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Sample records for selected transcript levels

  1. Selection Shapes Transcriptional Logic and Regulatory Specialization in Genetic Networks.

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    Fogelmark, Karl; Peterson, Carsten; Troein, Carl

    2016-01-01

    Living organisms need to regulate their gene expression in response to environmental signals and internal cues. This is a computational task where genes act as logic gates that connect to form transcriptional networks, which are shaped at all scales by evolution. Large-scale mutations such as gene duplications and deletions add and remove network components, whereas smaller mutations alter the connections between them. Selection determines what mutations are accepted, but its importance for shaping the resulting networks has been debated. To investigate the effects of selection in the shaping of transcriptional networks, we derive transcriptional logic from a combinatorially powerful yet tractable model of the binding between DNA and transcription factors. By evolving the resulting networks based on their ability to function as either a simple decision system or a circadian clock, we obtain information on the regulation and logic rules encoded in functional transcriptional networks. Comparisons are made between networks evolved for different functions, as well as with structurally equivalent but non-functional (neutrally evolved) networks, and predictions are validated against the transcriptional network of E. coli. We find that the logic rules governing gene expression depend on the function performed by the network. Unlike the decision systems, the circadian clocks show strong cooperative binding and negative regulation, which achieves tight temporal control of gene expression. Furthermore, we find that transcription factors act preferentially as either activators or repressors, both when binding multiple sites for a single target gene and globally in the transcriptional networks. This separation into positive and negative regulators requires gene duplications, which highlights the interplay between mutation and selection in shaping the transcriptional networks.

  2. Transcriptional blockages in a cell-free system by sequence-selective DNA alkylating agents.

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    Ferguson, L R; Liu, A P; Denny, W A; Cullinane, C; Talarico, T; Phillips, D R

    2000-04-14

    There is considerable interest in DNA sequence-selective DNA-binding drugs as potential inhibitors of gene expression. Five compounds with distinctly different base pair specificities were compared in their effects on the formation and elongation of the transcription complex from the lac UV5 promoter in a cell-free system. All were tested at drug levels which killed 90% of cells in a clonogenic survival assay. Cisplatin, a selective alkylator at purine residues, inhibited transcription, decreasing the full-length transcript, and causing blockage at a number of GG or AG sequences, making it probable that intrastrand crosslinks are the blocking lesions. A cyclopropylindoline known to be an A-specific alkylator also inhibited transcription, with blocks at adenines. The aniline mustard chlorambucil, that targets primarily G but also A sequences, was also effective in blocking the formation of full-length transcripts. It produced transcription blocks either at, or one base prior to, AA or GG sequences, suggesting that intrastrand crosslinks could again be involved. The non-alkylating DNA minor groove binder Hoechst 33342 (a bisbenzimidazole) blocked formation of the full-length transcript, but without creating specific blockage sites. A bisbenzimidazole-linked aniline mustard analogue was a more effective transcription inhibitor than either chlorambucil or Hoechst 33342, with different blockage sites occurring immediately as compared with 2 h after incubation. The blockages were either immediately prior to AA or GG residues, or four to five base pairs prior to such sites, a pattern not predicted from in vitro DNA-binding studies. Minor groove DNA-binding ligands are of particular interest as inhibitors of gene expression, since they have the potential ability to bind selectively to long sequences of DNA. The results suggest that the bisbenzimidazole-linked mustard does cause alkylation and transcription blockage at novel DNA sites. in addition to sites characteristic of

  3. Characteristics of functional enrichment and gene expression level of human putative transcriptional target genes.

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    Osato, Naoki

    2018-01-19

    Transcriptional target genes show functional enrichment of genes. However, how many and how significantly transcriptional target genes include functional enrichments are still unclear. To address these issues, I predicted human transcriptional target genes using open chromatin regions, ChIP-seq data and DNA binding sequences of transcription factors in databases, and examined functional enrichment and gene expression level of putative transcriptional target genes. Gene Ontology annotations showed four times larger numbers of functional enrichments in putative transcriptional target genes than gene expression information alone, independent of transcriptional target genes. To compare the number of functional enrichments of putative transcriptional target genes between cells or search conditions, I normalized the number of functional enrichment by calculating its ratios in the total number of transcriptional target genes. With this analysis, native putative transcriptional target genes showed the largest normalized number of functional enrichments, compared with target genes including 5-60% of randomly selected genes. The normalized number of functional enrichments was changed according to the criteria of enhancer-promoter interactions such as distance from transcriptional start sites and orientation of CTCF-binding sites. Forward-reverse orientation of CTCF-binding sites showed significantly higher normalized number of functional enrichments than the other orientations. Journal papers showed that the top five frequent functional enrichments were related to the cellular functions in the three cell types. The median expression level of transcriptional target genes changed according to the criteria of enhancer-promoter assignments (i.e. interactions) and was correlated with the changes of the normalized number of functional enrichments of transcriptional target genes. Human putative transcriptional target genes showed significant functional enrichments. Functional

  4. Signatures of DNA target selectivity by ETS transcription factors.

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    Poon, Gregory M K; Kim, Hye Mi

    2017-05-27

    The ETS family of transcription factors is a functionally heterogeneous group of gene regulators that share a structurally conserved, eponymous DNA-binding domain. DNA target specificity derives from combinatorial interactions with other proteins as well as intrinsic heterogeneity among ETS domains. Emerging evidence suggests molecular hydration as a fundamental feature that defines the intrinsic heterogeneity in DNA target selection and susceptibility to epigenetic DNA modification. This perspective invokes novel hypotheses in the regulation of ETS proteins in physiologic osmotic stress, their pioneering potential in heterochromatin, and the effects of passive and pharmacologic DNA demethylation on ETS regulation.

  5. Does selection against transcriptional interference shape retroelement-free regions in mammalian genomes?

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    Tobias Mourier

    Full Text Available BACKGROUND: Eukaryotic genomes are scattered with retroelements that proliferate through retrotransposition. Although retroelements make up around 40 percent of the human genome, large regions are found to be completely devoid of retroelements. This has been hypothesised to be a result of genomic regions being intolerant to insertions of retroelements. The inadvertent transcriptional activity of retroelements may affect neighbouring genes, which in turn could be detrimental to an organism. We speculate that such retroelement transcription, or transcriptional interference, is a contributing factor in generating and maintaining retroelement-free regions in the human genome. METHODOLOGY/PRINCIPAL FINDINGS: Based on the known transcriptional properties of retroelements, we expect long interspersed elements (LINEs to be able to display a high degree of transcriptional interference. In contrast, we expect short interspersed elements (SINEs to display very low levels of transcriptional interference. We find that genomic regions devoid of long interspersed elements (LINEs are enriched for protein-coding genes, but that this is not the case for regions devoid of short interspersed elements (SINEs. This is expected if genes are subject to selection against transcriptional interference. We do not find microRNAs to be associated with genomic regions devoid of either SINEs or LINEs. We further observe an increased relative activity of genes overlapping LINE-free regions during early embryogenesis, where activity of LINEs has been identified previously. CONCLUSIONS/SIGNIFICANCE: Our observations are consistent with the notion that selection against transcriptional interference has contributed to the maintenance and/or generation of retroelement-free regions in the human genome.

  6. Level of ubiquitinated histone H2B in chromatin is coupled to ongoing transcription

    International Nuclear Information System (INIS)

    Davie, J.R.; Murphy, L.C.

    1990-01-01

    The relationship between transcription and ubiquitination of the histones was investigated. Previous studies have shown that ubiquitinated (u) histone H2B and, to a lesser extend, mono- and polyubiquitinated histone H2A are enriched in transcriptionally active gene-enriched chromatin fractions. Here, the authors show that treatment of T-47D-5 human breast cancer cells with actinomycin D or 5,6-dichloro-1-β-D-ribofuranosylbenzimidazole, inhibitors of heterogeneous nuclear RNA synthesis, selectively reduced the level of uH2B, but not uH2A, uH2A.Z, or polyubiquitinated H2A, in chromatin. Treatment of the cells with low levels of actinomycin D slightly reduced the level of uH2B, suggesting that inhibition of ribosomal RNA synthesis does not have a profound effect on the level of uH2B in chromatin. These results demonstrate that maintenance of the levels of uH2B in chromatin is dependent upon ongoing transcription, particularly the synthesis of hnRNA. Thus, histone H2B would be ubiquitinated when the nucleosome was opened during transcription. Ubiquitination of histone H2B may impede nucleosome refolding, facilitating subsequent rounds of transcription

  7. Calcium regulates caveolin-1 expression at the transcriptional level

    International Nuclear Information System (INIS)

    Yang, Xiao-Yan; Huang, Cheng-Cheng; Kan, Qi-Ming; Li, Yan; Liu, Dan; Zhang, Xue-Cheng; Sato, Toshinori; Yamagata, Sadako; Yamagata, Tatsuya

    2012-01-01

    Highlights: ► Caveolin-1 expression is regulated by calcium signaling at the transcriptional level. ► An inhibitor of or siRNA to L-type calcium channel suppressed caveolin-1 expression. ► Cyclosporine A or an NFAT inhibitor markedly reduced caveolin-1 expression. ► Caveolin-1 regulation by calcium signaling is observed in several mouse cell lines. -- Abstract: Caveolin-1, an indispensable component of caveolae serving as a transformation suppressor protein, is highly expressed in poorly metastatic mouse osteosarcoma FBJ-S1 cells while highly metastatic FBJ-LL cells express low levels of caveolin-1. Calcium concentration is higher in FBJ-S1 cells than in FBJ-LL cells; therefore, we investigated the possibility that calcium signaling positively regulates caveolin-1 in mouse FBJ-S1 cells. When cells were treated with the calcium channel blocker nifedipine, cyclosporin A (a calcineurin inhibitor), or INCA-6 (a nuclear factor of activated T-cells [NFAT] inhibitor), caveolin-1 expression at the mRNA and protein levels decreased. RNA silencing of voltage-dependent L-type calcium channel subunit alpha-1C resulted in suppression of caveolin-1 expression. This novel caveolin-1 regulation pathway was also identified in mouse NIH 3T3 cells and Lewis lung carcinoma cells. These results indicate that caveolin-1 is positively regulated at the transcriptional level through a novel calcium signaling pathway mediated by L-type calcium channel/Ca 2+ /calcineurin/NFAT.

  8. DNA template dependent accuracy variation of nucleotide selection in transcription.

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    Harriet Mellenius

    Full Text Available It has been commonly assumed that the effect of erroneous transcription of DNA genes into messenger RNAs on peptide sequence errors are masked by much more frequent errors of mRNA translation to protein. We present a theoretical model of transcriptional accuracy. It uses experimentally estimated standard free energies of double-stranded DNA and RNA/DNA hybrids and predicts a DNA template dependent transcriptional accuracy variation spanning several orders of magnitude. The model also identifies high-error as well a high-accuracy transcription motifs. The source of the large accuracy span is the context dependent variation of the stacking free energy of pairs of correct and incorrect base pairs in the ever moving transcription bubble. Our model predictions have direct experimental support from recent single molecule based identifications of transcriptional errors in the C. elegans transcriptome. Our conclusions challenge the general view that amino acid substitution errors in proteins are mainly caused by translational errors. It suggests instead that transcriptional error hotspots are the dominating source of peptide sequence errors in some DNA template contexts, while mRNA translation is the major cause of protein errors in other contexts.

  9. Genomic and chromatin signals underlying transcription start-site selection

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    Valen, Eivind; Sandelin, Albin Gustav

    2011-01-01

    A central question in cellular biology is how the cell regulates transcription and discerns when and where to initiate it. Locating transcription start sites (TSSs), the signals that specify them, and ultimately elucidating the mechanisms of regulated initiation has therefore been a recurrent theme....... In recent years substantial progress has been made towards this goal, spurred by the possibility of applying genome-wide, sequencing-based analysis. We now have a large collection of high-resolution datasets identifying locations of TSSs, protein-DNA interactions, and chromatin features over whole genomes...

  10. Selective activation of human heat shock gene transcription by nitrosourea antitumor drugs mediated by isocyanate-induced damage and activation of heat shock transcription factor.

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    Kroes, R A; Abravaya, K; Seidenfeld, J; Morimoto, R I

    1991-01-01

    Treatment of cultured human tumor cells with the chloroethylnitrosourea antitumor drug 1,3-bis(2-chloroethyl)-1-nitrosourea (BCNU) selectively induces transcription and protein synthesis of a subset of the human heat shock or stress-induced genes (HSP90 and HSP70) with little effect on other stress genes or on expression of the c-fos, c-myc, or beta-actin genes. The active component of BCNU and related compounds appears to be the isocyanate moiety that causes carbamoylation of proteins and nucleic acids. Transcriptional activation of the human HSP70 gene by BCNU is dependent on the heat shock element and correlates with the level of heat shock transcription factor and its binding to the heat shock element in vivo. Unlike activation by heat or heavy metals, BCNU-mediated activation is strongly dependent upon new protein synthesis. This suggests that BCNU-induced, isocyanate-mediated damage to newly synthesized protein(s) may be responsible for activation of the heat shock transcription factor and increased transcription of the HSP90 and HSP70 genes. Images PMID:2052560

  11. Pairwise comparisons of ten porcine tissues identify differential transcriptional regulation at the gene, isoform, promoter and transcription start site level

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    Farajzadeh, Leila; Hornshøj, Henrik; Momeni, Jamal; Thomsen, Bo; Larsen, Knud; Hedegaard, Jakob; Bendixen, Christian; Madsen, Lone Bruhn

    2013-01-01

    Highlights: •Transcriptome sequencing yielded 223 mill porcine RNA-seq reads, and 59,000 transcribed locations. •Establishment of unique transcription profiles for ten porcine tissues including four brain tissues. •Comparison of transcription profiles at gene, isoform, promoter and transcription start site level. •Highlights a high level of regulation of neuro-related genes at both gene, isoform, and TSS level. •Our results emphasize the pig as a valuable animal model with respect to human biological issues. -- Abstract: The transcriptome is the absolute set of transcripts in a tissue or cell at the time of sampling. In this study RNA-Seq is employed to enable the differential analysis of the transcriptome profile for ten porcine tissues in order to evaluate differences between the tissues at the gene and isoform expression level, together with an analysis of variation in transcription start sites, promoter usage, and splicing. Totally, 223 million RNA fragments were sequenced leading to the identification of 59,930 transcribed gene locations and 290,936 transcript variants using Cufflinks with similarity to approximately 13,899 annotated human genes. Pairwise analysis of tissues for differential expression at the gene level showed that the smallest differences were between tissues originating from the porcine brain. Interestingly, the relative level of differential expression at the isoform level did generally not vary between tissue contrasts. Furthermore, analysis of differential promoter usage between tissues, revealed a proportionally higher variation between cerebellum (CBE) versus frontal cortex and cerebellum versus hypothalamus (HYP) than in the remaining comparisons. In addition, the comparison of differential transcription start sites showed that the number of these sites is generally increased in comparisons including hypothalamus in contrast to other pairwise assessments. A comprehensive analysis of one of the tissue contrasts, i

  12. Pairwise comparisons of ten porcine tissues identify differential transcriptional regulation at the gene, isoform, promoter and transcription start site level

    DEFF Research Database (Denmark)

    Farajzadeh, Leila; Hornshøj, Henrik; Momeni, Jamal

    2013-01-01

    , isoform, and transcription start site (TSS), and promoter level showed that several of the genes differed at all four levels. Interestingly, these genes were mainly annotated to the "electron transport chain" and neuronal differentiation, emphasizing that "tissue important" genes are regulated at several...

  13. Allele frequencies of variants in ultra conserved elements identify selective pressure on transcription factor binding.

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    Toomas Silla

    Full Text Available Ultra-conserved genes or elements (UCGs/UCEs in the human genome are extreme examples of conservation. We characterized natural variations in 2884 UCEs and UCGs in two distinct populations; Singaporean Chinese (n = 280 and Italian (n = 501 by using a pooled sample, targeted capture, sequencing approach. We identify, with high confidence, in these regions the abundance of rare SNVs (MAF5% are more often found in relatively less-conserved nucleotides within UCEs, compared to rare variants. Moreover, prevalent variants are less likely to overlap transcription factor binding site. Using SNPfold we found no significant influence of RNA secondary structure on UCE conservation. All together, these results suggest UCEs are not under selective pressure as a stretch of DNA but are under differential evolutionary pressure on the single nucleotide level.

  14. Allele frequencies of variants in ultra conserved elements identify selective pressure on transcription factor binding.

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    Silla, Toomas; Kepp, Katrin; Tai, E Shyong; Goh, Liang; Davila, Sonia; Catela Ivkovic, Tina; Calin, George A; Voorhoeve, P Mathijs

    2014-01-01

    Ultra-conserved genes or elements (UCGs/UCEs) in the human genome are extreme examples of conservation. We characterized natural variations in 2884 UCEs and UCGs in two distinct populations; Singaporean Chinese (n = 280) and Italian (n = 501) by using a pooled sample, targeted capture, sequencing approach. We identify, with high confidence, in these regions the abundance of rare SNVs (MAFpower for association studies. By combining our data with 1000 Genome Project data, we show in three independent datasets that prevalent UCE variants (MAF>5%) are more often found in relatively less-conserved nucleotides within UCEs, compared to rare variants. Moreover, prevalent variants are less likely to overlap transcription factor binding site. Using SNPfold we found no significant influence of RNA secondary structure on UCE conservation. All together, these results suggest UCEs are not under selective pressure as a stretch of DNA but are under differential evolutionary pressure on the single nucleotide level.

  15. Screening for impact of popular herbs improving mental abilities on the transcriptional level of brain transporters

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    Mrozikiewicz Przemyslaw M.

    2014-06-01

    Full Text Available There are a number of compounds that can modify the activity of ABC (ATP-binding cassette and SLC (solute carrier transporters in the blood-brain barrier (BBB. The aim of this study was to investigate the effect of natural and synthetic substances on the expression level of genes encoding transporters present in the BBB (mdr1a, mdr1b, mrp1, mrp2, oatp1a4, oatp1a5 and oatp1c1. Our results showed that verapamil caused the greatest reduction in the mRNA level while other synthetic (piracetam, phenobarbital and natural (codeine, cyclosporine A, quercetin substances showed a selective inhibitory effect. Further, the extract from the roots of Panax ginseng C. A. Meyer exhibited a decrease of transcription against selected transporters whereas the extract from Ginkgo biloba L. leaves resulted in an increase of the expression level of tested genes, except for mrp2. Extract from the aerial parts of Hypericum perforatum L. was the only one to cause an increased mRNA level for mdr1 and oatp1c1. These findings suggest that herbs can play an important role in overcoming the BBB and multidrug resistance to pharmacotherapy of brain cancer and mental disorders, based on the activity of selected drug-metabolizing enzymes and transporters located in the BBB

  16. YY1 binding association with sex-biased transcription revealed through X-linked transcript levels and allelic binding analyses.

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    Chen, Chih-Yu; Shi, Wenqiang; Balaton, Bradley P; Matthews, Allison M; Li, Yifeng; Arenillas, David J; Mathelier, Anthony; Itoh, Masayoshi; Kawaji, Hideya; Lassmann, Timo; Hayashizaki, Yoshihide; Carninci, Piero; Forrest, Alistair R R; Brown, Carolyn J; Wasserman, Wyeth W

    2016-11-18

    Sex differences in susceptibility and progression have been reported in numerous diseases. Female cells have two copies of the X chromosome with X-chromosome inactivation imparting mono-allelic gene silencing for dosage compensation. However, a subset of genes, named escapees, escape silencing and are transcribed bi-allelically resulting in sexual dimorphism. Here we conducted in silico analyses of the sexes using human datasets to gain perspectives into such regulation. We identified transcription start sites of escapees (escTSSs) based on higher transcription levels in female cells using FANTOM5 CAGE data. Significant over-representations of YY1 transcription factor binding motif and ChIP-seq peaks around escTSSs highlighted its positive association with escapees. Furthermore, YY1 occupancy is significantly biased towards the inactive X (Xi) at long non-coding RNA loci that are frequent contacts of Xi-specific superloops. Our study suggests a role for YY1 in transcriptional activity on Xi in general through sequence-specific binding, and its involvement at superloop anchors.

  17. Changes at transcriptional level during liver regeneration in the rat

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    Subba Rao, M.N.; Netrawali, M.S.; Pradhan, D.S.; Sreenivasan, A.

    1976-01-01

    A great upheaval in RNA synthetic pattern is known to occur during the early periods after partial hepatectomy. Such changes are being studied in regenerating rat liver with a view to understanding regulatory mechanisms of eukaryotic transcription. Follwoing partial hepatectomy, RNA synthesis is rat liver showed graded increase during 4 to 18 hours. At these time intervals, a significant enhancement could be discerned both in template efficiency of chromatin and in RNA polymerase activity in this tissue. Further examination revealed that the activity of RNA polymerase II (extra-nucleolar enzyme) stimulated to a much greater extent as compared to that of RNA polymerase I (nucleolar enzyme). Partial hepatectomy also resulted in significant alterations in turnovers of chromosomal acidic proteins in liver. 32 P-orthophosphate injected intraperitoneally was used in these studies. (author)

  18. Effect of low dose radiation on POMC transcription level in mouse hypothalamus and immune organs

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    Wan Hong; Liu Shuzheng

    1998-01-01

    Objective: To disclose the changes in mRNA transcription level of POMC in the hypothalamus and immune organs after low dose radiation. Method: In situ hybridization was used to examine the changes of POMC mRNA transcription level in mouse hypothalamus and immune organs following whole body irradiation (WBI) with 75 mGy X-rays. Results: There was a basal expression of POMC mRNA in both the hypothalamus and immune organs. POMC mRNA-positive neutron were located in the arcuate nucleus of hypothalamus. WBI with 75 mGy X-rays could significantly down-regulate the POMC transcription level that was remarkable within 1h and remained low in the observation period of 12h. POMC transcription level in mouse immune organs increased with time within 8h after irradiation and then began to decrease but still remained at a higher than normal level. The changes of POMC transcription level were more marked in the spleen than in other immune organs. Conclusion: These findings suggest that the immediate decrease of POMC transcription level in the hypothalamus might be the direct cause of the down-regulation of the hypothalamus-pituitary-adrenocortical axis after WBI with 75 mGy X-rays, accompanied with an increase in POMC transcription in immune organs

  19. Quantitative expression analysis of selected transcription factors in pavement, basal and trichome cells of mature leaves from Arabidopsis thaliana.

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    Schliep, Martin; Ebert, Berit; Simon-Rosin, Ulrike; Zoeller, Daniela; Fisahn, Joachim

    2010-05-01

    Gene expression levels of several transcription factors from Arabidopsis thaliana that were described previously to be involved in leaf development and trichome formation were analysed in trichome, basal and pavement cells of mature leaves. Single cell samples of these three cells types were collected by glass micro-capillaries. Real-time reverse transcription (RT)-PCR was used to analyse expression patterns of the following transcription factors: MYB23, MYB55, AtHB1, FILAMENTOUS FLOWER (FIL)/YABBY1 (YAB1), TRIPTYCHON (TRY) and CAPRICE (CPC). A difference in the expression patterns of TRY and CPC was revealed. Contrary to the CPC expression pattern, no transcripts of TRY could be detected in pavement cells. FIL/YAB1 was exclusively expressed in trichome cells. AtHB1 was highly expressed throughout all three cell types. MYB55 was higher expressed in basal cells than in trichome and pavement cells. MYB23 showed a pattern of low expression in pavement cells, medium in basal cells and high expression in trichomes. Expression patterns obtained by single cell sampling and real-time RT-PCR were compared to promoter GUS fusions of the selected transcription factors. Therefore, we regenerated two transgenic Arabidopsis lines that expressed the GUS reporter gene under control of the promoters of MYB55 and YAB1. In conclusion, despite their function in leaf morphogenesis, all six transcription factors were detected in mature leaves. Furthermore, single cell sampling and promoter GUS staining patterns demonstrated the predominant presence of MYB55 in basal cells as compared to pavement cells and trichomes.

  20. Does selection against transcriptional interference shape retroelement-free regions in mammalian genomes?

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    Mourier, Tobias; Willerslev, Eske

    2008-01-01

    in generating and maintaining retroelement-free regions in the human genome. METHODOLOGY/PRINCIPAL FINDINGS: Based on the known transcriptional properties of retroelements, we expect long interspersed elements (LINEs) to be able to display a high degree of transcriptional interference. In contrast, we expect......BACKGROUND: Eukaryotic genomes are scattered with retroelements that proliferate through retrotransposition. Although retroelements make up around 40 percent of the human genome, large regions are found to be completely devoid of retroelements. This has been hypothesised to be a result of genomic...... activity of LINEs has been identified previously. CONCLUSIONS/SIGNIFICANCE: Our observations are consistent with the notion that selection against transcriptional interference has contributed to the maintenance and/or generation of retroelement-free regions in the human genome....

  1. Sex differences in depressive, anxious behaviors and hippocampal transcript levels in a genetic rat model.

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    Mehta, N S; Wang, L; Redei, E E

    2013-10-01

    Major depressive disorder (MDD) is a common, debilitating illness with high prevalence of comorbid anxiety. The incidence of depression and of comorbid anxiety is much higher in women than in men. These gender biases appear after puberty and their etiology is mostly unknown. Selective breeding of the Wistar Kyoto (WKY) rat strain, an accepted model of adult and adolescent depression, resulted in two fully inbred substrains. Adult WKY more immobile (WMI) rats of both sexes consistently show increased depression-like behavior in the forced swim test when compared with the control WKY less immobile (WLI) strain. In contrast, here we show that while adult female WMIs and WLIs both display high anxiety-like behaviors, only WLI males, but not WMI males, show this behavior. Moreover, the behavioral profile of WMI males is consistent from early adolescence to adulthood, but the high depression- and anxiety-like behaviors of the female WMIs appear only in adulthood. These sex-specific behavioral patterns are paralleled by marked sex differences in hippocampal gene expression differences established by genome-wide transcriptional analyses of 13th generation WMIs and WLIs. Moreover, sex- and age-specific differences in transcript levels of selected genes are present in the hippocampus of the current, fully inbred WMIs and WLIs. Thus, the contribution of specific genes and/or the influence of the gonadal hormonal environment to depression- and anxiety-like behaviors may differ between male and female WMIs, resulting in their distinct behavioral and transcriptomic profiles despite shared sequences of the somatic chromosomes. © 2013 John Wiley & Sons Ltd and International Behavioural and Neural Genetics Society.

  2. Transcript-level annotation of Affymetrix probesets improves the interpretation of gene expression data

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    Tu Kang

    2007-06-01

    Full Text Available Abstract Background The wide use of Affymetrix microarray in broadened fields of biological research has made the probeset annotation an important issue. Standard Affymetrix probeset annotation is at gene level, i.e. a probeset is precisely linked to a gene, and probeset intensity is interpreted as gene expression. The increased knowledge that one gene may have multiple transcript variants clearly brings up the necessity of updating this gene-level annotation to a refined transcript-level. Results Through performing rigorous alignments of the Affymetrix probe sequences against a comprehensive pool of currently available transcript sequences, and further linking the probesets to the International Protein Index, we generated transcript-level or protein-level annotation tables for two popular Affymetrix expression arrays, Mouse Genome 430A 2.0 Array and Human Genome U133A Array. Application of our new annotations in re-examining existing expression data sets shows increased expression consistency among synonymous probesets and strengthened expression correlation between interacting proteins. Conclusion By refining the standard Affymetrix annotation of microarray probesets from the gene level to the transcript level and protein level, one can achieve a more reliable interpretation of their experimental data, which may lead to discovery of more profound regulatory mechanism.

  3. The predictive nature of transcript expression levels on protein expression in adult human brain.

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    Bauernfeind, Amy L; Babbitt, Courtney C

    2017-04-24

    Next generation sequencing methods are the gold standard for evaluating expression of the transcriptome. When determining the biological implications of such studies, the assumption is often made that transcript expression levels correspond to protein levels in a meaningful way. However, the strength of the overall correlation between transcript and protein expression is inconsistent, particularly in brain samples. Following high-throughput transcriptomic (RNA-Seq) and proteomic (liquid chromatography coupled with tandem mass spectrometry) analyses of adult human brain samples, we compared the correlation in the expression of transcripts and proteins that support various biological processes, molecular functions, and that are located in different areas of the cell. Although most categories of transcripts have extremely weak predictive value for the expression of their associated proteins (R 2 values of < 10%), transcripts coding for protein kinases and membrane-associated proteins, including those that are part of receptors or ion transporters, are among those that are most predictive of downstream protein expression levels. The predictive value of transcript expression for corresponding proteins is variable in human brain samples, reflecting the complex regulation of protein expression. However, we found that transcriptomic analyses are appropriate for assessing the expression levels of certain classes of proteins, including those that modify proteins, such as kinases and phosphatases, regulate metabolic and synaptic activity, or are associated with a cellular membrane. These findings can be used to guide the interpretation of gene expression results from primate brain samples.

  4. Relaxed selection against accidental binding of transcription factors with conserved chromatin contexts.

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    Babbitt, G A

    2010-10-15

    The spurious (or nonfunctional) binding of transcription factors (TF) to the wrong locations on DNA presents a formidable challenge to genomes given the relatively low ceiling for sequence complexity within the short lengths of most binding motifs. The high potential for the occurrence of random motifs and subsequent nonfunctional binding of many transcription factors should theoretically lead to natural selection against the occurrence of spurious motif throughout the genome. However, because of the active role that chromatin can influence over eukaryotic gene regulation, it may also be expected that many supposed spurious binding sites could escape purifying selection if (A) they simply occur in regions of high nucleosome occupancy or (B) their surrounding chromatin was dynamically involved in their identity and function. We compared nucleosome occupancy and the presence/absence of functionally conserved chromatin context to the strength of selection against spurious binding of various TF binding motifs in Saccharomyces yeast. While we find no direct relationship with nucleosome occupancy, we find strong evidence that transcription factors spatially associated with evolutionarily conserved chromatin states are under relaxed selection against accidental binding. Transcription factors (with/without) a conserved chromatin context were found to occur on average, (87.7%/49.3%) of their expected frequencies. Functional binding motifs with conserved chromatin contexts were also significantly shorter in length and more often clustered. These results indicate a role of chromatin context dependency in relaxing selection against spurious binding in nearly half of all TF binding motifs throughout the yeast genome. 2010 Elsevier B.V. All rights reserved.

  5. Nucleotide Selectivity at a Preinsertion Checkpoint of T7 RNA Polymerase Transcription Elongation.

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    E, Chao; Duan, Baogen; Yu, Jin

    2017-04-20

    Nucleotide selection is crucial for transcription fidelity control, in particular, for viral T7 RNA polymerase (RNAP) lack of proofreading activity. It has been recognized that multiple kinetic checkpoints exist prior to full nucleotide incorporation. In this work, we implemented intensive atomistic molecular dynamics (MD) simulations to quantify how strong the nucleotide selection is at the initial checkpoint of an elongation cycle of T7 RNAP. The incoming nucleotides bind into a preinsertion site where a critical tyrosine residue locates nearby to assist the nucleotide selection. We calculated the relative binding free energy between a noncognate nucleotide and a cognate one at a preinsertion configuration via alchemical simulations, showing that a small selection free energy or the binding free energy difference (∼3 k B T) exists between the two nucleotides. Indeed, another preinsertion configuration favored by the noncognate nucleotides was identified, which appears to be off path for further nucleotide insertion and additionally assists the nucleotide selection. By chemical master equation (CME) approach, we show that the small selection free energy at the preinsertion site along with the off-path noncognate nucleotide filtering can help substantially to reduce the error rate and to maintain the elongation rate high in the T7 RNAP transcription.

  6. Portfolio Selection Using Level Crossing Analysis

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    Bolgorian, Meysam; Shirazi, A. H.; Jafari, G. R.

    Asset allocation is one of the most important and also challenging issues in finance. In this paper using level crossing analysis we introduce a new approach for portfolio selection. We introduce a portfolio index that is obtained based on minimizing the waiting time to receive known return and risk values. By the waiting time, we mean time that a special level is observed in average. The advantage of this approach is that the investors are able to set their goals based on gaining return and knowing the average waiting time and risk value at the same time. As an example we use our model for forming portfolio of stocks in Tehran Stock Exchange (TSE).

  7. Effect of low dose ionizing radiation on Bcl-2 transcription level of Peyer's patches in mouse

    International Nuclear Information System (INIS)

    Liu Jiamei; Chen Dong; Zheng Yongchen; Liu Shuzheng

    2001-01-01

    Objective: To study the effect of whole body irradiation (WBI) with different doses of X-rays on apoptosis in cells of mouse Peyer's patches and its molecular mechanism. Methods: RT-PCR was used to detect the changes of Bcl-2 transcription level. Agarose electrophoresis and flow cytometry were used to detect the changes of DNA and apoptotic bodies in Peyer's patches after WBI with different doses of X-rays. Results: The apoptotic was increased and Bcl-2 transcription level was decreased in Peyer's patches after 2 Gy X-rays. The apoptotic rate was decreased and Bcl-2 transcription level was increased in Peyer's patches after 75 mGy X-rays. Conclusion: Bcl-2 participates in the regulation of radiation-induced apoptosis in Peyer's patches

  8. Glucose levels and genetic variants across transcriptional pathways: interaction effects with BMI

    NARCIS (Netherlands)

    Povel, C.M.; Feskens, E.J.M.; Imholz, S.; Blaak, E.E.; Boer, J.M.A.; Dollé, M.E.T.

    2010-01-01

    Objective: Much of the genetic variation in glucose levels remains to be discovered. Especially, research on gene–environment interactions is scarce. Overweight is one of the main risk factors for hyperglycemia. As transcriptional regulation is important for both weight maintenance and glucose

  9. Selection of reference genes for transcriptional analysis of edible tubers of potato (Solanum tuberosum L..

    Directory of Open Access Journals (Sweden)

    Roberta Fogliatto Mariot

    Full Text Available Potato (Solanum tuberosum yield has increased dramatically over the last 50 years and this has been achieved by a combination of improved agronomy and biotechnology efforts. Gene studies are taking place to improve new qualities and develop new cultivars. Reverse transcriptase quantitative polymerase chain reaction (RT-qPCR is a bench-marking analytical tool for gene expression analysis, but its accuracy is highly dependent on a reliable normalization strategy of an invariant reference genes. For this reason, the goal of this work was to select and validate reference genes for transcriptional analysis of edible tubers of potato. To do so, RT-qPCR primers were designed for ten genes with relatively stable expression in potato tubers as observed in RNA-Seq experiments. Primers were designed across exon boundaries to avoid genomic DNA contamination. Differences were observed in the ranking of candidate genes identified by geNorm, NormFinder and BestKeeper algorithms. The ranks determined by geNorm and NormFinder were very similar and for all samples the most stable candidates were C2, exocyst complex component sec3 (SEC3 and ATCUL3/ATCUL3A/CUL3/CUL3A (CUL3A. According to BestKeeper, the importin alpha and ubiquitin-associated/ts-n genes were the most stable. Three genes were selected as reference genes for potato edible tubers in RT-qPCR studies. The first one, called C2, was selected in common by NormFinder and geNorm, the second one is SEC3, selected by NormFinder, and the third one is CUL3A, selected by geNorm. Appropriate reference genes identified in this work will help to improve the accuracy of gene expression quantification analyses by taking into account differences that may be observed in RNA quality or reverse transcription efficiency across the samples.

  10. Selection of reference genes for transcriptional analysis of edible tubers of potato (Solanum tuberosum L.).

    Science.gov (United States)

    Mariot, Roberta Fogliatto; de Oliveira, Luisa Abruzzi; Voorhuijzen, Marleen M; Staats, Martijn; Hutten, Ronald C B; Van Dijk, Jeroen P; Kok, Esther; Frazzon, Jeverson

    2015-01-01

    Potato (Solanum tuberosum) yield has increased dramatically over the last 50 years and this has been achieved by a combination of improved agronomy and biotechnology efforts. Gene studies are taking place to improve new qualities and develop new cultivars. Reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) is a bench-marking analytical tool for gene expression analysis, but its accuracy is highly dependent on a reliable normalization strategy of an invariant reference genes. For this reason, the goal of this work was to select and validate reference genes for transcriptional analysis of edible tubers of potato. To do so, RT-qPCR primers were designed for ten genes with relatively stable expression in potato tubers as observed in RNA-Seq experiments. Primers were designed across exon boundaries to avoid genomic DNA contamination. Differences were observed in the ranking of candidate genes identified by geNorm, NormFinder and BestKeeper algorithms. The ranks determined by geNorm and NormFinder were very similar and for all samples the most stable candidates were C2, exocyst complex component sec3 (SEC3) and ATCUL3/ATCUL3A/CUL3/CUL3A (CUL3A). According to BestKeeper, the importin alpha and ubiquitin-associated/ts-n genes were the most stable. Three genes were selected as reference genes for potato edible tubers in RT-qPCR studies. The first one, called C2, was selected in common by NormFinder and geNorm, the second one is SEC3, selected by NormFinder, and the third one is CUL3A, selected by geNorm. Appropriate reference genes identified in this work will help to improve the accuracy of gene expression quantification analyses by taking into account differences that may be observed in RNA quality or reverse transcription efficiency across the samples.

  11. A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing

    KAUST Repository

    Zhang, Runxuan

    2017-04-05

    Alternative splicing generates multiple transcript and protein isoforms from the same gene and thus is important in gene expression regulation. To date, RNA-sequencing (RNA-seq) is the standard method for quantifying changes in alternative splicing on a genome-wide scale. Understanding the current limitations of RNA-seq is crucial for reliable analysis and the lack of high quality, comprehensive transcriptomes for most species, including model organisms such as Arabidopsis, is a major constraint in accurate quantification of transcript isoforms. To address this, we designed a novel pipeline with stringent filters and assembled a comprehensive Reference Transcript Dataset for Arabidopsis (AtRTD2) containing 82,190 non-redundant transcripts from 34 212 genes. Extensive experimental validation showed that AtRTD2 and its modified version, AtRTD2-QUASI, for use in Quantification of Alternatively Spliced Isoforms, outperform other available transcriptomes in RNA-seq analysis. This strategy can be implemented in other species to build a pipeline for transcript-level expression and alternative splicing analyses.

  12. A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing

    KAUST Repository

    Zhang, Runxuan; Calixto, Cristiane  P.  G.; Marquez, Yamile; Venhuizen, Peter; Tzioutziou, Nikoleta A.; Guo, Wenbin; Spensley, Mark; Entizne, Juan Carlos; Lewandowska, Dominika; ten  Have, Sara; Frei  dit  Frey, Nicolas; Hirt, Heribert; James, Allan B.; Nimmo, Hugh G.; Barta, Andrea; Kalyna, Maria; Brown, John  W.  S.

    2017-01-01

    Alternative splicing generates multiple transcript and protein isoforms from the same gene and thus is important in gene expression regulation. To date, RNA-sequencing (RNA-seq) is the standard method for quantifying changes in alternative splicing on a genome-wide scale. Understanding the current limitations of RNA-seq is crucial for reliable analysis and the lack of high quality, comprehensive transcriptomes for most species, including model organisms such as Arabidopsis, is a major constraint in accurate quantification of transcript isoforms. To address this, we designed a novel pipeline with stringent filters and assembled a comprehensive Reference Transcript Dataset for Arabidopsis (AtRTD2) containing 82,190 non-redundant transcripts from 34 212 genes. Extensive experimental validation showed that AtRTD2 and its modified version, AtRTD2-QUASI, for use in Quantification of Alternatively Spliced Isoforms, outperform other available transcriptomes in RNA-seq analysis. This strategy can be implemented in other species to build a pipeline for transcript-level expression and alternative splicing analyses.

  13. Biological effects of tolerable level chronic boron intake on transcription factors.

    Science.gov (United States)

    Orenay Boyacioglu, Seda; Korkmaz, Mehmet; Kahraman, Erkan; Yildirim, Hatice; Bora, Selin; Ataman, Osman Yavuz

    2017-01-01

    The mechanism of boron effect on human transcription and translation has not been fully understood. In the current study it was aimed to reveal the role of boron on the expression of certain transcription factors that play key roles in many cellular pathways on human subjects chronically exposed to low amounts of boron. The boron concentrations in drinking water samples were 1.57±0.06mg/l for boron group while the corresponding value for the control group was 0.016±0.002mg/l. RNA isolation was performed using PAX gene RNA kit on the blood samples from the subjects. The RNA was then reverse transcribed into cDNA and analyzed using the Human Transcription Factors RT 2 Profiler™ PCR Arrays. While the boron amount in urine was detected as 3.56±1.47mg/day in the boron group, it was 0.72±0.30mg/day in the control group. Daily boron intake of the boron and control groups were calculated to be 6.98±3.39 and 1.18±0.41mg/day, respectively. The expression levels of the transcription factor genes were compared between the boron and control groups and no statistically significant difference was detected (P>0.05). The data suggest that boron intake at 6.98±3.39mg/day, which is the dose at which beneficial effects might be seen, does not result in toxicity at molecular level since the expression levels of transcription factors are not changed. Although boron intake over this level will seem to increase RNA synthesis, further examination of the topic is needed using new molecular epidemiological data. Copyright © 2016 Elsevier GmbH. All rights reserved.

  14. Rearing Water Treatment Induces Microbial Selection Influencing the Microbiota and Pathogen Associated Transcripts of Cod (Gadus morhua Larvae

    Directory of Open Access Journals (Sweden)

    Ragnhild I. Vestrum

    2018-05-01

    Full Text Available We have previously shown that K-selection and microbial stability in the rearing water increases survival and growth of Atlantic cod (Gadus morhua larvae, and that recirculating aquaculture systems (RAS are compatible with this. Here, we have assessed how water treatment influenced the larval microbiota and host responses at the gene expression level. Cod larvae were reared with two different rearing water systems: a RAS and a flow-through system (FTS. The water microbiota was examined using a 16S rDNA PCR/DGGE strategy. RNA extracted from larvae at 8, 13, and 17 days post hatching was used for microbiota and microarray gene expression analysis. Bacterial cDNA was synthesized and used for 16S rRNA amplicon 454 pyrosequencing of larval microbiota. Both water and larval microbiota differed significantly between the systems, and the larval microbiota appeared to become more dissimilar between systems with time. In total 4 phyla were identified for all larvae: Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. The most profound difference in larval microbiota was a high abundance of Arcobacter (Epsilonproteobacteria in FTS larvae (34 ± 9% of total reads. Arcobacter includes several species that are known pathogens for humans and animals. Cod larval transcriptome responses were investigated using an oligonucleotide gene expression microarray covering approximately 24,000 genes. Interestingly, FTS larvae transcriptional profiles revealed an overrepresentation of upregulated transcripts associated with responses to pathogens and infections, such as c1ql3-like, pglyrp-2-like and zg16, compared to RAS larvae. In conclusion, distinct water treatment systems induced differences in the larval microbiota. FTS larvae showed up-regulation of transcripts associated with responses to microbial stress. These results are consistent with the hypothesis that RAS promotes K-selection and microbial stability by maintaining a microbial load close to the

  15. Glucocorticoids selectively inhibit the transcription of the interleukin 1β gene and decrease the stability of interleukin 1β mRNA

    International Nuclear Information System (INIS)

    Lee, S.W.; Tsou, A.P.; Chan, H.; Thomas, J.; Petrie, K.; Eugui, E.M.; Allison, A.C.

    1988-01-01

    Transcription of the interleukin 1β (IL-1β) gene was studied by mRNA hybridization with a cDNA probe in the human promonocytic cell line U-937. Phorbol ester and lipopolysaccharide increased the steady-state level of Il-1β mRNA. Glucocorticoids markedly decreased IL-1β mRNA levels by two mechanisms. Transcription of the IL-1 gene was inhibited, as shown by in vitro transcription assays with nuclei isolated from glucocorticoid-treated cells. Moreover, kinetic analyses and pulse-labeling of mRNAs showed that glucocorticoids selectively decrease the stability of IL-1β mRNA, without affecting the stability of β-actin and FOS mRNAs. Inhibition of the formation and effects IL-1 is a mechanism by which glucocorticoids can exert antiinflammatory and immunosuppressive effects

  16. The Complex Transcriptional Response of Acaryochloris marina to Different Oxygen Levels

    Directory of Open Access Journals (Sweden)

    Miguel A. Hernández-Prieto

    2017-02-01

    Full Text Available Ancient oxygenic photosynthetic prokaryotes produced oxygen as a waste product, but existed for a long time under an oxygen-free (anoxic atmosphere, before an oxic atmosphere emerged. The change in oxygen levels in the atmosphere influenced the chemistry and structure of many enzymes that contained prosthetic groups that were inactivated by oxygen. In the genome of Acaryochloris marina, multiple gene copies exist for proteins that are normally encoded by a single gene copy in other cyanobacteria. Using high throughput RNA sequencing to profile transcriptome responses from cells grown under microoxic and hyperoxic conditions, we detected 8446 transcripts out of the 8462 annotated genes in the Cyanobase database. Two-thirds of the 50 most abundant transcripts are key proteins in photosynthesis. Microoxic conditions negatively affected the levels of expression of genes encoding photosynthetic complexes, with the exception of some subunits. In addition to the known regulation of the multiple copies of psbA, we detected a similar transcriptional pattern for psbJ and psbU, which might play a key role in the altered components of photosystem II. Furthermore, regulation of genes encoding proteins important for reactive oxygen species-scavenging is discussed at genome level, including, for the first time, specific small RNAs having possible regulatory roles under varying oxygen levels.

  17. The Complex Transcriptional Response of Acaryochloris marina to Different Oxygen Levels

    Science.gov (United States)

    Hernández-Prieto, Miguel A.; Lin, Yuankui; Chen, Min

    2016-01-01

    Ancient oxygenic photosynthetic prokaryotes produced oxygen as a waste product, but existed for a long time under an oxygen-free (anoxic) atmosphere, before an oxic atmosphere emerged. The change in oxygen levels in the atmosphere influenced the chemistry and structure of many enzymes that contained prosthetic groups that were inactivated by oxygen. In the genome of Acaryochloris marina, multiple gene copies exist for proteins that are normally encoded by a single gene copy in other cyanobacteria. Using high throughput RNA sequencing to profile transcriptome responses from cells grown under microoxic and hyperoxic conditions, we detected 8446 transcripts out of the 8462 annotated genes in the Cyanobase database. Two-thirds of the 50 most abundant transcripts are key proteins in photosynthesis. Microoxic conditions negatively affected the levels of expression of genes encoding photosynthetic complexes, with the exception of some subunits. In addition to the known regulation of the multiple copies of psbA, we detected a similar transcriptional pattern for psbJ and psbU, which might play a key role in the altered components of photosystem II. Furthermore, regulation of genes encoding proteins important for reactive oxygen species-scavenging is discussed at genome level, including, for the first time, specific small RNAs having possible regulatory roles under varying oxygen levels. PMID:27974439

  18. Ultraviolet-B effects on transcript levels for photosynthetic genes are not mediated through carbohydrate metabolism

    International Nuclear Information System (INIS)

    Mackerness, S.A.H.; Surplus, S.L.; Jordan, B.R.; Thomas, B.

    1997-01-01

    The relationship between UV-B-induced changes in gene expression and carbohydrate levels in pea seedlings has been investigated. The effect of supplementary UV-B radiation on the transcript abundance for two photosynthetic genes, photosynthesis, respiration and the levels of carbohydrates was determined in fully expanded leaves of 17-d-old pea seedlings under high (HL: 350 μmol m −2 s −1 ) and low (LL: 150 μmol m −2 s 1 ) light. Supplementary UV-B caused down regulation of the photosynthetic genes in green leaves under LL and to a lesser extent under HL. In contrast to previous studies, UV-B radiation resulted in a decrease in glucose levels rather than an increase under LL. Sucrose and starch levels were not affected until longer exposure. Effects of UV-B on carbohydrate levels were, however, minimal under HL. The effects on transcript levels were most marked under LL and therefore could not be attributed to elevated carbohydrate levels. Comparison of UV-B effects on carbohydrates in source (leaf) and sink (green buds) organs indicated that changes in carbohydrates in response to UV-B are probably indirect and arise from effects of UV-B on photosynthesis in source organs. (author)

  19. Nucleolin is regulated both at the level of transcription and translation

    International Nuclear Information System (INIS)

    Bicknell, Katrina; Brooks, Gavin; Kaiser, Pete; Chen Hongying; Dove, Brian K.; Hiscox, Julian A.

    2005-01-01

    Nucleolin is a multi-functional protein that is located to the nucleolus. In tissue culture cells, the stability of nucleolin is related to the proliferation status of the cell. During development, rat cardiomyocytes proliferate actively with increases in the mass of the heart being due to both hyperplasia and hypertrophy. The timing of this shift in the phenotype of the myocyte from one capable of undergoing hyperplasia to one that can grow only by hypertrophy occurs within 4 days of post-natal development. Thus, cardiomyocytes are an ideal model system in which to study the regulation of nucleolin during growth in vivo. Using Western blot and quantitative RT-PCR (TaqMan) we found that the amount of nucleolin is regulated both at the level of transcription and translation during the development of the cardiomyocyte. However, in cells which had exited the cell cycle and were subsequently given a hypertrophic stimulus, nucleolin was regulated post-transcriptionally

  20. Transcriptional feedback regulation of YUCCA genes in response to auxin levels in Arabidopsis.

    Science.gov (United States)

    Suzuki, Masashi; Yamazaki, Chiaki; Mitsui, Marie; Kakei, Yusuke; Mitani, Yuka; Nakamura, Ayako; Ishii, Takahiro; Soeno, Kazuo; Shimada, Yukihisa

    2015-08-01

    The IPyA pathway, the major auxin biosynthesis pathway, is transcriptionally regulated through a negative feedback mechanism in response to active auxin levels. The phytohormone auxin plays an important role in plant growth and development, and levels of active free auxin are determined by biosynthesis, conjugation, and polar transport. Unlike conjugation and polar transport, little is known regarding the regulatory mechanism of auxin biosynthesis. We discovered that expression of genes encoding indole-3-pyruvic acid (IPyA) pathway enzymes is regulated by elevated or reduced active auxin levels. Expression levels of TAR2, YUC1, YUC2, YUC4, and YUC6 were downregulated in response to synthetic auxins [1-naphthaleneacetic acid (NAA) and 2,4-dichlorophenoxyacetic acid (2,4-D)] exogenously applied to Arabidopsis thaliana L. seedlings. Concomitantly, reduced levels of endogenous indole-3-acetic acid (IAA) were observed. Alternatively, expression of these YUCCA genes was upregulated by the auxin biosynthetic inhibitor kynurenine in Arabidopsis seedlings, accompanied by reduced IAA levels. These results indicate that expression of YUCCA genes is regulated by active auxin levels. Similar results were also observed in auxin-overproduction and auxin-deficient mutants. Exogenous application of IPyA to Arabidopsis seedlings preincubated with kynurenine increased endogenous IAA levels, while preincubation with 2,4-D reduced endogenous IAA levels compared to seedlings exposed only to IPyA. These results suggest that in vivo conversion of IPyA to IAA was enhanced under reduced auxin levels, while IPyA to IAA conversion was depressed in the presence of excess auxin. Based on these results, we propose that the IPyA pathway is transcriptionally regulated through a negative feedback mechanism in response to active auxin levels.

  1. ZFP226 is a novel artificial transcription factor for selective activation of tumor suppressor KIBRA.

    Science.gov (United States)

    Schelleckes, Katrin; Schmitz, Boris; Lenders, Malte; Mewes, Mirja; Brand, Stefan-Martin; Brand, Eva

    2018-03-09

    KIBRA has been suggested as a key regulator of the hippo pathway, regulating organ size, cell contact inhibition as well as tissue regeneration and tumorigenesis. Recently, alterations of KIBRA expression caused by promotor methylation have been reported for several types of cancer. Our current study aimed to design an artificial transcription factor capable of re-activating expression of the tumor suppressor KIBRA and the hippo pathway. We engineered a new gene named 'ZFP226' encoding for a ~23 kDa fusion protein. ZFP226 belongs to the Cys2-His2 zinc finger type and recognizes a nine base-pair DNA sequence 5'-GGC-GGC-GGC-3' in the KIBRA core promoter P1a. ZFP226 showed nuclear localization in human immortalized kidney epithelial cells and activated the KIBRA core promoter (p < 0.001) resulting in significantly increased KIBRA mRNA and protein levels (p < 0.001). Furthermore, ZFP226 led to activation of hippo signaling marked by elevated YAP and LATS phosphorylation. In Annexin V flow cytometry assays ZFP226 overexpression showed strong pro-apoptotic capacity on MCF-7 breast cancer cells (p < 0.01 early-, p < 0.001 late-apoptotic cells). We conclude that the artificial transcription factor ZFP226 can be used for target KIBRA and hippo pathway activation. This novel molecule may represent a molecular tool for the development of future applications in cancer treatment.

  2. Deciphering Mineral Homeostasis in Barley Seed Transfer Cells at Transcriptional Level.

    Directory of Open Access Journals (Sweden)

    Behrooz Darbani

    Full Text Available In addition to the micronutrient inadequacy of staple crops for optimal human nutrition, a global downtrend in crop-quality has emerged from intensive breeding for yield. This trend will be aggravated by elevated levels of the greenhouse gas carbon dioxide. Therefore, crop biofortification is inevitable to ensure a sustainable supply of minerals to the large part of human population who is dietary dependent on staple crops. This requires a thorough understanding of plant-mineral interactions due to the complexity of mineral homeostasis. Employing RNA sequencing, we here communicate transfer cell specific effects of excess iron and zinc during grain filling in our model crop plant barley. Responding to alterations in mineral contents, we found a long range of different genes and transcripts. Among them, it is worth to highlight the auxin and ethylene signaling factors Arfs, Abcbs, Cand1, Hps4, Hac1, Ecr1, and Ctr1, diurnal fluctuation components Sdg2, Imb1, Lip1, and PhyC, retroelements, sulfur homeostasis components Amp1, Hmt3, Eil3, and Vip1, mineral trafficking components Med16, Cnnm4, Aha2, Clpc1, and Pcbps, and vacuole organization factors Ymr155W, RabG3F, Vps4, and Cbl3. Our analysis introduces new interactors and signifies a broad spectrum of regulatory levels from chromatin remodeling to intracellular protein sorting mechanisms active in the plant mineral homeostasis. The results highlight the importance of storage proteins in metal ion toxicity-resistance and chelation. Interestingly, the protein sorting and recycling factors Exoc7, Cdc1, Sec23A, and Rab11A contributed to the response as well as the polar distributors of metal-transporters ensuring the directional flow of minerals. Alternative isoform switching was found important for plant adaptation and occurred among transcripts coding for identical proteins as well as transcripts coding for protein isoforms. We also identified differences in the alternative-isoform preference between

  3. Deciphering Mineral Homeostasis in Barley Seed Transfer Cells at Transcriptional Level.

    Science.gov (United States)

    Darbani, Behrooz; Noeparvar, Shahin; Borg, Søren

    2015-01-01

    In addition to the micronutrient inadequacy of staple crops for optimal human nutrition, a global downtrend in crop-quality has emerged from intensive breeding for yield. This trend will be aggravated by elevated levels of the greenhouse gas carbon dioxide. Therefore, crop biofortification is inevitable to ensure a sustainable supply of minerals to the large part of human population who is dietary dependent on staple crops. This requires a thorough understanding of plant-mineral interactions due to the complexity of mineral homeostasis. Employing RNA sequencing, we here communicate transfer cell specific effects of excess iron and zinc during grain filling in our model crop plant barley. Responding to alterations in mineral contents, we found a long range of different genes and transcripts. Among them, it is worth to highlight the auxin and ethylene signaling factors Arfs, Abcbs, Cand1, Hps4, Hac1, Ecr1, and Ctr1, diurnal fluctuation components Sdg2, Imb1, Lip1, and PhyC, retroelements, sulfur homeostasis components Amp1, Hmt3, Eil3, and Vip1, mineral trafficking components Med16, Cnnm4, Aha2, Clpc1, and Pcbps, and vacuole organization factors Ymr155W, RabG3F, Vps4, and Cbl3. Our analysis introduces new interactors and signifies a broad spectrum of regulatory levels from chromatin remodeling to intracellular protein sorting mechanisms active in the plant mineral homeostasis. The results highlight the importance of storage proteins in metal ion toxicity-resistance and chelation. Interestingly, the protein sorting and recycling factors Exoc7, Cdc1, Sec23A, and Rab11A contributed to the response as well as the polar distributors of metal-transporters ensuring the directional flow of minerals. Alternative isoform switching was found important for plant adaptation and occurred among transcripts coding for identical proteins as well as transcripts coding for protein isoforms. We also identified differences in the alternative-isoform preference between the treatments

  4. Transcription-Replication Conflict Orientation Modulates R-Loop Levels and Activates Distinct DNA Damage Responses.

    Science.gov (United States)

    Hamperl, Stephan; Bocek, Michael J; Saldivar, Joshua C; Swigut, Tomek; Cimprich, Karlene A

    2017-08-10

    Conflicts between transcription and replication are a potent source of DNA damage. Co-transcriptional R-loops could aggravate such conflicts by creating an additional barrier to replication fork progression. Here, we use a defined episomal system to investigate how conflict orientation and R-loop formation influence genome stability in human cells. R-loops, but not normal transcription complexes, induce DNA breaks and orientation-specific DNA damage responses during conflicts with replication forks. Unexpectedly, the replisome acts as an orientation-dependent regulator of R-loop levels, reducing R-loops in the co-directional (CD) orientation but promoting their formation in the head-on (HO) orientation. Replication stress and deregulated origin firing increase the number of HO collisions leading to genome-destabilizing R-loops. Our findings connect DNA replication to R-loop homeostasis and suggest a mechanistic basis for genome instability resulting from deregulated DNA replication, observed in cancer and other disease states. Copyright © 2017 Elsevier Inc. All rights reserved.

