WorldWideScience

Sample records for loci high variation

  1. Population structure of African buffalo inferred from mtDNA sequences and microsatellite loci: high variation but low differentiation

    DEFF Research Database (Denmark)

    Simonsen, Bo Thisted; Siegismund, H R; Arctander, P

    1998-01-01

    The African buffalo (Syncerus caffer) is widespread throughout sub-Saharan Africa and is found in most major vegetation types, wherever permanent sources of water are available, making it physically able to disperse through a wide range of habitats. Despite this, the buffalo has been assumed...... and analysis of variation at six microsatellite loci among 11 localities in eastern and southern Africa. High levels of genetic variability were found, suggesting that reported severe population bottlenecks due to outbreak of rinderpest during the last century did not strongly reduce the genetic variability...

  2. Four loci explain 83% of size variation in the horse.

    Directory of Open Access Journals (Sweden)

    Shokouh Makvandi-Nejad

    Full Text Available Horse body size varies greatly due to intense selection within each breed. American Miniatures are less than one meter tall at the withers while Shires and Percherons can exceed two meters. The genetic basis for this variation is not known. We hypothesize that the breed population structure of the horse should simplify efforts to identify genes controlling size. In support of this, here we show with genome-wide association scans (GWAS that genetic variation at just four loci can explain the great majority of horse size variation. Unlike humans, which are naturally reproducing and possess many genetic variants with weak effects on size, we show that horses, like other domestic mammals, carry just a small number of size loci with alleles of large effect. Furthermore, three of our horse size loci contain the LCORL, HMGA2 and ZFAT genes that have previously been found to control human height. The LCORL/NCAPG locus is also implicated in cattle growth and HMGA2 is associated with dog size. Extreme size diversification is a hallmark of domestication. Our results in the horse, complemented by the prior work in cattle and dog, serve to pinpoint those very few genes that have played major roles in the rapid evolution of size during domestication.

  3. Sequencing of a patient with balanced chromosome abnormalities and neurodevelopmental disease identifies disruption of multiple high risk loci by structural variation.

    Directory of Open Access Journals (Sweden)

    Jonathon Blake

    Full Text Available Balanced chromosome abnormalities (BCAs occur at a high frequency in healthy and diseased individuals, but cost-efficient strategies to identify BCAs and evaluate whether they contribute to a phenotype have not yet become widespread. Here we apply genome-wide mate-pair library sequencing to characterize structural variation in a patient with unclear neurodevelopmental disease (NDD and complex de novo BCAs at the karyotype level. Nucleotide-level characterization of the clinically described BCA breakpoints revealed disruption of at least three NDD candidate genes (LINC00299, NUP205, PSMD14 that gave rise to abnormal mRNAs and could be assumed as disease-causing. However, unbiased genome-wide analysis of the sequencing data for cryptic structural variation was key to reveal an additional submicroscopic inversion that truncates the schizophrenia- and bipolar disorder-associated brain transcription factor ZNF804A as an equally likely NDD-driving gene. Deep sequencing of fluorescent-sorted wild-type and derivative chromosomes confirmed the clinically undetected BCA. Moreover, deep sequencing further validated a high accuracy of mate-pair library sequencing to detect structural variants larger than 10 kB, proposing that this approach is powerful for clinical-grade genome-wide structural variant detection. Our study supports previous evidence for a role of ZNF804A in NDD and highlights the need for a more comprehensive assessment of structural variation in karyotypically abnormal individuals and patients with neurocognitive disease to avoid diagnostic deception.

  4. Sequencing of a Patient with Balanced Chromosome Abnormalities and Neurodevelopmental Disease Identifies Disruption of Multiple High Risk Loci by Structural Variation

    Science.gov (United States)

    Blake, Jonathon; Riddell, Andrew; Theiss, Susanne; Gonzalez, Alexis Perez; Haase, Bettina; Jauch, Anna; Janssen, Johannes W. G.; Ibberson, David; Pavlinic, Dinko; Moog, Ute; Benes, Vladimir; Runz, Heiko

    2014-01-01

    Balanced chromosome abnormalities (BCAs) occur at a high frequency in healthy and diseased individuals, but cost-efficient strategies to identify BCAs and evaluate whether they contribute to a phenotype have not yet become widespread. Here we apply genome-wide mate-pair library sequencing to characterize structural variation in a patient with unclear neurodevelopmental disease (NDD) and complex de novo BCAs at the karyotype level. Nucleotide-level characterization of the clinically described BCA breakpoints revealed disruption of at least three NDD candidate genes (LINC00299, NUP205, PSMD14) that gave rise to abnormal mRNAs and could be assumed as disease-causing. However, unbiased genome-wide analysis of the sequencing data for cryptic structural variation was key to reveal an additional submicroscopic inversion that truncates the schizophrenia- and bipolar disorder-associated brain transcription factor ZNF804A as an equally likely NDD-driving gene. Deep sequencing of fluorescent-sorted wild-type and derivative chromosomes confirmed the clinically undetected BCA. Moreover, deep sequencing further validated a high accuracy of mate-pair library sequencing to detect structural variants larger than 10 kB, proposing that this approach is powerful for clinical-grade genome-wide structural variant detection. Our study supports previous evidence for a role of ZNF804A in NDD and highlights the need for a more comprehensive assessment of structural variation in karyotypically abnormal individuals and patients with neurocognitive disease to avoid diagnostic deception. PMID:24625750

  5. Genetic variation of twenty autosomal STR loci and evaluate the ...

    African Journals Online (AJOL)

    SAM

    2014-03-12

    Mar 12, 2014 ... the second objective of the study was to evaluate the importance of these loci for forensic genetic purposes. ... of discrimination values for all tested loci was from 75 to 96%; therefore, those loci can be safely used to establish a ..... lists the frequency distribution of individual alleles within a given genetic ...

  6. Standing genetic variation in contingency loci drives the rapid adaptation of Campylobacter jejuni to a novel host.

    Directory of Open Access Journals (Sweden)

    John P Jerome

    2011-01-01

    Full Text Available The genome of the food-borne pathogen Campylobacter jejuni contains multiple highly mutable sites, or contingency loci. It has been suggested that standing variation at these loci is a mechanism for rapid adaptation to a novel environment, but this phenomenon has not been shown experimentally. In previous work we showed that the virulence of C. jejuni NCTC11168 increased after serial passage through a C57BL/6 IL-10(-/- mouse model of campylobacteriosis. Here we sought to determine the genetic basis of this adaptation during passage. Re-sequencing of the 1.64 Mb genome to 200-500 X coverage allowed us to define variation in 23 contingency loci to an unprecedented depth both before and after in vivo adaptation. Mutations in the mouse-adapted C. jejuni were largely restricted to the homopolymeric tracts of thirteen contingency loci. These changes cause significant alterations in open reading frames of genes in surface structure biosynthesis loci and in genes with only putative functions. Several loci with open reading frame changes also had altered transcript abundance. The increase in specific phases of contingency loci during in vivo passage of C. jejuni, coupled with the observed virulence increase and the lack of other types of genetic changes, is the first experimental evidence that these variable regions play a significant role in C. jejuni adaptation and virulence in a novel host.

  7. Interactions Between SNP Alleles at Multiple Loci and Variation in Skin Pigmentation in 122 Caucasians

    Directory of Open Access Journals (Sweden)

    Sumiko Anno

    2007-01-01

    Full Text Available This study was undertaken to clarify the molecular basis for human skin color variation and the environmental adaptability to ultraviolet irradiation, with the ultimate goal of predicting the impact of changes in future environments on human health risk. One hundred twenty-two Caucasians living in Toledo, Ohio participated. Back and cheek skin were assayed for melanin as a quantitative trait marker. Buccal cell samples were collected and used for DNA extraction. DNA was used for SNP genotyping using the Masscode™ system, which entails two-step PCR amplification and a platform chemistry which allows cleavable mass spectrometry tags. The results show gene-gene interaction between SNP alleles at multiple loci (not necessarily on the same chromosome contributes to inter-individual skin color variation while suggesting a high probability of linkage disequilibrium. Confirmation of these findings requires further study with other ethic groups to analyze the associations between SNP alleles at multiple loci and human skin color variation. Our overarching goal is to use remote sensing data to clarify the interaction between atmospheric environments and SNP allelic frequency and investigate human adaptability to ultraviolet irradiation. Such information should greatly assist in the prediction of the health effects of future environmental changes such as ozone depletion and increased ultraviolet exposure. If such health effects are to some extent predictable, it might be possible to prepare for such changes in advance and thus reduce the extent of their impact.

  8. The effect of subdivision on variation at multi-allelic loci under balancing selection

    DEFF Research Database (Denmark)

    Schierup, M H; Vekemans, X; Charlesworth, D

    2000-01-01

    Simulations are used to investigate the expected pattern of variation at loci under different forms of multi-allelic balancing selection in a finite island model of a subdivided population. The objective is to evaluate the effect of restricted migration among demes on the distribution of polymorp......Simulations are used to investigate the expected pattern of variation at loci under different forms of multi-allelic balancing selection in a finite island model of a subdivided population. The objective is to evaluate the effect of restricted migration among demes on the distribution...

  9. Evidence of novel fine-scale structural variation at autism spectrum disorder candidate loci

    Directory of Open Access Journals (Sweden)

    Hedges Dale J

    2012-04-01

    Full Text Available Abstract Background Autism spectrum disorders (ASD represent a group of neurodevelopmental disorders characterized by a core set of social-communicative and behavioral impairments. Gamma-aminobutyric acid (GABA is the major inhibitory neurotransmitter in the brain, acting primarily via the GABA receptors (GABR. Multiple lines of evidence, including altered GABA and GABA receptor expression in autistic patients, indicate that the GABAergic system may be involved in the etiology of autism. Methods As copy number variations (CNVs, particularly rare and de novo CNVs, have now been implicated in ASD risk, we examined the GABA receptors and genes in related pathways for structural variation that may be associated with autism. We further extended our candidate gene set to include 19 genes and regions that had either been directly implicated in the autism literature or were directly related (via function or ancestry to these primary candidates. For the high resolution CNV screen we employed custom-designed 244 k comparative genomic hybridization (CGH arrays. Collectively, our probes spanned a total of 11 Mb of GABA-related and additional candidate regions with a density of approximately one probe every 200 nucleotides, allowing a theoretical resolution for detection of CNVs of approximately 1 kb or greater on average. One hundred and sixty-eight autism cases and 149 control individuals were screened for structural variants. Prioritized CNV events were confirmed using quantitative PCR, and confirmed loci were evaluated on an additional set of 170 cases and 170 control individuals that were not included in the original discovery set. Loci that remained interesting were subsequently screened via quantitative PCR on an additional set of 755 cases and 1,809 unaffected family members. Results Results include rare deletions in autistic individuals at JAKMIP1, NRXN1, Neuroligin4Y, OXTR, and ABAT. Common insertion/deletion polymorphisms were detected at several

  10. Genetic variation at loci controlling quality traits in spring wheat

    International Nuclear Information System (INIS)

    Ali, N.; Iqbal, M.; Asif, M.

    2013-01-01

    Selection for quality traits in bread wheat (Triticum aestivum L.) during early breeding generations requires quick analytical methods that need small grain samples. Marker assisted selection can be useful for the improvement of quality traits in wheat. The present study was conducted to screen 117 Pakistani adapted spring wheat varieties with DNA markers linked with genes controlling composition of low and high molecular weight glutenin subunits (LMW-GS and HMW-GS, respectively), starch viscosity, Polyphenol oxidase (PPO) activity and grain hardness. DNA fragments associated with the presence/absence of quality related genes were amplified using Polymerase chain reaction (PCR) and detected using agarose gel electrophoresis. Positive allele of beta-secalin, which indicates presence of 1B.1R translocation, was found in 77 (66%) varieties. The marker PPO05 was found in 30 (26%) varieties, indicating lower PPO activity. Grain hardness controlled by Pinb-D1b allele was present in 49 (42%) varieties. Allele Wx-B1b which confers superior noodle quality was found in 48 (41%) varieties. HMW-GS encoded by Glu-D1d allele that exerts a positive effect on dough strength was present in 115 (98%) varieties. LMW-GS alleles Glu-A3d and Glu-B3 were observed in 21 (18%) and 76 (65%) varieties, respectively. Results of the present study may help wheat breeders in selecting parents for improving desirable quality attributes of future wheat varieties. The varieties, identified having desirable quality genes, in this study can be used in the wheat breeding programs aiming to improve quality traits. Early generation marker assisted selection can help to efficiently utilize resources of a breeding program. (author)

  11. Genetic effects at pleiotropic loci are context-dependent with consequences for the maintenance of genetic variation in populations.

    Directory of Open Access Journals (Sweden)

    Heather A Lawson

    2011-09-01

    Full Text Available Context-dependent genetic effects, including genotype-by-environment and genotype-by-sex interactions, are a potential mechanism by which genetic variation of complex traits is maintained in populations. Pleiotropic genetic effects are also thought to play an important role in evolution, reflecting functional and developmental relationships among traits. We examine context-dependent genetic effects at pleiotropic loci associated with normal variation in multiple metabolic syndrome (MetS components (obesity, dyslipidemia, and diabetes-related traits. MetS prevalence is increasing in Western societies and, while environmental in origin, presents substantial variation in individual response. We identify 23 pleiotropic MetS quantitative trait loci (QTL in an F(16 advanced intercross between the LG/J and SM/J inbred mouse strains (Wustl:LG,SM-G16; n = 1002. Half of each family was fed a high-fat diet and half fed a low-fat diet; and additive, dominance, and parent-of-origin imprinting genotypic effects were examined in animals partitioned into sex, diet, and sex-by-diet cohorts. We examine the context-dependency of the underlying additive, dominance, and imprinting genetic effects of the traits associated with these pleiotropic QTL. Further, we examine sequence polymorphisms (SNPs between LG/J and SM/J as well as differential expression of positional candidate genes in these regions. We show that genetic associations are different in different sex, diet, and sex-by-diet settings. We also show that over- or underdominance and ecological cross-over interactions for single phenotypes may not be common, however multidimensional synthetic phenotypes at loci with pleiotropic effects can produce situations that favor the maintenance of genetic variation in populations. Our findings have important implications for evolution and the notion of personalized medicine.

  12. Novel association strategy with copy number variation for identifying new risk Loci of human diseases.

    Directory of Open Access Journals (Sweden)

    Xianfeng Chen

    2010-08-01

    Full Text Available Copy number variations (CNV are important causal genetic variations for human disease; however, the lack of a statistical model has impeded the systematic testing of CNVs associated with disease in large-scale cohort.Here, we developed a novel integrated strategy to test CNV-association in genome-wide case-control studies. We converted the single-nucleotide polymorphism (SNP signal to copy number states using a well-trained hidden Markov model. We mapped the susceptible CNV-loci through SNP site-specific testing to cope with the physiological complexity of CNVs. We also ensured the credibility of the associated CNVs through further window-based CNV-pattern clustering. Genome-wide data with seven diseases were used to test our strategy and, in total, we identified 36 new susceptible loci that are associated with CNVs for the seven diseases: 5 with bipolar disorder, 4 with coronary artery disease, 1 with Crohn's disease, 7 with hypertension, 9 with rheumatoid arthritis, 7 with type 1 diabetes and 3 with type 2 diabetes. Fifteen of these identified loci were validated through genotype-association and physiological function from previous studies, which provide further confidence for our results. Notably, the genes associated with bipolar disorder converged in the phosphoinositide/calcium signaling, a well-known affected pathway in bipolar disorder, which further supports that CNVs have impact on bipolar disorder.Our results demonstrated the effectiveness and robustness of our CNV-association analysis and provided an alternative avenue for discovering new associated loci of human diseases.

  13. High-density genotyping of immune loci in Koreans and Europeans identifies eight new rheumatoid arthritis risk loci.

    Science.gov (United States)

    Kim, Kwangwoo; Bang, So-Young; Lee, Hye-Soon; Cho, Soo-Kyung; Choi, Chan-Bum; Sung, Yoon-Kyoung; Kim, Tae-Hwan; Jun, Jae-Bum; Yoo, Dae Hyun; Kang, Young Mo; Kim, Seong-Kyu; Suh, Chang-Hee; Shim, Seung-Cheol; Lee, Shin-Seok; Lee, Jisoo; Chung, Won Tae; Choe, Jung-Yoon; Shin, Hyoung Doo; Lee, Jong-Young; Han, Bok-Ghee; Nath, Swapan K; Eyre, Steve; Bowes, John; Pappas, Dimitrios A; Kremer, Joel M; Gonzalez-Gay, Miguel A; Rodriguez-Rodriguez, Luis; Ärlestig, Lisbeth; Okada, Yukinori; Diogo, Dorothée; Liao, Katherine P; Karlson, Elizabeth W; Raychaudhuri, Soumya; Rantapää-Dahlqvist, Solbritt; Martin, Javier; Klareskog, Lars; Padyukov, Leonid; Gregersen, Peter K; Worthington, Jane; Greenberg, Jeffrey D; Plenge, Robert M; Bae, Sang-Cheol

    2015-03-01

    A highly polygenic aetiology and high degree of allele-sharing between ancestries have been well elucidated in genetic studies of rheumatoid arthritis. Recently, the high-density genotyping array Immunochip for immune disease loci identified 14 new rheumatoid arthritis risk loci among individuals of European ancestry. Here, we aimed to identify new rheumatoid arthritis risk loci using Korean-specific Immunochip data. We analysed Korean rheumatoid arthritis case-control samples using the Immunochip and genome-wide association studies (GWAS) array to search for new risk alleles of rheumatoid arthritis with anticitrullinated peptide antibodies. To increase power, we performed a meta-analysis of Korean data with previously published European Immunochip and GWAS data for a total sample size of 9299 Korean and 45,790 European case-control samples. We identified eight new rheumatoid arthritis susceptibility loci (TNFSF4, LBH, EOMES, ETS1-FLI1, COG6, RAD51B, UBASH3A and SYNGR1) that passed a genome-wide significance threshold (p<5×10(-8)), with evidence for three independent risk alleles at 1q25/TNFSF4. The risk alleles from the seven new loci except for the TNFSF4 locus (monomorphic in Koreans), together with risk alleles from previously established RA risk loci, exhibited a high correlation of effect sizes between ancestries. Further, we refined the number of single nucleotide polymorphisms (SNPs) that represent potentially causal variants through a trans-ethnic comparison of densely genotyped SNPs. This study demonstrates the advantage of dense-mapping and trans-ancestral analysis for identification of potentially causal SNPs. In addition, our findings support the importance of T cells in the pathogenesis and the fact of frequent overlap of risk loci among diverse autoimmune diseases. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

  14. Identification of the sequence variations of 15 autosomal STR loci in a Chinese population.

    Science.gov (United States)

    Chen, Wenjing; Cheng, Jianding; Ou, Xueling; Chen, Yong; Tong, Dayue; Sun, Hongyu

    2014-01-01

    DNA sequence variation including base(s) changes and insertion or deletion in the primer binding region may cause a null allele and, if this changes the length of the amplified fragment out of the allelic ladder, off-ladder (OL) alleles may be detected. In order to provide accurate and reliable DNA evidence for forensic DNA analysis, it is essential to clarify sequence variations in prevalently used STR loci. Suspected null alleles and OL alleles of PlowerPlex16® System from 21,934 unrelated Chinese individuals were verified by alternative systems and sequenced. A total of 17 cases with null alleles were identified, including 12 kinds of point mutations in 16 cases and a 19-base deletion in one case. The total frequency of null alleles was 7.751 × 10(-4). Eight hundred and forty-four OL alleles classified as being of 97 different kinds were observed at 15 STR loci of the PowerPlex®16 system except vWA. All the frequencies of OL alleles were under 0.01. Null alleles should be confirmed by alternative primers and OL alleles should be named appropriately. Particular attention should be paid to sequence variation, since incorrect designation could lead to false conclusions.

  15. A Set of Plastid Loci for Use in Multiplex Fragment Length Genotyping for Intraspecific Variation in Pinus (Pinaceae

    Directory of Open Access Journals (Sweden)

    Austin M. Wofford

    2014-04-01

    Full Text Available Premise of the study: Recently released Pinus plastome sequences support characterization of 15 plastid simple sequence repeat (cpSSR loci originally published for P. contorta and P. thunbergii. This allows selection of loci for single-tube PCR multiplexed genotyping in any subsection of the genus. Methods: Unique placement of primers and primer conservation across the genus were investigated, and a set of six loci were selected for single-tube multiplexing. We compared interspecific variation between cpSSRs and nucleotide sequences ofycf1 and tested intraspecific variation for cpSSRs using 911 samples in the P. ponderosa species complex. Results: The cpSSR loci contain mononucleotide and complex repeats with additional length variation in flanking regions. They are not located in hypervariable regions, and most primers are conserved across the genus. A single PCR per sample multiplexed for six loci yielded 45 alleles in 911 samples. Discussion: The protocol allows efficient genotyping of many samples. The cpSSR loci are too variable for Pinus phylogenies but are useful for the study of genetic structure within and among populations. The multiplex method could easily be extended to other plant groups by choosing primers for cpSSR loci in a plastome alignment for the target group.

  16. A set of plastid loci for use in multiplex fragment length genotyping for intraspecific variation in Pinus (Pinaceae)1

    Science.gov (United States)

    Wofford, Austin M.; Finch, Kristen; Bigott, Adam; Willyard, Ann

    2014-01-01

    • Premise of the study: Recently released Pinus plastome sequences support characterization of 15 plastid simple sequence repeat (cpSSR) loci originally published for P. contorta and P. thunbergii. This allows selection of loci for single-tube PCR multiplexed genotyping in any subsection of the genus. • Methods: Unique placement of primers and primer conservation across the genus were investigated, and a set of six loci were selected for single-tube multiplexing. We compared interspecific variation between cpSSRs and nucleotide sequences of ycf1 and tested intraspecific variation for cpSSRs using 911 samples in the P. ponderosa species complex. • Results: The cpSSR loci contain mononucleotide and complex repeats with additional length variation in flanking regions. They are not located in hypervariable regions, and most primers are conserved across the genus. A single PCR per sample multiplexed for six loci yielded 45 alleles in 911 samples. • Discussion: The protocol allows efficient genotyping of many samples. The cpSSR loci are too variable for Pinus phylogenies but are useful for the study of genetic structure within and among populations. The multiplex method could easily be extended to other plant groups by choosing primers for cpSSR loci in a plastome alignment for the target group. PMID:25202625

  17. Variation in sperm displacement and its association with accessory gland protein loci in Drosophila melanogaster.

    Science.gov (United States)

    Clark, A G; Aguadé, M; Prout, T; Harshman, L G; Langley, C H

    1995-01-01

    Genes that influence mating and/or fertilization success may be targets for strong natural selection. If females remate frequently relative to the duration of sperm storage and rate of sperm use, sperm displacement may be an important component of male reproductive success. Although it has long been known that mutant laboratory stocks of Drosophila differ in sperm displacement, the magnitude of the naturally occurring genetic variation in this character has not been systematically quantified. Here we report the results of a screen for variation in sperm displacement among 152 lines of Drosophilia melanogaster that were made homozygous for second and/or third chromosomes recovered from natural populations. Sperm displacement was assayed by scoring the progeny of cn;bw females that had been mated sequentially to cn;bw and tested males in either order. Highly significant differences were seen in both the ability to displace sperm that is resident in the female's reproductive tract and in the ability to resist displacement by subsequent sperm. Most lines exhibited nearly complete displacement, having nearly all progeny sired by the second male, but several lines had as few as half the progeny fathered by the second male. Lines that were identified in the screen for naturally occurring variation in sperm displacement were also characterized for single-strand conformation polymorphisms (SSCP) at seven accessory gland protein (Acp) genes, Glucose dehydrogenase (Gld), and Esterase-6 (Est-6). Acp genes encode proteins that are in some cases known to be transmitted to the female in the seminal fluid and are likely candidates for genes that might mediate the phenomenon of sperm displacement. Significant associations were found between particular Acp alleles at four different loci (Acp26Aa/Ab, Acp29B, Acp36DE and Acp53E) and the ability of males to resist displacement by subsequent sperm. There was no correlation between the ability to displace resident sperm and the ability

  18. Adaptive genetic variation at three loci in South African vervet monkeys (Chlorocebus pygerythrus and the role of selection within primates

    Directory of Open Access Journals (Sweden)

    Willem G. Coetzer

    2018-06-01

    Full Text Available Vervet monkeys (Chlorocebus pygerythrus are one of the most widely distributed non-human primate species found in South Africa. They occur across all the South African provinces, inhabiting a large variety of habitats. These habitats vary sufficiently that it can be assumed that various factors such as pathogen diversity could influence populations in different ways. In turn, these factors could lead to varied levels of selection at specific fitness linked loci. The Toll-like receptor (TLR gene family, which play an integral role in vertebrate innate immunity, is a group of fitness linked loci which has been the focus of much research. In this study, we assessed the level of genetic variation at partial sequences of two TLR loci (TLR4 and 7 and a reproductively linked gene, acrosin (ACR, across the different habitat types within the vervet monkey distribution range. Gene variation and selection estimates were also made among 11–21 primate species. Low levels of genetic variation for all three gene regions were observed within vervet monkeys, with only two polymorphic sites identified for TLR4, three sites for TLR7 and one site for ACR. TLR7 variation was positively correlated with high mean annual rainfall, which was linked to increased pathogen abundance. The observed genetic variation at TLR4 might have been influenced by numerous factors including pathogens and climatic conditions. The ACR exonic regions showed no variation in vervet monkeys, which could point to the occurrence of a selective sweep. The TLR4 and TLR7 results for the among primate analyses was mostly in line with previous studies, indicating a higher rate of evolution for TLR4. Within primates, ACR coding regions also showed signs of positive selection, which was congruent with previous reports on mammals. Important additional information to the already existing vervet monkey knowledge base was gained from this study, which can guide future research projects on this highly

  19. Genetic variation and selection of MHC class I loci differ in two congeneric frogs.

    Science.gov (United States)

    Kiemnec-Tyburczy, Karen M; Tracy, Karen E; Lips, Karen R; Zamudio, Kelly R

    2018-04-01

    Major histocompatibility complex (MHC) genes encode proteins in the acquired immune response pathway that often show distinctive selection-driven patterns in wild vertebrate populations. We examined genetic variation and signatures of selection in the MHC class I alpha 1 (A1)- and alpha 2 (A2)-domain encoding exons of two frog congeners [Agalychnis callidryas (n = 20) and A. lemur (n = 20)] from a single locality in Panama. We also investigated how historical demographic processes may have impacted MHC genetic diversity by analyzing a neutral mitochondrial marker. We found that both MHC domains were highly variable in both species, with both species likely expressing three loci. Our analyses revealed different signatures of selection between the two species, most notably that the A. callidryas A2 domain had experienced positive selection while the A2 domain of A. lemur had not. Diversifying selection acted on the same number of A1 and A2 allelic lineages, but on a higher percentage of A1 sites compared to A2 sites. Neutrality tests of mitochondrial haplotypes predominately indicated that the two species were at genetic equilibrium when the samples were collected. In addition, two historical tests of demography indicated both species have had relatively stable population sizes over the past 100,000 years; thus large population size changes are unlikely to have greatly influenced MHC diversity in either species during this time period. In conclusion, our results suggest that the impact of selection on MHC diversity varied between these two closely related species, likely due to a combination of distinct ecological conditions and past pathogenic pressures.

  20. Common genetic variation and novel loci associated with volumetric mammographic density.

    Science.gov (United States)

    Brand, Judith S; Humphreys, Keith; Li, Jingmei; Karlsson, Robert; Hall, Per; Czene, Kamila

    2018-04-17

    Mammographic density (MD) is a strong and heritable intermediate phenotype of breast cancer, but much of its genetic variation remains unexplained. We conducted a genetic association study of volumetric MD in a Swedish mammography screening cohort (n = 9498) to identify novel MD loci. Associations with volumetric MD phenotypes (percent dense volume, absolute dense volume, and absolute nondense volume) were estimated using linear regression adjusting for age, body mass index, menopausal status, and six principal components. We also estimated the proportion of MD variance explained by additive contributions from single-nucleotide polymorphisms (SNP-based heritability [h 2 SNP ]) in 4948 participants of the cohort. In total, three novel MD loci were identified (at P associated with breast cancer in available meta-analysis data including 122,977 breast cancer cases and 105,974 control subjects (P < 0.05). h 2 SNP (SE) estimates for percent dense, absolute dense, and nondense volume were 0.29 (0.07), 0.31 (0.07), and 0.25 (0.07), respectively. Corresponding ratios of h 2 SNP to previously observed narrow-sense h 2 estimates in the same cohort were 0.46, 0.72, and 0.41, respectively. These findings provide new insights into the genetic basis of MD and biological mechanisms linking MD to breast cancer risk. Apart from identifying three novel loci, we demonstrate that at least 25% of the MD variance is explained by common genetic variation with h 2 SNP /h 2 ratios varying between dense and nondense MD components.

  1. Genetic variation observed at three tetrameric short tandem repeat loci HumTHO1, TPOX, and CSF1PO--in five ethnic population groups of northeastern India.

    Science.gov (United States)

    Ranjan, D; Kashyap, V K

    2001-01-01

    This paper portrays the genetic variation observed at three tetrameric short tandem repeat (STR) loci HumTHO1, TPOX, and CSF1PO in five ethnic population groups from northeastern India. The study also specifies the suitability of use of these markers for forensic testing. The populations studied included three tribal groups (Kuki, Naga and Hmar), one Mongoloid caste group (Meitei), and a religious caste group (Manipuri Muslims). The loci were highly polymorphic in the populations, and all loci met Hardy-Weinberg expectations. No evidence for association of alleles among the loci was detected. The probability of match for the three loci of the most frequent genotype in the five population groups ranged between 2.6 x 10(-4) and 6.6 x 10(-5). The average heterozygosity among the population groups was approximately 70% with the overall extent of gene differentiation among the five groups being high (Gst = 0.046). Genetic affinity among the populations reveal very close association between the Kuki, Hmar, Naga, and Meitei. The Manipuri Muslims, despite being found in the same region, have had no admixture with these populations and maintain a substantial distance with the other groups. The genetic polymorphism data suggest that the studied systems can be used for human identity testing to estimate the frequency of a multiple locus STR DNA profile in population groups of northeastern India.

  2. Variation in the complex carbohydrate biosynthesis loci of Acinetobacter baumannii genomes.

    Directory of Open Access Journals (Sweden)

    Johanna J Kenyon

    Full Text Available Extracellular polysaccharides are major immunogenic components of the bacterial cell envelope. However, little is known about their biosynthesis in the genus Acinetobacter, which includes A. baumannii, an important nosocomial pathogen. Whether Acinetobacter sp. produce a capsule or a lipopolysaccharide carrying an O antigen or both is not resolved. To explore these issues, genes involved in the synthesis of complex polysaccharides were located in 10 complete A. baumannii genome sequences, and the function of each of their products was predicted via comparison to enzymes with a known function. The absence of a gene encoding a WaaL ligase, required to link the carbohydrate polymer to the lipid A-core oligosaccharide (lipooligosaccharide forming lipopolysaccharide, suggests that only a capsule is produced. Nine distinct arrangements of a large capsule biosynthesis locus, designated KL1 to KL9, were found in the genomes. Three forms of a second, smaller variable locus, likely to be required for synthesis of the outer core of the lipid A-core moiety, were designated OCL1 to OCL3 and also annotated. Each K locus includes genes for capsule export as well as genes for synthesis of activated sugar precursors, and for glycosyltransfer, glycan modification and oligosaccharide repeat-unit processing. The K loci all include the export genes at one end and genes for synthesis of common sugar precursors at the other, with a highly variable region that includes the remaining genes in between. Five different capsule loci, KL2, KL6, KL7, KL8 and KL9 were detected in multiply antibiotic resistant isolates belonging to global clone 2, and two other loci, KL1 and KL4, in global clone 1. This indicates that this region is being substituted repeatedly in multiply antibiotic resistant isolates from these clones.

  3. Quantitative trait loci affecting phenotypic variation in the vacuolated lens mouse mutant, a multigenic mouse model of neural tube defects

    NARCIS (Netherlands)

    Korstanje, Ron; Desai, Jigar; Lazar, Gloria; King, Benjamin; Rollins, Jarod; Spurr, Melissa; Joseph, Jamie; Kadambi, Sindhuja; Li, Yang; Cherry, Allison; Matteson, Paul G.; Paigen, Beverly; Millonig, James H.

    Korstanje R, Desai J, Lazar G, King B, Rollins J, Spurr M, Joseph J, Kadambi S, Li Y, Cherry A, Matteson PG, Paigen B, Millonig JH. Quantitative trait loci affecting phenotypic variation in the vacuolated lens mouse mutant, a multigenic mouse model of neural tube defects. Physiol Genomics 35:

  4. Genetic variation at minisatellite loci D1S7, D4S139, D5S110 and D17S79 among three population groups of eastern India.

    Science.gov (United States)

    Dutta, R; Kashyap, V K

    2001-04-01

    Genetic variation at four minisatellite loci D1S7, D4S139, D5S110 and D17S79 in three predominant population groups of eastern India, namely Brahmin, Kayastha and Garo, are reported in this study. The Brahmin and Kayastha are of Indo-Caucasoid origin while the Garo community represents the Indo-Mongoloid ethnic group. The methodology employed comprised generation of HaeIII-restricted fragments of isolated DNA, Southern blotting, and hybridization using chemiluminescent probes MS1, pH30, LH1 and V1 for the four loci. All four loci were highly polymorphic in the population groups. Heterozygosity values for the four loci ranged between 0.68 and 0.95. Neither departure from Hardy Weinberg expectations nor evidence of any association across alleles among the selected loci was observed. The gene differentiation value among the loci is moderate (GST = 0.027). A neighbour-joining tree constructed on the basis of the generated data shows very low genetic distance between the Brahmin and Kayastha communities in relation to the Garo. Our results based on genetic distance analysis are consistent with results of earlier studies based on serological markers and linguistic as well as morphological affiliations of these populations and their Indo-Caucasoid and Indo-Mongoloid origin. The minisatellite loci studied here were found to be not only useful in showing significant genetic variation between the populations but also to be suitable for human identity testing among eastern Indian populations.

  5. High genetic diversity and fine-scale spatial structure in the marine flagellate Oxyrrhis marina (Dinophyceae uncovered by microsatellite loci.

    Directory of Open Access Journals (Sweden)

    Chris D Lowe

    2010-12-01

    Full Text Available Free-living marine protists are often assumed to be broadly distributed and genetically homogeneous on large spatial scales. However, an increasing application of highly polymorphic genetic markers (e.g., microsatellites has provided evidence for high genetic diversity and population structuring on small spatial scales in many free-living protists. Here we characterise a panel of new microsatellite markers for the common marine flagellate Oxyrrhis marina. Nine microsatellite loci were used to assess genotypic diversity at two spatial scales by genotyping 200 isolates of O. marina from 6 broad geographic regions around Great Britain and Ireland; in one region, a single 2 km shore line was sampled intensively to assess fine-scale genetic diversity. Microsatellite loci resolved between 1-6 and 7-23 distinct alleles per region in the least and most variable loci respectively, with corresponding variation in expected heterozygosities (H(e of 0.00-0.30 and 0.81-0.93. Across the dataset, genotypic diversity was high with 183 genotypes detected from 200 isolates. Bayesian analysis of population structure supported two model populations. One population was distributed across all sampled regions; the other was confined to the intensively sampled shore, and thus two distinct populations co-occurred at this site. Whilst model-based analysis inferred a single UK-wide population, pairwise regional F(ST values indicated weak to moderate population sub-division (0.01-0.12, but no clear correlation between spatial and genetic distance was evident. Data presented in this study highlight extensive genetic diversity for O. marina; however, it remains a substantial challenge to uncover the mechanisms that drive genetic diversity in free-living microorganisms.

  6. Analysis of natural allelic variation at seed dormancy loci of Arabidopsis thaliana

    NARCIS (Netherlands)

    Alonso-Blanco, C.; Bentsink, L.; Hanhart, C.J.; Vries, de M.H.C.; Koornneef, M.

    2003-01-01

    Arabidopsis accessions differ largely in their seed dormancy behavior. To understand the genetic basis of this intraspecific variation we analyzed two accessions: the laboratory strain Landsberg erecta (Ler) with low dormancy and the strong-dormancy accession Cape Verde Islands (Cvi). We used a

  7. Variation in Sperm Displacement and Its Association with Accessory Gland Protein Loci in Drosophila Melanogaster

    OpenAIRE

    Clark, A. G.; Aguade, M.; Prout, T.; Harshman, L. G.; Langley, C. H.

    1995-01-01

    Genes that influence mating and/or fertilization success may be targets for strong natural selection. If females remate frequently relative to the duration of sperm storage and rate of sperm use, sperm displacement may be an important component of male reproductive success. Although it has long been known that mutant laboratory stocks of Drosophila differ in sperm displacement, the magnitude of the naturally occurring genetic variation in this character has not been systematically quantified....

  8. Genetic Variation of pln Loci Among Probiotic Lactobacillus plantarum Group Strains with Antioxidant and Cholesterol-Lowering Ability.

    Science.gov (United States)

    Devi, Sundru Manjulata; Halami, Prakash M

    2017-10-13

    In the present study, 14 different plantaricin-encoding genes of pln loci were studied and compared to available sequences from public domain database of probiotic Lactobacillus plantarum strains. Based upon the presence and absence of selected genes, pln locus was grouped into eight clusters. Further, quantitative real-time PCR (qRT-PCR) analysis for seven genes has discriminated the complex pln locus into five types which includes WCFS1 (in Lactobacillus plantarum subsp. plantarum MCC 2976 and MCC 2974 and Lactobacillus paraplantarum MCC 2978), closely related to J51 (in Lb. paraplantarum MCC 2973 and MCC 2977), J23 (in Lb. plantarum MTCC 5422), NC8 (in Lb. paraplantarum MTCC 9483), and a new E1 type (in Lb. plantarum subsp. plantarum E1). It was observed that the plnA, EF, NC8βα, NC81F, NC8HK, and G were expressed in E1 strain. Further, southern hybridization confirmed the chromosome-encoded plantaricin in Lb. plantarum group (LPG) strains. Several PCR assays and DNA sequence analysis of the regions amplified in pln loci of E1 isolate suggested a hybrid variant of NC8 and J51 plantaritypes. This indicates the wide distribution of plantaricin with remarkable variation, diversity, and plasticity among the LPG strains of vegetable origin. Further, the selected strains were able to reduce the growth of Kocuria rhizophila ATCC 9341 by 40-54% within 6 h of co-incubation under in vitro pathogen exclusion assay. These isolates also possessed cholesterol-lowering and antioxidant activity suggesting their application in the development of functional foods.

  9. Null alleles and sequence variations at primer binding sites of STR loci within multiplex typing systems.

    Science.gov (United States)

    Yao, Yining; Yang, Qinrui; Shao, Chengchen; Liu, Baonian; Zhou, Yuxiang; Xu, Hongmei; Zhou, Yueqin; Tang, Qiqun; Xie, Jianhui

    2018-01-01

    Rare variants are widely observed in human genome and sequence variations at primer binding sites might impair the process of PCR amplification resulting in dropouts of alleles, named as null alleles. In this study, 5 cases from routine paternity testing using PowerPlex ® 21 System for STR genotyping were considered to harbor null alleles at TH01, FGA, D5S818, D8S1179, and D16S539, respectively. The dropout of alleles was confirmed by using alternative commercial kits AGCU Expressmarker 22 PCR amplification kit and AmpFℓSTR ® . Identifiler ® Plus Kit, and sequencing results revealed a single base variation at the primer binding site of each STR locus. Results from the collection of previous reports show that null alleles at D5S818 were frequently observed in population detected by two PowerPlex ® typing systems and null alleles at D19S433 were mostly observed in Japanese population detected by two AmpFℓSTR™ typing systems. Furthermore, the most popular mutation type appeared the transition from C to T with G to A, which might have a potential relationship with DNA methylation. Altogether, these results can provide helpful information in forensic practice to the elimination of genotyping discrepancy and the development of primer sets. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. Replication of linkage to quantitative trait loci: variation in location and magnitude of the lod score.

    Science.gov (United States)

    Hsueh, W C; Göring, H H; Blangero, J; Mitchell, B D

    2001-01-01

    Replication of linkage signals from independent samples is considered an important step toward verifying the significance of linkage signals in studies of complex traits. The purpose of this empirical investigation was to examine the variability in the precision of localizing a quantitative trait locus (QTL) by analyzing multiple replicates of a simulated data set with the use of variance components-based methods. Specifically, we evaluated across replicates the variation in both the magnitude and the location of the peak lod scores. We analyzed QTLs whose effects accounted for 10-37% of the phenotypic variance in the quantitative traits. Our analyses revealed that the precision of QTL localization was directly related to the magnitude of the QTL effect. For a QTL with effect accounting for > 20% of total phenotypic variation, > 90% of the linkage peaks fall within 10 cM from the true gene location. We found no evidence that, for a given magnitude of the lod score, the presence of interaction influenced the precision of QTL localization.

  11. Allelic variation at Glu-1 loci and its association with grain quality of ...

    African Journals Online (AJOL)

    The high molecular weight glutenin subunits (HMW-GS) are important determinants of wheat flour quality. The HMW-GS patterns of the major released wheat cultivars in Sudan, in addition to some advanced lines, were analyzed using SDS-PAGE. The associations of the HMW-GS quality scores (Glu-1 QS) with the flour ...

  12. CoLIde: a bioinformatics tool for CO-expression-based small RNA Loci Identification using high-throughput sequencing data.

    Science.gov (United States)

    Mohorianu, Irina; Stocks, Matthew Benedict; Wood, John; Dalmay, Tamas; Moulton, Vincent

    2013-07-01

    Small RNAs (sRNAs) are 20-25 nt non-coding RNAs that act as guides for the highly sequence-specific regulatory mechanism known as RNA silencing. Due to the recent increase in sequencing depth, a highly complex and diverse population of sRNAs in both plants and animals has been revealed. However, the exponential increase in sequencing data has also made the identification of individual sRNA transcripts corresponding to biological units (sRNA loci) more challenging when based exclusively on the genomic location of the constituent sRNAs, hindering existing approaches to identify sRNA loci. To infer the location of significant biological units, we propose an approach for sRNA loci detection called CoLIde (Co-expression based sRNA Loci Identification) that combines genomic location with the analysis of other information such as variation in expression levels (expression pattern) and size class distribution. For CoLIde, we define a locus as a union of regions sharing the same pattern and located in close proximity on the genome. Biological relevance, detected through the analysis of size class distribution, is also calculated for each locus. CoLIde can be applied on ordered (e.g., time-dependent) or un-ordered (e.g., organ, mutant) series of samples both with or without biological/technical replicates. The method reliably identifies known types of loci and shows improved performance on sequencing data from both plants (e.g., A. thaliana, S. lycopersicum) and animals (e.g., D. melanogaster) when compared with existing locus detection techniques. CoLIde is available for use within the UEA Small RNA Workbench which can be downloaded from: http://srna-workbench.cmp.uea.ac.uk.

  13. Quantitative trait loci for maysin synthesis in maize (Zea mays L.) lines selected for high silk maysin content.

    Science.gov (United States)

    Meyer, J D F; Snook, M E; Houchins, K E; Rector, B G; Widstrom, N W; McMullen, M D

    2007-06-01

    Maysin is a naturally occurring C-glycosyl flavone found in maize (Zea mays L.) silk tissue that confers resistance to corn earworm (Helicoverpa zea, Boddie). Recently, two new maize populations were derived for high silk maysin. The two populations were named the exotic populations of maize (EPM) and the southern inbreds of maize (SIM). Quantitative trait locus (QTL) analysis was employed to determine which loci were responsible for elevated maysin levels in inbred lines derived from the EPM and SIM populations. The candidate genes consistent with QTL position included the p (pericarp color), c2 (colorless2), whp1 (white pollen1) and in1 (intensifier1) loci. The role of these loci in controlling high maysin levels in silks was tested by expression analysis and use of the loci as genetic markers onto the QTL populations. These studies support p, c2 and whp1, but not in1, as loci controlling maysin. Through this study, we determined that the p locus regulates whp1 transcription and that increased maysin in these inbred lines was primarily due to alleles at both structural and regulatory loci promoting increased flux through the flavone pathway by increasing chalcone synthase activity.

  14. Allelic variation at the vernalization and photoperiod sensitivity loci in Chinese winter wheat cultivars (Triticum aestivum L.

    Directory of Open Access Journals (Sweden)

    Xiangfen eZhang

    2015-07-01

    Full Text Available A total of 205 wheat cultivars from the Yellow and Huai valley of China were used to identify allelic variations of vernalization and photoperiod response genes, as well as the copy number variations (CNVs of Ppd-B1 and Vrn-A1 genes. A novel Vrn-D1 allele with 174-bp insertion in the promoter region of the recessive allele vrn-D1 was discovered in three Chinese wheat cultivars and designated as Vrn-D1c. Quantitative real-time polymerase chain reaction showed that cultivars with the Vrn-D1c allele exhibited significantly higher expression of the Vrn-D1 gene than that in cultivars with the recessive allele vrn-D1, indicating that the 174-bp insertion of Vrn-D1c contributed to the increase in Vrn-D1 gene expression and caused early heading and flowering. The five new cis-elements (Box II-like, 3-AF1 binding site, TC-rich repeats, Box-W1 and CAT-box in the 174-bp insertion possibly promoted the basal activity level of Vrn-D1 gene. Two new polymorphism combinations of photoperiod genes were identified and designated as Ppd-D1_Hapl-IX and Ppd-D1_Hapl-X. Association of the CNV of Ppd-B1 gene with the heading and flowering days showed that the cultivars with Ppd-B1_Hapl-VI demonstrated the earliest heading and flowering times, and those with Ppd-B1_Hapl-IV presented the latest heading and flowering times in three cropping seasons. Distribution of the vernalization and photoperiod response genes indicated that all recessive alleles at the four vernalization response loci, Ppd-B1_Hapl-I at Ppd-B1 locus, and Ppd-D1_Hapl-I at the Ppd-D1 locus were predominant in Chinese winter wheat cultivars. This study can provide useful information for wheat breeding programs to screen wheat cultivars with relatively superior adaptability and maturity.

  15. Genetic Variations in Pattern Recognition Receptor Loci Are Associated with Anti-TNF Response in Patients with Rheumatoid Arthritis.

    Directory of Open Access Journals (Sweden)

    Jacob Sode

    Full Text Available To determine whether genetic variation within genes related to the Toll-like receptor, inflammasome and interferon-γ pathways contributes to the differences in treatment response to tumour necrosis factor inhibitors (anti-TNF in patients with rheumatoid arthritis (RA.In a retrospective case-case study, we assessed 23 functional single nucleotide polymorphisms (SNPs in 15 genes. We included 538 anti-TNF naïve Danish RA patients from the nationwide DANBIO database. Multivariable logistic regression analyses were performed to detect associations (p-value<0.05 between genotypes and European League Against Rheumatism (EULAR treatment responses. False Discovery Rate corrections for multiple testing (q-value and stratified analyses were performed to investigate association with individual therapies and IgM-rheumatoid factor (RF status.Six of twenty successfully genotyped polymorphisms were nominally associated with EULAR treatment response. Three of these were in weak to moderate linkage disequilibrium with polymorphisms previously reported associated with anti-TNF treatment response. TLR5(rs5744174 variant allele carriers (odds ratio(OR = 1.7(1.1-2.5,p = 0.010,q = 0.46 and TLR1(rs4833095 homozygous variant carriers (OR = 2.8(1.1-7.4,p = 0.037,q = 0.46 had higher odds for a positive treatment response. NLRP3(rs10754558 variant allele carriers (odds ratio(OR = 0.6(0.4-1.0,p = 0.045,q = 0.46 were more likely to have a negative treatment response. The association in TLR5(rs5744174 remained significant after correction for multiple comparisons among patients negative for RF (OR = 6.2(2.4-16.3,p = 0.0002,q = 0.024. No other association withstood correction for multiple testing. Post hoc analyses showed that change in Patient Global score on a visual analogue scale (VAS and change in pain VAS were the main factors responsible for the association.We reproduced previously reported associations between genetic variation in the TLR10/1/6 gene cluster, TLR5

  16. Salinity tolerance loci revealed in rice using high-throughput non-invasive phenotyping

    KAUST Repository

    Al-Tamimi, Nadia Ali; Brien, Chris; Oakey, Helena; Berger, Bettina; Saade, Stephanie; Ho, Yung Shwen; Schmö ckel, Sandra M.; Tester, Mark A.; Negrã o, Só nia

    2016-01-01

    High-throughput phenotyping produces multiple measurements over time, which require new methods of analyses that are flexible in their quantification of plant growth and transpiration, yet are computationally economic. Here we develop such analyses and apply this to a rice population genotyped with a 700k SNP high-density array. Two rice diversity panels, indica and aus, containing a total of 553 genotypes, are phenotyped in waterlogged conditions. Using cubic smoothing splines to estimate plant growth and transpiration, we identify four time intervals that characterize the early responses of rice to salinity. Relative growth rate, transpiration rate and transpiration use efficiency (TUE) are analysed using a new association model that takes into account the interaction between treatment (control and salt) and genetic marker. This model allows the identification of previously undetected loci affecting TUE on chromosome 11, providing insights into the early responses of rice to salinity, in particular into the effects of salinity on plant growth and transpiration.

  17. Salinity tolerance loci revealed in rice using high-throughput non-invasive phenotyping

    KAUST Repository

    Al-Tamimi, Nadia Ali

    2016-11-17

    High-throughput phenotyping produces multiple measurements over time, which require new methods of analyses that are flexible in their quantification of plant growth and transpiration, yet are computationally economic. Here we develop such analyses and apply this to a rice population genotyped with a 700k SNP high-density array. Two rice diversity panels, indica and aus, containing a total of 553 genotypes, are phenotyped in waterlogged conditions. Using cubic smoothing splines to estimate plant growth and transpiration, we identify four time intervals that characterize the early responses of rice to salinity. Relative growth rate, transpiration rate and transpiration use efficiency (TUE) are analysed using a new association model that takes into account the interaction between treatment (control and salt) and genetic marker. This model allows the identification of previously undetected loci affecting TUE on chromosome 11, providing insights into the early responses of rice to salinity, in particular into the effects of salinity on plant growth and transpiration.

  18. High mutation rates explain low population genetic divergence at copy-number-variable loci in Homo sapiens.

    Science.gov (United States)

    Hu, Xin-Sheng; Yeh, Francis C; Hu, Yang; Deng, Li-Ting; Ennos, Richard A; Chen, Xiaoyang

    2017-02-22

    Copy-number-variable (CNV) loci differ from single nucleotide polymorphic (SNP) sites in size, mutation rate, and mechanisms of maintenance in natural populations. It is therefore hypothesized that population genetic divergence at CNV loci will differ from that found at SNP sites. Here, we test this hypothesis by analysing 856 CNV loci from the genomes of 1184 healthy individuals from 11 HapMap populations with a wide range of ancestry. The results show that population genetic divergence at the CNV loci is generally more than three times lower than at genome-wide SNP sites. Populations generally exhibit very small genetic divergence (G st  = 0.05 ± 0.049). The smallest divergence is among African populations (G st  = 0.0081 ± 0.0025), with increased divergence among non-African populations (G st  = 0.0217 ± 0.0109) and then among African and non-African populations (G st  = 0.0324 ± 0.0064). Genetic diversity is high in African populations (~0.13), low in Asian populations (~0.11), and intermediate in the remaining 11 populations. Few significant linkage disequilibria (LDs) occur between the genome-wide CNV loci. Patterns of gametic and zygotic LDs indicate the absence of epistasis among CNV loci. Mutation rate is about twice as large as the migration rate in the non-African populations, suggesting that the high mutation rates play dominant roles in producing the low population genetic divergence at CNV loci.

  19. An integrative genetic study of rice metabolism, growth and stochastic variation reveals potential C/N partitioning loci

    DEFF Research Database (Denmark)

    Li, Baohua; Zhang, Yuanyuan; Mohammadi, Seyed Abolghasem

    2016-01-01

    metabolites suggesting that they may influence carbon and nitrogen partitioning, with one locus co-localizing with SUSIBA2 (WRKY78). Comparing QTLs for metabolomic and a variety of growth related traits identified few overlaps. Interestingly, the rice population displayed fewer loci controlling stochastic...

  20. Cultivar identification by means of isoenzymes 2. Genetic variation at 4 enzyme loci in diploid ryegrass lolium-spp

    DEFF Research Database (Denmark)

    Nielsen, G.; Østergaard, H.; Johansen, Henrik

    1985-01-01

    gel electrophoresis. Cultivars were pairwise compared by means of allelic frequencies assuming Hardy-Weinberg proportions. At first, the comparisons were carried out for each locus separately. The 2 loci Pgi-2 and Got-3 distinguished perennial ryegrass cultivars fairly well, but the discrimination...

  1. High density genetic mapping identifies new susceptibility loci for rheumatoid arthritis

    Science.gov (United States)

    Eyre, Steve; Bowes, John; Diogo, Dorothée; Lee, Annette; Barton, Anne; Martin, Paul; Zhernakova, Alexandra; Stahl, Eli; Viatte, Sebastien; McAllister, Kate; Amos, Christopher I.; Padyukov, Leonid; Toes, Rene E.M.; Huizinga, Tom W.J.; Wijmenga, Cisca; Trynka, Gosia; Franke, Lude; Westra, Harm-Jan; Alfredsson, Lars; Hu, Xinli; Sandor, Cynthia; de Bakker, Paul I.W.; Davila, Sonia; Khor, Chiea Chuen; Heng, Khai Koon; Andrews, Robert; Edkins, Sarah; Hunt, Sarah E; Langford, Cordelia; Symmons, Deborah; Concannon, Pat; Onengut-Gumuscu, Suna; Rich, Stephen S; Deloukas, Panos; Gonzalez-Gay, Miguel A.; Rodriguez-Rodriguez, Luis; Ärlsetig, Lisbeth; Martin, Javier; Rantapää-Dahlqvist, Solbritt; Plenge, Robert; Raychaudhuri, Soumya; Klareskog, Lars; Gregersen, Peter K; Worthington, Jane

    2012-01-01

    Summary Using the Immunochip custom single nucleotide polymorphism (SNP) array, designed for dense genotyping of 186 genome wide association study (GWAS) confirmed loci we analysed 11,475 rheumatoid arthritis cases of European ancestry and 15,870 controls for 129,464 markers. The data were combined in meta-analysis with GWAS data from additional independent cases (n=2,363) and controls (n=17,872). We identified fourteen novel loci; nine were associated with rheumatoid arthritis overall and 5 specifically in anti-citrillunated peptide antibody positive disease, bringing the number of confirmed European ancestry rheumatoid arthritis loci to 46. We refined the peak of association to a single gene for 19 loci, identified secondary independent effects at six loci and association to low frequency variants (minor allele frequency <0.05) at 4 loci. Bioinformatic analysis of the data generated strong hypotheses for the causal SNP at seven loci. This study illustrates the advantages of dense SNP mapping analysis to inform subsequent functional investigations. PMID:23143596

  2. No variation and low synonymous substitution rates in coral mtDNA despite high nuclear variation

    Directory of Open Access Journals (Sweden)

    Hellberg Michael E

    2006-03-01

    Full Text Available Abstract Background The mitochondrial DNA (mtDNA of most animals evolves more rapidly than nuclear DNA, and often shows higher levels of intraspecific polymorphism and population subdivision. The mtDNA of anthozoans (corals, sea fans, and their kin, by contrast, appears to evolve slowly. Slow mtDNA evolution has been reported for several anthozoans, however this slow pace has been difficult to put in phylogenetic context without parallel surveys of nuclear variation or calibrated rates of synonymous substitution that could permit quantitative rate comparisons across taxa. Here, I survey variation in the coding region of a mitochondrial gene from a coral species (Balanophyllia elegans known to possess high levels of nuclear gene variation, and estimate synonymous rates of mtDNA substitution by comparison to another coral (Tubastrea coccinea. Results The mtDNA surveyed (630 bp of cytochrome oxidase subunit I was invariant among individuals sampled from 18 populations spanning 3000 km of the range of B. elegans, despite high levels of variation and population subdivision for allozymes over these same populations. The synonymous substitution rate between B. elegans and T. coccinea (0.05%/site/106 years is similar to that in most plants, but 50–100 times lower than rates typical for most animals. In addition, while substitutions to mtDNA in most animals exhibit a strong bias toward transitions, mtDNA from these corals does not. Conclusion Slow rates of mitochondrial nucleotide substitution result in low levels of intraspecific mtDNA variation in corals, even when nuclear loci vary. Slow mtDNA evolution appears to be the basal condition among eukaryotes. mtDNA substitution rates switch from slow to fast abruptly and unidirectionally. This switch may stem from the loss of just one or a few mitochondrion-specific DNA repair or replication genes.

  3. Copy number and haplotype variation at the VRN-A1 and central FR-A2 loci are associated with frost tolerance in hexaploid wheat.

    Science.gov (United States)

    Zhu, Jie; Pearce, Stephen; Burke, Adrienne; See, Deven Robert; Skinner, Daniel Z; Dubcovsky, Jorge; Garland-Campbell, Kimberly

    2014-05-01

    The interaction between VRN - A1 and FR - A2 largely affect the frost tolerance of hexaploid wheat. Frost tolerance is critical for wheat survival during cold winters. Natural variation for this trait is mainly associated with allelic differences at the VERNALIZATION 1 (VRN1) and FROST RESISTANCE 2 (FR2) loci. VRN1 regulates the transition between vegetative and reproductive stages and FR2, a locus including several tandemly duplicated C-REPEAT BINDING FACTOR (CBF) transcription factors, regulates the expression of Cold-regulated genes. We identified sequence and copy number variation at these two loci among winter and spring wheat varieties and characterized their association with frost tolerance. We identified two FR-A2 haplotypes-'FR-A2-S' and 'FR-A2-T'-distinguished by two insertion/deletions and ten single nucleotide polymorphisms within the CBF-A12 and CBF-A15 genes. Increased copy number of CBF-A14 was frequently associated with the FR-A2-T haplotype and with higher CBF14 transcript levels in response to cold. Factorial ANOVAs revealed significant interactions between VRN1 and FR-A2 for frost tolerance in both winter and spring panels suggesting a crosstalk between vernalization and cold acclimation pathways. The model including these two loci and their interaction explained 32.0 and 20.7 % of the variation in frost tolerance in the winter and spring panels, respectively. The interaction was validated in a winter wheat F 4:5 population segregating for both genes. Increased VRN-A1 copy number was associated with improved frost tolerance among varieties carrying the FR-A2-T allele but not among those carrying the FR-A2-S allele. These results suggest that selection of varieties carrying the FR-A2-T allele and three copies of the recessive vrn-A1 allele would be a good strategy to improve frost tolerance in wheat.

  4. Limited phylogeographic signal in sex-linked and autosomal loci despite geographically, ecologically, and phenotypically concordant structure of mtDNA variation in the Holarctic avian genus Eremophila.

    Directory of Open Access Journals (Sweden)

    Sergei V Drovetski

    Full Text Available Phylogeographic studies of Holarctic birds are challenging because they involve vast geographic scale, complex glacial history, extensive phenotypic variation, and heterogeneous taxonomic treatment across countries, all of which require large sample sizes. Knowledge about the quality of phylogeographic information provided by different loci is crucial for study design. We use sequences of one mtDNA gene, one sex-linked intron, and one autosomal intron to elucidate large scale phylogeographic patterns in the Holarctic lark genus Eremophila. The mtDNA ND2 gene identified six geographically, ecologically, and phenotypically concordant clades in the Palearctic that diverged in the Early-Middle Pleistocene and suggested paraphyly of the horned lark (E. alpestris with respect to the Temminck's lark (E. bilopha. In the Nearctic, ND2 identified five subclades which diverged in the Late Pleistocene. They overlapped geographically and were not concordant phenotypically or ecologically. Nuclear alleles provided little information on geographic structuring of genetic variation in horned larks beyond supporting the monophyly of Eremophila and paraphyly of the horned lark. Multilocus species trees based on two nuclear or all three loci provided poor support for haplogroups identified by mtDNA. The node ages calculated using mtDNA were consistent with the available paleontological data, whereas individual nuclear loci and multilocus species trees appeared to underestimate node ages. We argue that mtDNA is capable of discovering independent evolutionary units within avian taxa and can provide a reasonable phylogeographic hypothesis when geographic scale, geologic history, and phenotypic variation in the study system are too complex for proposing reasonable a priori hypotheses required for multilocus methods. Finally, we suggest splitting the currently recognized horned lark into five Palearctic and one Nearctic species.

  5. The role of copy number variation in susceptibility to amyotrophic lateral sclerosis: genome-wide association study and comparison with published loci.

    Directory of Open Access Journals (Sweden)

    Louise V Wain

    2009-12-01

    Full Text Available The genetic contribution to sporadic amyotrophic lateral sclerosis (ALS has not been fully elucidated. There are increasing efforts to characterise the role of copy number variants (CNVs in human diseases; two previous studies concluded that CNVs may influence risk of sporadic ALS, with multiple rare CNVs more important than common CNVs. A little-explored issue surrounding genome-wide CNV association studies is that of post-calling filtering and merging of raw CNV calls. We undertook simulations to define filter thresholds and considered optimal ways of merging overlapping CNV calls for association testing, taking into consideration possibly overlapping or nested, but distinct, CNVs and boundary estimation uncertainty.In this study we screened Illumina 300K SNP genotyping data from 730 ALS cases and 789 controls for copy number variation. Following quality control filters using thresholds defined by simulation, a total of 11321 CNV calls were made across 575 cases and 621 controls. Using region-based and gene-based association analyses, we identified several loci showing nominally significant association. However, the choice of criteria for combining calls for association testing has an impact on the ranking of the results by their significance. Several loci which were previously reported as being associated with ALS were identified here. However, of another 15 genes previously reported as exhibiting ALS-specific copy number variation, only four exhibited copy number variation in this study. Potentially interesting novel loci, including EEF1D, a translation elongation factor involved in the delivery of aminoacyl tRNAs to the ribosome (a process which has previously been implicated in genetic studies of spinal muscular atrophy were identified but must be treated with caution due to concerns surrounding genomic location and platform suitability.Interpretation of CNV association findings must take into account the effects of filtering and combining

  6. Genetic Diversity and Sequence Variations at Growth Hormone Loci among Composite and Hereford Populations of Beef Cattle

    Directory of Open Access Journals (Sweden)

    ALAN J. LYMBERY

    2000-07-01

    Full Text Available A total of 194 Hereford and 235 composite breed cattle from Wokalup Research Station were used in this study. The aims of the study were to: Investigate polymorphisms in the growth hormone gene in the composite and purebred Hereford herds from the Wokalup selection experiment, compare genetic diversity in the growth hormone gene of the breeds, sequencing and compare the sequences of growth hormone loci between composite and purebred Hereford herds with published sequence from Genebank. The genomic DNA was extracted using Wizard genomic DNA purification system from Promega. Two fragments of growth hormone gene were amplified using PCR and continued with RFLP. Each genotype in both loci was sequenced. PCR products of each genotypes were cloned into PCR II, transformed, colonies selection, plasmid DNA extraction continued with cycle sequencing. Polymorphisms were found in both breeds of cattle in both loci of GH-L1 and GH-L2 of the growth hormone gene by PCR-RFLP analysis. Sequencing analysis confirmed the RFLPs data, polymorphism detected using AluI at GH-L1 is due to substitution between leusin/ valine at position 127, while polymorphism at the MspI restriction site was caused by transition of C to T at +837 position.

  7. Efficient Differentiation of Mycobacterium tuberculosis Strains of the W-Beijing Family from Russia using Highly Polymorphic VNTR Loci

    International Nuclear Information System (INIS)

    Surikova, O. V.; Voitech, D. S.; Kuzmicheva, G.; Tatkov, S. I.; Mokrousov, I. V.; Narvskaya, O. V.; Rot, M. A.; Soolingen, D. van; Filipenko, M. L.

    2005-01-01

    The W-Beijing family is a widespread Mycobacterium tuberculosis clonal lineage that frequently causes epidemic outbreaks. This family is genetically homogeneous and conserved, so ETR-VNTR (exact tandem repeat-variable number of tandem repeats) typing is insufficient for strain differentiation, due to a common ETR-A to E profile (42435). This leads to the false clustering in molecular epidemiological studies, especially in the regions of predominance of the W-Beijing family. In this study, we searched for VNTR loci with a high evolutionary rate of polymorphism in the W-Beijing genome. Here we further evaluated VNTR typing on a set of 99 Mycobacterium tuberculosis clinical isolates and reference strains. These isolates were characterized and classified into several genotype families based on three ETR loci (A, C, E) and eight additional loci [previously described as QUB (Queen's University Belfast) or MIRU (Mycobacterial Interspersed Repetitive Units) or Mtubs]. Ninety-nine strains were divided into 74 VNTR-types, 51 isolates of the W-Beijing family identified by IS6110 RFLP-typing (the restriction fragment length polymorphism-typing) and/or spoligotyping were subdivided into 30 VNTR-types. HGDI (the Hunter-Gaston discriminatory index) for all studied loci was close to that of IS6110 RFLP typing, a 'gold standard' method for subtyping M. tuberculosis complex strains. The QUB 26 and QUB 18 loci located in the PPE genes were highly polymorphic and more discriminative than other loci (HGDI is 0.8). Statistically significant increase of tandem repeats number in loci ETR-A, -E, QUB 26, QUB 18, QUB 11B, Mtub21 was revealed in the W-Beijing group compared to genetically divergent non-W-Beijing strains. Thirty-six isolates were subjected to IS6110 RFLP typing. The congruence between results of the IS6110 RFLP typing and 11-loci VNTR typing was estimated on 23 isolates of the W-Beijing family. These isolates were subdivided into 9 IS6110-RFLP types and 13 VNTR types. The poor

  8. Characterization of ten highly polymorphic microsatellite loci for the intertidal mussel Perna perna, and cross species amplification within the genus

    Directory of Open Access Journals (Sweden)

    Coelho Nelson C

    2012-10-01

    Full Text Available Abstract Background The brown mussel Perna perna (Linnaeus, 1758 is a dominant constituent of intertidal communities and a strong invader with multiple non-native populations distributed around the world. In a previous study, two polymorphic microsatellite loci were developed and used to determine population-level genetic diversity in invasive and native P. perna populations. However, higher number of microsatellite markers are required for reliable population genetic studies. In this context, in order to understand P. perna origins and history of invasion and to compare population genetic structure in native versus invaded areas, we developed 10 polymorphic microsatellite markers. Findings Described microsatellite markers were developed from an enriched genomic library. Analyses and characterization of loci using 20 individuals from a population in Western Sahara revealed on average 11 alleles per locus (range: 5–27 and mean gene diversity of 0.75 (range: 0.31 - 0.95. One primer pair revealed possible linkage disequilibrium while heterozygote deficiency was significant at four loci. Six of these markers cross-amplified in P. canaliculus (origin: New Zealand. Conclusions Developed markers will be useful in addressing a variety of questions concerning P. perna, including dispersal scales, genetic variation and population structure, in both native and invaded areas.

  9. Discovery and Fine-Mapping of Glycaemic and Obesity-Related Trait Loci Using High-Density Imputation.

    Directory of Open Access Journals (Sweden)

    Momoko Horikoshi

    2015-07-01

    Full Text Available Reference panels from the 1000 Genomes (1000G Project Consortium provide near complete coverage of common and low-frequency genetic variation with minor allele frequency ≥0.5% across European ancestry populations. Within the European Network for Genetic and Genomic Epidemiology (ENGAGE Consortium, we have undertaken the first large-scale meta-analysis of genome-wide association studies (GWAS, supplemented by 1000G imputation, for four quantitative glycaemic and obesity-related traits, in up to 87,048 individuals of European ancestry. We identified two loci for body mass index (BMI at genome-wide significance, and two for fasting glucose (FG, none of which has been previously reported in larger meta-analysis efforts to combine GWAS of European ancestry. Through conditional analysis, we also detected multiple distinct signals of association mapping to established loci for waist-hip ratio adjusted for BMI (RSPO3 and FG (GCK and G6PC2. The index variant for one association signal at the G6PC2 locus is a low-frequency coding allele, H177Y, which has recently been demonstrated to have a functional role in glucose regulation. Fine-mapping analyses revealed that the non-coding variants most likely to drive association signals at established and novel loci were enriched for overlap with enhancer elements, which for FG mapped to promoter and transcription factor binding sites in pancreatic islets, in particular. Our study demonstrates that 1000G imputation and genetic fine-mapping of common and low-frequency variant association signals at GWAS loci, integrated with genomic annotation in relevant tissues, can provide insight into the functional and regulatory mechanisms through which their effects on glycaemic and obesity-related traits are mediated.

  10. Discovery and Fine-Mapping of Glycaemic and Obesity-Related Trait Loci Using High-Density Imputation.

    Science.gov (United States)

    Horikoshi, Momoko; Mӓgi, Reedik; van de Bunt, Martijn; Surakka, Ida; Sarin, Antti-Pekka; Mahajan, Anubha; Marullo, Letizia; Thorleifsson, Gudmar; Hӓgg, Sara; Hottenga, Jouke-Jan; Ladenvall, Claes; Ried, Janina S; Winkler, Thomas W; Willems, Sara M; Pervjakova, Natalia; Esko, Tõnu; Beekman, Marian; Nelson, Christopher P; Willenborg, Christina; Wiltshire, Steven; Ferreira, Teresa; Fernandez, Juan; Gaulton, Kyle J; Steinthorsdottir, Valgerdur; Hamsten, Anders; Magnusson, Patrik K E; Willemsen, Gonneke; Milaneschi, Yuri; Robertson, Neil R; Groves, Christopher J; Bennett, Amanda J; Lehtimӓki, Terho; Viikari, Jorma S; Rung, Johan; Lyssenko, Valeriya; Perola, Markus; Heid, Iris M; Herder, Christian; Grallert, Harald; Müller-Nurasyid, Martina; Roden, Michael; Hypponen, Elina; Isaacs, Aaron; van Leeuwen, Elisabeth M; Karssen, Lennart C; Mihailov, Evelin; Houwing-Duistermaat, Jeanine J; de Craen, Anton J M; Deelen, Joris; Havulinna, Aki S; Blades, Matthew; Hengstenberg, Christian; Erdmann, Jeanette; Schunkert, Heribert; Kaprio, Jaakko; Tobin, Martin D; Samani, Nilesh J; Lind, Lars; Salomaa, Veikko; Lindgren, Cecilia M; Slagboom, P Eline; Metspalu, Andres; van Duijn, Cornelia M; Eriksson, Johan G; Peters, Annette; Gieger, Christian; Jula, Antti; Groop, Leif; Raitakari, Olli T; Power, Chris; Penninx, Brenda W J H; de Geus, Eco; Smit, Johannes H; Boomsma, Dorret I; Pedersen, Nancy L; Ingelsson, Erik; Thorsteinsdottir, Unnur; Stefansson, Kari; Ripatti, Samuli; Prokopenko, Inga; McCarthy, Mark I; Morris, Andrew P

    2015-07-01

    Reference panels from the 1000 Genomes (1000G) Project Consortium provide near complete coverage of common and low-frequency genetic variation with minor allele frequency ≥0.5% across European ancestry populations. Within the European Network for Genetic and Genomic Epidemiology (ENGAGE) Consortium, we have undertaken the first large-scale meta-analysis of genome-wide association studies (GWAS), supplemented by 1000G imputation, for four quantitative glycaemic and obesity-related traits, in up to 87,048 individuals of European ancestry. We identified two loci for body mass index (BMI) at genome-wide significance, and two for fasting glucose (FG), none of which has been previously reported in larger meta-analysis efforts to combine GWAS of European ancestry. Through conditional analysis, we also detected multiple distinct signals of association mapping to established loci for waist-hip ratio adjusted for BMI (RSPO3) and FG (GCK and G6PC2). The index variant for one association signal at the G6PC2 locus is a low-frequency coding allele, H177Y, which has recently been demonstrated to have a functional role in glucose regulation. Fine-mapping analyses revealed that the non-coding variants most likely to drive association signals at established and novel loci were enriched for overlap with enhancer elements, which for FG mapped to promoter and transcription factor binding sites in pancreatic islets, in particular. Our study demonstrates that 1000G imputation and genetic fine-mapping of common and low-frequency variant association signals at GWAS loci, integrated with genomic annotation in relevant tissues, can provide insight into the functional and regulatory mechanisms through which their effects on glycaemic and obesity-related traits are mediated.

  11. Variabilidade genética em algumas criações comerciais brasileiras de escargots (Helix aspersa, Müller, 1774 Genetic variation at eight isoenzyme loci in subpopulations of the edible snail (Helix aspersa, Müller, 1774

    Directory of Open Access Journals (Sweden)

    B.F. Vasconcellos

    2006-04-01

    Full Text Available Descreveram-se os marcadores isoenzimáticos e estimou-se a variabilidade genética de 20 subpopulações brasileiras de escargots (Helix aspersa. O estudo dos oito locos foi feito por eletroforese em gel de amido, em amostras com 30 indivíduos cada, obtidas em criatórios dos estados de Santa Catarina, São Paulo e Rio de Janeiro (uma, duas e 17 amostras, respectivamente. Observou-se polimorfismo nos locos das enzimas LAP, 6-PGD, PEP 2, PEP 1 e MDH, com três alelos nos três primeiros locos e dois nos demais. Os locos da ME, da SOD e da PGI apresentaram-se monomórficos. As freqüências gênicas de sete amostras ajustaram-se ao modelo de Hardy-Weinberg (PIn order to assess genetic variability in subpopulations of Helix aspersa, eight isoenzyme loci in 30 individuals in each of 20 subpopulations, obtained from breeders in Santa Catarina (1, São Paulo(2 and Rio de Janeiro (17 states of Brazil, were examined. Polymorphic loci included LAP, 6-PGD, PEP 2, PEP 1 and MDH, with three alelles at each of the first three loci and two at each of the others. The ME, SOD and PGI loci were monomorphic. Gene frequencies in 7 of 20 subpopulations were consistent with the Hardy-Wienberg equilibrium (P<0.05, and 6 were consistent with Wright model, indicating that these subpopulations did not meet requirements for genotypic equilibrium to be achieved. Despite the fact that some F values were high, F IS and F IT were not significantly different from zero (P³0.05. Although small, the F ST value (0.0485 was significant, suggesting small differences among populations. Most of the low genetic variation at isoenzyme loci was observed within subpopulations rather than among subpopulations, suggesting a small genetic basis for these samples. Estimated genetic distances among pairs of subpopulations also were low.

  12. High-density genetic mapping identifies new susceptibility loci for rheumatoid arthritis

    NARCIS (Netherlands)

    Eyre, Steve; Bowes, John; Diogo, Dorothee; Lee, Annette; Barton, Anne; Martin, Paul; Zhernakova, Alexandra; Stahl, Eli; Viatte, Sebastien; McAllister, Kate; Amos, Christopher I.; Padyukov, Leonid; Toes, Rene E. M.; Huizinga, Tom W. J.; Wijmenga, Cisca; Trynka, Gosia; Franke, Lude; Westra, Harm-Jan; Alfredsson, Lars; Hu, Xinli; Sandor, Cynthia; de Bakker, Paul I. W.; Davila, Sonia; Khor, Chiea Chuen; Heng, Khai Koon; Andrews, Robert; Edkins, Sarah; Hunt, Sarah E.; Langford, Cordelia; Symmons, Deborah; Concannon, Pat; Onengut-Gumuscu, Suna; Rich, Stephen S.; Deloukas, Panos; Gonzalez-Gay, Miguel A.; Rodriguez-Rodriguez, Luis; Arlsetig, Lisbeth; Martin, Javier; Rantapaa-Dahlqvist, Solbritt; Plenge, Robert M.; Raychaudhuri, Soumya; Klareskog, Lars; Gregersen, Peter K.; Worthington, Jane

    2012-01-01

    Using the Immunochip custom SNP array, which was designed for dense genotyping of 186 loci identified through genome-wide association studies (GWAS), we analyzed 11,475 individuals with rheumatoid arthritis (cases) of European ancestry and 15,870 controls for 129,464 markers. We combined these data

  13. Targeted exonic sequencing of GWAS loci in the high extremes of the plasma lipids distribution

    NARCIS (Netherlands)

    Patel, Aniruddh P.; Peloso, Gina M.; Pirruccello, James P.; Johansen, Christopher T.; Dubé, Joseph B.; Larach, Daniel B.; Ban, Matthew R.; Dallinge-Thie, Geesje M.; Gupta, Namrata; Boehnke, Michael; Abecasis, Gonçalo R.; Kastelein, John J. P.; Hovingh, G. Kees; Hegele, Robert A.; Rader, Daniel J.; Kathiresan, Sekar

    2016-01-01

    Genome-wide association studies (GWAS) for plasma lipid levels have mapped numerous genomic loci, with each region often containing many protein-coding genes. Targeted re-sequencing of exons is a strategy to pinpoint causal variants and genes. We performed solution-based hybrid selection of 9008

  14. Introgression study reveals two quantitative trait loci involved in interspecific variation in memory retention among Nasonia wasp species

    NARCIS (Netherlands)

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

    2014-01-01

    Genes involved in the process of memory formation have been studied intensively in model organisms; however, little is known about the mechanisms that are responsible for natural variation in memory dynamics. There is substantial variation in memory retention among closely related species in the

  15. High-Resolution Genome-Wide Linkage Mapping Identifies Susceptibility Loci for BMI in the Chinese Population

    DEFF Research Database (Denmark)

    Zhang, Dong Feng; Pang, Zengchang; Li, Shuxia

    2012-01-01

    The genetic loci affecting the commonly used BMI have been intensively investigated using linkage approaches in multiple populations. This study aims at performing the first genome-wide linkage scan on BMI in the Chinese population in mainland China with hypothesis that heterogeneity in genetic...... linkage could exist in different ethnic populations. BMI was measured from 126 dizygotic twins in Qingdao municipality who were genotyped using high-resolution Affymetrix Genome-Wide Human SNP arrays containing about 1 million single-nucleotide polymorphisms (SNPs). Nonparametric linkage analysis...... in western countries. Multiple loci showing suggestive linkage were found on chromosome 1 (lod score 2.38 at 242 cM), chromosome 8 (2.48 at 95 cM), and chromosome 14 (2.2 at 89.4 cM). The strong linkage identified in the Chinese subjects that is consistent with that found in populations of European origin...

  16. Recruitment of PfSET2 by RNA polymerase II to variant antigen encoding loci contributes to antigenic variation in P. falciparum.

    Directory of Open Access Journals (Sweden)

    Uchechi E Ukaegbu

    2014-01-01

    Full Text Available Histone modifications are important regulators of gene expression in all eukaryotes. In Plasmodium falciparum, these epigenetic marks regulate expression of genes involved in several aspects of host-parasite interactions, including antigenic variation. While the identities and genomic positions of many histone modifications have now been cataloged, how they are targeted to defined genomic regions remains poorly understood. For example, how variant antigen encoding loci (var are targeted for deposition of unique histone marks is a mystery that continues to perplex the field. Here we describe the recruitment of an ortholog of the histone modifier SET2 to var genes through direct interactions with the C-terminal domain (CTD of RNA polymerase II. In higher eukaryotes, SET2 is a histone methyltransferase recruited by RNA pol II during mRNA transcription; however, the ortholog in P. falciparum (PfSET2 has an atypical architecture and its role in regulating transcription is unknown. Here we show that PfSET2 binds to the unphosphorylated form of the CTD, a property inconsistent with its recruitment during mRNA synthesis. Further, we show that H3K36me3, the epigenetic mark deposited by PfSET2, is enriched at both active and silent var gene loci, providing additional evidence that its recruitment is not associated with mRNA production. Over-expression of a dominant negative form of PfSET2 designed to disrupt binding to RNA pol II induced rapid var gene expression switching, confirming both the importance of PfSET2 in var gene regulation and a role for RNA pol II in its recruitment. RNA pol II is known to transcribe non-coding RNAs from both active and silent var genes, providing a possible mechanism by which it could recruit PfSET2 to var loci. This work unifies previous reports of histone modifications, the production of ncRNAs, and the promoter activity of var introns into a mechanism that contributes to antigenic variation by malaria parasites.

  17. High Resolution of Quantitative Traits Into Multiple Loci via Interval Mapping

    OpenAIRE

    Jansen, Ritsert C.; Stam, Piet

    1994-01-01

    A very general method is described for multiple linear regression of a quantitative phenotype on genotype [putative quantitative trait loci (QTLs) and markers] in segregating generations obtained from line crosses. The method exploits two features, (a) the use of additional parental and F1 data, which fixes the joint QTL effects and the environmental error, and (b) the use of markers as cofactors, which reduces the genetic background noise. As a result, a significant increase of QTL detection...

