WorldWideScience

Sample records for strong genetic determinants

  1. Genetic modification and genetic determinism

    Directory of Open Access Journals (Sweden)

    Vorhaus Daniel B

    2006-06-01

    Full Text Available Abstract In this article we examine four objections to the genetic modification of human beings: the freedom argument, the giftedness argument, the authenticity argument, and the uniqueness argument. We then demonstrate that each of these arguments against genetic modification assumes a strong version of genetic determinism. Since these strong deterministic assumptions are false, the arguments against genetic modification, which assume and depend upon these assumptions, are therefore unsound. Serious discussion of the morality of genetic modification, and the development of sound science policy, should be driven by arguments that address the actual consequences of genetic modification for individuals and society, not by ones propped up by false or misleading biological assumptions.

  2. Genetic and other factors determining mannose-binding lectin levels in American Indians: the Strong Heart Study

    DEFF Research Database (Denmark)

    Best, Lyle G; Ferrell, Robert E; Decroo, Susan

    2009-01-01

    were selected for analysis of circulating MBL levels by double sandwich ELISA method. Mean MBL levels were compared between genotypic groups and multivariate regression was used to determine other independent factors influencing MBL2 expression. RESULTS: Our results confirm the effects of variant...... structural (B, C, and D) and promoter (H and Y) alleles that have been seen in other populations. In addition, MBL levels were found to be positively associated with male gender and hemoglobin A1c levels, but inversely related to triglyceride levels. Correlation was not found between MBL and other markers...

  3. <strong>On Determinism in Modal Transition Systemsstrong>

    DEFF Research Database (Denmark)

    Benes, Nikola; Kretinsky, Jan; Larsen, Kim Guldstrand

    2009-01-01

    Modal transition systems (MTS) is a formalism which extends the classical notion of labelled transition systems by introducing transitions of two types: must transitions that have to be present in any implementation of the MTS and may transitions that are allowed but not required. The MTS framewo....... In the present article, we provide a comprehensive account of the MTS framework in the deterministic setting. We study a number of problems previously considered on MTS and point out to what extend we can expect better results under the restriction of determinism....

  4. Genetic determinants of facial clefting

    DEFF Research Database (Denmark)

    Jugessur, Astanand; Shi, Min; Gjessing, Håkon Kristian

    2009-01-01

    BACKGROUND: Facial clefts are common birth defects with a strong genetic component. To identify fetal genetic risk factors for clefting, 1536 SNPs in 357 candidate genes were genotyped in two population-based samples from Scandinavia (Norway: 562 case-parent and 592 control-parent triads; Denmark...

  5. Strong genetic overlap between executive functions and intelligence.

    Science.gov (United States)

    Engelhardt, Laura E; Mann, Frank D; Briley, Daniel A; Church, Jessica A; Harden, K Paige; Tucker-Drob, Elliot M

    2016-09-01

    Executive functions (EFs) are cognitive processes that control, monitor, and coordinate more basic cognitive processes. EFs play instrumental roles in models of complex reasoning, learning, and decision making, and individual differences in EFs have been consistently linked with individual differences in intelligence. By middle childhood, genetic factors account for a moderate proportion of the variance in intelligence, and these effects increase in magnitude through adolescence. Genetic influences on EFs are very high, even in middle childhood, but the extent to which these genetic influences overlap with those on intelligence is unclear. We examined genetic and environmental overlap between EFs and intelligence in a racially and socioeconomically diverse sample of 811 twins ages 7 to 15 years (M = 10.91, SD = 1.74) from the Texas Twin Project. A general EF factor representing variance common to inhibition, switching, working memory, and updating domains accounted for substantial proportions of variance in intelligence, primarily via a genetic pathway. General EF continued to have a strong, genetically mediated association with intelligence even after controlling for processing speed. Residual variation in general intelligence was influenced only by shared and nonshared environmental factors, and there remained no genetic variance in general intelligence that was unique of EF. Genetic variance independent of EF did remain, however, in a more specific perceptual reasoning ability. These results provide evidence that genetic influences on general intelligence are highly overlapping with those on EF. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

  6. Strong Genetic Overlap Between Executive Functions and Intelligence

    Science.gov (United States)

    Engelhardt, Laura E.; Mann, Frank D.; Briley, Daniel A.; Church, Jessica A.; Harden, K. Paige; Tucker-Drob, Elliot M.

    2016-01-01

    Executive functions (EFs) are cognitive processes that control, monitor, and coordinate more basic cognitive processes. EFs play instrumental roles in models of complex reasoning, learning, and decision-making, and individual differences in EFs have been consistently linked with individual differences in intelligence. By middle childhood, genetic factors account for a moderate proportion of the variance in intelligence, and these effects increase in magnitude through adolescence. Genetic influences on EFs are very high, even in middle childhood, but the extent to which these genetic influences overlap with those on intelligence is unclear. We examined genetic and environmental overlap between EFs and intelligence in a racially and socioeconomically diverse sample of 811 twins ages 7-15 years (M = 10.91, SD = 1.74) from the Texas Twin Project. A general EF factor representing variance common to inhibition, switching, working memory, and updating domains accounted for substantial proportions of variance in intelligence, primarily via a genetic pathway. General EF continued to have a strong, genetically-mediated association with intelligence even after controlling for processing speed. Residual variation in general intelligence was influenced only by shared and nonshared environmental factors, and there remained no genetic variance in general intelligence that was unique of EF. Genetic variance independent of EF did remain, however, in a more specific perceptual reasoning ability. These results provide evidence that genetic influences on general intelligence are highly overlapping with those on EF. PMID:27359131

  7. GENETIC DETERMINATIONS OF MENTALITY

    Directory of Open Access Journals (Sweden)

    L. V. Osadcha

    2015-12-01

    Full Text Available Purpose. The article is devoted to clarifying the role of physicality and psycho-physical characteristics of a person as a preconditions of the mentality forming. It is conducted a retrospective analysis of discourse on the mentality, the history of the concept, its temporal characteristics and collective conditioning. The concept of mentality has been widely studied in various fields of socio-humanities such as: history, psychology, and even marginal context of scientific discourses, including the esoteric. This study attempted to analyse the mentality phenomenon through the prism of the concept of experience. Methodology. The concept of experience was acquired by essential justification through the representatives of the phenomenological approach - the late Edmund Husserl, Maurice Merleau-Ponty, Bernhard Valdenfels. On the other hand the concept of mentality as a form of collective unconscious experience was entered to the scientific vocabulary by the representatives of the French historical science - M. Bloch, L. Febvre, J. Le Goff and others. At the intersection of these two methods, historical and phenomenological, the genetic method has been established – as a history of coverage and experience of internalization. Thanks to the application of genetic method the transition of phenomenon into the concept was examined. Novelty. The problem of change dynamics of mental phenomenon, in particular psycho-physical nature of a person, which has been only mentioned in F. Braudel works but has not received the adequate theoretical coverage, is analysed. To explain the practices of physicality and causality of this factor the action component of the cultural the overview of developments of such authors as V. Rozin (2005, M. Epstein (2005, N. Brunov (2003, A. Soares, M. Farhangmehr, A. Shoham (2007, D. Vaskul, F. Vannini Hospital (2012 was committed. Conclusions. The transition to paradoxical behaviour that is oriented on sign, and not on signalling

  8. Computing strong metric dimension of some special classes of graphs by genetic algorithms

    Directory of Open Access Journals (Sweden)

    Kratica Jozef

    2008-01-01

    Full Text Available In this paper we consider the NP-hard problem of determining the strong metric dimension of graphs. The problem is solved by a genetic algorithm that uses binary encoding and standard genetic operators adapted to the problem. This represents the first attempt to solve this problem heuristically. We report experimental results for the two special classes of ORLIB test instances: crew scheduling and graph coloring.

  9. Genetic determinants of common epilepsies

    DEFF Research Database (Denmark)

    2014-01-01

    not previously implicated in epilepsy and provides further evidence about the genetic architecture of these disorders, with the ultimate aim of assisting in disease classification and prognosis. The data suggest that specific loci can act pleiotropically raising risk for epilepsy broadly, or can have effects......BACKGROUND: The epilepsies are a clinically heterogeneous group of neurological disorders. Despite strong evidence for heritability, genome-wide association studies have had little success in identification of risk loci associated with epilepsy, probably because of relatively small sample sizes...... and insufficient power. We aimed to identify risk loci through meta-analyses of genome-wide association studies for all epilepsy and the two largest clinical subtypes (genetic generalised epilepsy and focal epilepsy). METHODS: We combined genome-wide association data from 12 cohorts of individuals with epilepsy...

  10. A strong genetic footprint of the re-introduction history of Alpine ibex (Capra ibex ibex).

    Science.gov (United States)

    Biebach, Iris; Keller, Lukas F

    2009-12-01

    A population's neutral genetic variation is a composite of its size, degree of isolation and demographic history. Bottlenecks and founder events increase genetic drift, leading to the loss of genetic variation and increased genetic differentiation among populations. Gene flow has the opposite effects. Thus, gene flow can override the genetic patterns caused by founder events. Using 37 microsatellite loci, we investigated the effects of serial bottlenecks on genetic variation and differentiation among 42 Alpine ibex populations in Switzerland with known re-introduction histories. We detected a strong footprint of re-introduction events on contemporary genetic structure, with re-introduction history explaining a substantial part of the genetic differentiation among populations. As a result of the translocation of a considerable number of individuals from the sole formerly surviving population in northern Italy, most of the genetic variation of the ancestral population is now present in the combined re-introduced Swiss populations. However, re-introductions split up the genetic variation among populations, such that each contemporary Swiss population showed lower genetic variation than the ancestral population. As expected, serial bottlenecks had different effects on the expected heterozygosity (He) and standardized number of alleles (sNa). While loss of sNa was higher in the first bottlenecks than in subsequent ones, He declined to a similar degree with each bottleneck. Thus, genetic drift was detected with each bottleneck, even when no loss of sNa was observed. Overall, more than a hundred years after the beginning of this successful re-introduction programme, re-introduction history was the main determinant of today's genetic structure.

  11. Genetic resources of teak (Tectona grandis Linn. f.)—strong genetic structure among natural populations

    DEFF Research Database (Denmark)

    Hansen, Ole Kim; Changtragoon, Suchitra; Ponoy, Bundit

    2015-01-01

    Twenty-nine provenances of teak (Tectona grandis Linn. f.) representing the full natural distribution range of the species were genotyped with microsatellite DNA markers to analyse genetic diversity and population genetic structure. Provenances originating from the semi-moist east coast of India...... of genetic diversity supports the hypothesis that teak has its centre of origin in India, from where it spread eastwards. The analysis of molecular variance (AMOVA) gave an overall highly significant F st value of 0.227—population pairwise F st values were in the range 0.01–0.48. Applying the G......″st differentiation parameter, the estimated overall differentiation was 0.632, implying a strong genetic structure among populations. A neighbour-joining (NJ) tree, using the pairwise population matrix of G″st values as input, contained three distinct groups: (1) the eight provenances from Thailand and Laos, (2...

  12. Sex Determination, Sex Ratios, and Genetic Conflict

    NARCIS (Netherlands)

    Werren, John H.; Beukeboom, Leo W.

    1998-01-01

    Genetic mechanisms of sex determination are unexpectedly diverse and change rapidly during evolution. We review the role of genetic conflict as the driving force behind this diversity and turnover. Genetic conflict occurs when different components of a genetic system are subject to selection in

  13. A Strong Case for Viral Genetic Factors in HIV Virulence

    Directory of Open Access Journals (Sweden)

    Joshua T. Herbeck

    2011-03-01

    Full Text Available HIV infections show great variation in the rate of progression to disease, and the role of viral genetic factors in this variation had remained poorly characterized until recently. Now a series of four studies [1–4] published within a year has filled this important gap and has demonstrated a robust effect of the viral genotype on HIV virulence.

  14. Total and regional fat distribution is strongly influenced by genetic factors in young and elderly twins

    DEFF Research Database (Denmark)

    Malis, Charlotte; Rasmussen, Eva L; Poulsen, Pernille

    2005-01-01

    OBJECTIVE: Indirect estimates of obesity such as BMI seem to be strongly influenced by genetic factors in twins. Precise measurements of total and regional fat as determined by direct techniques such as DXA scan have only been applied in a few twin studies. The aim of the present study was to est......OBJECTIVE: Indirect estimates of obesity such as BMI seem to be strongly influenced by genetic factors in twins. Precise measurements of total and regional fat as determined by direct techniques such as DXA scan have only been applied in a few twin studies. The aim of the present study...... was to estimate the heritability (h(2)) of total and regional fat distribution in young and elderly Danish twins. RESEARCH METHODS AND PROCEDURES: Monozygotic (108) and dizygotic (88) twins in two age groups (25 to 32 and 58 to 66 years) underwent anthropometric measurements and DXA scans. Intraclass correlations...... genetic component (h(2)) of total (h(2)(young) = 0.83, h(2)(elderly) = 0.86) and regional fat percentages (trunk, h(2)(young) = 0.82, h(2)(elderly) = 0.85; lower body, h(2)(young) = 0.83, h(2)(elderly) = 0.81; and trunk/lower body, h(2)(young) = 0.83, h(2)(elderly) = 0.71) in both the young and elderly...

  15. Genetic determinants of eating disorders

    NARCIS (Netherlands)

    Slof-Op 't Landt, Margarita Cornelia Theodora

    2011-01-01

    In this thesis, a series of studies on different aspects of the genetics of eating disorders is presented. The heritability of disordered eating behavior and attitudes in relation with body mass index (BMI) was evaluated in a large adolescent twin-family sample ascertained through the Netherlands

  16. Genetic determinants of statin intolerance

    Directory of Open Access Journals (Sweden)

    Pollex Rebecca L

    2007-03-01

    Full Text Available Abstract Background Statin-related skeletal muscle disorders range from benign myalgias – such as non-specific muscle aches or joint pains without elevated serum creatinine kinase (CK concentration – to true myositis with >10-fold elevation of serum CK, to rhabdomyolysis and myoglobinuria. The genetic basis of statin-related muscle disorders is largely unknown. Because mutations in the COQ2 gene are associated with severe inherited myopathy, we hypothesized that common, mild genetic variation in COQ2 would be associated with inter-individual variation in statin intolerance. We studied 133 subjects who developed myopathy on statin monotherapy and 158 matched controls who tolerated statins without incident or complaint. Results COQ2 genotypes, based on two single nucleotide polymorphisms (SNP1 and SNP2 and a 2-SNP haplotype, all showed significant associations with statin intolerance. Specifically, the odds ratios (with 95% confidence intervals for increased risk of statin intolerance among homozygotes for the rare alleles were 2.42 (0.99 to 5.89, 2.33 (1.13 to 4.81 and 2.58 (1.26 to 5.28 for SNP1 and SNP2 genotypes, and the 2-SNP haplotype, respectively. Conclusion These preliminary pharmacogenetic results, if confirmed, are consistent with the idea that statin intolerance which is manifested primarily through muscle symptoms is associated with genomic variation in COQ2 and thus perhaps with the CoQ10 pathway.

  17. Genetic determinants of HDL metabolism.

    Science.gov (United States)

    Ossoli, A; Gomaraschi, M; Franceschini, G; Calabresi, L

    2014-01-01

    Plasma high density lipoproteins (HDL) comprise a highly heterogeneous family of lipoprotein particles, with subclasses that can be separated and identified according to density, size, surface charge as well as shape and protein composition. There is evidence that these subclasses may differ in their functional properties. The individual plasma HDL cholesterol (HDL-C) level is generally taken as a snapshot of the steady-state concentration of all circulating HDL subclasses together, but this is insufficient to capture the structural and functional variation in HDL particles. HDL are continuously remodeled and metabolized in plasma and interstitial fluids, through the interaction with a large number of factors, including structural proteins, membrane transporters, enzymes, transfer proteins and receptors. Genetic variation in these factors can lead to essential changes in plasma HDL levels, and to remarkable changes in HDL particle density, size, surface charge, shape, and composition in lipids and apolipoproteins. This review discusses the impact of rare mutations and common variants in genes encoding factors involved in HDL remodeling and metabolism on plasma HDL-C levels and particle distribution. The study of the effects of human genetic variation in major players in HDL metabolism provides important clues on how individual factors modulate the formation, maturation, remodeling and catabolism of HDL.

  18. Determination of strong ion gap in healthy dogs.

    Science.gov (United States)

    Fettig, Pamela K; Bailey, Dennis B; Gannon, Kristi M

    2012-08-01

    To determine and compare reference intervals of the strong ion gap (SIG) in a group of healthy dogs determined with 2 different equations. Prospective observational study. Tertiary referral and teaching hospital. Fifty-four healthy dogs. None. Serum biochemistry and blood gas analyses were performed for each dog. From these values, SIG was calculated using 2 different equations: SIG(1) = SID(a) {[Na (+)] + [K(+)] - [Cl(-)]+ [2 × Ca(2+)] + [2 × Mg(2+)] - [L-lactate]}- SID(e) {TCO(2) + A(-)} and SIG(2) = [albumin] × 4.9-anion gap. Reference intervals were established for each SIG equation using the mean ± 1.96 × standard deviation (SD). For SIG(1), the median was 7.13 mEq/L (range, 1.05-11.30 mEq/L) and the derived reference interval was 1.85-10.61 mEq/L. Median SIG(2) was -0.22 mEq/L (range, -5.34-6.61 mEq/L) and the mean SIG(2) was -0.09 mEq/L (95% confidence interval for the mean, -0.82-0.65 mEq/L). The derived reference interval was -5.36-5.18 mEq/L. The results of the SIG calculations were significantly different (P SIG yielded significantly different results and cannot be used interchangeably. The authors believe SIG(2) to be a more accurate reflection of acid-base status in healthy dogs, and recommend that this calculation be used for future studies. © Veterinary Emergency and Critical Care Society 2012.

  19. Is umbilical coiling genetically determined?

    Science.gov (United States)

    Ayala, Nina K; Ernst, Linda M; Miller, Emily S

    2018-02-21

    Abnormal umbilical cord coiling is associated with adverse perinatal outcomes; however, the etiology of the umbilical coiling pattern is poorly understood. Retrospective cohort of all twin deliveries >20 weeks in 2014. Pregnancies were dichotomized by chorionicity and the umbilical coiling index (UCI) and placental cord insertion location were compared. In cases with one or both cords hypercoiled, the direction and pattern of coiling were compared by chorionicity. A similar analysis was performed stratified by zygosity. Three hundred sisty two twin pairs were included; 26 (7.2%) monochorionic and 174 (87.0%) definitively dizygotic. Concordance in the UCI and coiling category were similar between dichorionic and monochorionic as well as dizygous and monozygous gestations, (73.2% vs 80.8%, p = 0.399 and 71.4% vs 80.8%, p = 0.399, respectively). Analyses of the coiling direction and pattern also demonstrated no difference by chorionicity or zygosity. These data do not support a genetic basis for umbilical cord coiling.

  20. Determination of stability constants using genetic algorithms

    NARCIS (Netherlands)

    Hartnett, Margaret K.; Bos, M.; van der Linden, W.E.; Diamond, Dermot

    1995-01-01

    A genetic algorithm (GA)-simplex hybrid approach has been developed for the determination of stability constants using calorimetric and polarographic data obtained from literature sources. The GA determined both the most suitable equilibrium model for the systems studied and the values of the

  1. Trapped in the extinction vortex? Strong genetic effects in a declining vertebrate population

    Directory of Open Access Journals (Sweden)

    Larsson Mikael

    2010-02-01

    Full Text Available Abstract Background Inbreeding and loss of genetic diversity are expected to increase the extinction risk of small populations, but detailed tests in natural populations are scarce. We combine long-term population and fitness data with those from two types of molecular markers to examine the role of genetic effects in a declining metapopulation of southern dunlins Calidris alpina schinzii, an endangered shorebird. Results The decline is associated with increased pairings between related individuals, including close inbreeding (as revealed by both field observations of parentage and molecular markers. Furthermore, reduced genetic diversity seems to affect individual fitness at several life stages. Higher genetic similarity between mates correlates negatively with the pair's hatching success. Moreover, offspring produced by related parents are more homozygous and suffer from increased mortality during embryonic development and possibly also after hatching. Conclusions Our results demonstrate strong genetic effects in a rapidly declining population, emphasizing the importance of genetic factors for the persistence of small populations.

  2. Understanding sex determination in the mouse: genetics ...

    Indian Academy of Sciences (India)

    profiles of the male and female gonads, firstly during primary sex determination, but also in the adult gonad, thereby regulating cellular behaviour during ... XX males (here, I was referring to the start of my Sxr work). She wrote back saying ..... Mouse genetics is providing increasingly sophisticated tools for the study of sex ...

  3. Understanding sex determination in the mouse: genetics ...

    Indian Academy of Sciences (India)

    Recent years have seen a rapid growth in mouse genetics resources that support research into fundamental mechanisms in organogenesis, including those controlling mammalian sex determinations. Numerous mouse mutants have shed light on molecular pathways of cell fate specification during gonadogenesis and the ...

  4. Reliably determining data leakage in the presence of strong attackers

    NARCIS (Netherlands)

    Bortolameotti, R.; Peter, A.; Everts, M.H.; Jonker, W.; Hartel, P.

    2016-01-01

    We address the problem of determining what data has been leaked from a system after its recovery from a successful attack. This is a forensic process which is relevant to give a better understanding of the impact of a data breach, but more importantly it is becoming mandatory according to the recent

  5. Genetic determinants of hepatic steatosis in man

    Science.gov (United States)

    Hooper, Amanda J.; Adams, Leon A.; Burnett, John R.

    2011-01-01

    Hepatic steatosis is one of the most common liver disorders in the general population. The main cause of hepatic steatosis is nonalcoholic fatty liver disease (NAFLD), representing the hepatic component of the metabolic syndrome, which is characterized by type 2 diabetes, obesity, and dyslipidemia. Insulin resistance and excess adiposity are considered to play key roles in the pathogenesis of NAFLD. Although the risk factors for NAFLD are well established, the genetic basis of hepatic steatosis is largely unknown. Here we review recent progress on genomic variants and their association with hepatic steatosis and discuss the potential impact of these genetic studies on clinical practice. Identifying the genetic determinants of hepatic steatosis will lead to a better understanding of the pathogenesis and progression of NAFLD. PMID:21245030

  6. GENETIC SEX DETERMINATION IN HEAVY BREED CHICKEN

    Directory of Open Access Journals (Sweden)

    BENCSIK ALENA

    2007-01-01

    Full Text Available We have used a non-invasive method to predetermine the sex of chicken embryosthat relies on the bio electromagnetic field generated by the embryonic cells. Tovalidate this method in poultry, on the basis of sexual dimorphism, the genetic sex of120 chicken eggs of heavy breed. One group consisted of 60 eggs with determinedgenetic sex ZZ (cock, abbr. M. The other group consisted of 60 eggs withdetermined genetic sex ZY (hen, abbr. F. After hatching, the chicks were identifiedand the genetic sex was checked repeatedly using the pendulum. The phenoypic sexof the birds was assessed after 60 days at the time the sexual dimorphism wasvisible. From the 60 eggs sexed and incubated for each group, a hatching rate of90%, for the group M and 91,66% for the group F was obtained. The genetic sex ofindividuals determined at the age of one day showed that all individuals of the groupM were cocks (ZZ and all individuals of the group F were hens (ZW. Thephenotypic sex determination performed 60 days later showed that of 54 individualsof the group M, 41 were cocks (77,36%. In the group F from 55 individuals 42 werehens (77,78%. The prediction rate for the group M (77,36% was relativlycomparable with that for the group F (77,78%. This method is non-invasive,relatively rapid, simple and inexpensive with application in effective breedingregimes of poultry production.

  7. Genetic markers cannot determine Jewish descent.

    Science.gov (United States)

    Falk, Raphael

    2014-01-01

    Humans differentiate, classify, and discriminate: social interaction is a basic property of human Darwinian evolution. Presumably inherent differential physical as well as behavioral properties have always been criteria for identifying friend or foe. Yet, biological determinism is a relatively modern term, and scientific racism is, oddly enough, largely a consequence or a product of the Age of Enlightenment and the establishment of the notion of human equality. In recent decades ever-increasing efforts and ingenuity were invested in identifying Biblical Israelite genotypic common denominators by analysing an assortment of phenotypes, like facial patterns, blood types, diseases, DNA-sequences, and more. It becomes overwhelmingly clear that although Jews maintained detectable vertical genetic continuity along generations of socio-religious-cultural relationship, also intensive horizontal genetic relations were maintained both between Jewish communities and with the gentile surrounding. Thus, in spite of considerable consanguinity, there is no Jewish genotype to identify.

  8. Genetic markers cannot determine Jewish descent

    Science.gov (United States)

    Falk, Raphael

    2015-01-01

    Humans differentiate, classify, and discriminate: social interaction is a basic property of human Darwinian evolution. Presumably inherent differential physical as well as behavioral properties have always been criteria for identifying friend or foe. Yet, biological determinism is a relatively modern term, and scientific racism is, oddly enough, largely a consequence or a product of the Age of Enlightenment and the establishment of the notion of human equality. In recent decades ever-increasing efforts and ingenuity were invested in identifying Biblical Israelite genotypic common denominators by analysing an assortment of phenotypes, like facial patterns, blood types, diseases, DNA-sequences, and more. It becomes overwhelmingly clear that although Jews maintained detectable vertical genetic continuity along generations of socio-religious-cultural relationship, also intensive horizontal genetic relations were maintained both between Jewish communities and with the gentile surrounding. Thus, in spite of considerable consanguinity, there is no Jewish genotype to identify. PMID:25653666

  9. Burden analysis of rare microdeletions suggests a strong impact of neurodevelopmental genes in genetic generalised epilepsies

    DEFF Research Database (Denmark)

    Lal, Dennis; Ruppert, Ann-Kathrin; Trucks, Holger

    2015-01-01

    Genetic generalised epilepsy (GGE) is the most common form of genetic epilepsy, accounting for 20% of all epilepsies. Genomic copy number variations (CNVs) constitute important genetic risk factors of common GGE syndromes. In our present genome-wide burden analysis, large (≥ 400 kb) and rare (...%) autosomal microdeletions with high calling confidence (≥ 200 markers) were assessed by the Affymetrix SNP 6.0 array in European case-control cohorts of 1,366 GGE patients and 5,234 ancestry-matched controls. We aimed to: 1) assess the microdeletion burden in common GGE syndromes, 2) estimate the relative...... a strong impact of fundamental neurodevelopmental processes in the pathogenesis of common GGE syndromes....

  10. Determination of genetic diversity among Turkish durum wheat ...

    African Journals Online (AJOL)

    Wheat landraces represent an important source of genetic variation that can be used for future wheat breeding program. The rich wheat landraces from Turkey have not been sufficiently analyzed genetically. For this reason, genetic diversity and relationship of the landraces must be determined. In this study, genetic diversity ...

  11. Self-Conscious Shyness: Growth during Toddlerhood, Strong Role of Genetics, and No Prediction from Fearful Shyness.

    Science.gov (United States)

    Eggum-Wilkens, Natalie D; Lemery-Chalfant, Kathryn; Aksan, Nazan; Goldsmith, H Hill

    2015-01-01

    Fearful and self-conscious subtypes of shyness have received little attention in the empirical literature. Study aims included: 1) determining if fearful shyness predicted self-conscious shyness, 2) describing development of self-conscious shyness, and 3) examining genetic and environmental contributions to fearful and self-conscious shyness. Observed self-conscious shyness was examined at 19, 22, 25, and 28 months in same-sex twins (MZ = 102, DZ = 111, missing zygosity = 3 pairs). Self-conscious shyness increased across toddlerhood, but onset was earlier than predicted by theory. Fearful shyness (observed [6 and 12 months] and parents' reports [12 and 22 months]) was not predictive of self-conscious shyness. Independent genetic factors made strong contributions to parent-reported (but not observed) fearful shyness (additive genetic influence = .69 and .72 at 12 and 22 months, respectively) and self-conscious shyness (additive genetic influence = .90 for the growth model intercept). Results encourage future investigation of patterns of change and interrelations in shyness subtypes.

  12. Low genetic diversity and strong population structure shaped by anthropogenic habitat fragmentation in a critically endangered primate, Trachypithecus leucocephalus.

    Science.gov (United States)

    Wang, W; Qiao, Y; Li, S; Pan, W; Yao, M

    2017-06-01

    Habitat fragmentation may strongly impact population genetic structure and reduce the genetic diversity and viability of small and isolated populations. The white-headed langur (Trachypithecus leucocephalus) is a critically endangered primate species living in a highly fragmented and human-modified habitat in southern China. We examined the population genetic structure and genetic diversity of the species and investigated the environmental and anthropogenic factors that may have shaped its population structure. We used 214 unique multi-locus genotypes from 41 social groups across the main distribution area of T. leucocephalus, and found strong genetic structure and significant genetic differentiation among local populations. Our landscape genetic analyses using a causal modelling framework suggest that a large habitat gap and geographical distance represent the primary landscape elements shaping genetic structure, yet high levels of genetic differentiation also exist between patches separated by a small habitat gap or road. This is the first comprehensive study that has evaluated the population genetic structure and diversity of T. leucocephalus using nuclear markers. Our results indicate strong negative impacts of anthropogenic land modifications and habitat fragmentation on primate genetic connectivity between forest patches. Our analyses suggest that two management units of the species could be defined, and indicate that habitat continuity should be enforced and restored to reduce genetic isolation and enhance population viability.

  13. Focusing light through strongly scattering media using genetic algorithm with SBR discriminant

    Science.gov (United States)

    Zhang, Bin; Zhang, Zhenfeng; Feng, Qi; Liu, Zhipeng; Lin, Chengyou; Ding, Yingchun

    2018-02-01

    In this paper, we have experimentally demonstrated light focusing through strongly scattering media by performing binary amplitude optimization with a genetic algorithm. In the experiments, we control 160 000 mirrors of digital micromirror device to modulate and optimize the light transmission paths in the strongly scattering media. We replace the universal target-position-intensity (TPI) discriminant with signal-to-background ratio (SBR) discriminant in genetic algorithm. With 400 incident segments, a relative enhancement value of 17.5% with a ground glass diffuser is achieved, which is higher than the theoretical value of 1/(2π )≈ 15.9 % for binary amplitude optimization. According to our repetitive experiments, we conclude that, with the same segment number, the enhancement for the SBR discriminant is always higher than that for the TPI discriminant, which results from the background-weakening effect of SBR discriminant. In addition, with the SBR discriminant, the diameters of the focus can be changed ranging from 7 to 70 μm at arbitrary positions. Besides, multiple foci with high enhancement are obtained. Our work provides a meaningful reference for the study of binary amplitude optimization in the wavefront shaping field.

  14. Strong incidence of Pseudomonas aeruginosa on bacterial rrs and ITS genetic structures of cystic fibrosis sputa.

    Directory of Open Access Journals (Sweden)

    Laurence Pages-Monteiro

    Full Text Available Cystic fibrosis (CF lungs harbor a complex community of interacting microbes, including pathogens like Pseudomonas aeruginosa. Meta-taxogenomic analysis based on V5-V6 rrs PCR products of 52 P. aeruginosa-positive (Pp and 52 P. aeruginosa-negative (Pn pooled DNA extracts from CF sputa suggested positive associations between P. aeruginosa and Stenotrophomonas and Prevotella, but negative ones with Haemophilus, Neisseria and Burkholderia. Internal Transcribed Spacer analyses (RISA from individual DNA extracts identified three significant genetic structures within the CF cohorts, and indicated an impact of P. aeruginosa. RISA clusters Ip and IIIp contained CF sputa with a P. aeruginosa prevalence above 93%, and of 24.2% in cluster IIp. Clusters Ip and IIIp showed lower RISA genetic diversity and richness than IIp. Highly similar cluster IIp RISA profiles were obtained from two patients harboring isolates of a same P. aeruginosa clone, suggesting convergent evolution in the structure of their microbiota. CF patients of cluster IIp had received significantly less antibiotics than patients of clusters Ip and IIIp but harbored the most resistant P. aeruginosa strains. Patients of cluster IIIp were older than those of Ip. The effects of P. aeruginosa on the RISA structures could not be fully dissociated from the above two confounding factors but several trends in these datasets support the conclusion of a strong incidence of P. aeruginosa on the genetic structure of CF lung microbiota.

  15. Genetic determinants of cocaine-associated agranulocytosis.

    Science.gov (United States)

    Buxton, Jane A; Omura, John; Kuo, Margot; Ross, Colin; Tzemis, Despina; Purssell, Roy; Gardy, Jennifer; Carleton, Bruce

    2015-06-13

    Drug-induced agranulocytosis is a recognized adverse drug event associated with serious infectious complications. Levamisole is an antihelminthic and immunomodulator withdrawn from North American markets in 2005 after reports of agranulocytosis. Previous studies of levamisole, suggest that the human leukocyte antigen (HLA)-B27 confers a genetic predisposition to this adverse drug event. Since 2009, emergency room visits due to agranulocytosis in individuals consuming levamisole-adulterated crack-cocaine have increased. We performed a case-control study using a genotyping assay and novel gene chip to test the association between cocaine-associated agranulocytosis (CAA) and HLA-B27 and to identify pharmacokinetic and pharmacodynamic gene variants associated with the phenotype. Fifty-one CAA cases were identified through a provincial physician reporting system between 2008 and 2011. We examined eight of these cases and 26 matched controls. Genotyping revealed a significant association between HLA-B27 and CAA (odds ratio [OR] 9.2, 95% confidence interval [CI], 1.54-54.6). We also observed a similar association with the HLA-B27 tag single nucleotide polymorphism rs4349859 (OR 9.2, 95% CI 1.5-54.6) and rs13202464 (OR 6.7, 95% CI 1.1-41). Further associations were identified with variants in the ARBCC12 (OR 10.0, 95% CI 2.7-36.8) and CYP11A1 (OR 7.4, 95% CI 2.1-26.6) genes, while a novel protective association was observed with variants in the ARDB1 gene (OR 0.06, 95% CI 0.007-0.46). We confirmed the association of HLA-B27 with CAA and identified additional susceptibility variants. Health care providers should inform people who are identified as having CAA that it is genetically determined and can recur with continued cocaine use. The severity of infections and subsequent hospitalization, and the risk of recurrence may prompt health-promoting behaviour changes of the affected individuals. These genetic associations warrant the attention of public health and knowledge

  16. Genetic backgrounds determine brown remodeling of white fat in rodents

    Directory of Open Access Journals (Sweden)

    Giulia Ferrannini

    2016-10-01

    Conclusion: Rodent genetic background determines the brown remodeling of different white fat depots. This study provides new insights into the role of genetic variation in fat remodeling in susceptibility to metabolic diseases.

  17. Population genetics inference for longitudinally-sampled mutants under strong selection.

    Science.gov (United States)

    Lacerda, Miguel; Seoighe, Cathal

    2014-11-01

    Longitudinal allele frequency data are becoming increasingly prevalent. Such samples permit statistical inference of the population genetics parameters that influence the fate of mutant variants. To infer these parameters by maximum likelihood, the mutant frequency is often assumed to evolve according to the Wright-Fisher model. For computational reasons, this discrete model is commonly approximated by a diffusion process that requires the assumption that the forces of natural selection and mutation are weak. This assumption is not always appropriate. For example, mutations that impart drug resistance in pathogens may evolve under strong selective pressure. Here, we present an alternative approximation to the mutant-frequency distribution that does not make any assumptions about the magnitude of selection or mutation and is much more computationally efficient than the standard diffusion approximation. Simulation studies are used to compare the performance of our method to that of the Wright-Fisher and Gaussian diffusion approximations. For large populations, our method is found to provide a much better approximation to the mutant-frequency distribution when selection is strong, while all three methods perform comparably when selection is weak. Importantly, maximum-likelihood estimates of the selection coefficient are severely attenuated when selection is strong under the two diffusion models, but not when our method is used. This is further demonstrated with an application to mutant-frequency data from an experimental study of bacteriophage evolution. We therefore recommend our method for estimating the selection coefficient when the effective population size is too large to utilize the discrete Wright-Fisher model. Copyright © 2014 by the Genetics Society of America.

  18. Determination of genetic relationships among elite thermosensitive ...

    Indian Academy of Sciences (India)

    Allahabad Agricultural Institute-Deemed University, Allahabad 211 007, India; Rice Section, Division of Genetics, Indian Agricultural Research Institute, New Delhi 110 012, India; Directorate of Rice Research, Rajendra Nagar, Hyderabad 500 030, India; Department of Genetics and Biochemistry, Clemson University, ...

  19. Genetically Determined Height and Coronary Artery Disease

    NARCIS (Netherlands)

    Nelson, Christopher P.; Hamby, Stephen E.; Saleheen, Danish; Hopewell, Jenna C.; Zeng, Lingyao; Assimes, Themistocles L.; Kanoni, Stavroula; Willenborg, Christina; Burgess, Stephen; Amouyel, Phillipe; Anand, Sonia; Blankenberg, Stefan; Boehm, Bernhard O.; Clarke, Robert J.; Collins, Rory; Dedoussis, George; Farrall, Martin; Franks, Paul W.; Groop, Leif; Hall, Alistair S.; Hamsten, Anders; Hengstenberg, Christian; Hovingh, G. Kees; Ingelsson, Erik; Kathiresan, Sekar; Kee, Frank; König, Inke R.; Kooner, Jaspal; Lehtimäki, Terho; März, Winifred; McPherson, Ruth; Metspalu, Andres; Nieminen, Markku S.; O'Donnell, Christopher J.; Palmer, Colin N. A.; Peters, Annette; Perola, Markus; Reilly, Muredach P.; Ripatti, Samuli; Roberts, Robert; Salomaa, Veikko; Shah, Svati H.; Schreiber, Stefan; Siegbahn, Agneta; Thorsteinsdottir, Unnur; Veronesi, Giovani; Wareham, Nicholas; Willer, Cristen J.; Zalloua, Pierre A.; Erdmann, Jeanette; Deloukas, Panos; Watkins, Hugh; Schunkert, Heribert; Danesh, John; Thompson, John R.; Samani, Nilesh J.; Assimes, Themistocles; Goldstein, Benjamin A.; Stirrups, Kathleen; Cazier, Jean-Baptiste; Johansson, Åsa; Lee, Jong-Young; Chambers, John C.; Esko, Tõnu; Folkersen, Lasse; Goel, Anuj; Grundberg, Elin; Havulinna, Aki S.; Ho, Weang K.; Hopewell, Jemma C.; Eriksson, Niclas; Kleber, Marcus E.; Kristiansson, Kati; Lundmark, Per; Lyytikäinen, Leo-Pekka; Rafelt, Suzanne; Shungin, Dmitry; Strawbridge, Rona J.; Thorleifsson, Gudmar; Tikkanen, Emmi; van Zuydam, Natalie; Voight, Benjamin F.; Waite, Lindsay L.; Zhang, Weihua; Ziegler, Andreas; Absher, Devin; Altshuler, David; Balmforth, Anthony J.; Barroso, Inês; Braund, Peter S.; Burgdorf, Christof; Claudi-Boehm, Simone; Cox, David; Dimitriou, Maria; Do, Ron; Doney, Alex S. F.; El Mokhtari, NourEddine; Eriksson, Per; Fischer, Krista; Fontanillas, Pierre; Franco-Cereceda, Anders; Gigante, Bruna; Gustafsson, Stefan; Hager, Jörg; Hallmans, Göran; Han, Bok-Ghee; Hunt, Sarah E.; Kang, Hyun M.; Illig, Thomas; Kessler, Thorsten; Knowles, Joshua W.; Kolovou, Genovefa; Kuusisto, Johanna; Langenberg, Claudia; Langford, Cordelia; Leander, Karin; Lokki, Marja-Liisa; Lundmark, Anders; McCarthy, Mark I.; Meisinger, Christa; Melander, Olle; Mihailov, Evelin; Maouche, Seraya; Morris, Andrew D.; Müller-Nurasyid, Martina; Nikus, Kjell; Peden, John F.; Rayner, N. William; Rasheed, Asif; Rosinger, Silke; Rubin, Diana; Rumpf, Moritz P.; Schäfer, Arne; Sivananthan, Mohan; Song, Ci; Stewart, Alexandre F. R.; Tan, Sian-Tsung; Thorgeirsson, Gudmundur; van der Schoot, C. Ellen; Wagner, Peter J.; Wells, George A.; Wild, Philipp S.; Yang, Tsun-Po; Amouyel, Philippe; Arveiler, Dominique; Basart, Hanneke; Boehnke, Michael; Boerwinkle, Eric; Brambilla, Paolo; Cambien, Francois; Cupples, Adrienne L.; de Faire, Ulf; Dehghan, Abbas; Diemert, Patrick; Epstein, Stephen E.; Evans, Alun; Ferrario, Marco M.; Ferrières, Jean; Gauguier, Dominique; Go, Alan S.; Goodall, Alison H.; Gudnason, Villi; Hazen, Stanley L.; Holm, Hilma; Iribarren, Carlos; Jang, Yangsoo; Kähönen, Mika; Kim, Hyo-Soo; Klopp, Norman; Koenig, Wolfgang; Kratzer, Wolfgang; Kuulasmaa, Kari; Laakso, Markku; Laaksonen, Reijo; Lee, Ji-Young; Lind, Lars; Ouwehand, Willem H.; Parish, Sarah; Park, Jeong E.; Pedersen, Nancy L.; Quertermous, Thomas; Rader, Daniel J.; Schadt, Eric; Sinisalo, Juha; Stark, Klaus; Stefansson, Kari; Trégouët, David-Alexandre; Virtamo, Jarmo; Wallentin, Lars; Zimmermann, Martina E.; Sandhu, Manjinder S.; Pastinen, Tomi; Syvänen, Ann-Christine; Blankenberg, Stefan S.; Clarke, Robert; O'Donnell, Christopher; März, Winfried; Kooner, Jaspal S.

    2015-01-01

    BACKGROUND The nature and underlying mechanisms of an inverse association between adult height and the risk of coronary artery disease (CAD) are unclear. METHODS We used a genetic approach to investigate the association between height and CAD, using 180 height-associated genetic variants. We tested

  20. Exploring Relationships Among Belief in Genetic Determinism, Genetics Knowledge, and Social Factors

    Science.gov (United States)

    Gericke, Niklas; Carver, Rebecca; Castéra, Jérémy; Evangelista, Neima Alice Menezes; Marre, Claire Coiffard; El-Hani, Charbel N.

    2017-12-01

    Genetic determinism can be described as the attribution of the formation of traits to genes, where genes are ascribed more causal power than what scientific consensus suggests. Belief in genetic determinism is an educational problem because it contradicts scientific knowledge, and is a societal problem because it has the potential to foster intolerant attitudes such as racism and prejudice against sexual orientation. In this article, we begin by investigating the very nature of belief in genetic determinism. Then, we investigate whether knowledge of genetics and genomics is associated with beliefs in genetic determinism. Finally, we explore the extent to which social factors such as gender, education, and religiosity are associated with genetic determinism. Methodologically, we gathered and analyzed data on beliefs in genetic determinism, knowledge of genetics and genomics, and social variables using the "Public Understanding and Attitudes towards Genetics and Genomics" (PUGGS) instrument. Our analyses of PUGGS responses from a sample of Brazilian university freshmen undergraduates indicated that (1) belief in genetic determinism was best characterized as a construct built up by two dimensions or belief systems: beliefs concerning social traits and beliefs concerning biological traits; (2) levels of belief in genetic determination of social traits were low, which contradicts prior work; (3) associations between knowledge of genetics and genomics and levels of belief in genetic determinism were low; and (4) social factors such as age and religiosity had stronger associations with beliefs in genetic determinism than knowledge. Although our study design precludes causal inferences, our results raise questions about whether enhancing genetic literacy will decrease or prevent beliefs in genetic determinism.

  1. Early environmental exposures influence schizophrenia expression even in the presence of strong genetic predisposition.

    Science.gov (United States)

    Husted, Janice A; Ahmed, Rashid; Chow, Eva W C; Brzustowicz, Linda M; Bassett, Anne S

    2012-05-01

    There are few studies of environmental factors in familial forms of schizophrenia. We investigated whether childhood adversity or environmental factors were associated with schizophrenia in a familial sample where schizophrenia is associated with the NOSA1P gene. We found that a cumulative adversity index including childhood illness, family instability and cannabis use was significantly associated with narrow schizophrenia, independent of NOSA1P risk genotype, previously measured childhood trauma, covariates and familial clustering (adjusted odds ratio (95% confidence interval)=1.55 (1.01, 2.38)). The results provide further support that early environmental exposures influence schizophrenia expression even in the presence of strong genetic predisposition. Copyright © 2012 Elsevier B.V. All rights reserved.

  2. Mature habitats associated with genetic divergence despite strong dispersal ability in an arthropod

    Directory of Open Access Journals (Sweden)

    Taylor Derek J

    2007-04-01

    Full Text Available Abstract Background Populations may be bound by contemporary gene flow, selective sweeps, and extinction-recolonization processes. Indeed, existing molecular estimates indicate that species with low levels of gene flow are rare. However, strong priority effects and local selective regimes may hinder gene flow (despite dispersal sending populations on independent evolutionary trajectories. In this scenario (the monopolization hypothesis, population differentiation will increase with time and genealogical evidence should yield ample private haplotypes. Cyclical parthenogens (e.g. rotifers and cladocerans such as Daphnia have an increased capacity for rapid local adaptation and priority effects because sexual reproduction is followed by multiple generations of clonal selection and massive egg bank formation. We aimed to better understand the history of population differentiation and ongoing gene flow in Daphnia rosea s.l., by comparing population and regional divergences in mature unglaciated areas and younger previously glaciated areas. We also examined the timing and paths of colonization of previously-glaciated areas to assess the dispersal limitations of D. rosea s.l. We used DNA sequence variation (84 populations and >400 individuals at the mitochondrial ND2 and nuclear HSP90 loci from Holarctic populations for our genetic analyses. Results The genetic evidence indicated pronounced historical structure. Holarctic mtDNA phylogenies of D. rosea s.l. revealed three geographically restricted and divergent clades: European, Siberian and Japanese/American. The Japanese/American clade showed marked population genetic structure (FST > 0.8 that was weakly associated with geographic distance, and a high proportion of private haplotypes. Populations from older unglaciated habitats (i.e., Japan showed higher DNA sequence divergences than populations from presumed younger habitats (i.e. non-Beringian North America with nDNA and with mtDNA. Mismatch

  3. Genetic compatibility determines endophyte-grass combinations.

    Directory of Open Access Journals (Sweden)

    Kari Saikkonen

    Full Text Available Even highly mutually beneficial microbial-plant interactions, such as mycorrhizal- and rhizobial-plant exchanges, involve selfishness, cheating and power-struggles between the partners, which depending on prevailing selective pressures, lead to a continuum of interactions from antagonistic to mutualistic. Using manipulated grass-endophyte combinations in a five year common garden experiment, we show that grass genotypes and genetic mismatches constrain genetic combinations between the vertically (via host seeds transmitted endophytes and the out-crossing host, thereby reducing infections in established grass populations. Infections were lost in both grass tillers and seedlings in F(1 and F(2 generations, respectively. Experimental plants were collected as seeds from two different environments, i.e., meadows and nearby riverbanks. Endophyte-related benefits to the host included an increased number of inflorescences, but only in meadow plants and not until the last growing season of the experiment. Our results illustrate the importance of genetic host specificity and trans-generational maternal effects on the genetic structure of a host population, which act as destabilizing forces in endophyte-grass symbioses. We propose that (1 genetic mismatches may act as a buffering mechanism against highly competitive endophyte-grass genotype combinations threatening the biodiversity of grassland communities and (2 these mismatches should be acknowledged, particularly in breeding programmes aimed at harnessing systemic and heritable endophytes to improve the agriculturally valuable characteristics of cultivars.

  4. Determination of genetic polymorphism among indigenous and ...

    African Journals Online (AJOL)

    Bullseye

    1Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India. 2Centre for Plant ... are currently considered as the molecular markers of choice and are rapidly being adapted by plant researchers for ... rate of photosynthetic activity because of its C4 pathway, leading to higher ...

  5. Genetic Diseases and Genetic Determinism Models in French Secondary School Biology Textbooks

    Science.gov (United States)

    Castera, Jeremy; Bruguiere, Catherine; Clement, Pierre

    2008-01-01

    The presentation of genetic diseases in French secondary school biology textbooks is analysed to determine the major conceptions taught in the field of human genetics. References to genetic diseases, and the processes by which they are explained (monogeny, polygeny, chromosomal anomaly and environmental influence) are studied in recent French…

  6. [Elucidation of key genes in sex determination in genetics teaching].

    Science.gov (United States)

    Li, Meng; He, Zhumei

    2014-06-01

    Sex is an important and complex feature of organisms, which is controlled by the genetic and environmental factors. The genetic factors, i.e., genes, are vital in sex determination. However, not all the related genes play the same roles, and some key genes play a vital role in the sex determination and differentiation. With the development of the modern genetics, a great progress on the key genes has been made in sex determination. In this review, we summarize the mechanism of sex determination and the strategy of how to study the key genes in sex determination. It will help us to understand the mechanism of sex determination better in the teaching of genetics.

  7. Determination of the neutron flux in the reactor zones with the strong neutron absorption and leakage

    International Nuclear Information System (INIS)

    Ljubenov, V.; Milosevic, M.

    2004-01-01

    The procedures for the numerical and experimental determination of the neutron flux in the zones with the strong neutron absorption and leakage are described in this paper. Numerical procedure is based on the SCALE-4.4a code system application with the use of Dancoff factor determined by the VEGA2DAN code. Experimental methodology consists of the irradiated foils activity measurement, and foil averaged neutron absorption cross-section determination via mentioned SCALE- 4.4a calculation procedure. The proposed procedures have been applied for the determination of the neutron flux in the internal neutron converter used with the RB reactor core configuration number 114. (author) [sr

  8. Precision determination of the strong interaction shift and width in pionic hydrogen

    International Nuclear Information System (INIS)

    Anagnostopoulos, D.F.; Covita, D.D.S.; Santos, J.M.F. dos; Veloso, J.F.C.A.; Fuhrmann, H.; Gruber, A.; Hirtl, A.; Ishiwatari, T.; Marton, J.; Schmid, P.; Zmeskal, J.; Gotta, D.; Hennebach, M.; Nekipelov, M.; Indelicato, P.; Jensen, T.; Bigot, E.O. Le; Trassinelli, M.; Simons, L.M.

    2005-01-01

    The new pionic hydrogen experiment at PSI aims at an improvement in the determination of the strong interaction ground state shift and width of the pionic hydrogen atom. High precision x-ray crystal spectroscopy is used to extract isospin separated scattering lengths with accuracies on the percent level. Compared to previous efforts, the energy resolution and statistics could be improved considerably and the background is much reduced. The response function of the Johann-type crystal spectrometer has been determined with a novel method with unprecedented accuracy. The inherent difficulties of the exotic atom's method result, from the fact that the formation of a sufficient amount of pionic hydrogen atoms requires a hydrogen target pressure of several bar at least. For the extraction of a strong interaction shift, an extrapolation method to vacuum conditions proved to be successful. This contribution mostly discusses the strategy to extract a result for the strong interaction width from the data.(author)

  9. Exploring Relationships among Belief in Genetic Determinism, Genetics Knowledge, and Social Factors

    Science.gov (United States)

    Gericke, Niklas; Carver, Rebecca; Castéra, Jérémy; Evangelista, Neima Alice Menezes; Marre, Claire Coiffard; El-Hani, Charbel N.

    2017-01-01

    Genetic determinism can be described as the attribution of the formation of traits to genes, where genes are ascribed more causal power than what scientific consensus suggests. Belief in genetic determinism is an educational problem because it contradicts scientific knowledge, and is a societal problem because it has the potential to foster…

  10. Genetic variability of indigenous cowpea genotypes as determined ...

    African Journals Online (AJOL)

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

  11. How genetic determinism and genetic diseases are presented in textbooks of 14 countries

    OpenAIRE

    Silva, Carla; Ferreira, Cláudia; Carvalho, Graça Simões de

    2009-01-01

    The purpose of the present study was to analyse whether "Genetic Determinism" and "Genetic anomalies" are present in the textbooks of 14 countries and, being present, how these issues are addresses, for the age group of 14 to 18 years old. These countries are involved in the international project “Biohead-citzen”(European Project FP6 STREP Biohead-Citizen; CIT2-CT2004-506015) in which one of the topics is "Human Genetics" Results show that both terms “Genetic program" and "Genetic information...

  12. GENETICALLY DETERMINED WAY OF COGNITION IN THE RUSSIAN TRADITION

    Directory of Open Access Journals (Sweden)

    Tatyana M. Klimenkova

    2016-01-01

    Full Text Available It is reviles stages of cognition and comprehension according to natural genetic determinate pass of cognition, modern discovery in methodology and archetype code of cognition/comprehension, saving up in Slavonic culture.

  13. Genetic determinism of oil acidity among some DELI oil palm ...

    African Journals Online (AJOL)

    Genetic determinism of oil acidity among some DELI oil palm (Elaeis guineensis Jacq.) progenies. Benoit Constant Likeng-Li-Ngue, Joseph Martin Bell, Georges Franck Ngando-Ebongue, Godswill Ntsefong Ntsomboh, Hermine Bille Ngalle ...

  14. Temporal genetic stability in natural populations of the waterflea Daphnia magna in response to strong selection pressure.

    Science.gov (United States)

    Orsini, Luisa; Marshall, Hollie; Cuenca Cambronero, Maria; Chaturvedi, Anurag; Thomas, Kelley W; Pfrender, Michael E; Spanier, Katina I; De Meester, Luc

    2016-12-01

    Studies monitoring changes in genetic diversity and composition through time allow a unique understanding of evolutionary dynamics and persistence of natural populations. However, such studies are often limited to species with short generation times that can be propagated in the laboratory or few exceptional cases in the wild. Species that produce dormant stages provide powerful models for the reconstruction of evolutionary dynamics in the natural environment. A remaining open question is to what extent dormant egg banks are an unbiased representation of populations and hence of the species' evolutionary potential, especially in the presence of strong environmental selection. We address this key question using the water flea Daphnia magna, which produces dormant stages that accumulate in biological archives over time. We assess temporal genetic stability in three biological archives, previously used in resurrection ecology studies showing adaptive evolutionary responses to rapid environmental change. We show that neutral genetic diversity does not decline with the age of the population and it is maintained in the presence of strong selection. In addition, by comparing temporal genetic stability in hatched and unhatched populations from the same biological archive, we show that dormant egg banks can be consulted to obtain a reliable measure of genetic diversity over time, at least in the multidecadal time frame studied here. The stability of neutral genetic diversity through time is likely mediated by the buffering effect of the resting egg bank. © 2016 John Wiley & Sons Ltd.

  15. Finding the genetic determinants of adverse reactions to radiotherapy.

    Science.gov (United States)

    Rattay, T; Talbot, C J

    2014-05-01

    Individual variation in radiosensitivity is thought to be at least partly determined by genetic factors. The remaining difference between individuals is caused by comorbidities, variation in treatment, body habitus and stochastic factors. Evidence for the heritability of radiosensitivity comes from rare genetic disorders and from cell-based studies. To what extent common and rare genetic variants might explain the genetic component of radiosensitivity has not been fully elucidated. If the genetic variants accounting for this heritability were to be determined, they could be incorporated into any future predictive statistical model of adverse reactions to radiotherapy. With the evolution of DNA sequencing and bioinformatics, radiogenomics has emerged as a new research field with the aim of finding the genetic determinants of adverse reactions to radiotherapy. Similar to the investigation of other complex genetic disease traits, early studies in radiogenomics involved candidate gene association studies--many plagued by false associations caused by low sample sizes and problematic experimental design. More recently, some promising genetic associations (e.g. with tumour necrosis factor) have emerged from large multi-institutional cohorts with built-in replication. At the same time, several small- to medium-sized genome-wide association studies (GWAS) have been or are about to be published. These studies will probably lead to an increasing number of genetic polymorphisms that may predict adverse reactions to radiotherapy. The future of the field is to create large patient cohorts for multiple cancer types, to validate the genetic loci and build reliable predictive models. For example, the REQUITE project involves multiple groups in Europe and North America. For further discovery studies, larger GWAS will be necessary to include rare sequence variants through next generation sequencing. Ultimately, radiogenomics seeks to predict which cancer patients will show

  16. Genetic determinants of serum vitamin B12 and their relation to body mass index

    DEFF Research Database (Denmark)

    Allin, Kristine H; Friedrich, Nele; Pietzner, Maik

    2017-01-01

    for associations between (1) serum vitamin B12 levels and body mass index (BMI), (2) genetic variants and serum vitamin B12 levels, and (3) genetic variants and BMI. The effect of a genetically determined decrease in serum vitamin B12 on BMI was estimated by instrumental variable regression. Decreased serum...... vitamin B12 associated with increased BMI (P genetic risk score based on eight vitamin B12 associated variants associated strongly with serum vitamin B12 (P ... was associated with a 0.09 kg/m(2) (95% CI 0.05; 0.13) increase in BMI (P = 3 × 10(-5)), whereas a genetically induced 20% decrease in serum vitamin B12 had no effect on BMI [-0.03 (95% CI -0.22; 0.16) kg/m(2)] (P = 0.74). Nevertheless, the strongest serum vitamin B12 variant, FUT2 rs602662, which was excluded...

  17. Genetic markers cannot determine Jewish descent

    Directory of Open Access Journals (Sweden)

    Raphael eFalk

    2015-01-01

    Full Text Available Social interaction is a basic property of human Darwinian evolution. Presumably inherent differential physical as well as behavioural properties have always been criteria for identifying friend or foe. Yet, biological determinism is a relatively modern term, and scientific racism is, oddly enough, largely a consequence or a product of the Age of Enlightenment and the establishment of the notion of human equality. In recent decades ever-increasing efforts and ingenuity were invested in identifying Biblical Israelite genotypic common denominators by analysing assorted phenotypes, like facial patterns, blood types, diseases, DNA-sequences, and more. It becomes overwhelmingly clear that although Jews by their socio-religious-cultural relationship maintained also considerable consanguinity, there is no Jewish genotype to identify.

  18. Polygyny and strong genetic structuring within an isolated population of the wood ant Formica rufa

    Directory of Open Access Journals (Sweden)

    Wouter Dekoninck

    2014-12-01

    Full Text Available Social structuring of populations within some Formica species exhibits considerable variation going from monodomous and monogynous populations to polydomous, polygynous populations. The wood ant species Formica rufa appears to be mainly monodomous and monogynous throughout most of its distribution area in central and northern Europe. Only occasionally it was mentioned that F. rufa can have both polygynous and monogynous colonies in the same geographical region. We studied an isolated polydomous F. rufa population in a deciduous mixed forest in the north-west of Belgium. The level of polydomy within the colonies varied from monodomous to 11 nests per colony. Our genetic analysis of eight variable microsatellites suggest an oligo- to polygynous structure for at least the major part of the sampled nests. Relatedness amongst nest mate workers varies considerable within the population and colonies but confirms in general a polygynous structure. Additionally high genetic diversity (e.g. up to 8 out of 11 alleles per nest for the most variable locus and high within nest genetic variance (93% indicate that multiple queens contribute to the gene pool of workers of the same nest. Moreover significant genetic structuring among colonies indicates that gene flow between colonies is restricted and that exchange of workers between colonies is very limited. Finally we explain how possible factors as budding and the absence of Serviformica can explain the differences in genetic structure within this polygynous F. rufa population.

  19. Microsatellites reveal a strong subdivision of genetic structure in Chinese populations of the mite Tetranychus urticae Koch (Acari: Tetranychidae

    Directory of Open Access Journals (Sweden)

    Sun Jing-Tao

    2012-02-01

    Full Text Available Abstract Background Two colour forms of the two-spotted spider mite (Tetranychus urticae Koch coexist in China: a red (carmine form, which is considered to be native and a green form which is considered to be invasive. The population genetic diversity and population genetic structure of this organism were unclear in China, and there is a controversy over whether they constitute distinct species. To address these issues, we genotyped a total of 1,055 individuals from 18 red populations and 7 green populations in China using eight microsatellite loci. Results We identified 109 alleles. We found a highly significant genetic differentiation among the 25 populations (global FST = 0.506, global FST {ENA} = 0.473 and a low genetic diversity in each population. In addition, genetic diversity of the red form mites was found to be higher than the green form. Pearson correlations between statistics of variation (AR and HE and geographic coordinates (latitude and longitude showed that the genetic diversity of the red form was correlated with latitude. Using Bayesian clustering, we divided the Chinese mite populations into five clades which were well congruent with their geographic distributions. Conclusions Spider mites possess low levels of genetic diversity, limit gene flow between populations and significant and IBD (isolation by distance effect. These factors in turn contribute to the strong subdivision of genetic structure. In addition, population genetic structure results don't support the separation of the two forms of spider mite into two species. The morphological differences between the two forms of mites may be a result of epigenetic effects.

  20. Pubertal onset in girls is strongly influenced by genetic variation affecting FSH action

    DEFF Research Database (Denmark)

    Hagen, Casper P; Sørensen, Kaspar; Aksglaede, Lise

    2014-01-01

    Age at pubertal onset varies substantially in healthy girls. Although genetic factors are responsible for more than half of the phenotypic variation, only a small part has been attributed to specific genetic polymorphisms identified so far. Follicle-stimulating hormone (FSH) stimulates ovarian...... follicle maturation and estradiol synthesis which is responsible for breast development. We assessed the effect of three polymorphisms influencing FSH action on age at breast deveopment in a population-based cohort of 964 healthy girls. Girls homozygous for FSHR -29AA (reduced FSH receptor expression...

  1. Genetic determinants of depression: Recent findings and future directions

    Science.gov (United States)

    Dunn, Erin C.; Brown, Ruth C.; Dai, Yael; Rosand, Jonathan; Nugent, Nicole R.; Amstadter, Ananda B.; Smoller, Jordan W.

    2014-01-01

    Depression is one of the most prevalent, disabling, and costly mental health conditions in the United States. One promising avenue for preventing depression and informing its clinical treatment lies in uncovering both the genetic and environmental determinants of the disorder as well as their interaction (i.e. gene-environment intervention; GxE). The overarching goal of this review paper is to translate recent findings from studies of genetic association and GxE related to depression, particularly for readers without in-depth knowledge of genetics or genetic methods. This review is organized into three major sections. In the first section, we summarize what is currently known about the genetic determinants of depression, focusing on findings from genome-wide association studies (GWAS). In the second section, we review findings from studies of GxE, which seek to simultaneously examine the role of genes and exposure to specific environments or experiences in the etiology of depression. In the third section, we describe the challenges to genetic discovery in depression and promising strategies for making progress. PMID:25563565

  2. A Neolithic expansion, but strong genetic structure, in the independent history of New Guinea.

    Science.gov (United States)

    Bergström, Anders; Oppenheimer, Stephen J; Mentzer, Alexander J; Auckland, Kathryn; Robson, Kathryn; Attenborough, Robert; Alpers, Michael P; Koki, George; Pomat, William; Siba, Peter; Xue, Yali; Sandhu, Manjinder S; Tyler-Smith, Chris

    2017-09-15

    New Guinea shows human occupation since ~50 thousand years ago (ka), independent adoption of plant cultivation ~10 ka, and great cultural and linguistic diversity today. We performed genome-wide single-nucleotide polymorphism genotyping on 381 individuals from 85 language groups in Papua New Guinea and find a sharp divide originating 10 to 20 ka between lowland and highland groups and a lack of non-New Guinean admixture in the latter. All highlanders share ancestry within the last 10 thousand years, with major population growth in the same period, suggesting population structure was reshaped following the Neolithic lifestyle transition. However, genetic differentiation between groups in Papua New Guinea is much stronger than in comparable regions in Eurasia, demonstrating that such a transition does not necessarily limit the genetic and linguistic diversity of human societies. Copyright © 2017, American Association for the Advancement of Science.

  3. A Neolithic expansion, but strong genetic structure, in the independent history of New Guinea

    Science.gov (United States)

    Bergström, Anders; Oppenheimer, Stephen J; Mentzer, Alexander J; Auckland, Kathryn; Robson, Kathryn; Attenborough, Robert; Alpers, Michael P; Koki, George; Pomat, William; Siba, Peter; Xue, Yali; Sandhu, Manjinder S; Tyler-Smith, Chris

    2018-01-01

    New Guinea shows human occupation since ~50 thousand years ago (kya), independent adoption of plant cultivation ~10 kya, and great cultural and linguistic diversity today. We performed genome-wide SNP genotyping on 381 individuals from 85 language groups in Papua New Guinea (PNG) and find a sharp divide originating 10-20 kya between lowland and highland groups, and a lack of non-New Guinean admixture in the latter. All highlanders share ancestry within the last 10 kya, with major population growth in the same period, suggesting population structure was reshaped following the Neolithic lifestyle transition. However, genetic differentiation between groups in PNG is much stronger than in comparable regions in Eurasia, demonstrating that such a transition does not necessarily limit the genetic and linguistic diversity of human societies. PMID:28912245

  4. Candidate genes detected in transcriptome studies are strongly dependent on genetic background.

    Directory of Open Access Journals (Sweden)

    Pernille Sarup

    2011-01-01

    Full Text Available Whole genome transcriptomic studies can point to potential candidate genes for organismal traits. However, the importance of potential candidates is rarely followed up through functional studies and/or by comparing results across independent studies. We have analysed the overlap of candidate genes identified from studies of gene expression in Drosophila melanogaster using similar technical platforms. We found little overlap across studies between putative candidate genes for the same traits in the same sex. Instead there was a high degree of overlap between different traits and sexes within the same genetic backgrounds. Putative candidates found using transcriptomics therefore appear very sensitive to genetic background and this can mask or override effects of treatments. The functional importance of putative candidate genes emerging from transcriptome studies needs to be validated through additional experiments and in future studies we suggest a focus on the genes, networks and pathways affecting traits in a consistent manner across backgrounds.

  5. Winemaking and bioprocesses strongly shaped the genetic diversity of the ubiquitous yeast Torulaspora delbrueckii.

    Directory of Open Access Journals (Sweden)

    Warren Albertin

    Full Text Available The yeast Torulaspora delbrueckii is associated with several human activities including oenology, bakery, distillery, dairy industry, etc. In addition to its biotechnological applications, T. delbrueckii is frequently isolated in natural environments (plant, soil, insect. T. delbrueckii is thus a remarkable ubiquitous yeast species with both wild and anthropic habitats, and appears to be a perfect yeast model to search for evidence of human domestication. For that purpose, we developed eight microsatellite markers that were used for the genotyping of 110 strains from various substrates and geographical origins. Microsatellite analysis showed four genetic clusters: two groups contained most nature strains from Old World and Americas respectively, and two clusters were associated with winemaking and other bioprocesses. Analysis of molecular variance (AMOVA confirmed that human activities significantly shaped the genetic variability of T. delbrueckii species. Natural isolates are differentiated on the basis of geographical localisation, as expected for wild population. The domestication of T. delbrueckii probably dates back to the Roman Empire for winemaking (∼ 1900 years ago, and to the Neolithic era for bioprocesses (∼ 4000 years ago. Microsatellite analysis also provided valuable data regarding the life-cycle of the species, suggesting a mostly diploid homothallic life. In addition to population genetics and ecological studies, the microsatellite tool will be particularly useful for further biotechnological development of T. delbrueckii strains for winemaking and other bioprocesses.

  6. Winemaking and bioprocesses strongly shaped the genetic diversity of the ubiquitous yeast Torulaspora delbrueckii.

    Science.gov (United States)

    Albertin, Warren; Chasseriaud, Laura; Comte, Guillaume; Panfili, Aurélie; Delcamp, Adline; Salin, Franck; Marullo, Philippe; Bely, Marina

    2014-01-01

    The yeast Torulaspora delbrueckii is associated with several human activities including oenology, bakery, distillery, dairy industry, etc. In addition to its biotechnological applications, T. delbrueckii is frequently isolated in natural environments (plant, soil, insect). T. delbrueckii is thus a remarkable ubiquitous yeast species with both wild and anthropic habitats, and appears to be a perfect yeast model to search for evidence of human domestication. For that purpose, we developed eight microsatellite markers that were used for the genotyping of 110 strains from various substrates and geographical origins. Microsatellite analysis showed four genetic clusters: two groups contained most nature strains from Old World and Americas respectively, and two clusters were associated with winemaking and other bioprocesses. Analysis of molecular variance (AMOVA) confirmed that human activities significantly shaped the genetic variability of T. delbrueckii species. Natural isolates are differentiated on the basis of geographical localisation, as expected for wild population. The domestication of T. delbrueckii probably dates back to the Roman Empire for winemaking (∼ 1900 years ago), and to the Neolithic era for bioprocesses (∼ 4000 years ago). Microsatellite analysis also provided valuable data regarding the life-cycle of the species, suggesting a mostly diploid homothallic life. In addition to population genetics and ecological studies, the microsatellite tool will be particularly useful for further biotechnological development of T. delbrueckii strains for winemaking and other bioprocesses.

  7. Molecular and Genetic Determinants of Glioma Cell Invasion

    Directory of Open Access Journals (Sweden)

    Kenta Masui

    2017-12-01

    Full Text Available A diffusely invasive nature is a major obstacle in treating a malignant brain tumor, “diffuse glioma”, which prevents neurooncologists from surgically removing the tumor cells even in combination with chemotherapy and radiation. Recently updated classification of diffuse gliomas based on distinct genetic and epigenetic features has culminated in a multilayered diagnostic approach to combine histologic phenotypes and molecular genotypes in an integrated diagnosis. However, it is still a work in progress to decipher how the genetic aberrations contribute to the aggressive nature of gliomas including their highly invasive capacity. Here we depict a set of recent discoveries involving molecular genetic determinants of the infiltrating nature of glioma cells, especially focusing on genetic mutations in receptor tyrosine kinase pathways and metabolic reprogramming downstream of common cancer mutations. The specific biology of glioma cell invasion provides an opportunity to explore the genotype-phenotype correlation in cancer and develop novel glioma-specific therapeutic strategies for this devastating disease.

  8. Genetic determinants of heart failure: facts and numbers.

    Science.gov (United States)

    Czepluch, Frauke S; Wollnik, Bernd; Hasenfuß, Gerd

    2018-02-19

    The relevance of gene mutations leading to heart diseases and hence heart failure has become evident. The risk for and the course of heart failure depends on genomic variants and mutations underlying the so-called genetic predisposition. Genetic contribution to heart failure is highly heterogenous and complex. For any patient with a likely inherited heart failure syndrome, genetic counselling is recommended and important. In the last few years, novel sequencing technologies (named next-generation sequencing - NGS) have dramatically improved the availability of molecular testing, the efficiency of genetic analyses, and moreover reduced the cost for genetic testing. Due to this development, genetic testing has become increasingly accessible and NGS-based sequencing is now applied in clinical routine diagnostics. One of the most common reasons of heart failure are cardiomyopathies such as the dilated or the hypertrophic cardiomyopathy. Nearly 100 disease-associated genes have been identified for cardiomyopathies. The knowledge of a pathogenic mutation can be used for genetic counselling, risk and prognosis determination, therapy guidance and hence for a more effective treatment. Besides, family cascade screening for a known familial, pathogenic mutation can lead to an early diagnosis in affected individuals. At that timepoint, a preventative intervention could be used to avoid or delay disease onset or delay disease progression. Understanding the cellular basis of genetic heart failure syndromes in more detail may provide new insights into the molecular biology of physiological and impaired cardiac (cell) function. As our understanding of the molecular and genetic pathophysiology of heart failure will increase, this might help to identify novel therapeutic targets and may lead to the development of new and specific treatment options in patients with heart failure. © 2018 The Authors. ESC Heart Failure published by John Wiley & Sons Ltd on behalf of the European

  9. Strongly enhanced colorectal cancer risk stratification by combining family history and genetic risk score

    Directory of Open Access Journals (Sweden)

    Weigl K

    2018-01-01

    Full Text Available Korbinian Weigl,1,2 Jenny Chang-Claude,3,4 Phillip Knebel,5 Li Hsu,6 Michael Hoffmeister,1 Hermann Brenner1,2,7 1Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ, Heidelberg, 2German Cancer Consortium (DKTK, German Cancer Research Center (DKFZ, Heidelberg, 3Unit of Genetic Epidemiology, German Cancer Research Center (DKFZ, Heidelberg, 4University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, 5Department for General, Visceral and Transplantation Surgery, University Heidelberg, Heidelberg, Germany; 6Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; 7Division of Preventive Oncology, German Cancer Research Center (DKFZ and National Center for Tumor Diseases (NCT, Heidelberg, Germany Background and aim: Family history (FH and genetic risk scores (GRSs are increasingly used for risk stratification for colorectal cancer (CRC screening. However, they were mostly considered alternatively rather than jointly. The aim of this study was to assess the potential of individual and joint risk stratification for CRC by FH and GRS.Patients and methods: A GRS was built based on the number of risk alleles in 53 previously identified single-nucleotide polymorphisms among 2,363 patients with a first diagnosis of CRC and 2,198 controls in DACHS [colorectal cancer: chances for prevention through screening], a population-based case-control study in Germany. Associations between GRS and FH with CRC risk were quantified by multiple logistic regression.Results: A total of 316 cases (13.4% and 214 controls (9.7% had a first-degree relative (FDR with CRC (adjusted odds ratio [aOR] 1.86, 95% CI 1.52–2.29. A GRS in the highest decile was associated with a 3.0-fold increased risk of CRC (aOR 3.00, 95% CI 2.24–4.02 compared with the lowest decile. This association was tentatively more pronounced in older age groups. FH and GRS were essentially unrelated, and their

  10. Automatic Creation of Machine Learning Workflows with Strongly Typed Genetic Programming

    Czech Academy of Sciences Publication Activity Database

    Křen, T.; Pilát, M.; Neruda, Roman

    2017-01-01

    Roč. 26, č. 5 (2017), č. článku 1760020. ISSN 0218-2130 R&D Projects: GA ČR GA15-19877S Grant - others:GA MŠk(CZ) LM2015042 Institutional support: RVO:67985807 Keywords : genetic programming * machine learning workflows * asynchronous evolutionary algorithm Subject RIV: IN - Informatics, Computer Science OBOR OECD: Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8) Impact factor: 0.778, year: 2016

  11. A Strong Impact of Genetic Background on Gut Microflora in Mice

    Directory of Open Access Journals (Sweden)

    R. Steven Esworthy

    2010-01-01

    Full Text Available Genetic background affects susceptibility to ileocolitis in mice deficient in two intracellular glutathione peroxidases, GPx1 and GPx2. The C57BL/6 (B6 GPx1/2 double-knockout (DKO mice have mild ileocolitis, and 129S1/Sv (129 DKO mice have severe inflammation. We used diet to modulate ileocolitis; a casein-based defined diet with AIN76A micronutrients (AIN attenuates inflammation compared to conventional LabDiets. Because luminal microbiota induce DKO ileocolitis, we assessed bacterial composition with automated ribosomal intergenic-spacer analysis (ARISA on cecal DNA. We found that mouse strain had the strongest impact on the composition of microbiota than diet and GPx genotypes. In comparing AIN and LabDiet, DKO mice were more resistant to change than the non-DKO or WT mice. However, supplementing yeast and inulin to AIN diet greatly altered microflora profiles in the DKO mice. From 129 DKO strictly, we found overgrowth of Escherichia coli. We conclude that genetic background predisposes mice to colonization of potentially pathogenic E. coli.

  12. Genetic determinants of P wave duration and PR segment

    NARCIS (Netherlands)

    Verweij, Niek; Mateo Leach, Irene; van den Boogaard, Malou; van Veldhuisen, Dirk J.; Christoffels, Vincent M.; Hillege, Hans L.; van Gilst, Wiek H.; Barnett, Phil; de Boer, Rudolf A.; van der Harst, Pim

    2014-01-01

    The PR interval on the ECG reflects atrial depolarization and atrioventricular nodal delay which can be partially differentiated by P wave duration and PR segment, respectively. Genome-wide association studies have identified several genetic loci for PR interval, but it remains to be determined

  13. Determination of genetic diversity among some almond accessions

    Directory of Open Access Journals (Sweden)

    Pinar Hasan

    2015-01-01

    Full Text Available More recently the use of different molecular markers in fruit species to determine particularly genetic diversity, genetic relationships and cultivar identification has been gained more importance. In the study, 13 randomly amplified polimorfic DNA (RAPD and 4 inter-simple sequence repeat (ISSR markers were used to evaluate genetic relationships among 95 almong accessions (26 foreign cultivars and 69 national cultivars and selections. The all plant material found in Almond Germplasm Repository in Gaziantep, Turkey. Both RAPD and ISSR markers distinguished the almond cultivars and selections in various levels. 17 RAPD and ISSR markers yielded a total of 73 scorable bands, which 51 are polymorphic. The two marker system exhibited variation with regard to average band sizes and polymorphism ratio. The average polymorphism was higher in ISSR (88% compared to RAPD (74%. RAPD and ISSR marker systems were found to be useful for determining genetic diversity among almong genotypes and cultivars. Combining of two dendrograms obtained through these markers show different clustering of 96 almond specimens without geographical isolation. These results supported that almonds in Turkey indicated considerable genetic diversity.