  5. Epalrestat increases intracellular glutathione levels in Schwann cells through transcription regulation

    Directory of Open Access Journals (Sweden)

    Keisuke Sato

    2014-01-01

    Full Text Available Epalrestat (EPS, approved in Japan, is the only aldose reductase inhibitor that is currently available for the treatment of diabetic neuropathy. Here we report that EPS at near-plasma concentration increases the intracellular levels of glutathione (GSH, which is important for protection against oxidative injury, through transcription regulation. Treatment of Schwann cells with EPS caused a dramatic increase in intracellular GSH levels. EPS increased the mRNA levels of γ-glutamylcysteine synthetase (γ-GCS, the enzyme catalyzing the first and rate-limiting step in de novo GSH synthesis. Nuclear factor erythroid 2-related factor 2 (Nrf2 is a key transcription factor that plays a central role in regulating the expression of γ-GCS. ELISA revealed that EPS increased nuclear Nrf2 levels. Knockdown of Nrf2 by siRNA suppressed the EPS-induced GSH biosynthesis. Furthermore, pretreatment with EPS reduced the cytotoxicity induced by H2O2, tert-butylhydroperoxide, 2,2'-azobis (2-amidinopropane dihydrochloride, and menadione, indicating that EPS plays a role in protecting against oxidative stress. This is the first study to show that EPS induces GSH biosynthesis via the activation of Nrf2. We suggest that EPS has new beneficial properties that may prevent the development and progression of disorders caused by oxidative stress.

  6. Transcription initiation patterns indicate divergent strategies for gene regulation at the chromatin level.

    Directory of Open Access Journals (Sweden)

    Elizabeth A Rach

    2011-01-01

    Full Text Available The application of deep sequencing to map 5' capped transcripts has confirmed the existence of at least two distinct promoter classes in metazoans: "focused" promoters with transcription start sites (TSSs that occur in a narrowly defined genomic span and "dispersed" promoters with TSSs that are spread over a larger window. Previous studies have explored the presence of genomic features, such as CpG islands and sequence motifs, in these promoter classes, but virtually no studies have directly investigated the relationship with chromatin features. Here, we show that promoter classes are significantly differentiated by nucleosome organization and chromatin structure. Dispersed promoters display higher associations with well-positioned nucleosomes downstream of the TSS and a more clearly defined nucleosome free region upstream, while focused promoters have a less organized nucleosome structure, yet higher presence of RNA polymerase II. These differences extend to histone variants (H2A.Z and marks (H3K4 methylation, as well as insulator binding (such as CTCF, independent of the expression levels of affected genes. Notably, differences are conserved across mammals and flies, and they provide for a clearer separation of promoter architectures than the presence and absence of CpG islands or the occurrence of stalled RNA polymerase. Computational models support the stronger contribution of chromatin features to the definition of dispersed promoters compared to focused start sites. Our results show that promoter classes defined from 5' capped transcripts not only reflect differences in the initiation process at the core promoter but also are indicative of divergent transcriptional programs established within gene-proximal nucleosome organization.

  7. Intracellular delivery of cell-penetrating peptide-transcriptional factor fusion protein and its role in selective osteogenesis

    Directory of Open Access Journals (Sweden)

    Suh JS

    2014-03-01

    Full Text Available Jin Sook Suh,1,* Jue Yeon Lee,2,* Yoon Jung Choi,1 Hyung Keun You,3 Seong-Doo Hong,4 Chong Pyoung Chung,2 Yoon Jeong Park1,2 1Dental Regenerative Biotechnology, Dental Research Institute, School of Dentistry, Seoul National University, Seoul, 2Central Research Institute, Nano Intelligent Biomedical Engineering Corporation (NIBEC, Seoul, 3Department of Periodontology, College of Dentistry, Wonkwang University, Iksan, 4Department of Oral Pathology, School of Dentistry, Seoul National University, Seoul, Republic of Korea *These authors contributed equally to this work Abstract: Protein-transduction technology has been attempted to deliver macromolecular materials, including protein, nucleic acids, and polymeric drugs, for either diagnosis or therapeutic purposes. Herein, fusion protein composed of an arginine-rich cell-penetrating peptide, termed low-molecular-weight protamine (LMWP, and a transcriptional coactivator with a PDZ-binding motif (TAZ protein was prepared and applied in combination with biomaterials to increase bone-forming capacity. TAZ has been recently identified as a specific osteogenic stimulating transcriptional coactivator in human mesenchymal stem cell (hMSC differentiation, while simultaneously blocking adipogenic differentiation. However, TAZ by itself cannot penetrate the cells, and thus needs a transfection tool for translocalization. The LMWP-TAZ fusion proteins were efficiently translocalized into the cytosol of hMSCs. The hMSCs treated with cell-penetrating LMWP-TAZ exhibited increased expression of osteoblastic genes and protein, producing significantly higher quantities of mineralized matrix compared to free TAZ. In contrast, adipogenic differentiation of the hMSCs was blocked by treatment of LMWP-TAZ fusion protein, as reflected by reduced marker-protein expression, adipocyte fatty acid-binding protein 2, and peroxisome proliferator-activated receptor-γ messenger ribonucleic acid levels. LMWP-TAZ was applied in

  8. Acrylamide levels in selected Colombian foods.

    Science.gov (United States)

    Pacetti, Deborah; Gil, Elizabeth; Frega, Natale G; Álvarez, Lina; Dueñas, Pilar; Garzón, Angélica; Lucci, Paolo

    2015-01-01

    Acrylamide (AA) levels in conventional (n = 112) and traditional (n = 43) Colombian foods were analysed by gas chromatography with mass spectrometry (GC/MS) detection. Samples included: infant powdered formula, coffee and chocolate powders, corn snacks, bakery products and tuber-, meat- and vegetable-based foods. There was a wide variability in AA levels among different foods and within different brands of the same food, especially for coffee powder, breakfast cereals biscuits and French fries samples. Among the conventional foods tested, the highest mean AA value was found in bakery products, such as biscuit (1104 µg kg(-1)) and wafer (1449 µg kg(-1)), followed by potato chips (916 µg kg(-1)). On the other hand, among the traditional foods, higher AA amounts were detected in fried platano (2813 µg kg(-1)) and yuca (3755 µg kg(-1)) compared to other products. Interestingly, the arepa, a traditional Colombian bakery product made with corn flour, showed a lower AA content (< 75 µg kg(-1)) when compared with similar bakery products tested, such as soft bread (102-594 µg kg(-1)), which is a made with wheat flour.

  9. Transcriptional profiling at whole population and single cell levels reveals somatosensory neuron molecular diversity

    Science.gov (United States)

    Chiu, Isaac M; Barrett, Lee B; Williams, Erika K; Strochlic, David E; Lee, Seungkyu; Weyer, Andy D; Lou, Shan; Bryman, Gregory S; Roberson, David P; Ghasemlou, Nader; Piccoli, Cara; Ahat, Ezgi; Wang, Victor; Cobos, Enrique J; Stucky, Cheryl L; Ma, Qiufu; Liberles, Stephen D; Woolf, Clifford J

    2014-01-01

    The somatosensory nervous system is critical for the organism's ability to respond to mechanical, thermal, and nociceptive stimuli. Somatosensory neurons are functionally and anatomically diverse but their molecular profiles are not well-defined. Here, we used transcriptional profiling to analyze the detailed molecular signatures of dorsal root ganglion (DRG) sensory neurons. We used two mouse reporter lines and surface IB4 labeling to purify three major non-overlapping classes of neurons: 1) IB4+SNS-Cre/TdTomato+, 2) IB4−SNS-Cre/TdTomato+, and 3) Parv-Cre/TdTomato+ cells, encompassing the majority of nociceptive, pruriceptive, and proprioceptive neurons. These neurons displayed distinct expression patterns of ion channels, transcription factors, and GPCRs. Highly parallel qRT-PCR analysis of 334 single neurons selected by membership of the three populations demonstrated further diversity, with unbiased clustering analysis identifying six distinct subgroups. These data significantly increase our knowledge of the molecular identities of known DRG populations and uncover potentially novel subsets, revealing the complexity and diversity of those neurons underlying somatosensation. DOI: http://dx.doi.org/10.7554/eLife.04660.001 PMID:25525749

  10. Uridine 5'-Monophosphate Synthase Is Transcriptionally Regulated by Pyrimidine Levels in Nicotiana plumbaginifolia

    Science.gov (United States)

    Santoso; Thornburg

    1998-02-01

    To understand the regulation and expression of pyrimidine biosynthesis in plants, we have examined the effect of the metabolic inhibitor 5-fluoroorotic acid (FOA) on uridine-5'-monophosphate synthase (UMPSase) expression in cell cultures of Nicotiana plumbaginifolia. UMPSase is the rate-limiting step of pyrimidine biosynthesis in plants. Addition of FOA causes an up-regulation of UMPSase enzyme activity in cell cultures after a lag phase of several days. Western-blot analysis demonstrated that the up-regulation in enzyme activity was caused by increased expression of the UMPSase protein. Northern-blot analysis demonstrated a higher level of UMPSase mRNA in the FOA-induced tissues than in control tissues. Run-on transcriptional assays showed that the UMPSase gene was transcriptionally activated after FOA treatment. The mechanism of toxicity of FOA is through thymine starvation. We found that addition of thymine abrogated the FOA-mediated up-regulation of UMPSase. In addition, methotrexate and aminopterin, which affect thymine levels by inhibiting dihydrofolate reductase, also up-regulate UMPSase in N. plumbaginifolia cells.

  11. Uridine 5′-Monophosphate Synthase Is Transcriptionally Regulated by Pyrimidine Levels in Nicotiana plumbaginifolia1

    Science.gov (United States)

    Santoso, Djoko; Thornburg, Robert

    1998-01-01

    To understand the regulation and expression of pyrimidine biosynthesis in plants, we have examined the effect of the metabolic inhibitor 5-fluoroorotic acid (FOA) on uridine-5′-monophosphate synthase (UMPSase) expression in cell cultures of Nicotiana plumbaginifolia. UMPSase is the rate-limiting step of pyrimidine biosynthesis in plants. Addition of FOA causes an up-regulation of UMPSase enzyme activity in cell cultures after a lag phase of several days. Western-blot analysis demonstrated that the up-regulation in enzyme activity was caused by increased expression of the UMPSase protein. Northern-blot analysis demonstrated a higher level of UMPSase mRNA in the FOA-induced tissues than in control tissues. Run-on transcriptional assays showed that the UMPSase gene was transcriptionally activated after FOA treatment. The mechanism of toxicity of FOA is through thymine starvation. We found that addition of thymine abrogated the FOA-mediated up-regulation of UMPSase. In addition, methotrexate and aminopterin, which affect thymine levels by inhibiting dihydrofolate reductase, also up-regulate UMPSase in N. plumbaginifolia cells. PMID:9490773

  12. Alu-miRNA interactions modulate transcript isoform diversity in stress response and reveal signatures of positive selection

    Science.gov (United States)

    Pandey, Rajesh; Bhattacharya, Aniket; Bhardwaj, Vivek; Jha, Vineet; Mandal, Amit K.; Mukerji, Mitali

    2016-09-01

    Primate-specific Alus harbor different regulatory features, including miRNA targets. In this study, we provide evidence for miRNA-mediated modulation of transcript isoform levels during heat-shock response through exaptation of Alu-miRNA sites in mature mRNA. We performed genome-wide expression profiling coupled with functional validation of miRNA target sites within exonized Alus, and analyzed conservation of these targets across primates. We observed that two miRNAs (miR-15a-3p and miR-302d-3p) elevated in stress response, target RAD1, GTSE1, NR2C1, FKBP9 and UBE2I exclusively within Alu. These genes map onto the p53 regulatory network. Ectopic overexpression of miR-15a-3p downregulates GTSE1 and RAD1 at the protein level and enhances cell survival. This Alu-mediated fine-tuning seems to be unique to humans as evident from the absence of orthologous sites in other primate lineages. We further analyzed signatures of selection on Alu-miRNA targets in the genome, using 1000 Genomes Phase-I data. We found that 198 out of 3177 Alu-exonized genes exhibit signatures of selection within Alu-miRNA sites, with 60 of them containing SNPs supported by multiple evidences (global-FST > 0.3, pair-wise-FST > 0.5, Fay-Wu’s H  2.0, high ΔDAF) and implicated in p53 network. We propose that by affecting multiple genes, Alu-miRNA interactions have the potential to facilitate population-level adaptations in response to environmental challenges.

  13. Transcript levels, alternative splicing and proteolytic cleavage of TFIIIA control 5S rRNA accumulation during Arabidopsis thaliana development.

    Science.gov (United States)

    Layat, Elodie; Cotterell, Sylviane; Vaillant, Isabelle; Yukawa, Yasushi; Tutois, Sylvie; Tourmente, Sylvette

    2012-07-01

    Ribosome biogenesis is critical for eukaryotic cells and requires coordinated synthesis of the protein and rRNA moieties of the ribosome, which are therefore highly regulated. 5S ribosomal RNA, an essential component of the large ribosomal subunit, is transcribed by RNA polymerase III and specifically requires transcription factor IIIA (TFIIIA). To obtain insight into the regulation of 5S rRNA transcription, we have investigated the expression of 5S rRNA and the exon-skipped (ES) and exon-including (EI) TFIIIA transcripts, two transcript isoforms that result from alternative splicing of the TFIIIA gene, and TFIIIA protein amounts with respect to requirements for 5S rRNA during development. We show that 5S rRNA quantities are regulated through distinct but complementary mechanisms operating through transcriptional and post-transcriptional control of TFIIIA transcripts as well as at the post-translational level through proteolytic cleavage of the TFIIIA protein. During the reproductive phase, high expression of the TFIIIA gene together with low proteolytic cleavage contributes to accumulation of functional, full-length TFIIIA protein, and results in 5S rRNA accumulation in the seed. In contrast, just after germination, the levels of TFIIIA-encoding transcripts are low and stable. Full-length TFIIIA protein is undetectable, and the level of 5S rRNA stored in the embryo progressively decreases. After day 4, in correlation with the reorganization of 5S rDNA chromatin to a mature state, full-length TFIIIA protein with transcriptional activity accumulates and permits de novo transcription of 5S rRNA. © 2012 The Authors. The Plant Journal © 2012 Blackwell Publishing Ltd.

  14. Intracellular delivery of cell-penetrating peptide-transcriptional factor fusion protein and its role in selective osteogenesis

    Science.gov (United States)

    Suh, Jin Sook; Lee, Jue Yeon; Choi, Yoon Jung; You, Hyung Keun; Hong, Seong-Doo; Chung, Chong Pyoung; Park, Yoon Jeong

    2014-01-01

    Protein-transduction technology has been attempted to deliver macromolecular materials, including protein, nucleic acids, and polymeric drugs, for either diagnosis or therapeutic purposes. Herein, fusion protein composed of an arginine-rich cell-penetrating peptide, termed low-molecular-weight protamine (LMWP), and a transcriptional coactivator with a PDZ-binding motif (TAZ) protein was prepared and applied in combination with biomaterials to increase bone-forming capacity. TAZ has been recently identified as a specific osteogenic stimulating transcriptional coactivator in human mesenchymal stem cell (hMSC) differentiation, while simultaneously blocking adipogenic differentiation. However, TAZ by itself cannot penetrate the cells, and thus needs a transfection tool for translocalization. The LMWP-TAZ fusion proteins were efficiently translocalized into the cytosol of hMSCs. The hMSCs treated with cell-penetrating LMWP-TAZ exhibited increased expression of osteoblastic genes and protein, producing significantly higher quantities of mineralized matrix compared to free TAZ. In contrast, adipogenic differentiation of the hMSCs was blocked by treatment of LMWP-TAZ fusion protein, as reflected by reduced marker-protein expression, adipocyte fatty acid-binding protein 2, and peroxisome proliferator-activated receptor-γ messenger ribonucleic acid levels. LMWP-TAZ was applied in alginate gel for the purpose of localization and controlled release. The LMWP-TAZ fusion protein-loaded alginate gel matrix significantly increased bone formation in rabbit calvarial defects compared with alginate gel matrix mixed with free TAZ protein. The protein transduction of TAZ fused with cell-penetrating LMWP peptide was able selectively to stimulate osteogenesis in vitro and in vivo. Taken together, this fusion protein-transduction technology for osteogenic protein can thus be applied in combination with biomaterials for tissue regeneration and controlled release for tissue

  15. Distribution of blood lead levels in schoolchildren in selected cape ...

    African Journals Online (AJOL)

    Objective. To determine blood lead levels among children attending schools in selected Cape Peninsula suburbs, and to assess the impact of a reduction in the lead content of petrol. Design. A cross-sectional analytical study of children's blood lead levels and associated risk factors. Setting. Selected inner city, suburban, ...

  16. Codon and amino acid usage in two major human pathogens of genus Bartonella--optimization between replicational-transcriptional selection, translational control and cost minimization.

    Science.gov (United States)

    Das, Sabyasachi; Paul, Sandip; Chatterjee, Sanjib; Dutta, Chitra

    2005-01-01

    Intra-genomic variation in synonymous codon and amino acid usage in two human pathogens Bartonella henselae and B. quintana has been carried out through multivariate analysis. Asymmetric mutational bias, coupled with replicational-transcriptional selection, has been identified as the prime selection force behind synonymous codon selection--a characteristic of the genus Bartonella, not exhibited by any other alpha-proteobacterial genome. Distinct codon usage patterns and low synonymous divergence values between orthologous sequences of highly expressed genes from the two Bartonella species indicate that there exists a residual intra-strand synonymous codon bias in the highly expressed genes, possibly operating at the level of translation. In the case of amino acid usage, the mean hydropathy level and aromaticity are the major sources of variation, both having nearly equal impact, while strand-specific mutational pressure and gene expressivity strongly influence the inter-strand variations. In both species under study, the highly expressed gene products tend not to contain heavy and/or aromatic residues, following the cost-minimization hypothesis in spite of their intracellular lifestyle. The codon and amino acid usage in these two human pathogens are, therefore, consequences of a complex balance between replicational-transcriptional selection, translational control, protein hydropathy and cost minimization.

  17. Inflammation response at the transcriptional level of HepG2 cells induced by multi-walled carbon nanotubes

    International Nuclear Information System (INIS)

    Piret, Jean-Pascal; Vankoningsloo, Sebastien; Noel, Florence; Saout, Christelle; Toussaint, Olivier; Mendoza, Jorge Mejia; Lucas, Stephane

    2011-01-01

    Poor information are currently available about the biological effects of multi-walled carbon nanotubes (MWCNT) on the liver. In this study, we evaluated the effects of MWCNT at the transcriptional level on the classical in vitro model of HepG2 hepatocarcinoma cells. The expression levels of 96 transcript species implicated in the inflammatory and immune responses was studied after a 24h incubation of HepG2 cells in presence of raw MWCNT dispersed in water by stirring. Among the 46 transcript species detected, only a few transcripts including mRNA coding for interleukine-7, chemokines receptor of the C-C families CCR7, as well as Endothelin-1, were statistically more abundant after treatment with MWCNT. Altogether, these data indicate that MWCNT can only induce a weak inflammatory response in HepG2 cells.

  18. Inflammation response at the transcriptional level of HepG2 cells induced by multi-walled carbon nanotubes

    Science.gov (United States)

    Piret, Jean-Pascal; Vankoningsloo, Sébastien; Noël, Florence; Mejia Mendoza, Jorge; Lucas, Stéphane; Saout, Christelle; Toussaint, Olivier

    2011-07-01

    Poor information are currently available about the biological effects of multi-walled carbon nanotubes (MWCNT) on the liver. In this study, we evaluated the effects of MWCNT at the transcriptional level on the classical in vitro model of HepG2 hepatocarcinoma cells. The expression levels of 96 transcript species implicated in the inflammatory and immune responses was studied after a 24h incubation of HepG2 cells in presence of raw MWCNT dispersed in water by stirring. Among the 46 transcript species detected, only a few transcripts including mRNA coding for interleukine-7, chemokines receptor of the C-C families CCR7, as well as Endothelin-1, were statistically more abundant after treatment with MWCNT. Altogether, these data indicate that MWCNT can only induce a weak inflammatory response in HepG2 cells.

  19. Dual targeting of gene delivery by genetic modification of adenovirus serotype 5 fibers and cell-selective transcriptional control.

    Science.gov (United States)

    Work, L M; Ritchie, N; Nicklin, S A; Reynolds, P N; Baker, A H

    2004-08-01

    Adenovirus (Ad)-mediated gene delivery is a promising approach for genetic manipulation of the vasculature and is being used in both preclinical models and clinical trials. However, safety concerns relating to infection of nontarget tissue and the poor infectivity of vascular cells compared to other cell types necessitates Ad vector refinement. Here, we combine a transductional targeting approach to improve vascular cell infectivity through RGD peptide insertion into adenovirus fibers, combined with transcriptional targeting to endothelial cells using a approximately 1 kb fragment of the fms-like tyrosine kinase receptor-1 (FLT-1) promoter. Single- and double-modified vectors were characterized in human cell lines that either support or have silenced FLT-1 expression. In rat hepatocytes and endothelial cells, the double modification substantially shifted transduction profiles toward vascular endothelial cells. Furthermore, in intact aortae derived from spontaneously hypertensive rats that display enhanced alphav integrin expression on dysfunctional endothelium, enhanced levels of transduction were observed using the double-modified vector but not in aortae derived from normotensive control rats. Our data indicate that Ad-mediated transduction can be beneficially modified in vitro and in vivo by combining fiber modification and a cell-selective promoter within a single-component vector system.

  20. TAS1R3 and UCN2 Transcript Levels in Blood Cells Are Associated With Sugary and Fatty Food Consumption in Children.

    Science.gov (United States)

    Priego, T; Sánchez, J; Picó, C; Ahrens, W; De Henauw, S; Kourides, Y; Lissner, L; Molnár, D; Moreno, L A; Russo, P; Siani, A; Veidebaum, T; Palou, A

    2015-09-01

    New types of dietary exposure biomarkers are needed to implement effective strategies for obesity prevention in children. Of special interest are biomarkers of consumption of food rich in simple sugars and fat because their intake has been associated with obesity development. Peripheral blood cells (PBCs) represent a promising new tool for identifying novel, transcript-based biomarkers. This study aimed to study potential associations between the transcripts of taste receptor type 1 member 3 (TAS1R3) and urocortin II (UCN2) genes in PBCs and the frequency of sugary and fatty food consumption in children. Four hundred sixty-three children from the IDEFICS cohort were selected to include a similar number of boys and girls, both normal-weight and overweight, belonging to eight European countries. Anthropometric parameters (measured at baseline and in a subset of 193 children after 2 years), food consumption frequency and transcript levels of TAS1R3 and UCN2 genes in PBCs were measured. Children with low-frequency consumption of sugary foods displayed higher TAS1R3 expression levels with respect to those with intermediate or high frequency. In turn, children with high-frequency consumption of fatty foods showed lower UCN2 expression levels with respect to those with low or intermediate frequency. Moreover, transcripts of TAS1R3 were related with body mass index and fat-mass changes after a 2-year follow-up period, with low expression levels of this gene being related with increased fat accumulation over time. The transcripts of TAS1R3 and UCN2 in PBCs may be considered potential biomarkers of consumption of sugary and fatty food, respectively, to complement data of food-intake questionnaires.

  1. Terrestrial radiation level in selected asphalt plants in Port Harcourt ...

    African Journals Online (AJOL)

    Terrestrial radiation level in selected asphalt plants in Port Harcourt, Nigeria. ... An environmental radiation survey in asphalt processing plants in Rivers State was been carried out ... Therefore the results show significant radiological risk.

  2. Waveband specific transcriptional control of select genetic pathways in vertebrate skin (Xiphophorus maculatus).

    Science.gov (United States)

    Walter, Ronald B; Boswell, Mikki; Chang, Jordan; Boswell, William T; Lu, Yuan; Navarro, Kaela; Walter, Sean M; Walter, Dylan J; Salinas, Raquel; Savage, Markita

    2018-05-10

    Evolution occurred exclusively under the full spectrum of sunlight. Conscription of narrow regions of the solar spectrum by specific photoreceptors suggests a common strategy for regulation of genetic pathways. Fluorescent light (FL) does not possess the complexity of the solar spectrum and has only been in service for about 60 years. If vertebrates evolved specific genetic responses regulated by light wavelengths representing the entire solar spectrum, there may be genetic consequences to reducing the spectral complexity of light. We utilized RNA-Seq to assess changes in the transcriptional profiles of Xiphophorus maculatus skin after exposure to FL ("cool white"), or narrow wavelength regions of light between 350 and 600 nm (i.e., 50 nm or 10 nm regions, herein termed "wavebands"). Exposure to each 50 nm waveband identified sets of genes representing discrete pathways that showed waveband specific transcriptional modulation. For example, 350-400 or 450-500 nm waveband exposures resulted in opposite regulation of gene sets marking necrosis and apoptosis (i.e., 350-400 nm; necrosis suppression, apoptosis activation, while 450-500 nm; apoptosis suppression, necrosis activation). Further investigation of specific transcriptional modulation employing successive 10 nm waveband exposures between 500 and 550 nm showed; (a) greater numbers of genes may be transcriptionally modulated after 10 nm exposures, than observed for 50 nm or FL exposures, (b) the 10 nm wavebands induced gene sets showing greater functional specificity than 50 nm or FL exposures, and (c) the genetic effects of FL are primarily due to 30 nm between 500 and 530 nm. Interestingly, many genetic pathways exhibited completely opposite transcriptional effects after different waveband exposures. For example, the epidermal growth factor (EGF) pathway exhibits transcriptional suppression after FL exposure, becomes highly active after 450-500 nm waveband exposure, and again, exhibits strong

  3. RNA-SEQ reveals transcriptional level changes of poplar roots in different forms of nitrogen treatments

    Directory of Open Access Journals (Sweden)

    Chunpu eQu

    2016-02-01

    Full Text Available Poplar has emerged as a model plant for understanding molecular mechanisms of tree growth, development and response to environment. Long-term application of different forms of nitrogen (such as NO3--N and NH4+-N may cause morphological changes of poplar roots; however, the molecular level changes are still not well known. In this study, we analyzed the expression profiling of poplar roots treated by three forms of nitrogen: S1 (NH4+, S2 (NH4NO3 and S3 (NO3- by using RNA-SEQ technique. We found 463 genes significantly differentially expressed in roots by different N treatments, of which a total of 116 genes were found to differentially express between S1 and S2, 173 genes between S2 and S3, and 327 genes between S1 and S3. A cluster analysis shows significant difference in many transcription factor families and functional genes family under different N forms. Through an analysis of Mapman metabolic pathway, we found that the significantly differentially expressed genes are associated with fermentation, glycolysis and tricarboxylic acid cycle (TCA, secondary metabolism, hormone metabolism, and transport processing. Interestingly, we did not find significantly differentially expressed genes in N metabolism pathway, mitochondrial electron transport / ATP synthesis and mineral nutrition. We also found abundant candidate genes (20 transcription factors and 30 functional genes regulating morphology changes of poplar roots under the three N forms. The results obtained are beneficial to a better understanding of the potential molecular and cellular mechanisms regulating root morphology changes under different N treatments.

  4. The Relationship Between Transcript Expression Levels of Nuclear Encoded (TFAM, NRF1 and Mitochondrial Encoded (MT-CO1 Genes in Single Human Oocytes During Oocyte Maturation

    Directory of Open Access Journals (Sweden)

    Ghaffari Novin M.

    2015-06-01

    Full Text Available In some cases of infertility in women, human oocytes fail to mature when they reach the metaphase II (MII stage. Mitochondria plays an important role in oocyte maturation. A large number of mitochondrial DNA (mtDNA, copied in oocytes, is essential for providing adenosine triphosphate (ATP during oocyte maturation. The purpose of this study was to identify the relationship between transcript expression levels of the mitochondrial encoded gene (MT-CO1 and two nuclear encoded genes, nuclear respiratory factor 1 (NRF1 and mitochondrial transcription factor A (TFAM in various stages of human oocyte maturation. Nine consenting patients, age 21-35 years old, with male factors were selected for ovarian stimulation and intracytoplasmic sperm injection (ICSI procedures. mRNA levels of mitochondrial- related genes were performed by singlecell TaqMan® quantitative real-time polymerase chain reaction (qRT-PCR. There was no significant relationship between the relative expression levels in germinal vesicle (GV stage oocytes (p = 0.62. On the contrary, a significant relationship was seen between the relative expression levels of TFAM and NRF1 and the MT-CO1 genes at the stages of metaphase I (MI and MII (p = 0.03 and p = 0.002. A relationship exists between the transcript expression levels of TFAM and NRF1, and MT-CO1 genes in various stages of human oocyte maturation.

  5. A Bayesian random effects discrete-choice model for resource selection: Population-level selection inference

    Science.gov (United States)

    Thomas, D.L.; Johnson, D.; Griffith, B.

    2006-01-01

    Modeling the probability of use of land units characterized by discrete and continuous measures, we present a Bayesian random-effects model to assess resource selection. This model provides simultaneous estimation of both individual- and population-level selection. Deviance information criterion (DIC), a Bayesian alternative to AIC that is sample-size specific, is used for model selection. Aerial radiolocation data from 76 adult female caribou (Rangifer tarandus) and calf pairs during 1 year on an Arctic coastal plain calving ground were used to illustrate models and assess population-level selection of landscape attributes, as well as individual heterogeneity of selection. Landscape attributes included elevation, NDVI (a measure of forage greenness), and land cover-type classification. Results from the first of a 2-stage model-selection procedure indicated that there is substantial heterogeneity among cow-calf pairs with respect to selection of the landscape attributes. In the second stage, selection of models with heterogeneity included indicated that at the population-level, NDVI and land cover class were significant attributes for selection of different landscapes by pairs on the calving ground. Population-level selection coefficients indicate that the pairs generally select landscapes with higher levels of NDVI, but the relationship is quadratic. The highest rate of selection occurs at values of NDVI less than the maximum observed. Results for land cover-class selections coefficients indicate that wet sedge, moist sedge, herbaceous tussock tundra, and shrub tussock tundra are selected at approximately the same rate, while alpine and sparsely vegetated landscapes are selected at a lower rate. Furthermore, the variability in selection by individual caribou for moist sedge and sparsely vegetated landscapes is large relative to the variability in selection of other land cover types. The example analysis illustrates that, while sometimes computationally intense, a

  6. The Transcription Bubble of the RNA Polymerase-Promoter Open Complex Exhibits Conformational Heterogeneity and Millisecond-Scale Dynamics : Implications for Transcription Start-Site Selection

    NARCIS (Netherlands)

    Robb, Nicole C.; Cordes, Thorben; Hwang, Ling Chin; Gryte, Kristofer; Duchi, Diego; Craggs, Timothy D.; Santoso, Yusdi; Weiss, Shimon; Ebright, Richard H.; Kapanidis, Achillefs N.

    2013-01-01

    Bacterial transcription is initiated after RNA polymerase (RNAP) binds to promoter DNA, melts similar to 14 bp around the transcription start site and forms a single-stranded "transcription bubble" within a catalytically active RNAP-DNA open complex (RPo). There is significant flexibility in the

  7. [Early monitoring of BCR-ABL transcript levels and cytogenetic in assessing the prognosis of chronic myeloid leukemia].

    Science.gov (United States)

    Huang, Qin; Zhang, Xiao-yan; Li, Yan; Wang, Xiao-min

    2013-10-15

    To explore the prognostic significance of early monitoring of BCR-ABL transcript levels and cytogenetic evaluations for chronic myeloid leukemia in chronic phase (CML-CP). From July 2007 to May 2012, 56 CML-CP patients received oral imatinib 400 mg/d. The BCR-ABL transcript levels were monitored and cytogenetic examinations performed after 3 and 6 months respectively. The median follow-up time was 48 months. The 3-month BCR-ABL transcript levels ≤ 10% of patients 5-year overall survival (OS) and progression-free survival (PFS) were better than BCR-ABL transcript levels >10% of patients (OS: 100% vs 84.6%, P = 0.011; PFS: 94.6% vs 67.7%, P = 0.045); cytogenetics: Ph(+) ≤ 35 % of patients 5-year OS and PFS better than Ph(+) > 35% of patients (OS: 100% vs 76.2%, P = 0.001; PFS: 95.2% vs 38.1%, P = 0.001); the 6-month BCR-ABL transcripts level ≤ 1% of patients 5-year OS and PFS also better than BCR-ABL transcript levels> 1% of patients (OS: 100% vs 71.4%, P = 0.000; PFS: 95.2% vs 47.6%, P = 0.001); Ph(+) = 0% and Ph(+)> 0% patients, 5-year OS and PFS were significantly different (OS: 100% vs 68.6%, P = 0.000; PFS: 95.3% vs 45.7%, P = 0.000). Early molecular biology and cytogenetics monitoring have some significance in the prognostic assessment of CML-CP. And individualized treatment strategies should be based upon the monitoring results in conjunctions with comprehensive judgments.

  8. Exposure level from selected base station tower around Kuala Nerus

    African Journals Online (AJOL)

    Health risk due to RF radiation exposure from base station tower (BST) has been debated for years leading to public concerns. Thus, this preliminary study aims to measure, evaluate and analyze the exposure level on three selected BST around Kuala Nerus. The measurement of exposure level in terms of voltage ...

  9. Mitochondrial Biogenesis in Diverse Cauliflower Cultivars under Mild and Severe Drought. Impaired Coordination of Selected Transcript and Proteomic Responses, and Regulation of Various Multifunctional Proteins

    Directory of Open Access Journals (Sweden)

    Michał Rurek

    2018-04-01

    Full Text Available Mitochondrial responses under drought within Brassica genus are poorly understood. The main goal of this study was to investigate mitochondrial biogenesis of three cauliflower (Brassica oleracea var. botrytis cultivars with varying drought tolerance. Diverse quantitative changes (decreases in abundance mostly in the mitochondrial proteome were assessed by two-dimensional gel electrophoresis (2D PAGE coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS. Respiratory (e.g., complex II, IV (CII, CIV and ATP synthase subunits, transporter (including diverse porin isoforms and matrix multifunctional proteins (e.g., components of RNA editing machinery were diversely affected in their abundance under two drought levels. Western immunoassays showed additional cultivar-specific responses of selected mitochondrial proteins. Dehydrin-related tryptic peptides (found in several 2D spots immunopositive with dehydrin-specific antisera highlighted the relevance of mitochondrial dehydrin-like proteins for the drought response. The abundance of selected mRNAs participating in drought response was also determined. We conclude that mitochondrial biogenesis was strongly, but diversely affected in various cauliflower cultivars, and associated with drought tolerance at the proteomic and functional levels. However, discussed alternative oxidase (AOX regulation at the RNA and protein level were largely uncoordinated due to the altered availability of transcripts for translation, mRNA/ribosome interactions, and/or miRNA impact on transcript abundance and translation.

  10. Mitochondrial Biogenesis in Diverse Cauliflower Cultivars under Mild and Severe Drought. Impaired Coordination of Selected Transcript and Proteomic Responses, and Regulation of Various Multifunctional Proteins

    Science.gov (United States)

    Rurek, Michał; Czołpińska, Magdalena; Staszak, Aleksandra Maria; Nowak, Witold; Krzesiński, Włodzimierz; Spiżewski, Tomasz

    2018-01-01

    Mitochondrial responses under drought within Brassica genus are poorly understood. The main goal of this study was to investigate mitochondrial biogenesis of three cauliflower (Brassica oleracea var. botrytis) cultivars with varying drought tolerance. Diverse quantitative changes (decreases in abundance mostly) in the mitochondrial proteome were assessed by two-dimensional gel electrophoresis (2D PAGE) coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS). Respiratory (e.g., complex II, IV (CII, CIV) and ATP synthase subunits), transporter (including diverse porin isoforms) and matrix multifunctional proteins (e.g., components of RNA editing machinery) were diversely affected in their abundance under two drought levels. Western immunoassays showed additional cultivar-specific responses of selected mitochondrial proteins. Dehydrin-related tryptic peptides (found in several 2D spots) immunopositive with dehydrin-specific antisera highlighted the relevance of mitochondrial dehydrin-like proteins for the drought response. The abundance of selected mRNAs participating in drought response was also determined. We conclude that mitochondrial biogenesis was strongly, but diversely affected in various cauliflower cultivars, and associated with drought tolerance at the proteomic and functional levels. However, discussed alternative oxidase (AOX) regulation at the RNA and protein level were largely uncoordinated due to the altered availability of transcripts for translation, mRNA/ribosome interactions, and/or miRNA impact on transcript abundance and translation. PMID:29642585

  11. Increased DHT levels in androgenic alopecia have been selected for to protect men from prostate cancer.

    Science.gov (United States)

    Bhargava, Shiva

    2014-04-01

    Androgenic alopecia, a condition characterized by increased levels of DHT could have been selected for due to the benefits that prostaglandin D2 (PGD(2)) has on the prostate. A DHT metabolite can increase the transcription of prostaglandin D2 synthase through estrogen receptor beta. The increase of PGD(2) can decrease the risk of prostate cancer and proliferation of prostate cancer cells. Therefore, the mechanisms behind male pattern baldness may also curtail the advancement of prostate cancer. Copyright © 2014 Elsevier Ltd. All rights reserved.

  12. Site selection handbook: Workshop on site selection for low-level radioactive waste disposal facilities

    International Nuclear Information System (INIS)

    1987-10-01

    The Low-Level Radioactive Waste Policy Amendments Act of 1985 (LLRWPAA) requires the Department of Energy (DOE) to provide technical assistance to ''...those compact regions, host States and nonmember States determined by the Secretary to require assistance.'' Technical assistance has been defined to include, but not be limited to, ''technical guidelines for site selection.'' This site selection workshop was developed to assist States and Compacts in developing new low-level radioactive waste (LLW) disposal sites in accordance with the requirements of the LLRWPAA. The workshop comprises a series of lectures, discussion topics, and exercises, supported by this Site Selection Workshop Handbook, designed to examine various aspects of a comprehensive site selection program. It is not an exhaustive treatment of all aspects of site selection, nor is it prescriptive. The workshop focuses on the major elements of site selection and the tools that can be used to implement the site selection program

  13. Groundwater levels for selected wells in Upper Kittitas County, Washington

    Science.gov (United States)

    Fasser, E.T.; Julich, R.J.

    2011-01-01

    Groundwater levels for selected wells in Upper Kittitas County, Washington, are presented on an interactive, web-based map to document the spatial distribution of groundwater levels in the study area measured during spring 2011. Groundwater-level data and well information were collected by the U.S. Geological Survey using standard techniques and are stored in the U.S. Geological Survey National Water Information System, Groundwater Site-Inventory database.

  14. The genome-wide identification and transcriptional levels of DNA methyltransferases and demethylases in globe artichoke.

    Science.gov (United States)

    Gianoglio, Silvia; Moglia, Andrea; Acquadro, Alberto; Comino, Cinzia; Portis, Ezio

    2017-01-01

    Changes to the cytosine methylation status of DNA, driven by the activity of C5 methyltransferases (C5-MTases) and demethylases, exert an important influence over development, transposon movement, gene expression and imprinting. Three groups of C5-MTase enzymes have been identified in plants, namely MET (methyltransferase 1), CMT (chromomethyltransferases) and DRM (domains rearranged methyltransferases). Here the repertoire of genes encoding C5-MTase and demethylase by the globe artichoke (Cynara cardunculus var. scolymus) is described, based on sequence homology, a phylogenetic analysis and a characterization of their functional domains. A total of ten genes encoding C5-MTase (one MET, five CMTs and four DRMs) and five demethylases was identified. An analysis of their predicted product's protein structure suggested an extensive level of conservation has been retained by the C5-MTases. Transcriptional profiling based on quantitative real time PCR revealed a number of differences between the genes encoding maintenance and de novo methyltransferases, sometimes in a tissue- or development-dependent manner, which implied a degree of functional specialization.

  15. The genome-wide identification and transcriptional levels of DNA methyltransferases and demethylases in globe artichoke.

    Directory of Open Access Journals (Sweden)

    Silvia Gianoglio

    Full Text Available Changes to the cytosine methylation status of DNA, driven by the activity of C5 methyltransferases (C5-MTases and demethylases, exert an important influence over development, transposon movement, gene expression and imprinting. Three groups of C5-MTase enzymes have been identified in plants, namely MET (methyltransferase 1, CMT (chromomethyltransferases and DRM (domains rearranged methyltransferases. Here the repertoire of genes encoding C5-MTase and demethylase by the globe artichoke (Cynara cardunculus var. scolymus is described, based on sequence homology, a phylogenetic analysis and a characterization of their functional domains. A total of ten genes encoding C5-MTase (one MET, five CMTs and four DRMs and five demethylases was identified. An analysis of their predicted product's protein structure suggested an extensive level of conservation has been retained by the C5-MTases. Transcriptional profiling based on quantitative real time PCR revealed a number of differences between the genes encoding maintenance and de novo methyltransferases, sometimes in a tissue- or development-dependent manner, which implied a degree of functional specialization.

  16. Effect of biotin on transcription levels of key enzymes and glutamate efflux in glutamate fermentation by Corynebacterium glutamicum.

    Science.gov (United States)

    Cao, Yan; Duan, Zuoying; Shi, Zhongping

    2014-02-01

    Biotin is an important factor affecting the performance of glutamate fermentation by biotin auxotrophic Corynebacterium glutamicum and glutamate is over-produced only when initial biotin content is controlled at suitable levels or initial biotin is excessive but with Tween 40 addition during fermentation. The transcription levels of key enzymes at pyruvate, isocitrate and α-ketoglutarate metabolic nodes, as well as transport protein (TP) of glutamate were investigated under the conditions of varied biotin contents and Tween 40 supplementation. When biotin was insufficient, the genes encoding key enzymes and TP were down-regulated in the early production phase, in particular, the transcription level of isocitrate dehydrogenase (ICDH) which was only 2% of that of control. Although the cells' morphology transformation and TP level were not affected, low transcription level of ICDH led to lower final glutamate concentration (64 g/L). When biotin was excessive, the transcription levels of key enzymes were at comparable levels as those of control with ICDH as an exception, which was only 3-22% of control level throughout production phase. In this case, little intracellular glutamate accumulation (1.5 mg/g DCW) and impermeable membrane resulted in non glutamate secretion into broth, even though the quantity of TP was more than 10-folds of control level. Addition of Tween 40 when biotin was excessive stimulated the expression of all key enzymes and TP, intracellular glutamate content was much higher (10-12 mg/g DCW), and final glutamate concentration reached control level (75-80 g/L). Hence, the membrane alteration and TP were indispensable in glutamate secretion. Biotin and Tween 40 influenced the expression level of ICDH and glutamate efflux, thereby influencing glutamate production.

  17. B-chromosome effects on Hsp70 gene expression does not occur at transcriptional level in the grasshopper Eyprepocnemis plorans.

    Science.gov (United States)

    Navarro-Domínguez, Beatriz; Cabrero, Josefa; Camacho, Juan Pedro M; López-León, María Dolores

    2016-10-01

    As intragenomic parasites, B chromosomes can elicit stress in the host genome, thus inducing a response for host adaptation to this kind of continuous parasitism. In the grasshopper Eyprepocnemis plorans, B-chromosome presence has been previously associated with a decrease in the amount of the heat-shock protein 70 (HSP70). To investigate whether this effect is already apparent at transcriptional level, we analyze the expression levels of the Hsp70 gene in gonads and somatic tissues of males and females with and without B chromosomes from two populations, where the predominant B chromosome variants (B2 and B24) exhibit different levels of parasitism, by means of quantitative real-time PCR (qPCR) on complementary DNA (cDNA). The results revealed the absence of significant differences for Hsp70 transcripts associated with B-chromosome presence in virtually all samples. This indicates that the decrease in HSP70 protein levels, formerly reported in this species, may not be a consequence of transcriptional down-regulation of Hsp70 genes, but the result of post-transcriptional regulation. These results will help to design future studies oriented to identifying factors modulating Hsp70 expression, and will also contribute to uncover the biological role of B chromosomes in eukaryotic genomes.

  18. Targeting of breast metastases using a viral gene vector with tumour-selective transcription.

    LENUS (Irish Health Repository)

    Rajendran, Simon

    2012-01-31

    BACKGROUND: Adeno-associated virus (AAV) vectors have significant potential as gene delivery vectors for cancer gene therapy. However, broad AAV2 tissue tropism results in nonspecific gene expression. MATERIALS AND METHODS: We investigated use of the C-X-C chemokine receptor type 4 (CXCR4) promoter to restrict AAV expression to tumour cells, in subcutaneous MCF-7 xenograft mouse models of breast cancer and in patient samples, using bioluminescent imaging and flow cytometric analysis. RESULTS: Higher transgene expression levels were observed in subcutaneous MCF-7 tumours relative to normal tissue (muscle) using the CXCR4 promoter, unlike a ubiquitously expressing Cytomegalovirus promoter construct, with preferential AAVCXCR4 expression in epithelial tumour and CXCR4-positive cells. Transgene expression following intravenously administered AAVCXCR4 in a model of liver metastasis was detected specifically in livers of tumour bearing mice. Ex vivo analysis using patient samples also demonstrated higher AAVCXCR4 expression in tumour compared with normal liver tissue. CONCLUSION: This study demonstrates for the first time, the potential for systemic administration of AAV2 vector for tumour-selective gene therapy.

  19. CAR gene cluster and transcript levels of carotenogenic genes in Rhodotorula mucilaginosa.

    Science.gov (United States)

    Landolfo, Sara; Ianiri, Giuseppe; Camiolo, Salvatore; Porceddu, Andrea; Mulas, Giuliana; Chessa, Rossella; Zara, Giacomo; Mannazzu, Ilaria

    2018-01-01

    A molecular approach was applied to the study of the carotenoid biosynthetic pathway of Rhodotorula mucilaginosa. At first, functional annotation of the genome of R. mucilaginosa C2.5t1 was carried out and gene ontology categories were assigned to 4033 predicted proteins. Then, a set of genes involved in different steps of carotenogenesis was identified and those coding for phytoene desaturase, phytoene synthase/lycopene cyclase and carotenoid dioxygenase (CAR genes) proved to be clustered within a region of ~10 kb. Quantitative PCR of the genes involved in carotenoid biosynthesis showed that genes coding for 3-hydroxy-3-methylglutharyl-CoA reductase and mevalonate kinase are induced during exponential phase while no clear trend of induction was observed for phytoene synthase/lycopene cyclase and phytoene dehydrogenase encoding genes. Thus, in R. mucilaginosa the induction of genes involved in the early steps of carotenoid biosynthesis is transient and accompanies the onset of carotenoid production, while that of CAR genes does not correlate with the amount of carotenoids produced. The transcript levels of genes coding for carotenoid dioxygenase, superoxide dismutase and catalase A increased during the accumulation of carotenoids, thus suggesting the activation of a mechanism aimed at the protection of cell structures from oxidative stress during carotenoid biosynthesis. The data presented herein, besides being suitable for the elucidation of the mechanisms that underlie carotenoid biosynthesis, will contribute to boosting the biotechnological potential of this yeast by improving the outcome of further research efforts aimed at also exploring other features of interest.

  20. Bayesian Group Bridge for Bi-level Variable Selection.

    Science.gov (United States)

    Mallick, Himel; Yi, Nengjun

    2017-06-01

    A Bayesian bi-level variable selection method (BAGB: Bayesian Analysis of Group Bridge) is developed for regularized regression and classification. This new development is motivated by grouped data, where generic variables can be divided into multiple groups, with variables in the same group being mechanistically related or statistically correlated. As an alternative to frequentist group variable selection methods, BAGB incorporates structural information among predictors through a group-wise shrinkage prior. Posterior computation proceeds via an efficient MCMC algorithm. In addition to the usual ease-of-interpretation of hierarchical linear models, the Bayesian formulation produces valid standard errors, a feature that is notably absent in the frequentist framework. Empirical evidence of the attractiveness of the method is illustrated by extensive Monte Carlo simulations and real data analysis. Finally, several extensions of this new approach are presented, providing a unified framework for bi-level variable selection in general models with flexible penalties.

  1. High-level radioactive waste repositories site selection plan

    International Nuclear Information System (INIS)

    Castanon, A.; Recreo, F.

    1985-01-01

    A general vision of the high level nuclear waste (HLNW) and/or nuclear spent fuel facilities site selection processes is given, according to the main international nuclear safety regulatory organisms quidelines and the experience from those countries which have reached a larger development of their national nuclear programs. (author)

  2. Attention to Hierarchical Level Influences Attentional Selection of Spatial Scale

    Science.gov (United States)

    Flevaris, Anastasia V.; Bentin, Shlomo; Robertson, Lynn C.

    2011-01-01

    Ample evidence suggests that global perception may involve low spatial frequency (LSF) processing and that local perception may involve high spatial frequency (HSF) processing (Shulman, Sullivan, Gish, & Sakoda, 1986; Shulman & Wilson, 1987; Robertson, 1996). It is debated whether SF selection is a low-level mechanism associating global…

  3. The Wheat NAC Transcription Factor TaNAC2L Is Regulated at the Transcriptional and Post-Translational Levels and Promotes Heat Stress Tolerance in Transgenic Arabidopsis.

    Science.gov (United States)

    Guo, Weiwei; Zhang, Jinxia; Zhang, Ning; Xin, Mingming; Peng, Huiru; Hu, Zhaorong; Ni, Zhongfu; Du, Jinkun

    2015-01-01

    Heat stress poses a serious threat to global crop production. In efforts that aim to mitigate the adverse effects of heat stress on crops, a variety of genetic tools are being used to develop plants with improved thermotolerance. The characterization of important regulators of heat stress tolerance provides essential information for this aim. In this study, we examine the wheat (Triticum aestivum) NAC transcription factor gene TaNAC2L. High temperature induced TaNAC2L expression in wheat and overexpression of TaNAC2L in Arabidopsis thaliana enhanced acquired heat tolerance without causing obvious alterations in phenotype compared with wild type under normal conditions. TaNAC2L overexpression also activated the expression of heat-related genes in the transgenic Arabidopsis plants, suggesting that TaNAC2L may improve heat tolerance by regulating the expression of stress-responsive genes. Notably, TaNAC2L is also regulated at the post-translational level and might be degraded via a proteasome-mediated pathway. Thus, this wheat transcription factor may have potential uses in enhancing thermotolerance in crops.

  4. The Wheat NAC Transcription Factor TaNAC2L Is Regulated at the Transcriptional and Post-Translational Levels and Promotes Heat Stress Tolerance in Transgenic Arabidopsis.

    Directory of Open Access Journals (Sweden)

    Weiwei Guo

    Full Text Available Heat stress poses a serious threat to global crop production. In efforts that aim to mitigate the adverse effects of heat stress on crops, a variety of genetic tools are being used to develop plants with improved thermotolerance. The characterization of important regulators of heat stress tolerance provides essential information for this aim. In this study, we examine the wheat (Triticum aestivum NAC transcription factor gene TaNAC2L. High temperature induced TaNAC2L expression in wheat and overexpression of TaNAC2L in Arabidopsis thaliana enhanced acquired heat tolerance without causing obvious alterations in phenotype compared with wild type under normal conditions. TaNAC2L overexpression also activated the expression of heat-related genes in the transgenic Arabidopsis plants, suggesting that TaNAC2L may improve heat tolerance by regulating the expression of stress-responsive genes. Notably, TaNAC2L is also regulated at the post-translational level and might be degraded via a proteasome-mediated pathway. Thus, this wheat transcription factor may have potential uses in enhancing thermotolerance in crops.

  5. Development and validation of quantitative PCR assays to measure cytokine transcript levels in the Florida manatee (Trichechus manatus latirostris)

    Science.gov (United States)

    Ferrante, Jason; Hunter, Margaret; Wellehan, James F.X.

    2018-01-01

    Cytokines have important roles in the mammalian response to viral and bacterial infections, trauma, and wound healing. Because of early cytokine production after physiologic stresses, the regulation of messenger RNA (mRNA) transcripts can be used to assess immunologic responses before changes in protein production. To detect and assess early immune changes in endangered Florida manatees (Trichechus manatus latirostris), we developed and validated a panel of quantitative PCR assays to measure mRNA transcription levels for the cytokines interferon (IFN)-γ; interleukin (IL)-2, -6, and -10; tumor necrosis factor-α, and the housekeeping genes glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and β-actin (reference genes). Assays were successfully validated using blood samples from free-ranging, apparently healthy manatees from the east and west coasts of central Florida. No cytokine or housekeeping gene transcription levels were significantly different among age classes or sexes. However, the transcription levels for GAPDH, IL-2, IL-6, and IFN-γ were significantly higher (Puse as a reference gene in future studies. Our assays can aid in the investigation of manatee immune response to physical trauma and novel or ongoing environmental stressors.

  6. Yeast tRNAPhe expressed in human cells can be selected by HIV-1 for use as a reverse transcription primer

    International Nuclear Information System (INIS)

    Kelly, Nathan J.; Morrow, Casey D.

    2003-01-01

    All naturally occurring human immune deficiency viruses (HIV-1) select and use tRNA Lys,3 as the primer for reverse transcription. Studies to elucidate the mechanism of tRNA selection from the intracellular milieu have been hampered due to the difficulties in manipulating the endogenous levels of tRNA Lys,3 . We have previously described a mutant HIV-1 with a primer binding site (PBS) complementary to yeast tRNA Phe (psHIV-Phe) that relies on transfection of yeast tRNA Phe for infectivity. To more accurately recapitulate the selection process, a cDNA was designed for the intracellular expression of the yeast tRNA Phe . Increasing amounts of the plasmid encoding tRNA Phe resulted in a corresponding increase in levels of yeast tRNA Phe in the cell. The yeast tRNA Phe isolated from cells transfected with the cDNA for yeast tRNA Phe , or in the cell lines expressing yeast tRNA Phe , were aminoacylated, indicating that the expressed yeast tRNA Phe was incorporated into tRNA biogenesis pathways and translation. Increasing the cytoplasmic levels of tRNA Phe resulted in increased encapsidation of tRNA Phe in viruses with a PBS complementary to tRNA Phe (psHIV-Phe) or tRNA Lys,3 (wild-type HIV-1). Production of infectious psHIV-Phe was dependent on the amount of cotransfected tRNA Phe cDNA. Increasing amounts of plasmids encoding yeast tRNA Phe produced an increase of infectious psHIV-Phe that plateaued at a level lower than that from the transfection of the wild-type genome, which uses tRNA Lys,3 as the primer for reverse transcription. Cell lines were generated that expressed yeast tRNA Phe at levels approximately 0.1% of that for tRNA Lys,3 . Even with this reduced level of yeast tRNA Phe , the cell lines complemented psHIV-Phe over background levels. The results of these studies demonstrate that intracellular levels of primer tRNA can have a direct effect on HIV-1 infectivity and further support the role for PBS-tRNA complementarity in the primer selection process

  7. A modified scintigrafic technique for amputation level selection in diabetics

    International Nuclear Information System (INIS)

    Dwars, B.J.; Rauwerda, J.A.; Broek, T.A.A. van den; Rij, G.L. van; Hollander, W. den; Heidendal, G.A.K.

