Sample records for showed high genetic

  1. The yeast Starmerella bacillaris (synonym Candida zemplinina) shows high genetic diversity in winemaking environments.

    PubMed

    Masneuf-Pomarede, Isabelle; Juquin, Elodie; Miot-Sertier, Cécile; Renault, Philippe; Laizet, Yec'han; Salin, Franck; Alexandre, Hervé; Capozzi, Vittorio; Cocolin, Luca; Colonna-Ceccaldi, Benoit; Englezos, Vasileios; Girard, Patrick; Gonzalez, Beatriz; Lucas, Patrick; Mas, Albert; Nisiotou, Aspasia; Sipiczki, Matthias; Spano, Giuseppe; Tassou, Chrysoula; Bely, Marina; Albertin, Warren

    2015-08-01

    The yeast Candida zemplinina (Starmerella bacillaris) is frequently isolated from grape and wine environments. Its enological use in mixed fermentation with Saccharomyces cerevisiae has been extensively investigated these last few years, and several interesting features including low ethanol production, fructophily, glycerol and other metabolites production, have been described. In addition, molecular tools allowing the characterization of yeast populations have been developed, both at the inter- and intraspecific levels. However, most of these fingerprinting methods are not compatible with population genetics or ecological studies. In this work, we developed 10 microsatellite markers for the C. zemplinina species that were used for the genotyping of 163 strains from nature or various enological regions (28 vineyards/wineries from seven countries). We show that the genetic diversity of C. zemplinina is shaped by geographical localization. Populations isolated from winemaking environments are quite diverse at the genetic level: neither clonal-like behaviour nor specific genetic signature were associated with the different vineyards/wineries. Altogether, these results suggest that C. zemplinina is not under selective pressure in winemaking environments. PMID:26071435

  2. Granular cell astrocytomas show a high frequency of allelic loss but are not a genetically defined subset.

    PubMed

    Castellano-Sanchez, Amilcar A; Ohgaki, Hiroko; Yokoo, Hideako; Scheithauer, Bernd W; Burger, Peter C; Hamilton, Ronald L; Finkelstein, Sydney D; Brat, Daniel J

    2003-04-01

    Granular cell astrocytomas (GCA) are an uncommon morphologic variant of infiltrative glioma that contains a prominent population of atypical granular cells. As a rule, they are biologically aggressive compared to similar tumors without granular features. We sought to determine whether GCAs possess distinct genotypic alterations that might reflect their unique morphology or clinical behavior. Eleven GCAs occurring in 7 men and 4 women ranging in age from 46 to 75 years were investigated for genetic alterations of known significance in glial tumorigenesis, including LOH at 1p, 9p, 10q, 17p, and 19q, point mutations of TP53, deletions of p16(CDKN2A) and p14ARF, as well as EGFR amplifications. Tumors included had an infiltrative growth pattern and consisted of large, round cells packed with eosinophilic, PAS-positive granules that varied in quantity, ranging from 30 to 100% of tumor cells. Three tumors were of WHO grade II, one was grade III, and 7 were grade IV lesions. Overall, the tumors showed higher frequencies of LOH at 1p, 9p, 10q, 17p, and 19q than typical infiltrating astrocytomas of similar grades. Losses on 9p and 10q occurred in nearly all cases, including low grade lesions. TP53 mutations were identified in 2 grade IV GCAs, while combined p14ARF and p16(CDKN2A) homozygous deletions were noted in only one grade IV lesion. None showed EGFR amplification. We found no genetic alterations specific for GCA. Instead, it appears that granular cell change occurs across genetic subsets. The high frequency of allelic loss, especially on 9p and 10q, may confer aggressive growth potential and be related to their rapid clinical progression. PMID:12744472

  3. A new genome scan for primary nonsyndromic vesicoureteric reflux emphasizes high genetic heterogeneity and shows linkage and association with various genes already implicated in urinary tract development

    PubMed Central

    Darlow, J M; Dobson, M G; Darlay, R; Molony, C M; Hunziker, M; Green, A J; Cordell, H J; Puri, P; Barton, D E

    2014-01-01

    Primary vesicoureteric reflux (VUR), the retrograde flow of urine from the bladder toward the kidneys, results from a developmental anomaly of the vesicoureteric valve mechanism, and is often associated with other urinary tract anomalies. It is the most common urological problem in children, with an estimated prevalence of 1–2%, and is a major cause of hypertension in childhood and of renal failure in childhood or adult life. We present the results of a genetic linkage and association scan using 900,000 markers. Our linkage results show a large number of suggestive linkage peaks, with different results in two groups of families, suggesting that VUR is even more genetically heterogeneous than previously imagined. The only marker achieving P?

  4. Genetic transformation of Neisseria gonorrhoeae shows a strand preference.

    PubMed

    Duffin, Paul M; Seifert, H Steven

    2012-09-01

    Natural transformation is the main means of horizontal genetic exchange in the obligate human pathogen Neisseria gonorrhoeae. Neisseria spp. have been shown to preferentially take up and transform their own DNA by recognizing a non-palindromic 10 or 12 nucleotide DNA uptake sequence (DUS10 or DUS12). We investigated the ability of the DUS12 to enhance single-stranded DNA (ssDNA) transformation. Given the non-palindromic nature of the DUS12, we tested whether both strands of the DUS equally enhance transformation. Recombinant single-stranded M13 phage harboring transforming DNA with the Watson DUS12, the Crick DUS12, or no DUS (DUS0) were constructed and circular ssDNA was purified. Southern blots of the purified DNA probed with strand-specific oligonucleotide probes showed > 10,000 : 1 ratio of ssDNA to contaminating dsDNA. The Crick strand of the DUS12 enhanced ssDNA transformation 180- to 470-fold over DUS0 ssDNA, whereas the Watson strand of the DUS only modestly enhanced ssDNA transformation in two strains of N. gonorrhoeae. These data confirm that ssDNA efficiently transforms N. gonorrhoeae, but that there is a strand preference and that part of this strand preference is a greater efficiency of the Crick strand of the DUS12 in enhancing transformation. PMID:22676068

  5. High Points of Human Genetics

    ERIC Educational Resources Information Center

    Stern, Curt

    1975-01-01

    Discusses such high points of human genetics as the study of chromosomes, somatic cell hybrids, the population formula: the Hardy-Weinberg Law, biochemical genetics, the single-active X Theory, behavioral genetics and finally how genetics can serve humanity. (BR)

  6. Genetic dissection of a behavioral quantitative trait locus shows that Rgs2 modulates anxiety in mice

    Microsoft Academic Search

    Binnaz Yalcin; Saffron A G Willis-Owen; Jan Fullerton; Anjela Meesaq; Robert M Deacon; J Nicholas P Rawlins; Richard R Copley; Andrew P Morris; Jonathan Flint; Richard Mott

    2004-01-01

    Here we present a strategy to determine the genetic basis of variance in complex phenotypes that arise from natural, as opposed to induced, genetic variation in mice. We show that a commercially available strain of outbred mice, MF1, can be treated as an ultrafine mosaic of standard inbred strains and accordingly used to dissect a known quantitative trait locus influencing

  7. Young adult female fragile X premutation carriers show age-and genetically-modulated cognitive impairments

    E-print Network

    Nguyen, Danh

    the biological basis for fragile X syndrome (FXS), which results in intellectual dis- ability (HagermanYoung adult female fragile X premutation carriers show age- and genetically-modulated cognitive Article history: Accepted 3 January 2011 Available online 3 February 2011 Keywords: Fragile X premutation

  8. 13. VIEW, LOOKING WEST FROM LEFT TO RIGHT, SHOWING HIGH ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    13. VIEW, LOOKING WEST FROM LEFT TO RIGHT, SHOWING HIGH PRESSURE AIR FLASK ROOM AND PUMP ROOM - U.S. Naval Submarine Base, New London Submarine Escape Training Tank, Albacore & Darter Roads, Groton, New London County, CT

  9. 3. VIEW SHOWING CREST OF DAM, LOOKING NORTHWEST High ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    3. VIEW SHOWING CREST OF DAM, LOOKING NORTHWEST - High Mountain Dams in Upalco Unit, Milk Lake Dam, Ashley National Forest, 9.4 miles Northwest of Swift Creek Campground, Mountain Home, Duchesne County, UT

  10. 4. VIEW SHOWING ROCKLINED SPILLWAY, LOOKING NORTHWEST High Mountain ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    4. VIEW SHOWING ROCK-LINED SPILLWAY, LOOKING NORTHWEST - High Mountain Dams in Upaco Unit, Superior Lake Dam, Ashley National Forest, 12.4 miles Northwest of Swift Creek Campground, Mountain Home, Duchesne County, UT

  11. 5. VIEW SHOWING DOWNSTREAM FACE DAM, LOOKING SOUTHEAST High ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    5. VIEW SHOWING DOWNSTREAM FACE DAM, LOOKING SOUTHEAST - High Mountain Dams in Upalco Unit, Milk Lake Dam, Ashley National Forest, 9.4 miles Northwest of Swift Creek Campground, Mountain Home, Duchesne County, UT

  12. 26. VIEW OF PUMP ROOM, SHOWING PORTIONS OF HIGH PRESSURE ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    26. VIEW OF PUMP ROOM, SHOWING PORTIONS OF HIGH PRESSURE AIR SYSTEM AT LEFT AND CENTER AND OVERFLOW STORAGE TANK AT RIGHT, LOOKING NORTHWEST - U.S. Naval Submarine Base, New London Submarine Escape Training Tank, Albacore & Darter Roads, Groton, New London County, CT

  13. 23. VIEW SHOWING HIGH WATER IN ROWDY CREEK WITH COLLAPSED ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    23. VIEW SHOWING HIGH WATER IN ROWDY CREEK WITH COLLAPSED SECTION IN CREEK, LOOKING NORTH TO SOUTH FROM END OF UNCOLLAPSED SECTION Winter 1931-32 - Rowdy Creek Bridge, Spanning Rowdy Creek at Fred Haight Drive, Smith River, Del Norte County, CA

  14. Introducing High School Students to Human Genetics.

    ERIC Educational Resources Information Center

    Haddow, Paula K.; And Others

    1988-01-01

    Considers six key concepts in human genetics in a question-and-answer format designed to help guide students to an understanding of the concept. Lists eight workshops in human genetics for high school biology teachers and four curriculum material packages on human genetics. (CW)

  15. Graphene oxide immobilized enzymes show high thermal and solvent stability.

    PubMed

    Hermanová, So?a; Zarevúcká, Marie; Bouša, Daniel; Pumera, Martin; Sofer, Zden?k

    2015-03-19

    The thermal and solvent tolerance of enzymes is highly important for their industrial use. We show here that the enzyme lipase from Rhizopus oryzae exhibits exceptionally high thermal stability and high solvent tolerance and even increased activity in acetone when immobilized onto a graphene oxide (GO) nanosupport prepared by Staudenmaier and Brodie methods. We studied various forms of immobilization of the enzyme: by physical adsorption, covalent attachment, and additional crosslinking. The activity recovery was shown to be dependent on the support type, enzyme loading and immobilization procedure. Covalently immobilized lipase showed significantly better resistance to heat inactivation (the activity recovery was 65% at 70 °C) in comparison with the soluble counterpart (the activity recovery was 65% at 40 °C). Physically adsorbed lipase achieved over 100% of the initial activity in a series of organic solvents. These findings, showing enhanced thermal stability and solvent tolerance of graphene oxide immobilized enzyme, will have a profound impact on practical industrial scale uses of enzymes for the conversion of lipids into fuels. PMID:25757536

  16. Highly reflective reasoners show no signs of belief inhibition.

    PubMed

    Svedholm-Häkkinen, Annika M

    2015-01-01

    The processes underlying individual differences in reasoning performance are not entirely understood. What do people who do well on reasoning tasks where beliefs and logic conflict do differently from other people? Because abundant evidence shows that even poorer reasoners detect these conflicts, it has been suggested that individual differences in reasoning performance arise from inhibition failures later in the reasoning process. The present paper argues that a minority of highly skilled reasoners may deviate from this general reasoning process from an early stage. Two studies investigated signs of belief inhibition using a lexical access paradigm (Study 1) and a negative priming paradigm (Study 2). Study 1 showed that while other people exhibited signs of belief inhibition following a belief-logic conflict, people with the highest disposition for cognitive reflection did not. In Study 2, this finding was replicated and similar results were also obtained when comparing groups with higher and lower general cognitive ability. Two possible explanations are discussed. The reasoners with a highly reflective cognitive style or high general cognitive ability may have engaged and inhibited belief processing but if so, they may have been exceptionally efficient at recovering from it, wherefore no belief inhibition effects were found. An alternative account is that these reasoners started Type 2 processing directly, without first engaging in and then inhibiting belief-based processing. Under either explanation, the results indicate that individual differences in reasoning may partly arise from differences that occur early in the reasoning process. PMID:25499057

  17. A framework genetic map for Miscanthus sinensis from RNAseq-based markers shows recent tetraploidy

    PubMed Central

    2012-01-01

    Background Miscanthus (subtribe Saccharinae, tribe Andropogoneae, family Poaceae) is a genus of temperate perennial C4 grasses whose high biomass production makes it, along with its close relatives sugarcane and sorghum, attractive as a biofuel feedstock. The base chromosome number of Miscanthus (x = 19) is different from that of other Saccharinae and approximately twice that of the related Sorghum bicolor (x = 10), suggesting large-scale duplications may have occurred in recent ancestors of Miscanthus. Owing to the complexity of the Miscanthus genome and the complications of self-incompatibility, a complete genetic map with a high density of markers has not yet been developed. Results We used deep transcriptome sequencing (RNAseq) from two M. sinensis accessions to define 1536 single nucleotide variants (SNVs) for a GoldenGate™ genotyping array, and found that simple sequence repeat (SSR) markers defined in sugarcane are often informative in M. sinensis. A total of 658 SNP and 210 SSR markers were validated via segregation in a full sibling F1 mapping population. Using 221 progeny from this mapping population, we constructed a genetic map for M. sinensis that resolves into 19 linkage groups, the haploid chromosome number expected from cytological evidence. Comparative genomic analysis documents a genome-wide duplication in Miscanthus relative to Sorghum bicolor, with subsequent insertional fusion of a pair of chromosomes. The utility of the map is confirmed by the identification of two paralogous C4-pyruvate, phosphate dikinase (C4-PPDK) loci in Miscanthus, at positions syntenic to the single orthologous gene in Sorghum. Conclusions The genus Miscanthus experienced an ancestral tetraploidy and chromosome fusion prior to its diversification, but after its divergence from the closely related sugarcane clade. The recent timing of this tetraploidy complicates discovery and mapping of genetic markers for Miscanthus species, since alleles and fixed differences between paralogs are comparable. These difficulties can be overcome by careful analysis of segregation patterns in a mapping population and genotyping of doubled haploids. The genetic map for Miscanthus will be useful in biological discovery and breeding efforts to improve this emerging biofuel crop, and also provide a valuable resource for understanding genomic responses to tetraploidy and chromosome fusion. PMID:22524439

  18. Histidine decarboxylase knockout mice, a genetic model of Tourette syndrome, show repetitive grooming after induced fear.

    PubMed

    Xu, Meiyu; Li, Lina; Ohtsu, Hiroshi; Pittenger, Christopher

    2015-05-19

    Tics, such as are seen in Tourette syndrome (TS), are common and can cause profound morbidity, but they are poorly understood. Tics are potentiated by psychostimulants, stress, and sleep deprivation. Mutations in the gene histidine decarboxylase (Hdc) have been implicated as a rare genetic cause of TS, and Hdc knockout mice have been validated as a genetic model that recapitulates phenomenological and pathophysiological aspects of the disorder. Tic-like stereotypies in this model have not been observed at baseline but emerge after acute challenge with the psychostimulant d-amphetamine. We tested the ability of an acute stressor to stimulate stereotypies in this model, using tone fear conditioning. Hdc knockout mice acquired conditioned fear normally, as manifested by freezing during the presentation of a tone 48h after it had been paired with a shock. During the 30min following tone presentation, knockout mice showed increased grooming. Heterozygotes exhibited normal freezing and intermediate grooming. These data validate a new paradigm for the examination of tic-like stereotypies in animals without pharmacological challenge and enhance the face validity of the Hdc knockout mouse as a pathophysiologically grounded model of tic disorders. PMID:25841792

  19. Resistance to oxidative stress shows low heritability and high common environmental variance in a wild bird.

    PubMed

    Losdat, S; Helfenstein, F; Blount, J D; Richner, H

    2014-09-01

    Oxidative stress was recently demonstrated to affect several fitness-related traits and is now well recognized to shape animal life-history evolution. However, very little is known about how much resistance to oxidative stress is determined by genetic and environmental effects and hence about its potential for evolution, especially in wild populations. In addition, our knowledge of phenotypic sexual dimorphism and cross-sex genetic correlations in resistance to oxidative stress remains extremely limited despite important evolutionary implications. In free-living great tits (Parus major), we quantified heritability, common environmental effect, sexual dimorphism and cross-sex genetic correlation in offspring resistance to oxidative stress by performing a split-nest cross-fostering experiment where 155 broods were split, and all siblings (n = 791) translocated and raised in two other nests. Resistance to oxidative stress was measured as both oxidative damage to lipids and erythrocyte resistance to a controlled free-radical attack. Both measurements of oxidative stress showed low additive genetic variances, high common environmental effects and phenotypic sexual dimorphism with males showing a higher resistance to oxidative stress. Cross-sex genetic correlations were not different from unity, and we found no substantial heritability in resistance to oxidative stress at adult age measured on 39 individuals that recruited the subsequent year. Our study shows that individual ability to resist to oxidative stress is primarily influenced by the common environment and has a low heritability with a consequent low potential for evolution, at least at an early stage of life. PMID:25040169

  20. Chromosome 2p Shows Significant Linkage to Antihypertensive Response in the British Genetics of Hypertension Study

    Microsoft Academic Search

    Sandosh Padmanabhan; Chris Wallace; Patricia B. Munroe; Richard Dobson; Morris Brown; Nilesh Samani; David Clayton; Martin Farrall; John Webster; Mark Lathrop; Mark Caulfield; Anna F. Dominiczak; John M. Connell

    2010-01-01

    There is a lack of consistently linked loci influencing blood pressure and hypertension status, and this may be because of genetic or phenotypic heterogeneity. We hypothesize that stratification of subjects by response to antihypertensive drug groups could be used to stringently define subsets that will have reduced genetic and etiologic heterogeneity, by partitioning contrasting mechanisms of hypertension and, thus, enhancing

  1. Genetic and morphological patterns show variation in frequency of hybrids between Ipomopsis (Polemoniaceae) zones of sympatry

    Microsoft Academic Search

    G Aldridge; D R Campbell

    2009-01-01

    Variation in rates of hybridization among zones of sympatry between a pair of species provides a useful window into the effect of local conditions on the evolution of reproductive isolation. We employed floral morphological traits and neutral genetic markers to quantify the frequency of individuals intermediate to the two parental species in two zones of sympatry between Ipomopsis aggregata and

  2. Genetic segregation analysis of familial mitral valve prolapse shows no linkage to fibrillar collagen genes

    Microsoft Academic Search

    P Wordsworth; D Ogilvie; F Akhras; G Jackson; B Sykes

    1989-01-01

    Three pedigrees were identified in which mitral valve prolapse seemed to be inherited as a mendelian autosomal dominant trait. The segregation of the genes encoding the major fibrillar collagens present in valve tissue, collagens I and III, was analysed by use of restriction enzyme site variants as genetic markers. In one pedigree there was discordance between the segregation of the

  3. That 70s show: regulation, evolution and development beyond molecular genetics.

    PubMed

    Suárez-Díaz Edna; García-Deister Vivette

    2015-01-01

    This paper argues that the "long 1970s" (1969-1983) is an important though often overlooked period in the development of a rich landscape in the research of metabolism, development, and evolution. The period is marked by: shrinking public funding of basic science, shifting research agendas in molecular biology, the incorporation of new phenomena and experimental tools from previous biological research at the molecular level, and the development of recombinant DNA techniques. Research was reoriented towards eukaryotic cells and development, and in particular towards "giant" RNA processing and transcription. We will here focus on three different models of developmental regulation published in that period: the two models of eukaryotic genetic regulation at the transcriptional level that were developed by Georgii P. Georgiev on the one hand, and by Roy Britten and Eric Davidson on the other; and the model of genetic sufficiency and evolution of regulatory genes proposed by Emile Zuckerkandl. These three bases illustrate the range of exploratory hypotheses that characterised the challenging landscape of gene regulation in the 1970s, a period that in hindsight can be labelled as transitional, between the biology at the laboratory bench of the preceding period, and the biology of genetic engineering and intensive data-driven research that followed. PMID:26013314

  4. Genetic Variability of Show Jumping Attributes in Young Horses Commencing Competing.

    PubMed

    Próchniak, Tomasz; Rozempolska-Ruci?ska, Iwona; Zi?ba, Grzegorz; ?ukaszewicz, Marek

    2015-08-01

    The aim of the study was to select traits that may constitute a prospective criterion for breeding value prediction of young horses. The results of 1,232 starts of 894 four-, five-, six-, and seven-year-old horses, obtained during jumping championships for young horses which had not been evaluated in, alternative to championships, training centres were analyed. Nine traits were chosen of those recorded: ranking in the championship, elimination (y/n), conformation, rating of style on day one, two, and three, and penalty points on day one, two, and three of a championship. (Co)variance components were estimated via the Gibbs sampling procedure and adequate (co)variance component ratios were calculated. Statistical classifications were trait dependent but all fitted random additive genetic and permanent environment effects. It was found that such characteristics as penalty points and jumping style are potential indicators of jumping ability, and the genetic variability of the traits was within the range of 14% to 27%. Given the low genetic correlations between the conformation and other results achieved on the parkour, the relevance of assessment of conformation in four-years-old horses has been questioned. PMID:26104516

  5. Bulinus globosus (Planorbidae; Gastropoda) populations in the Lake Victoria basin and coastal Kenya show extreme nuclear genetic differentiation.

    PubMed

    Nyakaana, Silvester; Stothard, J Russell; Nalugwa, Allen; Webster, Bonnie L; Lange, Charles N; Jřrgensen, Aslak; Rollinson, David; Kristensen, Thomas K

    2013-11-01

    Bulinus globosus, a key intermediate host for Schistosoma haematobium that causes urinary schistosomiasis, is a hermaphroditic freshwater Planorbid snail species that inhabits patchy and transient water bodies prone to large seasonal variations in water availability. Although capable of self-fertilizing, this species has been reported to be preferentially out crossing. In this study, we characterized the population genetic structure of 19 B. globosus populations sampled across the Lake Victoria basin and coastal Kenya using four polymorphic microsatellite loci. Population genetic structure was characterized and quantified using FST statistics and Bayesian clustering algorithms. The four loci used in this study contained sufficient statistical power to detect low levels of population genetic differentiation and were highly polymorphic with the number of alleles per locus across populations ranging from 16 to 22. Average observed and expected heterozygosities across loci in each population ranged from 0.13 to 0.69 and from 0.39 to 0.79, respectively. Twenty-five of the seventy-six possible population-locus comparisons significantly deviated from Hardy-Weinberg equilibrium proportions after Bonferroni corrections, mostly due to the deficiency of heterozygotes. Significant genetic differentiation was observed between populations and Bayesian inferences identified 15 genetic clusters. The excess homozygosity, significant inbreeding and population genetic differentiation observed in B. globosus populations are likely to be due to the habitat patchiness, mating system and the proneness to cyclic extinction and recolonization in transient habitats. PMID:23266524

  6. Genetic segregation analysis of familial mitral valve prolapse shows no linkage to fibrillar collagen genes.

    PubMed Central

    Wordsworth, P; Ogilvie, D; Akhras, F; Jackson, G; Sykes, B

    1989-01-01

    Three pedigrees were identified in which mitral valve prolapse seemed to be inherited as a mendelian autosomal dominant trait. The segregation of the genes encoding the major fibrillar collagens present in valve tissue, collagens I and III, was analysed by use of restriction enzyme site variants as genetic markers. In one pedigree there was discordance between the segregation of the disease and markers for all three collagen genes. In another, there was discordance between the disease and markers for both collagen I loci. This is evidence against the disease being generally the result of mutations of the genes encoding the major fibrillar collagens. PMID:2930669

  7. High-Resolution Genome-Wide Mapping of Genetic Alterations in Human Glial Brain Tumors

    E-print Network

    Ford, James

    High-Resolution Genome-Wide Mapping of Genetic Alterations in Human Glial Brain Tumors Markus and showed that gliomas can be clustered into distinct genetic subgroups. A subset of detected alterations are key genetic events in gliomagenesis. Recurrent genomic regions of alteration in copy number, including

  8. Genetic Structure and Demographic History Should Inform Conservation: Chinese Cobras Currently Treated as Homogenous Show Population Divergence

    PubMed Central

    Lin, Long-Hui; Qu, Yan-Fu; Li, Hong; Zhou, Kai-Ya; Ji, Xiang

    2012-01-01

    An understanding of population structure and genetic diversity is crucial for wildlife conservation and for determining the integrity of wildlife populations. The vulnerable Chinese cobra (Naja atra) has a distribution from the mouth of the Yangtze River down to northern Vietnam and Laos, within which several large mountain ranges and water bodies may influence population structure. We combined 12 microsatellite loci and 1117 bp of the mitochondrial cytochrome b gene to explore genetic structure and demographic history in this species, using 269 individuals from various localities in Mainland China and Vietnam. High levels of genetic variation were identified for both mtDNA and microsatellites. mtDNA data revealed two main (Vietnam + southern China + southwestern China; eastern + southeastern China) and one minor (comprising only two individuals from the westernmost site) clades. Microsatellite data divided the eastern + southeastern China clade further into two genetic clusters, which include individuals from the eastern and southeastern regions, respectively. The Luoxiao and Nanling Mountains may be important barriers affecting the diversification of lineages. In the haplotype network of cytchrome b, many haplotypes were represented within a “star” cluster and this and other tests suggest recent expansion. However, microsatellite analyses did not yield strong evidence for a recent bottleneck for any population or genetic cluster. The three main clusters identified here should be considered as independent management units for conservation purposes. The release of Chinese cobras into the wild should cease unless their origin can be determined, and this will avoid problems arising from unnatural homogenization. PMID:22558439

  9. Highly structured genetic diversity of the Mycobacterium tuberculosis population in

    E-print Network

    Choisy, Marc

    Highly structured genetic diversity of the Mycobacterium tuberculosis population in Djibouti S, Djibouti Ville, Djibouti Abstract Djibouti is an East African country with a high tuberculosis incidence with pulmonary tuberculosis (TB) were included. Genetic characterization of Mycobacterium tuberculosis, using

  10. Molecular Typing of Australian Scedosporium Isolates Showing Genetic Variability and Numerous S. aurantiacum

    PubMed Central

    Delhaes, Laurence; Harun, Azian; Chen, Sharon C.A.; Nguyen, Quoc; Slavin, Monica; Heath, Christopher H.; Maszewska, Krystyna; Halliday, Catriona; Robert, Vincent; Sorrell, Tania C.

    2008-01-01

    One hundred clinical isolates from a prospective nationwide study of scedosporiosis in Australia (2003–2005) and 46 additional isolates were genotyped by internal transcribed spacer–restriction fragment length polymorphism (ITS-RFLP) analysis, ITS sequencing, and M13 PCR fingerprinting. ITS-RFLP and PCR fingerprinting identified 3 distinct genetic groups. The first group corresponded to Scedosporium prolificans (n = 83), and the other 2 comprised isolates previously identified as S. apiospermum: one of these corresponded to S. apiospermum (n = 33) and the other to the newly described species S. aurantiacum (n = 30). Intraspecies variation was highest for S. apiospermum (58%), followed by S. prolificans (45%) and S. aurantiacum (28%) as determined by PCR fingerprinting. ITS sequence variation of 2.2% was observed among S. apiospermum isolates. No correlation was found between genotype of strains and their geographic origin, body site from which they were cultured, or colonization versus invasive disease. Twelve S. prolificans isolates from 2 suspected case clusters were examined by amplified fragment length polymorphism analysis. No specific clusters were confirmed. PMID:18258122

  11. Genetic and morphological patterns show variation in frequency of hybrids between Ipomopsis (Polemoniaceae) zones of sympatry.

    PubMed

    Aldridge, G; Campbell, D R

    2009-03-01

    Variation in rates of hybridization among zones of sympatry between a pair of species provides a useful window into the effect of local conditions on the evolution of reproductive isolation. We employed floral morphological traits and neutral genetic markers to quantify the frequency of individuals intermediate to the two parental species in two zones of sympatry between Ipomopsis aggregata and I. tenuituba, using clustering methods that make no a priori assumptions about population structure. The sites differed not only in the frequency of intermediate individuals, but also in climate, pollinator abundance and behavior and spatial structure of plant populations. Both floral traits, which are likely to be under natural selection and molecular markers, which are quasi-neutral, indicated more population structure at one site than the other, the pattern being more pronounced for floral morphology. One likely explanation for this difference between sites is that local ecological conditions, particularly pollinator choice of flowers, have promoted different rates of hybridization between these species. Hence, the evolution of reproductive isolation might depend in part on local conditions, and thus differ among populations of the same pair of species. PMID:18971956

  12. Systems Level Analysis of Systemic Sclerosis Shows a Network of Immune and Profibrotic Pathways Connected with Genetic Polymorphisms

    PubMed Central

    Mahoney, J. Matthew; Taroni, Jaclyn; Martyanov, Viktor; Wood, Tammara A.; Greene, Casey S.; Pioli, Patricia A.; Hinchcliff, Monique E.; Whitfield, Michael L.

    2015-01-01

    Systemic sclerosis (SSc) is a rare systemic autoimmune disease characterized by skin and organ fibrosis. The pathogenesis of SSc and its progression are poorly understood. The SSc intrinsic gene expression subsets (inflammatory, fibroproliferative, normal-like, and limited) are observed in multiple clinical cohorts of patients with SSc. Analysis of longitudinal skin biopsies suggests that a patient's subset assignment is stable over 6–12 months. Genetically, SSc is multi-factorial with many genetic risk loci for SSc generally and for specific clinical manifestations. Here we identify the genes consistently associated with the intrinsic subsets across three independent cohorts, show the relationship between these genes using a gene-gene interaction network, and place the genetic risk loci in the context of the intrinsic subsets. To identify gene expression modules common to three independent datasets from three different clinical centers, we developed a consensus clustering procedure based on mutual information of partitions, an information theory concept, and performed a meta-analysis of these genome-wide gene expression datasets. We created a gene-gene interaction network of the conserved molecular features across the intrinsic subsets and analyzed their connections with SSc-associated genetic polymorphisms. The network is composed of distinct, but interconnected, components related to interferon activation, M2 macrophages, adaptive immunity, extracellular matrix remodeling, and cell proliferation. The network shows extensive connections between the inflammatory- and fibroproliferative-specific genes. The network also shows connections between these subset-specific genes and 30 SSc-associated polymorphic genes including STAT4, BLK, IRF7, NOTCH4, PLAUR, CSK, IRAK1, and several human leukocyte antigen (HLA) genes. Our analyses suggest that the gene expression changes underlying the SSc subsets may be long-lived, but mechanistically interconnected and related to a patients underlying genetic risk. PMID:25569146

  13. Human Genetics Education in the High School: A Pilot Program.

    ERIC Educational Resources Information Center

    Haddow, Paula K.

    1982-01-01

    Describes and evaluates a two-day workshop on human genetics for high school biology teachers which involved: (1) a series of lectures by professionals in medical genetics, ethics, and genetic counseling; (2) demonstrations; (3) question-and-answer sessions; (4) a curriculum packet; and (5) a follow-up bimonthly newsletter. (DC)

  14. Small RNAs encoded within genetic islands of Salmonella typhimurium show host-induced expression and role in virulence

    PubMed Central

    Padalon-Brauch, Gilly; Hershberg, Ruth; Elgrably-Weiss, Maya; Baruch, Kobi; Rosenshine, Ilan; Margalit, Hanah; Altuvia, Shoshy

    2008-01-01

    The emergence of pathogenic strains of enteric bacteria and their adaptation to unique niches are associated with the acquisition of foreign DNA segments termed ‘genetic islands’. We explored these islands for the occurrence of small RNA (sRNA) encoding genes. Previous systematic screens for enteric bacteria sRNAs were mainly carried out using the laboratory strain Escherichia coli K12, leading to the discovery of ?80 new sRNA genes. These searches were based on conservation within closely related members of enteric bacteria and thus, sRNAs, unique to pathogenic strains were excluded. Here we describe the identification and characterization of 19 novel unique sRNA genes encoded within the ‘genetic islands’ of the virulent strain Salmonella typhimurium. We show that the expression of many of the island-encoded genes is associated with stress conditions and stationary phase. Several of these sRNA genes are induced when Salmonella resides within macrophages. One sRNA, IsrJ, was further examined and found to affect the translocation efficiency of virulence-associated effector proteins into nonphagocytic cells. In addition, we report that unlike the majority of the E. coli sRNAs that are trans regulators, many of the island-encoded sRNAs affect the expression of cis-encoded genes. Our study suggests that the island encoded sRNA genes play an important role within the network that regulates bacterial adaptation to environmental changes and stress conditions and thus controls virulence. PMID:18267966

  15. High-throughput olfactory conditioning and memory retention test show variation in Nasonia parasitic wasps.

    PubMed

    Hoedjes, K M; Steidle, J L M; Werren, J H; Vet, L E M; Smid, H M

    2012-10-01

    Most of our knowledge on learning and memory formation results from extensive studies on a small number of animal species. Although features and cellular pathways of learning and memory are highly similar in this diverse group of species, there are also subtle differences. Closely related species of parasitic wasps display substantial variation in memory dynamics and can be instrumental to understanding both the adaptive benefit of and mechanisms underlying this variation. Parasitic wasps of the genus Nasonia offer excellent opportunities for multidisciplinary research on this topic. Genetic and genomic resources available for Nasonia are unrivaled among parasitic wasps, providing tools for genetic dissection of mechanisms that cause differences in learning. This study presents a robust, high-throughput method for olfactory conditioning of Nasonia using a host encounter as reward. A T-maze olfactometer facilitates high-throughput memory retention testing and employs standardized odors of equal detectability, as quantified by electroantennogram recordings. Using this setup, differences in memory retention between Nasonia species were shown. In both Nasonia vitripennis and Nasonia longicornis, memory was observed up to at least 5 days after a single conditioning trial, whereas Nasonia giraulti lost its memory after 2 days. This difference in learning may be an adaptation to species-specific differences in ecological factors, for example, host preference. The high-throughput methods for conditioning and memory retention testing are essential tools to study both ultimate and proximate factors that cause variation in learning and memory formation in Nasonia and other parasitic wasp species. PMID:22804968

  16. The genetic landscape of high-risk neuroblastoma

    Cancer.gov

    Published on Office of Cancer Genomics (http://ocg.cancer.gov) Home > The genetic landscape of high-risk neuroblastoma The genetic landscape of high-risk neuroblastoma [1] Pugh TJ, Morozova O, Attiyeh EF, Asgharzadeh S, Wei JS, Auclair D, Carter SL,

  17. The genetic landscape of high-risk neuroblastoma

    Cancer.gov

    Published on Office of Cancer Genomics (https://ocg.cancer.gov) Home > The genetic landscape of high-risk neuroblastoma The genetic landscape of high-risk neuroblastoma [1] Pugh TJ, Morozova O, Attiyeh EF, Asgharzadeh S, Wei JS, Auclair D, Carter SL,

  18. GENETIC DIFFERENCES AMONG SOURCES OF HIGH PROTEIN IN SOYBEAN SEEDS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    There is much research that documents the genetic diversity between high and low protein concentration in soybean seeds but almost no information about genetic diversity among lines with high protein concentrations. The objective of this research was to identify germplasm accessions with difference...

  19. highly conserved and shows little variation in sequence over 12 isolates. CP is also essential

    E-print Network

    Paris-Sud XI, Université de

    is ideally suited to maize. Wheat and other small grain cereals have been affected by different strains diploperennis are resistant to MSV but cultivars and hybrids show varying susceptibility. Sweetcorns are highly susceptible to MSV but many new varieties of tropical maize show high levels of tolerance, although resis

  20. Stem and progenitor cells in myelodysplastic syndromes show aberrant stage-specific expansion and harbor genetic and epigenetic alterations

    PubMed Central

    Will, Britta; Zhou, Li; Vogler, Thomas O.; Ben-Neriah, Susanna; Schinke, Carolina; Tamari, Roni; Yu, Yiting; Bhagat, Tushar D.; Bhattacharyya, Sanchari; Barreyro, Laura; Heuck, Christoph; Mo, Yonkai; Parekh, Samir; McMahon, Christine; Pellagatti, Andrea; Boultwood, Jacqueline; Montagna, Cristina; Silverman, Lewis; Maciejewski, Jaroslaw; Greally, John M.; Ye, B. Hilda; List, Alan F.; Steidl, Christian

    2012-01-01

    Even though hematopoietic stem cell (HSC) dysfunction is presumed in myelodysplastic syndrome (MDS), the exact nature of quantitative and qualitative alterations is unknown. We conducted a study of phenotypic and molecular alterations in highly fractionated stem and progenitor populations in a variety of MDS subtypes. We observed an expansion of the phenotypically primitive long-term HSCs (lineage?/CD34+/CD38?/CD90+) in MDS, which was most pronounced in higher-risk cases. These MDS HSCs demonstrated dysplastic clonogenic activity. Examination of progenitors revealed that lower-risk MDS is characterized by expansion of phenotypic common myeloid progenitors, whereas higher-risk cases revealed expansion of granulocyte-monocyte progenitors. Genome-wide analysis of sorted MDS HSCs revealed widespread methylomic and transcriptomic alterations. STAT3 was an aberrantly hypomethylated and overexpressed target that was validated in an independent cohort and found to be functionally relevant in MDS HSCs. FISH analysis demonstrated that a very high percentage of MDS HSC (92% ± 4%) carry cytogenetic abnormalities. Longitudinal analysis in a patient treated with 5-azacytidine revealed that karyotypically abnormal HSCs persist even during complete morphologic remission and that expansion of clonotypic HSCs precedes clinical relapse. This study demonstrates that stem and progenitor cells in MDS are characterized by stage-specific expansions and contain epigenetic and genetic alterations. PMID:22753872

  1. Admixture facilitates genetic adaptations to high altitude in Tibet.

    PubMed

    Jeong, Choongwon; Alkorta-Aranburu, Gorka; Basnyat, Buddha; Neupane, Maniraj; Witonsky, David B; Pritchard, Jonathan K; Beall, Cynthia M; Di Rienzo, Anna

    2014-01-01

    Admixture is recognized as a widespread feature of human populations, renewing interest in the possibility that genetic exchange can facilitate adaptations to new environments. Studies of Tibetans revealed candidates for high-altitude adaptations in the EGLN1 and EPAS1 genes, associated with lower haemoglobin concentration. However, the history of these variants or that of Tibetans remains poorly understood. Here we analyse genotype data for the Nepalese Sherpa, and find that Tibetans are a mixture of ancestral populations related to the Sherpa and Han Chinese. EGLN1 and EPAS1 genes show a striking enrichment of high-altitude ancestry in the Tibetan genome, indicating that migrants from low altitude acquired adaptive alleles from the highlanders. Accordingly, the Sherpa and Tibetans share adaptive haemoglobin traits. This admixture-mediated adaptation shares important features with adaptive introgression. Therefore, we identify a novel mechanism, beyond selection on new mutations or on standing variation, through which populations can adapt to local environments. PMID:24513612

  2. Brain fiber architecture, genetics, and intelligence: a high angular resolution diffusion imaging (HARDI) study.

    PubMed

    Chiang, Ming-Chang; Barysheva, Marina; Lee, Agatha D; Madsen, Sarah; Klunder, Andrea D; Toga, Arthur W; Mcmahon, Katie L; de Zubicaray, Greig I; Meredith, Matthew; Wright, Margaret J; Srivastava, Anuj; Balov, Nikolay; Thompson, Paul M

    2008-01-01

    We developed an analysis pipeline enabling population studies of HARDI data, and applied it to map genetic influences on fiber architecture in 90 twin subjects. We applied tensor-driven 3D fluid registration to HARDI, resampling the spherical fiber orientation distribution functions (ODFs) in appropriate Riemannian manifolds, after ODF regularization and sharpening. Fitting structural equation models (SEM) from quantitative genetics, we evaluated genetic influences on the Jensen-Shannon divergence (JSD), a novel measure of fiber spatial coherence, and on the generalized fiber anisotropy (GFA) a measure of fiber integrity. With random-effects regression, we mapped regions where diffusion profiles were highly correlated with subjects' intelligence quotient (IQ). Fiber complexity was predominantly under genetic control, and higher in more highly anisotropic regions; the proportion of genetic versus environmental control varied spatially. Our methods show promise for discovering genes affecting fiber connectivity in the brain. PMID:18979850

  3. Executive deficits in Individuals at High Genetic Risk of Schizophrenia 

    E-print Network

    Dimitrova, R

    2012-11-28

    Background. Studies of individuals at high genetic risk (HR) of schizophrenia have shown subtle deficits in the domains of executive functions. However, executive abilities also depend on working memory, which is one of the most prominent...

  4. High-resolution genetic mapping with pooled sequencing

    E-print Network

    Edwards, Matthew Douglas

    Background: Modern genetics has been transformed by high-throughput sequencing. New experimental designs in model organisms involve analyzing many individuals, pooled and sequenced in groups for increased efficiency. ...

  5. High volume molecular genetic identification of single nucleotide polymorphisms using Genetic Bit Analysis Application to human genetic diagnosis

    SciTech Connect

    Boyce-Jacino, M.T.; Reynolds, J.; Nikiforov, T. [Molecular Tool, Inc., Baltimore, MD (United States)] [and others

    1994-09-01

    The most common type of genetic disease-associated mutation is the single nucleotide polymorphism (SNP). Because most genetic diseases can be caused by multiple SNPs in the same gene, effective routine diagnosis of complex genetic diseases is dependent on a simple and reliable method of interrogating SNP sites. Molecular Tool`s solid phase assay capable of direct genotyping (single base sequencing) of SNP sites, Genetic Bit Analysis (GBA), involves hybridization-capture of a single-stranded PCR product to a sequence-specific, microtiter plate-bound oligonucleotide primer. The captured PCR product then acts as template for single-base extension of the capture primer across the polymorphic site, enabling direct determination of the base composition of the polymorphism through a simple colormetric assay. Genotyping in a high volume, semi-automated, processing system with a current capacity of 100 SNP interrogations per technician per day enables the screening of candidate mutations rapidly and cost-effectively, critically important to comprehensive genetic diagnosis. Using this gel-free technology, we have developed prototype diagnostic tests for CFTR and ApoE polymorphisms which enable direct sequencing of the polymorphic base at each site of interest. Routine clinical diagnosis of genetically complex diseases such as cystic fibrosis is dependent on this combination of robust biochemistry and simple format. Additionally, the ability to transfer the format and biochemistry to any disease gene of interest enables the broad application of this technology to clinical diagnostics, especially for genetically complex diseases.

  6. Genetic polymorphisms in monoamine neurotransmitter systems show only weak association with acute post-surgical pain in humans

    Microsoft Academic Search

    Hyungsuk Kim; Hyewon Lee; Janet Rowan; Jaime Brahim; Raymond A Dionne

    2006-01-01

    BACKGROUND: Candidate gene studies on the basis of biological hypotheses have been a practical approach to identify relevant genetic variation in complex traits. Based on previous reports and the roles in pain pathways, we have examined the effects of variations of loci in the genes of monoamine neurotransmitter systems including metabolizing enzymes, receptors and transporters on acute clinical pain responses

  7. An informed genetic algorithm for the high school timetabling problem

    Microsoft Academic Search

    Rushil Raghavjee; Nelishia Pillay

    2010-01-01

    The high school timetabling problem differs drastically from one school to another and from country to country. The South African high school problem has not been researched. This paper presents a genetic algorithm (GA) to solve this problem for a particular high school. A two-phase approach is taken. The first phase uses a GA to evolve a timetable that meets

  8. Differential analysis of high-throughput quantitative genetic interaction data

    PubMed Central

    2012-01-01

    Synthetic genetic arrays have been very effective at measuring genetic interactions in yeast in a high-throughput manner and recently have been expanded to measure quantitative changes in interaction, termed 'differential interactions', across multiple conditions. Here, we present a strategy that leverages statistical information from the experimental design to produce a novel, quantitative differential interaction score, which performs favorably compared to previous differential scores. We also discuss the added utility of differential genetic-similarity in differential network analysis. Our approach is preferred for differential network analysis, and our implementation, written in MATLAB, can be found at http://chianti.ucsd.edu/~gbean/compute_differential_scores.m. PMID:23268787

  9. Application of Genetic Programming to High Energy Physics Event Selection

    E-print Network

    Link, J M; Anjos, J C; Bediaga, I; Castromonte, C; Göbel, C; Machado, A A; Magnin, J; Massafferri, A; De Miranda, J M; Pepe, I M; Polycarpo, E; Dos Reis, A C; Carrillo, S; Casimiro, E; Cuautle, E; Sánchez-Hernández, A; Uribe, C; Vázquez, F; Agostino, L; Cinquini, L; Cumalat, J P; O'Reilly, B; Segoni, I; Stenson, K; Butler, J N; Cheung, H W K; Chiodini, G; Gaines, I; Garbincius, P H; Garren, L A; Gottschalk, E; Kasper, P H; Kreymer, A E; Kutschke, R; Wang, M; Benussi, L; Bertani, M; Bianco, S; Fabbri, Franco Luigi; Pacetti, S; Zallo, A; Reyes, M; Cawlfield, C; Kim, D Y; Rahimi, A; Wiss, J; Gardner, R; Kryemadhi, A; Chung, Y S; Kang, J S; Ko, B R; Kwak, J W; Lee, K B; Cho, K; Park, H; Alimonti, G; Barberis, S; Boschini, M; Cerutti, A; D'Angelo, P; Di Corato, M; Dini, P; Edera, L; Erba, S; Inzani, P; Leveraro, F; Malvezzi, S; Menasce, D; Mezzadri, M; Moroni, L; Pedrini, D; Pontoglio, C; Prelz, F; Rovere, M; Sala, S; Davenport, T F; Arena, V; Boca, G; Bonomi, G; Gianini, G; Liguori, G; Lopes-Pegna, D; Merlo, M M; Pantea, D; Ratti, S P; Riccardi, C; Vitulo, P; Hernández, H; López, A M; Méndez, H; Paris, A; Quinones, J; Ramírez, J E; Zhang, Y; Wilson, J R; Handler, T; Mitchell, R; Engh, D; Hosack, M; Johns, W E; Luiggi, E; Moore, J E; Nehring, M; Sheldon, P D; Vaandering, E W; Webster, M; Sheaff, M

    2005-01-01

    We review genetic programming principles, their application to FOCUS data samples, and use the method to study the doubly Cabibbo suppressed decay D+ -> K+ pi+ pi- relative to its Cabibbo favored counterpart, D+ -> K- pi+ pi+. We find that this technique is able to improve upon more traditional analysis methods. To our knowledge, this is the first application of the genetic programming technique to High Energy Physics data.

  10. Application of Genetic Programming to High Energy Physics Event Selection

    E-print Network

    The FOCUS Collaboration; J. M. Link

    2005-05-12

    We review genetic programming principles, their application to FOCUS data samples, and use the method to study the doubly Cabibbo suppressed decay D+ -> K+ pi+ pi- relative to its Cabibbo favored counterpart, D+ -> K- pi+ pi+. We find that this technique is able to improve upon more traditional analysis methods. To our knowledge, this is the first application of the genetic programming technique to High Energy Physics data.

  11. Childhood hyperactivity scores are highly heritable and show sibling competition effects: Twin study evidence

    Microsoft Academic Search

    Anita Thapar; Amaia Hervas; Peter McGuffin I

    1995-01-01

    Hyperactivity has consistently been shown to be familial. Until recently however, due to a lack of systematic twin evidence,\\u000a it has remained uncertain to what extent familial transmission can be explained by genetic factors. We used a systematically\\u000a ascertained population-based sample of twin pairs aged between 8 and 16 years old to explore the role of genetic influences\\u000a on maternally

  12. Pulsed-field gel electrophoresis used to investigate genetic diversity of Haemophilus influenzae type b isolates in Australia shows differences between Aboriginal and non-Aboriginal isolates.

    PubMed

    Moor, P E; Collignon, P C; Gilbert, G L

    1999-05-01

    We used pulsed-field gel electrophoresis to study the epidemiology and population structure of Haemophilus influenzae type b. DNAs from 187 isolates recovered between 1985 and 1993 from Aboriginal children (n = 76), non-Aboriginal children (n = 106), and non-Aboriginal adults (n = 5) in urban and rural regions across Australia were digested with the SmaI restriction endonuclease. Patterns of 13 to 17 well-resolved fragments (size range, approximately 8 to 500 kb) defining 67 restriction fragment length polymorphism (RFLP) types were found. Two types predominated. One type (n = 37) accounted for 35 (46%) of the isolates from Aboriginals and 2 (2%) of the isolates from non-Aboriginals, and the other type (n = 41) accounted for 2 (3%) of the isolates from Aboriginals and 39 (35%) of the isolates from non-Aboriginals. Clustering revealed seven groups at a genetic distance of approximately 50% similarity in a tree-like dendrogram. They included two highly divergent groups representing 50 (66%) isolates from Aboriginals and 6 (5%) isolates from non-Aboriginals and another genetically distinct group representing 7 (9%) isolates from Aboriginals and 81 (73%) isolates from non-Aboriginals. The results showed a heterogeneous clonal population structure, with the isolates of two types accounting for 42% of the sample. There was no association between RFLP type and the diagnosis of meningitis or epiglottitis, age, sex, date of collection, or geographic location, but there was a strong association between the origin of isolates from Aboriginal children and RFLP type F2a and the origin of isolates from non-Aboriginal children and RFLP type A8b. The methodology discriminated well among the isolates (D = 0.91) and will be useful for the monitoring of postvaccine isolates of H. influenzae type b. PMID:10203516

  13. A genetic algorithm model for high heat flux flow boiling

    Microsoft Academic Search

    Pasquale M. Sforza

    1997-01-01

    A new genetic algorithm model is introduced in a recently developed turbulent-boundary-layer scheme for the calculation of heat transfer in high heat flux subcooled boiling flows. Such flows, often desired for cooling of rocket nozzles and nuclear components, are characterized by high fluid velocities and extremely small bubbles that exist in a thin layer adjacent to the heated wall. The

  14. DNA Barcode Detects High Genetic Structure within Neotropical Bird Species

    PubMed Central

    Tavares, Erika Sendra; Gonçalves, Priscila; Miyaki, Cristina Yumi; Baker, Allan J.

    2011-01-01

    Background Towards lower latitudes the number of recognized species is not only higher, but also phylogeographic subdivision within species is more pronounced. Moreover, new genetically isolated populations are often described in recent phylogenies of Neotropical birds suggesting that the number of species in the region is underestimated. Previous COI barcoding of Argentinean bird species showed more complex patterns of regional divergence in the Neotropical than in the North American avifauna. Methods and Findings Here we analyzed 1,431 samples from 561 different species to extend the Neotropical bird barcode survey to lower latitudes, and detected even higher geographic structure within species than reported previously. About 93% (520) of the species were identified correctly from their DNA barcodes. The remaining 41 species were not monophyletic in their COI sequences because they shared barcode sequences with closely related species (N?=?21) or contained very divergent clusters suggestive of putative new species embedded within the gene tree (N?=?20). Deep intraspecific divergences overlapping with among-species differences were detected in 48 species, often with samples from large geographic areas and several including multiple subspecies. This strong population genetic structure often coincided with breaks between different ecoregions or areas of endemism. Conclusions The taxonomic uncertainty associated with the high incidence of non-monophyletic species and discovery of putative species obscures studies of historical patterns of species diversification in the Neotropical region. We showed that COI barcodes are a valuable tool to indicate which taxa would benefit from more extensive taxonomic revisions with multilocus approaches. Moreover, our results support hypotheses that the megadiversity of birds in the region is associated with multiple geographic processes starting well before the Quaternary and extending to more recent geological periods. PMID:22163311

  15. Disproportionate Cochlear Length in Genus Homo Shows a High Phylogenetic Signal during Apes’ Hearing Evolution

    PubMed Central

    Braga, J.; Loubes, J-M.; Descouens, D.; Dumoncel, J.; Thackeray, J. F.; Kahn, J-L.; de Beer, F.; Riberon, A.; Hoffman, K.; Balaresque, P.; Gilissen, E.

    2015-01-01

    Changes in lifestyles and body weight affected mammal life-history evolution but little is known about how they shaped species’ sensory systems. Since auditory sensitivity impacts communication tasks and environmental acoustic awareness, it may have represented a deciding factor during mammal evolution, including apes. Here, we statistically measure the influence of phylogeny and allometry on the variation of five cochlear morphological features associated with hearing capacities across 22 living and 5 fossil catarrhine species. We find high phylogenetic signals for absolute and relative cochlear length only. Comparisons between fossil cochleae and reconstructed ape ancestral morphotypes show that Australopithecus absolute and relative cochlear lengths are explicable by phylogeny and concordant with the hypothetized ((Pan,Homo),Gorilla) and (Pan,Homo) most recent common ancestors. Conversely, deviations of the Paranthropus oval window area from these most recent common ancestors are not explicable by phylogeny and body weight alone, but suggest instead rapid evolutionary changes (directional selection) of its hearing organ. Premodern (Homo erectus) and modern human cochleae set apart from living non-human catarrhines and australopiths. They show cochlear relative lengths and oval window areas larger than expected for their body mass, two features corresponding to increased low-frequency sensitivity more recent than 2 million years ago. The uniqueness of the “hypertrophied” cochlea in the genus Homo (as opposed to the australopiths) and the significantly high phylogenetic signal of this organ among apes indicate its usefulness to identify homologies and monophyletic groups in the hominid fossil record. PMID:26083484

  16. European Invasion of North American Pinus strobus at Large and Fine Scales: High Genetic Diversity and Fine-Scale Genetic Clustering over Time in the Adventive Range

    PubMed Central

    Mandák, Bohumil; Hadincová, V?roslava; Mahelka, Václav; Wildová, Radka

    2013-01-01

    Background North American Pinus strobus is a highly invasive tree species in Central Europe. Using ten polymorphic microsatellite loci we compared various aspects of the large-scale genetic diversity of individuals from 30 sites in the native distribution range with those from 30 sites in the European adventive distribution range. To investigate the ascertained pattern of genetic diversity of this intercontinental comparison further, we surveyed fine-scale genetic diversity patterns and changes over time within four highly invasive populations in the adventive range. Results Our data show that at the large scale the genetic diversity found within the relatively small adventive range in Central Europe, surprisingly, equals the diversity found within the sampled area in the native range, which is about thirty times larger. Bayesian assignment grouped individuals into two genetic clusters separating North American native populations from the European, non-native populations, without any strong genetic structure shown over either range. In the case of the fine scale, our comparison of genetic diversity parameters among the localities and age classes yielded no evidence of genetic diversity increase over time. We found that SGS differed across age classes within the populations under study. Old trees in general completely lacked any SGS, which increased over time and reached its maximum in the sapling stage. Conclusions Based on (1) the absence of difference in genetic diversity between the native and adventive ranges, together with the lack of structure in the native range, and (2) the lack of any evidence of any temporal increase in genetic diversity at four highly invasive populations in the adventive range, we conclude that population amalgamation probably first happened in the native range, prior to introduction. In such case, there would have been no need for multiple introductions from previously isolated populations, but only several introductions from genetically diverse populations. PMID:23874648

  17. A new two-phase dimeticone pediculicide shows high efficacy in a comparative bioassay

    PubMed Central

    2009-01-01

    Background Dimeticones kill head lice by physical means. Here we assessed in a comparative bioassay the ex vivo efficacy of "NYDA® sensitiv", a new two-phase dimeticone-based pediculicide similar to a product established on the market, but without fragrances. Methods We compared efficacy of the new product to a positive dimeticone control group, a sample of four other insecticidal and natural head lice products marketed in Germany, and an untreated control. In a bioassay, lice were exposed ex vivo to products and examined for activity for up to 24 hours, following a standard protocol. Results After 6 and 24 hours, 13.7 and 88.5% of untreated control lice did not show major vital signs. In contrast, no lice showed major vital signs 5 minutes after treatment with the new product or the control dimeticone group (NYDA®). This effect persisted at all observation points (100% efficacy). Efficacy of 0.5% permethrin (Infectopedicul®) ranged between 76 and 96% in evaluations between 5 min and 6 hours. All lice treated with a coconut-based compound (mosquito® Läuseshampoo) did not show major vital signs after 5 min, but mortality was only 58% after one hour. Pyrethrum extract (Goldgeist® forte) showed an efficacy of 22 - 52% between 5 min and 3 hours after treatment; after 6 hours, 76% of lice were judged dead. An oxyphthirine®-based compound (Liberalice DUO LP-PRO®) killed 22 - 54% of lice in the first 6 hours. Conclusions The two-phase dimeticone compound NYDA® sensitiv is highly efficacious. The removal of fragrances as compared to an established dimeticone product did not affect in vitro efficacy. PMID:20003435

  18. Elitist Genetic Algorithm Models: Optimization of High Performance Concrete Mixes

    Microsoft Academic Search

    M. A. Jayaram; M. C. Nataraja; C. N. Ravikumar

    2009-01-01

    This article elaborates the development of elitist Genetic Algorithm (GA) models for the optimization of high volume fly ash concrete (HVFAC) mix. The model consists of two stages. In the first stage, a huge database of 350 mix designs garnered through standard research publications were statstistically analyzed to elicit upper and lower bounds of certain range constraints and rational ratio

  19. High and low sensation seeking adolescents show distinct patterns of brain activity during reward processing

    PubMed Central

    Cservenka, Anita; Herting, Megan M.; Seghete, Kristen L. Mackiewicz; Hudson, Karen A.; Nagel, Bonnie J.

    2012-01-01

    Previous research has shown that personality characteristics, such as sensation seeking (SS), are strong predictors of risk-taking behavior during adolescence. However, the relationship between levels of SS and brain response has not been studied during this time period. Given the prevalence of risky behavior during adolescence, it is important to understand neurobiological differences in reward sensitivity between youth with high and low SS personalities. To this end, we used functional magnetic resonance imaging (fMRI) to examine differences in brain activity in an adolescent sample that included 27 high (HSS) and 27 low sensation seekers (LSS), defined by the Impulsive Sensation Seeking scale of the Zuckerman-Kuhlman Personality Questionnaire (Zuckerman et al., 1993). In the scanner, participants played a modified Wheel of Fortune decision-making task (Cservenka and Nagel, 2012) that resulted in trials with monetary Wins or No Wins. We compared age- and sex-matched adolescent HSS and LSS (mean age = 13.94 ± 1.05) on brain activity by contrasting Win versus No Win trials. Our findings indicate that HSS show greater bilateral insular and prefrontal cortex (PFC) brain response on Win vs. No Win compared to LSS. Analysis of simple effects showed that while LSS showed comparable brain activity in these areas during Wins and No Wins, HSS showed significant differences in brain response to winning (activation) versus not winning (deactivation), with between-group comparison suggesting significant differences in brain response, largely to reward absence. Group differences in insular activation between reward receipt and absence may suggest weak autonomic arousal to negative outcomes in HSS compared with LSS. Additionally, since the PFC is important for goal-directed behavior and attention, the current results may reflect that HSS allocate fewer attentional resources to negative outcomes than LSS. This insensitivity to reward absence in HSS may lead to a greater likelihood of maladaptive choices when negative consequences are not considered, and may be an early neural marker of decreased loss sensitivity that has been seen in addiction. This neurobiological information may ultimately be helpful in establishing prevention strategies aimed at reducing youth risk-taking and suggests value in further examination of neural associations with personality characteristics during adolescence. PMID:23142276

  20. Biological Invasions: Paradox Lost and Paradise Gained A new study shows how an invasive snail species accrues elevated genetic

    E-print Network

    Hufbauer, Ruth A.

    Dispatches Biological Invasions: Paradox Lost and Paradise Gained A new study shows how an invasive human interference in animal and plant dispersal, biological invasions are wreaking havoc that can become economically and ecologically threatening. Recent studies of biological invasions, however

  1. Low levels of nestmate discrimination despite high genetic differentiation in the invasive pharaoh ant

    PubMed Central

    2010-01-01

    Background Ants typically distinguish nestmates from non-nestmates based on the perception of colony-specific chemicals, particularly cuticular hydrocarbons present on the surface of the ants' exoskeleton. These recognition cues are believed to play an important role in the formation of vast so-called supercolonies that have been described for some invasive ant species, but general conclusions about the role of these cues are hampered by only few species being studied. Here we use data on cuticular hydrocarbons, aggression and microsatellite genetic markers to investigate the interdependence of chemical recognition cues, genetic distance and nestmate discrimination in the pharaoh ant (Monomorium pharaonis), a widespread pest species, and ask whether introduced populations of this species are genetically differentiated and exhibit intraspecific aggression. Results Microsatellite analyses of a total of 35 colonies from four continents revealed extremely high levels of genetic differentiation between almost all colonies (FST = 0.751 ± 0.006 SE) and very low within-colony diversity. This implies that at least 34 and likely hundreds more independent lineages of this ant have spread worldwide. Aggression tests involving workers from 14 different colonies showed only low levels of aggression, even between colonies that were geographically and/or genetically very distant. Chemical analyses of groups of worker ants showed that all colonies had the same cuticular compounds, which varied only quantitatively among colonies. There was a positive correlation between geographical and genetic distance, but no other significant relationships were detected between aggression, chemical profile, genetic distance and geographical distance. Conclusions The pharaoh ant has a global invasion history of numerous independent introductions resulting in genetically highly differentiated colonies typically displaying surprisingly low levels of intraspecific aggression, a behaviour that may have evolved in the native range or by lineage selection in the introduced range. PMID:20591186

  2. Nanoscale anatase TiO2 with dominant {1 1 1} facets shows high photocatalytic activity

    NASA Astrophysics Data System (ADS)

    Zhang, Jun; Qian, Lisha; Yang, Lingxia; Tao, Xi; Su, Kunpeng; Wang, Hongbo; Xi, Junhua; Ji, Zhenguo

    2014-08-01

    In this work, we report a novel synthesis of nanoscale anatase TiO2 with dominant highly active {1 1 1} facets by a simple one-step hydrothermal route with the assistance of NH4F and HF. In this progress, the exposed crystal facets of TiO2 can been directly tuned by controlling the mole ratio of NH4+ and F-. When the mole ratio of NH4+ and F-reach 1:2, nanoscale anatase TiO2 with dominant {1 1 1} facets can be obtained. Nanoscale anatase TiO2 with exposed {1 0 1} or {0 0 1} facets will be prepared when there is only ammonia or HF added respectively. Such nano-TiO2 with exposed highly active {1 1 1} facets has large specific surface area and shows excellent photocatalytic activity: as much as 2-3 times than that of TiO2 nanosheets with exposed {0 0 1} facets and commercial Degussa P25 which confirms the {1 1 1} facets have higher photocatalytic activity than {0 0 1} and {1 0 1} facets. The higher photocatalytic activity of {1 1 1} facets can be ascribed to the fact that all Ti and O atoms on the surface are unsaturated Ti5c, Ti3c and O2c modes which produces a higher adsorption and degradation ability. The present work demonstrates a explore of hydrothermal synthetic method for controlling preparation of nano-materials.

  3. A novel lectin from Agrocybe aegerita shows high binding selectivity for terminal N-acetylglucosamine.

    PubMed

    Jiang, Shuai; Chen, Yijie; Wang, Man; Yin, Yalin; Pan, Yongfu; Gu, Bianli; Yu, Guojun; Li, Yamu; Wong, Barry Hon Cheung; Liang, Yi; Sun, Hui

    2012-04-15

    A novel lectin was isolated from the mushroom Agrocybe aegerita (designated AAL-2) by affinity chromatography with GlcNAc (N-acetylglucosamine)-coupled Sepharose 6B after ammonium sulfate precipitation. The AAL-2 coding sequence (1224 bp) was identified by performing a homologous search of the five tryptic peptides identified by MS against the translated transcriptome of A. aegerita. The molecular mass of AAL-2 was calculated to be 43.175 kDa from MS, which was consistent with the data calculated from the amino acid sequence. To analyse the carbohydrate-binding properties of AAL-2, a glycan array composed of 465 glycan candidates was employed, and the result showed that AAL-2 bound with high selectivity to terminal non-reducing GlcNAc residues, and further analysis revealed that AAL-2 bound to terminal non-reducing GlcNAc residues with higher affinity than previously well-known GlcNAc-binding lectins such as WGA (wheatgerm agglutinin) and GSL-II (Griffonia simplicifolia lectin-II). ITC (isothermal titration calorimetry) showed further that GlcNAc bound to AAL-2 in a sequential manner with moderate affinity. In the present study, we also evaluated the anti-tumour activity of AAL-2. The results showed that AAL-2 could bind to the surface of hepatoma cells, leading to induced cell apoptosis in vitro. Furthermore, AAL-2 exerted an anti-hepatoma effect via inhibition of tumour growth and prolongation of survival time of tumour-bearing mice in vivo. PMID:22268569

  4. Culturable associated-bacteria of the sponge Theonella swinhoei show tolerance to high arsenic concentrations

    PubMed Central

    Keren, Ray; Lavy, Adi; Mayzel, Boaz; Ilan, Micha

    2015-01-01

    Sponges are potent filter feeders and as such are exposed to high fluxes of toxic trace elements, which can accumulate in their body over time. Such is the case of the Red Sea sponge Theonella swinhoei, which has been shown to accumulate up to 8500 mg/Kg of the highly toxicelement arsenic. T. swinhoei is known to harbor a multitude of sponge-associated bacteria, so it is hypothesized that the associated-bacteria will be tolerant to high arsenic concentration. This study also investigates the fate of the arsenic accumulated in the sponge to test if the associated-bacteria have an important role in the arsenic accumulation process of their host, since bacteria are key players in the natural arsenic cycle. Separation of the sponge to sponge cells and bacteria enriched fractions showed that arsenic is accumulated by the bacteria. Sponge-associated, arsenic-tolerant bacteria were cultured in the presence of 5 mM of either arsenate or arsenite (equivalent to 6150 mg/Kg arsenic, dry weight). The 54 isolated bacteria were grouped to 15 operational taxonomic units (OTUs) and isolates belonging to 12 OTUs were assessed for tolerance to arsenate at increased concentrations up to 100 mM. Eight of the 12 OTUs tolerated an order of magnitude increase in the concentration of arsenate, and some exhibited external biomineralization of arsenic–magnesium salts. The biomineralization of this unique mineral was directly observed in bacteria for the first time. These results may provide an explanation for the ability of the sponge to accumulate considerable amounts of arsenic. Furthermore arsenic-mineralizing bacteria can potentially be used for the study of bioremediation, as arsenic toxicity affects millions of people worldwide. PMID:25762993

  5. Genetic correlations between field test results of Swedish Warmblood Riding Horses as 4-year-olds and lifetime performance results in dressage and show jumping

    Microsoft Academic Search

    Lena Wallin; Erling Strandberg; Jan Philipsson

    2003-01-01

    The main objective of this study was to estimate genetic correlations between traits of young sport horses (4 years old) evaluated in the Swedish Riding Horse Quality Test (RHQT) and later competition results in dressage and show jumping. The data comprised 3708 Warmblood horses born between 1968 and 1982 that had participated in the RHQT as 4-year-olds and 25?605 horses

  6. Male and female secondary sexual traits show different patterns of quantitative genetic and environmental variation in the horned beetle Onthophagus sagittarius.

    PubMed

    Watson, N L; Simmons, L W

    2010-11-01

    The expression of secondary sexual traits in females has often been attributed to a correlated response to selection on male traits. In rare cases, females have secondary sexual traits that are not homologous structures to secondary sexual traits in males and are thus less likely to have evolved in females because of correlated selection. In this study, we used the dung beetle Onthophagus sagittarius, a species with sex-specific horns, to examine the environmental and quantitative genetic control of horn expression in males and females. Offspring subjected to different brood mass manipulations (dung addition/removal) were found to differ significantly in body size. Brood mass manipulation also had a significant effect on the length of male horns; however, female horn length was found to be relatively impervious to the treatment, showing stronger patterns of additive genetic variance than males. We found no correlations between horn expression in males and females. We therefore conclude that the horns of O. sagittarius females are unlikely to result from genetic correlations between males and females. Rather, our data suggest that they may be under independent genetic control. PMID:20831732

  7. Microsatellite Typing of Clinical and Environmental Cryptococcus neoformans var. grubii Isolates from Cuba Shows Multiple Genetic Lineages

    Microsoft Academic Search

    Maria-Teresa Illnait-Zaragozi; Gerardo F. Martínez-Machín; Carlos M. Fernández-Andreu; Teun Boekhout; Jacques F. Meis; Corné H. W. Klaassen; Francoise Dromer

    2010-01-01

    BackgroundHuman cryptococcal infections have been associated with bird droppings as a likely source of infection. Studies toward the local and global epidemiology of Cryptococcus spp. have been hampered by the lack of rapid, discriminatory, and exchangeable molecular typing methods.Methodology\\/Principal FindingsWe selected nine microsatellite markers for high-resolution fingerprinting from the genome of C. neoformans var. grubii. This panel of markers was

  8. High frequency of cephalic neural crest cells shows coexistence of neurogenic, melanogenic, and osteogenic differentiation capacities

    PubMed Central

    Calloni, Giordano W.; Le Douarin, Nicole M.; Dupin, Elisabeth

    2009-01-01

    The neural crest (NC) is a vertebrate innovation that distinguishes vertebrates from other chordates and was critical for the development and evolution of a “New Head and Brain.” In early vertebrates, the NC was the source of dermal armor of fossil jawless fish. In extant vertebrates, including mammals, the NC forms the peripheral nervous system, melanocytes, and the cartilage and bone of the face. Here, we show that in avian embryos, a large majority of cephalic NC cells (CNCCs) have the ability to differentiate into cell types as diverse as neurons, melanocytes, osteocytes, and chondrocytes. Moreover, we find that the morphogen Sonic hedgehog (Shh) acts on CNCCs to increase endochondral osteogenesis while having no effect on osteoblasts prone to membranous ossification. We have developed culture conditions that demonstrate that “neural–mesenchymal” differentiation abilities are present in more than 90% of CNCCs. A highly multipotent progenitor (able to yield neurons, glia, melanocytes, myofibroblasts, chondrocytes, and osteocytes) comprises 7–13% of the clonogenic cells in the absence and presence of Shh, respectively. This progenitor is a good candidate for a cephalic NC stem cell. PMID:19447928

  9. Efficient screening of long terminal repeat retrotransposons that show high insertion polymorphism via high-throughput sequencing of the primer binding site.

    PubMed

    Monden, Yuki; Fujii, Nobuyuki; Yamaguchi, Kentaro; Ikeo, Kazuho; Nakazawa, Yoshiko; Waki, Takamitsu; Hirashima, Keita; Uchimura, Yosuke; Tahara, Makoto

    2014-05-01

    Retrotransposons have been used frequently for the development of molecular markers by using their insertion polymorphisms among cultivars, because multiple copies of these elements are dispersed throughout the genome and inserted copies are inherited genetically. Although a large number of long terminal repeat (LTR) retrotransposon families exist in the higher eukaryotic genomes, the identification of families that show high insertion polymorphism has been challenging. Here, we performed an efficient screening of these retrotransposon families using an Illumina HiSeq2000 sequencing platform with comprehensive LTR library construction based on the primer binding site (PBS), which is located adjacent to the 5' LTR and has a motif that is universal and conserved among LTR retrotransposon families. The paired-end sequencing library of the fragments containing a large number of LTR sequences and their insertion sites was sequenced for seven strawberry (Fragaria × ananassa Duchesne) cultivars and one diploid wild species (Fragaria vesca L.). Among them, we screened 24 families with a "unique" insertion site that appeared only in one cultivar and not in any others, assuming that this type of insertion should have occurred quite recently. Finally, we confirmed experimentally the selected LTR families showed high insertion polymorphisms among closely related cultivars. PMID:25072847

  10. Dietary Differentiation and the Evolution of Population Genetic Structure in a Highly Mobile Carnivore

    PubMed Central

    Pilot, Ma?gorzata; J?drzejewski, W?odzimierz; Sidorovich, Vadim E.; Meier-Augenstein, Wolfram; Hoelzel, A. Rus

    2012-01-01

    Recent studies on highly mobile carnivores revealed cryptic population genetic structures correlated to transitions in habitat types and prey species composition. This led to the hypothesis that natal-habitat-biased dispersal may be responsible for generating population genetic structure. However, direct evidence for the concordant ecological and genetic differentiation between populations of highly mobile mammals is rare. To address this we analyzed stable isotope profiles (?13C and ?15N values) for Eastern European wolves (Canis lupus) as a quantifiable proxy measure of diet for individuals that had been genotyped in an earlier study (showing cryptic genetic structure), to provide a quantitative assessment of the relationship between individual foraging behavior and genotype. We found a significant correlation between genetic distances and dietary differentiation (explaining 46% of the variation) in both the marginal test and crucially, when geographic distance was accounted for as a co-variable. These results, interpreted in the context of other possible mechanisms such as allopatry and isolation by distance, reinforce earlier studies suggesting that diet and associated habitat choice are influencing the structuring of populations in highly mobile carnivores. PMID:22768075

  11. X-ray survival characteristics and genetic analysis for nine saccharomyces deletion mutants that show altered radiation sensitivity

    SciTech Connect

    Game, John C.; Williamson, Marsha S.; Baccari, Clelia

    2004-01-07

    The availability of a genome-wide set of Saccharomyces deletion mutants provides a chance to identify all the yeast genes involved in DNA repair. Using X-rays, we are screening these mutants to identify additional genes that show increased sensitivity to the lethal effects of ionizing radiation. For each mutant identified as sensitive, we are confirming that the sensitivity phenotype co-segregates with the deletion allele and are obtaining multipoint survival-versus-dose assays in at least two haploid and one homozygous diploid strains. We present data for deletion mutants involving the genes DOT1, MDM20, NAT3, SPT7, SPT20, GCN5, HFI1, DCC1 and VID21/EAF1, and discuss their potential roles in repair. Eight of these genes have a clear radiation-sensitive phenotype when deleted, but the ninth, GCN5, has at most a borderline phenotype. None of the deletions confer substantial sensitivity to ultra-violet radiation, although one or two may confer marginal sensitivity. The DOT1 gene is of interest because its only known function is to methylate one lysine residue in the core of the histone H3 protein. We find that histone H3 mutants (supplied by K. Struhl) in which this residue is replaced by other amino-acids are also X-ray sensitive, seeming to confirm that methylation of the lysine-79 residue is required for effective repair of radiation damage.

  12. Microsatellite Typing of Clinical and Environmental Cryptococcus neoformans var. grubii Isolates from Cuba Shows Multiple Genetic Lineages

    PubMed Central

    Illnait-Zaragozi, Maria-Teresa; Martínez-Machín, Gerardo F.; Fernández-Andreu, Carlos M.; Boekhout, Teun; Meis, Jacques F.; Klaassen, Corné H. W.

