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Sample records for reveals suggestive qtls

  1. QTL Analysis of High Thermotolerance with Superior and Downgraded Parental Yeast Strains Reveals New Minor QTLs and Converges on Novel Causative Alleles Involved in RNA Processing

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    Yang, Yudi; Foulquié-Moreno, Maria R.; Clement, Lieven; Erdei, Éva; Tanghe, An; Schaerlaekens, Kristien; Dumortier, Françoise; Thevelein, Johan M.

    2013-01-01

    Revealing QTLs with a minor effect in complex traits remains difficult. Initial strategies had limited success because of interference by major QTLs and epistasis. New strategies focused on eliminating major QTLs in subsequent mapping experiments. Since genetic analysis of superior segregants from natural diploid strains usually also reveals QTLs linked to the inferior parent, we have extended this strategy for minor QTL identification by eliminating QTLs in both parent strains and repeating the QTL mapping with pooled-segregant whole-genome sequence analysis. We first mapped multiple QTLs responsible for high thermotolerance in a natural yeast strain, MUCL28177, compared to the laboratory strain, BY4742. Using single and bulk reciprocal hemizygosity analysis we identified MKT1 and PRP42 as causative genes in QTLs linked to the superior and inferior parent, respectively. We subsequently downgraded both parents by replacing their superior allele with the inferior allele of the other parent. QTL mapping using pooled-segregant whole-genome sequence analysis with the segregants from the cross of the downgraded parents, revealed several new QTLs. We validated the two most-strongly linked new QTLs by identifying NCS2 and SMD2 as causative genes linked to the superior downgraded parent and we found an allele-specific epistatic interaction between PRP42 and SMD2. Interestingly, the related function of PRP42 and SMD2 suggests an important role for RNA processing in high thermotolerance and underscores the relevance of analyzing minor QTLs. Our results show that identification of minor QTLs involved in complex traits can be successfully accomplished by crossing parent strains that have both been downgraded for a single QTL. This novel approach has the advantage of maintaining all relevant genetic diversity as well as enough phenotypic difference between the parent strains for the trait-of-interest and thus maximizes the chances of successfully identifying additional minor

  2. QTL analysis of high thermotolerance with superior and downgraded parental yeast strains reveals new minor QTLs and converges on novel causative alleles involved in RNA processing.

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    Yudi Yang

    Full Text Available Revealing QTLs with a minor effect in complex traits remains difficult. Initial strategies had limited success because of interference by major QTLs and epistasis. New strategies focused on eliminating major QTLs in subsequent mapping experiments. Since genetic analysis of superior segregants from natural diploid strains usually also reveals QTLs linked to the inferior parent, we have extended this strategy for minor QTL identification by eliminating QTLs in both parent strains and repeating the QTL mapping with pooled-segregant whole-genome sequence analysis. We first mapped multiple QTLs responsible for high thermotolerance in a natural yeast strain, MUCL28177, compared to the laboratory strain, BY4742. Using single and bulk reciprocal hemizygosity analysis we identified MKT1 and PRP42 as causative genes in QTLs linked to the superior and inferior parent, respectively. We subsequently downgraded both parents by replacing their superior allele with the inferior allele of the other parent. QTL mapping using pooled-segregant whole-genome sequence analysis with the segregants from the cross of the downgraded parents, revealed several new QTLs. We validated the two most-strongly linked new QTLs by identifying NCS2 and SMD2 as causative genes linked to the superior downgraded parent and we found an allele-specific epistatic interaction between PRP42 and SMD2. Interestingly, the related function of PRP42 and SMD2 suggests an important role for RNA processing in high thermotolerance and underscores the relevance of analyzing minor QTLs. Our results show that identification of minor QTLs involved in complex traits can be successfully accomplished by crossing parent strains that have both been downgraded for a single QTL. This novel approach has the advantage of maintaining all relevant genetic diversity as well as enough phenotypic difference between the parent strains for the trait-of-interest and thus maximizes the chances of successfully identifying

  3. Intersubspecific subcongenic mouse strain analysis reveals closely linked QTLs with opposite effects on body weight.

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    Mollah, Md Bazlur R; Ishikawa, Akira

    2011-06-01

    A previous genome-wide QTL study revealed many QTLs affecting postnatal body weight and growth in an intersubspecific backcross mouse population between the C57BL/6J (B6) strain and wild Mus musculus castaneus mice captured in the Philippines. Subsequently, several closely linked QTLs for body composition traits were revealed in an F(2) intercross population between B6 and B6.Cg-Pbwg1, a congenic strain on the B6 genetic background carrying the growth QTL Pbwg1 on proximal chromosome 2. However, no QTL affecting body weight has been duplicated in the F(2) population, except for mapping an overdominant QTL that causes heterosis of body weight. In this study, we developed 17 intersubspecific subcongenic strains with overlapping and nonoverlapping castaneus regions from the B6.Cg-Pbwg1 congenic strain in order to search for and genetically dissect QTLs affecting body weight into distinct closely linked loci. Phenotypic comparisons of several developed subcongenic strains with the B6 strain revealed that two closely linked but distinct QTLs that regulate body weight, named Pbwg1.11 and Pbwg1.12, are located on an 8.9-Mb region between D2Mit270 and D2Mit472 and on the next 3.6-Mb region between D2Mit205 and D2Mit182, respectively. Further analyses using F(2) segregating populations obtained from intercrosses between B6 and each of the two selected subcongenic strains confirmed the presence of these two body weight QTLs. Pbwg1.11 had an additive effect on body weight at 6, 10, and 13 weeks of age, and its castaneus allele decreased it. In contrast, the castaneus allele at Pbwg1.12 acted in a dominant fashion and surprisingly increased body weight at 6, 10, and 13 weeks of age despite the body weight of wild castaneus mice being 60% of that of B6 mice. These findings illustrate the complex genetic nature of body weight regulation and support the importance of subcongenic mouse analysis to dissect closely linked loci.

  4. Integrative modeling of eQTLs and cis-regulatory elements suggests mechanisms underlying cell type specificity of eQTLs.

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    Christopher D Brown

    Full Text Available Genetic variants in cis-regulatory elements or trans-acting regulators frequently influence the quantity and spatiotemporal distribution of gene transcription. Recent interest in expression quantitative trait locus (eQTL mapping has paralleled the adoption of genome-wide association studies (GWAS for the analysis of complex traits and disease in humans. Under the hypothesis that many GWAS associations tag non-coding SNPs with small effects, and that these SNPs exert phenotypic control by modifying gene expression, it has become common to interpret GWAS associations using eQTL data. To fully exploit the mechanistic interpretability of eQTL-GWAS comparisons, an improved understanding of the genetic architecture and causal mechanisms of cell type specificity of eQTLs is required. We address this need by performing an eQTL analysis in three parts: first we identified eQTLs from eleven studies on seven cell types; then we integrated eQTL data with cis-regulatory element (CRE data from the ENCODE project; finally we built a set of classifiers to predict the cell type specificity of eQTLs. The cell type specificity of eQTLs is associated with eQTL SNP overlap with hundreds of cell type specific CRE classes, including enhancer, promoter, and repressive chromatin marks, regions of open chromatin, and many classes of DNA binding proteins. These associations provide insight into the molecular mechanisms generating the cell type specificity of eQTLs and the mode of regulation of corresponding eQTLs. Using a random forest classifier with cell specific CRE-SNP overlap as features, we demonstrate the feasibility of predicting the cell type specificity of eQTLs. We then demonstrate that CREs from a trait-associated cell type can be used to annotate GWAS associations in the absence of eQTL data for that cell type. We anticipate that such integrative, predictive modeling of cell specificity will improve our ability to understand the mechanistic basis of human

  5. First interspecific genetic linkage map for Castanea sativa x Castanea crenata revealed QTLs for resistance to Phytophthora cinnamomi.

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    Santos, Carmen; Nelson, Charles Dana; Zhebentyayeva, Tetyana; Machado, Helena; Gomes-Laranjo, José; Costa, Rita Lourenço

    2017-01-01

    The Japanese chestnut (Castanea crenata) carries resistance to Phytophthora cinnamomi, the destructive and widespread oomycete causing ink disease. The European chestnut (Castanea sativa), carrying little to no disease resistance, is currently threatened by the presence of the oomycete pathogen in forests, orchards and nurseries. Determining the genetic basis of P. cinnamomi resistance, for further selection of molecular markers and candidate genes, is a prominent issue for implementation of marker assisted selection in the breeding programs for resistance. In this study, the first interspecific genetic linkage map of C. sativa x C. crenata allowed the detection of QTLs for P. cinnamomi resistance. The genetic map was constructed using two independent, control-cross mapping populations. Chestnut populations were genotyped using 452 microsatellite and single nucleotide polymorphism molecular markers derived from the available chestnut transcriptomes. The consensus genetic map spans 498,9 cM and contains 217 markers mapped with an average interval of 2.3 cM. For QTL analyses, the progression rate of P. cinnamomi lesions in excised shoots inoculated was used as the phenotypic metric. Using non-parametric and composite interval mapping approaches, two QTLs were identified for ink disease resistance, distributed in two linkage groups: E and K. The presence of QTLs located in linkage group E regarding P. cinnamomi resistance is consistent with a previous preliminary study developed in American x Chinese chestnut populations, suggesting the presence of common P. cinnamomi defense mechanisms across species. Results presented here extend the genomic resources of Castanea genus providing potential tools to assist the ongoing and future chestnut breeding programs.

  6. First interspecific genetic linkage map for Castanea sativa x Castanea crenata revealed QTLs for resistance to Phytophthora cinnamomi.

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    Carmen Santos

    Full Text Available The Japanese chestnut (Castanea crenata carries resistance to Phytophthora cinnamomi, the destructive and widespread oomycete causing ink disease. The European chestnut (Castanea sativa, carrying little to no disease resistance, is currently threatened by the presence of the oomycete pathogen in forests, orchards and nurseries. Determining the genetic basis of P. cinnamomi resistance, for further selection of molecular markers and candidate genes, is a prominent issue for implementation of marker assisted selection in the breeding programs for resistance. In this study, the first interspecific genetic linkage map of C. sativa x C. crenata allowed the detection of QTLs for P. cinnamomi resistance. The genetic map was constructed using two independent, control-cross mapping populations. Chestnut populations were genotyped using 452 microsatellite and single nucleotide polymorphism molecular markers derived from the available chestnut transcriptomes. The consensus genetic map spans 498,9 cM and contains 217 markers mapped with an average interval of 2.3 cM. For QTL analyses, the progression rate of P. cinnamomi lesions in excised shoots inoculated was used as the phenotypic metric. Using non-parametric and composite interval mapping approaches, two QTLs were identified for ink disease resistance, distributed in two linkage groups: E and K. The presence of QTLs located in linkage group E regarding P. cinnamomi resistance is consistent with a previous preliminary study developed in American x Chinese chestnut populations, suggesting the presence of common P. cinnamomi defense mechanisms across species. Results presented here extend the genomic resources of Castanea genus providing potential tools to assist the ongoing and future chestnut breeding programs.

  7. Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non-coding genes

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    Hasin-Brumshtein, Yehudit; Khan, Arshad H.; Hormozdiari, Farhad; Pan, Calvin; Parks, Brian W.; Petyuk, Vladislav A.; Piehowski, Paul D.; Brümmer, Anneke; Pellegrini, Matteo; Xiao, Xinshu; Eskin, Eleazar; Smith, Richard D.; Lusis, Aldons J.; Smith, Desmond J.

    2016-09-13

    Previous studies had shown that the integration of genome wide expression profiles, in metabolic tissues, with genetic and phenotypic variance, provided valuable insight into the underlying molecular mechanisms. We used RNA-Seq to characterize hypothalamic transcriptome in 99 inbred strains of mice from the Hybrid Mouse Diversity Panel (HMDP), a reference resource population for cardiovascular and metabolic traits. We report numerous novel transcripts supported by proteomic analyses, as well as novel non coding RNAs. High resolution genetic mapping of transcript levels in HMDP, reveals bothlocalandtransexpression Quantitative Trait Loci (eQTLs) demonstrating 2transeQTL 'hotspots' associated with expression of hundreds of genes. We also report thousands of alternative splicing events regulated by genetic variants. Finally, comparison with about 150 metabolic and cardiovascular traits revealed many highly significant associations. Our data provide a rich resource for understanding the many physiologic functions mediated by the hypothalamus and their genetic regulation.

  8. Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non-coding genes

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    Hasin-Brumshtein, Yehudit; Khan, Arshad H; Hormozdiari, Farhad; Pan, Calvin; Parks, Brian W; Petyuk, Vladislav A; Piehowski, Paul D; Brümmer, Anneke; Pellegrini, Matteo; Xiao, Xinshu; Eskin, Eleazar; Smith, Richard D; Lusis, Aldons J; Smith, Desmond J

    2016-01-01

    Previous studies had shown that the integration of genome wide expression profiles, in metabolic tissues, with genetic and phenotypic variance, provided valuable insight into the underlying molecular mechanisms. We used RNA-Seq to characterize hypothalamic transcriptome in 99 inbred strains of mice from the Hybrid Mouse Diversity Panel (HMDP), a reference resource population for cardiovascular and metabolic traits. We report numerous novel transcripts supported by proteomic analyses, as well as novel non coding RNAs. High resolution genetic mapping of transcript levels in HMDP, reveals both local and trans expression Quantitative Trait Loci (eQTLs) demonstrating 2 trans eQTL 'hotspots' associated with expression of hundreds of genes. We also report thousands of alternative splicing events regulated by genetic variants. Finally, comparison with about 150 metabolic and cardiovascular traits revealed many highly significant associations. Our data provide a rich resource for understanding the many physiologic functions mediated by the hypothalamus and their genetic regulation. DOI: http://dx.doi.org/10.7554/eLife.15614.001 PMID:27623010

  9. A model incorporating potential skewed X-inactivation in MZ girls suggests that X-linked QTLs exist for several social behaviours including autism spectrum disorder.

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    Loat, C S; Haworth, C M A; Plomin, R; Craig, I W

    2008-11-01

    Sex differences in the frequency and patterns of behaviours are frequently observed and largely unexplained. We have investigated the possible role of X-linked genes in the aetiology of social behaviour problems, including those involved in autistic spectrum disorders. A novel approach has been implemented. This is based on predictions following from stochastic patterns of X-inactivation of lower concordance of monozygous female (MZF) twins than MZM twins for behaviours underpinned by X-linked QTLs and the converse that DZF twins are expected to correlate more strongly for X-linked traits than DZM twins because unlike males, females always have at least one X chromosome in common. These expectations were tested in an ongoing longitudinal cohort study in which all twins born in England and Wales between 1994 and 1996 were invited to take part. 1000 each of MZF, MZM, DZF and DZM pairs from TEDS were tested at 7 and 8 years of age. The results suggest the persistent influence of X-linked genes on cognition and social behaviour problems, including those involved in autistic spectrum disorders, from early to middle childhood. This emphasises the potential importance of X-linked genes in the developmental trajectories of behaviour and mental health and the need to stratify genetic analysis of behaviours by gender.

  10. Fine mapping quantitative resistances to downy mildew in lettuce revealed multiple sub-QTLs with plant stage dependent effects reducing or even promoting the infection.

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    den Boer, Erik; Zhang, Ningwen W; Pelgrom, Koen; Visser, Richard G F; Niks, Rients E; Jeuken, Marieke J W

    2013-12-01

    Three regions with quantitative resistance to downy mildew of non-host and wild lettuce species, Lactuca saligna , disintegrate into seventeen sub-QTLs with plant-stage-dependent effects, reducing or even promoting the infection. Previous studies on the genetic dissection of the complete resistance of wild lettuce, Lactuca saligna, to downy mildew revealed 15 introgression regions that conferred plant stage dependent quantitative resistances (QTLs). Three backcross inbred lines (BILs), carrying an individual 30-50 cM long introgression segment from L. saligna in a cultivated lettuce, L. sativa, background, reduced infection by 60-70 % at young plant stage and by 30-50 % at adult plant stage in field situations. We studied these three quantitative resistances in order to narrow down their mapping interval and determine their number of loci, either single or multiple. We performed recombinant screenings and developed near isogenic lines (NILs) with smaller overlapping L. saligna introgressions (substitution mapping). In segregating introgression line populations, recombination was suppressed up to 17-fold compared to the original L. saligna × L. sativa F 2 population. Recombination suppression depended on the chromosome region and was stronger suppressed at the smallest introgression lengths. Disease evaluation of the NILs revealed that the resistance of all three BILs was not explained by a single locus but by multiple sub-QTLs. The 17 L. saligna-derived sub-QTLs had a smaller and plant stage dependent resistance effect, some segments reducing; others even promoting downy mildew infection. Implications for lettuce breeding are outlined.

  11. Re-evaluation of the inheritance for root-knot nematode resistance in the Upland cotton germplasm line M-120 RNR revealed two epistatic QTLs conferring resistance.

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    He, Yajun; Kumar, Pawan; Shen, Xinlian; Davis, Richard F; Van Becelaere, Guillermo; May, O Lloyd; Nichols, Robert L; Chee, Peng W

    2014-06-01

    We report a second major QTL for root-knot nematode resistance in the highly resistant Upland cotton line M-120RNR and show epistasis between two resistant QTLs with different mechanisms conferring resistance. In an earlier study, we identified a major QTL on Chromosome 11 associated with resistance to root-knot nematode in the M-120 RNR Upland cotton line (Gossypium hirsutum L.) of the Auburn 623 RNR source. Herein, we re-evaluated the genetics of the resistance to root-knot nematode in the M-120 RNR × Pima S-6 population by linkage mapping using recently published SSR markers. The QTL analysis detected two regions significantly associated with the resistance phenotype. In addition to the QTL previously identified on Chromosome 11 (qMi-C11), a major QTL was identified on Chromosome 14 (qMi-C14). The resistance locus on qMi-C11 originated from the Clevewilt parent, while the qMi-C14 locus originated from the other resistant parent, Mexico Wild Jack Jones. The qMi-C14 locus had logarithms of odds score of 17 and accounted for 45 % of the total phenotype variation in egg production. It was also associated with galling index, but the percent variation explained was only 6 %, suggesting that the qMi-C11 locus had a much stronger effect on root gall suppression than egg production, while the qMi-C14 locus had a stronger effect on egg production than galling. The results also suggest that the transgressive segregation observed in the development of Auburn 623 RNR was due to the pyramiding of at least two main effect QTLs as well as an additive-by-additive epistatic effects between the two resistant loci. The SSRs markers tightly linked to the qMi-C11 and qMi-C14 loci will greatly facilitate the improvement of RKN resistance in cotton via marker-assisted breeding.

  12. Trans-eQTLs reveal that independent genetic variants associated with a complex phenotype converge on intermediate genes, with a major role for the HLA.

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    Rudolf S N Fehrmann

    2011-08-01

    Full Text Available For many complex traits, genetic variants have been found associated. However, it is still mostly unclear through which downstream mechanism these variants cause these phenotypes. Knowledge of these intermediate steps is crucial to understand pathogenesis, while also providing leads for potential pharmacological intervention. Here we relied upon natural human genetic variation to identify effects of these variants on trans-gene expression (expression quantitative trait locus mapping, eQTL in whole peripheral blood from 1,469 unrelated individuals. We looked at 1,167 published trait- or disease-associated SNPs and observed trans-eQTL effects on 113 different genes, of which we replicated 46 in monocytes of 1,490 different individuals and 18 in a smaller dataset that comprised subcutaneous adipose, visceral adipose, liver tissue, and muscle tissue. HLA single-nucleotide polymorphisms (SNPs were 10-fold enriched for trans-eQTLs: 48% of the trans-acting SNPs map within the HLA, including ulcerative colitis susceptibility variants that affect plausible candidate genes AOAH and TRBV18 in trans. We identified 18 pairs of unlinked SNPs associated with the same phenotype and affecting expression of the same trans-gene (21 times more than expected, P<10(-16. This was particularly pronounced for mean platelet volume (MPV: Two independent SNPs significantly affect the well-known blood coagulation genes GP9 and F13A1 but also C19orf33, SAMD14, VCL, and GNG11. Several of these SNPs have a substantially higher effect on the downstream trans-genes than on the eventual phenotypes, supporting the concept that the effects of these SNPs on expression seems to be much less multifactorial. Therefore, these trans-eQTLs could well represent some of the intermediate genes that connect genetic variants with their eventual complex phenotypic outcomes.

  13. Identification of antioxidant capacity -related QTLs in Brassica oleracea.

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    Sotelo, Tamara; Cartea, María Elena; Velasco, Pablo; Soengas, Pilar

    2014-01-01

    Brassica vegetables possess high levels of antioxidant metabolites associated with beneficial health effects including vitamins, carotenoids, anthocyanins, soluble sugars and phenolics. Until now, no reports have been documented on the genetic basis of the antioxidant activity (AA) in Brassicas and the content of metabolites with AA like phenolics, anthocyanins and carotenoids. For this reason, this study aimed to: (1) study the relationship among different electron transfer (ET) methods for measuring AA, (2) study the relationship between these methods and phenolic, carotenoid and anthocyanin content, and (3) find QTLs of AA measured with ET assays and for phenolic, carotenoid and anthocyanin contents in leaves and flower buds in a DH population of B. oleracea as an early step in order to identify genes related to these traits. Low correlation coefficients among different methods for measuring AA suggest that it is necessary to employ more than one method at the same time. A total of 19 QTLs were detected for all traits. For AA methods, seven QTLs were found in leaves and six QTLs were found in flower buds. Meanwhile, for the content of metabolites with AA, two QTLs were found in leaves and four QTLs were found in flower buds. AA of the mapping population is related to phenolic compounds but also to carotenoid content. Three genomic regions determined variation for more than one ET method measuring AA. After the syntenic analysis with A. thaliana, several candidate genes related to phenylpropanoid biosynthesis are proposed for the QTLs found.

  14. QTLs for heading date and plant height under multiple environments in rice.

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    Han, Zhongmin; Hu, Wei; Tan, Cong; Xing, Yongzhong

    2017-02-01

    Both heading date and plant height are important traits related to grain yield in rice. In this study, a recombinant inbred lines (RILs) population was used to map quantitative trait loci (QTLs) for both traits under 3 long-day (LD) environments and 1 short-day (SD) environment. A total of eight QTLs for heading date and three QTLs for plant height were detected by composite interval mapping under LD conditions. Additional one QTL for heading date and three QTLs for plant height were identified by Two-QTL model under LD conditions. Among them, major QTLs qHd7.1, qHd7.2 and qHd8 for heading date, and qPh1 and qPh7.1 for plant height were commonly detected. qHd7.1 and qHd7.2 were mapped to small regions of less than 1 cM. Genome position comparison of previously cloned genes with QTLs detected in this study revealed that qHd5 and qPh3.1 were two novel QTLs. The alleles of these QTLs increasing trait values were dispersed in both parents, which well explained the transgressive segregation observed in this population. In addition, the interaction between qHd7.1 and qHd8 was detected under all LD conditions. Multiple-QTL model analysis revealed that all QTLs and their interactions explained over 80% of heading date variation and 50% of plant height variation. Two heading date QTLs were detected under SD condition. Of them, qHd10 were commonly identified under LD condition. The difference in QTL detection between LD and SD conditions indicated most heading date QTLs are sensitive to photoperiod. These findings will benefit breeding design for heading date and plant height in rice.

  15. Identification of novel QTLs for isolate-specific partial resistance to Plasmodiophora brassicae in Brassica rapa.

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    Jingjing Chen

    Full Text Available Plasmodiophora brassicae, the causal agent of clubroot disease of the Brassica crops, is widespread in the world. Quantitative trait loci (QTLs for partial resistance to 4 different isolates of P. brassicae (Pb2, Pb4, Pb7, and Pb10 were investigated using a BC1F1 population from a cross between two subspecies of Brassica rapa, i.e. Chinese cabbage inbred line C59-1 as a susceptible recurrent parent and turnip inbred line ECD04 as a resistant donor parent. The BC1F2 families were assessed for resistance under controlled conditions. A linkage map constructed with simple sequence repeats (SSR, unigene-derived microsatellite (UGMS markers, and specific markers linked to published clubroot resistance (CR genes of B. rapa was used to perform QTL mapping. A total of 6 QTLs residing in 5 CR QTL regions of the B. rapa chromosomes A01, A03, and A08 were identified to account for 12.2 to 35.2% of the phenotypic variance. Two QTL regions were found to be novel except for 3 QTLs in the respective regions of previously identified Crr1, Crr2, and Crr3. QTL mapping results indicated that 1 QTL region was common for partial resistance to the 2 isolates of Pb2 and Pb7, whereas the others were specific for each isolate. Additionally, synteny analysis between B. rapa and Arabidopsis thaliana revealed that all CR QTL regions were aligned to a single conserved crucifer blocks (U, F, and R on 3 Arabidopsis chromosomes where 2 CR QTLs were detected in A. thaliana. These results suggest that some common ancestral genomic regions were involved in the evolution of CR genes in B. rapa.

  16. Identification of Novel QTLs for Isolate-Specific Partial Resistance to Plasmodiophora brassicae in Brassica rapa

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    Zhan, Zhongxiang; Zhang, Teng; Zhang, Chunyu; Piao, Zhongyun

    2013-01-01

    Plasmodiophora brassicae, the causal agent of clubroot disease of the Brassica crops, is widespread in the world. Quantitative trait loci (QTLs) for partial resistance to 4 different isolates of P. brassicae (Pb2, Pb4, Pb7, and Pb10) were investigated using a BC1F1 population from a cross between two subspecies of Brassica rapa, i.e. Chinese cabbage inbred line C59-1 as a susceptible recurrent parent and turnip inbred line ECD04 as a resistant donor parent. The BC1F2 families were assessed for resistance under controlled conditions. A linkage map constructed with simple sequence repeats (SSR), unigene-derived microsatellite (UGMS) markers, and specific markers linked to published clubroot resistance (CR) genes of B. rapa was used to perform QTL mapping. A total of 6 QTLs residing in 5 CR QTL regions of the B. rapa chromosomes A01, A03, and A08 were identified to account for 12.2 to 35.2% of the phenotypic variance. Two QTL regions were found to be novel except for 3 QTLs in the respective regions of previously identified Crr1, Crr2, and Crr3. QTL mapping results indicated that 1 QTL region was common for partial resistance to the 2 isolates of Pb2 and Pb7, whereas the others were specific for each isolate. Additionally, synteny analysis between B. rapa and Arabidopsis thaliana revealed that all CR QTL regions were aligned to a single conserved crucifer blocks (U, F, and R) on 3 Arabidopsis chromosomes where 2 CR QTLs were detected in A. thaliana. These results suggest that some common ancestral genomic regions were involved in the evolution of CR genes in B. rapa. PMID:24376876

  17. (QTLs) underlying drought tolerance at g

    African Journals Online (AJOL)

    user

    2012-08-14

    Aug 14, 2012 ... use for quantitative trait locus (QTLs) underlying ... Key words: Soybean, molecular marker linkage map, quantitative trait loci (QTLs), drought tolerance, .... database (http://129.186.26.94/SSR.html) and was synthesized by. AuGCT Biotechnology. Data analysis. Phenotypic data for the BC1F4 population ...

  18. Identification of QTLs for root characteristics in maize grown in hydroponics and analysis of their overlap with QTLs for grain yield in the field at two water regimes.

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    Tuberosa, Roberto; Sanguineti, Maria Corinna; Landi, Pierangelo; Giuliani, Marcella Michela; Salvi, Silvio; Conti, Sergio

    2002-01-01

    We investigated the overlap among quantitative trait loci (QTLs) in maize for seminal root traits measured in hydroponics with QTLs for grain yield under well-watered (GY-WW) and water-stressed (GY-WS) field conditions as well as for a drought tolerance index (DTI) computed as GY-WS/GY-WW. In hydroponics, 11, 7, 9, and 10 QTLs were identified for primary root length (R1L), primary root diameter (R1D), primary root weight (R1W), and for the weight of the adventitious seminal roots (R2W), respectively. In the field, 7, 8, and 9 QTLs were identified for GY-WW, GY-WS, and DTI, respectively. Despite the weak correlation of root traits in hydroponics with GY-WW, GY-WS, and DTI, a noticeable overlap between the corresponding QTLs was observed. QTLs for R2W most frequently and consistently overlapped with QTLs for GY-WW, GY-WS, and/or DTI. At four QTL regions, an increase in R2W was positively associated with GY-WW, GY-WS, and/or DTI. A 10 cM interval on chromosome 1 between PGAMCTA205 and php20644 showed the strongest effect on R1L, R1D, R2W, GY-WW, GY-WS, and DTI. These results indicate the feasibility of using hydroponics in maize to identify QTL regions controlling root traits at an early growth stage and also influencing GY in the field. A comparative analysis of the QTL regions herein identified with those described in previous studies investigating root traits in different maize populations revealed a number of QTLs in common.

  19. Genomic affinities revealed by GISH suggests intergenomic restructuring between parental genomes of the paleopolyploid genus Zea.

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    González, Graciela Esther; Poggio, Lidia

    2015-10-01

    The present work compares the molecular affinities, revealed by GISH, with the analysis of meiotic pairing in intra- and interspecific hybrids between species of Zea obtained in previous works. The joint analysis of these data provided evidence about the evolutionary relationships among the species from the paleopolyploid genus Zea (maize and teosintes). GISH and meiotic pairing of intraspecific hybrids revealed high genomic affinity between maize (Zea mays subsp. mays) and both Zea mays subsp. parviglumis and Zea mays subsp. mexicana. On the other hand, when Zea mays subsp. huehuetenanguensis DNA was probed on maize chromosomes, a lower affinity was detected, and the pattern of hybridization suggested intergenomical restructuring between the parental genomes of maize. When DNA from Zea luxurians was used as probe, homogeneous hybridization signals were observed through all maize chromosomes. Lower genomic affinity was observed when DNA from Zea diploperennis was probed on maize chromosomes, especially at knob regions. Maize chromosomes hybridized with Zea perennis DNA showed hybridization signals on four chromosome pairs: two chromosome pairs presented hybridization signal in only one chromosomal arm, whereas four chromosome pairs did not show any hybridization. These results are in agreement with previous GISH studies, which have identified the genomic source of the chromosomes involved in the meiotic configurations of Z. perennis × maize hybrids. These findings allow postulating that maize has a parental genome not shared with Z. perennis, and the existence of intergenomic restructuring between the parental genomes of maize. Moreover, the absence of hybridization signals in all maize knobs indicate that these heterochromatic regions were lost during the Z. perennis genome evolution.

  20. Body Composition QTLs Identified in Intercross Populations Are Reproducible in Consomic Mouse Strains.

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    Lin, Cailu; Fesi, Brad D; Marquis, Michael; Bosak, Natalia P; Theodorides, Maria L; Avigdor, Mauricio; McDaniel, Amanda H; Duke, Fujiko F; Lysenko, Anna; Khoshnevisan, Amin; Gantick, Brian R; Arayata, Charles J; Nelson, Theodore M; Bachmanov, Alexander A; Reed, Danielle R

    2015-01-01

    Genetic variation contributes to individual differences in obesity, but defining the exact relationships between naturally occurring genotypes and their effects on fatness remains elusive. As a step toward positional cloning of previously identified body composition quantitative trait loci (QTLs) from F2 crosses of mice from the C57BL/6ByJ and 129P3/J inbred strains, we sought to recapture them on a homogenous genetic background of consomic (chromosome substitution) strains. Male and female mice from reciprocal consomic strains originating from the C57BL/6ByJ and 129P3/J strains were bred and measured for body weight, length, and adiposity. Chromosomes 2, 7, and 9 were selected for substitution because previous F2 intercross studies revealed body composition QTLs on these chromosomes. We considered a QTL confirmed if one or both sexes of one or both reciprocal consomic strains differed significantly from the host strain in the expected direction after correction for multiple testing. Using these criteria, we confirmed two of two QTLs for body weight (Bwq5-6), three of three QTLs for body length (Bdln3-5), and three of three QTLs for adiposity (Adip20, Adip26 and Adip27). Overall, this study shows that despite the biological complexity of body size and composition, most QTLs for these traits are preserved when transferred to consomic strains; in addition, studying reciprocal consomic strains of both sexes is useful in assessing the robustness of a particular QTL.

  1. Body Composition QTLs Identified in Intercross Populations Are Reproducible in Consomic Mouse Strains.

    Directory of Open Access Journals (Sweden)

    Cailu Lin

    Full Text Available Genetic variation contributes to individual differences in obesity, but defining the exact relationships between naturally occurring genotypes and their effects on fatness remains elusive. As a step toward positional cloning of previously identified body composition quantitative trait loci (QTLs from F2 crosses of mice from the C57BL/6ByJ and 129P3/J inbred strains, we sought to recapture them on a homogenous genetic background of consomic (chromosome substitution strains. Male and female mice from reciprocal consomic strains originating from the C57BL/6ByJ and 129P3/J strains were bred and measured for body weight, length, and adiposity. Chromosomes 2, 7, and 9 were selected for substitution because previous F2 intercross studies revealed body composition QTLs on these chromosomes. We considered a QTL confirmed if one or both sexes of one or both reciprocal consomic strains differed significantly from the host strain in the expected direction after correction for multiple testing. Using these criteria, we confirmed two of two QTLs for body weight (Bwq5-6, three of three QTLs for body length (Bdln3-5, and three of three QTLs for adiposity (Adip20, Adip26 and Adip27. Overall, this study shows that despite the biological complexity of body size and composition, most QTLs for these traits are preserved when transferred to consomic strains; in addition, studying reciprocal consomic strains of both sexes is useful in assessing the robustness of a particular QTL.

  2. Identification of QTLs associated with oil content in a high-oil Brassica napus cultivar and construction of a high-density consensus map for QTLs comparison in B. napus.

    Directory of Open Access Journals (Sweden)

    Xiaodong Wang

    Full Text Available Increasing seed oil content is one of the most important goals in breeding of rapeseed (B. napus L.. To dissect the genetic basis of oil content in B. napus, a large and new double haploid (DH population containing 348 lines was obtained from a cross between 'KenC-8' and 'N53-2', two varieties with >10% difference in seed oil content, and this population was named the KN DH population. A genetic linkage map consisting of 403 markers was constructed, which covered a total length of 1783.9 cM with an average marker interval of 4.4 cM. The KN DH population was phenotyped in eight natural environments and subjected to quantitative trait loci (QTL analysis for oil content. A total of 63 identified QTLs explaining 2.64-17.88% of the phenotypic variation were identified, and these QTLs were further integrated into 24 consensus QTLs located on 11 chromosomes using meta-analysis. A high-density consensus map with 1335 marker loci was constructed by combining the KN DH map with seven other published maps based on the common markers. Of the 24 consensus QTLs in the KN DH population, 14 were new QTLs including five new QTLs in A genome and nine in C genome. The analysis revealed that a larger population with significant differences in oil content gave a higher power detecting new QTLs for oil content, and the construction of the consensus map provided a new clue for comparing the QTLs detected in different populations. These findings enriched our knowledge of QTLs for oil content and should be a potential in marker-assisted breeding of B. napus.

  3. Literacy for QTLS achieving the minimum core

    CERN Document Server

    Hickey, Julia

    2013-01-01

    Literacy for QTLS is written specifically with the needs of all those training to teach or currently working in the lifelong learning sector in mind. This highly practical and easy-to-use text will help you identify your areas of strength and weakness, develop your knowledge and skills in order to pass the national literacy test and adopt strategies that you can use to support the language and literacy skills of your own learners.Packed with test-your-knowledge questions, examples and recommendations for best practice, this book, closely linked to the QTLS standards, is essential reading for a

  4. Identification and introgression of QTLs implicated in resistance to ...

    Indian Academy of Sciences (India)

    Sorghum downy mildew caused by Peronosclerospora sorghi is a major disease of maize and resistance is under the control of polygenes which necessitated identification of quantitative-trait loci (QTLs) for initiating marker-assisted introgression of resistant QTLs in elite susceptible inbred lines. In the present study, QTLs ...

  5. Genome anchored QTLs for biomass productivity in hybrid Populus grown under contrasting environments.

    Directory of Open Access Journals (Sweden)

    Wellington Muchero

    Full Text Available Traits related to biomass production were analyzed for the presence of quantitative trait loci (QTLs in a Populus trichocarpa × P. deltoides F(2 population. A genetic linkage map composed of 841 SSR, AFLP, and RAPD markers and phenotypic data from 310 progeny were used to identify genomic regions harboring biomass QTLs. Twelve intervals were identified, of which BM-1, BM-2, and BM-7 were identified in all three years for both height and diameter. One putative QTL, BM-7, and one suggestive QTL exhibited significant evidence of over-dominance in all three years for both traits. Conversely, QTLs BM-4 and BM-6 exhibited evidence of under-dominance in both environments for height and diameter. Seven of the nine QTLs were successfully anchored, and QTL peak positions were estimated for each one on the P. trichocarpa genome assembly using flanking SSR markers with known physical positions. Of the 3,031 genes located in genome-anchored QTL intervals, 1,892 had PFAM annotations. Of these, 1,313, representing 255 unique annotations, had at least one duplicate copy in a QTL interval identified on a separate scaffold. This observation suggests that some QTLs identified in this study may have shared the same ancestral sequence prior to the salicoid genome duplication in Populus.

  6. Fractal analysis reveals subclasses of neurons and suggests an explanation of their spontaneous activity.

    Science.gov (United States)

    Favela, Luis H; Coey, Charles A; Griff, Edwin R; Richardson, Michael J

    2016-07-28

    The present work used fractal time series analysis (detrended fluctuation analysis; DFA) to examine the spontaneous activity of single neurons in an anesthetized animal model, specifically, the mitral cells in the rat main olfactory bulb. DFA bolstered previous research in suggesting two subclasses of mitral cells. Although there was no difference in the fractal scaling of the interspike interval series at the shorter timescales, there was a significant difference at longer timescales. Neurons in Group B exhibited fractal, power-law scaled interspike intervals, whereas neurons in Group A exhibited random variation. These results raise questions about the role of these different cells within the olfactory bulb and potential explanations of their dynamics. Specifically, self-organized criticality has been proposed as an explanation of fractal scaling in many natural systems, including neural systems. However, this theory is based on certain assumptions that do not clearly hold in the case of spontaneous neural activity, which likely reflects intrinsic cell dynamics rather than activity driven by external stimulation. Moreover, it is unclear how self-organized criticality might account for the random dynamics observed in Group A, and how these random dynamics might serve some functional role when embedded in the typical activity of the olfactory bulb. These theoretical considerations provide direction for additional experimental work. Published by Elsevier Ireland Ltd.

  7. Genome analysis of canine astroviruses reveals genetic heterogeneity and suggests possible inter-species transmission.

    Science.gov (United States)

    Mihalov-Kovács, Eszter; Martella, Vito; Lanave, Gianvito; Bodnar, Livia; Fehér, Enikő; Marton, Szilvia; Kemenesi, Gábor; Jakab, Ferenc; Bányai, Krisztián

    2017-03-15

    Canine astrovirus RNA was detected in the stools of 17/63 (26.9%) samples, using either a broadly reactive consensus RT-PCR for astroviruses or random RT-PCR coupled with massive deep sequencing. The complete or nearly complete genome sequence of five canine astroviruses was reconstructed that allowed mapping the genome organization and to investigate the genetic diversity of these viruses. The genome was about 6.6kb in length and contained three open reading frames (ORFs) flanked by a 5' UTR, and a 3' UTR plus a poly-A tail. ORF1a and ORF1b overlapped by 43 nucleotides while the ORF2 overlapped by 8 nucleotides with the 3' end of ORF1b. Upon genome comparison, four strains (HUN/2012/2, HUN/2012/6, HUN/2012/115, and HUN/2012/135) were more related genetically to each other and to UK canine astroviruses (88-96% nt identity), whilst strain HUN/2012/126 was more divergent (75-76% nt identity). In the ORF1b and ORF2, strains HUN/2012/2, HUN/2012/6, and HUN/2012/135 were related genetically to other canine astroviruses identified formerly in Europe and China, whereas strain HUN/2012/126 was related genetically to a divergent canine astrovirus strain, ITA/2010/Zoid. For one canine astrovirus, HUN/2012/8, only a 3.2kb portion of the genome, at the 3' end, could be determined. Interestingly, this strain possessed unique genetic signatures (including a longer ORF1b/ORF2 overlap and a longer 3'UTR) and it was divergent in both ORF1b and ORF2 from all other canine astroviruses, with the highest nucleotide sequence identity (68% and 63%, respectively) to a mink astrovirus, thus suggesting a possible event of interspecies transmission. The genetic heterogeneity of canine astroviruses may pose a challenge for the diagnostics and for future prophylaxis strategies. Copyright © 2016 Elsevier B.V. All rights reserved.

  8. Molecular Mapping of QTLs for Yield and Yield-Related Traits in Oryza sativa cv Swarna × O. nivara (IRGC81848 Backcross Population

    Directory of Open Access Journals (Sweden)

    B.P. MALLIKARJUNA SWAMY

    2011-09-01

    Full Text Available Advanced backcross QTL analysis was used to identify QTLs for seven yield and yield-related traits in a BC2F2 population from the cross between a popular Oryza sativa cv Swarna and O. nivara IRGC81848. Transgressive segregants with more than 15% increased effect over Swarna were observed for all the traits except days to heading and days to 50% flowering. Thirty QTLs were detected for seven yield and yield-related traits using interval and composite interval mapping. Enhancing alleles at 13 (45% of these QTLs were derived from O. nivara, and enhancing alleles at all the QTLs for stem diameter and rachis diameter were derived from O. nivara. Three stem diameter QTLs, two rachis diameter QTLs and one number of secondary branches QTL identified by both Interval and composite interval mapping contributed more than 15% of the total phenotypic variance. The QTL epistasis was significant for stem diameter and plot yield. The most significant QTLs qSD7.2, qSD8.1 and qSD9.1 for stem diameter, qRD9.1 for rachis diameter and qNSB1.1 for number of secondary branches are good targets to evaluate their use in marker-assisted selection. O. nivara is a good source of novel alleles for yield related traits and reveals major effect QTLs suitable for marker-assisted selection.

  9. Isolate dependency of Brassica rapa resistance QTLs to Botrytis cinerea.

    Directory of Open Access Journals (Sweden)

    Wei eZhang

    2016-02-01

    Full Text Available Generalist necrotrophic pathogens including Botrytis cinerea cause significant yield and financial losses on Brassica crops. However, there is little knowledge about the mechanisms underlying the complex interactions encoded by both host and pathogen genomes in this interaction. This potentially includes multiple layers of plant defense and pathogen virulence mechanisms that could complicate in breeding broad spectrum resistance within Brassica species. Glucosinolates are a diverse group of defense metabolites that play a key role in interaction between Brassica and biotic attackers. In this study, we utilized a collection of diverse B. cinerea isolates to investigate resistance within the B. rapa R500 x IMB211 recombinant inbred line population. We tested variation on lesion development and glucosinolate accumulation in parental lines and all population lines. We then mapped quantitative trait loci (QTL for both resistances to B. cinerea and defense metabolites in this population. Phenotypic analysis and QTL mapping demonstrate that the genetic basis of resistance to B. cinerea in B. rapa is isolate specific and polygenic with transgressive segregation that both parents contribute resistance alleles. QTLs controlling defensive glucosinolates are highly dependent on pathogen infection. An overlap of two QTLs identified between resistance to B. cinerea and defense metabolites also showed isolate specific effects. This work suggests that directly searching for resistance loci may not be the best approach at improving resistance in B. rapa to necrotrophic pathogen.

  10. Genetic mapping of quantitative trait loci (QTLs) with effects on ...

    African Journals Online (AJOL)

    Genetic mapping of quantitative trait loci (QTLs) with effects on resistance to flower bud thrips ( Megalurothrips sjostedti ) identified in recombinant inbred lines of cowpea ( Vigna unguiculata (L.) Walp)

  11. Sustainable deployment of QTLs conferring quantitative resistance to crops: first lessons from a stochastic model.

    Science.gov (United States)

    Bourget, Romain; Chaumont, Loïc; Durel, Charles-Eric; Sapoukhina, Natalia

    2015-05-01

    Quantitative plant disease resistance is believed to be more durable than qualitative resistance, since it exerts less selective pressure on the pathogens. However, the process of progressive pathogen adaptation to quantitative resistance is poorly understood, which makes it difficult to predict its durability or to derive principles for its sustainable deployment. Here, we study the dynamics of pathogen adaptation in response to quantitative plant resistance affecting pathogen reproduction rate and its colonizing capacity. We developed a stochastic model for the continuous evolution of a pathogen population within a quantitatively resistant host. We assumed that pathogen can adapt to a host by the progressive restoration of reproduction rate or of colonizing capacity, or of both. Our model suggests that a combination of quantitative trait loci (QTLs) affecting distinct pathogen traits was more durable if the evolution of repressed traits was antagonistic. Otherwise, quantitative resistance that depressed only pathogen reproduction was more durable. In order to decelerate the progressive pathogen adaptation, QTLs that decrease the pathogen's maximum capacity to colonize must be combined with QTLs that decrease the spore production per lesion or the infection efficiency or that increase the latent period. Our theoretical framework can help breeders to develop principles for sustainable deployment of QTLs. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

  12. Detection of QTLs for seedling characteristics in barley (Hordeum vulgare L.) grown under hydroponic culture condition.

    Science.gov (United States)

    Wang, Qifei; Sun, Genlou; Ren, Xifeng; Wang, Jibin; Du, Binbin; Li, Chengdao; Sun, Dongfa

    2017-11-07

    Seedling characteristics play significant roles in the growth and development of barley (Hordeum vulgare L.), including stable stand establishment, water and nutrients uptake, biotic resistance and abiotic stresses, and can influence yield and quality. However, the genetic mechanisms underlying seedling characteristics in barley are largely unknown and little research has been done. In the present work, 21 seedling-related characteristics are assessed in a barley double haploid (DH) population, grown under hydroponic conditions. Of them, leaf age (LAG), shoot height (SH), maximum root length (MRL), main root number (MRN) and seedling fresh weight (SFW) were investigated at the 13th, 20th, 27th, and 34th day after germination. The objectives were to identify quantitative trait loci (QTLs) underlying these seedling characteristics using a high-density linkage map and to reveal the QTL expression pattern by comparing the QTLs among four different seedling growth stages. A total of 70 QTLs were distributed over all chromosomes except 4H, and, individually, accounted for 5.01%-77.78% of phenotypic variation. Out of the 70 detected QTLs, 23 showed a major effect on 14 seedling-related characteristics. Ten co-localized chromosomal regions on 2H (five regions), 3H (two regions) and 7H (three regions) involved 39 QTLs (55.71%), each simultaneously influenced more than one trait. Meanwhile, 9 co-localized genomic regions involving 22 QTLs for five seedling characteristics (LAG, SH, MRL, MRN and SFW) at the 13th, 20th, 27th and 34th day-old seedling were common for two or more growth stages of seedling. QTL in the vicinity of Vrs1 locus on chromosome 2H with the favorable alleles from Huadamai 6 was found to have the largest main effects on multiple seedling-related traits. Six QTL cluster regions associated with 16 seedling-related characteristics were observed on chromosome 2H, 3H and 7H. The majority of the 29 regions identified for five seedling characteristics were

  13. Identification and introgression of QTLs implicated in resistance to ...

    Indian Academy of Sciences (India)

    2015-12-08

    Dec 8, 2015 ... of polygenes which necessitated identification of quantitative-trait loci (QTLs) for initiating marker-assisted introgression of resistant QTLs in elite ... High heritability was observed for the disease reaction. The final map generated using 87 ..... disease and insect resistance genes in maize. Mol. Plant Microbe.

  14. Development of molecular map and identification of QTLs linked to ...

    Indian Academy of Sciences (India)

    A number of genetic maps for Fusarium wilt resistance in chickpea have been reported in earlier studies, however QTLs identified for Fusarium wilt resistance were unstable. Hence, the present study aims to map novel molecular markers and to identify QTLs for Fusarium wilt resistance in chickpea. An intraspecific linkage ...

  15. Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations.

    Directory of Open Access Journals (Sweden)

    Alexandra C Nica

    2010-04-01

    Full Text Available The recent success of genome-wide association studies (GWAS is now followed by the challenge to determine how the reported susceptibility variants mediate complex traits and diseases. Expression quantitative trait loci (eQTLs have been implicated in disease associations through overlaps between eQTLs and GWAS signals. However, the abundance of eQTLs and the strong correlation structure (LD in the genome make it likely that some of these overlaps are coincidental and not driven by the same functional variants. In the present study, we propose an empirical methodology, which we call Regulatory Trait Concordance (RTC that accounts for local LD structure and integrates eQTLs and GWAS results in order to reveal the subset of association signals that are due to cis eQTLs. We simulate genomic regions of various LD patterns with both a single or two causal variants and show that our score outperforms SNP correlation metrics, be they statistical (r(2 or historical (D'. Following the observation of a significant abundance of regulatory signals among currently published GWAS loci, we apply our method with the goal to prioritize relevant genes for each of the respective complex traits. We detect several potential disease-causing regulatory effects, with a strong enrichment for immunity-related conditions, consistent with the nature of the cell line tested (LCLs. Furthermore, we present an extension of the method in trans, where interrogating the whole genome for downstream effects of the disease variant can be informative regarding its unknown primary biological effect. We conclude that integrating cellular phenotype associations with organismal complex traits will facilitate the biological interpretation of the genetic effects on these traits.

  16. Genome anchored QTLs for biomass productivity in Hybrid Populus: Heterosis and detection across Contrasting Environments.

    Energy Technology Data Exchange (ETDEWEB)

    Muchero, Wellington [ORNL; Sewell, Mitchell [ORNL; Gunter, Lee E [ORNL; Tschaplinski, Timothy J [ORNL; Yin, Tongming [ORNL; DiFazio, Steven P [West Virginia University; Tuskan, Gerald A [ORNL

    2013-01-01

    Traits related to biomass production were analyzed for the presence of quantitative trait loci (QTLs) in an interspecific F2 population derived from an outbred Populus trichocarpa P. deltoides parental cross. Three years of phenotypic data for stem growth traits (height and diameter) were collected from two parental, two F1 and 339 F2 trees in a clonal trial replicated both within and among two environmentally contrasting sites in the North American Pacific Northwest. A genetic linkage map comprised of 841 SSR, AFLP, and RAPD markers and phenotypic data from 310 progeny were used to identify genomic regions harboring QTL using the Multiple-QTL Model (MQM) package of the statistical program MapQTL 6. A total of twelve QTLs, nine putative and three suggestive, were identified with eight of these being identified at both sites in at least one experiment. Of these, three putative QTL BM-1, BM-2, BM-7, on LGs I, II, and XIV, respectively, were identified in all three years for both height and diameter. Two QTLs BM-2 and BM-7, on LG II and XIV, respectively, exhibited significant evidence of over-dominance in all three years for both traits. Conversely a QTL on BM-6 LG XIII exhibited out-breeding depression in two years for both height and diameter. The remaining nine QTLs showed difference levels of dominance and additive effects. Seven of the nine QTL were successfully anchored and QTL peak positions were estimated for each one on the P. trichocarpa genome assembly using flanking SSR markers with known physical positions positions. QTL BM-7 on LG XIV had been anchored on the genome assembly in a previous study, therefore eight QTLs identified in this study were assigned genome assembly positions. Physical distances encompassed by each QTL regions ranged from 1.3 to 8.8 Mb.

  17. Identification of SSR and RAPD markers associated with QTLs of ...

    African Journals Online (AJOL)

    SERVER

    2008-04-03

    Apr 3, 2008 ... 5′-GAC AGG CCA A-3′. RAPD. 8. 650. 5′-AGT ATG CAG C-3′. RAPD. 9. The alleles of identified QTLs of studied traits trans- mitted to F2 plants and F3 families are from both parents based on their negative and positive additive effects. All of identified QTLs had small additive effects and other.

  18. QTLs for resistance to powdery mildew in pepper under natural and artificial infections.

    Science.gov (United States)

    Lefebvre, V; Daubèze, A-M; Rouppe van der Voort, J; Peleman, J; Bardin, M; Palloix, A

    2003-08-01

    Epidemics of powdery mildew due to Leveillula taurica is an increasing problem in pepper production areas, particularly in coastal regions or greenhouse cultivation. The highly resistant genitor 'H3' was submitted to genetic analysis and QTL mapping in order to promote the introgression of its oligogenic resistance into large and sweet-fruited cultivars. The doubled-haploid progeny from the cross 'H3' (resistant) by 'Vania' (susceptible) was tested for resistance under both natural field infection and artificial inoculation tests, and QTL detection was compared for those two methods. Seven genomic regions including additive QTLs and epistatic interactions were detected, explaining altogether the major part of genotypic variance. Two genomic regions were common to both the evaluation methods, whereas other QTLs were method-specific, reflecting the environment dependence of powdery mildew epidemics. Orthologies with tomato genomic regions carrying resistance genes to L. taurica and Oidium lycopersicum were revealed by comparative mapping with pepper. Tight linkages between the detected QTLs and virus resistance or fruit color traits in pepper were also shown, which adds to the agronomic importance of these regions in pepper breeding programs.

  19. Bipartite Community Structure of eQTLs.

    Directory of Open Access Journals (Sweden)

    John Platig

    2016-09-01

    Full Text Available Genome Wide Association Studies (GWAS and expression quantitative trait locus (eQTL analyses have identified genetic associations with a wide range of human phenotypes. However, many of these variants have weak effects and understanding their combined effect remains a challenge. One hypothesis is that multiple SNPs interact in complex networks to influence functional processes that ultimately lead to complex phenotypes, including disease states. Here we present CONDOR, a method that represents both cis- and trans-acting SNPs and the genes with which they are associated as a bipartite graph and then uses the modular structure of that graph to place SNPs into a functional context. In applying CONDOR to eQTLs in chronic obstructive pulmonary disease (COPD, we found the global network "hub" SNPs were devoid of disease associations through GWAS. However, the network was organized into 52 communities of SNPs and genes, many of which were enriched for genes in specific functional classes. We identified local hubs within each community ("core SNPs" and these were enriched for GWAS SNPs for COPD and many other diseases. These results speak to our intuition: rather than single SNPs influencing single genes, we see groups of SNPs associated with the expression of families of functionally related genes and that disease SNPs are associated with the perturbation of those functions. These methods are not limited in their application to COPD and can be used in the analysis of a wide variety of disease processes and other phenotypic traits.

  20. Association mapping of flowering time QTLs and insight into their contributions to rapeseed growth habits

    Directory of Open Access Journals (Sweden)

    Nian eWang

    2016-03-01

    Full Text Available Plants have developed sophisticated systems to adapt to local conditions during evolution, domestication and natural or artificial selection. The selective pressures of these different growing conditions have caused significant genomic divergence within species. The flowering time trait is the most crucial factor because it helps plants to maintain sustainable development. Controlling flowering at appropriate times can also prevent plants from suffering from adverse growth conditions, such as drought, winter hardness, and disease. Hence, discovering the genome-wide genetic mechanisms that influence flowering time variations and understanding their contributions to adaptation should be a central goal of plant genetics and genomics. A global core collection panel with 448 inbred rapeseed lines was first planted in four independent environments, and their flowering time traits were evaluated. We then performed a genome-wide association mapping of flowering times with a 60 K SNP array for this core collection. With quality control and filtration, 20,342 SNP markers were ultimately used for further analyses. In total, 312 SNPs showed marker-trait associations in all four environments, and they were based on a threshold p value of 4.06x10-4; the 40 QTLs showed significant association with flowering time variations. To explore flowering time QTLs and genes related to growth habits in rapeseed, selection signals related to divergent habits were screened at the genome-wide level and 117 genomic regions were found. Comparing locations of flowering time QTLs and genes with these selection regions revealed that 20 flowering time QTLs and 224 flowering time genes overlapped with 24 and 81 selected regions, respectively. Based on this study, a number of marker-trait associations and candidate genes for flowering time variations in rapeseed were revealed. Moreover, we also showed that both flowering time QTLs and genes play important roles in rapeseed growth

  1. Microsatellite panels suggested for parentage testing in cattle: informativeness revealed in Finnish Ayrshire and Holstein-Friesian populations (Research Note

    Directory of Open Access Journals (Sweden)

    P. BREDBACKA

    2008-12-01

    Full Text Available Informativeness of eleven microsatellite markers suggested for parentage control in cattle by the International Society for Animal Genetics (ISAG was studied in Finnish Ayrshire and Holstein-Friesian populations. Calculations were based on a sample of 100 non-sib artificial insemination bulls. Assuming one known parent the nine loci suggested for routine testing exhibited exclusion probabilities of 99.84% in the Ayrshires and 99.91% in the Holstein-Friesians. The addition of markers INRA23 and TGLA53, recommended for further investigations, increased the attained values to 99.94% in Ayrshires and to 99.98% in Holstein-Friesians. The recommended core set of six microsatellites provided a combined exclusion probability of 98.25% in Ayrshires and 99.32% in Holstein-Friesians. Although the combined values were high in general, a relatively low level of polymorphism was detected in some instances.;

  2. Satellite telemetry reveals higher fishing mortality rates than previously estimated, suggesting overfishing of an apex marine predator.

    Science.gov (United States)

    Byrne, Michael E; Cortés, Enric; Vaudo, Jeremy J; Harvey, Guy C McN; Sampson, Mark; Wetherbee, Bradley M; Shivji, Mahmood

    2017-08-16

    Overfishing is a primary cause of population declines for many shark species of conservation concern. However, means of obtaining information on fishery interactions and mortality, necessary for the development of successful conservation strategies, are often fisheries-dependent and of questionable quality for many species of commercially exploited pelagic sharks. We used satellite telemetry as a fisheries-independent tool to document fisheries interactions, and quantify fishing mortality of the highly migratory shortfin mako shark (Isurus oxyrinchus) in the western North Atlantic Ocean. Forty satellite-tagged shortfin mako sharks tracked over 3 years entered the Exclusive Economic Zones of 19 countries and were harvested in fisheries of five countries, with 30% of tagged sharks harvested. Our tagging-derived estimates of instantaneous fishing mortality rates (F = 0.19-0.56) were 10-fold higher than previous estimates from fisheries-dependent data (approx. 0.015-0.024), suggesting data used in stock assessments may considerably underestimate fishing mortality. Additionally, our estimates of F were greater than those associated with maximum sustainable yield, suggesting a state of overfishing. This information has direct application to evaluations of stock status and for effective management of populations, and thus satellite tagging studies have potential to provide more accurate estimates of fishing mortality and survival than traditional fisheries-dependent methodology. © 2017 The Author(s).

  3. Identification of metabolic QTLs and candidate genes for glucosinolate synthesis in Brassica oleracea leaves, seeds and flower buds.

    Science.gov (United States)

    Sotelo, Tamara; Soengas, Pilar; Velasco, Pablo; Rodríguez, Víctor M; Cartea, María Elena

    2014-01-01

    Glucosinolates are major secondary metabolites found in the Brassicaceae family. These compounds play an essential role in plant defense against biotic and abiotic stresses, but more interestingly they have beneficial effects on human health. We performed a genetic analysis in order to identify the genome regions regulating glucosinolates biosynthesis in a DH mapping population of Brassica oleracea. In order to obtain a general overview of regulation in the whole plant, analyses were performed in the three major organs where glucosinolates are synthesized (leaves, seeds and flower buds). Eighty two significant QTLs were detected, which explained a broad range of variability in terms of individual and total glucosinolate (GSL) content. A meta-analysis rendered eighteen consensus QTLs. Thirteen of them regulated more than one glucosinolate and its content. In spite of the considerable variability of glucosinolate content and profiles across the organ, some of these consensus QTLs were identified in more than one tissue. Consensus QTLs control the GSL content by interacting epistatically in complex networks. Based on in silico analysis within the B. oleracea genome along with synteny with Arabidopsis, we propose seven major candidate loci that regulate GSL biosynthesis in the Brassicaceae family. Three of these loci control the content of aliphatic GSL and four of them control the content of indolic glucosinolates. GSL-ALK plays a central role in determining aliphatic GSL variation directly and by interacting epistatically with other loci, thus suggesting its regulatory effect.

  4. Structure-function analyses of a PL24 family ulvan lyase reveal key features and suggest its catalytic mechanism.

    Science.gov (United States)

    Ulaganathan, ThirumalaiSelvi; Helbert, William; Kopel, Moran; Banin, Ehud; Cygler, Miroslaw

    2018-01-30

    Ulvan is a major cell wall component of green algae of the genus Ulva and some marine bacteria encode enzymes that can degrade this polysaccharide. The first ulvan degrading lyases have been recently characterized and several putative ulvan lyases have been recombinantly expressed, confirmed as ulvan lyases and partially characterized. Two families of ulvan degrading lyases, PL24 and PL25, have recently been established. The PL24 lyase LOR_107 from the bacterial Alteromonadales sp. strain LOR degrades ulvan endolytically, cleaving the bond at the C4 of a glucuronic acid. However, the mechanism and LOR_107 structural features involved are unknown. We present here the crystal structure of LOR_107, representing the first PL24 family structure. We found that LOR_107 adopts a seven-bladed β-propeller fold with a deep canyon on one side of the protein. Comparative sequence analysis revealed a cluster of conserved residues within this canyon, and site-directed mutagenesis disclosed several residues essential for catalysis. We also found that LOR_107 uses the His/Tyr catalytic mechanism, common to several PL families. We captured a tetrasaccharide substrate in the structures of two inactive mutants, which indicated a two-step binding event, with the first substrate interaction near the top of the canyon coordinated by Arg-320, followed by sliding of the substrate into the canyon toward the active-site residues. Surprisingly, the LOR_107 structure was very similar to that of PL25 family PLSV_3936, despite only ~14% sequence identity between the two enzymes. On the basis of our structural and mutational analyses, we propose a catalytic mechanism for LOR_107 that differs from the typical His/Tyr mechanism. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

  5. Transcriptome data reveal Syndermatan relationships and suggest the evolution of endoparasitism in Acanthocephala via an epizoic stage.

    Science.gov (United States)

    Wey-Fabrizius, Alexandra R; Herlyn, Holger; Rieger, Benjamin; Rosenkranz, David; Witek, Alexander; Welch, David B Mark; Ebersberger, Ingo; Hankeln, Thomas

    2014-01-01

    The taxon Syndermata comprises the biologically interesting wheel animals ("Rotifera": Bdelloidea + Monogononta + Seisonidea) and thorny-headed worms (Acanthocephala), and is central for testing superordinate phylogenetic hypotheses (Platyzoa, Gnathifera) in the metazoan tree of life. Recent analyses of syndermatan phylogeny suggested paraphyly of Eurotatoria (free-living bdelloids and monogononts) with respect to endoparasitic acanthocephalans. Data of epizoic seisonids, however, were absent, which may have affected the branching order within the syndermatan clade. Moreover, the position of Seisonidea within Syndermata should help in understanding the evolution of acanthocephalan endoparasitism. Here, we report the first phylogenomic analysis that includes all four higher-ranked groups of Syndermata. The analyzed data sets comprise new transcriptome data for Seison spec. (Seisonidea), Brachionus manjavacas (Monogononta), Adineta vaga (Bdelloidea), and Paratenuisentis ambiguus (Acanthocephala). Maximum likelihood and Bayesian trees for a total of 19 metazoan species were reconstructed from up to 410 functionally diverse proteins. The results unanimously place Monogononta basally within Syndermata, and Bdelloidea appear as the sister group to a clade comprising epizoic Seisonidea and endoparasitic Acanthocephala. Our results support monophyly of Syndermata, Hemirotifera (Bdelloidea + Seisonidea + Acanthocephala), and Pararotatoria (Seisonidea + Acanthocephala), rejecting monophyly of traditional Rotifera and Eurotatoria. This serves as an indication that early acanthocephalans lived epizoically or as ectoparasites on arthropods, before their complex lifecycle with arthropod intermediate and vertebrate definite hosts evolved.

  6. Transcriptome data reveal Syndermatan relationships and suggest the evolution of endoparasitism in Acanthocephala via an epizoic stage.

    Directory of Open Access Journals (Sweden)

    Alexandra R Wey-Fabrizius

    Full Text Available The taxon Syndermata comprises the biologically interesting wheel animals ("Rotifera": Bdelloidea + Monogononta + Seisonidea and thorny-headed worms (Acanthocephala, and is central for testing superordinate phylogenetic hypotheses (Platyzoa, Gnathifera in the metazoan tree of life. Recent analyses of syndermatan phylogeny suggested paraphyly of Eurotatoria (free-living bdelloids and monogononts with respect to endoparasitic acanthocephalans. Data of epizoic seisonids, however, were absent, which may have affected the branching order within the syndermatan clade. Moreover, the position of Seisonidea within Syndermata should help in understanding the evolution of acanthocephalan endoparasitism. Here, we report the first phylogenomic analysis that includes all four higher-ranked groups of Syndermata. The analyzed data sets comprise new transcriptome data for Seison spec. (Seisonidea, Brachionus manjavacas (Monogononta, Adineta vaga (Bdelloidea, and Paratenuisentis ambiguus (Acanthocephala. Maximum likelihood and Bayesian trees for a total of 19 metazoan species were reconstructed from up to 410 functionally diverse proteins. The results unanimously place Monogononta basally within Syndermata, and Bdelloidea appear as the sister group to a clade comprising epizoic Seisonidea and endoparasitic Acanthocephala. Our results support monophyly of Syndermata, Hemirotifera (Bdelloidea + Seisonidea + Acanthocephala, and Pararotatoria (Seisonidea + Acanthocephala, rejecting monophyly of traditional Rotifera and Eurotatoria. This serves as an indication that early acanthocephalans lived epizoically or as ectoparasites on arthropods, before their complex lifecycle with arthropod intermediate and vertebrate definite hosts evolved.

  7. Transcriptome Data Reveal Syndermatan Relationships and Suggest the Evolution of Endoparasitism in Acanthocephala via an Epizoic Stage

    Science.gov (United States)

    Rieger, Benjamin; Rosenkranz, David; Witek, Alexander; Welch, David B. Mark; Ebersberger, Ingo; Hankeln, Thomas

    2014-01-01

    The taxon Syndermata comprises the biologically interesting wheel animals (“Rotifera”: Bdelloidea + Monogononta + Seisonidea) and thorny-headed worms (Acanthocephala), and is central for testing superordinate phylogenetic hypotheses (Platyzoa, Gnathifera) in the metazoan tree of life. Recent analyses of syndermatan phylogeny suggested paraphyly of Eurotatoria (free-living bdelloids and monogononts) with respect to endoparasitic acanthocephalans. Data of epizoic seisonids, however, were absent, which may have affected the branching order within the syndermatan clade. Moreover, the position of Seisonidea within Syndermata should help in understanding the evolution of acanthocephalan endoparasitism. Here, we report the first phylogenomic analysis that includes all four higher-ranked groups of Syndermata. The analyzed data sets comprise new transcriptome data for Seison spec. (Seisonidea), Brachionus manjavacas (Monogononta), Adineta vaga (Bdelloidea), and Paratenuisentis ambiguus (Acanthocephala). Maximum likelihood and Bayesian trees for a total of 19 metazoan species were reconstructed from up to 410 functionally diverse proteins. The results unanimously place Monogononta basally within Syndermata, and Bdelloidea appear as the sister group to a clade comprising epizoic Seisonidea and endoparasitic Acanthocephala. Our results support monophyly of Syndermata, Hemirotifera (Bdelloidea + Seisonidea + Acanthocephala), and Pararotatoria (Seisonidea + Acanthocephala), rejecting monophyly of traditional Rotifera and Eurotatoria. This serves as an indication that early acanthocephalans lived epizoically or as ectoparasites on arthropods, before their complex lifecycle with arthropod intermediate and vertebrate definite hosts evolved. PMID:24520404

  8. The genome of the xerotolerant mold Wallemia sebi reveals adaptations to osmotic stress and suggests cryptic sexual reproduction

    Energy Technology Data Exchange (ETDEWEB)

    Mahajabeen, Padamsee; Kumas, T. K. Arun; Riley, Robert; Binder, Manfred; Boyd, Alex; Calvo, Ann M.; Furukawa, Kentaro; Hesse, Cedar; Hohmann, Stefan; James, Tim Y.; LaButti, Kurt; Lapidus, Alla; Lindquist, Erika; Lucas, Susan; Miller, Kari; Shantappa, Sourabha; Grigoriev, Igor V.; Hibbett, David S.; McLaughlin, David J.; Spatafora, Joseph W.; Aime, Mary C.

    2011-09-03

    Wallemia (Wallemiales, Wallemiomycetes) is a genus of xerophilic Fungi of uncertain phylogenetic position within Basidiomycota. Most commonly found as food contaminants, species of Wallemia have also been isolated from hypersaline environments. The ability to tolerate environments with reduced water activity is rare in Basidiomycota. We sequenced the genome of W. sebi in order to understand its adaptations for surviving in osmotically challenging environments, and we performed phylogenomic and ultrastructural analyses to address its systematic placement and reproductive biology. W. sebi has a compact genome (9.8 Mb), with few repeats and the largest fraction of genes with functional domains compared with other Basidiomycota. We applied several approaches to searching for osmotic stress-related proteins. In silico analyses identied 93 putative osmotic stress proteins; homology searches showed the HOG (High Osmolarity Glycerol) pathway to be mostly conserved. Despite the seemingly reduced genome, several gene family expansions and a high number of transporters (549) were found that also provide clues to the ability of W. sebito colonize harsh environments. Phylogenetic analyses of a 71-protein dataset support the position of Wallemia as the earliest diverging lineage of Agaricomycotina, which is conrmed by septal pore ultrastructure that shows the septal pore apparatus as a variant of the Tremella-type. Mating type gene homologs were idented although we found no evidence of meiosis during conidiogenesis, suggesting there may be aspects of the life cycle of W. sebi that remain cryptic

  9. New evidence of QTLs attributed to salinity tolerance in rice

    African Journals Online (AJOL)

    STORAGESEVER

    2008-12-17

    Dec 17, 2008 ... All these results reinforced the idea that, new QTLs of this study play an important role in the growth of rice at seedling in Iranian local population under salinity condition. Key words: Composite interval mapping, ion exchange, molecular markers, salt tolerance, simple sequence repeat. INTRODUCTION.

  10. Identification of QTLs with main, epistatic and QTL by environment ...

    Indian Academy of Sciences (India)

    correlation with seed yield (Smith and Camper 1975). HSW as main component of plants is .... (2009). QTL clusters and/or colocated QTLs for different traits have been reported in many previous studies (Yang et al. 2013). Salas et al. (2006) found nine clusters on LGs: E, A2,. A1, C2, M, D2, F, L and C1 for seed shape.

  11. Mapping QTLs for submergence tolerance during germination in rice

    African Journals Online (AJOL)

    STORAGESEVER

    2008-08-04

    Aug 4, 2008 ... Quantitative trait loci were identified using single-point analysis. (SPA), interval mapping (IM) and composite interval mapping (CIM). The primary analysis was performed using SPA and IM using. QGene 3.4 software (Nelson, 1997). The QTLs detected by SPA and IM corresponded well, therefore the results ...

  12. Mapping QTLs for submergence tolerance during germination in rice ...

    African Journals Online (AJOL)

    To understand the genetic bases of tolerance and to identify relevant quantitative trait loci (QTLs), KHAIYAN (Aus type) was crossed with IR64, a semi-dwarf, modern variety moderately sensitive to anaerobic conditions during germination. Results of screening of BC2F2 lines showed that survival percentage in ...

  13. Identification of QTLs with main, epistatic and QTL by environment ...

    Indian Academy of Sciences (India)

    Identification of QTLs with main, epistatic and QTL by environment interaction effects for seed shape and hundred-seed weight in soybean across multiple years. HUIZHEN LIANG LANJIE XU YONGLIANG YU HONGQI YANG WEII DONG HAIYANG ZHANG. RESEARCH NOTE Volume 95 Issue 2 June 2016 pp 475-477 ...

  14. Development of molecular map and identification of QTLs linked to ...

    Indian Academy of Sciences (India)

    2015-12-01

    ). The composite interval map- ping was used to identify putative Fusarium wilt resistance. QTLs in every linkage group considering the wilt data of. 2007 and 2008. A walk speed of 2 cM and a minimum. LOD score of 3.0 were ...

  15. Fine-mapping and cross-validation of QTLs linked to fatty acid composition in multiple independent interspecific crosses of oil palm.

    Science.gov (United States)

    Ting, Ngoot-Chin; Yaakub, Zulkifli; Kamaruddin, Katialisa; Mayes, Sean; Massawe, Festo; Sambanthamurthi, Ravigadevi; Jansen, Johannes; Low, Leslie Eng Ti; Ithnin, Maizura; Kushairi, Ahmad; Arulandoo, Xaviar; Rosli, Rozana; Chan, Kuang-Lim; Amiruddin, Nadzirah; Sritharan, Kandha; Lim, Chin Ching; Nookiah, Rajanaidu; Amiruddin, Mohd Din; Singh, Rajinder

    2016-04-14

    The commercial oil palm (Elaeis guineensis Jacq.) produces a mesocarp oil (commonly called 'palm oil') with approximately equal proportions of saturated and unsaturated fatty acids (FAs). An increase in unsaturated FAs content or iodine value (IV) as a measure of the degree of unsaturation would help to open up new markets for the oil. One way to manipulate the fatty acid composition (FAC) in palm oil is through introgression of favourable alleles from the American oil palm, E. oleifera, which has a more unsaturated oil. In this study, a segregating E. oleifera x E. guineensis (OxG) hybrid population for FAC is used to identify quantitative trait loci (QTLs) linked to IV and various FAs. QTL analysis revealed 10 major and two putative QTLs for IV and six FAs, C14:0, C16:0, C16:1, C18:0, C18:1 and C18:2 distributed across six linkage groups (LGs), OT1, T2, T3, OT4, OT6 and T9. The major QTLs for IV and C16:0 on LGOT1 explained 60.0 - 69.0 % of the phenotypic trait variation and were validated in two independent BC2 populations. The genomic interval contains several key structural genes in the FA and oil biosynthesis pathways such as PATE/FATB, HIBCH, BASS2, LACS4 and DGAT1 and also a relevant transcription factor (TF), WRI1. The literature suggests that some of these genes can exhibit pleiotropic effects in the regulatory networks of these traits. Using the whole genome sequence data, markers tightly linked to the candidate genes were also developed. Clustering trait values according to the allelic forms of these candidate markers revealed significant differences in the IV and FAs of the palms in the mapping and validation crosses. The candidate gene approach described and exploited here is useful to identify the potential causal genes linked to FAC and can be adopted for marker-assisted selection (MAS) in oil palm.