  14. Precision determination of the strong coupling constant within a global PDF analysis arXiv

    CERN Document Server

    Ball, Richard D.; Del Debbio, Luigi; Forte, Stefano; Kassabov, Zahari; Rojo, Juan; Slade, Emma; Ubiali, Maria

    We present a determination of the strong coupling constant $\\alpha_s(m_Z)$ based on the NNPDF3.1 determination of parton distributions, which for the first time includes constraints from jet production, top-quark pair differential distributions, and the $Z$ $p_T$ distributions using exact NNLO theory. Our result is based on a novel extension of the NNPDF methodology - the correlated replica method - which allows for a simultaneous determination of $\\alpha_s$ and the PDFs with all correlations between them fully taken into account. We study in detail all relevant sources of experimental, methodological and theoretical uncertainty. At NNLO we find $\\alpha_s(m_Z) = 0.1185 \\pm 0.0005^\\text{(exp)}\\pm 0.0001^\\text{(meth)}$, showing that methodological uncertainties are negligible. We conservatively estimate the theoretical uncertainty due to missing higher order QCD corrections (N$^3$LO and beyond) from half the shift between the NLO and NNLO $\\alpha_s$ values, finding $\\Delta\\alpha^{\\rm th}_s =0.0011$.

  15. Application of genetic algorithm in radio ecological models parameter determination

    International Nuclear Information System (INIS)

    Pantelic, G.

    2006-01-01

    The method of genetic algorithms was used to determine the biological half-life of 137 Cs in cow milk after the accident in Chernobyl. Methodologically genetic algorithms are based on the fact that natural processes tend to optimize themselves and therefore this method should be more efficient in providing optimal solutions in the modeling of radio ecological and environmental events. The calculated biological half-life of 137 Cs in milk is (32 ± 3) days and transfer coefficient from grass to milk is (0.019 ± 0.005). (authors)

  16. Application of genetic algorithm in radio ecological models parameter determination

    Energy Technology Data Exchange (ETDEWEB)

    Pantelic, G. [Institute of Occupatioanl Health and Radiological Protection ' Dr Dragomir Karajovic' , Belgrade (Serbia)

    2006-07-01

    The method of genetic algorithms was used to determine the biological half-life of 137 Cs in cow milk after the accident in Chernobyl. Methodologically genetic algorithms are based on the fact that natural processes tend to optimize themselves and therefore this method should be more efficient in providing optimal solutions in the modeling of radio ecological and environmental events. The calculated biological half-life of 137 Cs in milk is (32 {+-} 3) days and transfer coefficient from grass to milk is (0.019 {+-} 0.005). (authors)

  17. Strong evidence for a genetic contribution to late-onset Alzheimer's disease mortality: a population-based study.

    Directory of Open Access Journals (Sweden)

    John S K Kauwe

    Full Text Available Alzheimer's disease (AD is an international health concern that has a devastating effect on patients and families. While several genetic risk factors for AD have been identified much of the genetic variance in AD remains unexplained. There are limited published assessments of the familiality of Alzheimer's disease. Here we present the largest genealogy-based analysis of AD to date.We assessed the familiality of AD in The Utah Population Database (UPDB, a population-based resource linking electronic health data repositories for the state with the computerized genealogy of the Utah settlers and their descendants. We searched UPDB for significant familial clustering of AD to evaluate the genetic contribution to disease. We compared the Genealogical Index of Familiality (GIF between AD individuals and randomly selected controls and estimated the Relative Risk (RR for a range of family relationships. Finally, we identified pedigrees with a significant excess of AD deaths.The GIF analysis showed that pairs of individuals dying from AD were significantly more related than expected. This excess of relatedness was observed for both close and distant relationships. RRs for death from AD among relatives of individuals dying from AD were significantly increased for both close and more distant relatives. Multiple pedigrees had a significant excess of AD deaths.These data strongly support a genetic contribution to the observed clustering of individuals dying from AD. This report is the first large population-based assessment of the familiality of AD mortality and provides the only reported estimates of relative risk of AD mortality in extended relatives to date. The high-risk pedigrees identified show a true excess of AD mortality (not just multiple cases and are greater in depth and width than published AD pedigrees. The presence of these high-risk pedigrees strongly supports the possibility of rare predisposition variants not yet identified.

  18. Strong genetic structure corresponds to small-scale geographic breaks in the Australian alpine grasshopper Kosciuscola tristis.

    Science.gov (United States)

    Slatyer, Rachel A; Nash, Michael A; Miller, Adam D; Endo, Yoshinori; Umbers, Kate D L; Hoffmann, Ary A

    2014-10-02

    Mountain landscapes are topographically complex, creating discontinuous 'islands' of alpine and sub-alpine habitat with a dynamic history. Changing climatic conditions drive their expansion and contraction, leaving signatures on the genetic structure of their flora and fauna. Australia's high country covers a small, highly fragmented area. Although the area is thought to have experienced periods of relative continuity during Pleistocene glacial periods, small-scale studies suggest deep lineage divergence across low-elevation gaps. Using both DNA sequence data and microsatellite markers, we tested the hypothesis that genetic partitioning reflects observable geographic structuring across Australia's mainland high country, in the widespread alpine grasshopper Kosciuscola tristis (Sjösted). We found broadly congruent patterns of regional structure between the DNA sequence and microsatellite datasets, corresponding to strong divergence among isolated mountain regions. Small and isolated mountains in the south of the range were particularly distinct, with well-supported divergence corresponding to climate cycles during the late Pliocene and Pleistocene. We found mixed support, however, for divergence among other mountain regions. Interestingly, within areas of largely contiguous alpine and sub-alpine habitat around Mt Kosciuszko, microsatellite data suggested significant population structure, accompanied by a strong signature of isolation-by-distance. Consistent patterns of strong lineage divergence among different molecular datasets indicate genetic breaks between populations inhabiting geographically distinct mountain regions. Three primary phylogeographic groups were evident in the highly fragmented Victorian high country, while within-region structure detected with microsatellites may reflect more recent population isolation. Despite the small area of Australia's alpine and sub-alpine habitats, their low topographic relief and lack of extensive glaciation

  19. Arithmetic, reading and writing performance has a strong genetic component: A study in primary school children

    NARCIS (Netherlands)

    de Zeeuw, L.E.J.; van Beijsterveldt, C.E.M.; Glasner, T.J.; de Geus, E.J.C.; Boomsma, D.I.

    2016-01-01

    Even children attending the same primary school and taught by the same teacher differ greatly in their performance. In the Netherlands, performance at the end of primary school determines the enrollment in a particular level of secondary education. Identifying the impact of genes and the environment

  20. Self-Conscious Shyness: Growth during Toddlerhood, Strong Role of Genetics, and No Prediction from Fearful Shyness

    OpenAIRE

    Eggum-Wilkens, Natalie D.; Lemery-Chalfant, Kathryn; Aksan, Nazan; Goldsmith, H. Hill

    2014-01-01

    Fearful and self-conscious subtypes of shyness have received little attention in the empirical literature. Study aims included: 1) determining if fearful shyness predicted self-conscious shyness, 2) describing development of self-conscious shyness, and 3) examining genetic and environmental contributions to fearful and self-conscious shyness. Observed self-conscious shyness was examined at 19, 22, 25, and 28 months in same-sex twins (MZ = 102, DZ = 111, missing zygosity = 3 pairs). Self-consc...

  1. Using vibrational Cooper minima to determine strong-field molecular-dissociation pathways

    Science.gov (United States)

    Severt, T.; Zohrabi, M.; Armstrong, G. S. J.; McKenna, J.; Gaire, B.; Kling, Nora G.; Ablikim, U.; Carnes, K. D.; Esry, B. D.; Ben-Itzhak, I.

    2015-05-01

    We explore the possibility of using vibrational ``Cooper minima'' (VCM) locations as a method to determine dissociation pathways of molecules in a strong laser field. As a test case, we study the laser-induced dissociation of an O2+ion beam by several wavelengths (λ = 800 , 400, and 266 nm) using a coincidence three-dimensional momentum imaging technique. Vibrational structure is observed in the kinetic energy release spectra, revealing a suppression of the dissociation of certain vibrational levels, which is a manifestation of the VCM effect. Previously, it has been shown in H2+that first-order time-dependent perturbation theory can be used to predict the locations of the VCM. We explore if the VCM locations predicted by perturbation theory can help uniquely identify dissociation pathways in O2+and consider its utility for other systems. Supported by the Chemical Sciences, Geosciences, and Biosciences Division, Office of Basic Energy Sciences, Office of Science, U.S. Department of Energy. TS was partially supported by NSF-REU under Grant No. PHY-0851599.

  2. Teachers' Conceptions About the Genetic Determinism of Human Behaviour: A Survey in 23 Countries

    Science.gov (United States)

    Castéra, Jérémy; Clément, Pierre

    2012-07-01

    This work analyses the answers to a questionnaire from 8,285 in-service and pre-service teachers from 23 countries, elaborated by the Biohead-Citizen research project, to investigate teachers' conceptions related to the genetic determinism of human behaviour. A principal components analysis is used to assess the main trends in all the interviewed teachers' conceptions. This illustrates that innatism is present in two distinct ways: in relation to individuals (e.g. genetic determinism to justify intellectual likeness between individuals such as twins) or in relation to groups of humans (e.g. genetic determinism to justify gender differences or the superiority of some human ethnic groups). A between-factor analysis discriminates between countries, showing very significant differences. There is more innatism among teachers' conceptions in African countries and Lebanon than in European countries, Brazil and Australia. Among the other controlled parameters, only two are significantly independent of the country: the level of training and the level of knowledge of biology. A co-inertia analysis shows a strong correlation between non-citizen attitudes towards and innatist conceptions of genetic determinism regarding human groups. We discuss these findings and their implications for education.

  3. Genetically determined patozoospermia. Literature review and research results

    Directory of Open Access Journals (Sweden)

    E. E. Bragina

    2015-01-01

    Full Text Available Genetic factors (chromosomal aberrations and point mutations are the cause of infertility in 10–15 % of men with impaired fertility. Homogeneous structural and functional defects in the sperm or the total terato-, asthenozoospermia – rare cases of genetically determined male infertility, are autosomal recessive diseases. Currently, described 4 types of «syndromic» spermopatology. 1. Primary ciliary dyskinesia (PCD in men with total asthenozoospermia. Affects axoneme structures (microtubules, dynein arms, radial spokes. It identified more than 20 chromosomal loci responsible for the development of the PCD. 2. Dysplasia of the fibrous sheath of sperm tail in men with asthenozoospermia. The shortened and thickened sperm tail observed with disorganization of vertical columns and cross ribs of the fibrous sheath. Candidate genes – genes family ACAP. 3. Globozoospermia in men with teratozoospermia characterized by the presence of sperm with round heads, primary lack of acrosome and disorganization middle part of the flagellum. Found mutations or deletions of genes SPATA16, PICK1 and DPY19L2. 4. Syndrome decapitated spermatozoa in men with teratozoospermia (microcephaly. Abnormalities in the spermiogenesis development of connecting part jf the tail and proximal (morphologically normal centrioles.In 2012–2014 years we have studied the ultrastructure of 2267 semen samples of men with impaired fertility. Globozoospermia revealed in 7 patients, dysplasia of the fibrous sheath – 13, decapitated sperm – in one. PCD was revealed in 4 patients (lack of axoneme dynein arms was found in 1 patient, absence of axoneme radial spokes – in 3 patients.The problem of genetically determined patozoospermya must be taken into account when the assisted reproductive technologies practises. There are few cases of successful assisted reproductive technologies with sperm of these patients. We don»t know the etiological factors of syndromic spermopatologe, so

  4. Genetic signature of strong recent positive selection at interleukin-32 gene in goat

    Directory of Open Access Journals (Sweden)

    Akhtar Rasool Asif

    2017-07-01

    Full Text Available Objective Identification of the candidate genes that play key roles in phenotypic variations can provide new information about evolution and positive selection. Interleukin (IL-32 is involved in many biological processes, however, its role for the immune response against various diseases in mammals is poorly understood. Therefore, the current investigation was performed for the better understanding of the molecular evolution and the positive selection of single nucleotide polymorphisms in IL-32 gene. Methods By using fixation index (FST based method, IL-32 (9375 gene was found to be outlier and under significant positive selection with the provisional combined allocation of mean heterozygosity and FST. Using nucleotide sequences of 11 mammalian species from National Center for Biotechnology Information database, the evolutionary selection of IL-32 gene was determined using Maximum likelihood model method, through four models (M1a, M2a, M7, and M8 in Codeml program of phylogenetic analysis by maximum liklihood. Results IL-32 is detected under positive selection using the FST simulations method. The phylogenetic tree revealed that goat IL-32 was in close resemblance with sheep IL-32. The coding nucleotide sequences were compared among 11 species and it was found that the goat IL-32 gene shared identity with sheep (96.54%, bison (91.97%, camel (58.39%, cat (56.59%, buffalo (56.50%, human (56.13%, dog (50.97%, horse (54.04%, and rabbit (53.41% respectively. Conclusion This study provides evidence for IL-32 gene as under significant positive selection in goat.

  5. Genetic signature of strong recent positive selection at interleukin-32 gene in goat.

    Science.gov (United States)

    Asif, Akhtar Rasool; Qadri, Sumayyah; Ijaz, Nabeel; Javed, Ruheena; Ansari, Abdur Rahman; Awais, Muhammd; Younus, Muhammad; Riaz, Hasan; Du, Xiaoyong

    2017-07-01

    Identification of the candidate genes that play key roles in phenotypic variations can provide new information about evolution and positive selection. Interleukin (IL)-32 is involved in many biological processes, however, its role for the immune response against various diseases in mammals is poorly understood. Therefore, the current investigation was performed for the better understanding of the molecular evolution and the positive selection of single nucleotide polymorphisms in IL-32 gene. By using fixation index ( F ST ) based method, IL-32 (9375) gene was found to be outlier and under significant positive selection with the provisional combined allocation of mean heterozygosity and F ST . Using nucleotide sequences of 11 mammalian species from National Center for Biotechnology Information database, the evolutionary selection of IL-32 gene was determined using Maximum likelihood model method, through four models (M1a, M2a, M7, and M8) in Codeml program of phylogenetic analysis by maximum liklihood. IL-32 is detected under positive selection using the F ST simulations method. The phylogenetic tree revealed that goat IL-32 was in close resemblance with sheep IL-32. The coding nucleotide sequences were compared among 11 species and it was found that the goat IL-32 gene shared identity with sheep (96.54%), bison (91.97%), camel (58.39%), cat (56.59%), buffalo (56.50%), human (56.13%), dog (50.97%), horse (54.04%), and rabbit (53.41%) respectively. This study provides evidence for IL-32 gene as under significant positive selection in goat.

  6. Determination and optimization of a strong promoter element from Bacillus amyloliquefaciens by using a promoter probe vector.

    Science.gov (United States)

    Liao, Yuling; Wang, Bin; Ye, Yanrui; Pan, Li

    2018-01-01

    To construct a promoter probe vector, pBE-bgaB, to screen strong promoters from Bacillus amyloliquefaciens. 266 colonies containing active promoter elements from the genomic DNA of B. amyloliquefaciens were identified. Among these, promoter P41 exhibited the strongest β-Gal activity in Escherichia coli and B. amyloliquefaciens. Sequence analysis showed that promoter P41 contained P ykuN , a ykuN gene encoding flavodoxin. Optimization of the ribosome-binding site from P41 to P 382 improved β-Gal activity by ~ 200%. A new strong promoter for protein expression and genetic engineering of Bacillus species.

  7. Determination of tropane alkaloids by heart cutting reversed phase - Strong cation exchange two dimensional liquid chromatography.

    Science.gov (United States)

    Long, Zhen; Zhang, Yanhai; Gamache, Paul; Guo, Zhimou; Steiner, Frank; Du, Nana; Liu, Xiaoda; Jin, Yan; Liu, Xingguo; Liu, Lvye

    2018-01-01

    Current Chinese Pharmacopoeia (ChP) standards apply liquid extraction combined with one dimensional liquid chromatography (1DLC) method for determining alkaloids in herbal medicines. The complex pretreatments lead to a low analytical efficiency and possible component loss. In this study, a heart cutting reversed phase - strong cation exchange two dimensional liquid chromatography (RP - SCX 2DLC) approach was optimized for simultaneously quantifying tropane alkaloids (anisodine, scopolamine and hyoscyamine) in herbal medicines and herbal medicine tablets without further treatment of the filtered extract. The chromatographic conditions were systematically optimized in terms of column type, mobile phase composition and flow rate. To improve peak capacity and obtain symmetric peak shape of alkaloids, a polar group embedded C18 column combined with chaotropic salts was used in the first dimension. To remove the disturbance of non-alkaloids, achieve unique selectivity and acquire symmetric peak shape of alkaloids, an SCX column combined with phosphate buffer was used in the second dimension. Method validation was performed in terms of linearity, precision (0.54-0.82%), recovery (94.1-105.2%), limit of detection (LOD) and limit of quantification (LOQ) of the three analytes varied between 0.067-0.115mgL -1 and 0.195-0.268mgL -1 , respectively. The method demonstrated superiority over 1DLC method in respect of resolution (less alkaloid co-eluted), sample preparation (no pretreatment procedure) and transfer rate (minimum component loss). The optimized RP - SCX 2DLC approach was subsequently applied to quantify target alkaloids in five herbal medicines and herbal medicine tablets from three different manufactures. The results demonstrated that the developed heart cutting RP - SCX 2DLC approach represented a new, strategically significant methodology for the quality evaluation of tropane alkaloid in related herbal medicines that involve complex chemical matrix. Copyright

  8. Application of genetic algorithms to focal mechanism determination

    Science.gov (United States)

    Kobayashi, Reiji; Nakanishi, Ichiro

    1994-04-01

    Genetic algorithms are a new class of methods for global optimization. They resemble Monte Carlo techniques, but search for solutions more efficiently than uniform Monte Carlo sampling. In the field of geophysics, genetic algorithms have recently been used to solve some non-linear inverse problems (e.g., earthquake location, waveform inversion, migration velocity estimation). We present an application of genetic algorithms to focal mechanism determination from first-motion polarities of P-waves and apply our method to two recent large events, the Kushiro-oki earthquake of January 15, 1993 and the SW Hokkaido (Japan Sea) earthquake of July 12, 1993. Initial solution and curvature information of the objective function that gradient methods need are not required in our approach. Moreover globally optimal solutions can be efficiently obtained. Calculation of polarities based on double-couple models is the most time-consuming part of the source mechanism determination. The amount of calculations required by the method designed in this study is much less than that of previous grid search methods.

  9. Genetic determinant of trabecular bone score (TBS) and bone mineral density: A bivariate analysis.

    Science.gov (United States)

    Ho-Pham, Lan T; Hans, Didier; Doan, Minh C; Mai, Linh D; Nguyen, Tuan V

    2016-11-01

    This study sought to estimate the extent of genetic influence on the variation in trabecular bone score (TBS). We found that genetic factors accounted for ~45% of variance in TBS, and that the co-variation between TBS and bone density is partially determined by genetic factors. Trabecular bone score has emerged as an important predictor of fragility fracture, but factors underlying the individual differences in TBS have not been explored. In this study, we sought to determine the genetic contribution to the variation of TBS in the general population. The study included 556 women and 189 men from 265 families. The individuals aged 53years (SD 11). We measured lumbar spine bone mineral density (BMD; Hologic Horizon) and then derived the TBS from the same Hologic scan where BMD was derived. A biometric model was applied to the data to partition the variance of TBS into two components: one due to additive genetic factors, and one due to environmental factors. The index of heritability was estimated as the ratio of genetic variance to total variance of a trait. Bivariate genetic analysis was conducted to estimate the genetic correlation between TBS and BMD measurements. TBS was strongly correlated with lumbar spine BMD (r=0.73; P<0.001). On average TBS in men was higher than women, after adjusting age and height which are significantly associated with both TBS and lumbar spine BMD. The age and height adjusted index of heritability of TBS was 0.46 (95% CI, 0.39-0.54), which was not much different from that of LSBMD (0.44; 95% CI, 0.31-0.55). Moreover, the genetic correlation between TBS and LSBMD was 0.35 (95% CI, 0.21-0.46), between TBS and femoral neck BMD was 0.21 (95% CI, 0.10-0.33). Approximately 45% of the variance in TBS is under genetic influence, and this effect magnitude is similar to that of lumbar spine BMD. This finding provides a scientific justification for the search for specific genetic variants that may be associated with TBS and fracture risk

  10. Genetic Determinants of Epigenetic Patterns: Providing Insight into Disease.

    Science.gov (United States)

    Cazaly, Emma; Charlesworth, Jac; Dickinson, Joanne L; Holloway, Adele F

    2015-03-26

    The field of epigenetics and our understanding of the mechanisms that regulate the establishment, maintenance and heritability of epigenetic patterns continue to grow at a remarkable rate. This information is providing increased understanding of the role of epigenetic changes in disease, insight into the underlying causes of these epigenetic changes and revealing new avenues for therapeutic intervention. Epigenetic modifiers are increasingly being pursued as therapeutic targets in a range of diseases, with a number of agents targeting epigenetic modifications already proving effective in diseases such as cancer. Although it is well established that DNA mutations and aberrant expression of epigenetic modifiers play a key role in disease, attention is now turning to the interplay between genetic and epigenetic factors in complex disease etiology. The role of genetic variability in determining epigenetic profiles, which can then be modified by environmental and stochastic factors, is becoming more apparent. Understanding the interplay between genetic and epigenetic factors is likely to aid in identifying individuals most likely to benefit from epigenetic therapies. This goal is coming closer to realization because of continual advances in laboratory and statistical tools enabling improvements in the integration of genomic, epigenomic and phenotypic data.

  11. Determination of nonlinear genetic architecture using compressed sensing.

    Science.gov (United States)

    Ho, Chiu Man; Hsu, Stephen D H

    2015-01-01

    One of the fundamental problems of modern genomics is to extract the genetic architecture of a complex trait from a data set of individual genotypes and trait values. Establishing this important connection between genotype and phenotype is complicated by the large number of candidate genes, the potentially large number of causal loci, and the likely presence of some nonlinear interactions between different genes. Compressed Sensing methods obtain solutions to under-constrained systems of linear equations. These methods can be applied to the problem of determining the best model relating genotype to phenotype, and generally deliver better performance than simply regressing the phenotype against each genetic variant, one at a time. We introduce a Compressed Sensing method that can reconstruct nonlinear genetic models (i.e., including epistasis, or gene-gene interactions) from phenotype-genotype (GWAS) data. Our method uses L1-penalized regression applied to nonlinear functions of the sensing matrix. The computational and data resource requirements for our method are similar to those necessary for reconstruction of linear genetic models (or identification of gene-trait associations), assuming a condition of generalized sparsity, which limits the total number of gene-gene interactions. An example of a sparse nonlinear model is one in which a typical locus interacts with several or even many others, but only a small subset of all possible interactions exist. It seems plausible that most genetic architectures fall in this category. We give theoretical arguments suggesting that the method is nearly optimal in performance, and demonstrate its effectiveness on broad classes of nonlinear genetic models using simulated human genomes and the small amount of currently available real data. A phase transition (i.e., dramatic and qualitative change) in the behavior of the algorithm indicates when sufficient data is available for its successful application. Our results indicate

  12. The 5-HT2A receptor binding pattern in the human brain is strongly genetically determined

    DEFF Research Database (Denmark)

    Pinborg, Lars H; Arfan, Haroon; Haugbol, Steven

    2007-01-01

    With the appropriate radiolabeled tracers, positron emission tomography (PET) enables in vivo human brain imaging of markers for neurotransmission, including neurotransmitter synthesis, receptors, and transporters. Whereas structural imaging studies have provided compelling evidence that the human...... variability in cortical 5-HT(2A) receptor binding as measured with [(18)F]altanserin PET imaging. The intraclass correlation coefficients were 0.67 for dizygotic and 0.87 for monozygotic twin pairs. For comparison, the intraclass correlation coefficient was 0.93 in a group of six male healthy subjects...

  13. Low-Dose Radiation Cataract and Genetic Determinants of Radiosensitivity

    Energy Technology Data Exchange (ETDEWEB)

    Kleiman, Norman Jay [Columbia University

    2013-11-30

    The lens of the eye is one of the most radiosensitive tissues in the body. Ocular ionizing radiation exposure results in characteristic, dose related, progressive lens changes leading to cataract formation. While initial, early stages of lens opacification may not cause visual disability, the severity of such changes progressively increases with dose until vision is impaired and cataract extraction surgery may be required. Because of the transparency of the eye, radiation induced lens changes can easily be followed non-invasively over time. Thus, the lens provides a unique model system in which to study the effects of low dose ionizing radiation exposure in a complex, highly organized tissue. Despite this observation, considerable uncertainties remain surrounding the relationship between dose and risk of developing radiation cataract. For example, a growing number of human epidemiological findings suggest significant risk among various groups of occupationally and accidentally exposed individuals and confidence intervals that include zero dose. Nevertheless, questions remain concerning the relationship between lens opacities, visual disability, clinical cataract, threshold dose and/or the role of genetics in determining radiosensitivity. Experimentally, the response of the rodent eye to radiation is quite similar to that in humans and thus animal studies are well suited to examine the relationship between radiation exposure, genetic determinants of radiosensitivity and cataractogenesis. The current work has expanded our knowledge of the low-dose effects of X-irradiation or high-LET heavy ion exposure on timing and progression of radiation cataract and has provided new information on the genetic, molecular, biochemical and cell biological features which contribute to this pathology. Furthermore, findings have indicated that single and/or multiple haploinsufficiency for various genes involved in DNA repair and cell cycle checkpoint control, such as Atm, Brca1 or Rad9

  14. Determination of nuclear friction in strongly damped reactions from prescission neutron multiplicities

    Energy Technology Data Exchange (ETDEWEB)

    Wilczynski, J. [Soltan Inst. for Nuclear Studies, Otwock-Swierk (Poland); Siwek-Wilczynska, K. [Warsaw Univ., Inst. of Experimental Physics, Warsaw (Poland); Wilschut, H.W. [Kernfysisch Verneller Instituut, Groningen (Netherlands)

    1996-12-31

    The neutron multiplicities in non-fusion reactions have been calculated in the frame of classical equation of motion with friction (Lagrange-Rayleigh equations) The calculated data were compared with the reported neutron multiplicities data. The results shown an evidence of the onset of a strong two-body dissipation at unexpected low temperatures, already at about 2 MeV. 3 refs, 1 fig.

  15. Plexcitons: The Role of Oscillator Strengths and Spectral Widths in Determining Strong Coupling

    Energy Technology Data Exchange (ETDEWEB)

    Thomas, Reshmi [School; Thomas, Anoop [School; Pullanchery, Saranya [School; Joseph, Linta [School; Somasundaran, Sanoop Mambully [School; Swathi, Rotti Srinivasamurthy [School; Gray, Stephen K. [Center; Thomas, K. George [School

    2018-01-05

    Strong coupling interactions between plasmon and exciton-based excitations have been proposed to be useful in the design of optoelectronic systems. However, the role of various optical parameters dictating the plasmon-exciton (plexciton) interactions is less understood. Herein, we propose an inequality for achieving strong coupling between plasmons and excitons through appropriate variation of their oscillator strengths and spectral widths. These aspects are found to be consistent with experiments on two sets of free-standing plexcitonic systems obtained by (i) linking fluorescein isothiocyanate on Ag nanoparticles of varying sizes through silane coupling and (ii) electrostatic binding of cyanine dyes on polystyrenesulfonate-coated Au nanorods of varying aspect ratios. Being covalently linked on Ag nanoparticles, fluorescein isothiocyanate remains in monomeric state, and its high oscillator strength and narrow spectral width enable us to approach the strong coupling limit. In contrast, in the presence of polystyrenesulfonate, monomeric forms of cyanine dyes exist in equilibrium with their aggregates: Coupling is not observed for monomers and H-aggregates whose optical parameters are unfavorable. The large aggregation number, narrow spectral width, and extremely high oscillator strength of J-aggregates of cyanines permit effective delocalization of excitons along the linear assembly of chromophores, which in turn leads to efficient coupling with the plasmons. Further, the results obtained from experiments and theoretical models are jointly employed to describe the plexcitonic states, estimate the coupling strengths, and rationalize the dispersion curves. The experimental results and the theoretical analysis presented here portray a way forward to the rational design of plexcitonic systems attaining the strong coupling limits.

  16. Genetic and metabolic determinants of human epigenetic variation.

    Science.gov (United States)

    Haggarty, Paul

    2015-07-01

    Epigenetics has emerged in recent years as one of the most important biological mechanisms linking exposures across the life course to long-term health. This article reviews recent developments in our understanding of the metabolic and genetic determinants of epigenetic variation in human populations. Epigenetic status is influenced by a range of environmental exposures, including diet and nutrition, social status, the early emotional environment, and infertility and its treatment. The period around conception is particularly sensitive to environmental exposures with evidence for effects on epigenetic imprinting within the offspring. Epigenetic status is also influenced by genotype, and genetic variation in methylene tetrahydrofolate reductase, and the DNA methytransferase and ten-eleven translocation methylcytosine dioxygenase proteins has been linked to the epigenetic status, biological function and disease. Epigenetics is at the heart of a series of feedback loops linking the environment to the human genome in a way that allows crosstalk between the genome and the environment it exists within. It offers the potential for modification of adverse epigenetic states resulting from events/exposures at earlier life stages. We need to better understand the nutritional programming of epigenetic states, the persistence of these marks in time and their effect on biological function and health in current and future generations.

  17. Quantification of genetically modified soya using strong anion exchange chromatography and time-of-flight mass spectrometry.

    Science.gov (United States)

    Chang, Po-Chih; Reddy, P Muralidhar; Ho, Yen-Peng

    2014-09-01

    Stable-isotope dimethyl labeling was applied to the quantification of genetically modified (GM) soya. The herbicide-resistant gene-related protein 5-enolpyruvylshikimate-3-phosphate synthase (CP4 EPSPS) was labeled using a dimethyl labeling reagent, formaldehyde-H2 or -D2. The identification and quantification of CP4 EPSPS was performed using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). The CP4 EPSPS protein was separated from high abundance proteins using strong anion exchange chromatography and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Then, the tryptic peptides from the samples and reference were labeled with formaldehyde-H2 and formaldehyde-D2, respectively. The two labeled pools were mixed and analyzed using MALDI-MS. The data showed a good correlation between the peak ratio of the H- and D-labeled peptides and the GM soya percentages at 0.5, 1, 3, and 5 %, with R (2) of 0.99. The labeling reagents are readily available. The labeling experiments and the detection procedures are simple. The approach is useful for the quantification of GM soya at a level as low as 0.5 %.

  18. Genetic evidence strongly support an essential role for PfPV1 in intra-erythrocytic growth of P. falciparum.

    Directory of Open Access Journals (Sweden)

    Trang Chu

    Full Text Available Upon invading the host erythrocyte, the human malaria parasite P. falciparum lives and replicates within a membrane bound compartment referred to as the parasitophorous vacuole. Recently, interest in this compartment and its protein content has grown, due to the important roles these play in parasite egress and protein traffic to the host cell. Surprisingly, the function of many proteins within this compartment has not been experimentally addressed. Here, we study the importance of one of these proteins, termed PfPV1, for intra-erythrocytic parasite survival. Despite numerous attempts to inactivate the gene encoding PfPV1, we were unable to recover deletion mutants. Control experiments verified that the pv1 gene locus was per se open for gene targeting experiments, allowing us to exclude technical limitations in our experimental strategy. Our data provide strong genetic evidence that PfPV1 is essential for survival of blood stage P. falciparum, and further highlight the importance of parasitophorous vacuole proteins in this part of the parasite's life cycle.

  19. Genetic Determinism vs. Phenotypic Plasticity in Protist Morphology

    Czech Academy of Sciences Publication Activity Database

    Mulot, M.; Marcisz, K.; Grandgirard, L.; Lara, E.; Kosakyan, Anush; Robroek, B. J. M.; Lamentowicz, M.; Payne, R. J.; Mitchell, E.A.D.

    2017-01-01

    Roč. 64, č. 6 (2017), s. 729-739 ISSN 1066-5234 Institutional support: RVO:60077344 Keywords : Body size * protozoa * soil moisture * testate amoebae * water table depth Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Genetics and heredity (medical genetics to be 3) Impact factor: 2.692, year: 2016

  20. The determination of the rotation period and magnetic field geometry of the strongly magnetic roAp star HD 154708

    NARCIS (Netherlands)

    Hubrig, S.; Mathys, G.; Kurtz, D.W.; Schöller, M.; Elkin, V.G.; Henrichs, H.F.

    2009-01-01

    We obtained 13 spectropolarimetric observations of the strongly magnetic rapidly oscillating Ap star HD 154708 over 3 months with the multimode instrument FORS 1, installed at the 8-m Kueyen telescope of the Very Large Telescope. These observations have been used for the determination of the

  1. Determinations of the QCD strong coupling αsub(s) and the scale Λsub(QCD)

    International Nuclear Information System (INIS)

    Duke, D.W.; Roberts, R.G.

    1984-08-01

    The authors review determinations, via experiment of the strong coupling of QCD, αsub(s). In almost every case, the results are used of perturbative QCD to make the necessary extraction from data. These include scaling violations of deep inelastic scattering, e + e - annihilation experiments (including quarkonium decays) and lepton pair production. Finally estimates for Λ from lattice calculations are listed. (author)

  2. Determination of nuclear friction in strongly damped reactions from prescission neutron multiplicities

    Science.gov (United States)

    Wilczyński, J.; Siwek-Wilczyńska, K.; Wilschut, H. W.

    1996-07-01

    Nonfusion, fissionlike reactions in collisions of four heavy systems (well below the fusion extra-push energy threshold), for which Hinde and co-workers had measured the prescission neutron multiplicities, have been analyzed in terms of the deterministic dynamic model of Feldmeier coupled to a time-dependent statistical cascade calculation. In order to reproduce the measured prescission multiplicities and the observed (nearly symmetric) mass divisions, the energy dissipation must be dramatically changed with regard to the standard one-body dissipation: In the entrance channel, in the process of forming a composite system, the energy dissipation has to be reduced to at least half of the one-body dissipation strength (kinsmononucleus shape to scission) it must be increased by a factor ranging for the studied reactions from kouts=4 to kouts=12. These results are compared with the temperature dependence of the friction coefficient, recently deduced by Hofman, Back, and Paul from data on the prescission giant dipole resonance emission in fusion-fission reactions. The combined picture of the temperature dependence of the friction coefficient, for both fusion-fission and nonfusion reactions, may indicate the onset of strong two-body dissipation already at a nuclear temperature of about 2 MeV.

  3. 75 FR 8299 - Draft Environmental Impact Statement; Determination of Regulated Status of Alfalfa Genetically...

    Science.gov (United States)

    2010-02-24

    ...] Draft Environmental Impact Statement; Determination of Regulated Status of Alfalfa Genetically... making a determination on the status of the Monsanto Company and Forage Genetics International alfalfa... status of the Monsanto Company and Forage Genetics International alfalfa lines designated as events J101...

  4. Determining the pathogenicity of genetic variants associated with cardiac channelopathies.

    Science.gov (United States)

    Campuzano, Oscar; Allegue, Catarina; Fernandez, Anna; Iglesias, Anna; Brugada, Ramon

    2015-01-22

    Advancements in genetic screening have generated massive amounts of data on genetic variation; however, a lack of clear pathogenic stratification has left most variants classified as being of unknown significance. This is a critical limitation for translating genetic data into clinical practice. Genetic screening is currently recommended in the guidelines for diagnosis and treatment of cardiac channelopathies, which are major contributors to sudden cardiac death in young people. We propose to characterize the pathogenicity of genetic variants associated with cardiac channelopathies using a stratified scoring system. The development of this system was considered by using all of the tools currently available to define pathogenicity. The use of this scoring system could help clinicians to understand the limitations of genetic associations with a disease, and help them better define the role that genetics can have in their clinical routine.

  5. Genetic determinants and stroke in children with sickle cell disease,

    Directory of Open Access Journals (Sweden)

    Daniela O.W. Rodrigues

    Full Text Available Abstract Objective: To verify genetic determinants associated with stroke in children with sickle cell disease (SCD. Methods: Prospective cohort with 110 children submitted to neonatal screening by the Neonatal Screening Program, between 1998 and 2007, with SCD diagnosis, followed at a regional reference public service for hemoglobinopathies. The analyzed variables were type of hemoglobinopathy, gender, coexistence with alpha thalassemia (α-thal, haplotypes of the beta globin chain cluster, and stroke. The final analysis was conducted with 66 children with sickle cell anemia (SCA, using the chi-squared test in the program SPSS® version 14.0. Results: Among children with SCD, 60% had SCA. The prevalence of coexistence with α-thal was 30.3% and the Bantu haplotype (CAR was identified in 89.2%. The incidence of stroke was significantly higher in those with SCA (27.3% vs. 2.3%; p = 0.001 and males (24.1% vs. 9.6%; p = 0.044. The presence of α-thal (p = 0.196, the CAR haplotype (p = 0.543, and socioeconomic factors were not statistically significant in association with the occurrence of stroke. Conclusion: There is a high incidence of stroke in male children and in children with SCA. Coexistence with α-thal and haplotypes of the beta globin chain cluster did not show any significant association with stroke. The heterogeneity between previously evaluated populations, the non-reproducibility between studies, and the need to identify factors associated with stroke in patients with SCA indicate the necessity of conducting further research to demonstrate the relevance of genetic factors in stroke related to SCD.

  6. Genetic determinants and stroke in children with sickle cell disease.

    Science.gov (United States)

    Rodrigues, Daniela O W; Ribeiro, Luiz C; Sudário, Lysla C; Teixeira, Maria T B; Martins, Marina L; Pittella, Anuska M O L; Junior, Irtis de O Fernandes

    To verify genetic determinants associated with stroke in children with sickle cell disease (SCD). Prospective cohort with 110 children submitted to neonatal screening by the Neonatal Screening Program, between 1998 and 2007, with SCD diagnosis, followed at a regional reference public service for hemoglobinopathies. The analyzed variables were type of hemoglobinopathy, gender, coexistence with alpha thalassemia (α-thal), haplotypes of the beta globin chain cluster, and stroke. The final analysis was conducted with 66 children with sickle cell anemia (SCA), using the chi-squared test in the program SPSS ® version 14.0. Among children with SCD, 60% had SCA. The prevalence of coexistence with α-thal was 30.3% and the Bantu haplotype (CAR) was identified in 89.2%. The incidence of stroke was significantly higher in those with SCA (27.3% vs. 2.3%; p=0.001) and males (24.1% vs. 9.6%; p=0.044). The presence of α-thal (p=0.196), the CAR haplotype (p=0.543), and socioeconomic factors were not statistically significant in association with the occurrence of stroke. There is a high incidence of stroke in male children and in children with SCA. Coexistence with α-thal and haplotypes of the beta globin chain cluster did not show any significant association with stroke. The heterogeneity between previously evaluated populations, the non-reproducibility between studies, and the need to identify factors associated with stroke in patients with SCA indicate the necessity of conducting further research to demonstrate the relevance of genetic factors in stroke related to SCD. Copyright © 2016 Sociedade Brasileira de Pediatria. Published by Elsevier Editora Ltda. All rights reserved.

  7. Genetic determinants of growth hormone and GH-related phenotypes.

    Science.gov (United States)

    Hallengren, Erik; Almgren, Peter; Svensson, Malin; Gallo, Widet; Engström, Gunnar; Persson, Margaretha; Melander, Olle

    2017-10-24

    Higher fasting Growth Hormone (GH) has been associated with increased cardiovascular morbidity and mortality. Our objective was to find genetic determinants of fasting GH in order to facilitate future efforts of analyzing the association between fasting growth hormone and cardiovascular disease. A genome-wide association study (GWAS) was performed in a discovery cohort of 4134 persons (58% females; age 46-68 yrs), linking SNPs to fasting hs-GH. Fifteen SNPs were replicated in an independent cohort of 5262 persons (28.9% females; age 56-85 yrs). The best performing SNP was analyzed vs GH-related variables in a third independent cohort (n = 24,047; 61% females; age 44-73 yrs). A candidate gene approach searched for significant SNPs in the genes GH1 and GHR in the discovery cohort and was replicated as previously described. In the GWAS, the minor allele of rs7208736 was associated with lower GH in the discovery cohort (p = 5.15*10^-6) and the replication cohort (p = 0.005). The GH reducing allele was associated with lower BMI (P = 0.026) and waist (P = 0.021) in males only. In the candidate gene approach rs13153388 in the GHR-gene was associated with elevated GH-levels (P = 0.003) in the discovery cohort only and reduced height (P = 0.003). In the first GWAS ever for GH, we identify a novel locus on chromosome 17 associated with fasting GH levels, suggesting novel biological mechanisms behind GH secretion and GH-related traits. The candidate gene approach identified a genetic variant in the GHR, which was associated with an elevation of fasting hs-GH and lower height suggesting reduced GHR ligand sensitivity. Our findings need further replication.

  8. Diabetes mellitus unawareness is a strong determinant of mortality in patients manifesting myocardial infarction.

    Science.gov (United States)

    Figueiredo, Valéria N; Godoi, Filipe Canela de Souza; Martins, Nestor S; Quinaglia e Silva, Jose C; Nadruz, Wilson; Coelho, Otavio R; Sposito, Andrei C

    2013-11-01

    Often, as diabetes mellitus type 2 (T2DM) evolves insidiously, prevention is commenced late and diagnosis is made when vascular damage has been set. Hence, our hypothesis is that T2DM awareness may influence the outcome of atherothrombotic events. A consecutive cohort of patients manifesting ST-elevation myocardial infarction (MI) was classified according to the presence and awareness of the diagnosis of T2DM: known diabetes (kT2DM, n = 72), unknown diabetes (uT2DM, n = 80) and no diabetes (ND, n = 333). Medical history, laboratory data, and angiographic findings including myocardial blush grade (MBG) were prospectively obtained. The primary endpoint was in-hospital death and secondary endpoint was major adverse cardiac events (MACE) defined as sudden cardiac death, fatal MI and nonfatal MI that occurred from 30 days of study entry onwards. With the exception of glycated hemoglobin (p = 0.001) and triglycerides (p = 0.04), no differences were found between groups for all other biochemical, clinical or angiographic admission characteristics. Myocardial tissue reperfusion defined as MBG 3 was observed in 62% in the ND group, 50% in the kT2DM group and 23% in the uT2DM group (p = 0.01). All-cause in-hospital mortality was higher in uT2DM (16.7%) than in kT2DM (8.4%) and both groups had a higher mortality rate as compared with the ND group (3.8%, p = 0.01). During follow-up (653 ± 26 days), the incidence of MACE was higher in uT2DM than in kT2DM and in both compared to the ND group (p = 0.002). Unawareness of T2DM diagnosis is strongly associated with a poor short- and long-term outcome after MI.

  9. The plant pathogen Pseudomonas syringae pv. tomato is genetically monomorphic and under strong selection to evade tomato immunity.

    Directory of Open Access Journals (Sweden)

    Rongman Cai

    2011-08-01

    Full Text Available Recently, genome sequencing of many isolates of genetically monomorphic bacterial human pathogens has given new insights into pathogen microevolution and phylogeography. Here, we report a genome-based micro-evolutionary study of a bacterial plant pathogen, Pseudomonas syringae pv. tomato. Only 267 mutations were identified between five sequenced isolates in 3,543,009 nt of analyzed genome sequence, which suggests a recent evolutionary origin of this pathogen. Further analysis with genome-derived markers of 89 world-wide isolates showed that several genotypes exist in North America and in Europe indicating frequent pathogen movement between these world regions. Genome-derived markers and molecular analyses of key pathogen loci important for virulence and motility both suggest ongoing adaptation to the tomato host. A mutational hotspot was found in the type III-secreted effector gene hopM1. These mutations abolish the cell death triggering activity of the full-length protein indicating strong selection for loss of function of this effector, which was previously considered a virulence factor. Two non-synonymous mutations in the flagellin-encoding gene fliC allowed identifying a new microbe associated molecular pattern (MAMP in a region distinct from the known MAMP flg22. Interestingly, the ancestral allele of this MAMP induces a stronger tomato immune response than the derived alleles. The ancestral allele has largely disappeared from today's Pto populations suggesting that flagellin-triggered immunity limits pathogen fitness even in highly virulent pathogens. An additional non-synonymous mutation was identified in flg22 in South American isolates. Therefore, MAMPs are more variable than expected differing even between otherwise almost identical isolates of the same pathogen strain.

  10. Seagrass radiation after Messinian salinity crisis reflected by strong genetic structuring and out-of-Africa scenario (Ruppiaceae.

    Directory of Open Access Journals (Sweden)

    Ludwig Triest

    Full Text Available Many aquatic plant and seagrass species are widespread and the origin of their continent-wide ranges might result from high gene flow levels. The response of species when extending northwards since the Last Glacial Maximum can be opposed to the structuring of their populations that survived glaciation cycles in southern regions. The peri-Mediterranean is a complex series of sea basins, coastlines, islands and river deltas with a unique history since the Messinian Crisis that potentially influenced allopatric processes of aquatic life. We tested whether vast ranges across Europe and the peri-Mediterranean of a global seagrass group (Ruppia species complexes can be explained by either overall high levels of gene flow or vicariance through linking population genetics, phylogeography and shallow phylogenetics. A multigene approach identified haplogroup lineages of two species complexes, of ancient and recent hybrids with most of the diversity residing in the South. High levels of connectivity over long distances were only observed at recently colonized northern ranges and in recently-filled seas following the last glaciation. A strong substructure in the southern Mediterranean explained an isolation-by-distance model across Europe. The oldest lineages of the southern Mediterranean Ruppia dated back to the period between the end of the Messinian and Late Pliocene. An imprint of ancient allopatric origin was left at basin level, including basal African lineages. Thus both vicariance in the South and high levels of connectivity in the North explained vast species ranges. Our findings highlight the need for interpreting global distributions of these seagrass and euryhaline species in the context of their origin and evolutionary significant units for setting up appropriate conservation strategies.

  11. Genetic Determinism in the Genetics Curriculum: An Exploratory Study of the Effects of Mendelian and Weldonian Emphases

    Science.gov (United States)

    Jamieson, Annie; Radick, Gregory

    2017-01-01

    Twenty-first-century biology rejects genetic determinism, yet an exaggerated view of the power of genes in the making of bodies and minds remains a problem. What accounts for such tenacity? This article reports an exploratory study suggesting that the common reliance on Mendelian examples and concepts at the start of teaching in basic genetics is…

  12. Precipitation variability as a strong determinant on tree cover across global tropics

    Science.gov (United States)

    Xu, X.; Medvigy, D.; Guan, K.; Trugman, A. T.; Good, S. P.; Rodriguez-Iturbe, I.

    2017-12-01

    Tropical and subtropical ecosystems support a significant carbon sink and storage and provide various ecosystem services. One challenge for these ecosystems is the changing precipitation variability (PV), which is likely to become more extreme under on-going climate change. However, there is a lack of consensus in the determining role of PV on tropical tree cover, which is a widely-used indicator for ecosystem state and functions in the tropics, as well as the underlying mechanism. Here, we ask whether changes in PV by themselves are likely to lead to changes in tropical tree cover. Using a combination of climate, soil and remotely-sensed tree cover data, we comprehensively assess the effects of PV on tree cover spatial variations at intra-seasonal, seasonal and inter-annual scales. We find that PV contributes 33% -56% to the total explained spatial variation (65% -79%) in tree cover. The contribution of PV depends on mean annual precipitation (MAP) and is highest under intermediate MAP (500 - 1500 mm). In general, tree cover increases with rainy day frequency and wet season length but shows mixed responses to inter-annual precipitation variability. We further use a biophysical model to show that the PV-tree cover relation can be explained by tree-grass water competition. Our results suggest that tropical tree cover can decrease by 3-5% overall and by up to 20% in Amazonia under projected changes in PV at the end of this century.

  13. Intellectual Properties Rights-A strong determinant of economic growth in agriculture

    Directory of Open Access Journals (Sweden)

    Manju Chaudhary

    2010-03-01

    Full Text Available

    In the past few decades the subject of intellectual property rights (IPRs has occupied center stage in debates about globalization, economic development and poverty elimination. This study concerns the strengthening of IPRs in the plant breeding industry and its effect on agriculture in India. In India, most of the population relies on agriculture for its livelihood. India is self-sufficient in wheat and paddy, but deficient in other agricultural products. Patents are good indicators of research and development output. Patent analysis makes it possible to map out the trend of technological change and life cycle of a technology – growth, development, maturity and decline. Patent information and patent statistical analysis have been used for examining present, technological status and to forecast future trends. One can determine the directions of corporate R&D and market interests by analyzing patent data. The present study is an attempt to analyze patents granted in India in the field of agriculture and importance of biotechnology-based innovations in agriculture

  14. Biased Random-Key Genetic Algorithms for the Winner Determination Problem in Combinatorial Auctions.

    Science.gov (United States)

    de Andrade, Carlos Eduardo; Toso, Rodrigo Franco; Resende, Mauricio G C; Miyazawa, Flávio Keidi

    2015-01-01

    In this paper we address the problem of picking a subset of bids in a general combinatorial auction so as to maximize the overall profit using the first-price model. This winner determination problem assumes that a single bidding round is held to determine both the winners and prices to be paid. We introduce six variants of biased random-key genetic algorithms for this problem. Three of them use a novel initialization technique that makes use of solutions of intermediate linear programming relaxations of an exact mixed integer linear programming model as initial chromosomes of the population. An experimental evaluation compares the effectiveness of the proposed algorithms with the standard mixed linear integer programming formulation, a specialized exact algorithm, and the best-performing heuristics proposed for this problem. The proposed algorithms are competitive and offer strong results, mainly for large-scale auctions.

  15. Genetic architecture of sex determination in fish: Applications to sex ratio control in aquaculture

    Directory of Open Access Journals (Sweden)

    Paulino eMartínez

    2014-09-01

    Full Text Available Controlling the sex ratio is essential in finfish farming. A balanced sex ratio is usually good for broodstock management, since it enables to develop appropriate breeding schemes. However, in some species the production of monosex populations is desirable because the existence of sexual dimorphism, primarily in growth or first time of sexual maturation, but also in color or shape, can render one sex more valuable. The knowledge of the genetic architecture of sex determination (SD is convenient for controlling sex ratio and for the implementation of breeding programs. Unlike mammals and birds, which show highly conserved master genes that control a conserved genetic network responsible for gonad differentiation (GD, a huge diversity of SD mechanisms has been reported in fish. Despite theory predictions, more than one gene is in many cases involved in fish SD and genetic differences have been observed in the GD network. Environmental factors also play a relevant role and epigenetic mechanisms are becoming increasingly recognized for the establishment and maintenance of the GD pathways. Although major genetic factors are frequently involved in fish SD, these observations strongly suggest that SD in this group resembles a complex trait. Accordingly, the application of quantitative genetics combined with genomic tools is desirable to address its study and in fact, when applied, it has frequently demonstrated a multigene trait interacting with environmental factors in model and cultured fish species. This scenario has notable implications for aquaculture and, depending upon the species, from chromosome manipulation or environmental control techniques up to classical selection or marker assisted selection programs, are being applied. In this review, we selected four relevant species or fish groups to illustrate this diversity and hence the technologies that can be used by the industry for the control of sex ratio: turbot and European sea bass, two

  16. Methods for determining the genetic affinity of microorganisms and viruses

    Science.gov (United States)

    Fox, George E. (Inventor); Willson, III, Richard C. (Inventor); Zhang, Zhengdong (Inventor)

    2012-01-01

    Selecting which sub-sequences in a database of nucleic acid such as 16S rRNA are highly characteristic of particular groupings of bacteria, microorganisms, fungi, etc. on a substantially phylogenetic tree. Also applicable to viruses comprising viral genomic RNA or DNA. A catalogue of highly characteristic sequences identified by this method is assembled to establish the genetic identity of an unknown organism. The characteristic sequences are used to design nucleic acid hybridization probes that include the characteristic sequence or its complement, or are derived from one or more characteristic sequences. A plurality of these characteristic sequences is used in hybridization to determine the phylogenetic tree position of the organism(s) in a sample. Those target organisms represented in the original sequence database and sufficient characteristic sequences can identify to the species or subspecies level. Oligonucleotide arrays of many probes are especially preferred. A hybridization signal can comprise fluorescence, chemiluminescence, or isotopic labeling, etc.; or sequences in a sample can be detected by direct means, e.g. mass spectrometry. The method's characteristic sequences can also be used to design specific PCR primers. The method uniquely identifies the phylogenetic affinity of an unknown organism without requiring prior knowledge of what is present in the sample. Even if the organism has not been previously encountered, the method still provides useful information about which phylogenetic tree bifurcation nodes encompass the organism.

  17. Young Adults’ Belief in Genetic Determinism, and Knowledge and Attitudes towards Modern Genetics and Genomics: The PUGGS Questionnaire

    Science.gov (United States)

    Carver, Rebecca Bruu; Castéra, Jérémy; Gericke, Niklas; Evangelista, Neima Alice Menezes

    2017-01-01

    In this paper we present the development and validation a comprehensive questionnaire to assess college students’ knowledge about modern genetics and genomics, their belief in genetic determinism, and their attitudes towards applications of modern genetics and genomic-based technologies. Written in everyday language with minimal jargon, the Public Understanding and Attitudes towards Genetics and Genomics (PUGGS) questionnaire is intended for use in research on science education and public understanding of science, as a means to investigate relationships between knowledge, determinism and attitudes about modern genetics, which are to date little understood. We developed a set of core ideas and initial items from reviewing the scientific literature on genetics and previous studies on public and student knowledge and attitudes about genetics. Seventeen international experts from different fields (e.g., genetics, education, philosophy of science) reviewed the initial items and their feedback was used to revise the questionnaire. We validated the questionnaire in two pilot tests with samples of university freshmen students. The final questionnaire contains 45 items, including both multiple choice and Likert scale response formats. Cronbach alpha showed good reliability for each section of the questionnaire. In conclusion, the PUGGS questionnaire is a reliable tool for investigating public understanding and attitudes towards modern genetics and genomic-based technologies. PMID:28114357

  18. Young Adults' Belief in Genetic Determinism, and Knowledge and Attitudes towards Modern Genetics and Genomics: The PUGGS Questionnaire.

    Directory of Open Access Journals (Sweden)

    Rebecca Bruu Carver

    Full Text Available In this paper we present the development and validation a comprehensive questionnaire to assess college students' knowledge about modern genetics and genomics, their belief in genetic determinism, and their attitudes towards applications of modern genetics and genomic-based technologies. Written in everyday language with minimal jargon, the Public Understanding and Attitudes towards Genetics and Genomics (PUGGS questionnaire is intended for use in research on science education and public understanding of science, as a means to investigate relationships between knowledge, determinism and attitudes about modern genetics, which are to date little understood. We developed a set of core ideas and initial items from reviewing the scientific literature on genetics and previous studies on public and student knowledge and attitudes about genetics. Seventeen international experts from different fields (e.g., genetics, education, philosophy of science reviewed the initial items and their feedback was used to revise the questionnaire. We validated the questionnaire in two pilot tests with samples of university freshmen students. The final questionnaire contains 45 items, including both multiple choice and Likert scale response formats. Cronbach alpha showed good reliability for each section of the questionnaire. In conclusion, the PUGGS questionnaire is a reliable tool for investigating public understanding and attitudes towards modern genetics and genomic-based technologies.

  19. Constant, cycling, hot and cold thermal environments: strong effects on mean viability but not on genetic estimates

    DEFF Research Database (Denmark)

    Ketola, Tarmo; Kellermann, Vanessa; Kristensen, Torsten Nygård

    2012-01-01

    and their fluctuations. How species will respond to these changes is uncertain, particularly as there is a lack of studies which compare genetic performances in constant vs. fluctuating environments. In this study, we used a nested full-sib/half-sib breeding design to examine how the genetic variances and heritabilities...

  20. Genetic Determinants of Non-syndromic Hearing Impairment

    NARCIS (Netherlands)

    R.L.P. Santos (Regie)

    2006-01-01

    textabstractCongenital hearing impairment (HI) affects 1-2 per 1000 neonates, of which half would be genetic in etiology. Of the genetic cases, 70% would be non-syndromic in nature. To date ~120 non-syndromic (NS) HI loci have been mapped, for which 39 NSHI genes have been identified. For the

  1. Determination of genetic relatedness among selected rice ( Oryza ...

    African Journals Online (AJOL)

    For plant improvement programs, genetic variation information among different cultivars is very important. Genetic variation among 26 rice (Oryza sativa, L.) accessions, consisting of 13 Iranian and 13 Malaysian cultivars was investigated using microsatellite markers distributed across the rice genome. All the 21 selected ...

  2. Genetic Essentialism: On the Deceptive Determinism of DNA

    Science.gov (United States)

    Dar-Nimrod, Ilan; Heine, Steven J.

    2011-01-01

    This article introduces the notion of genetic essentialist biases: cognitive biases associated with essentialist thinking that are elicited when people encounter arguments that genes are relevant for a behavior, condition, or social group. Learning about genetic attributions for various human conditions leads to a particular set of thoughts…

  3. The major genetic determinants of HIV-1 control affect HLA class I peptide presentation

    NARCIS (Netherlands)

    Pereyra, Florencia; Jia, Xiaoming; McLaren, Paul J.; Telenti, Amalio; de Bakker, Paul I. W.; Walker, Bruce D.; Ripke, Stephan; Brumme, Chanson J.; Pulit, Sara L.; Carrington, Mary; Kadie, Carl M.; Carlson, Jonathan M.; Heckerman, David; Graham, Robert R.; Plenge, Robert M.; Deeks, Steven G.; Gianniny, Lauren; Crawford, Gabriel; Sullivan, Jordan; Gonzalez, Elena; Davies, Leela; Camargo, Amy; Moore, Jamie M.; Beattie, Nicole; Gupta, Supriya; Crenshaw, Andrew; Burtt, Noël P.; Guiducci, Candace; Gupta, Namrata; Gao, Xiaojiang; Qi, Ying; Yuki, Yuko; Piechocka-Trocha, Alicja; Cutrell, Emily; Rosenberg, Rachel; Moss, Kristin L.; Lemay, Paul; O'Leary, Jessica; Schaefer, Todd; Verma, Pranshu; Toth, Ildiko; Block, Brian; Baker, Brett; Rothchild, Alissa; Lian, Jeffrey; Proudfoot, Jacqueline; Alvino, Donna Marie L.; Vine, Seanna; Addo, Marylyn M.; Allen, Todd M.; Altfeld, Marcus; Henn, Matthew R.; Le Gall, Sylvie; Streeck, Hendrik; Haas, David W.; Kuritzkes, Daniel R.; Robbins, Gregory K.; Shafer, Robert W.; Gulick, Roy M.; Shikuma, Cecilia M.; Haubrich, Richard; Riddler, Sharon; Sax, Paul E.; Daar, Eric S.; Ribaudo, Heather J.; Agan, Brian; Agarwal, Shanu; Ahern, Richard L.; Allen, Brady L.; Altidor, Sherly; Altschuler, Eric L.; Ambardar, Sujata; Anastos, Kathryn; Anderson, Ben; Anderson, Val; Andrady, Ushan; Antoniskis, Diana; Bangsberg, David; Barbaro, Daniel; Barrie, William; Bartczak, J.; Barton, Simon; Basden, Patricia; Basgoz, Nesli; Bazner, Suzane; Bellos, Nicholaos C.; Benson, Anne M.; Berger, Judith; Bernard, Nicole F.; Bernard, Annette M.; Birch, Christopher; Bodner, Stanley J.; Bolan, Robert K.; Boudreaux, Emilie T.; Bradley, Meg; Braun, James F.; Brndjar, Jon E.; Brown, Stephen J.; Brown, Katherine; Brown, Sheldon T.; Burack, Jedidiah; Bush, Larry M.; Cafaro, Virginia; Campbell, Omobolaji; Campbell, John; Carlson, Robert H.; Carmichael, J. Kevin; Casey, Kathleen K.; Cavacuiti, Chris; Celestin, Gregory; Chambers, Steven T.; Chez, Nancy; Chirch, Lisa M.; Cimoch, Paul J.; Cohen, Daniel; Cohn, Lillian E.; Conway, Brian; Cooper, David A.; Cornelson, Brian; Cox, David T.; Cristofano, Michael V.; Cuchural, George; Czartoski, Julie L.; Dahman, Joseph M.; Daly, Jennifer S.; Davis, Benjamin T.; Davis, Kristine; Davod, Sheila M.; DeJesus, Edwin; Dietz, Craig A.; Dunham, Eleanor; Dunn, Michael E.; Ellerin, Todd B.; Eron, Joseph J.; Fangman, John J. W.; Farel, Claire E.; Ferlazzo, Helen; Fidler, Sarah; Fleenor-Ford, Anita; Frankel, Renee; Freedberg, Kenneth A.; French, Neel K.; Fuchs, Jonathan D.; Fuller, Jon D.; Gaberman, Jonna; Gallant, Joel E.; Gandhi, Rajesh T.; Garcia, Efrain; Garmon, Donald; Gathe, Joseph C.; Gaultier, Cyril R.; Gebre, Wondwoosen; Gilman, Frank D.; Gilson, Ian; Goepfert, Paul A.; Gottlieb, Michael S.; Goulston, Claudia; Groger, Richard K.; Gurley, T. Douglas; Haber, Stuart; Hardwicke, Robin; Hardy, W. David; Harrigan, P. Richard; Hawkins, Trevor N.; Heath, Sonya; Hecht, Frederick M.; Henry, W. Keith; Hladek, Melissa; Hoffman, Robert P.; Horton, James M.; Hsu, Ricky K.; Huhn, Gregory D.; Hunt, Peter; Hupert, Mark J.; Illeman, Mark L.; Jaeger, Hans; Jellinger, Robert M.; John, Mina; Johnson, Jennifer A.; Johnson, Kristin L.; Johnson, Heather; Johnson, Kay; Joly, Jennifer; Jordan, Wilbert C.; Kauffman, Carol A.; Khanlou, Homayoon; Killian, Robert K.; Kim, Arthur Y.; Kim, David D.; Kinder, Clifford A.; Kirchner, Jeffrey T.; Kogelman, Laura; Kojic, Erna Milunka; Korthuis, P. Todd; Kurisu, Wayne; Kwon, Douglas S.; LaMar, Melissa; Lampiris, Harry; Lanzafame, Massimiliano; Lederman, Michael M.; Lee, David M.; Lee, Jean M. L.; Lee, Marah J.; Lee, Edward T. Y.; Lemoine, Janice; Levy, Jay A.; Llibre, Josep M.; Liguori, Michael A.; Little, Susan J.; Liu, Anne Y.; Lopez, Alvaro J.; Loutfy, Mono R.; Loy, Dawn; Mohammed, Debbie Y.; Man, Alan; Mansour, Michael K.; Marconi, Vincent C.; Markowitz, Martin; Marques, Rui; Martin, Jeffrey N.; Martin, Harold L.; Mayer, Kenneth Hugh; McElrath, M. Juliana; McGhee, Theresa A.; McGovern, Barbara H.; McGowan, Katherine; McIntyre, Dawn; Mcleod, Gavin X.; Menezes, Prema; Mesa, Greg; Metroka, Craig E.; Meyer-Olson, Dirk; Miller, Andy O.; Montgomery, Kate; Mounzer, Karam C.; Nagami, Ellen H.; Nagin, Iris; Nahass, Ronald G.; Nelson, Margret O.; Nielsen, Craig; Norene, David L.; O'Connor, David H.; Ojikutu, Bisola O.; Okulicz, Jason; Oladehin, Olakunle O.; Oldfield, Edward C.; Olender, Susan A.; Ostrowski, Mario; Owen, William F.; Pae, Eunice; Parsonnet, Jeffrey; Pavlatos, Andrew M.; Perlmutter, Aaron M.; Pierce, Michael N.; Pincus, Jonathan M.; Pisani, Leandro; Price, Lawrence Jay; Proia, Laurie; Prokesch, Richard C.; Pujet, Heather Calderon; Ramgopal, Moti; Rathod, Almas; Rausch, Michael; Ravishankar, J.; Rhame, Frank S.; Richards, Constance Shamuyarira; Richman, Douglas D.; Rodes, Berta; Rodriguez, Milagros; Rose, Richard C.; Rosenberg, Eric S.; Rosenthal, Daniel; Ross, Polly E.; Rubin, David S.; Rumbaugh, Elease; Saenz, Luis; Salvaggio, Michelle R.; Sanchez, William C.; Sanjana, Veeraf M.; Santiago, Steven; Schmidt, Wolfgang; Schuitemaker, Hanneke; Sestak, Philip M.; Shalit, Peter; Shay, William; Shirvani, Vivian N.; Silebi, Vanessa I.; Sizemore, James M.; Skolnik, Paul R.; Sokol-Anderson, Marcia; Sosman, James M.; Stabile, Paul; Stapleton, Jack T.; Starrett, Sheree; Stein, Francine; Stellbrink, Hans-Jurgen; Sterman, F. Lisa; Stone, Valerie E.; Stone, David R.; Tambussi, Giuseppe; Taplitz, Randy A.; Tedaldi, Ellen M.; Theisen, William; Torres, Richard; Tosiello, Lorraine; Tremblay, Cecile; Tribble, Marc A.; Trinh, Phuong D.; Tsao, Alice; Ueda, Peggy; Vaccaro, Anthony; Valadas, Emilia; Vanig, Thanes J.; Vecino, Isabel; Vega, Vilma M.; Veikley, Wenoah; Wade, Barbara H.; Walworth, Charles; Wanidworanun, Chingchai; Ward, Douglas J.; Warner, Daniel A.; Weber, Robert D.; Webster, Duncan; Weis, Steve; Wheeler, David A.; White, David J.; Wilkins, Ed; Winston, Alan; Wlodaver, Clifford G.; van't Wout, Angelique; Wright, David P.; Yang, Otto O.; Yurdin, David L.; Zabukovic, Brandon W.; Zachary, Kimon C.; Zeeman, Beth; Zhao, Meng

    2010-01-01

    Infectious and inflammatory diseases have repeatedly shown strong genetic associations within the major histocompatibility complex (MHC); however, the basis for these associations remains elusive. To define host genetic effects on the outcome of a chronic viral infection, we performed genome-wide

  4. A rapid, strong, and convergent genetic response to urban habitat fragmentation in four divergent and widespread vertebrates

    Science.gov (United States)

    Delaney, Kathleen Semple; Riley, Seth P.D.; Fisher, Robert N.

    2010-01-01

    Background: Urbanization is a major cause of habitat fragmentation worldwide. Ecological and conservation theory predicts many potential impacts of habitat fragmentation on natural populations, including genetic impacts. Habitat fragmentation by urbanization causes populations of animals and plants to be isolated in patches of suitable habitat that are surrounded by non-native vegetation or severely altered vegetation, asphalt, concrete, and human structures. This can lead to genetic divergence between patches and in turn to decreased genetic diversity within patches through genetic drift and inbreeding. Methodology/Principal Findings: We examined population genetic patterns using microsatellites in four common vertebrate species, three lizards and one bird, in highly fragmented urban southern California. Despite significant phylogenetic, ecological, and mobility differences between these species, all four showed similar and significant reductions in gene flow over relatively short geographic and temporal scales. For all four species, the greatest genetic divergence was found where development was oldest and most intensive. All four animals also showed significant reduction in gene flow associated with intervening roads and freeways, the degree of patch isolation, and the time since isolation. Conclusions/Significance: Despite wide acceptance of the idea in principle, evidence of significant population genetic changes associated with fragmentation at small spatial and temporal scales has been rare, even in smaller terrestrial vertebrates, and especially for birds. Given the striking pattern of similar and rapid effects across four common and widespread species, including a volant bird, intense urbanization may represent the most severe form of fragmentation, with minimal effective movement through the urban matrix.

  5. A rapid, strong, and convergent genetic response to urban habitat fragmentation in four divergent and widespread vertebrates.

    Directory of Open Access Journals (Sweden)

    Kathleen Semple Delaney

    2010-09-01

    Full Text Available Urbanization is a major cause of habitat fragmentation worldwide. Ecological and conservation theory predicts many potential impacts of habitat fragmentation on natural populations, including genetic impacts. Habitat fragmentation by urbanization causes populations of animals and plants to be isolated in patches of suitable habitat that are surrounded by non-native vegetation or severely altered vegetation, asphalt, concrete, and human structures. This can lead to genetic divergence between patches and in turn to decreased genetic diversity within patches through genetic drift and inbreeding.We examined population genetic patterns using microsatellites in four common vertebrate species, three lizards and one bird, in highly fragmented urban southern California. Despite significant phylogenetic, ecological, and mobility differences between these species, all four showed similar and significant reductions in gene flow over relatively short geographic and temporal scales. For all four species, the greatest genetic divergence was found where development was oldest and most intensive. All four animals also showed significant reduction in gene flow associated with intervening roads and freeways, the degree of patch isolation, and the time since isolation.Despite wide acceptance of the idea in principle, evidence of significant population genetic changes associated with fragmentation at small spatial and temporal scales has been rare, even in smaller terrestrial vertebrates, and especially for birds. Given the striking pattern of similar and rapid effects across four common and widespread species, including a volant bird, intense urbanization may represent the most severe form of fragmentation, with minimal effective movement through the urban matrix.

  6. A rapid, strong, and convergent genetic response to urban habitat fragmentation in four divergent and widespread vertebrates.

    Science.gov (United States)

    Delaney, Kathleen Semple; Riley, Seth P D; Fisher, Robert N

    2010-09-16

    Urbanization is a major cause of habitat fragmentation worldwide. Ecological and conservation theory predicts many potential impacts of habitat fragmentation on natural populations, including genetic impacts. Habitat fragmentation by urbanization causes populations of animals and plants to be isolated in patches of suitable habitat that are surrounded by non-native vegetation or severely altered vegetation, asphalt, concrete, and human structures. This can lead to genetic divergence between patches and in turn to decreased genetic diversity within patches through genetic drift and inbreeding. We examined population genetic patterns using microsatellites in four common vertebrate species, three lizards and one bird, in highly fragmented urban southern California. Despite significant phylogenetic, ecological, and mobility differences between these species, all four showed similar and significant reductions in gene flow over relatively short geographic and temporal scales. For all four species, the greatest genetic divergence was found where development was oldest and most intensive. All four animals also showed significant reduction in gene flow associated with intervening roads and freeways, the degree of patch isolation, and the time since isolation. Despite wide acceptance of the idea in principle, evidence of significant population genetic changes associated with fragmentation at small spatial and temporal scales has been rare, even in smaller terrestrial vertebrates, and especially for birds. Given the striking pattern of similar and rapid effects across four common and widespread species, including a volant bird, intense urbanization may represent the most severe form of fragmentation, with minimal effective movement through the urban matrix.

  7. Genetic determinants of heat resistance in Escherichia coli.

    Science.gov (United States)

    Mercer, Ryan G; Zheng, Jinshui; Garcia-Hernandez, Rigoberto; Ruan, Lifang; Gänzle, Michael G; McMullen, Lynn M

    2015-01-01

    Escherichia coli AW1.7 is a heat resistant food isolate and the occurrence of pathogenic strains with comparable heat resistance may pose a risk to food safety. To identify the genetic determinants of heat resistance, 29 strains of E. coli that differed in their of heat resistance were analyzed by comparative genomics. Strains were classified as highly heat resistant strains, exhibiting a D60-value of more than 6 min; moderately heat resistant strains, exhibiting a D60-value of more than 1 min; or as heat sensitive. A ~14 kb genomic island containing 16 predicted open reading frames encoding putative heat shock proteins and proteases was identified only in highly heat resistant strains. The genomic island was termed the locus of heat resistance (LHR). This putative operon is flanked by mobile elements and possesses >99% sequence identity to genomic islands contributing to heat resistance in Cronobacter sakazakii and Klebsiella pneumoniae. An additional 41 LHR sequences with >87% sequence identity were identified in 11 different species of β- and γ-proteobacteria. Cloning of the full length LHR conferred high heat resistance to the heat sensitive E. coli AW1.7ΔpHR1 and DH5α. The presence of the LHR correlates perfectly to heat resistance in several species of Enterobacteriaceae and occurs at a frequency of 2% of all E. coli genomes, including pathogenic strains. This study suggests the LHR has been laterally exchanged among the β- and γ-proteobacteria and is a reliable indicator of high heat resistance in E. coli.

  8. Genetic determinants of reutericyclin biosynthesis in Lactobacillus reuteri.

    Science.gov (United States)

    Lin, Xiaoxi B; Lohans, Christopher T; Duar, Rebbeca; Zheng, Jinshui; Vederas, John C; Walter, Jens; Gänzle, Michael

    2015-03-01

    Reutericyclin is a unique antimicrobial tetramic acid produced by some strains of Lactobacillus reuteri. This study aimed to identify the genetic determinants of reutericyclin biosynthesis. Comparisons of the genomes of reutericyclin-producing L. reuteri strains with those of non-reutericyclin-producing strains identified a genomic island of 14 open reading frames (ORFs) including genes coding for a nonribosomal peptide synthetase (NRPS), a polyketide synthase (PKS), homologues of PhlA, PhlB, and PhlC, and putative transport and regulatory proteins. The protein encoded by rtcN is composed of a condensation domain, an adenylation domain likely specific for d-leucine, and a thiolation domain. rtcK codes for a PKS that is composed of a ketosynthase domain, an acyl-carrier protein domain, and a thioesterase domain. The products of rtcA, rtcB, and rtcC are homologous to the diacetylphloroglucinol-biosynthetic proteins PhlABC and may acetylate the tetramic acid moiety produced by RtcN and RtcK, forming reutericyclin. Deletion of rtcN or rtcABC in L. reuteri TMW1.656 abrogated reutericyclin production but did not affect resistance to reutericyclin. Genes coding for transport and regulatory proteins could be deleted only in the reutericyclin-negative L. reuteri strain TMW1.656ΔrtcN, and these deletions eliminated reutericyclin resistance. The genomic analyses suggest that the reutericyclin genomic island was horizontally acquired from an unknown source during a unique event. The combination of PhlABC homologues with both an NRPS and a PKS has also been identified in the lactic acid bacteria Streptococcus mutans and Lactobacillus plantarum, suggesting that the genes in these organisms and those in L. reuteri share an evolutionary origin. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  9. Genetic determinants of heat resistance in Escherichia coli

    Directory of Open Access Journals (Sweden)

    Ryan eMercer

    2015-09-01

    Full Text Available Escherichia coli AW1.7 is a heat resistant food isolate and the occurrence of pathogenic strains with comparable heat resistance may pose a risk to food safety. To identify the genetic determinants of heat resistance, 29 strains of E. coli that differed in their of heat resistance were analyzed by comparative genomics. Strains were classified as highly heat resistant strains, exhibiting a D60-value of more than 6 min; moderately heat resistant strains, exhibiting a D60-value of more than 1 min; or as heat sensitive. A ~14 kb genomic island containing 16 predicted open reading frames encoding putative heat shock proteins and proteases was identified only in highly heat resistant strains. The genomic island was termed the locus of heat resistance (LHR. This putative operon is flanked by mobile elements and possesses >99% sequence identity to genomic islands contributing to heat resistance in Cronobacter sakazakii and Klebsiella pneumoniae. An additional 41 LHR sequences with >87% sequence identity were identified in 11 different species of β- and γ-proteobacteria. Cloning of the full length LHR conferred high heat resistance to the heat sensitive E. coli AW1.7ΔpHR1 and DH5α. The presence of the LHR correlates perfectly to heat resistance in several species of Enterobacteriaceae and occurs at a frequency of 2% of all E. coli genomes, including pathogenic strains. This study suggests the LHR has been laterally exchanged among the β- and γ-proteobacteria and is a reliable indicator of high heat resistance in E. coli.

  10. Genetic determinants of heat resistance in Escherichia coli

    Science.gov (United States)

    Mercer, Ryan G.; Zheng, Jinshui; Garcia-Hernandez, Rigoberto; Ruan, Lifang; Gänzle, Michael G.; McMullen, Lynn M.

    2015-01-01

    Escherichia coli AW1.7 is a heat resistant food isolate and the occurrence of pathogenic strains with comparable heat resistance may pose a risk to food safety. To identify the genetic determinants of heat resistance, 29 strains of E. coli that differed in their of heat resistance were analyzed by comparative genomics. Strains were classified as highly heat resistant strains, exhibiting a D60-value of more than 6 min; moderately heat resistant strains, exhibiting a D60-value of more than 1 min; or as heat sensitive. A ~14 kb genomic island containing 16 predicted open reading frames encoding putative heat shock proteins and proteases was identified only in highly heat resistant strains. The genomic island was termed the locus of heat resistance (LHR). This putative operon is flanked by mobile elements and possesses >99% sequence identity to genomic islands contributing to heat resistance in Cronobacter sakazakii and Klebsiella pneumoniae. An additional 41 LHR sequences with >87% sequence identity were identified in 11 different species of β- and γ-proteobacteria. Cloning of the full length LHR conferred high heat resistance to the heat sensitive E. coli AW1.7ΔpHR1 and DH5α. The presence of the LHR correlates perfectly to heat resistance in several species of Enterobacteriaceae and occurs at a frequency of 2% of all E. coli genomes, including pathogenic strains. This study suggests the LHR has been laterally exchanged among the β- and γ-proteobacteria and is a reliable indicator of high heat resistance in E. coli. PMID:26441869

  11. The influence of fragmentation models on the determination of the strong coupling constant in e+e- annihilation into hadrons

    International Nuclear Information System (INIS)

    Behrend, H.J.; Chen, C.; Fenner, H.; Schachter, M.J.; Schroeder, V.; Sindt, H.; D'Agostini, G.; Apel, W.D.; Banerjee, S.; Bodenkamp, J.; Chrobaczek, D.; Engler, J.; Fluegge, G.; Fries, D.C.; Fues, W.; Gamerdinger, K.; Hopp, G.; Kuester, H.; Mueller, H.; Randoll, H.; Schmidt, G.; Schneider, H.; Boer, W. de; Buschhorn, G.; Grindhammer, G.; Grosse-Wiesmann, P.; Gunderson, B.; Kiesling, C.; Kotthaus, R.; Kruse, U.; Lierl, H.; Lueers, D.; Oberlack, H.; Schacht, P.; Colas, P.; Cordier, A.; Davier, M.; Fournier, D.; Grivaz, J.F.; Haissinski, J.; Journe, V.; Klarsfeld, A.; Laplanche, F.; Le Diberder, F.; Mallik, U.; Veillet, J.J.; Field, J.H.; George, R.; Goldberg, M.; Grossetete, B.; Hamon, O.; Kapusta, F.; Kovacs, F.; London, G.; Poggioli, L.; Rivoal, M.; Aleksan, R.; Bouchez, J.; Carnesecchi, G.; Cozzika, G.; Ducros, Y.; Gaidot, A.; Jadach, S.; Lavagne, Y.; Pamela, J.; Pansart, J.P.; Pierre, F.