    2010-01-01

    Background Human cryptococcal infections have been associated with bird droppings as a likely source of infection. Studies toward the local and global epidemiology of Cryptococcus spp. have been hampered by the lack of rapid, discriminatory, and exchangeable molecular typing methods. Methodology/Principal Findings We selected nine microsatellite markers for high-resolution fingerprinting from the genome of C. neoformans var. grubii. This panel of markers was applied to a collection of clinical (n?=?122) and environmental (n?=?68; from pigeon guano) C. neoformans var. grubii isolates from Cuba. All markers proved to be polymorphic. The average number of alleles per marker was 9 (range 5–51). A total of 104 genotypes could be distinguished. The discriminatory power of this panel of markers was 0.993. Multiple clusters of related genotypes could be discriminated that differed in only one or two microsatellite markers. These clusters were assigned as microsatellite complexes. The majority of environmental isolates (>70%) fell into 1 microsatellite complex containing only few clinical isolates (49 environmental versus 2 clinical). Clinical isolates were segregated over multiple microsatellite complexes. Conclusions/Significance A large genotypic variation exists in C. neoformans var. grubii. The genotypic segregation between clinical and environmental isolates from pigeon guano suggests additional source(s) of human cryptococcal infections. The selected panel of microsatellite markers is an excellent tool to study the epidemiology of C. neoformans var. grubii. PMID:20161737

  13. Amerindians show no association of PC-1 gene Gln121 allele and obesity: a thrifty gene population genetics.

    PubMed

    Rey, Diego; Fernandez-Honrado, Mercedes; Areces, Cristina; Algora, Manuel; Abd-El-Fatah-Khalil, Sedeka; Enriquez-de-Salamanca, Mercedes; Coca, Carmen; Arribas, Ignacio; Arnaiz-Villena, Antonio

    2012-07-01

    PC-1 Gln121 gene is a risk factor for type 2 diabetes, obesity and insulin resistance in European/American Caucasoids and Orientals. We have aimed to correlate for the first time this gene in Amerindians with obesity and their corresponding individuals genotypes with obesity in order to establish preventive medicine programs for this population and also studying the evolution of gene frequencies in world populations. Central obesity was diagnosed by waist circumference perimeter and food intake independent HDL-cholesterol plasma levels were measured. HLA genes were determined in order to more objectively ascertain participants Amerindians origin. 321 Amerindian blood donors who were healthy according to the blood doning parameters were studied. No association was found between PC-1 Gln121 variant and obesity. Significant HDL-cholesterol lower values were found in the PC-1 Lys121 bearing gene individuals versus PC-1 Gln121 bearing gene ones (45.1 ± 12.7 vs. 48.7 ± 15.2 mg/dl, p < 0.05). Population analyses showed a world geographical gradient in the PC-1 Gln121 allele frequency: around 9% in Orientals, 15% in European Caucasoids and 76% in Negroids. The conclusions are: (1) No association of PC-1 Gln121 gene is found with obesity in Amerindians when association is well established in Europeans. (2) PC-1 Gln121 gene is associated to higher levels of HDL-cholesterol than the alternative PC-1 Lys121 allele. This may be specific for Amerindians. (3) Amerindians have an intermediate frequency of this possible PC-1 Gln121 thrifty gene when compared with Negroid African Americans (78.5%) or Han Chinese (7.5%, p < 0.0001). Historical details of African and other groups may support the hypothesis that PC-1 Gln121 is indeed a thrifty gene. PMID:22327785

  14. Complete genome sequence analysis of goatpox virus isolated from China shows high variation.

    PubMed

    Zeng, Xiancheng; Chi, Xuelin; Li, Wei; Hao, Wenbo; Li, Ming; Huang, Xiaohong; Huang, Yifan; Rock, Daniel L; Luo, Shuhong; Wang, Shihua

    2014-09-17

    Goatpox virus (GTPV), a member of the Capripoxvirus genus of the Poxviridae family, is the causative agent of variolo caprina (goatpox). GTPV can cause significant economic losses of domestic ruminants in endemic regions and can threaten breeding stocks. In this study, we report on the compilation of the complete genomic sequence of an isolated GTPV field strain FZ (GTPV_FZ). The 150,194bp GTPV genome consists of a central coding region bounded by two identical 2301bp inverted terminal repeats and contains 151 putative genes. Comparative genomic analysis reveals the apparent genetic relationships among Capripoxviruses are close, but sufficient genomic variants in the field isolate strain FZ have been identified to distinguish it from other GTPV strains and other Capripoxvirus species. Phylogenetic analysis based on the p32 and complete GTPV genome can be used to differentiate SPPVs, GTPVs and LSDVs. These data may contribute to the epidemiological study of the Chinese capripoxvirus and help to develop more specific detection methods to distinguish GTPVs, SPPVs and LSDVs. PMID:25113672

  15. High risks of losing genetic diversity in an endemic Mauritian gecko: implications for conservation.

    PubMed

    Buckland, Steeves; Cole, Nik C; Groombridge, Jim J; Küpper, Clemens; Burke, Terry; Dawson, Deborah A; Gallagher, Laura E; Harris, Stephen

    2014-01-01

    Genetic structure can be a consequence of recent population fragmentation and isolation, or a remnant of historical localised adaptation. This poses a challenge for conservationists since misinterpreting patterns of genetic structure may lead to inappropriate management. Of 17 species of reptile originally found in Mauritius, only five survive on the main island. One of these, Phelsuma guimbeaui (lowland forest day gecko), is now restricted to 30 small isolated subpopulations following severe forest fragmentation and isolation due to human colonisation. We used 20 microsatellites in ten subpopulations and two mitochondrial DNA (mtDNA) markers in 13 subpopulations to: (i) assess genetic diversity, population structure and genetic differentiation of subpopulations; (ii) estimate effective population sizes and migration rates of subpopulations; and (iii) examine the phylogenetic relationships of haplotypes found in different subpopulations. Microsatellite data revealed significant population structure with high levels of genetic diversity and isolation by distance, substantial genetic differentiation and no migration between most subpopulations. MtDNA, however, showed no evidence of population structure, indicating that there was once a genetically panmictic population. Effective population sizes of ten subpopulations, based on microsatellite markers, were small, ranging from 44 to 167. Simulations suggested that the chance of survival and allelic diversity of some subpopulations will decrease dramatically over the next 50 years if no migration occurs. Our DNA-based evidence reveals an urgent need for a management plan for the conservation of P. guimbeaui. We identified 18 threatened and 12 viable subpopulations and discuss a range of management options that include translocation of threatened subpopulations to retain maximum allelic diversity, and habitat restoration and assisted migration to decrease genetic erosion and inbreeding for the viable subpopulations. PMID:24963708

  16. Source-sink estimates of genetic introgression show influence of hatchery strays on wild chum salmon populations in Prince William Sound, Alaska.

    PubMed

    Jasper, James R; Habicht, Christopher; Moffitt, Steve; Brenner, Rich; Marsh, Jennifer; Lewis, Bert; Creelman Fox, Elisabeth; Grauvogel, Zac; Rogers Olive, Serena D; Grant, W Stewart

    2013-01-01

    The extent to which stray, hatchery-reared salmon affect wild populations is much debated. Although experiments show that artificial breeding and culture influence the genetics of hatchery salmon, little is known about the interaction between hatchery and wild salmon in a natural setting. Here, we estimated historical and contemporary genetic population structures of chum salmon (Oncorhynchus keta) in Prince William Sound (PWS), Alaska, with 135 single nucleotide polymorphism (SNP) markers. Historical population structure was inferred from the analysis of DNA from fish scales, which had been archived since the late 1960's for several populations in PWS. Parallel analyses with microsatellites and a test based on Hardy-Weinberg proportions showed that about 50% of the fish-scale DNA was cross-contaminated with DNA from other fish. These samples were removed from the analysis. We used a novel application of the classical source-sink model to compare SNP allele frequencies in these archived fish-scales (1964-1982) with frequencies in contemporary samples (2008-2010) and found a temporal shift toward hatchery allele frequencies in some wild populations. Other populations showed markedly less introgression, despite moderate amounts of hatchery straying. The extent of introgression may reflect similarities in spawning time and life-history traits between hatchery and wild fish, or the degree that hybrids return to a natal spawning area. The source-sink model is a powerful means of detecting low levels of introgression over several generations. PMID:24349150

  17. Source-Sink Estimates of Genetic Introgression Show Influence of Hatchery Strays on Wild Chum Salmon Populations in Prince William Sound, Alaska

    PubMed Central

    Jasper, James R.; Habicht, Christopher; Moffitt, Steve; Brenner, Rich; Marsh, Jennifer; Lewis, Bert; Creelman Fox, Elisabeth; Grauvogel, Zac; Rogers Olive, Serena D.; Grant, W. Stewart

    2013-01-01

    The extent to which stray, hatchery-reared salmon affect wild populations is much debated. Although experiments show that artificial breeding and culture influence the genetics of hatchery salmon, little is known about the interaction between hatchery and wild salmon in a natural setting. Here, we estimated historical and contemporary genetic population structures of chum salmon (Oncorhynchus keta) in Prince William Sound (PWS), Alaska, with 135 single nucleotide polymorphism (SNP) markers. Historical population structure was inferred from the analysis of DNA from fish scales, which had been archived since the late 1960’s for several populations in PWS. Parallel analyses with microsatellites and a test based on Hardy-Weinberg proportions showed that about 50% of the fish-scale DNA was cross-contaminated with DNA from other fish. These samples were removed from the analysis. We used a novel application of the classical source-sink model to compare SNP allele frequencies in these archived fish-scales (1964–1982) with frequencies in contemporary samples (2008–2010) and found a temporal shift toward hatchery allele frequencies in some wild populations. Other populations showed markedly less introgression, despite moderate amounts of hatchery straying. The extent of introgression may reflect similarities in spawning time and life-history traits between hatchery and wild fish, or the degree that hybrids return to a natal spawning area. The source-sink model is a powerful means of detecting low levels of introgression over several generations. PMID:24349150

  18. Genetics

    MedlinePLUS

    Homozygous; Inheritance; Heterozygous; Inheritance patterns; Heredity and disease; Heritable; Genetic markers ... The chromosomes are made up of strands of genetic information called DNA. Each chromosome contains sections of ...

  19. Using Show Homes (and Sponsorships) to Persuade Commissioning Relevancy and Factory Crafted High Performance Modular Homes 

    E-print Network

    Thomas-Rees, S.; Chasar, D.; Beal, D.; Chandra, S.

    2007-01-01

    demonstrating that incentive programs encourage high performance building practices and are vital to integrating commissioning procedures into the marketplace. Blower door and duct leakage tests were conducted to quantify as built conditions validating modular...

  20. Study Shows Aspirin Reduces Colorectal Cancer in Those at High Risk

    Cancer.gov

    Findings from the first large clinical trial of its kind indicate that taking high doses of aspirin daily for at least 2 years substantially reduces the risk of colorectal cancer among people at increased risk of the disease.

  1. I. INTRODUCTION A lot of studies show that hydrogen has a high

    E-print Network

    Paris-Sud XI, Université de

    from water and hydrocarbons, alcohol or biomass with high H2 yields with limited costs [1-5]. This paper is devoted to a comparative study of syngas (H2+CO) production from various alcohol (methanol a Statarc reactor to produce syngas Khadija Arabi, Olivier Aubry, Ahmed Khacef, Jean-Marie Cormier GREMI

  2. Targeted exome sequencing for mitochondrial disorders reveals high genetic heterogeneity

    PubMed Central

    2013-01-01

    Background Mitochondrial disorders are difficult to diagnose due to extreme genetic and phenotypic heterogeneities. Methods We explored the utility of targeted next-generation sequencing for the diagnosis of mitochondrial disorders in 148 patients submitted for clinical testing. A panel of 447 nuclear genes encoding mitochondrial respiratory chain complexes, and other genes inducing secondary mitochondrial dysfunction or that cause diseases which mimic mitochondrial disorders were tested. Results We identified variants considered to be possibly disease-causing based on family segregation data and/or variants already known to cause disease in twelve genes in thirteen patients. Rare or novel variants of unknown significance were identified in 45 additional genes for various metabolic, genetic or neurogenetic disorders. Conclusions Primary mitochondrial defects were confirmed only in four patients indicating that majority of patients with suspected mitochondrial disorders are presumably not the result of direct impairment of energy production. Our results support that clinical and routine laboratory ascertainment for mitochondrial disorders are challenging due to significant overlapping non-specific clinical symptoms and lack of specific biomarkers. While next-generation sequencing shows promise for diagnosing suspected mitochondrial disorders, the challenges remain as the underlying genetic heterogeneity may be greater than suspected and it is further confounded by the similarity of symptoms with other conditions as we report here. PMID:24215330

  3. Network Intrusion Detection Method Based on High Speed and Precise Genetic Algorithm Neural Network

    Microsoft Academic Search

    Jingwen Tian; Meijuan Gao

    2009-01-01

    Aimed at the network intrusion behaviors are characterized with uncertainty, complexity, diversity and dynamic tendency and the advantages of neural network, an intrusion detection method based on high speed and precise genetic algorithm neural network is presented in this paper. The high speed and precise genetic algorithm neural network is combined the adaptive and floating-point code genetic algorithm with BP

  4. African elephants show high levels of interest in the skulls and ivory of their own species

    PubMed Central

    McComb, Karen; Baker, Lucy; Moss, Cynthia

    2005-01-01

    An important area of biology involves investigating the origins in animals of traits that are thought of as uniquely human. One way that humans appear unique is in the importance they attach to the dead bodies of other humans, particularly those of their close kin, and the rituals that they have developed for burying them. In contrast, most animals appear to show only limited interest in the carcasses or associated remains of dead individuals of their own species. African elephants (Loxodonta africana) are unusual in that they not only give dramatic reactions to the dead bodies of other elephants, but are also reported to systematically investigate elephant bones and tusks that they encounter, and it has sometimes been suggested that they visit the bones of relatives. Here, we use systematic presentations of object arrays to demonstrate that African elephants show higher levels of interest in elephant skulls and ivory than in natural objects or the skulls of other large terrestrial mammals. However, they do not appear to specifically select the skulls of their own relatives for investigation so that visits to dead relatives probably result from a more general attraction to elephant remains. PMID:17148317

  5. Biochemical Characterization of a First Fungal Esterase from Rhizomucor miehei Showing High Efficiency of Ester Synthesis

    PubMed Central

    Liu, Yu; Xu, Haibo; Yan, Qiaojuan; Yang, Shaoqing; Duan, Xiaojie; Jiang, Zhengqiang

    2013-01-01

    Background Esterases with excellent merits suitable for commercial use in ester production field are still insufficient. The aim of this research is to advance our understanding by seeking for more unusual esterases and revealing their characterizations for ester synthesis. Methodology/Principal Findings A novel esterase-encoding gene from Rhizomucor miehei (RmEstA) was cloned and expressed in Escherichia coli. Sequence analysis revealed a 975-bp ORF encoding a 324-amino-acid polypeptide belonging to the hormone-sensitive lipase (HSL) family IV and showing highest similarity (44%) to the Paenibacillus mucilaginosus esterase/lipase. Recombinant RmEstA was purified to homogeneity: it was 34 kDa by SDS-PAGE and showed optimal pH and temperature of 6.5 and 45°C, respectively. The enzyme was stable to 50°C, under a broad pH range (5.0–10.6). RmEstA exhibited broad substrate specificity toward p-nitrophenol esters and short-acyl-chain triglycerols, with highest activities (1,480 U mg?1 and 228 U mg?1) for p-nitrophenyl hexanoate and tributyrin, respectively. RmEstA efficiently synthesized butyl butyrate (92% conversion yield) when immobilized on AOT-based organogel. Conclusion RmEstA has great potential for industrial applications. RmEstA is the first reported esterase from Rhizomucor miehei. PMID:24204998

  6. Genetic diversity of planktonic eukaryotes in high mountain lakes (Central Pyrenees, Spain).

    PubMed

    Triadó-Margarit, Xavier; Casamayor, Emilio O

    2012-09-01

    The genetic diversity of planktonic eukaryotic microorganisms (size range 3-40 µm) inhabiting 11 alpine lakes of the Central Pyrenees (Spain) was analysed by cloning and sequencing of the 18S rRNA gene. The selected lakes covered a wide range of environmental conditions representative of the regional landscape heterogeneity. Overall, we obtained 953 sequences (averaged length 750 bp) that were grouped in 343 representative OTUs (98% identity). The genetic richness was high, and the 18S rRNA gene sequences spread within nine high-rank taxonomic groups and grouped in 26 eukaryal classes. Most of the sequences affiliated with Stramenopiles (> 55% of total sequences, mostly Chrysophyceae), Cryptophyta and Alveolata (15% each). Three groups had relative abundance < 5%, i.e. Opisthokonta (mostly Fungi), Viridiplantae (mostly Chlorophyceae) and Rhizaria (cercomonads). Finally, minor groups were related to Katablepharidophyta, Euglenozoa and Telonemida. The lakes showed a different community structure being pH, and phosphorous and Chl a concentrations the main environmental drivers. The novelty level was high, and a quarter of the retrieved OTUs were notably divergent (< 97% identity) from any previously known sequence, mainly for Rhizaria and Opisthokonta. More than 50% of the sequences affiliated with clusters exclusively formed by uncultured protists. Cryptophyta and Viridiplantae showed the largest number of sequences closely related to cultured counterparts. This work is the first description of the genetic diversity of eukaryotic assemblages in ultraoligotrophic high mountain lakes, and the study unveils alpine environments as an important reservoir of microbial eukaryotic biodiversity. PMID:22672082

  7. Map showing high-purity silica sand of Middle Ordovician age in the Midwestern states

    USGS Publications Warehouse

    Ketner, Keith B.

    1979-01-01

    Certain quartz sands of Middle Ordovician age in the Midwestern States are well known for their purity and are exploited for a wide variety of industrial uses. The principal Middle Ordovician formations containing high-purity sands are the St. Peter Sandstone which crops out extensively from Minnesota to Arkansas; the Everton Formation principally of Arkansas; and the Oil Creek, McLish, and Tulip Creek Formations (all of the Simpson Group) of Oklahoma. The St. Peter and sandy beds in the other formations are commonly called "sandstones," but a more appropriate term is "sands" for in most fresh exposures they are completely uncemented or very weakly cemented. On exposure to air, uncemented sands usually become "case hardened" where evaporating ground water precipitates mineral matter at the surface; but this is a surficial effect. This report summarizes the available information on the extent of exposures, range of grain size, and chemical composition of the Middle Ordovician sands.

  8. Cloacal Lactobacillus isolates from broilers show high prevalence of resistance towards macrolide and lincosamide antibiotics.

    PubMed

    Cauwerts, K; Pasmans, F; Devriese, L A; Martel, A; Haesebrouck, F; Decostere, A

    2006-04-01

    Eighty-seven Lactobacillus strains isolated from cloacal swabs of broiler chickens derived from 20 different farms in Belgium were identified to species level and tested for susceptibility to macrolide and lincosamide antibiotics. Five different Lactobacillus species were identified as being predominantly present in the cloacae of broilers: Lactobacillus crispatus, Lactobacillus salivarius subsp. salivarius, Lactobacillus amylovorus, Lactobacillus gallinarum and Lactobacillu sreuteri. Acquired resistance prevalence to macrolides and lincosamides was very high in the investigated lactobacilli: 89% of the strains were resistant to either or both lincosamide and macrolide class antibiotics. The vast majority of these resistant strains (96%) displayed constitutive resistance. More than one-half of the macrolide and/or lincosamide resistant strains carried an erm(B), erm(C), mef(A), lnu(A) gene or a combination of these genes. PMID:16595310

  9. High genetic variation in marginal fragmented populations at extreme climatic conditions of the Patagonian Cypress Austrocedrus chilensis.

    PubMed

    Arana, María Verónica; Gallo, Leonardo A; Vendramin, Giovanni G; Pastorino, Mario J; Sebastiani, Federico; Marchelli, Paula

    2010-03-01

    Knowledge about current patterns of genetic structure of populations together with the evolutionary history of a species helps to understand and predict the adaptation of populations to future climate change. We assayed variation at nuclear microsatellite markers among peripheral vs. continuous populations of the temperate South American species Austrocedrus chilensis, to investigate the role of historical vs. demographical forces in shaping population genetic structure. This species occurs in continuous populations in the west and central distribution range, but becomes highly fragmented at the eastern limit, which comprised ice-free areas during Quaternary glaciations and has extreme climatic conditions at present times. Bayesian analysis methods identified two contrasting patterns of genetic structure; (I) populations from humid, mesic and peri-glacial regions formed a single deme with relatively low genetic differentiation and high admixture levels whereas (II) a highly heterogeneous genetic structure with low level of admixture was found in the steppe, towards the east and northeast limit of the distribution range. In the steppe, population fragmentation, restricted gene flow and isolation-by-distance were also inferred. In addition, several small steppe populations showed high genetic diversity and divergent gene pools, suggesting that they constitute ancient refuges from pre-Holocene glaciations with just a subgroup of them contributing significantly to post-glacial spread. These results are discussed in relation to patterns of genetic variation found for other temperate species and the contribution of the particular southern Andes topography and climate to post-glacial spread. PMID:19919852

  10. Hydroxyeicosapentaenoic acids from the Pacific krill show high ligand activities for PPARs.

    PubMed

    Yamada, Hidetoshi; Oshiro, Eriko; Kikuchi, Sayaka; Hakozaki, Mayuka; Takahashi, Hideyuki; Kimura, Ken-Ichi

    2014-05-01

    PPARs regulate the expression of genes for energy metabolism in a ligand-dependent manner. PPARs can influence fatty acid oxidation, the level of circulating triglycerides, glucose uptake and insulin sensitivity. Here, we demonstrate that 5-hydroxyeicosapentaenoic acid (HEPE), 8-HEPE, 9-HEPE, 12-HEPE and 18-HEPE (hydroxylation products of EPA) obtained from methanol extracts of Pacific krill (Euphausia pacifica) can act as PPAR ligands. Two of these products, 8-HEPE and 9-HEPE, enhanced the transcription levels of GAL4-PPARs to a significantly greater extent than 5-HEPE, 12-HEPE, 18-HEPE, EPA, and EPA ethyl-ester. 8-HEPE also activated significantly higher transcription of GAL4-PPAR?, GAL4-PPAR?, and GAL4-PPAR? than EPA at concentrations greater than 4, 64, and 64 ?M, respectively. We also demonstrated that 8-HEPE increased the expression levels of genes regulated by PPARs in FaO, 3T3-F442A, and C2C12 cells. Furthermore, 8-HEPE enhanced adipogenesis and glucose uptake. By contrast, at the same concentrations, EPA showed weak or little effect, indicating that 8-HEPE was the more potent inducer of physiological effects. PMID:24668940

  11. Hydroxyeicosapentaenoic acids from the Pacific krill show high ligand activities for PPARs[S

    PubMed Central

    Yamada, Hidetoshi; Oshiro, Eriko; Kikuchi, Sayaka; Hakozaki, Mayuka; Takahashi, Hideyuki; Kimura, Ken-ichi

    2014-01-01

    PPARs regulate the expression of genes for energy metabolism in a ligand-dependent manner. PPARs can influence fatty acid oxidation, the level of circulating triglycerides, glucose uptake and insulin sensitivity. Here, we demonstrate that 5-hydroxyeicosapentaenoic acid (HEPE), 8-HEPE, 9-HEPE, 12-HEPE and 18-HEPE (hydroxylation products of EPA) obtained from methanol extracts of Pacific krill (Euphausia pacifica) can act as PPAR ligands. Two of these products, 8-HEPE and 9-HEPE, enhanced the transcription levels of GAL4-PPARs to a significantly greater extent than 5-HEPE, 12-HEPE, 18-HEPE, EPA, and EPA ethyl-ester. 8-HEPE also activated significantly higher transcription of GAL4-PPAR?, GAL4-PPAR?, and GAL4-PPAR? than EPA at concentrations greater than 4, 64, and 64 ?M, respectively. We also demonstrated that 8-HEPE increased the expression levels of genes regulated by PPARs in FaO, 3T3-F442A, and C2C12 cells. Furthermore, 8-HEPE enhanced adipogenesis and glucose uptake. By contrast, at the same concentrations, EPA showed weak or little effect, indicating that 8-HEPE was the more potent inducer of physiological effects. PMID:24668940

  12. A cDNA clone highly expressed in ripe banana fruit shows homology to pectate lyases.

    PubMed Central

    Dominguez-Puigjaner, E; LLop, I; Vendrell, M; Prat, S

    1997-01-01

    A cDNA clone (Ban17), encoding a protein homologous to pectate lyase, has been isolated from a cDNA library from climacteric banana fruit by means of differential screening. Northern analysis showed that Ban17 mRNA is first detected in early climacteric fruit, reaches a steady-state maximum at the climacteric peak, and declines thereafter in overripe fruit. Accumulation of the Ban17 transcript can be induced in green banana fruit by exogenous application of ethylene. The demonstrates that expression of this gene is under hormonal control, its induction being regulated by the rapid increase in ethylene production at the onset of ripening. The deduced amino acid sequence derived from the Ban17 cDNA shares significant identity with pectate lyases from pollen and plant pathogenic bacteria of the genus Erwinia. Similarity to bacterial pectate lyases that were proven to break down the pectic substances of the plant cell wall suggest that Ban17 might play a role in the loss of mesocarp firmness during fruit ripening. PMID:9232883

  13. Genetic Connectivity of the Moth Pollinated Tree Glionnetia sericea in a Highly Fragmented Habitat

    PubMed Central

    Finger, Aline; Valentin, Terence; Ghazoul, Jaboury

    2014-01-01

    Long-distance gene flow is thought to be one prerequisite for the persistence of plant species in fragmented environments. Human influences have led to severe fragmentation of native habitats in the Seychelles islands, with many species surviving only in small and isolated populations. The endangered Seychelles endemic tree Glionnetia sericea is restricted to altitudes between 450 m and 900 m where the native forest vegetation has been largely lost and replaced with exotic invasives over the last 200 years. This study explores the genetic and ecological consequences of population fragmentation in this species by analysing patterns of genetic diversity in a sample of adults, juveniles and seeds, and by using controlled pollination experiments. Our results show no decrease in genetic diversity and no increase in genetic structuring from adult to juvenile cohorts. Despite significant inbreeding in some populations, there is no evidence of higher inbreeding in juvenile cohorts relative to adults. A Bayesian structure analysis and a tentative paternity analysis indicate extensive historical and contemporary gene flow among remnant populations. Pollination experiments and a paternity analysis show that Glionnetia sericea is self-compatible. Nevertheless, outcrossing is present with 7% of mating events resulting from pollen transfer between populations. Artificial pollination provided no evidence for pollen limitation in isolated populations. The highly mobile and specialized hawkmoth pollinators (Agrius convolvuli and Cenophodes tamsi; Sphingidae) appear to promote extensive gene flow, thus mitigating the potential negative ecological and genetic effects of habitat fragmentation in this species. We conclude that contemporary gene flow is sufficient to maintain genetic connectivity in this rare and restricted Seychelles endemic, in contrast to other island endemic tree species with limited contemporary gene flow. PMID:25347541

  14. High-throughput neuroimaging-genetics computational infrastructure.

    PubMed

    Dinov, Ivo D; Petrosyan, Petros; Liu, Zhizhong; Eggert, Paul; Hobel, Sam; Vespa, Paul; Woo Moon, Seok; Van Horn, John D; Franco, Joseph; Toga, Arthur W

    2014-01-01

    Many contemporary neuroscientific investigations face significant challenges in terms of data management, computational processing, data mining, and results interpretation. These four pillars define the core infrastructure necessary to plan, organize, orchestrate, validate, and disseminate novel scientific methods, computational resources, and translational healthcare findings. Data management includes protocols for data acquisition, archival, query, transfer, retrieval, and aggregation. Computational processing involves the necessary software, hardware, and networking infrastructure required to handle large amounts of heterogeneous neuroimaging, genetics, clinical, and phenotypic data and meta-data. Data mining refers to the process of automatically extracting data features, characteristics and associations, which are not readily visible by human exploration of the raw dataset. Result interpretation includes scientific visualization, community validation of findings and reproducible findings. In this manuscript we describe the novel high-throughput neuroimaging-genetics computational infrastructure available at the Institute for Neuroimaging and Informatics (INI) and the Laboratory of Neuro Imaging (LONI) at University of Southern California (USC). INI and LONI include ultra-high-field and standard-field MRI brain scanners along with an imaging-genetics database for storing the complete provenance of the raw and derived data and meta-data. In addition, the institute provides a large number of software tools for image and shape analysis, mathematical modeling, genomic sequence processing, and scientific visualization. A unique feature of this architecture is the Pipeline environment, which integrates the data management, processing, transfer, and visualization. Through its client-server architecture, the Pipeline environment provides a graphical user interface for designing, executing, monitoring validating, and disseminating of complex protocols that utilize diverse suites of software tools and web-services. These pipeline workflows are represented as portable XML objects which transfer the execution instructions and user specifications from the client user machine to remote pipeline servers for distributed computing. Using Alzheimer's and Parkinson's data, we provide several examples of translational applications using this infrastructure. PMID:24795619

  15. High genetic load in the Pacific oyster Crassostrea gigas.

    PubMed Central

    Launey, S; Hedgecock, D

    2001-01-01

    The causes of inbreeding depression and the converse phenomenon of heterosis or hybrid vigor remain poorly understood despite their scientific and agricultural importance. In bivalve molluscs, related phenomena, marker-associated heterosis and distortion of marker segregation ratios, have been widely reported over the past 25 years. A large load of deleterious recessive mutations could explain both phenomena, according to the dominance hypothesis of heterosis. Using inbred lines derived from a natural population of Pacific oysters and classical crossbreeding experiments, we compare the segregation ratios of microsatellite DNA markers at 6 hr and 2-3 months postfertilization in F(2) or F(3) hybrid families. We find evidence for strong and widespread selection against identical-by-descent marker homozygotes. The marker segregation data, when fit to models of selection against linked deleterious recessive mutations and extrapolated to the whole genome, suggest that the wild founders of inbred lines carried a minimum of 8-14 highly deleterious recessive mutations. This evidence for a high genetic load strongly supports the dominance theory of heterosis and inbreeding depression and establishes the oyster as an animal model for understanding the genetic and physiological causes of these economically important phenomena. PMID:11560902

  16. High-Performance Single Cell Genetic Analysis Using Microfluidic Emulsion Generator Arrays

    PubMed Central

    Zeng, Yong; Novak, Richard; Shuga, Joe; Smith, Martyn T.; Mathies, Richard A.

    2010-01-01

    High-throughput genetic and phenotypic analysis at the single cell level is critical to advance our understanding of the molecular mechanisms underlying cellular function and dysfunction. Here we describe a high-performance single cell genetic analysis (SCGA) technique that combines high-throughput microfluidic emulsion generation with single cell multiplex PCR. Microfabricated emulsion generator array (MEGA) devices containing 4, 32 and 96 channels are developed to confer a flexible capability of generating up to 3.4 × 106 nanoliter-volume droplets per hour. Hybrid glass-polydimethylsiloxane diaphragm micropumps integrated into the MEGA chips afford uniform droplet formation, controlled generation frequency, and effective transportation and encapsulation of primer functionalized microbeads and cells. A multiplex single cell PCR method is developed to detect and quantify both wild type and mutant/pathogenic cells. In this method, microbeads functionalized with multiple forward primers targeting specific genes from different cell types are used for solid-phase PCR in droplets. Following PCR, the droplets are lysed, the beads are pooled and rapidly analyzed by multi-color flow cytometry. Using E. coli bacterial cells as a model, we show that this technique enables digital detection of pathogenic E. coli O157 cells in a high background of normal K12 cells, with a detection limit on the order of 1:105. This result demonstrates that multiplex SCGA is a promising tool for high-throughput quantitative digital analysis of genetic variation in complex populations. PMID:20192178

  17. High genetic diversity in the remnant island population of hihi and the genetic consequences of re-introduction.

    PubMed

    Brekke, Patricia; Bennett, Peter M; Santure, Anna W; Ewen, John G

    2011-01-01

    The maintenance of genetic diversity is thought to be fundamental for the conservation of threatened species. It is therefore important to understand how genetic diversity is affected by the re-introduction of threatened species. We use establishment history and genetic data from the remnant and re-introduced populations of a New Zealand endemic bird, the hihi Notiomystis cincta, to understand genetic diversity loss and quantify the genetic effects of re-introduction. Our data do not support any recent bottleneck events in the remnant population. Furthermore, all genetic diversity measures indicate the remnant hihi population has retained high levels of genetic diversity relative to other New Zealand avifauna with similar histories of decline. Genetic diversity (N(A) , alleles per locus, allelic richness, F(IS) and H(S) ) did not significantly decrease in new hihi populations founded through re-introduction when compared to their source populations, except in the Kapiti Island population (allelic richness and H(S) ) which had very slow post-re-introduction population growth. The N(e) /N(c) ratio in the remnant population was high, but decreased in first-level re-introductions, which together with significant genetic differentiation between populations (F(ST) & Fisher's exact tests) suggest that extant populations are diverging as a result of founder effects and drift. Importantly, simulations of future allele loss predict that the number of alleles lost will be higher in populations with a slow population growth, fewer founding individuals and with nonrandom mating. Interestingly, this species has very high levels of extra-pair paternity which may reduce reproductive variance by allowing social and floater males to reproduce a life history trait that together with a large remnant population size may help maintain higher levels of genetic diversity than expected. PMID:21073589

  18. High genetic homogeneity of an intertidal marine invertebrate along 8000 km of the Atlantic coast

    E-print Network

    Solé-Cava, Antonio M.

    High genetic homogeneity of an intertidal marine invertebrate along 8000 km of the Atlantic coast diagnostic characters in benthic invertebrate species. Almost invariably, genetic studies have demonstrated.28) so that P. nigra has genetic variation levels more related with other invertebrates than to their

  19. New applications of the genetic algorithm for the interpretation of high-resolution spectra1

    E-print Network

    Nijmegen, University of

    804 New applications of the genetic algorithm for the interpretation of high-resolution spectra1 W. An alternative approach is unassigned fits of the spectra using genetic algorithms (GAs) with special cost, genetic algorithm, biomolecules, structure, van der Waals clusters. Résumé : La spectroscopie électronique

  20. Local Search Genetic Algorithm for Optimization of Highly Reliable Communications Networks

    E-print Network

    Smith, Alice E.

    Local Search Genetic Algorithm for Optimization of Highly Reliable Communications Networks Berna Turkey berna@rorqual.cc.metu.edu.tr Abstract This paper presents a genetic algorithm (GA. Genetic algorithms (GA) have recently found their way in combinatorial optimization approaches to reliable

  1. Discovery in genetic skin disease: the impact of high throughput genetic technologies.

    PubMed

    Maruthappu, Thiviyani; Scott, Claire A; Kelsell, David P

    2014-01-01

    The last decade has seen considerable advances in our understanding of the genetic basis of skin disease, as a consequence of high throughput sequencing technologies including next generation sequencing and whole exome sequencing. We have now determined the genes underlying several monogenic diseases, such as harlequin ichthyosis, Olmsted syndrome, and exfoliative ichthyosis, which have provided unique insights into the structure and function of the skin. In addition, through genome wide association studies we now have an understanding of how low penetrance variants contribute to inflammatory skin diseases such as psoriasis vulgaris and atopic dermatitis, and how they contribute to underlying pathophysiological disease processes. In this review we discuss strategies used to unravel the genes underlying both monogenic and complex trait skin diseases in the last 10 years and the implications on mechanistic studies, diagnostics, and therapeutics. PMID:25093584

  2. Discovery in Genetic Skin Disease: The Impact of High Throughput Genetic Technologies

    PubMed Central

    Maruthappu, Thiviyani; Scott, Claire A.; Kelsell, David P.

    2014-01-01

    The last decade has seen considerable advances in our understanding of the genetic basis of skin disease, as a consequence of high throughput sequencing technologies including next generation sequencing and whole exome sequencing. We have now determined the genes underlying several monogenic diseases, such as harlequin ichthyosis, Olmsted syndrome, and exfoliative ichthyosis, which have provided unique insights into the structure and function of the skin. In addition, through genome wide association studies we now have an understanding of how low penetrance variants contribute to inflammatory skin diseases such as psoriasis vulgaris and atopic dermatitis, and how they contribute to underlying pathophysiological disease processes. In this review we discuss strategies used to unravel the genes underlying both monogenic and complex trait skin diseases in the last 10 years and the implications on mechanistic studies, diagnostics, and therapeutics. PMID:25093584

  3. High-quality DNA from fingernails for genetic analysis.

    PubMed

    Preuner, Sandra; Danzer, Martin; Pröll, Johannes; Pötschger, Ulrike; Lawitschka, Anita; Gabriel, Christian; Lion, Thomas

    2014-07-01

    The availability of high-quality germline DNA is an important prerequisite for a variety of genetic analyses. We have shown previously that fingernail clippings provide an optimal source of autologous, constitutional DNA for PCR-based applications. However, most existing protocols for nucleic acid purification from nails do not provide sufficiently high yields of pure and intact DNA for more demanding downstream analyses such as next generation sequencing (NGS). We have extensively tested and systematically modified a number of different protocols for DNA purification from nail material to optimize the yield and quality. The integrity of DNA was determined by PCR amplification of short (<300 bp), mid-range (>400 bp), and long-range (>2 kb) sequences using different target genes. Among the methods tested, the Prepfiler Forensic DNA Extraction kit was identified as the most appropriate approach to isolation of high-quality DNA from nail clippings. A standardized input of 20 mg nail material (1 to 10 pieces of fingernail clippings) yielded a mean of 1 ?g DNA (range, 0.5 to 2.3 ?g). Subsequent PCR-analysis revealed efficient amplifiability of short and mid-range targets in 93% and 90%, and long-range fragments in 60% of the samples tested. The adequacy for next generation sequencing applications was demonstrated by successful high-resolution HLA-typing in ten transplant recipients. Hence, the protocol presented facilitates the exploitation of fingernail material even for demanding genomic analyses both in research and diagnostics. PMID:24795088

  4. Population Genetic Structure of a Centipede Species with High Levels of Developmental Instability

    PubMed Central

    Fusco, Giuseppe; Le?niewska, Ma?gorzata; Congiu, Leonardo; Bertorelle, Giorgio

    2015-01-01

    European populations of the geophilomorph centipede Haplophilus subterraneus show a high proportion of individuals with morphological anomalies, suggesting high levels of developmental instability. The broad geographic distribution of this phenomenon seems to exclude local environmental causes, but the source of instability is still to be identified. The goal of the present study was to collect quantitative data on the occurrence of phenodeviants in different populations, along with data on the patterns of genetic variation within and between populations, in order to investigate possible association between developmental instability and genetic features. In a sample of 11 populations of H. subterraneus, distributed in western and central Europe, we looked for phenodeviants, in particular with respect to trunk morphology, and studied genetic variation through the genotyping of microsatellite loci. Overall, no support was found to the idea that developmental instability in H. subterraneus is related to a specific patterns of genetic variation, including inbreeding estimates. We identified a major genetic partition that subdivides French populations from the others, and a low divergence among northwestern areas, which are possibly related to the post-glacial recolonization from southern refugia and/or to recent anthropogenic soil displacements. A weak correlation between individual number of leg bearing segments and the occurrence of trunk anomalies seems to support a trade-off between these two developmental traits. These results, complemented by preliminary data on developmental stability in two related species, suggest that the phenomenon has not a simple taxonomic distribution, while it exhibits an apparent localization in central and eastern Europe. PMID:26029915

  5. Genetic mapping of high caries experience on human chromosome 13

    PubMed Central

    2013-01-01

    Background Our previous genome-wide linkage scan mapped five loci for caries experience. The purpose of this study was to fine map one of these loci, the locus 13q31.1, in order to identify genetic contributors to caries. Methods Seventy-two pedigrees from the Philippines were studied. Caries experience was recorded and DNA was extracted from blood samples obtained from all subjects. Sixty-one single nucleotide polymorphisms (SNPs) in 13q31.1 were genotyped. Association between caries experience and alleles was tested. We also studied 1,481 DNA samples obtained from saliva of subjects from the USA, 918 children from Brazil, and 275 children from Turkey, in order to follow up the results found in the Filipino families. We used the AliBaba2.1 software to determine if the nucleotide changes of the associated SNPs changed the prediction of the presence of transcription-binding site sequences and we also analyzed the gene expression of the genes selected based on binding predictions. Mutation analysis was also performed in 33 Filipino individuals of a segment of 13q31.1 that is highly conserved in mammals. Results Statistically significant association with high caries experience was found for 11 markers in 13q31.1 in the Filipino families. Haplotype analysis also confirmed these results. In the populations used for follow-up purposes, associations were found between high caries experience and a subset of these markers. Regarding the prediction of the transcription-binding site, the base change of the SNP rs17074565 was found to change the predicted-binding of genes that could be involved in the pathogenesis of caries. When the sequence has the allele C of rs17074565, the potential transcription factors binding the sequence are GR and GATA1. When the subject carries the G allele of rs17074565, the potential transcription factor predicted to bind to the sequence is GATA3. The expression of GR in whole saliva was higher in individuals with low caries experience when compared to individuals with high caries experience (p =?0.046). No mutations were found in the highly conserved sequence. Conclusions Genetic factors contributing to caries experience may exist in 13q31.1. The rs17074565 is located in an intergenic region and is predicted to disrupt the binding sites of two different transcription factors that might be involved with caries experience. GR expression in saliva may be a biomarker for caries risk and should be further explored. PMID:24192446

  6. AFLP analysis reveals high genetic diversity but low population structure in Coccidioides posadasii isolates from Mexico and Argentina

    PubMed Central

    2013-01-01

    Background Coccidioides immitis and C. posadasii cause coccidioidomycosis, a disease that is endemic to North and South America, but for Central America, the incidence of coccidioidomycosis has not been clearly established. Several studies suggest genetic variability in these fungi; however, little definitive information has been discovered about the variability of Coccidioides fungi in Mexico (MX) and Argentina (AR). Thus, the goals for this work were to study 32 Coccidioides spp. isolates from MX and AR, identify the species of these Coccidioides spp. isolates, analyse their phenotypic variability, examine their genetic variability and investigate the Coccidioides reproductive system and its level of genetic differentiation. Methods Coccidioides spp. isolates from MX and AR were taxonomically identified by phylogenetic inference analysis using partial sequences of the Ag2/PRA gene and their phenotypic characteristics analysed. The genetic variability, reproductive system and level of differentiation were estimated using AFLP markers. The level of genetic variability was assessed measuring the percentage of polymorphic loci, number of effective allele, expected heterocygosity and Index of Association (IA). The degree of genetic differentiation was determined by AMOVA. Genetic similarities among isolates were estimated using Jaccard index. The UPGMA was used to contsruct the corresponding dendrogram. Finally, a network of haplotypes was built to evaluate the genealogical relationships among AFLP haplotypes. Results All isolates of Coccidioides spp. from MX and AR were identified as C. posadasii. No phenotypic variability was observed among the C. posadasii isolates from MX and AR. Analyses of genetic diversity and population structure were conducted using AFLP markers. Different estimators of genetic variability indicated that the C. posadasii isolates from MX and AR had high genetic variability. Furthermore, AMOVA, dendrogram and haplotype network showed a small genetic differentiation among the C. posadasii populations analysed from MX and AR. Additionally, the IA calculated for the isolates suggested that the species has a recombinant reproductive system. Conclusions No phenotypic variability was observed among the C. posadasii isolates from MX and AR. The high genetic variability observed in the isolates from MX and AR and the small genetic differentiation observed among the C. posadasii isolates analysed, suggest that this species could be distributed as a single genetic population in Latin America. PMID:24004977

  7. High Quality Typhoon Cloud Image Restoration by Combining Genetic Algorithm with Contourlet Transform

    SciTech Connect

    Zhang Changjiang; Wang Xiaodong [College of Mathematics, Physics and Information Engineering, Zhejiang Normal University, Jinhua (China)

    2008-11-06

    An efficient typhoon cloud image restoration algorithm is proposed. Having implemented contourlet transform to a typhoon cloud image, noise is reduced in the high sub-bands. Weight median value filter is used to reduce the noise in the contourlet domain. Inverse contourlet transform is done to obtain the de-noising image. In order to enhance the global contrast of the typhoon cloud image, in-complete Beta transform (IBT) is used to determine non-linear gray transform curve so as to enhance global contrast for the de-noising typhoon cloud image. Genetic algorithm is used to obtain the optimal gray transform curve. Information entropy is used as the fitness function of the genetic algorithm. Experimental results show that the new algorithm is able to well enhance the global for the typhoon cloud image while well reducing the noises in the typhoon cloud image.

  8. Analysis of STR markers reveals high genetic structure in Portuguese native cattle.

    PubMed

    Ginja, Catarina; Telo Da Gama, Luís; Penedo, Maria Cecilia T

    2010-01-01

    Genetic structure and diversity of 13 Portuguese native and 3 imported cattle breeds were assessed with 39 microsatellites. Allelic richness per locus was high, with an overall average of 8.3 +/- 2.5. The mean observed and expected heterozygosities were 0.673 +/- 0.043 and 0.691 +/- 0.034, respectively. The mean number of alleles per breed ranged between 5.36 +/- 1.27 and 7.87 +/- 2.66. Brava de Lide and Mirandesa breeds had the lowest genetic diversity, whereas Minhota, Arouquesa, and Mertolenga had the highest. Significant (P < 0.05) heterozygote deficit was detected in all breeds except Garvonesa, Marinhoa, Minhota, and Limousin. Hardy-Weinberg deviations are most probably due to inbreeding, particularly in Alentejana, Brava de Lide, Mertolenga, and Ramo Grande (F(is) > 0, P < 0.0001). Based on the principal component and the Neighbor-Net analyses, Mirandesa was the most genetically distinct breed. Even though admixture was detected across all breeds (6.7%, q < 0.800), the molecular structure was consistent with original breed designations, with the exception of Cachena that had a clear influence of Barrosă (K = 15). Mertolenga showed substructure with independent clustering of red speckled animals. The percentage animals correctly assigned was >or=90 in all breeds except Cachena, Garvonesa, and Preta (q >or= 0.800). The results obtained here confirmed that high levels of genetic diversity exist within Portuguese native cattle and that the breeds are highly structured. Conservation measures should be implemented for all native breeds to minimize inbreeding. PMID:19965912

  9. MHC ANTIGEN BINDING LOCUS DRB1 SHOWS STRONG SIGNAL OF SELECTION AND HIGH VARIABILITY IN FUNDULUS HETERCLITUS POPULATIONS

    EPA Science Inventory

    The major histocompatibility system provides a unique complex of genetic loci in vertebrates to assess genetic diversity and to look for the effects of selection on the adaptive immune system. Studies using mammals and birds have demonstrated relationships between MHC genotyp...

  10. MHC ANTIGEN-BINDING LOCUS SHOWS STRONG SIGNAL OF SELECTION AND HIGH VARIABILITY IN FUNDULUS HETEROCLITUS POPULATIONS

    EPA Science Inventory

    The major histocompatibility system provides a unique genetic locus in vertebrates to assess genetic diversity and to look for the effects of selecti.on on the immune system. Fish population studies using MHC are fairly new, and thus far they have focused on endangered population...

  11. A Web-Based Genetic Polymorphism Learning Approach for High School Students and Science Teachers

    ERIC Educational Resources Information Center

    Amenkhienan, Ehichoya; Smith, Edward J.

    2006-01-01

    Variation and polymorphism are concepts that are central to genetics and genomics, primary biological disciplines in which high school students and undergraduates require a solid foundation. From 1998 through 2002, a web-based genetics education program was developed for high school teachers and students. The program included an exercise on using…

  12. High school students' problem-solving performance on realistic genetics problems

    Microsoft Academic Search

    Susie Johnston Slack; Jim Stewart

    1990-01-01

    Problem solving is recognized as a valuable educational experience in science. Thus genetics, essentially a problem-solving science included in almost all high school biology courses, offers a fruitful area for studying student problem-solving performance. The research reported in this article describes the performance of 30 high school students solving 119 problems generated by the computer program GENETICS CONSTRUCTION KIT (Jungck

  13. High school students' understanding and problem solving in population genetics

    Microsoft Academic Search

    Patti D. Soderberg

    2005-01-01

    This study is an investigation of student understanding of population genetics and how students developed, used and revised conceptual models to solve problems. The students in this study participated in three rounds of problem solving. The first round involved the use of a population genetics model to predict the number of carriers in a population. The second round required them

  14. Transcriptome sequencing for high throughput SNP development and genetic mapping in Pea

    PubMed Central

    2014-01-01

    Background Pea has a complex genome of 4.3 Gb for which only limited genomic resources are available to date. Although SNP markers are now highly valuable for research and modern breeding, only a few are described and used in pea for genetic diversity and linkage analysis. Results We developed a large resource by cDNA sequencing of 8 genotypes representative of modern breeding material using the Roche 454 technology, combining both long reads (400 bp) and high coverage (3.8 million reads, reaching a total of 1,369 megabases). Sequencing data were assembled and generated a 68 K unigene set, from which 41 K were annotated from their best blast hit against the model species Medicago truncatula. Annotated contigs showed an even distribution along M. truncatula pseudochromosomes, suggesting a good representation of the pea genome. 10 K pea contigs were found to be polymorphic among the genetic material surveyed, corresponding to 35 K SNPs. We validated a subset of 1538 SNPs through the GoldenGate assay, proving their ability to structure a diversity panel of breeding germplasm. Among them, 1340 were genetically mapped and used to build a new consensus map comprising a total of 2070 markers. Based on blast analysis, we could establish 1252 bridges between our pea consensus map and the pseudochromosomes of M. truncatula, which provides new insight on synteny between the two species. Conclusions Our approach created significant new resources in pea, i.e. the most comprehensive genetic map to date tightly linked to the model species M. truncatula and a large SNP resource for both academic research and breeding. PMID:24521263

  15. High Genetic Diversity and Structured Populations of the Oriental Fruit Moth in Its Range of Origin

    PubMed Central

    Zheng, Yan; Peng, Xiong; Liu, Gaoming; Pan, Hongyan; Dorn, Silvia; Chen, Maohua

    2013-01-01

    The oriental fruit moth Grapholita (?=?Cydia) molesta is a key fruit pest globally. Despite its economic importance, little is known about its population genetics in its putative native range that includes China. We used five polymorphic microsatellite loci and two mitochondrial gene sequences to characterize the population genetic diversity and genetic structure of G. molesta from nine sublocations in three regions of a major fruit growing area of China. Larval samples were collected throughout the season from peach, and in late season, after host switch by the moth to pome fruit, also from apple and pear. We found high numbers of microsatellite alleles and mitochondrial DNA haplotypes in all regions, together with a high number of private alleles and of haplotypes at all sublocations, providing strong evidence that the sampled area belongs to the origin of this species. Samples collected from peach at all sublocations were geographically structured, and a significant albeit weak pattern of isolation-by-distance was found among populations, likely reflecting the low flight capacity of this moth. Interestingly, populations sampled from apple and pear in the late season showed a structure differing from that of populations sampled from peach throughout the season, indicating a selective host switch of a certain part of the population only. The recently detected various olfactory genotypes in G. molesta may underly this selective host switch. These genetic data yield, for the first time, an understanding of population dynamics of G. molesta in its native range, and of a selective host switch from peach to pome fruit, which may have a broad applicability to other global fruit production areas for designing suitable pest management strategies. PMID:24265692

  16. A genetically encoded, high-signal-to-noise maltose sensor

    SciTech Connect

    Marvin, Jonathan S.; Schreiter, Eric R.; Echevarría, Ileabett M.; Looger, Loren L. (Puerto Rico); (HHMI)

    2012-10-23

    We describe the generation of a family of high-signal-to-noise single-wavelength genetically encoded indicators for maltose. This was achieved by insertion of circularly permuted fluorescent proteins into a bacterial periplasmic binding protein (PBP), Escherichia coli maltodextrin-binding protein, resulting in a four-color family of maltose indicators. The sensors were iteratively optimized to have sufficient brightness and maltose-dependent fluorescence increases for imaging, under both one- and two-photon illumination. We demonstrate that maltose affinity of the sensors can be tuned in a fashion largely independent of the fluorescent readout mechanism. Using literature mutations, the binding specificity could be altered to moderate sucrose preference, but with a significant loss of affinity. We use the soluble sensors in individual E. coli bacteria to observe rapid maltose transport across the plasma membrane, and membrane fusion versions of the sensors on mammalian cells to visualize the addition of maltose to extracellular media. The PBP superfamily includes scaffolds specific for a number of analytes whose visualization would be critical to the reverse engineering of complex systems such as neural networks, biosynthetic pathways, and signal transduction cascades. We expect the methodology outlined here to be useful in the development of indicators for many such analytes.

  17. Genetics

    NSDL National Science Digital Library

    Jennifer Doherty

    This activity helps students to understand basic principles of genetics, including relationships of genotype to phenotype, concepts of recessive and dominant alleles, and how understanding meiosis and fertilization provides the basis for understanding inheritance, as summarized in Punnett squares. The Student Handout includes an analysis of the inheritance of albinism that teaches all of these concepts, a Coin Toss Genetics activity that helps students understand the probabilistic nature of Punnett square predictions, and an analysis of the inheritance of sickle cell anemia that reinforces the basic concepts and introduces some of the complexities of genetics. The Genetics Supplement includes two additional activities, an analysis of student data on the sex makeup of sibships and pedigree analyses of recessive and dominant alleles with challenge questions that introduce the role of mutations and an evaluation of Punnett squares and pedigrees as models of inheritance.

  18. Genetic structure in a fragmented Northern Hemisphere rainforest: large effective sizes and high connectivity among populations of the epiphytic lichen Lobaria pulmonaria.

    PubMed

    Hilmo, Olga; Lundemo, Sverre; Holien, Hĺkon; Stengrundet, Kirsti; Stenřien, Hans K

    2012-07-01

    An extraordinary diversity of epiphytic lichens is found in the boreal rainforest of central Norway, the highest-latitude rainforest in the world. These rainforest relicts are located in ravine systems, and clear cutting has increased the distance between remaining patches. We hypothesized that the relatively small lichen populations in the remaining forest stands have suffered a depletion of genetic diversity through bottlenecks and founder events. To test this hypothesis, we assessed genetic diversity and structure in the populations of the tripartite lichen Lobaria pulmonaria using eight SSR loci. We sampled thalli growing on Picea abies branches and propagules deposited in snow at three localities. Contrary to expectations, we found high genetic diversity in lichen and snow samples, and high effective sizes of the studied populations. Also, limited genetic differentiation between populations, high historical migration rates, and a high proportion of first generation immigrants were estimated, implying high connectivity across distances <30km. Almost all genetic variation was attributed to variation within sites; spatial genetic structures within populations were absent or appeared on small scales (5-10m). The high genetic diversity in the remaining old boreal rainforests shows that even relict forest patches might be suitable for conservation of genetic diversity. PMID:22571538

  19. A tellurium-substituted Lindqvist-type polyoxoniobate showing high H(2) evolution catalyzed by tellurium nanowires via photodecomposition.

    PubMed

    Son, Jung-Ho; Wang, Jiarui; Osterloh, Frank E; Yu, Ping; Casey, William H

    2014-01-25

    A new tellurium-substituted Lindqvist-type polyoxoniobate [H2TeNb5O19](5-) was synthesized as a tetramethylammonium salt. When irradiated with a Xe lamp, a water-methanol solution of this cluster showed exceptionally high H2-evolution activity suggesting cocatalysis by the hexaniobate cluster and metallic tellurium, both of which are formed as photodecomposition products. PMID:24292440

  20. Evaluation of four genetic variants in han chinese subjects with high myopia.

    PubMed

    Ye, Zimeng; Luo, Huaichao; Gong, Bo; Lin, Ying; Shuai, Ping; Wang, Pu; Ye, Changning; Yang, Zhenglin; Wang, Wanjun; Shi, Yi

    2015-01-01

    High myopia is one of the leading causes of blindness worldwide. However, the exact etiology of high myopia remains unraveled despite numerous attempts of elucidation. Previous genome-wide association study (GWAS) has revealed that four single nucleotide polymorphisms (SNPs), including rs2969180, rs1652333, rs9307551, and rs7837791, were associated with high myopia in Caucasians. The present study was conducted to investigate whether these genetic variants were associated with high myopia in Han Chinese. These four SNPs were genotyped by SNaPshot method in a Han Chinese cohort composed of 827 patients with high myopia and 988 healthy controls. Among the SNPs genotyped, only rs9307551 was found to be significantly associated with high myopia in this study. Carriers of rs9307551A allele, AA, and AC genotypes had an increased risk of high myopia (OR = 1.33, 95% CI 1.14-1.54; OR = 1.75, 95% CI 1.28-2.38; OR = 1.59, 95% CI 1.24-2.01, resp.). Interestingly, when split by gender, the association between rs9307551 and high myopia proved to be gender-specific with significance observed only in females but not males. These findings suggested that the SNP of rs9307551 showed a gender-specific association with high myopia in the Han Chinese population. In addition, LOC100506035, a lincRNA gene, might play a crucial role in the susceptibility to high myopia. PMID:25628894

  1. 31-Year-Old Female Shows Marked Improvement in Depression, Agitation, and Panic Attacks after Genetic Testing Was Used to Inform Treatment

    PubMed Central

    Lawrence, Scott

    2014-01-01

    This case describes a 31-year-old female Caucasian patient with complaints of ongoing depression, agitation, and severe panic attacks. The patient was untreated until a recent unsuccessful trial of citalopram followed by venlafaxine which produced a partial response. Genetic testing was performed to assist in treatment decisions and revealed the patient to be heterozygous for polymorphisms in 5HT2C, ANK3, and MTHFR and homozygous for a polymorphism in SLC6A4 and the low activity (Met/Met) COMT allele. In response to genetic results and clinical presentation, venlafaxine was maintained and lamotrigine was added leading to remission of agitation and depression. PMID:24744941

  2. 31-year-old female shows marked improvement in depression, agitation, and panic attacks after genetic testing was used to inform treatment.

    PubMed

    Lawrence, Scott

    2014-01-01

    This case describes a 31-year-old female Caucasian patient with complaints of ongoing depression, agitation, and severe panic attacks. The patient was untreated until a recent unsuccessful trial of citalopram followed by venlafaxine which produced a partial response. Genetic testing was performed to assist in treatment decisions and revealed the patient to be heterozygous for polymorphisms in 5HT2C, ANK3, and MTHFR and homozygous for a polymorphism in SLC6A4 and the low activity (Met/Met) COMT allele. In response to genetic results and clinical presentation, venlafaxine was maintained and lamotrigine was added leading to remission of agitation and depression. PMID:24744941

  3. Awareness of Societal Issues Among High School Biology Teachers Teaching Genetics

    Microsoft Academic Search

    Reuven Lazarowitz; Ilit Bloch

    2005-01-01

    The purpose of this study was to investigate how aware high school biology teachers are of societal issues (values, moral,\\u000a ethic, and legal issues) while teaching genetics, genetics engineering, molecular genetics, human heredity, and evolution.\\u000a The study includes a short historical review of World War II atrocities during the Holocaust when scientists from all the\\u000a above-mentioned disciplines had been involved

  4. A genetic mechanism for Tibetan high-altitude adaptation.

    PubMed

    Lorenzo, Felipe R; Huff, Chad; Myllymäki, Mikko; Olenchock, Benjamin; Swierczek, Sabina; Tashi, Tsewang; Gordeuk, Victor; Wuren, Tana; Ri-Li, Ge; McClain, Donald A; Khan, Tahsin M; Koul, Parvaiz A; Guchhait, Prasenjit; Salama, Mohamed E; Xing, Jinchuan; Semenza, Gregg L; Liberzon, Ella; Wilson, Andrew; Simonson, Tatum S; Jorde, Lynn B; Kaelin, William G; Koivunen, Peppi; Prchal, Josef T

    2014-09-01

    Tibetans do not exhibit increased hemoglobin concentration at high altitude. We describe a high-frequency missense mutation in the EGLN1 gene, which encodes prolyl hydroxylase 2 (PHD2), that contributes to this adaptive response. We show that a variant in EGLN1, c.[12C>G; 380G>C], contributes functionally to the Tibetan high-altitude phenotype. PHD2 triggers the degradation of hypoxia-inducible factors (HIFs), which mediate many physiological responses to hypoxia, including erythropoiesis. The PHD2 p.[Asp4Glu; Cys127Ser] variant exhibits a lower K(m) value for oxygen, suggesting that it promotes increased HIF degradation under hypoxic conditions. Whereas hypoxia stimulates the proliferation of wild-type erythroid progenitors, the proliferation of progenitors with the c.[12C>G; 380G>C] mutation in EGLN1 is significantly impaired under hypoxic culture conditions. We show that the c.[12C>G; 380G>C] mutation originated ?8,000 years ago on the same haplotype previously associated with adaptation to high altitude. The c.[12C>G; 380G>C] mutation abrogates hypoxia-induced and HIF-mediated augmentation of erythropoiesis, which provides a molecular mechanism for the observed protection of Tibetans from polycythemia at high altitude. PMID:25129147

  5. Transcriptome analysis of the Bombyx mori fat body after constant high temperature treatment shows differences between the sexes.

    PubMed

    Wang, Hua; Fang, Yan; Wang, Lipeng; Zhu, Wenjuan; Ji, Haipeng; Wang, Haiying; Xu, Shiqing; Sima, Yanghu

    2014-09-01

    Ambient temperature plays a large role in insect growth, development and even their distribution. The elucidation of the associated molecular mechanism that underlies the effect of constant high temperature will enables us to further understand the stress responses. We constructed four digital gene expression libraries from the fat body of female and male Bombyx mori. Differential gene expression was analyzed after constant high temperature treatment. The results showed that there were significant changes to the gene expression in the fat body after heat treatment, especially in binding, catalytic, cellular and metabolic processes. Constant high temperature may induce more traditional cryoprotectants, such as glycerol, glycogen, sorbitol and lipids, to protect cells from damage, and induce heat oxidative stress in conjunction with the heat shock proteins. The data also indicated a difference between males and females. The heat shock protein-related genes were up-regulated in both sexes but the expression of Hsp25.4 and DnaJ5 were down-regulated in the male fat body of B. mori. This is the first report of such a result. Constant high temperature also affected the expression of other functional genes and differences were observed between male and female fat bodies in the expression of RPS2, RPL37A and MREL. These findings provide abundant data on the effect of high temperature on insects at the molecular level. The data will also be beneficial to the study of differences between the sexes, manifested in variations in gene expression under high temperature. PMID:24972568

  6. High Genetic Diversity Despite the Potential for Stepping-Stone Colonizations in an Invasive Species of Gecko on Moorea, French Polynesia

    PubMed Central

    Tonione, Maria A.; Reeder, Natalie; Moritz, Craig C.

    2011-01-01

    Invasive species often have reduced genetic diversity, but the opposite can be true if there have been multiple introductions and genetic admixture. Reduced diversity is most likely soon after establishment, in remote locations, when there is lower propagule pressure and with stepping-stone colonizations. The common house gecko (Hemidactylus frenatus) was introduced to Moorea, French Polynesia in the remote eastern Pacific within the last two decades and accordingly is expected to exhibit low diversity. In contrast, we show that H. frenatus on Moorea has exceptionally high genetic diversity, similar to that near the native range in Asia and much higher than reported for other Pacific island reptiles. The high diversity in this recently founded population likely reflects extensive genetic admixture in source population(s) and a life history that promotes retention of diversity. These observations point to the importance of understanding range-wide dynamics of genetic admixture in highly invasive species. PMID:22073211

  7. Sex-stratified Genome-wide Association Studies Including 270,000 Individuals Show Sexual Dimorphism in Genetic Loci for Anthropometric Traits

    PubMed Central

    Jackson, Anne U.; Monda, Keri L.; Kilpeläinen, Tuomas O.; Esko, Tőnu; Mägi, Reedik; Li, Shengxu; Workalemahu, Tsegaselassie; Feitosa, Mary F.; Croteau-Chonka, Damien C.; Day, Felix R.; Fall, Tove; Ferreira, Teresa; Gustafsson, Stefan; Locke, Adam E.; Mathieson, Iain; Scherag, Andre; Vedantam, Sailaja; Wood, Andrew R.; Liang, Liming; Steinthorsdottir, Valgerdur; Thorleifsson, Gudmar; Dermitzakis, Emmanouil T.; Dimas, Antigone S.; Karpe, Fredrik; Min, Josine L.; Nicholson, George; Clegg, Deborah J.; Person, Thomas; Krohn, Jon P.; Bauer, Sabrina; Buechler, Christa; Eisinger, Kristina; Bonnefond, Amélie; Froguel, Philippe; Hottenga, Jouke-Jan; Prokopenko, Inga; Waite, Lindsay L.; Harris, Tamara B.; Smith, Albert Vernon; Shuldiner, Alan R.; McArdle, Wendy L.; Caulfield, Mark J.; Munroe, Patricia B.; Grönberg, Henrik; Chen, Yii-Der Ida; Li, Guo; Beckmann, Jacques S.; Johnson, Toby; Thorsteinsdottir, Unnur; Teder-Laving, Maris; Khaw, Kay-Tee; Wareham, Nicholas J.; Zhao, Jing Hua; Amin, Najaf; Oostra, Ben A.; Kraja, Aldi T.; Province, Michael A.; Cupples, L. Adrienne; Heard-Costa, Nancy L.; Kaprio, Jaakko; Ripatti, Samuli; Surakka, Ida; Collins, Francis S.; Saramies, Jouko; Tuomilehto, Jaakko; Jula, Antti; Salomaa, Veikko; Erdmann, Jeanette; Hengstenberg, Christian; Loley, Christina; Schunkert, Heribert; Lamina, Claudia; Wichmann, H. Erich; Albrecht, Eva; Gieger, Christian; Hicks, Andrew A.; Johansson, Ĺsa; Pramstaller, Peter P.; Kathiresan, Sekar; Speliotes, Elizabeth K.; Penninx, Brenda; Hartikainen, Anna-Liisa; Jarvelin, Marjo-Riitta; Gyllensten, Ulf; Boomsma, Dorret I.; Campbell, Harry; Wilson, James F.; Chanock, Stephen J.; Farrall, Martin; Goel, Anuj; Medina-Gomez, Carolina; Rivadeneira, Fernando; Estrada, Karol; Uitterlinden, André G.; Hofman, Albert; Zillikens, M. Carola; den Heijer, Martin; Kiemeney, Lambertus A.; Maschio, Andrea; Hall, Per; Tyrer, Jonathan; Teumer, Alexander; Völzke, Henry; Kovacs, Peter; Tönjes, Anke; Mangino, Massimo; Spector, Tim D.; Hayward, Caroline; Rudan, Igor; Hall, Alistair S.; Samani, Nilesh J.; Attwood, Antony Paul; Sambrook, Jennifer G.; Hung, Joseph; Palmer, Lyle J.; Lokki, Marja-Liisa; Sinisalo, Juha; Boucher, Gabrielle; Huikuri, Heikki; Lorentzon, Mattias; Ohlsson, Claes; Eklund, Niina; Eriksson, Johan G.; Barlassina, Cristina; Rivolta, Carlo; Nolte, Ilja M.; Snieder, Harold; Van der Klauw, Melanie M.; Van Vliet-Ostaptchouk, Jana V.; Gejman, Pablo V.; Shi, Jianxin; Jacobs, Kevin B.; Wang, Zhaoming; Bakker, Stephan J. L.; Mateo Leach, Irene; Navis, Gerjan; van der Harst, Pim; Martin, Nicholas G.; Medland, Sarah E.; Montgomery, Grant W.; Yang, Jian; Chasman, Daniel I.; Ridker, Paul M.; Rose, Lynda M.; Lehtimäki, Terho; Raitakari, Olli; Absher, Devin; Iribarren, Carlos; Basart, Hanneke; Hovingh, Kees G.; Hyppönen, Elina; Power, Chris; Anderson, Denise; Beilby, John P.; Hui, Jennie; Jolley, Jennifer; Sager, Hendrik; Bornstein, Stefan R.; Schwarz, Peter E. H.; Kristiansson, Kati; Perola, Markus; Lindström, Jaana; Swift, Amy J.; Uusitupa, Matti; Atalay, Mustafa; Lakka, Timo A.; Rauramaa, Rainer; Bolton, Jennifer L.; Fowkes, Gerry; Fraser, Ross M.; Price, Jackie F.; Fischer, Krista; Krjutškov, Kaarel; Metspalu, Andres; Mihailov, Evelin; Langenberg, Claudia; Luan, Jian'an; Ong, Ken K.; Chines, Peter S.; Keinanen-Kiukaanniemi, Sirkka M.; Saaristo, Timo E.; Edkins, Sarah; Franks, Paul W.; Hallmans, Göran; Shungin, Dmitry; Morris, Andrew David; Palmer, Colin N. A.; Erbel, Raimund; Moebus, Susanne; Nöthen, Markus M.; Pechlivanis, Sonali; Hveem, Kristian; Narisu, Narisu; Hamsten, Anders; Humphries, Steve E.; Strawbridge, Rona J.; Tremoli, Elena; Grallert, Harald; Thorand, Barbara; Illig, Thomas; Koenig, Wolfgang; Müller-Nurasyid, Martina; Peters, Annette; Boehm, Bernhard O.; Kleber, Marcus E.; März, Winfried; Winkelmann, Bernhard R.; Kuusisto, Johanna; Laakso, Markku; Arveiler, Dominique; Cesana, Giancarlo; Kuulasmaa, Kari; Virtamo, Jarmo; Yarnell, John W. G.; Kuh, Diana; Wong, Andrew; Lind, Lars; de Faire, Ulf; Gigante, Bruna; Magnusson, Patrik K. E.; Pedersen, Nancy L.; Dedoussis, George; Dimitriou, Maria; Kolovou, Genovefa; Kanoni, Stavroula; Stirrups, Kathleen; Bonnycastle, Lori L.; Njřlstad, Inger; Wilsgaard, Tom; Ganna, Andrea; Rehnberg, Emil; Hingorani, Aroon; Kivimaki, Mika; Kumari, Meena; Assimes, Themistocles L.; Barroso, Inęs; Boehnke, Michael; Borecki, Ingrid B.; Deloukas, Panos; Fox, Caroline S.; Frayling, Timothy; Groop, Leif C.; Haritunians, Talin; Hunter, David

    2013-01-01

    Given the anthropometric differences between men and women and previous evidence of sex-difference in genetic effects, we conducted a genome-wide search for sexually dimorphic associations with height, weight, body mass index, waist circumference, hip circumference, and waist-to-hip-ratio (133,723 individuals) and took forward 348 SNPs into follow-up (additional 137,052 individuals) in a total of 94 studies. Seven loci displayed significant sex-difference (FDR<5%), including four previously established (near GRB14/COBLL1, LYPLAL1/SLC30A10, VEGFA, ADAMTS9) and three novel anthropometric trait loci (near MAP3K1, HSD17B4, PPARG), all of which were genome-wide significant in women (P<5×10?8), but not in men. Sex-differences were apparent only for waist phenotypes, not for height, weight, BMI, or hip circumference. Moreover, we found no evidence for genetic effects with opposite directions in men versus women. The PPARG locus is of specific interest due to its role in diabetes genetics and therapy. Our results demonstrate the value of sex-specific GWAS to unravel the sexually dimorphic genetic underpinning of complex traits. PMID:23754948

  8. Genetic variation and recombination of RdRp and HSP 70h genes of Citrus tristeza virus isolates from orange trees showing symptoms of citrus sudden death disease

    Microsoft Academic Search

    Clarissa PC Gomes; Tatsuya Nagata; Waldir C de Jesus; Carlos R Borges Neto; Georgios J Pappas Jr; Darren P Martin

    2008-01-01

    BACKGROUND: Citrus sudden death (CSD), a disease that rapidly kills orange trees, is an emerging threat to the Brazilian citrus industry. Although the causal agent of CSD has not been definitively determined, based on the disease's distribution and symptomatology it is suspected that the agent may be a new strain of Citrus tristeza virus (CTV). CTV genetic variation was therefore

  9. Viral reverse transcriptases show selective high affinity binding to DNA-DNA primer-templates that resemble the polypurine tract.

    PubMed

    Nair, Gauri R; Dash, Chandravanu; Le Grice, Stuart F J; DeStefano, Jeffrey J

    2012-01-01

    Previous results using a SELEX (Systematic Evolution of Ligands by Exponential Enrichment)-based approach that selected DNA primer-template duplexes binding with high affinity to HIV reverse transcriptase (RT) showed that primers mimicking the 3' end, and in particular the six nt terminal G tract, of the RNA polypurine tract (PPT; HIV PPT: 5'-AAAAGAAAAGGGGGG-3') were preferentially selected. In this report, two viral (Moloney murine leukemia virus (MuLV) and avian myeloblastosis virus (AMV)) and one retrotransposon (Ty3) RTs were used for selection. Like HIV RT, both viral RTs selected duplexes with primer strands mimicking the G tract at the PPT 3' end (AMV PPT: 5'-AGGGAGGGGGA-3'; MuLV PPT: 5'-AGAAAAAGGGGGG-3'). In contrast, Ty3, whose PPT lacks a G tract (5'-GAGAGAGAGGAA-3') showed no selective binding to any duplex sequences. Experiments were also conducted with DNA duplexes (termed DNA PPTs) mimicking the RNA PPT-DNA duplex of each virus and a control duplex with a random DNA sequence. Retroviral RTs bound with high affinity to all viral DNA PPT constructs, with HIV and MuLV RTs showing comparable binding to the counterpart DNA PPT duplexes and reduced affinity to the AMV DNA PPT. AMV RT showed similar behavior with a modest preference for its own DNA PPT. Ty3 RT showed no preferential binding for its own or any other DNA PPT and viral RTs bound the Ty3 DNA PPT with relatively low affinity. In contrast, binding affinity of HIV RT to duplexes containing the HIV RNA PPT was less dependent on the G tract, which is known to be pivotal for efficient extension. We hypothesize that the G tract on the RNA PPT helps shift the binding orientation of RT to the 3' end of the PPT where extension can occur. PMID:22848574

  10. Viral Reverse Transcriptases Show Selective High Affinity Binding to DNA-DNA Primer-Templates that Resemble the Polypurine Tract

    PubMed Central

    Nair, Gauri R.; Dash, Chandravanu; Le Grice, Stuart F. J.; DeStefano, Jeffrey J.