    1989-01-01

    A modified 123 I-antipyrine cutaneous washout technique for the selection of amputation levels is described. The modifications imply a reduction of time needed for the examination by simultaneous recordings on different levels, and a better patient acceptance by reducing inconvenience. Furthermore, both skin perfusion pressure (SPP) and skin blood flow (SBF) are determined from each clearance curve. In a prospective study among 26 diabetic patients presenting with ulcers or gangrene of the foot, both SPP and SBF were determined preoperatively on the selected level of surgery and on adjacent amputation sites. These 26 patients underwent 12 minor foot amputations and 17 major lower limb amputations. Two of these amputations failed to heal. SBF values appeared indicative for the degree of peripheral vascular disease, as low SBF values were found with low SPP values. SPP determinations revealed good predictive values: All surgical procedures healed when SPP>20 mmHg, but 2 out of 3 failed when SPP<2 mmHg. If SPP values would have been decisive, the amputation would have been converted to a lower level in 6 out of 17 cases. This modified scintigrafic technique provides accurate objective information for amputation level selection. (orig.)

  8. Modified scintigrafic technique for amputation level selection in diabetics

    Energy Technology Data Exchange (ETDEWEB)

    Dwars, B.J.; Rauwerda, J.A.; Broek, T.A.A. van den; Rij, G.L. van; Hollander, W. den; Heidendal, G.A.K.

    1989-01-01

    A modified /sup 123/I-antipyrine cutaneous washout technique for the selection of amputation levels is described. The modifications imply a reduction of time needed for the examination by simultaneous recordings on different levels, and a better patient acceptance by reducing inconvenience. Furthermore, both skin perfusion pressure (SPP) and skin blood flow (SBF) are determined from each clearance curve. In a prospective study among 26 diabetic patients presenting with ulcers or gangrene of the foot, both SPP and SBF were determined preoperatively on the selected level of surgery and on adjacent amputation sites. These 26 patients underwent 12 minor foot amputations and 17 major lower limb amputations. Two of these amputations failed to heal. SBF values appeared indicative for the degree of peripheral vascular disease, as low SBF values were found with low SPP values. SPP determinations revealed good predictive values: All surgical procedures healed when SPP>20 mmHg, but 2 out of 3 failed when SPP<2 mmHg. If SPP values would have been decisive, the amputation would have been converted to a lower level in 6 out of 17 cases. This modified scintigrafic technique provides accurate objective information for amputation level selection.

  9. Suitability of Yin Yang 1 transcript and protein levels for biomarker studies in B cell non-Hodgkin lymphoma.

    Science.gov (United States)

    Arribas Arranz, Jéssica; Winter, Dalia Nilufar; Drexler, Hans Günter; Eberth, Sonja

    2018-01-01

    Yin Yang 1 (YY1) is a transcription factor that plays an important role during all stages of B cell differentiation. Several studies reported upregulation of YY1 in B cell derived lymphoma, indicating that it might act as an oncogene. Furthermore, aberrant YY1 expression has been associated with survival in some entities of B cell non-Hodgkin lymphoma (B-NHL), suggesting that YY1 could be a valuable biomarker in B-NHL. However, studies are controversial and methodologically disparate, partially because some studies are based on transcript levels while others rely on YY1 protein data. Therefore, we aimed to investigate the dependence of YY1 protein levels on YY1 transcription. A panel of human cell lines representing different B-NHL subtypes was used to test for the correlation of YY1 mRNA and protein levels which were determined by quantitative PCR and immunoblotting. To analyze YY1 mRNA and YY1 protein stability cells were treated with actinomycin-D and cycloheximide, respectively. siRNAs were transfected to knockdown YY1 . Kaplan-Meier survival analyses were performed with data from published patient cohorts. Pearson's correlation analyses were assessed and statistical power was examined by Student's t-test. In the analyzed panel of B-NHL cell lines YY1 transcript levels do not correlate with their cellular protein amounts. YY1 protein levels were unaffected by transient block of transcription or by targeting YY1 mRNA using siRNA. Additionally, global inhibition of translation up to 48 h did not alter protein levels of YY1, indicating that YY1 is a highly stable protein in B-NHL. Furthermore, in a retrospective analysis of two different B-NHL cohorts, YY1 transcript levels had no impact on patients' survival probabilities. Our results point out the necessity to focus on YY1 protein expression to understand the potential role of YY1 as an oncogene and to unravel its suitability as clinical biomarker in B-NHL.

  10. Circadian transcription factor BMAL1 regulates innate immunity against select RNA viruses.

    Science.gov (United States)

    Majumdar, Tanmay; Dhar, Jayeeta; Patel, Sonal; Kondratov, Roman; Barik, Sailen

    2017-02-01

    BMAL1 (brain and muscle ARNT-like protein 1, also known as MOP3 or ARNT3) belongs to the family of the basic helix-loop-helix (bHLH)-PAS domain-containing transcription factors, and is a key component of the molecular oscillator that generates circadian rhythms. Here, we report that BMAL1-deficient cells are significantly more susceptible to infection by two major respiratory viruses of the Paramyxoviridae family, namely RSV and PIV3. Embryonic fibroblasts from Bmal1 -/- mice produced nearly 10-fold more progeny virus than their wild type controls. These results were supported by animal studies whereby pulmonary infection of RSV produced a more severe disease and morbidity in Bmal1 -/- mice. These results show that BMAL1 can regulate cellular innate immunity against specific RNA viruses.

  11. Process for Selecting System Level Assessments for Human System Technologies

    Science.gov (United States)

    Watts, James; Park, John

    2006-01-01

    The integration of many life support systems necessary to construct a stable habitat is difficult. The correct identification of the appropriate technologies and corresponding interfaces is an exhaustive process. Once technologies are selected secondary issues such as mechanical and electrical interfaces must be addressed. The required analytical and testing work must be approached in a piecewise fashion to achieve timely results. A repeatable process has been developed to identify and prioritize system level assessments and testing needs. This Assessment Selection Process has been defined to assess cross cutting integration issues on topics at the system or component levels. Assessments are used to identify risks, encourage future actions to mitigate risks, or spur further studies.

  12. Evaluation and selection of candidate high-level waste forms

    International Nuclear Information System (INIS)

    1982-03-01

    Seven candidate waste forms being developed under the direction of the Department of Energy's National High-Level Waste (HLW) Technology Program, were evaluated as potential media for the immobilization and geologic disposal of high-level nuclear wastes. The evaluation combined preliminary waste form evaluations conducted at DOE defense waste-sites and independent laboratories, peer review assessments, a product performance evaluation, and a processability analysis. Based on the combined results of these four inputs, two of the seven forms, borosilicate glass and a titanate based ceramic, SYNROC, were selected as the reference and alternative forms for continued development and evaluation in the National HLW Program. Both the glass and ceramic forms are viable candidates for use at each of the DOE defense waste-sites; they are also potential candidates for immobilization of commercial reprocessing wastes. This report describes the waste form screening process, and discusses each of the four major inputs considered in the selection of the two forms

  13. Using Poisson mixed-effects model to quantify transcript-level gene expression in RNA-Seq.

    Science.gov (United States)

    Hu, Ming; Zhu, Yu; Taylor, Jeremy M G; Liu, Jun S; Qin, Zhaohui S

    2012-01-01

    RNA sequencing (RNA-Seq) is a powerful new technology for mapping and quantifying transcriptomes using ultra high-throughput next-generation sequencing technologies. Using deep sequencing, gene expression levels of all transcripts including novel ones can be quantified digitally. Although extremely promising, the massive amounts of data generated by RNA-Seq, substantial biases and uncertainty in short read alignment pose challenges for data analysis. In particular, large base-specific variation and between-base dependence make simple approaches, such as those that use averaging to normalize RNA-Seq data and quantify gene expressions, ineffective. In this study, we propose a Poisson mixed-effects (POME) model to characterize base-level read coverage within each transcript. The underlying expression level is included as a key parameter in this model. Since the proposed model is capable of incorporating base-specific variation as well as between-base dependence that affect read coverage profile throughout the transcript, it can lead to improved quantification of the true underlying expression level. POME can be freely downloaded at http://www.stat.purdue.edu/~yuzhu/pome.html. yuzhu@purdue.edu; zhaohui.qin@emory.edu Supplementary data are available at Bioinformatics online.

  14. Selective transcription and cellular proliferation induced by PDGF require histone deacetylase activity

    International Nuclear Information System (INIS)

    Catania, Annunziata; Iavarone, Carlo; Carlomagno, Stella M.; Chiariello, Mario

    2006-01-01

    Histone deacetylases (HDACs) are key regulatory enzymes involved in the control of gene expression and their inhibition by specific drugs has been widely correlated to cell cycle arrest, terminal differentiation, and apoptosis. Here, we investigated whether HDAC activity was required for PDGF-dependent signal transduction and cellular proliferation. Exposure of PDGF-stimulated NIH3T3 fibroblasts to the HDAC inhibitor trichostatin A (TSA) potently repressed the expression of a group of genes correlated to PDGF-dependent cellular growth and pro-survival activity. Moreover, we show that TSA interfered with STAT3-dependent transcriptional activity induced by PDGF. Still, neither phosphorylation nor nuclear translocation and DNA-binding in vitro and in vivo of STAT3 were affected by using TSA to interfere with PDGF stimulation. Finally, TSA treatment resulted in the suppression of PDGF-dependent cellular proliferation without affecting cellular survival of NIH3T3 cells. Our data indicate that inhibition of HDAC activity antagonizes the mitogenic effect of PDGF, suggesting that these drugs may specifically act on the expression of STAT-dependent, PDGF-responsive genes

  15. Transcription factor levels enable metabolic diversification of single cells of environmental bacteria.

    Science.gov (United States)

    Guantes, Raúl; Benedetti, Ilaria; Silva-Rocha, Rafael; de Lorenzo, Víctor

    2016-05-01

    Transcriptional noise is a necessary consequence of the molecular events that drive gene expression in prokaryotes. However, some environmental microorganisms that inhabit polluted sites, for example, the m-xylene degrading soil bacterium Pseudomonas putida mt-2 seem to have co-opted evolutionarily such a noise for deploying a metabolic diversification strategy that allows a cautious exploration of new chemical landscapes. We have examined this phenomenon under the light of deterministic and stochastic models for activation of the main promoter of the master m-xylene responsive promoter of the system (Pu) by its cognate transcriptional factor (XylR). These analyses consider the role of co-factors for Pu activation and determinants of xylR mRNA translation. The model traces the onset and eventual disappearance of the bimodal distribution of Pu activity along time to the growth-phase dependent abundance of XylR itself, that is, very low in exponentially growing cells and high in stationary. This tenet was validated by examining the behaviour of a Pu-GFP fusion in a P. putida strain in which xylR expression was engineered under the control of an IPTG-inducible system. This work shows how a relatively simple regulatory scenario (for example, growth-phase dependent expression of a limiting transcription factor) originates a regime of phenotypic diversity likely to be advantageous in competitive environmental settings.

  16. Does positive selection drive transcription factor binding site turnover? A test with Drosophila cis-regulatory modules.

    Directory of Open Access Journals (Sweden)

    Bin Z He

    2011-04-01

    Full Text Available Transcription factor binding site(s (TFBS gain and loss (i.e., turnover is a well-documented feature of cis-regulatory module (CRM evolution, yet little attention has been paid to the evolutionary force(s driving this turnover process. The predominant view, motivated by its widespread occurrence, emphasizes the importance of compensatory mutation and genetic drift. Positive selection, in contrast, although it has been invoked in specific instances of adaptive gene expression evolution, has not been considered as a general alternative to neutral compensatory evolution. In this study we evaluate the two hypotheses by analyzing patterns of single nucleotide polymorphism in the TFBS of well-characterized CRM in two closely related Drosophila species, Drosophila melanogaster and Drosophila simulans. An important feature of the analysis is classification of TFBS mutations according to the direction of their predicted effect on binding affinity, which allows gains and losses to be evaluated independently along the two phylogenetic lineages. The observed patterns of polymorphism and divergence are not compatible with neutral evolution for either class of mutations. Instead, multiple lines of evidence are consistent with contributions of positive selection to TFBS gain and loss as well as purifying selection in its maintenance. In discussion, we propose a model to reconcile the finding of selection driving TFBS turnover with constrained CRM function over long evolutionary time.

  17. Low-level waste disposal site selection demonstration

    International Nuclear Information System (INIS)

    Rogers, V.C.

    1984-01-01

    This paper discusses the results of recent studies undertaken at EPRI related to low-level waste disposal technology. The initial work provided an overview of the state of the art including an assessment of its influence upon transportation costs and waste form requirements. The paper discusses work done on the overall system design aspects and computer modeling of disposal site performance characteristics. The results of this analysis are presented and provide a relative ranking of the importance of disposal parameters. This allows trade-off evaluations to be made of factors important in the design of a shallow land burial facility. To help minimize the impact of a shortage of low-level radioactive waste disposal sites, EPRI is closely observing the development of bellweather projects for developing new sites. The purpose of this activity is to provide information about lessons learned in those projects in order to expedite the development of additional disposal facilities. This paper describes most of the major stems in selecting a low-level radioactive waste disposal site in Texas. It shows how the Texas Low-Level Radioactive Waste Disposal Authority started with a wide range of potential siting areas in Texas and narrowed its attention down to a few preferred sites. The parameters used to discriminate between large areas of Texas and, eventually, 50 candidate disposal sites are described, along with the steps in the process. The Texas process is compared to those described in DOE and EPRI handbooks on site selection and to pertinent NRC requirements. The paper also describes how an inventory of low-level waste specific to Texas was developed and applied in preliminary performance assessments of two candidate sites. Finally, generic closure requirements and closure operations for low-level waste facilities in arid regions are given

  18. A synthetic interaction screen identifies factors selectively required for proliferation and TERT transcription in p53-deficient human cancer cells.

    Directory of Open Access Journals (Sweden)

    Li Xie

    Full Text Available Numerous genetic and epigenetic alterations render cancer cells selectively dependent on specific genes and regulatory pathways, and represent potential vulnerabilities that can be therapeutically exploited. Here we describe an RNA interference (RNAi-based synthetic interaction screen to identify genes preferentially required for proliferation of p53-deficient (p53- human cancer cells. We find that compared to p53-competent (p53+ human cancer cell lines, diverse p53- human cancer cell lines are preferentially sensitive to loss of the transcription factor ETV1 and the DNA damage kinase ATR. In p53- cells, RNAi-mediated knockdown of ETV1 or ATR results in decreased expression of the telomerase catalytic subunit TERT leading to growth arrest, which can be reversed by ectopic TERT expression. Chromatin immunoprecipitation analysis reveals that ETV1 binds to a region downstream of the TERT transcriptional start-site in p53- but not p53+ cells. We find that the role of ATR is to phosphorylate and thereby stabilize ETV1. Our collective results identify a regulatory pathway involving ETV1, ATR, and TERT that is preferentially important for proliferation of diverse p53- cancer cells.

  19. Regulation of Budding Yeast CENP-A levels Prevents Misincorporation at Promoter Nucleosomes and Transcriptional Defects.

    Directory of Open Access Journals (Sweden)

    Erica M Hildebrand

    2016-03-01

    Full Text Available The exclusive localization of the histone H3 variant CENP-A to centromeres is essential for accurate chromosome segregation. Ubiquitin-mediated proteolysis helps to ensure that CENP-A does not mislocalize to euchromatin, which can lead to genomic instability. Consistent with this, overexpression of the budding yeast CENP-A(Cse4 is lethal in cells lacking Psh1, the E3 ubiquitin ligase that targets CENP-A(Cse4 for degradation. To identify additional mechanisms that prevent CENP-A(Cse4 misincorporation and lethality, we analyzed the genome-wide mislocalization pattern of overexpressed CENP-A(Cse4 in the presence and absence of Psh1 by chromatin immunoprecipitation followed by high throughput sequencing. We found that ectopic CENP-A(Cse4 is enriched at promoters that contain histone H2A.Z(Htz1 nucleosomes, but that H2A.Z(Htz1 is not required for CENP-A(Cse4 mislocalization. Instead, the INO80 complex, which removes H2A.Z(Htz1 from nucleosomes, promotes the ectopic deposition of CENP-A(Cse4. Transcriptional profiling revealed gene expression changes in the psh1Δ cells overexpressing CENP-A(Cse4. The down-regulated genes are enriched for CENP-A(Cse4 mislocalization to promoters, while the up-regulated genes correlate with those that are also transcriptionally up-regulated in an htz1Δ strain. Together, these data show that regulating centromeric nucleosome localization is not only critical for maintaining centromere function, but also for ensuring accurate promoter function and transcriptional regulation.

  20. FLO11 gene length and transcriptional level affect biofilm-forming ability of wild flor strains of Saccharomyces cerevisiae.

    Science.gov (United States)

    Zara, Giacomo; Zara, Severino; Pinna, Claudia; Marceddu, Salvatore; Budroni, Marilena

    2009-12-01

    In Saccharomyces cerevisiae, FLO11 encodes an adhesin that is associated with different phenotypes, such as adherence to solid surfaces, hydrophobicity, mat and air-liquid biofilm formation. In the present study, we analysed FLO11 allelic polymorphisms and FLO11-associated phenotypes of 20 flor strains. We identified 13 alleles of different lengths, varying from 3.0 to 6.1 kb, thus demonstrating that FLO11 is highly polymorphic. Two alleles of 3.1 and 5.0 kb were cloned into strain BY4742 to compare the FLO11-associated phenotypes in the same genetic background. We show that there is a significant correlation between biofilm-forming ability and FLO11 length both in different and in the same genetic backgrounds. Moreover, we propose a multiple regression model that allows prediction of air-liquid biofilm-forming ability on the basis of transcription levels and lengths of FLO11 alleles in a population of S. cerevisiae flor strains. Considering that transcriptional differences are only partially explained by the differences in the promoter sequences, our results are consistent with the hypothesis that FLO11 transcription levels are strongly influenced by genetic background and affect biofilm-forming ability.

  1. Control of transcriptional repression of the vitellogenin receptor gene in largemouth bass (Micropterus salmoides) by select estrogen receptors isotypes.

    Science.gov (United States)

    Dominguez, Gustavo A; Bisesi, Joseph H; Kroll, Kevin J; Denslow, Nancy D; Sabo-Attwood, Tara

    2014-10-01

    The vitellogenin receptor (Vtgr) plays an important role in fish reproduction. This receptor functions to incorporate vitellogenin (Vtg), a macromolecule synthesized and released from the liver in the bloodstream, into oocytes where it is processed into yolk. Although studies have focused on the functional role of Vtgr in fish, the mechanistic control of this gene is still unexplored. Here we report the identification and analysis of the first piscine 5' regulatory region of the vtgr gene which was cloned from largemouth bass (Micropterus salmoides). Using this putative promoter sequence, we investigated a role for hormones, including insulin and 17β-estradiol (E2), in transcriptional regulation through cell-based reporter assays. No effect of insulin was observed, however, E2 was able to repress transcriptional activity of the vtgr promoter through select estrogen receptor subtypes, Esr1 and Esr2a but not Esr2b. Electrophoretic mobility shift assay demonstrated that Esr1 likely interacts with the vtgr promoter region through half ERE and/or SP1 sites, in part. Finally we also show that ethinylestradiol (EE2), but not bisphenol-A (BPA), represses promoter activity similarly to E2. These results reveal for the first time that the Esr1 isoform may play an inhibitory role in the expression of LMB vtgr mRNA under the influence of E2, and potent estrogens such as EE2. In addition, this new evidence suggests that vtgr may be a target of select endocrine disrupting compounds through environmental exposures. © The Author 2014. Published by Oxford University Press on behalf of the Society of Toxicology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  2. Prospective comparison of noninvasive techniques for amputation level selection

    International Nuclear Information System (INIS)

    Malone, J.M.; Anderson, G.G.; Lalka, S.G.; Hagaman, R.M.; Henry, R.; McIntyre, K.E.; Bernhard, V.M.

    1987-01-01

    This study prospectively compared the following tests for their accuracy in amputation level selection: transcutaneous oxygen, transcutaneous carbon dioxide, transcutaneous oxygen-to-transcutaneous carbon dioxide, foot-to-chest transcutaneous oxygen, intradermal xenon-133, ankle-brachial index, and absolute popliteal artery Doppler systolic pressure. All metabolic parameters had a high degree of statistical accuracy in predicting amputation healing whereas none of the other tests had statistical reliability. Amputation site healing was not affected by the presence of diabetes mellitus nor were the test results for any of the metabolic parameters

  3. Azimuth selection for sea level measurements using geodetic GPS receivers

    Science.gov (United States)

    Wang, Xiaolei; Zhang, Qin; Zhang, Shuangcheng

    2018-03-01

    Based on analysis of Global Positioning System (GPS) multipath signals recorded by a geodetic GPS receiver, GPS Reflectometry (GPS-R) has demonstrated unique advantages in relation to sea level monitoring. Founded on multipath reflectometry theory, sea level changes can be measured by GPS-R through spectral analysis of recorded signal-to-noise ratio data. However, prior to estimating multipath parameters, it is necessary to define azimuth and elevation angle mask to ensure the reflecting zones are on water. Here, a method is presented to address azimuth selection, a topic currently under active development in the field of GPS-R. Data from three test sites: the Kachemak Bay GPS site PBAY in Alaska (USA), Friday Harbor GPS site SC02 in the San Juan Islands (USA), and Brest Harbor GPS site BRST in Brest (France) are analyzed. These sites are located in different multipath environments, from a rural coastal area to a busy harbor, and they experience different tidal ranges. Estimates by the GPS tide gauges at azimuths selected by the presented method are compared with measurements from physical tide gauges and acceptable correspondence found for all three sites.

  4. Reducing pesticide level in wine by selective filtration

    Directory of Open Access Journals (Sweden)

    Lempereur Valérie

    2014-01-01

    Full Text Available Wine Pesticide residues, even when below grape regulatory limit, are a concern for consumers and have an impact on the export potential of wine in certain markets. A consortium of European SMEs (www.adfimax.com has developed a product that reduces the level of mycotoxins and pesticides in wine while keeping all other wine parameter identical. The product is derived from renewable vegetable fiber. The production process includes both activation and micronisation. The usage recommendation is to substitute only the pre-coat, typically perlite, by the product at 1 or 1.5 kg⋅m−2 without changing the other layer (body feed typically kieselguhr. This paper describes the results of numerous industrial trials that were performed in France, Luxemburg, Germany and Spain. The impact of the product on the wine oenological characteristics was evaluated for different wine (white, red and rosé in different countries and for different grape variety (including Cabernet sauvignon, Merlot and Gamay. Results showed a reduction of the test wine pesticide level of 50% to 60% for all pesticides compared to the blank. Level of pesticide analyzed in the cake where extremely high at a level of a 1,000 times greater than the filtered wine showing the ability of the product to selectively capture the pesticides molecules.

  5. PPARγ activates ABCA1 gene transcription but reduces the level of ABCA1 protein in HepG2 cells

    International Nuclear Information System (INIS)

    Mogilenko, Denis A.; Shavva, Vladimir S.; Dizhe, Ella B.; Orlov, Sergey V.; Perevozchikov, Andrej P.

    2010-01-01

    Research highlights: → PPARγ activates ABCA1 gene expression but decreases ABCA1 protein content in human hepatoma cell line HepG2. → Treatment of HepG2 cells with PPARγ agonist GW1929 leads to dissociation of LXRβ from ABCA1-LXRβ complex. → Inhibition of protein kinases MEK1/2 abolishes PPARγ-mediated dissociation of LXRβ from ABCA1/LXRβ complex. → Activation of PPARγ leads to increasing of the level of LXRβ associated with LXRE within ABCA1 gene promoter. -- Abstract: Synthesis of ABCA1 protein in liver is necessary for high-density lipoproteins (HDL) formation in mammals. Nuclear receptor PPARγ is known as activator of ABCA1 expression, but details of PPARγ-mediated regulation of ABCA1 at both transcriptional and post-transcriptional levels in hepatocytes have not still been well elucidated. In this study we have shown, that PPARγ activates ABCA1 gene transcription in human hepatoma cells HepG2 through increasing of LXRβ binding with promoter region of ABCA1 gene. Treatment of HepG2 cells with PPARγ agonist GW1929 leads to dissociation of LXRβ from ABCA1/LXRβ complex and to nuclear translocation of this nuclear receptor resulting in reduction of ABCA1 protein level 24 h after treatment. Inhibition of protein kinases MEK1/2 abolishes PPARγ-mediated dissociation of LXRβ from ABCA1/LXRβ complex, but does not block PPARγ-dependent down-regulation of ABCA1 protein in HepG2 cells. These data suggest that PPARγ may be important for regulation of the level of hepatic ABCA1 protein and indicate the new interplays between PPARγ, LXRβ and MEK1/2 in regulation of ABCA1 mRNA and protein expression.

  6. Increased levels of NOTCH1, NF-kappaB, and other interconnected transcription factors characterize primitive sets of hematopoietic stem cells.

    Science.gov (United States)

    Panepucci, Rodrigo Alexandre; Oliveira, Lucila Habib B; Zanette, Dalila Luciola; Viu Carrara, Rita de Cassia; Araujo, Amélia Goes; Orellana, Maristela Delgado; Bonini de Palma, Patrícia Vianna; Menezes, Camila C B O; Covas, Dimas Tadeu; Zago, Marco Antonio

    2010-03-01

    As previously shown, higher levels of NOTCH1 and increased NF-kappaB signaling is a distinctive feature of the more primitive umbilical cord blood (UCB) CD34+ hematopoietic stem cells (HSCs), as compared to bone marrow (BM). Differences between BM and UCB cell composition also account for this finding. The CD133 marker defines a more primitive cell subset among CD34+ HSC with a proposed hemangioblast potential. To further evaluate the molecular basis related to the more primitive characteristics of UCB and CD133+ HSC, immunomagnetically purified human CD34+ and CD133+ cells from BM and UCB were used on gene expression microarrays studies. UCB CD34+ cells contained a significantly higher proportion of CD133+ cells than BM (70% and 40%, respectively). Cluster analysis showed that BM CD133+ cells grouped with the UCB cells (CD133+ and CD34+) rather than to BM CD34+ cells. Compared with CD34+ cells, CD133+ had a higher expression of many transcription factors (TFs). Promoter analysis on all these TF genes revealed a significantly higher frequency (than expected by chance) of NF-kappaB-binding sites (BS), including potentially novel NF-kappaB targets such as RUNX1, GATA3, and USF1. Selected transcripts of TF related to primitive hematopoiesis and self-renewal, such as RUNX1, GATA3, USF1, TAL1, HOXA9, HOXB4, NOTCH1, RELB, and NFKB2 were evaluated by real-time PCR and were all significantly positively correlated. Taken together, our data indicate the existence of an interconnected transcriptional network characterized by higher levels of NOTCH1, NF-kappaB, and other important TFs on more primitive HSC sets.

  7. Chorionic gonadotropin regulates the transcript level of VHL, p53, and HIF-2alpha in human granulosa lutein cells.

    Science.gov (United States)

    Herr, D; Keck, C; Tempfer, C; Pietrowski, Detlef

    2004-12-01

    The ovarian corpus luteum plays a critical role in reproduction being the primary source of circulating progesterone. After ovulation the corpus luteum is build by avascular granulosa lutein cells through rapid vascularization regulated by gonadotropic hormones. The present study was performed to investigate whether this process might be influenced by the human chorionic gonadotropin (hCG)-dependent expression of different tumor suppressor genes and hypoxia dependent transcription factors. RNA was isolated from cultured granulosa lutein cells, transcribed into cDNA, and the transcript level of following genes were determined: RB-1, VHL, NF-1, NF-2, Wt-1, p53, APC, and hypoxia inducible factor-1 (HIF-1), -2, and -3alpha. Additionally, the influence of hCG on the expression of VHL, p53, and HIf2alpha were investigated. We demonstrate that in human granulosa lutein cells the tumor suppressor genes RB-1, VHL, NF-1, NF-2, Wt-1, p53, and APC and the hypoxia dependent transcription factors HIF-1alpha, -2alpha, and -3alpha are expressed. In addition, we showed that hCG regulates the expression of p53, VHL, and HIF-2alpha. Our results indicate that hCG may determine the growth and development of the corpus luteum by mediating hypoxic and apoptotic pathways in human granulosa lutein cells. Copyright 2004 Wiley-Liss, Inc.

  8. tortuga refines Notch pathway gene expression in the zebrafish presomitic mesoderm at the post-transcriptional level.

    Science.gov (United States)

    Dill, Kariena K; Amacher, Sharon L

    2005-11-15

    We have identified the zebrafish tortuga (tor) gene by an ENU-induced mutation that disrupts the presomitic mesoderm (PSM) expression of Notch pathway genes. In tor mutants, Notch pathway gene expression persists in regions of the PSM where expression is normally off in wild type embryos. The expression of hairy/Enhancer of split-related 1 (her1) is affected first, followed by the delta genes deltaC and deltaD, and finally, by another hairy/Enhancer of split-related gene, her7. In situ hybridization with intron-specific probes for her1 and deltaC indicates that transcriptional bursts of expression are normal in tor mutants, suggesting that tor normally functions to refine her1 and deltaC message levels downstream of transcription. Despite the striking defects in Notch pathway gene expression, somite boundaries form normally in tor mutant embryos, although somitic mesoderm defects are apparent later, when cells mature to form muscle fibers. Thus, while the function of Notch pathway genes is required for proper somite formation, the tor mutant phenotype suggests that precise oscillations of Notch pathway transcripts are not essential for establishing segmental pattern in the presomitic mesoderm.

  9. Maternal protein restriction induced-hypertension is associated to oxidative disruption at transcriptional and functional levels in the medulla oblongata.

    Science.gov (United States)

    de Brito Alves, José L; de Oliveira, Jéssica M D; Ferreira, Diorginis J S; Barros, Monique A de V; Nogueira, Viviane O; Alves, Débora S; Vidal, Hubert; Leandro, Carol G; Lagranha, Cláudia J; Pirola, Luciano; da Costa-Silva, João H

    2016-12-01

    Maternal protein restriction during pregnancy and lactation predisposes the adult offspring to sympathetic overactivity and arterial hypertension. Although the underlying mechanisms are poorly understood, dysregulation of the oxidative balance has been proposed as a putative trigger of neural-induced hypertension. The aim of the study was to evaluate the association between the oxidative status at transcriptional and functional levels in the medulla oblongata and maternal protein restriction induced-hypertension. Wistar rat dams were fed a control (normal protein; 17% protein) or a low protein ((Lp); 8% protein) diet during pregnancy and lactation, and male offspring was studied at 90 days of age. Direct measurements of baseline arterial blood pressure (ABP) and heart rate (HR) were recorded in awakened offspring. In addition, quantitative RT-PCR was used to assess the mRNA expression of superoxide dismutase 1 (SOD1) and 2 (SOD2), catalase (CAT), glutathione peroxidase (GPx), Glutamatergic receptors (Grin1, Gria1 and Grm1) and GABA(A)-receptor-associated protein like 1 (Gabarapl1). Malondialdehyde (MDA) levels, CAT and SOD activities were examined in ventral and dorsal medulla. Lp rats exhibited higher ABP. The mRNA expression levels of SOD2, GPx and Gabarapl1 were down regulated in medullary tissue of Lp rats (Pmedulla. Taken together, our data suggest that maternal protein restriction induced-hypertension is associated with medullary oxidative dysfunction at transcriptional level and with impaired antioxidant capacity in the ventral medulla. © 2016 John Wiley & Sons Australia, Ltd.

  10. Identification and analysis of evolutionary selection pressures acting at the molecular level in five forkhead subfamilies.

    Science.gov (United States)

    Fetterman, Christina D; Rannala, Bruce; Walter, Michael A

    2008-09-24

    Members of the forkhead gene family act as transcription regulators in biological processes including development and metabolism. The evolution of forkhead genes has not been widely examined and selection pressures at the molecular level influencing subfamily evolution and differentiation have not been explored. Here, in silico methods were used to examine selection pressures acting on the coding sequence of five multi-species FOX protein subfamily clusters; FoxA, FoxD, FoxI, FoxO and FoxP. Application of site models, which estimate overall selection pressures on individual codons throughout the phylogeny, showed that the amino acid changes observed were either neutral or under negative selection. Branch-site models, which allow estimated selection pressures along specified lineages to vary as compared to the remaining phylogeny, identified positive selection along branches leading to the FoxA3 and Protostomia clades in the FoxA cluster and the branch leading to the FoxO3 clade in the FoxO cluster. Residues that may differentiate paralogs were identified in the FoxA and FoxO clusters and residues that differentiate orthologs were identified in the FoxA cluster. Neutral amino acid changes were identified in the forkhead domain of the FoxA, FoxD and FoxP clusters while positive selection was identified in the forkhead domain of the Protostomia lineage of the FoxA cluster. A series of residues under strong negative selection adjacent to the N- and C-termini of the forkhead domain were identified in all clusters analyzed suggesting a new method for refinement of domain boundaries. Extrapolation of domains among cluster members in conjunction with selection pressure information allowed prediction of residue function in the FoxA, FoxO and FoxP clusters and exclusion of known domain function in residues of the FoxA and FoxI clusters. Consideration of selection pressures observed in conjunction with known functional information allowed prediction of residue function and

  11. Identification and analysis of evolutionary selection pressures acting at the molecular level in five forkhead subfamilies

    Directory of Open Access Journals (Sweden)

    Rannala Bruce

    2008-09-01

    Full Text Available Abstract Background Members of the forkhead gene family act as transcription regulators in biological processes including development and metabolism. The evolution of forkhead genes has not been widely examined and selection pressures at the molecular level influencing subfamily evolution and differentiation have not been explored. Here, in silico methods were used to examine selection pressures acting on the coding sequence of five multi-species FOX protein subfamily clusters; FoxA, FoxD, FoxI, FoxO and FoxP. Results Application of site models, which estimate overall selection pressures on individual codons throughout the phylogeny, showed that the amino acid changes observed were either neutral or under negative selection. Branch-site models, which allow estimated selection pressures along specified lineages to vary as compared to the remaining phylogeny, identified positive selection along branches leading to the FoxA3 and Protostomia clades in the FoxA cluster and the branch leading to the FoxO3 clade in the FoxO cluster. Residues that may differentiate paralogs were identified in the FoxA and FoxO clusters and residues that differentiate orthologs were identified in the FoxA cluster. Neutral amino acid changes were identified in the forkhead domain of the FoxA, FoxD and FoxP clusters while positive selection was identified in the forkhead domain of the Protostomia lineage of the FoxA cluster. A series of residues under strong negative selection adjacent to the N- and C-termini of the forkhead domain were identified in all clusters analyzed suggesting a new method for refinement of domain boundaries. Extrapolation of domains among cluster members in conjunction with selection pressure information allowed prediction of residue function in the FoxA, FoxO and FoxP clusters and exclusion of known domain function in residues of the FoxA and FoxI clusters. Conclusion Consideration of selection pressures observed in conjunction with known

  12. Low-level radioactive waste technology: a selected, annotated bibliography

    International Nuclear Information System (INIS)

    Fore, C.S.; Vaughan, N.D.; Hyder, L.K.

    1980-10-01

    This annotated bibliography of 447 references contains scientific, technical, economic, and regulatory information relevant to low-level radioactive waste technology. The bibliography focuses on environmental transport, disposal site, and waste treatment studies. The publication covers both domestic and foreign literature for the period 1952 to 1979. Major chapters selected are Chemical and Physical Aspects; Container Design and Performance; Disposal Site; Environmental Transport; General Studies and Reviews; Geology, Hydrology and Site Resources; Regulatory and Economic Aspects; Transportation Technology; Waste Production; and Waste Treatment. Specialized data fields have been incorporated into the data file to improve the ease and accuracy of locating pertinent references. Specific radionuclides for which data are presented are listed in the Measured Radionuclides field, and specific parameters which affect the migration of these radionuclides are presented in the Measured Parameters field. In addition, each document referenced in this bibliography has been assigned a relevance number to facilitate sorting the documents according to their pertinence to low-level radioactive waste technology. The documents are rated 1, 2, 3, or 4, with 1 indicating direct applicability to low-level radioactive waste technology and 4 indicating that a considerable amount of interpretation is required for the information presented to be applied. The references within each chapter are arranged alphabetically by leading author, corporate affiliation, or title of the document. Indexes are provide for (1) author(s), (2) keywords, (3) subject category, (4) title, (5) geographic location, (6) measured parameters, (7) measured radionuclides, and (8) publication description

  13. Low-level radioactive waste technology: a selected, annotated bibliography

    Energy Technology Data Exchange (ETDEWEB)

    Fore, C.S.; Vaughan, N.D.; Hyder, L.K.

    1980-10-01

    This annotated bibliography of 447 references contains scientific, technical, economic, and regulatory information relevant to low-level radioactive waste technology. The bibliography focuses on environmental transport, disposal site, and waste treatment studies. The publication covers both domestic and foreign literature for the period 1952 to 1979. Major chapters selected are Chemical and Physical Aspects; Container Design and Performance; Disposal Site; Environmental Transport; General Studies and Reviews; Geology, Hydrology and Site Resources; Regulatory and Economic Aspects; Transportation Technology; Waste Production; and Waste Treatment. Specialized data fields have been incorporated into the data file to improve the ease and accuracy of locating pertinent references. Specific radionuclides for which data are presented are listed in the Measured Radionuclides field, and specific parameters which affect the migration of these radionuclides are presented in the Measured Parameters field. In addition, each document referenced in this bibliography has been assigned a relevance number to facilitate sorting the documents according to their pertinence to low-level radioactive waste technology. The documents are rated 1, 2, 3, or 4, with 1 indicating direct applicability to low-level radioactive waste technology and 4 indicating that a considerable amount of interpretation is required for the information presented to be applied. The references within each chapter are arranged alphabetically by leading author, corporate affiliation, or title of the document. Indexes are provide for (1) author(s), (2) keywords, (3) subject category, (4) title, (5) geographic location, (6) measured parameters, (7) measured radionuclides, and (8) publication description.

  14. Alterations in the neuropeptide galanin system in major depressive disorder involve levels of transcripts, methylation, and peptide

    Science.gov (United States)

    Barde, Swapnali; Rüegg, Joelle; Prud’homme, Josée; Ekström, Tomas J.; Palkovits, Miklos; Turecki, Gustavo; Bagdy, Gyorgy; Ihnatko, Robert; Theodorsson, Elvar; Juhasz, Gabriella; Diaz-Heijtz, Rochellys; Mechawar, Naguib; Hökfelt, Tomas G. M.

    2016-01-01

    Major depressive disorder (MDD) is a substantial burden to patients, families, and society, but many patients cannot be treated adequately. Rodent experiments suggest that the neuropeptide galanin (GAL) and its three G protein-coupled receptors, GAL1–3, are involved in mood regulation. To explore the translational potential of these results, we assessed the transcript levels (by quantitative PCR), DNA methylation status (by bisulfite pyrosequencing), and GAL peptide by RIA of the GAL system in postmortem brains from depressed persons who had committed suicide and controls. Transcripts for all four members were detected and showed marked regional variations, GAL and galanin receptor 1 (GALR1) being most abundant. Striking increases in GAL and GALR3 mRNA levels, especially in the noradrenergic locus coeruleus and the dorsal raphe nucleus, in parallel with decreased DNA methylation, were found in both male and female suicide subjects as compared with controls. In contrast, GAL and GALR3 transcript levels were decreased, GALR1 was increased, and DNA methylation was increased in the dorsolateral prefrontal cortex of male suicide subjects, however, there were no changes in the anterior cingulate cortex. Thus, GAL and its receptor GALR3 are differentially methylated and expressed in brains of MDD subjects in a region- and sex-specific manner. Such an epigenetic modification in GALR3, a hyperpolarizing receptor, might contribute to the dysregulation of noradrenergic and serotonergic neurons implicated in the pathogenesis of MDD. Thus, one may speculate that a GAL3 antagonist could have antidepressant properties by disinhibiting the firing of these neurons, resulting in increased release of noradrenaline and serotonin in forebrain areas involved in mood regulation. PMID:27940914

  15. Radon gas exposure levels in some selected areas in Egypt

    International Nuclear Information System (INIS)

    Ali, E.M.; Taha, T.M.; Gomaa, M.A.; El-Hussein, A.M.; Ahmed, A.A.

    2005-01-01

    During a summer season of 2003, the atmospheric concentrations of radon gas were measured indoor every one-hour for twenty-four hour measurements in some selected areas, using Pylon-AB4. Two hundreds and forty samples were monitored to determine the concentration of radon gas at each location using high-efficiency Lucas type continuous passive cell. The average values of radon gas concentration were taken in three time intervals 6.00:18.00, 18.00:6.00 and whole day. The average values of indoor radon gas of two locations using three time intervals were 4.82±0.63, 9±0.71 and 6.9±0.33 and 9.6±0.23, 11.82±0.42 and 9.37±0.7 Bq/m /h. respectively. The exposure levels were within the ICRP and EPA recommendations

  16. Low-level radioactive waste technology: a selected, annotated bibliography

    International Nuclear Information System (INIS)

    Fore, C.S.; Carrier, R.F.; Brewster, R.H.; Hyder, L.K.; Barnes, K.A.

    1981-10-01

    This annotated bibliography of 416 references represents the third in a series to be published by the Hazardous Materials Information Center containing scientific, technical, economic, and regulatory information relevant to low-level radioactive waste technology. The bibliography focuses on disposal site, environmental transport, and waste treatment studies as well as general reviews on the subject. The publication covers both domestic and foreign literature for the period 1951 to 1981. Major chapters selected are Chemical and Physical Aspects; Container Design and Performance; Disposal Site; Environmental Transport; General Studies and Reviews; Geology, Hydrology, and Site Resources; Regulatory and Economic Aspects; Social Aspects; Transportation Technology; Waste Production; and Waste Treatment. Entries in each of the chapters are further classified as a field study, laboratory study, theoretical study, or general overview involving one or more of these research areas

  17. Selectivity and Efficiency of Late Transgene Expression by Transcriptionally Targeted Oncolytic Adenoviruses Are Dependent on the Transgene Insertion Strategy

    Science.gov (United States)

    Quirin, Christina; Rohmer, Stanimira; Fernández-Ulibarri, Inés; Behr, Michael; Hesse, Andrea; Engelhardt, Sarah; Erbs, Philippe; Enk, Alexander H.

    2011-01-01

    Abstract Key challenges facing cancer therapy are the development of tumor-specific drugs and potent multimodal regimens. Oncolytic adenoviruses possess the potential to realize both aims by restricting virus replication to tumors and inserting therapeutic genes into the virus genome, respectively. A major effort in this regard is to express transgenes in a tumor-specific manner without affecting virus replication. Using both luciferase as a sensitive reporter and genetic prodrug activation, we show that promoter control of E1A facilitates highly selective expression of transgenes inserted into the late transcription unit. This, however, required multistep optimization of late transgene expression. Transgene insertion via internal ribosome entry site (IRES), splice acceptor (SA), or viral 2A sequences resulted in replication-dependent expression. Unexpectedly, analyses in appropriate substrates and with matching control viruses revealed that IRES and SA, but not 2A, facilitated indirect transgene targeting via tyrosinase promoter control of E1A. Transgene expression via SA was more selective (up to 1,500-fold) but less effective than via IRES. Notably, we also revealed transgene-dependent interference with splicing. Hence, the prodrug convertase FCU1 (a cytosine deaminase–uracil phosphoribosyltransferase fusion protein) was expressed only after optimizing the sequence surrounding the SA site and mutating a cryptic splice site within the transgene. The resulting tyrosinase promoter-regulated and FCU1-encoding adenovirus combined effective oncolysis with targeted prodrug activation therapy of melanoma. Thus, prodrug activation showed potent bystander killing and increased cytotoxicity of the virus up to 10-fold. We conclude that armed oncolytic viruses can be improved substantially by comparing and optimizing strategies for targeted transgene expression, thereby implementing selective and multimodal cancer therapies. PMID:20939692

  18. Transcriptional control of megakaryocyte development.

    Science.gov (United States)

    Goldfarb, A N

    2007-10-15

    Megakaryocytes are highly specialized cells that arise from a bipotent megakaryocytic-erythroid progenitor (MEP). This developmental leap requires coordinated activation of megakaryocyte-specific genes, radical changes in cell cycle properties, and active prevention of erythroid differentiation. These programs result from upregulation of megakaryocyte-selective transcription factors, downregulation of erythroid-selective transcription factors and ongoing mediation of common erythro-megakaryocytic transcription factors. Unlike most developmental programs, no single lineage-unique family of master regulators exerts executive control over the megakaryocytic plan. Rather, an assemblage of non-unique factors and signals converge to determine lineage and differentiation. In human megakaryopoiesis, hereditary disorders of platelet production have confirmed contributions from three distinct transcription factor families. Murine models have extended this repertoire to include multiple additional factors. At a mechanistic level, the means by which these non-unique factors collaborate in the establishment of a perfectly unique cell type remains a central question.

  19. A hairpin within YAP mRNA 3′UTR functions in regulation at post-transcription level

    Energy Technology Data Exchange (ETDEWEB)

    Gao, Yuen; Wang, Yuan; Feng, Jinyan; Feng, Guoxing; Zheng, Minying; Yang, Zhe; Xiao, Zelin; Lu, Zhanping [State Key Laboratory of Medicinal Chemical Biology, Department of Cancer Research, College of Life Sciences, Nankai University, Tianjin 300071 (China); Ye, Lihong [State Key Laboratory of Medicinal Chemical Biology, Department of Biochemistry, College of Life Sciences, Nankai University, Tianjin 300071 (China); Zhang, Xiaodong, E-mail: zhangxd@nankai.edu.cn [State Key Laboratory of Medicinal Chemical Biology, Department of Cancer Research, College of Life Sciences, Nankai University, Tianjin 300071 (China)

    2015-04-03

    The central dogma of gene expression is that DNA is transcribed into messenger RNAs, which in turn serve as the template for protein synthesis. Recently, it has been reported that mRNAs display regulatory roles that rely on their ability to compete for microRNA binding, independent of their protein-coding function. However, the regulatory mechanism of mRNAs remains poorly understood. Here, we report that a hairpin within YAP mRNA 3′untranslated region (3′UTR) functions in regulation at post-transcription level through generating endogenous siRNAs (esiRNAs). Bioinformatics analysis for secondary structure showed that YAP mRNA displayed a hairpin structure (termed standard hairpin, S-hairpin) within its 3′UTR. Surprisingly, we observed that the overexpression of S-hairpin derived from YAP 3′UTR (YAP-sh) increased the luciferase reporter activities of transcriptional factor NF-κB and AP-1 in 293T cells. Moreover, we identified that a fragment from YAP-sh, an esiRNA, was able to target mRNA 3′UTR of NF2 (a member of Hippo-signaling pathway) and YAP mRNA 3′UTR itself in hepatoma cells. Thus, we conclude that the YAP-sh within YAP mRNA 3′UTR may serve as a novel regulatory element, which functions in regulation at post-transcription level. Our finding provides new insights into the mechanism of mRNAs in regulatory function. - Highlights: • An S-hairpin within YAP mRNA 3′UTR possesses regulatory function. • YAP-sh acts as a regulatory element for YAP at post-transcription level. • YAP-sh-3p20, an esiRNA derived from YAP-sh, targets mRNAs of YAP and NF2. • YAP-sh-3p20 depresses the proliferation of HepG2 cells in vitro.

  20. A hairpin within YAP mRNA 3′UTR functions in regulation at post-transcription level

    International Nuclear Information System (INIS)

    Gao, Yuen; Wang, Yuan; Feng, Jinyan; Feng, Guoxing; Zheng, Minying; Yang, Zhe; Xiao, Zelin; Lu, Zhanping; Ye, Lihong; Zhang, Xiaodong

    2015-01-01

    The central dogma of gene expression is that DNA is transcribed into messenger RNAs, which in turn serve as the template for protein synthesis. Recently, it has been reported that mRNAs display regulatory roles that rely on their ability to compete for microRNA binding, independent of their protein-coding function. However, the regulatory mechanism of mRNAs remains poorly understood. Here, we report that a hairpin within YAP mRNA 3′untranslated region (3′UTR) functions in regulation at post-transcription level through generating endogenous siRNAs (esiRNAs). Bioinformatics analysis for secondary structure showed that YAP mRNA displayed a hairpin structure (termed standard hairpin, S-hairpin) within its 3′UTR. Surprisingly, we observed that the overexpression of S-hairpin derived from YAP 3′UTR (YAP-sh) increased the luciferase reporter activities of transcriptional factor NF-κB and AP-1 in 293T cells. Moreover, we identified that a fragment from YAP-sh, an esiRNA, was able to target mRNA 3′UTR of NF2 (a member of Hippo-signaling pathway) and YAP mRNA 3′UTR itself in hepatoma cells. Thus, we conclude that the YAP-sh within YAP mRNA 3′UTR may serve as a novel regulatory element, which functions in regulation at post-transcription level. Our finding provides new insights into the mechanism of mRNAs in regulatory function. - Highlights: • An S-hairpin within YAP mRNA 3′UTR possesses regulatory function. • YAP-sh acts as a regulatory element for YAP at post-transcription level. • YAP-sh-3p20, an esiRNA derived from YAP-sh, targets mRNAs of YAP and NF2. • YAP-sh-3p20 depresses the proliferation of HepG2 cells in vitro

  1. The effect of preferred music genre selection versus preferred song selection on experimentally induced anxiety levels.

    Science.gov (United States)

    Walworth, Darcy DeLoach

    2003-01-01

    The purpose of this study was to investigate the differences of experimentally induced anxiety levels reached by subjects listening to no music (n = 30), subjects listening to music selected by the experimenter from the subject's preferred genre or artist listed as relaxing (n = 30), and subjects listening to a specific song they listed as relaxing (n = 30). Subjects consisted of 90 individuals, male and female, randomly assigned to one of the three groups mentioned above. Subjects in either music group filled out a questionnaire prior to participating in the study indicating their preference of music used for relaxation purposes. Subjects in Experimental Group 1 marked their preferred genres and/or artists, and Experimental Group 2 marked specific songs used for relaxation purposes. While the experimenter hypothesized subjects in Experimental Group 2 would show less anxiety than both the control group and Experimental Group 1, there were no significant differences found between the 2 music groups in anxiety levels reached. However, there was a statistically significant difference between the no music control group and both music groups in the anxiety level reached by subjects. Subjects listening to music, both songs chosen by the experimenter and subject selected songs, showed significantly less anxiety than subjects not listening to music.

  2. Caffeine and theobromine levels in selected Nigerian beverages.

    Science.gov (United States)

    Eteng, M U; Eyong, E U; Eka, O U; Umoh, I B; Ebong, P E; Ettarh, R R

    1999-01-01

    Caffeine and theobromine contents (mg/g) were determined in samples of selected Nigerian beverage products. The beverages were cocoa (Milo, Bournvita, Rosevita and Enervita), coffee (Nescafe, Bongo, and Maxwell House decaffeinated) and tea (Lipton). The theobromine contents of samples of Milo, Bournvita, Rosevita, Enervita, Nescafe, Bongo, Maxwell House decaffeinated coffee and Lipton were 62.10+/-5.21, 64.80+/-6.72, 82.80+/-4.43, 80.37+/-6.80, 27.00+/-4.31, 14.67+/-2.90, 23.46+/-3.13 and 12.60+/-1.52, respectively. The corresponding caffeine contents of these samples were 2.78+/-0.43 (Milo), 3.17+/-0.36 (Bournvita), 0.92+/-0.51 (Rosevita), 1.05+/-0.68 (Enervita), 93.66+/-8.91 (Nescafe), 6.47+/-2.42 (Bongo), 37.22+/-5.34 (Lipton), and 0.21+/-0.11 (Maxwell House decaffeinated coffee). Semi-processed cocoa beverages (Rosevita and Enervita) had significantly (p Nescafe contained significantly (p < 0.05) higher levels of caffeine compared to Maxwell House (decaffeinated coffee) and Bongo. Levels of caffeine in Lipton tea were moderate.

  3. Level selection in leg amputation for arterial occlusive disease

    DEFF Research Database (Denmark)

    Holstein, P

    1982-01-01

    In 102 leg amputations for arterial occlusion including 84 below-knee (BK), 16 above-knee (AD) and 2 through-knee (TK) amputations, the amputation level was determined by means of clinical criteria. The healing results and the selection of levels were then compared with sealed preoperative...... measurements of the skin perfusion pressure (SPP). Out of 62 BK amputations with an SPP above 30 mmHg wound healing failed in only 2 cases (3 per cent). Out of 13 BK amputations with an SPP between 20 and 30 mmHg 7 cases (54 per cent) failed and out of 9 BK amputations with an SPP below 20 mmHg no less than 8...... cases (89 per cent) failed to heal. The difference in failure rate is significant (P less than 0.0001). Out of the 15 failed BK amputations at low pressures (below 30 mmHg) only one case had local signs of ischaemia, which might have warned the surgeons. On the other hand, in 13 out of the 18 cases...

  4. Effect of DNA methylation profile on OATP3A1 and OATP4A1 transcript levels in colorectal cancer.

    Science.gov (United States)

    Rawłuszko-Wieczorek, Agnieszka Anna; Horst, Nikodem; Horbacka, Karolina; Bandura, Artur Szymon; Świderska, Monika; Krokowicz, Piotr; Jagodziński, Paweł Piotr

    2015-08-01

    Epidemiological studies indicate that 17β-estradiol (E2) prevents colorectal cancer (CRC). Organic anion transporting polypeptides (OATPs) are involved in the cellular uptake of various endogenous and exogenous substrates, including hormone conjugates. Because transfer of estrone sulfate (E1-S) can contribute to intra-tissue conversion of estrone to the biologically active form -E2, it is evident that the expression patterns of OATPs may be relevant to the analysis of CRC incidence and therapy. We therefore evaluated DNA methylation and transcript levels of two members of the OATP family, OATP3A1 and OATP4A1, that may be involved in E1-S transport in colorectal cancer patients. We detected a significant reduction in OATP3A1 and a significant increase in OATP4A1 mRNA levels in cancerous tissue, compared with histopathologically unchanged tissue (n=103). Moreover, we observed DNA hypermethylation in the OATP3A1 promoter region in a small subset of CRC patients and in HCT116 and Caco-2 colorectal cancer cell lines. We also observed increased OATP3A1 transcript following treatment with 5-aza-2-deoxycytidine and sodium butyrate. The OATP4A1 promoter region was hypomethylated in analyzed tissues and CRC cell lines and was not affected by these treatments. Our results suggest a potential mechanism for OATP3A1 downregulation that involves DNA methylation during colorectal carcinogenesis. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

  5. Transcriptional repressor domain of MBD1 is intrinsically disordered and interacts with its binding partners in a selective manner.

    KAUST Repository

    Hameed, Umar Farook Shahul

    2014-05-09

    Methylation of DNA CpG sites is a major mechanism of epigenetic gene silencing and plays important roles in cell division, development and carcinogenesis. One of its regulators is the 64-residue C-terminal Transcriptional Repressor Domain (the TRD) of MBD1, which recruits several repressor proteins such as MCAF1, HDAC3 and MPG that are essential for the gene silencing. Using NMR spectroscopy, we have characterized the solution structure of the C-terminus of MBD1 (MBD1-c, residues D507 to Q605), which included the TRD (A529 to P592). Surprisingly, the MBD1-c is intrinsically disordered. Despite its lack of a tertiary folding, MBD1-c could still bind to different partner proteins in a selective manner. MPG and MCAF1Δ8 showed binding to both the N-terminal and C-terminal residues of MBD1-c but HDAC3 preferably bound to the C-terminal region. This study reveals how MBD1-c discriminates different binding partners, and thus, expands our understanding of the mechanisms of gene regulation by MBD1.