    1983-01-01

    Hadronic events obtained with the CELLO detector at PETRA were compared with first-order QCD predictions using two different models for the fragmentation of quarks and gluons, the Hoyer model and the Lund model. Both models are in reasonable agreement with the data, although they do not completely reproduce the details of many distributions. Several methods have been applied to determine the strong coupling constant αsub(s). Although within one model the value of αsub(s) varies by 20% among the different methods, the values determined using the Lund model are 30% or more larger (depending on the method used) than the values determined with the Hoyer model. Our results using the Hoyer model are in agreement with previous results based on this approach. (orig.)

  12. Determining causes of genetic isolation in a large carnivore (Ursus americanus population to direct contemporary conservation measures.

    Directory of Open Access Journals (Sweden)

    Agnès Pelletier

    Full Text Available The processes leading to genetic isolation influence a population's local extinction risk, and should thus be identified before conservation actions are implemented. Natural or human-induced circumstances can result in historical or contemporary barriers to gene flow and/or demographic bottlenecks. Distinguishing between these hypotheses can be achieved by comparing genetic diversity and differentiation in isolated vs. continuous neighboring populations. In Ontario, American black bears (Ursus americanus are continuously distributed, genetically diverse, and exhibit an isolation-by-distance structuring pattern, except on the Bruce Peninsula (BP. To identify the processes that led to the genetic isolation of BP black bears, we modelled various levels of historical and contemporary migration and population size reductions using forward simulations. We compared simulation results with empirical genetic indices from Ontario black bear populations under different levels of geographic isolation, and conducted additional simulations to determine if translocations could help achieve genetic restoration. From a genetic standpoint, conservation concerns for BP black bears are warranted because our results show that: i a recent demographic bottleneck associated with recently reduced migration best explains the low genetic diversity on the BP; and ii under sustained isolation, BP black bears could lose between 70% and 80% of their rare alleles within 100 years. Although restoring migration corridors would be the most effective method to enhance long-term genetic diversity and prevent inbreeding, it is unrealistic to expect connectivity to be re-established. Current levels of genetic diversity could be maintained by successfully translocating 10 bears onto the peninsula every 5 years. Such regular translocations may be more practical than landscape restoration, because areas connecting the peninsula to nearby mainland black bear populations have been

  13. Influence of the larval phase on connectivity: strong differences in the genetic structure of brooders and broadcasters in the Ophioderma longicauda species complex.

    Science.gov (United States)

    Weber, A A-T; Mérigot, B; Valière, S; Chenuil, A

    2015-12-01

    Closely related species with divergent life history traits are excellent models to infer the role of such traits in genetic diversity and connectivity. Ophioderma longicauda is a brittle star species complex composed of different genetic clusters, including brooders and broadcasters. These species diverged very recently and some of them are sympatric and ecologically syntopic, making them particularly suitable to study the consequences of their trait differences. At the scale of the geographic distribution of the broadcasters (Mediterranean Sea and northeastern Atlantic), we sequenced the mitochondrial marker COI and genotyped an intron (i51) for 788 individuals. In addition, we sequenced 10 nuclear loci newly developed from transcriptome sequences, for six sympatric populations of brooders and broadcasters from Greece. At the large scale, we found a high genetic structure within the brooders (COI: 0.07 lecithotrophic larval stage allows on average a 50-fold increase in migration rates, a 280-fold increase in effective size and a threefold to fourfold increase in genetic diversity. Our work, investigating complementary genetic markers on sympatric and syntopic taxa, highlights the strong impact of the larval phase on connectivity and genetic diversity. © 2015 John Wiley & Sons Ltd.

  14. No Genetic Diversity at Molecular Markers and Strong Phenotypic Plasticity in Populations of Ranunculus nodiflorus, an Endangered Plant Species in France

    Science.gov (United States)

    Noel, Florence; Machon, Nathalie; Porcher, Emmanuelle

    2007-01-01

    Background and Aims Although conservation biology has long focused on population dynamics and genetics, phenotypic plasticity is likely to play a significant role in population viability. Here, an investigation is made into the relative contribution of genetic diversity and phenotypic plasticity to the phenotypic variation in natural populations of Ranunculus nodiflorus, a rare annual plant inhabiting temporary puddles in the Fontainebleau forest (Paris region, France) and exhibiting metapopulation dynamics. Methods The genetic diversity and phenotypic plasticity of quantitative traits (morphological and fitness components) were measured in five populations, using a combination of field measurements, common garden experiments and genotyping at microsatellite loci. Key Results It is shown that populations exhibit almost undetectable genetic diversity at molecular markers, and that the variation in quantitative traits observed among populations is due to a high level of phenotypic plasticity. Despite the lack of genetic diversity, the natural population of R. nodiflorus exhibits large population sizes and does not appear threatened by extinction; this may be attributable to large phenotypic plasticity, enabling the production of numerous seeds under a wide range of environmental conditions. Conclusions Efficient conservation of the populations can only be based on habitat management, to favour the maintenance of microenvironmental variation and the resulting strong phenotypic plasticity. In contrast, classical actions aiming to improve genetic diversity are useless in the present case. PMID:17468109

  15. 76 FR 37767 - Pioneer Hi-Bred International, Inc.; Determination of Nonregulated Status for Corn Genetically...

    Science.gov (United States)

    2011-06-28

    ...] Pioneer Hi-Bred International, Inc.; Determination of Nonregulated Status for Corn Genetically Engineered... Pioneer Hi-Bred International, Inc., designated as event DP-32138-1, which has been genetically engineered... by Pioneer Hi-Bred International, Inc., in its petition for a determination of nonregulated status...

  16. Why Are High Altitude Natives So Strong at High Altitude? Nature vs. Nurture: Genetic Factors vs. Growth and Development.

    Science.gov (United States)

    Brutsaert, Tom

    Among high-altitude natives there is evidence of a general hypoxia tolerance leading to enhanced performance and/or increased capacity in several important domains. These domains likely include an enhanced physical work capacity, an enhanced reproductive capacity, and an ability to resist several common pathologies of chronic high-altitude exposure. The "strength" of the high-altitude native in this regard may have both a developmental and a genetic basis, although there is better evidence for the former (developmental effects) than for the latter. For example, early-life hypoxia exposure clearly results in lung growth and remodeling leading to an increased O2 diffusing capacity in adulthood. Genetic research has yet to reveal a population genetic basis for enhanced capacity in high-altitude natives, but several traits are clearly under genetic control in Andean and Tibetan populations e.g., resting and exercise arterial O2 saturation (SaO2). This chapter reviews the effects of nature and nurture on traits that are relevant to the process of gas exchange, including pulmonary volumes and diffusion capacity, the maximal oxygen consumption (VO2max), the SaO2, and the alveolar-arterial oxygen partial pressure difference (A-aDO2) during exercise.

  17. Strong genetic structure among coral populations within a conservation priority region, the Bird's Head Seascape (Papua, Indonesia

    Directory of Open Access Journals (Sweden)

    Craig John Starger

    2015-11-01

    Full Text Available Marine Protected Areas (MPAs are widely considered to be one of the best strategies available for protecting species diversity and ecosystem processes in marine environments. While data on connectivity and genetic structure of marine populations are critical to designing appropriately sized and spaced networks of MPAs, such data are rarely available. This study examines genetic structure in reef-building corals from Papua and West Papua, Indonesia, one of the most biodiverse and least disturbed coral reef regions in the world. We focused on two common reef-building corals, Pocillopora damicornis (Linnaeus 1758 and Seriatopora hystrix (family: Pocilloporidae, from three regions under different management regimes: Teluk Cenderawasih, Raja Ampat, and southwest Papua. Analyses of molecular variance, assignment tests, and genetical bandwidth mapping based on microsatellite variation revealed significant genetic structure in both species, although there were no clear regional filters to gene flow among regions. Overall, P. damicornis populations were less structured (FST = 0.139, p < 0.00001 than S. hystrix (FST = 0.357, p < 0.00001. Despite occurring in one of the most pristine marine habitats in Indonesia, populations of both species showed evidence of recent declines. Furthermore, exclusion of individual populations from connectivity analyses resulted in marked increases in self-recruitment. Maintaining connectivity within and among regions of Eastern Indonesia will require coral conservation on the local scales and regional networks of MPAs. 

  18. Strong population genetic structuring in an annual fish, Nothobranchius furzeri, suggests multiple savannah refugia in southern Mozambique

    Czech Academy of Sciences Publication Activity Database

    Bartáková, V.; Reichard, M.; Janko, Karel; Polačik, M.; Blažek, R.; Reichwald, K.; Cellerino, A.; Bryja, J.

    2013-01-01

    Roč. 13, č. 196 (2013), s. 1-15 ISSN 1471-2148 Institutional support: RVO:67985904 Keywords : temporary pool * pyhlogeography * population genetics Subject RIV: EG - Zoology Impact factor: 3.407, year: 2013 http://www.biomedcentral.com/1471-2148/13/196

  19. Genetic Determinants of P Wave Duration and PR Segment

    NARCIS (Netherlands)

    Verweij, Niek; Mateo Leach, Irene; van den Boogaard, Malou; van Veldhuisen, Dirk J.; Christoffels, Vincent M.; Hillege, Hans L.; van Gilst, Wiek H.; Barnett, Phil; de Boer, Rudolf A.; van der Harst, Pim

    Background-The PR interval on the ECG reflects atrial depolarization and atrioventricular nodal delay which can be partially differentiated by P wave duration and PR segment, respectively. Genome-wide association studies have identified several genetic loci for PR interval, but it remains to be

  20. Genetic determination of polyhydroxyalkanoate metabolism in Rhodobacter capsulatus SB1003

    Czech Academy of Sciences Publication Activity Database

    Ulbrich, P.; Strnad, Hynek; Hejkalová, V.; Pačes, Jan

    2002-01-01

    Roč. 48, č. 4 (2002), s. 157-159 ISSN 0015-5500 R&D Projects: GA MŠk LN00A079 Institutional research plan: CEZ:AV0Z5052915 Keywords : bacterial genomes * gene organization * polyhydroxyalkanoates Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 0.615, year: 2002

  1. Non-genetic determinants of mosquito competence for malaria parasites.

    Directory of Open Access Journals (Sweden)

    Thierry Lefèvre

    Full Text Available Understanding how mosquito vectors and malaria parasites interact is of fundamental interest, and it also offers novel perspectives for disease control. Both the genetic and environmental contexts are known to affect the ability of mosquitoes to support malaria development and transmission, i.e., vector competence. Although the role of environment has long been recognized, much work has focused on host and parasite genetic effects. However, the last few years have seen a surge of studies revealing a great diversity of ways in which non-genetic factors can interfere with mosquito-Plasmodium interactions. Here, we review the current evidence for such environmentally mediated effects, including ambient temperature, mosquito diet, microbial gut flora, and infection history, and we identify additional factors previously overlooked in mosquito-Plasmodium interactions. We also discuss epidemiological implications, and the evolutionary consequences for vector immunity and parasite transmission strategies. Finally, we propose directions for further research and argue that an improved knowledge of non-genetic influences on mosquito-Plasmodium interactions could aid in implementing conventional malaria control measures and contribute to the design of novel strategies.

  2. CYP/PON genetic variations as determinant of organophosphate ...

    Indian Academy of Sciences (India)

    GURPREET KAUR

    This paper is aimed to review the impact of endogenous and exogenous factors on a mechanistic pathway of organophosphate pesticide biotransformation and various risk associated with it among the human population. Understanding the genetic polymorphism of genes involved in pesticide metabolism and highlighting ...

  3. Genetical genomic determinants of alcohol consumption in rats and humans

    Czech Academy of Sciences Publication Activity Database

    Tabakoff, B.; Saba, L.; Printz, M.; Flodman, P.; Hodgkinson, C.; Goldman, D.; Koob, G.; Richardson, H.N.; Kechris, K.; Bell, R.L.; Hübner, N.; Heinig, M.; Pravenec, Michal; Mangion, J.; Legault, L.; Dongier, M.; Conigrave, K.M.; Whitfield, J.B.; Saunders, J.; Grant, B.; Hoffman, P.L.

    2009-01-01

    Roč. 7, - (2009), s. 70-70 ISSN 1741-7007 R&D Projects: GA MŠk(CZ) 1M0520 Grant - others:Howard Hughes Medical Institute(US) 55005624 Institutional research plan: CEZ:AV0Z50110509 Keywords : alcohol consumption * rat * gene expression profiles Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.636, year: 2009

  4. Population Genetics of the São Tomé Caecilian (Gymnophiona: Dermophiidae: Schistometopum thomense) Reveals Strong Geographic Structuring

    Science.gov (United States)

    Stoelting, Ricka E.; Measey, G. John; Drewes, Robert C.

    2014-01-01

    Islands provide exciting opportunities for exploring ecological and evolutionary mechanisms. The oceanic island of São Tomé in the Gulf of Guinea exhibits high diversity of fauna including the endemic caecilian amphibian, Schistometopum thomense. Variation in pigmentation, morphology and size of this taxon over its c. 45 km island range is extreme, motivating a number of taxonomic, ecological, and evolutionary hypotheses to explain the observed diversity. We conducted a population genetic study of S. thomense using partial sequences of two mitochondrial DNA genes (ND4 and 16S), together with morphological examination, to address competing hypotheses of taxonomic or clinal variation. Using Bayesian phylogenetic analysis and Spatial Analysis of Molecular Variance, we found evidence of four geographic clades, whose range and approximated age (c. 253 Kya – 27 Kya) are consistent with the spread and age of recent volcanic flows. These clades explained 90% of variation in ND4 (φCT = 0.892), and diverged by 4.3% minimum pairwise distance at the deepest node. Most notably, using Mismatch Distributions and Mantel Tests, we identified a zone of population admixture that dissected the island. In the northern clade, we found evidence of recent population expansion (Fu's Fs = −13.08 and Tajima's D = −1.80) and limited dispersal (Mantel correlation coefficient = 0.36, p = 0.01). Color assignment to clades was not absolute. Paired with multinomial regression of chromatic data, our analyses suggested that the genetic groups and a latitudinal gradient together describe variation in color of S. thomense. We propose that volcanism and limited dispersal ability are the likely proximal causes of the observed genetic structure. This is the first population genetic study of any caecilian and demonstrates that these animals have deep genetic divisions over very small areas in accordance with previous speculations of low dispersal abilities. PMID:25171066

  5. Genetic determinants of mate recognition in Brachionus manjavacas (Rotifera

    Directory of Open Access Journals (Sweden)

    Kubanek Julia

    2009-09-01

    Full Text Available Abstract Background Mate choice is of central importance to most animals, influencing population structure, speciation, and ultimately the survival of a species. Mating behavior of male brachionid rotifers is triggered by the product of a chemosensory gene, a glycoprotein on the body surface of females called the mate recognition pheromone. The mate recognition pheromone has been biochemically characterized, but little was known about the gene(s. We describe the isolation and characterization of the mate recognition pheromone gene through protein purification, N-terminal amino acid sequence determination, identification of the mate recognition pheromone gene from a cDNA library, sequencing, and RNAi knockdown to confirm the functional role of the mate recognition pheromone gene in rotifer mating. Results A 29 kD protein capable of eliciting rotifer male circling was isolated by high-performance liquid chromatography. Two transcript types containing the N-terminal sequence were identified in a cDNA library; further characterization by screening a genomic library and by polymerase chain reaction revealed two genes belonging to each type. Each gene begins with a signal peptide region followed by nearly perfect repeats of an 87 to 92 codon motif with no codons between repeats and the final motif prematurely terminated by the stop codon. The two Type A genes contain four and seven repeats and the two Type B genes contain three and five repeats, respectively. Only the Type B gene with three repeats encodes a peptide with a molecular weight of 29 kD. Each repeat of the Type B gene products contains three asparagines as potential sites for N-glycosylation; there are no asparagines in the Type A genes. RNAi with Type A double-stranded RNA did not result in less circling than in the phosphate-buffered saline control, but transfection with Type B double-stranded RNA significantly reduced male circling by 17%. The very low divergence between repeat units

  6. Strong population genetic structuring in an annual fish, Nothobranchius furzeri, suggests multiple savannah refugia in southern Mozambique

    Czech Academy of Sciences Publication Activity Database

    Bartáková, Veronika; Reichard, Martin; Janko, Karel; Polačik, Matej; Blažek, Radim; Reichwald, K.; Cellerino, A.; Bryja, Josef

    2013-01-01

    Roč. 13, č. 196 (2013), s. 196 ISSN 1471-2148 R&D Projects: GA ČR GA206/09/0815; GA ČR GBP505/12/G112 Institutional support: RVO:68081766 Keywords : Temporary pool * Phylogeography * Population genetics * Cyprinodontiformes * Senescence * Pluvials * Pleistocene climate changes * Dispersal * Founder effect * Killifish Subject RIV: EG - Zoology Impact factor: 3.407, year: 2013 http://www.biomedcentral.com/1471-2148/13/196

  7. Genetic determinants and stroke in children with sickle cell disease

    Directory of Open Access Journals (Sweden)

    Daniela O.W. Rodrigues

    2016-11-01

    Conclusion: There is a high incidence of stroke in male children and in children with SCA. Coexistence with α‐thal and haplotypes of the beta globin chain cluster did not show any significant association with stroke. The heterogeneity between previously evaluated populations, the non‐reproducibility between studies, and the need to identify factors associated with stroke in patients with SCA indicate the necessity of conducting further research to demonstrate the relevance of genetic factors in stroke related to SCD.

  8. Genetical genomic determinants of alcohol consumption in rats and humans

    Directory of Open Access Journals (Sweden)

    Mangion Jonathan

    2009-10-01

    Full Text Available Abstract Background We have used a genetical genomic approach, in conjunction with phenotypic analysis of alcohol consumption, to identify candidate genes that predispose to varying levels of alcohol intake by HXB/BXH recombinant inbred rat strains. In addition, in two populations of humans, we assessed genetic polymorphisms associated with alcohol consumption using a custom genotyping array for 1,350 single nucleotide polymorphisms (SNPs. Our goal was to ascertain whether our approach, which relies on statistical and informatics techniques, and non-human animal models of alcohol drinking behavior, could inform interpretation of genetic association studies with human populations. Results In the HXB/BXH recombinant inbred (RI rats, correlation analysis of brain gene expression levels with alcohol consumption in a two-bottle choice paradigm, and filtering based on behavioral and gene expression quantitative trait locus (QTL analyses, generated a list of candidate genes. A literature-based, functional analysis of the interactions of the products of these candidate genes defined pathways linked to presynaptic GABA release, activation of dopamine neurons, and postsynaptic GABA receptor trafficking, in brain regions including the hypothalamus, ventral tegmentum and amygdala. The analysis also implicated energy metabolism and caloric intake control as potential influences on alcohol consumption by the recombinant inbred rats. In the human populations, polymorphisms in genes associated with GABA synthesis and GABA receptors, as well as genes related to dopaminergic transmission, were associated with alcohol consumption. Conclusion Our results emphasize the importance of the signaling pathways identified using the non-human animal models, rather than single gene products, in identifying factors responsible for complex traits such as alcohol consumption. The results suggest cross-species similarities in pathways that influence predisposition to consume

  9. The Genetic Determinism of Biochemical Systems Polymorphous From the Blood Serum in Pigs

    Directory of Open Access Journals (Sweden)

    Nicoleta Işfan

    2010-05-01

    Full Text Available The study of genetic markers and identification of new markers make the subject of an increasing number of research projects in various fields such as genetics of immunology, biochemical genetics, molecular genetics, quantitative genetics and the genetic amelioration of animals. The information provided by electrophoresis graphs has been used to determine the frequency of various categories of alleles (for the loci of pre-albumin, transferines and serum amylases, the frequency of various phenotypes and the genetic structure for each and every locus and, simultaneously, for the loci being studied. The discussion over the varieties of serum proteins was carried on for the purpose of using them as genetic markers, in order to appreciate the levels of genetic unity or diversity within the stock of swine that has been studied. A pair of simple alleles has been determined for each of the three loci. When the three loci were studied simultaneously, out of the 27 possible combinations, only 15 have been found. The sample studied has found to be genetically balanced for every of the three loci. However, when the simultaneous study has been applied, the same sample has not been found genetically balanced.

  10. Strong genetic influence on a UK nationwide test of educational achievement at the end of compulsory education at age 16.

    Science.gov (United States)

    Shakeshaft, Nicholas G; Trzaskowski, Maciej; McMillan, Andrew; Rimfeld, Kaili; Krapohl, Eva; Haworth, Claire M A; Dale, Philip S; Plomin, Robert

    2013-01-01

    We have previously shown that individual differences in educational achievement are highly heritable in the early and middle school years in the UK. The objective of the present study was to investigate whether similarly high heritability is found at the end of compulsory education (age 16) for the UK-wide examination, called the General Certificate of Secondary Education (GCSE). In a national twin sample of 11,117 16-year-olds, heritability was substantial for overall GCSE performance for compulsory core subjects (58%) as well as for each of them individually: English (52%), mathematics (55%) and science (58%). In contrast, the overall effects of shared environment, which includes all family and school influences shared by members of twin pairs growing up in the same family and attending the same school, accounts for about 36% of the variance of mean GCSE scores. The significance of these findings is that individual differences in educational achievement at the end of compulsory education are not primarily an index of the quality of teachers or schools: much more of the variance of GCSE scores can be attributed to genetics than to school or family environment. We suggest a model of education that recognizes the important role of genetics. Rather than a passive model of schooling as instruction (instruere, 'to build in'), we propose an active model of education (educare, 'to bring out') in which children create their own educational experiences in part on the basis of their genetic propensities, which supports the trend towards personalized learning.

  11. Genetic Determinants of Unruptured Intracranial Aneurysms in the General Population.

    Science.gov (United States)

    Peymani, Abbas; Adams, Hieab H H; Cremers, Lotte G M; Krestin, Gabriel; Hofman, Albert; van Duijn, Cornelia M; Uitterlinden, André G; van der Lugt, Aad; Vernooij, Meike W; Ikram, M Arfan

    2015-10-01

    Genome-wide association studies have identified single-nucleotide polymorphisms (SNPs) for intracranial aneurysms in clinical samples. In addition, SNPs have been discovered for blood pressure, one of the strongest risk factors for intracranial aneurysms. We studied the role of these genetic variants on occurrence and size of unruptured intracranial aneurysms, discovered incidentally in a general community-dwelling population. In 4890 asymptomatic participants from the Rotterdam Study, 120 intracranial aneurysms were identified on brain imaging and segmented for maximum diameter and volume. Genetic risk scores (GRS) were calculated for intracranial aneurysms (10 SNPs), systolic blood pressure (33 SNPs), and diastolic blood pressure (41 SNPs). The GRS for intracranial aneurysms was not statistically significantly associated with presence of aneurysms in this population (OR, 1.16; 95% CI, 0.96-1.40; P=0.119), but showed a significant association with both maximum diameter (difference in log-transformed mm per SD increase of GRS, 0.10; 95% CI, 0.02-0.19; P=0.018) and volume (difference in log-transformed µL per SD increase of GRS, 0.21; 95% CI, 0.01-0.41; P=0.040) of aneurysms. GRSs for blood pressures were associated with neither presence nor size of aneurysms. Genetic variants previously identified for intracranial aneurysms in clinical studies relate to the size rather than the presence of incidentally discovered, unruptured intracranial aneurysms in the general population. © 2015 American Heart Association, Inc.

  12. Analyses of historical and current populations of black grouse in Central Europe reveal strong effects of genetic drift and loss of genetic diversity

    NARCIS (Netherlands)

    Segelbacher, G.; Strand, T.M.; Quintela, M.; Axelsson, T.; Jansman, H.A.H.; Koelewijn, H.P.; Hoglund, J.

    2014-01-01

    Black grouse (Tetrao tetrix) in Central Europe have undergone a severe contraction of their range in recent decades with only a few small isolated remaining populations. Here we compare genetic diversity of two contemporary isolated populations (Sallandse Heuvelrug, Netherlands and Luneburger Heide,

  13. Genetic determinants of serum vitamin B12 and their relation to body mass index.

    Science.gov (United States)

    Allin, Kristine H; Friedrich, Nele; Pietzner, Maik; Grarup, Niels; Thuesen, Betina H; Linneberg, Allan; Pisinger, Charlotta; Hansen, Torben; Pedersen, Oluf; Sandholt, Camilla H

    2017-02-01

    Lower serum vitamin B12 levels have been related to adverse metabolic health profiles, including adiposity. We used a Mendelian randomization design to test whether this relation might be causal. We included two Danish population-based studies (n total  = 9311). Linear regression was used to test for associations between (1) serum vitamin B12 levels and body mass index (BMI), (2) genetic variants and serum vitamin B12 levels, and (3) genetic variants and BMI. The effect of a genetically determined decrease in serum vitamin B12 on BMI was estimated by instrumental variable regression. Decreased serum vitamin B12 associated with increased BMI (P vitamin B12 associated variants associated strongly with serum vitamin B12 (P vitamin B12 was associated with a 0.09 kg/m 2 (95% CI 0.05; 0.13) increase in BMI (P = 3 × 10 -5 ), whereas a genetically induced 20% decrease in serum vitamin B12 had no effect on BMI [-0.03 (95% CI -0.22; 0.16) kg/m 2 ] (P = 0.74). Nevertheless, the strongest serum vitamin B12 variant, FUT2 rs602662, which was excluded from the B12 genetic risk score due to potential pleiotropic effects, showed a per allele effect of 0.15 kg/m 2 (95% CI 0.01; 0.32) on BMI (P = 0.03). This association was accentuated including two German cohorts (n total  = 5050), with a combined effect of 0.19 kg/m 2 (95% CI 0.08; 0.30) (P = 4 × 10 -4 ). We found no support for a causal role of decreased serum vitamin B12 levels in obesity. However, our study suggests that FUT2, through its regulation of the cross-talk between gut microbes and the human host, might explain a part of the observational association between serum vitamin B12 and BMI.

  14. Genetic structure of the date palm (Phoenix dactylifera) in the Old World reveals a strong differentiation between eastern and western populations.

    Science.gov (United States)

    Zehdi-Azouzi, Salwa; Cherif, Emira; Moussouni, Souhila; Gros-Balthazard, Muriel; Abbas Naqvi, Summar; Ludeña, Bertha; Castillo, Karina; Chabrillange, Nathalie; Bouguedoura, Nadia; Bennaceur, Malika; Si-Dehbi, Farida; Abdoulkader, Sabira; Daher, Abdourahman; Terral, Jean-Frederic; Santoni, Sylvain; Ballardini, Marco; Mercuri, Antonio; Ben Salah, Mohamed; Kadri, Karim; Othmani, Ahmed; Littardi, Claudio; Salhi-Hannachi, Amel; Pintaud, Jean-Christophe; Aberlenc-Bertossi, Frédérique

    2015-07-01

    Date palms (Phoenix dactylifera, Arecaceae) are of great economic and ecological value to the oasis agriculture of arid and semi-arid areas. However, despite the availability of a large date palm germplasm spreading from the Atlantic shores to Southern Asia, improvement of the species is being hampered by a lack of information on global genetic diversity and population structure. In order to contribute to the varietal improvement of date palms and to provide new insights on the influence of geographic origins and human activity on the genetic structure of the date palm, this study analysed the diversity of the species. Genetic diversity levels and population genetic structure were investigated through the genotyping of a collection of 295 date palm accessions ranging from Mauritania to Pakistan using a set of 18 simple sequence repeat (SSR) markers and a plastid minisatellite. Using a Bayesian clustering approach, the date palm genotypes can be structured into two different gene pools: the first, termed the Eastern pool, consists of accessions from Asia and Djibouti, whilst the second, termed the Western pool, consists of accessions from Africa. These results confirm the existence of two ancient gene pools that have contributed to the current date palm diversity. The presence of admixed genotypes is also noted, which points at gene flows between eastern and western origins, mostly from east to west, following a human-mediated diffusion of the species. This study assesses the distribution and level of genetic diversity of accessible date palm resources, provides new insights on the geographic origins and genetic history of the cultivated component of this species, and confirms the existence of at least two domestication origins. Furthermore, the strong genetic structure clearly established here is a prerequisite for any breeding programme exploiting the effective polymorphism related to each gene pool. © The Author 2015. Published by Oxford University Press on

  15. Breast magnetic resonance imaging significance for breast cancer diagnostic in women with genetic predisposition and a strong family history

    Directory of Open Access Journals (Sweden)

    M. S. Karpova

    2013-01-01

    Full Text Available Screening of breast cancer with mammography recommended to women over 40 has been shown to decrease breast cancer mortality. But mam- mography has much lower accuracy in young women with BRCA1/2 mutations and women with a strong family history. Therefore new screening methods in young high-risk women are necessary to detect early-stage cancer.

  16. The Major Genetic Determinants of HIV-1 Control Affect HLA Class I Peptide Presentation

    OpenAIRE

    Pereyra, Florencia; Jia, Xiaoming; McLaren, Paul J.; Telenti, Amalio; de Bakker, Paul I.W.; Walker, Bruce D.; Jia, Xiaoming; McLaren, Paul J.; Ripke, Stephan; Brumme, Chanson J.; Pulit, Sara L.; Telenti, Amalio; Carrington, Mary; Kadie, Carl M.; Carlson, Jonathan M.

    2010-01-01

    Infectious and inflammatory diseases have repeatedly shown strong genetic associations within the major histocompatibility complex (MHC); however, the basis for these associations remains elusive. To define host genetic effects on the outcome of a chronic viral infection, we performed genome-wide association analysis in a multiethnic cohort of HIV-1 controllers and progressors, and we analyzed the effects of individual amino acids within the classical human leukocyte antigen (HLA) proteins. W...

  17. Measurement of Inclusive Jet Production in Deep-Inelastic Scattering at High Q$^{2}$ and Determination of the Strong Coupling

    CERN Document Server

    Aktas, A.; Andreev, V.; Anthonis, T.; Antunovic, B.; Aplin, S.; Asmone, A.; Astvatsatourov, A.; Backovic, S.; Baghdasaryan, A.; Baranov, P.; Barrelet, E.; Bartel, W.; Baudrand, S.; Beckingham, M.; Begzsuren, K.; Behnke, O.; Behrendt, O.; Belousov, A.; Berger, N.; Bizot, J.C.; Boenig, M.-O.; Boudry, V.; Bozovic-Jelisavcic, I.; Bracinik, J.; Brandt, G.; Brinkmann, M.; Brisson, V.; Bruncko, D.; Busser, F.W.; Bunyatyan, A.; Buschhorn, G.; Bystritskaya, L.; Campbell, A.J.; Cantun Avila, K.B.; Cassol-Brunner, F.; Cerny, K.; Cerny, V.; Chekelian, V.; Cholewa, A.; Contreras, J.G.; Coughlan, J.A.; Cozzika, G.; Cvach, J.; Dainton, J.B.; Daum, K.; Deak, M.; de Boer, Y.; Delcourt, B.; Del Degan, M.; Delvax, J.; De Roeck, A.; De Wolf, E.A.; Diaconu, C.; Dodonov, V.; Dubak, A.; Eckerlin, Guenter; Efremenko, V.; Egli, S.; Eichler, R.; Eisele, F.; Eliseev, A.; Elsen, E.; Essenov, S.; Falkiewicz, A.; Faulkner, P.J.W.; Favart, L.; Fedotov, A.; Felst, R.; Feltesse, J.; Ferencei, J.; Finke, L.; Fleischer, M.; Fomenko, A.; Franke, G.; Frisson, T.; Gabathuler, E.; Gayler, J.; Ghazaryan, Samvel; Ginzburgskaya, S.; Glazov, A.; Glushkov, I.; Goerlich, L.; Goettlich, M.; Gogitidze, N.; Gorbounov, S.; Gouzevitch, M.; Grab, C.; Greenshaw, T.; Grell, B.R.; Grindhammer, G.; Habib, S.; Haidt, D.; Hansson, M.; Heinzelmann, G.; Helebrant, C.; Henderson, R.C.W.; Henschel, H.; Herrera, G.; Hildebrandt, M.; Hiller, K.H.; Hoffmann, D.; Horisberger, R.; Hovhannisyan, A.; Hreus, T.; Jacquet, M.; Janssen, M.E.; Janssen, X.; Jemanov, V.; Jonsson, L.; Johnson, D.P.; Jung, Andreas Werner; Jung, H.; Kapichine, M.; Katzy, J.; Kenyon, I.R.; Kiesling, Christian M.; Klein, M.; Kleinwort, C.; Klimkovich, T.; Kluge, T.; Knutsson, A.; Korbel, V.; Kostka, P.; Kraemer, M.; Krastev, K.; Kretzschmar, J.; Kropivnitskaya, A.; Kruger, K.; Landon, M.P.J.; Lange, W.; Lastovicka-Medin, G.; Laycock, P.; Lebedev, A.; Leibenguth, G.; Lendermann, V.; Levonian, S.; Li, G.; Lindfeld, L.; Lipka, K.; Liptaj, A.; List, B.; List, J.; Loktionova, N.; Lopez-Fernandez, R.; Lubimov, V.; Lucaci-Timoce, A.-I.; Lytkin, L.; Makankine, A.; Malinovski, E.; Marage, P.; Marti, Ll.; Martisikova, M.; Martyn, H.-U.; Maxfield, S.J.; Mehta, A.; Meier, K.; Meyer, A.B.; Meyer, H.; Meyer, J.; Michels, V.; Mikocki, S.; Milcewicz-Mika, I.; Mohamed, A.; Moreau, F.; Morozov, A.; Morris, J.V.; Mozer, Matthias Ulrich; Muller, K.; Murin, P.; Nankov, K.; Naroska, B.; Naumann, Th.; Newman, Paul R.; Niebuhr, C.; Nikiforov, A.; Nowak, G.; Nowak, K.; Nozicka, M.; Oganezov, R.; Olivier, B.; Olsson, J.E.; Osman, S.; Ozerov, D.; Palichik, V.; Panagoulias, I.; Pandurovic, M.; Papadopoulou, Th.; Pascaud, C.; Patel, G.D.; Peng, H.; Perez, E.; Perez-Astudillo, D.; Perieanu, A.; Petrukhin, A.; Picuric, I.; Piec, S.; Pitzl, D.; Placakyte, R.; Polifka, R.; Povh, B.; Preda, T.; Prideaux, P.; Radescu, V.; Rahmat, A.J.; Raicevic, N.; Ravdandorj, T.; Reimer, P.; Risler, C.; Rizvi, E.; Robmann, P.; Roland, B.; Roosen, R.; Rostovtsev, A.; Rurikova, Z.; Rusakov, S.; Salvaire, F.; Sankey, D.P.C.; Sauter, M.; Sauvan, E.; Schmidt, S.; Schmitt, S.; Schmitz, C.; Schoeffel, L.; Schoning, A.; Schultz-Coulon, H.-C.; Sefkow, F.; Shaw-West, R.N.; Sheviakov, I.; Shtarkov, L.N.; Sloan, T.; Smiljanic, Ivan; Smirnov, P.; Soloviev, Y.; South, D.; Spaskov, V.; Specka, Arnd E.; Staykova, Z.; Steder, M.; Stella, B.; Stiewe, J.; Straumann, U.; Sunar, D.; Sykora, T.; Tchoulakov, V.; Thompson, G.; Thompson, P.D.; Toll, T.; Tomasz, F.; Tran, T.H.; Traynor, D.; Trinh, T.N.; Truol, P.; Tsakov, I.; Tseepeldorj, B.; Tsipolitis, G.; Tsurin, I.; Turnau, J.; Tzamariudaki, E.; Urban, K.; Utkin, D.; Valkarova, A.; Vallee, C.; Van Mechelen, P.; Vargas Trevino, A.; Vazdik, Y.; Vinokurova, S.; Volchinski, V.; Weber, G.; Weber, R.; Wegener, D.; Werner, C.; Wessels, M.; Wissing, Ch.; Wolf, R.; Wunsch, E.; Xella, S.; Yan, W.; Yeganov, V.; Zacek, J.; Zalesak, J.; Zhang, Z.; Zhelezov, A.; Zhokin, A.; Zhu, Y.C.; Zimmermann, T.; Zohrabyan, H.; Zomer, F.

    2007-01-01

    Inclusive jet production is studied in neutral current deep-inelastic positron-proton scattering at large four momentum transfer squared Q^2>150 GeV^2 with the H1 detector at HERA. Single and double differential inclusive jet cross sections are measured as a function of Q^2 and of the transverse energy E_T of the jets in the Breit frame. The measurements are found to be well described by calculations at next-to-leading order in perturbative QCD. The running of the strong coupling is demonstrated and the value of alpha_s(M_Z) is determined. The ratio of the inclusive jet cross section to the inclusive neutral current cross section is also measured and used to extract a precise value for alpha_s(M_Z)=0.1193+/-0.0014(exp.)^{+0.0047}_{-0.0030}(th.)+/-0.0016(pdf).

  18. Impact of beauty and charm H1-ZEUS combined measurements on PDFs and determination of the strong coupling

    Science.gov (United States)

    Vafaee, A.; Khorramian, A.

    2017-11-01

    In this QCD analysis, we investigate the impact of recent measurements of heavy-flavor charm and beauty cross sections data sets on the simultaneous determination of Parton Distribution Functions (PDFs) and the strong coupling, αs(M2Z). We perform three different fits based on Variable-Flavour Number Scheme (VFNS) at the Leading Order (LO) and Next-to-Leading Order (NLO) and choose the full HERA run I and II combined data as a new measurement of inclusive Deep Inelastic Scattering (DIS) cross sections for our base data set. We show that including charm and beauty cross sections data reduces the uncertainty of gluon distribution and improves the fit quality up to 4.1% from leading order to next-to-leading order and up to 1.7% for only NLO without and with beauty and charm data contributions.

  19. Determination of the strong coupling constant $\\alpha_s$ in multijet production with the ATLAS detector at the LHC.

    CERN Document Server

    Llorente Merino, Javier; The ATLAS collaboration

    2018-01-01

    A measurement of transverse energy--energy correlations and its asymmetry in $pp$ collisions recorded by the ATLAS detector at the LHC at $\\sqrt{s} = 8$ TeV is presented. The results are intepreted as a precision test of Quantum Chromodynamics, used to determine the strong coupling constant $\\alpha_s(m_Z)$ and to test asymptotic freedom up to scales close to 1 TeV. A global fit to the transverse energy--energy correlation distributions yields $\\alpha_{\\mathrm{s}}(m_Z) = 0.1162 \\pm 0.0011 \\mbox{ (exp.)}^{+0.0084}_{-0.0070} \\mbox{ (theo.)}$, while a global fit to the asymmetry distributions yields a value of $\\alpha_{\\mathrm{s}}(m_Z) = 0.1196 \\pm 0.0013 \\mbox{ (exp.)}^{+0.0075}_{-0.0045} \\mbox{ (theo.)}$.

  20. Genetic Determinism in the Genetics Curriculum. An Exploratory Study of the Effects of Mendelian and Weldonian Emphases

    Science.gov (United States)

    Jamieson, Annie; Radick, Gregory

    2017-12-01

    Twenty-first-century biology rejects genetic determinism, yet an exaggerated view of the power of genes in the making of bodies and minds remains a problem. What accounts for such tenacity? This article reports an exploratory study suggesting that the common reliance on Mendelian examples and concepts at the start of teaching in basic genetics is an eliminable source of support for determinism. Undergraduate students who attended a standard `Mendelian approach' university course in introductory genetics on average showed no change in their determinist views about genes. By contrast, students who attended an alternative course which, inspired by the work of a critic of early Mendelism, W. F. R. Weldon (1860-1906), replaced an emphasis on Mendel's peas with an emphasis on developmental contexts and their role in bringing about phenotypic variability, were less determinist about genes by the end of teaching. Improvements in both the new Weldonian curriculum and the study design are in view for the future.

  1. Populations genetically rifting within a complex geological system: The case of strong structure and low genetic diversity in the migratory freshwater catfish, Bagrus docmak, in East Africa

    OpenAIRE

    Basiita, Rose Komugisha; Zenger, Kyall Richard; Jerry, Dean Robert

    2017-01-01

    Abstract The complex geological history of East Africa has been a driving factor in the rapid evolution of teleost biodiversity. While there is some understanding of how macroevolutionary drivers have shaped teleost speciation in East Africa, there is a paucity of research into how the same biogeographical factors have affected microevolutionary processes within lakes and rivers. To address this deficiency, population genetic diversity, demography, and structure were investigated in a widely ...

  2. Genetic determinants for enhanced glycerol growth of Saccharomyces cerevisiae.

    Science.gov (United States)

    Swinnen, Steve; Ho, Ping-Wei; Klein, Mathias; Nevoigt, Elke

    2016-07-01

    The yeast Saccharomyces cerevisiae generally shows a low natural capability to utilize glycerol as the sole source of carbon, particularly when synthetic medium is used and complex supplements are omitted. Nevertheless, wild type isolates have been identified that show a moderate growth under these conditions. In the current study we made use of intraspecies diversity to identify targets suitable for reverse metabolic engineering of the non-growing laboratory strain CEN.PK113-1A. A genome-wide genetic mapping experiment using pooled-segregant whole-genome sequence analysis was conducted, and one major and several minor genetic loci were identified responsible for the superior glycerol growth phenotype of the previously selected S. cerevisiae strain CBS 6412-13A. Downscaling of the major locus by fine-mapping and reciprocal hemizygosity analysis allowed the parallel identification of two superior alleles (UBR2CBS 6412-13A and SSK1CBS 6412-13A). These alleles together with the previously identified GUT1CBS 6412-13A allele were used to replace the corresponding alleles in the strain CEN.PK113-1A. In this way, glycerol growth could be established reaching a maximum specific growth rate of 0.08h(-1). Further improvement to a maximum specific growth rate of 0.11h(-1) could be achieved by heterologous expression of the glycerol facilitator FPS1 from Cyberlindnera jadinii. Copyright © 2016 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

  3. Genetic determinants of hyaloid and retinal vasculature in zebrafish

    Directory of Open Access Journals (Sweden)

    Hyde David R

    2007-10-01

    Full Text Available Abstract Background The retinal vasculature is a capillary network of blood vessels that nourishes the inner retina of most mammals. Developmental abnormalities or microvascular complications in the retinal vasculature result in severe human eye diseases that lead to blindness. To exploit the advantages of zebrafish for genetic, developmental and pharmacological studies of retinal vasculature, we characterised the intraocular vasculature in zebrafish. Results We show a detailed morphological and developmental analysis of the retinal blood supply in zebrafish. Similar to the transient hyaloid vasculature in mammalian embryos, vessels are first found attached to the zebrafish lens at 2.5 days post fertilisation. These vessels progressively lose contact with the lens and by 30 days post fertilisation adhere to the inner limiting membrane of the juvenile retina. Ultrastructure analysis shows these vessels to exhibit distinctive hallmarks of mammalian retinal vasculature. For example, smooth muscle actin-expressing pericytes are ensheathed by the basal lamina of the blood vessel, and vesicle vacuolar organelles (VVO, subcellular mediators of vessel-retinal nourishment, are present. Finally, we identify 9 genes with cell membrane, extracellular matrix and unknown identity that are necessary for zebrafish hyaloid and retinal vasculature development. Conclusion Zebrafish have a retinal blood supply with a characteristic developmental and adult morphology. Abnormalities of these intraocular vessels are easily observed, enabling application of genetic and chemical approaches in zebrafish to identify molecular regulators of hyaloid and retinal vasculature in development and disease.

  4. Genetic determinants of glycated hemoglobin levels in the Greenlandic Inuit population

    DEFF Research Database (Denmark)

    Appel, Emil V R; Moltke, Ida; Jørgensen, Marit E

    2018-01-01

    We previously showed that a common genetic variant leads to a remarkably increased risk of type 2 diabetes (T2D) in the small and historically isolated Greenlandic population. Motivated by this, we aimed at discovering novel genetic determinants for glycated hemoglobin (HbA1C) and at estimating...

  5. Genetic Determinism in School Textbooks: A Comparative Study Conducted among Sixteen Countries

    Science.gov (United States)

    Castera, Jeremy; Clement, Pierre; Abrougui, Mondher; Nisiforou, Olympia; Valanides, Nicos; Turcinaviciene, Jurga; Sarapuu, Tago; Agorram, Boujemaa; Calado, Florbela; Bogner, Franz; Carvalho, Graca

    2008-01-01

    Genetic concepts have significantly evolved over the last ten years, and are now less connected to innate ideas and reductionism. Unique reference to genetic determinism has been replaced by the interaction between the genes and their environment (epigenetics). Our analyses relate to how current school biology textbooks present this new paradigm…

  6. Determination of the strong coupling constant from the inclusive jet cross section in pp- collisions at sqrt s=1.96 TeV

    NARCIS (Netherlands)

    Abazov, V.M.; et al., [Unknown; Ancu, L.S.; de Jong, S.J.; Filthaut, F.; Galea, C.F.; Hegeman, J.G.; Houben, P.; Meijer, M.M.; Svoisky, P.; van den Berg, P.J.; van Leeuwen, W.M.

    2009-01-01

    We determine the strong coupling constant alpha(s) and its energy dependence from the p(T) dependence of the inclusive jet cross section in pp collisions at s=1.96 TeV. The strong coupling constant is determined over the transverse momentum range 50 < p(T)< 145 GeV. Using perturbative QCD

  7. Genetics of sex determination in the haplodiploid wasp Nasonia ...

    Indian Academy of Sciences (India)

    The parasitoid wasp Nasonia vitripennis reproduces by haplodiploidy; males are haploid and females are diploid. Sex determination in Nasonia is not governed by complementary alleles at one or more sex loci. As in most other insects, the sex-determining pathway consists of the basal switch doublesex that is ...

  8. Low Genetic Diversity and Strong Geographical Structure of the Critically Endangered White-Headed Langur (Trachypithecus leucocephalus) Inferred from Mitochondrial DNA Control Region Sequences.

    Science.gov (United States)

    Wang, Weiran; Qiao, Yu; Pan, Wenshi; Yao, Meng

    2015-01-01

    Many Asian colobine monkey species are suffering from habitat destruction and population size decline. There is a great need to understand their genetic diversity, population structure and demographic history for effective species conservation. The white-headed langur (Trachypithecus leucocephalus) is a Critically Endangered colobine species endemic to the limestone karst forests in southwestern China. We analyzed the mitochondrial DNA (mtDNA) control region sequences of 390 fecal samples from 40 social groups across the main distribution areas, which represented one-third of the total extant population. Only nine haplotypes and 10 polymorphic sites were identified, indicating remarkably low genetic diversity in the species. Using a subset of 77 samples from different individuals, we evaluated genetic variation, population structure, and population demographic history. We found very low values of haplotype diversity (h = 0.570 ± 0.056) and nucleotide diversity (π = 0.00323 ± 0.00044) in the hypervariable region I (HVRI) of the mtDNA control region. Distribution of haplotypes displayed marked geographical pattern, with one population (Chongzuo, CZ) showing a complete lack of genetic diversity (having only one haplotype), whereas the other population (Fusui, FS) having all nine haplotypes. We detected strong population genetic structure among habit patches (ΦST = 0.375, P population size and modest population expansion in the last 2,000 years. Our results indicate different genetic diversity and possibly distinct population history for different local populations, and suggest that CZ and FS should be considered as one evolutionarily significant unit (ESU) and two management units (MUs) pending further investigation using nuclear markers.

  9. Genetic determinants of serum testosterone concentrations in men.

    Directory of Open Access Journals (Sweden)

    Claes Ohlsson

    2011-10-01

    Full Text Available Testosterone concentrations in men are associated with cardiovascular morbidity, osteoporosis, and mortality and are affected by age, smoking, and obesity. Because of serum testosterone's high heritability, we performed a meta-analysis of genome-wide association data in 8,938 men from seven cohorts and followed up the genome-wide significant findings in one in silico (n = 871 and two de novo replication cohorts (n = 4,620 to identify genetic loci significantly associated with serum testosterone concentration in men. All these loci were also associated with low serum testosterone concentration defined as <300 ng/dl. Two single-nucleotide polymorphisms at the sex hormone-binding globulin (SHBG locus (17p13-p12 were identified as independently associated with serum testosterone concentration (rs12150660, p = 1.2×10(-41 and rs6258, p = 2.3×10(-22. Subjects with ≥ 3 risk alleles of these variants had 6.5-fold higher risk of having low serum testosterone than subjects with no risk allele. The rs5934505 polymorphism near FAM9B on the X chromosome was also associated with testosterone concentrations (p = 5.6×10(-16. The rs6258 polymorphism in exon 4 of SHBG affected SHBG's affinity for binding testosterone and the measured free testosterone fraction (p<0.01. Genetic variants in the SHBG locus and on the X chromosome are associated with a substantial variation in testosterone concentrations and increased risk of low testosterone. rs6258 is the first reported SHBG polymorphism, which affects testosterone binding to SHBG and the free testosterone fraction and could therefore influence the calculation of free testosterone using law-of-mass-action equation.

  10. Population genomic analysis suggests strong influence of river network on spatial distribution of genetic variation in invasive saltcedar across the southwestern United States

    Science.gov (United States)

    Lee, Soo-Rang; Jo, Yeong-Seok; Park, Chan-Ho; Friedman, Jonathan M.; Olson, Matthew S.

    2018-01-01

    Understanding the complex influences of landscape and anthropogenic elements that shape the population genetic structure of invasive species provides insight into patterns of colonization and spread. The application of landscape genomics techniques to these questions may offer detailed, previously undocumented insights into factors influencing species invasions. We investigated the spatial pattern of genetic variation and the influences of landscape factors on population similarity in an invasive riparian shrub, saltcedar (Tamarix L.) by analysing 1,997 genomewide SNP markers for 259 individuals from 25 populations collected throughout the southwestern United States. Our results revealed a broad-scale spatial genetic differentiation of saltcedar populations between the Colorado and Rio Grande river basins and identified potential barriers to population similarity along both river systems. River pathways most strongly contributed to population similarity. In contrast, low temperature and dams likely served as barriers to population similarity. We hypothesize that large-scale geographic patterns in genetic diversity resulted from a combination of early introductions from distinct populations, the subsequent influence of natural selection, dispersal barriers and founder effects during range expansion.

  11. Impact of strong selection for the PrP major gene on genetic variability of four French sheep breeds (Open Access publication

    Directory of Open Access Journals (Sweden)

    Pantano Thais

    2008-11-01

    Full Text Available Abstract Effective selection on the PrP gene has been implemented since October 2001 in all French sheep breeds. After four years, the ARR "resistant" allele frequency increased by about 35% in young males. The aim of this study was to evaluate the impact of this strong selection on genetic variability. It is focussed on four French sheep breeds and based on the comparison of two groups of 94 animals within each breed: the first group of animals was born before the selection began, and the second, 3–4 years later. Genetic variability was assessed using genealogical and molecular data (29 microsatellite markers. The expected loss of genetic variability on the PrP gene was confirmed. Moreover, among the five markers located in the PrP region, only the three closest ones were affected. The evolution of the number of alleles, heterozygote deficiency within population, expected heterozygosity and the Reynolds distances agreed with the criteria from pedigree and pointed out that neutral genetic variability was not much affected. This trend depended on breed, i.e. on their initial states (population size, PrP frequencies and on the selection strategies for improving scrapie resistance while carrying out selection for production traits.

  12. So Far Away, Yet So Close: Strong Genetic Structure in Homonota uruguayensis (Squamata, Phyllodactylidae), a Species with Restricted Geographic Distribution in the Brazilian and Uruguayan Pampas

    Science.gov (United States)

    Felappi, Jéssica F.; Vieira, Renata C.; Fagundes, Nelson J. R.; Verrastro, Laura V.

    2015-01-01

    The Pampas is a biologically rich South American biome, but is poorly represented in phylogeographic studies. While the Pleistocene glacial cycles may have affected the evolutionary history of species distributed in forested biomes, little is known about their effects on the habitats that remained stable through glacial cycles. The South American Pampas have been covered by grasslands during both glacial and interglacial periods and therefore represent an interesting system to test whether the genetic structure in such environments is less pronounced. In this study, we sampled Pampean populations of Homonota uruguayensis from Southern Brazil and Uruguay to assess the tempo and mode of population divergence, using both morphological measurements and molecular markers. Our results indicate that, in spite of its narrow geographic distribution, populations of H. uruguayensis show high levels of genetic structure. We found four major well-supported mtDNA clades with strong geographic associations. Estimates of their divergence times fell between 3.16 and 1.82 million years before the present. Populations from the central portion of the species distribution, on the border between Uruguay and Brazil, have high genetic diversity and may have undergone a population expansion approximately 250,000 years before the present. The high degree of genetic structure is reflected in the analyses of morphological characters, and most individuals could be correctly assigned to their parental population based on morphology alone. Finally, we discuss the biogeographic and conservation implications of these findings. PMID:25692471

  13. So far away, yet so close: strong genetic structure in Homonota uruguayensis (Squamata, Phyllodactylidae, a species with restricted geographic distribution in the Brazilian and Uruguayan Pampas.

    Directory of Open Access Journals (Sweden)

    Jéssica F Felappi

    Full Text Available The Pampas is a biologically rich South American biome, but is poorly represented in phylogeographic studies. While the Pleistocene glacial cycles may have affected the evolutionary history of species distributed in forested biomes, little is known about their effects on the habitats that remained stable through glacial cycles. The South American Pampas have been covered by grasslands during both glacial and interglacial periods and therefore represent an interesting system to test whether the genetic structure in such environments is less pronounced. In this study, we sampled Pampean populations of Homonota uruguayensis from Southern Brazil and Uruguay to assess the tempo and mode of population divergence, using both morphological measurements and molecular markers. Our results indicate that, in spite of its narrow geographic distribution, populations of H. uruguayensis show high levels of genetic structure. We found four major well-supported mtDNA clades with strong geographic associations. Estimates of their divergence times fell between 3.16 and 1.82 million years before the present. Populations from the central portion of the species distribution, on the border between Uruguay and Brazil, have high genetic diversity and may have undergone a population expansion approximately 250,000 years before the present. The high degree of genetic structure is reflected in the analyses of morphological characters, and most individuals could be correctly assigned to their parental population based on morphology alone. Finally, we discuss the biogeographic and conservation implications of these findings.

  14. Ecological and genetic determinants of Pepino Mosaic Virus emergence.

    Science.gov (United States)

    Moreno-Pérez, Manuel G; Pagán, Israel; Aragón-Caballero, Liliana; Cáceres, Fátima; Fraile, Aurora; García-Arenal, Fernando

    2014-03-01

    Virus emergence is a complex phenomenon, which generally involves spread to a new host from a wild host, followed by adaptation to the new host. Although viruses account for the largest fraction of emerging crop pathogens, knowledge about their emergence is incomplete. We address here the question of whether Pepino Mosaic Virus (PepMV) emergence as a major tomato pathogen worldwide could have involved spread from wild to cultivated plant species and host adaptation. For this, we surveyed natural populations of wild tomatoes in southern Peru for PepMV infection. PepMV incidence, genetic variation, population structure, and accumulation in various hosts were analyzed. PepMV incidence in wild tomatoes was high, and a strain not yet reported in domestic tomato was characterized. This strain had a wide host range within the Solanaceae, multiplying efficiently in most assayed Solanum species and being adapted to wild tomato hosts. Conversely, PepMV isolates from tomato crops showed evidence of adaptation to domestic tomato, possibly traded against adaptation to wild tomatoes. Phylogenetic reconstructions indicated that the most probable ancestral sequence came from a wild Solanum species. A high incidence of PepMV in wild tomato relatives would favor virus spread to crops and its efficient multiplication in different Solanum species, including tomato, allowing its establishment as an epidemic pathogen. Later, adaptation to tomato, traded off against adaptation to other Solanum species, would isolate tomato populations from those in other hosts. Virus emergence is a complex phenomenon involving multiple ecological and genetic factors and is considered to involve three phases: virus encounter with the new host, virus adaptation to the new host, and changes in the epidemiological dynamics. We analyze here if this was the case in the recent emergence of Pepino Mosaic Virus (PepMV) in tomato crops worldwide. We characterized a new strain of PepMV infecting wild tomato

  15. Determinants of Public Attitudes to Genetically Modified Salmon

    Science.gov (United States)

    Amin, Latifah; Azad, Md. Abul Kalam; Gausmian, Mohd Hanafy; Zulkifli, Faizah

    2014-01-01

    The objective of this paper is to assess the attitude of Malaysian stakeholders to genetically modified (GM) salmon and to identify the factors that influence their acceptance of GM salmon using a structural equation model. A survey was carried out on 434 representatives from various stakeholder groups in the Klang Valley region of Malaysia. Public attitude towards GM salmon was measured using self-developed questionnaires with seven-point Likert scales. The findings of this study have confirmed that public attitudes towards GM salmon is a complex issue and should be seen as a multi-faceted process. The most important direct predictors for the encouragement of GM salmon are the specific application-linked perceptions about religious acceptability of GM salmon followed by perceived risks and benefits, familiarity, and general promise of modern biotechnology. Encouragement of GM salmon also involves the interplay among other factors such as general concerns of biotechnology, threatening the natural order of things, the need for labeling, the need for patenting, confidence in regulation, and societal values. The research findings can serve as a database that will be useful for understanding the social construct of public attitude towards GM foods in a developing country. PMID:24489695

  16. Genetic Determinants of Mycophenolate Related Anemia and Leukopenia Following Transplantation

    Science.gov (United States)

    Jacobson, PA; Schladt, D; Oetting, WS; Leduc, R; Guan, W; Matas, AJ; Lamba, V; Mannon, RB; Julian, BA; Israni, A

    2013-01-01

    Mycophenolate related anemia and leukopenia are well-known toxicities after transplantation. Toxicity leads to dose reduction, addition of colony-stimulating factors or erythropoietin, or discontinuation of immunosuppressive therapy. The causes of and risk factors associated with toxicity are unclear. Methods We studied the association between mycophenolate related anemia and leukopenia and 2,724 single nucleotide plymorphisms (SNP) in 978 patients undergoing living or deceased donor kidney transplant. Patients were followed to time of first anemia (hemoglobin leukopenia (white blood cell [WBC] count leukopenia in 224 (22.9%). In single SNP analyses, none of the SNPs were associated with time to leukopenia at a false discovery rate (FDR) of 20%. However, SNPs from the IL12A, HUS, CYP2C8 genes were associated with time to anemia allowing for an FDR of 20%. To assess the independence of these SNPs as predictors of anemia, we conducted a multi-SNP analysis including one SNP from each of the three genes. All three SNPs were associated with time to anemia, after adjusting for recipient age, weight, posttransplant dialysis and antiviral drug use and stratifying by clinical center. Conclusion While these SNPs require validation in an independent population, our results suggest genetics may play a role in risk of mycophenolate related hematologic toxicity. This may ultimately provide for better management of maintenance immunosuppression and gives insights into potential mechanism(s) by which toxicity occurs. PMID:21107304

  17. Genetic Determinants of Serum Testosterone Concentrations in Men

    Science.gov (United States)

    Maggio, Marcello; Coviello, Andrea D.; Ferrucci, Luigi; Heier, Margit; Hofman, Albert; Holliday, Kate L.; Jansson, John-Olov; Kähönen, Mika; Karasik, David; Karlsson, Magnus K.; Kiel, Douglas P.; Liu, Yongmei; Ljunggren, Östen; Lorentzon, Mattias; Lyytikäinen, Leo-Pekka; Meitinger, Thomas; Mellström, Dan; Melzer, David; Miljkovic, Iva; Nauck, Matthias; Nilsson, Maria; Penninx, Brenda; Pye, Stephen R.; Vasan, Ramachandran S.; Reincke, Martin; Rivadeneira, Fernando; Tajar, Abdelouahid; Teumer, Alexander; Uitterlinden, André G.; Ulloor, Jagadish; Viikari, Jorma; Völker, Uwe; Völzke, Henry; Wichmann, H. Erich; Wu, Tsung-Sheng; Zhuang, Wei Vivian; Ziv, Elad; Wu, Frederick C. W.; Raitakari, Olli; Eriksson, Anna; Bidlingmaier, Martin; Harris, Tamara B.; Murray, Anna; de Jong, Frank H.; Murabito, Joanne M.; Bhasin, Shalender; Vandenput, Liesbeth; Haring, Robin

    2011-01-01

    Testosterone concentrations in men are associated with cardiovascular morbidity, osteoporosis, and mortality and are affected by age, smoking, and obesity. Because of serum testosterone's high heritability, we performed a meta-analysis of genome-wide association data in 8,938 men from seven cohorts and followed up the genome-wide significant findings in one in silico (n = 871) and two de novo replication cohorts (n = 4,620) to identify genetic loci significantly associated with serum testosterone concentration in men. All these loci were also associated with low serum testosterone concentration defined as testosterone concentration (rs12150660, p = 1.2×10−41 and rs6258, p = 2.3×10−22). Subjects with ≥3 risk alleles of these variants had 6.5-fold higher risk of having low serum testosterone than subjects with no risk allele. The rs5934505 polymorphism near FAM9B on the X chromosome was also associated with testosterone concentrations (p = 5.6×10−16). The rs6258 polymorphism in exon 4 of SHBG affected SHBG's affinity for binding testosterone and the measured free testosterone fraction (ptestosterone concentrations and increased risk of low testosterone. rs6258 is the first reported SHBG polymorphism, which affects testosterone binding to SHBG and the free testosterone fraction and could therefore influence the calculation of free testosterone using law-of-mass-action equation. PMID:21998597

  18. Genetic diversity of bovine Neospora caninum determined by microsatellite markers.

    Science.gov (United States)

    Salehi, N; Gottstein, B; Haddadzadeh, H R

    2015-10-01

    Neospora caninum is one of the most significant parasitic organisms causing bovine abortion worldwide. Despite the economic impact of this infection, relatively little is known about the genetic diversity of this parasite. In this study, using Nc5 and ITS1 nested PCR, N. caninum has been detected in 12 brain samples of aborted fetuses from 298 seropositive dairy cattle collected from four different regions in Tehran, Iran. These specimen (Nc-Iran) were genotyped in multilocus using 9 different microsatellite markers previously described (MS4, MS5, MS6A, MS6B, MS7, MS8, MS10, MS12 and MS21). Microsatellite amplification was completely feasible in 2 samples, semi-completely in 8 samples, and failed in 2 samples. Within the two completely performed allelic profiles of Nc-Iran strains, unique multilocus profiles were obtained for both and novel allelic patterns were found in the MS8 and MS10 microsatellite markers. The Jaccard's similarity index showed significant difference between these two strains and from other standard isolates derived from GenBank such as Nc-Liv, Nc-SweB1, Nc-GER1, KBA1, and KBA2. All samples originating from the same area showed identical allelic numbers and a correlation between the number of repeats and geographic districts was observed. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  19. 75 FR 20560 - Syngenta Biotechnology, Inc.; Determination of Nonregulated Status for Corn Genetically...

    Science.gov (United States)

    2010-04-20

    ...] Syngenta Biotechnology, Inc.; Determination of Nonregulated Status for Corn Genetically Engineered for... are advising the public of our determination that a corn line developed by Syngenta Biotechnology, Inc... Biotechnology, Inc., in its petition for a determination of nonregulated status, our analysis of other...

  20. Determination of genetic variability of Asian rice ( Oryza sativa L ...

    African Journals Online (AJOL)

    The microsatellite or simple sequence repeat (SSR) marker analysis was done to determine the allelic diversity and relationship among thirty-five Asian cultivars of rice including 19 aromatic, 13 nonaromatic and 3 japonica type cultivars. A total of 144 alleles were detected at the 32 SSR loci, of which 141 (98%) were ...

  1. Genetics of sex determination in the haplodiploid wasp Nasonia ...

    Indian Academy of Sciences (India)

    2010-09-06

    Sep 6, 2010 ... sperm. Unfertilized eggs develop into haploid males that only have a maternally inherited genome. Fertilized eggs develop into diploid females that have inherited a maternal and a paternal genome. Early observations on sex determination in Nasonia. Absence of CSD in Nasonia has been known for a ...

  2. Determination of the genetic marker of the mutagenized strains of ...

    African Journals Online (AJOL)

    Bacillus cereus and Pseudomonas aeruginosa were isolated from the effluent of the Kaduna refining and petrochemical company, using standard methods. These were UV-irradiated for 30mins and thereafter subjected to nitrous acid treatment. Determination of essential amino acids required by both parents and mutants ...

  3. The PMCA pumps in genetically determined neuronal pathologies.

    Science.gov (United States)

    Calì, Tito; Brini, Marisa; Carafoli, Ernesto

    2018-01-10

    Ca 2+ signals regulate most aspects of animal cell life. They are of particular importance to the nervous system, in which they regulate specific functions, from neuronal development to synaptic plasticity. The homeostasis of cell Ca 2+ must thus be very precisely regulated: in all cells Ca 2+ pumps transport it from the cytosol to the extracellular medium (the Plasma Membrane Ca 2+ ATPases, hereafter referred to as PMCA pumps) or to the lumen of intracellular organelles (the Sarco/Endoplasmatic Reticulum Ca 2+ ATPase and the Secretory Pathway Ca 2+ ATPase, hereafter referred to as SERCA and SPCA pumps, respectively). In neurons and other excitable cells a powerful plasma membrane Na + /Ca 2+ exchanger (NCX) also exports Ca 2+ from cells. Quantitatively, the PMCA pumps are of minor importance to the bulk regulation of neuronal Ca 2+ . However, they are important in the regulation of Ca 2+ in specific sub-plasma membrane microdomains which contain a number of enzymes that are relevant to neuronal function. The PMCA pumps (of which 4 basic isoforms are expressed in animal cells) are P-type ATPases that are characterized by a long C-terminal cytosolic tail which is the site of interaction with most of the regulatory factors of the pump, the most important being calmodulin. In resting neurons, at low intracellular Ca 2+ the C-terminal tail of the PMCA interacts with the main body of the protein keeping it in an autoinhibited state. Local Ca 2+ increase activates calmodulin that removes the C-terminal tail from the inhibitory sites. Dysregulation of the Ca 2+ signals are incompatible with healthy neuronal life. A number of genetic mutations of PMCA pumps are associated with pathological phenotypes, those of the neuron-specific PMCA 2 and PMCA 3 being the best characterized. PMCA 2 mutations are associated with deafness and PMCA 3 mutations are linked to cerebellar ataxias. Biochemical analysis of the mutated pumps overexpressed in model cells have revealed their

  4. Overview of the genetic determinants of primary aldosteronism

    Directory of Open Access Journals (Sweden)

    Al-Salameh A

    2014-04-01

    Full Text Available Abdallah Al-Salameh,1 Régis Cohen,2 Rachel Desailloud3 1Service de Diabétologie, Endocrinologie et Maladies Métaboliques, Centre Hospitalier de Creil, Creil, France; 2Service d'Endocrinologie, Centre Hospitalier de Saint-Denis, Saint-Denis, France; 3Service d'Endocrinologie, Diabétologie et Nutrition, Centre Hospitalier Universitaire d'Amiens, Amiens, France Abstract: Primary aldosteronism is the most common cause of secondary hypertension. The syndrome accounts for 10% of all cases of hypertension and is primarily caused by bilateral adrenal hyperplasia or aldosterone-producing adenoma. Over the last few years, the use of exome sequencing has significantly improved our understanding of this syndrome. Somatic mutations in the KCNJ5, ATP1A1, ATP2B3 or CACNA1D genes are present in more than half of all cases of aldosterone-producing adenoma (~40%, ~6%, ~1% and ~8%, respectively. Germline gain-of-function mutations in KCNJ5 are now known to cause familial hyperaldosteronism type III, and an additional form of genetic hyperaldosteronism has been reported in patients with germline mutations in CACNA1D. These genes code for channels that control ion homeostasis across the plasma membrane of zona glomerulosa cells. Moreover, all these mutations modulate the same pathway, in which elevated intracellular calcium levels lead to aldosterone hyperproduction and (in some cases adrenal cell proliferation. From a clinical standpoint, the discovery of these mutations has potential implications for patient management. The mutated channels could be targeted by drugs, in order to control hormonal and overgrowth-related manifestations. Furthermore, some of these mutations are associated with high cell turnover and may be amenable to diagnosis via the sequencing of cell-free (circulating DNA. However, genotype-phenotype correlations in patients harboring these mutations have yet to be characterized. Despite this recent progress, much remains to be done to

  5. Genetic variants are major determinants of CSF antibody levels in multiple sclerosis.

    Science.gov (United States)

    Goris, An; Pauwels, Ine; Gustavsen, Marte W; van Son, Brechtje; Hilven, Kelly; Bos, Steffan D; Celius, Elisabeth Gulowsen; Berg-Hansen, Pål; Aarseth, Jan; Myhr, Kjell-Morten; D'Alfonso, Sandra; Barizzone, Nadia; Leone, Maurizio A; Martinelli Boneschi, Filippo; Sorosina, Melissa; Liberatore, Giuseppe; Kockum, Ingrid; Olsson, Tomas; Hillert, Jan; Alfredsson, Lars; Bedri, Sahl Khalid; Hemmer, Bernhard; Buck, Dorothea; Berthele, Achim; Knier, Benjamin; Biberacher, Viola; van Pesch, Vincent; Sindic, Christian; Bang Oturai, Annette; Søndergaard, Helle Bach; Sellebjerg, Finn; Jensen, Poul Erik H; Comabella, Manuel; Montalban, Xavier; Pérez-Boza, Jennifer; Malhotra, Sunny; Lechner-Scott, Jeannette; Broadley, Simon; Slee, Mark; Taylor, Bruce; Kermode, Allan G; Gourraud, Pierre-Antoine; Sawcer, Stephen J; Andreassen, Bettina Kullle; Dubois, Bénédicte; Harbo, Hanne F

    2015-03-01

    Immunological hallmarks of multiple sclerosis include the production of antibodies in the central nervous system, expressed as presence of oligoclonal bands and/or an increased immunoglobulin G index-the level of immunoglobulin G in the cerebrospinal fluid compared to serum. However, the underlying differences between oligoclonal band-positive and -negative patients with multiple sclerosis and reasons for variability in immunoglobulin G index are not known. To identify genetic factors influencing the variation in the antibody levels in the cerebrospinal fluid in multiple sclerosis, we have performed a genome-wide association screen in patients collected from nine countries for two traits, presence or absence of oligoclonal bands (n = 3026) and immunoglobulin G index levels (n = 938), followed by a replication in 3891 additional patients. We replicate previously suggested association signals for oligoclonal band status in the major histocompatibility complex region for the rs9271640*A-rs6457617*G haplotype, correlated with HLA-DRB1*1501, and rs34083746*G, correlated with HLA-DQA1*0301 (P comparing two haplotypes = 8.88 × 10(-16)). Furthermore, we identify a novel association signal of rs9807334, near the ELAC1/SMAD4 genes, for oligoclonal band status (P = 8.45 × 10(-7)). The previously reported association of the immunoglobulin heavy chain locus with immunoglobulin G index reaches strong evidence for association in this data set (P = 3.79 × 10(-37)). We identify two novel associations in the major histocompatibility complex region with immunoglobulin G index: the rs9271640*A-rs6457617*G haplotype (P = 1.59 × 10(-22)), shared with oligoclonal band status, and an additional independent effect of rs6457617*G (P = 3.68 × 10(-6)). Variants identified in this study account for up to 2-fold differences in the odds of being oligoclonal band positive and 7.75% of the variation in immunoglobulin G index. Both traits are associated with clinical features of disease such

  6. Genetic variants are major determinants of CSF antibody levels in multiple sclerosis

    Science.gov (United States)

    Pauwels, Ine; Gustavsen, Marte W.; van Son, Brechtje; Hilven, Kelly; Bos, Steffan D.; Celius, Elisabeth Gulowsen; Berg-Hansen, Pål; Aarseth, Jan; Myhr, Kjell-Morten; D’Alfonso, Sandra; Barizzone, Nadia; Leone, Maurizio A.; Martinelli Boneschi, Filippo; Sorosina, Melissa; Liberatore, Giuseppe; Kockum, Ingrid; Olsson, Tomas; Hillert, Jan; Alfredsson, Lars; Bedri, Sahl Khalid; Hemmer, Bernhard; Buck, Dorothea; Berthele, Achim; Knier, Benjamin; Biberacher, Viola; van Pesch, Vincent; Sindic, Christian; Bang Oturai, Annette; Søndergaard, Helle Bach; Sellebjerg, Finn; Jensen, Poul Erik H.; Comabella, Manuel; Montalban, Xavier; Pérez-Boza, Jennifer; Malhotra, Sunny; Lechner-Scott, Jeannette; Broadley, Simon; Slee, Mark; Taylor, Bruce; Kermode, Allan G.; Gourraud, Pierre-Antoine; Sawcer, Stephen J.; Andreassen, Bettina Kullle; Dubois, Bénédicte; Harbo, Hanne F.

    2015-01-01

    Immunological hallmarks of multiple sclerosis include the production of antibodies in the central nervous system, expressed as presence of oligoclonal bands and/or an increased immunoglobulin G index—the level of immunoglobulin G in the cerebrospinal fluid compared to serum. However, the underlying differences between oligoclonal band-positive and -negative patients with multiple sclerosis and reasons for variability in immunoglobulin G index are not known. To identify genetic factors influencing the variation in the antibody levels in the cerebrospinal fluid in multiple sclerosis, we have performed a genome-wide association screen in patients collected from nine countries for two traits, presence or absence of oligoclonal bands (n = 3026) and immunoglobulin G index levels (n = 938), followed by a replication in 3891 additional patients. We replicate previously suggested association signals for oligoclonal band status in the major histocompatibility complex region for the rs9271640*A-rs6457617*G haplotype, correlated with HLA-DRB1*1501, and rs34083746*G, correlated with HLA-DQA1*0301 (P comparing two haplotypes = 8.88 × 10−16). Furthermore, we identify a novel association signal of rs9807334, near the ELAC1/SMAD4 genes, for oligoclonal band status (P = 8.45 × 10−7). The previously reported association of the immunoglobulin heavy chain locus with immunoglobulin G index reaches strong evidence for association in this data set (P = 3.79 × 10−37). We identify two novel associations in the major histocompatibility complex region with immunoglobulin G index: the rs9271640*A-rs6457617*G haplotype (P = 1.59 × 10−22), shared with oligoclonal band status, and an additional independent effect of rs6457617*G (P = 3.68 × 10−6). Variants identified in this study account for up to 2-fold differences in the odds of being oligoclonal band positive and 7.75% of the variation in immunoglobulin G index. Both traits are associated with clinical features of disease such

  7. 78 FR 37201 - Pioneer Hi-Bred International, Inc.; Determination of Nonregulated Status of Maize Genetically...

    Science.gov (United States)

    2013-06-20

    ...] Pioneer Hi-Bred International, Inc.; Determination of Nonregulated Status of Maize Genetically Engineered... Hi-Bred International Inc., designated as maize event DP-[Oslash][Oslash]4114-3, which has been... by Pioneer Hi-Bred International, Inc., in its petition for a determination of nonregulated status...

  8. Comparison of French and Estonian Students' Conceptions in Genetic Determinism of Human Behaviours

    Science.gov (United States)

    Castera, Jeremy; Sarapuu, Tago; Clement, Pierre

    2013-01-01

    Innatism is the belief that most of the human personality can be determined by genes. This ideology is dangerous, especially when it claims to be scientific. The present study investigates conceptions of 1060 students from Estonia and France related to genetic determinism of some human behaviours. Factors taken into account included students'…

  9. Determinism and Underdetermination in Genetics: Implications for Students' Engagement in Argumentation and Epistemic Practices

    Science.gov (United States)

    Jiménez-Aleixandre, María Pilar

    2014-02-01

    In the last two decades science studies and science education research have shifted from an interest in products (of science or of learning), to an interest in processes and practices. The focus of this paper is on students' engagement in epistemic practices (Kelly in Teaching scientific inquiry: Recommendations for research and implementation. Sense Publishers, Rotterdam, pp 99-117, 2008), or on their practical epistemologies (Wickman in Sci Educ 88(3):325-344, 2004). In order to support these practices in genetics classrooms we need to take into account domain-specific features of the epistemology of genetics, in particular issues about determinism and underdetermination. I suggest that certain difficulties may be related to the specific nature of causality in genetics, and in particular to the correspondence between a given set of factors and a range of potential effects, rather than a single one. The paper seeks to bring together recent developments in the epistemology of biology and of genetics, on the one hand, with science education approaches about epistemic practices, on the other. The implications of these perspectives for current challenges in learning genetics are examined, focusing on students' engagement in epistemic practices, as argumentation, understood as using evidence to evaluate knowledge claims. Engaging in argumentation in genetics classrooms is intertwined with practices such as using genetics models to build explanations, or framing genetics issues in their social context. These challenges are illustrated with studies making part of our research program in the USC.