  16. Improved resolution in the position of drought-related QTLs in a single mapping population of rice by meta-analysis

    Directory of Open Access Journals (Sweden)

    Courtois Brigitte

    2009-06-01

    Full Text Available Abstract Background Meta-analysis of QTLs combines the results of several QTL detection studies and provides narrow confidence intervals for meta-QTLs, permitting easier positional candidate gene identification. It is usually applied to multiple mapping populations, but can be applied to one. Here, a meta-analysis of drought related QTLs in the Bala × Azucena mapping population compiles data from 13 experiments and 25 independent screens providing 1,650 individual QTLs separated into 5 trait categories; drought avoidance, plant height, plant biomass, leaf morphology and root traits. A heat map of the overlapping 1 LOD confidence intervals provides an overview of the distribution of QTLs. The programme BioMercator is then used to conduct a formal meta-analysis at example QTL clusters to illustrate the value of meta-analysis of QTLs in this population. Results The heat map graphically illustrates the genetic complexity of drought related traits in rice. QTLs can be linked to their physical position on the rice genome using Additional file 1 provided. Formal meta-analysis on chromosome 1, where clusters of QTLs for all trait categories appear close, established that the sd1 semi-dwarfing gene coincided with a plant height meta-QTL, that the drought avoidance meta-QTL was not likely to be associated with this gene, and that this meta-QTL was not pleiotropic with close meta-QTLs for leaf morphology and root traits. On chromosome 5, evidence suggests that a drought avoidance meta-QTL was pleiotropic with leaf morphology and plant biomass meta-QTLs, but not with meta-QTLs for root traits and plant height 10 cM lower down. A region of dense root QTL activity graphically visible on chromosome 9 was dissected into three meta-QTLs within a space of 35 cM. The confidence intervals for meta-QTLs obtained ranged from 5.1 to 14.5 cM with an average of 9.4 cM, which is approximately 180 genes in rice. Additional file 1 Alignment of markers on the Bala

  17. Mapping quantitative trait loci (QTLs) for fatty acid composition in an interspecific cross of oil palm

    Science.gov (United States)

    Singh, Rajinder; Tan, Soon G; Panandam, Jothi M; Rahman, Rahimah Abdul; Ooi, Leslie CL; Low, Eng-Ti L; Sharma, Mukesh; Jansen, Johannes; Cheah, Suan-Choo

    2009-01-01

    Background Marker Assisted Selection (MAS) is well suited to a perennial crop like oil palm, in which the economic products are not produced until several years after planting. The use of DNA markers for selection in such crops can greatly reduce the number of breeding cycles needed. With the use of DNA markers, informed decisions can be made at the nursery stage, regarding which individuals should be retained as breeding stock, which are satisfactory for agricultural production, and which should be culled. The trait associated with oil quality, measured in terms of its fatty acid composition, is an important agronomic trait that can eventually be tracked using molecular markers. This will speed up the production of new and improved oil palm planting materials. Results A map was constructed using AFLP, RFLP and SSR markers for an interspecific cross involving a Colombian Elaeis oleifera (UP1026) and a Nigerian E. guinneensis (T128). A framework map was generated for the male parent, T128, using Joinmap ver. 4.0. In the paternal (E. guineensis) map, 252 markers (199 AFLP, 38 RFLP and 15 SSR) could be ordered in 21 linkage groups (1815 cM). Interval mapping and multiple-QTL model (MQM) mapping (also known as composite interval mapping, CIM) were used to detect quantitative trait loci (QTLs) controlling oil quality (measured in terms of iodine value and fatty acid composition). At a 5% genome-wide significance threshold level, QTLs associated with iodine value (IV), myristic acid (C14:0), palmitic acid (C16:0), palmitoleic acid (C16:1), stearic acid (C18:0), oleic acid (C18:1) and linoleic acid (C18:2) content were detected. One genomic region on Group 1 appears to be influencing IV, C14:0, C16:0, C18:0 and C18:1 content. Significant QTL for C14:0, C16:1, C18:0 and C18:1 content was detected around the same locus on Group 15, thus revealing another major locus influencing fatty acid composition in oil palm. Additional QTL for C18:0 was detected on Group 3. A minor QTL

  18. Mapping quantitative trait loci (QTLs for fatty acid composition in an interspecific cross of oil palm

    Directory of Open Access Journals (Sweden)

    Sharma Mukesh

    2009-08-01

    Full Text Available Abstract Background Marker Assisted Selection (MAS is well suited to a perennial crop like oil palm, in which the economic products are not produced until several years after planting. The use of DNA markers for selection in such crops can greatly reduce the number of breeding cycles needed. With the use of DNA markers, informed decisions can be made at the nursery stage, regarding which individuals should be retained as breeding stock, which are satisfactory for agricultural production, and which should be culled. The trait associated with oil quality, measured in terms of its fatty acid composition, is an important agronomic trait that can eventually be tracked using molecular markers. This will speed up the production of new and improved oil palm planting materials. Results A map was constructed using AFLP, RFLP and SSR markers for an interspecific cross involving a Colombian Elaeis oleifera (UP1026 and a Nigerian E. guinneensis (T128. A framework map was generated for the male parent, T128, using Joinmap ver. 4.0. In the paternal (E. guineensis map, 252 markers (199 AFLP, 38 RFLP and 15 SSR could be ordered in 21 linkage groups (1815 cM. Interval mapping and multiple-QTL model (MQM mapping (also known as composite interval mapping, CIM were used to detect quantitative trait loci (QTLs controlling oil quality (measured in terms of iodine value and fatty acid composition. At a 5% genome-wide significance threshold level, QTLs associated with iodine value (IV, myristic acid (C14:0, palmitic acid (C16:0, palmitoleic acid (C16:1, stearic acid (C18:0, oleic acid (C18:1 and linoleic acid (C18:2 content were detected. One genomic region on Group 1 appears to be influencing IV, C14:0, C16:0, C18:0 and C18:1 content. Significant QTL for C14:0, C16:1, C18:0 and C18:1 content was detected around the same locus on Group 15, thus revealing another major locus influencing fatty acid composition in oil palm. Additional QTL for C18:0 was detected on Group 3

  19. Fine Mapping of Bone Structure and Strength QTLs in Heterogeneous Stock Rat

    Science.gov (United States)

    Alam, Imranul; Koller, Daniel L.; Cañete, Toni; Blázquez, Gloria; Mont-Cardona, Carme; López-Aumatell, Regina; Martínez-Membrives, Esther; Díaz-Morán, Sira; Tobeña, Adolf; Fernández-Teruel, Alberto; Stridh, Pernilla; Diez, Margarita; Olsson, Tomas; Johannesson, Martina; Baud, Amelie; Econs, Michael J.; Foroud, Tatiana

    2015-01-01

    We previously demonstrated that skeletal structure and strength phenotypes vary considerably in heterogeneous stock (HS) rats. These phenotypes were found to be strongly heritable, suggesting that the HS rat model represents a unique genetic resource for dissecting the complex genetic etiology underlying bone fragility. The purpose of this study was to identify and localize genes associated with bone structure and strength phenotypes using 1524 adult male and female HS rats between 17 to 20 weeks of age. Structure measures included femur length, neck width, head width; femur and lumbar spine (L3-5) areas obtained by DXA; and cross-sectional areas (CSA) at the midshaft, distal femur and femoral neck, and the 5th lumbar vertebra measured by CT. In addition, measures of strength of the whole femur and femoral neck were obtained. Approximately 70,000 polymorphic SNPs distributed throughout the rat genome were selected for genotyping, with a mean linkage disequilibrium coefficient between neighboring SNPs of 0.95. Haplotypes were estimated across the entire genome for each rat using a multipoint haplotype reconstruction method, which calculates the probability of descent at each locus from each of the 8 HS founder strains. The haplotypes were then tested for association with each structure and strength phenotype via a mixed model with covariate adjustment. We identified quantitative trait loci (QTLs) for structure phenotypes on chromosomes 3, 8, 10, 12, 17 and 20, and QTLs for strength phenotypes on chromosomes 5, 10 and 11 that met a conservative genome-wide empiric significance threshold (FDR=5%; P<3 × 10−6). Importantly, most QTLs were localized to very narrow genomic regions (as small as 0.3Mb and up to 3 Mb), each harboring a small set of candidate genes, both novel and previously shown to have roles in skeletal development and homeostasis. PMID:26297441

  20. Localization of QTLs for in vitro plant regeneration in tomato

    Directory of Open Access Journals (Sweden)

    Nuez Fernando

    2011-10-01

    Full Text Available Abstract Background Low regeneration ability limits biotechnological breeding approaches. The influence of genotype in the regeneration response is high in both tomato and other important crops. Despite the various studies that have been carried out on regeneration genetics, little is known about the key genes involved in this process. The aim of this study was to localize the genetic factors affecting regeneration in tomato. Results We developed two mapping populations (F2 and BC1 derived from a previously selected tomato cultivar (cv. Anl27 with low regeneration ability and a high regeneration accession of the wild species Solanum pennellii (PE-47. The phenotypic assay indicated dominance for bud induction and additive effects for both the percentage of explants with shoots and the number of regenerated shoots per explant. Two linkage maps were developed and six QTLs were identified on five chromosomes (1, 3, 4, 7 and 8 in the BC1 population by means of the Interval Mapping and restricted Multiple QTL Mapping methods. These QTLs came from S. pennellii, with the exception of the minor QTL located on chromosome 8, which was provided by cv. Anl27. The main QTLs correspond to those detected on chromosomes 1 and 7. In the F2 population, a QTL on chromosome 7 was identified on a similar region as that detected in the BC1 population. Marker segregation distortion was observed in this population in those areas where the QTLs of BC1 were detected. Furthermore, we located two tomato candidate genes using a marker linked to the high regeneration gene: Rg-2 (a putative allele of Rg-1 and LESK1, which encodes a serine/threonine kinase and was proposed as a marker for regeneration competence. As a result, we located a putative allele of Rg-2 in the QTL detected on chromosome 3 that we named Rg-3. LESK1, which is also situated on chromosome 3, is outside Rg-3. In a preliminary exploration of the detected QTL peaks, we found several genes that may be related

  1. Localization of QTLs for in vitro plant regeneration in tomato.

    Science.gov (United States)

    Trujillo-Moya, Carlos; Gisbert, Carmina; Vilanova, Santiago; Nuez, Fernando

    2011-10-20

    Low regeneration ability limits biotechnological breeding approaches. The influence of genotype in the regeneration response is high in both tomato and other important crops. Despite the various studies that have been carried out on regeneration genetics, little is known about the key genes involved in this process. The aim of this study was to localize the genetic factors affecting regeneration in tomato. We developed two mapping populations (F2 and BC1) derived from a previously selected tomato cultivar (cv. Anl27) with low regeneration ability and a high regeneration accession of the wild species Solanum pennellii (PE-47). The phenotypic assay indicated dominance for bud induction and additive effects for both the percentage of explants with shoots and the number of regenerated shoots per explant. Two linkage maps were developed and six QTLs were identified on five chromosomes (1, 3, 4, 7 and 8) in the BC1 population by means of the Interval Mapping and restricted Multiple QTL Mapping methods. These QTLs came from S. pennellii, with the exception of the minor QTL located on chromosome 8, which was provided by cv. Anl27. The main QTLs correspond to those detected on chromosomes 1 and 7. In the F2 population, a QTL on chromosome 7 was identified on a similar region as that detected in the BC1 population. Marker segregation distortion was observed in this population in those areas where the QTLs of BC1 were detected. Furthermore, we located two tomato candidate genes using a marker linked to the high regeneration gene: Rg-2 (a putative allele of Rg-1) and LESK1, which encodes a serine/threonine kinase and was proposed as a marker for regeneration competence. As a result, we located a putative allele of Rg-2 in the QTL detected on chromosome 3 that we named Rg-3. LESK1, which is also situated on chromosome 3, is outside Rg-3. In a preliminary exploration of the detected QTL peaks, we found several genes that may be related to regeneration. In this study we have

  2. eQTLs Regulating Transcript Variations Associated with Rapid Internode Elongation in Deepwater Rice.

    Science.gov (United States)

    Kuroha, Takeshi; Nagai, Keisuke; Kurokawa, Yusuke; Nagamura, Yoshiaki; Kusano, Miyako; Yasui, Hideshi; Ashikari, Motoyuki; Fukushima, Atsushi

    2017-01-01

    To avoid low oxygen, oxygen deficiency or oxygen deprivation, deepwater rice cultivated in flood planes can develop elongated internodes in response to submergence. Knowledge of the gene regulatory networks underlying rapid internode elongation is important for an understanding of the evolution and adaptation of major crops in response to flooding. To elucidate the genetic and molecular basis controlling their deepwater response we used microarrays and performed expression quantitative trait loci (eQTL) and phenotypic QTL (phQTL) analyses of internode samples of 85 recombinant inbred line (RIL) populations of non-deepwater (Taichung 65)- and deepwater rice (Bhadua). After evaluating the phenotypic response of the RILs exposed to submergence, confirming the genotypes of the populations, and generating 188 genetic markers, we identified 10,047 significant eQTLs comprised of 2,902 cis-eQTLs and 7,145 trans-eQTLs and three significant eQTL hotspots on chromosomes 1, 4, and 12 that affect the expression of many genes. The hotspots on chromosomes 1 and 4 located at different position from phQTLs detected in this study and other previous studies. We then regarded the eQTL hotspots as key regulatory points to infer causal regulatory networks of deepwater response including rapid internode elongation. Our results suggest that the downstream regulation of the eQTL hotspots on chromosomes 1 and 4 is independent, and that the target genes are partially regulated by SNORKEL1 and SNORKEL2 genes (SK1/2), key ethylene response factors. Subsequent bioinformatic analyses, including gene ontology-based annotation and functional enrichment analysis and promoter enrichment analysis, contribute to enhance our understanding of SK1/2-dependent and independent pathways. One remarkable observation is that the functional categories related to photosynthesis and light signaling are significantly over-represented in the candidate target genes of SK1/2. The combined results of these

  3. Dissecting the genetics of the human transcriptome identifies novel trait-related trans-eQTLs and corroborates the regulatory relevance of non-protein coding loci†.

    Science.gov (United States)

    Kirsten, Holger; Al-Hasani, Hoor; Holdt, Lesca; Gross, Arnd; Beutner, Frank; Krohn, Knut; Horn, Katrin; Ahnert, Peter; Burkhardt, Ralph; Reiche, Kristin; Hackermüller, Jörg; Löffler, Markus; Teupser, Daniel; Thiery, Joachim; Scholz, Markus

    2015-08-15

    Genetics of gene expression (eQTLs or expression QTLs) has proved an indispensable tool for understanding biological pathways and pathomechanisms of trait-associated SNPs. However, power of most genome-wide eQTL studies is still limited. We performed a large eQTL study in peripheral blood mononuclear cells of 2112 individuals increasing the power to detect trans-effects genome-wide. Going beyond univariate SNP-transcript associations, we analyse relations of eQTLs to biological pathways, polygenetic effects of expression regulation, trans-clusters and enrichment of co-localized functional elements. We found eQTLs for about 85% of analysed genes, and 18% of genes were trans-regulated. Local eSNPs were enriched up to a distance of 5 Mb to the transcript challenging typically implemented ranges of cis-regulations. Pathway enrichment within regulated genes of GWAS-related eSNPs supported functional relevance of identified eQTLs. We demonstrate that nearest genes of GWAS-SNPs might frequently be misleading functional candidates. We identified novel trans-clusters of potential functional relevance for GWAS-SNPs of several phenotypes including obesity-related traits, HDL-cholesterol levels and haematological phenotypes. We used chromatin immunoprecipitation data for demonstrating biological effects. Yet, we show for strongly heritable transcripts that still little trans-chromosomal heritability is explained by all identified trans-eSNPs; however, our data suggest that most cis-heritability of these transcripts seems explained. Dissection of co-localized functional elements indicated a prominent role of SNPs in loci of pseudogenes and non-coding RNAs for the regulation of coding genes. In summary, our study substantially increases the catalogue of human eQTLs and improves our understanding of the complex genetic regulation of gene expression, pathways and disease-related processes. © The Author 2015. Published by Oxford University Press.

  4. Genetic mapping of QTLs controlling fatty acids provided insights into the genetic control of fatty acid synthesis pathway in peanut (Arachis hypogaea L..

    Directory of Open Access Journals (Sweden)

    Ming Li Wang

    Full Text Available Peanut, a high-oil crop with about 50% oil content, is either crushed for oil or used as edible products. Fatty acid composition determines the oil quality which has high relevance to consumer health, flavor, and shelf life of commercial products. In addition to the major fatty acids, oleic acid (C18:1 and linoleic acid (C18:2 accounting for about 80% of peanut oil, the six other fatty acids namely palmitic acid (C16:0, stearic acid (C18:0, arachidic acid (C20:0, gadoleic acid (C20:1, behenic acid (C22:0, and lignoceric acid (C24:0 are accounted for the rest 20%. To determine the genetic basis and to improve further understanding on effect of FAD2 genes on these fatty acids, two recombinant inbred line (RIL populations namely S-population (high oleic line 'SunOleic 97R' × low oleic line 'NC94022' and T-population (normal oleic line 'Tifrunner' × low oleic line 'GT-C20' were developed. Genetic maps with 206 and 378 marker loci for the S- and the T-population, respectively were used for quantitative trait locus (QTL analysis. As a result, a total of 164 main-effect (M-QTLs and 27 epistatic (E-QTLs QTLs associated with the minor fatty acids were identified with 0.16% to 40.56% phenotypic variation explained (PVE. Thirty four major QTLs (>10% of PVE mapped on five linkage groups and 28 clusters containing more than three QTLs were also identified. These results suggest that the major QTLs with large additive effects would play an important role in controlling composition of these minor fatty acids in addition to the oleic and linoleic acids in peanut oil. The interrelationship among these fatty acids should be considered while breeding for improved peanut genotypes with good oil quality and desired fatty acid composition.

  5. SNP-based discovery of salinity-tolerant QTLs in a bi-parental population of rice (Oryza sativa).

    Science.gov (United States)

    Gimhani, D R; Gregorio, Glenn B; Kottearachchi, N S; Samarasinghe, W L G

    2016-12-01

    Breeding for salt tolerance is the most promising approach to enhance the productivity of saline prone areas. However, polygenic inheritance of salt tolerance in rice acts as a bottleneck in conventional breeding for salt tolerance. Hence, we set our goals to construct a single nucleotide polymorphism (SNP)-based molecular map employing high-throughput SNP marker technology and to investigate salinity tolerant QTLs with closest flanking markers using an elite rice background. Seedling stage salinity responses were assessed in a population of 281 recombinant inbred lines (RILs) derived from the cross between At354 (salt tolerant) and Bg352 (salt susceptible), by 11 morpho-physiological indices under a hydroponic system. Selected extreme 94 RILs were genotyped using Illumina Infinium rice 6K SNP array and densely saturated molecular map spanning 1460.81 cM of the rice genome with an average interval of 1.29 cM between marker loci was constructed using 1135 polymorphic SNP markers. The results revealed 83 significant QTLs for 11 salt responsive traits explaining 12.5-46.7 % of phenotypic variation in respective traits. Of them, 72 QTLs responsible for 10 traits were co-localized together forming 14 QTL hotspots at 14 different genomic regions. The all QTL hotspots were flanked less than 1 Mb intervals and therefore the SNP loci associated with these QTL hotspots would be important in candidate gene discovery for salt tolerance.

  6. Molecular Mapping of QTLs Associated with Lodging Resistance in Dry Direct-Seeded Rice (Oryza sativa L.

    Directory of Open Access Journals (Sweden)

    Shailesh Yadav

    2017-08-01

    Full Text Available Dry direct-seeded rice (DSR is an alternative crop establishment method with less water and labor requirement through mechanization. It provides better opportunities for a second crop during the cropping season and therefore, a feasible alternative system to transplanted lowland rice. However, lodging is one of the major constraints in attaining high yield in DSR. Identification of QTLs for lodging resistance and their subsequent use in improving varieties under DSR will be an efficient breeding strategy to address the problem. In order to map the QTLs associated with lodging resistance, a set of 253 BC3F4 lines derived from a backcross between Swarna and Moroberekan were evaluated in two consecutive years. A total of 12 QTLs associated with lodging resistance traits [culm length (qCL, culm diameter (qCD, and culm strength (qCS] were mapped on chromosomes 1, 2, 6, and 7 using 193 polymorphic SNP markers. Two major and consistent effect QTLs, namely qCD1.1 (with R2 of 10% and qCS1.1 (with R2 of 14% on chromosome 1 with id1003559 being the peak SNP marker (flanking markers; id1001973-id1006772 were identified as a common genomic region associated with important lodging resistance traits. In silico analysis revealed the presence of Gibberellic Acid 3 beta-hydroxylase along with 34 other putative candidate genes in the marker interval region of id1001973-id1006772. The positive alleles for culm length, culm diameter, and culm strength were contributed by the upland adaptive parent Moroberekan. Our results identified significant positive correlation between lodging related traits (culm length diameter and strength and grain yield under DSR, indicating the role of lodging resistant traits in grain yield improvement under DSR. Deployment of the identified alleles influencing the culm strength and culm diameter in marker assisted introgression program may facilitate the lodging resistance under DSR.

  7. Candidate genes and QTLs for fruit ripening and softening in melon.

    Science.gov (United States)

    Moreno, Eduard; Obando, Javier M; Dos-Santos, Noelia; Fernández-Trujillo, J Pablo; Monforte, Antonio J; Garcia-Mas, Jordi

    2008-02-01

    Different factors affect the quality of melon fruit and among them long shelf life is critical from the consumer's point of view. In melon, cultivars showing both climacteric and non-climacteric ripening types are found. In this study we have investigated climacteric ripening and fruit softening using a collection of near-isogenic lines (NILs) derived from the non-climacteric melon parental lines PI 161375 (SC) and "Piel de Sapo" (PS). Surprisingly, we found that QTL eth3.5 in NIL SC3-5b induced a climacteric-ripening phenotype with increased respiration and ethylene levels. Data suggest that the non-climacteric phenotypes from PI 161375 and "Piel de Sapo" may be the result of mutations in different genes. Several QTLs for fruit flesh firmness were also detected. Candidate genes putatively involved in ethylene regulation, biosynthesis and perception and cell wall degradation were mapped and some colocations with QTLs were observed. These results may provide additional data towards understanding of non-climacteric ripening in melon.

  8. Mapping of QTLs for Germination Characteristics under Non-stress and Drought Stress in Rice

    Directory of Open Access Journals (Sweden)

    Zahra MARDANI

    2013-11-01

    Full Text Available Identification of genetic factors controlling traits associated with seed germination under drought stress conditions, leads to identification and development of drought tolerant varieties. Present study by using a population of F2:4 derived from a cross between a drought tolerant variety, Gharib (indica and a drought sensitive variety, Sepidroud (indica, is to identify and compare QTLs associated with germination traits under drought stress and non-stress conditions. Through QTL analysis, using composite interval mapping, regarding traits such as germination rate (GR, germination percentage (GP, radicle length (RL, plumule length (PL, coleorhiza length (COL and coleoptile length (CL, totally 13 QTLs were detected under pole drought stress (−8 MPa poly ethylene glycol 6000 and 9 QTLs under non-stress conditions. Of the QTLs identified under non-stress conditions, QTLs associated with COL (qCOL-5 and GR (qGR-1 explained 21.28% and 19.73% of the total phenotypic variations, respectively. Under drought stress conditions, QTLs associated with COL (qCOL-3 and PL (qPL-5 explained 18.34% and 18.22% of the total phenotypic variations, respectively. A few drought-tolerance-related QTLs identified in previous studies are near the QTLs detected in this study, and several QTLs in this study are novel alleles. The major QTLs like qGR-1, qGP-4, qRL-12 and qCL-4 identified in both conditions for traits GR, GP, RL and CL, respectively, should be considered as the important and stable trait-controlling QTLs in rice seed germination. Those major or minor QTLs could be used to significantly improve drought tolerance by marker-assisted selection in rice.

  9. Analysis of QTLs for Flag Leaf Shape and Its Response to Elevated CO2 in Rice (Oryza sativa

    Directory of Open Access Journals (Sweden)

    Gui-zhi FAN

    2007-03-01

    Full Text Available To understand the responses of flag leaf shape in rice to elevated CO2 environment and their genetic characteristics, quantitative trait loci (QTLs for flag leaf shape in rice were mapped onto the molecular marker linkage map of chromosome segment substitution lines (CSSLs derived from a cross between a japonica variety Asominori and an indica variety IR24 under free air carbon dioxide enrichment (FACE, 200 μmol/mol above current levels and current CO2 concentration (Ambient, about 370 μmol/mol. Three flag-leaf traits, flag-leaf length (LL, width (LW and the ratio of LL to LW (RLW, were estimated for each CSSL and their parental varieties. The differences in LL, LW and RLW between parents and in LL and LW within IR24 between FACE and Ambient were significant at 1% level. The continuous distributions and transgressive segregations of LL, LW and RLW were also observed in CSSL population, showing that the three traits were quantitatively inherited under both FACE and Ambient. A total of 16 QTLs for the three traits were detected on chromosomes 1, 2, 3, 4, 6, 8 and 11 with LOD (Log10-likelihood ratio scores ranging from 3.0 to 6.7. Among them, four QTLs (qLL-6*, qLL-8*, qLW-4*, and qRLW-6* were commonly detected under both FACE and Ambient. Therefore, based on the different responses to elevated CO2 in comparison with current CO2 level, it can be suggested that the expressions of several QTLs associated with flag-leaf shape in rice could be induced by the high CO2 level.

  10. Molecular Simulations Reveal an Unresolved Conformation of the Type IA Protein Kinase A Regulatory Subunit and Suggest Its Role in the cAMP Regulatory Mechanism.

    Science.gov (United States)

    Hirakis, Sophia P; Malmstrom, Robert D; Amaro, Rommie E

    2017-08-01

    We identify a previously unresolved, unrecognized, and highly stable conformation of the protein kinase A (PKA) regulatory subunit RIα. This conformation, which we term the "Flipback" structure, bridges conflicting characteristics in crystallographic structures and solution experiments of the PKA RIα heterotetramer. Our simulations reveal a hinge residue, G235, in the B/C helix that is conserved through all isoforms of RI. Brownian dynamics simulations suggest that the Flipback conformation plays a role in cAMP association to the A domain of the R subunit.

  11. A trans-Amazonian screening of mtDNA reveals deep intraspecific divergence in forest birds and suggests a vast underestimation of species diversity.

    Directory of Open Access Journals (Sweden)

    Borja Milá

    Full Text Available The Amazonian avifauna remains severely understudied relative to that of the temperate zone, and its species richness is thought to be underestimated by current taxonomy. Recent molecular systematic studies using mtDNA sequence reveal that traditionally accepted species-level taxa often conceal genetically divergent subspecific lineages found to represent new species upon close taxonomic scrutiny, suggesting that intraspecific mtDNA variation could be useful in species discovery. Surveys of mtDNA variation in Holarctic species have revealed patterns of variation that are largely congruent with species boundaries. However, little information exists on intraspecific divergence in most Amazonian species. Here we screen intraspecific mtDNA genetic variation in 41 Amazonian forest understory species belonging to 36 genera and 17 families in 6 orders, using 758 individual samples from Ecuador and French Guiana. For 13 of these species, we also analyzed trans-Andean populations from the Ecuadorian Chocó. A consistent pattern of deep intraspecific divergence among trans-Amazonian haplogroups was found for 33 of the 41 taxa, and genetic differentiation and genetic diversity among them was highly variable, suggesting a complex range of evolutionary histories. Mean sequence divergence within families was the same as that found in North American birds (13%, yet mean intraspecific divergence in Neotropical species was an order of magnitude larger (2.13% vs. 0.23%, with mean distance between intraspecific lineages reaching 3.56%. We found no clear relationship between genetic distances and differentiation in plumage color. Our results identify numerous genetically and phenotypically divergent lineages which may result in new species-level designations upon closer taxonomic scrutiny and thorough sampling, although lineages in the tropical region could be older than those in the temperate zone without necessarily representing separate species. In

  12. A three-tier phenotyping approach for hunting QTLs related to heat tolerance in bread wheat

    DEFF Research Database (Denmark)

    Sharma, Dew Kumari; Rosenqvist, Eva; Ottosen, Carl-Otto

    - with a top-to-bottom (forward) approach: Tier 1: Phenotyping: As a starting point,the quantification of heat tolerance was done by the chlorophyll fluorescence parameter, Fv/Fm, as a measure of maximum quantum efficiency of PSII photochemistry after heat stress treatment (40°C for 72h). This way......, stomatal conductance and transpiration rate, suggesting that the tolerant cultivars had better evaporative cooling and stay green characteristics under heat stress. Further, cultivar Fv/Fm and dry matter content also showed a significant positive correlation. Tier 3: Linking phenotypic differences to QTLs......, wheat is sensitive to heat stress, particularly at the reproductive phase. Heat tolerance is a complex trait. In the present study, a combined approach of physiological phenotyping and quantitative genetics was used to dissect the complex nature of heat tolerance into photosynthesis related traits...

  13. Fluorescence microscopy of Streptomyces conjugation suggests DNA-transfer at the lateral walls and reveals the spreading of the plasmid in the recipient mycelium.

    Science.gov (United States)

    Thoma, Lina; Vollmer, Bernd; Muth, Günther

    2016-02-01

    Conjugative DNA-transfer in mycelial streptomycetes is a unique process, manifested on agar plates by the formation of circular growth retardation zones called pocks. Because pock size correlates with the extent of the transconjugant zone, it was suggested that pocks reflect the spreading of the transferred plasmid in the recipient mycelium. However, this concept has not been experimentally proven yet. The use of an eGFP-encoding derivative of the conjugative pIJ303 plasmid and Streptomyces lividans T7-mCherry as recipient enabled us to differentiate donor, recipient and transconjugant hyphae in mating experiments by fluorescence microscopy. Microscopic observation of the conjugation process suggested DNA-transfer via the lateral walls. At the contact sites mCherry was never observed in the donor, indicating that the conjugative DNA-transfer does not involve interfusion of cytoplasms of donor and recipient. The spreading of the transferred plasmid to the older parts of the recipient mycelium was demonstrated. This spreading was impaired when plasmid-encoded spd genes were inactivated. Deletion of the FtsK-like DNA-translocase encoding tra gene from the plasmid and mating experiments with strains containing chromosomal copies of tra either in the donor and/or in the recipient revealed that Tra had an essential role in intramycelial plasmid spreading. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

  14. 7,8-benzoflavone binding to human cytochrome P450 3A4 reveals complex fluorescence quenching, suggesting binding at multiple protein sites.

    Science.gov (United States)

    Marsch, Glenn A; Carlson, Benjamin T; Guengerich, F Peter

    2017-03-20

    Human cytochrome P450 (P450) 3A4 is involved in the metabolism of one-half of marketed drugs and shows cooperative interactions with some substrates and other ligands. The interaction between P450 3A4 and the known allosteric effector 7,8-benzoflavone (α-naphthoflavone, αNF) was characterized using steady-state fluorescence spectroscopy. The binding interaction of P450 3A4 and αNF effectively quenched the fluorescence of both the enzyme and ligand. The Hill Equation and Stern-Volmer fluorescence quenching models were used to evaluate binding of ligand to enzyme. P450 3A4 fluorescence was quenched by titration with αNF; at the relatively higher [αNF]/[P450 3A4] ratios in this experiment, two weaker quenching interactions were revealed (Kd 1.8-2.5 and 6.5 μM). A range is given for the stronger interaction since αNF quenching of P450 3A4 fluorescence changed the protein spectral profile: quenching of 315 nm emission was slightly more efficient (Kd 1.8 μM) than the quenching of protein fluorescence at 335 and 355 nm (Kd 2.5 and 2.1 μM, respectively). In the reverse titration, αNF fluorescence was quenched by P450 3A4; at the lower [αNF]/[P450 3A4] ratios here, two strong quenching interactions were revealed (Kd 0.048 and 1.0 μM). Thus, four binding interactions of αNF to P450 3A4 are suggested by this study, one of which may be newly recognized and which could affect studies of drug oxidations by this important enzyme.

  15. A genome-wide association study for equine recurrent airway obstruction in European Warmblood horses reveals a suggestive new quantitative trait locus on chromosome 13.

    Science.gov (United States)

    Schnider, D; Rieder, S; Leeb, T; Gerber, V; Neuditschko, M

    2017-12-01

    Recurrent airway obstruction (RAO), also known as heaves, is an asthma-like respiratory disease. Its development is strongly influenced by environmental risk factors such as sensitization and exposure to moldy hay, straw bedding and stabling indoors. A hereditary component has been documented in previous studies; however, so far no causative genetic variant that influences the risk of developing RAO has been identified. In this study, we revised an existing dataset and selected 384 horses for genotyping on the Affymetrix high-density equine SNP array. We performed an allelic case-control genome-wide association study, which revealed a suggestively significant association on equine chromosome 13 at 32 843 309 bp. This SNP is located in the protein-coding gene TXNDC11, which is possibly involved in the folding process of the multiprotein complexes DUOX1 and DUOX2. In humans, these proteins are known to take part in regulating the production of H2 O2 in the respiratory tract epithelium as well as in MUC5AC mucin expression. Therefore, TXNDC11 may be considered a functional candidate gene, and further research is needed to explore its potential role in RAO-affected horses. © 2017 Stichting International Foundation for Animal Genetics.

  16. Mapping of QTLs related with wood quality and developmental characteristics in hybrids (Eucalyptus grandis x Eucalyptus urophylla Mapeamento de QTLs para características de qualidade da madeira e crescimento em híbridos (Eucalyptus grandis x Eucalyptus urophylla

    Directory of Open Access Journals (Sweden)

    Rodrigo Barros Rocha

    2007-02-01

    Full Text Available The present work aimed to characterize and identify QTLs for wood quality and growth traits in E. grandis x E. urophylla hybrids. For this purpose a RAPD linkage map was developed for the hybrids (LOD=3 and r=0.40 containing 52 markers and 12 linkage groups. Traits related to wood quality and growth were evaluated in the QTL analyses. QTL analyses were performed using chi-square tests, single-marker, interval mapping and composite interval mapping analyses. All approaches led to the identification of similar QTLs associated with wood density, cellulose pulp yield and percentage of extractives, which were detected and confirmed by both the interval mapping and composite interval mapping methodologies. Some QTLs regions were confirmed only by the composite interval mapping methodology: percentage of soluble lignin, percentage of insoluble lignin, CBH and total height. Overlapping QTLs regions were detected, and these, can be the result of major genes involved in the regulation and control of the growth traits by epistatic interactions. In order to evaluate the effect of early selection using RAPD molecular data, molecular markers adjacent to QTLs were used genotype selection. The analysis of selection differential values suggests that for all the traits the phenotypic selection at seven years should generate larger genetic gains than early selection assisted by molecular markers and the combination of the strategies should elevate the selection efficiency.O presente trabalho teve como objetivos a caracterização e identificação de QTLs para características de crescimento e de qualidade da madeira em híbridos de eucalipto derivados do cruzamento entre E. grandis e E. urophylla. Para isso foi desenvolvido um mapa de ligação RAPD pouco saturado (LOD = 3 e r = 0,40 contendo 52 marcas e 12 grupos de ligação. Características de qualidade da madeira e características de crescimento foram avaliadas quanto à presença de QTLs. Foram utilizadas

  17. Comparative analysis of QTLs affecting domestication traits between two domesticated x wild pearl millet ( Pennisetum glaucum L., Poaceae) crosses.

    Science.gov (United States)

    Poncet, V.; Martel, E.; Allouis, S.; Devos, M.; Lamy, F.; Sarr, A.; Robert, T.

    2002-05-01

    Comparative mapping of Quantitative trait loci (QTLs) involved in domestication of adaptative syndrome traits of pearl millet was realized at the intra-specific level using two F(2) populations derived from domesticated ( Pennisetum glaucum ssp. glaucum) x wild ( Pennisetum glaucum ssp. monodii) crosses. The two domesticated parents analyzed differ in their geographical origins, agronomic characteristics and life cycles. In both populations, two regions of the genome were identified on linkage groups 6 and 7, that controlled most of the key morphological differences. The importance of these two linkage groups reveals their central role both in the developmental control of spikelet structure and in the domestication process of this crop. In contrast, QTLs involved in traits that are components of yield and measure differences in resource allocation (such as the shape of the spike, the number of spikes per plant and plant height) show a low level of correspondence among our two crosses. The results of the comparative mapping between cereals, although preliminary, reveal that genes involved in seed-shattering could correspond in maize, rice and sorghum. The evolutionary significance of our results, and especially the relationships between genome organization and cereal domestication, are discussed. The potential use of these results in pearl millet genetic-resources enhancement are presented.

  18. GWAS of follicular lymphoma reveals allelic heterogeneity at 6p21.32 and suggests shared genetic susceptibility with diffuse large B-cell lymphoma.

    Directory of Open Access Journals (Sweden)

    Karin E Smedby

    2011-04-01

    Full Text Available Non-Hodgkin lymphoma (NHL represents a diverse group of hematological malignancies, of which follicular lymphoma (FL is a prevalent subtype. A previous genome-wide association study has established a marker, rs10484561 in the human leukocyte antigen (HLA class II region on 6p21.32 associated with increased FL risk. Here, in a three-stage genome-wide association study, starting with a genome-wide scan of 379 FL cases and 791 controls followed by validation in 1,049 cases and 5,790 controls, we identified a second independent FL-associated locus on 6p21.32, rs2647012 (OR(combined  = 0.64, P(combined  = 2 × 10(-21 located 962 bp away from rs10484561 (r(2<0.1 in controls. After mutual adjustment, the associations at the two SNPs remained genome-wide significant (rs2647012:OR(adjusted  = 0.70, P(adjusted  =  4 × 10(-12; rs10484561:OR(adjusted  = 1.64, P(adjusted  = 5 × 10(-15. Haplotype and coalescence analyses indicated that rs2647012 arose on an evolutionarily distinct haplotype from that of rs10484561 and tags a novel allele with an opposite (protective effect on FL risk. Moreover, in a follow-up analysis of the top 6 FL-associated SNPs in 4,449 cases of other NHL subtypes, rs10484561 was associated with risk of diffuse large B-cell lymphoma (OR(combined  = 1.36, P(combined  =  1.4 × 10(-7. Our results reveal the presence of allelic heterogeneity within the HLA class II region influencing FL susceptibility and indicate a possible shared genetic etiology with diffuse large B-cell lymphoma. These findings suggest that the HLA class II region plays a complex yet important role in NHL.

  19. Deep sequencing reveals direct targets of gammaherpesvirus-induced mRNA decay and suggests that multiple mechanisms govern cellular transcript escape.

    Directory of Open Access Journals (Sweden)

    Karen Clyde

    Full Text Available One characteristic of lytic infection with gammaherpesviruses, including Kaposi's sarcoma-associated herpesvirus (KSHV, Epstein-Barr virus (EBV and murine herpesvirus 68 (MHV68, is the dramatic suppression of cellular gene expression in a process known as host shutoff. The alkaline exonuclease proteins (KSHV SOX, MHV-68 muSOX and EBV BGLF5 have been shown to induce shutoff by destabilizing cellular mRNAs. Here we extend previous analyses of cellular mRNA abundance during lytic infection to characterize the effects of SOX and muSOX, in the absence of other viral genes, utilizing deep sequencing technology (RNA-seq. Consistent with previous observations during lytic infection, the majority of transcripts are downregulated in cells expressing either SOX or muSOX, with muSOX acting as a more potent shutoff factor than SOX. Moreover, most cellular messages fall into the same expression class in both SOX- and muSOX-expressing cells, indicating that both factors target similar pools of mRNAs. More abundant mRNAs are more efficiently downregulated, suggesting a concentration effect in transcript targeting. However, even among highly expressed genes there are mRNAs that escape host shutoff. Further characterization of select escapees reveals multiple mechanisms by which cellular genes can evade downregulation. While some mRNAs are directly refractory to SOX, the steady state levels of others remain unchanged, presumably as a consequence of downstream effects on mRNA biogenesis. Collectively, these studies lay the framework for dissecting the mechanisms underlying the susceptibility of mRNA to destruction during lytic gammaherpesvirus infection.

  20. Molecular epidemiology of Coxiella burnetii in French livestock reveals the existence of three main genotype clusters and suggests species-specific associations as well as regional stability.

    Science.gov (United States)

    Joulié, Aurelien; Sidi-Boumedine, Karim; Bailly, Xavier; Gasqui, Patrick; Barry, Séverine; Jaffrelo, Lydia; Poncet, Charles; Abrial, David; Yang, Elise; Leblond, Agnès; Rousset, Elodie; Jourdain, Elsa

    2017-03-01

    Q fever is a worldwide zoonosis caused by the bacterium Coxiella burnetii. In domestic ruminants, Q fever main clinical manifestations are abortions. Although the clinical signs may differ between ruminant species, C. burnetii's genetic diversity remains understudied in enzootic areas. Here, we focused on France, where Q fever is enzootic, with the aims to (a) identify potential associations between C. burnetii genotypes and ruminant host species; (b) assess the distribution of C. burnetii genotypes both within French farms and across France's major livestock-farming regions; and (c) suggest a subset of markers for future genotypic studies. We used DNA samples collected between 2006 and 2015 from 301 females (160 cows, 76 ewes, 65 goats) aborted of Q fever within 7 different farming regions. C. burnetii diversity was determined using a multiple-locus variable-number of tandem repeat analysis (MLVA) considering 17 markers. Using a phylogenetic approach, we identified 3 main genotypic clusters divided into 12 sub-clusters. These clusters were significantly associated with ruminant species: almost all the cattle genotypes were found in a "cattle-specific" cluster whereas small ruminants genotypes essentially grouped into the two other clusters. The clusters also proved stable over space and time, some genotypes being more specifically observed in certain farming regions. We also observed some within-farm diversity but this diversity was restricted to a same genotypic cluster. Finally, we identified 6 MLVA markers that maximized the representativeness of the diversity described. Overall, we highlighted that molecular epidemiology is a relevant approach to assess C. burnetii's genetic diversity and to reveal the existence of species-specific associations and regional stability. These results will be valuable in the field to trace genotype circulation among ruminants and from ruminants to humans. Ultimately, the potential links between genotypes and virulence traits need

  1. Deep sequencing reveals direct targets of gammaherpesvirus-induced mRNA decay and suggests that multiple mechanisms govern cellular transcript escape.

    Science.gov (United States)

    Clyde, Karen; Glaunsinger, Britt A

    2011-05-09

    One characteristic of lytic infection with gammaherpesviruses, including Kaposi's sarcoma-associated herpesvirus (KSHV), Epstein-Barr virus (EBV) and murine herpesvirus 68 (MHV68), is the dramatic suppression of cellular gene expression in a process known as host shutoff. The alkaline exonuclease proteins (KSHV SOX, MHV-68 muSOX and EBV BGLF5) have been shown to induce shutoff by destabilizing cellular mRNAs. Here we extend previous analyses of cellular mRNA abundance during lytic infection to characterize the effects of SOX and muSOX, in the absence of other viral genes, utilizing deep sequencing technology (RNA-seq). Consistent with previous observations during lytic infection, the majority of transcripts are downregulated in cells expressing either SOX or muSOX, with muSOX acting as a more potent shutoff factor than SOX. Moreover, most cellular messages fall into the same expression class in both SOX- and muSOX-expressing cells, indicating that both factors target similar pools of mRNAs. More abundant mRNAs are more efficiently downregulated, suggesting a concentration effect in transcript targeting. However, even among highly expressed genes there are mRNAs that escape host shutoff. Further characterization of select escapees reveals multiple mechanisms by which cellular genes can evade downregulation. While some mRNAs are directly refractory to SOX, the steady state levels of others remain unchanged, presumably as a consequence of downstream effects on mRNA biogenesis. Collectively, these studies lay the framework for dissecting the mechanisms underlying the susceptibility of mRNA to destruction during lytic gammaherpesvirus infection.

  2. QTLs for seed vigor-related traits identified in maize seeds germinated under artificial aging conditions.

    Directory of Open Access Journals (Sweden)

    Zanping Han

    Full Text Available High seed vigor is important for agricultural production due to the associated potential for increased growth and productivity. However, a better understanding of the underlying molecular mechanisms is required because the genetic basis for seed vigor remains unknown. We used single-nucleotide polymorphism (SNP markers to map quantitative trait loci (QTLs for four seed vigor traits in two connected recombinant inbred line (RIL maize populations under four treatment conditions during seed germination. Sixty-five QTLs distributed between the two populations were identified and a meta-analysis was used to integrate genetic maps. Sixty-one initially identified QTLs were integrated into 18 meta-QTLs (mQTLs. Initial QTLs with contribution to phenotypic variation values of R(2>10% were integrated into mQTLs. Twenty-three candidate genes for association with seed vigor traits coincided with 13 mQTLs. The candidate genes had functions in the glycolytic pathway and in protein metabolism. QTLs with major effects (R(2>10% were identified under at least one treatment condition for mQTL2, mQTL3-2, and mQTL3-4. Candidate genes included a calcium-dependent protein kinase gene (302810918 involved in signal transduction that mapped in the mQTL3-2 interval associated with germination energy (GE and germination percentage (GP, and an hsp20/alpha crystallin family protein gene (At5g51440 that mapped in the mQTL3-4 interval associated with GE and GP. Two initial QTLs with a major effect under at least two treatment conditions were identified for mQTL5-2. A cucumisin-like Ser protease gene (At5g67360 mapped in the mQTL5-2 interval associated with GP. The chromosome regions for mQTL2, mQTL3-2, mQTL3-4, and mQTL5-2 may be hot spots for QTLs related to seed vigor traits. The mQTLs and candidate genes identified in this study provide valuable information for the identification of additional quantitative trait genes.

  3. Detection of elevated CO2 responsive QTLs for yield and its ...

    African Journals Online (AJOL)

    STORAGESEVER

    2008-06-03

    . Accepted 12 May, 2008. A mapping population of IR24 (indica) chromosome segment substitution lines (CSSLs.) in Asominori. (japonica) background was used to detect quantitative trait loci (QTLs) for response to elevated ...

  4. Coupling of MIC-3 overexpression with the chromosomes 11 and 14 root-knot nematode (RKN) (Meloidogyne incognita) resistance QTLs provides insights into the regulation of the RKN resistance response in Upland cotton (Gossypium hirsutum).

    Science.gov (United States)

    Wubben, Martin J; Callahan, Franklin E; Jenkins, Johnie N; Deng, Dewayne D

    2016-09-01

    Genetic analysis of MIC-3 transgene with RKN resistance QTLs provides insight into the resistance regulatory mechanism and provides a framework for testing additional hypotheses. Resistance to root-knot nematode (RKN) (Meloidogyne incognita) in Upland cotton (Gossypium hirsutum) is mediated by two major quantitative trait loci (QTL) located on chromosomes 11 and 14. The MIC-3 (Meloidogyne Induced Cotton3) protein accumulates specifically within the immature galls of RKN-resistant plants that possess these QTLs. Recently, we showed that MIC-3 overexpression in an RKN-susceptible cotton genotype suppressed RKN egg production but not RKN-induced root galling. In this study, the MIC-3 overexpression construct T-DNA in the single-copy transgenic line '14-7-1' was converted into a codominant molecular marker that allowed the marker assisted selection of F2:3 cotton lines, derived from a cross between 14-7-1 and M-240 RNR, having all possible combinations of the chromosomes 11 and 14 QTLs with and without the MIC-3 overexpression construct. Root-knot nematode reproduction (eggs g(-1) root) and severity of RKN-induced root galling were assessed in these lines. We discovered that the addition of MIC-3 overexpression suppressed RKN reproduction in lines lacking both resistance QTLs and in lines having only the chromosome 14 QTL, suggesting an additive effect of the MIC-3 construct with this QTL. In contrast, MIC-3 overexpression did not improve resistance in lines having the single chromosome 11 QTL or in lines having both resistance QTLs, suggesting an epistatic interaction between the chromosome 11 QTL and the MIC-3 construct. Overexpression of MIC-3 did not affect the severity of RKN-induced root galling regardless of QTL genotype. These data provide new insights into the relative order of action of the chromosomes 11 and 14 QTLs and their potential roles in regulating MIC-3 expression as part of the RKN resistance response.

  5. QTLs associated with agronomic traits in the Attila × CDC Go spring wheat population evaluated under conventional management.

    Science.gov (United States)

    Zou, Jun; Semagn, Kassa; Iqbal, Muhammad; Chen, Hua; Asif, Mohammad; N'Diaye, Amidou; Navabi, Alireza; Perez-Lara, Enid; Pozniak, Curtis; Yang, Rong-Cai; Randhawa, Harpinder; Spaner, Dean

    2017-01-01

    QTLs (one for flowering time and plant height each, and two for maturity and kernel weight each) were common between the conventional and organic management systems, which suggests issues in directly utilizing gene discovery results based on conventional management to make in detail selection (decision) for organic management.

  6. QTLs associated with agronomic traits in the Attila × CDC Go spring wheat population evaluated under conventional management.

    Directory of Open Access Journals (Sweden)

    Jun Zou

    QTLs (one for flowering time and plant height each, and two for maturity and kernel weight each were common between the conventional and organic management systems, which suggests issues in directly utilizing gene discovery results based on conventional management to make in detail selection (decision for organic management.

  7. Mapping QTLs Linked to Some Traits Related to Drought Stress in Rice

    Directory of Open Access Journals (Sweden)

    H. Sabouri

    2012-08-01

    Full Text Available Identification of markers linked to genes controlling drought tolerance is necessary to breed high-yielding rice varieties for drought-prone areas. In the current study, some traits associated with drought tolerance in rice were investigated using microsatellite marker. One hundred and ninety two individuals and families derived from a cross between two genetically divergent, Shahpasand (tolerant and IR28 (sensitive, were grown in Gonbad Kavous University to detect QTLs for traits related to drought tolerance on chromosomes 1 and 6. Linkage map was derived using 33 polymorphic markers in 2 linkage groups in parents and 192 F2 individuals. This map covered 366 cM of the rice genome. A total of 16 QTLs were detected for traits. The co-location of QTLs for traits for drought tolerance was shown to be on chromosome 1 in RM8115-RM5638 and chromosome 6 in RM7434-RM162 and RM4608-RM217 intervals. The results showed that QTLs controlling LFI (qLFI-1 overlapped with the QTLs for leaf rolling (qROL-1 on chromosome 1. Three QTLs were mapped for fertility (FER. Two QTLs were showed the large effects on the ROL and FER that explained 14.11% and 14.65%, respectively, of the total phenotypic variations. These QTLs may be useful for development of new varieties with a high level of grain yield under drought conditions. Since these regions explained significant percentage of the phenotypic variations, they have potential for being applied in selection programs using a marker for drought tolerance.

  8. Additive QTLs on three chromosomes control flowering time in woodland strawberry (Fragaria vesca L.)

    OpenAIRE

    Samia Samad; Takeshi Kurokura; Elli Koskela; Tuomas Toivainen; Vipul Patel; Katriina Mouhu; Daniel James Sargent; Timo Hytönen

    2017-01-01

    Flowering time is an important trait that affects survival, reproduction and yield in both wild and cultivated plants. Therefore, many studies have focused on the identification of flowering time quantitative trait locus (QTLs) in different crops, and molecular control of this trait has been extensively investigated in model species. Here we report the mapping of QTLs for flowering time and vegetative traits in a large woodland strawberry mapping population that was phenotyped both under fiel...

  9. Differential effects on nematode development of two QTLs for resistance to Meloidogyne incognita in cotton

    Science.gov (United States)

    QTLs qMi-C11 and qMi-C14 impart resistance to Meloidogyne incognita in cotton. Breeders had backcrossed both QTLs into Coker 201 (C201; susceptible) to create M-120 RNR (M-120; highly resistant), and we crossed C201 and M-120 to create near isogenic lines with either qMi-C11 or qMi-C14. Previous wor...

  10. Limited statistical evidence for shared genetic effects of eQTLs and autoimmune-disease-associated loci in three major immune-cell types.

    Science.gov (United States)

    Chun, Sung; Casparino, Alexandra; Patsopoulos, Nikolaos A; Croteau-Chonka, Damien C; Raby, Benjamin A; De Jager, Philip L; Sunyaev, Shamil R; Cotsapas, Chris

    2017-04-01

    Most autoimmune-disease-risk effects identified by genome-wide association studies (GWAS) localize to open chromatin with gene-regulatory activity. GWAS loci are also enriched in expression quantitative trait loci (eQTLs), thus suggesting that most risk variants alter gene expression. However, because causal variants are difficult to identify, and cis-eQTLs occur frequently, it remains challenging to identify specific instances of disease-relevant changes to gene regulation. Here, we used a novel joint likelihood framework with higher resolution than that of previous methods to identify loci where autoimmune-disease risk and an eQTL are driven by a single shared genetic effect. Using eQTLs from three major immune subpopulations, we found shared effects in only ∼25% of the loci examined. Thus, we show that a fraction of gene-regulatory changes suggest strong mechanistic hypotheses for disease risk, but we conclude that most risk mechanisms are not likely to involve changes in basal gene expression.

  11. A gene expression signature classifying telomerase and ALT immortalization reveals an hTERT regulatory network and suggests a mesenchymal stem cell origin for ALT

    DEFF Research Database (Denmark)

    Lafferty-Whyte, K; Cairney, C J; Will, M B

    2009-01-01

    Telomere length is maintained by two known mechanisms, the activation of telomerase or alternative lengthening of telomeres (ALT). The molecular mechanisms regulating the ALT phenotype are poorly understood and it is unknown how the decision of which pathway to activate is made at the cellular...... level. We have shown earlier that active repression of telomerase gene expression by chromatin remodelling of the promoters is one mechanism of regulation; however, other genes and signalling networks are likely to be required to regulate telomerase and maintain the ALT phenotype. Using gene expression...... this signature revealed a regulatory signalling network consistent with a model of human telomerase reverse transcriptase (hTERT) repression in ALT cell lines and liposarcomas. This network expands on our existing knowledge of hTERT regulation and provides a platform to understand differential regulation of h...

  12. Fine Mapping of QTLs for Ascochyta Blight Resistance in Pea Using Heterogeneous Inbred Families

    Directory of Open Access Journals (Sweden)

    Ambuj B. Jha

    2017-05-01

    Full Text Available Ascochyta blight (AB is an important disease of pea which can cause severe grain yield loss under wet conditions. In our previous study, we identified two quantitative trait loci (QTLs abIII-1 and abI-IV-2 for AB resistance and these QTLs were consistent across locations and/or years in an inter-specific pea population (PR-19 developed from a cross between Alfetta (Pisum sativum and P651 (P. fulvum. The objectives of this study were to fine map the abIII-1 and abI-IV-2 QTLs using a high density single nucleotide polymorphism (SNP-based genetic linkage map and analyze identified markers in heterogeneous inbred family (HIF populations. Selective genotyping of 51 PR-19 recombinant inbred lines was performed using genotyping-by-sequencing (GBS and the resulting high density genetic linkage map was used to identify eight new SNP markers within the abI-IV-2 QTL, whereas no additional SNPs were identified within the abIII-1 QTL. Two HIF populations HIF-224 (143 lines and HIF-173 (126 lines were developed from F6 RILs PR-19-224 and PR-19-173, respectively. The HIF populations evaluated under field conditions in 2015 and 2016 showed a wide range of variation for reaction to AB resistance. Lodging score had significant positive (P < 0.001 correlation with AB scores. HIFs were genotyped using SNP markers within targeted QTLs. The genotypic and phenotypic data of the HIFs were used to identify two new QTLs, abI-IV-2.1 and abI-IV-2.2 for AB resistance within the abI-IV-2 QTL. These QTLs individually explained 5.5 to 14% of the total phenotypic variation. Resistance to lodging was also associated with these two QTLs. Identified SNP markers will be useful in marker assisted selection for development of pea cultivars with improved AB resistance.

  13. Regional Association Analysis of MetaQTLs Delineates Candidate Grain Size Genes in Rice

    Directory of Open Access Journals (Sweden)

    Anurag V. Daware

    2017-05-01

    Full Text Available Molecular mapping studies which aim to identify genetic basis of diverse agronomic traits are vital for marker-assisted crop improvement. Numerous Quantitative Trait Loci (QTLs mapped in rice span long genomic intervals with hundreds to thousands of genes, which limits their utilization for marker-assisted genetic enhancement of rice. Although potent, fine mapping of QTLs is challenging task as it requires screening of large number of segregants to identify suitable recombination events. Association mapping offers much higher resolution as compared to QTL mapping, but detects considerable number of spurious QTLs. Therefore, combined use of QTL and association mapping strategies can provide advantages associated with both these methods. In the current study, we utilized meta-analysis approach to identify metaQTLs associated with grain size/weight in diverse Indian indica and aromatic rice accessions. Subsequently, attempt has been made to narrow-down identified grain size/weight metaQTLs through individual SNP- as well as haplotype-based regional association analysis. The study identified six different metaQTL regions, three of which were successfully revalidated, and substantially scaled-down along with GS3 QTL interval (positive control by regional association analysis. Consequently, two potential candidate genes within two reduced metaQTLs were identified based on their differential expression profiles in different tissues/stages of rice accessions during seed development. The developed strategy has broader practical utility for rapid delineation of candidate genes and natural alleles underlying QTLs associated with complex agronomic traits in rice as well as major crop plants enriched with useful genetic and genomic information.

  14. Structure of the first representative of Pfam family PF09410 (DUF2006) reveals a structural signature of the calycin superfamily that suggests a role in lipid metabolism

    Energy Technology Data Exchange (ETDEWEB)

    Chiu, Hsiu-Ju; Bakolitsa, Constantina; Skerra, Arne; Lomize, Andrei; Carlton, Dennis; Miller, Mitchell D.; Krishna, S. Sri; Abdubek, Polat; Astakhova, Tamara; Axelrod, Herbert L.; Clayton, Thomas; Deller, Marc C.; Duan, Lian; Feuerhelm, Julie; Grant, Joanna C.; Grzechnik, Slawomir K.; Han, Gye Won; Jaroszewski, Lukasz; Jin, Kevin K.; Klock, Heath E.; Knuth, Mark W.; Kozbial, Piotr; Kumar, Abhinav; Marciano, David; McMullan, Daniel; Morse, Andrew T.; Nigoghossian, Edward; Okach, Linda; Paulsen, Jessica; Reyes, Ron; Rife, Christopher L.; van den Bedem, Henry; Weekes, Dana; Xu, Qingping; Hodgson, Keith O.; Wooley, John; Elsliger, Marc-Andre; Deacon, Ashley M.; Godzik, Adam; Lesley, Scott A.; Wilson, Ian A. (SLAC); (Michigan); (TU Munchen)

    2015-10-15

    The first structural representative of the domain of unknown function DUF2006 family, also known as Pfam family PF09410, comprises a lipocalin-like fold with domain duplication. The finding of the calycin signature in the N-terminal domain, combined with remote sequence similarity to two other protein families (PF07143 and PF08622) implicated in isoprenoid metabolism and the oxidative stress response, support an involvement in lipid metabolism. Clusters of conserved residues that interact with ligand mimetics suggest that the binding and regulation sites map to the N-terminal domain and to the interdomain interface, respectively.

  15. Structure of the first representative of Pfam family PF09410 (DUF2006) reveals a structural signature of the calycin superfamily that suggests a role in lipid metabolism.

    Science.gov (United States)

    Chiu, Hsiu Ju; Bakolitsa, Constantina; Skerra, Arne; Lomize, Andrei; Carlton, Dennis; Miller, Mitchell D; Krishna, S Sri; Abdubek, Polat; Astakhova, Tamara; Axelrod, Herbert L; Clayton, Thomas; Deller, Marc C; Duan, Lian; Feuerhelm, Julie; Grant, Joanna C; Grzechnik, Slawomir K; Han, Gye Won; Jaroszewski, Lukasz; Jin, Kevin K; Klock, Heath E; Knuth, Mark W; Kozbial, Piotr; Kumar, Abhinav; Marciano, David; McMullan, Daniel; Morse, Andrew T; Nigoghossian, Edward; Okach, Linda; Paulsen, Jessica; Reyes, Ron; Rife, Christopher L; van den Bedem, Henry; Weekes, Dana; Xu, Qingping; Hodgson, Keith O; Wooley, John; Elsliger, Marc André; Deacon, Ashley M; Godzik, Adam; Lesley, Scott A; Wilson, Ian A

    2010-10-01

    The first structural representative of the domain of unknown function DUF2006 family, also known as Pfam family PF09410, comprises a lipocalin-like fold with domain duplication. The finding of the calycin signature in the N-terminal domain, combined with remote sequence similarity to two other protein families (PF07143 and PF08622) implicated in isoprenoid metabolism and the oxidative stress response, support an involvement in lipid metabolism. Clusters of conserved residues that interact with ligand mimetics suggest that the binding and regulation sites map to the N-terminal domain and to the interdomain interface, respectively.

  16. Genetic and epigenetic profiling of CLL disease progression reveals limited somatic evolution and suggests a relationship to memory-cell development.

    Science.gov (United States)

    Smith, E N; Ghia, E M; DeBoever, C M; Rassenti, L Z; Jepsen, K; Yoon, K-A; Matsui, H; Rozenzhak, S; Alakus, H; Shepard, P J; Dai, Y; Khosroheidari, M; Bina, M; Gunderson, K L; Messer, K; Muthuswamy, L; Hudson, T J; Harismendy, O; Barrett, C L; Jamieson, C H M; Carson, D A; Kipps, T J; Frazer, K A

    2015-04-10

    We examined genetic and epigenetic changes that occur during disease progression from indolent to aggressive forms of chronic lymphocytic leukemia (CLL) using serial samples from 27 patients. Analysis of DNA mutations grouped the leukemia cases into three categories: evolving (26%), expanding (26%) and static (47%). Thus, approximately three-quarters of the CLL cases had little to no genetic subclonal evolution. However, we identified significant recurrent DNA methylation changes during progression at 4752 CpGs enriched for regions near Polycomb 2 repressive complex (PRC2) targets. Progression-associated CpGs near the PRC2 targets undergo methylation changes in the same direction during disease progression as during normal development from naive to memory B cells. Our study shows that CLL progression does not typically occur via subclonal evolution, but that certain CpG sites undergo recurrent methylation changes. Our results suggest CLL progression may involve developmental processes shared in common with the generation of normal memory B cells.

  17. Primordial germ cell development in the marmoset monkey as revealed by pluripotency factor expression: suggestion of a novel model of embryonic germ cell translocation.

    Science.gov (United States)

    Aeckerle, N; Drummer, C; Debowski, K; Viebahn, C; Behr, R

    2015-01-01

    Primordial germ cells (PGCs) are the embryonic progenitors of sperm and egg cells. Mammalian PGCs are thought to actively migrate from the yolk sac endoderm over long distances across the embryo to reach the somatic genital ridges. The general principles of mammalian PGC development were discovered in mice. In contrast, little is known about PGC development in primates due to extremely limited access to primate embryos. Here, we analyzed 12 well preserved marmoset monkey (Callithrix jacchus) embryos covering the phase from PGC emergence in the endoderm to the formation of the sexually differentiated gonad (embryonic day (E) 50 to E95). We show using immunohistochemistry that the pluripotency factors OCT4A and NANOG specifically mark PGCs throughout the period studied. In contrast, SALL4 and LIN28 were first expressed ubiquitously and only later down-regulated in somatic tissues. We further show, for the first time, that PGCs are located in the endoderm in E50 embryos in close spatial proximity to the prospective genital ridge, making a long-range migration of PGCs dispensable. At E65, PGCs are already present in the primitive gonad, while significantly later embryonic stages still exhibit PGCs at their original endodermal site, revealing a wide spatio-temporal window of PGC distribution. Our findings challenge the 'dogma' of active long-range PGC migration from the endoderm to the gonads. We therefore favor an alternative model based primarily on passive translocation of PGCs from the mesenchyme that surrounds the gut to the prospective gonad through the intercalar expansion of mesenchymal tissue which contains the PGCs. In summary, we (i) show differential pluripotency factor expression during primate embryo development and (ii) provide a schematic model for embryonic PGC translocation. © The Author 2014. Published by Oxford University Press on behalf of the European Society of Human Reproduction and Embryology.

  18. Identification of QTL-s for drought tolerance in maize, II: Yield and yield components

    Directory of Open Access Journals (Sweden)

    Nikolić Ana

    2013-01-01

    Full Text Available Grain yield is the primary trait of interest in maize breeding programs. Worldwide, drought is the most pervasive limitation to the achievement of yield potential in maize. Drought tolerance of maize has been considerably improved through conventional breeding. Traditional breeding methods have numerous limitations, so development of new molecular genetics techniques could help in elucidation of genetic basis of drought tolerance .In order to map QTLs underlying yield and yield components under drought 116 F3 families of DTP79xB73 cross were evaluated in the field trials. Phenotypic correlations calculated using Pearson’s coefficients were high and significant. QTL detection was performed using composite interval mapping option in WinQTL Cartographer v 2.5. Over all nine traits 45 QTLs were detected: five for grain yield per plant and 40 for eight yield components. These QTLs were distributed on all chromosomes except on chromosome 9. Percent of phenotypic variability determined for the identified QTLs for all the traits was in the range from 27.46 to 95.85%. Different types of gene action were found for the QTLs identified for analyzed traits. [Projekat Ministarstva nauke Republike Srbije, br. TR31068

  19. Mapping QTLs associated to germination stability following dry-heat treatment in rice seed.

    Science.gov (United States)

    Lee, Seung-Yeob; Kim, Yong-Hwan; Lee, Gang-Seob

    2017-07-01

    Using 164 recombinant inbred lines (RILs) derived from a cross between Milyang 23 (indica/japonica) and Gihobyeo (japonica) in rice, dry-heat tolerance was evaluated for the seeds of parents and RILs, whose dormancy was naturally broken in six months after harvesting. Mapping QTLs associated to dry-heat tolerance was carried out through interval mapping using Qgene 3.0. Seed germination after dry-heat treatments (90 °C for 24 h) showed a significant difference between the two parents, when evaluated for percentage germination and mean germination time. Milyang 23 was highly tolerant to the dry-heat treatment, while Gihobyeo was sensitive. Three QTLs (qDHT 1, qDHT 5, and qDHT 7) conferring the dry-heat tolerance were mapped to chromosomes 1, 5 and 7, respectively. qDHT 1 on chromosome 1 was tightly linked at 4 cM from ME1-1. The phenotypic variation explained by the three QTLs was 27.18% of the total variance in the 164 RIL populations, and the parental additive effects of three QTLs affected the Milyang 23 allele increased dry-heat tolerance. The detection of new QTLs associated with dry-heat tolerance will provide important information for disease and insect control, using dry-heat treatment in organic or low input sustainable agriculture.

  20. Quantitative resistance can lead to evolutionary changes in traits not targeted by the resistance QTLs

    Science.gov (United States)

    Van den Berg, Femke; Lannou, Christian; Gilligan, Christopher A; van de Bosch, Frank

    2014-01-01

    This paper addresses the general concern in plant pathology that the introduction of quantitative resistance in the landscape can lead to increased pathogenicity. Hereto, we study the hypothetical case of a quantitative trait loci (QTL) acting on pathogen spore production per unit lesion area. To regain its original fitness, the pathogen can break the QTL, restoring its spore production capacity leading to an increased spore production per lesion. Or alternatively, it can increase its lesion size, also leading to an increased spore production per lesion. A data analysis shows that spore production per lesion (affected by the resistance QTL) and lesion size (not targeted by the QTL) are positively correlated traits, suggesting that a change in magnitude of a trait not targeted by the QTL (lesion size) might indirectly affect the targeted trait (spore production per lesion). Secondly, we model the effect of pathogen adaptation towards increased lesion size and analyse its consequences for spore production per lesion. The model calculations show that when the pathogen is unable to overcome the resistance associated QTL, it may compensate for its reduced fitness by indirect selection for increased pathogenicity on both the resistant and susceptible cultivar, but whereby the QTLs remain effective. PMID:24665339

  1. Proteome analysis of male accessory gland secretions in oriental fruit flies reveals juvenile hormone-binding protein, suggesting impact on female reproduction.

    Science.gov (United States)

    Wei, Dong; Li, Hui-Min; Tian, Chuan-Bei; Smagghe, Guy; Jia, Fu-Xian; Jiang, Hong-Bo; Dou, Wei; Wang, Jin-Jun

    2015-11-19

    In insects, the accessory gland proteins (Acps) secreted by male accessory glands (MAGs) account for the majority of seminal fluids proteins. Mixed with sperm, they are transferred to the female at mating and so impact reproduction. In this project, we identified 2,927 proteins in the MAG secretions of the oriental fruit fly Bactrocera dorsalis, an important agricultural pest worldwide, using LC-MS analysis, and all sequences containing open reading frames were analyzed using signalP. In total, 90 Acps were identified. About one third (26) of these 90 Acps had a specific functional description, while the other two thirds (64) had no functional description including dozens of new classes of proteins. Hence, several of these novel Acps were abundant in the MAG secretions, and we confirmed their MAG-specific expression by qPCR. Finally and interestingly, one of these novel proteins was functionally predicted as juvenile hormone-binding protein, suggesting the impact of Acps with reproductive events in the female. Our results will aid in the development of an experimental method to identify Acps in insects, and in turn this information with new Acps in B. dorsalis will pave the way of further exploration their function in reproduction and potential development as new insecticide targets.

  2. Complete plastid genome sequencing of Trochodendraceae reveals a significant expansion of the inverted repeat and suggests a Paleogene divergence between the two extant species.

    Directory of Open Access Journals (Sweden)

    Yan-xia Sun

    Full Text Available The early-diverging eudicot order Trochodendrales contains only two monospecific genera, Tetracentron and Trochodendron. Although an extensive fossil record indicates that the clade is perhaps 100 million years old and was widespread throughout the Northern Hemisphere during the Paleogene and Neogene, the two extant genera are both narrowly distributed in eastern Asia. Recent phylogenetic analyses strongly support a clade of Trochodendrales, Buxales, and Gunneridae (core eudicots, but complete plastome analyses do not resolve the relationships among these groups with strong support. However, plastid phylogenomic analyses have not included data for Tetracentron. To better resolve basal eudicot relationships and to clarify when the two extant genera of Trochodendrales diverged, we sequenced the complete plastid genome of Tetracentron sinense using Illumina technology. The Tetracentron and Trochodendron plastomes possess the typical gene content and arrangement that characterize most angiosperm plastid genomes, but both genomes have the same unusual ∼4 kb expansion of the inverted repeat region to include five genes (rpl22, rps3, rpl16, rpl14, and rps8 that are normally found in the large single-copy region. Maximum likelihood analyses of an 83-gene, 88 taxon angiosperm data set yield an identical tree topology as previous plastid-based trees, and moderately support the sister relationship between Buxaceae and Gunneridae. Molecular dating analyses suggest that Tetracentron and Trochodendron diverged between 44-30 million years ago, which is congruent with the fossil record of Trochodendrales and with previous estimates of the divergence time of these two taxa. We also characterize 154 simple sequence repeat loci from the Tetracentron sinense and Trochodendron aralioides plastomes that will be useful in future studies of population genetic structure for these relict species, both of which are of conservation concern.

  3. Comparative analyses of QTLs influencing obesity and metabolic phenotypes in pigs and humans

    DEFF Research Database (Denmark)

    Pant, Sameer Dinkar; Karlskov-Mortensen, Peter; Jacobsen, Mette Juul

    2015-01-01

    60k SNP Beadchip and a combined linkage disequilibrium-linkage analysis was used to identify genome-wide significant associations for collected phenotypes. We identified 229 QTLs which associated with adiposity- and metabolic phenotypes at genome-wide significant levels. Subsequently comparative...... analyses were performed to identify the extent of overlap between previously identified QTLs in both humans and pigs. The combined analysis of a large number of obesity phenotypes has provided insight in the genetic architecture of the molecular mechanisms underlying these traits indicating that QTLs......The pig is a well-known animal model used to investigate genetic and mechanistic aspects of human disease biology. They are particularly useful in the context of obesity and metabolic diseases because other widely used models (e.g. mice) do not completely recapitulate key pathophysiological...

  4. Molecular mapping of QTLs conferring stay-green in grain sorghum (Sorghum bicolor L. Moench).

    Science.gov (United States)

    Xu, W; Subudhi, P K; Crasta, O R; Rosenow, D T; Mullet, J E; Nguyen, H T

    2000-06-01

    Drought resistance is of enormous importance in crop production. The identification of genetic factors involved in plant response to drought stress provides a strong foundation for improving drought tolerance. Stay-green is a drought resistance trait in sorghum (Sorghum bicolor L. Moench) that gives plants resistance to premature senescence under severe soil moisture stress during the post-flowering stage. The objective of this study was to map quantitative trait loci (QTLs) that control the stay-green and chlorophyll content in sorghum. By using a restriction fragment length polymorphism (RFLP) map, developed from a recombinant inbred line (RIL) population, we identified four stay-green QTLs, located on three linkage groups. The QTLs (Stg1 and Stg2) are on linkage group A, with the other two, Stg3 and Stg4, on linkage groups D and J, respectively. Two stay-green QTLs, Stg1 and Stg2, explaining 13-20% and 20-30% of the phenotypic variability, respectively, were consistently identified in all trials at different locations in two years. Three QTLs for chlorophyll content (Chl1, Chl2, and Chl3), explaining 25-30% of the phenotypic variability were also identified under post-flowering drought stress. All coincided with the three stay-green QTL regions (Stg1, Stg2, and Stg3) accounting for 46% of the phenotypic variation. The Stg1 and Stg2 regions also contain the genes for key photosynthetic enzymes, heat shock proteins, and an abscisic acid (ABA) responsive gene. Such spatial arrangement shows that linkage group A is important for drought- and heat-stress tolerance and yield production in sorghum. High-resolution mapping and cloning of the consistent stay-green QTLs may help to develop drought-resistant hybrids and to understand the mechanism of drought-induced senescence in plants.

  5. Bilaterally Asymmetric Effects of Quantitative Trait Loci (QTLs): QTLs That Affect Laxity in the Right Versus Left Coxofemoral (Hip) Joints of the Dog (Canis familiaris)

    OpenAIRE

    Chase, Kevin; Lawler, Dennis F.; Adler, Fred R.; Ostrander, Elaine A.; Lark, Karl G.

    2004-01-01

    In dogs hip joint laxity that can lead to degenerative joint disease (DJD) is frequent and heritable, providing a genetic model for some aspects of the human disease. We have used Portuguese water dogs (PWDs) to identify Quantitative trait loci (QTLs) that regulate laxity in the hip joint.A population of 286 PWDs, each characterized by ca. 500 molecular genetic markers, was analyzed for subluxation of the hip joint as measured by the Norberg angle, a quantitative radiographic measure of laxit...

  6. Bilaterally asymmetric effects of quantitative trait loci (QTLs): QTLs that affect laxity in the right versus left coxofemoral (hip) joints of the dog (Canis familiaris).

    Science.gov (United States)

    Chase, Kevin; Lawler, Dennis F; Adler, Fred R; Ostrander, Elaine A; Lark, Karl G

    2004-01-30

    In dogs hip joint laxity that can lead to degenerative joint disease (DJD) is frequent and heritable, providing a genetic model for some aspects of the human disease. We have used Portuguese water dogs (PWDs) to identify Quantitative trait loci (QTLs) that regulate laxity in the hip joint. A population of 286 PWDs, each characterized by ca. 500 molecular genetic markers, was analyzed for subluxation of the hip joint as measured by the Norberg angle, a quantitative radiographic measure of laxity. A significant directed asymmetry was observed, such that greater laxity was observed in the left than the right hip. This asymmetry was not heritable. However, the average Norberg angle was highly heritable as were the Norberg angles of either the right or left hips. After correction for pedigree effects, two QTLs were identified using the metrics of the left and right hips as separate data sets. Both are on canine chromosome 1 (CFA1), separated by about 95 Mb. One QTL, associated with the SSR marker FH2524 was significant for the left, but not the right hip. The other, associated with FH2598, was significant for the right but not the left hip. For both QTLs, some extreme phenotypes were best explained by specific interactions between haplotypes. Copyright 2003 Wiley-Liss, Inc.

  7. Identification of quantitative trait locus (QTLs) for γ-aminobutyric acid ...

    African Journals Online (AJOL)

    Identification of quantitative trait locus (QTLs) for γ-aminobutyric acid content in grain of barley. ... These results are beneficial for understanding the genetic basis of GABA and developing the markers linked with GABA for marker-assisted selection breeding in barley. Key words: γ-Aminobutyric acid (GABA), quantitative trait ...

  8. Cross-Population Joint Analysis of eQTLs: Fine Mapping and Functional Annotation

    Science.gov (United States)

    Wen, Xiaoquan; Luca, Francesca; Pique-Regi, Roger

    2015-01-01

    Mapping expression quantitative trait loci (eQTLs) has been shown as a powerful tool to uncover the genetic underpinnings of many complex traits at molecular level. In this paper, we present an integrative analysis approach that leverages eQTL data collected from multiple population groups. In particular, our approach effectively identifies multiple independent cis-eQTL signals that are consistent across populations, accounting for population heterogeneity in allele frequencies and linkage disequilibrium patterns. Furthermore, by integrating genomic annotations, our analysis framework enables high-resolution functional analysis of eQTLs. We applied our statistical approach to analyze the GEUVADIS data consisting of samples from five population groups. From this analysis, we concluded that i) jointly analysis across population groups greatly improves the power of eQTL discovery and the resolution of fine mapping of causal eQTL ii) many genes harbor multiple independent eQTLs in their cis regions iii) genetic variants that disrupt transcription factor binding are significantly enriched in eQTLs (p-value = 4.93 × 10-22). PMID:25906321

  9. Mapping of genes for flower-related traits and QTLs for flowering ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 95; Issue 1. Mapping of genes for flower-related traits and QTLs for flowering time in an interspecific population of Gossypium hirsutum × G. darwinii. Shuwen Zhang Qianqian Lan Xiang Gao Biao Yang Caiping Cai Tianzhen Zhang Baoliang Zhou. Research Note Volume 95 ...

  10. Mapping of genes for flower-related traits and QTLs for flowering ...

    Indian Academy of Sciences (India)

    Mapping of genes for flower-related traits and QTLs for flowering time in an interspecific population of Gossypium hirsutum × G. darwinii. Shuwen Zhang, Qianqian Lan, Xiang Gao, Biao Yang, Caiping Cai, Tianzhen Zhang and Baoliang Zhou. J. Genet. 95, 197–201. Table 1. Loci composition and recombination distances of ...

  11. Detection of obesity QTLs on mouse chromosomes 1 and 7 by selective DNA pooling

    Energy Technology Data Exchange (ETDEWEB)

    Taylor, B.A.; Phillips, S.J. [Jackson Lab., Bar Harbor, ME (United States)

    1996-06-15

    The inheritance of obesity has been analyzed in an intercross between the lean 129/Sv mouse strain and the obesity-prone EL/Suz mouse strain. The weights of three major fat pads were determined on 4-month-old mice, and the sum of these weights, divided by body weight, was used as an adiposity index. The strategy of selective DNA pooling was used as a primary screen to identify putative quantitative trait loci (QTLs) affecting adiposity index. DNA pools representing the leanest 15% and fattest 15% of the F2 progeny were compared for differential allelic enrichment using widely dispersed microsatellite variants. To evaluate putative QTLs, individual genotyping and interval mapping were employed to estimate QTL effects and assess statistical significance. One QTL affecting adiposity index, which accounted for 12.3% of phenotypic variance in gender-merged data, was mapped to the central region of Chromosome (Chr) 7. The QTL allele inherited from EL conferred increased adiposity. A second QTL that accounts for 6.3% of phenotypic variance was identified on Chr 1 near D1Mitt211. At both QTLs, the data are consistent with dominant inheritance of the allele contributing to obesity. The possible relationships between these QTLs and previously described obesity QYLs, major obesity mutations, and candidate genes are discussed. 42 refs., 3 figs., 3 tabs.

  12. Mapping of genes for flower-related traits and QTLs for flowering ...

    Indian Academy of Sciences (India)

    tion of linkage maps and QTLs. J. Hered. 93, 77–78. Wang S. C., Basten J. and Zeng Z. B. 2005 Windows QTL. Cartographer 2.5. Department of Statistics, North Carolina State. University, Raleigh. Zhang J., Wu Y. T., Guo W. Z. and Zhang T. Z. 2000 Fast screening of microsatellite markers in cotton with PAGE/silver staining.