  6. Transcriptional repressor domain of MBD1 is intrinsically disordered and interacts with its binding partners in a selective manner.

    KAUST Repository

    Hameed, Umar Farook Shahul; Lim, Jackwee; Zhang, Qian; Wasik, Mariusz A; Yang, Daiwen; Swaminathan, Kunchithapadam

    2014-01-01

    Methylation of DNA CpG sites is a major mechanism of epigenetic gene silencing and plays important roles in cell division, development and carcinogenesis. One of its regulators is the 64-residue C-terminal Transcriptional Repressor Domain (the TRD) of MBD1, which recruits several repressor proteins such as MCAF1, HDAC3 and MPG that are essential for the gene silencing. Using NMR spectroscopy, we have characterized the solution structure of the C-terminus of MBD1 (MBD1-c, residues D507 to Q605), which included the TRD (A529 to P592). Surprisingly, the MBD1-c is intrinsically disordered. Despite its lack of a tertiary folding, MBD1-c could still bind to different partner proteins in a selective manner. MPG and MCAF1Δ8 showed binding to both the N-terminal and C-terminal residues of MBD1-c but HDAC3 preferably bound to the C-terminal region. This study reveals how MBD1-c discriminates different binding partners, and thus, expands our understanding of the mechanisms of gene regulation by MBD1.

  7. Elevated androgen levels induce hyperinsulinemia through increase in Ins1 transcription in pancreatic beta cells in female rats.

    Science.gov (United States)

    Mishra, Jay S; More, Amar S; Kumar, Sathish

    2018-01-22

    Hyperandrogenism is associated with hyperinsulinemia and insulin resistance in adult females. We tested whether androgens dysregulate pancreatic beta cell function to induce hyperinsulinemia through transcriptional regulation of insulin gene (Ins) in the islets. Adult female Wistar rats implanted with dihydrotestosterone (DHT; 7.5-mg, 90-d release) or placebo pellets were examined after 10 weeks. DHT exposure increased plasma DHT levels by 2-fold similar to that in polycystic ovary syndrome in women. DHT exposure induced hyperinsulinemia with increased HOMA-IR index in fasting state and glucose intolerance and exaggerated insulin responses following glucose tolerance test. DHT females had no change in islet number, size and beta cell proliferation/apoptosis but exhibited significant mitochondrial dysfunction (higher ADP/ATP ratio, decreased mtDNA copy number, increased reactive oxygen production and downregulation of mitochondrial biogenesis) and enhanced glucose-stimulated insulin secretion. Ins expression was increased in DHT islets. In vitro incubation of control islets with DHT dose-dependently stimulated Ins transcription. Analysis of Ins1 gene revealed a putative androgen responsive element in the promoter. Chromatin-immunoprecipitation assays showed that androgen receptors bind to this element in response to DHT stimulation. Furthermore, reporter assays showed that the promoter element is highly responsive to androgens. Insulin stimulated glucose uptake in skeletal muscle was decreased with associated decrease in IRβ expression in DHT females. Our studies identified a novel androgen-mediated mechanism for the control of Ins expression via transcriptional regulation providing a molecular mechanism linking elevated androgens and hyperinsulemia. Decreased IRβ expression in the skeletal muscles may contribute, in part, to glucose intolerance in this model. © The Author(s) 2018. Published by Oxford University Press on behalf of Society for the Study of

  8. Plasmodium falciparum spermidine synthase inhibition results in unique perturbation-specific effects observed on transcript, protein and metabolite levels

    Directory of Open Access Journals (Sweden)

    Louw Abraham I

    2010-04-01

    Full Text Available Abstract Background Plasmodium falciparum, the causative agent of severe human malaria, has evolved to become resistant to previously successful antimalarial chemotherapies, most notably chloroquine and the antifolates. The prevalence of resistant strains has necessitated the discovery and development of new chemical entities with novel modes-of-action. Although much effort has been invested in the creation of analogues based on existing drugs and the screening of chemical and natural compound libraries, a crucial shortcoming in current Plasmodial drug discovery efforts remains the lack of an extensive set of novel, validated drug targets. A requirement of these targets (or the pathways in which they function is that they prove essential for parasite survival. The polyamine biosynthetic pathway, responsible for the metabolism of highly abundant amines crucial for parasite growth, proliferation and differentiation, is currently under investigation as an antimalarial target. Chemotherapeutic strategies targeting this pathway have been successfully utilized for the treatment of Trypanosomes causing West African sleeping sickness. In order to further evaluate polyamine depletion as possible antimalarial intervention, the consequences of inhibiting P. falciparum spermidine synthase (PfSpdSyn were examined on a morphological, transcriptomic, proteomic and metabolic level. Results Morphological analysis of P. falciparum 3D7 following application of the PfSpdSyn inhibitor cyclohexylamine confirmed that parasite development was completely arrested at the early trophozoite stage. This is in contrast to untreated parasites which progressed to late trophozoites at comparable time points. Global gene expression analyses confirmed a transcriptional arrest in the parasite. Several of the differentially expressed genes mapped to the polyamine biosynthetic and associated metabolic pathways. Differential expression of corresponding parasite proteins involved in

  9. Selected radionuclides important to low-level radioactive waste management

    International Nuclear Information System (INIS)

    1996-11-01

    The purpose of this document is to provide information to state representatives and developers of low level radioactive waste (LLW) management facilities about the radiological, chemical, and physical characteristics of selected radionuclides and their behavior in the environment. Extensive surveys of available literature provided information for this report. Certain radionuclides may contribute significantly to the dose estimated during a radiological performance assessment analysis of an LLW disposal facility. Among these are the radionuclides listed in Title 10 of the Code of Federal Regulations Part 61.55, Tables 1 and 2 (including alpha emitting transuranics with half-lives greater than 5 years). This report discusses these radionuclides and other radionuclides that may be significant during a radiological performance assessment analysis of an LLW disposal facility. This report not only includes essential information on each radionuclide, but also incorporates waste and disposal information on the radionuclide, and behavior of the radionuclide in the environment and in the human body. Radionuclides addressed in this document include technetium-99, carbon-14, iodine-129, tritium, cesium-137, strontium-90, nickel-59, plutonium-241, nickel-63, niobium-94, cobalt-60, curium -42, americium-241, uranium-238, and neptunium-237

  10. Selected radionuclides important to low-level radioactive waste management

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-11-01

    The purpose of this document is to provide information to state representatives and developers of low level radioactive waste (LLW) management facilities about the radiological, chemical, and physical characteristics of selected radionuclides and their behavior in the environment. Extensive surveys of available literature provided information for this report. Certain radionuclides may contribute significantly to the dose estimated during a radiological performance assessment analysis of an LLW disposal facility. Among these are the radionuclides listed in Title 10 of the Code of Federal Regulations Part 61.55, Tables 1 and 2 (including alpha emitting transuranics with half-lives greater than 5 years). This report discusses these radionuclides and other radionuclides that may be significant during a radiological performance assessment analysis of an LLW disposal facility. This report not only includes essential information on each radionuclide, but also incorporates waste and disposal information on the radionuclide, and behavior of the radionuclide in the environment and in the human body. Radionuclides addressed in this document include technetium-99, carbon-14, iodine-129, tritium, cesium-137, strontium-90, nickel-59, plutonium-241, nickel-63, niobium-94, cobalt-60, curium -42, americium-241, uranium-238, and neptunium-237.

  11. High level of microsynteny and purifying selection affect the evolution of WRKY family in Gramineae.

    Science.gov (United States)

    Jin, Jing; Kong, Jingjing; Qiu, Jianle; Zhu, Huasheng; Peng, Yuancheng; Jiang, Haiyang

    2016-01-01

    The WRKY gene family, which encodes proteins in the regulation processes of diverse developmental stages, is one of the largest families of transcription factors in higher plants. In this study, by searching for interspecies gene colinearity (microsynteny) and dating the age distributions of duplicated genes, we found 35 chromosomal segments of subgroup I genes of WRKY family (WRKY I) in four Gramineae species (Brachypodium, rice, sorghum, and maize) formed eight orthologous groups. After a stepwise gene-by-gene reciprocal comparison of all the protein sequences in the WRKY I gene flanking areas, highly conserved regions of microsynteny were found in the four Gramineae species. Most gene pairs showed conserved orientation within syntenic genome regions. Furthermore, tandem duplication events played the leading role in gene expansion. Eventually, environmental selection pressure analysis indicated strong purifying selection for the WRKY I genes in Gramineae, which may have been followed by gene loss and rearrangement. The results presented in this study provide basic information of Gramineae WRKY I genes and form the foundation for future functional studies of these genes. High level of microsynteny in the four grass species provides further evidence that a large-scale genome duplication event predated speciation.

  12. Sleep Dependent Synaptic Down-Selection (II: Single Neuron Level Benefits for Matching, Selectivity, and Specificity

    Directory of Open Access Journals (Sweden)

    Atif eHashmi

    2013-10-01

    Full Text Available In a companion paper (Nere et al., this volume, we used computer simulations to show that a strategy of activity-dependent, on-line net synaptic potentiation during wake, followed by off-line synaptic depression during sleep, can provide a parsimonious account for several memory benefits of sleep at the systems level, including the consolidation of procedural and declarative memories, gist extraction, and integration of new with old memories. In this paper, we consider the theoretical benefits of this two-step process at the single neuron level and employ the theoretical notion of Matching between brain and environment to measure how this process increases the ability of the neuron to capture regularities in the environment and model them internally. We show that down-selection during sleep is beneficial for increasing or restoring Matching after learning, after integrating new with old memories, and after forgetting irrelevant material. By contrast, alternative schemes, such as additional potentiation in wake, potentiation in sleep, or synaptic renormalization in wake, decrease Matching. We also argue that, by selecting appropriate loops through the brain that tie feedforward synapses with feedback ones in the same dendritic domain, different subsets of neurons can learn to specialize for different contingencies and form sequences of nested perception-action loops. By potentiating such loops when interacting with the environment in wake, and depressing them when disconnected from the environment in sleep, neurons can learn to match the long-term statistical structure of the environment while avoiding spurious modes of functioning and catastrophic interference. Finally, such a two-step process has the additional benefit of desaturating the neuron's ability to learn and of maintaining cellular homeostasis. Thus, sleep-dependent synaptic renormalization offers a parsimonious account for both cellular and systems-level effects of sleep on learning

  13. Amino acid limitation induces down-regulation of WNT5a at transcriptional level

    International Nuclear Information System (INIS)

    Wang Zuguang; Chen Hong

    2009-01-01

    An aberrant WNT signaling contributes to the development and progression of multiple cancers. WNT5a is one of the WNT signaling molecules. This study was designed to test the hypothesis that amino acid deprivation induces changes in the WNT signaling pathway in colon cancer cells. Results showed that targets of the amino acid response pathway, ATF3 and p21, were induced in the human colon cancer cell line SW480 during amino acid limitation. There was a significant decrease in the WNT5a mRNA level following amino acid deprivation. The down-regulation of WNT5a mRNA by amino acid deprivation is not due to mRNA destabilization. There is a reduction of nuclear β-catenin protein level by amino acid limitation. Under amino acid limitation, phosphorylation of ERK1/2 was increased and the blockage of ERK1/2 by the inhibitor U0126 partially restored WNT5a mRNA level. In conclusion, amino acid limitation in colon cancer cells induces phosphorylation of ERK1/2, which then down-regulates WNT5a expression.

  14. 1,25-Dihydroxyvitamin D3 inhibits cytokine production by human blood monocytes at the post-transcriptional level

    DEFF Research Database (Denmark)

    Müller, K; Haahr, P M; Diamant, M

    1992-01-01

    was not caused by impaired production of mRNA. Taken together, the study demonstrates a vitamin D-induced inhibitory effect of LPS-driven monokine production, which is most likely a vitamin D-receptor mediated phenomenon exerted at a post-transcriptional, presecretory level. Impaired monokine production may...... be of importance in 1,25-(OH)2D3-mediated inhibition of lymphocyte functions in vitro.......1,25-Dihydroxyvitamin D3 [1,25-(OH)2D3] inhibits lymphocyte proliferation and production of antibodies and lymphokines such as interleukin (IL)-2 and interferon gamma. These lymphocyte functions are dependent upon cytokines, including IL-1 alpha, IL-1 beta, IL-6 and tumour necrosis factor alpha...

  15. Sulfate-driven elemental sparing is regulated at the transcriptional and posttranscriptional levels in a filamentous cyanobacterium.

    Science.gov (United States)

    Gutu, Andrian; Alvey, Richard M; Bashour, Sami; Zingg, Daniel; Kehoe, David M

    2011-03-01

    Sulfur is an essential nutrient that can exist at growth-limiting concentrations in freshwater environments. The freshwater cyanobacterium Fremyella diplosiphon (also known as Tolypothrix sp. PCC 7601) is capable of remodeling the composition of its light-harvesting antennae, or phycobilisomes, in response to changes in the sulfur levels in its environment. Depletion of sulfur causes these cells to cease the accumulation of two forms of a major phycobilisome protein called phycocyanin and initiate the production of a third form of phycocyanin, which possesses a minimal number of sulfur-containing amino acids. Since phycobilisomes make up approximately 50% of the total protein in these cells, this elemental sparing response has the potential to significantly influence the fitness of this species under low-sulfur conditions. This response is specific for sulfate and occurs over the physiological range of sulfate concentrations likely to be encountered by this organism in its natural environment. F. diplosiphon has two separate sulfur deprivation responses, with low sulfate levels activating the phycobilisome remodeling response and low sulfur levels activating the chlorosis or bleaching response. The phycobilisome remodeling response results from changes in RNA abundance that are regulated at both the transcriptional and posttranscriptional levels. The potential of this response, and the more general bleaching response of cyanobacteria, to provide sulfur-containing amino acids during periods of sulfur deprivation is examined.

  16. Sulfate-Driven Elemental Sparing Is Regulated at the Transcriptional and Posttranscriptional Levels in a Filamentous Cyanobacterium▿ †

    Science.gov (United States)

    Gutu, Andrian; Alvey, Richard M.; Bashour, Sami; Zingg, Daniel; Kehoe, David M.

    2011-01-01

    Sulfur is an essential nutrient that can exist at growth-limiting concentrations in freshwater environments. The freshwater cyanobacterium Fremyella diplosiphon (also known as Tolypothrix sp. PCC 7601) is capable of remodeling the composition of its light-harvesting antennae, or phycobilisomes, in response to changes in the sulfur levels in its environment. Depletion of sulfur causes these cells to cease the accumulation of two forms of a major phycobilisome protein called phycocyanin and initiate the production of a third form of phycocyanin, which possesses a minimal number of sulfur-containing amino acids. Since phycobilisomes make up approximately 50% of the total protein in these cells, this elemental sparing response has the potential to significantly influence the fitness of this species under low-sulfur conditions. This response is specific for sulfate and occurs over the physiological range of sulfate concentrations likely to be encountered by this organism in its natural environment. F. diplosiphon has two separate sulfur deprivation responses, with low sulfate levels activating the phycobilisome remodeling response and low sulfur levels activating the chlorosis or bleaching response. The phycobilisome remodeling response results from changes in RNA abundance that are regulated at both the transcriptional and posttranscriptional levels. The potential of this response, and the more general bleaching response of cyanobacteria, to provide sulfur-containing amino acids during periods of sulfur deprivation is examined. PMID:21239582

  17. Optimisation of transgene action at the post-transcriptional level: high quality parthenocarpic fruits in industrial tomatoes

    Directory of Open Access Journals (Sweden)

    Defez Roberto

    2002-01-01

    Full Text Available Abstract Background Genetic engineering of parthenocarpy confers to horticultural plants the ability to produce fruits under environmental conditions that curtail fruit productivity and quality. The DefH9-iaaM transgene, whose predicted action is to confer auxin synthesis specifically in the placenta, ovules and derived tissues, has been shown to confer parthenocarpy to several plant species (tobacco, eggplant, tomato and varieties. Results UC82 tomato plants, a typical cultivar used by the processing industry, transgenic for the DefH9-iaaM gene produce parthenocarpic fruits that are malformed. UC82 plants transgenic for the DefH9-RI-iaaM, a DefH9-iaaM derivative gene modified in its 5'ULR by replacing 53 nucleotides immediately upstream of the AUG initiation codon with an 87 nucleotides-long sequence derived from the rolA intron sequence, produce parthenocarpic fruits of high quality. In an in vitro translation system, the iaaM mRNA, modified in its 5'ULR is translated 3–4 times less efficiently than the original transcript. An optimal expressivity of parthenocarpy correlates with a reduced transgene mRNA steady state level in DefH9-RI-iaaM flower buds in comparison to DefH9-iaaM flower buds. Consistent with the known function of the iaaM gene, flower buds transgenic for the DefH9-RI-iaaM gene contain ten times more IAA than control untransformed flower buds, but five times less than DefH9-iaaM flower buds. Conclusions By using an auxin biosynthesis transgene downregulated at the post-transcriptional level, an optimal expressivity of parthenocarpy has been achieved in a genetic background not suitable for the original transgene. Thus, the method allows the generation of a wider range of expressivity of the desired trait in transgenic plants.

  18. Complex mutual regulation of facilitates chromatin transcription (FACT) subunits on both mRNA and protein levels in human cells.

    Science.gov (United States)

    Safina, Alfiya; Garcia, Henry; Commane, Mairead; Guryanova, Olga; Degan, Seamus; Kolesnikova, Kateryna; Gurova, Katerina V

    2013-08-01

    Facilitates chromatin transcription (FACT) is a chromatin remodeling complex with two subunits: SSRP1 and SPT16. Mechanisms controlling FACT levels are of interest, since the complex is not expressed in most differentiated cells, but is frequently upregulated in cancer, particularly in poorly differentiated, aggressive tumors. Moreover, inhibition of FACT expression or function in tumor cells interferes with their survival. Here we demonstrate that SSRP1 and SPT16 protein levels decline upon induction of cellular differentiation or senescence in vitro and that similar declines in protein levels for both SSRP1 and SPT16 occur upon RNAi-mediated knockdown of either SSRP1 or SPT16. The interdependence of SSRP1 and SPT16 protein levels was found to be due to their association with SSRP1 and SPT16 mRNAs, which stabilizes the proteins. In particular, presence of SSRP1 mRNA is critical for SPT16 protein stability. In addition, binding of SSRP1 and SPT16 mRNAs to the FACT complex increases the stability and efficiency of translation of the mRNAs. These data support a model in which the FACT complex is stable when SSRP1 mRNA is present, but quickly degrades when SSRP1 mRNA levels drop. In the absence of FACT complex, SSRP1 and SPT16 mRNAs are unstable and inefficiently translated, making reactivation of FACT function unlikely in normal cells. Thus, we have described a complex and unusual mode of regulation controlling cellular FACT levels that results in amplified and stringent control of FACT activity. The FACT dependence of tumor cells suggests that mechanisms controlling FACT levels could be targeted for anticancer therapy.

  19. Effects of the lipid regulating drug clofibric acid on PPARα-regulated gene transcript levels in common carp (Cyprinus carpio) at pharmacological and environmental exposure levels.

    Science.gov (United States)

    Corcoran, Jenna; Winter, Matthew J; Lange, Anke; Cumming, Rob; Owen, Stewart F; Tyler, Charles R

    2015-04-01

    In mammals, the peroxisome proliferator-activated receptor α (PPARα) plays a key role in regulating various genes involved in lipid metabolism, bile acid synthesis and cholesterol homeostasis, and is activated by a diverse group of compounds collectively termed peroxisome proliferators (PPs). Specific PPs have been detected in the aquatic environment; however little is known on their pharmacological activity in fish. We investigated the bioavailability and persistence of the human PPARα ligand clofibric acid (CFA) in carp, together with various relevant endpoints, at a concentration similar to therapeutic levels in humans (20mg/L) and for an environmentally relevant concentration (4μg/L). Exposure to pharmacologically-relevant concentrations of CFA resulted in increased transcript levels of a number of known PPARα target genes together with increased acyl-coA oxidase (Acox1) activity, supporting stimulation of lipid metabolism pathways in carp which are known to be similarly activated in mammals. Although Cu,Zn-superoxide dismutase (Sod1) activity was not affected, mRNA levels of several biotransformation genes were also increased, paralleling previous reports in mammals and indicating a potential role in hepatic detoxification for PPARα in carp. Importantly, transcription of some of these genes (and Acox1 activity) were affected at exposure concentrations comparable with those reported in effluent discharges. Collectively, these data suggest that CFA is pharmacologically active in carp and has the potential to invoke PPARα-related responses in fish exposed in the environment, particularly considering that CFA may represent just one of a number of PPAR-active compounds present to which wild fish may be exposed. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

  20. Serotonin markers show altered transcription levels in an experimental pig model of mitral regurgitation

    DEFF Research Database (Denmark)

    Cremer, Signe Emilie; Zois, Nora Elisabeth; Moesgaard, S. G.

    2015-01-01

    surgically induced MR or sham-operation, resulting in three MR groups: control (CON, n = 12), mild MR (mMR, n = 10) and severe MR (sMR, n = 6). The gene expression levels of 5-HT1BR, 5-HT2AR, 5-HT2BR, SERT and TPH-1 were analysed using quantitative PCR (qPCR) in the mitral valve (MV), anterior papillary......-uptake transporter (SERT) in MMVD-affected valves, increased valvular 5-HT synthesis and decreased clearance have been suggested. It remains unknown how haemodynamic changes associated with mitral regurgitation (MR) affect 5-HT markers in the mitral valve, myocardium and circulation. Twenty-eight pigs underwent...... muscle (AP) and left ventricle (LV). MV 5-HT2BR was also analysed with immunohistochemistry (IHC) in relation to histological lesions and valvular myofibroblasts. All 5-HTR mRNAs were up-regulated in MV compared to AP and LV (P SERT and TPH-1 were up-regulated in AP and LV compared...

  1. Profiling of Human Molecular Pathways Affected by Retrotransposons at the Level of Regulation by Transcription Factor Proteins

    Science.gov (United States)

    Nikitin, Daniil; Penzar, Dmitry; Garazha, Andrew; Sorokin, Maxim; Tkachev, Victor; Borisov, Nicolas; Poltorak, Alexander; Prassolov, Vladimir; Buzdin, Anton A.

    2018-01-01

    Endogenous retroviruses and retrotransposons also termed retroelements (REs) are mobile genetic elements that were active until recently in human genome evolution. REs regulate gene expression by actively reshaping chromatin structure or by directly providing transcription factor binding sites (TFBSs). We aimed to identify molecular processes most deeply impacted by the REs in human cells at the level of TFBS regulation. By using ENCODE data, we identified ~2 million TFBS overlapping with putatively regulation-competent human REs located in 5-kb gene promoter neighborhood (~17% of all TFBS in promoter neighborhoods; ~9% of all RE-linked TFBS). Most of REs hosting TFBS were highly diverged repeats, and for the evolutionary young (0–8% diverged) elements we identified only ~7% of all RE-linked TFBS. The gene-specific distributions of RE-linked TFBS generally correlated with the distributions for all TFBS. However, several groups of molecular processes were highly enriched in the RE-linked TFBS regulation. They were strongly connected with the immunity and response to pathogens, with the negative regulation of gene transcription, ubiquitination, and protein degradation, extracellular matrix organization, regulation of STAT signaling, fatty acids metabolism, regulation of GTPase activity, protein targeting to Golgi, regulation of cell division and differentiation, development and functioning of perception organs and reproductive system. By contrast, the processes most weakly affected by the REs were linked with the conservative aspects of embryo development. We also identified differences in the regulation features by the younger and older fractions of the REs. The regulation by the older fraction of the REs was linked mainly with the immunity, cell adhesion, cAMP, IGF1R, Notch, Wnt, and integrin signaling, neuronal development, chondroitin sulfate and heparin metabolism, and endocytosis. The younger REs regulate other aspects of immunity, cell cycle progression and

  2. Profiling of Human Molecular Pathways Affected by Retrotransposons at the Level of Regulation by Transcription Factor Proteins

    Directory of Open Access Journals (Sweden)

    Daniil Nikitin

    2018-01-01

    Full Text Available Endogenous retroviruses and retrotransposons also termed retroelements (REs are mobile genetic elements that were active until recently in human genome evolution. REs regulate gene expression by actively reshaping chromatin structure or by directly providing transcription factor binding sites (TFBSs. We aimed to identify molecular processes most deeply impacted by the REs in human cells at the level of TFBS regulation. By using ENCODE data, we identified ~2 million TFBS overlapping with putatively regulation-competent human REs located in 5-kb gene promoter neighborhood (~17% of all TFBS in promoter neighborhoods; ~9% of all RE-linked TFBS. Most of REs hosting TFBS were highly diverged repeats, and for the evolutionary young (0–8% diverged elements we identified only ~7% of all RE-linked TFBS. The gene-specific distributions of RE-linked TFBS generally correlated with the distributions for all TFBS. However, several groups of molecular processes were highly enriched in the RE-linked TFBS regulation. They were strongly connected with the immunity and response to pathogens, with the negative regulation of gene transcription, ubiquitination, and protein degradation, extracellular matrix organization, regulation of STAT signaling, fatty acids metabolism, regulation of GTPase activity, protein targeting to Golgi, regulation of cell division and differentiation, development and functioning of perception organs and reproductive system. By contrast, the processes most weakly affected by the REs were linked with the conservative aspects of embryo development. We also identified differences in the regulation features by the younger and older fractions of the REs. The regulation by the older fraction of the REs was linked mainly with the immunity, cell adhesion, cAMP, IGF1R, Notch, Wnt, and integrin signaling, neuronal development, chondroitin sulfate and heparin metabolism, and endocytosis. The younger REs regulate other aspects of immunity, cell cycle

  3. Declining job security level and workers' perfomance in selected ...

    African Journals Online (AJOL)

    Abstract. The study assessed bank workers' level of job security and also investigated the relationship between job security level and job performance among employees of the banks. ... These comprised both permanent and contract workers.

  4. Effects of the lipid regulating drug clofibric acid on PPARα-regulated gene transcript levels in common carp (Cyprinus carpio) at pharmacological and environmental exposure levels

    Energy Technology Data Exchange (ETDEWEB)

    Corcoran, Jenna, E-mail: J.F.Corcoran@exeter.ac.uk [University of Exeter, Biosciences, College of Life & Environmental Sciences, Exeter EX4 4QD (United Kingdom); Winter, Matthew J., E-mail: M.Winter@exeter.ac.uk [AstraZeneca Global Environment, Brixham Laboratory, Freshwater Quarry, Brixham TQ5 8BA (United Kingdom); Lange, Anke, E-mail: A.Lange@exeter.ac.uk [University of Exeter, Biosciences, College of Life & Environmental Sciences, Exeter EX4 4QD (United Kingdom); Cumming, Rob, E-mail: Rob.Cumming@astrazeneca.com [AstraZeneca Global Environment, Brixham Laboratory, Freshwater Quarry, Brixham TQ5 8BA (United Kingdom); Owen, Stewart F., E-mail: Stewart.Owen@astrazeneca.com [AstraZeneca Global Environment, Brixham Laboratory, Freshwater Quarry, Brixham TQ5 8BA (United Kingdom); Tyler, Charles R., E-mail: C.R.Tyler@exeter.ac.uk [University of Exeter, Biosciences, College of Life & Environmental Sciences, Exeter EX4 4QD (United Kingdom)

    2015-04-15

    Highlights: • CFA appears to have a low propensity to bioconcentrate and has a plasma half-life of <4 days in carp. • CFA increases levels of mRNA of a number of genes known to be regulated by PPARα in mammals. • PPARα activation changes levels of mRNA of genes involved with several detoxification/ biotransformation system components in carp. • CFA alters levels of mRNA and activity of the inducible β-oxidation pathway enzyme Acox1, a known indicator of peroxisome proliferator exposure. - Abstract: In mammals, the peroxisome proliferator-activated receptor α (PPARα) plays a key role in regulating various genes involved in lipid metabolism, bile acid synthesis and cholesterol homeostasis, and is activated by a diverse group of compounds collectively termed peroxisome proliferators (PPs). Specific PPs have been detected in the aquatic environment; however little is known on their pharmacological activity in fish. We investigated the bioavailability and persistence of the human PPARα ligand clofibric acid (CFA) in carp, together with various relevant endpoints, at a concentration similar to therapeutic levels in humans (20 mg/L) and for an environmentally relevant concentration (4 μg/L). Exposure to pharmacologically-relevant concentrations of CFA resulted in increased transcript levels of a number of known PPARα target genes together with increased acyl-coA oxidase (Acox1) activity, supporting stimulation of lipid metabolism pathways in carp which are known to be similarly activated in mammals. Although Cu,Zn-superoxide dismutase (Sod1) activity was not affected, mRNA levels of several biotransformation genes were also increased, paralleling previous reports in mammals and indicating a potential role in hepatic detoxification for PPARα in carp. Importantly, transcription of some of these genes (and Acox1 activity) were affected at exposure concentrations comparable with those reported in effluent discharges. Collectively, these data suggest that CFA

  5. Effects of the lipid regulating drug clofibric acid on PPARα-regulated gene transcript levels in common carp (Cyprinus carpio) at pharmacological and environmental exposure levels

    International Nuclear Information System (INIS)

    Corcoran, Jenna; Winter, Matthew J.; Lange, Anke; Cumming, Rob; Owen, Stewart F.; Tyler, Charles R.

    2015-01-01

    Highlights: • CFA appears to have a low propensity to bioconcentrate and has a plasma half-life of <4 days in carp. • CFA increases levels of mRNA of a number of genes known to be regulated by PPARα in mammals. • PPARα activation changes levels of mRNA of genes involved with several detoxification/ biotransformation system components in carp. • CFA alters levels of mRNA and activity of the inducible β-oxidation pathway enzyme Acox1, a known indicator of peroxisome proliferator exposure. - Abstract: In mammals, the peroxisome proliferator-activated receptor α (PPARα) plays a key role in regulating various genes involved in lipid metabolism, bile acid synthesis and cholesterol homeostasis, and is activated by a diverse group of compounds collectively termed peroxisome proliferators (PPs). Specific PPs have been detected in the aquatic environment; however little is known on their pharmacological activity in fish. We investigated the bioavailability and persistence of the human PPARα ligand clofibric acid (CFA) in carp, together with various relevant endpoints, at a concentration similar to therapeutic levels in humans (20 mg/L) and for an environmentally relevant concentration (4 μg/L). Exposure to pharmacologically-relevant concentrations of CFA resulted in increased transcript levels of a number of known PPARα target genes together with increased acyl-coA oxidase (Acox1) activity, supporting stimulation of lipid metabolism pathways in carp which are known to be similarly activated in mammals. Although Cu,Zn-superoxide dismutase (Sod1) activity was not affected, mRNA levels of several biotransformation genes were also increased, paralleling previous reports in mammals and indicating a potential role in hepatic detoxification for PPARα in carp. Importantly, transcription of some of these genes (and Acox1 activity) were affected at exposure concentrations comparable with those reported in effluent discharges. Collectively, these data suggest that CFA

  6. Assessment of complex water pollution with heavy metals and Pyrethroid pesticides on transcript levels of metallothionein and immune related genes.

    Science.gov (United States)

    Ghazy, Haneen A; Abdel-Razek, Mohamed A S; El Nahas, Abeer F; Mahmoud, Shawky

    2017-09-01

    Alteration of immunological function of an aquatic organism can be used as an indicator for evaluating the direct effect of exposure to pollutants. The aim of this work is to assess the impact of complex water pollution with special reference to Pyrethroid pesticides and heavy metals on mRNA transcript levels of Metallothionine and some immune related genes of Nile tilapia (Oreochromas Niloticus). Residues of six heavy metals and six Pyrethroid were assessed in water as well as fish tissues at three different sites of Lake Burullus, located at Northern Egypt. Variations of water physicochemical properties associated with different levels of heavy metals at the three different sections were recorded. Tissue residues of Fe, Mn and Zn, Cu, Ni exceed water levels in contrast to elevated water level of Pb. All assessed Pyrethroids are detected in fish tissue samples with higher concentration (3-42 folds) than that found in water samples especially Cypermethrin. Significant down-regulation of expression levels of metallothionein (MT) at the three sections of the lake was observed. The expression of immune related genes (IgM) and inflammatory cytokines (TNF, IL.8 and IL.1) were affected. IgM and TNF were significantly down-regulated at eastern and western section of the lake; meanwhile the expression of IL8 is down regulated at the three sections of the lack. IL1 was significantly up-regulated at eastern and middle sections. We conclude that, variable gene expression of MT and immune-related genes at the three sections of the lack impose different response to complex water pollution in relation to variable aquatic environment. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. The transcriptional profiling of human in vivo-generated plasma cells identifies selective imbalances in monoclonal gammopathies.

    Directory of Open Access Journals (Sweden)

    Luis M Valor

    Full Text Available Plasma cells (PC represent the heterogeneous final stage of the B cells (BC differentiation process. To characterize the transition of BC into PC, transcriptomes from human naïve BC were compared to those of three functionally-different subsets of human in vivo-generated PC: i tonsil PC, mainly consisting of early PC; ii PC released to the blood after a potent booster-immunization (mostly cycling plasmablasts; and, iii bone marrow CD138+ PC that represent highly mature PC and include the long-lived PC compartment. This transcriptional transition involves subsets of genes related to key processes for PC maturation: the already known protein processing, apoptosis and homeostasis, and of new discovery including histones, macromolecule assembly, zinc-finger transcription factors and neuromodulation. This human PC signature is partially reproduced in vitro and is conserved in mouse. Moreover, the present study identifies genes that define PC subtypes (e.g., proliferation-associated genes for circulating PC and transcriptional-related genes for tonsil and bone marrow PC and proposes some putative transcriptional regulators of the human PC signatures (e.g., OCT/POU, XBP1/CREB, E2F, among others. Finally, we also identified a restricted imbalance of the present PC transcriptional program in monoclonal gammopathies that correlated with PC malignancy.

  8. Depletion of polycistronic transcripts using short interfering RNAs: cDNA synthesis method affects levels of non-targeted genes determined by quantitative PCR.

    Science.gov (United States)

    Hanning, Jennifer E; Groves, Ian J; Pett, Mark R; Coleman, Nicholas

    2013-05-21

    Short interfering RNAs (siRNAs) are often used to deplete viral polycistronic transcripts, such as those encoded by human papillomavirus (HPV). There are conflicting data in the literature concerning how siRNAs targeting one HPV gene can affect levels of other genes in the polycistronic transcripts. We hypothesised that the conflict might be partly explained by the method of cDNA synthesis used prior to transcript quantification. We treated HPV16-positive cervical keratinocytes with siRNAs targeting the HPV16 E7 gene and used quantitative PCR to compare transcript levels of E7 with those of E6 and E2, viral genes located upstream and downstream of the target site respectively. We compared our findings from cDNA generated using oligo-dT primers alone with those from cDNA generated using a combination of random hexamer and oligo-dT primers. Our data show that when polycistronic transcripts are targeted by siRNAs, there is a period when untranslatable cleaved mRNA upstream of the siRNA binding site remains detectable by PCR, if cDNA is generated using random hexamer primers. Such false indications of mRNA abundance are avoided using oligo-dT primers. The period corresponds to the time taken for siRNA activity and degradation of the cleaved transcripts. Genes downstream of the siRNA binding site are detectable during this interval, regardless of how the cDNA is generated. These data emphasise the importance of the cDNA synthesis method used when measuring transcript abundance following siRNA depletion of polycistronic transcripts. They provide a partial explanation for erroneous reports suggesting that siRNAs targeting HPV E7 can have gene-specific effects.

  9. Serum levels of selected vitamins and trace elements in Nigerian ...

    African Journals Online (AJOL)

    Folic acid, vitamins and Zinc play essential role in DNA methylation but alcohol consumption is known to affect the levels of these micronutrients leading to risk of developing various illnesses and certain cancers. This study determined the levels of DNA methylation dependent-micronutrients (folate, vitamin B12, vitamin B6, ...

  10. Comparing Content in Selected GCE A Levels and Advanced GNVQs.

    Science.gov (United States)

    Holding, Gordon; And Others

    1996-01-01

    In an action research project, four British further education colleges compared mandatory units of three Advanced General National Vocational Qualifications (GNVQs)--business, art and design, and health and social care--with related General Certificate of Education Advanced Level (GCE A-level) syllabuses. Activities included a detailed comparison…

  11. Serum Lipids and Lipoproteins Levels and Selected Trace Metals In ...

    African Journals Online (AJOL)

    This study aim to determine the serum levels of trace metals and correlate same with serum levels of lipoproteins (an established marker of HBP) in newly diagnosed hypertensives (NDH) A total of 50 NDH subjects (24 males and 26 females) attending Ladoke Akintola University of Technology Teaching Hospital, Osogbo ...

  12. Selection and evaluation of potential reference genes for gene expression analysis in the brown planthopper, Nilaparvata lugens (Hemiptera: Delphacidae using reverse-transcription quantitative PCR.

    Directory of Open Access Journals (Sweden)

    Miao Yuan

    Full Text Available The brown planthopper (BPH, Nilaparvata lugens (Hemiptera, Delphacidae, is one of the most important rice pests. Abundant genetic studies on BPH have been conducted using reverse-transcription quantitative real-time PCR (qRT-PCR. Using qRT-PCR, the expression levels of target genes are calculated on the basis of endogenous controls. These genes need to be appropriately selected by experimentally assessing whether they are stably expressed under different conditions. However, such studies on potential reference genes in N. lugens are lacking. In this paper, we presented a systematic exploration of eight candidate reference genes in N. lugens, namely, actin 1 (ACT, muscle actin (MACT, ribosomal protein S11 (RPS11, ribosomal protein S15e (RPS15, alpha 2-tubulin (TUB, elongation factor 1 delta (EF, 18S ribosomal RNA (18S, and arginine kinase (AK and used four alternative methods (BestKeeper, geNorm, NormFinder, and the delta Ct method to evaluate the suitability of these genes as endogenous controls. We examined their expression levels among different experimental factors (developmental stage, body part, geographic population, temperature variation, pesticide exposure, diet change, and starvation following the MIQE (Minimum Information for publication of Quantitative real time PCR Experiments guidelines. Based on the results of RefFinder, which integrates four currently available major software programs to compare and rank the tested candidate reference genes, RPS15, RPS11, and TUB were found to be the most suitable reference genes in different developmental stages, body parts, and geographic populations, respectively. RPS15 was the most suitable gene under different temperature and diet conditions, while RPS11 was the most suitable gene under different pesticide exposure and starvation conditions. This work sheds light on establishing a standardized qRT-PCR procedure in N. lugens, and serves as a starting point for screening for reference genes for

  13. Declining Job Security Level and Workers' Perfomance In Selected ...

    African Journals Online (AJOL)

    tween job security level and job performance among employees of the banks. The study ..... My financial income is likely to be unstable and uncertain due ..... when job satisfaction and motivation were sufficiently high, the negative influence of.

  14. Yakima tribal perspectives on high level selection process

    International Nuclear Information System (INIS)

    Jim, R.; Wittman, J.; Tousley, D.R.; Hovis, J.B.

    1987-01-01

    When Congress went through the arduous process of fashioning a comprehensive plan for resolution of the nation's long-standing nuclear waste problem, it explicitly recognized that past federal efforts in this area had been inadequate. Congress also recognized that the primary reasons for the failure of earlier federal efforts was failure on the part of the federal government to seriously deal with very real technical questions about the geologic adequacy of prospective repository sites, and failure to address the concerns of state, tribal, and local governments in the repository selection and development process

  15. Novel system uses probasin-based promoter, transcriptional silencers and amplification loop to induce high-level prostate expression

    Directory of Open Access Journals (Sweden)

    Yu Hong

    2007-02-01

    Full Text Available Abstract Background Despite several effective treatment options available for prostate cancer, it remains the second leading cause of cancer death in American men. Thus, there is a great need for new treatments to improve outcomes. One such strategy is to eliminate cancer through the expression of cytotoxic genes specifically in prostate cells by gene therapy vectored delivery. To prevent systemic toxicity, tissue- and/or cancer-specific gene expression is required. However, the use of tissue- or cancer-specific promoters to target transgene expression has been hampered by their weak activity. Results To address this issue, we have developed a regulation strategy that includes feedback amplification of gene expression along with a differentially suppressible tetracycline regulated expression system (DiSTRES. By differentially suppressing expression of the tetracycline-regulated transcriptional activator (tTA and silencer (tTS genes based on the cell origin, this leads to the activation and silencing of the TRE promoter, respectively. In vitro transduction of LNCaP cells with Ad/GFPDiSTRES lead to GFP expression levels that were over 30-fold higher than Ad/CMV-GFP. Furthermore, Ad/FasL-GFPDiSTRES demonstrated cytotoxic effects in prostate cancer cells known to be resistant to Fas-mediated apoptosis. Conclusion Prostate-specific regulation from the DiSTRES system, therefore, serves as a promising new regulation strategy for future applications in the field of cancer gene therapy and gene therapy as a whole.

  16. Employee performance appraisal and productivity levels in selected ...

    African Journals Online (AJOL)

    The focus of this study was on performance appraisal of academic staff of Universities in Nigeria and their productivity levels. The prime problem that necessitated this study was to examine the effectiveness of the subjective methods used in appraising qualitative work attributes of the employees and to assess the extent to ...

  17. Nitrite reductase expression is regulated at the post-transcriptional level by the nitrogen source in Nicotiana plumbaginifolia and Arabidopsis thaliana.

    Science.gov (United States)

    Crété, P; Caboche, M; Meyer, C

    1997-04-01

    Higher plant nitrite reductase (NiR) is a monomeric chloroplastic protein catalysing the reduction of nitrite, the product of nitrate reduction, to ammonium. The expression of this enzyme is controlled at the transcriptional level by light and by the nitrogen source. In order to study the post-transcriptional regulation of NiR, Nicotiana plumbaginifolia and Arabidopsis thaliana were transformed with a chimaeric NiR construct containing the tobacco leaf NiR1 coding sequence driven by the CaMV 35S RNA promoter. Transformed plants did not show any phenotypic difference when compared with the wild-type, although they overexpressed NiR activity in the leaves. When these plants were grown in vitro on media containing either nitrate or ammonium as sole nitrogen source, NiR mRNA derived from transgene expression was constitutively expressed, whereas NiR activity and protein level were strongly reduced on ammonium-containing medium. These results suggest that, together with transcriptional control, post-transcriptional regulation by the nitrogen source is operating on NiR expression. This post-transcriptional regulation of tobacco leaf NiR1 expression was observed not only in the closely related species N. plumbaginifolia but also in the more distant species A. thaliana.

  18. A review of selected derived intervention levels for Hong Kong

    International Nuclear Information System (INIS)

    Tang, S.L.; Tso, M.Y.W.; Leung, J.K.C.

    1993-01-01

    A review on the computation of derived intervention levels (DILs) for the internal pathways of exposure namely inhalation of plume and of resuspended radionuclides and ingestion of contaminated food and water is provided. The main parameters which depend on individual metabolism and habit (i.e., inhalation rate and food consumption pattern) of local population are revised. The DILs so calculated are very different from those based on parameters adopted by the Radiological Protection Advisory Group (RPAG) of the Hong Kong Government. Thus it is worthwhile to have an intensive review on the DILs based on more realistic local parameters. (6 tabs.)

  19. [Construction of Corynebacterium crenatum AS 1.542 δ argR and analysis of transcriptional levels of the related genes of arginine biosynthetic pathway].

    Science.gov (United States)

    Chen, Xuelan; Tang, Li; Jiao, Haitao; Xu, Feng; Xiong, Yonghua

    2013-01-04

    ArgR, coded by the argR gene from Corynebacterium crenatum AS 1.542, acts as a negative regulator in arginine biosynthetic pathway. However, the effect of argR on transcriptional levels of the related biosynthetic genes has not been reported. Here, we constructed a deletion mutant of argR gene: C. crenatum AS 1.542 Delta argR using marker-less knockout technology, and compared the changes of transcriptional levels of the arginine biosynthetic genes between the mutant strain and the wild-type strain. We used marker-less knockout technology to construct C. crenatum AS 1.542 Delta argR and analyzed the changes of the relate genes at the transcriptional level using real-time fluorescence quantitative PCR. C. crenatum AS 1.542 Delta argR was successfully obtained and the transcriptional level of arginine biosynthetic genes in this mutant increased significantly with an average of about 162.1 folds. The arginine biosynthetic genes in C. crenatum are clearly controlled by the negative regulator ArgR. However, the deletion of this regulator does not result in a clear change in arginine production in the bacteria.

  20. Physical interactions among plant MADS-box transcription factors and their biological relevance

    NARCIS (Netherlands)

    Nougalli Tonaco, I.A.

    2008-01-01

    The biological interpretation of the genome starts from transcription, and many different signaling pathways are integrated at this level. Transcription factors play a central role in the transcription process, because they select the down-stream genes and determine their spatial and temporal

  1. Association of neuropeptide Y (NPY, interleukin-1B (IL1B genetic variants and correlation of IL1B transcript levels with vitiligo susceptibility.

    Directory of Open Access Journals (Sweden)

    Naresh C Laddha

    Full Text Available BACKGROUND: Vitiligo is a depigmenting disorder resulting from loss of functional melanocytes in the skin. NPY plays an important role in induction of immune response by acting on a variety of immune cells. NPY synthesis and release is governed by IL1B. Moreover, genetic variability in IL1B is reported to be associated with elevated NPY levels. OBJECTIVES: Aim of the present study was to explore NPY promoter -399T/C (rs16147 and exon2 +1128T/C (rs16139 polymorphisms as well as IL1B promoter -511C/T (rs16944 polymorphism and to correlate IL1B transcript levels with vitiligo. METHODS: PCR-RFLP method was used to genotype NPY -399T/C SNP in 454 patients and 1226 controls; +1128T/C SNP in 575 patients and 1279 controls and IL1B -511C/T SNP in 448 patients and 785 controls from Gujarat. IL1B transcript levels in blood were also assessed in 105 controls and 95 patients using real-time PCR. RESULTS: Genotype and allele frequencies for NPY -399T/C, +1128T/C and IL1B -511C/T SNPs differed significantly (p<0.0001, p<0.0001; p = 0.0161, p = 0.0035 and p<0.0001, p<0.0001 between patients and controls. 'TC' haplotype containing minor alleles of NPY polymorphisms was significantly higher in patients and increased the risk of vitiligo by 2.3 fold (p<0.0001. Transcript levels of IL1B were significantly higher, in patients compared to controls (p = 0.0029, in patients with active than stable vitiligo (p = 0.015, also in female patients than male patients (p = 0.026. Genotype-phenotype correlation showed moderate association of IL1B -511C/T polymorphism with higher IL1B transcript levels. Trend analysis revealed significant difference between patients and controls for IL1B transcript levels with respect to different genotypes. CONCLUSION: Our results suggest that NPY -399T/C, +1128T/C and IL1B -511C/T polymorphisms are associated with vitiligo and IL1B -511C/T SNP influences its transcript levels leading to increased risk for vitiligo in

  2. Combinations of ERK and p38 MAPK inhibitors ablate tumor necrosis factor-alpha (TNF-alpha ) mRNA induction. Evidence for selective destabilization of TNF-alpha transcripts.

    Science.gov (United States)

    Rutault, K; Hazzalin, C A; Mahadevan, L C

    2001-03-02

    Tumor necrosis factor-alpha (TNF-alpha) is a potent proinflammatory cytokine whose synthesis and secretion are implicated in diverse pathologies. Hence, inhibition of TNF-alpha transcription or translation and neutralization of its protein product represent major pharmaceutical strategies to control inflammation. We have studied the role of ERK and p38 mitogen-activated protein (MAP) kinase in controlling TNF-alpha mRNA levels in differentiated THP-1 cells and in freshly purified human monocytes. We show here that it is possible to produce virtually complete inhibition of lipopolysaccharide-stimulated TNF-alpha mRNA accumulation by using a combination of ERK and p38 MAP kinase inhibitors. Furthermore, substantial inhibition is achievable using combinations of 1 microm of each inhibitor, whereas inhibitors used individually are incapable of producing complete inhibition even at high concentrations. Finally, addressing mechanisms involved, we show that inhibition of p38 MAP kinase selectively destabilizes TNF-alpha transcripts but does not affect degradation of c-jun transcripts. These results impinge on the controversy in the literature surrounding the mode of action of MAP kinase inhibitors on TNF-alpha mRNA and suggest the use of combinations of MAP kinase inhibitors as an effective anti-inflammatory strategy.

  3. Pesticides residue levels in selected fruits from some Ghanaian markets

    International Nuclear Information System (INIS)

    Bempah, K.C.

    2009-02-01

    The amount of some pesticide residues in fruits was monitored at five (5) Accra Metropolis markets. Locally produced fruits (pawpaw and tomato) and imported apples were purchased from two supermarkets and three urban markets in Accra metropolis and analyzed by gas chromatography equipped with electron capture detector for pesticide residues. A total of 220 samples of fruits were extracted and analyzed for pesticide residues, mainly organochlorines (γ-HCH, δ-HCH, aldrin, heptachlor, γ-chlordane, heptachlor epoxide, α-endosulfan, p,p'-DDE, endrin, β-endosulfan, o,p'-DDT, endrin aldehyde, p,p'- DDT, endrin ketone and methoxychlor). The data showed that most of the fruit samples analyzed contain residues of the monitored pesticides above the accepted maximum residue limit (MRL) as adopted by the FAO/WHO Codex Alimentarius Commission (CAC). The results obtained showed that 38.6 % fruit samples showed results above the MRL, 48.7 % were below the MRL and 12.7 % contained no detectable level of the monitored pesticides. Data analysis of health risk estimates indicated that, particularly γ-HCH, δ-HCH, o,p'-DDT, p,p'-DDE or p,p'-DDT do not pose a direct hazard to human health, although present in the three fruits (pawpaw, tomato and apple). However, heptachlor, heptachlor epoxide, endrin aldehyde, and endrin ketone levels exceeded the reference dose, indicating a great potential for systemic toxicity, especially in children who are considered to be the most vulnerable population subgroup. Lastly, the public is aware of pesticide residues in fruits and advocates for the curtailing of pesticide use on horticulture produce or strong educational programmes for farmers on control and safer use of pesticides. (au)

  4. Selection of a tool to decision making for site selection for high level waste

    International Nuclear Information System (INIS)

    Madeira, J.G.; Alvin, A.C.M.; Martins, V.B.; Monteiro, N.A.

    2016-01-01

    The aim of this paper is to create a panel comparing some of the key decision-making support tools used in situations with the characteristics of the problem of selecting suitable areas for constructing a final deep geologic repository. The tools addressed in this work are also well known and with easy implementation. The decision-making process in matters of this kind is, in general, complex due to its multi-criteria nature and the conflicting opinions of various stakeholders. Thus, a comprehensive study was performed with the literature in this subject, specifically in documents of the International Atomic Energy Agency (IAEA), regarding the importance of the criteria involved in the decision-making process. Therefore, we highlighted six judgment attributes for selecting a decision support tool, suitable for the problem. For this study, we have selected the following multi-criteria tools: AHP, Delphi, Brainstorm, Nominal Group Technique and AHP-Delphi. Finally, the AHP-Delphi method has demonstrated to be more appropriate for managing the inherent multiple attributes to the problem proposed. (authors)

  5. Selection of a tool to support decision making for site selection for high level waste - 15010

    International Nuclear Information System (INIS)

    Madeira, J.G.; Alvim, A.C.M.; Martins, V.B.; Monteiro, N.A.

    2015-01-01

    The aim of this paper is to create a panel comparing some of the key decision-making support tools used in situations with the characteristics of the problem of selecting suitable areas for constructing a final deep geologic repository. The tools presented in this work are also well-known and with easy implementation. The decision making process in issues of this kind is, in general, complex due to its multi-criteria nature and the conflicting opinions of various of stakeholders. Thus a comprehensive study was performed with the literature on this subject, specifically documents of the International Atomic Energy Agency - IAEA, regarding the importance of the criteria involved in the decision making process. Therefore, we highlighted 6 judgments attributes for selecting an adequate support tool: -) transparency and reliability, -) subjectivity, -) updating and adapting, -) multi-criteria analysis, -) ease of deployment, and -) application time. We have selected the following key decision-making support tools: AHP, Delphi, Brainstorm, Nominal Group Technique, and AHP-Delphi. Finally, the AHP-Delphi method has demonstrated to be more appropriate for managing the inherent multiple attributes to the problem proposed

  6. Transcript levels of several epigenome regulatory genes in bovine somatic donor cells are not correlated with their cloning efficiency.

    Science.gov (United States)

    Zhou, Wenli; Sadeghieh, Sanaz; Abruzzese, Ronald; Uppada, Subhadra; Meredith, Justin; Ohlrichs, Charletta; Broek, Diane; Polejaeva, Irina

    2009-09-01

    Among many factors that potentially affect somatic cell nuclear transfer (SCNT) embryo development is the donor cell itself. Cloning potentials of somatic donor cells vary greatly, possibly because the cells have different capacities to be reprogrammed by ooplasma. It is therefore intriguing to identify factors that regulate the reprogrammability of somatic donor cells. Gene expression analysis is a widely used tool to investigate underlying mechanisms of various phenotypes. In this study, we conducted a retrospective analysis investigating whether donor cell lines with distinct cloning efficiencies express different levels of genes involved in epigenetic reprogramming including histone deacetylase-1 (HDAC1), -2 (HDAC2); DNA methyltransferase-1 (DNMT1), -3a (DNMT3a),-3b (DNMT3b), and the bovine homolog of yeast sucrose nonfermenting-2 (SNF2L), a SWI/SNF family of ATPases. Cell samples from 12 bovine donor cell lines were collected at the time of nuclear transfer experiments and expression levels of the genes were measured using quantitative polymerase chain reaction (PCR). Our results show that there are no significant differences in expression levels of these genes between donor cell lines of high and low cloning efficiency defined as live calving rates, although inverse correlations are observed between in vitro embryo developmental rates and expression levels of HDAC2 and SNF2L. We also show that selection of stable reference genes is important for relative quantification, and different batches of cells can have different gene expression patterns. In summary, we demonstrate that expression levels of these epigenome regulatory genes in bovine donor cells are not correlated with cloning potential. The experimental design and data analysis method reported here can be applied to study any genes expressed in donor cells.

  7. Integrated mRNA and microRNA analysis identifies genes and small miRNA molecules associated with transcriptional and post-transcriptional-level responses to both drought stress and re-watering treatment in tobacco.

    Science.gov (United States)

    Chen, Qiansi; Li, Meng; Zhang, Zhongchun; Tie, Weiwei; Chen, Xia; Jin, Lifeng; Zhai, Niu; Zheng, Qingxia; Zhang, Jianfeng; Wang, Ran; Xu, Guoyun; Zhang, Hui; Liu, Pingping; Zhou, Huina

    2017-01-10

    Drought stress is one of the most severe problem limited agricultural productivity worldwide. It has been reported that plants response to drought-stress by sophisticated mechanisms at both transcriptional and post-transcriptional levels. However, the precise molecular mechanisms governing the responses of tobacco leaves to drought stress and water status are not well understood. To identify genes and miRNAs involved in drought-stress responses in tobacco, we performed both mRNA and small RNA sequencing on tobacco leaf samples from the following three treatments: untreated-control (CL), drought stress (DL), and re-watering (WL). In total, we identified 798 differentially expressed genes (DEGs) between the DL and CL (DL vs. CL) treatments and identified 571 DEGs between the WL and DL (WL vs. DL) treatments. Further analysis revealed 443 overlapping DEGs between the DL vs. CL and WL vs. DL comparisons, and, strikingly, all of these genes exhibited opposing expression trends between these two comparisons, strongly suggesting that these overlapping DEGs are somehow involved in the responses of tobacco leaves to drought stress. Functional annotation analysis showed significant up-regulation of genes annotated to be involved in responses to stimulus and stress, (e.g., late embryogenesis abundant proteins and heat-shock proteins) antioxidant defense (e.g., peroxidases and glutathione S-transferases), down regulation of genes related to the cell cycle pathway, and photosynthesis processes. We also found 69 and 56 transcription factors (TFs) among the DEGs in, respectively, the DL vs. CL and the WL vs. DL comparisons. In addition, small RNA sequencing revealed 63 known microRNAs (miRNA) from 32 families and 368 novel miRNA candidates in tobacco. We also found that five known miRNA families (miR398, miR390, miR162, miR166, and miR168) showed differential regulation under drought conditions. Analysis to identify negative correlations between the differentially expressed mi

  8. Absence of 60-Hz, 0.1-mT magnetic field-induced changes in oncogene transcription rates or levels in CEM-CM3 cells.

    Science.gov (United States)

    Jahreis, G P; Johnson, P G; Zhao, Y L; Hui, S W

    1998-12-22

    Our objective was to assess the reproducibility of the 60-Hz magnetic field-induced, time-dependent transcription changes of c-fos, c-jun and c-myc oncogenes in CEM-CM3 cells reported by Phillips et al. (Biochim. Biophys. Acta, 1132 (1992) 140-144). Cells were exposed to a 60-Hz magnetic field (MF) at 0.1 mT (rms), generated by a pair of Helmholtz coils energized in a reinforcing (MF) mode, or to a null magnetic field when the coils were energized in a bucking (sham) mode. After MF or sham exposure for 15, 30, 60 or 120 min, nuclei and cytoplasmic RNA were extracted. Transcription rates were measured by a nuclear run-on assay, and values were normalized against either their zero-time exposure values, or against those of the c-G3PDH (housekeeping) gene at the same time points. There was no significant difference, at P=0.05, detected between MF and either sham-exposed or control cells at any time point. Transcript levels of the oncogenes were measured by Northern analysis and normalized as above. No significant difference (P=0.05) in transcript levels between MF and either sham-exposed or control cells was detected.