  10. Determination of Optimal Double Sampling Plan using Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    Sampath Sundaram

    2012-03-01

    Full Text Available Normal 0 false false false EN-US X-NONE X-NONE MicrosoftInternetExplorer4 Designing double sampling plan requires identification of sample sizes and acceptance numbers. In this paper a genetic algorithm has been designed for the selection of optimal acceptance numbers and sample sizes for the specified producer’s risk and consumer’s risk. Implementation of the algorithm has been illustrated numerically for different choices of quantities involved in a double sampling plan   

  1. Genetic and metabolic determinants of methotrexate-induced mucositis in pediatric acute lymphoblastic leukemia

    NARCIS (Netherlands)

    den Hoed, M. A. H.; Lopez-Lopez, E.; te Winkel, M. L.; Tissing, W.; de Rooij, J. D. E.; Gutierrez-Camino, A.; Garcia-Orad, A.; den Boer, E.; Pieters, R.; Pluijm, S. M. F.; de Jonge, R.; van den Heuvel-Eibrink, M. M.

    Methotrexate (MTX) is an effective and toxic chemotherapeutic drug in the treatment of pediatric acute lymphoblastic leukemia (ALL). In this prospective study, we aimed to identify metabolic and genetic determinants of MTX toxicity. One hundred and thirty-four Dutch pediatric ALL patients were

  2. Teachers' Conceptions about the Genetic Determinism of Human Behaviour: A Survey in 23 Countries

    Science.gov (United States)

    Castéra, Jérémy; Clément, Pierre

    2014-01-01

    This work analyses the answers to a questionnaire from 8,285 in-service and pre-service teachers from 23 countries, elaborated by the Biohead-Citizen research project, to investigate teachers' conceptions related to the genetic determinism of human behaviour. A principal components analysis is used to assess the main trends in all the interviewed…

  3. Common Genetic Determinants of Intraocular Pressure and Primary Open-Angle Glaucoma

    NARCIS (Netherlands)

    van Koolwijk, Leonieke M. E.; Ramdas, Wishal D.; Ikram, M. Kamran; Jansonius, Nomdo M.; Pasutto, Francesca; Hysi, Pirro G.; Macgregor, Stuart; Janssen, Sarah F.; Hewitt, Alex W.; Viswanathan, Ananth C.; ten Brink, Jacoline B.; Hosseini, S. Mohsen; Amin, Najaf; Despriet, Dominiek D. G.; Willemse-Assink, Jacqueline J. M.; Kramer, Rogier; Rivadeneira, Fernando; Struchalin, Maksim; Aulchenko, Yurii S.; Weisschuh, Nicole; Zenkel, Matthias; Mardin, Christian Y.; Gramer, Eugen; Welge-Luessen, Ulrich; Montgomery, Grant W.; Carbonaro, Francis; Young, Terri L.; Bellenguez, Celine; McGuffin, Peter; Foster, Paul J.; Topouzis, Fotis; Mitchell, Paul; Wang, Jie Jin; Wong, Tien Y.; Czudowska, Monika A.; Hofman, Albert; Uitterlinden, Andre G.; Wolfs, Roger C. W.; de Jong, Paulus T. V. M.; Oostra, Ben A.; Paterson, Andrew D.; Mackey, David A.; Bergen, Arthur A. B.; Reis, Andre; Hammond, Christopher J.; Vingerling, Johannes R.; Lemij, Hans G.; Klaver, Caroline C. W.; van Duijn, Cornelia M.

    2012-01-01

    Intraocular pressure (IOP) is a highly heritable risk factor for primary open-angle glaucoma and is the only target for current glaucoma therapy. The genetic factors which determine IOP are largely unknown. We performed a genome-wide association study for IOP in 11,972 participants from 4

  4. Life history determines genetic structure and evolutionary potential of host–parasite interactions

    OpenAIRE

    Barrett, Luke G.; Thrall, Peter H.; Burdon, Jeremy J.; Linde, Celeste C.

    2008-01-01

    Measures of population genetic structure and diversity of disease-causing organisms are commonly used to draw inferences regarding their evolutionary history and potential to generate new variation in traits that determine interactions with their hosts. Parasite species exhibit a range of population structures and life-history strategies, including different transmission modes, life-cycle complexity, off-host survival mechanisms and dispersal ability. These are important determinants of the f...

  5. Beliefs in genetic determinism and attitudes towards psychiatric genetic research: psychometric scale properties, construct associations, demographic correlates, and cross-cultural comparisons.

    Science.gov (United States)

    Voracek, Martin; Swami, Viren; Loibl, Lisa Mariella; Furnham, Adrian

    2007-12-01

    Using two new scales, this study examined beliefs in genetic determinism and attitudes towards psychiatric genetic research in student samples from Austria, Malaysia, Romania, and the United Kingdom. For both constructs, effects of culture were detectable, whereas those related to key demographics were either small and inconsistent across samples (political orientation and religiosity) or zero (sex and age). Judged from factorial dimensionality and internal consistency, the psychometric properties of both scales were satisfactory. Belief in genetic determinism had lower prevalence and corresponded only modestly to positive attitudes towards psychiatric genetic research which had higher prevalence. The correlations of both constructs with a preference of inequality among social groups (social dominance orientation) were modest and inconsistent across samples. Both scales appear appropriate for cross-cultural applications, in particular for research into lay theories and public perceptions regarding genetic vs environmental effects on human behavior, mental disorders, and behavioral and psychiatric genetic research related to these.

  6. Strong correlation between cross-amplification success and genetic distance across all members of 'True Salamanders' (Amphibia: Salamandridae) revealed by Salamandra salamandra-specific microsatellite loci.

    Science.gov (United States)

    Hendrix, Ralf; Susanne Hauswaldt, J; Veith, Michael; Steinfartz, Sebastian

    2010-11-01

    The unpredictable and low cross-amplification success of microsatellite loci tested for congeneric amphibian species has mainly been explained by the size and complexity of amphibian genomes, but also by taxonomy that is inconsistent with phylogenetic relationships among taxa. Here, we tested whether the cross-amplification success of nine new and 11 published microsatellite loci cloned for an amphibian source species, the fire salamander (Salamandra salamandra), correlated with the genetic distance across all members of True Salamanders (genera Chioglossa, Lyciasalamandra, Mertensiella and Salamandra that form a monophyletic clade within the family of Salamandridae) serving as target species. Cross-amplification success varied strongly among the species and showed a highly significant negative relationship with genetic distance and amplification success. Even though lineages of S. salamandra and Lyciasalamndra have separated more than 30 Ma, a within genus amplification success rate of 65% was achieved for species of Lyciasalamandra thus demonstrating that an efficient cross-species amplification of microsatellite loci in amphibians is feasible even across large evolutionary distances. A decrease in genome size, on the other hand, paralleled also a decrease in amplified loci and therefore contradicted previous results and expectations that amplification success should increase with a decrease in genome size. However, in line with other studies, our comprehensive dataset clearly shows that cross-amplification success of microsatellite loci is well explained by phylogenetic divergence between species. As taxonomic classifications on the species and genus level do not necessarily mirror phylogenetic divergence between species, the pure belonging of species to the same taxonomic units (i.e. species or genus) might be less useful to predict cross-amplification success of microsatellite loci between such species. © 2010 Blackwell Publishing Ltd.

  7. Individual Differences in the Speed of Facial Emotion Recognition Show Little Specificity but Are Strongly Related with General Mental Speed: Psychometric, Neural and Genetic Evidence

    Science.gov (United States)

    Liu, Xinyang; Hildebrandt, Andrea; Recio, Guillermo; Sommer, Werner; Cai, Xinxia; Wilhelm, Oliver

    2017-01-01

    Facial identity and facial expression processing are crucial socio-emotional abilities but seem to show only limited psychometric uniqueness when the processing speed is considered in easy tasks. We applied a comprehensive measurement of processing speed and contrasted performance specificity in socio-emotional, social and non-social stimuli from an individual differences perspective. Performance in a multivariate task battery could be best modeled by a general speed factor and a first-order factor capturing some specific variance due to processing emotional facial expressions. We further tested equivalence of the relationships between speed factors and polymorphisms of dopamine and serotonin transporter genes. Results show that the speed factors are not only psychometrically equivalent but invariant in their relation with the Catechol-O-Methyl-Transferase (COMT) Val158Met polymorphism. However, the 5-HTTLPR/rs25531 serotonin polymorphism was related with the first-order factor of emotion perception speed, suggesting a specific genetic correlate of processing emotions. We further investigated the relationship between several components of event-related brain potentials with psychometric abilities, and tested emotion specific individual differences at the neurophysiological level. Results revealed swifter emotion perception abilities to go along with larger amplitudes of the P100 and the Early Posterior Negativity (EPN), when emotion processing was modeled on its own. However, after partialling out the shared variance of emotion perception speed with general processing speed-related abilities, brain-behavior relationships did not remain specific for emotion. Together, the present results suggest that speed abilities are strongly interrelated but show some specificity for emotion processing speed at the psychometric level. At both genetic and neurophysiological levels, emotion specificity depended on whether general cognition is taken into account or not. These

  8. Individual Differences in the Speed of Facial Emotion Recognition Show Little Specificity but Are Strongly Related with General Mental Speed: Psychometric, Neural and Genetic Evidence

    Directory of Open Access Journals (Sweden)

    Xinyang Liu

    2017-08-01

    Full Text Available Facial identity and facial expression processing are crucial socio-emotional abilities but seem to show only limited psychometric uniqueness when the processing speed is considered in easy tasks. We applied a comprehensive measurement of processing speed and contrasted performance specificity in socio-emotional, social and non-social stimuli from an individual differences perspective. Performance in a multivariate task battery could be best modeled by a general speed factor and a first-order factor capturing some specific variance due to processing emotional facial expressions. We further tested equivalence of the relationships between speed factors and polymorphisms of dopamine and serotonin transporter genes. Results show that the speed factors are not only psychometrically equivalent but invariant in their relation with the Catechol-O-Methyl-Transferase (COMT Val158Met polymorphism. However, the 5-HTTLPR/rs25531 serotonin polymorphism was related with the first-order factor of emotion perception speed, suggesting a specific genetic correlate of processing emotions. We further investigated the relationship between several components of event-related brain potentials with psychometric abilities, and tested emotion specific individual differences at the neurophysiological level. Results revealed swifter emotion perception abilities to go along with larger amplitudes of the P100 and the Early Posterior Negativity (EPN, when emotion processing was modeled on its own. However, after partialling out the shared variance of emotion perception speed with general processing speed-related abilities, brain-behavior relationships did not remain specific for emotion. Together, the present results suggest that speed abilities are strongly interrelated but show some specificity for emotion processing speed at the psychometric level. At both genetic and neurophysiological levels, emotion specificity depended on whether general cognition is taken into account

  9. Application of genetic algorithms for determination biological half-life of 137 Cs in milk

    International Nuclear Information System (INIS)

    Pantelic, G.

    1998-01-01

    Genetic algorithm an optimization method involving natural selection mechanisms, was used to determine biological half-life of sup 1 sup 3 sup 7 Cs in the milk, after the Chernobyl accident, based on a two compartment linear system model. Genetic algorithms operate on populations of strings. Reproduction, crossover and mutation are applied to successive string population to create new string population. A model parameter estimation is performed by minimizing square differences between fitting function and experimental data. The calculated biological half-life of sup 1 sup 3 sup 7 Cs in milk is (32(+(-) days (author)

  10. Determination of the proton structure and the strong coupling from inclusive jet cross sections at the LHC

    CERN Document Server

    Sieber, Georg; Rabbertz, Klaus

    This thesis presents the sensitivity study of PDFs and $\\alpha_\\mathrm{S}$ to the inclusive jet cross section at a center-of-mass energy of $\\sqrt{s}$ = 7 TeV. The data corresponds to an integrated luminosity of 5 fb$^{-1}$ collected with the CMS detector in 2011. Next-to-leading order calculations have been compared to the measurement and found agreement within uncertainties. The PDF sensitivity has been studied using the HERAFitter framework. It was found that the inclusive jet cross section constrains the quark and gluon PDFs in the high-$x$ region and reduces the PDF uncertainties. Furthermore the strong coupling has been extracted using fixed global PDF sets.

  11. The Major Genetic Determinants of HIV-1 Control Affect HLA Class I Peptide Presentation

    Science.gov (United States)

    Pereyra, Florencia; Jia, Xiaoming; McLaren, Paul J.; Telenti, Amalio; de Bakker, Paul I.W.; Walker, Bruce D.; Jia, Xiaoming; McLaren, Paul J.; Ripke, Stephan; Brumme, Chanson J.; Pulit, Sara L.; Telenti, Amalio; Carrington, Mary; Kadie, Carl M.; Carlson, Jonathan M.; Heckerman, David; de Bakker, Paul I.W.; Pereyra, Florencia; de Bakker, Paul I.W.; Graham, Robert R.; Plenge, Robert M.; Deeks, Steven G.; Walker, Bruce D.; Gianniny, Lauren; Crawford, Gabriel; Sullivan, Jordan; Gonzalez, Elena; Davies, Leela; Camargo, Amy; Moore, Jamie M.; Beattie, Nicole; Gupta, Supriya; Crenshaw, Andrew; Burtt, Noël P.; Guiducci, Candace; Gupta, Namrata; Carrington, Mary; Gao, Xiaojiang; Qi, Ying; Yuki, Yuko; Pereyra, Florencia; Piechocka-Trocha, Alicja; Cutrell, Emily; Rosenberg, Rachel; Moss, Kristin L.; Lemay, Paul; O’Leary, Jessica; Schaefer, Todd; Verma, Pranshu; Toth, Ildiko; Block, Brian; Baker, Brett; Rothchild, Alissa; Lian, Jeffrey; Proudfoot, Jacqueline; Alvino, Donna Marie L.; Vine, Seanna; Addo, Marylyn M.; Allen, Todd M.; Altfeld, Marcus; Henn, Matthew R.; Le Gall, Sylvie; Streeck, Hendrik; Walker, Bruce D.; Haas, David W.; Kuritzkes, Daniel R.; Robbins, Gregory K.; Shafer, Robert W.; Gulick, Roy M.; Shikuma, Cecilia M.; Haubrich, Richard; Riddler, Sharon; Sax, Paul E.; Daar, Eric S.; Ribaudo, Heather J.; Agan, Brian; Agarwal, Shanu; Ahern, Richard L.; Allen, Brady L.; Altidor, Sherly; Altschuler, Eric L.; Ambardar, Sujata; Anastos, Kathryn; Anderson, Ben; Anderson, Val; Andrady, Ushan; Antoniskis, Diana; Bangsberg, David; Barbaro, Daniel; Barrie, William; Bartczak, J.; Barton, Simon; Basden, Patricia; Basgoz, Nesli; Bazner, Suzane; Bellos, Nicholaos C.; Benson, Anne M.; Berger, Judith; Bernard, Nicole F.; Bernard, Annette M.; Birch, Christopher; Bodner, Stanley J.; Bolan, Robert K.; Boudreaux, Emilie T.; Bradley, Meg; Braun, James F.; Brndjar, Jon E.; Brown, Stephen J.; Brown, Katherine; Brown, Sheldon T.; Burack, Jedidiah; Bush, Larry M.; Cafaro, Virginia; Campbell, Omobolaji; Campbell, John; Carlson, Robert H.; Carmichael, J. Kevin; Casey, Kathleen K.; Cavacuiti, Chris; Celestin, Gregory; Chambers, Steven T.; Chez, Nancy; Chirch, Lisa M.; Cimoch, Paul J.; Cohen, Daniel; Cohn, Lillian E.; Conway, Brian; Cooper, David A.; Cornelson, Brian; Cox, David T.; Cristofano, Michael V.; Cuchural, George; Czartoski, Julie L.; Dahman, Joseph M.; Daly, Jennifer S.; Davis, Benjamin T.; Davis, Kristine; Davod, Sheila M.; Deeks, Steven G.; DeJesus, Edwin; Dietz, Craig A.; Dunham, Eleanor; Dunn, Michael E.; Ellerin, Todd B.; Eron, Joseph J.; Fangman, John J.W.; Farel, Claire E.; Ferlazzo, Helen; Fidler, Sarah; Fleenor-Ford, Anita; Frankel, Renee; Freedberg, Kenneth A.; French, Neel K.; Fuchs, Jonathan D.; Fuller, Jon D.; Gaberman, Jonna; Gallant, Joel E.; Gandhi, Rajesh T.; Garcia, Efrain; Garmon, Donald; Gathe, Joseph C.; Gaultier, Cyril R.; Gebre, Wondwoosen; Gilman, Frank D.; Gilson, Ian; Goepfert, Paul A.; Gottlieb, Michael S.; Goulston, Claudia; Groger, Richard K.; Gurley, T. Douglas; Haber, Stuart; Hardwicke, Robin; Hardy, W. David; Harrigan, P. Richard; Hawkins, Trevor N.; Heath, Sonya; Hecht, Frederick M.; Henry, W. Keith; Hladek, Melissa; Hoffman, Robert P.; Horton, James M.; Hsu, Ricky K.; Huhn, Gregory D.; Hunt, Peter; Hupert, Mark J.; Illeman, Mark L.; Jaeger, Hans; Jellinger, Robert M.; John, Mina; Johnson, Jennifer A.; Johnson, Kristin L.; Johnson, Heather; Johnson, Kay; Joly, Jennifer; Jordan, Wilbert C.; Kauffman, Carol A.; Khanlou, Homayoon; Killian, Robert K.; Kim, Arthur Y.; Kim, David D.; Kinder, Clifford A.; Kirchner, Jeffrey T.; Kogelman, Laura; Kojic, Erna Milunka; Korthuis, P. Todd; Kurisu, Wayne; Kwon, Douglas S.; LaMar, Melissa; Lampiris, Harry; Lanzafame, Massimiliano; Lederman, Michael M.; Lee, David M.; Lee, Jean M.L.; Lee, Marah J.; Lee, Edward T.Y.; Lemoine, Janice; Levy, Jay A.; Llibre, Josep M.; Liguori, Michael A.; Little, Susan J.; Liu, Anne Y.; Lopez, Alvaro J.; Loutfy, Mono R.; Loy, Dawn; Mohammed, Debbie Y.; Man, Alan; Mansour, Michael K.; Marconi, Vincent C.; Markowitz, Martin; Marques, Rui; Martin, Jeffrey N.; Martin, Harold L.; Mayer, Kenneth Hugh; McElrath, M. Juliana; McGhee, Theresa A.; McGovern, Barbara H.; McGowan, Katherine; McIntyre, Dawn; Mcleod, Gavin X.; Menezes, Prema; Mesa, Greg; Metroka, Craig E.; Meyer-Olson, Dirk; Miller, Andy O.; Montgomery, Kate; Mounzer, Karam C.; Nagami, Ellen H.; Nagin, Iris; Nahass, Ronald G.; Nelson, Margret O.; Nielsen, Craig; Norene, David L.; O’Connor, David H.; Ojikutu, Bisola O.; Okulicz, Jason; Oladehin, Olakunle O.; Oldfield, Edward C.; Olender, Susan A.; Ostrowski, Mario; Owen, William F.; Pae, Eunice; Parsonnet, Jeffrey; Pavlatos, Andrew M.; Perlmutter, Aaron M.; Pierce, Michael N.; Pincus, Jonathan M.; Pisani, Leandro; Price, Lawrence Jay; Proia, Laurie; Prokesch, Richard C.; Pujet, Heather Calderon; Ramgopal, Moti; Rathod, Almas; Rausch, Michael; Ravishankar, J.; Rhame, Frank S.; Richards, Constance Shamuyarira; Richman, Douglas D.; Robbins, Gregory K.; Rodes, Berta; Rodriguez, Milagros; Rose, Richard C.; Rosenberg, Eric S.; Rosenthal, Daniel; Ross, Polly E.; Rubin, David S.; Rumbaugh, Elease; Saenz, Luis; Salvaggio, Michelle R.; Sanchez, William C.; Sanjana, Veeraf M.; Santiago, Steven; Schmidt, Wolfgang; Schuitemaker, Hanneke; Sestak, Philip M.; Shalit, Peter; Shay, William; Shirvani, Vivian N.; Silebi, Vanessa I.; Sizemore, James M.; Skolnik, Paul R.; Sokol-Anderson, Marcia; Sosman, James M.; Stabile, Paul; Stapleton, Jack T.; Starrett, Sheree; Stein, Francine; Stellbrink, Hans-Jurgen; Sterman, F. Lisa; Stone, Valerie E.; Stone, David R.; Tambussi, Giuseppe; Taplitz, Randy A.; Tedaldi, Ellen M.; Telenti, Amalio; Theisen, William; Torres, Richard; Tosiello, Lorraine; Tremblay, Cecile; Tribble, Marc A.; Trinh, Phuong D.; Tsao, Alice; Ueda, Peggy; Vaccaro, Anthony; Valadas, Emilia; Vanig, Thanes J.; Vecino, Isabel; Vega, Vilma M.; Veikley, Wenoah; Wade, Barbara H.; Walworth, Charles; Wanidworanun, Chingchai; Ward, Douglas J.; Warner, Daniel A.; Weber, Robert D.; Webster, Duncan; Weis, Steve; Wheeler, David A.; White, David J.; Wilkins, Ed; Winston, Alan; Wlodaver, Clifford G.; Wout, Angelique van’t; Wright, David P.; Yang, Otto O.; Yurdin, David L.; Zabukovic, Brandon W.; Zachary, Kimon C.; Zeeman, Beth; Zhao, Meng

    2011-01-01

    Infectious and inflammatory diseases have repeatedly shown strong genetic associations within the major histocompatibility complex (MHC); however, the basis for these associations remains elusive. To define host genetic effects on the outcome of a chronic viral infection, we performed genome-wide association analysis in a multiethnic cohort of HIV-1 controllers and progressors, and we analyzed the effects of individual amino acids within the classical human leukocyte antigen (HLA) proteins. We identified >300 genome-wide significant single-nucleotide polymorphisms (SNPs) within the MHC and none elsewhere. Specific amino acids in the HLA-B peptide binding groove, as well as an independent HLA-C effect, explain the SNP associations and reconcile both protective and risk HLA alleles. These results implicate the nature of the HLA–viral peptide interaction as the major factor modulating durable control of HIV infection. PMID:21051598

  12. Genetic and pharmacokinetic determinants of response to transdermal nicotine in white, black, and Asian nonsmokers.

    Science.gov (United States)

    Dempsey, D A; St Helen, G; Jacob, P; Tyndale, R F; Benowitz, N L

    2013-12-01

    The aim of the study was to examine genetic, pharmacokinetic, and demographic factors that influence sensitivity to nicotine in never-smokers. Sixty never-smokers, balanced for gender and race (white, black, and Asian), wore 7-mg nicotine skin patches for up to 8 h. Serial plasma nicotine concentrations and subjective and cardiovascular effects were measured, and genetic variation in the CYP2A6 gene, encoding the primary enzyme responsible for nicotine metabolism, was assessed. Nicotine toxicity requiring patch removal developed in nine subjects and was strongly associated with rate of increase and peak concentrations of plasma nicotine. Toxicity and subjective and cardiovascular effects of nicotine were associated with the presence of reduced-function CYP2A6 alleles, presumably reflecting slow nicotine metabolic inactivation. This study has implications for understanding individual differences in responses to nicotine medications, particularly when they are used for treating medical conditions in nonsmokers, and possibly in vulnerability to developing nicotine dependence.

  13. A putative causal relationship between genetically determined female body shape and posttraumatic stress disorder.

    Science.gov (United States)

    Polimanti, Renato; Amstadter, Ananda B; Stein, Murray B; Almli, Lynn M; Baker, Dewleen G; Bierut, Laura J; Bradley, Bekh; Farrer, Lindsay A; Johnson, Eric O; King, Anthony; Kranzler, Henry R; Maihofer, Adam X; Rice, John P; Roberts, Andrea L; Saccone, Nancy L; Zhao, Hongyu; Liberzon, Israel; Ressler, Kerry J; Nievergelt, Caroline M; Koenen, Karestan C; Gelernter, Joel

    2017-11-27

    The nature and underlying mechanisms of the observed increased vulnerability to posttraumatic stress disorder (PTSD) in women are unclear. We investigated the genetic overlap of PTSD with anthropometric traits and reproductive behaviors and functions in women. The analysis was conducted using female-specific summary statistics from large genome-wide association studies (GWAS) and a cohort of 3577 European American women (966 PTSD cases and 2611 trauma-exposed controls). We applied a high-resolution polygenic score approach and Mendelian randomization analysis to investigate genetic correlations and causal relationships. We observed an inverse association of PTSD with genetically determined anthropometric traits related to body shape, independent of body mass index (BMI). The top association was related to BMI-adjusted waist circumference (WC adj ; R = -0.079, P body shape and PTSD, which could be mediated by evolutionary mechanisms involved in human sexual behaviors.

  14. On the model dependence of the determination of the strong coupling constant in second order QCD from e+e--annihilation into hadrons

    International Nuclear Information System (INIS)

    Achterberg, O.; D'Agostini, G.; Apel, W.D.; Engler, J.; Fluegge, G.; Forstbauer, B.; Fries, D.C.; Fues, W.; Gamerdinger, K.; Henkes, T.; Hopp, G.; Krueger, M.; Kuester, H.; Mueller, H.; Randoll, H.; Schmidt, G.; Schneider, H.; Boer, W. de; Buschhorn, G.; Grindhammer, G.; Grosse-Wiesmann, P.; Gunderson, B.; Kiesling, C.; Kotthaus, R.; Kruse, U.; Lierl, H.; Lueers, D.; Oberlack, H.; Schacht, P.; Bonneaud, G.; Colas, P.; Cordier, A.; Davier, M.; Fournier, D.; Grivaz, J.F.; Haissinski, J.; Journe, V.; Laplanche, F.; Le Diberder, F.; Mallik, U.; Ros, E.; Veillet, J.J.; Behrend, H.J.; Fenner, H.; Schachter, M.J.; Schroeder, V.; Sindt, H.

    1983-12-01

    Hadronic events obtained with the CELLO detector at PETRA are compared with second order QCD predictions using different models for the fragmentation of quarks and gluons into hadrons. We find that the model dependence in the determination of the strong coupling constant persists when going from first to second order QCD calculations. (orig.)

  15. A putative causal relationship between genetically determined female body shape and posttraumatic stress disorder

    Directory of Open Access Journals (Sweden)

    Renato Polimanti

    2017-11-01

    Full Text Available Abstract Background The nature and underlying mechanisms of the observed increased vulnerability to posttraumatic stress disorder (PTSD in women are unclear. Methods We investigated the genetic overlap of PTSD with anthropometric traits and reproductive behaviors and functions in women. The analysis was conducted using female-specific summary statistics from large genome-wide association studies (GWAS and a cohort of 3577 European American women (966 PTSD cases and 2611 trauma-exposed controls. We applied a high-resolution polygenic score approach and Mendelian randomization analysis to investigate genetic correlations and causal relationships. Results We observed an inverse association of PTSD with genetically determined anthropometric traits related to body shape, independent of body mass index (BMI. The top association was related to BMI-adjusted waist circumference (WCadj; R = –0.079, P < 0.001, Q = 0.011. We estimated a relative decrease of 64.6% (95% confidence interval = 27.5–82.7 in the risk of PTSD per 1-SD increase in WCadj. MR-Egger regression intercept analysis showed no evidence of pleiotropic effects in this association (Ppleiotropy = 0.979. We also observed associations of genetically determined WCadj with age at first sexual intercourse and number of sexual partners (P = 0.013 and P < 0.001, respectively. Conclusions There is a putative causal relationship between genetically determined female body shape and PTSD, which could be mediated by evolutionary mechanisms involved in human sexual behaviors.

  16. GENETIC SEX DETERMINATION IN HEAVY BREED CHICKEN EMBRYOS USING AN UNCONVENTIONAL METHOD

    Directory of Open Access Journals (Sweden)

    I. BENCSIK

    2007-05-01

    Full Text Available We have used a non-invasive method to predetermine the sex of chicken embryosthat relies on the bio electromagnetic field generated by the embryonic cells. Tovalidate this method in poultry, on the basis of sexual dimorphism, the genetic sex of120 chicken eggs of heavy breed. One group consisted of 60 eggs with determinedgenetic sex ZZ (cock, abbr. M. The other group consisted of 60 eggs withdetermined genetic sex ZY (hen, abbr. F. After hatching, the chicks were identifiedand the genetic sex was checked repeatedly using the pendulum. The phenoypic sexof the birds was assessed after 60 days at the time the sexual dimorphism wasvisible. From the 60 eggs sexed and incubated for each group, a hatching rate of90%, for the group M and 91,66% for the group F was obtained. The genetic sex ofindividuals determined at the age of one day showed that all individuals of thegroup M were cocks (ZZ and all individuals of the group F were hens (ZW. Thephenotypic sex determination performed 60 days later showed that of 54 individualsof the group M, 41 were cocks (77,36%. In the group F from 55 individuals 42 werehens (77,78%. The prediction rate for the group M (77,36% was relativlycomparable with that for the group F (77,78%. This method is non-invasive,relatively rapid, simple and inexpensive with application in effective breedingregimes of poultry production.

  17. Genetic and Nongenetic Determinants of Cell Growth Variation Assessed by High-Throughput Microscopy

    Science.gov (United States)

    Ziv, Naomi; Siegal, Mark L.; Gresham, David

    2013-01-01

    In microbial populations, growth initiation and proliferation rates are major components of fitness and therefore likely targets of selection. We used a high-throughput microscopy assay, which enables simultaneous analysis of tens of thousands of microcolonies, to determine the sources and extent of growth rate variation in the budding yeast (Saccharomyces cerevisiae) in different glucose environments. We find that cell growth rates are regulated by the extracellular concentration of glucose as proposed by Monod (1949), but that significant heterogeneity in growth rates is observed among genetically identical individuals within an environment. Yeast strains isolated from different geographic locations and habitats differ in their growth rate responses to different glucose concentrations. Inheritance patterns suggest that the genetic determinants of growth rates in different glucose concentrations are distinct. In addition, we identified genotypes that differ in the extent of variation in growth rate within an environment despite nearly identical mean growth rates, providing evidence that alleles controlling phenotypic variability segregate in yeast populations. We find that the time to reinitiation of growth (lag) is negatively correlated with growth rate, yet this relationship is strain-dependent. Between environments, the respirative activity of individual cells negatively correlates with glucose abundance and growth rate, but within an environment respirative activity and growth rate show a positive correlation, which we propose reflects differences in protein expression capacity. Our study quantifies the sources of genetic and nongenetic variation in cell growth rates in different glucose environments with unprecedented precision, facilitating their molecular genetic dissection. PMID:23938868

  18. Populations genetically rifting within a complex geological system: The case of strong structure and low genetic diversity in the migratory freshwater catfish,Bagrus docmak,in East Africa.

    Science.gov (United States)

    Basiita, Rose Komugisha; Zenger, Kyall Richard; Jerry, Dean Robert

    2017-08-01

    The complex geological history of East Africa has been a driving factor in the rapid evolution of teleost biodiversity. While there is some understanding of how macroevolutionary drivers have shaped teleost speciation in East Africa, there is a paucity of research into how the same biogeographical factors have affected microevolutionary processes within lakes and rivers. To address this deficiency, population genetic diversity, demography, and structure were investigated in a widely distributed and migratory (potamodromous) African teleost species, Ssemutundu ( Bagrus docmak ). Samples were acquired from five geographical locations in East Africa within two major drainage basins; the Albertine Rift and Lake Victoria Basin. Individuals ( N  = 175) were genotyped at 12 microsatellite loci and 93 individuals sequenced at the mitochondrial DNA control region. Results suggested populations from Lakes Edward and Victoria had undergone a severe historic bottleneck resulting in very low nucleotide diversity (π = 0.004 and 0.006, respectively) and negatively significant Fu values (-3.769 and -5.049; p  < .05). Heterozygosity deficiencies and restricted effective population size ( N eLD ) suggested contemporary exposure of these populations to stress, consistent with reports of the species decline in the East African Region. High genetic structuring between drainages was detected at both historical (ɸ ST  = 0.62 for mtDNA; p  < .001) and contemporary (microsatellite F ST  = 0.460; p  < .001) levels. Patterns of low genetic diversity and strong population structure revealed are consistent with speciation patterns that have been linked to the complex biogeography of East Africa, suggesting that these biogeographical features have operated as both macro- and micro-evolutionary forces in the formation of the East African teleost fauna.

  19. Maxillary canine displacement and genetically determined predisposition to disturbed development of the dentition.

    Science.gov (United States)

    Stahl, Franka; Grabowski, Rosemarie

    2003-05-01

    The relationship between maxillary canine displacement and the simultaneous occurrence of "genetically determined predisposition to disturbed development of the dentition" as defined by Hoffmeister was investigated in 675 patients. Panoramic radiographs taken of each patient during the first and the second mixed dentition periods were evaluated. Canine inclination and the distance between the tip of the canine and a line connecting the cusps of the molars were computed in five different age groups according to Dausch-Neumann. Statistical analysis revealed 34 patients with "potential canine displacement", who exhibited further symptoms of "genetically determined predisposition to disturbed development of the dentition" significantly more frequently than the total group. The symptoms concerned were agenesia, displaced tooth buds, rotated or tilted incisors, aplasia and microdontia of lateral incisors. Careful follow-ups in patients with a predisposition to disturbed dental development enables risks to be anticipated and canine displacement to be detected at an early stage.

  20. Determining Optimal Replacement Policy with an Availability Constraint via Genetic Algorithms

    OpenAIRE

    Zong, Shengliang; Chai, Guorong; Su, Yana

    2017-01-01

    We develop a model and a genetic algorithm for determining an optimal replacement policy for power equipment subject to Poisson shocks. If the time interval of two consecutive shocks is less than a threshold value, the failed equipment can be repaired. We assume that the operating time after repair is stochastically nonincreasing and the repair time is exponentially distributed with a geometric increasing mean. Our objective is to minimize the expected average cost under an availability requi...

  1. Genetic and Epigenetic Determinants of Lung Cancer Subtype: Adenocarcinoma to Small Cell Conversion

    Science.gov (United States)

    2016-10-01

    calendar NCI $ 166,700 Elucidating the regulation of mitosis by BRAF V600E in lung cancer The goals of this proposal are to analyze how mutant BRAF...AWARD NUMBER: W81XWH-14-1-0223 TITLE: Genetic and Epigenetic Determinants of Lung Cancer Subtype: Adenocarcinoma to Small Cell Conversion...PRINCIPAL INVESTIGATOR: Charles M. Rudin, MD PhD CONTRACTING ORGANIZATION: Sloan Kettering Institute for Cancer Research New York, NY 10065 REPORT DATE

  2. Genetic polymorphism of vitamin D receptor determines its metabolism and efficiency

    OpenAIRE

    O.A. Yakovleva; O.M. Nikolova; I.A. Doroshkevych; N.V. Shcherbeniuk

    2017-01-01

    The review represents the results of researches of vitamin D receptor characteristics and its genetic polymorphism, which is variable in different populations, and also depends on age and gender. This polymorphism determines the association of vitamin D different concentration with the probability of bronchial asthma or chronic obstructive pulmonary disease development, and therefore the different efficacy of drug correction of vitamin D deficiency. However, the scientific data are contradict...

  3. Aortic root dimensions are predominantly determined by genetic factors: a classical twin study

    Energy Technology Data Exchange (ETDEWEB)

    Celeng, Csilla; Kolossvary, Marton; Kovacs, Attila; Molnar, Andrea Agnes; Szilveszter, Balint; Karolyi, Mihaly; Jermendy, Adam L.; Karady, Julia; Merkely, Bela; Maurovich-Horvat, Pal [Semmelweis University, MTA-SE Cardiovascular Imaging Research Group, Heart and Vascular Center, Budapest (Hungary); Horvath, Tamas [Budapest University of Technology and Economics, Department of Hydrodynamic Systems, Budapest (Hungary); Tarnoki, Adam D.; Tarnoki, David L. [Semmelweis University, Department of Radiology and Oncotherapy, Budapest (Hungary); Voros, Szilard [Global Genomics Group, Atlanta, GA (United States); Jermendy, Gyoergy [Bajcsy-Zsilinszky Hospital, Medical Department, Budapest (Hungary)

    2017-06-15

    Previous studies using transthoracic echocardiography (TTE) observed moderate heritability of aortic root dimensions. Computed tomography angiography (CTA) might provide more accurate heritability estimates. Our primary aim was to assess the heritability of the aortic root with CTA. Our secondary aim was to derive TTE-based heritability and compare this with the CTA-based results. In the BUDAPEST-GLOBAL study 198 twin subjects (118 monozygotic, 80 dizygotic; age 56.1 ± 9.4 years; 126 female) underwent CTA and TTE. We assessed the diameter of the left ventricular outflow tract (LVOT), annulus, sinus of Valsalva, sinotubular junction and ascending aorta. Heritability was assessed using ACDE model (A additive genetic, C common environmental, D dominant genetic, E unique environmental factors). Based on CTA, additive genetic effects were dominant (LVOT: A = 0.67, E = 0.33; annulus: A = 0.76, E = 0.24; sinus of Valsalva: A = 0.83, E = 0.17; sinotubular junction: A = 0.82, E = 0.18; ascending aorta: A = 0.75, E = 0.25). TTE-derived measurements showed moderate to no genetic influence (LVOT: A = 0.38, E = 0.62; annulus: C = 0.47, E = 0.53; sinus of Valsalva: C = 0.63, E = 0.37; sinotubular junction: C = 0.45, E = 0.55; ascending aorta: A = 0.67, E = 0.33). CTA-based assessment suggests that aortic root dimensions are predominantly determined by genetic factors. TTE-based measurements showed moderate to no genetic influence. The choice of measurement method has substantial impact on heritability estimates. (orig.)

  4. Determination of genetic relatedness from low-coverage human genome sequences using pedigree simulations.

    Science.gov (United States)

    Martin, Michael D; Jay, Flora; Castellano, Sergi; Slatkin, Montgomery

    2017-08-01

    We develop and evaluate methods for inferring relatedness among individuals from low-coverage DNA sequences of their genomes, with particular emphasis on sequences obtained from fossil remains. We suggest the major factors complicating the determination of relatedness among ancient individuals are sequencing depth, the number of overlapping sites, the sequencing error rate and the presence of contamination from present-day genetic sources. We develop a theoretical model that facilitates the exploration of these factors and their relative effects, via measurement of pairwise genetic distances, without calling genotypes, and determine the power to infer relatedness under various scenarios of varying sequencing depth, present-day contamination and sequencing error. The model is validated by a simulation study as well as the analysis of aligned sequences from present-day human genomes. We then apply the method to the recently published genome sequences of ancient Europeans, developing a statistical treatment to determine confidence in assigned relatedness that is, in some cases, more precise than previously reported. As the majority of ancient specimens are from animals, this method would be applicable to investigate kinship in nonhuman remains. The developed software grups (Genetic Relatedness Using Pedigree Simulations) is implemented in Python and freely available. © 2017 John Wiley & Sons Ltd.

  5. Placebo Responses in Genetically Determined Intellectual Disability: A Meta-Analysis.

    Directory of Open Access Journals (Sweden)

    Aurore Curie

    Full Text Available Genetically determined Intellectual Disability (ID is an intractable condition that involves severe impairment of mental abilities such as learning, reasoning and predicting the future. As of today, little is known about the placebo response in patients with ID.To determine if placebo response exists in patients with genetically determined ID.We searched Medline/PubMed, EMBASE, CENTRAL and PsycINFO to find all placebo-controlled double-blind randomized clinical trials (RCTs in patients with genetically determined ID, published up to April 2013, focusing on core ID symptoms.Two investigators extracted outcome data independently.Bias-corrected standardized mean difference (Hedge's g was computed for each outcome measure, using the Comprehensive Meta-Analysis software. A priori defined patient sub-groups were analyzed using a mixed-effect model. The relationship between pre-defined continuous variable moderators (age, IQ, year of publication and trial duration and effect size was analyzed using meta-regression.Twenty-two placebo-controlled double-blind RCTs met the inclusion criteria (n = 721, mean age = 17.1 years, 62% men, mean trial duration = 35 weeks. There was a significant overall placebo response from pre- to post-treatment in patients with ID (g = 0.468, p = 0.002, both for "subjective outcomes" (a third-person's evaluation of the patient (g = 0.563, p = 0.022 and "objective outcomes" (direct evaluation of the patient's abilities (g = 0.434, p = 0.036. Individuals with higher IQ had higher response to placebo (p = 0.02 and no placebo response was observed in ID patients with comorbid dementia. A significant effect of age (p = 0.02 was found, indicating higher placebo responses in treatment of younger patients.Results suggest that patients with genetically determined ID improve in the placebo arm of RCTs. Several mechanisms may contribute to placebo effects in ID, including expectancy, implicit learning and "placebo-by-proxy" induced by

  6. Genetic sex determination in Astatotilapia calliptera, a prototype species for the Lake Malawi cichlid radiation

    Science.gov (United States)

    Peterson, Erin N.; Cline, Maggie E.; Moore, Emily C.; Roberts, Natalie B.; Roberts, Reade B.

    2017-06-01

    East African cichlids display extensive variation in sex determination systems. The species Astatotilapia calliptera is one of the few cichlids that reside both in Lake Malawi and in surrounding waterways. A. calliptera is of interest in evolutionary studies as a putative immediate outgroup species for the Lake Malawi species flock and possibly as a prototype ancestor-like species for the radiation. Here, we use linkage mapping to test association of sex in A. calliptera with loci that have been previously associated with genetic sex determination in East African cichlid species. We identify a male heterogametic XY system segregating at linkage group (LG) 7 in an A. calliptera line that originated from Lake Malawi, at a locus previously shown to act as an XY sex determination system in multiple species of Lake Malawi cichlids. Significant association of genetic markers and sex produce a broad genetic interval of approximately 26 megabases (Mb) using the Nile tilapia genome to orient markers; however, we note that the marker with the strongest association with sex is near a gene that acts as a master sex determiner in other fish species. We demonstrate that alleles of the marker are perfectly associated with sex in Metriaclima mbenjii, a species from the rock-dwelling clade of Lake Malawi. While we do not rule out the possibility of other sex determination loci in A. calliptera, this study provides a foundation for fine mapping of the cichlid sex determination gene on LG7 and evolutionary context regarding the origin and persistence of the LG7 XY across diverse, rapidly evolving lineages.

  7. Genetic diversity of pomegranate germplasm collection from Spain determined by fruit, seed, leaf and flower characteristics.

    Science.gov (United States)

    Martinez-Nicolas, Juan J; Melgarejo, Pablo; Legua, Pilar; Garcia-Sanchez, Francisco; Hernández, Francisca

    2016-01-01

    Background. Miguel Hernandez University (Spain) created a germplasm bank of the varieties of pomegranate from different Southeastern Spain localities in order to preserve the crop's wide genetic diversity. Once this collection was established, the next step was to characterize the phenotype of these varieties to determine the phenotypic variability that existed among all the different pomegranate genotypes, and to understand the degree of polymorphism of the morphometric characteristics among varieties. Methods. Fifty-three pomegranate (Punica granatum L.) accessions were studied in order to determine their degree of polymorphism and to detect similarities in their genotypes. Thirty-one morphometric characteristics were measured in fruits, arils, seeds, leaves and flowers, as well as juice characteristics including content, pH, titratable acidity, total soluble solids and maturity index. ANOVA, principal component analysis, and cluster analysis showed that there was a considerable phenotypic diversity (and presumably genetic). Results. The cluster analysis produced a dendrogram with four main clusters. The dissimilarity level ranged from 1 to 25, indicating that there were varieties that were either very similar or very different from each other, with varieties from the same geographical areas being more closely related. Within each varietal group, different degrees of similarity were found, although there were no accessions that were identical. These results highlight the crop's great genetic diversity, which can be explained not only by their different geographical origins, but also to the fact that these are native plants that have not come from genetic improvement programs. The geographic origin could be, in the cases where no exchanges of plant material took place, a key criterion for cultivar clustering. Conclusions. As a result of the present study, we can conclude that among all the parameters analyzed, those related to fruit and seed size as well as the

  8. Measured dose to ovaries and testes from Hodgkin's fields and determination of genetically significant dose

    International Nuclear Information System (INIS)

    Niroomand-Rad, A.; Cumberlin, R.

    1993-01-01

    The purpose of this study was to determine the genetically significant dose from therapeutic radiation exposure with Hodgkin's fields by estimating the doses to ovaries and testes. Phantom measurements were performed to verify estimated doses to ovaries and testes from Hodgkin's fields. Thermoluminescent LiF dosimeters (TLD-100) of 1 x 3 x 3 mm 3 dimensions were embedded in phantoms and exposed to standard mantle and paraaortic fields using Co-60, 4 MV, 6 MV, and 10 MV photon beams. The results show that measured doses to ovaries and testes are about two to five times higher than the corresponding graphically estimated doses for Co-60 and 4 MVX photon beams as depicted in ICRP publication 44. In addition, the measured doses to ovaries and testes are about 30% to 65% lower for 10 MV photon beams than for their corresponding Co-60 photon beams. The genetically significant dose from Hodgkin's treatment (less than 0.01 mSv) adds about 4% to the genetically significant dose contribution to medical procedures and adds less than 1% to the genetically significant dose from all sources. Therefore, the consequence to society is considered to be very small. The consequences for the individual patient are, likewise, small. 28 refs., 3 figs., 5 tabs

  9. Determination of the Genetic Architecture Underlying Short Wavelength Sensitivity in Lake Malawi Cichlids.

    Science.gov (United States)

    Nandamuri, Sri Pratima; Dalton, Brian E; Carleton, Karen L

    2017-06-01

    African cichlids are an exemplary system to study organismal diversity and rapid speciation. Species differ in external morphology including jaw shape and body coloration, but also differ in sensory systems including vision. All cichlids have 7 cone opsin genes with species differing broadly in which opsins are expressed. The differential opsin expression results in closely related species with substantial differences in spectral sensitivity of their photoreceptors. In this work, we take a first step in determining the genetic basis of opsin expression in cichlids. Using a second generation cross between 2 species with different opsin expression patterns, we make a conservative estimate that short wavelength opsin expression is regulated by a few loci. Genetic mapping in 96 F2 hybrids provides clear evidence of a cis-regulatory region for SWS1 opsin that explains 34% of the variation in expression between the 2 species. Additionally, in situ hybridization has shown that SWS1 and SWS2B opsins are coexpressed in individual single cones in the retinas of F2 progeny. Results from this work will contribute to a better understanding of the genetic architecture underlying opsin expression. This knowledge will help answer long-standing questions about the evolutionary processes fundamental to opsin expression variation and how this contributes to adaptive cichlid divergence. © The American Genetic Association 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  10. Determination of human cytomegalovirus genetic diversity in different patient populations in Costa Rica

    Directory of Open Access Journals (Sweden)

    Ahumada-Ruiz Sara

    2004-01-01

    Full Text Available Seroprevalence of HCMV in Costa Rica is greater than 95% in adults; primary infections occur early in life and is the most frequent congenital infection in newborns. The objectives of this study were to determine the genetic variability and genotypes of HCMV gB gene in Costa Rica. Samples were collected from alcoholics, pregnant women, blood donors, AIDS patients, hematology-oncology (HO children and HCMV isolates from neonates with cytomegalic inclusion disease. A semi-nested PCR system was used to obtain a product of 293-296 bp of the gB gene to be analyzed by Single Stranded Conformational Polymorphism (SSCP and sequencing to determine the genetic polymorphic pattern and genotypes, respectively. AIDS patients showed the highest polymorphic diversity with 14 different patterns while fifty-six percent of HO children samples showed the same polymorphic pattern, suggesting in this group a possible nosocomial infection. In neonates three genotypes (gB1, gB2 and gB3, were determined while AIDS patients and blood donors only showed one (gB2. Of all samples analyzed only genotypes gB1, 2 and 3 were determined, genotype gB2 was the most frequent (73% and mixed infections were not detected. The results of the study indicate that SSCP could be an important tool to detect HCMV intra-hospital infections and suggests a need to include additional study populations to better determine the genotype diversity and prevalence.

  11. Determination of the strong coupling constant from the inclusive jet cross section in ppbar collisions at sqrt(s)=1.96 TeV

    Energy Technology Data Exchange (ETDEWEB)

    Abazov, V.M.; /Dubna, JINR; Abbott, B.; /Oklahoma U.; Abolins, M.; /Michigan State U.; Acharya, B.S.; /Tata Inst.; Adams, M.; /Illinois U., Chicago; Adams, T.; /Florida State U.; Aguilo, E.; /Alberta U. /Simon Fraser U. /York U., Canada /McGill U.; Ahsan, M.; /Kansas State U.; Alexeev, G.D.; /Dubna, JINR; Alkhazov, G.; /St. Petersburg, INP; Alton, A.; /Michigan U. /Northeastern U.

    2009-11-01

    We determine the strong coupling constant {alpha}{sub s} and its energy dependence from the p{sub T} dependence of the inclusive jet cross section in p{bar p} collisions at {radical}s = 1.96 TeV. The strong coupling constant is determined over the transverse momentum range 50 < p{sub T} < 145 GeV. Using perturbative QCD calculations to order {Omicron}({alpha}{sub s}{sup 3}) combined with {Omicron}({alpha}{sub s}{sup 4}) contributions from threshold corrections, we obtain {alpha}{sub s}(M{sub Z}) = 0.1173{sub -0.0049}{sup +0.0041}. This is the most precise result obtained at a hadron-hadron collider.

  12. Genetic determination of high productivity in experimental hybrid combinations of sugar beet (Beta vulgaris L.

    Directory of Open Access Journals (Sweden)

    М. О. Корнєєва

    2016-05-01

    Full Text Available Purpose. Creation of experimental sugar beet hybrid combinations of high sugar yield values and defining gene­tic determination of their heterotic effect. Methods. Diallel crossing and topcrossing, genetic analysis of quantitative traits. Results. The authors have studied the frequency of occurrence of sugar beet heterotic hybrid combinations for «sugar yield» trait created on the basis of two pollinator lines to be genetically valuable for productivity elements, CMS lines and single-cross sterile hybrids with the use of diallel and topcrossing system of controlled hybridization. The share of parental components’ effect and their interaction in CMS hybrids variability for productivity was determined. Expediency of heterotic forecasting based on high combining ability lines was substabtiated. Promising high-yielding sugar beet combinations were selected that exceeded the group standard by 4.1–16.3%. Conclusions. The theory of genetic balance by M. V. Turbin was confirmed. Such hybrids as [CMS 5OT 4]MGP 1 (116.3%, [CMS 1OT 2]MGP 1 (112.5% and [CMS 3OT 5]MGP 1 (113.2% were recognized as the best for their productivity, MGP 1 and MGP 2 lines – as the best for their combining ability.

  13. Genetic and modifying factors that determine the risk of brain tumors

    DEFF Research Database (Denmark)

    Montelli, Terezinha de Cresci Braga; Peraçoli, Maria Terezinha Serrão; Rogatto, Silvia Regina

    2011-01-01

    Some modifying factors may determine the risk of brain tumors. Until now, it could not be attempted to identify people at risk and also to improve significantly disease progression. Current therapy consists of surgical resection, followed by radiation therapy and chemotherapy. Despite...... of these treatments, the prognosis for patients is poor. In this review, we highlight general aspects concerning genetic alterations in brain tumors, namely astrocytomas, glioblastomas, oligodendrogliomas, medulloblastomas and ependymomas. The influence of these genetic alterations in patients' prognosis is discussed....... Mutagen sensitivity is associated with cancer risk. The convincing studies that linked DNA damages and DNA repair alterations with brain tumors are also described. Another important modifying factor is immunity. General immune response against cancer, tumor microenvironment and immune response, mechanisms...

  14. Determining Optimal Replacement Policy with an Availability Constraint via Genetic Algorithms

    Directory of Open Access Journals (Sweden)

    Shengliang Zong

    2017-01-01

    Full Text Available We develop a model and a genetic algorithm for determining an optimal replacement policy for power equipment subject to Poisson shocks. If the time interval of two consecutive shocks is less than a threshold value, the failed equipment can be repaired. We assume that the operating time after repair is stochastically nonincreasing and the repair time is exponentially distributed with a geometric increasing mean. Our objective is to minimize the expected average cost under an availability requirement. Based on this average cost function, we propose the genetic algorithm to locate the optimal replacement policy N to minimize the average cost rate. The results show that the GA is effective and efficient in finding the optimal solutions. The availability of equipment has significance effect on the optimal replacement policy. Many practical systems fit the model developed in this paper.

  15. Genetic determinants of hair and eye colours in the Scottish and Danish populations

    DEFF Research Database (Denmark)

    Mengel-From, Jonas; Wong, Terence H; Morling, Niels

    2009-01-01

    BACKGROUND: Eye and hair colour is highly variable in the European population, and is largely genetically determined. Both linkage and association studies have previously been used to identify candidate genes underlying this variation. Many of the genes found were previously known as underlying...... mutant mouse phenotypes or human genetic disease, but others, previously unsuspected as pigmentation genes, have also been discovered. RESULTS: We assayed the hair of a population of individuals of Scottish origin using tristimulus colorimetry, in order to produce a quantitative measure of hair colour....... Cluster analysis of this data defined two groups, with overlapping borders, which corresponded to visually assessed dark versus red/light hair colour. The Danish population was assigned into categorical hair colour groups. Both cohorts were also assessed for eye colour. DNA from the Scottish group...

  16. Relation between chloroguanide bioactivation to cycloguanil and the genetically determined metabolism of mephenytoin in humans.

    Science.gov (United States)

    Funck-Brentano, C; Bosco, O; Jacqz-Aigrain, E; Keundjian, A; Jaillon, P

    1992-05-01

    It has been suggested recently that the bioactivation of chloroguanide hydrochloride (proguanil) to its active antimalarial metabolite cycloguanil cosegregates with the genetically determined polymorphism of mephenytoin hydroxylation. We determined the chloroguanide to cycloguanil ratio in urine after oral administration of a single dose of 200 mg proguanil either alone or together with 100 mg racemic mephenytoin or 40 mg dextromethorphan in a randomized crossover study performed in 24 healthy subjects. The mephenytoin hydroxylation index was also determined after administration of 100 mg racemic mephenytoin either alone or together with 200 mg proguanil. Two subjects were poor metabolizers and one subject was an intermediate metabolizer of mephenytoin. These three subjects had chloroguanide to cycloguanil ratios of more than 50. The 21 subjects with the extensive metabolizer phenotype for mephenytoin hydroxylation had chloroguanide to cycloguanil ratios of less than 10. The chloroguanide to cycloguanil ratio was not significantly altered by mephenytoin or dextromethorphan coadministration. The trend toward a correlation between chloroguanide/cycloguanil ratio and log mephenytoin hydroxylation index did not reach statistical significance. Inclusion of the dextromethorphan metabolic ratio into the model did not improve the relationship. These findings confirm that the bioactivation of chloroguanide to cycloguanil cosegregates with the genetically determined activity of the CYP2C family. However, the chloroguanide to cycloguanil ratio and the mephenytoin hydroxylation index do not similarly reflect the variable activity of CYP2C.

  17. Unfolding an under-determined neutron spectrum using genetic algorithm based Monte Carlo

    International Nuclear Information System (INIS)

    Suman, V.; Sarkar, P.K.

    2011-01-01

    Spallation in addition to the other photon-neutron reactions in target materials and different components in accelerators may result in production of huge amount of energetic protons which further leads to the production of neutron and contributes to the main component of the total dose. For dosimetric purposes in accelerator facilities the detector measurements doesn't provide directly the actual neutron flux values but a cumulative picture. To obtain Neutron spectrum from the measured data, response functions of the measuring instrument together with the measurements are used into many unfolding techniques which are frequently used for unfolding the hidden spectral information. Here we discuss a genetic algorithm based unfolding technique which is in the process of development. Genetic Algorithm is a stochastic method based on natural selection, which mimics Darwinian theory of survival of the best. The above said method has been tested to unfold the neutron spectra obtained from a reaction carried out at an accelerator facility, with energetic carbon ions on thick silver target along with its respective neutron response of BC501A liquid scintillation detector. The problem dealt here is under-determined where the number of measurements is less than the required energy bin information. The results so obtained were compared with those obtained using the established unfolding code FERDOR, which unfolds data for completely determined problems. It is seen that the genetic algorithm based solution has a reasonable match with the results of FERDOR, when smoothening carried out by Monte Carlo is taken into consideration. This method appears to be a promising candidate for unfolding neutron spectrum in cases of under-determined and over-determined, where measurements are more. The method also has advantages of flexibility, computational simplicity and works well without need of any initial guess spectrum. (author)

  18. A Large-Scale Genetic Analysis Reveals a Strong Contribution of the HLA Class II Region to Giant Cell Arteritis Susceptibility

    Science.gov (United States)

    Carmona, F. David; Mackie, Sarah L.; Martín, Jose-Ezequiel; Taylor, John C.; Vaglio, Augusto; Eyre, Stephen; Bossini-Castillo, Lara; Castañeda, Santos; Cid, Maria C.; Hernández-Rodríguez, José; Prieto-González, Sergio; Solans, Roser; Ramentol-Sintas, Marc; González-Escribano, M. Francisca; Ortiz-Fernández, Lourdes; Morado, Inmaculada C.; Narváez, Javier; Miranda-Filloy, José A.; Martínez-Berriochoa, Agustín; Unzurrunzaga, Ainhoa; Hidalgo-Conde, Ana; Madroñero-Vuelta, Ana B.; Fernández-Nebro, Antonio; Ordóñez-Cañizares, M. Carmen; Escalante, Begoña; Marí-Alfonso, Begoña; Sopeña, Bernardo; Magro, César; Raya, Enrique; Grau, Elena; Román, José A.; de Miguel, Eugenio; López-Longo, F. Javier; Martínez, Lina; Gómez-Vaquero, Carmen; Fernández-Gutiérrez, Benjamín; Rodríguez-Rodríguez, Luis; Díaz-López, J. Bernardino; Caminal-Montero, Luis; Martínez-Zapico, Aleida; Monfort, Jordi; Tío, Laura; Sánchez-Martín, Julio; Alegre-Sancho, Juan J.; Sáez-Comet, Luis; Pérez-Conesa, Mercedes; Corbera-Bellalta, Marc; García-Villanueva, M. Jesús; Fernández-Contreras, M. Encarnación; Sanchez-Pernaute, Olga; Blanco, Ricardo; Ortego-Centeno, Norberto; Ríos-Fernández, Raquel; Callejas, José L.; Fanlo-Mateo, Patricia; Martínez-Taboada, Víctor M.; Beretta, Lorenzo; Lunardi, Claudio; Cimmino, Marco A.; Gianfreda, Davide; Santilli, Daniele; Ramirez, Giuseppe A.; Soriano, Alessandra; Muratore, Francesco; Pazzola, Giulia; Addimanda, Olga; Wijmenga, Cisca; Witte, Torsten; Schirmer, Jan H.; Moosig, Frank; Schönau, Verena; Franke, Andre; Palm, Øyvind; Molberg, Øyvind; Diamantopoulos, Andreas P.; Carette, Simon; Cuthbertson, David; Forbess, Lindsy J.; Hoffman, Gary S.; Khalidi, Nader A.; Koening, Curry L.; Langford, Carol A.; McAlear, Carol A.; Moreland, Larry; Monach, Paul A.; Pagnoux, Christian; Seo, Philip; Spiera, Robert; Sreih, Antoine G.; Warrington, Kenneth J.; Ytterberg, Steven R.; Gregersen, Peter K.; Pease, Colin T.; Gough, Andrew; Green, Michael; Hordon, Lesley; Jarrett, Stephen; Watts, Richard; Levy, Sarah; Patel, Yusuf; Kamath, Sanjeet; Dasgupta, Bhaskar; Worthington, Jane; Koeleman, Bobby P.C.; de Bakker, Paul I.W.; Barrett, Jennifer H.; Salvarani, Carlo; Merkel, Peter A.; González-Gay, Miguel A.; Morgan, Ann W.; Martín, Javier

    2015-01-01

    We conducted a large-scale genetic analysis on giant cell arteritis (GCA), a polygenic immune-mediated vasculitis. A case-control cohort, comprising 1,651 case subjects with GCA and 15,306 unrelated control subjects from six different countries of European ancestry, was genotyped by the Immunochip array. We also imputed HLA data with a previously validated imputation method to perform a more comprehensive analysis of this genomic region. The strongest association signals were observed in the HLA region, with rs477515 representing the highest peak (p = 4.05 × 10−40, OR = 1.73). A multivariate model including class II amino acids of HLA-DRβ1 and HLA-DQα1 and one class I amino acid of HLA-B explained most of the HLA association with GCA, consistent with previously reported associations of classical HLA alleles like HLA-DRB1∗04. An omnibus test on polymorphic amino acid positions highlighted DRβ1 13 (p = 4.08 × 10−43) and HLA-DQα1 47 (p = 4.02 × 10−46), 56, and 76 (both p = 1.84 × 10−45) as relevant positions for disease susceptibility. Outside the HLA region, the most significant loci included PTPN22 (rs2476601, p = 1.73 × 10−6, OR = 1.38), LRRC32 (rs10160518, p = 4.39 × 10−6, OR = 1.20), and REL (rs115674477, p = 1.10 × 10−5, OR = 1.63). Our study provides evidence of a strong contribution of HLA class I and II molecules to susceptibility to GCA. In the non-HLA region, we confirmed a key role for the functional PTPN22 rs2476601 variant and proposed other putative risk loci for GCA involved in Th1, Th17, and Treg cell function. PMID:25817017

  19. Psychological determinants of willingness to taste and purchase genetically modified food.

    Science.gov (United States)

    Townsend, Ellen; Campbell, Scott

    2004-10-01

    Decreasing acceptance of biotechnologies over time has been reported in Europe. Studies claim that attitudes are negative, even hostile, and that people are very worried about genetic engineering in food and medicine. However, such studies are mostly based on surveys and these have significant methodological problems, such as low response rates, which may indicate that only those with strong views respond, thus biasing the sample. Here an alternative method, involving "topic-blind" recruitment of participants and a behavioral measure (food tasting), was used. We show that in a topic-blind sample of 100 individuals, 93% willingly tasted and ate what they believed to be genetically modified (GM) food in an experimental setting, and 48% said they would buy GM food in the future, results that are surprising in the context of other reports about attitudes and intentions toward GM food. Purchasers and nonpurchasers differed in their attitudes toward GM food on key risk-related scales (particularly on a dread-not dread scale--a measure of integral affect--and an ethical-unethical scale). Despite these differences, however, and despite their negative attitude, most nonpurchasers (85.7%) still tasted the GM apple. Incidental affect (state stress and trait worry) was not found to influence risk-related judgments about GM food. Integral affect (dread of GM plants and animals used for food) and concerns about the future risks of GM animals in food were found to be key predictors of willingness to purchase GM food.

  20. Genetic determinants of both ethanol and acetaldehyde metabolism influence alcohol hypersensitivity and drinking behaviour among Scandinavians.

    Science.gov (United States)

    Linneberg, A; Gonzalez-Quintela, A; Vidal, C; Jørgensen, T; Fenger, M; Hansen, T; Pedersen, O; Husemoen, L L N

    2010-01-01

    Although hypersensitivity reactions following intake of alcoholic drinks are common in Caucasians, the underlying mechanisms and clinical significance are not known. In contrast, in Asians, alcohol-induced asthma and flushing have been shown to be because of a single nucleotide polymorphism (SNP), the acetaldehyde dehydrogenase 2 (ALDH2) 487lys, causing decreased acetaldehyde (the metabolite of ethanol) metabolism and high levels of histamine. However, the ALDH2 487lys is absent in Caucasians. To investigate the genetic determinants of self-reported alcohol-induced hypersensitivity reactions in Caucasians. The study included two population-based studies of 1216 and 6784 adults living in Copenhagen. Assessment of alcohol consumption and hypersensitivity reactions (in a subgroup) was performed by a questionnaire and was related to common SNPs of genes encoding alcohol dehydrogenases (ADHs) and ALDHs. In both populations, alcohol drinkers with a genetically determined fast metabolism of ethanol (the A allele of the ADH1b rs1229984) had an increased risk of alcohol-induced hypersensitivity reactions (odds ratio AA/AG vs. GG in combined populations: 1.82, 95% CI 1.04-3.17). In both populations, a common SNP encoding ALDH1b1 (rs2228093) was found to be significantly associated with alcohol-induced hypersensitivity (odds ratio TT vs. CC in combined populations: 2.53, 95% CI 1.31-4.90). Our data support that alcohol sensitivity in Caucasians is genetically determined and suggest that a histamine-releasing effect of acetaldehyde represents a plausible biological mechanism. Furthermore, we present the first report of a clinically significant SNP within the acetaldehyde-metabolizing system in a Caucasian population.

  1. Determining Relative Importance and Effective Settings for Genetic Algorithm Control Parameters.

    Science.gov (United States)

    Mills, K L; Filliben, J J; Haines, A L

    2015-01-01

    Setting the control parameters of a genetic algorithm to obtain good results is a long-standing problem. We define an experiment design and analysis method to determine relative importance and effective settings for control parameters of any evolutionary algorithm, and we apply this method to a classic binary-encoded genetic algorithm (GA). Subsequently, as reported elsewhere, we applied the GA, with the control parameter settings determined here, to steer a population of cloud-computing simulators toward behaviors that reveal degraded performance and system collapse. GA-steered simulators could serve as a design tool, empowering system engineers to identify and mitigate low-probability, costly failure scenarios. In the existing GA literature, we uncovered conflicting opinions and evidence regarding key GA control parameters and effective settings to adopt. Consequently, we designed and executed an experiment to determine relative importance and effective settings for seven GA control parameters, when applied across a set of numerical optimization problems drawn from the literature. This paper describes our experiment design, analysis, and results. We found that crossover most significantly influenced GA success, followed by mutation rate and population size and then by rerandomization point and elite selection. Selection method and the precision used within the chromosome to represent numerical values had least influence. Our findings are robust over 60 numerical optimization problems.

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

    Science.gov (United States)

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

    2017-02-22

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

  3. Multilevel selection 2: Estimating the genetic parameters determining inheritance and response to selection.

    Science.gov (United States)

    Bijma, Piter; Muir, William M; Ellen, Esther D; Wolf, Jason B; Van Arendonk, Johan A M

    2007-01-01

    Interactions among individuals are universal, both in animals and in plants and in natural as well as domestic populations. Understanding the consequences of these interactions for the evolution of populations by either natural or artificial selection requires knowledge of the heritable components underlying them. Here we present statistical methodology to estimate the genetic parameters determining response to multilevel selection of traits affected by interactions among individuals in general populations. We apply these methods to obtain estimates of genetic parameters for survival days in a population of layer chickens with high mortality due to pecking behavior. We find that heritable variation is threefold greater than that obtained from classical analyses, meaning that two-thirds of the full heritable variation is hidden to classical analysis due to social interactions. As a consequence, predicted responses to multilevel selection applied to this population are threefold greater than classical predictions. This work, combined with the quantitative genetic theory for response to multilevel selection presented in an accompanying article in this issue, enables the design of selection programs to effectively reduce competitive interactions in livestock and plants and the prediction of the effects of social interactions on evolution in natural populations undergoing multilevel selection.

  4. A population genetics perspective on the determinants of intra-tumor heterogeneity.

    Science.gov (United States)

    Hu, Zheng; Sun, Ruping; Curtis, Christina

    2017-04-01

    Cancer results from the acquisition of somatic alterations in a microevolutionary process that typically occurs over many years, much of which is occult. Understanding the evolutionary dynamics that are operative at different stages of progression in individual tumors might inform the earlier detection, diagnosis, and treatment of cancer. Although these processes cannot be directly observed, the resultant spatiotemporal patterns of genetic variation amongst tumor cells encode their evolutionary histories. Such intra-tumor heterogeneity is pervasive not only at the genomic level, but also at the transcriptomic, phenotypic, and cellular levels. Given the implications for precision medicine, the accurate quantification of heterogeneity within and between tumors has become a major focus of current research. In this review, we provide a population genetics perspective on the determinants of intra-tumor heterogeneity and approaches to quantify genetic diversity. We summarize evidence for different modes of evolution based on recent cancer genome sequencing studies and discuss emerging evolutionary strategies to therapeutically exploit tumor heterogeneity. This article is part of a Special Issue entitled: Evolutionary principles - heterogeneity in cancer?, edited by Dr. Robert A. Gatenby. Copyright © 2017 Elsevier B.V. All rights reserved.

  5. Are host genetics the predominant determinant of persistent nasal Staphylococcus aureus carriage in humans?

    Science.gov (United States)

    Ruimy, Raymond; Angebault, Cécile; Djossou, Félix; Dupont, Claire; Epelboin, Loïc; Jarraud, Sophie; Lefevre, Laurence Armand; Bes, Michèle; Lixandru, Brandusa Elena; Bertine, Mélanie; El Miniai, Assiya; Renard, Magaly; Bettinger, Régis Marc; Lescat, Mathilde; Clermont, Olivier; Peroz, Gilles; Lina, Gerard; Tavakol, Mehri; Vandenesch, François; van Belkum, Alex; Rousset, François; Andremont, Antoine

    2010-09-15

    Staphylococcus aureus nasal carriage is influenced by multifactorial interactions which are difficult to study in open populations. Therefore, we concomitantly assessed the epidemiological, microbiological, and human-genetic carriage-related factors in a nearly closed population. In 2006 and 2008, we collected nasal S. aureus strains, human DNA, and epidemiological data from 154 adult Wayampi Amerindians living in an isolated village in the Amazonian forest. The genetics of the strains (multilocus sequence type, spa type, and toxin-content type), epidemiological risk factors, antibiotic exposure, and allelic polymorphism of human genes putatively involved in carriage of the persistent carriers were compared with those of other volunteers. Overall carriage prevalence was 41.7% in 2006 and 57.8% in 2008, but the overall prevalence of persistent carriage was only 26%. The rare and phylogenetically distant multilocus sequence type ST1223 was present in 18.5% of the carriers in 2006 and 34.8% in 2008. No epidemiological factors or antibiotic exposure were significantly associated with persistent carriage, but single nucleotide polymorphism distribution in C-reactive proteins C2042T and C1184T and interleukin-4 C524T genes was significantly associated (P=.02, by global test). Host genetic factors appeared to be the predominant determinant for S. aureus persistent nasal carriage in humans.

  6. Genetic polymorphism of vitamin D receptor determines its metabolism and efficiency

    Directory of Open Access Journals (Sweden)

    O.A. Yakovleva

    2017-04-01

    Full Text Available The review represents the results of researches of vitamin D receptor characteristics and its genetic polymorphism, which is variable in different populations, and also depends on age and gender. This polymorphism determines the association of vitamin D different concentration with the probability of bronchial asthma or chronic obstructive pulmonary disease development, and therefore the different efficacy of drug correction of vitamin D deficiency. However, the scientific data are contradictory, the molecular mechanisms of connection between vitamin D and bronchial tonus or allergic reactions remain unclear, which emphasizes the importance of studies to clarify the role of vitamin D in inflammatory, immune disorders in bronchial obstructive syndrome.

  7. Genetic determinism and evolutionary reconstruction of a host jump in a plant virus

    DEFF Research Database (Denmark)

    Vassilakos, Nikon; Simon, Vincent; Tzima, Aliki

    2016-01-01

    In spite of their widespread occurrence, only few host jumps by plant viruses have been evidenced and the molecular bases of even fewer have been determined. A combination of three independent approaches, 1) experimental evolution followed by reverse genetics analysis, 2) positive selection...... analysis, and 3) locus-by-locus analysis of molecular variance (AMOVA) allowed reconstructing the Potato virus Y (PVY; genus Potyvirus, family Potyviridae) jump to pepper (Capsicum annuum), probably from other solanaceous plants. Synthetic chimeras between infectious cDNA clones of two PVY isolates...

  8. A new method for ABO genotyping to avoid discrepancy between genetic and serological determinations.

    Science.gov (United States)

    Shintani-Ishida, Kaori; Zhu, Bao-Li; Maeda, Hitoshi; Uemura, Koichi; Yoshida, Ken-Ichi

    2008-01-01

    In Japan and elsewhere, ABO genotyping is frequently used in forensic practice for identification of a decomposed body. However, the phenotype deduced from the genotyping data is occasionally inconsistent with the real phenotype. In this paper, we report a simple ABO genotyping method in which five single nucleotide polymorphism at nps 220, 261, 796, 802, and 803 are analyzed simultaneously to avoid discrepancies between genetic and serological determinations in ABO*A204, *O303, *O207, *cis-AB01 and *cis-AB02 alleles. This method can be used for the genotyping of badly decomposed remains or old bloodstains.

  9. Genetics

    Science.gov (United States)

    ... Likelihood of getting certain diseases Mental abilities Natural talents An abnormal trait (anomaly) that is passed down ... one of them has a genetic disorder. Information Human beings have cells with 46 chromosomes . These consist ...

  10. Computer simulations to determine the efficacy of different genome resource banking strategies for maintaining genetic diversity.

    Science.gov (United States)

    Harnal, V K; Wildt, D E; Bird, D M; Monfort, S L; Ballou, J D

    2002-04-01

    Genome resource banks (GRBs) and assisted reproductive techniques are increasingly recognized as useful tools for the management and conservation of biodiversity, including endangered species. Cryotechnology permits long-term storage of valuable genetic material. Although, the actual application to endangered species management requires technical knowledge about sperm freezing and thawing, a systematic understanding of the quantitative impacts of various germ plasm storage and use scenarios is also mandatory. In this study, various GRB strategies were analyzed using the historical data from three managed populations of endangered species with varied pedigrees (Eld's deer, Przewalski's horse, and Sumatran tiger). The following types of sperm banks were assessed: (1) a "Wild Bank" consisting of sperm (i.e., genes) from 5 to 10 males unrelated to the managed population and to each other; and (2) a "Best Male" bank containing sperm from only the most genetically valuable males alive in the ex situ population at the time the bank was established. These different bank types were then used to evaluate the effectiveness of different bank usage frequencies. The efficiency of each scenario was assessed by examining the level of inbreeding and gene diversity in the population. Overall, a sperm usage frequency of five times per year was determined to be the most efficient and "wild banks" were highly successful at enhancing genetic diversity. The value of a GRB established from the ex situ population depends on how closely related the banked males are to future generations. A GRB will have significantly less benefit when banked males also produce many successful offspring, or when donors are already genetically over-represented in the population at the time of establishing the GRB.

  11. Determination of interrill soil erodibility coefficient based on Fuzzy and Fuzzy-Genetic Systems

    Directory of Open Access Journals (Sweden)

    Habib Palizvan Zand

    2017-02-01

    Full Text Available Introduction: Although the fuzzy logic science has been used successfully in various sudies of hydrology and soil erosion, but in literature review no article was found about its performance for estimating of interrill erodibility. On the other hand, studies indicate that genetic algorithm techniques can be used in fuzzy models and finding the appropriate membership functions for linguistic variables and fuzzy rules. So this study was conducted to develop the fuzzy and fuzzy–genetics models and investigation of their performance in the estimation of soil interrill erodibility factor (Ki. Materials and Methods: For this reason 36 soil samples with different physical and chemical properties were collected from west of Azerbaijan province . soilsamples were also taken from the Ap or A horizon of each soil profile. The samples were air-dried , sieved and Some soil characteristics such as soil texture, organic matter (OM, cation exchange capacity (CEC, sodium adsorption ratio (SAR, EC and pH were determined by the standard laboratory methods. Aggregates size distributions (ASD were determined by the wet-sieving method and fractal dimension of soil aggregates (Dn was also calculated. In order to determination of soil interrill erodibility, the flume experiment performed by packing soil a depth of 0.09-m in 0.5 × 1.0 m. soil was saturated from the base and adjusted to 9% slope and was subjected to at least 90 min rainfall . Rainfall intensity treatments were 20, 37 and 47 mm h-1. During each rainfall event, runoff was collected manually in different time intervals, being less than 60 s at the beginning, up to 15 min near the end of the test. At the end of the experiment, the volumes of runoff samples and the mass of sediment load at each time interval were measured. Finally interrill erodibility values were calculated using Kinnell (11 Equation. Then by statistical analyses Dn and sand percent of the soils were selected as input variables and Ki as

  12. Strong genetic structure revealed by multilocus patterns of variation in Giardia duodenalis isolates of patients from Galicia (NW-Iberian Peninsula).