    2012-01-01

    Previous results using a SELEX (Systematic Evolution of Ligands by Exponential Enrichment)-based approach that selected DNA primer-template duplexes binding with high affinity to HIV reverse transcriptase (RT) showed that primers mimicking the 3? end, and in particular the six nt terminal G tract, of the RNA polypurine tract (PPT; HIV PPT: 5?-AAAAGAAAAGGGGGG-3?) were preferentially selected. In this report, two viral (Moloney murine leukemia virus (MuLV) and avian myeloblastosis virus (AMV)) and one retrotransposon (Ty3) RTs were used for selection. Like HIV RT, both viral RTs selected duplexes with primer strands mimicking the G tract at the PPT 3? end (AMV PPT: 5?-AGGGAGGGGGA-3?; MuLV PPT: 5?-AGAAAAAGGGGGG-3?). In contrast, Ty3, whose PPT lacks a G tract (5?-GAGAGAGAGGAA-3?) showed no selective binding to any duplex sequences. Experiments were also conducted with DNA duplexes (termed DNA PPTs) mimicking the RNA PPT-DNA duplex of each virus and a control duplex with a random DNA sequence. Retroviral RTs bound with high affinity to all viral DNA PPT constructs, with HIV and MuLV RTs showing comparable binding to the counterpart DNA PPT duplexes and reduced affinity to the AMV DNA PPT. AMV RT showed similar behavior with a modest preference for its own DNA PPT. Ty3 RT showed no preferential binding for its own or any other DNA PPT and viral RTs bound the Ty3 DNA PPT with relatively low affinity. In contrast, binding affinity of HIV RT to duplexes containing the HIV RNA PPT was less dependent on the G tract, which is known to be pivotal for efficient extension. We hypothesize that the G tract on the RNA PPT helps shift the binding orientation of RT to the 3? end of the PPT where extension can occur. PMID:22848574

  11. Detecting Genetic Association of Common Human Facial Morphological Variation Using High Density 3D Image Registration

    PubMed Central

    Hu, Sile; Zhou, Hang; Guo, Jing; Jin, Li; Tang, Kun

    2013-01-01

    Human facial morphology is a combination of many complex traits. Little is known about the genetic basis of common facial morphological variation. Existing association studies have largely used simple landmark-distances as surrogates for the complex morphological phenotypes of the face. However, this can result in decreased statistical power and unclear inference of shape changes. In this study, we applied a new image registration approach that automatically identified the salient landmarks and aligned the sample faces using high density pixel points. Based on this high density registration, three different phenotype data schemes were used to test the association between the common facial morphological variation and 10 candidate SNPs, and their performances were compared. The first scheme used traditional landmark-distances; the second relied on the geometric analysis of 15 landmarks and the third used geometric analysis of a dense registration of ?30,000 3D points. We found that the two geometric approaches were highly consistent in their detection of morphological changes. The geometric method using dense registration further demonstrated superiority in the fine inference of shape changes and 3D face modeling. Several candidate SNPs showed potential associations with different facial features. In particular, one SNP, a known risk factor of non-syndromic cleft lips/palates, rs642961 in the IRF6 gene, was validated to strongly predict normal lip shape variation in female Han Chinese. This study further demonstrated that dense face registration may substantially improve the detection and characterization of genetic association in common facial variation. PMID:24339768

  12. Genetics

    NSDL National Science Digital Library

    National Science Teachers Association (NSTA)

    2005-04-01

    What affects how physical characteristics are transmitted from parent to offspring? This is a question that can be answered at many levels. Molecular biologists examine the pattern of nucleotides in deoxyribonucleic acid (DNA) and the effect of mutations on the proteins produced. Classical geneticists explore the patterns by which traits are transmitted through families. Medical geneticists attempt to describe and develop treatments for diseases that have a genetic component. Genetic engineers analyze how traits can be altered in organisms through modern technology. These are only a few of the strategies that scientists employ to explain the nature of heredity. Explore historical perspectives on the study of genetics and investigate how cutting-edge technology is being used to expand our understanding of heredity.

  13. Spatio-temporal Genetic Structure of a Tropical Bee Species Suggests High Dispersal Over a Fragmented Landscape

    PubMed Central

    Suni, Sevan S.; Bronstein, Judith L.; Brosi, Berry J.

    2014-01-01

    Habitat destruction threatens biodiversity by reducing the amount of available resources and connectivity among geographic areas. For organisms living in fragmented habitats, population persistence may depend on dispersal, which maintains gene flow among fragments and can prevent inbreeding within them. It is centrally important to understand patterns of dispersal for bees living in fragmented areas given the importance of pollination systems and recently documented declines in bee populations. We used population and landscape genetic techniques to characterize patterns of dispersal over a large fragmented area in southern Costa Rica for the orchid bee species Euglossa championi. First, we estimated levels of genetic differentiation among forest fragments as ?pt, an analog to the traditional summary statistic Fst, as well as two statistics that may more adequately represent levels of differentiation, G’st and Dest. Second, we used a Bayesian approach to determine the number and composition of genetic groups in our sample. Third we investigated how genetic differentiation changes with distance. Fourth, we determined the extent to which deforested areas restrict dispersal. Finally, we estimated the extent to which there were temporal differences in allele frequencies within the same forest fragments. Within years we found low levels of differentiation even over 80 km, and no effect of land use type on level of genetic differentiation. However, we found significant genetic differentiation between years. Taken together our results suggest that there are high levels of gene flow over this geographic area, and that individuals show low site fidelity over time. PMID:24659825

  14. Spatio-temporal Genetic Structure of a Tropical Bee Species Suggests High Dispersal Over a Fragmented Landscape.

    PubMed

    Suni, Sevan S; Bronstein, Judith L; Brosi, Berry J

    2014-03-01

    Habitat destruction threatens biodiversity by reducing the amount of available resources and connectivity among geographic areas. For organisms living in fragmented habitats, population persistence may depend on dispersal, which maintains gene flow among fragments and can prevent inbreeding within them. It is centrally important to understand patterns of dispersal for bees living in fragmented areas given the importance of pollination systems and recently documented declines in bee populations. We used population and landscape genetic techniques to characterize patterns of dispersal over a large fragmented area in southern Costa Rica for the orchid bee species Euglossa championi. First, we estimated levels of genetic differentiation among forest fragments as ?pt, an analog to the traditional summary statistic F st, as well as two statistics that may more adequately represent levels of differentiation, G'st and Dest . Second, we used a Bayesian approach to determine the number and composition of genetic groups in our sample. Third we investigated how genetic differentiation changes with distance. Fourth, we determined the extent to which deforested areas restrict dispersal. Finally, we estimated the extent to which there were temporal differences in allele frequencies within the same forest fragments. Within years we found low levels of differentiation even over 80 km, and no effect of land use type on level of genetic differentiation. However, we found significant genetic differentiation between years. Taken together our results suggest that there are high levels of gene flow over this geographic area, and that individuals show low site fidelity over time. PMID:24659825

  15. Mitochondrial DNA markers reveal high genetic diversity but low genetic differentiation in the black fly Simulium tani Takaoka & Davies along an elevational gradient in Malaysia.

    PubMed

    Low, Van Lun; Adler, Peter H; Takaoka, Hiroyuki; Ya'cob, Zubaidah; Lim, Phaik Eem; Tan, Tiong Kai; Lim, Yvonne A L; Chen, Chee Dhang; Norma-Rashid, Yusoff; Sofian-Azirun, Mohd

    2014-01-01

    The population genetic structure of Simulium tani was inferred from mitochondria-encoded sequences of cytochrome c oxidase subunits I (COI) and II (COII) along an elevational gradient in Cameron Highlands, Malaysia. A statistical parsimony network of 71 individuals revealed 71 haplotypes in the COI gene and 43 haplotypes in the COII gene; the concatenated sequences of the COI and COII genes revealed 71 haplotypes. High levels of genetic diversity but low levels of genetic differentiation were observed among populations of S. tani at five elevations. The degree of genetic diversity, however, was not in accordance with an altitudinal gradient, and a Mantel test indicated that elevation did not have a limiting effect on gene flow. No ancestral haplotype of S. tani was found among the populations. Pupae with unique structural characters at the highest elevation showed a tendency to form their own haplotype cluster, as revealed by the COII gene. Tajima's D, Fu's Fs, and mismatch distribution tests revealed population expansion of S. tani in Cameron Highlands. A strong correlation was found between nucleotide diversity and the levels of dissolved oxygen in the streams where S. tani was collected. PMID:24941043

  16. Genetic selection of mice for high voluntary wheel running: effect on skeletal muscle glucose uptake

    E-print Network

    Garland Jr., Theodore

    Genetic selection of mice for high voluntary wheel running: effect on skeletal muscle glucose: effect on skeletal muscle glucose uptake. J Appl Physiol 91: 1289­1297, 2001.--Effects of genetic glucose uptake were stud- ied in mice with the following treatments for 8 wk: 1) access to unlocked wheels

  17. The Effect of Different Molecular Models on High School Students' Conceptions of Molecular Genetics

    ERIC Educational Resources Information Center

    Rotbain, Yosi; Stavy, Ruth; Marbach-Ad, Gili

    2008-01-01

    Our main goal in this study was to explore whether the use of models in high school molecular genetics instruction can contribute to students' understanding of concepts and processes in genetics. Three hundred and nineteen students from four comparable groups of 11th- and 12th-grade students participated. The control group (116 students) was…

  18. Academic Tasks in High School Biology: A Genetics Unit. R&D Rep. 6197.

    ERIC Educational Resources Information Center

    French, Barbara A. Schmidt; Sanford, Julie P.

    The relationship between classroom work and student understanding of genetics content is examined in this descriptive study of an introductory high school biology class. Classroom observations and examnations of student assignments related to a genetics unit were made. Factors affecting the teacher's management of the work system and the apparent…

  19. High-Throughput Association Testing on DNA Pools to Identify Genetic Variants that Confer Susceptibility

    E-print Network

    California at Berkeley, University of

    High-Throughput Association Testing on DNA Pools to Identify Genetic Variants that Confer designed for nine candidate genetic variants in DNA repair and cell cycle/apoptotic regulatory genes, including Cyclin D1 [codon 870 splice site variant (A>G)]; BRCA1, P871L; ERCC2, K751Q; FAS Ŕ1377 (G>A); h

  20. "The Show"

    ERIC Educational Resources Information Center

    Gehring, John

    2004-01-01

    For the past 16 years, the blue-collar city of Huntington, West Virginia, has rolled out the red carpet to welcome young wrestlers and their families as old friends. They have come to town chasing the same dream for a spot in what many of them call "The Show". For three days, under the lights of an arena packed with 5,000 fans, the state's best…

  1. Comparison of Fluorescence In Situ Hybridization and Chromogenic In Situ Hybridization for Low and High Throughput HER2 Genetic Testing

    PubMed Central

    Poulsen, Tim S.; Espersen, Maiken L. M.; Kofoed, Vibeke; Dabetic, Tanja; Hřgdall, Estrid; Balslev, Eva

    2013-01-01

    The purpose was to evaluate and compare 5 different HER2 genetic assays with different characteristics that could affect the performance to analyze the human epidermal growth factor 2 (HER2) gene copy number under low and high throughput conditions. The study included 108 tissue samples from breast cancer patients with HER2 immunohistochemistry (IHC) results scored as 0/1+, 2+, and 3+. HER2 genetic status was analysed using chromogenic in situ hybridization (CISH) and fluorescence in situ hybridization (FISH). Scoring results were documented through digital image analysis. The cancer region of interest was identified from a serial H&E stained slide following tissue cores were transferred to a tissue microarrays (TMA). When using TMA in a routine flow, all patients will be tested for HER2 status with IHC followed by CISH or FISH, thereby providing individual HER2 results. In conclusion, our results show that the differences between the HER2 genetic assays do not have an effect on the analytic performance and the CISH technology is superior to high throughput HER2 genetic testing due to scanning speed, while the IQ-FISH may still be a choice for fast low throughput HER2 genetic testing. PMID:24383005

  2. DRD4 Long Allele Carriers Show Heightened Attention to High-Priority Items Relative to Low-Priority Items

    PubMed Central

    Gorlick, Marissa A.; Worthy, Darrell A.; Knopik, Valerie S.; McGeary, John E.; Beevers, Christopher G.; Maddox, W. Todd

    2014-01-01

    Humans with 7 or more repeats in exon III of the DRD4 gene (long DRD4 carriers) sometimes demonstrate impaired attention, as seen in ADHD, and at other times demonstrate heightened attention, as seen in addictive behavior. Though the clinical effects of DRD4 are the focus of much work, this gene may not necessarily serve as a ‘risk’ gene for attentional deficits, but as a plasticity gene where attention is heightened for priority items in the environment and impaired for minor items. Here we examine the role of DRD4 in two tasks that benefit from selective attention to high-priority information. We examine a category learning task where performance is supported by focusing on features and updating verbal rules. Here selective attention to the most salient features is associated with good performance. In addition, we examine the Operation Span Task (OSPAN), a working memory capacity task that relies on selective attention to update and maintain items in memory while also performing a secondary task. Long DRD4 carriers show superior performance relative to short DRD4 homozygotes (six or less tandem repeats) in both the category learning and OSPAN tasks. These results suggest that DRD4 may serve as a ‘plasticity’ gene where individuals with the long allele show heightened selective attention to high-priority items in the environment, which can be beneficial in the appropriate context. PMID:25244120

  3. Genetic Analysis of Diffuse High-Grade Astrocytomas in Infancy Defines a Novel Molecular Entity.

    PubMed

    Gielen, Gerrit H; Gessi, Marco; Buttarelli, Francesca R; Baldi, Caterina; Hammes, Jennifer; Zur Muehlen, Anja; Doerner, Evelyn; Denkhaus, Dorota; Warmuth-Metz, Monika; Giangaspero, Felice; Lauriola, Libero; von Bueren, André O; Kramm, Christof M; Waha, Andreas; Pietsch, Torsten

    2015-07-01

    Pediatric high-grade gliomas are considered to be different when compared to adult high-grade gliomas in their pathogenesis and biological behavior. Recently, common genetic alterations, including mutations in the H3F3A/ATRX/DAXX pathway, have been described in approximately 30% of the pediatric cases. However, only few cases of infant high-grade gliomas have been analyzed so far. We investigated the molecular features of 35 infants with diffuse high-grade astrocytomas, including 8 anaplastic astrocytomas [World Health Organization (WHO) grade III] and 27 glioblastomas (WHO grade IV) by immunohistochemistry, multiplex ligation probe-dependent amplification (MLPA), pyrosequencing of glioma-associated genes and molecular inversion probe (MIP) assay. MIP and MLPA analyses showed that chromosomal alterations are significantly less frequent in infants compared with high-grade gliomas in older children and adults. We only identified H3F3A K27M in 2 of 34 cases (5.9%), with both tumors located in the posterior fossa. PDGFRA amplifications were absent, and CDKN2A loss could be observed only in two cases. Conversely, 1q gain (22.7%) and 6q loss (18.2%) were identified in a subgroup of tumors. Loss of SNORD located on chromosome 14q32 was observed in 27.3% of the infant tumors, a focal copy number change not previously described in gliomas. Our findings indicate that infant high-grade gliomas appear to represent a distinct genetic entity suggesting a different pathogenesis and biological behavior. PMID:25231549

  4. Genetic dissection of an alien chromosomal segment may enable the production of a rice (Oryza sativa L.) genotype showing shoot developmental instability.

    PubMed

    Itoh, Youki; Sato, Yoshikazu

    2015-04-01

    During the course of evolutionary history, organisms have acquired genes which cooperate harmoniously and subsequently express a stable pattern of development. In an earlier study we introduced a large chromosomal segment of chromosome 6 from a rice (Oryza sativa L.) ecotype, carrying the two flowering-time genes, which showed complex epistatic interactions in relation to environmental change, into a different ecotype by successive backcrossings. Four-near-isogenic lines (NILs) with respect to these two loci were obtained by subsequent hybridization with the recurrent parent. In the study reported here, these four NILs were the major plant material used to evaluate changes in days to leaf appearance (DLA) during shoot development using a quadratic-polynomial regression. The regressions were regarded as developmental norms because of the high values of R (2). Absolute Y-residuals (AYRs) (or size of deviation) of DLA from the norms were significantly affected by genotype. Dissections of the alien chromosomal segment resulted in one NIL that showed an increased level of AYR. Since this NIL also expressed a low survival rate in a stress environment, we suggest that the increased level of AYR during development might indicate an increased level of instability in shoot development. PMID:25677854

  5. Breeding high-yielding drought-tolerant rice: genetic variations and conventional and molecular approaches

    PubMed Central

    Kumar, Arvind; Dixit, Shalabh; Ram, T.; Yadaw, R. B.; Mishra, K. K.; Mandal, N. P.

    2014-01-01

    The increased occurrence and severity of drought stress have led to a high yield decline in rice in recent years in drought-affected areas. Drought research at the International Rice Research Institute (IRRI) over the past decade has concentrated on direct selection for grain yield under drought. This approach has led to the successful development and release of 17 high-yielding drought-tolerant rice varieties in South Asia, Southeast Asia, and Africa. In addition to this, 14 quantitative trait loci (QTLs) showing a large effect against high-yielding drought-susceptible popular varieties were identified using grain yield as a selection criterion. Six of these (qDTY 1.1, qDTY 2.2, qDTY 3.1, qDTY 3.2, qDTY 6.1, and qDTY 12.1) showed an effect against two or more high-yielding genetic backgrounds in both the lowland and upland ecosystem, indicating their usefulness in increasing the grain yield of rice under drought. The yield of popular rice varieties IR64 and Vandana has been successfully improved through a well-planned marker-assisted backcross breeding approach, and QTL introgression in several other popular varieties is in progress. The identification of large-effect QTLs for grain yield under drought and the higher yield increase under drought obtained through the use of these QTLs (which has not been reported in other cereals) indicate that rice, because of its continuous cultivation in two diverse ecosystems (upland, drought tolerant, and lowland, drought susceptible), has benefited from the existence of larger genetic variability than in other cereals. This can be successfully exploited using marker-assisted breeding. PMID:25205576

  6. Regional genetic differentiation among northern high-latitude island populations of a broadcast-spawning coral

    NASA Astrophysics Data System (ADS)

    Nakajima, Y.; Nishikawa, A.; Iguchi, A.; Sakai, K.

    2012-12-01

    Knowledge of genetic connectivity is useful for understanding of the recovery potential of coral populations after various disturbances, such as coral mass bleaching. Population genetic studies in corals are mostly restricted to Australian and Caribbean species; studies in the northern Pacific are relatively limited. Using microsatellite markers, the population genetics of Acropora sp. 1 was examined between two regions in Japan, the Okinawa-Aka and Bonin Islands, which are separated by approximately 1,500 km of open water in a high-latitude area. Statistically significant but small genetic differentiation in Acropora sp. 1 was detected between and within these regions. Genetic diversity was not obviously reduced in populations of the Bonin Islands, which are relatively isolated. Thus, some level of connectivity appears to be maintained between the two regions, likely because of the high dispersal ability of this broadcast spawner.

  7. High Genetic Diversity and Clonal Growth in Relict Populations of Olea europaea subsp. laperrinei (Oleaceae) from Hoggar, Algeria

    PubMed Central

    BAALI-CHERIF, DJAMEL; BESNARD, GUILLAUME

    2005-01-01

    • Background and Aims The Laperrine's olive (Olea europaea subsp. laperrinei) is an endemic tree from Saharan massifs. Its populations have substantially regressed since the Pleistocene and are presently distributed in a fragmented habitat. Long-term persistence of this taxon is uncertain and programmes of preservation have to be urgently implemented. To define a conservation strategy, the genetic diversity and breeding system of this tree have to be investigated. • Methods One hundred and eleven ramets were prospected in the laperrinei populations from the Tamanrasset region, southern Algeria. Genetic polymorphism was revealed at nuclear and chloroplast DNA (cpDNA) microsatellite loci allowing a comparative assessment of the genetic diversity of laperrinei and Mediterranean populations based on bi-parental and maternal markers. Additionally, nuclear microsatellite markers enabled the genotypes to be identified unambiguously. • Key Results Based on nuclear microsatellite data, the total diversity was high (Ht = 0·61) in laperrinei populations and similar to that observed in western Mediterranean populations. A substantial cpDNA diversity (Ht = 0·19) was also observed. Genetically identical ramets originated from the same stump (which can cover >80?m2) were identified in each population. Sixteen per cent of genets exhibited more than one ramet. In addition, several cases of somatic mutations were unambiguously revealed in distinct ramets stemming from the same stump. • Conclusions These data show that highly isolated and small laperrinei populations are able to maintain a high genetic diversity. This supports the existence of relict trees persisting for a very long time (probably since the last humid transition, 3000 years ago). It is proposed that the very long persistence associated with an asexual multiplication of highly adapted trees could be a strategy of survival in extreme conditions avoiding a mutational meltdown due to reproduction in reduced populations. PMID:16043438

  8. Sex-biased gene expression on the avian Z chromosome: highly expressed genes show higher male-biased expression.

    PubMed

    Naurin, Sara; Hasselquist, Dennis; Bensch, Staffan; Hansson, Bengt

    2012-01-01

    Dosage compensation, the process whereby expression of sex-linked genes remains similar between sexes (despite heterogamety) and balanced with autosomal expression, was long believed to be essential. However, recent research has shown that several lineages, including birds, butterflies, monotremes and sticklebacks, lack chromosome-wide dosage compensation mechanisms and do not completely balance the expression of sex-linked and autosomal genes. To obtain further understanding of avian sex-biased gene expression, we studied Z-linked gene expression in the brain of two songbirds of different genera (zebra finch, Taeniopygia guttata, and common whitethroat, Sylvia communis) using microarray technology. In both species, the male-bias in gene expression was significantly higher for Z than for autosomes, although the ratio of Z-linked to autosomal expression (Z:A) was relatively close to one in both sexes (range: 0.89-1.01). Interestingly, the Z-linked male-bias in gene expression increased with expression level, and genes with low expression showed the lowest degree of sex-bias. These results support the view that the heterogametic females have up-regulated their single Z-linked homologues to a high extent when the W-chromosome degraded and thereby managed to largely balance their Z:A expression with the exception of highly expressed genes. The male-bias in highly expressed genes points towards male-driven selection on Z-linked loci, and this and other possible hypotheses are discussed. PMID:23056488

  9. A Highly Efficient Function Optimization with Genetic Programming

    Microsoft Academic Search

    Joao C. F. Pujol; Riccardo Poli

    2004-01-01

    This paper describes a new approach for function optimization that uses a novel representation for the parameters to be optimized. By using genetic programming using, the new method evolves functions that transform initial random values for the parameters into optimal ones. Moreover, the new approach addresses the scalability problem by using a representation that, in principle, is independent of the

  10. High genome heterozygosity and endemic genetic recombination in the wheat stripe rust fungus

    PubMed Central

    Zheng, Wenming; Huang, Lili; Huang, Jinqun; Wang, Xiaojie; Chen, Xianming; Zhao, Jie; Guo, Jun; Zhuang, Hua; Qiu, Chuangzhao; Liu, Jie; Liu, Huiquan; Huang, Xueling; Pei, Guoliang; Zhan, Gangming; Tang, Chunlei; Cheng, Yulin; Liu, Minjie; Zhang, Jinshan; Zhao, Zhongtao; Zhang, Shijie; Han, Qingmei; Han, Dejun; Zhang, Hongchang; Zhao, Jing; Gao, Xiaoning; Wang, Jianfeng; Ni, Peixiang; Dong, Wei; Yang, Linfeng; Yang, Huanming; Xu, Jin-Rong; Zhang, Gengyun; Kang, Zhensheng

    2013-01-01

    Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most destructive diseases of wheat. Here we report a 110-Mb draft sequence of Pst isolate CY32, obtained using a ‘fosmid-to-fosmid’ strategy, to better understand its race evolution and pathogenesis. The Pst genome is highly heterozygous and contains 25,288 protein-coding genes. Compared with non-obligate fungal pathogens, Pst has a more diverse gene composition and more genes encoding secreted proteins. Re-sequencing analysis indicates significant genetic variation among six isolates collected from different continents. Approximately 35% of SNPs are in the coding sequence regions, and half of them are non-synonymous. High genetic diversity in Pst suggests that sexual reproduction has an important role in the origin of different regional races. Our results show the effectiveness of the ‘fosmid-to-fosmid’ strategy for sequencing dikaryotic genomes and the feasibility of genome analysis to understand race evolution in Pst and other obligate pathogens. PMID:24150273

  11. Sci Show

    NSDL National Science Digital Library

    The Sci Show, an entertaining series of quirky YouTube videos, tackles topics ranging from â??How Do Polarized Sunglasses Workâ?ť to â??Strong Interaction: The Four Fundamental Forces of Physics.â?ť Most episodes are less than five minutes long, but they pack a wallop of handy science info. Anyone short on time but long on big questions will benefit from the series. Episodes will be helpful to teachers and parents looking to spark enthusiasm in young minds. Viewers may want to start with recent episodes like â??Todayâ??s Mass Extinction,â?ť and the â??Worldâ??s First See-Through Animalâ?ť and â??How Do Animals Change Color?â?ť before digging into the archives for gems like â??The Truth About Gingersâ?ť and â??The Science of Lying.â?ť

  12. High genetic diversity among Stenotrophomonas maltophilia strains despite their originating at a single hospital.

    PubMed

    Valdezate, Sylvia; Vindel, Ana; Martín-Dávila, Pilar; Del Saz, Begońa Sánchez; Baquero, Fernando; Cantón, Rafael

    2004-02-01

    The levels of genetic relatedness of 139 Stenotrophomonas maltophilia strains recovered from 105 hospitalized non-cystic fibrosis patients (51% from medical wards, 35% from intensive care units, and 14% from surgical wards) and 7 environmental sources in the same hospital setting during a 4-year period were typed by the pulsed-field gel electrophoresis (PFGE) technique. A total of 99 well-defined distinct XbaI PFGE patterns were identified (Simpson's discrimination index, 0.996). The dendrogram showed a Dice similarity coefficient ranging from 28 to 80%. Two major clusters (I and II), three minor clusters (III, IV, and V), and two independent branches were observed when using a 36% Dice coefficient, indicating a high diversity of genetic relatedness. It is of note that 84% of strains were grouped within two major clonal lineages. No special cluster gathering was found among strains belonging to the same sample type specimen, patients' infection or colonization status, and ward of precedence. Despite this fact, three different clones (A, B, and C) recovered from respiratory samples from six, three, and two patients, respectively, and two clones, D and E, in two bacteremic patients each, were identified. Isolation of an S. maltophilia strain belonging to the clone A profile in a bronchoscope demonstrated a common source from this clone. This study revealed a high genetic diversity of S. maltophilia isolates despite their origin from a single hospital, which may be related to the wide environmental distribution of this pathogen. However, few clones could be transmitted among different patients, yielding outbreak situations. PMID:14766838

  13. The genetic architecture of Down syndrome phenotypes revealed by high-resolution analysis

    E-print Network

    Gerstein, Mark

    The genetic architecture of Down syndrome phenotypes revealed by high-resolution analysis of human, CA, and approved May 29, 2009 (received for review December 30, 2008) Down syndrome (DS), or trisomy

  14. Genetic structure in striped skunks (Mephitis mephitis) on the southern high plains of Texas

    USGS Publications Warehouse

    Hansen, L.A.; Mathews, N.E.; Hansen, R.W.; Vander Lee, B. A.; Scott, Lutz R.

    2003-01-01

    Genetic variation within populations reflects population-level social and demographic processes and influences how a population behaves as an evolutionary unit. We examined partitioning of genetic variation in striped skunks (Mephitis mephitis) from the Southern High Plains of Texas during 1994-1995. Sixty-nine male and 35 female skunks were sampled on four 12.8-km2 study plots. Plot centers ranged from 17.6 to 61.6 km apart. We used multi-locus DNA fingerprinting with 2 probes, pV47 and CTTxAGG, to test 3 hypotheses: (1) females are more genetically similar to other females than males are to other males on the same plot (indicating greater female philopatry than male philopatry), (2) genetic similarity is greater within plots than among plots (indicating partitioning of genetic variation in space), and (3) genetic similarity of males decreases as the distance separating males increases (indicating geographic distance affects rates of gene flow). In general, males on a plot had lower average genetic similarity than females. Genetic similarity within plots was not different from genetic similarity among plots for males or for females. Genetic similarity of males did not decrease with increasing distance among plots. The lack of geographical genetic structure in striped skunks suggests at the scale of this study (<60 km) that gene flow of biparentally inherited genes is not distance-mediated. However, the higher similarity values for females than for males on the same plot supports an effect of male-biased dispersal and female philopatry on partitioning of genetic variation between sexes.

  15. Genetic analyses of several Drosophila ananassae-complex species show a low-frequency major gene for parthenogenesis that maps to chromosome 2.

    PubMed

    Matsuda, Muneo; Tobari, Yoshiko N

    2004-04-01

    Parthenogenetic strains of several species have been found in the genus Drosophila. The mode of diploidization in the eggs of females has been found to be post-meiotic nuclear fusion. The genetic basis for this parthenogenesis is not understood but is believed to be under the control of a complex polygenic system. We found parthenogenetic females in an isofemale strain (LAE345) of D. pallidosa-like collected in 1981 at Lae, Papua New Guinea, and established a parthenogenetically reproducing strain. Parthenogenetic strains of D. ananassae and D. pallidosa collected at Taputimu, American Samoa had also been established by Futch (1972). D. ananassae, D. pallidosa and D. pallidosa-like are very closely related species belonging to the ananassae complex of the ananassae species subgroup of the melanogaster species group. Using these three species, we found that more than 80% of females from parthenogenetic strains produced progeny parthenogenetically and that inter-specific hybrid females also produced impaternate progeny. In the present report, we demonstrate that the mode of parthenogenesis of D. ananassae appears to be the post-meiotic nuclear doubling of a single meiotic product, and that a major gene responsible for the parthenogenesis maps to the left arm of the second chromosome of D. ananassae. We also suggest that the genetic basis for parthenogenesis capacity may be identical among the three closely related species. We discuss the function of the gene required for parthenogenesis and its significance for the evolutionary process. PMID:15219153

  16. Dictyostelium discoideum has a highly Q/N-rich proteome and shows an unusual resilience to protein aggregation

    PubMed Central

    Malinovska, Liliana; Palm, Sandra; Gibson, Kimberley; Verbavatz, Jean-Marc; Alberti, Simon

    2015-01-01

    Many protein-misfolding diseases are caused by proteins carrying prion-like domains. These proteins show sequence similarity to yeast prion proteins, which can interconvert between an intrinsically disordered and an aggregated prion state. The natural presence of prions in yeast has provided important insight into disease mechanisms and cellular proteostasis. However, little is known about prions in other organisms, and it is not yet clear whether the findings in yeast can be generalized. Using bioinformatics tools, we show that Dictyostelium discoideum has the highest content of prion-like proteins of all organisms investigated to date, suggesting that its proteome has a high overall aggregation propensity. To study mechanisms regulating these proteins, we analyze the behavior of several well-characterized prion-like proteins, such as an expanded version of human huntingtin exon 1 (Q103) and the prion domain of the yeast prion protein Sup35 (NM), in D. discoideum. We find that these proteins remain soluble and are innocuous to D. discoideum, in contrast to other organisms, where they form cytotoxic cytosolic aggregates. However, when exposed to conditions that compromise molecular chaperones, these proteins aggregate and become cytotoxic. We show that the disaggregase Hsp101, a molecular chaperone of the Hsp100 family, dissolves heat-induced aggregates and promotes thermotolerance. Furthermore, prion-like proteins accumulate in the nucleus, where they are targeted by the ubiquitin–proteasome system. Our data suggest that D. discoideum has undergone specific adaptations that increase the proteostatic capacity of this organism and allow for an efficient regulation of its prion-like proteome. PMID:25941378

  17. Dictyostelium discoideum has a highly Q/N-rich proteome and shows an unusual resilience to protein aggregation.

    PubMed

    Malinovska, Liliana; Palm, Sandra; Gibson, Kimberley; Verbavatz, Jean-Marc; Alberti, Simon

    2015-05-19

    Many protein-misfolding diseases are caused by proteins carrying prion-like domains. These proteins show sequence similarity to yeast prion proteins, which can interconvert between an intrinsically disordered and an aggregated prion state. The natural presence of prions in yeast has provided important insight into disease mechanisms and cellular proteostasis. However, little is known about prions in other organisms, and it is not yet clear whether the findings in yeast can be generalized. Using bioinformatics tools, we show that Dictyostelium discoideum has the highest content of prion-like proteins of all organisms investigated to date, suggesting that its proteome has a high overall aggregation propensity. To study mechanisms regulating these proteins, we analyze the behavior of several well-characterized prion-like proteins, such as an expanded version of human huntingtin exon 1 (Q103) and the prion domain of the yeast prion protein Sup35 (NM), in D. discoideum. We find that these proteins remain soluble and are innocuous to D. discoideum, in contrast to other organisms, where they form cytotoxic cytosolic aggregates. However, when exposed to conditions that compromise molecular chaperones, these proteins aggregate and become cytotoxic. We show that the disaggregase Hsp101, a molecular chaperone of the Hsp100 family, dissolves heat-induced aggregates and promotes thermotolerance. Furthermore, prion-like proteins accumulate in the nucleus, where they are targeted by the ubiquitin-proteasome system. Our data suggest that D. discoideum has undergone specific adaptations that increase the proteostatic capacity of this organism and allow for an efficient regulation of its prion-like proteome. PMID:25941378

  18. Schizophrenics 'show new mutations' -Health News -NHS Choices http://www.nhs.uk/news/2011/08August/Pages/sporadic-genetic-mutation-schizophrenia.aspx[8/9/2011 10:05:12 AM

    E-print Network

    Schizophrenics 'show new mutations' - Health News - NHS Choices http://www.nhs.uk/news/2011) Mental health (125) QA articles (83) Diabetes (80) Swine flu (38) Special reports (2) Share: Save they have `fundamentally transformed' the understanding of the genetics of schizophrenia," BBC News has

  19. Tree Rings Show Recent High Summer-Autumn Precipitation in Northwest Australia Is Unprecedented within the Last Two Centuries

    PubMed Central

    O'Donnell, Alison J.; Cook, Edward R.; Palmer, Jonathan G.; Turney, Chris S. M.; Page, Gerald F. M.; Grierson, Pauline F.

    2015-01-01

    An understanding of past hydroclimatic variability is critical to resolving the significance of recent recorded trends in Australian precipitation and informing climate models. Our aim was to reconstruct past hydroclimatic variability in semi-arid northwest Australia to provide a longer context within which to examine a recent period of unusually high summer-autumn precipitation. We developed a 210-year ring-width chronology from Callitris columellaris, which was highly correlated with summer-autumn (Dec–May) precipitation (r = 0.81; 1910–2011; p < 0.0001) and autumn (Mar–May) self-calibrating Palmer drought severity index (scPDSI, r = 0.73; 1910–2011; p < 0.0001) across semi-arid northwest Australia. A linear regression model was used to reconstruct precipitation and explained 66% of the variance in observed summer-autumn precipitation. Our reconstruction reveals inter-annual to multi-decadal scale variation in hydroclimate of the region during the last 210 years, typically showing periods of below average precipitation extending from one to three decades and periods of above average precipitation, which were often less than a decade. Our results demonstrate that the last two decades (1995–2012) have been unusually wet (average summer-autumn precipitation of 310 mm) compared to the previous two centuries (average summer-autumn precipitation of 229 mm), coinciding with both an anomalously high frequency and intensity of tropical cyclones in northwest Australia and the dominance of the positive phase of the Southern Annular Mode. PMID:26039148

  20. Tree Rings Show Recent High Summer-Autumn Precipitation in Northwest Australia Is Unprecedented within the Last Two Centuries.

    PubMed

    O'Donnell, Alison J; Cook, Edward R; Palmer, Jonathan G; Turney, Chris S M; Page, Gerald F M; Grierson, Pauline F

    2015-01-01

    An understanding of past hydroclimatic variability is critical to resolving the significance of recent recorded trends in Australian precipitation and informing climate models. Our aim was to reconstruct past hydroclimatic variability in semi-arid northwest Australia to provide a longer context within which to examine a recent period of unusually high summer-autumn precipitation. We developed a 210-year ring-width chronology from Callitris columellaris, which was highly correlated with summer-autumn (Dec-May) precipitation (r = 0.81; 1910-2011; p < 0.0001) and autumn (Mar-May) self-calibrating Palmer drought severity index (scPDSI, r = 0.73; 1910-2011; p < 0.0001) across semi-arid northwest Australia. A linear regression model was used to reconstruct precipitation and explained 66% of the variance in observed summer-autumn precipitation. Our reconstruction reveals inter-annual to multi-decadal scale variation in hydroclimate of the region during the last 210 years, typically showing periods of below average precipitation extending from one to three decades and periods of above average precipitation, which were often less than a decade. Our results demonstrate that the last two decades (1995-2012) have been unusually wet (average summer-autumn precipitation of 310 mm) compared to the previous two centuries (average summer-autumn precipitation of 229 mm), coinciding with both an anomalously high frequency and intensity of tropical cyclones in northwest Australia and the dominance of the positive phase of the Southern Annular Mode. PMID:26039148

  1. Essay Contest Reveals Misconceptions of High School Students in Genetics Content

    PubMed Central

    Mills Shaw, Kenna R.; Van Horne, Katie; Zhang, Hubert; Boughman, Joann

    2008-01-01

    National educational organizations have called upon scientists to become involved in K–12 education reform. From sporadic interaction with students to more sustained partnerships with teachers, the engagement of scientists takes many forms. In this case, scientists from the American Society of Human Genetics (ASHG), the Genetics Society of America (GSA), and the National Society of Genetic Counselors (NSGC) have partnered to organize an essay contest for high school students as part of the activities surrounding National DNA Day. We describe a systematic analysis of 500 of 2443 total essays submitted in response to this contest over 2 years. Our analysis reveals the nature of student misconceptions in genetics, the possible sources of these misconceptions, and potential ways to galvanize genetics education. PMID:18245328

  2. Migration and dispersal may drive to high genetic variation and significant genetic mixing: the case of two agriculturally important, continental hoverflies (Episyrphus balteatus and Sphaerophoria scripta).

    PubMed

    Raymond, Lucie; Plantegenest, Manuel; Vialatte, Aude

    2013-11-01

    Population structure of pests and beneficial species is an important issue when designing management strategies to optimize ecosystem services. In this study, we investigated for the first time the population structure at a continental scale of two migratory species of hoverflies providing both pest regulation and pollination services [Episyrphus balteatus and Sphaerophoria scripta (Diptera: Syrphidae)]. To achieve this objective, we used two sets of 12 species-specific microsatellite markers on a large-scale sampling from all over Europe. Our findings showed a high level of genetic mixing resulting in a lack of genetic differentiation at a continental scale and a great genetic diversity in the two species. All the pairwise FST values between European localities were less 0.05 in the two species. These low values reflect a large-scale genetic mixing probably caused by the existence of frequent migratory movements in the two species. Mantel tests revealed isolation-by-distance pattern on the East-West axis, but not on the North-South axis. This isolation-by-distance pattern confirms the existence of North-South migratory movements in both directions and suggests an important step by step dispersal. Population features shown by this study are common in invasive species and pests, but are not often observed in beneficial species. They reflect great colonization abilities and a high adaptive potential when dealing with a changing environment. Our results highlight the two studied species as particularly interesting beneficial insects for pollination and pest predation in the current context of global change. PMID:24138027

  3. Genetics

    NSDL National Science Digital Library

    The Tech Museum of Innovation

    2004-01-01

    This online tutorial from the TheTech Museum of Innovation focuses on genetics. The interactive topics will initially introduce the user to the DNA, chromosomes, and the make up of human genes. Further topics will examine forensic science, the history of forensics, fingerprinting, and cloning background research and community response to cloning. Finally, the resource provides connections to gallery exhibits, science labs, and a design challenge that engages the learner to write a persuasive letter to a group or organization responsible for cloning or DNA decision making. Copyright 2005 International Technology Education Association

  4. Genetic variation and recombination of RdRp and HSP 70h genes of Citrus tristeza virus isolates from orange trees showing symptoms of citrus sudden death disease

    PubMed Central

    Gomes, Clarissa PC; Nagata, Tatsuya; de Jesus, Waldir C; Neto, Carlos R Borges; Pappas, Georgios J; Martin, Darren P

    2008-01-01

    Background Citrus sudden death (CSD), a disease that rapidly kills orange trees, is an emerging threat to the Brazilian citrus industry. Although the causal agent of CSD has not been definitively determined, based on the disease's distribution and symptomatology it is suspected that the agent may be a new strain of Citrus tristeza virus (CTV). CTV genetic variation was therefore assessed in two Brazilian orange trees displaying CSD symptoms and a third with more conventional CTV symptoms. Results A total of 286 RNA-dependent-RNA polymerase (RdRp) and 284 heat shock protein 70 homolog (HSP70h) gene fragments were determined for CTV variants infecting the three trees. It was discovered that, despite differences in symptomatology, the trees were all apparently coinfected with similar populations of divergent CTV variants. While mixed CTV infections are common, the genetic distance between the most divergent population members observed (24.1% for RdRp and 11.0% for HSP70h) was far greater than that in previously described mixed infections. Recombinants of five distinct RdRp lineages and three distinct HSP70h lineages were easily detectable but respectively accounted for only 5.9 and 11.9% of the RdRp and HSP70h gene fragments analysed and there was no evidence of an association between particular recombinant mosaics and CSD. Also, comparisons of CTV population structures indicated that the two most similar CTV populations were those of one of the trees with CSD and the tree without CSD. Conclusion We suggest that if CTV is the causal agent of CSD, it is most likely a subtle feature of population structures within mixed infections and not merely the presence (or absence) of a single CTV variant within these populations that triggers the disease. PMID:18199320

  5. Genetic score based on high-risk genetic polymorphisms and early onset of ischemic heart disease in an Italian cohort of ischemic patients.

    PubMed

    Vecoli, Cecilia; Adlerstein, Daniel; Shehi, Erlet; Bigazzi, Federico; Sampietro, Tiziana; Foffa, Ilenia; Carpeggiani, Clara; L'abbate, Antonio; Andreassi, Maria Grazia

    2014-05-01

    Several single-nucleotide polymorphisms (SNPs) have been recognized as associated with ischemic heart disease (IHD) although the optimal set of risk genotypes has not be identified. This study aimed to examine whether identified high-risk SNPs are associated with early onset of IHD. In the GENOCOR study, 44 high-risk SNPs were genotyped in 114 patients with early onset of IHD (46.2 ± 5.1 years) and 384 patients with late onset of IHD (60.7 ± 5.9 years). The associations between individual SNPs and early onset IHD were assessed. A multilocus genetic risk score (GRS) for each associated risk genetic markers was constructed by summing the number of risk alleles. The SNPs significantly associated with IHD were: -482C>T of Apolipoprotein C III gene (ApoC3, p=0.02); 1171 5A>6A of Matrix metalloproteinase 3 stromelisine I gene (p=0.01); G98T of Selectin E gene (p=0.05); C/G of 9p21.3 locus (p=0.01). Likelihood ratio test showed a strong interaction for increasing risk of early IHD between the presence of ApoC3 and 9p21.3 locus with hypertriglyceridemia (p=0.0008, 0.0011) as well as between 9p21.3 locus and smoking (p=0.0010) after correction for multiple testing. The OR for premature IHD for GRS unit was 1.3 (95% CI 1.1-1.6, p=0.001). Patients in the top tertile of GRS were estimated to have a 3.2-fold (95% CI 1.5-6.8; p=0.001) increased risk of early IHD compared with those in the bottom tertile. The results show that currently identified high-risk SNPs confer an additive biomarker for cardiovascular events. GRS may provide important incremental information on the genetic component of IHD. PMID:24656450

  6. Genetic Structure Is Associated with Phenotypic Divergence in Floral Traits and Reproductive Investment in a High-Altitude Orchid from the Iron Quadrangle, Southeastern Brazil

    PubMed Central

    Leles, Bruno; Chaves, Anderson V.; Russo, Philip; Batista, Joăo A. N.; Lovato, Maria Bernadete

    2015-01-01

    Knowledge of the role of Neotropical montane landscapes in shaping genetic connectivity and local adaptation is essential for understanding the evolutionary processes that have shaped the extraordinary species diversity in these regions. In the present study, we examined the landscape genetics, estimated genetic diversity, and explored genetic relationships with morphological variability and reproductive strategies in seven natural populations of Cattleya liliputana (Orchidaceae). Nuclear microsatellite markers were used for genetic analyses. Spatial Bayesian clustering and population-based analyses revealed significant genetic structuring and high genetic diversity (He = 0.733 ± 0.03). Strong differentiation was found between populations over short spatial scales (FST = 0.138, p < 0.001), reflecting the landscape discontinuity and isolation. Monmonier´s maximum difference algorithm, Bayesian analysis on STRUCTURE and principal component analysis identified one major genetic discontinuity between populations. Divergent genetic groups showed phenotypic divergence in flower traits and reproductive strategies. Increased sexual reproductive effort was associated with rock outcrop type and may be a response to adverse conditions for growth and vegetative reproduction. Here we discuss the effect of restricted gene flow, local adaptation and phenotypic plasticity as drivers of population differentiation in Neotropical montane rock outcrops. PMID:25756994

  7. Efficient photoinduced charge accumulation in reduced graphene oxide coupled with titania nanosheets to show highly enhanced and persistent conductance.

    PubMed

    Cai, Xingke; Sakai, Nobuyuki; Ozawa, Tadashi C; Funatsu, Asami; Ma, Renzhi; Ebina, Yasuo; Sasaki, Takayoshi

    2015-06-01

    Tuning of the electrical properties of graphene via photoexcitation of a heteroassembled material has started to attract attention for electronic and optoelectronic applications. Actually photoinduced carrier doping from the hexagonal boron nitride (h-BN) substrate greatly modulated the transport property of the top layer graphene, showing promising potential for this approach. However, for practical applications, the large scale production of this two-dimensional heterostructure is needed. Here, a superlattice film constructed from reduced graphene oxide (rGO) and photoactive titania nanosheets (Ti0.87O2(0.52-)) was employed as a channel to construct a field effect transistor (FET) device, and its UV light response on the electrical transport property was examined. The UV light illumination induced significant improvement of the electrical conductance by ?7 times on the basis of simultaneous enhancements of the electron carrier concentration and its mobility in rGO. Furthermore, the polarity of the FET response changed from ambipolar to n-type unipolar. Such modulated properties persisted in vacuum even after the UV light was turned off. These interesting behaviors may be explained in terms of photomodulation effects from Ti0.87O2(0.52-) nanosheets. The photoexcited electrons in Ti0.87O2(0.52-) are injected into rGO to increase the electron carrier concentration as high as 7.6 × 10(13) cm(-2). On the other hand, the holes are likely trapped in the Ti0.87O2(0.52-) nanosheets. These photocarriers undergo reduction and oxidation of oxygen and water molecules adsorbed in the film, respectively, which act as carrier scattering centers, contributing to the enhancement of the carrier mobility. Since the film likely contains more water molecules than oxygen, upon extinction of UV light, a major portion of electrons (?80% of the concentration at the UV off) survives in rGO, showing the highly enhanced conductance for days. This surpassing photomodulated FET response and its persistency observed in the present superlattice system of rGO/Ti0.87O2(0.52-) are noteworthy compared with previous studies such as the device with a heteroassembly of graphene/h-BN. PMID:25945510

  8. Genetic analysis of axial length genes in high grade myopia from Indian population?

    PubMed Central

    Sharmila, Ferdinamarie; Abinayapriya; Ramprabhu, Karthikeyan; Kumaramanickavel, Govindasamy; R.R.Sudhir; Sripriya, Sarangapani

    2014-01-01

    Purpose To study the putative association of Membrane frizzled related protein (MFRP) and Visual system homeobox protein (VSX2) gene variants with axial length (AL) in myopia. Method A total of 189 samples with (N = 98) and without (N = 91) myopia were genotyped for the MRFP and VSX2 variations in ABI Prism 3100 AVANT genetic analyzer. Genotype/haplotype analysis was performed using PLINK, Haploview and THESIAS softwares. Results Fifteen variations were observed in the MFRP gene of which, rs36015759 (c.492C > T, T164T) in exon 5 was distributed at a high frequency in the controls and significantly associated with a low risk for myopia (P = 4.10 ? e? 07 OR < 1.0). An increased frequency for the coding haplotype block [CGTCGG] harboring rs36015759 was observed in controls (31%) than cases (8%) that also correlated with a decreased mean AL (? 1.35085; P = 0.000444) by THESIAS analysis. The ‘T’ allele of rs36015759 was predicted to abolish the binding site for splicing enhancer (SRp40) by FASTSNP analysis. Conclusion Myopia is a complex disorder influenced by genetic and environmental factors. Our work shows evidence of association of a specific MFRP haplotype which was more prevalent in controls with decreased AL. However, replication and functional studies are warranted to confirm these findings. PMID:25606400

  9. Construction of a high-density high-resolution genetic map and its integration with BAC-based physical map in channel catfish

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Construction of genetic linkage map is essential for genetic and genomic studies. Recent advances in sequencing and genotyping technologies made it possible to generate high-density and high-resolution genetic linkage maps, especially for the organisms lacking extensive genomic resources. In the pre...

  10. Genealogical surveys show a high rate of non-paternal surname transmission with regional differences in Argentina.

    PubMed

    Muzzio, M; Motti, J M B; Chiarullo, S M; Bravi, C M; Bailliet, G

    2012-02-01

    Surnames are a vertically transmitted cultural trait that in Argentina follows the paternal line of descent when the paternity is known. There was a lack of empirical information regarding non-paternal surname transmissions among the general population, so we performed 2,550 genealogical interviews, which included 6,954 surname passes, in different regions of this country. We compared the proportion of non-paternal transmissions between the propositus and parental generation and found no significant difference between them (p<0.01). Inter-population comparisons allowed us to describe 4 regional groups. We also drew models and simulations to estimate how many generations it would take to find that only half of the population maintained the paternal transmission. The lowest proportion of non-paternal transmission was 7.3%, estimating 9 generations (between 225 and 315 years) to find that, at most, half its population keeps following the paternal transmission; the highest proportion was 23%, taking 3 generations (75-105 years). Our results show a high proportion of unrecognized paternities among the general population, a very quick loss of association between male lineages and surnames, and regional proportions with significant differences between each other. PMID:22305123

  11. Construction of High-Density Genetic Map in Barley through Restriction-Site Associated DNA Sequencing

    PubMed Central

    Zhou, Gaofeng; Zhang, Qisen; Zhang, Xiao-qi; Tan, Cong; Li, Chengdao

    2015-01-01

    Genetic maps in barley are usually constructed from a limited number of molecular markers such as SSR (simple sequence repeat) and DarT (diversity arrays technology). These markers must be first developed before being used for genotyping. Here, we introduce a new strategy based on sequencing progeny of a doubled haploid population from Baudin × AC Metcalfe to construct a genetic map in barley. About 13,547 polymorphic SNP tags with >93% calling rate were selected to construct the genetic map. A total of 12,998 SNP tags were anchored to seven linkage groups which spanned a cumulative 967.6 cM genetic distance. The high-density genetic map can be used for QTL mapping and the assembly of WGS and BAC contigs. The genetic map was evaluated for its effectiveness and efficiency in QTL mapping and candidate gene identification. A major QTL for plant height was mapped at 105.5 cM on chromosome 3H. This QTL with LOD value of 13.01 explained 44.5% of phenotypic variation. This strategy will enable rapid and efficient establishment of high-density genetic maps in other species. PMID:26182149

  12. Genetic algorithms

    NASA Technical Reports Server (NTRS)

    Wang, Lui; Bayer, Steven E.

    1991-01-01

    Genetic algorithms are mathematical, highly parallel, adaptive search procedures (i.e., problem solving methods) based loosely on the processes of natural genetics and Darwinian survival of the fittest. Basic genetic algorithms concepts are introduced, genetic algorithm applications are introduced, and results are presented from a project to develop a software tool that will enable the widespread use of genetic algorithm technology.

  13. High Genetic Diversity and Novelty in Eukaryotic Plankton Assemblages Inhabiting Saline Lakes in the Qaidam Basin

    PubMed Central

    Wang, Jiali; Wang, Fang; Chu, Limin; Wang, Hao; Zhong, Zhiping; Liu, Zhipei; Gao, Jianyong; Duan, Hairong

    2014-01-01

    Saline lakes are intriguing ecosystems harboring extremely productive microbial communities in spite of their extreme environmental conditions. We performed a comprehensive analysis of the genetic diversity (18S rRNA gene) of the planktonic microbial eukaryotes (nano- and picoeukaryotes) in six different inland saline lakes located in the Qaidam Basin. The novelty level are high, with about 11.23% of the whole dataset showing <90% identity to any previously reported sequence in GenBank. At least 4 operational taxonomic units (OTUs) in mesosaline lakes, while up to eighteen OTUs in hypersaline lakes show very low CCM and CEM scores, indicating that these sequences are highly distantly related to any existing sequence. Most of the 18S rRNA gene sequence reads obtained in investigated mesosaline lakes is closely related to Holozoa group (48.13%), whereas Stramenopiles (26.65%) and Alveolates (10.84%) are the next most common groups. Hypersaline lakes in the Qaidam Basin are also dominated by Holozoa group, accounting for 26.65% of the total number of sequence reads. Notably, Chlorophyta group are only found in high abundance in Lake Gasikule (28.00%), whereas less represented in other hypersaline lakes such as Gahai (0.50%) and Xiaochaidan (1.15%). Further analysis show that the compositions of planktonic eukaryotic assemblages are also most variable between different sampling sites in the same lake. Out of the parameters, four show significant correlation to this CCA: altitude, calcium, sodium and potassium concentrations. Overall, this study shows important gaps in the current knowledge about planktonic microbial eukaryotes inhabiting Qaidam Basin (hyper) saline water bodies. The identified diversity and novelty patterns among eukaryotic plankton assemblages in saline lake are of great importance for understanding and interpreting their ecology and evolution. PMID:25401703

  14. High genetic diversity and novelty in eukaryotic plankton assemblages inhabiting saline lakes in the Qaidam basin.

    PubMed

    Wang, Jiali; Wang, Fang; Chu, Limin; Wang, Hao; Zhong, Zhiping; Liu, Zhipei; Gao, Jianyong; Duan, Hairong

    2014-01-01

    Saline lakes are intriguing ecosystems harboring extremely productive microbial communities in spite of their extreme environmental conditions. We performed a comprehensive analysis of the genetic diversity (18S rRNA gene) of the planktonic microbial eukaryotes (nano- and picoeukaryotes) in six different inland saline lakes located in the Qaidam Basin. The novelty level are high, with about 11.23% of the whole dataset showing <90% identity to any previously reported sequence in GenBank. At least 4 operational taxonomic units (OTUs) in mesosaline lakes, while up to eighteen OTUs in hypersaline lakes show very low CCM and CEM scores, indicating that these sequences are highly distantly related to any existing sequence. Most of the 18S rRNA gene sequence reads obtained in investigated mesosaline lakes is closely related to Holozoa group (48.13%), whereas Stramenopiles (26.65%) and Alveolates (10.84%) are the next most common groups. Hypersaline lakes in the Qaidam Basin are also dominated by Holozoa group, accounting for 26.65% of the total number of sequence reads. Notably, Chlorophyta group are only found in high abundance in Lake Gasikule (28.00%), whereas less represented in other hypersaline lakes such as Gahai (0.50%) and Xiaochaidan (1.15%). Further analysis show that the compositions of planktonic eukaryotic assemblages are also most variable between different sampling sites in the same lake. Out of the parameters, four show significant correlation to this CCA: altitude, calcium, sodium and potassium concentrations. Overall, this study shows important gaps in the current knowledge about planktonic microbial eukaryotes inhabiting Qaidam Basin (hyper) saline water bodies. The identified diversity and novelty patterns among eukaryotic plankton assemblages in saline lake are of great importance for understanding and interpreting their ecology and evolution. PMID:25401703

  15. Genetic variants on chromosome 1q41 influence ocular axial length and high myopia.

    PubMed

    Fan, Qiao; Barathi, Veluchamy A; Cheng, Ching-Yu; Zhou, Xin; Meguro, Akira; Nakata, Isao; Khor, Chiea-Chuen; Goh, Liang-Kee; Li, Yi-Ju; Lim, Wan'e; Ho, Candice E H; Hawthorne, Felicia; Zheng, Yingfeng; Chua, Daniel; Inoko, Hidetoshi; Yamashiro, Kenji; Ohno-Matsui, Kyoko; Matsuo, Keitaro; Matsuda, Fumihiko; Vithana, Eranga; Seielstad, Mark; Mizuki, Nobuhisa; Beuerman, Roger W; Tai, E-Shyong; Yoshimura, Nagahisa; Aung, Tin; Young, Terri L; Wong, Tien-Yin; Teo, Yik-Ying; Saw, Seang-Mei

    2012-01-01

    As one of the leading causes of visual impairment and blindness, myopia poses a significant public health burden in Asia. The primary determinant of myopia is an elongated ocular axial length (AL). Here we report a meta-analysis of three genome-wide association studies on AL conducted in 1,860 Chinese adults, 929 Chinese children, and 2,155 Malay adults. We identified a genetic locus on chromosome 1q41 harboring the zinc-finger 11B pseudogene ZC3H11B showing genome-wide significant association with AL variation (rs4373767, ??=?-0.16 mm per minor allele, P(meta)?=2.69 × 10(-10)). The minor C allele of rs4373767 was also observed to significantly associate with decreased susceptibility to high myopia (per-allele odds ratio (OR)?=0.75, 95% CI: 0.68-0.84, P(meta)?=4.38 × 10(-7)) in 1,118 highly myopic cases and 5,433 controls. ZC3H11B and two neighboring genes SLC30A10 and LYPLAL1 were expressed in the human neural retina, retinal pigment epithelium, and sclera. In an experimental myopia mouse model, we observed significant alterations to gene and protein expression in the retina and sclera of the unilateral induced myopic eyes for the murine genes ZC3H11A, SLC30A10, and LYPLAL1. This supports the likely role of genetic variants at chromosome 1q41 in influencing AL variation and high myopia. PMID:22685421

  16. A Transition Zone Showing Highly Discontinuous or Alternating Levels of Stem Cell and Proliferation Markers Characterizes the Development of PTEN-Haploinsufficient Colorectal Cancer

    PubMed Central

    Arvai, Kevin J.; Hsu, Ya-Hsuan; Lee, Lobin A.; Jones, Dan

    2015-01-01

    Background Stepwise acquisition of oncogene mutations and deletion/inactivation of tumor suppressor genes characterize the development of colorectal cancer (CRC). These genetic events interact with discrete morphologic transitions from hyperplastic mucosa to adenomatous areas, followed by in situ malignant transformation and finally invasive carcinoma. The goal of this study was to identify tissue markers of the adenoma-carcinoma morphogenetic transitions in CRC. Methods and Findings We analyzed the patterns of expression of growth regulatory and stem cell markers across these distinct morphologic transition zones in 735 primary CRC tumors. In 202 cases with preserved adenoma-adenocarcinoma transition, we identified, in 37.1% of cases, a zone of adenomatous epithelium, located immediately adjacent to the invasive component, that showed rapidly alternating intraglandular stretches of PTEN+ and PTEN- epithelium. This zone exactly overlapped with similar alternating expression of Ki-67 and inversely with the transforming growth factor-beta (TGF-?) growth regulator SMAD4. These zones also show parallel alternating levels and/or subcellular localization of multiple cancer stem/progenitor cell (CSC) markers, including ?-catenin/CTNNB1, ALDH1, and CD44. PTEN was always re-expressed in the invasive tumor in these cases, unlike those with complete loss of PTEN expression. Genomic microarray analysis of CRC with prominent CSC-like expansions demonstrated a high frequency of PTEN genomic deletion/haploinsufficiency in tumors with CSC-like transition zones (62.5%) but not in tumors with downregulated but non-alternating PTEN expression (14.3%). There were no significant differences in the levels of KRAS mutation or CTNNB1 mutation in CSC-like tumors as compared to unselected CRC cases. Conclusions In conclusion, we have identified a distinctive CSC-like pre-invasive transition zone in PTEN-haploinsufficient CRC that shows convergent on-off regulation of the PTEN/AKT, TGF-?/SMAD and Wnt/?-catenin pathways. This bottleneck-like zone is usually followed by the emergence of invasive tumors with intact PTEN expression but dysregulated TP53 and uniformly high proliferation rates. PMID:26098881

  17. Genetic algorithms: the philosopher's stone or an effective solution for high-level TPG?

    Microsoft Academic Search

    Alessandro Fin; Franco Fummi

    2003-01-01

    The paper examines the potentialities of genetic algorithms (GAs) with respect to the development of high-level TPGs. It summarizes at first the most relevant test pattern generation techniques based on genetic algorithms (GAs). This analysis distinguishes the considered techniques with respect to the abstraction level of the design under test. In particular, the effectiveness of gate-level GA-based TPGs is compared

  18. RAPD and ISSR markers indicate high genetic variation within Lobathallia radiosa in Turkey

    Microsoft Academic Search

    Ertu?rul Yüzba??o?lu; Mehmet Gökhan Hal?c?; Muhammer Karabacak; Ahmet Aksoy

    2011-01-01

    Randomly amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR) methods were used for investigating genetic\\u000a variation within L. radiosa and for delimiting species within the genus Lobothallia. Ten RAPD and 11 ISSR primers produced a total of 261 and 260 reproducible bands, respectively, and all of which were polymorphic\\u000a for the two markers, suggesting high genetic variability within

  19. Population structure and genetic diversity of black redhorse (Moxostoma duquesnei) in a highly fragmented watershed

    USGS Publications Warehouse

    Reid, S.M.; Wilson, C.C.; Mandrak, N.E.; Carl, L.M.

    2008-01-01

    Dams have the potential to affect population size and connectivity, reduce genetic diversity, and increase genetic differences among isolated riverine fish populations. Previous research has reported adverse effects on the distribution and demographics of black redhorse (Moxostoma duquesnei), a threatened fish species in Canada. However, effects on genetic diversity and population structure are unknown. We used microsatellite DNA markers to assess the number of genetic populations in the Grand River (Ontario) and to test whether dams have resulted in a loss of genetic diversity and increased genetic differentiation among populations. Three hundred and seventy-seven individuals from eight Grand River sites were genotyped at eight microsatellite loci. Measures of genetic diversity were moderately high and not significantly different among populations; strong evidence of recent population bottlenecks was not detected. Pairwise FST and exact tests identified weak (global FST = 0.011) but statistically significant population structure, although little population structuring was detected using either genetic distances or an individual-based clustering method. Neither geographic distance nor the number of intervening dams were correlated with pairwise differences among populations. Tests for regional equilibrium indicate that Grand River populations were either in equilibrium between gene flow and genetic drift or that gene flow is more influential than drift. While studies on other species have identified strong dam-related effects on genetic diversity and population structure, this study suggests that barrier permeability, river fragment length and the ecological characteristics of affected species can counterbalance dam-related effects. ?? 2007 Springer Science+Business Media B.V.

  20. A High-Throughput Arabidopsis Reverse Genetics System

    PubMed Central

    Sessions, Allen; Burke, Ellen; Presting, Gernot; Aux, George; McElver, John; Patton, David; Dietrich, Bob; Ho, Patrick; Bacwaden, Johana; Ko, Cynthia; Clarke, Joseph D.; Cotton, David; Bullis, David; Snell, Jennifer; Miguel, Trini; Hutchison, Don; Kimmerly, Bill; Mitzel, Theresa; Katagiri, Fumiaki; Glazebrook, Jane; Law, Marc; Goff, Stephen A.

    2002-01-01

    A collection of Arabidopsis lines with T-DNA insertions in known sites was generated to increase the efficiency of functional genomics. A high-throughput modified thermal asymetric interlaced (TAIL)-PCR protocol was developed and used to amplify DNA fragments flanking the T-DNA left borders from ?100,000 transformed lines. A total of 85,108 TAIL-PCR products from 52,964 T-DNA lines were sequenced and compared with the Arabidopsis genome to determine the positions of T-DNAs in each line. Predicted T-DNA insertion sites, when mapped, showed a bias against predicted coding sequences. Predicted insertion mutations in genes of interest can be identified using Arabidopsis Gene Index name searches or by BLAST (Basic Local Alignment Search Tool) search. Insertions can be confirmed by simple PCR assays on individual lines. Predicted insertions were confirmed in 257 of 340 lines tested (76%). This resource has been named SAIL (Syngenta Arabidopsis Insertion Library) and is available to the scientific community at www.tmri.org. PMID:12468722

  1. Informed consent form challenges for genetic research in a developing Arab country with high risk for genetic disease.

    PubMed

    Nair, Satish Chandrasekhar; Ibrahim, Halah

    2015-04-01

    The prevalence of genetic disease is high in the Middle East, particularly in the United Arab Emirates. Our study assesses the information provided in, and the readability ease of, informed consent forms (ICF) for genetic research studies. A multicenter retrospective cross-sectional review of 54 ICFs was conducted to assess compliance by comparing them with standard good clinical practice guidelines for developing consent forms. Readability of the forms was determined using the Flesch-Kincaid scale. Overall Good Clinical Practice compliance for the ICFs averaged at 63 %. Information regarding privacy, confidentiality, specimen collection and storage were absent from the majority of the ICFs. Readability ease score was low (36.7?±?4.6) and required college-level (11.8?±?1.4) reading skills to understand the information. Our study highlights the need to improve the readability and information contained in the ICFs for genetic research studies in our setting. Our findings may be generalized to similar cultures in the Middle East and Asia. PMID:25228356

  2. High-throughput Genetic Screen for Synaptogenic Factors: Identification of LRP6 as Critical for Excitatory Synapse Development

    PubMed Central

    Sharma, Kamal; Choi, Se-Young; Zhang, Yong; Nieland, Thomas J.F.; Long, Shunyou; Li, Min; Huganir, Richard

    2014-01-01

    SUMMARY Genetic screens in invertebrates have discovered many synaptogenic genes and pathways. However, similar genetic studies have not been possible in mammals. We have optimized an automated high-throughput platform that employs automated liquid handling and imaging of primary mammalian neurons. Using this platform we have screened 3200 shRNAs targeting 800 proteins. One of the hits identified was LRP6, a co-receptor for canonical Wnt ligands. LRP6 regulates excitatory synaptogenesis, and is selectively localized to excitatory synapses. In vivo knockdown of LRP6 leads to a reduction in the number of functional synapses. Moreover, we show that the canonical Wnt ligand, Wnt8A, promotes synaptogenesis via LRP6. These results provide a proof of principle for using a high content approach to screen for synaptogenic factors in the mammalian nervous system, and identify and characterize a Wnt ligand receptor complex that is critical for development of functional synapses in vivo. PMID:24316074

  3. Population genetic structure of Carchesium polypinum (Ciliophora: Peritrichia) in four Chinese lakes inferred from ISSR fingerprinting: high diversity but low differentiation.

    PubMed

    Zhang, Wen-Jing; Yang, Jun; Yu, Yu-He; Shu, Shao-Wu; Shen, Yun-Fen

    2006-01-01

    Although the peritrichous ciliate Carchesium polypinum is common in freshwater, its population genetic structure is largely unknown. We used inter-simple sequence repeat (ISSR) fingerprinting to analyze the genetic structure of 48 different isolates of the species from four lakes in Wuhan, central China. Using eight polymorphic primers, 81 discernible DNA fragments were detected, among which 76 (93.83%) were polymorphic, indicating high genetic diversity at the isolate level. Further, Nei's gene diversity (h) and Shannon's Information index (I) between the different isolates both revealed a remarkable genetic diversity, higher than previously indicated by their morphology. At the same time, substantial gene flow was found. So the main factors responsible for the high level of diversity within populations are probably due to conjugation (sexual reproduction) and wide distribution of swarmers. Analysis of molecular variance (AMOVA) showed that there was low genetic differentiation among the four populations probably due to common ancestry and flooding events. The cluster analysis and principal component analysis (PCA) suggested that genotypes isolated from the same lake displayed a higher genetic similarity than those from different lakes. Both analyses separated C. polypinum isolates into subgroups according to the geographical locations. However, there is only a weak positive correlation between the genetic distance and geographical distance, suggesting a minor effect of geographical distance on the distribution of genetic diversity between populations of C. polypinum at the local level. In conclusion, our studies clearly demonstrated that a single morphospecies may harbor high levels of genetic diversity, and that the degree of resolution offered by morphology as a marker for measuring distribution patterns of genetically distinct entities is too low. PMID:16968453

  4. High local genetic diversity of canine parvovirus from Ecuador.

    PubMed

    Aldaz, Jaime; García-Díaz, Juan; Calleros, Lucía; Sosa, Katia; Iraola, Gregorio; Marandino, Ana; Hernández, Martín; Panzera, Yanina; Pérez, Ruben

    2013-09-27

    Canine parvovirus (CPV) comprises three antigenic variants (2a, 2b, and 2c) that are distributed globally with different frequencies and levels of genetic variability. CPVs from central Ecuador were herein analyzed to characterize the strains and to provide new insights into local viral diversity, evolution, and pathogenicity. Variant prevalence was analyzed by PCR and partial sequencing for 53 CPV-positive samples collected during 2011 and 2012. The full-length VP2 gene was sequenced in 24 selected strains and a maximum-likelihood phylogenetic tree was constructed using both Ecuadorian and worldwide strains. Ecuadorian CPVs have a remarkable genetic diversity that includes the circulation of all three variants and the existence of different evolutionary groups or lineages. CPV-2c was the most prevalent variant (54.7%), confirming the spread of this variant in America. Ecuadorian CPV-2c strains clustered in two lineages, which represent the first evidence of polyphyletic CPV-2c circulating in South America. CPV-2a strains constituted 41.5% of the samples and clustered in a single lineage. The two detected CPV-2b strains (3.8%) were clearly polyphyletic and appeared related to Ecuadorian CPV-2a or foreign CPV-2b strains. Besides the substitution at residue 426 that is used to identify the variants, two amino acid changes occurred in Ecuadorian strains: Val139Iso and Thr440Ser. Ser(440) occurred in a biologically relevant domain of VP2 and is here described for the first time in CPV. The associations of Ecuadorian CPV-2c and CPV-2a with clinical symptoms indicate that dull mentation, hemorrhagic gastroenteritis and hypothermia occurred more frequently in infection with CPV-2c than with CPV-2a. PMID:23850438

  5. Fine-scale genetic structure and clinal variation in silene acaulis despite high gene flow

    PubMed

    Gehring; Delph

    1999-06-01

    We investigated whether the distribution of genes reflects the patchy distribution of individuals of Silene acaulis on Pennsylvania Mountain in central Colorado. Five polymorphic protein loci were analysed using both F-statistics and spatial autocorrelation. Low thetaPOP (FST) indicated little genetic differentiation between populations approximately 1 km apart. This indicates high gene flow within our study site, perhaps as a result of long-distance pollen dispersal. Despite little differentiation between populations, there was clinal variation at the 6-Pgd-1 locus and significant within-population genetic structure (indicated by both thetaPATCH and spatial autocorrelation). We infer that this fine-scale genetic structure is the result of limited seed dispersal combined with genetic drift. The level of genetic structure varied markedly among populations, with the greatest genetic structure (highest Moran's I and thetaPATCH values) in two low-altitude, small, low-density populations. Intensive sampling such as used in this study may reveal similar patterns of fine-scale genetic differentiation in other patchily distributed plant species, particularly those with limited seed dispersal. PMID:10383684

  6. Combined analyses of kinship and FST suggest potential drivers of chaotic genetic patchiness in high gene-flow populations

    PubMed Central

    Iacchei, Matthew; Ben-Horin, Tal; Selkoe, Kimberly A; Bird, Christopher E; García-Rodríguez, Francisco J; Toonen, Robert J

    2013-01-01

    We combine kinship estimates with traditional F-statistics to explain contemporary drivers of population genetic differentiation despite high gene flow. We investigate range-wide population genetic structure of the California spiny (or red rock) lobster (Panulirus interruptus) and find slight, but significant global population differentiation in mtDNA (?ST = 0.006, P = 0.001; Dest_Chao = 0.025) and seven nuclear microsatellites (FST = 0.004, P < 0.001; Dest_Chao = 0.03), despite the species’ 240- to 330-day pelagic larval duration. Significant population structure does not correlate with distance between sampling locations, and pairwise FST between adjacent sites often exceeds that among geographically distant locations. This result would typically be interpreted as unexplainable, chaotic genetic patchiness. However, kinship levels differ significantly among sites (pseudo-F16,988 = 1.39, P = 0.001), and ten of 17 sample sites have significantly greater numbers of kin than expected by chance (P < 0.05). Moreover, a higher proportion of kin within sites strongly correlates with greater genetic differentiation among sites (Dest_Chao, R2 = 0.66, P < 0.005). Sites with elevated mean kinship were geographically proximate to regions of high upwelling intensity (R2 = 0.41, P = 0.0009). These results indicate that P. interruptus does not maintain a single homogenous population, despite extreme dispersal potential. Instead, these lobsters appear to either have substantial localized recruitment or maintain planktonic larval cohesiveness whereby siblings more likely settle together than disperse across sites. More broadly, our results contribute to a growing number of studies showing that low FST and high family structure across populations can coexist, illuminating the foundations of cryptic genetic patterns and the nature of marine dispersal. PMID:23802550

  7. High Genetic Diversity vs. Low Genetic Differentiation in Nouelia insignis (Asteraceae), a Narrowly Distributed and Endemic Species in China, Revealed by ISSR Fingerprinting

    PubMed Central

    LUAN, SHANSHAN; CHIANG, TZEN-YUH; GONG, XUN

    2006-01-01

    • Background and Aims Nouelia insignis Franch., a monotypic genus of the Asteraceae, is an endangered species endemic in Yunnan and Sichuan Provinces of China. Most of the populations are seriously threatened. Some of them are even at the brink of extinction. In this study, the genetic diversity and differentiation between populations of this species were examined in two drainage areas. • Methods DNA fingerprinting based on inter-simple sequence repeat polymorphisms was employed to detect the genetic variation and population structure in the species. • Key Results Genetic diversity at species level was high with P = 65·05?% (percentage of polymorphic loci) and Ht = 0·2248 (total genetic diversity). The coefficient of genetic differentiation among populations, Gst, which was estimated by partitioning the total gene diversity, was 0·2529; whereas, the genetic differentiation between populations in the Jinsha and Nanpan drainage areas was unexpectedly low (Gst = 0·0702). • Conclusions Based on the genetic analyses of the DNA fingerprinting, recent habitat fragmentation may not have led to genetic differentiation or the loss of genetic diversity in the rare species. Spatial apportionment of fingerprinting polymorphisms provides a footprint of historical migration across geographical barriers. The high diversity detected in this study holds promise for conservation and restoration efforts to save the endangered species from extinction. PMID:16807255

  8. Pediatric High-grade Glioma: Molecular Genetic Clues for Innovative Therapeutic Approaches

    Microsoft Academic Search

    Brian R. Rood; Tobey J. MacDonald

    2005-01-01

    High grade glioma remains the most intractable childhood tumor of the central nervous system. The molecular genetics of childhood high grade glioma remain largely unknown in comparison to that of their adult counterparts. In an era of molecularly targeted therapies, this dearth of knowledge will present particular challenges to those who must design and implement the next generation of therapeutic

  9. High genetic diversity and population differentiation in Boechera fecunda, a rare relative of Arabidopsis.

    PubMed

    Song, Bao-Hua; Mitchell-Olds, Thomas

    2007-10-01

    Conservation of endangered species becomes a critical issue with the increasing rates of extinction. In this study, we use 13 microsatellite loci and 27 single-copy nuclear loci to investigate the population genetics of Boechera fecunda, a rare relative of Arabidopsis thaliana, known from only 21 populations in Montana. We investigated levels of genetic diversity and population structure in comparison to its widespread congener, Boechera stricta, which shares similar life history and mating system. Despite its rarity, B. fecunda had levels of genetic diversity similar to B. stricta for both microsatellites and nucleotide polymorphism. Populations of B. fecunda are highly differentiated, with a majority of genetic diversity existing among populations (F(ST) = 0.57). Differences in molecular diversity and allele frequencies between western and eastern population groups suggest they experienced very different evolutionary histories. PMID:17784916

  10. Multilocus nested haplotype networks extended with DNA fingerprints show common origin and fine-scale, ongoing genetic divergence in a wild microbial metapopulation

    Microsoft Academic Search

    IGNAZIO CARBONE; LINDA M. KOHN

    2001-01-01

    Nested haplotype networks for three loci in a haploid, fungal plant pathogen, Sclerotinia sclerotiorum , in two natural, Norwegian populations of the woodland buttercup, Ranunculus ficaria , were extended with DNA fingerprints to determine fine-scale population diver- gence. To preserve the cladistic structure in the network for both nonrecombinant and postrecombinant haplotypes in highly recombinant clades, recombinant events were not

  11. ARCING HIGH IMPEDANCE FAULT DETECTION USING REAL CODED GENETIC ALGORITHM

    Microsoft Academic Search

    Naser Zamanan; Jan Sykulski; A. K. Al-Othman

    Safety and reliability are two of the most important aspects of electric power supply systems. Sensitivity and robustness to detect and isolate faults can influence the safety and reliability of such systems. Overcurrent relays are generally used to protect the high voltage feeders in distribution systems. Downed conductors, tree branches touching conductors, and failing insulators often cause high-impedance faults in

  12. High-seas Biodiversity and Genetic Resources: Science and Policy Questions

    NSDL National Science Digital Library

    Richard Blaustein (freelance writer; )

    2010-06-01

    Global efforts to protect marine genetic resources and high-seas biodiversity peak in 2010, a very eventful year for the conservation and study of high-seas biodiversity, with developments that put relevant policy and scientific directions at a significant crossroads. With these timely developments come important conservation, equity, and research questions: How do we protect deep-seas biodiversity against irresponsible exploitation in hard-to-monitor areas? How do we equitably govern the use of marine genetic resources while also fostering advanced scientific research?