  13. Phenotyping mouse chromosome substitution strains reveal multiple QTLs for febrile seizure susceptibility.

    NARCIS (Netherlands)

    Hessel, E.V.; Gassen, K.L.I. van; Wolterink-Donselaar, I.G.; Stienen, P.J.; Fernandes, C.; Brakkee, J.H.; Kas, M.J.; Graan, P.N. de

    2009-01-01

    Febrile seizures (FS) are the most common seizure type in children and recurrent FS are a risk factor for developing temporal lobe epilepsy. Although the mechanisms underlying FS are largely unknown, recent family, twin and animal studies indicate that genetics are important in FS susceptibility.

  14. QTL mapping of root traits in phosphorus-deficient soils reveals important genomic regions for improving NDVI and grain yield in barley.

    Science.gov (United States)

    Gong, Xue; McDonald, Glenn

    2017-09-01

    Major QTLs for root rhizosheath size are not correlated with grain yield or yield response to phosphorus. Important QTLs were found to improve phosphorus efficiency. Root traits are important for phosphorus (P) acquisition, but they are often difficult to characterize and their breeding values are seldom assessed under field conditions. This has shed doubts on using seedling-based criteria of root traits to select and breed for P efficiency. Eight root traits were assessed under controlled conditions in a barley doubled-haploid population in soils differing in P levels. The population was also phenotyped for grain yield, normalized difference vegetation index (NDVI), grain P uptake and P utilization efficiency at maturity (PutE GY ) under field conditions. Several quantitative traits loci (QTLs) from the root screening and the field trials were co-incident. QTLs for root rhizosheath size and root diameter explained the highest phenotypic variation in comparison to QTLs for other root traits. Shared QTLs were found between root diameter and grain yield, and total root length and PutE GY . A common major QTL for rhizosheath size and NDVI was mapped to the HvMATE gene marker on chromosome 4H. Collocations between major QTLs for NDVI and grain yield were detected on chromosomes 6H and 7H. When results from BIP and MET were combined, QTLs detected for grain yield were also those QTLs found for NDVI. QTLs qGY5H, qGY6H and qGY7Hb on 7H were robust QTLs in improving P efficiency. A selection of multiple loci may be needed to optimize the breeding outcomes due to the QTL x Environment interaction. We suggest that rhizosheath size alone is not a reliable trait to predict P efficiency or grain yield.

  15. High Density Linkage Map Construction and Mapping of Yield Trait QTLs in Maize (Zea mays) Using the Genotyping-by-Sequencing (GBS) Technology

    Science.gov (United States)

    Su, Chengfu; Wang, Wei; Gong, Shunliang; Zuo, Jinghui; Li, Shujiang; Xu, Shizhong

    2017-01-01

    Increasing grain yield is the ultimate goal for maize breeding. High resolution quantitative trait loci (QTL) mapping can help us understand the molecular basis of phenotypic variation of yield and thus facilitate marker assisted breeding. The aim of this study is to use genotyping-by-sequencing (GBS) for large-scale SNP discovery and simultaneous genotyping of all F2 individuals from a cross between two varieties of maize that are in clear contrast in yield and related traits. A set of 199 F2 progeny derived from the cross of varieties SG-5 and SG-7 were generated and genotyped by GBS. A total of 1,046,524,604 reads with an average of 5,258,918 reads per F2 individual were generated. This number of reads represents an approximately 0.36-fold coverage of the maize reference genome Zea_mays.AGPv3.29 for each F2 individual. A total of 68,882 raw SNPs were discovered in the F2 population, which, after stringent filtering, led to a total of 29,927 high quality SNPs. Comparative analysis using these physically mapped marker loci revealed a higher degree of synteny with the reference genome. The SNP genotype data were utilized to construct an intra-specific genetic linkage map of maize consisting of 3,305 bins on 10 linkage groups spanning 2,236.66 cM at an average distance of 0.68 cM between consecutive markers. From this map, we identified 28 QTLs associated with yield traits (100-kernel weight, ear length, ear diameter, cob diameter, kernel row number, corn grains per row, ear weight, and grain weight per plant) using the composite interval mapping (CIM) method and 29 QTLs using the least absolute shrinkage selection operator (LASSO) method. QTLs identified by the CIM method account for 6.4% to 19.7% of the phenotypic variation. Small intervals of three QTLs (qCGR-1, qKW-2, and qGWP-4) contain several genes, including one gene (GRMZM2G139872) encoding the F-box protein, three genes (GRMZM2G180811, GRMZM5G828139, and GRMZM5G873194) encoding the WD40-repeat protein, and

  16. IDENTIFICACIÓN DE QTLs ASOCIADOS A CARACTERES DE ARQUITECTURA VEGETAL EN YUCA (Manihot esculenta

    Directory of Open Access Journals (Sweden)

    Camilo López

    2015-11-01

    Full Text Available RESUMENLa yuca (Manihot esculenta es el cuarto cultivo en importancia a nivel mundial como fuente de calorías para la población humana después del arroz, el azúcar y el maíz, posicionándose por esta razón como un cultivo primordial para la seguridad alimentaria. Su arquitectura ha sido considerada como un factor clave que subyace a la fisiología del rendimiento, relacionando características morfológicas con productividad. En este trabajo se evaluaron diferentes características de arquitectura vegetal en yuca. Los caracteres fueron evaluados en una población F1 compuesta por 133 hermanos completos (familia K sembrados en dos lugares biogeográficamente diferentes: La Vega (Cundinamarca y Arauca (Arauca en Colombia. Las características evaluadas relacionadas con la arquitectura vegetal fueron altura de la planta (AT, número de brotes (NB, longitud entrenudos (LE, número de raíces (NR, peso de raíces (PR, pigmentación del peciolo (PP, área de la hoja (AH y tipo de hoja (TH. A partir de los datos obtenidos y empleando un mapa genético de alta densidad basado en SNPs (Single Nucleotide Polymorphisms se llevó a cabo un análisis de QTLs (Quantitative Trait Loci. Se lograron identificar tres QTLs para La Vega asociados con los caracteres altura total, número de brotes y área de la hoja. Para Arauca se detectaron tres QTLs asociados con altura total, longitud de entrenudos y número de brotes. Los QTLs se distribuyeron en cuatro grupos de ligamiento y explicaron entre 18,93 y 41,92 % de la variación genética.ABSTRACTCassava (Manihot esculenta is the fourth most important crop worldwide as a source of calories for the human population after rice, sugar and corn and therefore it is considered as a staple crop. Cassava’s architecture has been considered as a key factor underlying the physiology of yield, relating morphological traits with productivity. In this work different characteristics of plant architecture were evaluated in

  17. Meta-Analyses of QTLs Associated with Protein and Oil Contents and Compositions in Soybean [Glycine max (L.) Merr.] Seed.

    Science.gov (United States)

    Van, Kyujung; McHale, Leah K

    2017-06-01

    Soybean [Glycine max (L.) Merr.] is a valuable and nutritious crop in part due to the high protein meal and vegetable oil produced from its seed. Soybean producers desire cultivars with both elevated seed protein and oil concentrations as well as specific amino acid and fatty acid profiles. Numerous studies have identified quantitative trait loci (QTLs) associated with seed composition traits, but validation of these QTLs has rarely been carried out. In this study, we have collected information, including genetic location and additive effects, on each QTL for seed contents of protein and oil, as well as amino acid and fatty acid compositions from over 80 studies. Using BioMercator V. 4.2, a meta-QTL analysis was performed with genetic information comprised of 175 QTLs for protein, 205 QTLs for oil, 156 QTLs for amino acids, and 113 QTLs for fatty acids. A total of 55 meta-QTL for seed composition were detected on 6 out of 20 chromosomes. Meta-QTL possessed narrower confidence intervals than the original QTL and candidate genes were identified within each meta-QTL. These candidate genes elucidate potential natural genetic variation in genes contributing to protein and oil biosynthesis and accumulation, providing meaningful information to further soybean breeding programs.

  18. Plastic expression of heterochrony quantitative trait loci (hQTLs) for leaf growth in the common bean (Phaseolus vulgaris).

    Science.gov (United States)

    Jiang, Libo; Clavijo, Jose A; Sun, Lidan; Zhu, Xuli; Bhakta, Mehul S; Gezan, Salvador A; Carvalho, Melissa; Vallejos, C Eduardo; Wu, Rongling

    2015-08-01

    Heterochrony, that is, evolutionary changes in the relative timing of developmental events and processes, has emerged as a key concept that links evolution and development. Genes associated with heterochrony encode molecular components of developmental timing mechanisms. However, our understanding of how heterochrony genes alter the expression of heterochrony in response to environmental changes remains very limited. We applied functional mapping to find quantitative trait loci (QTLs) responsible for growth trajectories of leaf area and leaf mass in the common bean (Phaseolus vulgaris) grown in two contrasting environments. We identified three major QTLs pleiotropically expressed under the two environments. Further characterization of the temporal pattern of these QTLs indicates that they are heterochrony QTLs (hQTLs) in terms of their role in influencing four heterochronic parameters: the timing of the inflection point, the timing of maximum acceleration and deceleration, and the duration of linear growth. The pattern of gene action by the hQTLs on each parameter was unique, being environmentally dependent and varying between two allometrically related leaf growth traits. These results provide new insights into the complexity of genetic mechanisms that control trait formation in plants and provide novel findings that will be of use in studying the evolutionary trends. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

  19. IDENTIFICACIÓN DE QTLs ASOCIADOS A CARACTERES DE ARQUITECTURA VEGETAL EN YUCA (Manihot esculenta

    Directory of Open Access Journals (Sweden)

    Ruben Eduardo MORA MORENO

    2016-01-01

    Full Text Available La yuca (Manihot esculenta es el cuarto cultivo en importancia a nivel mundial como fuente de calorías para la población humana después del arroz, el azúcar y el maíz, posicionándose por esta razón como un cultivo primordial para la seguridad alimentaria. Su arquitectura ha sido considerada como un factor clave que subyace a la fisiología del rendimiento, relacionando características morfológicas con productividad. En este trabajo se evaluaron diferentes características de arquitectura vegetal en yuca. Los caracteres fueron evaluados en una población F1 compuesta por 133 hermanos completos (familia K sembrados en dos lugares biogeográficamente diferentes: La Vega (Cundinamarca y Arauca (Arauca en Colombia. Las características evaluadas relacionadas con la arquitectura vegetal fueron altura de la planta (AT, número de brotes (NB, longitud entrenudos (LE, número de raíces (NR, peso de raíces (PR, pigmentación del peciolo (PP, área de la hoja (AH y tipo de hoja (TH. A partir de los datos obtenidos y empleando un mapa genético de alta densidad basado en SNPs (Single Nucleotide Polymorphisms se llevó a cabo un análisis de QTLs (Quantitative Trait Loci. Se lograron identificar tres QTLs para La Vega asociados con los caracteres altura total, número de brotes y área de la hoja. Para Arauca se detectaron tres QTLs asociados con altura total, longitud de entrenudos y número de brotes. Los QTLs se distribuyeron en cuatro grupos de ligamiento y explicaron entre 18,93 y 41,92 % de la variación genética.

  20. Body Composition QTLs Identified in Intercross Populations Are Reproducible in Consomic Mouse Strains

    OpenAIRE

    Lin, Cailu; Fesi, Brad D.; Marquis, Michael; Bosak, Natalia P.; Theodorides, Maria L.; Avigdor, Mauricio; McDaniel, Amanda H.; Duke, Fujiko F.; Lysenko, Anna; Khoshnevisan, Amin; Gantick, Brian R.; Arayata, Charles J.; Nelson, Theodore M.; Bachmanov, Alexander A.; Reed, Danielle R.

    2015-01-01

    Genetic variation contributes to individual differences in obesity, but defining the exact relationships between naturally occurring genotypes and their effects on fatness remains elusive. As a step toward positional cloning of previously identified body composition quantitative trait loci (QTLs) from F2 crosses of mice from the C57BL/6ByJ and 129P3/J inbred strains, we sought to recapture them on a homogenous genetic background of consomic (chromosome substitution) strains. Male and female m...

  1. SNP-Based Linkage Mapping for Validation of QTLs for Resistance to Ascochyta Blight in Lentil.

    Science.gov (United States)

    Sudheesh, Shimna; Rodda, Matthew S; Davidson, Jenny; Javid, Muhammad; Stephens, Amber; Slater, Anthony T; Cogan, Noel O I; Forster, John W; Kaur, Sukhjiwan

    2016-01-01

    Lentil (Lens culinaris Medik.) is a self-pollinating, diploid, annual, cool-season, food legume crop that is cultivated throughout the world. Ascochyta blight (AB), caused by Ascochyta lentis Vassilievsky, is an economically important and widespread disease of lentil. Development of cultivars with high levels of durable resistance provides an environmentally acceptable and economically feasible method for AB control. A detailed understanding of the genetic basis of AB resistance is hence highly desirable, in order to obtain insight into the number and influence of resistance genes. Genetic linkage maps based on single nucleotide polymorphisms (SNP) and simple sequence repeat (SSR) markers have been developed from three recombinant inbred line (RIL) populations. The IH × NF map contained 460 loci across 1461.6 cM, while the IH × DIG map contained 329 loci across 1302.5 cM and the third map, NF × DIG contained 330 loci across 1914.1 cM. Data from these maps were combined with a map from a previously published study through use of bridging markers to generate a consensus linkage map containing 689 loci distributed across seven linkage groups (LGs), with a cumulative length of 2429.61 cM at an average density of one marker per 3.5 cM. Trait dissection of AB resistance was performed for the RIL populations, identifying totals of two and three quantitative trait loci (QTLs) explaining 52 and 69% of phenotypic variation for resistance to infection in the IH × DIG and IH × NF populations, respectively. Presence of common markers in the vicinity of the AB_IH1- and AB_IH2.1/AB_IH2.2-containing regions on both maps supports the inference that a common genomic region is responsible for conferring resistance and is associated with the resistant parent, Indianhead. The third QTL was derived from Northfield. Evaluation of markers associated with AB resistance across a diverse lentil germplasm panel revealed that the identity of alleles associated with AB_IH1 predicted the

  2. SNP-based linkage mapping for validation of QTLs for resistance to ascochyta blight in lentil

    Directory of Open Access Journals (Sweden)

    Shimna Sudheesh

    2016-11-01

    Full Text Available Lentil (Lens culinaris Medik. is a self-pollinating, diploid, annual, cool-season, food legume crop that is cultivated throughout the world. Ascochyta blight (AB, caused by Ascochyta lentis Vassilievsky, is an economically important and widespread disease of lentil. Development of cultivars with high levels of durable resistance provides an environmentally acceptable and economically feasible method for AB control. A detailed understanding of the genetic basis of AB resistance is hence highly desirable, in order to obtain insight into the number and influence of resistance genes. Genetic linkage maps based on single nucleotide polymorphisms (SNP and simple sequence repeat (SSR markers have been developed from three recombinant inbred line (RIL populations. The IH x NF map contained 460 loci across 1461.6 cM, while the IH x DIG map contained 329 loci across 1302.5 cM and the third map, NF x DIG contained 330 loci across 1914.1 cM. Data from these maps were combined with a map from a previously published study through use of bridging markers to generate a consensus linkage map containing 689 loci distributed across 7 linkage groups (LGs, with a cumulative length of 2429.61 cM at an average density of one marker per 3.5 cM. Trait dissection of AB resistance was performed for the RIL populations, identifying totals of two and three quantitative trait loci (QTLs explaining 52% and 69% of phenotypic variation for resistance to infection in the IH x DIG and IH x NF populations, respectively. Presence of common markers in the vicinity of the AB_IH1- and AB_IH2.1/AB_IH2.2-containing regions on both maps supports the inference that a common genomic region is responsible for conferring resistance and is associated with the resistant parent, Indianhead. The third QTL was derived from Northfield. Evaluation of markers associated with AB resistance across a diverse lentil germplasm panel revealed that the identity of alleles associated with AB_IH1 predicted

  3. LOD score exclusion analyses for candidate QTLs using random population samples.

    Science.gov (United States)

    Deng, Hong-Wen

    2003-11-01

    While extensive analyses have been conducted to test for, no formal analyses have been conducted to test against, the importance of candidate genes as putative QTLs using random population samples. Previously, we developed an LOD score exclusion mapping approach for candidate genes for complex diseases. Here, we extend this LOD score approach for exclusion analyses of candidate genes for quantitative traits. Under this approach, specific genetic effects (as reflected by heritability) and inheritance models at candidate QTLs can be analyzed and if an LOD score is < or = -2.0, the locus can be excluded from having a heritability larger than that specified. Simulations show that this approach has high power to exclude a candidate gene from having moderate genetic effects if it is not a QTL and is robust to population admixture. Our exclusion analysis complements association analysis for candidate genes as putative QTLs in random population samples. The approach is applied to test the importance of Vitamin D receptor (VDR) gene as a potential QTL underlying the variation of bone mass, an important determinant of osteoporosis.

  4. Identification of QTLs conferring resistance to downy mildew in legacy cultivars of lettuce.

    Science.gov (United States)

    Simko, Ivan; Atallah, Amy J; Ochoa, Oswaldo E; Antonise, Rudie; Galeano, Carlos H; Truco, Maria Jose; Michelmore, Richard W

    2013-10-07

    Many cultivars of lettuce (Lactuca sativa L.), the most popular leafy vegetable, are susceptible to downy mildew disease caused by Bremia lactucae. Cultivars Iceberg and Grand Rapids that were released in the 18th and 19th centuries, respectively, have high levels of quantitative resistance to downy mildew. We developed a population of recombinant inbred lines (RILs) originating from a cross between these two legacy cultivars, constructed a linkage map, and identified two QTLs for resistance on linkage groups 2 (qDM2.1) and 5 (qDM5.1) that determined resistance under field conditions in California and the Netherlands. The same QTLs determined delayed sporulation at the seedling stage in laboratory experiments. Alleles conferring elevated resistance at both QTLs originate from cultivar Iceberg. An additional QTL on linkage group 9 (qDM9.1) was detected through simultaneous analysis of all experiments with mixed-model approach. Alleles for elevated resistance at this locus originate from cultivar Grand Rapids.

  5. Fine-Mapping Angiotensin-Converting Enzyme Gene: Separate QTLs Identified for Hypertension and for ACE Activity

    Science.gov (United States)

    Chung, Chia-Min; Wang, Ruey-Yun; Fann, Cathy S. J.; Chen, Jaw-Wen; Jong, Yuh-Shiun; Jou, Yuh-Shan; Yang, Hsin-Chou; Kang, Chih-Sen; Chen, Chien-Chung; Chang, Huan-Cheng; Pan, Wen-Harn

    2013-01-01

    Angiotensin-converting enzyme (ACE) has been implicated in multiple biological system, particularly cardiovascular diseases. However, findings associating ACE insertion/deletion polymorphism with hypertension or other related traits are inconsistent. Therefore, in a two-stage approach, we aimed to fine-map ACE in order to narrow-down the function-specific locations. We genotyped 31 single nucleotide polymorphisms (SNPs) of ACE from 1168 individuals from 305 young-onset (age ≤40) hypertension pedigrees, and found four linkage disequilibrium (LD) blocks. A tag-SNP, rs1800764 on LD block 2, upstream of and near the ACE promoter, was significantly associated with young-onset hypertension (p = 0.04). Tag-SNPs on all LD blocks were significantly associated with ACE activity (p-value: 10–16 to ACE activity were found between exon13 and intron18 and between intron 20 and 3′UTR, as revealed by measured haplotype analysis. These two major QTLs of ACE activity and the moderate effect variant upstream of ACE promoter for young-onset hypertension were replicated by another independent association study with 842 subjects. PMID:23469169

  6. A genetic map of melon highly enriched with fruit quality QTLs and EST markers, including sugar and carotenoid metabolism genes.

    Science.gov (United States)

    Harel-Beja, R; Tzuri, G; Portnoy, V; Lotan-Pompan, M; Lev, S; Cohen, S; Dai, N; Yeselson, L; Meir, A; Libhaber, S E; Avisar, E; Melame, T; van Koert, P; Verbakel, H; Hofstede, R; Volpin, H; Oliver, M; Fougedoire, A; Stalh, C; Fauve, J; Copes, B; Fei, Z; Giovannoni, J; Ori, N; Lewinsohn, E; Sherman, A; Burger, J; Tadmor, Y; Schaffer, A A; Katzir, N

    2010-08-01

    A genetic map of melon enriched for fruit traits was constructed, using a recombinant inbred (RI) population developed from a cross between representatives of the two subspecies of Cucumis melo L.: PI 414723 (subspecies agrestis) and 'Dulce' (subspecies melo). Phenotyping of 99 RI lines was conducted over three seasons in two locations in Israel and the US. The map includes 668 DNA markers (386 SSRs, 76 SNPs, six INDELs and 200 AFLPs), of which 160 were newly developed from fruit ESTs. These ESTs include candidate genes encoding for enzymes of sugar and carotenoid metabolic pathways that were cloned from melon cDNA or identified through mining of the International Cucurbit Genomics Initiative database (http://www.icugi.org/). The map covers 1,222 cM with an average of 2.672 cM between markers. In addition, a skeleton physical map was initiated and 29 melon BACs harboring fruit ESTs were localized to the 12 linkage groups of the map. Altogether, 44 fruit QTLs were identified: 25 confirming QTLs described using other populations and 19 newly described QTLs. The map includes QTLs for fruit sugar content, particularly sucrose, the major sugar affecting sweetness in melon fruit. Six QTLs interacting in an additive manner account for nearly all the difference in sugar content between the two genotypes. Three QTLs for fruit flesh color and carotenoid content were identified. Interestingly, no clear colocalization of QTLs for either sugar or carotenoid content was observed with over 40 genes encoding for enzymes involved in their metabolism. The RI population described here provides a useful resource for further genomics and metabolomics studies in melon, as well as useful markers for breeding for fruit quality.

  7. Dissection of a genetically complex cluster of growth and obesity QTLs on mouse chromosome 2 using subcongenic intercrosses.

    Science.gov (United States)

    Farber, Charles R; Medrano, Juan F

    2007-09-01

    In a previous study we characterized the B6.CAST-(D2Mit329-D2Mit457)N(6) (B62D) congenic strain, which possesses CAST/EiJ (CAST) chromosome 2 donor alleles from 74 to 180 Mbp on a C57BL6/J (B6) background. This strain exhibited significant decreases in body weight and adiposity attributable to the weight gain 2 (Wg2) quantitative trait locus (QTL). To refine the location of Wg2, we used a two-stage genetic dissection strategy consisting of a B62D x B6 backcross, which mapped Wg2 to the proximal portion of the B62D donor region, followed by the development of seven overlapping subcongenic F(2) intercrosses targeting the Wg2 genomic interval. Surprisingly, five of the seven intercrosses displayed significant differences, dependent on genotype, in body weight and/or fat pad mass. These effects were the result of at least four independent QTLs that were named Wg2a, b, c, and d. In contrast to the lean and low body weight phenotype of the B62D parental strain, mice homozygous for CAST congenic alleles (cast/cast) at Wg2a were significantly heavier at 6 and 9 weeks of age, while cast/cast mice at Wg2c had higher levels of total fat. Consistent with the prior observed effects of Wg2, cast/cast mice at Wg2b displayed significant decreases in 6- and 9-week body weight as well as a decrease in total fat pad mass. All of the QTLs had additive effects on body composition except Wg2d, which displayed underdominance for total fat mass. Significant differences in weight and adiposity were also observed in genetically identical b6/b6 homozygous mice across the panel of subcongenics, suggesting either maternal or paternal contributions to body composition. These data represent a significant advancement toward the identification of mouse chromosome 2 growth and obesity quantitative trait genes.

  8. Integrating mRNA and miRNA Weighted Gene Co-Expression Networks with eQTLs in the Nucleus Accumbens of Subjects with Alcohol Dependence.

    Directory of Open Access Journals (Sweden)

    Mohammed Mamdani

    Full Text Available Alcohol consumption is known to lead to gene expression changes in the brain. After performing weighted gene co-expression network analyses (WGCNA on genome-wide mRNA and microRNA (miRNA expression in Nucleus Accumbens (NAc of subjects with alcohol dependence (AD; N = 18 and of matched controls (N = 18, six mRNA and three miRNA modules significantly correlated with AD were identified (Bonferoni-adj. p≤ 0.05. Cell-type-specific transcriptome analyses revealed two of the mRNA modules to be enriched for neuronal specific marker genes and downregulated in AD, whereas the remaining four mRNA modules were enriched for astrocyte and microglial specific marker genes and upregulated in AD. Gene set enrichment analysis demonstrated that neuronal specific modules were enriched for genes involved in oxidative phosphorylation, mitochondrial dysfunction and MAPK signaling. Glial-specific modules were predominantly enriched for genes involved in processes related to immune functions, i.e. cytokine signaling (all adj. p≤ 0.05. In mRNA and miRNA modules, 461 and 25 candidate hub genes were identified, respectively. In contrast to the expected biological functions of miRNAs, correlation analyses between mRNA and miRNA hub genes revealed a higher number of positive than negative correlations (χ2 test p≤ 0.0001. Integration of hub gene expression with genome-wide genotypic data resulted in 591 mRNA cis-eQTLs and 62 miRNA cis-eQTLs. mRNA cis-eQTLs were significantly enriched for AD diagnosis and AD symptom counts (adj. p = 0.014 and p = 0.024, respectively in AD GWAS signals in a large, independent genetic sample from the Collaborative Study on Genetics of Alcohol (COGA. In conclusion, our study identified putative gene network hubs coordinating mRNA and miRNA co-expression changes in the NAc of AD subjects, and our genetic (cis-eQTL analysis provides novel insights into the etiological mechanisms of AD.

  9. Discovery of Consistent QTLs of Wheat Spike-Related Traits under Nitrogen Treatment at Different Development Stages

    Directory of Open Access Journals (Sweden)

    Zhiying Deng

    2017-12-01

    Full Text Available Spike-related traits such as spike length (Sl, fertile spikelet number (Fsn, sterile spikelet number (Ssn, grain number per spike (Gns, and thousand-kernel weight (Tkw are important factors influencing wheat yield. However, reliably stable markers that can be used for molecular breeding in different environments have not yet been identified. In this study, a double haploid (DH population was used for quantitative trait locus (QTL mapping of five spike-related traits under four different nitrogen (N supply dates in two locations and years. Seventy additive QTLs with phenotypic variation ranging from 4.12 to 34.74% and 10 major epistatic QTLs were identified. Eight important chromosomal regions on five chromosomes (1B, 2B, 2D, 5D, and 6A were found. Sixteen stable QTLs were detected for which N application had little effect. Among those stable QTLs, QSl.sdau-2D-1, and QSl.sdau-2D-2, with phenotypic variation explained (PVE of 10.4 and 24.2%, respectively, were flanked by markers Xwmc112 and Xcfd53 in the same order. The QTLs QSsn.sdau-2B-1, QFsn.sdau-2B-1, and QGns.sdau-2B, with PVE ranging from 4.37 to 28.43%, collocated in the Xwmc179-Xbarc373 marker interval. The consistent kernel wheat QTL (QTkw.sdau-6A on the long arm of chromosome 6A, flanked by SSR markers Xbarc1055 and Xwmc553, showed PVE of 5.87–15.18%. Among these stable QTLs, the two flanking markers Xwmc112 and Xcfd53 have been validated using different varieties and populations for selecting Sl. Therefore, these results will be of great value for marker-assisted selection (MAS in breeding programs and will accelerate the understanding of the genetic relationships among spike-related traits at the molecular level.

  10. Identification of candidate genes of QTLs for seed weight in Brassica napus through comparative mapping among Arabidopsis and Brassica species

    Science.gov (United States)

    2012-01-01

    Background Map-based cloning of quantitative trait loci (QTLs) in polyploidy crop species remains a challenge due to the complexity of their genome structures. QTLs for seed weight in B. napus have been identified, but information on candidate genes for identified QTLs of this important trait is still rare. Results In this study, a whole genome genetic linkage map for B. napus was constructed using simple sequence repeat (SSR) markers that covered a genetic distance of 2,126.4 cM with an average distance of 5.36 cM between markers. A procedure was developed to establish colinearity of SSR loci on B. napus with its two progenitor diploid species B. rapa and B. oleracea through extensive bioinformatics analysis. With the aid of B. rapa and B. oleracea genome sequences, the 421 homologous colinear loci deduced from the SSR loci of B. napus were shown to correspond to 398 homologous loci in Arabidopsis thaliana. Through comparative mapping of Arabidopsis and the three Brassica species, 227 homologous genes for seed size/weight were mapped on the B. napus genetic map, establishing the genetic bases for the important agronomic trait in this amphidiploid species. Furthermore, 12 candidate genes underlying 8 QTLs for seed weight were identified, and a gene-specific marker for BnAP2 was developed through molecular cloning using the seed weight/size gene distribution map in B. napus. Conclusions Our study showed that it is feasible to identify candidate genes of QTLs using a SSR-based B. napus genetic map through comparative mapping among Arabidopsis and B. napus and its two progenitor species B. rapa and B. oleracea. Identification of candidate genes for seed weight in amphidiploid B. napus will accelerate the process of isolating the mapped QTLs for this important trait, and this approach may be useful for QTL identification of other traits of agronomic significance. PMID:23216693

  11. The impact of methylation quantitative trait loci (mQTLs) on active smoking-related DNA methylation changes.

    Science.gov (United States)

    Gao, Xu; Thomsen, Hauke; Zhang, Yan; Breitling, Lutz Philipp; Brenner, Hermann

    2017-01-01

    Methylation quantitative trait loci (mQTLs) are the genetic variants that may affect the DNA methylation patterns of CpG sites. However, their roles in influencing the disturbances of smoking-related epigenetic changes have not been well established. This study was conducted to address whether mQTLs exist in the vicinity of smoking-related CpG sites (± 50 kb) and to examine their associations with smoking exposure and all-cause mortality in older adults. We obtained DNA methylation profiles in whole blood samples by Illumina Infinium Human Methylation 450 BeadChip array of two independent subsamples of the ESTHER study (discovery set, n = 581; validation set, n = 368) and their corresponding genotyping data using the Illumina Infinium OncoArray BeadChip. After correction for multiple testing (FDR), we successfully identified that 70 out of 151 previously reported smoking-related CpG sites were significantly associated with 192 SNPs within the 50 kb search window of each locus. The 192 mQTLs significantly influenced the active smoking-related DNA methylation changes, with percentage changes ranging from 0.01 to 18.96%, especially for the weakly/moderately smoking-related CpG sites. However, these identified mQTLs were not directly associated with active smoking exposure or all-cause mortality. Our findings clearly demonstrated that if not dealt with properly, the mQTLs might impair the power of epigenetic-based models of smoking exposure to a certain extent. In addition, such genetic variants could be the key factor to distinguish between the heritable and smoking-induced impact on epigenome disparities. These mQTLs are of special importance when DNA methylation markers measured by Illumina Infinium assay are used for any comparative population studies related to smoking-related cancers and chronic diseases.

  12. Sunflower Resistance to Broomrape (Orobanche cumana) Is Controlled by Specific QTLs for Different Parasitism Stages

    Science.gov (United States)

    Louarn, Johann; Boniface, Marie-Claude; Pouilly, Nicolas; Velasco, Leonardo; Pérez-Vich, Begoña; Vincourt, Patrick; Muños, Stéphane

    2016-01-01

    Orobanche cumana (sunflower broomrape) is an obligatory and non-photosynthetic root parasitic plant that specifically infects the sunflower. It is located in Europe and in Asia, where it can cause yield losses of over 80%. More aggressive races have evolved, mainly around the Black Sea, and broomrape can rapidly spread to new areas. Breeding for resistance seems to be the most efficient and sustainable approach to control broomrape infestation. In our study, we used a population of 101 recombinant inbred lines (RILs), derived from a cross between the two lines HA89 and LR1 (a line derived from an interspecific cross with Helianthus debilis). Rhizotrons, pots and field experiments were used to characterize all RILs for their resistance to O. cumana race F parasitism at three post vascular connection life stages: (i) early attachment of the parasite to the sunflower roots, (ii) young tubercle and (iii) shoot emergence. In addition, RIL resistance to race G at young tubercle development stage was evaluated in pots. The entire population was genotyped, and QTLs were mapped. Different QTLs were identified for each race (F from Spain and G from Turkey) and for the three stages of broomrape development. The results indicate that there are several quantitative resistance mechanisms controlling the infection by O. cumana that can be used in sunflower breeding. PMID:27242810

  13. Interaction between QTLs induces an advance in ethylene biosynthesis during melon fruit ripening.

    Science.gov (United States)

    Vegas, Juan; Garcia-Mas, Jordi; Monforte, Antonio Jose

    2013-06-01

    The coexistence of both climacteric and non-climacteric genotypes and the availability of a set of genetic and genomic resources make melon a suitable model for genetic studies of fruit ripening. We have previously described a QTL, ETHQB3.5, which induces climacteric fruit ripening in the near-isogenic line (NIL) SC3-5 that harbors an introgression on linkage group (LG) III from the non-climacteric melon accession PI 161375 in the, also non-climacteric cultivar, "Piel de Sapo" genetic background. In the current study, a new major QTL, ETHQV6.3, on LG VI was detected on an additional introgression in the same NIL. These QTLs are capable, individually, of inducing climacteric ripening in the non-climacteric background, the effects of ETHQV6.3 being greater than that of ETHQB3.5. The QTLs interact epistatically, advancing the timing of ethylene biosynthesis during ripening and, therefore, the climacteric responses. ETHQV6.3 was fine-mapped to a 4.5 Mb physical region of the melon genome, probably in the centromeric region of LG VI. The results presented will be of value in the molecular identification of the gene underlying ETHQV6.3.

  14. QTLs for agronomic traits in the Mediterranean environment identified in recombinant inbred lines of the cross 'Arta' × ¤H. spontaneum¤ 41-1

    DEFF Research Database (Denmark)

    Baum, M.; Grando, S.; Backes, G.

    2003-01-01

    ). The linkage map extended to 890 cM. Agronomic traits such as grain yield, biological yield, days to heading, plant height, cold tolerance and others were evaluated at the ICARDA research stations Tel Hadya and Breda during the years 1996-97 and 1997-98. QTLs for agronomic traits related to drought resistance...... were localized. For the most-important character 'plant height under drought stress', QTLs on 2H, 3H and 7H were detected. The 'plant height' QTLs, specially the one on 3H, showed pleiotropic effects on traits such as days to heading, grain yield and biological yield. QTLs were also identified...... for other traits associated with adaptation to the Mediterranean environment such as cold tolerance, days to heading and tiller number. The identification of QTLs for agronomic traits is a first step to analyze and to dissect complex characters such as adaptation to drought tolerance....

  15. A High-Density Integrated DArTseq SNP-Based Genetic Map of Pisum fulvum and Identification of QTLs Controlling Rust Resistance

    Directory of Open Access Journals (Sweden)

    Eleonora Barilli

    2018-02-01

    Full Text Available Pisum fulvum, a wild relative of pea is an important source of allelic diversity to improve the genetic resistance of cultivated species against fungal diseases of economic importance like the pea rust caused by Uromyces pisi. To unravel the genetic control underlying resistance to this fungal disease, a recombinant inbred line (RIL population was generated from a cross between two P. fulvum accessions, IFPI3260 and IFPI3251, and genotyped using Diversity Arrays Technology. A total of 9,569 high-quality DArT-Seq and 8,514 SNPs markers were generated. Finally, a total of 12,058 markers were assembled into seven linkage groups, equivalent to the number of haploid chromosomes of P. fulvum and P. sativum. The newly constructed integrated genetic linkage map of P. fulvum covered an accumulated distance of 1,877.45 cM, an average density of 1.19 markers cM−1 and an average distance between adjacent markers of 1.85 cM. The composite interval mapping revealed three QTLs distributed over two linkage groups that were associated with the percentage of rust disease severity (DS%. QTLs UpDSII and UpDSIV were located in the LGs II and IV respectively and were consistently identified both in adult plants over 3 years at the field (Córdoba, Spain and in seedling plants under controlled conditions. Whenever they were detected, their contribution to the total phenotypic variance varied between 19.8 and 29.2. A third QTL (UpDSIV.2 was also located in the LGIVand was environmentally specific as was only detected for DS % in seedlings under controlled conditions. It accounted more than 14% of the phenotypic variation studied. Taking together the data obtained in the study, it could be concluded that the expression of resistance to fungal diseases in P. fulvum originates from the resistant parent IFPI3260.

  16. LMNA Sequences of 60,706 Unrelated Individuals Reveal 132 Novel Missense Variants in A-Type Lamins and Suggest a Link between Variant p.G602S and Type 2 Diabetes

    Directory of Open Access Journals (Sweden)

    Alyssa Florwick

    2017-06-01

    Full Text Available Mutations in LMNA, encoding nuclear intermediate filament proteins lamins A and C, cause multiple diseases (‘laminopathies’ including muscular dystrophy, dilated cardiomyopathy, familial partial lipodystrophy (FPLD2, insulin resistance syndrome and progeria. To assess the prevalence of LMNA missense mutations (‘variants’ in a broad, ethnically diverse population, we compared missense alleles found among 60,706 unrelated individuals in the ExAC cohort to those identified in 1,404 individuals in the laminopathy database (UMD-LMNA. We identified 169 variants in the ExAC cohort, of which 37 (∼22% are disease-associated including p.I299V (allele frequency 0.0402%, p.G602S (allele frequency 0.0262% and p.R644C (allele frequency 0.124%, suggesting certain LMNA mutations are more common than previously recognized. Independent analysis of LMNA variants via the type 2 diabetes (T2D Knowledge Portal showed that variant p.G602S associated significantly with type 2 diabetes (p = 0.02; odds ratio = 4.58, and was more frequent in African Americans (allele frequency 0.297%. The FPLD2-associated variant I299V was most prevalent in Latinos (allele frequency 0.347%. The ExAC cohort also revealed 132 novel LMNA missense variants including p.K108E (limited to individuals with psychiatric disease; predicted to perturb coil-1B, p.R397C and p.R427C (predicted to perturb filament biogenesis, p.G638R and p.N660D (predicted to perturb prelamin A processing, and numerous Ig-fold variants predicted to perturb phenotypically characteristic protein–protein interactions. Overall, this two-pronged strategy— mining a large database for missense variants in a single gene (LMNA, coupled to knowledge about the structure, biogenesis and functions of A-type lamins— revealed an unexpected number of LMNA variants, including novel variants predicted to perturb lamin assembly or function. Interestingly, this study also correlated novel variant p.K108E with psychiatric

  17. Hypnosis, suggestion, and suggestibility: an integrative model.

    Science.gov (United States)

    Lynn, Steven Jay; Laurence, Jean-Roch; Kirsch, Irving

    2015-01-01

    This article elucidates an integrative model of hypnosis that integrates social, cultural, cognitive, and neurophysiological variables at play both in and out of hypnosis and considers their dynamic interaction as determinants of the multifaceted experience of hypnosis. The roles of these variables are examined in the induction and suggestion stages of hypnosis, including how they are related to the experience of involuntariness, one of the hallmarks of hypnosis. It is suggested that studies of the modification of hypnotic suggestibility; cognitive flexibility; response sets and expectancies; the default-mode network; and the search for the neurophysiological correlates of hypnosis, more broadly, in conjunction with research on social psychological variables, hold much promise to further understanding of hypnosis.

  18. Meta-analysis to refine map position and reduce confidence intervals for delayed canopy wilting QTLs in soybean

    Science.gov (United States)

    Slow canopy wilting in soybean has been identified as a potentially beneficial trait for ameliorating drought effects on yield. Previous research identified QTLs for slow wilting from two different bi-parental populations and this information was combined with data from three other populations to id...

  19. Development of pyramidal lines with two major QTLs conferring resistance to sheath blight in rice (Oryza sativa L.)

    Science.gov (United States)

    Hossain, Md Kamal; Jena, Kshirod; Bhuiyan, Md Atiqur Rahman; Ratnam, Wickneswari

    2014-09-01

    Sheath blight is an emerging threat in rice cultivation. It is animportant disease caused by the soil-borne necrotrophic pathogenic fungus, Rhizoctonia solani Kühn. However, to date neither known major genes for quantitative resistance, nor any rice lines immune to this disease has been identified. The disease resistance is quantitative in nature. Numerous genes are involved in this resistance process. There are few quantitative trait loci (QTLs) detected conferring improved resistance against the disease. Teqing and Tetepshowimproved resistance having QTLs, qSB-9 and qSBR11-1, respectively. Since, these QTLs demonstrates additive effects, pyramiding of these QTLs might be an option to increase the sheath blight resistance in rice. Nine rice cultivars were screened at greenhouse conditions. Results showed that Tetep and Teqing had the lowest disease ratings. UKMRC2a new high yielding cultivar was as recipient parent. Crosses between UKMRC2 and Teqing, and UKMRC2 and Tetep were made and confirmed. Subsequently 4-way crosses between the two F1s were performed to develop pyramidal lines.

  20. Conditional entropy in variation-adjusted windows detects selection signatures associated with expression quantitative trait loci (eQTLs).

    Science.gov (United States)

    Handelman, Samuel K; Seweryn, Michal; Smith, Ryan M; Hartmann, Katherine; Wang, Danxin; Pietrzak, Maciej; Johnson, Andrew D; Kloczkowski, Andrzej; Sadee, Wolfgang

    2015-01-01

    Over the past 50,000 years, shifts in human-environmental or human-human interactions shaped genetic differences within and among human populations, including variants under positive selection. Shaped by environmental factors, such variants influence the genetics of modern health, disease, and treatment outcome. Because evolutionary processes tend to act on gene regulation, we test whether regulatory variants are under positive selection. We introduce a new approach to enhance detection of genetic markers undergoing positive selection, using conditional entropy to capture recent local selection signals. We use conditional logistic regression to compare our Adjusted Haplotype Conditional Entropy (H|H) measure of positive selection to existing positive selection measures. H|H and existing measures were applied to published regulatory variants acting in cis (cis-eQTLs), with conditional logistic regression testing whether regulatory variants undergo stronger positive selection than the surrounding gene. These cis-eQTLs were drawn from six independent studies of genotype and RNA expression. The conditional logistic regression shows that, overall, H|H is substantially more powerful than existing positive-selection methods in identifying cis-eQTLs against other Single Nucleotide Polymorphisms (SNPs) in the same genes. When broken down by Gene Ontology, H|H predictions are particularly strong in some biological process categories, where regulatory variants are under strong positive selection compared to the bulk of the gene, distinct from those GO categories under overall positive selection. . However, cis-eQTLs in a second group of genes lack positive selection signatures detectable by H|H, consistent with ancient short haplotypes compared to the surrounding gene (for example, in innate immunity GO:0042742); under such other modes of selection, H|H would not be expected to be a strong predictor.. These conditional logistic regression models are adjusted for Minor allele

  1. Identification of QTLs of resistance to white mold in common bean from multiple markers by using Bayesian analysis.

    Science.gov (United States)

    Lara, L A C; Santos, J B; Balestre, M; Lima, I A; Pamplona, A K A; Veloso, J S; Silva, P H

    2015-02-06

    In this study, we identified simple sequence repeat, ampli-fied fragment length polymorphism, and sequence-related amplified poly-morphism markers linked to quantitative trait loci (QTLs) for resistance to white mold disease in common bean progenies derived from a cross between lines CNFC 9506 and RP-2, evaluated using the oxalic acid test and using Bayesian analysis. DNA was extracted from 186 F₂ plants and their parental lines for molecular analysis. Fifteen experiments were car-ried out for phenotypic analysis, which included 186 F₂:₄ progenies, the F₁ generation, the F₂ generation, and the lines CNFC 9506, RP-2, and G122 as common treatments. A completely randomized experimental design with 3 replications was used in controlled environments. The adjusted means for the F₂:₄ generation were to identify QTLs by Bayesian shrink-age analysis. Significant differences were observed among the progenies for the reaction to white mold. The moving away method under the Bayes-ian approach was effective for identifying QTLs when it was not possible to obtain a genetic map because of low marker density. Using the Wald test, 25 markers identified QTLs for resistance to white mold, as well as 16 simple sequence repeats, 7 amplified fragment length polymorphisms, and 2 sequence-related amplified polymorphisms. The markers BM184, BM211, and PV-gaat001 showed low distances from QTLs related white mold resistance. In addition, these markers showed, signal effects with increasing resistance to white mold and high heritability in the analysis with oxalic acid, and thus, are promising for marker-assisted selection.

  2. Construction of a SSR-based genetic map and identification of QTLs for catechins content in tea plant (Camellia sinensis).

    Science.gov (United States)

    Ma, Jian-Qiang; Yao, Ming-Zhe; Ma, Chun-Lei; Wang, Xin-Chao; Jin, Ji-Qiang; Wang, Xue-Min; Chen, Liang

    2014-01-01

    Catechins are the most important bioactive compounds in tea, and have been demonstrated to possess a wide variety of pharmacological activities. To characterize quantitative trait loci (QTLs) for catechins content in the tender shoots of tea plant, we constructed a moderately saturated genetic map using 406 simple sequence repeat (SSR) markers, based on a pseudo-testcross population of 183 individuals derived from an intraspecific cross of two Camellia sinensis varieties with diverse catechins composition. The map consisted of fifteen linkage groups (LGs), corresponding to the haploid chromosome number of tea plant (2n = 2x = 30). The total map length was 1,143.5 cM, with an average locus spacing of 2.9 cM. A total of 25 QTLs associated with catechins content were identified over two measurement years. Of these, nine stable QTLs were validated across years, and clustered into four main chromosome regions on LG03, LG11, LG12 and LG15. The population variability explained by each QTL was predominantly at moderate-to-high levels and ranged from 2.4% to 71.0%, with an average of 17.7%. The total number of QTL for each trait varied from four to eight, while the total population variability explained by all QTLs for a trait ranged between 38.4% and 79.7%. This is the first report on the identification of QTL for catechins content in tea plant. The results of this study provide a foundation for further cloning and functional characterization of catechin QTLs for utilization in improvement of tea plant.

  3. Dissection of QTLs for Hull Silicon Content on the Short Arm of Rice Chromosome 6

    Directory of Open Access Journals (Sweden)

    Ji-rong WU

    2010-06-01

    Full Text Available The QTL qHUS6 for hull silicon content in rice was previously located on the short arm of rice chromosome 6. By using an F2:3 population segregating in the RM587–RM19784 region harboring qHUS6 in an isogenic background, two QTLs for hull silicon content were detected, of which qHUS6-1 was located in the distal region and qHUS6-2 in the region proximal to the centromere. Three rice plants carrying small heterozygous segments in the target region were selected, of which two covered the qHUS6-1 region and the other covered the qHUS6-2 region. Three F2:3 populations were derived from the selfed seeds of the three plants, respectively. QTL mapping was performed using the two populations segregating in the qHUS6-1 region, and qHUS6-1 was delimited to a 147.0-kb region flanked by the markers RM510 and RM19417. Five groups of F3 lines with different genotypic compositions in the qHUS6-2 region were selected from the other F2:3 population. Two QTLs were separated with two-way ANOVA, of which qHUS6-2a was located in the interval defined by RM19706–RM19795 and qHUS6-2b in the interval RM314–RM19665.

  4. A GENOME-WIDE EXPLORATION SUGGESTS AN OLIGOGENIC MODEL OF INHERITANCE FOR THE TAFI ACTIVITY AND ITS ANTIGEN LEVELS

    Science.gov (United States)

    Sabater-Lleal, Maria; Buil, Alfonso; Souto, Juan Carlos; Almasy, Laura; Borrell, Montserrat; Lathrop, Mark; Blangero, John; Fontcuberta, Jordi; Soria, José Manuel

    2008-01-01

    Thrombin-Activatable Fibrinolysis Inhibitor (TAFI) is a protein that attenuates fibrinolysis potently. A considerable proportion of its variability levels is genetically determined. It has been associated with arterial and venous thrombosis. We conducted a genomewide linkage scan for genes affecting variation in plasma TAFI levels in 398 subjects from 21 extended Spanish families. The data were analyzed by a variance-component linkage method. A strong linkage was found on the long arm of Chromosome 13, near the DNA marker D13S156, where the structural gene encoding for TAFI is located. In addition, other new linkage signals were detected on chromosome regions 5p and 7q. More importantly, we performed another multipoint linkage analysis of functional TAFI conditioned on TAFI antigen levels. We detected a strong linkage signal on Chromosome 19 (LOD = 3.0, p = 0.0001) suggesting a novel QTL in this region involved in the specific functional activity of TAFI, regardless of the TAFI antigen levels. One notable aspect of this study is the identification of new QTLs that reveal a clearer picture of the genetic determinants responsible for variation in TAFI levels. Another is the replication of the linkage signal of the CPB2 gene, which confirms an important genetic determinant for TAFI antigen levels. These results strongly suggest an oligogenic mode of inheritance for TAFI, in which CPB2 gene accounts for a proportion of the variation of the phenotype together with other unknown genes that may represent potential risk factors for thrombotic disease. PMID:18563448

  5. Open to Suggestion.

    Science.gov (United States)

    Journal of Reading, 1987

    1987-01-01

    Offers (1) suggestions for improving college students' study skills; (2) a system for keeping track of parent, teacher, and community contacts; (3) suggestions for motivating students using tic tac toe; (4) suggestions for using etymology to improve word retention; (5) a word search grid; and (6) suggestions for using postcards in remedial reading…

  6. Identification of QTLs for Resistance to Sclerotinia Stem Rot and BnaC.IGMT5.a as a Candidate Gene of the Major Resistant QTL SRC6 in Brassica napus

    Science.gov (United States)

    Wu, Jian; Cai, Guangqin; Tu, Jiangying; Li, Lixia; Liu, Sheng; Luo, Xinping; Zhou, Lipeng; Fan, Chuchuan; Zhou, Yongming

    2013-01-01

    Stem rot caused by Sclerotinia sclerotiorum in many important dicotyledonous crops, including oilseed rape (Brassica napus), is one of the most devastating fungal diseases and imposes huge yield loss each year worldwide. Currently, breeding for Sclerotinia resistance in B. napus, as in other crops, can only rely on germplasms with quantitative resistance genes. Thus, the identification of quantitative trait locus (QTL) for S. sclerotiorum resistance/tolerance in this crop holds immediate promise for the genetic improvement of the disease resistance. In this study, ten QTLs for stem resistance (SR) at the mature plant stage and three QTLs for leaf resistance (LR) at the seedling stage in multiple environments were mapped on nine linkage groups (LGs) of a whole genome map for B. napus constructed with SSR markers. Two major QTLs, LRA9 on LG A9 and SRC6 on LG C6, were repeatedly detected across all environments and explained 8.54–15.86% and 29.01%–32.61% of the phenotypic variations, respectively. Genotypes containing resistant SRC6 or LRA9 allele showed a significant reduction in disease lesion after pathogen infection. Comparative mapping with Arabidopsis and data mining from previous gene profiling experiments identified that the Arabidopsis homologous gene of IGMT5 (At1g76790) was related to the SRC6 locus. Four copies of the IGMT5 gene in B. napus were isolated through homologous cloning, among which, only BnaC.IGMT5.a showed a polymorphism between parental lines and can be associated with the SRC6. Furthermore, two parental lines exhibited a differential expression pattern of the BnaC.IGMT5.a gene in responding to pathogen inoculation. Thus, our data suggested that BnaC.IGMT5.a was very likely a candidate gene of this major resistance QTL. PMID:23844081

  7. Identification of QTLs for resistance to sclerotinia stem rot and BnaC.IGMT5.a as a candidate gene of the major resistant QTL SRC6 in Brassica napus.

    Directory of Open Access Journals (Sweden)

    Jian Wu

    Full Text Available Stem rot caused by Sclerotinia sclerotiorum in many important dicotyledonous crops, including oilseed rape (Brassica napus, is one of the most devastating fungal diseases and imposes huge yield loss each year worldwide. Currently, breeding for Sclerotinia resistance in B. napus, as in other crops, can only rely on germplasms with quantitative resistance genes. Thus, the identification of quantitative trait locus (QTL for S. sclerotiorum resistance/tolerance in this crop holds immediate promise for the genetic improvement of the disease resistance. In this study, ten QTLs for stem resistance (SR at the mature plant stage and three QTLs for leaf resistance (LR at the seedling stage in multiple environments were mapped on nine linkage groups (LGs of a whole genome map for B. napus constructed with SSR markers. Two major QTLs, LRA9 on LG A9 and SRC6 on LG C6, were repeatedly detected across all environments and explained 8.54-15.86% and 29.01%-32.61% of the phenotypic variations, respectively. Genotypes containing resistant SRC6 or LRA9 allele showed a significant reduction in disease lesion after pathogen infection. Comparative mapping with Arabidopsis and data mining from previous gene profiling experiments identified that the Arabidopsis homologous gene of IGMT5 (At1g76790 was related to the SRC6 locus. Four copies of the IGMT5 gene in B. napus were isolated through homologous cloning, among which, only BnaC.IGMT5.a showed a polymorphism between parental lines and can be associated with the SRC6. Furthermore, two parental lines exhibited a differential expression pattern of the BnaC.IGMT5.a gene in responding to pathogen inoculation. Thus, our data suggested that BnaC.IGMT5.a was very likely a candidate gene of this major resistance QTL.

  8. Profiling RNA-Seq at multiple resolutions markedly increases the number of causal eQTLs in autoimmune disease.

    Science.gov (United States)

    Odhams, Christopher A; Cunninghame Graham, Deborah S; Vyse, Timothy J

    2017-10-01

    Genome-wide association studies have identified hundreds of risk loci for autoimmune disease, yet only a minority (~25%) share genetic effects with changes to gene expression (eQTLs) in immune cells. RNA-Seq based quantification at whole-gene resolution, where abundance is estimated by culminating expression of all transcripts or exons of the same gene, is likely to account for this observed lack of colocalisation as subtle isoform switches and expression variation in independent exons can be concealed. We performed integrative cis-eQTL analysis using association statistics from twenty autoimmune diseases (560 independent loci) and RNA-Seq data from 373 individuals of the Geuvadis cohort profiled at gene-, isoform-, exon-, junction-, and intron-level resolution in lymphoblastoid cell lines. After stringently testing for a shared causal variant using both the Joint Likelihood Mapping and Regulatory Trait Concordance frameworks, we found that gene-level quantification significantly underestimated the number of causal cis-eQTLs. Only 5.0-5.3% of loci were found to share a causal cis-eQTL at gene-level compared to 12.9-18.4% at exon-level and 9.6-10.5% at junction-level. More than a fifth of autoimmune loci shared an underlying causal variant in a single cell type by combining all five quantification types; a marked increase over current estimates of steady-state causal cis-eQTLs. Causal cis-eQTLs detected at different quantification types localised to discrete epigenetic annotations. We applied a linear mixed-effects model to distinguish cis-eQTLs modulating all expression elements of a gene from those where the signal is only evident in a subset of elements. Exon-level analysis detected disease-associated cis-eQTLs that subtly altered transcription globally across the target gene. We dissected in detail the genetic associations of systemic lupus erythematosus and functionally annotated the candidate genes. Many of the known and novel genes were concealed at gene

  9. High-Density Linkage Map Construction and Mapping of Salt-Tolerant QTLs at Seedling Stage in Upland Cotton Using Genotyping by Sequencing (GBS

    Directory of Open Access Journals (Sweden)

    Latyr Diouf

    2017-12-01

    Full Text Available Over 6% of agricultural land is affected by salinity. It is becoming obligatory to use saline soils, so growing salt-tolerant plants is a priority. To gain an understanding of the genetic basis of upland cotton tolerance to salinity at seedling stage, an intra-specific cross was developed from CCRI35, tolerant to salinity, as female with Nan Dan (NH, sensitive to salinity, as the male. A genetic map of 5178 SNP markers was developed from 277 F2:3 populations. The map spanned 4768.098 cM, with an average distance of 0.92 cM. A total of 66 QTLs for 10 traits related to salinity were detected in three environments (0, 110, and 150 mM salt treatment. Only 14 QTLs were consistent, accounting for 2.72% to 9.87% of phenotypic variation. Parental contributions were found to be in the ratio of 3:1, 10 QTLs from the sensitive and four QTLs from the resistant parent. Five QTLs were located in At and nine QTLs in the Dt sub-genome. Moreover, eight clusters were identified, in which 12 putative key genes were found to be related to salinity. The GBS-SNPs-based genetic map developed is the first high-density genetic map that has the potential to provide deeper insights into upland cotton salinity tolerance. The 12 key genes found in this study could be used for QTL fine mapping and cloning for further studies.

  10. A statistical model for estimating maternal-zygotic interactions and parent-of-origin effects of QTLs for seed development.

    Directory of Open Access Journals (Sweden)

    Yanchun Li

    Full Text Available Proper development of a seed requires coordinated exchanges of signals among the three components that develop side by side in the seed. One of these is the maternal integument that encloses the other two zygotic components, i.e., the diploid embryo and its nurturing annex, the triploid endosperm. Although the formation of the embryo and endosperm contains the contributions of both maternal and paternal parents, maternally and paternally derived alleles may be expressed differently, leading to a so-called parent-of-origin or imprinting effect. Currently, the nature of how genes from the maternal and zygotic genomes interact to affect seed development remains largely unknown. Here, we present a novel statistical model for estimating the main and interaction effects of quantitative trait loci (QTLs that are derived from different genomes and further testing the imprinting effects of these QTLs on seed development. The experimental design used is based on reciprocal backcrosses toward both parents, so that the inheritance of parent-specific alleles could be traced. The computing model and algorithm were implemented with the maximum likelihood approach. The new strategy presented was applied to study the mode of inheritance for QTLs that control endoreduplication traits in maize endosperm. Monte Carlo simulation studies were performed to investigate the statistical properties of the new model with the data simulated under different imprinting degrees. The false positive rate of imprinting QTL discovery by the model was examined by analyzing the simulated data that contain no imprinting QTL. The reciprocal design and a series of analytical and testing strategies proposed provide a standard procedure for genomic mapping of QTLs involved in the genetic control of complex seed development traits in flowering plants.

  11. Manufacturer's Suggested Retail Prices

    NARCIS (Netherlands)

    Rosenkranz, S.|info:eu-repo/dai/nl/157222241

    2003-01-01

    Based on arguments of the `reference- dependent' theory of consumer choice we assume that a retailer's discount of a manufacturer's suggested retail price changes consumers' demand. We can show that the producer benefits from suggesting a retail price. If consumers are additionally sufficiently

  12. Identification of QTLs associated with resistance to Phomopsis pod blight (Diaporthe toxica) in Lupinus albus.

    Science.gov (United States)

    Cowley, Raymond; Luckett, David J; Ash, Gavin J; Harper, John D I; Vipin, Cina A; Raman, Harsh; Ellwood, Simon

    2014-05-01

    Phomopsis blight in Lupinus albus is caused by a fungal pathogen, Diaporthe toxica. It can invade all plant parts, leading to plant material becoming toxic to grazing animals, and potentially resulting in lupinosis. Identifying sources of resistance and breeding for resistance remains the best strategy for controlling Phomopsis and reducing lupinosis risks. However, loci associated with resistance to Phomopsis blight have not yet been identified. In this study, quantitative trait locus (QTL) analysis identified genomic regions associated with resistance to Phomopsis pod blight (PPB) using a linkage map of L. albus constructed previously from an F8 recombinant inbred line population derived from a cross between Kiev-Mutant (susceptible to PPB) and P27174 (resistant to PPB). Phenotyping was undertaken using a detached pod assay. In total, we identified eight QTLs for resistance to PPB on linkage group (LG) 3, LG6, LG10, LG12, LG17 and LG27 from different phenotyping environments. However, at least one QTL, QTL-5 on LG10 was consistently detected in both phenotyping environments and accounted for up to 28.2% of the total phenotypic variance. The results of this study showed that the QTL-2 on LG3 interacts epistatically with QTL-5 and QTL-6, which map on LG10 and LG12, respectively.

  13. Fine-mapping QTLs in advanced intercross lines and other outbred populations.

    Science.gov (United States)

    Gonzales, Natalia M; Palmer, Abraham A

    2014-08-01

    Quantitative genetic studies in model organisms, particularly in mice, have been extremely successful in identifying chromosomal regions that are associated with a wide variety of behavioral and other traits. However, it is now widely understood that identification of the underlying genes will be far more challenging. In the last few years, a variety of populations have been utilized in an effort to more finely map these chromosomal regions with the goal of identifying specific genes. The common property of these newer populations is that linkage disequilibrium spans relatively short distances, which permits fine-scale mapping resolution. This review focuses on advanced intercross lines (AILs) which are the simplest such population. As originally proposed in 1995 by Darvasi and Soller, an AIL is the product of intercrossing two inbred strains beyond the F2 generation. Unlike recombinant inbred strains, AILs are maintained as outbred populations; brother-sister matings are specifically avoided. Each generation of intercrossing beyond the F2 further degrades linkage disequilibrium between adjacent makers, which allows for fine-scale mapping of quantitative trait loci (QTLs). Advances in genotyping technology and techniques for the statistical analysis of AILs have permitted rapid advances in the application of AILs. We review some of the analytical issues and available software, including QTLRel, EMMA, EMMAX, GEMMA, TASSEL, GRAMMAR, WOMBAT, Mendel, and others.

  14. Genes and quality trait loci (QTLs) associated with firmness in Malus x domestica

    KAUST Repository

    Marondedze, Claudius

    2013-03-31

    Fruit firmness, a quality quantitative trait, has long been established as a key textural property and one of the essential parameters for estimating ripening and shelf life of apples. Loss of firmness, also referred to as fruit softening, is undesirable in apples and represents a serious problem for growers in many countries. This results in the reduction of apple shelf life and in turn influences its commercialization. Low firmness impacts negatively on the sensory values of juiciness, crunchiness and crispness. Fruit firmness is affected by the inheritance of alleles at multiple loci and their possible interactions with the environment. Identification of these loci is key for the determination of genetic candidate markers that can be implemented in marker assisted selection and breeding for trees and/or cultivars that can yield firmer fruits with economic value. In turn, this technique can help reduce the time needed to evaluate plants and new cultivars could become available faster. This review provides an overview of quantitative trait loci (QTL), including additional putative QTLs that we have identified, and genes associated with firmness and their importance to biotechnology, the breeding industry and eventually the consumers.

  15. Marker-based linkage map of Andean common bean (Phaseolus vulgaris L.) and mapping of QTLs underlying popping ability traits

    Science.gov (United States)

    2012-01-01

    Background Nuña bean is a type of ancient common bean (Phaseolus vulgaris L.) native to the Andean region of South America, whose seeds possess the unusual property of popping. The nutritional features of popped seeds make them a healthy low fat and high protein snack. However, flowering of nuña bean only takes place under short-day photoperiod conditions, which means a difficulty to extend production to areas where such conditions do not prevail. Therefore, breeding programs of adaptation traits will facilitate the diversification of the bean crops and the development of new varieties with enhanced healthy properties. Although the popping trait has been profusely studied in maize (popcorn), little is known about the biology and genetic basis of the popping ability in common bean. To obtain insights into the genetics of popping ability related traits of nuña bean, a comprehensive quantitative trait loci (QTL) analysis was performed to detect single-locus and epistatic QTLs responsible for the phenotypic variance observed in these traits. Results A mapping population of 185 recombinant inbred lines (RILs) derived from a cross between two Andean common bean genotypes was evaluated for three popping related traits, popping dimension index (PDI), expansion coefficient (EC), and percentage of unpopped seeds (PUS), in five different environmental conditions. The genetic map constructed included 193 loci across 12 linkage groups (LGs), covering a genetic distance of 822.1 cM, with an average of 4.3 cM per marker. Individual and multi-environment QTL analyses detected a total of nineteen single-locus QTLs, highlighting among them the co-localized QTLs for the three popping ability traits placed on LGs 3, 5, 6, and 7, which together explained 24.9, 14.5, and 25.3% of the phenotypic variance for PDI, EC, and PUS, respectively. Interestingly, epistatic interactions among QTLs have been detected, which could have a key role in the genetic control of popping. Conclusions

  16. Marker-based linkage map of Andean common bean (Phaseolus vulgaris L. and mapping of QTLs underlying popping ability traits

    Directory of Open Access Journals (Sweden)

    Yuste-Lisbona Fernando J

    2012-08-01

    Full Text Available Abstract Background Nuña bean is a type of ancient common bean (Phaseolus vulgaris L. native to the Andean region of South America, whose seeds possess the unusual property of popping. The nutritional features of popped seeds make them a healthy low fat and high protein snack. However, flowering of nuña bean only takes place under short-day photoperiod conditions, which means a difficulty to extend production to areas where such conditions do not prevail. Therefore, breeding programs of adaptation traits will facilitate the diversification of the bean crops and the development of new varieties with enhanced healthy properties. Although the popping trait has been profusely studied in maize (popcorn, little is known about the biology and genetic basis of the popping ability in common bean. To obtain insights into the genetics of popping ability related traits of nuña bean, a comprehensive quantitative trait loci (QTL analysis was performed to detect single-locus and epistatic QTLs responsible for the phenotypic variance observed in these traits. Results A mapping population of 185 recombinant inbred lines (RILs derived from a cross between two Andean common bean genotypes was evaluated for three popping related traits, popping dimension index (PDI, expansion coefficient (EC, and percentage of unpopped seeds (PUS, in five different environmental conditions. The genetic map constructed included 193 loci across 12 linkage groups (LGs, covering a genetic distance of 822.1 cM, with an average of 4.3 cM per marker. Individual and multi-environment QTL analyses detected a total of nineteen single-locus QTLs, highlighting among them the co-localized QTLs for the three popping ability traits placed on LGs 3, 5, 6, and 7, which together explained 24.9, 14.5, and 25.3% of the phenotypic variance for PDI, EC, and PUS, respectively. Interestingly, epistatic interactions among QTLs have been detected, which could have a key role in the genetic control of

  17. Pyramids of QTLs enhance host-plant resistance and Bt-mediated resistance to leaf-chewing insects in soybean.

    Science.gov (United States)

    Ortega, María A; All, John N; Boerma, H Roger; Parrott, Wayne A

    2016-04-01

    QTL-M and QTL-E enhance soybean resistance to insects. Pyramiding these QTLs with cry1Ac increases protection against Bt-tolerant pests, presenting an opportunity to effectively deploy Bt with host-plant resistance genes. Plant resistance to leaf-chewing insects minimizes the need for insecticide applications, reducing crop production costs and pesticide concerns. In soybean [Glycine max (L.) Merr.], resistance to a broad range of leaf-chewing insects is found in PI 229358 and PI 227687. PI 229358's resistance is conferred by three quantitative trait loci (QTLs): M, G, and H. PI 227687's resistance is conferred by QTL-E. The letters indicate the soybean Linkage groups (LGs) on which the QTLs are located. This study aimed to determine if pyramiding PI 229358 and PI 227687 QTLs would enhance soybean resistance to leaf-chewing insects, and if pyramiding these QTLs with Bt (cry1Ac) enhances resistance against Bt-tolerant pests. The near-isogenic lines (NILs): Benning(ME), Benning(MGHE), and Benning(ME+cry1Ac) were developed. Benning(ME) and Benning(MGHE) were evaluated in detached-leaf and greenhouse assays with soybean looper [SBL, Chrysodeixis includens (Walker)], corn earworm [CEW, Helicoverpa zea (Boddie)], fall armyworm [FAW, Spodoptera frugiperda (J.E. Smith)], and velvetbean caterpillar [VBC, Anticarsia gemmatalis (Hübner)]; and in field-cage assays with SBL. Benning(ME+cry1Ac) was tested in detached-leaf assays against SBL, VBC, and Southern armyworm [SAW, Spodoptera eridania (Cramer)]. In the detached-leaf assay, Benning(ME) showed the strongest antibiosis against CEW, FAW, and VBC. In field-cage conditions, Benning(ME) and Benning(MGHE) suffered 61 % less defoliation than Benning. Benning(ME+cry1Ac) was more resistant than Benning(ME) and Benning (cry1Ac) against SBL and SAW. Agriculturally relevant levels of resistance in soybean can be achieved with just two loci, QTL-M and QTL-E. ME+cry1Ac could present an opportunity to protect the durability of Bt

  18. Suggestive Objects at Work

    DEFF Research Database (Denmark)

    Ratner, Helene Gad

    2009-01-01

    In Western secular societies, spiritual life is no longer limited to classical religious institutions but can also be found at workplace organizations. While spirituality is conventionally understood as a subjective and internal process, this paper proposes the concept of ‘suggestive objects’, co...... scaffolding. This has deep implications for our understanding of the sacred, including a better appreciation of the way that suggestive objects make the sacred durable, the way they organize it....

  19. Suggestive techniques in advertising

    OpenAIRE

    Sora, Olena

    2011-01-01

    In my thesis I focused on a detailed analysis of suggestive techniques that appear in contemporary advertising. The issue of the effects of advertising has existed for many years and still staying timely. On the one side there are entrepreneurs and advertising agencies that are trying to influence opinions and suggest motivation for consuming. On the other side there is a potential customer, who is trying to obtain information about the product he needs and at the same time not letting anybod...

  20. Room-Temperature Energy-Sampling Kβ X-ray Emission Spectroscopy of the Mn4Ca Complex of Photosynthesis Reveals Three Manganese-Centered Oxidation Steps and Suggests a Coordination Change Prior to O2 Formation.

    Science.gov (United States)

    Zaharieva, Ivelina; Chernev, Petko; Berggren, Gustav; Anderlund, Magnus; Styring, Stenbjörn; Dau, Holger; Haumann, Michael

    2016-08-02

    In oxygenic photosynthesis, water is oxidized and dioxygen is produced at a Mn4Ca complex bound to the proteins of photosystem II (PSII). Valence and coordination changes in its catalytic S-state cycle are of great interest. In room-temperature (in situ) experiments, time-resolved energy-sampling X-ray emission spectroscopy of the Mn Kβ1,3 line after laser-flash excitation of PSII membrane particles was applied to characterize the redox transitions in the S-state cycle. The Kβ1,3 line energies suggest a high-valence configuration of the Mn4Ca complex with Mn(III)3Mn(IV) in S0, Mn(III)2Mn(IV)2 in S1, Mn(III)Mn(IV)3 in S2, and Mn(IV)4 in S3 and, thus, manganese oxidation in each of the three accessible oxidizing transitions of the water-oxidizing complex. There are no indications of formation of a ligand radical, thus rendering partial water oxidation before reaching the S4 state unlikely. The difference spectra of both manganese Kβ1,3 emission and K-edge X-ray absorption display different shapes for Mn(III) oxidation in the S2 → S3 transition when compared to Mn(III) oxidation in the S1 → S2 transition. Comparison to spectra of manganese compounds with known structures and oxidation states and varying metal coordination environments suggests a change in the manganese ligand environment in the S2 → S3 transition, which could be oxidation of five-coordinated Mn(III) to six-coordinated Mn(IV). Conceivable options for the rearrangement of (substrate) water species and metal-ligand bonding patterns at the Mn4Ca complex in the S2 → S3 transition are discussed.

  1. [Psychoanalysis and suggestion].

    Science.gov (United States)

    Thomä, H

    1977-01-01

    In the history of psychoanalysis the problem of suggestion has been a central one. At first it involved the necessity to establish the psychoanalytic technique as independent scientific paradigm in contrast to persuasion and hypnosis. However, it was not only the symptom-oriented suggestion that had to be given up for scientific reasons and reasons of treatment technique. Since professional and human factors as well could have influenced the psychoanalytic situation to revert to the traditional "suggestion", Freud has given some technical considerations (e.g. the mirror-analogy), that were meant to counteract the confusion of the psychoanalytic technique with the persuasive one that had to come up to late. The discovery of the transference phenomena has further complicated the problem. It became obvious that the capacity of the analyst to exert an influence and to have impact, originated in very basic human categories and their specific psychogenetic developments and distortions. This understanding contributed to the development of psychoanalytic theories of suggestibility. Until the present day the discovery of the transference phenomena has determined the discussions of psychoanalytic technique in term of the relationship between the special and general therapeutic factors (i.e. interpretation versus relationship). The departure from the therapeutic mode of persuasive suggestion and the introduction of psychoanalytic technique signaled the revolutionary paradigm of Sigmund Freud, i.e. the active participation of the patient and the process of observation. Often scientific problems related to this pradigm and suggestion are discussed concurrently.

  2. Open to Suggestion.

    Science.gov (United States)

    Journal of Reading, 1986

    1986-01-01

    Offers (1) suggestions on how to teach students the importance of regular study habits for learning to spell, (2) story ideas to help students get started with creative writing, and (3) a model of a daily record assignment book to help students organize and remember their homework assignments. (SRT)

  3. Comparative Analysis of Root Traits and the Associated QTLs for Maize Seedlings Grown in Paper Roll, Hydroponics and Vermiculite Culture System.

    Science.gov (United States)

    Liu, Zhigang; Gao, Kun; Shan, Shengchen; Gu, Riling; Wang, Zhangkui; Craft, Eric J; Mi, Guohua; Yuan, Lixing; Chen, Fanjun

    2017-01-01

    Root system architecture (RSA) plays an important role in the acquisition of both nitrogen (N) and phosphorus (P) from the environment. Currently RSA is rarely considered as criteria for selection to improve nutrient uptake efficiency in crop breeding. Under field conditions roots can be greatly influenced by uncontrolled environment factors. Therefore, it is necessary to develop fast selection methods for evaluating root traits of young seedlings in the lab which can then be related to high nutrient efficiency of adult plants in the field. Here, a maize recombination inbred line (RILs) population was used to compare the genetic relationship between RSA and nitrogen and phosphorous efficiency traits. The phenotypes of eight RSA-related traits were evaluated in young seedlings using three different growth systems (i.e., paper roll, hydroponics and vermiculite), and then subjected to correlation analysis with N efficiency and P efficiency related traits measured under field conditions. Quantitative trait loci (QTL) of RSA were determined and QTL co-localizations across different growth systems were further analyzed. Phenotypic associations were observed for most of RSA traits among all three culture systems. RSA-related traits in hydroponics and vermiculite weakly correlated with Nitrogen (NupE) uptake efficiency ( r = 0.17-0.31) and Phosphorus (PupE) uptake efficiency ( r = 0.22-0.34). This correlation was not found in the paper roll growth system. A total of 14 QTLs for RSA were identified in paper rolls, 18 in hydroponics, and 14 in vermiculite. Co-localization of QTLs for RSA traits were identified in six chromosome regions of bin 1.04/1.05, 1.06, 2.04/2.05, 3.04, 4.05, and 5.04/5.05. The results suggest the problem of using the phenotype from one growth system to predict those in another growth system. Assessing RSA traits at the seedling stage using either hydroponics or a vermiculite system appears better suited than the paper roll system as an important index

  4. Comparative Analysis of Root Traits and the Associated QTLs for Maize Seedlings Grown in Paper Roll, Hydroponics and Vermiculite Culture System

    Science.gov (United States)

    Liu, Zhigang; Gao, Kun; Shan, Shengchen; Gu, Riling; Wang, Zhangkui; Craft, Eric J.; Mi, Guohua; Yuan, Lixing; Chen, Fanjun

    2017-01-01

    Root system architecture (RSA) plays an important role in the acquisition of both nitrogen (N) and phosphorus (P) from the environment. Currently RSA is rarely considered as criteria for selection to improve nutrient uptake efficiency in crop breeding. Under field conditions roots can be greatly influenced by uncontrolled environment factors. Therefore, it is necessary to develop fast selection methods for evaluating root traits of young seedlings in the lab which can then be related to high nutrient efficiency of adult plants in the field. Here, a maize recombination inbred line (RILs) population was used to compare the genetic relationship between RSA and nitrogen and phosphorous efficiency traits. The phenotypes of eight RSA-related traits were evaluated in young seedlings using three different growth systems (i.e., paper roll, hydroponics and vermiculite), and then subjected to correlation analysis with N efficiency and P efficiency related traits measured under field conditions. Quantitative trait loci (QTL) of RSA were determined and QTL co-localizations across different growth systems were further analyzed. Phenotypic associations were observed for most of RSA traits among all three culture systems. RSA-related traits in hydroponics and vermiculite weakly correlated with Nitrogen (NupE) uptake efficiency (r = 0.17–0.31) and Phosphorus (PupE) uptake efficiency (r = 0.22–0.34). This correlation was not found in the paper roll growth system. A total of 14 QTLs for RSA were identified in paper rolls, 18 in hydroponics, and 14 in vermiculite. Co-localization of QTLs for RSA traits were identified in six chromosome regions of bin 1.04/1.05, 1.06, 2.04/2.05, 3.04, 4.05, and 5.04/5.05. The results suggest the problem of using the phenotype from one growth system to predict those in another growth system. Assessing RSA traits at the seedling stage using either hydroponics or a vermiculite system appears better suited than the paper roll system as an important

  5. Bridging the Rice Yield Gaps under Drought: QTLs, Genes, and their Use in Breeding Programs

    Directory of Open Access Journals (Sweden)

    Nitika Sandhu

    2017-04-01

    Full Text Available Rice is the staple food for more than half of the world’s population. Although rice production has doubled in the last 30 years as a result of the development of high-yield, widely adaptable, resource-responsive, semi-dwarf varieties, the threat of a food crisis remains as severe as it was 60 years ago due to the ever-increasing population, water scarcity, labor scarcity, shifting climatic conditions, pest/diseases, loss of productive land to housing, industries, rising sea levels, increasing incidences of drought, flood, urbanization, soil erosion, reduction in soil nutrient status, and environmental issues associated with high-input agriculture. Among these, drought is predicted to be the most severe stress that reduces rice yield. Systematic research on drought over the last 10 years has been conducted across institutes on physiology, breeding, molecular genetics, biotechnology, and cellular and molecular biology. This has provided a better understanding of plant drought mechanisms and has helped scientists to devise better strategies to reduce rice yield losses under drought stress. These include the identification of quantitative trait loci (QTLs for grain yield under drought as well as many agronomically important traits related to drought tolerance, marker-assisted pyramiding of genetic regions that increase yield under drought, development of efficient techniques for genetic transformation, complete sequencing and annotation of rice genomes, and synteny studies of rice and other cereal genomes. Conventional and marker-assisted breeding rice lines containing useful introgressed genes or loci have been field tested and released as varieties. Still, there is a long way to go towards developing drought-tolerant rice varieties by exploiting existing genetic diversity, identifying superior alleles for drought tolerance, understanding interactions among alleles for drought tolerance and their interaction with genetic backgrounds, and

  6. A maximum likelihood QTL analysis reveals common genome regions controlling resistance to Salmonella colonization and carrier-state

    Directory of Open Access Journals (Sweden)

    Thanh-Son Tran

    2012-05-01

    Full Text Available Abstract Background The serovars Enteritidis and Typhimurium of the Gram-negative bacterium Salmonella enterica are significant causes of human food poisoning. Fowl carrying these bacteria often show no clinical disease, with detection only established post-mortem. Increased resistance to the carrier state in commercial poultry could be a way to improve food safety by reducing the spread of these bacteria in poultry flocks. Previous studies identified QTLs for both resistance to carrier state and resistance to Salmonella colonization in the same White Leghorn inbred lines. Until now, none of the QTLs identified was common to the two types of resistance. All these analyses were performed using the F2 inbred or backcross option of the QTLExpress software based on linear regression. In the present study, QTL analysis was achieved using Maximum Likelihood with QTLMap software, in order to test the effect of the QTL analysis method on QTL detection. We analyzed the same phenotypic and genotypic data as those used in previous studies, which were collected on 378 animals genotyped with 480 genome-wide SNP markers. To enrich these data, we added eleven SNP markers located within QTLs controlling resistance to colonization and we looked for potential candidate genes co-localizing with QTLs. Results In our case the QTL analysis method had an important impact on QTL detection. We were able to identify new genomic regions controlling resistance to carrier-state, in particular by testing the existence of two segregating QTLs. But some of the previously identified QTLs were not confirmed. Interestingly, two QTLs were detected on chromosomes 2 and 3, close to the locations of the major QTLs controlling resistance to colonization and to candidate genes involved in the immune response identified in other, independent studies. Conclusions Due to the lack of stability of the QTLs detected, we suggest that interesting regions for further studies are those that were

  7. Identification of QTLs associated with oil content and mapping FAD2 genes and their relative contribution to oil quality in peanut (Arachis hypogaea L.).