    Science.gov (United States)

    Gabín-García, Luis B; Bartolomé, Carolina; Abal-Fabeiro, José L; Méndez, Santiago; Llovo, José; Maside, Xulio

    2017-03-01

    We report a survey of genetic variation at three coding loci in Giardia duodenalis of assemblages A and B obtained from stool samples of patients from Santiago de Compostela (Galicia, NW-Iberian Peninsula). The mean pooled synonymous diversity for assemblage A was nearly five times lower than for assemblage B (0.77%±0.30% and 4.14%±1.65%, respectively). Synonymous variation in both assemblages was in mutation-drift equilibrium and an excess of low-frequency nonsynonymous variants suggested the action of purifying selection at the three loci. Differences between isolates contributed to 40% and 60% of total genetic variance in assemblages A and B, respectively, which revealed a significant genetic structure. These results, together with the lack of evidence for recombination, support that (i) Giardia assemblages A and B are in demographic equilibrium and behave as two genetically isolated populations, (ii) infections are initiated by a reduced number of individuals, which may be genetically diverse and even belong to different assemblages, and (iii) parasites reproduce clonally within the host. However, the observation of invariant loci in some isolates means that mechanisms for the homogenization of the genetic content of the two diploid nuclei in each individual must exist. Copyright © 2016 Elsevier B.V. All rights reserved.

  13. The puzzle of Italian rice origin and evolution: determining genetic divergence and affinity of rice germplasm from Italy and Asia.

    Directory of Open Access Journals (Sweden)

    Xingxing Cai

    Full Text Available The characterization of genetic divergence and relationships of a set of germplasm is essential for its efficient applications in crop breeding and understanding of the origin/evolution of crop varieties from a given geographical region. As the largest rice producing country in Europe, Italy holds rice germplasm with abundant genetic diversity. Although Italian rice varieties and the traditional ones in particular have played important roles in rice production and breeding, knowledge concerning the origin and evolution of Italian traditional varieties is still limited. To solve the puzzle of Italian rice origin, we characterized genetic divergence and relationships of 348 rice varieties from Italy and Asia based on the polymorphisms of microsatellite fingerprints. We also included common wild rice O. rufipogon as a reference in the characterization. Results indicated relatively rich genetic diversity (H(e = 0.63-0.65 in Italian rice varieties. Further analyses revealed a close genetic relationship of the Italian traditional varieties with those from northern China, which provides strong genetic evidence for tracing the possible origin of early established rice varieties in Italy. These findings have significant implications for the rice breeding programs, in which appropriate germplasm can be selected from a given region and utilized for transferring unique genetic traits based on its genetic diversity and evolutionary relationships.

  14. Variation in Recombination Rate and Its Genetic Determinism in Sheep Populations.

    Science.gov (United States)

    Petit, Morgane; Astruc, Jean-Michel; Sarry, Julien; Drouilhet, Laurence; Fabre, Stéphane; Moreno, Carole R; Servin, Bertrand

    2017-10-01

    Recombination is a complex biological process that results from a cascade of multiple events during meiosis. Understanding the genetic determinism of recombination can help to understand if and how these events are interacting. To tackle this question, we studied the patterns of recombination in sheep, using multiple approaches and data sets. We constructed male recombination maps in a dairy breed from the south of France (the Lacaune breed) at a fine scale by combining meiotic recombination rates from a large pedigree genotyped with a 50K SNP array and historical recombination rates from a sample of unrelated individuals genotyped with a 600K SNP array. This analysis revealed recombination patterns in sheep similar to other mammals but also genome regions that have likely been affected by directional and diversifying selection. We estimated the average recombination rate of Lacaune sheep at 1.5 cM/Mb, identified ∼50,000 crossover hotspots on the genome, and found a high correlation between historical and meiotic recombination rate estimates. A genome-wide association study revealed two major loci affecting interindividual variation in recombination rate in Lacaune, including the RNF212 and HEI10 genes and possibly two other loci of smaller effects including the KCNJ15 and FSHR genes. The comparison of these new results to those obtained previously in a distantly related population of domestic sheep (the Soay) revealed that Soay and Lacaune males have a very similar distribution of recombination along the genome. The two data sets were thus combined to create more precise male meiotic recombination maps in Sheep. However, despite their similar recombination maps, Soay and Lacaune males were found to exhibit different heritabilities and QTL effects for interindividual variation in genome-wide recombination rates. This highlights the robustness of recombination patterns to underlying variation in their genetic determinism. Copyright © 2017 by the Genetics Society

  15. $K^{0} \\leftrightharpoons \\overline{K}^0$ transitions monitored by strong interactions a new determination of the $K_{L} - K_{S}$ mass difference

    CERN Document Server

    Angelopoulos, Angelos; Backenstoss, Gerhard; Bargassa, P; Behnke, O; Benelli, A; Bertin, V; Blanc, F; Bloch, P; Carlson, P J; Carroll, M; Cawley, E; Chertok, M B; Danielsson, M; Dejardin, M; Derré, J; Ealet, A; Eleftheriadis, C; Fetscher, W; Fidecaro, Maria; Filipcic, A; Francis, D; Fry, J; Gabathuler, Erwin; Gamet, R; Gerber, H J; Go, A; Haselden, A; Haymen, P J; Henry-Coüannier, F; Hollander, R W; Jon-And, K; Kettle, P R; Kokkas, P; Kreuger, R; Le Gac, R; Leimgruber, F; Mandic, I; Manthos, N; Marel, Gérard; Mikuz, M; Miller, J; Montanet, François; Müller, A; Nakada, Tatsuya; Pagels, B; Papadopoulos, I M; Pavlopoulos, P; Polivka, G; Rickenbach, R; Roberts, B L; Ruf, T; Sakelliou, L; Schäfer, M; Schaller, L A; Schietinger, T; Schopper, A; Tauscher, Ludwig; Thibault, C; Touchard, F; Touramanis, C; van Eijk, C W E; Vlachos, S; Weber, P; Wigger, O; Wolter, M; Zavrtanik, D; Zimmerman, D

    2001-01-01

    The CPLEAR set-up (modified) has been used to determine the K/sub L/- K/sub S/ mass difference by a method where neutral-kaon strangeness oscillations are monitored through kaon strong interactions, rather than semileptonic decays, thus requiring no assumptions on CPT invariance for the decay amplitudes. The result, Delta m= (0.5343+or-0.0063/sub stat/+or-0.0025/sub syst/)*10/sup 10/ h(cross) /s, provides a valuable input for CPT tests. (22 refs).

  16. The importance of genetic verification for determination of Atlantic salmon in north Pacific waters

    Science.gov (United States)

    Nielsen, J.L.; Williams, I.; Sage, G.K.; Zimmerman, C.E.

    2003-01-01

    Genetic analyses of two unknown but putative Atlantic salmon Salmo salar captured in the Copper River drainage, Alaska, demonstrated the need for validation of morphologically unusual fishes. Mitochondrial DNA sequences (control region and cytochrome b) and data from two nuclear genes [first internal transcribed spacer (ITS-1) sequence and growth hormone (GH1) amplification product] indicated that the fish caught in fresh water on the Martin River was a coho salmon Oncorhynchus kisutch, while the other fish caught in the intertidal zone of the Copper River delta near Grass Island was an Atlantic salmon. Determination of unusual or cryptic fish based on limited physical characteristics and expected seasonal spawning run timing will add to the controversy over farmed Atlantic salmon and their potential effects on native Pacific species. It is clear that determination of all putative collections of Atlantic salmon found in Pacific waters requires validation. Due to uncertainty of fish identification in the field using plastic morphometric characters, it is recommended that genetic analyses be part of the validation process. ?? 2003 The Fisheries Society of the British Isles.

  17. CNS repair and axon regeneration: Using genetic variation to determine mechanisms.

    Science.gov (United States)

    Tedeschi, Andrea; Omura, Takao; Costigan, Michael

    2017-01-01

    The importance of genetic diversity in biological investigation has been recognized since the pioneering studies of Gregor Johann Mendel and Charles Darwin. Research in this area has been greatly informed recently by the publication of genomes from multiple species. Genes regulate and create every part and process in a living organism, react with the environment to create each living form and morph and mutate to determine the history and future of each species. The regenerative capacity of neurons differs profoundly between animal lineages and within the mammalian central and peripheral nervous systems. Here, we discuss research that suggests that genetic background contributes to the ability of injured axons to regenerate in the mammalian central nervous system (CNS), by controlling the regulation of specific signaling cascades. We detail the methods used to identify these pathways, which include among others Activin signaling and other TGF-β superfamily members. We discuss the potential of altering these pathways in patients with CNS damage and outline strategies to promote regeneration and repair by combinatorial manipulation of neuron-intrinsic and extrinsic determinants. Copyright © 2016 Elsevier Inc. All rights reserved.

  18. Prevalence of genetic determinants and phenotypic resistance to ciprofloxacin in Campylobacter jejuni from lithuania

    DEFF Research Database (Denmark)

    Aksomaitiene, Jurgita; Ramonaite, Sigita; Olsen, John E.

    2018-01-01

    Recently, the number of reports on isolation of ciprofloxacin resistant Campylobacter jejuni has increased worldwide. The aim of this study was to determine the prevalence of resistance to ciprofloxacin and its genetic determinants among C. jejuni isolated from humans (n = 100), poultry products (n...... = 96) and wild birds (n = 96) in Lithuania. 91.4% of the C. jejuni isolates were phenotypically resistant to ciprofloxacin. DNA sequence analyses of the gyrA gene from 292 isolates revealed that a change in amino acid sequence, Thr86Ile, was the main substition conferring resistance to ciprofloxacin...... forty-five C. jejuni isolates showed one or more silent mutations, and 32.4% of examined isolates possessed six silent mutations. In addition to the ciprofloxacin resistant isolates harboring only Thr86Ile point mutation (110 isolates), the current study identified resistant isolates (n = 101) harboring...

  19. Life history determines genetic structure and evolutionary potential of host-parasite interactions.

    Science.gov (United States)

    Barrett, Luke G; Thrall, Peter H; Burdon, Jeremy J; Linde, Celeste C

    2008-12-01

    Measures of population genetic structure and diversity of disease-causing organisms are commonly used to draw inferences regarding their evolutionary history and potential to generate new variation in traits that determine interactions with their hosts. Parasite species exhibit a range of population structures and life-history strategies, including different transmission modes, life-cycle complexity, off-host survival mechanisms and dispersal ability. These are important determinants of the frequency and predictability of interactions with host species. Yet the complex causal relationships between spatial structure, life history and the evolutionary dynamics of parasite populations are not well understood. We demonstrate that a clear picture of the evolutionary potential of parasitic organisms and their demographic and evolutionary histories can only come from understanding the role of life history and spatial structure in influencing population dynamics and epidemiological patterns.

  20. AFLP analysis of genetic diversity in determinate and indeterminate snap bean accessions

    Directory of Open Access Journals (Sweden)

    Felipe Aranha de Andrade

    2016-01-01

    Full Text Available The present study aimed to estimate and characterize the genetic divergence between determinate and indeterminate snap bean accessions from the Universidade Estadual de Londrina (UEL germplasm bank based on amplified fragment length polymorphism (AFLP markers. A total of 40 and 32 accessions with determinate and indeterminate growth habits, respectively, were characterized for this purpose. Seven combinations of primers corresponding to EcoR1 and Mse1 were tested for the AFLP analysis, and the combinations E-AAG/M-CTC, E-ACT/M-CTT and E-ACC/M-CTT were selected. The resulting products were denatured and subjected to capillary electrophoresis. The Jaccard distance was used to estimate the genetic distances between accessions, and the Unweighted Pair Cluster Method with Arithmetic Mean (UPGMA, principal coordinates analysis (PCoA and Bayesian statistics were used for the clustering analysis. The three combinations of primer/enzyme revealed 485 informative loci in total, and the combination E-ACC/M-CTT detected the greatest number of informative loci (49%. The analysis of dissimilarity frequency distribution showed that the distribution was uniform, ranging from 0.1285 to 0.7310 with a mean of 0.4801, and the accessions with indeterminate growth habits exhibited greater variability than the accessions with determinate growth habits. The clustering UPGMA, PCoA and Bayesian analyses showed the formation of two large clusters, wherein there is a possible association between snap bean growth habit and gene pool. The determinate accessions may be more closely associated with the Andean gene pool, while the indeterminate ones may be associated with the Mesoamerican gene pool. The Bayesian analysis showed accessions intermediate to both groups, suggesting introgression between the Andean and Mesoamerican gene pools.

  1. Genetic Risk Determinants for Cigarette Smoking Dependence in Mexican Mestizo Families.

    Science.gov (United States)

    Svyryd, Yevgeniya; Ramírez-Venegas, Alejandra; Sánchez-Hernández, Beatriz; Aguayo-Gómez, Adolfo; Luna-Muñoz, Leonora; Arteaga-Vázquez, Jazmín; Regalado-Pineda, Justino; Mutchinick, Osvaldo M

    2016-05-01

    Tobacco smoking is a leading cause of mortality in developed and developing countries. Despite antitobacco and smoke-free policies, the prevalence of active smokers in Mexican urban populations has remained stable. Mexican smokers differ from Caucasian and other ethnic groups, probably due to sociocultural and genetic background characteristics. This study explored the effect of known genetic variants on smoking behavior in Mexico City residents. Three hundred sixty-four Mexican Mestizo Mexico City residents from 87 families with at least one smoker were assessed for association of 12 gene variants of six candidate genes (CHRNA4, CHRNB2, DRD2, ANKK1, SLC6A3, and CYP2A6) with cigarette consumption, age of initiation and smoking duration. The Family Based Association Test, an extension of the Transmission Disequilibrium Test, was used to perform family-based association analysis. The Family Based Association Test showed statistically significant association between the rs2072658 polymorphism of the CHRNB2 gene and smoking-related phenotypes such as: smoking status (SS), age of onset (AO), years of smoking, and psychological dependence (PD) evaluated by the Glover-Nilsson Smoking Behavior Questionnaire. After Bonferroni correction, only the association with AO remained significant (P = .003). Statistically significant association was also observed for the CYP2A6 rs28399433 T allele with SS (P = .003) and PD (P = .003). Our results indicate effects of the rs2072658 CHRNB2 and rs28399433 CYP2A6 gene variants on AO, SS and PD in Mexican Mestizo smokers. A mild effect of other analyzed gene variants, which may contribute to a putative polygenic predisposition for smoking, is suggested. The understanding of genetic and environmental determinants in the Mexican population is important for other Latin American populations as well, living in their own countries or moving to other ones, particular due to the current migration characteristics and particular genetic background

  2. Determination of the strong coupling constant α{sub s} (m{sub Z}) from measurements of the total cross section for top-antitop-quark production

    Energy Technology Data Exchange (ETDEWEB)

    Klijnsma, Thomas; Dissertori, Guenther [ETH Zurich, Institute for Particle Physics, Zurich (Switzerland); Bethke, Siegfried [Max-Planck-Institute of Physics, Munich (Germany); Salam, Gavin P. [CERN, Theoretical Physics Department, Geneva (Switzerland); CNRS, UMR 7589, LPTHE, Paris (France)

    2017-11-15

    We present a determination of the strong coupling constant α{sub s} (m{sub Z}) using inclusive top-quark pair production cross section measurements performed at the LHC and at the Tevatron. Following a procedure first applied by the CMS Collaboration, we extract individual values of α{sub s} (m{sub Z}) from measurements by different experiments at several centre-of-mass energies, using QCD predictions complete in NNLO perturbation theory, supplemented with NNLL approximations to all orders, and suitable sets of parton distribution functions. The determinations are then combined using a likelihood-based approach, where special emphasis is put on a consistent treatment of theoretical uncertainties and of correlations between various sources of systematic uncertainties. Our final combined result is α{sub s} (m{sub Z}) = 0.1177{sup +0.0034}{sub -0.0036}. (orig.)

  3. Genetics

    International Nuclear Information System (INIS)

    Hubitschek, H.E.

    1975-01-01

    Progress is reported on the following research projects: genetic effects of high LET radiations; genetic regulation, alteration, and repair; chromosome replication and the division cycle of Escherichia coli; effects of radioisotope decay in the DNA of microorganisms; initiation and termination of DNA replication in Bacillus subtilis; mutagenesis in mouse myeloma cells; lethal and mutagenic effects of near-uv radiation; effect of 8-methoxypsoralen on photodynamic lethality and mutagenicity in Escherichia coli; DNA repair of the lethal effects of far-uv; and near uv irradiation of bacterial cells

  4. Determinants of human adipose tissue gene expression: impact of diet, sex, metabolic status, and cis genetic regulation.

    Directory of Open Access Journals (Sweden)

    Nathalie Viguerie

    2012-09-01

    Full Text Available Weight control diets favorably affect parameters of the metabolic syndrome and delay the onset of diabetic complications. The adaptations occurring in adipose tissue (AT are likely to have a profound impact on the whole body response as AT is a key target of dietary intervention. Identification of environmental and individual factors controlling AT adaptation is therefore essential. Here, expression of 271 transcripts, selected for regulation according to obesity and weight changes, was determined in 515 individuals before, after 8-week low-calorie diet-induced weight loss, and after 26-week ad libitum weight maintenance diets. For 175 genes, opposite regulation was observed during calorie restriction and weight maintenance phases, independently of variations in body weight. Metabolism and immunity genes showed inverse profiles. During the dietary intervention, network-based analyses revealed strong interconnection between expression of genes involved in de novo lipogenesis and components of the metabolic syndrome. Sex had a marked influence on AT expression of 88 transcripts, which persisted during the entire dietary intervention and after control for fat mass. In women, the influence of body mass index on expression of a subset of genes persisted during the dietary intervention. Twenty-two genes revealed a metabolic syndrome signature common to men and women. Genetic control of AT gene expression by cis signals was observed for 46 genes. Dietary intervention, sex, and cis genetic variants independently controlled AT gene expression. These analyses help understanding the relative importance of environmental and individual factors that control the expression of human AT genes and therefore may foster strategies aimed at improving AT function in metabolic diseases.

  5. A Co-Association Network Analysis of the Genetic Determination of Pig Conformation, Growth and Fatness

    Science.gov (United States)

    Puig-Oliveras, Anna; Ballester, Maria; Corominas, Jordi; Revilla, Manuel; Estellé, Jordi; Fernández, Ana I.; Ramayo-Caldas, Yuliaxis; Folch, Josep M.

    2014-01-01

    Background Several QTLs have been identified for major economically relevant traits in livestock, such as growth and meat quality, revealing the complex genetic architecture of these traits. The use of network approaches considering the interactions of multiple molecules and traits provides useful insights into the molecular underpinnings of complex traits. Here, a network based methodology, named Association Weight Matrix, was applied to study gene interactions and pathways affecting pig conformation, growth and fatness traits. Results The co-association network analysis underpinned three transcription factors, PPARγ, ELF1, and PRDM16 involved in mesoderm tissue differentiation. Fifty-four genes in the network belonged to growth-related ontologies and 46 of them were common with a similar study for growth in cattle supporting our results. The functional analysis uncovered the lipid metabolism and the corticotrophin and gonadotrophin release hormone pathways among the most important pathways influencing these traits. Our results suggest that the genes and pathways here identified are important determining either the total body weight of the animal and the fat content. For instance, a switch in the mesoderm tissue differentiation may determinate the age-related preferred pathways being in the puberty stage those related with the miogenic and osteogenic lineages; on the contrary, in the maturity stage cells may be more prone to the adipocyte fate. Hence, our results demonstrate that an integrative genomic co-association analysis is a powerful approach for identifying new connections and interactions among genes. Conclusions This work provides insights about pathways and key regulators which may be important determining the animal growth, conformation and body proportions and fatness traits. Molecular information concerning genes and pathways here described may be crucial for the improvement of genetic breeding programs applied to pork meat production. PMID:25503799

  6. A co-association network analysis of the genetic determination of pig conformation, growth and fatness.

    Directory of Open Access Journals (Sweden)

    Anna Puig-Oliveras

    Full Text Available Several QTLs have been identified for major economically relevant traits in livestock, such as growth and meat quality, revealing the complex genetic architecture of these traits. The use of network approaches considering the interactions of multiple molecules and traits provides useful insights into the molecular underpinnings of complex traits. Here, a network based methodology, named Association Weight Matrix, was applied to study gene interactions and pathways affecting pig conformation, growth and fatness traits.The co-association network analysis underpinned three transcription factors, PPARγ, ELF1, and PRDM16 involved in mesoderm tissue differentiation. Fifty-four genes in the network belonged to growth-related ontologies and 46 of them were common with a similar study for growth in cattle supporting our results. The functional analysis uncovered the lipid metabolism and the corticotrophin and gonadotrophin release hormone pathways among the most important pathways influencing these traits. Our results suggest that the genes and pathways here identified are important determining either the total body weight of the animal and the fat content. For instance, a switch in the mesoderm tissue differentiation may determinate the age-related preferred pathways being in the puberty stage those related with the miogenic and osteogenic lineages; on the contrary, in the maturity stage cells may be more prone to the adipocyte fate. Hence, our results demonstrate that an integrative genomic co-association analysis is a powerful approach for identifying new connections and interactions among genes.This work provides insights about pathways and key regulators which may be important determining the animal growth, conformation and body proportions and fatness traits. Molecular information concerning genes and pathways here described may be crucial for the improvement of genetic breeding programs applied to pork meat production.

  7. Genetics

    DEFF Research Database (Denmark)

    Christensen, Kaare; McGue, Matt

    2016-01-01

    The sequenced genomes of individuals aged ≥80 years, who were highly educated, self-referred volunteers and with no self-reported chronic diseases were compared to young controls. In these data, healthy ageing is a distinct phenotype from exceptional longevity and genetic factors that protect...

  8. Genetic variation of silver fir progeny from Tisovik Reserve population determined via microsatellite and isozyme markers

    Directory of Open Access Journals (Sweden)

    Pawlaczyk Ewa Maria

    2017-03-01

    Full Text Available Progeny from 19 family lines of silver fir (Abies alba Mill. from a small, native and isolated population from the Tisovik Reserve (Belarusian part of Białowieża Primeval Forest growing in an experimental plot near Hajnówka (Polish part of Białowieża Primeval Forest were analysed in terms of 4 nuclear microsatellite DNA loci and 9 isozyme systems with 14 loci. The aim of this study was to determine the genetic variation within and between progeny lines. Analysis of isozyme loci showed that all progeny lines, except the progeny lines T6 and T16, were characterised by an excess of heterozygotes and 20% of the detected variation occurred between progeny. Progeny formed two groups. Microsatellite loci showed that 6 progeny lines demonstrated an excess of heterozygotes and 12 an excess of homozygotes. On an average, the population was in the Hardy-Weinberg equilibrium. Analysis of molecular variance (AMOVA showed that 14% of the detected variation occurred between offspring and the remaining 86% within progeny lines. The most distinct progeny line was Tl, where the highest number of alleles per locus was detected. Generally, progeny of Tisovik is characterised by high level of differentiation as the offspring of isolated population that have limited number of individuals to crossing (only 20. In some progeny line, the private alleles that are detected may be the result of pollination from Polish part of Białowieża Forest where in 1920s and 1930s of XX century had planted the seedling of silver fir of unknown origin. The substructuring of population is observed, and the detected deficiency of heterozygotes may be ostensible as a result of the Wahlund effect. Such pattern of genetic structure could also be an effect of harsh environmental conditions exerting selection pressure and modifying the genetic composition of this population.

  9. Response to enemies in the invasive plant Lythrum salicaria is genetically determined

    Science.gov (United States)

    Joshi, Srijana; Tielbörger, Katja

    2012-01-01

    Background and Aims The enemy release hypothesis assumes that invasive plants lose their co-evolved natural enemies during introduction into the new range. This study tested, as proposed by the evolution of increased competitive ability (EICA) hypothesis, whether escape from enemies results in a decrease in defence ability in plants from the invaded range. Two straightforward aspects of the EICA are examined: (1) if invasives have lost their enemies and their defence, they should be more negatively affected by their full natural pre-invasion herbivore spectrum than their native conspecifics; and (2) the genetic basis of evolutionary change in response to enemy release in the invasive range has not been taken sufficiently into account. Methods Lythrum salicaria (purple loosestrife) from several populations in its native (Europe) and invasive range (North America) was exposed to all above-ground herbivores in replicated natural populations in the native range. The experiment was performed both with plants raised from field-collected seeds as well as with offspring of these where maternal effects were removed. Key Results Absolute and relative leaf damage was higher for introduced than for native plants. Despite having smaller height growth rate, invasive plants attained a much larger final size than natives irrespective of damage, indicating large tolerance rather than effective defence. Origin effects on response to herbivory and growth were stronger in second-generation plants, suggesting that invasive potential through enemy release has a genetic basis. Conclusions The findings support two predictions of the EICA hypothesis – a genetically determined difference between native and invasive plants in plant vigour and response to enemies – and point to the importance of experiments that control for maternal effects and include the entire spectrum of native range enemies. PMID:22492331

  10. Determination of the Spatial Distribution in Hydraulic Conductivity Using Genetic Algorithm Optimization

    Science.gov (United States)

    Aksoy, A.; Lee, J. H.; Kitanidis, P. K.

    2016-12-01

    Heterogeneity in hydraulic conductivity (K) impacts the transport and fate of contaminants in subsurface as well as design and operation of managed aquifer recharge (MAR) systems. Recently, improvements in computational resources and availability of big data through electrical resistivity tomography (ERT) and remote sensing have provided opportunities to better characterize the subsurface. Yet, there is need to improve prediction and evaluation methods in order to obtain information from field measurements for better field characterization. In this study, genetic algorithm optimization, which has been widely used in optimal aquifer remediation designs, was used to determine the spatial distribution of K. A hypothetical 2 km by 2 km aquifer was considered. A genetic algorithm library, PGAPack, was linked with a fast Fourier transform based random field generator as well as a groundwater flow and contaminant transport simulation model (BIO2D-KE). The objective of the optimization model was to minimize the total squared error between measured and predicted field values. It was assumed measured K values were available through ERT. Performance of genetic algorithm in predicting the distribution of K was tested for different cases. In the first one, it was assumed that observed K values were evaluated using the random field generator only as the forward model. In the second case, as well as K-values obtained through ERT, measured head values were incorporated into evaluation in which BIO2D-KE and random field generator were used as the forward models. Lastly, tracer concentrations were used as additional information in the optimization model. Initial results indicated enhanced performance when random field generator and BIO2D-KE are used in combination in predicting the spatial distribution in K.

  11. The role of nutrition and genetics as key determinants of the positive height trend.

    Science.gov (United States)

    Grasgruber, P; Cacek, J; Kalina, T; Sebera, M

    2014-12-01

    The aim of this study was to identify the most important variables determining current differences in physical stature in Europe and some of its overseas offshoots such as Australia, New Zealand and USA. We collected data on the height of young men from 45 countries and compared them with long-term averages of food consumption from the FAOSTAT database, various development indicators compiled by the World Bank and the CIA World Factbook, and frequencies of several genetic markers. Our analysis demonstrates that the most important factor explaining current differences in stature among nations of European origin is the level of nutrition, especially the ratio between the intake of high-quality proteins from milk products, pork meat and fish, and low-quality proteins from wheat. Possible genetic factors such as the distribution of Y haplogroup I-M170, combined frequencies of Y haplogroups I-M170 and R1b-U106, or the phenotypic distribution of lactose tolerance emerge as comparably important, but the available data are more limited. Moderately significant positive correlations were also found with GDP per capita, health expenditure and partly with the level of urbanization that influences male stature in Western Europe. In contrast, male height correlated inversely with children's mortality and social inequality (Gini index). These results could inspire social and nutritional guidelines that would lead to the optimization of physical growth in children and maximization of the genetic potential, both at the individual and national level. Copyright © 2014 The Authors. Published by Elsevier B.V. All rights reserved.

  12. Genetic determinants of telomere length and risk of common cancers: a Mendelian randomization study.

    Science.gov (United States)

    Zhang, Chenan; Doherty, Jennifer A; Burgess, Stephen; Hung, Rayjean J; Lindström, Sara; Kraft, Peter; Gong, Jian; Amos, Christopher I; Sellers, Thomas A; Monteiro, Alvaro N A; Chenevix-Trench, Georgia; Bickeböller, Heike; Risch, Angela; Brennan, Paul; Mckay, James D; Houlston, Richard S; Landi, Maria Teresa; Timofeeva, Maria N; Wang, Yufei; Heinrich, Joachim; Kote-Jarai, Zsofia; Eeles, Rosalind A; Muir, Ken; Wiklund, Fredrik; Grönberg, Henrik; Berndt, Sonja I; Chanock, Stephen J; Schumacher, Fredrick; Haiman, Christopher A; Henderson, Brian E; Amin Al Olama, Ali; Andrulis, Irene L; Hopper, John L; Chang-Claude, Jenny; John, Esther M; Malone, Kathleen E; Gammon, Marilie D; Ursin, Giske; Whittemore, Alice S; Hunter, David J; Gruber, Stephen B; Knight, Julia A; Hou, Lifang; Le Marchand, Loic; Newcomb, Polly A; Hudson, Thomas J; Chan, Andrew T; Li, Li; Woods, Michael O; Ahsan, Habibul; Pierce, Brandon L

    2015-09-15

    Epidemiological studies have reported inconsistent associations between telomere length (TL) and risk for various cancers. These inconsistencies are likely attributable, in part, to biases that arise due to post-diagnostic and post-treatment TL measurement. To avoid such biases, we used a Mendelian randomization approach and estimated associations between nine TL-associated SNPs and risk for five common cancer types (breast, lung, colorectal, ovarian and prostate cancer, including subtypes) using data on 51 725 cases and 62 035 controls. We then used an inverse-variance weighted average of the SNP-specific associations to estimate the association between a genetic score representing long TL and cancer risk. The long TL genetic score was significantly associated with increased risk of lung adenocarcinoma (P = 6.3 × 10(-15)), even after exclusion of a SNP residing in a known lung cancer susceptibility region (TERT-CLPTM1L) P = 6.6 × 10(-6)). Under Mendelian randomization assumptions, the association estimate [odds ratio (OR) = 2.78] is interpreted as the OR for lung adenocarcinoma corresponding to a 1000 bp increase in TL. The weighted TL SNP score was not associated with other cancer types or subtypes. Our finding that genetic determinants of long TL increase lung adenocarcinoma risk avoids issues with reverse causality and residual confounding that arise in observational studies of TL and disease risk. Under Mendelian randomization assumptions, our finding suggests that longer TL increases lung adenocarcinoma risk. However, caution regarding this causal interpretation is warranted in light of the potential issue of pleiotropy, and a more general interpretation is that SNPs influencing telomere biology are also implicated in lung adenocarcinoma risk. © The Author 2015. Published by Oxford University Press.

  13. Genetic determinants of freckle occurrence in the Spanish population: Towards ephelides prediction from human DNA samples.

    Science.gov (United States)

    Hernando, Barbara; Ibañez, Maria Victoria; Deserio-Cuesta, Julio Alberto; Soria-Navarro, Raquel; Vilar-Sastre, Inca; Martinez-Cadenas, Conrado

    2018-03-01

    Prediction of human pigmentation traits, one of the most differentiable externally visible characteristics among individuals, from biological samples represents a useful tool in the field of forensic DNA phenotyping. In spite of freckling being a relatively common pigmentation characteristic in Europeans, little is known about the genetic basis of this largely genetically determined phenotype in southern European populations. In this work, we explored the predictive capacity of eight freckle and sunlight sensitivity-related genes in 458 individuals (266 non-freckled controls and 192 freckled cases) from Spain. Four loci were associated with freckling (MC1R, IRF4, ASIP and BNC2), and female sex was also found to be a predictive factor for having a freckling phenotype in our population. After identifying the most informative genetic variants responsible for human ephelides occurrence in our sample set, we developed a DNA-based freckle prediction model using a multivariate regression approach. Once developed, the capabilities of the prediction model were tested by a repeated 10-fold cross-validation approach. The proportion of correctly predicted individuals using the DNA-based freckle prediction model was 74.13%. The implementation of sex into the DNA-based freckle prediction model slightly improved the overall prediction accuracy by 2.19% (76.32%). Further evaluation of the newly-generated prediction model was performed by assessing the model's performance in a new cohort of 212 Spanish individuals, reaching a classification success rate of 74.61%. Validation of this prediction model may be carried out in larger populations, including samples from different European populations. Further research to validate and improve this newly-generated freckle prediction model will be needed before its forensic application. Together with DNA tests already validated for eye and hair colour prediction, this freckle prediction model may lead to a substantially more detailed

  14. A Large-Scale Genetic Analysis Reveals a Strong Contribution of the HLA Class II Region to Giant Cell Arteritis Susceptibility

    NARCIS (Netherlands)

    David Carmona, F.; Mackie, Sarah L.; Martin, Jose-Ezequiel; Taylor, John C.; Vaglio, Augusto; Eyre, Stephen; Bossini-Castillo, Lara; Castaneda, Santos; Cid, Maria C.; Hernandez-Rodriguez, Jose; Prieto-Gonzalez, Sergio; Solans, Roser; Ramentol-Sintas, Marc; Francisca Gonzalez-Escribano, M.; Ortiz-Fernandez, Lourdes; Morado, Inmaculada C.; Narvaez, Javier; Miranda-Filloy, Jose A.; Beretta, Lorenzo; Lunardi, Claudio; Cimmino, Marco A.; Gianfreda, Davide; Santilli, Daniele; Ramirez, Giuseppe A.; Soriano, Alessandra; Muratore, Francesco; Pazzola, Giulia; Addimanda, Olga; Wijmenga, Cisca; Witte, Torsten; Schirmer, Jan H.; Moosig, Frank; Schoenau, Verena; Franke, Andre; Palm, Oyvind; Molberg, Oyvind; Diamantopoulos, Andreas P.; Carette, Simon; Cuthbertson, David; Forbess, Lindsy J.; Hoffman, Gary S.; Khalidi, Nader A.; Koening, Curry L.; Langford, Carol A.; McAlear, Carol A.; Moreland, Larry; Monach, Paul A.; Pagnoux, Christian; Seo, Philip; Spiera, Robert; Sreih, Antoine G.; Warrington, Kenneth J.; Ytterberg, Steven R.; Gregersen, Peter K.; Pease, Colin T.; Gough, Andrew; Green, Michael; Hordon, Lesley; Jarrett, Stephen; Watts, Richard; Levy, Sarah; Patel, Yusuf; Kamath, Sanjeet; Dasgupta, Bhaskar; Worthington, Jane; Koeleman, Bobby P. C.; de Bakker, Paul I. W.; Barrett, Jennifer H.; Salvarani, Carlo; Merkel, Peter A.; Gonzalez-Gay, Miguel A.; Morgan, Ann W.; Martin, Javier

    2015-01-01

    We conducted a large-scale genetic analysis on giant cell arteritis (GCA), a polygenic immune-mediated vasculitis. A case-control cohort, comprising 1,651 case subjects with GCA and 15,306 unrelated control subjects from six different countries of European ancestry, was genotyped by the Immunochip

  15. The geographical and environmental determinants of genetic diversity for four alpine conifers of the European Alps.

    Science.gov (United States)

    Mosca, E; Eckert, A J; Di Pierro, E A; Rocchini, D; La Porta, Nicola; Belletti, P; Neale, D B

    2012-11-01

    Climate is one of the most important drivers of local adaptation in forest tree species. Standing levels of genetic diversity and structure within and among natural populations of forest trees are determined by the interplay between climatic heterogeneity and the balance between selection and gene flow. To investigate this interplay, single nucleotide polymorphisms (SNPs) were genotyped in 24 to 37 populations from four subalpine conifers, Abies alba Mill., Larix decidua Mill., Pinus cembra L. and Pinus mugo Turra, across their natural ranges in the Italian Alps and Apennines. Patterns of population structure were apparent using a Bayesian clustering program, STRUCTURE, which identified three to five genetic groups per species. Geographical correlates with these patterns, however, were only apparent for P. cembra. Multivariate environmental variables [i.e. principal components (PCs)] were subsequently tested for association with SNPs using a Bayesian generalized linear mixed model. The majority of the SNPs, ranging from six in L. decidua to 18 in P. mugo, were associated with PC1, corresponding to winter precipitation and seasonal minimum temperature. In A. alba, four SNPs were associated with PC2, corresponding to the seasonal minimum temperature. Functional annotation of those genes with the orthologs in Arabidopsis revealed several genes involved in abiotic stress response. This study provides a detailed assessment of population structure and its association with environment and geography in four coniferous species in the Italian mountains. © 2012 Blackwell Publishing Ltd.

  16. A genome scan conducted in a multigenerational pedigree with convergent strabismus supports a complex genetic determinism.

    Directory of Open Access Journals (Sweden)

    Anouk Georges

    Full Text Available A genome-wide linkage scan was conducted in a Northern-European multigenerational pedigree with nine of 40 related members affected with concomitant strabismus. Twenty-seven members of the pedigree including all affected individuals were genotyped using a SNP array interrogating > 300,000 common SNPs. We conducted parametric and non-parametric linkage analyses assuming segregation of an autosomal dominant mutation, yet allowing for incomplete penetrance and phenocopies. We detected two chromosome regions with near-suggestive evidence for linkage, respectively on chromosomes 8 and 18. The chromosome 8 linkage implied a penetrance of 0.80 and a rate of phenocopy of 0.11, while the chromosome 18 linkage implied a penetrance of 0.64 and a rate of phenocopy of 0. Our analysis excludes a simple genetic determinism of strabismus in this pedigree.

  17. Analyzing the determinants of the voting behavior using a genetic algorithm

    Directory of Open Access Journals (Sweden)

    Marcos Vizcaíno-González

    2016-09-01

    Full Text Available Using data about votes emitted by funds in meetings held by United States banks from 2003 to 2013, we apply a genetic algorithm to a set of financial variables in order to detect the determinants of the vote direction. Our findings indicate that there are three main explanatory factors: the market value of the firm, the shareholder activism measured as the total number of funds voting, and the temporal context, which reflects the influence of recent critical events affecting the banking industry, including bankruptcies, reputational failures, and mergers and acquisitions. As a result, considering that voting behavior has been empirically linked to reputational harms, these findings can be considered as a useful insight about the keys that should be taken into account in order to achieve an effective reputational risk management strategy.

  18. Environmental and genetic factors determine whether the mosquito Aedes aegypti lays eggs without a blood meal.

    Science.gov (United States)

    Ariani, Cristina V; Smith, Sophia C L; Osei-Poku, Jewelna; Short, Katherine; Juneja, Punita; Jiggins, Francis M

    2015-04-01

    Some mosquito strains or species are able to lay eggs without taking a blood meal, a trait named autogeny. This may allow populations to persist through times or places where vertebrate hosts are scarce. Autogenous egg production is highly dependent on the environment in some species, but the ideal conditions for its expression in Aedes aegypti mosquitoes are unknown. We found that 3.2% of females in a population of Ae. aegypti from Kenya were autogenous. Autogeny was strongly influenced by temperature, with many more eggs laid at 28°C compared with 22°C. Good nutrition in larval stages and feeding on higher concentrations of sugar solution during the adult stage both result in more autogenous eggs being produced. The trait also has a genetic basis, as not all Ae. aegypti genotypes can lay autogenously. We conclude that Ae. aegypti requires a favorable environment and a suitable genotype to be able to lay eggs without a blood meal. © The American Society of Tropical Medicine and Hygiene.

  19. Genetic determinants and clinico-pathological outcomes of helicobacter pylori infection.

    Science.gov (United States)

    Oluwasola, A O

    2014-06-01

    Helicobacter pylori is a spiral Gram-negative bacterium with a relatively small genome and is known to be the most common human bacterial infection worldwide, infecting about half of the world's population. The bacterium represents one of the most successful human pathogens, inducing severe clinical symptoms only in a small subset of individuals, thus signifying a highly balanced degree of co-evolution of H. pylori and humans. The prevalence of Helicobacter pylori infection varies greatly among countries and among population groups within the same country, but is falling in most developed countries. The clinical course of H. pylori infection is highly variable and is influenced by both microbial and host factors including genetic susceptibility while the pattern and distribution of inflammation correlate strongly with the risk of clinical sequelae, namely duodenal or gastric ulcers, mucosal atrophy, gastric carcinoma, or gastric lymphoma. Cytokine gene polymorphisms directly influence inter-individual variation in the magnitude of cytokine response, and this clearly contributes to an individual's ultimate clinical outcome. Polymorphisms in genes coding for innate immune factors have also been incriminated in the pathogenesis of H. pylori related disease, while promoter hypermethylation of tumor suppressor genes is considered an important factor in carcinogenesis and known to be present in H. pylori associated gastric tumors. Functional genomics may fill many of the gaps in our understanding of the pathogenesis of H. pylori infection and accelerate the development of novel therapies, including H. pylori specific antimicrobial agents.

  20. 76 FR 8707 - Syngenta Seeds, Inc.; Determination of Nonregulated Status for Corn Genetically Engineered To...

    Science.gov (United States)

    2011-02-15

    ... Organisms and Products Altered or Produced Through Genetic Engineering Which Are Plant Pests or Which There... genetic engineering that are plant pests or that there is reason to believe are plant pests. Such...

  1. 76 FR 78232 - Monsanto Co.; Determination of Nonregulated Status for Soybean Genetically Engineered To Have a...

    Science.gov (United States)

    2011-12-16

    ... Through Genetic Engineering Which Are Plant Pests or Which There Is Reason to Believe Are Plant Pests... environment) of organisms and products altered or produced through genetic engineering that are plant pests or...

  2. 75 FR 32356 - Pioneer Hi-Bred International, Inc.; Determination of Nonregulated Status for Genetically...

    Science.gov (United States)

    2010-06-08

    ... Organisms and Products Altered or Produced Through Genetic Engineering Which Are Plant Pests or Which There... genetic engineering that are plant pests or that there is reason to believe are plant pests. Such...

  3. Genomic selection strategies in breeding programs: Strong positive interaction between application of genotypic information and intensive use of young bulls on genetic gain

    DEFF Research Database (Denmark)

    Buch, Line Hjortø; Sørensen, Morten Kargo; Berg, Peer

    2012-01-01

    ) a positive interaction exists between the use of genotypic information and a short generation interval on ΔGAG and (iii) the inclusion of an indicator trait in the selection index will only result in a negligible increase in ΔGAG if genotypic information about the breeding goal trait is known. We examined......We tested the following hypotheses: (i) breeding schemes with genomic selection are superior to breeding schemes without genomic selection regarding annual genetic gain of the aggregate genotype (ΔGAG), annual genetic gain of the functional traits and rate of inbreeding per generation (ΔF), (ii...... four breeding schemes with or without genomic selection and with or without intensive use of young bulls using pseudo-genomic stochastic simulations. The breeding goal consisted of a milk production trait and a functional trait. The two breeding schemes with genomic selection resulted in higher ΔGAG...

  4. Genetic background strongly modifies the severity of symptoms of Hirschsprung disease, but not hearing loss in rats carrying Ednrb(sl mutations.

    Directory of Open Access Journals (Sweden)

    Ruihua Dang

    Full Text Available Hirschsprung disease (HSCR is thought to result as a consequence of multiple gene interactions that modulate the ability of enteric neural crest cells to populate the developing gut. However, it remains unknown whether the single complete deletion of important HSCR-associated genes is sufficient to result in HSCR disease. In this study, we found that the null mutation of the Ednrb gene, thought indispensable for enteric neuron development, is insufficient to result in HSCR disease when bred onto a different genetic background in rats carrying Ednrb(sl mutations. Moreover, we found that this mutation results in serious congenital sensorineural deafness, and these strains may be used as ideal models of Waardenburg Syndrome Type 4 (WS4. Furthermore, we evaluated how the same changed genetic background modifies three features of WS4 syndrome, aganglionosis, hearing loss, and pigment disorder in these congenic strains. We found that the same genetic background markedly changed the aganglionosis, but resulted in only slight changes to hearing loss and pigment disorder. This provided the important evidence, in support of previous studies, that different lineages of neural crest-derived cells migrating along with various pathways are regulated by different signal molecules. This study will help us to better understand complicated diseases such as HSCR and WS4 syndrome.

  5. 78 FR 66891 - Monsanto Co.; Determination of Nonregulated Status of Soybean Genetically Engineered for...

    Science.gov (United States)

    2013-11-07

    ... Products Altered or Produced Through Genetic Engineering Which Are Plant Pests or Which There Is Reason to... movement, or release into the environment) of organisms and products altered or produced through genetic engineering that are plant pests or that there is reason to believe are plant pests. Such genetically...

  6. Genetic structure of wild pea (Pisum sativum subsp. elatius) populations in the northern part of the Fertile Crescent reflects moderate cross-pollination and strong effect of geographic but not environmental distance.

    Science.gov (United States)

    Smýkal, Petr; Trněný, Oldřich; Brus, Jan; Hanáček, Pavel; Rathore, Abhishek; Roma, Rani Das; Pechanec, Vilém; Duchoslav, Martin; Bhattacharyya, Debjyoti; Bariotakis, Michalis; Pirintsos, Stergios; Berger, Jens; Toker, Cengiz

    2018-01-01

    Knowledge of current genetic diversity and mating systems of crop wild relatives (CWR) in the Fertile Crescent is important in crop genetic improvement, because western agriculture began in the area after the cold-dry period known as Younger Dryas about 12,000 years ago and these species are also wild genepools of the world's most important food crops. Wild pea (Pisum sativum subsp. elatius) is an important source of genetic diversity for further pea crop improvement harbouring traits useful in climate change context. The genetic structure was assessed on 187 individuals of Pisum sativum subsp. elatius from fourteen populations collected in the northern part of the Fertile Crescent using 18,397 genome wide single nucleotide polymorphism DARTseq markers. AMOVA showed that 63% of the allelic variation was distributed between populations and 19% between individuals within populations. Four populations were found to contain admixed individuals. The observed heterozygosity ranged between 0.99 to 6.26% with estimated self-pollination rate between 47 to 90%. Genetic distances of wild pea populations were correlated with geographic but not environmental (climatic) distances and support a mixed mating system with predominant self-pollination. Niche modelling with future climatic projections showed a local decline in habitats suitable for wild pea, making a strong case for further collection and ex situ conservation.

  7. Genetic Determinism of Sensitivity to Corynespora cassiicola Exudates in Rubber Tree (Hevea brasiliensis).

    Science.gov (United States)

    Tran, Dinh Minh; Clément-Demange, André; Déon, Marine; Garcia, Dominique; Le Guen, Vincent; Clément-Vidal, Anne; Soumahoro, Mouman; Masson, Aurélien; Label, Philippe; Le, Mau Tuy; Pujade-Renaud, Valérie

    2016-01-01

    An indirect phenotyping method was developed in order to estimate the susceptibility of rubber tree clonal varieties to Corynespora Leaf Fall (CLF) disease caused by the ascomycete Corynespora cassiicola. This method consists in quantifying the impact of fungal exudates on detached leaves by measuring the induced electrolyte leakage (EL%). The tested exudates were either crude culture filtrates from diverse C. cassiicola isolates or the purified cassiicolin (Cas1), a small secreted effector protein produced by the aggressive isolate CCP. The test was found to be quantitative, with the EL% response proportional to toxin concentration. For eight clones tested with two aggressive isolates, the EL% response to the filtrates positively correlated to the response induced by conidial inoculation. The toxicity test applied to 18 clones using 13 toxinic treatments evidenced an important variability among clones and treatments, with a significant additional clone x treatment interaction effect. A genetic linkage map was built using 306 microsatellite markers, from the F1 population of the PB260 x RRIM600 family. Phenotyping of the population for sensitivity to the purified Cas1 effector and to culture filtrates from seven C. cassiicola isolates revealed a polygenic determinism, with six QTL detected on five chromosomes and percentages of explained phenotypic variance varying from 11 to 17%. Two common QTL were identified for the CCP filtrate and the purified cassiicolin, suggesting that Cas1 may be the main effector of CCP filtrate toxicity. The CCP filtrate clearly contrasted with all other filtrates. The toxicity test based on Electrolyte Leakage Measurement offers the opportunity to assess the sensitivity of rubber genotypes to C. cassiicola exudates or purified effectors for genetic investigations and early selection, without risk of spreading the fungus in plantations. However, the power of this test for predicting field susceptibility of rubber clones to CLF will have

  8. Genetic diversity of Streptococcus suis isolates as determined by comparative genome hybridization

    Directory of Open Access Journals (Sweden)

    Thi Hoa

    2011-07-01

    Full Text Available Abstract Background Streptococcus suis is a zoonotic pathogen that causes infections in young piglets. S. suis is a heterogeneous species. Thirty-three different capsular serotypes have been described, that differ in virulence between as well as within serotypes. Results In this study, the correlation between gene content, serotype, phenotype and virulence among 55 S. suis strains was studied using Comparative Genome Hybridization (CGH. Clustering of CGH data divided S. suis isolates into two clusters, A and B. Cluster A isolates could be discriminated from cluster B isolates based on the protein expression of extracellular factor (EF. Cluster A contained serotype 1 and 2 isolates that were correlated with virulence. Cluster B mainly contained serotype 7 and 9 isolates. Genetic similarity was observed between serotype 7 and serotype 2 isolates that do not express muramidase released protein (MRP and EF (MRP-EF-, suggesting these isolates originated from a common founder. Profiles of 25 putative virulence-associated genes of S. suis were determined among the 55 isolates. Presence of all 25 genes was shown for cluster A isolates, whereas cluster B isolates lacked one or more putative virulence genes. Divergence of S. suis isolates was further studied based on the presence of 39 regions of difference. Conservation of genes was evaluated by the definition of a core genome that contained 78% of all ORFs in P1/7. Conclusions In conclusion, we show that CGH is a valuable method to study distribution of genes or gene clusters among isolates in detail, yielding information on genetic similarity, and virulence traits of S. suis isolates.

  9. Genetic and immunologic determinants of intravesical BCG therapy in non-muscle-invasive urothelial bladder cancer

    Directory of Open Access Journals (Sweden)

    Wojciech Krajewski

    2014-03-01

    Full Text Available Bladder cancer (BCA is one of the most common cancers. In 2010 in Poland, 6296 people developed bladder cancer and 3110 people died of it. Immunotherapy with BCG (Bacillus Calmette-Guérin is by far the most effective adjuvant therapy. Noninfiltrating muscle membrane changes, that is, stages Ta, Tis and T1 qualify for BCG immunotherapy. BCG immunotherapy comprises series of bladder instillations, containing attenuated strain of Mycobacterium bovis. The effectiveness of immunotherapy in non-invasive bladder cancer is 70% 5-year survival without recurrence of the tumor. The treatment leads to a reduction of the residual tumor mass, but also to the delay and/or prevention of relapse, disease progression and ultimately death. Cytokines, as key mediators of immune response, play an important role in the pathogenesis of bladder cancer, which occurrence is stimulated by the inflammatory process. BCG immunotherapy provokes an intensive immunological response by the increase of cytokine production. Genetic variants determine inter-individual differences in the incidence of this cancer, as well as the response to the therapy. This is evidenced by the presence of differences in genetic variants of cytokines correlated with the varied risk of bladder cancer incidence. It is believed that concentrations of particular cytokines in urine after installation of BCG may indicate response to the therapy. Increased levels of Th1 cytokines – IFN-γ, IL-2 and TNF-α are correlated with longer survival time without recurrence, whereas high levels of Th2 cytokines such as IL-10, predict unsuccessful BCG therapy.

  10. Genetic determinants of age-related macular degeneration in diverse populations from the PAGE study.

    Science.gov (United States)

    Restrepo, Nicole A; Spencer, Kylee L; Goodloe, Robert; Garrett, Tiana A; Heiss, Gerardo; Bůžková, Petra; Jorgensen, Neal; Jensen, Richard A; Matise, Tara C; Hindorff, Lucia A; Klein, Barbara E K; Klein, Ronald; Wong, Tien Y; Cheng, Ching-Yu; Cornes, Belinda K; Tai, E-Shyong; Ritchie, Marylyn D; Haines, Jonathan L; Crawford, Dana C

    2014-09-09

    Substantial progress has been made in identifying susceptibility variants for AMD in European populations; however, few studies have been conducted to understand the role these variants play in AMD risk in diverse populations. The present study aims to examine AMD risk across diverse populations in known and suspected AMD complement factor and lipid-related loci. Targeted genotyping was performed across study sites for AMD and lipid trait-associated single nucleotide polymorphism (SNPs). Genetic association tests were performed at individual sites and then meta-analyzed using logistic regression assuming an additive genetic model stratified by self-described race/ethnicity. Participants included cases with early or late AMD and controls with no signs of AMD as determined by fundus photography. Populations included in this study were European Americans, African Americans, Mexican Americans, and Singaporeans from the Population Architecture using Genomics and Epidemiology (PAGE) study. Index variants of AMD, rs1061170 (CFH) and rs10490924 (ARMS2), were associated with AMD at P=3.05×10(-8) and P=6.36×10(-6), respectively, in European Americans. In general, none of the major AMD index variants generalized to our non-European populations with the exception of rs10490924 in Mexican Americans at an uncorrected P value<0.05. Four lipid-associated SNPS (LPL rs328, TRIB1 rs6987702, CETP rs1800775, and KCTD10/MVK rs2338104) were associated with AMD in African Americans and Mexican Americans (P<0.05), but these associations did not survive strict corrections for multiple testing. While most associations did not generalize in the non-European populations, variants within lipid-related genes were found to be associated with AMD. This study highlights the need for larger well-powered studies in non-European populations. Copyright 2014 The Association for Research in Vision and Ophthalmology, Inc.

  11. Genetic Determinants of Circulating Interleukin-1 Receptor Antagonist Levels and Their Association With Glycemic Traits

    Science.gov (United States)

    Nuotio, Marja-Liisa; Shah, Sonia; Blankenberg, Stefan; Brunner, Eric J.; Carstensen, Maren; Gieger, Christian; Grallert, Harald; Jula, Antti; Kähönen, Mika; Kettunen, Johannes; Kivimäki, Mika; Koenig, Wolfgang; Kristiansson, Kati; Langenberg, Claudia; Lehtimäki, Terho; Luotola, Kari; Marzi, Carola; Müller, Christian; Peters, Annette; Prokisch, Holger; Raitakari, Olli; Rathmann, Wolfgang; Roden, Michael; Salmi, Marko; Schramm, Katharina; Swerdlow, Daniel; Tabak, Adam G.; Thorand, Barbara; Wareham, Nick; Wild, Philipp S.; Zeller, Tanja; Hingorani, Aroon D.; Witte, Daniel R.; Kumari, Meena; Perola, Markus; Salomaa, Veikko

    2014-01-01

    The proinflammatory cytokine interleukin (IL)-1β is implicated in the development of insulin resistance and β-cell dysfunction, whereas higher circulating levels of IL-1 receptor antagonist (IL-1RA), an endogenous inhibitor of IL-1β, has been suggested to improve glycemia and β-cell function in patients with type 2 diabetes. To elucidate the protective role of IL-1RA, this study aimed to identify genetic determinants of circulating IL-1RA concentration and to investigate their associations with immunological and metabolic variables related to cardiometabolic risk. In the analysis of seven discovery and four replication cohort studies, two single nucleotide polymorphisms (SNPs) were independently associated with circulating IL-1RA concentration (rs4251961 at the IL1RN locus [n = 13,955, P = 2.76 × 10−21] and rs6759676, closest gene locus IL1F10 [n = 13,994, P = 1.73 × 10−17]). The proportion of the variance in IL-1RA explained by both SNPs combined was 2.0%. IL-1RA–raising alleles of both SNPs were associated with lower circulating C-reactive protein concentration. The IL-1RA–raising allele of rs6759676 was also associated with lower fasting insulin levels and lower HOMA insulin resistance. In conclusion, we show that circulating IL-1RA levels are predicted by two independent SNPs at the IL1RN and IL1F10 loci and that genetically raised IL-1RA may be protective against the development of insulin resistance. PMID:24969107

  12. Genetic determinants of semi-dwarf characters induced in Oryza sativa for upland rice cultivation

    International Nuclear Information System (INIS)

    Clement, G.; Poisson, C.

    1988-01-01

    Numerous semi-dwarf mutants have been obtained by applying gamma irradiation to tall upland varieties. They show better lodging resistance and retain their adaptation to upland cultivation conditions (MARIE, 1974). These mutants are also of interest as cross breeding parents. If the breeder knows the genes for semi-dwarfness, he can use different ones so as to avoid the risk of a narrow genetic base. Five induced mutants and one deviant from a sixth one, were used in this study. The semi-dwarf characters were analysed in two steps: Comparison of the stem morphology of the conventional varieties and of the induced mutants; Studying the behaviour of hybrid F 1 and F 2 segregations. Three types of genetic control for induced semi-dwarfness have been found on the basis of the six mutants used: A recessive single-gene determinant in IRAT 115; A recessive single-gene determinant different from the preceding one and common to IRAT 13, IRAT 177, IRAT 250 and IRAT 257; A semi-dominant single-gene determinant in IRAT 194. For his hybridization programme, the rice breeder therefore has at his disposal various upland semi-dwarf mutants, which are capable of transmitting this character in accordance with simple Mendelian rules. However, he has to test also their general cross breeding value. IRAT 13, from which most IRAT varieties released so far originated (including IRAT 104, IRAT 170 and IRAT 112), is undoubtedly a good parent. Mutants IRAT 177, IRAT 250 and IRAT 257, which have the same gene for semi-dwarfness, have been used more recently. They exhibit an excellent ability for combination with tall upland varieties, while being differentiated by a few features (better recombination for seed shedding or resistance to Pyricularia oryzae with IRAT 257 and for grain character with IRAT 177 or 250). The recombination observed in the crosses involving IRAT 115 and conventional upland varieties seems poor. Paradoxically, IRAT 115 has been found to become an excellent parent after

  13. High-throughput double quantitative competitive polymerase chain reaction for determination of genetically modified organisms.

    Science.gov (United States)

    Mavropoulou, Anastasia K; Koraki, Theodora; Ioannou, Penelope C; Christopoulos, Theodore K

    2005-08-01

    Quantitative competitive polymerase chain reaction (PCR), especially the double competitive PCR methods (DC-PCR), have evolved as reliable approaches to quantification of genetically modified organisms (GMO) in food. However, DC-PCR is a low-throughput method because it requires titration of each sample with various amounts of a competitive internal standard, a protocol that involves several PCRs per sample followed by electrophoresis and densitometry. To address this drawback, we have developed a new method for GMO quantification, namely, a high-throughput double quantitative competitive PCR (HT-DCPCR). In HT-DCPCR, electrophoresis and densitometry are replaced by a rapid, microtiter well-based bioluminometric hybridization assay and there is no need for titration of each sample. The determination of GM soya was chosen as a model. We have constructed internal standards (DNA competitors) both for the 35S promoter sequence and for a plant-specific reference gene (lectin). The competitors have identical size and share the same primer binding sites with the target sequences but differ in a 24-bp internal segment. Each target sequence (35S and lectin) is coamplified with a constant amount (1000 copies) of the respective competitor. The four amplified fragments are hybridized with specific probes and captured on a universal solid phase to achieve simplicity and high throughput. The hybrids are determined by using streptavidin conjugated to the photoprotein aequorin. The ratio of the luminescence values obtained for the target and the competitor is linearly related to the starting amount of target DNA. The limit of quantification for the 35S promoter is 24 copies. The proposed method was evaluated by determining the GMO content of soybean powder certified reference materials. Also HT-DCPCR was compared to real-time PCR in a variety of real samples.

  14. Breast cancer: determining the genetic profile from ultrasound-guided percutaneous biopsy specimens obtained during the diagnostic workups.

    Science.gov (United States)

    López Ruiz, J A; Zabalza Estévez, I; Mieza Arana, J A

    2016-01-01

    To evaluate the possibility of determining the genetic profile of primary malignant tumors of the breast from specimens obtained by ultrasound-guided percutaneous biopsies during the diagnostic imaging workup. This is a retrospective study in 13 consecutive patients diagnosed with invasive breast cancer by B-mode ultrasound-guided 12 G core needle biopsy. After clinical indication, the pathologist decided whether the paraffin block specimens seemed suitable (on the basis of tumor size, validity of the sample, and percentage of tumor cells) before sending them for genetic analysis with the MammaPrint® platform. The size of the tumors on ultrasound ranged from 0.6cm to 5cm. In 11 patients the preserved specimen was considered valid and suitable for use in determining the genetic profile. In 1 patient (with a 1cm tumor) the pathologist decided that it was necessary to repeat the core biopsy to obtain additional samples. In 1 patient (with a 5cm tumor) the specimen was not considered valid by the genetic laboratory. The percentage of tumor cells in the samples ranged from 60% to 70%. In 11/13 cases (84.62%) it was possible to do the genetic analysis on the previously diagnosed samples. In most cases, regardless of tumor size, it is possible to obtain the genetic profile from tissue specimens obtained with ultrasound-guided 12 G core biopsy preserved in paraffin blocks. Copyright © 2015 SERAM. Published by Elsevier España, S.L.U. All rights reserved.

  15. Genetic and non-genetic determinants of raltegravir penetration into cerebrospinal fluid: a single arm pharmacokinetic study.

    Directory of Open Access Journals (Sweden)

    Daniel H Johnson

    Full Text Available Antiretroviral drugs vary in their central nervous system penetration, with better penetration possibly conferring neurocognitive benefit during human immunodeficiency virus (HIV therapy. The efflux transporter gene ABCB1 is expressed in the blood-brain barrier, and an ABCB1 variant (3435C → T has been reported to affect ABCB1 expression. The integrase inhibitor raltegravir is a substrate for ABCB1. We examined whether ABCB1 3435C → T affects raltegravir disposition into cerebrospinal fluid (CSF, and explored associations with polymorphisms in other membrane transporter genes expressed in the blood-brain barrier.Forty healthy, HIV-negative adults of European descent (20 homozygous for ABCB1 3435 C/C, 20 homozygous for 3435 T/T, each group divided equally between males and females were given raltegravir 400 mg twice daily for 7 days. With the final dose, plasma was collected for pharmacokinetic analysis at 9 timepoints over 12 hours, and CSF collected 4 hours post dose.The 4-hour CSF concentration correlated more strongly with 2-hour (r(2=0.76, P=1.12 x 10(-11 than 4-hour (r(2=0.47, P=6.89 x 10(-6 single timepoint plasma concentration, and correlated strongly with partial plasma area-under-the-curve values (AUC0-4h r(2=0.86, P=5.15 x 10(-16. There was no significant association between ABCB1 3435C → T and ratios of CSF-to-plasma AUC or concentration (p>0.05 for each comparison. In exploratory analyses, CSF-to-plasma ratios were not associated with 276 polymorphisms across 16 membrane transporter genes.Among HIV-negative adults, CSF raltegravir concentrations do not differ by ABCB1 3435C → T genotype but strongly correlate with plasma exposure.ClinicalTrials.gov NCT00729924 http://clinicaltrials.gov/show/NCT00729924.

  16. Mutation in the 3'untranslated region of APP as a genetic determinant of cerebral amyloid angiopathy.

    Science.gov (United States)

    Nicolas, Gaël; Wallon, David; Goupil, Claudia; Richard, Anne-Claire; Pottier, Cyril; Dorval, Véronique; Sarov-Rivière, Mariana; Riant, Florence; Hervé, Dominique; Amouyel, Philippe; Guerchet, Maelenn; Ndamba-Bandzouzi, Bebene; Mbelesso, Pascal; Dartigues, Jean-François; Lambert, Jean-Charles; Preux, Pierre-Marie; Frebourg, Thierry; Campion, Dominique; Hannequin, Didier; Tournier-Lasserve, Elisabeth; Hébert, Sébastien S; Rovelet-Lecrux, Anne

    2016-01-01

    Aβ-related cerebral amyloid angiopathy (CAA) is a major cause of primary non-traumatic brain hemorrhage. In families with an early onset of the disease, CAA can be due to amyloid precursor protein (APP) pathogenic variants or duplications. APP duplications lead to a ~1.5-fold increased APP expression, resulting in Aβ overproduction and deposition in the walls of leptomeningeal vessels. We hypothesized that rare variants in the 3'untranslated region (UTR) of APP might lead to APP overexpression in patients with CAA and no APP pathogenic variant or duplication. We performed direct sequencing of the whole APP 3'UTR in 90 patients with CAA and explored the functional consequences of one previously unreported variant. We identified three sequence variants in four patients, of which a two-base pair deletion (c.*331_*332del) was previously unannotated and absent from 175 controls of same ethnicity. This latter variant was associated with increased APP expression in vivo and in vitro. Bioinformatics and functional assays showed that the APP c.*331_*332del variant affected APP messenger RNA (mRNA) structure and binding of two microRNAs (miR-582-3p and miR-892b), providing a mechanism for the observed effects on APP expression. These results identify APP 3'UTR sequence variants as genetic determinants of Aβ-CAA.

  17. Determination of edge plasma parameters by a genetic algorithm analysis of spectral line shapes

    International Nuclear Information System (INIS)

    Marandet, Y.; Genesio, P.; Godbert-Mouret, L.; Koubiti, M.; Stamm, R.; Capes, H.; Guirlet, R.

    2003-01-01

    Comparing an experimental and a theoretical line shape can be achieved by a genetic algorithm (GA) based on an analogy to the mechanisms of natural selection. Such an algorithm is able to deal with complex non-linear models, and can avoid local minima. We have used this optimization tool in the context of edge plasma spectroscopy, for a determination of the temperatures and fractions of the various populations of neutral deuterium emitting the D α line in 2 configurations of Tore-Supra: ergodic divertor and toroidal pumped limiter. Using the GA fit, the neutral emitters are separated into up to 4 populations which can be identified as resulting from molecular dissociation reactions, charge exchange, or reflection. In all the edge plasmas studied, a significant fraction of neutrals emit in the line wings, leading to neutrals with a temperature up to a few hundreds eV if a Gaussian line shape is assumed. This conclusion could be modified if the line wing exhibits a non Gaussian behavior

  18. Genomewide Identification of Genetic Determinants of Antimicrobial Drug Resistance in Pseudomonas aeruginosa▿

    Science.gov (United States)

    Dötsch, Andreas; Becker, Tanja; Pommerenke, Claudia; Magnowska, Zofia; Jänsch, Lothar; Häussler, Susanne

    2009-01-01

    The emergence of antimicrobial drug resistance is of enormous public concern due to the increased risk of delayed treatment of infections, the increased length of hospital stays, the substantial increase in the cost of care, and the high risk of fatal outcomes. A prerequisite for the development of effective therapy alternatives is a detailed understanding of the diversity of bacterial mechanisms that underlie drug resistance, especially for problematic gram-negative bacteria such as Pseudomonas aeruginosa. This pathogen has impressive chromosomally encoded mechanisms of intrinsic resistance, as well as the potential to mutate, gaining resistance to current antibiotics. In this study we have screened the comprehensive nonredundant Harvard PA14 library for P. aeruginosa mutants that exhibited either increased or decreased resistance against 19 antibiotics commonly used in the clinic. This approach identified several genes whose inactivation sensitized the bacteria to a broad spectrum of different antimicrobials and uncovered novel genetic determinants of resistance to various classes of antibiotics. Knowledge of the enhancement of bacterial susceptibility to existing antibiotics and of novel resistance markers or modifiers of resistance expression may lay the foundation for effective therapy alternatives and will be the basis for the development of new strategies in the control of problematic multiresistant gram-negative bacteria. PMID:19332674

  19. Determination of optimum allocation and pricing of distributed generation using genetic algorithm methodology

    Science.gov (United States)

    Mwakabuta, Ndaga Stanslaus

    Electric power distribution systems play a significant role in providing continuous and "quality" electrical energy to different classes of customers. In the context of the present restrictions on transmission system expansions and the new paradigm of "open and shared" infrastructure, new approaches to distribution system analyses, economic and operational decision-making need investigation. This dissertation includes three layers of distribution system investigations. In the basic level, improved linear models are shown to offer significant advantages over previous models for advanced analysis. In the intermediate level, the improved model is applied to solve the traditional problem of operating cost minimization using capacitors and voltage regulators. In the advanced level, an artificial intelligence technique is applied to minimize cost under Distributed Generation injection from private vendors. Soft computing techniques are finding increasing applications in solving optimization problems in large and complex practical systems. The dissertation focuses on Genetic Algorithm for investigating the economic aspects of distributed generation penetration without compromising the operational security of the distribution system. The work presents a methodology for determining the optimal pricing of distributed generation that would help utilities make a decision on how to operate their system economically. This would enable modular and flexible investments that have real benefits to the electric distribution system. Improved reliability for both customers and the distribution system in general, reduced environmental impacts, increased efficiency of energy use, and reduced costs of energy services are some advantages.

  20. An Image Segmentation Based on a Genetic Algorithm for Determining Soil Coverage by Crop Residues

    Science.gov (United States)

    Ribeiro, Angela; Ranz, Juan; Burgos-Artizzu, Xavier P.; Pajares, Gonzalo; Sanchez del Arco, Maria J.; Navarrete, Luis

    2011-01-01

    Determination of the soil coverage by crop residues after ploughing is a fundamental element of Conservation Agriculture. This paper presents the application of genetic algorithms employed during the fine tuning of the segmentation process of a digital image with the aim of automatically quantifying the residue coverage. In other words, the objective is to achieve a segmentation that would permit the discrimination of the texture of the residue so that the output of the segmentation process is a binary image in which residue zones are isolated from the rest. The RGB images used come from a sample of images in which sections of terrain were photographed with a conventional camera positioned in zenith orientation atop a tripod. The images were taken outdoors under uncontrolled lighting conditions. Up to 92% similarity was achieved between the images obtained by the segmentation process proposed in this paper and the templates made by an elaborate manual tracing process. In addition to the proposed segmentation procedure and the fine tuning procedure that was developed, a global quantification of the soil coverage by residues for the sampled area was achieved that differed by only 0.85% from the quantification obtained using template images. Moreover, the proposed method does not depend on the type of residue present in the image. The study was conducted at the experimental farm “El Encín” in Alcalá de Henares (Madrid, Spain). PMID:22163966

  1. Genetically Determined MBL Deficiency Is Associated with Protection against Chronic Cardiomyopathy in Chagas Disease.

    Directory of Open Access Journals (Sweden)

    Paola Rosa Luz

    2016-01-01

    Full Text Available Chagas disease (CD is caused by Trypanosoma cruzi, whose sugar moieties are recognized by mannan binding lectin (MBL, a soluble pattern-recognition molecule that activates the lectin pathway of complement. MBL levels and protein activity are affected by polymorphisms in the MBL2 gene. We sequenced the MBL2 promoter and exon 1 in 196 chronic CD patients and 202 controls. The MBL2*C allele, which causes MBL deficiency, was associated with protection against CD (P = 0.007, OR = 0.32. Compared with controls, genotypes with this allele were completely absent in patients with the cardiac form of the disease (P = 0.003. Furthermore, cardiac patients with genotypes causing MBL deficiency presented less heart damage (P = 0.003, OR = 0.23, compared with cardiac patients having the XA haplotype causing low MBL levels, but fully capable of activating complement (P = 0.005, OR = 7.07. Among the patients, those with alleles causing MBL deficiency presented lower levels of cytokines and chemokines possibly implicated in symptom development (IL9, p = 0.013; PDGFB, p = 0.036 and RANTES, p = 0.031. These findings suggest a protective effect of genetically determined MBL deficiency against the development and progression of chronic CD cardiomyopathy.

  2. Common genetic determinants of intraocular pressure and primary open-angle glaucoma.

    Directory of Open Access Journals (Sweden)

    Leonieke M E van Koolwijk

    Full Text Available Intraocular pressure (IOP is a highly heritable risk factor for primary open-angle glaucoma and is the only target for current glaucoma therapy. The genetic factors which determine IOP are largely unknown. We performed a genome-wide association study for IOP in 11,972 participants from 4 independent population-based studies in The Netherlands. We replicated our findings in 7,482 participants from 4 additional cohorts from the UK, Australia, Canada, and the Wellcome Trust Case-Control Consortium 2/Blue Mountains Eye Study. IOP was significantly associated with rs11656696, located in GAS7 at 17p13.1 (p=1.4×10(-8, and with rs7555523, located in TMCO1 at 1q24.1 (p=1.6×10(-8. In a meta-analysis of 4 case-control studies (total N = 1,432 glaucoma cases, both variants also showed evidence for association with glaucoma (p=2.4×10(-2 for rs11656696 and p=9.1×10(-4 for rs7555523. GAS7 and TMCO1 are highly expressed in the ciliary body and trabecular meshwork as well as in the lamina cribrosa, optic nerve, and retina. Both genes functionally interact with known glaucoma disease genes. These data suggest that we have identified two clinically relevant genes involved in IOP regulation.

  3. Early onset epileptic encephalopathy or genetically determined encephalopathy with early onset epilepsy? Lessons learned from TSC.

    Science.gov (United States)

    Curatolo, Paolo; Aronica, Eleonora; Jansen, Anna; Jansen, Floor; Kotulska, Katarzyna; Lagae, Lieven; Moavero, Romina; Jozwiak, Sergiusz

    2016-03-01

    In tuberous sclerosis complex (TSC) a relationship has been shown between early and refractory seizures and intellectual disability. However, it is uncertain whether epilepsy in TSC is simply a marker in infants who are destined to develop an encephalopathic process or if seizures play a causal role in developing an encephalopathy. This paper summarizes the key points discussed during a European TSC workshop held in Rome, and reviews the experimental and clinical evidence in support of the two theories. There are many factors that influence the appearance of both early seizure onset and the encephalopathy resulting in neurodevelopmental deficits. Experimental studies show that as a consequence of the TSC genes mutation, mammalian target of Rapamycin (mTOR) overactivation determines an alteration in cellular morphology with cytomegalic neurons, altered synaptogenesis and an imbalance between excitation/inhibition, thus providing a likely neuroanatomical substrate for the early appearance of refractory seizures and for the encephalopathic process. At the clinical level, early signs of altered developmental trajectories are often unrecognized before 12 months of age. Evidence from experimental research shows that encephalopathy in TSC might have a genetic cause, and mTOR activation caused by TSC gene mutation can be directly responsible for the early appearance of seizures and encephalopathy. Copyright © 2015 European Paediatric Neurology Society. Published by Elsevier Ltd. All rights reserved.

  4. Measurement of inclusive jet production in deep-inelastic scattering at high Q{sup 2} and determination of the strong coupling

    Energy Technology Data Exchange (ETDEWEB)

    Aktas, A. [DESY, Hamburg (Germany); Alexa, C. [National Institute for Physics and Nuclear Engineering (NIPNE), Bucharest (Romania); Andreev, V. [Lebedev Physical Institute, Moscow (RU)] (and others)

    2007-05-15

    Inclusive jet production is studied in neutral current deep-inelastic positron-proton scattering at large four momentum transfer squared Q{sup 2} > 150 GeV{sup 2} with the H1 detector at HERA. Single and double differential inclusive jet cross sections are measured as a function of Q{sup 2} and of the transverse energy E{sub T} of the jets in the Breit frame. The measurements are found to be well described by calculations at next-to-leading order in perturbative QCD. The running of the strong coupling is demonstrated and the value of {alpha}{sub s}(M{sub Z}) is determined. The ratio of the inclusive jet cross section to the inclusive neutral current cross section is also measured and used to extract a precise value for {alpha}{sub s}(M{sub Z})=0.1193{+-}0.0014(exp.){sup +0.0047}{sub -0.0030}(th.){+-}0.0016(pdf). (orig.)