  13. Patients with type 1 diabetes show signs of vascular dysfunction in response to multiple high-fat meals

    PubMed Central

    2014-01-01

    Background A high-fat diet promotes postprandial systemic inflammation and metabolic endotoxemia. We investigated the effects of three consecutive high-fat meals on endotoxemia, inflammation, vascular function, and postprandial lipid metabolism in patients with type 1 diabetes. Methods Non-diabetic controls (n?=?34) and patients with type 1 diabetes (n?=?37) were given three high-caloric, fat-containing meals during one day. Blood samples were drawn at fasting (8:00) and every two hours thereafter until 18:00. Applanation tonometry was used to assess changes in the augmentation index during the investigation day. Results Three consecutive high-fat meals had only a modest effect on serum LPS-activity levels and inflammatory markers throughout the day in both groups. Of note, patients with type 1 diabetes were unable to decrease the augmentation index in response to the high-fat meals. The most profound effects of the consecutive fat loads were seen in chylomicron and HDL-metabolism. The triglyceride-rich lipoprotein remnant marker, apoB-48, was elevated in patients compared to controls both at fasting (p?=?0.014) and postprandially (p?=?0.035). The activities of the HDL-associated enzymes PLTP (p?high-fat meals, early signs of vascular dysfunction alongside accumulation of chylomicron remnants, higher augmentation index, and decreased PON-1 activity were observed in patients with type 1 diabetes. The high-fat meals had no significant impact on postprandial LPS-activity in non-diabetic subjects or patients with type 1 diabetes suggesting that metabolic endotoxemia may be more central in patients with chronic metabolic disturbances such as obesity, type 2 diabetes, or diabetic kidney disease. PMID:24959195

  14. Range-wide analysis of genetic structure in a widespread, highly mobile species (Odocoileus hemionus) reveals the importance of historical biogeography.

    PubMed

    Latch, Emily K; Reding, Dawn M; Heffelfinger, James R; Alcalá-Galván, Carlos H; Rhodes, Olin E

    2014-07-01

    Highly mobile species that thrive in a wide range of habitats are expected to show little genetic differentiation across their range. A limited but growing number of studies have revealed that patterns of broad-scale genetic differentiation can and do emerge in vagile, continuously distributed species. However, these patterns are complex and often shaped by both historical and ecological factors. Comprehensive surveys of genetic variation at a broad scale and at high resolution are useful for detecting cryptic spatial genetic structure and for investigating the relative roles of historical and ecological processes in structuring widespread, highly mobile species. In this study, we analysed 10 microsatellite loci from over 1900 samples collected across the full range of mule deer (Odocoileus hemionus), one of the most widely distributed and abundant of all large mammal species in North America. Through both individual- and population-based analyses, we found evidence for three main genetic lineages, one corresponding to the 'mule deer' morphological type and two to the 'black-tailed deer' type. Historical biogeographic events likely are the primary drivers of genetic divergence in this species; boundaries of the three lineages correspond well with predictions based on Pleistocene glacial cycles, and substructure within each lineage demonstrates island vicariance. However, across large geographic areas, including the entire mule deer lineage, we found that genetic variation fit an isolation-by-distance pattern rather than discrete clusters. A lack of genetic structure across wide geographic areas of the continental west indicates that ecological processes have not resulted in restrictions to gene flow sufficient for spatial genetic structure to emerge. Our results have important implications for our understanding of evolutionary mechanisms of divergence, as well as for taxonomy, conservation and management. PMID:24863151

  15. The Botrytis cinerea type III polyketide synthase shows unprecedented high catalytic efficiency toward long chain acyl-CoAs.

    PubMed

    Jeya, Marimuthu; Kim, Tae-Su; Tiwari, Manish Kumar; Li, Jinglin; Zhao, Huimin; Lee, Jung-Kul

    2012-11-01

    BPKS from Botrytis cinerea is a novel type III polyketide synthase that accepts C(4)-C(18) aliphatic acyl-CoAs and benzoyl-CoA as the starters to form pyrones, resorcylic acids and resorcinols through sequential condensation with malonyl-CoA. The catalytic efficiency (k(cat)/K(m)) of BPKS was 2.8 × 10(5) s(-1) M(-1) for palmitoyl-CoA, the highest ever reported. Substrate docking analyses addressed the unique features of BPKS such as its high activity and high specificity toward long chain acyl-CoAs. PMID:22945364

  16. Many Infants Prenatally Exposed to High Levels of Alcohol Show One Particular Anomaly of the Corpus Callosum

    Microsoft Academic Search

    Fred L. Bookstein; Paul D. Connor; Janet E. Huggins; Helen M. Barr; Kristi D. Pimentel; Ann P. Streissguth

    2007-01-01

    Introduction: Effects of prenatal alcohol exposure on the brain are seen at every age. The earlier they can be quantified, the better the prognosis for the affected child. Here we show measurable alcohol effects at birth on a structure currently used for nosology only much later in life. Methods: Midline shape of the corpus callosum was imaged in infants via

  17. High altitude hypoxia environment changes of the content of RAAS and ACE2 Genetics polymorphisms

    Microsoft Academic Search

    Wenhua Li; Liu Zhong

    2011-01-01

    Objective To study the function of the rennin- angiotensin-aldoterone system(RAAS) under high altitude hypoxia environment and objective to investigate the effects of high altitude hypoxia on the angiotensin conversion enzyme 2(ACE2) Genetics polymorphisms. Methods Forty male adult Sprague Dawley( SD) rats, under high altitude hypoxia environment were divided randomly into 4 groups: the control group(D group, Xi'an area 5m above

  18. High genetic diversity at the regional scale and possible speciation in Sebacina epigaea and S. incrustans

    PubMed Central

    2013-01-01

    Background Phylogenetic studies, particularly those based on rDNA sequences from plant roots and basidiomata, have revealed a strikingly high genetic diversity in the Sebacinales. However, the factors determining this genetic diversity at higher and lower taxonomic levels within this order are still unknown. In this study, we analysed patterns of genetic variation within two morphological species, Sebacina epigaea and S. incrustans, based on 340 DNA haplotype sequences of independent genetic markers from the nuclear (ITS?+?5.8S?+?D1/D2, RPB2) and mitochondrial (ATP6) genomes for 98 population samples. By characterising the genetic population structure within these species, we provide insights into species boundaries and the possible factors responsible for genetic diversity at a regional geographic scale. Results We found that recombination events are relatively common between natural populations within Sebacina epigaea and S. incrustans, and play a significant role in generating intraspecific genetic diversity. Furthermore, we also found that RPB2 and ATP6 genes display higher levels of intraspecific synonymous polymorphism. Phylogenetic and demographic analyses based on nuclear and mitochondrial loci revealed three distinct phylogenetic lineages within of each of the morphospecies S. epigaea and S. incrustans: one major and widely distributed lineage, and two geographically restricted lineages, respectively. We found almost no differential morphological or ecological characteristics that could be used to discriminate between these lineages. Conclusions Our results suggest that recombination and negative selection have played significant roles in generating genetic diversity within these morphological species at small geographical scales. Concordance between gene genealogies identified lineages/cryptic species that have evolved independently for a relatively long period of time. These putative species were not associated with geographic provenance, geographic barrier, host preference or distinct phenotypic innovations. PMID:23697379

  19. Recombineering: highly efficient in vivo genetic engineering using single-strand oligos.

    PubMed

    Sawitzke, James A; Thomason, Lynn C; Bubunenko, Mikhail; Li, Xintian; Costantino, Nina; Court, Donald L

    2013-01-01

    Recombineering provides the ability to make rapid, precise, and inexpensive genetic alterations to any DNA sequence, either in the chromosome or cloned onto a vector that replicates in E. coli (or other recombineering-proficient bacteria), and to do so in a highly efficient manner. Complicated genetic constructs that are impossible to make with in vitro genetic engineering can be created in days with recombineering. Recombineering with single-strand DNA (ssDNA) can be used to create single or multiple clustered point mutations, small or large (up to 10kb) deletions, and small (10-20 base) insertions such as sequence tags. Using optimized conditions, point mutations can be made with such high frequencies that they can be found without selection. This technology excels at creating both directed and random mutations. PMID:24182922

  20. Genetic algorithm-support vector regression for high reliability SHM system based on FBG sensor network

    NASA Astrophysics Data System (ADS)

    Zhang, XiaoLi; Liang, DaKai; Zeng, Jie; Asundi, Anand

    2012-02-01

    Structural Health Monitoring (SHM) based on fiber Bragg grating (FBG) sensor network has attracted considerable attention in recent years. However, FBG sensor network is embedded or glued in the structure simply with series or parallel. In this case, if optic fiber sensors or fiber nodes fail, the fiber sensors cannot be sensed behind the failure point. Therefore, for improving the survivability of the FBG-based sensor system in the SHM, it is necessary to build high reliability FBG sensor network for the SHM engineering application. In this study, a model reconstruction soft computing recognition algorithm based on genetic algorithm-support vector regression (GA-SVR) is proposed to achieve the reliability of the FBG-based sensor system. Furthermore, an 8-point FBG sensor system is experimented in an aircraft wing box. The external loading damage position prediction is an important subject for SHM system; as an example, different failure modes are selected to demonstrate the SHM system's survivability of the FBG-based sensor network. Simultaneously, the results are compared with the non-reconstruct model based on GA-SVR in each failure mode. Results show that the proposed model reconstruction algorithm based on GA-SVR can still keep the predicting precision when partial sensors failure in the SHM system; thus a highly reliable sensor network for the SHM system is facilitated without introducing extra component and noise.

  1. Genetic algorithm-based feature selection in high-resolution NMR spectra

    PubMed Central

    Cho, Hyun-Woo; Jeong, Myong K.; Park, Youngja; Ziegler, Thomas R.; Jones, Dean P.

    2011-01-01

    High-resolution nuclear magnetic resonance (NMR) spectroscopy has provided a new means for detection and recognition of metabolic changes in biological systems in response to pathophysiological stimuli and to the intake of toxins or nutrition. To identify meaningful patterns from NMR spectra, various statistical pattern recognition methods have been applied to reduce their complexity and uncover implicit metabolic patterns. In this paper, we present a genetic algorithm (GA)-based feature selection method to determine major metabolite features to play a significant role in discrimination of samples among different conditions in high-resolution NMR spectra. In addition, an orthogonal signal filter was employed as a preprocessor of NMR spectra in order to remove any unwanted variation of the data that is unrelated to the discrimination of different conditions. The results of k-nearest neighbors and the partial least squares discriminant analysis of the experimental NMR spectra from human plasma showed the potential advantage of the features obtained from GA-based feature selection combined with an orthogonal signal filter. PMID:21472035

  2. Amerindians show association to obesity with adiponectin gene SNP45 and SNP276: population genetics of a food intake control and "thrifty" gene.

    PubMed

    Arnaiz-Villena, Antonio; Fernández-Honrado, Mercedes; Rey, Diego; Enríquez-de-Salamanca, Mercedes; Abd-El-Fatah-Khalil, Sedeka; Arribas, Ignacio; Coca, Carmen; Algora, Manuel; Areces, Cristina

    2013-02-01

    Adiponectin gene polymorphisms SNP45 and SNP276 have been related to metabolic syndrome (MS) and related pathologies, including obesity. However results of associations are contradictory depending on which population is studied. In the present study, these adiponectin SNPs are for the first time studied in Amerindians. Allele frequencies are obtained and comparison with obesity and other MS related parameters are performed. Amerindians were also defined by characteristic HLA genes. Our main results are: (1) SNP276 T is associated to low diastolic blood pressure in Amerindians, (2) SNP45 G allele is correlated with obesity in female but not in male Amerindians, (3) SNP45/SNP276 T/G haplotype in total obese/non-obese subjects tends to show a linkage with non-obese Amerindians, (4) SNP45/SNP276 T/T haplotype is linked to obese Amerindian males. Also, a world population study is carried out finding that SNP45 T and SNP276 T alleles are the most frequent in African Blacks and are found significantly in lower frequencies in Europeans and Asians. This together with the fact that there is a linkage of this haplotype to obese Amerindian males suggest that evolutionary forces related to famine (or population density in relation with available food) may have shaped world population adiponectin polymorphism frequencies. PMID:23108996

  3. Utilizing high-fidelity crucial conversation simulation in genetic counseling training.

    PubMed

    Holt, R Lynn; Tofil, Nancy M; Hurst, Christina; Youngblood, Amber Q; Peterson, Dawn Taylor; Zinkan, J Lynn; White, Marjorie Lee; Clemons, Jason L; Robin, Nathaniel H

    2013-06-01

    Genetics professionals are often required to deliver difficult news to patients and families. This is a challenging task, but one that many genetics trainees have limited opportunity to master during training. This is true for several reasons, including relative scarcity of these events and an understandable hesitation of supervisors allowing a trainee to provide such high stakes information. Medical simulation is effective in other health care disciplines giving trainees opportunities of "hands on" education in similar high stakes situations. We hypothesized that crucial conversations simulation would be effective for genetics trainees to gain experience in communication and counseling skills in a realistic clinical scenario. To test this hypothesis, we designed a prenatal counseling scenario requiring disclosure of an abnormal amniocentesis result and discussion of pregnancy management options; we challenged participants to address common counseling questions. Three medical genetics resident physicians and five genetic counseling students participated. Genetics and simulation experts observed the session via live video feed from a different room. A behavioral checklist was completed in real time assessing trainee's performance and documenting medical information discussed. Debriefing immediately followed the session and included simulation and genetics experts and the actor parents. Participants completed open-ended post evaluations. There was a trend towards participants being more likely to discuss issues the child could have while an infant/toddler rather than issues that could emerge as the child with Down Syndrome transitions to adulthood and end of life (P=.069). All participants found the simulation helpful, notably that it was more realistic than role-playing with colleagues. PMID:23633180

  4. Highly resolved early Eocene food webs show development of modern trophic structure after the end-Cretaceous extinction.

    PubMed

    Dunne, Jennifer A; Labandeira, Conrad C; Williams, Richard J

    2014-05-01

    Generalities of food web structure have been identified for extant ecosystems. However, the trophic organization of ancient ecosystems is unresolved, as prior studies of fossil webs have been limited by low-resolution, high-uncertainty data. We compiled highly resolved, well-documented feeding interaction data for 700 taxa from the 48 million-year-old latest early Eocene Messel Shale, which contains a species assemblage that developed after an interval of protracted environmental and biotal change during and following the end-Cretaceous extinction. We compared the network structure of Messel lake and forest food webs to extant webs using analyses that account for scale dependence of structure with diversity and complexity. The Messel lake web, with 94 taxa, displays unambiguous similarities in structure to extant webs. While the Messel forest web, with 630 taxa, displays differences compared to extant webs, they appear to result from high diversity and resolution of insect-plant interactions, rather than substantive differences in structure. The evidence presented here suggests that modern trophic organization developed along with the modern Messel biota during an 18 Myr interval of dramatic post-extinction change. Our study also has methodological implications, as the Messel forest web analysis highlights limitations of current food web data and models. PMID:24648225

  5. High-Pitched Notes during Vocal Contests Signal Genetic Diversity in Ocellated Antbirds

    PubMed Central

    Araya-Ajoy, Yi-men; Chaves-Campos, Johel; Kalko, Elisabeth K. V.; DeWoody, J. Andrew

    2009-01-01

    Animals use honest signals to assess the quality of competitors during aggressive interactions. Current theory predicts that honest signals should be costly to produce and thus reveal some aspects of the phenotypic or genetic quality of the sender. In songbirds, research indicates that biomechanical constraints make the production of some acoustic features costly. Furthermore, recent studies have found that vocal features are related to genetic diversity. We linked these two lines of research by evaluating if constrained acoustic features reveal male genetic diversity during aggressive interactions in ocellated antbirds (Phaenostictus mcleannani). We recorded the aggressive vocalizations of radiotagged males at La Selva Biological Station in Costa Rica, and found significant variation in the highest frequency produced among individuals. Moreover, we detected a negative relationship between the frequency of the highest pitched note and vocalization duration, suggesting that high pitched notes might constrain the duration of vocalizations through biomechanical and/or energetic limitations. When we experimentally exposed wild radiotagged males to simulated acoustic challenges, the birds increased the pitch of their vocalization. We also found that individuals with higher genetic diversity (as measured by zygosity across 9 microsatellite loci) produced notes of higher pitch during aggressive interactions. Overall, our results suggest that the ability to produce high pitched notes is an honest indicator of male genetic diversity in male-male aggressive interactions. PMID:19956580

  6. AFLP Polymorphisms Allow High Resolution Genetic Analysis of American Tegumentary Leishmaniasis Agents Circulating in Panama and Other Members of the Leishmania Genus

    PubMed Central

    Restrepo, Carlos M.; De La Guardia, Carolina; Sousa, Octavio E.; Calzada, José E.; Fernández, Patricia L.; Lleonart, Ricardo

    2013-01-01

    American Tegumentary Leishmaniasis is caused by parasites of the genus Leishmania, and causes significant health problems throughout the Americas. In Panama, Leishmania parasites are endemic, causing thousands of new cases every year, mostly of the cutaneous form. In the last years, the burden of the disease has increased, coincident with increasing disturbances in its natural sylvatic environments. The study of genetic variation in parasites is important for a better understanding of the biology, population genetics, and ultimately the evolution and epidemiology of these organisms. Very few attempts have been made to characterize genetic polymorphisms of parasites isolated from Panamanian patients of cutaneous leishmaniasis. Here we present data on the genetic variability of local isolates of Leishmania, as well as specimens from several other species, by means of Amplified Fragment Length Polymorphisms (AFLP), a technique seldom used to study genetic makeup of parasites. We demonstrate that this technique allows detection of very high levels of genetic variability in local isolates of Leishmania panamensis in a highly reproducible manner. The analysis of AFLP fingerprints generated by unique selective primer combinations in L. panamensis suggests a predominant clonal mode of reproduction. Using fluorescently labeled primers, many taxon-specific fragments were identified which may show potential as species diagnostic fragments. The AFLP permitted a high resolution genetic analysis of the Leishmania genus, clearly separating certain groups among L. panamensis specimens and highly related species such as L. panamensis and L. guyanensis. The phylogenetic networks reconstructed from our AFLP data are congruent with established taxonomy for the genus Leishmania, even when using single selective primer combinations. Results of this study demonstrate that AFLP polymorphisms can be informative for genetic characterization in Leishmania parasites, at both intra and inter-specific levels. PMID:24039881

  7. High Genetic Diversity of Anaplasma marginale Detected from Philippine Cattle

    PubMed Central

    YBAŃEZ, Adrian Patalinghug; YBAŃEZ, Rochelle Haidee D.; CLAVERIA, Florencia G.; CRUZ-FLORES, Mary Jane; XUENAN, Xuen; YOKOYAMA, Naoaki; INOKUMA, Hisashi

    2014-01-01

    ABSTRACT A total of 658 cattle in 6 provinces in the Philippines were screened for Anaplasma marginale infection by using a diagnostic heat-shock operon (groEL) gene-PCR assay. The screening-positive samples were further tested using the major surface antigen protein 1a (Msp1a) gene-PCR assay. Screening PCR results showed 130 cattle (19.8%) were positive for the A. marginale infection. Subsequent amplification using the Msp1a gene only showed 93 samples (14.1%) to be positive. In addition, 37 tandem-repeat structures, including 20 novel structures, and 41 distinct genotypes were identified. Interestingly, multiple infections of 4 different genotypes were also observed in A. marginale-infected cattle. The present study demonstrated the prevalence and characterization of diverse genotypes of A. marginale in the Philippine cattle. PMID:24717413

  8. The HapMap project has raised high hopes for mapping genetic determinants of complex human

    E-print Network

    Rosenberg, Noah

    The HapMap project has raised high hopes for mapping genetic determinants of complex human disease for mapping studies in human populations around the world. The HapMap project has characterized haplotype structures across the genome for four human populations with the goal of enabling genome-wide sets of SNPs

  9. HIGH LEVELS OF GENETIC VARIABILITY IN THE HAPLOID MOSS PLAGIOMNIUM CILIARE

    Microsoft Academic Search

    ROBERT WYATT; IRENEUSZ J. ODRZYKOSKI; ANN STONEBURNER

    1989-01-01

    Horizontal starch-gel electrophoresis was used to measure variability at 14 enzyme loci from 13 natural populations of the dioecious moss Plagiomniwn ciliare. Overall levels of genetic polymorphism were unexpectedly high for a haploid organism. Using a 1% frequency criterion, 71% of the loci surveyed were polymorphic for the species as a whole. The number of alleles per polymorphic locus for

  10. Biodiversity of Costa Rican salamanders: Implications of high levels of genetic differentiation and

    E-print Network

    Wake, David B.

    Biodiversity of Costa Rican salamanders: Implications of high levels of genetic differentiation, December 10, 1999 Although salamanders are characteristic amphibians in Holarctic temperate habitats, there are but three. Despite this phylogenetic constraint, Costa Rica has many species; the number of salamander

  11. Fine-scale genetic structure and clinal variation in Silene acaulis despite high gene flow

    Microsoft Academic Search

    JANET L. GEHRING; Lynda F Delph

    1999-01-01

    We investigated whether the distribution of genes reflects the patchy distribution of individuals of Silene acaulis on Pennsylvania Mountain in central Colorado. Five polymorphic protein loci were analysed using both F-statistics and spatial autocorrelation. Low ?POP (FST) indicated little genetic differentiation between populations ?1 km apart. This indicates high gene flow within our study site, perhaps as a result of

  12. A high resolution genetic map anchoring scaffolds of the sequenced watermelon genome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    As part of our ongoing efforts to sequence and map the watermelon (Citrullus spp.) genome, we have constructed a high-density genetic linkage map. The map positioned 234 watermelon genome sequence scaffolds (an average size of 1.41 Mb) that cover about 330 Mb and account for 93.5% of the 353 Mb of ...

  13. Genetic Contribution to High Neonatally Lethal Malformation Rate in the United Arab Emirates

    Microsoft Academic Search

    A. Dawodu; L. Al-Gazali; E. Varady; M. Varghese; K. Nath; V. Rajan

    2005-01-01

    Objectives: We examined the contribution of genetic disorders to congenital anomalies (CA) causing neonatal deaths in the Al Ain Medical District (AMD) in the United Arab Emirates (UAE) because of the high consanguineous marriage rate in the community. Methods: Charts of all neonatal deaths in the three perinatal units, which accounted for 99% of all births in AMD (1992–2000), were

  14. New Classes of Alanine Racemase Inhibitors Identified by High-Throughput Screening Show Antimicrobial Activity against Mycobacterium tuberculosis

    PubMed Central

    Anthony, Karen G.; Strych, Ulrich; Yeung, Kacheong R.; Shoen, Carolyn S.; Perez, Oriana; Krause, Kurt L.; Cynamon, Michael H.; Aristoff, Paul A.; Koski, Raymond A.

    2011-01-01

    Background In an effort to discover new drugs to treat tuberculosis (TB) we chose alanine racemase as the target of our drug discovery efforts. In Mycobacterium tuberculosis, the causative agent of TB, alanine racemase plays an essential role in cell wall synthesis as it racemizes L-alanine into D-alanine, a key building block in the biosynthesis of peptidoglycan. Good antimicrobial effects have been achieved by inhibition of this enzyme with suicide substrates, but the clinical utility of this class of inhibitors is limited due to their lack of target specificity and toxicity. Therefore, inhibitors that are not substrate analogs and that act through different mechanisms of enzyme inhibition are necessary for therapeutic development for this drug target. Methodology/Principal Findings To obtain non-substrate alanine racemase inhibitors, we developed a high-throughput screening platform and screened 53,000 small molecule compounds for enzyme-specific inhibitors. We examined the ‘hits’ for structural novelty, antimicrobial activity against M. tuberculosis, general cellular cytotoxicity, and mechanism of enzyme inhibition. We identified seventeen novel non-substrate alanine racemase inhibitors that are structurally different than any currently known enzyme inhibitors. Seven of these are active against M. tuberculosis and minimally cytotoxic against mammalian cells. Conclusions/Significance This study highlights the feasibility of obtaining novel alanine racemase inhibitor lead compounds by high-throughput screening for development of new anti-TB agents. PMID:21637807

  15. A High-Throughput Arabidopsis Reverse Genetics System

    Microsoft Academic Search

    Allen Sessions; Ellen Burke; Gernot Presting; John McElver; David Patton; Bob Dietrich; Patrick Ho; Johana Bacwaden; Cynthia Ko; Joseph D. Clarke; David Cotton; David Bullis; Jennifer Snell; Trini Miguel; Theresa Mitzel; Fumiaki Katagiri; Jane Glazebrook; Marc Law; Stephen A. Goff

    2002-01-01

    A collection of Arabidopsis lines with T-DNA insertions in known sites was generated to increase the efficiency of func- tional genomics. A high-throughput modified thermal asymetric interlaced (TAIL)-PCR protocol was developed and used to amplify DNA fragments flanking the T-DNA left borders from ? 100,000 transformed lines. A total of 85,108 TAIL-PCR products from 52,964 T-DNA lines were sequenced and

  16. High genetic diversity on a sample of pre-Columbian bone remains from Guane territories in northwestern Colombia.

    PubMed

    Casas-Vargas, Andrea; Gómez, Alberto; Briceńo, Ignacio; Díaz-Matallana, Marcela; Bernal, Jaime E; Rodríguez, José Vicente

    2011-12-01

    Ancient DNA was recovered from 17 individuals found in a rock shelter in the district of "La Purnia" (Santander, Colombia). This region is the homeland of pre-Columbian Guane, whom spread over the "Río Suarez" to the "Río de Oro", and were surrounded to the west by the Central Andes, south and east by foothills of Eastern Andes, and north by the "Chicamocha" river canyon. Guanes established in a region that straddles the Andes and the northern Amazon basin, possibly making it an unavoidable conduit for people moving to and from South America. We amplified mtDNA hypervariable region I (HVI) segments from ancient bone remains, and the resulting sequences were compared with both ancient and modern mitochondrial haplogroups from American and non-American populations. Samples showed a distribution of 35% for haplogroup A, 41% for haplogroup B and 24% for haplogroup D. Nine haplotypes were found in 17 samples, indicating an unusually high genetic diversity on a single site ancient population. Among them, three haplotypes have not been previously found in America, two are shared in Asia, and one is a private haplotype. Despite geographical barriers that eventually isolated them, an important influence of gene flow from neighboring pre-Columbian communities, mainly Muiscas, could explain the high genetic polymorphism of this community before the Spanish conquest, and argues against Guanes as being a genetic isolate. PMID:21990065

  17. Unexpected genetic differentiation between recently recolonized populations of a long-lived and highly vagile marine mammal

    PubMed Central

    Bonin, Carolina A; Goebel, Michael E; Forcada, Jaume; Burton, Ronald S; Hoffman, Joseph I

    2013-01-01

    Many species have been heavily exploited by man leading to local extirpations, yet few studies have attempted to unravel subsequent recolonization histories. This has led to a significant gap in our knowledge of the long-term effects of exploitation on the amount and structure of contemporary genetic variation, with important implications for conservation. The Antarctic fur seal provides an interesting case in point, having been virtually exterminated in the nineteenth century but subsequently staged a dramatic recovery to recolonize much of its original range. Consequently, we evaluated the hypothesis that South Georgia (SG), where a few million seals currently breed, was the main source of immigrants to other locations including Livingston Island (LI), by genotyping 366 individuals from these two populations at 17 microsatellite loci and sequencing a 263 bp fragment of the mitochondrial hypervariable region 1. Contrary to expectations, we found highly significant genetic differences at both types of marker, with 51% of LI individuals carrying haplotypes that were not observed in 246 animals from SG. Moreover, the youngest of three sequentially founded colonies at LI showed greater similarity to SG at mitochondrial DNA than microsatellites, implying temporal and sex-specific variation in recolonization. Our findings emphasize the importance of relict populations and provide insights into the mechanisms by which severely depleted populations can recover while maintaining surprisingly high levels of genetic diversity. PMID:24198934

  18. Characterization of new bacterial catabolic genes and mobile genetic elements by high throughput genetic screening of a soil metagenomic library.

    PubMed

    Jacquiod, Samuel; Demančche, Sandrine; Franqueville, Laure; Ausec, Luka; Xu, Zhuofei; Delmont, Tom O; Dunon, Vincent; Cagnon, Christine; Mandic-Mulec, Ines; Vogel, Timothy M; Simonet, Pascal

    2014-11-20

    A mix of oligonucleotide probes was used to hybridize soil metagenomic DNA from a fosmid clone library spotted on high density membranes. The pooled radio-labeled probes were designed to target genes encoding glycoside hydrolases GH18, dehalogenases, bacterial laccases and mobile genetic elements (integrases from integrons and insertion sequences). Positive hybridizing spots were affiliated to the corresponding clones in the library and the metagenomic inserts were sequenced. After assembly and annotation, new coding DNA sequences related to genes of interest were identified with low protein similarity against the closest hits in databases. This work highlights the sensitivity of DNA/DNA hybridization techniques as an effective and complementary way to recover novel genes from large metagenomic clone libraries. This study also supports that some of the identified catabolic genes might be associated with horizontal transfer events. PMID:24721211

  19. The Genetic and Environmental Etiology of High Math Performance in 10YearOld Twins

    Microsoft Academic Search

    Stephen A. Petrill; Yulia Kovas; Sara A. Hart; Lee A. Thompson; Robert Plomin

    2009-01-01

    The genetic and environmental etiology of high math performance (at or above the 85%tile) was examined in a population-based\\u000a sample of 10-year-old twins (nMZ = 1,279, nDZ = 2,305). Math skills were assessed using a web-based battery of math performance tapping skills related to the UK National\\u000a Math Curriculum. Probandwise concordance rates and liability threshold models indicated that genetic and shared environmental\\u000a influences were

  20. Spatial genetic analysis reveals high connectivity of tiger (Panthera tigris) populations in the Satpura–Maikal landscape of Central India

    PubMed Central

    Sharma, Sandeep; Dutta, Trishna; Maldonado, Jesús E; Wood, Thomas C; Panwar, Hemendra Singh; Seidensticker, John

    2013-01-01

    We investigated the spatial genetic structure of the tiger meta-population in the Satpura–Maikal landscape of central India using population- and individual-based genetic clustering methods on multilocus genotypic data from 273 individuals. The Satpura–Maikal landscape is classified as a global-priority Tiger Conservation Landscape (TCL) due to its potential for providing sufficient habitat that will allow the long-term persistence of tigers. We found that the tiger meta-population in the Satpura–Maikal landscape has high genetic variation and very low genetic subdivision. Individual-based Bayesian clustering algorithms reveal two highly admixed genetic populations. We attribute this to forest connectivity and high gene flow in this landscape. However, deforestation, road widening, and mining may sever this connectivity, impede gene exchange, and further exacerbate the genetic division of tigers in central India. PMID:23403813

  1. Spatial genetic analysis reveals high connectivity of tiger (Panthera tigris) populations in the Satpura-Maikal landscape of Central India.

    PubMed

    Sharma, Sandeep; Dutta, Trishna; Maldonado, Jesús E; Wood, Thomas C; Panwar, Hemendra Singh; Seidensticker, John

    2012-01-01

    We investigated the spatial genetic structure of the tiger meta-population in the Satpura-Maikal landscape of central India using population- and individual-based genetic clustering methods on multilocus genotypic data from 273 individuals. The Satpura-Maikal landscape is classified as a global-priority Tiger Conservation Landscape (TCL) due to its potential for providing sufficient habitat that will allow the long-term persistence of tigers. We found that the tiger meta-population in the Satpura-Maikal landscape has high genetic variation and very low genetic subdivision. Individual-based Bayesian clustering algorithms reveal two highly admixed genetic populations. We attribute this to forest connectivity and high gene flow in this landscape. However, deforestation, road widening, and mining may sever this connectivity, impede gene exchange, and further exacerbate the genetic division of tigers in central India. PMID:23403813

  2. Metabolic characterization of a strain (BM90) of Delftia tsuruhatensis showing highly diversified capacity to degrade low molecular weight phenols.

    PubMed

    Juárez-Jiménez, Belén; Manzanera, Maximino; Rodelas, Belén; Martínez-Toledo, Maria Victoria; Gonzalez-López, Jesus; Crognale, Silvia; Pesciaroli, Chiara; Fenice, Massimiliano

    2010-06-01

    A novel bacterium, strain BM90, previously isolated from Tyrrhenian Sea, was metabolically characterized testing its ability to use 95 different carbon sources by the Biolog system. The bacterium showed a broad capacity to use fatty-, organic- and amino-acids; on the contrary, its ability to use carbohydrates was extremely scarce. Strain BM90 was identified and affiliated to Delftia tsuruhatensis by molecular techniques based on 16S rRNA gene sequencing. D. tsuruhatensis BM90, cultivated in shaken cultures, was able to grow on various phenolic compounds and to remove them from its cultural broth. The phenols used, chosen for their presence in industrial or agro-industrial effluents, were grouped on the base of their chemical characteristics. These included benzoic acid derivatives, cinnamic acid derivatives, phenolic aldehyde derivatives, acetic acid derivatives and other phenolic compounds such as catechol and p-hydroxyphenylpropionic acid. When all the compounds (24) were gathered in the same medium (total concentration: 500 mg/l), BM90 caused the complete depletion of 18 phenols and the partial removal of two others. Only four phenolic compounds were not removed. Flow cytometry studies were carried out to understand the physiological state of BM90 cells in presence of the above phenols in various conditions. At the concentrations tested, a certain toxic effect was exerted only by the four compounds that were not metabolized by the bacterium. PMID:19946734

  3. Nationwide Surveillance Study of Clostridium difficile in Australian Neonatal Pigs Shows High Prevalence and Heterogeneity of PCR Ribotypes

    PubMed Central

    Knight, Daniel R.; Squire, Michele M.

    2014-01-01

    Clostridium difficile is an important enteric pathogen of humans and the cause of diarrhea and enteritis in neonatal pigs. Outside Australia, prevalence in piglets can be up to 73%, with a single PCR ribotype (RT), 078, predominating. We investigated the prevalence and genotype of C. difficile in Australian pig herds. Rectal swabs (n = 229) were collected from piglets aged <7 days from 21 farms across Australia. Selective culture for C. difficile was performed and isolates characterized by PCR for toxin genes and PCR ribotyping. C. difficile was isolated from 52% of samples by direct culture on chromogenic agar and 67% by enrichment culture (P = 0.001). No association between C. difficile recovery or genotype and diarrheic status of either farm or piglets was found. The majority (87%; 130/154) of isolates were toxigenic. Typing revealed 23 different RTs, several of which are known to cause disease in humans, including RT014, which was isolated most commonly (23%; 36/154). RT078 was not detected. This study shows that colonization of Australian neonatal piglets with C. difficile is widespread in the herds sampled. PMID:25326297

  4. Abnormal Mammary Adipose Tissue Environment of Brca1 Mutant Mice Show a Persistent Deposition of Highly Vascularized Multilocular Adipocytes.

    PubMed

    Jones, Laundette P; Buelto, Destiney; Tago, Elaine; Owusu-Boaitey, Kwadwo E

    2011-12-01

    A major challenge to breast cancer research is the identification of alterations in the architecture and composition of the breast that are associated with breast cancer progression. The aim of the present investigation was to characterize the mammary adipose phenotype from Brca1 mutant mice in the expectation that this would shed light on the role of the mammary tissue environment in the early stages of breast tumorigenesis. We observed that histological sections of mammary tissue from adult Brca1 mutant mice abnormally display small, multilocular adipocytes that are reminiscent of brown adipose tissue (BAT) as compared to wildtype mice. Using a marker for BAT, the uncoupling protein 1 (UCP1), we demonstrated that these multilocular adipose regions in Brca1 mutant mice stain positive for UCP1. Transcriptionally, UCP1 mRNA levels in the Brca1 mutant mice were elevated greater than 50-fold compared to age-matched mammary glands from wildtype mice. Indeed, BAT has characteristics that are favorable for tumor growth, including high vascularity. Therefore, we also demonstrated that the multilocular brown adipose phenotype in the mammary fat pad of Brca1 mutant mice displayed regions of increased vascularity as evidenced by a significant increase in the protein expression of CD31, a marker for angiogenesis. This Brca1 mutant mouse model should provide a physiologically relevant context to determine whether brown adipose tissue can play a role in breast cancer development. PMID:24501658

  5. Global gene analysis of oocytes from early stages in human folliculogenesis shows high expression of novel genes in reproduction.

    PubMed

    Markholt, S; Grřndahl, M L; Ernst, E H; Andersen, C Yding; Ernst, E; Lykke-Hartmann, K

    2012-02-01

    The pool of primordial follicles in humans is laid down during embryonic development and follicles can remain dormant for prolonged intervals, often decades, until individual follicles resume growth. The mechanisms that induce growth and maturation of primordial follicles are poorly understood but follicles once activated either continue growth or undergo atresia. We have isolated pure populations of oocytes from human primordial, intermediate and primary follicles using laser capture micro-dissection microscopy and evaluated the global gene expression profiles by whole-genome microarray analysis. The array data were confirmed by qPCR for selected genes. A total of 6301 unique genes were identified as significantly expressed representing enriched specific functional categories such as 'RNA binding', 'translation initiation' and 'structural molecule activity'. Several genes, some not previously known to be associated with early oocyte development, were identified with exceptionally high expression levels, such as the anti-proliferative transmembrane protein with an epidermal growth factor-like and two follistatin-like domains (TMEFF2), the Rho-GTPase-activating protein oligophrenin 1 (OPHN1) and the mitochondrial-encoded ATPase6 (ATP6). Thus, the present study provides not only a technique to capture and perform transcriptome analysis of the sparse material of human oocytes from the earliest follicle stages but further includes a comprehensive basis for our understanding of the regulatory factors and pathways present during early human folliculogenesis. PMID:22238370

  6. Genetic Characterization of Highly Pathogenic Avian Influenza (H5N8) Virus from Domestic Ducks, England, November 2014

    PubMed Central

    Banks, Jill; Marston, Denise A.; Ellis, Richard J.; Brookes, Sharon M.; Brown, Ian H.

    2015-01-01

    Genetic sequences of a highly pathogenic avian influenza (H5N8) virus in England have high homology to those detected in mainland Europe and Asia during 2014. Genetic characterization suggests this virus is an avian-adapted virus without specific affinity for zoonoses. Spatio-temporal detections of H5N8 imply a role for wild birds in virus spread. PMID:25898126

  7. Genetic Characterization of Highly Pathogenic Avian Influenza (H5N8) Virus from Domestic Ducks, England, November 2014.

    PubMed

    Hanna, Amanda; Banks, Jill; Marston, Denise A; Ellis, Richard J; Brookes, Sharon M; Brown, Ian H

    2015-05-01

    Genetic sequences of a highly pathogenic avian influenza (H5N8) virus in England have high homology to those detected in mainland Europe and Asia during 2014. Genetic characterization suggests this virus is an avian-adapted virus without specific affinity for zoonoses. Spatio-temporal detections of H5N8 imply a role for wild birds in virus spread. PMID:25898126

  8. T cells from chronic bone infection show reduced proliferation and a high proportion of CD28- CD4 T cells

    PubMed Central

    Kumar, G; Roger, P-M; Ticchioni, M; Trojani, C; Bernard de Dompsur, R; Bronsard, N; Carles, M; Bernard, E

    2014-01-01

    Chronic bone infection is associated with bone resorption. From animal studies, CD3/CD28-activated T cells are known to enhance osteoclastogenesis and bone resorption. Because CD28 is expressed constitutively on T cells and its expression is down-regulated by chronic exposure to the inflammatory environment, we characterized co-stimulatory molecule expression on T cells from chronically infected patients. We used cytofluorometric techniques to phenotypically characterize T cells, its co-stimulatory molecules and perforin secretion from infected and non-infected human bones. Chronic bone infection was defined as infection lasting for more than a month. We show a higher T cell activation [human leucocyte antigen D-related (HLA-DR+)] in infected compared to non-infected bones: median being 16 versus 7%, P?=?0·009 for CD4 T cells, and 33 versus 15%, P?=?0·038 for CD8 T cells, respectively. However, T cell proliferation (Ki67+) was lower for CD8 T cells in infected bones: 26 versus 34%, P?=?0·045. In contrast, we detected no difference in apoptosis and regulatory T cells. In infected bone, we found higher CD28-negative CD4+ T cells compared to non-infected bone: 20 versus 8%, respectively (P?=?0·005); this T cell subset had higher CD11b expression and perforin secretion. Chronically infected human bones are characterized by an increase of CD28-negative CD4+ T cells, indicating long-term activated cells with cytotoxic ability. Therefore, this alteration of co-stimulatory molecules may modify interactions with osteoclasts and impact bone resorption. PMID:24298980

  9. Remotely sensed forest cover loss shows high spatial and temporal variation across Sumatera and Kalimantan, Indonesia 2000-2008

    NASA Astrophysics Data System (ADS)

    Broich, Mark; Hansen, Matthew; Stolle, Fred; Potapov, Peter; Arunarwati Margono, Belinda; Adusei, Bernard

    2011-01-01

    The Indonesian islands of Sumatera and Kalimantan (the Indonesian part of the island of Borneo) are a center of significant and rapid forest cover loss in the humid tropics with implications for carbon dynamics, biodiversity conservation, and local livelihoods. The aim of our research was to analyze and interpret annual trends of forest cover loss for different sub-regions of the study area. We mapped forest cover loss for 2000-2008 using multi-resolution remote sensing data from the Landsat enhanced thematic mapper plus (ETM +) and moderate resolution imaging spectroradiometer (MODIS) sensors and analyzed annual trends per island, province, and official land allocation zone. The total forest cover loss for Sumatera and Kalimantan 2000-2008 was 5.39 Mha, which represents 5.3% of the land area and 9.2% of the year 2000 forest cover of these two islands. At least 6.5% of all mapped forest cover loss occurred in land allocation zones prohibiting clearing. An additional 13.6% of forest cover loss occurred where clearing is legally restricted. The overall trend of forest cover loss increased until 2006 and decreased thereafter. The trends for Sumatera and Kalimantan were distinctly different, driven primarily by the trends of Riau and Central Kalimantan provinces, respectively. This analysis shows that annual mapping of forest cover change yields a clearer picture than a one-time overall national estimate. Monitoring forest dynamics is important for national policy makers, especially given the commitment of Indonesia to reducing greenhouse gas emissions as part of the reducing emissions from deforestation and forest degradation in developing countries initiative (REDD +). The improved spatio-temporal detail of forest change monitoring products will make it possible to target policies and projects in meeting this commitment. Accurate, annual forest cover loss maps will be integral to many REDD + objectives, including policy formulation, definition of baselines, detection of displacement, and the evaluation of the permanence of emission reduction.

  10. A scalable pipeline for highly effective genetic modification of a malaria parasite.

    PubMed

    Pfander, Claudia; Anar, Burcu; Schwach, Frank; Otto, Thomas D; Brochet, Mathieu; Volkmann, Katrin; Quail, Michael A; Pain, Arnab; Rosen, Barry; Skarnes, William; Rayner, Julian C; Billker, Oliver

    2011-12-01

    In malaria parasites, the systematic experimental validation of drug and vaccine targets by reverse genetics is constrained by the inefficiency of homologous recombination and by the difficulty of manipulating adenine and thymine (A+T)-rich DNA of most Plasmodium species in Escherichia coli. We overcame these roadblocks by creating a high-integrity library of Plasmodium berghei genomic DNA (>77% A+T content) in a bacteriophage N15-based vector that can be modified efficiently using the lambda Red method of recombineering. We built a pipeline for generating P. berghei genetic modification vectors at genome scale in serial liquid cultures on 96-well plates. Vectors have long homology arms, which increase recombination frequency up to tenfold over conventional designs. The feasibility of efficient genetic modification at scale will stimulate collaborative, genome-wide knockout and tagging programs for P. berghei. PMID:22020067

  11. Investigating Population Genetic Structure in a Highly Mobile Marine Organism: The Minke Whale Balaenoptera acutorostrata acutorostrata in the North East Atlantic

    PubMed Central

    Quintela, María; Skaug, Hans J.; Řien, Nils; Haug, Tore; Seliussen, Bjřrghild B.; Solvang, Hiroko K.; Pampoulie, Christophe; Kanda, Naohisa; Pastene, Luis A.; Glover, Kevin A.

    2014-01-01

    Inferring the number of genetically distinct populations and their levels of connectivity is of key importance for the sustainable management and conservation of wildlife. This represents an extra challenge in the marine environment where there are few physical barriers to gene-flow, and populations may overlap in time and space. Several studies have investigated the population genetic structure within the North Atlantic minke whale with contrasting results. In order to address this issue, we analyzed ten microsatellite loci and 331 bp of the mitochondrial D-loop on 2990 whales sampled in the North East Atlantic in the period 2004 and 2007–2011. The primary findings were: (1) No spatial or temporal genetic differentiations were observed for either class of genetic marker. (2) mtDNA identified three distinct mitochondrial lineages without any underlying geographical pattern. (3) Nuclear markers showed evidence of a single panmictic population in the NE Atlantic according STRUCTURE's highest average likelihood found at K?=?1. (4) When K?=?2 was accepted, based on the Evanno's test, whales were divided into two more or less equally sized groups that showed significant genetic differentiation between them but without any sign of underlying geographic pattern. However, mtDNA for these individuals did not corroborate the differentiation. (5) In order to further evaluate the potential for cryptic structuring, a set of 100 in silico generated panmictic populations was examined using the same procedures as above showing genetic differentiation between two artificially divided groups, similar to the aforementioned observations. This demonstrates that clustering methods may spuriously reveal cryptic genetic structure. Based upon these data, we find no evidence to support the existence of spatial or cryptic population genetic structure of minke whales within the NE Atlantic. However, in order to conclusively evaluate population structure within this highly mobile species, more markers will be required. PMID:25268591

  12. Landscape scale genetic effects of habitat fragmentation on a high gene flow species: Speyeria idalia (Nymphalidae).

    PubMed

    Williams, Barry L; Brawn, Jeffrey D; Paige, Ken N

    2003-01-01

    Detection of the genetic effects of recent habitat fragmentation in natural populations can be a difficult task, especially for high gene flow species. Previous analyses of mitochondrial DNA data from across the current range of Speyeria idalia indicated that the species exhibited high levels of gene flow among populations, with the exception of an isolated population in the eastern portion of its range. However, some populations are found on isolated habitat patches, which were recently separated from one another by large expanses of uninhabitable terrain, in the form of row crop agriculture. The goal of this study was to compare levels of genetic differentiation and diversity among populations found in relatively continuous habitat to populations in both recently and historically isolated habitat. Four microsatellite loci were used to genotype over 300 individuals from five populations in continuous habitat, five populations in recently fragmented habitat, and one historically isolated population. Results from the historically isolated population were concordant with previous analyses and suggest significant differentiation. Also, microsatellite data were consistent with the genetic effects of habitat fragmentation for the recently isolated populations, in the form of increased differentiation and decreased genetic diversity when compared to nonfragmented populations. These results suggest that given the appropriate control populations, microsatellite markers can be used to detect the effects of recent habitat fragmentation in natural populations, even at a large geographical scale in high gene flow species. PMID:12492874

  13. Genetic Diversity Analysis of Highly Incomplete SNP Genotype Data with Imputations: An Empirical Assessment

    PubMed Central

    Fu, Yong-Bi

    2014-01-01

    Genotyping by sequencing (GBS) recently has emerged as a promising genomic approach for assessing genetic diversity on a genome-wide scale. However, concerns are not lacking about the uniquely large unbalance in GBS genotype data. Although some genotype imputation has been proposed to infer missing observations, little is known about the reliability of a genetic diversity analysis of GBS data, with up to 90% of observations missing. Here we performed an empirical assessment of accuracy in genetic diversity analysis of highly incomplete single nucleotide polymorphism genotypes with imputations. Three large single-nucleotide polymorphism genotype data sets for corn, wheat, and rice were acquired, and missing data with up to 90% of missing observations were randomly generated and then imputed for missing genotypes with three map-independent imputation methods. Estimating heterozygosity and inbreeding coefficient from original, missing, and imputed data revealed variable patterns of bias from assessed levels of missingness and genotype imputation, but the estimation biases were smaller for missing data without genotype imputation. The estimates of genetic differentiation were rather robust up to 90% of missing observations but became substantially biased when missing genotypes were imputed. The estimates of topology accuracy for four representative samples of interested groups generally were reduced with increased levels of missing genotypes. Probabilistic principal component analysis based imputation performed better in terms of topology accuracy than those analyses of missing data without genotype imputation. These findings are not only significant for understanding the reliability of the genetic diversity analysis with respect to large missing data and genotype imputation but also are instructive for performing a proper genetic diversity analysis of highly incomplete GBS or other genotype data. PMID:24626289

  14. Genetic diversity analysis of highly incomplete SNP genotype data with imputations: an empirical assessment.

    PubMed

    Fu, Yong-Bi

    2014-05-01

    Genotyping by sequencing (GBS) recently has emerged as a promising genomic approach for assessing genetic diversity on a genome-wide scale. However, concerns are not lacking about the uniquely large unbalance in GBS genotype data. Although some genotype imputation has been proposed to infer missing observations, little is known about the reliability of a genetic diversity analysis of GBS data, with up to 90% of observations missing. Here we performed an empirical assessment of accuracy in genetic diversity analysis of highly incomplete single nucleotide polymorphism genotypes with imputations. Three large single-nucleotide polymorphism genotype data sets for corn, wheat, and rice were acquired, and missing data with up to 90% of missing observations were randomly generated and then imputed for missing genotypes with three map-independent imputation methods. Estimating heterozygosity and inbreeding coefficient from original, missing, and imputed data revealed variable patterns of bias from assessed levels of missingness and genotype imputation, but the estimation biases were smaller for missing data without genotype imputation. The estimates of genetic differentiation were rather robust up to 90% of missing observations but became substantially biased when missing genotypes were imputed. The estimates of topology accuracy for four representative samples of interested groups generally were reduced with increased levels of missing genotypes. Probabilistic principal component analysis based imputation performed better in terms of topology accuracy than those analyses of missing data without genotype imputation. These findings are not only significant for understanding the reliability of the genetic diversity analysis with respect to large missing data and genotype imputation but also are instructive for performing a proper genetic diversity analysis of highly incomplete GBS or other genotype data. PMID:24626289

  15. High-resolution deep Northeast Pacific radiocarbon record shows little change in ventilation rate during the last deglaciation

    NASA Astrophysics Data System (ADS)

    Lund, D. C.; Mix, A. C.

    2010-12-01

    The rise in atmospheric carbon dioxide during the last deglaciation is thought to be driven by release of carbon sequestered in the abyssal ocean. This mechanism requires a poorly ventilated deep Pacific during the Last Glacial Maximum (LGM) and enhanced ventilation during the deglaciation. Here we evaluate the plausibility of this scenario using planktonic and benthic foraminiferal radiocarbon data from a high-sedimentation rate core (~25 cm/kyr) collected in the deep (2700 m) Northeast Pacific. We estimate that the mean benthic-planktonic (B-P) age was 1620±190 years during the LGM (n=10 pairs). This value is indistinguishable from the mean B-P difference for the deglaciation (1500±230; n=20 pairs) and the difference between surface and deep water 14C ages today (1560±70 years). Furthermore, our time series of benthic ?14C parallels atmospheric ?14C with an offset of 300±50‰ from 22 to 10 kyr BP. These data suggest the ventilation rate of the deep NE Pacific remained nearly constant during the deglaciation, consistent with lower resolution data from this region (Okazaki et al., 2010). Between 22 and 16 kyr BP, ?14C in the deep NE Pacific varied between 0 and 100‰, well above the -200‰ values estimated at intermediate depths off of Baja California during the Mystery Interval (Marchitto et al., 2007). The deep NE Pacific apparently did not contain water of adequate age to source deglacial ?14C anomalies shallower in the water column. Given that Antarctic Intermediate Water is also an unlikely source (de Pol-Holz et al., 2010; Rose et al., 2010), an alternative explanation is necessary for the extreme 14C depletions in the eastern tropical Pacific. De Pol-Holz, R. D., et al. 2010. No signature of abyssal carbon in intermediate waters off Chile during deglaciation. Nature Geoscience 3, 192-195. Marchitto, T., Lehman, S., Ortiz, J., Fluckiger, J. & van Geen, A. 2007. Marine radiocarbon evidence for the mechanism of deglacial atmospheric CO2 rise. Science 316, 1456-1459. Okazaki et al. 2010. Deepwater formation in the North Pacific during the Last Glacial Termination. Science 329, 200-204. Rose, K. A., et al. 2010. Upper-ocean-to-atmosphere offsets imply fast deglacial radiocarbon release, Nature 466, 1093-1097.

  16. High-grade endometrial stromal sarcomas: a clinicopathologic study of a group of tumors with heterogenous morphologic and genetic features.

    PubMed

    Sciallis, Andrew P; Bedroske, Patrick P; Schoolmeester, John K; Sukov, William R; Keeney, Gary L; Hodge, Jennelle C; Bell, Debra A

    2014-09-01

    The existence of a "high-grade endometrial stromal sarcoma" category of tumors has been a controversial subject owing to, among other things, the difficulty in establishing consistent diagnostic criteria. Currently, the recommended classification for such tumors is undifferentiated uterine/endometrial sarcoma. Interest in this subject has recently increased markedly with the identification of recurrent molecular genetic abnormalities. At Mayo Clinic, a group of neoplasms has been observed that morphologically resemble, either cytologically or architecturally, classic "low-grade" endometrial stromal sarcoma but feature obvious deviations, specifically, 17 tumors with unequivocally high-grade morphology. These high-grade tumors displayed 3 morphologic themes: (1) tumors with a component that is identical to low-grade ESS that transitions abruptly into an obviously higher-grade component; (2) tumors composed exclusively of high-grade cells with uniform nuclear features but with a permeative pattern of infiltration; (3) tumors similar to the second group but with a different, yet characteristic, cytomorphology featuring enlarged round to ovoid cells (larger than those found in low-grade ESS) with smooth nuclear membranes and distinct chromatin clearing but lacking prominent nucleoli. We collected clinicopathologic data, applied immunohistochemical studies, and also tested tumors by fluorescence in situ hybridization for abnormalities in JAZF1, PHF1, YWHAE, and CCND1. Tumors from these 3 groups were found to be immunohistochemically and genetically distinct from one another. Most notable was the fact that category 3 contained all the cases that tested positive for YWHAE rearrangement, did not show any classic translocations for JAZF1, PHF1, or CCND1, often presented at a high stage, and behaved aggressively. This study demonstrates the morphologic, immunophenotypic, and molecular genetic heterogeneity that exists within "undifferentiated endometrial sarcomas" as currently defined and lends credence to the effort of subclassifying some tumors as truly "high-grade endometrial stromal sarcomas." Our study also shows that, in the context of undifferentiated endometrial sarcomas, recognition of cytomorphologic features on routine hematoxylin and eosin-stained sections may be used to select tumors with specific molecular genetic changes-that is, translocations involving YWHAE. Our conclusions will help further efforts towards proper sub-classification of these tumors which will aid in diagnosis and potentially affect clinical management. PMID:25133706

  17. Genetic risk factors in two Utah pedigrees at high risk for suicide

    PubMed Central

    Coon, H; Darlington, T; Pimentel, R; Smith, K R; Huff, C D; Hu, H; Jerominski, L; Hansen, J; Klein, M; Callor, W B; Byrd, J; Bakian, A; Crowell, S E; McMahon, W M; Rajamanickam, V; Camp, N J; McGlade, E; Yurgelun-Todd, D; Grey, T; Gray, D

    2013-01-01

    We have used unique population-based data resources to identify 22 high-risk extended pedigrees that show clustering of suicide over twice that expected from demographically adjusted incidence rates. In this initial study of genetic risk factors, we focused on two high-risk pedigrees. In the first of these (pedigree 12), 10/19 (53%) of the related suicides were female, and the average age at death was 30.95. In the second (pedigree 5), 7/51 (14%) of the suicides were female and the average age at death was 36.90. Six decedents in pedigree 12 and nine in pedigree 5 were genotyped with the Illumina HumanExome BeadChip. Genotypes were analyzed using the Variant Annotation, Analysis, and Search program package that computes likelihoods of risk variants using the functional impact of the DNA variation, aggregative scoring of multiple variants across each gene and pedigree structure. We prioritized variants that were: (1) shared across pedigree members, (2) rare in other Utah suicides not related to these pedigrees, (3) ? 5% in genotyping data from 398 other Utah population controls and (4) ?5% frequency in publicly available sequence data from 1358 controls and/or in dbSNP. Results included several membrane protein genes (ANO5, and TMEM141 for pedigree 12 and FAM38A and HRCT1 for pedigree 5). Other genes with known neuronal involvement and/or previous associations with psychiatric conditions were also identified, including NFKB1, CASP9, PLXNB1 and PDE11A in pedigree 12, and THOC1, and AUTS2 in pedigree 5. Although the study is limited to variants included on the HumanExome BeadChip, these findings warrant further exploration, and demonstrate the utility of this high-risk pedigree resource to identify potential genes or gene pathways for future development of targeted interventions. PMID:24252905

  18. The genetic landscape of high-risk neuroblastoma

    PubMed Central

    Pugh, Trevor J.; Morozova, Olena; Attiyeh, Edward F.; Asgharzadeh, Shahab; Wei, Jun S.; Auclair, Daniel; Carter, Scott L.; Cibulskis, Kristian; Hanna, Megan; Kiezun, Adam; Kim, Jaegil; Lawrence, Michael S.; Lichenstein, Lee; McKenna, Aaron; Pedamallu, Chandra Sekhar; Ramos, Alex H.; Shefler, Erica; Sivachenko, Andrey; Sougnez, Carrie; Stewart, Chip; Ally, Adrian; Birol, Inanc; Chiu, Readman; Corbett, Richard D.; Hirst, Martin; Jackman, Shaun D.; Kamoh, Baljit; Khodabakshi, Alireza Hadj; Krzywinski, Martin; Lo, Allan; Moore, Richard A.; Mungall, Karen L.; Qian, Jenny; Tam, Angela; Thiessen, Nina; Zhao, Yongjun; Cole, Kristina A.; Diamond, Maura; Diskin, Sharon J.; Mosse, Yael P.; Wood, Andrew C.; Ji, Lingyun; Sposto, Richard; Badgett, Thomas; London, Wendy B.; Moyer, Yvonne; Gastier-Foster, Julie M.; Smith, Malcolm A.; Auvil, Jaime M. Guidry; Gerhard, Daniela S.; Hogarty, Michael D.; Jones, Steven J. M.; Lander, Eric S.; Gabriel, Stacey B.; Getz, Gad; Seeger, Robert C.; Khan, Javed; Marra, Marco A.; Meyerson, Matthew; Maris, John M.

    2013-01-01

    Neuroblastoma is a malignancy of the developing sympathetic nervous system that often presents with widespread metastatic disease, resulting in survival rates of less than 50%1. To determine the spectrum of somatic mutation in high-risk neuroblastoma, we studied 240 cases using a combination of whole exome, genome and transcriptome sequencing as part of the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) initiative. Here we report a low median exonic mutation frequency of 0.60 per megabase (0.48 non-silent), and remarkably few recurrently mutated genes in these tumors. Genes with significant somatic mutation frequencies included ALK (9.2% of cases), PTPN11 (2.9%), ATRX (2.5%, an additional 7.1% had focal deletions), MYCN (1.7%, a recurrent p.Pro44Leu alteration), and NRAS (0.83%). Rare, potentially pathogenic germline variants were significantly enriched in ALK, CHEK2, PINK1, and BARD1. The relative paucity of recurrent somatic mutations in neuroblastoma challenges current therapeutic strategies reliant upon frequently altered oncogenic drivers. PMID:23334666

  19. High-Throughput Automated Phenotyping of Two Genetic Mouse Models of Huntington's Disease.

    PubMed

    Balci, Fuat; Oakeshott, Stephen; Shamy, Jul Lea; El-Khodor, Bassem F; Filippov, Igor; Mushlin, Richard; Port, Russell; Connor, David; Paintdakhi, Ahmad; Menalled, Liliana; Ramboz, Sylvie; Howland, David; Kwak, Seung; Brunner, Dani

    2013-01-01

    Phenotyping with traditional behavioral assays constitutes a major bottleneck in the primary screening, characterization, and validation of genetic mouse models of disease, leading to downstream delays in drug discovery efforts. We present a novel and comprehensive one-stop approach to phenotyping, the PhenoCube™. This system simultaneously captures the cognitive performance, motor activity, and circadian patterns of group-housed mice by use of home-cage operant conditioning modules (IntelliCage) and custom-built computer vision software. We evaluated two different mouse models of Huntington's Disease (HD), the R6/2 and the BACHD in the PhenoCube™ system. Our results demonstrated that this system can efficiently capture and track alterations in both cognitive performance and locomotor activity patterns associated with these disease models. This work extends our prior demonstration that PhenoCube™ can characterize circadian dysfunction in BACHD mice and shows that this system, with the experimental protocols used, is a sensitive and efficient tool for a first pass high-throughput screening of mouse disease models in general and mouse models of neurodegeneration in particular. PMID:23863947

  20. High-Throughput Automated Phenotyping of Two Genetic Mouse Models of Huntington's Disease

    PubMed Central

    Balci, Fuat; Oakeshott, Stephen; Shamy, Jul Lea; El-Khodor, Bassem F.; Filippov, Igor; Mushlin, Richard; Port, Russell; Connor, David; Paintdakhi, Ahmad; Menalled, Liliana; Ramboz, Sylvie; Howland, David; Kwak, Seung; Brunner, Dani

    2013-01-01

    Phenotyping with traditional behavioral assays constitutes a major bottleneck in the primary screening, characterization, and validation of genetic mouse models of disease, leading to downstream delays in drug discovery efforts. We present a novel and comprehensive one-stop approach to phenotyping, the PhenoCube™. This system simultaneously captures the cognitive performance, motor activity, and circadian patterns of group-housed mice by use of home-cage operant conditioning modules (IntelliCage) and custom-built computer vision software. We evaluated two different mouse models of Huntington’s Disease (HD), the R6/2 and the BACHD in the PhenoCube™ system. Our results demonstrated that this system can efficiently capture and track alterations in both cognitive performance and locomotor activity patterns associated with these disease models. This work extends our prior demonstration that PhenoCube™ can characterize circadian dysfunction in BACHD mice and shows that this system, with the experimental protocols used, is a sensitive and efficient tool for a first pass high-throughput screening of mouse disease models in general and mouse models of neurodegeneration in particular. PMID:23863947

  1. High Prevalence, Genetic Diversity and Intracellular Growth Ability of Legionella in Hot Spring Environments

    PubMed Central

    Zhou, Haijian; Wang, Huanxin; Xu, Ying; Zhao, Mingqiang; Guan, Hong; Li, Machao; Shao, Zhujun

    2013-01-01

    Background Legionella is the causative agent of Legionnaires' disease, and hot springs are a major source of outbreaks of this disease. It is important from a public health perspective to survey hot spring environments for the presence of Legionella. Methods Prospective surveillance of the extent of Legionella pollution was conducted at three hot spring recreational areas in Beijing, China in 2011. Pulsed-field gel electrophoresis (PFGE) and sequence-based typing (SBT) were used to describe the genetic polymorphism of isolates. The intracellular growth ability of the isolates was determined by interacting with J774 cells and plating the dilutions onto BCYE agar plates. Results Overall, 51.9% of spring water samples showed Legionella-positive, and their concentrations ranged from 1 CFU/liter to 2,218 CFU/liter. The positive rates of Legionella were significantly associated with a free chlorine concentration of ?0.2 mg/L, urea concentration of ?0.05 mg/L, total microbial counts of ?400 CFU/ml and total coliform of ?3 MPN/L (p<0.01). The Legionella concentrations were significantly associated with sample temperature, pH, total microbial counts and total coliform (p<0.01). Legionella pneumophila was the most frequently isolated species (98.9%), and the isolated serogroups included serogroups 3 (25.3%), 6 (23.4%), 5 (19.2%), 1 (18.5%), 2 (10.2%), 8 (0.4%), 10 (0.8%), 9 (1.9%) and 12 (0.4%). Two hundred and twenty-eight isolates were analyzed by PFGE and 62 different patterns were obtained. Fifty-seven L. pneumophila isolates were selected for SBT analysis and divided into 35 different sequence types with 5 main clonal groups. All the 57 isolates had high intracellular growth ability. Conclusions Our results demonstrated high prevalence and genetic polymorphism of Legionella in springs in Beijing, China, and the SBT and intracellular growth assay results suggested that the Legionella isolates of hot spring environments were pathogenic. Improved control and prevention strategies are urgently needed. PMID:23527075

  2. Nutrition and Feeding of Show Poultry 

    E-print Network

    Cartwright, A. Lee

    2003-11-03

    The championship potential of a chicken or turkey is determined by genetics, but proper nutrition can help an animal achieve that genetic potential. This publication outlines four principles critical to developing a nutrition program for show...

  3. Genetic diversity of high-elevation populations of an endangered medicinal plant

    PubMed Central

    Nag, Akshay; Ahuja, Paramvir Singh; Sharma, Ram Kumar

    2015-01-01

    Intraspecific genetic variation in natural populations governs their potential to overcome challenging ecological and environmental conditions. In addition, knowledge of this variation is critical for the conservation and management of endangered plant taxa. Found in the Himalayas, Podophyllum hexandrum is an endangered high-elevation plant species that has great medicinal importance. Here we report on the genetic diversity analysis of 24 P. hexandrum populations (209 individuals), representing the whole of the Indian Himalayas. In the present study, seven amplified fragment length polymorphism (AFLP) primer pairs generated 1677 fragments, of which 866 were found to be polymorphic. Neighbour joining clustering, principal coordinate analysis and STRUCTURE analysis clustered 209 individuals from 24 populations of the Indian Himalayan mountains into two major groups with a significant amount of gene flow (Nm = 2.13) and moderate genetic differentiation Fst(0.196), G?st(0.20). This suggests that, regardless of geographical location, all of the populations from the Indian Himalayas are intermixed and are composed broadly of two types of genetic populations. High variance partitioned within populations (80 %) suggests that most of the diversity is restricted to the within-population level. These results suggest two possibilities about the ancient population structure of P. hexandrum: either all of the populations in the geographical region of the Indian Himalayas are remnants of a once-widespread ancient population, or they originated from two types of genetic populations, which coexisted a long time ago, but subsequently separated as a result of long-distance dispersal and natural selection. High variance partitioned within the populations indicates that these populations have evolved in response to their respective environments over time, but low levels of heterozygosity suggest the presence of historical population bottlenecks. PMID:25416728

  4. Genetic diversity of high-elevation populations of an endangered medicinal plant.

    PubMed

    Nag, Akshay; Ahuja, Paramvir Singh; Sharma, Ram Kumar

    2014-01-01

    Intraspecific genetic variation in natural populations governs their potential to overcome challenging ecological and environmental conditions. In addition, knowledge of this variation is critical for the conservation and management of endangered plant taxa. Found in the Himalayas, Podophyllum hexandrum is an endangered high-elevation plant species that has great medicinal importance. Here we report on the genetic diversity analysis of 24 P. hexandrum populations (209 individuals), representing the whole of the Indian Himalayas. In the present study, seven amplified fragment length polymorphism (AFLP) primer pairs generated 1677 fragments, of which 866 were found to be polymorphic. Neighbour joining clustering, principal coordinate analysis and STRUCTURE analysis clustered 209 individuals from 24 populations of the Indian Himalayan mountains into two major groups with a significant amount of gene flow (Nm = 2.13) and moderate genetic differentiation Fst(0.196), G'st(0.20). This suggests that, regardless of geographical location, all of the populations from the Indian Himalayas are intermixed and are composed broadly of two types of genetic populations. High variance partitioned within populations (80 %) suggests that most of the diversity is restricted to the within-population level. These results suggest two possibilities about the ancient population structure of P. hexandrum: either all of the populations in the geographical region of the Indian Himalayas are remnants of a once-widespread ancient population, or they originated from two types of genetic populations, which coexisted a long time ago, but subsequently separated as a result of long-distance dispersal and natural selection. High variance partitioned within the populations indicates that these populations have evolved in response to their respective environments over time, but low levels of heterozygosity suggest the presence of historical population bottlenecks. PMID:25416728

  5. Pathways and barriers to genetic testing and screening: Molecular genetics meets the high-risk family. Final report

    SciTech Connect

    Duster, T.

    1998-11-01

    The proliferation of genetic screening and testing is requiring increasing numbers of Americans to integrate genetic knowledge and interventions into their family life and personal experience. This study examines the social processes that occur as families at risk for two of the most common autosomal recessive diseases, sickle cell disease (SC) and cystic fibrosis (CF), encounter genetic testing. Each of these diseases is found primarily in a different ethnic/racial group (CF in Americans of North European descent and SC in Americans of West African descent). This has permitted them to have a certain additional lens on the role of culture in integrating genetic testing into family life and reproductive planning. A third type of genetic disorder, the thalassemias was added to the sample in order to extent the comparative frame and to include other ethnic and racial groups.

  6. Human high-altitude adaptation: forward genetics meets the HIF pathway

    PubMed Central

    Bigham, Abigail W.

    2014-01-01

    Humans have adapted to the chronic hypoxia of high altitude in several locations, and recent genome-wide studies have indicated a genetic basis. In some populations, genetic signatures have been identified in the hypoxia-inducible factor (HIF) pathway, which orchestrates the transcriptional response to hypoxia. In Tibetans, they have been found in the HIF2A (EPAS1) gene, which encodes for HIF-2?, and the prolyl hydroxylase domain protein 2 (PHD2, also known as EGLN1) gene, which encodes for one of its key regulators, PHD2. High-altitude adaptation may be due to multiple genes that act in concert with one another. Unraveling their mechanism of action can offer new therapeutic approaches toward treating common human diseases characterized by chronic hypoxia. PMID:25319824

  7. On the Origin of Tibetans and Their Genetic Basis in Adapting High-Altitude Environments

    PubMed Central

    Zhang, Feng; Lin, Hongbin; Wang, Xumin; Wan, Ning; Ye, Zhenqing; Weng, Haiyu; Zhang, Lili; Li, Xin; Yan, Jiangwei; Wang, Panpan; Wu, Tingting; Cheng, Longfei; Wang, Jing; Wang, Duen-Mei; Ma, Xu; Yu, Jun

    2011-01-01

    Since their arrival in the Tibetan Plateau during the Neolithic Age, Tibetans have been well-adapted to extreme environmental conditions and possess genetic variation that reflect their living environment and migratory history. To investigate the origin of Tibetans and the genetic basis of adaptation in a rigorous environment, we genotyped 30 Tibetan individuals with more than one million SNP markers. Our findings suggested that Tibetans, together with the Yi people, were descendants of Tibeto-Burmans who diverged from ancient settlers of East Asia. The valleys of the Hengduan Mountain range may be a major migration route. We also identified a set of positively-selected genes that belong to functional classes of the embryonic, female gonad, and blood vessel developments, as well as response to hypoxia. Most of these genes were highly correlated with population-specific and beneficial phenotypes, such as high infant survival rate and the absence of chronic mountain sickness. PMID:21386899

  8. Human high-altitude adaptation: forward genetics meets the HIF pathway.

    PubMed

    Bigham, Abigail W; Lee, Frank S

    2014-10-15

    Humans have adapted to the chronic hypoxia of high altitude in several locations, and recent genome-wide studies have indicated a genetic basis. In some populations, genetic signatures have been identified in the hypoxia-inducible factor (HIF) pathway, which orchestrates the transcriptional response to hypoxia. In Tibetans, they have been found in the HIF2A (EPAS1) gene, which encodes for HIF-2?, and the prolyl hydroxylase domain protein 2 (PHD2, also known as EGLN1) gene, which encodes for one of its key regulators, PHD2. High-altitude adaptation may be due to multiple genes that act in concert with one another. Unraveling their mechanism of action can offer new therapeutic approaches toward treating common human diseases characterized by chronic hypoxia. PMID:25319824

  9. Genetic variability of the high-affinity IgE receptor ?-subunit (Fc?RI?)

    Microsoft Academic Search

    Daniel P. Potaczek; Chiharu Nishiyama; Marek Sanak; Andrew Szczeklik; Ko Okumura

    2009-01-01

    Our knowledge on the variability of FCER1A gene encoding for ?-subunit of the high-affinity immunoglobulin E receptor (Fc?RI) that plays a central role in the pathogenesis\\u000a of allergy and related disorders, has been recently much extended. Last findings from FCER1A mutational screening and genetic association studies, followed by functional analyses of the polymorphisms, are briefly summarized\\u000a in this mini-review. The

  10. Genetic testing among high-risk individuals in families with hereditary nonpolyposis colorectal cancer

    Microsoft Academic Search

    M Ponz de Leon; P Benatti; C Di Gregorio; M Pedroni; L Losi; M Genuardi; A Viel; M Fornasarig; E Lucci-Cordisco; M Anti; G Ponti; F Borghi; I Lamberti; L Roncucci

    2004-01-01

    Hereditary nonpolyposis colorectal cancer (HNPCC) is frequently associated with constitutional mutations in a class of genes involved in DNA mismatch repair. We identified 32 kindreds, with germline mutations in one of three genes hMSH2, hMLH1 or hMSH6. In this study, we purposed to evaluate how many high-risk individuals in each family underwent genetic testing: moreover, we assessed how many mutation-positive

  11. A scalable pipeline for highly effective genetic modification of a malaria parasite

    Microsoft Academic Search

    Claudia Pfander; Burcu Anar; Frank Schwach; Thomas D Otto; Mathieu Brochet; Katrin Volkmann; Michael A Quail; Arnab Pain; Barry Rosen; William Skarnes; Julian C Rayner; Oliver Billker

    2011-01-01

    In malaria parasites, the systematic experimental validation of drug and vaccine targets by reverse genetics is constrained by the inefficiency of homologous recombination and by the difficulty of manipulating adenine and thymine (A+T)-rich DNA of most Plasmodium species in Escherichia coli. We overcame these roadblocks by creating a high-integrity library of Plasmodium berghei genomic DNA (>77% A+T content) in a

  12. Effect of bead and illustrations models on high school students' achievement in molecular genetics

    NASA Astrophysics Data System (ADS)

    Rotbain, Yosi; Marbach-Ad, Gili; Stavy, Ruth

    2006-05-01

    Our main goal in this study was to explore whether the use of models in molecular genetics instruction in high school can contribute to students' understanding of concepts and processes in genetics. Three comparable groups of 11th and 12th graders participated: The control group (116 students) was taught in the traditional lecture format, while the others received instructions which integrated a bead model (71 students), or an illustration model (71 students). Similar instructions and the same guiding questions accompanied the two models. We used three instruments: a multiple-choice and an open-ended written questionnaire, as well as personal interviews. Five of the multiple-choice questions were also given to students before receiving their genetics instruction (pretest). We found that students who used one of the two types of models improved their knowledge in molecular genetics compared to the control group. However, the open-ended questions revealed that bead model activity was significantly more effective than illustration activity. On the basis of these findings we conclude that, though it is advisable to use a three-dimensional model, such as the bead model, engaging students in activities with illustrations can still improve their achievement in comparison to traditional instruction.