    Science.gov (United States)

    Pandey, Manish K; Wang, Ming Li; Qiao, Lixian; Feng, Suping; Khera, Pawan; Wang, Hui; Tonnis, Brandon; Barkley, Noelle A; Wang, Jianping; Holbrook, C Corley; Culbreath, Albert K; Varshney, Rajeev K; Guo, Baozhu

    2014-12-10

    Peanut is one of the major source for human consumption worldwide and its seed contain approximately 50% oil. Improvement of oil content and quality traits (high oleic and low linoleic acid) in peanut could be accelerated by exploiting linked markers through molecular breeding. The objective of this study was to identify QTLs associated with oil content, and estimate relative contribution of FAD2 genes (ahFAD2A and ahFAD2B) to oil quality traits in two recombinant inbred line (RIL) populations. Improved genetic linkage maps were developed for S-population (SunOleic 97R × NC94022) with 206 (1780.6 cM) and T-population (Tifrunner × GT-C20) with 378 (2487.4 cM) marker loci. A total of 6 and 9 QTLs controlling oil content were identified in the S- and T-population, respectively. The contribution of each QTL towards oil content variation ranged from 3.07 to 10.23% in the S-population and from 3.93 to 14.07% in the T-population. The mapping positions for ahFAD2A (A sub-genome) and ahFAD2B (B sub-genome) genes were assigned on a09 and b09 linkage groups. The ahFAD2B gene (26.54%, 25.59% and 41.02% PVE) had higher phenotypic effect on oleic acid (C18:1), linoleic acid (C18:2), and oleic/linoleic acid ratio (O/L ratio) than ahFAD2A gene (8.08%, 6.86% and 3.78% PVE). The FAD2 genes had no effect on oil content. This study identified a total of 78 main-effect QTLs (M-QTLs) with up to 42.33% phenotypic variation (PVE) and 10 epistatic QTLs (E-QTLs) up to 3.31% PVE for oil content and quality traits. A total of 78 main-effect QTLs (M-QTLs) and 10 E-QTLs have been detected for oil content and oil quality traits. One major QTL (more than 10% PVE) was identified in both the populations for oil content with source alleles from NC94022 and GT-C20 parental genotypes. FAD2 genes showed high effect for oleic acid (C18:1), linoleic acid (C18:2), and O/L ratio while no effect on total oil content. The information on phenotypic effect of FAD2 genes for oleic acid, linoleic acid and O

  8. Identification of QTLs controlling grain protein concentration using a high-density SNP and SSR linkage map in barley (Hordeum vulgare L.).

    Science.gov (United States)

    Fan, Chaofeng; Zhai, Huijie; Wang, Huifang; Yue, Yafei; Zhang, Minghu; Li, Jinghui; Wen, Shaozhe; Guo, Ganggang; Zeng, Yawen; Ni, Zhongfu; You, Mingshan

    2017-07-11

    Grain protein concentration (GPC) is a major determinant of quality in barley (Hordeum vulgare L.). Breeding barley cultivars with high GPC has practical value for feed and food properties. The aim of the present study was to identify quantitative trait loci (QTLs) for GPC that could be detected under multiple environments. A population of 190 recombinant inbred lines (RILs) deriving from a cross between Chinese landrace ZGMLEL with high GPC (> 20%) and Australian cultivar Schooner was used for linkage and QTL analyses. The genetic linkage map spanned 2353.48 cM in length with an average locus interval of 2.33 cM. GPC was evaluated under six environments for the RIL population and the two parental lines. In total, six environmentally stable QTLs for GPC were detected on chromosomes 2H (1), 4H (1), 6H (1), and 7H (3) and the increasing alleles were derived from ZGMLEL. Notably, the three QTLs on chromosome 7H (QGpc.ZiSc-7H.1, QGpc.ZiSc-7H.2, and QGpc.ZiSc-7H.3) that linked in coupling phase were firstly identified. Moreover, the genetic effects of stable QTLs on chromosomes 2H, 6H and 7H were validated using near isogenic lines (NILs). Collectively, the identified QTLs expanded our knowledge about the genetic basis of GPC in barley and could be selected to develop cultivars with high grain protein concentration.

  9. QTLs for straw quality characteristics identified in recombinant inbred lines of a Hordeum vulgare x H spontaneum cross in a Mediterranean environment

    DEFF Research Database (Denmark)

    Grando, S.; Baum, M.; Ceccarelli, S.

    2005-01-01

    Barley straw is commonly used as animal feed in many developing countries. Even a small increase in its nutritive value can have a large impact on animal production, and hence, on rural livelihood and human nutrition. Straw quality is strongly affected by environmental factors and is, therefore...... neutral detergent fiber, acid detergent fiber, lignin, digestible organic matter in dry matter, voluntary intake, crude protein, and straw morphology (the percentage of blades, sheaths, and stems). Localization of QTLs was performed using Windows QTL Cartographer, version 2.0. Seventy-three QTLs were...... identified, the majority of which (17) in the driest of the four environments. Only six QTLs were identified. ed in two environments; in five cases, one of the two was the wettest environment. This is discussed in relation to the possibility of improving straw quality in favorable environments where yields...

  10. QTLs for resistance to the false brome rust Puccinia brachypodii in the model grass Brachypodium distachyon L.

    Science.gov (United States)

    Barbieri, Mirko; Marcel, Thierry C; Niks, Rients E; Francia, Enrico; Pasquariello, Marianna; Mazzamurro, Valentina; Garvin, David F; Pecchioni, Nicola

    2012-02-01

    The potential of the model grass Brachypodium distachyon L. (Brachypodium) for studying grass-pathogen interactions is still underexploited. We aimed to identify genomic regions in Brachypodium associated with quantitative resistance to the false brome rust fungus Puccinia brachypodii . The inbred lines Bd3-1 and Bd1-1, differing in their level of resistance to P. brachypodii, were crossed to develop an F(2) population. This was evaluated for reaction to a virulent isolate of P. brachypodii at both the seedling and advanced growth stages. To validate the results obtained on the F(2), resistance was quantified in F(2)-derived F(3) families in two experiments. Disease evaluations showed quantitative and transgressive segregation for resistance. A new AFLP-based Brachypodium linkage map consisting of 203 loci and spanning 812 cM was developed and anchored to the genome sequence with SSR and SNP markers. Three false brome rust resistance QTLs were identified on chromosomes 2, 3, and 4, and they were detected across experiments. This study is the first quantitative trait analysis in Brachypodium. Resistance to P. brachypodii was governed by a few QTLs: two acting at the seedling stage and one acting at both seedling and advanced growth stages. The results obtained offer perspectives to elucidate the molecular basis of quantitative resistance to rust fungi.

  11. Linkage disequilibrium, SNP frequency change due to selection, and association mapping in popcorn chromosome regions containing QTLs for quality traits

    Directory of Open Access Journals (Sweden)

    Geísa Pinheiro Paes

    2016-03-01

    Full Text Available Abstract The objectives of this study were to assess linkage disequilibrium (LD and selection-induced changes in single nucleotide polymorphism (SNP frequency, and to perform association mapping in popcorn chromosome regions containing quantitative trait loci (QTLs for quality traits. Seven tropical and two temperate popcorn populations were genotyped for 96 SNPs chosen in chromosome regions containing QTLs for quality traits. The populations were phenotyped for expansion volume, 100-kernel weight, kernel sphericity, and kernel density. The LD statistics were the difference between the observed and expected haplotype frequencies (D, the proportion of D relative to the expected maximum value in the population, and the square of the correlation between the values of alleles at two loci. Association mapping was based on least squares and Bayesian approaches. In the tropical populations, D-values greater than 0.10 were observed for SNPs separated by 100-150 Mb, while most of the D-values in the temperate populations were less than 0.05. Selection for expansion volume indirectly led to increase in LD values, population differentiation, and significant changes in SNP frequency. Some associations were observed for expansion volume and the other quality traits. The candidate genes are involved with starch, storage protein, lipid, and cell wall polysaccharides synthesis.

  12. Linkage disequilibrium, SNP frequency change due to selection, and association mapping in popcorn chromosome regions containing QTLs for quality traits.

    Science.gov (United States)

    Paes, Geísa Pinheiro; Viana, José Marcelo Soriano; Silva, Fabyano Fonseca E; Mundim, Gabriel Borges

    2016-03-01

    The objectives of this study were to assess linkage disequilibrium (LD) and selection-induced changes in single nucleotide polymorphism (SNP) frequency, and to perform association mapping in popcorn chromosome regions containing quantitative trait loci (QTLs) for quality traits. Seven tropical and two temperate popcorn populations were genotyped for 96 SNPs chosen in chromosome regions containing QTLs for quality traits. The populations were phenotyped for expansion volume, 100-kernel weight, kernel sphericity, and kernel density. The LD statistics were the difference between the observed and expected haplotype frequencies (D), the proportion of D relative to the expected maximum value in the population, and the square of the correlation between the values of alleles at two loci. Association mapping was based on least squares and Bayesian approaches. In the tropical populations, D-values greater than 0.10 were observed for SNPs separated by 100-150 Mb, while most of the D-values in the temperate populations were less than 0.05. Selection for expansion volume indirectly led to increase in LD values, population differentiation, and significant changes in SNP frequency. Some associations were observed for expansion volume and the other quality traits. The candidate genes are involved with starch, storage protein, lipid, and cell wall polysaccharides synthesis.

  13. Introgression of QTLs Controlling Spikelet Fertility Maintains Membrane Integrity and Grain Yield in Improved White Ponni Derived Progenies Exposed to Heat Stress

    Directory of Open Access Journals (Sweden)

    P. Vivitha

    2017-01-01

    Full Text Available To increase the thermotolerance of improved White Ponni (IWP, two quantitative trait loci (QTLs, qHTSF1.1 and qHTSF4.1, controlling spikelet fertility under high-temperature stress, were introgressed from Nagina 22 into IWP through marker-assisted breeding. The progenies were subjected to foreground selection of target QTLs using simple sequence repent markers RM431 and RM5757 linked to qHTSF1.1 and qHTSF4.1, respectively. At each generation, foreground selection with single target QTL or both QTLs was done together. The QTL-positive plants were forwarded to next generation by selfing. The F2:3 progenies were subjected to phenotypic analyses under high-temperature stress at the flowering stage. Chlorophyll stability index, malondialdehyde content, grain yield, and yield-related components of the F2:3 progenies were measured. The progenies IWP-295, IWP-277 and IWP-246 harboring both qHTSF1.1 and qHTSF4.1 showed higher fertility percentages under high-temperature stress at the flowering stage. These QTLs were responsible for maintaining membrane integrity and yield under elevated temperature conditions.

  14. Mapping QTLs for 100-seed weight in an interspecific soybean cross of Williams 82 (Glycine max) x PI 366121 (Glycine soja)

    Science.gov (United States)

    100-seed weight is a critical component for soybean quality and yield. The objective of the present study was to identify quantitative trait loci (QTLs) for 100-seed weight using 169 recombinant inbred lines (RILs) derived from the cross of Williams 82 x PI 366121. The parental lines and RILs were g...

  15. Identification of QTLs for grain yield and grain-related traits of maize (Zea mays L.) using an AFLP-map, different testers, and cofactor analysis

    NARCIS (Netherlands)

    Ajimone Marsan, P.; Gorni, C.; Chitto, A.; Redaelli, R.; Vijk, van R.; Stam, P.; Motto, M.

    2001-01-01

    Abstract We exploited the AFLP?1(AFLP? is a registered trademark of Keygene, N.V.) technique to map and characterise quantitative trait loci (QTLs) for grain yield and two grain-related traits of a maize segregating population. Two maize elite inbred lines were crossed to produce 229 F2 individuals

  16. Mapping QTLs for Fertility Restoration of Different Cytoplasmic Male Sterility Types in Rice Using Two Oryza sativa ×O. rufipogon Backcross Inbred Line Populations.

    Science.gov (United States)

    Hu, Biao-Lin; Xie, Jian-Kun; Wan, Yong; Zhang, Jin-Wei; Zhang, Fan-Tao; Li, Xia

    2016-01-01

    Hybrid rice breeding using cytoplasmic male sterility/fertility restoration (CMS/Rf) systems plays an important role in ensuring global food security. Two backcross inbred line (BIL) populations derived from either Xieqingzao B (XB)//XB/Dongxiang wild rice (DWR) (XXD) or XB//DWR/XB (XDX) were used to detect quantitative trait loci (QTLs) for fertility restoration of Dwarf wild abortive- (DA-), Indonesia Paddy- (ID-), and DWR-type CMS in rice. Lines with ID- and DA-type CMS were testcrossed with both the XXD- and XDX-BILs, while the line with DWR-type CMS was testcrossed with the XDX-BILs only. A total of 16 QTLs for fertility restoration of CMS systems were identified, including three for DWR-type CMS, six for DA-type CMS, and seven for ID-type CMS. All of the additive alleles in the QTLs were derived from Oryza rufipogon. Eleven QTLs were clustered in five chromosomal regions, indicating that common Rf loci restored different CMS systems, and the favorable O. rufipogon alleles could be used to develop restorer lines for various CMS types by marker-assisted selection.

  17. Meta-analysis of cotton fiber quality QTLs across diverse environments in a Gossypium hirsutum x G. barbadense RIL population

    Directory of Open Access Journals (Sweden)

    Giband Marc

    2010-06-01

    Full Text Available Abstract Background Cotton fibers (produced by Gossypium species are the premier natural fibers for textile production. The two tetraploid species, G. barbadense (Gb and G. hirsutum (Gh, differ significantly in their fiber properties, the former having much longer, finer and stronger fibers that are highly prized. A better understanding of the genetics and underlying biological causes of these differences will aid further improvement of cotton quality through breeding and biotechnology. We evaluated an inter-specific Gh × Gb recombinant inbred line (RIL population for fiber characteristics in 11 independent experiments under field and glasshouse conditions. Sites were located on 4 continents and 5 countries and some locations were analyzed over multiple years. Results The RIL population displayed a large variability for all major fiber traits. QTL analyses were performed on a per-site basis by composite interval mapping. Among the 651 putative QTLs (LOD > 2, 167 had a LOD exceeding permutation based thresholds. Coincidence in QTL location across data sets was assessed for the fiber trait categories strength, elongation, length, length uniformity, fineness/maturity, and color. A meta-analysis of more than a thousand putative QTLs was conducted with MetaQTL software to integrate QTL data from the RIL and 3 backcross populations (from the same parents and to compare them with the literature. Although the global level of congruence across experiments and populations was generally moderate, the QTL clustering was possible for 30 trait x chromosome combinations (5 traits in 19 different chromosomes where an effective co-localization of unidirectional (similar sign of additivity QTLs from at least 5 different data sets was observed. Most consistent meta-clusters were identified for fiber color on chromosomes c6, c8 and c25, fineness on c15, and fiber length on c3. Conclusions Meta-analysis provided a reliable means of integrating phenotypic and

  18. QTL analysis of root morphology, flowering time, and yield reveals trade-offs in response to drought in Brassica napus.

    Science.gov (United States)

    Fletcher, Richard S; Mullen, Jack L; Heiliger, Annie; McKay, John K

    2015-01-01

    Drought escape and dehydration avoidance represent alternative strategies for drought adaptation in annual crops. The mechanisms underlying these two strategies are reported to have a negative correlation, suggesting a trade-off. We conducted a quantitative trait locus (QTL) analysis of flowering time and root mass, traits representing each strategy, in Brassica napus to understand if a trade-off exists and what the genetic basis might be. Our field experiment used a genotyped population of doubled haploid lines and included both irrigated and rainfed treatments, allowing analysis of plasticity in each trait. We found strong genetic correlations among all traits, suggesting a trade-off among traits may exist. Summing across traits and treatments we found 20 QTLs, but many of these co-localized to two major QTLs, providing evidence that the trade-off is genetically constrained. To understand the mechanistic relationship between root mass, flowering time, and QTLs, we analysed the data by conditioning upon correlated traits. Our results suggest a causal model where such QTLs affect root mass directly as well as through their impacts on flowering time. Additionally, we used draft Brassica genomes to identify orthologues of well characterized Arabidopsis thaliana flowering time genes as candidate genes. This research provides valuable clues to breeding for drought adaptation as it is the first to analyse the inheritance of the root system in B. napus in relation to drought. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  19. Tagging QTLs for late blight resistance and plant maturity from diploid wild relatives in a cultivated potato (Solanum tuberosum) background.

    Science.gov (United States)

    Sliwka, J; Jakuczun, H; Lebecka, R; Marczewski, W; Gebhardt, C; Zimnoch-Guzowska, E

    2007-06-01

    Phytophthora infestans causes an economically important disease of potato called late blight. The epidemic is controlled chemically but resistant potatoes can become an environment-friendly and financially justified alternative solution. The use of diploid Solanum tuberosum derived from European tetraploid cultivars enabled the introgression of novel genes encoding foliage resistance and tuber resistance from other species into the modern cultivated potato gene pool. This study evaluated the resistance of the obtained hybrids, its quality, expression in leaflets and tubers and its relation to the length of vegetation period. We also identified genetic loci involved in late blight resistance and the length of vegetation period. A family of 156 individuals segregating for resistance to late blight was assessed by three laboratory methods: detached leaflet, tuber slice and whole tuber test, repeatedly over 5 years. Length of vegetation period was estimated by a field test over 2 years. The phenotypic distributions of all traits were close to normal. Using sequence-specific PCR markers of known chromosomal position on the potato genetic map, six quantitative trait loci (QTLs) for resistance and length of vegetation period were identified. The most significant and robust QTL were located on chromosomes III (explaining 17.3% of variance observed in whole tuber tests), IV (15.5% of variance observed in slice tests), X (15.6% of variance observed in leaflet tests) and V (19.9% of variance observed in length of vegetation period). Genetic characterization of these novel resistance sources can be valuable for potato breeders and the knowledge that the most prominent QTLs for resistance and vegetation period length do not overlap in this material is promising with respect to breeding early potatoes resistant to P. infestans.

  20. Panicle blast 1 (Pb1) resistance is dependent on at least four QTLs in the rice genome.

    Science.gov (United States)

    Inoue, Haruhiko; Nakamura, Mitsuru; Mizubayashi, Tatsumi; Takahashi, Akira; Sugano, Shoji; Fukuoka, Shuuichi; Hayashi, Nagao

    2017-12-01

    Rice blast is the most serious disease afflicting rice and there is an urgent need for the use of disease resistance (R) genes in blast tolerance breeding programs. Pb1 is classified as a quantitative resistance gene and it does not have fungal specificity. Pb1-mediated resistance develops in the latter stages of growth. However, some cultivars, such as Kanto209 (K209), cultivar name Satojiman, despite possessing Pb1, do not exert resistance to rice blast during the reproductive stage. We found that the expression of WRKY45 gene downstream of Pb1 was weakly induced by rice blast inoculation at the full heading stage in K209. Genetic analysis using the SNP-based Golden Gate assay of K209 crossing with Koshihikari Aichi SBL (KASBL) found at least four regions related to the resistance in the rice genome (Chr8, Chr9, Chr7, Chr11). Mapping of QTL related to Chr7 confirmed the existence of factors that were required for the resistance of Pb1 in the 22 to 23 Mbp region of the rice genome. We clarified how the K209 cultivar is vulnerable to the blast disease despite possessing Pb1 and found the DNA marker responsible for the quantitative resistance of Pb1. We identified the QTL loci required for Pb1-mediated resistance to rice panicle blast. Pb1 was negatively dependent on at least three QTLs, 7, 9 and 11, and positively dependent on one, QTL 8, in the K209 genome. This finding paves the way for creating a line to select optimal QTLs in order to make use of Pb1-mediated resistance more effectively.

  1. High-density genetic map construction and QTLs analysis of grain yield-related traits in sesame (Sesamum indicum L.) based on RAD-Seq techonology.

    Science.gov (United States)

    Wu, Kun; Liu, Hongyan; Yang, Minmin; Tao, Ye; Ma, Huihui; Wu, Wenxiong; Zuo, Yang; Zhao, Yingzhong

    2014-10-10

    Sesame (Sesamum indicum L., 2n = 26) is an important oilseed crop with an estimated genome size of 369 Mb. The genetic basis, including the number and locations of quantitative trait loci (QTLs) of sesame grain yield and quality remain poorly understood, due in part to the lack of reliable markers and genetic maps. Here we report on the construction of a hitherto most high-density genetic map of sesame using the restriction-site associated DNA sequencing (RAD-seq) combined with 89 PCR markers, and the identification of grain yield-related QTLs using a recombinant inbred line (RIL) population. In total, 3,769 single-nucleotide polymorphism (SNP) markers were identified from RAD-seq, and 89 polymorphic PCR markers were identified including 44 expressed sequence tag-simple sequence repeats (EST-SSRs), 10 genomic-SSRs and 35 Insertion-Deletion markers (InDels). The final map included 1,230 markers distributed on 14 linkage groups (LGs) and was 844.46 cM in length with an average of 0.69 cM between adjacent markers. Using this map and RIL population, we detected 13 QTLs on 7 LGs and 17 QTLs on 10 LGs for seven grain yield-related traits by the multiple interval mapping (MIM) and the mixed linear composite interval mapping (MCIM), respectively. Three major QTLs had been identified using MIM with R2 > 10.0% or MCIM with ha 2 > 5.0%. Two co-localized QTL groups were identified that partially explained the correlations among five yield-related traits. Three thousand eight hundred and four pairs of new DNA markers including SNPs and InDels were developed by RAD-seq, and a so far most high-density genetic map was constructed based on these markers in combination with SSR markers. Several grain yield-related QTLs had been identified using this population and genetic map. We report here the first QTL mapping of yield-related traits with a high-density genetic map using a RIL population in sesame. Results of this study solidified the basis for studying important agricultural

  2. Genome-wide Association Mapping of Quantitative Trait Loci (QTLs) for Contents of Eight Elements in Brown Rice (Oryza sativa L.).

    Science.gov (United States)

    Nawaz, Zarqa; Kakar, Kaleem U; Li, Xiao-bai; Li, Shan; Zhang, Bin; Shou, Hui-xia; Shu, Qing-yao

    2015-09-16

    An association mapping of quantitative trait loci (QTLs) regulating the concentrations of eight elements in brown rice (Oryza sativa L.) was performed using USDA mini-core subset cultivated in two different environments. In addition, correlation between the grain elemental concentrations was also studied. A total of 60 marker loci associated with 8 grain elemental concentrations were identified, and these loci were clustered into 37 genomic regions. Twenty new QTLs were found to be associated with important elements such as Zn, Fe, and P, along with others. Fe concentration was associated with the greatest number of markers in two environments. In addition, several important elemental/metal transporter genes were identified in a few mapped regions. Positive correlation was observed within all grain elemental concentrations. In summary, the results provide insight into the genetic basis of rice grain element accumulation and may help in the identification of genes associated with the accumulation of Zn, Fe, and other essential elements in rice.

  3. Pyramiding of drought yield QTLs into a high quality Malaysian rice cultivar MRQ74 improves yield under reproductive stage drought.

    Science.gov (United States)

    Shamsudin, Noraziyah Abd Aziz; Swamy, B P Mallikarjuna; Ratnam, Wickneswari; Sta Cruz, Ma Teressa; Sandhu, Nitika; Raman, Anitha K; Kumar, Arvind

    2016-12-01

    With the objective of improving the grain yield (GY) of the Malaysian high quality rice cultivar MRQ74 under reproductive stage drought stress (RS), three drought yield QTLs, viz. qDTY 2.2, qDTY 3.1 , and qDTY 12.1 were pyramided by marker assisted breeding (MAB). Foreground selection using QTL specific markers, recombinant selection using flanking markers, and background selections were performed in every generation. BC1F3 derived pyramided lines (PLs) with different combinations of qDTY 2.2, qDTY 3.1 , and qDTY 12.1 were evaluated under both RS and non-stress (NS) during the dry season (DS) of 2013 and 2014 at IRRI. The GY reductions in RS trials compared to NS trials ranged from 79 to 99 %. Plant height (PH) was reduced and days to flowering (DTF) was delayed under RS. Eleven BC1F5 MRQ74 PLs with yield advantages of 1009 to 3473 kg ha(-1) under RS and with yields equivalent to MRQ74 under NS trials were identified as promising drought tolerance PLs. Five best PLs, IR 98010-126-708-1-4, IR 98010-126-708-1-3, IR 98010-126-708-1-5, IR 99616-44-94-1-1, and IR 99616-44-94-1-2 with a yield advantage of more than 1000 kg ha(-1) under RS and with yield potential equivalent to that of MRQ74 under NS were selected. The effect of three drought grain yield QTLs under RS in MRQ74 was validated. Under NS, PLs with two qDTY combinations (qDTY 2.2 + qDTY 12.1 ) performed better than PLs with other qDTY combinations, indicating the presence of a positive interaction between qDTY 2.2 and qDTY 12.1 in the MRQ74 background. Drought tolerant MRQ74 PLs with a yield advantage of more than 1000 kg ha(-1) under RS were developed. Differential yield advantages of different combinations of the qDTYs indicate a differential synergistic relationship among qDTYs.

  4. A major QTL, which is co-located with cly1, and two minor QTLs are associated with glume opening angle in barley (Hordeum vulgare L.

    Directory of Open Access Journals (Sweden)

    Xinzhong Zhang

    2016-10-01

    Full Text Available Cleistogamous and chasmogamous are two opposing phenomena for flowering in barley. Cleistogamy limits the rate of outcrossing, and increases the cost of producing hybrid barley seeds. Selecting chasmogamous lines with a large glume opening angle is essential for the utilization of barley heterosis. In the current study, 247 DH lines derived from a cross between Yangnongpi7 and Yang0187 were used to identify and validate QTLs associated with the glume opening angle in different environments using SSR markers. Three QTLs associated with barley glume opening angle were mapped on chromosomes 2H and 7H. The major QTL QGOA-2H-2 was mapped on chromosome 2H with the flanking markers of KDH and GBM1498, explaining 63.92% of the phenotypic variation. The marker KDH was developed from the gene Cly1, the candidate gene for QGOA-2H-2. This new marker can be used to identify barley chasmogamous lines with a large glume opening angle. The two minor QTLs were validated at all three locations across two seasons after removing DH lines carrying the candidate gene Cly1 of QGOA-2H-2.

  5. Characterization of opaque2 modifier QTLs and candidate genes in recombinant inbred lines derived from the K0326Y quality protein maize inbred

    KAUST Repository

    Holding, David R.

    2010-11-13

    Quality protein maize (QPM) is a high lysine-containing corn that is based on genetic modification of the opaque2 (o2) mutant. In QPM, modifier genes convert the starchy endosperm of o2 to the vitreous phenotype of wild type maize. There are multiple, unlinked o2 modifier loci (Opm) in QPM and their nature and mode of action are unknown. We previously identified seven Opm QTLs and characterized 16 genes that are differentially up-regulated at a significant level in K0326Y QPM, compared to the starchy endosperm mutant W64Ao2. In order to further characterize these Opm QTLs and the genes up-regulated in K0326Y QPM, we created a population of 314 recombinant inbred lines (RILs) from a cross between K0326Y QPM and W64Ao2. The RILs were characterized for three traits associated with endosperm texture: vitreousness, density and hardness. Genetic linkage analysis of the RIL population confirmed three of the previously identified QTLs associated with o2 endosperm modification in K0326Y QPM. Many of the genes up-regulated in K0326Y QPM showed substantially higher levels of expression in vitreous compared with opaque RILs. These included genes associated with the upstream regulation of the ethylene response pathway, and a gene encoding a regulatory subunit of pyrophosphate-dependent fructose-6-phosphate 1-phosphotransferase, an adaptive enzyme of the glycolytic pathway. © 2010 Springer-Verlag.

  6. Mapping of QTLs for frost tolerance and heading time using SSR ...

    African Journals Online (AJOL)

    The progeny of individual F2 plants were used as F2:3 families for the assessment of LT50 and heading time. Single marker analysis revealed that seven markers with total of 27% of phenotypic variance determination linked to LT50 and five markers linked to the heading time. Two markers that were located on 2B and 5A ...

  7. A RAD tag derived marker based eggplant linkage map and the location of QTLs determining anthocyanin pigmentation.

    Directory of Open Access Journals (Sweden)

    Lorenzo Barchi

    Full Text Available Both inter- and intra-specific maps have been developed in eggplant (Solanum melongena L.. The former benefit from an enhanced frequency of marker polymorphism, but their relevance to marker-assisted crop breeding is limited. Combining the restriction-site associated DNA strategy with high throughput sequencing has facilitated the discovery of a large number of functional single nucleotide polymorphism (SNP markers discriminating between the two eggplant mapping population parental lines '305E40' and '67/3'. A set of 347 de novo SNPs, together with 84 anchoring markers, were applied to the F(2 mapping population bred from the cross '305E40' x '67/3' to construct a linkage map. In all, 415 of the 431 markers were assembled into twelve major and one minor linkage group, spanning 1,390 cM, and the inclusion of established markers allowed each linkage group to be assigned to one of the 12 eggplant chromosomes. The map was then used to discover the genetic basis of seven traits associated with anthocyanin content. Each of the traits proved to be controlled by between one and six quantitative trait loci (QTL, of which at least one was a major QTL. Exploitation of syntenic relationships between the eggplant and tomato genomes facilitated the identification of potential candidate genes for the eggplant QTLs related to anthocyanin accumulation. The intra-specific linkage map should have utility for elucidating the genetic basis of other phenotypic traits in eggplant.

  8. Identification of QTLs Associated with Callogenesis and Embryogenesis in Oil Palm Using Genetic Linkage Maps Improved with SSR Markers

    Science.gov (United States)

    Ting, Ngoot-Chin; Jansen, Johannes; Nagappan, Jayanthi; Ishak, Zamzuri; Chin, Cheuk-Weng; Tan, Soon-Guan; Cheah, Suan-Choo; Singh, Rajinder

    2013-01-01

    Clonal reproduction of oil palm by means of tissue culture is a very inefficient process. Tissue culturability is known to be genotype dependent with some genotypes being more amenable to tissue culture than others. In this study, genetic linkage maps enriched with simple sequence repeat (SSR) markers were developed for dura (ENL48) and pisifera (ML161), the two fruit forms of oil palm, Elaeis guineensis. The SSR markers were mapped onto earlier reported parental maps based on amplified fragment length polymorphism (AFLP) and restriction fragment length polymorphism (RFLP) markers. The new linkage map of ENL48 contains 148 markers (33 AFLPs, 38 RFLPs and 77 SSRs) in 23 linkage groups (LGs), covering a total map length of 798.0 cM. The ML161 map contains 240 markers (50 AFLPs, 71 RFLPs and 119 SSRs) in 24 LGs covering a total of 1,328.1 cM. Using the improved maps, two quantitative trait loci (QTLs) associated with tissue culturability were identified each for callusing rate and embryogenesis rate. A QTL for callogenesis was identified in LGD4b of ENL48 and explained 17.5% of the phenotypic variation. For embryogenesis rate, a QTL was detected on LGP16b in ML161 and explained 20.1% of the variation. This study is the first attempt to identify QTL associated with tissue culture amenity in oil palm which is an important step towards understanding the molecular processes underlying clonal regeneration of oil palm. PMID:23382832

  9. Identification of QTLs associated with callogenesis and embryogenesis in oil palm using genetic linkage maps improved with SSR markers.

    Directory of Open Access Journals (Sweden)

    Ngoot-Chin Ting

    Full Text Available Clonal reproduction of oil palm by means of tissue culture is a very inefficient process. Tissue culturability is known to be genotype dependent with some genotypes being more amenable to tissue culture than others. In this study, genetic linkage maps enriched with simple sequence repeat (SSR markers were developed for dura (ENL48 and pisifera (ML161, the two fruit forms of oil palm, Elaeis guineensis. The SSR markers were mapped onto earlier reported parental maps based on amplified fragment length polymorphism (AFLP and restriction fragment length polymorphism (RFLP markers. The new linkage map of ENL48 contains 148 markers (33 AFLPs, 38 RFLPs and 77 SSRs in 23 linkage groups (LGs, covering a total map length of 798.0 cM. The ML161 map contains 240 markers (50 AFLPs, 71 RFLPs and 119 SSRs in 24 LGs covering a total of 1,328.1 cM. Using the improved maps, two quantitative trait loci (QTLs associated with tissue culturability were identified each for callusing rate and embryogenesis rate. A QTL for callogenesis was identified in LGD4b of ENL48 and explained 17.5% of the phenotypic variation. For embryogenesis rate, a QTL was detected on LGP16b in ML161 and explained 20.1% of the variation. This study is the first attempt to identify QTL associated with tissue culture amenity in oil palm which is an important step towards understanding the molecular processes underlying clonal regeneration of oil palm.

  10. REVIEW: Genetic Diversity: Detection of Gene Variation at the DNA Level and Utilization of Gene Markers on Locating QTLs

    Directory of Open Access Journals (Sweden)

    SUTARNO

    2003-01-01

    Full Text Available Advanced techniques of molecular biology have provided the opportunity to study genetic diversity within and among breeds at the single gene level. Many DNA markers, either of genomic DNA or cytoplasmic DNA, have been generated recently by utilizing molecular techniques, such as RFLP, microsatellites, PCR-RFLP, RAPD, sequencing etc. PCR-based techniques have recently progressed rapidly for the detection of both known- and unknown-mutation detections that may be applied in locating gene marker for economically important traits. There are basically two different approaches of locating quantitative trait loci (QTLs, candidate gene and random approaches. The first approach is based on prior supporting knowledge of physiological and biochemical evidence, showing that the gene is involved in the trait(s of interest, while the random marker approach attempts to locate gene markers by measuring genotypes at a large number of loci with unknown phenotypic effects, in the hope that the loci are linked to a QTL influencing the trait of interest.

  11. A dense SNP genetic map constructed using restriction site-associated DNA sequencing enables detection of QTLs controlling apple fruit quality.

    Science.gov (United States)

    Sun, Rui; Chang, Yuansheng; Yang, Fengqiu; Wang, Yi; Li, Hui; Zhao, Yongbo; Chen, Dongmei; Wu, Ting; Zhang, Xinzhong; Han, Zhenhai

    2015-10-05

    Genetic map based quantitative trait locus (QTL) analysis is an important method for studying important horticultural traits in apple. To facilitate molecular breeding studies of fruit quality traits in apple, we aim to construct a high density map which was efficient for QTL mapping and possible to search for candidate genes directly in mapped QTLs regions. A total of 1733 F1 seedlings derived from 'Jonathan' × 'Golden Delicious' was used for the map constructionand QTL analysis. The SNP markers were developed by restriction site-associated DNA sequencing (RADseq). Phenotyping data of fruit quality traits were calculated in 2008-2011. Once QTLs were mapped, candidate genes were searched for in the corresponding regions of the apple genome sequence underlying the QTLs. Then some of the candidate genes were validated using real-time PCR. A high-density genetic map with 3441 SNP markers from 297 individuals was generated. Of the 3441 markers, 2017 were mapped to 'Jonathan' with a length of 1343.4 cM and the average distance between markers was 0.67 cM, 1932 were mapped to 'Golden Delicious' with a length of 1516.0 cM and the average distance between markers was 0.78 cM. Twelve significant QTLs linked to the control of fruit weight, fruit firmness, sugar content and fruit acidity were mapped to seven linkage groups. Based on gene annotation, 80, 64 and 17 genes related to fruit weight, fruit firmness and fruit acidity, respectively, were analyzed.Among the 17 candidate genes associated with control of fruit acidity, changes in the expression of MDP0000582174 (MdMYB4) were in agreement with the pattern of changes in malic acid content in apple during ripening, and the relative expression of MDP0000239624 (MdME) was significantly correlated withfruit acidity. We demonstrated the construction of a dense SNP genetic map in apple using next generation sequencing and that the increased resolution enabled the detection of narrow interval QTLs linked to the three fruit

  12. Identification of a Rice stripe necrosis virus resistance locus and yield component QTLs using Oryza sativa × O. glaberrima introgression lines

    Science.gov (United States)

    2010-01-01

    Background Developing new population types based on interspecific introgressions has been suggested by several authors to facilitate the discovery of novel allelic sources for traits of agronomic importance. Chromosome segment substitution lines from interspecific crosses represent a powerful and useful genetic resource for QTL detection and breeding programs. Results We built a set of 64 chromosome segment substitution lines carrying contiguous chromosomal segments of African rice Oryza glaberrima MG12 (acc. IRGC103544) in the genetic background of Oryza sativa ssp. tropical japonica (cv. Caiapó). Well-distributed simple-sequence repeats markers were used to characterize the introgression events. Average size of the substituted chromosomal segments in the substitution lines was about 10 cM and covered the whole donor genome, except for small regions on chromosome 2 and 4. Proportions of recurrent and donor genome in the substitution lines were 87.59% and 7.64%, respectively. The remaining 4.78% corresponded to heterozygotes and missing data. Strong segregation distortion was found on chromosomes 3 and 6, indicating the presence of interspecific sterility genes. To illustrate the advantages and the power of quantitative trait loci (QTL) detection using substitution lines, a QTL detection was performed for scored traits. Transgressive segregation was observed for several traits measured in the population. Fourteen QTLs for plant height, tiller number per plant, panicle length, sterility percentage, 1000-grain weight and grain yield were located on chromosomes 1, 3, 4, 6 and 9. Furthermore, a highly significant QTL controlling resistance to the Rice stripe necrosis virus was located between SSR markers RM202-RM26406 (44.5-44.8 cM) on chromosome 11. Conclusions Development and phenotyping of CSSL libraries with entire genome coverage represents a useful strategy for QTL discovery. Mapping of the RSNV locus represents the first identification of a genetic factor

  13. Deepening sleep by hypnotic suggestion.

    Science.gov (United States)

    Cordi, Maren J; Schlarb, Angelika A; Rasch, Björn

    2014-06-01

    Slow wave sleep (SWS) plays a critical role in body restoration and promotes brain plasticity; however, it markedly declines across the lifespan. Despite its importance, effective tools to increase SWS are rare. Here we tested whether a hypnotic suggestion to "sleep deeper" extends the amount of SWS. Within-subject, placebo-controlled crossover design. Sleep laboratory at the University of Zurich, Switzerland. Seventy healthy females 23.27 ± 3.17 y. Participants listened to an auditory text with hypnotic suggestions or a control tape before napping for 90 min while high-density electroencephalography was recorded. After participants listened to the hypnotic suggestion to "sleep deeper" subsequent SWS was increased by 81% and time spent awake was reduced by 67% (with the amount of SWS or wake in the control condition set to 100%). Other sleep stages remained unaffected. Additionally, slow wave activity was significantly enhanced after hypnotic suggestions. During the hypnotic tape, parietal theta power increases predicted the hypnosis-induced extension of SWS. Additional experiments confirmed that the beneficial effect of hypnotic suggestions on SWS was specific to the hypnotic suggestion and did not occur in low suggestible participants. Our results demonstrate the effectiveness of hypnotic suggestions to specifically increase the amount and duration of slow wave sleep (SWS) in a midday nap using objective measures of sleep in young, healthy, suggestible females. Hypnotic suggestions might be a successful tool with a lower risk of adverse side effects than pharmacological treatments to extend SWS also in clinical and elderly populations.

  14. Deepening Sleep by Hypnotic Suggestion

    Science.gov (United States)

    Cordi, Maren J.; Schlarb, Angelika A.; Rasch, Björn

    2014-01-01

    Study Objectives: Slow wave sleep (SWS) plays a critical role in body restoration and promotes brain plasticity; however, it markedly declines across the lifespan. Despite its importance, effective tools to increase SWS are rare. Here we tested whether a hypnotic suggestion to “sleep deeper” extends the amount of SWS. Design: Within-subject, placebo-controlled crossover design. Setting: Sleep laboratory at the University of Zurich, Switzerland. Participants: Seventy healthy females 23.27 ± 3.17 y. Intervention: Participants listened to an auditory text with hypnotic suggestions or a control tape before napping for 90 min while high-density electroencephalography was recorded. Measurements and Results: After participants listened to the hypnotic suggestion to “sleep deeper” subsequent SWS was increased by 81% and time spent awake was reduced by 67% (with the amount of SWS or wake in the control condition set to 100%). Other sleep stages remained unaffected. Additionally, slow wave activity was significantly enhanced after hypnotic suggestions. During the hypnotic tape, parietal theta power increases predicted the hypnosis-induced extension of SWS. Additional experiments confirmed that the beneficial effect of hypnotic suggestions on SWS was specific to the hypnotic suggestion and did not occur in low suggestible participants. Conclusions: Our results demonstrate the effectiveness of hypnotic suggestions to specifically increase the amount and duration of slow wave sleep (SWS) in a midday nap using objective measures of sleep in young, healthy, suggestible females. Hypnotic suggestions might be a successful tool with a lower risk of adverse side effects than pharmacological treatments to extend SWS also in clinical and elderly populations. Citation: Cordi MJ, Schlarb AA, Rasch B. Deepening sleep by hypnotic suggestion. SLEEP 2014;37(6):1143-1152. PMID:24882909

  15. Detection of elevated CO 2 responsive QTLs for yield and its ...

    African Journals Online (AJOL)

    Transgressive segregation and continuous distribution in the CSSLs were observed for elevated CO2 response values (the value in FACE minus that in Ambient), in panicle number per plant (PN), grain number per panicle (GN), 1000 grain weight (GW) and yield per plant (YD), suggesting that all the tested traits responding ...

  16. Effects of defoliating insect resistance QTLs and a cry1Ac transgene in soybean near-isogenic lines.

    Science.gov (United States)

    Zhu, S; Walker, D R; Boerma, H R; All, J N; Parrott, W A

    2008-02-01

    The crystal proteins coded by transgenes from Bacillus thuringiensis (Bt) have shown considerable value in providing effective insect resistance in a number of crop species, including soybean, Glycine max (L.) Merr. Additional sources of soybean insect resistance would be desirable to manage the development of tolerance/resistance to crystal proteins by defoliating insects and to sustain the deployment of Bt crops. The objective of this study was to evaluate the effects and interactions of three insect resistance quantitative trait loci (QTLs; QTL-M, QTL-H, and QTL-G) originating from Japanese soybean PI 229358 and a cry1Ac gene in a "Benning" genetic background. A set of 16 BC(6)F(2)-derived near isogenic lines (NILs) was developed using marker-assisted backcrosses and evaluated for resistance to soybean looper [SBL, Pseudoplusia includens (Walker)] and corn earworm [CEW, Helicoverpa zea (Boddie)] in field cage, greenhouse, and detached leaf assays. Both Bt and QTL-M had significantly reduced defoliation by both SBL and CEW and reduced larval weight of CEW. The antibiosis QTL-G had a significant effect on reducing CEW larval weight and also a significant effect on reducing defoliation by SBL and CEW in some assays. The antixenosis QTL-H had no main effect, but it appeared to function through interaction with QTL-M and QTL-G. Adding QTL-H and QTL-G further enhanced the resistance of the Bt and QTL-M combination to CEW in the field cage assay. These results should help guide the development of strategies for effective management of insect pests and for sustainable deployment of Bt genes.

  17. Identification of major QTLs underlying tomato spotted wilt virus resistance in peanut cultivar Florida-EP(TM) '113'.

    Science.gov (United States)

    Tseng, Yu-Chien; Tillman, Barry L; Peng, Ze; Wang, Jianping

    2016-09-06

    Spotted wilt caused by tomato spotted wilt virus (TSWV) is one of the major peanut (Arachis hypogaea L.) diseases in the southeastern United States. Occurrence, severity, and symptoms of spotted wilt disease are highly variable from season to season, making it difficult to efficiently evaluate breeding populations for resistance. Molecular markers linked to spotted wilt resistance could overcome this problem and allow selection of resistant lines regardless of environmental conditions. Florida-EP(TM) '113' is a spotted wilt resistant cultivar with a significantly lower infection frequency. However, the genetic basis is still unknown. The objective of this study is to map the major quantitative trait loci (QTLs) linked to spotted wilt resistance in Florida-EP(TM) '113'. Among 2,431 SSR markers located across the whole peanut genome screened between the two parental lines, 329 were polymorphic. Those polymorphic markers were used to further genotype a representative set of individuals in a segregating population. Only polymorphic markers on chromosome A01 showed co-segregation between genotype and phenotype. Genotyping by sequencing (GBS) of the representative set of individuals in the segregating population also depicted a strong association between several SNPs on chromosome A01 and the trait, indicating a major QTL on chromosome A01. Therefore marker density was enriched on the A01 chromosome. A linkage map with 23 makers on chromosome A01 was constructed, showing collinearity with the physical map. Combined with phenotypic data, a major QTL flanked by marker AHGS4584 and GM672 was identified on chromosome A01, with up to 22.7 % PVE and 9.0 LOD value. A major QTL controlling the spotted wilt resistance in Florida-EP(TM) '113' was identified. The resistance is most likely contributed by PI 576638, a hirsuta botanical-type line, introduced from Mexico with spotted wilt resistance. The flanking markers of this QTL can be used for further fine mapping and marker

  18. Hypnotic suggestion and cognitive neuroscience.

    Science.gov (United States)

    Oakley, David A; Halligan, Peter W

    2009-06-01

    The growing acceptance of consciousness as a legitimate field of enquiry and the availability of functional imaging has rekindled research interest in the use of hypnosis and suggestion to manipulate subjective experience and to gain insights into healthy and pathological cognitive functioning. Current research forms two strands. The first comprises studies exploring the cognitive and neural nature of hypnosis itself. The second employs hypnosis to explore known psychological processes using specifically targeted suggestions. An extension of this second approach involves using hypnotic suggestion to create clinically informed analogues of established structural and functional neuropsychological disorders. With functional imaging, this type of experimental neuropsychopathology offers a productive means of investigating brain activity involved in many symptom-based disorders and their related phenomenology.

  19. Adaptation of maize to temperate climates: mid-density genome-wide association genetics and diversity patterns reveal key genomic regions, with a major contribution of the Vgt2 (ZCN8 locus.

    Directory of Open Access Journals (Sweden)

    Sophie Bouchet

    Full Text Available The migration of maize from tropical to temperate climates was accompanied by a dramatic evolution in flowering time. To gain insight into the genetic architecture of this adaptive trait, we conducted a 50K SNP-based genome-wide association and diversity investigation on a panel of tropical and temperate American and European representatives. Eighteen genomic regions were associated with flowering time. The number of early alleles cumulated along these regions was highly correlated with flowering time. Polymorphism in the vicinity of the ZCN8 gene, which is the closest maize homologue to Arabidopsis major flowering time (FT gene, had the strongest effect. This polymorphism is in the vicinity of the causal factor of Vgt2 QTL. Diversity was lower, whereas differentiation and LD were higher for associated loci compared to the rest of the genome, which is consistent with selection acting on flowering time during maize migration. Selection tests also revealed supplementary loci that were highly differentiated among groups and not associated with flowering time in our panel, whereas they were in other linkage-based studies. This suggests that allele fixation led to a lack of statistical power when structure and relatedness were taken into account in a linear mixed model. Complementary designs and analysis methods are necessary to unravel the architecture of complex traits. Based on linkage disequilibrium (LD estimates corrected for population structure, we concluded that the number of SNPs genotyped should be at least doubled to capture all QTLs contributing to the genetic architecture of polygenic traits in this panel. These results show that maize flowering time is controlled by numerous QTLs of small additive effect and that strong polygenic selection occurred under cool climatic conditions. They should contribute to more efficient genomic predictions of flowering time and facilitate the dissemination of diverse maize genetic resources under a wide

  20. Plant genetic background increasing the efficiency and durability of major resistance genes to root-knot nematodes can be resolved into a few resistance QTLs

    Directory of Open Access Journals (Sweden)

    Arnaud eBarbary

    2016-05-01

    Full Text Available With the banning of most chemical nematicides, the control of root-knot nematodes (RKNs in vegetable crops is now based essentially on the deployment of single, major resistance genes (R-genes. However, these genes are rare and their efficacy is threatened by the capacity of RKNs to adapt. In pepper, several dominant R-genes are effective against RKNs, and their efficacy and durability have been shown to be greater in a partially resistant genetic background. However, the genetic determinants of this partial resistance were unknown. Here, a QTL analysis was performed on the F2:3 population from the cross between Yolo Wonder, an accession considered partially resistant or resistant, depending on the RKN species, and Doux Long des Landes, a susceptible cultivar. A genetic linkage map was constructed from 130 F2 individuals, and the 130 F3 families were tested for resistance to the three main RKN species, M. incognita, M. arenaria and M. javanica. For the first time in the pepper-RKN pathosystem, four major QTLs were identified and mapped to two clusters. The cluster on chromosome P1 includes three tightly linked QTLs with specific effects against individual RKN species. The fourth QTL, providing specific resistance to M. javanica, mapped to pepper chromosome P9, which is known to carry multiple NBS-LRR repeats, together with major R-genes for resistance to nematodes and other pathogens. The newly discovered cluster on chromosome P1 has a broad spectrum of action with major additive effects on resistance. These data highlight the role of host QTLs involved in plant-RKN interactions and provide innovative potential for the breeding of new pepper cultivars or rootstocks combining quantitative resistance and major R-genes, to increase both the efficacy and durability of RKN control by resistance genes.

  1. Construction of an interspecific genetic map based on InDel and SSR for mapping the QTLs affecting the initiation of flower primordia in pepper (Capsicum spp..

    Directory of Open Access Journals (Sweden)

    Shu Tan

    Full Text Available Re-sequencing permits the mining of genome-wide variations on a large scale and provides excellent resources for the research community. To accelerate the development and application of molecular markers and identify the QTLs affecting the flowering time-related trait in pepper, a total of 1,038 pairs of InDel and 674 SSR primers from different sources were used for genetic mapping using the F2 population (n = 154 derived from a cross between BA3 (C. annuum and YNXML (C. frutescens. Of these, a total of 224 simple PCR-based markers, including 129 InDels and 95 SSRs, were validated and integrated into a map, which was designated as the BY map. The BY map consisted of 13 linkage groups (LGs and spanned a total genetic distance of 1,249.77 cM with an average marker distance of 5.60 cM. Comparative analysis of the genetic and physical map based on the anchored markers showed that the BY map covered nearly the whole pepper genome. Based on the BY map, one major and five minor QTLs affecting the number of leaves on the primary axis (Nle were detected on chromosomes P2, P7, P10 and P11 in 2012. The major QTL on P2 was confirmed based on another subset of the same F2 population (n = 147 in 2014 with selective genotyping of markers from the BY map. With the accomplishment of pepper whole genome sequencing and annotations (release 2.0, 153 candidate genes were predicted to embed in the Nle2.2 region, of which 12 important flowering related genes were obtained. The InDel/SSR-based interspecific genetic map, QTLs and candidate genes obtained by the present study will be useful for the downstream isolation of flowering time-related gene and other genetic applications for pepper.

  2. QTLs for straw quality characteristics identified in recombinant inbred lines of a Hordeum vulgare x H. spontaneum cross in a Mediterranean environment.

    Science.gov (United States)

    Grando, S; Baum, M; Ceccarelli, S; Goodchild, A; El-Haramein, F Jaby; Jahoor, A; Backes, G

    2005-02-01

    Barley straw is commonly used as animal feed in many developing countries. Even a small increase in its nutritive value can have a large impact on animal production, and hence, on rural livelihood and human nutrition. Straw quality is strongly affected by environmental factors and is, therefore, difficult to improve with empirical breeding. The objective of this study was to identify molecular markers to facilitate the improvement of straw quality in barley. For this purpose, we have used the genetic linkage map that was already developed for recombinant inbred lines (RILs) of the cross between a Hordeum vulgare cultivar ('Arta') and a H. spontaneum line (H. spontaneum 41-1), covering a total of 890 cM. Straw parameters from RILs grown at Tel Hadya and Breda (ICARDA's research stations) in 2 years (1996/1997 and 1997/1998) were analyzed by NIRS for predicted nutritional characteristics including neutral detergent fiber, acid detergent fiber, lignin, digestible organic matter in dry matter, voluntary intake, crude protein, and straw morphology (the percentage of blades, sheaths, and stems). Localization of QTLs was performed using Windows QTL Cartographer, version 2.0. Seventy-three QTLs were identified, the majority of which (17) in the driest of the four environments. Only six QTLs were identified in two environments; in five cases, one of the two was the wettest environment. This is discussed in relation to the possibility of improving straw quality in favorable environments where yields are higher, rather than in dry environments where straw quality is already relatively good.

  3. Deepening sleep by hypnotic suggestion.

    OpenAIRE

    Cordi, Maren J.; Schlarb, Angelika A; Rasch, Björn

    2014-01-01

    STUDY OBJECTIVES Slow wave sleep (SWS) plays a critical role in body restoration and promotes brain plasticity; however it markedly declines across the lifespan. Despite its importance effective tools to increase SWS are rare. Here we tested whether a hypnotic suggestion to "sleep deeper" extends the amount of SWS. DESIGN Within subject placebo controlled crossover design. SETTING Sleep laboratory at the University of Zurich Switzerland. PARTICIPANTS Seventy healthy females 23.27 ± 3.17 y. IN...

  4. Genes and QTLs controlling inflorescence and stem branch architecture in Leymus (Poaceae: Triticeae) Wildrye.

    Science.gov (United States)

    Larson, Steven R; Kellogg, Elizabeth A; Jensen, Kevin B

    2013-01-01

    Grass inflorescence and stem branches show recognizable architectural differences among species. The inflorescence branches of Triticeae cereals and grasses, including wheat, barley, and 400-500 wild species, are usually contracted into a spike formation, with the number of flowering branches (spikelets) per node conserved within species and genera. Perennial Triticeae grasses of genus Leymus are unusual in that the number of spikelets per node varies, inflorescences may have panicle branches, and vegetative stems may form subterranean rhizomes. Leymus cinereus and L. triticoides show discrete differences in inflorescence length, branching architecture, node number, and density; number of spikelets per node and florets per spikelet; culm length and width; and perimeter of rhizomatous spreading. Quantitative trait loci controlling these traits were detected in 2 pseudo-backcross populations derived from the interspecific hybrids using a linkage map with 360 expressed gene sequence markers from Leymus tiller and rhizome branch meristems. Alignments of genes, mutations, and quantitative trait loci controlling similar traits in other grass species were identified using the Brachypodium genome reference sequence. Evidence suggests that loci controlling inflorescence and stem branch architecture in Leymus are conserved among the grasses, are governed by natural selection, and can serve as possible gene targets for improving seed, forage, and grain production.

  5. Mapeamento de QTLs para características de qualidade da madeira e crescimento em híbridos (Eucalyptus grandis x Eucalyptus urophylla)

    OpenAIRE

    Rodrigo Barros Rocha; Everaldo Gonçalves de Barros; Cosme Damião Cruz; Antônio Marcos Rosado; Elza Fernandes Araújo

    2007-01-01

    The present work aimed to characterize and identify QTLs for wood quality and growth traits in E. grandis x E. urophylla hybrids. For this purpose a RAPD linkage map was developed for the hybrids (LOD=3 and r=0.40) containing 52 markers and 12 linkage groups. Traits related to wood quality and growth were evaluated in the QTL analyses. QTL analyses were performed using chi-square tests, single-marker, interval mapping and composite interval mapping analyses. All approaches led to the identifi...

  6. QTL mapping of genes controlling plasma insulin and leptin concentrations: metabolic effect of obesity QTLs identified in an F2 intercross between C57BL/6J and DDD.Cg-A(y) inbred mice.

    Science.gov (United States)

    Suto, Jun-ichi

    2013-07-31

    DDD.Cg-A(y) female mice developed massive obesity as compared with B6.Cg-A(y) female mice. We previously identified quantitative trait loci (QTLs) for obesity on chromosomes 1, 6, 9 and 17 in F2 female mice, including F2A(y) (F2 mice with the A(y) allele) and F2 non- A(y) mice (F2 mice without the A(y) allele), produced by crossing C57BL/6J and DDD.Cg-A(y) strains. We here addressed the question whether the obesity QTLs share genetic bases with putative QTLs for plasma glucose, insulin and leptin concentrations. We performed QTL analyses for the first principal component (PC1) extracted from these metabolic measurements to identify the genes that contributed to the comprehensive evaluation of metabolic traits. By single QTL scans, we identified two significant QTLs for insulin concentration on chromosomes 6 and 12, three for leptin concentration on chromosomes 1, 6 and 17, and five for PC1 on chromosomes 1, 6, 12 (two loci) and 17. Although insulin and leptin concentrations and PC1 were not normally distributed in combined F2 mice, results of single QTL scans by parametric and non-parametric methods were very similar. Therefore, QTL scan by the parametric method was performed with the agouti locus genotype as a covariate. A significant QTL × covariate interaction was found for PC1 on chromosome 9. All obesity QTLs had significant metabolic effects. Thus, obesity- and diabetes-related traits in DDD.Cg-A(y) mice were largely controlled by QTLs on chromosomes 1, 6, 9, 12 and 17.

  7. The functional anatomy of suggested limb paralysis.

    Science.gov (United States)

    Deeley, Quinton; Oakley, David A; Toone, Brian; Bell, Vaughan; Walsh, Eamonn; Marquand, Andre F; Giampietro, Vincent; Brammer, Michael J; Williams, Steven C R; Mehta, Mitul A; Halligan, Peter W

    2013-02-01

    Suggestions of limb paralysis in highly hypnotically suggestible subjects have been employed to successfully model conversion disorders, revealing similar patterns of brain activation associated with attempted movement of the affected limb. However, previous studies differ with regard to the executive regions involved during involuntary inhibition of the affected limb. This difference may have arisen as previous studies did not control for differences in hypnosis depth between conditions and/or include subjective measures to explore the experience of suggested paralysis. In the current study we employed functional magnetic resonance imaging (fMRI) to examine the functional anatomy of left and right upper limb movements in eight healthy subjects selected for high hypnotic suggestibility during (i) hypnosis (NORMAL) and (ii) attempted movement following additional left upper limb paralysis suggestions (PARALYSIS). Contrast of left upper limb motor function during NORMAL relative to PARALYSIS conditions revealed greater activation of contralateral M1/S1 and ipsilateral cerebellum, consistent with the engagement of these regions in the completion of movements. By contrast, two significant observations were noted in PARALYSIS relative to NORMAL conditions. In conjunction with reports of attempts to move the paralysed limb, greater supplementary motor area (SMA) activation was observed, a finding consistent with the role of SMA in motor intention and planning. The anterior cingulate cortex (ACC, BA 24) was also significantly more active in PARALYSIS relative to NORMAL conditions - suggesting that ACC (BA 24) may be implicated in involuntary, as well as voluntary inhibition of prepotent motor responses. Copyright © 2012 Elsevier Ltd. All rights reserved.

  8. The first genetic and comparative map of white lupin (Lupinus albus L.): identification of QTLs for anthracnose resistance and flowering time, and a locus for alkaloid content.

    Science.gov (United States)

    Phan, Huyen T T; Ellwood, Simon R; Adhikari, Kedar; Nelson, Matthew N; Oliver, Richard P

    2007-04-01

    We report the first genetic linkage map of white lupin (Lupinus albus L.). An F8 recombinant inbred line population developed from Kiev mutant x P27174 was mapped with 220 amplified fragment length polymorphism and 105 gene-based markers. The genetic map consists of 28 main linkage groups (LGs) that varied in length from 22.7 cM to 246.5 cM and spanned a total length of 2951 cM. There were seven additional pairs and 15 unlinked markers, and 12.8% of markers showed segregation distortion at P albus were complex. Forty-five orthologous markers that mapped between M. truncatula and L. albus identified 17 small syntenic blocks, and each M. truncatula chromosome aligned to between one and six syntenic blocks in L. albus. Genetic mapping of three important traits: anthracnose resistance, flowering time, and alkaloid content allowed loci governing these traits to be defined. Two quantitative trait loci (QTLs) with significant effects were identified for anthracnose resistance on LG4 and LG17, and two QTLs were detected for flowering time on the top of LG1 and LG3. Alkaloid content was mapped as a Mendelian trait to LG11.

  9. The First Genetic and Comparative Map of White Lupin (Lupinus albus L.): Identification of QTLs for Anthracnose Resistance and Flowering Time, and a Locus for Alkaloid Content

    Science.gov (United States)

    Phan, Huyen T. T.; Ellwood, Simon R.; Adhikari, Kedar; Nelson, Matthew N.; Oliver, Richard P.

    2007-01-01

    Abstract We report the first genetic linkage map of white lupin (Lupinus albus L.). An F8 recombinant inbred line population developed from Kiev mutant × P27174 was mapped with 220 amplified fragment length polymorphism and 105 gene-based markers. The genetic map consists of 28 main linkage groups (LGs) that varied in length from 22.7 cM to 246.5 cM and spanned a total length of 2951 cM. There were seven additional pairs and 15 unlinked markers, and 12.8% of markers showed segregation distortion at P < 0.05. Syntenic relationships between Medicago truncatula and L. albus were complex. Forty-five orthologous markers that mapped between M. truncatula and L. albus identified 17 small syntenic blocks, and each M. truncatula chromosome aligned to between one and six syntenic blocks in L. albus. Genetic mapping of three important traits: anthracnose resistance, flowering time, and alkaloid content allowed loci governing these traits to be defined. Two quantitative trait loci (QTLs) with significant effects were identified for anthracnose resistance on LG4 and LG17, and two QTLs were detected for flowering time on the top of LG1 and LG3. Alkaloid content was mapped as a Mendelian trait to LG11. PMID:17526914

  10. Towards diverse visual suggestions on Flickr

    Science.gov (United States)

    Feki, Ghada; Ben Ammar, Anis; Ben Amar, Chokri

    2017-03-01

    With the great popularity of the photo sharing site Flickr, the research community is involved to produce innovative applications in order to enhance different Flickr services. In this paper, we present a new process for diverse visual suggestions generation on Flickr. We unify the social aspect of Flickr and the richness of Wikipedia to produce an important number of meanings illustrated by the diverse visual suggestions which can integrate the diversity aspect into the Flickr search. We conduct an experimental study to illustrate the effect of the fusion of the Wikipedia and Flickr knowledge on the diversity rate among the Flickr search and reveal the evolution of the diversity aspect through the returned images among the different results of search engines.

  11. Partitioning the Heritability of Tourette Syndrome and Obsessive Compulsive Disorder Reveals Differences in Genetic Architecture

    Science.gov (United States)

    Davis, Lea K.; Yu, Dongmei; Keenan, Clare L.; Gamazon, Eric R.; Konkashbaev, Anuar I.; Derks, Eske M.; Neale, Benjamin M.; Yang, Jian; Lee, S. Hong; Evans, Patrick; Barr, Cathy L.; Bellodi, Laura; Benarroch, Fortu; Berrio, Gabriel Bedoya; Bienvenu, Oscar J.; Bloch, Michael H.; Blom, Rianne M.; Bruun, Ruth D.; Budman, Cathy L.; Camarena, Beatriz; Campbell, Desmond; Cappi, Carolina; Cardona Silgado, Julio C.; Cath, Danielle C.; Cavallini, Maria C.; Chavira, Denise A.; Chouinard, Sylvain; Conti, David V.; Cook, Edwin H.; Coric, Vladimir; Cullen, Bernadette A.; Deforce, Dieter; Delorme, Richard; Dion, Yves; Edlund, Christopher K.; Egberts, Karin; Falkai, Peter; Fernandez, Thomas V.; Gallagher, Patience J.; Garrido, Helena; Geller, Daniel; Girard, Simon L.; Grabe, Hans J.; Grados, Marco A.; Greenberg, Benjamin D.; Gross-Tsur, Varda; Haddad, Stephen; Heiman, Gary A.; Hemmings, Sian M. J.; Hounie, Ana G.; Illmann, Cornelia; Jankovic, Joseph; Jenike, Michael A.; Kennedy, James L.; King, Robert A.; Kremeyer, Barbara; Kurlan, Roger; Lanzagorta, Nuria; Leboyer, Marion; Leckman, James F.; Lennertz, Leonhard; Liu, Chunyu; Lochner, Christine; Lowe, Thomas L.; Macciardi, Fabio; McCracken, James T.; McGrath, Lauren M.; Mesa Restrepo, Sandra C.; Moessner, Rainald; Morgan, Jubel; Muller, Heike; Murphy, Dennis L.; Naarden, Allan L.; Ochoa, William Cornejo; Ophoff, Roel A.; Osiecki, Lisa; Pakstis, Andrew J.; Pato, Michele T.; Pato, Carlos N.; Piacentini, John; Pittenger, Christopher; Pollak, Yehuda; Rauch, Scott L.; Renner, Tobias J.; Reus, Victor I.; Richter, Margaret A.; Riddle, Mark A.; Robertson, Mary M.; Romero, Roxana; Rosàrio, Maria C.; Rosenberg, David; Rouleau, Guy A.; Ruhrmann, Stephan; Ruiz-Linares, Andres; Sampaio, Aline S.; Samuels, Jack; Sandor, Paul; Sheppard, Brooke; Singer, Harvey S.; Smit, Jan H.; Stein, Dan J.; Strengman, E.; Tischfield, Jay A.; Valencia Duarte, Ana V.; Vallada, Homero; Van Nieuwerburgh, Filip; Veenstra-VanderWeele, Jeremy; Walitza, Susanne; Wang, Ying; Wendland, Jens R.; Westenberg, Herman G. M.; Shugart, Yin Yao; Miguel, Euripedes C.; McMahon, William; Wagner, Michael; Nicolini, Humberto; Posthuma, Danielle; Hanna, Gregory L.; Heutink, Peter; Denys, Damiaan; Arnold, Paul D.; Oostra, Ben A.; Nestadt, Gerald; Freimer, Nelson B.; Pauls, David L.; Wray, Naomi R.

    2013-01-01

    The direct estimation of heritability from genome-wide common variant data as implemented in the program Genome-wide Complex Trait Analysis (GCTA) has provided a means to quantify heritability attributable to all interrogated variants. We have quantified the variance in liability to disease explained by all SNPs for two phenotypically-related neurobehavioral disorders, obsessive-compulsive disorder (OCD) and Tourette Syndrome (TS), using GCTA. Our analysis yielded a heritability point estimate of 0.58 (se = 0.09, p = 5.64e-12) for TS, and 0.37 (se = 0.07, p = 1.5e-07) for OCD. In addition, we conducted multiple genomic partitioning analyses to identify genomic elements that concentrate this heritability. We examined genomic architectures of TS and OCD by chromosome, MAF bin, and functional annotations. In addition, we assessed heritability for early onset and adult onset OCD. Among other notable results, we found that SNPs with a minor allele frequency of less than 5% accounted for 21% of the TS heritability and 0% of the OCD heritability. Additionally, we identified a significant contribution to TS and OCD heritability by variants significantly associated with gene expression in two regions of the brain (parietal cortex and cerebellum) for which we had available expression quantitative trait loci (eQTLs). Finally we analyzed the genetic correlation between TS and OCD, revealing a genetic correlation of 0.41 (se = 0.15, p = 0.002). These results are very close to previous heritability estimates for TS and OCD based on twin and family studies, suggesting that very little, if any, heritability is truly missing (i.e., unassayed) from TS and OCD GWAS studies of common variation. The results also indicate that there is some genetic overlap between these two phenotypically-related neuropsychiatric disorders, but suggest that the two disorders have distinct genetic architectures. PMID:24204291

  12. Partitioning the heritability of Tourette syndrome and obsessive compulsive disorder reveals differences in genetic architecture.

    Directory of Open Access Journals (Sweden)

    Lea K Davis

    2013-10-01

    Full Text Available The direct estimation of heritability from genome-wide common variant data as implemented in the program Genome-wide Complex Trait Analysis (GCTA has provided a means to quantify heritability attributable to all interrogated variants. We have quantified the variance in liability to disease explained by all SNPs for two phenotypically-related neurobehavioral disorders, obsessive-compulsive disorder (OCD and Tourette Syndrome (TS, using GCTA. Our analysis yielded a heritability point estimate of 0.58 (se = 0.09, p = 5.64e-12 for TS, and 0.37 (se = 0.07, p = 1.5e-07 for OCD. In addition, we conducted multiple genomic partitioning analyses to identify genomic elements that concentrate this heritability. We examined genomic architectures of TS and OCD by chromosome, MAF bin, and functional annotations. In addition, we assessed heritability for early onset and adult onset OCD. Among other notable results, we found that SNPs with a minor allele frequency of less than 5% accounted for 21% of the TS heritability and 0% of the OCD heritability. Additionally, we identified a significant contribution to TS and OCD heritability by variants significantly associated with gene expression in two regions of the brain (parietal cortex and cerebellum for which we had available expression quantitative trait loci (eQTLs. Finally we analyzed the genetic correlation between TS and OCD, revealing a genetic correlation of 0.41 (se = 0.15, p = 0.002. These results are very close to previous heritability estimates for TS and OCD based on twin and family studies, suggesting that very little, if any, heritability is truly missing (i.e., unassayed from TS and OCD GWAS studies of common variation. The results also indicate that there is some genetic overlap between these two phenotypically-related neuropsychiatric disorders, but suggest that the two disorders have distinct genetic architectures.

  13. A high-density genetic map for anchoring genome sequences and identifying QTLs associated with dwarf vine in pumpkin (Cucurbita maxima Duch.).

    Science.gov (United States)

    Zhang, Guoyu; Ren, Yi; Sun, Honghe; Guo, Shaogui; Zhang, Fan; Zhang, Jie; Zhang, Haiying; Jia, Zhangcai; Fei, Zhangjun; Xu, Yong; Li, Haizhen

    2015-12-24

    Pumpkin (Cucurbita maxima Duch.) is an economically important crop belonging to the Cucurbitaceae family. However, very few genomic and genetic resources are available for this species. As part of our ongoing efforts to sequence the pumpkin genome, high-density genetic map is essential for anchoring and orienting the assembled scaffolds. In addition, a saturated genetic map can facilitate quantitative trait locus (QTL) mapping. A set of 186 F2 plants derived from the cross of pumpkin inbred lines Rimu and SQ026 were genotyped using the genotyping-by-sequencing approach. Using the SNPs we identified, a high-density genetic map containing 458 bin-markers was constructed, spanning a total genetic distance of 2,566.8 cM across the 20 linkage groups of C. maxima with a mean marker density of 5.60 cM. Using this map we were able to anchor 58 assembled scaffolds that covered about 194.5 Mb (71.7%) of the 271.4 Mb assembled pumpkin genome, of which 44 (183.0 Mb; 67.4%) were oriented. Furthermore, the high-density genetic map was used to identify genomic regions highly associated with an important agronomic trait, dwarf vine. Three QTLs on linkage groups (LGs) 1, 3 and 4, respectively, were recovered. One QTL, qCmB2, which was located in an interval of 0.42 Mb on LG 3, explained 21.4% phenotypic variations. Within qCmB2, one gene, Cma_004516, encoding the gibberellin (GA) 20-oxidase in the GA biosynthesis pathway, had a 1249-bp deletion in its promoter in bush type lines, and its expression level was significantly increased during the vine growth and higher in vine type lines than bush type lines, supporting Cma_004516 as a possible candidate gene controlling vine growth in pumpkin. A high-density pumpkin genetic map was constructed, which was used to successfully anchor and orient the assembled genome scaffolds, and to identify QTLs highly associated with pumpkin vine length. The map provided a valuable resource for gene cloning and marker assisted breeding in pumpkin and

  14. Estimativas de parÃmetros genÃticos e identificaÃÃo de QTLs candidatos em cajueiro.

    OpenAIRE

    Francisco Herbeth Costa dos Santos

    2012-01-01

    O conhecimento sobre os parÃmetros genÃticos, a identificaÃÃo de locos de caracterÃsticas quantitativas (QTL) e a seleÃÃo assistida por marcadores tÃm grande importÃncia para o melhoramento genÃtico vegetal. Objetivou-se com o presente estudo avaliar o potencial de produÃÃo de oitenta e quatro clones de cajueiro, estimar parÃmetros genÃticos e identificar QTLs associados à altura da planta, diÃmetro da copa, antracnose, mofo-preto, nÃmero de flores hermafroditas/panÃcula e peso da castanha. C...

  15. D-subgenome bias of Xcm resistance genes in tetraploid Gossypium (cotton) suggests that polyploid formation has created novel avenues for evolution.

    Science.gov (United States)

    Wright, R J; Thaxton, P M; El-Zik, K M; Paterson, A H

    1998-08-01

    A detailed RFLP map was used to determine the chromosomal locations and subgenomic distributions of cotton (Gossypium) genes/QTLs that confer resistance to the bacterial blight pathogen, Xanthomonas campestris pv. malvacearum (Xcm). Genetic mapping generally corroborated classic predictions regarding the number and dosage effects of genes conferring Xcm resistance. One recessive allele (b6) was a noteworthy exception to the genetic dominance of most plant resistance alleles. This recessive allele appeared to uncover additional QTLs from both resistant and ostensibly susceptible genotypes, some of which corresponded in location to resistance (R)-genes effective against other Xcm races. One putatively "defeated" resistance allele (B3) reduced severity of Xcm damage by "virulent" races. Among the six resistance genes derived from tetraploid cottons, five (83%) mapped to D-subgenome chromosomes-if each subgenome were equally likely to evolve new R-gene alleles, this level of bias would occur in only about 1.6% of cases. Possible explanations of this bias include biogeographic factors, differences in evolutionary rates between subgenomes, gene conversion or other intergenomic exchanges that escaped detection by genetic mapping, or other factors. A significant D-subgenome bias of Xcm resistance genes may suggest that polyploid formation has offered novel avenues for phenotypic response to selection.

  16. QTLs for Woolly Poplar Aphid (Phloeomyzus passerinii L.) Resistance Detected in an Inter-Specific Populus deltoides x P. nigra Mapping Population.

    Science.gov (United States)

    Carletti, Giorgia; Carra, Andrea; Allegro, Gianni; Vietto, Lorenzo; Desiderio, Francesca; Bagnaresi, Paolo; Gianinetti, Alberto; Cattivelli, Luigi; Valè, Giampiero; Nervo, Giuseppe

    2016-01-01

    The genus Populus represents one of the most economically important groups of forest trees. It is composed by approximately 30 species used for wood and non-wood products, phytoremediation and biomass. Poplar is subjected to several biological and environmental threats although, compared to annual crops, we know far less about the genetic bases of biotic stress resistance. Woolly poplar aphid (Phloeomyzus passerinii) is considered a main pest of cultivated poplars in European and American countries. In this work we present two high density linkage maps in poplar obtained by a genotyping by sequencing (GBS) approach and the identification of QTLs involved in Ph. passerinii resistance. A total of 5,667 polymorphic markers (5,606 SNPs and 61 SSRs) identified on expressed sequences have been used to genotype 131 plants of an F1 population P ×canadensis obtained by an interspecific mate between Populus deltoides (resistant to woolly poplar aphid) and Populus nigra (susceptible to woolly poplar aphid). The two linkage maps, obtained following the two-way pseudo-testcross mapping strategy, have been used to investigate the genetic bases of woolly poplar aphid resistance. One major QTL and two QTLs with minor effects (mapped on LGV, LGXVI and LG XIX) explaining the 65.8% of the genetic variance observed in the progeny in response to Ph. passerinii attack were found. The high density coverage of functional markers allowed the identification of three genes belonging to disease resistance pathway as putative candidates for P. deltoides resistance to woolly poplar aphid. This work is the first report on genetic of woolly poplar aphid genetic resistance and the resistant loci associated markers identified represent a valuable tool in resistance poplar breeding programs.