  5. Measurement of multijet production in ep collisions at high Q{sup 2} and determination of the strong coupling α{sub s}

    Energy Technology Data Exchange (ETDEWEB)

    Andreev, V.; Belousov, A.; Fomenko, A.; Gogitidze, N.; Lebedev, A.; Malinovski, E.; Rusakov, S.; Vazdik, Y. [Lebedev Physical Institute, Moscow (Russian Federation); Baghdasaryan, A.; Zohrabyan, H. [Yerevan Physics Institute, Yerevan (Armenia); Begzsuren, K.; Ravdandorj, T.; Tseepeldorj, B. [Institute of Physics and Technology of the Mongolian Academy of Sciences, Ulaanbaatar (Mongolia); Belov, P.; Brinkmann, M.; Britzger, D.; Campbell, A.J.; Dodonov, V.; Eckerlin, G.; Elsen, E.; Fleischer, M.; Gayler, J.; Ghazaryan, S.; Glazov, A.; Gouzevitch, M.; Haidt, D.; Kleinwort, C.; Krueger, K.; Levonian, S.; Lipka, K.; List, B.; List, J.; Lobodzinski, B.; Meyer, A.B.; Meyer, J.; Niebuhr, C.; Olsson, J.E.; Ozerov, D.; Pahl, P.; Petrukhin, A.; Pirumov, H.; Pitzl, D.; Placakyte, R.; Radescu, V.; Schmitt, S.; Sefkow, F.; Shushkevich, S.; South, D.; Steder, M.; Wuensch, E. [DESY, Hamburg (Germany); Boudry, V.; Specka, A. [LLR, Ecole Polytechnique, CNRS/IN2P3, Palaiseau (France); Brandt, G. [Oxford University, Department of Physics, Oxford (United Kingdom); Brisson, V.; Jacquet, M.; Pascaud, C.; Zhang, Z.; Zomer, F. [LAL, Universite Paris-Sud, CNRS/IN2P3, Orsay (France); Buniatyan, A.; Newman, P.R.; Thompson, P.D. [University of Birmingham, School of Physics and Astronomy, Birmingham (United Kingdom); Bylinkin, A.; Bystritskaya, L.; Fedotov, A.; Rostovtsev, A. [Institute for Theoretical and Experimental Physics, Moscow (Russian Federation); Cantun Avila, K.B.; Contreras, J.G. [CINVESTAV, Departamento de Fisica Aplicada, Merida, Yucatan (Mexico); Ceccopieri, F.; Favart, L.; Grebenyuk, A.; Hreus, T.; Janssen, X.; Roosen, R.; Mechelen, P. van [Inter-University Institute for High Energies ULB-VUB, Brussels and Universiteit Antwerpen, Antwerp (Belgium); Cerny, K.; Pokorny, B.; Polifka, R.; Salek, D.; Valkarova, A.; Zacek, J.; Zlebcik, R. [Charles University, Faculty of Mathematics and Physics, Pragua (Czech Republic); Chekelian, V.; Grindhammer, G.; Kiesling, C. [Max-Planck-Institut fuer Physik, Munich (Germany); Dainton, J.B.; Gabathuler, E.; Greenshaw, T.; Klein, M.; Kostka, P.; Kretzschmar, J.; Laycock, P.; Maxfield, S.J.; Mehta, A.; Patel, G.D. [University of Liverpool, Department of Physics, Liverpool (United Kingdom); Daum, K.; Meyer, H. [Fachbereich C, Universitaet Wuppertal, Wuppertal (Germany); Diaconu, C.; Hoffmann, D.; Sauvan, E.; Vallee, C. [CPPM, Aix-Marseille University, CNRS/IN2P3, Marseille (France); Dobre, M.; Rotaru, M. [National Institute for Physics and Nuclear Engineering (NIPNE), Bucharest (Romania); Dossanov, A. [Universitaet Hamburg, Institut fuer Experimentalphysik, Hamburg (Germany); Max-Planck-Institut fuer Physik, Munich (Germany); Egli, S.; Horisberger, R. [Paul Scherrer Institut, Villigen (Switzerland); Feltesse, J.; Perez, E.; Schoeffel, L. [CEA, DSM/Irfu, CE-Saclay, Gif-sur-Yvette (France); Ferencei, J. [Slovak Academy of Sciences, Institute of Experimental Physics, Kosice (Slovakia); Goerlich, L.; Mikocki, S.; Nowak, G.; Sopicki, P.; Turnau, J. [Institute for Nuclear Physics, Krakow (Poland); Grab, C. [Institut fuer Teilchenphysik, ETH, Zurich (Switzerland); Henderson, R.C.W. [University of Lancaster, Department of Physics, Lancaster (United Kingdom); Herbst, M.; Schultz-Coulon, H.C. [Universitaet Heidelberg, Kirchhoff-Institut fuer Physik, Heidelberg (Germany); Hladka, J.; Reimer, P. [Academy of Sciences of the Czech Republic, Institute of Physics, Prague (Czech Republic); Huber, F.; Sauter, M.; Schoening, A. [Universitaet Heidelberg, Physikalisches Institut, Heidelberg (Germany); Jung, H. [Inter-University Institute for High Energies ULB-VUB, Brussels and Universiteit Antwerpen, Antwerp (Belgium); DESY, Hamburg (Germany); Kapichine, M.; Morozov, A.; Spaskov, V. [Joint Institute for Nuclear Research, Dubna (Russian Federation); Kogler, R. [Universitaet Hamburg, Institut fuer Experimentalphysik, Hamburg (Germany); Landon, M.P.J.; Rizvi, E.; Traynor, D. [Queen Mary, University of London, School of Physics and Astronomy, London (United Kingdom); Lange, W.; Naumann, T. [DESY, Zeuthen (Germany); Martyn, H.U. [I. Physikalisches Institut der RWTH, Aachen (Germany); Mueller, K.; Robmann, P.; Straumann, U.; Truoel, P. [Physik-Institut der Universitaet Zuerich, Zurich (Switzerland); Picuric, I.; Raicevic, N. [University of Montenegro, Faculty of Science, Podgorica (Montenegro); Sankey, D.P.C. [STFC, Rutherford Appleton Laboratory, Didcot, Oxfordshire (United Kingdom); Soloviev, Y. [DESY, Hamburg (Germany); Lebedev Physical Institute, Moscow (Russian Federation); Stella, B. [Universita di Roma Tre, Dipartimento di Fisica, Rome (Italy); INFN Roma 3 (Italy); Sykora, T. [Inter-University Institute for High Energies ULB-VUB, Brussels and Universiteit Antwerpen, Antwerp (Belgium); Charles University, Faculty of Mathematics and Physics, Pragua (Czech Republic); Tsakov, I. [Institute for Nuclear Research and Nuclear Energy, Sofia (Bulgaria); Wegener, D. [Institut fuer Physik, TU Dortmund, Dortmund (Germany); Collaboration: H1 Collaboration

    2015-02-01

    Inclusive jet, dijet and trijet differential cross sections aremeasured in neutral current deep-inelastic scattering for exchanged boson virtualities 150 < Q{sup 2} < 15 000 GeV{sup 2} using the H1 detector at HERA. The data were taken in the years 2003 to 2007 and correspond to an integrated luminosity of 351 pb{sup -1}. Double differential jet cross sections are obtained using a regularised unfolding procedure. They are presented as a function of Q{sup 2} and the transverse momentum of the jet, P{sub T}{sup jet}, and as a function of Q{sup 2} and the proton's longitudinal momentum fraction, ξ, carried by the parton participating in the hard interaction. In addition normalised double differential jet cross sections aremeasured as the ratio of the jet cross sections to the inclusive neutral current cross sections in the respective Q{sup 2} bins of the jet measurements. Compared to earlier work, the measurements benefit from an improved reconstruction and calibration of the hadronic final state. The cross sections are compared to perturbative QCD calculations in next-to-leading order and are used to determine the running coupling and the value of the strong coupling constant as α{sub s}(MZ) = 0.1165 (8){sub exp} (38){sub pdf,theo}. (orig.)

  6. Genetic and Environmental Determinants of Otitis Media in an Indigenous Filipino Population.

    Science.gov (United States)

    Santos-Cortez, Regie Lyn P; Reyes-Quintos, Ma Rina T; Tantoco, Ma Leah C; Abbe, Izoduwa; Llanes, Erasmo Gonzalo D V; Ajami, Nadim J; Hutchinson, Diane S; Petrosino, Joseph F; Padilla, Carmencita D; Villarta, Romeo L; Gloria-Cruz, Teresa Luisa; Chan, Abner L; Cutiongco-de la Paz, Eva Maria; Chiong, Charlotte M; Leal, Suzanne M; Abes, Generoso T

    2016-11-01

    To identify genetic and environmental risk factors for otitis media in an indigenous Filipino population. Cross-sectional study. Indigenous Filipino community. Clinical history and information on breastfeeding, tobacco smoke exposure, and swimming were obtained from community members. Heads of households were interviewed for family history and personal beliefs on ear health. Height and weight were measured. Otoscopic findings were described for the presence and character of perforation or discharge. An A2ML1 duplication variant that confers otitis media susceptibility was Sanger sequenced in all DNA samples. Co-occurrence of middle ear bacteria detected by 16S rRNA gene sequencing was determined according to A2ML1 genotype and social cluster. The indigenous Filipino population has a ~50% prevalence of otitis media. Young age was associated with otitis media (4 age strata; P = .004); however, age was nonsignificant as a bistratal or continuous variable. There was no association between otitis media and sex, body mass index, breastfeeding, tobacco exposure, or deep swimming. In multivariate analyses, A2ML1 genotype is the strongest predictor of otitis media, with an odds ratio of 3.7 (95% confidence interval: 1.3-10.8; P = .005). When otitis media diagnoses were plotted across ages, otitis media was observed within the first year of life, and chronic otitis media persisted up to adulthood, particularly in A2ML1-variant carriers. Among indigenous Filipinos, A2ML1 genotype is the primary risk factor for otitis media and main determinant of disease progression, although age, the middle ear microbiome, and social clusters might modulate the effect of the A2ML1 genotype. © American Academy of Otolaryngology—Head and Neck Surgery Foundation 2016.

  7. 78 FR 13302 - Syngenta Biotechnology, Inc.; Determination of Nonregulated Status of Corn Genetically Engineered...

    Science.gov (United States)

    2013-02-27

    ... and products altered or produced through genetic engineering that are plant pests or that there is... regulations in 7 CFR part 340, ``Introduction of Organisms and Products Altered or Produced Through Genetic Engineering Which Are Plant Pests or Which There Is Reason to Believe Are Plant Pests,'' regulate, among other...

  8. 76 FR 63279 - Monsanto Co.; Determination of Nonregulated Status for Soybean Genetically Engineered for Insect...

    Science.gov (United States)

    2011-10-12

    ... and products altered or produced through genetic engineering that are plant pests or that there is... regulations in 7 CFR part 340, ``Introduction of Organisms and Products Altered or Produced Through Genetic Engineering Which Are Plant Pests or Which There Is Reason to Believe Are Plant Pests,'' regulate, among other...

  9. 77 FR 41350 - Monsanto Co.; Determination of Nonregulated Status of Soybean Genetically Engineered To Produce...

    Science.gov (United States)

    2012-07-13

    ... and products altered or produced through genetic engineering that are plant pests or that there is... regulations in 7 CFR part 340, ``Introduction of Organisms and Products Altered or Produced Through Genetic Engineering Which Are Plant Pests or Which There Is Reason to Believe Are Plant Pests,'' regulate, among other...

  10. 76 FR 80869 - Monsanto Co.; Determination of Nonregulated Status of Corn Genetically Engineered for Drought...

    Science.gov (United States)

    2011-12-27

    ... and products altered or produced through genetic engineering that are plant pests or that there is... in 7 CFR part 340, ``Introduction of Organisms and Products Altered or Produced Through Genetic Engineering Which Are Plant Pests or Which There Is Reason to Believe Are Plant Pests,'' regulate, among other...

  11. 76 FR 5780 - Determination of Regulated Status of Alfalfa Genetically Engineered for Tolerance to the...

    Science.gov (United States)

    2011-02-02

    ... part 340, ``Introduction of Organisms and Products Altered or Produced Through Genetic Engineering... and products altered or produced through genetic engineering that are plant pests or that there is... California by the Center for Food Safety, other associations, and several organic alfalfa growers. The...

  12. [Determining mitochondrial molecular markers suitable for genetic diversity analysis of Cordyceps militaris].

    Science.gov (United States)

    Zhang, Yongjie; Guo, Lihong; Zhang, Shu; Liu, Xingzhong

    2015-07-04

    To screen efficient molecular markers suitable for genetic diversity analysis of Cordyceps militaris from mitochondrial DNA. We amplified 12 mitochondrial DNA fragments and 3 nuclear DNA fragments from each of 20 C. militaris isolates and analyzed nucleotide variations on these DNA fragments. We revealed a greatly higher genetic variation in mitochondrial DNA fragments than in nuclear DNA fragments. Specifically, C. militaris isolates exhibited intron presence/absence diversity in some mitochondrial fragments, and more variable sites were found in mitochondrial fragments than in nuclear fragments. The extent of nucleotide variations also varied by mitochondrial fragment, and intronic proteins seemed to be more vulnerable to amino acid changes than exonic proteins. Genetic diversity increased with the number of molecular markers used. We recommended using (in order) nad3-cox2. cox2-nad5, cox2, cox3, cob, and cox1 for future genetic diversity and population genetic studies of C. militaris.

  13. Genetic adaptation of Pseudomonas aeruginosa during chronic lung infection of patients with cystic fibrosis: strong and weak mutators with heterogeneous genetic backgrounds emerge in mucA and/or lasR mutants

    DEFF Research Database (Denmark)

    Ciofu, Oana; Mandsberg, Lotte F.; Bjarnsholt, Thomas

    2010-01-01

    During the chronic lung infection of patients with cystic fibrosis (CF), Pseudomonas aeruginosa can survive for long periods due to adaptive evolution mediated by genetic variation. Hypermutability is considered to play an important role in this adaptive evolution and it has been demonstrated...

  14. The interaction of genetic determinants in the outcome of HCV infection: evidence for discrete immunological pathways.

    Science.gov (United States)

    Hydes, T J; Moesker, B; Traherne, J A; Ashraf, S; Alexander, G J; Dimitrov, B D; Woelk, C H; Trowsdale, J; Khakoo, S I

    2015-10-01

    Diversity within the innate and adaptive immune response to hepatitis C is important in determining spontaneous resolution (SR) and treatment response. The aim of this study was to analyze how these variables interact in combination; furthering our understanding of the mechanisms that drive successful immunological clearance. Multivariate analysis was performed on retrospectively collected data for 357 patients previously genotyped for interferon (IFN)-λ3/4, killer cell immunoglobulin (KIR), human leukocyte antigen (HLA) class I and II and tapasin. High resolution KIR genotyping was performed for individuals with chronic infection and haplotypes determined. Outcomes for SR, IFN response and cirrhosis were examined. Statistical analysis included univariate methods, χ(2) test for trend, multivariate logistic regression, synergy and principal component analysis (PCA). Although KIR2DL3:HLA-C1C1 (P = 0.027), IFN-λ3/4 rs12979860 CC (P = 0.027), tapasin G in individuals with aspartate at residue 114 of HLA-B (TapG:HLA-B(114D) ) (P = 0.007) and HLA-DRB1*04:01 (P = 0.014) were associated with SR with a strong additive influence (χ(2) test for trend P < 0.0001); favorable polymorphisms did not interact synergistically, nor did patients cluster by outcome. In the treatment cohort, IFN-λ3/4 rs12979860 CC was protective in hepatitis C virus (HCV) G1 infection and KIR2DL3:HLA-C1 in HCV G2/3. In common with SR, variables did not interact synergistically. Polymorphisms predictive of viral clearance did not predict disease progression. In summary, different individuals resolve HCV infection using discrete and non-interacting immunological pathways. These pathways are influenced by viral genotype. This work provides novel insights into the complexity of the interaction between host and viral factors in determining the outcome of HCV infection. © 2015 The Authors. Tissue Antigens published by John Wiley & Sons Ltd.

  15. Genetic determinants of LDL, lipoprotein(a), triglyceride-rich lipoproteins and HDL: concordance and discordance with cardiovascular disease risk

    DEFF Research Database (Denmark)

    Nordestgaard, Børge G; Tybjærg-Hansen, Anne

    2011-01-01

    To evaluate whether new and known genetic determinants of plasma levels of LDL cholesterol, lipoprotein(a), triglyceride-rich lipoproteins, and HDL cholesterol associate with the risk of cardiovascular disease expected from the effect on lipoprotein levels. Concordance or discordance...

  16. Performance Analysis of Combined Methods of Genetic Algorithm and K-Means Clustering in Determining the Value of Centroid

    Science.gov (United States)

    Adya Zizwan, Putra; Zarlis, Muhammad; Budhiarti Nababan, Erna

    2017-12-01

    The determination of Centroid on K-Means Algorithm directly affects the quality of the clustering results. Determination of centroid by using random numbers has many weaknesses. The GenClust algorithm that combines the use of Genetic Algorithms and K-Means uses a genetic algorithm to determine the centroid of each cluster. The use of the GenClust algorithm uses 50% chromosomes obtained through deterministic calculations and 50% is obtained from the generation of random numbers. This study will modify the use of the GenClust algorithm in which the chromosomes used are 100% obtained through deterministic calculations. The results of this study resulted in performance comparisons expressed in Mean Square Error influenced by centroid determination on K-Means method by using GenClust method, modified GenClust method and also classic K-Means.

  17. Regularized unfolding of jet cross sections in deep-inelastic ep scattering at HERA and determination of the strong coupling constant

    Energy Technology Data Exchange (ETDEWEB)

    Britzger, Daniel Andreas

    2013-10-15

    In this thesis double-differential cross sections for jet production in neutral current deep-inelastic e{sup {+-}}p scattering (DIS) are presented at the center-of-mass energy of {radical}(s)=319 GeV, and in the kinematic range of the squared four-momentum transfer 150< Q{sup 2}<15 000 GeV{sup 2} and the inelasticity 0.2determine the strong coupling constant {alpha}{sub s}(M{sub Z}) at the scale of the mass of the Z{sup 0} boson in the framework of perturbative quantum chromodynamics in next-to-leading order. Values are derived separately for the absolute

  18. Variability in alkaloid profiles in neotropical poison frogs (Dendrobatidae): genetic versus environmental determinants.

    Science.gov (United States)

    Daly, J W; Secunda, S I; Garraffo, H M; Spande, T F; Wisnieski, A; Nishihira, C; Cover, J F

    1992-08-01

    Dendrobatid frogs produce a diverse set of alkaloids, whose profiles appear characteristic of frogs of each species or, in the case of variable species, of each population. In the case of one widespread species, Dendrobates auratus, alkaloid profiles in extracts of skin are markedly different in three populations, one from a Pacific island, Isla Taboga, Panama, one from central mountains in Panama, and the third from the Caribbean coast in Costa Rica. The first contains three major classes of dendrobatid alkaloids, the histrionicotoxins, the pumiliotoxin-A class and the decahydroquinolines. The second contains mainly histrionicotoxins, pumiliotoxin-A class alkaloids and one indolizidine. The third contains histrionicotoxins, a homopumiliotoxin, one decahydroquinoline, and a variety of indolizidines, quinolizidines and pyrrolizidines. Frogs from Isla Taboga or a nearby island were introduced into the Manoa Valley, Oahu, Hawaii, in 1932. Remarkably, although alkaloids of the pumiliotoxin-A class and one decahydroquinoline are still major constituents in skin extracts of Hawaiian frogs descended from the 1932 founding population, histrionicotoxins are absent and a novel tricyclic alkaloid is present. Offspring of wild-caught parents from Hawaii, Panama or Costa Rica raised in indoor terrariums on a diet of crickets and fruit flies do not contain detectable amounts of skin alkaloids. Offspring raised in large outside terrariums in Hawaii and fed mainly wild-caught termites and fruit flies do contain the same profile of alkaloids as their wild-caught parents in Hawaii, but at reduced levels. The genetic, environmental and dietary determinants of alkaloid profiles in dendrobatid frogs remain obscure, in particular the underlying cause for total absence in terrarium-reared frogs.

  19. Behavioral versus genetic determination of lipoproteins andidentical twins discordant for exercise

    Energy Technology Data Exchange (ETDEWEB)

    Williams, Paul T.; Blanche, Patricia J.; Krauss, Ronald M.

    2004-06-01

    Lipoprotein and weight differences between vigorously active and sedentary MZ twins are used to: (1) estimate the effects of training while controlling for genotype; (2) estimate genetic concordance in the presence of divergent lifestyles.

  20. Thelytokous parthenogenesis, male clonality and genetic caste determination in the little fire ant: new evidence and insights from the lab.

    Science.gov (United States)

    Foucaud, J; Estoup, A; Loiseau, A; Rey, O; Orivel, J

    2010-08-01

    Previous studies indicate that some populations of the little fire ant, Wasmannia auropunctata, display an unusual reproduction system polymorphism. Although some populations have a classical haplodiploid reproduction system, in other populations queens are produced by thelytokous parthenogenesis, males are produced by a male clonality system and workers are produced sexually. An atypical genetic caste determination system was also suggested. However, these conclusions were indirectly inferred from genetic studies on field population samples. Here we set up experimental laboratory nests that allow the control of the parental relationships between individuals. The queens heading those nests originated from either putatively clonal or sexual populations. We characterized the male, queen and worker offspring they produced at 12 microsatellite loci. Our results unambiguously confirm the unique reproduction system polymorphism mentioned above and that male clonality is strictly associated with thelytokous parthenogenesis. We also observed direct evidence of the rare production of sexual gynes and arrhenotokous males in clonal populations. Finally, we obtained evidence of a genetic basis for caste determination. The evolutionary significance of the reproduction system polymorphism and genetic caste determination as well as future research opportunities are discussed.

  1. Genetic Relationship among Three Subspecies of Oncorhynchus masou Determined by Mitochondrial DNA Sequence Analysis

    OpenAIRE

    Ichiro, Oohara; Toshio, Okazaki; National Research Institute of Aquaculture; National Research Institute of Aquaculture

    1996-01-01

    It is generally accepted that there are 3 subspecies of Oncorhynchus masou in Japan, namely, Masu salmon (Oncorhynchus masou masou (Brevoort)), Amago salmon (O. masou ishikawae Jordan & McGregor), and Biwa salmon (O. masou rhodurus Jordan & McGregor or O. masou subsp. Kimura). Since the genetic relationship of these three taxa is not well known, there has been considerable confusion over their nomenclature. We have clarified the genetic relationship among these three taxa by partially sequenc...

  2. Demographic Histories, Isolation and Social Factors as Determinants of the Genetic Structure of Alpine Linguistic Groups

    Science.gov (United States)

    Coia, Valentina; Capocasa, Marco; Anagnostou, Paolo; Pascali, Vincenzo; Scarnicci, Francesca; Boschi, Ilaria; Battaggia, Cinzia; Crivellaro, Federica; Ferri, Gianmarco; Alù, Milena; Brisighelli, Francesca; Busby, George B. J.; Capelli, Cristian; Maixner, Frank; Cipollini, Giovanna; Viazzo, Pier Paolo; Zink, Albert; Destro Bisol, Giovanni

    2013-01-01

    Great European mountain ranges have acted as barriers to gene flow for resident populations since prehistory and have offered a place for the settlement of small, and sometimes culturally diverse, communities. Therefore, the human groups that have settled in these areas are worth exploring as an important potential source of diversity in the genetic structure of European populations. In this study, we present new high resolution data concerning Y chromosomal variation in three distinct Alpine ethno-linguistic groups, Italian, Ladin and German. Combining unpublished and literature data on Y chromosome and mitochondrial variation, we were able to detect different genetic patterns. In fact, within and among population diversity values observed vary across linguistic groups, with German and Italian speakers at the two extremes, and seem to reflect their different demographic histories. Using simulations we inferred that the joint effect of continued genetic isolation and reduced founding group size may explain the apportionment of genetic diversity observed in all groups. Extending the analysis to other continental populations, we observed that the genetic differentiation of Ladins and German speakers from Europeans is comparable or even greater to that observed for well known outliers like Sardinian and Basques. Finally, we found that in south Tyroleans, the social practice of Geschlossener Hof, a hereditary norm which might have favored male dispersal, coincides with a significant intra-group diversity for mtDNA but not for Y chromosome, a genetic pattern which is opposite to those expected among patrilocal populations. Together with previous evidence regarding the possible effects of “local ethnicity” on the genetic structure of German speakers that have settled in the eastern Italian Alps, this finding suggests that taking socio-cultural factors into account together with geographical variables and linguistic diversity may help unveil some yet to be understood

  3. Demographic histories, isolation and social factors as determinants of the genetic structure of Alpine linguistic groups.

    Directory of Open Access Journals (Sweden)

    Valentina Coia

    Full Text Available Great European mountain ranges have acted as barriers to gene flow for resident populations since prehistory and have offered a place for the settlement of small, and sometimes culturally diverse, communities. Therefore, the human groups that have settled in these areas are worth exploring as an important potential source of diversity in the genetic structure of European populations. In this study, we present new high resolution data concerning Y chromosomal variation in three distinct Alpine ethno-linguistic groups, Italian, Ladin and German. Combining unpublished and literature data on Y chromosome and mitochondrial variation, we were able to detect different genetic patterns. In fact, within and among population diversity values observed vary across linguistic groups, with German and Italian speakers at the two extremes, and seem to reflect their different demographic histories. Using simulations we inferred that the joint effect of continued genetic isolation and reduced founding group size may explain the apportionment of genetic diversity observed in all groups. Extending the analysis to other continental populations, we observed that the genetic differentiation of Ladins and German speakers from Europeans is comparable or even greater to that observed for well known outliers like Sardinian and Basques. Finally, we found that in south Tyroleans, the social practice of Geschlossener Hof, a hereditary norm which might have favored male dispersal, coincides with a significant intra-group diversity for mtDNA but not for Y chromosome, a genetic pattern which is opposite to those expected among patrilocal populations. Together with previous evidence regarding the possible effects of "local ethnicity" on the genetic structure of German speakers that have settled in the eastern Italian Alps, this finding suggests that taking socio-cultural factors into account together with geographical variables and linguistic diversity may help unveil some yet

  4. Shortest-path network analysis is a useful approach toward identifying genetic determinants of longevity.

    Directory of Open Access Journals (Sweden)

    J R Managbanag

    Full Text Available BACKGROUND: Identification of genes that modulate longevity is a major focus of aging-related research and an area of intense public interest. In addition to facilitating an improved understanding of the basic mechanisms of aging, such genes represent potential targets for therapeutic intervention in multiple age-associated diseases, including cancer, heart disease, diabetes, and neurodegenerative disorders. To date, however, targeted efforts at identifying longevity-associated genes have been limited by a lack of predictive power, and useful algorithms for candidate gene-identification have also been lacking. METHODOLOGY/PRINCIPAL FINDINGS: We have utilized a shortest-path network analysis to identify novel genes that modulate longevity in Saccharomyces cerevisiae. Based on a set of previously reported genes associated with increased life span, we applied a shortest-path network algorithm to a pre-existing protein-protein interaction dataset in order to construct a shortest-path longevity network. To validate this network, the replicative aging potential of 88 single-gene deletion strains corresponding to predicted components of the shortest-path longevity network was determined. Here we report that the single-gene deletion strains identified by our shortest-path longevity analysis are significantly enriched for mutations conferring either increased or decreased replicative life span, relative to a randomly selected set of 564 single-gene deletion strains or to the current data set available for the entire haploid deletion collection. Further, we report the identification of previously unknown longevity genes, several of which function in a conserved longevity pathway believed to mediate life span extension in response to dietary restriction. CONCLUSIONS/SIGNIFICANCE: This work demonstrates that shortest-path network analysis is a useful approach toward identifying genetic determinants of longevity and represents the first application of

  5. Prevalence of Genetic Determinants and Phenotypic Resistance to Ciprofloxacin in Campylobacter jejuni from Lithuania

    Directory of Open Access Journals (Sweden)

    Jurgita Aksomaitiene

    2018-02-01

    Full Text Available Recently, the number of reports on isolation of ciprofloxacin resistant Campylobacter jejuni has increased worldwide. The aim of this study was to determine the prevalence of resistance to ciprofloxacin and its genetic determinants among C. jejuni isolated from humans (n = 100, poultry products (n = 96 and wild birds (n = 96 in Lithuania. 91.4% of the C. jejuni isolates were phenotypically resistant to ciprofloxacin. DNA sequence analyses of the gyrA gene from 292 isolates revealed that a change in amino acid sequence, Thr86Ile, was the main substition conferring resistance to ciprofloxacin. This change was significantly associated with isolates from poultry products (P < 0.05 and humans (P < 0.05. A total of 26.7% of C. jejuni isolates from human (n = 47, poultry products (n = 30 and wild bird (n = 1, had a mutation from Ser at position 22, and six had an additional mutation from Ala at position 39. Eight isolates from poultry and two isolates from human, corresponding to 67.0% of isolates with MICs ≥128 μg/ml, showed missense mutations Thr86Ile (ACA → ATA and Ser22Gly (AGT → GGT together, whereas isolates without these mutations showed lower MIC values (from 4 to 64 μg/ml. Two hundred forty-five C. jejuni isolates showed one or more silent mutations, and 32.4% of examined isolates possessed six silent mutations. In addition to the ciprofloxacin resistant isolates harboring only Thr86Ile point mutation (110 isolates, the current study identified resistant isolates (n = 101 harboring additional point mutations (Ser22Gly, Ala39Ser, Arg48Lys, Thr85Ala Ala122Ser, Glu136Asp, Vall49Ile, and strains (n = 57 having only Glu136Asp point mutation. The study highlight the potential public health problem with elevated ciprofloxacin resistance in Campylobacters from poultry meat, wild birds and humans, and the need for extensive surveillance enabling to follow changes of antimicrobial resistance development in this species.

  6. Patterns of DNA methylation in development, division of labor and hybridization in an ant with genetic caste determination.

    Science.gov (United States)

    Smith, Chris R; Mutti, Navdeep S; Jasper, W Cameron; Naidu, Agni; Smith, Christopher D; Gadau, Jürgen

    2012-01-01

    DNA methylation is a common regulator of gene expression, including acting as a regulator of developmental events and behavioral changes in adults. Using the unique system of genetic caste determination in Pogonomyrmex barbatus, we were able to document changes in DNA methylation during development, and also across both ancient and contemporary hybridization events. Sodium bisulfite sequencing demonstrated in vivo methylation of symmetric CG dinucleotides in P. barbatus. We also found methylation of non-CpG sequences. This validated two bioinformatics methods for predicting gene methylation, the bias in observed to expected ratio of CpG dinucleotides and the density of CpG/TpG single nucleotide polymorphisms (SNP). Frequencies of genomic DNA methylation were determined for different developmental stages and castes using ms-AFLP assays. The genetic caste determination system (GCD) is probably the product of an ancestral hybridization event between P. barbatus and P. rugosus. Two lineages obligately co-occur within a GCD population, and queens are derived from intra-lineage matings whereas workers are produced from inter-lineage matings. Relative DNA methylation levels of queens and workers from GCD lineages (contemporary hybrids) were not significantly different until adulthood. Virgin queens had significantly higher relative levels of DNA methylation compared to workers. Worker DNA methylation did not vary among developmental stages within each lineage, but was significantly different between the currently hybridizing lineages. Finally, workers of the two genetic caste determination lineages had half as many methylated cytosines as workers from the putative parental species, which have environmental caste determination. These results suggest that DNA methylation may be a conserved regulatory mechanism moderating division of labor in both bees and ants. Current and historic hybridization appear to have altered genomic methylation levels suggesting a possible link

  7. Patterns of DNA methylation in development, division of labor and hybridization in an ant with genetic caste determination.

    Directory of Open Access Journals (Sweden)

    Chris R Smith

    Full Text Available BACKGROUND: DNA methylation is a common regulator of gene expression, including acting as a regulator of developmental events and behavioral changes in adults. Using the unique system of genetic caste determination in Pogonomyrmex barbatus, we were able to document changes in DNA methylation during development, and also across both ancient and contemporary hybridization events. METHODOLOGY/PRINCIPAL FINDINGS: Sodium bisulfite sequencing demonstrated in vivo methylation of symmetric CG dinucleotides in P. barbatus. We also found methylation of non-CpG sequences. This validated two bioinformatics methods for predicting gene methylation, the bias in observed to expected ratio of CpG dinucleotides and the density of CpG/TpG single nucleotide polymorphisms (SNP. Frequencies of genomic DNA methylation were determined for different developmental stages and castes using ms-AFLP assays. The genetic caste determination system (GCD is probably the product of an ancestral hybridization event between P. barbatus and P. rugosus. Two lineages obligately co-occur within a GCD population, and queens are derived from intra-lineage matings whereas workers are produced from inter-lineage matings. Relative DNA methylation levels of queens and workers from GCD lineages (contemporary hybrids were not significantly different until adulthood. Virgin queens had significantly higher relative levels of DNA methylation compared to workers. Worker DNA methylation did not vary among developmental stages within each lineage, but was significantly different between the currently hybridizing lineages. Finally, workers of the two genetic caste determination lineages had half as many methylated cytosines as workers from the putative parental species, which have environmental caste determination. CONCLUSIONS/SIGNIFICANCE: These results suggest that DNA methylation may be a conserved regulatory mechanism moderating division of labor in both bees and ants. Current and historic

  8. Genetic determination of the biological radiation response in inbred mice lines; Genetische Determination der biologischen Strahlenantwort in Mausinzuchtstaemmen

    Energy Technology Data Exchange (ETDEWEB)

    Gomolka, M.; Hornhardt, S.; Jung, T. [Bundesamt fuer Strahlenschutz Oberschleissheim (Germany). Institut fuer Strahlenhygiene

    2000-07-01

    Variation in radiation sensitivity and radiation resistance is influenced by the genetic constitution of an individual. Loss of function of genes involved in DNA repair, cell cycle or controlled cell death can have serious consequences on individual radiation sensitivity. For example, individuals suffering on the clinical syndrome of Ataxia telangiectasia exhibit radiation sensitivity in the order of 2-3 magnitudes higher than other cancer patients. For radiation protection it is important to clarify the role of genetic predisposition for radiation sensitivity in clinical healthy people. Therefore, data were collected from the literature describing the genetic variation (heritability) of radiation sensitivity in the mouse model. A heritability of 30-50% was calculated for 27 inbred mice lines by Roderick (1963) based on days of survival after a daily dose of 1 Gy {gamma}-irradiation. The following inbred lines were described in the literature as radiation sensitive (phenotypical markers were e.g., time of survival, mortality, reduction in fertility post exposure): SWR, RIII, NC, K, HLG, DBA, CBA, BALB/c, A, AKR. Radiation resistance was demonstrated in SJL, SEC, RF, MA, C58, C57BR, BDP and 129. Parameter of longevity, some physiological, biochemical and immunological parameters as given in the data bank of the Jackson Laboratory, U.S.A., were compared between radiation sensitive and radiation resistant inbred strains. No correlation was seen for the most of the parameters except for the development of breast cancer. In 6 out of 10 radiosensitive inbred strains breast cancer is described while only 1 of 8 strains exhibits breast cancer. The higher heritability of 30-50% in spite of a very complex phenotype like survival and the correlation between radiosensitivity and tumour incidence show that individual genetic susceptibility is important on the biological radiation reaction. (orig.) [German] Die phaenotypische Variation der Strahlensensitivitaet und

  9. The use of ISSR markers for species determination and a genetic study of the invasive lionfish in Guanahacabibes, Cuba

    Directory of Open Access Journals (Sweden)

    Elizabeth Labastida

    2015-11-01

    Full Text Available The red lionfish (Pterois volitans and devil fire-fish (Pterois miles are invasive species that pose a threat to the biodiversity and stability of coral reefs in the Western Atlantic, Gulf of Mexico and Caribbean Sea. Species identification of lionfish is uncertain in some parts of Cuba, and research has mainly been focused on their biology and ecology. The principal aim of this study was to determine highly polymorphic markers (Inter Simple Sequence Repeat, ISSR that could be used in research on lionfish population genetics in addition to confirming the presence of Pterois species in the Guanahacabibes National Park. The genetic profile or "fingerprint" of individuals collected in Mexico, formally identified as P. volitans, was compared with the genetic profile of specimens from Cuba. There were very few "diagnostic bands" and a high number of "common bands", demonstrating that the same species exists in both countries. Furthermore, Nei's genetic distance and the unrooted tree do not show significant differences between both localities. In light of these results, we can confirm the presence of P. volitans in the Guanahacabibes National Park, Cuba. This study demonstrates the functionality of ISSR as a molecular tool for species identification and their application for genetic population studies of this invasive fish species.

  10. Environmental versus geographical determinants of genetic structure in two subalpine conifers.

    Science.gov (United States)

    Mosca, Elena; González-Martínez, Santiago C; Neale, David B

    2014-01-01

    Alpine ecosystems are facing rapid human-induced environmental changes, and so more knowledge about tree adaptive potential is needed. This study investigated the relative role of isolation by distance (IBD) versus isolation by adaptation (IBA) in explaining population genetic structure in Abies alba and Larix decidua, based on 231 and 233 single nucleotide polymorphisms (SNPs) sampled across 36 and 22 natural populations, respectively, in the Alps and Apennines. Genetic structure was investigated for both geographical and environmental groups, using analysis of molecular variance (AMOVA). For each species, nine environmental groups were defined using climate variables selected from a multiple factor analysis. Complementary methods were applied to identify outliers based on these groups, and to test for IBD versus IBA. AMOVA showed weak but significant genetic structure for both species, with higher values in L. decidua. Among the potential outliers detected, up to two loci were found for geographical groups and up to seven for environmental groups. A stronger effect of IBD than IBA was found in both species; nevertheless, once spatial effects had been removed, temperature and soil in A. alba, and precipitation in both species, were relevant factors explaining genetic structure. Based on our findings, in the Alpine region, genetic structure seems to be affected by both geographical isolation and environmental gradients, creating opportunities for local adaptation. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

  11. Genetic determination of human facial morphology: links between cleft-lips and normal variation.

    Science.gov (United States)

    Boehringer, Stefan; van der Lijn, Fedde; Liu, Fan; Günther, Manuel; Sinigerova, Stella; Nowak, Stefanie; Ludwig, Kerstin U; Herberz, Ruth; Klein, Stefan; Hofman, Albert; Uitterlinden, Andre G; Niessen, Wiro J; Breteler, Monique M B; van der Lugt, Aad; Würtz, Rolf P; Nöthen, Markus M; Horsthemke, Bernhard; Wieczorek, Dagmar; Mangold, Elisabeth; Kayser, Manfred

    2011-11-01

    Recent genome-wide association studies have identified single nucleotide polymorphisms (SNPs) associated with non-syndromic cleft lip with or without cleft palate (NSCL/P), and other previous studies showed distinctly differing facial distance measurements when comparing unaffected relatives of NSCL/P patients with normal controls. Here, we test the hypothesis that genetic loci involved in NSCL/P also influence normal variation in facial morphology. We tested 11 SNPs from 10 genomic regions previously showing replicated evidence of association with NSCL/P for association with normal variation of nose width and bizygomatic distance in two cohorts from Germany (N=529) and the Netherlands (N=2497). The two most significant associations found were between nose width and SNP rs1258763 near the GREM1 gene in the German cohort (P=6 × 10(-4)), and between bizygomatic distance and SNP rs987525 at 8q24.21 near the CCDC26 gene (P=0.017) in the Dutch sample. A genetic prediction model explained 2% of phenotype variation in nose width in the German and 0.5% of bizygomatic distance variation in the Dutch cohort. Although preliminary, our data provide a first link between genetic loci involved in a pathological facial trait such as NSCL/P and variation of normal facial morphology. Moreover, we present a first approach for understanding the genetic basis of human facial appearance, a highly intriguing trait with implications on clinical practice, clinical genetics, forensic intelligence, social interactions and personal identity.

  12. Determination of deferasirox plasma concentrations: do gender, physical and genetic differences affect chelation efficacy?

    Science.gov (United States)

    Mattioli, Francesca; Puntoni, Matteo; Marini, Valeria; Fucile, Carmen; Milano, Giulia; Robbiano, Luigi; Perrotta, Silverio; Pinto, Valeria; Martelli, Antonietta; Forni, Gian Luca

    2015-04-01

    Bioavailability of deferasirox (DFX) is significantly affected by the timing of administration relative to times and to composition of meals. Its elimination half-life is also highly variable - in some patients as a result of gene polymorphisms. Understanding whether deferasirox plasma levels are related to specific characteristics of patients could help physicians to devise a drug regimen tailored the individual patient. We analyzed deferasirox plasma concentrations (CDFX ) in 80 patients with transfusion-dependent anemias, such as thalassemia, by a high performance liquid chromatography (HPLC) assay. We used a multivariate linear regression model to find significant associations between CDFX and clinical/demographical characteristics of patients. All patients were genotyped for UGT1A1. Fifty-six patients were female, 24 were male, the great majority (88%) affected by β-thalassemia, and 15 were children and adolescents. No statistical correlation was detectable between CDFX and DFX dose (P = 0.6). Age, time from last drug intake to blood sampling, and ferritin levels in the 6 months before study initiation were significantly and inversely associated with CDFX in univariate analysis. In the multivariate analysis, the only two factors independently and inversely associated with CDFX levels were time from last drug intake to blood sampling and ferritin levels (P = 0.006). A significant inverse correlation (P = 0.03) was observed between CDFX and UGT1A1*28 gene polymorphism, but only in patients with levels of lean body mass (LBM) below the median (P for interaction = 0.05). The results could indicate that a higher plasma DFX concentration could be associated with greater chelation efficacy. As a correlation between dose and CDFX was not demonstrated, it seems useful to monitor the concentrations to optimize and determine the most appropriate dose for each patient. Interesting results emerged from the analysis of genetic and physical characteristics of

  13. Microsatellite markers to determine population genetic structure in the golden anchovy, Coilia dussumieri.

    Science.gov (United States)

    Kathirvelpandian, A; Gopalakrishnan, A; Lakra, W S; Krishna, Gopal; Sharma, Rupam; Musammilu, K K; Basheer, V S; Jena, J K

    2014-06-01

    Coilia dussumieri (Valenciennes, 1848) commonly called as golden anchovy, constitutes a considerable fishery in the northern part of both the west and east coasts of India. Despite its clear-cut geographic isolation, the species is treated as a unit stock for fishery management purposes. We evaluated 32 microsatellite primer pairs from three closely related species (resource species) belonging to the family Engraulidae through cross-species amplification in C. dussumieri. Successful cross-priming was obtained with 10 loci, which were sequenced for confirmation of repeats. Loci were tested for delineating the genetic stock structure of four populations of C. dussumieri from both the coasts of India. The number of alleles per locus ranged from 8 to 18, with a mean of 12.3. Results of pairwise F ST indicated genetic stock structuring between the east and west coast populations of India and also validated the utilization of identified microsatellite markers in population genetic structure analysis.

  14. Asymmetrical Damage Partitioning in Bacteria: A Model for the Evolution of Stochasticity, Determinism, and Genetic Assimilation.

    Science.gov (United States)

    Chao, Lin; Rang, Camilla Ulla; Proenca, Audrey Menegaz; Chao, Jasper Ubirajara

    2016-01-01

    Non-genetic phenotypic variation is common in biological organisms. The variation is potentially beneficial if the environment is changing. If the benefit is large, selection can favor the evolution of genetic assimilation, the process by which the expression of a trait is transferred from environmental to genetic control. Genetic assimilation is an important evolutionary transition, but it is poorly understood because the fitness costs and benefits of variation are often unknown. Here we show that the partitioning of damage by a mother bacterium to its two daughters can evolve through genetic assimilation. Bacterial phenotypes are also highly variable. Because gene-regulating elements can have low copy numbers, the variation is attributed to stochastic sampling. Extant Escherichia coli partition asymmetrically and deterministically more damage to the old daughter, the one receiving the mother's old pole. By modeling in silico damage partitioning in a population, we show that deterministic asymmetry is advantageous because it increases fitness variance and hence the efficiency of natural selection. However, we find that symmetrical but stochastic partitioning can be similarly beneficial. To examine why bacteria evolved deterministic asymmetry, we modeled the effect of damage anchored to the mother's old pole. While anchored damage strengthens selection for asymmetry by creating additional fitness variance, it has the opposite effect on symmetry. The difference results because anchored damage reinforces the polarization of partitioning in asymmetric bacteria. In symmetric bacteria, it dilutes the polarization. Thus, stochasticity alone may have protected early bacteria from damage, but deterministic asymmetry has evolved to be equally important in extant bacteria. We estimate that 47% of damage partitioning is deterministic in E. coli. We suggest that the evolution of deterministic asymmetry from stochasticity offers an example of Waddington's genetic assimilation

  15. Strong Cosmic Censorship

    Science.gov (United States)

    Isenberg, James

    2017-01-01

    The Hawking-Penrose theorems tell us that solutions of Einstein's equations are generally singular, in the sense of the incompleteness of causal geodesics (the paths of physical observers). These singularities might be marked by the blowup of curvature and therefore crushing tidal forces, or by the breakdown of physical determinism. Penrose has conjectured (in his `Strong Cosmic Censorship Conjecture`) that it is generically unbounded curvature that causes singularities, rather than causal breakdown. The verification that ``AVTD behavior'' (marked by the domination of time derivatives over space derivatives) is generically present in a family of solutions has proven to be a useful tool for studying model versions of Strong Cosmic Censorship in that family. I discuss some of the history of Strong Cosmic Censorship, and then discuss what is known about AVTD behavior and Strong Cosmic Censorship in families of solutions defined by varying degrees of isometry, and discuss recent results which we believe will extend this knowledge and provide new support for Strong Cosmic Censorship. I also comment on some of the recent work on ``Weak Null Singularities'', and how this relates to Strong Cosmic Censorship.

  16. Genetically Determined Insulin Resistance is Characterized by Down-Regulation of Mitochondrial Oxidative Metabolism in Human Skeletal Muscle

    DEFF Research Database (Denmark)

    Kristensen, Jonas M; Skov, Vibe; Wojtaszewski, Jørgen

    2010-01-01

    Transcriptional profiling of skeletal muscle from patients with type 2 diabetes and high-risk individuals have demonstrated a co-ordinated down-regulation of oxidative phosphorylation (OxPhos) genes, suggesting a link between insulin resistance and mitochondrial dysfunction. However, whether...... mitochondrial dysfunction is a cause or consequence of insulin resistance remains to be clarified. In the present study, we tested the hypothesis that mitochondrial oxidative metabolism was down-regulated in skeletal muscle of patients with genetically determined insulin resistance. Skeletal muscle biopsies.......02), and complex V (ATP5B; p=0.005). Our data demonstrate that genetically determined insulin resistance is associated with a co-ordinated down-regulation of OxPhos components both at the transcriptional and translational level. These findings suggest that an impaired biological response to insulin in skeletal...

  17. Annual cycles of metabolic rate are genetically determined but can be shifted by phenotypic flexibility

    NARCIS (Netherlands)

    Versteegh, M. A.; Helm, B.; Gwinner, E.; Tieleman, B. I.

    2012-01-01

    Birds have adjusted their life history and physiological traits to the characteristics of the seasonally changing environments they inhabit. Annual cycles in physiology can result from phenotypic flexibility or from variation in its genetic basis. A key physiological trait that shows seasonal

  18. Characterization of North American Armillaria species: Genetic relationships determined by ribosomal DNA sequences and AFLP markers

    Science.gov (United States)

    M. -S. Kim; N. B. Klopfenstein; J. W. Hanna; G. I. McDonald

    2006-01-01

    Phylogenetic and genetic relationships among 10 North American Armillaria species were analysed using sequence data from ribosomal DNA (rDNA), including intergenic spacer (IGS-1), internal transcribed spacers with associated 5.8S (ITS + 5.8S), and nuclear large subunit rDNA (nLSU), and amplified fragment length polymorphism (AFLP) markers. Based on rDNA sequence data,...

  19. Markerless Escherichia coli rrn Deletion Strains for Genetic Determination of Ribosomal Binding Sites

    DEFF Research Database (Denmark)

    Quan, Selwyn; Skovgaard, Ole; McLaughlin, Robert E

    2015-01-01

    Single-copy rrn strains facilitate genetic ribosomal studies in Escherichia coli. Consecutive markerless deletion of rrn operons resulted in slower growth upon inactivation of the fourth copy, which was reversed by supplying transfer RNA genes encoded in rrn operons in trans. Removal of the sixth...

  20. Vector choice determines immunogenicity and potency of genetic vaccines against Angola Marburg virus in nonhuman primates

    NARCIS (Netherlands)

    Geisbert, Thomas W.; Bailey, Michael; Geisbert, Joan B.; Asiedu, Clement; Roederer, Mario; Grazia-Pau, Maria; Custers, Jerome; Jahrling, Peter; Goudsmit, Jaap; Koup, Richard; Sullivan, Nancy J.

    2010-01-01

    The immunogenicity and durability of genetic vaccines are influenced by the composition of gene inserts and choice of delivery vector. DNA vectors are a promising vaccine approach showing efficacy when combined in prime-boost regimens with recombinant protein or viral vectors, but they have shown

  1. Incidence, prevalence and genetic determinants of neonatal diabetes mellitus: a systematic review and meta-analysis protocol.

    Science.gov (United States)

    Nansseu, Jobert Richie N; Ngo-Um, Suzanne S; Balti, Eric V

    2016-11-10

    In the absence of existing data, the present review intends to determine the incidence, prevalence and/or genetic determinants of neonatal diabetes mellitus (NDM), with expected contribution to disease characterization. We will include cross-sectional, cohort or case-control studies which have reported the incidence, prevalence and/or genetic determinants of NDM between January 01, 2000 and May 31, 2016, published in English or French languages and without any geographical limitation. PubMed and EMBASE will be extensively screened to identify potentially eligible studies, completed by manual search. Two authors will independently screen, select studies, extract data, and assess the risk of bias; disagreements will be resolved by consensus. Clinical heterogeneity will be investigated by examining the design and setting (including geographic region), procedure used for genetic testing, calculation of incidence or prevalence, and outcomes in each study. Studies found to be clinically homogeneous will be pooled together through a random effects meta-analysis. Statistical heterogeneity will be assessed using the chi-square test of homogeneity and quantified using the I 2 statistic. In case of substantial heterogeneity, subgroup analyses will be undertaken. Publication bias will be assessed with funnel plots, complemented with the use of Egger's test of bias. This systematic review and meta-analysis is expected to draw a clear picture of phenotypic and genotypic presentations of NDM in order to better understand the condition and adequately address challenges in respect with its management. PROSPERO CRD42016039765.

  2. A microsatellite-based genetic linkage map and putative sex-determining genomic regions in Lake Victoria cichlids.

    Science.gov (United States)

    Kudo, Yu; Nikaido, Masato; Kondo, Azusa; Suzuki, Hikoyu; Yoshida, Kohta; Kikuchi, Kiyoshi; Okada, Norihiro

    2015-04-15

    Cichlid fishes in East Africa have undergone extensive adaptive radiation, which has led to spectacular diversity in their morphology and ecology. To date, genetic linkage maps have been constructed for several tilapias (riverine), Astatotilapia burtoni (Lake Tanganyika), and hybrid lines of Lake Malawi cichlids to facilitate genome-wide comparative analyses. In the present study, we constructed a genetic linkage map of the hybrid line of Lake Victoria cichlids, so that maps of cichlids from all the major areas of East Africa will be available. The genetic linkage map shown here is derived from the F2 progeny of an interspecific cross between Haplochromis chilotes and Haplochromis sauvagei and is based on 184 microsatellite and two single-nucleotide polymorphism (SNP) markers. Most of the microsatellite markers used in the present study were originally designed for other genetic linkage maps, allowing us to directly compare each linkage group (LG) among different cichlid groups. We found 25 LGs, the total length of which was 1133.2cM with an average marker spacing of about 6.09cM. Our subsequent linkage mapping analysis identified two putative sex-determining loci in cichlids. Interestingly, one of these two loci is located on cichlid LG5, on which the female heterogametic ZW locus and several quantitative trait loci (QTLs) related to adaptive evolution have been reported in Lake Malawi cichlids. We also found that V1R1 and V1R2, candidate genes for the fish pheromone receptor, are located very close to the recently detected sex-determining locus on cichlid LG5. The genetic linkage map study presented here may provide a valuable foundation for studying the chromosomal evolution of East African cichlids and the possible role of sex chromosomes in generating their genomic diversity. Copyright © 2015 Elsevier B.V. All rights reserved.

  3. Embryonic aneuploidy does not differ among genetic ancestry according to continental origin as determined by ancestry informative markers.

    Science.gov (United States)

    Franasiak, Jason M; Olcha, Meir; Shastri, Shefali; Molinaro, Thomas A; Congdon, Haley; Treff, Nathan R; Scott, Richard T

    2016-10-01

    Is embryonic aneuploidy, as determined by comprehensive chromosome screening (CCS), related to genetic ancestry, as determined by ancestry informative markers (AIMs)? In this study, when determining continental ancestry utilizing AIMs, genetic ancestry does not have an impact on embryonic aneuploidy. Aneuploidy is one of the best-characterized barriers to ART success and little information exists regarding ethnicity and whole chromosome aneuploidy in IVF. Classifying continental ancestry utilizing genetic profiles from a selected group of single nucleotide polymorphisms, termed AIMs, can determine ancestral origin with more accuracy than self-reported data. This is a retrospective cohort study of patients undergoing their first cycle of IVF with CCS at a single center from 2008 to 2014. There were 2328 patients identified whom had undergone IVF/CCS and AIM genotyping. All patients underwent IVF/ICSI and CCS after trophectoderm biopsy. Patients' serum was genotyped using 32 custom AIMs to identify continental origin. Admixture proportions were determined using Bayesian clustering algorithms. Patients were assigned to the population (European, African, East Asian or Central/South Asian) corresponding to their greatest admixture proportion. The mean number of embryos tested was 5.3 (range = 1-40) and the mode was 1. Patients' ethnic classifications revealed European (n = 1698), African (n = 103), East Asian (n = 206) or Central/South Asian (n = 321). When controlling for age and BMI, aneuploidy rate did not differ by genetic ancestry (P = 0.28). The study type (retrospective) and the ability to classify patients by continental rather than sub-continental origin as well as the predominantly European patient mix may impact generalizability. Post hoc power calculation revealed power to detect a 16.8% difference in embryonic aneuploidy between the two smallest sample size groups. These data do not support differences in embryonic aneuploidy among various genetic

  4. The principal genetic determinants for nasopharyngeal carcinoma in China involve the HLA class I antigen recognition groove.

    Directory of Open Access Journals (Sweden)

    Minzhong Tang

    Full Text Available Nasopharyngeal carcinoma (NPC is an epithelial malignancy facilitated by Epstein-Barr Virus infection. Here we resolve the major genetic influences for NPC incidence using a genome-wide association study (GWAS, independent cohort replication, and high-resolution molecular HLA class I gene typing including 4,055 study participants from the Guangxi Zhuang Autonomous Region and Guangdong province of southern China. We detect and replicate strong association signals involving SNPs, HLA alleles, and amino acid (aa variants across the major histocompatibility complex-HLA-A, HLA -B, and HLA -C class I genes (P(HLA-A-aa-site-62 = 7.4 × 10(-29; P (HLA-B-aa-site-116 = 6.5 × 10(-19; P (HLA-C-aa-site-156 = 6.8 × 10(-8 respectively. Over 250 NPC-HLA associated variants within HLA were analyzed in concert to resolve separate and largely independent HLA-A, -B, and -C gene influences. Multivariate logistical regression analysis collapsed significant associations in adjacent genes spanning 500 kb (OR2H1, GABBR1, HLA-F, and HCG9 as proxies for peptide binding motifs carried by HLA- A*11:01. A similar analysis resolved an independent association signal driven by HLA-B*13:01, B*38:02, and B*55:02 alleles together. NPC resistance alleles carrying the strongly associated amino acid variants implicate specific class I peptide recognition motifs in HLA-A and -B peptide binding groove as conferring strong genetic influence on the development of NPC in China.

  5. Strong Impact of an Axial Ligand on the Absorption by Chlorophyll a and b Pigments Determined by Gas-Phase Ion Spectroscopy Experiments

    DEFF Research Database (Denmark)

    Kjaer, Christina; Stockett, Mark H.; Pedersen, Bjarke Møller

    2016-01-01

    The microenvironments in photosynthetic proteins affect the absorption by chlorophyll (Chl) pigments. It is, however, a challenge to disentangle the impact on the transition energies of different perturbations, for example, the global electrostatics of the protein (nonbonded environmental effects......), exciton coupling between Chl's, conformational variations, and binding of an axial ligand to the magnesium center. This is needed to distinguish between the two most commonly proposed mechanisms for energy transport in photosynthetic proteins, relying on either weakly or strongly coupled pigments. Here...

  6. Populational genetic structure of free-living maned wolves (Chrysocyon brachyurus determined by proteic markers

    Directory of Open Access Journals (Sweden)

    P. S. R. De Mattos

    Full Text Available Electrophoretic analysis of presumptive twenty gene loci products was conducted in hemolisates and plasma samples of twenty-eight maned wolves (Chrysocyon brachyurus from an area in northeastern São Paulo State, Brazil. The area sampled was divided into three sub-areas, with the Mogi-Guaçu and Pardo rivers regarded as barriers to the gene flow. The polymorphism degree and heterozygosity level (intralocus and average estimated in this study were similar to those detected by other authors for maned wolves and other species of wild free-living canids. The samples of each sub-area and the total sample exhibited genotype frequencies consistent with the genetic equilibrium model. The values of the F-statistics evidenced absence of inbreeding and population subdivision and, consequently, low genetic distances were found among the samples of each area.

  7. Genetic variants are major determinants of CSF antibody levels in multiple sclerosis

    DEFF Research Database (Denmark)

    Goris, An; Pauwels, Ine; Gustavsen, Marte W

    2015-01-01

    Immunological hallmarks of multiple sclerosis include the production of antibodies in the central nervous system, expressed as presence of oligoclonal bands and/or an increased immunoglobulin G index-the level of immunoglobulin G in the cerebrospinal fluid compared to serum. However, the underlying...... differences between oligoclonal band-positive and -negative patients with multiple sclerosis and reasons for variability in immunoglobulin G index are not known. To identify genetic factors influencing the variation in the antibody levels in the cerebrospinal fluid in multiple sclerosis, we have performed...... of being oligoclonal band positive and 7.75% of the variation in immunoglobulin G index. Both traits are associated with clinical features of disease such as female gender, age at onset and severity. This is the largest study population so far investigated for the genetic influence on antibody levels...

  8. [Past and present of streptococcus pyogenes: some pathogenic factors and their genetic determination].

    Science.gov (United States)

    Totolian, A A

    2015-01-01

    In this review two aspects dealt with Streptococcus pyogenes--one of the leading agent responsible for infectious diseases and another related to their complications in humans worldwide--are given. In the first part of the review the comparative evaluation of laboratory diagnostic approaches and methods used in the second half of the twentieth century and molecular technologies developed during last twenty years are described. In the second part the role of the main microbial pathogenic factors as well as the data on intra- and interspecies genetic exchange with extrachromosomal genetic elements and their influence on biological properties of the pathogen are discussed. Essential for today possibilities for molecular epidemiology of streptococcal pathology approaches must be introduces in diagnostic laboratories within the country.

  9. Genetic mapping of the regulator gene determining enterotoxin synthesis in Vibrio cholerae

    International Nuclear Information System (INIS)

    Smirnova, N.I.; Livanova, L.F.; Shaginyan, I.A.; Motin, V.L.

    1986-01-01

    Data on the genetic mapping of mutation tox-7 (the mutation affecting the synthesis of the cholera toxin) were obtained by conjugation crosses between the atoxigenic donor strain Vibrio cholerae Eltor and the toxigenic recipient strain V. cholera classica. The molecular and genetic analysis of the Tox - recombinants indicated that, when the synthesis of the cholera toxin is disrupted in these strains, the tox-7 mutation (which impairs the regulator gene tox) is gained. Close linkage between the tox-7 and pur-63 mutations was established (during the selection procedure there was 81.1% combined transfer with respect to marker pur-63 situated in the donor strain chromosome more proximal than mutation tox-7). The markers were localized in the following order in the region under investigation: asp-cys-nal-pur-61-trp-his-pur-63-tox-7-ile

  10. Measurement of angular correlations of jets at {radical}(s)=1.96 TeV and determination of the strong coupling at high momentum transfers

    Energy Technology Data Exchange (ETDEWEB)

    Abazov, V.M. [Joint Institute for Nuclear Research, Dubna (Russian Federation); Abbott, B. [University of Oklahoma, Norman, OK 73019 (United States); Acharya, B.S. [Tata Institute of Fundamental Research, Mumbai (India); Adams, M. [University of Illinois at Chicago, Chicago, IL 60607 (United States); Adams, T. [Florida State University, Tallahassee, FL 32306 (United States); Alexeev, G.D. [Joint Institute for Nuclear Research, Dubna (Russian Federation); Alkhazov, G. [Petersburg Nuclear Physics Institute, St. Petersburg (Russian Federation); Alton, A. [University of Michigan, Ann Arbor, MI 48109 (United States); Alverson, G. [Northeastern University, Boston, MA 02115 (United States); Askew, A. [Florida State University, Tallahassee, FL 32306 (United States); Atkins, S. [Louisiana Tech University, Ruston, LA 71272 (United States); Augsten, K. [Czech Technical University in Prague, Prague (Czech Republic); Avila, C. [Universidad de los Andes, Bogota (Colombia); Badaud, F. [LPC, Universite Blaise Pascal, CNRS/IN2P3, Clermont (France); Bagby, L.; Baldin, B. [Fermi National Accelerator Laboratory, Batavia, IL 60510 (United States); Bandurin, D.V. [Florida State University, Tallahassee, FL 32306 (United States); Banerjee, S. [Tata Institute of Fundamental Research, Mumbai (India); Barberis, E. [Northeastern University, Boston, MA 02115 (United States); Baringer, P. [University of Kansas, Lawrence, KS 66045 (United States); and others

    2012-11-15

    We present a measurement of the average value of a new observable at hadron colliders that is sensitive to QCD dynamics and to the strong coupling constant, while being only weakly sensitive to parton distribution functions. The observable measures the angular correlations of jets and is defined as the number of neighboring jets above a given transverse momentum threshold which accompany a given jet within a given distance {Delta}R in the plane of rapidity and azimuthal angle. The ensemble average over all jets in an inclusive jet sample is measured and the results are presented as a function of transverse momentum of the inclusive jets, in different regions of {Delta}R and for different transverse momentum requirements for the neighboring jets. The measurement is based on a data set corresponding to an integrated luminosity of 0.7 fb{sup -1} collected with the D0 detector at the Fermilab Tevatron Collider in pp{sup Macron} collisions at {radical}(s)=1.96 TeV. The results are well described by a perturbative QCD calculation in next-to-leading order in the strong coupling constant, corrected for non-perturbative effects. From these results, we extract the strong coupling and test the QCD predictions for its running over a range of momentum transfers of 50-400 GeV.

  11. Determinants of Excess Genetic Risk of Acute Myocardial Infarction - A Matched Case-Control Study

    Czech Academy of Sciences Publication Activity Database

    Valenta, Zdeněk; Mazura, Ivan; Kolář, M.; Feglarová, Petra; Peleška, Jan; Tomečková, Marie; Kalina, Jan; Slovák, Dalibor; Zvárová, Jana

    2012-01-01

    Roč. 8, č. 1 (2012), s. 34-43 ISSN 1801-5603 R&D Projects: GA MŠk(CZ) 1M06014 Institutional support: RVO:67985807 Keywords : genome-wide association study * gene expression * myocardial infarction * genetic predisposition * predictive modeling Subject RIV: BB - Applied Statistics, Operational Research http://www.ejbi.org/img/ejbi/2012/1/Valenta_en.pdf

  12. Genetically determined differences in brain response to a primary food reward

    OpenAIRE

    Felsted, Jennifer A.; Ren, Xueying; Chouinard-Decorte, Francois; Small, Dana M.

    2010-01-01

    Combining genetic and neuroimaging techniques may elucidate the biological underpinnings of individual differences in neurophysiology and potential vulnerabilities to disease. The TaqIA A1 variant is associated with diminished DRD2 receptor density, higher body mass, and food reinforcement. It also moderates the relationship between brain response to food and future weight gain. This suggests that the polymorphism is associated with a fundamental difference in the neurophysiology of food that...

  13. Genetic determinants for gestational diabetes mellitus and related metabolic traits in Mexican women.

    Directory of Open Access Journals (Sweden)

    Alicia Huerta-Chagoya

    Full Text Available Epidemiological and physiological similarities among Gestational Diabetes Mellitus (GDM and Type 2 Diabetes (T2D suggest that both diseases, share a common genetic background. T2D risk variants have been associated to GDM susceptibility. However, the genetic architecture of GDM is not yet completely understood. We analyzed 176 SNPs for 115 loci previously associated to T2D, GDM and body mass index (BMI, as well as a set of 118 Ancestry Informative Markers (AIMs, in 750 pregnant Mexican women. Association with GDM was found for two of the most frequently replicated T2D loci: a TCF7L2 haplotype (CTTC: rs7901695, rs4506565, rs7903146, rs12243326; P=2.16 x 10(-06; OR=2.95 and a KCNQ1 haplotype (TTT: rs2237892, rs163184, rs2237897; P=1.98 x 10(-05; OR=0.55. In addition, we found two loci associated to glycemic traits: CENTD2 (60' OGTT glycemia: rs1552224, P=0.03727 and MTNR1B (HOMA B: rs1387153, P=0.05358. Remarkably, a major susceptibility SLC16A11 locus for T2D in Mexicans was not shown to play a role in GDM risk. The fact that two of the main T2D associated loci also contribute to the risk of developing GDM in Mexicans, confirm that both diseases share a common genetic background. However, lack of association with a Native American contribution T2D risk haplotype, SLC16A11, suggests that other genetic mechanisms may be in play for GDM.

  14. Mapping genetic determinants of coronary microvascular remodeling in the spontaneously hypertensive rat

    Czech Academy of Sciences Publication Activity Database

    Mancini, M.; Petretto, E.; Kleinert, C.; Scavone, A.; De, T.; Cook, S.; Šilhavý, Jan; Zídek, Václav; Pravenec, Michal; d´Amati, G.; Camici, P.G.

    2013-01-01

    Roč. 108, č. 1 (2013), s. 316 ISSN 0300-8428 R&D Projects: GA MŠk(CZ) LH11049; GA MŠk(CZ) LL1204; GA ČR(CZ) GAP301/12/0696 Institutional support: RVO:67985823 Keywords : arterial hypertension * coronary circulation * myocardial ischemia * spontaneously hypertensive rat * recombinant inbred strains Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.955, year: 2013

  15. Genetic determination of the biological radiation response in inbred mice lines

    International Nuclear Information System (INIS)

    Gomolka, M.; Hornhardt, S.; Jung, T.

    2000-01-01

    Variation in radiation sensitivity and radiation resistance is influenced by the genetic constitution of an individual. Loss of function of genes involved in DNA repair, cell cycle or controlled cell death can have serious consequences on individual radiation sensitivity. For example, individuals suffering on the clinical syndrome of Ataxia telangiectasia exhibit radiation sensitivity in the order of 2-3 magnitudes higher than other cancer patients. For radiation protection it is important to clarify the role of genetic predisposition for radiation sensitivity in clinical healthy people. Therefore, data were collected from the literature describing the genetic variation (heritability) of radiation sensitivity in the mouse model. A heritability of 30-50% was calculated for 27 inbred mice lines by Roderick (1963) based on days of survival after a daily dose of 1 Gy γ-irradiation. The following inbred lines were described in the literature as radiation sensitive (phenotypical markers were e.g., time of survival, mortality, reduction in fertility post exposure): SWR, RIII, NC, K, HLG, DBA, CBA, BALB/c, A, AKR. Radiation resistance was demonstrated in SJL, SEC, RF, MA, C58, C57BR, BDP and 129. Parameter of longevity, some physiological, biochemical and immunological parameters as given in the data bank of the Jackson Laboratory, U.S.A., were compared between radiation sensitive and radiation resistant inbred strains. No correlation was seen for the most of the parameters except for the development of breast cancer. In 6 out of 10 radiosensitive inbred strains breast cancer is described while only 1 of 8 strains exhibits breast cancer. The higher heritability of 30-50% in spite of a very complex phenotype like survival and the correlation between radiosensitivity and tumour incidence show that individual genetic susceptibility is important on the biological radiation reaction. (orig.) [de

  16. Genetic, clinical and pharmacological determinants of out-of-hospital cardiac arrest

    DEFF Research Database (Denmark)

    Blom, M T; van Hoeijen, D A; Bardai, A

    2014-01-01

    INTRODUCTION: Out-of-hospital cardiac arrest (OHCA) is a major public health problem. Recognising the complexity of the underlying causes of OHCA in the community, we aimed to establish the clinical, pharmacological, environmental and genetic factors and their interactions that may cause OHCA...... victims since June 2005, we prospectively collect medical history (through hospital and general practitioner), and current and previous medication use (through community pharmacy). In addition, we include DNA samples from OHCA victims with documented ventricular tachycardia/fibrillation during...

  17. Biochemical traits useful for the determination of genetic variation in a natural population of Myracrodruon urundeuva

    Directory of Open Access Journals (Sweden)

    Abdala Ludmila

    2002-01-01

    Full Text Available The objectives of this work were to analyze seeds from 20 trees of aroeira (Myracrodruon urundeuva Fr. All. of a natural population located in the region of Selvíria, State of Mato Grosso do Sul, Brazil, in order to evaluate their protein, lipid and carbohydrate contents, and to estimate their genetic variation. A completely randomized experimental design consisting of 20 treatments (families was set up, with two replications. Four types of proteins were detected: albumin (35.0 to 107.3 mg/g seed, globulin (3.4 to 9.3 mg/g, prolamin (60.0 to 135.2 mg/g and glutelin (118.0 to 286.0 mg/g. The lipid content varied between 200 and 334 mg/g seed. The total sugars also varied (26.5 to 46.3 mg/g seed, with a predominance of polyols (arabinitol, mannitol, glucitol and xylitol. The main monosaccharides detected were glucose and arabinose. Total hydrolysis of the sugars indicated the presence of neutral arabinan and xylan oligosaccharides. The starch content varied from 0.35 to 1.58 mg/g seed. These biochemical traits showed considerable genetic variability, indicating that only the collection of seeds from many different trees can provide a representative sample of the population for conservation and genetic improvement.

  18. Genetic Factors are Important Determinants of Impaired Growth Following Infant Cardiac Surgery

    Science.gov (United States)

    Burnham, Nancy; Ittenbach, Richard F.; Stallings, Virginia A.; Gerdes, Marsha; Zackai, Elaine; Bernbaum, Judy; Clancy, Robert R.; Gaynor, J. William

    2010-01-01

    Objectives To estimate the prevalence and identify the predictors of impaired growth following infant cardiac surgery. Methods Secondary analysis of a prospective study of the role of apolipoprotein E (APOE) gene polymorphisms on neurodevelopment in young children following infant cardiac surgery. Prevalence estimates for growth velocity were derived using anthropometric measures [weight (WT) and head circumference (HC)] obtained at birth and at 4-years of age. Genetic evaluation was also performed. Growth measure z-scores were calculated using World Health Organization Child Growth Standards. Growth velocity was evaluated using two different techniques: first by clustering the children into one of three growth velocity subgroups based on z-score: impaired growth (difference 0.5 SD), and, second, using continuous difference scores. Statistical analyses were conducted using a combination of proportional odds models for the ordered categories and simple linear regression for the continuous outcomes. Results Three hundred and nineteen full term subjects had complete anthropometric measures for WT and HC at birth and at 4-yrs. The cohort was 56% male. Genetic examinations were available for 97% (309/319) of the cohort (normal, 74% definite or suspected genetic abnormality, 26%). Frequency counts for WT categories were: impaired growth 37% stable growth 31% and improving growth 32%. Frequency counts for HC categories were: impaired growth 39% stable growth 28% and improving growth 33%. Presence of a definite or suspected genetic syndrome (p = 0.04) was found to be a predictor of impaired growth for WT, but not HC. When growth z-scores were used as continuous outcomes, the APOE ε2 allele was found to be predictive of lower z-scores for both WT (p = 0.02) and HC (p = 0.03). Conclusions Impaired growth for both WT and HC is common (both > 30%) in this cohort of children following infant cardiac surgery. Both the APOE ε2 allele and the presence of a definite or suspected

  19. The roles of standing genetic variation and evolutionary history in determining the evolvability of anti-predator strategies.

    Directory of Open Access Journals (Sweden)

    Daniel R O'Donnell

    Full Text Available Standing genetic variation and the historical environment in which that variation arises (evolutionary history are both potentially significant determinants of a population's capacity for evolutionary response to a changing environment. Using the open-ended digital evolution software Avida, we evaluated the relative importance of these two factors in influencing evolutionary trajectories in the face of sudden environmental change. We examined how historical exposure to predation pressures, different levels of genetic variation, and combinations of the two, affected the evolvability of anti-predator strategies and competitive abilities in the presence or absence of threats from new, invasive predator populations. We show that while standing genetic variation plays some role in determining evolutionary responses, evolutionary history has the greater influence on a population's capacity to evolve anti-predator traits, i.e. traits effective against novel predators. This adaptability likely reflects the relative ease of repurposing existing, relevant genes and traits, and the broader potential value of the generation and maintenance of adaptively flexible traits in evolving populations.

  20. Combining data from morphological traits and genetic markers to determine transmission cycles in the tape worm, Echinococcus granulosus.

    Science.gov (United States)

    Lymbery, A J

    1998-08-01

    Species of Echinococcus (Cestoda: Taeniidae) require 2 mammalian hosts to complete their life-cycle; a carnivorous definitive host, and a herbivorous or omnivorous intermediate host. For most species of Echinococcus, the definitive host range is restricted to 1 or a few species, but the intermediate host range is very broad. Programmes to control hydatid disease attempt to break the life-cycle of the parasite and their effectiveness is therefore enhanced by an understanding of local patterns of transmission. Although it is known that the rostellar hooks of protoscoleces may be influenced by the species of intermediate host in which they develop, the application of this knowledge to infer transmission cycles has been limited, because the intermediate host effect has not been isolated from other environmental and genetic components of phenotypic variance. This study presents a method for separating these potentially confounding genetic and environmental effects, by combining quantitative genetic analyses of hook traits with data on population structure from neutral genetic markers. The method was applied to 5 hook traits (hook number, total length of large hooks, blade length of large hooks, total length of small hooks, blade length of small hooks) measured on protoscoleces from 2 intermediate host types (sheep and macropod marsupials) in Australia. Although genetic variance was similar for all traits, they differed markedly in the extent of environmental variance attributed to development in different host types. Total length of small hooks was the trait most affected, with 49-60% of phenotypic variance being explained by environmental differences between intermediate host species. Blade length of small hooks was least affected, with none of the phenotypic variance due to intermediate host origin. These data suggest that hook measurements of adult worms from naturally infected definitive hosts could be used to determine the intermediate host species from which

  1. Identification of the UBP1 locus as a critical blood pressure determinant using a combination of mouse and human genetics

    DEFF Research Database (Denmark)

    Koutnikova, Hana; Laakso, Markku; Lu, Lu

    2009-01-01

    recombinant BXD strains of mice we identified a quantitative trait locus (QTL) for blood pressure (BP) on distal chromosome 9. The association analysis of markers encompassing the syntenic region on human chromosome 3 gave in an additive genetic model the strongest association for rs17030583 C/T and rs2291897...... G/A, located within the UBP1 locus, with systolic and diastolic BP (rs17030583: 1.3+/-0.4 mmHg p... complementarities of mouse and human genetic approaches, identifies the UBP1 locus as a critical blood pressure determinant. UBP1 plays a role in cholesterol and steroid metabolism via the transcriptional activation of CYP11A, the rate-limiting enzyme in pregnenolone and aldosterone biosynthesis. We suggest...

  2. Genetic Risk for Inflammatory Bowel Disease Is a Determinant of Crohn's Disease Development in Chronic Granulomatous Disease.

    Science.gov (United States)

    Huang, Chengrui; De Ravin, Suk See; Paul, Adam R; Heller, Theo; Ho, Nancy; Wu Datta, Lisa; Zerbe, Christa S; Marciano, Beatriz E; Kuhns, Douglas B; Kader, Howard A; Holland, Steven M; Malech, Harry L; Brant, Steven R

    2016-12-01

    Approximately, one-third to one-half of children with chronic granulomatous disease (CGD) develop gastrointestinal inflammation characteristic of idiopathic inflammatory bowel disease (IBD), usually Crohn's disease. We hypothesized that the overall IBD genetic risk, determined by IBD genetic risk score (GRS), might in part determine IBD development in CGD. We reviewed medical records to establish IBD diagnoses in CGD subjects seen at NIAID. IBD risk single nucleotide polymorphism genotypes were determined using the Immunochip, and GRS were estimated by Mangrove. Among 157 white patients with CGD, 55 were confirmed, 78 excluded, and 24 were uncertain for IBD. Two hundred one established, independent European IBD risk single nucleotide polymorphisms passed quality control. After sample quality control and removing non-IBD CGD patients with perianal disease, mean GRS for 40 unrelated patients with CGD-IBD was higher than 53 CGD non-IBD patients (in log2-scale 0.08 ± 1.62 versus -0.67 ± 1.64, P = 0.026) but lower than 239 IBD Genetics Consortium (IBDGC) young-onset Crohn's disease cases (0.76 ± 1.60, P = 0.025). GRS for non-IBD CGD was similar to 609 IBDGC controls (-0.69 ± 1.60, P = 0.95). Seven established IBD single nucleotide polymorphisms were nominally significant among CGD-IBD versus CGD non-IBD, including those near LACC1 (P = 0.005), CXCL14 (P = 0.007), and TNFSF15 (P = 0.016). The weight of the common IBD risk alleles are significant determinants of IBD in CGD. However, IBD risk gene burden among CGD children with IBD is significantly lower than that in nonsyndromic pediatric Crohn's disease, congruent with the concept that defective superoxide production in CGD is also a major IBD risk factor. Individual IBD genes might interact with the CGD defect to cause IBD in CGD.

  3. Growth-based determination and biochemical confirmation of genetic requirements for protein degradation in Saccharomyces cerevisiae.