  13. Application of Reverse Genetics for Producing Attenuated Vaccine Strains against Highly Pathogenic Avian Influenza Viruses

    PubMed Central

    UCHIDA, Yuko; TAKEMAE, Nobuhiro; SAITO, Takehiko

    2014-01-01

    ABSTRACT In this study, reverse genetics was applied to produce vaccine candidate strains against highly pathogenic avian influenza viruses (HPAIVs) of the H5N1 subtype. The H5 subtype vaccine strains were generated by a reverse genetics method in a biosafety level 2 facility. The strain contained the HA gene from the H5N1 subtype HPAIV attenuated by genetic modification at the cleavage site, the NA gene derived from the H5N1 subtype HPAI or the H5N3 subtype of avian influenza virus and internal genes from A/Puerto Rico/8/34. Vaccination with an inactivated recombinant virus with oil-emulsion completely protected chickens from a homologous viral challenge with a 640 HAU or 3,200 HAU/vaccination dose. Vaccination with a higher dose of antigen, 3,200 HAU, was effective at increasing survival and efficiently reduced viral shedding even when challenged by a virus of a different HA clade. The feasibility of differentiation of infected from vaccinated animals (DIVA) was demonstrated against a challenge with H5N1 HPAIVs when the recombinant H5N3 subtype viruses were used as the antigens of the vaccine. Our study demonstrated that the use of reverse genetics would be an option to promptly produce an inactivated vaccine with better matching of antigenicity to a circulating strain. PMID:24805906

  14. Exploration of genetically determined resistance against hepatitis C infection in high-risk injecting drug users.

    PubMed

    Sugden, P B; Cameron, B; Luciani, F; Lloyd, A R

    2014-08-01

    Genetic resistance to specific infections is well recognized. In hepatitis C virus (HCV) infection, genetic polymorphisms in IL-28B and the killer cell immunoglobulin-like receptors (KIR) and their HLA class I ligands have been shown to affect clearance of the virus following infection. There are limited data regarding resistance to established HCV infection. Reliable quantification of repeated exposure in high-risk populations, such as injecting drug users (IDU), is a key limitation of previous studies of resistance. Behavioural data and DNA from IDU (n = 210) in the Hepatitis C Incidence and Transmission Study in prisons (HITS-p) cohort were genotyped for polymorphisms in: IL-28B, peptidyl-prolyl isomerase A (PPIA), HLA-C and KIR2. To quantify risk, a composite risk index based on factors predictive of incident HCV infection was derived. Logistic regression analysis revealed the risk index was strongly associated with incident HCV infection (P < 0.0001). The upper tertile of the uninfected individuals had risk indices comparable to the incident cases, but remained uninfected. There were no significant differences in the frequencies of IL-28B or PPIA polymorphisms between these exposed-uninfected cases, or in the frequencies of KIR2-DL3, HLA-C1, or their combination. A framework for the investigation of genetic determinants of resistance to HCV infection has been developed. Several candidate gene associations were investigated and excluded. Further investigation of genetic determinants of resistance to HCV infection is warranted. PMID:24612442

  15. High-resolution genetic maps of Eucalyptus improve Eucalyptus grandis genome assembly.

    PubMed

    Bartholomé, Jérôme; Mandrou, Eric; Mabiala, André; Jenkins, Jerry; Nabihoudine, Ibouniyamine; Klopp, Christophe; Schmutz, Jeremy; Plomion, Christophe; Gion, Jean-Marc

    2015-06-01

    Genetic maps are key tools in genetic research as they constitute the framework for many applications, such as quantitative trait locus analysis, and support the assembly of genome sequences. The resequencing of the two parents of a cross between Eucalyptus urophylla and Eucalyptus grandis was used to design a single nucleotide polymorphism (SNP) array of 6000 markers evenly distributed along the E. grandis genome. The genotyping of 1025 offspring enabled the construction of two high-resolution genetic maps containing 1832 and 1773 markers with an average marker interval of 0.45 and 0.5 cM for E. grandis and E. urophylla, respectively. The comparison between genetic maps and the reference genome highlighted 85% of collinear regions. A total of 43 noncollinear regions and 13 nonsynthetic regions were detected and corrected in the new genome assembly. This improved version contains 4943 scaffolds totalling 691.3 Mb of which 88.6% were captured by the 11 chromosomes. The mapping data were also used to investigate the effect of population size and number of markers on linkage mapping accuracy. This study provides the most reliable linkage maps for Eucalyptus and version 2.0 of the E. grandis genome. PMID:25385325

  16. Quantitative genetic basis of fatty acid composition in the GIFT strain of Nile tilapia ( Oreochromis niloticus) selected for high growth

    Microsoft Academic Search

    Nguyen Hong Nguyen; Raul W. Ponzoni; Hoong Yip Yee; Khairul R. Abu-Bakar; Azhar Hamzah; Hooi Ling Khaw

    2010-01-01

    The quantitative genetic basis of fatty acid composition was examined in the Genetically Improved Farmed Tilapia (GIFT) strain of Nile tilapia selected for high breeding value for body weight and in the contemporaneous control selected for average breeding value. Gas chromatography analysis of 514 frozen fillet samples, obtained from the offspring of 104 sires and 154 dams from two generations

  17. Genetic analysis of bed bug populations reveals small propagule size within individual infestations but high genetic diversity across infestations from the eastern United States.

    PubMed

    Saenz, Virna L; Booth, Warren; Schal, Coby; Vargo, Edward L

    2012-07-01

    Bed bugs (Cimex lectularius L.) are a resurgent pest worldwide and infestations within the United States are increasing at a rapid rate. Because of the physical and psychological discomfort inflicted by their blood feeding habits, and allergies and secondary infections associated with bites, bed bugs are recognized as a significant public health problem. Although bed bug infestations are spreading and becoming more prevalent, we have a poor understanding of their dispersal patterns and sources of infestation. To help fill this gap, we conducted a genetic study of 21 bed bug infestations from the eastern United States, nearly all of which came from single rooms within residences. We genotyped samples comprised of 8-10 individuals per infestation at nine polymorphic microsatellite loci. Despite high genetic diversity across all infestations, with 5-17 alleles per locus (mean = 10.3 alleles per locus), we found low genetic diversity (1-4 alleles per locus) within all but one of the infestations. These results suggest that nearly all the studied infestations were started by a small propagule possibly consisting of a singly mated female and/or her progeny, or a female mated with multiple males that were highly related to her. All infestations were strongly genetically differentiated from each other (mean pairwise F(ST) between populations = 0.68) and we did not find strong evidence of a geographic pattern of genetic structure, indicating infestations located in closer proximity to each other were nearly as genetically differentiated as those located hundreds of kilometers away. The high level of genetic diversity across infestations from the eastern United States together with the lack of geographically organized structure is consistent with multiple introductions into the United States from foreign sources. PMID:22897047

  18. High genetic diversity in a small population: the case of Chilean blue whales.

    PubMed

    Torres-Florez, Juan P; Hucke-Gaete, Rodrigo; Rosenbaum, Howard; Figueroa, Christian C

    2014-04-01

    It is generally assumed that species with low population sizes have lower genetic diversities than larger populations and vice versa. However, this would not be the case for long-lived species with long generation times, and which populations have declined due to anthropogenic effects, such as the blue whale (Balaenoptera musculus). This species was intensively decimated globally to near extinction during the 20th century. Along the Chilean coast, it is estimated that at least 4288 blue whales were hunted from an apparently pre-exploitation population size (k) of a maximum of 6200 individuals (Southeastern Pacific). Thus, here, we describe the mtDNA (control region) and nDNA (microsatellites) diversities of the Chilean blue whale aggregation site in order to verify the expectation of low genetic diversity in small populations. We then compare our findings with other blue whale aggregations in the Southern Hemisphere. Interestingly, although the estimated population size is small compared with the pre-whaling era, there is still considerable genetic diversity, even after the population crash, both in mitochondrial (N = 46) and nuclear (N = 52) markers (Hd = 0.890 and Ho = 0.692, respectively). Our results suggest that this diversity could be a consequence of the long generation times and the relatively short period of time elapsed since the end of whaling, which has been observed in other heavily-exploited whale populations. The genetic variability of blue whales on their southern Chile feeding grounds was similar to that found in other Southern Hemisphere blue whale feeding grounds. Our phylogenetic analysis of mtDNA haplotypes does not show extensive differentiation of populations among Southern Hemisphere blue whale feeding grounds. The present study suggests that although levels of genetic diversity are frequently used as estimators of population health, these parameters depend on the biology of the species and should be taken into account in a monitoring framework study to obtain a more complete picture of the conservation status of a population. PMID:24834336

  19. High-Level Genetic Diversity and Complex Population Structure of Siberian Apricot (Prunus sibirica L.) in China as Revealed by Nuclear SSR Markers

    PubMed Central

    Wang, Zhe; Kang, Ming; Liu, Huabo; Gao, Jiao; Zhang, Zhengdong; Li, Yingyue; Wu, Rongling; Pang, Xiaoming

    2014-01-01

    Siberian apricot (Prunus sibirica L.), an ecologically and economically important tree species with a high degree of tolerance to a variety of extreme environmental conditions, is widely distributed across the mountains of northeastern and northern China, eastern and southeastern regions of Mongolia, Eastern Siberia, and the Maritime Territory of Russia. However, few studies have examined the genetic diversity and population structure of this species. Using 31 nuclear microsatellites, we investigated the level of genetic diversity and population structure of Siberian apricot sampled from 22 populations across China. The number of alleles per locus ranged from 5 to 33, with an average of 19.323 alleles. The observed heterozygosity and expected heterozygosity ranged from 0.037 to 0.874 and 0.040 to 0.924 with average values of 0.639 and 0.774, respectively. A STRUCTURE-based analysis clustered all of the populations into four genetic clusters. Significant genetic differentiation was observed between all population pairs. A hierarchical analysis of molecular variance attributed about 94% of the variation to within populations. No significant difference was detected between the wild and semi-wild groups, indicating that recent cultivation practices have had little impact on the genetic diversity of Siberian apricot. The Mantel test showed that the genetic distance among the populations was not significantly correlated with geographic distance (r?=?0.4651, p?=?0.9940). Our study represents the most comprehensive investigation of the genetic diversity and population structure of Siberian apricot in China to date, and it provides valuable information for the collection of genetic resources for the breeding of Siberian apricot and related species. PMID:24516551

  20. Drainage-independent genetic structure and high genetic diversity of endangered freshwater pearl mussels ( Margaritifera margaritifera ) in northern Europe

    Microsoft Academic Search

    Juergen Geist; Hĺkan Söderberg; Andreas Karlberg; Ralph Kuehn

    2010-01-01

    Freshwater pearl mussels (Margaritifera margaritifera) are among the most critically threatened bivalve molluscs worldwide. An understanding of spatial patterns of genetic diversity\\u000a is crucial for the development of integrative conservation strategies. We used microsatellites to study the genetic diversity\\u000a and differentiation of 14 populations of M. margaritifera in central Sweden, an area which was described as a major secondary contact

  1. The influence of genetic variation on innate immune activation in an environment with high infectious pressure.

    PubMed

    Boef, A G C; May, L; van Bodegom, D; Kuningas, M; Eriksson, U K; Westendorp, R G J

    2012-02-01

    Interleukin-10 (IL-10) production is under tight genetic control in populations living in affluent environments. However, little is known about the role of IL10 genetics on cytokine production in populations living in environments with high infectious pressure. We have previously reported that, in a rural Ghanaian population, the most common IL10 haplotype associates with a pro-inflammatory response. Here, we aim to replicate these findings in an independent sample of the same population 2 years later. IL-10 and tumour necrosis factor-? (TNF-?) protein concentrations were determined in whole-blood samples ex vivo stimulated with lipopolysaccharide and zymosan in 2006 (n=615) and 2008 (n=647). The association between IL10 single nucleotide polymorphisms and Z-scores of IL-10 and TNF-? levels was analysed in each population subset. The most common IL10 haplotype was associated with a significantly lower IL-10 production and nonsignificantly increased TNF-? levels. The correlation between repeated cytokine assays, based on 111 individuals with measurements in both 2006 and 2008, was r=0.53 (P<0.001) for IL-10 and r=0.36 (P<0.001) for TNF-?. The replication of our previously found effect of variation in the IL10 gene on IL-10 production and the correlation between repeated cytokine stimulation assays provide evidence that IL10 genetics have an important role in regulating the host response under high infectious pressure. PMID:21833021

  2. Dinucleotide repeat loci contribute highly informative genetic markers to the human chromosome 2 linkage map

    SciTech Connect

    Todd, S. (Eleanor Roosevelt Institute, Denver, CO (United States)); Sherman, S.L. (Emory Univ. School of Medicine, Atlanta, GA (United States)); Naylor, S.L. (Univ. of Texas Health Science Center, San Antonio, TX (United States))

    1993-06-01

    Microsatellite repeat loci can provide informative markers for genetic linkage. Currently, the human chromosome 2 genetic linkage map has very few highly polymorphic markers. Being such a large chromosome, it will require a large number of informative markers for the dense coverage desired to allow disease genes to be mapped quickly and accurately. Dinucleotide repeat loci from two anonymous chromosome 2 genomic DNA clones were sequenced so that oligonucleotide primers could be designed for amplifying each locus using the polymerase chain reaction (PCR). Five sets of PCR primers were also generated from nucleotide sequences in the GenBank Database of chromosome 2 genes containing dinucleotide repeats. In addition, one PCR primer pair was made that amplifies a restriction fragment length polymorphism on the TNP1 gene. These markers were placed on the CEPH genetic linkage map by screening the CEPH reference DNA panel with each primer set, combining these data with those of other markers previously placed on the map, and analyzing the combined data set using CRI-MAP and LINKAGE. The microsatellite loci are highly informative markers and the TNP1 locus, as expected, is only moderately informative. A map was constructed with 38 ordered loci (odds [ge] 1000:1) spanning 296 cM (male) and 476 cM (female) of chromosome 2 compared with 306 cM (male) and 529 cM (female) for a previous map of 20 markers. 32 refs., 2 figs., 3 tabs.

  3. Efficient high-resolution genetic mapping of mouse interspersed repetitive sequence PCR products, toward integrated genetic and physical mapping of the mouse genome.

    PubMed Central

    McCarthy, L; Hunter, K; Schalkwyk, L; Riba, L; Anson, S; Mott, R; Newell, W; Bruley, C; Bar, I; Ramu, E

    1995-01-01

    The ability to carry out high-resolution genetic mapping at high throughput in the mouse is a critical rate-limiting step in the generation of genetically anchored contigs in physical mapping projects and the mapping of genetic loci for complex traits. To address this need, we have developed an efficient, high-resolution, large-scale genome mapping system. This system is based on the identification of polymorphic DNA sites between mouse strains by using interspersed repetitive sequence (IRS) PCR. Individual cloned IRS PCR products are hybridized to a DNA array of IRS PCR products derived from the DNA of individual mice segregating DNA sequences from the two parent strains. Since gel electrophoresis is not required, large numbers of samples can be genotyped in parallel. By using this approach, we have mapped > 450 polymorphic probes with filters containing the DNA of up to 517 backcross mice, potentially allowing resolution of 0.14 centimorgan. This approach also carries the potential for a high degree of efficiency in the integration of physical and genetic maps, since pooled DNAs representing libraries of yeast artificial chromosomes or other physical representations of the mouse genome can be addressed by hybridization of filter representations of the IRS PCR products of such libraries. Images Fig. 1 Fig. 2 Fig. 4 Fig. 5 PMID:7777502

  4. High-density SNP-based genetic map development and linkage disequilibrium assessment in Brassica napus L

    PubMed Central

    2013-01-01

    Background High density genetic maps built with SNP markers that are polymorphic in various genetic backgrounds are very useful for studying the genetics of agronomical traits as well as genome organization and evolution. Simultaneous dense SNP genotyping of segregating populations and variety collections was applied to oilseed rape (Brassica napus L.) to obtain a high density genetic map for this species and to study the linkage disequilibrium pattern. Results We developed an integrated genetic map for oilseed rape by high throughput SNP genotyping of four segregating doubled haploid populations. A very high level of collinearity was observed between the four individual maps and a large number of markers (>59%) was common to more than two maps. The precise integrated map comprises 5764 SNP and 1603 PCR markers. With a total genetic length of 2250 cM, the integrated map contains a density of 3.27 markers (2.56 SNP) per cM. Genotyping of these mapped SNP markers in oilseed rape collections allowed polymorphism level and linkage disequilibrium (LD) to be studied across the different collections (winter vs spring, different seed quality types) and along the linkage groups. Overall, polymorphism level was higher and LD decayed faster in spring than in “00” winter oilseed rape types but this was shown to vary greatly along the linkage groups. Conclusions Our study provides a valuable resource for further genetic studies using linkage or association mapping, for marker assisted breeding and for Brassica napus sequence assembly and genome organization analyses. PMID:23432809

  5. Genetic Pool Information Reflects Highly Suitable Areas: The Case of Two Parapatric Endangered Species of Tuco-tucos (Rodentia: Ctenomiydae)

    PubMed Central

    Galiano, Daniel; Bernardo-Silva, Jorge; de Freitas, Thales R. O.

    2014-01-01

    Conservation of small mammals requires knowledge of the genetically and ecologically meaningful spatial scales at which species respond to habitat modifications. Conservation strategies can be improved through the use of ecological niche models and genetic data to classify areas of high environmental suitability. In this study, we applied a Maxent model integrated with genetic information (nucleotide diversity, haplotype diversity and Fu's Fs neutrality tests) to evaluate potential genetic pool populations with highly suitable areas for two parapatric endangered species of tuco-tucos (Ctenomys minutus and C. lami). Our results demonstrated that both species were largely influenced by vegetation and soil variables at a landscape scale and inhabit a highly specific niche. Ctenomys minutus was also influenced by the variable altitude; the species was associated with low altitudes (sea level). Our model of genetic data associated with environmental suitability indicate that the genetic pool data were associated with highly suitable areas for C. minutus. This pattern was not evident for C. lami, but this outcome could be a consequence of the restricted range of the species. The preservation of species requires not only detailed knowledge of their natural history and genetic structure but also information on the availability of suitable areas where species can survive, and such knowledge can aid significantly in conservation planning. This finding reinforces the use of these two techniques for planning conservation actions. PMID:24819251

  6. Family Process and High School Adjustment of Boys Who Showed Depressive Symptoms with and without Co-Occurring Conduct Problems in Early Adolescence.

    ERIC Educational Resources Information Center

    Capaldi, Deborah

    Family process and peer relationships for boys who showed depressive symptoms with or without co-occurring conduct problems in early adolescence were analyzed in this study. Also examined were outcomes in late adolescence and young adulthood including the relationship with parents and peers and graduation from high school for these boys. The…

  7. In many cases, tsunami waveheights and effects show a high variability along the coast. The possible causes are insecurities about the tectonic

    E-print Network

    Al Hanbali, Ahmad

    In many cases, tsunami waveheights and effects show a high variability along the coast area in propagation direction of a tsunami wave can produce largely amplified waves by near coast tsunami waveguiding, see [1]. The waveguiding is caused by the fact that different propagation speeds

  8. BORDERLINE PERSONALITY TRAITS AND SUBSTANCE USE: GENETIC FACTORS UNDERLIE THE ASSOCIATION WITH SMOKING AND EVER USE OF CANNABIS, BUT NOT WITH HIGH ALCOHOL CONSUMPTION

    PubMed Central

    Distel, Marijn A.; Trull, Tim J.; de Moor, Marleen M. H.; Vink, Jacqueline M.; Geels, Lot M.; van Beek, Jenny H. D. A.; Bartels, Meike; Willemsen, Gonneke; Thiery, Evert; Derom, Catherine A.; Neale, Michael C.; Boomsma, Dorret I.

    2013-01-01

    Borderline personality disorder (BPD) and substance use disorders often co-occur. Both disorders are heritable and family studies showed that there are familial factors that increase the risk for BPD as well as substance use/abuse. This is the first study that investigates whether the association of borderline personality traits (BPT) with substance use reflects an underlying genetic vulnerability or nongenetic familial influences. To this end we analyzed data of 5,638 Dutch and Belgian twins aged between 21–50 years from 3,567 families. Significant associations between BPT and high alcohol consumption (r = .192), regular smoking (r = .299), and ever use of cannabis (r = .254) were found. Bivariate genetic analyses showed that the associations of BPT and substance use had different etiologies. For regular smoking and for ever use of cannabis, the correlation with BPT was explained by common genetic factors. Interestingly, for high alcohol consumption and BPT the association was explained by unique environmental factors that influence both traits rather than common genetic factors. PMID:23281672

  9. High genetic differentiation and cross-shelf patterns of genetic diversity among Great Barrier Reef populations of Symbiodinium

    NASA Astrophysics Data System (ADS)

    Howells, E. J.; van Oppen, M. J. H.; Willis, B. L.

    2009-03-01

    The resilience of Symbiodinium harboured by corals is dependent on the genetic diversity and extent of connectivity among reef populations. This study presents genetic analyses of Great Barrier Reef (GBR) populations of clade C Symbiodinium hosted by the alcyonacean coral, Sinularia flexibilis. Allelic variation at four newly developed microsatellite loci demonstrated that Symbiodinium populations are genetically differentiated at all spatial scales from 16 to 1,360 km (pairwise ?ST = 0.01-0.47, mean = 0.22); the only exception being two neighbouring populations in the Cairns region separated by 17 km. This indicates that gene flow is restricted for Symbiodinium C hosted by S. flexibilis on the GBR. Patterns of population structure reflect longshore circulation patterns and limited cross-shelf mixing, suggesting that passive transport by currents is the primary mechanism of dispersal in Symbiodinium types that are acquired horizontally. There was no correlation between the genetic structure of Symbiodinium populations and their host S. flexibilis, most likely because different factors affect the dispersal and recruitment of each partner in the symbiosis. The genetic diversity of these Symbiodinium reef populations is on average 1.5 times lower on inshore reefs than on offshore reefs. Lower inshore diversity may reflect the impact of recent bleaching events on Sinularia assemblages, which have been more widespread and severe on inshore reefs, but may also have been shaped by historical sea level fluctuations or recent migration patterns.

  10. Predicting first episode psychosis in those at high risk for genetic or cognitive reasons.

    PubMed

    Lawrie, Stephen M; Stanfield, Andrew; Johnstone, Eve C; McIntosh, Andrew M

    2012-12-01

    Structural and functional magnetic resonance imaging (MRI) of patients with psychosis has advanced to the point where there are clear abnormalities at a group level between patients and groups of healthy controls, and suggestions of different patterns of abnormalities between groups of patients. A major area of research endeavour is being able to translate these group differences into clinically relevant predictions at an individual patient level. Here, we briefly summarize our main findings in cohorts at high risk of psychosis because they come from families in which several members have schizophrenia or bipolar disorder, or have educational impairments. We highlight consistent predictors of psychosis in those at high risk of schizophrenia for genetic or cognitive reasons, as compared with quite distinct profiles between those at genetic high risk of schizophrenia v. bipolar disorder on functional MRI during an executive language task. We also consider future research directions and ethical issues in the early diagnostic testing of people at high risk of psychosis. PMID:22967956

  11. High-Voltage Electroporation of Bacteria: Genetic Transformation of Campylobacter jejuni with Plasmid DNA

    NASA Astrophysics Data System (ADS)

    Miller, Jeff F.; Dower, William J.; Tompkins, Lucy S.

    1988-02-01

    Electroporation permits the uptake of DNA by mammalian cells and plant protoplasts because it induces transient permeability of the cell membrane. We investigated the utility of high-voltage electroporation as a method for genetic transformation of intact bacterial cells by using the enteric pathogen Campylobacter jejuni as a model system. This report demonstrates that the application of high-voltage discharges to bacterial cells permits genetic transformation. Our method involves exposure of a Campylobacter cell suspension to a high-voltage exponential decay discharge (5-13 kV/cm) for a brief period of time (resistance-capacitance time constant = 2.4-26 msec) in the presence of plasmid DNA. Electrical transformation of C. jejuni results in frequencies as high as 1.2 × 106 transformants per ? g of DNA. We have investigated the effects of pulse amplitude and duration, cell growth conditions, divalent cations, and DNA concentration on the efficiency of transformation. Transformants of C. jejuni obtained by electroporation contained structurally intact plasmid molecules. In addition, evidence is presented that indicates that C. jejuni possesses DNA restriction and modification systems. The use of electroporation as a method for transforming other bacterial species and guidelines for its implementation are also discussed.

  12. Analysis of genetic variation and diversity of Rice stripe virus populations through high-throughput sequencing

    PubMed Central

    Huang, Lingzhe; Li, Zefeng; Wu, Jianxiang; Xu, Yi; Yang, Xiuling; Fan, Longjiang; Fang, Rongxiang; Zhou, Xueping

    2015-01-01

    Plant RNA viruses often generate diverse populations in their host plants through error-prone replication and recombination. Recent studies on the genetic diversity of plant RNA viruses in various host plants have provided valuable information about RNA virus evolution and emergence of new diseases caused by RNA viruses. We analyzed and compared the genetic diversity of Rice stripe virus (RSV) populations in Oryza sativa (a natural host of RSV) and compared it with that of the RSV populations generated in an infection of Nicotiana benthamiana, an experimental host of RSV, using the high-throughput sequencing technology. From infected O. sativa and N. benthamiana plants, a total of 341 and 1675 site substitutions were identified in the RSV genome, respectively, and the average substitution ratio in these sites was 1.47 and 7.05 %, respectively, indicating that the RSV populations from infected N. benthamiana plant are more diverse than those from infected O. sativa plant. Our result gives a direct evidence that virus might allow higher genetic diversity for host adaptation. PMID:25852724

  13. High postmortem temperature in muscle has very similar consequences in two turkey genetic lines.

    PubMed

    Molette, C; Sérieye, V; Rossignol, M; Babilé, R; Fernandez, X; Rémignon, H

    2006-12-01

    In the present study, we artificially generated pale, soft, exudative turkey meat by holding muscles immediately after death at 40 degrees C for 6 h. Two genetic types (BUT9 and Label) were compared. When muscles were kept at 40 degrees C, BUT9 muscles exhibited higher lightness values than Label muscles. Drip, thawing, and cook losses were higher for muscles held at 40 degrees C, compared with those held at 4 degrees C, regardless of genetic type. A significant decrease in meat tenderness was found for muscles kept at 40 degrees C. For both genetic types, protein extractabilities either with low ionic strength or high ionic strength buffer decreased for muscles held at 40 degrees C. These fractions were analyzed by using SDS-PAGE, and proteins that differed from the 4 degrees C and 40 degrees C treatments were identified using a matrix-assisted laser desorption ionization time-of-flight mass spectrometer. We reported the alteration of various proteins, such as alpha-actinin, myosin heavy chain, myokinase, phosphorylase, and ATP synthase. PMID:17135686

  14. Development and Integration of Genome-Wide Polymorphic Microsatellite Markers onto a Reference Linkage Map for Constructing a High-Density Genetic Map of Chickpea.

    PubMed

    Khajuria, Yash Paul; Saxena, Maneesha S; Gaur, Rashmi; Chattopadhyay, Debasis; Jain, Mukesh; Parida, Swarup K; Bhatia, Sabhyata

    2015-01-01

    The identification of informative in silico polymorphic genomic and genic microsatellite markers by comparing the genome and transcriptome sequences of crop genotypes is a rapid, cost-effective and non-laborious approach for large-scale marker validation and genotyping applications, including construction of high-density genetic maps. We designed 1494 markers, including 1016 genomic and 478 transcript-derived microsatellite markers showing in-silico fragment length polymorphism between two parental genotypes (Cicer arietinum ICC4958 and C. reticulatum PI489777) of an inter-specific reference mapping population. High amplification efficiency (87%), experimental validation success rate (81%) and polymorphic potential (55%) of these microsatellite markers suggest their effective use in various applications of chickpea genetics and breeding. Intra-specific polymorphic potential (48%) detected by microsatellite markers in 22 desi and kabuli chickpea genotypes was lower than inter-specific polymorphic potential (59%). An advanced, high-density, integrated and inter-specific chickpea genetic map (ICC4958 x PI489777) having 1697 map positions spanning 1061.16 cM with an average inter-marker distance of 0.625 cM was constructed by assigning 634 novel informative transcript-derived and genomic microsatellite markers on eight linkage groups (LGs) of our prior documented, 1063 marker-based genetic map. The constructed genome map identified 88, including four major (7-23 cM) longest high-resolution genomic regions on LGs 3, 5 and 8, where the maximum number of novel genomic and genic microsatellite markers were specifically clustered within 1 cM genetic distance. It was for the first time in chickpea that in silico FLP analysis at genome-wide level was carried out and such a large number of microsatellite markers were identified, experimentally validated and further used in genetic mapping. To best of our knowledge, in the presently constructed genetic map, we mapped highest number of new sequence-based robust microsatellite markers (634) which is an advancement over the previously documented (~300 markers) inter-specific genetic maps. This advanced high-density map will serve as a foundation for large-scale marker validation and genotyping applications, including identification and targeted mapping of trait-specific genes/QTLs (quantitative trait loci) with sub-optimal use of resources and labour in chickpea. PMID:25974327

  15. Population analysis of Vibrio parahaemolyticus originating from different geographical regions demonstrates a high genetic diversity

    PubMed Central

    2014-01-01

    Background Vibrio parahaemolyticus is frequently isolated from environmental and seafood samples and associated with gastroenteritis outbreakes in American, European, Asian and African countries. To distinguish between different lineages of V. parahaemolyticus various genotyping techniques have been used, incl. multilocus sequence typing (MLST). Even though some studies have already applied MLST analysis to characterize V. parahaemolyticus strain sets, these studies have been restricted to specific geographical areas (e.g. U.S. coast, Thailand and Peru), have focused exclusively on pandemic or non-pandemic pathogenic isolates or have been based on a limited strain number. Results To generate a global picture of V. parahaemolyticus genotype distribution, a collection of 130 environmental and seafood related V. parahaemolyticus isolates of different geographical origins (Sri Lanka, Ecuador, North Sea and Baltic Sea as well as German retail) was subjected to MLST analysis after modification of gyrB and recA PCRs. The V. parahaemolyticus population was composed of 82 unique Sequence Types (STs), of which 68 (82.9%) were new to the pubMLST database. After translating the in-frame nucleotide sequences into amino acid sequences, less diversity was detectable: a total of 31 different peptide Sequence Types (pSTs) with 19 (61.3%) new pSTs were generated from the analyzed isolates. Most STs did not show a global dissemination, but some were supra-regionally distributed and clusters of STs were dependent on geographical origin. On peptide level no general clustering of strains from specific geographical regions was observed, thereby the most common pSTs were found on all continents (Asia, South America and Europe) and rare pSTs were restricted to distinct countries or even geographical regions. One lineage of pSTs associated only with strains from North and Baltic Sea strains was identified. Conclusions Our study reveals a high genetic diversity in the analyzed V. parahaemolyticus strain set as well as for geographical strain subsets, with a high proportion of newly discovered alleles and STs. Differences between the subsets were identified. Our data support the postulated population structure of V. parahaemolyticus which follows the ‘epidemic’ model of clonal expansion. Application of peptide based AA-MLST allowed the identification of reliable relationships between strains. PMID:24606756

  16. USF-1 genetic polymorphisms confer a high risk of nonalcoholic fatty liver disease in Chinese population

    PubMed Central

    Wang, Ying; Wang, Bai-Fang; Tong, Jing; Chang, Bing; Wang, Bing-Yuan

    2015-01-01

    Genetic polymorphisms in upstream transcription factor 1 (USF1) were investigated for their links to increased risk of nonalcoholic fatty liver disease (NAFLD) in Chinese population. Between January 2013 and April 2014, 174 patients with NAFLD in the First Affiliated Hospital of China Medical University were selected for this study. A group of 100 healthy subjects were identified as the control group. The MALDI-TOF-MS, a mass spectrometry based technique, was used to detect USF-1 genetic polymorphisms using PCR amplified DNA products. Furthermore, Automatic Chemistry Analyzer (ACA) was used to determine the clinical indicators. Genotypes, allele frequencies and clinical indicators were measured to assess NAFLD risk in relation to the SNPs. USF-1 rs6427573 genetic polymorphisms were associated with an increased risk of NAFLD (AA vs. GG: OR = 3.16, 95% CI = 1.56-6.43, P = 0.001; GA + AA vs. GG: OR = 1.87, 95% CI = 1.13-3.09, P = 0.015; GG + AA vs. AA: OR = 2.96, 95% CI = 1.49-5.88, P = 0.001; G vs. A: OR = 2.10, 95% CI = 1.43-3.09, P < 0.001). Similarly, rs2516839 polymorphisms also conferred a risk for NAFLD (AA vs. GG: OR = 2.49, 95% CI = 1.43-4.34, P = 0.001; GA + AA vs. GG: OR = 1.69, 95% CI = 1.02-2.78, P = 0.041). On the other hand, rs3737787 and rs2774279 showed no statistical significances in the NAFLD group and control group (P > 0.05). Two USF-1 genetic polymorphisms, rs6427573 and rs2516839, may present an increased risk of NAFLD. PMID:25932200

  17. Mapping of Genetic Abnormalities of Primary Tumours from Metastatic CRC by High-Resolution SNP Arrays

    PubMed Central

    Sayagués, José María; Fontanillo, Celia; Abad, María del Mar; González-González, María; Sarasquete, María Eugenia; del Carmen Chillon, Maria; Garcia, Eva; Bengoechea, Oscar; Fonseca, Emilio; Gonzalez-Diaz, Marcos; De Las Rivas, Javier

    2010-01-01

    Background For years, the genetics of metastatic colorectal cancer (CRC) have been studied using a variety of techniques. However, most of the approaches employed so far have a relatively limited resolution which hampers detailed characterization of the common recurrent chromosomal breakpoints as well as the identification of small regions carrying genetic changes and the genes involved in them. Methodology/Principal Findings Here we applied 500K SNP arrays to map the most common chromosomal lesions present at diagnosis in a series of 23 primary tumours from sporadic CRC patients who had developed liver metastasis. Overall our results confirm that the genetic profile of metastatic CRC is defined by imbalanced gains of chromosomes 7, 8q, 11q, 13q, 20q and X together with losses of the 1p, 8p, 17p and 18q chromosome regions. In addition, SNP-array studies allowed the identification of small (<1.3 Mb) and extensive/large (>1.5 Mb) altered DNA sequences, many of which contain cancer genes known to be involved in CRC and the metastatic process. Detailed characterization of the breakpoint regions for the altered chromosomes showed four recurrent breakpoints at chromosomes 1p12, 8p12, 17p11.2 and 20p12.1; interestingly, the most frequently observed recurrent chromosomal breakpoint was localized at 17p11.2 and systematically targeted the FAM27L gene, whose role in CRC deserves further investigations. Conclusions/Significance In summary, in the present study we provide a detailed map of the genetic abnormalities of primary tumours from metastatic CRC patients, which confirm and extend on previous observations as regards the identification of genes potentially involved in development of CRC and the metastatic process. PMID:21060790

  18. High-precision genetic mapping of behavioral traits in the diversity outbred mouse population

    PubMed Central

    Logan, R W; Robledo, R F; Recla, J M; Philip, V M; Bubier, J A; Jay, J J; Harwood, C; Wilcox, T; Gatti, D M; Bult, C J; Churchill, G A; Chesler, E J

    2013-01-01

    Historically our ability to identify genetic variants underlying complex behavioral traits in mice has been limited by low mapping resolution of conventional mouse crosses. The newly developed Diversity Outbred (DO) population promises to deliver improved resolution that will circumvent costly fine-mapping studies. The DO is derived from the same founder strains as the Collaborative Cross (CC), including three wild-derived strains. Thus the DO provides more allelic diversity and greater potential for discovery compared to crosses involving standard mouse strains. We have characterized 283 male and female DO mice using open-field, light–dark box, tail-suspension and visual-cliff avoidance tests to generate 38 behavioral measures. We identified several quantitative trait loci (QTL) for these traits with support intervals ranging from 1 to 3 Mb in size. These intervals contain relatively few genes (ranging from 5 to 96). For a majority of QTL, using the founder allelic effects together with whole genome sequence data, we could further narrow the positional candidates. Several QTL replicate previously published loci. Novel loci were also identified for anxiety- and activity-related traits. Half of the QTLs are associated with wild-derived alleles, confirming the value to behavioral genetics of added genetic diversity in the DO. In the presence of wild-alleles we sometimes observe behaviors that are qualitatively different from the expected response. Our results demonstrate that high-precision mapping of behavioral traits can be achieved with moderate numbers of DO animals, representing a significant advance in our ability to leverage the mouse as a tool for behavioral genetics PMID:23433259

  19. High-precision genetic mapping of behavioral traits in the diversity outbred mouse population.

    PubMed

    Logan, R W; Robledo, R F; Recla, J M; Philip, V M; Bubier, J A; Jay, J J; Harwood, C; Wilcox, T; Gatti, D M; Bult, C J; Churchill, G A; Chesler, E J

    2013-06-01

    Historically our ability to identify genetic variants underlying complex behavioral traits in mice has been limited by low mapping resolution of conventional mouse crosses. The newly developed Diversity Outbred (DO) population promises to deliver improved resolution that will circumvent costly fine-mapping studies. The DO is derived from the same founder strains as the Collaborative Cross (CC), including three wild-derived strains. Thus the DO provides more allelic diversity and greater potential for discovery compared to crosses involving standard mouse strains. We have characterized 283 male and female DO mice using open-field, light-dark box, tail-suspension and visual-cliff avoidance tests to generate 38 behavioral measures. We identified several quantitative trait loci (QTL) for these traits with support intervals ranging from 1 to 3?Mb in size. These intervals contain relatively few genes (ranging from 5 to 96). For a majority of QTL, using the founder allelic effects together with whole genome sequence data, we could further narrow the positional candidates. Several QTL replicate previously published loci. Novel loci were also identified for anxiety- and activity-related traits. Half of the QTLs are associated with wild-derived alleles, confirming the value to behavioral genetics of added genetic diversity in the DO. In the presence of wild-alleles we sometimes observe behaviors that are qualitatively different from the expected response. Our results demonstrate that high-precision mapping of behavioral traits can be achieved with moderate numbers of DO animals, representing a significant advance in our ability to leverage the mouse as a tool for behavioral genetics. PMID:23433259

  20. Multivariate genetic analysis of plant responses to water deficit and high temperature revealed contrasting adaptive strategies

    PubMed Central

    Vasseur, François; Bontpart, Thibaut; Dauzat, Myriam; Granier, Christine; Vile, Denis

    2014-01-01

    How genetic factors control plant performance under stressful environmental conditions is a central question in ecology and for crop breeding. A multivariate framework was developed to examine the genetic architecture of performance-related traits in response to interacting environmental stresses. Ecophysiological and life history traits were quantified in the Arabidopsis thaliana Ler×Cvi mapping population exposed to constant soil water deficit and high air temperature. The plasticity of the genetic variance–covariance matrix (G-matrix) was examined using mixed-effects models after regression into principal components. Quantitative trait locus (QTL) analysis was performed on the predictors of genotype effects and genotype by environment interactions (G×E). Three QTLs previously identified for flowering time had antagonistic G×E effects on carbon acquisition and the other traits (phenology, growth, leaf morphology, and transpiration). This resulted in a size-dependent response of water use efficiency (WUE) to high temperature but not soil water deficit, indicating that most of the plasticity of carbon acquisition and WUE to temperature is controlled by the loci that control variation of development, size, growth, and transpiration. A fourth QTL, MSAT2.22, controlled the response of carbon acquisition to specific combinations of watering and temperature irrespective of plant size and development, growth, and transpiration rate, which resulted in size-independent plasticity of WUE. These findings highlight how the strategies to optimize plant performance may differ in response to water deficit and high temperature (or their combination), and how different G×E effects could be targeted to improve plant tolerance to these stresses. PMID:25246443

  1. Molecular Evidence For High Levels of Intrapopulation Genetic Diversity in Woodrats (Neotoma Micropus)

    PubMed Central

    Mendez-Harclerode, Francisca M.; Strauss, Richard E.; Fulhorst, Charles F.; Milazzo, Mary L.; Ruthven, Donald C.; Bradley, Robert D.

    2009-01-01

    Nucleotide sequences from the mitochondrial control region and genotypes from 5 nuclear microsatellite loci were used to examine genetic structure and infer recent (within approximately the last 3,000 years) evolutionary history of a population (549 individuals) of the southern plains woodrat (Neotoma micropus). Observed heterozygosity values ranged from 0.61 to 0.89 across microsatellite loci and systematically were lower than expected heterozygosity values (0.66–0.95). Probability of unique identity using microsatellite data was high (1 individual in 66,005,424). Fifty-three mitochondrial haplotypes were obtained from 150 individuals. FST values estimated from sequence and microsatellite data were 0.061 and 0.011, respectively, and the RST for microsatellite data was 0.007. Within-group genetic variation ranged from 93.90% to 99.99% depending on whether sequence or microsatellite data were examined. Analyses of microsatellite data suggested that all sampled individuals belonged to a single population, albeit genetically diverse. However, combined data analyses suggested the presence of low levels of substructure attributable to maternal lineages within the population. Low nucleotide-diversity values (0.007–0.010) in addition to high haplotype-diversity values (0.915–0.933) indicate a high number of closely related haplotypes, and suggest that this population may have undergone a recent expansion. However, Fu's FS statistic did not fully support this finding, because it did not reveal a significant excess of recent mutations. A phylogenetic approach using the haplotype sequence data and a combined set including both haplotype and genotype data was used to test for evolutionary patterns and history. PMID:19890482

  2. Tuftsin-based, EGFR-targeting fusion protein and its enediyne-energized analog show high antitumor efficacy associated with CD47 down-regulation.

    PubMed

    Liu, Wen-Juan; Liu, Xiu-Jun; Li, Liang; Li, Yi; Zhang, Sheng-Hua; Zhen, Yong-Su

    2014-12-01

    Tuftsin (TF) is an immunomodulator tetrapeptide (Thr-Lys-Pro-Arg) that binds to the receptor neuropilin-1 (Nrp1) on the surface of cells. Many reports have described anti-tumor activity of tuftsin to relate with nonspecific activation of the host immune system. Lidamycin (LDM) that displays extremely potent cytotoxicity to cancer cells is composed of an apoprotein (LDP) and an enediyne chromophore (AE). In addition, Ec is an EGFR-targeting oligopeptide. In the present study, LDP was used as protein scaffold and the specific carrier for the highly potent AE. Genetically engineered fusion proteins LDP-TF and Ec-LDP-TF were prepared; then, the enediyne-energized fusion protein Ec-LDM-TF was generated by integration of AE into Ec-LDP-TF. The tuftsin-based fusion proteins LDP-TF and Ec-LDP-TF significantly enhanced the phagocytotic activity of macrophages as compared with LDP (P < 0.05). Ec-LDP-TF effectively bound to tumor cells and macrophages; furthermore, it markedly suppressed the growth of human epidermoid carcinoma A431 xenograft in athymic mice by 84.2 % (P < 0.05) with up-regulated expression of TNF-? and IFN-?. Ec-LDM-TF further augmented the therapeutic efficacy, inhibiting the growth of A431 xenograft by 90.9 % (P < 0.05); notably, the Ec-LDM-TF caused marked down-regulation of CD47 in A431 cells. Moreover, the best therapeutic effect was recorded in the group of animals treated with the combination of Ec-LDP-TF with Ec-LDM-TF. The results suggest that tuftsin-based, enediyne-energized, and EGFR-targeting fusion proteins exert highly antitumor efficacy with CD47 modulation. Tuftsin-based fusion proteins are potentially useful for treatment of EGFR- and CD47-overexpressing cancers. PMID:25164878

  3. Two Different High Throughput Sequencing Approaches Identify Thousands of De Novo Genomic Markers for the Genetically Depleted Bornean Elephant

    PubMed Central

    Sharma, Reeta; Goossens, Benoit; Kun-Rodrigues, Célia; Teixeira, Tatiana; Othman, Nurzhafarina; Boone, Jason Q.; Jue, Nathaniel K.; Obergfell, Craig; O'Neill, Rachel J.; Chikhi, Lounčs

    2012-01-01

    High throughput sequencing technologies are being applied to an increasing number of model species with a high-quality reference genome. The application and analyses of whole-genome sequence data in non-model species with no prior genomic information are currently under way. Recent sequencing technologies provide new opportunities for gathering genomic data in natural populations, laying the empirical foundation for future research in the field of conservation and population genomics. Here we present the case study of the Bornean elephant, which is the most endangered subspecies of Asian elephant and exhibits very low genetic diversity. We used two different sequencing platforms, the Roche 454 FLX (shotgun) and Illumina, GAIIx (Restriction site associated DNA, RAD) to evaluate the feasibility of the two methodologies for the discovery of de novo markers (single nucleotide polymorphism, SNPs and microsatellites) using low coverage data. Approximately, 6,683 (shotgun) and 14,724 (RAD) SNPs were detected within our elephant sequence dataset. Genotyping of a representative sample of 194 SNPs resulted in a SNP validation rate of ? 83 to 94% and 17% of the loci were polymorphic with a low diversity (Ho?=?0.057). Different numbers of microsatellites were identified through shotgun (27,226) and RAD (868) techniques. Out of all di-, tri-, and tetra-microsatellite loci, 1,706 loci had sufficient flanking regions (shotgun) while only 7 were found with RAD. All microsatellites were monomorphic in the Bornean but polymorphic in another elephant subspecies. Despite using different sample sizes, and the well known differences in the two platforms used regarding sequence length and throughput, the two approaches showed high validation rate. The approaches used here for marker development in a threatened species demonstrate the utility of high throughput sequencing technologies as a starting point for the development of genomic tools in a non-model species and in particular for a species with low genetic diversity. PMID:23185354

  4. Blacktip reef sharks, Carcharhinus melanopterus, have high genetic structure and varying demographic histories in their Indo-Pacific range.

    PubMed

    Vignaud, Thomas M; Mourier, Johann; Maynard, Jeffrey A; Leblois, Raphael; Spaet, Julia; Clua, Eric; Neglia, Valentina; Planes, Serge

    2014-11-01

    For free-swimming marine species like sharks, only population genetics and demographic history analyses can be used to assess population health/status as baseline population numbers are usually unknown. We investigated the population genetics of blacktip reef sharks, Carcharhinus melanopterus; one of the most abundant reef-associated sharks and the apex predator of many shallow water reefs of the Indian and Pacific Oceans. Our sampling includes 4 widely separated locations in the Indo-Pacific and 11 islands in French Polynesia with different levels of coastal development. Four-teen microsatellite loci were analysed for samples from all locations and two mitochondrial DNA fragments, the control region and cytochrome b, were examined for 10 locations. For microsatellites, genetic diversity is higher for the locations in the large open systems of the Red Sea and Australia than for the fragmented habitat of the smaller islands of French Polynesia. Strong significant structure was found for distant locations with FST values as high as ~0.3, and a smaller but still significant structure is found within French Polynesia. Both mitochondrial genes show only a few mutations across the sequences with a dominant shared haplotype in French Polynesia and New Caledonia suggesting a common lineage different to that of East Australia. Demographic history analyses indicate population expansions in the Red Sea and Australia that may coincide with sea level changes after climatic events. Expansions and flat signals are indicated for French Polynesia as well as a significant recent bottleneck for Moorea, the most human-impacted lagoon of the locations in French Polynesia. PMID:25251515

  5. Genetic evidence suggests that homosporous ferns with high chromosome numbers are diploid

    PubMed Central

    Haufler, Christopher H.; Soltis, Douglas E.

    1986-01-01

    Homosporous ferns have usually been considered highly polyploid because they have high chromosome numbers (average n = 57.05). In angiosperms, species with chromosome numbers higher than n = 14 generally have more isozymes than those with lower numbers, consistent with their polyploidy. By extrapolation, homosporous ferns would be expected to have many isozymes. However, ongoing surveys indicate that within fern genera, species having the lowest chromosome numbers have the number of isozymes considered typical of diploid seed plants. Only species above these lowest numbers have additional isozymes. Therefore, homosporous ferns either have gone through repeated cycles of polyploidy and gene silencing or were initiated with relatively high chromosome numbers. The latter possibility represents a radical departure from currently advocated hypotheses of fern evolution and suggests that there may be fundamental differences between the genomes of homosporous ferns and those of higher plants. These hypotheses can be tested by genetic, karyological, and molecular techniques. Images PMID:16593713

  6. Toward a more Uniform Sampling of Human Genetic Diversity: A Survey of Worldwide Populations by High-density Genotyping

    PubMed Central

    Xing, Jinchuan; Watkins, W. Scott; Shlien, Adam; Walker, Erin; Huff, Chad D.; Witherspoon, David J.; Zhang, Yuhua; Simonson, Tatum S.; Weiss, Robert B.; Schiffman, Joshua D.; Malkin, David; Woodward, Scott R.; Jorde, Lynn B.

    2010-01-01

    High-throughput genotyping data are useful for making inferences about human evolutionary history. However, the populations sampled to date are unevenly distributed, and some areas (e.g., South and Central Asia) have rarely been sampled in large-scale studies. To assess human genetic variation more evenly, we sampled 296 individuals from 13 worldwide populations that are not covered by previous studies. By combining these samples with a data set from our laboratory and the HapMap II samples, we assembled a final dataset of ~250,000 SNPs in 850 individuals from 40 populations. With more uniform sampling, the estimate of global genetic differentiation (FST) substantially decreases from ~16% with the HapMap II samples to ~11%. A panel of copy number variations typed in the same populations shows patterns of diversity similar to the SNP data, with highest diversity in African populations. This unique sample collection also permits new inferences about human evolutionary history. The comparison of haplotype variation among populations supports a single out-of-Africa migration event and suggests that the founding population of Eurasia may have been relatively large but isolated from Africans for a period of time. We also found a substantial affinity between populations from central Asia (Kyrgyzstani and Mongolian Buryat) and America, suggesting a central Asian contribution to New World founder populations. PMID:20643205

  7. Optimisation of a high speed rotating composite drive shaft using a genetic algorithm - Hybrid high modulus-high resistance carbon solutions

    E-print Network

    Montagnier, Olivier

    2011-01-01

    This study deals with the optimisation of subcritical and supercritical laminated composite drive shafts, based on a genetic algorithm. The first part focuses on the modelling of a composite drive shaft. Flexural vibrations in a simply supported composite drive shaft mounted on viscoelastic supports, including shear effects are studied. In particular, an analytic stability criterion is developed to ensure the integrity of the system. The torsional strength is then computed with the maximum stress criterion, assuming the coupling effects to be null. Torsional buckling of thin walled composite tubes is modelled using a combination between laminate theory and Fl\\"ugge theory. In the second part, the genetic algorithm is developed. The last part presents a comparative study between various composite materials solutions on a helicopter tail rotor driveline. In particular, hybrid tubes consisting of high modulus and high resistance carbon/epoxy plies are studied. These solutions make it possible to replace the conv...

  8. Genetic structuring in three closely related circumpolar plant species: AFLP versus microsatellite markers and high-arctic versus arctic-alpine distributions.

    PubMed

    Skrede, I; Borgen, L; Brochmann, C

    2009-03-01

    Genetic structuring in response to the glacial cycles has been investigated for many plant species, but exclusively high-arctic ones have not been studied. Such extremely cold-adapted species have probably experienced range reductions under the present climate. Here we compare three predominantly selfing species of Draba with different distributions and hardiness (D. subcapitata, high-arctic; D. nivalis, arctic to arctic-alpine; D. fladnizensis, arctic-alpine) for genetic structuring on the basis of two different types of molecular markers (10 microsatellite loci and 160 amplified fragment length polymorphisms (AFLPs)). The degree of genetic structuring within these species is of particular interest because it has been shown that they contain many cryptic biological species. The high-arctic D. subcapitata had less phylogeographic structure, less diversity and fewer private alleles than the other two species, suggesting that long-distance dispersal may occur more frequently in the high arctic, that hardy plants may have higher probability for establishment after dispersal under high-arctic conditions and that high-arctic species may have experienced a bottleneck during the present interglacial. In contrast, D. fladnizensis and D. nivalis showed distinct phylogeographic structure and more diversity, suggesting separate long-term refugia in Eurasia and North America/Beringia. The AFLP markers revealed more phylogeographic structuring than the microsatellites, possibly because of the higher number of loci surveyed and/or because structure at very large geographic scales is blurred by high mutation rate leading to homoplasy at microsatellite loci. The number of genetic groups detected was in any case insignificant compared with the numerous cryptic biological species known within these species, supporting rapid development of sterility barriers. PMID:19066622

  9. Better the Devil You Know? High-Risk Individuals’ Anticipated Psychological Responses to Genetic Testing for Melanoma Susceptibility

    Microsoft Academic Search

    Nadine A. Kasparian; Bettina Meiser; Phyllis N. Butow; R. F. Soames Job; Graham J. Mann

    2006-01-01

    \\u000a Purpose: The psychological consequences of genetic testing for mutations among individuals at increased risk of developing melanoma remain unexamined. The present study aimed to explore anticipated emotional, behavioral, cognitive, and familial responses to hypothetical genetic testing for melanoma susceptibility. Methods: Forty semi-structured interviews were undertaken with affected (n=20) and unaffected (n=20) individuals at either high or average risk of developing

  10. Application of somatic embryogenesis in high-value clonal forestry: Deployment, genetic control, and stability of cryopreserved clones

    Microsoft Academic Search

    Y. S. Park; J. D. Barrett; J. M. Bonga

    1998-01-01

    Summary  The most important advantage of cloning conifers by somatic embryogenesis (SE) is that the embryogenic tissue can be cryopreserved\\u000a without changing its genetic make-up and without loss of juvenility. This offers an opportunity to develop high-value clonal\\u000a varieties by defrosting and repropagating cryopreserved clones after genetic testing has shown which clones are the best performers.\\u000a In the current absence of

  11. Impact of virtual learning environment (VLE): A technological approach to genetics teaching on high school students' content knowledge, self-efficacy and career goal aspirations

    NASA Astrophysics Data System (ADS)

    Kandi, Kamala M.

    This study examines the effect of a technology-based instructional tool 'Geniverse' on the content knowledge gains, Science Self-Efficacy, Technology Self-Efficacy, and Career Goal Aspirations among 283 high school learners. The study was conducted in four urban high schools, two of which have achieved Adequate Yearly Progress (AYP) and two have not. Students in both types of schools were taught genetics either through Geniverse, a virtual learning environment or Dragon genetics, a paper-pencil activity embedded in traditional instructional method. Results indicated that students in all schools increased their knowledge of genetics using either type of instructional approach. Students who were taught using Geniverse demonstrated an advantage for genetics knowledge although the effect was small. These increases were more pronounced in the schools that had been meeting the AYP goal. The other significant effect for Geniverse was that students in the technology-enhanced classrooms increased in science Self-Efficacy while students in the non-technology enhanced classrooms decreased. In addition, students from Non-AYP schools showed an improvement in Science and Technology Self-Efficacy; however the effects were small. The implications of these results for the future use of technology-enriched classrooms were discussed. Keywords: Technology-based instruction, Self-Efficacy, career goals and Adequate Yearly Progress (AYP).

  12. Historical and biological determinants of genetic diversity in the highly endemic triploid sea lavender Limonium dufourii (Plumbaginaceae).

    PubMed

    Palop-Esteban, M; Segarra-Moragues, J G; González-Candelas, F

    2007-09-01

    Microsatellite markers were used to evaluate the genetic diversity and population genetic structure in the critically endangered Limonium dufourii (Plumbaginaceae), a highly endemic triploid species from the coasts of eastern Spain. Sixty-five alleles from 13 microsatellite regions were amplified in a sample of 122 individuals collected from the six extant populations. Microsatellite patterns were consistent with the triploid nature of L. dufourii. Alleles were unambiguously assigned to two different parental subgenomes in this hybrid species and the greater contribution of the diploid parental subgenome was confirmed. Eleven, 25 and 26 multilocus genotypes were recorded from the haploid, diploid and from the combined information of both subgenomes, respectively. Genetic diversity was mostly distributed among populations (72.06% of the total genetic variation). Genotypes from Marjal del Moro populations grouped into two highly structured clusters (88.41% of the total variance). The observed patterns of distribution of genetic diversity are interpreted to result from multiple hybridization events and isolation between populations. Threats to this species are mainly anthropogenic (urbanization and tourism pressure), although stochastic risks cannot be ignored. Therefore, in order to preserve extant genetic variation of L. dufourii, in situ strategies such as the preservation of its habitat are a high priority. Several recommendations in order to assist ex situ measures to guarantee the success of conservation strategies and maintain the relationships between individuals and populations are proposed. PMID:17850548

  13. Low genetic diversity and high differentiation among relict populations of the neotropical gymnosperm Podocarpus sellowii (Klotz.) in the Atlantic Forest.

    PubMed

    Dantas, Liliane G; Esposito, Tiago; de Sousa, Adna Cristina Barbosa; Félix, Leonardo; Amorim, Lidiane L B; Benko-Iseppon, Ana Maria; Batalha-Filho, Henrique; Pedrosa-Harand, Andrea

    2015-02-01

    Podocarpus sellowii (Podocarpaceae) is one of only a few gymnosperms native to Brazil and the sole species of the genus found in the northeastern region of that country. It has a very restricted distribution in this region, with only three known populations in highland forests (called Brejos de Altitude), which apparently have been isolated from each other since the Pleistocene. Due to this long-term isolation and the fact that these populations have few adult individuals and suffer great anthropogenic pressure, low genetic variability is expected, compromising their long-term viability. The present work assessed the genetic variability and structure of northeastern populations of P. sellowii to investigate the role of Pleistocene glaciations on the genetic relationships between them and to propose strategies for their conservation by analyzing the SSR and ISSR markers of adult and juvenile individuals. Low genetic diversity was found with both markers, associated with a high differentiation of the Brejo de Baturité population in relation to the others-suggesting their isolation at different points in time, probably during the Pleistocene. Actions directed towards increasing the genetic diversity of these populations will be needed, such as planting seedlings with high genetic variability-but the high degrees of differentiation observed between the populations must be taken into account. PMID:25532751

  14. Construction of a high-density, high-resolution genetic map and its integration with BAC-based physical map in channel catfish

    PubMed Central

    Li, Yun; Liu, Shikai; Qin, Zhenkui; Waldbieser, Geoff; Wang, Ruijia; Sun, Luyang; Bao, Lisui; Danzmann, Roy G.; Dunham, Rex; Liu, Zhanjiang

    2015-01-01

    Construction of genetic linkage map is essential for genetic and genomic studies. Recent advances in sequencing and genotyping technologies made it possible to generate high-density and high-resolution genetic linkage maps, especially for the organisms lacking extensive genomic resources. In the present work, we constructed a high-density and high-resolution genetic map for channel catfish with three large resource families genotyped using the catfish 250K single-nucleotide polymorphism (SNP) array. A total of 54,342 SNPs were placed on the linkage map, which to our knowledge had the highest marker density among aquaculture species. The estimated genetic size was 3,505.4 cM with a resolution of 0.22 cM for sex-averaged genetic map. The sex-specific linkage maps spanned a total of 4,495.1 cM in females and 2,593.7 cM in males, presenting a ratio of 1.7 : 1 between female and male in recombination fraction. After integration with the previously established physical map, over 87% of physical map contigs were anchored to the linkage groups that covered a physical length of 867 Mb, accounting for ?90% of the catfish genome. The integrated map provides a valuable tool for validating and improving the catfish whole-genome assembly and facilitates fine-scale QTL mapping and positional cloning of genes responsible for economically important traits. PMID:25428894

  15. Imaging through a highly scattering medium with structural similarity and genetic algorithm

    NASA Astrophysics Data System (ADS)

    Wu, Tengfei; Shao, Xiaopeng; Gong, Changmei; Dai, Weijia

    2014-10-01

    A method to recover the image of an object behind a highly scattering medium with higher accuracy is presented. Instead of the Pearson correlation coefficient (PCC) used in the existing methods, structural similarity (SSIM), which is known as an excellent evaluation indicator of image quality, is employed as the cost function for the wavefront optimization. Compared to PCC, better imaging quality can be acquired with SSIM, because the latter comprehensively analyzes the luminance, the contrast, and the structure of imaging results. By comparing the performances of the three commonly used global optimization algorithms, including a genetic algorithm (GA), particle swarm optimization and differential evolution algorithm, we verify that GA has the best reliability and stability to solve this multidimensional wavefront modulation problem among these global optimization algorithms, including in strong noise environments. This work can improve the quality of imaging through a highly scattering medium with a wavefront optimization technique and can be applied to the fields of optical detection or biomedical imaging.

  16. A High-Density Simple Sequence Repeat-Based Genetic Linkage Map of Switchgrass

    PubMed Central

    Liu, Linglong; Wu, Yanqi; Wang, Yunwen; Samuels, Tim

    2012-01-01

    Switchgrass (Panicum virgatum) has been identified as a promising cellulosic biofuel crop in the United States. Construction of a genetic linkage map is fundamental for switchgrass molecular breeding and the elucidation of its genetic mechanisms for economically important traits. In this study, a novel population consisting of 139 selfed progeny of a northern lowland genotype, NL 94 LYE 16X13, was used to construct a linkage map. A total of 2493 simple sequence repeat markers were screened for polymorphism. Of 506 polymorphic loci, 80.8% showed a goodness-of-fit of 1:2:1 segregation ratio. Among 469 linked loci on the framework map, 241 coupling vs. 228 repulsion phase linkages were detected that conformed to a 1:1 ratio, confirming disomic inheritance. A total of 499 loci were mapped to 18 linkage groups (LG), of which the cumulative length was 2085.2 cM, with an average marker interval of 4.2 cM. Nine homeologous LG pairs were identified based on multi-allele markers and comparative genomic analysis. Two clusters of segregation-distorted loci were identified on LG 5b and 9b, respectively. Comparative analysis indicated a one-to-one relationship between nine switchgrass homeologous groups and nine foxtail millet (Setaria italica) chromosomes, suggesting strong homology between the two species. The linkage map derived from selfing a heterozygous parent, instead of two separate maps usually constructed for a cross-fertilized species, provides a new genetic framework to facilitate genomics research, quantitative trait locus (QTL) mapping, and marker-assisted breeding. PMID:22413090

  17. Foraging segregation and genetic divergence between geographically proximate colonies of a highly mobile seabird

    USGS Publications Warehouse

    Wiley, Anne E.; Welch, Andreanna J.; Ostrom, P.H.; James, Helen F.; Stricker, C.A.; Fleischer, R.C.; Gandhi, H.; Adams, J.; Ainley, D.G.; Duvall, F.; Holmes, N.; Hu, D.; Judge, S.; Penniman, J.; Swindle, K.A.

    2012-01-01

    Foraging segregation may play an important role in the maintenance of animal diversity, and is a proposed mechanism for promoting genetic divergence within seabird species. However, little information exists regarding its presence among seabird populations. We investigated genetic and foraging divergence between two colonies of endangered Hawaiian petrels (Pterodroma sandwichensis) nesting on the islands of Hawaii and Kauai using the mitochondrial Cytochrome b gene and carbon, nitrogen and hydrogen isotope values (?? 13C, ?? 15N and ??D, respectively) of feathers. Genetic analyses revealed strong differentiation between colonies on Hawaii and Kauai, with ?? ST = 0. 50 (p < 0. 0001). Coalescent-based analyses gave estimates of <1 migration event per 1,000 generations. Hatch-year birds from Kauai had significantly lower ?? 13C and ?? 15N values than those from Hawaii. This is consistent with Kauai birds provisioning chicks with prey derived from near or north of the Hawaiian Islands, and Hawaii birds provisioning young with prey from regions of the equatorial Pacific characterized by elevated ?? 15N values at the food web base. ?? 15N values of Kauai and Hawaii adults differed significantly, indicating additional foraging segregation during molt. Feather ??D varied from -69 to 53???. This variation cannot be related solely to an isotopically homogeneous ocean water source or evaporative water loss. Instead, we propose the involvement of salt gland excretion. Our data demonstrate the presence of foraging segregation between proximately nesting seabird populations, despite high species mobility. This ecological diversity may facilitate population coexistence, and its preservation should be a focus of conservation strategies. ?? 2011 Springer-Verlag (outside the USA).

  18. Foraging segregation and genetic divergence between geographically proximate colonies of a highly mobile seabird.

    PubMed

    Wiley, Anne E; Welch, Andreanna J; Ostrom, Peggy H; James, Helen F; Stricker, Craig A; Fleischer, Robert C; Gandhi, Hasand; Adams, Josh; Ainley, David G; Duvall, Fern; Holmes, Nick; Hu, Darcy; Judge, Seth; Penniman, Jay; Swindle, Keith A

    2012-01-01

    Foraging segregation may play an important role in the maintenance of animal diversity, and is a proposed mechanism for promoting genetic divergence within seabird species. However, little information exists regarding its presence among seabird populations. We investigated genetic and foraging divergence between two colonies of endangered Hawaiian petrels (Pterodroma sandwichensis) nesting on the islands of Hawaii and Kauai using the mitochondrial Cytochrome b gene and carbon, nitrogen and hydrogen isotope values (?(13)C, ?(15)N and ?D, respectively) of feathers. Genetic analyses revealed strong differentiation between colonies on Hawaii and Kauai, with ?(ST) = 0.50 (p < 0.0001). Coalescent-based analyses gave estimates of <1 migration event per 1,000 generations. Hatch-year birds from Kauai had significantly lower ?(13)C and ?(15)N values than those from Hawaii. This is consistent with Kauai birds provisioning chicks with prey derived from near or north of the Hawaiian Islands, and Hawaii birds provisioning young with prey from regions of the equatorial Pacific characterized by elevated ?(15)N values at the food web base. ?(15)N values of Kauai and Hawaii adults differed significantly, indicating additional foraging segregation during molt. Feather ?D varied from -69 to 53‰. This variation cannot be related solely to an isotopically homogeneous ocean water source or evaporative water loss. Instead, we propose the involvement of salt gland excretion. Our data demonstrate the presence of foraging segregation between proximately nesting seabird populations, despite high species mobility. This ecological diversity may facilitate population coexistence, and its preservation should be a focus of conservation strategies. PMID:21837410

  19. Plasma membrane of Beta vulgaris storage root shows high water channel activity regulated by cytoplasmic pH and a dual range of calcium concentrations.

    PubMed

    Alleva, Karina; Niemietz, Christa M; Sutka, Moira; Maurel, Christophe; Parisi, Mario; Tyerman, Stephen D; Amodeo, Gabriela

    2006-01-01

    Plasma membrane vesicles isolated by two-phase partitioning from the storage root of Beta vulgaris show atypically high water permeability that is equivalent only to those reported for active aquaporins in tonoplast or animal red cells (Pf=542 microm s(-1)). The values were determined from the shrinking kinetics measured by stopped-flow light scattering. This high Pf was only partially inhibited by mercury (HgCl2) but showed low activation energy (Ea) consistent with water permeation through water channels. To study short-term regulation of water transport that could be the result of channel gating, the effects of pH, divalent cations, and protection against dephosphorylation were tested. The high Pf observed at pH 8.3 was dramatically reduced by medium acidification. Moreover, intra-vesicular acidification (corresponding to the cytoplasmic face of the membrane) shut down the aquaporins. De-phosphorylation was discounted as a regulatory mechanism in this preparation. On the other hand, among divalent cations, only calcium showed a clear effect on aquaporin activity, with two distinct ranges of sensitivity to free Ca2+ concentration (pCa 8 and pCa 4). Since the normal cytoplasmic free Ca2+ sits between these ranges it allows for the possibility of changes in Ca2+ to finely up- or down-regulate water channel activity. The calcium effect is predominantly on the cytoplasmic face, and inhibition corresponds to an increase in the activation energy for water transport. In conclusion, these findings establish both cytoplasmic pH and Ca2+ as important regulatory factors involved in aquaporin gating. PMID:16397000

  20. Optimization of high-order harmonic generation by genetic algorithm and wavelet time-frequency analysis of quantum dipole emission

    E-print Network

    Chu, Shih-I

    Optimization of high-order harmonic generation by genetic algorithm and wavelet time-frequency analysis of quantum dipole emission Xi Chu and Shih-I Chu Department of Chemistry, University of Kansas-dimensional quantum study of the coherent control of high-order harmonic generation HHG processes in intense pulsed

  1. Post-Doctoral Fellow in Cardiovascular Genetics A research position is available for a highly motivated post-doctoral fellow to join the

    E-print Network

    de Leon, Alex R.

    Post-Doctoral Fellow in Cardiovascular Genetics A research position is available for a highly laboratory is interested in molecular and genetic mechanisms of inherited cardiomyopathies and arrhythmias a combination of biochemical, genetic and cell biological approaches. The project is focused on the role of cell

  2. Mark-recapture using tetracycline and genetics reveal record-high bear density

    USGS Publications Warehouse

    Peacock, E.; Titus, K.; Garshelis, D.L.; Peacock, M.M.; Kuc, M.

    2011-01-01

    We used tetracycline biomarking, augmented with genetic methods to estimate the size of an American black bear (Ursus americanus) population on an island in Southeast Alaska. We marked 132 and 189 bears that consumed remote, tetracycline-laced baits in 2 different years, respectively, and observed 39 marks in 692 bone samples subsequently collected from hunters. We genetically analyzed hair samples from bait sites to determine the sex of marked bears, facilitating derivation of sex-specific population estimates. We obtained harvest samples from beyond the study area to correct for emigration. We estimated a density of 155 independent bears/100 km2, which is equivalent to the highest recorded for this species. This high density appears to be maintained by abundant, accessible natural food. Our population estimate (approx. 1,000 bears) could be used as a baseline and to set hunting quotas. The refined biomarking method for abundance estimation is a useful alternative where physical captures or DNA-based estimates are precluded by cost or logistics. Copyright ?? 2011 The Wildlife Society.

  3. Essay Contest Reveals Misconceptions of High School Students in Genetics Content

    Microsoft Academic Search

    K. R. Mills Shaw; K. Van Horne; H. Zhang; J. Boughman

    2008-01-01

    National educational organizations have called upon scientists to become involved in K-12 education reform. From sporadic interaction with students to more sustained partnerships with teachers, the engagement of scientists takes many forms. In this case, scientists from the American Society of Human Genetics (ASHG), the Genetics Society of America (GSA), and the National Society of Genetic Counselors (NSGC) have partnered

  4. High genetic diversity in a rare and endangered sunflower as compared to a common congener

    Microsoft Academic Search

    J. R. ELLIS; C. H. PASHLEY; J. M. BURKE; D. E. M C CAULEY

    2006-01-01

    Determining the genetic structure of isolated or fragmented species is of critical importance when planning a suitable conservation strategy. In this study, we use nuclear and chloroplast SSRs (simple sequence repeats) to investigate the population genetics of an extremely rare sunflower, Helianthus verticillatus Small, which is known from only three locations in North America. We investigated levels of genetic diversity

  5. Association between genetic subgroups of pancreatic ductal adenocarcinoma defined by high density 500 K SNP-arrays and tumor histopathology.

    PubMed

    Gutiérrez, María Laura; Muńoz-Bellvis, Luís; Abad, María del Mar; Bengoechea, Oscar; González-González, María; Orfao, Alberto; Sayagués, José María

    2011-01-01

    The specific genes and genetic pathways associated with pancreatic ductal adenocarcinoma are still largely unknown partially due to the low resolution of the techniques applied so far to their study. Here we used high-density 500 K single nucleotide polymorphism (SNP)-arrays to define those chromosomal regions which most commonly harbour copy number (CN) alterations and loss of heterozygozity (LOH) in a series of 20 PDAC tumors and we correlated the corresponding genetic profiles with the most relevant clinical and histopathological features of the disease. Overall our results showed that primary PDAC frequently display (>70%) extensive gains of chromosomes 1q, 7q, 8q and 20q, together with losses of chromosomes 1p, 9p, 12q, 17p and 18q, such chromosomal regions harboring multiple cancer- and PDAC-associated genes. Interestingly, these alterations clustered into two distinct genetic profiles characterized by gains of the 2q14.2, 3q22.1, 5q32, 10q26.13, 10q26.3, 11q13.1, 11q13.3, 11q13.4, 16q24.1, 16q24.3, 22q13.1, 22q13.31 and 22q13.32 chromosomal regions (group 1; n?=?9) versus gains at 1q21.1 and losses of the 1p36.11, 6q25.2, 9p22.1, 9p24.3, 17p13.3 and Xp22.33 chromosomal regions (group 2; n?=?11). From the clinical and histopathological point of view, group 1 cases were associated with smaller and well/moderately-differentiated grade I/II PDAC tumors, whereas and group 2 PDAC displayed a larger size and they mainly consisted of poorly-differentiated grade III carcinomas. These findings confirm the cytogenetic complexity and heterozygozity of PDAC and provide evidence for the association between tumor cytogenetics and its histopathological features. In addition, we also show that the altered regions identified harbor multiple cancer associate genes that deserve further investigation to determine their relevance in the pathogenesis of PDAC. PMID:21811587

  6. A Novel Extraction Method Combining Plasma with a Whole-Blood Fraction Shows Excellent Sensitivity and Reproducibility for Patients at High Risk for Invasive Aspergillosis

    PubMed Central

    Springer, Jan; Schloßnagel, Hannes; Heinz, Werner; Doedt, Thomas; Soeller, Rainer; Einsele, Hermann

    2012-01-01

    Diagnosis of invasive aspergillosis (IA) is still a major problem in routine clinical practice. Early diagnosis is essential for a good patient prognosis. PCR is a highly sensitive method for the detection of nucleic acids and could play an important role in improving the diagnosis of fungal infections. Therefore, a novel DNA extraction method, ultraclean production (UCP), was developed allowing purification of both cellular and cell-free circulating fungal DNA. In this prospective study we evaluated the commercially available UCP extraction system and compared it to an in-house system. Sixty-three patients at high risk for IA were screened twice weekly, and DNA extracted by both methods was cross-analyzed, in triplicate, by two different real-time PCR assays. The negative predictive values were high for all methods (94.3 to 100%), qualifying them as screening methods, but the sensitivity and diagnostic odds ratios were higher using the UCP extraction method. Sensitivity ranged from 33.3 to 66.7% using the in-house extracts to 100% using the UCP extraction method. Most of the unclassified patients showed no positive PCR results; however, single-positive PCR replicates were observed in some cases. These can bear clinical relevance but should be interpreted with additional clinical and laboratory data. The PCR assays from the UCP extracts showed greater reproducibility than the in-house method for probable IA patients. The standardized UCP extraction method yielded superior results, with regard to sensitivity and reproducibility, than the in-house method. This was independent of the PCR assay used to detect fungal DNA in the sample extracts. PMID:22593600

  7. Radiation-induced meningiomas in multiple regions, showing rapid recurrence and a high MIB 1 labeling index: a case report and review of the literature

    PubMed Central

    2014-01-01

    Combined chemotherapy and prophylactic cranial irradiation has improved the prognosis of children with acute leukemia. However cranial irradiation carries a latent risk of the induction of secondary intracranial tumors. We encountered a patient who developed multiple intracranial radiation-induced meningiomas (RIMs) 25 years after prophylactic cranial irradiation for the treatment of acute leukemia in childhood. The patient had 3 intracranial lesions, 1 of which showed rapid growth within 6 months; another of the tumors also enlarged within a short period. All of the tumors were surgically treated, and immunohistochemistry indicated a high MIB-1 labeling index in each of the multiple lesions. In the literature, the MIB-1 labeling indices of 27 tumors from 21 patients were examined. Among them, 12 recurrent tumors showed higher MIB-1 labeling indices compared to the MIB-1 labeling indices of the non-recurrent tumors. Overall, 11 of the patients with RIM had multiple lesions and 8 cases developed recurrence (72.7%). RIM cases with multiple lesions had higher MIB-1 labeling indices compared to the MIB-1 labeling indices of cases with single lesions. Collectively, these data showed that the MIB-1 labeling index is as important for predicting RIM recurrences, as it is for predicting sporadic meningioma (SM) recurrences. RIMs should be treated more aggressively than SMs because of their greater malignant potential. PMID:24767145

  8. High-resolution imaging of the fusiform face area (FFA) using multivariate non-linear classifiers shows diagnosticity for non-face categories.