  18. The Case for High Resolution Extended 6-Loci HLA Typing for Identifying Related Donors in the Indian Subcontinent.

    Science.gov (United States)

    Agarwal, Rajat Kumar; Kumari, Ankita; Sedai, Amit; Parmar, Lalith; Dhanya, Rakesh; Faulkner, Lawrence

    2017-09-01

    Three-loci low-resolution (LR) or intermediate-resolution HLA typing is generally considered adequate in the related blood and marrow transplantation (BMT) context. However, a single high-resolution (HR) mismatch may have a similar adverse impact on BMT outcome as an LR one. We sought to determine the frequency of mismatches that may go undetected when standard typing (LR or 3-loci HR) is used compared with 6-loci HR typing for related donor compatibility testing, and to assess its impact on relevant BMT outcomes. We analyzed data from a total of 2554 6-loci (HLA-A, -B, -C, -DRB1, -DQB1, and -DPB1) HR sequence-based typing (full typing [FT]) from 754 patients, 1011 siblings, and 789 parents done at DKMS Germany (www.DKMS.de) between January 1, 2014, and June 21, 2016. We also studied 38 cases in which the family had undergone 3-loci HLA typing (standard typing [ST]). Patients were from India (70%), Pakistan (22%), and Sri Lanka (8%). The IMGT/HLA database (www.ebi.ac.uk/ipd/imgt/hla) was used to tease out nonpermissive DPB1 mismatches. HLA disparity-related outcomes, such as rejection and graft-versus-host disease (GVHD) were assessed in a retrospective matched-pair cohort of 50 patients (25 with ST and 25 with FT) who underwent BMT for severe thalassemia from compatible related donors. We found fully matched (either 12/12 HR matches or with a single permissive DPB1 mismatch) related donors for 285 patients (38%). Of these donors, 89% were siblings and 11% were parents. The likelihood of matching on an individual locus on LR but not on HR was found to be 5%. A total of 9 donors (3%; 7 siblings and 2 parents) who would have been considered a full match by HR typing on A, B, and DRB1 alone were not a match by extended 6-loci HR typing. Five of these 9 donors had a mismatch on C or DQB1, and 4 had a nonpermissive DPB1 mismatch. In this group, 5 donors (56%) belonged to a consanguineous family, in 2 donors (22%) there was no reported consanguinity, and in 2 donors (22

  19. Structure and amount of genetic variation at minisatellite loci within the subspecies complex of Phoca vitulina (the harbour seal)

    NARCIS (Netherlands)

    Kappe, A.L.; Bijlsma, R.; Osterhaus, ADME; van Delden, W.; van de Zande, L.

    The structure and amount of genetic variation within and between three subspecies of the harbour seal Phoca vitulina was assessed by multilocus DNA fingerprinting. Bandsharing similarity indicates that the subspecies Phoca vitulina richarhsi (Alaska, East Pacific) is clearly separated from the other

  20. Genetic analysis of two STR loci (VWA and TPOX in the Iranian province of Khuzestan

    Directory of Open Access Journals (Sweden)

    Ali Mohammad Foroughmand

    2014-08-01

    Conclusion: The examined STR loci in this study have proven a relatively high genetic variation in the Iranian population. The data could be used for construction of a forensic genetic database for the Iranian population.

  1. High levels of heterozygosity found for 15 SSR loci in Solanum chacoense

    Science.gov (United States)

    Genetic variation is a necessary prerequisite for improving domesticated plants through breeding; without it, breeding progress would be impossible. Genetic variation can be readily ascertained with co-dominant DNA markers, such as simple sequence repeats (SSRs). Twenty-four SSR markers specifically...

  2. High-density genotyping of immune-related loci identifies new SLE risk variants in individuals with Asian ancestry.

    Science.gov (United States)

    Sun, Celi; Molineros, Julio E; Looger, Loren L; Zhou, Xu-Jie; Kim, Kwangwoo; Okada, Yukinori; Ma, Jianyang; Qi, Yuan-Yuan; Kim-Howard, Xana; Motghare, Prasenjeet; Bhattarai, Krishna; Adler, Adam; Bang, So-Young; Lee, Hye-Soon; Kim, Tae-Hwan; Kang, Young Mo; Suh, Chang-Hee; Chung, Won Tae; Park, Yong-Beom; Choe, Jung-Yoon; Shim, Seung Cheol; Kochi, Yuta; Suzuki, Akari; Kubo, Michiaki; Sumida, Takayuki; Yamamoto, Kazuhiko; Lee, Shin-Seok; Kim, Young Jin; Han, Bok-Ghee; Dozmorov, Mikhail; Kaufman, Kenneth M; Wren, Jonathan D; Harley, John B; Shen, Nan; Chua, Kek Heng; Zhang, Hong; Bae, Sang-Cheol; Nath, Swapan K

    2016-03-01

    Systemic lupus erythematosus (SLE) has a strong but incompletely understood genetic architecture. We conducted an association study with replication in 4,478 SLE cases and 12,656 controls from six East Asian cohorts to identify new SLE susceptibility loci and better localize known loci. We identified ten new loci and confirmed 20 known loci with genome-wide significance. Among the new loci, the most significant locus was GTF2IRD1-GTF2I at 7q11.23 (rs73366469, Pmeta = 3.75 × 10(-117), odds ratio (OR) = 2.38), followed by DEF6, IL12B, TCF7, TERT, CD226, PCNXL3, RASGRP1, SYNGR1 and SIGLEC6. We identified the most likely functional variants at each locus by analyzing epigenetic marks and gene expression data. Ten candidate variants are known to alter gene expression in cis or in trans. Enrichment analysis highlights the importance of these loci in B cell and T cell biology. The new loci, together with previously known loci, increase the explained heritability of SLE to 24%. The new loci share functional and ontological characteristics with previously reported loci and are possible drug targets for SLE therapeutics.

  3. Meta-analysis of genome-wide association studies identifies 8 novel loci involved in shape variation of human head hair.

    Science.gov (United States)

    Liu, Fan; Chen, Yan; Zhu, Gu; Hysi, Pirro G; Wu, Sijie; Adhikari, Kaustubh; Breslin, Krystal; Pospiech, Ewelina; Hamer, Merel A; Peng, Fuduan; Muralidharan, Charanya; Acuna-Alonzo, Victor; Canizales-Quinteros, Samuel; Bedoya, Gabriel; Gallo, Carla; Poletti, Giovanni; Rothhammer, Francisco; Bortolini, Maria Catira; Gonzalez-Jose, Rolando; Zeng, Changqing; Xu, Shuhua; Jin, Li; Uitterlinden, André G; Ikram, M Arfan; van Duijn, Cornelia M; Nijsten, Tamar; Walsh, Susan; Branicki, Wojciech; Wang, Sijia; Ruiz-Linares, Andrés; Spector, Timothy D; Martin, Nicholas G; Medland, Sarah E; Kayser, Manfred

    2018-02-01

    Shape variation of human head hair shows striking variation within and between human populations, while its genetic basis is far from being understood. We performed a series of genome-wide association studies (GWASs) and replication studies in a total of 28 964 subjects from 9 cohorts from multiple geographic origins. A meta-analysis of three European GWASs identified 8 novel loci (1p36.23 ERRFI1/SLC45A1, 1p36.22 PEX14, 1p36.13 PADI3, 2p13.3 TGFA, 11p14.1 LGR4, 12q13.13 HOXC13, 17q21.2 KRTAP, and 20q13.33 PTK6), and confirmed 4 previously known ones (1q21.3 TCHH/TCHHL1/LCE3E, 2q35 WNT10A, 4q21.21 FRAS1, and 10p14 LINC00708/GATA3), all showing genome-wide significant association with hair shape (P 5e-8). All except one (1p36.22 PEX14) were replicated with nominal significance in at least one of the 6 additional cohorts of European, Native American and East Asian origins. Three additional previously known genes (EDAR, OFCC1, and PRSS53) were confirmed at the nominal significance level. A multivariable regression model revealed that 14 SNPs from different genes significantly and independently contribute to hair shape variation, reaching a cross-validated AUC value of 0.66 (95% CI: 0.62-0.70) and an AUC value of 0.64 in an independent validation cohort, providing an improved accuracy compared with a previous model. Prediction outcomes of 2504 individuals from a multiethnic sample were largely consistent with general knowledge on the global distribution of hair shape variation. Our study thus delivers target genes and DNA variants for future functional studies to further evaluate the molecular basis of hair shape in humans. © The Author(s) 2017. Published by Oxford University Press.

  4. Meta-analysis of genome-wide association studies identifies 8 novel loci involved in shape variation of human head hair

    Science.gov (United States)

    Liu, Fan; Chen, Yan; Zhu, Gu; Hysi, Pirro G; Wu, Sijie; Adhikari, Kaustubh; Breslin, Krystal; Pośpiech, Ewelina; Hamer, Merel A; Peng, Fuduan; Muralidharan, Charanya; Acuna-Alonzo, Victor; Canizales-Quinteros, Samuel; Bedoya, Gabriel; Gallo, Carla; Poletti, Giovanni; Rothhammer, Francisco; Bortolini, Maria Catira; Gonzalez-Jose, Rolando; Zeng, Changqing; Xu, Shuhua; Jin, Li; Uitterlinden, André G; Ikram, M Arfan; van Duijn, Cornelia M; Nijsten, Tamar; Walsh, Susan; Branicki, Wojciech; Wang, Sijia; Ruiz-Linares, Andrés; Spector, Timothy D; Martin, Nicholas G; Medland, Sarah E; Kayser, Manfred

    2018-01-01

    Abstract Shape variation of human head hair shows striking variation within and between human populations, while its genetic basis is far from being understood. We performed a series of genome-wide association studies (GWASs) and replication studies in a total of 28 964 subjects from 9 cohorts from multiple geographic origins. A meta-analysis of three European GWASs identified 8 novel loci (1p36.23 ERRFI1/SLC45A1, 1p36.22 PEX14, 1p36.13 PADI3, 2p13.3 TGFA, 11p14.1 LGR4, 12q13.13 HOXC13, 17q21.2 KRTAP, and 20q13.33 PTK6), and confirmed 4 previously known ones (1q21.3 TCHH/TCHHL1/LCE3E, 2q35 WNT10A, 4q21.21 FRAS1, and 10p14 LINC00708/GATA3), all showing genome-wide significant association with hair shape (P < 5e-8). All except one (1p36.22 PEX14) were replicated with nominal significance in at least one of the 6 additional cohorts of European, Native American and East Asian origins. Three additional previously known genes (EDAR, OFCC1, and PRSS53) were confirmed at the nominal significance level. A multivariable regression model revealed that 14 SNPs from different genes significantly and independently contribute to hair shape variation, reaching a cross-validated AUC value of 0.66 (95% CI: 0.62–0.70) and an AUC value of 0.64 in an independent validation cohort, providing an improved accuracy compared with a previous model. Prediction outcomes of 2504 individuals from a multiethnic sample were largely consistent with general knowledge on the global distribution of hair shape variation. Our study thus delivers target genes and DNA variants for future functional studies to further evaluate the molecular basis of hair shape in humans. PMID:29220522

  5. High-throughput SNP genotyping in Cucurbita pepo for map construction and quantitative trait loci mapping.

    Science.gov (United States)

    Esteras, Cristina; Gómez, Pedro; Monforte, Antonio J; Blanca, José; Vicente-Dólera, Nelly; Roig, Cristina; Nuez, Fernando; Picó, Belén

    2012-02-22

    Cucurbita pepo is a member of the Cucurbitaceae family, the second- most important horticultural family in terms of economic importance after Solanaceae. The "summer squash" types, including Zucchini and Scallop, rank among the highest-valued vegetables worldwide. There are few genomic tools available for this species.The first Cucurbita transcriptome, along with a large collection of Single Nucleotide Polymorphisms (SNP), was recently generated using massive sequencing. A set of 384 SNP was selected to generate an Illumina GoldenGate assay in order to construct the first SNP-based genetic map of Cucurbita and map quantitative trait loci (QTL). We herein present the construction of the first SNP-based genetic map of Cucurbita pepo using a population derived from the cross of two varieties with contrasting phenotypes, representing the main cultivar groups of the species' two subspecies: Zucchini (subsp. pepo) × Scallop (subsp. ovifera). The mapping population was genotyped with 384 SNP, a set of selected EST-SNP identified in silico after massive sequencing of the transcriptomes of both parents, using the Illumina GoldenGate platform. The global success rate of the assay was higher than 85%. In total, 304 SNP were mapped, along with 11 SSR from a previous map, giving a map density of 5.56 cM/marker. This map was used to infer syntenic relationships between C. pepo and cucumber and to successfully map QTL that control plant, flowering and fruit traits that are of benefit to squash breeding. The QTL effects were validated in backcross populations. Our results show that massive sequencing in different genotypes is an excellent tool for SNP discovery, and that the Illumina GoldenGate platform can be successfully applied to constructing genetic maps and performing QTL analysis in Cucurbita. This is the first SNP-based genetic map in the Cucurbita genus and is an invaluable new tool for biological research, especially considering that most of these markers are located in

  6. A three-component system incorporating Ppd-D1, copy number variation at Ppd-B1, and numerous small-effect quantitative trait loci facilitates adaptation of heading time in winter wheat cultivars of worldwide origin.

    Science.gov (United States)

    Würschum, Tobias; Langer, Simon M; Longin, C Friedrich H; Tucker, Matthew R; Leiser, Willmar L

    2018-06-01

    The broad adaptability of heading time has contributed to the global success of wheat in a diverse array of climatic conditions. Here, we investigated the genetic architecture underlying heading time in a large panel of 1,110 winter wheat cultivars of worldwide origin. Genome-wide association mapping, in combination with the analysis of major phenology loci, revealed a three-component system that facilitates the adaptation of heading time in winter wheat. The photoperiod sensitivity locus Ppd-D1 was found to account for almost half of the genotypic variance in this panel and can advance or delay heading by many days. In addition, copy number variation at Ppd-B1 was the second most important source of variation in heading, explaining 8.3% of the genotypic variance. Results from association mapping and genomic prediction indicated that the remaining variation is attributed to numerous small-effect quantitative trait loci that facilitate fine-tuning of heading to the local climatic conditions. Collectively, our results underpin the importance of the two Ppd-1 loci for the adaptation of heading time in winter wheat and illustrate how the three components have been exploited for wheat breeding globally. © 2018 John Wiley & Sons Ltd.

  7. Intragenomic polymorphisms among high-copy loci: a genus-wide study of nuclear ribosomal DNA in Asclepias (Apocynaceae).

    Science.gov (United States)

    Weitemier, Kevin; Straub, Shannon C K; Fishbein, Mark; Liston, Aaron

    2015-01-01

    Despite knowledge that concerted evolution of high-copy loci is often imperfect, studies that investigate the extent of intragenomic polymorphisms and comparisons across a large number of species are rarely made. We present a bioinformatic pipeline for characterizing polymorphisms within an individual among copies of a high-copy locus. Results are presented for nuclear ribosomal DNA (nrDNA) across the milkweed genus, Asclepias. The 18S-26S portion of the nrDNA cistron of Asclepias syriaca served as a reference for assembly of the region from 124 samples representing 90 species of Asclepias. Reads were mapped back to each individual's consensus and at each position reads differing from the consensus were tallied using a custom perl script. Low frequency polymorphisms existed in all individuals (mean = 5.8%). Most nrDNA positions (91%) were polymorphic in at least one individual, with polymorphic sites being less frequent in subunit regions and loops. Highly polymorphic sites existed in each individual, with highest abundance in the "noncoding" ITS regions. Phylogenetic signal was present in the distribution of intragenomic polymorphisms across the genus. Intragenomic polymorphisms in nrDNA are common in Asclepias, being found at higher frequency than any other study to date. The high and variable frequency of polymorphisms across species highlights concerns that phylogenetic applications of nrDNA may be error-prone. The new analytical approach provided here is applicable to other taxa and other high-copy regions characterized by low coverage genome sequencing (genome skimming).

  8. The use of high-throughput DNA sequencing in the investigation of antigenic variation: application to Neisseria species.

    Directory of Open Access Journals (Sweden)

    John K Davies

    Full Text Available Antigenic variation occurs in a broad range of species. This process resembles gene conversion in that variant DNA is unidirectionally transferred from partial gene copies (or silent loci into an expression locus. Previous studies of antigenic variation have involved the amplification and sequencing of individual genes from hundreds of colonies. Using the pilE gene from Neisseria gonorrhoeae we have demonstrated that it is possible to use PCR amplification, followed by high-throughput DNA sequencing and a novel assembly process, to detect individual antigenic variation events. The ability to detect these events was much greater than has previously been possible. In N. gonorrhoeae most silent loci contain multiple partial gene copies. Here we show that there is a bias towards using the copy at the 3' end of the silent loci (copy 1 as the donor sequence. The pilE gene of N. gonorrhoeae and some strains of Neisseria meningitidis encode class I pilin, but strains of N. meningitidis from clonal complexes 8 and 11 encode a class II pilin. We have confirmed that the class II pili of meningococcal strain FAM18 (clonal complex 11 are non-variable, and this is also true for the class II pili of strain NMB from clonal complex 8. In addition when a gene encoding class I pilin was moved into the meningococcal strain NMB background there was no evidence of antigenic variation. Finally we investigated several members of the opa gene family of N. gonorrhoeae, where it has been suggested that limited variation occurs. Variation was detected in the opaK gene that is located close to pilE, but not at the opaJ gene located elsewhere on the genome. The approach described here promises to dramatically improve studies of the extent and nature of antigenic variation systems in a variety of species.

  9. A novel HURRAH protocol reveals high numbers of monomorphic MHC class II loci and two asymmetric multi-locus haplotypes in the Père David's deer.

    Directory of Open Access Journals (Sweden)

    Qiu-Hong Wan

    Full Text Available The Père David's deer is a highly inbred, but recovered, species, making it interesting to consider their adaptive molecular evolution from an immunological perspective. Prior to this study, genomic sequencing was the only method for isolating all functional MHC genes within a certain species. Here, we report a novel protocol for isolating MHC class II loci from a species, and its use to investigate the adaptive evolution of this endangered deer at the level of multi-locus haplotypes. This protocol was designated "HURRAH" based on its various steps and used to estimate the total number of MHC class II loci. We confirmed the validity of this novel protocol in the giant panda and then used it to examine the Père David's deer. Our results revealed that the Père David's deer possesses nine MHC class II loci and therefore has more functional MHC class II loci than the eight genome-sequenced mammals for which full MHC data are currently available. This could potentially account at least in part for the strong survival ability of this species in the face of severe bottlenecking. The results from the HURRAH protocol also revealed that: (1 All of the identified MHC class II loci were monomorphic at their antigen-binding regions, although DRA was dimorphic at its cytoplasmic tail; and (2 these genes constituted two asymmetric functional MHC class II multi-locus haplotypes: DRA1*01 ∼ DRB1 ∼ DRB3 ∼ DQA1 ∼ DQB2 (H1 and DRA1*02 ∼ DRB2 ∼ DRB4 ∼ DQA2 ∼ DQB1 (H2. The latter finding indicates that the current members of the deer species have lost the powerful ancestral MHC class II haplotypes of nine or more loci, and have instead fixed two relatively weak haplotypes containing five genes. As a result, the Père David's deer are currently at risk for increased susceptibility to infectious pathogens.

  10. Discovery and fine-mapping of adiposity loci using high density imputation of genome-wide association studies in individuals of African ancestry: African Ancestry Anthropometry Genetics Consortium.

    Science.gov (United States)

    Ng, Maggie C Y; Graff, Mariaelisa; Lu, Yingchang; Justice, Anne E; Mudgal, Poorva; Liu, Ching-Ti; Young, Kristin; Yanek, Lisa R; Feitosa, Mary F; Wojczynski, Mary K; Rand, Kristin; Brody, Jennifer A; Cade, Brian E; Dimitrov, Latchezar; Duan, Qing; Guo, Xiuqing; Lange, Leslie A; Nalls, Michael A; Okut, Hayrettin; Tajuddin, Salman M; Tayo, Bamidele O; Vedantam, Sailaja; Bradfield, Jonathan P; Chen, Guanjie; Chen, Wei-Min; Chesi, Alessandra; Irvin, Marguerite R; Padhukasahasram, Badri; Smith, Jennifer A; Zheng, Wei; Allison, Matthew A; Ambrosone, Christine B; Bandera, Elisa V; Bartz, Traci M; Berndt, Sonja I; Bernstein, Leslie; Blot, William J; Bottinger, Erwin P; Carpten, John; Chanock, Stephen J; Chen, Yii-Der Ida; Conti, David V; Cooper, Richard S; Fornage, Myriam; Freedman, Barry I; Garcia, Melissa; Goodman, Phyllis J; Hsu, Yu-Han H; Hu, Jennifer; Huff, Chad D; Ingles, Sue A; John, Esther M; Kittles, Rick; Klein, Eric; Li, Jin; McKnight, Barbara; Nayak, Uma; Nemesure, Barbara; Ogunniyi, Adesola; Olshan, Andrew; Press, Michael F; Rohde, Rebecca; Rybicki, Benjamin A; Salako, Babatunde; Sanderson, Maureen; Shao, Yaming; Siscovick, David S; Stanford, Janet L; Stevens, Victoria L; Stram, Alex; Strom, Sara S; Vaidya, Dhananjay; Witte, John S; Yao, Jie; Zhu, Xiaofeng; Ziegler, Regina G; Zonderman, Alan B; Adeyemo, Adebowale; Ambs, Stefan; Cushman, Mary; Faul, Jessica D; Hakonarson, Hakon; Levin, Albert M; Nathanson, Katherine L; Ware, Erin B; Weir, David R; Zhao, Wei; Zhi, Degui; Arnett, Donna K; Grant, Struan F A; Kardia, Sharon L R; Oloapde, Olufunmilayo I; Rao, D C; Rotimi, Charles N; Sale, Michele M; Williams, L Keoki; Zemel, Babette S; Becker, Diane M; Borecki, Ingrid B; Evans, Michele K; Harris, Tamara B; Hirschhorn, Joel N; Li, Yun; Patel, Sanjay R; Psaty, Bruce M; Rotter, Jerome I; Wilson, James G; Bowden, Donald W; Cupples, L Adrienne; Haiman, Christopher A; Loos, Ruth J F; North, Kari E

    2017-04-01

    Genome-wide association studies (GWAS) have identified >300 loci associated with measures of adiposity including body mass index (BMI) and waist-to-hip ratio (adjusted for BMI, WHRadjBMI), but few have been identified through screening of the African ancestry genomes. We performed large scale meta-analyses and replications in up to 52,895 individuals for BMI and up to 23,095 individuals for WHRadjBMI from the African Ancestry Anthropometry Genetics Consortium (AAAGC) using 1000 Genomes phase 1 imputed GWAS to improve coverage of both common and low frequency variants in the low linkage disequilibrium African ancestry genomes. In the sex-combined analyses, we identified one novel locus (TCF7L2/HABP2) for WHRadjBMI and eight previously established loci at P African ancestry individuals. An additional novel locus (SPRYD7/DLEU2) was identified for WHRadjBMI when combined with European GWAS. In the sex-stratified analyses, we identified three novel loci for BMI (INTS10/LPL and MLC1 in men, IRX4/IRX2 in women) and four for WHRadjBMI (SSX2IP, CASC8, PDE3B and ZDHHC1/HSD11B2 in women) in individuals of African ancestry or both African and European ancestry. For four of the novel variants, the minor allele frequency was low (African ancestry sex-combined and sex-stratified analyses, 26 BMI loci and 17 WHRadjBMI loci contained ≤ 20 variants in the credible sets that jointly account for 99% posterior probability of driving the associations. The lead variants in 13 of these loci had a high probability of being causal. As compared to our previous HapMap imputed GWAS for BMI and WHRadjBMI including up to 71,412 and 27,350 African ancestry individuals, respectively, our results suggest that 1000 Genomes imputation showed modest improvement in identifying GWAS loci including low frequency variants. Trans-ethnic meta-analyses further improved fine mapping of putative causal variants in loci shared between the African and European ancestry populations.

  11. Dynamics of genetic variation at gliadin-coding loci in bread wheat cultivars developed in small grains research center (Kragujevac during last 35 years

    Directory of Open Access Journals (Sweden)

    Novosljska-Dragovič Aleksandra

    2005-01-01

    Full Text Available Multiple alleles of gliadin-coding loci are well-known genetic markers of common wheat genotypes. Based on analysis of gliadin patterns in common wheat cultivars developed at the Small Grains Research Center in Kragujevac dynamics of genetic variability at gliadin-coding loci has been surveyed for the period of 35 years. It was shown that long-term breeding of the wheat cultivars involved gradual replacement of ancient alleles for those widely spread in some regions in the world, which belong to well-known cultivars-donor of some important traits. Developing cultivars whose pedigree involved much new foreign genetic material has increased genetic diversity as well as has changed frequency of alleles of gliadin-coding loci. So we can conclude that the genetic profile of modern Serbian cultivars has changed considerably. Genetic formula of gliadin was made for each the cultivar studied. The most frequent alleles of gliadin-coding loci among modern cultivars should be of great interest of breeders because these alleles are probably linked with genes that confer advantage to their carriers at present.

  12. Distinct high resolution genome profiles of early onset and late onset colorectal cancer integrated with gene expression data identify candidate susceptibility loci

    Directory of Open Access Journals (Sweden)

    Merok Marianne A

    2010-05-01

    Full Text Available Abstract Background Estimates suggest that up to 30% of colorectal cancers (CRC may develop due to an increased genetic risk. The mean age at diagnosis for CRC is about 70 years. Time of disease onset 20 years younger than the mean age is assumed to be indicative of genetic susceptibility. We have compared high resolution tumor genome copy number variation (CNV (Roche NimbleGen, 385 000 oligo CGH array in microsatellite stable (MSS tumors from two age groups, including 23 young at onset patients without known hereditary syndromes and with a median age of 44 years (range: 28-53 and 17 elderly patients with median age 79 years (range: 69-87. Our aim was to identify differences in the tumor genomes between these groups and pinpoint potential susceptibility loci. Integration analysis of CNV and genome wide mRNA expression data, available for the same tumors, was performed to identify a restricted candidate gene list. Results The total fraction of the genome with aberrant copy number, the overall genomic profile and the TP53 mutation spectrum were similar between the two age groups. However, both the number of chromosomal aberrations and the number of breakpoints differed significantly between the groups. Gains of 2q35, 10q21.3-22.1, 10q22.3 and 19q13.2-13.31 and losses from 1p31.3, 1q21.1, 2q21.2, 4p16.1-q28.3, 10p11.1 and 19p12, positions that in total contain more than 500 genes, were found significantly more often in the early onset group as compared to the late onset group. Integration analysis revealed a covariation of DNA copy number at these sites and mRNA expression for 107 of the genes. Seven of these genes, CLC, EIF4E, LTBP4, PLA2G12A, PPAT, RG9MTD2, and ZNF574, had significantly different mRNA expression comparing median expression levels across the transcriptome between the two groups. Conclusions Ten genomic loci, containing more than 500 protein coding genes, are identified as more often altered in tumors from early onset versus late

  13. Genetic Variation of 25 Y-Chromosomal and 15 Autosomal STR Loci in the Han Chinese Population of Liaoning Province, Northeast China.

    Science.gov (United States)

    Yao, Jun; Wang, Bao-Jie

    2016-01-01

    In the present study, we investigated the genetic characteristics of 25 Y-chromosomal and 15 autosomal short tandem repeat (STR) loci in 305 unrelated Han Chinese male individuals from Liaoning Province using AmpFISTR® Yfiler® Plus and IdentifilerTM PCR amplification kits. Population comparison was performed between Liaoning Han population and different ethnic groups to better understand the genetic background of the Liaoning Han population. For Y-STR loci, the overall haplotype diversity was 0.9997 and the discrimination capacity was 0.9607. Gene diversity values ranged from 0.4525 (DYS391) to 0.9617 (DYS385). Rst and two multi-dimensional scaling plots showed that minor differences were observed when the Liaoning Han population was compared to the Jilin Han Chinese, Beijing Han Chinese, Liaoning Manchu, Liaoning Mongolian, Liaoning Xibe, Shandong Han Chinese, Jiangsu Han Chinese, Anhui Han Chinese, Guizhou Han Chinese and Liaoning Hui populations; by contrast, major differences were observed when the Shanxi Han Chinese, Yunnan Bai, Jiangxi Han Chinese, Guangdong Han Chinese, Liaoning Korean, Hunan Tujia, Guangxi Zhuang, Gansu Tibetan, Xishuangbanna Dai, South Korean, Japanese and Hunan Miao populations. For autosomal STR loci, DP ranged from 0.9621 (D2S1338) to 0.8177 (TPOX), with PE distributing from 0.7521 (D18S51) to 0.2988 (TH01). A population comparison was performed and no statistically significant differences were detected at any STR loci between Liaoning Han, China Dong, and Shaanxi Han populations. The results showed that the 25 Y-STR and 15 autosomal STR loci in the Liaoning Han population were valuable for forensic applications and human genetics, and Liaoning Han was an independent endogenous ethnicity with a unique subpopulation structure.

  14. Genetic Variation of 25 Y-Chromosomal and 15 Autosomal STR Loci in the Han Chinese Population of Liaoning Province, Northeast China.

    Directory of Open Access Journals (Sweden)

    Jun Yao

    Full Text Available In the present study, we investigated the genetic characteristics of 25 Y-chromosomal and 15 autosomal short tandem repeat (STR loci in 305 unrelated Han Chinese male individuals from Liaoning Province using AmpFISTR® Yfiler® Plus and IdentifilerTM PCR amplification kits. Population comparison was performed between Liaoning Han population and different ethnic groups to better understand the genetic background of the Liaoning Han population. For Y-STR loci, the overall haplotype diversity was 0.9997 and the discrimination capacity was 0.9607. Gene diversity values ranged from 0.4525 (DYS391 to 0.9617 (DYS385. Rst and two multi-dimensional scaling plots showed that minor differences were observed when the Liaoning Han population was compared to the Jilin Han Chinese, Beijing Han Chinese, Liaoning Manchu, Liaoning Mongolian, Liaoning Xibe, Shandong Han Chinese, Jiangsu Han Chinese, Anhui Han Chinese, Guizhou Han Chinese and Liaoning Hui populations; by contrast, major differences were observed when the Shanxi Han Chinese, Yunnan Bai, Jiangxi Han Chinese, Guangdong Han Chinese, Liaoning Korean, Hunan Tujia, Guangxi Zhuang, Gansu Tibetan, Xishuangbanna Dai, South Korean, Japanese and Hunan Miao populations. For autosomal STR loci, DP ranged from 0.9621 (D2S1338 to 0.8177 (TPOX, with PE distributing from 0.7521 (D18S51 to 0.2988 (TH01. A population comparison was performed and no statistically significant differences were detected at any STR loci between Liaoning Han, China Dong, and Shaanxi Han populations. The results showed that the 25 Y-STR and 15 autosomal STR loci in the Liaoning Han population were valuable for forensic applications and human genetics, and Liaoning Han was an independent endogenous ethnicity with a unique subpopulation structure.

  15. Intragenomic polymorphisms among high-copy loci: a genus-wide study of nuclear ribosomal DNA in Asclepias (Apocynaceae

    Directory of Open Access Journals (Sweden)

    Kevin Weitemier

    2015-01-01

    Full Text Available Despite knowledge that concerted evolution of high-copy loci is often imperfect, studies that investigate the extent of intragenomic polymorphisms and comparisons across a large number of species are rarely made. We present a bioinformatic pipeline for characterizing polymorphisms within an individual among copies of a high-copy locus. Results are presented for nuclear ribosomal DNA (nrDNA across the milkweed genus, Asclepias. The 18S-26S portion of the nrDNA cistron of Asclepias syriaca served as a reference for assembly of the region from 124 samples representing 90 species of Asclepias. Reads were mapped back to each individual’s consensus and at each position reads differing from the consensus were tallied using a custom perl script. Low frequency polymorphisms existed in all individuals (mean = 5.8%. Most nrDNA positions (91% were polymorphic in at least one individual, with polymorphic sites being less frequent in subunit regions and loops. Highly polymorphic sites existed in each individual, with highest abundance in the “noncoding” ITS regions. Phylogenetic signal was present in the distribution of intragenomic polymorphisms across the genus. Intragenomic polymorphisms in nrDNA are common in Asclepias, being found at higher frequency than any other study to date. The high and variable frequency of polymorphisms across species highlights concerns that phylogenetic applications of nrDNA may be error-prone. The new analytical approach provided here is applicable to other taxa and other high-copy regions characterized by low coverage genome sequencing (genome skimming.

  16. Multiple cold resistance loci confer the high cold tolerance adaptation of Dongxiang wild rice (Oryza rufipogon) to its high-latitude habitat.

    Science.gov (United States)

    Mao, Donghai; Yu, Li; Chen, Dazhou; Li, Lanying; Zhu, Yuxing; Xiao, Yeqing; Zhang, Dechun; Chen, Caiyan

    2015-07-01

    Dongxiang wild rice is phylogenetically close to temperate japonica and contains multiple cold resistance loci conferring its adaptation to high-latitude habitat. Understanding the nature of adaptation in wild populations will benefit crop breeding in the development of climate-resilient crop varieties. Dongxiang wild rice (DXWR), the northernmost common wild rice known, possesses a high degree of cold tolerance and can survive overwintering in its native habitat. However, to date, it is still unclear how DXWR evolved to cope with low-temperature environment, resulting in limited application of DXWR in rice breeding programs. In this study, we carried out both QTL mapping and phylogenetic analysis to discern the genetic mechanism underlying the strong cold resistance. Through a combination of interval mapping and single locus analysis in two genetic populations, at least 13 QTLs for seedling cold tolerance were identified in DXWR. A phylogenetic study using both genome-wide InDel markers and markers associated with cold tolerance loci reveals that DXWR belongs to the Or-III group, which is most closely related to cold-tolerant Japonica rice rather than to the Indica cultivars that are predominant in the habitat where DXWR grows. Our study paves the way toward an understanding of the nature of adaptation to a northern habitat in O. rufipogon. The QTLs identified in DXWR in this study will be useful for molecular breeding of cold-tolerant rice.

  17. Genomewide Linkage Screen for Waldenström Macroglobulinemia Susceptibility Loci in High-Risk Families

    Science.gov (United States)

    McMaster, Mary L.; Goldin, Lynn R.; Bai, Yan; Ter-Minassian, Monica; Boehringer, Stefan; Giambarresi, Therese R.; Vasquez, Linda G.; Tucker, Margaret A.

    2006-01-01

    Waldenström macroglobulinemia (WM), a distinctive subtype of non-Hodgkin lymphoma that features overproduction of immunoglobulin M (IgM), clearly has a familial component; however, no susceptibility genes have yet been identified. We performed a genomewide linkage analysis in 11 high-risk families with WM that were informative for linkage, for a total of 122 individuals with DNA samples, including 34 patients with WM and 10 patients with IgM monoclonal gammopathy of undetermined significance (IgM MGUS). We genotyped 1,058 microsatellite markers (average spacing 3.5 cM), performed both nonparametric and parametric linkage analysis, and computed both two-point and multipoint linkage statistics. The strongest evidence of linkage was found on chromosomes 1q and 4q when patients with WM and with IgM MGUS were both considered affected; nonparametric linkage scores were 2.5 (P=.0089) and 3.1 (P=.004), respectively. Other locations suggestive of linkage were found on chromosomes 3 and 6. Results of two-locus linkage analysis were consistent with independent effects. The findings from this first linkage analysis of families at high risk for WM represent important progress toward identifying gene(s) that modulate susceptibility to WM and toward understanding its complex etiology. PMID:16960805

  18. Population genomics of Pacific lamprey: adaptive variation in a highly dispersive species.

    Science.gov (United States)

    Hess, Jon E; Campbell, Nathan R; Close, David A; Docker, Margaret F; Narum, Shawn R

    2013-06-01

    Unlike most anadromous fishes that have evolved strict homing behaviour, Pacific lamprey (Entosphenus tridentatus) seem to lack philopatry as evidenced by minimal population structure across the species range. Yet unexplained findings of within-region population genetic heterogeneity coupled with the morphological and behavioural diversity described for the species suggest that adaptive genetic variation underlying fitness traits may be responsible. We employed restriction site-associated DNA sequencing to genotype 4439 quality filtered single nucleotide polymorphism (SNP) loci for 518 individuals collected across a broad geographical area including British Columbia, Washington, Oregon and California. A subset of putatively neutral markers (N = 4068) identified a significant amount of variation among three broad populations: northern British Columbia, Columbia River/southern coast and 'dwarf' adults (F(CT) = 0.02, P ≪ 0.001). Additionally, 162 SNPs were identified as adaptive through outlier tests, and inclusion of these markers revealed a signal of adaptive variation related to geography and life history. The majority of the 162 adaptive SNPs were not independent and formed four groups of linked loci. Analyses with matsam software found that 42 of these outlier SNPs were significantly associated with geography, run timing and dwarf life history, and 27 of these 42 SNPs aligned with known genes or highly conserved genomic regions using the genome browser available for sea lamprey. This study provides both neutral and adaptive context for observed genetic divergence among collections and thus reconciles previous findings of population genetic heterogeneity within a species that displays extensive gene flow. © 2012 John Wiley & Sons Ltd.

  19. Three new loci for determining x chromosome inactivation patterns

    DEFF Research Database (Denmark)

    Bertelsen, Birgitte; Tümer, Zeynep; Ravn, Kirstine

    2011-01-01

    . The reliability of the loci was validated by showing a high correlation between the results obtained by employing the new loci and the AR locus using DNA from 15 females who were informative for all four loci. Altogether, we show that these loci can be applied easily in molecular diagnostic laboratories, either...

  20. Fast magnetic resonance imaging based on high degree total variation

    Science.gov (United States)

    Wang, Sujie; Lu, Liangliang; Zheng, Junbao; Jiang, Mingfeng

    2018-04-01

    In order to eliminating the artifacts and "staircase effect" of total variation in Compressive Sensing MRI, high degree total variation model is proposed for dynamic MRI reconstruction. the high degree total variation regularization term is used as a constraint to reconstruct the magnetic resonance image, and the iterative weighted MM algorithm is proposed to solve the convex optimization problem of the reconstructed MR image model, In addtion, one set of cardiac magnetic resonance data is used to verify the proposed algorithm for MRI. The results show that the high degree total variation method has a better reconstruction effect than the total variation and the total generalized variation, which can obtain higher reconstruction SNR and better structural similarity.

  1. High-throughput sequencing of core STR loci for forensic genetic investigations using the Roche Genome Sequencer FLX platform

    DEFF Research Database (Denmark)

    Fordyce, Sarah Louise; Avila Arcos, Maria del Carmen; Rockenbauer, Eszter

    2011-01-01

    repeat units. These methods do not allow for the full resolution of STR base composition that sequencing approaches could provide. Here we present an STR profiling method based on the use of the Roche Genome Sequencer (GS) FLX to simultaneously sequence multiple core STR loci. Using this method...

  2. A genome-wide analysis of putative functional and exonic variation associated with extremely high intelligence.

    Science.gov (United States)

    Spain, S L; Pedroso, I; Kadeva, N; Miller, M B; Iacono, W G; McGue, M; Stergiakouli, E; Davey Smith, G; Putallaz, M; Lubinski, D; Meaburn, E L; Plomin, R; Simpson, M A

    2016-08-01

    Although individual differences in intelligence (general cognitive ability) are highly heritable, molecular genetic analyses to date have had limited success in identifying specific loci responsible for its heritability. This study is the first to investigate exome variation in individuals of extremely high intelligence. Under the quantitative genetic model, sampling from the high extreme of the distribution should provide increased power to detect associations. We therefore performed a case-control association analysis with 1409 individuals drawn from the top 0.0003 (IQ >170) of the population distribution of intelligence and 3253 unselected population-based controls. Our analysis focused on putative functional exonic variants assayed on the Illumina HumanExome BeadChip. We did not observe any individual protein-altering variants that are reproducibly associated with extremely high intelligence and within the entire distribution of intelligence. Moreover, no significant associations were found for multiple rare alleles within individual genes. However, analyses using genome-wide similarity between unrelated individuals (genome-wide complex trait analysis) indicate that the genotyped functional protein-altering variation yields a heritability estimate of 17.4% (s.e. 1.7%) based on a liability model. In addition, investigation of nominally significant associations revealed fewer rare alleles associated with extremely high intelligence than would be expected under the null hypothesis. This observation is consistent with the hypothesis that rare functional alleles are more frequently detrimental than beneficial to intelligence.

  3. Identification and genetic mapping of highly polymorphic microsatellite loci from an EST database of the septoria tritici blotch pathogen Mycosphaerella graminicola.

    Science.gov (United States)

    Goodwin, Stephen B; van der Lee, Theo A J; Cavaletto, Jessica R; Te Lintel Hekkert, Bas; Crane, Charles F; Kema, Gert H J

    2007-05-01

    A database of 30,137 EST sequences from Mycosphaerella graminicola, the septoria tritici blotch fungus of wheat, was scanned with a custom software pipeline for di- and trinucleotide units repeated tandemly six or more times. The bioinformatics analysis identified 109 putative SSR loci, and for 99 of them, flanking primers were developed successfully and tested for amplification and polymorphism by PCR on five field isolates of diverse origin, including the parents of the standard M. graminicola mapping population. Seventy-seven of the 99 primer pairs generated an easily scored banding pattern and 51 were polymorphic, with up to four alleles per locus, among the isolates tested. Among these 51 loci, 23 were polymorphic between the parents of the mapping population. Twenty-one of these as well as two previously published microsatellite loci were positioned on the existing genetic linkage map of M. graminicola on 13 of the 24 linkage groups. Most (66%) of the primer pairs also amplified bands in the closely related barley pathogen Septoria passerinii, but only six were polymorphic among four isolates tested. A subset of the primer pairs also revealed polymorphisms when tested with DNA from the related banana black leaf streak (Black Sigatoka) pathogen, M. fijiensis. The EST database provided an excellent source of new, highly polymorphic microsatellite markers that can be multiplexed for high-throughput genetic analyses of M. graminicola and related species.

  4. Genetic variants near TIMP3 and high-density lipoprotein–associated loci influence susceptibility to age-related macular degeneration

    Science.gov (United States)

    Chen, Wei; Stambolian, Dwight; Edwards, Albert O.; Branham, Kari E.; Othman, Mohammad; Jakobsdottir, Johanna; Tosakulwong, Nirubol; Pericak-Vance, Margaret A.; Campochiaro, Peter A.; Klein, Michael L.; Tan, Perciliz L.; Conley, Yvette P.; Kanda, Atsuhiro; Kopplin, Laura; Li, Yanming; Augustaitis, Katherine J.; Karoukis, Athanasios J.; Scott, William K.; Agarwal, Anita; Kovach, Jaclyn L.; Schwartz, Stephen G.; Postel, Eric A.; Brooks, Matthew; Baratz, Keith H.; Brown, William L.; Brucker, Alexander J.; Orlin, Anton; Brown, Gary; Ho, Allen; Regillo, Carl; Donoso, Larry; Tian, Lifeng; Kaderli, Brian; Hadley, Dexter; Hagstrom, Stephanie A.; Peachey, Neal S.; Klein, Ronald; Klein, Barbara E. K.; Gotoh, Norimoto; Yamashiro, Kenji; Ferris, Frederick; Fagerness, Jesen A.; Reynolds, Robyn; Farrer, Lindsay A.; Kim, Ivana K.; Miller, Joan W.; Cortón, Marta; Carracedo, Angel; Sanchez-Salorio, Manuel; Pugh, Elizabeth W.; Doheny, Kimberly F.; Brion, Maria; DeAngelis, Margaret M.; Weeks, Daniel E.; Zack, Donald J.; Chew, Emily Y.; Heckenlively, John R.; Yoshimura, Nagahisa; Iyengar, Sudha K.; Francis, Peter J.; Katsanis, Nicholas; Seddon, Johanna M.; Haines, Jonathan L.; Gorin, Michael B.; Abecasis, Gonçalo R.; Swaroop, Anand; Johnson, Robert N.; Ai, Everett; McDonald, H. Richard; Stolarczuk, Margaret; Pavan, Peter Reed; Billiris, Karina K.; Iyer, Mohan; Menosky, Matthew M.; Pautler, Scott E.; Millard, Sharon M.; Hubbard, Baker; Aaberg, Thomas; DuBois, Lindy; Lyon, Alice; Anderson-Nelson, Susan; Jampol, Lee M.; Weinberg, David V.; Muñana, Annie; Rozenbajgier, Zuzanna; Orth, David; Cohen, Jack; MacCumber, Matthew; MacCumber, Matthew; Figliulo, Celeste; Porcz, Liz; Folk, James; Boldt, H. Culver; Russell, Stephen R.; Ivins, Rachel; Hinz, Connie J.; Barr, Charles C.; Bloom, Steve; Jaegers, Ken; Kritchman, Brian; Whittington, Greg; Heier, Jeffrey; Frederick, Albert R.; Morley, Michael G.; Topping, Trexler; Davis, Heather L.; Bressler, Susan B.; Bressler, Neil M.; Doll, Warren; Trese, Michael; Capone, Antonio; Garretson, Bruce R.; Hassan, Tarek S.; Ruby, Alan J.; Osentoski, Tammy; McCannel, Colin A.; Ruszczyk, Margaret J.; Grand, Gilbert; Blinder, Kevin; Holekamp, Nancy M.; Joseph, Daniel P.; Shah, Gaurav; Nobel, Ginny S.; Antoszyk, Andrew N.; Browning, David J.; Stallings, Alison H; Singerman, Lawrence J.; Miller, David; Novak, Michael; Pendergast, Scott; Zegarra, Hernando; Schura, Stephanie A.; Smith-Brewer, Sheila; Davidorf, Frederick H.; Chambers, Robert; Chorich, Louis; Salerno, Jill; Dreyer, Richard F.; Ma, Colin; Kopfer, Marcia R.; Klein, Michael L.; Wilson, David J.; Nolte, Susan K.; Grunwald, Juan E.; Brucker, Alexander J.; Dunaief, Josh; Fine, Stuart L.; Maguire, Albert M.; Stoltz, Robert A.; McRay, Monique N.; Fish, Gary Edd; Anand, Rajiv; Spencer, Rand; Arnwine, Jean; Chandra, Suresh R.; Altaweel, Michael; Blodi, Barbara; Gottlieb, Justin; Ip, Michael; Nork, T. Michael; Perry-Raymond, Jennie; Fine, Stuart L.; Maguire, Maureen G.; Brightwell-Arnold, Mary; Harkins, Sandra; Peskin, Ellen; Ying, Gui-Shuang; Kurinij, Natalie

    2010-01-01

    We executed a genome-wide association scan for age-related macular degeneration (AMD) in 2,157 cases and 1,150 controls. Our results validate AMD susceptibility loci near CFH (P < 10−75), ARMS2 (P < 10−59), C2/CFB (P < 10−20), C3 (P < 10−9), and CFI (P < 10−6). We compared our top findings with the Tufts/Massachusetts General Hospital genome-wide association study of advanced AMD (821 cases, 1,709 controls) and genotyped 30 promising markers in additional individuals (up to 7,749 cases and 4,625 controls). With these data, we identified a susceptibility locus near TIMP3 (overall P = 1.1 × 10−11), a metalloproteinase involved in degradation of the extracellular matrix and previously implicated in early-onset maculopathy. In addition, our data revealed strong association signals with alleles at two loci (LIPC, P = 1.3 × 10−7; CETP, P = 7.4 × 10−7) that were previously associated with high-density lipoprotein cholesterol (HDL-c) levels in blood. Consistent with the hypothesis that HDL metabolism is associated with AMD pathogenesis, we also observed association with AMD of HDL-c—associated alleles near LPL (P = 3.0 × 10−3) and ABCA1 (P = 5.6 × 10−4). Multilocus analysis including all susceptibility loci showed that 329 of 331 individuals (99%) with the highest-risk genotypes were cases, and 85% of these had advanced AMD. Our studies extend the catalog of AMD associated loci, help identify individuals at high risk of disease, and provide clues about underlying cellular pathways that should eventually lead to new therapies. PMID:20385819

  5. Highly polygenic variation in environmental perception determines dauer larvae formation in growing populations of Caenorhabditis elegans.

    Directory of Open Access Journals (Sweden)

    James W M Green

    Full Text Available Determining how complex traits are genetically controlled is a requirement if we are to predict how they evolve and how they might respond to selection. This requires understanding how distinct, and often more simple, life history traits interact and change in response to environmental conditions. In order to begin addressing such issues, we have been analyzing the formation of the developmentally arrested dauer larvae of Caenorhabditis elegans under different conditions.We find that 18 of 22 previously identified quantitative trait loci (QTLs affecting dauer larvae formation in growing populations, assayed by determining the number of dauer larvae present at food patch exhaustion, can be recovered under various environmental conditions. We also show that food patch size affects both the ability to detect QTLs and estimates of effect size, and demonstrate that an allele of nath-10 affects dauer larvae formation in growing populations. To investigate the component traits that affect dauer larvae formation in growing populations we map, using the same introgression lines, QTLs that affect dauer larvae formation in response to defined amounts of pheromone. This identifies 36 QTLs, again demonstrating the highly polygenic nature of the genetic variation underlying dauer larvae formation.These data indicate that QTLs affecting the number of dauer larvae at food exhaustion in growing populations of C. elegans are highly reproducible, and that nearly all can be explained by variation affecting dauer larvae formation in response to defined amounts of pheromone. This suggests that most variation in dauer larvae formation in growing populations is a consequence of variation in the perception of the food and pheromone environment (i.e. chemosensory variation and in the integration of these cues.

  6. Novel Associations of Nonstructural Loci with Paraoxonase Activity

    Directory of Open Access Journals (Sweden)

    Ellen E. Quillen

    2012-01-01

    Full Text Available The high-density-lipoprotein-(HDL- associated esterase paraoxonase 1 (PON1 is a likely contributor to the antioxidant and antiatherosclerotic capabilities of HDL. Two nonsynonymous mutations in the structural gene, PON1, have been associated with variation in activity levels, but substantial interindividual differences remain unexplained and are greatest for substrates other than the eponymous paraoxon. PON1 activity levels were measured for three substrates—organophosphate paraoxon, arylester phenyl acetate, and lactone dihydrocoumarin—in 767 Mexican American individuals from San Antonio, Texas. Genetic influences on activity levels for each substrate were evaluated by association with approximately one million single nucleotide polymorphism (SNPs while conditioning on PON1 genotypes. Significant associations were detected at five loci including regions on chromosomes 4 and 17 known to be associated with atherosclerosis and lipoprotein regulation and loci on chromosome 3 that regulate ubiquitous transcription factors. These loci explain 7.8% of variation in PON1 activity with lactone as a substrate, 5.6% with the arylester, and 3.0% with paraoxon. In light of the potential importance of PON1 in preventing cardiovascular disease/events, these novel loci merit further investigation.

  7. High throughput sequencing of small RNA component of leaves and inflorescence revealed conserved and novel miRNAs as well as phasiRNA loci in chickpea.

    Science.gov (United States)

    Srivastava, Sangeeta; Zheng, Yun; Kudapa, Himabindu; Jagadeeswaran, Guru; Hivrale, Vandana; Varshney, Rajeev K; Sunkar, Ramanjulu

    2015-06-01

    Among legumes, chickpea (Cicer arietinum L.) is the second most important crop after soybean. MicroRNAs (miRNAs) play important roles by regulating target gene expression important for plant development and tolerance to stress conditions. Additionally, recently discovered phased siRNAs (phasiRNAs), a new class of small RNAs, are abundantly produced in legumes. Nevertheless, little is known about these regulatory molecules in chickpea. The small RNA population was sequenced from leaves and flowers of chickpea to identify conserved and novel miRNAs as well as phasiRNAs/phasiRNA loci. Bioinformatics analysis revealed 157 miRNA loci for the 96 highly conserved and known miRNA homologs belonging to 38 miRNA families in chickpea. Furthermore, 20 novel miRNAs belonging to 17 miRNA families were identified. Sequence analysis revealed approximately 60 phasiRNA loci. Potential target genes likely to be regulated by these miRNAs were predicted and some were confirmed by modified 5' RACE assay. Predicted targets are mostly transcription factors that might be important for developmental processes, and others include superoxide dismutases, plantacyanin, laccases and F-box proteins that could participate in stress responses and protein degradation. Overall, this study provides an inventory of miRNA-target gene interactions for chickpea, useful for the comparative analysis of small RNAs among legumes. Copyright © 2015 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

  8. Accurate, high-throughput typing of copy number variation using paralogue ratios from dispersed repeats.

    Science.gov (United States)

    Armour, John A L; Palla, Raquel; Zeeuwen, Patrick L J M; den Heijer, Martin; Schalkwijk, Joost; Hollox, Edward J

    2007-01-01

    Recent work has demonstrated an unexpected prevalence of copy number variation in the human genome, and has highlighted the part this variation may play in predisposition to common phenotypes. Some important genes vary in number over a high range (e.g. DEFB4, which commonly varies between two and seven copies), and have posed formidable technical challenges for accurate copy number typing, so that there are no simple, cheap, high-throughput approaches suitable for large-scale screening. We have developed a simple comparative PCR method based on dispersed repeat sequences, using a single pair of precisely designed primers to amplify products simultaneously from both test and reference loci, which are subsequently distinguished and quantified via internal sequence differences. We have validated the method for the measurement of copy number at DEFB4 by comparison of results from >800 DNA samples with copy number measurements by MAPH/REDVR, MLPA and array-CGH. The new Paralogue Ratio Test (PRT) method can require as little as 10 ng genomic DNA, appears to be comparable in accuracy to the other methods, and for the first time provides a rapid, simple and inexpensive method for copy number analysis, suitable for application to typing thousands of samples in large case-control association studies.

  9. CoLIde: A bioinformatics tool for CO-expression based small RNA Loci Identification using high-throughput sequencing data

    OpenAIRE

    Mohorianu, Irina; Stocks, Matthew Benedict; Wood, John; Dalmay, Tamas; Moulton, Vincent

    2013-01-01

    Small RNAs (sRNAs) are 20–25 nt non-coding RNAs that act as guides for the highly sequence-specific regulatory mechanism known as RNA silencing. Due to the recent increase in sequencing depth, a highly complex and diverse population of sRNAs in both plants and animals has been revealed. However, the exponential increase in sequencing data has also made the identification of individual sRNA transcripts corresponding to biological units (sRNA loci) more challenging when based exclusively on the...

  10. Novel microsatellite loci for studies of Thamnophis Gartersnake genetic identity and hybridization

    Science.gov (United States)

    Sloss, Brian L.; Schuurman, Gregor W.; Paloski, Rori A.; Boyle, Owen D.; Kapfer, Joshua M.

    2012-01-01

    Butler’s Gartersnakes (BGS; Thamnophis butleri) are confined to open and semi-open canopy wetlands and adjacent uplands, habitats under threat of development in Wisconsin. To address issues of species identity and putative hybridization with congeneric snakes, a suite of 18 microsatellite loci capable of cross-species amplification of Plains Gartersnakes (T. radix) and Common Gartersnakes (T. sirtalis) was developed. All loci were polymorphic in BGS with mean number of alleles per locus of 16.11 (range = 3–41) and mean observed heterozygosity of 0.659 (range = 0.311–0.978). Loci amplified efficiently in the congeneric species with high levels of intra- and inter-specific variation. These loci will aid ongoing efforts to effectively identify and manage BGS in Wisconsin.

  11. Identification of mega-environments in Europe and effect of allelic variation at maturity E loci on adaptation of European soybean.

    Science.gov (United States)

    Kurasch, Alena K; Hahn, Volker; Leiser, Willmar L; Vollmann, Johann; Schori, Arnold; Bétrix, Claude-Alain; Mayr, Bernhard; Winkler, Johanna; Mechtler, Klemens; Aper, Jonas; Sudaric, Aleksandra; Pejic, Ivan; Sarcevic, Hrvoje; Jeanson, Patrice; Balko, Christiane; Signor, Marco; Miceli, Fabiano; Strijk, Peter; Rietman, Hendrik; Muresanu, Eugen; Djordjevic, Vuk; Pospišil, Ana; Barion, Giuseppe; Weigold, Peter; Streng, Stefan; Krön, Matthias; Würschum, Tobias

    2017-05-01

    Soybean cultivation holds great potential for a sustainable agriculture in Europe, but adaptation remains a central issue. In this large mega-environment (MEV) study, 75 European cultivars from five early maturity groups (MGs 000-II) were evaluated for maturity-related traits at 22 locations in 10 countries across Europe. Clustering of the locations based on phenotypic similarity revealed six MEVs in latitudinal direction and suggested several more. Analysis of maturity identified several groups of cultivars with phenotypic similarity that are optimally adapted to the different growing regions in Europe. We identified several haplotypes for the allelic variants at the E1, E2, E3 and E4 genes, with each E haplotype comprising cultivars from different MGs. Cultivars with the same E haplotype can exhibit different flowering and maturity characteristics, suggesting that the genetic control of these traits is more complex and that adaptation involves additional genetic pathways, for example temperature requirement. Taken together, our study allowed the first unified assessment of soybean-growing regions in Europe and illustrates the strong effect of photoperiod on soybean adaptation and MEV classification, as well as the effects of the E maturity loci for soybean adaptation in Europe. © 2017 John Wiley & Sons Ltd.

  12. High polymorphism in Est-SSR loci for cellulose synthase and β-amylase of sugarcane varieties (Saccharum spp.) used by the industrial sector for ethanol production.

    Science.gov (United States)

    Augusto, Raphael; Maranho, Rone Charles; Mangolin, Claudete Aparecida; Pires da Silva Machado, Maria de Fátima

    2015-01-01

    High and low polymorphisms in simple sequence repeats of expressed sequence tag (EST-SSR) for specific proteins and enzymes, such as β-amylase, cellulose synthase, xyloglucan endotransglucosylase, fructose 1,6-bisphosphate aldolase, and fructose 1,6-bisphosphatase, were used to illustrate the genetic divergence within and between varieties of sugarcane (Saccharum spp.) and to guide the technological paths to optimize ethanol production from lignocellulose biomass. The varieties RB72454, RB867515, RB92579, and SP813250 on the second stage of cutting, all grown in the state of Paraná (PR), and the varieties RB92579 and SP813250 cultured in the PR state and in Northeastern Brazil, state of Pernambuco (PE), were analyzed using five EST-SSR primers for EstC66, EstC67, EstC68, EstC69, and EstC91 loci. Genetic divergence was evident in the EstC67 and EstC69 loci for β-amylase and cellulose synthase, respectively, among the four sugarcane varieties. An extremely high level of genetic differentiation was also detected in the EstC67 locus from the RB82579 and SP813250 varieties cultured in the PR and PE states. High polymorphism in SSR of the cellulose synthase locus may explain the high variability of substrates used in pretreatment and enzymatic hydrolysis processes, which has been an obstacle to effective industrial adaptations.

  13. Amplification Biases and Consistent Recovery of Loci in a Double-Digest RAD-seq Protocol

    Science.gov (United States)

    DaCosta, Jeffrey M.; Sorenson, Michael D.

    2014-01-01

    A growing variety of “genotype-by-sequencing” (GBS) methods use restriction enzymes and high throughput DNA sequencing to generate data for a subset of genomic loci, allowing the simultaneous discovery and genotyping of thousands of polymorphisms in a set of multiplexed samples. We evaluated a “double-digest” restriction-site associated DNA sequencing (ddRAD-seq) protocol by 1) comparing results for a zebra finch (Taeniopygia guttata) sample with in silico predictions from the zebra finch reference genome; 2) assessing data quality for a population sample of indigobirds (Vidua spp.); and 3) testing for consistent recovery of loci across multiple samples and sequencing runs. Comparison with in silico predictions revealed that 1) over 90% of predicted, single-copy loci in our targeted size range (178–328 bp) were recovered; 2) short restriction fragments (38–178 bp) were carried through the size selection step and sequenced at appreciable depth, generating unexpected but nonetheless useful data; 3) amplification bias favored shorter, GC-rich fragments, contributing to among locus variation in sequencing depth that was strongly correlated across samples; 4) our use of restriction enzymes with a GC-rich recognition sequence resulted in an up to four-fold overrepresentation of GC-rich portions of the genome; and 5) star activity (i.e., non-specific cutting) resulted in thousands of “extra” loci sequenced at low depth. Results for three species of indigobirds show that a common set of thousands of loci can be consistently recovered across both individual samples and sequencing runs. In a run with 46 samples, we genotyped 5,996 loci in all individuals and 9,833 loci in 42 or more individuals, resulting in <1% missing data for the larger data set. We compare our approach to similar methods and discuss the range of factors (fragment library preparation, natural genetic variation, bioinformatics) influencing the recovery of a consistent set of loci among

  14. Genome-wide high-density SNP linkage search for glioma susceptibility loci: results from the Gliogene Consortium

    DEFF Research Database (Denmark)

    Shete, Sanjay; Lau, Ching C; Houlston, Richard S

    2011-01-01

    .S. families and obtained a maximum NPL score of 1.26 (P = 0.008) and the Z-score of 1.47 (P = 0.035). Accounting for the genetic heterogeneity using the ordered subset analysis approach, the combined analyses of 75 families resulted in a maximum NPL score of 3.81 (P = 0.00001). The genomic regions we have...... implicated in this study may offer novel insights into glioma susceptibility, focusing future work to identify genes that cause familial glioma.......-fold increased risk of glioma, the search for susceptibility loci in familial forms of the disease has been challenging because the disease is relatively rare, fatal, and heterogeneous, making it difficult to collect sufficient biosamples from families for statistical power. To address this challenge...

  15. Seasonal variations of the high-latitude F region for

    International Nuclear Information System (INIS)

    Sojka, J.J.; Schunk, R.W.; Raitt, W.J.

    1982-01-01

    We combined a plasma convection model with an inosphere-atmospheric composition model in order to study the seasonal variations of the high-latitude F region for strong convection. Our numerical study produced time-dependent, three-dimensional, ion density distributions for the ions NO + , O 2 + , N 2 + , O + , N + , and He + . We covered the high-latitude ionosphere above 42 0 N magnetic latitude and at altitudes between 160 and 800 km for a time period of one complete day. From our study we found the following: (1) For strong convection, the high-altitude ionosphere exhibits a significant UT variation both during winter and summer. (2) In general, the electron density is lower in winter than in summer. However, at certain universal times the electron density in the dayside polar cap is larger in winter than in summer owing to the effect of the mid-latitude 'winter anomaly' in combination with strong antisunward convection. (3) In both summer and winter, the major region of low electron density is associated with the main or mid-latitudde trough. The trough is deeper and its local time extend is much greater in winter than in summer. (4) Typically, the electron density exhibits a much larger variation with altitude in winter than in summer. (5) The ion composition and molecular/atomic ion transition altitude are highly UT dependent in both summer and winter. (6) The ion composition also displays a significant seasonal variation. However, at a given location the seasonal variation can be opposite at different universal times. (7) High-speed convection cells should display a marked seasonal variation, with a much larger concentration of molecular ions near the F region peak in summer than in winter

  16. Prenatal famine and genetic variation are independently and additively associated with DNA methylation at regulatory loci within IGF2/H19.

    Directory of Open Access Journals (Sweden)

    Elmar W Tobi

    Full Text Available Both the early environment and genetic variation may affect DNA methylation, which is one of the major molecular marks of the epigenome. The combined effect of these factors on a well-defined locus has not been studied to date. We evaluated the association of periconceptional exposure to the Dutch Famine of 1944-45, as an example of an early environmental exposure, and single nucleotide polymorphisms covering the genetic variation (tagging SNPs with DNA methylation at the imprinted IGF2/H19 region, a model for an epigenetically regulated genomic region. DNA methylation was measured at five differentially methylated regions (DMRs that regulate the imprinted status of the IGF2/H19 region. Small but consistent differences in DNA methylation were observed comparing 60 individuals with periconceptional famine exposure with unexposed same-sex siblings at all IGF2 DMRs (P(BH<0.05 after adjustment for multiple testing, but not at the H19 DMR. IGF2 DMR0 methylation was associated with IGF2 SNP rs2239681 (P(BH = 0.027 and INS promoter methylation with INS SNPs, including rs689, which tags the INS VNTR, suggesting a mechanism for the reported effect of the VNTR on INS expression (P(BH = 3.4 × 10(-3. Prenatal famine and genetic variation showed similar associations with IGF2/H19 methylation and their contributions were additive. They were small in absolute terms (<3%, but on average 0.5 standard deviations relative to the variation in the population. Our analyses suggest that environmental and genetic factors could have independent and additive similarly sized effects on DNA methylation at the same regulatory site.

  17. Speckle Noise Reduction via Nonconvex High Total Variation Approach

    Directory of Open Access Journals (Sweden)

    Yulian Wu

    2015-01-01

    Full Text Available We address the problem of speckle noise removal. The classical total variation is extensively used in this field to solve such problem, but this method suffers from the staircase-like artifacts and the loss of image details. In order to resolve these problems, a nonconvex total generalized variation (TGV regularization is used to preserve both edges and details of the images. The TGV regularization which is able to remove the staircase effect has strong theoretical guarantee by means of its high order smooth feature. Our method combines the merits of both the TGV method and the nonconvex variational method and avoids their main drawbacks. Furthermore, we develop an efficient algorithm for solving the nonconvex TGV-based optimization problem. We experimentally demonstrate the excellent performance of the technique, both visually and quantitatively.

  18. Genius loci / Madis Kõiv

    Index Scriptorium Estoniae

    Kõiv, Madis, 1929-2014

    2005-01-01

    Ettekanne 37. Kreutzwaldi päevadel Tartu Kirjandusmuuseumis 18.-19. dets. 1993, pealkirjaga "Kus on see Valga, kus on see Tartu...: Genius loci B. Kangro ja V. Uibopuu romaanides". Varem ilmunud: Akadeemia, 1994, nr. 4

  19. Molecular variation at the HLA-A, B, C, DRB1, DQA1, and DQB1 loci in full heritage American Indians in Arizona: private haplotypes and their evolution.

    Science.gov (United States)

    Williams, R; Chen, Y-F; Endres, R; Middleton, D; Trucco, M; Williams, J Dunn; Knowler, W

    2009-12-01

    A sample of 492 full heritage, unrelated residents of the Gila River Indian Community (GRIC) of Arizona were characterized for their high-resolution DNA alleles at the HLA-A, B, C, DRB1, DQA1, and DQB1 loci. Only five allelic categories are found at HLA-A, 10 at HLA-B, 8 at HLA-C and HLA-DR, and 4 at DQA1 and DQB1. There is little evidence for population structure at the 6 loci. Two 'private' alleles, B*5102 and B*4005, which are found nearly exclusively in American Indian populations in the desert southwest and northern Mexico, are likely new mutations after the first inhabitation of the area, the evolution of which are reflected in the contemporary distribution of their respective haplotypes. DRB1*1402 has the highest reported frequency of any specificity at the DRB1 locus, 0.7461, and serves as a sensitive probe for locating related east Asian populations. The haplotypes in this population also exhibit a highly restricted distribution and strong genetic disequilibria, which has important implications for matching solid organ and bone marrow allografts. It is shown that, when one considers HLA-A-B-DRB1 homozygotes as allograft donors for all full heritage members of the GRIC, 50% of the community would find a non-mismatched organ within the homozygotes for the six most common haplotypes. This raises questions about transplantation policy and whether, in the presence of high-frequency private alleles and a restricted number of haplotypes, the full heritage American Indian community of the desert southwest should act as its own pool of donors for its affected members.

  20. High Resolution Consensus Mapping of Quantitative Trait Loci for Fiber Strength, Length and Micronaire on Chromosome 25 of the Upland Cotton (Gossypium hirsutum L..

    Directory of Open Access Journals (Sweden)

    Zhen Zhang

    Full Text Available Cotton (Gossypium hirsutum L. is an important agricultural crop that provides renewable natural fiber resources for the global textile industry. Technological developments in the textile industry and improvements in human living standards have increased the requirement for supplies and better quality cotton. Upland cotton 0-153 is an elite cultivar harboring strong fiber strength genes. To conduct quantitative trait locus (QTL mapping for fiber quality in 0-153, we developed a population of 196 recombinant inbred lines (RILs from a cross between 0-153 and sGK9708. The fiber quality traits in 11 environments were measured and a genetic linkage map of chromosome 25 comprising 210 loci was constructed using this RIL population, mainly using simple sequence repeat markers and single nucleotide polymorphism markers. QTLs were identified across diverse environments using the composite interval mapping method. A total of 37 QTLs for fiber quality traits were identified on chromosome 25, of which 17 were stably expressed in at least in two environments. A stable fiber strength QTL, qFS-chr25-4, which was detected in seven environments and was located in the marker interval between CRI-SNP120491 and BNL2572, could explain 6.53%-11.83% of the observed phenotypic variations. Meta-analysis also confirmed the above QTLs with previous reports. Application of these QTLs could contribute to improving fiber quality and provide information for marker-assisted selection.

  1. High Resolution Consensus Mapping of Quantitative Trait Loci for Fiber Strength, Length and Micronaire on Chromosome 25 of the Upland Cotton (Gossypium hirsutum L.).

    Science.gov (United States)

    Zhang, Zhen; Li, Junwen; Muhammad, Jamshed; Cai, Juan; Jia, Fei; Shi, Yuzhen; Gong, Juwu; Shang, Haihong; Liu, Aiying; Chen, Tingting; Ge, Qun; Palanga, Koffi Kibalou; Lu, Quanwei; Deng, Xiaoying; Tan, Yunna; Li, Wei; Sun, Linyang; Gong, Wankui; Yuan, Youlu

    2015-01-01

    Cotton (Gossypium hirsutum L.) is an important agricultural crop that provides renewable natural fiber resources for the global textile industry. Technological developments in the textile industry and improvements in human living standards have increased the requirement for supplies and better quality cotton. Upland cotton 0-153 is an elite cultivar harboring strong fiber strength genes. To conduct quantitative trait locus (QTL) mapping for fiber quality in 0-153, we developed a population of 196 recombinant inbred lines (RILs) from a cross between 0-153 and sGK9708. The fiber quality traits in 11 environments were measured and a genetic linkage map of chromosome 25 comprising 210 loci was constructed using this RIL population, mainly using simple sequence repeat markers and single nucleotide polymorphism markers. QTLs were identified across diverse environments using the composite interval mapping method. A total of 37 QTLs for fiber quality traits were identified on chromosome 25, of which 17 were stably expressed in at least in two environments. A stable fiber strength QTL, qFS-chr25-4, which was detected in seven environments and was located in the marker interval between CRI-SNP120491 and BNL2572, could explain 6.53%-11.83% of the observed phenotypic variations. Meta-analysis also confirmed the above QTLs with previous reports. Application of these QTLs could contribute to improving fiber quality and provide information for marker-assisted selection.

  2. CNV Workshop: an integrated platform for high-throughput copy number variation discovery and clinical diagnostics.

    Science.gov (United States)

    Gai, Xiaowu; Perin, Juan C; Murphy, Kevin; O'Hara, Ryan; D'arcy, Monica; Wenocur, Adam; Xie, Hongbo M; Rappaport, Eric F; Shaikh, Tamim H; White, Peter S

    2010-02-04

    Recent studies have shown that copy number variations (CNVs) are frequent in higher eukaryotes and associated with a substantial portion of inherited and acquired risk for various human diseases. The increasing availability of high-resolution genome surveillance platforms provides opportunity for rapidly assessing research and clinical samples for CNV content, as well as for determining the potential pathogenicity of identified variants. However, few informatics tools for accurate and efficient CNV detection and assessment currently exist. We developed a suite of software tools and resources (CNV Workshop) for automated, genome-wide CNV detection from a variety of SNP array platforms. CNV Workshop includes three major components: detection, annotation, and presentation of structural variants from genome array data. CNV detection utilizes a robust and genotype-specific extension of the Circular Binary Segmentation algorithm, and the use of additional detection algorithms is supported. Predicted CNVs are captured in a MySQL database that supports cohort-based projects and incorporates a secure user authentication layer and user/admin roles. To assist with determination of pathogenicity, detected CNVs are also annotated automatically for gene content, known disease loci, and gene-based literature references. Results are easily queried, sorted, filtered, and visualized via a web-based presentation layer that includes a GBrowse-based graphical representation of CNV content and relevant public data, integration with the UCSC Genome Browser, and tabular displays of genomic attributes for each CNV. To our knowledge, CNV Workshop represents the first cohesive and convenient platform for detection, annotation, and assessment of the biological and clinical significance of structural variants. CNV Workshop has been successfully utilized for assessment of genomic variation in healthy individuals and disease cohorts and is an ideal platform for coordinating multiple associated

  3. CNV Workshop: an integrated platform for high-throughput copy number variation discovery and clinical diagnostics

    Directory of Open Access Journals (Sweden)

    Rappaport Eric F

    2010-02-01

    Full Text Available Abstract Background Recent studies have shown that copy number variations (CNVs are frequent in higher eukaryotes and associated with a substantial portion of inherited and acquired risk for various human diseases. The increasing availability of high-resolution genome surveillance platforms provides opportunity for rapidly assessing research and clinical samples for CNV content, as well as for determining the potential pathogenicity of identified variants. However, few informatics tools for accurate and efficient CNV detection and assessment currently exist. Results We developed a suite of software tools and resources (CNV Workshop for automated, genome-wide CNV detection from a variety of SNP array platforms. CNV Workshop includes three major components: detection, annotation, and presentation of structural variants from genome array data. CNV detection utilizes a robust and genotype-specific extension of the Circular Binary Segmentation algorithm, and the use of additional detection algorithms is supported. Predicted CNVs are captured in a MySQL database that supports cohort-based projects and incorporates a secure user authentication layer and user/admin roles. To assist with determination of pathogenicity, detected CNVs are also annotated automatically for gene content, known disease loci, and gene-based literature references. Results are easily queried, sorted, filtered, and visualized via a web-based presentation layer that includes a GBrowse-based graphical representation of CNV content and relevant public data, integration with the UCSC Genome Browser, and tabular displays of genomic attributes for each CNV. Conclusions To our knowledge, CNV Workshop represents the first cohesive and convenient platform for detection, annotation, and assessment of the biological and clinical significance of structural variants. CNV Workshop has been successfully utilized for assessment of genomic variation in healthy individuals and disease cohorts and

  4. Biology and applications of human minisatellite loci.

    Science.gov (United States)

    Armour, J A; Jeffreys, A J

    1992-12-01

    Highly repetitive minisatellites' include the most variable human loci described to date. They have proved invaluable in a wide variety of genetic analyses, and despite some controversies surrounding their practical implementation, have been extensively adopted in civil and forensic casework. Molecular analysis of internal allelic structure has provided detailed insights into the repeat-unit turnover mechanisms operating in germline mutations, which are ultimately responsible for the extreme variability seen at these loci.

  5. HLA class II variation in the Gila River Indian Community of Arizona: alleles, haplotypes, and a high frequency epitope at the HLA-DR locus.

    Science.gov (United States)

    Williams, R C; McAuley, J E

    1992-01-01

    A genetic distribution for the HLA class II loci is described for 349 "full-blooded" Pima and Tohono O'odham Indians (Pimans) in the Gila River Indian Community. A high frequency epitope in the *DRw52 family was defined by reactions with 31 alloantisera, which we have designated *DR3X6. It segregates as a codominant allele at HLA-DR with alleles *DR2, *DR4, and *DRw8, and has the highest frequency yet reported for an HLA-DR specificity, 0.735. It forms a common haplotype with *DRw52 and *DQw3 that is a valuable marker for genetic admixture and anthropological studies. Phenotype and allele frequencies, and haplotype frequencies for two and three loci, are presented. Variation at these loci is highly restricted, the mean heterozygosity for HLA-DR and HLA-DQ being 0.361. The Pimans represent a contemporary model for the Paleo-Indians who first entered North America 20,000 to 40,000 years ago.

  6. CpG island methylator phenotype-low (CIMP-low) colorectal cancer shows not only few methylated CIMP-high-specific CpG islands, but also low-level methylation at individual loci.

    Science.gov (United States)

    Kawasaki, Takako; Ohnishi, Mutsuko; Nosho, Katsuhiko; Suemoto, Yuko; Kirkner, Gregory J; Meyerhardt, Jeffrey A; Fuchs, Charles S; Ogino, Shuji

    2008-03-01

    The CpG island methylator phenotype (CIMP or CIMP-high) with widespread promoter methylation is a distinct phenotype in colorectal cancer. However, the concept of CIMP-low with less extensive CpG island methylation is still evolving. Our aim is to examine whether density of methylation in individual CpG islands was different between CIMP-low and CIMP-high tumors. Utilizing MethyLight technology and 889 population-based colorectal cancers, we quantified DNA methylation (methylation index, percentage of methylated reference) at 14 CpG islands, including 8 CIMP-high-specific loci (CACNA1G, CDKN2A (p16), CRABP1, IGF2, MLH1, NEUROG1, RUNX3 and SOCS1). Methylation positivity in each locus was defined as methylation index>4. Low-level methylation (methylation index>0, CIMP-high-specific locus was significantly more common in 340 CIMP-low tumors (1/8-5/8 methylation-positive loci) than 133 CIMP-high tumors (> or =6/8 methylation-positive loci) and 416 CIMP-0 tumors (0/8 methylation-positive loci) (PCIMP-high, low-level methylation, was not persistently more prevalent in CIMP-low tumors. In conclusion, compared to CIMP-high and CIMP-0 tumors, CIMP-low colorectal cancers show not only few methylated CIMP-high-specific CpG islands, but also more frequent low-level methylation at individual loci. Our data may provide supporting evidence for a difference in pathogenesis of DNA methylation between CIMP-low and CIMP-high tumors.

  7. Shared susceptibility loci at 2q33 region for lung and esophageal cancers in high-incidence areas of esophageal cancer in northern China.

    Directory of Open Access Journals (Sweden)

    Xue Ke Zhao

    Full Text Available Cancers from lung and esophagus are the leading causes of cancer-related deaths in China and share many similarities in terms of histological type, risk factors and genetic variants. Recent genome-wide association studies (GWAS in Chinese esophageal cancer patients have demonstrated six high-risk candidate single nucleotide polymorphisms (SNPs. Thus, the present study aimed to determine the risk of these SNPs predisposing to lung cancer in Chinese population.A total of 1170 lung cancer patients and 1530 normal subjects were enrolled in this study from high-incidence areas for esophageal cancer in Henan, northern China. Five milliliters of blood were collected from all subjects for genotyping. Genotyping of 20 high-risk SNP loci identified from genome-wide association studies (GWAS on esophageal, lung and gastric cancers was performed using TaqMan allelic discrimination assays. Polymorphisms were examined for deviation from Hardy-Weinberg equilibrium (HWE using Х2 test. Bonferroni correction was performed to correct the statistical significance of 20 SNPs with the risk of lung cancer. The Pearson's Х2 test was used to compare the distributions of gender, TNM stage, histopathological type, smoking and family history by lung susceptibility genotypes. Kaplan-Meier and Cox regression analyses were carried out to evaluate the associations between genetic variants and overall survival.Four of the 20 SNPs identified as high-risk SNPs in Chinese esophageal cancer showed increased risk for Chinese lung cancer, which included rs3769823 (OR = 1.26; 95% CI = 1.107-1.509; P = 0.02, rs10931936 (OR = 1.283; 95% CI = 1.100-1.495; P = 0.04, rs2244438 (OR = 1.294; 95% CI = 1.098-1.525; P = 0.04 and rs13016963 (OR = 1.268; 95% CI = 1.089-1.447; P = 0.04. All these SNPs were located at 2q33 region harboringgenes of CASP8, ALS2CR12 and TRAK2. However, none of these susceptibility SNPs was observed to be significantly associated with gender, TNM stage

  8. Shared susceptibility loci at 2q33 region for lung and esophageal cancers in high-incidence areas of esophageal cancer in northern China.

    Science.gov (United States)

    Zhao, Xue Ke; Mao, Yi Min; Meng, Hui; Song, Xin; Hu, Shou Jia; Lv, Shuang; Cheng, Rang; Zhang, Tang Juan; Han, Xue Na; Ren, Jing Li; Qi, Yi Jun; Wang, Li Dong

    2017-01-01

    Cancers from lung and esophagus are the leading causes of cancer-related deaths in China and share many similarities in terms of histological type, risk factors and genetic variants. Recent genome-wide association studies (GWAS) in Chinese esophageal cancer patients have demonstrated six high-risk candidate single nucleotide polymorphisms (SNPs). Thus, the present study aimed to determine the risk of these SNPs predisposing to lung cancer in Chinese population. A total of 1170 lung cancer patients and 1530 normal subjects were enrolled in this study from high-incidence areas for esophageal cancer in Henan, northern China. Five milliliters of blood were collected from all subjects for genotyping. Genotyping of 20 high-risk SNP loci identified from genome-wide association studies (GWAS) on esophageal, lung and gastric cancers was performed using TaqMan allelic discrimination assays. Polymorphisms were examined for deviation from Hardy-Weinberg equilibrium (HWE) using Х2 test. Bonferroni correction was performed to correct the statistical significance of 20 SNPs with the risk of lung cancer. The Pearson's Х2 test was used to compare the distributions of gender, TNM stage, histopathological type, smoking and family history by lung susceptibility genotypes. Kaplan-Meier and Cox regression analyses were carried out to evaluate the associations between genetic variants and overall survival. Four of the 20 SNPs identified as high-risk SNPs in Chinese esophageal cancer showed increased risk for Chinese lung cancer, which included rs3769823 (OR = 1.26; 95% CI = 1.107-1.509; P = 0.02), rs10931936 (OR = 1.283; 95% CI = 1.100-1.495; P = 0.04), rs2244438 (OR = 1.294; 95% CI = 1.098-1.525; P = 0.04) and rs13016963 (OR = 1.268; 95% CI = 1.089-1.447; P = 0.04). All these SNPs were located at 2q33 region harboringgenes of CASP8, ALS2CR12 and TRAK2. However, none of these susceptibility SNPs was observed to be significantly associated with gender, TNM stage, histopathological type

  9. Allelic heterogeneity and genetic modifier loci contribute to clinical variation in males with X-linked retinitis pigmentosa due to RPGR mutations.