  9. Association of Cocaine- and Amphetamine-Regulated Transcript (CART) Messenger RNA Level, Food Intake, and Growth in Channel Catfish

    Science.gov (United States)

    Cocaine-and Amphetamine-Regulated Transcript (CART) is a potent hypothalamic anorectic peptide in mammals and fish. We hypothesized that increased food intake is associated with changes in expression of CART mRNA within the brain of channel catfish. Objectives were to clone the CART gene, examine ...

  10. Untangling the Effect of Fatty Acid Addition at Species Level Revealed Different Transcriptional Responses of the Biogas Microbial Community Members

    DEFF Research Database (Denmark)

    Treu, Laura; Campanaro, Stefano; Kougias, Panagiotis

    2016-01-01

    In the present study, RNA-sequencing was used to elucidate the change of anaerobic digestion metatranscriptome after long chain fatty acids (oleate) exposure. To explore the general transcriptional behavior of the microbiome, the analysis was first performed on shotgun reads without considering...

  11. Profiling of histone H3 lysine 9 trimethylation levels predicts transcription factor activity and survival in acute myeloid leukemia

    DEFF Research Database (Denmark)

    Müller-Tidow, Carsten; Klein, Hans-Ulrich; Hascher, Antje

    2010-01-01

    Acute Myeloid Leukemia (AML) is commonly associated with alterations in transcription factors due to altered expression or gene mutations. These changes might induce leukemia- specific patterns of histone modifications. We used ChIP-Chip to analyze histone H3 Lysine 9 trimethylation (H3K9me3) pat...

  12. Association of Neuropeptide Y (NPY), Interleukin-1B (IL1B) Genetic Variants and Correlation of IL1B Transcript Levels with Vitiligo Susceptibility

    Science.gov (United States)

    Laddha, Naresh C.; Dwivedi, Mitesh; Mansuri, Mohmmad Shoab; Singh, Mala; Patel, Hetanshi H.; Agarwal, Nishtha; Shah, Anish M.; Begum, Rasheedunnisa

    2014-01-01

    Background Vitiligo is a depigmenting disorder resulting from loss of functional melanocytes in the skin. NPY plays an important role in induction of immune response by acting on a variety of immune cells. NPY synthesis and release is governed by IL1B. Moreover, genetic variability in IL1B is reported to be associated with elevated NPY levels. Objectives Aim of the present study was to explore NPY promoter −399T/C (rs16147) and exon2 +1128T/C (rs16139) polymorphisms as well as IL1B promoter −511C/T (rs16944) polymorphism and to correlate IL1B transcript levels with vitiligo. Methods PCR-RFLP method was used to genotype NPY -399T/C SNP in 454 patients and 1226 controls; +1128T/C SNP in 575 patients and 1279 controls and IL1B −511C/T SNP in 448 patients and 785 controls from Gujarat. IL1B transcript levels in blood were also assessed in 105 controls and 95 patients using real-time PCR. Results Genotype and allele frequencies for NPY −399T/C, +1128T/C and IL1B −511C/T SNPs differed significantly (pvitiligo by 2.3 fold (pvitiligo (p = 0.015), also in female patients than male patients (p = 0.026). Genotype-phenotype correlation showed moderate association of IL1B -511C/T polymorphism with higher IL1B transcript levels. Trend analysis revealed significant difference between patients and controls for IL1B transcript levels with respect to different genotypes. Conclusion Our results suggest that NPY −399T/C, +1128T/C and IL1B −511C/T polymorphisms are associated with vitiligo and IL1B −511C/T SNP influences its transcript levels leading to increased risk for vitiligo in Gujarat population. Up-regulation of IL1B transcript in patients advocates its possible role in autoimmune pathogenesis of vitiligo. PMID:25221996

  13. In vitro selection of DNA elements highly responsive to the human T-cell lymphotropic virus type I transcriptional activator, Tax.

    Science.gov (United States)

    Paca-Uccaralertkun, S; Zhao, L J; Adya, N; Cross, J V; Cullen, B R; Boros, I M; Giam, C Z

    1994-01-01

    The human T-cell lymphotropic virus type I (HTLV-I) transactivator, Tax, the ubiquitous transcriptional factor cyclic AMP (cAMP) response element-binding protein (CREB protein), and the 21-bp repeats in the HTLV-I transcriptional enhancer form a ternary nucleoprotein complex (L. J. Zhao and C. Z. Giam, Proc. Natl. Acad. Sci. USA 89:7070-7074, 1992). Using an antibody directed against the COOH-terminal region of Tax along with purified Tax and CREB proteins, we selected DNA elements bound specifically by the Tax-CREB complex in vitro. Two distinct but related groups of sequences containing the cAMP response element (CRE) flanked by long runs of G and C residues in the 5' and 3' regions, respectively, were preferentially recognized by Tax-CREB. In contrast, CREB alone binds only to CRE motifs (GNTGACG[T/C]) without neighboring G- or C-rich sequences. The Tax-CREB-selected sequences bear a striking resemblance to the 5' or 3' two-thirds of the HTLV-I 21-bp repeats and are highly inducible by Tax. Gel electrophoretic mobility shift assays, DNA transfection, and DNase I footprinting analyses indicated that the G- and C-rich sequences flanking the CRE motif are crucial for Tax-CREB-DNA ternary complex assembly and Tax transactivation but are not in direct contact with the Tax-CREB complex. These data show that Tax recruits CREB to form a multiprotein complex that specifically recognizes the viral 21-bp repeats. The expanded DNA binding specificity of Tax-CREB and the obligatory role the ternary Tax-CREB-DNA complex plays in transactivation reveal a novel mechanism for regulating the transcriptional activity of leucine zipper proteins like CREB.

  14. Supplementation of Nucleosides During Selection can Reduce Sequence Variant Levels in CHO Cells Using GS/MSX Selection System.

    Science.gov (United States)

    Tang, Danming; Lam, Cynthia; Louie, Salina; Hoi, Kam Hon; Shaw, David; Yim, Mandy; Snedecor, Brad; Misaghi, Shahram

    2018-01-01

    In the process of generating stable monoclonal antibody (mAb) producing cell lines, reagents such as methotrexate (MTX) or methionine sulfoximine (MSX) are often used. However, using such selection reagent(s) increases the possibility of having higher occurrence of sequence variants in the expressed antibody molecules due to the effects of MTX or MSX on de novo nucleotide synthesis. Since MSX inhibits glutamine synthase (GS) and results in both amino acid and nucleoside starvation, it is questioned whether supplementing nucleosides into the media could lower sequence variant levels without affecting titer. The results show that the supplementation of nucleosides to the media during MSX selection decreased genomic DNA mutagenesis rates in the selected cells, probably by reducing nucleotide mis-incorporation into the DNA. Furthermore, addition of nucleosides enhance clone recovery post selection and does not affect antibody expression. It is further observed that nucleoside supplements lowered DNA mutagenesis rates only at the initial stage of the clone selection and do not have any effect on DNA mutagenesis rates after stable cell lines are established. Therefore, the data suggests that addition of nucleosides during early stages of MSX selection can lower sequence variant levels without affecting titer or clone stability in antibody expression. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. ABCC5, ERCC2, XPA and XRCC1 transcript abundance levels correlate with cisplatin chemoresistance in non-small cell lung cancer cell lines

    Directory of Open Access Journals (Sweden)

    Khuder Sadik A

    2005-05-01

    Full Text Available Abstract Background Although 40–50% of non-small cell lung cancer (NSCLC tumors respond to cisplatin chemotherapy, there currently is no way to prospectively identify potential responders. The purpose of this study was to determine whether transcript abundance (TA levels of twelve selected DNA repair or multi-drug resistance genes (LIG1, ERCC2, ERCC3, DDIT3, ABCC1, ABCC4, ABCC5, ABCC10, GTF2H2, XPA, XPC and XRCC1 were associated with cisplatin chemoresistance and could therefore contribute to the development of a predictive marker. Standardized RT (StaRT-PCR, was employed to assess these genes in a set of NSCLC cell lines with a previously published range of sensitivity to cisplatin. Data were obtained in the form of target gene molecules relative to 106 β-actin (ACTB molecules. To cancel the effect of ACTB variation among the different cell lines individual gene expression values were incorporated into ratios of one gene to another. Each two-gene ratio was compared as a single variable to chemoresistance for each of eight NSCLC cell lines using multiple regression. In an effort to validate these results, six additional lines then were evaluated. Results Following validation, single variable models best correlated with chemoresistance (p ERCC2/XPC, ABCC5/GTF2H2, ERCC2/GTF2H2, XPA/XPC and XRCC1/XPC. All single variable models were examined hierarchically to achieve two variable models. The two variable model with the highest correlation was (ABCC5/GTF2H2, ERCC2/GTF2H2 with an R2 value of 0.96 (p Conclusion These results provide markers suitable for assessment of small fine needle aspirate biopsies in an effort to prospectively identify cisplatin resistant tumors.

  16. Active Center Control of Termination by RNA Polymerase III and tRNA Gene Transcription Levels In Vivo.

    Directory of Open Access Journals (Sweden)

    Keshab Rijal

    2016-08-01

    Full Text Available The ability of RNA polymerase (RNAP III to efficiently recycle from termination to reinitiation is critical for abundant tRNA production during cellular proliferation, development and cancer. Yet understanding of the unique termination mechanisms used by RNAP III is incomplete, as is its link to high transcription output. We used two tRNA-mediated suppression systems to screen for Rpc1 mutants with gain- and loss- of termination phenotypes in S. pombe. 122 point mutation mutants were mapped to a recently solved 3.9 Å structure of yeast RNAP III elongation complex (EC; they cluster in the active center bridge helix and trigger loop, as well as the pore and funnel, the latter of which indicate involvement of the RNA cleavage domain of the C11 subunit in termination. Purified RNAP III from a readthrough (RT mutant exhibits increased elongation rate. The data strongly support a kinetic coupling model in which elongation rate is inversely related to termination efficiency. The mutants exhibit good correlations of terminator RT in vitro and in vivo, and surprisingly, amounts of transcription in vivo. Because assessing in vivo transcription can be confounded by various parameters, we used a tRNA reporter with a processing defect and a strong terminator. By ruling out differences in RNA decay rates, the data indicate that mutants with the RT phenotype synthesize more RNA than wild type cells, and than can be accounted for by their increased elongation rate. Finally, increased activity by the mutants appears unrelated to the RNAP III repressor, Maf1. The results show that the mobile elements of the RNAP III active center, including C11, are key determinants of termination, and that some of the mutations activate RNAP III for overall transcription. Similar mutations in spontaneous cancer suggest this as an unforeseen mechanism of RNAP III activation in disease.

  17. Annual variation in the levels of transcripts of sex-specific genes in the mantle of the common mussel, Mytilus edulis.

    Directory of Open Access Journals (Sweden)

    Sandhya Anantharaman

    Full Text Available Mytilus species are used as sentinels for the assessment of environmental health but sex or stage in the reproduction cycle is rarely considered even though both parameters are likely to influence responses to pollution. We have validated the use of a qPCR assay for sex identification and related the levels of transcripts to the reproductive cycle. A temporal study of mantle of Mytilus edulis found transcripts of male-specific vitelline coat lysin (VCL and female-specific vitelline envelope receptor for lysin (VERL could identify sex over a complete year. The levels of VCL/VERL were proportional to the numbers of sperm/ova and are indicative of the stage of the reproductive cycle. Maximal levels of VCL and VERL were found in February 2009 declining to minima between July - August before increasing and re-attaining a peak in February 2010. Water temperature may influence these transitions since they coincide with minimal water temperature in February and maximal temperature in August. An identical pattern of variation was found for a cryptic female-specific transcript (H5 but a very different pattern was observed for oestrogen receptor 2 (ER2. ER2 varied in a sex-specific way with male > female for most of the cycle, with a female maxima in July and a male maxima in December. Using artificially spawned animals, the transcripts for VCL, VERL and H5 were shown to be present in gametes and thus their disappearance from mantle is indicative of spawning. VCL and VERL are present at equivalent levels in February and July-August but during gametogenesis (August to January and spawning (March to June VCL is present at lower relative amounts than VERL. This may indicate sex-specific control mechanisms for these processes and highlight a potential pressure point leading to reduced reproductive output if environmental factors cause asynchrony to gamete maturation or release.

  18. When selection ratios are high: predicting the expatriation willingness of prospective domestic entry-level job applicants

    NARCIS (Netherlands)

    Mol, S.T.; Born, M.P.; Willemsen, M.E.; van der Molen, H.T.; Derous, E.

    2009-01-01

    High expatriate selection ratios thwart the ability of multinational organizations to select expatriates. Reducing the selection ratio may be accomplished by selecting those applicants for entry level domestic positions who have expatriate aspirations. Regression analyses conducted on data from a

  19. Conserved XPB Core Structure and Motifs for DNA Unwinding:Implications for Pathway Selection of Transcription or ExcisionRepair

    Energy Technology Data Exchange (ETDEWEB)

    Fan, Li; Arval, Andrew S.; Cooper, Priscilla K.; Iwai, Shigenori; Hanaoka, Fumio; Tainer, John A.

    2005-04-01

    The human xeroderma pigmentosum group B (XPB) helicase is essential for transcription, nucleotide excision repair, and TFIIH functional assembly. Here, we determined crystal structures of an Archaeoglobus fulgidus XPB homolog (AfXPB) that characterize two RecA-like XPB helicase domains and discover a DNA damage recognition domain (DRD), a unique RED motif, a flexible thumb motif (ThM), and implied conformational changes within a conserved functional core. RED motif mutations dramatically reduce helicase activity, and the DRD and ThM, which flank the RED motif, appear structurally as well as functionally analogous to the MutS mismatch recognition and DNA polymerase thumb domains. Substrate specificity is altered by DNA damage, such that AfXPB unwinds dsDNA with 3' extensions, but not blunt-ended dsDNA, unless it contains a lesion, as shown for CPD or (6-4) photoproducts. Together, these results provide an unexpected mechanism of DNA unwinding with Implications for XPB damage verification in nucleotide excision repair.

  20. Subcellular location of Arabidopsis thaliana subfamily a1 β-galactosidases and developmental regulation of transcript levels of their coding genes.

    Science.gov (United States)

    Moneo-Sánchez, María; Izquierdo, Lucía; Martín, Ignacio; Labrador, Emilia; Dopico, Berta

    2016-12-01

    The aim of this work is to gain insight into the six members of the a1 subfamily of the β-galactosidases (BGAL) from Arabidopsis thaliana. First, the subcellular location of all these six BGAL proteins from a1 subfamily has been established in the cell wall by the construction of transgenic plants producing the enhanced green fluorescent protein (eGFP) fused to the BGAL proteins. BGAL12 is also located in the endoplasmic reticulum. Our study of the AtBGAL transcript accumulation along plant development indicated that all AtBGAL transcript appeared in initial stages of development, both dark- and light-grown seedlings, being AtBGAL1, AtBGAL2 and AtBGAL3 transcripts the predominant ones in the latter condition, mainly in the aerial part and with levels decreasing with age. The high accumulation of transcript of AtBGAL4 in basal internodes and in leaves at the end of development, and their strong increase after treatment both with BL and H 3 BO 3 point to an involvement of BGAL4 in cell wall changes leading to the cease of elongation and increased rigidity. The changes of AtBGAL transcript accumulation in relation to different stages and conditions of plant development, suggest that each of the different gene products have a plant-specific function and provides support for the proposed function of the subfamily a1 BGAL in plant cell wall remodelling for cell expansion or for cell response to stress conditions. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

  1. Diversity and Transcriptional Levels of RuBisCO Form II of Sulfur-Oxidizing γ-Proteobacteria in Coastal-Upwelling Waters with Seasonal Anoxia

    Directory of Open Access Journals (Sweden)

    Bárbara Léniz

    2017-07-01

    Full Text Available Seasonal wind-driven upwelling, high primary production in surface waters, and oxygen deficiency in subsurface waters characterize the coastal ecosystem of the subtropical eastern South Pacific (ESP, and shape the nature and dynamics of the microbial community structure and function. We investigated the diversity, abundance, and transcriptional levels of the gene encoding the large subunit form II of the RuBisCO enzyme (cbbM in the pelagic microbial community at a continental-shelf site off central Chile over 2 years. We focused on cbbM genes affiliated with the sulfur-oxidizing γ-proteobacteria cluster, whose members are known to dominate in oxygen-deficient marine environments and are highly abundant in the study area. Phylogenetic analysis of cbbM sequences suggests the presence of a novel group of chemolithoautotrophs, closely related to the SUP05/ARCTIC96BD-19 clade. Through (RT-qPCR, we studied the cbbM gene abundance and transcript dynamics over an annual cycle, finding a significantly higher number of cbbM copies per unit volume in months of active upwelling and at depths in which oxygen was scarce or absent. The same temporal pattern was observed at the transcriptional level. We also analyzed the relative expression of key genes for carbon, nitrogen and sulfur cycling in six metatranscriptomic datasets, for two characteristic periods within the annual cycle: the anoxic upwelling and the suboxic downwelling. Our results indicate that coastal waters of the subtropical ESP contain transcriptionally active populations of carbon fixing pelagic bacteria, whose dynamics is controlled, in large part, by fluctuations in oxygen levels. They also suggest that chemolithoautotrophic processes coupled to the sulfur and nitrogen cycles become increasingly important for the carbon economy of marine coastal waters as oxygen concentrations decline.

  2. Site selection criteria for the shallow land burial of low-level radioactive waste

    International Nuclear Information System (INIS)

    Falconer, K.L.; Hull, L.C.; Mizell, S.A.

    The shallow land burial of low-level waste must be accomplished in a manner that ensures the public and biosphere are protected from harmful amounts of radiation. This can be attained by selecting, designing, operating and closing sites such that contaminants never leave the site boundary in levels above regulatory limits. Site design, operation and closure are all functions of the characteristics of the site selected. As a result, the site selection process offers the most effective means for optimizing safe, efficient and economical low-level waste burial practices. The purpose of this document is to set forth criteria for the selection of shallow land burial sites. Criteria are standard rules, by which the ability of a site to meet waste management goals can be judged. They are comprehensive, universal, and qualitative and are applicable in any geologic environment. Site selection criteria provide the framework for the siting process

  3. Quantifying Temporal Autocorrelations for the Expression of Geobacter species mRNA Gene Transcripts at Variable Ammonium Levels during in situ U(VI) Bioremediation

    Science.gov (United States)

    Mouser, P. J.

    2010-12-01

    In order to develop decision-making tools for the prediction and optimization of subsurface bioremediation strategies, we must be able to link the molecular-scale activity of microorganisms involved in remediation processes with biogeochemical processes observed at the field-scale. This requires the ability to quantify changes in the in situ metabolic condition of dominant microbes and associate these changes to fluctuations in nutrient levels throughout the bioremediation process. It also necessitates a need to understand the spatiotemporal variability of the molecular-scale information to develop meaningful parameters and constraint ranges in complex bio-physio-chemical models. The expression of three Geobacter species genes (ammonium transporter (amtB), nitrogen fixation (nifD), and a housekeeping gene (recA)) were tracked at two monitoring locations that differed significantly in ammonium (NH4+) concentrations during a field-scale experiment where acetate was injected into the subsurface to simulate Geobacteraceae in a uranium-contaminated aquifer. Analysis of amtB and nifD mRNA transcript levels indicated that NH4+ was the primary form of fixed nitrogen during bioremediation. Overall expression levels of amtB were on average 8-fold higher at NH4+ concentrations of 300 μM or more than at lower NH4+ levels (average 60 μM). The degree of temporal correlation in Geobacter species mRNA expression levels was calculated at both locations using autocorrelation methods that describe the relationship between sample semi-variance and time lag. At the monitoring location with lower NH4+, a temporal correlation lag of 8 days was observed for both amtB and nifD transcript patterns. At the location where higher NH4+ levels were observed, no discernable temporal correlation lag above the sampling frequency (approximately every 2 days) was observed for amtB or nifD transcript fluctuations. Autocorrelation trends in recA expression levels at both locations indicated that

  4. Bone-remodeling transcript levels are independent of perching in end-of-lay white leghorn chickens.

    Science.gov (United States)

    Dale, Maurice D; Mortimer, Erin M; Kolli, Santharam; Achramowicz, Erik; Borchert, Glenn; Juliano, Steven A; Halkyard, Scott; Sietz, Nick; Gatto, Craig; Hester, Patricia Y; Rubin, David A

    2015-01-23

    Osteoporosis is a bone disease that commonly results in a 30% incidence of fracture in hens used to produce eggs for human consumption. One of the causes of osteoporosis is the lack of mechanical strain placed on weight-bearing bones. In conventionally-caged hens, there is inadequate space for chickens to exercise and induce mechanical strain on their bones. One approach is to encourage mechanical stress on bones by the addition of perches to conventional cages. Our study focuses on the molecular mechanism of bone remodeling in end-of-lay hens (71 weeks) with access to perches. We examined bone-specific transcripts that are actively involved during development and remodeling. Using real-time quantitative PCR, we examined seven transcripts (COL2A1 (collagen, type II, alpha 1), RANKL (receptor activator of nuclear factor kappa-B ligand), OPG (osteoprotegerin), PTHLH (PTH-like hormone), PTH1R (PTH/PTHLH type-1 receptor), PTH3R (PTH/PTHLH type-3 receptor), and SOX9 (Sry-related high mobility group box)) in phalange, tibia and femur. Our results indicate that the only significant effect was a difference among bones for COL2A1 (femur > phalange). Therefore, we conclude that access to a perch did not alter transcript expression. Furthermore, because hens have been used as a model for human bone metabolism and osteoporosis, the results indicate that bone remodeling due to mechanical loading in chickens may be a product of different pathways than those involved in the mammalian model.

  5. Bone-Remodeling Transcript Levels Are Independent of Perching in End-of-Lay White Leghorn Chickens

    Directory of Open Access Journals (Sweden)

    Maurice D. Dale

    2015-01-01

    Full Text Available Osteoporosis is a bone disease that commonly results in a 30% incidence of fracture in hens used to produce eggs for human consumption. One of the causes of osteoporosis is the lack of mechanical strain placed on weight-bearing bones. In conventionally-caged hens, there is inadequate space for chickens to exercise and induce mechanical strain on their bones. One approach is to encourage mechanical stress on bones by the addition of perches to conventional cages. Our study focuses on the molecular mechanism of bone remodeling in end-of-lay hens (71 weeks with access to perches. We examined bone-specific transcripts that are actively involved during development and remodeling. Using real-time quantitative PCR, we examined seven transcripts (COL2A1 (collagen, type II, alpha 1, RANKL (receptor activator of nuclear factor kappa-B ligand, OPG (osteoprotegerin, PTHLH (PTH-like hormone, PTH1R (PTH/PTHLH type-1 receptor, PTH3R (PTH/PTHLH type-3 receptor, and SOX9 (Sry-related high mobility group box in phalange, tibia and femur. Our results indicate that the only significant effect was a difference among bones for COL2A1 (femur > phalange. Therefore, we conclude that access to a perch did not alter transcript expression. Furthermore, because hens have been used as a model for human bone metabolism and osteoporosis, the results indicate that bone remodeling due to mechanical loading in chickens may be a product of different pathways than those involved in the mammalian model.

  6. Comparison of selection methods to deduce natural background levels for groundwater units

    NARCIS (Netherlands)

    Griffioen, J.; Passier, H.F.; Klein, J.

    2008-01-01

    Establishment of natural background levels (NBL) for groundwater is commonly performed to serve as reference when assessing the contamination status of groundwater units. We compare various selection methods to establish NBLs using groundwater quality data forfour hydrogeologically different areas

  7. Students' level of skillfulness and use of the internet in selected ...

    African Journals Online (AJOL)

    The study examined level of skillfulness and the use of the Internet for learning among secondary school students in Lagos State, Nigeria. The descriptive survey research method was adopted for the study. A sample of 450 students was randomly selected from the three secondary schools. One intact arm was selected from ...

  8. Population Level Purifying Selection and Gene Expression Shape Subgenome Evolution in Maize.

    Science.gov (United States)

    Pophaly, Saurabh D; Tellier, Aurélien

    2015-12-01

    The maize ancestor experienced a recent whole-genome duplication (WGD) followed by gene erosion which generated two subgenomes, the dominant subgenome (maize1) experiencing fewer deletions than maize2. We take advantage of available extensive polymorphism and gene expression data in maize to study purifying selection and gene expression divergence between WGD retained paralog pairs. We first report a strong correlation in nucleotide diversity between duplicate pairs, except for upstream regions. We then show that maize1 genes are under stronger purifying selection than maize2. WGD retained genes have higher gene dosage and biased Gene Ontologies consistent with previous studies. The relative gene expression of paralogs across tissues demonstrates that 98% of duplicate pairs have either subfunctionalized in a tissuewise manner or have diverged consistently in their expression thereby preventing functional complementation. Tissuewise subfunctionalization seems to be a hallmark of transcription factors, whereas consistent repression occurs for macromolecular complexes. We show that dominant gene expression is a strong determinant of the strength of purifying selection, explaining the inferred stronger negative selection on maize1 genes. We propose a novel expression-based classification of duplicates which is more robust to explain observed polymorphism patterns than the subgenome location. Finally, upstream regions of repressed genes exhibit an enrichment in transposable elements which indicates a possible mechanism for expression divergence. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  9. Glycogen synthase kinase-3 inhibitors suppress the AR-V7-mediated transcription and selectively inhibit cell growth in AR-V7-positive prostate cancer cells.

    Science.gov (United States)

    Nakata, Daisuke; Koyama, Ryokichi; Nakayama, Kazuhide; Kitazawa, Satoshi; Watanabe, Tatsuya; Hara, Takahito

    2017-06-01

    Recent evidence suggests that androgen receptor (AR) splice variants, including AR-V7, play a pivotal role in resistance to androgen blockade in prostate cancer treatment. The development of new therapeutic agents that can suppress the transcriptional activities of AR splice variants has been anticipated as the next generation treatment of castration-resistant prostate cancer. High-throughput screening of AR-V7 signaling inhibitors was performed using an AR-V7 reporter system. The effects of a glycogen synthase kinase-3 (GSK3) inhibitor, LY-2090314, on endogenous AR-V7 signaling were evaluated in an AR-V7-positive cell line, JDCaP-hr, by quantitative reverse transcription polymerase chain reaction. The relationship between AR-V7 signaling and β-catenin signaling was assessed using RNA interference. The effect of LY-2090314 on cell growth in various prostate cancer cell lines was also evaluated. We identified GSK3 inhibitors as transcriptional suppressors of AR-V7 using a high-throughput screen with an AR-V7 reporter system. LY-2090314 suppressed the reporter activity and endogenous AR-V7 activity in JDCaP-hr cells. Because silencing of β-catenin partly rescued the suppression, it was evident that the suppression was mediated, at least partially, via the activation of β-catenin signaling. AR-V7 signaling and β-catenin signaling reciprocally regulate each other in JDCaP-hr cells, and therefore, GSK3 inhibition can repress AR-V7 transcriptional activity by accumulating intracellular β-catenin. Notably, LY-2090314 selectively inhibited the growth of AR-V7-positive prostate cancer cells in vitro. Our findings demonstrate the potential of GSK3 inhibitors in treating advanced prostate cancer driven by AR splice variants. In vivo evaluation of AR splice variant-positive prostate cancer models will help illustrate the overall significance of GSK3 inhibitors in treating prostate cancer. © 2017 Wiley Periodicals, Inc.

  10. Foot-and-mouth disease virus leader proteinase inhibits dsRNA-induced type I interferon transcription by decreasing interferon regulatory factor 3/7 in protein levels

    International Nuclear Information System (INIS)

    Wang, Dang; Fang, Liurong; Luo, Rui; Ye, Rui; Fang, Ying; Xie, Lilan; Chen, Huanchun; Xiao, Shaobo

    2010-01-01

    Research highlights: → FMDV L pro inhibits poly(I:C)-induced IFN-α1/β mRNA expression. → L pro inhibits MDA5-mediated activation of the IFN-α1/β promoter. → L pro significantly reduced the transcription of multiple IRF-responsive genes. → L pro inhibits IFN-α1/β promoter activation by decreasing IRF-3/7 in protein levels. → The ability to process eIF-4G of L pro is not necessary to inhibit IFN-α1/β activation. -- Abstract: The leader proteinase (L pro ) of foot-and-mouth disease virus (FMDV) has been identified as an interferon-β (IFN-β) antagonist that disrupts the integrity of transcription factor nuclear factor κB (NF-κB). In this study, we showed that the reduction of double stranded RNA (dsRNA)-induced IFN-α1/β expression caused by L pro was also associated with a decrease of interferon regulatory factor 3/7 (IRF-3/7) in protein levels, two critical transcription factors for activation of IFN-α/β. Furthermore, overexpression of L pro significantly reduced the transcription of multiple IRF-responsive genes including 2',5'-OAS, ISG54, IP-10, and RANTES. Screening L pro mutants indicated that the ability to process eIF-4G of L pro is not required for suppressing dsRNA-induced activation of the IFN-α1/β promoter and decreasing IRF-3/7 expression. Taken together, our results demonstrate that, in addition to disrupting NF-κB, L pro also decreases IRF-3/7 expression to suppress dsRNA-induced type I IFN production, suggesting multiple strategies used by FMDV to counteract the immune response to viral infection.

  11. Foot-and-mouth disease virus leader proteinase inhibits dsRNA-induced type I interferon transcription by decreasing interferon regulatory factor 3/7 in protein levels

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Dang; Fang, Liurong; Luo, Rui; Ye, Rui; Fang, Ying; Xie, Lilan; Chen, Huanchun [Division of Animal Infectious Diseases, State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070 (China); Xiao, Shaobo, E-mail: shaoboxiao@yahoo.com [Division of Animal Infectious Diseases, State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070 (China)

    2010-08-13

    Research highlights: {yields} FMDV L{sup pro} inhibits poly(I:C)-induced IFN-{alpha}1/{beta} mRNA expression. {yields} L{sup pro} inhibits MDA5-mediated activation of the IFN-{alpha}1/{beta} promoter. {yields} L{sup pro} significantly reduced the transcription of multiple IRF-responsive genes. {yields} L{sup pro} inhibits IFN-{alpha}1/{beta} promoter activation by decreasing IRF-3/7 in protein levels. {yields} The ability to process eIF-4G of L{sup pro} is not necessary to inhibit IFN-{alpha}1/{beta} activation. -- Abstract: The leader proteinase (L{sup pro}) of foot-and-mouth disease virus (FMDV) has been identified as an interferon-{beta} (IFN-{beta}) antagonist that disrupts the integrity of transcription factor nuclear factor {kappa}B (NF-{kappa}B). In this study, we showed that the reduction of double stranded RNA (dsRNA)-induced IFN-{alpha}1/{beta} expression caused by L{sup pro} was also associated with a decrease of interferon regulatory factor 3/7 (IRF-3/7) in protein levels, two critical transcription factors for activation of IFN-{alpha}/{beta}. Furthermore, overexpression of L{sup pro} significantly reduced the transcription of multiple IRF-responsive genes including 2',5'-OAS, ISG54, IP-10, and RANTES. Screening L{sup pro} mutants indicated that the ability to process eIF-4G of L{sup pro} is not required for suppressing dsRNA-induced activation of the IFN-{alpha}1/{beta} promoter and decreasing IRF-3/7 expression. Taken together, our results demonstrate that, in addition to disrupting NF-{kappa}B, L{sup pro} also decreases IRF-3/7 expression to suppress dsRNA-induced type I IFN production, suggesting multiple strategies used by FMDV to counteract the immune response to viral infection.

  12. Micro-Level Adaptation, Macro-Level Selection, and the Dynamics of Market Partitioning.

    Science.gov (United States)

    García-Díaz, César; van Witteloostuijn, Arjen; Péli, Gábor

    2015-01-01

    This paper provides a micro-foundation for dual market structure formation through partitioning processes in marketplaces by developing a computational model of interacting economic agents. We propose an agent-based modeling approach, where firms are adaptive and profit-seeking agents entering into and exiting from the market according to their (lack of) profitability. Our firms are characterized by large and small sunk costs, respectively. They locate their offerings along a unimodal demand distribution over a one-dimensional product variety, with the distribution peak constituting the center and the tails standing for the peripheries. We found that large firms may first advance toward the most abundant demand spot, the market center, and release peripheral positions as predicted by extant dual market explanations. However, we also observed that large firms may then move back toward the market fringes to reduce competitive niche overlap in the center, triggering nonlinear resource occupation behavior. Novel results indicate that resource release dynamics depend on firm-level adaptive capabilities, and that a minimum scale of production for low sunk cost firms is key to the formation of the dual structure.

  13. UPF2-dependent nonsense-mediated mRNA decay pathway is essential for spermatogenesis by selectively eliminating longer 3'UTR transcripts

    DEFF Research Database (Denmark)

    Bao, Jianqiang; Vitting-Seerup, Kristoffer; Waage, Johannes Eichler

    2016-01-01

    During transcription, most eukaryotic genes generate multiple alternative cleavage and polyadenylation (APA) sites, leading to the production of transcript isoforms with variable lengths in the 3' untranslated region (3'UTR). In contrast to somatic cells, male germ cells, especially pachytene...

  14. In-Depth Global Analysis of Transcript Abundance Levels in Porcine Alveolar Macrophages Following Infection with Porcine Reproductive and Respiratory Syndrome Virus

    Directory of Open Access Journals (Sweden)

    Laura C. Miller

    2010-01-01

    Full Text Available Porcine reproductive and respiratory syndrome virus (PRRSV is a major pathogen of swine worldwide and causes considerable economic loss. Identifying specific cell signaling or activation pathways that associate with variation in PRRSV replication and macrophage function may lead to identification of novel gene targets for the control of PRRSV infection. Serial Analysis of Gene Expression (SAGE was used to create and survey the transcriptome of in vitro mock-infected and PRRSV strain VR-2332-infected porcine alveolar macrophages (PAM at 0, 6, 12, 16, and 24 hours after infection. The transcriptome data indicated changes in transcript abundance occurring in PRRSV-infected PAMs over time after infection with more than 590 unique tags with significantly altered transcript abundance levels identified (P<.01. Strikingly, innate immune genes (whose transcript abundances are typically altered in response to other pathogens or insults including IL-8, CCL4, and IL-1β showed no or very little change at any time point following infection.

  15. Selected Food Consumption Mediates the Association between Education Level and Metabolic Syndrome in Korean Adults.

    Science.gov (United States)

    Kim, Oh Yoen; Kwak, So-Young; Kim, Boeun; Kim, Young-Sun; Kim, Hye Young; Shin, Min-Jeong

    2017-01-01

    Low socioeconomic status (SES) is linked to higher incidence/mortality of cardiovascular disease, but emerging evidence inconsistently reported that education level, a proxy for SES, is related to cardiovascular risk and metabolic syndrome (MetS) in Koreans. Furthermore, limited information is available on whether dietary components would mediate the relationship between education level and cardiovascular risk. We hypothesized that selected food consumption mediates the association between education level and MetS prevalence. Data from the Korea National Health and Nutritional Examination Survey (2008-2011) were included in cross-sectional analyses (n = 11,029, 30-64 years). The possible mediating effect of selected food groups (fruits, raw vegetables, red meat, milk, and soft drinks) on the association between education level and MetS was tested using a multiple mediation model. Education level was negatively associated with MetS prevalence. The association between lower education level and higher MetS prevalence was partially mediated by selected food consumption (lower intakes of fruit, red meat and milk; higher intakes of vegetable and soft drink) after adjusted for covariates. Gender also modified the association between education level and MetS prevalence that was more prominent in women than in men. Selected food consumption substantially contributes to the association between education level and MetS in Korean adults, especially among women. © 2017 S. Karger AG, Basel.

  16. Radiological protection and the selection of management strategies for intermediate level wastes

    International Nuclear Information System (INIS)

    Hill, M.D.; Webb, G.A.M.

    1982-01-01

    This paper describes the steps involved in selecting management systems and an overall management strategy for intermediate level solid radioactive wastes. The radiological protection inputs to intermediate level waste management decisions are discussed, together with the results of preliminary radiological assessments of disposal options. Areas where further work is required are identified. (author)

  17. LSM Proteins Provide Accurate Splicing and Decay of Selected Transcripts to Ensure Normal Arabidopsis Development[W

    Science.gov (United States)

    Perea-Resa, Carlos; Hernández-Verdeja, Tamara; López-Cobollo, Rosa; Castellano, María del Mar; Salinas, Julio

    2012-01-01

    In yeast and animals, SM-like (LSM) proteins typically exist as heptameric complexes and are involved in different aspects of RNA metabolism. Eight LSM proteins, LSM1 to 8, are highly conserved and form two distinct heteroheptameric complexes, LSM1-7 and LSM2-8,that function in mRNA decay and splicing, respectively. A search of the Arabidopsis thaliana genome identifies 11 genes encoding proteins related to the eight conserved LSMs, the genes encoding the putative LSM1, LSM3, and LSM6 proteins being duplicated. Here, we report the molecular and functional characterization of the Arabidopsis LSM gene family. Our results show that the 11 LSM genes are active and encode proteins that are also organized in two different heptameric complexes. The LSM1-7 complex is cytoplasmic and is involved in P-body formation and mRNA decay by promoting decapping. The LSM2-8 complex is nuclear and is required for precursor mRNA splicing through U6 small nuclear RNA stabilization. More importantly, our results also reveal that these complexes are essential for the correct turnover and splicing of selected development-related mRNAs and for the normal development of Arabidopsis. We propose that LSMs play a critical role in Arabidopsis development by ensuring the appropriate development-related gene expression through the regulation of mRNA splicing and decay. PMID:23221597

  18. Groundwater Levels for Selected Wells in the Chehalis River Basin, Washington

    Science.gov (United States)

    Fasser, E.T.; Julich, R.J.

    2010-01-01

    Groundwater levels for selected wells in the Chehalis River basin, Washington, are presented on an interactive web-based map to document the spatial distribution of groundwater levels in the study area during late summer 2009. Groundwater level data and well information were collected by the U.S. Geological Survey using standard techniques. The data are stored in the USGS National Water Information System (NWIS), Ground-Water Site-Inventory (GWSI) System.

  19. Quantitative Analysis of High-Quality Officer Selection by Commandants Career-Level Education Board

    Science.gov (United States)

    2017-03-01

    impact on the organization and allocate resources to improve the human capital of this select group. From 2011 onward, CCLEB revamped the application...ANALYSIS OF HIGH-QUALITY OFFICER SELECTION BY COMMANDANT’S CAREER - LEVEL EDUCATION BOARD by Clifton N. Rateike March 2017 Thesis Advisor...of Management and Budget, Paperwork Reduction Project (0704-0188) Washington, DC 20503. 1. AGENCY USE ONLY (Leave blank) 2. REPORT DATE March

  20. Site selection procedure for high level radioactive waste disposal in Bulgaria

    International Nuclear Information System (INIS)

    Evstatiev, D.; Vachev, B.

    1993-01-01

    A combined site selection approach is implemented. Bulgaria's territory has been classified in three categories, presented on a 1:500000 scale map. The number of suitable sites has been reduced to 20 using the method of successive screening. The formulated site selection problem is a typical discrete multi-criteria decision making problem under uncertainty. A 5-level procedure using Expert Choice Rating and relative models is created. It is a part of a common procedure for evaluation and choice of variants for high level radwaste disposal construction. On this basis 7-8 more preferable sites are demonstrated. A new knowledge and information about the relative importance of the criteria and their subsets, about the level of criteria uncertainty and the reliability are gained. It is very useful for planning and managing of the next final stages of the site selection procedure. 7 figs., 8 refs., 4 suppls. (author)

  1. Site selection and characterization processes for deep geologic disposal of high level nuclear waste

    International Nuclear Information System (INIS)

    Costin, L.S.

    1997-10-01

    In this paper, the major elements of the site selection and characterization processes used in the US high level waste program are discussed. While much of the evolution of the site selection and characterization processes have been driven by the unique nature of the US program, these processes, which are well defined and documented, could be used as an initial basis for developing site screening, selection, and characterization programs in other countries. Thus, this paper focuses more on the process elements than the specific details of the US program

  2. Site selection and characterization processes for deep geologic disposal of high level nuclear waste

    International Nuclear Information System (INIS)

    Costin, L.S.

    1997-01-01

    In this paper, the major elements of the site selection and characterization processes used in the U. S. high level waste program are discussed. While much of the evolution of the site selection and characterization processes have been driven by the unique nature of the U. S. program, these processes, which are well-defined and documented, could be used as an initial basis for developing site screening, selection, and characterization programs in other countries. Thus, this paper focuses more on the process elements than the specific details of the U. S. program. (author). 3 refs., 2 tabs., 5 figs

  3. Site selection and characterization processes for deep geologic disposal of high level nuclear waste

    Energy Technology Data Exchange (ETDEWEB)

    Costin, L.S. [Sandia National Labs., Albuquerque, NM (United States)

    1997-12-31

    In this paper, the major elements of the site selection and characterization processes used in the U. S. high level waste program are discussed. While much of the evolution of the site selection and characterization processes have been driven by the unique nature of the U. S. program, these processes, which are well-defined and documented, could be used as an initial basis for developing site screening, selection, and characterization programs in other countries. Thus, this paper focuses more on the process elements than the specific details of the U. S. program. (author). 3 refs., 2 tabs., 5 figs.

  4. Selection for reproductive traits in white egg stock using independent culling levels

    Directory of Open Access Journals (Sweden)

    GS Schmidt

    2005-12-01

    Full Text Available The objective of this study was to report the response to selection for fertility and hatchability in white egg layers strains, based on sire and dam performance, and the effects of inbreeding on these traits. Two selected white egg strains (CC and DD from Embrapa´s poultry program under multiple trait selection were compared to a control strain (CCc. The control strain was established by randomly mating one male from each sire family to a non-related female from each dam family and was used to monitor genetic change in the selected lines. CC and DD were selected using family and individual information on hen-day egg production up to 40 weeks of age, egg weight, sexual maturity and 16-week-old body weight over five generations. Independent culling levels (ICL were also used during population expansion to eliminate sires and dams with low fertility (FERT and hatchability (HATC. Initially, FERT and HATC were over 90.0% in both selected and control strains. FERT and HATC of the selected and the control strains were compared during the last generation. FERT averages were 93.8, 93.8 and 94.4%, and HATCH averages were 93.2, 91.6 and 93.1% for CC, DD and CCc respectively. FERT and HATCH means were not different among strains. Estimated inbreeding increased at a rate of 0.4% per generation in all strains. Selection using ICL was able to effectively maintain the high initial FERT and HATC levels, and provide potential for high selection intensity in other traits. Inbreeding depression was not observed for any trait, indicating that selection compensated for any negative effects of inbreeding.

  5. Multi-level gene/MiRNA feature selection using deep belief nets and active learning.

    Science.gov (United States)

    Ibrahim, Rania; Yousri, Noha A; Ismail, Mohamed A; El-Makky, Nagwa M

    2014-01-01

    Selecting the most discriminative genes/miRNAs has been raised as an important task in bioinformatics to enhance disease classifiers and to mitigate the dimensionality curse problem. Original feature selection methods choose genes/miRNAs based on their individual features regardless of how they perform together. Considering group features instead of individual ones provides a better view for selecting the most informative genes/miRNAs. Recently, deep learning has proven its ability in representing the data in multiple levels of abstraction, allowing for better discrimination between different classes. However, the idea of using deep learning for feature selection is not widely used in the bioinformatics field yet. In this paper, a novel multi-level feature selection approach named MLFS is proposed for selecting genes/miRNAs based on expression profiles. The approach is based on both deep and active learning. Moreover, an extension to use the technique for miRNAs is presented by considering the biological relation between miRNAs and genes. Experimental results show that the approach was able to outperform classical feature selection methods in hepatocellular carcinoma (HCC) by 9%, lung cancer by 6% and breast cancer by around 10% in F1-measure. Results also show the enhancement in F1-measure of our approach over recently related work in [1] and [2].

  6. Reconstruction and analysis of transcription factor-miRNA co-regulatory feed-forward loops in human cancers using filter-wrapper feature selection.

    Directory of Open Access Journals (Sweden)

    Chen Peng

    Full Text Available BACKGROUND: As one of the most common types of co-regulatory motifs, feed-forward loops (FFLs control many cell functions and play an important role in human cancers. Therefore, it is crucial to reconstruct and analyze cancer-related FFLs that are controlled by transcription factor (TF and microRNA (miRNA simultaneously, in order to find out how miRNAs and TFs cooperate with each other in cancer cells and how they contribute to carcinogenesis. Current FFL studies rely on predicted regulation information and therefore suffer the false positive issue in prediction results. More critically, FFLs generated by existing approaches cannot represent the dynamic and conditional regulation relationship under different experimental conditions. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we proposed a novel filter-wrapper feature selection method to accurately identify co-regulatory mechanism by incorporating prior information from predicted regulatory interactions with parallel miRNA/mRNA expression datasets. By applying this method, we reconstructed 208 and 110 TF-miRNA co-regulatory FFLs from human pan-cancer and prostate datasets, respectively. Further analysis of these cancer-related FFLs showed that the top-ranking TF STAT3 and miRNA hsa-let-7e are key regulators implicated in human cancers, which have regulated targets significantly enriched in cellular process regulations and signaling pathways that are involved in carcinogenesis. CONCLUSIONS/SIGNIFICANCE: In this study, we introduced an efficient computational approach to reconstruct co-regulatory FFLs by accurately identifying gene co-regulatory interactions. The strength of the proposed feature selection method lies in the fact it can precisely filter out false positives in predicted regulatory interactions by quantitatively modeling the complex co-regulation of target genes mediated by TFs and miRNAs simultaneously. Moreover, the proposed feature selection method can be generally applied to

  7. Dominance behaviour in a non-aggressive flatfish, Senegalese sole (Solea senegalensis and brain mRNA abundance of selected transcripts.

    Directory of Open Access Journals (Sweden)

    Elvira Fatsini

    Full Text Available Dominance is defined as the preferential access to limited resources. The present study aimed to characterise dominance in a non-aggressive flatfish species, the Senegalese sole (Solea senegalensis by 1 identifying dominance categories and associated behaviours and 2 linking dominance categories (dominant and subordinate with the abundance of selected mRNA transcripts in the brain. Early juveniles (n = 74, 37 pairs were subjected to a dyadic dominance test, related to feeding, and once behavioural phenotypes had been described the abundance of ten selected mRNAs related to dominance and aggressiveness was measured in the brain. Late juveniles were subjected to two dyadic dominance tests (n = 34, 17 pairs, related to feeding and territoriality and one group test (n = 24, 4 groups of 6 fish. Sole feeding first were categorized as dominant and sole feeding second or not feeding as subordinate. Three social behaviours (i. "Resting the head" on another fish, ii. "Approaching" another fish, iii. "Swimming above another" fish were associated with dominance of feeding. Two other variables (i. Total time occupying the preferred area during the last 2 hours of the 24 h test, ii. Organisms occupying the preferred area when the test ended were representative of dominance in the place preference test. In all tests, dominant fish compared to subordinate fish displayed a significantly higher number of the behaviours "Rest the head" and "Approaches". Moreover, dominant sole dominated the sand at the end of the test, and in the group test dominated the area close to the feed delivery point before feed was delivered. The mRNA abundance of the selected mRNAs related to neurogenesis (nrd2 and neuroplasticity (c-fos in dominant sole compared to subordinate were significantly different. This is the first study to characterise dominance categories with associated behaviours and mRNA abundance in Senegalese sole and provides tools to study dominance related problems in

  8. Impact of Genomics Platform and Statistical Filtering on Transcriptional Benchmark Doses (BMD and Multiple Approaches for Selection of Chemical Point of Departure (PoD.

    Directory of Open Access Journals (Sweden)

    A Francina Webster

    Full Text Available Many regulatory agencies are exploring ways to integrate toxicogenomic data into their chemical risk assessments. The major challenge lies in determining how to distill the complex data produced by high-content, multi-dose gene expression studies into quantitative information. It has been proposed that benchmark dose (BMD values derived from toxicogenomics data be used as point of departure (PoD values in chemical risk assessments. However, there is limited information regarding which genomics platforms are most suitable and how to select appropriate PoD values. In this study, we compared BMD values modeled from RNA sequencing-, microarray-, and qPCR-derived gene expression data from a single study, and explored multiple approaches for selecting a single PoD from these data. The strategies evaluated include several that do not require prior mechanistic knowledge of the compound for selection of the PoD, thus providing approaches for assessing data-poor chemicals. We used RNA extracted from the livers of female mice exposed to non-carcinogenic (0, 2 mg/kg/day, mkd and carcinogenic (4, 8 mkd doses of furan for 21 days. We show that transcriptional BMD values were consistent across technologies and highly predictive of the two-year cancer bioassay-based PoD. We also demonstrate that filtering data based on statistically significant changes in gene expression prior to BMD modeling creates more conservative BMD values. Taken together, this case study on mice exposed to furan demonstrates that high-content toxicogenomics studies produce robust data for BMD modelling that are minimally affected by inter-technology variability and highly predictive of cancer-based PoD doses.

  9. Statistical selection of tide gauges for Arctic sea-level reconstruction

    DEFF Research Database (Denmark)

    Svendsen, Peter Limkilde; Andersen, Ole Baltazar; Nielsen, Allan Aasbjerg

    2015-01-01

    In this paper, we seek an appropriate selection of tide gauges for Arctic Ocean sea-level reconstruction based on a combination of empirical criteria and statistical properties (leverages). Tide gauges provide the only in situ observations of sea level prior to the altimetry era. However, tide...... the "influence" of each Arctic tide gauge on the EOF-based reconstruction through the use of statistical leverage and use this as an indication in selecting appropriate tide gauges, in order to procedurally identify poor-quality data while still including as much data as possible. To accommodate sparse...

  10. Transcript levels of ten caste-related genes in adult diploid males of Melipona quadrifasciata (Hymenoptera, Apidae: a comparison with haploid males, queens and workers

    Directory of Open Access Journals (Sweden)

    Andreia A. Borges

    2011-01-01

    Full Text Available In Hymenoptera, homozygosity at the sex locus results in the production of diploid males. In social species, these pose a double burden by having low fitness and drawing resources normally spent for increasing the work force of a colony. Yet, diploid males are of academic interest as they can elucidate effects of ploidy (normal males are haploid, whereas the female castes, the queens and workers, are diploid on morphology and life history. Herein we investigated expression levels of ten caste-related genes in the stingless bee Melipona quadrifasciata, comparing newly emerged and 5-day-old diploid males with haploid males, queens and workers. In diploid males, transcript levels for dunce and paramyosin were increased during the first five days of adult life, while those for diacylglycerol kinase and the transcriptional co-repressor groucho diminished. Two general trends were apparent, (i gene expression patterns in diploid males were overall more similar to haploid ones and workers than to queens, and (ii in queens and workers, more genes were up-regulated after emergence until day five, whereas in diploid and especially so in haploid males more genes were down-regulated. This difference between the sexes may be related to longevity, which is much longer in females than in males.

  11. Transcript levels of ten caste-related genes in adult diploid males of Melipona quadrifasciata (Hymenoptera, Apidae) - A comparison with haploid males, queens and workers.

    Science.gov (United States)

    Borges, Andreia A; Humann, Fernanda C; Oliveira Campos, Lucio A; Tavares, Mara G; Hartfelder, Klaus

    2011-10-01

    In Hymenoptera, homozygosity at the sex locus results in the production of diploid males. In social species, these pose a double burden by having low fitness and drawing resources normally spent for increasing the work force of a colony. Yet, diploid males are of academic interest as they can elucidate effects of ploidy (normal males are haploid, whereas the female castes, the queens and workers, are diploid) on morphology and life history. Herein we investigated expression levels of ten caste-related genes in the stingless bee Melipona quadrifasciata, comparing newly emerged and 5-day-old diploid males with haploid males, queens and workers. In diploid males, transcript levels for dunce and paramyosin were increased during the first five days of adult life, while those for diacylglycerol kinase and the transcriptional co-repressor groucho diminished. Two general trends were apparent, (i) gene expression patterns in diploid males were overall more similar to haploid ones and workers than to queens, and (ii) in queens and workers, more genes were up-regulated after emergence until day five, whereas in diploid and especially so in haploid males more genes were down-regulated. This difference between the sexes may be related to longevity, which is much longer in females than in males.

  12. Fluoroorotic acid-selected Nicotiana plumbaginifolia cell lines with a stable thymine starvation phenotype have lost the thymine-regulated transcriptional program.

    Science.gov (United States)

    Santoso, D; Thornburg, R

    2000-08-01

    We have selected 143 independent Nicotiana plumbaginifolia cell lines that survive in the presence of 5-fluoroorotic acid. These lines show several diverse phenotypes. The majority of these cell lines showed reduced levels of UMP synthase. However, one particular phenotype, which represents 14% of the total independent lines (20 cell lines), showed an unexpected, high level of UMP synthase and was therefore analyzed in detail. The selected cell lines showed no differences with wild-type cells with respect to uptake of orotic acid, affinity of UMP synthase for its substrates, or UMP synthase gene-copy number. Alternative detoxification mechanisms were also excluded. The elevated enzyme activity was correlated with elevated UMP synthase protein levels as well as elevated UMP synthase mRNA levels. In contrast to wild-type cell lines, the fluoroorotic acid-selected cell lines did not respond to thymine or to other biochemicals that affect thymine levels. In addition, there was also a concomitant up-regulation of aspartate transcarbamoylase, however, dihydroorotase and dihydroorotate dehydrogenase are not up-regulated in these cell lines.