    PubMed

    Hanson, Stephen José; Schmidt, Arielle

    2011-01-15

    Does the "fusiform face area" (FFA) code only for faces? This question continues to elude the neuroimaging field due to at least two kinds of problems: first, the relatively low spatial resolution of fMRI in which the FFA was defined and second, the potential bias inherent in prevailing statistical methods for analyzing the actual diagnosticity of cortical tissue. Using high-resolution (1 mm × 1 mm × 1 mm) imaging data of the fusiform face area (FFA) from 4 subjects who had categorized images as 'animal', 'car', 'face', or 'sculpture', we used multivariate linear and non-linear classifiers to decode the resultant voxel patterns. Prior to identifying the appropriate classifier we performed exploratory analysis to determine the nature of the distributions over classes and the voxel intensity pattern structure between classes. The FFA was visualized using non-metric multidimensional scaling revealing "string-like" sequences of voxels, which appeared in small non-contiguous clusters of categories, intertwined with other categories. Since this analysis suggested that feature space was highly non-linear, we trained various statistical classifiers on the class-conditional distributions (labelled) and separated the four categories with 100% reliability (over replications) and generalized to out-of-sample cases with high significance (up to 50%; p<.000001, chance=25%). The increased noise inherent in high-resolution neuroimaging data relative to standard resolution resisted any further gains in category performance above ~60% (with FACE category often having the highest bias per category) even coupled with various feature extraction/selection methods. A sensitivity/diagnosticity analysis for each classifier per voxel showed: (1) reliable (with S.E.<3%) sensitivity present throughout the FFA for all 4 categories, and (2) showed multi-selectivity; that is, many voxels were selective for more than one category with some high diagnosticity but at submaximal intensity. This work is clearly consistent with the characterization of the FFA as a distributed, object-heterogeneous similarity structure and bolsters the view that the FFA response to "FACE" stimuli in standard resolution may be primarily due to a linear bias, which has resulted from an averaging artefact. PMID:20736071

  9. A High-Performance Genetic Algorithm: Using Traveling Salesman Problem as a Case

    PubMed Central

    Tsai, Chun-Wei; Tseng, Shih-Pang; Yang, Chu-Sing

    2014-01-01

    This paper presents a simple but efficient algorithm for reducing the computation time of genetic algorithm (GA) and its variants. The proposed algorithm is motivated by the observation that genes common to all the individuals of a GA have a high probability of surviving the evolution and ending up being part of the final solution; as such, they can be saved away to eliminate the redundant computations at the later generations of a GA. To evaluate the performance of the proposed algorithm, we use it not only to solve the traveling salesman problem but also to provide an extensive analysis on the impact it may have on the quality of the end result. Our experimental results indicate that the proposed algorithm can significantly reduce the computation time of GA and GA-based algorithms while limiting the degradation of the quality of the end result to a very small percentage compared to traditional GA. PMID:24892038

  10. Construction of a high-density genetic map for sesame based on large scale marker development by specific length amplified fragment (SLAF) sequencing

    PubMed Central

    2013-01-01

    Background The genetics and molecular biology of sesame has only recently begun to be studied even though sesame is an important oil seed crop. A high-density genetic map for sesame has not been published yet due to a lack of sufficient molecular markers. Specific length amplified fragment sequencing (SLAF-seq) is a recently developed high-resolution strategy for large-scale de novo SNP discovery and genotyping. SLAF-seq was employed in this study to obtain sufficient markers to construct a high-density genetic map for sesame. Results In total, 28.21 Gb of data containing 201,488,285 pair-end reads was obtained after sequencing. The average coverage for each SLAF marker was 23.48-fold in the male parent, 23.38-fold in the female parent, and 14.46-fold average in each F2 individual. In total, 71,793 high-quality SLAFs were detected of which 3,673 SLAFs were polymorphic and 1,272 of the polymorphic markers met the requirements for use in the construction of a genetic map. The final map included 1,233 markers on the 15 linkage groups (LGs) and was 1,474.87 cM in length with an average distance of 1.20 cM between adjacent markers. To our knowledge, this map is the densest genetic linkage map to date for sesame. 'SNP_only’ markers accounted for 87.51% of the markers on the map. A total of 205 markers on the map showed significant (P?high-density genetic map for sesame. The map was constructed using an F2 population and the SLAF-seq approach, which allowed the efficient development of a large number of polymorphic markers in a short time. Results of this study will not only provide a platform for gene/QTL fine mapping, map-based gene isolation, and molecular breeding for sesame, but will also serve as a reference for positioning sequence scaffolds on a physical map, to assist in the process of assembling the sesame genome sequence. PMID:24060091

  11. The gibberellic-acid insensitive dwarfing gene sdw3 of barley is located on chromosome 2HS in a region that shows high colinearity with rice chromosome 7L

    Microsoft Academic Search

    S. Gottwald; N. Stein; A. Börner; T. Sasaki; A. Graner

    2004-01-01

    In this study, comparative high resolution genetic mapping of the GA-insensitive dwarfing gene sdw3 of barley revealed highly conserved macrosynteny of the target region on barley chromosome 2HS with rice chromosome 7L. A rice contig covering the sdw3-orthologous region was identified and subsequently exploited for marker saturation of the target interval in barley. This was achieved by (1) mapping of

  12. Construction of a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis) using genotyping-by-sequencing (GBS)

    PubMed Central

    Pootakham, Wirulda; Ruang-Areerate, Panthita; Jomchai, Nukoon; Sonthirod, Chutima; Sangsrakru, Duangjai; Yoocha, Thippawan; Theerawattanasuk, Kanikar; Nirapathpongporn, Kanlaya; Romruensukharom, Phayao; Tragoonrung, Somvong; Tangphatsornruang, Sithichoke

    2015-01-01

    Construction of linkage maps is crucial for genetic studies and marker-assisted breeding programs. Recent advances in next generation sequencing technologies allow for the generation of high-density linkage maps, especially in non-model species lacking extensive genomic resources. Here, we constructed a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis), the sole commercial producer of high-quality natural rubber. We applied a genotyping-by-sequencing (GBS) technique to simultaneously discover and genotype single nucleotide polymorphism (SNP) markers in two rubber tree populations. A total of 21,353 single nucleotide substitutions were identified, 55% of which represented transition events. GBS-based genetic maps of populations P and C comprised 1704 and 1719 markers and encompassed 2041 cM and 1874 cM, respectively. The average marker densities of these two maps were one SNP in 1.23–1.25 cM. A total of 1114 shared SNP markers were used to merge the two component maps. An integrated linkage map consisted of 2321 markers and spanned the cumulative length of 2052 cM. The composite map showed a substantial improvement in marker density, with one SNP marker in every 0.89 cM. To our knowledge, this is the most saturated genetic map in rubber tree to date. This integrated map allowed us to anchor 28,965 contigs, covering 135 Mb or 12% of the published rubber tree genome. We demonstrated that GBS is a robust and cost-effective approach for generating a common set of genome-wide SNP data suitable for constructing integrated linkage maps from multiple populations in a highly heterozygous agricultural species.

  13. Construction of a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis) using genotyping-by-sequencing (GBS).

    PubMed

    Pootakham, Wirulda; Ruang-Areerate, Panthita; Jomchai, Nukoon; Sonthirod, Chutima; Sangsrakru, Duangjai; Yoocha, Thippawan; Theerawattanasuk, Kanikar; Nirapathpongporn, Kanlaya; Romruensukharom, Phayao; Tragoonrung, Somvong; Tangphatsornruang, Sithichoke

    2015-01-01

    Construction of linkage maps is crucial for genetic studies and marker-assisted breeding programs. Recent advances in next generation sequencing technologies allow for the generation of high-density linkage maps, especially in non-model species lacking extensive genomic resources. Here, we constructed a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis), the sole commercial producer of high-quality natural rubber. We applied a genotyping-by-sequencing (GBS) technique to simultaneously discover and genotype single nucleotide polymorphism (SNP) markers in two rubber tree populations. A total of 21,353 single nucleotide substitutions were identified, 55% of which represented transition events. GBS-based genetic maps of populations P and C comprised 1704 and 1719 markers and encompassed 2041 cM and 1874 cM, respectively. The average marker densities of these two maps were one SNP in 1.23-1.25 cM. A total of 1114 shared SNP markers were used to merge the two component maps. An integrated linkage map consisted of 2321 markers and spanned the cumulative length of 2052 cM. The composite map showed a substantial improvement in marker density, with one SNP marker in every 0.89 cM. To our knowledge, this is the most saturated genetic map in rubber tree to date. This integrated map allowed us to anchor 28,965 contigs, covering 135 Mb or 12% of the published rubber tree genome. We demonstrated that GBS is a robust and cost-effective approach for generating a common set of genome-wide SNP data suitable for constructing integrated linkage maps from multiple populations in a highly heterozygous agricultural species. PMID:26074933

  14. Construction of a high-density DArTseq SNP-based genetic map and identification of genomic regions with segregation distortion in a genetic population derived from a cross between feral and cultivated-type watermelon.

    PubMed

    Ren, Runsheng; Ray, Rumiana; Li, Pingfang; Xu, Jinhua; Zhang, Man; Liu, Guang; Yao, Xiefeng; Kilian, Andrzej; Yang, Xingping

    2015-08-01

    Watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai] is an economically important vegetable crop grown extensively worldwide. To facilitate the identification of agronomically important traits and provide new information for genetic and genomic research on this species, a high-density genetic linkage map of watermelon was constructed using an F2 population derived from a cross between elite watermelon cultivar K3 and wild watermelon germplasm PI 189225. Based on a sliding window approach, a total of 1,161 bin markers representing 3,465 SNP markers were mapped onto 11 linkage groups corresponding to the chromosome pair number of watermelon. The total length of the genetic map is 1,099.2 cM, with an average distance between bins of 1.0 cM. The number of markers in each chromosome varies from 62 in chromosome 07 to 160 in chromosome 05. The length of individual chromosomes ranged between 61.8 cM for chromosome 07 and 140.2 cM for chromosome 05. A total of 616 SNP bin markers showed significant (P < 0.05) segregation distortion across all 11 chromosomes, and 513 (83.3 %) of these distorted loci showed distortion in favor of the elite watermelon cultivar K3 allele and 103 were skewed toward PI 189225. The number of SNPs and InDels per Mb varied considerably across the segregation distorted regions (SDRs) on each chromosome, and a mixture of dense and sparse SNPs and InDel SDRs coexisted on some chromosomes suggesting that SDRs were randomly distributed throughout the genome. Recombination rates varied greatly among each chromosome, from 2.0 to 4.2 centimorgans per megabase (cM/Mb). An inconsistency was found between the genetic and physical positions on the map for a segment on chromosome 11. The high-density genetic map described in the present study will facilitate fine mapping of quantitative trait loci, the identification of candidate genes, map-based cloning, as well as marker-assisted selection (MAS) in watermelon breeding programs. PMID:25702268

  15. Breeding loggerhead marine turtles Caretta caretta in Dry Tortugas National Park, USA, show high fidelity to diverse habitats near nesting beaches

    USGS Publications Warehouse

    Hart, Kristen M.; Zawada, David G.; Sartain, Autumn R.; Fujisaki, Ikuko

    2014-01-01

    We used satellite telemetry to identify in-water habitat used by individuals in the smallest North-west Atlantic subpopulation of adult nesting loggerhead turtles Caretta caretta during the breeding season. During 2010, 2011 and 2012 breeding periods, a total of 20 adult females used habitats proximal to nesting beaches with various levels of protection within Dry Tortugas National Park. We then used a rapid, high-resolution, digital imaging system to map habitat adjacent to nesting beaches, revealing the diversity and distribution of available benthic cover. Turtle behaviour showing measurable site-fidelity to these diverse habitats has implications for managing protected areas and human activities within them. Protecting diverse benthic areas adjacent to loggerhead turtle nesting beaches here and elsewhere could provide benefits for overall biodiversity conservation.

  16. Effects of the aspartic protease inhibitor from Lupinus bogotensis seeds on the growth and development of Hypothenemus hampei: an inhibitor showing high homology with storage proteins.

    PubMed

    Molina, Diana; Patińo, Luisa; Quintero, Mónica; Cortes, José; Bastos, Sara

    2014-02-01

    The coffee berry borer Hypothenemus hampei is a pest that causes great economic damage to coffee grains worldwide. Because the proteins consumed are digested by aspartic proteases in the insect's midgut, the inhibition of these proteases by transferring a gene encoding an aspartic protease inhibitor from Lupinus bogotensis Benth. to coffee plants could provide a promising strategy to control this pest. Five aspartic protease inhibitors from L. bogotensis (LbAPI) were accordingly purified and characterized. The gene encoding the L. bogotensis aspartic protease inhibitor (LbAPI), with the highest inhibitory activity against H. hampei, was expressed in Escherichia coli and the purified recombinant protein (rLbAPI), with a molecular mass of 15 kDa, was subsequently assessed for its ability to inhibit the aspartic protease activity present in the H. hampei midgut in vitro, as well as its effects on the growth and development of H. hampei in vivo. The in vitro experiments showed that rLbAPI was highly effective against aspartic proteases from H. hampei guts, with a half maximal inhibitory concentration (IC50) of 2.9 ?g. The in vivo experiments showed that the concentration of rLbAPI (w/w) in the artificial diet necessary to cause 50% mortality (LD50) of the larvae was 0.91%. The amino acid sequence of LbAPI had high homology (52-80%) to the seed storage proteins, vicilin and ?-conglutin, suggesting that this protein was generated by evolutionary events from a ?-conglutin precursor. Based on these results, LbAPI may have a dual function as storage protein, and as defense protein against H. hampei. These results provide a promising alternative to obtain a coffee plant resistant to H. hampei. PMID:24314849

  17. Genetic Signatures Reveal High-Altitude Adaptation in a Set of Ethiopian Populations

    PubMed Central

    Huerta-Sánchez, Emilia; DeGiorgio, Michael; Pagani, Luca; Tarekegn, Ayele; Ekong, Rosemary; Antao, Tiago; Cardona, Alexia; Montgomery, Hugh E.; Cavalleri, Gianpiero L.; Robbins, Peter A.; Weale, Michael E.; Bradman, Neil; Bekele, Endashaw; Kivisild, Toomas; Tyler-Smith, Chris; Nielsen, Rasmus

    2013-01-01

    The Tibetan and Andean Plateaus and Ethiopian highlands are the largest regions to have long-term high-altitude residents. Such populations are exposed to lower barometric pressures and hence atmospheric partial pressures of oxygen. Such “hypobaric hypoxia” may limit physical functional capacity, reproductive health, and even survival. As such, selection of genetic variants advantageous to hypoxic adaptation is likely to have occurred. Identifying signatures of such selection is likely to help understanding of hypoxic adaptive processes. Here, we seek evidence of such positive selection using five Ethiopian populations, three of which are from high-altitude areas in Ethiopia. As these populations may have been recipients of Eurasian gene flow, we correct for this admixture. Using single-nucleotide polymorphism genotype data from multiple populations, we find the strongest signal of selection in BHLHE41 (also known as DEC2 or SHARP1). Remarkably, a major role of this gene is regulation of the same hypoxia response pathway on which selection has most strikingly been observed in both Tibetan and Andean populations. Because it is also an important player in the circadian rhythm pathway, BHLHE41 might also provide insights into the mechanisms underlying the recognized impacts of hypoxia on the circadian clock. These results support the view that Ethiopian, Andean, and Tibetan populations living at high altitude have adapted to hypoxia differently, with convergent evolution affecting different genes from the same pathway. PMID:23666210

  18. High altitude genetic adaptation in Tibetans: no role of increased hemoglobin-oxygen affinity.

    PubMed

    Tashi, Tsewang; Feng, Tang; Koul, Parvaiz; Amaru, Ricardo; Hussey, Dottie; Lorenzo, Felipe R; RiLi, Ge; Prchal, Josef T

    2014-01-01

    High altitude exerts selective evolutionary pressure primarily due to its hypoxic environment, resulting in multiple adaptive responses. High hemoglobin-oxygen affinity is postulated to be one such adaptive change, which has been reported in Sherpas of the Himalayas. Tibetans have lived on the Qinghai-Tibetan plateau for thousands of years and have developed unique phenotypes, such as protection from polycythemia which has been linked to PDH2 mutation, resulting in the downregulation of the HIF pathway. In order to see if Tibetans also developed high hemoglobin-oxygen affinity as a part of their genetic adaptation, we conducted this study assessing hemoglobin-oxygen affinity and their fetal hemoglobin levels in Tibetan subjects from 3 different altitudes. We found normal hemoglobin-oxygen affinity in all subjects, fetal hemoglobin levels were normal in all except one and no hemoglobin variants in any of the subjects. We conclude that increased hemoglobin-oxygen affinity or increased fetal hemoglobin are not adaptive phenotypes of the Tibetan highlanders. PMID:24618341

  19. High altitude genetic adaptation in Tibetans: no role of increased hemoglobin-oxygen affinity

    PubMed Central

    Tashi, Tsewang; Feng, Tang; Koul, Parvaiz; Amaru, Ricardo; Hussey, Dottie; Lorenzo, Felipe R.; RiLi, Ge; Prchal, Josef T.

    2014-01-01

    High altitude exerts selective evolutionary pressure primarily due to its hypoxic environment, resulting in multiple adaptive responses. High hemoglobin-oxygen affinity is postulated to be one such adaptive change, which has been reported in Sherpas of the Himalayas. Tibetans have lived on the Qinghai-Tibetan plateau for thousands of years and have developed unique phenotypes, such as protection from polycythemia which has been linked to PDH2 mutation, resulting in downregulation of HIF pathway. In order to see if Tibetans also developed high hemoglobin-oxygen affinity as a part of their genetic adaptation, we conducted this study assessing hemoglobin-oxygen affinity and their fetal hemoglobin levels in Tibetan subjects from 3 different altitudes. We found normal hemoglobin-oxygen affinity in all subjects, fetal hemoglobin levels were normal in all except one and no hemoglobin variants in any of the subjects. We conclude that increased hemoglobin-oxygen affinity or increased fetal hemoglobin are not adaptive phenotypes of the Tibetan highlanders. PMID:24618341

  20. Cleft lip with or without cleft palate: identification of sporadic cases with a high level of genetic predisposition.

    PubMed Central

    Crawford, F C; Sofaer, J A

    1987-01-01

    Previous studies have suggested that asymmetry for certain bilaterally represented features may be an indicator of genetic predisposition to cleft lip with or without cleft palate and may therefore be of value in the individual assessment of recurrence risk, particularly for sporadic cases. An asymmetry score has been devised that may be of use in identifying those with a high level of genetic predisposition. Stepwise logistic regression selected nine variables that together correctly classified 85% of familial cleft patients and unrelated non-cleft controls. Applying the same regression equation to sporadic cases, 26% fell into the range occupied by the majority of familial patients, suggesting that these had a high level of genetic predisposition. PMID:3572999

  1. RNA-Seq bulked segregant analysis enables the identification of high-resolution genetic markers for breeding in hexaploid wheat.

    PubMed

    Ramirez-Gonzalez, Ricardo H; Segovia, Vanesa; Bird, Nicholas; Fenwick, Paul; Holdgate, Sarah; Berry, Simon; Jack, Peter; Caccamo, Mario; Uauy, Cristobal

    2015-06-01

    The identification of genetic markers linked to genes of agronomic importance is a major aim of crop research and breeding programmes. Here, we identify markers for Yr15, a major disease resistance gene for wheat yellow rust, using a segregating F2 population. After phenotyping, we implemented RNA sequencing (RNA-Seq) of bulked pools to identify single-nucleotide polymorphisms (SNP) associated with Yr15. Over 27 000 genes with SNPs were identified between the parents, and then classified based on the results from the sequenced bulks. We calculated the bulk frequency ratio (BFR) of SNPs between resistant and susceptible bulks, selecting those showing sixfold enrichment/depletion in the corresponding bulks (BFR > 6). Using additional filtering criteria, we reduced the number of genes with a putative SNP to 175. The 35 SNPs with the highest BFR values were converted into genome-specific KASP assays using an automated bioinformatics pipeline (PolyMarker) which circumvents the limitations associated with the polyploid wheat genome. Twenty-eight assays were polymorphic of which 22 (63%) mapped in the same linkage group as Yr15. Using these markers, we mapped Yr15 to a 0.77-cM interval. The three most closely linked SNPs were tested across varieties and breeding lines representing UK elite germplasm. Two flanking markers were diagnostic in over 99% of lines tested, thus providing a reliable haplotype for marker-assisted selection in these breeding programmes. Our results demonstrate that the proposed methodology can be applied in polyploid F2 populations to generate high-resolution genetic maps across target intervals. PMID:25382230

  2. A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map

    SciTech Connect

    Kelleher, Colin [University of British Columbia, Vancouver; CHIU, Dr. R. [Genome Sciences Centre, Vancouver, BC, Canada; Shin, Dr. H. [Genome Sciences Centre, Vancouver, BC, Canada; Krywinski, Martin [Genome Sciences Centre, Vancouver, BC, Canada; Fjell, Chris [Genome Sciences Centre, Vancouver, BC, Canada; Wilkin, Jennifer [University of British Columbia, Vancouver; Yin, Tongming [ORNL; Difazio, Stephen P. [West Virginia University

    2007-01-01

    As part of a larger project to sequence the Populus genome and generate genomic resources for this emerging model tree, we constructed a physical map of the Populus genome, representing one of the few such maps of an undomesticated, highly heterozygous plant species. The physical map, consisting of 2802 contigs, was constructed from fingerprinted bacterial artificial chromosome (BAC) clones. The map represents approximately 9.4-fold coverage of the Populus genome, which has been estimated from the genome sequence assembly to be 485 {+-} 10 Mb in size. BAC ends were sequenced to assist long-range assembly of whole-genome shotgun sequence scaffolds and to anchor the physical map to the genome sequence. Simple sequence repeat-based markers were derived from the end sequences and used to initiate integration of the BAC and genetic maps. A total of 2411 physical map contigs, representing 97% of all clones assigned to contigs, were aligned to the sequence assembly (JGI Populus trichocarpa, version 1.0). These alignments represent a total coverage of 384 Mb (79%) of the entire poplar sequence assembly and 295 Mb (96%) of linkage group sequence assemblies. A striking result of the physical map contig alignments to the sequence assembly was the co-localization of multiple contigs across numerous regions of the 19 linkage groups. Targeted sequencing of BAC clones and genetic analysis in a small number of representative regions showed that these co-aligning contigs represent distinct haplotypes in the heterozygous individual sequenced, and revealed the nature of these haplotype sequence differences.

  3. Male rats with same sex preference show high experimental anxiety and lack of anxiogenic-like effect of fluoxetine in the plus maze test.

    PubMed

    García-Cárdenas, Nallely; Olvera-Hernández, Sandra; Gómez-Quintanar, Blanca Nelly; Fernández-Guasti, Alonso

    2015-08-01

    Homosexual men show a 2-4 higher risk to suffer anxiety in comparison with heterosexuals. It is unknown if biological factors collaborate to increase such incidence. Fluoxetine produces differential brain activation in homosexuals as compared with heterosexuals, suggesting that it may produce a divergent behavioral effect dependant on sex-preference. The first aim was to evaluate experimental anxiety in male rats that show same-sex preference in the elevated plus maze (EPM). The second goal explored the putative differential effect of fluoxetine (10mg/kg) in male rats with female and same-sex preference in the EPM. To induce same-sex preference males were prenatally treated with letrozole (0.56?g/kg, 10-20 gestation days), while controls were males prenatally treated with letrozole that retain female-preference or which mothers received oil. In both groups we found animals with male preference, but the proportion was higher in males that prenatally received letrozole (10 vs. 27%). Males with same-sex preference spent less time and showed lower number of entries to the open arms of the EPM than males that prefer females, regardless of the prenatal treatment. In males with female preference, fluoxetine reduced the time spent and number of entries to the open arms that was absent in males with same-sex preference. These data suggest that biological factors contribute to the high levels of anxiety in subjects with same-sex preference and that fluoxetine in men may produce a divergent action depending on sexual orientation. PMID:26044966

  4. 6. VIEW SHOWING DOWNSTREAM FACE OF DAM, SHOWING SEEPAGE CONTROL ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    6. VIEW SHOWING DOWNSTREAM FACE OF DAM, SHOWING SEEPAGE CONTROL REINFORCEMENT, LOOKING SOUTHWEST - High Mountain Dams in Upalco Unit, East Timothy Lake Dam, Ashley National Forest, 8.4 miles North of Swift Creek Campground, Mountain Home, Duchesne County, UT

  5. Enhanced characteristics of genetically modified switchgrass (Panicum virgatum L.) for high biofuel production

    PubMed Central

    2013-01-01

    Background Lignocellulosic biomass is one of the most promising renewable and clean energy resources to reduce greenhouse gas emissions and dependence on fossil fuels. However, the resistance to accessibility of sugars embedded in plant cell walls (so-called recalcitrance) is a major barrier to economically viable cellulosic ethanol production. A recent report from the US National Academy of Sciences indicated that, “absent technological breakthroughs”, it was unlikely that the US would meet the congressionally mandated renewable fuel standard of 35 billion gallons of ethanol-equivalent biofuels plus 1 billion gallons of biodiesel by 2022. We here describe the properties of switchgrass (Panicum virgatum) biomass that has been genetically engineered to increase the cellulosic ethanol yield by more than 2-fold. Results We have increased the cellulosic ethanol yield from switchgrass by 2.6-fold through overexpression of the transcription factor PvMYB4. This strategy reduces carbon deposition into lignin and phenolic fermentation inhibitors while maintaining the availability of potentially fermentable soluble sugars and pectic polysaccharides. Detailed biomass characterization analyses revealed that the levels and nature of phenolic acids embedded in the cell-wall, the lignin content and polymer size, lignin internal linkage levels, linkages between lignin and xylans/pectins, and levels of wall-bound fucose are all altered in PvMYB4-OX lines. Genetically engineered PvMYB4-OX switchgrass therefore provides a novel system for further understanding cell wall recalcitrance. Conclusions Our results have demonstrated that overexpression of PvMYB4, a general transcriptional repressor of the phenylpropanoid/lignin biosynthesis pathway, can lead to very high yield ethanol production through dramatic reduction of recalcitrance. MYB4-OX switchgrass is an excellent model system for understanding recalcitrance, and provides new germplasm for developing switchgrass cultivars as biomass feedstocks for biofuel production. PMID:23651942

  6. Spatial and Temporal Genetic Analyses Show High Gene Flow Among European Corn Borer (Lepidoptera: Crambidae) Populations Across the Central U.S. Corn Belt

    Technology Transfer Automated Retrieval System (TEKTRAN)

    European corn borer, Ostrinia nubilalis, were sampled at 13 sites along two perpendicular 720 km transects intersecting in central Iowa, and two generations later at 4 of the same sites separated by 150-km in the cardinal directions. More than 50 moths from each sample location and time were genoty...

  7. Genetic isolation and morphological divergence mediated by high-energy rapids in two cichlid genera from the lower Congo rapids

    PubMed Central

    2010-01-01

    Background It is hypothesized that one of the mechanisms promoting diversification in cichlid fishes in the African Great Lakes has been the well-documented pattern of philopatry along shoreline habitats leading to high levels of genetic isolation among populations. However lake habitats are not the only centers of cichlid biodiversity - certain African rivers also contain large numbers of narrowly endemic species. Patterns of isolation and divergence in these systems have tended to be overlooked and are not well understood. Results We examined genetic and morphological divergence among populations of two narrowly endemic cichlid species, Teleogramma depressum and Lamprologus tigripictilis, from a 100 km stretch of the lower Congo River using both nDNA microsatellites and mtDNA markers along with coordinate-based morphological techniques. In L. tigripictilis, the strongest genetic break was concordant with measurable phenotypic divergence but no morphological disjunction was detected for T. depressum despite significant differentiation at mtDNA and nDNA microsatellite markers. Conclusions The genetic markers revealed patterns of philopatry and estimates of genetic isolation that are among the highest reported for any African cichlid species over a comparable geographic scale. We hypothesize that the high levels of philopatry observed are generated and maintained by the extreme hydrology of the lower Congo River. PMID:20482864

  8. Psychological impact of genetic testing in women from high-risk breast cancer families

    Microsoft Academic Search

    B Meiser; P Butow; M Friedlander; A Barratt; V Schnieden; M Watson; J Brown; K Tucker

    2002-01-01

    Psychological adjustment in 90 women (30 carriers and 60 non-carriers) who had undergone genetic testing for mutations in BRCA1 and BRCA2 breast\\/ovarian cancer susceptibility genes was compared with that of 53 women who were not offered genetic testing. Women were assessed prior to genetic testing and 7–10 days, 4 and 12 months after carrier status disclosure using self-administered questionnaires. Compared

  9. Am. J. Hum. Genet. 77:685693, 2005 High-Resolution Whole-Genome Association Study of Parkinson Disease

    E-print Network

    Jin, Jiashun

    of Parkinson disease (PD [MIM 168600]). Our findings contribute to the cre- ation of a genomic predispositionAm. J. Hum. Genet. 77:685­693, 2005 685 High-Resolution Whole-Genome Association Study of Parkinson Disease Demetrius M. Maraganore,1 Mariza de Andrade,2 Timothy G. Lesnick,2 Kari J. Strain,2 Matthew J

  10. Impact of a microRNA MIR137 susceptibility variant on brain function in people at high genetic risk of schizophrenia or bipolar disorder.

    PubMed

    Whalley, Heather C; Papmeyer, Martina; Romaniuk, Liana; Sprooten, Emma; Johnstone, Eve C; Hall, Jeremy; Lawrie, Stephen M; Evans, Kathryn L; Blumberg, Hilary P; Sussmann, Jessika E; McIntosh, Andrew M

    2012-11-01

    A recent 'mega-analysis' combining genome-wide association study data from over 40,000 individuals identified novel genetic loci associated with schizophrenia (SCZ) at genome-wide significance level. The strongest finding was a locus within an intron of a putative primary transcript for microRNA MIR137. In the current study, we examine the impact of variation at this locus (rs1625579, G/T; where T is the common and presumed risk allele) on brain activation during a sentence completion task that differentiates individuals with SCZ, bipolar disorder (BD), and their relatives from controls. We examined three groups of individuals performing a sentence completion paradigm: (i) individuals at high genetic risk of SCZ (n=44), (ii) individuals at high genetic risk of BD (n=90), and (iii) healthy controls (n=81) in order to test the hypothesis that genotype at rs1625579 would influence brain activation. Genotype groups were assigned as 'RISK-' for GT and GG individuals, and 'RISK+' for TT homozygotes. The main effect of genotype was significantly greater activation in the RISK- individuals in the posterior right medial frontal gyrus, BA 6. There was also a significant genotype(*)group interaction in the left amygdala and left pre/postcentral gyrus. This was due to differences between the controls (where individuals with the RISK- genotype showed greater activation than RISK+ subjects) and the SCZ high-risk group, where the opposite genotype effect was seen. These results suggest that the newly identified SCZ locus may influence brain activation in a manner that is partly dependent on the presence of existing genetic susceptibility for SCZ. PMID:22850735

  11. Impact of a microRNA MIR137 Susceptibility Variant on Brain Function in People at High Genetic Risk of Schizophrenia or Bipolar Disorder

    PubMed Central

    Whalley, Heather C; Papmeyer, Martina; Romaniuk, Liana; Sprooten, Emma; Johnstone, Eve C; Hall, Jeremy; Lawrie, Stephen M; Evans, Kathryn L; Blumberg, Hilary P; Sussmann, Jessika E; McIntosh, Andrew M

    2012-01-01

    A recent ‘mega-analysis' combining genome-wide association study data from over 40?000 individuals identified novel genetic loci associated with schizophrenia (SCZ) at genome-wide significance level. The strongest finding was a locus within an intron of a putative primary transcript for microRNA MIR137. In the current study, we examine the impact of variation at this locus (rs1625579, G/T; where T is the common and presumed risk allele) on brain activation during a sentence completion task that differentiates individuals with SCZ, bipolar disorder (BD), and their relatives from controls. We examined three groups of individuals performing a sentence completion paradigm: (i) individuals at high genetic risk of SCZ (n=44), (ii) individuals at high genetic risk of BD (n=90), and (iii) healthy controls (n=81) in order to test the hypothesis that genotype at rs1625579 would influence brain activation. Genotype groups were assigned as ‘RISK?' for GT and GG individuals, and ‘RISK+' for TT homozygotes. The main effect of genotype was significantly greater activation in the RISK? individuals in the posterior right medial frontal gyrus, BA 6. There was also a significant genotype*group interaction in the left amygdala and left pre/postcentral gyrus. This was due to differences between the controls (where individuals with the RISK? genotype showed greater activation than RISK+ subjects) and the SCZ high-risk group, where the opposite genotype effect was seen. These results suggest that the newly identified SCZ locus may influence brain activation in a manner that is partly dependent on the presence of existing genetic susceptibility for SCZ. PMID:22850735

  12. Unique Features of High-Density Lipoproteins in the Japanese: In Population and in Genetic Factors

    PubMed Central

    Yokoyama, Shinji

    2015-01-01

    Despite its gradual increase in the past several decades, the prevalence of atherosclerotic vascular disease is low in Japan. This is largely attributed to difference in lifestyle, especially food and dietary habits, and it may be reflected in certain clinical parameters. Plasma high-density lipoprotein (HDL) levels, a strong counter risk for atherosclerosis, are indeed high among the Japanese. Accordingly, lower HDL seems to contribute more to the development of coronary heart disease (CHD) than an increase in non-HDL lipoproteins at a population level in Japan. Interestingly, average HDL levels in Japan have increased further in the past two decades, and are markedly higher than in Western populations. The reasons and consequences for public health of this increase are still unknown. Simulation for the efficacy of raising HDL cholesterol predicts a decrease in CHD of 70% in Japan, greater than the extent by reducing low-density lipoprotein cholesterol predicted by simulation or achieved in a statin trial. On the other hand, a substantial portion of hyperalphalipoproteinemic population in Japan is accounted for by genetic deficiency of cholesteryl ester transfer protein (CETP), which is also commonly unique in East Asian populations. It is still controversial whether CETP mutations are antiatherogenic. Hepatic Schistosomiasis is proposed as a potential screening factor for historic accumulation of CETP deficiency in East Asia. PMID:25849946

  13. Pathogenic serum amyloid A 1.1 shows a long oligomer-rich fibrillation lag phase contrary to the highly amyloidogenic non-pathogenic SAA2.2.

    PubMed

    Srinivasan, Saipraveen; Patke, Sanket; Wang, Yun; Ye, Zhuqiu; Litt, Jeffrey; Srivastava, Sunit K; Lopez, Maria M; Kurouski, Dmitry; Lednev, Igor K; Kane, Ravi S; Colón, Wilfredo

    2013-01-25

    Serum amyloid A (SAA) is best known for being the main component of amyloid in the inflammation-related disease amyloid A (AA) amyloidosis. Despite the high sequence identity among different SAA isoforms, not all SAA proteins are pathogenic. In most mouse strains, the AA deposits mostly consist of SAA1.1. Conversely, the CE/J type mouse expresses a single non-pathogenic SAA2.2 protein that is 94% identical to SAA1.1. Here we show that SAA1.1 and SAA2.2 differ in their quaternary structure, fibrillation kinetics, prefibrillar oligomers, and fibril morphology. At 37 °C and inflammation-related SAA concentrations, SAA1.1 exhibits an oligomer-rich fibrillation lag phase of a few days, whereas SAA2.2 shows virtually no lag phase and forms small fibrils within a few hours. Deep UV resonance Raman, far UV-circular dichroism, atomic force microscopy, and fibrillation cross-seeding experiments suggest that SAA1.1 and SAA2.2 fibrils possess different morphology. Both the long-lived oligomers of pathogenic SAA1.1 and the fleeting prefibrillar oligomers of non-pathogenic SAA2.2, but not their respective amyloid fibrils, permeabilized synthetic bilayer membranes in vitro. This study represents the first comprehensive comparison between the biophysical properties of SAA isoforms with distinct pathogenicities, and the results suggest that structural and kinetic differences in the oligomerization-fibrillation of SAA1.1 and SAA2.2, more than their intrinsic amyloidogenicity, may contribute to their diverse pathogenicity. PMID:23223242

  14. BRAF V600E immunohistochemistry is reliable in primary and metastatic colorectal carcinoma regardless of treatment status and shows high intratumoral homogeneity.

    PubMed

    Bledsoe, Jacob R; Kamionek, Michal; Mino-Kenudson, Mari

    2014-10-01

    In colorectal carcinoma the evaluation of BRAF mutation status is increasingly being performed given its utility as a prognostic and predictive biomarker. However, there are conflicting reports of the sensitivity and specificity of BRAF V600E immunohistochemistry (IHC), and little is known about its reliability in tissues collected from metastatic sites or after chemotherapy, radiation therapy and/or targeted therapy. The degree of intratumoral staining heterogeneity is also not well established. We performed IHC for BRAF V600E (VE1) on 204 cases of colorectal carcinoma including 59 with the BRAF V600E mutation. These included primary (n=147) and metastatic/recurrent (n=57) tumors, collected before (n=133) or after (n=71) chemotherapy, radiation therapy and/or targeted therapy. Evaluation of a test cohort (39 cases) with knowledge of mutation status established a specific staining pattern for the mutation: diffuse cytoplasmic staining of near-uniform intensity, regardless of strength of staining. Using this pattern, pathologists at 3 levels of training independently performed blinded evaluation of the remaining cases. BRAF V600E staining was 96.3% sensitive and 98.5% specific for the mutation, including both pretreatment and posttreatment specimens. Fleiss ? for interobserver agreement was 0.96. Staining of whole sections of the BRAF mutants showed diffuse staining in all cases and uniform or near-uniform intensity in 91%. In 20 cases with both pretreatment and posttreatment specimens, there was 100% accuracy and agreement in staining between samples. We conclude that BRAF V600E IHC is reliable for the evaluation of mutational status in colorectal carcinoma regardless of site or prior treatment history, and staining shows a high degree of intratumoral homogeneity. PMID:24921639

  15. The Phenome-Wide Distribution of Genetic Variance.

    PubMed

    Blows, Mark W; Allen, Scott L; Collet, Julie M; Chenoweth, Stephen F; McGuigan, Katrina

    2015-07-01

    A general observation emerging from estimates of additive genetic variance in sets of functionally or developmentally related traits is that much of the genetic variance is restricted to few trait combinations as a consequence of genetic covariance among traits. While this biased distribution of genetic variance among functionally related traits is now well documented, how it translates to the broader phenome and therefore any trait combination under selection in a given environment is unknown. We show that 8,750 gene expression traits measured in adult male Drosophila serrata exhibit widespread genetic covariance among random sets of five traits, implying that pleiotropy is common. Ultimately, to understand the phenome-wide distribution of genetic variance, very large additive genetic variance-covariance matrices (G) are required to be estimated. We draw upon recent advances in matrix theory for completing high-dimensional matrices to estimate the 8,750-trait G and show that large numbers of gene expression traits genetically covary as a consequence of a single genetic factor. Using gene ontology term enrichment analysis, we show that the major axis of genetic variance among expression traits successfully identified genetic covariance among genes involved in multiple modes of transcriptional regulation. Our approach provides a practical empirical framework for the genetic analysis of high-dimensional phenome-wide trait sets and for the investigation of the extent of high-dimensional genetic constraint. PMID:26098335

  16. High genetic diversity and predominance of Rhinovirus A and C from Panamanian hospitalized children under five years with respiratory infections

    PubMed Central

    2012-01-01

    Background Human Rhinoviruses (HRVs) have high genetic diversity and three species have been described: HRV-A, HRV-B, and the recently recognized HRV-C, which has been rapidly identified worldwide. Findings In the present study, we report the frequency and diversity of Human Rhinovirus (HRV) strains circulating in Panama from children hospitalized with respiratory infections. Conclusions HRVs of species A, B and C have been identified with a predominance of HRV-A and HRV-C over HRV-B, and marked genetic diversity within each species. PMID:23116216

  17. A water-soluble extract from Cucurbita moschata shows anti-obesity effects by controlling lipid metabolism in a high fat diet-induced obesity mouse model.

    PubMed

    Choi, Hyounjeong; Eo, Haekwan; Park, Kyoungcheol; Jin, Mirim; Park, Eun-Jin; Kim, Seon-Hee; Park, Jeong Euy; Kim, Sunyoung

    2007-08-01

    During the screening of a variety of plant sources for their anti-obesity activity, it was found that a water-soluble extract, named PG105, prepared from stem parts of Cucurbita moschata, contains potent anti-obesity activities in a high fat diet-induced obesity mouse model. In this animal model, increases in body weight and fat storage were suppressed by 8-week oral administration of PG105 at 500 mg/kg, while the overall amount of food intake was not affected. Furthermore, PG105 protected the development of fatty liver and increased the hepatic beta-oxidation activity. Results from blood analysis showed that the levels of triglyceride and cholesterol were significantly lowered by PG105 administration, and also that the level of leptin was reduced, while that of adiponectin was increased. To understand the underlying mechanism at the molecular level, the effects of PG105 were examined on the expression of the genes involved in lipid metabolism by Northern blot analysis. In the liver of PG105-treated mice, the mRNA level of lipogenic genes such as SREBP-1c and SCD-1 was decreased, while that of lipolytic genes such as PPARalpha, ACO-1, CPT-1, and UCP-2 was modestly increased. Our data suggest that PG105 may have great potential as a novel anti-obesity agent in that both inhibition of lipid synthesis and acceleration of fatty acid breakdown are induced by this reagent. PMID:17548058

  18. Theoretical study of the dynamics and kinetics of the O + CS ? CO + S chemical laser reaction, where CO shows a very high vibrational excitation.

    PubMed

    Gamallo, Pablo; Francia, Rafael; Martínez, Rodrigo; Sayós, Ramón; González, Miguel

    2012-12-01

    The dynamics and kinetics of the O((3)P) + CS(X(1)?(+)) ? CO(X(1)?(+)) + S((3)P) chemical laser reaction was studied theoretically in detail for the first time, as a function of collision energy (0.0388-2.0 eV) and rovibrational excitation of CS. This was made using the quasi-classical trajectory (QCT) method and employing the best ab initio analytical ground potential energy surface (1(3)A' PES) available. A broad set of properties was determined, including scalar and vector properties, and the reaction mode. The behaviors observed and the considerable formation of OCS collision complexes were interpreted from some characteristics of the PES (early barrier, shallow minimum in the exit channel, and high exoergicity (mainly channeled into CO vibration; up to ?81% of the available energy)) and the kinematics. The QCT vibrational and rotational CO populations and the vector properties show a quite good agreement with experiments, but the QCT rate constants disagree. To better account for the kinetics, we performed CASPT2/aug-cc-pVTZ ab initio calculations on the stationary points along the minimum energy path of the ground and first excited (1(3)A'') PESs. The transition state theory, which can be satisfactorily applied here, leads to rate constants (100-2000 K) that are quite close to the measured ones, where comparison is possible (150-300 K). We expect that these results will encourage further theoretical and experimental developments. PMID:23131012

  19. A high-density genetic map of Arachis duranensis, a diploid ancestor of cultivated peanut

    PubMed Central

    2012-01-01

    Background Cultivated peanut (Arachis hypogaea) is an allotetraploid species whose ancestral genomes are most likely derived from the A-genome species, A. duranensis, and the B-genome species, A. ipaensis. The very recent (several millennia) evolutionary origin of A. hypogaea has imposed a bottleneck for allelic and phenotypic diversity within the cultigen. However, wild diploid relatives are a rich source of alleles that could be used for crop improvement and their simpler genomes can be more easily analyzed while providing insight into the structure of the allotetraploid peanut genome. The objective of this research was to establish a high-density genetic map of the diploid species A. duranensis based on de novo generated EST databases. Arachis duranensis was chosen for mapping because it is the A-genome progenitor of cultivated peanut and also in order to circumvent the confounding effects of gene duplication associated with allopolyploidy in A. hypogaea. Results More than one million expressed sequence tag (EST) sequences generated from normalized cDNA libraries of A. duranensis were assembled into 81,116 unique transcripts. Mining this dataset, 1236 EST-SNP markers were developed between two A. duranensis accessions, PI 475887 and Grif 15036. An additional 300 SNP markers also were developed from genomic sequences representing conserved legume orthologs. Of the 1536 SNP markers, 1054 were placed on a genetic map. In addition, 598 EST-SSR markers identified in A. hypogaea assemblies were included in the map along with 37 disease resistance gene candidate (RGC) and 35 other previously published markers. In total, 1724 markers spanning 1081.3 cM over 10 linkage groups were mapped. Gene sequences that provided mapped markers were annotated using similarity searches in three different databases, and gene ontology descriptions were determined using the Medicago Gene Atlas and TAIR databases. Synteny analysis between A. duranensis, Medicago and Glycine revealed significant stretches of conserved gene clusters spread across the peanut genome. A higher level of colinearity was detected between A. duranensis and Glycine than with Medicago. Conclusions The first high-density, gene-based linkage map for A. duranensis was generated that can serve as a reference map for both wild and cultivated Arachis species. The markers developed here are valuable resources for the peanut, and more broadly, to the legume research community. The A-genome map will have utility for fine mapping in other peanut species and has already had application for mapping a nematode resistance gene that was introgressed into A. hypogaea from A. cardenasii. PMID:22967170

  20. Using the Eastern Hellbender Salamander in a High School Genetics & Ecological Conservation Activity

    ERIC Educational Resources Information Center

    Chudyk, Sarah; McMillan, Amy; Lange, Catherine

    2014-01-01

    This article contains an original 5E lesson plan developed from conservation genetics research on the giant North American hellbender salamander, Cryptobranchus alleganiensis alleganiensis. The lesson plan provides background information on the hellbender, reviews basic genetics, and exposes students to the scientific process that is used during…

  1. High genetic diversity and population differentiation in Boechera fecunda , a rare relative of Arabidopsis

    Microsoft Academic Search

    BAO-HUA SONG; THOMAS MITCHELL-OLDS

    2007-01-01

    Conservation of endangered species becomes a critical issue with the increasing rates of extinction. In this study, we use 13 microsatellite loci and 27 single-copy nuclear loci to investigate the population genetics of Boechera fecunda, a rare relative of Arabidopsis thaliana, known from only 21 populations in Montana. We investigated levels of genetic diversity and population structure in comparison to

  2. Shallow gene pools in the high intertidal: extreme loss of genetic diversity in viviparous sea stars (Parvulastra).

    PubMed

    Keever, Carson C; Puritz, Jonathan B; Addison, Jason A; Byrne, Maria; Grosberg, Richard K; Toonen, Robert J; Hart, Michael W

    2013-10-23

    We document an extreme example of reproductive trait evolution that affects population genetic structure in sister species of Parvulastra cushion stars from Australia. Self-fertilization by hermaphroditic adults and brood protection of benthic larvae causes strong inbreeding and range-wide genetic poverty. Most samples were fixed for a single allele at nearly all nuclear loci; heterozygotes were extremely rare (0.18%); mitochondrial DNA sequences were more variable, but few populations shared haplotypes in common. Isolation-with-migration models suggest that these patterns are caused by population bottlenecks (relative to ancestral population size) and low gene flow. Loss of genetic diversity and low potential for dispersal between high-intertidal habitats may have dire consequences for extinction risk and potential for future adaptive evolution in response to climate and other selective agents. PMID:23925835

  3. The First High-Density Genetic Map Construction in Tree Peony (Paeonia Sect. Moutan) using Genotyping by Specific-Locus Amplified Fragment Sequencing

    PubMed Central

    Cai, Changfu; Cheng, Fang-Yun; Wu, Jing; Zhong, Yuan; Liu, Gaixiu

    2015-01-01

    Genetic linkage maps, permitting the elucidation of genome structure, are one of most powerful genomic tools to accelerate marker-assisted breeding. However, due to a lack of sufficient user-friendly molecular markers, no genetic linkage map has been developed for tree peonies (Paeonia Sect. Moutan), a group of important horticultural plants worldwide. Specific-locus amplified fragment sequencing (SLAF-seq) is a recent molecular marker development technology that enable the large-scale discovery and genotyping of sequence-based marker in genome-wide. In this study, we performed SLAF sequencing of an F1 population, derived from the cross P. ostti ‘FenDanBai’ × P. × suffruticosa ‘HongQiao’, to identify sufficient high-quality markers for the construction of high-density genetic linkage map in tree peonies. After SLAF sequencing, a total of 78 Gb sequencing data and 285,403,225 pair-end reads were generated. We detected 309,198 high-quality SLAFs from these data, of which 85,124 (27.5%) were polymorphic. Subsequently, 3518 of the polymorphic markers, which were successfully encoded in to Mendelian segregation types, and were in conformity with the criteria of high-quality markers, were defined as effective markers and used for genetic linkage mapping. Finally, we constructed an integrated genetic map, which comprised 1189 markers on the five linkage groups, and spanned 920.699 centiMorgans (cM) with an average inter-marker distance of 0.774 cM. There were 1115 ‘SNP-only’ markers, 18 ‘InDel-only’ markers, and 56 ‘SNP&InDel’ markers on the map. Among these markers, 450 (37.85%) showed significant segregation distortion (P < 0.05). In conclusion, this investigation reported the first large-scale marker development and high-density linkage map construction for tree peony. The results of this study will serve as a solid foundation not only for marker-assisted breeding, but also for genome sequence assembly for tree peony. PMID:26010095

  4. Genetic Risk Assessments in Individuals at High Risk for Inherited Breast Cancer in the Breast Oncology Care Setting

    PubMed Central

    Pal, Tuya; Vadaparampil, Susan T.

    2014-01-01

    Background It has become increasingly common to consider BRCA mutation status when determining optimal cancer risk management and treatment options in order to improve patient outcomes. Knowledge about the risk for hereditary cancer at or as close as possible to the time of diagnosis allows patients access to the most risk reduction options available. Methods This paper illustrates the role of genetic risk assessment for hereditary breast cancer, using hereditary breast and ovarian cancer (HBOC) syndrome as a model due to germline mutations in the BRCA1 and BRCA2. Specifically, the value of genetic counseling and testing for HBOC across the cancer prevention and control continuum is outlined as it pertains to breast cancer. Results In recognition of the importance of risk assessment for hereditary breast cancer, leading health professional organizations have developed specific guidelines and recommendations to providers for identification of women at increased risk for carrying a BRCA mutation. Conclusions Institutional efforts specific to genetic counseling and testing have resulted in the implementation of a model driven by physician recommendation as a referral system for high-risk breast cancer patients. Establishing an infrastructure to support research, education, and outreach initiatives focused on BRCA genetic counseling and testing will provide information that can improve the delivery of cancer genetics services. PMID:23037493

  5. Genetic population structure of the ectomycorrhizal fungus Pisolithus microcarpus suggests high gene flow in south-eastern Australia.

    PubMed

    Hitchcock, Catherine J; Chambers, Susan M; Cairney, John W G

    2011-02-01

    Pisolithus are ectomycorrhizal fungi that associate with roots of numerous plant species in natural and plantation forests worldwide. Despite the fact that Pisolithus spp. are present in plantation forests in many countries, knowledge of the genetic population structure of Pisolithus spp. remains limited. In this study, we have tested the hypothesis that a propensity for long-distance spore dispersal in Pisolithus microcarpus, along with the widespread distribution of potential eucalypt and acacia plant hosts in south-eastern Australia facilitates gene flow that limits population differentiation. Five polymorphic simple sequence repeat markers were used to investigate the population structure of P. microcarpus. Isolates were grouped according to geographical origin and isolate genotypes were analysed among the geographical populations. Pairwise F (ST) estimates indicated limited genetic differentiation among the geographical populations. Analysis of molecular variance revealed that most of the genetic variation present was within geographical populations, with only 1.3% of the genetic variation among P. microcarpus geographical populations. This was particularly pronounced for four geographical populations within a ca 7,000 km(2) area New South Wales, which were each separated by < 100 km and appeared to be genetically homogeneous. The lack of population structure is suggested to be due to a high degree of gene flow, via basidiospores, between the New South Wales geographical populations. PMID:20499111

  6. Genetic algorithm based optimization of pulse profile for MOPA based high power fiber lasers

    NASA Astrophysics Data System (ADS)

    Zhang, Jiawei; Tang, Ming; Shi, Jun; Fu, Songnian; Li, Lihua; Liu, Ying; Cheng, Xueping; Liu, Jian; Shum, Ping

    2015-03-01

    Although the Master Oscillator Power-Amplifier (MOPA) based fiber laser has received much attention for laser marking process due to its large tunabilty of pulse duration (from 10ns to 1ms), repetition rate (100Hz to 500kHz), high peak power and extraordinary heat dissipating capability, the output pulse deformation due to the saturation effect of fiber amplifier is detrimental for many applications. We proposed and demonstrated that, by utilizing Genetic algorithm (GA) based optimization technique, the input pulse profile from the master oscillator (current-driven laser diode) could be conveniently optimized to achieve targeted output pulse shape according to real parameters' constraints. In this work, an Yb-doped high power fiber amplifier is considered and a 200ns square shaped pulse profile is the optimization target. Since the input pulse with longer leading edge and shorter trailing edge can compensate the saturation effect, linear, quadratic and cubic polynomial functions are used to describe the input pulse with limited number of unknowns(<5). Coefficients of the polynomial functions are the optimization objects. With reasonable cost and hardware limitations, the cubic input pulse with 4 coefficients is found to be the best as the output amplified pulse can achieve excellent flatness within the square shape. Considering the bandwidth constraint of practical electronics, we examined high-frequency component cut-off effect of input pulses and found that the optimized cubic input pulses with 300MHz bandwidth is still quite acceptable to satisfy the requirement for the amplified output pulse and it is feasible to establish such a pulse generator in real applications.

  7. High-density genetic linkage maps of Phytophthora infestans reveal trisomic progeny and chromosomal rearrangements

    Microsoft Academic Search

    Lee van der T. A. J; Antonino Testa; Andrea Robold; Klooster van t J. W; F. Govers

    2004-01-01

    Detailed analysis of the inheritance of molecular markers was performed in the oomycete plant pathogen Phytophthora infestans. Linkage analysis in the sexual progeny of two Dutch field isolates (cross 71) resulted in a high-density map containing 508 markers on 13 major and 10 minor linkage groups. The map showed strong clustering of markers, particularly of markers originating from one parent,

  8. Characterization and genetic analysis of a very high tillering and dwarf rice (Oryza sativa L.) mutant

    E-print Network

    Mani, Dhananjay

    2009-05-15

    leaf stage whereas no tiller was observed in semi-dwarf rice cultivar, Cocodrie. Results showed that the production of high tiller numbers was the result of the release of axillary buds from a dormant stage rather than the initiation of additional...

  9. High variance in reproductive success generates a false signature of a genetic bottleneck in populations of constant size: a simulation study

    PubMed Central

    2013-01-01

    Background Demographic bottlenecks can severely reduce the genetic variation of a population or a species. Establishing whether low genetic variation is caused by a bottleneck or a constantly low effective number of individuals is important to understand a species’ ecology and evolution, and it has implications for conservation management. Recent studies have evaluated the power of several statistical methods developed to identify bottlenecks. However, the false positive rate, i.e. the rate with which a bottleneck signal is misidentified in demographically stable populations, has received little attention. We analyse this type of error (type I) in forward computer simulations of stable populations having greater than Poisson variance in reproductive success (i.e., variance in family sizes). The assumption of Poisson variance underlies bottleneck tests, yet it is commonly violated in species with high fecundity. Results With large variance in reproductive success (Vk ? 40, corresponding to a ratio between effective and census size smaller than 0.1), tests based on allele frequencies, allelic sizes, and DNA sequence polymorphisms (heterozygosity excess, M-ratio, and Tajima’s D test) tend to show erroneous signals of a bottleneck. Similarly, strong evidence of population decline is erroneously detected when ancestral and current population sizes are estimated with the model based method MSVAR. Conclusions Our results suggest caution when interpreting the results of bottleneck tests in species showing high variance in reproductive success. Particularly in species with high fecundity, computer simulations are recommended to confirm the occurrence of a population bottleneck. PMID:24131797

  10. Genetic Convergence in the Adaptation of Dogs and Humans to the High-Altitude Environment of the Tibetan Plateau

    PubMed Central

    Wang, Guo-Dong; Fan, Ruo-Xi; Zhai, Weiwei; Liu, Fei; Wang, Lu; Zhong, Li; Wu, Hong; Yang, He-Chuan; Wu, Shi-Fang; Zhu, Chun-Ling; Li, Yan; Gao, Yun; Ge, Ri-Li; Wu, Chung-I; Zhang, Ya-Ping

    2014-01-01

    The high-altitude hypoxic environment represents one of the most extreme challenges for mammals. Previous studies of humans on the Tibetan plateau and in the Andes Mountains have identified statistical signatures of selection in different sets of loci. Here, we first measured the hemoglobin levels in village dogs from Tibet and those from Chinese lowlands. We found that the hemoglobin levels are very similar between the two groups, suggesting that Tibetan dogs might share similar adaptive strategies as the Tibetan people. Through a whole-genome sequencing approach, we have identified EPAS1 and HBB as candidate genes for the hypoxic adaptation on the Tibetan plateau. The population genetic analysis shows a significant convergence between humans and dogs in Tibet. The similarities in the sets of loci that exhibit putative signatures of selection and the hemoglobin levels between humans and dogs of the same environment, but not between human populations in different regions, suggests an extraordinary landscape of convergent evolution between human beings and their best friend on the Tibetan plateau. PMID:25091388

  11. Genetic convergence in the adaptation of dogs and humans to the high-altitude environment of the tibetan plateau.

    PubMed

    Wang, Guo-Dong; Fan, Ruo-Xi; Zhai, Weiwei; Liu, Fei; Wang, Lu; Zhong, Li; Wu, Hong; Yang, He-Chuan; Wu, Shi-Fang; Zhu, Chun-Ling; Li, Yan; Gao, Yun; Ge, Ri-Li; Wu, Chung-I; Zhang, Ya-Ping

    2014-08-01

    The high-altitude hypoxic environment represents one of the most extreme challenges for mammals. Previous studies of humans on the Tibetan plateau and in the Andes Mountains have identified statistical signatures of selection in different sets of loci. Here, we first measured the hemoglobin levels in village dogs from Tibet and those from Chinese lowlands. We found that the hemoglobin levels are very similar between the two groups, suggesting that Tibetan dogs might share similar adaptive strategies as the Tibetan people. Through a whole-genome sequencing approach, we have identified EPAS1 and HBB as candidate genes for the hypoxic adaptation on the Tibetan plateau. The population genetic analysis shows a significant convergence between humans and dogs in Tibet. The similarities in the sets of loci that exhibit putative signatures of selection and the hemoglobin levels between humans and dogs of the same environment, but not between human populations in different regions, suggests an extraordinary landscape of convergent evolution between human beings and their best friend on the Tibetan plateau. PMID:25091388

  12. Genetic Affinities between Trans-Oceanic Populations of Non-Buoyant Macroalgae in the High Latitudes of the Southern Hemisphere

    PubMed Central

    Fraser, Ceridwen I.; Zuccarello, Giuseppe C.; Spencer, Hamish G.; Salvatore, Laura C.; Garcia, Gabriella R.; Waters, Jonathan M.

    2013-01-01

    Marine biologists and biogeographers have long been puzzled by apparently non-dispersive coastal taxa that nonetheless have extensive transoceanic distributions. We here carried out a broad-scale phylogeographic study to test whether two widespread Southern Hemisphere species of non-buoyant littoral macroalgae are capable of long-distance dispersal. Samples were collected from along the coasts of southern Chile, New Zealand and several subAntarctic islands, with the focus on high latitude populations in the path of the Antarctic Circumpolar Current or West Wind Drift. We targeted two widespread littoral macroalgal species: the brown alga Adenocystisutricularis (Ectocarpales, Heterokontophyta) and the red alga Bostrychiaintricata (Ceramiales, Rhodophyta). Phylogenetic analyses were performed using partial mitochondrial (COI), chloroplast (rbcL) and ribosomal nuclear (LSU / 28S) DNA sequence data. Numerous deeply-divergent clades were resolved across all markers in each of the target species, but close phylogenetic relationships – even shared haplotypes – were observed among some populations separated by large oceanic distances. Despite not being particularly buoyant, both Adenocystisutricularis and Bostrychiaintricata thus show genetic signatures of recent dispersal across vast oceanic distances, presumably by attachment to floating substrata such as wood or buoyant macroalgae. PMID:23894421

  13. Multilocus sequence typing reveals high genetic diversity and epidemic population structure for the fish pathogen Yersinia ruckeri.

    PubMed

    Bastardo, Asmine; Ravelo, Carmen; Romalde, Jesús L

    2012-08-01

    Yersinia ruckeri is the causative agent of enteric redmouth in fish and one of the major bacterial pathogens causing losses in salmonid aquaculture. Previously typing methods, including restriction enzyme analysis, pulsed-field gel electrophoresis and multilocus enzyme electrophoresis (MLEE) have indicated a clonal population structure. In this work, we describe a multilocus sequence typing (MLST) scheme for Y.ruckeri based on the internal fragment sequence of six housekeeping genes. This MLST scheme was applied to 103 Y.ruckeri strains from diverse geographic areas and hosts as well as environmental sources. Sequences obtained from this work were deposited and are available in a public database (http://publmst.org/yruckeri/). Thirty different sequence types (ST) were identified, 21 of which were represented by a single isolate, evidencing high genetic diversity. ST2 comprised more than one-third of the isolates and was most frequently observed among isolates from trout. Two major clonal complexes (CC) were identified by eBURST analysis showing a common evolutionary origin for 94 isolates forming 21 STs into CC1 and for 6 isolates of 6 STs in the CC2. It was also possible to associate some unique ST with isolates from recent outbreaks in vaccinated salmonid fish. PMID:22463110

  14. High prevalence of genetic variants previously associated with Brugada syndrome in new exome data.

    PubMed

    Risgaard, B; Jabbari, R; Refsgaard, L; Holst, A G; Haunsř, S; Sadjadieh, A; Winkel, B G; Olesen, M S; Tfelt-Hansen, J

    2013-11-01

    More than 300 variants in 12 genes have been associated with Brugada syndrome (BrS) which has a prevalence ranging between 1:2000 and 1:100,000. Until recently, there has been little knowledge regarding the distribution of genetic variations in the general population. This problem was partly solved, when exome data from the NHLI GO Exome Sequencing Project (ESP) was published. In this study, we aimed to report the prevalence of previously BrS-associated variants in the ESP population. We performed a search in ESP for variants previously associated with BrS. In addition, four variants in ESP were genotyped in a second Danish control population (n?=?536) with available electrocardiograms. In ESP, we identified 38 of 355 (10%) variants, distributed on 272 heterozygote carriers and two homozygote carriers. The genes investigated were on average screened in 6258 individuals. This corresponds to a surprisingly high genotype prevalence of 1:23 (274:6258). Genotyping the four common ESP-derived variants CACNA2D1 S709N, SCN5A F2004L, CACNB2 S143F, and CACNB2 T450I in the Danish controls, we found a genotype prevalence comparable with that found in ESP. We suggest that exome data are used in research, as an additive tool to predict the pathogenicity of variants in patients suspected for BrS. PMID:23414114

  15. High Genetic Differentiation between the M and S Molecular Forms of Anopheles gambiae in Africa

    PubMed Central

    Esnault, Caroline; Boulesteix, Matthieu; Duchemin, Jean Bernard; Koffi, Alphonsine A.; Chandre, Fabrice; Dabiré, Roch; Robert, Vincent; Simard, Frédéric; Tripet, Frédéric; Donnelly, Martin J.; Fontenille, Didier; Biémont, Christian

    2008-01-01

    Background Anopheles gambiae, a major vector of malaria, is widely distributed throughout sub-Saharan Africa. In an attempt to eliminate infective mosquitoes, researchers are trying to develop transgenic strains that are refractory to the Plasmodium parasite. Before any release of transgenic mosquitoes can be envisaged, we need an accurate picture of the differentiation between the two molecular forms of An. gambiae, termed M and S, which are of uncertain taxonomic status. Methodology/Principal Findings Insertion patterns of three transposable elements (TEs) were determined in populations from Benin, Burkina Faso, Cameroon, Ghana, Ivory Coast, Madagascar, Mali, Mozambique, Niger, and Tanzania, using Transposon Display, a TE-anchored strategy based on Amplified Fragment Length Polymorphism. The results reveal a clear differentiation between the M and S forms, whatever their geographical origin, suggesting an incipient speciation process. Conclusions/Significance Any attempt to control the transmission of malaria by An. gambiae using either conventional or novel technologies must take the M/S genetic differentiation into account. In addition, we localized three TE insertion sites that were present either in every individual or at a high frequency in the M molecular form. These sites were found to be located outside the chromosomal regions that are suspected of involvement in the speciation event between the two forms. This suggests that these chromosomal regions are either larger than previously thought, or there are additional differentiated genomic regions interspersed with undifferentiated regions. PMID:18414665

  16. Regularization approach to inductive genetic programming

    Microsoft Academic Search

    Nikolay I. Nikolaev; Hitoshi Iba

    2001-01-01

    Abstract, This paper presents an approach to regularization of inductive genetic programming tuned for learning polynomials. The objective is to achieve optimal evolutionary performance when searching high-order multivariate polynomials represented as tree structures. We show how to improve the genetic programming of polynomials by balancing its statistical bias with its variance. Bias reduction is achieved by employing a set of

  17. High genetic diversity in cryptic populations of the migratory sutchi catfish Pangasianodon hypophthalmus in the Mekong River.

    PubMed

    So, N; Maes, G E; Volckaert, F A M

    2006-02-01

    The detection and conservation of spawning units is of crucial importance in highly migratory species. The sutchi catfish Pangasianodon hypophthalmus (Pangasiidae; Teleostei) is a common large-sized tropical fish, which migrates annually to several upstream spawning sites on the Lower Mekong River and feeds on the huge floodplain of the Lower Mekong and Tonle Sap for the other half of the year. We hypothesised that because of the relative size of the feeding and spawning habitat, genetic variability would be high and homogeneous in foraging populations, but that spawning stocks would be distinct in space and time. To test these predictions, 567 individuals from 10 geographic locations separated by up to 1230 km along the Lower Mekong River were genotyped at seven microsatellite loci. The level of genetic diversity was much higher than other freshwater fish and reached values comparable to marine species (mean H(e)=0.757). All samples collected at the potential spawning sites deviated from Hardy-Weinberg expectations, suggesting admixture. Individual-based clustering methods revealed genetic heterogeneity and enabled the detection of three genetically distinct sympatric populations. There was no evidence of recent reduction in effective population size in any population. Contrasting with the vast extent of the feeding grounds, the shortage of spawning grounds seems to have moved sutchi catfish towards diachronous spawning. Hence the sustainable exploitation of this natural resource hinges on the conservation of the limited spawning grounds and open migration routes between the spawning and feeding grounds. PMID:16369576

  18. Genetic Profiling to Determine Risk of Relapse Free Survival in High-risk Localized Prostate Cancer

    PubMed Central

    Barnett, Christine M.; Heinrich, Michael C.; Lim, Jeong; Nelson, Dylan; Beadling, Carol; Warrick, Andrea; Neff, Tanaya; Higano, Celestia S.; Garzotto, Mark; Qian, David; Corless, Christopher L.; Thomas, George V.; Beer, Tomasz M.

    2014-01-01

    Purpose The characterization of actionable mutations in human tumors is a prerequisite for the development of individualized, targeted therapy. We examined the prevalence of potentially therapeutically actionable mutations in patients with high risk clinically localized prostate cancer. Experimental Design 48 samples of formalin fixed paraffin embedded prostatectomy tissue from a neoadjuvant chemotherapy trial were analyzed. DNA extracted from microdissected tumor was analyzed for 643 common solid tumor mutations in 53 genes using mass spectroscopy based sequencing. In addition, PTEN loss and ERG translocations were examined using immunohistochemistry in associated tissue microarrays. Association with relapse during 5 years of follow-up was examined in exploratory analyses of the potential clinical relevance of the genetic alterations. Results Of the 40 tumors evaluable for mutations, 10% had point mutations in potentially actionable cancer genes. Of the 47 tumors evaluable for IHC, 36% had PTEN loss and 40% had ERG rearrangement. Individual mutations were not frequent enough to determine associations with relapse. Using Kaplan-Meier analysis with a log-rank test, the 16 patients who had PTEN loss had a significantly shorter median relapse free survival, 19 vs. 106 months (p = .01). Conclusions This study confirms that point mutations in the most common cancer regulatory genes in prostate cancer are rare. However, the PIK3CA/AKT pathway was mutated in 10% of our samples. While point mutations alone did not have a statistically significant association with relapse, PTEN loss was associated with an increased relapse in high risk prostate cancer treated with chemotherapy followed by surgery. PMID:24352642

  19. Identification of genetic variants of lecithin cholesterol acyltransferase in individuals with high HDL?C levels.

    PubMed

    Naseri, Mohsen; Hedayati, Mehdi; Daneshpour, Maryam Sadat; Bandarian, Fatemeh; Azizi, Fereidoun

    2014-07-01

    Among the most common lipid abnormalities, a low level of high-density lipoprotein-cholesterol (HDL?C) is one of the first risk factors identified for coronary heart disease. Lecithin cholesterol acyltransferase (LCAT) has a pivotal role in the formation and maturation of HDL-C and in reverse cholesterol transport. To identify genetic loci associated with low HDL-C in a population-based cohort in Tehran, the promoter, coding regions and exon/intron boundaries of LCAT were amplified and sequenced in consecutive individuals (n=150) who had extremely low or high HDL-C levels but no other major lipid abnormalities. A total of 14 single-nucleotide polymorphisms (SNPs) were identified, of which 10 were found to be novel; the L393L, S232T and 16:67977696 C>A polymorphisms have been previously reported in the SNP Database (as rs5923, rs4986970 and rs11860115, respectively) and the non-synonymous R47M mutation has been reported in the Catalogue of Somatic Mutations in Cancer (COSM972635). Three of the SNPs identified in the present study (position 6,531 in exon 5, position 6,696 in exon 5 and position 5,151 in exon 1) led to an amino acid substitution. The most common variants were L393L (4886C/T) in exon 6 and Q177E, a novel mutation, in exon 5, and the prevalence of the heterozygous genotype of these two SNPs was significantly higher in the low HDL-C groups. Univariate conditional logistic regression odds ratios (ORs) were nominally significant for Q177E (OR, 5.64; P=0.02; 95% confidence interval, 1.2?26.2). However, this finding was attenuated following adjustment for confounders. Further studies using a larger sample size may enhance the determination of the role of these SNPs. PMID:24789697

  20. Antiviral resistance among highly pathogenic influenza A (H5N1) viruses isolated worldwide in 2002–2012 shows need for continued monitoring

    PubMed Central

    Govorkova, Elena A.; Baranovich, Tatiana; Seiler, Patrick; Armstrong, Jianling; Burnham, Andrew; Guan, Yi; Peiris, Malik; Webby, Richard J.; Webster, Robert G.

    2013-01-01

    Highly pathogenic (HP) H5N1 influenza viruses are evolving pathogens with the potential to cause sustained human-to-human transmission and pandemic virus spread. Specific antiviral drugs can play an important role in the early stages of a pandemic, but the emergence of drug-resistant variants can limit control options. The available data on the susceptibility of HP H5N1 influenza viruses to neuraminidase (NA) inhibitors and adamantanes is scarce, and there is no extensive analysis. Here, we systematically examined the prevalence of NA inhibitor and adamantane resistance among HP H5N1 influenza viruses that circulated worldwide during 2002–2012. The phenotypic fluorescence-based assay showed that both human and avian HP H5N1 viruses are susceptible to NA inhibitors oseltamivir and zanamivir with little variability over time and ~5.5-fold less susceptibility to oseltamivir of viruses of hemagglutinin (HA) clade 2 than of clade 1. Analysis of available sequence data revealed a low incidence of NA inhibitor–resistant variants. The established markers of NA inhibitor resistance (E119A, H274Y, and N294S, N2 numbering) were found in 2.4% of human and 0.8% of avian isolates, and the markers of reduced susceptibility (I117V, K150N, I222V/T/K, and S246N) were found in 0.8% of human and 2.9 % of avian isolates. The frequency of amantadine-resistant variants was higher among human (62.2%) than avian (31.6%) viruses with disproportionate distribution among different HA clades. As in human isolates, avian H5N1 viruses carry double L26I and S31N M2 mutations more often than a single S31N mutation. Overall, both human and avian HP H5N1 influenza viruses are susceptible to NA inhibitors; some proportion is still susceptible to amantadine in contrast to ~100% amantadine resistance among currently circulating seasonal human H1N1 and H3N2 viruses. Continued antiviral susceptibility monitoring of H5N1 viruses is needed to maintain therapeutic approaches for control of disease. PMID:23458714

  1. An ultra-high throughput mutational spectrometer for human genetic diagnostics

    E-print Network

    Forest, Craig Richard, 1978-

    2007-01-01

    Discovering the genetic causes of common diseases may require scanning for mutations in all of the genes in a million people, a significant undertaking. Such discoveries would revolutionize biotechnology, potentially ...