    Directory of Open Access Journals (Sweden)

    Abigail T Fahim

    Full Text Available Mutations in RPGR account for over 70% of X-linked retinitis pigmentosa (XlRP, characterized by retinal degeneration and eventual blindness. The clinical consequences of RPGR mutations are highly varied, even among individuals with the same mutation: males demonstrate a wide range of clinical severity, and female carriers may or may not be affected. This study describes the phenotypic diversity in a cohort of 98 affected males from 56 families with RPGR mutations, and demonstrates the contribution of genetic factors (i.e., allelic heterogeneity and genetic modifiers to this diversity. Patients were categorized as grade 1 (mild, 2 (moderate or 3 (severe according to specific clinical criteria. Patient DNAs were genotyped for coding SNPs in 4 candidate modifier genes with products known to interact with RPGR protein: RPGRIP1, RPGRIP1L, CEP290, and IQCB1. Family-based association testing was performed using PLINK. A wide range of clinical severity was observed both between and within families. Patients with mutations in exons 1-14 were more severely affected than those with ORF15 mutations, and patients with predicted null alleles were more severely affected than those predicted to make RPGR protein. Two SNPs showed association with severe disease: the minor allele (N of I393N in IQCB1 (p = 0.044 and the common allele (R of R744Q in RPGRIP1L (p = 0.049. These data demonstrate that allelic heterogeneity contributes to phenotypic diversity in XlRP and suggest that this may depend on the presence or absence of RPGR protein. In addition, common variants in 2 proteins known to interact with RPGR are associated with severe disease in this cohort.

  10. Population genetic data of the NGM SElect STR loci in Chinese Han population from Zhejiang region, China.

    Science.gov (United States)

    Zhou, Anju; Wu, Weiwei; Liu, Qiuling; Wu, Yeda; Lu, Dejian

    2013-03-01

    Genetic variations of the 17 NGM SElect STR loci in Chinese Han samples from the Zhejiang region were analyzed. The results show that the NGM SElect is a highly genetic informative system in Zhejiang Han, and this population shows quite different genetic data from other major populations in the world with the exception of the Fujian Han.

  11. High Resolution Global Electrical Conductivity Variations in the Earth's Mantle

    Science.gov (United States)

    Kelbert, A.; Sun, J.; Egbert, G. D.

    2013-12-01

    Electrical conductivity of the Earth's mantle is a valuable constraint on the water content and melting processes. In Kelbert et al. (2009), we obtained the first global inverse model of electrical conductivity in the mantle capable of providing constraints on the lateral variations in mantle water content. However, in doing so we had to compromise on the problem complexity by using the historically very primitive ionospheric and magnetospheric source assumptions. In particular, possible model contamination by the auroral current systems had greatly restricted our use of available data. We have now addressed this problem by inverting for the external sources along with the electrical conductivity variations. In this study, we still focus primarily on long period data that are dominated by quasi-zonal source fields. The improved understanding of the ionospheric sources allows us to invert the magnetic fields directly, without a correction for the source and/or the use of transfer functions. It allows us to extend the period range of available data to 1.2 days - 102 days, achieving better sensitivity to the upper mantle and transition zone structures. Finally, once the source effects in the data are accounted for, a much larger subset of observatories may be used in the electrical conductivity inversion. Here, we use full magnetic fields at 207 geomagnetic observatories, which include mid-latitude, equatorial and high latitude data. Observatory hourly means from the years 1958-2010 are employed. The improved quality and spatial distribution of the data set, as well as the high resolution modeling and inversion using degree and order 40 spherical harmonics mapped to a 2x2 degree lateral grid, all contribute to the much improved resolution of our models, representing a conceptual step forward in global electromagnetic sounding. We present a fully three-dimensional, global electrical conductivity model of the Earth's mantle as inferred from ground geomagnetic

  12. High-resolution copy-number variation map reflects human olfactory receptor diversity and evolution.

    Directory of Open Access Journals (Sweden)

    Yehudit Hasin

    2008-11-01

    Full Text Available Olfactory receptors (ORs, which are involved in odorant recognition, form the largest mammalian protein superfamily. The genomic content of OR genes is considerably reduced in humans, as reflected by the relatively small repertoire size and the high fraction ( approximately 55% of human pseudogenes. Since several recent low-resolution surveys suggested that OR genomic loci are frequently affected by copy-number variants (CNVs, we hypothesized that CNVs may play an important role in the evolution of the human olfactory repertoire. We used high-resolution oligonucleotide tiling microarrays to detect CNVs across 851 OR gene and pseudogene loci. Examining genomic DNA from 25 individuals with ancestry from three populations, we identified 93 OR gene loci and 151 pseudogene loci affected by CNVs, generating a mosaic of OR dosages across persons. Our data suggest that approximately 50% of the CNVs involve more than one OR, with the largest CNV spanning 11 loci. In contrast to earlier reports, we observe that CNVs are more frequent among OR pseudogenes than among intact genes, presumably due to both selective constraints and CNV formation biases. Furthermore, our results show an enrichment of CNVs among ORs with a close human paralog or lacking a one-to-one ortholog in chimpanzee. Interestingly, among the latter we observed an enrichment in CNV losses over gains, a finding potentially related to the known diminution of the human OR repertoire. Quantitative PCR experiments performed for 122 sampled ORs agreed well with the microarray results and uncovered 23 additional CNVs. Importantly, these experiments allowed us to uncover nine common deletion alleles that affect 15 OR genes and five pseudogenes. Comparison to the chimpanzee reference genome revealed that all of the deletion alleles are human derived, therefore indicating a profound effect of human-specific deletions on the individual OR gene content. Furthermore, these deletion alleles may be used

  13. High-resolution analysis of a QTL for resistance to Stagonospora nodorum glume blotch in wheat reveals presence of two distinct resistance loci in the target interval.

    Science.gov (United States)

    Shatalina, Margarita; Messmer, Monika; Feuillet, Catherine; Mascher, Fabio; Paux, Etienne; Choulet, Frédéric; Wicker, Thomas; Keller, Beat

    2014-03-01

    Stagonospora nodorum glume blotch (SNG), caused by the necrotrophic fungus Stagonospora nodorum, is one of the economically important diseases of bread wheat (Triticum aestivum L.). Resistance to SNG is known to be quantitative and previous studies of a recombinant inbred line (RIL) population identified a major quantitative trait locus (QTL) for resistance to SNG on the short arm of chromosome 3B. To localize this QTL (QSng.sfr-3BS) with high resolution, we constructed a genetic map for the QTL target region using information from sequenced flow-sorted chromosomes 3B of the two parental cultivars 'Arina' and 'Forno', the physical map of chromosome 3B of cultivar 'Chinese Spring' and BAC-clone sequences. The mapping population of near-isogenic lines (NIL) was evaluated for SNG resistance in field infection tests. NILs segregated for disease resistance as well as for plant height; additionally, we observed a high environmental influence on the trait. Our analysis detected a strong negative correlation of SNG resistance and plant height. Further analysis of the target region identified two linked loci associated with SNG resistance. One of them was also associated with plant height, revealing an effect of QSng.sfr-3BS on plant height that was hidden in the RIL population. This result demonstrates an unexpectedly high genetic complexity of resistance controlled by QSng.sfr-3BS and shows the importance of the study of QTL in mendelized form in NILs.

  14. Reduced Variance of Gene Expression at Numerous Loci in a Population of Chickens Selected for High Feather Pecking

    DEFF Research Database (Denmark)

    Hughes, A L; Buitenhuis, A J

    2010-01-01

    among populations with respect to mean expression scores, but numerous transcripts showed reduced variance in expression scores in the high FP population in comparison to control and low FP populations. The reduction in variance in the high FP population generally involved transcripts whose expression...

  15. INTERACTION BETWEEN THE ADH AND ALPHA-GPDH LOCI IN DROSOPHILA-MELANOGASTER - ADULT SURVIVAL AT HIGH-TEMPERATURE

    NARCIS (Netherlands)

    OUDMAN, L; VANDELDEN, W; KAMPING, A; BIJLSMA, R

    The role of high temperature resistance in the world-wide cline of Adh and alpha-Gpdh allele frequencies of Drosophila melanogaster was investigated. Experimental strains were used with different combinations of Adh and alpha-Gpdh alleles but with similar genetic background. The survival time of

  16. EPR: High load variation performances with the 'Tmode' core control

    International Nuclear Information System (INIS)

    Grossetete, A.

    2008-01-01

    The load variation performances on a PWR are directly linked to the core control design. This design is mainly characterized by the definition of the control rod banks and the way to both perform the banks movements and to modify the core boron concentration by injection of boric acid or water. The following paper presents the principles of the T mode, the new fully automatic core control mode for the EPR which provides high performance in terms of maneuverability and optimizes the effluents. First, the paper describes the division of the control rods into two control banks (Pbank for temperature and Hbank for power distribution). Then typical movements of these banks during power changes are shown. Then, the principle of the 3 control loops (Tave, AO, Pmax), used to obtain these desired control rod movements, is given. Finally, a load following transient simulation is presented. (authors)

  17. EPR: high load variation performances with the 'TMODE' core control

    International Nuclear Information System (INIS)

    Pairot, Frederic

    2008-01-01

    The load variation performances on a PWR are directly linked to the core control design. This design is mainly characterized by the definition of the control rod banks and the way to both perform the banks movements and to modify the core boron concentration by injection of boric acid or water. The following paper presents the principles of the T mode, the new fully automatic core control mode for the EPR which provides high performance in terms of maneuverability and optimizes the effluents. First, the paper describes the division of the control rods into two control banks (Pbank for temperature and Hbank for power distribution). Then typical movements of these banks during power changes are shown. Then, the principle of the 3 control loops (Tave, AO, Pmax), used to obtain these desired control rod movements, is given. Finally, a load following transient simulation is presented. (author)

  18. Double-digest RAD sequencing outperforms microsatellite loci at assigning paternity and estimating relatedness: A proof of concept in a highly promiscuous bird.

    Science.gov (United States)

    Thrasher, Derrick J; Butcher, Bronwyn G; Campagna, Leonardo; Webster, Michael S; Lovette, Irby J

    2018-02-17

    Information on genetic relationships among individuals is essential to many studies of the behaviour and ecology of wild organisms. Parentage and relatedness assays based on large numbers of single nucleotide polymorphism (SNP) loci hold substantial advantages over the microsatellite markers traditionally used for these purposes. We present a double-digest restriction site-associated DNA sequencing (ddRAD-seq) analysis pipeline that, as such, simultaneously achieves the SNP discovery and genotyping steps and which is optimized to return a statistically powerful set of SNP markers (typically 150-600 after stringent filtering) from large numbers of individuals (up to 240 per run). We explore the trade-offs inherent in this approach through a set of experiments in a species with a complex social system, the variegated fairy-wren (Malurus lamberti) and further validate it in a phylogenetically broad set of other bird species. Through direct comparisons with a parallel data set from a robust panel of highly variable microsatellite markers, we show that this ddRAD-seq approach results in substantially improved power to discriminate among potential relatives and considerably more precise estimates of relatedness coefficients. The pipeline is designed to be universally applicable to all bird species (and with minor modifications to many other taxa), to be cost- and time-efficient, and to be replicable across independent runs such that genotype data from different study periods can be combined and analysed as field samples are accumulated. © 2018 John Wiley & Sons Ltd.

  19. COMBO-FISH Enables High Precision Localization Microscopy as a Prerequisite for Nanostructure Analysis of Genome Loci

    Directory of Open Access Journals (Sweden)

    Rainer Kaufmann

    2010-10-01

    Full Text Available With the completeness of genome databases, it has become possible to develop a novel FISH (Fluorescence in Situ Hybridization technique called COMBO-FISH (COMBinatorial Oligo FISH. In contrast to other FISH techniques, COMBO-FISH makes use of a bioinformatics approach for probe set design. By means of computer genome database searching, several oligonucleotide stretches of typical lengths of 15–30 nucleotides are selected in such a way that all uniquely colocalize at the given genome target. The probes applied here were Peptide Nucleic Acids (PNAs—synthetic DNA analogues with a neutral backbone—which were synthesized under high purity conditions. For a probe repetitively highlighted in centromere 9, PNAs labeled with different dyes were tested, among which Alexa 488Ò showed reversible photobleaching (blinking between dark and bright state a prerequisite for the application of SPDM (Spectral Precision Distance/Position Determination Microscopy a novel technique of high resolution fluorescence localization microscopy. Although COMBO-FISH labeled cell nuclei under SPDM conditions sometimes revealed fluorescent background, the specific locus was clearly discriminated by the signal intensity and the resulting localization accuracy in the range of 10–20 nm for a detected oligonucleotide stretch. The results indicate that COMBO-FISH probes with blinking dyes are well suited for SPDM, which will open new perspectives on molecular nanostructural analysis of the genome.

  20. A Nondegenerate Code of Deleterious Variants in Mendelian Loci Contributes to Complex Disease Risk

    DEFF Research Database (Denmark)

    Blair, David R.; Lyttle, Christopher S.; Mortensen, Jonathan M.

    2013-01-01

    Although countless highly penetrant variants have been associated with Mendelian disorders, the genetic etiologies underlying complex diseases remain largely unresolved. By mining the medical records of over 110 million patients, we examine the extent to which Mendelian variation contributes to c...... of complex diseases. Overall, this study illustrates a complementary approach for mapping complex disease loci and provides unique predictions concerning the etiologies of specific diseases....

  1. Comparative Mapping of Seed Dormancy Loci Between Tropical and Temperate Ecotypes of Weedy Rice (Oryza sativa L.

    Directory of Open Access Journals (Sweden)

    Lihua Zhang

    2017-08-01

    Full Text Available Genotypic variation at multiple loci for seed dormancy (SD contributes to plant adaptation to diverse ecosystems. Weedy rice (Oryza sativa was used as a model to address the similarity of SD genes between distinct ecotypes. A total of 12 quantitative trait loci (QTL for SD were identified in one primary and two advanced backcross (BC populations derived from a temperate ecotype of weedy rice (34.3°N Lat.. Nine (75% of the 12 loci were mapped to the same positions as those identified from a tropical ecotype of weedy rice (7.1°N Lat.. The high similarity suggested that the majority of SD genes were conserved during the ecotype differentiation. These common loci are largely those collocated/linked with the awn, hull color, pericarp color, or plant height loci. Phenotypic correlations observed in the populations support the notion that indirect selections for the wild-type morphological characteristics, together with direct selections for germination time, were major factors influencing allelic distributions of SD genes across ecotypes. Indirect selections for crop-mimic traits (e.g., plant height and flowering time could also alter allelic frequencies for some SD genes in agroecosystems. In addition, 3 of the 12 loci were collocated with segregation distortion loci, indicating that some gametophyte development genes could also influence the genetic equilibria of SD loci in hybrid populations. The SD genes with a major effect on germination across ecotypes could be used as silencing targets to develop transgene mitigation (TM strategies to reduce the risk of gene flow from genetically modified crops into weed/wild relatives.

  2. Highly accurate symplectic element based on two variational principles

    Science.gov (United States)

    Qing, Guanghui; Tian, Jia

    2018-02-01

    For the stability requirement of numerical resultants, the mathematical theory of classical mixed methods are relatively complex. However, generalized mixed methods are automatically stable, and their building process is simple and straightforward. In this paper, based on the seminal idea of the generalized mixed methods, a simple, stable, and highly accurate 8-node noncompatible symplectic element (NCSE8) was developed by the combination of the modified Hellinger-Reissner mixed variational principle and the minimum energy principle. To ensure the accuracy of in-plane stress results, a simultaneous equation approach was also suggested. Numerical experimentation shows that the accuracy of stress results of NCSE8 are nearly the same as that of displacement methods, and they are in good agreement with the exact solutions when the mesh is relatively fine. NCSE8 has advantages of the clearing concept, easy calculation by a finite element computer program, higher accuracy and wide applicability for various linear elasticity compressible and nearly incompressible material problems. It is possible that NCSE8 becomes even more advantageous for the fracture problems due to its better accuracy of stresses.

  3. Combined Analyses of the ITS Loci and the Corresponding 16S rRNA Genes Reveal High Micro- and Macrodiversity of SAR11 Populations in the Red Sea

    Science.gov (United States)

    Ngugi, David Kamanda; Stingl, Ulrich

    2012-01-01

    Bacteria belonging to the SAR11 clade are among the most abundant prokaryotes in the pelagic zone of the ocean. 16S rRNA gene-based analyses indicate that they constitute up to 60% of the bacterioplankton community in the surface waters of the Red Sea. This extremely oligotrophic water body is further characterized by an epipelagic zone, which has a temperature above 24°C throughout the year, and a remarkable uniform temperature (∼22°C) and salinity (∼41 psu) from the mixed layer (∼200 m) to the bottom at over 2000 m depth. Despite these conditions that set it apart from other marine environments, the microbiology of this ecosystem is still vastly understudied. Prompted by the limited phylogenetic resolution of the 16S rRNA gene, we extended our previous study by sequencing the internal transcribed spacer (ITS) region of SAR11 in different depths of the Red Sea’s water column together with the respective 16S fragment. The overall diversity captured by the ITS loci was ten times higher than that of the corresponding 16S rRNA genes. Moreover, species estimates based on the ITS showed a highly diverse population of SAR11 in the mixed layer that became diminished in deep isothermal waters, which was in contrast to results of the related 16S rRNA genes. While the 16S rRNA gene-based sequences clustered into three phylogenetic subgroups, the related ITS fragments fell into several phylotypes that showed clear depth-dependent shifts in relative abundances. Blast-based analyses not only documented the observed vertical partitioning and universal co-occurrence of specific phylotypes in five other distinct oceanic provinces, but also highlighted the influence of ecosystem-specific traits (e.g., temperature, nutrient availability, and concentration of dissolved oxygen) on the population dynamics of this ubiquitous marine bacterium. PMID:23185592

  4. Combined analyses of the ITS loci and the corresponding 16S rRNA genes reveal high micro- and macrodiversity of SAR11 populations in the Red Sea.

    KAUST Repository

    Ngugi, David

    2012-11-20

    Bacteria belonging to the SAR11 clade are among the most abundant prokaryotes in the pelagic zone of the ocean. 16S rRNA gene-based analyses indicate that they constitute up to 60% of the bacterioplankton community in the surface waters of the Red Sea. This extremely oligotrophic water body is further characterized by an epipelagic zone, which has a temperature above 24 °C throughout the year, and a remarkable uniform temperature (~22 °C) and salinity (~41 psu) from the mixed layer (~200 m) to the bottom at over 2000 m depth. Despite these conditions that set it apart from other marine environments, the microbiology of this ecosystem is still vastly understudied. Prompted by the limited phylogenetic resolution of the 16S rRNA gene, we extended our previous study by sequencing the internal transcribed spacer (ITS) region of SAR11 in different depths of the Red Sea\\'s water column together with the respective 16S fragment. The overall diversity captured by the ITS loci was ten times higher than that of the corresponding 16S rRNA genes. Moreover, species estimates based on the ITS showed a highly diverse population of SAR11 in the mixed layer that became diminished in deep isothermal waters, which was in contrast to results of the related 16S rRNA genes. While the 16S rRNA gene-based sequences clustered into three phylogenetic subgroups, the related ITS fragments fell into several phylotypes that showed clear depth-dependent shifts in relative abundances. Blast-based analyses not only documented the observed vertical partitioning and universal co-occurrence of specific phylotypes in five other distinct oceanic provinces, but also highlighted the influence of ecosystem-specific traits (e.g., temperature, nutrient availability, and concentration of dissolved oxygen) on the population dynamics of this ubiquitous marine bacterium.

  5. Identification and genetic mapping of highly polymorphic microsatellite loci from an EST database of the septoria tritici blotch pathogen Mycosphaerella graminicola

    NARCIS (Netherlands)

    Goodwin, S.B.; Lee, van der T.A.J.; Cavaletto, J.R.; Lintel Hekkert, te B.; Crane, C.F.; Kema, G.H.J.

    2007-01-01

    A database of 30,137 EST sequences from Mycosphaerella graminicola, the septoria tritici blotch fungus of wheat, was scanned with a custom software pipeline for di- and trinucleotide units repeated tandemly six or more times. The bioinformatics analysis identified 109 putative SSR loci, and for 99

  6. A journey from a SSR-based low density map to a SNP-based high density map for identification of disease resistance quantitative trait loci in peanut

    Science.gov (United States)

    Mapping and identification of quantitative trait loci (QTLs) are important for efficient marker-assisted breeding. Diseases such as leaf spots and Tomato spotted wilt virus (TSWV) cause significant loses to peanut growers. The U.S. Peanut Genome Initiative (PGI) was launched in 2004, and expanded to...

  7. Isolation and characterization of 21 polymorphic microsatellite loci in the Japanese dace (Tribolodon hakonensis)

    Science.gov (United States)

    Koizumi, Noriyuki; Quinn, Thomas W.; Park, Myeongsoo; Fike, Jennifer A.; Nishida, Kazuya; Takemura, Takeshi; Watabe, Keiji; Mori, Atsushi

    2011-01-01

    Twenty one polymorphic microsatellite loci for the Japanese dace (Tribolodon hakonensis) were isolated and characterized. The number of observed alleles per locus in 32 individuals ranged from 3 to 30. The observed and expected heterozygosities ranged from 0.125 to 0.969 and from 0.175 to 0.973, respectively. All loci conformed to Hardy–Weinberg equilibrium, no linkage disequilibrium was observed between pairs of loci and no loci showed evidence of null alleles. These microsatellite loci will be useful for investigating the intraspecific genetic variation and population structure of this species.

  8. SSR allelic variation in almond (Prunus dulcis Mill.).

    Science.gov (United States)

    Xie, Hua; Sui, Yi; Chang, Feng-Qi; Xu, Yong; Ma, Rong-Cai

    2006-01-01

    Sixteen SSR markers including eight EST-SSR and eight genomic SSRs were used for genetic diversity analysis of 23 Chinese and 15 international almond cultivars. EST- and genomic SSR markers previously reported in species of Prunus, mainly peach, proved to be useful for almond genetic analysis. DNA sequences of 117 alleles of six of the 16 SSR loci were analysed to reveal sequence variation among the 38 almond accessions. For the four SSR loci with AG/CT repeats, no insertions or deletions were observed in the flanking regions of the 98 alleles sequenced. Allelic size variation of these loci resulted exclusively from differences in the structures of repeat motifs, which involved interruptions or occurrences of new motif repeats in addition to varying number of AG/CT repeats. Some alleles had a high number of uninterrupted repeat motifs, indicating that SSR mutational patterns differ among alleles at a given SSR locus within the almond species. Allelic homoplasy was observed in the SSR loci because of base substitutions, interruptions or compound repeat motifs. Substitutions in the repeat regions were found at two SSR loci, suggesting that point mutations operate on SSRs and hinder the further SSR expansion by introducing repeat interruptions to stabilize SSR loci. Furthermore, it was shown that some potential point mutations in the flanking regions are linked with new SSR repeat motif variation in almond and peach.

  9. Discovery and refinement of loci associated with lipid levels

    NARCIS (Netherlands)

    Willer, Cristen J.; Schmidt, Ellen M.; Sengupta, Sebanti; Peloso, Gina M.; Gustafsson, Stefan; Kanoni, Stavroula; Ganna, Andrea; Chen, Jin; Buchkovich, Martin L.; Mora, Samia; Beckmann, Jacques S.; Bragg-Gresham, Jennifer L.; Chang, Hsing-Yi; Demirkan, Ayşe; den Hertog, Heleen M.; Do, Ron; Donnelly, Louise A.; Ehret, Georg B.; Esko, Tõnu; Feitosa, Mary F.; Ferreira, Teresa; Fischer, Krista; Fontanillas, Pierre; Fraser, Ross M.; Freitag, Daniel F.; Gurdasani, Deepti; Heikkilä, Kauko; Hyppönen, Elina; Isaacs, Aaron; Jackson, Anne U.; Johansson, Asa; Johnson, Toby; Kaakinen, Marika; Kettunen, Johannes; Kleber, Marcus E.; Li, Xiaohui; Luan, Jian'an; Lyytikäinen, Leo-Pekka; Magnusson, Patrik K. E.; Mangino, Massimo; Mihailov, Evelin; Montasser, May E.; Müller-Nurasyid, Martina; Nolte, Ilja M.; O'Connell, Jeffrey R.; Palmer, Cameron D.; Perola, Markus; Petersen, Ann-Kristin; Sanna, Serena; Saxena, Richa; Service, Susan K.; Shah, Sonia; Shungin, Dmitry; Sidore, Carlo; Song, Ci; Strawbridge, Rona J.; Surakka, Ida; Tanaka, Toshiko; Teslovich, Tanya M.; Thorleifsson, Gudmar; van den Herik, Evita G.; Voight, Benjamin F.; Volcik, Kelly A.; Waite, Lindsay L.; Wong, Andrew; Wu, Ying; Zhang, Weihua; Absher, Devin; Asiki, Gershim; Barroso, Inês; Been, Latonya F.; Bolton, Jennifer L.; Bonnycastle, Lori L.; Brambilla, Paolo; Burnett, Mary S.; Cesana, Giancarlo; Dimitriou, Maria; Doney, Alex S. F.; Döring, Angela; Elliott, Paul; Epstein, Stephen E.; Eyjolfsson, Gudmundur Ingi; Gigante, Bruna; Goodarzi, Mark O.; Grallert, Harald; Gravito, Martha L.; Groves, Christopher J.; Hallmans, Göran; Hartikainen, Anna-Liisa; Hayward, Caroline; Hernandez, Dena; Hicks, Andrew A.; Holm, Hilma; Hung, Yi-Jen; Illig, Thomas; Jones, Michelle R.; Kaleebu, Pontiano; Kastelein, John J. P.; Khaw, Kay-Tee; Kim, Eric; Klopp, Norman; Komulainen, Pirjo; Kumari, Meena; Langenberg, Claudia; Lehtimäki, Terho; Lin, Shih-Yi; Lindström, Jaana; Loos, Ruth J. F.; Mach, François; McArdle, Wendy L.; Meisinger, Christa; Mitchell, Braxton D.; Müller, Gabrielle; Nagaraja, Ramaiah; Narisu, Narisu; Nieminen, Tuomo V. M.; Nsubuga, Rebecca N.; Olafsson, Isleifur; Ong, Ken K.; Palotie, Aarno; Papamarkou, Theodore; Pomilla, Cristina; Pouta, Anneli; Rader, Daniel J.; Reilly, Muredach P.; Ridker, Paul M.; Rivadeneira, Fernando; Rudan, Igor; Ruokonen, Aimo; Samani, Nilesh; Scharnagl, Hubert; Seeley, Janet; Silander, Kaisa; Stancáková, Alena; Stirrups, Kathleen; Swift, Amy J.; Tiret, Laurence; Uitterlinden, Andre G.; van Pelt, L. Joost; Vedantam, Sailaja; Wainwright, Nicholas; Wijmenga, Cisca; Wild, Sarah H.; Willemsen, Gonneke; Wilsgaard, Tom; Wilson, James F.; Young, Elizabeth H.; Zhao, Jing Hua; Adair, Linda S.; Arveiler, Dominique; Assimes, Themistocles L.; Bandinelli, Stefania; Bennett, Franklyn; Bochud, Murielle; Boehm, Bernhard O.; Boomsma, Dorret I.; Borecki, Ingrid B.; Bornstein, Stefan R.; Bovet, Pascal; Burnier, Michel; Campbell, Harry; Chakravarti, Aravinda; Chambers, John C.; Chen, Yii-Der Ida; Collins, Francis S.; Cooper, Richard S.; Danesh, John; Dedoussis, George; de Faire, Ulf; Feranil, Alan B.; Ferrières, Jean; Ferrucci, Luigi; Freimer, Nelson B.; Gieger, Christian; Groop, Leif C.; Gudnason, Vilmundur; Gyllensten, Ulf; Hamsten, Anders; Harris, Tamara B.; Hingorani, Aroon; Hirschhorn, Joel N.; Hofman, Albert; Hovingh, G. Kees; Hsiung, Chao Agnes; Humphries, Steve E.; Hunt, Steven C.; Hveem, Kristian; Iribarren, Carlos; Järvelin, Marjo-Riitta; Jula, Antti; Kähönen, Mika; Kaprio, Jaakko; Kesäniemi, Antero; Kivimaki, Mika; Kooner, Jaspal S.; Koudstaal, Peter J.; Krauss, Ronald M.; Kuh, Diana; Kuusisto, Johanna; Kyvik, Kirsten O.; Laakso, Markku; Lakka, Timo A.; Lind, Lars; Lindgren, Cecilia M.; Martin, Nicholas G.; März, Winfried; McCarthy, Mark I.; McKenzie, Colin A.; Meneton, Pierre; Metspalu, Andres; Moilanen, Leena; Morris, Andrew D.; Munroe, Patricia B.; Njølstad, Inger; Pedersen, Nancy L.; Power, Chris; Pramstaller, Peter P.; Price, Jackie F.; Psaty, Bruce M.; Quertermous, Thomas; Rauramaa, Rainer; Saleheen, Danish; Salomaa, Veikko; Sanghera, Dharambir K.; Saramies, Jouko; Schwarz, Peter E. H.; Sheu, Wayne H.-H.; Shuldiner, Alan R.; Siegbahn, Agneta; Spector, Tim D.; Stefansson, Kari; Strachan, David P.; Tayo, Bamidele O.; Tremoli, Elena; Tuomilehto, Jaakko; Uusitupa, Matti; van Duijn, Cornelia M.; Vollenweider, Peter; Wallentin, Lars; Wareham, Nicholas J.; Whitfield, John B.; Wolffenbuttel, Bruce H. R.; Ordovas, Jose M.; Boerwinkle, Eric; Palmer, Colin N. A.; Thorsteinsdottir, Unnur; Chasman, Daniel I.; Rotter, Jerome I.; Franks, Paul W.; Ripatti, Samuli; Cupples, L. Adrienne; Sandhu, Manjinder S.; Rich, Stephen S.; Boehnke, Michael; Deloukas, Panos; Kathiresan, Sekar; Mohlke, Karen L.; Ingelsson, Erik; Abecasis, Gonçalo R.

    2013-01-01

    Levels of low-density lipoprotein (LDL) cholesterol, high-density lipoprotein (HDL) cholesterol, triglycerides and total cholesterol are heritable, modifiable risk factors for coronary artery disease. To identify new loci and refine known loci influencing these lipids, we examined 188,577

  10. BPS Jumping Loci are Automorphic

    Science.gov (United States)

    Kachru, Shamit; Tripathy, Arnav

    2018-06-01

    We show that BPS jumping loci-loci in the moduli space of string compactifications where the number of BPS states jumps in an upper semi-continuous manner—naturally appear as Fourier coefficients of (vector space-valued) automorphic forms. For the case of T 2 compactification, the jumping loci are governed by a modular form studied by Hirzebruch and Zagier, while the jumping loci in K3 compactification appear in a story developed by Oda and Kudla-Millson in arithmetic geometry. We also comment on some curious related automorphy in the physics of black hole attractors and flux vacua.

  11. High-density SNP genotyping of tomato (Solanum lycopersicum L. reveals patterns of genetic variation due to breeding.

    Directory of Open Access Journals (Sweden)

    Sung-Chur Sim

    Full Text Available The effects of selection on genome variation were investigated and visualized in tomato using a high-density single nucleotide polymorphism (SNP array. 7,720 SNPs were genotyped on a collection of 426 tomato accessions (410 inbreds and 16 hybrids and over 97% of the markers were polymorphic in the entire collection. Principal component analysis (PCA and pairwise estimates of F(st supported that the inbred accessions represented seven sub-populations including processing, large-fruited fresh market, large-fruited vintage, cultivated cherry, landrace, wild cherry, and S. pimpinellifolium. Further divisions were found within both the contemporary processing and fresh market sub-populations. These sub-populations showed higher levels of genetic diversity relative to the vintage sub-population. The array provided a large number of polymorphic SNP markers across each sub-population, ranging from 3,159 in the vintage accessions to 6,234 in the cultivated cherry accessions. Visualization of minor allele frequency revealed regions of the genome that distinguished three representative sub-populations of cultivated tomato (processing, fresh market, and vintage, particularly on chromosomes 2, 4, 5, 6, and 11. The PCA loadings and F(st outlier analysis between these three sub-populations identified a large number of candidate loci under positive selection on chromosomes 4, 5, and 11. The extent of linkage disequilibrium (LD was examined within each chromosome for these sub-populations. LD decay varied between chromosomes and sub-populations, with large differences reflective of breeding history. For example, on chromosome 11, decay occurred over 0.8 cM for processing accessions and over 19.7 cM for fresh market accessions. The observed SNP variation and LD decay suggest that different patterns of genetic variation in cultivated tomato are due to introgression from wild species and selection for market specialization.

  12. Bats aloft: Variation in echolocation call structure at high altitudes

    Science.gov (United States)

    Bats alter their echolocation calls in response to changes in ecological and behavioral conditions, but little is known about how they adjust their call structure in response to changes in altitude. This study examines altitudinal variation in the echolocation calls of Brazilian free-tailed bats, T...

  13. Discovery and refinement of loci associated with lipid levels

    DEFF Research Database (Denmark)

    Willer, C. J.; Schmidt, E. M.; Sengupta, S.

    2013-01-01

    Levels of low-density lipoprotein (LDL) cholesterol, high-density lipoprotein (HDL) cholesterol, triglycerides and total cholesterol are heritable, modifiable risk factors for coronary artery disease. To identify new loci and refine known loci influencing these lipids, we examined 188,577 individ...... of using genetic data from individuals of diverse ancestry and provide insights into the biological mechanisms regulating blood lipids to guide future genetic, biological and therapeutic research.......Levels of low-density lipoprotein (LDL) cholesterol, high-density lipoprotein (HDL) cholesterol, triglycerides and total cholesterol are heritable, modifiable risk factors for coronary artery disease. To identify new loci and refine known loci influencing these lipids, we examined 188......,577 individuals using genome-wide and custom genotyping arrays. We identify and annotate 157 loci associated with lipid levels at P lipid levels in humans. Using dense genotyping in individuals of European, East Asian, South Asian and African ancestry...

  14. Variation in MHC genotypes in two populations of house sparrow (Passer domesticus) with different population histories.

    Science.gov (United States)

    Borg, Asa Alexandra; Pedersen, Sindre Andre; Jensen, Henrik; Westerdahl, Helena

    2011-10-01

    Small populations are likely to have a low genetic ability for disease resistance due to loss of genetic variation through inbreeding and genetic drift. In vertebrates, the highest genetic diversity of the immune system is located at genes within the major histocompatibility complex (MHC). Interestingly, parasite-mediated selection is thought to potentially maintain variation at MHC loci even in populations that are monomorphic at other loci. Therefore, general loss of genetic variation in the genome may not necessarily be associated with low variation at MHC loci. We evaluated inter- and intrapopulation variation in MHC genotypes between an inbred (Aldra) and a relatively outbred population (Hestmannøy) of house sparrows (Passer domesticus) in a metapopulation at Helgeland, Norway. Genomic (gDNA) and transcribed (cDNA) alleles of functional MHC class I and IIB loci, along with neutral noncoding microsatellite markers, were analyzed to obtain relevant estimates of genetic variation. We found lower allelic richness in microsatellites in the inbred population, but high genetic variation in MHC class I and IIB loci in both populations. This suggests that also the inbred population could be under balancing selection to maintain genetic variation for pathogen resistance.

  15. Intraspecific karyotypic polymorphism is highly concordant with allozyme variation in Lysimachia mauritiana (Primulaceae: Myrsinoideae) in Taiwan: implications for the colonization history and dispersal patterns of coastal plants

    Science.gov (United States)

    Kono, Yoshiko; Chung, Kuo-Fang; Chen, Chih-Hui; Hoshi, Yoshikazu; Setoguchi, Hiroaki; Chou, Chang-Hung; Oginuma, Kazuo; Peng, Ching-I

    2012-01-01

    Background and Aims Investigating intraspecific karyotypic and genetic variations jointly can provide unique insights into how historical, ecological and cytogenetic factors influence microevolution. A coastal herb, Lysimachia mauritiana, exhibits extensive karyotypic polymorphism and displays a complex cytogeographic pattern across the Ryukyus. To explore whether a similar degree of chromosomal variation exists south of the Ryukyus, and in an attempt to ascertain the mechanisms that may have generated the patterns, comprehensive sampling was conducted in Taiwan. Methods Karyotypes were analysed at mitotic metaphase for 550 individuals from 42 populations throughout Taiwan Proper and its adjacent islands. In addition, genetic variation was estimated using 12 allozymes (21 loci) of 314 individuals sampled from 12 localities. Key Results Four chromosome numbers and eight cytotypes, including four endemic cytotypes, were detected. Cytotype distributions were highly structured geographically, with single cytotypes present in most populations and four major cytotypes dominating the north, east and south of Taiwan and the Penghu Archipelago. Allozyme variation was very low and F-statistics indicated an extremely high level of population differentiation, implying limited gene flow among populations. Cluster analysis of allozyme variation uncovered four geographic groups, each corresponding perfectly to the four dominant cytotypes. The geographic structure of cytotype distribution and allozyme variation probably resulted from severe genetic drift triggered by genetic bottlenecks, suggesting that Taiwanese populations were likely to be derived from four independent founder events. In the few localities with multiple cytotypes, cytogeographic patterns and inferences of chromosomal evolution revealed a trend of northward dispersal, consistent with the course of the Kuroshio Current that has been influential in shaping the coastal biota of the region. Conclusions The data

  16. Genome-wide association mapping reveals a rich genetic architecture of stripe rust resistance loci in emmer wheat (Triticum turgidum ssp. dicoccum).

    Science.gov (United States)

    Liu, Weizhen; Maccaferri, Marco; Chen, Xianming; Laghetti, Gaetano; Pignone, Domenico; Pumphrey, Michael; Tuberosa, Roberto

    2017-11-01

    SNP-based genome scanning in worldwide domesticated emmer germplasm showed high genetic diversity, rapid linkage disequilibrium decay and 51 loci for stripe rust resistance, a large proportion of which were novel. Cultivated emmer wheat (Triticum turgidum ssp. dicoccum), one of the oldest domesticated crops in the world, is a potentially rich reservoir of variation for improvement of resistance/tolerance to biotic and abiotic stresses in wheat. Resistance to stripe rust (Puccinia striiformis f. sp. tritici) in emmer wheat has been under-investigated. Here, we employed genome-wide association (GWAS) mapping with a mixed linear model to dissect effective stripe rust resistance loci in a worldwide collection of 176 cultivated emmer wheat accessions. Adult plants were tested in six environments and seedlings were evaluated with five races from the United States and one from Italy under greenhouse conditions. Five accessions were resistant across all experiments. The panel was genotyped with the wheat 90,000 Illumina iSelect single nucleotide polymorphism (SNP) array and 5106 polymorphic SNP markers with mapped positions were obtained. A high level of genetic diversity and fast linkage disequilibrium decay were observed. In total, we identified 14 loci associated with field resistance in multiple environments. Thirty-seven loci were significantly associated with all-stage (seedling) resistance and six of them were effective against multiple races. Of the 51 total loci, 29 were mapped distantly from previously reported stripe rust resistance genes or quantitative trait loci and represent newly discovered resistance loci. Our results suggest that GWAS is an effective method for characterizing genes in cultivated emmer wheat and confirm that emmer wheat is a rich source of stripe rust resistance loci that can be used for wheat improvement.

  17. Variational methods for high-order multiphoton processes

    International Nuclear Information System (INIS)

    Gao, B.; Pan, C.; Liu, C.; Starace, A.F.

    1990-01-01

    Methods for applying the variationally stable procedure for Nth-order perturbative transition matrix elements of Gao and Starace [Phys. Rev. Lett. 61, 404 (1988); Phys. Rev. A 39, 4550 (1989)] to multiphoton processes involving systems other than atomic H are presented. Three specific cases are discussed: one-electron ions or atoms in which the electron--ion interaction is described by a central potential; two-electron ions or atoms in which the electronic states are described by the adiabatic hyperspherical representation; and closed-shell ions or atoms in which the electronic states are described by the multiconfiguration Hartree--Fock representation. Applications are made to the dynamic polarizability of He and the two-photon ionization cross section of Ar

  18. The loci controlling plasticity in flax

    Directory of Open Access Journals (Sweden)

    Bickel CL

    2012-02-01

    Full Text Available Cory L Bickel, Marshall Lukacs, Christopher A CullisCase Western Reserve University, Cleveland OH, USAAbstract: Flax undergoes heritable genomic changes in response to nutrient stress, including changes in total DNA content, rDNA copy number variation, and the appearance of Linum Insertion Sequence 1 (LIS-1. The nature of the genomic changes suggests a very different mechanism, which is not yet understood, from that of other DNA changes in response to stress, such as the activation of transposable elements. To identify the genes that control genomic changes in response to stress in flax, reciprocal crosses were made between a responsive flax line, Stormont cirrus, and an unresponsive line, Bethune. The ability of the F2 generation (from selfed F1 plants to respond to nutrient stress was assayed using the insertion of LIS-1 as the criteria for responsiveness. Twenty-nine out of 89 F2s responded at 5 weeks, suggesting that 3-4 dominant loci were all necessary for early LIS-1 insertion. Seventy out of 76 responded at 10 weeks, indicating two dominant loci independently capable of initiating LIS-1 insertion under prolonged nutrient stress. F1 plants and their progeny with either P1 or Bethune as the maternal parent were capable of responding with LIS-1 insertion, indicating that LIS-1 insertion is under nuclear genetic control and does not involve maternal factors. Thus, a small number of loci within the genome of Stormont cirrus appear to control the ability to respond to nutrient stress with LIS-1 insertion. A genetic map of the flax genome is currently under construction, and will be used to identify these loci within the genome.Keywords: nutrient stress, genomic plasticity, flax, Linum usitatissimum, LIS-1 

  19. High resolution analysis of temporal variation of airborne radionuclides

    International Nuclear Information System (INIS)

    Komura, K.; Yamaguchi, Y.; Manikandan, M.; Murata, Y.; Iida, T.; Moriizumi, J.

    2004-01-01

    One of the application of ultra low-background gamma spectrometry, we tried to measure temporal variation of airborne radionuclides at intervals of 1 to few hours in extreme case. Airborne radionuclides were collected on a filter paper made of quartz fiber at the Low Level Radioactivity Laboratory (LLRL), Kanazawa Univ. in Tatsunokuchi (since Nov. 2002), Hegra Island located 50 km from Noto peninsula (since Apr. 2003) to investigate influence of Asian continent and Shishiku plateau at 640 m above sea to know vertical difference (since Sep., 2003). Pb-210, Pb-212 and Be-7 were measured nondestructively by ultra low background Ge detectors in Ogoya Underground Laboratory (270 meter water Concentration of Rn-222 was monitored 1 hour intervals and wind direction and speed were recorded 10 min or 2 min intervals (Hegra Is.) as support data in data analyses. In the regular monitoring, sampling was made at 1-2 day (LLRL and Shishiku) or 1 week intervals (Hegra) to know daily and seasonal variations and similarity or difference between sampling locations. When drastic meteorological change, such as passage of front or typhoon, occurrence of inversion layer and snow fall etc., short sampling at 1-2 hours of intervals was conducted to find the corrlation with meteorological factors at single point or 2 points simultaneously. As a results, it was found that concentrations of Pb-210, Po-210, Pb-212 and Be-7 were found to vary very quickly in a short time (see Figure below) due mainly to horizontal or vertical mixing of air-masses. (authors)

  20. The influence of Glu-1 and Glu-3 loci on dough rheology and bread-making properties in wheat (Triticum aestivum L.) doubled haploid lines.

    Science.gov (United States)

    Langner, Monika; Krystkowiak, Karolina; Salmanowicz, Bolesław P; Adamski, Tadeusz; Krajewski, Paweł; Kaczmarek, Zygmunt; Surma, Maria

    2017-12-01

    The major determinants of wheat quality are Glu-1 and Glu-3 glutenin loci and environmental factors. Additive effects of alleles at the Glu-1 and Glu-3 loci, as well as their interactions, were evaluated for dough rheology and baking properties in four groups of wheat doubled haploid lines differing in high- and low-molecular-weight glutenin composition. Flour quality, Reomixer (Reologica Instruments, Lund, Sweden), dough extension, Farinograph (Brabender GmbH, Duisburg, Germany) and baking parameters were determined. Groups of lines with the alleles Glu-A3b and Glu-B3d were characterized by higher values of dough and baking parameters compared to those with the Glu-A3e and Glu-B3a alleles. Effects of interactions between allelic variants at the Glu-1 and Glu-3 loci on Reomixer parameters, dough extension tests and baking parameters were significant, although additive effects of individual alleles were not always significant. The allelic variants at Glu-B3 had a much greater effect on dough rheological parameters than the variants at Glu-A3 or Glu-D3 loci. The effect of allelic variations at the Glu-D3 loci on rheological parameters and bread-making quality was non-significant, whereas their interactions with a majority of alleles at the other Glu-1 × Glu-3 loci were significant. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  1. A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk.

    Science.gov (United States)

    Blair, David R; Lyttle, Christopher S; Mortensen, Jonathan M; Bearden, Charles F; Jensen, Anders Boeck; Khiabanian, Hossein; Melamed, Rachel; Rabadan, Raul; Bernstam, Elmer V; Brunak, Søren; Jensen, Lars Juhl; Nicolae, Dan; Shah, Nigam H; Grossman, Robert L; Cox, Nancy J; White, Kevin P; Rzhetsky, Andrey

    2013-09-26

    Although countless highly penetrant variants have been associated with Mendelian disorders, the genetic etiologies underlying complex diseases remain largely unresolved. By mining the medical records of over 110 million patients, we examine the extent to which Mendelian variation contributes to complex disease risk. We detect thousands of associations between Mendelian and complex diseases, revealing a nondegenerate, phenotypic code that links each complex disorder to a unique collection of Mendelian loci. Using genome-wide association results, we demonstrate that common variants associated with complex diseases are enriched in the genes indicated by this "Mendelian code." Finally, we detect hundreds of comorbidity associations among Mendelian disorders, and we use probabilistic genetic modeling to demonstrate that Mendelian variants likely contribute nonadditively to the risk for a subset of complex diseases. Overall, this study illustrates a complementary approach for mapping complex disease loci and provides unique predictions concerning the etiologies of specific diseases. Copyright © 2013 Elsevier Inc. All rights reserved.

  2. The role of height-associated loci identified in genome wide association studies in the determination of pediatric stature

    Directory of Open Access Journals (Sweden)

    Frackelton Edward C

    2010-06-01

    Full Text Available Abstract Background Human height is considered highly heritable and correlated with certain disorders, such as type 2 diabetes and cancer. Despite environmental influences, genetic factors are known to play an important role in stature determination. A number of genetic determinants of adult height have already been established through genome wide association studies. Methods To examine 51 single nucleotide polymorphisms (SNPs corresponding to the 46 previously reported genomic loci for height in 8,184 European American children with height measurements. We leveraged genotyping data from our ongoing GWA study of height variation in children in order to query the 51 SNPs in this pediatric cohort. Results Sixteen of these SNPs yielded at least nominally significant association to height, representing fifteen different loci including EFEMP1-PNPT1, GPR126, C6orf173, SPAG17, Histone class 1, HLA class III and GDF5-UQCC. Other loci revealed no evidence for association, including HMGA1 and HMGA2. For the 16 associated variants, the genotype score explained 1.64% of the total variation for height z-score. Conclusion Among 46 loci that have been reported to associate with adult height to date, at least 15 also contribute to the determination of height in childhood.

  3. Analysis of genetic stability at SSR loci during somatic embryogenesis in maritime pine (Pinus pinaster).

    Science.gov (United States)

    Marum, Liliana; Rocheta, Margarida; Maroco, João; Oliveira, M Margarida; Miguel, Célia

    2009-04-01

    Somatic embryogenesis (SE) is a propagation tool of particular interest for accelerating the deployment of new high-performance planting stock in multivarietal forestry. However, genetic conformity in in vitro propagated plants should be assessed as early as possible, especially in long-living trees such as conifers. The main objective of this work was to study such conformity based on genetic stability at simple sequence repeat (SSR) loci during somatic embryogenesis in maritime pine (Pinus pinaster Ait.). Embryogenic cell lines (ECLs) subjected to tissue proliferation during 6, 14 or 22 months, as well as emblings regenerated from several ECLs, were analyzed. Genetic variation at seven SSR loci was detected in ECLs under proliferation conditions for all time points, and in 5 out of 52 emblings recovered from somatic embryos. Three of these five emblings showed an abnormal phenotype consisting mainly of plagiotropism and loss of apical dominance. Despite the variation found in somatic embryogenesis-derived plant material, no correlation was established between genetic stability at the analyzed loci and abnormal embling phenotype, present in 64% of the emblings. The use of microsatellites in this work was efficient for monitoring mutation events during the somatic embryogenesis in P. pinaster. These molecular markers should be useful in the implementation of new breeding and deployment strategies for improved trees using SE.

  4. Polymorphisms within novel risk loci for type 2 diabetes determine beta-cell function.

    Directory of Open Access Journals (Sweden)

    Harald Staiger

    Full Text Available BACKGROUND: Type 2 diabetes arises when insulin resistance-induced compensatory insulin secretion exhausts. Insulin resistance and/or beta-cell dysfunction result from the interaction of environmental factors (high-caloric diet and reduced physical activity with a predisposing polygenic background. Very recently, genetic variations within four novel genetic loci (SLC30A8, HHEX, EXT2, and LOC387761 were reported to be more frequent in subjects with type 2 diabetes than in healthy controls. However, associations of these variations with insulin resistance and/or beta-cell dysfunction were not assessed. METHODOLOGY/PRINCIPAL FINDINGS: By genotyping of 921 metabolically characterized German subjects for the reported candidate single nucleotide polymorphisms (SNPs, we show that the major alleles of the SLC30A8 SNP rs13266634 and the HHEX SNP rs7923837 associate with reduced insulin secretion stimulated by orally or intravenously administered glucose, but not with insulin resistance. In contrast, the other reported type 2 diabetes candidate SNPs within the EXT2 and LOC387761 loci did not associate with insulin resistance or beta-cell dysfunction, respectively. CONCLUSIONS/SIGNIFICANCE: The HHEX and SLC30A8 genes encode for proteins that were shown to be required for organogenesis of the ventral pancreas and for insulin maturation/storage, respectively. Therefore, the major alleles of type 2 diabetes candidate SNPs within these genetic loci represent crucial alleles for beta-cell dysfunction and, thus, might confer increased susceptibility of beta-cells towards adverse environmental factors.

  5. Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts

    DEFF Research Database (Denmark)

    Aulchenko, Yurii S; Ripatti, Samuli; Lindqvist, Ida

    2008-01-01

    Recent genome-wide association (GWA) studies of lipids have been conducted in samples ascertained for other phenotypes, particularly diabetes. Here we report the first GWA analysis of loci affecting total cholesterol (TC), low-density lipoprotein (LDL) cholesterol, high-density lipoprotein (HDL) .......8% of variation in lipids and were also associated with increased intima media thickness (P = 0.001) and coronary heart disease incidence (P = 0.04). The genetic risk score improves the screening of high-risk groups of dyslipidemia over classical risk factors....

  6. Library Spirit and Genius Loci

    DEFF Research Database (Denmark)

    Dahlkild, Nan

    2009-01-01

    The architecture and design of Nyborg Public Library in the light of the concepts "Library Spirit" and "Genius Loci", related to contemporary social and cultural movements, the development of the early welfare state and the "Scandinavian Style".......The architecture and design of Nyborg Public Library in the light of the concepts "Library Spirit" and "Genius Loci", related to contemporary social and cultural movements, the development of the early welfare state and the "Scandinavian Style"....

  7. High-Cadence Transit Timing Variation Monitoring of Extrasolar Planets

    Directory of Open Access Journals (Sweden)

    Naef D.

    2011-02-01

    Full Text Available We report ground-based high-cadence transit timing observations of the extrasolar planet WASP-2b. We achieve a typical timing error of 15-30 sec. The data show no significant deviations from the predicted ephemeris.

  8. The Impact of Polymorphic Variations in the 5p15, 6p12, 6p21 and 15q25 Loci on the Risk and Prognosis of Portuguese Patients with Non-Small Cell Lung Cancer

    Science.gov (United States)

    de Mello, Ramon Andrade; Ferreira, Mónica; Soares-Pires, Filipa; Costa, Sandra; Cunha, João; Oliveira, Pedro; Hespanhol, Venceslau; Reis, Rui Manuel

    2013-01-01

    Introduction Polymorphic variants in the 5p15, 6p12, 6p21, and 15q25 loci were demonstrated to potentially contribute to lung cancer carcinogenesis. Therefore, this study was performed to assess the role of those variants in non-small cell lung cancer (NSCLC) risk and prognosis in a Portuguese population. Materials and Methods Blood from patients with NSCLC was prospectively collected. To perform an association study, DNA from these patients and healthy controls were genotyped for a panel of 19 SNPs using a Sequenom® MassARRAY platform. Kaplan-Meier curves were used to assess the overall survival (OS) and progression-free survival (PFS). Results One hundred and forty-four patients with NSCLC were successfully consecutively genotyped for the 19 SNPs. One SNP was associated with NSCLC risk: rs9295740 G/A. Two SNPs were associated with non-squamous histology: rs3024994 (VEGF intron 2) T/C and rs401681 C/T. Three SNPs were associated with response rate: rs3025035 (VEGF intron 7) C/T, rs833061 (VEGF –460) C/T and rs9295740 G/A. One SNP demonstrated an influence on PFS: rs401681 C/T at 5p15, p = 0.021. Four SNPs demonstrated an influence on OS: rs2010963 (VEGF +405 G/C), p = 0.042; rs3025010 (VEGF intron 5 C/T), p = 0.047; rs401681 C/T at 5p15, p = 0.046; and rs31489 C/A at 5p15, p = 0.029. Conclusions Our study suggests that SNPs in the 6p12, 6p21, and 5p15 loci may serve as risk, predictive and prognostic NSCLC biomarkers. In the future, SNPs identified in the genomes of patients may improve NSCLC screening strategies and therapeutic management as well. PMID:24039754

  9. Exploring Variation in Glycemic Control Across and Within Eight High-Income Countries

    DEFF Research Database (Denmark)

    Charalampopoulos, Dimitrios; Hermann, Julia M; Svensson, Jannet

    2018-01-01

    OBJECTIVE: International studies on childhood type 1 diabetes (T1D) have focused on whole-country mean HbA1c levels, thereby concealing potential variations within countries. We aimed to explore the variations in HbA1c across and within eight high-income countries to best inform international ben...

  10. Accurate, high-throughput typing of copy number variation using paralogue ratios from dispersed repeats.

    NARCIS (Netherlands)

    Armour, J.A.; Palla, R.; Zeeuwen, P.L.J.M.; Heijer, M. den; Schalkwijk, J.; Hollox, E.J.

    2007-01-01

    Recent work has demonstrated an unexpected prevalence of copy number variation in the human genome, and has highlighted the part this variation may play in predisposition to common phenotypes. Some important genes vary in number over a high range (e.g. DEFB4, which commonly varies between two and

  11. Genetic polymorphisms of 20 autosomal STR loci in the Vietnamese population from Yunnan Province, Southwest China.

    Science.gov (United States)

    Zhang, Xiufeng; Hu, Liping; Du, Lei; Nie, Aiting; Rao, Min; Pang, Jing Bo; Nie, Shengjie

    2017-05-01

    The genetic polymorphisms of 20 autosomal short tandem repeat (STR) loci included in the PowerPlex® 21 kit were evaluated in 522 healthy unrelated Vietnamese from Yunnan, China. All of the loci reached the Hardy-Weinberg equilibrium. These loci were examined to determine allele frequencies and forensic statistical parameters. The combined discrimination power and probability of excluding paternity of the 20 STR loci were 0.999999999999999999999991 26 and 0.999999975, respectively. Results suggested that the 20 STR loci are highly polymorphic, which is suitable for forensic personal identification and paternity testing.

  12. Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice

    OpenAIRE

    Yang, Wanneng; Guo, Zilong; Huang, Chenglong; Duan, Lingfeng; Chen, Guoxing; Jiang, Ni; Fang, Wei; Feng, Hui; Xie, Weibo; Lian, Xingming; Wang, Gongwei; Luo, Qingming; Zhang, Qifa; Liu, Qian; Xiong, Lizhong

    2014-01-01

    Even as the study of plant genomics rapidly develops through the use of high-throughput sequencing techniques, traditional plant phenotyping lags far behind. Here we develop a high-throughput rice phenotyping facility (HRPF) to monitor 13 traditional agronomic traits and 2 newly defined traits during the rice growth period. Using genome-wide association studies (GWAS) of the 15 traits, we identify 141 associated loci, 25 of which contain known genes such as the Green Revolution semi-dwarf gen...

  13. Anomalously high variation in postnatal development is ancestral for dinosaurs but lost in birds

    Science.gov (United States)

    Griffin, Christopher T.; Nesbitt, Sterling J.

    2016-12-01

    Compared with all other living reptiles, birds grow extremely fast and possess unusually low levels of intraspecific variation during postnatal development. It is now clear that birds inherited their high rates of growth from their dinosaurian ancestors, but the origin of the avian condition of low variation during development is poorly constrained. The most well-understood growth trajectories of later Mesozoic theropods (e.g., Tyrannosaurus, Allosaurus) show similarly low variation to birds, contrasting with higher variation in extant crocodylians. Here, we show that deep within Dinosauria, among the earliest-diverging dinosaurs, anomalously high intraspecific variation is widespread but then is lost in more derived theropods. This style of development is ancestral for dinosaurs and their closest relatives, and, surprisingly, this level of variation is far higher than in living crocodylians. Among early dinosaurs, this variation is widespread across Pangaea in the Triassic and Early Jurassic, and among early-diverging theropods (ceratosaurs), this variation is maintained for 165 million years to the end of the Cretaceous. Because the Late Triassic environment across Pangaea was volatile and heterogeneous, this variation may have contributed to the rise of dinosaurian dominance through the end of the Triassic Period.

  14. Building high resolution genetic variation map for Mongolians

    DEFF Research Database (Denmark)

    Guo, Xiaosen

    the paternal or maternal transmission, or carrying out the genetic disease studies based on the data of a small number of variants or partial genomic regions. In the study plan, first, we collected the genomic DNA of a representative Mongolian male individual, performed high coverage whole genome sequencing...... the pigmentation gene OCA2 play an important role in the convergent skin lightening of East Asians during recent human evolution. However, the genomics research on Mongolians, which attract strong research interests, still remains the levels of using the data of Y chromosome or Mitochondrial genome to explore...... the individual possesses a risk allele that may cause carnitine deficiency. Y haplogroup analysis located the paternal inheritance to the clade D3a, which is the one of oldest lineage in East Asians and present the most common in Tibeto- Burman populations. Through final population genetics analyses, we roughly...

  15. Cigarette price variation around high schools: evidence from Washington DC.

    Science.gov (United States)

    Cantrell, Jennifer; Ganz, Ollie; Anesetti-Rothermel, Andrew; Harrell, Paul; Kreslake, Jennifer M; Xiao, Haijun; Pearson, Jennifer L; Vallone, Donna; Kirchner, Thomas R

    2015-01-01

    This study examines lowest cigarette prices in all tobacco retail outlets in Washington D.C. (n=750) in relation to the type and number of high schools nearby, controlling for confounders. The lowest overall and Newport menthol prices were significantly lower at outlets near public non-charter and charter schools compared with outlets near private schools. Given higher smoking prevalence and more price-sensitive youth subgroups in U.S. public schools, exposure to low prices may contribute to tobacco-related health disparities in minority and low-income populations. Tobacco taxes combined with policies to minimize the increasing use of price as a marketing tool are critical. Copyright © 2014 Elsevier Ltd. All rights reserved.

  16. Core surface flow modelling from high-resolution secular variation

    DEFF Research Database (Denmark)

    Holme, R.; Olsen, Nils

    2006-01-01

    -flux hypothesis, but the spectrum of the SV implies that a conclusive test of frozen-flux is not possible. We parametrize the effects of diffusion as an expected misfit in the flow prediction due to departure from the frozen-flux hypothesis; at low spherical harmonic degrees, this contribution dominates...... the expected departure of the SV predictions from flow to the observed SV, while at high degrees the SV model uncertainty is dominant. We construct fine-scale core surface flows to model the SV. Flow non-uniqueness is a serious problem because the flows are sufficiently small scale to allow flow around non......-series of magnetic data and better parametrization of the external magnetic field....

  17. Variation in readmission expenditures after high-risk surgery.

    Science.gov (United States)

    Jacobs, Bruce L; He, Chang; Li, Benjamin Y; Helfand, Alex; Krishnan, Naveen; Borza, Tudor; Ghaferi, Amir A; Hollenbeck, Brent K; Helm, Jonathan E; Lavieri, Mariel S; Skolarus, Ted A

    2017-06-01

    The Hospital Readmissions Reduction Program reduces payments to hospitals with excess readmissions for three common medical conditions and recently extended its readmission program to surgical patients. We sought to investigate readmission intensity as measured by readmission cost for high-risk surgeries and examine predictors of higher readmission costs. We used the Healthcare Cost and Utilization Project's State Inpatient Database to perform a retrospective cohort study of patients undergoing major chest (aortic valve replacement, coronary artery bypass grafting, lung resection) and major abdominal (abdominal aortic aneurysm repair [open approach], cystectomy, esophagectomy, pancreatectomy) surgery in 2009 and 2010. We fit a multivariable logistic regression model with generalized estimation equations to examine patient and index admission factors associated with readmission costs. The 30-d readmission rate was 16% for major chest and 22% for major abdominal surgery (P readmission costs for both chest (odds ratio [OR]: 1.99; 95% confidence interval [CI]: 1.60-2.48) and abdominal surgeries (OR: 1.86; 95% CI: 1.24-2.78). Comorbidities, length of stay, and receipt of blood or imaging was associated with higher readmission costs for chest surgery patients. Readmission >3 wk after discharge was associated with lower costs among abdominal surgery patients. Readmissions after high-risk surgery are common, affecting about one in six patients. Predictors of higher readmission costs differ among major chest and abdominal surgeries. Better identifying patients susceptible to higher readmission costs may inform future interventions to either reduce the intensity of these readmissions or eliminate them altogether. Copyright © 2017 Elsevier Inc. All rights reserved.

  18. Genome-wide linkage in a highly consanguineous pedigree reveals two novel loci on chromosome 7 for non-syndromic familial Premature Ovarian Failure.

    Directory of Open Access Journals (Sweden)

    Sandrine Caburet

    Full Text Available BACKGROUND: The human condition known as Premature Ovarian Failure (POF is characterized by loss of ovarian function before the age of 40. A majority of POF cases are sporadic, but 10-15% are familial, suggesting a genetic origin of the disease. Although several causal mutations have been identified, the etiology of POF is still unknown for about 90% of the patients. METHODOLOGY/PRINCIPAL FINDINGS: We report a genome-wide linkage and homozygosity analysis in one large consanguineous Middle-Eastern POF-affected family presenting an autosomal recessive pattern of inheritance. We identified two regions with a LOD(max of 3.26 on chromosome 7p21.1-15.3 and 7q21.3-22.2, which are supported as candidate regions by homozygosity mapping. Sequencing of the coding exons and known regulatory sequences of three candidate genes (DLX5, DLX6 and DSS1 included within the largest region did not reveal any causal mutations. CONCLUSIONS/SIGNIFICANCE: We detect two novel POF-associated loci on human chromosome 7, opening the way to the identification of new genes involved in the control of ovarian development and function.

  19. Proposal for the Identification of Barley Varieties Based on the Genotypes for 2 Hordein and 39 Isoenzym Loci of 47 Reference Varieties

    DEFF Research Database (Denmark)

    Nielsen, G.; Johansen, Hanne Bay

    1986-01-01

    Fifty-nine spring and 7 winter barley varieties in lsquoThe Danish List of Varieties of Agricultural Crops, 1983/84rsquo were examined for variation at 39 isoenzyme and two hordein loci. Twenty-three isoenzyme loci had one allele only, and 16 loci had from two to five alleles. One hordein locus had...

  20. Multiple loci associated with renal function in African Americans.

    Directory of Open Access Journals (Sweden)

    Daniel Shriner

    Full Text Available The incidence of chronic kidney disease varies by ethnic group in the USA, with African Americans displaying a two-fold higher rate than European Americans. One of the two defining variables underlying staging of chronic kidney disease is the glomerular filtration rate. Meta-analysis in individuals of European ancestry has identified 23 genetic loci associated with the estimated glomerular filtration rate (eGFR. We conducted a follow-up study of these 23 genetic loci using a population-based sample of 1,018 unrelated admixed African Americans. We included in our follow-up study two variants in APOL1 associated with end-stage kidney disease discovered by admixture mapping in admixed African Americans. To address confounding due to admixture, we estimated local ancestry at each marker and global ancestry. We performed regression analysis stratified by local ancestry and combined the resulting regression estimates across ancestry strata using an inverse variance-weighted fixed effects model. We found that 11 of the 24 loci were significantly associated with eGFR in our sample. The effect size estimates were not significantly different between the subgroups of individuals with two copies of African ancestry vs. two copies of European ancestry for any of the 11 loci. In contrast, allele frequencies were significantly different at 10 of the 11 loci. Collectively, the 11 loci, including four secondary signals revealed by conditional analyses, explained 14.2% of the phenotypic variance in eGFR, in contrast to the 1.4% explained by the 24 loci in individuals of European ancestry. Our findings provide insight into the genetic basis of variation in renal function among admixed African Americans.

  1. Development of new VNTR markers for pike and assessment of variability at di- and tetranucleotide repeat microsatellite loci

    DEFF Research Database (Denmark)

    Hansen, Michael Møller; Taggart, J.B.; Meldrup, Dorte

    1999-01-01

    Levels of variation at six VNTR (variable number of tandem repeats) loci, one minisatellite and five microsatellite loci, isolated from tri- and tetranucleotide enriched DNA libraries for northern pike were generally low in two Danish populations (1-4 alleles; expected heterozygosity 0-0.57), tho......Levels of variation at six VNTR (variable number of tandem repeats) loci, one minisatellite and five microsatellite loci, isolated from tri- and tetranucleotide enriched DNA libraries for northern pike were generally low in two Danish populations (1-4 alleles; expected heterozygosity 0...

  2. Novel genetic loci associated with hippocampal volume.

    Science.gov (United States)

    Hibar, Derrek P; Adams, Hieab H H; Jahanshad, Neda; Chauhan, Ganesh; Stein, Jason L; Hofer, Edith; Renteria, Miguel E; Bis, Joshua C; Arias-Vasquez, Alejandro; Ikram, M Kamran; Desrivières, Sylvane; Vernooij, Meike W; Abramovic, Lucija; Alhusaini, Saud; Amin, Najaf; Andersson, Micael; Arfanakis, Konstantinos; Aribisala, Benjamin S; Armstrong, Nicola J; Athanasiu, Lavinia; Axelsson, Tomas; Beecham, Ashley H; Beiser, Alexa; Bernard, Manon; Blanton, Susan H; Bohlken, Marc M; Boks, Marco P; Bralten, Janita; Brickman, Adam M; Carmichael, Owen; Chakravarty, M Mallar; Chen, Qiang; Ching, Christopher R K; Chouraki, Vincent; Cuellar-Partida, Gabriel; Crivello, Fabrice; Den Braber, Anouk; Doan, Nhat Trung; Ehrlich, Stefan; Giddaluru, Sudheer; Goldman, Aaron L; Gottesman, Rebecca F; Grimm, Oliver; Griswold, Michael E; Guadalupe, Tulio; Gutman, Boris A; Hass, Johanna; Haukvik, Unn K; Hoehn, David; Holmes, Avram J; Hoogman, Martine; Janowitz, Deborah; Jia, Tianye; Jørgensen, Kjetil N; Karbalai, Nazanin; Kasperaviciute, Dalia; Kim, Sungeun; Klein, Marieke; Kraemer, Bernd; Lee, Phil H; Liewald, David C M; Lopez, Lorna M; Luciano, Michelle; Macare, Christine; Marquand, Andre F; Matarin, Mar; Mather, Karen A; Mattheisen, Manuel; McKay, David R; Milaneschi, Yuri; Muñoz Maniega, Susana; Nho, Kwangsik; Nugent, Allison C; Nyquist, Paul; Loohuis, Loes M Olde; Oosterlaan, Jaap; Papmeyer, Martina; Pirpamer, Lukas; Pütz, Benno; Ramasamy, Adaikalavan; Richards, Jennifer S; Risacher, Shannon L; Roiz-Santiañez, Roberto; Rommelse, Nanda; Ropele, Stefan; Rose, Emma J; Royle, Natalie A; Rundek, Tatjana; Sämann, Philipp G; Saremi, Arvin; Satizabal, Claudia L; Schmaal, Lianne; Schork, Andrew J; Shen, Li; Shin, Jean; Shumskaya, Elena; Smith, Albert V; Sprooten, Emma; Strike, Lachlan T; Teumer, Alexander; Tordesillas-Gutierrez, Diana; Toro, Roberto; Trabzuni, Daniah; Trompet, Stella; Vaidya, Dhananjay; Van der Grond, Jeroen; Van der Lee, Sven J; Van der Meer, Dennis; Van Donkelaar, Marjolein M J; Van Eijk, Kristel R; Van Erp, Theo G M; Van Rooij, Daan; Walton, Esther; Westlye, Lars T; Whelan, Christopher D; Windham, Beverly G; Winkler, Anderson M; Wittfeld, Katharina; Woldehawariat, Girma; Wolf, Christiane; Wolfers, Thomas; Yanek, Lisa R; Yang, Jingyun; Zijdenbos, Alex; Zwiers, Marcel P; Agartz, Ingrid; Almasy, Laura; Ames, David; Amouyel, Philippe; Andreassen, Ole A; Arepalli, Sampath; Assareh, Amelia A; Barral, Sandra; Bastin, Mark E; Becker, Diane M; Becker, James T; Bennett, David A; Blangero, John; van Bokhoven, Hans; Boomsma, Dorret I; Brodaty, Henry; Brouwer, Rachel M; Brunner, Han G; Buckner, Randy L; Buitelaar, Jan K; Bulayeva, Kazima B; Cahn, Wiepke; Calhoun, Vince D; Cannon, Dara M; Cavalleri, Gianpiero L; Cheng, Ching-Yu; Cichon, Sven; Cookson, Mark R; Corvin, Aiden; Crespo-Facorro, Benedicto; Curran, Joanne E; Czisch, Michael; Dale, Anders M; Davies, Gareth E; De Craen, Anton J M; De Geus, Eco J C; De Jager, Philip L; De Zubicaray, Greig I; Deary, Ian J; Debette, Stéphanie; DeCarli, Charles; Delanty, Norman; Depondt, Chantal; DeStefano, Anita; Dillman, Allissa; Djurovic, Srdjan; Donohoe, Gary; Drevets, Wayne C; Duggirala, Ravi; Dyer, Thomas D; Enzinger, Christian; Erk, Susanne; Espeseth, Thomas; Fedko, Iryna O; Fernández, Guillén; Ferrucci, Luigi; Fisher, Simon E; Fleischman, Debra A; Ford, Ian; Fornage, Myriam; Foroud, Tatiana M; Fox, Peter T; Francks, Clyde; Fukunaga, Masaki; Gibbs, J Raphael; Glahn, David C; Gollub, Randy L; Göring, Harald H H; Green, Robert C; Gruber, Oliver; Gudnason, Vilmundur; Guelfi, Sebastian; Håberg, Asta K; Hansell, Narelle K; Hardy, John; Hartman, Catharina A; Hashimoto, Ryota; Hegenscheid, Katrin; Heinz, Andreas; Le Hellard, Stephanie; Hernandez, Dena G; Heslenfeld, Dirk J; Ho, Beng-Choon; Hoekstra, Pieter J; Hoffmann, Wolfgang; Hofman, Albert; Holsboer, Florian; Homuth, Georg; Hosten, Norbert; Hottenga, Jouke-Jan; Huentelman, Matthew; Hulshoff Pol, Hilleke E; Ikeda, Masashi; Jack, Clifford R; Jenkinson, Mark; Johnson, Robert; Jönsson, Erik G; Jukema, J Wouter; Kahn, René S; Kanai, Ryota; Kloszewska, Iwona; Knopman, David S; Kochunov, Peter; Kwok, John B; Lawrie, Stephen M; Lemaître, Hervé; Liu, Xinmin; Longo, Dan L; Lopez, Oscar L; Lovestone, Simon; Martinez, Oliver; Martinot, Jean-Luc; Mattay, Venkata S; McDonald, Colm; McIntosh, Andrew M; McMahon, Francis J; McMahon, Katie L; Mecocci, Patrizia; Melle, Ingrid; Meyer-Lindenberg, Andreas; Mohnke, Sebastian; Montgomery, Grant W; Morris, Derek W; Mosley, Thomas H; Mühleisen, Thomas W; Müller-Myhsok, Bertram; Nalls, Michael A; Nauck, Matthias; Nichols, Thomas E; Niessen, Wiro J; Nöthen, Markus M; Nyberg, Lars; Ohi, Kazutaka; Olvera, Rene L; Ophoff, Roel A; Pandolfo, Massimo; Paus, Tomas; Pausova, Zdenka; Penninx, Brenda W J H; Pike, G Bruce; Potkin, Steven G; Psaty, Bruce M; Reppermund, Simone; Rietschel, Marcella; Roffman, Joshua L; Romanczuk-Seiferth, Nina; Rotter, Jerome I; Ryten, Mina; Sacco, Ralph L; Sachdev, Perminder S; Saykin, Andrew J; Schmidt, Reinhold; Schmidt, Helena; Schofield, Peter R; Sigursson, Sigurdur; Simmons, Andrew; Singleton, Andrew; Sisodiya, Sanjay M; Smith, Colin; Smoller, Jordan W; Soininen, Hilkka; Steen, Vidar M; Stott, David J; Sussmann, Jessika E; Thalamuthu, Anbupalam; Toga, Arthur W; Traynor, Bryan J; Troncoso, Juan; Tsolaki, Magda; Tzourio, Christophe; Uitterlinden, Andre G; Hernández, Maria C Valdés; Van der Brug, Marcel; van der Lugt, Aad; van der Wee, Nic J A; Van Haren, Neeltje E M; van 't Ent, Dennis; Van Tol, Marie-Jose; Vardarajan, Badri N; Vellas, Bruno; Veltman, Dick J; Völzke, Henry; Walter, Henrik; Wardlaw, Joanna M; Wassink, Thomas H; Weale, Michael E; Weinberger, Daniel R; Weiner, Michael W; Wen, Wei; Westman, Eric; White, Tonya; Wong, Tien Y; Wright, Clinton B; Zielke, Ronald H; Zonderman, Alan B; Martin, Nicholas G; Van Duijn, Cornelia M; Wright, Margaret J; Longstreth, W T; Schumann, Gunter; Grabe, Hans J; Franke, Barbara; Launer, Lenore J; Medland, Sarah E; Seshadri, Sudha; Thompson, Paul M; Ikram, M Arfan

    2017-01-18

    The hippocampal formation is a brain structure integrally involved in episodic memory, spatial navigation, cognition and stress responsiveness. Structural abnormalities in hippocampal volume and shape are found in several common neuropsychiatric disorders. To identify the genetic underpinnings of hippocampal structure here we perform a genome-wide association study (GWAS) of 33,536 individuals and discover six independent loci significantly associated with hippocampal volume, four of them novel. Of the novel loci, three lie within genes (ASTN2, DPP4 and MAST4) and one is found 200 kb upstream of SHH. A hippocampal subfield analysis shows that a locus within the MSRB3 gene shows evidence of a localized effect along the dentate gyrus, subiculum, CA1 and fissure. Further, we show that genetic variants associated with decreased hippocampal volume are also associated with increased risk for Alzheimer's disease (r g =-0.155). Our findings suggest novel biological pathways through which human genetic variation influences hippocampal volume and risk for neuropsychiatric illness.

  3. Quantitative trait loci and metabolic pathways

    Science.gov (United States)

    McMullen, M. D.; Byrne, P. F.; Snook, M. E.; Wiseman, B. R.; Lee, E. A.; Widstrom, N. W.; Coe, E. H.

    1998-01-01

    The interpretation of quantitative trait locus (QTL) studies is limited by the lack of information on metabolic pathways leading to most economic traits. Inferences about the roles of the underlying genes with a pathway or the nature of their interaction with other loci are generally not possible. An exception is resistance to the corn earworm Helicoverpa zea (Boddie) in maize (Zea mays L.) because of maysin, a C-glycosyl flavone synthesized in silks via a branch of the well characterized flavonoid pathway. Our results using flavone synthesis as a model QTL system indicate: (i) the importance of regulatory loci as QTLs, (ii) the importance of interconnecting biochemical pathways on product levels, (iii) evidence for “channeling” of intermediates, allowing independent synthesis of related compounds, (iv) the utility of QTL analysis in clarifying the role of specific genes in a biochemical pathway, and (v) identification of a previously unknown locus on chromosome 9S affecting flavone level. A greater understanding of the genetic basis of maysin synthesis and associated corn earworm resistance should lead to improved breeding strategies. More broadly, the insights gained in relating a defined genetic and biochemical pathway affecting a quantitative trait should enhance interpretation of the biological basis of variation for other quantitative traits. PMID:9482823

  4. Phylogenomic analyses of 539 highly informative loci dates a fully resolved time tree for the major clades of living turtles (Testudines).

    Science.gov (United States)

    Shaffer, H Bradley; McCartney-Melstad, Evan; Near, Thomas J; Mount, Genevieve G; Spinks, Phillip Q

    2017-10-01

    Accurate time-calibrated phylogenies are the centerpiece of many macroevolutionary studies, and the relationship between the size and scale of molecular data sets and the density and accuracy of fossil calibrations is a key element of time tree studies. Here, we develop a target capture array specifically for living turtles, compare its efficiency to an ultraconserved element (UCE) dataset, and present a time-calibrated molecular phylogeny based on 539 nuclear loci sequenced from 26 species representing the breadth of living turtle diversity plus outgroups. Our gene array, based on three fully sequenced turtle genomes, is 2.4 times more variable across turtles than a recently published UCE data set for an identical subset of 13 species, confirming that taxon-specific arrays return more informative data per sequencing effort than UCEs. We used our genomic data to estimate the ages of living turtle clades including a mid-late Triassic origin for crown turtles and a mid-Carboniferous split of turtles from their sister group, Archosauria. By specifically excluding several of the earliest potential crown turtle fossils and limiting the age of fossil calibration points to the unambiguous crown lineage Caribemys oxfordiensis from the Late Jurassic (Oxfordian, 163.5-157.3Ma) we corroborate a relatively ancient age for living turtles. We also provide novel age estimates for five of the ten testudine families containing more than a single species, as well as several intrafamilial clades. Most of the diversity of crown turtles appears to date to the Paleogene, well after the Cretaceous-Paleogene mass extinction 66mya. Copyright © 2017 Elsevier Inc. All rights reserved.

  5. Global assessment of genomic variation in cattle by genome resequencing and high-throughput genotyping

    DEFF Research Database (Denmark)

    Zhan, Bujie; Fadista, João; Thomsen, Bo

    2011-01-01

    Background Integration of genomic variation with phenotypic information is an effective approach for uncovering genotype-phenotype associations. This requires an accurate identification of the different types of variation in individual genomes. Results We report the integration of the whole genome...... of split-read and read-pair approaches proved to be complementary in finding different signatures. CNVs were identified on the basis of the depth of sequenced reads, and by using SNP and CGH arrays. Conclusions Our results provide high resolution mapping of diverse classes of genomic variation...

  6. Effects of Abrupt Variations of Solar Wind Dynamic Pressure on the High-Latitude Ionosphere

    Directory of Open Access Journals (Sweden)

    Igino Coco

    2011-01-01

    Full Text Available We show the results of a statistical study on the effects in the high-latitude ionosphere of abrupt variations of solar wind dynamic pressure, using Super Dual Auroral Radar Network (SuperDARN data in both hemispheres. We find that, during periods of quiet ionospheric conditions, the amount of radar backscatter increases when a variation in the dynamic pressure occurs, both positive (increase of the pressure and negative (decrease of the pressure. We also investigate the behaviour of the Cross-Polar Cap Potential (CPCP during pressure variations and show preliminary results.

  7. A high sensitivity process variation sensor utilizing sub-threshold operation

    OpenAIRE

    Meterelliyoz, Mesut; Song, Peilin; Stellari, Franco; Kulkarni, Jaydeep P.; Roy, Kaushik

    2008-01-01

    In this paper, we propose a novel low-power, bias-free, high-sensitivity process variation sensor for monitoring random variations in the threshold voltage. The proposed sensor design utilizes the exponential current-voltage relationship of sub-threshold operation thereby improving the sensitivity by 2.3X compared to the above-threshold operation. A test-chip containing 128 PMOS and 128 NMOS devices has been fabri...