  13. Fluoroorotic Acid-Selected Nicotiana plumbaginifolia Cell Lines with a Stable Thymine Starvation Phenotype Have Lost the Thymine-Regulated Transcriptional Program1

    Science.gov (United States)

    Santoso, Djoko; Thornburg, Robert

    2000-01-01

    We have selected 143 independent Nicotiana plumbaginifolia cell lines that survive in the presence of 5-fluoroorotic acid. These lines show several diverse phenotypes. The majority of these cell lines showed reduced levels of UMP synthase. However, one particular phenotype, which represents 14% of the total independent lines (20 cell lines), showed an unexpected, high level of UMP synthase and was therefore analyzed in detail. The selected cell lines showed no differences with wild-type cells with respect to uptake of orotic acid, affinity of UMP synthase for its substrates, or UMP synthase gene-copy number. Alternative detoxification mechanisms were also excluded. The elevated enzyme activity was correlated with elevated UMP synthase protein levels as well as elevated UMP synthase mRNA levels. In contrast to wild-type cell lines, the fluoroorotic acid-selected cell lines did not respond to thymine or to other biochemicals that affect thymine levels. In addition, there was also a concomitant up-regulation of aspartate transcarbamoylase, however, dihydroorotase and dihydroorotate dehydrogenase are not up-regulated in these cell lines. PMID:10938367

  14. Different Levels of DNA Methylation Detected in Human Sperms after Morphological Selection Using High Magnification Microscopy

    Directory of Open Access Journals (Sweden)

    Nino Guy Cassuto

    2016-01-01

    Full Text Available Objective. To analyze DNA methylation levels between two groups of spermatozoa taken from the same sample, following morphological selection by high magnification (HM at 6100x microscopy. A prospective study was conducted and studied 876 spermatozoa from 10 randomly selected men. Sperm morphology was characterized at HM according to criteria previously established. High-scoring Score 6 and low-scoring Score 0 sperm were selected. Sperm DNA methylation level was assessed using an immunoassay method targeting 5-methylcytosine residues by fluorescence microscopy with imaging analysis system to detect DNA methylation in single spermatozoon. Results. In total, 448 S6 spermatozoa and 428 S0 spermatozoa were analyzed. A strong relationship was found between sperm DNA methylation levels and sperm morphology observed at HM. Sperm DNA methylation level in the S6 group was significantly lower compared with that in the S0 group (p<10-6, OR = 2.4; and p<0.001, as determined using the Wilcoxon test. Conclusion. Differences in DNA methylation levels are associated with sperm morphology variations as observed at HM, which allows spermatozoa with abnormal levels to be discarded and ultimately decrease birth defects, malformations, and epigenetic diseases that may be transmitted from sperm to offspring in ICSI.

  15. Lead levels in deciduous teeth of children from selected urban areas ...

    African Journals Online (AJOL)

    1983-04-09

    Apr 9, 1983 ... Blood and urine levels are markers of recent ... The selected teeth were stored in plastic bags at _7° C. Before analysis remnants of roots (if ... varied from sample to sample, so that aqueous standards could not be used for ...

  16. M7--a high speed digital processor for second level trigger selections

    International Nuclear Information System (INIS)

    Droege, T.F.; Gaines, I.; Turner, K.J.

    1978-01-01

    A digital processor is described which reconstructs mass and momentum as a second-level trigger selection. The processor is a five-address, microprogramed, pipelined, ECL machine with simultaneous memory access to four operands which load two parallel multipliers and an ALU. Source data modules are extensions of the processor

  17. Applied Math & Science Levels Utilized in Selected Trade & Industrial Vocational Education. Final Report.

    Science.gov (United States)

    Gray, James R.

    Research identified and evaluated the level of applied mathematics and science used in selected trade and industrial (T&I) subjects taught in the Kentucky Vocational Education System. The random sample was composed of 52 programs: 21 carpentry, 20 electricity/electronics, and 11 machine shop. The 96 math content items that were identified as…

  18. Evaluation and comparison of alternative fleet-level selective maintenance models

    International Nuclear Information System (INIS)

    Schneider, Kellie; Richard Cassady, C.

    2015-01-01

    Fleet-level selective maintenance refers to the process of identifying the subset of maintenance actions to perform on a fleet of repairable systems when the maintenance resources allocated to the fleet are insufficient for performing all desirable maintenance actions. The original fleet-level selective maintenance model is designed to maximize the probability that all missions in a future set are completed successfully. We extend this model in several ways. First, we consider a cost-based optimization model and show that a special case of this model maximizes the expected value of the number of successful missions in the future set. We also consider the situation in which one or more of the future missions may be canceled. These models and the original fleet-level selective maintenance optimization models are nonlinear. Therefore, we also consider an alternative model in which the objective function can be linearized. We show that the alternative model is a good approximation to the other models. - Highlights: • Investigate nonlinear fleet-level selective maintenance optimization models. • A cost based model is used to maximize the expected number of successful missions. • Another model is allowed to cancel missions if reliability is sufficiently low. • An alternative model has an objective function that can be linearized. • We show that the alternative model is a good approximation to the other models

  19. Forced selection of a human immunodeficiency virus type 1 variant that uses a non-self tRNA primer for reverse transcription: Involvement of viral RNA sequences and the reverse transcriptase enzyme

    NARCIS (Netherlands)

    Abbink, Truus E. M.; Beerens, Nancy; Berkhout, Ben

    2004-01-01

    Human immunodeficiency virus type 1 uses the tRNA(3)(Lys) molecule as a selective primer for reverse transcription. This primer specificity is imposed by sequence complementarity between the tRNA primer and two motifs in the viral RNA genome: the primer-binding site (PBS) and the primer activation

  20. Lymphoid Progenitor Cells from Childhood Acute Lymphoblastic Leukemia Are Functionally Deficient and Express High Levels of the Transcriptional Repressor Gfi-1

    Directory of Open Access Journals (Sweden)

    Jessica Purizaca

    2013-01-01

    Full Text Available Acute lymphoblastic leukemia (ALL is the most frequent malignancy of childhood. Substantial progress on understanding the cell hierarchy within ALL bone marrow (BM has been recorded in the last few years, suggesting that both primitive cell fractions and committed lymphoid blasts with immature stem cell-like properties contain leukemia-initiating cells. Nevertheless, the biology of the early progenitors that initiate the lymphoid program remains elusive. The aim of the present study was to investigate the ability of lymphoid progenitors from B-cell precursor ALL BM to proliferate and undergo multilineage differentiation. By phenotype analyses, in vitro proliferation assays, and controlled culture systems, the lymphoid differentiation potentials were evaluated in BM primitive populations from B-cell precursor ALL pediatric patients. When compared to their normal counterparts, functional stem and progenitor cell contents were substantially reduced in ALL BM. Moreover, neither B nor NK or dendritic lymphoid-cell populations developed recurrently from highly purified ALL-lymphoid progenitors, and their proliferation and cell cycle status revealed limited proliferative capacity. Interestingly, a number of quiescence-associated transcription factors were elevated, including the transcriptional repressor Gfi-1, which was highly expressed in primitive CD34+ cells. Together, our findings reveal major functional defects in the primitive hematopoietic component of ALL BM. A possible contribution of high levels of Gfi-1 expression in the regulation of the stem/progenitor cell biology is suggested.

  1. Higher transcription levels in ascorbic acid biosynthetic and recycling genes were associated with higher ascorbic acid accumulation in blueberry.

    Science.gov (United States)

    Liu, Fenghong; Wang, Lei; Gu, Liang; Zhao, Wei; Su, Hongyan; Cheng, Xianhao

    2015-12-01

    In our preliminary study, the ripe fruits of two highbush blueberry (Vaccinium corymbosum L.) cultivars, cv 'Berkeley' and cv 'Bluecrop', were found to contain different levels of ascorbic acid. However, factors responsible for these differences are still unknown. In the present study, ascorbic acid content in fruits was compared with expression profiles of ascorbic acid biosynthetic and recycling genes between 'Bluecrop' and 'Berkeley' cultivars. The results indicated that the l-galactose pathway was the predominant route of ascorbic acid biosynthesis in blueberry fruits. Moreover, higher expression levels of the ascorbic acid biosynthetic genes GME, GGP, and GLDH, as well as the recycling genes MDHAR and DHAR, were associated with higher ascorbic acid content in 'Bluecrop' compared with 'Berkeley', which indicated that a higher efficiency ascorbic acid biosynthesis and regeneration was likely to be responsible for the higher ascorbic acid accumulation in 'Bluecrop'. Copyright © 2015 Elsevier Ltd. All rights reserved.

  2. Integrative Analysis Using Proteome and Transcriptome Data From Yeast to Unravel Regulatory Patterns at Post-Transcriptional Level

    DEFF Research Database (Denmark)

    Olivares Hernandez, Roberto; Usaite, Renata; Nielsen, Jens

    2010-01-01

    In this stud) we combined proteome and transcriptome data from six different published dataset to identify patterns that can provide new insight into the reasons for these deviations By using a categorization method and integrating genome-scale information we found that the relation between protein and mRNA...... is related to the gene function We could further identify that for genes belonging to amino acid biosynthetic pathways there is no translational regulation, meaning that there is generally a good correlation between mRNA and protein levels We also found that there is generally translational control for large...... proteins and there also evidence for a role of conserved motifs m the 3' untranslated regions in the mRNA-protein correlation, probably by controlling the level of mRNA Biotechnol Bioeng 2010,107 865-875...

  3. Technical factors in the site selection for a radioactive wastes storage of low and intermediate level

    International Nuclear Information System (INIS)

    Badillo A, V. E.; Ramirez S, J. R.; Palacios H, J. C.

    2009-10-01

    The storage on surface or near surface it is viable for wastes of low and intermediate level which contain radio nuclides of short half life that would decay at insignificant levels of radioactivity in some decades and also radio nuclides of long half life but in very low concentrations. The sites selection, for the construction of radioactive waste storages, that present an appropriate stability at long term, a foreseeable behavior to future and a capacity to fulfill other operational requirements, is one of the great tasks that confront the waste disposal agencies. In the selection of potential sites for the construction of a radioactive wastes storage of low and intermediate level, several basic judgments should be satisfied that concern to physiography, climatology, geologic, geo-hydrology, tectonic and seismic aspects; as well as factors like the population density, socioeconomic develops and existent infrastructure. the necessary technician-scientific investigations for the selection of a site for the construction of radioactive waste storages are presented in this work and they are compared with the pre-selection factors realized in specify areas in previous studies in different regions of the Mexican Republic. (Author)

  4. Sulfate-Driven Elemental Sparing Is Regulated at the Transcriptional and Posttranscriptional Levels in a Filamentous Cyanobacterium▿ †

    OpenAIRE

    Gutu, Andrian; Alvey, Richard M.; Bashour, Sami; Zingg, Daniel; Kehoe, David M.

    2011-01-01

    Sulfur is an essential nutrient that can exist at growth-limiting concentrations in freshwater environments. The freshwater cyanobacterium Fremyella diplosiphon (also known as Tolypothrix sp. PCC 7601) is capable of remodeling the composition of its light-harvesting antennae, or phycobilisomes, in response to changes in the sulfur levels in its environment. Depletion of sulfur causes these cells to cease the accumulation of two forms of a major phycobilisome protein called phycocyanin and ini...

  5. Cold acclimation induces distinctive changes in the chromatin state and transcript levels of COR genes in Cannabis sativa varieties with contrasting cold acclimation capacities.

    Science.gov (United States)

    Mayer, Boris F; Ali-Benali, Mohamed Ali; Demone, Jordan; Bertrand, Annick; Charron, Jean-Benoit

    2015-11-01

    Little is known about the capacity of Cannabis sativa to cold-acclimate and develop freezing tolerance. This study investigates the cold acclimation (CA) capacity of nine C. sativa varieties and the underlying genetic and epigenetic responses. The varieties were divided into three groups based on their contrasting CA capacities by comparing the survival of non-acclimated and cold-acclimated plants in whole-plant freeze tests. In response to the CA treatment, all varieties accumulated soluble sugars but only the varieties with superior capacity for CA could maintain higher levels throughout the treatment. In addition, the varieties that acclimated most efficiently accumulated higher transcript levels of cold-regulated (COR) genes and genes involved in de novo DNA methylation while displaying locus- and variety-specific changes in the levels of H3K9ac, H3K27me3 and methylcytosine (MeC) during CA. Furthermore, these hardy C. sativa varieties displayed significant increases in MeC levels at COR gene loci when deacclimated, suggesting a role for locus-specific DNA methylation in deacclimation. This study uncovers the molecular mechanisms underlying CA in C. sativa and reveals higher levels of complexity regarding how genetic, epigenetic and environmental factors intertwine. © 2014 Scandinavian Plant Physiology Society.

  6. BAG3 regulates total MAP1LC3B protein levels through a translational but not transcriptional mechanism.

    Science.gov (United States)

    Rodríguez, Andrea E; López-Crisosto, Camila; Peña-Oyarzún, Daniel; Salas, Daniela; Parra, Valentina; Quiroga, Clara; Morawe, Tobias; Chiong, Mario; Behl, Christian; Lavandero, Sergio

    2016-01-01

    Autophagy is mainly regulated by post-translational and lipid modifications of ATG proteins. In some scenarios, the induction of autophagy is accompanied by increased levels of certain ATG mRNAs such as MAP1LC3B/LC3B, ATG5 or ATG12. However, little is known about the regulation of ATG protein synthesis at the translational level. The cochaperone of the HSP70 system BAG3 (BCL2-associated athanogene 3) has been associated to LC3B lipidation through an unknown mechanism. In the present work, we studied how BAG3 controls autophagy in HeLa and HEK293 cells. Our results showed that BAG3 regulates the basal amount of total cellular LC3B protein by controlling its mRNA translation. This effect was apparently specific to LC3B because other ATG protein levels were not affected. BAG3 knockdown did not affect LC3B lipidation induced by nutrient deprivation or proteasome inhibition. We concluded that BAG3 maintains the basal amount of LC3B protein by controlling the translation of its mRNA in HeLa and HEK293 cells.

  7. Site selection criteria for shallow land burial of low-level radioactive waste

    International Nuclear Information System (INIS)

    Falconer, K.L.; Hull, L.C.; Mizell, S.A.

    1982-01-01

    Twelve site selection criteria are presented. These are: (1) site shall be of sufficient area and depth to accommodate the projected volume of waste and a three dimensional buffer zone; (2) site should allow waste to be buried either completely above or below the transition zone between the unsaturated and saturated zones; (3) site should be located where flooding will not jeopardize performance; (4) site should be located where erosion will not jeopardize performance; (5) site should be located in areas where hydrogeologic conditions allow reliable performance prediction; (6) site should be located where geologic hazards will not jeopardize performance; (7) site should be selected with considerations given to those characteristics of earth materials and water chemistry that favor increased residence times and/or attenuation of radionuclide concentrations within site boundaries; (8) site should be selected with consideration given to current and projected population distributions; (9) site should be selected with consideration given to current and projected land use and resource development; (10) site should be selected with consideration given to location of waste generation, access to all-weather highway and rail routes, and access utilities; (11) site should be selected consistent with federal laws and regulations; (12) site should not be located within areas that are protected from such use by federal laws and regulations. These criteria are considered preliminary and do not necessarily represent the position of the Department of Energy's Low-Level Waste Management Program

  8. Increased transcript level of poly(ADP-ribose) polymerase (PARP-1) in human tricuspid compared with bicuspid aortic valves correlates with the stenosis severity

    International Nuclear Information System (INIS)

    Nagy, Edit; Caidahl, Kenneth; Franco-Cereceda, Anders; Bäck, Magnus

    2012-01-01

    Highlights: ► Oxidative stress has been implicated in the pathomechanism of calcific aortic valve stenosis. ► We assessed the transcript levels for PARP-1 (poly(ADP-ribose) polymerase), acts as a DNA damage nick sensor in stenotic valves. ► Early stage of diseased tricuspid valves exhibited higher mRNA levels for PARP-1 compared to bicuspid valves. ► The mRNA levels for PARP-1 inversely correlated with the clinical stenosis severity in tricuspid valves. ► Our data demonstrated that DNA damage pathways might be associated with stenosis severity only in tricuspid valves. -- Abstract: Oxidative stress may contribute to the hemodynamic progression of aortic valve stenosis, and is associated with activation of the nuclear enzyme poly(ADP-ribose) polymerase (PARP) 1. The aim of the present study was to assess the transcriptional profile and the topological distribution of PARP-1 in human aortic valves, and its relation to the stenosis severity. Human stenotic aortic valves were obtained from 46 patients undergoing aortic valve replacement surgery and used for mRNA extraction followed by quantitative real-time PCR to correlate the PARP-1 expression levels with the non invasive hemodynamic parameters quantifying the stenosis severity. Primary isolated valvular interstitial cells (VICs) were used to explore the effects of cytokines and leukotriene C 4 (LTC 4 ) on valvular PARP-1 expression. The thickened areas of stenotic valves with tricuspid morphology expressed significantly higher levels of PARP-1 mRNA compared with the corresponding part of bicuspid valves (0.501 vs 0.243, P = 0.01). Furthermore, the quantitative gene expression levels of PARP-1 were inversely correlated with the aortic valve area (AVA) (r = −0.46, P = 0.0469) and AVA indexed for body surface area (BSA) (r = −0.498; P = 0.0298) only in tricuspid aortic valves. LTC 4 (1 nM) significantly elevated the mRNA levels of PARP-1 by 2.38-fold in VICs. Taken together, these data suggest that

  9. Antiandrogens act as selective androgen receptor modulators at the proteome level in prostate cancer cells.

    Science.gov (United States)

    Brooke, Greg N; Gamble, Simon C; Hough, Michael A; Begum, Shajna; Dart, D Alwyn; Odontiadis, Michael; Powell, Sue M; Fioretti, Flavia M; Bryan, Rosie A; Waxman, Jonathan; Wait, Robin; Bevan, Charlotte L

    2015-05-01

    Current therapies for prostate cancer include antiandrogens, inhibitory ligands of the androgen receptor, which repress androgen-stimulated growth. These include the selective androgen receptor modulators cyproterone acetate and hydroxyflutamide and the complete antagonist bicalutamide. Their activity is partly dictated by the presence of androgen receptor mutations, which are commonly detected in patients who relapse while receiving antiandrogens, i.e. in castrate-resistant prostate cancer. To characterize the early proteomic response to these antiandrogens we used the LNCaP prostate cancer cell line, which harbors the androgen receptor mutation most commonly detected in castrate-resistant tumors (T877A), analyzing alterations in the proteome, and comparing these to the effect of these therapeutics upon androgen receptor activity and cell proliferation. The majority are regulated post-transcriptionally, possibly via nongenomic androgen receptor signaling. Differences detected between the exposure groups demonstrate subtle changes in the biological response to each specific ligand, suggesting a spectrum of agonistic and antagonistic effects dependent on the ligand used. Analysis of the crystal structures of the AR in the presence of cyproterone acetate, hydroxyflutamide, and DHT identified important differences in the orientation of key residues located in the AF-2 and BF-3 protein interaction surfaces. This further implies that although there is commonality in the growth responses between androgens and those antiandrogens that stimulate growth in the presence of a mutation, there may also be influential differences in the growth pathways stimulated by the different ligands. This therefore has implications for prostate cancer treatment because tumors may respond differently dependent upon which mutation is present and which ligand is activating growth, also for the design of selective androgen receptor modulators, which aim to elicit differential proteomic

  10. Sustained Submicromolar H2O2 Levels Induce Hepcidin via Signal Transducer and Activator of Transcription 3 (STAT3)*

    Science.gov (United States)

    Millonig, Gunda; Ganzleben, Ingo; Peccerella, Teresa; Casanovas, Guillem; Brodziak-Jarosz, Lidia; Breitkopf-Heinlein, Katja; Dick, Tobias P.; Seitz, Helmut-Karl; Muckenthaler, Martina U.; Mueller, Sebastian

    2012-01-01

    The peptide hormone hepcidin regulates mammalian iron homeostasis by blocking ferroportin-mediated iron export from macrophages and the duodenum. During inflammation, hepcidin is strongly induced by interleukin 6, eventually leading to the anemia of chronic disease. Here we show that hepatoma cells and primary hepatocytes strongly up-regulate hepcidin when exposed to low concentrations of H2O2 (0.3–6 μm), concentrations that are comparable with levels of H2O2 released by inflammatory cells. In contrast, bolus treatment of H2O2 has no effect at low concentrations and even suppresses hepcidin at concentrations of >50 μm. H2O2 treatment synergistically stimulates hepcidin promoter activity in combination with recombinant interleukin-6 or bone morphogenetic protein-6 and in a manner that requires a functional STAT3-responsive element. The H2O2-mediated hepcidin induction requires STAT3 phosphorylation and is effectively blocked by siRNA-mediated STAT3 silencing, overexpression of SOCS3 (suppressor of cytokine signaling 3), and antioxidants such as N-acetylcysteine. Glycoprotein 130 (gp130) is required for H2O2 responsiveness, and Janus kinase 1 (JAK1) is required for adequate basal signaling, whereas Janus kinase 2 (JAK2) is dispensable upstream of STAT3. Importantly, hepcidin levels are also increased by intracellular H2O2 released from the respiratory chain in the presence of rotenone or antimycin A. Our results suggest a novel mechanism of hepcidin regulation by nanomolar levels of sustained H2O2. Thus, similar to cytokines, H2O2 provides an important regulatory link between inflammation and iron metabolism. PMID:22932892

  11. A Study on Site Selecting for National Project including High Level Radioactive Waste Disposal

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Kilyoo [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2016-10-15

    Many national projects are stopped since sites for the projects are not determined. The sites selections are hold by NIMBY for unpleasant facilities or by PYMFY for preferable facilities among local governments. The followings are the typical ones; NIMBY projects: high level radioactive waste disposal, THAAD, Nuclear power plant(NPP), etc. PIMFY projects: South-east new airport, KTX station, Research center for NPP decommission, etc. The site selection for high level radioactive waste disposal is more difficult problem, and thus government did not decide and postpone to a dead end street. Since it seems that there is no solution for site selection for high level radioactive waste disposal due to NIMBY among local governments, a solution method is proposed in this paper. To decide a high level radioactive waste disposal, the first step is to invite a bid by suggesting a package deal including PIMFY projects such as Research Center for NPP decommission. Maybe potential host local governments are asked to submit sealed bids indicating the minimum compensation sum that they would accept the high level radioactive waste disposal site. If there are more than one local government put in a bid, then decide an adequate site by considering both the accumulated PESS point and technical evaluation results. By considering how fairly preferable national projects and unpleasant national projects are distributed among local government, sites selection for NIMBY or PIMFY facilities is suggested. For NIMBY national projects, risk, cost benefit analysis is useful and required since it generates cost value to be used in the PESS. For many cases, the suggested method may be not adequate. However, similar one should be prepared, and be basis to decide sites for NIMBY or PIMFY national projects.

  12. Chitinase mRNA levels by quantitative PCR using the single standard DNA: acidic mammalian chitinase is a major transcript in the mouse stomach.

    Directory of Open Access Journals (Sweden)

    Misa Ohno

    Full Text Available Chitinases hydrolyze the β-1-4 glycosidic bonds of chitin, a major structural component of fungi, crustaceans and insects. Although mammals do not produce chitin or its synthase, they express two active chitinases, chitotriosidase (Chit1 and acidic mammalian chitinase (AMCase. These mammalian chitinases have attracted considerable attention due to their increased expression in individuals with a number of pathological conditions, including Gaucher disease, Alzheimer's disease and asthma. However, the contribution of these enzymes to the pathophysiology of these diseases remains to be determined. The quantification of the Chit1 and AMCase mRNA levels and the comparison of those levels with the levels of well-known reference genes can generate useful and biomedically relevant information. In the beginning, we established a quantitative real-time PCR system that uses standard DNA produced by ligating the cDNA fragments of the target genes. This system enabled us to quantify and compare the expression levels of the chitinases and the reference genes on the same scale. We found that AMCase mRNA is synthesized at extraordinarily high levels in the mouse stomach. The level of this mRNA in the mouse stomach was 7- to 10-fold higher than the levels of the housekeeping genes and was comparable to that the level of the mRNA for pepsinogen C (progastricsin, a major component of the gastric mucosa. Thus, AMCase mRNA is a major transcript in mouse stomach, suggesting that AMCase functions as a digestive enzyme that breaks down polymeric chitin and as part of the host defense against chitin-containing pathogens in the gastric contents. Our methodology is applicable to the quantification of mRNAs for multiple genes across multiple specimens using the same scale.

  13. The level of the transcription factor Pax6 is essential for controlling the balance between neural stem cell self-renewal and neurogenesis.

    Directory of Open Access Journals (Sweden)

    Stephen N Sansom

    2009-06-01

    Full Text Available Neural stem cell self-renewal, neurogenesis, and cell fate determination are processes that control the generation of specific classes of neurons at the correct place and time. The transcription factor Pax6 is essential for neural stem cell proliferation, multipotency, and neurogenesis in many regions of the central nervous system, including the cerebral cortex. We used Pax6 as an entry point to define the cellular networks controlling neural stem cell self-renewal and neurogenesis in stem cells of the developing mouse cerebral cortex. We identified the genomic binding locations of Pax6 in neocortical stem cells during normal development and ascertained the functional significance of genes that we found to be regulated by Pax6, finding that Pax6 positively and directly regulates cohorts of genes that promote neural stem cell self-renewal, basal progenitor cell genesis, and neurogenesis. Notably, we defined a core network regulating neocortical stem cell decision-making in which Pax6 interacts with three other regulators of neurogenesis, Neurog2, Ascl1, and Hes1. Analyses of the biological function of Pax6 in neural stem cells through phenotypic analyses of Pax6 gain- and loss-of-function mutant cortices demonstrated that the Pax6-regulated networks operating in neural stem cells are highly dosage sensitive. Increasing Pax6 levels drives the system towards neurogenesis and basal progenitor cell genesis by increasing expression of a cohort of basal progenitor cell determinants, including the key transcription factor Eomes/Tbr2, and thus towards neurogenesis at the expense of self-renewal. Removing Pax6 reduces cortical stem cell self-renewal by decreasing expression of key cell cycle regulators, resulting in excess early neurogenesis. We find that the relative levels of Pax6, Hes1, and Neurog2 are key determinants of a dynamic network that controls whether neural stem cells self-renew, generate cortical neurons, or generate basal progenitor cells

  14. Tracking and flavour tagging selection in the ATLAS High Level Trigger

    CERN Document Server

    Calvetti, Milene; The ATLAS collaboration

    2017-01-01

    In high-energy physics experiments, track based selection in the online environment is crucial for the efficient real time selection of the rare physics process of interest. This is of particular importance at the Large Hadron Collider (LHC), where the increasingly harsh collision environment is challenging the experiments to improve the performance of their online selection. Principal among these challenges is the increasing number of interactions per bunch crossing, known as pileup. In the ATLAS experiment the challenge has been addressed with multiple strategies. Firstly, specific trigger objects have been improved by building algorithms using detailed tracking and vertexing in specific detector regions to improve background rejection without loosing signal efficiency. Secondly, since 2015 all trigger areas have benefited from a new high performance Inner Detector (ID) software tracking system implemented in the High Level Trigger. Finally, performance will be further enhanced in future by the installation...

  15. Test methods for selection of materials of construction for high-level radioactive waste vitrification. Revision

    International Nuclear Information System (INIS)

    Bickford, D.F.; Corbett, R.A.; Morrison, W.S.

    1986-01-01

    Candidate materials of construction were evaluated for a facility at the Department of Energy's Savannah River Plant to vitrify high-level radioactive waste. Limited operating experience was available under the corrosive conditions of the complex vitrification process. The objective of the testing program was to provide a high degree of assurance that equipment will meet or exceed design lifetimes. To meet this objective in reasonable time and minimum cost, a program was designed consisting of a combination of coupon immersion and electrochemical laboratory tests and pilot-scale tests. Stainless steels and nickel-based alloys were tested. Alloys that were most resistant to general and local attack contained nickel, molybdenum (>9%), and chromium (where Cr + Mo > 30%). Alloy C-276 was selected as the reference material for process equipment. Stellite 6 was selected for abrasive service in the presence of formic acid. Alloy 690 and ALLCORR were selected for specific applications

  16. Selection of replacement material for the failed surface level gauge wire in Hanford waste tanks

    International Nuclear Information System (INIS)

    Anantatmula, R.P.; Pitman, S.G.; Lund, A.L.

    1995-10-01

    Surface level gauges fabricated from AISI Type 316 stainless steel (316) wire failed after only a few weeks of operation in underground storage tanks at the Hanford Site. The wire failure was determined to be due to chloride ion assisted corrosion of the 316 wire. Radiation-induced breakdown of the polyvinyl chloride (PVC) riser liners is suspected to be the primary source of the chloride ions. An extensive literature search followed by expert concurrence was undertaken to select a replacement material for the wire. Platinum (Pt)-20 % Iridium (Ir) alloy was selected as the replacement material from tile candidate materials, P-20% Ir, Pt-1O% Rhodium (Rh), Pt-20%Rh and Hastelloy C-22. The selection was made on the basis of the alloy's immunity towards acidic and basic environments as well as its adequate tensile properties in the fully annealed state

  17. A code for transcription initiation in mammalian genomes

    DEFF Research Database (Denmark)

    Frith, Martin C.; Valen, Eivind Dale; Krogh, Anders

    2007-01-01

    that initiation events are clustered on the chromosomes at multiple scales - clusters within clusters - indicating multiple regulatory processes. Within the smallest of such clusters, which can be interpreted as core promoters, the local DNA sequence predicts the relative transcription start usage of each...... of large- and small-scale effects: the selection of transcription start sites is largely governed by the local DNA sequence, whereas the transcriptional activity of a locus is regulated at a different level; it is affected by distal features or events such as enhancers and chromatin remodeling....

  18. Basal transcription machinery

    Indian Academy of Sciences (India)

    2007-03-29

    Mar 29, 2007 ... The holoenzyme of prokaryotic RNA polymerase consists of the core enzyme, made of two , , ' and subunits, which lacks promoter selectivity and a sigma () subunit which enables the core enzyme to initiate transcription in a promoter dependent fashion. A stress sigma factor s, in prokaryotes ...

  19. Dynamic usage of transcription start sites within core promoters

    DEFF Research Database (Denmark)

    Kawaji, Hideya; Frith, Martin C; Katayama, Shintaro

    2006-01-01

    BACKGROUND: Mammalian promoters do not initiate transcription at single, well defined base pairs, but rather at multiple, alternative start sites spread across a region. We previously characterized the static structures of transcription start site usage within promoters at the base pair level......, based on large-scale sequencing of transcript 5' ends. RESULTS: In the present study we begin to explore the internal dynamics of mammalian promoters, and demonstrate that start site selection within many mouse core promoters varies among tissues. We also show that this dynamic usage of start sites...... is associated with CpG islands, broad and multimodal promoter structures, and imprinting. CONCLUSION: Our results reveal a new level of biologic complexity within promoters--fine-scale regulation of transcription starting events at the base pair level. These events are likely to be related to epigenetic...

  20. Sex-Differences in Renal Expression of Selected Transporters and Transcription Factors in Lean and Obese Zucker Spontaneously Hypertensive Fatty Rats

    Directory of Open Access Journals (Sweden)

    Andrea Babelova

    2015-01-01

    Full Text Available The aim of this study was to identify sex-dependent expression of renal transporter mRNA in lean and obese Zucker spontaneously hypertensive fatty (ZSF1 rats and to investigate the interaction of the most altered transporter, organic anion transporter 2 (Oat2, with diabetes-relevant metabolites and drugs. Higher incidence of glomerulosclerosis, tubulointerstitial fibrosis, and protein casts in Bowman’s space and tubular lumen was detected by PAS staining in obese male compared to female ZSF1 rats. Real-time PCR on RNA isolated from kidney cortex revealed that Sglt1-2, Oat1-3, and Oct1 were higher expressed in kidneys of lean females. Oct2 and Mrp2 were higher expressed in obese males. Renal mRNA levels of transporters were reduced with diabetic nephropathy in females and the expression of transcription factors Hnf1β and Hnf4α in both sexes. The highest difference between lean and obese ZSF1 rats was found for Oat2. Therefore, we have tested the interaction of human OAT2 with various substances using tritium-labeled cGMP. Human OAT2 showed no interaction with diabetes-related metabolites, diabetic drugs, and ACE-inhibitors. However, OAT2-dependent uptake of cGMP was inhibited by furosemide. The strongly decreased expression of Oat2 and other transporters in female diabetic ZSF1 rats could possibly impair renal drug excretion, for example, of furosemide.

  1. A Time-Series Water Level Forecasting Model Based on Imputation and Variable Selection Method.

    Science.gov (United States)

    Yang, Jun-He; Cheng, Ching-Hsue; Chan, Chia-Pan

    2017-01-01

    Reservoirs are important for households and impact the national economy. This paper proposed a time-series forecasting model based on estimating a missing value followed by variable selection to forecast the reservoir's water level. This study collected data from the Taiwan Shimen Reservoir as well as daily atmospheric data from 2008 to 2015. The two datasets are concatenated into an integrated dataset based on ordering of the data as a research dataset. The proposed time-series forecasting model summarily has three foci. First, this study uses five imputation methods to directly delete the missing value. Second, we identified the key variable via factor analysis and then deleted the unimportant variables sequentially via the variable selection method. Finally, the proposed model uses a Random Forest to build the forecasting model of the reservoir's water level. This was done to compare with the listing method under the forecasting error. These experimental results indicate that the Random Forest forecasting model when applied to variable selection with full variables has better forecasting performance than the listing model. In addition, this experiment shows that the proposed variable selection can help determine five forecast methods used here to improve the forecasting capability.

  2. A Time-Series Water Level Forecasting Model Based on Imputation and Variable Selection Method

    Directory of Open Access Journals (Sweden)

    Jun-He Yang

    2017-01-01

    Full Text Available Reservoirs are important for households and impact the national economy. This paper proposed a time-series forecasting model based on estimating a missing value followed by variable selection to forecast the reservoir’s water level. This study collected data from the Taiwan Shimen Reservoir as well as daily atmospheric data from 2008 to 2015. The two datasets are concatenated into an integrated dataset based on ordering of the data as a research dataset. The proposed time-series forecasting model summarily has three foci. First, this study uses five imputation methods to directly delete the missing value. Second, we identified the key variable via factor analysis and then deleted the unimportant variables sequentially via the variable selection method. Finally, the proposed model uses a Random Forest to build the forecasting model of the reservoir’s water level. This was done to compare with the listing method under the forecasting error. These experimental results indicate that the Random Forest forecasting model when applied to variable selection with full variables has better forecasting performance than the listing model. In addition, this experiment shows that the proposed variable selection can help determine five forecast methods used here to improve the forecasting capability.

  3. A Time-Series Water Level Forecasting Model Based on Imputation and Variable Selection Method

    OpenAIRE

    Jun-He Yang; Ching-Hsue Cheng; Chia-Pan Chan

    2017-01-01

    Reservoirs are important for households and impact the national economy. This paper proposed a time-series forecasting model based on estimating a missing value followed by variable selection to forecast the reservoir's water level. This study collected data from the Taiwan Shimen Reservoir as well as daily atmospheric data from 2008 to 2015. The two datasets are concatenated into an integrated dataset based on ordering of the data as a research dataset. The proposed time-series forecasting m...

  4. Application of remote sensing technique to site selection for low and intermediate level radioactive waste

    International Nuclear Information System (INIS)

    Chen Zhangru; Jin Yuanxin; Liu Yuemiao; Hou Dewen

    2001-01-01

    Based on the relative criteria of selection of disposal site for low and intermediate level radioactive waste, the social-economic conditions, landform, morphologic properties, regional geological stability, hydrogeological and engineering geological characters of adjacent area of Anhui, Zhejiang and Jiangsu provinces were investigated. The geological interpretation of thematic mapper images, field reconnaissance and data analysis were conducted during the research work. The results show that three areas in the west part of Zhejiang Province were recommended as potential site for disposal of low and intermediate level radioactive waste. They are Bajiaotang area, Tiebanchong area and Changxing-Guangde-Anji nabes

  5. Selection of the host rock for high level radioactive waste repository in China

    International Nuclear Information System (INIS)

    Jin Yuanxin; Wang Wenguang; Chen Zhangru

    2001-01-01

    The authors has briefly introduced the experiences of the host rock selection and the host rock types in other countries for high level radioactive waste repository. The potential host rocks in China are investigated. They include granite, tuff, clay, basalt, salt, and loess. The report has expounded the distributions, scale, thickness, mineral and chemical composition, construction, petrogenesis and the ages of the rock. The possibility of these rocks as the host rock has been studied. The six pieces of distribution map of potential rocks have been made up. Through the synthetical study, it is considered that granite as the host rock of high level radioactive waste repository is possible

  6. Double level selection in a constitutional dynamic library of coordination driven supramolecular polygons.

    Science.gov (United States)

    Rancan, Marzio; Tessarolo, Jacopo; Casarin, Maurizio; Zanonato, Pier Luigi; Quici, Silvio; Armelao, Lidia

    2014-07-21

    A constitutional dynamic library (CDL) of Cu(II) metallo-supramolecular polygons has been studied as a bench test to examine an interesting selection case based on molecular recognition. Sorting of the CDL polygons is achieved through a proper guest that is hosted into the triangular metallo-macrocycle constituent. Two selection mechanisms are observed, a guest induced path and a guest templated self-assembly (virtual library approach). Remarkably, the triangular host can accommodate several guests with a degree of selectivity ranging from ∼1 to ∼10(4) for all possible guest pairs. A double level selection operates: guests drive the CDL toward the triangular polygon, and, at the same time, this is able to pick a specific guest from a set of competitive molecules, according to a selectivity-affinity correlation. Association constants of the host-guest systems have been determined. Guest competition and exchange studies have been analyzed through variable temperature UV-Vis absorption spectroscopy and single crystal X-ray diffraction studies. Molecular structures and electronic properties of the triangular polygon and of the host-guest systems also have been studied by means of all electrons density functional theory (DFT) and time-dependent density functional theory (TDDFT) calculations including dispersive contributions. DFT outcomes ultimately indicate the dispersive nature of the host-guest interactions, while TDDFT results allow a thorough assignment of the host and host-guests spectral features.

  7. Transcriptional Activities of the Microbial Consortium Living with the Marine Nitrogen-Fixing Cyanobacterium Trichodesmium Reveal Potential Roles in Community-Level Nitrogen Cycling.

    Science.gov (United States)

    Lee, Michael D; Webb, Eric A; Walworth, Nathan G; Fu, Fei-Xue; Held, Noelle A; Saito, Mak A; Hutchins, David A

    2018-01-01

    Trichodesmium is a globally distributed cyanobacterium whose nitrogen-fixing capability fuels primary production in warm oligotrophic oceans. Like many photoautotrophs, Trichodesmium serves as a host to various other microorganisms, yet little is known about how this associated community modulates fluxes of environmentally relevant chemical species into and out of the supraorganismal structure. Here, we utilized metatranscriptomics to examine gene expression activities of microbial communities associated with Trichodesmium erythraeum (strain IMS101) using laboratory-maintained enrichment cultures that have previously been shown to harbor microbial communities similar to those of natural populations. In enrichments maintained under two distinct CO 2 concentrations for ∼8 years, the community transcriptional profiles were found to be specific to the treatment, demonstrating a restructuring of overall gene expression had occurred. Some of this restructuring involved significant increases in community respiration-related transcripts under elevated CO 2 , potentially facilitating the corresponding measured increases in host nitrogen fixation rates. Particularly of note, in both treatments, community transcripts involved in the reduction of nitrate, nitrite, and nitrous oxide were detected, suggesting the associated organisms may play a role in colony-level nitrogen cycling. Lastly, a taxon-specific analysis revealed distinct ecological niches of consistently cooccurring major taxa that may enable, or even encourage, the stable cohabitation of a diverse community within Trichodesmium consortia. IMPORTANCE Trichodesmium is a genus of globally distributed, nitrogen-fixing marine cyanobacteria. As a source of new nitrogen in otherwise nitrogen-deficient systems, these organisms help fuel carbon fixation carried out by other more abundant photoautotrophs and thereby have significant roles in global nitrogen and carbon cycling. Members of the Trichodesmium genus tend to

  8. Attentional selection of levels within hierarchically organized figures is mediated by object-files

    Directory of Open Access Journals (Sweden)

    Mitchell Joseph Valdes-Sosa

    2014-12-01

    Full Text Available Objects frequently have a hierarchical organization (tree-branch-leaf. How do we select the level to be attended? This has been explored with compound letters: a global letter built from local letters. One explanation, backed by much empirical support, is that attentional competition is biased towards certain spatial frequency (SF bands across all locations and objects (a SF filter. This view assumes that the global and local letters are carried respectively by low and high SF bands, and that the bias can persist over time. Here we advocate a complementary view in which perception of hierarchical level is determined by how we represent each object-file. Although many properties bound to an object-file (i.e. position, color, even shape can mutate without affecting its persistence over time, we posit that same object-file cannot be used to store information from different hierarchical levels. Thus selection of level would be independent from locations but not from the way objects are represented at each moment. These views were contrasted via an attentional blink paradigm that presented letters within compound figures, but only one level at a time. Attending to two letters in rapid succession was easier if they were at the same- compared to different-levels, as predicted by both accounts. However, only the object-file account was able to explain why it was easier to report two targets on the same moving object compared to the same targets on distinct objects. The interference of different masks on target recognition was also easier to predict by the object-file account than by the SF filter. The methods introduced here allowed us to investigate attention to hierarchical levels and to objects within the same empirical framework. The data suggests that SF information is used to structure the internal organization of object representations, a process understood best by integrating object-file theory with previous models of hierarchical perception.

  9. Evolution of learning and levels of selection: a lesson from avian parent-offspring communication.

    Science.gov (United States)

    Lotem, Arnon; Biran-Yoeli, Inbar

    2014-02-01

    In recent years, it has become increasingly clear that the evolution of behavior may be better understood as the evolution of the learning mechanisms that produce it, and that such mechanisms should be modeled and tested explicitly. However, this approach, which has recently been applied to animal foraging and decision-making, has rarely been applied to the social and communicative behaviors that are likely to operate in complex social environments and be subject to multi-level selection. Here we use genetic, agent-based evolutionary simulations to explore how learning mechanisms may evolve to adjust the level of nestling begging (offspring signaling of need), and to examine the possible consequences of this process for parent-offspring conflict and communication. In doing so, we also provide the first step-by-step dynamic model of parent-offspring communication. The results confirm several previous theoretical predictions and demonstrate three novel phenomena. First, negatively frequency-dependent group-level selection can generate a stable polymorphism of learning strategies and parental responses. Second, while conventional reinforcement learning models fail to cope successfully with family dynamics at the nest, a newly developed learning model (incorporating behaviors that are consistent with recent experimental results on learning in nestling begging) produced effective learning, which evolved successfully. Third, while kin-selection affects the frequency of the different learning genes, its impact on begging slope and intensity was unexpectedly negligible, demonstrating that evolution is a complex process, and showing that the effect of kin-selection on behaviors that are shaped by learning may not be predicted by simple application of Hamilton's rule. Copyright © 2013 Elsevier Inc. All rights reserved.

  10. DETERMINATION OF DIVERSE ENVIRONMENTAL POLLUTION LEVEL FROM SELECTED AREAS OF RAWALPINDI, PAKISTAN

    Directory of Open Access Journals (Sweden)

    S. Pervez

    2017-08-01

    Full Text Available Anthropogenic contaminants arising from both stationary (power plants, industries and residential heating and mobile sources (road traffic can harm ambient air quality in urban areas. Depending upon their physical state, these pollutants are classified as liquid and vapor phases and are subsequently transported to the Earth’s surface through dry and wet deposition. After the deposition of these pollutants onto the surface of earth various health effects caused by these pollutants occurred like cardiovascular diseases and hypertension. In this study four different locations/sites were selected from the Rawalpindi city depending upon the population, traffic rush and industries to examine the noise level, concentration of carbon dioxide and heavy metals. Air sampler was used for the collection of air sample to analyze the heavy metal concentration, Quest electronic sound meter for measuring sound level and SIBATA for CO2 measurement. The study findings revealed that noise level was higher at all selected locations as described by WHO limit (70 dB being highest at Industrial area due to heavy machinery and lowest at green area. Concentration of all four heavy metals were high as compared with the prescribed limits. CO2 level reaches up to 300 ppm because of coal consumption during the winter season. The threshold values of all these selected parameters well above the prescribed limits defined by the authorities so to combat with this situation we should move towards more energy efficient fuels, proper maintenance of vehicles and machineries, traffic management and installation of noise barriers in industries as well as installation of catalytic convertors in vehicles to stop further air pollution.

  11. Monitoring of fluoride and iodide levels in drinking water using ion selective electrodes

    International Nuclear Information System (INIS)

    Ahmed, R.; Viqar-Un-Nisa; Hussain, M.; Tanwir, R.; Qureshi, S.A.

    2004-01-01

    Fluoride and iodide, the most important constituents of drinking water are essential as well as toxic depending on their levels. For their analysis in water mostly ion-selective electrodes, spectrophotometry, titrimetry and coulometry etc; have been used and literature has been briefly reviewed. Ion-selective electrodes offer an efficient method for the measurement of the two halides and were mostly used during this work. Fabrication of these electrodes is briefly described. Comparison of results obtained by ion selective electrode and coulometry is given. Recoveries of the added fluoride ions from the samples were good. A large number of water samples from Rawalpindi-Islamabad area were analyzed for fluoride and iodide. Levels of fluoride and iodide from two main water reservoirs of Rawalpindi and Islamabad are reported before and after treatment. Both surface and ground water samples were analyzed and results are compared and discussed. Some samples from northern areas were also analyzed for iodide and fluoride and compared. Intake of fluoride and iodide from water of different areas is also compared. Water samples, which caused bone deformation in certain areas in Punjab due to excess fluoride, were also analyzed for fluoride and results are presented. (author)

  12. Selective harmonic elimination strategy in eleven level inverter for PV system with unbalanced DC sources

    Science.gov (United States)

    Ghoudelbourk, Sihem.; Dib, D.; Meghni, B.; Zouli, M.

    2017-02-01

    The paper deals with the multilevel converters control strategy for photovoltaic system integrated in distribution grids. The objective of the proposed work is to design multilevel inverters for solar energy applications so as to reduce the Total Harmonic Distortion (THD) and to improve the power quality. The multilevel inverter power structure plays a vital role in every aspect of the power system. It is easier to produce a high-power, high-voltage inverter with the multilevel structure. The topologies of multilevel inverter have several advantages such as high output voltage, lower total harmonic distortion (THD) and reduction of voltage ratings of the power semiconductor switching devices. The proposed control strategy ensures an implementation of selective harmonic elimination (SHE) modulation for eleven levels. SHE is a very important and efficient strategy of eliminating selected harmonics by judicious selection of the firing angles of the inverter. Harmonics elimination technique eliminates the need of the expensive low pass filters in the system. Previous research considered that constant and equal DC sources with invariant behavior; however, this research extends earlier work to include variant DC sources, which are typical of lead-acid batteries when used in system PV. This Study also investigates methods to minimize the total harmonic distortion of the synthesized multilevel waveform and to help balance the battery voltage. The harmonic elimination method was used to eliminate selected lower dominant harmonics resulting from the inverter switching action.

  13. Selection criteria for container materials at the proposed Yucca Mountain high level nuclear waste repository

    International Nuclear Information System (INIS)

    Halsey, W.G.

    1989-11-01

    A geological repository has been proposed for the permanent disposal of the nation's high level nuclear waste at Yucca Mountain in the Nevada desert. The containers for this waste must remain intact for the unprecedented service lifetime of 1000 years. A combination of engineering, regulatory, and licensing requirements complicate the container material selection. In parallel to gathering information regarding the Yucca Mountain service environment and material performance data, a set of selection criteria have been established which compare candidate materials to the performance requirements, and allow a quantitative comparison of candidates. These criteria assign relative weighting to varied topic areas such as mechanical properties, corrosion resistance, fabricability, and cost. Considering the long service life of the waste containers, it is not surprising that the corrosion behavior of the material is a dominant factor. 7 refs

  14. Crossfostering in mice selectively bred for high and low levels of open-field thigmotaxis.

    Science.gov (United States)

    Leppänen, Pia K; Ewalds-Kvist, S Béatrice M

    2005-02-01

    The main purpose of this research was to investigate whether the difference in open-field (OF) thigmotaxis between mice selectively bred for high and low levels of wall-seeking behavior originated from genetic or acquired sources. Unfostered, infostered, and crossfostered mice were compared in two experiments in which the effects of strain, sex, and fostering on ambulation, defecation, exploration, grooming, latency to move, radial latency, rearing, thigmotaxis, and urination were studied. These experiments revealed that OF thigmotaxis was unaffected by the foster condition and thus genetically determined. The selected strains of mice also diverged repeatedly with regard to exploration and rearing. The findings are in line with the previously described existence of an inverse relationship between emotionality and exploration.

  15. Tracking and flavour tagging selection in the ATLAS High Level Trigger

    CERN Document Server

    Calvetti, Milene; The ATLAS collaboration

    2017-01-01

    In high-energy physics experiments, track based selection in the online environment is crucial for the detection of physics processes of interest for further study. This is of particular importance at the Large Hadron Collider (LHC), where the increasingly harsh collision environment is challenging participating experiments to improve the performance of their online selection. Principle among these challenges is the increasing number of interactions per bunch crossing, known as pileup. In the ATLAS experiment the challenge has been addressed with multiple strategies. Firstly, individual trigger groups focusing on specific physics objects have implemented novel algorithms which make use of the detailed tracking and vertexing performed within the trigger to improve rejection without losing efficiency. Secondly, since 2015 all trigger areas have also benefited from a new high performance inner detector software tracking system implemented in the High Level Trigger. Finally, performance will be further enhanced i...

  16. Level-1 trigger selection of electrons and photons with CMS for LHC Run-II.

    CERN Document Server

    AUTHOR|(CDS)2088114

    2016-01-01

    The CMS experiment has a sophisticated two-level online selection system that achieves a rejection factor of nearly $10^5$. The first, hardware-level trigger (L1) is based on coarse information coming from the calorimeters and the muon detectors while the High-Level Trigger combines fine-grain information from all subdetectors. During Run II, the LHC will increase its center of mass energy to 13 or 14 TeV, and progressively reach an instantaneous luminosity of $2\\times10^{34} \\mathrm{cm}^{-2}\\mathrm{s}^{-1}$. In order to guarantee a successful and ambitious physics programme in this intense environment, the CMS trigger and data acquisition system must be upgraded. The L1 calorimeter trigger hardware and architecture in particular has been redesigned to maintain the current thresholds even in presence of more demanding conditions (e.g., for electrons and photons) and improve the performance for the selection of $\\tau$ leptons. This design benefits from recent $\\mu$TCA technology, allowing sophisticated algorit...

  17. 17beta-estradiol induced vitellogenesis is inhibited by cortisol at the post-transcriptional level in Arctic char (Salvelinus alpinus

    Directory of Open Access Journals (Sweden)

    Modig Carina

    2004-09-01

    Full Text Available Abstract This study was performed to investigate stress effects on the synthesis of egg yolk precursor, vitellogenin (Vtg in Arctic char (Salvelinus alpinus. In particular the effect of cortisol (F was determined since this stress hormone has been suggested to interfere with vitellogenesis and is upregulated during sexual maturation in teleosts. Arctic char Vtg was purified and polyclonal antibodies were produced in order to develop tools to study regulation of vitellogenesis. The Vtg antibodies were used to develop an enzyme-linked immunosorbent assay. The corresponding Vtg cDNA was cloned from a hepatic cDNA library in order to obtain DNA probes to measure Vtg mRNA expression. Analysis of plasma from juvenile Arctic char, of both sexes, exposed to different steroids showed that production of Vtg was induced in a dose dependent fashion by 17β-estradiol (E2, estrone and estriol. Apart from estrogens a high dose of F also upregulated Vtg. In addition, F, progesterone (P and tamoxifen were tested to determine these compounds ability to modulate E2 induced Vtg synthesis at both the mRNA and protein level. Tamoxifen was found to inhibit E2 induced Vtg mRNA and protein upregulation. P did not alter the Vtg induction while F reduced the Vtg protein levels without affecting the Vtg mRNA levels. Furthermore the inhibition of Vtg protein was found to be dose dependent. Thus, the inhibitory effect of F on Vtg appears to be mediated at the post-transcriptional level.

  18. Available phosphorus levels for 95 to 120 kg barrows genetically selected for lean gain

    Directory of Open Access Journals (Sweden)

    Cláudio Luís Corrêa Arouca

    2012-06-01

    Full Text Available With the objective of evaluating available phosphorus (aP levels in diets for barrows selected for lean meat deposition, eighty commercial hybrid pigs with initial weight of 94.05±1.05 kg were used in this experiment. Pigs were allotted in a completely randomized block design, with five treatments (0.092, 0.156, 0.220, 0,284, and 0.348% of aP, eight replicates and two pigs per experimental unit. The average daily weight gain of pigs increased and the feed conversion improved quadratically with increasing aP in the diets up to the estimated levels of 0.21 and 0.20%, respectively. There was no effect of the dietary aP on average daily feed intake. However, aP intake, bone strength and concentration of phosphorus in the bones increased linearly with increasing aP in the diets. The levels of aP did not affect carcass traits; however, the alkaline phosphatase activity was improved and the values of serum inorganic phosphorus increased quadratically up to the estimated levels of 0.26 and 0.27% of aP, respectively. The available phosphorus levels of 0.21, 0.27, and 0.35%, corresponding to daily aP intakes of 6.34, 8.13, and 10.44 g result, respectively, in greatest performance, blood and bone parameters of 95 to 120 kg barrows selected for lean gain.

  19. Selective excitation of a vibrational level within the electronic ground state of a polyatomic molecule with ultra pulses

    CSIR Research Space (South Africa)

    de Clercq, L

    2010-09-01

    Full Text Available Coherent control of the upper vibrational level populations in the electronic ground state of a polyatomic molecule was simulated. Results indicate that selective excitation of a specific upper state level is possible...

  20. Five major controversial issues about fusion level selection in corrective surgery for adolescent idiopathic scoliosis: a narrative review.

    Science.gov (United States)

    Lee, Choon Sung; Hwang, Chang Ju; Lee, Dong-Ho; Cho, Jae Hwan

    2017-07-01

    Shoulder imbalance, coronal decompensation, and adding-on phenomenon following corrective surgery in patients with adolescent idiopathic scoliosis are known to be related to the fusion level selected. Although many studies have assessed the appropriate selection of the proximal and distal fusion level, no definite conclusions have been drawn thus far. We aimed to assess the problems with fusion level selection for corrective surgery in patients with adolescent idiopathic scoliosis, and to enhance understanding about these problems. This study is a narrative review. We conducted a literature search of fusion level selection in corrective surgery for adolescent idiopathic scoliosis. Accordingly, we selected and reviewed five debatable topics related to fusion level selection: (1) selective thoracic fusion; (2) selective thoracolumbar-lumbar (TL-L) fusion; (3) adding-on phenomenon; (4) distal fusion level selection for major TL-L curves; and (5) proximal fusion level selection and shoulder imbalance. Selective fusion can be chosen in specific curve types, although there is a risk of coronal decompensation or adding-on phenomenon. Generally, wider indications for selective fusions are usually associated with more frequent complications. Despite the determination of several indications for selective fusion to avoid such complications, no clear guidelines have been established. Although authors have suggested various criteria to prevent the adding-on phenomenon, no consensus has been reached on the appropriate selection of lower instrumented vertebra. The fusion level selection for major TL-L curves primarily focuses on whether distal fusion can terminate at L3, a topic that remains unclear. Furthermore, because of the presence of several related factors and complications, proximal level selection and shoulder imbalance has been constantly debated and remains controversial from its etiology to its prevention. Although several difficult problems in the diagnosis and

  1. Selective suppression of autocatalytic caspase-3 driven by two-step transcriptional amplified human telomerase reverse transcriptase promoter on ovarian carcinoma growth in vitro and in mice.

    Science.gov (United States)

    Song, Yue; Xin, Xing; Xia, Zhijun; Zhai, Xingyue; Shen, Keng

    2014-07-01

    The objective of our study was to construct recombinant adenovirus (rAd) AdHTVP2G5-rev-casp3, which expresses autocatalytic caspase-3 driven by human telomerase reverse transcriptase promoter (hTERTp) with a two-step transcription amplification (TSTA) system and investigate its antitumor effects on ovarian cancer in vitro and in vivo. Fluorescent detection was used to detect EGFP expression in various cells. Cell viabilities were determined using the Cell Counting Kit-8 and flow cytometry. RT-PCR and immunoblotting assays were used to detect cellular apoptotic activities. Tumor growth and survival of tumor-bearing mice were studied. The hTERTp-TSTA system showed the strongest activity in hTERT-positive cancer cells when compared with hTERTp and cytomeglovirus promoter (CMVp). In contrast, it showed no activity in hTERT‑negative HUVECs. AdHTVP2G5‑rev-casp3 markedly suppressed the survival of AO cells in a dose-dependent modality with a viability rate of 17.8 ± 3.5% at an MOI of 70, which was significantly lower than that by AdHT-rev-casp3 and Ad-rev-casp3 (rAds which express rev-caspase-3 driven by hTERTp and CMVp, respectively). In contrast, AdHTVP2G5‑rev-casp3 induced little HUVEC death with a viability rate of 92.7 ± 5.2% at the same MOI. Additionally, AdHTVP2G5-rev-casp3 (MOI=70) caused significant apoptosis in AO cells with an apoptotic rate of 42%. The tumor growth suppression rate of AdHTVP2G5-rev-casp3 was 81.52%, significantly higher than that of AdHT-rev-casp3 (54.94%) or Ad-rev-casp3 (21.35%). AdHTVP2G5-rev-casp3 significantly improved the survival of tumor-bearing mice with little liver damage, with a mean survival of 258 ± 28 days. These results showed that AdHTVP2G5-rev-casp3 caused effective apoptosis with significant tumor selectivity, strongly suppressed tumor growth and improved mouse survival with little liver toxicity. It can be a potent therapeutic agent for tumor targeted treatment of ovarian cancer.