  2. Multi-objective optimization of high-speed milling with parallel genetic simulated annealing

    Microsoft Academic Search

    Z. G. Wang; Y. S. Wong; M. Rahman; J. Sun

    2006-01-01

    In this paper, the optimization of multi-pass milling has been investigated in terms of two objectives: machining time and production cost. An advanced search algorithm—parallel genetic simulated annealing (PGSA)—was used to obtain the optimal cutting parameters. In the implementation of PGSA, the fitness assignment is based on the concept of a non-dominated sorting genetic algorithm (NSGA). An application example is

  3. “They Don’t Teach This in High School”: An Examination of the Portrayal of Teenage Pregnancy in the MTV Television Show 16 and Pregnant

    Microsoft Academic Search

    Elizabeth F. Smith

    2012-01-01

    This paper examines the depiction of teenage pregnancy on the MTV show 16 and Pregnant- a documentary style reality show. Using a qualitative textual analysis the author examines how he teen girls describe themselves, whether contraception was discussed and if it was how so, what options the teens discussed in regards to the pregnancy, the role of the father of

  4. A Combined Analysis of 48 Type 2 Diabetes Genetic Risk Variants Shows No Discriminative Value to Predict Time to First Prescription of a Glucose Lowering Drug in Danish Patients with Screen Detected Type 2 Diabetes

    PubMed Central

    Hornbak, Malene; Allin, Kristine Hřjgaard; Jensen, Majken Linnemann; Lau, Cathrine Juel; Witte, Daniel; Jřrgensen, Marit Eika; Sandbćk, Annelli; Lauritzen, Torsten; Andersson, Ĺsa; Pedersen, Oluf; Hansen, Torben

    2014-01-01

    Objective To investigate the genetic influence of 48 type 2 diabetes susceptibility variants on disease progression measured as risk of early prescription redemption of glucose lowering drugs in screen-detected patients with type 2 diabetes. Methods We studied type 2 diabetes progression in 1,480 patients with screen-detected type 2 diabetes from the ADDITION-Denmark study using information of redeemed prescriptions from the Register of Medicinal Products Statistics from 2001–2009 in Denmark. Patients were cluster randomized by general practitioners, who were randomized to treat type 2 diabetes according to either a conventional or a multifactorial intensive treatment algorithm. We investigated the genetic influence on diabetes progression by constructing a genetic risk score (GRS) of all 48 validated type 2 diabetes susceptibility variants, a GRS of 11 variants linked to ?-cell function and a GRS of 3 variants linked to insulin sensitivity and assessed the association between number of risk alleles and time from diagnosis until first redeemed prescription of either any glucose lowering drug or an insulin drug. Results The GRS linked to insulin sensitivity only nominally increased the risk of an early prescription redemption with an insulin drug by 39% (HR [95% C.I.]?=?1.39 [1.09–1.77], p?=?0.009] in patients randomized to the intensive treatment group. Furthermore, the strongest univariate predictors of diabetes progression for the intensive treatment group (measured as time to first insulin) were younger age (HR [95% C.I.]?=?0.96 [0.93–0.99]), increased BMI (1.05 [1.01–1.09]), increased HbA1c (1.50 [1.36–.66]), increased TG (1.24 [1.11–1.39]) and reduced fasting serum HDL (0.37 [0.17–0.80]) at baseline. Similar results were obtained for the conventional treatment group. Conclusion Higher levels of HbA1c, fasting circulating levels of triglyceride, lower HDL, larger BMI and younger age are significant determinants of early pharmacological intervention in type 2 diabetes. However, known common type 2 diabetes-associated gene variants do not appear to significantly affect disease progression. PMID:25157406

  5. Genome sequencing of a genetically tractable Pyrococcus furiosus strain reveals a highly dynamic genome.

    PubMed

    Bridger, Stephanie L; Lancaster, W Andrew; Poole, Farris L; Schut, Gerrit J; Adams, Michael W W

    2012-08-01

    The model archaeon Pyrococcus furiosus grows optimally near 100°C on carbohydrates and peptides. Its genome sequence (NCBI) was determined 12 years ago. A genetically tractable strain, COM1, was very recently reported, and here we describe its genome sequence. Of 1,909,827 bp in size, it is 1,571 bp longer (0.1%) than the reference NCBI sequence. The COM1 genome contains numerous chromosomal rearrangements, deletions, and single base changes. COM1 also has 45 full or partial insertion sequences (ISs) compared to 35 in the reference NCBI strain, and these have resulted in the direct deletion or insertional inactivation of 13 genes. Another seven genes were affected by chromosomal deletions and are predicted to be nonfunctional. In addition, the amino acid sequences of another 102 of the 2,134 predicted gene products are different in COM1. These changes potentially impact various cellular functions, including carbohydrate, peptide, and nucleotide metabolism; DNA repair; CRISPR-associated defense; transcriptional regulation; membrane transport; and growth at 72°C. For example, the IS-mediated inactivation of riboflavin synthase in COM1 resulted in a riboflavin requirement for growth. Nevertheless, COM1 grew on cellobiose, malto-oligosaccharides, and peptides in complex and minimal media at 98 and 72°C to the same extent as did both its parent strain and a new culture collection strain (DSMZ 3638). This was in spite of COM1 lacking several metabolic enzymes, including nonphosphorylating glyceraldehyde-3-phosphate dehydrogenase and beta-glucosidase. The P. furiosus genome is therefore of high plasticity, and the availability of the COM1 sequence will be critical for the future studies of this model hyperthermophile. PMID:22636780

  6. High genetic diversity in human immunodeficiency virus-type 1 in Jamaica.

    PubMed

    Heslop, O D; Smikle, M F; Vickers, I E; Christian, N A; Harvey, K M; Figueroa, J P; Brown, S E; Christie, C D C; Bain, B; Barton, E N

    2009-06-01

    The subtypes of the human immunodeficiency virus - type 1 (HIV-1) strains from 54 HIV-1 - infected persons including 44 strains which were typed previously by heteroduplex mobility assay (HMA) were determined by DNA sequencing and phylogenetic analysis. Of 54 HIV- infected persons, 92.5% were infected with HIV-1 subtype B and 7.5% with other HIV-1 subtypes including subtypes D (3.7%), A (1.9%) and J (1.9%). In the phylogenetic analysis, the subtype A virus found in the sample clustered with subtype A reference strains and a circulating recombinant form (CRF) reference strain which originates in Central Africa and is circulating in Cuba indicating a close relationship between these viruses. There was 86% concordance between HMA and DNA sequencing in assigning subtype B viruses. For the non-B subtype viruses, there was less concordance between the two methods (67%). The results confirm the predominance of HIV-1 subtype B strains and the high genetic diversity of HIV-1 strains in circulation in Jamaica. The efficacies and some limitations of the HMA as a method of HIV-1 subtyping also were noted. It is important that the HIV/AIDS epidemic in Jamaica be monitored meticulously for possible expansions in non-B subtypes and the emergence of inter-subtype recombinant forms. We recommend that the more expensive DNA sequencing and phylogenetic analysis, including HIV-1 genotyping for antiretroviral drug resistance testing, be used as an adjunct to the more cost-effective HMA to track the HIV/AIDS epidemic in Jamaica. PMID:20043524

  7. Phylogeography of the South China Field Mouse (Apodemus draco) on the Southeastern Tibetan Plateau Reveals High Genetic Diversity and Glacial Refugia

    PubMed Central

    Liu, Yang; Liao, Lihuan; Zhang, Xiuyue; Yue, Bisong

    2012-01-01

    The southeastern margin of the Tibetan Plateau (SEMTP) is a particularly interesting region due to its topographic complexity and unique geologic history, but phylogeographic studies that focus on this region are rare. In this study, we investigated the phylogeography of the South China field mouse, Apodemus draco, in order to assess the role of geologic and climatic events on the Tibetan Plateau in shaping its genetic structure. We sequenced mitochondrial cytochrome b (cyt b) sequences in 103 individuals from 47 sampling sites. In addition, 23 cyt b sequences were collected from GenBank for analyses. Phylogenetic, demographic and landscape genetic methods were conducted. Seventy-six cyt b haplotypes were found and the genetic diversity was extremely high (??=?0.0368; h?=?0.989). Five major evolutionary clades, based on geographic locations, were identified. Demographic analyses implied subclade 1A and subclade 1B experienced population expansions at about 0.052-0.013 Mya and 0.014-0.004 Mya, respectively. The divergence time analysis showed that the split between clade 1 and clade 2 occurred 0.26 Mya, which fell into the extensive glacial period (EGP, 0.5-0.17 Mya). The divergence times of other main clades (2.20-0.55 Mya) were congruent with the periods of the Qingzang Movement (3.6-1.7 Mya) and the Kun-Huang Movement (1.2-0.6 Mya), which were known as the most intense uplift events in the Tibetan Plateau. Our study supported the hypothesis that the SEMTP was a large late Pleistocene refugium, and further inferred that the Gongga Mountain Region and Hongya County were glacial refugia for A. draco in clade 1. We hypothesize that the evolutionary history of A. draco in the SEMTP primarily occurred in two stages. First, an initial divergence would have been shaped by uplift events of the Tibetan Plateau. Then, major glaciations in the Pleistocene added complexity to its demographic history and genetic structure. PMID:22666478

  8. High levels of genetic variability in the moss Ceratodon purpureus from continental Antarctica, subantarctic Heard and Macquarie Islands, and Australasia

    Microsoft Academic Search

    M. L. Skotnicki; A. M. Mackenzie; J. A. Ninham; P. M. Selkirk

    2004-01-01

    The random amplified polymorphic DNA (RAPD) technique, and DNA sequencing of the conserved nuclear ribosomal DNA internal transcribed spacer region (ITS1-5.8S-ITS2), have been used to assess levels of genetic diversity in the moss Ceratodon purpureus from several locations in Australasia, subantarctic Heard and Macquarie Islands, and continental Antarctica. Populations from Heard and Macquarie Islands and from Antarctica maintain high levels

  9. Characterization and genetic mapping of a short, highly repeated, interspersed DNA sequence from rice ( Oryza sativa L.)

    Microsoft Academic Search

    Xinping Zhao; Gary Kochert

    1992-01-01

    A short, highly repeated, interspersed DNA sequence from rice was characterized using a combination of techniques and genetically mapped to rice chromosomes by restriction fragment length polymorphism (RFLP) analysis. A consensus sequence (GGC)n, where n varies from 13–16, for the repeated sequence family was deduced from sequence analysis. Southern blot analysis, restriction mapping of repeat element-containing genomic clones, and DNA

  10. A Genetic and Correlation Analysis of Liver Cholesterol Concentration in Rat Recombinant Inbred Strains Fed a High Cholesterol Diet

    Microsoft Academic Search

    Anita Bottger; Egidius Lankhorst; Hein A. van Lith; L. F. M. van Zutphen; Václav Z??dek; Alena Musilová; Miroslava Šimáková; Rudolf Poledne; Vlasta B??lá; Vladim??r Křen; Michal Pravenec

    1998-01-01

    Liver cholesterol concentration in rats fed a high cholesterol diet, is under genetic control which is supported by significant differences observed among inbred strains. For instance, the Brown Norway (BN-Lx\\/Cub) rat developed a twofold higher liver cholesterol concentration than the spontaneously hypertensive rat (SHR\\/Ola). In the current study, we used 30 recombinant inbred (RI) strains, derived from BN-Lxand SHR progenitors,

  11. A high-density genetic map of Sorghum bicolor (L.) Moench based on 2926 AFLP®, RFLP and SSR markers

    Microsoft Academic Search

    M. A. Menz; R. R. Klein; J. E. Mullet; J. A. Obert; N. C. Unruh; P. E. Klein

    2002-01-01

    Using AFLP technology and a recombinant inbred line population derived from the sorghum cross of BTx623 × IS3620C, a high-density genetic map of the sorghum genome was constructed. The 1713 cM map encompassed 2926 loci distributed on ten linkage groups; 2454 of those loci are AFLP products generated from either the EcoRI\\/MseI or PstI\\/MseI enzyme combinations. Among the non-AFLP markers, 136

  12. High-efficiency transfection and drug selection of genetically transformed blood stages of the rodent malaria parasite Plasmodium berghei

    Microsoft Academic Search

    Chris J Janse; Jai Ramesar; Andrew P Waters

    2006-01-01

    This protocol describes a method of genetic transformation for the rodent malaria parasite Plasmodium berghei with a high transfection efficiency of 10?3–10?4. It provides methods for: (i) in vitro cultivation and purification of the schizont stage;(ii) transfection of DNA constructs containing drug-selectable markers into schizonts using the nonviral Nucleofector technology; and (iii) injection of transfected parasites into mice and subsequent

  13. Remnant populations of the regal fritillary ( Speyeria idalia ) in Pennsylvania: Local genetic structure in a high gene flow species

    Microsoft Academic Search

    Nusha Keyghobadi; Katherine P. Unger; Jason D. Weintraub; Dina M. Fonseca

    2006-01-01

    The Regal Fritillary butterfly, Speyeria idalia (Drury) (Lepidoptera: Nymphalidae), has been described as a high gene flow species. Supporting this assertion, previous studies\\u000a in the Great Plains, where it is still relatively widespread, have found evidence of gene flow across hundreds of kilometers.\\u000a Using mitochondrial and microsatellite loci, we examined the spatial genetic structure of a very isolated Pennsylvania population

  14. Analysis of Genetic Variations of Lamin A\\/C Gene (LMNA) by Denaturing High-Performance Liquid Chromatography

    Microsoft Academic Search

    Matthew R. G. Taylor; Misi L. Robinson; Luisa Mestroni

    2004-01-01

    The human LMNA gene, when mutated, has been shown to cause at least 7 human diseases: dilated cardiomyopathy, Emery Dreifuss muscular dystrophy, limb girdle muscular dystrophy, familial partial lipodystrophy, Charcot Marie tooth disease type II, mandibuloacral dysplasia, and Hutchinson-Gilford Progeria (OMIM #176670). This article describes a high-throughput method for screening the human lamin A\\/C (LMNA) gene for genetic mutations and

  15. The high Andes, gene flow and a stable hybrid zone shape the genetic structure of a wide-ranging South American parrot

    PubMed Central

    2011-01-01

    Background While the gene flow in some organisms is strongly affected by physical barriers and geographical distance, other highly mobile species are able to overcome such constraints. In southern South America, the Andes (here up to 6,900 m) may constitute a formidable barrier to dispersal. In addition, this region was affected by cycles of intercalating arid/moist periods during the Upper/Late Pleistocene and Holocene. These factors may have been crucial in driving the phylogeographic structure of the vertebrate fauna of the region. Here we test these hypotheses in the burrowing parrot Cyanoliseus patagonus (Aves, Psittaciformes) across its wide distributional range in Chile and Argentina. Results Our data show a Chilean origin for this species, with a single migration event across the Andes during the Upper/Late Pleistocene, which gave rise to all extant Argentinean mitochondrial lineages. Analyses suggest a complex population structure for burrowing parrots in Argentina, which includes a hybrid zone that has remained stable for several thousand years. Within this zone, introgression by expanding haplotypes has resulted in the evolution of an intermediate phenotype. Multivariate regressions show that present day climatic variables have a strong influence on the distribution of genetic heterogeneity, accounting for almost half of the variation in the data. Conclusions Here we show how huge barriers like the Andes and the regional environmental conditions imposed constraints on the ability of a parrot species to colonise new habitats, affecting the way in which populations diverged and thus, genetic structure. When contact between divergent populations was re-established, a stable hybrid zone was formed, functioning as a channel for genetic exchange between populations. PMID:21672266

  16. Construction and analysis of a high-density genetic linkage map in cabbage (Brassica oleracea L. var. capitata)

    PubMed Central

    2012-01-01

    Background Brassica oleracea encompass a family of vegetables and cabbage that are among the most widely cultivated crops. In 2009, the B. oleracea Genome Sequencing Project was launched using next generation sequencing technology. None of the available maps were detailed enough to anchor the sequence scaffolds for the Genome Sequencing Project. This report describes the development of a large number of SSR and SNP markers from the whole genome shotgun sequence data of B. oleracea, and the construction of a high-density genetic linkage map using a double haploid mapping population. Results The B. oleracea high-density genetic linkage map that was constructed includes 1,227 markers in nine linkage groups spanning a total of 1197.9 cM with an average of 0.98 cM between adjacent loci. There were 602 SSR markers and 625 SNP markers on the map. The chromosome with the highest number of markers (186) was C03, and the chromosome with smallest number of markers (99) was C09. Conclusions This first high-density map allowed the assembled scaffolds to be anchored to pseudochromosomes. The map also provides useful information for positional cloning, molecular breeding, and integration of information of genes and traits in B. oleracea. All the markers on the map will be transferable and could be used for the construction of other genetic maps. PMID:23033896

  17. The high frequency of genetic diseases in hypotonic infants referred by neuropediatrics.

    PubMed

    Vilchis, Zacil; Najera, Nayelli; Pérez-Duran, Javier; Najera, Zenyesen; Gonzalez, Lourdes; del Refugio Rivera, Maria; Queipo, Gloria

    2014-07-01

    Neonatal hypotonia is a relatively common cause of consultation in daily pediatric practice. It is part of the clinical presentation of a large group of heterogeneous diseases, many of which have an important and classifiable genetic background. Identification of the specific disorder can help optimize the management and treatment of the patient and inform genetic counseling for the family, and therefore input from clinical geneticists is critical at the earliest stages of medical management. Here we present 30 patients with hypotonia of unknown etiology referred by a neuropediatrician to clinical genetics. Clinical, genetic, and molecular evaluation of each patient was performed. Sixty-nine percent of the patients included in the study had a genetic disease, including eight with Prader-Willi syndrome, three with spinal muscular atrophy, one with Rett syndrome, and one with Sotos syndrome harboring a previously undescribed mutation. Our data demonstrate that a multidisciplinary approach used from the outset that includes molecular analysis can help improve diagnosis and management of hypotonic infants. PMID:24715477

  18. High resolution genetic map of the adenomatous polyposis coli gene (APC) region

    SciTech Connect

    Olschwang, S.; Laurent-Puig, P.; Melot, T. [Institut Curie, Paris (France)

    1995-05-08

    Familial adenomatous polyposis coli (APC) is a dominantly inherited colorectal cancer susceptibility disease caused by mutation in a gene called APC located on chromosome 5q21. Presymptomatic diagnosis of this condition is recommended because it enables restriction of the efficient but demanding prevention program to those relatives that are genetically affected. The large size of the APC gene makes the direct search for the casual alteration difficult to implement in routine diagnostic laboratories. Because APC appears to be genetically homogeneous with alteration in a single locus causing the disease, cosegregation analysis may represent an alternative efficient method for presymptomatic diagnosis. However, the reliability of the risk estimation by linkage analysis in APC families is hampered by the lack of a short range genetic map of the APC locus. A combined approach including genotyping of 65 APC families, analysis of the CEPH database, and complementary typing of both APC and CEPH families has made it possible to derive the following genetic map: Centromere-[D5S82-D5S49]-0.02-D5S122-0.01-D5S136-0.01-D5S135-0.02-[APC-D5S346-MCC]-0.04-[D5S81-D5S64]-Telomere. This order, which differs from previously proposed genetic maps, is fully compatible with recent physical mapping data. These data should contribute to increase the reliability of the presymptomatic test for APC. 42 refs., 1 fig., 3 tabs.

  19. Population genetics of Drosophila ananassae.

    PubMed

    Singh, Pranveer; Singh, Bashisth N

    2008-10-01

    Drosophila ananassae Doleschall is a cosmopolitan and domestic species. It occupies a unique status among Drosophila species due to certain peculiarities in its genetic behaviour and is of common occurrence in India. Quantitative genetics of sexual and non-sexual traits provided evidence for genetic control of these traits. D. ananassae exhibits high level of chromosomal polymorphism in its natural populations. Indian natural populations of D. ananassae show geographic differentiation of inversion polymorphism due to their adaptation to varying environments and natural selection operates to maintain three cosmopolitan inversions. Populations do not show divergence on temporal scale, an evidence for rigid polymorphism. D. ananassae populations show substantial degree of sub-structuring and exist as semi-isolated populations. Gene flow is low despite co-transportation with human goods. There is persistence of cosmopolitan inversions when populations are transferred to laboratory conditions, which suggests that heterotic buffering is associated with these inversions in D. ananassae. Populations collected from similar environmental conditions that initially show high degree of genetic similarity have diverged to different degrees in laboratory environment. This randomness could be due to genetic drift. Interracial hybridization does not lead to breakdown of heterosis associated with cosmopolitan inversions, which shows that there is lack of genetic co-adaptation in D. ananassae. Linkage disequilibrium between independent inversions in laboratory populations has often been observed, which is likely to be due to suppression of crossing-over and random genetic drift. No evidence for chromosomal interactions has been found in natural and laboratory populations of D. ananassae. This strengthens the previous suggestion that there is lack of genetic co-adaptation in D. ananassae. PMID:19061531

  20. Use of High Throughput Sequencing and Light Microscopy Show Contrasting Results in a Study of Phytoplankton Occurrence in a Freshwater Environment

    PubMed Central

    Xiao, Xi; Sogge, Hanne; Lagesen, Karin; Tooming-Klunderud, Ave; Jakobsen, Kjetill S.; Rohrlack, Thomas

    2014-01-01

    Assessing phytoplankton diversity is of primary importance for both basic and applied ecological studies. Following the advances in molecular methods, phytoplankton studies are switching from using classical microscopy to high throughput sequencing approaches. However, methodological comparisons of these approaches have rarely been reported. In this study, we compared the two methods, using a unique dataset of multiple water samples taken from a natural freshwater environment. Environmental DNA was extracted from 300 water samples collected weekly during 20 years, followed by high throughput sequencing of amplicons from the 16S and 18S rRNA hypervariable regions. For each water sample, phytoplankton diversity was also estimated using light microscopy. Our study indicates that species compositions detected by light microscopy and 454 high throughput sequencing do not always match. High throughput sequencing detected more rare species and picoplankton than light microscopy, and thus gave a better assessment of phytoplankton diversity. However, when compared to light microscopy, high throughput sequencing of 16S and 18S rRNA amplicons did not adequately identify phytoplankton at the species level. In summary, our study recommends a combined strategy using both morphological and molecular techniques. PMID:25171164

  1. Storytelling Slide Shows to Improve Diabetes and High Blood Pressure Knowledge and Self-Efficacy: Three-Year Results among Community Dwelling Older African Americans

    ERIC Educational Resources Information Center

    Bertera, Elizabeth M.

    2014-01-01

    This study combined the African American tradition of oral storytelling with the Hispanic medium of "Fotonovelas." A staggered pretest posttest control group design was used to evaluate four Storytelling Slide Shows on health that featured community members. A total of 212 participants were recruited for the intervention and 217 for the…

  2. Next Generation Statistical Genetics: Modeling, Penalization, and Optimization in High-Dimensional Data.

    PubMed

    Lange, Kenneth; Papp, Jeanette C; Sinsheimer, Janet S; Sobel, Eric M

    2014-01-01

    Statistical genetics is undergoing the same transition to big data that all branches of applied statistics are experiencing. With the advent of inexpensive DNA sequencing, the transition is only accelerating. This brief review highlights some modern techniques with recent successes in statistical genetics. These include: (a) lasso penalized regression and association mapping, (b) ethnic admixture estimation, (c) matrix completion for genotype and sequence data, (d) the fused lasso and copy number variation, (e) haplotyping, (f) estimation of relatedness, (g) variance components models, and (h) rare variant testing. For more than a century, genetics has been both a driver and beneficiary of statistical theory and practice. This symbiotic relationship will persist for the foreseeable future. PMID:24955378

  3. Next Generation Statistical Genetics: Modeling, Penalization, and Optimization in High-Dimensional Data

    PubMed Central

    Lange, Kenneth; Papp, Jeanette C.; Sinsheimer, Janet S.; Sobel, Eric M.

    2014-01-01

    Statistical genetics is undergoing the same transition to big data that all branches of applied statistics are experiencing. With the advent of inexpensive DNA sequencing, the transition is only accelerating. This brief review highlights some modern techniques with recent successes in statistical genetics. These include: (a) lasso penalized regression and association mapping, (b) ethnic admixture estimation, (c) matrix completion for genotype and sequence data, (d) the fused lasso and copy number variation, (e) haplotyping, (f) estimation of relatedness, (g) variance components models, and (h) rare variant testing. For more than a century, genetics has been both a driver and beneficiary of statistical theory and practice. This symbiotic relationship will persist for the foreseeable future. PMID:24955378

  4. A high-density collection of EMS-induced mutations for TILLING in Landsberg erecta genetic background of Arabidopsis

    PubMed Central

    2009-01-01

    Background Arabidopsis thaliana is the main model species for plant molecular genetics studies and world-wide efforts are devoted to identify the function of all its genes. To this end, reverse genetics by TILLING (Targeting Induced Local Lesions IN Genomes) in a permanent collection of chemically induced mutants is providing a unique resource in Columbia genetic background. In this work, we aim to extend TILLING resources available in A. thaliana by developing a new population of ethyl methanesulphonate (EMS) induced mutants in the second commonest reference strain. In addition, we pursue to saturate the number of EMS induced mutations that can be tolerated by viable and fertile plants. Results By mutagenizing with different EMS concentrations we have developed a permanent collection of 3712 M2/M3 independent mutant lines in the reference strain Landsberg erecta (Ler) of A. thaliana. This population has been named as the Arabidopsis TILLer collection. The frequency of mutations per line was maximized by using M1 plants with low but sufficient seed fertility. Application of TILLING to search for mutants in 14 genes identified 21 to 46 mutations per gene, which correspond to a total of 450 mutations. Missense mutations were found for all genes while truncations were selected for all except one. We estimated that, on average, these lines carry one mutation every 89 kb, Ler population providing a total of more than five million induced mutations. It is estimated that TILLer collection shows a two to three fold higher EMS mutation density per individual than previously reported A. thaliana population. Conclusions Analysis of TILLer collection demonstrates its usefulness for large scale TILLING reverse genetics in another reference genetic background of A. thaliana. Comparisons with TILLING populations in other organisms indicate that this new A. thaliana collection carries the highest chemically induced mutation density per individual known in diploid species. PMID:20003424

  5. Developing Genetic Epidemiological Models to Predict Risk for Nasopharyngeal Carcinoma in High-Risk Population of China

    PubMed Central

    Bei, Jin-Xin; Luo, Fu-Tian; Zeng, Yi-Xin; Jia, Wei-Hua

    2013-01-01

    To date, the only established model for assessing risk for nasopharyngeal carcinoma (NPC) relies on the sero-status of the Epstein-Barr virus (EBV). By contrast, the risk assessment models proposed here include environmental risk factors, family history of NPC, and information on genetic variants. The models were developed using epidemiological and genetic data from a large case-control study, which included 1,387 subjects with NPC and 1,459 controls of Cantonese origin. The predictive accuracy of the models were then assessed by calculating the area under the receiver-operating characteristic curves (AUC). To compare the discriminatory improvement of models with and without genetic information, we estimated the net reclassification improvement (NRI) and integrated discrimination index (IDI). Well-established environmental risk factors for NPC include consumption of salted fish and preserved vegetables and cigarette smoking (in pack years). The environmental model alone shows modest discriminatory ability (AUC?=?0.68; 95% CI: 0.66, 0.70), which is only slightly increased by the addition of data on family history of NPC (AUC?=?0.70; 95% CI: 0.68, 0.72). With the addition of data on genetic variants, however, our model’s discriminatory ability rises to 0.74 (95% CI: 0.72, 0.76). The improvements in NRI and IDI also suggest the potential usefulness of considering genetic variants when screening for NPC in endemic areas. If these findings are confirmed in larger cohort and population-based case-control studies, use of the new models to analyse data from NPC-endemic areas could well lead to earlier detection of NPC. PMID:23457511

  6. Construction of high-density genetic linkage maps for orange-spotted grouper Epinephelus coioides using multiplexed shotgun genotyping

    PubMed Central

    2013-01-01

    Background Orange-spotted grouper, Epinephelus coioides, is one of the most valuable fish species in China. Commercial production of orange-spotted grouper could be increased by developing higher growth rates and improving commercially important traits. Information on genetic markers associated with quantitative trait loci (QTL) can be used in breeding programs to identify and select individuals carrying desired traits. A high-density genetic linkage map is the basis for QTL study, and multiplexed shotgun genotyping (MSG) facilitates the development of single nucleotide polymorphisms (SNPs) and genotyping. In this study, the first high-density genetic linkage maps for groupers were generated on the basis of the MSG method. Results The sex-averaged map contained a total of 4,608 SNPs, which spanned 1581.7 cM, with a mean distance between SNPs of 0.34 cM. The 4,608 SNPs were located in 2,849 unique locations on the linkage map, with an average inter-location space at 0.56 cM. There were 2,516 SNPs on the female map, and the number of unique locus was 1,902. However, the male map contained more numbers of SNP (2,939) and unique locations (2,005). The total length of the female and male maps was 1,370.9 and 1,335.5 cM, respectively. Conclusions The high-resolution genetic linkage maps will be very useful for QTL analyses and marker-assisted selection (MAS) for economically important traits in molecular breeding of the orange-spotted grouper. PMID:24289265

  7. Measurement of the half-life of (198)Au in a nonmetal: High-precision measurement shows no host-material dependence 

    E-print Network

    Goodwin, J. R.; Nica, N.; Iacob, V. E.; Dibidad, A.; Hardy, John C.

    2010-01-01

    , for consistency we nevertheless followed the same procedure as in the previous measurement, including the use of the cryopump as a location for our sample. A 70% high-purity germanium detector was placed directly facing the sample on the cryopump axis just...

  8. High-resolution imaging of the fusiform face area (FFA) using multivariate non-linear classifiers shows diagnosticity for non-face categories

    Microsoft Academic Search

    Stephen José Hanson; Arielle Schmidt

    2011-01-01

    Does the “fusiform face area” (FFA) code only for faces? This question continues to elude the neuroimaging field due to at least two kinds of problems: first, the relatively low spatial resolution of fMRI in which the FFA was defined and second, the potential bias inherent in prevailing statistical methods for analyzing the actual diagnosticity of cortical tissue. Using high-resolution

  9. Glycinergic inhibition to the medial nucleus of the trapezoid body shows prominent facilitation and can sustain high levels of ongoing activity.

    PubMed

    Mayer, Florian; Albrecht, Otto; Dondzillo, Anna; Klug, Achim

    2014-12-01

    Neurons in the medial nucleus of the trapezoid body (MNTB) are well known for their prominent excitatory inputs, mediated by the calyx of Held. Less attention has been paid to the prominent inhibitory inputs that MNTB neurons also receive. Because of their auditory nature, both excitatory and inhibitory synapses are highly active in vivo. These high levels of activity are known to reduce excitatory synaptic currents considerably, such that in vivo synaptic currents produced by the calyx are smaller than typically measured in standard brain slice experiments. The goal of this study was to investigate the properties of the inhibitory inputs in the Mongolian gerbil (Meriones unguiculatus) under activity levels that correspond to those in the intact brain to facilitate a direct comparison between the two inputs. Our results suggest that inhibitory inputs to MNTB are largely mediated by a fast and phasic glycinergic component, and to a lesser degree by a GABAergic component. The glycinergic component can sustain prolonged high levels of activity. Even when challenged with stimulus patterns consisting of thousands of stimuli over tens of minutes, glycinergic inputs to MNTB maintain large conductances and fast decays and even facilitate substantially when the stimulation frequency is increased. The inhibition is mediated by a relatively small number of independent input fibers. The data presented here suggest that inhibitory inputs to MNTB sustain high levels of activity and need to be considered for a full understanding of mechanisms underlying processing of auditory information in MNTB. PMID:25185813

  10. SIGNIFICANT LINKAGE DISEQUILIBRIUM AND HIGH GENETIC DIVERSITY IN A POPULATION OF PLASMODIUM FALCIPARUM FROM AN AREA (REPUBLIC OF THE CONGO) HIGHLY ENDEMIC FOR MALARIA

    Microsoft Academic Search

    P. DURAND; Y. MICHALAKIS; S. CESTIER; B. OURY; M. C. LECLERC; M. TIBAYRENC; F. RENAUD

    2003-01-01

    A study based on 28 microsatellite loci was performed on 32 isolates of Plasmodium falciparum from Pointe Noire (Republic of the Congo) and compared with a cosmopolitan sample of 21 isolates collected from different countries in Africa, Latin America, and Asia. The Pointe Noire population exhibited very high genetic diversity (A 7.8 ± 2.6, He 0.79 ± 0.11). Significant linkage

  11. Autumn shows roundup

    Microsoft Academic Search

    Richard Bloss

    2002-01-01

    A report on three major American automation shows where innovative products and automated assembly technologies formed a focus. Products reviewed include grippers, actuators, assembly modules, dispensing controller and pneumatic components from a number of suppliers.

  12. Subsets of Finns with High HDL to Total Cholesterol Ratio Show Evidence for Linkage to Type 2 Diabetes on Chromosome 6q

    Microsoft Academic Search

    Corina Shtir; I. Sharon Nagakawa; William L. Duren; Karen N. Conneely; Laura J. Scott; Kaisa Silander; Timo T. Valle; Jaakko Tuomilehto; Thomas A. Buchanan; Richard N. Bergman; Francis S. Collins; Michael Boehnke; Richard M. Watanabe

    2007-01-01

    Objectives: The purpose of this study was to examine carefully heterogeneity underlying evidence for linkage to type 2 diabetes (T2DM) on chromosome 6q from two sets of FUSION families. Methods: Ordered subsets analysis (OSA) was performed on two sets of FUSION families. For OSA results showing significant improvement in evidence for linkage, T2DM-related phenotypes were compared between individuals with T2DM

  13. Ratios of Record High to Record Low Temperatures in Europe Show an Accelerating Trend Since 2000 Despite a Slowdown in Mean Temperature Trends

    NASA Astrophysics Data System (ADS)

    Beniston, M.

    2014-12-01

    The present study has examined the behavior of extreme high and low temperatures in Euirope since the mid-20th century, in terms of the ratio of number of days per year with record Tmax and record Tmin. The investigations have shown that there has been a clear and massive increase in the number of high Tmax: low Tmin ratios in the most recent decade of the 1951-2013 temperature record for 30 selected observation stations in Europe. This sharp increase is seen to occur despite an apparent hiatus - or at least a reduction in the rate of warming - since the early 2000s, as observed not only in Europe but on a hemispheric basis too. The «explosion» of record high:record low temperature ratios since 2000, despite relatively small increases in mean temperatures in the last 10-15 years of the observational record, can be explained by a non-linear (quadratic) relation between mean temperatures and the Tmax:Tmin record ratios. It is suggested here that the increases are probably a consequence of increasing dryness during the summer in the Mediterranean region (where today there are on average 30 more dry days than in the 1950s), and a reduction in the cold season conducive to snow days in Arctic summers and Northern European springs (with up to 40 days less freezing days than 60 years previously). Both effects can serve to amplify positive temperature feedbacks in the lower atmosphere that result in strong increases in the number of Tmax record high temperatures and correspondingly strong reductions in the number of Tmin record low temperatures.

  14. Genetic map of the human pseudoautosomal region reveals a high rate of recombination in female meiosis at the Xp telomere

    SciTech Connect

    Henke, A.; Fischer, C.; Rappold, G.A. (Univ. of Heidelberg (Germany))

    1993-12-01

    This paper describes the genetic map of the pseudoautosomal region bounded by the telomere of the short arms of the X and Y chromosomes. In males, meiotic exchange on Xp/Yp is confined to this region, leading to highly elevated recombination rates. The map was constructed using 11 pseudoautosomal probes (six of which are new) and typing individuals from 38 CEPH families. All markers have been physically mapped, thus providing the opportunity to compare genetic distance to physical distance through all intervals of the map. This comparison reveals an unexpected high rate of recombination in female meiosis between loci DXYS20 and DXYS78, within 20-80 kb from the telomere. Within this telemore-adjacent region no differences in male and female recombination rates are seen. Furthermore, data from this genetic map support the hypothesis of a linear gradient of recombination across most of the region in male meiosis and provide densely spaced anchor points for linkage studies especially in the telomeric portion of the pseudoautosomal region. 34 refs., 4 figs., 4 tabs.

  15. Candidate genetic analysis of plasma high-density lipoprotein-cholesterol and severity of coronary atherosclerosis

    PubMed Central

    Chen, Suet Nee; Cilingiroglu, Mehmet; Todd, Josh; Lombardi, Raffaella; Willerson, James T; Gotto, Antonio M; Ballantyne, Christie M; Marian, AJ

    2009-01-01

    Background Plasma level of high-density lipoprotein-cholesterol (HDL-C), a heritable trait, is an important determinant of susceptibility to atherosclerosis. Non-synonymous and regulatory single nucleotide polymorphisms (SNPs) in genes implicated in HDL-C synthesis and metabolism are likely to influence plasma HDL-C, apolipoprotein A-I (apo A-I) levels and severity of coronary atherosclerosis. Methods We genotyped 784 unrelated Caucasian individuals from two sets of populations (Lipoprotein and Coronary Atherosclerosis Study- LCAS, N = 333 and TexGen, N = 451) for 94 SNPs in 42 candidate genes by 5' nuclease assays. We tested the distribution of the phenotypes by the Shapiro-Wilk normality test. We used Box-Cox regression to analyze associations of the non-normally distributed phenotypes (plasma HDL-C and apo A-I levels) with the genotypes. We included sex, age, body mass index (BMI), diabetes mellitus (DM), and cigarette smoking as covariates. We calculated the q values as indicators of the false positive discovery rate (FDR). Results Plasma HDL-C levels were associated with sex (higher in females), BMI (inversely), smoking (lower in smokers), DM (lower in those with DM) and SNPs in APOA5, APOC2, CETP, LPL and LIPC (each q ?0.01). Likewise, plasma apo A-I levels, available in the LCAS subset, were associated with SNPs in CETP, APOA5, and APOC2 as well as with BMI, sex and age (all q values ?0.03). The APOA5 variant S19W was also associated with minimal lumen diameter (MLD) of coronary atherosclerotic lesions, a quantitative index of severity of coronary atherosclerosis (q = 0.018); mean number of coronary artery occlusions (p = 0.034) at the baseline and progression of coronary atherosclerosis, as indicated by the loss of MLD. Conclusion Putatively functional variants of APOA2, APOA5, APOC2, CETP, LPL, LIPC and SOAT2 are independent genetic determinants of plasma HDL-C levels. The non-synonymous S19W SNP in APOA5 is also an independent determinant of plasma apo A-I level, severity of coronary atherosclerosis and its progression. PMID:19878569

  16. The genetic signatures of pediatric high-grade glioma: no longer a one-act play.

    PubMed

    Diaz, Alexander K; Baker, Suzanne J

    2014-10-01

    Advances in understanding pediatric high-grade glioma (pHGG) genetics have revealed key differences between pHGG and adult HGG and have uncovered unique molecular drivers among subgroups within pHGG. The 3 core adult HGG pathways, the receptor tyrosine kinase-Ras-phosphatidylinositide 3-kinase, p53, and retinoblastoma networks, are also disrupted in pHGG, but they exhibit a different spectrum of effectors targeted by mutation. There are also similarities and differences in the genomic landscape of diffuse intrinsic pontine glioma (DIPG) and pediatric nonbrainstem (pNBS)-HGG. In 2012, histone H3 mutations were identified in nearly 80% of DIPGs and ~35% of pNBS-HGG. These were the first reports of histone mutations in human cancer, implicating novel biology in pediatric gliomagenesis. Additionally, DIPG and midline pNBS-HGG vary in the frequency and specific histone H3 amino acid substitution compared with pNBS-HGGs arising in the cerebral hemispheres, demonstrating a molecular difference among pHGG subgroups. The gene expression signatures as well as DNA methylation signatures of these tumors are also distinctive, reflecting a combination of the driving mutations and the developmental context from which they arise. These data collectively highlight unique selective pressures within the developing brainstem and solidify DIPG as a specific molecular and biological entity among pHGGs. Emerging studies continue to identify novel mutations that distinguish subgroups of pHGG. The molecular heterogeneity among pHGGs will undoubtedly have clinical implications moving forward. The discovery of unique oncogenic drivers is a critical first step in providing patients with appropriate, targeted therapies. Despite these insights, our vantage point has been largely limited to an in-depth analysis of protein coding sequences. Given the clear importance of histone mutations in pHGG, it will be interesting to see how aberrant epigenetic regulation contributes to tumorigenesis in the pediatric context. New mechanistic insights may allow for the identification of distinct vulnerabilities in this devastating spectrum of childhood tumors. PMID:25219808

  17. Casein secretion and cytological differentiation in mammary tissue from bulls of high or low genetic merit.

    PubMed

    Filep, R; Akers, R M

    2000-10-01

    We evaluated tissue content and secretion of milk proteins by mammary parenchymal explants prepared from tissue of mature Holstein bulls as a possible index for genetic merit. Explants from eight selection-line and eight control-line bulls were cultured for 48 or 96 h in medium with 5% fetal bovine serum with or without the addition of lactogenic hormones. Four selection-line and four control-line bulls were also treated for 7 d with estrogen and progesterone or placebo before tissue was removed on d 15 of the experiment. Overall, tissue content and secretion of casein were increased approximately twofold in selection-line bulls. Differences between genetic lines were evident only with the addition of lactogenic hormones. However, treatment of bulls with steroids was not necessary for casein secretion or detection of differences between genetic lines. Averaged for both lines, 96-h media concentrations of casein were 89-fold greater for explants cultured with added lactogenic hormones. Epithelial cells were classified as nonsecretory, droplet-containing, or degenerated. The appearance of droplet-containing cells was markedly increased in cultures supplemented with lactogenic hormones, and the cells were most often located within epithelial folds or pockets. Only occasionally did we observe areas of alveolar-like tissue. The data demonstrate that it is possible to induce the secretion of casein in mammary explants prepared from sexually mature bulls, that lactogenic hormones markedly stimulate secretion, and that differences in genetic merit may be expressed. PMID:11049066

  18. Using philosophy of science in curriculum development: an example from high school genetics

    Microsoft Academic Search

    Susan K. Johnson; Jim Stewart

    1990-01-01

    This paper describes a unique curriculum in which the students experience aspects of the ‘nature of science’ as they study classical genetics. In this curriculum, ‘Gregor Mendel’ presents his conceptual model of simple dominance and involves the students in a reproduction of his famous experiments with pea plants. The students read his paper and test his model using a computer

  19. High fidelity of RecA-catalyzed recombination: a watchdog of genetic diversity

    E-print Network

    Tlusty, Tsvi

    mismatches at the initial stages of recombi- nation, and the efficiency of recombination is strongly for the creation of genetic diversity (1,2). By reassembling sequences from homologous but not identical DNA speciation. Creation of new sequence combinations however has to be delicately balanced, to give the highest

  20. High genetic diversity in arbuscular mycorrhizal fungi: evidence for recombination events

    Microsoft Academic Search

    P. Vandenkoornhuyse; C. Leyval; I. Bonnin

    2001-01-01

    The genetic diversity of spores of two indigenous species of Glomus isolated from three soils of a long-term field experiment amended by different quantities of sewage sludges has been evaluated. Three populations of spores of Glomus claroideum (W2537) and three populations of spores of Glomus DAOM 225952 (W2538) were analysed using a microsatellite primer and aliquots of genomic DNA were

  1. The Mechanism of Bacillus anthracis Intracellular Germination Requires Multiple and Highly Diverse Genetic Loci

    Microsoft Academic Search

    Soumitra Barua; Matthew McKevitt; Kevin DeGiusti; Elaine E. Hamm; Jason Larabee; Salika Shakir; Katie Bryant; Theresa M. Koehler; Steven R. Blanke; David Dyer; Allison Gillaspy; Jimmy D. Ballard

    2009-01-01

    In an effort to better understand the mechanisms by which Bacillus anthracis establishes disease, experiments were undertaken to identify the genes essential for intracellular germination. Eighteen diverse genetic loci were identified via an enrichment protocol using a transposon-mutated library of B. anthracis spores, which was screened for mutants delayed in intracellular germination. Fourteen transposon mutants were identified in genes not

  2. Aedes aegypti in Brazil: genetically differentiated populations with high susceptibility to dengue and yellow fever viruses

    Microsoft Academic Search

    R Lourenço-de-Oliveira; M Vazeille; A. M. B de Filippis; A. B Failloux

    2004-01-01

    Aedes aegypti was eliminated from Brazil in 1955, but re-infested the country in the 1970s. Dengue outbreaks have occurred since 1981 and became endemic in several cities in Brazil after 1986. Urban yellow fever has not occurred since 1942, and only jungle yellow fever cases have been reported. A population genetic analysis using isoenzyme variation combined with an evaluation of

  3. High Genetic Diversity and Fine-Scale Spatial Structure in the Marine Flagellate Oxyrrhis marina (Dinophyceae)

    E-print Network

    Steve Kemp

    (Dinophyceae) Uncovered by Microsatellite Loci Chris D. Lowe*, David J. S. Montagnes, Laura E. Martin, Phillip for the common marine flagellate Oxyrrhis marina. Nine microsatellite loci were used to assess genotypic to assess fine-scale genetic diversity. Microsatellite loci resolved between 1­6 and 7­23 distinct alleles

  4. Determination of Escherichia coli Contamination with Chromocult Coliform Agar Showed a High Level of Discrimination Efficiency for Differing Fecal Pollution Levels in Tropical Waters of Kampala, Uganda

    PubMed Central

    Byamukama, Dennis; Kansiime, Frank; Mach, Robert L.; Farnleitner, Andreas H.

    2000-01-01

    Escherichia coli, total coliforms, fecal coliforms, and sulfite-reducing anaerobic spore formers from different polluted sites in a tropical environment were determined in order to test for their indication ability for fecal contamination. Quantification of E. coli contamination with Chromocult coliform agar proved to be efficient and feasible for determining fecal pollutions in the investigated area within 24 h. The other microbial parameters showed a lower ability to differentiate sites and cannot be recommended for monitoring fecal pollution in the studied tropical surface waters. PMID:10653767

  5. On-chip whole-animal manipulation for high-throughput subcellular-resolution in-vivo drug/genetic screening

    E-print Network

    Yanik, Mehmet Fatih

    Techniques for rapid and automated small-animal manipulation and immobilization are necessary for high-throughput in vivo genetic/drug screens using cellular and sub-cellular features in multicellular organisms. We present ...

  6. Do Elephants Show Empathy?

    Microsoft Academic Search

    Lucy A. Bates; Phyllis C. Lee; Norah Njiraini; Joyce H. Poole; Katito Sayialel; Soila Sayialel; Cynthia J. Moss; Richard W. Byrne

    2008-01-01

    Elephants show a rich social organization and display a number of unusual traits. In this paper, we analyse reports collected over a thirty-five year period, describing behaviour that has the potential to reveal signs of empathic understanding. These include coalition formation, the offering of protection and comfort to others, retrieving and 'babysitting' calves, aiding individuals that would otherwise have difficulty

  7. Show Me the Way

    ERIC Educational Resources Information Center

    Dicks, Matthew J.

    2005-01-01

    Because today's students have grown up steeped in video games and the Internet, most of them expect feedback, and usually gratification, very soon after they expend effort on a task. Teachers can get quick feedback to students by showing them videotapes of their learning performances. The author, a 3rd grade teacher describes how the seemingly…

  8. Demonstration Road Show

    NSDL National Science Digital Library

    2009-04-06

    The Idaho State University Department of Physics conducts science demonstration shows at S. E. Idaho schools. Four different presentations are currently available; "Forces and Motion", "States of Matter", "Electricity and Magnetism", and "Sound and Waves". Information provided includes descriptions of the material and links to other resources.

  9. Earthquake Damage Slide Show

    NSDL National Science Digital Library

    This slide show presents examples of various types of damage caused by earthquakes. Photos include structural failures in bridges and buildings, landshifts, landslides, liquefaction, fires, tsunamis, and human impacts. Supplemental notes are provided to aid instructors about the photos presented on each slide.

  10. Honored Teacher Shows Commitment.

    ERIC Educational Resources Information Center

    Ratte, Kathy

    1987-01-01

    Part of the acceptance speech of the 1985 National Council for the Social Studies Teacher of the Year, this article describes the censorship experience of this honored social studies teacher. The incident involved the showing of a videotape version of the feature film entitled "The Seduction of Joe Tynan." (JDH)

  11. What Do Maps Show?

    ERIC Educational Resources Information Center

    Geological Survey (Dept. of Interior), Reston, VA.

    This curriculum packet, appropriate for grades 4-8, features a teaching poster which shows different types of maps (different views of Salt Lake City, Utah), as well as three reproducible maps and reproducible activity sheets which complement the maps. The poster provides teacher background, including step-by-step lesson plans for four geography…

  12. GENETIC TRANSPOSITION IN TREE-ADJOINING GRAMMAR GUIDED GENETIC PROGRAMMING

    E-print Network

    McKay, Robert Ian

    GENETIC TRANSPOSITION IN TREE-ADJOINING GRAMMAR GUIDED GENETIC PROGRAMMING: THE DUPLICATION adjoining grammar guided genetic programming system (TAG3P). The results show that, on the problems tried genetic programming (TAG3P) [20] is a genetic programming system that uses tree-adjoining grammars (TAGs

  13. Producing Turkeys for Show

    E-print Network

    Thornberry, Fredrick D.

    2005-12-14

    hours of brooding. Follow directions on the label and do not over-medicate. Vaccinate poults for fowl pox at 8 to 10 weeks of age. In areas with high mosquito populations, poults should be vaccinated ini- tially at 3 to 4 weeks followed by a second...

  14. Show What You Know.

    ERIC Educational Resources Information Center

    Chadwell, Deana R.

    1991-01-01

    At South Medford High School, Oregon, all seniors must complete a senior project that requires the following: write a 10-page research paper on a topic of choice; carry out a project that relates to the research; and speak about what they learned from the project and answer questions before a board of judges. Offers tips for starting senior…

  15. High within-host genetic variation of the nematode Spirocerca lupi in a high-density urban dog population.

    PubMed

    de Waal, Pamela J; Gous, Annemarie; Clift, Sarah J; Greeff, Jaco M

    2012-06-01

    The nematode worm Spirocerca lupi has a cosmopolitan distribution and can cause the death of its final canid host, typically dogs. While its life cycle, which involves a coprophagous beetle intermediate host, a number of non-obligatory vertebrate paratenic hosts and a canid final host, is well understood, surprisingly little is known about its transmission dynamics and population genetic structure. Here we sequenced cox1 to quantify genetic variation and the factors that limit gene flow in a 300 km(2) area in South Africa. Three quarters of the genetic variation, was explained by differences between worms from the same host, whereas a quarter of the variation was explained by differences between worms from different hosts. With the help of a newly derived model we conclude that while the offspring from different infrapopulations mixes fairly frequently in new hosts, the level of admixture is not enough to homogenize the parasite populations among dogs. Small infrapopulation sizes along with clumped transmission may also result in members of infrapopulations being closely related. PMID:22226763

  16. A thromboxane A2/prostaglandin H2 receptor antagonist (S18886) shows high antithrombotic efficacy in an experimental model of stent-induced thrombosis.

    PubMed

    Vilahur, Gemma; Casaní, Laura; Badimon, Lina

    2007-09-01

    Acute thrombosis is a threat in patients undergoing percutaneous coronary intervention with stent implantation. Our objective was to determine if stent-induced thrombus formation could be inhibited by oral treatment with a thromboxane A(2)/prostaglandin H(2) receptor antagonist (TPr; S18886) as an alternative to standard therapy. Pigs were allocated in the following treatment (p.o) groups: I) clopidogrel (CLOP); II) ASA; III) S18886; IV) ASA+CLOP; and V) placebo-control. Damaged vessel was placed in the Badimon chamber containing a stent and perfused at 212/s. Antithrombotic effects were assessed as (111)In-platelet deposition (PD) in two series (60 and 180 min after drug intake). Fibrin(ogen) deposition, light transmittance aggregometry (LTA; collagen, U46619, and ADP), and bleeding time (BT) were also evaluated. After 60 min S18886 reduced PD < or =48%, 40%, and 35% vs placebo, CLOP-, and ASA-treated animals, respectively (P < 0.05), while ASA+CLOP showed a 58% reduction versus placebo (P < 0.01). After 3 hours, ASA+CLOP decreased PD by 55%, S18886 by 40%, CLOP alone by 28% (P < 0.05), and ASA showed no inhibition versus placebo. Similar effects were found in S18886- and ASA+CLOP-treated animals at both times. Fibrin(ogen) deposition followed the same pattern. Collagen-induced LTA was significantly reduced by ASA, ASA+CLOP, and S18886; S18886 abolished U46619-induced LTA; and, CLOP +/- ASA reduced ADP-induced LTA in a time-dependent manner. TPr blockade did not prolong BT, whereas CLOP +/- ASA significantly did (P < 0.0001). In conclusion, blockade of the TPr provided a fast and potent platelet inhibitory effect in a porcine model of in-stent thrombosis comparable to that of blocking both the ADP receptor and cyclooxygenase activation; in addition, TPr provided a more favorable bleeding risk profile. PMID:17849057

  17. High frequency regeneration via direct somatic embryogenesis and efficient Agrobacterium-mediated genetic transformation of tobacco.

    PubMed

    Pathi, Krishna Mohan; Tula, Suresh; Tuteja, Narendra

    2013-06-01

    A direct somatic embryogenesis protocol was developed for four cultivars of Nicotiana species, by using leaf disc as an explant. Direct somatic embryogenesis of Nicotiana by using BAP and IAA has not been investigated so far. This method does not require formation of callus tissues which leads to somaclonal variations. The frequency of somatic embryogenesis was strongly influenced by the plant growth hormones. The somatic embryos developing directly from explant tissue were noticed after 6 d of culture. Somatic embryogenesis of a high frequency (87-96%) was observed in cultures of the all four genotypes (Nicotiana tabacum, N. benthamiyana, N. xanthi, N. t cv petihavana). The results showed that the best medium for direct somatic embryogenesis was MS supplemented with 2.5 mg/l, 0.2 mg/l IAA and 2% sucrose. Subculture of somatic embryos onto hormone free MS medium resulted in their conversion into plants for all genotypes. About 95% of the regenerated somatic embryos germinated into complete plantlets. The plants showed morphological and growth characteristics similar to those of seed-derived plants. Explants were transformed using Agrobacterium tumifacious LBA4404 plasmid pCAMBIA1301 harboring the GUS gene. The regenerated transgenic plants were confirmed by PCR analysis and histochemical GUS assay. The transformation efficiency obtained by using the Agrobacterium- mediated transformation was more than 95%. This method takes 6 wk to accomplish complete transgenic plants through direct somatic embryogenesis. The transgenic plantlets were acclimatized successfully with 98% survival in greenhouse and they showed normal morphological characteristics and were fertile. The regeneration and transformation method described herein is very simple, highly efficient and fast for the introduction of any foreign gene directly in tobacco through direct somatic embryogenesis. PMID:23518589

  18. Neuropsychological Functioning in Adolescents and Young Adults at Genetic Risk for Schizophrenia and Affective Psychoses: Results from the Harvard and Hillside Adolescent High Risk Studies

    Microsoft Academic Search

    Larry J. Seidman; Anthony J. Giuliano; Christopher W. Smith; William S. Stone; Stephen J. Glatt; Eric Meyer; Stephen V. Faraone; Ming T. Tsuang; Barbara Cornblatt

    2006-01-01

    Siblings and offspring of persons with schizophrenia carry elevated genetic risk for the illness and manifest attentional and memory impairments. Because less is known about other neuropsychological functions and their specificity in adolescents, we conducted a genetic high-risk (HR) study of schizophrenia (HR-SCZ) and affective psychosis (HR- AFF). Participants (ages 12-25) were from the Harvard Adolescent High-Risk and Hillside Family

  19. Experimentally infected domestic ducks show efficient transmission of Indonesian H5N1 highly pathogenic avian influenza virus, but lack persistent viral shedding.

    PubMed

    Wibawa, Hendra; Bingham, John; Nuradji, Harimurti; Lowther, Sue; Payne, Jean; Harper, Jenni; Junaidi, Akhmad; Middleton, Deborah; Meers, Joanne

    2014-01-01

    Ducks are important maintenance hosts for avian influenza, including H5N1 highly pathogenic avian influenza viruses. A previous study indicated that persistence of H5N1 viruses in ducks after the development of humoral immunity may drive viral evolution following immune selection. As H5N1 HPAI is endemic in Indonesia, this mechanism may be important in understanding H5N1 evolution in that region. To determine the capability of domestic ducks to maintain prolonged shedding of Indonesian clade 2.1 H5N1 virus, two groups of Pekin ducks were inoculated through the eyes, nostrils and oropharynx and viral shedding and transmission investigated. Inoculated ducks (n?=?15), which were mostly asymptomatic, shed infectious virus from the oral route from 1 to 8 days post inoculation, and from the cloacal route from 2-8 dpi. Viral ribonucleic acid was detected from 1-15 days post inoculation from the oral route and 1-24 days post inoculation from the cloacal route (cycle threshold <40). Most ducks seroconverted in a range of serological tests by 15 days post inoculation. Virus was efficiently transmitted during acute infection (5 inoculation-infected to all 5 contact ducks). However, no evidence for transmission, as determined by seroconversion and viral shedding, was found between an inoculation-infected group (n?=?10) and contact ducks (n?=?9) when the two groups only had contact after 10 days post inoculation. Clinical disease was more frequent and more severe in contact-infected (2 of 5) than inoculation-infected ducks (1 of 15). We conclude that Indonesian clade 2.1 H5N1 highly pathogenic avian influenza virus does not persist in individual ducks after acute infection. PMID:24392085

  20. Show-Me Center

    NSDL National Science Digital Library

    The Show-Me Center is a partnership of four NSF-sponsored middle grades mathematics curriculum development Satellite Centers (University of Wisconsin, Michigan State University, University of Montana, and the Educational Development Center). The group's website provides "information and resources needed to support selection and implementation of standards-based middle grades mathematics curricula." The Video Showcase includes segments on Number, Algebra, Geometry, Measure, and Data Analysis, with information on ways to obtain the complete video set. The Curricula Showcase provides general information, unit goals, sample lessons and teacher pages spanning four projects: the Connected Mathematics Project (CMP), Mathematics in Context (MiC), MathScape: Seeing and Thinking Mathematically, and Middle Grades Math Thematics. The website also posts Show-Me Center newsletters, information on upcoming conferences and workshops, and links to resources including published articles and unpublished commentary on mathematics school reform.

  1. The Truman Show

    Microsoft Academic Search

    Rolf F. Nohr

    The Truman Show is hardly a film you would automatically speak about as a game. At first glance, it is tempting to interpret the story of\\u000a Truman Burbank — his perpetual subjection to the artificial (televisual) world of Seahaven and its gargantuan reality TV project,\\u000a his eventual escape from the “OmniCam Ecosphere” building and the paternalistic surveillance of director Christof

  2. Hydraulic sweep shows promise

    SciTech Connect

    Rintoul. B.

    1981-01-01

    One of the more imaginative approaches toward recovering oil from shallow tar sands is undergoing evaluation following a field test in California's Midway-Sunset field. The technique could make possible the recovery of about 67% of the oil in place, revealing the best steam flood projects in recovery efficiency, and it could be used in near solid bitumens where steam flooding does not work. The process is an in situ, or in place, operation performed through a drilled well and consists of conducting a high velocity water stream down the well through special piping. At the bottom of the 2 stings, water follows separate paths. A portion passes through a high speed, focused nozzel directed toward the pay zone. The rest of the water stream passes through a Venturi jet pump. The suction created by the Venturi effect lifts the sand/water slurry to the surface.

  3. Fine granules showing sustained drug release prepared by high-shear melt granulation using triglycerin full behenate and milled microcrystalline cellulose.

    PubMed

    Aoki, Hajime; Iwao, Yasunori; Uchimoto, Takeaki; Noguchi, Shuji; Kajihara, Ryusuke; Takahashi, Kana; Ishida, Masayuki; Terada, Yasuko; Suzuki, Yoshio; Itai, Shigeru

    2015-01-30

    This study aimed to prepare fine granules with a diameter less than 200?m and sustained drug release properties by melt granulation. Triglycerin full behenate (TR-FB) was examined as a new meltable binder (MB) by comparison of its properties with those of glycerin monostearate (GM), widely used as MB. The effect of milling microcrystalline cellulose (MCC), an excipient for melt granulation, on the granule properties was also investigated. TR-FB was more stable during heating and storage than GM, and produced smaller granules with narrower particle size distribution, larger yield in the 106-200?m range, uniform roundness and better sustained drug release profile than those prepared with GM. Granules prepared with milled MCC had almost the same physicochemical properties as those produced with intact MCC. However, milled MCC produced granules with a more rigid structure and smaller void space than intact MCC. Consequently, the granules produced with milled MCC showed better sustained drug release behavior than those prepared with intact MCC. We successfully prepared fine granules with sustained drug release properties and diameter of less than 200?m using TR-FB and milled MCC. PMID:25434591

  4. A High Resolution Case Study of a Patient with Recurrent Plasmodium vivax Infections Shows That Relapses Were Caused by Meiotic Siblings

    PubMed Central

    Bright, Andrew Taylor; Manary, Micah J.; Tewhey, Ryan; Arango, Eliana M.; Wang, Tina; Schork, Nicholas J.; Yanow, Stephanie K.; Winzeler, Elizabeth A.

    2014-01-01

    Plasmodium vivax infects a hundred million people annually and endangers 40% of the world's population. Unlike Plasmodium falciparum, P. vivax parasites can persist as a dormant stage in the liver, known as the hypnozoite, and these dormant forms can cause malaria relapses months or years after the initial mosquito bite. Here we analyze whole genome sequencing data from parasites in the blood of a patient who experienced consecutive P. vivax relapses over 33 months in a non-endemic country. By analyzing patterns of identity, read coverage, and the presence or absence of minor alleles in the initial polyclonal and subsequent monoclonal infections, we show that the parasites in the three infections are likely meiotic siblings. We infer that these siblings are descended from a single tetrad-like form that developed in the infecting mosquito midgut shortly after fertilization. In this natural cross we find the recombination rate for P. vivax to be 10 kb per centimorgan and we further observe areas of disequilibrium surrounding major drug resistance genes. Our data provide new strategies for studying multiclonal infections, which are common in all types of infectious diseases, and for distinguishing P. vivax relapses from reinfections in malaria endemic regions. This work provides a theoretical foundation for studies that aim to determine if new or existing drugs can provide a radical cure of P. vivax malaria. PMID:24901334

  5. Nanocomposites of tantalum-based pyrochlore and indium hydroxide showing high and stable photocatalytic activities for overall water splitting and carbon dioxide reduction.

    PubMed

    Hsieh, Meng-Chun; Wu, Guan-Chang; Liu, Wei-Guang; Goddard, William A; Yang, Chia-Min

    2014-12-15

    Nanocomposites of tantalum-based pyrochlore nanoparticles and indium hydroxide were prepared by a hydrothermal process for UV-driven photocatalytic reactions including overall water splitting, hydrogen production from photoreforming of methanol, and CO2 reduction with water to produce CO. The best catalyst was more than 20?times more active than sodium tantalate in overall water splitting and 3?times more active than Degussa P25 TiO2 in CO2 reduction. Moreover, the catalyst was very stable while generating stoichiometric products of H2 (or CO) and O2 throughout long-term photocatalytic reactions. After the removal of In(OH)3, the pyrochlore nanoparticles remained highly active for H2 production from pure water and aqueous methanol solution. Both experimental studies and density functional theory calculations suggest that the pyrochlore nanoparticles catalyzed the water reduction to produce H2, whereas In(OH)3 was the major active component for water oxidation to produce O2. PMID:25384922

  6. Light-harvesting mutants show differential gene expression upon shift to high light as a consequence of photosynthetic redox and reactive oxygen species metabolism

    PubMed Central

    Tikkanen, Mikko; Gollan, Peter J.; Mekala, Nageswara Rao; Isojärvi, Janne; Aro, Eva-Mari

    2014-01-01

    The amount of light energy that is harvested and directed to the photosynthetic machinery is regulated in order to control the production of reactive oxygen species (ROS) in leaf tissues. ROS have important roles as signalling factors that instigate and mediate a range of cellular responses, suggesting that the mechanisms regulating light-harvesting and photosynthetic energy transduction also affect cell signalling. In this study, we exposed wild-type (WT) Arabidopsis and mutants impaired in the regulation of photosynthetic light-harvesting (stn7, tap38 and npq4) to transient high light (HL) stress in order to study the role of these mechanisms for up- and downregulation of gene expression under HL stress. The mutants, all of which have disturbed regulation of excitation energy transfer and distribution, responded to transient HL treatment with surprising similarity to the WT in terms of general ‘abiotic stress-regulated’ genes associated with hydrogen peroxide and 12-oxo-phytodienoic acid signalling. However, we identified distinct expression profiles in each genotype with respect to induction of singlet oxygen and jasmonic acid-dependent responses. The results of this study suggest that the control of excitation energy transfer interacts with hormonal regulation. Furthermore, the photosynthetic pigment–protein complexes appear to operate as receptors that sense the energetic balance between the photosynthetic light reactions and downstream metabolism. PMID:24591716

  7. High-resolution profiling of stationary-phase survival reveals yeast longevity factors and their genetic interactions.

    PubMed

    Garay, Erika; Campos, Sergio E; González de la Cruz, Jorge; Gaspar, Ana P; Jinich, Adrian; Deluna, Alexander

    2014-02-01

    Lifespan is influenced by a large number of conserved proteins and gene-regulatory pathways. Here, we introduce a strategy for systematically finding such longevity factors in Saccharomyces cerevisiae and scoring the genetic interactions (epistasis) among these factors. Specifically, we developed an automated competition-based assay for chronological lifespan, defined as stationary-phase survival of yeast populations, and used it to phenotype over 5,600 single- or double-gene knockouts at unprecedented quantitative resolution. We found that 14% of the viable yeast mutant strains were affected in their stationary-phase survival; the extent of true-positive chronological lifespan factors was estimated by accounting for the effects of culture aeration and adaptive regrowth. We show that lifespan extension by dietary restriction depends on the Swr1 histone-exchange complex and that a functional link between autophagy and the lipid-homeostasis factor Arv1 has an impact on cellular lifespan. Importantly, we describe the first genetic interaction network based on aging phenotypes, which successfully recapitulated the core-autophagy machinery and confirmed a role of the human tumor suppressor PTEN homologue in yeast lifespan and phosphatidylinositol phosphate metabolism. Our quantitative analysis of longevity factors and their genetic interactions provides insights into the gene-network interactions of aging cells. PMID:24586198

  8. Co5/Co8-cluster-based coordination polymers showing high-connected self-penetrating networks: syntheses, crystal structures, and magnetic properties.

    PubMed

    Li, Dong-Sheng; Zhao, Jun; Wu, Ya-Pan; Liu, Bin; Bai, Liang; Zou, Kun; Du, Miao

    2013-07-15

    Two novel Co(II)-cluster-based coordination polymers--namely, [Co5(?3-OH)2(1,4-ndc)4(bix)2]n (1) and {[Co8(?3-OH)4(1,4-ndc)6(btp)(H2O)6]·H2O}n (2)--were prepared by hydrothermal reactions of Co(II) perchlorate with 1,4-naphthalenedicarboxylic acid (1,4-H2ndc) and different N-donor coligands (bix = 1,4-bis(imidazol-1-ylmethyl)benzene and btp = 4,4'-bis(triazol-1-ylmethyl)biphenyl). In 1, 10-connected [Co5(?3-OH)2(COO)8] clusters are extended by the ?4-1,4-ndc(2-) and trans-bix ligands to construct a rare, self-penetrating ile framework that can interestingly be regarded as the cross-link of two interpenetrating 6-connected pcu networks. While for 2, [Co8(?3-OH)4(COO)12] clusters serve as the 8-connected nodes, which are bridged by the ?4/?5-1,4-ndc(2-) and trans-btp ligands to afford the highest-connected uninodal self-penetrating (4(20).6(8)) network based on octacobalt clusters. A synthetic and structural comparison of 1 and 2 demonstrates that the features of auxiliary N-donor ligands play a key role in governing the in situ formed clusters and the final 3-D coordination frameworks. Magnetic susceptibility measurements indicate that complex 1 shows an antiferromagnetic interaction between the adjacent Co(II) ions, whereas 2 displays the dominant antiferromagnetic exchanges in 300-50 K and a ferrimagnetic-like behavior at lower temperatures. PMID:23819571

  9. High genetic diversity in gametophyte clones of Undaria pinnatifida from Vladivostok, Dalian and Qingdao revealed using microsatellite analysis

    NASA Astrophysics Data System (ADS)

    Shan, Tifeng; Pang, Shaojun; Liu, Feng; Xu, Na; Zhao, Xiaobo; Gao, Suqin

    2012-03-01

    Breeding practice for Undaria pinnatifida (Harvey) Suringar requires the screening of a large number of offspring from gametophyte crossings to obtain an elite variety for large-scale cultivation. To better understand the genetic relationships of different gametophyte cultures isolated from different sources, 20 microsatellite loci were screened and 53 gametophyte clone cultures analyzed for U. pinnatifida isolated from wild sporophytes in Vladivostok, Russia and from cultivated sporophytes from Dalian and Qingdao, China. One locus was abandoned because of poor amplification. At the sex-linked locus of Up-AC-2A8, 3 alleles were detected in 25 female gametophyte clones, with sizes ranging from 307 to 316 bp. At other loci, 3 to 7 alleles were detected with an average of 4.5 alleles per locus. The average number of alleles at each locus was 1.3 and 3.7 for Russian and Chinese gametophyte clones, respectively. The average gene diversity for Russian, Chinese, and for the combined total of gametophyte clones was 0.1, 0.4, and 0.5, respectively. Russian gametophyte clones had unique alleles at 7 out of the 19 loci. In cluster analysis, Russian and Chinese gametophyte clones were separated into two different groups according to genetic distance. Overall, high genetic diversity was detected in gametophyte clones isolated from the two countries. These gametophyte cultures were believed to be appropriate parental materials for conducting breeding programs in the future.

  10. The DNA Bank: High-Security Bank Accounts to Protect and Share Your Genetic Identity.

    PubMed

    den Dunnen, Johan T

    2015-07-01

    With the cost of genome sequencing decreasing every day, DNA information has the potential of affecting the lives of everyone. Surprisingly, an individual has little knowledge about his own DNA information, can rarely access it, and has hardly any control over its use. This may result in preventable, life-threatening situations, and also significantly inhibits scientific progress. What we urgently need is a "DNA bank," a resource providing a secure personal account where, similar to a financial institution, you can store your DNA sequence. Using this private and secure DNA bank account, you govern your sequence-related business. For any genetic study performed, the data generated must be transferred (paid) to your DNA account. Using your account, you regulate access, knowing for what purpose (informed consent) and only for the genetic data you are willing to share. The DNA account ensures you are in the driver's seat, know what is known, and control what is happening with it. PMID:25952467

  11. Quantifying multi-ethnic representation in genetic studies of high mortality diseases

    PubMed Central

    Chen, Rong; Dudley, Joel T.; Ruau, David; Butte, Atul J.

    2012-01-01

    Most GWASs were performed using study populations with Caucasian ethnicity or ancestry, and findings from one ethnic subpopulation might not always translate to another. We curated 4,573 genetic studies on 763 human diseases and identified 3,461 disease-susceptible SNPs with genome-wide significance; only 10% of these had been validated in at least two different ethnic populations. SNPs for autoimmune diseases demonstrated the lowest percentage of cross-ethnicity validation. We used the mortality data from the Center for Disease Control and Prevention and identified 19 diseases killing over 10,000 Americans per year that were still lacking publications of even a single cross-ethnic SNP. Fifteen of these diseases had never been studied in large GWAS in non-Caucasian populations, including chronic liver diseases and cirrhosis, leukemia, and non-Hodgkin’s lymphoma. Our results demonstrate that diseases killing most Americans are still lacking genetic studies across ethnicities. PMID:22779041

  12. Not So Giants: Mice Lacking Both Somatostatin and Cortistatin Have High GH Levels but Show No Changes in Growth Rate or IGF-1 Levels.

    PubMed

    Pedraza-Arévalo, S; Córdoba-Chacón, J; Pozo-Salas, A I; L-López, F; de Lecea, L; Gahete, M D; Castańo, J P; Luque, R M

    2015-06-01

    Somatostatin (SST) and cortistatin (CORT) are two highly related neuropeptides involved in the regulation of various endocrine secretions. In particular, SST and CORT are two primary negative regulators of GH secretion. Consequently, single SST or CORT knockout mice exhibit elevated GH levels; however, this does not lead to increased IGF-1 levels or somatic growth. This apparent lack of correspondence has been suggested to result from compensatory mechanisms between both peptides. To test this hypothesis, in this study we explored, for the first time, the consequences of simultaneously deleting endogenous SST and CORT by generating a double SST/CORT knockout mouse model and exploring its endocrine and metabolic phenotype. Our results demonstrate that simultaneous deletion of SST and CORT induced a drastic elevation of endogenous GH levels, which, surprisingly, did not lead to changes in growth rate or IGF-1 levels, suggesting the existence of additional factors/systems that, in the absence of endogenous SST and CORT, could counteract GH actions. Notably, elevation in circulating GH levels were not accompanied by changes in pituitary GH expression or by alterations in the expression of its main regulators (GHRH and ghrelin) or their receptors (GHRH receptor, GHS receptor, or SST/CORT receptors) at the hypothalamic or pituitary level. However, although double-SST/CORT knockout male mice exhibited normal glucose and insulin levels, they had improved insulin sensitivity compared with the control mice. Therefore, these results suggest the existence of an intricate interplay among the known (SST/CORT), and likely unknown, inhibitory components of the GH/IGF-1 axis to regulate somatic growth and glucose/insulin homeostasis. PMID:25830706

  13. Comparative genetic diversity and genetic structure of three Chinese silkworm species Bombyx mori L. (Lepidoptera: Bombycidae), Antheraea pernyi Guérin-Meneville and Samia cynthia ricini Donovan (Lepidoptera: Saturniidae).

    PubMed

    Liu, Yan-Qun; Qin, Li; Li, Yu-Ping; Wang, Huan; Xia, Run-Xi; Qi, Yong-Hong; Li, Xi-Sheng; Lu, Cheng; Xiang, Zhong-Huai

    2010-01-01

    The genetic diversity and genetic structure of three Chinese silkworm species Bombyx mori L., Antheraea pernyi Guérin-Meneville and Samia cynthia ricini Donovan were comparatively assessed based on RAPD markers. At the species level, A. pernyi and B. mori showed high levels of genetic diversity, whereas S. cynthia ricini showed low level of genetic diversity. However, at the strain level, A. pernyi had relatively highest genetic diversity and B. mori had lowest genetic diversity. Analysis of molecular variance (AMOVA) suggested that 60% and 72% of genetic variation resided within strains in A. pernyi and S. cynthia ricini, respectively, whereas only 16% of genetic variation occurred within strains in B. mori. In UPGMA dendrogram, individuals of A. pernyi and B. mori formed the strain-specific genetic clades, whereas those of S. cynthia ricini were distributed in a mixed way. The implications of these results for the conservation and utilization in breeding programs of three silkworm species are discussed. PMID:21271066

  14. Producing Turkeys for Show 

    E-print Network

    Thornberry, Fredrick D.