  8. Suppression of subthreshold characteristics variation for junctionless multigate transistors using high-k spacers

    International Nuclear Information System (INIS)

    Lou, Haijun; Zhang, Baili; Li, Dan; Lin, Xinnan; He, Jin; Chan, Mansun

    2015-01-01

    In this work, the high-k spacer is proposed to suppress the subthreshold characteristics variation of junctionless multigate transistor (JMT) with non-ideal sidewall angle for the first time. It is demonstrated that the variation of subthreshold characteristics induced by the changing sidewall angle is efficiently suppressed by high-k spacers due to the enhanced corner effect through the fringe capacitance, and the electrostatic integrity of JMTs is also improved at sub-22 nm gate length. Two key parameters of high-k spacer, the thickness and length, have been optimized in terms of the suppression of subthreshold characteristics variation. Then their optimal values are proposed. The benefit of high-k spacer makes JMTs more scalable. (paper)

  9. High-resolution copy number variation analysis of schizophrenia in Japan.

    Science.gov (United States)

    Kushima, I; Aleksic, B; Nakatochi, M; Shimamura, T; Shiino, T; Yoshimi, A; Kimura, H; Takasaki, Y; Wang, C; Xing, J; Ishizuka, K; Oya-Ito, T; Nakamura, Y; Arioka, Y; Maeda, T; Yamamoto, M; Yoshida, M; Noma, H; Hamada, S; Morikawa, M; Uno, Y; Okada, T; Iidaka, T; Iritani, S; Yamamoto, T; Miyashita, M; Kobori, A; Arai, M; Itokawa, M; Cheng, M-C; Chuang, Y-A; Chen, C-H; Suzuki, M; Takahashi, T; Hashimoto, R; Yamamori, H; Yasuda, Y; Watanabe, Y; Nunokawa, A; Someya, T; Ikeda, M; Toyota, T; Yoshikawa, T; Numata, S; Ohmori, T; Kunimoto, S; Mori, D; Iwata, N; Ozaki, N

    2017-03-01

    Recent schizophrenia (SCZ) studies have reported an increased burden of de novo copy number variants (CNVs) and identified specific high-risk CNVs, although with variable phenotype expressivity. However, the pathogenesis of SCZ has not been fully elucidated. Using array comparative genomic hybridization, we performed a high-resolution genome-wide CNV analysis on a mainly (92%) Japanese population (1699 SCZ cases and 824 controls) and identified 7066 rare CNVs, 70.0% of which were small (history of congenital/developmental phenotypes, and the rate of treatment resistance was significantly higher (odds ratio=2.79, P=0.0036). We found more severe clinical manifestations in patients with two clinically significant CNVs. Gene set analysis replicated previous findings (e.g., synapse, calcium signaling) and identified novel biological pathways including oxidative stress response, genomic integrity, kinase and small GTPase signaling. Furthermore, involvement of multiple SCZ candidate genes and biological pathways in the pathogenesis of SCZ was suggested in established SCZ-associated CNV loci. Our study shows the high genetic heterogeneity of SCZ and its clinical features and raises the possibility that genomic instability is involved in its pathogenesis, which may be related to the increased burden of de novo CNVs and variable expressivity of CNVs.

  10. Patterns of gene variation in central and marginal populations of Drosophila robusta.

    Science.gov (United States)

    Prakash, S

    1973-10-01

    follows: (1) The allele frequencies are similar in all populations at the XDH, Pep-1 and Hex-1 loci. (2) The alleles at the Est-1, Est-2, Amy loci and the AP-4(1.0) and the LAP-1(.90) alleles show north south clinal change in frequency. (3) There is north south and east west differentiation at the Pt-5, Pt-8 and Pt-9 loci and the allele AP-4(.81). (4) Polymorphism at loci such as Fum, B.Ox, Hex-8, Pep-2 and Pep-3 are restricted to only one or two of the populations. (5) Allele frequencies at the MDH and ODH loci fluctuate between populations. (6) Allele frequencies at many polymorphic loci such as Est-1, Est-2, LAP-1, AP-4, Pt-5, Pt-8, Pt-9, Pt-16, MDH, Fum change clinally within a gene arrangement. The pattern of gene variation in D. robusta is very complex and cannot be easily explained due to migration of neutral alleles between once-isolated populations or to semi-isolation of neutral alleles. The observations of the pattern of allele variation in different populations, high levels of polymorphism in the marginal populations which have small population size and low levels of polymorphism of the X chromosome loci all support the argument in favor of balancing selection as the main mechanism for the maintenance of these polymorphisms. Environmental factors must play a role in the maintenance of a great deal of these polymorphisms, since we observe clinal allele frequency changes even within a given inversion type.

  11. Neutral mutation as the source of genetic variation in life history traits.

    Science.gov (United States)

    Brcić-Kostić, Krunoslav

    2005-08-01

    The mechanism underlying the maintenance of adaptive genetic variation is a long-standing question in evolutionary genetics. There are two concepts (mutation-selection balance and balancing selection) which are based on the phenotypic differences between alleles. Mutation - selection balance and balancing selection cannot properly explain the process of gene substitution, i.e. the molecular evolution of quantitative trait loci affecting fitness. I assume that such loci have non-essential functions (small effects on fitness), and that they have the potential to evolve into new functions and acquire new adaptations. Here I show that a high amount of neutral polymorphism at these loci can exist in real populations. Consistent with this, I propose a hypothesis for the maintenance of genetic variation in life history traits which can be efficient for the fixation of alleles with very small selective advantage. The hypothesis is based on neutral polymorphism at quantitative trait loci and both neutral and adaptive gene substitutions. The model of neutral - adaptive conversion (NAC) assumes that neutral alleles are not neutral indefinitely, and that in specific and very rare situations phenotypic (relative fitness) differences between them can appear. In this paper I focus on NAC due to phenotypic plasticity of neutral alleles. The important evolutionary consequence of NAC could be the increased adaptive potential of a population. Loci responsible for adaptation should be fast evolving genes with minimally discernible phenotypic effects, and the recent discovery of genes with such characteristics implicates them as suitable candidates for loci involved in adaptation.

  12. Genetics analysis of 38 STR loci in Uygur population from Southern Xinjiang of China.

    Science.gov (United States)

    Yuan, Li; Liu, Haibo; Liao, Qinxiang; Xu, Xu; Chen, Wen; Hao, Shicheng

    2016-05-01

    The allele frequencies and statistical parameters of 38 autosomal short tandem repeat (STR) loci were analyzed in the Uygur population from Southern Xinjiang of China with 290 unrelated individuals. The results show these 38 STR loci have high or medium power of discrimination and probabilities of exclusion. All loci are in Hardy-Weinberg equilibrium. The genetic distances between the Uygur population and other Chinese populations were also estimated.

  13. Allelic interaction of F1 pollen sterility loci and abnormal chromosome behaviour caused pollen sterility in intersubspecific autotetraploid rice hybrids.

    Science.gov (United States)

    He, J H; Shahid, M Q; Li, Y J; Guo, H B; Cheng, X A; Liu, X D; Lu, Y G

    2011-08-01

    The intersubspecific hybrids of autotetraploid rice has many features that increase rice yield, but lower seed set is a major hindrance in its utilization. Pollen sterility is one of the most important factors which cause intersubspecific hybrid sterility. The hybrids with greater variation in seed set were used to study how the F(1) pollen sterile loci (S-a, S-b, and S-c) interact with each other and how abnormal chromosome behaviour and allelic interaction of F(1) sterility loci affect pollen fertility and seed set of intersubspecific autotetraploid rice hybrids. The results showed that interaction between pollen sterility loci have significant effects on the pollen fertility of autotetraploid hybrids, and pollen fertility further decreased with an increase in the allelic interaction of F(1) pollen sterility loci. Abnormal ultra-structure and microtubule distribution patterns during pollen mother cell (PMC) meiosis were found in the hybrids with low pollen fertility in interphase and leptotene, suggesting that the effect-time of pollen sterility loci interaction was very early. There were highly significant differences in the number of quadrivalents and bivalents, and in chromosome configuration among all the hybrids, and quadrivalents decreased with an increase in the seed set of autotetraploid hybrids. Many different kinds of chromosomal abnormalities, such as chromosome straggling, chromosome lagging, asynchrony of chromosome disjunction, and tri-fission were found during the various developmental stages of PMC meiosis. All these abnormalities were significantly higher in sterile hybrids than in fertile hybrids, suggesting that pollen sterility gene interactions tend to increase the chromosomal abnormalities which cause the partial abortion of male gametes and leads to the decline in the seed set of the autotetraploid rice hybrids. © 2011 The Author(s).

  14. High frequency variations of Earth Rotation Parameters from GPS and GLONASS observations.

    Science.gov (United States)

    Wei, Erhu; Jin, Shuanggen; Wan, Lihua; Liu, Wenjie; Yang, Yali; Hu, Zhenghong

    2015-01-28

    The Earth's rotation undergoes changes with the influence of geophysical factors, such as Earth's surface fluid mass redistribution of the atmosphere, ocean and hydrology. However, variations of Earth Rotation Parameters (ERP) are still not well understood, particularly the short-period variations (e.g., diurnal and semi-diurnal variations) and their causes. In this paper, the hourly time series of Earth Rotation Parameters are estimated using Global Positioning System (GPS), Global Navigation Satellite System (GLONASS), and combining GPS and GLONASS data collected from nearly 80 sites from 1 November 2012 to 10 April 2014. These new observations with combining different satellite systems can help to decorrelate orbit biases and ERP, which improve estimation of ERP. The high frequency variations of ERP are analyzed using a de-trending method. The maximum of total diurnal and semidiurnal variations are within one milli-arcseconds (mas) in Polar Motion (PM) and 0.5 milli-seconds (ms) in UT1-UTC. The semidiurnal and diurnal variations are mainly related to the ocean tides. Furthermore, the impacts of satellite orbit and time interval used to determinate ERP on the amplitudes of tidal terms are analyzed. We obtain some small terms that are not described in the ocean tide model of the IERS Conventions 2010, which may be caused by the strategies and models we used or the signal noises as well as artifacts. In addition, there are also small differences on the amplitudes between our results and IERS convention. This might be a result of other geophysical excitations, such as the high-frequency variations in atmospheric angular momentum (AAM) and hydrological angular momentum (HAM), which needs more detailed analysis with more geophysical data in the future.

  15. High Frequency Variations of Earth Rotation Parameters from GPS and GLONASS Observations

    Directory of Open Access Journals (Sweden)

    Erhu Wei

    2015-01-01

    Full Text Available The Earth’s rotation undergoes changes with the influence of geophysical factors, such as Earth’s surface fluid mass redistribution of the atmosphere, ocean and hydrology. However, variations of Earth Rotation Parameters (ERP are still not well understood, particularly the short-period variations (e.g., diurnal and semi-diurnal variations and their causes. In this paper, the hourly time series of Earth Rotation Parameters are estimated using Global Positioning System (GPS, Global Navigation Satellite System (GLONASS, and combining GPS and GLONASS data collected from nearly 80 sites from 1 November 2012 to 10 April 2014. These new observations with combining different satellite systems can help to decorrelate orbit biases and ERP, which improve estimation of ERP. The high frequency variations of ERP are analyzed using a de-trending method. The maximum of total diurnal and semidiurnal variations are within one milli-arcseconds (mas in Polar Motion (PM and 0.5 milli-seconds (ms in UT1-UTC. The semidiurnal and diurnal variations are mainly related to the ocean tides. Furthermore, the impacts of satellite orbit and time interval used to determinate ERP on the amplitudes of tidal terms are analyzed. We obtain some small terms that are not described in the ocean tide model of the IERS Conventions 2010, which may be caused by the strategies and models we used or the signal noises as well as artifacts. In addition, there are also small differences on the amplitudes between our results and IERS convention. This might be a result of other geophysical excitations, such as the high-frequency variations in atmospheric angular momentum (AAM and hydrological angular momentum (HAM, which needs more detailed analysis with more geophysical data in the future.

  16. Individuals and the variation needed for high species diversity in forest trees

    Science.gov (United States)

    James S. Clark

    2010-01-01

    In the past, explanations for high species diversity have been sought at the species level. Theory shows that coexistence requires substantial differences between species, but species-level data rarely provide evidence for such differences. Using data from forests in the southeastern United States, I show here that variation evident at the individual level provides for...

  17. A Genome Wide Study of Copy Number Variation Associated with Nasopharyngeal Carcinoma in Malaysian Chinese Identifies CNVs at 11q14.3 and 6p21.3 as Candidate Loci

    Science.gov (United States)

    Low, Joyce Siew Yong; Chin, Yoon Ming; Mushiroda, Taisei; Kubo, Michiaki; Govindasamy, Gopala Krishnan; Pua, Kin Choo; Yap, Yoke Yeow; Yap, Lee Fah; Subramaniam, Selva Kumar; Ong, Cheng Ai; Tan, Tee Yong; Khoo, Alan Soo Beng; Ng, Ching Ching

    2016-01-01

    Background Nasopharyngeal carcinoma (NPC) is a neoplasm of the epithelial lining of the nasopharynx. Despite various reports linking genomic variants to NPC predisposition, very few reports were done on copy number variations (CNV). CNV is an inherent structural variation that has been found to be involved in cancer predisposition. Methods A discovery cohort of Malaysian Chinese descent (NPC patients, n = 140; Healthy controls, n = 256) were genotyped using Illumina® HumanOmniExpress BeadChip. PennCNV and cnvPartition calling algorithms were applied for CNV calling. Taqman CNV assays and digital PCR were used to validate CNV calls and replicate candidate copy number variant region (CNVR) associations in a follow-up Malaysian Chinese (NPC cases, n = 465; and Healthy controls, n = 677) and Malay cohort (NPC cases, n = 114; Healthy controls, n = 124). Results Six putative CNVRs overlapping GRM5, MICA/HCP5/HCG26, LILRB3/LILRA6, DPY19L2, RNase3/RNase2 and GOLPH3 genes were jointly identified by PennCNV and cnvPartition. CNVs overlapping GRM5 and MICA/HCP5/HCG26 were subjected to further validation by Taqman CNV assays and digital PCR. Combined analysis in Malaysian Chinese cohort revealed a strong association at CNVR on chromosome 11q14.3 (Pcombined = 1.54x10-5; odds ratio (OR) = 7.27; 95% CI = 2.96–17.88) overlapping GRM5 and a suggestive association at CNVR on chromosome 6p21.3 (Pcombined = 1.29x10-3; OR = 4.21; 95% CI = 1.75–10.11) overlapping MICA/HCP5/HCG26 genes. Conclusion Our results demonstrated the association of CNVs towards NPC susceptibility, implicating a possible role of CNVs in NPC development. PMID:26730743

  18. A Genome Wide Study of Copy Number Variation Associated with Nasopharyngeal Carcinoma in Malaysian Chinese Identifies CNVs at 11q14.3 and 6p21.3 as Candidate Loci.

    Directory of Open Access Journals (Sweden)

    Joyce Siew Yong Low

    Full Text Available Nasopharyngeal carcinoma (NPC is a neoplasm of the epithelial lining of the nasopharynx. Despite various reports linking genomic variants to NPC predisposition, very few reports were done on copy number variations (CNV. CNV is an inherent structural variation that has been found to be involved in cancer predisposition.A discovery cohort of Malaysian Chinese descent (NPC patients, n = 140; Healthy controls, n = 256 were genotyped using Illumina® HumanOmniExpress BeadChip. PennCNV and cnvPartition calling algorithms were applied for CNV calling. Taqman CNV assays and digital PCR were used to validate CNV calls and replicate candidate copy number variant region (CNVR associations in a follow-up Malaysian Chinese (NPC cases, n = 465; and Healthy controls, n = 677 and Malay cohort (NPC cases, n = 114; Healthy controls, n = 124.Six putative CNVRs overlapping GRM5, MICA/HCP5/HCG26, LILRB3/LILRA6, DPY19L2, RNase3/RNase2 and GOLPH3 genes were jointly identified by PennCNV and cnvPartition. CNVs overlapping GRM5 and MICA/HCP5/HCG26 were subjected to further validation by Taqman CNV assays and digital PCR. Combined analysis in Malaysian Chinese cohort revealed a strong association at CNVR on chromosome 11q14.3 (Pcombined = 1.54x10-5; odds ratio (OR = 7.27; 95% CI = 2.96-17.88 overlapping GRM5 and a suggestive association at CNVR on chromosome 6p21.3 (Pcombined = 1.29x10-3; OR = 4.21; 95% CI = 1.75-10.11 overlapping MICA/HCP5/HCG26 genes.Our results demonstrated the association of CNVs towards NPC susceptibility, implicating a possible role of CNVs in NPC development.

  19. Biological, clinical and population relevance of 95 loci for blood lipids

    DEFF Research Database (Denmark)

    Teslovich, Tanya M; Musunuru, Kiran; Smith, Albert V

    2010-01-01

    polymorphisms (SNPs) near known lipid regulators (for example, CYP7A1, NPC1L1 and SCARB1) as well as in scores of loci not previously implicated in lipoprotein metabolism. The 95 loci contribute not only to normal variation in lipid traits but also to extreme lipid phenotypes and have an impact on lipid traits...... in three non-European populations (East Asians, South Asians and African Americans). Our results identify several novel loci associated with plasma lipids that are also associated with CAD. Finally, we validated three of the novel genes-GALNT2, PPP1R3B and TTC39B-with experiments in mouse models. Taken...

  20. Chromosomal localization of microsatellite loci in Drosophila mediopunctata

    Directory of Open Access Journals (Sweden)

    Renato Cavasini

    2015-03-01

    Full Text Available Drosophila mediopunctata has been used as a model organism for genetics and evolutionary studies in the last three decades. A linkage map with 48 microsatellite loci recently published for this species showed five syntenic groups, which had their homology determined to Drosophila melanogaster chromosomes. Then, by inference, each of the groups was associated with one of the five major chromosomes of D. mediopunctata. Our objective was to carry out a genetic (chromosomal analysis to increase the number of available loci with known chromosomal location. We made a simultaneous analysis of visible mutant phenotypes and microsatellite genotypes in a backcross of a standard strain and a mutant strain, which had each major autosome marked. Hence, we could establish the chromosomal location of seventeen loci; including one from each of the five major linkage groups previously published, and twelve new loci. Our results were congruent with the previous location and they open new possibilities to future work integrating microsatellites, chromosomal inversions, and genetic determinants of physiological and morphological variation.

  1. Asymmetric Bilateral Variations in the Musculocutaneous and Median Nerves with High Branching of Brachial Artery

    Directory of Open Access Journals (Sweden)

    Vandana Tomar

    2012-01-01

    Full Text Available Brachial Plexus is formed by the union of the anterior rami of cervical 5, 6, 7, 8 and thoracic 1 nerves. These nerves unite and divide to form the key nerves innervating the upper limb. Variations in the course of these nerves are clinically important to anesthetists, neurologists and orthopedicians. We report bilateral variations in the arterial and neural structures in the upper limb of a 65 year old cadaver. The muscles of the arm on one side were innervated by the median nerve with absence of musculocutaneous. While on the other side the musculocutaneous nerve contributed to the formation of the median nerve. There was a presence of high bifurcation of brachial artery on both sides. Knowledge of such variations in the innervations of muscles and the arterial supply of the limbs are important to remember before performing any reconstructive procedures or interventions on the limb.

  2. Genetic loci for retinal arteriolar microcirculation.

    Directory of Open Access Journals (Sweden)

    Xueling Sim

    Full Text Available Narrow arterioles in the retina have been shown to predict hypertension as well as other vascular diseases, likely through an increase in the peripheral resistance of the microcirculatory flow. In this study, we performed a genome-wide association study in 18,722 unrelated individuals of European ancestry from the Cohorts for Heart and Aging Research in Genomic Epidemiology consortium and the Blue Mountain Eye Study, to identify genetic determinants associated with variations in retinal arteriolar caliber. Retinal vascular calibers were measured on digitized retinal photographs using a standardized protocol. One variant (rs2194025 on chromosome 5q14 near the myocyte enhancer factor 2C MEF2C gene was associated with retinal arteriolar caliber in the meta-analysis of the discovery cohorts at genome-wide significance of P-value <5×10(-8. This variant was replicated in an additional 3,939 individuals of European ancestry from the Australian Twins Study and Multi-Ethnic Study of Atherosclerosis (rs2194025, P-value = 2.11×10(-12 in combined meta-analysis of discovery and replication cohorts. In independent studies of modest sample sizes, no significant association was found between this variant and clinical outcomes including coronary artery disease, stroke, myocardial infarction or hypertension. In conclusion, we found one novel loci which underlie genetic variation in microvasculature which may be relevant to vascular disease. The relevance of these findings to clinical outcomes remains to be determined.

  3. Novel Complete Probabilistic Models of Random Variation in High Frequency Performance of Nanoscale MOSFET

    Directory of Open Access Journals (Sweden)

    Rawid Banchuin

    2013-01-01

    Full Text Available The novel probabilistic models of the random variations in nanoscale MOSFET's high frequency performance defined in terms of gate capacitance and transition frequency have been proposed. As the transition frequency variation has also been considered, the proposed models are considered as complete unlike the previous one which take only the gate capacitance variation into account. The proposed models have been found to be both analytic and physical level oriented as they are the precise mathematical expressions in terms of physical parameters. Since the up-to-date model of variation in MOSFET's characteristic induced by physical level fluctuation has been used, part of the proposed models for gate capacitance is more accurate and physical level oriented than its predecessor. The proposed models have been verified based on the 65 nm CMOS technology by using the Monte-Carlo SPICE simulations of benchmark circuits and Kolmogorov-Smirnov tests as highly accurate since they fit the Monte-Carlo-based analysis results with 99% confidence. Hence, these novel models have been found to be versatile for the statistical/variability aware analysis/design of nanoscale MOSFET-based analog/mixed signal circuits and systems.

  4. [Identification of novel variable number tandem repeat (VNTR) loci in Mycobacterium avium and development of an effective means of VNTR typing].

    Science.gov (United States)

    Kurokawa, Kazuhiro; Uchiya, Kei-Ichi; Yagi, Tetsuya; Takahashi, Hiroyasu; Niimi, Masaki; Ichikawa, Kazuya; Inagaki, Takayuki; Moriyama, Makoto; Nikai, Toshiaki; Hayashi, Yuta; Nakagawa, Taku; Ogawa, Kenji

    2012-07-01

    To make more effective use of variable number tandem repeat (VNTR) typing, we identified novel VNTR loci in Mycobacterium avium and used them for modified M. avium tandem repeat-VNTR (MATR-VNTR) typing. Analysis of a DNA sample extracted from a clinical isolate (strain HN135) with the FLX system genome sequencer (Roche Diagnostic System) led to discovery of several novel VNTR loci. The allelic diversity of the novel VNTR loci was evaluated for 71 clinical isolates and compared with the diversity of the MATR-VNTR loci. To improve efficacy of MATR-VNTR typing, we tested typing using 2 sets of loci selected from the newly identified loci and the MATR loci, i.e., one set containing 7 and another 16 loci. Hunter Gaston's discriminatory index (HGDI) was calculated for these sets. Six VNTR loci were newly identified, of which 5 showed a high diversity. The HGDI was 0.980 for the improved new typing using a set of 7 loci, and 0.995 for another set of 16 loci, while it was 0.992 for the conventional MATR-VNTR typing. VNTR typing with the set of the 7 loci enabled a rapid analysis, and another set of 16 loci enabled a precise analysis, as compared with conventional MATR-VNTR typing. A method that uses only VNTR loci with relatively high allelic diversity is considered to be a useful tool for VNTR typing of MAC isolates.

  5. Genetic variation in laboratory and field populations of the vector of bluetongue virus, Culicoides variipennis (Diptera: Ceratopogonidae).

    Science.gov (United States)

    Tabachnick, W J

    1990-01-01

    Laboratory colonies and several natural populations of the biting midge Culicoides variipennis (Coquillett) were analyzed for genetic variation at 21 electrophoretic loci. The laboratory colonies maintained high levels of genetic variation measured by average expected heterozygosities (He = 0.142 +/- 0.008), although levels were lower than those observed in field collections (He = 0.198 +/- 0.009). A field population from Colorado, analyzed five times over a 1-yr period, showed a consistent trend in the change in gene frequencies at two loci. Genetic comparisons between natural populations were consistent with the existence of two subspecies. C. variipennis variipennis and C. variipennis sonorensis Wirth & Jones.

  6. Detecting population structure in a high gene-flow species, Atlantic herring (Clupea harengus): direct, simultaneous evaluation of neutral vs putatively selected loci

    DEFF Research Database (Denmark)

    André, C.; Larsson, L. C.; Laikre, L.

    2010-01-01

    In many marine fish species, genetic population structure is typically weak because populations are large, evolutionarily young and have a high potential for gene flow. We tested whether genetic markers influenced by natural selection are more efficient than the presumed neutral genetic markers t...

  7. Combined analyses of the ITS loci and the corresponding 16S rRNA genes reveal high micro- and macrodiversity of SAR11 populations in the Red Sea.

    KAUST Repository

    Ngugi, David; Stingl, Ulrich

    2012-01-01

    that of the corresponding 16S rRNA genes. Moreover, species estimates based on the ITS showed a highly diverse population of SAR11 in the mixed layer that became diminished in deep isothermal waters, which was in contrast to results of the related 16S rRNA genes. While

  8. Using genotyping-by-sequencing to develop broccoli markers for construction of a high-density linkage map and to identify quantitative trait loci associated with heat tolerance

    Science.gov (United States)

    Heat stress reduces the yield and quality of broccoli heads imposing seasonal and geographic limits to broccoli production. For the most part, the risk of producing broccoli with head defects (uneven beads, bracts in heads, etc.) induced by high temperatures has restricted commercial production in t...

  9. Autosomal and sex-linked microsatellite loci in the green oak leaf roller Tortrix viridana L.

    NARCIS (Netherlands)

    Schroeder, H.C.; Arens, P.F.P.; Smulders, M.J.M.

    2009-01-01

    Eight microsatellite markers were developed for the lepidopteran species Tortrix viridana using an enrichment protocol. The loci were highly variable with number of alleles ranging from four to 38. Six of the eight loci were in Hardy¿Weinberg equilibrium. The other two were linked to the

  10. Influence of variations in creep curve on creep behavior of a high-temperature structure

    International Nuclear Information System (INIS)

    Hada, Kazuhiko

    1986-01-01

    It is one of the key issues for a high-temperature structural design guideline to evaluate the influence of variations in creep curve on the creep behavior of a high-temperature structure. In the present paper, a comparative evaluation was made to clarify such influence. Additional consideration was given to the influence of the relationship between creep rupture life and minimum creep rate, i.e., the Monkman-Grant's relationship, on the creep damage evaluation. The consideration suggested that the Monkman-Grant's relationship be taken into account in evaluating the creep damage behavior, especially the creep damage variations. However, it was clarified that the application of the creep damage evaluation rule of ASME B and P.V. Code Case N-47 to the ''standard case'' which was predicted from the average creep property would predict the creep damage on the safe side. (orig./GL)

  11. Jump Variation Estimation with Noisy High Frequency Financial Data via Wavelets

    Directory of Open Access Journals (Sweden)

    Xin Zhang

    2016-08-01

    Full Text Available This paper develops a method to improve the estimation of jump variation using high frequency data with the existence of market microstructure noises. Accurate estimation of jump variation is in high demand, as it is an important component of volatility in finance for portfolio allocation, derivative pricing and risk management. The method has a two-step procedure with detection and estimation. In Step 1, we detect the jump locations by performing wavelet transformation on the observed noisy price processes. Since wavelet coefficients are significantly larger at the jump locations than the others, we calibrate the wavelet coefficients through a threshold and declare jump points if the absolute wavelet coefficients exceed the threshold. In Step 2 we estimate the jump variation by averaging noisy price processes at each side of a declared jump point and then taking the difference between the two averages of the jump point. Specifically, for each jump location detected in Step 1, we get two averages from the observed noisy price processes, one before the detected jump location and one after it, and then take their difference to estimate the jump variation. Theoretically, we show that the two-step procedure based on average realized volatility processes can achieve a convergence rate close to O P ( n − 4 / 9 , which is better than the convergence rate O P ( n − 1 / 4 for the procedure based on the original noisy process, where n is the sample size. Numerically, the method based on average realized volatility processes indeed performs better than that based on the price processes. Empirically, we study the distribution of jump variation using Dow Jones Industrial Average stocks and compare the results using the original price process and the average realized volatility processes.

  12. Microsatellite loci discovery from next-generation sequencing data and loci characterization in the epizoic barnacle Chelonibia testudinaria (Linnaeus, 1758

    Directory of Open Access Journals (Sweden)

    Christine Ewers-Saucedo

    2016-05-01

    Full Text Available Microsatellite markers remain an important tool for ecological and evolutionary research, but are unavailable for many non-model organisms. One such organism with rare ecological and evolutionary features is the epizoic barnacle Chelonibia testudinaria (Linnaeus, 1758. Chelonibia testudinaria appears to be a host generalist, and has an unusual sexual system, androdioecy. Genetic studies on host specificity and mating behavior are impeded by the lack of fine-scale, highly variable markers, such as microsatellite markers. In the present study, we discovered thousands of new microsatellite loci from next-generation sequencing data, and characterized 12 loci thoroughly. We conclude that 11 of these loci will be useful markers in future ecological and evolutionary studies on C. testudinaria.

  13. Microsatellite loci discovery from next-generation sequencing data and loci characterization in the epizoic barnacle Chelonibia testudinaria (Linnaeus, 1758)

    Science.gov (United States)

    Zardus, John D.; Wares, John P.

    2016-01-01

    Microsatellite markers remain an important tool for ecological and evolutionary research, but are unavailable for many non-model organisms. One such organism with rare ecological and evolutionary features is the epizoic barnacle Chelonibia testudinaria (Linnaeus, 1758). Chelonibia testudinaria appears to be a host generalist, and has an unusual sexual system, androdioecy. Genetic studies on host specificity and mating behavior are impeded by the lack of fine-scale, highly variable markers, such as microsatellite markers. In the present study, we discovered thousands of new microsatellite loci from next-generation sequencing data, and characterized 12 loci thoroughly. We conclude that 11 of these loci will be useful markers in future ecological and evolutionary studies on C. testudinaria. PMID:27231653

  14. High responders and low responders: factors associated with individual variation in response to standardized training.

    Science.gov (United States)

    Mann, Theresa N; Lamberts, Robert P; Lambert, Michael I

    2014-08-01

    The response to an exercise intervention is often described in general terms, with the assumption that the group average represents a typical response for most individuals. In reality, however, it is more common for individuals to show a wide range of responses to an intervention rather than a similar response. This phenomenon of 'high responders' and 'low responders' following a standardized training intervention may provide helpful insights into mechanisms of training adaptation and methods of training prescription. Therefore, the aim of this review was to discuss factors associated with inter-individual variation in response to standardized, endurance-type training. It is well-known that genetic influences make an important contribution to individual variation in certain training responses. The association between genotype and training response has often been supported using heritability estimates; however, recent studies have been able to link variation in some training responses to specific single nucleotide polymorphisms. It would appear that hereditary influences are often expressed through hereditary influences on the pre-training phenotype, with some parameters showing a hereditary influence in the pre-training phenotype but not in the subsequent training response. In most cases, the pre-training phenotype appears to predict only a small amount of variation in the subsequent training response of that phenotype. However, the relationship between pre-training autonomic activity and subsequent maximal oxygen uptake response appears to show relatively stronger predictive potential. Individual variation in response to standardized training that cannot be explained by genetic influences may be related to the characteristics of the training program or lifestyle factors. Although standardized programs usually involve training prescribed by relative intensity and duration, some methods of relative exercise intensity prescription may be more successful in creating

  15. Radon variations in active volcanoes and in regions with high seismicity: internal and external factors

    International Nuclear Information System (INIS)

    Segovia, N.; Cruz-Reyna, S. De la; Mena, M.

    1986-01-01

    The results of 4 years of observations of radon concentrations in soils of active volcanoes of Costa Rica and a highly seismic region in Mexico are discussed. A distinction is made between the influences of external (mostly meteorological) and internal (magmatic or tectonic) factors on the variation in radon levels. The geological meaning of the radon data can be thus enhanced if the external factors are excluded. (author)

  16. Determination of allele frequencies in nine short tandem repeat loci ...

    African Journals Online (AJOL)

    SERVER

    2008-04-17

    Apr 17, 2008 ... out the human genome. These loci are a rich source of highly polymorphic markers that may be detected using the polymerase chain reaction (PCR). PCR is a mimic of the normal cellular process of replication of DNA molecules. Each STR is distinguished by the number of times a sequence is repeated, ...

  17. Analysis and Comprehensive Analytical Modeling of Statistical Variations in Subthreshold MOSFET's High Frequency Characteristics

    Directory of Open Access Journals (Sweden)

    Rawid Banchuin

    2014-01-01

    Full Text Available In this research, the analysis of statistical variations in subthreshold MOSFET's high frequency characteristics defined in terms of gate capacitance and transition frequency, have been shown and the resulting comprehensive analytical models of such variations in terms of their variances have been proposed. Major imperfection in the physical level properties including random dopant fluctuation and effects of variations in MOSFET's manufacturing process, have been taken into account in the proposed analysis and modeling. The up to dated comprehensive analytical model of statistical variation in MOSFET's parameter has been used as the basis of analysis and modeling. The resulting models have been found to be both analytic and comprehensive as they are the precise mathematical expressions in terms of physical level variables of MOSFET. Furthermore, they have been verified at the nanometer level by using 65~nm level BSIM4 based benchmarks and have been found to be very accurate with smaller than 5 % average percentages of errors. Hence, the performed analysis gives the resulting models which have been found to be the potential mathematical tool for the statistical and variability aware analysis and design of subthreshold MOSFET based VHF circuits, systems and applications.

  18. High-resolution magnetic resonance imaging of diurnal variations in rheumatoid arthritis

    International Nuclear Information System (INIS)

    Nicholas, R.S.

    2000-09-01

    This thesis describes work that uses high-resolution magnetic resonance imaging (MRI) to give an insight into the aetiology of rheumatoid arthritis (RA) with particular reference to characterising diurnal changes in joint stiffness in the metacarpophalangeal (MCP) joints. The study was performed on a targeted 1.1 T MRI scanner using specialised sequences, including 3-dimensional gradient-echo, magnetisation transfer (MT) and multiple gradient-echo. These enabled tissue-dependent parameters such as MT ratio, effective transverse relaxation time (T 2 *) and proton density (ρ) to be made. Preliminary reproducibility studies of the MRI measurements showed that MT ratio could be measured in vivo to an accuracy of better than 8%. This variation is due to repositioning errors and physiological changes. Equivalent variations in T 2 * and p were 23% and 16% respectively; these poorer figures were contributed to errors in fitting the data to an exponential curve. An MRI study monitoring the diurnal variation of stiffness in RA demonstrated better characterisation of the disease state using MT and T 2 * maps compared to standard gradient-echo imaging. Features associated with arthritis such as bone erosions and cysts were found in the control group and an MT age dependence was measured in the soft tissue on the superior margin of the joint. This region also exhibited a diurnal variation in MT ratio for the patient group. The interaction between this region of tissue and other structures (e.g. the sheath of extensor tendon) within the joint could be a possible cause of joint stiffness. An incidental finding of this study was that Ritchie joint score also showed a diurnal variation. This study has demonstrated that MRI can be used to make reproducible measurements of the diurnal variations in RA. The indication is that the soft tissues in the superior aspect of the joint may be responsible for the symptom of joint stiffness in the MCP joints and future studies should be

  19. High temperature triggers latent variation among individuals: oviposition rate and probability for outbreaks.

    Directory of Open Access Journals (Sweden)

    Christer Björkman

    2011-01-01

    Full Text Available It is anticipated that extreme population events, such as extinctions and outbreaks, will become more frequent as a consequence of climate change. To evaluate the increased probability of such events, it is crucial to understand the mechanisms involved. Variation between individuals in their response to climatic factors is an important consideration, especially if microevolution is expected to change the composition of populations.Here we present data of a willow leaf beetle species, showing high variation among individuals in oviposition rate at a high temperature (20 °C. It is particularly noteworthy that not all individuals responded to changes in temperature; individuals laying few eggs at 20 °C continued to do so when transferred to 12 °C, whereas individuals that laid many eggs at 20 °C reduced their oviposition and laid the same number of eggs as the others when transferred to 12 °C. When transferred back to 20 °C most individuals reverted to their original oviposition rate. Thus, high variation among individuals was only observed at the higher temperature. Using a simple population model and based on regional climate change scenarios we show that the probability of outbreaks increases if there is a realistic increase in the number of warm summers. The probability of outbreaks also increased with increasing heritability of the ability to respond to increased temperature.If climate becomes warmer and there is latent variation among individuals in their temperature response, the probability for outbreaks may increase. However, the likelihood for microevolution to play a role may be low. This conclusion is based on the fact that it has been difficult to show that microevolution affect the probability for extinctions. Our results highlight the urge for cautiousness when predicting the future concerning probabilities for extreme population events.

  20. Characterization of Novel Gene Yr79 and Four Additional Quantitative Trait Loci for All-Stage and High-Temperature Adult-Plant Resistance to Stripe Rust in Spring Wheat PI 182103.

    Science.gov (United States)

    Feng, Junyan; Wang, Meinan; See, Deven R; Chao, Shiaoman; Zheng, Youliang; Chen, Xianming

    2018-06-01

    Stripe rust, caused by Puccinia striiformis f. sp. tritici, is an important disease of wheat worldwide. Exploring new resistance genes is essential for breeding resistant wheat cultivars. PI 182103, a spring wheat landrace originally from Pakistan, has shown a high level of resistance to stripe rust in fields for many years, but genes for resistance to stripe rust in the variety have not been studied. To map the resistance gene(s) in PI 182103, 185 recombinant inbred lines (RILs) were developed from a cross with Avocet Susceptible (AvS). The RIL population was genotyped with simple sequence repeat (SSR) and single nucleotide polymorphism markers and tested with races PST-100 and PST-114 at the seedling stage under controlled greenhouse conditions and at the adult-plant stage in fields at Pullman and Mt. Vernon, Washington under natural infection by the stripe rust pathogen in 2011, 2012, and 2013. A total of five quantitative trait loci (QTL) were detected. QyrPI182103.wgp-2AS and QyrPI182103.wgp-3AL were detected at the seedling stage, QyrPI182103.wgp-4DL was detected only in Mt. Vernon field tests, and QyrPI182103.wgp-5BS was detected in both seedling and field tests. QyrPI182103.wgp-7BL was identified as a high-temperature adult-plant resistance gene and detected in all field tests. Interactions among the QTL were mostly additive, but some negative interactions were detected. The 7BL QTL was mapped in chromosomal bin 7BL 0.40 to 0.45 and identified as a new gene, permanently designated as Yr79. SSR markers Xbarc72 and Xwmc335 flanking the Yr79 locus were highly polymorphic in various wheat genotypes, indicating that the molecular markers are useful for incorporating the new gene for potentially durable stripe rust resistance into new wheat cultivars.

  1. Application of a high-throughput genotyping method for loci exclusion in non-consanguineous Australian pedigrees with autosomal recessive retinitis pigmentosa.

    Science.gov (United States)

    Paterson, Rachel L; De Roach, John N; McLaren, Terri L; Hewitt, Alex W; Hoffmann, Ling; Lamey, Tina M

    2012-01-01

    Retinitis pigmentosa (RP) is the most common form of inherited blindness, caused by progressive degeneration of photoreceptor cells in the retina, and affects approximately 1 in 3,000 people. Over the past decade, significant progress has been made in gene therapy for RP and related diseases, making genetic characterization increasingly important. Recently, high-throughput technologies have provided an option for reasonably fast, cost-effective genetic characterization of autosomal recessive RP (arRP). The current study used a single nucleotide polymorphism (SNP) genotyping method to exclude up to 28 possible disease-causing genes in 31 non-consanguineous Australian families affected by arRP. DNA samples were collected from 59 individuals affected with arRP and 74 unaffected family members from 31 Australian families. Five to six SNPs were genotyped for 28 genes known to cause arRP or the related disease Leber congenital amaurosis (LCA). Cosegregation analyses were used to exclude possible causative genes from each of the 31 families. Bidirectional sequencing was used to identify disease-causing mutations in prioritized genes that were not excluded with cosegregation analyses. Two families were excluded from analysis due to identification of false paternity. An average of 28.9% of genes were excluded per family when only one affected individual was available, in contrast to an average of 71.4% or 89.8% of genes when either two, or three or more affected individuals were analyzed, respectively. A statistically significant relationship between the proportion of genes excluded and the number of affected individuals analyzed was identified using a multivariate regression model (pA) and USH2A in two families (c.2276 G>T). This study has shown that SNP genotyping cosegregation analysis can be successfully used to refine and expedite the genetic characterization of arRP in a non-consanguineous population; however, this method is effective only when DNA samples are

  2. Assessment of high to low frequency variations of isoprene emission rates using a neural network approach

    Science.gov (United States)

    Boissard, C.; Chervier, F.; Dutot, A. L.

    2007-08-01

    Using a statistical approach based on artificial neural networks, an emission algorithm (ISO_LF) accounting for high (instantaneous) to low (seasonal) frequency variations was developed for isoprene. ISO_LF was optimised using an isoprene emission data base (ISO-DB) specifically designed for this work. ISO-DB consists of 1321 emission rates collected in the literature, together with 34 environmental variables, measured or assessed using NCDC (National Climatic Data Center) or NCEP (National Centers for Environmental Predictions) meteorological databases. ISO-DB covers a large variety of emitters (25 species) and environmental conditions (10° S to 60° N). When only instantaneous environmental regressors (air temperature and photosynthetic active radiation, PAR) were used, a maximum of 60% of the overall isoprene variability was assessed and the highest emissions were underestimated. Considering a total of 9 high (instantaneous) to low (up to 3 weeks) frequency regressors, ISO_LF accounts for up to 91% of the isoprene emission variability, whatever the emission range, species or climate. Diurnal and seasonal variations are correctly reproduced for textit{Ulex europaeus} with a maximum factor of discrepancy of 4. ISO-LF was found to be mainly sensitive to air temperature cumulated over 3 weeks T21 and to instantaneous light L0 and air temperature T0 variations. T21, T0 and L0 only accounts for 76% of the overall variability. The use of ISO-LF for non stored monoterpene emissions was shown to give poor results.

  3. Genetic Variation and Population Structure in Jamunapari Goats Using Microsatellites, Mitochondrial DNA, and Milk Protein Genes

    Science.gov (United States)

    Rout, P. K.; Thangraj, K.; Mandal, A.; Roy, R.

    2012-01-01

    Jamunapari, a dairy goat breed of India, has been gradually declining in numbers in its home tract over the years. We have analysed genetic variation and population history in Jamunapari goats based on 17 microsatellite loci, 2 milk protein loci, mitochondrial hypervariable region I (HVRI) sequencing, and three Y-chromosomal gene sequencing. We used the mitochondrial DNA (mtDNA) mismatch distribution, microsatellite data, and bottleneck tests to infer the population history and demography. The mean number of alleles per locus was 9.0 indicating that the allelic variation was high in all the loci and the mean heterozygosity was 0.769 at nuclear loci. Although the population size is smaller than 8,000 individuals, the amount of variability both in terms of allelic richness and gene diversity was high in all the microsatellite loci except ILST 005. The gene diversity and effective number of alleles at milk protein loci were higher than the 10 other Indian goat breeds that they were compared to. Mismatch analysis was carried out and the analysis revealed that the population curve was unimodal indicating the expansion of population. The genetic diversity of Y-chromosome genes was low in the present study. The observed mean M ratio in the population was above the critical significance value (Mc) and close to one indicating that it has maintained a slowly changing population size. The mode-shift test did not detect any distortion of allele frequency and the heterozygosity excess method showed that there was no significant departure from mutation-drift equilibrium detected in the population. However, the effects of genetic bottlenecks were observed in some loci due to decreased heterozygosity and lower level of M ratio. There were two observed genetic subdivisions in the population supporting the observations of farmers in different areas. This base line information on genetic diversity, bottleneck analysis, and mismatch analysis was obtained to assist the conservation

  4. Investigation of population structure in Gulf of Mexico Seepiophila jonesi (Polychaeta, Siboglinidae using cross-amplified microsatellite loci

    Directory of Open Access Journals (Sweden)

    Chunya Huang

    2016-08-01

    presence of significant gene flow via larval dispersal in mixed oceanic currents. Discussion The ability to develop “universal” microsatellites reduces the costs associated with these analyses and allows researchers to track and investigate a wider array of taxa, which is particularly useful for organisms living at inaccessible locations such as the deep sea. Our study highlights that non-species specific microsatellites can be amplified across large evolutionary distances and still yield similar findings as species-specific loci. Further, these results show that S. jonesi collected from various localities in the GoM represents a single panmictic population, suggesting that dispersal of lecithotrophic larvae by deep sea currents is sufficient to homogenize populations. These data are consistent with the high levels of gene flow seen in Escarpia spp., which advocates that differences in microhabitats of seep localities lead to variation in biogeography of separate species.

  5. Air shower array designed for cosmic ray variation measurements and high energy gamma ray astronomy

    Energy Technology Data Exchange (ETDEWEB)

    Morello, C; Navarra, G [Consiglio Nazionale delle Ricerche, Turin (Italy). Lab. di Cosmo-Geofisica

    1981-08-15

    We describe an array for performing measurements of counting rates and arrival directions of extensive air showers at primary energy E/sub 0/ approx. equal to 3 x 10/sup 9/ eV. The aim of the research is to study the time variations and the anisotropies of cosmic rays and the observable gamma ray sources in the high energy region. The installation, composed of four large area scintillation counters and completely controlled by a microcomputer system, operates at mountain altitude (3500 m a.s.l.). The preanalysis of data, stability tests and periodic calibrations are performed by on-line programs. The method for obtaining the required stability and the corrections on temperature and gain variations are also described.

  6. Low density, variation in sintered density and high nitrogen in uranium dioxide

    International Nuclear Information System (INIS)

    Balakrishna, Palanki; Murty, B.N.; Anuradha, M.; Nageshwara Rao, P.; Jayaraj, R.N.; Ganguly, C.

    2000-01-01

    Low sintered density and density variation in sintered UO 2 were found to have been caused by non uniformity in the granule feed characteristics to the compacting press. The nitrogen impurity content of sintered UO 2 was found to be sintering furnace related and associated with low sintered density pellets. The problems of low density, variation in sintered density and high nitrogen could be solved by the replacement of the prevailing four punch precompaction by a single punch process; by the introduction of a vibro-sieve for the separation of fine particles from the press feed granules; by innovation in the powder feed shoe design for simultaneous and uniform dispensing of powder in all the die holes; by increasing the final compaction pressure and by modifying the gas flows and preheat temperature in the sintering furnace. (author)

  7. Young modulus variation of a brickwork masonry element submitted to high temperatures

    Directory of Open Access Journals (Sweden)

    Maciá, M. E.

    2013-03-01

    Full Text Available In order to understand the thermal behavior of the masonry elements submitted to high temperatures we need to know the variation of their thermal properties with regard to the temperature. Submitted to high temperatures clay brick masonry presents thermomechanical effects (as the variation of Young's modulus, the thermal expansion of the unit and the mortar, spalling, losses of resistance … as well as variation of the properties of the material as result of its degradation. In this article the variation of the module of elasticity of the unit and the mortar is described with regard to high temperatures according to the state of the knowledge. In this article is also exposed the results obtained from the experimental program carried out on elements of clay brick masonry submitted to high temperatures in order to observe the variation of Young's module related to temperature.

    La definición del comportamiento térmico de los elementos de fábrica sometidos a la acción del fuego requiere del conocimiento de la variación de sus propiedades termomecánicas con respecto a la temperatura. Ante las altas temperaturas la fábrica cerámica presenta efectos termomecánicos, como la variación del módulo de Young entre otros, así como la variación de las propiedades del material debidas a la degradación del mismo. En este artículo se describe la variación del módulo de elasticidad de la pieza y el mortero con respecto a altas temperaturas según el estado del conocimiento y se exponen los resultados obtenidos del programa experimental llevado a cabo sobre elementos de fábrica sometidos a altas temperaturas con el fin de observar la variación del módulo de Young con respecto a la temperatura.

  8. Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice

    Science.gov (United States)

    Yang, Wanneng; Guo, Zilong; Huang, Chenglong; Duan, Lingfeng; Chen, Guoxing; Jiang, Ni; Fang, Wei; Feng, Hui; Xie, Weibo; Lian, Xingming; Wang, Gongwei; Luo, Qingming; Zhang, Qifa; Liu, Qian; Xiong, Lizhong

    2014-01-01

    Even as the study of plant genomics rapidly develops through the use of high-throughput sequencing techniques, traditional plant phenotyping lags far behind. Here we develop a high-throughput rice phenotyping facility (HRPF) to monitor 13 traditional agronomic traits and 2 newly defined traits during the rice growth period. Using genome-wide association studies (GWAS) of the 15 traits, we identify 141 associated loci, 25 of which contain known genes such as the Green Revolution semi-dwarf gene, SD1. Based on a performance evaluation of the HRPF and GWAS results, we demonstrate that high-throughput phenotyping has the potential to replace traditional phenotyping techniques and can provide valuable gene identification information. The combination of the multifunctional phenotyping tools HRPF and GWAS provides deep insights into the genetic architecture of important traits. PMID:25295980

  9. Between-game variation of physical soccer performance measures in highly trained youth soccer players.

    Science.gov (United States)

    Doncaster, Greg; Unnithan, Viswanath

    2017-07-12

    To assess the between-game variation in measures of physical performance during 11 v 11 soccer match-play, over a short period of time, in highly trained youth soccer players. A single cohort observational study design was employed. Physical match performance data were collected from 17 male, highly trained youth soccer players (age: 13.3 ± 0.4 y) over three, 2 x 20min, 11 v 11 matches. Using 10 Hz GPS, the variables selected for analyses were total distance (TD), high-speed running (HSR), very high-speed running (VHSR), number of high-speed running efforts (HSReff) and number of very high-speed running efforts (VHSReff). Match data was also separated into cumulative 5 min epochs, to identify the peak 5 min epoch and the mean of the cumulative 5 min epochs for each match. Variability was quantified using the coefficient of variation (CV), Standard error of measurement (SEM) and intra-class correlation coefficient (ICC). Between- and within-player smallest worthwhile changes (SWC) were also calculated for each variable to aid in the interpretation of the data. Analysis of the variance between games reported a low CV for TD (3.8%) but larger CVs for HSR (33.3%), HSReff (35.4%) and VHSR and VHSReff (59.6 and 57.4 %, respectively). Analysis of 5 min epochs (peak and average) found an increase in the CVs beyond that of the values reported for the whole match. Between-player SWC in high intensity physical performance data ranged from 24.7 - 42.4 %, whereas within-player SWC ranged from 1.2 - 79.9%. The between-game variability of high and very high intensity activities in youth soccer players, across three soccer matches over a short period of time (2 weeks), is relatively 'large' and specific to the individual, thus highlighting the need for caution when interpreting physical performance data between games and players.

  10. High hardness-high toughness WC-20Co nanocomposites: Effect of VC variation and sintering temperature

    International Nuclear Information System (INIS)

    Kumar, Devender; Singh, K.

    2016-01-01

    WC-Co nanocomposites with variable VC content are synthesized by liquid phase sintering at two different temperatures. The as synthesized samples are characterized by X-ray diffraction (XRD), field emission scanning electron microscope (FE-SEM) and optical microscope. The mechanical properties are obtained by Vickers indentation method. The high content of VC, lead to high porosity when sintering temperature is increased from 1350 to 1400 °C. The relative density of all the samples is more than 95%. Microstructure reveals that agglomeration of W-Co-C and V-W-C increases at 1400 °C, which generates layered interfaces in radial direction and hence the material inhomogeneity. XRD pattern shows that the formation of η phase increases at 1400 °C, which is responsible to decrease the fracture toughness of the present samples. The average particle size of 102 nm, highest hardness of 1870.6 kgf/mm"2 with fracture toughness of 14.4 MN/mm"3"/"2 is observed in sample having 7.5 wt% VC, sintered at 1350 °C for one minute. This combination shows the highest hardness and reasonably high toughness as compared to conventionally sintered materials reported so far.

  11. Inheritance of microsatellite loci in the polyploid lake sturgeon (Acipenser fulvescens)

    Science.gov (United States)

    Pyatskowit, J.D.; Krueger, C.C.; Kincaid, H.L.; May, B.

    2001-01-01

    Inheritance in the expression of amplicons for four microsatellite primer pairs was determined using 10 families created from gametes of wild lake sturgeon (Acipenser fulvescens). Loci Afu34 and Afu68 expressed a maximum of two even-intensity bands per individual and had progeny genotype ratios that fit disomic inheritance (P > 0.05). Some variation exhibited at Afu34 and Afu68 was attributable to a null allele. Genotype expression at both loci also indicated that one female parent had transmitted unreduced gametes. Primer Afu39 amplified products that exhibited four gene doses, where genotype counts fit expected ratios for disomic inheritance (P > 0.05) indicating amplification of products from two disomic loci that share alleles. Meiotic drive was evident at the Afu39 loci based on a test for random segregation (P inheritance based on a single progeny potentially produced by a double reduction gamete. No evidence for proposed octoploid inheritance was observed.

  12. Isotopic composition of dissolved inorganic nitrogen in high mountain lakes: variation with altitude in the Pyrenees

    Science.gov (United States)

    Bartrons, M.; Camarero, L.; Catalan, J.

    2010-05-01

    Nitrogen deposition in remote areas has increased, but the effect on ecosystems is still poorly understood. For aquatic systems, knowledge of the main processes driving the observed variation is limited, as is knowledge of how changes in nitrogen supply affect lake biogeochemical and food web processes. Differences in dissolved inorganic nitrogen (DIN) between lakes cannot be understood without considering catchment characteristics. In mountains, catchment features (e.g., thermal conditions, land cover) vary considerably with elevation. The isotopic composition of nitrogen (δ15N) is increasingly used to study aquatic ecosystem dynamics. Here we explore the variability of δ15N in DIN in high mountain lakes and show that environmental conditions that change with altitude can affect the isotopic ratio. We measured ammonium and nitrate δ15N values in atmospheric deposition, epilimnetic water, deep chlorophyll maximum water (DCMW) and sediment pore water (SPW) from eight mountain lakes in the Pyrenees, both above and below the treeline. Lakes showed relatively uniform δ15N-NH4+ values in SPW (2.2±1.6‰), with no variation corresponding to catchment or lake characteristics. We suggest that organic matter diagenesis under similar sediment conditions is responsible for the low variation between the lakes. In the water column, the range of δ15N values was larger for ammonium (-9.4‰ to 7.4‰) than for nitrate (-11.4‰ to -3.4‰), as a result of higher variation both between and within lakes (epilimnetic vs. DCM water). For both compounds part of the difference correlated with altitude or catchment features (e.g., scree proportion). Based on concentration, chemical and isotopic tendencies, we suggest that patterns arise from the distinct relative contributions of two types of water flow paths to the lakes: one from snowpack melting, with little soil interaction; and another highly influenced by soil conditions. The snow-type flow path contributes low DIN

  13. Sun, Ocean, Nuclear Bombs, and Fossil Fuels: Radiocarbon Variations and Implications for High-Resolution Dating

    Science.gov (United States)

    Dutta, Koushik

    2016-06-01

    Radiocarbon, or 14C, is a radiometric dating method ideally suited for providing a chronological framework in archaeology and geosciences for timescales spanning the last 50,000 years. 14C is easily detectable in most common natural organic materials and has a half-life (5,730±40 years) relevant to these timescales. 14C produced from large-scale detonations of nuclear bombs between the 1950s and the early 1960s can be used for dating modern organic materials formed after the 1950s. Often these studies demand high-resolution chronology to resolve ages within a few decades to less than a few years. Despite developments in modern, high-precision 14C analytical methods, the applicability of 14C in high-resolution chronology is limited by short-term variations in atmospheric 14C in the past. This article reviews the roles of the principal natural drivers (e.g., solar magnetic activity and ocean circulation) and the anthropogenic perturbations (e.g., fossil fuel CO2 and 14C from nuclear and thermonuclear bombs) that are responsible for short-term 14C variations in the environment. Methods and challenges of high-resolution 14C dating are discussed.

  14. The signature of positive selection at randomly chosen loci.

    OpenAIRE

    Przeworski, Molly

    2002-01-01

    In Drosophila and humans, there are accumulating examples of loci with a significant excess of high-frequency-derived alleles or high levels of linkage disequilibrium, relative to a neutral model of a random-mating population of constant size. These are features expected after a recent selective sweep. Their prevalence suggests that positive directional selection may be widespread in both species. However, as I show here, these features do not persist long after the sweep ends: The high-frequ...

  15. Paleosecular variation analysis of high-latitude paleomagnetic data from the volcanic island of Jan Mayen

    Science.gov (United States)

    Cromwell, G.; Tauxe, L.; Staudigel, H.; Pedersen, L. R.; Constable, C.; Pedersen, R.; Duncan, R. A.; Staudigel, P.

    2009-12-01

    Recent investigation of high-latitude paleomagnetic data from the Erebus Volcanic Province (EVP), Antarctica shows a departure from magnetic dipole predictions for paleointensity data for the period 0-5 Ma. The average EVP paleointensity (31.5 +/- 2.4 μT) is equivalent to low-latitude measurements (1) or approximately half the strength predicted for a dipole at high-latitude. Also, paleosecular variation models (e.g., 2,3) predict dispersions of directions that are much lower than the high latitude observations. Observed low intensity values may be the result of reduced convective flow inside the tangent cylinder of the Earth’s core or insufficient temporal sampling (1). More high-latitude paleomagnetic data are necessary in order to investigate the cause of the depressed intensity values and to provide better geographic and temporal resolution for future statistical paleosecular variation models. To address this, we carried out two field seasons, one in Spitzbergen (79°N, 14°E) and one on the young volcanic island of Jan Mayen (71°N, 8°W). The latter sampling effort was guided by age analyses of samples obtained by P. Imsland (unpublished and 4). We will present new paleodirectional and paleointensity data from a total of 25 paleomagnetic sites. These data enhance the temporal resolution of global paleomagnetic data and allow for a more complete evaluation of the time-averaged magnetic field from 0-5 Ma. We will present a new analysis of paleosecular variation based on our new data, in combination with other recently published data sets. (1) Lawrence, K.P., L.Tauxe, H. Staudigel, C.G. Constable, A. Koppers, W. MacIntosh, C.L. Johnson, Paleomagnetic field properties at high southern latitude. Geochemistry Geophysics Geosystems 10 (2009). (2) McElhinny, M.W., P.L. McFadden, Paleosecular variation over the past 5 Myr based on a new generalized database. Geophysics Journal International 131 (1997), 240-252. (3) Tauxe, L., Kent, D.V., A simplified statistical

  16. The African Genome Variation Project shapes medical genetics in Africa

    Science.gov (United States)

    Gurdasani, Deepti; Carstensen, Tommy; Tekola-Ayele, Fasil; Pagani, Luca; Tachmazidou, Ioanna; Hatzikotoulas, Konstantinos; Karthikeyan, Savita; Iles, Louise; Pollard, Martin O.; Choudhury, Ananyo; Ritchie, Graham R. S.; Xue, Yali; Asimit, Jennifer; Nsubuga, Rebecca N.; Young, Elizabeth H.; Pomilla, Cristina; Kivinen, Katja; Rockett, Kirk; Kamali, Anatoli; Doumatey, Ayo P.; Asiki, Gershim; Seeley, Janet; Sisay-Joof, Fatoumatta; Jallow, Muminatou; Tollman, Stephen; Mekonnen, Ephrem; Ekong, Rosemary; Oljira, Tamiru; Bradman, Neil; Bojang, Kalifa; Ramsay, Michele; Adeyemo, Adebowale; Bekele, Endashaw; Motala, Ayesha; Norris, Shane A.; Pirie, Fraser; Kaleebu, Pontiano; Kwiatkowski, Dominic; Tyler-Smith, Chris; Rotimi, Charles; Zeggini, Eleftheria; Sandhu, Manjinder S.

    2014-01-01

    Given the importance of Africa to studies of human origins and disease susceptibility, detailed characterisation of African genetic diversity is needed. The African Genome Variation Project (AGVP) provides a resource to help design, implement and interpret genomic studies in sub-Saharan Africa (SSA) and worldwide. The AGVP represents dense genotypes from 1,481 and whole genome sequences (WGS) from 320 individuals across SSA. Using this resource, we find novel evidence of complex, regionally distinct hunter-gatherer and Eurasian admixture across SSA. We identify new loci under selection, including for malaria and hypertension. We show that modern imputation panels can identify association signals at highly differentiated loci across populations in SSA. Using WGS, we show further improvement in imputation accuracy supporting efforts for large-scale sequencing of diverse African haplotypes. Finally, we present an efficient genotype array design capturing common genetic variation in Africa, showing for the first time that such designs are feasible. PMID:25470054

  17. Evaluating the potential roles of the Gray and Extension loci in the coat coloration of Thoroughbred racing horses.

    Science.gov (United States)

    Sakamoto, Takahiro; Fawcett, Jeffrey A; Innan, Hideki

    2017-01-01

    Horses have substantial variation in coat color, and the genetic loci responsible for the coat color variations have been well investigated. It has been believed that some color variations should follow a single-locus Mendelian law. Examples include the Gray locus that causes the gray phenotype and the Extension locus that specifies the chestnut phenotype. We reevaluated the roles of the Gray and Extension loci by using a large number of mating records of Thoroughbred racing horses. We showed that the data indeed fits the Mendelian law extremely well for the two loci. Furthermore, we demonstrated that the Extension and Agouti loci might have an additional role in determining the degree of melanin that should distinguish bay, dark bay, and brown.

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

    Science.gov (United States)

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

    2013-01-01

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

  19. Effect of hormonal variation on in vivo high wavenumber Raman spectra improves cervical precancer detection

    Science.gov (United States)

    Duraipandian, Shiyamala; Zheng, Wei; Ng, Joseph; Low, Jeffrey J. H.; Ilancheran, A.; Huang, Zhiwei

    2012-03-01

    Raman spectroscopy is a unique analytical probe for molecular vibration and is capable of providing specific spectroscopic fingerprints of molecular compositions and structures of biological tissues. The aim of this study is to improve the classification accuracy of cervical precancer by characterizing the variations in the normal high wavenumber (HW - 2800-3700cm-1) Raman spectra arising from the menopausal status of the cervix. A rapidacquisition near-infrared (NIR) Raman spectroscopic system was used for in vivo tissue Raman measurements at 785 nm excitation. Individual HW Raman spectrum was measured with a 5s exposure time from both normal and precancer tissue sites of 15 patients recruited. The acquired Raman spectra were stratified based on the menopausal status of the cervix before the data analysis. Significant differences were noticed in Raman intensities of prominent band at 2924 cm-1 (CH3 stretching of proteins) and the broad water Raman band (in the 3100-3700 cm-1 range) with a peak at 3390 cm-1 in normal and dysplasia cervical tissue sites. Multivariate diagnostic decision algorithm based on principal component analysis (PCA) and linear discriminant analysis (LDA) was utilized to successfully differentiate the normal and precancer cervical tissue sites. By considering the variations in the Raman spectra of normal cervix due to the hormonal or menopausal status of women, the diagnostic accuracy was improved from 71 to 91%. By incorporating these variations prior to tissue classification, we can significantly improve the accuracy of cervical precancer detection using HW Raman spectroscopy.

  20. A CMOS high resolution, process/temperature variation tolerant RSSI for WIA-PA transceiver

    International Nuclear Information System (INIS)

    Yang Tao; Jiang Yu; Li Jie; Guo Jiangfei; Chen Hua; Han Jingyu; Guo Guiliang; Yan Yuepeng

    2015-01-01

    This paper presents a high resolution, process/temperature variation tolerant received signal strength indicator (RSSI) for wireless networks for industrial automation process automation (WIA-PA) transceiver fabricated in 0.18 μm CMOS technology. The active area of the RSSI is 0.24 mm 2 . Measurement results show that the proposed RSSI has a dynamic range more than 70 dB and the linearity error is within ±0.5 dB for an input power from −70 to 0 dBm (dBm to 50 Ω), the corresponding output voltage is from 0.81 to 1.657 V and the RSSI slope is 12.1 mV/dB while consuming all of 2 mA from a 1.8 V power supply. Furthermore, by the help of the integrated compensation circuit, the proposed RSSI shows the temperature error within ±1.5 dB from −40 to 85 °C, and process variation error within ±0.25 dB, which exhibits good temperature-independence and excellent robustness against process variation characteristics. (paper)

  1. Does the evolutionary conservation of microsatellite loci imply function?

    Energy Technology Data Exchange (ETDEWEB)

    Shriver, M.D.; Deka, R.; Ferrell, R.E. [Univ. of Pittsburgh, PA (United States)] [and others

    1994-09-01

    Microsatellites are highly polymorphic tandem arrays of short (1-6 bp) sequence motifs which have been found widely distributed in the genomes of all eukaryotes. We have analyzed allele frequency data on 16 microsatellite loci typed in the great apes (human, chimp, orangutan, and gorilla). The majority of these loci (13) were isolated from human genomic libraries; three were cloned from chimpanzee genomic DNA. Most of these loci are not only present in all apes species, but are polymorphic with comparable levels of heterozygosity and have alleles which overlap in size. The extent of divergence of allele frequencies among these four species were studies using the stepwise-weighted genetic distance (Dsw), which was previously shown to conform to linearity with evolutionary time since divergence for loci where mutations exist in a stepwise fashion. The phylogenetic tree of the great apes constructed from this distance matrix was consistent with the expected topology, with a high bootstrap confidence (82%) for the human/chimp clade. However, the allele frequency distributions of these species are 10 times more similar to each other than expected when they were calibrated with a conservative estimate of the time since separation of humans and the apes. These results are in agreement with sequence-based surveys of microsatellites which have demonstrated that they are highly (90%) conserved over short periods of evolutionary time (< 10 million years) and moderately (30%) conserved over long periods of evolutionary time (> 60-80 million years). This evolutionary conservation has prompted some authors to speculate that there are functional constraints on microsatellite loci. In contrast, the presence of directional bias of mutations with constraints and/or selection against aberrant sized alleles can explain these results.

  2. Characterization of variation and quantitative trait loci related to ...

    Indian Academy of Sciences (India)

    2012-04-13

    Apr 13, 2012 ... heterologous organisms for increasing the yield of .... to be genetically distant by morphological, biochemical and molecular analyses ... some modifications was used for the extraction of alkaloids from the dry samples of ...

  3. A microsatellite study for determination of allelic variation of Kurdish population-Kurdistan region-Iraq

    Science.gov (United States)

    Murad, Media J.; Amin, Bushra K.

    2017-09-01

    The purpose of this study was detecting genetic variations for the Kurdish population in Kurdistan region-Iraq, using fifteen autosomal STR loci. Buccal swabs were collected and depositing on Nucleic Card (Copan, Italia Spa) from 302 healthy unrelated Iraqi Kurds in five provinces of Kurdistan region-Iraq. Fifteen autosomal STR loci are D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818, FGA and Amelogenin included in the AmpFlSTR Identifiler® Direct PCR Amplification Kit (Applied Biosystems, Foster City, CA, USA). No significant departure from Hardy Weinberg Equilibrium (HWE) expectations were observed in 10 from 15 STR loci analyzed (a 5% significance level was taken). The exceptions were the CSF1PO, D3S1358, D13S317, D16S539 and D2S1338 loci. Statistical parameters of forensic efficiencies were estimated for the loci, based on allelic frequencies. The mean of observed heterozygosity, expected heterozygosity and PIC values across the 15 loci were 0.762, 0.797 and 0.768 respectively, indicating high gene diversity. The combined probability of exclusion, power of discrimination, probability of matching value for all the 15 STR loci were 0.9999968; 0.9999999 and 4.966×10-17, respectively. These parameters indicated the importance of the loci for forensic genetic purposes and paternity testing.

  4. Variations in pore characteristics in high volatile bituminous coals: Implications for coal bed gas content

    Science.gov (United States)

    Mastalerz, Maria; Drobniak, A.; Strapoc, D.; Solano-Acosta, W.; Rupp, J.

    2008-01-01

    The Seelyville Coal Member of the Linton Formation (Pennsylvanian) in Indiana was studied to: 1) understand variations in pore characteristics within a coal seam at a single location and compare these variations with changes occurring between the same coal at different locations, 2) elaborate on the influence of mineral-matter and maceral composition on mesopore and micropore characteristics, and 3) discuss implications of these variations for coal bed gas content. The coal is high volatile bituminous rank with R0 ranging from 0.57% to 0.60%. BET specific surface areas (determined by nitrogen adsorption) of the coals samples studied range from 1.8 to 22.9??m2/g, BJH adsorption mesopore volumes from 0.0041 to 0.0339??cm3/g, and micropore volumes (determined by carbon dioxide adsorption) from 0.0315 to 0.0540??cm3/g. The coals that had the largest specific surface areas and largest mesopore volumes occur at the shallowest depths, whereas the smallest values for these two parameters occur in the deepest coals. Micropore volumes, in contrast, are not depth-dependent. In the coal samples examined for this study, mineral-matter content influenced both specific surface area as well as mesopore and micropore volumes. It is especially clear in the case of micropores, where an increase in mineral-matter content parallels the decrease of micropore volume of the coal. No obvious relationships were observed between the total vitrinite content and pore characteristics but, after splitting vitrinite into individual macerals, we see that collotelinite influences both meso- and micropore volume positively, whereas collodetrinite contributes to the reduction of mesopore and micropore volumes. There are large variations in gas content within a single coal at a single location. Because of this variability, the entire thickness of the coal must be desorbed in order to determine gas content reliably and to accurately calculate the level of gas saturation. ?? 2008 Elsevier B.V. All

  5. Even between-lap pacing despite high within-lap variation during mountain biking.

    Science.gov (United States)

    Martin, Louise; Lambeth-Mansell, Anneliese; Beretta-Azevedo, Liane; Holmes, Lucy A; Wright, Rachel; St Clair Gibson, Alan

    2012-09-01

    Given the paucity of research on pacing strategies during competitive events, this study examined changes in dynamic high-resolution performance parameters to analyze pacing profiles during a multiple-lap mountain-bike race over variable terrain. A global-positioning-system (GPS) unit (Garmin, Edge 305, USA) recorded velocity (m/s), distance (m), elevation (m), and heart rate at 1 Hz from 6 mountain-bike riders (mean±SD age=27.2±5.0 y, stature=176.8±8.1 cm, mass=76.3±11.7 kg, VO2max=55.1±6.0 mL·kg(-1)·min1) competing in a multilap race. Lap-by-lap (interlap) pacing was analyzed using a 1-way ANOVA for mean time and mean velocity. Velocity data were averaged every 100 m and plotted against race distance and elevation to observe the presence of intralap variation. There was no significant difference in lap times (P=.99) or lap velocity (P=.65) across the 5 laps. Within each lap, a high degree of oscillation in velocity was observed, which broadly reflected changes in terrain, but high-resolution data demonstrated additional nonmonotonic variation not related to terrain. Participants adopted an even pace strategy across the 5 laps despite rapid adjustments in velocity during each lap. While topographical and technical variations of the course accounted for some of the variability in velocity, the additional rapid adjustments in velocity may be associated with dynamic regulation of self-paced exercise.

  6. Defining Allowable Physical Property Variations for High Accurate Measurements on Polymer Parts

    DEFF Research Database (Denmark)

    Mohammadi, Ali; Sonne, Mads Rostgaard; Madruga, Daniel González

    2015-01-01

    Measurement conditions and material properties have a significant impact on the dimensions of a part, especially for polymers parts. Temperature variation causes part deformations that increase the uncertainty of the measurement process. Current industrial tolerances of a few micrometres demand...... high accurate measurements in non-controlled ambient. Most of polymer parts are manufactured by injection moulding and their inspection is carried out after stabilization, around 200 hours. The overall goal of this work is to reach ±5μm in uncertainty measurements a polymer products which...

  7. A variational nodal diffusion method of high accuracy; Varijaciona nodalna difuziona metoda visoke tachnosti

    Energy Technology Data Exchange (ETDEWEB)

    Tomasevic, Dj; Altiparmarkov, D [Institut za Nuklearne Nauke Boris Kidric, Belgrade (Yugoslavia)

    1988-07-01

    A variational nodal diffusion method with accurate treatment of transverse leakage shape is developed and presented in this paper. Using Legendre expansion in transverse coordinates higher order quasi-one-dimensional nodal equations are formulated. Numerical solution has been carried out using analytical solutions in alternating directions assuming Legendre expansion of the RHS term. The method has been tested against 2D and 3D IAEA benchmark problem, as well as 2D CANDU benchmark problem. The results are highly accurate. The first order approximation yields to the same order of accuracy as the standard nodal methods with quadratic leakage approximation, while the second order reaches reference solution. (author)

  8. Identifying loci influencing grain number by microsatellite screening in bread wheat (Triticum aestivum L.).

    Science.gov (United States)

    Zhang, Dongling; Hao, Chenyang; Wang, Lanfen; Zhang, Xueyong

    2012-11-01

    Grain number (GN) is one of three major yield-related components in wheat. We used the Chinese wheat mini core collection to undertake a genome-wide association analysis of grain number using 531 SSR markers randomly located on all 21 chromosomes. Grain numbers of all accessions were measured in four trials, i.e. two environments in four growing seasons. Association analysis based on a mixed linear model (MLM) revealed that 27 SSR loci were significantly associated with mean GN (MGN) estimated by the best linear unbiased predictor (BLUP) method. These included numerous breeder favorable alleles with strong positive effects at 23 loci. Significant or extremely significant differences were detected on MGN between varieties conveying favored allele and varieties with other alleles. Moreover, statistical simulation showed that the favored alleles have additive genetic effects. Although modern varieties combined larger numbers of favored alleles, the numbers of favored alleles were not significantly different from those in landraces, especially those alleles contributing mostly to the phenotypic variation. These results indicate that there is still considerable genetic potential for use of markers for genome selection of GN for high yield in wheat.

  9. Quantitative trait loci associated with seed and seedling traits in Lactuca.

    Science.gov (United States)

    Argyris, Jason; Truco, María José; Ochoa, Oswaldo; Knapp, Steven J; Still, David W; Lenssen, Ger M; Schut, Johan W; Michelmore, Richard W; Bradford, Kent J

    2005-11-01

    Seed and seedling traits related to germination and stand establishment are important in the production of cultivated lettuce (Lactuca sativa L.). Six seed and seedling traits segregating in a L. sativa cv. Salinas x L. serriola recombinant inbred line population consisting of 103 F8 families revealed a total of 17 significant quantitative trait loci (QTL) resulting from three seed production environments. Significant QTL were identified for germination in darkness, germination at 25 and 35 degrees C, median maximum temperature of germination, hypocotyl length at 72 h post-imbibition, and plant (seedling) quality. Some QTL for germination and early seedling growth characteristics were co-located, suggestive of pleiotropic loci regulating these traits. A single QTL (Htg6.1) described 25 and 23% of the total phenotypic variation for high temperature germination in California- and Netherlands-grown populations, respectively, and was significant between 33 and 37 degrees C. Additionally, Htg6.1 showed significant epistatic interactions with other Htg QTL and a consistent effect across all the three seed production environments. L. serriola alleles increased germination at these QTL. The estimate of narrow-sense heritability (h2) of Htg6.1 was 0.84, indicating potential for L. serriola as a source of germination thermotolerance for lettuce introgression programs.

  10. Supervised machine learning reveals introgressed loci in the genomes of Drosophila simulans and D. sechellia.

    Science.gov (United States)

    Schrider, Daniel R; Ayroles, Julien; Matute, Daniel R; Kern, Andrew D

    2018-04-01

    Hybridization and gene flow between species appears to be common. Even though it is clear that hybridization is widespread across all surveyed taxonomic groups, the magnitude and consequences of introgression are still largely unknown. Thus it is crucial to develop the statistical machinery required to uncover which genomic regions have recently acquired haplotypes via introgression from a sister population. We developed a novel machine learning framework, called FILET (Finding Introgressed Loci via Extra-Trees) capable of revealing genomic introgression with far greater power than competing methods. FILET works by combining information from a number of population genetic summary statistics, including several new statistics that we introduce, that capture patterns of variation across two populations. We show that FILET is able to identify loci that have experienced gene flow between related species with high accuracy, and in most situations can correctly infer which population was the donor and which was the recipient. Here we describe a data set of outbred diploid Drosophila sechellia genomes, and combine them with data from D. simulans to examine recent introgression between these species using FILET. Although we find that these populations may have split more recently than previously appreciated, FILET confirms that there has indeed been appreciable recent introgression (some of which might have been adaptive) between these species, and reveals that this gene flow is primarily in the direction of D. simulans to D. sechellia.

  11. Variational data assimilation system with nesting model for high resolution ocean circulation

    Energy Technology Data Exchange (ETDEWEB)

    Ishikawa, Yoichi; Igarashi, Hiromichi; Hiyoshi, Yoshimasa; Sasaki, Yuji; Wakamatsu, Tsuyoshi; Awaji, Toshiyuki [Center for Earth Information Science and Technology, Japan Agency for Marine-Earth Science and Technology, 3173-25 Showa-machi, Kanazawa-Ku, Yokohama 236-0001 (Japan); In, Teiji [Japan Marine Science Foundation, 4-24, Minato-cho, Mutsu, Aomori, 035-0064 (Japan); Nakada, Satoshi [Graduate School of Maritime Science, Kobe University, 5-1-1, Fukae-minamimachi, Higashinada-Ku, Kobe, 658-0022 (Japan); Nishina, Kei, E-mail: ishikaway@jamstec.go.jp [Graduate School of Science, Kyoto University, Kitashirakawaoiwake-cho, Sakyo-Ku, Kyoto, 606-8502 (Japan)

    2015-10-15

    To obtain the high-resolution analysis fields for ocean circulation, a new incremental approach is developed using a four-dimensional variational data assimilation system with nesting models. The results show that there are substantial biases when using a classical method combined with data assimilation and downscaling, caused by different dynamics resulting from the different resolutions of the models used within the nesting models. However, a remarkable reduction in biases of the low-resolution model relative to the high-resolution model was observed using our new approach in narrow strait regions, such as the Tsushima and Tsugaru straits, where the difference in the dynamics represented by the high- and low-resolution models is substantial. In addition, error reductions are demonstrated in the downstream region of these narrow channels associated with the propagation of information through the model dynamics. (paper)

  12. Plant-symbiotic fungi as chemical engineers: multi-genome analysis of the clavicipitaceae reveals dynamics of alkaloid loci.

    Directory of Open Access Journals (Sweden)

    Christopher L Schardl

    Full Text Available The fungal family Clavicipitaceae includes plant symbionts and parasites that produce several psychoactive and bioprotective alkaloids. The family includes grass symbionts in the epichloae clade (Epichloë and Neotyphodium species, which are extraordinarily diverse both in their host interactions and in their alkaloid profiles. Epichloae produce alkaloids of four distinct classes, all of which deter insects, and some-including the infamous ergot alkaloids-have potent effects on mammals. The exceptional chemotypic diversity of the epichloae may relate to their broad range of host interactions, whereby some are pathogenic and contagious, others are mutualistic and vertically transmitted (seed-borne, and still others vary in pathogenic or mutualistic behavior. We profiled the alkaloids and sequenced the genomes of 10 epichloae, three ergot fungi (Claviceps species, a morning-glory symbiont (Periglandula ipomoeae, and a bamboo pathogen (Aciculosporium take, and compared the gene clusters for four classes of alkaloids. Results indicated a strong tendency for alkaloid loci to have conserved cores that specify the skeleton structures and peripheral genes that determine chemical variations that are known to affect their pharmacological specificities. Generally, gene locations in cluster peripheries positioned them near to transposon-derived, AT-rich repeat blocks, which were probably involved in gene losses, duplications, and neofunctionalizations. The alkaloid loci in the epichloae had unusual structures riddled with large, complex, and dynamic repeat blocks. This feature was not reflective of overall differences in repeat contents in the genomes, nor was it characteristic of most other specialized metabolism loci. The organization and dynamics of alkaloid loci and abundant repeat blocks in the epichloae suggested that these fungi are under selection for alkaloid diversification. We suggest that such selection is related to the variable life histories

  13. Genome-wide association study identifies five new schizophrenia loci.

    LENUS (Irish Health Repository)

    Ripke, Stephan

    2011-10-01

    We examined the role of common genetic variation in schizophrenia in a genome-wide association study of substantial size: a stage 1 discovery sample of 21,856 individuals of European ancestry and a stage 2 replication sample of 29,839 independent subjects. The combined stage 1 and 2 analysis yielded genome-wide significant associations with schizophrenia for seven loci, five of which are new (1p21.3, 2q32.3, 8p23.2, 8q21.3 and 10q24.32-q24.33) and two of which have been previously implicated (6p21.32-p22.1 and 18q21.2). The strongest new finding (P = 1.6 × 10(-11)) was with rs1625579 within an intron of a putative primary transcript for MIR137 (microRNA 137), a known regulator of neuronal development. Four other schizophrenia loci achieving genome-wide significance contain predicted targets of MIR137, suggesting MIR137-mediated dysregulation as a previously unknown etiologic mechanism in schizophrenia. In a joint analysis with a bipolar disorder sample (16,374 affected individuals and 14,044 controls), three loci reached genome-wide significance: CACNA1C (rs4765905, P = 7.0 × 10(-9)), ANK3 (rs10994359, P = 2.5 × 10(-8)) and the ITIH3-ITIH4 region (rs2239547, P = 7.8 × 10(-9)).