  2. Selective estrogen receptor modulators and betulinic acid act synergistically to target ERα and SP1 transcription factor dependent Pygopus expression in breast cancer.

    Science.gov (United States)

    Tzenov, Youlian R; Andrews, Phillip; Voisey, Kim; Gai, Luis; Carter, Beverley; Whelan, Kathryn; Popadiuk, Catherine; Kao, Kenneth R

    2016-06-01

    Estrogen and progesterone hormone receptor (ER and PR) expression in invasive breast cancer predicts response to hormone disruptive therapy. Pygopus2 (hPYGO2) encodes a chromatin remodelling protein important for breast cancer growth and cell cycle progression. The aims of this study were to determine the mechanism of expression of hPYGO2 in breast cancer and to examine how this expression is affected therapeutically. hPYGO2 and ER protein expression was examined in a breast tumour microarray by immunohistochemistry. hPYGO2 RNA and protein expression was examined in ER+ and ER- breast cancer cell lines in the presence of selective estrogen hormone receptor modulator drugs and the specificity protein-1 (SP1) inhibitor, betulinic acid (BA). The effects of these drugs on the ability for ER and SP1 to bind the hPYGO2 promoter and affect cell cycle progression were studied using chromatin immunoprecipitation assays. hPYGO2 was expressed in seven of eight lines and in nuclei of 98% of 65 breast tumours, including 3 Ductal carcinoma in situ and 62 invasive specimens representing ER-negative (22%) and ER-positive (78%) cases. Treatment with either 4-Hydroxytamoxifen (OHT) or fulvestrant reduced hPYGO2 mRNA 10-fold and protein 5-10-fold within 4 h. Promoter analysis indicated an ER/SP1 binding site at nt -225 to -531 of hPYGO2. SP1 RNA interference and BA reduced hPYGO2 protein and RNA expression by fivefold in both ER- and ER+ cells. Further attenuation was achieved by combining BA and 4-OHT resulting in eightfold reduction in cell growth. Our findings reveal a mechanistic link between hormone signalling and the growth transcriptional programme. The activation of its expression by ERα and/or SP1 suggests hPYGO2 as a theranostic target for hormone therapy responsive and refractory breast cancer. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

  3. Reference gene selection for quantitative reverse transcription-polymerase chain reaction normalization during in vitro adventitious rooting in Eucalyptus globulus Labill.

    Science.gov (United States)

    de Almeida, Márcia R; Ruedell, Carolina M; Ricachenevsky, Felipe K; Sperotto, Raul A; Pasquali, Giancarlo; Fett-Neto, Arthur G

    2010-09-20

    Eucalyptus globulus and its hybrids are very important for the cellulose and paper industry mainly due to their low lignin content and frost resistance. However, rooting of cuttings of this species is recalcitrant and exogenous auxin application is often necessary for good root development. To date one of the most accurate methods available for gene expression analysis is quantitative reverse transcription-polymerase chain reaction (qPCR); however, reliable use of this technique requires reference genes for normalization. There is no single reference gene that can be regarded as universal for all experiments and biological materials. Thus, the identification of reliable reference genes must be done for every species and experimental approach. The present study aimed at identifying suitable control genes for normalization of gene expression associated with adventitious rooting in E. globulus microcuttings. By the use of two distinct algorithms, geNorm and NormFinder, we have assessed gene expression stability of eleven candidate reference genes in E. globulus: 18S, ACT2, EF2, EUC12, H2B, IDH, SAND, TIP41, TUA, UBI and 33380. The candidate reference genes were evaluated in microccuttings rooted in vitro, in presence or absence of auxin, along six time-points spanning the process of adventitious rooting. Overall, the stability profiles of these genes determined with each one of the algorithms were very similar. Slight differences were observed in the most stable pair of genes indicated by each program: IDH and SAND for geNorm, and H2B and TUA for NormFinder. Both programs identified UBI and 18S as the most variable genes. To validate these results and select the most suitable reference genes, the expression profile of the ARGONAUTE1 gene was evaluated in relation to the most stable candidate genes indicated by each algorithm. Our study showed that expression stability varied between putative reference genes tested in E. globulus. Based on the AGO1 relative expression

  4. The Drosophila Translational Control Element (TCE) is required for high-level transcription of many genes that are specifically expressed in testes.

    Science.gov (United States)

    Katzenberger, Rebeccah J; Rach, Elizabeth A; Anderson, Ashley K; Ohler, Uwe; Wassarman, David A

    2012-01-01

    To investigate the importance of core promoter elements for tissue-specific transcription of RNA polymerase II genes, we examined testis-specific transcription in Drosophila melanogaster. Bioinformatic analyses of core promoter sequences from 190 genes that are specifically expressed in testes identified a 10 bp A/T-rich motif that is identical to the translational control element (TCE). The TCE functions in the 5' untranslated region of Mst(3)CGP mRNAs to repress translation, and it also functions in a heterologous gene to regulate transcription. We found that among genes with focused initiation patterns, the TCE is significantly enriched in core promoters of genes that are specifically expressed in testes but not in core promoters of genes that are specifically expressed in other tissues. The TCE is variably located in core promoters and is conserved in melanogaster subgroup species, but conservation dramatically drops in more distant species. In transgenic flies, short (300-400 bp) genomic regions containing a TCE directed testis-specific transcription of a reporter gene. Mutation of the TCE significantly reduced but did not abolish reporter gene transcription indicating that the TCE is important but not essential for transcription activation. Finally, mutation of testis-specific TFIID (tTFIID) subunits significantly reduced the transcription of a subset of endogenous TCE-containing but not TCE-lacking genes, suggesting that tTFIID activity is limited to TCE-containing genes but that tTFIID is not an obligatory regulator of TCE-containing genes. Thus, the TCE is a core promoter element in a subset of genes that are specifically expressed in testes. Furthermore, the TCE regulates transcription in the context of short genomic regions, from variable locations in the core promoter, and both dependently and independently of tTFIID. These findings set the stage for determining the mechanism by which the TCE regulates testis-specific transcription and understanding the

  5. A single amino acid change within the R2 domain of the VvMYB5b transcription factor modulates affinity for protein partners and target promoters selectivity

    Directory of Open Access Journals (Sweden)

    Granier Thierry

    2011-08-01

    Full Text Available Abstract Background Flavonoid pathway is spatially and temporally controlled during plant development and the transcriptional regulation of the structural genes is mostly orchestrated by a ternary protein complex that involves three classes of transcription factors (R2-R3-MYB, bHLH and WDR. In grapevine (Vitis vinifera L., several MYB transcription factors have been identified but the interactions with their putative bHLH partners to regulate specific branches of the flavonoid pathway are still poorly understood. Results In this work, we describe the effects of a single amino acid substitution (R69L located in the R2 domain of VvMYB5b and predicted to affect the formation of a salt bridge within the protein. The activity of the mutated protein (name VvMYB5bL, the native protein being referred as VvMYB5bR was assessed in different in vivo systems: yeast, grape cell suspensions, and tobacco. In the first two systems, VvMYB5bL exhibited a modified trans-activation capability. Moreover, using yeast two-hybrid assay, we demonstrated that modification of VvMYB5b transcriptional properties impaired its ability to correctly interact with VvMYC1, a grape bHLH protein. These results were further substantiated by overexpression of VvMYB5bR and VvMYB5bL genes in tobacco. Flowers from 35S::VvMYB5bL transgenic plants showed a distinct phenotype in comparison with 35S::VvMYB5bR and the control plants. Finally, significant differences in transcript abundance of flavonoid metabolism genes were observed along with variations in pigments accumulation. Conclusions Taken together, our findings indicate that VvMYB5bL is still able to bind DNA but the structural consequences linked to the mutation affect the capacity of the protein to activate the transcription of some flavonoid genes by modifying the interaction with its co-partner(s. In addition, this study underlines the importance of an internal salt bridge for protein conformation and thus for the establishment

  6. The -271 G>A polymorphism of kinase insert domain-containing receptor gene regulates its transcription level in patients with non-small cell lung cancer

    International Nuclear Information System (INIS)

    An, She-Juan; Chen, Zhi-Hong; Lin, Qiu-Xiong; Su, Jian; Chen, Hua-Jun; Lin, Jia-Ying; Wu, Yi-Long

    2009-01-01

    Kinase insert domain-containing receptor (KDR) plays a critical role in the metastasis of cancer and is used as a molecular target in cancer therapy. We investigated the characteristics of the -271 G>A polymorphism of the KDR gene to gain information that may benefit the development of individualized therapies for patients with non-small cell lung cancer (NSCLC). The -271 G>A polymorphism of the KDR gene in 106 lung cancer patients and 203 healthy control individuals was analyzed by polymerase chain reaction (PCR) and DNA sequencing methods. Real-time quantitative PCR and immunohistochemical methods were used to evaluate KDR mRNA and protein expression levels, respectively, in frozen tumor specimens. The -271 G>A polymorphism was associated with the mRNA expression level of the KDR gene in tumor tissues (t = 2.178, P = 0.032, independent samples t-test). Compared with the AG/GG genotype, the AA genotype was associated with higher KDR mRNA expression in tumor tissues. We found no relationship between the genotype and the KDR protein expression level and no significant difference in the distribution of the KDR gene polymorphism genotypes between lung cancer patients and the control group (χ 2 = 1.269, P = 0.264, Fisher's exact test). This study is the first to show that the -271 G>A polymorphism of the KDR gene may be a functional polymorphism related to the regulation of gene transcription. These findings may have important implications for therapies targeting KDR in patients with NSCLC

  7. A two level mutation-selection model of cultural evolution and diversity.

    Science.gov (United States)

    Salazar-Ciudad, Isaac

    2010-11-21

    Cultural evolution is a complex process that can happen at several levels. At the level of individuals in a population, each human bears a set of cultural traits that he or she can transmit to its offspring (vertical transmission) or to other members of his or her society (horizontal transmission). The relative frequency of a cultural trait in a population or society can thus increase or decrease with the relative reproductive success of its bearers (individual's level) or the relative success of transmission (called the idea's level). This article presents a mathematical model on the interplay between these two levels. The first aim of this article is to explore when cultural evolution is driven by the idea's level, when it is driven by the individual's level and when it is driven by both. These three possibilities are explored in relation to (a) the amount of interchange of cultural traits between individuals, (b) the selective pressure acting on individuals, (c) the rate of production of new cultural traits, (d) the individual's capacity to remember cultural traits and to the population size. The aim is to explore the conditions in which cultural evolution does not lead to a better adaptation of individuals to the environment. This is to contrast the spread of fitness-enhancing ideas, which make individual bearers better adapted to the environment, to the spread of "selfish" ideas, which spread well simply because they are easy to remember but do not help their individual bearers (and may even hurt them). At the same time this article explores in which conditions the adaptation of individuals is maximal. The second aim is to explore how these factors affect cultural diversity, or the amount of different cultural traits in a population. This study suggests that a larger interchange of cultural traits between populations could lead to cultural evolution not improving the adaptation of individuals to their environment and to a decrease of cultural diversity

  8. The future of event-level information repositories, indexing, and selection in ATLAS

    International Nuclear Information System (INIS)

    Barberis, D; Cranshaw, J; Malon, D; Gemmeren, P Van; Zhang, Q; Dimitrov, G; Nairz, A; Sorokoletov, R; Doherty, T; Quilty, D; Gallas, E J; Hrivnac, J; Nowak, M

    2014-01-01

    ATLAS maintains a rich corpus of event-by-event information that provides a global view of the billions of events the collaboration has measured or simulated, along with sufficient auxiliary information to navigate to and retrieve data for any event at any production processing stage. This unique resource has been employed for a range of purposes, from monitoring, statistics, anomaly detection, and integrity checking, to event picking, subset selection, and sample extraction. Recent years of data-taking provide a foundation for assessment of how this resource has and has not been used in practice, of the uses for which it should be optimized, of how it should be deployed and provisioned for scalability to future data volumes, and of the areas in which enhancements to functionality would be most valuable. This paper describes how ATLAS event-level information repositories and selection infrastructure are evolving in light of this experience, and in view of their expected roles both in wide-area event delivery services and in an evolving ATLAS analysis model in which the importance of efficient selective access to data can only grow.

  9. Development, evaluation, and selection of candidate high-level waste forms

    International Nuclear Information System (INIS)

    Bernadzikowski, T.A.; Allender, J.S.; Gordon, D.E.; Gould, T.H. Jr.

    1982-01-01

    The seven candidate waste forms, evaluated as potential media for the immobilization and gelogic disposal of high-level nuclear wastes were borosilicate glass, SYNROC, tailored ceramic, high-silica glass, FUETAP concrete, coated sol-gel particles, and glass marbles in a lead matrix. The evaluation, completed on August 1, 1981, combined preliminary waste form evaluations conducted at Department of Energy (DOE) defense waste-sites and at independent laboratories, peer review assessments, a product performance evaluation, and a processability analysis. Based on the combined results of these four inputs, two of the seven forms, borosilicate glass and a titanate-based ceramic, SYNROC, were selected as the reference and alternative forms, respectively, for continued development and evaluation in the National HLW Program. The borosilicate glass and ceramic forms were further compared during FY-1982 on the basis of risk assessments, cost comparisons, properties comparisons, and conformance with proposed regulatory and repository criteria. Both the glass and ceramic forms are viable candidates for use at DOE defense HLW sites; they are also candidates for immobilization of commercial reprocessing wastes. This paper describes the waste form screening process, discusses each of the four major inputs considered in the selection of the two forms in 1981, and presents a brief summary of the comparisons of the two forms during 1982 and the selection process to determine the final form for SRP defense HLW

  10. Assessment of heavy metal contamination, levels in topsoil at selected auto-workshops in Accra, Ghana

    International Nuclear Information System (INIS)

    Ziblim, M. Y.

    2015-07-01

    The research was conducted to assess the levels of contamination of heavy metals in the topsoil at selected auto-workshops in Accra to determine the anthropogenic and crustal contributions and the human heath risk associated with them. Soil samples collected from four auto-workshops were analysed using Atomic Absorption Spectrometer. Eleven (11) elements: Co, Fe, Cu, Mn, Cr, As, Hg, Zn, Pb, Ni, and Cd were identified in each sample collected from the auto-workshops. Pollution indices; contamintion factor (Cf) index of geoaccumulation (Igeo) and pollution load index (PLI) were used to assess the contamination levels. It revealed the extent of contamination at the auto-workshops for most of the elements which range from low to considerate contamintion. Lead (Pb) recorded the greatest contamination levels at the auto-electrical location. The results from the index of geoccumulation showed no pollution to highly pollution indicting high variations of pollution levels at different locations. The results of the PLI in almost all locations ranged from moderately to extremely polluted. Noncancer effect on children and adults due to exposure to the topsoil were also estimated with some selected metal elements. The hazard quotient (HQ) evaluation, showed ingestion to be the route of exposure to soil dust that results in a higher risk for heavy metals, followed by dermal contact. The effect due to inhalation of resuspended dust particles through the mouth and nose is relatively low. It was observed that, the auto-workshops are generally polluted with heavy metals and therefore posing ill-health effect to the humans and the environment. (au)

  11. Analysis of changes in water-level dynamics at selected sites in the Florida Everglades

    Science.gov (United States)

    Conrads, Paul; Benedict, Stephen T.

    2013-01-01

    The historical modification and regulation of the hydrologic patterns in the Florida Everglades have resulted in changes in the ecosystem of South Florida and the Florida Everglades. Since the 1970s, substantial focus has been given to the restoration of the Everglades ecosystem. The U.S. Geological Survey through its Greater Everglades Priority Ecosystem Science and National Water-Quality Assessment Programs has been providing scientific information to resource managers to assist in the Everglades restoration efforts. The current investigation included development of a simple method to identify and quantify changes in historical hydrologic behavior within the Everglades that could be used by researchers to identify responses of ecological communities to those changes. Such information then could be used by resource managers to develop appropriate water-management practices within the Everglades to promote restoration. The identification of changes in historical hydrologic behavior within the Everglades was accomplished by analyzing historical time-series water-level data from selected gages in the Everglades using (1) break-point analysis of cumulative Z-scores to identify hydrologic changes and (2) cumulative water-level frequency distribution curves to evaluate the magnitude of those changes. This analytical technique was applied to six long-term water-level gages in the Florida Everglades. The break-point analysis for the concurrent period of record (1978–2011) identified 10 common periods of changes in hydrologic behavior at the selected gages. The water-level responses at each gage for the 10 periods displayed similarity in fluctuation patterns, highlighting the interconnectedness of the Florida Everglades hydrologic system. While the patterns were similar, the analysis also showed that larger fluctuations in water levels between periods occurred in Water Conservation Areas 2 and 3 in contrast to those in Water Conservation Area 1 and the Everglades

  12. The level of selected coordinative motor abilities of basketball players aged 16-18.

    Science.gov (United States)

    Popowczak, M; Struzik, A; Rokita, A; Pietraszewski, B

    2015-10-01

    Coordinative abilities play a very important role in sport. Unfortunately, researchers do not confine appropriate attention to this issue. Therefore, the aim of this study was an attempt at analysing results of the selected coordinative motor abilities: kinesthetic differentiation, quick reaction and spatial orientation. It was intended to find out whether the results of trials determining manifestations of the particular coordinative abilities exhibit any mutual relationships. Forasmuch as a static torque is a parameter determining the level of force components of the ability of kinaesthetic differentiation, it would like to find out whether its maximum level influences the final result. Research was carried out on 20 young basketball players with the use of a torque meter and Fusion Smart Speed System. It was noticed a lack of statistically significant relationships between the results of trials assessing manifestations of the ability of kinaesthetic differentiation, quick reaction and spatial orientation. However, it was noted statistically significant correlation between the maximum static torque and the accuracy of releasing a particular value of a static torque. The accuracy of releasing a particular value of a static torque ought to be classified as a comprehensive ability that comprises manifestations of strength abilities and kinaesthetic differentiation. Presented trials to evaluation manifestations of the selected coordinative abilities could be used by coaches during a training process. Coaches should also focus on the development of muscle strength of the upper body and upper limbs of basketball players.

  13. Development of the Teacher Candidates’ Level of being Affected from Public Personnel Selection Examination Scale

    Directory of Open Access Journals (Sweden)

    Fatma SUSAR KIRMIZI

    2016-07-01

    Full Text Available This study aimed to develop a scale to evaluate teacher candidates' level of being affected from the public personnel selection examination. The participants of the study consisted of the final year students at Pamukkale University Education Faculty. The participants were 207 teacher candidates, of whom 143 were female and 64 were male. The validity and reliability study of the scale was conducted on the data gathered from teacher candidates studying at Art Teaching, Music Teaching, Turkish Language Teaching, Social Studies Education, Science Teaching, Psychological Counseling and Guidance Education, Elementary Education and Preschool Education departments of Pamukkale University Education Faculty. The Lawshe technique was used in the evaluation of the scale by experts. To determine the construct validity, factor analysis was performed on the data, and two sub-scales were identified. The factor loading values of the items in the first sub-scale ranged between 0,65 and 0,35, and those in the second sub-scale between 0,75 and 0,39. As a result of the analyses, the "Teacher Candidates' Level of Being Affected From Public Personnel Selection Examination Scale" (TCLBAPPSES including 33 items, 23 negative and 10 positive, and two sub-scales was produced. The Cronbach's Alpha reliability coefficient was found as 0,86 for the first sub-dimension, 0,73 for the second sub-dimension, and 0,91 for the whole scale. As a result, it can be argued that the scale is reliable

  14. Population-level resource selection by sympatric brown and American black bears in Alaska

    Science.gov (United States)

    Belant, Jerrold L.; Griffith, Brad; Zhang, Yingte; Follmann, Erich H.; Adams, Layne G.

    2010-01-01

    Distribution theory predicts that for two species living in sympatry, the subordinate species would be constrained from using the most suitable resources (e.g., habitat), resulting in its use of less suitable habitat and spatial segregation between species. We used negative binomial generalized linear mixed models with fixed effects to estimate seasonal population-level resource selection at two spatial resolutions for female brown bears (Ursus arctos) and female American black bears (U. americanus) in southcentral Alaska during May–September 2000. Black bears selected areas occupied by brown bears during spring which may be related to spatially restricted (i.e., restricted to low elevations) but dispersed or patchy availability of food. In contrast, black bears avoided areas occupied by brown bears during summer. Brown bears selected areas near salmon streams during summer, presumably to access spawning salmon. Use of areas with high berry production by black bears during summer appeared in response to avoidance of areas containing brown bears. Berries likely provided black bears a less nutritious, but adequate food source. We suggest that during summer, black bears were displaced by brown bears, which supports distribution theory in that black bears appeared to be partially constrained from areas containing salmon, resulting in their use of areas containing less nutritious forage. Spatial segregation of brown and American black bears apparently occurs when high-quality resources are spatially restricted and alternate resources are available to the subordinate species. This and previous work suggest that individual interactions between species can result in seasonal population-level responses.

  15. Changes in transcript levels of starch hydrolysis genes and raising citric acid production via carbon ion irradiation mutagenesis of Aspergillus niger.

    Directory of Open Access Journals (Sweden)

    Wei Hu

    Full Text Available The filamentous ascomycete Aspergillus niger is well known for its ability to accumulate citric acid for the hydrolysis of starchy materials. To improve citric acid productivity, heavy ion beam mutagenesis was utilized to produce mutant A.niger strains with enhanced production of citric acid in this work. It was demonstrated that a mutant HW2 with high concentration of citric acid was isolated after carbon ion irradiation with the energy of 80Mev/μ, which was obvious increase higher than the original strain from liquefied corn starch as a feedstock. More importantly, with the evidence from the expression profiles of key genes and enzyme activity involved in the starch hydrolysis process between original strain and various phenotype mutants, our results confirmed that different transcript levels of key genes involving in starch hydrolysis process between original strain and mutants could be a significant contributor to different citric acid concentration in A.niger, such as, amyR and glaA, which therefore opened a new avenue for constructing genetically engineered A.niger mutants for high-yield citric acid accumulation in the future. As such, this work demonstrated that heavy ion beam mutagenesis presented an efficient alternative strategy to be developed to generate various phenotype microbe species mutants for functional genes research.

  16. Development of an ultralow-light-level luminescence image analysis system for dynamic measurements of transcriptional activity in living and migrating cells.

    Science.gov (United States)

    Maire, E; Lelièvre, E; Brau, D; Lyons, A; Woodward, M; Fafeur, V; Vandenbunder, B

    2000-04-10

    We have developed an approach to study in single living epithelial cells both cell migration and transcriptional activation, which was evidenced by the detection of luminescence emission from cells transfected with luciferase reporter vectors. The image acquisition chain consists of an epifluorescence inverted microscope, connected to an ultralow-light-level photon-counting camera and an image-acquisition card associated to specialized image analysis software running on a PC computer. Using a simple method based on a thin calibrated light source, the image acquisition chain has been optimized following comparisons of the performance of microscopy objectives and photon-counting cameras designed to observe luminescence. This setup allows us to measure by image analysis the luminescent light emitted by individual cells stably expressing a luciferase reporter vector. The sensitivity of the camera was adjusted to a high value, which required the use of a segmentation algorithm to eliminate the background noise. Following mathematical morphology treatments, kinetic changes of luminescent sources were analyzed and then correlated with the distance and speed of migration. Our results highlight the usefulness of our image acquisition chain and mathematical morphology software to quantify the kinetics of luminescence changes in migrating cells.

  17. Changes in transcript levels of starch hydrolysis genes and raising citric acid production via carbon ion irradiation mutagenesis of Aspergillus niger.

    Science.gov (United States)

    Hu, Wei; Li, Wenjian; Chen, Hao; Liu, Jing; Wang, Shuyang; Chen, Jihong

    2017-01-01

    The filamentous ascomycete Aspergillus niger is well known for its ability to accumulate citric acid for the hydrolysis of starchy materials. To improve citric acid productivity, heavy ion beam mutagenesis was utilized to produce mutant A.niger strains with enhanced production of citric acid in this work. It was demonstrated that a mutant HW2 with high concentration of citric acid was isolated after carbon ion irradiation with the energy of 80Mev/μ, which was obvious increase higher than the original strain from liquefied corn starch as a feedstock. More importantly, with the evidence from the expression profiles of key genes and enzyme activity involved in the starch hydrolysis process between original strain and various phenotype mutants, our results confirmed that different transcript levels of key genes involving in starch hydrolysis process between original strain and mutants could be a significant contributor to different citric acid concentration in A.niger, such as, amyR and glaA, which therefore opened a new avenue for constructing genetically engineered A.niger mutants for high-yield citric acid accumulation in the future. As such, this work demonstrated that heavy ion beam mutagenesis presented an efficient alternative strategy to be developed to generate various phenotype microbe species mutants for functional genes research.

  18. Changes in transcript levels of starch hydrolysis genes and raising citric acid production via carbon ion irradiation mutagenesis of Aspergillus niger

    Science.gov (United States)

    Li, Wenjian; Chen, Hao; Liu, Jing; Wang, Shuyang; Chen, Jihong

    2017-01-01

    The filamentous ascomycete Aspergillus niger is well known for its ability to accumulate citric acid for the hydrolysis of starchy materials. To improve citric acid productivity, heavy ion beam mutagenesis was utilized to produce mutant A.niger strains with enhanced production of citric acid in this work. It was demonstrated that a mutant HW2 with high concentration of citric acid was isolated after carbon ion irradiation with the energy of 80Mev/μ, which was obvious increase higher than the original strain from liquefied corn starch as a feedstock. More importantly, with the evidence from the expression profiles of key genes and enzyme activity involved in the starch hydrolysis process between original strain and various phenotype mutants, our results confirmed that different transcript levels of key genes involving in starch hydrolysis process between original strain and mutants could be a significant contributor to different citric acid concentration in A.niger, such as, amyR and glaA, which therefore opened a new avenue for constructing genetically engineered A.niger mutants for high-yield citric acid accumulation in the future. As such, this work demonstrated that heavy ion beam mutagenesis presented an efficient alternative strategy to be developed to generate various phenotype microbe species mutants for functional genes research. PMID:28650980

  19. Selective effects of whey protein concentrate on glutathione levels and apoptosis in rats with mammary tumors.

    Science.gov (United States)

    Cheng, Shih-Hsuan; Tseng, Yang-Ming; Wu, Szu-Hsien; Tsai, Shih-Meng; Tsai, Li-Yu

    2017-09-01

    Glutathione (GSH) plays an important role in antioxidant defense and regulation of apoptosis. GSH deficiency is related to many diseases, including cancer, and increased GSH levels in cancer cells are associated with chemotherapy resistance because of resistance to apoptosis. In this study, we investigated the effects of whey protein concentrate (WPC), a precursor of GSH, in rats with mammary tumors induced by treatment with 7,12-dimethylbenz(a)anthracene (DMBA). DMBA treatment results in cellular changes that mimic the initiation and promotion of carcinogenesis of breast tissue. We aimed to examine the possible preventive effects of diets containing whey protein on DMBA-induced mammary tumors in rats. The results indicate that WPC (0.334 g/kg) supplementation significantly increased the liver GSH levels by 92%, and were accompanied by low Bax/Bcl-2 ratio (from 5 to 3) and cleaved caspase-3/procaspase-3 ratio (from 2.4 to 1.2) in DMBA-treated rats. Furthermore, tumor GSH levels were decreased by 47% in WPC-supplemented rats, which resulted in increased Bax/Bcl-2 ratio (from 0.9 to 2) and cleaved caspase-3/procaspase-3 ratio (from 1.1 to 2.7). In conclusion, supplementation with WPC could selectively deplete tumor GSH levels and, therefore, WPC supplementation might be a promising strategy to overcome treatment resistance in cancer therapy. Copyright © 2017 Elsevier Ltd. All rights reserved.

  20. Selection and ranking of patient video cases in paediatric neurology in relation to learner levels.

    Science.gov (United States)

    Balslev, Thomas; Muijtjens, Arno M M; Maarbjerg, Sabine Frølich; de Grave, Willem

    2018-05-01

    Teaching and learning with patient video cases may add authenticity, enhance diagnostic accuracy and improve chances of early diagnosis. The aim of this study is firstly to identify selection criteria for key Patient video cases (PVCs), secondly to identify trends in relevance of PVCs for learner levels and thirdly, to rank PVCs for learner levels. Based on a literature review, we identified criteria for key PVCs for use in paediatric neurology. We then performed a multi-round Delphi analysis to obtain agreement between 28 expert clinician teachers concerning key PVCs for four learner levels. We identified two major criteria: key PVCs should demonstrate key movements, and these movements should be subtle and/or difficult to note. The expert clinician teachers subsequently assessed a list of 14 topics for key PVCs. We found a clear, increasing trend in relevance scores, from medical students to young residents to experienced residents and specialists. For medical students and residents, epileptic spasms, Down syndrome, developmental delay, cerebral palsy and absence epilepsy were highly ranked. For specialists, conditions like chorea, focal seizures or eye movement disorders topped the ranking list, although ranking was less clear for this group of advanced learners. Key PVCs should demonstrate movements that are difficult to note for learners. Ranked lists of key PVCs for teaching and learning at different learner levels are now available and may help institutions build validated local libraries of PVCs. Copyright © 2017 European Paediatric Neurology Society. Published by Elsevier Ltd. All rights reserved.

  1. Astrocyte production of the chemokine macrophage inflammatory protein-2 is inhibited by the spice principle curcumin at the level of gene transcription

    Directory of Open Access Journals (Sweden)

    Santoro Thomas J

    2005-02-01

    -oxidant, epigallocatechin gallate. Conclusion Our results indicate that curcumin potently inhibits MIP-2 production at the level of gene transcription and offer further support for its potential use in the treatment of inflammatory conditions of the CNS.

  2. Astrocyte production of the chemokine macrophage inflammatory protein-2 is inhibited by the spice principle curcumin at the level of gene transcription.

    Science.gov (United States)

    Tomita, Michiyo; Holman, Brita J; Santoro, Christopher P; Santoro, Thomas J

    2005-02-25

    gallate. CONCLUSION: Our results indicate that curcumin potently inhibits MIP-2 production at the level of gene transcription and offer further support for its potential use in the treatment of inflammatory conditions of the CNS.

  3. Levels of selected metals in leaves of Cannabis sativa L. cultivated in Ethiopia.

    Science.gov (United States)

    Zerihun, Agalu; Chandravanshi, Bhagwan Singh; Debebe, Ayalew; Mehari, Bewketu

    2015-01-01

    Cannabis sativa L. is one of the illicit drug bearing plants. Cannabis products are the most widely trafficked drugs worldwide. The highest levels of cannabis production in the world take place in the African continent. A small volume of cannabis is produced in rural areas of Ethiopia, of which a small portion is exported to neighboring countries and the majority is consumed at home. The literature survey revealed that there is no report on the metal contents in cannabis cultivated in Ethiopia. The main objective of this study is to determine the level of selected metals in leaves of Cannabis sativa L. cultivated in Ethiopia. Cannabis sativa L. samples were collected from Metema (Amhara Region), Mekelle (Tigray Region), Sheshemene (Oromia Region) and Butajira (South Nations Nationality and Peoples (SNNP) Region) of Ethiopia. After proper sample pretreatment, the volumes of reagents used, digestion temperature and digestion time were optimized and using the optimized conditions the levels of metals were determined by flame atomic absorption spectrometry. The accuracy of the optimized procedure was evaluated by analyzing the digest of the spiked samples with standard solution and the percentage recoveries varied from 88 to 103%. The levels of metals determined (µg/g dry weight) were in the ranges Ca (657-1,511), Zn (321-380), Ni (124-172), Cu (122-176), Cd (3-10), Pb (8-10), and Cr (4-8). Zn was with the highest concentration among trace metals. A statistical analysis of variance (ANOVA) at 95% confidence level indicated that there is a significant difference in the levels of all the metals between the four sample means except Pb. The results indicate that the content of Pb and Cd exceeds the permissible amount for medicinal plants which form the raw materials for the finished products set by World Health Organization (WHO).

  4. A comparative study of noise pollution levels in some selected areas in Ilorin Metropolis, Nigeria.

    Science.gov (United States)

    Oyedepo, Olayinka S; Saadu, Abdullahi A

    2009-11-01

    The noise pollution is a major problem for the quality of life in urban areas. This study was conducted to compare the noise pollution levels at busy roads/road junctions, passengers loading parks, commercial, industrial and residential areas in Ilorin metropolis. A total number of 47-locations were selected within the metropolis. Statistical analysis shows significant difference (P noise pollution levels between industrial areas and low density residential areas, industrial areas and high density areas, industrial areas and passengers loading parks, industrial areas and commercial areas, busy roads/road junctions and low density areas, passengers loading parks and commercial areas and commercial areas and low density areas. There is no significant difference (P > 0.05) in noise pollution levels between industrial areas and busy roads/road junctions, busy roads/road junctions and high density areas, busy roads/road junctions and passengers loading parks, busy roads/road junctions and commercial areas, passengers loading parks and high density areas, passengers loading parks and commercial areas and commercial areas and high density areas. The results show that Industrial areas have the highest noise pollution levels (110.2 dB(A)) followed by busy roads/Road junctions (91.5 dB(A)), Passengers loading parks (87.8 dB(A)) and Commercial areas (84.4 dB(A)). The noise pollution levels in Ilorin metropolis exceeded the recommended level by WHO at 34 of 47 measuring points. It can be concluded that the city is environmentally noise polluted and road traffic and industrial machineries are the major sources of it. Noting the noise emission standards, technical control measures, planning and promoting the citizens awareness about the high noise risk may help to relieve the noise problem in the metropolis.

  5. Roka Listeria detection method using transcription mediated amplification to detect Listeria species in select foods and surfaces. Performance Tested Method(SM) 011201.

    Science.gov (United States)

    Hua, Yang; Kaplan, Shannon; Reshatoff, Michael; Hu, Ernie; Zukowski, Alexis; Schweis, Franz; Gin, Cristal; Maroni, Brett; Becker, Michael; Wisniewski, Michele

    2012-01-01

    The Roka Listeria Detection Assay was compared to the reference culture methods for nine select foods and three select surfaces. The Roka method used Half-Fraser Broth for enrichment at 35 +/- 2 degrees C for 24-28 h. Comparison of Roka's method to reference methods requires an unpaired approach. Each method had a total of 545 samples inoculated with a Listeria strain. Each food and surface was inoculated with a different strain of Listeria at two different levels per method. For the dairy products (Brie cheese, whole milk, and ice cream), our method was compared to AOAC Official Method(SM) 993.12. For the ready-to-eat meats (deli chicken, cured ham, chicken salad, and hot dogs) and environmental surfaces (sealed concrete, stainless steel, and plastic), these samples were compared to the U.S. Department of Agriculture/Food Safety and Inspection Service-Microbiology Laboratory Guidebook (USDA/FSIS-MLG) method MLG 8.07. Cold-smoked salmon and romaine lettuce were compared to the U.S. Food and Drug Administration/Bacteriological Analytical Manual, Chapter 10 (FDA/BAM) method. Roka's method had 358 positives out of 545 total inoculated samples compared to 332 positive for the reference methods. Overall the probability of detection analysis of the results showed better or equivalent performance compared to the reference methods.

  6. Growth arrest-specific transcript 5 associated snoRNA levels are related to p53 expression and DNA damage in colorectal cancer.

    Directory of Open Access Journals (Sweden)

    Jonathan Krell

    Full Text Available The growth arrest-specific transcript 5 gene (GAS5 encodes a long noncoding RNA (lncRNA and hosts a number of small nucleolar RNAs (snoRNAs that have recently been implicated in multiple cellular processes and cancer. Here, we investigate the relationship between DNA damage, p53, and the GAS5 snoRNAs to gain further insight into the potential role of this locus in cell survival and oncogenesis both in vivo and in vitro.We used quantitative techniques to analyse the effect of DNA damage on GAS5 snoRNA expression and to assess the relationship between p53 and the GAS5 snoRNAs in cancer cell lines and in normal, pre-malignant, and malignant human colorectal tissue and used biological techniques to suggest potential roles for these snoRNAs in the DNA damage response.GAS5-derived snoRNA expression was induced by DNA damage in a p53-dependent manner in colorectal cancer cell lines and their levels were not affected by DICER. Furthermore, p53 levels strongly correlated with GAS5-derived snoRNA expression in colorectal tissue.In aggregate, these data suggest that the GAS5-derived snoRNAs are under control of p53 and that they have an important role in mediating the p53 response to DNA damage, which may not relate to their function in the ribosome. We suggest that these snoRNAs are not processed by DICER to form smaller snoRNA-derived RNAs with microRNA (miRNA-like functions, but their precise role requires further evaluation. Furthermore, since GAS5 host snoRNAs are often used as endogenous controls in qPCR quantifications we show that their use as housekeeping genes in DNA damage experiments can lead to inaccurate results.

  7. Expression levels of transcription factors c-Fos and c-Jun and transmembrane protein HAb18G/CD147 in urothelial carcinoma of the bladder.

    Science.gov (United States)

    Huhe, Muren; Liu, Shuangshuang; Zhang, Yang; Zhang, Zheng; Chen, Zhinan

    2017-05-01

    The aim of the present study was to investigate the prognostic significance of the expression of transcription factors, c-Fos, c-Jun and transmembrane protein CD147, in urothelial carcinoma of the bladder (UCB). The current study investigated the clinical significance of these factors in the development, progression and survival analysis of UCB. Immunohistochemistry was employed to analyze c‑Fos, c‑Jun and CD147 expression in 41 UCB cases and 34 non‑cancerous human bladder tissues. These results were scored in a semi‑quantitative manner based on the intensity and percentage of tumor cells that presented immunoreactivity. Protein levels of CD147, c‑Fos and c‑Jun expression were upregulated in 22 (53.7%), 10 (24.4%) and 9 (22.0%) UCB cases, respectively. High levels of c‑Jun correlated with the AJCC cancer staging manual (7th edition; P=0.038). Univariate analysis revealed that upregulated CD147 (P=0.038) or c‑Jun (P=0.008) was associated with poor overall survival (OS), respectively. Further analysis revealed that either CD147‑c‑Fos‑c‑Jun co‑expression (P=0.004), or CD147‑c‑Jun co‑expression (P=0.037) and c‑Fos‑c‑Jun co‑expression (PCD147, c‑Jun or c‑Fos were independent risk indicators for death in UCB patients. Increased expression of c‑Jun or CD147, as well as co‑expression of CD147‑c‑Jun, c‑Jun‑c‑Fos or CD147‑c‑Jun‑c‑Fos has prognostic significance for UCB patients. Therefore, high CD147 and c‑Jun expression may serve roles in tumor progression and may be diagnostic and therapeutic targets in UCB whether alone or in combination.

  8. Evidence for changes in the transcription levels of two putative P-glycoprotein genes in sea lice (Lepeophtheirus salmonis) in response to emamectin benzoate exposure.

    Science.gov (United States)

    Tribble, Nicholas D; Burka, John F; Kibenge, Frederick S B

    2007-05-01

    Overexpression of P-glycoproteins (Pgps) is assumed to be a principal mechanism of resistance of nematodes and arthropods to macrocyclic lactones. Quantitative RT-PCR (Q-RT-PCR) was used to demonstrate changes in transcription levels of two putative P-glycoprotein genes, designated here as SL0525 and SL-Pgp1, in sea lice (Lepeophtheirus salmonis) following exposure to emamectin benzoate (EMB). Pre-adult L. salmonis were challenged in an EMB bioassay for 24h and gene expression was studied from lice surviving EMB concentrations of 0, 10, and 30ppb. Gene expression was measured using Q-RT-PCR with elongation factor 1 (eEF1alpha) as an internal reference gene. The results show that both target genes, SL0525 and SL-Pgp1, had significantly increased levels of expression with exposure to 10ppb EMB (p=0.11 and p=0.17, respectively) whereas the group exposed to 30ppb was on the verge of being significant (p=0.053) only in the expression of SL-Pgp1. Gene expression for SL0525 and SL-Pgp1 were increased over five-fold at 10ppb EMB. Therefore, the upregulation of these target genes may offer protection by increasing Pgp expression when lice are exposed to EMB. Our optimized Q-RT-PCR can be used to determine if over-expression of these genes could be the basis for development of resistance in sea lice and thus allow suitable alternative chemotherapeutic options to be assessed.

  9. The cost and benefit analysis of a contaminated area remediation: case study of dose level selection

    International Nuclear Information System (INIS)

    Lauria, D.C.

    2006-01-01

    In recent years there has been an increasing awareness of the radiological impact of non-nuclear industries that extract and/or process ores and minerals containing naturally occurring radioactive material (NORM). Without radiological rules, these industrial activities may result in significant radioactive contamination of installations and sites. Depending on the potential hazardous to the environment and public health, the radioactive contaminated sites may require remediation. The extent of the site cleanup is a function of the size, localization, complexity, potential risks and on possible future uses envisioned for the site. Since worker and public health, public anxiety and economics factors are involved; the selection of an appropriate dose level can be quite complicated. This paper discusses the selection of a dose level criterion to remedy a site, which was contaminated by wastes from monazite processing. The site is located in the Sao Paulo city; the most densely populated Brazilian City. In its 60,000 square meters of area, a preliminary survey showed contaminated zones covering an area of 6,500 square meters. In some places, contamination was found below the superficial layer of the soil, being the radionuclide vertical distribution not uniform. The 228 Ra soil activity concentration reached values up to 33,000 Bq/kg while those for 226 Ra reached values up to 6,700 Bq/kg. Based on pathway analysis model and considering both the current land use and a hypothetical residential scenario, the residual contamination levels of radionuclides in soil have been derived for dose values of 10 mSv/y (dose level for intervention), 5 mSv/y, 3 mSv/y, 1 mSv/y (dose limit for practices) and 0.3 mSv/y (dose constraint for practices). An optimized value o f annual dose of about 5 mSv/y would be a good option for intervention level, but taking into account the public concern and anxiety, the site location and size, and the remediation costs, it is suggested the

  10. The cost and benefit analysis of a contaminated area remediation: case study of dose level selection

    Energy Technology Data Exchange (ETDEWEB)

    Lauria, D.C. [Instituto de Radioproteccion e Dosimetria- IRD/CNEN, Av. Salvador Allende s/n, Barra de Tijuca, Rio de Janeiro- RJ (Brazil)]. e-mail: dejanira@ird.gov.br

    2006-07-01

    In recent years there has been an increasing awareness of the radiological impact of non-nuclear industries that extract and/or process ores and minerals containing naturally occurring radioactive material (NORM). Without radiological rules, these industrial activities may result in significant radioactive contamination of installations and sites. Depending on the potential hazardous to the environment and public health, the radioactive contaminated sites may require remediation. The extent of the site cleanup is a function of the size, localization, complexity, potential risks and on possible future uses envisioned for the site. Since worker and public health, public anxiety and economics factors are involved; the selection of an appropriate dose level can be quite complicated. This paper discusses the selection of a dose level criterion to remedy a site, which was contaminated by wastes from monazite processing. The site is located in the Sao Paulo city; the most densely populated Brazilian City. In its 60,000 square meters of area, a preliminary survey showed contaminated zones covering an area of 6,500 square meters. In some places, contamination was found below the superficial layer of the soil, being the radionuclide vertical distribution not uniform. The {sup 228} Ra soil activity concentration reached values up to 33,000 Bq/kg while those for {sup 226} Ra reached values up to 6,700 Bq/kg. Based on pathway analysis model and considering both the current land use and a hypothetical residential scenario, the residual contamination levels of radionuclides in soil have been derived for dose values of 10 mSv/y (dose level for intervention), 5 mSv/y, 3 mSv/y, 1 mSv/y (dose limit for practices) and 0.3 mSv/y (dose constraint for practices). An optimized value o f annual dose of about 5 mSv/y would be a good option for intervention level, but taking into account the public concern and anxiety, the site location and size, and the remediation costs, it is suggested

  11. Diacetyl levels and volatile profiles of commercial starter distillates and selected dairy foods.

    Science.gov (United States)

    Rincon-Delgadillo, M I; Lopez-Hernandez, A; Wijaya, I; Rankin, S A

    2012-03-01

    Starter distillates (SDL) are used as ingredients in the formulation of many food products such as cottage cheese, margarine, vegetable oil spreads, processed cheese, and sour cream to increase the levels of naturally occurring buttery aroma associated with fermentation. This buttery aroma results, in part, from the presence of the vicinal dicarbonyl, diacetyl, which imparts a high level of buttery flavor notes and is a key component of SDL. Diacetyl (2,3-butanedione) is a volatile product of citrate metabolism produced by certain bacteria, including Lactococcus lactis ssp. diacetylactis and Leuconostoc citrovorum. In the United States, SDL are regarded as generally recognized as safe ingredients, whereby usage in food products is limited by good manufacturing practices. Recently, diacetyl has been implicated as a causative agent in certain lung ailments in plant workers; however, little is published about the volatile composition of SDL and the levels of diacetyl or other flavoring components in finished dairy products. The objective of this work was to characterize the volatile compounds of commercial SDL and to quantitate levels of diacetyl and other Flavor and Extract Manufacturers Association-designated high-priority flavoring components found in 18 SDL samples and 24 selected dairy products. Headspace volatiles were assessed using a solid-phase microextraction and analyzed by gas chromatography-mass spectrometry. In addition to diacetyl (ranging from 1.2 to 22,000 μg/g), 40 compounds including 8 organic acids, 4 alcohols, 3 aldehydes, 7 esters, 3 furans, 10 ketones, 2 lactones, 2 sulfur-containing compounds, and 1 terpene were detected in the SDL. A total of 22 food samples were found to contain diacetyl ranging from 4.5 to 2,700 μg/100g. Other volatile compounds, including acetaldehyde, acetic acid, acetoin, benzaldehyde, butyric acid, formic acid, furfural, 2,3-heptanedione, 2,3-pentanedione, and propanoic acid, were also identified and quantified in SDL

  12. Comparison of selected foreign plans and practices for spent fuel and high-level waste management

    International Nuclear Information System (INIS)

    Schneider, K.J.; Mitchell, S.J.; Lakey, L.T.; Johnson, A.B. Jr.; Hazelton, R.F.; Bradley, D.J.

    1990-04-01

    This report describes the major parameters for management of spent nuclear fuel and high-level radioactive wastes in selected foreign countries as of December 1989 and compares them with those in the United States. The foreign countries included in this study are Belgium, Canada, France, the Federal Republic of Germany, Japan, Sweden, Switzerland, and the United Kingdom. All the countries are planning for disposal of spent fuel and/or high-level wastes in deep geologic repositories. Most countries (except Canada and Sweden) plan to reprocess their spent fuel and vitrify the resultant high-level liquid wastes; in comparison, the US plans direct disposal of spent fuel. The US is planning to use a container for spent fuel as the primary engineered barrier. The US has the most developed repository concept and has one of the earliest scheduled repository startup dates. The repository environment presently being considered in the US is unique, being located in tuff above the water table. The US also has the most prescriptive regulations and performance requirements for the repository system and its components. 135 refs., 8 tabs

  13. Selection of important initiating events for Level 1 probabilistic safety assessment study at Puspati TRIGA Reactor

    International Nuclear Information System (INIS)

    Maskin, M.; Charlie, F.; Hassan, A.; Prak Tom, P.; Ramli, Z.; Mohamed, F.

    2016-01-01

    Highlights: • Identifying possible important initiating events (IEs) for Level 1 probabilistic safety assessment performed on research nuclear reactor. • Methods in screening and grouping IEs are addressed. • Focusing only on internal IEs due to random failures of components. - Abstract: This paper attempts to present the results in identifying possible important initiating events (IEs) as comprehensive as possible to be applied in the development of Level-1 probabilistic safety assessment (PSA) study. This involves the approaches in listing and the methods in screening and grouping IEs, by focusing only on the internal IEs due to random failures of components and human errors with full power operational conditions and reactor core as the radioactivity source. Five approaches were applied in listing the IEs and each step of the methodology was described and commented. The criteria in screening and grouping the IEs were also presented. The results provided the information on how the Malaysian PSA team applied the approaches in selecting the most probable IEs as complete as possible in order to ensure the set of IEs was identified systematically and as representative as possible, hence providing confidence to the completeness of the PSA study. This study is perhaps one of the first to address classic comprehensive steps in identifying important IEs to be used in a Level-1 PSA study.

  14. Comparison of selected foreign plans and practices for spent fuel and high-level waste management

    Energy Technology Data Exchange (ETDEWEB)

    Schneider, K.J.; Mitchell, S.J.; Lakey, L.T.; Johnson, A.B. Jr.; Hazelton, R.F.; Bradley, D.J.

    1990-04-01

    This report describes the major parameters for management of spent nuclear fuel and high-level radioactive wastes in selected foreign countries as of December 1989 and compares them with those in the United States. The foreign countries included in this study are Belgium, Canada, France, the Federal Republic of Germany, Japan, Sweden, Switzerland, and the United Kingdom. All the countries are planning for disposal of spent fuel and/or high-level wastes in deep geologic repositories. Most countries (except Canada and Sweden) plan to reprocess their spent fuel and vitrify the resultant high-level liquid wastes; in comparison, the US plans direct disposal of spent fuel. The US is planning to use a container for spent fuel as the primary engineered barrier. The US has the most developed repository concept and has one of the earliest scheduled repository startup dates. The repository environment presently being considered in the US is unique, being located in tuff above the water table. The US also has the most prescriptive regulations and performance requirements for the repository system and its components. 135 refs., 8 tabs.

  15. MCG101-induced cancer anorexia-cachexia features altered expression of hypothalamic Nucb2 and Cartpt and increased plasma levels of cocaine- and amphetamine-regulated transcript peptides.

    Science.gov (United States)

    Burgos, Jonathan R; Iresjö, Britt-Marie; Smedh, Ulrika

    2016-04-01

    The aim of the present study was to explore central and peripheral host responses to an anorexia-cachexia producing tumor. We focused on neuroendocrine anorexigenic signals in the hypothalamus, brainstem, pituitary and from the tumor per se. Expression of mRNA for corticotropin-releasing hormone (CRH), cocaine- and amphetamine-regulated transcript (CART), nesfatin-1, thyrotropin (TSH) and the TSH receptor were explored. In addition, we examined changes in plasma TSH, CART peptides (CARTp) and serum amyloid P component (SAP). C57BL/6 mice were implanted with MCG101 tumors or sham-treated. A sham-implanted, pair‑fed (PF) group was included to delineate between primary tumor and secondary effects from reduced feeding. Food intake and body weight were measured daily. mRNA levels from microdissected mouse brain samples were assayed using qPCR, and plasma levels were determined using ELISA. MCG101 tumors expectedly induced anorexia and loss of body weight. Tumor-bearing (TB) mice exhibited an increase in nesfatin-1 mRNA as well as a decrease in CART mRNA in the paraventricular area (PVN). The CART mRNA response was secondary to reduced caloric intake whereas nesfatin-1 mRNA appeared to be tumor-specifically induced. In the pituitary, CART and TSH mRNA were upregulated in the TB and PF animals compared to the freely fed controls. Plasma levels for CARTp were significantly elevated in TB but not PF mice whereas levels of TSH were unaffected. The plasma CARTp response was correlated to the degree of inflammation represented by SAP. The increase in nesfatin-1 mRNA in the PVN highlights nesfatin-1 as a plausible candidate for causing tumor-induced anorexia. CART mRNA expression in the PVN is likely an adaptation to reduced caloric intake secondary to a cancer anorexia-cachexia syndrome (CACS)‑inducing tumor. The MCG101 tumor did not express CART mRNA, thus the elevation of plasma CARTp is host derived and likely driven by inflammation.

  16. Low-level overexpression of p53 promotes warfarin-induced calcification of porcine aortic valve interstitial cells by activating Slug gene transcription.

    Science.gov (United States)

    Gao, Li; Ji, Yue; Lu, Yan; Qiu, Ming; Shen, Yejiao; Wang, Yaqing; Kong, Xiangqing; Shao, Yongfeng; Sheng, Yanhui; Sun, Wei

    2018-03-09

    The most frequently used oral anti-coagulant warfarin has been implicated in inducing calcification of aortic valve interstitial cells (AVICs), whereas the mechanism is not fully understood. The low-level activation of p53 is found to be involved in osteogenic transdifferentiation and calcification of AVICs. Whether p53 participates in warfarin-induced AVIC calcification remains unknown. In this study, we investigated the role of low-level p53 overexpression in warfarin-induced porcine AVIC (pAVIC) calcification. Immunostaining, quantitative PCR, and Western blotting revealed that p53 was expressed in human and pAVICs and that p53 expression was slightly increased in calcific human aortic valves compared with non-calcific valves. Terminal deoxynucleotidyltransferase-mediated dUTP nick end labeling staining indicated that apoptosis slightly increased in calcific aortic valves than in non-calcific valves. Warfarin treatment led to a low-level increase of p53 mRNA and protein in both pAVICs and mouse aortic valves. Low-level overexpression of p53 in pAVICs via an adenovirus vector did not affect pAVIC apoptosis but promoted warfarin-induced calcium deposition and expression of osteogenic markers. shRNA-mediated p53 knockdown attenuated the pAVIC calcium deposition and osteogenic marker expression. Moreover, ChIP and luciferase assays showed that p53 was recruited to the slug promoter and activated slug expression in calcific pAVICs. Of note, overexpression of Slug increased osteogenic marker Runx2 expression, but not pAVIC calcium deposition, and Slug knockdown attenuated pAVIC calcification and p53-mediated pAVIC calcium deposition and expression of osteogenic markers. In conclusion, we found that p53 plays an important role in warfarin induced pAVIC calcification, and increased slug transcription by p53 is required for p53-mediated pAVIC calcification. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

  17. Site selection experience for a new low-level radioactive waste storage/disposal facility at the Savannah River Plant

    International Nuclear Information System (INIS)

    Towler, O.A.; Cook, J.R.; Helton, B.D.

    1985-10-01

    Preliminary performance criteria and site selection guides specific to the Savannah River Plant, were developed for a new low-level radioactive waste storage/disposal facility. These site selection guides were applied to seventeen potential sites identified at SRP. The potential site were ranked based on how well they met a set of characteristics considered important in site selection for a low-level radioactive waste disposal facility. The characteristics were given a weighting factor representing its relative importance in meeting site performance criteria. A candidate site was selected and will be the subject of a site characterization program

  18. Graphene–platinum nanocomposite as a sensitive and selective voltammetric sensor for trace level arsenic quantification

    Directory of Open Access Journals (Sweden)

    R. Kempegowda

    2014-01-01

    Full Text Available A simple protocol for the chemical modification of graphene with platinum nanoparticles and its subsequent electroanalytical application toward sensitive and selective determination of arsenic has been described. Chemical modification was carried out by the simultaneous and sequential chemical reduction of graphene oxide and hexachloroplatinic acid in the presence of ethylene glycol as a mild reducing agent. The synthesized graphene–platinum nanocomposite (Gr–nPt has been characterized through infrared spectroscopy, x-ray diffraction study, field emission scanning electron microscopy and cyclic voltammetry (CV techniques. CV and square-wave anodic stripping voltammetry have been used to quantify arsenic. The proposed nanostructure showed linearity in the concentration range 10–100 nM with a detection limit of 1.1 nM. The proposed sensor has been successfully applied to measure trace levels of arsenic present in natural sample matrices like borewell water, polluted lake water, agricultural soil, tomato and spinach leaves.