  17. Construction of a Genetic Linkage Map and Identification of QTLs for Seed Weight and Seed Size Traits in Lentil (Lens culinaris Medik.).

    Science.gov (United States)

    Verma, Priyanka; Goyal, Richa; Chahota, R K; Sharma, Tilak R; Abdin, M Z; Bhatia, Sabhyata

    2015-01-01

    Seed weight and seed size both are quantitative traits and have been considered as important components of grain yield, thus identification of quantitative trait loci (QTL) for seed traits in lentil (Lens culinaris) would be beneficial for the improvement of grain yield. Hence the main objective of this study was to identify QTLs for seed traits using an intraspecific mapping population derived from a cross between L. culinaris cv. Precoz (seed weight-5.1g, seed size-5.7mm) and L. culinaris cv. L830 (seed weight-2.2g, seed size-4mm) comprising 126 F8-RILs. For this, two microsatellite genomic libraries enriched for (GA/CT) and (GAA/CTT) motif were constructed which resulted in the development of 501 new genomic SSR markers. Six hundred forty seven SSR markers (including 146 previously published) were screened for parental polymorphism and 219 (33.8%) were found to be polymorphic among the parents. Of these 216 were mapped on seven linkage groups at LOD4.0 spanning 1183.7cM with an average marker density of 5.48cM. Phenotypic data from the RILs was used to identify QTLs for the seed weight and seed size traits by single marker analysis (SMA) followed by composite interval mapping (CIM) which resulted in one QTL each for the 2 traits (qSW and qSS) that were co-localized on LG4 and explained 48.4% and 27.5% of phenotypic variance respectively. The current study would serve as a strong foundation for further validation and fine mapping for utilization in lentil breeding programs.

  18. Construction of a Genetic Linkage Map and Identification of QTLs for Seed Weight and Seed Size Traits in Lentil (Lens culinaris Medik..

    Directory of Open Access Journals (Sweden)

    Priyanka Verma

    Full Text Available Seed weight and seed size both are quantitative traits and have been considered as important components of grain yield, thus identification of quantitative trait loci (QTL for seed traits in lentil (Lens culinaris would be beneficial for the improvement of grain yield. Hence the main objective of this study was to identify QTLs for seed traits using an intraspecific mapping population derived from a cross between L. culinaris cv. Precoz (seed weight-5.1g, seed size-5.7mm and L. culinaris cv. L830 (seed weight-2.2g, seed size-4mm comprising 126 F8-RILs. For this, two microsatellite genomic libraries enriched for (GA/CT and (GAA/CTT motif were constructed which resulted in the development of 501 new genomic SSR markers. Six hundred forty seven SSR markers (including 146 previously published were screened for parental polymorphism and 219 (33.8% were found to be polymorphic among the parents. Of these 216 were mapped on seven linkage groups at LOD4.0 spanning 1183.7cM with an average marker density of 5.48cM. Phenotypic data from the RILs was used to identify QTLs for the seed weight and seed size traits by single marker analysis (SMA followed by composite interval mapping (CIM which resulted in one QTL each for the 2 traits (qSW and qSS that were co-localized on LG4 and explained 48.4% and 27.5% of phenotypic variance respectively. The current study would serve as a strong foundation for further validation and fine mapping for utilization in lentil breeding programs.

  19. QTLs for Woolly Poplar Aphid (Phloeomyzus passerinii L. Resistance Detected in an Inter-Specific Populus deltoides x P. nigra Mapping Population.

    Directory of Open Access Journals (Sweden)

    Giorgia Carletti

    Full Text Available The genus Populus represents one of the most economically important groups of forest trees. It is composed by approximately 30 species used for wood and non-wood products, phytoremediation and biomass. Poplar is subjected to several biological and environmental threats although, compared to annual crops, we know far less about the genetic bases of biotic stress resistance. Woolly poplar aphid (Phloeomyzus passerinii is considered a main pest of cultivated poplars in European and American countries. In this work we present two high density linkage maps in poplar obtained by a genotyping by sequencing (GBS approach and the identification of QTLs involved in Ph. passerinii resistance. A total of 5,667 polymorphic markers (5,606 SNPs and 61 SSRs identified on expressed sequences have been used to genotype 131 plants of an F1 population P ×canadensis obtained by an interspecific mate between Populus deltoides (resistant to woolly poplar aphid and Populus nigra (susceptible to woolly poplar aphid. The two linkage maps, obtained following the two-way pseudo-testcross mapping strategy, have been used to investigate the genetic bases of woolly poplar aphid resistance. One major QTL and two QTLs with minor effects (mapped on LGV, LGXVI and LG XIX explaining the 65.8% of the genetic variance observed in the progeny in response to Ph. passerinii attack were found. The high density coverage of functional markers allowed the identification of three genes belonging to disease resistance pathway as putative candidates for P. deltoides resistance to woolly poplar aphid. This work is the first report on genetic of woolly poplar aphid genetic resistance and the resistant loci associated markers identified represent a valuable tool in resistance poplar breeding programs.

  20. The Terpene Synthase Gene Family of Carrot (Daucus carota L.: Identification of QTLs and Candidate Genes Associated with Terpenoid Volatile Compounds

    Directory of Open Access Journals (Sweden)

    Jens Keilwagen

    2017-11-01

    Full Text Available Terpenes are an important group of secondary metabolites in carrots influencing taste and flavor, and some of them might also play a role as bioactive substances with an impact on human physiology and health. Understanding the genetic and molecular basis of terpene synthases (TPS involved in the biosynthesis of volatile terpenoids will provide insights for improving breeding strategies aimed at quality traits and for developing specific carrot chemotypes possibly useful for pharmaceutical applications. Hence, a combination of terpene metabolite profiling, genotyping-by-sequencing (GBS, and genome-wide association study (GWAS was used in this work to get insights into the genetic control of terpene biosynthesis in carrots and to identify several TPS candidate genes that might be involved in the production of specific monoterpenes. In a panel of 85 carrot cultivars and accessions, metabolite profiling was used to identify 31 terpenoid volatile organic compounds (VOCs in carrot leaves and roots, and a GBS approach was used to provide dense genome-wide marker coverage (>168,000 SNPs. Based on this data, a total of 30 quantitative trait loci (QTLs was identified for 15 terpenoid volatiles. Most QTLs were detected for the monoterpene compounds ocimene, sabinene, β-pinene, borneol and bornyl acetate. We identified four genomic regions on three different carrot chromosomes by GWAS which are both associated with high significance (LOD ≥ 5.91 to distinct monoterpenes and to TPS candidate genes, which have been identified by homology-based gene prediction utilizing RNA-seq data. In total, 65 TPS candidate gene models in carrot were identified and assigned to known plant TPS subfamilies with the exception of TPS-d and TPS-h. TPS-b was identified as largest subfamily with 32 TPS candidate genes.

  1. FEM effective suggestion of guitar construction

    Directory of Open Access Journals (Sweden)

    Vladimír Dániel

    2006-01-01

    Full Text Available Modal analysis of the whole guitar construction was performed. The results of eigenfrequencies were obtained. Stress in strings affects not only static loading of material, but also shift of eigenfrequencies. From obtained natural frequencies for solved spectrum such frequencies were used which coincides with assumed ribs new positions of ribs were suggested. Other ribs which do not carry out the mechanical function were removed. Also static reaction was evaluated and new position of ribs was adjusted. For final model new eigenfrequencies were computed and compared with previous ones. Significant changes were revealed in low frequencies (bellow 400 Hz where fewer amounts of natural shapes were obtained. Approximately 50% were lost by adding of ribs. For chosen frequencies of equal temperament the harmonic analysis was performed. The analysis proved ability of oscillation for frequencies far of natural frequencies. The final model satisfies the requirement of minimization of static stress in material due to strings and allows very effective oscillation of top the guitar resonance board. In comparison with literature good agreement in amplitude size of front board and amount of modes in appropriate frequencies were achieved. Suggested model even offers higher amount of natural shapes in comparison with literature, namely in high frequencies. From additional comparison of eigenfrequencies and natural shapes the influence of ribs position on natural shapes was approved.

  2. Communicative, organizational and suggestive skills of high school teacher

    National Research Council Canada - National Science Library

    Марина Олександрівна Васильєва-Халатникова

    2015-01-01

    .... Communicative, organizational and suggestive skills of high school teacher are revealed and analyzed.Communicative ability of teacher - ability setting and forming a pedagogical and reasonable position about the students...

  3. Comparative Genomics Analyses Reveal Extensive Chromosome Colinearity and Novel Quantitative Trait Loci in Eucalyptus.

    Directory of Open Access Journals (Sweden)

    Fagen Li

    Full Text Available Dense genetic maps, along with quantitative trait loci (QTLs detected on such maps, are powerful tools for genomics and molecular breeding studies. In the important woody genus Eucalyptus, the recent release of E. grandis genome sequence allows for sequence-based genomic comparison and searching for positional candidate genes within QTL regions. Here, dense genetic maps were constructed for E. urophylla and E. tereticornis using genomic simple sequence repeats (SSR, expressed sequence tag (EST derived SSR, EST-derived cleaved amplified polymorphic sequence (EST-CAPS, and diversity arrays technology (DArT markers. The E. urophylla and E. tereticornis maps comprised 700 and 585 markers across 11 linkage groups, totaling at 1,208.2 and 1,241.4 cM in length, respectively. Extensive synteny and colinearity were observed as compared to three earlier DArT-based eucalypt maps (two maps with E. grandis × E. urophylla and one map of E. globulus and with the E. grandis genome sequence. Fifty-three QTLs for growth (10-56 months of age and wood density (56 months were identified in 22 discrete regions on both maps, in which only one colocalizaiton was found between growth and wood density. Novel QTLs were revealed as compared with those previously detected on DArT-based maps for similar ages in Eucalyptus. Eleven to 585 positional candidate genes were obained for a 56-month-old QTL through aligning QTL confidence interval with the E. grandis genome. These results will assist in comparative genomics studies, targeted gene characterization, and marker-assisted selection in Eucalyptus and the related taxa.

  4. A Novel QTL for Powdery Mildew Resistance in Nordic Spring Barley (Hordeum vulgare L. ssp. vulgare Revealed by Genome-Wide Association Study

    Directory of Open Access Journals (Sweden)

    Therése Bengtsson

    2017-11-01

    Full Text Available The powdery mildew fungus, Blumeria graminis f. sp. hordei is a worldwide threat to barley (Hordeum vulgare L. ssp. vulgare production. One way to control the disease is by the development and deployment of resistant cultivars. A genome-wide association study was performed in a Nordic spring barley panel consisting of 169 genotypes, to identify marker-trait associations significant for powdery mildew. Powdery mildew was scored during three years (2012–2014 in four different locations within the Nordic region. There were strong correlations between data from all locations and years. In total four QTLs were identified, one located on chromosome 4H in the same region as the previously identified mlo locus and three on chromosome 6H. Out of these three QTLs identified on chromosome 6H, two are in the same region as previously reported QTLs for powdery mildew resistance, whereas one QTL appears to be novel. The top NCBI BLASTn hit of the SNP markers within the novel QTL predicted the responsible gene to be the 26S proteasome regulatory subunit, RPN1, which is required for innate immunity and powdery mildew-induced cell death in Arabidopsis. The results from this study have revealed SNP marker candidates that can be exploited for use in marker-assisted selection and stacking of genes for powdery mildew resistance in barley.

  5. A Novel QTL for Powdery Mildew Resistance in Nordic Spring Barley (Hordeum vulgare L. ssp. vulgare) Revealed by Genome-Wide Association Study

    Science.gov (United States)

    Bengtsson, Therése; Åhman, Inger; Manninen, Outi; Reitan, Lars; Christerson, Therese; Due Jensen, Jens; Krusell, Lene; Jahoor, Ahmed; Orabi, Jihad

    2017-01-01

    The powdery mildew fungus, Blumeria graminis f. sp. hordei is a worldwide threat to barley (Hordeum vulgare L. ssp. vulgare) production. One way to control the disease is by the development and deployment of resistant cultivars. A genome-wide association study was performed in a Nordic spring barley panel consisting of 169 genotypes, to identify marker-trait associations significant for powdery mildew. Powdery mildew was scored during three years (2012–2014) in four different locations within the Nordic region. There were strong correlations between data from all locations and years. In total four QTLs were identified, one located on chromosome 4H in the same region as the previously identified mlo locus and three on chromosome 6H. Out of these three QTLs identified on chromosome 6H, two are in the same region as previously reported QTLs for powdery mildew resistance, whereas one QTL appears to be novel. The top NCBI BLASTn hit of the SNP markers within the novel QTL predicted the responsible gene to be the 26S proteasome regulatory subunit, RPN1, which is required for innate immunity and powdery mildew-induced cell death in Arabidopsis. The results from this study have revealed SNP marker candidates that can be exploited for use in marker-assisted selection and stacking of genes for powdery mildew resistance in barley. PMID:29184565

  6. From QTL to variety-harnessing the benefits of QTLs for drought, flood and salt tolerance in mega rice varieties of India through a multi-institutional network.

    Science.gov (United States)

    Singh, Renu; Singh, Yashi; Xalaxo, Suchit; Verulkar, S; Yadav, Neera; Singh, Shweta; Singh, Nisha; Prasad, K S N; Kondayya, K; Rao, P V Ramana; Rani, M Girija; Anuradha, T; Suraynarayana, Y; Sharma, P C; Krishnamurthy, S L; Sharma, S K; Dwivedi, J L; Singh, A K; Singh, P K; Nilanjay; Singh, N K; Kumar, Rajesh; Chetia, S K; Ahmad, T; Rai, M; Perraju, P; Pande, Anita; Singh, D N; Mandal, N P; Reddy, J N; Singh, O N; Katara, J L; Marandi, B; Swain, P; Sarkar, R K; Singh, D P; Mohapatra, T; Padmawathi, G; Ram, T; Kathiresan, R M; Paramsivam, K; Nadarajan, S; Thirumeni, S; Nagarajan, M; Singh, A K; Vikram, Prashant; Kumar, Arvind; Septiningshih, E; Singh, U S; Ismail, A M; Mackill, D; Singh, Nagendra K

    2016-01-01

    Rice is a staple cereal of India cultivated in about 43.5Mha area but with relatively low average productivity. Abiotic factors like drought, flood and salinity affect rice production adversely in more than 50% of this area. Breeding rice varieties with inbuilt tolerance to these stresses offers an economically viable and sustainable option to improve rice productivity. Availability of high quality reference genome sequence of rice, knowledge of exact position of genes/QTLs governing tolerance to abiotic stresses and availability of DNA markers linked to these traits has opened up opportunities for breeders to transfer the favorable alleles into widely grown rice varieties through marker-assisted backcross breeding (MABB). A large multi-institutional project, "From QTL to variety: marker-assisted breeding of abiotic stress tolerant rice varieties with major QTLs for drought, submergence and salt tolerance" was initiated in 2010 with funding support from Department of Biotechnology, Government of India, in collaboration with International Rice Research Institute, Philippines. The main focus of this project is to improve rice productivity in the fragile ecosystems of eastern, northeastern and southern part of the country, which bear the brunt of one or the other abiotic stresses frequently. Seven consistent QTLs for grain yield under drought, namely, qDTY1.1, qDTY2.1, qDTY2.2, qDTY3.1, qDTY3.2, qDTY9.1 and qDTY12.1 are being transferred into submergence tolerant versions of three high yielding mega rice varieties, Swarna-Sub1, Samba Mahsuri-Sub1 and IR 64-Sub1. To address the problem of complete submergence due to flash floods in the major river basins, the Sub1 gene is being transferred into ten highly popular locally adapted rice varieties namely, ADT 39, ADT 46, Bahadur, HUR 105, MTU 1075, Pooja, Pratikshya, Rajendra Mahsuri, Ranjit, and Sarjoo 52. Further, to address the problem of soil salinity, Saltol, a major QTL for salt tolerance is being transferred into

  7. Updated sesame genome assembly and fine mapping of plant height and seed coat color QTLs using a new high-density genetic map.

    Science.gov (United States)

    Wang, Linhai; Xia, Qiuju; Zhang, Yanxin; Zhu, Xiaodong; Zhu, Xiaofeng; Li, Donghua; Ni, Xuemei; Gao, Yuan; Xiang, Haitao; Wei, Xin; Yu, Jingyin; Quan, Zhiwu; Zhang, Xiurong

    2016-01-05

    Sesame is an important high-quality oil seed crop. The sesame genome was de novo sequenced and assembled in 2014 (version 1.0); however, the number of anchored pseudomolecules was higher than the chromosome number (2n = 2x = 26) due to the lack of a high-density genetic map with 13 linkage groups. We resequenced a permanent population consisting of 430 recombinant inbred lines and constructed a genetic map to improve the sesame genome assembly. We successfully anchored 327 scaffolds onto 13 pseudomolecules. The new genome assembly (version 2.0) included 97.5 % of the scaffolds greater than 150 kb in size present in assembly version 1.0 and increased the total pseudomolecule length from 233.7 to 258.4 Mb with 94.3 % of the genome assembled and 97.2 % of the predicted gene models anchored. Based on the new genome assembly, a bin map including 1,522 bins spanning 1090.99 cM was generated and used to identified 41 quantitative trait loci (QTLs) for sesame plant height and 9 for seed coat color. The plant height-related QTLs explained 3-24 % the phenotypic variation (mean value, 8 %), and 29 of them were detected in at least two field trials. Two major loci (qPH-8.2 and qPH-3.3) that contributed 23 and 18 % of the plant height were located in 350 and 928-kb spaces on Chr8 and Chr3, respectively. qPH-3.3, is predicted to be responsible for the semi-dwarf sesame plant phenotype and contains 102 candidate genes. This is the first report of a sesame semi-dwarf locus and provides an interesting opportunity for a plant architecture study of the sesame. For the sesame seed coat color, the QTLs of the color spaces L*, a*, and b* were detected with contribution rates of 3-46 %. qSCb-4.1 contributed approximately 39 % of the b* value and was located on Chr4 in a 199.9-kb space. A list of 32 candidate genes for the locus, including a predicted black seed coat-related gene, was determined by screening the newly anchored genome. This study offers a high

  8. Expression QTL-based analyses reveal candidate causal genes and loci across five tumor types

    Science.gov (United States)

    Li, Qiyuan; Stram, Alexander; Chen, Constance; Kar, Siddhartha; Gayther, Simon; Pharoah, Paul; Haiman, Christopher; Stranger, Barbara; Kraft, Peter; Freedman, Matthew L.

    2014-01-01

    The majority of trait-associated loci discovered through genome-wide association studies are located outside of known protein coding regions. Consequently, it is difficult to ascertain the mechanism underlying these variants and to pinpoint the causal alleles. Expression quantitative trait loci (eQTLs) provide an organizing principle to address both of these issues. eQTLs are genetic loci that correlate with RNA transcript levels. Large-scale data sets such as the Cancer Genome Atlas (TCGA) provide an ideal opportunity to systematically evaluate eQTLs as they have generated multiple data types on hundreds of samples. We evaluated the determinants of gene expression (germline variants and somatic copy number and methylation) and performed cis-eQTL analyses for mRNA expression and miRNA expression in five tumor types (breast, colon, kidney, lung and prostate). We next tested 149 known cancer risk loci for eQTL effects, and observed that 42 (28.2%) were significantly associated with at least one transcript. Lastly, we described a fine-mapping strategy for these 42 eQTL target–gene associations based on an integrated strategy that combines the eQTL level of significance and the regulatory potential as measured by DNaseI hypersensitivity. For each of the risk loci, our analyses suggested 1 to 81 candidate causal variants that may be prioritized for downstream functional analysis. In summary, our study provided a comprehensive landscape of the genetic determinants of gene expression in different tumor types and ranked the genes and loci for further functional assessment of known cancer risk loci. PMID:24907074

  9. 29 CFR 785.45 - Suggestion systems.

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 3 2010-07-01 2010-07-01 false Suggestion systems. 785.45 Section 785.45 Labor Regulations..., Medical Attention, Civic and Charitable Work, and Suggestion Systems § 785.45 Suggestion systems... general suggestion system is not working time, but if employees are permitted to work on suggestions...

  10. A suggested method for dispersion model evaluation.

    Science.gov (United States)

    Irwin, John S

    2014-03-01

    Too often operational atmospheric dispersion models are evaluated in their ability to replicate short-term concentration maxima, when in fact a valid model evaluation procedure would evaluate a model's ability to replicate ensemble-average patterns in hourly concentration values. A valid model evaluation includes two basic tasks: In Step 1 we should analyze the observations to provide average patterns for comparison with modeled patterns, and in Step 2 we should account for the uncertainties inherent in Step 1 so we can tell whether differences seen in a comparison of performance of several models are statistically significant. Using comparisons of model simulation results from AERMOD and ISCST3 with tracer concentration values collected during the EPRI Kincaid experiment, a candidate model evaluation procedure is demonstrated that assesses whether a model has the correct total mass at the receptor level (crosswind integrated concentration values) and whether a model is correctly spreading the mass laterally (lateral dispersion), and assesses the uncertainty in characterizing the transport. The use of the BOOT software (preferably using the ASTMD 6589 resampling procedure) is suggested to provide an objective assessment of whether differences in model performance between models are significant. Regulatory agencies can choose to treat modeling results as "pseudo-monitors," but air quality models actually only predict what they are constructed to predict, which certainly does not include the stochastic variations that result in observed short-term maxima (e.g., arc-maxima). Models predict the average concentration pattern of a collection of hours having very similar dispersive conditions. An easy-to-implement evaluation procedure is presented that challenges a model to properly estimate ensemble average concentration values, reveals where to look in a model to remove bias, and provides statistical tests to assess the significance of skill differences seen between

  11. Construction of a high-density linkage map and fine mapping of QTLs for growth and gonad related traits in blunt snout bream.

    Science.gov (United States)

    Wan, Shi-Ming; Liu, Hong; Zhao, Bo-Wen; Nie, Chun-Hong; Wang, Wei-Min; Gao, Ze-Xia

    2017-04-19

    High-density genetic maps based on SNPs are essential for fine mapping loci controlling specific traits for fish species. Using restriction-site associated DNA tag sequencing (RAD-Seq) technology, we identified 42,784 SNPs evenly distributed across the Megalobrama amblycephala genome. Based on 2 parents and 187 intra-specific hybridization progenies, a total of 14,648 high-confidence SNPs were assigned to 24 consensus linkage groups (LGs) of maternal and paternal map. The total length of the integrated map was 3,258.38 cM with an average distance of 0.57 cM among 5676 effective loci, thereby representing the first high-density genetic map reported for M. amblycephala. A total of eight positive quantitative trait loci (QTLs) were detected in QTL analysis. Of that, five QTL explained ≥35% of phenotypic variation for growth traits and three QTL explained ≥16% phenotypic variation for gonad related traits. A total of 176 mapped markers had significant hits in the zebrafish genome and almost all of the 24 putative-chromosomes of M. amblycephala were in relatively conserved synteny with chromosomes of zebrafish. Almost all M. amblycephala and zebrafish chromosomes had a 1:1 correspondence except for putative-chromosome 4, which mapped to two chromosomes of zebrafish caused by the difference in chromosome numbers between two species.

  12. High-density genetic map and identification of QTLs for responses to temperature and salinity stresses in the model brown alga Ectocarpus

    Science.gov (United States)

    Avia, Komlan; Coelho, Susana M.; Montecinos, Gabriel J.; Cormier, Alexandre; Lerck, Fiona; Mauger, Stéphane; Faugeron, Sylvain; Valero, Myriam; Cock, J. Mark; Boudry, Pierre

    2017-01-01

    Deciphering the genetic architecture of adaptation of brown algae to environmental stresses such as temperature and salinity is of evolutionary as well as of practical interest. The filamentous brown alga Ectocarpus sp. is a model for the brown algae and its genome has been sequenced. As sessile organisms, brown algae need to be capable of resisting the various abiotic stressors that act in the intertidal zone (e.g. osmotic pressure, temperature, salinity, UV radiation) and previous studies have shown that an important proportion of the expressed genes is regulated in response to hyposaline, hypersaline or oxidative stress conditions. Using the double digest RAD sequencing method, we constructed a dense genetic map with 3,588 SNP markers and identified 39 QTLs for growth-related traits and their plasticity under different temperature and salinity conditions (tolerance to high temperature and low salinity). GO enrichment tests within QTL intervals highlighted membrane transport processes such as ion transporters. Our study represents a significant step towards deciphering the genetic basis of adaptation of Ectocarpus sp. to stress conditions and provides a substantial resource to the increasing list of tools generated for the species. PMID:28256542

  13. QTLs for cell wall-bound phenolics in relation to the photosynthetic apparatus activity and leaf water status under drought stress at different growth stages of triticale.

    Science.gov (United States)

    Hura, Tomasz; Tyrka, Mirosław; Hura, Katarzyna; Ostrowska, Agnieszka; Dziurka, Kinga

    2017-04-01

    The present study aimed at identifying the regions of triticale genome responsible for cell wall saturation with phenolic compounds under drought stress during vegetative and generative growth. Moreover, the loci determining the activity of the photosynthetic apparatus, leaf water content (LWC) and osmotic potential (Ψ o) were identified, as leaf hydration and functioning of the photosynthetic apparatus under drought are associated with the content of cell wall-bound phenolics (CWPh). Compared with LWC and Ψ o, CWPh fluctuations were more strongly associated with changes in chlorophyll fluorescence. At the vegetative stage, CWPh fluctuations were due to the activity of three loci, of which only QCWPh.4B was also related to changes in F v/F m and ABS/CSm. In the other QTLs (QCWPh.6R.2 and QCWPh.6R.3), the genes of these loci determined also the changes in majority of chlorophyll fluorescence parameters. At the generative stage, the changes in CWPh in loci QCWPh.4B, QCWPh.3R and QCWPh.6R.1 corresponded to those in DIo/CSm. The locus QCWPh.6R.3, active at V stage, controlled majority of chlorophyll fluorescence parameters. This is the first study on mapping quantitative traits in triticale plants exposed to drought at different stages of development, and the first to present the loci for cell wall-bound phenolics.

  14. Reinventing suggestion systems for continuous improvement

    NARCIS (Netherlands)

    Schuring, R.W.; Luijten, Harald

    2001-01-01

    This article reports an experiment to increase the effectiveness of a suggestion system by deliberately applying principles of the kaizen and performance management. Design rules for suggestion systems are derived from these theories. The suggestion system that resulted differs from traditional

  15. Regulating professional behavior: codes of ethics or law? Suggested criteria.

    Science.gov (United States)

    Libman, Liron A

    2013-09-01

    This paper suggests considering a few parameters when making policy decisions as to the proper "tool" to regulate professional behavior: law or professional ethics. This is done on the background of understanding the place of codes of professional ethics between "pure" ethics and law. Suggested criteria are then illustrated using a few examples. Further discourse may reveal additional factors to support a more rational process of decision-making in this field.

  16. Two new behavioral QTLs, Emo4 and Reb1, map to mouse Chromosome 1: Congenic strains and candidate gene identification studies.

    Science.gov (United States)

    de Ledesma, Ana Maria Rodriguez; Desai, Aarti N; Bolivar, Valerie J; Symula, Derek J; Flaherty, Lorraine

    2006-02-01

    By use of newly developed subcongenic strains of mice from a parental B6.129-Il10-/- knockout/congenic strain, we have narrowed the critical region for a new behavioral QTL, called Emo4, for open-field activity to a segment of Chromosome 1 between Erbb4 (68.4Mb) and B3gnt7 (86.2 Mb). We have also uncovered an additional QTL governing repetitive beam breaks in the open field. This QTL, called Reb1, maps to the interval between Asb1 (91.4 Mb) and NM_172851 (100.0 Mb) and is one of the first QTLs mapped for this type of behavior. Genome-wide microarray expression analyses were then undertaken to help to identify candidate genes that may be the cause of these genetic differences in open-field performance. In this effort, we analyzed global gene expression differences in the amygdalae by use of Affymetrix GeneChips between B6, B6.129-Il10-/-, and B6.129R4. Several probe sets representing target Chr 1 genes were found that showed significantly differential expression in the subcongenic and congenic strains. Several candidate genes have been identified. One of these regions coincides with an homologous region in humans that has been associated with autism, a disease whose symptoms include repetitive actions. This study illustrates that the use of congenic strains combined with global gene expression analyses can produce a list of viable candidates. It further shows that caution should be observed when analyzing the effects of knockout/congenic strains because many of the gene expression differences in these comparisons could not be attributable to the ablated Il10 gene but rather to passenger gene effects.

  17. Suggested physical therapy protocol for reduction of lipomatosis ...

    African Journals Online (AJOL)

    Mohamed M. Khalaf

    2012-11-11

    Nov 11, 2012 ... The results revealed a significant improvement (P < 0.05) in BMI and the lower limb volumes. It could be concluded that, suggested physical therapy protocol consisting of a complete decongestive physical therapy program and diet regimen had an effect in the treatment of lipomatosis dolorosa of the legs in.

  18. Hypnotic suggestion: opportunities for cognitive neuroscience.

    Science.gov (United States)

    Oakley, David A; Halligan, Peter W

    2013-08-01

    Hypnosis uses the powerful effects of attention and suggestion to produce, modify and enhance a broad range of subjectively compelling experiences and behaviours. For more than a century, hypnotic suggestion has been used successfully as an adjunctive procedure to treat a wide range of clinical conditions. More recently, hypnosis has attracted a growing interest from a cognitive neuroscience perspective. Recent studies using hypnotic suggestion show how manipulating subjective awareness in the laboratory can provide insights into brain mechanisms involved in attention, motor control, pain perception, beliefs and volition. Moreover, they indicate that hypnotic suggestion can create informative analogues of clinical conditions that may be useful for understanding these conditions and their treatments.

  19. Petrographic observations suggestive of microbial mats from ...

    Indian Academy of Sciences (India)

    Petrographic observations of two Vindhyan black shales (Rampur Shale of the Semri Group and. Bijaigarh Shale of the Kaimur Group) revealed the following features: • general wavy lamination,. • contorted and folded thin shreds of organic matter,. • wavy pyritic laminae,. • 'teeth and socket' structure. These features are ...

  20. Petrographic observations suggestive of microbial mats from ...

    Indian Academy of Sciences (India)

    Petrographic observations of two Vindhyan black shales (Rampur Shale of the Semri Group and Bijaigarh Shale of the Kaimur Group)revealed the following features: general wavy lamination,; contorted and folded thin shreds of organic matter,; wavy pyritic laminae,; 'teeth and socket 'structure. These features are indirect ...

  1. Maltreated Children's Memory: Accuracy, Suggestibility, and Psychopathology

    Science.gov (United States)

    Eisen, Mitchell L.; Goodman, Gail S.; Qin, Jianjian; Davis, Suzanne; Crayton, John

    2007-01-01

    Memory, suggestibility, stress arousal, and trauma-related psychopathology were examined in 328 3- to 16-year-olds involved in forensic investigations of abuse and neglect. Children's memory and suggestibility were assessed for a medical examination and venipuncture. Being older and scoring higher in cognitive functioning were related to fewer…

  2. Query term suggestion in academic search

    NARCIS (Netherlands)

    Verberne, S.; Sappelli, M.; Kraaij, W.

    2014-01-01

    In this paper, we evaluate query term suggestion in the context of academic professional search. Our overall goal is to support scientists in their information seeking tasks. We set up an interactive search system in which terms are extracted from clicked documents and suggested to the user before

  3. Electrocardiographic features suggestive of a left. ventricular ...

    African Journals Online (AJOL)

    SA MEDICAL JOURNAL VOLUME 63 1 JANUARY 1983. 27. Electrocardiographic features suggestive of a left. ventricular' aneurysm following a high-velocity missile injury. A case report. T. H. DIAMOND, R. SMITH, D. P. MYBURGH, L. STEINGO. Summary. Electrocardiographic features suggestive of a transmural anterior ...

  4. Microsatellite mapping of QTLs affecting resistance to coccidiosis (Eimeria tenella) in a Fayoumi × White Leghorn cross

    Science.gov (United States)

    Pinard-van der Laan, Marie-Hélène; Bed'hom, Bertrand; Coville, Jean-Luc; Pitel, Frédérique; Feve, Katia; Leroux, Sophie; Legros, Hélène; Thomas, Aurélie; Gourichon, David; Repérant, Jean-Michel; Rault, Paul

    2009-01-01

    Background Avian coccidiosis is a major parasitic disease of poultry, causing severe economical loss to poultry production by affecting growth and feed efficiency of infected birds. Current control strategies using mainly drugs and more recently vaccination are showing drawbacks and alternative strategies are needed. Using genetic resistance that would limit the negative and very costly effects of the disease would be highly relevant. The purpose of this work was to detect for the first time QTL for disease resistance traits to Eimeria tenella in chicken by performing a genome scan in an F2 cross issued from a resistant Fayoumi line and a susceptible Leghorn line. Results The QTL analysis detected 21 chromosome-wide significant QTL for the different traits related to disease resistance (body weight growth, plasma coloration, hematocrit, rectal temperature and lesion) on 6 chromosomes. Out of these, a genome-wide very significant QTL for body weight growth was found on GGA1, five genome-wide significant QTL for body weight growth, plasma coloration and hematocrit and one for plasma coloration were found on GGA1 and GGA6, respectively. Two genome-wide suggestive QTL for plasma coloration and rectal temperature were found on GGA1 and GGA2, respectively. Other chromosme-wide significant QTL were identified on GGA2, GGA3, GGA6, GGA15 and GGA23. Parent-of-origin effects were found for QTL for body weight growth and plasma coloration on GGA1 and GGA3. Several QTL for different resistance phenotypes were identified as co-localized on the same location. Conclusion Using an F2 cross from resistant and susceptible chicken lines proved to be a successful strategy to identify QTL for different resistance traits to Eimeria tenella, opening the way for further gene identification and underlying mechanisms and hopefully possibilities for new breeding strategies for resistance to coccidiosis in the chicken. From the QTL regions identified, several candidate genes and relevant

  5. Microsatellite mapping of QTLs affecting resistance to coccidiosis (Eimeria tenella in a Fayoumi × White Leghorn cross

    Directory of Open Access Journals (Sweden)

    Gourichon David

    2009-01-01

    Full Text Available Abstract Background Avian coccidiosis is a major parasitic disease of poultry, causing severe economical loss to poultry production by affecting growth and feed efficiency of infected birds. Current control strategies using mainly drugs and more recently vaccination are showing drawbacks and alternative strategies are needed. Using genetic resistance that would limit the negative and very costly effects of the disease would be highly relevant. The purpose of this work was to detect for the first time QTL for disease resistance traits to Eimeria tenella in chicken by performing a genome scan in an F2 cross issued from a resistant Fayoumi line and a susceptible Leghorn line. Results The QTL analysis detected 21 chromosome-wide significant QTL for the different traits related to disease resistance (body weight growth, plasma coloration, hematocrit, rectal temperature and lesion on 6 chromosomes. Out of these, a genome-wide very significant QTL for body weight growth was found on GGA1, five genome-wide significant QTL for body weight growth, plasma coloration and hematocrit and one for plasma coloration were found on GGA1 and GGA6, respectively. Two genome-wide suggestive QTL for plasma coloration and rectal temperature were found on GGA1 and GGA2, respectively. Other chromosme-wide significant QTL were identified on GGA2, GGA3, GGA6, GGA15 and GGA23. Parent-of-origin effects were found for QTL for body weight growth and plasma coloration on GGA1 and GGA3. Several QTL for different resistance phenotypes were identified as co-localized on the same location. Conclusion Using an F2 cross from resistant and susceptible chicken lines proved to be a successful strategy to identify QTL for different resistance traits to Eimeria tenella, opening the way for further gene identification and underlying mechanisms and hopefully possibilities for new breeding strategies for resistance to coccidiosis in the chicken. From the QTL regions identified, several

  6. QTL mapping of fungicide sensitivity reveals novel genes and pleiotropy with melanization in the pathogen Zymoseptoria tritici.

    Science.gov (United States)

    Lendenmann, Mark H; Croll, Daniel; McDonald, Bruce A

    2015-07-01

    A major problem associated with the intensification of agriculture is the emergence of fungicide resistance. Azoles are ergosterol biosynthesis inhibitors that have been widely used in agriculture and medicine since the 1970s, leading to emergence of increasingly resistant fungal populations. The known genetic mechanisms underlying lower azole sensitivity include mutations affecting the CYP51 gene that encodes the target protein, but in many cases azole resistance is a more complex trait with an unknown genetic basis. We used quantitative trait locus (QTL) mapping to identify genes affecting azole sensitivity in two crosses of Zymoseptoria tritici, the most damaging wheat pathogen in Europe. Restriction site associated DNA sequencing (RADseq) was used to genotype 263 (cross 1) and 261 (cross 2) progeny at ∼ 8500 single nucleotide polymorphisms (SNP) and construct two dense linkage maps. Azole sensitivity was assessed using high-throughput digital image analysis of colonies growing on Petri dishes with or without the fungicide propiconazole. We identified three QTLs for azole sensitivity, including two that contained novel fungicide sensitivity genes. One of these two QTLs contained only 16 candidate genes, among which four most likely candidates were identified. The third QTL contained ERG6, encoding another protein involved in ergosterol biosynthesis. Known genes in QTLs affecting colony growth included CYP51 and PKS1, a gene affecting melanization in Z. tritici. PKS1 showed compelling evidence for pleiotropy, with a rare segregating allele that increased melanization while decreasing growth rate and propiconazole sensitivity. This study resolved the genetic architecture of an important agricultural trait and led to identification of novel genes that are likely to affect azole sensitivity in Z. tritici. It also provided insight into fitness costs associated with lowered azole sensitivity and suggests a novel fungicide mixture strategy. Copyright © 2015 Elsevier

  7. Measuring Children's Suggestibility in Forensic Interviews.

    Science.gov (United States)

    Volpini, Laura; Melis, Manuela; Petralia, Stefania; Rosenberg, Melina D

    2016-01-01

    According to the scientific literature, childrens' cognitive development is not complete until adolescence. Therefore, the problems inherent in children serving as witnesses are crucial. In preschool-aged children, false memories may be identified because of misinformation and insight bias. Additionally, they are susceptible of suggestions. The aim of this study was to verify the levels of suggestibility in children between three and 5 years of age. Ninety-two children were examined (44 male, 48 female; M = 4.5 years, SD = 9.62). We used the correlation coefficient (Pearson's r) and the averages variance by SPSS statistical program. The results concluded that: younger children are almost always more susceptible to suggestibility. The dimension of immediate recall was negatively correlates with that of total suggestibility (r = -0.357 p Forensic Sciences.

  8. Electrocardiographic features suggestive of a left. ventricular ...

    African Journals Online (AJOL)

    Abstract. Electrocardiographic features suggestive of a transmural anterior myocardial infarction with resultant left ventricular aneurysm formation were found in a 22-year-old man who had sustained a ballistic missile injury to his chest.

  9. Suggestions for Customer Strategy Updates : Finnish Customs

    OpenAIRE

    Kaisto, Raisa

    2014-01-01

    The case organization Finnish Customs wanted to be provided with new suggestions for their customer strategy updates. The first objective of this study was to study how the needs of the partnership and key customers are met in the customer strategy and provide suggestions for improvements. Another objective was to research the legislation influencing the customer strategy development. The customer strategy was created in 2004 and it was combined with other strategies in 2013. The customer...

  10. LSD enhances suggestibility in healthy volunteers.

    Science.gov (United States)

    Carhart-Harris, R L; Kaelen, M; Whalley, M G; Bolstridge, M; Feilding, A; Nutt, D J

    2015-02-01

    Lysergic acid diethylamide (LSD) has a history of use as a psychotherapeutic aid in the treatment of mood disorders and addiction, and it was also explored as an enhancer of mind control. The present study sought to test the effect of LSD on suggestibility in a modern research study. Ten healthy volunteers were administered with intravenous (i.v.) LSD (40-80 μg) in a within-subject placebo-controlled design. Suggestibility and cued mental imagery were assessed using the Creative Imagination Scale (CIS) and a mental imagery test (MIT). CIS and MIT items were split into two versions (A and B), balanced for 'efficacy' (i.e. A ≈ B) and counterbalanced across conditions (i.e. 50 % completed version 'A' under LSD). The MIT and CIS were issued 110 and 140 min, respectively, post-infusion, corresponding with the peak drug effects. Volunteers gave significantly higher ratings for the CIS (p = 0.018), but not the MIT (p = 0.11), after LSD than placebo. The magnitude of suggestibility enhancement under LSD was positively correlated with trait conscientiousness measured at baseline (p = 0.0005). These results imply that the influence of suggestion is enhanced by LSD. Enhanced suggestibility under LSD may have implications for its use as an adjunct to psychotherapy, where suggestibility plays a major role. That cued imagery was unaffected by LSD implies that suggestions must be of a sufficient duration and level of detail to be enhanced by the drug. The results also imply that individuals with high trait conscientiousness are especially sensitive to the suggestibility-enhancing effects of LSD.

  11. A high-resolution genetic map of yellow monkeyflower identifies chemical defense QTLs and recombination rate variation.

    Science.gov (United States)

    Holeski, Liza M; Monnahan, Patrick; Koseva, Boryana; McCool, Nick; Lindroth, Richard L; Kelly, John K

    2014-03-13

    Genotyping-by-sequencing methods have vastly improved the resolution and accuracy of genetic linkage maps by increasing both the number of marker loci as well as the number of individuals genotyped at these loci. Using restriction-associated DNA sequencing, we construct a dense linkage map for a panel of recombinant inbred lines derived from a cross between divergent ecotypes of Mimulus guttatus. We used this map to estimate recombination rate across the genome and to identify quantitative trait loci for the production of several secondary compounds (PPGs) of the phenylpropanoid pathway implicated in defense against herbivores. Levels of different PPGs are correlated across recombinant inbred lines suggesting joint regulation of the phenylpropanoid pathway. However, the three quantitative trait loci identified in this study each act on a distinct PPG. Finally, we map three putative genomic inversions differentiating the two parental populations, including a previously characterized inversion that contributes to life-history differences between the annual/perennial ecotypes. Copyright © 2014 Holeski et al.

  12. Evidence of Bos javanicus x Bos indicus hybridization and major QTLs for birth weight in Indonesian Peranakan Ongole cattle.

    Science.gov (United States)

    Hartati, Hartati; Utsunomiya, Yuri Tani; Sonstegard, Tad Stewart; Garcia, José Fernando; Jakaria, Jakaria; Muladno, Muladno

    2015-07-04

    Peranakan Ongole (PO) is a major Indonesian Bos indicus breed that derives from animals imported from India in the late 19(th) century. Early imports were followed by hybridization with the Bos javanicus subspecies of cattle. Here, we used genomic data to partition the ancestry components of PO cattle and map loci implicated in birth weight. We found that B. javanicus contributes about 6-7% to the average breed composition of PO cattle. Only two nearly fixed B. javanicus haplotypes were identified, suggesting that most of the B. javanicus variants are segregating under drift or by the action of balancing selection. The zebu component of the PO genome was estimated to derive from at least two distinct ancestral pools. Additionally, well-known loci underlying body size in other beef cattle breeds, such as the PLAG1 region on chromosome 14, were found to also affect birth weight in PO cattle. This study is the first attempt to characterize PO at the genome level, and contributes evidence of successful, stabilized B. indicus x B. javanicus hybridization. Additionally, previously described loci implicated in body size in worldwide beef cattle breeds also affect birth weight in PO cattle.

  13. Multi-allelic major effect genes interact with minor effect QTLs to control adaptive color pattern variation in Heliconius erato.

    Directory of Open Access Journals (Sweden)

    Riccardo Papa

    Full Text Available Recent studies indicate that relatively few genomic regions are repeatedly involved in the evolution of Heliconius butterfly wing patterns. Although this work demonstrates a number of cases where homologous loci underlie both convergent and divergent wing pattern change among different Heliconius species, it is still unclear exactly how many loci underlie pattern variation across the genus. To address this question for Heliconius erato, we created fifteen independent crosses utilizing the four most distinct color pattern races and analyzed color pattern segregation across a total of 1271 F2 and backcross offspring. Additionally, we used the most variable brood, an F2 cross between H. himera and the east Ecuadorian H. erato notabilis, to perform a quantitative genetic analysis of color pattern variation and produce a detailed map of the loci likely involved in the H. erato color pattern radiation. Using AFLP and gene based markers, we show that fewer major genes than previously envisioned control the color pattern variation in H. erato. We describe for the first time the genetic architecture of H. erato wing color pattern by assessing quantitative variation in addition to traditional linkage mapping. In particular, our data suggest three genomic intervals modulate the bulk of the observed variation in color. Furthermore, we also identify several modifier loci of moderate effect size that contribute to the quantitative wing pattern variation. Our results are consistent with the two-step model for the evolution of mimetic wing patterns in Heliconius and support a growing body of empirical data demonstrating the importance of major effect loci in adaptive change.

  14. Suggestions for Structuring a Research Article

    Science.gov (United States)

    Klein, James D.; Reiser, Robert A.

    2014-01-01

    Researchers often experience difficulty as they attempt to prepare journal articles that describe their work. The purpose of this article is to provide researchers in the field of education with a series of suggestions as to how to clearly structure each section of a research manuscript that they intend to submit for publication in a scholarly…

  15. Family Living: Suggestions for Effective Parenting.

    Science.gov (United States)

    Katz, Lilian G.; And Others

    Suggestions for effective parenting of preschool children are provided in 33 brief articles on children's feelings concerning self-esteem; fear; adopted children; the birth of a sibling; death; depression; and coping with stress, trauma, and divorce. Children's behavior is discussed in articles on toddlers' eating habits, punishment and…

  16. IRIT at TREC 2014 Contextual Suggestion Track

    Science.gov (United States)

    2014-11-01

    both criteria users preferences and geographical location criteria. 1 Introduction TREC3 2014 Contextual Suggestion track examines search techniques...Contextual Retrieval Framework We address here the contextual retrieval problem as a multi-criteria decision making ( MCDM ) problem. The difficulty here

  17. Studies and Suggestions on Prewriting Activities

    Science.gov (United States)

    Zheng, Shigao; Dai, Weiping

    2012-01-01

    This paper studies and suggests the need for writing instruction by which students can experience writing as a creative process in exploring and communicating meaning. The prewriting activities generate ideas which can encourage a free flow of thoughts and help students discover both what they want to say and how to say it on paper. Through the…

  18. Leadership Theories--Managing Practices, Challenges, Suggestions

    Science.gov (United States)

    Hawkins, Cheryl

    2009-01-01

    A shortage of community college executives due to the number of retirements occurring among current leaders is predicted. An examination of three leadership theories--servant-leadership, business leadership and transformational leadership--suggests techniques for potential community college leaders. Servant-leaders focus on the needs of their…

  19. Qualitative Research Articles: Guidelines, Suggestions and Needs

    Science.gov (United States)

    Crescentini, Alberto; Mainardi, Giuditta

    2009-01-01

    Purpose: The purpose of this paper is to give ideas and suggestions to avoid some typical problems of qualitative articles. The aim is not to debate quality in qualitative research but to indicate some practical solutions. Design/methodology/approach: The paper discusses the design of qualitative research and the structure of a qualitative article…

  20. Current Research: 2013 Summer Reading Suggestions

    Science.gov (United States)

    Journal of College Science Teaching, 2013

    2013-01-01

    To supplement the summer reading of National Science Teachers Association (NSTA) members, the NSTA Committee on Research in Science Education suggested a list of science education research articles that were published in the journals of NSTA's affiliates in 2012. These articles covered a variety of topics that include learning about…

  1. Integrating Composition and Literature: Some Practical Suggestions.

    Science.gov (United States)

    Daiker, Donald A.

    This paper suggests that it is possible to construct a course that integrates the teaching of composition with the teaching of literature without allowing the secondary goal of heightened literary understanding to overwhelm the primary goal of improved expository writing. It presents a syllabus for a four-week unit on Ernest Hemingway's "The Sun…

  2. Fine-mapping resolves Eae23 into two QTLs and implicates ZEB1 as a candidate gene regulating experimental neuroinflammation in rat.

    Directory of Open Access Journals (Sweden)

    Pernilla Stridh

    Full Text Available BACKGROUND: To elucidate mechanisms involved in multiple sclerosis (MS, we studied genetic regulation of experimental autoimmune encephalomyelitis (EAE in rats, assuming a conservation of pathogenic pathways. In this study, we focused on Eae23, originally identified to regulate EAE in a (LEW.1AV1xPVG.1AV1F2 cross. Our aim was to determine whether one or more genes within the 67 Mb region regulate EAE and to define candidate risk genes. METHODOLOGY/PRINCIPAL FINDINGS: We used high resolution quantitative trait loci (QTL analysis in the 10th generation (G10 of an advanced intercross line (AIL to resolve Eae23 into two QTLs that independently regulate EAE, namely Eae23a and Eae23b. We established a congenic strain to validate the effect of this region on disease. PVG alleles in Eae23 resulted in significant protection from EAE and attenuated CNS inflammation/demyelination. Disease amelioration was accompanied with increased levels of Foxp3(+ cells in the CNS of the congenic strain compared to DA. We then focused on candidate gene investigation in Eae23b, a 9 Mb region linked to all clinical phenotypes. Affymetrix exon arrays were used to study expression of the genes in Eae23b in the parental strains, where none showed differential expression. However, we found lower expression of exon 4 of ZEB1, which is specific for splice-variant Zfhep1. ZEB1 is an interleukin 2 (IL2 repressor involved in T cell development. The splice-specific variance prompted us to next analyze the expression of ZEB1 and its two splice variants, Zfhep1 and Zfhep2, in both lymph node and spleen. We demonstrated that ZEB1 splice-variants are differentially expressed; severity of EAE and higher IL2 levels were associated with down-regulation of Zfhep1 and up-regulation of Zfhep2. CONCLUSIONS/SIGNIFICANCE: We speculate that the balance between splice-variants of ZEB1 could influence the regulation of EAE. Further functional studies of ZEB1 and the splice-variants may unravel

  3. Atypical stab injury suggesting ritual suicide

    Directory of Open Access Journals (Sweden)

    Štěpánka Kučerová

    2016-11-01

    Full Text Available Sharp weapons have been one of the most common deadly tools in cases of homicide and suicide for a long time. Tentative incisions accompany the majority of suicides by sharp force and the absence of hesitation marks provokes questions about the manner of death. We present the bizarre fatality of a 41-year-old male with an isolated circumscribed incision on the right neck, where the body was found lying in a pool of blood in the shower of his apartment. The internal examination revealed a 4-cm-long channel-like defect running inwardly and downwardly along the right sternocleidomastoid region. The cause of death was external bleeding from an injured right carotid artery and internal jugular vein. The wound had clean non-contused margins without any conspicuous hesitation injuries. A fragment of a razor blade, found in blood splatters, was identified as the only potential injuring tool. The case was classified as a suicide.

  4. Does neuroimaging of suggestion elucidate hypnotic trance?

    Science.gov (United States)

    Raz, Amir

    2011-07-01

    Contemporary studies in the cognitive neuroscience of attention and suggestion shed new light on the underlying neural mechanisms that operationalize these effects. Without adhering to important caveats inherent to imaging of the living human brain, however, findings from brain imaging studies may enthrall more than explain. Scholars, practitioners, professionals, and consumers must realize that the influence words exert on focal brain activity is measurable but that these measurements are often difficult to interpret. While recent brain imaging research increasingly incorporates variations of suggestion and hypnosis, correlating overarching hypnotic experiences with specific brain substrates remains tenuous. This article elucidates the mounting role of cognitive neuroscience, including the relative merits and intrinsic limitations of neuroimaging, in better contextualizing trance-like concepts.

  5. Euthanasia and mental retardation: suggesting the unthinkable.

    Science.gov (United States)

    Hollander, R

    1989-04-01

    Current opinions on euthanasia of persons with mental retardation were discussed within the framework of the development of social policy towards this population. Historians of mental retardation have emphasized that incarceration and sterilization were the only two policy options available in the late 19th and early 20th centuries, but a third option, euthanasia, was also suggested. The significance of the euthanasia option as the nation struggled to find a solution to the question of how to deal with what was thought to be a sharp rise in the number of people with mental retardation in the United States in the late 19th and early 20th centuries was examined. The responses of service providers to suggestions that euthanasia be implemented were reviewed. The rejection of proposals for euthanasia on moral and religious grounds and on the basis that custodial institutions, based on eugenics principles, were able to achieve the same end through a scientifically justifiable means was explored.

  6. Overview of the SBS 2016 Suggestion Track

    DEFF Research Database (Denmark)

    Koolen, Marijn; Bogers, Toine; Jaap, Kamps

    2016-01-01

    The goal of the SBS 2016 Suggestion Track is to evaluate approaches for supporting users in searching collections of books who express their information needs both in a query and through example books. The track investigates the complex nature of relevance in book search and the role of traditional...... and user-generated book metadata in retrieval. We consolidated last year’s investigation into the nature of book suggestions from the LibraryThing forums and how they compare to book relevance judgements. Participants were encouraged to incorporate rich user profiles of both topic creators and other...... LibraryThing users to explore the relative value of recommendation and retrieval paradigms for book search....

  7. [Suggestions to improve dentist-endodontist collaboration].

    Science.gov (United States)

    Zabalegui, B; Zabalegui, I; Flores, L

    1989-01-01

    Referrals from the general dentist to the endodontist are in some occasions complicated with lack of proper communication among dentist-patient-specialist, resulting in the loss of confidence or even the patient. Suggestions to improve this communication are discussed, which will provide the patient a higher confidence in the indicated endodontic treatment and a better dental service. It will also enhance the prestige of the general dentists' and specialists' practice.

  8. Application for Suggesting Restaurants Using Clustering Algorithms

    Directory of Open Access Journals (Sweden)

    Iulia Alexandra IANCU

    2014-10-01

    Full Text Available The aim of this article is to present an application whose purpose is to make suggestions of restaurants to users. The application uses as input the descriptions of restaurants, reviews, user reviews available on the specialized Internet sites and blogs. In the application there are used processing techniques of natural language implemented using parsers, clustering algorithms and techniques for data collection from the Internet through web crawlers.

  9. Performance evaluation of the suggestion system.

    Science.gov (United States)

    Hadi, Mohammad; Sajjadi, Haniye Sadat; Baratpour, Sara; Toghiani, Ali

    2013-01-01

    This cross-sectional research evaluated the suggestion system of Isfahan University of Medical Sciences (IUMS) using CIPP model. The population consisted of all members of executive committee of suggestion system and the members of professional and general committee of IUMS; regarding to some limitations, sampling was not done. The tool of gathering data was a self-constructed questionnaire that its content validity approved by the professors' ideas, and calculating Cronbach's alpha confirmed its reliability. Collected data was analyzed using SPSS software. Analyzed data showed that the average score of the performance of the mentioned system was 50.47 +/- 14.8; based on this result it can be claimed that most of the participants (about 91%) evaluated the performance of the system moderate. The comparison of the average score of the four dimensions of CIPP model showed that the input dimension had the highest score and process, product and context dimensions were next on the hierarchy. Planning some programs for paying awards, facilitating and accelerating the personnel's and notifying the procedures of the suggestion system implementation are some useful strategy that could be used to increase the staff's participants.

  10. Preventing motor training through nocebo suggestions.

    Science.gov (United States)

    Pollo, Antonella; Carlino, Elisa; Vase, Lene; Benedetti, Fabrizio

    2012-11-01

    Although placebos have repeatedly been shown to increase physical performance and endurance, much less is known about the effect of their negative counterpart, nocebos. Here, we employ negative suggestions and a sham electrical stimulation as a nocebo conditioning procedure in healthy subjects performing a leg extension exercise to total exhaustion. Using two different protocols, we analyze the contribution of expectation alone or the combination of conditioning and expectation to the nocebo effect evaluated as the change of work performed and rate of perceived exertion. We find that it is possible to negatively modulate the physical performance in both cases, and we argue that this effect can effectively offset the outcome of training programs.

  11. Dinosaur Peptides Suggest Mechanisms of Protein Survival

    Energy Technology Data Exchange (ETDEWEB)

    San Antonio, James D.; Schweitzer, Mary H.; Jensen, Shane T.; Kalluri, Raghu; Buckley, Michael; Orgel, Joseph P.R.O. (Harvard-Med); (IIT); (NCSU); (UPENN); (Manchester); (Orthovita)

    2011-09-16

    Eleven collagen peptide sequences recovered from chemical extracts of dinosaur bones were mapped onto molecular models of the vertebrate collagen fibril derived from extant taxa. The dinosaur peptides localized to fibril regions protected by the close packing of collagen molecules, and contained few acidic amino acids. Four peptides mapped to collagen regions crucial for cell-collagen interactions and tissue development. Dinosaur peptides were not represented in more exposed parts of the collagen fibril or regions mediating intermolecular cross-linking. Thus functionally significant regions of collagen fibrils that are physically shielded within the fibril may be preferentially preserved in fossils. These results show empirically that structure-function relationships at the molecular level could contribute to selective preservation in fossilized vertebrate remains across geological time, suggest a 'preservation motif', and bolster current concepts linking collagen structure to biological function. This non-random distribution supports the hypothesis that the peptides are produced by the extinct organisms and suggests a chemical mechanism for survival.

  12. Health service marketing: a suggested model.

    Science.gov (United States)

    Zaltman, G; Vertinsky, I

    1971-07-01

    Focus is on social marketing in a health context, and attention is directed to the development of a psychosocial model of health-related behavior with emphasis on developing countries. Each component of the model is identified and defined, with some of the interactions among its components noted. There are both advantages and limitations to using the model in a social marketing context. The model's primary contribution at this stage of its development is in structuring and organizing diverse sources of knowledge and data. New relationships are suggested which were not previously considered in the literature. The relationship between risk-taking and perceived susceptibility is 1 example. The model also provides a basis for simulating health processes, providing a testing ground for health policies before their actual implementation. The model's perspective is uniquely appropriate for the development of social marketing strategies, and it promises to encompass health market behavior in various cultural settings.

  13. Chest magnetic resonance imaging: a protocol suggestion

    Directory of Open Access Journals (Sweden)

    Bruno Hochhegger

    2015-12-01

    Full Text Available Abstract In the recent years, with the development of ultrafast sequences, magnetic resonance imaging (MRI has been established as a valuable diagnostic modality in body imaging. Because of improvements in speed and image quality, MRI is now ready for routine clinical use also in the study of pulmonary diseases. The main advantage of MRI of the lungs is its unique combination of morphological and functional assessment in a single imaging session. In this article, the authors review most technical aspects and suggest a protocol for performing chest MRI. The authors also describe the three major clinical indications for MRI of the lungs: staging of lung tumors; evaluation of pulmonary vascular diseases; and investigation of pulmonary abnormalities in patients who should not be exposed to radiation.

  14. PEER SUGGESTIVE FEEDBACK IN ENGLISH SPEAKING CLASS

    Directory of Open Access Journals (Sweden)

    Agnes Widyaningrum

    2017-12-01

    Full Text Available Students learn English in Speaking Class should get enjoyable learning atmosphere in order to help them improve their speaking skill. Teacher‘s role as facilitator contributes in reducing students‘ anxiety when they have chance to speak. Nunan (1995 and Richards (2008 argue that speaking is an important skill in language learning whether it is as EFL or ESL that enable language learners to communicate not only in expressing view point but also in giving responses in their communication. This classroom study supports the idea to give positive suggestion as students‘ feedback given by their peers. Each student has their own chance to review and to be reviewed so that they can perform better in speaking class. This study is conducted in order to improve students‘ speaking skill in speaking class.

  15. An Integrative Genetic Study of Rice Metabolism, Growth and Stochastic Variation Reveals Potential C/N Partitioning Loci

    Science.gov (United States)

    Li, Baohua; Zhang, Yuanyuan; Mohammadi, Seyed Abolghasem; Huai, Dongxin; Zhou, Yongming; Kliebenstein, Daniel J.

    2016-07-01

    Studying the genetic basis of variation in plant metabolism has been greatly facilitated by genomic and metabolic profiling advances. In this study, we use metabolomics and growth measurements to map QTL in rice, a major staple crop. Previous rice metabolism studies have largely focused on identifying genes controlling major effect loci. To complement these studies, we conducted a replicated metabolomics analysis on a japonica (Lemont) by indica (Teqing) rice recombinant inbred line population and focused on the genetic variation for primary metabolism. Using independent replicated studies, we show that in contrast to other rice studies, the heritability of primary metabolism is similar to Arabidopsis. The vast majority of metabolic QTLs had small to moderate effects with significant polygenic epistasis. Two metabolomics QTL hotspots had opposing effects on carbon and nitrogen rich 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 variation for metabolism than was found in Arabidopsis. Thus, it is possible that domestication has differentially impacted stochastic metabolite variation more than average metabolite variation.

  16. Leishmania major: Parasite Interactions Suggesting Sexuality

    Directory of Open Access Journals (Sweden)

    Sousa Maria Auxiliadora de

    1997-01-01

    Full Text Available In five experiments, Leishmania (Leishmania major (MRHO/SU/59/P-strain grew poorly when seeded in FYTS medium supplemented with 15% fetal calf serum, but presented several peculiar pairs of promastigotes diametrically opposed and attached at their posterior ends (5.8-13.5%. As seen in Giemsa-stained smears, a ring-like line and/or an enlargement, generally occurred at the parasite junction. A close proximity of nuclei, which sometimes were difficult to distinguish from each other, was also observed at this junction. Several of these pairs appeared to be composed of fused cells in which the nuclei could be apparently fused, as shown by fluorescence microscopy to detect ß-tubulin and DNA, and by scanning electron microscopy. Under other culture conditions these pairs were absent or occurred at very low rates (0.2-2.2%. Such pairs differ markedly from longitudinally dividing cells and resemble those described in two other Leishmania species, as well as in Herpetomonas megaseliae and Phytomonas davidi, suggesting steps of a putative sexual process

  17. PROBLEMS AND SUGGESTIONS FOR OFFICE FURNITURE MANUFACTURE

    Directory of Open Access Journals (Sweden)

    Cevdet Söğütlü

    2016-12-01

    Full Text Available This study aims to identify the problems encountered in production lines for office furniture manufacturers and gives suggestions to the problems. For this response, a questionnaire was designed and conducted with directors or owners of 50 office furniture manufacturers of small, medium and large scale size enterprises which were randomly selected from different cities. The questionnaire aims to focus on identifying the fundamental obstacles for production, marketing, sales and law. The data from questionnaire was calculated with frequency numbers and percentages for statistical values. In respect to the scope of dependent variables for the study, relationships between the independent variables such as the size of the company scale and Chi Square Single Analysis of Variance (ANOVA were determined. According to the results, 52% of customers constitute owners. The biggest obstacle is the lack of qualified personnel in office furniture production while 46% of customers complain about pour designs. As a result, the study concludes with specific obstacles for logistics (30%, distributions (18%, unpaid bills after delivery (28%, and unconscious of the consumer (24% in the office furniture sector.

  18. Employee suggestion programs: the rewards of involvement.

    Science.gov (United States)

    Mishra, J M; McKendall, M

    1993-09-01

    Successful ESPs are the products of a great deal of effort by managers, administrators, teams, individuals, and reviewers, who are all striving to achieve the goals of increased profitability and enhanced employee involvement. A review of the literature indicates that there are several prescriptions that will increase the likelihood of a successful ESP (see the box). Today's American business prophets sound ceaseless calls to arms in the name of "world class performance," "global competitiveness," "total quality management," and a variety of other buzz terms. A burgeoning industry has evolved that promises, through speeches, teleconferences, seminars, and consulting contracts, to teach American organizations how to achieve excellence. In the face of a sputtering economy and unrelenting competitive pressure, today's managers must translate these laudatory ideals into hands-on reality without sacrificing the firm's profit margin to experimentation. If any idea can help an organization achieve improvement through a workable program, then that idea and that program deserve real consideration. An ESP represents an opportunity to tap the intelligence and resourcefulness of an organization's employees, and by doing so, reap significant cost savings. Those companies and managers that have an ESP program uniformly list economic advantages first when describing the benefits of their employee suggestion programs. But there is another deeper and longer term benefit inherent in an ESP. These programs allow employees to become involved in their organization; they drive deaccession to lower levels, they give employees more responsibility, they foster creative approaches to work, and they encourage creativity in pursuit of company goals.(ABSTRACT TRUNCATED AT 250 WORDS)

  19. Cross-Disorder Genome-Wide Analyses Suggest a Complex Genetic Relationship Between Tourette Syndrome and Obsessive-Compulsive Disorder

    Science.gov (United States)

    Yu, Dongmei; Mathews, Carol A.; Scharf, Jeremiah M.; Neale, Benjamin M.; Davis, Lea K.; Gamazon, Eric R.; Derks, Eske M.; Evans, Patrick; Edlund, Christopher K.; Crane, Jacquelyn; Fagerness, Jesen A.; Osiecki, Lisa; Gallagher, Patience; Gerber, Gloria; Haddad, Stephen; Illmann, Cornelia; McGrath, Lauren M.; Mayerfeld, Catherine; Arepalli, Sampath; Barlassina, Cristina; Barr, Cathy L.; Bellodi, Laura; Benarroch, Fortu; Berrió, Gabriel Bedoya; Bienvenu, O. Joseph; Black, Donald; Bloch, Michael H.; Brentani, Helena; Bruun, Ruth D.; Budman, Cathy L.; Camarena, Beatriz; Campbell, Desmond D.; Cappi, Carolina; Cardona Silgado, Julio C.; Cavallini, Maria C.; Chavira, Denise A.; Chouinard, Sylvain; Cook, Edwin H.; Cookson, M. R.; Coric, Vladimir; Cullen, Bernadette; Cusi, Daniele; Delorme, Richard; Denys, Damiaan; Dion, Yves; Eapen, Valsama; Egberts, Karin; Falkai, Peter; Fernandez, Thomas; Fournier, Eduardo; Garrido, Helena; Geller, Daniel; Gilbert, Donald; Girard, Simon L.; Grabe, Hans J.; Grados, Marco A.; Greenberg, Benjamin D.; Gross-Tsur, Varda; Grünblatt, Edna; Hardy, John; Heiman, Gary A.; Hemmings, Sian M.J.; Herrera, Luis D.; Hezel, Dianne M.; Hoekstra, Pieter J.; Jankovic, Joseph; Kennedy, James L.; King, Robert A.; Konkashbaev, Anuar I.; Kremeyer, Barbara; Kurlan, Roger; Lanzagorta, Nuria; Leboyer, Marion; Leckman, James F.; Lennertz, Leonhard; Liu, Chunyu; Lochner, Christine; Lowe, Thomas L.; Lupoli, Sara; Macciardi, Fabio; Maier, Wolfgang; Manunta, Paolo; Marconi, Maurizio; McCracken, James T.; Mesa Restrepo, Sandra C.; Moessner, Rainald; Moorjani, Priya; Morgan, Jubel; Muller, Heike; Murphy, Dennis L.; Naarden, Allan L.; Ochoa, William Cornejo; Ophoff, Roel A.; Pakstis, Andrew J.; Pato, Michele T.; Pato, Carlos N.; Piacentini, John; Pittenger, Christopher; Pollak, Yehuda; Rauch, Scott L.; Renner, Tobias; Reus, Victor I.; Richter, Margaret A.; Riddle, Mark A.; Robertson, Mary M.; Romero, Roxana; Rosário, Maria C.; Rosenberg, David; Ruhrmann, Stephan; Sabatti, Chiara; Salvi, Erika; Sampaio, Aline S.; Samuels, Jack; Sandor, Paul; Service, Susan K.; Sheppard, Brooke; Singer, Harvey S.; Smit, Jan H.; Stein, Dan J.; Strengman, Eric; Tischfield, Jay A.; Turiel, Maurizio; Valencia Duarte, Ana V.; Vallada, Homero; Veenstra-VanderWeele, Jeremy; Walitza, Susanne; Walkup, John; Wang, Ying; Weale, Mike; Weiss, Robert; Wendland, Jens R.; Westenberg, Herman G.M.; Yao, Yin; Hounie, Ana G.; Miguel, Euripedes C.; Nicolini, Humberto; Wagner, Michael; Ruiz-Linares, Andres; Cath, Danielle C.; McMahon, William; Posthuma, Danielle; Oostra, Ben A.; Nestadt, Gerald; Rouleau, Guy A.; Purcell, Shaun; Jenike, Michael A.; Heutink, Peter; Hanna, Gregory L.; Conti, David V.; Arnold, Paul D.; Freimer, Nelson; Stewart, S. Evelyn; Knowles, James A.; Cox, Nancy J.; Pauls, David L.

    2014-01-01

    Obsessive-compulsive disorder (OCD) and Tourette Syndrome (TS) are highly heritable neurodevelopmental disorders that are thought to share genetic risk factors. However, the identification of definitive susceptibility genes for these etiologically complex disorders remains elusive. Here, we report a combined genome-wide association study (GWAS) of TS and OCD in 2723 cases (1310 with OCD, 834 with TS, 579 with OCD plus TS/chronic tics (CT)), 5667 ancestry-matched controls, and 290 OCD parent-child trios. Although no individual single nucleotide polymorphisms (SNPs) achieved genome-wide significance, the GWAS signals were enriched for SNPs strongly associated with variations in brain gene expression levels, i.e. expression quantitative loci (eQTLs), suggesting the presence of true functional variants that contribute to risk of these disorders. Polygenic score analyses identified a significant polygenic component for OCD (p=2×10−4), predicting 3.2% of the phenotypic variance in an independent data set. In contrast, TS had a smaller, non-significant polygenic component, predicting only 0.6% of the phenotypic variance (p=0.06). No significant polygenic signal was detected across the two disorders, although the sample is likely underpowered to detect a modest shared signal. Furthermore, the OCD polygenic signal was significantly attenuated when cases with both OCD and TS/CT were included in the analysis (p=0.01). Previous work has shown that TS and OCD have some degree of shared genetic variation. However, the data from this study suggest that there are also distinct components to the genetic architectures of TS and OCD. Furthermore, OCD with co-occurring TS/CT may have different underlying genetic susceptibility compared to OCD alone. PMID:25158072

  20. Evaluation of the improvement suggestion system in a nuclear facility

    Energy Technology Data Exchange (ETDEWEB)

    Carnaval, Joao Paulo Rodrigues; Moraes, Geice Almeida, E-mail: joaocarnaval@inb.gov.br, E-mail: geice@inb.gov.br [Industrias Nucleares do Brasil S.A (INB), Resende, RJ (Brazil)

    2017-11-01

    This work evaluated methods for processing improvement suggestions of a nuclear factory, with the intention to verify those which best fits to the company purposes. Two methods for processing improvement suggestions were applied in the studied organization. The first one was guided to the processing suggestions by specific independent sectors of the company and the second one was conducted to the processing of suggestions by a multidisciplinary team. It has been concluded that a multidisciplinary team focused on research and development would be the best option to the implementation of improvement suggestions and technological innovation on this facility, instead of multi sector processing which revealed to be excessive bureaucratic before the expected goals. This study can be used by nuclear facilities to optimize an existing system of improvements analysis or even guide them for the implantation of a new one. It is more significant for the companies certified on ISO and OHSAS standards for the quality management, environmental and safety and occupational health systems which requires that the continuous improvement must exist and to be demonstrated. But it is also relevant for nuclear plants aiming to implement an Integrated Management System certified on ISO Standards. (author)

  1. Convergent evidence from mouse and human studies suggests the involvement of zinc finger protein 326 gene in antidepressant treatment response.

    Directory of Open Access Journals (Sweden)

    Ying-Jay Liou

    Full Text Available OBJECTIVES: The forced swim test (FST is a commonly used model to predict antidepressant efficacy. Uncovering the genetic basis of the model may unravel the mechanism of antidepressant treatment. METHODS: FVB/NJ (FVB and C57BL/6J (B6 were first identified as the response and non-response strains to fluoxetine (a serotonin-specific reuptake inhibitor antidepressant treatment in the mouse FST. Simple-interval (SIM and composite-interval (CIM mappings were applied to map the quantitative trait loci (QTLs of the anti-immobility effect of fluoxetine in FST (FST(FLX in 865 male B6×FVB-F2 mice. The brain mRNA expressions of the gene with the maximum QTL-linkage signal for FST(FLX after the FST were compared between B6 and FVB mice and also compared between fluoxetine and saline treatment. The association of the variants in the human homologue of the mouse FST(FLX-QTL gene with major depressive disorder (MDD and antidepressant response were investigated in 1080 human subjects (MDD/control = 582/498. RESULTS: One linkage signal for FST(FLX-QTL was detected at an intronic SNP (rs6215396 of the mouse Zfp326 gene (maximal CIM-LOD = 9.36. The Zfp326 mRNA expression in the FVB thalamus was significantly down-regulated by fluoxetine in the FST, and the higher FVB-to-B6 Zfp326 mRNA expressions in the frontal cortex, striatum and hypothalamus diminished after fluoxetine treatment. Two coding-synonymous SNPs (rs2816881 and rs10922744 in the human homologue of Zfp326, ZNF326, were significantly associated with the 8-week antidepressant treatment response in the MDD patients (Bonferroni-corrected p = 0.004-0.028. CONCLUSIONS: The findings suggest the involvement of the Zfp326 and ZNF326 genes in antidepressant treatment response.

  2. QTL analysis of a red junglefowl x White Leghorn intercross reveals trade-off in resource allocation between behavior and production traits.

    Science.gov (United States)

    Schütz, Karin; Kerje, Susanne; Carlborg, Orjan; Jacobsson, Lina; Andersson, Leif; Jensen, Per

    2002-11-01

    contrafreeloading. Significant QTLs were found for PC1 and PC4 scores on chromosomes 27 and 7, respectively. The location of the QTLs coincided with known QTLs for growth rate and body weight. The results suggest a trade-off between energy-demanding behavior and high production and that some of this may be caused by genetic linkage or pleiotropic gene effects.

  3. High-Throughput Phenotyping and QTL Mapping Reveals the Genetic Architecture of Maize Plant Growth1[OPEN

    Science.gov (United States)

    Huang, Chenglong; Wu, Di; Qiao, Feng; Li, Wenqiang; Duan, Lingfeng; Wang, Ke; Xiao, Yingjie; Chen, Guoxing; Liu, Qian; Yang, Wanneng

    2017-01-01

    With increasing demand for novel traits in crop breeding, the plant research community faces the challenge of quantitatively analyzing the structure and function of large numbers of plants. A clear goal of high-throughput phenotyping is to bridge the gap between genomics and phenomics. In this study, we quantified 106 traits from a maize (Zea mays) recombinant inbred line population (n = 167) across 16 developmental stages using the automatic phenotyping platform. Quantitative trait locus (QTL) mapping with a high-density genetic linkage map, including 2,496 recombinant bins, was used to uncover the genetic basis of these complex agronomic traits, and 988 QTLs have been identified for all investigated traits, including three QTL hotspots. Biomass accumulation and final yield were predicted using a combination of dissected traits in the early growth stage. These results reveal the dynamic genetic architecture of maize plant growth and enhance ideotype-based maize breeding and prediction. PMID:28153923

  4. Mapeamento de QTLs associados à produção de frutos e sementes em híbridos de Citrus Sunki vs. Poncirus trifoliata QTL mapping linked to fruit set and seeds in Citrus Sunki vs. Poncirus trifoliata hybrids

    Directory of Open Access Journals (Sweden)

    Amauri Siviero

    2002-12-01

    Full Text Available O grupo dos citros apresenta acentuada juvenilidade manifestada pela incapacidade de florescimento, vigor e formação de espinhos. No caso da laranja 'valência', os híbridos de trifoliata, utilizados como porta-enxertos, induzem maior precocidade e produtividade. O número de sementes do fruto (NSF constitui importante característica da variedade candidata a porta-enxerto de citros. O presente estudo teve como objetivo detectar QTLs associados às características número de frutos por planta (NF e número de sementes por fruto em uma progênie F1 derivada de um cruzamento entre Citrus sunki e Poncirus trifoliata 'Rubidoux'. Os grupos de ligação (GL dos parentais foram obtidos usando a estratégia 'pseudotestcross' e marcadores do tipo RAPD. A contagem do número de frutos por planta e o número médio de sementes por fruto foi realizada usando 80 indivíduos da progênie. A detecção dos QTLs foi realizada pelo método de mapeamento por intervalo composto utilizando o programa QTLCartographer. Foram detectados um QTL associado à frutificação e um QTL ligado ao número de sementes situados no GL 4 e GL 5 no mapa de P. trifoliata, respectivamente.Citrus group shows juvenility strong due incapacity to flowering, vigor and thorn formation. Trifoliata hybrids used as rootstocks to induce early production and better field for 'Valencia' orange scion. Seeds number per fruit is very important characteristic to citrus rootstocks candidate. The present study has as objective to detect quantitative trait loci (QTL associated to fruiting and seeds production in F1 progeny obtained of Citrus sunki vs. Poncirus trifoliata cross. Linkage groups (LG of parents were built by pseudotestcross strategy using RAPD markers. Fruits/plant and seeds/fruit numbers were counting using 80 individuals of progeny. QTL detection was made with composite interval mapping using the QTL Cartographer. QTL linked to fruiting and seed production in LG 4 and LG 5 of the P

  5. Differential adaptation to multi-stressed conditions of wine fermentation revealed by variations in yeast regulatory networks.