    Science.gov (United States)

    Watts, Sheldon G; Crowder, Justin J; Coffey, Samuel Z; Rubenstein, Eric M

    2015-02-16

    Regulated protein degradation is crucial for virtually every cellular function. Much of what is known about the molecular mechanisms and genetic requirements for eukaryotic protein degradation was initially established in Saccharomyces cerevisiae. Classical analyses of protein degradation have relied on biochemical pulse-chase and cycloheximide-chase methodologies. While these techniques provide sensitive means for observing protein degradation, they are laborious, time-consuming, and low-throughput. These approaches are not amenable to rapid or large-scale screening for mutations that prevent protein degradation. Here, a yeast growth-based assay for the facile identification of genetic requirements for protein degradation is described. In this assay, a reporter enzyme required for growth under specific selective conditions is fused to an unstable protein. Cells lacking the endogenous reporter enzyme but expressing the fusion protein can grow under selective conditions only when the fusion protein is stabilized (i.e. when protein degradation is compromised). In the growth assay described here, serial dilutions of wild-type and mutant yeast cells harboring a plasmid encoding a fusion protein are spotted onto selective and non-selective medium. Growth under selective conditions is consistent with degradation impairment by a given mutation. Increased protein abundance should be biochemically confirmed. A method for the rapid extraction of yeast proteins in a form suitable for electrophoresis and western blotting is also demonstrated. A growth-based readout for protein stability, combined with a simple protocol for protein extraction for biochemical analysis, facilitates rapid identification of genetic requirements for protein degradation. These techniques can be adapted to monitor degradation of a variety of short-lived proteins. In the example presented, the His3 enzyme, which is required for histidine biosynthesis, was fused to Deg1-Sec62. Deg1-Sec62 is targeted for

  4. Genetic determinants of UV-susceptibility in non-melanoma skin cancer.

    Directory of Open Access Journals (Sweden)

    Marleen M Welsh

    Full Text Available A milieu of cytokines and signaling molecules are involved in the induction of UV-induced immune suppression and thus the etiology of non-melanoma skin cancer (NMSC. Targeting the UV-induced immunosuppression pathway, and using a large population based study of NMSC, we have investigated the risk associated with functional variants in 10 genes (IL10, IL4, IL4R, TNF, TNFR2, HTR2A, HRH2, IL12B, PTGS2, and HAL. The most prominent single genetic effect was observed for IL10. There was increasing risk for both basal cell carcinoma (BCC and squamous cell carcinoma (SCC with increasing number of variant IL10 haplotypes (BCC: p(trend = 0.0048; SCC: p(trend = 0.031. Having two IL10 GC haplotypes was associated with increased odds ratios of BCC and SCC (OR(BCC = 1.5, 95% CI 1.1-1.9; OR(SCC = 1.4, 95% CI 1.0-1.9, and these associations were largely confined to women (OR(BCC = 2.2, 95% CI 1.4-3.4; SCC: OR(SCC = 1.8, 95% CI 1.1-3.0. To examine how combinations of these variants contribute to risk of BCC and SCC, we used multifactor dimensionality reduction (MDR and classification and regression trees (CART. Results from both of these methods found that in men, a combination of skin type, burns, IL10, IL4R, and possibly TNFR2 were important in both BCC and SCC. In women, skin type, burns, and IL10 were the most critical risk factors in SCC, with risk of BCC involving these same factors plus genetic variants in HTR2A, IL12B and IL4R. These data suggest differential genetic susceptibility to UV-induced immune suppression and skin cancer risk by gender.

  5. Occurrence of Diverse Antimicrobial Resistance Determinants in Genetically Unrelated Biocide Tolerant Klebsiella pneumoniae.

    Directory of Open Access Journals (Sweden)

    Amitabha Mondal

    Full Text Available Nosocomial infections due to Klebsiella pneumoniae is a significant problem in health care settings worldwide. In this study, we examined the antimicrobial susceptibility, genetic profiles and mechanisms of antibiotic resistance in K. pneumoniae isolates of Indian origin. To our knowledge this is the first report demonstrating the high prevalence of β-lactamases, aminoglycoside modifying enzymes, quinolone resistance genes besides demonstrating the involvement of active efflux in K. pneumoniae Indian isolates. This study has enabled us to correlate the phenotypic and genotypic characteristics in K. pneumoniae, providing an important base for continued monitoring and epidemiological studies of this emerging nosocomial pathogen in Indian hospitals.

  6. Genetic context determines susceptibility to intraocular pressure elevation in a mouse pigmentary glaucoma

    Directory of Open Access Journals (Sweden)

    Cosma Ioan M

    2006-07-01

    Full Text Available Abstract Background DBA/2J (D2 mice develop an age-related form of glaucoma. Their eyes progressively develop iris pigment dispersion and iris atrophy followed by increased intraocular pressure (IOP and glaucomatous optic nerve damage. Mutant alleles of the Gpnmb and Tyrp1 genes are necessary for the iris disease, but it is unknown whether alleles of other D2 gene(s are necessary for the distinct later stages of disease. We initiated a study of congenic strains to further define the genetic requirements and disease mechanisms of the D2 glaucoma. Results To further understand D2 glaucoma, we created congenic strains of mice on the C57BL/6J (B6 genetic background. B6 double-congenic mice carrying D2-derived Gpnmb and Tyrp1 mutations develop a D2-like iris disease. B6 single-congenics with only the Gpnmb and Tyrp1 mutations develop milder forms of iris disease. Genetic epistasis experiments introducing a B6 tyrosinase mutation into the congenic strains demonstrated that both the single and double-congenic iris diseases are rescued by interruption of melanin synthesis. Importantly, our experiments analyzing mice at ages up to 27 months indicate that the B6 double-congenic mice are much less prone to IOP elevation and glaucoma than are D2 mice. Conclusion As demonstrated here, the Gpnmb and Tyrp1 iris phenotypes are both individually dependent on tyrosinase function. These results support involvement of abnormal melanosomal events in the diseases caused by each gene. In the context of the inbred D2 mouse strain, the glaucoma phenotype is clearly influenced by more genes than just Gpnmb and Tyrp1. Despite the outward similarity of pigment-dispersing iris disease between D2 and the B6 double-congenic mice, the congenic mice are much less susceptible to developing high IOP and glaucoma. These new congenic strains provide a valuable new resource for further studying the genetic and mechanistic complexity of this form of glaucoma.

  7. Molecular responses of genetically modified maize to abiotic stresses as determined through proteomic and metabolomic analyses.

    Directory of Open Access Journals (Sweden)

    Rafael Fonseca Benevenuto

    Full Text Available Some genetically modified (GM plants have transgenes that confer tolerance to abiotic stressors. Meanwhile, other transgenes may interact with abiotic stressors, causing pleiotropic effects that will affect the plant physiology. Thus, physiological alteration might have an impact on the product safety. However, routine risk assessment (RA analyses do not evaluate the response of GM plants exposed to different environmental conditions. Therefore, we here present a proteome profile of herbicide-tolerant maize, including the levels of phytohormones and related compounds, compared to its near-isogenic non-GM variety under drought and herbicide stresses. Twenty differentially abundant proteins were detected between GM and non-GM hybrids under different water deficiency conditions and herbicide sprays. Pathway enrichment analysis showed that most of these proteins are assigned to energetic/carbohydrate metabolic processes. Among phytohormones and related compounds, different levels of ABA, CA, JA, MeJA and SA were detected in the maize varieties and stress conditions analysed. In pathway and proteome analyses, environment was found to be the major source of variation followed by the genetic transformation factor. Nonetheless, differences were detected in the levels of JA, MeJA and CA and in the abundance of 11 proteins when comparing the GM plant and its non-GM near-isogenic variety under the same environmental conditions. Thus, these findings do support molecular studies in GM plants Risk Assessment analyses.

  8. Population genetics of traditionally managed maize : farming practice as a determinant of genetic structure and identity of maize landraces in Mexico

    NARCIS (Netherlands)

    Heerwaarden, van J.

    2007-01-01

    A large amount of crop genetic diversity is being maintained in farmers' fields worldwide. The population genetics of traditionally managed landraces is therefore of interest to the conservation of genetic resources. The growing trend towards agricultural modernization and the prospect of

  9. Genetic determinants of facial clefting: analysis of 357 candidate genes using two national cleft studies from Scandinavia.

    Directory of Open Access Journals (Sweden)

    Astanand Jugessur

    Full Text Available Facial clefts are common birth defects with a strong genetic component. To identify fetal genetic risk factors for clefting, 1536 SNPs in 357 candidate genes were genotyped in two population-based samples from Scandinavia (Norway: 562 case-parent and 592 control-parent triads; Denmark: 235 case-parent triads.We used two complementary statistical methods, TRIMM and HAPLIN, to look for associations across these two national samples. TRIMM tests for association in each gene by using multi-SNP genotypes from case-parent triads directly without the need to infer haplotypes. HAPLIN on the other hand estimates the full haplotype distribution over a set of SNPs and estimates relative risks associated with each haplotype. For isolated cleft lip with or without cleft palate (I-CL/P, TRIMM and HAPLIN both identified significant associations with IRF6 and ADH1C in both populations, but only HAPLIN found an association with FGF12. For isolated cleft palate (I-CP, TRIMM found associations with ALX3, MKX, and PDGFC in both populations, but only the association with PDGFC was identified by HAPLIN. In addition, HAPLIN identified an association with ETV5 that was not detected by TRIMM.Strong associations with seven genes were replicated in the Scandinavian samples and our approach effectively replicated the strongest previously known association in clefting--with IRF6. Based on two national cleft cohorts of similar ancestry, two robust statistical methods and a large panel of SNPs in the most promising cleft candidate genes to date, this study identified a previously unknown association with clefting for ADH1C and provides additional candidates and analytic approaches to advance the field.

  10. Neighbourhood density and genetic relatedness interact to determine fruit set and abortion rates in a continuous tropical tree population.

    Science.gov (United States)

    Jones, F A; Comita, L S

    2008-12-07

    Tropical trees may show positive density dependence in fruit set and maturation due to pollen limitation in low-density populations. However, pollen from closely related individuals in the local neighbourhood might reduce fruit set or increase fruit abortion in self-incompatible tree species. We investigated the role of neighbourhood density and genetic relatedness on individual fruit set and abortion in the neotropical tree Jacaranda copaia in a large forest plot in central Panama. Using nested neighbourhood models, we found a strong positive effect of increased conspecific density on fruit set and maturation. However, high neighbourhood genetic relatedness interacted with density to reduce total fruit set and increase the proportion of aborted fruit. Our results imply a fitness advantage for individuals growing in high densities as measured by fruit set, but realized fruit set is lowered by increased neighbourhood relatedness. We hypothesize that the mechanism involved is increased visitation by density-dependent invertebrate pollinators in high-density populations, which increases pollen quantity and carry-over and increases fruit set and maturation, coupled with self-incompatibility at early and late stages due to biparental inbreeding that lowers fruit set and increases fruit abortion. Implications for the reproductive ecology and conservation of tropical tree communities in continuous and fragmented habitats are discussed.

  11. Association of baseline vitamin D level with genetic determinants and virologic response in patients with chronic hepatitis B.

    Science.gov (United States)

    Yu, Rui; Tan, Deming; Ning, Qin; Niu, Junqi; Bai, Xuefan; Chen, Shijun; Cheng, Jun; Yu, Yanyan; Wang, Hao; Xu, Min; Shi, Guangfeng; Wan, Mobin; Chen, Xinyue; Tang, Hong; Sheng, Jifang; Dou, Xiaoguang; Shi, Junping; Ren, Hong; Wang, Maorong; Zhang, Hongfei; Gao, Zhiliang; Chen, Chengwei; Ma, Hong; Jia, Jidong; Hou, Jinlin; Xie, Qing; Sun, Jian

    2018-02-01

    The role of vitamin D in individuals with chronic hepatitis B (CHB) is unclear. We aimed to explore the association of baseline vitamin D level with genetic determinants and week-104 treatment outcome in CHB patients. Baseline serum 25-hydroxycholecalciferol (25(OH)D) levels and genetic polymorphism within GC, DHCR7, and CYP2R1 were determined in stored serum of 560 patients who were enrolled into a multicenter, randomized, controlled study and completed 104 weeks of telbivudine monotherapy or telbivudine-based optimized therapy. Virologic response was defined as hepatitis B virus DNA <300 copies/mL (52 IU/mL) at week 104. The mean 25(OH)D value was 29.64 ng/mL. The percentage of patients with vitamin D insufficiency (<30 ng/mL) and vitamin D deficiency (<20 ng/mL) were 55.0% and 20.9%, respectively. Gender, season, latitude, and GC rs2282679 polymorphism were independent factors of vitamin D status. Patients with sufficient vitamin D (≥30 ng/mL) achieved a higher virologic response rate than those with vitamin D insufficiency (81.7% vs. 67.2%, P < 0.001). The area under the curve of 25(OH)D to predict virologic response was 0.65 (P < 0.001; 95% confidence interval, 0.62-0.67). On multivariate analysis, 25(OH)D level was an independent predictor of virologic response, but not associated with hepatitis B envelope antigen (HBeAg) seroconversion or alanine aminotransferase (ALT) normalization. Vitamin D insufficiency was highly prevalent in treatment-naïve CHB patients in mainland China. Latitude and genetic determinants affect vitamin D status. Baseline vitamin D level can predict week-104 virologic response, but not HBeAg seroconversion or ALT normalization. © 2017 The Japan Society of Hepatology.

  12. Haploid Mammalian Genetic Screen Identifies UBXD8 as a Key Determinant of HMGCR Degradation and Cholesterol Biosynthesis.

    Science.gov (United States)

    Loregger, Anke; Raaben, Matthijs; Tan, Josephine; Scheij, Saskia; Moeton, Martina; van den Berg, Marlene; Gelberg-Etel, Hila; Stickel, Elmer; Roitelman, Joseph; Brummelkamp, Thijn; Zelcer, Noam

    2017-11-01

    The cellular demand for cholesterol requires control of its biosynthesis by the mevalonate pathway. Regulation of HMGCR (3-hydroxy-3-methylglutaryl coenzyme A reductase), a rate-limiting enzyme in this pathway and the target of statins, is a key control point herein. Accordingly, HMGCR is subject to negative and positive regulation. In particular, the ability of oxysterols and intermediates of the mevalonate pathway to stimulate its proteasomal degradation is an exquisite example of metabolically controlled feedback regulation. To define the genetic determinants that govern this process, we conducted an unbiased haploid mammalian genetic screen. We generated human haploid cells with mNeon fused to endogenous HMGCR using CRISPR/Cas9 and used these cells to interrogate regulation of HMGCR abundance in live cells. This resulted in identification of known and new regulators of HMGCR, and among the latter, UBXD8 (ubiquitin regulatory X domain-containing protein 8), a gene that has not been previously implicated in this process. We demonstrate that UBXD8 is an essential determinant of metabolically stimulated degradation of HMGCR and of cholesterol biosynthesis in multiple cell types. Accordingly, UBXD8 ablation leads to aberrant cholesterol synthesis due to loss of feedback control. Mechanistically, we show that UBXD8 is necessary for sterol-stimulated dislocation of ubiquitylated HMGCR from the endoplasmic reticulum membrane en route to proteasomal degradation, a function dependent on its UBX domain. We establish UBXD8 as a previously unrecognized determinant that couples flux across the mevalonate pathway to control of cholesterol synthesis and demonstrate the feasibility of applying mammalian haploid genetics to study metabolic traits. © 2017 The Authors.

  13. Breast cancer genetic counseling among Dutch patients from Turkish and Moroccan descent : participation determinants and perspectives of patients and healthcare professionals

    NARCIS (Netherlands)

    Baars, J E; van Dulmen, A M; Velthuizen, M E; van Riel, E; Ausems, M G E M

    2017-01-01

    Lower participation rates in cancer genetic counseling are observed among different ethnic minorities. The goal of our study is to gain insight into determinants of Turkish and Moroccan patients' participation in breast cancer genetic counseling and DNA testing, from the point of view of healthcare

  14. Breast cancer genetic counseling among Dutch patients from Turkish and Moroccan descent: participation determinants, and perspectives of patients and healthcare professionals.

    NARCIS (Netherlands)

    Baars, J.E.; Dulmen, S. van; Veldhuizen, M.E. van; Riel, E. van; Ausems, M.G.E.M.

    2017-01-01

    Abstract Lower participation rates in cancer genetic counseling are observed among different ethnic minorities. The goal of our study is to gain insight into determinants of Turkish and Moroccan patients’ participation in breast cancer genetic counseling and DNA testing, from the point of view of

  15. Breast cancer genetic counseling among Dutch patients from Turkish and Moroccan descent: participation determinants and perspectives of patients and healthcare professionals

    NARCIS (Netherlands)

    Baars, J.E.; Dulmen, A.M. van; Velthuizen, M.E.; Riel, E. van; Ausems, M.G.E.M.

    2017-01-01

    Lower participation rates in cancer genetic counseling are observed among different ethnic minorities. The goal of our study is to gain insight into determinants of Turkish and Moroccan patients' participation in breast cancer genetic counseling and DNA testing, from the point of view of healthcare

  16. The European Prader-Willi Syndrome Clinical Research Database: An Aid in the Investigation of a Rare Genetically Determined Neurodevelopmental Disorder

    Science.gov (United States)

    Holland, A.; Whittington, J.; Cohen, O.; Curfs, L.; Delahaye, F.; Dudley, O.; Horsthemke, B.; Lindgren, A. -C.; Nourissier, C.; Sharma, N.; Vogels, A.

    2009-01-01

    Background: Prader-Willi Syndrome (PWS) is a rare genetically determined neurodevelopmental disorder with a complex phenotype that changes with age. The rarity of the syndrome and the need to control for different variables such as genetic sub-type, age and gender limits clinical studies of sufficient size in any one country. A clinical research…

  17. Genetic determinants of the release of mannoproteins of enological interest by Saccharomyces cerevisiae.

    Science.gov (United States)

    Gonzalez-Ramos, Daniel; Gonzalez, Ramon

    2006-12-13

    Cell wall mannoproteins released by Saccharomyces cerevisiae during wine fermentation and aging have recently attracted the attention of enologists and researchers in enology due to their positive effect over a number of technological and quality properties of the wines, including protein and tartaric stability, aroma and color stability, astringency, mouthfeel, malolactic fermentation, or foam properties of sparkling wines. This work has investigated the effect of deletions involving genes related to cell wall biogenesis on the release of mannoproteins, as well as the effect of the released mannoproteins on wine protein stability. When available, the phenotypes have been studied in different genetic backgrounds, in haploid or diploid strains, and in homo- or heterozygosis. Strains deleted for GAS1, GPI7, or KNR4 release higher amounts of mannoproteins and polysaccharides to the medium. These increased amounts of mannoproteins and polysaccharides lead to a stronger stability of Sauvignon Blanc wines against protein haze.

  18. EXPERIMENTAL DETERMINATION OF ELECTRICAL AND MECHANICAL PARAMETERS OF DC MOTOR USING GENETIC ELMAN NEURAL NETWORK

    Directory of Open Access Journals (Sweden)

    ARIF A. AL-QASSAR

    2008-08-01

    Full Text Available The most suitable and generalized neural network that represents the control system dynamics is the Elman Neural Network (ENN. This is due to its ability to memorize and emulate the system states. Moreover, ENNs learned by Genetic algorithms are found to be more representative to system order in terms of its structural complexity in comparison to those learned by back propagation algorithm. This facility is utilized efficiently to find the minimum ENN structure that represents the discrete-time state space model of the DC motor. Then by comparing the ENN weights with the well-known discrete-time state space equation in terms of the motor physical parameters (moment of inertia, torque constant, armature inductance, etc., these parameters can be obtained.

  19. Neonatal Screening: Some Ethical Issues of Expanding Spectrum for Genetically Determined Diseases

    Directory of Open Access Journals (Sweden)

    S. S. Deryabina

    2015-01-01

    Full Text Available The article considers philosophical questions of neonatal screening technology. The main focus is on ethical and methodological issues that inevitably arise when expanding the number of scanned nosologies and applying genetic research methods. Questions concerning the existing discrepancy between technical capacity and the practical level of healthcare delivery and the probabilistic nature of results obtained by molecular testing are analyzed in terms of methodology. Access to information about the DNA-testing of newborns and the linkage between neonatal screening and prenatal diagnostics are among the most topical ethical problems raised within this article. One of the purposes of this article is to draw the attention of the public — especially it concerns current and prospective parents and volunteer organizations — to these contemporary problems.

  20. Farming termites determine the genetic population structure of Termitomyces fungal symbionts

    DEFF Research Database (Denmark)

    Nobre, Tânia; Fernandes, Cecília; Boomsma, Jacobus J

    2011-01-01

    population structure of Termitomyces fungus gardens across 74 colonies of Macrotermes bellicosus in four west and central African countries. We confirm earlier, more limited, studies showing that the Termitomyces symbionts of M. bellicosus are normally transmitted vertically and clonally by dispersing males....... We also document that the symbionts associated with this termite species belong to three main lineages that do not constitute a monophyletic group. The most common lineage occurs over the entire geographical region that we studied, including west, central and southern Africa, where it is also...... associated with the alternative termite hosts Macrotermes subhyalinus and Macrotermes natalensis. While Termitomyces associated with these alternative hosts are horizontally transmitted and recombine freely, the genetic population structure of the same Termitomyces associated with M. bellicosus is consistent...

  1. Identification of novel genetic determinants of erythrocyte membrane fatty acid composition among Greenlanders

    DEFF Research Database (Denmark)

    Andersen, Mette Korre; Jørsboe, Emil; Sandholt, Camilla Helene

    2016-01-01

    Fatty acids (FAs) are involved in cellular processes important for normal body function, and perturbation of FA balance has been linked to metabolic disturbances, including type 2 diabetes. An individual's level of FAs is affected by diet, lifestyle, and genetic variation. We aimed to improve......-28) and docosahexaenoic acid (rs6035106 in DTD1, 0.137% (0.025), p = 6.4x10-8), respectively. For a missense variant (rs80356779) in CPT1A, we identified a number of novel FA associations, the strongest with 11-eicosenoic acid (0.473% (0.035), p = 2.6x10-38), and for variants in FADS2 (rs174570), LPCAT3 (rs2110073...

  2. Genetic Determinants of RNA Editing Levels of ADAR Targets in Drosophila melanogaster

    Directory of Open Access Journals (Sweden)

    Yerbol Z. Kurmangaliyev

    2016-02-01

    Full Text Available RNA editing usually affects only a fraction of expressed transcripts and there is a vast amount of variation in editing levels of ADAR (adenosine deaminase, RNA-specific targets. Here we explore natural genetic variation affecting editing levels of particular sites in 81 natural strains of Drosophila melanogaster. The analysis of associations between editing levels and single-nucleotide polymorphisms allows us to map putative cis-regulatory regions affecting editing of 16 A-to-I editing sites (cis-RNA editing quantitative trait loci or cis-edQTLs, P < 10−8. The observed changes in editing levels are validated by independent molecular technique. All identified regulatory variants are located in close proximity of modulated editing sites. Moreover, colocalized editing sites are often regulated by same loci. Similar to expression and splicing QTL studies, the characterization of edQTLs will greatly expand our understanding of cis-regulatory evolution of gene expression.

  3. Determination of genetic polymorphism in Guney Karaman local Turkish sheep breed by using STR markers

    Science.gov (United States)

    Karslı, Taki; Balcıoǧlu, Murat Soner

    2017-04-01

    The objective of this study was to assess genetic diversity of Güney Karaman Turkish local sheep breed. A total of 29 samples were genotyped by using 14 STR markers. All markers were polymorphic. The number of alleles in Güney Karaman sheep breed ranged from 3 to 11 per locus, with a mean of 7.42. The average observed and expected heterozygosity was 0.659 and 0.794, respectively. Mean inbreeding coefficient (Fis) value was found 0.175. The PIC values ranged from 0.569 to 0.860 with a mean of 0.743. The findings of this research demonstrate at moderate level gene diversity and heterozygosity with lower inbreeding in Güney Karaman sheep breed.

  4. Genetic, nongenetic and epigenetic risk determinants in developmental programming of type 2 diabetes

    DEFF Research Database (Denmark)

    Vaag, Allan; Brøns, Charlotte; Gillberg, Linn

    2014-01-01

    Low birthweight (LBW) individuals and offspring of women with gestational diabetes mellitus (GDM) exhibit increased risk of developing type 2 diabetes (T2D) and associated cardiometabolic traits in adulthood, which for both groups may be mediated by adverse events and developmental changes in fetal...... factors. Indeed, it has been shown that genetic changes influencing risk of diabetes may also be associated with reduced fetal growth as a result of reduced insulin secretion and/or action. Similarly, increased risk of T2D among offspring could be explained by T2D susceptibility genes shared between...... the mother and her offspring. Epigenetic mechanisms may explain the link between factors operating in fetal life and later risk of developing T2D, but so far convincing evidence is lacking for epigenetic changes as a prime and direct cause of T2D. This review addresses recent literature on the early origins...

  5. Genetic heterogeneity of Campylobacter concisus determined by pulsed field gel electrophoresis-based macrorestriction profiling

    DEFF Research Database (Denmark)

    Matsheka, M.I.; Elisha, B.G.; Lastovica, A.L.

    2002-01-01

    1 for pulsed field gel electrophoresis-based genotyping. Subsequently, 53 strains of C concisus, principally from cases of diarrhoea in children, were examined. Fifty-one distinct patterns were obtained, indicating the high discriminatory potential of the method. Patterns comprised between one...... comprised of several genomospecies. The pulsed field gel electrophoresis typing method described here has considerable potential for molecular epidemiological studies of C concisus and may be a useful adjunctive method for helping to resolve key taxonomic issues for this species....... and 14 restriction fragments, with type and reference strains of two well-defined genomospecies of oral and faecal origin containing six and 12 fragments respectively. Our results show that C concisus is genetically diverse and suggest the species as currently defined to be a taxonomic continuum...

  6. Dynamical patterning modules: physico-genetic determinants of morphological development and evolution

    International Nuclear Information System (INIS)

    Newman, Stuart A; Bhat, Ramray

    2008-01-01

    The shapes and forms of multicellular organisms arise by the generation of new cell states and types and changes in the numbers and rearrangements of the various kinds of cells. While morphogenesis and pattern formation in all animal species are widely recognized to be mediated by the gene products of an evolutionarily conserved 'developmental-genetic toolkit', the link between these molecular players and the physics underlying these processes has been generally ignored. This paper introduces the concept of 'dynamical patterning modules' (DPMs), units consisting of one or more products of the 'toolkit' genes that mobilize physical processes characteristic of chemically and mechanically excitable meso- to macroscopic systems such as cell aggregates: cohesion, viscoelasticity, diffusion, spatiotemporal heterogeneity based on lateral inhibition and multistable and oscillatory dynamics. We suggest that ancient toolkit gene products, most predating the emergence of multicellularity, assumed novel morphogenetic functions due to change in the scale and context inherent to multicellularity. We show that DPMs, acting individually and in concert with each other, constitute a 'pattern language' capable of generating all metazoan body plans and organ forms. The physical dimension of developmental causation implies that multicellular forms during the explosive radiation of animal body plans in the middle Cambrian, approximately 530 million years ago, could have explored an extensive morphospace without concomitant genotypic change or selection for adaptation. The morphologically plastic body plans and organ forms generated by DPMs, and their ontogenetic trajectories, would subsequently have been stabilized and consolidated by natural selection and genetic drift. This perspective also solves the apparent 'molecular homology-analogy paradox', whereby widely divergent modern animal types utilize the same molecular toolkit during development by proposing, in contrast to the Neo

  7. Dynamical patterning modules: physico-genetic determinants of morphological development and evolution

    Science.gov (United States)

    Newman, Stuart A.; Bhat, Ramray

    2008-03-01

    The shapes and forms of multicellular organisms arise by the generation of new cell states and types and changes in the numbers and rearrangements of the various kinds of cells. While morphogenesis and pattern formation in all animal species are widely recognized to be mediated by the gene products of an evolutionarily conserved 'developmental-genetic toolkit', the link between these molecular players and the physics underlying these processes has been generally ignored. This paper introduces the concept of 'dynamical patterning modules' (DPMs), units consisting of one or more products of the 'toolkit' genes that mobilize physical processes characteristic of chemically and mechanically excitable meso- to macroscopic systems such as cell aggregates: cohesion, viscoelasticity, diffusion, spatiotemporal heterogeneity based on lateral inhibition and multistable and oscillatory dynamics. We suggest that ancient toolkit gene products, most predating the emergence of multicellularity, assumed novel morphogenetic functions due to change in the scale and context inherent to multicellularity. We show that DPMs, acting individually and in concert with each other, constitute a 'pattern language' capable of generating all metazoan body plans and organ forms. The physical dimension of developmental causation implies that multicellular forms during the explosive radiation of animal body plans in the middle Cambrian, approximately 530 million years ago, could have explored an extensive morphospace without concomitant genotypic change or selection for adaptation. The morphologically plastic body plans and organ forms generated by DPMs, and their ontogenetic trajectories, would subsequently have been stabilized and consolidated by natural selection and genetic drift. This perspective also solves the apparent 'molecular homology-analogy paradox', whereby widely divergent modern animal types utilize the same molecular toolkit during development by proposing, in contrast to the Neo

  8. Determination of Genetic Diversity Using 15 Simple Sequence Repeats Markers in Long Term Selected Japanese Quail Lines.

    Science.gov (United States)

    Karabağ, Kemal; Balcıoğlu, Murat Soner; Karlı, Taki; Alkan, Sezai

    2016-12-01

    Japanese quail is still used as a model for poultry research because of their usefulness as laying, meat, and laboratory animals. Microsatellite markers are the most widely used molecular markers, due to their relative ease of scoring and high levels of polymorphism. The objective of the research was to determine genetic diversity and population genetic structures of selected Japanese quail lines (high body weight 1 [HBW1], HBW2, low body weight [LBW], and layer [L]) throughout 15th generations and an unselected control (C). A total of 69 individuals from five quail lines were genotyped by fifteen microsatellite markers. When analyzed profiles of the markers the observed (H o ) and expected (H e ) heterozygosity ranged from 0.04 (GUJ0027) to 0.64 (GUJ0087) and 0.21 (GUJ0027) to 0.84 (GUJ0037), respectively. Also, H o and H e were separated from 0.30 (L and LBW) to 0.33 (C and HBW2) and from 0.52 (HBW2) to 0.58 (L and LBW), respectively. The mean polymorphic information content (PIC) ranged from 0.46 (HBW2) to 0.52 (L). Approximately half of the markers were informative (PIC≥0.50). Genetic distances were calculated from 0.09 (HBW1 and HBW2) to 0.33 (C and L). Phylogenetic dendrogram showed that the quail lines were clearly defined by the microsatellite markers used here. Bayesian model-based clustering supported the results from the phylogenetic tree. These results reflect that the set of studied markers can be used effectively to capture the magnitude of genetic variability in selected Japanese quail lines. Also, to identify markers and alleles which are specific to the divergence lines, further generations of selection are required.

  9. Determination of the strong coupling constant from the measurement of inclusive multijet event cross sections in pp collisions at $\\sqrt{s} = 8~\\mathrm{TeV}$

    CERN Document Server

    CMS Collaboration

    2017-01-01

    A measurement of inclusive multijet event cross sections is presented from proton-proton collisions recorded at $\\sqrt{s} = 8\\,$TeV with the CMS detector and corresponding to an integrated luminosity of $19.7\\,\\mathrm{fb}^{-1}$. Jets are reconstructed with the anti-k$_t$ clustering algorithm for a jet size parameter $R=0.7$ in a phase space region ranging up to jet transverse momenta $p_\\mathrm{T}$ of $2.0\\,$TeV and an absolute rapidity of $|y|=2.5$. The inclusive 2-jet and 3-jet event cross sections are measured as a function of the average $p_\\mathrm{T}$ of the two leading jets. The data are well described by predictions at next-to-leading order in perturbative quantum chromodynamics and additionally are compared to several Monte Carlo event generators. The strong coupling constant at the scale of the Z boson mass is inferred from a fit of the ratio of the 3-jet over 2-jet event cross section giving $\\alpha_s(M_Z) = 0.1150\\,\\pm0.0010\\,\\textrm{(exp)}\\,\\pm0.0013\\,\\textrm{(PDF)}\\, \\pm0.0015\\,\\textrm{(NP)}\\,^{+...

  10. The molecular genetics of sex determination and sex reversal in mammals.

    Science.gov (United States)

    Quinn, Alexander; Koopman, Peter

    2012-10-01

    The process of sex determination in mammals normally unfolds in three distinct stages: (1) establishment of chromosomal sex at fertilization (XX or XY); (2) commitment to the appropriate pathway of gonadal differentiation with respect to chromosomal sex, through the action (or absence) of the Y chromosome gene SRY; and (3) correct development of secondary sexual characteristics, including internal and external genitalia, in accordance with gonadal sex. At any of these three steps, the process of sex determination can go awry, leading to disorders of sexual development. In this article, we review the typical mechanism and process of mammalian sex determination, with an emphasis on the well-characterized mouse and human models. We also consider aberrant mammalian sex determination, focusing on examples of sex reversal stemming from gene defects. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

  11. Determination of complex reaction mechanisms: analysis of chemical, biological, and genetic networks

    National Research Council Canada - National Science Library

    Ross, John; Schreiber, Igor; Vlad, Marcel O

    2006-01-01

    ... Systems, 40 5 Response of Systems to Pulse Perturbations, 46 5.1 5.2 Theory, 46 An Example: The Glycolytic Pathway, 53 6 Experimental Test of the Pulse Perturbation Method for Determining Causa...

  12. Population differentiation determined from putative neutral and divergent adaptive genetic markers in Eulachon (Thaleichthys pacificus, Osmeridae), an anadromous Pacific smelt.

    Science.gov (United States)

    Candy, John R; Campbell, Nathan R; Grinnell, Matthew H; Beacham, Terry D; Larson, Wesley A; Narum, Shawn R

    2015-11-01

    Twelve eulachon (Thaleichthys pacificus, Osmeridae) populations ranging from Cook Inlet, Alaska and along the west coast of North America to the Columbia River were examined by restriction-site-associated DNA (RAD) sequencing to elucidate patterns of neutral and adaptive variation in this high geneflow species. A total of 4104 single-nucleotide polymorphisms (SNPs) were discovered across the genome, with 193 putatively adaptive SNPs as determined by F(ST) outlier tests. Estimates of population structure in eulachon with the putatively adaptive SNPs were similar, but provided greater resolution of stocks compared with a putatively neutral panel of 3911 SNPs or previous estimates with 14 microsatellites. A cline of increasing measures of genetic diversity from south to north was found in the adaptive panel, but not in the neutral markers (SNPs or microsatellites). This may indicate divergent selective pressures in differing freshwater and marine environments between regional eulachon populations and that these adaptive diversity patterns not seen with neutral markers could be a consideration when determining genetic boundaries for conservation purposes. Estimates of effective population size (N(e)) were similar with the neutral SNP panel and microsatellites and may be utilized to monitor population status for eulachon where census sizes are difficult to obtain. Greater differentiation with the panel of putatively adaptive SNPs provided higher individual assignment accuracy compared to the neutral panel or microsatellites for stock identification purposes. This study presents the first SNPs that have been developed for eulachon, and analyses with these markers highlighted the importance of integrating genome-wide neutral and adaptive genetic variation for the applications of conservation and management. © 2015 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.

  13. Natural genetic variation for morphological and molecular determinants of plant growth and yield.

    Science.gov (United States)

    Nunes-Nesi, Adriano; Nascimento, Vitor de Laia; de Oliveira Silva, Franklin Magnum; Zsögön, Agustin; Araújo, Wagner L; Sulpice, Ronan

    2016-05-01

    The rates of increase in yield of the main commercial crops have been steadily falling in many areas worldwide. This generates concerns because there is a growing demand for plant biomass due to the increasing population. Plant yield should thus be improved in the context of climate change and decreasing natural resources. It is a major challenge which could be tackled by improving and/or altering light-use efficiency, CO2 uptake and fixation, primary metabolism, plant architecture and leaf morphology, and developmental plant processes. In this review, we discuss some of the traits which could lead to yield increase, with a focus on how natural genetic variation could be harnessed. Moreover, we provide insights for advancing our understanding of the molecular aspects governing plant growth and yield, and propose future avenues for improvement of crop yield. We also suggest that knowledge accumulated over the last decade in the field of molecular physiology should be integrated into new ideotypes. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  14. Determination of the Cascade Reservoir Operation for Optimal Firm-Energy Using Genetic Algorithms

    Directory of Open Access Journals (Sweden)

    Azmeri

    2013-08-01

    Full Text Available Indonesia today face a new paradigm in water management where aim to apply integrated water resources management has become unavoidable task in purpose of achieving greater level of effectiveness and efficiency. On of most interesting case study is the case of Citarum river, one of the most potential river for water supply in West Java, Indonesia. Alongside the river, Saguling, Cirata and Djuanda Reservoirs had been constructed in series/cascade. Saguling and Cirata reservoirs are particularly operated for hydroelectric power and Djuanda is multipurpose reservoir mainly operated for irrigation and contribute domestic water supply for Jakarta (capital city of Indonesia. Basically all reservoirs are relying on same resources, therefore this condition has considered addressing management and operational problem. Therefore, an approach toward new management and operation system are urgently required in order to achieve the effective and efficient output and to avoid conflicts of water used. This study aims to obtain energy production from Citarum Cascade Reservoir System using Genetic Algorithms optimization with the objective function to maximize firm-energy. Firm-energy is the minimum energy requirements must be available in a certain time period. Then, the result obtained by using the energy produced by GA is compared to the conventional searching technique of Non-Linier Programming (NLP. The GA derived operating curves reveal the higher energy and firm-energy than NLP model

  15. The determination of genetic markers of age-related cancer pathologies in populations from Kazakhstan

    Directory of Open Access Journals (Sweden)

    Leyla Bulatovna Djansugurova

    2013-05-01

    Full Text Available Aging associates with a variety of pathological conditions such as cancer, cardiovascular, neurodegenerative, autoimmune diseases, and metabolic disorders. The oncogenic alterations overlap frequently with the genes linked to aging. Here, we show that several aging related genes may serve as the genetic risk factors for cervical and esophagus cancers. In our study, we analyzed samples obtained from 115 patients with esophageal and 207 patients with cervical cancer. The control groups were selected to match the ethnicity and age of cancer patients. We examined the genes involved in the processes of xenobiotics detoxification (GSTM1 and GSTT1, DNA repair (XRCC1 and XRCC3, and cell cycle regulation and apoptosis (CCND1 and TP53. Our study revealed that deletions of GSTT1 and GSTM1 genes or the distinct point mutations of XRCC1 gene are associated with cervical and esophageal cancers. These results will lead to development of screening for detection of individuals susceptible to esophageal and cervical cancers. Introduction of the screening programs will allow the early and effective preventive measures that will reduce cancer incidence and mortality in Kazakhstan.

  16. Genetic determinants of mycophenolate-related anemia and leukopenia after transplantation.

    Science.gov (United States)

    Jacobson, Pamala A; Schladt, David; Oetting, William S; Leduc, Robert; Guan, Weihau; Matas, Arthur J; Lamba, Vishal; Mannon, Roslyn B; Julian, Bruce A; Israni, Ajay

    2011-02-15

    Mycophenolate-related anemia and leukopenia are well-known toxicities after transplantation. Toxicity leads to dose reduction, addition of colony-stimulating factors or erythropoietin, or discontinuation of immunosuppressive therapy. The causes of and risk factors associated with toxicity are unclear. We studied the association between mycophenolate-related anemia and leukopenia and 2724 single nucleotide polymorphisms (SNP) in 978 patients undergoing living or deceased donor kidney transplant. Patients were followed up to time of first anemia (hemoglobinleukopenia (white blood cell [WBC] count leukopenia in 224 (22.9%). In single SNP analyses, none of the SNPs were associated with time to leukopenia at a false discovery rate (FDR) of 20%. However, SNPs from the IL12A, HUS, CYP2C8 genes were associated with time to anemia, allowing for an FDR of 20%. To assess the independence of these SNPs as predictors of anemia, we conducted a multi-SNP analysis including one SNP from each of the three genes. All three SNPs were associated with time to anemia, after adjusting for recipient age, weight, posttransplant dialysis and antiviral drug use, and stratifying by clinical center. Although these SNPs require validation in an independent population, our results suggest that genetics may play a role in risk of mycophenolate-related hematologic toxicity. This may ultimately provide for better management of maintenance immunosuppression and gives insights into potential mechanism(s) by which toxicity occurs.

  17. Genetic Determinants of RNA Editing Levels of ADAR Targets in Drosophila melanogaster.

    Science.gov (United States)

    Kurmangaliyev, Yerbol Z; Ali, Sammi; Nuzhdin, Sergey V

    2015-12-12

    RNA editing usually affects only a fraction of expressed transcripts and there is a vast amount of variation in editing levels of ADAR (adenosine deaminase, RNA-specific) targets. Here we explore natural genetic variation affecting editing levels of particular sites in 81 natural strains of Drosophila melanogaster. The analysis of associations between editing levels and single-nucleotide polymorphisms allows us to map putative cis-regulatory regions affecting editing of 16 A-to-I editing sites (cis-RNA editing quantitative trait loci or cis-edQTLs, P < 10(-8)). The observed changes in editing levels are validated by independent molecular technique. All identified regulatory variants are located in close proximity of modulated editing sites. Moreover, colocalized editing sites are often regulated by same loci. Similar to expression and splicing QTL studies, the characterization of edQTLs will greatly expand our understanding of cis-regulatory evolution of gene expression. Copyright © 2016 Kurmangaliyev et al.

  18. Alcohol Dehydrogenase-1B (rs1229984 and Aldehyde Dehydrogenase-2 (rs671 Genotypes Are Strong Determinants of the Serum Triglyceride and Cholesterol Levels of Japanese Alcoholic Men.

    Directory of Open Access Journals (Sweden)

    Akira Yokoyama

    Full Text Available Elevated serum triglyceride (TG and high-density-lipoprotein cholesterol (HDL-C levels are common in drinkers. The fast-metabolizing alcohol dehydrogenase-1B encoded by the ADH1B*2 allele (vs. ADH1B*1/*1 genotype and inactive aldehyde dehydrogenase-2 encoded by the ALDH2*2 allele (vs. ALDH2*1/*1 genotype modify ethanol metabolism and are prevalent (≈90% and ≈40%, respectively in East Asians. We attempted to evaluate the associations between the ADH1B and ALDH2 genotypes and lipid levels in alcoholics.The population consisted of 1806 Japanese alcoholic men (≥40 years who had undergone ADH1B and ALDH2 genotyping and whose serum TG, total cholesterol, and HDL-C levels in the fasting state had been measured within 3 days after admission.High serum levels of TG (≥150 mg/dl, HDL-C (>80 mg/dl, and low-density-lipoprotein cholesterol (LDL-C calculated by the Friedewald formula ≥140 mg/dl were observed in 24.3%, 16.8%, and 15.6%, respectively, of the subjects. Diabetes, cirrhosis, smoking, and body mass index (BMI affected the serum lipid levels. Multivariate analysis revealed that the presence of the ADH1B*2 allele and the active ALDH2*1/*1 genotype increased the odds ratio (OR; 95% confidence interval for a high TG level (2.22 [1.67-2.94] and 1.39 [0.99-1.96], respectively, and decreased the OR for a high HDL-C level (0.37 [0.28-0.49] and 0.51 [0.37-0.69], respectively. The presence of the ADH1B*2 allele decreased the OR for a high LDL-C level (0.60 [0.45-0.80]. The ADH1B*2 plus ALDH2*1/*1 combination yielded the highest ORs for high TG levels and lowest OR for a high HDL-C level. The genotype effects were more prominent in relation to the higher levels of TG (≥220 mg/dl and HDL-C (≥100 mg/dl.The fast-metabolizing ADH1B and active ALDH2, and especially a combination of the two were strongly associated with higher serum TG levels and lower serum HDL-C levels of alcoholics. The fast-metabolizing ADH1B was associated with lower serum LDL

  19. Genetically determined differences in brain response to a primary food reward.

    Science.gov (United States)

    Felsted, Jennifer A; Ren, Xueying; Chouinard-Decorte, Francois; Small, Dana M

    2010-02-17

    Combining genetic and neuroimaging techniques may elucidate the biological underpinnings of individual differences in neurophysiology and potential vulnerabilities to disease. The TaqIA A1 variant is associated with diminished dopamine D(2) receptor density, higher body mass, and food reinforcement. It also moderates the relationship between brain response to food and future weight gain. This suggests that the polymorphism is associated with a fundamental difference in the neurophysiology of food that may predispose toward overeating. An alternative possibility is that factors, such as impulsivity, eating style, reward drive, and perception, which may covary with the polymorphism, influence reward coding and eating behavior. To distinguish between these alternatives, we used functional magnetic resonance imaging to measure neural response to the ingestion of palatable and caloric milkshakes in healthy subjects with (A1+; n = 13) and without (A1-; n = 13) the TaqIA A1 allele. The groups were selected from a larger group to be matched for linked individual factors such as age, gender, education, body mass index, impulsivity, eating style, and perceptual responses to the milkshake. We demonstrate an interaction between genotype (A1+ vs A1-) and stimulus (milkshake vs a tasteless/odorless baseline) in the midbrain, thalamus, and orbital frontal cortex; whereas A1- shows increased responses to milkshake, A1+ shows decreased responses to milkshake relative to baseline. This interaction occurs despite similar ratings of milkshake pleasantness, intensity, and familiarity. We therefore conclude that there is a specific association between the TaqIA A1 polymorphism and brain response during ingestion of a palatable food.

  20. What determines the acceptability of genetically modified food that can improve human nutrition?

    Science.gov (United States)

    Purchase, Iain F H

    2005-09-01

    It has been predicted that by 2025 there will be an annual shortfall of cereals for feeding the human population of 68.5 million tones. One possible solution is the use of genetically modified (GM) crops, which are already grown extensively (59 million ha of GM crops were planted in 2002) in the USA, South America, Africa and China. Nevertheless, there is considerable disagreement about the advisability of using such crops, particularly in Europe. Obviously, the safety of the food derived from the GM crops is a primary consideration. Safety assessment relies on establishing that the food is substantially equivalent to its non-GM counterpart and specific testing for allergenicity of proteins and toxicity of metabolites and the whole food. There appears to be international agreement on the principles of safety assessment. Safety to the environment is equally important, but will not be covered in this presentation. The public's perception of the risk of new technology is critical to its acceptance. Perception of risk, in turn, depends on the credibility of the source of the information and trust in the regulatory process. In many countries, the public appears to have lost its trust in the scientists and government dealing with GM food, making the acceptability of GM crops uncertain. Of equal importance are the socio-economic factors that impinge on the viability of GM produce. These include intellectual property protection, trade liberalization (through subsidy and tariff barriers in developed countries) and the intensity of bio safety regulations. The socio-economic interests of developed and developing countries may diverge and may even be contradictory in any one country. Acceptance of GM crops will thus depend on detailed issues surrounding particular crops and economies.

  1. Copy number ratios determined by two digital polymerase chain reaction systems in genetically modified grains

    Science.gov (United States)

    Pérez Urquiza, M.; Acatzi Silva, A. I.

    2014-02-01

    Three certified reference materials produced from powdered seeds to measure the copy number ratio sequences of p35S/hmgA in maize containing MON 810 event, p35S/Le1 in soybeans containing GTS 40-3-2 event and DREB1A/acc1 in wheat were produced according to the ISO Guides 34 and 35. In this paper, we report digital polymerase chain reaction (dPCR) protocols, performance parameters and results of copy number ratio content of genetically modified organisms (GMOs) in these materials using two new dPCR systems to detect and quantify molecular deoxyribonucleic acid: the BioMark® (Fluidigm) and the OpenArray® (Life Technologies) systems. These technologies were implemented at the National Institute of Metrology in Mexico (CENAM) and in the Reference Center for GMO Detection from the Ministry of Agriculture (CNRDOGM), respectively. The main advantage of this technique against the more-used quantitative polymerase chain reaction (qPCR) is that it generates an absolute number of target molecules in the sample, without reference to standards or an endogenous control, which is very useful when not much information is available for new developments or there are no standard reference materials in the market as in the wheat case presented, or when it was not possible to test the purity of seeds as in the maize case presented here. Both systems reported enhanced productivity, increased reliability and reduced instrument footprint. In this paper, the performance parameters and uncertainty of measurement obtained with both systems are presented and compared.

  2. What determines the acceptability of genetically modified food that can improve human nutrition?

    International Nuclear Information System (INIS)

    Purchase, Iain F.H.

    2005-01-01

    It has been predicted that by 2025 there will be an annual shortfall of cereals for feeding the human population of 68.5 million tonnes. One possible solution is the use of genetically modified (GM) crops, which are already grown extensively (59 million ha of GM crops were planted in 2002) in the USA, South America, Africa and China. Nevertheless, there is considerable disagreement about the advisability of using such crops, particularly in Europe. Obviously, the safety of the food derived from the GM crops is a primary consideration. Safety assessment relies on establishing that the food is substantially equivalent to its non-GM counterpart and specific testing for allergenicity of proteins and toxicity of metabolites and the whole food. There appears to be international agreement on the principles of safety assessment. Safety to the environment is equally important, but will not be covered in this presentation. The public's perception of the risk of new technology is critical to its acceptance. Perception of risk, in turn, depends on the credibility of the source of the information and trust in the regulatory process. In many countries, the public appears to have lost its trust in the scientists and government dealing with GM food, making the acceptability of GM crops uncertain. Of equal importance are the socio-economic factors that impinge on the viability of GM produce. These include intellectual property protection, trade liberalisation (through subsidy and tariff barriers in developed countries) and the intensity of bio safety regulations. The socio-economic interests of developed and developing countries may diverge and may even be contradictory in any one country. Acceptance of GM crops will thus depend on detailed issues surrounding particular crops and economies

  3. Genetic Determinants of Cisplatin Resistance in Patients With Advanced Germ Cell Tumors.

    Science.gov (United States)

    Bagrodia, Aditya; Lee, Byron H; Lee, William; Cha, Eugene K; Sfakianos, John P; Iyer, Gopa; Pietzak, Eugene J; Gao, Sizhi Paul; Zabor, Emily C; Ostrovnaya, Irina; Kaffenberger, Samuel D; Syed, Aijazuddin; Arcila, Maria E; Chaganti, Raju S; Kundra, Ritika; Eng, Jana; Hreiki, Joseph; Vacic, Vladimir; Arora, Kanika; Oschwald, Dayna M; Berger, Michael F; Bajorin, Dean F; Bains, Manjit S; Schultz, Nikolaus; Reuter, Victor E; Sheinfeld, Joel; Bosl, George J; Al-Ahmadie, Hikmat A; Solit, David B; Feldman, Darren R

    2016-11-20

    Purpose Owing to its exquisite chemotherapy sensitivity, most patients with metastatic germ cell tumors (GCTs) are cured with cisplatin-based chemotherapy. However, up to 30% of patients with advanced GCT exhibit cisplatin resistance, which requires intensive salvage treatment, and have a 50% risk of cancer-related death. To identify a genetic basis for cisplatin resistance, we performed whole-exome and targeted sequencing of cisplatin-sensitive and cisplatin-resistant GCTs. Methods Men with GCT who received a cisplatin-containing chemotherapy regimen and had available tumor tissue were eligible to participate in this study. Whole-exome sequencing or targeted exon-capture-based sequencing was performed on 180 tumors. Patients were categorized as cisplatin sensitive or cisplatin resistant by using a combination of postchemotherapy parameters, including serum tumor marker levels, radiology, and pathology at surgical resection of residual disease. Results TP53 alterations were present exclusively in cisplatin-resistant tumors and were particularly prevalent among primary mediastinal nonseminomas (72%). TP53 pathway alterations including MDM2 amplifications were more common among patients with adverse clinical features, categorized as poor risk according to the International Germ Cell Cancer Collaborative Group (IGCCCG) model. Despite this association, TP53 and MDM2 alterations predicted adverse prognosis independent of the IGCCCG model. Actionable alterations, including novel RAC1 mutations, were detected in 55% of cisplatin-resistant GCTs. Conclusion In GCT, TP53 and MDM2 alterations were associated with cisplatin resistance and inferior outcomes, independent of the IGCCCG model. The finding of frequent TP53 alterations among mediastinal primary nonseminomas may explain the more frequent chemoresistance observed with this tumor subtype. A substantial portion of cisplatin-resistant GCTs harbor actionable alterations, which might respond to targeted therapies. Genomic

  4. Fine-scale variation and genetic determinants of alternative splicing across individuals.

    Directory of Open Access Journals (Sweden)

    Jasmin Coulombe-Huntington

    2009-12-01

    Full Text Available Recently, thanks to the increasing throughput of new technologies, we have begun to explore the full extent of alternative pre-mRNA splicing (AS in the human transcriptome. This is unveiling a vast layer of complexity in isoform-level expression differences between individuals. We used previously published splicing sensitive microarray data from lymphoblastoid cell lines to conduct an in-depth analysis on splicing efficiency of known and predicted exons. By combining publicly available AS annotation with a novel algorithm designed to search for AS, we show that many real AS events can be detected within the usually unexploited, speculative majority of the array and at significance levels much below standard multiple-testing thresholds, demonstrating that the extent of cis-regulated differential splicing between individuals is potentially far greater than previously reported. Specifically, many genes show subtle but significant genetically controlled differences in splice-site usage. PCR validation shows that 42 out of 58 (72% candidate gene regions undergo detectable AS, amounting to the largest scale validation of isoform eQTLs to date. Targeted sequencing revealed a likely causative SNP in most validated cases. In all 17 incidences where a SNP affected a splice-site region, in silico splice-site strength modeling correctly predicted the direction of the micro-array and PCR results. In 13 other cases, we identified likely causative SNPs disrupting predicted splicing enhancers. Using Fst and REHH analysis, we uncovered significant evidence that 2 putative causative SNPs have undergone recent positive selection. We verified the effect of five SNPs using in vivo minigene assays. This study shows that splicing differences between individuals, including quantitative differences in isoform ratios, are frequent in human populations and that causative SNPs can be identified using in silico predictions. Several cases affected disease-relevant genes and

  5. [Crohns disease and ulcerative colitis - current view on genetic determination, immunopathogenesis and biologic therapy].

    Science.gov (United States)

    Buc, M

    2017-01-01

    Crohns disease (CD) and ulcerative colitis (UC) are chronic inflammatory disorders of the intestine, also called inflammatory bowel diseases (IBD), which are not caused by pathogenic microorganisms but result from non-specific inflammatory processes in the bowel. IBD are polygenic diseases, as evidenced by the genome-wide association studies (GWAS), which have discovered more than 200 genes or genetic regions to be associated with IBD. Some of them are specific for CD or UC; however, there are 110 overlapping genes. In the pathogenesis of CD, activation of adaptive immunity mediated by TH1, TH17, or TH1/TH17 cells is induced because of disturbances in the mechanisms of innate immunity and autophagocytosis. By comparison, the major events that trigger autoimmune processes in UC are an increased translocation of commensal bacteria into the submucosa because of loose inter-epithelial connections with subsequent activation of ILC2, TH9, TH2, and NKT cells. Knowledge of the pathogenesis of a disease enables an effective therapy, which is especially true for biological therapy. It is noteworthy that monoclonal antibodies directed against the major protagonists underlying both CD and UC have failed. It points to the complexity of immunopathologic processes that run in both diseases. One can suppose that a blockade of one inflammatory pathway is circumvented by an alternative pathway. TNF is the principal pro-inflammatory cytokine that plays a major role in CD and UC as well. It was therefore decided to treat IBD patients with anti-TNF monoclonal antibodies, infliximab or adalimumab. Approximately one half of the CD patients and one third of the UC patients respond to this treatment.

  6. Home Environment as Strong Determinant in Academic Involvement of Female Students in Dhekia Gram Panchayat of Saltora C.D. Block, Bankura District

    Directory of Open Access Journals (Sweden)

    Ayanika Sarkar

    2017-11-01

    Full Text Available Education is a learnt behaviour, which shapes and moulds the nature of a human being by transforming him/her into a human resource and helps in social progress. Children start learning in the lap of their parents. They are bought up by accumulating the knowledge gained from the interaction with the family members. This interaction varies from one family to another. Even when they start going to an institution for the formal education, home environment leaves an influence on his/her attitude towards education. In addition to institutional influence, proper understanding of the impact of home environment is essential for taking due care in development of human resource. Backwardness of the female students in different hierarchies of the educational sector is a major concern in India as well as in West Bengal since a very long period. In spite of ample efforts to increase the rate of enrolment and to develop the quality of education in both national and state level, the progress in terms of actual involvement in educational activities is not up to the mark in many cases. In the light of this background, a grass-root level study has been conducted to understand the role of home environment on determining the academic involvement of the female students belonging to different hierarchies of tribe-caste continuum in a rural context of Bankura District, West Bengal. It aims to identify the major components of home environment, which determine the level of cohort specific academic involvement in the type of families from different social background. In order to retrieve various perspectives on their home environment, we surveyed female students reading in VIII —XII and belonging to the age group 13 to 18 years. From the micro level analysis, it has been found that caste and tribal identity based disparity as well as family type wise differences in level of academic involvement (LAI is profound in the study area. Home environment is having a significant

  7. Other paradigms: growth rate constants and tumor burden determined using computed tomography data correlate strongly with the overall survival of patients with renal cell carcinoma.

    Science.gov (United States)

    Stein, Wilfred D; Huang, Hui; Menefee, Michael; Edgerly, Maureen; Kotz, Herb; Dwyer, Andrew; Yang, James; Bates, Susan E

    2009-01-01

    In solid tumors, where curative therapies still elude oncologists, novel paradigms are needed to assess the efficacy of new therapies and those already approved. We used radiologic measurements obtained in patients with metastatic renal cell carcinoma enrolled in a phase II study of the epothilone B analog, ixabepilone (Ixempra), to address this issue. Using a novel 2-phase mathematical equation, we used the radiologic measurements to estimate the concomitant rates of tumor regression and growth (regression and growth rate constants). Eighty-one patients were enrolled on the ixabepilone trial at the time of this analysis. Growth rate constants were determined using computed tomography measurements obtained exclusively while a patient was enrolled on study. The growth rate constants of renal cell carcinomas treated with ixabepilone were significantly reduced compared with those of tumors in patients who received placebo in a previous trial. Furthermore, a correlation with overall survival was found for both the growth rate constant and the initial tumor burden; and this correlation was even stronger when both the growth rate constant and the initial tumor burden were combined. The readily amenable mathematical model described herein has potential applications to many tumor types that can be assessed with imaging modalities. Because the growth rate constant seems to be a surrogate for survival, assessment could aid in the evaluation of relative efficacies of different therapies and perhaps in assessing the potential individual benefit of an experimental therapy.

  8. Genetically determined differences in the resistance to myocardial infarction in Wistar and August rats.

    Science.gov (United States)

    Belkina, L M; Saltykova, V A; Pshennikova, M G

    2001-06-01

    In intact August rats, the cardiac contractile function at rest was by 76% higher than in Wistar rats, while their hearts, both intact and after acute myocardial infarction, were more resistant to isometric load than the hearts of Wistar rats. Postinfarction mortality in August rats was 18% vs. 70% in Wistar rats. Adrenoreactivity of the myocardium in August rats was decreased compared to that in Wistar rats. These peculiarities can determine high resistance of August rats to myocardial infarction.

  9. Determination of the strong coupling constant α{sub s}(m{sub Z}) in next-to-next-to-leading order QCD using H1 jet cross section measurements

    Energy Technology Data Exchange (ETDEWEB)

    Andreev, V.; Belousov, A.; Fomenko, A.; Gogitidze, N.; Lebedev, A.; Malinovski, E.; Soloviev, Y.; Vazdik, Y. [Lebedev Physical Institute, Moscow (Russian Federation); Baghdasaryan, A.; Zohrabyan, H. [Yerevan Physics Institute, Yerevan (Armenia); Begzsuren, K.; Ravdandorj, T. [Institute of Physics and Technology of the Mongolian Academy of Sciences, Ulaanbaatar (Mongolia); Bertone, V. [Vrije University, Department of Physics and Astronomy, Amsterdam (Netherlands); National Institute for Subatomic Physics (NIKHEF), Amsterdam (Netherlands); Bolz, A.; Britzger, D.; Huber, F.; Sauter, M.; Schoening, A. [Universitaet Heidelberg, Physikalisches Institut, Heidelberg (Germany); Boudry, V.; Specka, A. [LLR, Ecole Polytechnique, CNRS/IN2P3, Palaiseau (France); Brandt, G. [Universitaet Goettingen, II. Physikalisches Institut, Goettingen (Germany); Brisson, V.; Jacquet, M.; Pascaud, C.; Zhang, Z.; Zomer, F. [LAL, Universite Paris-Sud, CNRS/IN2P3, Orsay (France); Buniatyan, A.; Newman, P.R.; Thompson, P.D. [University of Birmingham, School of Physics and Astronomy, Birmingham (United Kingdom); Bylinkin, A. [Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region (Russian Federation); Bystritskaya, L.; Fedotov, A. [Institute for Theoretical and Experimental Physics, Moscow (Russian Federation); Campbell, A.J.; Dodonov, V.; Eckerlin, G.; Elsen, E.; Fleischer, M.; Gayler, J.; Ghazaryan, S.; Haidt, D.; Jung, H.; Katzy, J.; Kleinwort, C.; Kruecker, D.; Krueger, K.; Levonian, S.; Lipka, K.; List, B.; List, J.; Meyer, A.B.; Meyer, J.; Niebuhr, C.; Olsson, J.E.; Pirumov, H.; Pitzl, D.; Placakyte, R.; Schmitt, S.; Sefkow, F.; South, D.; Steder, M.; Wuensch, E.; Zlebcik, R. [DESY, Hamburg (Germany); Cantun Avila, K.B.; Contreras, J.G. [CINVESTAV, Departamento de Fisica Aplicada, Merida, Yucatan (Mexico); Cerny, K.; Salek, D.; Valkarova, A.; Zacek, J. [Charles University, Faculty of Mathematics and Physics, Prague (Czech Republic); Chekelian, V.; Grindhammer, G.; Kiesling, C.; Lobodzinski, B. [Max-Planck-Institut fuer Physik, Munich (Germany); Cvach, J.; Hladky, J.; Reimer, P. [Academy of Sciences of the Czech Republic, Institute of Physics, Prague (Czech Republic); Currie, J. [Durham University, Institute for Particle Physics Phenomenology, Ogden Centre for Fundamental Physics, Durham (United Kingdom); Dainton, J.B.; Gabathuler, E.; Greenshaw, T.; Klein, M.; Kostka, P.; Kretzschmar, J.; Laycock, P.; Maxfield, S.J.; Mehta, A.; Patel, G.D. [University of Liverpool, Department of Physics, Liverpool (United Kingdom); Daum, K.; Meyer, H. [Fachbereich C, Universitaet Wuppertal, Wuppertal (Germany); Diaconu, C.; Hoffmann, D.; Vallee, C. [Aix Marseille Universite, CNRS/IN2P3, CPPM UMR 7346, Marseille (France); Dobre, M.; Rotaru, M. [Horia Hulubei National Institute for R and D in Physics and Nuclear Engineering (IFIN-HH), Bucharest (Romania); Egli, S.; Horisberger, R.; Ozerov, D. [Paul Scherrer Institute, Villigen (Switzerland); Favart, L.; Grebenyuk, A.; Hreus, T.; Janssen, X.; Roosen, R.; Mechelen, P.Van [Brussels and Universiteit Antwerpen, Inter-University Institute for High Energies ULB-VUB, Antwerp (Belgium); Feltesse, J.; Schoeffel, L. [Irfu/SPP, CE Saclay, Gif-sur-Yvette (France); Gehrmann, T.; Mueller, K.; Niehues, J.; Robmann, P.; Straumann, U.; Truoel, P. [Physik-Institut der Universitaet Zuerich, Zurich (Switzerland); Goerlich, L.; Mikocki, S.; Nowak, G.; Sopicki, P. [Polish Academy of Sciences, Institute of Nuclear Physics, Krakow (Poland); Gouzevitch, M.; Petrukhin, A. [IPNL, Universite Claude Bernard Lyon 1, CNRS/IN2P3, Villeurbanne (France); Grab, C.; Huss, A. [ETH Zuerich, Institut fuer Teilchenphysik, Zurich (Switzerland); Gwenlan, C.; Radescu, V. [Oxford University, Department of Physics, Oxford (United Kingdom); Henderson, R.C.W. [University of Lancaster, Department of Physics, Lancaster (United Kingdom); Jung, A.W. [Purdue University, Department of Physics and Astronomy, West Lafayette, IN (United States); Kapichine, M.; Morozov, A.; Spaskov, V. [Joint Institute for Nuclear Research, Dubna (Russian Federation); Kogler, R. [Universitaet Hamburg, Institut fuer Experimentalphysik, Hamburg (Germany); Landon, M.P.J.; Rizvi, E.; Traynor, D. [Queen Mary University of London, School of Physics and Astronomy, London (United Kingdom); Lange, W.; Naumann, T. [DESY, Zeuthen (Germany); Martyn, H.U. [I. Physikalisches Institut der RWTH, Aachen (Germany); Perez, E. [CERN, Geneva (Switzerland); Picuric, I.; Raicevic, N. [University of Montenegro, Faculty of Science, Podgorica (Montenegro); Polifka, R. [Charles University, Faculty of Mathematics and Physics, Prague (Czech Republic); University of Toronto, Department of Physics, Toronto, ON (Canada); Rabbertz, K. [Karlsruher Institut fuer Technologie (KIT), Institut fuer Experimentelle Teilchenphysik (ETP), Karlsruhe (Germany); Rostovtsev, A. [Institute for Information Transmission Problems RAS, Moscow (Russian Federation); Sankey, D.P.C. [STFC, Rutherford Appleton Laboratory, Didcot, Oxfordshire (United Kingdom); Sauvan, E. [Aix Marseille Universite, CNRS/IN2P3, CPPM UMR 7346, Marseille (France); Universite de Savoie, CNRS/IN2P3, LAPP, Annecy-le-Vieux (France); Shushkevich, S. [Lomonosov Moscow State University, Skobeltsyn Institute of Nuclear Physics, Moscow (Russian Federation); Stella, B. [Universita di Roma Tre, Dipartimento di Fisica, Rome (Italy); INFN Roma 3 (Italy); Sutton, M.R. [University of Sussex, Department of Physics and Astronomy, Brighton (United Kingdom); Sykora, T. [Brussels and Universiteit Antwerpen, Inter-University Institute for High Energies ULB-VUB, Antwerp (Belgium); Charles University, Faculty of Mathematics and Physics, Prague (Czech Republic); Tsakov, I. [Institute for Nuclear Research and Nuclear Energy, Sofia (Bulgaria); Tseepeldorj, B. [Institute of Physics and Technology of the Mongolian Academy of Sciences, Ulaanbaatar (MN); Ulaanbaatar University, Ulaanbaatar (MN); Wegener, D. [TU Dortmund, Institut fuer Physik, Dortmund (DE); Collaboration: H1 Collaboration

    2017-11-15

    The strong coupling constant α{sub s} is determined from inclusive jet and dijet cross sections in neutral-current deep-inelastic ep scattering (DIS) measured at HERA by the H1 collaboration using next-to-next-to-leading order (NNLO) QCD predictions. The dependence of the NNLO predictions and of the resulting value of α{sub s}(m{sub Z}) at the Z-boson mass m{sub Z} are studied as a function of the choice of the renormalisation and factorisation scales. Using inclusive jet and dijet data together, the strong coupling constant is determined to be α{sub s}(m{sub Z}) = 0.1157(20){sub exp}(29){sub th}. Complementary, α{sub s}(m{sub Z}) is determined together with parton distribution functions of the proton (PDFs) from jet and inclusive DIS data measured by the H1 experiment. The value α{sub s}(m{sub Z}) = 0.1142(28){sub tot} obtained is consistent with the determination from jet data alone. The impact of the jet data on the PDFs is studied. The running of the strong coupling is tested at different values of the renormalisation scale and the results are found to be in agreement with expectations. (orig.)

  10. The Decision Support System (DSS) Application to Determination of Diabetes Mellitus Patient Menu Using a Genetic Algorithm Method

    Science.gov (United States)

    Zuliyana, Nia; Suseno, Jatmiko Endro; Adi, Kusworo

    2018-02-01

    Composition of foods containing sugar in people with Diabetes Mellitus should be balanced, so an app is required for facilitate the public and nutritionists in determining the appropriate food menu with calorie requirement of diabetes patient. This research will be recommended to determination of food variation for using Genetic Algorithm. The data used is nutrient content of food obtained from Tabel Komposisi Pangan Indonesia (TKPI). The requirement of caloric value the patient can be used the PERKENI 2015 method. Then the data is processed to determine the best food menu consisting of energy (E), carbohydrate (K), fat (L) and protein (P) requirements. The system is comparised with variation of Genetic Algorithm parameters is the total of chromosomes, Probability of Crossover (Pc) and Probability of Mutation (Pm). Maximum value of the probability generation of crossover and probability of mutation will be the more variations of food that will come out. For example, patient with gender is women aged 61 years old, height 160 cm, weight 55 kg, will be resulted number of calories: (E=1621.4, K=243.21, P=60.80, L=45.04), with the gene=4, chromosomes=3, generation=3, Pc=0.2, and Pm=0.2. The result obtained is the three varians: E=1607.25, K=198.877, P=95.385, L=47.508), (E=1633.25, K=196.677, P=85.885, L=55.758), (E=1630.90, K=177.455, P=85.245, L=64.335).

  11. The Decision Support System (DSS Application to Determination of Diabetes Mellitus Patient Menu Using a Genetic Algorithm Method

    Directory of Open Access Journals (Sweden)

    Zuliyana Nia

    2018-01-01

    Full Text Available Composition of foods containing sugar in people with Diabetes Mellitus should be balanced, so an app is required for facilitate the public and nutritionists in determining the appropriate food menu with calorie requirement of diabetes patient. This research will be recommended to determination of food variation for using Genetic Algorithm. The data used is nutrient content of food obtained from Tabel Komposisi Pangan Indonesia (TKPI. The requirement of caloric value the patient can be used the PERKENI 2015 method. Then the data is processed to determine the best food menu consisting of energy (E, carbohydrate (K, fat (L and protein (P requirements. The system is comparised with variation of Genetic Algorithm parameters is the total of chromosomes, Probability of Crossover (Pc and Probability of Mutation (Pm. Maximum value of the probability generation of crossover and probability of mutation will be the more variations of food that will come out. For example, patient with gender is women aged 61 years old, height 160 cm, weight 55 kg, will be resulted number of calories: (E=1621.4, K=243.21, P=60.80, L=45.04, with the gene=4, chromosomes=3, generation=3, Pc=0.2, and Pm=0.2. The result obtained is the three varians: E=1607.25, K=198.877, P=95.385, L=47.508, (E=1633.25, K=196.677, P=85.885, L=55.758, (E=1630.90, K=177.455, P=85.245, L=64.335.

  12. A haploid genetic screen identifies the G1/S regulatory machinery as a determinant of Wee1 inhibitor sensitivity.

    Science.gov (United States)

    Heijink, Anne Margriet; Blomen, Vincent A; Bisteau, Xavier; Degener, Fabian; Matsushita, Felipe Yu; Kaldis, Philipp; Foijer, Floris; van Vugt, Marcel A T M

    2015-12-08

    The Wee1 cell cycle checkpoint kinase prevents premature mitotic entry by inhibiting cyclin-dependent kinases. Chemical inhibitors of Wee1 are currently being tested clinically as targeted anticancer drugs. Wee1 inhibition is thought to be preferentially cytotoxic in p53-defective cancer cells. However, TP53 mutant cancers do not respond consistently to Wee1 inhibitor treatment, indicating the existence of genetic determinants of Wee1 inhibitor sensitivity other than TP53 status. To optimally facilitate patient selection for Wee1 inhibition and uncover potential resistance mechanisms, identification of these currently unknown genes is necessary. The aim of this study was therefore to identify gene mutations that determine Wee1 inhibitor sensitivity. We performed a genome-wide unbiased functional genetic screen in TP53 mutant near-haploid KBM-7 cells using gene-trap insertional mutagenesis. Insertion site mapping of cells that survived long-term Wee1 inhibition revealed enrichment of G1/S regulatory genes, including SKP2, CUL1, and CDK2. Stable depletion of SKP2, CUL1, or CDK2 or chemical Cdk2 inhibition rescued the γ-H2AX induction and abrogation of G2 phase as induced by Wee1 inhibition in breast and ovarian cancer cell lines. Remarkably, live cell imaging showed that depletion of SKP2, CUL1, or CDK2 did not rescue the Wee1 inhibition-induced karyokinesis and cytokinesis defects. These data indicate that the activity of the DNA replication machinery, beyond TP53 mutation status, determines Wee1 inhibitor sensitivity, and could serve as a selection criterion for Wee1-inhibitor eligible patients. Conversely, loss of the identified S-phase genes could serve as a mechanism of acquired resistance, which goes along with development of severe genomic instability.

  13. Mammalian Cardiovascular Patterning as Determined by Hemodynamic Forces and Blood Vessel Genetics

    Science.gov (United States)

    Anderson, Gregory Arthur

    Cardiovascular development is a process that involves the timing of multiple molecular events, and numerous subtle three-dimensional conformational changes. Traditional developmental biology techniques have provided large quantities of information as to how these complex organ systems develop. However, the major drawback of the majority of current developmental biological imaging is that they are two-dimensional in nature. It is now well recognized that circulation of blood is required for normal patterning and remodeling of blood vessels. Normal blood vessel formation is dependent upon a complex network of signaling pathways, and genetic mutations in these pathways leads to impaired vascular development, heart failure, and lethality. As such, it is not surprising that mutant mice with aberrant cardiovascular patterning are so common, since normal development requires proper coordination between three systems: the heart, the blood, and the vasculature. This thesis describes the implementation of a three-dimensional imaging technique, optical projection tomography (OPT), in conjunction with a computer-based registration algorithm to statistically analyze developmental differences in groups of wild-type mouse embryos. Embryos that differ by only a few hours' gestational time are shown to have developmental differences in blood vessel formation and heart development progression that can be discerned. This thesis describes how we analyzed mouse models of cardiovascular perturbation by OPT to detect morphological differences in embryonic development in both qualitative and quantitative ways. Both a blood vessel specific mutation and a cardiac specific mutation were analyzed, providing evidence that developmental defects of these types can be quantified. Finally, we describe the implementation of OPT imaging to identify statistically significant phenotypes from three different mouse models of cardiovascular perturbation across a range of developmental time points. Image

  14. Genetic determinants of cardiovascular events among women with migraine: a genome-wide association study.

    Directory of Open Access Journals (Sweden)

    Markus Schürks

    Full Text Available Migraine is associated with an increased risk for cardiovascular disease (CVD. Both migraine and CVD are highly heritable. However, the genetic liability for CVD among migraineurs is unclear.We performed a genome-wide association study for incident CVD events during 12 years of follow-up among 5,122 migraineurs participating in the population-based Women's Genome Health Study. Migraine was self-reported and CVD events were confirmed after medical records review. We calculated odds ratios (OR and 95% confidence intervals (CI and considered a genome-wide p-value <5×10(-8 as significant.Among the 5,122 women with migraine 164 incident CVD events occurred during follow-up. No SNP was associated with major CVD, ischemic stroke, myocardial infarction, or CVD death at the genome-wide level; however, five SNPs showed association with p<5×10(-6. Among migraineurs with aura rs7698623 in MEPE (OR = 6.37; 95% CI 3.15-12.90; p = 2.7×10(-7 and rs4975709 in IRX4 (OR = 5.06; 95% CI 2.66-9.62; p = 7.7×10(-7 appeared to be associated with ischemic stroke, rs2143678 located close to MDF1 with major CVD (OR = 3.05; 95% CI 1.98-4.69; p = 4.3×10(-7, and the intergenic rs1406961 with CVD death (OR = 12.33; 95% CI 4.62-32.87; p = 5.2×10(-7. Further, rs1047964 in BACE1 appeared to be associated with CVD death among women with any migraine (OR = 4.67; 95% CI 2.53-8.62; p = 8.0×10(-7.Our results provide some suggestion for an association of five SNPs with CVD events among women with migraine; none of the results was genome-wide significant. Four associations appeared among migraineurs with aura, two of those with ischemic stroke. Although our population is among the largest with migraine and incident CVD information, these results must be treated with caution, given the limited number of CVD events among women with migraine and the low minor allele frequencies for three of the SNPs. Our results await independent replication

  15. Genetically determined ancestry is more informative than self-reported race in HIV-infected and -exposed children

    Science.gov (United States)

    Spector, Stephen A.; Brummel, Sean S.; Nievergelt, Caroline M.; Maihofer, Adam X.; Singh, Kumud K.; Purswani, Murli U.; Williams, Paige L.; Hazra, Rohan; Van Dyke, Russell; Seage, George R.