  14. Retrospectively reported month-to-month variation in sleeping problems of people naturally exposed to high-amplitude annual variation in daylength and/or temperature

    Directory of Open Access Journals (Sweden)

    Arcady A. Putilov

    Full Text Available Compared to literature on seasonal variation in mood and well-being, reports on seasonality of trouble sleeping are scarce and contradictive. To extend geography of such reports on example of people naturally exposed to high-amplitude annual variation in daylength and/or temperature. Participants were the residents of Turkmenia, West Siberia, South and North Yakutia, Chukotka, and Alaska. Health and sleep-wake adaptabilities, month-to-month variation in sleeping problems, well-being and behaviors were self-assessed. More than a half of 2398 respondents acknowledged seasonality of sleeping problems. Four of the assessed sleeping problems demonstrated three different patterns of seasonal variation. Rate of the problems significantly increased in winter months with long nights and cold days (daytime sleepiness and difficulties falling and staying asleep as well as in summer months with either long days (premature awakening and difficulties falling and staying asleep or hot nights and days (all 4 sleeping problems. Individual differences between respondents in pattern and level of seasonality of sleeping problems were significantly associated with differences in several other domains of individual variation, such as gender, age, ethnicity, physical health, morning-evening preference, sleep quality, and adaptability of the sleep-wake cycle. These results have practical relevance to understanding of the roles playing by natural environmental factors in seasonality of sleeping problems as well as to research on prevalence of sleep disorders and methods of their prevention and treatment in regions with large seasonal differences in temperature and daylength.

  15. Environmental variation, vegetation distribution, carbon dynamics and water/energy exchange at high latitudes

    Science.gov (United States)

    McGuire, A.D.; Wirth, C.; Apps, M.; Beringer, J.; Clein, J.; Epstein, H.; Kicklighter, D.W.; Bhatti, J.; Chapin, F. S.; De Groot, B.; Efremov, D.; Eugster, W.; Fukuda, M.; Gower, T.; Hinzman, L.; Huntley, B.; Jia, G.J.; Kasischke, E.; Melillo, J.; Romanovsky, V.; Shvidenko, A.; Vaganov, E.; Walker, D.

    2002-01-01

    The responses of high latitude ecosystems to global change involve complex interactions among environmental variables, vegetation distribution, carbon dynamics, and water and energy exchange. These responses may have important consequences for the earth system. In this study, we evaluated how vegetation distribution, carbon stocks and turnover, and water and energy exchange are related to environmental variation spanned by the network of the IGBP high latitude transects. While the most notable feature of the high latitude transects is that they generally span temperature gradients from southern to northern latitudes, there are substantial differences in temperature among the transects. Also, along each transect temperature co-varies with precipitation and photosynthetically active radiation, which are also variable among the transects. Both climate and disturbance interact to influence latitudinal patterns of vegetation and soil carbon storage among the transects, and vegetation distribution appears to interact with climate to determine exchanges of heat and moisture in high latitudes. Despite limitations imposed by the data we assembled, the analyses in this study have taken an important step toward clarifying the complexity of interactions among environmental variables, vegetation distribution, carbon stocks and turnover, and water and energy exchange in high latitude regions. This study reveals the need to conduct coordinated global change studies in high latitudes to further elucidate how interactions among climate, disturbance, and vegetation distribution influence carbon dynamics and water and energy exchange in high latitudes.

  16. High and uneven levels of 45S rDNA site-number variation across wild populations of a diploid plant genus (Anacyclus, Asteraceae).

    Science.gov (United States)

    Rosato, Marcela; Álvarez, Inés; Nieto Feliner, Gonzalo; Rosselló, Josep A

    2017-01-01

    The nuclear genome harbours hundreds to several thousand copies of ribosomal DNA. Despite their essential role in cellular ribogenesis few studies have addressed intrapopulation, interpopulation and interspecific levels of rDNA variability in wild plants. Some studies have assessed the extent of rDNA variation at the sequence and copy-number level with large sampling in several species. However, comparable studies on rDNA site number variation in plants, assessed with extensive hierarchical sampling at several levels (individuals, populations, species) are lacking. In exploring the possible causes for ribosomal loci dynamism, we have used the diploid genus Anacyclus (Asteraceae) as a suitable system to examine the evolution of ribosomal loci. To this end, the number and chromosomal position of 45S rDNA sites have been determined in 196 individuals from 47 populations in all Anacyclus species using FISH. The 45S rDNA site-number has been assessed in a significant sample of seed plants, which usually exhibit rather consistent features, except for polyploid plants. In contrast, the level of rDNA site-number variation detected in Anacyclus is outstanding in the context of angiosperms particularly regarding populations of the same species. The number of 45S rDNA sites ranged from four to 11, accounting for 14 karyological ribosomal phenotypes. Our results are not even across species and geographical areas, and show that there is no clear association between the number of 45S rDNA loci and the life cycle in Anacyclus. A single rDNA phenotype was detected in several species, but a more complex pattern that included intra-specific and intra-population polymorphisms was recorded in A. homogamos, A. clavatus and A. valentinus, three weedy species showing large and overlapping distribution ranges. It is likely that part of the cytogenetic changes and inferred dynamism found in these species have been triggered by genomic rearrangements resulting from contemporary

  17. Mapping autism risk loci using genetic linkage and chromosomal rearrangements

    Science.gov (United States)

    Szatmari, Peter; Paterson, Andrew; Zwaigenbaum, Lonnie; Roberts, Wendy; Brian, Jessica; Liu, Xiao-Qing; Vincent, John; Skaug, Jennifer; Thompson, Ann; Senman, Lili; Feuk, Lars; Qian, Cheng; Bryson, Susan; Jones, Marshall; Marshall, Christian; Scherer, Stephen; Vieland, Veronica; Bartlett, Christopher; Mangin, La Vonne; Goedken, Rhinda; Segre, Alberto; Pericak-Vance, Margaret; Cuccaro, Michael; Gilbert, John; Wright, Harry; Abramson, Ruth; Betancur, Catalina; Bourgeron, Thomas; Gillberg, Christopher; Leboyer, Marion; Buxbaum, Joseph; Davis, Kenneth; Hollander, Eric; Silverman, Jeremy; Hallmayer, Joachim; Lotspeich, Linda; Sutcliffe, James; Haines, Jonathan; Folstein, Susan; Piven, Joseph; Wassink, Thomas; Sheffield, Val; Geschwind, Daniel; Bucan, Maja; Brown, Ted; Cantor, Rita; Constantino, John; Gilliam, Conrad; Herbert, Martha; Lajonchere, Clara; Ledbetter, David; Lese-Martin, Christa; Miller, Janet; Nelson, Stan; Samango-Sprouse, Carol; Spence, Sarah; State, Matthew; Tanzi, Rudolph; Coon, Hilary; Dawson, Geraldine; Devlin, Bernie; Estes, Annette; Flodman, Pamela; Klei, Lambertus; Mcmahon, William; Minshew, Nancy; Munson, Jeff; Korvatska, Elena; Rodier, Patricia; Schellenberg, Gerard; Smith, Moyra; Spence, Anne; Stodgell, Chris; Tepper, Ping Guo; Wijsman, Ellen; Yu, Chang-En; Rogé, Bernadette; Mantoulan, Carine; Wittemeyer, Kerstin; Poustka, Annemarie; Felder, Bärbel; Klauck, Sabine; Schuster, Claudia; Poustka, Fritz; Bölte, Sven; Feineis-Matthews, Sabine; Herbrecht, Evelyn; Schmötzer, Gabi; Tsiantis, John; Papanikolaou, Katerina; Maestrini, Elena; Bacchelli, Elena; Blasi, Francesca; Carone, Simona; Toma, Claudio; Van Engeland, Herman; De Jonge, Maretha; Kemner, Chantal; Koop, Frederieke; Langemeijer, Marjolein; Hijmans, Channa; Staal, Wouter; Baird, Gillian; Bolton, Patrick; Rutter, Michael; Weisblatt, Emma; Green, Jonathan; Aldred, Catherine; Wilkinson, Julie-Anne; Pickles, Andrew; Le Couteur, Ann; Berney, Tom; Mcconachie, Helen; Bailey, Anthony; Francis, Kostas; Honeyman, Gemma; Hutchinson, Aislinn; Parr, Jeremy; Wallace, Simon; Monaco, Anthony; Barnby, Gabrielle; Kobayashi, Kazuhiro; Lamb, Janine; Sousa, Ines; Sykes, Nuala; Cook, Edwin; Guter, Stephen; Leventhal, Bennett; Salt, Jeff; Lord, Catherine; Corsello, Christina; Hus, Vanessa; Weeks, Daniel; Volkmar, Fred; Tauber, Maïté; Fombonne, Eric; Shih, Andy; Meyer, Kacie

    2007-01-01

    Autism spectrum disorders (ASD) are common, heritable neurodevelopmental conditions. The genetic architecture of ASD is complex, requiring large samples to overcome heterogeneity. Here we broaden coverage and sample size relative to other studies of ASD by using Affymetrix 10K single nucleotide polymorphism (SNP) arrays and 1168 families with ≥ 2 affected individuals to perform the largest linkage scan to date, while also analyzing copy number variation (CNV) in these families. Linkage and CNV analyses implicate chromosome 11p12-p13 and neurexins, respectively, amongst other candidate loci. Neurexins team with previously-implicated neuroligins for glutamatergic synaptogenesis, highlighting glutamate-related genes as promising candidates for ASD. PMID:17322880

  18. Association mapping of partitioning loci in barley

    Directory of Open Access Journals (Sweden)

    Mackay Ian J

    2008-02-01

    Full Text Available Abstract Background Association mapping, initially developed in human disease genetics, is now being applied to plant species. The model species Arabidopsis provided some of the first examples of association mapping in plants, identifying previously cloned flowering time genes, despite high population sub-structure. More recently, association genetics has been applied to barley, where breeding activity has resulted in a high degree of population sub-structure. A major genotypic division within barley is that between winter- and spring-sown varieties, which differ in their requirement for vernalization to promote subsequent flowering. To date, all attempts to validate association genetics in barley by identifying major flowering time loci that control vernalization requirement (VRN-H1 and VRN-H2 have failed. Here, we validate the use of association genetics in barley by identifying VRN-H1 and VRN-H2, despite their prominent role in determining population sub-structure. Results By taking barley as a typical inbreeding crop, and seasonal growth habit as a major partitioning phenotype, we develop an association mapping approach which successfully identifies VRN-H1 and VRN-H2, the underlying loci largely responsible for this agronomic division. We find a combination of Structured Association followed by Genomic Control to correct for population structure and inflation of the test statistic, resolved significant associations only with VRN-H1 and the VRN-H2 candidate genes, as well as two genes closely linked to VRN-H1 (HvCSFs1 and HvPHYC. Conclusion We show that, after employing appropriate statistical methods to correct for population sub-structure, the genome-wide partitioning effect of allelic status at VRN-H1 and VRN-H2 does not result in the high levels of spurious association expected to occur in highly structured samples. Furthermore, we demonstrate that both VRN-H1 and the candidate VRN-H2 genes can be identified using association mapping

  19. Relaxed impact craters on Ganymede: Regional variation and high heat flows

    Science.gov (United States)

    Singer, Kelsi N.; Bland, Michael T.; Schenk, Paul M.; McKinnon, William B.

    2018-01-01

    Viscously relaxed craters provide a window into the thermal history of Ganymede, a satellite with copious geologic signs of past high heat flows. Here we present measurements of relaxed craters in four regions for which suitable imaging exists: near Anshar Sulcus, Tiamat Sulcus, northern Marius Regio, and Ganymede's south pole. We describe a technique to measure apparent depth, or depth of the crater with respect to the surrounding terrain elevation. Measured relaxation states are compared with results from finite element modeling to constrain heat flow scenarios [see companion paper: Bland et al. (2017)]. The presence of numerous, substantially relaxed craters indicates high heat flows—in excess of 30–40 mW m−2 over 2 Gyr, with many small (heat flows. Crater relaxation states are bimodal for some equatorial regions but not in the region studied near the south pole, which suggests regional variations in Ganymede's thermal history.

  20. Variation of Mechanical Properties of High RRR And Reactor Grade Niobium With Heat Treatments

    Energy Technology Data Exchange (ETDEWEB)

    Ganapati Myneni; H. Umezawa

    2003-06-01

    Superconducting rf cavities used as accelerating structures in particle accelerators are made from high purity niobium with residual resistance ratios greater than 250. Reactor grade niobium is also used to make wave-guide and/or end group components for these accelerating structures. The major impurities in this type of niobium are interstitially dissolved gases such as hydrogen, nitrogen, and oxygen in addition to carbon. After fabricating the niobium accelerating structures, they are subjected to heat treatments for several hours in vacuum at temperatures of up to 900 C for degassing hydrogen or up to 1400 C for improving the thermal conductivity of niobium considerably. These heat treatments are affecting the mechanical properties of niobium drastically. In this paper the variation of the mechanical properties of high purity and reactor grade niobium with heat treatments in a vacuum of {approx} 10{sup -6} Torr and temperatures from 600 C to 1250 C for periods of 10 to 6 hours are presented.

  1. Relaxed impact craters on Ganymede: Regional variation and high heat flows

    Science.gov (United States)

    Singer, Kelsi N.; Bland, Michael T.; Schenk, Paul M.; McKinnon, William B.

    2018-05-01

    Viscously relaxed craters provide a window into the thermal history of Ganymede, a satellite with copious geologic signs of past high heat flows. Here we present measurements of relaxed craters in four regions for which suitable imaging exists: near Anshar Sulcus, Tiamat Sulcus, northern Marius Regio, and Ganymede's south pole. We describe a technique to measure apparent depth, or depth of the crater with respect to the surrounding terrain elevation. Measured relaxation states are compared with results from finite element modeling to constrain heat flow scenarios [see companion paper: Bland et al. (2017)]. The presence of numerous, substantially relaxed craters indicates high heat flows-in excess of 30-40 mW m-2 over 2 Gyr, with many small (heat flows. Crater relaxation states are bimodal for some equatorial regions but not in the region studied near the south pole, which suggests regional variations in Ganymede's thermal history.

  2. High variation in manufacturer-declared serving size of packaged discretionary foods in Australia.

    Science.gov (United States)

    Haskelberg, Hila; Neal, Bruce; Dunford, Elizabeth; Flood, Victoria; Rangan, Anna; Thomas, Beth; Cleanthous, Xenia; Trevena, Helen; Zheng, Jazzmin Miaobing; Louie, Jimmy Chun Yu; Gill, Timothy; Wu, Jason H Y

    2016-05-28

    Despite the potential of declared serving size to encourage appropriate portion size consumption, most countries including Australia have not developed clear reference guidelines for serving size. The present study evaluated variability in manufacturer-declared serving size of discretionary food and beverage products in Australia, and how declared serving size compared with the 2013 Australian Dietary Guideline (ADG) standard serve (600 kJ). Serving sizes were obtained from the Nutrition Information Panel for 4466 packaged, discretionary products in 2013 at four large supermarkets in Sydney, Australia, and categorised into fifteen categories in line with the 2013 ADG. For unique products that were sold in multiple package sizes, the percentage difference between the minimum and the maximum serving size across different package sizes was calculated. A high variation in serving size was found within the majority of food and beverage categories - for example, among 347 non-alcoholic beverages (e.g. soft drinks), the median for serving size was 250 (interquartile range (IQR) 250, 355) ml (range 100-750 ml). Declared serving size for unique products that are available in multiple package sizes also showed high variation, particularly for chocolate-based confectionery, with median percentage difference between minimum and maximum serving size of 183 (IQR 150) %. Categories with a high proportion of products that exceeded the 600 kJ ADG standard serve included cakes and muffins, pastries and desserts (≥74 % for each). High variability in declared serving size may confound interpretation and understanding of consumers interested in standardising and controlling their portion selection. Future research is needed to assess if and how standardising declared serving size might affect consumer behaviour.

  3. Eighteen microsatellite loci in Salix arbutifolia (Salicaceae) and cross-species amplification in Salix and Populus species.

    Science.gov (United States)

    Hoshikawa, Takeshi; Kikuchi, Satoshi; Nagamitsu, Teruyoshi; Tomaru, Nobuhiro

    2009-07-01

    Salix arbutifolia is a riparian dioecious tree species that is of conservation concern in Japan because of its highly restricted distribution. Eighteen polymorphic loci of dinucleotide microsatellites were isolated and characterized. Among these, estimates of the expected heterozygosity ranged from 0.350 to 0.879. Cross-species amplification was successful at 9-13 loci among six Salix species and at three loci in one Populus species. © 2009 Blackwell Publishing Ltd.

  4. Advanced Nongray Radiation Module in the LOCI Framework for Combustion CFD, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — In this STTR, an innovative, efficient and high fidelity computational tool to predict radiative heat transfer will be implemented in the LOCI framework. Radiative...

  5. Genetic Variation in the Nuclear and Organellar Genomes Modulates Stochastic Variation in the Metabolome, Growth, and Defense

    Science.gov (United States)

    Joseph, Bindu; Corwin, Jason A.; Kliebenstein, Daniel J.

    2015-01-01

    Recent studies are starting to show that genetic control over stochastic variation is a key evolutionary solution of single celled organisms in the face of unpredictable environments. This has been expanded to show that genetic variation can alter stochastic variation in transcriptional processes within multi-cellular eukaryotes. However, little is known about how genetic diversity can control stochastic variation within more non-cell autonomous phenotypes. Using an Arabidopsis reciprocal RIL population, we showed that there is significant genetic diversity influencing stochastic variation in the plant metabolome, defense chemistry, and growth. This genetic diversity included loci specific for the stochastic variation of each phenotypic class that did not affect the other phenotypic classes or the average phenotype. This suggests that the organism's networks are established so that noise can exist in one phenotypic level like metabolism and not permeate up or down to different phenotypic levels. Further, the genomic variation within the plastid and mitochondria also had significant effects on the stochastic variation of all phenotypic classes. The genetic influence over stochastic variation within the metabolome was highly metabolite specific, with neighboring metabolites in the same metabolic pathway frequently showing different levels of noise. As expected from bet-hedging theory, there was more genetic diversity and a wider range of stochastic variation for defense chemistry than found for primary metabolism. Thus, it is possible to begin dissecting the stochastic variation of whole organismal phenotypes in multi-cellular organisms. Further, there are loci that modulate stochastic variation at different phenotypic levels. Finding the identity of these genes will be key to developing complete models linking genotype to phenotype. PMID:25569687

  6. Isotopic composition of dissolved inorganic nitrogen in high mountain lakes: variation with altitude in the Pyrenees

    Directory of Open Access Journals (Sweden)

    M. Bartrons

    2010-05-01

    Full Text Available Nitrogen deposition in remote areas has increased, but the effect on ecosystems is still poorly understood. For aquatic systems, knowledge of the main processes driving the observed variation is limited, as is knowledge of how changes in nitrogen supply affect lake biogeochemical and food web processes. Differences in dissolved inorganic nitrogen (DIN between lakes cannot be understood without considering catchment characteristics. In mountains, catchment features (e.g., thermal conditions, land cover vary considerably with elevation. The isotopic composition of nitrogen (δ15N is increasingly used to study aquatic ecosystem dynamics. Here we explore the variability of δ15N in DIN in high mountain lakes and show that environmental conditions that change with altitude can affect the isotopic ratio.

    We measured ammonium and nitrate δ15N values in atmospheric deposition, epilimnetic water, deep chlorophyll maximum water (DCMW and sediment pore water (SPW from eight mountain lakes in the Pyrenees, both above and below the treeline. Lakes showed relatively uniform δ15N-NH4+ values in SPW (2.2±1.6‰, with no variation corresponding to catchment or lake characteristics. We suggest that organic matter diagenesis under similar sediment conditions is responsible for the low variation between the lakes.

    In the water column, the range of δ15N values was larger for ammonium (−9.4‰ to 7.4‰ than for nitrate (−11.4‰ to −3.4‰, as a result of higher variation both between and within lakes (epilimnetic vs. DCM water. For both compounds part of the difference correlated with altitude or catchment features (e.g., scree proportion. Based on concentration, chemical and isotopic tendencies, we suggest that patterns arise from the distinct relative contributions of two types of water flow paths to the lakes: one from snowpack melting, with little soil

  7. The African Genome Variation Project shapes medical genetics in Africa.

    Science.gov (United States)

    Gurdasani, Deepti; Carstensen, Tommy; Tekola-Ayele, Fasil; Pagani, Luca; Tachmazidou, Ioanna; Hatzikotoulas, Konstantinos; Karthikeyan, Savita; Iles, Louise; Pollard, Martin O; Choudhury, Ananyo; Ritchie, Graham R S; Xue, Yali; Asimit, Jennifer; Nsubuga, Rebecca N; Young, Elizabeth H; Pomilla, Cristina; Kivinen, Katja; Rockett, Kirk; Kamali, Anatoli; Doumatey, Ayo P; Asiki, Gershim; Seeley, Janet; Sisay-Joof, Fatoumatta; Jallow, Muminatou; Tollman, Stephen; Mekonnen, Ephrem; Ekong, Rosemary; Oljira, Tamiru; Bradman, Neil; Bojang, Kalifa; Ramsay, Michele; Adeyemo, Adebowale; Bekele, Endashaw; Motala, Ayesha; Norris, Shane A; Pirie, Fraser; Kaleebu, Pontiano; Kwiatkowski, Dominic; Tyler-Smith, Chris; Rotimi, Charles; Zeggini, Eleftheria; Sandhu, Manjinder S

    2015-01-15

    Given the importance of Africa to studies of human origins and disease susceptibility, detailed characterization of African genetic diversity is needed. The African Genome Variation Project provides a resource with which to design, implement and interpret genomic studies in sub-Saharan Africa and worldwide. The African Genome Variation Project represents dense genotypes from 1,481 individuals and whole-genome sequences from 320 individuals across sub-Saharan Africa. Using this resource, we find novel evidence of complex, regionally distinct hunter-gatherer and Eurasian admixture across sub-Saharan Africa. We identify new loci under selection, including loci related to malaria susceptibility and hypertension. We show that modern imputation panels (sets of reference genotypes from which unobserved or missing genotypes in study sets can be inferred) can identify association signals at highly differentiated loci across populations in sub-Saharan Africa. Using whole-genome sequencing, we demonstrate further improvements in imputation accuracy, strengthening the case for large-scale sequencing efforts of diverse African haplotypes. Finally, we present an efficient genotype array design capturing common genetic variation in Africa.

  8. The African Genome Variation Project shapes medical genetics in Africa

    Science.gov (United States)

    Gurdasani, Deepti; Carstensen, Tommy; Tekola-Ayele, Fasil; Pagani, Luca; Tachmazidou, Ioanna; Hatzikotoulas, Konstantinos; Karthikeyan, Savita; Iles, Louise; Pollard, Martin O.; Choudhury, Ananyo; Ritchie, Graham R. S.; Xue, Yali; Asimit, Jennifer; Nsubuga, Rebecca N.; Young, Elizabeth H.; Pomilla, Cristina; Kivinen, Katja; Rockett, Kirk; Kamali, Anatoli; Doumatey, Ayo P.; Asiki, Gershim; Seeley, Janet; Sisay-Joof, Fatoumatta; Jallow, Muminatou; Tollman, Stephen; Mekonnen, Ephrem; Ekong, Rosemary; Oljira, Tamiru; Bradman, Neil; Bojang, Kalifa; Ramsay, Michele; Adeyemo, Adebowale; Bekele, Endashaw; Motala, Ayesha; Norris, Shane A.; Pirie, Fraser; Kaleebu, Pontiano; Kwiatkowski, Dominic; Tyler-Smith, Chris; Rotimi, Charles; Zeggini, Eleftheria; Sandhu, Manjinder S.

    2015-01-01

    Given the importance of Africa to studies of human origins and disease susceptibility, detailed characterization of African genetic diversity is needed. The African Genome Variation Project provides a resource with which to design, implement and interpret genomic studies in sub-Saharan Africa and worldwide. The African Genome Variation Project represents dense genotypes from 1,481 individuals and whole-genome sequences from 320 individuals across sub-Saharan Africa. Using this resource, we find novel evidence of complex, regionally distinct hunter-gatherer and Eurasian admixture across sub-Saharan Africa. We identify new loci under selection, including loci related to malaria susceptibility and hypertension. We show that modern imputation panels (sets of reference genotypes from which unobserved or missing genotypes in study sets can be inferred) can identify association signals at highly differentiated loci across populations in sub-Saharan Africa. Using whole-genome sequencing, we demonstrate further improvements in imputation accuracy, strengthening the case for large-scale sequencing efforts of diverse African haplotypes. Finally, we present an efficient genotype array design capturing common genetic variation in Africa.

  9. Quantitative Trait Loci in Inbred Lines

    NARCIS (Netherlands)

    Jansen, R.C.

    2001-01-01

    Quantitative traits result from the influence of multiple genes (quantitative trait loci) and environmental factors. Detecting and mapping the individual genes underlying such 'complex' traits is a difficult task. Fortunately, populations obtained from crosses between inbred lines are relatively

  10. Understanding Students' Transition to High School: Demographic Variation and the Role of Supportive Relationships.

    Science.gov (United States)

    Benner, Aprile D; Boyle, Alaina E; Bakhtiari, Farin

    2017-10-01

    The transition to high school is disruptive for many adolescents, yet little is known about the supportive relational processes that might attenuate the challenges students face as they move from middle to high school, particularly for students from more diverse backgrounds. Identifying potential buffers that protect youth across this critical educational transition is important for informing more effective support services for youth. In this study, we investigated how personal characteristics (gender, nativity, parent education level) and changes in support from family, friends, and school influenced changes in socioemotional adjustment and academic outcomes across the transition from middle to high school. The data were drawn from 252 students (50% females, 85% Latina/o). The results revealed declines in students' grades and increases in depressive symptoms and feelings of loneliness across the high school transition, with key variation by student nativity and gender. Additionally, stable/increasing friend support and school belonging were both linked to less socioemotional disruptions as students moved from middle to high school. Increasing/stable school belonging was also linked to increases in school engagement across the high school transition. These findings suggest that when high school transitions disrupt supportive relationships with important others in adolescents' lives, adolescents' socioemotional well-being and, to a lesser extent, their academic engagement are also compromised. Thus, in designing transition support activities, particularly for schools serving more low-income and race/ethnic minority youth, such efforts should strive to acclimate new high school students by providing inclusive, caring environments and positive connections with educators and peers.

  11. Understanding human genetic variation in the era of high-throughput sequencing

    OpenAIRE

    Knight, Julian C.

    2010-01-01

    The EMBO/EMBL symposium ‘Human Variation: Cause and Consequence' highlighted advances in understanding the molecular basis of human genetic variation and its myriad implications for biology, human origins and disease.

  12. Exome chip meta-analysis identifies novel loci and East Asian-specific coding variants that contribute to lipid levels and coronary artery disease

    DEFF Research Database (Denmark)

    Lu, Xiangfeng; Peloso, Gina M; Liu, Dajiang J

    2017-01-01

    Most genome-wide association studies have been of European individuals, even though most genetic variation in humans is seen only in non-European samples. To search for novel loci associated with blood lipid levels and clarify the mechanism of action at previously identified lipid loci, we used a...

  13. Genomic analysis of natural selection and phenotypic variation in high-altitude mongolians.

    Directory of Open Access Journals (Sweden)

    Jinchuan Xing

    Full Text Available Deedu (DU Mongolians, who migrated from the Mongolian steppes to the Qinghai-Tibetan Plateau approximately 500 years ago, are challenged by environmental conditions similar to native Tibetan highlanders. Identification of adaptive genetic factors in this population could provide insight into coordinated physiological responses to this environment. Here we examine genomic and phenotypic variation in this unique population and present the first complete analysis of a Mongolian whole-genome sequence. High-density SNP array data demonstrate that DU Mongolians share genetic ancestry with other Mongolian as well as Tibetan populations, specifically in genomic regions related with adaptation to high altitude. Several selection candidate genes identified in DU Mongolians are shared with other Asian groups (e.g., EDAR, neighboring Tibetan populations (including high-altitude candidates EPAS1, PKLR, and CYP2E1, as well as genes previously hypothesized to be associated with metabolic adaptation (e.g., PPARG. Hemoglobin concentration, a trait associated with high-altitude adaptation in Tibetans, is at an intermediate level in DU Mongolians compared to Tibetans and Han Chinese at comparable altitude. Whole-genome sequence from a DU Mongolian (Tianjiao1 shows that about 2% of the genomic variants, including more than 300 protein-coding changes, are specific to this individual. Our analyses of DU Mongolians and the first Mongolian genome provide valuable insight into genetic adaptation to extreme environments.

  14. Pairing and Blocking in High-K Isomers: Variation of the Collective Parameter gR

    Directory of Open Access Journals (Sweden)

    Stone N.J.

    2013-12-01

    Full Text Available Using the principle of additivity, the quasi-particle contribution to magnetism in high-K isomers of Lu - Re has been estimated. Based on these estimates band structure branching ratio data is used to explore the behavior of the collective contribution as the number and neutron/proton nature (Np, Nn, of the quasi-particle excitations, change. A striking systematic variation of the collective g-factor gR with the difference, Np – Nn, is revealed. Basic ideas of pairing, its quenching by quasi-particle excitation and the consequent changes to moment of inertia and collective magnetism are discussed. The new found systematic behaviour of gR opens a fresh window on these effects amenable to detailed theoretical investigation.

  15. High Sequence Variations in Mitochondrial DNA Control Region among Worldwide Populations of Flathead Mullet Mugil cephalus

    Directory of Open Access Journals (Sweden)

    Brian Wade Jamandre

    2014-01-01

    Full Text Available The sequence and structure of the complete mtDNA control region (CR of M. cephalus from African, Pacific, and Atlantic populations are presented in this study to assess its usefulness in phylogeographic studies of this species. The mtDNA CR sequence variations among M. cephalus populations largely exceeded intraspecific polymorphisms that are generally observed in other vertebrates. The length of CR sequence varied among M. cephalus populations due to the presence of indels and variable number of tandem repeats at the 3′ hypervariable domain. The high evolutionary rate of the CR in this species probably originated from these mutations. However, no excessive homoplasic mutations were noticed. Finally, the star shaped tree inferred from the CR polymorphism stresses a rapid radiation worldwide, in this species. The CR still appears as a good marker for phylogeographic investigations and additional worldwide samples are warranted to further investigate the genetic structure and evolution in M. cephalus.

  16. Monitoring Mars LOD Variations from a High Altitude Circular Equatorial Orbit: Theory and Simulation

    Science.gov (United States)

    Barriot, J.; Dehant, V.; Duron, J.

    2003-12-01

    We compute the perturbations of a high altitude circular equatorial orbit of a martian probe under the influence of an annual variation of the martian lenght of day. For this purpose, we use the first order perturbations of the newtonian equations of motion, where the small parameter is given from the hourglass model of Chao and Rubincam, which allow a simple computation of CO2 exchanges during the martian year. We are able to demonstrate that the perturbations contains two components: the first one is a sine/cosine modulation at the orbit frequency, the second one is composed of terms of the form exp(t)*sin(t), so the orbit may not stable in the long term (several martian years), with perturbations growing exponentially. We give the full theory and numbers.

  17. Variation of minority charge carrier lifetime in high-resistance p-type silicon under irradiation

    International Nuclear Information System (INIS)

    Basheleishvili, Z.V.; Garnyk, V.S.; Gorin, S.N.; Pagava, T.A.

    1984-01-01

    The minority carrier lifetime (tau) variation was studied in the process of p-type silicon bombardment with fast 8 MeV electrons. The irradiation and all measurements were carried out at room temperature. The tau quantity was measured by the photoconductivity attenuation method at a low injection level 20% measurement error; the resistivity was measured by the four-probe method (10% error). The resistivity and minority charge carrier lifetime tau are shown to increase with the exposure dose. It is supposed that as radiation dose increases, the rearrangement of the centres responsible for reducing the lifetime occurs and results in a tau increase in the material being irradiated, however the tau value observed in the original samples is not attained. The restoration of the minority carrier lifetime in p-type high-resistance silicon with a growing exposure dose might proceed due to reduction in the free carrier concentration

  18. Sequencing Chromosomal Abnormalities Reveals Neurodevelopmental Loci that Confer Risk across Diagnostic Boundaries

    DEFF Research Database (Denmark)

    Talkowski, Michael E.; Rosenfeld, Jill A.; Blumenthal, Ian

    2012-01-01

    Sequencing of balanced chromosomal abnormalities, combined with convergent genomic studies of gene expression, copy-number variation, and genome-wide association, identifies 22 new loci that contribute to autism and related neurodevelopmental disorders. These data support a polygenic risk model...

  19. Multiancestry association study identifies new asthma risk loci that colocalize with immune-cell enhancer marks

    DEFF Research Database (Denmark)

    Demenais, Florence; Margaritte-Jeannin, Patricia; Barnes, Kathleen C

    2018-01-01

    We examined common variation in asthma risk by conducting a meta-analysis of worldwide asthma genome-wide association studies (23,948 asthma cases, 118,538 controls) of individuals from ethnically diverse populations. We identified five new asthma loci, found two new associations at two known...

  20. Multiancestry association study identifies new asthma risk loci that colocalize with immune-cell enhancer marks

    NARCIS (Netherlands)

    Demenais, Florence; Margaritte-Jeannin, Patricia; Barnes, Kathleen C; Cookson, William O C; Altmüller, Janine; Ang, Wei; Barr, R Graham; Beaty, Terri H; Becker, Allan B; Beilby, John; Bisgaard, Hans; Bjornsdottir, Unnur Steina; Bleecker, Eugene; Bønnelykke, Klaus; Boomsma, Dorret I; Bouzigon, Emmanuelle; Brightling, Christopher E; Brossard, Myriam; Brusselle, Guy G; Burchard, Esteban; Burkart, Kristin M; Bush, Andrew; Chan-Yeung, Moira; Chung, Kian Fan; Couto Alves, Alexessander; Curtin, John A; Custovic, Adnan; Daley, Denise; de Jongste, Johan C; Del-Rio-Navarro, Blanca E; Donohue, Kathleen M; Duijts, Liesbeth; Eng, Celeste; Eriksson, Johan G; Farrall, Martin; Fedorova, Yuliya; Feenstra, Bjarke; Ferreira, Manuel A; Freidin, Maxim B; Gajdos, Zofia; Gauderman, Jim; Gehring, Ulrike; Geller, Frank; Genuneit, Jon; Gharib, Sina A; Gilliland, Frank; Granell, Raquel; Graves, Penelope E; Gudbjartsson, Daniel F; Haahtela, Tari; Heckbert, Susan R; Heederik, Dick; Heinrich, Joachim; Heliövaara, Markku; Henderson, John; Himes, Blanca E; Hirose, Hiroshi; Hirschhorn, Joel N; Hofman, Albert; Holt, Patrick; Hottenga, Jouke; Hudson, Thomas J; Hui, Jennie; Imboden, Medea; Ivanov, Vladimir; Jaddoe, Vincent W V; James, Alan; Janson, Christer; Jarvelin, Marjo-Riitta; Jarvis, Deborah; Jones, Graham; Jonsdottir, Ingileif; Jousilahti, Pekka; Kabesch, Michael; Kähönen, Mika; Kantor, David B; Karunas, Alexandra S; Khusnutdinova, Elza; Koppelman, Gerard H; Kozyrskyj, Anita L; Kreiner, Eskil; Kubo, Michiaki; Kumar, Rajesh; Kumar, Ashish; Kuokkanen, Mikko; Lahousse, Lies; Laitinen, Tarja; Laprise, Catherine; Lathrop, Mark; Lau, Susanne; Lee, Young-Ae; Lehtimäki, Terho; Letort, Sébastien; Levin, Albert M; Li, Guo; Liang, Liming; Loehr, Laura R; London, Stephanie J; Loth, Daan W; Manichaikul, Ani; Marenholz, Ingo; Martinez, Fernando J; Matheson, Melanie C; Mathias, Rasika A; Matsumoto, Kenji; Mbarek, Hamdi; McArdle, Wendy L; Melbye, Mads; Melén, Erik; Meyers, Deborah; Michel, Sven; Mohamdi, Hamida; Musk, Arthur W; Myers, Rachel A; Nieuwenhuis, Maartje A E; Noguchi, Emiko; O'Connor, George T; Ogorodova, Ludmila M; Palmer, Cameron D; Palotie, Aarno; Park, Julie E; Pennell, Craig E; Pershagen, Göran; Polonikov, Alexey; Postma, Dirkje S; Probst-Hensch, Nicole; Puzyrev, Valery P; Raby, Benjamin A; Raitakari, Olli T; Ramasamy, Adaikalavan; Rich, Stephen S; Robertson, Colin F; Romieu, Isabelle; Salam, Muhammad T; Salomaa, Veikko; Schlünssen, Vivi; Scott, Robert; Selivanova, Polina A; Sigsgaard, Torben; Simpson, Angela; Siroux, Valérie; Smith, Lewis J; Solodilova, Maria; Standl, Marie; Stefansson, Kari; Strachan, David P; Stricker, Bruno H; Takahashi, Atsushi; Thompson, Philip J; Thorleifsson, Gudmar; Thorsteinsdottir, Unnur; Tiesler, Carla M T; Torgerson, Dara G; Tsunoda, Tatsuhiko; Uitterlinden, André G; van der Valk, Ralf J P; Vaysse, Amaury; Vedantam, Sailaja; von Berg, Andrea; von Mutius, Erika; Vonk, Judith M; Waage, Johannes; Wareham, Nick J; Weiss, Scott T; White, Wendy B; Wickman, Magnus; Widén, Elisabeth; Willemsen, Gonneke; Williams, L Keoki; Wouters, Inge M; Yang, James J; Zhao, Jing Hua; Moffatt, Miriam F; Ober, Carole; Nicolae, Dan L

    We examined common variation in asthma risk by conducting a meta-analysis of worldwide asthma genome-wide association studies (23,948 asthma cases, 118,538 controls) of individuals from ethnically diverse populations. We identified five new asthma loci, found two new associations at two known asthma

  1. Identification of seven loci affecting mean telomere length and their association with disease

    NARCIS (Netherlands)

    Codd, V.; Nelson, C.P.; Albrecht, E.; Mangino, M.; Deelen, J.; Buxton, J.L.; Hottenga, J.J.; Fischer, K.; Esko, T.; Surakka, I.; Broer, L.; Nyholt, DR; Mateo Leach, I.; Salo, P.; Hägg, S.; Matthews, M.K.; Palmen, J.; Norata, G.D.; O'Reilly, P.F.; Saleheen, D.; Amin, N.; Balmforth, A.J.; Beekman, M.; de Boer, R.A.; Böhringer, S.; Braund, P.S.; Burton, P.R.; de Craen, A.J.; Denniff, M.; Dong, Y.; Douroudis, K.; Dubinina, E.; Eriksson, J.G.; Garlaschelli, K.; Guo, D.; Hartikainen, A.L.; Henders, A.K.; Houwing-Duistermaat, J.J.; Kananen, L.; Karssen, L.C.; Kettunen, J.; Klopp, N.; Lagou, V.; van Leeuwen, E.; Madden, P.A.; Mägi, R.; Magnusson, P.K.E.; Männistö, S.; McCarthy, M.I.; Medland, S.E.; Mihailov, E.; Montgomery, G.W.; Oostra, B.A.; Palotie, A.; Peters, A.; Pollard, H.; Pouta, A.; Prokopenko, I.; Ripatti, S.; Salomaa, V.; Suchiman, H.E.D.; Valdes, A.M.; Verweij, N.; Viñuela, A.; Wang, X.; Wichmann, H. E.; Widen, E.; Willemsen, G.; Wright, M.J.; Xia, K.; Xiao, X.; van Veldhuisen, D.J.; Catapano, A.L.; Tobin, M.D.; Hall, A.S.; Blakemore, A.I.F.; van Gilst, W.H.; Zhu, H.; Erdmann, J.; Reilly, M.P.; Kathiresan, S.; Schunkert, H.; Talmud, P.J.; Pedersen, N.L.; Perola, M.; Ouwehand, W.; Kaprio, J.; Martin, N.G.; van Duijn, C.M.; Hovatta, I.; Gieger, C.; Metspalu, A.; Boomsma, D.I.; Järvelin, M.R.; Slagboom, P.E.; Thompson, J.R.; Spector, T.D.; van der Harst, P.; Samani, N.J.

    2013-01-01

    Interindividual variation in mean leukocyte telomere length (LTL) is associated with cancer and several age-associated diseases. We report here a genome-wide meta-analysis of 37,684 individuals with replication of selected variants in an additional 10,739 individuals. We identified seven loci,

  2. Identification of seven loci affecting mean telomere length and their association with disease

    NARCIS (Netherlands)

    Codd, Veryan; Nelson, Christopher P.; Albrecht, Eva; Mangino, Massimo; Deelen, Joris; Buxton, Jessica L.; Hottenga, Jouke Jan; Fischer, Krista; Esko, Tonu; Surakka, Ida; Broer, Linda; Nyholt, Dale R.; Mateo Leach, Irene; Salo, Perttu; Hagg, Sara; Matthews, Mary K.; Palmen, Jutta; Norata, Giuseppe D.; O'Reilly, Paul F.; Saleheen, Danish; Amin, Najaf; Balmforth, Anthony J.; Beekman, Marian; de Boer, Rudolf A.; Bohringer, Stefan; Braund, Peter S.; Burton, Paul R.; de Craen, Anton J. M.; Denniff, Matthew; Dong, Yanbin; Douroudis, Konstantinos; Dubinina, Elena; Eriksson, Johan G.; Garlaschelli, Katia; Guo, Dehuang; Hartikainen, Anna-Liisa; Henders, Anjali K.; Houwing-Duistermaat, Jeanine J.; Kananen, Laura; Karssen, Lennart C.; Kettunen, Johannes; Klopp, Norman; Lagou, Vasiliki; van Leeuwen, Elisabeth M.; Madden, Pamela A.; Maegi, Reedik; Verweij, Niek; van Veldhuisen, Dirk J.; van Gilst, Wiek H.; van der Harst, Pim

    Interindividual variation in mean leukocyte telomere length (LTL) is associated with cancer and several age-associated diseases. We report here a genome-wide meta-analysis of 37,684 individuals with replication of selected variants in an additional 10,739 individuals. We identified seven loci,

  3. High-resolution proxies for wood density variations in Terminalia superba

    Science.gov (United States)

    De Ridder, Maaike; Van den Bulcke, Jan; Vansteenkiste, Dries; Van Loo, Denis; Dierick, Manuel; Masschaele, Bert; De Witte, Yoni; Mannes, David; Lehmann, Eberhard; Beeckman, Hans; Van Hoorebeke, Luc; Van Acker, Joris

    2011-01-01

    Background and Aims Density is a crucial variable in forest and wood science and is evaluated by a multitude of methods. Direct gravimetric methods are mostly destructive and time-consuming. Therefore, faster and semi- to non-destructive indirect methods have been developed. Methods Profiles of wood density variations with a resolution of approx. 50 µm were derived from one-dimensional resistance drillings, two-dimensional neutron scans, and three-dimensional neutron and X-ray scans. All methods were applied on Terminalia superba Engl. & Diels, an African pioneer species which sometimes exhibits a brown heart (limba noir). Key Results The use of X-ray tomography combined with a reference material permitted direct estimates of wood density. These X-ray-derived densities overestimated gravimetrically determined densities non-significantly and showed high correlation (linear regression, R2 = 0·995). When comparing X-ray densities with the attenuation coefficients of neutron scans and the amplitude of drilling resistance, a significant linear relation was found with the neutron attenuation coefficient (R2 = 0·986) yet a weak relation with drilling resistance (R2 = 0·243). When density patterns are compared, all three methods are capable of revealing the same trends. Differences are mainly due to the orientation of tree rings and the different characteristics of the indirect methods. Conclusions High-resolution X-ray computed tomography is a promising technique for research on wood cores and will be explored further on other temperate and tropical species. Further study on limba noir is necessary to reveal the causes of density variations and to determine how resistance drillings can be further refined. PMID:21131386

  4. Variations of bubble cavitation and temperature elevation during lesion formation by high-intensity focused ultrasound.

    Science.gov (United States)

    Zhou, Yufeng; Gao, Xiaobin Wilson

    2013-08-01

    High-intensity focused ultrasound (HIFU) is emerging as an effective therapeutic modality in both thermal ablations for solid tumor/cancer and soft-tissue fragmentation. Mechanical and thermal effects, which play an important role in the HIFU treatment simultaneously, are dependent on the operating parameters and may vary with the progress of therapy. Mechanical erosion in the shape of a "squid," a "dumbbell" lesion with both mechanical and thermal lesions, or a "tadpole" lesion with mechanical erosion at the center and thermal necrosis on the boundary in the transparent gel phantom could be produced correspondingly with the pulse duration of 5-30 ms, which is much longer than histotripsy burst but shorter than the time for tissue boiling, and pulse repetition frequency (PRF) of 0.2-5 Hz. Meanwhile, variations of bubble cavitation (both inertial and stable cavitation) and temperature elevation in the focal region (i.e., z = -2.5, 0, and 2.5 mm) were measured by passive cavitation detection (PCD) and thermocouples during the therapeutic procedure, respectively. Stable cavitation increased with the pulse duration, PRF, and the number of pulses delivered. However, inertial cavitation was found to increase initially and then decrease with long pulse duration and high PRF. Temperature in the pre-focal region is always higher than those at the focal and post-focal position in all tests. Great variations of PCD signals and temperature elevation are due to the generation and persistence of large bubble, which is resistant to collapse and occurs with the increase of pulse duration and PRF. Similar lesion pattern and variations were also observed in ex vivo porcine kidneys. Hyperechoes in the B-mode ultrasound image were comparable to the shape and size of lesions in the dissected tissue. Thermal lesion volume increased with the increase of pulse duration and PRF, but mechanical erosion reached its maximum volume with the pulse duration of 20 ms and PRF of 1

  5. Energy spectra variations of high energy electrons in magnetic storms observed by ARASE and HIMAWARI

    Science.gov (United States)

    Takashima, T.; Higashio, N.; Mitani, T.; Nagatsuma, T.; Yoshizumi, M.

    2017-12-01

    The ARASE spacecraft was launched in December 20, 2016 to investigate mechanisms for acceleration and loss of relativistic electrons in the radiation belts during space storms. The six particle instruments with wide energy range (a few eV to 10MeV) are onboard the ARASE spacecraft. Especially, two particle instruments, HEP and XEP observe high energy electron with energy range from 70keV to over 10Mev. Those instruments observed several geomagnetic storms caused by coronal hole high speed streams or coronal mass ejections from March in 2017. The relativistic electrons in the outer radiation belt were disappeared/increased and their energy spectra were changed dynamically in some storms observed by XEP/HEP onboard the ARASE spacecraft. In the same time, SEDA-e with energy range 200keV-4.5MeV for electron on board the HIMAWARI-8, Japanese weather satellite on GEO, observed increase of relativistic electron in different local time. We will report on energy spectra variations of high energy electrons including calibrations of differential flux between XEP and HEP and discuss comparisons with energy spectra between ARAE and HIMAWARI that observed each storm in different local time.

  6. Geometric variations in high index-contrast waveguides, coupled mode theory in curvilinear coordinates.

    Science.gov (United States)

    Skorobogatiy, Maksim; Jacobs, Steven; Johnson, Steven; Fink, Yoel

    2002-10-21

    Perturbation theory formulation of Maxwell's equations gives a theoretically elegant and computationally efficient way of describing small imperfections and weak interactions in electro-magnetic systems. It is generally appreciated that due to the discontinuous field boundary conditions in the systems employing high dielectric contrast profiles standard perturbation formulations fail when applied to the problem of shifted material boundaries. In this paper we developed a novel coupled mode and perturbation theory formulations for treating generic non-uniform (varying along the direction of propagation) perturbations of a waveguide cross-section based on Hamiltonian formulation of Maxwell equations in curvilinear coordinates. We show that our formulation is accurate and rapidly converges to an exact result when used in a coupled mode theory framework even for the high index-contrast discontinuous dielectric profiles. Among others, our formulation allows for an efficient numerical evaluation of induced PMD due to a generic distortion of a waveguide profile, analysis of mode filters, mode converters and other optical elements such as strong Bragg gratings, tapers, bends etc., and arbitrary combinations of thereof. To our knowledge, this is the first time perturbation and coupled mode theories are developed to deal with arbitrary non-uniform profile variations in high index-contrast waveguides.

  7. Variation in mortality of ischemic and hemorrhagic strokes in relation to high temperature

    Science.gov (United States)

    Lim, Youn-Hee; Kim, Ho; Hong, Yun-Chul

    2013-01-01

    Outdoor temperature has been reported to have a significant influence on the seasonal variations of stroke mortality, but few studies have investigated the effect of high temperature on the mortality of ischemic and hemorrhagic strokes. The main study goal was to examine the effect of temperature, particularly high temperature, on ischemic and hemorrhagic strokes. We investigated the association between outdoor temperature and stroke mortality in four metropolitan cities in Korea during 1992-2007. We used time series analysis of the age-adjusted mortality rate for ischemic and hemorrhagic stroke deaths by using generalized additive and generalized linear models, and estimated the percentage change of mortality rate associated with a 1°C increase of mean temperature. The temperature-responses for the hemorrhagic and ischemic stroke mortality differed, particularly in the range of high temperature. The estimated percentage change of ischemic stroke mortality above a threshold temperature was 5.4 % (95 % CI, 3.9-6.9 %) in Seoul, 4.1 % (95 % CI, 1.6-6.6 %) in Incheon, 2.3 % (-0.2 to 5.0 %) in Daegu and 3.6 % (0.7-6.6 %) in Busan, after controlling for daily mean humidity, mean air pressure, day of the week, season, and year. Additional adjustment of air pollution concentrations in the model did not change the effects. Hemorrhagic stroke mortality risk significantly decreased with increasing temperature without a threshold in the four cities after adjusting for confounders. These findings suggest that the mortality of hemorrhagic and ischemic strokes show different patterns in relation to outdoor temperature. High temperature was harmful for ischemic stroke but not for hemorrhagic stroke. The risk of high temperature to ischemic stroke did not differ by age or gender.

  8. Discovery of novel heart rate-associated loci using the Exome Chip

    DEFF Research Database (Denmark)

    van den Berg, Marten E; Warren, Helen R; Cabrera, Claudia P

    2017-01-01

    Resting heart rate is a heritable trait, and an increase in heart rate is associated with increased mortality risk. Genome-wide association study analyses have found loci associated with resting heart rate, at the time of our study these loci explained 0.9% of the variation. This study aims to di......) and fetal muscle samples by including our novel variants.Our findings advance the knowledge of the genetic architecture of heart rate, and indicate new candidate genes for follow-up functional studies....

  9. Novel genetic loci underlying human intracranial volume identified through genome-wide association

    OpenAIRE

    Adams, Hieab HH; Hibar, Derrek P; Chouraki, Vincent; Stein, Jason L; Nyquist, Paul A; Renter��a, Miguel E; Trompet, Stella; Arias-Vasquez, Alejandro; Seshadri, Sudha; Desrivi��res, Sylvane; Beecham, Ashley H; Jahanshad, Neda; Wittfeld, Katharina; Van der Lee, Sven J; Abramovic, Lucija

    2016-01-01

    Intracranial volume reflects the maximally attained brain size during development, and remains stable with loss of tissue in late life. It is highly heritable, but the underlying genes remain largely undetermined. In a genome-wide association study of 32,438 adults, we discovered five previously unknown loci for intracranial volume and confirmed two known signals. Four of the loci were also associated with adult human stature, but these remained associated with intracranial volume after adjus...

  10. Genetic loci involved in antibody response to Mycobacterium avium ssp. paratuberculosis in cattle.

    Directory of Open Access Journals (Sweden)

    Giulietta Minozzi

    Full Text Available BACKGROUND: Mycobacterium avium subsp. paratuberculosis (MAP causes chronic enteritis in a wide range of animal species. In cattle, MAP causes a chronic disease called Johne's disease, or paratuberculosis, that is not treatable and the efficacy of vaccine control is controversial. The clinical phase of the disease is characterised by diarrhoea, weight loss, drop in milk production and eventually death. Susceptibility to MAP infection is heritable with heritability estimates ranging from 0.06 to 0.10. There have been several studies over the last few years that have identified genetic loci putatively associated with MAP susceptibility, however, with the availability of genome-wide high density SNP maker panels it is now possible to carry out association studies that have higher precision. METHODOLOGY/PRINCIPAL FINDINGS: The objective of the current study was to localize genes having an impact on Johne's disease susceptibility using the latest bovine genome information and a high density SNP panel (Illumina BovineSNP50 BeadChip to perform a case/control, genome-wide association analysis. Samples from MAP case and negative controls were selected from field samples collected in 2007 and 2008 in the province of Lombardy, Italy. Cases were defined as animals serologically positive for MAP by ELISA. In total 966 samples were genotyped: 483 MAP ELISA positive and 483 ELISA negative. Samples were selected randomly among those collected from 119 farms which had at least one positive animal. CONCLUSION/SIGNIFICANCE: THE ANALYSIS OF THE GENOTYPE DATA IDENTIFIED SEVERAL CHROMOSOMAL REGIONS ASSOCIATED WITH DISEASE STATUS: a region on chromosome 12 with high significance (P<5x10(-6, while regions on chromosome 9, 11, and 12 had moderate significance (P<5x10(-5. These results provide evidence for genetic loci involved in the humoral response to MAP. Knowledge of genetic variations related to susceptibility will facilitate the incorporation of this information

  11. Gene transposition causing natural variation for growth in Arabidopsis thaliana.

    Science.gov (United States)

    Vlad, Daniela; Rappaport, Fabrice; Simon, Matthieu; Loudet, Olivier

    2010-05-13

    A major challenge in biology is to identify molecular polymorphisms responsible for variation in complex traits of evolutionary and agricultural interest. Using the advantages of Arabidopsis thaliana as a model species, we sought to identify new genes and genetic mechanisms underlying natural variation for shoot growth using quantitative genetic strategies. More quantitative trait loci (QTL) still need be resolved to draw a general picture as to how and where in the pathways adaptation is shaping natural variation and the type of molecular variation involved. Phenotypic variation for shoot growth in the Bur-0 x Col-0 recombinant inbred line set was decomposed into several QTLs. Nearly-isogenic lines generated from the residual heterozygosity segregating among lines revealed an even more complex picture, with major variation controlled by opposite linked loci and masked by the segregation bias due to the defective phenotype of SG3 (Shoot Growth-3), as well as epistasis with SG3i (SG3-interactor). Using principally a fine-mapping strategy, we have identified the underlying gene causing phenotypic variation at SG3: At4g30720 codes for a new chloroplast-located protein essential to ensure a correct electron flow through the photosynthetic chain and, hence, photosynthesis efficiency and normal growth. The SG3/SG3i interaction is the result of a structural polymorphism originating from the duplication of the gene followed by divergent paralogue's loss between parental accessions. Species-wide, our results illustrate the very dynamic rate of duplication/transposition, even over short periods of time, resulting in several divergent--but still functional-combinations of alleles fixed in different backgrounds. In predominantly selfing species like Arabidopsis, this variation remains hidden in wild populations but is potentially revealed when divergent individuals outcross. This work highlights the need for improved tools and algorithms to resolve structural variation

  12. Characterisation of 12 microsatellite loci in the Vietnamese commercial clam Lutraria rhynchaena Jonas 1844 (Heterodonta: Bivalvia: Mactridae) through next-generation sequencing.

    Science.gov (United States)

    Thai, Binh Thanh; Tan, Mun Hua; Lee, Yin Peng; Gan, Han Ming; Tran, Trang Thi; Austin, Christopher M

    2016-05-01

    The marine clam Lutraria rhynchaena is gaining popularity as an aquaculture species in Asia. Lutraria populations are present in the wild throughout Vietnam and several stocks have been established and translocated for breeding and aquaculture grow-out purposes. In this study, we demonstrate the feasibility of utilising Illumina next-generation sequencing technology to streamline the identification and genotyping of microsatellite loci from this clam species. Based on an initial partial genome scan, 48 microsatellite markers with similar melting temperatures were identified and characterised. The 12 most suitable polymorphic loci were then genotyped using 51 individuals from a population in Quang Ninh Province, North Vietnam. Genetic variation was low (mean number of alleles per locus = 2.6; mean expected heterozygosity = 0.41). Two loci showed significant deviation from Hardy-Weinberg equilibrium (HWE) and the presence of null alleles, but there was no evidence of linkage disequilibrium among loci. Three additional populations were screened (n = 7-36) to test the geographic utility of the 12 loci, which revealed 100 % successful genotyping in two populations from central Vietnam (Nha Trang). However, a second population from north Vietnam (Co To) could not be successfully genotyped and morphological evidence and mitochondrial variation suggests that this population represents a cryptic species of Lutraria. Comparisons of the Qang Ninh and Nha Trang populations, excluding the 2 loci out of HWE, revealed statistically significant allelic variation at 4 loci. We reported the first microsatellite loci set for the marine clam Lutraria rhynchaena and demonstrated its potential in differentiating clam populations. Additionally, a cryptic species population of Lutraria rhynchaena was identified during initial loci development, underscoring the overlooked diversity of marine clam species in Vietnam and the need to genetically characterise population representatives prior

  13. Unexpectedly high genetic variation in large unisexual clumps of the subdioecious plant Honckenya peploides

    DEFF Research Database (Denmark)

    Sánchez-Vilas, Julia; Philipp, Marianne; Retuerto, Rubén

    2010-01-01

    Honckenya peploides is a subdioecious dune plant that reproduces both sexually and by clonal growth. In northwest Spain this species was found to exhibit an extreme spatial segregation of the sexes, and our objective was to investigate genetic variation in unisexual clumps. Genetic variation was ...

  14. List of isozyme loci - RGP gmap98 | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us RGP gmap98 List of isozyme loci Data detail Data name List of isozyme loci DOI 10.18908/lsdb...he present high-density linkage map, and that were putatively identified as isozyme genes. Data file File name: rgp_gmap98_iso...gmap98/LATEST/rgp_gmap98_isozyme_loci.zip File size: 611 B Simple search URL http://togodb.biosciencedbc.jp/...0001 were considered as functionally identical clones. And we have selected the ones that hit the isozyme ge...his Database Database Description Download License Update History of This Database Site Policy | Contact Us List of isozyme loci - RGP gmap98 | LSDB Archive ...

  15. Spatial variations in composition in high-critical-current-density Bi-2223 tapes

    International Nuclear Information System (INIS)

    Holesinger, T. G.; Bingert, J. F.; Teplitsky, M.; Li, Q.; Parrella, R.; Rupich, M. P.; Riley, G. N. Jr.

    2000-01-01

    A detailed compositional analysis of high-critical-current-density (J c ) (55 and 65 kA/cm2 at 77 K) (Bi, Pb) 2 Sr 2 Ca 2 Cu 3 O y (Bi-2223) tapes was undertaken by energy dispersive spectroscopy in the transmission electron microscope. Structural features were coupled with characteristic compositions of the Bi-2223 phase. The average of all compositional measurements of the Bi-2223 phase was determined to be Bi 1.88 Pb 0.23 Sr 1.96 Ca 1.95 Cu 2.98 O y . However, spatial variations in the Bi-2223 composition and differing phase equilibria were found throughout the filament structure. In particular, a considerable range of Bi-2223 compositions can be found within a single tape, and the lead content of the Bi-2223 phase is significantly depressed in the vicinity of lead-rich phases. The depletion of lead in the Bi-2223 phase around the 3221 phases may be a current-limiting microstructure in these tapes. (c) 2000 Materials Research Society

  16. Characteristics of Japanese inflammatory bowel disease susceptibility loci.

    Science.gov (United States)

    Arimura, Yoshiaki; Isshiki, Hiroyuki; Onodera, Kei; Nagaishi, Kanna; Yamashita, Kentaro; Sonoda, Tomoko; Matsumoto, Takayuki; Takahashi, Atsushi; Takazoe, Masakazu; Yamazaki, Keiko; Kubo, Michiaki; Fujimiya, Mineko; Imai, Kohzoh; Shinomura, Yasuhisa

    2014-08-01

    There are substantial differences in inflammatory bowel disease (IBD) genetics depending on the populations examined. We aimed to identify Japanese population-specific or true culprit susceptibility genes through a meta-analysis of past genetic studies of Japanese IBD. For this study, we reviewed 2,703 articles. The review process consisted of three screening stages: we initially searched for relevant studies and then relevant single nucleotide polymorphisms (SNPs). Finally, we adjusted them for the meta-analysis. To maximize our chances of analysis, we introduced proxy SNPs during the first stage. To minimize publication bias, no significant SNPs and solitary SNPs without pairs were combined to be reconsidered during the third stage. Additionally, two SNPs were newly genotyped. Finally, we conducted a meta-analysis of 37 published studies in 50 SNPs located at 22 loci corresponding to the total number of 4,853 Crohn's disease (CD), 5,612 ulcerative colitis (UC) patients, and 14,239 healthy controls. We confirmed that the NKX2-3 polymorphism is associated with common susceptibility to IBD and that HLA-DRB1*0450 alleles increase susceptibility to CD but reduce risk for UC while HLA-DRB1*1502 alleles increase susceptibility to UC but reduce CD risk. Moreover, we found individual disease risk loci: TNFSF15 and TNFα to CD and HLA-B*5201, and NFKBIL1 to UC. The genetic risk of HLA was substantially high (odds ratios ranged from 1.54 to 2.69) while that of common susceptibility loci to IBD was modest (odds ratio ranged from 1.13 to 1.24). Results indicate that Japanese IBD susceptibility loci identified by the meta-analysis are closely associated with the HLA regions.

  17. Immunogenetic variation and differential pathogen exposure in free-ranging cheetahs across Namibian farmlands.

    Directory of Open Access Journals (Sweden)

    Aines Castro-Prieto

    Full Text Available Genes under selection provide ecologically important information useful for conservation issues. Major histocompatibility complex (MHC class I and II genes are essential for the immune defence against pathogens from intracellular (e.g. viruses and extracellular (e.g. helminths origins, respectively. Serosurvey studies in Namibian cheetahs (Acinonyx juabuts revealed higher exposure to viral pathogens in individuals from north-central than east-central regions. Here we examined whether the observed differences in exposure to viruses influence the patterns of genetic variation and differentiation at MHC loci in 88 free-ranging Namibian cheetahs.Genetic variation at MHC I and II loci was assessed through single-stranded conformation polymorphism (SSCP analysis and sequencing. While the overall allelic diversity did not differ, we observed a high genetic differentiation at MHC class I loci between cheetahs from north-central and east-central Namibia. No such differentiation in MHC class II and neutral markers were found.Our results suggest that MHC class I variation mirrors the variation in selection pressure imposed by viruses in free-ranging cheetahs across Namibian farmland. This is of high significance for future management and conservation programs of this species.

  18. Development of Microsatellite Loci for the Riparian Tree Species Melaleuca argentea (Myrtaceae Using 454 Sequencing

    Directory of Open Access Journals (Sweden)

    Paul G. Nevill

    2013-05-01

    Full Text Available Premise of the study: Microsatellite primers were developed for Melaleuca argentea (Myrtaceae to evaluate genetic diversity and population genetic structure of this broadly distributed northern Australian riparian tree species. Methods and Results: 454 GS-FLX shotgun sequencing was used to obtain 5860 sequences containing putative microsatellite motifs. Two multiplex PCRs were optimized to genotype 11 polymorphic microsatellite loci. These loci were screened for variation in individuals from two populations in the Pilbara region, northwestern Western Australia. Overall, observed heterozygosities ranged from 0.27 to 0.86 (mean: 0.52 and the number of alleles per locus ranged from two to 13 (average: 4.3. Conclusions: These microsatellite loci will be useful in future studies of the evolutionary history and population and spatial genetic structure in M. argentea, and inform the development of seed sourcing strategies for the species.

  19. Annotation of loci from genome-wide association studies using tissue-specific quantitative interaction proteomics

    DEFF Research Database (Denmark)

    Lundby, Alicia; Rossin, Elizabeth J.; Steffensen, Annette B.

    2014-01-01

    Genome-wide association studies (GWAS) have identified thousands of loci associated with complex traits, but it is challenging to pinpoint causal genes in these loci and to exploit subtle association signals. We used tissue-specific quantitative interaction proteomics to map a network of five genes...... involved in the Mendelian disorder long QT syndrome (LOTS). We integrated the LOTS network with GWAS loci from the corresponding common complex trait, QT-interval variation, to identify candidate genes that were subsequently confirmed in Xenopus laevis oocytes and zebrafish. We used the LOTS protein...... network to filter weak GWAS signals by identifying single-nucleotide polymorphisms (SNPs) in proximity to genes in the network supported by strong proteomic evidence. Three SNPs passing this filter reached genome-wide significance after replication genotyping. Overall, we present a general strategy...

  20. High natural gene expression variation in the reef-building coral Acropora millepora: potential for acclimative and adaptive plasticity.

    Science.gov (United States)

    Granados-Cifuentes, Camila; Bellantuono, Anthony J; Ridgway, Tyrone; Hoegh-Guldberg, Ove; Rodriguez-Lanetty, Mauricio

    2013-04-08

    Ecosystems worldwide are suffering the consequences of anthropogenic impact. The diverse ecosystem of coral reefs, for example, are globally threatened by increases in sea surface temperatures due to global warming. Studies to date have focused on determining genetic diversity, the sequence variability of genes in a species, as a proxy to estimate and predict the potential adaptive response of coral populations to environmental changes linked to climate changes. However, the examination of natural gene expression variation has received less attention. This variation has been implicated as an important factor in evolutionary processes, upon which natural selection can act. We acclimatized coral nubbins from six colonies of the reef-building coral Acropora millepora to a common garden in Heron Island (Great Barrier Reef, GBR) for a period of four weeks to remove any site-specific environmental effects on the physiology of the coral nubbins. By using a cDNA microarray platform, we detected a high level of gene expression variation, with 17% (488) of the unigenes differentially expressed across coral nubbins of the six colonies (jsFDR-corrected, p natural variation between reef corals when assessing experimental gene expression differences. The high transcriptional variation detected in this study is interpreted and discussed within the context of adaptive potential and phenotypic plasticity of reef corals. Whether this variation will allow coral reefs to survive to current challenges remains unknown.

  1. An Evaluation of Subseasonal Intensity Variation of the South Asian High in the CMIP5 Models

    Science.gov (United States)

    Shang, W.; Ren, X.

    2017-12-01

    The South Asian High (SAH) is a vital member among the Asian summer monsoon circulations in the upper troposphere located over the Tibetan Plateau and its surrounding areas during boreal summer. This study presents an evaluation of the characteristics of SAH's subseasonal intensity variation simulated by 18 coupled models from the Coupled Model Intercomparison Project (CMIP5). The empirical orthogonal function (EOF) analysis is used on subseasonal anomalies in 100hPa geopotential height over 20°-40°N, 35°-110°E for June, July and August from 1979 to 2005. The first EOF mode from the ERA-Interim (denoted as observation) shows a monopole pattern capturing the strengthening/weakening of SAH. The power spectrum analysis of the corresponding principal component (PC1) time series shows a period about 10-30 days. In general, all the 18 coupled models can reproduce the monopole pattern and its subseasonal oscillation to a certain extent. The four well-simulated models are: ACCESS1-3, HadGEM2-CC, MRI-CGCM3 and BNU-ESM, which EOF1 show strong positive anomalies in the 100hPa geopotential height over the SAH's region and weak negative anomalies in their north side. Lead-lag regression shows that the evolution of the EOF1 from day -12 to +3 in the above four models is also reasonably simulated. In the observation, positive rainfall band moves northward from the equatorial Indian Ocean, the Bay of Bengals and the Western North Pacific to the north of Indian Peninsula, south of Tibetan Plateau and Southeast China, accompanied by the increasing intensity of SAH. In the above four models, the northward movement of anomalous rainfall band can be well reproduced. In the observation, the spatial pattern of anomalies in integrated apparent heat source and integrated apparent moisture sink resemble that of rainfall, thus corresponding to anomalous condensation heat release. The anomalous heating stimulates positive height anomalies with an anomalous anticyclonic circulation to its

  2. Variations in energy, flux, and brightness of pulsating aurora measured at high time resolution

    Directory of Open Access Journals (Sweden)

    H. Dahlgren

    2017-03-01

    Full Text Available High-resolution multispectral optical and incoherent scatter radar data are used to study the variability of pulsating aurora. Two events have been analysed, and the data combined with electron transport and ion chemistry modelling provide estimates of the energy and energy flux during both the ON and OFF periods of the pulsations. Both the energy and energy flux are found to be reduced during each OFF period compared with the ON period, and the estimates indicate that it is the number flux of foremost higher-energy electrons that is reduced. The energies are found never to drop below a few kilo-electronvolts during the OFF periods for these events. The high-resolution optical data show the occurrence of dips in brightness below the diffuse background level immediately after the ON period has ended. Each dip lasts for about a second, with a reduction in brightness of up to 70 % before the intensity increases to a steady background level again. A different kind of variation is also detected in the OFF period emissions during the second event, where a slower decrease in the background diffuse emission is seen with its brightness minimum just before the ON period, for a series of pulsations. Since the dips in the emission level during OFF are dependent on the switching between ON and OFF, this could indicate a common mechanism for the precipitation during the ON and OFF phases. A statistical analysis of brightness rise, fall, and ON times for the pulsations is also performed. It is found that the pulsations are often asymmetric, with either a slower increase of brightness or a slower fall.

  3. Genome scan for nonadditive heterotic trait loci reveals mainly underdominant effects in Saccharomyces cerevisiae.

    Science.gov (United States)

    Laiba, Efrat; Glikaite, Ilana; Levy, Yael; Pasternak, Zohar; Fridman, Eyal

    2016-04-01

    The overdominant model of heterosis explains the superior phenotype of hybrids by synergistic allelic interaction within heterozygous loci. To map such genetic variation in yeast, we used a population doubling time dataset of Saccharomyces cerevisiae 16 × 16 diallel and searched for major contributing heterotic trait loci (HTL). Heterosis was observed for the majority of hybrids, as they surpassed their best parent growth rate. However, most of the local heterozygous loci identified by genome scan were surprisingly underdominant, i.e., reduced growth. We speculated that in these loci adverse effects on growth resulted from incompatible allelic interactions. To test this assumption, we eliminated these allelic interactions by creating hybrids with local hemizygosity for the underdominant HTLs, as well as for control random loci. Growth of hybrids was indeed elevated for most hemizygous to HTL genes but not for control genes, hence validating the results of our genome scan. Assessing the consequences of local heterozygosity by reciprocal hemizygosity and allele replacement assays revealed the influence of genetic background on the underdominant effects of HTLs. Overall, this genome-wide study on a multi-parental hybrid population provides a strong argument against single gene overdominance as a major contributor to heterosis, and favors the dominance complementation model.

  4. High-Amplitude, Rapid Photometric Variation of the New Polar Master OT J132104.0+560957.8

    Science.gov (United States)

    2015-02-05

    HIGH-AMPLITUDE, RAPID PHOTOMETRIC VARIATION OF THE NEW POLAR MASTER OT J132104.04+560957.8 LITTLEFIELD, COLIN;1,2 GARNAVICH, PETER;1 MAGNO, KATRINA;1...18.5 during each photometric cycle, becoming so faint that we could no longer detect it. The data showed a period of roughly 91 minutes with each...TYPE 3. DATES COVERED 00-00-2015 to 00-00-2015 4. TITLE AND SUBTITLE High-Amplitude, Rapid Photometric Variation Of The New Polar Master OT

  5. Nonlinear selection and a blend of convergent, divergent and parallel evolution shapes natural variation in glucosinolates

    DEFF Research Database (Denmark)

    Kliebenstein, Daniel James; Cacho, N. Ivalú

    2016-01-01

    and traits that is highly similar both within and between species. Further, early field trials with single gene recreations of natural variation are showing that selection is highly fluctuating both from site to site and from year to year within a location. This review goes into the specific ecological......The molecular mechanisms underlying organismal fitness in complex environments is just beginning to be illuminated. One of the pre-eminent model systems that span the molecular to field fitness chasm is the natural variation in glucosinolate defence metabolites within the Capparales. In this system......, evolutionary and molecular observations for each of the major loci controlling natural variation in glucosinolates....

  6. Genetic variation of cowslip (Primula veris L. populations (West Poland

    Directory of Open Access Journals (Sweden)

    Maria Morozowska

    2011-01-01

    Full Text Available Genetic variation of twelve Polish populations of Primula veris L. from western Poland was investigated in respect of six enzyme systems: 6-phosphogluconate dehydrogenase (6PGD, diaphorase (DIA, menadione reductase (MNR, formate dehydrogenase (FDH, isocitrate dehydrogenase (IDH and glutamate oxaloacetate transaminase (GOT. Only two of them (6PGD and DIA were polymorphic and all populations were compared according to four loci and eight alleles. For 6PGD only one out of the two detected loci (locus 6PGD-2 was polymorphic and consisted of three alleles a, b and c. For DIA each of two detected loci had two alleles. For 6PGD-2 one population was monomorphic and four populations were monomorphic for DIA-1 and DIA-2. The rest of the populations were polymorphic with low frequency of heterozygotes. The low heterozygosity level, found in the examined populations, was confirmed by high values of the fixation index (F. The level of genetic differentiation among GST populations specified for each polymorphic loci, was equal to 0.045 for 6PGD-2 and had the value of 0.078 for DIA-2 and 0.186 for DIA-1. Nm value for polymorphic loci was 1.10 for DIA-1 and 2.94 for DIA-2, and for 6PGD-2 was 5.33, what indicates some gene flow between the examined populations. The dendrogram constructed on the basis of genotype frequencies showed that the populations were divided into two groups, however the most southern population No. 2 was clearly similar to the northern population No. 8.

  7. Seasonal variations of the high-latitude geomagnetic field intensity in the northern hemisphere

    International Nuclear Information System (INIS)

    Rivin, Yu.R.; Chkhaidze, Z.Sh.

    1994-01-01

    Seasonal variation of the geomagnetic field three components is investigated using the data of the USA observatories chain separately for polar region, auroral zone and middle latitudes beginning from 1950. The variation consists of an annual and half-yearly waves. main attention is paid to time variability of the annual wave phase in the auroral zone, that is connected with superposition of waves of western and eastern jets

  8. The variation of acute treatment costs of trauma in high-income countries

    Directory of Open Access Journals (Sweden)

    Willenberg Lynsey

    2012-08-01

    Full Text Available Abstract Background In order to assist health service planning, understanding factors that influence higher trauma treatment costs is essential. The majority of trauma costing research reports the cost of trauma from the perspective of the receiving hospital. There has been no comprehensive synthesis and little assessment of the drivers of cost variation, such as country, trauma, subgroups and methods. The aim of this review is to provide a synthesis of research reporting the trauma treatment costs and factors associated with higher treatment costs in high income countries. Methods A systematic search for articles relating to the cost of acute trauma care was performed and included studies reporting injury severity scores (ISS, per patient cost/charge estimates; and costing methods. Cost and charge values were indexed to 2011 cost equivalents and converted to US dollars using purchasing power parities. Results A total of twenty-seven studies were reviewed. Eighty-one percent of these studies were conducted in high income countries including USA, Australia, Europe and UK. Studies either reported a cost (74.1% or charge estimate (25.9% for the acute treatment of trauma. Across studies, the median per patient cost of acute trauma treatment was $22,448 (IQR: $11,819-$33,701. However, there was variability in costing methods used with 18% of studies providing comprehensive cost methods. Sixty-three percent of studies reported cost or charge items incorporated in their cost analysis and 52% reported items excluded in their analysis. In all publications reviewed, predictors of cost included Injury Severity Score (ISS, surgical intervention, hospital and intensive care, length of stay, polytrauma and age. Conclusion The acute treatment cost of trauma is higher than other disease groups. Research has been largely conducted in high income countries and variability exists in reporting costing methods as well as the actual costs. Patient populations studied

  9. The variation of acute treatment costs of trauma in high-income countries.

    Science.gov (United States)

    Willenberg, Lynsey; Curtis, Kate; Taylor, Colman; Jan, Stephen; Glass, Parisa; Myburgh, John

    2012-08-21

    In order to assist health service planning, understanding factors that influence higher trauma treatment costs is essential. The majority of trauma costing research reports the cost of trauma from the perspective of the receiving hospital. There has been no comprehensive synthesis and little assessment of the drivers of cost variation, such as country, trauma, subgroups and methods. The aim of this review is to provide a synthesis of research reporting the trauma treatment costs and factors associated with higher treatment costs in high income countries. A systematic search for articles relating to the cost of acute trauma care was performed and included studies reporting injury severity scores (ISS), per patient cost/charge estimates; and costing methods. Cost and charge values were indexed to 2011 cost equivalents and converted to US dollars using purchasing power parities. A total of twenty-seven studies were reviewed. Eighty-one percent of these studies were conducted in high income countries including USA, Australia, Europe and UK. Studies either reported a cost (74.1%) or charge estimate (25.9%) for the acute treatment of trauma. Across studies, the median per patient cost of acute trauma treatment was $22,448 (IQR: $11,819-$33,701). However, there was variability in costing methods used with 18% of studies providing comprehensive cost methods. Sixty-three percent of studies reported cost or charge items incorporated in their cost analysis and 52% reported items excluded in their analysis. In all publications reviewed, predictors of cost included Injury Severity Score (ISS), surgical intervention, hospital and intensive care, length of stay, polytrauma and age. The acute treatment cost of trauma is higher than other disease groups. Research has been largely conducted in high income countries and variability exists in reporting costing methods as well as the actual costs. Patient populations studied and the cost methods employed are the primary drivers for the

  10. Environmental and geographic variables are effective surrogates for genetic variation in conservation planning.

    Science.gov (United States)

    Hanson, Jeffrey O; Rhodes, Jonathan R; Riginos, Cynthia; Fuller, Richard A

    2017-11-28

    Protected areas buffer species from anthropogenic threats and provide places for the processes that generate and maintain biodiversity to continue. However, genetic variation, the raw material for evolution, is difficult to capture in conservation planning, not least because genetic data require considerable resources to obtain and analyze. Here we show that freely available environmental and geographic distance variables can be highly effective surrogates in conservation planning for representing adaptive and neutral intraspecific genetic variation. We obtained occurrence and genetic data from the IntraBioDiv project for 27 plant species collected over the European Alps using a gridded sampling scheme. For each species, we identified loci that were potentially under selection using outlier loci methods, and mapped their main gradients of adaptive and neutral genetic variation across the grid cells. We then used the cells as planning units to prioritize protected area acquisitions. First, we verified that the spatial patterns of environmental and geographic variation were correlated, respectively, with adaptive and neutral genetic variation. Second, we showed that these surrogates can predict the proportion of genetic variation secured in randomly generated solutions. Finally, we discovered that solutions based only on surrogate information secured substantial amounts of adaptive and neutral genetic variation. Our work paves the way for widespread integration of surrogates for genetic variation into conservation planning.

  11. Genetic variation among pelt sheep population using microsatellite ...

    African Journals Online (AJOL)

    Genetic variation in three Iranian pelt sheep breeds namely: Gray Shiraz, Zandi and Karakul were investigated using fifteen microsatellite loci. Genomic DNA was extracted from 360 blood samples by extraction kits and salting-out procedure with some modifications. The total number of alleles ranged from 6 to12 in loci.

  12. Reliable Detection of Herpes Simplex Virus Sequence Variation by High-Throughput Resequencing.

    Science.gov (United States)

    Morse, Alison M; Calabro, Kaitlyn R; Fear, Justin M; Bloom, David C; McIntyre, Lauren M

    2017-08-16

    High-throughput sequencing (HTS) has resulted in data for a number of herpes simplex virus (HSV) laboratory strains and clinical isolates. The knowledge of these sequences has been critical for investigating viral pathogenicity. However, the assembly of complete herpesviral genomes, including HSV, is complicated due to the existence of large repeat regions and arrays of smaller reiterated sequences that are commonly found in these genomes. In addition, the inherent genetic variation in populations of isolates for viruses and other microorganisms presents an additional challenge to many existing HTS sequence assembly pipelines. Here, we evaluate two approaches for the identification of genetic variants in HSV1 strains using Illumina short read sequencing data. The first, a reference-based approach, identifies variants from reads aligned to a reference sequence and the second, a de novo assembly approach, identifies variants from reads aligned to de novo assembled consensus sequences. Of critical importance for both approaches is the reduction in the number of low complexity regions through the construction of a non-redundant reference genome. We compared variants identified in the two methods. Our results indicate that approximately 85% of variants are identified regardless of the approach. The reference-based approach to variant discovery captures an additional 15% representing variants divergent from the HSV1 reference possibly due to viral passage. Reference-based approaches are significantly less labor-intensive and identify variants across the genome where de novo assembly-based approaches are limited to regions where contigs have been successfully assembled. In addition, regions of poor quality assembly can lead to false variant identification in de novo consensus sequences. For viruses with a well-assembled reference genome, a reference-based approach is recommended.

  13. Spatial and temporal variations in traffic-related particulate matter at New York City high schools

    Science.gov (United States)

    Patel, Molini M.; Chillrud, Steven N.; Correa, Juan C.; Feinberg, Marian; Hazi, Yair; Deepti, K. C.; Prakash, Swati; Ross, James M.; Levy, Diane; Kinney, Patrick L.