    Science.gov (United States)

    Brion, Christian; Ambroset, Chloé; Sanchez, Isabelle; Legras, Jean-Luc; Blondin, Bruno

    2013-10-04

    Variation of gene expression can lead to phenotypic variation and have therefore been assumed to contribute the diversity of wine yeast (Saccharomyces cerevisiae) properties. However, the molecular bases of this variation of gene expression are unknown. We addressed these questions by carrying out an integrated genetical-genomic study in fermentation conditions. We report here quantitative trait loci (QTL) mapping based on expression profiling in a segregating population generated by a cross between a derivative of the popular wine strain EC1118 and the laboratory strain S288c. Most of the fermentation traits studied appeared to be under multi-allelic control. We mapped five phenotypic QTLs and 1465 expression QTLs. Several expression QTLs overlapped in hotspots. Among the linkages unraveled here, several were associated with metabolic processes essential for wine fermentation such as glucose sensing or nitrogen and vitamin metabolism. Variations affecting the regulation of drug detoxification and export (TPO1, PDR12 or QDR2) were linked to variation in four genes encoding transcription factors (PDR8, WAR1, YRR1 and HAP1). We demonstrated that the allelic variation of WAR1 and TPO1 affected sorbic and octanoic acid resistance, respectively. Moreover, analysis of the transcription factors phylogeny suggests they evolved with a specific adaptation of the strains to wine fermentation conditions. Unexpectedly, we found that the variation of fermentation rates was associated with a partial disomy of chromosome 16. This disomy resulted from the well known 8-16 translocation. This large data set made it possible to decipher the effects of genetic variation on gene expression during fermentation and certain wine fermentation properties. Our findings shed a new light on the adaptation mechanisms required by yeast to cope with the multiple stresses generated by wine fermentation. In this context, the detoxification and export systems appear to be of particular importance

  6. Detection of quantitative trait loci for agronomic, yield, grain and disease characters in spring barley (Hordeum vulgare L.).

    Science.gov (United States)

    Thomas, W T; Powell, W; Waugh, R; Chalmers, K J; Barua, U M; Jack, P; Lea, V; Forster, B P; Swanston, J S; Ellis, R P; Hanson, P R; Lance, R C

    1995-11-01

    Quantitative trait loci (QTLs) have been revealed for characters in a segregating population from a spring barley cross between genotypes adapted to North-West Europe. Transgressive segregation was found for all the characters, which was confirmed by the regular detection of positive and negative QTLs from both parents. A QTL for all the agronomic, yield and grain characters measured except thousand grain weight was found in the region of the denso dwarfing gene locus. There were considerable differences between the location of QTLs found in the present study and those found in previous studies of North American germ plasm, revealing the diversity between the two gene pools. Thirty-one QTLs were detected in more than one environment for the 13 characters studied, although many more were detected in just one environment. Whilst biometrical analyses suggested the presence of epistasis in the genetic control of some characters, there was little evidence of interactions between the QTLs apart from those associated with yield. QTLs of large effect sometimes masked the presence of QTLs of smaller effect.

  7. Cross-disorder genome-wide analyses suggest a complex genetic relationship between Tourette's syndrome and OCD.

    Science.gov (United States)

    Yu, Dongmei; Mathews, Carol A; Scharf, Jeremiah M; Neale, Benjamin M; Davis, Lea K; Gamazon, Eric R; Derks, Eske M; Evans, Patrick; Edlund, Christopher K; Crane, Jacquelyn; Fagerness, Jesen A; Osiecki, Lisa; Gallagher, Patience; Gerber, Gloria; Haddad, Stephen; Illmann, Cornelia; McGrath, Lauren M; Mayerfeld, Catherine; Arepalli, Sampath; Barlassina, Cristina; Barr, Cathy L; Bellodi, Laura; Benarroch, Fortu; Berrió, Gabriel Bedoya; Bienvenu, O Joseph; Black, Donald W; Bloch, Michael H; Brentani, Helena; Bruun, Ruth D; Budman, Cathy L; Camarena, Beatriz; Campbell, Desmond D; Cappi, Carolina; Silgado, Julio C Cardona; Cavallini, Maria C; Chavira, Denise A; Chouinard, Sylvain; Cook, Edwin H; Cookson, M R; Coric, Vladimir; Cullen, Bernadette; Cusi, Daniele; Delorme, Richard; Denys, Damiaan; Dion, Yves; Eapen, Valsama; Egberts, Karin; Falkai, Peter; Fernandez, Thomas; Fournier, Eduardo; Garrido, Helena; Geller, Daniel; Gilbert, Donald L; Girard, Simon L; Grabe, Hans J; Grados, Marco A; Greenberg, Benjamin D; Gross-Tsur, Varda; Grünblatt, Edna; Hardy, John; Heiman, Gary A; Hemmings, Sian M J; Herrera, Luis D; Hezel, Dianne M; Hoekstra, Pieter J; Jankovic, Joseph; Kennedy, James L; King, Robert A; Konkashbaev, Anuar I; Kremeyer, Barbara; Kurlan, Roger; Lanzagorta, Nuria; Leboyer, Marion; Leckman, James F; Lennertz, Leonhard; Liu, Chunyu; Lochner, Christine; Lowe, Thomas L; Lupoli, Sara; Macciardi, Fabio; Maier, Wolfgang; Manunta, Paolo; Marconi, Maurizio; McCracken, James T; Mesa Restrepo, Sandra C; Moessner, Rainald; Moorjani, Priya; Morgan, Jubel; Muller, Heike; Murphy, Dennis L; Naarden, Allan L; Nurmi, Erika; Ochoa, William Cornejo; Ophoff, Roel A; Pakstis, Andrew J; Pato, Michele T; Pato, Carlos N; Piacentini, John; Pittenger, Christopher; Pollak, Yehuda; Rauch, Scott L; Renner, Tobias; Reus, Victor I; Richter, Margaret A; Riddle, Mark A; Robertson, Mary M; Romero, Roxana; Rosário, Maria C; Rosenberg, David; Ruhrmann, Stephan; Sabatti, Chiara; Salvi, Erika; Sampaio, Aline S; Samuels, Jack; Sandor, Paul; Service, Susan K; Sheppard, Brooke; Singer, Harvey S; Smit, Jan H; Stein, Dan J; Strengman, Eric; Tischfield, Jay A; Turiel, Maurizio; Valencia Duarte, Ana V; Vallada, Homero; Veenstra-VanderWeele, Jeremy; Walitza, Susanne; Wang, Ying; Weale, Mike; Weiss, Robert; Wendland, Jens R; Westenberg, Herman G M; Shugart, Yin Yao; Hounie, Ana G; Miguel, Euripedes C; Nicolini, Humberto; Wagner, Michael; Ruiz-Linares, Andres; Cath, Danielle C; McMahon, William; Posthuma, Danielle; Oostra, Ben A; Nestadt, Gerald; Rouleau, Guy A; Purcell, Shaun; Jenike, Michael A; Heutink, Peter; Hanna, Gregory L; Conti, David V; Arnold, Paul D; Freimer, Nelson B; Stewart, S Evelyn; Knowles, James A; Cox, Nancy J; Pauls, David L

    2015-01-01

    Obsessive-compulsive disorder (OCD) and Tourette's syndrome are highly heritable neurodevelopmental disorders that are thought to share genetic risk factors. However, the identification of definitive susceptibility genes for these etiologically complex disorders remains elusive. The authors report a combined genome-wide association study (GWAS) of Tourette's syndrome and OCD. The authors conducted a GWAS in 2,723 cases (1,310 with OCD, 834 with Tourette's syndrome, 579 with OCD plus Tourette's syndrome/chronic tics), 5,667 ancestry-matched controls, and 290 OCD parent-child trios. GWAS summary statistics were examined for enrichment of functional variants associated with gene expression levels in brain regions. Polygenic score analyses were conducted to investigate the genetic architecture within and across the two disorders. Although no individual single-nucleotide polymorphisms (SNPs) achieved genome-wide significance, the GWAS signals were enriched for SNPs strongly associated with variations in brain gene expression levels (expression quantitative loci, or eQTLs), suggesting the presence of true functional variants that contribute to risk of these disorders. Polygenic score analyses identified a significant polygenic component for OCD (p=2×10(-4)), predicting 3.2% of the phenotypic variance in an independent data set. In contrast, Tourette's syndrome had a smaller, nonsignificant polygenic component, predicting only 0.6% of the phenotypic variance (p=0.06). No significant polygenic signal was detected across the two disorders, although the sample is likely underpowered to detect a modest shared signal. Furthermore, the OCD polygenic signal was significantly attenuated when cases with both OCD and co-occurring Tourette's syndrome/chronic tics were included in the analysis (p=0.01). Previous work has shown that Tourette's syndrome and OCD have some degree of shared genetic variation. However, the data from this study suggest that there are also distinct

  8. Bifurcation Analysis of an Existing Mathematical Model Reveals Novel Treatment Strategies and Suggests Potential Cure for Type 1 Diabetes

    DEFF Research Database (Denmark)

    Nielsen, Kenneth Hagde Mandrup; Ottesen, Johnny T.; Pociot, Flemming

    2014-01-01

    Type 1 diabetes is a disease with serious personal and socioeconomic consequences that has attracted the attention of modellers recently. But as models of this disease tend to be complicated, there has been only limited mathematical analysis to date. Here we address this problem by providing a bi...

  9. Bifurcation analysis of an existing mathematical model reveals novel treatment strategies and suggests potential cure for type 1 diabetes.

    Science.gov (United States)

    Nielsen, Kenneth H M; Pociot, Flemming M; Ottesen, Johnny T

    2014-09-01

    Type 1 diabetes is a disease with serious personal and socioeconomic consequences that has attracted the attention of modellers recently. But as models of this disease tend to be complicated, there has been only limited mathematical analysis to date. Here we address this problem by providing a bifurcation analysis of a previously published mathematical model for the early stages of type 1 diabetes in diabetes-prone NOD mice, which is based on the data available in the literature. We also show positivity and the existence of a family of attracting trapping regions in the positive 5D cone, converging towards a smaller trapping region, which is the intersection over the family. All these trapping regions are compact sets, and thus, practical weak persistence is guaranteed. We conclude our analysis by proposing 4 novel treatment strategies: increasing the phagocytic ability of resting macrophages or activated macrophages, increasing the phagocytic ability of resting and activated macrophages simultaneously and lastly, adding additional macrophages to the site of inflammation. The latter seems counter-intuitive at first glance, but nevertheless it appears to be the most promising, as evidenced by recent results. © The Authors 2013. Published by Oxford University Press on behalf of the Institute of Mathematics and its Applications. All rights reserved.

  10. Diatom centromeres suggest a mechanism for nuclear DNA acquisition.

    Science.gov (United States)

    Diner, Rachel E; Noddings, Chari M; Lian, Nathan C; Kang, Anthony K; McQuaid, Jeffrey B; Jablanovic, Jelena; Espinoza, Josh L; Nguyen, Ngocquynh A; Anzelmatti, Miguel A; Jansson, Jakob; Bielinski, Vincent A; Karas, Bogumil J; Dupont, Christopher L; Allen, Andrew E; Weyman, Philip D

    2017-07-18

    Centromeres are essential for cell division and growth in all eukaryotes, and knowledge of their sequence and structure guides the development of artificial chromosomes for functional cellular biology studies. Centromeric proteins are conserved among eukaryotes; however, centromeric DNA sequences are highly variable. We combined forward and reverse genetic approaches with chromatin immunoprecipitation to identify centromeres of the model diatom Phaeodactylum tricornutum We observed 25 unique centromere sequences typically occurring once per chromosome, a finding that helps to resolve nuclear genome organization and indicates monocentric regional centromeres. Diatom centromere sequences contain low-GC content regions but lack repeats or other conserved sequence features. Native and foreign sequences with similar GC content to P. tricornutum centromeres can maintain episomes and recruit the diatom centromeric histone protein CENH3, suggesting nonnative sequences can also function as diatom centromeres. Thus, simple sequence requirements may enable DNA from foreign sources to persist in the nucleus as extrachromosomal episomes, revealing a potential mechanism for organellar and foreign DNA acquisition.

  11. Expression analysis in intestinal mucosa reveals complex relations among genes under the association peaks in celiac disease

    Science.gov (United States)

    Plaza-Izurieta, Leticia; Fernandez-Jimenez, Nora; Irastorza, Iñaki; Jauregi-Miguel, Amaia; Romero-Garmendia, Irati; Vitoria, Juan Carlos; Bilbao, Jose Ramon

    2015-01-01

    Celiac disease is a chronic immune-mediated disorder with an important genetic component. To date, there are 57 independent association signals from 39 non-HLA loci, and a total of 66 candidate genes have been proposed. We aimed to scrutinize the functional implication of 45 of those genes by analyzing their expression in the disease tissue of celiac patients (at diagnosis/treatment) compared with non-celiac controls. Moreover, we investigated the SNP genotype effect in gene expression and performed coexpression analyses. Several genes showed differential expression among disease groups, most of them related to immune response. Multiple trans-eQTLs but only four cis-eQTLs were found, and surprisingly the genotype effect seems to be stimulus dependent as it differs among groups. Coexpression levels vary from higher to lower levels in active patients at diagnosis, treated patients and non-celiac controls respectively. A subset of 18 genes tightly correlated in both groups of patients but not in controls was identified. Interestingly, this subset of genes was influenced by the genotype of three SNPs. One of the SNPs, rs1018326 on chromosome two is on top of a known lincRNA whose function is not yet described, and whose expression seems to be upregulated in active disease when comparing biopsy pairs from the same individuals. Our results strongly suggest that the effects of disease-associated SNPs go far beyond the oversimplistic idea of transcriptional control at a nearby locus. Further investigations are needed to determine how each variant disrupts fine-tuning mechanisms in the genome that eventually lead to disease. PMID:25388004

  12. On the Effects of Suggested Prices in Gasoline Markets

    NARCIS (Netherlands)

    R.P. Faber (Riemer); M.C.W. Janssen (Maarten)

    2008-01-01

    textabstractThis article analyzes the role of suggested prices in the Dutch retail market for gasoline. Suggested prices are announced by large oil companies with the suggestion that retailers follow them. There are at least two competing rationales for the existence of suggested prices: they may

  13. Childhood stress in healthcare settings: awareness and suggested interventions.

    Science.gov (United States)

    Al-Yateem, Nabeel S; Banni Issa, Wegdan; Rossiter, Rachel

    2015-06-01

    Pivotal to healthy adulthood is a supportive and nurturing environment that enables successful progression through the developmental tasks of childhood and adolescence. For many children there are events that disrupt this development. Illness, injury, painful medical interventions, and hospitalization have been reported by children and families as causing medical trauma and psychological stress. Frequently pediatric health professionals focus primarily on achieving positive physical treatment outcomes. Creating an environment that will support the developmental tasks of childhood and limit the trauma and distress associated with illness and treatment is also required. Strategies and practices to deliver holistic and comprehensive pediatric care are well established in many Western settings. Opportunity exists to broaden the focus of pediatric care in developing healthcare systems such as the United Arab Emirates (UAE) to encompass psychological well-being. The study focused on two key objectives, firstly to assess healthcare professionals' awareness of the stressful and potentially traumatic nature of healthcare settings and treatment for children. Second the study explored the views of healthcare participants regarding possible strategies to minimize medically induced stress and trauma for children and adolescents in UAE healthcare settings. The study utilized a mixed methods design in which participants views were examined through administration of a survey comprised of close-ended questions that were analyzed quantitatively and open-ended questions analyzed qualitatively. One hundred and seventeen healthcare professionals from a range of disciplines in two government hospitals completed the survey. Data revealed that one third of the participating healthcare professionals were unaware of or did not think that their healthcare settings could provoke stress for pediatric patients. Respondents suggested three main strategies to minimize stress for children and

  14. High-Throughput Phenotyping and QTL Mapping Reveals the Genetic Architecture of Maize Plant Growth.

    Science.gov (United States)

    Zhang, Xuehai; Huang, Chenglong; Wu, Di; Qiao, Feng; Li, Wenqiang; Duan, Lingfeng; Wang, Ke; Xiao, Yingjie; Chen, Guoxing; Liu, Qian; Xiong, Lizhong; Yang, Wanneng; Yan, Jianbing

    2017-03-01

    With increasing demand for novel traits in crop breeding, the plant research community faces the challenge of quantitatively analyzing the structure and function of large numbers of plants. A clear goal of high-throughput phenotyping is to bridge the gap between genomics and phenomics. In this study, we quantified 106 traits from a maize (Zea mays) recombinant inbred line population (n = 167) across 16 developmental stages using the automatic phenotyping platform. Quantitative trait locus (QTL) mapping with a high-density genetic linkage map, including 2,496 recombinant bins, was used to uncover the genetic basis of these complex agronomic traits, and 988 QTLs have been identified for all investigated traits, including three QTL hotspots. Biomass accumulation and final yield were predicted using a combination of dissected traits in the early growth stage. These results reveal the dynamic genetic architecture of maize plant growth and enhance ideotype-based maize breeding and prediction. © 2017 American Society of Plant Biologists. All Rights Reserved.

  15. Gestational Pityriasis Rosea: Suggestions for Approaching Affected Pregnant Women.

    Science.gov (United States)

    Monastirli, Alexandra; Pasmatzi, Efstathia; Badavanis, George; Tsambaos, Dionysios

    2016-12-01

    pityriasis rosea, for intrauterine fetal death. All miscarrying women reportedly revealed an aggressive course of widespread eruption and severe constitutional symptoms; all of them had HHV-6 DNA in the plasma, placenta, skin lesions, and fetal tissues, whereas HHV-7 DNA was detected in the plasma and skin lesions in 3 out of 8 (37.5%) miscarrying women. HHV-6 DNA was found only in the plasma of 2 out of 31 women (6.45%) with normal pregnancy, whereas HHV-7 DNA was detected in the plasma of 3 (9.45%) and in the skin lesions of 2 women (6.45%) with normal pregnancy. The total abortion rate in women who developed pityriasis rosea during their pregnancy (13%) does not differ from that observed in the general population. Nevertheless, it is markedly higher in cases affected during the first 15 gestational weeks (57%) (4,5). Surprisingly, this devastating impact of pityriasis rosea on the outcome of pregnancy is almost completely unknown not only to the public but also to many members of the medical community. It is also largely unknown that, particularly during the first 15 gestational weeks, all pregnant women should avoid any contact with patients known to have pityriasis rosea. Since we have received a considerable number of requests for consultation with pregnant women with pityriasis rosea over the last few years, our group has compiled suggestions approaching the affected patients: 1. If an eruption suggestive for pityriasis rosea occurs in a pregnant woman, the following factors should be excluded: a. Exposure to drugs prior to the development of the rash (biologic agents, captopril, clonidine, hydrochlorothiazide, atenolol, lamotrigine, nortriptyline, barbiturates, metronidazole, terbinafine, omeprazole, non-steroidal anti-inflammatory drugs, and isotretinoin), which are capable of inducing a pityriasis rosea-like eruption (6) and b. Disorders included in the differential diagnosis (syphilis and infections due to parvovirus, herpes virus, cytomegalovirus, and Epstein

  16. Disorganized Cortical Patches Suggest Prenatal Origin of Autism

    Science.gov (United States)

    ... 2014 Disorganized cortical patches suggest prenatal origin of autism NIH-funded study shows disrupted cell layering process ... study suggests that brain irregularities in children with autism can be traced back to prenatal development. “While ...

  17. Suggestions on Writing for Publication in Language Learning Journals

    OpenAIRE

    George M. Jacobs

    1999-01-01

    This article provides suggestions on writing for journals in the field of language learning. These suggestions are presented in three sections. The first section discusses how to begin. Suggestions in this section are that we appreciate the benefits of writing for publication, develop good ideas, work efficiently, ponder options as to what type of writing to do, choose a good topic, consider replication of other's research, and cooperate with others. The second section presents suggestions on...

  18. Android Emotions Revealed

    DEFF Research Database (Denmark)

    Vlachos, Evgenios; Schärfe, Henrik

    2012-01-01

    in which case an android robot like the Geminoid|DK –a duplicate of an Original person- reveals emotions convincingly; when following an empirical perspective, or when following a theoretical one. The methodology includes the processes of acquiring the empirical data, and gathering feedback on them. Our...

  19. An effective suggestion method for keyword search of databases

    KAUST Repository

    Huang, Hai

    2016-09-09

    This paper solves the problem of providing high-quality suggestions for user keyword queries over databases. With the assumption that the returned suggestions are independent, existing query suggestion methods over databases score candidate suggestions individually and return the top-k best of them. However, the top-k suggestions have high redundancy with respect to the topics. To provide informative suggestions, the returned k suggestions are expected to be diverse, i.e., maximizing the relevance to the user query and the diversity with respect to topics that the user might be interested in simultaneously. In this paper, an objective function considering both factors is defined for evaluating a suggestion set. We show that maximizing the objective function is a submodular function maximization problem subject to n matroid constraints, which is an NP-hard problem. An greedy approximate algorithm with an approximation ratio O((Formula presented.)) is also proposed. Experimental results show that our suggestion outperforms other methods on providing relevant and diverse suggestions. © 2016 Springer Science+Business Media New York

  20. Two functionally distinct members of the MATE (multi-drug and toxic compound extrusion) family of transporters potentially underlie two major aluminum tolerance QTLs in maize.

    Science.gov (United States)

    Maron, Lyza G; Piñeros, Miguel A; Guimarães, Claudia T; Magalhaes, Jurandir V; Pleiman, Jennifer K; Mao, Chuanzao; Shaff, Jon; Belicuas, Silvia N J; Kochian, Leon V

    2010-03-01

    Crop yields are significantly reduced by aluminum (Al) toxicity on acidic soils, which comprise up to 50% of the world's arable land. Al-activated release of ligands (such as organic acids) from the roots is a major Al tolerance mechanism in plants. In maize, Al-activated root citrate exudation plays an important role in tolerance. However, maize Al tolerance is a complex trait involving multiple genes and physiological mechanisms. Recently, transporters from the MATE family have been shown to mediate Al-activated citrate exudation in a number of plant species. Here we describe the cloning and characterization of two MATE family members in maize, ZmMATE1 and ZmMATE2, which co-localize to major Al tolerance QTL. Both genes encode plasma membrane proteins that mediate significant anion efflux when expressed in Xenopus oocytes. ZmMATE1 expression is mostly concentrated in root tissues, is up-regulated by Al and is significantly higher in Al-tolerant maize genotypes. In contrast, ZmMATE2 expression is not specifically localized to any particular tissue and does not respond to Al. [(14)C]-citrate efflux experiments in oocytes demonstrate that ZmMATE1 is a citrate transporter. In addition, ZmMATE1 expression confers a significant increase in Al tolerance in transgenic Arabidopsis. Our data suggests that ZmMATE1 is a functional homolog of the Al tolerance genes recently characterized in sorghum, barley and Arabidopsis, and is likely to underlie the largest maize Al tolerance QTL found on chromosome 6. However, ZmMATE2 most likely does not encode a citrate transporter, and could be involved in a novel Al tolerance mechanism.

  1. Genome-wide analysis of ivermectin response by Onchocerca volvulus reveals that genetic drift and soft selective sweeps contribute to loss of drug sensitivity.

    Science.gov (United States)

    Doyle, Stephen R; Bourguinat, Catherine; Nana-Djeunga, Hugues C; Kengne-Ouafo, Jonas A; Pion, Sébastien D S; Bopda, Jean; Kamgno, Joseph; Wanji, Samuel; Che, Hua; Kuesel, Annette C; Walker, Martin; Basáñez, Maria-Gloria; Boakye, Daniel A; Osei-Atweneboana, Mike Y; Boussinesq, Michel; Prichard, Roger K; Grant, Warwick N

    2017-07-01

    Treatment of onchocerciasis using mass ivermectin administration has reduced morbidity and transmission throughout Africa and Central/South America. Mass drug administration is likely to exert selection pressure on parasites, and phenotypic and genetic changes in several Onchocerca volvulus populations from Cameroon and Ghana-exposed to more than a decade of regular ivermectin treatment-have raised concern that sub-optimal responses to ivermectin's anti-fecundity effect are becoming more frequent and may spread. Pooled next generation sequencing (Pool-seq) was used to characterise genetic diversity within and between 108 adult female worms differing in ivermectin treatment history and response. Genome-wide analyses revealed genetic variation that significantly differentiated good responder (GR) and sub-optimal responder (SOR) parasites. These variants were not randomly distributed but clustered in ~31 quantitative trait loci (QTLs), with little overlap in putative QTL position and gene content between the two countries. Published candidate ivermectin SOR genes were largely absent in these regions; QTLs differentiating GR and SOR worms were enriched for genes in molecular pathways associated with neurotransmission, development, and stress responses. Finally, single worm genotyping demonstrated that geographic isolation and genetic change over time (in the presence of drug exposure) had a significantly greater role in shaping genetic diversity than the evolution of SOR. This study is one of the first genome-wide association analyses in a parasitic nematode, and provides insight into the genomics of ivermectin response and population structure of O. volvulus. We argue that ivermectin response is a polygenically-determined quantitative trait (QT) whereby identical or related molecular pathways but not necessarily individual genes are likely to determine the extent of ivermectin response in different parasite populations. Furthermore, we propose that genetic drift

  2. Genome-wide analysis of ivermectin response by Onchocerca volvulus reveals that genetic drift and soft selective sweeps contribute to loss of drug sensitivity.

    Directory of Open Access Journals (Sweden)

    Stephen R Doyle

    2017-07-01

    Full Text Available Treatment of onchocerciasis using mass ivermectin administration has reduced morbidity and transmission throughout Africa and Central/South America. Mass drug administration is likely to exert selection pressure on parasites, and phenotypic and genetic changes in several Onchocerca volvulus populations from Cameroon and Ghana-exposed to more than a decade of regular ivermectin treatment-have raised concern that sub-optimal responses to ivermectin's anti-fecundity effect are becoming more frequent and may spread.Pooled next generation sequencing (Pool-seq was used to characterise genetic diversity within and between 108 adult female worms differing in ivermectin treatment history and response. Genome-wide analyses revealed genetic variation that significantly differentiated good responder (GR and sub-optimal responder (SOR parasites. These variants were not randomly distributed but clustered in ~31 quantitative trait loci (QTLs, with little overlap in putative QTL position and gene content between the two countries. Published candidate ivermectin SOR genes were largely absent in these regions; QTLs differentiating GR and SOR worms were enriched for genes in molecular pathways associated with neurotransmission, development, and stress responses. Finally, single worm genotyping demonstrated that geographic isolation and genetic change over time (in the presence of drug exposure had a significantly greater role in shaping genetic diversity than the evolution of SOR.This study is one of the first genome-wide association analyses in a parasitic nematode, and provides insight into the genomics of ivermectin response and population structure of O. volvulus. We argue that ivermectin response is a polygenically-determined quantitative trait (QT whereby identical or related molecular pathways but not necessarily individual genes are likely to determine the extent of ivermectin response in different parasite populations. Furthermore, we propose that genetic

  3. The Hardy-Weinberg Equilibrium--Some Helpful Suggestions.

    Science.gov (United States)

    Ortiz, Mary T.; Taras, Loretta; Stavroulakis, Anthea M.

    2000-01-01

    Describes an approach that provides mathematical tips and helpful suggestions for presenting the Hardy-Weinberg equilibrium to predict allele frequencies, phenotypes, and genotypes in populations. (ASK)

  4. Vocabulary of definitions of life suggests a definition.

    Science.gov (United States)

    Trifonov, Edward N

    2011-10-01

    Analysis of the vocabulary of 123 tabulated definitions of life reveals nine groups of defining terms (definientia) of which the groups (self-)reproduction and evolution (variation) appear as the minimal set for a concise and inclusive definition: Life is self-reproduction with variations.

  5. Therapeutic suggestion has no effect on postoperative morphine requirements

    NARCIS (Netherlands)

    W.H. van der Laan (W.); B.L. van Leeuwen (B.); P.S. Sebel (P.); E. Winograd (E.); P. Baumann (P.); B. Bonke (Benno)

    1996-01-01

    textabstractThis study was designed to confirm the effect of therapeutic intraoperative auditory suggestion on recovery from anesthesia, to establish the effect of preoperative suggestion, and to assess implicit memory for intraoperative information using an indirect memory task. Sixty consenting

  6. Students' Suggestions for Eliminating Bullying at a University

    Science.gov (United States)

    Meriläinen, Matti; Puhakka, Helena; Sinkkonen, Hanna-Maija

    2015-01-01

    Students' suggestions for how to eliminate bullying at universities were gathered as part of an e-questionnaire sent to each university student (N = 10,551) at a Finnish university. The suggestions (n = 2804) regarding how to address bullying at universities were divided into the following four classes: support (944), punishment (78), support and…

  7. Prevalence of lower urinary tract symptoms suggestive of benign ...

    African Journals Online (AJOL)

    Prevalence of lower urinary tract symptoms suggestive of benign prostatic hyperplasia in primary care, Port Harcourt, Nigeria. ... The prevalence of LUTS suggestive of BPH was 72.2% using the IPSS, and 60% had an enlarged prostate that was diagnosed through a digital rectal examination. The prevalence of bothersome ...

  8. Theory-of-Mind Development Influences Suggestibility and Source Monitoring

    Science.gov (United States)

    Bright-Paul, Alexandra; Jarrold, Christopher; Wright, Daniel B.

    2008-01-01

    According to the mental-state reasoning model of suggestibility, 2 components of theory of mind mediate reductions in suggestibility across the preschool years. The authors examined whether theory-of-mind performance may be legitimately separated into 2 components and explored the memory processes underlying the associations between theory of mind…

  9. Exploration of Opinion-aware Approach to Contextual Suggestion

    Science.gov (United States)

    2014-11-01

    are selected since they cover 1 http://www.yelp.com Report Documentation Page Form ApprovedOMB No. 0704-0188 Public reporting burden for the collection...suggestion are crawled. Approximately 60,442 candidate sug- gestions are crawled for all contexts, resulting in average 1208 candidate suggestions per

  10. User Simulations for Interactive Search : Evaluating Personalized Query Suggestion

    NARCIS (Netherlands)

    Verberne, S.; Sappelli, M.; Järvelin, K.; Kraaij, W.

    2015-01-01

    In this paper, we address the question “what is the influence of user search behaviour on the effectiveness of personalized query suggestion?”. We implemented a method for query suggestion that generates candidate follow-up queries from the documents clicked by the user. This is a potentially

  11. Enhancing business intelligence by means of suggestive reviews.

    Science.gov (United States)

    Qazi, Atika; Raj, Ram Gopal; Tahir, Muhammad; Cambria, Erik; Syed, Karim Bux Shah

    2014-01-01

    Appropriate identification and classification of online reviews to satisfy the needs of current and potential users pose a critical challenge for the business environment. This paper focuses on a specific kind of reviews: the suggestive type. Suggestions have a significant influence on both consumers' choices and designers' understanding and, hence, they are key for tasks such as brand positioning and social media marketing. The proposed approach consists of three main steps: (1) classify comparative and suggestive sentences; (2) categorize suggestive sentences into different types, either explicit or implicit locutions; (3) perform sentiment analysis on the classified reviews. A range of supervised machine learning approaches and feature sets are evaluated to tackle the problem of suggestive opinion mining. Experimental results for all three tasks are obtained on a dataset of mobile phone reviews and demonstrate that extending a bag-of-words representation with suggestive and comparative patterns is ideal for distinguishing suggestive sentences. In particular, it is observed that classifying suggestive sentences into implicit and explicit locutions works best when using a mixed sequential rule feature representation. Sentiment analysis achieves maximum performance when employing additional preprocessing in the form of negation handling and target masking, combined with sentiment lexicons.

  12. Suggestibility, intelligence, memory recall and personality: an experimental study.

    Science.gov (United States)

    Gudjonsson, G H

    1983-01-01

    A new suggestibility test, potentially useful in the context of police interrogation, was administered to 45 subjects who also completed the Wechsler Adult Intelligence Scale and the Eysenck Personality Questionnaire. Suggestibility was significantly related to low intelligence, poor memory recall, neuroticism and social desirability.

  13. Using suggestion to model different types of automatic writing.

    Science.gov (United States)

    Walsh, E; Mehta, M A; Oakley, D A; Guilmette, D N; Gabay, A; Halligan, P W; Deeley, Q

    2014-05-01

    Our sense of self includes awareness of our thoughts and movements, and our control over them. This feeling can be altered or lost in neuropsychiatric disorders as well as in phenomena such as "automatic writing" whereby writing is attributed to an external source. Here, we employed suggestion in highly hypnotically suggestible participants to model various experiences of automatic writing during a sentence completion task. Results showed that the induction of hypnosis, without additional suggestion, was associated with a small but significant reduction of control, ownership, and awareness for writing. Targeted suggestions produced a double dissociation between thought and movement components of writing, for both feelings of control and ownership, and additionally, reduced awareness of writing. Overall, suggestion produced selective alterations in the control, ownership, and awareness of thought and motor components of writing, thus enabling key aspects of automatic writing, observed across different clinical and cultural settings, to be modelled. Copyright © 2014. Published by Elsevier Inc.

  14. Revealing the programming process

    DEFF Research Database (Denmark)

    Bennedsen, Jens; Caspersen, Michael Edelgaard

    2005-01-01

    One of the most important goals of an introductory programming course is that the students learn a systematic approach to the development of computer programs. Revealing the programming process is an important part of this; however, textbooks do not address the issue -- probably because...... the textbook medium is static and therefore ill-suited to expose the process of programming. We have found that process recordings in the form of captured narrated programming sessions are a simple, cheap, and efficient way of providing the revelation.We identify seven different elements of the programming...

  15. TypeScript revealed

    CERN Document Server

    Maharry, Dan

    2013-01-01

    TypeScript Revealed is a quick 100-page guide to Anders Hejlsberg's new take on JavaScript. With this brief, fast-paced introduction to TypeScript, .NET, Web and Windows 8 application developers who are already familiar with JavaScript will easily get up to speed with TypeScript and decide whether or not to start incorporating it into their own development. TypeScript is 'JavaScript for Application-scale development'; a superset of JavaScript that brings to it an additional object-oriented-like syntax familiar to .NET programmers that compiles down into simple, clean JavaScript that any browse

  16. Mechanisms of eyewitness suggestibility: tests of the explanatory role hypothesis.

    Science.gov (United States)

    Rindal, Eric J; Chrobak, Quin M; Zaragoza, Maria S; Weihing, Caitlin A

    2017-10-01

    In a recent paper, Chrobak and Zaragoza (Journal of Experimental Psychology: General, 142(3), 827-844, 2013) proposed the explanatory role hypothesis, which posits that the likelihood of developing false memories for post-event suggestions is a function of the explanatory function the suggestion serves. In support of this hypothesis, they provided evidence that participant-witnesses were especially likely to develop false memories for their forced fabrications when their fabrications helped to explain outcomes they had witnessed. In three experiments, we test the generality of the explanatory role hypothesis as a mechanism of eyewitness suggestibility by assessing whether this hypothesis can predict suggestibility errors in (a) situations where the post-event suggestions are provided by the experimenter (as opposed to fabricated by the participant), and (b) across a variety of memory measures and measures of recollective experience. In support of the explanatory role hypothesis, participants were more likely to subsequently freely report (E1) and recollect the suggestions as part of the witnessed event (E2, source test) when the post-event suggestion helped to provide a causal explanation for a witnessed outcome than when it did not serve this explanatory role. Participants were also less likely to recollect the suggestions as part of the witnessed event (on measures of subjective experience) when their explanatory strength had been reduced by the presence of an alternative explanation that could explain the same outcome (E3, source test + warning). Collectively, the results provide strong evidence that the search for explanatory coherence influences people's tendency to misremember witnessing events that were only suggested to them.

  17. Mysterious Blob Galaxies Revealed

    Science.gov (United States)

    2005-01-01

    [figure removed for brevity, see original site] [figure removed for brevity, see original site] Figure 1Figure 2Figure 3 This image composite shows a giant galactic blob (red, figure 2) and the three merging galaxies NASA's Spitzer Space Telescope discovered within it (yellow, figure 3). Blobs are intensely glowing clouds of hot hydrogen gas that envelop faraway galaxies. They are about 10 times as large as the galaxies they surround. Visible-light images like the one shown in figure 2, reveal the vast extent of blobs, but don't provide much information about their host galaxies. Using its heat-seeking infrared eyes, Spitzer was able to see the dusty galaxies tucked inside one well-known blob located 11 billion light-years away. The findings reveal three monstrously bright galaxies, trillions of times brighter than the Sun, in the process of merging together (figure 3). Spitzer also observed three other blobs located in the same cosmic neighborhood, all of which were found to be glaringly bright. One of these blobs is also known to be a galactic merger, only between two galaxies instead of three. It remains to be seen whether the final two blobs studied also contain mergers. The Spitzer data were acquired by its multiband imaging photometer. The visible-light image was taken by the Blanco Telescope at the Cerro Tololo Inter-American Observatory, Chile.

  18. Suggestion and veridicality in the reconstruction of sexual trauma, or can a bait of suggestion catch a carp of falsehood?

    Science.gov (United States)

    Good, M I

    1996-01-01

    Freud used the term suggestion in psychoanalysis in different ways, including suggestion as an integral part of the transference and suggestion in the sense of undue influence or technical error. This distinction can be expressed in terms of the patient's suggestibility (capacity for transference) and the analyst's unwarranted suggestion or persuasion representing countertransference, theoretical bias, or a departure from technical neutrality. Whether suggestion is explicit or implicit, the effects of suggestion and suggestibility may be mutual and reciprocal. To the extent that a psychoanalyst maintains the goal of technical neutrality, undue suggestion is likely to be minimal. To the extent that it occurs for transferential or countertransferential reasons, suggestion may itself be analyzed. Problems of suggestion are more likely to occur and persist when they are part of the analyst's theoretical orientation, influencing the course of the analysis and expressing compromise formations for both patient and analyst. At times, even tentatively stated words or unintended behaviors of the analyst can have a dynamic impact that may not be readily analyzed. The analytic situation itself may have retrospective (nachträglich) action. A previously published case is described in which an apparent enactment led the analyst to urge a reconstruction of sexual abuse even though the patient never actually recalled what was presumed to have been fellatio. The need for technical neutrality and alternative reconstructions in such cases is considered. The degree to which the personality and goals of the analyst influence the course of reconstruction remains a vexing issue for psychoanalysis as a scientific endeavor. There is a need for detailed analytic case studies in which alternative reconstructions can be compared by investigating opportunities for external confirmation or falsification.

  19. Baby Teeth Link Autism and Heavy Metals, NIH Study Suggests

    Science.gov (United States)

    ... Release Thursday, June 1, 2017 Baby teeth link autism and heavy metals, NIH study suggests Cross-section ... Sinai Health System Baby teeth from children with autism contain more toxic lead and less of the ...

  20. Even Your Bones Can Get Fat, Mouse Study Suggests

    Science.gov (United States)

    ... medlineplus.gov/news/fullstory_166422.html Even Your Bones Can Get Fat, Mouse Study Suggests But running rodents improved their ... the hows and whys behind exercise's impact on bone fat composition remains murky. She said her current focus ...

  1. Using Neurolinguistic Programming: Some Suggestions for the Remedial Teacher.

    Science.gov (United States)

    Burton, Grace M.

    1986-01-01

    The use of neurolinguistic programming techniques is suggested as a means of enhancing rapport with students. Mirroring, digital mirroring, analog mirroring, metaphors, knowing persons, and how these aid in presenting content are each discussed. (MNS)

  2. Neurogenesis suggests independent evolution of opercula in serpulid polychaetes

    DEFF Research Database (Denmark)

    Brinkmann, Nora; Wanninger, Andreas

    2009-01-01

    BACKGROUND: The internal phylogenetic relationships of Annelida, one of the key lophotrochozoan lineages, are still heavily debated. Recent molecular analyses suggest that morphologically distinct groups, such as the polychaetes, are paraphyletic assemblages, thus questioning the homology...

  3. Sexual Harrassment: Suggested Policy and Procedures for Handling Complaints.

    Science.gov (United States)

    Academe, 1983

    1983-01-01

    AAUP guidelines on establishing institutional policy and procedures for handling sexual harassment complaints are outlined. Sexual harassment is defined and procedures for both bringing and resolving a complaint are suggested. (MSE)

  4. Study Suggests Brain Is Hard-Wired for Chronic Pain

    Science.gov (United States)

    ... News Release Tuesday, September 17, 2013 NIH-funded study suggests brain is hard-wired for chronic pain ... Apkarian, Ph.D., a senior author of the study and professor of physiology at Northwestern University Feinberg ...

  5. Eye Problems May Be Tied to Zika, Lab Study Suggests

    Science.gov (United States)

    ... 165947.html Eye Problems May Be Tied to Zika, Lab Study Suggests Work with monkeys indicates birth ... 25, 2017 (HealthDay News) -- Scientists exploring how the Zika virus passes from pregnant monkeys to their fetuses ...

  6. Overview of the TREC 2014 Contextual Suggestion Track

    Science.gov (United States)

    2014-11-01

    Section 6 which contains the results . 1.2 Task Description The contextual suggestion track investigates search techniques for complex information needs...split into two files: examples2014.csv, profiles2014-70.csv, and profiles2014-100.csv. exam - ples2014.csv contains a list of 100 suggestions which each...Chamber Music Festival Description Santa Fe Chamber Music Festival is music that moves you, played by artists who astound and dazzle you with their

  7. Highlighting Impact and the Impact of Highlighting: PRB Editors' Suggestions

    OpenAIRE

    Antonoyiannakis, Manolis

    2016-01-01

    Associate Editor Manolis Antonoyiannakis discusses the highlighting, as Editors' Suggestions, of a small percentage of the papers published each week. We highlight papers primarily for their importance and impact in their respective fields, or because we find them particularly interesting or elegant. It turns out that the additional layer of scrutiny involved in the selection of papers as Editors' Suggestions is associated with a significantly elevated and sustained citation impact.

  8. Hypnosis, hypnotic suggestibility, memory, and involvement in films.

    Science.gov (United States)

    Maxwell, Reed; Lynn, Steven Jay; Condon, Liam

    2015-05-01

    Our research extends studies that have examined the relation between hypnotic suggestibility and experiential involvement and the role of an hypnotic induction in enhancing experiential involvement (e.g., absorption) in engaging tasks. Researchers have reported increased involvement in reading (Baum & Lynn, 1981) and music-listening (Snodgrass & Lynn, 1989) tasks during hypnosis. We predicted a similar effect for film viewing: greater experiential involvement in an emotional (The Champ) versus a non-emotional (Scenes of Toronto) film. We tested 121 participants who completed measures of absorption and trait dissociation and the Harvard Group Scale of Hypnotic Susceptibility and then viewed the two films after either an hypnotic induction or a non-hypnotic task (i.e., anagrams). Experiential involvement varied as a function of hypnotic suggestibility and film clip. Highly suggestible participants reported more state depersonalization than less suggestible participants, and depersonalization was associated with negative affect; however, we observed no significant correlation between hypnotic suggestibility and trait dissociation. Although hypnosis had no effect on memory commission or omission errors, contrary to the hypothesis that hypnosis facilitates absorption in emotionally engaging tasks, the emotional film was associated with more commission and omission errors compared with the non-emotional film. Copyright © 2014 Elsevier Inc. All rights reserved.

  9. Suggestions on Writing for Publication in Language Learning Journals

    Directory of Open Access Journals (Sweden)

    George M. Jacobs

    1999-01-01

    Full Text Available This article provides suggestions on writing for journals in the field of language learning. These suggestions are presented in three sections. The first section discusses how to begin. Suggestions in this section are that we appreciate the benefits of writing for publication, develop good ideas, work efficiently, ponder options as to what type of writing to do, choose a good topic, consider replication of other's research, and cooperate with others. The second section presents suggestions on doing the actual writing. Here, it is suggested that we connect ideas, delve deeply into the ideas we present, strive to write the reader friendly manner, use visuals, and improve our writing by noticing how other journal authors write. The third section concerns relations with editors. The advice given is that we choose carefully the journal to which we submit our work, follow that journal's directions to contributors, include a cover letter, be prepared to wait patiently, welcome critical feedback from editors and reviewers, and view editors as colleagues.

  10. Feasibility of Music and Hypnotic Suggestion to Manage Chronic Pain.

    Science.gov (United States)

    Johnson, Alisa J; Kekecs, Zoltan; Roberts, R Lynae; Gavin, Russell; Brown, Kathleen; Elkins, Gary R

    2017-01-01

    The authors investigated the feasibility and possible effects of hypnotic suggestion and music for chronic pain. Ten people completed the 2-week intervention that consisted of daily listening to hypnotic suggestions combined with music. Averaged subjective pain intensity, pain bothersomeness, overall distress, anxiety, and depression decreased from baseline to endpoint. Participants rated pre- and postlistening pain intensity and pain bothersomeness decreased for each session. Information provided during end-of-study interviews indicated all participants were satisfied with treatment and felt they benefited from being in the study. Means and standard deviations are reported for outcome measures and a case study is provided. This preliminary study supports the use of a combined hypnotic suggestion and music intervention for chronic pain.

  11. Suggested Interactivity: Seeking Perceived Affordances for Information Visualization.

    Science.gov (United States)

    Boy, Jeremy; Eveillard, Louis; Detienne, Françoise; Fekete, Jean-Daniel

    2016-01-01

    In this article, we investigate methods for suggesting the interactivity of online visualizations embedded with text. We first assess the need for such methods by conducting three initial experiments on Amazon's Mechanical Turk. We then present a design space for Suggested Interactivity (i. e., visual cues used as perceived affordances-SI), based on a survey of 382 HTML5 and visualization websites. Finally, we assess the effectiveness of three SI cues we designed for suggesting the interactivity of bar charts embedded with text. Our results show that only one cue (SI3) was successful in inciting participants to interact with the visualizations, and we hypothesize this is because this particular cue provided feedforward.

  12. Therapeutic suggestion has not effect on postoperative morphine requirements.

    Science.gov (United States)

    van der Laan, W H; van Leeuwen, B L; Sebel, P S; Winograd, E; Baumann, P; Bonke, B

    1996-01-01

    This study was designed to confirm the effect of therapeutic intraoperative auditory suggestion on recovery from anesthesia, to establish the effect of preoperative suggestion, and to assess implicit memory for intraoperative information using an indirect memory task. Sixty consenting unpremedicated patients scheduled for elective gynecologic surgery were randomly divided into three equal groups: Group 1 received a tape of therapeutic suggestions preoperatively, and the story of Robinson Crusoe intraoperatively; Group 2 heard the story of Peter Pan preoperatively and therapeutic suggestions intraoperatively; Group 3 heard the Crusoe story preoperatively and the Peter Pan story intraoperatively. A standardized anesthetic technique was used with fentanyl, propofol, isoflurane, and nitrous oxide. After surgery, all patients received patient-controlled analgesia (PCA) with a standardized regimen. In the 24 h postsurgery, morphine use was recorded every 6 h and at 24 h an indirect memory test (free association) was used to test for memory of the stories. Anxiety scores were measured before surgery and at 6 and 24 h postsurgery. There were no significant differences between groups for postoperative morphine use, pain or nausea scores, anxiety scores, or days spent in hospital after surgery. Seven of 20 patients who heard the Pan story intraoperative gave a positive association with the word "Hook," whereas 2 of 20 who did not hear the story gave such an association. Indirect memory for the Pan story was established using confidence interval (CI) analysis. (The 95% CI for difference in proportion did not include zero). No indirect memory for the Crusoe story could be demonstrated. This study did not confirm previous work which suggested that positive therapeutic auditory suggestions, played intraoperatively, reduced PCA morphine requirements. In contrast, a positive implicit memory effect was found for a story presented intraoperatively.

  13. Establishment of prevention: what do dentists in northern Germany suggest?

    Science.gov (United States)

    Hussein, R J; Schneller, T; Dierks, M-L; Walter, U

    2013-11-01

    Dentists' suggestions for the establishment of preventive care were investigated on 3 levels; dentist, dental associations and unions (DAU), and health care system (HCS). Associations between categories of suggestions and dentists' characteristics were explored. A postal survey was sent to 2,075 dentists practicing in Bremen and Lower Saxony. The answers on 3 open-ended questions were analysed in a qualitative manner based on the quality control protocol (QCP) of the Federal Joint Committee. Quantitative methods were used for exploring associations between categories of suggestions and gender as well as age. Response rate was 33% (n=685). Dentists made 2,120 suggestions (dentist=752, DAU= 574, HCS= 794). The majority of dentists (90%) suggested educating and motivating patients. Dentists stated that support from DAU is needed in educating the public (50%), offering preventive-oriented training (35%), and in advertising for prophylaxis (18%). On the HCS level, about 60% of the suggestions concerned remunerating prophylaxis and expanding the existing bonus system. Significantly more female (p=0.010) and younger dentists (p=0.031) contributed to educating patients than male and older dentists. Education is the key message of this work. Essential topics such as prevention for elderly and risk groups were not a focal point. Education on the DAU and HCS levels can be realised through organising nation-wide health campaigns. Funding options for prevention and regulating multidisciplinary work between dentists and other health-care providers should be examined. These changes can contribute enormously to further establish prevention. © Georg Thieme Verlag KG Stuttgart · New York.

  14. Overview of the TREC 2013 Contextual Suggestion Track

    Science.gov (United States)

    2013-11-01

    Mechanical Turk and the University of Waterloo, where asked to complete an online survey. In the survey sample suggestions were presented to users in a random...re s taurant−and− grocery −s tore−johnson−c i t y 0 . . . 78 http ://www. r e d l i o n l e w i s t o n . com/ m e r i w e t h e r s a m e r i c a n g r...Team Runids: UAmsTF30WU This systems extracts suggestions for sightseeing, shopping , eating, and drinking from Wikitravel pages dedicated to US

  15. Children's suggestibility research: Things to know before interviewing a child

    Directory of Open Access Journals (Sweden)

    Amelia Courtney Hritz

    2015-01-01

    Full Text Available Children's testimony is often the only evidence of alleged abuse. Thus, the importance of conducting forensic interviews that are free from bias and misleading information is immense, as these could lead to false reports. In the current paper, we review unexpected findings in children's suggestibility that illustrate the difficulty in distinguishing between false and accurate reports. We explore situations in which a younger person's memory account may be more accurate than that of an adult, when a single suggestive interview may be as detrimental as multiple interviews, and when children can make inaccurate reports spontaneously. We conclude with recommendations for interviewers to decrease false reporting by both children and adults.

  16. Suggested guidelines for gas emission monitoring at danish landfills

    DEFF Research Database (Denmark)

    Kjeldsen, Peter; Scheutz, Charlotte

    2015-01-01

    Landfill gas is produced on waste disposal sites receiving organic waste resulting in emission of methane. Regulation requires that the landfill gas is managed in order to reduce emissions, but very few suggestions exist to how the landfill gas management activities are monitored, what requirements...... to the ability of the landfill gas management to reduce the emission should be set up, and how criteria are developed for when the monitoring activities can be terminated. Monitoring procedures are suggested centred on a robust method for measuring the total methane emission from the site, and quantitative...

  17. Studies and Suggestions on English Vocabulary Teaching and Learning

    Science.gov (United States)

    Zheng, Shigao

    2012-01-01

    To improve vocabulary learning and teaching in ELT settings, two questionnaires are designed and directed to more than 100 students and teachers in one of China's key universities. The findings suggest that an enhanced awareness of cultural difference, metaphorical competence, and learners' autonomy in vocabulary acquisition will effectively…

  18. Animal Rights: Selected Resources and Suggestions for Further Study.

    Science.gov (United States)

    Davidoff, Donald J.

    1989-01-01

    Presents an annotated list of selected resources intended to serve as a guide to the growing amount of material on animal rights. Suggestions to aid in additional research include subject headings used to find books, indexes used to locate periodical articles, sources for locating organizations, and a selected list of animal rights organizations.…

  19. Farm Women, Farming Systems, and Agricultural Structure: Suggestions for Scholarship.

    Science.gov (United States)

    Flora, Cornelia Butler

    1981-01-01

    Suggests research agenda to analyze the class struggle occurring with farm women. Views the household as the unit of analysis, both internally from a farming-systems perspective and externally as responding to shifts in policy and technology. Available from: Rural Sociological Society, 325 Morgan Hall, University of Tennessee, Knoxville, TN 37916.…

  20. Barriers to Policy Change and a Suggested Path for Change

    Science.gov (United States)

    Jing, Yijia

    2013-01-01

    China's one-child policy has been an unprecedented policy experiment in human history. Despite its significant achievements, the policy has induced equally significant potential problems. As problems of the one-child policy have been widely noticed and suggestions for adjustments are available, the leadership transition of China in 2012 and 2013…

  1. Economic Literacy and Efficacy: Suggestions for Research. Draft.

    Science.gov (United States)

    Wentworth, Donald R.

    Economic literacy and economic efficacy are addressed by examining basic goals and assumptions of economic education and by suggesting areas that need systematic attention and investigation. To clarify goals, an operational definition of economic literacy must be developed and used in a criterion-referenced testing instrument. A definition of…

  2. Suggested physical therapy protocol for reduction of lipomatosis ...

    African Journals Online (AJOL)

    The purpose of this study was to investigate the efficacy of suggested physical therapy protocol in lipomatosis dolorosa of the legs. Twenty female patients with stage I lipomatosis dolorosa of the legs ranged in age from 30 to 45 years. They received a complete decongestive physical therapy program and diet regimen.

  3. Government policy and technological innovation-a suggested typology

    NARCIS (Netherlands)

    Dolfsma, Wilfred; Seo, DongBack

    2013-01-01

    Reports on the effects of government's role in stimulating technological development provide a mixed picture. Some policies have had the expected, stimulating effect and other policies have not. We suggest that specific characteristics of technologies that government has sought to stimulate have not

  4. Suggestions for Revising Iranian Library Laws and Regulations.

    Science.gov (United States)

    Harvey, John F.

    The present Iranian library laws are incomplete, obsolete, and ineffective. Certain aspects of the Iranian school and public library standards described are based on the assumption that the laws will be improved in accordance with these suggestions. In a general way, this document attempts to build on the present laws and supplement them as well…

  5. Halloween Costumes May Suggest Influence of Violent Models on Children.

    Science.gov (United States)

    Owen, John W.; Sterling, Bruce S.

    Halloween costumes may be used to examine the influence violent models have on children. On Halloween evening observers recorded the frequency of violent and nonviolent costumes worn by children. When all of the data are inspected they suggest that children confronted with several aggressive models may be more likely to identify with the…

  6. Sexually Abused Children: Identification and Suggestions for Intervention.

    Science.gov (United States)

    Brassard, Marla R.; And Others

    1983-01-01

    This article is designed to help school psychologists: (1) identify victims of child abuse; (2) interview a victim and the victim's parents; (3) know who to notify when sexual abuse is suspected; and (4) identify suggested intervention and treatment approaches that are appropriate in the practice of school psychology. (Author/PN)

  7. Hotel Employees' Japanese Language Experiences: Implications and Suggestions.

    Science.gov (United States)

    Makita-Discekici, Yasuko

    1998-01-01

    Analyzes the Japanese language learning experiences of 13 hotel employees in Guam. Results of the study present implications and suggestions for a Japanese language program for the hotel industry. The project began as a result of hotel employees frustrations when they were unable to communicate effectively with their Japanese guests. (Auth/JL)

  8. Automatic annotation suggestions for audiovisual archives: Evaluation aspects

    NARCIS (Netherlands)

    Gazendam, L.J.B.; Malaisé, V.; de Jong, A.; Wartena, C.; Brugman, H.; Schreiber, A.Th.

    2009-01-01

    In the context of large and ever growing archives, generating annotation suggestions automatically from textual resources related to the documents to be archived is an interesting option in theory. It could save a lot of work in the time consuming and expensive task of manual annotation and it could

  9. Suggestions for Improving Ugandan Higher Education to Produce ...

    African Journals Online (AJOL)

    Every country invests in formal education to develop and empower its citizens with the capacity needed to practically work and transform their surrounding environmental resources into productive employment after graduation. The high and growing rate of graduate unemployment in Uganda suggests however, that most of ...

  10. A Suggested Journalism Curriculum for California Junior Colleges.

    Science.gov (United States)

    Margosian, Arthur

    The purpose of this study was to develop a suggested journalism curriculum for California junior colleges, based upon the functions and content of journalism programs as they should be, as perceived by a representative group of junior college instructrs and editors of daily and weekly newspapers in California. Data were collected from…

  11. Suggesting a General ESP Model for Adult Learners

    Science.gov (United States)

    Al-Jumaily, Samir

    2011-01-01

    The study suggests a general model that could guarantee the cooperation between teachers and their students to overcome the difficulties encountered in ESP learning. It tries to join together different perspectives in the research of adult education, specifically in the teaching of English for Specific Purposes. It also provides some sort of trust…

  12. Suggestion in Education: The Historical Path of Suggestopedia.

    Science.gov (United States)

    Lindeman, Mary L.

    Although techniques of autosuggestion in personal development have a long history in some Eastern cultures, suggestibility as a character trait first came into focus in the West with the "animal magnetism" of Franz Mesmer. The uncovering of the nature and phenomena of hypnosis resulted in a steady and enduring interest in this state of…

  13. Coping with loneliness: what do older adults suggest?

    NARCIS (Netherlands)

    Schoenmakers, E.; van Tilburg, T.; Fokkema, C.M.

    2012-01-01

    Objectives: A limited amount of information is available on how older adults cope with loneliness. Two ways of coping are distinguished here, i.e., active coping by improving relationships and regulative coping by lowering expectations about relationships. We explore how often older adults suggest

  14. A Privacy-by-Design Contextual Suggestion System for Tourism

    NARCIS (Netherlands)

    Efraimidis, Pavlos; Drosatos, George; Arampatzis, Avi; Stamatelatos, Giorgos; Athanasiadis, Ioannis

    2016-01-01

    We focus on personal data generated by the sensors and through the everyday usage of smart devices and take advantage of these data to build a non-invasive contextual suggestion system for tourism. The system, which we call Pythia, exploits the computational capabilities of modern smart devices to

  15. Editor's Note Responding to suggestions from the research ...

    African Journals Online (AJOL)

    Admin

    Editor's Note. Responding to suggestions from the research fellowship of the Institute of African Studies for a re-branding of the. Research Review, which began publication in the early 1960s soon after the establishment of the Institute, the old title has now been replaced with a new title — Contemporary Journal of African ...

  16. De-Problematizing 'GMOs': Suggestions for Communicating about Genetic Engineering.

    Science.gov (United States)

    Blancke, Stefaan; Grunewald, Wim; De Jaeger, Geert

    2017-03-01

    The public debates concerning genetic engineering (GE) involve many non-scientific issues. The ensuing complexity is one reason why biotechnologists are reluctant to become involved. By sharing our personal experiences in science communication and suggesting ways to de-problematize GE, we aim to inspire our colleagues to engage with the public. Copyright © 2016 Elsevier Ltd. All rights reserved.

  17. Asthma control - Practical suggestions for practicing doctors in family ...

    African Journals Online (AJOL)

    ... the 'Goals of asthma management' as set out in the Global Initiative for Asthma (GINA) guidelines. Despite the availability of useful asthma therapies and treatment strategies, the morbidity from asthma has remained significant. This review includes practical suggestions on optimal asthma control for the family practitioner.

  18. A SUGGESTED CHECKLIST FOR ASSESSING A SCIENCE PROGRAM.

    Science.gov (United States)

    Office of Education (DHEW), Washington, DC.

    SUGGESTIONS AND A CHECKLIST FOR THE EVALUATION OF ELEMENTARY AND SECONDARY SCHOOL SCIENCE PROGRAMS ARE CONTAINED IN THIS UNITED STATES OFFICE OF EDUCATION BULLETIN. AN INTRODUCTORY SECTION DEALS WITH THE IMPORTANCE OF (1) BROAD FACULTY PARTICIPATION, AND (2) UP-TO-DATE CONTENT AND METHODS IN PROGRAM EVALUATION. EXPLANATIONS FOR THE CONSTRUCTION…

  19. 32 CFR Enclosure - Suggested Format, Affidavit of Service by Mail

    Science.gov (United States)

    2010-07-01

    ... 32 National Defense 1 2010-07-01 2010-07-01 false Suggested Format, Affidavit of Service by Mail Enclosure National Defense Department of Defense OFFICE OF THE SECRETARY OF DEFENSE PERSONNEL, MILITARY AND CIVILIAN UNSATISFACTORY PERFORMANCE OF READY RESERVE OBLIGATION Definitions. Pt. 100, Encl. Enclosure...

  20. Evaluation of patients with symptoms suggestive of chronic polyneuropathy

    DEFF Research Database (Denmark)

    Johannsen, L; Smith, T; Havsager, A M

    2001-01-01

    OBJECTIVES: The aim of this study was to determine the diagnostic yield and to describe the spectrum of diagnosis encountered by evaluation of patients with symptoms suggestive of chronic polyneuropathy. METHODS: We prospectively evaluated 198 patients referred to a department of neurology with s...

  1. Explicit grammar teaching in EAL classrooms: Suggestions from ...

    African Journals Online (AJOL)

    The development of the subject English Additional Language (EAL) to serve as a strong support subject in explicitly teaching learners the grammar of English is suggested as an interim solution to the effects of the non-implementation of the 1997 South African Language in Education Policy. To identify specific grammatical ...

  2. Webis at TREC 2014: Web, Session, and Contextual Suggestion Tracks

    Science.gov (United States)

    2014-11-01

    much to improve the result ranking. 4. CONTEXTUAL SUGGESTION TRACK The research question we examine in the Contextual Sug- gestion track is whether a... gestions we build upon state-of-the-art tools. Our first run uses descriptions without explanations while an explanation is added in the second run

  3. Mind the gap: suggestions for bridging the divide between formal ...

    African Journals Online (AJOL)

    These alternatives can be termed informal social security which, although providing a certain degree of security, functions outside the protection and recognition of the formal system. The article offers suggestions for mechanisms to enhance offers cooperation between these two social security systems that can assist ...

  4. Suggestions for the Classical Shelves of a School Library.

    Science.gov (United States)

    Colebourn, R., Comp.; Cleeve, Marigold, Comp.

    This bibliography is suggested for use by students and teachers of Latin, Greek and ancient civilizations. Entries are compiled under the headings of: (1) bibliographies and journals including booklists, periodicals, and books for teachers; (2) reference works in literature, mythology, history and antiquities, and language; (3) texts and…

  5. Dissociation, personality, suggestibility, alexithymia, and problems with emotional regulation: A correlational study

    Directory of Open Access Journals (Sweden)

    Ángeles Serrano

    2016-12-01

    Full Text Available The present paper explores the relationship between psychological and somatic dissociation and different personality and emotional variables, including suggestibility, alexithymia, and emotional regulation and dysregulation. The results with a sample of 355 partipants of a normal population reveal that there is a positive relationship between both types of dissociation, suggestibility and emotional dysregulation. Likewise, there were different patterns of personality associated both to psychological and somatic dissociation. Correlations found in this study put forward the importance to take into account both types of dissociactive symptoms, psychological and somatic ones.

  6. Source memory and eyewitness suggestibility in older adults.

    Science.gov (United States)

    Multhaup, K S; De Leonardis, D M; Johnson, M K

    1999-01-01

    The authors investigated the influence of test format on the source-memory performance of older adults (N = 128). Each participant viewed a picture and wrote a description of the scene. Then half of the participants (control group) read a text that accurately described the scene; the other half (misled group) read a text that contained misinformation. After writing another scene description, the participants were given a surprise memory test. Half were given a yes/no recognition test, and half were given a source-monitoring test. The misled yes/no participants mistakenly indicated more often than the control yes/no participants that misleading-text items were in the picture (suggestibility effect). There was no suggestibility effect for source-monitoring participants. The data are discussed in terms of the source monitoring framework.

  7. Auto Spell Suggestion for High Quality Speech Synthesis in Hindi

    Science.gov (United States)

    Kabra, Shikha; Agarwal, Ritika

    2014-02-01

    The goal of Text-to-Speech (TTS) synthesis in a particular language is to convert arbitrary input text to intelligible and natural sounding speech. However, for a particular language like Hindi, which is a highly confusing language (due to very close spellings), it is not an easy task to identify errors/mistakes in input text and an incorrect text degrade the quality of output speech hence this paper is a contribution to the development of high quality speech synthesis with the involvement of Spellchecker which generates spell suggestions for misspelled words automatically. Involvement of spellchecker would increase the efficiency of speech synthesis by providing spell suggestions for incorrect input text. Furthermore, we have provided the comparative study for evaluating the resultant effect on to phonetic text by adding spellchecker on to input text.

  8. Analysis of existing risk assessments, and list of suggestions

    CERN Document Server

    Heimsch, Laura

    2016-01-01

    The scope of this project was to analyse risk assessments made at CERN and extracting some crucial information about the different methodologies used, profiles of people who make the risk assessments, and gathering information of whether the risk matrix was used and if the acceptable level of risk was defined. Second step of the project was to trigger discussion inside HSE about risk assessment by suggesting a risk matrix and a risk assessment template.

  9. Oncologic prevention and suggested working standards in primary health care

    Directory of Open Access Journals (Sweden)

    Konstantinović Dejan

    2016-01-01

    Full Text Available On the ground of the available data, this paper presents the problem of malignant diseases in Central Serbia, and most common carcinogens. Division of carcinogens, cancerogenesis and natural history of disease, early detection of cancer and palliative management are explained. The role and capacities of primary health care doctors in treatment of patients with suspect malignant disease are presented. Authors are suggesting standards for medical tasks and contemporary principles in approach to patients with malignant diseases in everyday practice.

  10. Children's suggestibility research: Things to know before interviewing a child

    OpenAIRE

    Hritz, Amelia Courtney; Royer, Caisa Elizabeth; Helm, Rebecca K.; Burd, Kayla A.; Ojeda, Karen; Ceci, Stephen J.

    2015-01-01

    Children's testimony is often the only evidence of alleged abuse. Thus, the importance of conducting forensic interviews that are free from bias and misleading information is immense, as these could lead to false reports. In the current paper, we review unexpected findings in children's suggestibility that illustrate the difficulty in distinguishing between false and accurate reports. We explore situations in which a younger person's memory account may be more accurate than that of an adult, ...

  11. Epistemological Suggestions in „Entropy Low and Economic Process”

    Directory of Open Access Journals (Sweden)

    Emil Dinga

    2006-06-01

    Full Text Available The paper is aimed to derive, on criticism basis (following, especially, the critic rationalism, as method, epistemological suggestions from the crucial work of Nicholas Georgescu-Roegen, “The Entropy Law and the Economic Process”, in order to these suggestions or challenges constitute going points for further logical assessments or polemical debates. By this way, four basic epistemological suggestions are identified: a inconsistency between the analytical description of the economic process and its evolutionist nature (that implies qualitative changes; b logical and epistemological bases for the possibility of a theoretical economic science (i.e. of a theory of the economic science; c impact of the qualitative changes of the economic process on the non-linearity of the economic models for prognosis; d logics, based on the entropy law, to pass off the rationality of optimality and to enter the rationality of sustainability. Each of these suggestions (explicit or implicit mentioned in the evocated work plays as rational, for the authors, to formulate epistemological assessments, critics or proposals for solutions aimed at to pass over the arisen epistemological or methodological problems. The authors believe that the entropic paradigm proposed by Nicholas Georgescu-Roegen for the economic epistemology and methodology is one of the most interesting, from the philosophic and logic points of view, having abundant resources to open a re-conceptualization of the logical bases of the economic science, to rethink the theoreticity of the sciences that study fields where evolutive processes are going, and to think, with more maturity, to the way in which the human rationality could answer the challenges the entropy law arises.

  12. CHINESE EFL UNDERGRADUATES’ ACADEMIC WRITING: RHETORICAL DIFFICULTIES AND SUGGESTIONS

    Directory of Open Access Journals (Sweden)

    Xiaoyun Bian

    2016-07-01

    Full Text Available Difficulties encountered by students in L2 academic writing has been a subject of research for several decades. However, to date, there still remains a lack of detailed and in-depth investigation into this area of interest. This qualitative study thoroughly investigated the rhetorical difficulties faced by Chinese EFL undergraduate academic writers, and collected suggestions on how to address these rhetorical issues. To be sufficiently detailed and thorough, this study divided students' difficulties into process- and product-related difficulties, and used triangulated data from supervisors' perspectives, students' perspectives, and supervisors' comments to address research questions. Although there were no strong generalizations derived from data from different perspectives and sources, the findings of this study showed supervisor perceptions of the rhetorical difficulties the students experienced were almost identical. In nature these rhetorical difficulties were culturallyembedded and genre-related issues; and the degree of difficulty experienced by each student varied. In this study, supervisors and students both suggested that, to solve rhetorical difficulties, teacher student communication should be improved. This study provided empirical evidence to contrastive rhetoric theory and socio-cultural theory. It also offered suggestions on how to strengthen future research in this area of inquiry, and how to improve academic writing teaching in L2 educational contexts.

  13. A Privacy-by-Design Contextual Suggestion System for Tourism

    Directory of Open Access Journals (Sweden)

    Pavlos S. Efraimidis

    2016-05-01

    Full Text Available We focus on personal data generated by the sensors and through the everyday usage of smart devices and take advantage of these data to build a non-invasive contextual suggestion system for tourism. The system, which we call Pythia, exploits the computational capabilities of modern smart devices to offer high quality personalized POI (point of interest recommendations. To protect user privacy, we apply a privacy by design approach within all of the steps of creating Pythia. The outcome is a system that comprises important architectural and operational innovations. The system is designed to process sensitive personal data, such as location traces, browsing history and web searches (query logs, to automatically infer user preferences and build corresponding POI-based user profiles. These profiles are then used by a contextual suggestion engine to anticipate user choices and make POI recommendations for tourists. Privacy leaks are minimized by implementing an important part of the system functionality at the user side, either as a mobile app or as a client-side web application, and by taking additional precautions, like data generalization, wherever necessary. As a proof of concept, we present a prototype that implements the aforementioned mechanisms on the Android platform accompanied with certain web applications. Even though the current prototype focuses only on location data, the results from the evaluation of the contextual suggestion algorithms and the user experience feedback from volunteers who used the prototype are very positive.

  14. Public opinion and organ donation suggestions for overcoming barriers.

    Science.gov (United States)

    Cantarovich, Félix

    2005-01-01

    Getting organs for transplantation depends on people's decision; thus, public opinion is essential to finding a solution to this problem. Efforts to improve organ shortage focus on: 1) Living, unrelated donation, 2) increasing marginal donors and 3) proposing economic support for donors. Paradoxically, no initiative has been suggested to modify public opinion towards cadaver donors. Several reasons explain the resistance to donating cadaver organs: Lack of awareness, religious uncertainties, distrust of medicine, hostility to new ideas, and misinformation. Education should be used to reshape public opinion about the use of organs for transplantation. Society should accept that "using" body parts is moral and offers a source of health for everybody. The concept that using cadaver organs implies sharing a source of health might be a social agreement between all members of Society. Suggestions for improving organ shortage include: 1) Society should understand that during one's life one may be just as easily a potential organ receiver as one is an organ donor. 2) Cadaver organs are an irreplaceable source of health. 3) As self-interest is one obstacle to donating cadaver organs, the "concept that allowing the use of our organs after death represents a chance of sharing health for everybody" may be useful for a change of attitude. Even though a poll among transplant professionals supported this suggestion, an international public survey should be carried out to evaluate people's reaction to this message.

  15. A query suggestion workflow for life science IR-systems.

    Science.gov (United States)

    Esch, Maria; Chen, Jinbo; Weise, Stephan; Hassani-Pak, Keywan; Scholz, Uwe; Lange, Matthias

    2014-06-13

    Information Retrieval (IR) plays a central role in the exploration and interpretation of integrated biological datasets that represent the heterogeneous ecosystem of life sciences. Here, keyword based query systems are popular user interfaces. In turn, to a large extend, the used query phrases determine the quality of the search result and the effort a scientist has to invest for query refinement. In this context, computer aided query expansion and suggestion is one of the most challenging tasks for life science information systems. Existing query front-ends support aspects like spelling correction, query refinement or query expansion. However, the majority of the front-ends only make limited use of enhanced IR algorithms to implement comprehensive and computer aided query refinement workflows. In this work, we present the design of a multi-stage query suggestion workflow and its implementation in the life science IR system LAILAPS. The presented workflow includes enhanced tokenisation, word breaking, spelling correction, query expansion and query suggestion ranking. A spelling correction benchmark with 5,401 queries and manually selected use cases for query expansion demonstrate the performance of the implemented workflow and its advantages compared with state-of-the-art systems.

  16. Perinatal pathology: practice suggestions for limited-resource settings.

    Science.gov (United States)

    Roberts, Drucilla J

    2013-06-01

    The practice of perinatal pathology in much of the world suffers, as do all subspecialties of anatomic pathology, from inadequate resources (equipment, consumables, and both professional and technical personnel), from lack of education (not only of the pathologist but also of the clinicians responsible for sending the specimens, and the technicians processing the specimens), and from lack of appropriate government sector support. Perinatal pathology has significant public health-related utility and should be championing its service by providing maternal and fetal/infant mortality and morbidity data to governmental health ministries. It is with this pathologic data that informed decisions can be made on health-related courses of action and allocation of resources. These perinatal pathology data are needed to develop appropriate public health initiatives, specifically toward achieving the Millennium Developmental Goals as the best way to effectively decrease infant and maternal deaths and to determine causes of perinatal mortality and morbidity. The following overview will focus on the utility of perinatal pathology specifically as related to its public health function and will suggest methods to improve its service in resource-poor settings. This article is offered not as a critique of the current practice that most pathologists find themselves working in globally, but to provide suggestions for improving perinatal pathology services, which could be implemented with the limited available resources and manpower most pathology departments currently have. In addition, we offer suggestions for graded improvements ("ramping up") over time.

  17. Mitochondrial genomes suggest that hexapods and crustaceans are mutually paraphyletic

    Science.gov (United States)

    Cook, Charles E; Yue, Qiaoyun; Akam, Michael

    2005-01-01

    For over a century the relationships between the four major groups of the phylum Arthropoda (Chelicerata, Crustacea, Hexapoda and Myriapoda) have been debated. Recent molecular evidence has confirmed a close relationship between the Crustacea and the Hexapoda, and has included the suggestion of a paraphyletic Hexapoda. To test this hypothesis we have sequenced the complete or near-complete mitochondrial genomes of three crustaceans (Parhyale hawaiensis, Squilla mantis and Triops longicaudatus), two collembolans (Onychiurus orientalis and Podura aquatica) and the insect Thermobia domestica. We observed rearrangement of transfer RNA genes only in O. orientalis, P. aquatica and P. hawaiensis. Of these, only the rearrangement in O. orientalis, an apparent autapomorphy for the collembolan family Onychiuridae, was phylogenetically informative. We aligned the nuclear and amino acid sequences from the mitochondrial protein-encoding genes of these taxa with their homologues from other arthropod taxa for phylogenetic analysis. Our dataset contains many more Crustacea than previous molecular phylogenetic analyses of the arthropods. Neighbour-joining, maximum-likelihood and Bayesian posterior probabilities all suggest that crustaceans and hexapods are mutually paraphyletic. A crustacean clade of Malacostraca and Branchiopoda emerges as sister to the Insecta sensu stricto and the Collembola group with the maxillopod crustaceans. Some, but not all, analyses strongly support this mutual paraphyly but statistical tests do not reject the null hypotheses of a monophyletic Hexapoda or a monophyletic Crustacea. The dual monophyly of the Hexapoda and Crustacea has rarely been questioned in recent years but the idea of both groups' paraphyly dates back to the nineteenth century. We suggest that the mutual paraphyly of both groups should seriously be considered. PMID:16024395

  18. Solid-State Lighting 2017 Suggested Research Topics

    Energy Technology Data Exchange (ETDEWEB)

    None, None

    2017-09-29

    A 2017 update to the Solid-State Lighting R&D Plan that is divided into two documents. The first document describes a list of suggested SSL priority research topics and the second document provides context and background, including information drawn from technical, market, and economic studies. Widely referenced by industry and government both here and abroad, these documents reflect SSL stakeholder inputs on key R&D topics that will improve efficacy, reduce cost, remove barriers to adoption, and add value for LED and OLED lighting solutions over the next three to five years, and discuss those applications that drive and prioritize the specific R&D.

  19. A suggestion for multidisciplinarity: the fluorescence phenomenon observation

    Directory of Open Access Journals (Sweden)

    Jorge Roberto Pimentel

    2014-05-01

    Full Text Available Multidisciplinary approaches involving daily phenomena are valuable teaching tools to stimulate reflections in order to comprehend that scientific knowledge is developed in a collective process, as well as to understand the importance that scientific research cannot be done in a unique area of knowledge for the full understanding of any phenomenon. We suggest the fluorescence phenomenon observation in some materials, objects and living organisms so that students realize the interaction between Physics, Chemistry and Biology, generally regarded as not correlated disciplines.

  20. Vietnam’s public debt : Problems and Suggested solutions

    OpenAIRE

    Van Nguyen, Thuy

    2014-01-01

    Public debt crisis currently becomes a common concern of many countries. In Vietnam, public debt is at risk level and tends to increase rapidly. This thesis analyzed the current situation and causes of Vietnam’s public debt, and suggested some solutions to control public debt. The research flows from the cases in European countries and Japan to Vietnam to study the con-text of public debt crisis and policy-responses of those countries. The study was conducted by means of the qualitative ...