    2005-12-14

    cobs, peanut hulls or rice hulls make good litter. Never place poults on a slick surface such as newspaper, plastic, butcher paper, etc. Construct a cardboard brooder guard (brooder circle) to keep poults near heat, water and feed. The brooder guard... should be 18 inches high and must be a minimum of 5 feet in diameter for 50 poults. When poults are 7 days old, remove the guard and allow them full freedom of the pen. Electric heat lamps (infrared bulbs) are good heat sources for brooding poults. Two...

  15. High level of genetic differentiation of Juniperus phoenicea (Cupressaceae) in the Mediterranean region: geographic implications

    Microsoft Academic Search

    Adam Boraty?ski; Andrzej Lewandowski; Krystyna Boraty?ska; Jose M. Montserrat; Angel Romo

    2009-01-01

    Fourteen natural populations of Juniperus phoenicea L. from the quite entire species range have been compared using isoenzyme polymorphism. Among 17 loci, 5 (Got1, 6Pgd3, Pgi2, Pgm2 and Shdh2) appeared to be differentiated sufficiently to provide useful information for discrimination between the subspecies phoenicea and turbinata (Guss.) Nyman. Two distinct groups of populations were detected using the Nei’s genetic distance

  16. Multiple genetic variants along candidate pathways influence plasma high-density lipoprotein cholesterol concentrations

    Microsoft Academic Search

    Yingchang Lu; M. E. T. Dollé; Sandra Imholz; R. van't Slot; W. M. M. Verschuren; C. Wijmenga; E. J. M. Feskens; J. M. A. Boer

    2008-01-01

    The known genetic variants determining plasma HDL cholesterol (HDL-C) levels explain only part of its variation. Three hundred eighty-four single nucleotide polymorphisms (SNPs) across 251 genes based on pathways potentially relevant to HDL-C metabolism were selected and genotyped in 3,575 subjects from the Doetinchem cohort, which was examined thrice over 11 years. Three hundred fifty-three SNPs in 239 genes passed

  17. High dispersal ability and low genetic differentiation in the widespread butterfly species Melanargia galathea

    Microsoft Academic Search

    Jan Christian Habel; Marius Junker; Thomas Schmitt

    2010-01-01

    Agricultural intensification caused a fragmentation of flower-rich extensively used meadows which resulted in the reduction\\u000a of the abundance of species of these habitats. The abundance pattern and the dispersal behaviour of species influence the\\u000a connectivity of local populations. In this context exchange rates can be directly measured by mark release recapture (MRR)\\u000a studies and indirectly by genetic analysis. Both approaches

  18. High yield potential, shuttle breeding, genetic diversity, and a new international wheat improvement strategy

    Microsoft Academic Search

    Rodomiro Ortiz; Richard Trethowan; Guillermo Ortiz Ferrara; Masa Iwanaga; John H. Dodds; Jonathan H. Crouch; Jose Crossa; Hans-Joachim Braun

    2007-01-01

    The main elements of the international wheat improvement program of the Centro Internacional de Mejoramiento de Maíz y Trigo\\u000a (CIMMYT), also known as the International Maize and Wheat Improvement Center, have been shuttle breeding at two contrasting\\u000a locations in Mexico, wide adaptation, durable rust and Septoria resistances, international multisite testing, and the appropriate\\u000a use of genetic variation to enhance yield

  19. An Escherichia coli strain, PGB01, isolated from feral pigeon Faeces, thermally fit to survive in pigeon, shows high level resistance to trimethoprim.

    PubMed

    Kumar, Arvind; Tiwary, Bipransh Kumar; Kachhap, Sangita; Nanda, Ashis Kumar; Chakraborty, Ranadhir

    2015-01-01

    In this study, of the hundred Escherichia coli strains isolated from feral Pigeon faeces, eighty five strains were resistant to one or more antibiotics and fifteen sensitive to all the antibiotics tested. The only strain (among all antibiotic-resistant E. coli isolates) that possessed class 1 integron was PGB01. The dihydrofolate reductase gene of the said integron was cloned, sequenced and expressed in E. coli JM109. Since PGB01 was native to pigeon's gut, we have compared the growth of PGB01 at two different temperatures, 42°C (normal body temperature of pigeon) and 37°C (optimal growth temperature of E. coli; also the human body temperature), with E. coli K12. It was found that PGB01 grew better than the laboratory strain E. coli K12 at 37°C as well as at 42°C. In the thermal fitness assay, it was observed that the cells of PGB01 were better adapted to 42°C, resembling the average body temperature of pigeon. The strain PGB01 also sustained more microwave mediated thermal stress than E. coli K12 cells. The NMR spectra of the whole cells of PGB01 varied from E. coli K12 in several spectral peaks relating some metabolic adaptation to thermotolerance. On elevating the growth temperature from 37°C to 42°C, susceptibility to kanamycin (both strains were sensitive to it) of E. coli K12 was increased, but in case of PGB01 no change in susceptibility took place. We have also attempted to reveal the basis of trimethoprim resistance phenotype conferred by the dfrA7 gene homologue of PGB01. Molecular Dynamics (MD) simulation study of docked complexes, PGB01-DfrA7 and E. coli TMP-sensitive-Dfr with trimethoprim (TMP) showed loss of some of the hydrogen and hydrophobic interaction between TMP and mutated residues in PGB01-DfrA7-TMP complex compared to TMP-sensitive-Dfr-TMP complex. This loss of interaction entails decrease in affinity of TMP for PGB01-DfrA7 compared to TMP-sensitive-Dfr. PMID:25750990

  20. American History Picture Show

    NSDL National Science Digital Library

    Ms. Bennion

    2009-11-23

    In class we read Katie's Picture Show, a book about a girl who discovers art first-hand one day at an art museum in London. She realizes she can climb into the paintings, explore her surroundings, and even solve problems for the subjects of the paintings. As part of our unit on American history, we are going to use art to further learn about some of the important events we have been discussing. Each of these works of art depicts an important event in American History. When you click on a picture, you will be able to see the name of the event as well as the artist who created it. You will be using all three pictures for this assignment.Use the websites ...

  1. Using High-Throughput Sequencing to Leverage Surveillance of Genetic Diversity and Oseltamivir Resistance: A Pilot Study during the 2009 Influenza A(H1N1) Pandemic

    PubMed Central

    Téllez-Sosa, Juan; Rodríguez, Mario Henry; Gómez-Barreto, Rosa E.; Valdovinos-Torres, Humberto; Hidalgo, Ana Cecilia; Cruz-Hervert, Pablo; Luna, René Santos; Carrillo-Valenzo, Erik; Ramos, Celso; García-García, Lourdes; Martínez-Barnetche, Jesús

    2013-01-01

    Background Influenza viruses display a high mutation rate and complex evolutionary patterns. Next-generation sequencing (NGS) has been widely used for qualitative and semi-quantitative assessment of genetic diversity in complex biological samples. The “deep sequencing” approach, enabled by the enormous throughput of current NGS platforms, allows the identification of rare genetic viral variants in targeted genetic regions, but is usually limited to a small number of samples. Methodology and Principal Findings We designed a proof-of-principle study to test whether redistributing sequencing throughput from a high depth-small sample number towards a low depth-large sample number approach is feasible and contributes to influenza epidemiological surveillance. Using 454-Roche sequencing, we sequenced at a rather low depth, a 307 bp amplicon of the neuraminidase gene of the Influenza A(H1N1) pandemic (A(H1N1)pdm) virus from cDNA amplicons pooled in 48 barcoded libraries obtained from nasal swab samples of infected patients (n ?=? 299) taken from May to November, 2009 pandemic period in Mexico. This approach revealed that during the transition from the first (May-July) to second wave (September-November) of the pandemic, the initial genetic variants were replaced by the N248D mutation in the NA gene, and enabled the establishment of temporal and geographic associations with genetic diversity and the identification of mutations associated with oseltamivir resistance. Conclusions NGS sequencing of a short amplicon from the NA gene at low sequencing depth allowed genetic screening of a large number of samples, providing insights to viral genetic diversity dynamics and the identification of genetic variants associated with oseltamivir resistance. Further research is needed to explain the observed replacement of the genetic variants seen during the second wave. As sequencing throughput rises and library multiplexing and automation improves, we foresee that the approach presented here can be scaled up for global genetic surveillance of influenza and other infectious diseases. PMID:23843978

  2. Genetic relatedness in viscous populations

    Microsoft Academic Search

    David C. Queller

    1994-01-01

    Summary Hamilton's inclusive fitness rule shows that the evolution of altruism is facilitated by high genetic relatedness of altruists to their beneficiaries. But the evolution of altruism is inhibited when the beneficiaries are also close competitors of the altruist, as will often be true in structured or viscous populations. However, Hamilton's rule still gives the correct condition for the evolution

  3. A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map and analysis of haplotype variation

    SciTech Connect

    Kelleher, Colin [University of British Columbia, Vancouver; Chiu, Readman [Genome Sciences Centre, Vancouver, BC, Canada; Shin, Heesun [Genome Sciences Centre, Vancouver, BC, Canada; Bosdet, Ian [Genome Sciences Centre, Vancouver, BC, Canada; Krywinski, Martin [Genome Sciences Centre, Vancouver, BC, Canada; Fjell, Chris [Genome Sciences Centre, Vancouver, BC, Canada; Wilkin, Jennifer [University of British Columbia, Vancouver; Yin, Tongming [ORNL; DiFazio, Stephen P [ORNL; Ali, Johar [Genome Sciences Centre, Vancouver, BC, Canada; Asano, Jennifer [Genome Sciences Centre, Vancouver, BC, Canada; Chan, Susanna [Genome Sciences Centre, Vancouver, BC, Canada; Cloutier, Alison [Genome Sciences Centre, Vancouver, BC, Canada; Girn, Noreen [Genome Sciences Centre, Vancouver, BC, Canada; Leach, Stephen [Genome Sciences Centre, Vancouver, BC, Canada; Lee, Darlene [Genome Sciences Centre, Vancouver, BC, Canada; Mathewson, Carrie [Genome Sciences Centre, Vancouver, BC, Canada; Olson, Teika [Genome Sciences Centre, Vancouver, BC, Canada; O'Connor, Katie [Genome Sciences Centre, Vancouver, BC, Canada; Prabhu, Anna-Liisa [Genome Sciences Centre, Vancouver, BC, Canada; Smailus, Duane [Genome Sciences Centre, Vancouver, BC, Canada; Stott, Jeffery [Genome Sciences Centre, Vancouver, BC, Canada; Tsai, Miranda [Genome Sciences Centre, Vancouver, BC, Canada; Wye, Natasaja [Genome Sciences Centre, Vancouver, BC, Canada; Yang, George [Genome Sciences Centre, Vancouver, BC, Canada; Zhuang, Jun [Genome Sciences Centre, Vancouver, BC, Canada; Holt, Robert A. [Genome Sciences Centre, Vancouver, BC, Canada; Putnam, Nicholas [Genome Sciences Centre, Vancouver, BC, Canada; Vrebalov, Julia [Cornell University; Giovannoni, James [Cornell University; Grimwood, Jane [Stanford University; Schmutz, Jeremy [Stanford University; Rokhsar, Daniel [U.S. Department of Energy, Joint Genome Institute; Jones, Steven [Genome Sciences Centre, Vancouver, BC, Canada; Marra, Marco [Genome Sciences Centre, Vancouver, BC, Canada; Tuskan, Gerald A [ORNL; Bohlmann, J. [University of British Columbia, Vancouver; Ellis, Brian [University of British Columbia, Vancouver; Ritland, Kermit [University of British Columbia, Vancouver; Douglas, Carl [University of British Columbia, Vancouver; Schein, Jacqueline [Genome Sciences Centre, Vancouver, BC, Canada

    2007-01-01

    As part of a larger project to sequence the Populus genome and generate genomic resources for this emerging model tree, we constructed a physical map of the Populus genome, representing one of the first maps of an undomesticated, highly heterozygous plant species. The physical map, consisting of 2,802 contigs, was constructed from fingerprinted bacterial artificial chromosome (BAC) clones. The map represents approximately 9.4-fold coverage of the 485+10 Mb Populus genome, as estimated from the genome sequence assembly. BAC ends were sequenced to aid in long-range assembly of whole genome shotgun sequence scaffolds and to anchor the physical map to the genome sequence. Simple sequence repeat (SSR)-based markers were derived from the end sequences and used to initiate integration of the BAC and genetic maps. 2,411 physical map contigs, representing 97% of all clones assigned to contigs, were aligned to the sequence assembly (JGI Populus trichocarpa v1.0). These alignments represent a total coverage of 384 Mb (79%) of the entire poplar sequence assembly and 295 Mb (96%) of linkage group sequence assemblies. A striking result of the physical map contig alignments to the sequence assembly was the co-localization of multiple contigs across numerous regions of the 19 linkage groups. Targeted sequencing of BAC clones and genetic analysis in a small number of representative regions showed that these co-aligning contigs represent distinct haplotypes in the heterozygous individual sequenced, and revealed the nature of these haplotype sequence differences.

  4. Genetic mapping to 10q23.3-q24.2, in a large Italian pedigree, of a new syndrome showing bilateral cataracts, gastroesophageal reflux, and spastic paraparesis with amyotrophy.

    PubMed Central

    Seri, M; Cusano, R; Forabosco, P; Cinti, R; Caroli, F; Picco, P; Bini, R; Morra, V B; De Michele, G; Lerone, M; Silengo, M; Pela, I; Borrone, C; Romeo, G; Devoto, M

    1999-01-01

    We have recently observed a large pedigree with a new rare autosomal dominant spastic paraparesis. In three subsequent generations, 13 affected individuals presented with bilateral cataracts, gastroesophageal reflux with persistent vomiting, and spastic paraparesis with amyotrophy. Bilateral cataracts occurred in all affected individuals, with the exception of one patient who presented with a chorioretinal dystrophy, whereas clinical signs of spastic paraparesis showed a variable expressivity. Using a genomewide mapping approach, we mapped the disorder to the long arm of chromosome 10 on band q23.3-q24.2, in a 12-cM chromosomal region where additional neurologic disorders have been localized. The spectrum of phenotypic manifestations in this family is reminiscent of a smaller pedigree, reported recently, confirming the possibility of a new syndrome. Finally, the anticipation of symptoms suggests that an unstable trinucleotide repeat may be responsible for the condition. PMID:9973297

  5. Human Genetics in Rheumatoid Arthritis Guides a High-Throughput Drug Screen of the CD40 Signaling Pathway

    PubMed Central

    Li, Gang; Diogo, Dorothée; Wu, Di; Spoonamore, Jim; Dancik, Vlado; Franke, Lude; Kurreeman, Fina; Rossin, Elizabeth J.; Duclos, Grant; Hartland, Cathy; Zhou, Xuezhong; Li, Kejie; Liu, Jun; De Jager, Philip L.; Siminovitch, Katherine A.; Zhernakova, Alexandra; Raychaudhuri, Soumya; Bowes, John; Eyre, Steve; Padyukov, Leonid; Gregersen, Peter K.; Worthington, Jane; Gupta, Namrata; Clemons, Paul A.; Stahl, Eli; Tolliday, Nicola; Plenge, Robert M.

    2013-01-01

    Although genetic and non-genetic studies in mouse and human implicate the CD40 pathway in rheumatoid arthritis (RA), there are no approved drugs that inhibit CD40 signaling for clinical care in RA or any other disease. Here, we sought to understand the biological consequences of a CD40 risk variant in RA discovered by a previous genome-wide association study (GWAS) and to perform a high-throughput drug screen for modulators of CD40 signaling based on human genetic findings. First, we fine-map the CD40 risk locus in 7,222 seropositive RA patients and 15,870 controls, together with deep sequencing of CD40 coding exons in 500 RA cases and 650 controls, to identify a single SNP that explains the entire signal of association (rs4810485, P?=?1.4×10?9). Second, we demonstrate that subjects homozygous for the RA risk allele have ?33% more CD40 on the surface of primary human CD19+ B lymphocytes than subjects homozygous for the non-risk allele (P?=?10?9), a finding corroborated by expression quantitative trait loci (eQTL) analysis in peripheral blood mononuclear cells from 1,469 healthy control individuals. Third, we use retroviral shRNA infection to perturb the amount of CD40 on the surface of a human B lymphocyte cell line (BL2) and observe a direct correlation between amount of CD40 protein and phosphorylation of RelA (p65), a subunit of the NF-?B transcription factor. Finally, we develop a high-throughput NF-?B luciferase reporter assay in BL2 cells activated with trimerized CD40 ligand (tCD40L) and conduct an HTS of 1,982 chemical compounds and FDA–approved drugs. After a series of counter-screens and testing in primary human CD19+ B cells, we identify 2 novel chemical inhibitors not previously implicated in inflammation or CD40-mediated NF-?B signaling. Our study demonstrates proof-of-concept that human genetics can be used to guide the development of phenotype-based, high-throughput small-molecule screens to identify potential novel therapies in complex traits such as RA. PMID:23696745

  6. Human genetics in rheumatoid arthritis guides a high-throughput drug screen of the CD40 signaling pathway.

    PubMed

    Li, Gang; Diogo, Dorothée; Wu, Di; Spoonamore, Jim; Dancik, Vlado; Franke, Lude; Kurreeman, Fina; Rossin, Elizabeth J; Duclos, Grant; Hartland, Cathy; Zhou, Xuezhong; Li, Kejie; Liu, Jun; De Jager, Philip L; Siminovitch, Katherine A; Zhernakova, Alexandra; Raychaudhuri, Soumya; Bowes, John; Eyre, Steve; Padyukov, Leonid; Gregersen, Peter K; Worthington, Jane; Gupta, Namrata; Clemons, Paul A; Stahl, Eli; Tolliday, Nicola; Plenge, Robert M

    2013-05-01

    Although genetic and non-genetic studies in mouse and human implicate the CD40 pathway in rheumatoid arthritis (RA), there are no approved drugs that inhibit CD40 signaling for clinical care in RA or any other disease. Here, we sought to understand the biological consequences of a CD40 risk variant in RA discovered by a previous genome-wide association study (GWAS) and to perform a high-throughput drug screen for modulators of CD40 signaling based on human genetic findings. First, we fine-map the CD40 risk locus in 7,222 seropositive RA patients and 15,870 controls, together with deep sequencing of CD40 coding exons in 500 RA cases and 650 controls, to identify a single SNP that explains the entire signal of association (rs4810485, P?=?1.4×10(-9)). Second, we demonstrate that subjects homozygous for the RA risk allele have ?33% more CD40 on the surface of primary human CD19+ B lymphocytes than subjects homozygous for the non-risk allele (P?=?10(-9)), a finding corroborated by expression quantitative trait loci (eQTL) analysis in peripheral blood mononuclear cells from 1,469 healthy control individuals. Third, we use retroviral shRNA infection to perturb the amount of CD40 on the surface of a human B lymphocyte cell line (BL2) and observe a direct correlation between amount of CD40 protein and phosphorylation of RelA (p65), a subunit of the NF-?B transcription factor. Finally, we develop a high-throughput NF-?B luciferase reporter assay in BL2 cells activated with trimerized CD40 ligand (tCD40L) and conduct an HTS of 1,982 chemical compounds and FDA-approved drugs. After a series of counter-screens and testing in primary human CD19+ B cells, we identify 2 novel chemical inhibitors not previously implicated in inflammation or CD40-mediated NF-?B signaling. Our study demonstrates proof-of-concept that human genetics can be used to guide the development of phenotype-based, high-throughput small-molecule screens to identify potential novel therapies in complex traits such as RA. PMID:23696745

  7. Genetic alterations activating kinase and cytokine receptor signaling in high-risk acute lymphoblastic leukemia

    Cancer.gov

    Activated kinase-like B-ALL does not harbor the BCR-ABL translocation, but it exhibits a very similar gene expression profile. The genetic alterations discovered in this study, which were validated by recurrence testing in a larger cohort, specifically affect cytokine receptors and regulators of kinase signaling. Moreover, several of the novel or rare alterations identified in this study induced cancerous phenotypes in cell lines and mouse xenograft models, and demonstrated sensitivity to tyrosine kinase inhibitors that are already used in the clinic.

  8. Managing Beef Cattle for Show

    E-print Network

    Herd, Dennis B.; Boleman, Chris; Boleman, Larry L.

    2001-11-16

    in show diets because of its rapid digestion and tendency to cause acido- sis (see the section on health). Oats are excellent for growth and development of steers or heifers. A mixture similar in nutrient content to oats can be formulated with a high...

  9. Low genetic diversity and high genetic divergence caused by inbreeding and geographical isolation in the populations of endangered species Loropetalum subcordatum (Hamamelidaceae) endemic to China

    Microsoft Academic Search

    Wei GongLei; Lei Gu; Dianxiang Zhang

    2010-01-01

    Loropetalum subcordatum (Hamamelidaceae) is one of the most endangered angiosperm species in China. It is narrowly distributed in a few localities\\u000a in the evergreen broadleaved forest of southern China. Up to now only a few dozen remnant individuals have been found in the\\u000a four extant populations. In this project, we studied its genetic diversity and population genetic structure using the

  10. Murine Albino-Deletion Complex: High-Resolution Microsatellite Map and Genetically Anchored Yac Framework Map

    PubMed Central

    Rikke, B. A.; Johnson, D. K.; Johnson, T. E.

    1997-01-01

    The murine albino-deletion complex developed as part of the Oak Ridge specific-locus test covers 6-11 cM of chromosome 7. This complex has proven to be a valuable resource for localizing traits to a small target region suitable for positional cloning. In this study, we mapped the endpoints of deletions in this complex using all of the available Mit simple-sequence length polymorphism (SSLP) markers. Concurrently, this mapping has determined the map order of nearly all of the SSLP markers, most of which were previously unresolved. The SSLP-based deletion map was confirmed and genetic distances were determined using the European Collaborative Interspecific Backcross panel of nearly a thousand mice. The average SSLP marker resolution is 0.3-0.4 cM, comparable to the cloning capacity of yeast artificial chromosomes (YACs). The SSLP markers were then used to construct a genetically anchored YAC framework map that further confirms the deletion map. We find that the largest deleted region distal to Tyr is about two to three times larger than the largest proximal deleted region, and the original C3H/101 regions flanking the deletions (moved to an St2A c(ch)/c(ch) background) are smaller than anticipated, which we suggest may result from increased recombination rates immediately flanking the deleted regions. PMID:9335613

  11. High-resolution genetic mapping of maize pan-genome sequence anchors

    PubMed Central

    Lu, Fei; Romay, Maria C.; Glaubitz, Jeffrey C.; Bradbury, Peter J.; Elshire, Robert J.; Wang, Tianyu; Li, Yu; Li, Yongxiang; Semagn, Kassa; Zhang, Xuecai; Hernandez, Alvaro G.; Mikel, Mark A.; Soifer, Ilya; Barad, Omer; Buckler, Edward S.

    2015-01-01

    In addition to single-nucleotide polymorphisms, structural variation is abundant in many plant genomes. The structural variation across a species can be represented by a ‘pan-genome', which is essential to fully understand the genetic control of phenotypes. However, the pan-genome's complexity hinders its accurate assembly via sequence alignment. Here we demonstrate an approach to facilitate pan-genome construction in maize. By performing 18 trillion association tests we map 26 million tags generated by reduced representation sequencing of 14,129 maize inbred lines. Using machine-learning models we select 4.4 million accurately mapped tags as sequence anchors, 1.1 million of which are presence/absence variations. Structural variations exhibit enriched association with phenotypic traits, indicating that it is a significant source of adaptive variation in maize. The ability to efficiently map ultrahigh-density pan-genome sequence anchors enables fine characterization of structural variation and will advance both genetic research and breeding in many crops. PMID:25881062

  12. Genetic diversity increases population productivity in a sessile marine invertebrate.

    PubMed

    Aguirre, J David; Marshall, Dustin J

    2012-05-01

    Reductions in genetic diversity can have widespread ecological consequences: populations with higher genetic diversity are more stable, productive and resistant to disturbance or disease than populations with lower genetic diversity. These ecological effects of genetic diversity differ from the more familiar evolutionary consequences of depleting genetic diversity, because ecological effects manifest within a single generation. If common, genetic diversity effects have the potential to change the way we view and manage populations, but our understanding of these effects is far from complete, and the role of genetic diversity in sexually reproducing animals remains unclear. Here, we examined the effects of genetic diversity in a sexually reproducing marine invertebrate in the field. We manipulated the genetic diversity of experimental populations and then measured individual survival, growth, and fecundity, as well as the size of offspring produced by individuals in high and low genetic diversity populations. Overall, we found greater genetic diversity increased performance across all metrics, and that complementarity effects drove the increased productivity of our high-diversity populations. Our results show that differences in genetic diversity among populations can have pervasive effects on population productivity within remarkably short periods of time. PMID:22764499

  13. Cholesterol oxidase with high catalytic activity from Pseudomonas aeruginosa: Screening, molecular genetic analysis, expression and characterization.

    PubMed

    Doukyu, Noriyuki; Nihei, Shyou

    2015-07-01

    An extracellular cholesterol oxidase producer, Pseudomonas aeruginosa strain PA157, was isolated by a screening method to detect 6?-hydroperoxycholest-4-en-3-one-forming cholesterol oxidase. On the basis of a putative cholesterol oxidase gene sequence in the genome sequence data of P. aeruginosa strain PAO1, the cholesterol oxidase gene from strain PA157 was cloned. The mature form of the enzyme was overexpressed in Escherichia coli cells. The overexpressed enzyme formed inclusion bodies in recombinant E. coli cells grown at 20°C and 30°C. A soluble and active PA157 enzyme was obtained when the recombinant cells were grown at 10°C. The purified enzyme was stable at pH 5.5 to 10 and was most active at pH 7.5-8.0, showing optimal activity at pH 7.0 and 70°C. The enzyme retained about 90% of its activity after incubation for 30 min at 70°C. The enzyme oxidized 3?-hydroxysteroids such as cholesterol, ?-cholestanol, and ?-sitosterol at high rates. The Km value and Vmax value for the cholesterol were 92.6 ?M and 15.9 ?mol/min/mg of protein, respectively. The Vmax value of the enzyme was higher than those of commercially available cholesterol oxidases. This is the first report to characterize a cholesterol oxidase from P. aeruginosa. PMID:25573142

  14. High Genetic Diversity Detected in Olives beyond the Boundaries of the Mediterranean Sea

    PubMed Central

    Sheikh-Hassani, Massoma; Ataei, Saeedeh; Cultrera, Nicolň G. M.; Pandolfi, Saverio; Baldoni, Luciana

    2014-01-01

    Background Olive trees (Olea europaea subsp. europaea var. europaea) naturally grow in areas spanning the Mediterranean basin and towards the East, including the Middle East. In the Iranian plateau, the presence of olives has been documented since very ancient times, though the early history of the crop in this area is shrouded in uncertainty. Methods The varieties presently cultivated in Iran and trees of an unknown cultivation status, surviving under extreme climate and soil conditions, were sampled from different provinces and compared with a set of Mediterranean cultivars. All samples were analyzed using SSR and chloroplast markers to establish the relationships between Iranian olives and Mediterranean varieties, to shed light on the origins of Iranian olives and to verify their contribution to the development of the current global olive variation. Results Iranian cultivars and ecotypes, when analyzed using SSR markers, clustered separately from Mediterranean cultivars and showed a high number of private alleles, on the contrary, they shared the same single chlorotype with the most widespread varieties cultivated in the Mediterranean. Conclusion We hypothesized that Iranian and Mediterranean olive trees may have had a common origin from a unique center in the Near East region, possibly including the western Iranian area. The present pattern of variation may have derived from different environmental conditions, distinct levels and selection criteria, and divergent breeding opportunities found by Mediterranean and Iranian olives.These unexpected findings emphasize the importance of studying the Iranian olive germplasm as a promising but endangered source of variation. PMID:24709858

  15. High-precision mapping of protein–protein interfaces: an integrated genetic strategy combining en masse mutagenesis and DNA-level parallel analysis on a yeast two-hybrid platform

    PubMed Central

    Pajunen, Maria; Turakainen, Hilkka; Poussu, Eini; Peränen, Johan; Vihinen, Mauno; Savilahti, Harri

    2007-01-01

    Understanding networks of protein–protein interactions constitutes an essential component on a path towards comprehensive description of cell function. Whereas efficient techniques are readily available for the initial identification of interacting protein partners, practical strategies are lacking for the subsequent high-resolution mapping of regions involved in protein–protein interfaces. We present here a genetic strategy to accurately map interacting protein regions at amino acid precision. The system is based on parallel construction, sampling and analysis of a comprehensive insertion mutant library. The methodology integrates Mu in vitro transposition-based random pentapeptide mutagenesis of proteins, yeast two-hybrid screening and high-resolution genetic footprinting. The strategy is general and applicable to any interacting protein pair. We demonstrate the feasibility of the methodology by mapping the region in human JFC1 that interacts with Rab8A, and we show that the association is mediated by the Slp homology domain 1. PMID:17702760

  16. Personalized prostate cancer screening among men with high risk genetic predisposition- study protocol for a prospective cohort study

    PubMed Central

    2014-01-01

    Background Prostate cancer screening among the general population is highly debatable. Nevertheless, screening among high-risk groups is appealing. Prior data suggests that men carrying mutations in the BRCA1& 2 genes may be at increased risk of developing prostate cancer. Additionally, they appear to develop prostate cancer at a younger age and with a more aggressive course. However, prior studies did not systematically perform prostate biopsies and thus cannot determine the true prevalence of prostate cancer in this population. Methods This will be a prospective diagnostic trial of screening for prostate cancer among men with genetic predisposition. The target population is males (40–70 year old) carrying a BRCA1 and/or BRCA2 germ line mutation. They will be identified via our Genetic counseling unit. All men after signing an informed consent will undergo the following tests: PSA, free to total PSA, MRI of prostate and prostate biopsy. The primary endpoint will be to estimate the prevalence, stage and grade of prostate cancer in this population. Additionally, the study aims to estimate the impact of these germ line mutations on benign prostatic hyperplasia. Furthermore, this study aims to create a bio-bank of tissue, urine and serum of this unique cohort for future investigations. Finally, this study will identify an inception cohort for future interventional studies of primary and secondary prevention. Discussion The proposed research is highly translational and focuses not only on the clinical results, but on the future specimens that will be used to advance our understanding of prostate cancer patho-physiology. Most importantly, these high-risk germ-line mutation carriers are ideal candidates for primary and secondary prevention initiatives. Trial registration ClinicalTrials.gov: NCT02053805. PMID:25047061

  17. From Structure to Systems: High-Resolution, Quantitative Genetic Analysis of RNA Polymerase II

    PubMed Central

    Braberg, Hannes; Jin, Huiyan; Moehle, Erica A.; Chan, Yujia A.; Wang, Shuyi; Shales, Michael; Benschop, Joris J.; Morris, John H.; Qiu, Chenxi; Hu, Fuqu; Tang, Leung K.; Fraser, James S.; Holstege, Frank C.P.; Hieter, Philip; Guthrie, Christine; Kaplan, Craig D.; Krogan, Nevan J.

    2014-01-01

    SUMMARY RNA polymerase II (RNAPII) lies at the core of dynamic control of gene expression. Using 53 RNAPII point mutants, we generated a point mutant epistatic miniarray profile (pE-MAP) comprising ~60,000 quantitative genetic interactions in Saccharomyces cerevisiae. This analysis enabled functional assignment of RNAPII subdomains and uncovered connections between individual regions and other protein complexes. Using splicing microarrays and mutants that alter elongation rates in vitro, we found an inverse relationship between RNAPII speed and in vivo splicing efficiency. Furthermore, the pE-MAP classified fast and slow mutants that favor upstream and downstream start site selection, respectively. The striking coordination of polymerization rate with transcription initiation and splicing suggests that transcription rate is tuned to regulate multiple gene expression steps. The pE-MAP approach provides a powerful strategy to understand other multifunctional machines at amino acid resolution. PMID:23932120

  18. A Defined Zebrafish Line for High-Throughput Genetics and Genomics: NHGRI-1

    PubMed Central

    LaFave, Matthew C.; Varshney, Gaurav K.; Vemulapalli, Meghana; Mullikin, James C.; Burgess, Shawn M.

    2014-01-01

    Substantial intrastrain variation at the nucleotide level complicates molecular and genetic studies in zebrafish, such as the use of CRISPRs or morpholinos to inactivate genes. In the absence of robust inbred zebrafish lines, we generated NHGRI-1, a healthy and fecund strain derived from founder parents we sequenced to a depth of ?50×. Within this strain, we have identified the majority of the genome that matches the reference sequence and documented most of the variants. This strain has utility for many reasons, but in particular it will be useful for any researcher who needs to know the exact sequence (with all variants) of a particular genomic region or who wants to be able to robustly map sequences back to a genome with all possible variants defined. PMID:25009150

  19. Genetic Differentiation among Long-Toed Salamander ( Ambystoma macrodactylum ) Populations

    Microsoft Academic Search

    David A. Tallmon; W. Chris Funk; William W. Dunlap; Fred W. Allendorf; J. D. McEachran

    2000-01-01

    We examined the genetic population structure of Long-Toed Salamanders (Am- bystoma macrodactylum) from the Bitterroot Mountains of Idaho and Montana to better understand their evolutionary history and genetic population structure. Pop- ulations show high levels of within-population genetic variation at six polymorphic allozyme loci (Hs 5 0.09 for all 18 loci examined; range 0.04-0.14). There is very little divergence among

  20. A high resolution genetic linkage map of soybean based on 357 recombinant inbred lines genotyped with BARCSoySNP6K

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of this study was to construct a high density genetic map of soybean (Glycine max L. Merr) using a high throughput single nucleotide polymorphism (SNP) genotyping on 357 F7 recombinant inbred lines (RILs) from a cross of ‘Wyandot’ × PI 567301B. Of 5,403 SNP loci scored from the Infiniu...

  1. High Genetic Diversity and Distinctiveness of Rear-Edge Climate Relicts Maintained by Ancient Tetraploidisation for Alnus glutinosa

    PubMed Central

    Lepais, Olivier; Muller, Serge D.; Ben Saad-Limam, Samia; Benslama, Mohamed; Rhazi, Laila; Belouahem-Abed, Djamila; Daoud-Bouattour, Amina; Gammar, Amor Mokhtar; Ghrabi-Gammar, Zeineb; Bacles, Cécile Fanny Emilie

    2013-01-01

    Populations located at the rear-edge of a species’ distribution may have disproportionate ecological and evolutionary importance for biodiversity conservation in a changing global environment. Yet genetic studies of such populations remain rare. This study investigates the evolutionary history of North-African low latitude marginal populations of Alnus glutinosa Gaertn., a European tree species that plays a significant ecological role as a keystone of riparian ecosystems. We genotyped 551 adults from 19 populations located across North Africa at 12 microsatellite loci and applied a coalescent-based simulation approach to reconstruct the demographic and evolutionary history of these populations. Surprisingly, Moroccan trees were tetraploids demonstrating a strong distinctiveness of these populations within a species otherwise known as diploid. Best-fitting models of demographic reconstruction revealed the relict nature of Moroccan populations that were found to have withstood past climate change events and to be much older than Algerian and Tunisian populations. This study highlights the complex demographic history that can be encountered in rear-edge distribution margins that here consist of both old stable climate relict and more recent populations, distinctively diverse genetically both quantitatively and qualitatively. We emphasize the high evolutionary and conservation value of marginal rear-edge populations of a keystone riparian species in the context of on-going climate change in the Mediterranean region. PMID:24098677

  2. Patterns of molecular genetic variation among African elephant populations

    Microsoft Academic Search

    Kenine E. Comstock; Nicholas Georgiadis; Jill Pecon-Slattery; Alfred L. Roca; Elaine A. Ostrander; Stephen J. O'Brien; Samuel K. Wasser

    2002-01-01

    The highly threatened African elephants have recently been subdivided into two species, Loxodonta africana (savannah or bush elephant) and L. cyclotis (forest elephant) based on morphological and molecular studies. A molecular genetic assessment of 16 microsatellite loci across 20 populations (189 individuals) affirms species level genetic differentiation and provides robust genotypic assessment of species affiliation. Savannah elephant popula- tions show

  3. Human-Competitive Machine Intelligence by Means of Genetic Algorithms

    E-print Network

    Fernandez, Thomas

    Human-Competitive Machine Intelligence by Means of Genetic Algorithms John R. Koza Section Holland's expectation that the genetic algorithm would have "applications to ... artificial intelligence" by showing examples of the automatic creation of human-competitive computer programs from a high

  4. Analysis of Molecular Genetics Content in Spanish Secondary School Textbooks

    ERIC Educational Resources Information Center

    Martinez-Gracia, M. V.; Gil-Quilez, M. J.; Osada, J.

    2006-01-01

    The treatment of molecular biology in thirty-four Spanish high school biology textbooks has been analysed using a check-list made up of twenty-three items. The study showed a tendency to confuse the genetic code with genetic information. The treatment of DNA transcription, regulation of gene expression and translation were presented as masses of…

  5. ORIGINAL ARTICLE Genetic and morphological patterns show variation

    E-print Network

    Campbell, Diane

    of individuals intermediate to the two parental species in two zones of sympatry between Ipomopsis aggregata Ipomopsis (Polemoniaceae) zones of sympatry G Aldridge1 and DR Campbell2 1 Rocky Mountain Biological online 29 October 2008 Keywords: Ipomopsis; hybrid zones; hybridization rate; mosaic hybrid zone

  6. Remarkably low genetic variation but high population differentiation in the climbing perch, Anabas testudineus (Anabantidae), based on the mtDNA control region.

    PubMed

    Jamsari, A F J; Muchlisin, Z A; Musri, M; Siti Azizah, M N

    2010-01-01

    Anabas testudineus (Anabantidae) is an important food fish in Southeast Asia. We analyzed the mitochondrial DNA control region sequence data to evaluate the genetic variability and population structure of this species. Sixty specimens were collected from four populations in Sumatra and two populations in Peninsular Malaysia. We found a very low level of genetic variability, with five of the six populations exhibiting total absence of genetic variation. Based on analysis of molecular variance, 84.72% of the total variation was among populations and 15.28% within populations. A geographical division based on FST values indicated highly significant genetic differentiation among populations from the four drainage systems: Aceh, Sumatra Utara, Pulau Pinang, and Terengganu (FST ranging from 0.633 to 1.000). No phylogeographic relationships among populations were detected, despite the generation of four distinct clades in a neighbor-joining phylogenetic tree. PMID:20845309

  7. Generation by reverse genetics of an effective, stable, live-attenuated newcastle disease virus vaccine based on a currently circulating, highly virulent Indonesian strain.

    PubMed

    Xiao, Sa; Nayak, Baibaswata; Samuel, Arthur; Paldurai, Anandan; Kanabagattebasavarajappa, Mallikarjuna; Prajitno, Teguh Y; Bharoto, Eny E; Collins, Peter L; Samal, Siba K

    2012-01-01

    Newcastle disease virus (NDV) can cause severe disease in chickens. Although NDV vaccines exist, there are frequent reports of outbreaks in vaccinated chickens. During 2009-2010, despite intense vaccination, NDV caused major outbreaks among commercial poultry farms in Indonesia. These outbreaks raised concern regarding the protective immunity of current vaccines against circulating virulent strains in Indonesia. In this study, we investigated whether a recombinant attenuated Indonesian NDV strain could provide better protection against prevalent Indonesian viruses. A reverse genetics system for the highly virulent NDV strain Banjarmasin/010/10 (Ban/010) isolated in Indonesia in 2010 was constructed. The Ban/010 virus is classified in genotype VII of class II NDV, which is genetically distinct from the commercial vaccine strains B1 and LaSota, which belong to genotype II, and shares only 89 and 87% amino acid identity for the protective antigens F and HN, respectively. A mutant virus, named Ban/AF, was developed in which the virulent F protein cleavage site motif "RRQKR?F" was modified to an avirulent motif "GRQGR?L" by three amino acid substitutions (underlined). The Ban/AF vaccine virus did not produce syncytia or plaques in cell culture, even in the presence of added protease. Pathogenicity tests showed that Ban/AF was completely avirulent. Ban/AF replicated efficiently during 10 consecutive passages in chickens and remained genetically stable. Serological analysis showed that Ban/AF induced higher neutralization and hemagglutination inhibition antibody titers against the prevalent viruses than the commercial vaccines B1 or LaSota. Both Ban/AF and commercial vaccines provided protection against clinical disease and mortality after challenge with virulent NDV strain Ban/010 (genotype VII) or GB Texas (genotype II). However, Ban/AF significantly reduced challenge virus shedding from the vaccinated birds compared to B1 vaccine. These results suggest that Ban/AF can provide better protection than commercial vaccines and is a promising vaccine candidate against NDV strains circulating in Indonesia. PMID:23285174

  8. High genetic diversity and absence of founder effects in a worldwide aquatic invader.

    PubMed

    Lejeusne, Christophe; Saunier, Alice; Petit, Nicolas; Béguer, Mélanie; Otani, Michio; Carlton, James T; Rico, Ciro; Green, Andy J

    2014-01-01

    The introduced oriental shrimp Palaemon macrodactylus has recently become widespread in temperate estuaries worldwide. However, this recent worldwide spread outside of its native range arises after a previous introduction to the US Pacific coast, where it was restricted for more than 30 years. Using a phylogeographic approach, the present work investigates the genetic history of the invasion of this decapod worldwide. Japan acted as the main native source area for worldwide introduced populations, but other native areas (likely South Korea and China) may act as source populations as well. The recently introduced European and NW Atlantic populations result from colonization from both Japan and an unknown area of the native range, although colonization from the NE Pacific could not be ruled out. Most introduced populations had higher haplotypic diversity than most native populations. P. macrodactylus has a strong potential to become one of the most widespread introduced species and may become the dominant estuarine shrimp in Europe. The ecological and economic consequences of this invasion remain to be thoroughly evaluated. PMID:25060780

  9. Genetic and Molecular Predictors of High Vancomycin MIC in Staphylococcus aureus Bacteremia Isolates

    PubMed Central

    Turnidge, John D.; Munckhof, Wendy J.; Robinson, J. Owen; Korman, Tony M.; O'Sullivan, Matthew V. N.; Anderson, Tara L.; Roberts, Sally A.; Warren, Sanchia J. C.; Coombs, Geoffrey W.; Tan, Hui-Leen; Gao, Wei; Johnson, Paul D. R.; Howden, Benjamin P.

    2014-01-01

    An elevated vancomycin MIC is associated with poor outcomes in Staphylococcus aureus bacteremia (SAB) and is reported in patients with methicillin-susceptible S. aureus (MSSA) bacteremia in the absence of vancomycin treatment. Here, using DNA microarray and phenotype analysis, we investigated the genetic predictors and accessory gene regulator (agr) function and their relationship with elevated vancomycin MIC using blood culture isolates from a multicenter binational cohort of patients with SAB. Specific clonal complexes were associated with elevated (clonal complex 8 [CC8] [P < 0.001]) or low (CC22 [P < 0.001], CC88 [P < 0.001], and CC188 [P = 0.002]) vancomycin MIC. agr dysfunction (P = 0.014) or agr genotype II (P = 0.043) were also associated with an elevated vancomycin MIC. Specific resistance and virulence genes were also linked to an elevated vancomycin MIC, including blaZ (P = 0.002), sea (P < 0.001), clfA (P < 0.001), splA (P = 0.001), and the arginine catabolic mobile element (ACME) locus (P = 0.02). These data suggest that inherent organism characteristics may explain the link between elevated vancomycin MICs and poor outcomes in patients with SAB, regardless of the antibiotic treatment received. A consideration of clonal specificity should be included in future research when attempting to ascertain treatment effects or clinical outcomes. PMID:25031442

  10. Multilocus Sequence Analysis of Nectar Pseudomonads Reveals High Genetic Diversity and Contrasting Recombination Patterns

    PubMed Central

    Álvarez-Pérez, Sergio; de Vega, Clara; Herrera, Carlos M.

    2013-01-01

    The genetic and evolutionary relationships among floral nectar-dwelling Pseudomonas ‘sensu stricto’ isolates associated to South African and Mediterranean plants were investigated by multilocus sequence analysis (MLSA) of four core housekeeping genes (rrs, gyrB, rpoB and rpoD). A total of 35 different sequence types were found for the 38 nectar bacterial isolates characterised. Phylogenetic analyses resulted in the identification of three main clades [nectar groups (NGs) 1, 2 and 3] of nectar pseudomonads, which were closely related to five intrageneric groups: Pseudomonas oryzihabitans (NG 1); P. fluorescens, P. lutea and P. syringae (NG 2); and P. rhizosphaerae (NG 3). Linkage disequilibrium analysis pointed to a mostly clonal population structure, even when the analysis was restricted to isolates from the same floristic region or belonging to the same NG. Nevertheless, signatures of recombination were observed for NG 3, which exclusively included isolates retrieved from the floral nectar of insect-pollinated Mediterranean plants. In contrast, the other two NGs comprised both South African and Mediterranean isolates. Analyses relating diversification to floristic region and pollinator type revealed that there has been more unique evolution of the nectar pseudomonads within the Mediterranean region than would be expected by chance. This is the first work analysing the sequence of multiple loci to reveal geno- and ecotypes of nectar bacteria. PMID:24116076

  11. High-Performance Single Cell Genetic Analysis Using Microfluidic Emulsion Generator Arrays

    E-print Network

    California at Berkeley, University of

    ) Primary Contact & Position Primary Contact E-mail Primary Contact Cell Phone Secondary Organization Name (if applicable) Secondary Contact & Position Secondary Contact E-mail Secondary Contact Cell Phone Provide Frontier Fiesta Sponsorship Talent Show/Showcase Variety Show Joe Koppel MilitaryAppreciation 5k

  12. Identifying genetic relatives without compromising privacy

    PubMed Central

    He, Dan; Furlotte, Nicholas A.; Hormozdiari, Farhad; Joo, Jong Wha J.; Wadia, Akshay; Ostrovsky, Rafail; Sahai, Amit; Eskin, Eleazar

    2014-01-01

    The development of high-throughput genomic technologies has impacted many areas of genetic research. While many applications of these technologies focus on the discovery of genes involved in disease from population samples, applications of genomic technologies to an individual’s genome or personal genomics have recently gained much interest. One such application is the identification of relatives from genetic data. In this application, genetic information from a set of individuals is collected in a database, and each pair of individuals is compared in order to identify genetic relatives. An inherent issue that arises in the identification of relatives is privacy. In this article, we propose a method for identifying genetic relatives without compromising privacy by taking advantage of novel cryptographic techniques customized for secure and private comparison of genetic information. We demonstrate the utility of these techniques by allowing a pair of individuals to discover whether or not they are related without compromising their genetic information or revealing it to a third party. The idea is that individuals only share enough special-purpose cryptographically protected information with each other to identify whether or not they are relatives, but not enough to expose any information about their genomes. We show in HapMap and 1000 Genomes data that our method can recover first- and second-order genetic relationships and, through simulations, show that our method can identify relationships as distant as third cousins while preserving privacy. PMID:24614977

  13. Genetic Counseling

    MedlinePLUS

    ... this page It's been added to your dashboard . Genetic counseling Genetic counseling is a service to help ... child care and genetic testing. Who should get genetic counseling? Anyone who has unanswered questions about origins ...

  14. Sequence-tagged high-density genetic maps of Zoysia japonica provide insights into genome evolution in Chloridoideae.

    PubMed

    Wang, Fangfang; Singh, Ratnesh; Genovesi, Anthony D; Wai, Ching Man; Huang, Xiaoen; Chandra, Ambika; Yu, Qingyi

    2015-06-01

    Zoysiagrass (Zoysia spp.), belonging to the genus Zoysia in the subfamily Chloridoideae, is widely used in domestic lawns, sports fields and as forage. We constructed high-density genetic maps of Zoysia japonica using a restriction site-associated DNA sequencing (RAD-Seq) approach and an F1 mapping population derived from a cross between 'Carrizo' and 'El Toro'. Two linkage maps were constructed, one for each of the parents. A map consisting of 2408 RAD markers distributed on 21 linkage groups was constructed for 'Carrizo'. Another map with 1230 RAD markers mapped on 20 linkage groups was constructed for 'El Toro'. The average distance between adjacent markers of the two maps was at 0.56 and 1.4 cM, respectively. Comparative genomics analysis was carried out among zoysiagrass, rice and sorghum genomes and a highly conserved collinearity in the gene order was observed among the three genomes. Chromosome collinearity was disrupted at centromeric regions for each chromosome pair between zoysiagrass and sorghum genomes. However, no obvious synteny gaps were observed across the centromeric regions between zoysiagrass and rice genomes. Two homologous chromosomes for each of the 10 sorghum chromosomes were found in the zoysiagrass genome, indicating an allotetraploid origin for zoysiagrass. The reduction of the basic chromosome number from 12 to 10 in chloridoids and panicoids took place via independent single-step nested chromosome fusion events after the two subfamilies diverged from a common ancestor. The genetic maps will assist in genome sequence assembly, targeted gene isolation and comparative genomic analyses among grasses. PMID:25846381

  15. High prevalence and genetic diversity of porcine bocaviruses in pigs in the USA, and identification of multiple novel porcine bocaviruses.

    PubMed

    Jiang, Yong-Hou; Xiao, Chao-Ting; Yin, Shuang-Hui; Gerber, Priscilla F; Halbur, Patrick G; Opriessnig, Tanja

    2014-02-01

    Viruses in the genus Bocavirus are associated with respiratory and enteric disease in dogs and cattle. In addition, novel porcine bocaviruses (PBoVs) have been identified in domestic and wild pigs in recent years, but are of unknown relevance to date. The objectives of this study were to determine the prevalence ra tes and genetic diversity of PBoVs in pigs in the USA. Using newly established multiplex real-time PCR assays, 385 lung, lymph node, serum and faecal samples from pigs with various disease conditions were investigated. A high PBoV prevalence rate ranging from 21.3 to 50.8 % was identified in the investigated samples and often two or more PBoV species were detected in the same sample. Cloning and sequencing analysis of the partial non-structural protein NS1 and the capsid proteins VP1 and VP2 of DNA samples positive for PBoV groups 1 (n = 6), 2 (n = 16) and 3 (n = 42), including subgroups 3A, 3B or 3C, revealed a high genetic diversity especially for the PBoV G3 VP2 gene, whereas the PBoV group 1 VP1 gene displayed a low nucleotide polymorphism. Using primer walking, 18 partial or nearly complete genomes of PBoVs were obtained and six of the 18 nearly complete genomes represented novel PBoV species. Recombination analysis using partial NS1, VP1 and VP2 genes and the nearly complete genomes indicated possible recombination events within and between PBoVs. Further studies will be required to reveal the possible pathogenic role of these diverse PBoVs. PMID:24243729

  16. Genome-wide polymorphisms show unexpected targets of natural selection

    PubMed Central

    Pespeni, Melissa H.; Garfield, David A.; Manier, Mollie K.; Palumbi, Stephen R.

    2012-01-01

    Natural selection can act on all the expressed genes of an individual, leaving signatures of genetic differentiation or diversity at many loci across the genome. New power to assay these genome-wide effects of selection comes from associating multi-locus patterns of polymorphism with gene expression and function. Here, we performed one of the first genome-wide surveys in a marine species, comparing purple sea urchins, Strongylocentrotus purpuratus, from two distant locations along the species' wide latitudinal range. We examined 9112 polymorphic loci from upstream non-coding and coding regions of genes for signatures of selection with respect to gene function and tissue- and ontogenetic gene expression. We found that genetic differentiation (FST) varied significantly across functional gene classes. The strongest enrichment occurred in the upstream regions of E3 ligase genes, enzymes known to regulate protein abundance during development and environmental stress. We found enrichment for high heterozygosity in genes directly involved in immune response, particularly NALP genes, which mediate pro-inflammatory signals during bacterial infection. We also found higher heterozygosity in immune genes in the southern population, where disease incidence and pathogen diversity are greater. Similar to the major histocompatibility complex in mammals, balancing selection may enhance genetic diversity in the innate immune system genes of this invertebrate. Overall, our results show that how genome-wide polymorphism data coupled with growing databases on gene function and expression can combine to detect otherwise hidden signals of selection in natural populations. PMID:21993504

  17. High prevalence of genetic variants previously associated with LQT syndrome in new exome data.

    PubMed

    Refsgaard, Lena; Holst, Anders G; Sadjadieh, Golnaz; Haunsř, Stig; Nielsen, Jonas B; Olesen, Morten S

    2012-08-01

    To date, hundreds of variants in 13 genes have been associated with long QT syndrome (LQTS). The prevalence of LQTS is estimated to be between 1:2000 and 1:5000. The knowledge of genetic variation in the general population has until recently been limited, but newly published data from NHLBI GO Exome Sequencing Project (ESP) has provided important knowledge on this topic. We aimed to investigate the prevalence of previously LQTS-associated variants in ESP (5400 individuals), in order to identify possible false-positive LQTS variants. With this aim, we performed a search for previously published LQTS-associated variants in ESP. In addition, a PolyPhen-2 prediction was conducted, and the four most prevalent LQTS-associated variants with significant functional effects present in ESP were genotyped in a second control population. We identified 33 missense variants previously associated with LQTS in ESP. These 33 variants affected 173 alleles and this corresponded to a LQTS prevalence of 1:31 in the ESP population. PolyPhen-2 predicted 30% of the 33 variants present in ESP to be benign compared with 13% among LQTS-associated variants not present in ESP (P=0.019). Genotyping of the four variants KCNH2 P347S; SCN5A: S216L, V1951L; and CAV3 T78M in the control population (n=704) revealed prevalences comparable to those of ESP. Thus, we identified a much higher prevalence of previously LQTS-associated variants than expected in exome data from population studies. Great caution regarding the possible disease causation of some of these variants has to be taken, especially when used for risk stratification in family members. PMID:22378279

  18. High prevalence of genetic variants previously associated with LQT syndrome in new exome data

    PubMed Central

    Refsgaard, Lena; Holst, Anders G; Sadjadieh, Golnaz; Haunsř, Stig; Nielsen, Jonas B; Olesen, Morten S

    2012-01-01

    To date, hundreds of variants in 13 genes have been associated with long QT syndrome (LQTS). The prevalence of LQTS is estimated to be between 1:2000 and 1:5000. The knowledge of genetic variation in the general population has until recently been limited, but newly published data from NHLBI GO Exome Sequencing Project (ESP) has provided important knowledge on this topic. We aimed to investigate the prevalence of previously LQTS-associated variants in ESP (5400 individuals), in order to identify possible false-positive LQTS variants. With this aim, we performed a search for previously published LQTS-associated variants in ESP. In addition, a PolyPhen-2 prediction was conducted, and the four most prevalent LQTS-associated variants with significant functional effects present in ESP were genotyped in a second control population. We identified 33 missense variants previously associated with LQTS in ESP. These 33 variants affected 173 alleles and this corresponded to a LQTS prevalence of 1:31 in the ESP population. PolyPhen-2 predicted 30% of the 33 variants present in ESP to be benign compared with 13% among LQTS-associated variants not present in ESP (P=0.019). Genotyping of the four variants KCNH2 P347S; SCN5A: S216L, V1951L; and CAV3 T78M in the control population (n=704) revealed prevalences comparable to those of ESP. Thus, we identified a much higher prevalence of previously LQTS-associated variants than expected in exome data from population studies. Great caution regarding the possible disease causation of some of these variants has to be taken, especially when used for risk stratification in family members. PMID:22378279

  19. Medical genetics

    SciTech Connect

    Nora, J.J.; Fraser, F.C.

    1989-01-01

    This book presents a discussion of medical genetics for the practitioner treating or counseling patients with genetic disease. It includes a discussion of the relationship of heredity and diseases, the chromosomal basis for heredity, gene frequencies, and genetics of development and maldevelopment. The authors also focus on teratology, somatic cell genetics, genetics and cancer, genetics of behavior.

  20. Genetic interest assessment

    NASA Astrophysics Data System (ADS)

    Doughney, Erin

    Genetics is becoming increasingly integrated into peoples' lives. Different measures have been taken to try and better genetics education. This thesis examined undergraduate students at the University of North Texas not majoring in the life sciences interest in genetic concepts through the means of a Likert style survey. ANOVA analysis showed there was variation amongst the interest level in different genetic concepts. In addition age and lecture were also analyzed as contributing factors to students' interest. Both age and lecture were evaluated to see if they contributed to the interest of students in genetic concepts and neither showed statistical significance. The Genetic Interest Assessment (GIA) serves to help mediate the gap between genetic curriculum and students' interest.

  1. An automatic scanning method for high throughput microscopic system to facilitate medical genetic diagnosis: an initial study

    NASA Astrophysics Data System (ADS)

    Qiu, Yuchen; Chen, Xiaodong; Li, Zheng; Li, Yuhua; Chen, Wei R.; Zheng, Bin; Li, Shibo; Liu, Hong

    2012-03-01

    The purpose of this paper is to report a new automatic scanning scheme for high throughput microscopic systems aiming to facilitate disease diagnosis in genetic laboratories. To minimize the impact of the random vibration and mechanical drifting of the scanning stage in microscopic image acquisition, auto-focusing operations are usually applied repeatedly during the scanning process. Such methods ensure the acquisition of well focused images for clinical diagnosis, but are time consuming. The technique investigated in this preliminary study applies the auto-focusing operations at a limited number of locations on the slide. For the rest of the imaging field, the focusing position is quickly adjusted through linear interpolation. In this initial validation study, blood pathological slides containing both metaphase and interphase cells are scanned. For a selected area of 6.9mm×6.9mm, a number of 2×2, 3×2, 3×3, and 4×4 positions are evenly sampled for auto-focusing operations. Respectively, 25, 29, 40, and 41 clinically meaningful cells are identified for each sampling scheme. For the specific case investigated, the results demonstrate that the 4 position auto-focusing scheme could obtain the adequate number of clinically meaningful cells for the diagnosis. The schemes with more auto-focusing operations provide an option for high reliability diagnosis when clinically necessary. More comprehensive research is planned, and that may lead to optimal design of trade-off for developing the scanning scheme of the high throughput microscopic systems.

  2. Dispersal and genetic structure in the American marten, Martes americana.

    PubMed

    Broquet, T; Johnson, C A; Petit, E; Thompson, I; Burel, F; Fryxell, J M

    2006-05-01

    Natal dispersal in a vagile carnivore, the American marten (Martes americana), was studied by comparing radio-tracking data and microsatellite genetic structure in two populations occupying contrasting habitats. The genetic differentiation determined among groups of individuals using F(ST) indices appeared to be weak in both landscapes, and showed no increase with geographical distance. Genetic structure investigated using pairwise genetic distances between individuals conversely showed a pattern of isolation by distance (IBD), but only in the population occurring in a homogeneous high-quality habitat, therefore showing the advantage of individual-based analyses in detecting within-population processes and local landscape effects. The telemetry study of juveniles revealed a leptokurtic distribution of dispersal distances in both populations, and estimates of the mean squared parent-offspring axial distance (sigma2) inferred both from the genetic pattern of IBD and from the radio-tracking survey showed that most juveniles make little contribution to gene flow. PMID:16629821

  3. Serotonin release in the caudal nidopallium of adult laying hens genetically selected for high and low feather pecking behavior: an in vivo microdialysis study.

    PubMed

    Kops, Marjolein S; Kjaer, Joergen B; Güntürkün, Onur; Westphal, Koen G C; Korte-Bouws, Gerdien A H; Olivier, Berend; Bolhuis, J Elizabeth; Korte, S Mechiel

    2014-07-15

    Severe feather pecking (FP) is a detrimental behavior causing welfare problems in laying hens. Divergent genetic selection for FP in White Leghorns resulted in strong differences in FP incidences between lines. More recently, it was shown that the high FP (HFP) birds have increased locomotor activity as compared to hens of the low FP (LFP) line, but whether these lines differ in central serotonin (5-hydroxytryptamine, 5-HT) release is unknown. We compared baseline release levels of central 5-HT, and the metabolite 5-HIAA in the limbic and prefrontal subcomponents of the caudal nidopallium by in vivo microdialysis in adult HFP and LFP laying hens from the ninth generation of selection. A single subcutaneous d-fenfluramine injection (0.5 mg/kg) was given to release neuronal serotonin in order to investigate presynaptic storage capacity. The present study shows that HFP hens had higher baseline levels of 5-HT in the caudal nidopallium as compared to LFP laying hens. Remarkably, no differences in plasma tryptophan levels (precursor of 5-HT) between the lines were observed. d-fenfluramine increased 5-HT levels in both lines similarly indirectly suggesting that presynaptic storage capacity was the same. The present study shows that HFP hens release more 5-HT under baseline conditions in the caudal nidopallium as compared to the LFP birds. This suggests that HFP hens are characterized by a higher tonic 5-HT release. PMID:24720936

  4. Isolation and characterization of nine microsatellite markers from Coffea arabica L., showing wide cross-species amplifications

    Microsoft Academic Search

    A. Baruah; V. Naik; P. S. Hendre; R. Rajkumar; P. Rajendrakumar; R. K. Aggarwal

    2003-01-01

    Genetic improvement of coffee ( Coffea arabica L.) is constrained by low genetic diversity and lack of genetic markers, suitable screening tools, information on the genetic make- up of available gene pool and long generation time. In this context, use of DNA markers such as microsatellites that provide high genetic-resolution becomes highly desirable. Here, we report the development of nine

  5. Genetic characterisation of Toxoplasma gondii in wildlife from North America revealed widespread and high prevalence of the fourth clonal type

    USGS Publications Warehouse

    Dubey, J.P.; Velmurugan, G.V.; Ragendran, C.; Yabsley, M.J.; Thomas, N.J.; Beckmen, K.B.; Sinnett, D.; Ruid, D.; Hart, J.; Fair, P.A.; McFee, W.E.; Shearn-Bochsler, V.; Kwok, O.C.H.; Ferreira, L.R.; Choudhary, S.; Faria, E.B.; Zhou, H.; Felix, T.A.; Su, C.

    2011-01-01

    Little is known of the genetic diversity of Toxoplasma gondii circulating in wildlife. In the present study wild animals, from the USA were examined for T. gondii infection. Tissues of naturally exposed animals were bioassayed in mice for isolation of viable parasites. Viable T. gondii was isolated from 31 animals including, to our knowledge for the first time, from a bald eagle (Haliaeetus leucocephalus), five gray wolves (Canis lupus), a woodrat (Neotoma micropus), and five Arctic foxes (Alopex lagopus). Additionally, 66 T. gondii isolates obtained previously, but not genetically characterised, were revived in mice. Toxoplasma gondii DNA isolated from these 97 samples (31+66) was characterised using 11 PCR-restriction fragment length polymorphism (RFLP) markers (SAG1, 5'- and 3'-SAG2, alt.SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1 and Apico). A total of 95 isolates were successfully genotyped. In addition to clonal Types II, and III, 12 different genotypes were found. These genotype data were combined with 74 T. gondii isolates previously characterised from wildlife from North America and a composite data set of 169 isolates comprised 22 genotypes, including clonal Types II, III and 20 atypical genotypes. Phylogenetic network analysis showed limited diversity with dominance of a recently designated fourth clonal type (Type 12) in North America, followed by the Type II and III lineages. These three major lineages together accounted for 85% of strains in North America. The Type 12 lineage includes previously identified Type A and X strains from sea otters. This study revealed that the Type 12 lineage accounts for 46.7% (79/169) of isolates and is dominant in wildlife of North America. No clonal Type I strain was identified among these wildlife isolates. These results suggest that T. gondii strains in wildlife from North America have limited diversity, with the occurrence of only a few major clonal types.

  6. Genetic overlap of schizophrenia and bipolar disorder in a high-density linkage survey in the Portuguese Island population.

    PubMed

    Fanous, Ayman H; Middleton, Frank A; Gentile, Karen; Amdur, Richard L; Maher, Brion S; Zhao, Zhongming; Sun, Jingchun; Medeiros, Helena; Carvalho, Celia; Ferreira, Susana R; Macedo, Antonio; Knowles, James A; Azevedo, Maria H; Pato, Michele T; Pato, Carlos N

    2012-06-01

    Recent family and genome-wide association studies strongly suggest shared genetic risk factors for schizophrenia (SZ) and bipolar disorder (BP). However, linkage studies have not been used to test for statistically significant genome-wide overlap between them. Forty-seven Portuguese families with sibpairs concordant for SZ, BP, or psychosis (PSY, which includes either SZ or psychotic BP) were genotyped for over 57,000 markers using the Affymetrix 50K Xba SNP array. NPL and Kong and Cox LOD scores were calculated in Merlin for all three phenotypes. Empirical significance was determined using 1,000 gene-dropping simulations. Significance of genome-wide genetic overlap between SZ and BP was determined by the number of simulated BP scans having the same number of loci jointly linked with the real SZ scan, and vice versa. For all three phenotypes, a number of regions previously linked in this sample remained so. For BP, chromosome 1p36 achieved significance (11.54-15.71 MB, LOD = 3.51), whereas it was not even suggestively linked at lower marker densities, as did chromosome 11q14.1 (89.32-90.15 MB, NPL = 4.15). Four chromosomes had loci at which both SZ and BP had NPL ? 1.98, which was more than would be expected by chance (empirical P = 0.01 using simulated SZ scans; 0.07 using simulated BP scans), although they did not necessarily meet criteria for suggestive linkage individually. These results suggest that high-density marker maps may provide greater power and precision in linkage studies than lower density maps. They also further support the hypothesis that SZ and BP share at least some risk alleles. PMID:22461138

  7. A genetic algorithm for the design space exploration of datapaths during high-level synthesis

    Microsoft Academic Search

    Vyas Krishnan; Srinivas Katkoori

    2006-01-01

    High-level synthesis is comprised of interdependent tasks such as scheduling, allocation, and module selection. For today's very large-scale integration (VLSI) designs, the cost of solving the combined scheduling, allocation, and module selection problem by exhaustive search is prohibitive. However, to meet design objectives, an extensive design space exploration is often critical to obtaining superior designs. We present a framework for

  8. Solvent-free liquid crystals and liquids based on genetically engineered supercharged polypeptides with high elasticity.

    PubMed

    Liu, Kai; Pesce, Diego; Ma, Chao; Tuchband, Michael; Shuai, Min; Chen, Dong; Su, Juanjuan; Liu, Qing; Gerasimov, Jennifer Y; Kolbe, Anke; Zajaczkowski, Wojciech; Pisula, Wojciech; Müllen, Klaus; Clark, Noel A; Herrmann, Andreas

    2015-04-17

    A series of solvent-free elastin-like polypeptide liquid crystals and liquids are developed by electrostatic complexation of supercharged elastin-like polypeptides with surfactants. The smectic mesophases exhibit a high elasticity and the values can be easily tuned by varying the alkyl chain lengths of the surfactants or the lengths of the elastin-like polypeptides. PMID:25732045

  9. High Genetic Diversity of Nontypeable Haemophilus influenzae Isolates from Two Children Attending a Day Care Center?

    PubMed Central

    LaCross, Nathan C.; Marrs, Carl F.; Patel, Mayuri; Sandstedt, Sara A.; Gilsdorf, Janet R.

    2008-01-01

    Twenty-one nontypeable Haemophilus influenzae (NTHi) isolates from the throats of two healthy children were genotyped by multilocus sequence typing. Nine unique sequence types (STs) were identified. These STs were scattered throughout the phylogenetic tree of reported NTHi STs, demonstrating the high level of NTHi diversity found in colonized children. PMID:18845825

  10. Genetically predisposed offspring with schizotypal features: An ultra high-risk group for schizophrenia?

    Microsoft Academic Search

    Vaibhav A. Diwadkar; Debra M. Montrose; Diana Dworakowski; John A. Sweeney; Matcheri S. Keshavan

    2006-01-01

    Biomarkers proposed in the schizophrenia diathesis have included neurocognitive deficits in domains such as working memory that implicate prefrontal systems. However, the relationship between these biomarkers and psychopathological markers such as schizotypy has not been systematically assessed, particularly in adolescent offspring of schizophrenia patients. Convergence between these markers may identify individuals at especially high risk for schizophrenia. In the current

  11. High genetic differentiation among remnant populations of the endangered Caesalpinia echinata Lam. (Leguminosae-Caesalpinioideae)

    Microsoft Academic Search

    M. A. CARDOSO; J. PROVAN; W. POWELL; P. C. G. FERREIRA; D. E. DE OLIVEIRA

    1998-01-01

    Forest fragments along the Atlantic coastland of Brazil have been highly impacted by extensive human activities for the last 400 years. Caesalpinia echinata (Leguminosae- Caesalpinioideae), brazilwood, was overexploited during this period due to its economi- cal importance as a dye. As a result, the species has become endangered and today its total population size is very restricted. We have assessed

  12. Increasing Cottonseed Utilization Through Breeding and Genetic Engineering to Produce High Levels of (+)-Gossypol in Seed

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cottonseed is composed of ~22.5% of high quality protein. The estimate of world cottonseed production for 2006 is over 42.5 million metric tons (National Agricultural Statistics Service, USDA, 2005), which translates to an estimated 9.56 million metric tons of protein available for use as a food/fe...

  13. High genetic diversity among Mycobacterium tuberculosis complex strains from Sierra Leone

    Microsoft Academic Search

    Susanne Homolka; Erik Post; Barbara Oberhauser; Abu Garawani George; Lars Westman; Foday Dafae; Sabine Rüsch-Gerdes; Stefan Niemann

    2008-01-01

    BACKGROUND: Among tuberculosis (TB) high incidence regions, Sub-Saharan Africa is particularly affected with approx. 1.6 million new cases every year. Besides this dramatic situation, data on the diversity of Mycobacterium tuberculosis complex (MTBC) strains causing this epidemic in this area are only sparsely available. Here we analyzed the population structure of strains from Sierra Leone with a special focus on

  14. Human genetics

    SciTech Connect

    Carlson, E.A.

    1984-01-01

    This text provides full and balanced coverage of the concepts requisite for a thorough understanding of human genetics. Applications to both the individual and society are integrated throughout the lively and personal narrative, and the essential principles of heredity are clearly presented to prepare students for informed participation in public controversies. High-interest, controversial topics, including recombinant DNA technology, oncogenes, embryo transfer, environmental mutagens and carcinogens, IQ testing, and eugenics encourage understanding of important social issues.

  15. Genetic Engineering

    Microsoft Academic Search

    J. F. Kreuze; J. P. T. Valkonen; M. Ghislain

    Genetic transformation through direct gene transfer methods holds promise for introducing novel traits to sweetpotato in cases\\u000a where no solutions by conventional breeding are available. This may be if the trait is not known in sweetpotato or it is governed\\u000a by complex inheritance. Sweetpotato is clonally propagated, highly heterozygous, polyploid and out-crossing – in other words,\\u000a a challenging crop to

  16. The Influence of Self-Efficacy Beliefs and Metacognitive Prompting on Genetics Problem Solving Ability among High School Students in Kenya

    ERIC Educational Resources Information Center

    Aurah, Catherine Muhonja

    2013-01-01

    Within the framework of social cognitive theory, the influence of self-efficacy beliefs and metacognitive prompting on genetics problem solving ability among high school students in Kenya was examined through a mixed methods research design. A quasi-experimental study, supplemented by focus group interviews, was conducted to investigate both the…

  17. 476. Human Mesenchymal Stem Cells Genetically Modified To Express High Levels of Erythropoietin Through Transfer of an Artificial Chromosome Engineered Using the ACE System

    Microsoft Academic Search

    Sandra Vanderbyl; Neil MacDonald; Tom Stodola; Adele Telenius; Sandra Stewart; Harry C. Ledebur; Carl F. Perez

    2004-01-01

    The ACE System is a versatile, reliable system for genetically modifying cell therapies, generating transgenic animals, and engineering mammalian cells for high expression of a recombinant protein. Key components of the ACE System include an artificial chromosome (Platform ACE) encoding multiple (>50) DNA site-specific integration sites (acceptor sites); a targeting vector (ACE Targeting Vector) encoding both a Platform ACE-specific DNA

  18. High-density genetic map construction and identification of a locus controlling weeping trait in an ornamental woody plant (Prunus mume Sieb. et Zucc)

    PubMed Central

    Zhang, Jie; Zhang, Qixiang; Cheng, Tangren; Yang, Weiru; Pan, Huitang; Zhong, Junjun; Huang, Long; Liu, Enze

    2015-01-01

    High-density genetic map is a valuable tool for fine mapping locus controlling a specific trait especially for perennial woody plants. In this study, we firstly constructed a high-density genetic map of mei (Prunus mume) using SLAF markers, developed by specific locus amplified fragment sequencing (SLAF-seq). The linkage map contains 8,007 markers, with a mean marker distance of 0.195 cM, making it the densest genetic map for the genus Prunus. Though weeping trees are used worldwide as landscape plants, little is known about weeping controlling gene(s) (Pl). To test the utility of the high-density genetic map, we did fine-scale mapping of this important ornamental trait. In total, three statistic methods were performed progressively based on the result of inheritance analysis. Quantitative trait loci (QTL) analysis initially revealed that a locus on linkage group 7 was strongly responsible for weeping trait. Mutmap-like strategy and extreme linkage analysis were then applied to fine map this locus within 1.14 cM. Bioinformatics analysis of the locus identified some candidate genes. The successful localization of weeping trait strongly indicates that the high-density map constructed using SLAF markers is a worthy reference for mapping important traits for woody plants. PMID:25776277

  19. Genetic Linkage Analysis of the Lesser Grain Borer Rhyzopertha dominica Identifies Two Loci That Confer High-Level Resistance to the Fumigant Phosphine

    Microsoft Academic Search

    David I. Schlipalius; Qiang Cheng; Paul E. B. Reilly; Patrick J. Collins; Paul R. Ebert

    High levels of inheritable resistance to phosphine in Rhyzopertha dominica have recently been detected in Australia and in an effort to isolate the genes responsible for resistance we have used random amplified DNA fingerprinting (RAF) to produce a genetic linkage map of R. dominica. The map consists of 94 dominant DNA markers with an average distance between markers of 4.6

  20. High-density genetic map construction and identification of a locus controlling weeping trait in an ornamental woody plant (Prunus mume Sieb. et Zucc).

    PubMed

    Zhang, Jie; Zhang, Qixiang; Cheng, Tangren; Yang, Weiru; Pan, Huitang; Zhong, Junjun; Huang, Long; Liu, Enze

    2015-06-01

    High-density genetic map is a valuable tool for fine mapping locus controlling a specific trait especially for perennial woody plants. In this study, we firstly constructed a high-density genetic map of mei (Prunus mume) using SLAF markers, developed by specific locus amplified fragment sequencing (SLAF-seq). The linkage map contains 8,007 markers, with a mean marker distance of 0.195 cM, making it the densest genetic map for the genus Prunus. Though weeping trees are used worldwide as landscape plants, little is known about weeping controlling gene(s) (Pl). To test the utility of the high-density genetic map, we did fine-scale mapping of this important ornamental trait. In total, three statistic methods were performed progressively based on the result of inheritance analysis. Quantitative trait loci (QTL) analysis initially revealed that a locus on linkage group 7 was strongly responsible for weeping trait. Mutmap-like strategy and extreme linkage analysis were then applied to fine map this locus within 1.14 cM. Bioinformatics analysis of the locus identified some candidate genes. The successful localization of weeping trait strongly indicates that the high-density map constructed using SLAF markers is a worthy reference for mapping important traits for woody plants. PMID:25776277