    Relatively little is known about exposures to traffic-related particulate matter at schools located in dense urban areas. The purpose of this study was to examine the influences of diesel traffic proximity and intensity on ambient concentrations of fine particulate matter (PM 2.5) and black carbon (BC), an indicator of diesel exhaust particles, at New York City (NYC) high schools. Outdoor PM 2.5 and BC were monitored continuously for 4-6 weeks at each of 3 NYC schools and 1 suburban school located 40 km upwind of the city. Traffic count data were obtained using an automated traffic counter or video camera. BC concentrations were 2-3 fold higher at urban schools compared with the suburban school, and among the 3 urban schools, BC concentrations were higher at schools located adjacent to highways. PM 2.5 concentrations were significantly higher at urban schools than at the suburban school, but concentrations did not vary significantly among urban schools. Both hourly average counts of trucks and buses and meteorological factors such as wind direction, wind speed, and humidity were significantly associated with hourly average ambient BC and PM 2.5 concentrations in multivariate regression models. An increase of 443 trucks/buses per hour was associated with a 0.62 μg/m 3 increase in hourly average BC at an NYC school located adjacent to a major interstate highway. Car traffic counts were not associated with BC. The results suggest that local diesel vehicle traffic may be important sources of airborne fine particles in dense urban areas and consequently may contribute to local variations in PM 2.5 concentrations. In urban areas with higher levels of diesel traffic, local, neighborhood-scale monitoring of pollutants such as BC, which compared to PM 2.5, is a more specific indicator of diesel exhaust particles, may more accurately represent population exposures.

  14. Rapid detection of SMARCB1 sequence variation using high resolution melting

    Directory of Open Access Journals (Sweden)

    Ashley David M

    2009-12-01

    Full Text Available Abstract Background Rhabdoid tumors are rare cancers of early childhood arising in the kidney, central nervous system and other organs. The majority are caused by somatic inactivating mutations or deletions affecting the tumor suppressor locus SMARCB1 [OMIM 601607]. Germ-line SMARCB1 inactivation has been reported in association with rhabdoid tumor, epitheloid sarcoma and familial schwannomatosis, underscoring the importance of accurate mutation screening to ascertain recurrence and transmission risks. We describe a rapid and sensitive diagnostic screening method, using high resolution melting (HRM, for detecting sequence variations in SMARCB1. Methods Amplicons, encompassing the nine coding exons of SMARCB1, flanking splice site sequences and the 5' and 3' UTR, were screened by both HRM and direct DNA sequencing to establish the reliability of HRM as a primary mutation screening tool. Reaction conditions were optimized with commercially available HRM mixes. Results The false negative rate for detecting sequence variants by HRM in our sample series was zero. Nine amplicons out of a total of 140 (6.4% showed variant melt profiles that were subsequently shown to be false positive. Overall nine distinct pathogenic SMARCB1 mutations were identified in a total of 19 possible rhabdoid tumors. Two tumors had two distinct mutations and two harbored SMARCB1 deletion. Other mutations were nonsense or frame-shifts. The detection sensitivity of the HRM screening method was influenced by both sequence context and specific nucleotide change and varied from 1: 4 to 1:1000 (variant to wild-type DNA. A novel method involving digital HRM, followed by re-sequencing, was used to confirm mutations in tumor specimens containing associated normal tissue. Conclusions This is the first report describing SMARCB1 mutation screening using HRM. HRM is a rapid, sensitive and inexpensive screening technology that is likely to be widely adopted in diagnostic laboratories to

  15. Rapid detection of SMARCB1 sequence variation using high resolution melting

    International Nuclear Information System (INIS)

    Dagar, Vinod; Chow, Chung-Wo; Ashley, David M; Algar, Elizabeth M

    2009-01-01

    Rhabdoid tumors are rare cancers of early childhood arising in the kidney, central nervous system and other organs. The majority are caused by somatic inactivating mutations or deletions affecting the tumor suppressor locus SMARCB1 [OMIM 601607]. Germ-line SMARCB1 inactivation has been reported in association with rhabdoid tumor, epitheloid sarcoma and familial schwannomatosis, underscoring the importance of accurate mutation screening to ascertain recurrence and transmission risks. We describe a rapid and sensitive diagnostic screening method, using high resolution melting (HRM), for detecting sequence variations in SMARCB1. Amplicons, encompassing the nine coding exons of SMARCB1, flanking splice site sequences and the 5' and 3' UTR, were screened by both HRM and direct DNA sequencing to establish the reliability of HRM as a primary mutation screening tool. Reaction conditions were optimized with commercially available HRM mixes. The false negative rate for detecting sequence variants by HRM in our sample series was zero. Nine amplicons out of a total of 140 (6.4%) showed variant melt profiles that were subsequently shown to be false positive. Overall nine distinct pathogenic SMARCB1 mutations were identified in a total of 19 possible rhabdoid tumors. Two tumors had two distinct mutations and two harbored SMARCB1 deletion. Other mutations were nonsense or frame-shifts. The detection sensitivity of the HRM screening method was influenced by both sequence context and specific nucleotide change and varied from 1: 4 to 1:1000 (variant to wild-type DNA). A novel method involving digital HRM, followed by re-sequencing, was used to confirm mutations in tumor specimens containing associated normal tissue. This is the first report describing SMARCB1 mutation screening using HRM. HRM is a rapid, sensitive and inexpensive screening technology that is likely to be widely adopted in diagnostic laboratories to facilitate whole gene mutation screening

  16. GWAS identifies four novel eosinophilic esophagitis loci

    NARCIS (Netherlands)

    Sleiman, Patrick M. A.; Wang, Mei-Lun; Cianferoni, Antonella; Aceves, Seema; Gonsalves, Nirmala; Nadeau, Kari; Bredenoord, Albert J.; Furuta, Glenn T.; Spergel, Jonathan M.; Hakonarson, Hakon

    2014-01-01

    Eosinophilic esophagitis (EoE) is an allergic disorder characterized by infiltration of the oesophagus with eosinophils. We had previously reported association of the TSLP/WDR36 locus with EoE. Here we report genome-wide significant associations at four additional loci; c11orf30 and STAT6, which

  17. Genetic Diversity of Three Spotted Seahorse, Hippocampus trimaculatus (Leach, 1814 in India Using Four Microsatellite Loci

    Directory of Open Access Journals (Sweden)

    Muthusamy THANGARAJ

    2012-11-01

    Full Text Available Seahorse populations are declining year by year not only in India but also throughout the world, because of over-fishing and increasing demand in Chinese market. The three spotted seahorse, Hippocampus trimaculatus is one of the dominant species and distributed all along the Indian coast. To study the genetic structure is very essential to conserve these species effectively. Hippocampus trimaculatus samples (n = 60/population were collected from Mullimunai in Palk Bay, Tuticorin in Gulf of Mannar and Vizhinjam in south Malabar in India as by-catch in small trawlnets. Microsatellites are being widely applied in animal genome mapping and phylogenetic analysis because of their co-dominant inheritance and high degree of polymorphism. The molecular polymorphism of microsatellite DNA has proved to be a potent tool in the analysis of several aspects of population genetics. In the present study, four microsatellite primers were used to investigate the genetic difference and structure of three selected populations of H. trimaculatus. The result showed the overall FST value (0.0989 of the microsatellite loci between Mullimunai and Vizhinjam was significantly different. The genetic distance between Mullimunai and Tuticorin was 0.183; between Tuticorin and Vizhinjam was 0.461; and Mullimunai and Vizhinjam was 0.837. There was no statistical evidence of recent severe bottlenecks in any of the three populations. Continuous monitoring of microsatellite variations within the populations of all the three locations was suggested to determine whether genetic variation within the populations is stabilized between year classes.

  18. Loci influencing blood pressure identified using a cardiovascular gene-centric array.

    Science.gov (United States)

    Ganesh, Santhi K; Tragante, Vinicius; Guo, Wei; Guo, Yiran; Lanktree, Matthew B; Smith, Erin N; Johnson, Toby; Castillo, Berta Almoguera; Barnard, John; Baumert, Jens; Chang, Yen-Pei Christy; Elbers, Clara C; Farrall, Martin; Fischer, Mary E; Franceschini, Nora; Gaunt, Tom R; Gho, Johannes M I H; Gieger, Christian; Gong, Yan; Isaacs, Aaron; Kleber, Marcus E; Mateo Leach, Irene; McDonough, Caitrin W; Meijs, Matthijs F L; Mellander, Olle; Molony, Cliona M; Nolte, Ilja M; Padmanabhan, Sandosh; Price, Tom S; Rajagopalan, Ramakrishnan; Shaffer, Jonathan; Shah, Sonia; Shen, Haiqing; Soranzo, Nicole; van der Most, Peter J; Van Iperen, Erik P A; Van Setten, Jessica; Van Setten, Jessic A; Vonk, Judith M; Zhang, Li; Beitelshees, Amber L; Berenson, Gerald S; Bhatt, Deepak L; Boer, Jolanda M A; Boerwinkle, Eric; Burkley, Ben; Burt, Amber; Chakravarti, Aravinda; Chen, Wei; Cooper-Dehoff, Rhonda M; Curtis, Sean P; Dreisbach, Albert; Duggan, David; Ehret, Georg B; Fabsitz, Richard R; Fornage, Myriam; Fox, Ervin; Furlong, Clement E; Gansevoort, Ron T; Hofker, Marten H; Hovingh, G Kees; Kirkland, Susan A; Kottke-Marchant, Kandice; Kutlar, Abdullah; Lacroix, Andrea Z; Langaee, Taimour Y; Li, Yun R; Lin, Honghuang; Liu, Kiang; Maiwald, Steffi; Malik, Rainer; Murugesan, Gurunathan; Newton-Cheh, Christopher; O'Connell, Jeffery R; Onland-Moret, N Charlotte; Ouwehand, Willem H; Palmas, Walter; Penninx, Brenda W; Pepine, Carl J; Pettinger, Mary; Polak, Joseph F; Ramachandran, Vasan S; Ranchalis, Jane; Redline, Susan; Ridker, Paul M; Rose, Lynda M; Scharnag, Hubert; Schork, Nicholas J; Shimbo, Daichi; Shuldiner, Alan R; Srinivasan, Sathanur R; Stolk, Ronald P; Taylor, Herman A; Thorand, Barbara; Trip, Mieke D; van Duijn, Cornelia M; Verschuren, W Monique; Wijmenga, Cisca; Winkelmann, Bernhard R; Wyatt, Sharon; Young, J Hunter; Boehm, Bernhard O; Caulfield, Mark J; Chasman, Daniel I; Davidson, Karina W; Doevendans, Pieter A; Fitzgerald, Garret A; Gums, John G; Hakonarson, Hakon; Hillege, Hans L; Illig, Thomas; Jarvik, Gail P; Johnson, Julie A; Kastelein, John J P; Koenig, Wolfgang; März, Winfried; Mitchell, Braxton D; Murray, Sarah S; Oldehinkel, Albertine J; Rader, Daniel J; Reilly, Muredach P; Reiner, Alex P; Schadt, Eric E; Silverstein, Roy L; Snieder, Harold; Stanton, Alice V; Uitterlinden, André G; van der Harst, Pim; van der Schouw, Yvonne T; Samani, Nilesh J; Johnson, Andrew D; Munroe, Patricia B; de Bakker, Paul I W; Zhu, Xiaofeng; Levy, Daniel; Keating, Brendan J; Asselbergs, Folkert W

    2013-04-15

    Blood pressure (BP) is a heritable determinant of risk for cardiovascular disease (CVD). To investigate genetic associations with systolic BP (SBP), diastolic BP (DBP), mean arterial pressure (MAP) and pulse pressure (PP), we genotyped ∼50 000 single-nucleotide polymorphisms (SNPs) that capture variation in ∼2100 candidate genes for cardiovascular phenotypes in 61 619 individuals of European ancestry from cohort studies in the USA and Europe. We identified novel associations between rs347591 and SBP (chromosome 3p25.3, in an intron of HRH1) and between rs2169137 and DBP (chromosome1q32.1 in an intron of MDM4) and between rs2014408 and SBP (chromosome 11p15 in an intron of SOX6), previously reported to be associated with MAP. We also confirmed 10 previously known loci associated with SBP, DBP, MAP or PP (ADRB1, ATP2B1, SH2B3/ATXN2, CSK, CYP17A1, FURIN, HFE, LSP1, MTHFR, SOX6) at array-wide significance (P < 2.4 × 10(-6)). We then replicated these associations in an independent set of 65 886 individuals of European ancestry. The findings from expression QTL (eQTL) analysis showed associations of SNPs in the MDM4 region with MDM4 expression. We did not find any evidence of association of the two novel SNPs in MDM4 and HRH1 with sequelae of high BP including coronary artery disease (CAD), left ventricular hypertrophy (LVH) or stroke. In summary, we identified two novel loci associated with BP and confirmed multiple previously reported associations. Our findings extend our understanding of genes involved in BP regulation, some of which may eventually provide new targets for therapeutic intervention.

  19. Signatures of selection in loci governing major colour patterns in Heliconius butterflies and related species

    Directory of Open Access Journals (Sweden)

    Joron Mathieu

    2010-11-01

    Full Text Available Abstract Background Protein-coding change is one possible genetic mechanism underlying the evolution of adaptive wing colour pattern variation in Heliconius butterflies. Here we determine whether 38 putative genes within two major Heliconius patterning loci, HmYb and HmB, show evidence of positive selection. Ratios of nonsynonymous to synonymous nucleotide changes (ω were used to test for selection, as a means of identifying candidate genes within each locus that control wing pattern. Results Preliminary analyses using 454 transcriptome and Bacterial Artificial Chromosome (BAC sequences from three Heliconius species highlighted a cluster of genes within each region showing relatively higher rates of sequence evolution. Other genes within the region appear to be highly constrained, and no ω estimates exceeded one. Three genes from each locus with the highest average pairwise ω values were amplified from additional Heliconius species and races. Two selected genes, fizzy-like (HmYb and DALR (HmB, were too divergent for amplification across species and were excluded from further analysis. Amongst the remaining genes, HM00021 and Kinesin possessed the highest background ω values within the HmYb and HmB loci, respectively. After accounting for recombination, these two genes both showed evidence of having codons with a signature of selection, although statistical support for this signal was not strong in any case. Conclusions Tests of selection reveal a cluster of candidate genes in each locus, suggesting that weak directional selection may be occurring within a small region of each locus, but coding changes alone are unlikely to explain the full range of wing pattern diversity. These analyses pinpoint many of the same genes believed to be involved in the control of colour patterning in Heliconius that have been identified through other studies implementing different research methods.

  20. Predicting spatial variations of tree species richness in tropical forests from high-resolution remote sensing.

    Science.gov (United States)

    Fricker, Geoffrey A; Wolf, Jeffrey A; Saatchi, Sassan S; Gillespie, Thomas W

    2015-10-01

    There is an increasing interest in identifying theories, empirical data sets, and remote-sensing metrics that can quantify tropical forest alpha diversity at a landscape scale. Quantifying patterns of tree species richness in the field is time consuming, especially in regions with over 100 tree species/ha. We examine species richness in a 50-ha plot in Barro Colorado Island in Panama and test if biophysical measurements of canopy reflectance from high-resolution satellite imagery and detailed vertical forest structure and topography from light detection and ranging (lidar) are associated with species richness across four tree size classes (>1, 1-10, >10, and >20 cm dbh) and three spatial scales (1, 0.25, and 0.04 ha). We use the 2010 tree inventory, including 204,757 individuals belonging to 301 species of freestanding woody plants or 166 ± 1.5 species/ha (mean ± SE), to compare with remote-sensing data. All remote-sensing metrics became less correlated with species richness as spatial resolution decreased from 1.0 ha to 0.04 ha and tree size increased from 1 cm to 20 cm dbh. When all stems with dbh > 1 cm in 1-ha plots were compared to remote-sensing metrics, standard deviation in canopy reflectance explained 13% of the variance in species richness. The standard deviations of canopy height and the topographic wetness index (TWI) derived from lidar were the best metrics to explain the spatial variance in species richness (15% and 24%, respectively). Using multiple regression models, we made predictions of species richness across Barro Colorado Island (BCI) at the 1-ha spatial scale for different tree size classes. We predicted variation in tree species richness among all plants (adjusted r² = 0.35) and trees with dbh > 10 cm (adjusted r² = 0.25). However, the best model results were for understory trees and shrubs (dbh 1-10 cm) (adjusted r² = 0.52) that comprise the majority of species richness in tropical forests. Our results indicate that high

  1. Discrimination of candidate subgenome-specific loci by linkage map construction with an S1 population of octoploid strawberry (Fragaria × ananassa).

    Science.gov (United States)

    Nagano, Soichiro; Shirasawa, Kenta; Hirakawa, Hideki; Maeda, Fumi; Ishikawa, Masami; Isobe, Sachiko N

    2017-05-12

    The strawberry, Fragaria × ananassa, is an allo-octoploid (2n = 8x = 56) and outcrossing species. Although it is the most widely consumed berry crop in the world, its complex genome structure has hindered its genetic and genomic analysis, and thus discrimination of subgenome-specific loci among the homoeologous chromosomes is needed. In the present study, we identified candidate subgenome-specific single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) loci, and constructed a linkage map using an S 1 mapping population of the cultivar 'Reikou' with an IStraw90 Axiom® SNP array and previously published SSR markers. The 'Reikou' linkage map consisted of 11,574 loci (11,002 SNPs and 572 SSR loci) spanning 2816.5 cM of 31 linkage groups. The 11,574 loci were located on 4738 unique positions (bin) on the linkage map. Of the mapped loci, 8999 (8588 SNPs and 411 SSR loci) showed a 1:2:1 segregation ratio of AA:AB:BB allele, which suggested the possibility of deriving loci from candidate subgenome-specific sequences. In addition, 2575 loci (2414 SNPs and 161 SSR loci) showed a 3:1 segregation of AB:BB allele, indicating they were derived from homoeologous genomic sequences. Comparative analysis of the homoeologous linkage groups revealed differences in genome structure among the subgenomes. Our results suggest that candidate subgenome-specific loci are randomly located across the genomes, and that there are small- to large-scale structural variations among the subgenomes. The mapped SNPs and SSR loci on the linkage map are expected to be seed points for the construction of pseudomolecules in the octoploid strawberry.

  2. Genetic analysis of 20 autosomal STR loci in the Miao ethnic group from Yunnan Province, Southwest China.

    Science.gov (United States)

    Zhang, Xiufeng; Hu, Liping; Du, Lei; Nie, Aiting; Rao, Min; Pang, Jing Bo; Xiran, Zeng; Nie, Shengjie

    2017-05-01

    The genetic polymorphisms of 20 autosomal short tandem repeat (STR) loci included in the PowerPlex ® 21 kit were evaluated from 748 unrelated healthy individuals of the Miao ethnic minority living in the Yunnan province in southwestern China. All of the loci reached Hardy-Weinberg equilibrium. These loci were examined to determine allele frequencies and forensic statistical parameters. The genetic relationship between the Miao population and other Chinese populations were also estimated. The combined discrimination power and probability of excluding paternity of the 20 STR loci were 0.999 999 999 999 999 999 999 991 26 and 0.999 999 975, respectively. The results suggested that the 20 STR loci were highly polymorphic, which makes them suitable for forensic personal identification and paternity testing. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. A HIGH ORDER SOLUTION OF THREE DIMENSIONAL TIME DEPENDENT NONLINEAR CONVECTIVE-DIFFUSIVE PROBLEM USING MODIFIED VARIATIONAL ITERATION METHOD

    Directory of Open Access Journals (Sweden)

    Pratibha Joshi

    2014-12-01

    Full Text Available In this paper, we have achieved high order solution of a three dimensional nonlinear diffusive-convective problem using modified variational iteration method. The efficiency of this approach has been shown by solving two examples. All computational work has been performed in MATHEMATICA.

  4. High-resolution records of non-dipole variations in the intensity of the Earth's magnetic field

    NARCIS (Netherlands)

    de Groot, L.V.

    2013-01-01

    Our understanding of the short-term behavior of the Earth’s magnetic field is currently mainly hampered by a lack of high-resolution records of geomagnetic intensity variations that are well distributed over the globe and cover the same timespan. Over the past decades many efforts have been made to

  5. Development of the 16 X-STR loci typing system and genetic analysis in a Shanghai Han population from China.

    Science.gov (United States)

    Sun, Kuan; Zhao, Shumin; Tian, Huaizhou; Zhang, Suhua; Li, Chengtao

    2013-11-01

    This study developed a new multiplex PCR system that simultaneously amplifies 16 X-STR loci in the same PCR reaction, and the polymorphism and mutation rates of these 16 X-STR loci were explored in a Shanghai Han population from China. These loci included DXS10134, DXS10159, DXS6789, DXS6795, DXS6800, DXS6803, DXS6807, DXS6810, DXS7132, DXS7424, DXS8378, DXS9902, GATA165B12, GATA172D05, GATA31E08, and HPRTB. Samples from 591 unrelated individuals (293 males and 298 females) and 400 two-generation families were successfully analyzed using this multiplex system. Allele frequencies and mutation rates of the 16 loci were investigated, with the comparison of allele frequency distributions among different populations performed. Polymorphism information contents of these loci were all >0.6440 except the locus DXS6800 (0.4706). Nine cases of mutations were detected in the 16 loci from the investigation of 9232 meioses. Pairwise comparisons of allele frequency distributions showed significant differences for most loci among populations from different countries and ethnic groups but not among the Han population living in other areas of China. These results suggest that the 16 X-STR loci system provides highly informative polymorphic data for paternity testing and forensic identification in the Han population in Shanghai, China, as a complementary tool. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Isozyme variation in wild and cultivated pineapple

    Science.gov (United States)

    Isozyme variation was studied in 161 accessions of pineapple including four species of Ananas and one of Pseudananas. Six enzyme systems (ADH, GPI, PGM, SKDH, TPI, UGPP) involving seven putative loci revealed 35 electromorphs . Considerable variation exists within and between species of Ananas. Sixt...

  7. Quantitative Trait Loci Analysis of Allelopathy in Rice

    DEFF Research Database (Denmark)

    Jensen, L B; Courtois, B; Olofsdotter, M

    2008-01-01

    The allelopathic potential of rice (Oryza sativa L.) against Echinochloa crus-galli (L.) Beauv. was investigated under both laboratory and greenhouse conditions. A population of 150 recombinant inbred lines (RILs) was derived through single-seed descent from a cross between the indica cultivar AC...... the population phenotype was normally distributed. Two quantitative trait loci (QTLs) were located on chromosomes 4 and 7, explaining 20% of the phenotypic variation. A second relay seeding experiment was set up, this time including charcoal in the perlite. This screening showed that the allelopathic rice...... varieties did not have any effect on the weed species when grown with charcoal, the charcoal reversing the effect of any potential allelochemicals exuded from the rice roots. The second phenotypic experiment was conducted under greenhouse conditions in pots. Thirteen QTLs were detected for four different...

  8. Discovery of new risk loci for IgA nephropathy implicates genes involved in immunity against intestinal pathogens

    Science.gov (United States)

    Kiryluk, Krzysztof; Li, Yifu; Scolari, Francesco; Sanna-Cherchi, Simone; Choi, Murim; Verbitsky, Miguel; Fasel, David; Lata, Sneh; Prakash, Sindhuri; Shapiro, Samantha; Fischman, Clara; Snyder, Holly J.; Appel, Gerald; Izzi, Claudia; Viola, Battista Fabio; Dallera, Nadia; Vecchio, Lucia Del; Barlassina, Cristina; Salvi, Erika; Bertinetto, Francesca Eleonora; Amoroso, Antonio; Savoldi, Silvana; Rocchietti, Marcella; Amore, Alessandro; Peruzzi, Licia; Coppo, Rosanna; Salvadori, Maurizio; Ravani, Pietro; Magistroni, Riccardo; Ghiggeri, Gian Marco; Caridi, Gianluca; Bodria, Monica; Lugani, Francesca; Allegri, Landino; Delsante, Marco; Maiorana, Mariarosa; Magnano, Andrea; Frasca, Giovanni; Boer, Emanuela; Boscutti, Giuliano; Ponticelli, Claudio; Mignani, Renzo; Marcantoni, Carmelita; Di Landro, Domenico; Santoro, Domenico; Pani, Antonello; Polci, Rosaria; Feriozzi, Sandro; Chicca, Silvana; Galliani, Marco; Gigante, Maddalena; Gesualdo, Loreto; Zamboli, Pasquale; Maixnerová, Dita; Tesar, Vladimir; Eitner, Frank; Rauen, Thomas; Floege, Jürgen; Kovacs, Tibor; Nagy, Judit; Mucha, Krzysztof; Pączek, Leszek; Zaniew, Marcin; Mizerska-Wasiak, Małgorzata; Roszkowska-Blaim, Maria; Pawlaczyk, Krzysztof; Gale, Daniel; Barratt, Jonathan; Thibaudin, Lise; Berthoux, Francois; Canaud, Guillaume; Boland, Anne; Metzger, Marie; Panzer, Ulf; Suzuki, Hitoshi; Goto, Shin; Narita, Ichiei; Caliskan, Yasar; Xie, Jingyuan; Hou, Ping; Chen, Nan; Zhang, Hong; Wyatt, Robert J.; Novak, Jan; Julian, Bruce A.; Feehally, John; Stengel, Benedicte; Cusi, Daniele; Lifton, Richard P.; Gharavi, Ali G.

    2014-01-01

    We performed a genome-wide association study (GWAS) of IgA nephropathy (IgAN), the most common form of glomerulonephritis, with discovery and follow-up in 20,612 individuals of European and East Asian ancestry. We identified six novel genome-wide significant associations, four in ITGAM-ITGAX, VAV3 and CARD9 and two new independent signals at HLA-DQB1 and DEFA. We replicated the nine previously reported signals, including known SNPs in the HLA-DQB1 and DEFA loci. The cumulative burden of risk alleles is strongly associated with age at disease onset. Most loci are either directly associated with risk of inflammatory bowel disease (IBD) or maintenance of the intestinal epithelial barrier and response to mucosal pathogens. The geo-spatial distribution of risk alleles is highly suggestive of multi-locus adaptation and the genetic risk correlates strongly with variation in local pathogens, particularly helminth diversity, suggesting a possible role for host-intestinal pathogen interactions in shaping the genetic landscape of IgAN. PMID:25305756

  9. Quantitative trait loci mapping of heat tolerance in broccoli (Brassica oleracea var. italica) using genotyping-by-sequencing.

    Science.gov (United States)

    Branham, Sandra E; Stansell, Zachary J; Couillard, David M; Farnham, Mark W

    2017-03-01

    Five quantitative trait loci and one epistatic interaction were associated with heat tolerance in a doubled haploid population of broccoli evaluated in three summer field trials. Predicted rising global temperatures due to climate change have generated a demand for crops that are resistant to yield and quality losses from heat stress. Broccoli (Brassica oleracea var. italica) is a cool weather crop with high temperatures during production decreasing both head quality and yield. Breeding for heat tolerance in broccoli has potential to both expand viable production areas and extend the growing season but breeding efficiency is constrained by limited genetic information. A doubled haploid (DH) broccoli population segregating for heat tolerance was evaluated for head quality in three summer fields in Charleston, SC, USA. Multiple quantitative trait loci (QTL) mapping of 1,423 single nucleotide polymorphisms developed through genotyping-by-sequencing identified five QTL and one positive epistatic interaction that explained 62.1% of variation in heat tolerance. The QTL identified here can be used to develop markers for marker-assisted selection and to increase our understanding of the molecular mechanisms underlying plant response to heat stress.

  10. Balancing selection and heterogeneity across the classical human leukocyte antigen loci: a meta-analytic review of 497 population studies.

    Science.gov (United States)

    Solberg, Owen D; Mack, Steven J; Lancaster, Alex K; Single, Richard M; Tsai, Yingssu; Sanchez-Mazas, Alicia; Thomson, Glenys

    2008-07-01

    This paper presents a meta-analysis of high-resolution human leukocyte antigen (HLA) allele frequency data describing 497 population samples. Most of the datasets were compiled from studies published in eight journals from 1990 to 2007; additional datasets came from the International Histocompatibility Workshops and from the AlleleFrequencies.net database. In all, these data represent approximately 66,800 individuals from throughout the world, providing an opportunity to observe trends that may not have been evident at the time the data were originally analyzed, especially with regard to the relative importance of balancing selection among the HLA loci. Population genetic measures of allele frequency distributions were summarized across populations by locus and geographic region. A role for balancing selection maintaining much of HLA variation was confirmed. Further, the breadth of this meta-analysis allowed the ranking of the HLA loci, with DQA1 and HLA-C showing the strongest balancing selection and DPB1 being compatible with neutrality. Comparisons of the allelic spectra reported by studies since 1990 indicate that most of the HLA alleles identified since 2000 are very-low-frequency alleles. The literature-based allele-count data, as well as maps summarizing the geographic distributions for each allele, are available online.

  11. Genome-Wide Characterization of Simple Sequence Repeat (SSR) Loci in Chinese Jujube and Jujube SSR Primer Transferability

    Science.gov (United States)

    Xiao, Jing; Zhao, Jin; Liu, Mengjun; Liu, Ping; Dai, Li; Zhao, Zhihui

    2015-01-01

    Chinese jujube (Ziziphus jujuba), an economically important species in the Rhamnaceae family, is a popular fruit tree in Asia. Here, we surveyed and characterized simple sequence repeats (SSRs) in the jujube genome. A total of 436,676 SSR loci were identified, with an average distance of 0.93 Kb between the loci. A large proportion of the SSRs included mononucleotide, dinucleotide and trinucleotide repeat motifs, which accounted for 64.87%, 24.40%, and 8.74% of all repeats, respectively. Among the mononucleotide repeats, A/T was the most common, whereas AT/TA was the most common dinucleotide repeat. A total of 30,565 primer pairs were successfully designed and screened using a series of criteria. Moreover, 725 of 1,000 randomly selected primer pairs were effective among 6 cultivars, and 511 of these primer pairs were polymorphic. Sequencing the amplicons of two SSRs across three jujube cultivars revealed variations in the repeats. The transferability of jujube SSR primers proved that 35/64 SSRs could be transferred across family boundary. Using jujube SSR primers, clustering analysis results from 15 species were highly consistent with the Angiosperm Phylogeny Group (APGIII) System. The genome-wide characterization of SSRs in Chinese jujube is very valuable for whole-genome characterization and marker-assisted selection in jujube breeding. In addition, the transferability of jujube SSR primers could provide a solid foundation for their further utilization. PMID:26000739

  12. Identification of Multiple Loci Associated with Social Parasitism in Honeybees.

    Science.gov (United States)

    Wallberg, Andreas; Pirk, Christian W; Allsopp, Mike H; Webster, Matthew T

    2016-06-01

    In colonies of the honeybee Apis mellifera, the queen is usually the only reproductive female, which produces new females (queens and workers) by laying fertilized eggs. However, in one subspecies of A. mellifera, known as the Cape bee (A. m. capensis), worker bees reproduce asexually by thelytoky, an abnormal form of meiosis where two daughter nucleii fuse to form single diploid eggs, which develop into females without being fertilized. The Cape bee also exhibits a suite of phenotypes that facilitate social parasitism whereby workers lay such eggs in foreign colonies so their offspring can exploit their resources. The genetic basis of this switch to social parasitism in the Cape bee is unknown. To address this, we compared genome variation in a sample of Cape bees with other African populations. We find genetic divergence between these populations to be very low on average but identify several regions of the genome with extreme differentiation. The regions are strongly enriched for signals of selection in Cape bees, indicating that increased levels of positive selection have produced the unique set of derived phenotypic traits in this subspecies. Genetic variation within these regions allows unambiguous genetic identification of Cape bees and likely underlies the genetic basis of social parasitism. The candidate loci include genes involved in ecdysteroid signaling and juvenile hormone and dopamine biosynthesis, which may regulate worker ovary activation and others whose products localize at the centrosome and are implicated in chromosomal segregation during meiosis. Functional analysis of these loci will yield insights into the processes of reproduction and chemical signaling in both parasitic and non-parasitic populations and advance understanding of the process of normal and atypical meiosis.

  13. Identification of Multiple Loci Associated with Social Parasitism in Honeybees.

    Directory of Open Access Journals (Sweden)

    Andreas Wallberg

    2016-06-01

    Full Text Available In colonies of the honeybee Apis mellifera, the queen is usually the only reproductive female, which produces new females (queens and workers by laying fertilized eggs. However, in one subspecies of A. mellifera, known as the Cape bee (A. m. capensis, worker bees reproduce asexually by thelytoky, an abnormal form of meiosis where two daughter nucleii fuse to form single diploid eggs, which develop into females without being fertilized. The Cape bee also exhibits a suite of phenotypes that facilitate social parasitism whereby workers lay such eggs in foreign colonies so their offspring can exploit their resources. The genetic basis of this switch to social parasitism in the Cape bee is unknown. To address this, we compared genome variation in a sample of Cape bees with other African populations. We find genetic divergence between these populations to be very low on average but identify several regions of the genome with extreme differentiation. The regions are strongly enriched for signals of selection in Cape bees, indicating that increased levels of positive selection have produced the unique set of derived phenotypic traits in this subspecies. Genetic variation within these regions allows unambiguous genetic identification of Cape bees and likely underlies the genetic basis of social parasitism. The candidate loci include genes involved in ecdysteroid signaling and juvenile hormone and dopamine biosynthesis, which may regulate worker ovary activation and others whose products localize at the centrosome and are implicated in chromosomal segregation during meiosis. Functional analysis of these loci will yield insights into the processes of reproduction and chemical signaling in both parasitic and non-parasitic populations and advance understanding of the process of normal and atypical meiosis.

  14. An Updated and Comprehensive Meta-Analysis of Association Between Seven Hot Loci Polymorphisms from Eight GWAS and Glioma Risk.

    Science.gov (United States)

    Wu, Qiang; Peng, Yanyan; Zhao, Xiaotao

    2016-09-01

    Eight genome-wide association studies (GWASs) found that seven loci (rs2736100, rs4295627, rs4977756, rs498872, rs11979158, rs2252586, rs6010620) polymorphisms could elevate the risk of glioma, one of the most common types of primary brain cancer in adults. However, the replication studies about these seven loci obtained inconsistent results. In order to derive a more accurate estimation about the relationship between the selected single-nucleotide polymorphism (SNP) and susceptibility to glioma, we conducted a meta-analysis containing all eligible published case control studies to evaluate the association. An overall literature search was conducted using the database of PubMed, Science Direct, China national knowledge infrastructure (CNKI), and Embase. Seventeen articles with 25 studies were included in the meta-analysis. Glioma risk (odds ratio, OR; 95 % confidential interval, 95 %CI) was estimated with the random-effect model or the fixed-effects model. STATA 12.0 was applied to analyze all statistical data. Results showed that seven hot loci were all associated with increased risk of glioma (rs2736100, OR = 1.28, 95 %CI = 1.23-1.32; rs4295627, OR = 1.34, 95 %CI = 1.21-1.47; rs4977756, OR = 1.24, 95 %CI = 1.20-1.28; rs498872, OR = 1.24, 95 %CI = 1.15-1.33; rs6010620, OR = 1.29, 95 %CI = 1.24-1.35; rs11979158: OR = 1.18, 95 %CI = 1.10-1.25; rs2252586: OR = 1.18, 95 %CI = 1.10-1.25). Additionally, subgroup analysis by stages of glioma found that variation of rs11979158 had stronger relationship with high-grade (OR = 1.32, 95 %CI = 1.19-1.45) than low-grade glioma (OR = 1.12, 95 % CI = 1.03-1.21). Similarly, stratified analysis of rs2252586 by stages revealed the similar trend, with OR of 1.26 (95 %CI = 1.17-1.35) in high-grade glioma and OR of 1.15 (95 %CI = 1.08-1.22) in low-grade glioma. In summary, the present study showed that mutations of the seven loci could elevate

  15. Biofouling likely serves as a major mode of dispersal for the polychaete tubeworm Hydroides elegans as inferred from microsatellite loci.

    Science.gov (United States)

    Pettengill, J B; Wendt, D E; Schug, M D; Hadfield, M G

    2007-01-01

    The polychaete tubeworm Hydroides elegans (Haswell) is a biofouling species with relatively limited larval dispersal. Four highly polymorphic microsatellite loci were used to make inferences about the migration and global population structure of 137 individuals from seven sub-populations located in the Atlantic, Pacific, and Indian Oceans and in the Mediterranean Sea. The results of the genetic analyses suggest minimal population sub-structure (F(st) = 0.09). Estimates of pairwise F(st) and migration rates using the coalescent-based method of MIGRATE suggest that there is little genetic differentiation between certain populations. Variation in relatedness among pairs of populations is consistent with a suite of local and global factors. The most likely explanation for close genetic relatedness among certain populations over such vast distances is the regular and consistent transport of adults and larvae on the hulls and in the ballast water of ships, respectively.

  16. Natural epigenetic variation within and among six subspecies of the house sparrow, Passer domesticus.

    Science.gov (United States)

    Riyahi, Sepand; Vilatersana, Roser; Schrey, Aaron W; Ghorbani Node, Hassan; Aliabadian, Mansour; Senar, Juan Carlos

    2017-11-01

    Epigenetic modifications can respond rapidly to environmental changes and can shape phenotypic variation in accordance with environmental stimuli. One of the most studied epigenetic marks is DNA methylation. In the present study, we used the methylation-sensitive amplified polymorphism (MSAP) technique to investigate the natural variation in DNA methylation within and among subspecies of the house sparrow, Passer domesticus We focused on five subspecies from the Middle East because they show great variation in many ecological traits and because this region is the probable origin for the house sparrow's commensal relationship with humans. We analysed house sparrows from Spain as an outgroup. The level of variation in DNA methylation was similar among the five house sparrow subspecies from the Middle East despite high phenotypic and environmental variation, but the non-commensal subspecies was differentiated from the other four (commensal) Middle Eastern subspecies. Further, the European subspecies was differentiated from all other subspecies in DNA methylation. Our results indicate that variation in DNA methylation does not strictly follow subspecies designations. We detected a correlation between methylation level and some morphological traits, such as standardized bill length, and we suggest that part of the high morphological variation in the native populations of the house sparrow is influenced by differentially methylated regions in specific loci throughout the genome. We also detected 10 differentially methylated loci among subspecies and three loci that differentiated between commensal or non-commensal status. Therefore, the MSAP technique detected larger scale differences among the European and non-commensal subspecies, but did not detect finer scale differences among the other Middle Eastern subspecies. © 2017. Published by The Company of Biologists Ltd.

  17. Resolving the Complex Genetic Basis of Phenotypic Variation and Variability of Cellular Growth.

    Science.gov (United States)

    Ziv, Naomi; Shuster, Bentley M; Siegal, Mark L; Gresham, David

    2017-07-01

    In all organisms, the majority of traits vary continuously between individuals. Explaining the genetic basis of quantitative trait variation requires comprehensively accounting for genetic and nongenetic factors as well as their interactions. The growth of microbial cells can be characterized by a lag duration, an exponential growth phase, and a stationary phase. Parameters that characterize these growth phases can vary among genotypes (phenotypic variation), environmental conditions (phenotypic plasticity), and among isogenic cells in a given environment (phenotypic variability). We used a high-throughput microscopy assay to map genetic loci determining variation in lag duration and exponential growth rate in growth rate-limiting and nonlimiting glucose concentrations, using segregants from a cross of two natural isolates of the budding yeast, Saccharomyces cerevisiae We find that some quantitative trait loci (QTL) are common between traits and environments whereas some are unique, exhibiting gene-by-environment interactions. Furthermore, whereas variation in the central tendency of growth rate or lag duration is explained by many additive loci, differences in phenotypic variability are primarily the result of genetic interactions. We used bulk segregant mapping to increase QTL resolution by performing whole-genome sequencing of complex mixtures of an advanced intercross mapping population grown in selective conditions using glucose-limited chemostats. We find that sequence variation in the high-affinity glucose transporter HXT7 contributes to variation in growth rate and lag duration. Allele replacements of the entire locus, as well as of a single polymorphic amino acid, reveal that the effect of variation in HXT7 depends on genetic, and allelic, background. Amplifications of HXT7 are frequently selected in experimental evolution in glucose-limited environments, but we find that HXT7 amplifications result in antagonistic pleiotropy that is absent in naturally

  18. Epigenetic variation contributes to environmental adaptation of Arabidopsis thaliana

    NARCIS (Netherlands)

    Kooke, R.; Keurentjes, J.J.B.

    2015-01-01

    Epigenetic variation is frequently observed in plants and direct relationships between differences in DNA methylation and phenotypic responses to changing environments have often been described. The identification of contributing genetic loci, however, was until recently hampered by the lack of

  19. Radiation-induced mutation at minisatellite loci

    International Nuclear Information System (INIS)

    Dubrova, Y.E.; Nesterov, V.N.; Krouchinsky, N.G.

    1997-01-01

    We are studying the radiation-induced increase of mutation rate in minisatellite loci in mice and humans. Minisatellite mutations were scored by multilocus DNA fingerprint analysis in the progeny of γ-irradiated and non-irradiated mice. The frequency of mutation in offspring of irradiated males was 1.7 higher that in the control group. Germline mutation at human minisatellite loci was studied among children born in heavily polluted areas of the Mogilev district of Belarus after the Chernobyl accident and in a control population. The frequency of mutation assayed both by DNA fingerprinting and by eight single locus probes was found to be two times higher in the exposed families than in the control group. Furthermore, mutation rate was correlated with the parental radiation dose for chronic exposure 137 Cs, consistent with radiation-induction of germline mutation. The potential use of minisatellites in monitoring germline mutation in humans will be discussed

  20. High spatial variation in terrestrial arthropod species diversity and composition near the Greenland ice cap

    DEFF Research Database (Denmark)

    Hansen, Rikke Reisner; Hansen, Oskar Liset Pryds; Bowden, Joseph James

    2016-01-01

    Arthropods form a major part of the terrestrial species diversity in the Arctic, and are particularly sensitive to temporal changes in the abiotic environment. It is assumed that most Arctic arthropods are habitat generalists and that their diversity patterns exhibit low spatial variation....... The empirical basis for this assumption, however, is weak. We examine the degree of spatial variation in species diversity and assemblage structure among five habitat types at two sites of similar abiotic conditions and plant species composition in southwest Greenland, using standardized field collection...... methods for spiders, beetles and butterflies. We employed non-metric multidimensional scaling, species richness estimation, community dissimilarity and indicator species analysis to test for local (within site)- and regional (between site)-scale differences in arthropod communities. To identify specific...

  1. SU-E-T-636: Investigation of Dose Variation in High Dose Radiation Brachytherapy

    Energy Technology Data Exchange (ETDEWEB)

    Hyvarinen, M; Leventouri, T; Casey, C; Long, S [Florida Atlantic University, Boca Raton, FL (United States); Pella, S [South Florida Radiation Oncology and Florida Atlantic University, Boca Raton, FL (United States); Dumitru, N [University of Bucharest, Bucharest-magurele, Ilfov (Romania); Herrera, R [Louis Stokes VA Medical Center, Cleveland, OH (United States)

    2014-06-15

    Purpose: The purpose of this study is to revise most of the HDR types of treatments with their applicators and their localization challenges. Since every millimeter of misplacement counts the study will look into the necessity of increasing the immobilization for several types of applicators Methods: The study took over 136 plans generated by the treatment planning system (TPS) looking into the applicator's placement in regard to the organs at risk (OR) and simulated the three possible displacements at the hottest dose point on the critical organ for several accessories to evaluate the variation of the delivered dose at the point due to the displacement. Results: Significant dose variation was obtained for the Contura, Savi, MLM and Prostate applicators. Conclusion: This study data indicates that an improvement of the immobilization devices for HDR is absolutely necessary. Better applicator fixation devices are required too. Developing new immobilization devices for all the applicators is recommended. Florida Atlantic University may provide Travel reimbursements.

  2. The study of height variation on outdoor ventilation for Singapore's high-rise residential housing estates

    OpenAIRE

    Rou Xuan Lee; Steve Kardinal Jusuf; Nyuk Hien Wong

    2015-01-01

    This article is concerned with external ventilation levels within a multi-story Housing and Development Board (HDB) residential estate, focusing toward a deeper understanding of wind flow with respect to different levels of height variation (HV). This study analyzed through parametric study, using numerical simulations with the realizable k – ε turbulence model, the various scenarios of HV within a typical residential HDB estate or precinct. It is found that external wind flow within the prec...

  3. Inferring Variation in Copy Number Using High Throughput Sequencing Data in R.

    Science.gov (United States)

    Knaus, Brian J; Grünwald, Niklaus J

    2018-01-01

    Inference of copy number variation presents a technical challenge because variant callers typically require the copy number of a genome or genomic region to be known a priori . Here we present a method to infer copy number that uses variant call format (VCF) data as input and is implemented in the R package vcfR . This method is based on the relative frequency of each allele (in both genic and non-genic regions) sequenced at heterozygous positions throughout a genome. These heterozygous positions are summarized by using arbitrarily sized windows of heterozygous positions, binning the allele frequencies, and selecting the bin with the greatest abundance of positions. This provides a non-parametric summary of the frequency that alleles were sequenced at. The method is applicable to organisms that have reference genomes that consist of full chromosomes or sub-chromosomal contigs. In contrast to other software designed to detect copy number variation, our method does not rely on an assumption of base ploidy, but instead infers it. We validated these approaches with the model system of Saccharomyces cerevisiae and applied it to the oomycete Phytophthora infestans , both known to vary in copy number. This functionality has been incorporated into the current release of the R package vcfR to provide modular and flexible methods to investigate copy number variation in genomic projects.

  4. Novel genetic loci associated with hippocampal volume

    OpenAIRE

    Hibar, Derrek P.; Adams, Hieab H. H.; Jahanshad, Neda; Chauhan, Ganesh; Stein, Jason L.; Hofer, Edith; Renteria, Miguel E.; Bis, Joshua C.; Arias-Vasquez, Alejandro; Ikram, M. Kamran; Desrivieres, Sylvane; Vernooij, Meike W.; Abramovic, Lucija; Alhusaini, Saud; Amin, Najaf

    2017-01-01

    International audience; The hippocampal formation is a brain structure integrally involved in episodic memory, spatial navigation, cognition and stress responsiveness. Structural abnormalities in hippocampal volume and shape are found in several common neuropsychiatric disorders. To identify the genetic underpinnings of hippocampal structure here we perform a genome-wide association study (GWAS) of 33,536 individuals and discover six independent loci significantly associated with hippocampal ...

  5. The signature of positive selection at randomly chosen loci.

    Science.gov (United States)

    Przeworski, Molly

    2002-03-01

    In Drosophila and humans, there are accumulating examples of loci with a significant excess of high-frequency-derived alleles or high levels of linkage disequilibrium, relative to a neutral model of a random-mating population of constant size. These are features expected after a recent selective sweep. Their prevalence suggests that positive directional selection may be widespread in both species. However, as I show here, these features do not persist long after the sweep ends: The high-frequency alleles drift to fixation and no longer contribute to polymorphism, while linkage disequilibrium is broken down by recombination. As a result, loci chosen without independent evidence of recent selection are not expected to exhibit either of these features, even if they have been affected by numerous sweeps in their genealogical history. How then can we explain the patterns in the data? One possibility is population structure, with unequal sampling from different subpopulations. Alternatively, positive selection may not operate as is commonly modeled. In particular, the rate of fixation of advantageous mutations may have increased in the recent past.

  6. Genetic diversity of Pinus halepensis Mill. populations detected by RAPD loci

    OpenAIRE

    Gómez , Aránzazu; Alía , Ricardo; Bueno , María

    2001-01-01

    International audience; Genetic diversity of Pinus halepensis Mill. was analysed in nine populations (six Spanish populations and one each from Tunisia, France and Greece). Twenty four RAPD loci were amplified with 60 megagametophyte DNA samples from each population. Populations' contribution to Nei gene diversity and to allelic richness were calculated. Results showed higher within population genetic variation but also a $G_{{\\rm ST}} = 13.6\\%$ higher than those detected in previous studies ...

  7. The 4.8 hour variation of Cygnus X-3 at high X-ray energies

    International Nuclear Information System (INIS)

    Pietsch, W.; Kendziorra, E.; Staubert, R.; Trumper, J.

    1976-01-01

    During a balloon observation of Cygnus X-3 on 1975 February 20, an intensity variation has been found which is in phase with the low-energy X-ray 4.8 hour sinusoidal light curve. The measured relative amplitude in the range 32--64 keV is 0.37 (+0.31, -0.29). Compared with the results at lower energies there is no indication for an energy dependence of the relative amplitude up to 64 keV. The encountered low-intensity source spectrum is compared with previous measurements

  8. Identification of High-Variation Fields based on Open Satellite Imagery

    DEFF Research Database (Denmark)

    Jeppesen, Jacob Høxbroe; Jacobsen, Rune Hylsberg; Nyholm Jørgensen, Rasmus

    2017-01-01

    . The categorization is based on vegetation indices derived from Sentinel-2 satellite imagery. A case study on 7678 winter wheat fields is presented, which employs open data and open source software to analyze the satellite imagery. Furthermore, the method can be automated to deliver categorizations at every update......This paper proposes a simple method for categorizing fields on a regional level, with respect to intra-field variations. It aims to identify fields where the potential benefits of applying precision agricultural practices are highest from an economic and environmental perspective...

  9. Genetic structure and gene flow among Komodo dragon populations inferred by microsatellite loci analysis.

    Science.gov (United States)

    Ciofi, C; Bruford, M W

    1999-12-01

    A general concern for the conservation of endangered species is the maintenance of genetic variation within populations, particularly when they become isolated and reduced in size. Estimates of gene flow and effective population size are therefore important for any conservation initiative directed to the long-term persistence of a species in its natural habitat. In the present study, 10 microsatellite loci were used to assess the level of genetic variability among populations of the Komodo dragon Varanus komodoensis. Effective population size was calculated and gene flow estimates were compared with palaeogeographic data in order to assess the degree of vulnerability of four island populations. Rinca and Flores, currently separated by an isthmus of about 200 m, retained a high level of genetic diversity and showed a high degree of genetic similarity, with gene flow values close to one migrant per generation. The island of Komodo showed by far the highest levels of genetic divergence, and its allelic distinctiveness was considered of great importance in the maintenance of genetic variability within the species. A lack of distinct alleles and low levels of gene flow and genetic variability were found for the small population of Gili Motang island, which was identified as vulnerable to stochastic threats. Our results are potentially important for both the short- and long-term management of the Komodo dragon, and are critical in view of future re-introduction or augmentation in areas where the species is now extinct or depleted.

  10. A meta-analysis of thyroid-related traits reveals novel loci and gender-specific differences in the regulation of thyroid function.

    Directory of Open Access Journals (Sweden)

    Eleonora Porcu

    Full Text Available Thyroid hormone is essential for normal metabolism and development, and overt abnormalities in thyroid function lead to common endocrine disorders affecting approximately 10% of individuals over their life span. In addition, even mild alterations in thyroid function are associated with weight changes, atrial fibrillation, osteoporosis, and psychiatric disorders. To identify novel variants underlying thyroid function, we performed a large meta-analysis of genome-wide association studies for serum levels of the highly heritable thyroid function markers TSH and FT4, in up to 26,420 and 17,520 euthyroid subjects, respectively. Here we report 26 independent associations, including several novel loci for TSH (PDE10A, VEGFA, IGFBP5, NFIA, SOX9, PRDM11, FGF7, INSR, ABO, MIR1179, NRG1, MBIP, ITPK1, SASH1, GLIS3 and FT4 (LHX3, FOXE1, AADAT, NETO1/FBXO15, LPCAT2/CAPNS2. Notably, only limited overlap was detected between TSH and FT4 associated signals, in spite of the feedback regulation of their circulating levels by the hypothalamic-pituitary-thyroid axis. Five of the reported loci (PDE8B, PDE10A, MAF/LOC440389, NETO1/FBXO15, and LPCAT2/CAPNS2 show strong gender-specific differences, which offer clues for the known sexual dimorphism in thyroid function and related pathologies. Importantly, the TSH-associated loci contribute not only to variation within the normal range, but also to TSH values outside the reference range, suggesting that they may be involved in thyroid dysfunction. Overall, our findings explain, respectively, 5.64% and 2.30% of total TSH and FT4 trait variance, and they improve the current knowledge of the regulation of hypothalamic-pituitary-thyroid axis function and the consequences of genetic variation for hypo- or hyperthyroidism.

  11. A Meta-Analysis of Thyroid-Related Traits Reveals Novel Loci and Gender-Specific Differences in the Regulation of Thyroid Function

    Science.gov (United States)

    Volpato, Claudia B.; Wilson, Scott G.; Cappola, Anne R.; Bos, Steffan D.; Deelen, Joris; den Heijer, Martin; Freathy, Rachel M.; Lahti, Jari; Liu, Chunyu; Lopez, Lorna M.; Nolte, Ilja M.; O'Connell, Jeffrey R.; Tanaka, Toshiko; Trompet, Stella; Arnold, Alice; Bandinelli, Stefania; Beekman, Marian; Böhringer, Stefan; Brown, Suzanne J.; Buckley, Brendan M.; Camaschella, Clara; de Craen, Anton J. M.; Davies, Gail; de Visser, Marieke C. H.; Ford, Ian; Forsen, Tom; Frayling, Timothy M.; Fugazzola, Laura; Gögele, Martin; Hattersley, Andrew T.; Hermus, Ad R.; Hofman, Albert; Houwing-Duistermaat, Jeanine J.; Jensen, Richard A.; Kajantie, Eero; Kloppenburg, Margreet; Lim, Ee M.; Masciullo, Corrado; Mariotti, Stefano; Minelli, Cosetta; Mitchell, Braxton D.; Nagaraja, Ramaiah; Netea-Maier, Romana T.; Palotie, Aarno; Persani, Luca; Piras, Maria G.; Psaty, Bruce M.; Räikkönen, Katri; Richards, J. Brent; Rivadeneira, Fernando; Sala, Cinzia; Sabra, Mona M.; Sattar, Naveed; Shields, Beverley M.; Soranzo, Nicole; Starr, John M.; Stott, David J.; Sweep, Fred C. G. J.; Usala, Gianluca; van der Klauw, Melanie M.; van Heemst, Diana; van Mullem, Alies; H.Vermeulen, Sita; Visser, W. Edward; Walsh, John P.; Westendorp, Rudi G. J.; Widen, Elisabeth; Zhai, Guangju; Cucca, Francesco; Deary, Ian J.; Eriksson, Johan G.; Ferrucci, Luigi; Fox, Caroline S.; Jukema, J. Wouter; Kiemeney, Lambertus A.; Pramstaller, Peter P.; Schlessinger, David; Shuldiner, Alan R.; Slagboom, Eline P.; Uitterlinden, André G.; Vaidya, Bijay; Visser, Theo J.; Wolffenbuttel, Bruce H. R.; Meulenbelt, Ingrid; Rotter, Jerome I.; Spector, Tim D.; Hicks, Andrew A.; Toniolo, Daniela; Sanna, Serena; Peeters, Robin P.; Naitza, Silvia

    2013-01-01

    Thyroid hormone is essential for normal metabolism and development, and overt abnormalities in thyroid function lead to common endocrine disorders affecting approximately 10% of individuals over their life span. In addition, even mild alterations in thyroid function are associated with weight changes, atrial fibrillation, osteoporosis, and psychiatric disorders. To identify novel variants underlying thyroid function, we performed a large meta-analysis of genome-wide association studies for serum levels of the highly heritable thyroid function markers TSH and FT4, in up to 26,420 and 17,520 euthyroid subjects, respectively. Here we report 26 independent associations, including several novel loci for TSH (PDE10A, VEGFA, IGFBP5, NFIA, SOX9, PRDM11, FGF7, INSR, ABO, MIR1179, NRG1, MBIP, ITPK1, SASH1, GLIS3) and FT4 (LHX3, FOXE1, AADAT, NETO1/FBXO15, LPCAT2/CAPNS2). Notably, only limited overlap was detected between TSH and FT4 associated signals, in spite of the feedback regulation of their circulating levels by the hypothalamic-pituitary-thyroid axis. Five of the reported loci (PDE8B, PDE10A, MAF/LOC440389, NETO1/FBXO15, and LPCAT2/CAPNS2) show strong gender-specific differences, which offer clues for the known sexual dimorphism in thyroid function and related pathologies. Importantly, the TSH-associated loci contribute not only to variation within the normal range, but also to TSH values outside the reference range, suggesting that they may be involved in thyroid dysfunction. Overall, our findings explain, respectively, 5.64% and 2.30% of total TSH and FT4 trait variance, and they improve the current knowledge of the regulation of hypothalamic-pituitary-thyroid axis function and the consequences of genetic variation for hypo- or hyperthyroidism. PMID:23408906

  12. Genetic susceptibility loci, pesticide exposure and prostate cancer risk.

    Directory of Open Access Journals (Sweden)

    Stella Koutros

    Full Text Available Uncovering SNP (single nucleotide polymorphisms-environment interactions can generate new hypotheses about the function of poorly characterized genetic variants and environmental factors, like pesticides. We evaluated SNP-environment interactions between 30 confirmed prostate cancer susceptibility loci and 45 pesticides and prostate cancer risk in 776 cases and 1,444 controls in the Agricultural Health Study. We used unconditional logistic regression to estimate odds ratios (ORs and 95% confidence intervals (CIs. Multiplicative SNP-pesticide interactions were calculated using a likelihood ratio test. After correction for multiple tests using the False Discovery Rate method, two interactions remained noteworthy. Among men carrying two T alleles at rs2710647 in EH domain binding protein 1 (EHBP1 SNP, the risk of prostate cancer in those with high malathion use was 3.43 times those with no use (95% CI: 1.44-8.15 (P-interaction= 0.003. Among men carrying two A alleles at rs7679673 in TET2, the risk of prostate cancer associated with high aldrin use was 3.67 times those with no use (95% CI: 1.43, 9.41 (P-interaction= 0.006. In contrast, associations were null for other genotypes. Although additional studies are needed and the exact mechanisms are unknown, this study suggests known genetic susceptibility loci may modify the risk between pesticide use and prostate cancer.

  13. Genetic and epigenetic variation in 5S ribosomal RNA genes reveals genome dynamics in Arabidopsis thaliana.

    Science.gov (United States)

    Simon, Lauriane; Rabanal, Fernando A; Dubos, Tristan; Oliver, Cecilia; Lauber, Damien; Poulet, Axel; Vogt, Alexander; Mandlbauer, Ariane; Le Goff, Samuel; Sommer, Andreas; Duborjal, Hervé; Tatout, Christophe; Probst, Aline V

    2018-04-06

    Organized in tandem repeat arrays in most eukaryotes and transcribed by RNA polymerase III, expression of 5S rRNA genes is under epigenetic control. To unveil mechanisms of transcriptional regulation, we obtained here in depth sequence information on 5S rRNA genes from the Arabidopsis thaliana genome and identified differential enrichment in epigenetic marks between the three 5S rDNA loci situated on chromosomes 3, 4 and 5. We reveal the chromosome 5 locus as the major source of an atypical, long 5S rRNA transcript characteristic of an open chromatin structure. 5S rRNA genes from this locus translocated in the Landsberg erecta ecotype as shown by linkage mapping and chromosome-specific FISH analysis. These variations in 5S rDNA locus organization cause changes in the spatial arrangement of chromosomes in the nucleus. Furthermore, 5S rRNA gene arrangements are highly dynamic with alterations in chromosomal positions through translocations in certain mutants of the RNA-directed DNA methylation pathway and important copy number variations among ecotypes. Finally, variations in 5S rRNA gene sequence, chromatin organization and transcripts indicate differential usage of 5S rDNA loci in distinct ecotypes. We suggest that both the usage of existing and new 5S rDNA loci resulting from translocations may impact neighboring chromatin organization.

  14. Identification of new susceptibility loci for type 2 diabetes and shared etiological pathways with coronary heart disease

    DEFF Research Database (Denmark)

    Zhao, Wei; Rasheed, Asif; Tikkanen, Emmi

    2017-01-01

    To evaluate the shared genetic etiology of type 2 diabetes (T2D) and coronary heart disease (CHD), we conducted a genome-wide, multi-ancestry study of genetic variation for both diseases in up to 265,678 subjects for T2D and 260,365 subjects for CHD. We identify 16 previously unreported loci for ...

  15. Population structure of the African savannah elephant inferred from mitochondrial control region sequences and nuclear microsatellite loci

    DEFF Research Database (Denmark)

    Nyakaana, S; Arctander, P; Siegismund, H R

    2002-01-01

    Two hundred and thirty-six mitochondrial DNA nucleotide sequences were used in combination with polymorphism at four nuclear microsatellite loci to assess the amount and distribution of genetic variation within and between African savannah elephants. They were sampled from 11 localities in easter...

  16. In-silico QTL mapping of postpubertal mammary ductal development in the mouse uncovers potential human breast cancer risk loci

    Science.gov (United States)

    Genetic background plays a dominant role in mammary gland development and breast cancer (BrCa). Despite this, the role of genetics is only partially understood. This study used strain-dependent variation in an inbred mouse mapping panel, to identify quantitative trait loci (QTL) underlying structura...

  17. Human red cell 2,3-diphosphoglycerate mutase and monophosphoglycerate mutase: genetic evidence for two separate loci.

    Science.gov (United States)

    Chen, S H; Anderson, J E; Giblett, E R

    1977-01-01

    Rare genetic variants of human red cell 2,3-diphosphoglycerate mutase (DPGM) and monophosphoglycerate mutase (MPGM) were compared by starch gel electrophoresis. The isozyme patterns showed that genetic variation of the enzymes were independent from each other, thus DPGM and MPGM must be controlled by two separate loci. Images Fig. 1 PMID:195467

  18. Microgeographic body size variation in a high elevation Andean anole (Anolis mariarum; Squamata, Polychrotidae

    Directory of Open Access Journals (Sweden)

    Brian C Bock

    2009-12-01

    Full Text Available Intra-specific body size variation is common and often is assumed to be adaptive. Studies of body size variation among sites should include or consider environmental and ecological variables in their designs. Additionally, reciprocal transplant or common garden studies will support which variables are really contributing to the observed body size variation. This study analyzed the microgeographic body size variation in Anolis mariarum, a small lizard endemic to Antioquia, Colombia. Parameters such as body size, shape, and lepidosis variation were quantified in 217 adult A. mariarum, belonging to six populations separated by less than 80km. Results showed that significant body size variation was not related to differences among sites in mean annual temperature, but covaried with mean annual precipitation, with the largest individuals occurring in dryer sites. Mark-recapture data obtained from 115 individuals from both the wettest and dryest sites from October 2004 to April 2005 showed that growth rates were higher at the latter. Eight males from each site were captured at the end of the mark- recapture study and reared for two months under identical conditions in a common garden study. Individuals from both sites grew faster when reared in the laboratory with food provided ad libitum. Although growth rates of males from the two populations did not differ significantly in the laboratory, males from the dryest site still maintained a significantly larger asymptotic body size in their growth trajectories. Multivariate analyses also demonstrated that both males and females from the six populations differed in terms of body shape and lepidosis. However, only female body size was found to covary significantly with an environmental gradient (precipitation. A. mariarum does not conform to Bergmann’s rule, but the relationship found between mean body size and asympotic growth with mean annual precipitation at these sites needs further analysis

  19. Molecular screening of deafness in Algeria: high genetic heterogeneity involving DFNB1 and the Usher loci, DFNB2/USH1B, DFNB12/USH1D and DFNB23/USH1F.

    Science.gov (United States)

    Ammar-Khodja, Fatima; Faugère, Valérie; Baux, David; Giannesini, Claire; Léonard, Susana; Makrelouf, Mohamed; Malek, Rahia; Djennaoui, Djamel; Zenati, Akila; Claustres, Mireille; Roux, Anne-Françoise

    2009-01-01

    A systematic approach, involving haplotyping and genotyping, to the molecular diagnosis of non-syndromic deafness within 50 families and 9 sporadic cases from Algeria is described. Mutations at the DFNB1 locus (encompassing the GJB2 and GJB6 genes) are responsible for more than half of autosomal recessive prelingual non-syndromic deafness in various populations. A c.35delG mutation can account for up to 85% of GJB2 mutations and two large deletions del(GJB6-D13S1830) and del(GJB6-D13S1854) have also been reported in several population groups. In view of the genetic heterogeneity a strategy was developed which involved direct analysis of DFNB1. In negative familial cases, haplotype analysis was carried out, where possible, to exclude DFNB1 mutations. Following this, haplotype analysis of five Usher syndrome loci, sometimes involved in autosomal non-syndromic hearing loss, was carried out to identify cases in which Usher gene sequencing was indicated. When homozygosity was observed at a locus in a consanguineous family, the corresponding gene was exhaustively sequenced. Pathogenic DFNB1 genotypes were identified in 40% of the cases. Of the 21 cases identified with 2 pathogenic mutations, c.35delG represented 76% of the mutated alleles. The additional mutations were one nonsense, two missense and one splicing mutation. Four additional patients were identified with a single DFNB1 mutation. None carried the large deletions. Three families with non-syndromic deafness carried novel unclassified variants (UVs) in MYO7A (1 family) and CDH23 (2 families) of unknown pathogenic effect. Additionally, molecular diagnosis was carried out on two Usher type I families and pathogenic mutations in MYO7A and PCDH15 were found.

  20. Diurnal variation in ruminal pH on the digestibility of highly digestible perennial ryegrass during continuous culture fermentation.

    Science.gov (United States)

    Wales, W J; Kolver, E S; Thorne, P L; Egan, A R

    2004-06-01

    Dairy cows grazing high-digestibility pastures exhibit pronounced diurnal variation in ruminal pH, with pH being below values considered optimal for digestion. Using a dual-flow continuous culture system, the hypothesis that minimizing diurnal variation in pH would improve digestion of pasture when pH was low, but not at a higher pH, was tested. Four treatments were imposed, with pH either allowed to exhibit normal diurnal variation around an average pH of 6.1 or 5.6, or maintained at constant pH. Digesta samples were collected during the last 3 d of each of four, 9-d experimental periods. A constant pH at 5.6 compared with a constant pH of 6.1 reduced the digestibility of organic matter (OM), neutral detergent (NDF), and acid detergent fiber (ADF) by 7, 14, and 21%, respectively. When pH was allowed to vary (averaging 5.6), digestion of OM, NDF, and ADF were reduced by 15,30, and 36%, respectively, compared with pH varying at 6.1. There was little difference in digestion parameters when pH was either constant or varied with an average pH of 6.1. However, when average pH was 5.6, maintaining a constant pH significantly increased digestion of OM, NDF, and ADF by 5, 25, and 24% compared with a pH that exhibited normal diurnal variation. These in vitro results show that gains in digestibility and potential milk production can be made by minimizing diurnal variation in ruminal pH, but only when ruminal pH is low (5.6). However, larger gains in productivity can be achieved by increasing average daily ruminal pH from 5.6 to 6.1.

  1. Impact of ecological diversity on genetic and phytochemical variation injuniperus excelsa from high elevation zones of quetta valley, pakistan

    International Nuclear Information System (INIS)

    Seed, S.; Barozai, M.Y.K.; Ahmed, A.; Tareen, R.B.

    2017-01-01

    Juniperusexcelsa (Cupressaceae) is an evergreen tree and the second most diverse group of the conifers distributed abundantly in high elevation zones of Balochistan. Genetic and phytochemical variations in three naturally occurring populations of J.excelsa were analysed. Genetic variability was assessed by different molecular markers (RAPD, ISSR and URP) with an objective to use genetic diversity as a key to conserve the taxon which is also known as living fossil as dominated in Mesozoic era. Genetic diversity was assessed by polymorphic bands to generate a dendrogram based on UPGMA. Using tested markers, 116 bands were amplified out of which 67 bands were polymorphic with an average value of 8.37 (57%) bands per primer. Based on data, a cluster dendrogram was prepared that exhibited the mean genetic similarity matrix as 0.57 and two major clusters diverge at 0.49. The genetic similarity coefficient among all accessions ranged from 0.35 to 0.90. In phytochemical analysis, total phenolic and flavonoid contents were estimated and compared among all accessions. Ecological characteristics of the study sites were measured to check their impact on genetic and chemical variation. Soil properties were analyzed for Principal Component Analysis. Chemical variation of J. excelsa of three sites revealed by dissimilarity matrix exhibiting genetic distance based on TPC and Flavonoids. Cluster analysis represent two major groups. Mean concentration of TPC and flavonoids were 56+-9.15 and 150+-27.9 mg/g respectively. PCA of soil considered three factors had Eigen values >1 and explain cumulatively 4.60 %, 26.02% and 10.36 % of the variance. First factor was positively correlated with second and fifth, but negatively correlated with other factors. In conclusion, molecular marker profiling together with phytochemical variation of total phenolic and flavonoid content in all accessions of Juniperusexcelsa and impact of ecological diversity on Genetic and chemical variation can be used

  2. The Transiting System GJ1214: High-Precision Defocused Transit Observations and a Search for Evidence of Transit Timing Variation

    DEFF Research Database (Denmark)

    Harpsøe, Kennet Bomann West; Hardis, S.; Hinse, T. C.

    2012-01-01

    Aims: We present 11 high-precision photometric transit observations of the transiting super-Earth planet GJ1214b. Combining these data with observations from other authors, we investigate the ephemeris for possible signs of transit timing variations (TTVs) using a Bayesian approach. Methods......: The observations were obtained using telescope-defocusing techniques, and achieve a high precision with random errors in the photometry as low as 1mmag per point. To investigate the possibility of TTVs in the light curve, we calculate the overall probability of a TTV signal using Bayesian methods. Results...

  3. Discovery and fine mapping of serum protein loci through transethnic meta-analysis.

    Science.gov (United States)

    Franceschini, Nora; van Rooij, Frank J A; Prins, Bram P; Feitosa, Mary F; Karakas, Mahir; Eckfeldt, John H; Folsom, Aaron R; Kopp, Jeffrey; Vaez, Ahmad; Andrews, Jeanette S; Baumert, Jens; Boraska, Vesna; Broer, Linda; Hayward, Caroline; Ngwa, Julius S; Okada, Yukinori; Polasek, Ozren; Westra, Harm-Jan; Wang, Ying A; Del Greco M, Fabiola; Glazer, Nicole L; Kapur, Karen; Kema, Ido P; Lopez, Lorna M; Schillert, Arne; Smith, Albert V; Winkler, Cheryl A; Zgaga, Lina; Bandinelli, Stefania; Bergmann, Sven; Boban, Mladen; Bochud, Murielle; Chen, Y D; Davies, Gail; Dehghan, Abbas; Ding, Jingzhong; Doering, Angela; Durda, J Peter; Ferrucci, Luigi; Franco, Oscar H; Franke, Lude; Gunjaca, Grog; Hofman, Albert; Hsu, Fang-Chi; Kolcic, Ivana; Kraja, Aldi; Kubo, Michiaki; Lackner, Karl J; Launer, Lenore; Loehr, Laura R; Li, Guo; Meisinger, Christa; Nakamura, Yusuke; Schwienbacher, Christine; Starr, John M; Takahashi, Atsushi; Torlak, Vesela; Uitterlinden, André G; Vitart, Veronique; Waldenberger, Melanie; Wild, Philipp S; Kirin, Mirna; Zeller, Tanja; Zemunik, Tatijana; Zhang, Qunyuan; Ziegler, Andreas; Blankenberg, Stefan; Boerwinkle, Eric; Borecki, Ingrid B; Campbell, Harry; Deary, Ian J; Frayling, Timothy M; Gieger, Christian; Harris, Tamara B; Hicks, Andrew A; Koenig, Wolfgang; O' Donnell, Christopher J; Fox, Caroline S; Pramstaller, Peter P; Psaty, Bruce M; Reiner, Alex P; Rotter, Jerome I; Rudan, Igor; Snieder, Harold; Tanaka, Toshihiro; van Duijn, Cornelia M; Vollenweider, Peter; Waeber, Gerard; Wilson, James F; Witteman, Jacqueline C M; Wolffenbuttel, Bruce H R; Wright, Alan F; Wu, Qingyu; Liu, Yongmei; Jenny, Nancy S; North, Kari E; Felix, Janine F; Alizadeh, Behrooz Z; Cupples, L Adrienne; Perry, John R B; Morris, Andrew P

    2012-10-05

    Many disorders are associated with altered serum protein concentrations, including malnutrition, cancer, and cardiovascular, kidney, and inflammatory diseases. Although these protein concentrations are highly heritable, relatively little is known about their underlying genetic determinants. Through transethnic meta-analysis of European-ancestry and Japanese genome-wide association studies, we identified six loci at genome-wide significance (p Japanese individuals) and three loci for total protein (TNFRS13B, 6q21.3, and ELL2, in up to 25,539 European-ancestry and 10,168 Japanese individuals). We observed little evidence of heterogeneity in allelic effects at these loci between groups of European and Japanese ancestry but obtained substantial improvements in the resolution of fine mapping of potential causal variants by leveraging transethnic differences in the distribution of linkage disequilibrium. We demonstrated a functional role for the most strongly associated serum albumin locus, HPN, for which Hpn knockout mice manifest low plasma albumin concentrations. Other loci associated with serum albumin harbor genes related to ribosome function, protein translation, and proteasomal degradation, whereas those associated with serum total protein include genes related to immune function. Our results highlight the advantages of transethnic meta-analysis for the discovery and fine mapping of complex trait loci and have provided initial insights into the underlying genetic architecture of serum protein concentrations and their association with human disease. Copyright © 2012 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  4. [Relationship between genetic polymorphisms of 3 SNP loci in 5-HTT gene and paranoid schizophrenia].

    Science.gov (United States)

    Xuan, Jin-Feng; Ding, Mei; Pang, Hao; Xing, Jia-Xin; Sun, Yi-Hua; Yao, Jun; Zhao, Yi; Li, Chun-Mei; Wang, Bao-Jie

    2012-12-01

    To investigate the population genetic data of 3 SNP loci (rs25533, rs34388196 and rs1042173) of 5-hydroxytryptamine transporter (5-HTT) gene and the association with paranoid schizophrenia. Three SNP loci of 5-HTT gene were examined in 132 paranoid schizophrenia patients and 150 unrelated healthy individuals of Northern Chinese Han population by PCR-RFLP technique. The Hardy-Weinberg equilibrium test was performed using the chi-square test and the data of haplotype frequency and population genetics parameters were statistically analyzed. Among these three SNP loci, four haplotypes were obtained. There were no statistically significant differences between the patient group and the control group (P > 0.05). The DP values of the 3 SNP loci were 0.276, 0.502 and 0.502. The PIC of them were 0.151, 0.281 and 0.281. The PE of them were 0.014, 0.072 and 0.072. The three SNP loci and four haplotypes of 5-HTT gene have no association with paranoid schizophrenia, while the polymorphism still have high potential application in forensic practice.

  5. A revised nomenclature for transcribed human endogenous retroviral loci

    Science.gov (United States)

    2011-01-01

    Background Endogenous retroviruses (ERVs) and ERV-like sequences comprise 8% of the human genome. A hitherto unknown proportion of ERV loci are transcribed and thus contribute to the human transcriptome. A small proportion of these loci encode functional proteins. As the role of ERVs in normal and diseased biological processes is not yet established, transcribed ERV loci are of particular interest. As more transcribed ERV loci are likely to be identified in the near future, the development of a systematic nomenclature is important to ensure that all information on each locus can be easily retrieved. Results Here we present a revised nomenclature of transcribed human endogenous retroviral loci that sorts loci into groups based on Repbase classifications. Each symbol is of the format ERV + group symbol + unique number. Group symbols are based on a mixture of Repbase designations and well-supported symbols used in the literature. The presented guidelines will allow newly identified loci to be easily incorporated into the scheme. Conclusions The naming system will be employed by the HUGO Gene Nomenclature Committee for naming transcribed human ERV loci. We hope that the system will contribute to clarifying a certain aspect of a sometimes confusing nomenclature for human endogenous retroviruses. The presented system may also be employed for naming transcribed loci of human non-ERV repeat loci. PMID:21542922

  6. Genetic analysis of variation in human meiotic recombination.

    Directory of Open Access Journals (Sweden)

    Reshmi Chowdhury

    2009-09-01

    Full Text Available The number of recombination events per meiosis varies extensively among individuals. This recombination phenotype differs between female and male, and also among individuals of each gender. In this study, we used high-density SNP genotypes of over 2,300 individuals and their offspring in two datasets to characterize recombination landscape and to map the genetic variants that contribute to variation in recombination phenotypes. We found six genetic loci that are associated with recombination phenotypes. Two of these (RNF212 and an inversion on chromosome 17q21.31 were previously reported in the Icelandic population, and this is the first replication in any other population. Of the four newly identified loci (KIAA1462, PDZK1, UGCG, NUB1, results from expression studies provide support for their roles in meiosis. Each of the variants that we identified explains only a small fraction of the individual variation in recombination. Notably, we found different sequence variants associated with female and male recombination phenotypes, suggesting that they are regulated by different genes. Characterization of genetic variants that influence natural variation in meiotic recombination will lead to a better understanding of normal meiotic events as well as of non-disjunction, the primary cause of pregnancy loss.

  7. Electrostatic Swelling and Conformational Variation Observed in High-Generation Polyelectrolyte Dendrimers

    International Nuclear Information System (INIS)

    Butler, Paul D.; Chen, Wei-Ren; Herwig, Kenneth W.; Hong, Kunlun; Liu, Yun; Porcar, L.; Shew, Chwen-Yang; Smith, Gregory Scott; Chen, Hsin-Lung; Chen, Chun-Yu; Li, Xin; Liu, Emily

    2010-01-01

    A coordinated study combining small angle neutron scattering (SANS) and small angle x-ray scattering (SAXS) measurements was conducted to investigate the structural characteristics of aqueous (D2O) generation 7 and 8 (G7 and G8) PAMAM dendrimer solutions as a function of molecular protonation at room temperature. The change in intra-molecular conformation was clearly exhibited in the data analysis by separating the variation in the inter-molecular correlation. Our results unambiguously demonstrate an increased molecular size and evolved intra-molecular density profile upon increasing the molecular protonation. This is contrary to the existing understanding that in higher generation polyelectrolyte dendrimers, steric crowding stiffens the local motion of dendrimer segments exploring additional available intra-dendrimer volume and therefore inhibits the electrostatic swelling. Our observation is relevant to elucidation of the general microscopic picture of polyelectrolyte dendrimer structure, as well as the development of dendrimer-based packages with based on the stimuli-responsive principle.

  8. High variation and very low differentiation in wide ranging plains zebra (Equus quagga): insights from mtDNA and microsatellites.

    Science.gov (United States)

    Lorenzen, Eline D; Arctander, Peter; Siegismund, Hans R

    2008-06-01

    Patterns of genetic differentiation in the plains zebra (Equus quagga) were analysed using mitochondrial DNA control region variation and seven microsatellites. The six morphologically defined subspecies of plains zebra lacked the population genetic structure indicative of distinct evolutionary units. Both marker sets showed high levels of genetic variation and very low levels of differentiation. There was no geographical structuring of mitochondrial DNA haplotypes in the phylogenetic tree, and the plains zebra showed the lowest overall differentiation recorded in any African ungulate studied so far. Arid-adapted African ungulates have shown significant regional genetic structuring in support of the Pleistocene refuge theory. This was not the case in the zebra, and the data are discussed in relation to the impact of Pleistocene climate change on a nonbovid member of the savannah ungulate community. The only other species showing a similar absence of genetic structuring is the African buffalo (Syncerus caffer), but this taxon lacks the high levels of morphological variation present in the plains zebra.

  9. Genomic copy number variations in three Southeast Asian populations.

    Science.gov (United States)

    Ku, Chee-Seng; Pawitan, Yudi; Sim, Xueling; Ong, Rick T H; Seielstad, Mark; Lee, Edmund J D; Teo, Yik-Ying; Chia, Kee-Seng; Salim, Agus

    2010-07-01

    Research on the role of copy number variations (CNVs) in the genetic risk of diseases in Asian populations has been hampered by a relative lack of reference CNV maps for Asian populations outside the East Asians. In this article, we report the population characteristics of CNVs in Chinese, Malay, and Asian Indian populations in Singapore. Using the Illumina Human 1M Beadchip array, we identify 1,174 CNV loci in these populations that corroborated with findings when the same samples were typed on the Affymetrix 6.0 platform. We identify 441 novel loci not previously reported in the Database of Genomic Variations (DGV). We observe a considerable number of loci that span all three populations and were previously unreported, as well as population-specific loci that are quite common in the respective populations. From this we observe the distribution of CNVs in the Asian Indian population to be considerably different from the Chinese and Malay populations. About half of the deletion loci and three-quarters of duplication loci overlap UCSC genes. Tens of loci show population differentiation and overlap with genes previously known to be associated with genetic risk of diseases. One of these loci is the CYP2A6 deletion, previously linked to reduced susceptibility to lung cancer. (c) 2010 Wiley-Liss, Inc.