  1. Six Suggestions for Research on Games in Cognitive Science.

    Science.gov (United States)

    Chabris, Christopher F

    2017-04-01

    Games are more varied and occupy more of daily life than ever before. At the same time, the tools available to study game play and players are more powerful than ever, especially massive data sets from online platforms and computational engines that can accurately evaluate human decisions. This essay offers six suggestions for future cognitive science research on games: (1) Don't forget about chess, (2) Look beyond action games and chess, (3) Use (near)-optimal play to understand human play and players, (4) Investigate social phenomena, (5) Raise the standards for studies of games as treatments, (6) Talk to real experts. Copyright © 2017 Cognitive Science Society, Inc.

  2. Is homosexuality familial? A review, some data, and a suggestion.

    Science.gov (United States)

    Pillard, R C; Poumadere, J; Carretta, R A

    1981-10-01

    This report summarizes evidence that sexual orientation is familial. Family studies report that homosexual subjects have more homosexual siblings than do heterosexual subjects and more than would be expected given population frequencies. Twin studies find in general a higher concordance in sexual orientation among monozygotic than among dizygotic twins. Evidence for associated psychopathology in homosexual subjects or their relatives is inconclusive. Possible sources of bias in these reports are discussed and a suggestion is offered that family studies should be undertaken in which the sexual orientation of relatives would be directly ascertained by interview.

  3. Partnership-Based Health Care: Suggestions for Effective Application

    Directory of Open Access Journals (Sweden)

    Teddie M Potter

    2015-06-01

    Full Text Available Societal transformation often starts with one visionary and a compelling idea. However, if there are no followers, the idea quickly becomes marginalized. It “takes a village” to build a movement, and the more system layers that can be addressed, the more likely the transformation will take hold. This article describes the framework for creating the necessary changes for partnership-based health care. It also makes suggestions for ensuring successful application of partnership-based systems change. This article is for all readers seeking to apply partnership principles in their own fields of influence.

  4. Making academic research more relevant: A few suggestions

    Directory of Open Access Journals (Sweden)

    Abinash Panda

    2014-09-01

    Full Text Available Academic research in the domain of management scholarship, though steeped in scientific and methodological rigour, is generally found to be of little relevance to practice. The authors of this paper have revisited the rigour-relevance debate in light of recent developments and with special reference to the management research scenario in India. The central thesis of the argument is that the gulf between rigour and relevance needs to be bridged to make academic research more relevant to business organizations and practitioners. They have offered some suggestions to enhance the relevance of academic research to practice.

  5. Mental illness stigma in the Israeli context: deliberations and suggestions.

    Science.gov (United States)

    Tal, Amir; Roe, David; Corrigan, Patrick W

    2007-11-01

    In this paper we deliberate mental illness stigma in the Israeli context and suggest ways to reduce it, emphasizing the community's role in the rehabilitation of persons with mental illness. A literature review of Israeli and international literature of mental illness stigma. Community mental health, in addition to its traditional focus on developing community-based services, should focus also on community-based interventions such as the delivery of anti-stigma interventions. Providing individualized rehabilitation services in the community while addressing stigma-induced social barriers may create a better recovery ground for Israelis with mental illness.

  6. Genome-Wide Association Study Reveals the Genetic Architecture Underlying Salt Tolerance-Related Traits in Rapeseed (Brassica napus L.

    Directory of Open Access Journals (Sweden)

    Jinxiong Shen

    2017-04-01

    Full Text Available Soil salinity is a serious threat to agriculture sustainability worldwide. Salt tolerance at the seedling stage is crucial for plant establishment and high yield in saline soils; however, little information is available on rapeseed (Brassica napus L. salt tolerance. We evaluated salt tolerance in different rapeseed accessions and conducted a genome-wide association study (GWAS to identify salt tolerance-related quantitative trait loci (QTL. A natural population comprising 368 B. napus cultivars and inbred lines was genotyped with a Brassica 60K Illumina Infinium SNP array. The results revealed that 75 single-nucleotide polymorphisms (SNPs distributed across 14 chromosomes were associated with four salt tolerance-related traits. These SNPs integrated into 25 QTLs that explained 4.21–9.23% of the phenotypic variation in the cultivars. Additionally, 38 possible candidate genes were identified in genomic regions associated with salt tolerance indices. These genes fell into several functional groups that are associated with plant salt tolerance, including transcription factors, aquaporins, transporters, and enzymes. Thus, salt tolerance in rapeseed involves complex molecular mechanisms. Our results provide valuable information for studying the genetic control of salt tolerance in B. napus seedlings and may facilitate marker-based breeding for rapeseed salt tolerance.

  7. Genome-Wide Association Study Reveals the Genetic Architecture Underlying Salt Tolerance-Related Traits in Rapeseed (Brassica napus L.).

    Science.gov (United States)

    Wan, Heping; Chen, Lunlin; Guo, Jianbin; Li, Qun; Wen, Jing; Yi, Bin; Ma, Chaozhi; Tu, Jinxing; Fu, Tingdong; Shen, Jinxiong

    2017-01-01

    Soil salinity is a serious threat to agriculture sustainability worldwide. Salt tolerance at the seedling stage is crucial for plant establishment and high yield in saline soils; however, little information is available on rapeseed (Brassica napus L.) salt tolerance. We evaluated salt tolerance in different rapeseed accessions and conducted a genome-wide association study (GWAS) to identify salt tolerance-related quantitative trait loci (QTL). A natural population comprising 368 B. napus cultivars and inbred lines was genotyped with a Brassica 60K Illumina Infinium SNP array. The results revealed that 75 single-nucleotide polymorphisms (SNPs) distributed across 14 chromosomes were associated with four salt tolerance-related traits. These SNPs integrated into 25 QTLs that explained 4.21-9.23% of the phenotypic variation in the cultivars. Additionally, 38 possible candidate genes were identified in genomic regions associated with salt tolerance indices. These genes fell into several functional groups that are associated with plant salt tolerance, including transcription factors, aquaporins, transporters, and enzymes. Thus, salt tolerance in rapeseed involves complex molecular mechanisms. Our results provide valuable information for studying the genetic control of salt tolerance in B. napus seedlings and may facilitate marker-based breeding for rapeseed salt tolerance.

  8. Children Undergoing Radiotherapy: Swedish Parents’ Experiences and Suggestions for Improvement

    Science.gov (United States)

    Mullaney, Tara; Nilsson, Kristina; Wickart-Johansson, Gun; Svärd, Anna-Maja; Nyholm, Tufve; Lindh, Jack; Lindh, Viveca

    2015-01-01

    Approximately 300 children, from 0 to 18 years old, are diagnosed with cancer in Sweden every year. Of these children, 80–90 of them undergo radiotherapy treatment for their cancer. Although radiotherapy is an encounter with advanced technology, few studies have investigated the child’s and the parent’s view of the procedure. As part of an ongoing multicenter study aimed to improve patient preparation and the care environment in pediatric radiotherapy, this article reports the findings from interviews with parents at baseline. The aim of the present study was twofold: to describe parents’ experience when their child undergoes radiotherapy treatment, and to report parents’ suggestions for improvements during radiotherapy for their children. Sixteen mothers and sixteen fathers of children between 2–16 years old with various cancer diagnoses were interviewed. Data were analyzed using content analysis. The findings showed that cancer and treatment turns people’s lives upside down, affecting the entire family. Further, the parents experience the child’s suffering and must cope with intense feelings. Radiotherapy treatment includes preparation by skilled and empathetic staff. The parents gradually find that they can deal with the process; and lastly, parents have suggestions for improvements during the radiotherapy treatment. An overarching theme emerged: that despair gradually turns to a sense of security, with a sustained focus on and close interaction with the child. In conclusion, an extreme burden was experienced around the start of radiotherapy, though parents gradually coped with the process. PMID:26509449

  9. Synesthesia in twins: incomplete concordance in monozygotes suggests extragenic factors.

    Science.gov (United States)

    Bosley, Hannah G; Eagleman, David M

    2015-06-01

    Colored-sequence synesthesia (CSS) is a neurological condition in which sequential stimuli such as letters, numbers, or days of the week trigger simultaneous, involuntary color perception. Although the condition appears to run in families and several studies have sought a genetic link, the genetic contribution to synesthesia remains unclear. We conducted the first comparative twin study of CSS and found that CSS has a pairwise concordance of 73.9% in monozygotic twins, and a pairwise concordance of 36.4% in dizygotic twins. In line with previous studies, our results suggest a heritable element of synesthesia. However, consonant with the findings of previous single-pair case studies, our large sample size verifies that synesthesia is not completely conferred by genetics; if it were, monozygotic twins should have 100% concordance. These findings implicate a genetic mechanism of CSS that may work differently than previously thought: collectively, our data suggest that synesthesia is a heritable condition with incomplete penetrance that is substantially influenced by epigenetic and environmental factors. Copyright © 2015 Elsevier B.V. All rights reserved.

  10. Current and Suggested focus on Sustainability in Pyrometallurgy

    Science.gov (United States)

    See, J. B.; Robertson, D. G. C.; Mackey, P. J.

    The production of iron and steel and non-ferrous metals by pyrometallurgical processes will remain a critical element in meeting the demand for materials in both developed and developing nations. Given the important need to reduce and minimise greenhouse gas emissions the technological focus of future pyrometallurgical R&D by universities and industry alike must concentrate on sustainability issues such as improved energy efficiency, recycling and waste minimization. Continued efforts are also needed on process optimization and new process development with a view to reducing capital and operating costs of the new large "mega" plants. Using the academic and industrial backgrounds of the authors, the present paper reviews the current status of R&D in pyrometallurgy in university departments with a particular emphasis on sustainability issues. The role of industry and government laboratories is also reviewed although primarily for developed countries. The paper also includes comments and suggestions on the future requirements for education and R&D in pyrometallurgy in developed countries to maximise sustainability. It is also suggested that future R&D in pyrometallurgy will be even more concentrated in developing countries — most notably China.

  11. ONLINE PSYCHOTHERAPY: GROWING DEMAND AND SUGGESTIONS FOR ITS REGULATION

    Directory of Open Access Journals (Sweden)

    Carmelita Gomes Rodrigues

    2017-01-01

    Full Text Available Online psychotherapy is a form of psychotherapy conducted by means of synchronous Internet sessions that are still not allowed in Brazil, except in a few instances defined by the Resolution 011/2012 of the Federal Council of Psychology. Such restriction is based on the understanding that the research available is insufficient to authorize a widespread use of this type of service. Studies on therapeutic alliance in psychological care provided exclusively over the internet show that the establishment of the therapeutic relationship in synchronous online calls occurs much like it does in face-to-face therapeutic processes, considering both, its benefits and challenges. This article aims to broaden the understanding of the online psychotherapy and to question its prohibition, signaling the dangers it entails, vis-a-vis the increasing demand for the service and its widespread use in disregard with the current restrictions. This article also makes suggestions for the regulation of the service in Brazil.

  12. Friend suggestion in social network based on user log

    Science.gov (United States)

    Kaviya, R.; Vanitha, M.; Sumaiya Thaseen, I.; Mangaiyarkarasi, R.

    2017-11-01

    Simple friend recommendation algorithms such as similarity, popularity and social aspects is the basic requirement to be explored to methodically form high-performance social friend recommendation. Suggestion of friends is followed. No tags of character were followed. In the proposed system, we use an algorithm for network correlation-based social friend recommendation (NC-based SFR).It includes user activities like where one lives and works. A new friend recommendation method, based on network correlation, by considering the effect of different social roles. To model the correlation between different networks, we develop a method that aligns these networks through important feature selection. We consider by preserving the network structure for a more better recommendations so that it significantly improves the accuracy for better friend-recommendation.

  13. Genomic analysis suggests higher susceptibility of children to air pollution

    DEFF Research Database (Denmark)

    van Leeuwen, Danitsja M; Pedersen, Marie; Hendriksen, Peter J M

    2008-01-01

    Differences in biological responses to exposure to hazardous airborne substances between children and adults have been reported, suggesting children to be more susceptible. Aim of this study was to improve our understanding of differences in susceptibility in cancer risk associated with air...... pollution by comparing genome-wide gene expression profiles in peripheral blood of children and their parents. Gene expression analysis was performed in blood from children and parents living in two different regions in the Czech Republic with different levels of air pollution. Data were analyzed by two...... in relation to air pollution exposure at the transcriptome level. The findings underline the necessity of implementing environmental health policy measures specifically for protecting children's health....

  14. Crisis Phones - Suicide Prevention Versus Suggestion/Contagion Effects.

    Science.gov (United States)

    Stack, Steven

    2015-01-01

    There has been no systematic work on the short- or long-term impact of the installation of crisis phones on suicides from bridges. The present study addresses this issue. Data refer to 219 suicides from 1954 through 2013 on the Skyway Bridge in St. Petersburg, Florida. Six crisis phones with signs were installed in July 1999. In the first decade after installation, the phones were used by 27 suicidal persons and credited with preventing 26 or 2.6 suicides a year. However, the net suicide count increased from 48 in the 13 years before installation of phones to 106 the following 13 years or by 4.5 additional suicides/year (t =3.512, p < .001). Although the phones prevented some suicides, there was a net increase after installation. The findings are interpreted with reference to suggestion/contagion effects including the emergence of a controversial bridge suicide blog.

  15. MOOCs for Teacher Professional Development: Reflections and Suggested Actions

    Directory of Open Access Journals (Sweden)

    Pradeep Kumar Misra

    2018-02-01

    Full Text Available Teacher Professional Development (TPD has become a major policy priority within education systems worldwide. But keeping teachers professionally up-to-date and providing them professional development opportunities on continuing basis is a big challenge. Massive Open Online Courses (MOOCs can be a cost and resource effective means to complement the traditional methods of professional development of teachers. This optimism is based on the assumption that use of MOOCs will facilitate mass training of teachers as per their convenience and ease. The other assumption is that being MOOCs-based training, it will be easy to adapt it to different cultures and languages. Considering these assumptions, this concept paper which is based on reviews of different reports, documents and research papers - discusses the challenges of TPD, reflects upon promises of using MOOCs for TPD; details initiatives and experiences of using MOOCs for TPD; and suggests actions for promoting the use of MOOCs for TPD.

  16. Sexual health and older adults: suggestions for social science research.

    Science.gov (United States)

    Hinchliff, Sharron

    2016-11-01

    The body of evidence on older adults' sexual health is beginning to grow. However, it remains an under-researched area particularly within the social sciences. This viewpoint outlines four considerations for those who carry out social science research in this area: 1. defining the age category "older adults"; 2. being clear about the types of sex under research; 3. capturing a range of diverse voices; and 4. considering the use of qualitative research methods to explore the topic in depth. These suggestions are aimed at helping researchers to avoid some of the pitfalls of research in this area, as well as improving the evidence base in order to advance recognition of the issues and drive change in service provision. Copyright © 2016 Elsevier Inc. All rights reserved.

  17. Large decadal scale changes of polar ozone suggest solar influence

    Directory of Open Access Journals (Sweden)

    B.-M. Sinnhuber

    2006-01-01

    Full Text Available Long-term measurements of polar ozone show an unexpectedly large decadal scale variability in the mid-stratosphere during winter. Negative ozone anomalies are strongly correlated with the flux of energetic electrons in the radiation belt, which is modulated by the 11-year solar cycle. The magnitude of the observed decadal ozone changes (≈20% is much larger than any previously reported solar cycle effect in the atmosphere up to this altitude. The early-winter ozone anomalies subsequently propagate downward into the lower stratosphere and may even influence total ozone and meteorological conditions during spring. These findings suggest a previously unrecognized mechanism by which solar variability impacts on climate through changes in polar ozone.

  18. A review of cyberbullying and suggestions for online psychological therapy

    Directory of Open Access Journals (Sweden)

    Mairéad Foody

    2015-09-01

    Full Text Available Investigations of cyberbullying are beginning to emerge in the scientific literature because of their implications for child and adolescent development. In particular, cyberbullying victimisation has been associated with similar negative consequences to traditional or face-to-face bullying such as lower academic achievement, anxiety, and sometimes even suicide. Research has also started to emerge investigating the impact of such incidences on the life of adults. The literature in this area has been steadily growing over the last decade and this review highlights the current situation in terms of relevant features and the psychological impact on victims. The selection process consisted of a comprehensive search that was conducted in January 2015 in the following databases: PsychInfo, ERIC, Web of Science and Medline. A total of 19 papers were included. We conclude with suggestions for online psychological treatment for victims and bullies as a means of coping with the distress caused from cyberbullying experiences.

  19. Suggested benchmarks for shape optimization for minimum stress concentration

    DEFF Research Database (Denmark)

    Pedersen, Pauli

    2008-01-01

    Shape optimization for minimum stress concentration is vital, important, and difficult. New formulations and numerical procedures imply the need for good benchmarks. The available analytical shape solutions rely on assumptions that are seldom satisfied, so here, we suggest alternative benchmarks....... The existence of singularities forces us to separate the design modeling (parameterization) from the analysis modeling, which from a practical point of view, is finite element (FE) modeling. Furthermore, the obtained stress concentrations depend highly on the FE modeling and cannot be used as a primary...... procedure is avoided. As examples, we use a sensitive stress concentration problem for fillets or cavities in tension (or compression). These problems are solved as three dimensional (axisymmetric) and as plane stress and plane strain cases. Further cases with design of shapes for a T-head fillet are also...

  20. Persistent Web References – Best Practices and New Suggestions

    DEFF Research Database (Denmark)

    Zierau, Eld; Nyvang, Caroline; Kromann, Thomas Hvid

    In this paper, we suggest adjustments to best practices for persistent web referencing; adjustments that aim at preservation and long time accessibility of web referenced resources in general, but with focus on web references in web archives. Web referencing is highly relevant and crucial...... for various research fields, since an increasing number of references point to resources that only exist on the web. However, present practices using URL and date reference cannot be regarded as persistent due to the volatile nature of the Internet, - and present practices for references to web archives only....... In order to explain needed change of practices based on the wPID, the paper includes a thorough description of the challenges in web references. This description is based on the perspectives from computer science, web collection and Digital Humanities....

  1. Membrane proteomics of phagosomes suggests a connection to autophagy

    Energy Technology Data Exchange (ETDEWEB)

    Shui, Wenqing; Sheu, Leslie; Liu, Jun; Smart, Brian; Petzold, Christopher J.; Hsieh, Tsung-yen; Pitcher, Austin; Keasling*, Jay D.; Bertozzi*, Carolyn R.

    2008-11-25

    Phagocytosis is the central process by which macrophage cellsinternalize and eliminate infectious microbes as well as apoptoticcells. During maturation, phagosomes containing engulfed particlesfuse with various endosomal compartments through theaction of regulatory molecules on the phagosomal membrane. Inthis study, we performed a proteomic analysis of the membranefraction from latex bead-containing (LBC) phagosomes isolatedfrom macrophages. The profile, which comprised 546 proteins,suggests diverse functions of the phagosome and potential connectionsto secretory processes, toll-like receptor signaling, andautophagy. Many identified proteins were not previously knownto reside in the phagosome. We characterized several proteins inLBC phagosomes that change in abundance on induction of autophagy,a process that has been previously implicated in the hostdefense against microbial pathogens. These observations suggestcrosstalk between autophagy and phagocytosis that may be relevantto the innate immune response of macrophages.

  2. Suggestions for teacher education from concept mapping studies

    Directory of Open Access Journals (Sweden)

    Priit Reiska

    2015-03-01

    Full Text Available In order to enhance primary and secondary education, teaching and learning methods need to be continuously developed as well as, of course, promote teaching quality dependent on teacher personality, teacher professional development, teacher self-development, etc. Teacher professional development gives the novice teacher access to a wide set of teaching methods and assessment opportunities, especially geared to flexible learning and assessment methods, which can be considered for adoption. One such flexible method is the use of concept mapping. This article describes the results of several studies, where concept mapping method was used, giving many didactical suggestions for using concept mapping for learning and especially for assessment. Additionally, considerations are introduced on using concept maps as a research instrument.

  3. Seasonal survival probabilities suggest low migration mortality in migrating bats.

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    Simone Giavi

    Full Text Available Migration is adaptive if survival benefits are larger than costs of residency. Many aspects of bat migration ecology such as migratory costs, stopover site use and fidelity are largely unknown. Since many migrating bats are endangered, such information is urgently needed to promote conservation. We selected the migrating Leisler's bat (Nyctalus leisleri as model species and collected capture-recapture data in southern Switzerland year round during 6 years. We estimated seasonal survival and site fidelity with Cormack-Jolly-Seber models that accounted for the presence of transients fitted with Bayesian methods and assessed differences between sexes and seasons. Activity peaked in autumn and spring, whereas very few individuals were caught during summer. We hypothesize that the study site is a migratory stopover site used during fall and spring migration for most individuals, but there is also evidence for wintering. Additionally, we found strong clues for mating during fall. Summer survival that included two major migratory journeys was identical to winter survival in males and slightly higher in females, suggesting that the migratory journeys did not bear significant costs in terms of survival. Transience probability was in both seasons higher in males than in females. Our results suggest that, similarly to birds, Leisler's bat also use stopover sites during migration with high site fidelity. In contrast to most birds, the stopover site was also used for mating and migratory costs in terms of survival seemed to be low. Transients' analyses highlighted strong individual variation in site use which makes particularly challenging the study and modelling of their populations as well as their conservation.

  4. An hypnotic suggestion: review of hypnosis for clinical emergency care.

    Science.gov (United States)

    Iserson, Kenneth V

    2014-04-01

    Hypnosis has been used in medicine for nearly 250 years. Yet, emergency clinicians rarely use it in emergency departments or prehospital settings. This review describes hypnosis, its historical use in medicine, several neurophysiologic studies of the procedure, its uses and potential uses in emergency care, and a simple technique for inducing hypnosis. It also discusses reasons why the technique has not been widely adopted, and suggests methods of increasing its use in emergency care, including some potential research areas. A limited number of clinical studies and case reports suggest that hypnosis may be effective in a wide variety of conditions applicable to emergency medical care. These include providing analgesia for existing pain (e.g., fractures, burns, and lacerations), providing analgesia and sedation for painful procedures (e.g., needle sticks, laceration repair, and fracture and joint reductions), reducing acute anxiety, increasing children's cooperation for procedures, facilitating the diagnosis and treatment of acute psychiatric conditions, and providing analgesia and anxiolysis for obstetric/gynecologic problems. Although it is safe, fast, and cost-effective, emergency clinicians rarely use hypnosis. This is due, in part, to the myths surrounding hypnosis and its association with alternative-complementary medicine. Genuine barriers to its increased clinical use include a lack of assured effectiveness and a lack of training and training requirements. Based on the results of further research, hypnosis could become a powerful and safe nonpharmacologic addition to the emergency clinician's armamentarium, with the potential to enhance patient care in emergency medicine, prehospital care, and remote medical settings. Copyright © 2014 Elsevier Inc. All rights reserved.

  5. Seasonal survival probabilities suggest low migration mortality in migrating bats.

    Science.gov (United States)

    Giavi, Simone; Moretti, Marco; Bontadina, Fabio; Zambelli, Nicola; Schaub, Michael

    2014-01-01

    Migration is adaptive if survival benefits are larger than costs of residency. Many aspects of bat migration ecology such as migratory costs, stopover site use and fidelity are largely unknown. Since many migrating bats are endangered, such information is urgently needed to promote conservation. We selected the migrating Leisler's bat (Nyctalus leisleri) as model species and collected capture-recapture data in southern Switzerland year round during 6 years. We estimated seasonal survival and site fidelity with Cormack-Jolly-Seber models that accounted for the presence of transients fitted with Bayesian methods and assessed differences between sexes and seasons. Activity peaked in autumn and spring, whereas very few individuals were caught during summer. We hypothesize that the study site is a migratory stopover site used during fall and spring migration for most individuals, but there is also evidence for wintering. Additionally, we found strong clues for mating during fall. Summer survival that included two major migratory journeys was identical to winter survival in males and slightly higher in females, suggesting that the migratory journeys did not bear significant costs in terms of survival. Transience probability was in both seasons higher in males than in females. Our results suggest that, similarly to birds, Leisler's bat also use stopover sites during migration with high site fidelity. In contrast to most birds, the stopover site was also used for mating and migratory costs in terms of survival seemed to be low. Transients' analyses highlighted strong individual variation in site use which makes particularly challenging the study and modelling of their populations as well as their conservation.

  6. [Cervical Pott's disease revealed by retropharyngeal abscesses].

    Science.gov (United States)

    Benhammou, A; Bencheikh, R; Benbouzid, M-A; Boulaich, M; Essakali, L; Kzadri, M

    2007-12-01

    Retropharyngeal abscesses are exceptional in adults. The etiologies are numerous, cervical spine tuberculosis is one of them. We report two cases of cervical Pott's disease revealed by a retropharyngeal abscess. The clinical presentation was non-specific, dominated by oropharyngeal obstruction. Radiological findings suggested the diagnosis, showing a retropharyngeal collection with vertebral osteolysis. The bacteriological and histological assessment confirmed the diagnosis. The evolution was favorable after treatment by antituberculosis drugs. Vertebral tuberculosis is rare. Cervical involvement is exceptional, and retropharyngeal abscesses can be the revealing feature of this condition. Symptoms are not specific. The diagnosis is based on radiological and bacteriological assessment. Treatment with antituberculosis drugs leads to a good outcome.

  7. Association Mapping Reveals Genetic Loci Associated with Important Agronomic Traits in Lentinula edodes, Shiitake Mushroom.

    Science.gov (United States)

    Li, Chuang; Gong, Wenbing; Zhang, Lin; Yang, Zhiquan; Nong, Wenyan; Bian, Yinbing; Kwan, Hoi-Shan; Cheung, Man-Kit; Xiao, Yang

    2017-01-01

    Association mapping is a robust approach for the detection of quantitative trait loci (QTLs). Here, by genotyping 297 genome-wide molecular markers of 89 Lentinula edodes cultivars in China, the genetic diversity, population structure and genetic loci associated with 11 agronomic traits were examined. A total of 873 alleles were detected in the tested strains with a mean of 2.939 alleles per locus, and the Shannon's information index was 0.734. Population structure analysis revealed two robustly differentiated groups among the Chinese L. edodes cultivars (FST = 0.247). Using the mixed linear model, a total of 43 markers were detected to be significantly associated with four traits. The number of markers associated with traits ranged from 9 to 26, and the phenotypic variations explained by each marker varied from 12.07% to 31.32%. Apart from five previously reported markers, the remaining 38 markers were newly reported here. Twenty-one markers were identified as simultaneously linked to two to four traits, and five markers were associated with the same traits in cultivation tests performed in two consecutive years. The 43 traits-associated markers were related to 97 genes, and 24 of them were related to 10 traits-associated markers detected in both years or identified previously, 13 of which had a >2-fold expression change between the mycelium and primordium stages. Our study has provided candidate markers for marker-assisted selection (MAS) and useful clues for understanding the genetic architecture of agronomic traits in the shiitake mushroom.

  8. Cytological Findings Suggesting Sexuality in Phytomonas davidi (Protozoa: Kinetoplastida

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    Maria Auxiliadora de Sousa

    1997-03-01

    Full Text Available On few occasions, Phytomonas davidi (McGhee & Postell isolate cultures in LIT (liver infusion-tryptose medium around 27oC presented, as seen in Giemsa-stained smears, a set of peculiar morphological features, among them being noticeable the pairs of apposed cells attached by their posterior ends, where occurred a stained line and/or a dilatation, usually bulb-like in shape; sometimes this dilatation could occupy one of the cells or hold both together. In some pairs, the nucleus of each parasite seemed migrating towards the other, entering into such dilatation; in others, both nuclei were inside it, sometimes in close proximity or seeming fused; peculiar chromatin arrangements involving both nuclei were occasionally observed. Several mono or binucleate round forms bearing one or two flagella, as well as flagellate slender cells without nucleus were concomitantly seen there. In some instances, an intriguing small stained body occurred beside a single large nucleus, either in pairs presenting the bulb-like structure or in round cells. These cytological findings seemed steps of a dynamic process suggesting sexuality, since in several of them nuclear interactions following fusion of two parasites appeared to occur

  9. Molecular spectroscopic study for suggested mechanism of chrome tanned leather.

    Science.gov (United States)

    Nashy, Elshahat H A; Osman, Osama; Mahmoud, Abdel Aziz; Ibrahim, Medhat

    2012-03-01

    Collagen represents the structural protein of the extracellular matrix, which gives strength of hides and/or skin under tanning process. Chrome tan is the most important tanning agent all over the world. The methods for production of leather evolved over several centuries as art and engineering with little understanding of the underlying science. The present work is devoted to suggest the most probable mechanistic action of chrome tan on hide proteins. First the affect of Cr upon hide protein is indicated by the studied mechanical properties. Then the spectroscopic characterization of the hide protein as well as chrome tanned leather was carried out with Horizontal Attenuated Total Reflection (HATR) FT-IR. The obtained results indicate how the chromium can attached with the active sites of collagen. Molecular modeling confirms that chromium can react with amino as well as carboxylate groups. Four schemes were obtained to describe the possible interactions of chrome tan with hide proteins. Copyright © 2011 Elsevier B.V. All rights reserved.

  10. Improving therapeutic use of homework: suggestions from mental health clinicians.

    Science.gov (United States)

    Kelly, Peter J; Deane, Frank P

    2011-10-01

    The majority of mental health clinicians report the use of homework to support their case management, but practitioner surveys indicate that homework is not routinely used. To examine barriers that mental health case managers experience in implementing homework and to identify strategies to promote successful homework administration. One hundred thirty-four surveys were completed by mental health case managers. The survey examined their use of homework for individuals diagnosed with a severe mental health problem. It also asked them to identify barriers to regularly implement homework and describe strategies to promote more regular use of homework. On average, homework was used at 50% of clinical contacts. The primary reasons for not using homework included allocating insufficient time at appointments, perceived client resistance for using homework and concerns that the client was too unwell. Strategies used to overcome these difficulties included prioritising the use of homework and ensuring that homework assignments were achievable. Clinicians are able to identify a range of practical strategies to promote the use of homework. Discussion focuses on the application of the suggested strategies to promote regular use of homework. This includes discussion of possible training approaches to enhance systematic homework administration.

  11. Reaction mechanism of azoreductases suggests convergent evolution with quinone oxidoreductases.

    Science.gov (United States)

    Ryan, Ali; Wang, Chan-Ju; Laurieri, Nicola; Westwood, Isaac; Sim, Edith

    2010-08-01

    Azoreductases are involved in the bioremediation by bacteria of azo dyes found in waste water. In the gut flora, they activate azo pro-drugs, which are used for treatment of inflammatory bowel disease, releasing the active component 5-aminosalycilic acid. The bacterium P. aeruginosa has three azoreductase genes, paAzoR1, paAzoR2 and paAzoR3, which as recombinant enzymes have been shown to have different substrate specificities. The mechanism of azoreduction relies upon tautomerisation of the substrate to the hydrazone form. We report here the characterization of the P. aeruginosa azoreductase enzymes, including determining their thermostability, cofactor preference and kinetic constants against a range of their favoured substrates. The expression levels of these enzymes during growth of P. aeruginosa are altered by the presence of azo substrates. It is shown that enzymes that were originally described as azoreductases, are likely to act as NADH quinone oxidoreductases. The low sequence identities observed among NAD(P)H quinone oxidoreductase and azoreductase enzymes suggests convergent evolution.

  12. Modelling of Arabidopsis LAX3 expression suggests auxin homeostasis.

    Science.gov (United States)

    Mellor, Nathan; Péret, Benjamin; Porco, Silvana; Sairanen, Ilkka; Ljung, Karin; Bennett, Malcolm; King, John

    2015-02-07

    Emergence of new lateral roots from within the primary root in Arabidopsis has been shown to be regulated by the phytohormone auxin, via the expression of the auxin influx carrier LAX3, mediated by the ARF7/19 IAA14 signalling module (Swarup et al., 2008). A single cell model of the LAX3 and IAA14 auxin response was formulated and used to demonstrate that hysteresis and bistability may explain the experimentally observed 'all-or-nothing' LAX3 spatial expression pattern in cortical cells containing a gradient of auxin concentrations. The model was tested further by using a parameter fitting algorithm to match model output with qRT-PCR mRNA expression data following exogenous auxin treatment. It was found that the model is able to show good agreement with the data, but only when the exogenous auxin signal is degraded over time, at a rate higher than that measured in the experimental medium, suggesting the triggering of an endogenous auxin homeostasis mechanism. Testing the model over a more physiologically relevant range of extracellular auxin shows bistability and hysteresis still occur when using the optimised parameters, providing the rate of LAX3 active auxin transport is sufficiently high relative to passive diffusion. Copyright © 2014 Elsevier Ltd. All rights reserved.

  13. In vitro model suggests oxidative stress involved in keratoconus disease

    Science.gov (United States)

    Karamichos, D.; Hutcheon, A. E. K.; Rich, C. B.; Trinkaus-Randall, V.; Asara, J. M.; Zieske, J. D.

    2014-04-01

    Keratoconus (KC) affects 1:2000 people and is a disorder where cornea thins and assumes a conical shape. Advanced KC requires surgery to maintain vision. The role of oxidative stress in KC remains unclear. We aimed to identify oxidative stress levels between human corneal keratocytes (HCKs), fibroblasts (HCFs) and keratoconus cells (HKCs). Cells were cultured in 2D and 3D systems. Vitamin C (VitC) and TGF-β3 (T3) were used for 4 weeks to stimulate self-assembled extracellular matrix (ECM). No T3 used as controls. Samples were analyzed using qRT-PCR and metabolomics. qRT-PCR data showed low levels of collagen I and V, as well as keratocan for HKCs, indicating differentiation to a myofibroblast phenotype. Collagen type III, a marker for fibrosis, was up regulated in HKCs. We robustly detected more than 150 metabolites of the targeted 250 by LC-MS/MS per condition and among those metabolites several were related to oxidative stress. Lactate levels, lactate/malate and lactate/pyruvate ratios were elevated in HKCs, while arginine and glutathione/oxidized glutathione ratio were reduced. Similar patterns found in both 2D and 3D. Our data shows that fibroblasts exhibit enhanced oxidative stress compared to keratocytes. Furthermore the HKC cells exhibit the greatest level suggesting they may have a myofibroblast phenotype.

  14. Dehumanizing Communication Reified among Undergraduates and Lecturers: Issues and Suggestions

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    Duvie Adanma Nnekwu

    2014-10-01

    Full Text Available This paper discusses dehumanizing communication reified among undergraduates and t lecturers. Dehumanization is the act of degrading people with respect to their best qualities and denial of humanness to others. On the other hand, communication is human interaction and learning. Communication becomes rude when it is deliberately directed resulting in dehumanizing communication. The paper, therefore, examines dehumanizing communication in terms of its being intentional and unintentional and dehumanizing communication between lecturers and students and among students. It also took a swipe on the effects of dehumanizing communication on students and lecturers as well as proffer solutions to mitigating effect of dehumanizing communication between lecturer and students and among students. The suggested solutions among others include inter-group dialogue programme among contending groups in the student community, establishment of multicultural centers on campus in order to bring contending groups together (i.e. lecturers and students of all races and ethnicity. A compulsory course on “pedagogy of positiveness” is also recommended in the university curriculum to instill in the students the value of respecting people who may be different. Keywords: Dehumanization, Intentional and Unintentional Communication, Reified, Lecturers, Undergraduates, Teaching and Learning, Classroom

  15. Demystifying Survey Research: Practical Suggestions for Effective Question Design

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    Deborah H. Charbonneau

    2007-12-01

    Full Text Available Objective ‐ Recent research has yielded several studies helpful for understanding the use of the survey technique in various library environments. Despite this, there has been limited discussion to guide library practitioners preparing survey questions. The aim of this article is to provide practical suggestions for effective questions when designing written surveys.Methods ‐ Advice and important considerations to help guide the process of developing survey questions are drawn from a review of the literature and personal experience.Results ‐ Basic techniques can be incorporated to improve survey questions, such as choosing appropriate question forms and incorporating the use of scales. Attention should be paid to the flow and ordering of the survey questions. Careful wording choices can also help construct clear, simple questions. Conclusion ‐ A well‐designed survey questionnaire can be a valuable source of data. By following some basic guidelines when constructing written survey questions, library and information professionals can have useful data collection instruments at their disposal.

  16. Current Situation in Vocational Schools: Issues and Some Suggested Solutions

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    Reha Metin ALKAN

    2014-12-01

    Full Text Available Vocational Schools which have undertaken various missions throughout history were established in order to train intermediate staff s with suff icient knowledge and skills in their fields, in accordance with the requirements of trade, industry and services sectors and they are the most important components of ‘vocational and technical education system' today. Analyzing the education given in the vocational schools in accordance with the national and international requirements, developing technologies and the needs of business world and making the necessary arrangements in line with these will contribute to the employability and preferability of graduates of these schools in an eff icient way. Many industrialists/businessmen in our country stated that they experienced serious problems in the supply of qualified staff with suff icient knowledge and skills needed in sectors. Although much progress has been achieved in this subject, it is a fact that there are still a lot of work to be done. In this study, current situation and main troubles in vocational schools are discussed in the light of the experiences gained at Hitit University Vocational School which was established about 40 years ago in Çorum and which is one of the first high schools in Turkey and some solutions are suggested in accordance with the problems mentioned.

  17. Foreign accents: suggested competencies for improving communicative pronunciation.

    Science.gov (United States)

    Sikorski, Lorna D

    2005-05-01

    In the past 20 years, many speech-language pathologists (SLPs) have joined their English as a Second Language (ESL) colleagues to address the pronunciation skills of second language speakers of English. This paper introduces SLPs to the ESL term "communicative pronunciation" as the underpinning for the commonly accepted terms "accent modification" or "accent reduction." Initially, professionals in both speech pathology and ESL felt that accent intervention was outside the scope of speech pathology practice, though that stance is softening. If an essential part of our mission as speech pathologists is to improve communicative competence for all persons, then making pronunciation more intelligible falls under that heading. This article on foreign accents limits discussion to: (1) the rationale for intervening with foreign accented adults; (2) an outline of a broader scope and definition of effective instruction for this population; (3) suggestions for trainer preparation; (4) recommendations for productive literature searches; and (5) a brief discussion of principles guiding assessment and instruction planning. The article includes relevant research and references outside the field of speech pathology that should stimulate future productive research efforts as well as more in-depth papers on specific instruction and assessment issues. While this article is intended to stand alone, readers may benefit from the content and references in another article in this issue by the same author.

  18. Clinical and biomarker assessment of demyelinating events suggesting multiple sclerosis.

    Science.gov (United States)

    Gajofatto, A; Bongianni, M; Zanusso, G; Bianchi, M R; Turatti, M; Benedetti, M D; Monaco, S

    2013-11-01

    Initial demyelinating event (IDE) diagnosis and prognosis are not straightforward. To identify potential diagnostic markers and outcome predictors of IDEs suggestive of multiple sclerosis (MS), that is, clinically isolated syndromes (CISs). Clinically isolated syndrome cases (i.e., subjects with an IDE compatible with MS onset and no alternative explanation) with at least 1.5 years' follow-up were retrospectively identified. All cases underwent clinical, neurophysiological, MRI, and cerebrospinal fluid (CSF) assessment, including exploratory tau, 14-3-3, and cystatin C testing. CIS recovery, conversion to MS, and long-term neurological disability were used as outcome measures. Patients with neuromyelitis optica spectrum disorders, idiopathic acute transverse myelitis (IATM), Creutzfeldt-Jacob disease, and non-inflammatory/non-neurodegenerative disorders served as controls for CSF analysis. Forty-six CIS cases were included. Severe presentation was associated with incomplete recovery, while presence of at least 3 periventricular lesions on baseline MRI correlated with MS conversion. Initial pyramidal tract involvement, incomplete CIS recovery, and number of relapses predicted neurological disability. CSF tau, 14-3-3, and cystatin C did not correlate with any outcome measure. CIS cases had significantly lower tau and cystatin C levels compared to IATM. An extensive diagnostic evaluation of patients with an IDE is worthwhile to make prognostic predictions. More robust molecular biomarkers are needed. © 2013 John Wiley & Sons A/S.

  19. Partners in Science: A Suggested Framework for Inclusive Research

    Science.gov (United States)

    Pandya, R. E.

    2012-12-01

    Public participation in scientific research, also known as citizen science, is effective on many levels: it produces sound, publishable science and data, helps participants gain scientific knowledge and learn about the methods and practices of modern science, and can help communities advance their own priorities. Unfortunately, the demographics of citizen science programs do not reflect the demographics of the US; in general people of color and less affluent members of society are under-represented. To understand the reasons for this disparity, it is useful to look to the broader research about participation in science in a variety of informal and formal settings. From this research, the causes for unequal participation in science can be grouped into three broad categories: accessibility challenges, cultural differences, and a gap between scientific goals and community priorities. Many of these challenges are addressed in working with communities to develop an integrated program of scientific research, education, and community action that addresses community priorities and invites community participation at every stage of the process from defining the question to applying the results. In the spectrum of ways to engage the public in scientific research, this approach of "co-creation" is the most intensive. This talk will explore several examples of co-creation of science, including collaborations with tribal communities around climate change adaptation, work in the Louisiana Delta concerning land loss, and the link between weather and disease in Africa. We will articulate some of the challenges of working this intensively with communities, and suggest a general framework for guiding this kind of work with communities. This model of intensive collaboration at every stage is a promising one for adding to the diversity of citizen science efforts. It also provides a powerful strategy for science more generally, and may help us diversify our field, ensure the use and

  20. Opsin clines in butterflies suggest novel roles for insect photopigments.

    Science.gov (United States)

    Frentiu, Francesca D; Yuan, Furong; Savage, Wesley K; Bernard, Gary D; Mullen, Sean P; Briscoe, Adriana D

    2015-02-01

    Opsins are ancient molecules that enable animal vision by coupling to a vitamin-derived chromophore to form light-sensitive photopigments. The primary drivers of evolutionary diversification in opsins are thought to be visual tasks related to spectral sensitivity and color vision. Typically, only a few opsin amino acid sites affect photopigment spectral sensitivity. We show that opsin genes of the North American butterfly Limenitis arthemis have diversified along a latitudinal cline, consistent with natural selection due to environmental factors. We sequenced single nucleotide (SNP) polymorphisms in the coding regions of the ultraviolet (UVRh), blue (BRh), and long-wavelength (LWRh) opsin genes from ten butterfly populations along the eastern United States and found that a majority of opsin SNPs showed significant clinal variation. Outlier detection and analysis of molecular variance indicated that many SNPs are under balancing selection and show significant population structure. This contrasts with what we found by analysing SNPs in the wingless and EF-1 alpha loci, and from neutral amplified fragment length polymorphisms, which show no evidence of significant locus-specific or genome-wide structure among populations. Using a combination of functional genetic and physiological approaches, including expression in cell culture, transgenic Drosophila, UV-visible spectroscopy, and optophysiology, we show that key BRh opsin SNPs that vary clinally have almost no effect on spectral sensitivity. Our results suggest that opsin diversification in this butterfly is more consistent with natural selection unrelated to spectral tuning. Some of the clinally varying SNPs may instead play a role in regulating opsin gene expression levels or the thermostability of the opsin protein. Lastly, we discuss the possibility that insect opsins might have important, yet-to-be elucidated, adaptive functions in mediating animal responses to abiotic factors, such as temperature or photoperiod

  1. Niche convergence suggests functionality of the nocturnal fovea

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    Gillian L. Moritz

    2014-07-01

    Full Text Available The fovea is a declivity of the retinal surface associated with maximum visual acuity. Foveae are widespread across vertebrates, but among mammals they are restricted to haplorhine primates (tarsiers, monkeys, apes, and humans, which are primarily diurnal. Thus primates have long contributed to the prevailing view that the fovea is a functional adaptation to diurnal color vision. The foveae of nocturnal taxa, such as tarsiers, are widely interpreted as vestigial traits and therefore evidence of a diurnal ancestry. This enduring premise has been central to adaptive hypotheses on the origins of anthropoid primates; however, the question of whether the fovea of tarsiers is a functionless anachronism or a nocturnal adaptation remains open. To address this question, we focused on the diets of tarsiers (Tarsius and scops owls (Otus, two taxa united by numerous anatomical homoplasies, including foveate vision. A functional interpretation of these homoplasies predicts dietary convergence and competition. This prediction can be tested with an analysis of carbon and nitrogen stable isotopes in tissues, which integrate dietary information. As predicted, the isotopic niches of Tarsius and Otus overlapped. In both Borneo and the Philippines, the δ13C values were indistinguishable, whereas the δ15N values of Otus were marginally higher than those of Tarsius. Our results indicate that both diets consisted mainly of ground-dwelling prey and raise the possibility of some resource partitioning. Taken together, our isotopic analysis supports a functional interpretation of the many homoplasies shared by tarsiers and scops owls, including a retinal fovea. We suggest that the fovea might function similarly in tarsiers and scops owls by calibrating the auditory localization pathway. The integration of auditory localization and visual fixation during prey detection and acquisition might be critical at low light levels.

  2. Rising maternal circulating GH during murine pregnancy suggests placental regulation

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    Kathryn L Gatford

    2017-06-01

    Full Text Available Placenta-derived hormones including growth hormone (GH in humans contribute to maternal adaptation to pregnancy, and intermittent maternal GH administration increases foetal growth in several species. Both patterns and abundance of circulating GH are important for its activity, but their changes during pregnancy have only been reported in humans and rats. The aim of the present study was to characterise circulating profiles and secretory characteristics of GH in non-pregnant female mice and throughout murine pregnancy. Circulating GH concentrations were measured in whole blood (2 μL collected every 10 min for 6 h in non-pregnant diestrus female C57Bl/6J mice (n = 9, and pregnant females at day 8.5–9.5 (early pregnancy, n = 8, day 12.5–13.5 (mid-pregnancy, n = 7 and day 17.5 after mating (late pregnancy, n = 7. Kinetics and secretory patterns of GH secretion were determined by deconvolution analysis, while orderliness and regularity of serial GH concentrations were calculated by approximate entropy analysis. Circulating GH was pulsatile in all groups. Mean circulating GH and total and basal GH secretion rates increased markedly from early to mid-pregnancy, and then remained elevated. Pulse frequency and pulsatile GH secretion rate were similar between groups. The irregularity of GH pulses was higher in all pregnant groups than that in non-pregnant mice. Increased circulating GH in murine pregnancy is consistent with an important role for this hormone in maternal adaptation to pregnancy and placental development. The timing of increased basal secretion from mid-pregnancy, concurrent with the formation of the chorioallantoic placenta and initiation of maternal blood flow through it, suggests regulation of pituitary secretion by placenta-derived factors.

  3. Pre-hospital Obstacles in Thrombolytic Therapy and Suggested Solutions

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    Betül Tekin Güveli

    2015-12-01

    Full Text Available INTRODUCTION: Acute ischemic stroke is frequently encountered in emergency neurology clinics. Especially when administered within 3 hours of symptom onset, thrombolytic therapy is important in reducing ischemic injury and neurological disability. In this study, we aimed to investigate the demographic and clinical characteristics according to application time, to identify situations which pose an obstacle to thrombolytic therapy and to review the thrombolytic therapy results in patients diagnosed with acute ischemic stroke. METHODS: The patients diagnosed with acute ischemic stroke were evaluated and their age, gender, complaints, risk factors, previous history of stroke, with whom they live, how they arrived at the hospital and their application time information were recorded. Those who were admitted within 3 hours of symptom onset were assessed as early, those admitted after 3 hours were assessed as late admission. Then the rate of thrombolytic therapy, final results and the clinical status in early admission patients and the reasons for delay in late admission patients were discussed. RESULTS: Among 361 acute ischemic stroke patients, the mean age was 66±14,1. 111 patients were admitted within 3 hours of symptom onset, 246 patients were admitted after three hours. Patients arriving to emergency room with 112 Ambulance Service were admitted earlier than those brought in by family, and this difference was statistically significant. The most common causes of time loss in late admissions were the patients being referred from other centers and the unawareness of family about the importance of the disease. There were 13 patients treated with thrombolytic therapy, and complications occurred in one patient. DISCUSSION AND CONCLUSION: Thrombolytic therapy is important in acute ischemic stroke for suitable patients.Our study suggested that the most important factors in spreading of performing the thrombolytic therapy are informing the public about

  4. Precise synaptic efficacy alignment suggests potentiation dominated learning

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    Christoph eHartmann

    2016-01-01

    Full Text Available Recent evidence suggests that parallel synapses from the same axonal branch onto the same dendritic branch have almost identical strength. It has been proposed that this alignment is only possible through learning rules that integrate activity over long time spans. However, learning mechanisms such as spike-timing-dependent plasticity (STDP are commonly assumed to be temporally local. Here, we propose that the combination of temporally local STDP and a multiplicative synaptic normalization mechanism is sufficient to explain the alignment of parallel synapses.To address this issue, we introduce three increasingly complex models: First, we model the idealized interaction of STDP and synaptic normalization in a single neuron as a simple stochastic process and derive analytically that the alignment effect can be described by a so-called Kesten process. From this we can derive that synaptic efficacy alignment requires potentiation-dominated learning regimes. We verify these conditions in a single-neuron model with independent spiking activities but more realistic synapses. As expected, we only observe synaptic efficacy alignment for long-term potentiation-biased STDP. Finally, we explore how well the findings transfer to recurrent neural networks where the learning mechanisms interact with the correlated activity of the network. We find that due to the self-reinforcing correlations in recurrent circuits under STDP, alignment occurs for both long-term potentiation- and depression-biased STDP, because the learning will be potentiation dominated in both cases due to the potentiating events induced by correlated activity. This is in line with recent results demonstrating a dominance of potentiation over depression during waking and normalization during sleep. This leads us to predict that individual spine pairs will be more similar in the morning than they are after sleep depriviation.In conclusion, we show that synaptic normalization in conjunction with

  5. Genomic and archaeological evidence suggest a dual origin of domestic dogs.

    Science.gov (United States)

    Frantz, Laurent A F; Mullin, Victoria E; Pionnier-Capitan, Maud; Lebrasseur, Ophélie; Ollivier, Morgane; Perri, Angela; Linderholm, Anna; Mattiangeli, Valeria; Teasdale, Matthew D; Dimopoulos, Evangelos A; Tresset, Anne; Duffraisse, Marilyne; McCormick, Finbar; Bartosiewicz, László; Gál, Erika; Nyerges, Éva A; Sablin, Mikhail V; Bréhard, Stéphanie; Mashkour, Marjan; Bălăşescu, Adrian; Gillet, Benjamin; Hughes, Sandrine; Chassaing, Olivier; Hitte, Christophe; Vigne, Jean-Denis; Dobney, Keith; Hänni, Catherine; Bradley, Daniel G; Larson, Greger

    2016-06-03

    The geographic and temporal origins of dogs remain controversial. We generated genetic sequences from 59 ancient dogs and a complete (28x) genome of a late Neolithic dog (dated to ~4800 calendar years before the present) from Ireland. Our analyses revealed a deep split separating modern East Asian and Western Eurasian dogs. Surprisingly, the date of this divergence (~14,000 to 6400 years ago) occurs commensurate with, or several millennia after, the first appearance of dogs in Europe and East Asia. Additional analyses of ancient and modern mitochondrial DNA revealed a sharp discontinuity in haplotype frequencies in Europe. Combined, these results suggest that dogs may have been domesticated independently in Eastern and Western Eurasia from distinct wolf populations. East Eurasian dogs were then possibly transported to Europe with people, where they partially replaced European Paleolithic dogs. Copyright © 2016, American Association for the Advancement of Science.

  6. Suggestions on the development strategy of shale gas in China

    Directory of Open Access Journals (Sweden)

    Dazhong Dong

    2016-12-01

    Full Text Available From the aspects of shale gas resource condition, main exploration and development progress, important breakthrough in key technologies and equipment, this paper systematically summarized and analyzed current situation of shale gas development in China and pointed out five big challenges such as misunderstandings, lower implementation degree and higher economic uncertainty of shale gas resource, and still no breakthrough in exploration and development core technologies and equipment for shale gas buried depth more than 3500 m, higher cost and other non-technical factors that restrict the development pace. Aiming at the above challenges, we put forward five suggestions to promote the shale gas development in China: (1 Make strategies and set goals according to our national conditions and exploration and development stages. That is, make sure to realize shale gas annual production of 20 × 109 m3, and strives to reach 30 × 109 m3. (2 Attach importance to the research of accumulation and enrichment geological theory and exploration & development key engineering technologies for lower production and lower pressure marine shale gas reservoir, and at the same time orderly promote the construction of non-marine shale gas exploration & development demonstration areas. (3 The government should introduce further policies and set special innovation funds to support the companies to carry out research and development of related technologies and equipment, especially to strengthen the research and development of technology, equipment and process for shale gas bellow 3500 m in order to achieve breakthrough in deep shale gas. (4 Continue to promote the geological theory, innovation in technology and management, and strengthen cost control on drilling, fracturing and the whole process in order to realize efficient, economic and scale development of China's shale gas. (5 Reform the mining rights management system, establish information platform of shale

  7. Behavioral connectivity among bighorn sheep suggests potential for disease spread

    Science.gov (United States)

    Borg, Nathan J.; Mitchell, Michael S.; Lukacs, Paul M.; Mack, Curt M.; Waits, Lisette P.; Krausman, Paul R.

    2017-01-01

    Connectivity is important for population persistence and can reduce the potential for inbreeding depression. Connectivity between populations can also facilitate disease transmission; respiratory diseases are one of the most important factors affecting populations of bighorn sheep (Ovis canadensis). The mechanisms of connectivity in populations of bighorn sheep likely have implications for spread of disease, but the behaviors leading to connectivity between bighorn sheep groups are not well understood. From 2007–2012, we radio-collared and monitored 56 bighorn sheep in the Salmon River canyon in central Idaho. We used cluster analysis to define social groups of bighorn sheep and then estimated connectivity between these groups using a multi-state mark-recapture model. Social groups of bighorn sheep were spatially segregated and linearly distributed along the Salmon River canyon. Monthly probabilities of movement between adjacent male and female groups ranged from 0.08 (±0.004 SE) to 0.76 (±0.068) for males and 0.05 (±0.132) to 0.24 (±0.034) for females. Movements of males were extensive and probabilities of movement were considerably higher during the rut. Probabilities of movement for females were typically smaller than those of males and did not change seasonally. Whereas adjacent groups of bighorn sheep along the Salmon River canyon were well connected, connectivity between groups north and south of the Salmon River was limited. The novel application of a multi-state model to a population of bighorn sheep allowed us to estimate the probability of movement between adjacent social groups and approximate the level of connectivity across the population. Our results suggest high movement rates of males during the rut are the most likely to result in transmission of pathogens among both male and female groups. Potential for disease spread among female groups was smaller but non-trivial. Land managers can plan grazing of domestic sheep for spring and summer

  8. Literature Suggests Information Professionals Have Adopted New Roles

    Directory of Open Access Journals (Sweden)

    Robin E. Miller

    2017-03-01

    note, the majority of articles included in the review were about academic libraries. The authors searched a wide range of databases, following the guidance of Hemingway and Brereton (2009. The focus on peer-reviewed literature discovered through database searches may be the reason that the majority of included articles address academic libraries. This limitation was acknowledged by the authors. While trade and grey literature published by professional associations and consortia may be more difficult to locate in databases, such literature might expand the subject matter to information professionals working outside of higher education. The inclusion and exclusion criteria employed by the authors reveal ambiguities in LIS professional rhetoric that this research may be unable to overcome. The search terms “librarian/s roles” and “information professional/s roles” were employed to search several databases. However, the authors do not define “role,” nor do they identify other terms they considered and discarded. Research about the “skills” of librarians was also excluded, though the 114 articles ultimately included do discuss librarian “competencies,” “expertise,” “knowledge,” and “training.” “Papers referring to specific positions or specific occupational groups” (p. 39 were excluded, though the article does not explain the distinction between a librarian’s “role” and “professional responsibilities.” For example, the authors indicate that the role of “embedded librarian” dominated the scholarly conversation in the included literature, but the exclusion criteria indicate that “embedded librarianship” is a “type” of librarianship that was excluded from systematic review (2015. New positions and titles in information organizations may well represent emerging roles in areas like scholarly communication, assessment, outreach, emerging technology, and instructional design. Are these roles, professional responsibilities

  9. Genetic architecture of growth traits in Populus revealed by integrated quantitative trait locus (QTL) analysis and association studies.

    Science.gov (United States)

    Du, Qingzhang; Gong, Chenrui; Wang, Qingshi; Zhou, Daling; Yang, Haijiao; Pan, Wei; Li, Bailian; Zhang, Deqiang

    2016-02-01

    Deciphering the genetic architecture underlying polygenic traits in perennial species can inform molecular marker-assisted breeding. Recent advances in high-throughput sequencing have enabled strategies that integrate linkage-linkage disequilibrium (LD) mapping in Populus. We used an integrated method of quantitative trait locus (QTL) dissection with a high-resolution linkage map and multi-gene association mapping to decipher the nature of genetic architecture (additive, dominant, and epistatic effects) of potential QTLs for growth traits in a Populus linkage population (1200 progeny) and a natural population (435 individuals). Seventeen QTLs for tree height, diameter at breast height, and stem volume mapped to 11 linkage groups (logarithm of odds (LOD) ≥ 2.5), and explained 2.7-18.5% of the phenotypic variance. After comparative mapping and transcriptome analysis, 187 expressed genes (10 046 common single nucleotide polymorphisms (SNPs)) were selected from the segmental homology regions (SHRs) of 13 QTLs. Using multi-gene association models, we observed 202 significant SNPs in 63 promising genes from 10 QTLs (P ≤ 0.0001; FDR ≤ 0.10) that exhibited reproducible associations with additive/dominant effects, and further determined 11 top-ranked genes tightly linked to the QTLs. Epistasis analysis uncovered a uniquely interconnected gene-gene network for each trait. This study opens up opportunities to uncover the causal networks of interacting genes in plants using an integrated linkage-LD mapping approach. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

  10. Compensation in Swedish infrastructure projects and suggestions on policy improvements

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    Jesper Persson

    2015-07-01

    were never explicitly mentioned in permits, but in practice a ratio of 1:1 (often measured as area or length was usually applied. The compensation measures typically consisted in recreating the same kind of natural asset that was affected, in a location close to the damaged area. In the two cases specially studied, the road and railway planning processes were not properly adjusted to integrate compensation issues, resulting in unnecessary bureaucracy and insufficient co-ordination between different projects, such as between the environmental-impact assessment process and the compensation process or between closely related sub-projects in the same region. To meet the EU’s goal of no net loss of biodiversity, we suggest that policy requirements should be made stricter and that incentives for voluntary compensation should be created. In line with the goals of Swedish national transport policy and the European Landscape Convention, account should be taken of social and cultural aspects, and there should be a shift from a narrow focus on individual projects to a broader planning approach, since this would allow compensation measures to be taken where they can deliver the greatest environmental benefits.

  11. Tadpole begging reveals high quality.

    Science.gov (United States)

    Dugas, M B; Strickler, S A; Stynoski, J L

    2017-05-01

    Parents can benefit from allocating limited resources nonrandomly among offspring, and offspring solicitation (i.e. begging) is often hypothesized to evolve because it contains information valuable to choosy parents. We tested the predictions of three 'honest begging' hypotheses - Signal of Need, Signal of Quality and Signal of Hunger - in the tadpoles of a terrestrial frog (Oophaga pumilio). In this frog, mothers provision tadpoles with trophic eggs, and when mothers visit, tadpoles perform a putative begging signal by stiffening their bodies and vibrating rapidly. We assessed the information content of intense tadpole begging with an experimental manipulation of tadpole condition (need/quality) and food deprivation (hunger). This experiment revealed patterns consistent with the Signal of Quality hypothesis and directly counter to predictions of Signal of Need and Signal of Hunger. Begging effort and performance were higher in more developed and higher condition tadpoles and declined with food deprivation. Free-living mothers were unlikely to feed tadpoles of a nonbegging species experimentally cross-fostered with their own, and allocated larger meals to more developed tadpoles and those that vibrated at higher speed. Mother O. pumilio favour their high-quality young, and because their concurrent offspring are reared in separate nurseries, must do so by making active allocation decisions. Our results suggest that these maternal choices are based at least in part on offspring signals, indicating that offspring solicitation can evolve to signal high quality. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

  12. Is working memory working against suggestion susceptibility? Results from extended version of DRM paradigm

    Directory of Open Access Journals (Sweden)

    Maciaszek Patrycja

    2016-04-01

    Full Text Available The paper investigates relationship between working memory efficiency, defined as the result of its’ processing & storage capacity (Oberauer et al., 2003 and the tendency to (1 create assosiative memory distortions (false memories, FM; (2 yield under the influence of external, suggesting factors. Both issues were examined using extended version of Deese-Roediger-McDermott procedure (1959, 1995, modified in order to meet the study demands. Suggestion was contained in an ostentatious feedback information the participants (N=88 received during the DRM procedure. Working memory (WM was measured by standardized tasks (n-back, Jaeggi et al., 2010; automatic-ospan, Unsworth et al., 2005. Study included 3 conditions, differing in the quality of suggestion (positive, negative or neutral. Participants were assigned into 3 groups, depending on results they achieved completing the WM tasks. Obtained results alongside the previously set hypothesis, revealed that (1 WM impacts individuals’ tendency to create false memories in DRM and (2 that the individuals showing higher rates in WM tasks are less willing to yield to suggestion compared to those with lesser ones. It also showed that the greater amount to shift (Gudjonsson, 2003, emerges under the negative suggestion condition (collating positive. Notwithstanding that the interaction effect did not achieve saliency, both analyzed factors (WM and suggesting content are considered as meaningful to explain memory suggestion susceptibility in presented study. Although, obtained results emphasize the crucial role of WM efficiency, that is believed to decide the magnitude of feedback that is influential in every subject. Therefore, issue demands further exploration.

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

    Directory of Open Access Journals (Sweden)

    Claudia Gonzaga-Jauregui

    2015-08-01

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

  14. Quantitative trait loci for plant height in Maresi × CamB barley population and their associations with yield-related traits under different water regimes.

    Science.gov (United States)

    Mikołajczak, Krzysztof; Kuczyńska, Anetta; Krajewski, Paweł; Sawikowska, Aneta; Surma, Maria; Ogrodowicz, Piotr; Adamski, Tadeusz; Krystkowiak, Karolina; Górny, Andrzej G; Kempa, Michał; Szarejko, Iwona; Guzy-Wróbelska, Justyna; Gudyś, Kornelia

    2017-02-01

    High-yielding capacity of the modern barley varieties is mostly dependent on the sources of semi-dwarfness associated with the sdw1/denso locus. The objective of the study was to identify quantitative trait loci (QTLs) associated with the plant height and yield potential of barley recombinant inbred lines (RILs) grown under various soil moisture regimes. The plant material was developed from a hybrid between the Maresi (European cv.) and CamB (Syrian cv.). A total of 103 QTLs affecting analysed traits were detected and 36 of them showed stable effects over environments. In total, ten QTLs were found to be significant only under water shortage conditions. Nine QTLs affecting the length of main stem were detected on 2H-6H chromosomes. In four of the detected QTLs, alleles contributed by Maresi had negative effects on that trait, the most significant being the QLSt-3H.1-1 in the 3H.1 linkage group. The close linkage between QTLs identified around the sdw1/denso locus, with positive alleles contributed by Maresi, indicates that the semi-dwarf cv. Maresi could serve as a donor of favourable traits resulting in grain yield improvement, also under water scarcity. Molecular analyses revealed that the Syrian cv. also contributed alleles which increased the yield potential. Available barley resources of genomic annotations were employed to the biological interpretation of detected QTLs. This approach revealed 26 over-represented Gene Ontology terms. In the projected support intervals of QGWSl-5H.3-2 and QLSt-5H.3 on the chromosome 5H, four genes annotated to 'response to stress' were found. It suggests that these QTL-regions may be involved in a response of plant to a wide range of environmental disturbances.

  15. Stable isotopes in fossil hominin tooth enamel suggest a fundamental dietary shift in the Pliocene

    Science.gov (United States)

    Lee-Thorp, Julia A.; Sponheimer, Matt; Passey, Benjamin H.; de Ruiter, Darryl J.; Cerling, Thure E.

    2010-01-01

    Accumulating isotopic evidence from fossil hominin tooth enamel has provided unexpected insights into early hominin dietary ecology. Among the South African australopiths, these data demonstrate significant contributions to the diet of carbon originally fixed by C4 photosynthesis, consisting of C4 tropical/savannah grasses and certain sedges, and/or animals eating C4 foods. Moreover, high-resolution analysis of tooth enamel reveals strong intra-tooth variability in many cases, suggesting seasonal-scale dietary shifts. This pattern is quite unlike that seen in any great apes, even ‘savannah’ chimpanzees. The overall proportions of C4 input persisted for well over a million years, even while environments shifted from relatively closed (ca 3 Ma) to open conditions after ca 1.8 Ma. Data from East Africa suggest a more extreme scenario, where results for Paranthropus boisei indicate a diet dominated (approx. 80%) by C4 plants, in spite of indications from their powerful ‘nutcracker’ morphology for diets of hard objects. We argue that such evidence for engagement with C4 food resources may mark a fundamental transition in the evolution of hominin lineages, and that the pattern had antecedents prior to the emergence of Australopithecus africanus. Since new isotopic evidence from Aramis suggests that it was not present in Ardipithecus ramidus at 4.4 Ma, we suggest that the origins lie in the period between 3 and 4 Myr ago. PMID:20855312

  16. Cellular and Molecular Changes Associated with Onion Skin Formation Suggest Involvement of Programmed Cell Death

    Science.gov (United States)

    Galsurker, Ortal; Doron-Faigenboim, Adi; Teper-Bamnolker, Paula; Daus, Avinoam; Fridman, Yael; Lers, Amnon; Eshel, Dani

    2017-01-01

    Skin formation of onion (Allium cepa L.) bulb involves scale desiccation accompanied by scale senescence, resulting in cell death and tissue browning. Understanding the mechanism of skin formation is essential to improving onion skin and bulb qualities. Although onion skin plays a crucial role in postharvest onion storage and shelf life, its formation is poorly understood. We investigated the mode of cell death in the outermost scales that are destined to form the onion skin. Surprisingly, fluorescein diacetate staining and scanning electron microscopy indicated that the outer scale desiccates from the inside out. This striking observation suggests that cell death in the outer scales, during skin formation, is an internal and organized process that does not derive only from air desiccation. DNA fragmentation, a known hallmark of programmed cell death (PCD), was revealed in the outer scales and gradually decreased toward the inner scales of the bulb. Transmission electron microscopy further revealed PCD-related structural alterations in the outer scales which were absent from the inner scales. De novo transcriptome assembly for three different scales: 1st (outer), 5th (intermediate) and 8th (inner) fleshy scales identified 2,542 differentially expressed genes among them. GO enrichment for cluster analysis revealed increasing metabolic processes in the outer senescent scale related to defense response, PCD processes, carbohydrate metabolism and flavonoid biosynthesis, whereas increased metabolism and developmental growth processes were identified in the inner scales. High expression levels of PCD-related genes were identified in the outer scale compared to the inner ones, highlighting the involvement of PCD in outer-skin development. These findings suggest that a program to form the dry protective skin exists and functions only in the outer scales of onion. PMID:28119713

  17. [Vulvar oedema revealing systemic mastocytosis].

    Science.gov (United States)

    Deveza, E; Locatelli, F; Girardin, M; Valmary-Degano, S; Daguindau, E; Aubin, F; Humbert, P; Pelletier, F

    2015-11-01

    Systemic mastocytosis is characterised by abnormal proliferation of mast cells in various organs. We report an original case of systemic mastocytosis revealed by vulvar oedema. A 24-year-old patient was examined in the dermatology department for vulvar oedema appearing during sexual intercourse. She presented vasomotor dysfunction of the lower limbs, urticaria on the trunk on exertion, diarrhoea and bone pains. Laboratory tests showed serum tryptase of 29.7μg and plasma histamine at twice the normal value. Myelogram results showed infiltration by dysmorphic mast cells. Screening for c-kit D816V mutation was positive. Duodenal biopsies revealed mast-cell clusters with aggregation involving over 15 mast cells. CD2 staining was inconclusive and CD25 staining could not be done. Trabecular osteopenia was found, and we thus made a diagnosis of indolent systemic mastocytosis (ISM variant Ia) as per the WHO 2008 criteria. Symptomatic treatment was initiated (antiH1, H2, antileukotrienes) and clinical and laboratory follow-up was instituted. The cutaneous signs leading to diagnosis in this patient of systemic mastocytosis involving several organs were seemingly minimal signs associated with mastocyte degranulation. This is the third recorded case of mastocytosis revealed by vulvar oedema and the first case revealing systemic involvement. The two previously reported cases of vulvar oedema revealed cutaneous mastocytosis alone. Mastocytosis, whether systemic or cutaneous, must be included among the differential diagnoses considered in the presence of vulvar oedema. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

  18. The Clavibacter michiganensis subsp. michiganensis-tomato interactome reveals the perception of pathogen by the host and suggests mechanisms of infection

    Energy Technology Data Exchange (ETDEWEB)

    Savidor, Alon [Tel Aviv University; Teper, [Tel Aviv University; Gartemann, KH [Tel Aviv University; Eichenlaub, R [Tel Aviv University; Chalupowicz, L [Tel Aviv University; Manulis-Sasson, S [Tel Aviv University; Barash, I [Tel Aviv University; Tews, H [Tel Aviv University; Mayer, K [Tel Aviv University; Giannone, Richard J [ORNL; Hettich, Robert {Bob} L [ORNL; Sessa, G [Tel Aviv University

    2012-01-01

    The Gram-positive bacterium Clavibacter michiganensis subsp. michiganensis (Cmm) causes wilt and canker disease of tomato (Solanum lycopersicum). Mechanisms of Cmm pathogenicity and tomato response to Cmm infection are not well understood. To explore the interaction between Cmm and tomato, multidimensional protein identification technology (MudPIT) and tandem mass spectrometry were used to analyze in vitro and in planta generated samples. The results show that during infection Cmm senses the plant environment, transmits signals, induces, and then secretes multiple hydrolytic enzymes, including serine proteases of the Pat-1, Ppa, and Sbt familes, the CelA, XysA, and NagA glycosyl hydrolases, and other cell wall-degrading enzymes. Tomato induction of pathogenesis-related (PR) proteins, LOX1, and other defense-related proteins during infection indicates that the plant senses the invading bacterium and mounts a basal defense response, although partial with some suppressed components including class III peroxidases and a secreted serine peptidase. The tomato ethylene-synthesizing enzyme ACC-oxidase was induced during infection with the wild-type Cmm but not during infection with an endophytic Cmm strain, identifying Cmm-triggered host synthesis of ethylene as an important factor in disease symptom development. The proteomic data were also used to improve Cmm genome annotation, and thousands of Cmm gene models were confirmed or expanded.

  19. GWAS of follicular lymphoma reveals allelic heterogeneity at 6p21.32 and suggests shared genetic susceptibility with diffuse large B-cell lymphoma

    DEFF Research Database (Denmark)

    Smedby, Karin E; Foo, Jia Nee; Skibola, Christine F

    2011-01-01

    Non-Hodgkin lymphoma (NHL) represents a diverse group of hematological malignancies, of which follicular lymphoma (FL) is a prevalent subtype. A previous genome-wide association study has established a marker, rs10484561 in the human leukocyte antigen (HLA) class II region on 6p21.32 associated w...

  20. Analysis of the whole transcriptome from gingivo-buccal squamous cell carcinoma reveals deregulated immune landscape and suggests targets for immunotherapy.

    Directory of Open Access Journals (Sweden)

    Richa Singh

    Full Text Available Gingivo-buccal squamous cell carcinoma (GBSCC is one of the most common oral cavity cancers in India with less than 50% patients surviving past 5 years. Here, we report a whole transcriptome profile on a batch of GBSCC tumours with diverse tobacco usage habits. The study provides an entire landscape of altered expression with an emphasis on searching for targets with therapeutic potential.Whole transcriptomes of 12 GBSCC tumours and adjacent normal tissues were sequenced and analysed to explore differential expression of genes. Expression changes were further compared with those in TCGA head and neck cohort (n = 263 data base and validated in an independent set of 10GBSCC samples.Differentially expressed genes (n = 2176 were used to cluster the patients based on their tobacco habits, resulting in 3 subgroups. Immune response was observed to be significantly aberrant, along with cell adhesion and lipid metabolism processes. Different modes of immune evasion were seen across 12 tumours with up-regulation or consistent expression of CD47, unlike other immune evasion genes such as PDL1, FUT4, CTLA4 and BTLA which were downregulated in a few samples. Variation in infiltrating immune cell signatures across tumours also indicates heterogeneity in immune evasion strategies. A few actionable genes such as ITGA4, TGFB1 and PTGS1/COX1 were over expressed in most samples.This study found expression deregulation of key immune evasion genes, such as CD47 and PDL1, and reasserts their potential as effective immunotherapeutic targets for GBSCC, which requires further clinical studies. Present findings reiterate the idea of using transcriptome profiling to guide precision therapeutic strategies.

  1. In silico peptide-binding predictions of passerine MHC class I reveal similarities across distantly related species, suggesting convergence on the level of protein function

    DEFF Research Database (Denmark)

    Follin, Elna; Karlsson, Maria; Lundegaard, Claus

    2013-01-01

    compared to most mammals. To elucidate the reason for this large number of genes, we compared 14 MHC class I alleles (α1–α3 domains), from great reed warbler, house sparrow and tree sparrow, via phylogenetic analysis, homology modelling and in silico peptide-binding predictions to investigate...... is of functional significance. The MHC class I allomorphs from house sparrow and tree sparrow, species that diverged 10 million years ago (MYA), had overlapping peptide-binding specificities, and these similarities across species were also confirmed in phylogenetic analyses based on amino acid sequences. Notably......, there were also overlapping peptide-binding specificities in the allomorphs from house sparrow and great reed warbler, although these species diverged 30 MYA. This overlap was not found in a tree based on amino acid sequences. Our interpretation is that convergent evolution on the level of the protein...

  2. Coalescent Modelling Suggests Recent Secondary-Contact of Cryptic Penguin Species.

    Science.gov (United States)

    Grosser, Stefanie; Burridge, Christopher P; Peucker, Amanda J; Waters, Jonathan M

    2015-01-01

    Molecular genetic analyses present powerful tools for elucidating demographic and biogeographic histories of taxa. Here we present genetic evidence showing a dynamic history for two cryptic lineages within Eudyptula, the world's smallest penguin. Specifically, we use a suite of genetic markers to reveal that two congeneric taxa ('Australia' and 'New Zealand') co-occur in southern New Zealand, with only low levels of hybridization. Coalescent modelling suggests that the Australian little penguin only recently expanded into southern New Zealand. Analyses conducted under time-dependent molecular evolutionary rates lend support to the hypothesis of recent anthropogenic turnover, consistent with shifts detected in several other New Zealand coastal vertebrate taxa. This apparent turnover event highlights the dynamic nature of the region's coastal ecosystem.

  3. Association Analysis Suggests SOD2 as a Newly Identified Candidate Gene Associated With Leprosy Susceptibility.

    Science.gov (United States)

    Ramos, Geovana Brotto; Salomão, Heloisa; Francio, Angela Schneider; Fava, Vinícius Medeiros; Werneck, Renata Iani; Mira, Marcelo Távora

    2016-08-01

    Genetic studies have identified several genes and genomic regions contributing to the control of host susceptibility to leprosy. Here, we test variants of the positional and functional candidate gene SOD2 for association with leprosy in 2 independent population samples. Family-based analysis revealed an association between leprosy and allele G of marker rs295340 (P = .042) and borderline evidence of an association between leprosy and alleles C and A of markers rs4880 (P = .077) and rs5746136 (P = .071), respectively. Findings were validated in an independent case-control sample for markers rs295340 (P = .049) and rs4880 (P = .038). These results suggest SOD2 as a newly identified gene conferring susceptibility to leprosy. © The Author 2016. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.

  4. Evidence from phylogenetic and genome fingerprinting analyses suggests rapidly changing variation in Halorubrum and Haloarcula populations

    Directory of Open Access Journals (Sweden)

    Nikhil eRam Mohan

    2014-04-01

    Full Text Available Halobacteria require high NaCl concentrations for growth and are the dominant inhabitants of hypersaline environments above 15% NaCl. They are well documented to be highly recombinogenic, both in frequency and in the range of exchange partners. In this study, we examine the genetic and genomic variation of cultured, naturally co-occurring environmental populations of Halobacteria. Sequence data from multiple loci (~2500bp identified closely related strains belonging to the genera Halorubrum and Haloarcula. Genome fingerprinting using a random priming PCR amplification method to analyze these isolates revealed diverse banding patterns within and across each of the genera and surprisingly even for isolates that are identical at the nucleotide level for five protein coding sequenced loci. This variance in genome structure even between identical multilocus sequence analysis (MLSA haplotypes suggests that accumulation of variation is rapid, perhaps occurring every generation.