    2016-01-01

    Abstract The Pediatric HIV/AIDS Cohort Study (PHACS), the largest ongoing longitudinal study of perinatal HIV-infected (PHIV) and HIV-exposed, uninfected (PHEU) children in the United States, comprises the Surveillance Monitoring of Antiretroviral Therapy [ART] Toxicities (SMARTT) Study in PHEU children and the Adolescent Master Protocol (AMP) that includes PHIV and PHEU children ≥7 years. Although race/ethnicity is often used to assess health outcomes, this approach remains controversial and may fail to accurately reflect the backgrounds of ancestry-diverse populations as represented in the PHACS participants. In this study, we compared genetically determined ancestry (GDA) and self-reported race/ethnicity (SRR) in the PHACS cohort. GDA was estimated using a highly discriminative panel of 41 single nucleotide polymorphisms and compared to SRR. Because SRR was similar between the PHIV and PHEU, and between the AMP and SMARTT cohorts, data for all unique 1958 participants were combined. According to SRR, 63% of study participants identified as Black/African-American, 27% White, and 34% Hispanic. Using the highest percentage of ancestry/ethnicity to identify GDA, 9.5% of subjects were placed in the incorrect superpopulation based on SRR. When ≥50% or ≥75% GDA of a given superpopulation was required, 12% and 25%, respectively, of subjects were placed in the incorrect superpopulation based on SRR, and the percent of subjects classified as multiracial increased. Of 126 participants with unidentified SRR, 71% were genetically identified as Eurasian. GDA provides a more robust assessment of race/ethnicity when compared to self-report, and study participants with unidentified SRR could be assigned GDA using genetic markers. In addition, identification of continental ancestry removes the taxonomic identification of race as a variable when identifying risk for clinical outcomes. PMID:27603370

  16. Differences in the mannose oligomer specificities of the closely related lectins from Galanthus nivalis and Zea mays strongly determine their eventual anti-HIV activity

    Directory of Open Access Journals (Sweden)

    Fouquaert Elke

    2011-02-01

    Full Text Available Abstract Background In a recent report, the carbohydrate-binding specificities of the plant lectins Galanthus nivalis (GNA and the closely related lectin from Zea mays (GNAmaize were determined by glycan array analysis and indicated that GNAmaize recognizes complex-type N-glycans whereas GNA has specificity towards high-mannose-type glycans. Both lectins are tetrameric proteins sharing 64% sequence similarity. Results GNAmaize appeared to be ~20- to 100-fold less inhibitory than GNA against HIV infection, syncytia formation between persistently HIV-1-infected HuT-78 cells and uninfected CD4+ T-lymphocyte SupT1 cells, HIV-1 capture by DC-SIGN and subsequent transmission of DC-SIGN-captured virions to uninfected CD4+ T-lymphocyte cells. In contrast to GNA, which preferentially selects for virus strains with deleted high-mannose-type glycans on gp120, prolonged exposure of HIV-1 to dose-escalating concentrations of GNAmaize selected for mutant virus strains in which one complex-type glycan of gp120 was deleted. Surface Plasmon Resonance (SPR analysis revealed that GNA and GNAmaize interact with HIV IIIB gp120 with affinity constants (KD of 0.33 nM and 34 nM, respectively. Whereas immobilized GNA specifically binds mannose oligomers, GNAmaize selectively binds complex-type GlcNAcβ1,2Man oligomers. Also, epitope mapping experiments revealed that GNA and the mannose-specific mAb 2G12 can independently bind from GNAmaize to gp120, whereas GNAmaize cannot efficiently bind to gp120 that contained prebound PHA-E (GlcNAcβ1,2man specific or SNA (NeuAcα2,6X specific. Conclusion The markedly reduced anti-HIV activity of GNAmaize compared to GNA can be explained by the profound shift in glycan recognition and the disappearance of carbohydrate-binding sites in GNAmaize that have high affinity for mannose oligomers. These findings underscore the need for mannose oligomer recognition of therapeutics to be endowed with anti-HIV activity and that mannose, but

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

    Science.gov (United States)

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

    2011-10-01

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

  18. Genetic determinants of antimicrobial resistance in Gram positive bacteria from organic foods.

    Science.gov (United States)

    Fernández-Fuentes, Miguel Angel; Abriouel, Hikmate; Ortega Morente, Elena; Pérez Pulido, Rubén; Gálvez, Antonio

    2014-02-17

    Bacterial biocide resistance is becoming a matter of concern. In the present study, a collection of biocide-resistant, Gram-positive bacteria from organic foods (including 11 isolates from genus Bacillus, 25 from Enterococcus and 10 from Staphylococcus) were analyzed for genes associated to biocide resistance efflux pumps and antibiotic resistance. The only qac-genes detected were qacA/B (one Bacillus cereus isolate) and smr (one B. cereus and two Staphylococcus saprophyticus isolates). Efflux pump genes efrA and efrB genes were detected in Staphylococcus (60% of isolates), Bacillus (54.54%) and Enterococcus (24%); sugE was detected in Enterococcus (20%) and in one Bacillus licheniformis; mepA was detected in Staphylococcus (60%) and in one Enterococcus isolate (which also carried mdeA), and norE gene was detected only in one Enterococcus faecium and one S. saprophyticus isolate. An amplicon for acrB efflux pump was detected in all but one isolate. When minimal inhibitory concentrations (MICs) were determined, it was found that the addition of reserpine reduced the MICs by eight fold for most of the biocides and isolates, corroborating the role of efflux pumps in biocide resistance. Erythromycin resistance gene ermB was detected in 90% of Bacillus isolates, and in one Staphylococcus, while ereA was detected only in one Bacillus and one Staphyloccus, and ereB only in one Staphylococcus. The ATP-dependent msrA gene (which confers resistance to macrolides, lincosamides and type B streptogramins) was detected in 60% of Bacillus isolates and in all staphylococci, which in addition carried msrB. The lincosamide and streptogramin A resistance gene lsa was detected in Staphylococcus (40%), Bacillus (27.27%) and Enterococcus (8%) isolates. The aminoglycoside resistance determinant aph (3_)-IIIa was detected in Staphylococcus (40%) and Bacillus (one isolate), aph(2_)-1d in Bacillus (27.27%) and Enterococcus (8%), aph(2_)-Ib in Bacillus (one isolate), and the bifunctional aac

  19. Identification of viruses infecting cucurbits and determination of genetic diversity of Cucumber mosaic virus in Lorestan province, Iran

    Directory of Open Access Journals (Sweden)

    Hasanvand Vahid

    2017-06-01

    Full Text Available Various viral pathogens infect Cucurbitaceae and cause economic losses. The aim of the present study was to detect plant viral pathogens including Cucumber mosaic virus (CMV, Cucumber green mottle mosaic virus (CGMMV, Zucchini yellow mosaic virus (ZYMV, Cucurbit yellow stunting disorder virus (CYSDV and Cucurbit chlorotic yellows virus (CCYV in Lorestan province, in western Iran, and also to determine CMV genetic diversity in Iranian populations. A total of 569 symptomatic leaf samples were collected in 2013 and 2014 from cucurbits growing regions in Lorestan province. The collected samples were assessed for viral diseases by ELISA. The results showed virus incidences in most regions. Then, the infection of 40 samples to CMV was confirmed by RT-PCR. Moreover, to distinguish between the two groups (I and II of CMV, PCR products were digested by two restriction enzymes XhoI and EcoRI. Results of the digestion showed that the isolates of Lorestan belonged to group I. The CMV-coat protein gene of eight isolates from different regions and hosts was sequenced and phylogenetic analysis was performed. Subsequent analyses showed even more genetic variation among Lorestan isolates. The phylogenetic tree revealed that Lorestan province isolates belonged to two IA and IB subgroups and could be classified together with East Azerbaijan province isolates. The results of the present study indicate a wide distribution of CMV, ZYMV, CGMMV, CYSDV and CCYV viruses in cucurbits fields of Lorestan province and for the first time subgroup IB of CMV was reported on melon from Iran.

  20. PARAOXONASE 1 (PON1) AS A GENETIC DETERMINANT OF SUSCEPTIBILITY TO ORGANOPHOSPHATE TOXICITY

    Science.gov (United States)

    Costa, Lucio G.; Giordano, Gennaro; Cole, Toby B.; Marsillach, Judit; Furlong, Clement E.

    2012-01-01

    Paraoxonase (PON1) is an A-esterase capable of hydrolyzing the active metabolites (oxons) of a number of organophosphorus (OP) insecticides such as parathion, diazinon and chlorpyrifos. PON1 activity is highest in liver and in plasma. Human PON1 displays two polymorphisms in the coding region (Q192R and L55M) and several polymorphisms in the promoter and the 3’-UTR regions. The Q192R polymorphism imparts differential catalytic activity toward some OP substrates, while the polymorphism at position –108 (C/T) is the major contributor of differences in the levels of PON1 expression. Both contribute to determining an individual's PON1 “status”. Animal studies have shown that PON1 is an important determinant of OP toxicity. Administration of exogenous PON1 to rats or mice protects them from the toxicity of specific OPs. PON1 knockout mice display a high sensitivity to the toxicity of diazoxon and chlorpyrifos oxon, but not of paraoxon. In vitro catalytic efficiencies of purified PON192 alloforms for hydrolysis of specific oxon substrates accurately predict the degree of in vivo protection afforded by each isoform. Evidence is slowly emerging that a low PON1 status may increase susceptibility to OP toxicity in humans. Low PON1 activity may also contribute to the developmental toxicity and neurotoxicity of OPs, as shown by animal and human studies. PMID:22884923

  1. Eggplant and related species are promising genetic resources to dissect the plant immune response to Pseudomonas syringae and Xanthomonas euvesicatoria and to identify new resistance determinants.

    Science.gov (United States)

    Clarke, Christopher R; Hayes, Byron W; Runde, Brendan J; Wicker, Emmanuel; Vinatzer, Boris A

    2014-10-01

    The apparent lack of durability of many resistance (R) genes highlights the need for the constant identification of new genetic sources of resistance for the breeding of new disease-resistant crop cultivars. To this end, we screened a collection of accessions of eggplant and close relatives for resistance against Pseudomonas syringae pv. tomato (Pto) and Xanthomonas euvesicatoria (Xeu), foliar plant pathogens of many solanaceous crops. Both pathogens caused substantial disease on most genotypes of eggplant and its relatives. Promisingly, however, some of the genotypes were fully or partially resistant to either of the pathogens, suggesting the presence of effective resistance determinants in these genotypes. Segregation of resistance to the growth of Xeu following infiltration in F2 progeny from a cross of a resistant and susceptible genotype suggests that resistance to Xeu is inherited as a multigenic trait. With regard to Pto, a mutant strain lacking all 28 functional type III secreted effectors, and a Pseudomonas fluorescens strain expressing a P. syringae type III secretion system (T3SS), both elicit a strong cell death response on most eggplant lines. Several genotypes thus appear to harbour a mechanism for the direct recognition of a component of the T3SS. Therefore, eggplant and its close relatives are promising resources to unravel novel aspects of plant immunity and to identify new candidate R genes that could be employed in other Solanaceae in which Xeu and Pto cause agriculturally relevant diseases. © 2014 BSPP AND JOHN WILEY & SONS LTD.

  2. Genetic studies on sex determination and colouration in Nile tilapia (Oreochromis niloticus L.)

    International Nuclear Information System (INIS)

    Karayuecel, I.

    1999-05-01

    The present study was undertaken to investigate colour and sex determination mechanisms through the application of androgenesis, gynogenesis and controlled breeding programme with the objective of producing all red males in O. niloticus. The highest yield of androgenetic haploid to pigmentation stage was 24.6±3.5% (relative to controls) with optimal UV irradiation dose of 450JM -2 for 5 minutes. The highest survival rate of diploid androgens was 0.07±0.07% (relative to controls) to yolk sac stage using a heat shock of 42.5 deg. C for 3 minutes 30 seconds applied at 25 minutes after fertilisation. All paternal inheritance of diploid androgenetic tilapia was verified using DNA fingerprinting. The mean recombination frequency of the red skin colour gene in meiotic gynogens was 0.12±0.04. All maternal inheritance of meiotic gynogens was verified using the isozyme locus ADA*. Analyses of sex ratios of meiotic gynogens suggested that male progenies were produced by an epistatic sex determining locus (SDL-2 with two alleles SR and sr) causing female to male sex reversal in the homozygous phase (srsr) but with limited penetrance. A close linkage was found between a sex determining locus (SDL-2) and the red gene. No significant difference was found between colour genotypes (namely homozygous red, heterozygous red and wild type) in terms of total fecundity, ISI (inter spawning interval), egg size and survival rate. Overall mean ISI was 26.3±1.0 days. Mean total fecundity was 1096 eggs. Fecundity varied over successive spawns but this variation did not appear to be related to spawning periodicity. Hormonal and thermal feminization were compared on all YY male progeny of O. niloticus. While similar female percentages of 32.0±5.2 and 33.8±1.5% were produced, significantly higher intersex percentages of 18.5±2.5 and 1.6±0.8 were observed in heat and DES treated groups, respectively. Heat treatment groups showed the lowest survival rate of 62.6±9.8% compared to the

  3. Genetic studies on sex determination and colouration in Nile tilapia (Oreochromis niloticus L.)

    Energy Technology Data Exchange (ETDEWEB)

    Karayuecel, I

    1999-05-01

    The present study was undertaken to investigate colour and sex determination mechanisms through the application of androgenesis, gynogenesis and controlled breeding programme with the objective of producing all red males in O. niloticus. The highest yield of androgenetic haploid to pigmentation stage was 24.6{+-}3.5% (relative to controls) with optimal UV irradiation dose of 450JM{sup -2} for 5 minutes. The highest survival rate of diploid androgens was 0.07{+-}0.07% (relative to controls) to yolk sac stage using a heat shock of 42.5 deg. C for 3 minutes 30 seconds applied at 25 minutes after fertilisation. All paternal inheritance of diploid androgenetic tilapia was verified using DNA fingerprinting. The mean recombination frequency of the red skin colour gene in meiotic gynogens was 0.12{+-}0.04. All maternal inheritance of meiotic gynogens was verified using the isozyme locus ADA*. Analyses of sex ratios of meiotic gynogens suggested that male progenies were produced by an epistatic sex determining locus (SDL-2 with two alleles SR and sr) causing female to male sex reversal in the homozygous phase (srsr) but with limited penetrance. A close linkage was found between a sex determining locus (SDL-2) and the red gene. No significant difference was found between colour genotypes (namely homozygous red, heterozygous red and wild type) in terms of total fecundity, ISI (inter spawning interval), egg size and survival rate. Overall mean ISI was 26.3{+-}1.0 days. Mean total fecundity was 1096 eggs. Fecundity varied over successive spawns but this variation did not appear to be related to spawning periodicity. Hormonal and thermal feminization were compared on all YY male progeny of O. niloticus. While similar female percentages of 32.0{+-}5.2 and 33.8{+-}1.5% were produced, significantly higher intersex percentages of 18.5{+-}2.5 and 1.6{+-}0.8 were observed in heat and DES treated groups, respectively. Heat treatment groups showed the lowest survival rate of 62

  4. Genetically Determined Insulin Resistance is Characterized by Down-Regulation of Mitochondrial Oxidative Metabolism in Human Skeletal Muscle

    DEFF Research Database (Denmark)

    Kristensen, Jonas M; Skov, Vibe; Wojtaszewski, Jørgen

    2010-01-01

    mitochondrial dysfunction is a cause or consequence of insulin resistance remains to be clarified. In the present study, we tested the hypothesis that mitochondrial oxidative metabolism was down-regulated in skeletal muscle of patients with genetically determined insulin resistance. Skeletal muscle biopsies......Transcriptional profiling of skeletal muscle from patients with type 2 diabetes and high-risk individuals have demonstrated a co-ordinated down-regulation of oxidative phosphorylation (OxPhos) genes, suggesting a link between insulin resistance and mitochondrial dysfunction. However, whether...... Set Enrichment Analysis (GSEA) and Gene Map Annotator and Pathway Profiler (GenMAPP). In carriers of a INSR mutation reduced insulin-stimulated total and non-oxidative glucose disposal and impaired insulin signaling through Akt and glycogen synthase were associated with a co-ordinated down...

  5. Accurate determination of genetic identity for a single cacao bean, using molecular markers with a nanofluidic system, ensures cocoa authentication.

    Science.gov (United States)

    Fang, Wanping; Meinhardt, Lyndel W; Mischke, Sue; Bellato, Cláudia M; Motilal, Lambert; Zhang, Dapeng

    2014-01-15

    Cacao (Theobroma cacao L.), the source of cocoa, is an economically important tropical crop. One problem with the premium cacao market is contamination with off-types adulterating raw premium material. Accurate determination of the genetic identity of single cacao beans is essential for ensuring cocoa authentication. Using nanofluidic single nucleotide polymorphism (SNP) genotyping with 48 SNP markers, we generated SNP fingerprints for small quantities of DNA extracted from the seed coat of single cacao beans. On the basis of the SNP profiles, we identified an assumed adulterant variety, which was unambiguously distinguished from the authentic beans by multilocus matching. Assignment tests based on both Bayesian clustering analysis and allele frequency clearly separated all 30 authentic samples from the non-authentic samples. Distance-based principle coordinate analysis further supported these results. The nanofluidic SNP protocol, together with forensic statistical tools, is sufficiently robust to establish authentication and to verify gourmet cacao varieties. This method shows significant potential for practical application.

  6. Determining Risk of Colorectal Cancer and Starting Age of Screening Based on Lifestyle, Environmental, and Genetic Factors.

    Science.gov (United States)

    Jeon, Jihyoun; Du, Mengmeng; Schoen, Robert E; Hoffmeister, Michael; Newcomb, Polly A; Berndt, Sonja I; Caan, Bette; Campbell, Peter T; Chan, Andrew T; Chang-Claude, Jenny; Giles, Graham G; Gong, Jian; Harrison, Tabitha A; Huyghe, Jeroen R; Jacobs, Eric J; Li, Li; Lin, Yi; Le Marchand, Loïc; Potter, John D; Qu, Flora; Bien, Stephanie A; Zubair, Niha; Macinnis, Robert J; Buchanan, Daniel D; Hopper, John L; Cao, Yin; Nishihara, Reiko; Rennert, Gad; Slattery, Martha L; Thomas, Duncan C; Woods, Michael O; Prentice, Ross L; Gruber, Stephen B; Zheng, Yingye; Brenner, Hermann; Hayes, Richard B; White, Emily; Peters, Ulrike; Hsu, Li

    2018-02-16

    Guidelines for initiating colorectal cancer (CRC) screening are based on family history but do not consider lifestyle, environmental, or genetic risk factors. We developed models to determine risk of CRC, based on lifestyle and environmental factors and genetic variants, and to identify an optimal age to begin screening. We collected data from 9748 CRC cases and 10,590 controls in the Genetics and Epidemiology of Colorectal Cancer Consortium and the Colorectal Transdisciplinary study, from 1992 through 2005. Half of the participants were used to develop the risk determination model and the other half were used to evaluate the discriminatory accuracy (validation set). Models of CRC risk were created based on family history, 19 lifestyle and environmental factors (E-score), and 63 CRC-associated single-nucleotide polymorphisms identified in genome-wide association studies (G-score). We evaluated the discriminatory accuracy of the models by calculating area under the receiver operating characteristic curve (AUC) values, adjusting for study, age, and endoscopy findings for the validation set. We used the models to project the 10-year absolute risk of CRC for a given risk profile and recommend ages to begin screening, in comparison to CRC risk for an average individual at 50 years of age, using external population incidence rates for non-Hispanic whites from the Surveillance, Epidemiology, and End Results Program registry. In our models, E-score and G-score each determined risk of CRC with greater accuracy than family history. A model that combined both scores and family history estimated CRC risk with an AUC value of 0.63 (95% CI, 0.62-0.64) for men and 0.62 (95% CI, 0.61-0.63) for women; AUC values based on only family history ranged from 0.53 to 0.54 and those based only E-score or G-score ranged from 0.59 to 0.60. Although screening is recommended to begin at age 50 years for individuals with no family history of CRC, starting ages calculated based on combined E

  7. A major determinant of cyclophilin dependence and cyclosporine susceptibility of hepatitis C virus identified by a genetic approach.

    Directory of Open Access Journals (Sweden)

    Feng Yang

    2010-09-01

    Full Text Available Since the advent of genome-wide small interfering RNA screening, large numbers of cellular cofactors important for viral infection have been discovered at a rapid pace, but the viral targets and the mechanism of action for many of these cofactors remain undefined. One such cofactor is cyclophilin A (CyPA, upon which hepatitis C virus (HCV replication critically depends. Here we report a new genetic selection scheme that identified a major viral determinant of HCV's dependence on CyPA and susceptibility to cyclosporine A. We selected mutant viruses that were able to infect CyPA-knockdown cells which were refractory to infection by wild-type HCV produced in cell culture. Five independent selections revealed related mutations in a single dipeptide motif (D316 and Y317 located in a proline-rich region of NS5A domain II, which has been implicated in CyPA binding. Engineering the mutations into wild-type HCV fully recapitulated the CyPA-independent and CsA-resistant phenotype and four putative proline substrates of CyPA were mapped to the vicinity of the DY motif. Circular dichroism analysis of wild-type and mutant NS5A peptides indicated that the D316E/Y317N mutations (DEYN induced a conformational change at a major CyPA-binding site. Furthermore, nuclear magnetic resonance experiments suggested that NS5A with DEYN mutations adopts a more extended, functional conformation in the putative CyPA substrate site in domain II. Finally, the importance of this major CsA-sensitivity determinant was confirmed in additional genotypes (GT other than GT 2a. This study describes a new genetic approach to identifying viral targets of cellular cofactors and identifies a major regulator of HCV's susceptibility to CsA and its derivatives that are currently in clinical trials.

  8. A Pragmatic Study Shows Failure of Dental Composite Fillings Is Genetically Determined: A Contribution to the Discussion on Dental Amalgams.

    Science.gov (United States)

    Vieira, Alexandre R; Silva, Marília B; Souza, Kesia K A; Filho, Arnôldo V A; Rosenblatt, Aronita; Modesto, Adriana

    2017-01-01

    Composite resins for posterior tooth restorations have become a viable alternative to dental amalgam. Failures sometimes cannot be easily explained, and we hypothesize that a genetic component may influence longevity of restorations. We aimed to determine if there is any evidence for a difference in the performance of amalgams versus composite resin in extensive posterior restorations. We also aimed to determine if risk factors such as age, sex, smoking tobacco, alcohol drinking, diabetes status, and periodontal health status may have a role in the failures of extensive anterior composite restorations. Finally, we investigated if genetic variation in matrix metalloproteinases that are present in the mineralized dentin is associated with failure of composite resin. The data used to perform this research were obtained from the Dental Registry and DNA Repository project after screening 4,856 patients. All restorations were evaluated at times of 1, 2, and 5 years after the restoration placement. 6,266 amalgam and 2,010 composite restorations were analyzed in a total of 807 patients in a period of approximately 10 years (period corresponding to the database existence). An additional 443 extensive direct composite resin restorations in anterior teeth were also studied. Failure rates of amalgam and composite restorations are similar, and by the end of 5 years, composites outperformed amalgams slightly. Failures of anterior composite restorations occurred more often in males who smoked tobacco ( p  = 0.05), despite a similar number of females and males that smoked tobacco in the sample (116 individuals smoked tobacco, 54 females and 62 males). Alcohol drinking increased failure rate within 2 years ( p  = 0.03). We found a statistically significant association between matrix metalloproteinase 2 rs9923304 and failure of composite restorations ( p  = 0.007). Composite resins can replace amalgam restorations. Smoking tobacco and drinking alcohol will

  9. A Pragmatic Study Shows Failure of Dental Composite Fillings Is Genetically Determined: A Contribution to the Discussion on Dental Amalgams

    Directory of Open Access Journals (Sweden)

    Alexandre R. Vieira

    2017-11-01

    Full Text Available Composite resins for posterior tooth restorations have become a viable alternative to dental amalgam. Failures sometimes cannot be easily explained, and we hypothesize that a genetic component may influence longevity of restorations. We aimed to determine if there is any evidence for a difference in the performance of amalgams versus composite resin in extensive posterior restorations. We also aimed to determine if risk factors such as age, sex, smoking tobacco, alcohol drinking, diabetes status, and periodontal health status may have a role in the failures of extensive anterior composite restorations. Finally, we investigated if genetic variation in matrix metalloproteinases that are present in the mineralized dentin is associated with failure of composite resin. The data used to perform this research were obtained from the Dental Registry and DNA Repository project after screening 4,856 patients. All restorations were evaluated at times of 1, 2, and 5 years after the restoration placement. 6,266 amalgam and 2,010 composite restorations were analyzed in a total of 807 patients in a period of approximately 10 years (period corresponding to the database existence. An additional 443 extensive direct composite resin restorations in anterior teeth were also studied. Failure rates of amalgam and composite restorations are similar, and by the end of 5 years, composites outperformed amalgams slightly. Failures of anterior composite restorations occurred more often in males who smoked tobacco (p = 0.05, despite a similar number of females and males that smoked tobacco in the sample (116 individuals smoked tobacco, 54 females and 62 males. Alcohol drinking increased failure rate within 2 years (p = 0.03. We found a statistically significant association between matrix metalloproteinase 2 rs9923304 and failure of composite restorations (p = 0.007. Composite resins can replace amalgam restorations. Smoking tobacco and drinking alcohol

  10. Spectrophotometric determination of fluoxetine by molecularly imprinted polypyrrole and optimization by experimental design, artificial neural network and genetic algorithm

    Science.gov (United States)

    Nezhadali, Azizollah; Motlagh, Maryam Omidvar; Sadeghzadeh, Samira

    2018-02-01

    A selective method based on molecularly imprinted polymer (MIP) solid-phase extraction (SPE) using UV-Vis spectrophotometry as a detection technique was developed for the determination of fluoxetine (FLU) in pharmaceutical and human serum samples. The MIPs were synthesized using pyrrole as a functional monomer in the presence of FLU as a template molecule. The factors that affecting the preparation and extraction ability of MIP such as amount of sorbent, initiator concentration, the amount of monomer to template ratio, uptake shaking rate, uptake time, washing buffer pH, take shaking rate, Taking time and polymerization time were considered for optimization. First a Plackett-Burman design (PBD) consists of 12 randomized runs were applied to determine the influence of each factor. The other optimization processes were performed using central composite design (CCD), artificial neural network (ANN) and genetic algorithm (GA). At optimal condition the calibration curve showed linearity over a concentration range of 10- 7-10- 8 M with a correlation coefficient (R2) of 0.9970. The limit of detection (LOD) for FLU was obtained 6.56 × 10- 9 M. The repeatability of the method was obtained 1.61%. The synthesized MIP sorbent showed a good selectivity and sensitivity toward FLU. The MIP/SPE method was used for the determination of FLU in pharmaceutical, serum and plasma samples, successfully.

  11. Determination of the genetic structure of remnant Morus boninensis Koidz. trees to establish a conservation program on the Bonin Islands, Japan.

    Science.gov (United States)

    Tani, Naoki; Yoshimaru, Hiroshi; Kawahara, Takayuki; Hoshi, Yoshio; Nobushima, Fuyuo; Yasui, Takaya

    2006-10-11

    Morus boninensis, is an endemic plant of the Bonin (Ogasawara) Islands of Japan and is categorized as "critically endangered" in the Japanese red data book. However, little information is available about its ecological, evolutionary and genetic status, despite the urgent need for guidelines for the conservation of the species. Therefore, we adopted Moritz's MU concept, based on the species' current genetic structure, to define management units and to select mother tree candidates for seed orchards. Nearly all individuals of the species were genotyped on the basis of seven microsatellite markers. Genetic diversity levels in putative natural populations were higher than in putative man-made populations with the exception of those on Otouto-jima Island. This is because a limited number of maternal trees are likely to have been used for seed collection to establish the man-made populations. A model-based clustering analysis clearly distinguished individuals into nine clusters, with a large difference in genetic composition between the population on Otouto-jima Island, the putative natural populations and the putative man-made populations. The Otouto-jima population appeared to be genetically differentiated from the others; a finding that was also supported by pairwise FST and RST analysis. Although multiple clusters were detected in the putative man-made populations, the pattern of genetic diversity was monotonous in comparison to the natural populations. The genotyping by microsatellite markers revealed strong genetic structures. Typically, artificial propagation of this species has ignored the genetic structure, relying only on seeds from Otouto-jima for replanting on other islands, because of a problem with inter-specific hybridization on Chichi-jima and Haha-jima Islands. However, this study demonstrates that we should be taking into consideration the genetic structure of the species when designing a propagation program for the conservation of this species.

  12. Determination of the genetic structure of remnant Morus boninensis Koidz. trees to establish a conservation program on the Bonin Islands, Japan

    Directory of Open Access Journals (Sweden)

    Nobushima Fuyuo

    2006-10-01

    Full Text Available Abstract Background Morus boninensis, is an endemic plant of the Bonin (Ogasawara Islands of Japan and is categorized as "critically endangered" in the Japanese red data book. However, little information is available about its ecological, evolutionary and genetic status, despite the urgent need for guidelines for the conservation of the species. Therefore, we adopted Moritz's MU concept, based on the species' current genetic structure, to define management units and to select mother tree candidates for seed orchards. Results Nearly all individuals of the species were genotyped on the basis of seven microsatellite markers. Genetic diversity levels in putative natural populations were higher than in putative man-made populations with the exception of those on Otouto-jima Island. This is because a limited number of maternal trees are likely to have been used for seed collection to establish the man-made populations. A model-based clustering analysis clearly distinguished individuals into nine clusters, with a large difference in genetic composition between the population on Otouto-jima Island, the putative natural populations and the putative man-made populations. The Otouto-jima population appeared to be genetically differentiated from the others; a finding that was also supported by pairwise FST and RST analysis. Although multiple clusters were detected in the putative man-made populations, the pattern of genetic diversity was monotonous in comparison to the natural populations. Conclusion The genotyping by microsatellite markers revealed strong genetic structures. Typically, artificial propagation of this species has ignored the genetic structure, relying only on seeds from Otouto-jima for replanting on other islands, because of a problem with inter-specific hybridization on Chichi-jima and Haha-jima Islands. However, this study demonstrates that we should be taking into consideration the genetic structure of the species when designing a

  13. Genetic determination of the meso-diaminopimelate biosynthetic pathway of mycobacteria.

    Science.gov (United States)

    Cirillo, J D; Weisbrod, T R; Banerjee, A; Bloom, B R; Jacobs, W R

    1994-07-01

    The increasing incidence of multiple-drug-resistant mycobacterial infections indicates that the development of new methods for treatment of mycobacterial diseases should be a high priority. meso-Diaminopimelic acid (DAP), a key component of a highly immunogenic subunit of the mycobacterial peptidoglycan layer, has been implicated as a potential virulence factor. The mycobacterial DAP biosynthetic pathway could serve as a target for design of new antimycobacterial agents as well as the construction of in vivo selection systems. We have isolated the asd, dapA, dapB, dapD, and dapE genes involved in the DAP biosynthetic pathway of Mycobacterium bovis BCG. These genes were isolated by complementation of Escherichia coli mutations with an expression library of BCG DNA. Our analysis of these genes suggests that BCG may use more than one pathway for biosynthesis of DAP. The nucleotide sequence of the BCG dapB gene was determined. The activity of the product of this gene in Escherichia coli provided evidence that the gene may encode a novel bifunctional dihydrodipicolinate reductase and DAP dehydrogenase.

  14. 76 FR 63278 - Bayer CropScience LP; Determination of Nonregulated Status for Cotton Genetically Engineered for...

    Science.gov (United States)

    2011-10-12

    ... part 340, ``Introduction of Organisms and Products Altered or Produced Through Genetic Engineering... and products altered or produced through genetic engineering that are plant pests or that there is...

  15. 78 FR 51706 - Bayer CropScience LP; Determination of Nonregulated Status of Soybean Genetically Engineered for...

    Science.gov (United States)

    2013-08-21

    ... part 340, ``Introduction of Organisms and Products Altered or Produced Through Genetic Engineering... and products altered or produced through genetic engineering that are plant pests or that there is...

  16. Genetic polymorphisms in catalase and CYP1B1 determine DNA adduct formation by bento(a)pyrene ex vivo

    NARCIS (Netherlands)

    Schults, Marten A.; Chiu, Roland K.; Nagle, Peter; Kleinjans, J C; van Schooten, Frederik Jan; Godschalk, Roger W.

    Genetic polymorphisms can partially explain the large inter-individual variation in DNA adduct levels following exposure to polycyclic aromatic hydrocarbons. Effects of genetic polymorphisms on DNA adduct formation are difficult to assess in human studies because exposure misclassification

  17. 78 FR 25941 - Stine Seed Farm, Inc.; Extension of a Determination of Nonregulated Status of Corn Genetically...

    Science.gov (United States)

    2013-05-03

    ..., ``Introduction of Organisms and Products Altered or Produced Through Genetic Engineering Which Are Plant Pests or... produced through genetic engineering that are plant pests or that there is reason to believe are plant...

  18. 77 FR 42693 - Monsanto Company and KWS SAAT AG; Determination of Nonregulated Status of Sugar Beet Genetically...

    Science.gov (United States)

    2012-07-20

    ... Through Genetic Engineering Which Are Plant Pests or Which There Is Reason to Believe Are Plant Pests... environment) of organisms and products altered or produced through genetic engineering that are plant pests or...

  19. Genetic Determinants of C1 Inhibitor Deficiency Angioedema Age of Onset.

    Science.gov (United States)

    Gianni, Panagiota; Loules, Gedeon; Zamanakou, Maria; Kompoti, Maria; Csuka, Dorottya; Psarros, Fotis; Magerl, Markus; Moldovan, Dimitru; Maurer, Marcus; Speletas, Matthaios G; Farkas, Henriette; Germenis, Anastasios E

    2017-01-01

    In view of the large heterogeneity in the clinical presentation of hereditary angioedema due to C1 inhibitor deficiency (C1-INH-HAE), great efforts are being made towards detecting measurable biological determinants of disease severity that can help to improve the management of the disease. Considering the central role that plasma kallikrein plays in bradykinin production, we investigated the contribution of the functional polymorphism KLKB1-428G/A to the disease phenotype. We studied 249 C1-INH-HAE patients from 114 European families, and we explored possible associations of C1-INH-HAE clinical features with carriage of KLKB1-428G/A, combined or not with that of the functional F12-46C/T polymorphism. Carriers of the G allele of the KLKB1-428G/A polymorphism exhibited a significantly delayed disease onset (i.e., by 4.1 years [p < 0.001], depending on the zygocity status), while carriers of both the KLKB1-428G/A and the F12-46C/T polymorphism displayed an 8.8-year delay in disease onset (p < 0.001) and a 64% lower probability of needing long-term prophylactic treatment (p = 0.019). These findings support our initial hypothesis that functional alterations in genes of proteins involved in bradykinin metabolism and function affect the clinical phenotype and possibly contribute to the pathogenesis of C1-INH-HAE. Given that an earlier onset of symptoms is inversely correlated with the subsequent course of the disease and, eventually, the need for long-term prophylaxis, these polymorphisms may be helpful prognostic biomarkers of disease severity. © 2017 S. Karger AG, Basel.

  20. Antibiotic resistance determinants and genetic analysis of Salmonella enterica isolated from food in Morocco.

    Science.gov (United States)

    Murgia, Manuela; Bouchrif, Brahim; Timinouni, Mohammed; Al-Qahtani, Ahmed; Al-Ahdal, Mohammed N; Cappuccinelli, Pietro; Rubino, Salvatore; Paglietti, Bianca

    2015-12-23

    Antimicrobial-resistant non-typhoidal Salmonella (NTS) are an important cause of infection in Africa, but there is a lack of information on their molecular mechanisms of resistance and epidemiology. This study contributes to fill this gap through the characterization by pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), plasmid profiling and analysis of antibiotic-resistance determinants of 94 Salmonella enterica strains isolated from food in Morocco. PFGE revealed considerable heterogeneity among the strains, showing 32 pulsotypes. MLST of strains representative of the different serovars evidenced 13 sequence types (STs), three of which were newly identified (ST1694, ST1768 and ST1818) and nine not previously reported in Morocco. Thirty-four strains harbored from one to four plasmids, of IncI1 group in S. Mbandaka, IncFIIA in S. Typhimurium, IncL/M in S. Hadar and S. Blockley. For the first time in Morocco an intact Salmonella Genomic Island 1 (SGI1) carrying the resistance genes aadA2, floR, tetG, blaPSE-1 and sul1 was detected in S. Typhimurium DT104. In serovar Hadar resistance to ampicillin, tetracycline and streptomycin was associated to blaTEM-1, tetA and strA genes respectively, whereas one mutation in gyrA (Asp87Asn) and one in parC (Thr54Ser) genes conferred resistance to nalidixic acid. These findings improve the information on foodborne Salmonella in Morocco, evidencing the presence of MDR strains potentially dangerous to humans, and provide useful data for future studies. Copyright © 2015 Elsevier B.V. All rights reserved.

  1. Mild Salt-Sensitive Hypertension in Genetically Determined Low Nephron Number is Associated with Chloride but Not Sodium Retention.

    Science.gov (United States)

    Benz, Kerstin; Schlote, Julia; Daniel, Christoph; Kopp, Christoph; Dahlmann, Anke; Schröder, Agnes; Cordasic, Nada; Klanke, Bernd; Hilgers, Karl; Titze, Jens; Amann, Kerstin

    2018-01-01

    One potential pathomechanism how low nephron number leads to hypertension in later life is altered salt handling. We therefore evaluated changes in electrolyte and water content in wildtype (wt) and GDNF+/- mice with a 30% reduction of nephron number. 32 GDNF+/- and 36 wt mice were fed with low salt (LSD, 0.03%, normal drinking water) or high salt (HSD, 4%, 0.9% drinking water) diet for 4 weeks. Blood pressure was continuously measured by telemetry in a subgroup. At the end of the experiment and after standardized ashing processes electrolyte- and water contents of the skin and the total body were determined. We found higher blood pressure in high salt treated GDNF+/-compared to wt mice. Of interest, we could not confirm an increase in total-body sodium as predicted by prevailing explanations, but found increased total body and skin chloride that interestingly correlated with relative kidney weight. We hereby firstly report significant total body and skin chloride retention in salt sensitive hypertension of GDNF+/-mice with genetically determined lower nephron number. Thus, in contrast to the prevailing opinion our data argue for the involvement of non-volume related mechanisms. © 2018 The Author(s). Published by S. Karger AG, Basel.

  2. The social and economic origins of genetic determinism: a case history of the American Eugenics Movement, 1900-1940 and its lessons for today.

    Science.gov (United States)

    Allen, G E

    1997-01-01

    Eugenics, the attempt to improve the genetic quality of the human species by 'better breeding', developed as a worldwide movement between 1900 and 1940. It was particularly prominent in the United States, Britain and Germany, and in those countries was based on the then-new science of Mendelian genetics. Eugenicists developed research programs to determine the degree in which traits such as Huntington's chorea, blindness, deafness, mental retardation (feeblemindedness), intelligence, alcoholism, schizophrenia, manic depression, rebelliousness, nomadism, prostitution and feeble inhibition were genetically determined. Eugenicists were also active in the political arena, lobbying in the United States for immigration restriction and compulsory sterilization laws for those deemed genetically unfit; in Britain they lobbied for incarceration of genetically unfit and in Germany for sterilization and eventually euthanasia. In all these countries one of the major arguments was that of efficiency: that it was inefficient to allow genetic defects to be multiplied and then have to try and deal with the consequences of state care for the offspring. National socialists called genetically defective individuals 'useless eaters' and argued for sterilization or euthanasia on economic grounds. Similar arguments appeared in the United States and Britain as well. At the present time (1997) much research and publicity is being given to claims about a genetic basis for all the same behaviors (alcoholism, manic depression, etc.), again in an economic context--care for people with such diseases is costing too much. There is an important lesson to learn from the past: genetic arguments are put forward to mask the true--social and economic--causes of human behavioral defects.

  3. Search for genetic markers determining the efficiency of therapy with bisphosphonates in Russian women with postmenopausal osteoporosis: A pilot study

    Directory of Open Access Journals (Sweden)

    M. Yu. Krylov

    2016-01-01

    Full Text Available Many clinical observations show that patient’s genetic background is of great importance in determining the efficiency of treatment.Subjects and methods. The instigation included 50 postmenopausal women with osteoporosis (OP, who were followed up at the Laboratory of osteoporosis, V.A. Nasonova Research Institute of Rheumatology. Body mineral density (BMD in the lumbar spine (LI-IV, femoral neck (FN, and total hip was measured using dual-energy X-ray absorptiometry before and 12 months after treatment with bisphosphonates (BP. To estimate BMD changes, the investigators used ΔBMD in percent (Δ, %.Results and discussion. The whole group showed a positive effect of BP therapy during a year, which was most pronounced in the lumbar spine (mean ΔBMD, about 4%, and a small increment in the proximal hip BMD (mean ΔBMD, about 2%. An analysis indicated a statistically significant correlation of MCP1 -2518A>G polymorphism with changes in LI-IV BMD after 12-month BP therapy. Thus, the female patients who were A allele carriers had a twice lower increase in LI-IV BMD due to BP therapy than those without this allele. The genetic variants of the CCR5 gene, which were related to Δ32 deletion, and IL1β -511C/T polymorphism were also associated with changes in FN BMD following 12-month BP therapy. The BMD increase due to BP therapy in the carriers of the CCR5 Δ32 mutation (wt/Δ32 genotype was 3.5-fold than that in the carriers of the wild type gene (wt/wt genotype. Examination of IL1 -511C/T polymorphism demonstrated that the FN BMD increment in the carriers of the CC genotype was significantly higher than in those of the CT genotype (4.2±4.8 and 1.0±3.7%, respectively; р = 0.023. Our investigation revealed no significant relationship between VDR, LEPR, IL10, MHTFR, PPARG, SPP1, and CCR5(G/A gene polymorphisms and 12-month BP therapy-induced BMD changes in the three study skeletal regions. The findings may suggest that genetic testing may be used to

  4. Testing strong interaction theories

    International Nuclear Information System (INIS)

    Ellis, J.

    1979-01-01

    The author discusses possible tests of the current theories of the strong interaction, in particular, quantum chromodynamics. High energy e + e - interactions should provide an excellent means of studying the strong force. (W.D.L.)

  5. Determining resistance to mastitis in a bovine subject comprises detecting the presence or absence of a genetic marker that is linked to a trait indicative of mastitis resistance

    DEFF Research Database (Denmark)

    2007-01-01

    The invention relates to a method for determining mastitis resistance in bovine subjects, wherein mastitis resistance comprise resistance to both sub-clinical and clinical mastitis. In particular, the method of the invention involves identification of genetic markers and/or Quantitative Trait Locus...... (QTL) for the determination of mastitis resistance in a bovine subject. The determination of mastitis resistance involves resolution of the specific microsatellite status. Furthermore, the invention relates to a diagnostic kit for detection of genetic marker(s) associated with mastitis resistance....... The method and kit of the present invention can be applied for selection of bovine subjects for breeding purposes. Thus, the invention provides a method of genetically selecting bovine subjects with mastitis resistance, thereby yielding cows less prone to mastitis...

  6. Genetic and environmental determinants of violence risk in psychotic disorders: a multivariate quantitative genetic study of 1.8 million Swedish twins and siblings.

    Science.gov (United States)

    Sariaslan, A; Larsson, H; Fazel, S

    2016-09-01

    Patients diagnosed with psychotic disorders (for example, schizophrenia and bipolar disorder) have elevated risks of committing violent acts, particularly if they are comorbid with substance misuse. Despite recent insights from quantitative and molecular genetic studies demonstrating considerable pleiotropy in the genetic architecture of these phenotypes, there is currently a lack of large-scale studies that have specifically examined the aetiological links between psychotic disorders and violence. Using a sample of all Swedish individuals born between 1958 and 1989 (n=3 332 101), we identified a total of 923 259 twin-sibling pairs. Patients were identified using the National Patient Register using validated algorithms based on International Classification of Diseases (ICD) 8-10. Univariate quantitative genetic models revealed that all phenotypes (schizophrenia, bipolar disorder, substance misuse, and violent crime) were highly heritable (h(2)=53-71%). Multivariate models further revealed that schizophrenia was a stronger predictor of violence (r=0.32; 95% confidence interval: 0.30-0.33) than bipolar disorder (r=0.23; 0.21-0.25), and large proportions (51-67%) of these phenotypic correlations were explained by genetic factors shared between each disorder, substance misuse, and violence. Importantly, we found that genetic influences that were unrelated to substance misuse explained approximately a fifth (21%; 20-22%) of the correlation with violent criminality in bipolar disorder but none of the same correlation in schizophrenia (Pbipolar disorder<0.001; Pschizophrenia=0.55). These findings highlight the problems of not disentangling common and unique sources of covariance across genetically similar phenotypes as the latter sources may include aetiologically important clues. Clinically, these findings underline the importance of assessing risk of different phenotypes together and integrating interventions for psychiatric disorders, substance misuse, and violence.

  7. Temperamento: características e determinação genética Temperament: characteristics and genetic determination

    Directory of Open Access Journals (Sweden)

    Patrícia do Carmo Pereira Ito

    2002-01-01

    Full Text Available Este estudo investigou características temperamentais de uma amostra de crianças de 7 a 14 anos, verificando inclusive a influência exercida pela genética na determinação do temperamento. Uma amostra de 26 pais forneceu dados sobre o temperamento de 26 pares de gêmeos (15 monozigóticos, 11 dizigóticos, os quais totalizavam 52 sujeitos. Para coleta de dados foi utilizada a Escala Pavlovian Temperament Survey, versão infantil, que investiga três fatores de temperamento: Força de Excitação (FE, Força de Inibição (FI e Mobilidade (MO. Resultados obtidos indicaram que a partir da percepção dos pais, esta amostra de sujeitos possuía como característica predominante de temperamento a mobilidade. Análise de variância (MANOVA indicou que as características temperamentais variavam quando consideradas as variáveis sexo e faixa etária. Considerando-se a gemealidade, correlações obtidas entre pares de gêmeos monozigóticos e dizigóticos evidenciaram a influência exercida pela genética na determinação dos três fatores de temperamento.This study investigated the temperament characteristics of a sample of children from 7 to 14 years old, verifying the influence of genetics in the determination of temperament. A sample of 26 parents provided data about temperament of 26 pairs of twins (15 monozigotic, 11 dizigotic, totalizing 52 subjects. For the data gathering, the Pavlovian Temperament Survey - PTS, child version was used, which investigates three temperament factors: Strength of Excitation (SE, Strength of Inhibition (SI and Mobility (MO. The results showed that, from parents' perception, this sample had mobility as the predominant temperament characteristic. Analysis of variance (MANOVA indicated that temperament characteristics varied when considering variables such as sex and age group. The correlation obtained from pairs of monozigotic and dizigotic twins made evident the influence of genetic determination on the three

  8. Methods to determine the relative value of genetic traits in dairy cows to reduce greenhouse gas emissions along the chain.

    Science.gov (United States)

    van Middelaar, C E; Berentsen, P B M; Dijkstra, J; van Arendonk, J A M; de Boer, I J M

    2014-01-01

    Current decisions on breeding in dairy farming are mainly based on economic values of heritable traits, as earning an income is a primary objective of farmers. Recent literature, however, shows that breeding also has potential to reduce greenhouse gas (GHG) emissions. The objective of this paper was to compare 2 methods to determine GHG values of genetic traits. Method 1 calculates GHG values using the current strategy (i.e., maximizing labor income), whereas method 2 is based on minimizing GHG per kilogram of milk and shows what can be achieved if the breeding results are fully directed at minimizing GHG emissions. A whole-farm optimization model was used to determine results before and after 1 genetic standard deviation improvement (i.e., unit change) of milk yield and longevity. The objective function of the model differed between method 1 and 2. Method 1 maximizes labor income; method 2 minimizes GHG emissions per kilogram of milk while maintaining labor income and total milk production at least at the level before the change in trait. Results show that the full potential of the traits to reduce GHG emissions given the boundaries that were set for income and milk production (453 and 441kg of CO2 equivalents/unit change per cow per year for milk yield and longevity, respectively) is about twice as high as the reduction based on maximizing labor income (247 and 210kg of CO2 equivalents/unit change per cow per year for milk yield and longevity, respectively). The GHG value of milk yield is higher than that of longevity, especially when the focus is on maximizing labor income. Based on a sensitivity analysis, it was shown that including emissions from land use change and using different methods for handling the interaction between milk and meat production can change results, generally in favor of milk yield. Results can be used by breeding organizations that want to include GHG values in their breeding goal. To verify GHG values, the effect of prices and emissions

  9. Genetically determined optic neuropathies

    DEFF Research Database (Denmark)

    Milea, Dan; Amati-Bonneau, Patrizia; Reynier, Pascal

    2010-01-01

    The present review focuses on recent advances in the knowledge of hereditary optic neuropathies resulting from retinal ganglion cell degeneration, mostly due to mitochondrial dysfunctions.......The present review focuses on recent advances in the knowledge of hereditary optic neuropathies resulting from retinal ganglion cell degeneration, mostly due to mitochondrial dysfunctions....

  10. Evolving Attractive Faces Using Morphing Technology and a Genetic Algorithm: A New Approach to Determining Ideal Facial Aesthetics

    Science.gov (United States)

    Wong, Brian J. F.; Karmi, Koohyar; Devcic, Zlatko; McLaren, Christine E.; Chen, Wen-Pin

    2013-01-01

    Objectives The objectives of this study were to: 1) determine if a genetic algorithm in combination with morphing software can be used to evolve more attractive faces; and 2) evaluate whether this approach can be used as a tool to define or identify the attributes of the ideal attractive face. Study Design Basic research study incorporating focus group evaluations. Methods Digital images were acquired of 250 female volunteers (18–25 y). Randomly selected images were used to produce a parent generation (P) of 30 synthetic faces using morphing software. Then, a focus group of 17 trained volunteers (18–25 y) scored each face on an attractiveness scale ranging from 1 (unattractive) to 10 (attractive). A genetic algorithm was used to select 30 new pairs from the parent generation, and these were morphed using software to produce a new first generation (F1) of faces. The F1 faces were scored by the focus group, and the process was repeated for a total of four iterations of the algorithm. The algorithm mimics natural selection by using the attractiveness score as the selection pressure; the more attractive faces are more likely to morph. All five generations (P-F4) were then scored by three focus groups: a) surgeons (n = 12), b) cosmetology students (n = 44), and c) undergraduate students (n = 44). Morphometric measurements were made of 33 specific features on each of the 150 synthetic faces, and correlated with attractiveness scores using univariate and multivariate analysis. Results The average facial attractiveness scores increased with each generation and were 3.66 (+0.60), 4.59 (±0.73), 5.50 (±0.62), 6.23 (±0.31), and 6.39 (±0.24) for P and F1–F4 generations, respectively. Histograms of attractiveness score distributions show a significant shift in the skew of each curve toward more attractive faces with each generation. Univariate analysis identified nasal width, eyebrow arch height, and lip thickness as being significantly correlated with attractiveness

  11. Evolving attractive faces using morphing technology and a genetic algorithm: a new approach to determining ideal facial aesthetics.

    Science.gov (United States)

    Wong, Brian J F; Karimi, Koohyar; Devcic, Zlatko; McLaren, Christine E; Chen, Wen-Pin

    2008-06-01

    The objectives of this study were to: 1) determine if a genetic algorithm in combination with morphing software can be used to evolve more attractive faces; and 2) evaluate whether this approach can be used as a tool to define or identify the attributes of the ideal attractive face. Basic research study incorporating focus group evaluations. Digital images were acquired of 250 female volunteers (18-25 y). Randomly selected images were used to produce a parent generation (P) of 30 synthetic faces using morphing software. Then, a focus group of 17 trained volunteers (18-25 y) scored each face on an attractiveness scale ranging from 1 (unattractive) to 10 (attractive). A genetic algorithm was used to select 30 new pairs from the parent generation, and these were morphed using software to produce a new first generation (F1) of faces. The F1 faces were scored by the focus group, and the process was repeated for a total of four iterations of the algorithm. The algorithm mimics natural selection by using the attractiveness score as the selection pressure; the more attractive faces are more likely to morph. All five generations (P-F4) were then scored by three focus groups: a) surgeons (n = 12), b) cos-metology students (n = 44), and c) undergraduate students (n = 44). Morphometric measurements were made of 33 specific features on each of the 150 synthetic faces, and correlated with attractiveness scores using univariate and multivariate analysis. The average facial attractiveness scores increased with each generation and were 3.66 (+0.60), 4.59 (+/-0.73), 5.50 (+/-0.62), 6.23 (+/-0.31), and 6.39 (+/-0.24) for P and F1-F4 generations, respectively. Histograms of attractiveness score distributions show a significant shift in the skew of each curve toward more attractive faces with each generation. Univariate analysis identified nasal width, eyebrow arch height, and lip thickness as being significantly correlated with attractiveness scores. Multivariate analysis identified a

  12. Determination of the turbulent viscosity inside a strongly heated rectangular jet: experimental and numerical studies; Determination de la viscosite turbulente dans un jet rectangulaire fortement chauffe: etudes experimentale et numerique

    Energy Technology Data Exchange (ETDEWEB)

    Sarh, B.; Gokalp, I.; Sanders, H. [Centre National de la Recherche Scientifique (CNRS), 45 - Orleans-la-Source (France)

    1997-12-31

    In the framework of the studies carried out by the LCSR on variable density flows and diffusion turbulent flames, this paper deals with the study of the influence of density variation on the characteristics of a heated rectangular turbulent jet emerging in a stagnant surrounding atmosphere and more particularly on the determination of turbulent viscosity. The dynamical field is measured using laser-Doppler anemometry while the thermal field is measured using cold wire anemometry. A numerical predetermination of the characteristics of this jet, based on a k-{epsilon} modeling, is carried out. (J.S.) 6 refs.

  13. Identification of Combined Genetic Determinants of Liver Stiffness within the SREBP1c-PNPLA3 Pathway

    Directory of Open Access Journals (Sweden)

    Frank Lammert

    2013-10-01

    Full Text Available The common PNPLA3 (adiponutrin variant, p.I148M, was identified as a genetic determinant of liver fibrosis. Since the expression of PNPLA3 is induced by sterol regulatory element binding protein 1c (SREBP1c, we investigate two common SREBP1c variants (rs2297508 and rs11868035 for their association with liver stiffness. In 899 individuals (aged 17–83 years, 547 males with chronic liver diseases, hepatic fibrosis was non-invasively phenotyped by transient elastography (TE. The SREBP1c single nucleotide polymorphisms (SNPs were genotyped using PCR-based assays with 5'-nuclease and fluorescence detection. The SREBP1c rs11868035 variant affected liver fibrosis significantly (p = 0.029: median TE levels were 7.2, 6.6 and 6.0 kPa in carriers of (TT (n = 421, (CT (n = 384 and (CC (n = 87 genotypes, respectively. Overall, the SREBP1c SNP was associated with low TE levels (5.0–8.0 kPa. Carriers of both PNPLA3 and SREBP1c risk genotypes displayed significantly (p = 0.005 higher median liver stiffness, as compared to patients carrying none of these variants. The common SREBP1c variant may affect early stages of liver fibrosis. Our study supports a role of the SREBP1c-PNPLA3 pathway as a “disease module” that promotes hepatic fibrogenesis.

  14. Genetic-relatedness of peri-implants and buccal Candida albicans isolates determined by RAPD-PCR.

    Science.gov (United States)

    Bertone, Adriana M; Rosa, Alcira C; Nastri, Natalia; Santillán, Hector D; Ariza, Yamila; Iovannitti, Cristina A; Jewtuchowicz, Virginia M

    2016-12-01

    Molecular techniques have been used in recent studies to identify a wide range of potential bacterial pathogens in periimplant pockets of the oral cavity. However, the prevalence and molecular epidemiology of yeasts and species distribution related to periimplantitis are as yet unknown. The aim of this study was to determine the prevalence and distribution of yeasts in periimplant biofilm and to study genetic relatedness of Candida albicans. Yeasts recovered from periimplant biofilm samples (n=89) and buccal samples (n=120) were studied in 40 immunocompetent nonsmoking patients who visited the dental clinic of the Asociación Implantodontológica Argentina, Buenos Aires, Argentina, and had received oral rehabilitation with implants for more than five years. Yeasts recovered from samples were studied by typing assays using RAPDPCR. The prevalence of yeasts in the periimplant sulcus was 73% (n=29). C. albicans was the most prevalent species identified in this study population. The RAPD analysis showed identical genotypes in most C. albicans spp. from the two different sampling sites: buccal and periimplant. These findings suggest that periimplant biofilm is an ecological niche that favors the growth of yeast species. Most C. albicans found in periimplant biofilm originate from the endogenous infection caused by commensal strains. Sociedad Argentina de Investigación Odontológica.

  15. Role of mouse Wdr13 in placental growth; a genetic evidence for lifetime body weight determination by placenta during development

    Science.gov (United States)

    Singh, Vijay Pratap; Alex, Jomini Liza; Lakshmi, B. Jyothi; Sailasree, S Purnima; Raj, T. Avinash; Kumar, Satish

    2015-01-01

    Placental development is essential for implantation and growth of foetus in the uterus of eutherian mammals. Numerous growth factors are responsible for placental development and cell lineage differentiation. Gene knockout mice have shown role of various genes in the placenta. Here using Wdr13 knockout mice, we show that this gene is important for proper placental development. Wdr13, a X-linked gene, expresses in multiple trophoblast cell types of placenta and the mutant placenta had reduced size after 17.5 dpc due to reduction of junctional zone (JZ) and labyrinth zone (LZ). We observed reduction in levels of angiopoietin-2 and cd44 mRNA in Wdr13 mutant placenta as compared to that in the wild type. Our findings show that Wdr13 is required for normal placental development and cell differentiation. Wdr13 heterozygous female placenta when the mutant allele was of maternal origin showed similar defects as those in case of Wdr13 null placenta. Using two types of heterozygous females carrying either maternally and paternally derived mutant Wdr13 allele we provide genetic evidence that development of placenta determines body weight of mice for the entire life. PMID:26306915

  16. Determination of genetic toxicity and potential carcinogenicity in vitro--challenges post the Seventh Amendment to the European Cosmetics Directive.

    Science.gov (United States)

    Tweats, D J; Scott, A D; Westmoreland, C; Carmichael, P L

    2007-01-01

    Genetic toxicology and its role in the detection of carcinogens is currently undergoing a period of reappraisal. There is an increasing interest in developing alternatives to animal testing and the three R's of reduction, refinement and replacement are the basis for EU and national animal protection laws the Seventh Amendment to the EU Cosmetics Directive will ban the marketing of cosmetic/personal care products that contain ingredients that have been tested in animal models. Thus in vivo tests such as the bone marrow micronucleus test, which has a key role in current testing strategies for genotoxicity, will not be available for this class of products. The attrition rate for new, valuable and safe chemicals tested in an in vitro-only testing battery, using the in vitro tests currently established for genotoxicity screening, will greatly increase once this legislation is in place. In addition there has been an explosion of knowledge concerning the cellular and molecular events leading to carcinogenesis. This knowledge has not yet been fully factored into screening chemicals for properties that are not directly linked to mutation induction. Thus there is a pressing need for new, more accurate approaches to determine genotoxicity and carcinogenicity. However, a considerable challenge is presented for these new approaches to be universally accepted and new tests sufficiently validated by March 2009 when the animal testing and marketing bans associated with the Seventh Amendment are due to come into force. This commentary brings together ideas and approaches from several international workshops and meetings to consider these issues.

  17. Common genetic variations in the CYP2R1 and GC genes are determinants of vitamin D status in Danes

    DEFF Research Database (Denmark)

    Nissen, Ioanna

    (SNPs) in CYP2R1, CYP24A1, CYP27B1, C10orf88, DHCR7/NADSYN1, GC and VDR genes to be associated with vitamin D status. The main hypothesis of this work was that genetically determined variation in vitamin D metabolism would influence the effect of vitamin D sources (vitamin D......-supplementation and ultraviolet (UV)-B) on vitamin D status. This was done by assessing the association between 25 SNPs located in the CYP2R1, CYP24A1, CYP27B1, C10orf88, DHCR7/NADSYN1, GC and VDR genes and vitamin D status in 756 participants in the VitmaD study in late summer (paper I), at the end of a winter season (paper II......Vitamin D is considered a key fat-soluble vitamin critically important for good bone- and overall health throughout life. Vitamin D deficiency increases the risk of developing rickets, osteomalacia and osteoporosis, and moreover increases the risk of various non-skeletal adverse health outcomes...

  18. Stirring Strongly Coupled Plasma

    CERN Document Server

    Fadafan, Kazem Bitaghsir; Rajagopal, Krishna; Wiedemann, Urs Achim

    2009-01-01

    We determine the energy it takes to move a test quark along a circle of radius L with angular frequency w through the strongly coupled plasma of N=4 supersymmetric Yang-Mills (SYM) theory. We find that for most values of L and w the energy deposited by stirring the plasma in this way is governed either by the drag force acting on a test quark moving through the plasma in a straight line with speed v=Lw or by the energy radiated by a quark in circular motion in the absence of any plasma, whichever is larger. There is a continuous crossover from the drag-dominated regime to the radiation-dominated regime. In the crossover regime we find evidence for significant destructive interference between energy loss due to drag and that due to radiation as if in vacuum. The rotating quark thus serves as a model system in which the relative strength of, and interplay between, two different mechanisms of parton energy loss is accessible via a controlled classical gravity calculation. We close by speculating on the implicati...

  19. Genetic and physical maps around the sex-determining M-locus of the dioecious plant asparagus.

    Science.gov (United States)

    Telgmann-Rauber, Alexa; Jamsari, Ari; Kinney, Michael S; Pires, J Chris; Jung, Christian

    2007-09-01

    Asparagus officinalis L. is a dioecious plant. A region called the M-locus located on a pair of homomorphic sex chromosomes controls the sexual dimorphism in asparagus. The aim of this work was to clone the region determining sex in asparagus from its position in the genome. The structure of the region encompassing M should be investigated and compared to the sex-determining regions in other dioecious model species. To establish an improved basis for physical mapping, a high-resolution genetic map was enriched with AFLP markers closely linked to the target locus by carrying out a bulked segregant analysis. By screening a BAC library with AFLP- and STS-markers followed by chromosome walking, a physical map with eight contigs could be established. However, the gaps between the contigs could not be closed due to a plethora of repetitive elements. Surprisingly, two of the contigs on one side of the M-locus did not overlap although they have been established with two markers, which mapped in a distance as low as 0.25 cM flanking the sex locus. Thus, the clustering of the markers indicates a reduced recombination frequency within the M-region. On the opposite side of the M-locus, a contig was mapped in a distance of 0.38 cM. Four closely linked BAC clones were partially sequenced and 64 putative ORFs were identified. Interestingly, only 25% of the ORFs showed sequence similarity to known proteins and ESTs. In addition, an accumulation of repetitive sequences and a low gene density was revealed in the sex-determining region of asparagus. Molecular cytogenetic and sequence analysis of BACs flanking the M-locus indicate that the BACs contain highly repetitive sequences that localize to centromeric and pericentromeric locations on all asparagus chromosomes, which hindered the localization of the M-locus to the single pair of sex chromosomes. We speculate that dioecious Silene, papaya and Asparagus species may represent three stages in the evolution of XX, XY sex

  20. Antimicrobial resistance, genetic resistance determinants for ceftriaxone and molecular epidemiology of Neisseria gonorrhoeae isolates in Nanjing, China.

    Science.gov (United States)

    Chen, Shao-Chun; Yin, Yue-Ping; Dai, Xiu-Qin; Unemo, Magnus; Chen, Xiang-Sheng

    2014-11-01

    Antimicrobial resistance (AMR) in Neisseria gonorrhoeae is a major problem worldwide. This study investigated the AMR, genetic ceftriaxone resistance determinants and molecular epidemiology of N. gonorrhoeae in Nanjing, China. N. gonorrhoeae isolates were collected in 2007 (n = 198) and 2012 (n = 80). The susceptibility to ceftriaxone, spectinomycin, ciprofloxacin and tetracycline was determined using an agar-dilution method. The ceftriaxone resistance determinants penA, mtrR and penB were examined using sequencing. N. gonorrhoeae multi-antigen sequence typing (NG-MAST) was performed for molecular epidemiology. All isolates were resistant to ciprofloxacin, 42.4% produced β-lactamase and 34.9% showed high-level resistance to tetracycline (MIC ≥16 mg/L). In total, 5.4% of isolates were resistant to ceftriaxone; however, all of these isolates were obtained in 2007 and the susceptibility to ceftriaxone appeared to have increased. All isolates were susceptible to spectinomycin. No penA mosaic alleles were found. Non-mosaic penA alleles with A501T and G542S alterations, an H105Y alteration in mtrR and an A102D/N alteration in porB1b were statistically associated with decreased susceptibility or resistance to ceftriaxone. The most prevalent NG-MAST sequence types (STs) were ST568 (n = 13), ST270 (n = 9) and ST421 (n = 7). ST270 was the most common ST in isolates with decreased susceptibility or resistance to ceftriaxone. Ceftriaxone, ideally 500 mg and together with azithromycin (1-2 g), should be recommended for treatment of gonorrhoea in Nanjing, China. However, N. gonorrhoeae strains with resistance to ceftriaxone have been found in Nanjing. NG-MAST and ceftriaxone resistance determinant analysis can be valuable to supplement the antimicrobial resistance surveillance in China, which needs to be further strengthened. © The Author 2014. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights

  1. Determinants of consumer attitudes and purchase intentions with regard to genetically modified foods: Results of a cross-national survey

    DEFF Research Database (Denmark)

    Bredahl, Lone

    2000-01-01

    Executive summary 1. Previous research has shown consumers to be highly sceptical towards genetic modification in food production. So far, however, little research has tried to explain how consumers form attitudes and make decisions with regard to genetically modified foods. 2. The paper presents...... the results of a survey which was carried out in Denmark, Germany, Italy and the United Kingdom to investigate the formation of consumer attitudes towards genetic modification in food production and of purchase decisions with regard to genetically modified yoghurt and beer. Altogether, 2031 consumers were...... interviewed in the four countries. 3. Results show that attitude formation and decision-making are more comparable among Danish, German and British consumers than with Italian consumers. Likewise, Italian consumers turned out to be significantly less negative towards genetic modification in foods than...

  2. Is It Possible to Predict Strong Earthquakes?

    Science.gov (United States)

    Polyakov, Y. S.; Ryabinin, G. V.; Solovyeva, A. B.; Timashev, S. F.

    2015-07-01

    The possibility of earthquake prediction is one of the key open questions in modern geophysics. We propose an approach based on the analysis of common short-term candidate precursors (2 weeks to 3 months prior to strong earthquake) with the subsequent processing of brain activity signals generated in specific types of rats (kept in laboratory settings) who reportedly sense an impending earthquake a few days prior to the event. We illustrate the identification of short-term precursors using the groundwater sodium-ion concentration data in the time frame from 2010 to 2014 (a major earthquake occurred on 28 February 2013) recorded at two different sites in the southeastern part of the Kamchatka Peninsula, Russia. The candidate precursors are observed as synchronized peaks in the nonstationarity factors, introduced within the flicker-noise spectroscopy framework for signal processing, for the high-frequency component of both time series. These peaks correspond to the local reorganizations of the underlying geophysical system that are believed to precede strong earthquakes. The rodent brain activity signals are selected as potential "immediate" (up to 2 weeks) deterministic precursors because of the recent scientific reports confirming that rodents sense imminent earthquakes and the population-genetic model of K irshvink (Soc Am 90, 312-323, 2000) showing how a reliable genetic seismic escape response system may have developed over the period of several hundred million years in certain animals. The use of brain activity signals, such as electroencephalograms, in contrast to conventional abnormal animal behavior observations, enables one to apply the standard "input-sensor-response" approach to determine what input signals trigger specific seismic escape brain activity responses.

  3. Conservation of Sex-Linked Markers among Conspecific Populations of a Viviparous Skink, Niveoscincus ocellatus, Exhibiting Genetic and Temperature-Dependent Sex Determination

    Science.gov (United States)

    Burridge, Christopher P; Ezaz, Tariq; Wapstra, Erik

    2018-01-01

    Abstract Sex determination systems are exceptionally diverse and have undergone multiple and independent evolutionary transitions among species, particularly reptiles. However, the mechanisms underlying these transitions have not been established. Here, we tested for differences in sex-linked markers in the only known reptile that is polymorphic for sex determination system, the spotted snow skink, Niveoscincus ocellatus, to quantify the genomic differences that have accompanied this transition. In a highland population, sex is determined genetically, whereas in a lowland population, offspring sex ratio is influenced by temperature. We found a similar number of sex-linked loci in each population, including shared loci, with genotypes consistent with male heterogamety (XY). However, population-specific linkage disequilibrium suggests greater differentiation of sex chromosomes in the highland population. Our results suggest that transitions between sex determination systems can be facilitated by subtle genetic differences. PMID:29659810

  4. Strong interaction at finite temperature

    Indian Academy of Sciences (India)

    Abstract. We review two methods discussed in the literature to determine the effective parameters of strongly interacting particles as they move through a heat bath. The first one is the general method of chiral perturbation theory, which may be readily applied to this problem. The other is the method of thermal QCD sum rules ...

  5. Environmental and Historical Determinants of Patterns of Genetic Differentiation in Wild Soybean (Glycine soja Sieb. et Zucc).

    Science.gov (United States)

    He, Shui-Lian; Wang, Yun-Sheng; Li, De-Zhu; Yi, Ting-Shuang

    2016-03-08

    Wild soybean, the direct progenitor of cultivated soybean, inhabits a wide distribution range across the mainland of East Asia and the Japanese archipelago. A multidisciplinary approach combining analyses of population genetics based on 20 nuclear microsatellites and one plastid locus were applied to reveal the genetic variation of wild soybean, and the contributions of geographical, environmental factors and historic climatic change on its patterns of genetic differentiation. High genetic diversity and significant genetic differentiation were revealed in wild soybean. Wild soybean was inferred to be limited to southern and central China during the Last Glacial Maximum (LGM) and experienced large-scale post-LGM range expansion into northern East Asia. A substantial northward range shift has been predicted to occur by the 2080s. A stronger effect of isolation by environment (IBE) versus isolation by geographical distance (IBD) was found for genetic differentiation in wild soybean, which suggested that environmental factors were responsible for the adaptive eco-geographical differentiation. This study indicated that IBE and historical climatic change together shaped patterns of genetic variation and differentiation of wild soybean. Different conservation measures should be implemented on different populations according to their adaptive potential to future changes in climate and human-induced environmental changes.

  6. Genetic background (DDD/Sgn versus C57BL/6J) strongly influences postnatal growth of male mice carrying the A(y) allele at the agouti locus: identification of quantitative trait loci associated with diabetes and body weight loss.

    Science.gov (United States)

    Suto, Jun-ichi; Satou, Kunio

    2013-05-04

    Mice carrying the A(y) allele at the agouti locus become obese and are heavier than their non-A(y) littermates. However, this does not hold true for the genetic background of the DDD mouse strain. At 22 weeks of age, DDD.Cg-A(y) females are heavier than DDD females, whereas DDD.Cg-A(y) males are lighter than DDD males. This study aimed to determine the possible cause and identify the genes responsible for the lower body weight of DDD.Cg-A(y) males. Growth curves of DDD.Cg-A(y) mice were analyzed and compared with those of B6.Cg-A(y) mice from 5 to 25 weeks. In DDD.Cg-A(y) males, body weight gain stopped between 16 and 17 weeks and the body weight gradually decreased; thus, the lower body weight was a consequence of body weight loss. Quantitative trait locus (QTL) mapping was performed in backcrossed (BC) males of DDD × (B6 × DDD.Cg-A(y)) F(1)-A(y) mice. For the body weight at 25 weeks, significant QTLs were identified on chromosomes 1 and 4. The DDD allele was associated with a lower body weight at both loci. In particular, the QTL on chromosome 4 interacted with the A(y) allele. Furthermore, suggestive QTLs for plasma glucose and high molecular weight adiponectin levels were coincidentally mapped to chromosome 4. The DDD allele was associated with increased glucose and decreased adiponectin levels. When the body weight at 25 weeks and plasma glucose levels were considered as dependent and independent variables, respectively, BC A(y) males were classified into two groups according to statistical analysis using the partition method. Mice of one group had significantly higher glucose and lower adiponectin levels than those of the other group and exhibited body weight loss as observed with DDD-A(y) males. The lower body weight of DDD.Cg-A(y) male mice was a consequence of body weight loss. Diabetes mellitus has been suggested to be a possible contributory factor causing body weight loss. The QTL on distal chromosome 4 contained the major responsible genes. This QTL

  7. Population genetic structure of the common warthog (Phacochoerus africanus) in Uganda: evidence for a strong philopatry among warthogs and social structure breakdown in a disturbed population

    DEFF Research Database (Denmark)

    Muwanka, V.B.; Nyakaana, S.; Siegismund, Hans Redlef

    2007-01-01

    populations from five localities in Uganda are genetically structured using both mitochondrial control region sequence and microsatellite allele length variation. Four of the localities (Queen Elizabeth, Murchison Falls, Lake Mburo and Kidepo Valley) are national parks with relatively good wildlife protection......Fine-scale genetic structure of large mammals is rarely analysed. Yet it is potentially important in estimating gene flow between the now fragmented wildlife habitats and in predicting re-colonization following local extinction events. In this study, we examined the extent to which warthog...... geographical distances between populations, significant genetic differentiation was observed in all pair-wise population comparisons at the two marker sets (mtDNA FST = 0.21-0.79, P 

  8. An open-source genetic algorithm for determining optimal seed distributions for low-dose-rate prostate brachytherapy.

    Science.gov (United States)

    McGeachy, P; Madamesila, J; Beauchamp, A; Khan, R

    2015-01-01

    An open source optimizer that generates seed distributions for low-dose-rate prostate brachytherapy was designed, tested, and validated. The optimizer was a simple genetic algorithm (SGA) that, given a set of prostate and urethra contours, determines the optimal seed distribution in terms of coverage of the prostate with the prescribed dose while avoiding hotspots within the urethra. The algorithm was validated in a retrospective study on 45 previously contoured low-dose-rate prostate brachytherapy patients. Dosimetric indices were evaluated to ensure solutions adhered to clinical standards. The SGA performance was further benchmarked by comparing solutions obtained from a commercial optimizer (inverse planning simulated annealing [IPSA]) with the same cohort of 45 patients. Clinically acceptable target coverage by the prescribed dose (V100) was obtained for both SGA and IPSA, with a mean ± standard deviation of 98 ± 2% and 99.5 ± 0.5%, respectively. For the prostate D90, SGA and IPSA yielded 177 ± 8 Gy and 186 ± 7 Gy, respectively, which were both clinically acceptable. Both algorithms yielded reasonable dose to the rectum, with V100 < 0.3 cc. A reduction in dose to the urethra was seen using SGA. SGA solutions showed a slight prostate volume dependence, with smaller prostates (<25 cc) yielding less desirable, although still clinically viable, dosimetric outcomes. SGA plans used, on average, fewer needles than IPSA (21 vs. 24, respectively), which may lead to a reduction in urinary toxicity and edema that alters post-implant dosimetry. An open source SGA was validated that provides a research tool for the brachytherapy community. Copyright © 2015 American Brachytherapy Society. Published by Elsevier Inc. All rights reserved.

  9. CRISPR/Cas9 knockouts reveal genetic interaction between strain-transcendent erythrocyte determinants ofPlasmodium falciparuminvasion.

    Science.gov (United States)

    Kanjee, Usheer; Grüring, Christof; Chaand, Mudit; Lin, Kai-Min; Egan, Elizabeth; Manzo, Jale; Jones, Patrick L; Yu, Tiffany; Barker, Robert; Weekes, Michael P; Duraisingh, Manoj T

    2017-10-31

    During malaria blood-stage infections, Plasmodium parasites interact with the RBC surface to enable invasion followed by intracellular proliferation. Critical factors involved in invasion have been identified using biochemical and genetic approaches including specific knockdowns of genes of interest from primary CD34 + hematopoietic stem cells (cRBCs). Here we report the development of a robust in vitro culture system to produce RBCs that allow the generation of gene knockouts via CRISPR/Cas9 using the immortal JK-1 erythroleukemia line. JK-1 cells spontaneously differentiate, generating cells at different stages of erythropoiesis, including terminally differentiated nucleated RBCs that we term "jkRBCs." A screen of small-molecule epigenetic regulators identified several bromodomain-specific inhibitors that promote differentiation and enable production of synchronous populations of jkRBCs. Global surface proteomic profiling revealed that jkRBCs express all known P falciparum host receptors in a similar fashion to cRBCs and that multiple P falciparum strains invade jkRBCs at comparable levels to cRBCs and RBCs. Using CRISPR/Cas9, we deleted two host factors, basigin (BSG) and CD44, for which no natural nulls exist. BSG interacts with the parasite ligand Rh5, a prominent vaccine candidate. A BSG knockout was completely refractory to parasite invasion in a strain-transcendent manner, confirming the essential role for BSG during invasion. CD44 was recently identified in an RNAi screen of blood group genes as a host factor for invasion, and we show that CD44 knockout results in strain-transcendent reduction in invasion. Furthermore, we demonstrate a functional interaction between these two determinants in mediating P falciparum erythrocyte invasion. Published under the PNAS license.

  10. Phenotype microarray analysis may unravel genetic determinants of the stress response by Rhodococcus aetherivorans BCP1 and Rhodococcus opacus R7.

    Science.gov (United States)

    Cappelletti, Martina; Fedi, Stefani; Zampolli, Jessica; Di Canito, Alessandra; D'Ursi, Pasqualina; Orro, Alessandro; Viti, Carlo; Milanesi, Luciano; Zannoni, Davide; Di Gennaro, Patrizia

    In the present study, the response of Rhodococcus aetherivorans BCP1 and Rhodococcus opacus R7 to various stress conditions and several antimicrobials was examined by PM in relation with genetic determinants, as revealed by annotation analysis of the two genomes. Comparison between metabolic activities and genetic features of BCP1 and R7 provided new insight into the environmental persistence of these two members of the genus Rhodococcus. Copyright © 2016 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

  11. Genetic determinants in HIV-1 Gag and Env V3 are related to viral response to combination antiretroviral therapy with a protease inhibitor.

    Science.gov (United States)

    Ho, Sarah K; Perez, Elena E; Rose, Stephanie L; Coman, Roxana M; Lowe, Amanda C; Hou, Wei; Ma, Changxing; Lawrence, Robert M; Dunn, Ben M; Sleasman, John W; Goodenow, Maureen M

    2009-08-24

    To identify novel viral determinants in HIV-1 protease, Gag, and envelope V3 that relate to outcomes to initial protease inhibitor-based antiretroviral therapy. A longitudinal cohort study of protease inhibitor-naive, HIV-infected individuals was designed to identify genetic variables in viral Gag and envelope sequences associated with response to antiretroviral therapy. Genetic and statistic