  10. Seasonal variations of cadmium and zinc in Arrhenatherum elatius, a perennial grass species from highly contaminated soils

    International Nuclear Information System (INIS)

    Deram, Annabelle; Denayer, Franck-Olivier; Petit, Daniel; Van Haluwyn, Chantal

    2006-01-01

    There is interest in studying bioaccumulation in plants because they form the base of the food chain as well as their potential use in phytoextraction. From this viewpoint, our study deals with the seasonal variation, from January to July, of Cd and Zn bioaccumulation in three metallicolous populations of Arrhenatherum elatius, a perennial grass with a high biomass production. In heavily polluted soils, while Zn bioaccumulation is weak, A. elatius accumulates more Cd than reported gramineous plants, with concentration of up to 100 μg g -1 . Our results also showed seasonal variations of bioaccumulation, underlying the necessity for in situ studies to specify the date of sampling and also the phenology of the collected plant sample. In our experimental conditions, accumulation is lower in June, leading us to the hypothesis of restriction in heavy metals translocation from roots to aerial parts during seed production. - Cd and Zn bioaccumulation varies seasonally in a perennial grass

  11. Seasonal variations of cadmium and zinc in Arrhenatherum elatius, a perennial grass species from highly contaminated soils

    Energy Technology Data Exchange (ETDEWEB)

    Deram, Annabelle [Institut Lillois d' Ingenierie de la Sante, Universite Droit et Sante de Lille, EA 2690, 42 rue Ambroise Pare, 59120 Loos (France)]. E-mail: aderam@ilis.univ-lille2.fr; Denayer, Franck-Olivier [Institut Lillois d' Ingenierie de la Sante, Universite Droit et Sante de Lille, EA 2690, 42 rue Ambroise Pare, 59120 Loos (France); Petit, Daniel [Laboratoire de Genetique et Evolution des Populations Vegetales, UPRESA-CNRS 8016, Bat SN2, Universite des Sciences et Techniques de Lille, 59655 Villeneuve d' Ascq, F59655 France (France); Van Haluwyn, Chantal [Faculte des Sciences Pharmaceutiques et Biologiques, Departement de Botanique, Universite Droit et Sante de Lille, EA 2690, B.P. 83, 59006 Lille Cedex (France)

    2006-03-15

    There is interest in studying bioaccumulation in plants because they form the base of the food chain as well as their potential use in phytoextraction. From this viewpoint, our study deals with the seasonal variation, from January to July, of Cd and Zn bioaccumulation in three metallicolous populations of Arrhenatherum elatius, a perennial grass with a high biomass production. In heavily polluted soils, while Zn bioaccumulation is weak, A. elatius accumulates more Cd than reported gramineous plants, with concentration of up to 100 {mu}g g{sup -1}. Our results also showed seasonal variations of bioaccumulation, underlying the necessity for in situ studies to specify the date of sampling and also the phenology of the collected plant sample. In our experimental conditions, accumulation is lower in June, leading us to the hypothesis of restriction in heavy metals translocation from roots to aerial parts during seed production. - Cd and Zn bioaccumulation varies seasonally in a perennial grass.

  12. [SSR loci information analysis in transcriptome of Andrographis paniculata].

    Science.gov (United States)

    Li, Jun-Ren; Chen, Xiu-Zhen; Tang, Xiao-Ting; He, Rui; Zhan, Ruo-Ting

    2018-06-01

    To study the SSR loci information and develop molecular markers, a total of 43 683 Unigenes in transcriptome of Andrographis paniculata were used to explore SSR. The distribution frequency of SSR and the basic characteristics of repeat motifs were analyzed using MicroSAtellite software, SSR primers were designed by Primer 3.0 software and then validated by PCR. Moreover, the gene function analysis of SSR Unigene was obtained by Blast. The results showed that 14 135 SSR loci were found in the transcriptome of A. paniculata, which distributed in 9 973 Unigenes with a distribution frequency of 32.36%. Di-nucleotide and Tri-nucleotide repeat were the main types, accounted for 75.54% of all SSRs. The repeat motifs of AT/AT and CCG/CGG were the predominant repeat types of Di-nucleotide and Tri-nucleotide, respectively. A total of 4 740 pairs of SSR primers with the potential to produce polymorphism were designed for maker development. Ten pairs of primers in 20 pairs of randomly picked primers produced fragments with expected molecular size. The gene function of Unigenes containing SSR were mostly related to the basic metabolism function of A. paniculata. The SSR markers in transcriptome of A. paniculata show rich type, strong specificity and high potential of polymorphism, which will benefit the candidate gene mining and marker-assisted breeding. Copyright© by the Chinese Pharmaceutical Association.

  13. School and class-level variations and patterns of physical activity: a multilevel analysis of Danish high school students.

    Science.gov (United States)

    Steenholt, Carina Bjørnskov; Pisinger, Veronica Sofie Clara; Danquah, Ida Høgstedt; Tolstrup, Janne Schurmann

    2018-02-14

    There is limited knowledge of physical activity (PA) patterns among high school students. High schools plays an important role as context for the students, but it is uncertain to what extent schools influence student participation in PA during leisure time. The purpose of this study is to describe patterns of PA and assess variations between schools and classes in PA, in a large cohort of Danish high school students. Self-reported cross-sectional data came from The Danish National Youth Study, comprising a total of 70,674 students attending 119 different schools and 3213 classes. Multilevel logistic regressions were applied to evaluate the association between socio-demographic variables and patterns of PA, and to assess the impact of schools and classes on PA measures. Students whose parents have achieved a lower level of education, older students and girls of perceived ethnic minority generally participated less in several forms of PA during leisure time. Substantial variations between schools were observed in terms of participation in PA at school during leisure time and in terms of use of active transportation to and from school. The school-level accounted for 9% (intra-class correlation coefficient (ICC) = 0.09 (95% CI: 0.06-0.11)) and 8% (ICC = 0.08 (95% CI: 0.07-0.11)) of the variation for participation in PA during leisure time and active transportation. Overall, students whose parents achieved a lower level of education, older students and girls of perceived ethnic minority represent vulnerable groups in relation to participation in several forms of PA during leisure time. The ICCs indicate that schools, in particular, have the potential to influence participation in PA at school during leisure time and active transportation to and from school. Thus, high schools should encourage and facilitate activities aimed at engaging students in PA during leisure time as well as encourage active transportation.

  14. Characterization of microsatellite loci in Phormia regina towards expanding molecular applications in forensic entomology.

    Science.gov (United States)

    Farncombe, K M; Beresford, D; Kyle, C J

    2014-07-01

    Forensic entomology involves the use of insects and arthropods to assist a spectrum of medico-criminal investigations that range from identifying cases of abuse, corpse movements, and most commonly, post mortem interval estimates. Many of these applications focus on the use of blowflies given their predicable life history characteristics in their larval stages. Molecular tools have become increasingly important in the unambiguous identification of larval blowfly species, however, these same tools have the potential to broaden the array of molecular applications in forensic entomology to include individual identifications and population assignments. Herein, we establish a microsatellite profiling system for the blowfly, Phormiaregina (Diptera: Calliphoridae). The goal being to create a system to identify the population genetic structure of this species and subsequently establish if these data are amenable to identifying corpse movements based on the geographic distribution of specific genetic clusters of blowflies. Using next generation sequencing technology, we screened a partial genomic DNA sequence library of P.regina, searching for di-, tetra-, and penta-nucleotide microsatellite loci. We identified and developed primers for 84 highly repetitive segments of DNA, of which 14 revealed consistent genotypes and reasonable levels of genetic variation (4-26 alleles/locus; heterozygosity ranged from 0.385 to 0.909). This study provides the first step in assessing the utility of microsatellite markers to track the movements and sources of corpses via blowflies. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  15. Quantitative trait loci for magnitude of the plasma cortisol response to confinement in rainbow trout.

    Science.gov (United States)

    Quillet, E; Krieg, F; Dechamp, N; Hervet, C; Bérard, A; Le Roy, P; Guyomard, R; Prunet, P; Pottinger, T G

    2014-04-01

    Better understanding of the mechanisms underlying interindividual variation in stress responses and their links with production traits is a key issue for sustainable animal breeding. In this study, we searched for quantitative trait loci (QTL) controlling the magnitude of the plasma cortisol stress response and compared them to body size traits in five F2 full-sib families issued from two rainbow trout lines divergently selected for high or low post-confinement plasma cortisol level. Approximately 1000 F2 individuals were individually tagged and exposed to two successive acute confinement challenges (1 month interval). Post-stress plasma cortisol concentrations were determined for each fish. A medium density genome scan was carried out (268 markers, overall marker spacing less than 10 cM). QTL detection was performed using qtlmap software, based on an interval mapping method (http://www.inra.fr/qtlmap). Overall, QTL of medium individual effects on cortisol responsiveness (confinement stressor are distinct traits sharing only part of their genetic control. Chromosomal location of the steroidogenic acute regulatory protein (STAR) makes it a good potential candidate gene for one of the QTL. Finally, comparison of body size traits QTL (weight, length and body conformation) with cortisol-associated QTL did not support evidence for negative genetic relationships between the two types of traits. © 2014 Stichting International Foundation for Animal Genetics.

  16. Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture

    Science.gov (United States)

    Estrada, Karol; Styrkarsdottir, Unnur; Evangelou, Evangelos; Hsu, Yi-Hsiang; Duncan, Emma L; Ntzani, Evangelia E; Oei, Ling; Albagha, Omar M E; Amin, Najaf; Kemp, John P; Koller, Daniel L; Li, Guo; Liu, Ching-Ti; Minster, Ryan L; Moayyeri, Alireza; Vandenput, Liesbeth; Willner, Dana; Xiao, Su-Mei; Yerges-Armstrong, Laura M; Zheng, Hou-Feng; Alonso, Nerea; Eriksson, Joel; Kammerer, Candace M; Kaptoge, Stephen K; Leo, Paul J; Thorleifsson, Gudmar; Wilson, Scott G; Wilson, James F; Aalto, Ville; Alen, Markku; Aragaki, Aaron K; Aspelund, Thor; Center, Jacqueline R; Dailiana, Zoe; Duggan, David J; Garcia, Melissa; Garcia-Giralt, Natàlia; Giroux, Sylvie; Hallmans, Göran; Hocking, Lynne J; Husted, Lise Bjerre; Jameson, Karen A; Khusainova, Rita; Kim, Ghi Su; Kooperberg, Charles; Koromila, Theodora; Kruk, Marcin; Laaksonen, Marika; Lacroix, Andrea Z; Lee, Seung Hun; Leung, Ping C; Lewis, Joshua R; Masi, Laura; Mencej-Bedrac, Simona; Nguyen, Tuan V; Nogues, Xavier; Patel, Millan S; Prezelj, Janez; Rose, Lynda M; Scollen, Serena; Siggeirsdottir, Kristin; Smith, Albert V; Svensson, Olle; Trompet, Stella; Trummer, Olivia; van Schoor, Natasja M; Woo, Jean; Zhu, Kun; Balcells, Susana; Brandi, Maria Luisa; Buckley, Brendan M; Cheng, Sulin; Christiansen, Claus; Cooper, Cyrus; Dedoussis, George; Ford, Ian; Frost, Morten; Goltzman, David; González-Macías, Jesús; Kähönen, Mika; Karlsson, Magnus; Khusnutdinova, Elza; Koh, Jung-Min; Kollia, Panagoula; Langdahl, Bente Lomholt; Leslie, William D; Lips, Paul; Ljunggren, Östen; Lorenc, Roman S; Marc, Janja; Mellström, Dan; Obermayer-Pietsch, Barbara; Olmos, José M; Pettersson-Kymmer, Ulrika; Reid, David M; Riancho, José A; Ridker, Paul M; Rousseau, François; Slagboom, P Eline; Tang, Nelson LS; Urreizti, Roser; Van Hul, Wim; Viikari, Jorma; Zarrabeitia, María T; Aulchenko, Yurii S; Castano-Betancourt, Martha; Grundberg, Elin; Herrera, Lizbeth; Ingvarsson, Thorvaldur; Johannsdottir, Hrefna; Kwan, Tony; Li, Rui; Luben, Robert; Medina-Gómez, Carolina; Palsson, Stefan Th; Reppe, Sjur; Rotter, Jerome I; Sigurdsson, Gunnar; van Meurs, Joyce B J; Verlaan, Dominique; Williams, Frances MK; Wood, Andrew R; Zhou, Yanhua; Gautvik, Kaare M; Pastinen, Tomi; Raychaudhuri, Soumya; Cauley, Jane A; Chasman, Daniel I; Clark, Graeme R; Cummings, Steven R; Danoy, Patrick; Dennison, Elaine M; Eastell, Richard; Eisman, John A; Gudnason, Vilmundur; Hofman, Albert; Jackson, Rebecca D; Jones, Graeme; Jukema, J Wouter; Khaw, Kay-Tee; Lehtimäki, Terho; Liu, Yongmei; Lorentzon, Mattias; McCloskey, Eugene; Mitchell, Braxton D; Nandakumar, Kannabiran; Nicholson, Geoffrey C; Oostra, Ben A; Peacock, Munro; Pols, Huibert A P; Prince, Richard L; Raitakari, Olli; Reid, Ian R; Robbins, John; Sambrook, Philip N; Sham, Pak Chung; Shuldiner, Alan R; Tylavsky, Frances A; van Duijn, Cornelia M; Wareham, Nick J; Cupples, L Adrienne; Econs, Michael J; Evans, David M; Harris, Tamara B; Kung, Annie Wai Chee; Psaty, Bruce M; Reeve, Jonathan; Spector, Timothy D; Streeten, Elizabeth A; Zillikens, M Carola; Thorsteinsdottir, Unnur; Ohlsson, Claes; Karasik, David; Richards, J Brent; Brown, Matthew A; Stefansson, Kari; Uitterlinden, André G; Ralston, Stuart H; Ioannidis, John P A; Kiel, Douglas P; Rivadeneira, Fernando

    2012-01-01

    Bone mineral density (BMD) is the most important predictor of fracture risk. We performed the largest meta-analysis to date on lumbar spine and femoral neck BMD, including 17 genome-wide association studies and 32,961 individuals of European and East Asian ancestry. We tested the top-associated BMD markers for replication in 50,933 independent subjects and for risk of low-trauma fracture in 31,016 cases and 102,444 controls. We identified 56 loci (32 novel)associated with BMD atgenome-wide significant level (P<5×10−8). Several of these factors cluster within the RANK-RANKL-OPG, mesenchymal-stem-cell differentiation, endochondral ossification and the Wnt signalling pathways. However, we also discovered loci containing genes not known to play a role in bone biology. Fourteen BMD loci were also associated with fracture risk (P<5×10−4, Bonferroni corrected), of which six reached P<5×10−8 including: 18p11.21 (C18orf19), 7q21.3 (SLC25A13), 11q13.2 (LRP5), 4q22.1 (MEPE), 2p16.2 (SPTBN1) and 10q21.1 (DKK1). These findings shed light on the genetic architecture and pathophysiological mechanisms underlying BMD variation and fracture susceptibility. PMID:22504420

  17. Isolation and characterization of 23 polymorphic microsatellite loci for a West Indian iguana (Cyclura pinguis) from the British Virgin Islands.

    Science.gov (United States)

    Lau, Jennie; Alberts, Allison C; Chemnick, Leona G; Gerber, Glenn P; Jones, Kenneth C; Mitchell, Adele A; Ryder, Oliver A

    2009-09-01

    Twenty-three polymorphic microsatellite markers were identified and characterized for Cyclura pinguis, a critically endangered species of lizard (Sauria: Iguanidae) native to Anegada Island in the British Virgin Islands. We examined variation at these loci for 39 C. pinguis, finding up to five alleles per locus and an average expected heterozygosity of 0.55. Allele frequency estimates for these microsatellite loci will be used to characterize genetic diversity of captive and wild C. pinguis populations and to estimate relatedness among adult iguanas at the San Diego Zoo that form the nucleus of a captive breeding programme for this critically endangered species. © 2009 Blackwell Publishing Ltd.

  18. Low and high frequency Madden-Julian oscillations in austral summer: interannual variations

    Energy Technology Data Exchange (ETDEWEB)

    Izumo, Takeshi [Research Institute For Global Change (JAMSTEC), Yokohama (Japan); LOCEAN, IRD-CNRS-UPMC, Paris (France); Masson, Sebastien; Vialard, Jerome; Madec, Gurvan [LOCEAN, IRD-CNRS-UPMC, Paris (France); Boyer Montegut, Clement de [IFREMER, Brest (France); Behera, Swadhin K. [Research Institute For Global Change (JAMSTEC), Yokohama (Japan); Takahashi, Keiko [Earth Simulator Center (JAMSTEC), Yokohama (Japan); Yamagata, Toshio [Research Institute For Global Change (JAMSTEC), Yokohama (Japan); University of Tokyo, Tokyo (Japan)

    2010-09-15

    The Madden-Julian oscillation (MJO) is the main component of intraseasonal variability of the tropical convection, with clear climatic impacts at an almost-global scale. Based on satellite observations, it is shown that there are two types of austral-summer MJO events (broadly defined as 30-120 days convective variability with eastward propagation of about 5 m/s). Equatorial MJO events have a period of 30-50 days and tend to be symmetric about the equator, whereas MJO events centered near 8 S tend to have a longer period of 55-100 days. The lower-frequency variability is associated with a strong upper-ocean response, having a clear signature in both sea surface temperature and its diurnal cycle. These two MJO types have different interannual variations, and are modulated by the Indian Ocean Dipole (IOD). Following a negative IOD event, the lower-frequency southern MJO variability increases, while the higher-frequency equatorial MJO strongly diminishes. We propose two possible explanations for this change in properties of the MJO. One possibility is that changes in the background atmospheric circulation after an IOD favour the development of the low-frequency MJO. The other possibility is that the shallower thermocline ridge and mixed layer depth, by enhancing SST intraseasonal variability and thus ocean-atmosphere coupling in the southwest Indian Ocean (the breeding ground of southern MJO onset), favour the lower-frequency southern MJO variability. (orig.)

  19. An outbreak of mumps with genetic strain variation in a highly vaccinated student population in Scotland.

    Science.gov (United States)

    Willocks, L J; Guerendiain, D; Austin, H I; Morrison, K E; Cameron, R L; Templeton, K E; DE Lima, V R F; Ewing, R; Donovan, W; Pollock, K G J

    2017-11-01

    An outbreak of mumps within a student population in Scotland was investigated to assess the effect of previous vaccination on infection and clinical presentation, and any genotypic variation. Of the 341 cases, 79% were aged 18-24. Vaccination status was available for 278 cases of whom 84% had received at least one dose of mumps containing vaccine and 62% had received two. The complication rate was 5·3% (mainly orchitis), and 1·2% were admitted to hospital. Genetic sequencing of mumps virus isolated from cases across Scotland classified 97% of the samples as genotype G. Two distinct clusters of genotype G were identified, one circulating before the outbreak and the other thereafter, suggesting the virus that caused this outbreak was genetically different from the previously circulating virus. Whilst the poor vaccine effectiveness we found may be due to waning immunity over time, a contributing factor may be that the current mumps vaccine is less effective against some genotypes. Although the general benefits of the measles-mumps-rubella (MMR) vaccine should continue to be promoted, there may be value in reassessing the UK vaccination schedule and the current mumps component of the MMR vaccine.

  20. Mechanical Properties Variation of B500SD High Ductility Reinforcement Regarding its Corrosion Degree

    Directory of Open Access Journals (Sweden)

    Cobo, A.

    2011-12-01

    Full Text Available Corrosion effects on reinforcement become evident in the bar section reduction and in the variation of mechanical properties related to ductility. In this research work, 96 B500SD steel bars, previously subjected to different corrosion variables, have been tested. Results show that the elongation of the bars diminishes and the ratio between the maximum tensile stress and the elastic limit increases as the corrosion degree advances. These phenomena can be explained by studying the necking effect and the different steel composition through the manufacture process.

    Los efectos de la corrosión sobre las armaduras se manifiestan por la pérdida de sección y la variación de las propiedades mecánicas relacionadas con la ductilidad. En este trabajo se han ensayado a tracción 96 barras de acero B500SD que previamente se han sometido a niveles variables de corrosión. Los resultados muestran que los alargamientos de las barras disminuyen y el cociente entre la tensión máxima y el límite elástico aumenta conforme el nivel de corrosión avanza. A partir del estudio del efecto de entalla y de la distinta constitución metalográfica del acero a nivel de sección debido a su procedimiento de fabricación, se pueden explicar los fenómenos anteriores.

  1. [Discriminatory power of variable number on tandem repeats loci for genotyping Mycobacterium tuberculosis strains in China].

    Science.gov (United States)

    Chen, H X; Cai, C; Liu, J Y; Zhang, Z G; Yuan, M; Jia, J N; Sun, Z G; Huang, H R; Gao, J M; Li, W M

    2017-06-10

    Objective: Using the standard genotype method, variable number of tandem repeats (VNTR), we constructed a VNTR database to cover all provinces and proposed a set of optimized VNTR loci combinations for each province, in order to improve the preventive and control programs on tuberculosis, in China. Methods: A total of 15 loci VNTR was used to analyze 4 116 Mycobacterium tuberculosis strains, isolated from national survey of Drug Resistant Tuberculosis, in 2007. Hunter-Gaston Index (HGI) was also used to analyze the discriminatory power of each VNTR site. A set combination of 12-VNTR, 10-VNTR, 8-VNTR and 5-VNTR was respectively constructed for each province, based on 1) epidemic characteristics of M. tuberculosis lineages in China, with high discriminatory power and genetic stability. Results: Through the completed 15 loci VNTR patterns of 3 966 strains under 96.36 % (3 966/4 116) coverage, we found seven high HGI loci (including QUB11b and MIRU26) as well as low stable loci (including QUB26, MIRU16, Mtub21 and QUB11b) in several areas. In all the 31 provinces, we found an optimization VNTR combination as 10-VNTR loci in Inner Mongolia, Chongqing and Heilongjiang, but with 8-VNTR combination shared in other provinces. Conclusions: It is necessary to not only use the VNTR database for tracing the source of infection and cluster of M. tuberculosis in the nation but also using the set of optimized VNTR combinations in monitoring those local epidemics and M. tuberculosis (genetics in local) population.

  2. Efficient assembly of de novo human artificial chromosomes from large genomic loci

    Directory of Open Access Journals (Sweden)

    Stromberg Gregory

    2005-07-01

    Full Text Available Abstract Background Human Artificial Chromosomes (HACs are potentially useful vectors for gene transfer studies and for functional annotation of the genome because of their suitability for cloning, manipulating and transferring large segments of the genome. However, development of HACs for the transfer of large genomic loci into mammalian cells has been limited by difficulties in manipulating high-molecular weight DNA, as well as by the low overall frequencies of de novo HAC formation. Indeed, to date, only a small number of large (>100 kb genomic loci have been reported to be successfully packaged into de novo HACs. Results We have developed novel methodologies to enable efficient assembly of HAC vectors containing any genomic locus of interest. We report here the creation of a novel, bimolecular system based on bacterial artificial chromosomes (BACs for the construction of HACs incorporating any defined genomic region. We have utilized this vector system to rapidly design, construct and validate multiple de novo HACs containing large (100–200 kb genomic loci including therapeutically significant genes for human growth hormone (HGH, polycystic kidney disease (PKD1 and ß-globin. We report significant differences in the ability of different genomic loci to support de novo HAC formation, suggesting possible effects of cis-acting genomic elements. Finally, as a proof of principle, we have observed sustained ß-globin gene expression from HACs incorporating the entire 200 kb ß-globin genomic locus for over 90 days in the absence of selection. Conclusion Taken together, these results are significant for the development of HAC vector technology, as they enable high-throughput assembly and functional validation of HACs containing any large genomic locus. We have evaluated the impact of different genomic loci on the frequency of HAC formation and identified segments of genomic DNA that appear to facilitate de novo HAC formation. These genomic loci

  3. Investigation of Interfraction Variations of MammoSite Balloon Applicator in High-Dose-Rate Brachytherapy of Partial Breast Irradiation

    International Nuclear Information System (INIS)

    Kim, Yongbok; Johnson, Mark M.S.; Trombetta, Mark G.; Parda, David S.; Miften, Moyed

    2008-01-01

    Purpose: To measure the interfraction changes of the MammoSite applicator and evaluate their dosimetric effect on target coverage and sparing of organs at risk. Methods and Materials: A retrospective evaluation of the data from 19 patients who received 10 fractions (34 Gy) of high-dose-rate partial breast irradiation was performed. A computed tomography-based treatment plan was generated for Fraction 1, and a computed tomography scan was acquired just before the delivery of each fraction to ensure a consistent shape of the balloon. The eccentricity, asymmetry, and planning target volume (PTV) for plan evaluation purposes (PTV E VAL), as well as trapped air gaps, were measured for all patients. Furthermore, 169 computed tomography-based treatment plans were retrospectively generated for Fractions 2-10. Interfraction dosimetric variations were evaluated using the %PTV E VAL coverage, target dose homogeneity index, target dose conformal index, and maximum doses to the organs at risks. Results: The average variation of eccentricity and asymmetry from Fraction 1 values of 3.5% and 1.1 mm was -0.4% ± 1.6% and -0.1 ± 0.6 mm. The average trapped air gap volume was dramatically reduced from before treatment (3.7 cm 3 ) to Fraction 1 (0.8 cm 3 ). The PTV E VAL volume change was insignificant. The average variation for the %PTV E VAL, target dose homogeneity, and target dose conformal index from Fraction 1 values of 94.7%, 0.64, and 0.85 was 0.15% ± 2.4%, -0.35 ± 2.4%, and -0.34 ± 4.9%, respectively. The average Fraction 1 maximum skin and ipsilateral lung dose of 3.2 Gy and 2.0 Gy varied by 0.08 ± 0.47 and -0.16 ± 0.29 Gy, respectively. Conclusion: The interfraction variations were patient specific and fraction dependent. Although the average interfraction dose variations for the target and organs at risk were not clinically significant, the maximum variations could be clinically significant

  4. Runoff and sediment variation in the areas with high and coarse sediment yield of the middle Yellow River

    Science.gov (United States)

    Zhang, Pan; Yao, Wenyi; Xiao, Peiqing; Sun, Weiying

    2018-02-01

    Massive water and soil conservation works (WSCW) have been conducted in the areas with high and coarse sediment yield of the middle Yellow River since 1982. With the impending effects of climate change, it is necessary to reconsider the effects of WSCW on runoff and sediment variation at decadal and regional scales. Using long-term official and synthesized data, the WSCW impacts on reducing water and soil loss were studied in Sanchuanhe River watershed. Results showed that the sediment and runoff generated from this area showed a decreasing trend in the past 50 years. A great progress has been achieved in erosion control since the 1970s. After the 4 soil and water conservation harnessing stages during the period from 1970 to 2006, the sediment and runoff yield showed decreases with the extension of harnessing. The results revealed that human activities exerted the largest effects on the sediment reduction and explained 66.6% of the variation in the specific sediment yield. The contribution of rainfall variation to runoff reduction was as large as human activities. A great benefit have been obtained in water and soil loss control in this area.

  5. High Levels of Sample-to-Sample Variation Confound Data Analysis for Non-Invasive Prenatal Screening of Fetal Microdeletions.

    Directory of Open Access Journals (Sweden)

    Tianjiao Chu

    Full Text Available Our goal was to test the hypothesis that inter-individual genomic copy number variation in control samples is a confounding factor in the non-invasive prenatal detection of fetal microdeletions via the sequence-based analysis of maternal plasma DNA. The database of genomic variants (DGV was used to determine the "Genomic Variants Frequency" (GVF for each 50kb region in the human genome. Whole genome sequencing of fifteen karyotypically normal maternal plasma and six CVS DNA controls samples was performed. The coefficient of variation of relative read counts (cv.RTC for these samples was determined for each 50kb region. Maternal plasma from two pregnancies affected with a chromosome 5p microdeletion was also sequenced, and analyzed using the GCREM algorithm. We found strong correlation between high variance in read counts and GVF amongst controls. Consequently we were unable to confirm the presence of the microdeletion via sequencing of maternal plasma samples obtained from two sequential affected pregnancies. Caution should be exercised when performing NIPT for microdeletions. It is vital to develop our understanding of the factors that impact the sensitivity and specificity of these approaches. In particular, benign copy number variation amongst controls is a major confounder, and their effects should be corrected bioinformatically.

  6. Assessment of intra and interregional genetic variation in the Eastern Red-backed Salamander, Plethodon cinereus, via analysis of novel microsatellite markers.

    Directory of Open Access Journals (Sweden)

    Alexander C Cameron

    Full Text Available The red-backed salamander (Plethodon cinereus has long-served as a model system in ecology, evolution, and behavior, and studies surveying molecular variation in this species have become increasingly common over the past decade. However, difficulties are commonly encountered when extending microsatellite markers to populations that are unstudied from a genetic perspective due to high levels of genetic differentiation across this species' range. To ameliorate this issue, we used 454 pyrosequencing to identify hundreds of microsatellite loci. We then screened 40 of our top candidate loci in populations in Virginia, Pennsylvania, and Ohio-including an isolated island population ~ 4.5 km off the shore of Lake Erie (South Bass Island. We identified 25 loci that are polymorphic in a well-studied region of Virginia and 11 of these loci were polymorphic in populations located in the genetically unstudied regions of Ohio and Pennsylvania. Use of these loci to examine patterns of variation within populations revealed that South Bass Island has low diversity in comparison to other sites. However, neither South Bass Island nor isolated populations around Cleveland are inbred. Assessment of variation between populations revealed three well defined genetic clusters corresponding to Virginia, mainland Ohio/Pennsylvania, and South Bass Island. Comparisons of our results to those of others working in various parts of the range are consistent with the idea that differentiation is lower in regions that were once glaciated. However, these comparisons also suggest that well differentiated isolated populations in the formerly glaciated portion of the range are not uncommon. This work provides novel genetic resources that will facilitate population genetic studies in a part of the red-backed salamander's range that has not previously been studied in this manner. Moreover, this work refines our understanding of how neutral variation is distributed in this ecologically

  7. Passenger comfort on high-speed trains: effect of tunnel noise on the subjective assessment of pressure variations.

    Science.gov (United States)

    Sanok, Sandra; Mendolia, Franco; Wittkowski, Martin; Rooney, Daniel; Putzke, Matthias; Aeschbach, Daniel

    2015-01-01

    When passing through a tunnel, aerodynamic effects on high-speed trains may impair passenger comfort. These variations in atmospheric pressure are accompanied by transient increases in sound pressure level. To date, it is unclear whether the latter influences the perceived discomfort associated with the variations in atmospheric pressure. In a pressure chamber of the DLR-Institute of Aerospace Medicine, 71 participants (M = 28.3 years ± 8.1 SD) rated randomised pressure changes during two conditions according to a crossover design. The pressure changes were presented together with tunnel noise such that the sound pressure level was transiently elevated by either +6 dB (low noise condition) or +12 dB (high noise condition) above background noise level (65 dB(A)). Data were combined with those of a recent study, in which identical pressure changes were presented without tunnel noise (Schwanitz et al., 2013, 'Pressure Variations on a Train - Where is the Threshold to Railway Passenger Discomfort?' Applied Ergonomics 44 (2): 200-209). Exposure-response relationships for the combined data set comprising all three noise conditions show that pressure discomfort increases with the magnitude and speed of the pressure changes but decreases with increasing tunnel noise. Practitioner Summary: In a pressure chamber, we systematically examined how pressure discomfort, as it may be experienced by railway passengers, is affected by the presence of tunnel noise during pressure changes. It is shown that across three conditions (no noise, low noise (+6 dB), high noise (+12 dB)) pressure discomfort decreases with increasing tunnel noise.

  8. Ethnic Variations of Trajectories in Suicide Ideation and Attempt: From Middle School to High School.

    Science.gov (United States)

    Kim, Jahun; Pike, Kenneth; McCauley, Elizabeth; Vander Stoep, Ann

    2018-02-14

    The purpose of this study was to compare patterns of suicide ideation and suicide attempt in three ethnic groups. We analyzed data from 463 students with ethnic backgrounds of African American (AA), Asian American (ASA), and European American (EA) for 6 years. The best fit model was a three-trajectory class model for all groups. The majority of adolescents belonged in the nonideators trajectory. The high level of ideation was found in the high ideators (4%), high-fluctuating ideators (8%), and high-decreasing ideators (4%) trajectory in AA, ASA, and EA, respectively. In the AA group, being a member of ideators was not a significant predictor of suicide attempt. In the ASA group, being a member of high-fluctuating ideators was a significant predictor. In the EA group, being a member of both ideators predicted suicide attempt. The timing of onset, patterns of change, and peak time in the ideators trajectories in the three ethnic groups were markedly different. The high level of attempts found in the ASA-AA group was not explained by having suicide ideation. Findings suggest the need for in-depth examination of suicide behaviors across ethnic groups and culturally adapted preventive efforts with distinct developmental timing for adolescents from different ethnic backgrounds. © 2018 The American Association of Suicidology.

  9. Spatial and temporal patterns of sea ice variations in Vilkitsky strait, Russian High Arctic

    Science.gov (United States)

    Ci, T.; Cheng, X.; Hui, F.

    2013-12-01

    The Arctic Ocean has been greatly affected by climate change. Future predications show an even more drastic reduction of the ice cap which will open new areas for the exploration of natural resources and maritime transportation.Shipping through the Arctic Ocean via the Northern Sea Route (NSR) could save about 40% of the sailing distance from Asia (Yokohama) to Europe (Rotterdam) compared to the traditional route via the Suez Canal. Vilkitsky strait is the narrowest and northest portion of the Northern Sea Route with heaviest traffic between the Taimyr Peninsular and the Severnaya Zemlya archipelago. The preliminary results of sea ice variations are presented by using moderate-resolution imaging spectro radiometer(MODIS) data with 250-m resolution in the Vilkitsky strait during 2009-2012. Temporally, the first rupture on sea ice in Vilkitsky strait usually comes up in April and sea ice completely break into pieces in early June. The strait would be ice-free between August and late September. The frequency of ice floes grows while temperature falls down in October. There are always one or two months suitable for transport. Spatially, Sea ice on Laptev sea side breaks earlier than that of Kara sea side while sea ice in central of strait breaks earlier than in shoreside. The phenomena are directly related with the direction of sea wind and ocean current. In summmary, study on Spatial and temporal patterns in this area is significant for the NSR. An additional research issue to be tackled is to seeking the trends of ice-free duration in the context of global warming. Envisat ASAR data will also be used in this study.

  10. Microsatellite loci isolated from the scleractinian coral, Acropora nobilis.

    Science.gov (United States)

    Isomura, Naoko; Hidaka, Michio

    2008-05-01

    We report the isolation and characterization of eight microsatellite loci from the scleractinian coral, Acropora nobilis. The microsatellite loci were obtained using compound SSR primers or an enrichment protocol. All the loci were polymorphic with four to eight alleles per locus and observed heterozygosities ranging from 0.22 to 0.76. Some of the primers developed for the two congeners, Acropora palmata and Acropora millepora were applicable to A. nobilis. These loci are useful for studying the connectivity among A. nobilis populations in Okinawa, southern Japan. © 2007 The Authors.

  11. An evaluation of multiple-schedule variations to reduce high-rate requests in the picture exchange communication system.

    Science.gov (United States)

    Landa, Robin; Hanley, Gregory P

    2016-06-01

    Using procedures similar to those of Tiger, Hanley, and Heal (2006), we compared two multiple-schedule variations (S+/S- and S+ only) to treat high-rate requests for edible items in the Picture Exchange Communication System (PECS). Two individuals with autism participated, after they showed persistent requests for edible items after PECS training. Stimulus control was achieved only with the multiple schedule that involved presentation of a discriminative stimulus during reinforcement components and its removal during extinction components (S+ only). Discriminated requests were maintained for the 1 participant who experienced schedule thinning. © 2016 Society for the Experimental Analysis of Behavior.

  12. Identification of six new susceptibility loci for invasive epithelial ovarian cancer

    NARCIS (Netherlands)

    Kuchenbaecker, K.B.; Ramus, S.J.; Tyrer, J.; Lee, A.; Shen, H.C.; Beesley, J.; Lawrenson, K.; McGuffog, L.; Healey, S.; Lee, J.M.; Spindler, T.J.; Lin, Y.G.; Pejovic, T.; Bean, Y.; Li, Q.; Coetzee, S.; Hazelett, D.; Miron, A.; Southey, M.; Terry, M.B.; Goldgar, D.E.; Buys, S.S.; Janavicius, R.; Dorfling, C.M.; Rensburg, E.J. van; Neuhausen, S.L.; Ding, Y.C.; Hansen, T.V.; Jonson, L.; Gerdes, A.M.; Ejlertsen, B.; Barrowdale, D.; Dennis, J.; Benitez, J.; Osorio, A.; Garcia, M.J.; Komenaka, I.; Weitzel, J.N.; Ganschow, P.; Peterlongo, P.; Bernard, L.; Viel, A.; Bonanni, B.; Peissel, B.; Manoukian, S.; Radice, P.; Papi, L.; Ottini, L.; Fostira, F.; Konstantopoulou, I.; Garber, J.; Frost, D.; Perkins, J.; Platte, R.; Ellis, S.; Embrace, .; Godwin, A.K.; Schmutzler, R.K.; Meindl, A.; Engel, C.; Sutter, C.; Sinilnikova, O.M.; Damiola, F.; Mazoyer, S.; Stoppa-Lyonnet, D.; Claes, K.; Leeneer, K. De; Kirk, J.; Rodriguez, G.C.; Piedmonte, M.; O'Malley, D.M.; Hoya, M. de la; Caldes, T.; Aittomaki, K.; Nevanlinna, H.; Collee, J.M.; Rookus, M.A.; Oosterwijk, J.C; Tihomirova, L.; Tung, N.; Hamann, U.; Isaccs, C.; Tischkowitz, M.; Imyanitov, E.N.; Caligo, M.A.; Campbell, I.G.; Hogervorst, F.B.; Olah, E.; Diez, O.; Blanco, I.; Brunet, J.; Lazaro, C.; Pujana, M.A.; Jakubowska, A.; Gronwald, J.; Lubinski, J.; Sukiennicki, G.; Massuger, L.F.A.G.; Altena, A.M. van; Aben, K.K.H.; Kiemeney, B.; Mensenkamp, A.R.; Kets, M.; Hoogerbrugge, N.; Ligtenberg, M.J.L.; et al.,

    2015-01-01

    Genome-wide association studies (GWAS) have identified 12 epithelial ovarian cancer (EOC) susceptibility alleles. The pattern of association at these loci is consistent in BRCA1 and BRCA2 mutation carriers who are at high risk of EOC. After imputation to 1000 Genomes Project data, we assessed

  13. Identification of six new susceptibility loci for invasive epithelial ovarian cancer

    NARCIS (Netherlands)

    K.B. Kuchenbaecker (Karoline); S.J. Ramus (Susan); J.P. Tyrer (Jonathan); A. Lee (Andrew); H.C. Shen (Howard C.); J. Beesley (Jonathan); K. Lawrenson (Kate); L. McGuffog (Lesley); S. Healey (Sue); J.M. Lee (Janet M.); T.J. Spindler (Tassja J.); Y.G. Lin (Yvonne G.); T. Pejovic (Tanja); Y. Bean (Yukie); Q. Li (Qiyuan); S. Coetzee (Simon); D. Hazelett (Dennis); A. Miron (Alexander); M.C. Southey (Melissa); M.B. Terry (Mary Beth); D. Goldgar (David); S.S. Buys (Saundra); R. Janavicius (Ramunas); C.M. Dorfling (Cecilia); E.J. van Rensburg (Elizabeth); S.L. Neuhausen (Susan); Y.C. Ding (Yuan); T.V.O. Hansen (Thomas); L. Jønson (Lars); A.-M. Gerdes (Anne-Marie); B. Ejlertsen (Bent); D. Barrowdale (Daniel); J. Dennis (Joe); J. Benítez (Javier); A. Osorio (Ana); M.J. Garcia (Maria Jose); I. Komenaka (Ian); J.N. Weitzel (Jeffrey); P. Ganschow (Pamela); P. Peterlongo (Paolo); L. Bernard (Loris); A. Viel (Alessandra); B. Bonnani (Bernardo); B. Peissel (Bernard); S. Manoukian (Siranoush); P. Radice (Paolo); L. Papi (Laura); L. Ottini (Laura); F. Fostira (Florentia); I. Konstantopoulou (I.); J. Garber (Judy); D. Frost (Debra); J. Perkins (Jo); R. Platte (Radka); S.D. Ellis (Steve); A.K. Godwin (Andrew K.); R.K. Schmutzler (Rita); A. Meindl (Alfons); C. Engel (Christoph); C. Sutter (Christian); O. Sinilnikova (Olga); F. Damiola (Francesca); S. Mazoyer (Sylvie); D. Stoppa-Lyonnet (Dominique); K.B.M. Claes (Kathleen B.M.); K. De Leeneer (Kim); J. Kirk (Judy); G. Rodriguez (Gustavo); M. Piedmonte (Marion); D.M. O'Malley (David M.); M. de La Hoya (Miguel); T. Caldes (Trinidad); K. Aittomäki (Kristiina); H. Nevanlinna (Heli); J.M. Collée (Margriet); M.A. Rookus (Matti); J.C. Oosterwijk (Jan); L. Tihomirova (Laima); N. Tung (Nadine); U. Hamann (Ute); C. Isaccs (Claudine); M. Tischkowitz (Marc); E.N. Imyanitov (Evgeny); M.A. Caligo (Maria); I. Campbell (Ian); F.B.L. Hogervorst (Frans); E. Olah; O. Díez (Orland); I. Blanco (Ignacio); J. Brunet (Joan); C. Lazaro (Conxi); M.A. Pujana (Miguel); A. Jakubowska (Anna); J. Gronwald (Jacek); J. Lubinski (Jan); G. Sukiennicki (Grzegorz); R.B. Barkardottir (Rosa); M. Plante (Marie); J. Simard (Jacques); P. Soucy (Penny); M. Montagna (Marco); S. Tognazzo (Silvia); P.J. Teixeira; V.S. Pankratz (Shane); X. Wang (Xianshu); N.M. Lindor (Noralane); C. Szabo (Csilla); N. Kauff (Noah); J. Vijai (Joseph); C.A. Aghajanian (Carol A.); G. Pfeiler (Georg); A. Berger (Andreas); C.F. Singer (Christian); M.-K. Tea; C. Phelan (Catherine); M.H. Greene (Mark H.); P.L. Mai (Phuong); G. Rennert (Gad); A.-M. Mulligan (Anna-Marie); S. Tchatchou (Sandrine); I.L. Andrulis (Irene); G. Glendon (Gord); A.E. Toland (Amanda); U.B. Jensen (Uffe Birk); T.A. Kruse (Torben); M. Thomassen (Mads); A. Bojesen (Anders); J. Zidan (Jamal); E. Friedman (Eitan); Y. Laitman (Yael); M. Soller (Maria); A. Liljegren (Annelie); B. Arver (Brita Wasteson); Z. Einbeigi (Zakaria); M. Stenmark-Askmalm (Marie); O.I. Olopade (Olufunmilayo I.); R.L. Nussbaum (Robert L.); T.R. Rebbeck (Timothy R.); K.L. Nathanson (Katherine); S.M. Domchek (Susan); K.H. Lu (Karen); B.Y. Karlan (Beth Y.); C. Walsh (Christine); K.J. Lester (Kathryn); R. Hein (Rebecca); A.B. Ekici (Arif); M.W. Beckmann (Matthias); P.A. Fasching (Peter); D. Lambrechts (Diether); E. Van Nieuwenhuysen (Els); I. Vergote (Ignace); S. Lambrechts (Sandrina); E. Dicks (Ed); J.A. Doherty (Jennifer A.); K.G. Wicklund (Kristine G.); M.A. Rossing (Mary Anne); A. Rudolph (Anja); J. Chang-Claude (Jenny); S. Wang-Gohrke (Shan); U. Eilber (Ursula); K.B. Moysich (Kirsten B.); K. Odunsi (Kunle); L. Sucheston (Lara); S. Lele (Shashi); L. Wilkens (Lynne); M.T. Goodman (Marc); P.J. Thompson (Pamela J.); Y.B. Shvetsov (Yurii B.); I.B. Runnebaum (Ingo); M. Dürst (Matthias); P. Hillemanns (Peter); T. Dörk (Thilo); N.N. Antonenkova (Natalia); N.V. Bogdanova (Natalia); A. Leminen (Arto); L.M. Pelttari (Liisa); R. Butzow (Ralf); F. Modugno (Francesmary); J.L. Kelley (Joseph L.); R. Edwards (Robert); R.B. Ness (Roberta); A. Du Bois (Andreas); P.U. Heitz; I. Schwaab (Ira); P. Harter (Philipp); K. Matsuo (Keitaro); N. Hosono (Naoya); S. Orsulic (Sandra); A. Jensen (Allan); M. Kjaer (Michael); E. Høgdall (Estrid); H.N. Hasmad (Hanis Nazihah); M.A. Noor Azmi (Mat Adenan); S.-H. Teo (Soo-Hwang); Y.L. Woo (Yin Ling); B.L. Fridley (Brooke); E.L. Goode (Ellen); J.M. Cunningham (Julie); R.A. Vierkant (Robert); F. Bruinsma (Fiona); G.G. Giles (Graham G.); D. Liang (Dong); M.A.T. Hildebrandt (Michelle A.T.); X. Wu (Xifeng); D.A. Levine (Douglas); M. Bisogna (Maria); A. Berchuck (Andrew); E. Iversen (Erik); J.M. Schildkraut (Joellen); P. Concannon (Patrick); R.P. Weber (Rachel Palmieri); D.W. Cramer (Daniel); K.L. Terry (Kathryn); E.M. Poole (Elizabeth); S. Tworoger (Shelley); E.V. Bandera (Elisa); I. Orlow (Irene); S.H. Olson (Sara); C. Krakstad (Camilla); H.B. Salvesen (Helga); I.L. Tangen (Ingvild L.); L. Bjorge (Line); A.M. van Altena (Anne); K.K.H. Aben (Katja); L.A.L.M. Kiemeney (Bart); L.F. Massuger (Leon); M. Kellar (Melissa); A. Brooks-Wilson (Angela); L.E. Kelemen (Linda); L.S. Cook (Linda S.); N.D. Le (Nhu D.); C. Cybulski (Cezary); H. Yang (Hannah); J. Lissowska (Jolanta); L.A. Brinton (Louise); N. Wentzensen (N.); C.K. Høgdall (Claus); L. Lundvall (Lene); L. Nedergaard (Lotte); H. Baker (Helen); H. Song (Honglin); D. Eccles (Diana); I. McNeish (Ian); J. Paul (James); K. Carty (Karen); N. Siddiqui (Nadeem); R. Glasspool (Rosalind); A.S. Whittemore (Alice S.); J.H. Rothstein (Joseph H.); W.P. McGuire; W. Sieh (Weiva); B.-T. Ji (Bu-Tian); W. Zheng (Wei); X.-O. Shu (Xiao-Ou); Y. Gao; B. Rosen (Barry); H. Risch (Harvey); J. McLaughlin (John); S.A. Narod (Steven A.); A.N.A. Monteiro (Alvaro N.); A. Chen (Ann); H.-Y. Lin (Hui-Yi); J. Permuth-Wey (Jenny); T.F. Sellers; Y.-Y. Tsai (Ya-Yu); Z. Chen (Zhihua); A. Ziogas (Argyrios); H. Anton-Culver (Hoda); A. Gentry-Maharaj (Aleksandra); U. Menon (Usha); P. harrington (Patricia); A.W. Lee (Alice W.); A.H. Wu (Anna H.); C.L. Pearce (Celeste); G. Coetzee (Gerry); M.C. Pike (Malcolm C.); A. Dansonka-Mieszkowska (Agnieszka); A. Timorek (Agnieszka); I.K. Rzepecka (Iwona); J. Kupryjanczyk (Jolanta); M. Freedman (Matthew); H. Noushmehr (Houtan); D.F. Easton (Douglas F.); K. Offit (Kenneth); F.J. Couch (Fergus); S.A. Gayther (Simon); P.P.D.P. Pharoah (Paul P.D.P.); A.C. Antoniou (Antonis C.); G. Chenevix-Trench (Georgia)

    2015-01-01

    textabstractGenome-wide association studies (GWAS) have identified 12 epithelial ovarian cancer (EOC) susceptibility alleles. The pattern of association at these loci is consistent in BRCA1 and BRCA2 mutation carriers who are at high risk of EOC. After imputation to 1000 Genomes Project data, we

  14. Novel Centromeric Loci of the Wine and Beer Yeast Dekkera bruxellensis CEN1 and CEN2

    DEFF Research Database (Denmark)

    Ishchuk, Olena P.; Vojvoda Zeljko, Tanja; Schifferdecker, Anna J.

    2016-01-01

    The wine and beer yeast Dekkera bruxellensis thrives in environments that are harsh and limiting, especially in concentrations with low oxygen and high ethanol. Its different strains' chromosomes greatly vary in number (karyotype). This study isolates two novel centromeric loci (CEN1 and CEN2...

  15. Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index

    NARCIS (Netherlands)

    Speliotes, Elizabeth K.; Willer, Cristen J.; Berndt, Sonja I.; Monda, Keri L.; Thorleifsson, Gudmar; Jackson, Anne U.; Allen, Hana Lango; Lindgren, Cecilia M.; Luan, Jian'an; Maegi, Reedik; Randall, Joshua C.; Vedantam, Sailaja; Winkler, Thomas W.; Qi, Lu; Workalemahu, Tsegaselassie; Heid, Iris M.; Steinthorsdottir, Valgerdur; Stringham, Heather M.; Weedon, Michael N.; Wheeler, Eleanor; Wood, Andrew R.; Ferreira, Teresa; Weyant, Robert J.; Segre, Ayellet V.; Estrada, Karol; Liang, Liming; Nemesh, James; Park, Ju-Hyun; Gustafsson, Stefan; Kilpelaenen, Tuomas O.; Yang, Jian; Bouatia-Naji, Nabila; Esko, Tonu; Feitosa, Mary F.; Kutalik, Zoltan; Mangino, Massimo; Raychaudhuri, Soumya; Scherag, Andre; Smith, Albert Vernon; Welch, Ryan; Zhao, Jing Hua; Aben, Katja K.; Absher, Devin M.; Amin, Najaf; Dixon, Anna L.; Fisher, Eva; Glazer, Nicole L.; Goddard, Michael E.; Heard-Costa, Nancy L.; van Meurs, Joyce B. J.

    2010-01-01

    Obesity is globally prevalent and highly heritable, but its underlying genetic factors remain largely elusive. To identify genetic loci for obesity susceptibility, we examined associations between body mass index and similar to 2.8 million SNPs in up to 123,865 individuals with targeted follow up of

  16. Five willow varieties cultivated across diverse field environments reveal stem density variation associated with high tension wood abundance

    Directory of Open Access Journals (Sweden)

    Nicolas eBerthod

    2015-10-01

    Full Text Available Sustainable and inexpensive production of biomass is necessary to make biofuel production feasible, but represents a challenge. Five short rotation coppice (SRC willow cultivars, selected for high biomass yield, were cultivated on sites at four diverse regions of Quebec to determine their bioenergy potential in contrasting environments. Wood composition and anatomical traits were characterized. Tree height and stem diameter were measured to evaluate growth performance of the cultivars according to the diverse pedoclimatic conditions. Each cultivar showed very specific responses to its environment. While no significant variation in lignin content was observed between sites, there was variation between cultivars. Surprisingly, the pattern of substantial genotype variability in stem density was maintained across all sites. However, wood anatomy did differ between sites in a cultivar (producing high and low density wood, suggesting a probable response to an abiotic stress. Furthermore, twice as many cellulose-rich G-fibers, comprising over 50 % of secondary xylem, were also found in the high density wood, a finding with potential to bring higher value to the lignocellulosic bioethanol industry

  17. Variation in access to sugar-sweetened beverages in vending machines across rural, town and urban high schools.

    Science.gov (United States)

    Adachi-Mejia, A M; Longacre, M R; Skatrud-Mickelson, M; Li, Z; Purvis, L A; Titus, L J; Beach, M L; Dalton, M A

    2013-05-01

    The 2010 Dietary Guidelines for Americans include reducing consumption of sugar-sweetened beverages. Among the many possible routes of access for youth, school vending machines provide ready availability of sugar-sweetened beverages. The purpose of this study was to determine variation in high school student access to sugar-sweetened beverages through vending machines by geographic location - urban, town or rural - and to offer an approach for analysing school vending machine content. Cross-sectional observational study. Between October 2007 and May 2008, trained coders recorded beverage vending machine content and machine-front advertising in 113 machines across 26 schools in New Hampshire and Vermont, USA. Compared with town schools, urban schools were significantly less likely to offer sugar-sweetened beverages (P = 0.002). Rural schools also offered more sugar-sweetened beverages than urban schools, but this difference was not significant. Advertisements for sugar-sweetened beverages were highly prevalent in town schools. High school students have ready access to sugar-sweetened beverages through their school vending machines. Town schools offer the highest risk of exposure; school vending machines located in towns offer up to twice as much access to sugar-sweetened beverages in both content and advertising compared with urban locations. Variation by geographic region suggests that healthier environments are possible and some schools can lead as inspirational role models. Copyright © 2013 The Royal Society for Public Health. Published by Elsevier Ltd. All rights reserved.

  18. A Simple Ensemble Simulation Technique for Assessment of Future Variations in Specific High-Impact Weather Events

    Science.gov (United States)

    Taniguchi, Kenji

    2018-04-01

    To investigate future variations in high-impact weather events, numerous samples are required. For the detailed assessment in a specific region, a high spatial resolution is also required. A simple ensemble simulation technique is proposed in this paper. In the proposed technique, new ensemble members were generated from one basic state vector and two perturbation vectors, which were obtained by lagged average forecasting simulations. Sensitivity experiments with different numbers of ensemble members, different simulation lengths, and different perturbation magnitudes were performed. Experimental application to a global warming study was also implemented for a typhoon event. Ensemble-mean results and ensemble spreads of total precipitation, atmospheric conditions showed similar characteristics across the sensitivity experiments. The frequencies of the maximum total and hourly precipitation also showed similar distributions. These results indicate the robustness of the proposed technique. On the other hand, considerable ensemble spread was found in each ensemble experiment. In addition, the results of the application to a global warming study showed possible variations in the future. These results indicate that the proposed technique is useful for investigating various meteorological phenomena and the impacts of global warming. The results of the ensemble simulations also enable the stochastic evaluation of differences in high-impact weather events. In addition, the impacts of a spectral nudging technique were also examined. The tracks of a typhoon were quite different between cases with and without spectral nudging; however, the ranges of the tracks among ensemble members were comparable. It indicates that spectral nudging does not necessarily suppress ensemble spread.

  19. Nasal variation in relation to high-altitude adaptations among Tibetans and Andeans.

    Science.gov (United States)

    Butaric, Lauren N; Klocke, Ross P

    2018-05-01

    High-altitude (>2500 m) populations face several pressures, including hypoxia and cold-dry air, resulting in greater respiratory demand to obtain more oxygen and condition inspired air. While cardiovascular and pulmonary adaptations to high-altitude hypoxia have been extensively studied, adaptations of upper-respiratory structures, e.g., nasal cavity, remain untested. This study investigates whether nasal morphology presents adaptations to hypoxic (larger noses) and/or cold-dry (tall/narrow noses) conditions among high-altitude samples. CT scans of two high- and four low-altitude samples from diverse climates were collected (n = 130): high-altitude Tibetans and Peruvians; low-altitude Peruvians, Southern Chinese (temperate), Mongolian-Buriats (cold-dry), and Southeast Asians (hot-wet). Facial and nasal distances were calculated from 3D landmarks placed on digitally-modeled crania. Temperature, precipitation, and barometric pressure data were also obtained. Principal components analysis and analyses of variance primarily indicate size-related differences among the cold-dry (Mongolian-Buriats) and hot-wet (Southeast Asians) adapted groups. Two-block partial least squares (PLS) analysis show weak relationships between size-standardized nasal dimensions and environmental variables. However, among PLS1 (85.90% of covariance), Tibetans display relatively larger nasal cavities related to lower temperatures and barometric pressure; regression analyses also indicate high-altitude Tibetans possess relatively larger internal nasal breadths and heights for their facial size. Overall, nasal differences relate to climate among the cold-dry and hot-wet groups. Specific nasal adaptations were not identified among either Peruvian group, perhaps due to their relatively recent migration history and population structure. However, high-altitude Tibetans seem to exhibit a compromise in nasal morphology, serving in increased oxygen uptake, and air-conditioning processes. © 2018

  20. Identification of New Resistance Loci to African Stem Rust Race TTKSK in Tetraploid Wheats Based on Linkage and Genome-Wide Association Mapping.

    Science.gov (United States)

    Laidò, Giovanni; Panio, Giosuè; Marone, Daniela; Russo, Maria A; Ficco, Donatella B M; Giovanniello, Valentina; Cattivelli, Luigi; Steffenson, Brian; de Vita, Pasquale; Mastrangelo, Anna M

    2015-01-01

    Stem rust, caused by Puccinia graminis Pers. f. sp. tritici Eriks. and E. Henn. (Pgt), is one of the most destructive diseases of wheat. Races of the pathogen in the "Ug99 lineage" are of international concern due to their virulence for widely used stem rust resistance genes and their spread throughout Africa. Disease resistant cultivars provide one of the best means for controlling stem rust. To identify quantitative trait loci (QTL) conferring resistance to African stem rust race TTKSK at the seedling stage, we evaluated an association mapping (AM) panel consisting of 230 tetraploid wheat accessions under greenhouse conditions. A high level of phenotypic variation was observed in response to race TTKSK in the AM panel, allowing for genome-wide association mapping of resistance QTL in wild, landrace, and cultivated tetraploid wheats. Thirty-five resistance QTL were identified on all chromosomes, and seventeen are of particular interest as identified by multiple associations. Many of the identified resistance loci were coincident with previously identified rust resistance genes; however, nine on chromosomes 1AL, 2AL, 4AL, 5BL, and 7BS may be novel. To validate AM results, a biparental population of 146 recombinant inbred lines was also considered, which derived from a cross between the resistant cultivar "Cirillo" and susceptible "Neodur." The stem rust resistance of Cirillo was conferred by a single gene on the distal region of chromosome arm 6AL in an interval map coincident with the resistance gene Sr13, and confirmed one of the resistance loci identified by AM. A search for candidate resistance genes was carried out in the regions where QTL were identified, and many of them corresponded to NBS-LRR genes and protein kinases with LRR domains. The results obtained in the present study are of great interest as a high level of genetic variability for resistance to race TTKSK was described in a germplasm panel comprising most of the tetraploid wheat sub-species.

  1. Process Inference from High Frequency Temporal Variations in Dissolved Organic Carbon (DOC) Dynamics Across Nested Spatial Scales

    Science.gov (United States)

    Tunaley, C.; Tetzlaff, D.; Lessels, J. S.; Soulsby, C.

    2014-12-01

    In order to understand aquatic ecosystem functioning it is critical to understand the processes that control the spatial and temporal variations in DOC. DOC concentrations are highly dynamic, however, our understanding at short, high frequency timescales is still limited. Optical sensors which act as a proxy for DOC provide the opportunity to investigate near-continuous DOC variations in order to understand the hydrological and biogeochemical processes that control concentrations at short temporal scales. Here we present inferred 15 minute stream water DOC data for a 12 month period at three nested scales (1km2, 3km2 and 31km2) for the Bruntland Burn, a headwater catchment in NE Scotland. High frequency data were measured using FDOM and CDOM probes which work by measuring the fluorescent component and coloured component, respectively, of DOC when exposed to ultraviolet light. Both FDOM and CDOM were strongly correlated (r2 >0.8) with DOC allowing high frequency estimations. Results show the close coupling of DOC with discharge throughout the sampling period at all three spatial scales. However, analysis at the event scale highlights anticlockwise hysteresis relationships between DOC and discharge due to the delay in DOC being flushed from the increasingly large areas of peaty soils as saturation zones expand and increase hydrological connectivity. Lag times vary between events dependent on antecedent conditions. During a 10 year drought period in late summer 2013 it was apparent that very small changes in discharge on a 15 minute timescale result in high increases in DOC. This suggests transport limitation during this period where DOC builds up in the soil and is not flushed regularly, therefore any subsequent increase in discharge results in large DOC peaks. The high frequency sensors also reveal diurnal variability during summer months related to the photo-oxidation, evaporative and biological influences of DOC during the day. This relationship is less

  2. Fitness of allozyme variants in Drosophila pseudoobscura. II. Selection at the Est-5, Odh and Mdh-2 loci

    Energy Technology Data Exchange (ETDEWEB)

    Marinkovic, D; Ayala, F J

    1975-01-01

    We have studied the effects on fitness of allelic variation at three gene loci (Est-5, Odh, and Mdh-2) coding for enzymes in Drosophila pseudoobscura. Genotype has a significant effect on fitness for all six parameters measured (female fecundity, male mating capacity, egg-to-adult survival under near-optimal and under competitive conditions, and rate of development under near-optimal and under competitive conditions). No single genotype is best for all six fitness parameters; rather, genotypes with superior performance during a certain stage of the life-cycle may have low fitness at some other stage, or in different environmental conditions. Heterozygotes are sometimes best when all fitness parameters are considered. There are significant interactions between loci. The various forms of balancing selection uncovered in our experiments may account for the polymorphisms occurring in natural populations of D. pseudoobscura at the three loci studied. (auth)

  3. Structural Examination of RIASEC Scales in High School Students: Variation across Ethnicity and Method

    Science.gov (United States)

    Gupta, Saurabh; Tracey, Terence J. G.; Gore, Paul A., Jr.

    2008-01-01

    The structural validity of Holland's model of vocational interests across racial/ethnic groups was examined in the population of high school juniors in two states. The fit of the circumplex model to Holland's RIASEC types as assessed by the UNIACT-R was evaluated for the general sample and five subgroups: Caucasian/Euro-Americans, African…

  4. Variation of low temperature internal friction of microplastic deformation of high purity molybdenum single crystals

    International Nuclear Information System (INIS)

    Pal-Val, P.P.; Kaufmann, H.J.

    1984-01-01

    Amplitude and temperature spectra of ultrasound absorption in weakly deformed high purity molybdenum single crystals of different orientations were measured. The results were discussed in terms of parameter changes related to quasiparticle or dislocation oscillations, respectively, dislocation point defect interactions as well as defect generation at microplastic deformation. (author)

  5. Variation by Gender in Abu Dhabi High School Students' Interests in Physics

    Science.gov (United States)

    Badri, Masood; Mazroui, Karima Al; Al Rashedi, Asma; Yang, Guang

    2016-01-01

    Abu Dhabi high school students' interest in physics in different contexts was investigated with a survey conducted in connection with the international project, The Relevance of Science Education (ROSE). The sample consisted of 2248 students in public and private schools. Means of most items that belong to the school physics context for both girls…

  6. Variation of low temperature internal friction of microplastic deformation of high purity molybdenum single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Pal-Val, P.P. (AN Ukrainskoj SSR, Kharkov. Fiziko-Tekhnicheskij Inst. Nizkikh Temperatur); Kaufmann, H.J. (Akademie der Wissenschaften der DDR, Berlin)

    1984-08-01

    Amplitude and temperature spectra of ultrasound absorption in weakly deformed high purity molybdenum single crystals of different orientations were measured. The results were discussed in terms of parameter changes related to quasiparticle or dislocation oscillations, respectively, dislocation point defect interactions as well as defect generation at microplastic deformation.

  7. High throughput olfactory conditioning and memory retention test reveal variation in Nasonia parasitic wasps

    NARCIS (Netherlands)

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

    2012-01-01

    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

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

    NARCIS (Netherlands)

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

    2012-01-01

    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

  9. Variations in Star Excursion Balance Test Performance Between High School and Collegiate Football Players.

    Science.gov (United States)

    McCann, Ryan S; Kosik, Kyle B; Beard, Megan Q; Terada, Masafumi; Pietrosimone, Brian G; Gribble, Phillip A

    2015-10-01

    The Star Excursion Balance Test (SEBT) is a reliable inexpensive tool used to assess dynamic postural control deficits and efficacy in the prediction of musculoskeletal injuries, but with little previous consideration for performance differences across age and skill levels. The purpose of this study was to examine differences in SEBT scores between high school and collegiate football players. Three-hundred eighteen high school football players and 180 National Collegiate Athletic Association Division I collegiate football players volunteered to participate. Star Excursion Balance Test scores were obtained bilaterally for anterior (ANT), posterolateral (PL), and posteromedial (PM) directions, and for an overall composite (COMP) score. The mean of 3 trials from each leg was normalized to stance leg length and presented as a percentage score. Bilaterally averaged scores were compared between high school and collegiate football players using separate independent t-tests. A multiple linear backward regression determined the amount of variance in SEBT scores explained by age, mass, and height. Compared with collegiate athletes, high school athletes had lower PL (72.8 ± 11.4% vs. 77.1 ± 10.2%; p football players.

  10. An experimental investigation on bending stiffness and neutral axis depth variation of over-reinforced high strength concrete beams

    International Nuclear Information System (INIS)

    Mohammadhassani, Mohammad; Bin Jumaat, Mohd Zamin; Chemrouk, Mohamed; Akbar Maghsoudi, Ali; Jameel, Mohammed; Akib, Shatirah

    2011-01-01

    Highlights: → Improvement of the assessment of correspond stress for calculation of modules of elasticity → better evaluation of cracked moment of inertia. → Low distinction of neutral axis depth → low bending stiffness variation. → Rate of slope in the line connecting the origin of first crack to yield point of N.A.D-LOAD graph → rate of ductility of beam section. - Abstract: The present work is an attempt to study the neutral axis variation and the evolution of the moment inertia with the loading of over reinforced high strength concrete sections in conjunction with ACI 318-05. In this sense, four high strength concrete beams, having different tension reinforcement quantities expressed as proportions of the balanced steel ratio (0.75ρ b , 0.85ρ b , ρ b , 1.2ρ b ) were tested. Measurements of the deflection and the reinforcement and concrete strains of all specimens were made during the loading process. The load-neutral axis depth variation and the load-section stiffness curves were drawn. The slope of the line connecting the origin of the first crack to the initial yielding of the failure point in the neutral axis depth-load graphs shows the rate of ductility; ductile behaviour in the beam increases as the slope becomes steeper. Based on the results of this study, it is recommended that the modulus of elasticity of concrete E c be reviewed and evaluated at a stress higher than 0.5f ' c for the determination of the cracked moment of inertia.

  11. Relative variations of gut microbiota in disordered cholesterol metabolism caused by high-cholesterol diet and host genetics.

    Science.gov (United States)

    Bo, Tao; Shao, Shanshan; Wu, Dongming; Niu, Shaona; Zhao, Jiajun; Gao, Ling

    2017-08-01

    Recent studies performed provide mechanistic insight into effects of the microbiota on cholesterol metabolism, but less focus was given to how cholesterol impacts the gut microbiota. In this study, ApoE -/- Sprague Dawley (SD) rats and their wild-type counterparts (n = 12) were, respectively, allocated for two dietary condition groups (normal chow and high-cholesterol diet). Total 16S rDNA of fecal samples were extracted and sequenced by high-throughput sequencing to determine differences in microbiome composition. Data were collected and performed diversity analysis and phylogenetic analysis. The influence of cholesterol on gut microbiota was discussed by using cholesterol dietary treatment as exogenous cholesterol disorder factor and genetic modification as endogenous metabolic disorder factor. Relative microbial variations were compared to illustrate the causality and correlation of cholesterol and gut microbiota. It turned out comparing to genetically modified rats, exogenous cholesterol intake may play more effective role in changing gut microbiota profile, although the serum cholesterol level of genetically modified rats was even higher. Relative abundance of some representative species showed that the discrepancies due to dietary variation were more obvious, whereas some low abundance species changed because of genetic disorders. Our results partially demonstrated that gut microbiota are relatively more sensitive to dietary variation. Nevertheless, considering the important effect of bacteria in cholesterol metabolism, the influence to gut flora by "genetically caused cholesterol disorder" cannot be overlooked. Manipulation of gut microbiota might be an effective target for preventing cholesterol-related metabolic disorders. © 2017 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

  12. lociNGS: a lightweight alternative for assessing suitability of next-generation loci for evolutionary analysis.

    Directory of Open Access Journals (Sweden)

    Sarah M Hird

    Full Text Available Genomic enrichment methods and next-generation sequencing produce uneven coverage for the portions of the genome (the loci they target; this information is essential for ascertaining the suitability of each locus for further analysis. lociNGS is a user-friendly accessory program that takes multi-FASTA formatted loci, next-generation sequence alignments and demographic data as input and collates, displays and outputs information about the data. Summary information includes the parameters coverage per locus, coverage per individual and number of polymorphic sites, among others. The program can output the raw sequences used to call loci from next-generation sequencing data. lociNGS also reformats subsets of loci in three commonly used formats for multi-locus phylogeographic and population genetics analyses - NEXUS, IMa2 and Migrate. lociNGS is available at https://github.com/SHird/lociNGS and is dependent on installation of MongoDB (freely available at http://www.mongodb.org/downloads. lociNGS is written in Python and is supported on MacOSX and Unix; it is distributed under a GNU General Public License.

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

    Science.gov (United States)

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

    2011-11-01

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

  14. A high-throughput FTIR spectroscopy approach to assess adaptive variation in the chemical composition of pollen.

    Science.gov (United States)

    Zimmermann, Boris; Bağcıoğlu, Murat; Tafinstseva, Valeria; Kohler, Achim; Ohlson, Mikael; Fjellheim, Siri

    2017-12-01

    The two factors defining male reproductive success in plants are pollen quantity and quality, but our knowledge about the importance of pollen quality is limited due to methodological constraints. Pollen quality in terms of chemical composition may be either genetically fixed for high performance independent of environmental conditions, or it may be plastic to maximize reproductive output under different environmental conditions. In this study, we validated a new approach for studying the role of chemical composition of pollen in adaptation to local climate. The approach is based on high-throughput Fourier infrared (FTIR) characterization and biochemical interpretation of pollen chemical composition in response to environmental conditions. The study covered three grass species, Poa alpina , Anthoxanthum odoratum , and Festuca ovina . For each species, plants were grown from seeds of three populations with wide geographic and climate variation. Each individual plant was divided into four genetically identical clones which were grown in different controlled environments (high and low levels of temperature and nutrients). In total, 389 samples were measured using a high-throughput FTIR spectrometer. The biochemical fingerprints of pollen were species and population specific, and plastic in response to different environmental conditions. The response was most pronounced for temperature, influencing the levels of proteins, lipids, and carbohydrates in pollen of all species. Furthermore, there is considerable variation in plasticity of the chemical composition of pollen among species and populations. The use of high-throughput FTIR spectroscopy provides fast, cheap, and simple assessment of the chemical composition of pollen. In combination with controlled-condition growth experiments and multivariate analyses, FTIR spectroscopy opens up for studies of the adaptive role of pollen that until now has been difficult with available methodology. The approach can easily be

  15. Study on fluorescence-sensitization of 3 variations of scintillators in high speed autoradiography

    International Nuclear Information System (INIS)

    Wang Zhenli; Liu Guimin

    1993-01-01

    The sensitizing effects of POPOP, PBD and PPO were compared in 3 H-TdR incorporation experiment, 3 H-TdR low and high concentration twice labelling experiment and a cell migration tracer experiment. The results indicate that 7.5% PPO in xylene with an exposure time of 48 h is most satisfactory. The efficiency was increased for 15-20 times

  16. Cross-linguistic vowel variation in trilingual speakers of Saterland Frisian, Low German, and High German.

    Science.gov (United States)

    Peters, Jörg; Heeringa, Wilbert J; Schoormann, Heike E

    2017-08-01

    The present study compares the acoustic realization of Saterland Frisian, Low German, and High German vowels by trilingual speakers in the Saterland. The Saterland is a rural municipality in northwestern Germany. It offers the unique opportunity to study trilingualism with languages that differ both by their vowel inventories and by external factors, such as their social status and the autonomy of their speech communities. The objective of the study was to examine whether the trilingual speakers differ in their acoustic realizations of vowel categories shared by the three languages and whether those differences can be interpreted as effects of either the differences in the vowel systems or of external factors. Monophthongs produced in a /hVt/ frame revealed that High German vowels show the most divergent realizations in terms of vowel duration and formant frequencies, whereas Saterland Frisian and Low German vowels show small differences. These findings suggest that vowels of different languages are likely to share the same phonological space when the speech communities largely overlap, as is the case with Saterland Frisian and Low German, but may resist convergence if at least one language is shared with a larger, monolingual speech community, as is the case with High German.

  17. SSR allelic variation of rice variety Hangxiangnuo bred by space mutation

    International Nuclear Information System (INIS)

    Yang Tifeng; Liu Chuanguang; Pan Dajian; Fan Zhilan; Li Chen; Chen Jianyou; Liu Bin; Jiang Yijun; Gao Yun; Zhou Hanqin

    2011-01-01

    Hangxiangnuo, an indica fragrant glutinous rice mutant, was induced by space environment. Comparing with its wild type Nanfengnuo, the yield and blast resistance of Hangxiangnuo are improved significantly and the grain shape became slender and with fragrance. To understand the mechanisms of space mutation and identify the changes at molecular level associated with phenotypic variations, SSR allelic variation analysis were performed on Hangxiangnuo and Nanfengnuo in this study. The results showed that 45 loci were polymorphic among the 156 SSR loci tested throughout the genome, the frequency of variation was 28.85%. Among the polymorphic loci, 42 loci only showed variations in the molecular weight of the amplified bands, only on locus increased the number of amplification bands in Hangxiangnuo and two loci were differed by heterozygous loci (with two amplification bands at one locus) detected in Nanfengnuo and homozygous loci in Hangxiangnuo. It suggests that the change of some loci in mutants was due to the normal segregation and recombination of heterozygous loci of the wild type. The variation frequencies among different chromosomes were quite different, with the highest one at 50.00% detected on chromosomes 7, 8 and 12, and the lowest at 6.25% on chromosome 6. The polymorphic loci were clustered on chromosomes throughout the genome indicating that large DNA segments mutation is one of the major variation patterns induced by space environment. Some of reported QTLs involved in grain shape, yield, fragrance and blast resistance were found to be located exactly in the mutated regions. Therefore, further study is needed to confirm that these QTLs are responsible for the trait variations. (authors)

  18. A note on variational multiscale methods for high-contrast heterogeneous porous media flows with rough source terms

    KAUST Repository

    Calo, Victor M.

    2011-09-01

    In this short note, we discuss variational multiscale methods for solving porous media flows in high-contrast heterogeneous media with rough source terms. Our objective is to separate, as much as possible, subgrid effects induced by the media properties from those due to heterogeneous source terms. For this reason, enriched coarse spaces designed for high-contrast multiscale problems are used to represent the effects of heterogeneities of the media. Furthermore, rough source terms are captured via auxiliary correction equations that appear in the formulation of variational multiscale methods [23]. These auxiliary equations are localized and one can use additive or multiplicative constructions for the subgrid corrections as discussed in the current paper. Our preliminary numerical results show that one can capture the effects due to both spatial heterogeneities in the coefficients (such as permeability field) and source terms (e.g., due to singular well terms) in one iteration. We test the cases for both smooth source terms and rough source terms and show that with the multiplicative correction, the numerical approximations are more accurate compared to the additive correction. © 2010 Elsevier Ltd.

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

    Directory of Open Access Journals (Sweden)

    Zhang Xuegong

    2011-06-01

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

  20. Seasonal and diurnal variations of methane and carbon dioxide in the highly polluted Kathmandu Valley, Nepal

    Science.gov (United States)

    Mahata, Khadak; Panday, Arnico; Rupakheti, Maheswar; Lawrence, Mark

    2016-04-01

    Anthropogenic emissions of carbon dioxide and methane - key greenhouse gases (GHGs) - are primary causes of global warming and resultant impacts. The atmospheric warming is more pronounced and likely to cause more serious damage in vulnerable areas such as the Hindukush-Karakorum-Himalayan region (HKH). The HKH region is a data gap region according to the 5th Assessment report of the intergovernmental panel on climate change (IPCC). In order to understand the mixing ratios and variability of the key GHGs in the foothills of the Central Himalaya, we carried out continuous measurements of CO2, CH4, CO, and water vapor at Bode (an urban site in the Kathmandu valley, Nepal) for a year (March 2013 - Feb 2014), and again at Bode and at Chanban (a background outside the Valley) for 3 months (July 15 - Oct 3, 2015), with two state-of-the-art cavity ring-down instruments (Picarro G2401). The measurements were carried out as a part of the international air pollution measurement campaign: SusKat- ABC (Sustainable atmosphere for the Kathmandu Valley - Atmospheric Brown Clouds). The annual average CO2 and CH4 concentrations at Bode were 419 ± 24 and 2.192 ± 0.224 ppm, respectively, which are notably higher than those observed at the background site at Mauna Loa Observatory in the same period. The CO2concentration at Bode was high during the pre-monsoon period and low during the monsoon, while CH4 was high in winter and lower during the pre-monsoon period. The monthly CO2concentration was highest in April. Forest fires and agro-waste burning in the region, and the local emissions in the Kathmandu valley were the main sources of the high CO2 in the pre-monsoon period. CH4 showed a maximum in September due to additional emissions from paddy fields. Seasonally, winter has the highest CH4 concentration which is due to brick production, which is a seasonal activity, and other local sources combined with the shallow mixing layer height in winter. The diurnal pattern of CO2 and CH4

  1. Genome-wide association studies of autoimmune vitiligo identify 23 new risk loci and highlight key pathways and regulatory variants.

    Science.gov (United States)

    Jin, Ying; Andersen, Genevieve; Yorgov, Daniel; Ferrara, Tracey M; Ben, Songtao; Brownson, Kelly M; Holland, Paulene J; Birlea, Stanca A; Siebert, Janet; Hartmann, Anke; Lienert, Anne; van Geel, Nanja; Lambert, Jo; Luiten, Rosalie M; Wolkerstorfer, Albert; Wietze van der Veen, J P; Bennett, Dorothy C; Taïeb, Alain; Ezzedine, Khaled; Kemp, E Helen; Gawkrodger, David J; Weetman, Anthony P; Kõks, Sulev; Prans, Ele; Kingo, Külli; Karelson, Maire; Wallace, Margaret R; McCormack, Wayne T; Overbeck, Andreas; Moretti, Silvia; Colucci, Roberta; Picardo, Mauro; Silverberg, Nanette B; Olsson, Mats; Valle, Yan; Korobko, Igor; Böhm, Markus; Lim, Henry W; Hamzavi, Iltefat; Zhou, Li; Mi, Qing-Sheng; Fain, Pamela R; Santorico, Stephanie A; Spritz, Richard A

    2016-11-01

    Vitiligo is an autoimmune disease in which depigmented skin results from the destruction of melanocytes, with epidemiological association with other autoimmune diseases. In previous linkage and genome-wide association studies (GWAS1 and GWAS2), we identified 27 vitiligo susceptibility loci in patients of European ancestry. We carried out a third GWAS (GWAS3) in European-ancestry subjects, with augmented GWAS1 and GWAS2 controls, genome-wide imputation, and meta-analysis of all three GWAS, followed by an independent replication. The combined analyses, with 4,680 cases and 39,586 controls, identified 23 new significantly associated loci and 7 suggestive loci. Most encode immune and apoptotic regulators, with some also associated with other autoimmune diseases, as well as several melanocyte regulators. Bioinformatic analyses indicate a predominance of causal regulatory variation, some of which corresponds to expression quantitative trait loci (eQTLs) at these loci. Together, the identified genes provide a framework for the genetic architecture and pathobiology of vitiligo, highlight relationships with other autoimmune diseases and melanoma, and offer potential targets for treatment.

  2. Genetic variability and population structure in loci related to milk production traits in native Argentine Creole and commercial Argentine Holstein cattle

    Directory of Open Access Journals (Sweden)

    Golijow C.D.

    1999-01-01

    Full Text Available Many cattle breeds have been subjected to high selection pressure for production traits. Consequently, population genetic structure and allelic distribution could differ in breeds under high selection pressure compared to unselected breeds. Analysis of k-casein, aS1-casein and prolactin gene frequencies was made for Argentine Creole (AC and Argentine Holstein (AH cattle herds. The calculated FST values measured the degree of genetic differentiation of subpopulations, depending on the variances of gene frequencies.The AC breed had considerably more variation among herds at the aS1-casein and k-casein loci. Conservation strategies should consider the entire AC population in order to maintain the genetic variability found in this native breed.

  3. Dominant Epistasis Between Two Quantitative Trait Loci Governing Sporulation Efficiency in Yeast Saccharomyces cerevisiae

    Science.gov (United States)

    Bergman, Juraj; Mitrikeski, Petar T.

    2015-01-01

    Summary Sporulation efficiency in the yeast Saccharomyces cerevisiae is a well-established model for studying quantitative traits. A variety of genes and nucleotides causing different sporulation efficiencies in laboratory, as well as in wild strains, has already been extensively characterised (mainly by reciprocal hemizygosity analysis and nucleotide exchange methods). We applied a different strategy in order to analyze the variation in sporulation efficiency of laboratory yeast strains. Coupling classical quantitative genetic analysis with simulations of phenotypic distributions (a method we call phenotype modelling) enabled us to obtain a detailed picture of the quantitative trait loci (QTLs) relationships underlying the phenotypic variation of this trait. Using this approach, we were able to uncover a dominant epistatic inheritance of loci governing the phenotype. Moreover, a molecular analysis of known causative quantitative trait genes and nucleotides allowed for the detection of novel alleles, potentially responsible for the observed phenotypic variation. Based on the molecular data, we hypothesise that the observed dominant epistatic relationship could be caused by the interaction of multiple quantitative trait nucleotides distributed across a 60--kb QTL region located on chromosome XIV and the RME1 locus on chromosome VII. Furthermore, we propose a model of molecular pathways which possibly underlie the phenotypic variation of this trait. PMID:27904371

  4. RNA-Seq Highlights High Clonal Variation in Monoclonal Antibody Producing CHO Cells

    DEFF Research Database (Denmark)

    Orellana, Camila A.; Marcellin, Esteban; Palfreyman, Robin W.