  5. Bacteriophage T5 tail tube structure suggests a trigger mechanism for Siphoviridae DNA ejection.

    Science.gov (United States)

    Arnaud, Charles-Adrien; Effantin, Grégory; Vivès, Corinne; Engilberge, Sylvain; Bacia, Maria; Boulanger, Pascale; Girard, Eric; Schoehn, Guy; Breyton, Cécile

    2017-12-05

    The vast majority of phages, bacterial viruses, possess a tail ensuring host recognition, cell wall perforation and safe viral DNA transfer from the capsid to the host cytoplasm. Long flexible tails are formed from the tail tube protein (TTP) polymerised as hexameric rings around and stacked along the tape measure protein (TMP). Here, we report the crystal structure of T5 TTP pb6 at 2.2 Å resolution. Pb6 is unusual in forming a trimeric ring, although structure analysis reveals homology with all classical TTPs and related tube proteins of bacterial puncturing devices (type VI secretion system and R-pyocin). Structures of T5 tail tubes before and after interaction with the host receptor were determined by cryo-electron microscopy at 6 Å resolution. Comparison of these two structures reveals that host-binding information is not propagated to the capsid through conformational changes in the tail tube, suggesting a role of the TMP in this information transduction process.

  6. Phylogenetic analyses suggest multiple changes of substrate specificity within the Glycosyl hydrolase 20 family

    Directory of Open Access Journals (Sweden)

    Horner David S

    2008-07-01

    Full Text Available Abstract Background Beta-N-acetylhexosaminidases belonging to the glycosyl hydrolase 20 (GH20 family are involved in the removal of terminal β-glycosidacally linked N-acetylhexosamine residues. These enzymes, widely distributed in microorganisms, animals and plants, are involved in many important physiological and pathological processes, such as cell structural integrity, energy storage, pathogen defence, viral penetration, cellular signalling, fertilization, development of carcinomas, inflammatory events and lysosomal storage diseases. Nevertheless, only limited analyses of phylogenetic relationships between GH20 genes have been performed until now. Results Careful phylogenetic analyses of 233 inferred protein sequences from eukaryotes and prokaryotes reveal a complex history for the GH20 family. In bacteria, multiple gene duplications and lineage specific gene loss (and/or horizontal gene transfer are required to explain the observed taxonomic distribution. The last common ancestor of extant eukaryotes is likely to have possessed at least one GH20 family member. At least one gene duplication before the divergence of animals, plants and fungi as well as other lineage specific duplication events have given rise to multiple paralogous subfamilies in eukaryotes. Phylogenetic analyses also suggest that a second, divergent subfamily of GH20 family genes present in animals derive from an independent prokaryotic source. Our data suggest multiple convergent changes of functional roles of GH20 family members in eukaryotes. Conclusion This study represents the first detailed evolutionary analysis of the glycosyl hydrolase GH20 family. Mapping of data concerning physiological function of GH20 family members onto the phylogenetic tree reveals that apparently convergent and highly lineage specific changes in substrate specificity have occurred in multiple GH20 subfamilies.

  7. Suggestive evidence for association of the circadian genes PERIOD3 and ARNTL with bipolar disorder.

    Science.gov (United States)

    Nievergelt, Caroline M; Kripke, Daniel F; Barrett, Thomas B; Burg, Elyssa; Remick, Ronald A; Sadovnick, A Dessa; McElroy, Susan L; Keck, Paul E; Schork, Nicholas J; Kelsoe, John R

    2006-04-05

    Bipolar affective disorder (BPAD) is suspected to arise in part from malfunctions of the circadian system, a system that enables adaptation to a daily and seasonally cycling environment. Genetic variations altering functions of genes involved with the input to the circadian clock, in the molecular feedback loops constituting the circadian oscillatory mechanism itself, or in the regulatory output systems could influence BPAD as a result. Several human circadian system genes have been identified and localized recently, and a comparison with linkage hotspots for BPAD has revealed some correspondences. We have assessed evidence for linkage and association involving polymorphisms in 10 circadian clock genes (ARNTL, CLOCK, CRY2, CSNK1epsilon, DBP, GSK3beta, NPAS2, PER1, PER2, and PER3) to BPAD. Linkage analysis in 52 affected families showed suggestive evidence for linkage to CSNK1epsilon. This finding was not substantiated in the association study. Fifty-two SNPs in 10 clock genes were genotyped in 185 parent proband triads. Single SNP TDT analyses showed no evidence for association to BPAD. However, more powerful haplotype analyses suggest two candidates deserving further studies. Haplotypes in ARNTL and PER3 were found to be significantly associated with BPAD via single-gene permutation tests (PG = 0.025 and 0.008, respectively). The most suggestive haplotypes in PER3 showed a Bonferroni-corrected P-value of PGC = 0.07. These two genes have previously been implicated in circadian rhythm sleep disorders and affective disorders. With correction for the number of genes considered and tests conducted, these data do not provide statistically significant evidence for association. However, the trends for ARNTL and PER3 are suggestive of their involvement in bipolar disorder and warrant further study in a larger sample. Copyright 2006 Wiley-Liss, Inc.

  8. Revealing and Concealing in Antiquity

    DEFF Research Database (Denmark)

    Secrecy and the act of concealing and revealing knowledge effectually segregate the initiated and the uninitiated. The act of sharing or hiding knowledge plays a central role in all human relations private or public, political or religious. This volume explores the concept of secrecy and its impl...

  9. Preliminary data suggest rates of male military sexual trauma may be higher than previously reported.

    Science.gov (United States)

    Sheppard, Sean C; Hickling, Edward J; Earleywine, Mitch; Hoyt, Tim; Russo, Amanda R; Donati, Matthew R; Kip, Kevin E

    2015-11-01

    Stigma associated with disclosing military sexual trauma (MST) makes estimating an accurate base rate difficult. Anonymous assessment may help alleviate stigma. Although anonymous research has found higher rates of male MST, no study has evaluated whether providing anonymity sufficiently mitigates the impact of stigma on accurate reporting. This study used the unmatched count technique (UCT), a form of randomized response techniques, to gain information about the accuracy of base rate estimates of male MST derived via anonymous assessment of Operation Enduring Freedom (OEF)/Operation Iraqi Freedom (OIF) combat veterans. A cross-sectional convenience sample of 180 OEF/OIF male combat veterans, recruited via online websites for military populations, provided data about history of MST via traditional anonymous self-report and the UCT. The UCT revealed a rate of male MST more than 15 times higher than the rate derived via traditional anonymous assessment (1.1% vs. 17.2%). These data suggest that anonymity does not adequately mitigate the impact of stigma on disclosure of male MST. Results, though preliminary, suggest that published rates of male MST may substantially underestimate the true rate of this problem. The UCT has significant potential to improve base rate estimation of sensitive behaviors in the military. (c) 2015 APA, all rights reserved).

  10. Invasion by P. falciparum Merozoites Suggests a Hierarchy of Molecular Interactions.

    Directory of Open Access Journals (Sweden)

    2005-12-01

    Full Text Available Central to the pathology of malaria disease are the repeated cycles of parasite invasion and destruction of human erythrocytes. In Plasmodium falciparum, the most virulent species causing malaria, erythrocyte invasion involves several specific receptor-ligand interactions that direct the pathway used to invade the host cell, with parasites varying in their dependency on these different pathways. Gene disruption of a key invasion ligand in the 3D7 parasite strain, the P. falciparum reticulocyte binding-like homolog 2b (PfRh2b, resulted in the parasite invading via a novel pathway. Here, we show results that suggest the molecular basis for this novel pathway is not due to a molecular switch but is instead mediated by the redeployment of machinery already present in the parent parasite but masked by the dominant role of PfRh2b. This would suggest that interactions directing invasion are organized hierarchically, where silencing of dominant invasion ligands reveal underlying alternative pathways. This provides wild parasites with the ability to adapt to immune-mediated selection or polymorphism in erythrocyte receptors and has implications for the use of invasion-related molecules in candidate vaccines.

  11. Demyelination in mild cognitive impairment suggests progression path to Alzheimer's disease.

    Directory of Open Access Journals (Sweden)

    Cristian Carmeli

    Full Text Available The preclinical Alzheimer's disease (AD - amnestic mild cognitive impairment (MCI - is manifested by phenotypes classified into exclusively memory (single-domain MCI (sMCI and multiple-domain MCI (mMCI. We suggest that typical MCI-to-AD progression occurs through the sMCI-to-mMCI sequence as a result of the extension of initial pathological processes. To support this hypothesis, we assess myelin content with a Magnetization Transfer Ratio (MTR in 21 sMCI and 21 mMCI patients and in 42 age-, sex-, and education-matched controls. A conjunction analysis revealed MTR reduction shared by sMCI and mMCI groups in the medial temporal lobe and posterior structures including white matter (WM: splenium, posterior corona radiata and gray matter (GM: hippocampus; parahippocampal and lingual gyri. A disjunction analysis showed the spread of demyelination to prefrontal WM and insula GM in executive mMCI. Our findings suggest that demyelination starts in the structures affected by neurofibrillary pathology; its presence correlates with the clinical picture and indicates the method of MCI-to-AD progression. In vivo staging of preclinical AD can be developed in terms of WM/GM demyelination.

  12. Evolutionary breakpoints in the gibbon suggest association between cytosine methylation and karyotype evolution.

    Science.gov (United States)

    Carbone, Lucia; Harris, R Alan; Vessere, Gery M; Mootnick, Alan R; Humphray, Sean; Rogers, Jane; Kim, Sung K; Wall, Jeffrey D; Martin, David; Jurka, Jerzy; Milosavljevic, Aleksandar; de Jong, Pieter J

    2009-06-01

    Gibbon species have accumulated an unusually high number of chromosomal changes since diverging from the common hominoid ancestor 15-18 million years ago. The cause of this increased rate of chromosomal rearrangements is not known, nor is it known if genome architecture has a role. To address this question, we analyzed sequences spanning 57 breaks of synteny between northern white-cheeked gibbons (Nomascus l. leucogenys) and humans. We find that the breakpoint regions are enriched in segmental duplications and repeats, with Alu elements being the most abundant. Alus located near the gibbon breakpoints (other Alus. Bisulphite allelic sequencing reveals that these gibbon Alus have a lower average density of methylated cytosine that their human orthologues. The finding of higher CpG content and lower average CpG methylation suggests that the gibbon Alu elements are epigenetically distinct from their human orthologues. The association between undermethylation and chromosomal rearrangement in gibbons suggests a correlation between epigenetic state and structural genome variation in evolution.

  13. Evolutionary breakpoints in the gibbon suggest association between cytosine methylation and karyotype evolution.

    Directory of Open Access Journals (Sweden)

    Lucia Carbone

    2009-06-01

    Full Text Available Gibbon species have accumulated an unusually high number of chromosomal changes since diverging from the common hominoid ancestor 15-18 million years ago. The cause of this increased rate of chromosomal rearrangements is not known, nor is it known if genome architecture has a role. To address this question, we analyzed sequences spanning 57 breaks of synteny between northern white-cheeked gibbons (Nomascus l. leucogenys and humans. We find that the breakpoint regions are enriched in segmental duplications and repeats, with Alu elements being the most abundant. Alus located near the gibbon breakpoints (<150 bp have a higher CpG content than other Alus. Bisulphite allelic sequencing reveals that these gibbon Alus have a lower average density of methylated cytosine that their human orthologues. The finding of higher CpG content and lower average CpG methylation suggests that the gibbon Alu elements are epigenetically distinct from their human orthologues. The association between undermethylation and chromosomal rearrangement in gibbons suggests a correlation between epigenetic state and structural genome variation in evolution.

  14. Natural Selection and Functional Potentials of Human Noncoding Elements Revealed by Analysis of Next Generation Sequencing Data.

    Science.gov (United States)

    Jha, Pankaj; Lu, Dongsheng; Xu, Shuhua

    2015-01-01

    Noncoding DNA sequences (NCS) have attracted much attention recently due to their functional potentials. Here we attempted to reveal the functional roles of noncoding sequences from the point of view of natural selection that typically indicates the functional potentials of certain genomic elements. We analyzed nearly 37 million single nucleotide polymorphisms (SNPs) of Phase I data of the 1000 Genomes Project. We estimated a series of key parameters of population genetics and molecular evolution to characterize sequence variations of the noncoding genome within and between populations, and identified the natural selection footprints in NCS in worldwide human populations. Our results showed that purifying selection is prevalent and there is substantial constraint of variations in NCS, while positive selectionis more likely to be specific to some particular genomic regions and regional populations. Intriguingly, we observed larger fraction of non-conserved NCS variants with lower derived allele frequency in the genome, indicating possible functional gain of non-conserved NCS. Notably, NCS elements are enriched for potentially functional markers such as eQTLs, TF motif, and DNase I footprints in the genome. More interestingly, some NCS variants associated with diseases such as Alzheimer's disease, Type 1 diabetes, and immune-related bowel disorder (IBD) showed signatures of positive selection, although the majority of NCS variants, reported as risk alleles by genome-wide association studies, showed signatures of negative selection. Our analyses provided compelling evidence of natural selection forces on noncoding sequences in the human genome and advanced our understanding of their functional potentials that play important roles in disease etiology and human evolution.

  15. Genetic Architecture of Natural Variation in Rice Nonphotochemical Quenching Capacity Revealed by Genome-Wide Association Study

    Directory of Open Access Journals (Sweden)

    Quanxiu Wang

    2017-10-01

    Full Text Available The photoprotective processes conferred by nonphotochemical quenching (NPQ serve fundamental roles in maintaining plant fitness and sustainable yield. So far, few loci have been reported to be involved in natural variation of NPQ capacity in rice (Oryza sativa, and the extents of variation explored are very limited. Here we conducted a genome-wide association study (GWAS for NPQ capacity using a diverse worldwide collection of 529 O. sativa accessions. A total of 33 significant association loci were identified. To check the validity of the GWAS signals, three F2 mapping populations with parents selected from the association panel were constructed and assayed. All QTLs detected in mapping populations could correspond to at least one GWAS signal, indicating the GWAS results were quite reliable. OsPsbS1 was repeatedly detected and explained more than 40% of the variation in the whole association population in two years, and demonstrated to be a common major QTL in all three mapping populations derived from inter-group crosses. We revealed 43 single nucleotide polymorphisms (SNPs and 7 insertions and deletions (InDels within a 6,997-bp DNA fragment of OsPsbS1, but found no non-synonymous SNPs or InDels in the coding region, indicating the PsbS1 protein sequence is highly conserved. Haplotypes with the 2,674-bp insertion in the promoter region exhibited significantly higher NPQ values and higher expression levels of OsPsbS1. The OsPsbS1 RNAi plants and CRISPR/Cas9 mutants exhibited drastically decreased NPQ values. OsPsbS1 had specific and high-level expression in green tissues of rice. However, we didn't find significant function for OsPsbS2, the other rice PsbS homologue. Manipulation of the significant loci or candidate genes identified may enhance photoprotection and improve photosynthesis and yield in rice.

  16. Genome-wide association analysis reveals genetic loci and candidate genes for feeding behavior and eating efficiency in Duroc boars.

    Directory of Open Access Journals (Sweden)

    Rongrong Ding

    Full Text Available Efficient use of feed resources is a challenge in the pork industry because the largest variability in expenditure is attributed to the cost of fodder. Efficiency of feeding is directly related to feeding behavior. In order to identify genomic regions controlling feeding behavior and eating efficiency traits, 338 Duroc boars were used in this study. The Illumina Porcine SNP60K BeadChip was used for genotyping. Data pertaining to individual daily feed intake (DFI, total daily time spent in feeder (TPD, number of daily visits to feeder (NVD, average duration of each visit (TPV, mean feed intake per visit (FPV, mean feed intake rate (FR, and feed conversion ratio (FCR were collected for these pigs. Despite the limited sample size, the genome-wide association study was acceptable to detect candidate regions association with feeding behavior and eating efficiency traits in pigs. We detected three genome-wide (P < 1.40E-06 and 11 suggestive (P < 2.79E-05 single nucleotide polymorphism (SNP-trait associations. Six SNPs were located in genomic regions where quantitative trait loci (QTLs have previously been reported for feeding behavior and eating efficiency traits in pigs. Five candidate genes (SERPINA3, MYC, LEF1, PITX2, and MAP3K14 with biochemical and physiological roles that were relevant to feeding behavior and eating efficiency were discovered proximal to significant or suggestive markers. Gene ontology analysis indicated that most of the candidate genes were involved in the development of the hypothalamus (GO:0021854, P < 0.0398. Our results provide new insights into the genetic basis of feeding behavior and eating efficiency in pigs. Furthermore, some significant SNPs identified in this study could be incorporated into artificial selection programs for Duroc-related pigs to select for increased feeding efficiency.

  17. [Cervicofacial cellulitis revealing cutaneous lymphomas].

    Science.gov (United States)

    Benbouzid, M A; Bencheikh, R; Benhammou, A; El Edghiri, H; Boulaich, M; Essakali, L; Kzadri, M

    2007-06-01

    The cervicofacial localization of cutaneous lymphomas is rare. These lymphomas usually present as a long-lasting and treatment-refractory papule or nodule. Lymphomas can also be revealed by cervicofacial cellulitis. We report 2 cases of cervicofacial cellulitis revealing a cutaneous lymphoma. The diagnosis was proved by multiple biopsies, performed because there was no clinical improvement in spite of an aggressive and adequate antibiotherapy. Our 2 patients were treated by radio and chemotherapy. Cutaneous lymphomas are lymphocytic proliferations stemming from cutaneous lymphoid tissue, without nodal, medullary, or visceral localization. Their clinical presentation is quite polymorphic, and cellulitis is one of the modes of revelation, especially forehead and neck localization. They have no portal of entry and are resistant to treatment. The diagnosis relies on histology, and biopsies must be performed if there is a suspicion of lymphoma. The treatment is radio and chemotherapy, and the evolution depends on the tumoral stage.

  18. Decision Making and Revealed Preference

    DEFF Research Database (Denmark)

    de la Rosa, Leonidas Enrique

    If our decision-making processes are to some extent shaped by evolutionary pressures and our environment is different from that to which we adapted, some of our choices will not be in our best interest. But revealed preference is the only tool that we have so far to conduct a normative analysis. ....... Given advances in evolutionary psychology and neuroscience, I propose one way to model those evolutionary pressures that will hopefully prove useful in expanding normative economics.......If our decision-making processes are to some extent shaped by evolutionary pressures and our environment is different from that to which we adapted, some of our choices will not be in our best interest. But revealed preference is the only tool that we have so far to conduct a normative analysis...

  19. Urticarial vasculitis reveals unsuspected thyroiditis.

    Science.gov (United States)

    Ferreira, Olga; Mota, Alberto; Baudrier, Teresa; Azevedo, Filomena

    2012-01-01

    A 38-year-old woman presented with erythematous, violaceous plaques with a serpiginous and unusual appearance located on the left shoulder, left thigh, and right buttock, evolving for 5 days, which eventually became generalized. A skin biopsy revealed leukocytoclastic vasculitis and a diagnosis of urticarial vasculitis was made. The complete blood count, biochemistry, complement levels, and other immunological test results were unremarkable. However, antithyroid antibody titers were increased. Despite having normal thyroid function tests and an absence of specific symptoms, the patient underwent a thyroid ultrasound, which revealed features of thyroiditis, and was subsequently referred to an endocrinologist. Several diseases can be associated with urticarial vasculitis, namely infections and autoimmune connective-tissue disorders such as systemic lupus erythematosus and Sjögren syndrome. Thyroiditis is an uncommon association.

  20. Perceived reasons for, opinions about, and suggestions for elders considering suicide: elderly outpatients' perspectives.

    Science.gov (United States)

    Chen, Ying-Jen; Tsai, Yun-Fang; Ku, Yan-Chiou; Lee, Shwu-Hua; Lee, Hsiu-Lan

    2014-07-01

    The purposes of this study were to explore elderly outpatients' perceived reasons for, opinions of, and suggestions for elderly people considering suicide in Taiwan. Elderly outpatients (N = 83) were recruited in 2011-2012 by convenience sampling from three randomly selected medical centers in Taiwan. Data were collected in individual interviews using a semi-structured guide and analyzed by content analysis. Findings revealed that most participants had heard of elderly suicide, with television news as the main source for their information. Their opinions about elderly suicide reflected judgmental attitudes, negative emotional reactions, expectations of social welfare, and could happen after losing one's meaning in life. Their suggestions for elderly people considering suicide fell into four major themes: give up suicidal ideas, seek help, enhance social welfare, and attend religious activities. Since television news was the main source for participants' information about elderly suicide, this mass medium should be used in suicide prevention to disseminate suicide knowledge, increase access to help, and strengthen suicide-protective factors among the elderly. Furthermore, no participants mentioned depression as a reason for attempted or completed suicide among older people despite depression being a well-known suicide-risk factor. Future suicide-prevention programs should emphasize the role of depression in suicide among older people. Participants also did not suggest that older people considering suicide seek help from the health system. Thus, older people should be educated about the role of the health system in suicide prevention and trained as gatekeepers to recognize signs of suicide ideation and respond appropriately.

  1. Improving working memory performance in brain-injured patients using hypnotic suggestion.

    Science.gov (United States)

    Lindeløv, Jonas K; Overgaard, Rikke; Overgaard, Morten

    2017-04-01

    Working memory impairment is prevalent in brain injured patients across lesion aetiologies and severities. Unfortunately, rehabilitation efforts for this impairment have hitherto yielded small or no effects. Here we show in a randomized actively controlled trial that working memory performance can be effectively restored by suggesting to hypnotized patients that they have regained their pre-injury level of working memory functioning. Following four 1-h sessions, 27 patients had a medium-sized improvement relative to 22 active controls (Bayes factors of 342 and 37.5 on the two aggregate outcome measures) and a very large improvement relative to 19 passive controls (Bayes factor = 1.7 × 1013). This was a long-term effect as revealed by no deterioration following a 6.7 week no-contact period (Bayes factors = 7.1 and 1.3 in favour of no change). To control for participant-specific effects, the active control group was crossed over to the working memory suggestion and showed superior improvement. By the end of the study, both groups reached a performance level at or above the healthy population mean with standardized mean differences between 1.55 and 2.03 relative to the passive control group. We conclude that, if framed correctly, hypnotic suggestion can effectively improve working memory following acquired brain injury. The speed and consistency with which this improvement occurred, indicate that there may be a residual capacity for normal information processing in the injured brain. © The Author (2017). Published by Oxford University Press on behalf of the Guarantors of Brain. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  2. Effects of microgravity on muscle and cerebral cortex: a suggested interaction

    Science.gov (United States)

    D'Amelio, F.; Fox, R. A.; Wu, L. C.; Daunton, N. G.; Corcoran, M. L.

    The ``slow'' antigravity muscle adductor longus was studied in rats after 14 days of spaceflight (SF). The techniques employed included standard methods for light microscopy, neural cell adhesion molecule (N-CAM) immunocytochemistry and electron microscopy. Light and electron microscopy revealed myofiber atrophy, segmental necrosis and regenerative myofibers. Regenerative myofibers were N-CAM immunoreactive (N-CAM-IR). The neuromuscular junctions showed axon terminals with a decrease or absence of synaptic vesicles, degenerative changes, vacant axonal spaces and changes suggestive of axonal sprouting. No alterations of muscle spindles was seen either by light or electron microscopy. These observations suggest that muscle regeneration and denervation and synaptic remodeling at the level of the neuromuscular junction may take place during spaceflight. In a separate study, GABA immunoreactivity (GABA-IR) was evaluated at the level of the hindlimb representation of the rat somatosensory cortex after 14 days of hindlimb unloading by tail suspension (``simulated'' microgravity). A reduction in number of GABA-immunoreactive cells with respect to the control animals was observed in layer Va and Vb. GABA-IR terminals were also reduced in the same layers, particularly those terminals surrounding the soma and apical dendrites of pyramidal cells in layer Vb. On the basis of previous morphological and behavioral studies of the neuromuscular system after spaceflight and hindlimb suspension it is suggested that after limb unloading there are alterations of afferent signaling and feedback information from intramuscular receptors to the cerebral cortex due to modifications in the reflex organization of hindlimb muscle groups. We propose that the changes observed in GABA immunoreactivity of cells and terminals is an expression of changes in their modulatory activity to compensate for the alterations in the afferent information.

  3. Systems genomics study reveals expression quantitative trait loci, regulator genes and pathways associated with boar taint in pigs

    DEFF Research Database (Denmark)

    Drag, Markus; Hansen, Mathias Brygger; Kadarmideen, Haja

    2018-01-01

    to identify expression quantitative trait loci (eQTLs) with potential effects on boar taint compounds to improve breeding possibilities for reduced boar taint. Danish Landrace male boars with low, medium and high genetic merit for skatole and human nose score (HNS) were slaughtered at ~100 kg. Gene expression...

  4. Exome sequencing of bilateral testicular germ cell tumors suggests independent development lineages.

    Science.gov (United States)

    Brabrand, Sigmund; Johannessen, Bjarne; Axcrona, Ulrika; Kraggerud, Sigrid M; Berg, Kaja G; Bakken, Anne C; Bruun, Jarle; Fosså, Sophie D; Lothe, Ragnhild A; Lehne, Gustav; Skotheim, Rolf I

    2015-02-01

    Intratubular germ cell neoplasia, the precursor of testicular germ cell tumors (TGCTs), is hypothesized to arise during embryogenesis from developmentally arrested primordial germ cells (PGCs) or gonocytes. In early embryonal life, the PGCs migrate from the yolk sac to the dorsal body wall where the cell population separates before colonizing the genital ridges. However, whether the malignant transformation takes place before or after this separation is controversial. We have explored the somatic exome-wide mutational spectra of bilateral TGCT to provide novel insight into the in utero critical time frame of malignant transformation and TGCT pathogenesis. Exome sequencing was performed in five patients with bilateral TGCT (eight tumors), of these three patients in whom both tumors were available (six tumors) and two patients each with only one available tumor (two tumors). Selected loci were explored by Sanger sequencing in 71 patients with bilateral TGCT. From the exome-wide mutational spectra, no identical mutations in any of the three bilateral tumor pairs were identified. Exome sequencing of all eight tumors revealed 87 somatic non-synonymous mutations (median 10 per tumor; range 5-21), some in already known cancer genes such as CIITA, NEB, platelet-derived growth factor receptor α (PDGFRA), and WHSC1. SUPT6H was found recurrently mutated in two tumors. We suggest independent development lineages of bilateral TGCT. Thus, malignant transformation into intratubular germ cell neoplasia is likely to occur after the migration of PGCs. We reveal possible drivers of TGCT pathogenesis, such as mutated PDGFRA, potentially with therapeutic implications for TGCT patients. Copyright © 2014 Neoplasia Press, Inc. Published by Elsevier Inc. All rights reserved.

  5. Exome Sequencing of Bilateral Testicular Germ Cell Tumors Suggests Independent Development Lineages12

    Science.gov (United States)

    Brabrand, Sigmund; Johannessen, Bjarne; Axcrona, Ulrika; Kraggerud, Sigrid M.; Berg, Kaja G.; Bakken, Anne C.; Bruun, Jarle; Fosså, Sophie D.; Lothe, Ragnhild A.; Lehne, Gustav; Skotheim, Rolf I.

    2015-01-01

    Intratubular germ cell neoplasia, the precursor of testicular germ cell tumors (TGCTs), is hypothesized to arise during embryogenesis from developmentally arrested primordial germ cells (PGCs) or gonocytes. In early embryonal life, the PGCs migrate from the yolk sac to the dorsal body wall where the cell population separates before colonizing the genital ridges. However, whether the malignant transformation takes place before or after this separation is controversial. We have explored the somatic exome-wide mutational spectra of bilateral TGCT to provide novel insight into the in utero critical time frame of malignant transformation and TGCT pathogenesis. Exome sequencing was performed in five patients with bilateral TGCT (eight tumors), of these three patients in whom both tumors were available (six tumors) and two patients each with only one available tumor (two tumors). Selected loci were explored by Sanger sequencing in 71 patients with bilateral TGCT. From the exome-wide mutational spectra, no identical mutations in any of the three bilateral tumor pairs were identified. Exome sequencing of all eight tumors revealed 87 somatic non-synonymous mutations (median 10 per tumor; range 5-21), some in already known cancer genes such as CIITA, NEB, platelet-derived growth factor receptor α (PDGFRA), and WHSC1. SUPT6H was found recurrently mutated in two tumors. We suggest independent development lineages of bilateral TGCT. Thus, malignant transformation into intratubular germ cell neoplasia is likely to occur after the migration of PGCs. We reveal possible drivers of TGCT pathogenesis, such as mutated PDGFRA, potentially with therapeutic implications for TGCT patients. PMID:25748235

  6. Exome Sequencing of Bilateral Testicular Germ Cell Tumors Suggests Independent Development Lineages

    Directory of Open Access Journals (Sweden)

    Sigmund Brabrand

    2015-02-01

    Full Text Available Intratubular germ cell neoplasia, the precursor of testicular germ cell tumors (TGCTs, is hypothesized to arise during embryogenesis from developmentally arrested primordial germ cells (PGCs or gonocytes. In early embryonal life, the PGCs migrate from the yolk sac to the dorsal body wall where the cell population separates before colonizing the genital ridges. However, whether the malignant transformation takes place before or after this separation is controversial. We have explored the somatic exome-wide mutational spectra of bilateral TGCT to provide novel insight into the in utero critical time frame of malignant transformation and TGCT pathogenesis. Exome sequencing was performed in five patients with bilateral TGCT (eight tumors, of these three patients in whom both tumors were available (six tumors and two patients each with only one available tumor (two tumors. Selected loci were explored by Sanger sequencing in 71 patients with bilateral TGCT. From the exome-wide mutational spectra, no identical mutations in any of the three bilateral tumor pairs were identified. Exome sequencing of all eight tumors revealed 87 somatic non-synonymous mutations (median 10 per tumor; range 5-21, some in already known cancer genes such as CIITA, NEB, platelet-derived growth factor receptor α (PDGFRA, and WHSC1. SUPT6H was found recurrently mutated in two tumors. We suggest independent development lineages of bilateral TGCT. Thus, malignant transformation into intratubular germ cell neoplasia is likely to occur after the migration of PGCs. We reveal possible drivers of TGCT pathogenesis, such as mutated PDGFRA, potentially with therapeutic implications for TGCT patients.

  7. Different inward and outward conduction mechanisms in NaVMs suggested by molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Song Ke

    2014-07-01

    Full Text Available Rapid and selective ion transport is essential for the generation and regulation of electrical signaling pathways in living organisms. Here, we use molecular dynamics (MD simulations with an applied membrane potential to investigate the ion flux of bacterial sodium channel NaVMs. 5.9 µs simulations with 500 mM NaCl suggest different mechanisms for inward and outward flux. The predicted inward conductance rate of ∼27±3 pS, agrees with experiment. The estimated outward conductance rate is 15±3 pS, which is considerably lower. Comparing inward and outward flux, the mean ion dwell time in the selectivity filter (SF is prolonged from 13.5±0.6 ns to 20.1±1.1 ns. Analysis of the Na+ distribution revealed distinct patterns for influx and efflux events. In 32.0±5.9% of the simulation time, the E53 side chains adopted a flipped conformation during outward conduction, whereas this conformational change was rarely observed (2.7±0.5% during influx. Further, simulations with dihedral restraints revealed that influx is less affected by the E53 conformational flexibility. In contrast, during outward conduction, our simulations indicate that the flipped E53 conformation provides direct coordination for Na+. The free energy profile (potential of mean force calculations indicates that this conformational change lowers the putative barriers between sites SCEN and SHFS during outward conduction. We hypothesize that during an action potential, the increased Na+ outward transition propensities at depolarizing potentials might increase the probability of E53 conformational changes in the SF. Subsequently, this might be a first step towards initiating slow inactivation.

  8. Transparency masters for mathematics revealed

    CERN Document Server

    Berman, Elizabeth

    1980-01-01

    Transparency Masters for Mathematics Revealed focuses on master diagrams that can be used for transparencies for an overhead projector or duplicator masters for worksheets. The book offers information on a compilation of master diagrams prepared by John R. Stafford, Jr., audiovisual supervisor at the University of Missouri at Kansas City. Some of the transparencies are designed to be shown horizontally. The initial three masters are number lines and grids that can be used in a mathematics course, while the others are adaptations of text figures which are slightly altered in some instances. The

  9. Patterns of evolution of MHC class II genes of crows (Corvus suggest trans-species polymorphism

    Directory of Open Access Journals (Sweden)

    John A. Eimes

    2015-03-01

    Full Text Available A distinguishing characteristic of genes that code for the major histocompatibility complex (MHC is that alleles often share more similarity between, rather than within species. There are two likely mechanisms that can explain this pattern: convergent evolution and trans-species polymorphism (TSP, in which ancient allelic lineages are maintained by balancing selection and retained by descendant species. Distinguishing between these two mechanisms has major implications in how we view adaptation of immune genes. In this study we analyzed exon 2 of the MHC class IIB in three passerine bird species in the genus Corvus: jungle crows (Corvus macrorhynchos japonensis American crows (C. brachyrhynchos and carrion crows (C. corone orientalis. Carrion crows and American crows are recently diverged, but allopatric, sister species, whereas carrion crows and jungle crows are more distantly related but sympatric species, and possibly share pathogens linked to MHC IIB polymorphisms. These patterns of evolutionary divergence and current geographic ranges enabled us to test for trans-species polymorphism and convergent evolution of the MHC IIB in crows. Phylogenetic reconstructions of MHC IIB sequences revealed several well supported interspecific clusters containing all three species, and there was no biased clustering of variants among the sympatric carrion crows and jungle crows. The topologies of phylogenetic trees constructed from putatively selected sites were remarkably different than those constructed from putatively neutral sites. In addition, trees constructed using non-synonymous substitutions from a continuous fragment of exon 2 had more, and generally more inclusive, supported interspecific MHC IIB variant clusters than those constructed from the same fragment using synonymous substitutions. These phylogenetic patterns suggest that recombination, especially gene conversion, has partially erased the signal of allelic ancestry in these species. While

  10. To Reveal Thy Heart Perchance to Reveal the World

    Directory of Open Access Journals (Sweden)

    Robert B. Faux

    2005-05-01

    Full Text Available Ronald PELIAS, a professor of speech communications, employs a variety of writing methods as examples of alternative ways to do research and to share with the reader a seldom seen and seldom considered aspect of academic life: Heart. In the early chapters of the book, PELIAS sets out to establish a way to place his Heart in the foreground; baring his emotional vulnerability, his humanness, his being in the world. Later chapters of the book encompass an autoethnographic study of academic life in which the previously revealed Heart is placed in context. In this review essay I discuss PELIAS' book in relation to the larger literature on autoethnography and subjectivist research; I follow this by discussing the need for and usefulness of such alternative methods using PELIAS' autoethnography of academic life as a context. URN: urn:nbn:de:0114-fqs050279

  11. Biannual cycles of organochlorine pesticide enantiomers in arctic air suggest changing sources and pathways

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    Bidleman, T. F.; Jantunen, L. M.; Hung, H.; Ma, J.; Stern, G. A.; Rosenberg, B.; Racine, J.

    2014-09-01

    Air samples collected during 1994-2000 at the Canadian arctic air monitoring station Alert (82°30' N, 62°20' W) were analyzed by enantiospecific gas chromatography - mass spectrometry for α-hexachlorocyclohexane (α-HCH), trans-chlordane (TC) and cis-chlordane (CC). Results were expressed as enantiomer fractions (EF = quantities of (+)/[(+) + (-)] enantiomers), where EFs = 0.5, 0.5 indicate racemic composition, and preferential depletion of (+) and (-) enantiomers, respectively. Long-term average EFs were close to racemic values for α-HCH (0.504 ± 0.004, n = 197) and CC (0.505 ± 0.004, n = 162), and deviated farther from racemic for TC (0.470 ± 0.013, n = 165). Digital filtration analysis revealed biannual cycles of lower α-HCH EFs in summer-fall and higher EFs in winter-spring. These cycles suggest volatilization of partially degraded α-HCH with EF 0.5 during the cold season. The contribution of sea-volatilized α-HCH was only 11% at Alert, vs. 32% at Resolute Bay (74.68° N, 94.90° W) in 1999. EFs of TC also followed biannual cycles of lower and higher values in the warm and cold seasons. These were in phase with low and high cycles of the TC/CC ratio (expressed as FTC = TC/(TC + CC)), which suggests greater contribution of microbially "weathered" TC in summer-fall vs. winter-spring. CC was closer to racemic than TC and displayed seasonal cycles only in 1997-1998. EF profiles are likely to change with rising contribution of secondary emission sources, weathering of residues in the environment, and loss of ice cover in the Arctic. Enantiomer-specific analysis could provide added forensic capability to air monitoring programs.

  12. Annual cycles of organochlorine pesticide enantiomers in Arctic air suggest changing sources and pathways

    Science.gov (United States)

    Bidleman, T. F.; Jantunen, L. M.; Hung, H.; Ma, J.; Stern, G. A.; Rosenberg, B.; Racine, J.

    2015-02-01

    Air samples collected during 1994-2000 at the Canadian Arctic air monitoring station Alert (82°30' N, 62°20' W) were analysed by enantiospecific gas chromatography-mass spectrometry for α-hexachlorocyclohexane (α-HCH), trans-chlordane (TC) and cis-chlordane (CC). Results were expressed as enantiomer fractions (EF = peak areas of (+)/[(+) + (-)] enantiomers), where EFs = 0.5, 0.5 indicate racemic composition, and preferential depletion of (+) and (-) enantiomers, respectively. Long-term average EFs were close to racemic values for α -HCH (0.504 ± 0.004, n = 197) and CC (0.505 ± 0.004, n = 162), and deviated farther from racemic for TC (0.470 ± 0.013, n = 165). Digital filtration analysis revealed annual cycles of lower α-HCH EFs in summer-fall and higher EFs in winter-spring. These cycles suggest volatilization of partially degraded α-HCH with EF 0.5 during the cold season. The contribution of sea-volatilized α-HCH was only 11% at Alert, vs. 32% at Resolute Bay (74.68° N, 94.90° W) in 1999. EFs of TC also followed annual cycles of lower and higher values in the warm and cold seasons. These were in phase with low and high cycles of the TC/CC ratio (expressed as FTC = TC/(TC+CC)), which suggests greater contribution of microbially "weathered" TC in summer-fall versus winter-spring. CC was closer to racemic than TC and displayed seasonal cycles only in 1997-1998. EF profiles are likely to change with rising contribution of secondary emission sources, weathering of residues in the environment, and loss of ice cover in the Arctic. Enantiomer-specific analysis could provide added forensic capability to air monitoring programs.

  13. Genotyping of Burkholderia mallei from an outbreak of glanders in Bahrain suggests multiple introduction events.

    Science.gov (United States)

    Scholz, Holger C; Pearson, Talima; Hornstra, Heidie; Projahn, Michaela; Terzioglu, Rahime; Wernery, Renate; Georgi, Enrico; Riehm, Julia M; Wagner, David M; Keim, Paul S; Joseph, Marina; Johnson, Bobby; Kinne, Joerg; Jose, Shanti; Hepp, Crystal M; Witte, Angela; Wernery, Ulrich

    2014-09-01

    Glanders, caused by the gram-negative bacterium Burkholderia mallei, is a highly infectious zoonotic disease of solipeds causing severe disease in animals and men. Although eradicated from many Western countries, it recently emerged in Asia, the Middle-East, Africa, and South America. Due to its rareness, little is known about outbreak dynamics of the disease and its epidemiology. We investigated a recent outbreak of glanders in Bahrain by applying high resolution genotyping (multiple locus variable number of tandem repeats, MLVA) and comparative whole genome sequencing to B. mallei isolated from infected horses and a camel. These results were compared to samples obtained from an outbreak in the United Arab Emirates in 2004, and further placed into a broader phylogeographic context based on previously published B. mallei data. The samples from the outbreak in Bahrain separated into two distinct clusters, suggesting a complex epidemiological background and evidence for the involvement of multiple B. mallei strains. Additionally, the samples from Bahrain were more closely related to B. mallei isolated from horses in the United Arab Emirates in 2004 than other B. mallei which is suggestive of repeated importation to the region from similar geographic sources. High-resolution genotyping and comparative whole genome analysis revealed the same phylogenetic patterns among our samples. The close relationship of the Dubai/UAE B. mallei populations to each other may be indicative of a similar geographic origin that has yet to be identified for the infecting strains. The recent emergence of glanders in combination with worldwide horse trading might pose a new risk for human infections.

  14. Genotyping of Burkholderia mallei from an outbreak of glanders in Bahrain suggests multiple introduction events.

    Directory of Open Access Journals (Sweden)

    Holger C Scholz

    2014-09-01

    Full Text Available Glanders, caused by the gram-negative bacterium Burkholderia mallei, is a highly infectious zoonotic disease of solipeds causing severe disease in animals and men. Although eradicated from many Western countries, it recently emerged in Asia, the Middle-East, Africa, and South America. Due to its rareness, little is known about outbreak dynamics of the disease and its epidemiology.We investigated a recent outbreak of glanders in Bahrain by applying high resolution genotyping (multiple locus variable number of tandem repeats, MLVA and comparative whole genome sequencing to B. mallei isolated from infected horses and a camel. These results were compared to samples obtained from an outbreak in the United Arab Emirates in 2004, and further placed into a broader phylogeographic context based on previously published B. mallei data. The samples from the outbreak in Bahrain separated into two distinct clusters, suggesting a complex epidemiological background and evidence for the involvement of multiple B. mallei strains. Additionally, the samples from Bahrain were more closely related to B. mallei isolated from horses in the United Arab Emirates in 2004 than other B. mallei which is suggestive of repeated importation to the region from similar geographic sources.High-resolution genotyping and comparative whole genome analysis revealed the same phylogenetic patterns among our samples. The close relationship of the Dubai/UAE B. mallei populations to each other may be indicative of a similar geographic origin that has yet to be identified for the infecting strains. The recent emergence of glanders in combination with worldwide horse trading might pose a new risk for human infections.

  15. Clinically isolated syndrome suggestive of multiple sclerosis: voxelwise regional investigation of white and gray matter.

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    Raz, Eytan; Cercignani, Mara; Sbardella, Emilia; Totaro, Porzia; Pozzilli, Carlo; Bozzali, Marco; Pantano, Patrizia

    2010-01-01

    To quantify white matter (WM) and gray matter (GM) damage in patients who presented with clinically isolated syndrome (CIS), which is suggestive of multiple sclerosis (MS), by combining volume-based morphometry (VBM) and tract-based spatial statistics (TBSS). This prospective HIPAA-compliant study was approved by the institutional review board. Written informed consent was obtained from all participants. In this study, 34 consecutive patients (21 women, 13 men; mean age, 31.7 years +/- 7.7 [standard deviation]) who presented with CIS were recruited. The magnetic resonance (MR) examination included dual-echo fast spin-echo, three-dimensional T1, and diffusion-tensor imaging. Sixteen matched healthy volunteers served as control subjects. T2 lesion volumes were assessed with a semiautomatic technique. VBM and TBSS were used for the GM and WM analyses, respectively, to compare regional GM volumes and fractional anisotropy (FA) values in the two groups. TBSS analysis revealed a pattern of diffuse FA reductions in patients with CIS at the cluster level (P < .05). Regions of decreased FA involved most of the WM pathways, including the corticospinal tracts, corpus callosum, and superior and inferior longitudinal fasciculi. There were no significant differences between the two groups in terms of global GM, WM, or cerebrospinal fluid volume or in terms of regional GM volume. Diffuse WM damage not accompanied by any change in GM or WM volume is observed in patients with CIS. This suggests that WM involvement plays a relevant role in the early phases of MS. Subsequently detected GM damage may be secondary to WM alterations.

  16. Characterisation of cell death inducing Phytophthora capsici CRN effectors suggests diverse activities in the host nucleus

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    Remco eStam

    2013-10-01

    Full Text Available Plant-Microbe interactions are complex associations that feature recognition of Pathogen Associated Molecular Patterns by the plant immune system and dampening of subsequent responses by pathogen encoded secreted effectors. With large effector repertoires now identified in a range of sequenced microbial genomes, much attention centres on understanding their roles in immunity or disease. These studies not only allow identification of pathogen virulence factors and strategies, they also provide an important molecular toolset suited for studying immunity in plants. The Phytophthora intracellular effector repertoire encodes a large class of proteins that translocate into host cells and exclusively target the host nucleus. Recent functional studies have implicated the CRN protein family as an important class of diverse effectors that target distinct subnuclear compartments and modify host cell signalling. Here, we characterised three necrosis inducing CRNs and show that there are differences in the levels of cell death. We show that only expression of CRN20_624 has an additive effect on PAMP induced cell death but not AVR3a induced ETI. Given their distinctive phenotypes, we assessed localisation of each CRN with a set of nuclear markers and found clear differences in CRN subnuclear distribution patterns. These assays also revealed that expression of CRN83_152 leads to a distinct change in nuclear chromatin organisation, suggesting a distinct series of events that leads to cell death upon over-expression. Taken together, our results suggest diverse functions carried by CRN C-termini, which can be exploited to identify novel processes that take place in the host nucleus and are required for immunity or susceptibility.

  17. Altered gene synchrony suggests a combined hormone-mediated dysregulated state in major depression.

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    Chris Gaiteri

    2010-04-01

    Full Text Available Coordinated gene transcript levels across tissues (denoted "gene synchrony" reflect converging influences of genetic, biochemical and environmental factors; hence they are informative of the biological state of an individual. So could brain gene synchrony also integrate the multiple factors engaged in neuropsychiatric disorders and reveal underlying pathologies? Using bootstrapped Pearson correlation for transcript levels for the same genes across distinct brain areas, we report robust gene transcript synchrony between the amygdala and cingulate cortex in the human postmortem brain of normal control subjects (n = 14; Control/Permutated data, p<0.000001. Coordinated expression was confirmed across distinct prefrontal cortex areas in a separate cohort (n = 19 subjects and affected different gene sets, potentially reflecting regional network- and function-dependent transcriptional programs. Genewise regional transcript coordination was independent of age-related changes and array technical parameters. Robust shifts in amygdala-cingulate gene synchrony were observed in subjects with major depressive disorder (MDD, denoted here "depression" (n = 14; MDD/Permutated data, p<0.000001, significantly affecting between 100 and 250 individual genes (10-30% false discovery rate. Biological networks and signal transduction pathways corresponding to the identified gene set suggested putative dysregulated functions for several hormone-type factors previously implicated in depression (insulin, interleukin-1, thyroid hormone, estradiol and glucocorticoids; p<0.01 for association with depression-related networks. In summary, we showed that coordinated gene expression across brain areas may represent a novel molecular probe for brain structure/function that is sensitive to disease condition, suggesting the presence of a distinct and integrated hormone-mediated corticolimbic homeostatic, although maladaptive and pathological, state in major depression.

  18. Comparative Chromosome Painting and NOR Distribution Suggest a Complex Hybrid Origin of Triploid Lepidodactylus lugubris (Gekkonidae.

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    Vladimir A Trifonov

    Full Text Available Parthenogenesis, unisexuality and triploidy are interesting but poorly studied phenomena occurring in some reptile species. The mourning gecko (Lepidodactylus lugubris represents a complex of diploid and triploid parthenogenetic mostly all-female populations (males occur quite rarely widely distributed in coastal areas of the Indian and Pacific Oceans. Here, we study karyotypes of a male and two female L. lugubris (LLU triploid individuals (3n = 66 using comparative painting with Gekko japonicus, Hemidactylus turcicus and H. platyurus chromosome specific probes to visualize the homologous regions and to reveal genus specific rearrangements. Also, we applied a 28S ribosomal DNA probe and Ag-staining to detect nucleolus organizer regions (NORs. Our results suggest that the karyotype of L. lugubris underwent a chromosome fission and a fusion after its divergence from a common ancestor of the Gekko-Hemidactylus group. The NORs were found to be located on one out of three homologs on each of LLU8, LLU15 and LLU18, thus further confirming a hybrid origin of triploid individuals. It seems that three different bisexual populations might have contributed to the origin of this triploid parthenogenetic population. We postulate that the heterozygosity in NOR localization is maintained in the triploid clone studied by the absence of recombination as described in whiptail lizards. The pattern of NOR localizations and homologous regions in males and females, as well as the absence of other detectable karyotypic differences, suggest that males arise spontaneously in all female populations and do not arise from independent hybridizations with different species.

  19. Cloaked similarity between HIV-1 and SARS-CoV suggests an anti-SARS strategy

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    Kliger Yossef

    2003-09-01

    Full Text Available Abstract Background Severe acute respiratory syndrome (SARS is a febrile respiratory illness. The disease has been etiologically linked to a novel coronavirus that has been named the SARS-associated coronavirus (SARS-CoV, whose genome was recently sequenced. Since it is a member of the Coronaviridae, its spike protein (S2 is believed to play a central role in viral entry by facilitating fusion between the viral and host cell membranes. The protein responsible for viral-induced membrane fusion of HIV-1 (gp41 differs in length, and has no sequence homology with S2. Results Sequence analysis reveals that the two viral proteins share the sequence motifs that construct their active conformation. These include (1 an N-terminal leucine/isoleucine zipper-like sequence, and (2 a C-terminal heptad repeat located upstream of (3 an aromatic residue-rich region juxtaposed to the (4 transmembrane segment. Conclusions This study points to a similar mode of action for the two viral proteins, suggesting that anti-viral strategy that targets the viral-induced membrane fusion step can be adopted from HIV-1 to SARS-CoV. Recently the FDA approved Enfuvirtide, a synthetic peptide corresponding to the C-terminal heptad repeat of HIV-1 gp41, as an anti-AIDS agent. Enfuvirtide and C34, another anti HIV-1 peptide, exert their inhibitory activity by binding to a leucine/isoleucine zipper-like sequence in gp41, thus inhibiting a conformational change of gp41 required for its activation. We suggest that peptides corresponding to the C-terminal heptad repeat of the S2 protein may serve as inhibitors for SARS-CoV entry.

  20. Facial cellulitis revealing choreo-acanthocytosis: a case report.

    Science.gov (United States)

    Samia, Younes; Yosra, Cherif; Foued, Bellazreg; Mouna, Aissi; Olfa, Berriche; Jihed, Souissi; Hammadi, Braham; Mahbouba, Frih-Ayed; Amel, Letaief; Habib, Sfar Mohamed

    2014-01-01

    We report a 62 year-old-man with facial cellulitis revealing choreo-acanthocytosis (ChAc). He showed chorea that started 20 years ago. The orofacial dyskinisia with tongue and cheek biting resulted in facial cellulitis. The peripheral blood smear revealed acanthocytosis of 25%. The overall of chorea, orofacial dyskinetic disorder, peripheral neuropathy, disturbed behavior, acanthocytosis and the atrophy of caudate nuclei was suggestive of a diagnosis of ChAc. To our knowledge no similar cases of facial cellulitis revealing choreo-acanthocytosis (ChAc) were found in a review of the literature.

  1. Brain Abscess and Keratoacanthoma Suggestive of Hyper IgE Syndrome

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    Soheyla Alyasin

    2015-01-01

    Full Text Available Hyper immunoglobulin-E (IgE syndrome is an autosomal immune deficiency disease. It is characterized by an increase in IgE and eosinophil count with both T-cell and B-cell malfunction. Here, we report an 8-year-old boy whose disease started with an unusual skin manifestation. When 6 months old he developed generalized red, nontender nodules and pathologic report of the skin lesion was unremarkable (inflammatory. Then he developed a painless, cold abscess. At the age of 4 years, he developed a seronegative polyarticular arthritis. Another skin biopsy was taken which was in favor of Keratoacanthoma. Laboratory workup for immune deficiency showed high eosinophil count and high level of immunoglobulin-E, due to some diagnostic criteria (NIH sores: 41 in 9-year-olds, he was suggestive of hyper IgE syndrome. At the age of 8, the patient developed an abscess in the left inguinal region. While in hospital, the patient developed generalized tonic colonic convulsion and fever. Brain computed tomography scan revealed an abscess in the right frontal lobe. Subsequently magnetic resonance imaging (MRI of the brain indicated expansion of the existing abscess to contralateral frontal lobe (left side. After evacuating the abscesses and administrating intravenous antibiotic, the patient’s condition improved dramatically and fever stopped.

  2. Nuclear genomes distinguish cryptic species suggested by their DNA barcodes and ecology.

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    Janzen, Daniel H; Burns, John M; Cong, Qian; Hallwachs, Winnie; Dapkey, Tanya; Manjunath, Ramya; Hajibabaei, Mehrdad; Hebert, Paul D N; Grishin, Nick V

    2017-08-01

    DNA sequencing brings another dimension to exploration of biodiversity, and large-scale mitochondrial DNA cytochrome oxidase I barcoding has exposed many potential new cryptic species. Here, we add complete nuclear genome sequencing to DNA barcoding, ecological distribution, natural history, and subtleties of adult color pattern and size to show that a widespread neotropical skipper butterfly known as Udranomia kikkawai (Weeks) comprises three different species in Costa Rica. Full-length barcodes obtained from all three century-old Venezuelan syntypes of U. kikkawai show that it is a rainforest species occurring from Costa Rica to Brazil. The two new species are Udranomia sallydaleyae Burns, a dry forest denizen occurring from Costa Rica to Mexico, and Udranomia tomdaleyi Burns, which occupies the junction between the rainforest and dry forest and currently is known only from Costa Rica. Whereas the three species are cryptic, differing but slightly in appearance, their complete nuclear genomes totaling 15 million aligned positions reveal significant differences consistent with their 0.00065-Mbp (million base pair) mitochondrial barcodes and their ecological diversification. DNA barcoding of tropical insects reared by a massive inventory suggests that the presence of cryptic species is a widespread phenomenon and that further studies will substantially increase current estimates of insect species richness.

  3. A Meta-Analysis Suggests Different Neural Correlates for Implicit and Explicit Learning.

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    Loonis, Roman F; Brincat, Scott L; Antzoulatos, Evan G; Miller, Earl K

    2017-10-11

    A meta-analysis of non-human primates performing three different tasks (Object-Match, Category-Match, and Category-Saccade associations) revealed signatures of explicit and implicit learning. Performance improved equally following correct and error trials in the Match (explicit) tasks, but it improved more after correct trials in the Saccade (implicit) task, a signature of explicit versus implicit learning. Likewise, error-related negativity, a marker for error processing, was greater in the Match (explicit) tasks. All tasks showed an increase in alpha/beta (10-30 Hz) synchrony after correct choices. However, only the implicit task showed an increase in theta (3-7 Hz) synchrony after correct choices that decreased with learning. In contrast, in the explicit tasks, alpha/beta synchrony increased with learning and decreased thereafter. Our results suggest that explicit versus implicit learning engages different neural mechanisms that rely on different patterns of oscillatory synchrony. Copyright © 2017 Elsevier Inc. All rights reserved.

  4. Linear sign in cystic brain lesions ≥5 mm: A suggestive feature of perivascular space.

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    Sung, Jinkyeong; Jang, Jinhee; Choi, Hyun Seok; Jung, So-Lyung; Ahn, Kook-Jin; Kim, Bum-Soo

    2017-11-01

    To determine the prevalence of a linear sign within enlarged perivascular space (EPVS) and chronic lacunar infarction (CLI) ≥ 5 mm on T2-weighted imaging (T2WI) and time-of-flight (TOF) magnetic resonance angiography (MRA), and to evaluate the diagnostic value of the linear signs for EPVS over CLI. This study included 101 patients with cystic lesions ≥ 5 mm on brain MRI including TOF MRA. After classification of cystic lesions into EPVS or CLI, two readers assessed linear signs on T2WI and TOF MRA. We compared the prevalence and the diagnostic performance of linear signs. Among 46 EPVS and 51 CLI, 84 lesions (86.6%) were in basal ganglia. The prevalence of T2 and TOF linear signs was significantly higher in the EPVS than in the CLI (P linear signs showed high sensitivity (> 80%). TOF linear sign showed significantly higher specificity (100%) and accuracy (92.8% and 90.7%) than T2 linear sign (P linear signs were more frequently observed in EPVS than CLI. They showed high sensitivity in differentiation of them, especially for basal ganglia. TOF sign showed higher specificity and accuracy than T2 sign. • Linear sign is a suggestive feature of EPVS. • Time-of-flight magnetic resonance angiography can reveal the lenticulostriate artery within perivascular spaces. • Linear sign helps differentiation of EPVS and CLI, especially in basal ganglia.

  5. Elevated [11C]-D-deprenyl uptake in chronic Whiplash Associated Disorder suggests persistent musculoskeletal inflammation.

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    Clas Linnman

    Full Text Available There are few diagnostic tools for chronic musculoskeletal pain as structural imaging methods seldom reveal pathological alterations. This is especially true for Whiplash Associated Disorder, for which physical signs of persistent injuries to the neck have yet to be established. Here, we sought to visualize inflammatory processes in the neck region by means Positron Emission Tomography using the tracer (11C-D-deprenyl, a potential marker for inflammation. Twenty-two patients with enduring pain after a rear impact car accident (Whiplash Associated Disorder grade II and 14 healthy controls were investigated. Patients displayed significantly elevated tracer uptake in the neck, particularly in regions around the spineous process of the second cervical vertebra. This suggests that whiplash patients have signs of local persistent peripheral tissue inflammation, which may potentially serve as a diagnostic biomarker. The present investigation demonstrates that painful processes in the periphery can be objectively visualized and quantified with PET and that (11C-D-deprenyl is a promising tracer for these purposes.

  6. Genotype heterogeneity of Mycobacterium tuberculosis within geospatial hotspots suggests foci of imported infection in Sydney, Australia.

    Science.gov (United States)

    Gurjav, Ulziijargal; Jelfs, Peter; Hill-Cawthorne, Grant A; Marais, Ben J; Sintchenko, Vitali

    2016-06-01

    In recent years the State of New South Wales (NSW), Australia, has maintained a low tuberculosis incidence rate with little evidence of local transmission. Nearly 90% of notified tuberculosis cases occurred in people born in tuberculosis-endemic countries. We analyzed geographic, epidemiological and genotypic data of all culture-confirmed tuberculosis cases to identify the bacterial and demographic determinants of tuberculosis hotspot areas in NSW. Standard 24-loci mycobacterium interspersed repetitive unit-variable number tandem repeat (MIRU-24) typing was performed on all isolates recovered between 2009 and 2013. In total 1692/1841 (91.9%) cases with confirmed Mycobacterium tuberculosis infection had complete MIRU-24 and demographic data and were included in the study. Despite some year-to-year variability, spatio-temporal analysis identified four tuberculosis hotspots. The incidence rate and the relative risk of tuberculosis in these hotspots were 2- to 10-fold and 4- to 8-fold higher than the state average, respectively. MIRU-24 profiles of M. tuberculosis isolates associated with these hotspots revealed high levels of heterogeneity. This suggests that these spatio-temporal hotspots, within this low incidence setting, can represent areas of predominantly imported infection rather than clusters of cases due to local transmission. These findings provide important epidemiological insight and demonstrate the value of combining tuberculosis genotyping and spatiotemporal data to guide better-targeted public health interventions. Copyright © 2015 Elsevier B.V. All rights reserved.

  7. GPS suggests low physical activity in urban Hispanic school children: a proof of concept study.

    Science.gov (United States)

    Carrel, Aaron L; Sledge, Jeffrey S; Ventura, Stephen J; Eickhoff, Jens C; Allen, David B

    2014-01-01

    Urban environments can increase risk for development of obesity, insulin resistance (IR), and type 2 diabetes mellitus (T2DM) by limiting physical activity. This study examined, in a cohort of urban Hispanic youth, the relationship between daily physical activity (PA) measured by GPS, insulin resistance and cardiovascular fitness. Hispanic middle school children (n = 141) were assessed for body mass index (BMI), IR (homeostasis model [HOMA-IR]), cardiovascular fitness (progressive aerobic cardiovascular endurance run [PACER]). PA was measured (GPS-PA) and energy expenditure estimated (GPS-EE) utilizing a global positioning mapping device worn for up to 7 days. Students (mean age 12.7 ± 1.2 years, 52% female) spent 98% of waking time in sedentary activities, 1.7% in moderate intensity PA, and 0.3% in vigorous intensity. GPS analysis revealed extremely low amounts of physical movement during waking hours. The degree of low PA confounded correlation analysis with PACER or HOMA-IR. Levels of moderate and vigorous intensity PA, measured by GPS, were extremely low in these urban Hispanic youth, possibly contributing to high rates of obesity and IR. Physical movement patterns suggest barriers to PA in play options near home, transportation to school, and in school recess time. GPS technology can objectively and accurately evaluate initiatives designed to reduce obesity and its morbidities by increasing PA.

  8. Tissue accumulation of microplastics in mice and biomarker responses suggest widespread health risks of exposure

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    Deng, Yongfeng; Zhang, Yan; Lemos, Bernardo; Ren, Hongqiang

    2017-04-01

    Microplastics (MPs) are a significant environmental health issue and increasingly greater source of concern. MPs have been detected in oceans, rivers, sediments, sewages, soil and even table salts. MPs exposure on marine organisms and humans has been documented, but information about the toxicity of MPs in mammal is limited. Here we used fluorescent and pristine polystyrene microplastics (PS-MPs) particles with two diameters (5 μm and 20 μm) to investigate the tissue distribution, accumulation, and tissue-specific health risk of MPs in mice. Results indicated that MPs accumulated in liver, kidney and gut, with a tissue-accumulation kinetics and distribution pattern that was strongly depended on the MPs particle size. In addition, analyses of multiple biochemical biomarkers and metabolomic profiles suggested that MPs exposure induced disturbance of energy and lipid metabolism as well as oxidative stress. Interestingly, blood biomarkers of neurotoxicity were also altered. Our results uncovered the distribution and accumulation of MPs across mice tissues and revealed significant alteration in several biomarkers that indicate potential toxicity from MPs exposure. Collectively, our data provided new evidence for the adverse consequences of MPs.

  9. Novel analysis of oceanic surface water metagenomes suggests importance of polyphosphate metabolism in oligotrophic environments.

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    Ben Temperton

    Full Text Available Polyphosphate is a ubiquitous linear homopolymer of phosphate residues linked by high-energy bonds similar to those found in ATP. It has been associated with many processes including pathogenicity, DNA uptake and multiple stress responses across all domains. Bacteria have also been shown to use polyphosphate as a way to store phosphate when transferred from phosphate-limited to phosphate-rich media--a process exploited in wastewater treatment and other environmental contaminant remediation. Despite this, there has, to date, been little research into the role of polyphosphate in the survival of marine bacterioplankton in oligotrophic environments. The three main proteins involved in polyphosphate metabolism, Ppk1, Ppk2 and Ppx are multi-domain and have differential inter-domain and inter-gene conservation, making unbiased analysis of relative abundance in metagenomic datasets difficult. This paper describes the development of a novel Isofunctional Homolog Annotation Tool (IHAT to detect homologs of genes with a broad range of conservation without bias of traditional expect-value cutoffs. IHAT analysis of the Global Ocean Sampling (GOS dataset revealed that genes associated with polyphosphate metabolism are more abundant in environments where available phosphate is limited, suggesting an important role for polyphosphate metabolism in marine oligotrophs.

  10. Suggested alternative starch utilization system from the human gut bacterium Bacteroides thetaiotaomicron.

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    Chaudet, Marcia M; Rose, David R

    2016-06-01

    The human digestive system is host to a highly populated ecosystem of bacterial species that significantly contributes to our assimilation of dietary carbohydrates. Bacteroides thetaiotaomicron is a member of this ecosystem, and participates largely in the role of the gut microbiome by breaking down dietary complex carbohydrates. This process of acquiring glycans from the colon lumen is predicted to rely on the mechanisms of proteins that are part of a classified system known as polysaccharide utilization loci (PUL). These loci are responsible for binding substrates at the cell outer membrane, internalizing them, and then hydrolyzing them within the periplasm into simple sugars. Here we report our investigation into specific components of a PUL, and suggest an alternative starch utilization system in B. thetaiotaomicron. Our analysis of an outer membrane binding protein, a SusD homolog, highlights its contribution to this PUL by acquiring starch-based sugars from the colon lumen. Through our structural characterization of two Family GH31 α-glucosidases, we reveal the flexibility of this bacterium with respect to utilizing a range of starch-derived glycans with an emphasis on branched substrates. With these results we demonstrate the predicted function of a gene locus that is capable of contributing to starch hydrolysis in the human colon.

  11. Multilocus Sequence Typing of Borrelia burgdorferi Suggests Existence of Lineages with Differential Pathogenic Properties in Humans

    Science.gov (United States)

    Hanincova, Klara; Mukherjee, Priyanka; Ogden, Nicholas H.; Margos, Gabriele; Wormser, Gary P.; Reed, Kurt D.; Meece, Jennifer K.; Vandermause, Mary F.; Schwartz, Ira

    2013-01-01

    The clinical manifestations of Lyme disease, caused by Borrelia burgdorferi, vary considerably in different patients, possibly due to infection by strains with varying pathogenicity. Both rRNA intergenic spacer and ospC typing methods have proven to be useful tools for categorizing B. burgdorferi strains that vary in their tendency to disseminate in humans. Neither method, however, is suitable for inferring intraspecific relationships among strains that are important for understanding the evolution of pathogenicity and the geographic spread of disease. In this study, multilocus sequence typing (MLST) was employed to investigate the population structure of B. burgdorferi recovered from human Lyme disease patients. A total of 146 clinical isolates from patients in New York and Wisconsin were divided into 53 sequence types (STs). A goeBURST analysis, that also included previously published STs from the northeastern and upper Midwestern US and adjoining areas of Canada, identified 11 major and 3 minor clonal complexes, as well as 14 singletons. The data revealed that patients from New York and Wisconsin were infected with two distinct, but genetically and phylogenetically closely related, populations of B. burgdorferi. Importantly, the data suggest the existence of B. burgdorferi lineages with differential capabilities for dissemination in humans. Interestingly, the data also indicate that MLST is better able to predict the outcome of localized or disseminated infection than is ospC typing. PMID:24069170

  12. Eighteenth-Century Observations of Algol: The First Suggestion of an Exoplanet?

    Science.gov (United States)

    French, Linda M.

    2017-10-01

    In November of 1782, 18-year old John Goodricke of York, England, was amazed to observe the star Algol (Beta Persei) dim by more than one magnitude and then return to full brightness over a period of seven hours. Goodricke and his mentor, Edward Pigott, speculated that the dimming could only have been caused by a "dark body" passing in front of Algol. Over the succeeding months, the two were able to refine the period between what we now know to be eclipses to 2.87 days. They would determine the periods of other variable stars, including the first two Cepheid variables known. Yet in their lifetime, their suggestion that Algol's variation was due to an eclipse was not accepted. Most astronomers believed the variations were due to spots on the surface of a single star. Only a century later, with the advent of astronomical spectroscopy, was Algol's true nature revealed. Goodricke and Pigott's work is one of the first studies of stellar variation; their methods and occasional pitfalls are ones to which modern astronomers can relate.

  13. Methamphetamine administration targets multiple immune subsets and induces phenotypic alterations suggestive of immunosuppression.

    Directory of Open Access Journals (Sweden)

    Robert Harms

    Full Text Available Methamphetamine (Meth is a widely abused stimulant and its users are at increased risk for multiple infectious diseases. To determine the impact of meth on the immune system, we utilized a murine model that simulates the process of meth consumption in a typical addict. Our phenotypic analysis of leukocytes from this dose escalation model revealed that meth affected key immune subsets. Meth administration led to a decrease in abundance of natural killer (NK cells and the remaining NK cells possessed a phenotype suggesting reduced responsiveness. Dendritic cells (DCs and Gr-1(high monocytes/macrophages were also decreased in abundance while Gr-1(low monocytes/macrophages appear to show signs of perturbation. CD4 and CD8 T cell subsets were affected by methamphetamine, both showing a reduction in antigen-experienced subsets. CD4 T cells also exhibited signs of activation, with increased expression of CD150 on CD226-expressing cells and an expansion of KLRG1(+, FoxP3(- cells. These results exhibit that meth has the ability to disrupt immune homeostasis and impact key subsets of leukocytes which may leave users more vulnerable to pathogens.

  14. Communication Games Reveal Preparation Contextuality

    Science.gov (United States)

    Hameedi, Alley; Tavakoli, Armin; Marques, Breno; Bourennane, Mohamed

    2017-12-01

    A communication game consists of distributed parties attempting to jointly complete a task with restricted communication. Such games are useful tools for studying limitations of physical theories. A theory exhibits preparation contextuality whenever its predictions cannot be explained by a preparation noncontextual model. Here, we show that communication games performed in operational theories reveal the preparation contextuality of that theory. For statistics obtained in a particular family of communication games, we show a direct correspondence with correlations in spacelike separated events obeying the no-signaling principle. Using this, we prove that all mixed quantum states of any finite dimension are preparation contextual. We report on an experimental realization of a communication game involving three-level quantum systems from which we observe a strong violation of the constraints of preparation noncontextuality.

  15. Plan competitions reveal entrepreneurial talent

    Energy Technology Data Exchange (ETDEWEB)

    Madison, Alison L.

    2011-05-15

    Monthly economic diversity column for Tri-City Herald business section. Excerpt below: There’s something to be said for gaining valuable real-world experience in a structured, nurturing environment. Take for instance learning to scuba dive in the comfort of my resort pool rather than immediately hanging out with sharks while I figure out little things like oxygen tanks and avoiding underwater panic attacks. Likewise, graduate students are getting some excellent, supportive real-world training through university business plan competitions. These competitions are places where smart minds, new technologies, months of preparation and coaching, and some healthy pre-presentation jitters collide to reveal not only solid new business ideas, but also some promising entrepreneurial talent. In fact, professionals from around our region descend upon college campuses every spring to judge these events, which help to bridge the gap between academics and the real technology and business-driven economy.

  16. Revealing Non-Covalent Interactions

    Science.gov (United States)

    Johnson, Erin R.; Keinan, Shahar; Mori-Sánchez, Paula; Contreras-García, Julia; Cohen, Aron J.; Yang, Weitao

    2010-01-01

    Molecular structure does not easily identify the intricate non-covalent interactions that govern many areas of biology and chemistry, including design of new materials and drugs. We develop an approach to detect non-covalent interactions in real space, based on the electron density and its derivatives. Our approach reveals underlying chemistry that compliments the covalent structure. It provides a rich representation of van der Waals interactions, hydrogen bonds, and steric repulsion in small molecules, molecular complexes, and solids. Most importantly, the method, requiring only knowledge of the atomic coordinates, is efficient and applicable to large systems, such as proteins or DNA. Across these applications, a view of non-bonded interactions emerges as continuous surfaces rather than close contacts between atom pairs, offering rich insight into the design of new and improved ligands. PMID:20394428

  17. Genetic architecture of cold tolerance in rice (Oryza sativa) determined through high resolution genome-wide analysis

    Science.gov (United States)

    Shakiba, Ehsan; Edwards, Jeremy D.; Jodari, Farman; Duke, Sara E.; Baldo, Angela M.; Korniliev, Pavel; McCouch, Susan R.; Eizenga, Georgia C.

    2017-01-01

    Cold temperature is an important abiotic stress which negatively affects morphological development and seed production in rice (Oryza sativa L.). At the seedling stage, cold stress causes poor germination, seedling injury and poor stand establishment; and at the reproductive stage cold decreases seed yield. The Rice Diversity Panel 1 (RDP1) is a global collection of over 400 O. sativa accessions representing the five major subpopulations from the INDICA and JAPONICA varietal groups, with a genotypic dataset consisting of 700,000 SNP markers. The objectives of this study were to evaluate the RDP1 accessions for the complex, quantitatively inherited cold tolerance traits at the germination and reproductive stages, and to conduct genome-wide association (GWA) mapping to identify SNPs and candidate genes associated with cold stress at these stages. GWA mapping of the germination index (calculated as percent germination in cold divided by warm treatment) revealed 42 quantitative trait loci (QTLs) associated with cold tolerance at the seedling stage, including 18 in the panel as a whole, seven in temperate japonica, six in tropical japonica, 14 in JAPONICA, and nine in INDICA, with five shared across all subpopulations. Twenty-two of these QTLs co-localized with 32 previously reported cold tolerance QTLs. GWA mapping of cold tolerance at the reproductive stage detected 29 QTLs, including seven associated with percent sterility, ten with seed weight per panicle, 14 with seed weight per plant and one region overlapping for two traits. Fifteen co-localized with previously reported QTLs for cold tolerance or yield components. Candidate gene ontology searches revealed these QTLs were associated with significant enrichment for genes related to with lipid metabolism, response to stimuli, response to biotic stimuli (suggesting cross-talk between biotic and abiotic stresses), and oxygen binding. Overall the JAPONICA accessions were more tolerant to cold stress than INDICA

  18. Genetic architecture of cold tolerance in rice (Oryza sativa) determined through high resolution genome-wide analysis.

    Science.gov (United States)

    Shakiba, Ehsan; Edwards, Jeremy D; Jodari, Farman; Duke, Sara E; Baldo, Angela M; Korniliev, Pavel; McCouch, Susan R; Eizenga, Georgia C

    2017-01-01

    Cold temperature is an important abiotic stress which negatively affects morphological development and seed production in rice (Oryza sativa L.). At the seedling stage, cold stress causes poor germination, seedling injury and poor stand establishment; and at the reproductive stage cold decreases seed yield. The Rice Diversity Panel 1 (RDP1) is a global collection of over 400 O. sativa accessions representing the five major subpopulations from the INDICA and JAPONICA varietal groups, with a genotypic dataset consisting of 700,000 SNP markers. The objectives of this study were to evaluate the RDP1 accessions for the complex, quantitatively inherited cold tolerance traits at the germination and reproductive stages, and to conduct genome-wide association (GWA) mapping to identify SNPs and candidate genes associated with cold stress at these stages. GWA mapping of the germination index (calculated as percent germination in cold divided by warm treatment) revealed 42 quantitative trait loci (QTLs) associated with cold tolerance at the seedling stage, including 18 in the panel as a whole, seven in temperate japonica, six in tropical japonica, 14 in JAPONICA, and nine in INDICA, with five shared across all subpopulations. Twenty-two of these QTLs co-localized with 32 previously reported cold tolerance QTLs. GWA mapping of cold tolerance at the reproductive stage detected 29 QTLs, including seven associated with percent sterility, ten with seed weight per panicle, 14 with seed weight per plant and one region overlapping for two traits. Fifteen co-localized with previously reported QTLs for cold tolerance or yield components. Candidate gene ontology searches revealed these QTLs were associated with significant enrichment for genes related to with lipid metabolism, response to stimuli, response to biotic stimuli (suggesting cross-talk between biotic and abiotic stresses), and oxygen binding. Overall the JAPONICA accessions were more tolerant to cold stress than INDICA

  19. Genetic architecture of cold tolerance in rice (Oryza sativa determined through high resolution genome-wide analysis.

    Directory of Open Access Journals (Sweden)

    Ehsan Shakiba

    Full Text Available Cold temperature is an important abiotic stress which negatively affects morphological development and seed production in rice (Oryza sativa L.. At the seedling stage, cold stress causes poor germination, seedling injury and poor stand establishment; and at the reproductive stage cold decreases seed yield. The Rice Diversity Panel 1 (RDP1 is a global collection of over 400 O. sativa accessions representing the five major subpopulations from the INDICA and JAPONICA varietal groups, with a genotypic dataset consisting of 700,000 SNP markers. The objectives of this study were to evaluate the RDP1 accessions for the complex, quantitatively inherited cold tolerance traits at the germination and reproductive stages, and to conduct genome-wide association (GWA mapping to identify SNPs and candidate genes associated with cold stress at these stages. GWA mapping of the germination index (calculated as percent germination in cold divided by warm treatment revealed 42 quantitative trait loci (QTLs associated with cold tolerance at the seedling stage, including 18 in the panel as a whole, seven in temperate japonica, six in tropical japonica, 14 in JAPONICA, and nine in INDICA, with five shared across all subpopulations. Twenty-two of these QTLs co-localized with 32 previously reported cold tolerance QTLs. GWA mapping of cold tolerance at the reproductive stage detected 29 QTLs, including seven associated with percent sterility, ten with seed weight per panicle, 14 with seed weight per plant and one region overlapping for two traits. Fifteen co-localized with previously reported QTLs for cold tolerance or yield components. Candidate gene ontology searches revealed these QTLs were associated with significant enrichment for genes related to with lipid metabolism, response to stimuli, response to biotic stimuli (suggesting cross-talk between biotic and abiotic stresses, and oxygen binding. Overall the JAPONICA accessions were more tolerant to cold stress than

  20. Do author-suggested reviewers rate submissions more favorably than editor-suggested reviewers? A study on atmospheric chemistry and physics.

    Directory of Open Access Journals (Sweden)

    Lutz Bornmann

    Full Text Available BACKGROUND: Ratings in journal peer review can be affected by sources of bias. The bias variable investigated here was the information on whether authors had suggested a possible reviewer for their manuscript, and whether the editor had taken up that suggestion or had chosen a reviewer that had not been suggested by the authors. Studies have shown that author-suggested reviewers rate manuscripts more favorably than editor-suggested reviewers do. METHODOLOGY/PRINCIPAL FINDINGS: Reviewers' ratings on three evaluation criteria and the reviewers' final publication recommendations were available for 552 manuscripts (in total 1145 reviews that were submitted to Atmospheric Chemistry and Physics, an interactive open access journal using public peer review (authors' and reviewers' comments are publicly exchanged. Public peer review is supposed to bring a new openness to the reviewing process that will enhance its objectivity. In the statistical analysis the quality of a manuscript was controlled for to prevent favorable reviewers' ratings from being attributable to quality instead of to the bias variable. CONCLUSIONS/SIGNIFICANCE: Our results agree with those from other studies that editor-suggested reviewers rated manuscripts between 30% and 42% less favorably than author-suggested reviewers. Against this backdrop journal editors should consider either doing without the use of author-suggested reviewers or, if they are used, bringing in more than one editor-suggested reviewer for the review process (so that the review by author-suggested reviewers can be put in perspective.