    2018-01-01

    The development of next-generation sequencing technologies has opened new opportunities to better characterize complex eukaryotic cells. Chinese hamster ovary (CHO) cells play a primary role in therapeutic protein production, with currently five of the top ten blockbuster drugs produced in CHO......-regulation of genes encoding secreted glycoproteins is found to be the most significant change. The large number of significant differences even between subclones challenges the notion of identifying and manipulating a few key genes to generate high production CHO cell lines....

  5. VARIATION OF SUBSTRUCTURES OF PEARLITIC HEAT RESISTANT STEEL AFTER HIGH TEMPERATURE AGING

    Institute of Scientific and Technical Information of China (English)

    R.C.Yang; K.Chen; H.X.Feng; H.Wang

    2004-01-01

    The observations of dislocations, substructures and other microstructural details were conducted mainly by means of transmission electron microscope (TEM) and scanning electron microscope (SEM) for 12Cr1Mo V pearlitic heat-resistant steel. It is shown that during the high temperature long-term aging, the disordered and jumbled phasetransformed dislocations caused by normalized cooling are recovered and rearranged into cell substructures, and then the dislocation density is reduced gradually. Finally a low density linear dislocation configuration and a stabler dislocation network are formed and ferritic grains grow considerably.

  6. Variation of the Plasma Density in a Glow Discharge Upon the Application of A High Voltage

    International Nuclear Information System (INIS)

    Akman, S.

    2004-01-01

    It is emphasized and demonstrated that, during the formation of an ion-matrix sheath in a glow discharge upon the application of a high voltage pulse, the existing neutral plasma density should change as well. An explicit and practical expression for the neutral plasma density in terms of the gas pressure, secondary electron emission coefficient and the applied voltage is derived, so that the consequent sheath behavior can be formulated correctly. The theoretical result is compared with the data of an experiment, particularly designed and performed to test its validity, and found to be in good agreement with the latter

  7. Microgeographic and temporal genetic variation in populations of the bluetongue virus vector Culicoides variipennis (Diptera: Ceratopogonidae).

    Science.gov (United States)

    Tabachnick, W J

    1992-05-01

    Seven Colorado populations of the bluetongue virus vector Culicoides varipennis (Coquillett) were analyzed for genetic variation at 19-21 isozyme loci. Permanent populations, which overwinter as larvae, showed little temporal genetic change at 19 loci. PGD and MDH showed seasonal changes in gene frequencies, attributable to selection at two permanent populations. Two temporary populations showed low heterozygosity compared with permanent populations. Independent estimates of gene flow, calculated using FST and the private allele method, were Nm* = 2.15 and 6.95, respectively. Colorado C. variipennis permanent populations showed high levels of gene flow which prevented significant genetic differentiation due to genetic drift. Temporary populations showed significant gene frequency differences from nearby permanent populations due to the "founder effect" associated with chance colonization.

  8. Enhanced, targeted sampling of high-dimensional free-energy landscapes using variationally enhanced sampling, with an application to chignolin.

    Science.gov (United States)

    Shaffer, Patrick; Valsson, Omar; Parrinello, Michele

    2016-02-02

    The capabilities of molecular simulations have been greatly extended by a number of widely used enhanced sampling methods that facilitate escaping from metastable states and crossing large barriers. Despite these developments there are still many problems which remain out of reach for these methods which has led to a vigorous effort in this area. One of the most important problems that remains unsolved is sampling high-dimensional free-energy landscapes and systems that are not easily described by a small number of collective variables. In this work we demonstrate a new way to compute free-energy landscapes of high dimensionality based on the previously introduced variationally enhanced sampling, and we apply it to the miniprotein chignolin.

  9. Enhanced, targeted sampling of high-dimensional free-energy landscapes using variationally enhanced sampling, with an application to chignolin

    Science.gov (United States)

    Shaffer, Patrick; Valsson, Omar; Parrinello, Michele

    2016-01-01

    The capabilities of molecular simulations have been greatly extended by a number of widely used enhanced sampling methods that facilitate escaping from metastable states and crossing large barriers. Despite these developments there are still many problems which remain out of reach for these methods which has led to a vigorous effort in this area. One of the most important problems that remains unsolved is sampling high-dimensional free-energy landscapes and systems that are not easily described by a small number of collective variables. In this work we demonstrate a new way to compute free-energy landscapes of high dimensionality based on the previously introduced variationally enhanced sampling, and we apply it to the miniprotein chignolin. PMID:26787868

  10. DETERMINING THE COMPOSITION OF HIGH TEMPERATURE COMBUSTION PRODUCTS OF FOSSIL FUEL BASED ON VARIATIONAL PRINCIPLES AND GEOMETRIC PROGRAMMING

    Directory of Open Access Journals (Sweden)

    Velibor V Vujović

    2011-01-01

    Full Text Available This paper presents the algorithm and results of a computer program for calculation of complex equilibrium composition for the high temperature fossil fuel combustion products. The method of determining the composition of high temperatures combustion products at the temperatures appearing in the open cycle MHD power generation is given. The determination of combustion product composition is based on minimization of the Gibbs free energy. The number of equations to be solved is reduced by using variational principles and a method of geometric programming and is equal to the sum of the numbers of elements and phases. A short description of the computer program for the calculation of the composition and an example of the results are also given.

  11. Nonparametric functional mapping of quantitative trait loci.

    Science.gov (United States)

    Yang, Jie; Wu, Rongling; Casella, George

    2009-03-01

    Functional mapping is a useful tool for mapping quantitative trait loci (QTL) that control dynamic traits. It incorporates mathematical aspects of biological processes into the mixture model-based likelihood setting for QTL mapping, thus increasing the power of QTL detection and the precision of parameter estimation. However, in many situations there is no obvious functional form and, in such cases, this strategy will not be optimal. Here we propose to use nonparametric function estimation, typically implemented with B-splines, to estimate the underlying functional form of phenotypic trajectories, and then construct a nonparametric test to find evidence of existing QTL. Using the representation of a nonparametric regression as a mixed model, the final test statistic is a likelihood ratio test. We consider two types of genetic maps: dense maps and general maps, and the power of nonparametric functional mapping is investigated through simulation studies and demonstrated by examples.

  12. Linkage analysis: Inadequate for detecting susceptibility loci in complex disorders?

    Energy Technology Data Exchange (ETDEWEB)

    Field, L.L.; Nagatomi, J. [Univ. of Calgary, Alberta (Canada)

    1994-09-01

    Insulin-dependent diabetes mellitus (IDDM) may provide valuable clues about approaches to detecting susceptibility loci in other oligogenic disorders. Numerous studies have demonstrated significant association between IDDM and a VNTR in the 5{prime} flanking region of the insulin (INS) gene. Paradoxically, all attempts to demonstrate linkage of IDDM to this VNTR have failed. Lack of linkage has been attributed to insufficient marker locus information, genetic heterogeneity, or high frequency of the IDDM-predisposing allele in the general population. Tyrosine hydroxylase (TH) is located 2.7 kb from INS on the 5` side of the VNTR and shows linkage disequilibrium with INS region loci. We typed a highly polymorphic microsatellite within TH in 176 multiplex families, and performed parametric (lod score) linkage analysis using various intermediate reduced penetrance models for IDDM (including rare and common disease allele frequencies), as well as non-parametric (affected sib pair) linkage analysis. The scores significantly reject linkage for recombination values of .05 or less, excluding the entire 19 kb region containing TH, the 5{prime} VNTR, the INS gene, and IGF2 on the 3{prime} side of INS. Non-parametric linkage analysis also provided no significant evidence for linkage (mean TH allele sharing 52.5%, P=.12). These results have important implications for efforts to locate genes predisposing to complex disorders, strongly suggesting that regions which are significantly excluded by linkage methods may nevertheless contain predisposing genes readily detectable by association methods. We advocate that investigators routinely perform association analyses in addition to linkage analyses.

  13. Jet Impingement Heat Transfer at High Reynolds Numbers and Large Density Variations

    DEFF Research Database (Denmark)

    Jensen, Michael Vincent; Walther, Jens Honore

    2010-01-01

    Jet impingement heat transfer from a round gas jet to a flat wall has been investigated numerically in a configuration with H/D=2, where H is the distance from the jet inlet to the wall and D is the jet diameter. The jet Reynolds number was 361000 and the density ratio across the wall boundary...... layer was 3.3 due to a substantial temperature difference of 1600K between jet and wall. Results are presented which indicate very high heat flux levels and it is demonstrated that the jet inlet turbulence intensity significantly influences the heat transfer results, especially in the stagnation region....... The results also show a noticeable difference in the heat transfer predictions when applying different turbulence models. Furthermore calculations were performed to study the effect of applying temperature dependent thermophysical properties versus constant properties and the effect of calculating the gas...

  14. Variational Multiscale Finite Element Method for Flows in Highly Porous Media

    KAUST Repository

    Iliev, O.; Lazarov, R.; Willems, J.

    2011-01-01

    We present a two-scale finite element method (FEM) for solving Brinkman's and Darcy's equations. These systems of equations model fluid flows in highly porous and porous media, respectively. The method uses a recently proposed discontinuous Galerkin FEM for Stokes' equations by Wang and Ye and the concept of subgrid approximation developed by Arbogast for Darcy's equations. In order to reduce the "resonance error" and to ensure convergence to the global fine solution, the algorithm is put in the framework of alternating Schwarz iterations using subdomains around the coarse-grid boundaries. The discussed algorithms are implemented using the Deal.II finite element library and are tested on a number of model problems. © 2011 Society for Industrial and Applied Mathematics.

  15. Variational Multiscale Finite Element Method for Flows in Highly Porous Media

    KAUST Repository

    Iliev, O.

    2011-10-01

    We present a two-scale finite element method (FEM) for solving Brinkman\\'s and Darcy\\'s equations. These systems of equations model fluid flows in highly porous and porous media, respectively. The method uses a recently proposed discontinuous Galerkin FEM for Stokes\\' equations by Wang and Ye and the concept of subgrid approximation developed by Arbogast for Darcy\\'s equations. In order to reduce the "resonance error" and to ensure convergence to the global fine solution, the algorithm is put in the framework of alternating Schwarz iterations using subdomains around the coarse-grid boundaries. The discussed algorithms are implemented using the Deal.II finite element library and are tested on a number of model problems. © 2011 Society for Industrial and Applied Mathematics.

  16. Searches for high frequency variations in the 8-B neutrino flux at the Sudbury neutrino observatory

    Energy Technology Data Exchange (ETDEWEB)

    Rielage, Keith [Los Alamos National Laboratory; Seibert, Stanley R [Los Alamos National Laboratory; Hime, Andrew [Los Alamos National Laboratory; Elliott, Steven R [Los Alamos National Laboratory; Stonehill, L C [Los Alamos National Laboratory; Wouters, J M [Los Alamos National Laboratory; Aharmim, B [LAURENTIAN UNIV; Ahmed, S N [QUEEN' S UNIV; Anthony, A E [UNIV OF TEXAS; Barros, N [PORTUGAL; Beier, E W [UNIV OF PA; Bellerive, A [CARLETON UNIV; Belttran, B [UNIV OF ALBERTA; Bergevin, M [LBNL; Biller, S D [UNIV OF OXFORD; Boudjemline, K [CARLETON UNIV; Burritt, T H [UNIV OF WASHINGTON; Cai, B [QUEEN' S UNIV; Chan, Y D [LBNL; Chauhan, D [LAURENTIAN UNIV; Chen, M [QUEEN' S UNIV; Cleveland, B T [UNIV OF OXFORD; Cox - Mobrand, G A [UNIV OF WASHINGTON; Dai, X [QUEEN' S UNIV; Deng, H [UNIV OF PA; Detwiler, J [LBNL; Dimarco, M [QUEEN' S UNIV; Doe, P J [UNIV OF WASHINGTON; Drouin, P - L [CARLTON UNIV; Duba, C A [UNIV OF WASHINGTON; Duncan, F A [SNOLAB, SUDBURY; Dunford, M [UNIV OF PA; Earle, E D [QUEEN' S UNIV; Evans, H C [QUEEN' S UNIV; Ewan, G T [QUEEN' S UNIV; Farine, J [LAURENTTIAN UNIV; Fergani, H [UNIV OF OXFORD; Fleurot, F [LAURENTIAN UNIV; Ford, R J [SNOLAB, SUDBURY; Formaggilo, J A [MASSACHUSETTS INST. OF TECH.; Gagnon, N [UNIV OF WASHINGTON; Goon, J Tm [LOUISIANA STATE UNIV; Guillian, E [QUEEN' S UNIV; Habib, S [UNIV OF ALBERTA; Hahn, R L [BNL; Hallin, A L [UNIV OF ALBERTA; Hallman, E D [LAURENTIAN UNIV; Harvey, P J [QUEEN' S UNIV; Hazama, R [UNIV OF WASHINGTON; Heintzelman, W J [UNIV OF PA; Heise, J [SNOLAB, SUDBURY; Helmer, R L [TRIUMF; Howard, C [UNIV OF ALBERTA; Howe, M A [UNIV OF WASHINGTON; Huang, M [UNIV OF TEXAS; Jamieson, B [UNIV OF BRITISH COLUMBIA; Jelley, N A [UNIV OF OXFORD; Keeter, K J [SNOLAB, SUDBURY; Klein, J R [UNIV OF TEXAS; Kos, M [QUEEN' S UNIV; Kraus, C [QUEEN' S UNIV; Krauss, C B [UNIV OF ALBERTA; Kutter, T [LOUISIANA STATE UNIV; Kyba, C C M [UNIV OF PA; Law, J [UNIV OF GUELPH; Lawson, I T [SNOLAB, SUDBURY; Lesko, K T [LBNL; Leslie, J R [QUEEN' S UNIV; Loach, J C [UNIV OF OXFORD; Maclellan, R [QUEEN' S UNIV; Majerus, S [UNIV OF OXFORD; Mak, H B [QUEEN' S UNIV; Maneira, J [PORTUGAL; Martin, R [QUEEN' S UNIV; Mccauley, N [UNIV OF PA; Mc Donald, A B [QUEEN' S UNIV; Mcgee, S [UNIV OF WASHINGTON; Miffin, C [CARLETON UNIV; Miller, M L [MASSACHUSETTS INST. OF TECH.; Monreal, B [MASSACHUSETTS INST. OF TECH.; Monroe, J [MASSACHUSETTS INST. OF TECH; Morissette, B [SNOLAB, SUDBURY; Nickel, B G [UNIV OF GUELPH; Noble, A J [QUEEN' S UNIV; O' Keeffe, H M [UNIV OF OXFORD; Oblath, N S [UNIV OF WASHINGTON; Orebi Gann, G D [UNIV OF OXFORD; Oser, S M [UNIV OF BRITISH COLUMBIA; Ott, R A [MASSACHUSETTS INST. OF TECH.; Peeters, S J M [UNIV OF OXFORD; Poon, A W P [LBNL; Prior, G [LBNL; Reitzner, S D [UNIV OF GUELPH; Robertson, B C [QUEEN' S UNIV; Robertson, R G H [UNIV OF WASHINGTON; Rollin, E [CARLETON UNIV; Schwendener, M H [LAURENTIAN UNIV; Secrest, J A [UNIV OF PA; Seibert, S R [UNIV OF TEXAS; Simard, O [CARLETON UNIV; Sinclair, D [CARLETON UNIV; Sinclair, L [CARLETON UNIV; Skensved, P [QUEEN' S UNIV; Sonley, T J [MASSACHUSETTS INST. OF TECH.; Tesic, G [CARLETON UNIV; Tolich, N [UNIV OF WASHINGTON; Tsui, T [UNIV OF BRITISH COLUMBIA; Tunnell, C D [UNIV OF TEXAS; Van Berg, R [UNIV OF PA; Van Devender, B A [UNIV OF WASHINGTON; Virtue, C J [LAURENTIAN UNIV; Wall, B L [UNIV OF WASHINGTON; Waller, D [CARLETON UNIV; Wan Chan Tseung, H [UNIV OF OXFORD; West, N [UNIV OF OXFORD; Wilkerson, J F [UNIV OF WASHINGTON; Wilson, J R [UNIV OF OXFORD; Wright, A [QUEEN' S UNIV; Yeh, M [BNL; Zhang, F [CARLETON UNIV; Zuber, K [UNIV OF OXFORD

    2009-01-01

    We have peformed three searches for high-frequency signals in the solar neutrino flux measured by the Sudbury Neutrino Observatory (SNO), motivated by the possibility that solar g-mode oscillations could affect the production or propagation of solar {sup 8}B neutrinos. The first search looked for any significant peak in the frequency range l/day to 144/day, with a sensitivity to sinusoidal signals with amplitudes of 12% or greater. The second search focused on regions in which g-mode signals have been claimed by experiments aboard the SoHO satellite, and was sensitive to signals with amplitudes of 10% or greater. The third search looked for extra power across the entire frequency band. No statistically significant signal was detected in any of the three searches.

  17. Variation by Gender in Abu Dhabi High School Students' Interests in Physics

    Science.gov (United States)

    Badri, Masood; Mazroui, Karima Al; Al Rashedi, Asma; Yang, Guang

    2016-04-01

    Abu Dhabi high school students' interest in physics in different contexts was investigated with a survey conducted in connection with the international project, The Relevance of Science Education (ROSE). The sample consisted of 2248 students in public and private schools. Means of most items that belong to the school physics context for both girls and boys were below the score of (3.0). The most interesting topics for both genders were connected with fantasy items. The least interesting items (particularly for girls) were connected with artifacts and technological processes. Girls assigned the highest scores for "why we dream" and "life and death." Boys assigned the highest scores for "inventions and discoveries" and "life outside of earth." The main message of the study is that new curricular approaches and textbooks can be developed through combining technological and human contexts. The implications for curriculum development, teacher professional development programs, and other education strategies in Abu Dhabi are discussed in light of the ROSE survey.

  18. Theory in Highly Cited Studies of Sexual Minority Parent Families: Variations and Implications.

    Science.gov (United States)

    Farr, Rachel H; Tasker, Fiona; Goldberg, Abbie E

    2017-01-01

    This article includes a systematic review and citation analysis of the literature regarding sexual minority parent families, particularly attending to what theories have been used, and how. We consider the importance of theoretical frameworks for future research and implications for policy, practice, and law related to sexual minority parent families. Our review targets 30 highly cited studies located through Google Scholar (as an interdisciplinary search engine) and published within a specific timeframe (2005-2010). We highlight the dominant theoretical models employed across disciplines studying sexual minority parent families. Although the majority of studies reviewed referred to theoretical models or perspectives, explicit theoretical grounding was frequently lacking. Instead, the empirical work reviewed appeared to have a predominantly applied focus in addressing public debates on sexual minority parent families. We provide recommendations for how theory might be more fully integrated into the social science literature on sexual minority parents and their children.

  19. Unraveling possible association between quantitative trait loci (QTL ...

    African Journals Online (AJOL)

    Unraveling possible association between quantitative trait loci (QTL) for partial resistance and nonhost resistance in food barley ( Hordeum vulgaris L.) ... Abstract. Many quantitative trait loci (QTLs) in different barley populations were discovered for resistance to Puccinia hordei and heterologous rust species. Partial ...

  20. Genetic evidence of multiple loci in dystocia - difficult labour

    Directory of Open Access Journals (Sweden)

    Westgren Magnus

    2010-06-01

    Full Text Available Abstract Background Dystocia, difficult labour, is a common but also complex problem during childbirth. It can be attributed to either weak contractions of the uterus, a large infant, reduced capacity of the pelvis or combinations of these. Previous studies have indicated that there is a genetic component in the susceptibility of experiencing dystocia. The purpose of this study was to identify susceptibility genes in dystocia. Methods A total of 104 women in 47 families were included where at least two sisters had undergone caesarean section at a gestational length of 286 days or more at their first delivery. Study of medical records and a telephone interview was performed to identify subjects with dystocia. Whole-genome scanning using Affymetrix genotyping-arrays and non-parametric linkage (NPL analysis was made in 39 women exhibiting the phenotype of dystocia from 19 families. In 68 women re-sequencing was performed of candidate genes showing suggestive linkage: oxytocin (OXT on chromosome 20 and oxytocin-receptor (OXTR on chromosome 3. Results We found a trend towards linkage with suggestive NPL-score (3.15 on chromosome 12p12. Suggestive linkage peaks were observed on chromosomes 3, 4, 6, 10, 20. Re-sequencing of OXT and OXTR did not reveal any causal variants. Conclusions Dystocia is likely to have a genetic component with variations in multiple genes affecting the patient outcome. We found 6 loci that could be re-evaluated in larger patient cohorts.

  1. Genetic evidence of multiple loci in dystocia - difficult labour

    Science.gov (United States)

    2010-01-01

    Background Dystocia, difficult labour, is a common but also complex problem during childbirth. It can be attributed to either weak contractions of the uterus, a large infant, reduced capacity of the pelvis or combinations of these. Previous studies have indicated that there is a genetic component in the susceptibility of experiencing dystocia. The purpose of this study was to identify susceptibility genes in dystocia. Methods A total of 104 women in 47 families were included where at least two sisters had undergone caesarean section at a gestational length of 286 days or more at their first delivery. Study of medical records and a telephone interview was performed to identify subjects with dystocia. Whole-genome scanning using Affymetrix genotyping-arrays and non-parametric linkage (NPL) analysis was made in 39 women exhibiting the phenotype of dystocia from 19 families. In 68 women re-sequencing was performed of candidate genes showing suggestive linkage: oxytocin (OXT) on chromosome 20 and oxytocin-receptor (OXTR) on chromosome 3. Results We found a trend towards linkage with suggestive NPL-score (3.15) on chromosome 12p12. Suggestive linkage peaks were observed on chromosomes 3, 4, 6, 10, 20. Re-sequencing of OXT and OXTR did not reveal any causal variants. Conclusions Dystocia is likely to have a genetic component with variations in multiple genes affecting the patient outcome. We found 6 loci that could be re-evaluated in larger patient cohorts. PMID:20587075

  2. Multiple loci are associated with white blood cell phenotypes.

    Directory of Open Access Journals (Sweden)

    Michael A Nalls

    2011-06-01

    Full Text Available White blood cell (WBC count is a common clinical measure from complete blood count assays, and it varies widely among healthy individuals. Total WBC count and its constituent subtypes have been shown to be moderately heritable, with the heritability estimates varying across cell types. We studied 19,509 subjects from seven cohorts in a discovery analysis, and 11,823 subjects from ten cohorts for replication analyses, to determine genetic factors influencing variability within the normal hematological range for total WBC count and five WBC subtype measures. Cohort specific data was supplied by the CHARGE, HeamGen, and INGI consortia, as well as independent collaborative studies. We identified and replicated ten associations with total WBC count and five WBC subtypes at seven different genomic loci (total WBC count-6p21 in the HLA region, 17q21 near ORMDL3, and CSF3; neutrophil count-17q21; basophil count- 3p21 near RPN1 and C3orf27; lymphocyte count-6p21, 19p13 at EPS15L1; monocyte count-2q31 at ITGA4, 3q21, 8q24 an intergenic region, 9q31 near EDG2, including three previously reported associations and seven novel associations. To investigate functional relationships among variants contributing to variability in the six WBC traits, we utilized gene expression- and pathways-based analyses. We implemented gene-clustering algorithms to evaluate functional connectivity among implicated loci and showed functional relationships across cell types. Gene expression data from whole blood was utilized to show that significant biological consequences can be extracted from our genome-wide analyses, with effect estimates for significant loci from the meta-analyses being highly corellated with the proximal gene expression. In addition, collaborative efforts between the groups contributing to this study and related studies conducted by the COGENT and RIKEN groups allowed for the examination of effect homogeneity for genome-wide significant associations across

  3. Allele frequency distribution for 15 autosomal STR loci in Afridi Pathan population of Uttar Pradesh, India.

    Science.gov (United States)

    Noor, Sabahat; Ali, Shahnaz; Eaaswarkhanth, Muthukrishnan; Haque, Ikramul

    2009-11-01

    Allele frequencies of the 15 autosomal short tandem repeat (STR) loci D8S1179, D21S11, D7S820, CSF1PO D19S433, vWA, TPOX, D18S51, D3S1358, THO1, D13S317, D16S539, D2S1338, D5S818 and FGA were determined in Afridi Pathan population of Uttar Pradesh, India. All the 15 STR loci studied were found to be highly polymorphic with respect to observed heterozygosity values. Adherence to the expectations of the Hardy-Weinberg equilibrium (HWE) was confirmed for all the loci with an exception of TPOX and FGA. The allele 12 in CSF1PO was found to be most frequent. The power of discrimination was found to be high ranging from a minimum of 0.858 for the locus CSFIPO to maximum of 0.962 for the locus FGA, thereby facilitating the validation and efficiency of these STR markers in human identification. Population differentiation test between the studied and neighboring populations revealed significant differences at several loci suggesting the endogamous nature of the studied population. To the best of our knowledge, Afridi Pathan population has not been explored genetically for generating forensic data on STR markers. Therefore, STR allele frequency data of this unique population is a valuable contribution to the existing DNA database on Indian populations.

  4. Biallelic and Genome Wide Association Mapping of Germanium Tolerant Loci in Rice (Oryza sativa L..

    Directory of Open Access Journals (Sweden)

    Partha Talukdar

    Full Text Available Rice plants accumulate high concentrations of silicon. Silicon has been shown to be involved in plant growth, high yield, and mitigating biotic and abiotic stresses. However, it has been demonstrated that inorganic arsenic is taken up by rice through silicon transporters under anaerobic conditions, thus the ability to efficiently take up silicon may be considered either a positive or a negative trait in rice. Germanium is an analogue of silicon that produces brown lesions in shoots and leaves, and germanium toxicity has been used to identify mutants in silicon and arsenic transport. In this study, two different genetic mapping methods were performed to determine the loci involved in germanium sensitivity in rice. Genetic mapping in the biparental cross of Bala × Azucena (an F6 population and a genome wide association (GWA study with 350 accessions from the Rice Diversity Panel 1 were conducted using 15 μM of germanic acid. This identified a number of germanium sensitive loci: some co-localised with previously identified quantitative trait loci (QTL for tissue silicon or arsenic concentration, none co-localised with Lsi1 or Lsi6, while one single nucleotide polymorphism (SNP was detected within 200 kb of Lsi2 (these are genes known to transport silicon, whose identity was discovered using germanium toxicity. However, examining candidate genes that are within the genomic region of the loci detected above reveals genes homologous to both Lsi1 and Lsi2, as well as a number of other candidate genes, which are discussed.

  5. Variation in the stress response between high- and low-neuroticism female undergraduates across the menstrual cycle.

    Science.gov (United States)

    Liu, Qing; Zhou, Renlai; Oei, Tian P S; Wang, Qingguo; Zhao, Yan; Liu, Yanfeng

    2013-09-01

    This study was undertaken to elucidate possible relationships between menstrual cycle stage, neuroticism and behavioral and physiological responses to a cognitive challenge. The study investigated the differences between high neuroticism and low neuroticism groups across the menstrual cycle (luteal, menstrual and ovulatory stages). The Stroop color-naming task was used as a stressor. During the task, the galvanic skin response (GSR), heart rate (HR) and HR variability (HRV) were simultaneously recorded by a polygraph. The results showed a significant difference in reaction times (RT) on the Stroop task between the high- and low-neuroticism groups during menstruation. However, there were no significant RT differences between groups during the luteal or ovulatory cycle stages. The GSR of the high-neuroticism group during menstruation was significantly lower than it was in the luteal and ovulatory stages. Moreover, during menstruation, the cardiovascular responses (high-frequency HRV (HF) and low-frequency HRV (LF)) and accuracy on the Stroop task were positively correlated, while the correlations between HF, LF and the RT were negative. The results demonstrate that during menstruation, there were consistent variations in female behavior and physiology when facing a cognitive stressor. Specifically, the high-neuroticism group was more sensitive to the stressor than the low neuroticism group, with decreased reaction time on the Stroop task, and increased GSR and HRV.

  6. Browns Ferry Nuclear Plant: variation in test intervals for high-pressure coolant injection (HPCI) system

    International Nuclear Information System (INIS)

    Christie, R.F.; Stetkar, J.W.

    1985-01-01

    The change in availability of the high-pressure coolant injection system (HPCIS) due to a change in pump and valve test interval from monthly to quarterly was analyzed. This analysis started by using the HPCIS base line evaluation produced as part of the Browns Ferry Nuclear Plant (BFN) Probabilistic Risk Assessment (PRA). The base line evaluation showed that the dominant contributors to the unavailability of the HPCI system are hardware failures and the resultant downtime for unscheduled maintenance. The effect of changing the pump and valve test interval from monthly to quarterly was analyzed by considering the system unavailability due to hardware failures, the unavailability due to testing, and the unavailability due to human errors that potentially could occur during testing. The magnitude of the changes in unavailability affected by the change in test interval are discussed. The analysis showed a small increase in the availability of the HPCIS to respond to loss of coolant accidents (LOCAs) and a small decrease in the availability of the HPCIS to respond to transients which require HPCIS actuation. In summary, the increase in test interval from monthly to quarterly does not significantly impact the overall HPCIS availability

  7. Detection of genomic variation by selection of a 9 mb DNA region and high throughput sequencing.

    Directory of Open Access Journals (Sweden)

    Sergey I Nikolaev

    Full Text Available Detection of the rare polymorphisms and causative mutations of genetic diseases in a targeted genomic area has become a major goal in order to understand genomic and phenotypic variability. We have interrogated repeat-masked regions of 8.9 Mb on human chromosomes 21 (7.8 Mb and 7 (1.1 Mb from an individual from the International HapMap Project (NA12872. We have optimized a method of genomic selection for high throughput sequencing. Microarray-based selection and sequencing resulted in 260-fold enrichment, with 41% of reads mapping to the target region. 83% of SNPs in the targeted region had at least 4-fold sequence coverage and 54% at least 15-fold. When assaying HapMap SNPs in NA12872, our sequence genotypes are 91.3% concordant in regions with coverage > or = 4-fold, and 97.9% concordant in regions with coverage > or = 15-fold. About 81% of the SNPs recovered with both thresholds are listed in dbSNP. We observed that regions with low sequence coverage occur in close proximity to low-complexity DNA. Validation experiments using Sanger sequencing were performed for 46 SNPs with 15-20 fold coverage, with a confirmation rate of 96%, suggesting that DNA selection provides an accurate and cost-effective method for identifying rare genomic variants.

  8. Iodine monoxide at a clean marine coastal site: observations of high frequency variations and inhomogeneous distributions

    Directory of Open Access Journals (Sweden)

    R. Commane

    2011-07-01

    Full Text Available The first in situ point observations of iodine monoxide (IO at a clean marine site were made using a laser-induced fluorescence instrument deployed at Mace Head, Ireland in August 2007. IO mixing ratios of up to 49.8 pptv (equivalent to pmol mol−1; 1 s average were observed at day-time low tide, well in excess of previous observed spatially-averaged maxima. A strong anti-correlation of IO mixing ratios with tide height was evident and the high time resolution of the observations showed IO peaked in the hour after low tide. The temporal delay in peak IO compared to low tide has not been observed previously but coincides with the time of peak aerosol number previously observed at Mace Head.

    A long path-differential optical absorption spectroscopy instrument (with a 2 × 6.8 km folded path across Roundstone Bay was also based at the site for 3 days during the point measurement observation period. Both instruments show similar temporal trends but the point measurements of IO are a factor of ~6–10 times greater than the spatially averaged IO mixing ratios, providing direct empirical evidence of the presence of inhomogeneities in the IO mixing ratio near the intertidal region.

  9. Admixture mapping of 15,280 African Americans identifies obesity susceptibility loci on chromosomes 5 and X.

    Directory of Open Access Journals (Sweden)

    Ching-Yu Cheng

    2009-05-01

    Full Text Available The prevalence of obesity (body mass index (BMI > or =30 kg/m(2 is higher in African Americans than in European Americans, even after adjustment for socioeconomic factors, suggesting that genetic factors may explain some of the difference. To identify genetic loci influencing BMI, we carried out a pooled analysis of genome-wide admixture mapping scans in 15,280 African Americans from 14 epidemiologic studies. Samples were genotyped at a median of 1,411 ancestry-informative markers. After adjusting for age, sex, and study, BMI was analyzed both as a dichotomized (top 20% versus bottom 20% and a continuous trait. We found that a higher percentage of European ancestry was significantly correlated with lower BMI (rho = -0.042, P = 1.6x10(-7. In the dichotomized analysis, we detected two loci on chromosome X as associated with increased African ancestry: the first at Xq25 (locus-specific LOD = 5.94; genome-wide score = 3.22; case-control Z = -3.94; and the second at Xq13.1 (locus-specific LOD = 2.22; case-control Z = -4.62. Quantitative analysis identified a third locus at 5q13.3 where higher BMI was highly significantly associated with greater European ancestry (locus-specific LOD = 6.27; genome-wide score = 3.46. Further mapping studies with dense sets of markers will be necessary to identify the alleles in these regions of chromosomes X and 5 that may be associated with variation in BMI.

  10. Genome-wide mapping of virulence in brown planthopper identifies loci that break down host plant resistance.

    Science.gov (United States)

    Jing, Shengli; Zhang, Lei; Ma, Yinhua; Liu, Bingfang; Zhao, Yan; Yu, Hangjin; Zhou, Xi; Qin, Rui; Zhu, Lili; He, Guangcun

    2014-01-01

    Insects and plants have coexisted for over 350 million years and their interactions have affected ecosystems and agricultural practices worldwide. Variation in herbivorous insects' virulence to circumvent host resistance has been extensively documented. However, despite decades of investigation, the genetic foundations of virulence are currently unknown. The brown planthopper (Nilaparvata lugens) is the most destructive rice (Oryza sativa) pest in the world. The identification of the resistance gene Bph1 and its introduction in commercial rice varieties prompted the emergence of a new virulent brown planthopper biotype that was able to break the resistance conferred by Bph1. In this study, we aimed to construct a high density linkage map for the brown planthopper and identify the loci responsible for its virulence in order to determine their genetic architecture. Based on genotyping data for hundreds of molecular markers in three mapping populations, we constructed the most comprehensive linkage map available for this species, covering 96.6% of its genome. Fifteen chromosomes were anchored with 124 gene-specific markers. Using genome-wide scanning and interval mapping, the Qhp7 locus that governs preference for Bph1 plants was mapped to a 0.1 cM region of chromosome 7. In addition, two major QTLs that govern the rate of insect growth on resistant rice plants were identified on chromosomes 5 (Qgr5) and 14 (Qgr14). This is the first study to successfully locate virulence in the genome of this important agricultural insect by marker-based genetic mapping. Our results show that the virulence which overcomes the resistance conferred by Bph1 is controlled by a few major genes and that the components of virulence originate from independent genetic characters. The isolation of these loci will enable the elucidation of the molecular mechanisms underpinning the rice-brown planthopper interaction and facilitate the development of durable approaches for controlling this most

  11. Genome-wide mapping of virulence in brown planthopper identifies loci that break down host plant resistance.

    Directory of Open Access Journals (Sweden)

    Shengli Jing

    Full Text Available Insects and plants have coexisted for over 350 million years and their interactions have affected ecosystems and agricultural practices worldwide. Variation in herbivorous insects' virulence to circumvent host resistance has been extensively documented. However, despite decades of investigation, the genetic foundations of virulence are currently unknown. The brown planthopper (Nilaparvata lugens is the most destructive rice (Oryza sativa pest in the world. The identification of the resistance gene Bph1 and its introduction in commercial rice varieties prompted the emergence of a new virulent brown planthopper biotype that was able to break the resistance conferred by Bph1. In this study, we aimed to construct a high density linkage map for the brown planthopper and identify the loci responsible for its virulence in order to determine their genetic architecture. Based on genotyping data for hundreds of molecular markers in three mapping populations, we constructed the most comprehensive linkage map available for this species, covering 96.6% of its genome. Fifteen chromosomes were anchored with 124 gene-specific markers. Using genome-wide scanning and interval mapping, the Qhp7 locus that governs preference for Bph1 plants was mapped to a 0.1 cM region of chromosome 7. In addition, two major QTLs that govern the rate of insect growth on resistant rice plants were identified on chromosomes 5 (Qgr5 and 14 (Qgr14. This is the first study to successfully locate virulence in the genome of this important agricultural insect by marker-based genetic mapping. Our results show that the virulence which overcomes the resistance conferred by Bph1 is controlled by a few major genes and that the components of virulence originate from independent genetic characters. The isolation of these loci will enable the elucidation of the molecular mechanisms underpinning the rice-brown planthopper interaction and facilitate the development of durable approaches for

  12. Stable isotope ratios in freshwater mussel shells as high resolution recorders of riverine environmental variation

    Science.gov (United States)

    Kukolich, S.; Kendall, C.; Dettman, D. L.

    2017-12-01

    The geochemical record stored in growth increments of freshwater mussel shells reveals annual to sub-annual changes in environmental conditions during the lifetime of the organism. The carbon, nitrogen, and oxygen stable isotope composition of aragonite shells responds to changes in water chemistry, temperature, streamflow, turbidity, growth rate, size, age, and reproduction. The goals of this study are to determine how stable isotopes can be used to reconstruct the conditions in which the mussels lived and to illuminate any vital effects that might obscure the isotopic record of those conditions. Previous research has suggested that annual δ13C values decrease in older freshwater mussel shells due to lower growth rates and greater incorporation of dietary carbon into the shell with increasing age. However, a high-resolution, seasonal investigation of δ13C, δ15N, and δ18O as they relate to organism age has not yet been attempted in freshwater mussels. A total of 28 Unionid mussels of three different species were collected live in 2011 in the Tennessee River near Paducah, Kentucky, USA. In this study, we analyzed the shell nacre and external organic layers for stable carbon, nitrogen, and oxygen isotope ratios, focusing on growth bands formed between 2006 and 2011. We present a time series of shell δ13C, δ18O, and δ15N values with monthly resolution. We also compare the shell-derived geochemical time series to a time series of the δ13C and δ15N of particulate organic matter, δ13C of DIC, δ18OWater, and water temperature in which the mussels lived. Results show that environmental factors such as water temperature and primary productivity dominate shell chemistry while animal age has little or no effect.

  13. EARLY HEAD START FAMILIES' EXPERIENCES WITH STRESS: UNDERSTANDING VARIATIONS WITHIN A HIGH-RISK, LOW-INCOME SAMPLE.

    Science.gov (United States)

    Hustedt, Jason T; Vu, Jennifer A; Bargreen, Kaitlin N; Hallam, Rena A; Han, Myae

    2017-09-01

    The federal Early Head Start program provides a relevant context to examine families' experiences with stress since participants qualify on the basis of poverty and risk. Building on previous research that has shown variations in demographic and economic risks even among qualifying families, we examined possible variations in families' perceptions of stress. Family, parent, and child data were collected to measure stressors and risk across a variety of domains in families' everyday lives, primarily from self-report measures, but also including assay results from child cortisol samples. A cluster analysis was employed to examine potential differences among groups of Early Head Start families. Results showed that there were three distinct subgroups of families, with some families perceiving that they experienced very high levels of stress while others perceived much lower levels of stress despite also experiencing poverty and heightened risk. These findings have important implications in that they provide an initial step toward distinguishing differences in low-income families' experiences with stress, thereby informing interventions focused on promoting responsive caregiving as a possible mechanism to buffer the effects of family and social stressors on young children. © 2017 Michigan Association for Infant Mental Health.

  14. Structural-morphological variations in pseudo-barrier films of anode aluminium oxide under irradiation with high-energy particles

    International Nuclear Information System (INIS)

    Chernykh, M.A.; Belov, V.T.

    1988-01-01

    Comparative study of structural-morphological variations under electron beam effect in pseudo-barrier films of anode aluminium oxide, obtained in seven different solutions and proton or X-rays pre-irradiated to determine structure peculiarities of anode aluminium oxides, is presented. Such study is a matter of interest from the solid-phase transformation theory point of view and for anode aluminium films application under radiation. Stability increase of pseudo-barrier films of anode aluminium oxide to the effect of UEhMV-100 K microscope electron beam at standard modes of operation (75 kV) due to proton or X-rays irradiation is found. Difference in structural-monorphological variations obtained in different solutions of anode aluminium films under high-energy particles irradiation is determined. Strucural-phase microinhomogeneity of amorphous pseudo-barrier films of anode aluminium oxide and its influence on solid-phase transformations character under electron bean of maximal intensity are detected

  15. Quantitative Trait Loci Associated with Drought Tolerance in Brachypodium distachyon

    Directory of Open Access Journals (Sweden)

    Yiwei Jiang

    2017-05-01

    Full Text Available The temperate wild grass Brachypodium distachyon (Brachypodium serves as model system for studying turf and forage grasses. Brachypodium collections show diverse responses to drought stress, but little is known about the genetic mechanisms of drought tolerance of this species. The objective of this study was to identify quantitative trait loci (QTLs associated with drought tolerance traits in Brachypodium. We assessed leaf fresh weight (LFW, leaf dry weight (LDW, leaf water content (LWC, leaf wilting (WT, and chlorophyll fluorescence (Fv/Fm under well-watered and drought conditions on a recombinant inbred line (RIL population from two parents (Bd3-1 and Bd1-1 known to differ in their drought adaptation. A linkage map of the RIL population was constructed using 467 single nucleotide polymorphism (SNP markers obtained from genotyping-by-sequencing. The Bd3-1/Bd1-1 map spanned 1,618 cM and had an average distance of 3.5 cM between adjacent single nucleotide polymorphisms (SNPs. Twenty-six QTLs were identified in chromosome 1, 2, and 3 in two experiments, with 14 of the QTLs under well-watered conditions and 12 QTLs under drought stress. In Experiment 1, a QTL located on chromosome 2 with a peak at 182 cM appeared to simultaneously control WT, LWC, and Fv/Fm under drought stress, accounting for 11–18.7% of the phenotypic variation. Allelic diversity of candidate genes DREB2B, MYB, and SPK, which reside in one multi-QTL region, may play a role in the natural variation in whole plant drought tolerance in Brachypodium. Co-localization of QTLs for multiple drought-related traits suggest that the gene(s involved are important regulators of drought tolerance in Brachypodium.

  16. Alzheimer's Disease Risk Polymorphisms Regulate Gene Expression in the ZCWPW1 and the CELF1 Loci.

    Directory of Open Access Journals (Sweden)

    Celeste M Karch

    Full Text Available Late onset Alzheimer's disease (LOAD is a genetically complex and clinically heterogeneous disease. Recent large-scale genome wide association studies (GWAS have identified more than twenty loci that modify risk for AD. Despite the identification of these loci, little progress has been made in identifying the functional variants that explain the association with AD risk. Thus, we sought to determine whether the novel LOAD GWAS single nucleotide polymorphisms (SNPs alter expression of LOAD GWAS genes and whether expression of these genes is altered in AD brains. The majority of LOAD GWAS SNPs occur in gene dense regions under large linkage disequilibrium (LD blocks, making it unclear which gene(s are modified by the SNP. Thus, we tested for brain expression quantitative trait loci (eQTLs between LOAD GWAS SNPs and SNPs in high LD with the LOAD GWAS SNPs in all of the genes within the GWAS loci. We found a significant eQTL between rs1476679 and PILRB and GATS, which occurs within the ZCWPW1 locus. PILRB and GATS expression levels, within the ZCWPW1 locus, were also associated with AD status. Rs7120548 was associated with MTCH2 expression, which occurs within the CELF1 locus. Additionally, expression of several genes within the CELF1 locus, including MTCH2, were highly correlated with one another and were associated with AD status. We further demonstrate that PILRB, as well as other genes within the GWAS loci, are most highly expressed in microglia. These findings together with the function of PILRB as a DAP12 receptor supports the critical role of microglia and neuroinflammation in AD risk.

  17. Geomagnetic Paleointensity Variations as a Cheap, High-Resolution Geochronometer for Recent Mid-Ocean Ridge Processes

    Science.gov (United States)

    DYMENT, J.; HEMOND, C.

    2001-12-01

    of the data confirms the quality of the oceanic crust as a recorder of the geomagnetic variations. Future work in the framework of Project GIMNAUT include 1) the processing and interpretation of the available magnetic signals to obtain a detailed sequence of the geomagnetic fluctuations for the last 800 ka; 2) the dating of collected samples with different radiochronologic methods such as K-Ar and Ar-Ar for samples older than 100-150 ka and 230Th-238U for samples aged between 300-10 ka; and 3) the calibration of the geomagnetic intensity variation sequence as a high resolution geochronometer for the last 800 ka. Such a magnetic geochronometer would present an obvious interest for mid-ocean ridge studies, because of its low cost and simplicity of operation: it would only require the addition of a deep-sea magnetometer onto existing means of investigation such as submersibles, ROVs or AUVs. Beyond this application, this magnetic geochronometer could also be used for accurate dating of pelagic sedimentary sequences, through the analysis of relative paleointensities on cores, or of continental or island volcanic flows, through the determination of absolute paleointensities by the Thellier-Thellier method. (*) N. Arnaud, C. Bassoullet, M.. Benoit, A. Briais, F. Chabaux, A.K. Chaubey, A. Chauvin, P. Gente, H. Guillou, H. Horen, M. Kitazawa, B. Le Gall, M. Maia, M. Ravilly

  18. Understanding human DNA sequence variation.

    Science.gov (United States)

    Kidd, K K; Pakstis, A J; Speed, W C; Kidd, J R

    2004-01-01

    Over the past century researchers have identified normal genetic variation and studied that variation in diverse human populations to determine the amounts and distributions of that variation. That information is being used to develop an understanding of the demographic histories of the different populations and the species as a whole, among other studies. With the advent of DNA-based markers in the last quarter century, these studies have accelerated. One of the challenges for the next century is to understand that variation. One component of that understanding will be population genetics. We present here examples of many of the ways these new data can be analyzed from a population perspective using results from our laboratory on multiple individual DNA-based polymorphisms, many clustered in haplotypes, studied in multiple populations representing all major geographic regions of the world. These data support an "out of Africa" hypothesis for human dispersal around the world and begin to refine the understanding of population structures and genetic relationships. We are also developing baseline information against which we can compare findings at different loci to aid in the identification of loci subject, now and in the past, to selection (directional or balancing). We do not yet have a comprehensive understanding of the extensive variation in the human genome, but some of that understanding is coming from population genetics.

  19. Solar cycle variations of the energetic H/He intensity ratio at high heliolatitudes and in the ecliptic plane

    Directory of Open Access Journals (Sweden)

    D. Lario

    Full Text Available We study the variability of the heliospheric energetic proton-to-helium abundance ratios during different phases of the solar cycle. We use energetic particle, solar wind, and magnetic field data from the Ulysses, ACE and IMP-8 spacecraft to compare the H/He intensity ratio at high heliographic latitudes and in the ecliptic plane. During the first out-of-ecliptic excursion of Ulysses (1992–1996, the HI-SCALE instrument measured corotating energetic particle intensity enhancements characterized by low values (< 10 of the 0.5–1.0 MeV nucleon-1 H/He intensity ratio. During the second out-of-ecliptic excursion of Ulysses (1999–2002, the more frequent occurrence of solar energetic particle events resulted in almost continuously high (< 20 values of the H/He ratio, even at the highest heliolatitudes reached by Ulysses. Comparison with in-ecliptic measurements from an identical instrument on the ACE spacecraft showed similar H/He values at ACE and Ulysses, suggesting a remarkable uniformity of energetic particle intensities in the solar maximum heliosphere at high heliolatitudes and in the ecliptic plane. In-ecliptic observations of the H/He intensity ratio from the IMP-8 spacecraft show variations between solar maximum and solar minimum similar to those observed by Ulysses at high heliographic latitudes. We suggest that the variation of the H/He intensity ratio throughout the solar cycle is due to the different level of transient solar activity, as well as the different structure and duration that corotating solar wind structures have under solar maximum and solar minimum conditions. During solar minimum, the interactions between the two different types of solar wind streams (slow vs. fast are strong and long-lasting, allowing for a continuous and efficient acceleration of interstellar pickup He +. During solar maximum, transient events of solar origin (characterized by high values of the H/He ratio are able to globally

  20. Intraspecific variation in cadmium tolerance and accumulation of a high-biomass tropical tree Averrhoa carambola L.: implication for phytoextraction.

    Science.gov (United States)

    Dai, Zi-yun; Shu, Wen-sheng; Liao, Bin; Wan, Cai-yun; Li, Jin-tian

    2011-06-01

    Averrhoa carambola L., a high-biomass tropical tree, has recently been shown to be a strong accumulator of cadmium (Cd) and has great potential for Cd phytoextraction. In the present study, field studies and a controlled-environment experiment were combined to establish the extent of variation in Cd tolerance and accumulation at the cultivar level using 14 to 19 cultivars of A. carambola. The results indicated that all cultivars tested could accumulate Cd at high but different levels, and that Cd tolerance also varied greatly between these cultivars. It is confirmed that the high Cd tolerance and accumulation capacity are species-level and constitutional traits in A. carambola. However, no correlation was detected between tolerance index and accumulation of Cd in different cultivars, suggesting that the two traits are independent in this woody Cd accumulator. More importantly, cultivar Wuchuan Sweet (WCT) was shown to have the highest Cd-extraction potential; it yielded a high shoot biomass of 30 t ha(-1) in 230 d, and extracted 330 g ha(-1) Cd in the aerial tissues grown in Cd-contaminated field soil, which accounted for 12.8% of the total soil Cd in the top 20 cm of the soil profile.

  1. Variations in airborne bacterial communities at high altitudes over the Noto Peninsula (Japan) in response to Asian dust events

    Science.gov (United States)

    Maki, Teruya; Hara, Kazutaka; Iwata, Ayumu; Lee, Kevin C.; Kawai, Kei; Kai, Kenji; Kobayashi, Fumihisa; Pointing, Stephen B.; Archer, Stephen; Hasegawa, Hiroshi; Iwasaka, Yasunobu

    2017-10-01

    Aerosol particles, including airborne microorganisms, are transported through the free troposphere from the Asian continental area to the downwind area in East Asia and can influence climate changes, ecosystem dynamics, and human health. However, the variations present in airborne bacterial communities in the free troposphere over downwind areas are poorly understood, and there are few studies that provide an in-depth examination of the effects of long-range transport of aerosols (natural and anthropogenic particles) on bacterial variations. In this study, the vertical distributions of airborne bacterial communities at high altitudes were investigated and the bacterial variations were compared between dust events and non-dust events.Aerosols were collected at three altitudes from ground level to the free troposphere (upper level: 3000 or 2500 m; middle level: 1200 or 500 m; and low level: 10 m) during Asian dust events and non-dust events over the Noto Peninsula, Japan, where westerly winds carry aerosols from the Asian continental areas. During Asian dust events, air masses at high altitudes were transported from the Asian continental area by westerly winds, and laser imaging detection and ranging (lidar) data indicated high concentrations of non-spherical particles, suggesting that dust-sand particles were transported from the central desert regions of Asia. The air samples collected during the dust events contained 10-100 times higher concentrations of microscopic fluorescent particles and optical particle counter (OPC) measured particles than in non-dust events. The air masses of non-dust events contained lower amounts of dust-sand particles. Additionally, some air samples showed relatively high levels of black carbon, which were likely transported from the Asian continental coasts. Moreover, during the dust events, microbial particles at altitudes of > 1200 m increased to the concentrations ranging from 1. 2 × 106 to 6. 6 × 106 particles m-3. In contrast

  2. Drivers of inter-annual variation and long-term change in High-Arctic spider species abundances

    DEFF Research Database (Denmark)

    Bowden, Joseph J.; Hansen, Oskar L. P.; Olsen, Kent

    2018-01-01

    Understanding how species abundances vary in space and time is a central theme in ecology, yet there are few long-term field studies of terrestrial invertebrate abundances and the determinants of their dynamics. This is particularly relevant in the context of rapid climate change occurring...... in the Arctic. Arthropods can serve as strong indicators of ecosystem change due to their sensitivity to increasing temperatures and other environmental variables. We used spider samples collected by pitfall trapping from three different habitats (fen, mesic and arid heath) in High-Arctic Greenland to assess...... interpretation of long-term trends. We used model selection to determine which climatic variables and/or previous years’ abundance best explained annual variation in species abundances over this period. We identified and used 28 566 adult spiders that comprised eight species. Most notably, the abundances of some...

  3. Variations in depression care and outcomes among high-risk mothers from different racial/ethnic groups.

    Science.gov (United States)

    Huang, Hsiang; Chan, Ya-Fen; Katon, Wayne; Tabb, Karen; Sieu, Nida; Bauer, Amy M; Wasse, Jessica Knaster; Unützer, Jürgen

    2012-08-01

    PURPOSE. To examine variations in depression care and outcomes among high-risk pregnant and parenting women from different racial/ethnic groups served in community health centres. As part of a collaborative care programme that provides depression treatment in primary care clinics for high-risk mothers, 661 women with probable depression (Patient Health Questionnaire-9 ≥ 10), who self-reported race/ethnicity as Latina (n = 393), White (n = 126), Black (n = 75) or Asian (n = 67), were included in the study. Primary outcomes include quality of depression care and improvement in depression. A Cox proportional hazard model adjusting for sociodemographic and clinical characteristics was used to examine time to treatment response. We observed significant differences in both depression processes and outcomes across ethnic groups. After adjusting for other variables, Blacks were found to be significantly less likely to improve than Latinas [hazard ratio (HR): 0.53, 95% confidence interval (CI): 0.44-0.65]. Other factors significantly associated with depression improvement were pregnancy (HR: 1.52, 95% CI: 1.27-1.82), number of clinic visits (HR: 1.26, 95% CI: 1.17-1.36) and phone contacts (HR: 1.45, 95% CI: 1.32-1.60) by the care manager in the first month of treatment. After controlling for depression severity, having suicidal thoughts at baseline was significantly associated with a decreased likelihood of depression improvement (HR: 0.75, 95% CI: 0.67-0.83). In this racially and ethnically diverse sample of pregnant and parenting women treated for depression in primary care, the intensity of care management was positively associated with improved depression. There was also appreciable variation in depression outcomes between Latina and Black patients.

  4. Variations of the high-level Balmer line spectrum of the helium-strong star σ Orionis E

    Science.gov (United States)

    Smith, M. A.; Bohlender, D. A.

    2007-12-01

    Using the high-level Balmer lines and continuum, we trace the density structure of two magnetospheric disk segments of the prototypical Bp star σ Orionis E (B2p) as these segments occult portions of the star during the rotational cycle. High-resolution spectra of the Balmer lines ≥H9 and Balmer edge were obtained on seven nights in January-February 2007 at an average sampling of 0.01 cycles. We measured equivalent width variations due to the star occultations by two disk segments 0.4 cycles apart and constructed differential spectra of the migrations of the corresponding absorptions across the Balmer line profiles. We first estimated the rotational and magnetic obliquity angles. We then simulated the observed Balmer jump variation using the model atmosphere codes synspec/circus and evaluated the disk geometry and gas thermodynamics. We find that the two occultations are caused by two disk segments. The first of these transits quickly, indicating that the segment resides in a range of distances, perhaps 2.5-6 R*, from the star. The second consists of a more slowly moving segment situated closer to the surface and causing two semi-resolved absorbing maxima. During its transit this segment brushes across the star's “lower” limb. Judging from the line visibility up to H23-H24 during the occultations, both disk segments have mean densities near 1012 cm-3 and are opaque in the lines and continuum. They have semiheights less than 1/2 R*, and their temperatures are near 10 500 K and 12 000 K, respectively. In all, the disks of Bp stars have a much more complicated geometry than has been anticipated, as evidenced by their (sometimes) non-coplanarity, de-centerness, and from star to star, differences in disk height. Based on observations obtained at the the Dominion Astrophysical Observatory, Herzberg Institute of Astrophysics, National Research Council of Canada.

  5. Substructure of a Tunisian Berber population as inferred from 15 autosomal short tandem repeat loci.

    Science.gov (United States)

    Khodjet-El-Khil, Houssein; Fadhlaoui-Zid, Karima; Gusmão, Leonor; Alves, Cíntia; Benammar-Elgaaied, Amel; Amorim, Antonio

    2008-08-01

    Currently, language and cultural practices are the only criteria to distinguish between Berber autochthonous Tunisian populations. To evaluate these populations' possible genetic structure and differentiation, we have analyzed 15 autosomal short tandem repeat loci (CSF1PO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, FGA, TH01, TPOX, VWA, D2S1338, and D19S433) in three southern Tunisian Berber groups: Sened, Matmata, and Chenini-Douiret. The exact test of population differentiation based on allele frequencies at the 15 loci shows significant P values at 7 loci between Chenini-Douiret and both Sened and Matmata, whereas just 5 loci show significant P values between Sened and Matmata. Comparative analyses between the three Berber groups based on genetic distances show that P values for F(ST) distances are significant between the three Berber groups. Population analysis performed using Structure shows a clear differentiation between these Berber groups, with strong genetic isolation of Chenini-Douiret. These results confirm at the autosomal level the high degree of heterogeneity of Tunisian Berber populations that had been previously reported for uniparental markers.

  6. Evaluation of European Schizophrenia GWAS Loci in Asian Populations via Comprehensive Meta-Analyses.

    Science.gov (United States)

    Xiao, Xiao; Luo, Xiong-Jian; Chang, Hong; Liu, Zichao; Li, Ming

    2017-08-01

    Schizophrenia is a severe and highly heritable neuropsychiatric disorder. Recent genetic analyses including genome-wide association studies (GWAS) have implicated multiple genome-wide significant variants for schizophrenia among European populations. However, many of these risk variants were not largely validated in other populations of different ancestry such as Asians. To validate whether these European GWAS significant loci are associated with schizophrenia in Asian populations, we conducted a systematic literature search and meta-analyses on 19 single nucleotide polymorphisms (SNPs) in Asian populations by combining all available case-control and family-based samples, including up to 30,000 individuals. We employed classical fixed (or random) effects inverse variance weighted methods to calculate summary odds ratios (ORs) and 95 % confidence intervals (CIs). Among the 19 GWAS loci, we replicated the risk associations of nine markers (e.g., SNPs at VRK2, ITIH3/4, NDST3, NOTCH4) surpassing significance level (two-tailed P Asian replication samples and initial European GWAS findings, and the successful replications of these GWAS loci in a different ethnic group provide stronger evidence for their clinical associations with schizophrenia. Further studies, focusing on the molecular mechanisms of these GWAS significant loci, will become increasingly important for understanding of the pathogenesis to schizophrenia.

  7. Activation of int-1 and int-2 loci in GRf mammary tumors.

    Science.gov (United States)

    Gray, D A; Jackson, D P; Percy, D H; Morris, V L

    1986-10-30

    The Mtv-2 locus is known to be associated with a high mammary tumor incidence (97%) and early development of mammary tumors (3-13 months) in GR mice. However, it was not previously known whether the provirus which resides at the Mtv-2 locus is tumorigenic in and of itself or whether reintegration of proviruses generated from Mtv-2 is required for tumorigenesis. Foster-nursing GR mice on C57/BL mice eliminates the milk-borne source of GR virus, and allows the study of Mtv-2 derived proviruses alone. Using this approach, we have tested predictions which follow from the "positional" versus "reintegrational" models of tumorigenesis. Specifically, we have examined tumors from primary foster-nursed (GRf) mice to determine if MMTV proviruses derived from Mtv-2 were scattered randomly throughout the genome or were clustered in the vicinity of the int-1 and int-2 loci, which are thought to be associated with mammary tumorigenesis. It was found that the majority of spontaneous GRf mammary tumors that were tested have MMTV proviral integrations in either or both of the int-1 and int-2 loci and have transcription of either or both of the int loci. Tumors induced by Mtv-2, therefore, appear to have arisen via a mechanism similar to the activation of the int loci by exogenous (milk-borne) MMTV proviruses.

  8. Fine-mapping and initial characterization of QT interval loci in African Americans.

    Directory of Open Access Journals (Sweden)

    Christy L Avery

    Full Text Available The QT interval (QT is heritable and its prolongation is a risk factor for ventricular tachyarrhythmias and sudden death. Most genetic studies of QT have examined European ancestral populations; however, the increased genetic diversity in African Americans provides opportunities to narrow association signals and identify population-specific variants. We therefore evaluated 6,670 SNPs spanning eleven previously identified QT loci in 8,644 African American participants from two Population Architecture using Genomics and Epidemiology (PAGE studies: the Atherosclerosis Risk in Communities study and Women's Health Initiative Clinical Trial. Of the fifteen known independent QT variants at the eleven previously identified loci, six were significantly associated with QT in African American populations (P≤1.20×10(-4: ATP1B1, PLN1, KCNQ1, NDRG4, and two NOS1AP independent signals. We also identified three population-specific signals significantly associated with QT in African Americans (P≤1.37×10(-5: one at NOS1AP and two at ATP1B1. Linkage disequilibrium (LD patterns in African Americans assisted in narrowing the region likely to contain the functional variants for several loci. For example, African American LD patterns showed that 0 SNPs were in LD with NOS1AP signal rs12143842, compared with European LD patterns that indicated 87 SNPs, which spanned 114.2 Kb, were in LD with rs12143842. Finally, bioinformatic-based characterization of the nine African American signals pointed to functional candidates located exclusively within non-coding regions, including predicted binding sites for transcription factors such as TBX5, which has been implicated in cardiac structure and conductance. In this detailed evaluation of QT loci, we identified several African Americans SNPs that better define the association with QT and successfully narrowed intervals surrounding established loci. These results demonstrate that the same loci influence variation in QT

  9. Genome-wide association study identifies six new loci influencing pulse pressure and mean arterial pressure

    Science.gov (United States)

    Wain, Louise V; Verwoert, Germaine C; O’Reilly, Paul F; Shi, Gang; Johnson, Toby; Johnson, Andrew D; Bochud, Murielle; Rice, Kenneth M; Henneman, Peter; Smith, Albert V; Ehret, Georg B; Amin, Najaf; Larson, Martin G; Mooser, Vincent; Hadley, David; Dörr, Marcus; Bis, Joshua C; Aspelund, Thor; Esko, Tõnu; Janssens, A Cecile JW; Zhao, Jing Hua; Heath, Simon; Laan, Maris; Fu, Jingyuan; Pistis, Giorgio; Luan, Jian’an; Arora, Pankaj; Lucas, Gavin; Pirastu, Nicola; Pichler, Irene; Jackson, Anne U; Webster, Rebecca J; Zhang, Feng; Peden, John F; Schmidt, Helena; Tanaka, Toshiko; Campbell, Harry; Igl, Wilmar; Milaneschi, Yuri; Hotteng, Jouke-Jan; Vitart, Veronique; Chasman, Daniel I; Trompet, Stella; Bragg-Gresham, Jennifer L; Alizadeh, Behrooz Z; Chambers, John C; Guo, Xiuqing; Lehtimäki, Terho; Kühnel, Brigitte; Lopez, Lorna M; Polašek, Ozren; Boban, Mladen; Nelson, Christopher P; Morrison, Alanna C; Pihur, Vasyl; Ganesh, Santhi K; Hofman, Albert; Kundu, Suman; Mattace-Raso, Francesco US; Rivadeneira, Fernando; Sijbrands, Eric JG; Uitterlinden, Andre G; Hwang, Shih-Jen; Vasan, Ramachandran S; Wang, Thomas J; Bergmann, Sven; Vollenweider, Peter; Waeber, Gérard; Laitinen, Jaana; Pouta, Anneli; Zitting, Paavo; McArdle, Wendy L; Kroemer, Heyo K; Völker, Uwe; Völzke, Henry; Glazer, Nicole L; Taylor, Kent D; Harris, Tamara B; Alavere, Helene; Haller, Toomas; Keis, Aime; Tammesoo, Mari-Liis; Aulchenko, Yurii; Barroso, Inês; Khaw, Kay-Tee; Galan, Pilar; Hercberg, Serge; Lathrop, Mark; Eyheramendy, Susana; Org, Elin; Sõber, Siim; Lu, Xiaowen; Nolte, Ilja M; Penninx, Brenda W; Corre, Tanguy; Masciullo, Corrado; Sala, Cinzia; Groop, Leif; Voight, Benjamin F; Melander, Olle; O’Donnell, Christopher J; Salomaa, Veikko; d’Adamo, Adamo Pio; Fabretto, Antonella; Faletra, Flavio; Ulivi, Sheila; Del Greco, M Fabiola; Facheris, Maurizio; Collins, Francis S; Bergman, Richard N; Beilby, John P; Hung, Joseph; Musk, A William; Mangino, Massimo; Shin, So-Youn; Soranzo, Nicole; Watkins, Hugh; Goel, Anuj; Hamsten, Anders; Gider, Pierre; Loitfelder, Marisa; Zeginigg, Marion; Hernandez, Dena; Najjar, Samer S; Navarro, Pau; Wild, Sarah H; Corsi, Anna Maria; Singleton, Andrew; de Geus, Eco JC; Willemsen, Gonneke; Parker, Alex N; Rose, Lynda M; Buckley, Brendan; Stott, David; Orru, Marco; Uda, Manuela; van der Klauw, Melanie M; Zhang, Weihua; Li, Xinzhong; Scott, James; Chen, Yii-Der Ida; Burke, Gregory L; Kähönen, Mika; Viikari, Jorma; Döring, Angela; Meitinger, Thomas; Davies, Gail; Starr, John M; Emilsson, Valur; Plump, Andrew; Lindeman, Jan H; ’t Hoen, Peter AC; König, Inke R; Felix, Janine F; Clarke, Robert; Hopewell, Jemma C; Ongen, Halit; Breteler, Monique; Debette, Stéphanie; DeStefano, Anita L; Fornage, Myriam; Mitchell, Gary F; Smith, Nicholas L; Holm, Hilma; Stefansson, Kari; Thorleifsson, Gudmar; Thorsteinsdottir, Unnur; Samani, Nilesh J; Preuss, Michael; Rudan, Igor; Hayward, Caroline; Deary, Ian J; Wichmann, H-Erich; Raitakari, Olli T; Palmas, Walter; Kooner, Jaspal S; Stolk, Ronald P; Jukema, J Wouter; Wright, Alan F; Boomsma, Dorret I; Bandinelli, Stefania; Gyllensten, Ulf B; Wilson, James F; Ferrucci, Luigi; Schmidt, Reinhold; Farrall, Martin; Spector, Tim D; Palmer, Lyle J; Tuomilehto, Jaakko; Pfeufer, Arne; Gasparini, Paolo; Siscovick, David; Altshuler, David; Loos, Ruth JF; Toniolo, Daniela; Snieder, Harold; Gieger, Christian; Meneton, Pierre; Wareham, Nicholas J; Oostra, Ben A; Metspalu, Andres; Launer, Lenore; Rettig, Rainer; Strachan, David P; Beckmann, Jacques S; Witteman, Jacqueline CM; Erdmann, Jeanette; van Dijk, Ko Willems; Boerwinkle, Eric; Boehnke, Michael; Ridker, Paul M; Jarvelin, Marjo-Riitta; Chakravarti, Aravinda; Abecasis, Goncalo R; Gudnason, Vilmundur; Newton-Cheh, Christopher; Levy, Daniel; Munroe, Patricia B; Psaty, Bruce M; Caulfield, Mark J; Rao, Dabeeru C

    2012-01-01

    Numerous genetic loci influence systolic blood pressure (SBP) and diastolic blood pressure (DBP) in Europeans 1-3. We now report genome-wide association studies of pulse pressure (PP) and mean arterial pressure (MAP). In discovery (N=74,064) and follow-up studies (N=48,607), we identified at genome-wide significance (P= 2.7×10-8 to P=2.3×10-13) four novel PP loci (at 4q12 near CHIC2/PDGFRAI, 7q22.3 near PIK3CG, 8q24.12 in NOV, 11q24.3 near ADAMTS-8), two novel MAP loci (3p21.31 in MAP4, 10q25.3 near ADRB1) and one locus associated with both traits (2q24.3 near FIGN) which has recently been associated with SBP in east Asians. For three of the novel PP signals, the estimated effect for SBP was opposite to that for DBP, in contrast to the majority of common SBP- and DBP-associated variants which show concordant effects on both traits. These findings indicate novel genetic mechanisms underlying blood pressure variation, including pathways that may differentially influence SBP and DBP. PMID:21909110

  10. Allozyme variation in spineless Pejibaye (Bactris gasipaes Kunth)

    Science.gov (United States)

    Isozyme variation was studied in 161 accessions of pineapple including four species of Ananas and one of Pseudananas. Six enzyme systems (ADH, GPI, PGM, SKDH, TPI, UGPP) involving seven putative loci revealed 35 electromorphs . Considerable variation exists within and between species of Ananas. Sixt...

  11. Cell-type-specific enrichment of risk-associated regulatory elements at ovarian cancer susceptibility loci.

    Science.gov (United States)

    Coetzee, Simon G; Shen, Howard C; Hazelett, Dennis J; Lawrenson, Kate; Kuchenbaecker, Karoline; Tyrer, Jonathan; Rhie, Suhn K; Levanon, Keren; Karst, Alison; Drapkin, Ronny; Ramus, Susan J; Couch, Fergus J; Offit, Kenneth; Chenevix-Trench, Georgia; Monteiro, Alvaro N A; Antoniou, Antonis; Freedman, Matthew; Coetzee, Gerhard A; Pharoah, Paul D P; Noushmehr, Houtan; Gayther, Simon A

    2015-07-01

    Understanding the regulatory landscape of the human genome is a central question in complex trait genetics. Most single-nucleotide polymorphisms (SNPs) associated with cancer risk lie in non-protein-coding regions, implicating regulatory DNA elements as functional targets of susceptibility variants. Here, we describe genome-wide annotation of regions of open chromatin and histone modification in fallopian tube and ovarian surface epithelial cells (FTSECs, OSECs), the debated cellular origins of high-grade serous ovarian cancers (HGSOCs) and in endometriosis epithelial cells (EECs), the likely precursor of clear cell ovarian carcinomas (CCOCs). The regulatory architecture of these cell types was compared with normal human mammary epithelial cells and LNCaP prostate cancer cells. We observed similar positional patterns of global enhancer signatures across the three different ovarian cancer precursor cell types, and evidence of tissue-specific regulatory signatures compared to non-gynecological cell types. We found significant enrichment for risk-associated SNPs intersecting regulatory biofeatures at 17 known HGSOC susceptibility loci in FTSECs (P = 3.8 × 10(-30)), OSECs (P = 2.4 × 10(-23)) and HMECs (P = 6.7 × 10(-15)) but not for EECs (P = 0.45) or LNCaP cells (P = 0.88). Hierarchical clustering of risk SNPs conditioned on the six different cell types indicates FTSECs and OSECs are highly related (96% of samples using multi-scale bootstrapping) suggesting both cell types may be precursors of HGSOC. These data represent the first description of regulatory catalogues of normal precursor cells for different ovarian cancer subtypes, and provide unique insights into the tissue specific regulatory variation with respect to the likely functional targets of germline genetic susceptibility variants for ovarian cancer. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  12. Evaluating the Feasibility of Five Candidate DNA Barcoding Loci for Philippine Lasianthus Jack (Lasiantheae: Rubiaceae).

    Science.gov (United States)

    Arshed, Muhammad Jefte C; Valdez, Marcos B; Alejandro, Grecebio Jonathan D

    2017-01-01

    The pantropical genus Lasianthus Jack is identified for high phenotypic plasticity making traditional taxonomic identification difficult. Having some members with important medicinal properties, a precise complimentary identification through DNA barcoding is needed for species delineation. In this study, 12 samples representing six Philippine Lasianthus species were used to determine the most efficient barcoding loci among the cpDNA markers ( mat K, rbc L, rps 16, and trn T-F) and nrDNA (ITS) based on the criteria of universality, discriminatory power, and resolution of species. The results revealed that ITS has the recommended primer universality, greatest interspecific divergences, and average resolution of species. Among the cpDNA markers, mat K and rbc L are recommended but with minimal resolution of species. While trn T-F showed moderate interspecific variations and resolution of Lasianthus species, rps 16 has the lowest interspecific divergence and resolution of species. Consequently, ITS is the potential ideal DNA barcode for Lasianthus species. ITS, mat K, and rps 16 markers have the excellent amplification and sequence qualityITS marker has the highest interspecific divergence with the maximum values, followed by mat K, rbc L, trn T-F, and rps 16, respectivelyAll markers except rps 16 yielded average resolution to Lasianthus speciesITS marker is the most ideal locus in terms of excellent universality, high interspecific discriminatory ability, and average species resolution. Abbreviations used: ITS: Internal Transcribe Spacer, mat K: maturase K, rbc L: ribulose-1,5-biphospahte-carboxylase, rps 16: ribosomal protein 16 small subunit gene.

  13. Multiple Linkage Disequilibrium Mapping Methods to Validate Additive Quantitative Trait Loci in Korean Native Cattle (Hanwoo

    Directory of Open Access Journals (Sweden)

    Yi Li

    2015-07-01

    Full Text Available The efficiency of genome-wide association analysis (GWAS depends on power of detection for quantitative trait loci (QTL and precision for QTL mapping. In this study, three different strategies for GWAS were applied to detect QTL for carcass quality traits in the Korean cattle, Hanwoo; a linkage disequilibrium single locus regression method (LDRM, a combined linkage and linkage disequilibrium analysis (LDLA and a BayesCπ approach. The phenotypes of 486 steers were collected for weaning weight (WWT, yearling weight (YWT, carcass weight (CWT, backfat thickness (BFT, longissimus dorsi muscle area, and marbling score (Marb. Also the genotype data for the steers and their sires were scored with the Illumina bovine 50K single nucleotide polymorphism (SNP chips. For the two former GWAS methods, threshold values were set at false discovery rate <0.01 on a chromosome-wide level, while a cut-off threshold value was set in the latter model, such that the top five windows, each of which comprised 10 adjacent SNPs, were chosen with significant variation for the phenotype. Four major additive QTL from these three methods had high concordance found in 64.1 to 64.9Mb for Bos taurus autosome (BTA 7 for WWT, 24.3 to 25.4Mb for BTA14 for CWT, 0.5 to 1.5Mb for BTA6 for BFT and 26.3 to 33.4Mb for BTA29 for BFT. Several candidate genes (i.e. glutamate receptor, ionotropic, ampa 1 [GRIA1], family with sequence similarity 110, member B [FAM110B], and thymocyte selection-associated high mobility group box [TOX] may be identified close to these QTL. Our result suggests that the use of different linkage disequilibrium mapping approaches can provide more reliable chromosome regions to further pinpoint DNA makers or causative genes in these regions.

  14. Quantitative trait loci controlling leaf appearance and curd initiation of cauliflower in relation to temperature.

    Science.gov (United States)

    Hasan, Yaser; Briggs, William; Matschegewski, Claudia; Ordon, Frank; Stützel, Hartmut; Zetzsche, Holger; Groen, Simon; Uptmoor, Ralf

    2016-07-01

    QTL regions on chromosomes C06 and C09 are involved in temperature dependent time to curd induction in cauliflower. Temperature is the main environmental factor influencing curding time of cauliflower (Brassica oleracea var. botrytis). Temperatures above 20-22 °C inhibit development towards curding even in many summer cultivars. To identify quantitative trait loci (QTL) controlling curding time and its related traits in a wide range of different temperature regimes from 12 to 27 °C, a doubled haploid (DH) mapping population segregating for curding time was developed and days to curd initiation (DCI), leaf appearance rate (LAR), and final leaf number (FLN) were measured. The population was genotyped with 176 single nucleotide polymorphism (SNP) markers. Composite interval mapping (CIM) revealed repeatedly detected QTL for DCI on C06 and C09. The estimated additive effect increased at high temperatures. Significant QTL × environment interactions (Q × E) for FLN and DCI on C06 and C09 suggest that these hotspot regions have major influences on temperature mediated curd induction. 25 % of the DH lines did not induce curds at temperatures higher than 22 °C. Applying a binary model revealed a QTL with LOD >15 on C06. Nearly all lines carrying the allele of the reliable early maturing parental line (PL) on that locus induced curds at high temperatures while only half of the DH lines carrying the allele of the unreliable PL reached the generative phase during the experiment. Large variation in LAR was observed. QTL for LAR were detected repeatedly in several environments on C01, C04 and C06. Negative correlations between LAR and DCI and QTL co-localizations on C04 and C06 suggest that LAR has also effects on development towards curd induction.

  15. Gutzwiller-RVB theory of high temperature superconductivity. Results from renormalized mean field theory and variational Monte Carlo calculations

    International Nuclear Information System (INIS)

    Edegger, B.

    2007-01-01

    We consider the theory of high temperature superconductivity from the viewpoint of a strongly correlated electron system. In particular, we discuss Gutzwiller projected wave functions, which incorporate strong correlations by prohibiting double occupancy in orbitals with strong on-site repulsion. After a general overview on high temperature superconductivity, we discuss Anderson's resonating valence bond (RVB) picture and its implementation by renormalized mean field theory (RMFT) and variational Monte Carlo (VMC) techniques. In the following, we present a detailed review on RMFT and VMC results with emphasis on our recent contributions. Especially, we are interested in spectral features of Gutzwiller-Bogolyubov quasiparticles obtained by extending VMC and RMFT techniques to excited states. We explicitly illustrate this method to determine the quasiparticle weight and provide a comparison with angle resolved photoemission spectroscopy (ARPES) and scanning tunneling microscopy (STM). We conclude by summarizing recent successes and by discussing open questions, which must be solved for a thorough understanding of high temperature superconductivity by Gutzwiller projected wave functions. (orig.)

  16. Influence of the seasonal variation of environmental conditions on biogas upgrading in an outdoors pilot scale high rate algal pond.

    Science.gov (United States)

    Marín, David; Posadas, Esther; Cano, Patricia; Pérez, Víctor; Lebrero, Raquel; Muñoz, Raúl

    2018-05-01

    The influence of the daily and seasonal variations of environmental conditions on the quality of the upgraded biogas was evaluated in an outdoors pilot scale high rate algal pond (HRAP) interconnected to an external absorption column (AC) via a conical settler. The high alkalinity in the cultivation broth resulted in a constant biomethane composition during the day regardless of the monitored month, while the high algal-bacterial activity during spring and summer boosted a superior biomethane quality. CO 2 concentrations in the upgraded biogas ranged from 0.1% in May to 11.6% in December, while a complete H 2 S removal was always achieved regardless of the month. A limited N 2 and O 2 stripping from the scrubbing cultivation broth was recorded in the upgraded biogas at a recycling liquid/biogas ratio in the AC of 1. Finally, CH 4 concentration in the upgraded biogas ranged from 85.6% in December to 99.6% in August. Copyright © 2018 Elsevier Ltd. All rights reserved.

  17. Gutzwiller-RVB theory of high temperature superconductivity. Results from renormalized mean field theory and variational Monte Carlo calculations

    Energy Technology Data Exchange (ETDEWEB)

    Edegger, B.

    2007-08-10

    We consider the theory of high temperature superconductivity from the viewpoint of a strongly correlated electron system. In particular, we discuss Gutzwiller projected wave functions, which incorporate strong correlations by prohibiting double occupancy in orbitals with strong on-site repulsion. After a general overview on high temperature superconductivity, we discuss Anderson's resonating valence bond (RVB) picture and its implementation by renormalized mean field theory (RMFT) and variational Monte Carlo (VMC) techniques. In the following, we present a detailed review on RMFT and VMC results with emphasis on our recent contributions. Especially, we are interested in spectral features of Gutzwiller-Bogolyubov quasiparticles obtained by extending VMC and RMFT techniques to excited states. We explicitly illustrate this method to determine the quasiparticle weight and provide a comparison with angle resolved photoemission spectroscopy (ARPES) and scanning tunneling microscopy (STM). We conclude by summarizing recent successes and by discussing open questions, which must be solved for a thorough understanding of high temperature superconductivity by Gutzwiller projected wave functions. (orig.)

  18. International variations in the gestational age distribution of births: an ecological study in 34 high-income countries.

    Science.gov (United States)

    Delnord, Marie; Mortensen, Laust; Hindori-Mohangoo, Ashna D; Blondel, Béatrice; Gissler, Mika; Kramer, Michael R; Richards, Jennifer L; Deb-Rinker, Paromita; Rouleau, Jocelyn; Morisaki, Naho; Nassar, Natasha; Bolumar, Francisco; Berrut, Sylvie; Nybo Andersen, Anne-Marie; Kramer, Michael S; Zeitlin, Jennifer

    2018-04-01

    Few studies have investigated international variations in the gestational age (GA) distribution of births. While preterm births (22-36 weeks GA) and early term births (37-38 weeks) are at greater risk of adverse health outcomes compared to full term births (39-40 weeks), it is not known if countries with high preterm birth rates also have high early term birth rates. We examined rate associations between preterm and early term births and mean term GA by mode of delivery onset. We used routine aggregate data on the GA distribution of singleton live births from up to 34 high-income countries/regions in 1996, 2000, 2004, 2008 and 2010 to study preterm and early term births overall and by spontaneous or indicated onset. Pearson correlation coefficients were adjusted for clustering in time trend analyses. Preterm and early term births ranged from 4.1% to 8.2% (median 5.5%) and 15.6% to 30.8% (median 22.2%) of live births in 2010, respectively. Countries with higher preterm birth rates in 2004-2010 had higher early term birth rates (r > 0.50, P birth rates suggest that common risk factors could underpin shifts in the GA distribution. Targeting m