  19. Low-level radioactive waste technology: a selected, annotated bibliography. [416 references

    Energy Technology Data Exchange (ETDEWEB)

    Fore, C.S.; Carrier, R.F.; Brewster, R.H.; Hyder, L.K.; Barnes, K.A.

    1981-10-01

    This annotated bibliography of 416 references represents the third in a series to be published by the Hazardous Materials Information Center containing scientific, technical, economic, and regulatory information relevant to low-level radioactive waste technology. The bibliography focuses on disposal site, environmental transport, and waste treatment studies as well as general reviews on the subject. The publication covers both domestic and foreign literature for the period 1951 to 1981. Major chapters selected are Chemical and Physical Aspects; Container Design and Performance; Disposal Site; Environmental Transport; General Studies and Reviews; Geology, Hydrology, and Site Resources; Regulatory and Economic Aspects; Social Aspects; Transportation Technology; Waste Production; and Waste Treatment. Entries in each of the chapters are further classified as a field study, laboratory study, theoretical study, or general overview involving one or more of these research areas.

  20. Levels of use of selected components of the Comprehensive Basic Nursing Programme

    Directory of Open Access Journals (Sweden)

    N. S. Gwele

    1996-03-01

    Full Text Available Change in nursing education in South Africa has been characterised by the predominance of the use of power-coercive strategies to effect change. Changes in nursing curricula are legislated through the South African Nursing Council. The Comprehensive Basic Nursing Programme (CBNP became mandatory for all institutions offering basic professional nurse preparation education programmes in this country in 1985. This was a comparative descriptive study aimed at examining the levels of use of 47 nurse educators at four nursing colleges regarding their behaviours and skills in implementing four selected components of the CBNP. The components of the CBNP which formed the focus for this study were teaching to produce nurses capable of (a rendering comprehensive health care, (b nursing holistically, (c thinking critically, and (d learning independently.

  1. Utilities of gossip across organizational levels : Multilevel selection, free-riders, and teams.

    Science.gov (United States)

    Kniffin, Kevin M; Wilson, David Sloan

    2005-09-01

    Gossip is a subject that has been studied by researchers from an array of disciplines with various foci and methods. We measured the content of language use by members of a competitive sports team across 18 months, integrating qualitative ethnographic methods with quantitative sampling and analysis. We hypothesized that the use of gossip will vary significantly depending on whether it is used for self-serving or group-serving purposes. Our results support a model of gossip derived from multilevel selection theory that expects gossip to serve group-beneficial rules when rewards are partitioned at the group level on a scale that permits mutual monitoring. We integrate our case study with earlier studies of gossip conducted by anthropologists, psychologists, and management researchers.

  2. Selective removal of cesium and strontium using porous frameworks from high level nuclear waste.

    Science.gov (United States)

    Aguila, Briana; Banerjee, Debasis; Nie, Zimin; Shin, Yongsoon; Ma, Shengqian; Thallapally, Praveen K

    2016-05-01

    Efficient and cost-effective removal of radioactive (137)Cs and (90)Sr found in spent fuel is an important step for safe, long-term storage of nuclear waste. Solid-state materials such as resins and titanosilicate zeolites have been assessed for the removal of Cs and Sr from aqueous solutions, but there is room for improvement in terms of capacity and selectivity. Herein, we report the Cs(+) and Sr(2+) exchange potential of an ultra stable MOF, namely, MIL-101-SO3H, as a function of different contact times, concentrations, pH levels, and in the presence of competing ions. Our preliminary results suggest that MOFs with suitable ion exchange groups can be promising alternate materials for cesium and strontium removal.

  3. Farm level evaluation of biomass energy operated seed dryer at selected sites of Bangladesh

    International Nuclear Information System (INIS)

    Rahman, S.M.M.; Bhuiyan, M.G.K.; Rahman, M.A.; Baqui, M.A.; Bala, B.K.

    2006-01-01

    Drying is one of the major problem in post harvest and processing of farm produce specially paddy seed in Bangladesh resulting tremendous shortage of quality seed. Evaluation through demonstrations was undertaken for the resource poor farmers at the selected sites to have practical experience of the IRRI-BRRI seed dryer. Viability of the dried paddy was more than 90% after six months of storage. The farmers were satisfied on the performance of the dryer. 68-100% farmers were motivated to hire the dyer during Boro and Aus seasons. Thus, the farm level evaluation and adoption of seed dryer will give a better alternative, aware and motivate the farmers on producing quality seed through proper drying and will contribute increased production

  4. The selection, licensing, and operation of a low-level radioactive waste incinerator

    International Nuclear Information System (INIS)

    Arrowsmith, H.W.; Dalton, D.

    1990-01-01

    The Scientific Ecology Group has just completed the selection, procurement, licensing, and start-up of a low-level radioactive waste incinerator. This incinerator is the only commercial radioactive waste incinerator in the US and was licensed by the Environmental Protection Agency, the State of Tennessee, the City of Oak Ridge, and the Tennessee Valley Authority. This incinerator has a thermal capacity of 13,000,000 BTUs and can burn approximately 1,000 pounds per hour of typical radioactive waste. Waste to be incinerated is sorted in a new waste sorting system at the SEG facility. The sorting is essential to assure that the incinerator will not be damaged by any unexpected waste and to maintain the purity of the incinerator off-gas. The volume reduction expected for typical waste is approximately 100:1. After burning, the incinerator ash is compacted or vitrified before shipment to burial sites

  5. Comparison of low-level waste disposal programs of DOE and selected international countries

    International Nuclear Information System (INIS)

    Meagher, B.G.; Cole, L.T.

    1996-06-01

    The purpose of this report is to examine and compare the approaches and practices of selected countries for disposal of low-level radioactive waste (LLW) with those of the US Department of Energy (DOE). The report addresses the programs for disposing of wastes into engineered LLW disposal facilities and is not intended to address in-situ options and practices associated with environmental restoration activities or the management of mill tailings and mixed LLW. The countries chosen for comparison are France, Sweden, Canada, and the United Kingdom. The countries were selected as typical examples of the LLW programs which have evolved under differing technical constraints, regulatory requirements, and political/social systems. France was the first country to demonstrate use of engineered structure-type disposal facilities. The UK has been actively disposing of LLW since 1959. Sweden has been disposing of LLW since 1983 in an intermediate-depth disposal facility rather than a near-surface disposal facility. To date, Canada has been storing its LLW but will soon begin operation of Canada's first demonstration LLW disposal facility

  6. Denitration of simulated high-level liquid wastes and selective removal of cesium with zeolites

    Energy Technology Data Exchange (ETDEWEB)

    Mimura, Hitoshi; Kanno, Takuji [Tohoku Univ., Sendai (Japan). Research Inst. of Mineral Dressing and Metallurgy; Kimura, Toshiya

    1982-03-01

    Denitration of high-level liquid wastes (HLW) from nuclear fuel reprocessing has been studied. Selective removal of Cs has been also examined with various types of zeolites. The following zeolites were used in this study; Na-synthetic mordenite (NaSM), Na-natural mordenite (NaNM), Na-natural clinoptilolite (NaCP) and H-synthetic mordenites (HSM). The effective denitration is found in the simulated HLW (15 components, 2N HNO/sub 3/ soln.) containing platinum group elements in the case of the addition of formic acid, and the pH of the solution shows the value of 5.4 when the excess formic acid ((HCOOH)/(HNO/sub 3/) = 2.0) was added. Platinum group elements may react as a catalyst for the decomposition of nitric acid and the excess formic acid. The break-through properties of NaSM column are poor for the simulated HLW, and the selective removal of Cs appears to be difficult. On the other hand, good results are obtained in the denitrated HLW, i.e., break-through capacity, total capacity and column utilization are 59.4 (meq./100 g zeolite), 147 (meq./100 g zeolite) and 40.4 (%), respectively. The break-through properties of NaSM and NaNM are superior to those of HSM. The break-through capacity and column utilization increase with an increase in column temperature.

  7. Denitration of simulated high-level liquid wastes and selective removal of cesium with zeolites

    International Nuclear Information System (INIS)

    Mimura, Hitoshi; Kanno, Takuji; Kimura, Toshiya.

    1982-01-01

    Denitration of high-level liquid wastes (HLW) from nuclear fuel reprocessing has been studied. Selective removal of Cs has been also examined with various types of zeolites. The following zeolites were used in this study; Na-synthetic mordenite (NaSM), Na-natural mordenite (NaNM), Na-natural clinoptilolite (NaCP) and H-synthetic mordenites (HSM). The effective denitration is found in the simulated HLW (15 components, 2N HNO 3 soln.) containing platinum group elements in the case of the addition of formic acid, and the pH of the solution shows the value of 5.4 when the excess formic acid ([HCOOH]/[HNO 3 ] = 2.0) was added. Platinum group elements may react as a catalyst for the decomposition of nitric acid and the excess formic acid. The break-through properties of NaSM column are poor for the simulated HLW, and the selective removal of Cs appears to be difficult. On the other hand, good results are obtained in the denitrated HLW, i.e., break-through capacity, total capacity and column utilization are 59.4 (meq./100 g zeolite), 147 (meq./100 g zeolite) and 40.4 (%), respectively. The break-through properties of NaSM and NaNM are superior to those of HSM. The break-through capacity and column utilization increase with an increase in column temperature. (author)

  8. Selection and evaluation of inner material candidates for Spanish high level radioactive waste canisters

    International Nuclear Information System (INIS)

    Puig, Francesc; Dies, Javier; Sevilla, Manuel; Pablo, Joan de; Pueyo, Juan Jose; Miralles, Lourdes; Martinez-Esparza, Aurora

    2007-01-01

    This paper summarizes the work carried out to analyse different alternatives related to the inner material selection of the Spanish high level waste canister for long term storage. The preliminary repository design considers granitic or clay formations, compacted bentonite sealing, corrosion allowing steel canisters and glass bead filling between the fuel assemblies and canister walls. This filling material will have the primary role of avoiding the possibility of a criticality event, which becomes an issue of major importance once the container is finally breached by corrosion and flooded by groundwater. In the first place, a complete set of requirements have been devised as evaluation criteria for candidate materials examination and selection; resulting in a compilation of demands significantly deeper and more exhaustive than any other similar work found in literature, including over 20 requirements and some other general aspects that could involve improvements in repository performance. Secondly, eight materials or material families (cast iron or steel, borosilicate glass, spinel, depleted uranium, dehydrated zeolites, hematite, phosphates and olivine) have been chosen and examined in detail, extracting some relevant conclusions. Either cast iron, borosilicate glass, spinel or depleted uranium are considered to look quite promising for the mentioned purpose. (authors)

  9. The Drosophila Translational Control Element (TCE is required for high-level transcription of many genes that are specifically expressed in testes.

    Directory of Open Access Journals (Sweden)

    Rebeccah J Katzenberger

    Full Text Available To investigate the importance of core promoter elements for tissue-specific transcription of RNA polymerase II genes, we examined testis-specific transcription in Drosophila melanogaster. Bioinformatic analyses of core promoter sequences from 190 genes that are specifically expressed in testes identified a 10 bp A/T-rich motif that is identical to the translational control element (TCE. The TCE functions in the 5' untranslated region of Mst(3CGP mRNAs to repress translation, and it also functions in a heterologous gene to regulate transcription. We found that among genes with focused initiation patterns, the TCE is significantly enriched in core promoters of genes that are specifically expressed in testes but not in core promoters of genes that are specifically expressed in other tissues. The TCE is variably located in core promoters and is conserved in melanogaster subgroup species, but conservation dramatically drops in more distant species. In transgenic flies, short (300-400 bp genomic regions containing a TCE directed testis-specific transcription of a reporter gene. Mutation of the TCE significantly reduced but did not abolish reporter gene transcription indicating that the TCE is important but not essential for transcription activation. Finally, mutation of testis-specific TFIID (tTFIID subunits significantly reduced the transcription of a subset of endogenous TCE-containing but not TCE-lacking genes, suggesting that tTFIID activity is limited to TCE-containing genes but that tTFIID is not an obligatory regulator of TCE-containing genes. Thus, the TCE is a core promoter element in a subset of genes that are specifically expressed in testes. Furthermore, the TCE regulates transcription in the context of short genomic regions, from variable locations in the core promoter, and both dependently and independently of tTFIID. These findings set the stage for determining the mechanism by which the TCE regulates testis-specific transcription and

  10. Studies for a common selection software environment in ATLAS from the Level-2 Trigger to the offline reconstruction

    CERN Document Server

    Wiedenmann, W; Baines, J T M; Bee, C P; Biglietti, M; Bogaerts, A; Boisvert, V; Bosman, M; Brandt, S; Caron, B; Casado, M P; Cataldi, G; Cavalli, D; Cervetto, M; Comune, G; Corso-Radu, A; Di Mattia, A; Díaz-Gómez, M; Dos Anjos, A; Drohan, J; Ellis, Nick; Elsing, M; Epp, B; Etienne, F; Falciano, S; Farilla, A; George, S; Ghete, V M; González, S; Grothe, M; Kaczmarska, A; Karr, K M; Khomich, A; Konstantinidis, N P; Krasny, W; Li, W; Lowe, A; Luminari, L; Meessen, C; Mello, A G; Merino, G; Morettini, P; Moyse, E; Nairz, A; Negri, A; Nikitin, N V; Nisati, A; Padilla, C; Parodi, F; Pérez-Réale, V; Pinfold, J L; Pinto, P; Polesello, G; Qian, Z; Resconi, S; Rosati, S; Scannicchio, D A; Schiavi, C; Schörner-Sadenius, T; Segura, E; De Seixas, J M; Shears, T G; Sivoklokov, S Yu; Smizanska, M; Soluk, R A; Stanescu, C; Tapprogge, Stefan; Touchard, F; Vercesi, V; Watson, A T; Wengler, T; Werner, P; Wheeler, S; Wickens, F J; Wielers, M; Zobernig, G; NSS-MIC 2003 - IEEE Nuclear Science Symposium and Medical Imaging Conference, Part 1

    2004-01-01

    The Atlas High Level Trigger's primary function of event selection will be accomplished with a Level-2 trigger farm and an Event Filter farm, both running software components developed in the Atlas offline reconstruction framework. While this approach provides a unified software framework for event selection, it poses strict requirements on offline components critical for the Level-2 trigger. A Level-2 decision in Atlas must typically be accomplished within 10 ms and with multiple event processing in concurrent threads. In order to address these constraints, prototypes have been developed that incorporate elements of the Atlas Data Flow -, High Level Trigger -, and offline framework software. To realize a homogeneous software environment for offline components in the High Level Trigger, the Level-2 Steering Controller was developed. With electron/gamma- and muon-selection slices it has been shown that the required performance can be reached, if the offline components used are carefully designed and optimized ...

  11. DHT selectively reverses Smad3-mediated/TGF-beta-induced responses through transcriptional down-regulation of Smad3 in prostate epithelial cells.

    Science.gov (United States)

    Song, Kyung; Wang, Hui; Krebs, Tracy L; Wang, Bingcheng; Kelley, Thomas J; Danielpour, David

    2010-10-01

    Androgens suppress TGF-β responses in the prostate through mechanisms that are not fully explored. We have recently reported that 5α-dihydrotestosterone (DHT) suppresses the ability of TGF-β to inhibit proliferation and induce apoptosis of prostatic epithelial cells and provided evidence that such suppression was fueled by transcriptional down-regulation of TGF-β receptor II (ΤβRII). We now show that androgen receptor (AR) activated by DHT suppresses the TGF-β-induced phosphorylation of Sma- and Mad-related protein (Smad)3 in LNCaP cells overexpressing TβRII under the control of a cytomegalovirus promoter, which is not regulated by DHT, suggesting that transcriptional repression of TβRII alone does not fully account for the impact of DHT on TGF-β responses. Instead, we demonstrate that such suppression occurs through loss of total Smad3, resulting from transcriptional suppression of Smad3. We provide evidence that DHT down-regulates the promoter activity of Smad3 in various prostate cancer cell lines, including NRP-154+AR, DU145+AR, LNCaP, and VCaP, at least partly through androgen-dependent inactivation of Sp1. Moreover, we show that overexpression of Smad3 reverses the ability of DHT to protect against TGF-β-induced apoptosis in NRP-154+AR, supporting our model that loss of Smad3 by DHT is involved in the protection against TGF-β-induced apoptosis. Together, these findings suggest that deregulated/enhanced expression and activation of AR in prostate carcinomas may intercept the tumor suppressor function of TGF-β through transcriptional suppression of Smad3, thereby providing new mechanistic insight into the development of castration-resistant prostate cancer.

  12. High levels of absorption in orientation-unbiased, radio-selected 3CR Active Galaxies

    Science.gov (United States)

    Wilkes, Belinda J.; Haas, Martin; Barthel, Peter; Leipski, Christian; Kuraszkiewicz, Joanna; Worrall, Diana; Birkinshaw, Mark; Willner, Steven P.

    2014-08-01

    A critical problem in understanding active galaxies (AGN) is the separation of intrinsic physical differences from observed differences that are due to orientation. Obscuration of the active nucleus is anisotropic and strongly frequency dependent leading to complex selection effects for observations in most wavebands. These can only be quantified using a sample that is sufficiently unbiased to test orientation effects. Low-frequency radio emission is one way to select a close-to orientation-unbiased sample, albeit limited to the minority of AGN with strong radio emission.Recent Chandra, Spitzer and Herschel observations combined with multi-wavelength data for a complete sample of high-redshift (1half the sample is significantly obscured with ratios of unobscured: Compton thin (22 24.2) = 2.5:1.4:1 in these high-luminosity (log L(0.3-8keV) ~ 44-46) sources. These ratios are consistent with current expectations based on modelingthe Cosmic X-ray Background. A strong correlation with radio orientation constrains the geometry of the obscuring disk/torus to have a ~60 degree opening angle and ~12 degree Compton-thick cross-section. The deduced ~50% obscured fraction of the population contrasts with typical estimates of ~20% obscured in optically- and X-ray-selected high-luminosity samples. Once the primary nuclear emission is obscured, AGN X-ray spectra are frequently dominated by unobscured non-nuclear or scattered nuclear emission which cannot be distinguished from direct nuclear emission with a lower obscuration level unless high quality data is available. As a result, both the level of obscuration and the estimated instrinsic luminosities of highly-obscured AGN are likely to be significantly (*10-1000) underestimated for 25-50% of the population. This may explain the lower obscured fractions reported for optical and X-ray samples which have no independent measure of the AGN luminosity. Correcting AGN samples for these underestimated luminosities would result in

  13. Changes in Air CO2 Concentration Differentially Alter Transcript Levels of NtAQP1 and NtPIP2;1 Aquaporin Genes in Tobacco Leaves

    Directory of Open Access Journals (Sweden)

    Francesca Secchi

    2016-04-01

    Full Text Available The aquaporin specific control on water versus carbon pathways in leaves is pivotal in controlling gas exchange and leaf hydraulics. We investigated whether Nicotiana tabacum aquaporin 1 (NtAQP1 and Nicotiana tabacum plasma membrane intrinsic protein 2;1 (NtPIP2;1 gene expression varies in tobacco leaves subjected to treatments with different CO2 concentrations (ranging from 0 to 800 ppm, inducing changes in photosynthesis, stomatal regulation and water evaporation from the leaf. Changes in air CO2 concentration ([CO2] affected net photosynthesis (Pn and leaf substomatal [CO2] (Ci. Pn was slightly negative at 0 ppm air CO2; it was one-third that of ambient controls at 200 ppm, and not different from controls at 800 ppm. Leaves fed with 800 ppm [CO2] showed one-third reduced stomatal conductance (gs and transpiration (E, and their gs was in turn slightly lower than in 200 ppm– and in 0 ppm–treated leaves. The 800 ppm air [CO2] strongly impaired both NtAQP1 and NtPIP2;1 gene expression, whereas 0 ppm air [CO2], a concentration below any in vivo possible conditions and specifically chosen to maximize the gene expression alteration, increased only the NtAQP1 transcript level. We propose that NtAQP1 expression, an aquaporin devoted to CO2 transport, positively responds to CO2 scarcity in the air in the whole range 0–800 ppm. On the contrary, expression of NtPIP2;1, an aquaporin not devoted to CO2 transport, is related to water balance in the leaf, and changes in parallel with gs. These observations fit in a model where upregulation of leaf aquaporins is activated at low Ci, while downregulation occurs when high Ci saturates photosynthesis and causes stomatal closure.

  14. Antisense oligonucleotides targeting translation inhibitory elements in 5' UTRs can selectively increase protein levels.

    Science.gov (United States)

    Liang, Xue-Hai; Sun, Hong; Shen, Wen; Wang, Shiyu; Yao, Joyee; Migawa, Michael T; Bui, Huynh-Hoa; Damle, Sagar S; Riney, Stan; Graham, Mark J; Crooke, Rosanne M; Crooke, Stanley T

    2017-09-19

    A variety of diseases are caused by deficiencies in amounts or activity of key proteins. An approach that increases the amount of a specific protein might be of therapeutic benefit. We reasoned that translation could be specifically enhanced using trans-acting agents that counter the function of negative regulatory elements present in the 5' UTRs of some mRNAs. We recently showed that translation can be enhanced by antisense oligonucleotides (ASOs) that target upstream open reading frames. Here we report the amount of a protein can also be selectively increased using ASOs designed to hybridize to other translation inhibitory elements in 5' UTRs. Levels of human RNASEH1, LDLR, and ACP1 and of mouse ACP1 and ARF1 were increased up to 2.7-fold in different cell types and species upon treatment with chemically modified ASOs targeting 5' UTR inhibitory regions in the mRNAs encoding these proteins. The activities of ASOs in enhancing translation were sequence and position dependent and required helicase activity. The ASOs appear to improve the recruitment of translation initiation factors to the target mRNA. Importantly, ASOs targeting ACP1 mRNA significantly increased the level of ACP1 protein in mice, suggesting that this approach has therapeutic and research potentials. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  15. The expression of pre- and postcopulatory sexually selected traits reflects levels of dietary stress in guppies.

    Directory of Open Access Journals (Sweden)

    Md Moshiur Rahman

    Full Text Available Environmental and ecological conditions can shape the evolution of life history traits in many animals. Among such factors, food or nutrition availability can play an important evolutionary role in moderating an animal's life history traits, particularly sexually selected traits. Here, we test whether diet quantity and/or composition in the form of omega-3 long chain polyunsaturated fatty acids (here termed 'n3LC' influence the expression of pre- and postcopulatory traits in the guppy (Poecilia reticulata, a livebearing poeciliid fish. We assigned males haphazardly to one of two experimental diets supplemented with n3LC, and each of these diet treatments was further divided into two diet 'quantity' treatments. Our experimental design therefore explored the main and interacting effects of two factors (n3LC content and diet quantity on the expression of precopulatory (sexual behaviour and sexual ornamentation, including the size, number and spectral properties of colour spots and postcopulatory (the velocity, viability, number and length of sperm sexually selected traits. Our study revealed that diet quantity had significant effects on most of the pre- and postcopulatory traits, while n3LC manipulation had a significant effect on sperm traits and in particular on sperm viability. Our analyses also revealed interacting effects of diet quantity and n3LC levels on courtship displays, and the area of orange and iridescent colour spots in the males' colour patterns. We also confirmed that our dietary manipulations of n3LC resulted in the differential uptake of n3LC in body and testes tissues in the different n3LC groups. This study reveals the effects of diet quantity and n3LC on behavioural, ornamental and ejaculate traits in P. reticulata and underscores the likely role that diet plays in maintaining the high variability in these condition-dependent sexual traits.

  16. Corticosteroid receptors adopt distinct cyclical transcriptional signatures.

    Science.gov (United States)

    Le Billan, Florian; Amazit, Larbi; Bleakley, Kevin; Xue, Qiong-Yao; Pussard, Eric; Lhadj, Christophe; Kolkhof, Peter; Viengchareun, Say; Fagart, Jérôme; Lombès, Marc

    2018-05-07

    Mineralocorticoid receptors (MRs) and glucocorticoid receptors (GRs) are two closely related hormone-activated transcription factors that regulate major pathophysiologic functions. High homology between these receptors accounts for the crossbinding of their corresponding ligands, MR being activated by both aldosterone and cortisol and GR essentially activated by cortisol. Their coexpression and ability to bind similar DNA motifs highlight the need to investigate their respective contributions to overall corticosteroid signaling. Here, we decipher the transcriptional regulatory mechanisms that underlie selective effects of MRs and GRs on shared genomic targets in a human renal cellular model. Kinetic, serial, and sequential chromatin immunoprecipitation approaches were performed on the period circadian protein 1 ( PER1) target gene, providing evidence that both receptors dynamically and cyclically interact at the same target promoter in a specific and distinct transcriptional signature. During this process, both receptors regulate PER1 gene by binding as homo- or heterodimers to the same promoter region. Our results suggest a novel level of MR-GR target gene regulation, which should be considered for a better and integrated understanding of corticosteroid-related pathophysiology.-Le Billan, F., Amazit, L., Bleakley, K., Xue, Q.-Y., Pussard, E., Lhadj, C., Kolkhof, P., Viengchareun, S., Fagart, J., Lombès, M. Corticosteroid receptors adopt distinct cyclical transcriptional signatures.

  17. What's New in Children's Literature for the Children of Louisiana? A Selected Annotated Bibliography with Readability Levels (Selected) and Associated Louisiana Content Standards

    Science.gov (United States)

    Webre, Elizabeth C.

    2011-01-01

    An annotated list of children's books published within the last 15 years and related to Louisiana culture, environment, and economics are linked to the Louisiana Content Standards. Readability levels of selected books are included, providing guidance as to whether a book is appropriate for independent student use. The thirty-three books listed are…

  18. Induction of annexin-1 at transcriptional and posttranscriptional level in rat brain by methylprednisolone and the 21-aminosteroid U74389F

    NARCIS (Netherlands)

    Voermans, PH; Go, KG; TerHorst, GJ; Ruiters, MHJ; Solito, E; Parente, L

    1996-01-01

    BRAIN tissue of rats pretreated with methylprednisolone or with the 21-aminosteroid U74389F, and that of untreated control rats, was assessed for the expression of annexin-l (Anx-1) and the transcription of its mRNA. For this purpose Anx-1 cDNA was amplified and simultaneously a T7-RNA-polymerase

  19. Classical Mus musculus Igκ enhancers support transcription but not high level somatic hypermutation from a V-lambda promoter in chicken DT40 cells.

    Directory of Open Access Journals (Sweden)

    Naga Rama Kothapalli

    2011-04-01

    Full Text Available Somatic hypermutation (SHM of immunoglobulin genes is initiated by activation-induced cytidine deaminase (AID in activated B cells. This process is strictly dependent on transcription. Hence, cis-acting transcriptional control elements have been proposed to target SHM to immunoglobulin loci. The Mus musculus Igκ locus is regulated by the intronic enhancer (iE/MAR and the 3' enhancer (3'E, and multiple studies using transgenic and knock-out approaches in mice and cell lines have reported somewhat contradictory results about the function of these enhancers in AID-mediated sequence diversification. Here we show that the M. musculus iE/MAR and 3'E elements are active solely as transcriptional enhancer when placed in the context of the IGL locus in Gallus gallus DT40 cells, but they are very inefficient in targeting AID-mediated mutation events to this locus. This suggests that either key components of the cis-regulatory targeting elements reside outside the murine Igκ transcriptional enhancer sequences, or that the targeting of AID activity to Ig loci occurs by largely species-specific mechanisms.

  20. SOXE transcription factors form selective dimers on non-compact DNA motifs through multifaceted interactions between dimerization and high-mobility group domains.

    Science.gov (United States)

    Huang, Yong-Heng; Jankowski, Aleksander; Cheah, Kathryn S E; Prabhakar, Shyam; Jauch, Ralf

    2015-05-27

    The SOXE transcription factors SOX8, SOX9 and SOX10 are master regulators of mammalian development directing sex determination, gliogenesis, pancreas specification and neural crest development. We identified a set of palindromic SOX binding sites specifically enriched in regulatory regions of melanoma cells. SOXE proteins homodimerize on these sequences with high cooperativity. In contrast to other transcription factor dimers, which are typically rigidly spaced, SOXE group proteins can bind cooperatively at a wide range of dimer spacings. Using truncated forms of SOXE proteins, we show that a single dimerization (DIM) domain, that precedes the DNA binding high mobility group (HMG) domain, is sufficient for dimer formation, suggesting that DIM : HMG rather than DIM:DIM interactions mediate the dimerization. All SOXE members can also heterodimerize in this fashion, whereas SOXE heterodimers with SOX2, SOX4, SOX6 and SOX18 are not supported. We propose a structural model where SOXE-specific intramolecular DIM:HMG interactions are allosterically communicated to the HMG of juxtaposed molecules. Collectively, SOXE factors evolved a unique mode to combinatorially regulate their target genes that relies on a multifaceted interplay between the HMG and DIM domains. This property potentially extends further the diversity of target genes and cell-specific functions that are regulated by SOXE proteins.

  1. SOXE transcription factors form selective dimers on non-compact DNA motifs through multifaceted interactions between dimerization and high-mobility group domains

    Science.gov (United States)

    Huang, Yong-Heng; Jankowski, Aleksander; Cheah, Kathryn S. E.; Prabhakar, Shyam; Jauch, Ralf

    2015-01-01

    The SOXE transcription factors SOX8, SOX9 and SOX10 are master regulators of mammalian development directing sex determination, gliogenesis, pancreas specification and neural crest development. We identified a set of palindromic SOX binding sites specifically enriched in regulatory regions of melanoma cells. SOXE proteins homodimerize on these sequences with high cooperativity. In contrast to other transcription factor dimers, which are typically rigidly spaced, SOXE group proteins can bind cooperatively at a wide range of dimer spacings. Using truncated forms of SOXE proteins, we show that a single dimerization (DIM) domain, that precedes the DNA binding high mobility group (HMG) domain, is sufficient for dimer formation, suggesting that DIM : HMG rather than DIM:DIM interactions mediate the dimerization. All SOXE members can also heterodimerize in this fashion, whereas SOXE heterodimers with SOX2, SOX4, SOX6 and SOX18 are not supported. We propose a structural model where SOXE-specific intramolecular DIM:HMG interactions are allosterically communicated to the HMG of juxtaposed molecules. Collectively, SOXE factors evolved a unique mode to combinatorially regulate their target genes that relies on a multifaceted interplay between the HMG and DIM domains. This property potentially extends further the diversity of target genes and cell-specific functions that are regulated by SOXE proteins. PMID:26013289

  2. Xylan degradation by the human gut Bacteroides xylanisolvens XB1A(T) involves two distinct gene clusters that are linked at the transcriptional level.

    Science.gov (United States)

    Despres, Jordane; Forano, Evelyne; Lepercq, Pascale; Comtet-Marre, Sophie; Jubelin, Gregory; Chambon, Christophe; Yeoman, Carl J; Berg Miller, Margaret E; Fields, Christopher J; Martens, Eric; Terrapon, Nicolas; Henrissat, Bernard; White, Bryan A; Mosoni, Pascale

    2016-05-04

    Plant cell wall (PCW) polysaccharides and especially xylans constitute an important part of human diet. Xylans are not degraded by human digestive enzymes in the upper digestive tract and therefore reach the colon where they are subjected to extensive degradation by some members of the symbiotic microbiota. Xylanolytic bacteria are the first degraders of these complex polysaccharides and they release breakdown products that can have beneficial effects on human health. In order to understand better how these bacteria metabolize xylans in the colon, this study was undertaken to investigate xylan breakdown by the prominent human gut symbiont Bacteroides xylanisolvens XB1A(T). Transcriptomic analyses of B. xylanisolvens XB1A(T) grown on insoluble oat-spelt xylan (OSX) at mid- and late-log phases highlighted genes in a polysaccharide utilization locus (PUL), hereafter called PUL 43, and genes in a fragmentary remnant of another PUL, hereafter referred to as rPUL 70, which were highly overexpressed on OSX relative to glucose. Proteomic analyses supported the up-regulation of several genes belonging to PUL 43 and showed the important over-production of a CBM4-containing GH10 endo-xylanase. We also show that PUL 43 is organized in two operons and that the knockout of the PUL 43 sensor/regulator HTCS gene blocked the growth of the mutant on insoluble OSX and soluble wheat arabinoxylan (WAX). The mutation not only repressed gene expression in the PUL 43 operons but also repressed gene expression in rPUL 70. This study shows that xylan degradation by B. xylanisolvens XB1A(T) is orchestrated by one PUL and one PUL remnant that are linked at the transcriptional level. Coupled to studies on other xylanolytic Bacteroides species, our data emphasize the importance of one peculiar CBM4-containing GH10 endo-xylanase in xylan breakdown and that this modular enzyme may be used as a functional marker of xylan degradation in the human gut. Our results also suggest that B. xylanisolvens

  3. Rationally designed, heterologous S. cerevisiae transcripts expose novel expression determinants

    Science.gov (United States)

    Ben-Yehezkel, Tuval; Atar, Shimshi; Zur, Hadas; Diament, Alon; Goz, Eli; Marx, Tzipy; Cohen, Rafael; Dana, Alexandra; Feldman, Anna; Shapiro, Ehud; Tuller, Tamir

    2015-01-01

    Deducing generic causal relations between RNA transcript features and protein expression profiles from endogenous gene expression data remains a major unsolved problem in biology. The analysis of gene expression from heterologous genes contributes significantly to solving this problem, but has been heavily biased toward the study of the effect of 5′ transcript regions and to prokaryotes. Here, we employ a synthetic biology driven approach that systematically differentiates the effect of different regions of the transcript on gene expression up to 240 nucleotides into the ORF. This enabled us to discover new causal effects between features in previously unexplored regions of transcripts, and gene expression in natural regimes. We rationally designed, constructed, and analyzed 383 gene variants of the viral HRSVgp04 gene ORF, with multiple synonymous mutations at key positions along the transcript in the eukaryote S. cerevisiae. Our results show that a few silent mutations at the 5′UTR can have a dramatic effect of up to 15 fold change on protein levels, and that even synonymous mutations in positions more than 120 nucleotides downstream from the ORF 5′end can modulate protein levels up to 160%–300%. We demonstrate that the correlation between protein levels and folding energy increases with the significance of the level of selection of the latter in endogenous genes, reinforcing the notion that selection for folding strength in different parts of the ORF is related to translation regulation. Our measured protein abundance correlates notably(correlation up to r = 0.62 (p=0.0013)) with mean relative codon decoding times, based on ribosomal densities (Ribo-Seq) in endogenous genes, supporting the conjecture that translation elongation and adaptation to the tRNA pool can modify protein levels in a causal/direct manner. This report provides an improved understanding of transcript evolution, design principles of gene expression regulation, and suggests simple

  4. Cortisol levels and expression of selected stress- and apoptosis-related genes in the embryos of Atlantic cod, Gadus morhua following short-term exposure to air

    DEFF Research Database (Denmark)

    Marlowe, Christopher; Caipang, A.; Fagutao, Ferdinand F.

    2015-01-01

    Embryos (morula stage) of Atlantic cod, Gadus morhua L., were collected and subjected to air exposure for 2 min. followed by recovery at ambient conditions in the rearing container. Total immunoreactive cortisol and transcription of selected stress- and apoptosis-related genes of the embryos were...

  5. Selection of liquid-level monitoring method for the Oak Ridge National Laboratory inactive liquid low-level waste tanks, remedial investigation/feasibility study

    International Nuclear Information System (INIS)

    1994-11-01

    Several of the inactive liquid low-level waste (LLLW) tanks at Oak Ridge National Laboratory contain residual wastes in liquid or solid (sludge) form or both. A plan of action has been developed to ensure that potential environmental impacts from the waste remaining in the inactive LLLW tank systems are minimized. This document describes the evaluation and selection of a methodology for monitoring the level of the liquid in inactive LLLW tanks. Criteria are established for comparison of existing level monitoring and leak testing methods; a preferred method is selected and a decision methodology for monitoring the level of the liquid in the tanks is presented for implementation. The methodology selected can be used to continuously monitor the tanks pending disposition of the wastes for treatment and disposal. Tanks that are empty, are scheduled to be emptied in the near future, or have liquid contents that are very low risk to the environment were not considered to be candidates for installing level monitoring. Tanks requiring new monitoring equipment were provided with conductivity probes; tanks with existing level monitoring instrumentation were not modified. The resulting data will be analyzed to determine inactive LLLW tank liquid level trends as a function of time

  6. Dissecting the expression relationships between RNA-binding proteins and their cognate targets in eukaryotic post-transcriptional regulatory networks

    Science.gov (United States)

    Nishtala, Sneha; Neelamraju, Yaseswini; Janga, Sarath Chandra

    2016-05-01

    RNA-binding proteins (RBPs) are pivotal in orchestrating several steps in the metabolism of RNA in eukaryotes thereby controlling an extensive network of RBP-RNA interactions. Here, we employed CLIP (cross-linking immunoprecipitation)-seq datasets for 60 human RBPs and RIP-ChIP (RNP immunoprecipitation-microarray) data for 69 yeast RBPs to construct a network of genome-wide RBP- target RNA interactions for each RBP. We show in humans that majority (~78%) of the RBPs are strongly associated with their target transcripts at transcript level while ~95% of the studied RBPs were also found to be strongly associated with expression levels of target transcripts when protein expression levels of RBPs were employed. At transcript level, RBP - RNA interaction data for the yeast genome, exhibited a strong association for 63% of the RBPs, confirming the association to be conserved across large phylogenetic distances. Analysis to uncover the features contributing to these associations revealed the number of target transcripts and length of the selected protein-coding transcript of an RBP at the transcript level while intensity of the CLIP signal, number of RNA-Binding domains, location of the binding site on the transcript, to be significant at the protein level. Our analysis will contribute to improved modelling and prediction of post-transcriptional networks.

  7. Evaluation of an Improved Branch-Site Likelihood Method for Detecting Positive Selection at the Molecular Level

    DEFF Research Database (Denmark)

    Zhang, Jianzhi; Nielsen, Rasmus; Yang, Ziheng

    2005-01-01

    of interest, while test 2 had acceptable false-positive rates and appeared robust against violations of model assumptions. As test 2 is a direct test of positive selection on the lineages of interest, it is referred to as the branch-site test of positive selection and is recommended for use in real data......Detecting positive Darwinian selection at the DNA sequence level has been a subject of considerable interest. However, positive selection is difficult to detect because it often operates episodically on a few amino acid sites, and the signal may be masked by negative selection. Several methods have...... been developed to test positive selection that acts on given branches (branch methods) or on a subset of sites (site methods). Recently, Yang, Z., and R. Nielsen (2002. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol. Biol. Evol. 19...

  8. Topography of sound level representation in the FM sweep selective region of the pallid bat auditory cortex.

    Science.gov (United States)

    Measor, Kevin; Yarrow, Stuart; Razak, Khaleel A

    2018-05-26

    Sound level processing is a fundamental function of the auditory system. To determine how the cortex represents sound level, it is important to quantify how changes in level alter the spatiotemporal structure of cortical ensemble activity. This is particularly true for echolocating bats that have control over, and often rapidly adjust, call level to actively change echo level. To understand how cortical activity may change with sound level, here we mapped response rate and latency changes with sound level in the auditory cortex of the pallid bat. The pallid bat uses a 60-30 kHz downward frequency modulated (FM) sweep for echolocation. Neurons tuned to frequencies between 30 and 70 kHz in the auditory cortex are selective for the properties of FM sweeps used in echolocation forming the FM sweep selective region (FMSR). The FMSR is strongly selective for sound level between 30 and 50 dB SPL. Here we mapped the topography of level selectivity in the FMSR using downward FM sweeps and show that neurons with more monotonic rate level functions are located in caudomedial regions of the FMSR overlapping with high frequency (50-60 kHz) neurons. Non-monotonic neurons dominate the FMSR, and are distributed across the entire region, but there is no evidence for amplitopy. We also examined how first spike latency of FMSR neurons change with sound level. The majority of FMSR neurons exhibit paradoxical latency shift wherein the latency increases with sound level. Moreover, neurons with paradoxical latency shifts are more strongly level selective and are tuned to lower sound level than neurons in which latencies decrease with level. These data indicate a clustered arrangement of neurons according to monotonicity, with no strong evidence for finer scale topography, in the FMSR. The latency analysis suggests mechanisms for strong level selectivity that is based on relative timing of excitatory and inhibitory inputs. Taken together, these data suggest how the spatiotemporal

  9. Growth, Morphology and Growth Related Hormone Level in Kappaphycus alvarezii Produced by Mass Selection in Gorontalo Waters, Indonesia

    Directory of Open Access Journals (Sweden)

    Siti Fadilah

    2016-01-01

    Full Text Available The use of high quality seed can support the success of the seaweed cultivation. This study was conducted to evaluate the growth performance, morphology and growth related hormone level of brown strain seaweed Kappaphycus alvarezii seed produced by mass selection. Selection was performed in the Tomini Gulf, Gorontalo, based on mass selection of seaweed seed protocol with a slight modification in cut-off 10% of the highest daily growth rate. Selection was carried out for four generations. The selected 4th generation of seed was then used in cultivation performance test in the Celebes Sea, North Gorontalo, for three production cycles. The results showed that the selected K. alvarezii has higher clump weight and daily growth rate, longer thallus, more number of branches, and shorter internodes compared to the unselected control and seaweed from the farmer as external control. Furthermore, total sugar content, levels of kinetin hormone and kinetin:indole-3-acetic acid ratio were higher in selected seaweeds than that of unselected control and external control. Thus, mass selection method could be used to produce high growth of seed, and kinetin and indole-3-acetic acid play an important role in growth of K. alvarezii.

  10. Molecular Tools for the Selective Detection of Nine Diatom Species Biomarkers of Various Water Quality Levels

    Directory of Open Access Journals (Sweden)

    Lucia Cimarelli

    2015-05-01

    Full Text Available Our understanding of the composition of diatom communities and their response to environmental changes is currently limited by laborious taxonomic identification procedures. Advances in molecular technologies are expected to contribute more efficient, robust and sensitive tools for the detection of these ecologically relevant microorganisms. There is a need to explore and test phylogenetic markers as an alternative to the use of rRNA genes, whose limited sequence divergence does not allow the accurate discrimination of diatoms at the species level. In this work, nine diatom species belonging to eight genera, isolated from epylithic environmental samples collected in central Italy, were chosen to implement a panel of diatoms covering the full range of ecological status of freshwaters. The procedure described in this work relies on the PCR amplification of specific regions in two conserved diatom genes, elongation factor 1-a (eEF1-a and silicic acid transporter (SIT, as a first step to narrow down the complexity of the targets, followed by microarray hybridization experiments. Oligonucleotide probes with the potential to discriminate closely related species were designed taking into account the genetic polymorphisms found in target genes. These probes were tested, refined and validated on a small-scale prototype DNA chip. Overall, we obtained 17 highly specific probes targeting eEF1-a and SIT, along with 19 probes having lower discriminatory power recognizing at the same time two or three species. This basic array was validated in a laboratory setting and is ready for tests with crude environmental samples eventually to be scaled-up to include a larger panel of diatoms. Its possible use for the simultaneous detection of diatoms selected from the classes of water quality identified by the European Water Framework Directive is discussed.

  11. ENHANCED DOE HIGH LEVEL WASTE MELTER THROUGHPUT STUDIES: SRNL GLASS SELECTION STRATEGY

    Energy Technology Data Exchange (ETDEWEB)

    Raszewski, F; Tommy Edwards, T; David Peeler, D

    2008-01-23

    The Department of Energy has authorized a team of glass formulation and processing experts at the Savannah River National Laboratory (SRNL), the Pacific Northwest National Laboratory (PNNL), and the Vitreous State Laboratory (VSL) at Catholic University of America to develop a systematic approach to increase high level waste melter throughput (by increasing waste loading with minimal or positive impacts on melt rate). This task is aimed at proof-of-principle testing and the development of tools to improve waste loading and melt rate, which will lead to higher waste throughput. Four specific tasks have been proposed to meet these objectives (for details, see WSRC-STI-2007-00483): (1) Integration and Oversight, (2) Crystal Accumulation Modeling (led by PNNL)/Higher Waste Loading Glasses (led by SRNL), (3) Melt Rate Evaluation and Modeling, and (4) Melter Scale Demonstrations. Task 2, Crystal Accumulation Modeling/Higher Waste Loading Glasses is the focus of this report. The objective of this study is to provide supplemental data to support the possible use of alternative melter technologies and/or implementation of alternative process control models or strategies to target higher waste loadings (WLs) for the Defense Waste Processing Facility (DWPF)--ultimately leading to higher waste throughputs and a reduced mission life. The glass selection strategy discussed in this report was developed to gain insight into specific technical issues that could limit or compromise the ability of glass formulation efforts to target higher WLs for future sludge batches at the Savannah River Site (SRS). These technical issues include Al-dissolution, higher TiO{sub 2} limits and homogeneity issues for coupled-operations, Al{sub 2}O{sub 3} solubility, and nepheline formation. To address these technical issues, a test matrix of 28 glass compositions has been developed based on 5 different sludge projections for future processing. The glasses will be fabricated and characterized based on

  12. Evaluation of noise level at intensive care units in selected hospitals of Sanandaj

    Directory of Open Access Journals (Sweden)

    Nammam Ali Azadi

    2015-08-01

    Conclusion: We found the noise levels were always above the EPA thresholds at all three hospitals both during the day and night. It is recommended to train hospital officials and staffs for keeping noise levels to an acceptable level.

  13. Area selection for a geological repository of high level radioactive waste in China

    International Nuclear Information System (INIS)

    Jin Yuanxin; Wang Ju; Chen Weiming; Guo Yonghai; Su Rui; Zhao Honggang; Xu Guoqing

    2012-01-01

    China started research on HLW disposal in 1985 and 6 areas, including Northwest, Southwest, East China, South China, Inner Mongolia and Xinjiang area, are selected. The results show that the Northwest area has obvious comprehensive advantages, which can be considered as the first area for site selection, while site characterization and comparison research in the area should be continued. (authors)

  14. Early and Late Trisporoids Differentially Regulate β-Carotene Production and Gene Transcript Levels in the Mucoralean Fungi Blakeslea trispora and Mucor mucedo

    Science.gov (United States)

    Sahadevan, Yamuna; Richter-Fecken, Mareike; Kaerger, Kerstin; Voigt, Kerstin

    2013-01-01

    The multistep cleavage of carotenoids in Mucorales during the sexual phase results in a cocktail of trisporic acid (C18) sex pheromones. We hypothesized that the C18 trisporoid intermediates have a specific regulatory function for sex pheromone production and carotenogenesis that varies with genus/species and vegetative and sexual phases of their life cycles. Real-time quantitative PCR kinetics determined for Blakeslea trispora displayed a very high transcript turnover in the gene for carotenoid cleavage dioxygenase, tsp3, during the sexual phase. An in vivo enzyme assay and chromatographic analysis led to the identification of β-apo-12′-carotenal as the first apocarotenoid involved in trisporic acid biosynthesis in B. trispora. Supplementation of C18 trisporoids, namely D'orenone, methyl trisporate C, and trisporin C, increased tsp3 transcripts in the plus compared to minus partners. Interestingly, the tsp1 gene, which is involved in trisporic acid biosynthesis, was downregulated compared to tsp3 irrespective of asexual or sexual phase. Only the minus partners of both B. trispora and Mucor mucedo had enhanced β-carotene production after treatment with C20 apocarotenoids, 15 different trisporoids, and their analogues. We conclude that the apocarotenoids and trisporoids influence gene transcription and metabolite production, depending upon the fungal strain, corresponding genus, and developmental phase, representing a “chemical dialect” during sexual communication. PMID:24056470

  15. Comparison of transcriptional heterogeneity of eight genes between batch Desulfovibrio vulgaris biofilm and planktonic culture at a single-cell level

    Directory of Open Access Journals (Sweden)

    Zhenhua eQi

    2016-04-01

    Full Text Available Sulfate-reducing bacteria (SRB biofilm formed on metal surfaces can change the physicochemical properties of metals and cause metal corrosion. To enhance understanding of differential gene expression in Desulfovibrio vulgaris under planktonic and biofilm growth modes, a single-cell based RT-qPCR approach was applied to determine gene expression levels of 8 selected target genes in four sets of the 31 individual cells isolated from each growth condition (i.e., biofilm formed on a stainless steel (SS) and planktonic cultures, exponential and stationary phases. The results showed obvious gene-expression heterogeneity for the target genes among D. vulgaris single cells of both biofilm and planktonic cultures. In addition, an increased gene-expression heterogeneity in the D. vulgaris biofilm when compared with the planktonic culture was also observed for seven out of eight selected genes, which may be contributing to the increased complexity in terms of structures and morphology in the biofilm. Moreover, the results showed up-regulation of DVU0281 gene encoding exopolysaccharide biosynthesis protein, and down-regulation of genes involved in energy metabolism (i.e., DVU0434 and DVU0588, stress responses (i.e., DVU2410 and response regulator (i.e., DVU3062 in the D. vulgaris biofilm cells. Finally, the gene (DVU2571 involved in iron transportation was found down-regulated, and two genes (DVU1340 and DVU1397 involved in ferric uptake repressor and iron storage were up-regulated in D. vulgaris biofilm, suggesting their possible roles in maintaining normal metabolism of the D. vulgaris biofilm under environments of high concentration of iron. This study showed that the single-cell based analysis could be a useful approach in deciphering metabolism of microbial biofilms.

  16. DOE hearing on the draft area recommendation report for the Crystalline Repository Project, Lake Region High School, Bridgton, Maine, April 5, 1986: Volume 5: Transcript of proceedings

    International Nuclear Information System (INIS)

    1986-01-01

    This document contains a transcript of the comments of 15 witnesses. These meetings were held to hear the public's comments regarding the selection of a site for a second high-level radioactive waste repository

  17. DOE hearing on the draft area recommendation report for the Crystalline Repository Project, Ada High School Gymnasium, Ada, Minnesota, April 3, 1986: Transcript of proceedings

    International Nuclear Information System (INIS)

    1986-01-01

    This document contains a transcript of the comments of 64 witnesses. These meetings were held to hear the public's comments regarding the selection of a site for a second high-level radioactive waste repository

  18. DOE hearing on the draft area recommendation report for the Crystalline Repository Project, Penobscot Community Building, Indian Island, Maine: Volume 2, April 1, 1986: Transcript of proceedings

    International Nuclear Information System (INIS)

    1986-01-01

    This document contains a transcript of the comments of 10 witnesses. These meetings were held to hear public comments regarding the selection of a site for a second high-level nuclear waste repository

  19. DOE hearing on the draft area recommendation report for the Crystalline Repository Project, Kennett High School, Conway, New Hampshire, April 14, 1986: Volume 1: Transcript of proceedings

    International Nuclear Information System (INIS)

    1986-01-01

    This document contains a transcript of the comments of 18 witnesses. These meetings were held to hear public comments regarding the selection of a site for a second high-level nuclear waste repository

  20. DOE hearing on the draft area recommendation report for the Crystalline Repository Project, State Museum Auditorium, Trenton, New Jersey, April 10, 1986: Transcript of proceedings

    International Nuclear Information System (INIS)

    1986-01-01

    This document contains a transcript of the comments of a single witness. These meetings were held to hear public comments regarding the selection of a site for a second high-level nuclear waste repository

  1. DOE hearing on the draft area recommendation report for the Crystalline Repository Project, Mattanawcook Academy, Lincoln, Maine: Volume 2, April 4, 1986: Transcript of proceedings

    International Nuclear Information System (INIS)

    1986-01-01

    This document contains a transcript of the comments of 11 witnesses. These meetings were held to hear public comments regarding the selection of a site for a second high-level nuclear waste repository

  2. DOE hearing on the draft area recommendation report for the Crystalline Repository Project, Concord City Auditorium, Concord, New Hampshire: Volume 1, April 4, 1986: Transcript of proceedings

    International Nuclear Information System (INIS)

    1986-01-01

    This document contains a transcript of the comments of 29 witnesses. These meetings were held to hear public comments regarding the selection of a site for a second high-level nuclear waste repository

  3. DOE hearing on the draft area recommendation report for the Crystalline Repository Project, Calais High School, Calais, Maine, April 8, 1986: Volume 2: Transcript of proceedings

    International Nuclear Information System (INIS)

    1986-01-01

    This document contains a transcript of the comments of 32 witnesses. These meetings were held to hear the public's comments regarding the selection of a site for a second high-level radioactive waste repository

  4. DOE hearing on the draft area recommendation report for the Crystalline Repository Project, Kennett High School, Conway, New Hampshire: Volume 2, April 14, 1986: Transcript of proceedings

    International Nuclear Information System (INIS)

    1986-01-01

    This document contains a transcript of the comments of 15 witnesses. These meetings were held to hear public comments regarding the selection of a site for a second high-level nuclear waste repository

  5. DOE hearing on the draft area recommendation report for the Crystalline Repository Project, Foley High School, Foley, Minnesota, April 7, 1986: Transcript of proceedings

    International Nuclear Information System (INIS)

    1986-01-01

    This document contains a transcript of the comments of 40 witnesses. These meetings were held to hear public comments regarding the selection of a site for a second high-level nuclear waste repository

  6. DOE hearing on the draft area recommendation report for the Crystalline Repository Project, Portland High School, Portland, Maine: Volume 1, March 25, 1986: Transcript of proceedings

    International Nuclear Information System (INIS)

    1986-01-01

    This document contains a transcript of the comments of 13 witnesses. These meetings were held to hear public comments regarding the selection of a site for a second high-level nuclear waste repository

  7. DOE hearing on the Draft Area Recommendation Report for the Crystalline Repository Project, Ashland High School, Ashland, Wisconsin, Session 1: Transcript of proceedings

    International Nuclear Information System (INIS)

    1986-01-01

    This document contains a transcript of the comments of more than 35 witnesses. These meetings were held to hear public comments regarding the selection of a site for a second high-level nuclear waste repository

  8. DOE hearing on the draft area recommendation report for the Crystalline Repository Project, Concord City Auditorium, Concord, New Hampshire: Volume 2, April 4, 1986: Transcript of proceedings

    International Nuclear Information System (INIS)

    1987-01-01

    This document contains a transcript of the comments of 42 witnesses. These meetings were held to hear public comments regarding the selection of a site for a second high-level nuclear waste repository

  9. DOE hearing on the draft area recommendation report for the Crystalline Repository Project, Loganville High School, Loganville, Georgia, March 25, 1986: Transcript of Proceedings

    International Nuclear Information System (INIS)

    1986-01-01

    This document contains a transcript of the comments of 32 witnesses. These meetings were held to hear public comments regarding the selection of a site for a second high-level nuclear waste repository

  10. DOE hearing on the draft area recommendation report for the Crystalline Repository project, Waupaca, Wisconsin, April 8, 1986: Transcript of Proceedings

    International Nuclear Information System (INIS)

    1986-01-01

    This document contains a transcript of the comments of 29 witnesses. These meetings were held to hear public comments regarding the selection of a site for a second high-level nuclear waste repository

  11. DOE hearing on the Draft Area Recommendation Report for the Crystalline Repository Project, Lakes Region High School, Bridgton, Maine: Volume 5: Transcript of proceedings

    International Nuclear Information System (INIS)

    1986-01-01

    This document contains a transcript of the comments of 17 witnesses. These meetings were held to hear public comments regarding the selection of a site for a second high-level nuclear waste repository

  12. DOE hearing on the draft area recommendation report for the Crystalline Repository Project, Ironwood Theater, Ironwood, Michigan, April 10, 1986: Transcript of proceedings

    International Nuclear Information System (INIS)

    1986-01-01

    This document contains a transcript of the comments of 22 witnesses. These meetings were held to hear public comments regarding the selection of a site for a second high-level nuclear waste repository. TEM

  13. DOE hearing on the draft area recommendation report for the Crystalline Repository Project, Concord City Auditorium, Concord, New Hampshire: Volume 4, April 3, 1986: Transcript of proceedings

    International Nuclear Information System (INIS)

    1986-01-01

    This document contains a transcript of the comments of 36 witnesses. These meetings were held to hear public comments regarding the selection of a site for a second high-level nuclear waste repository

  14. DOE hearing on the Draft Area Recommendation Report for the Crystalline Repository Project, Capitol Hill Armory, St. Paul, Minnesota: Transcript of proceedings

    International Nuclear Information System (INIS)

    1986-01-01

    This document contains a transcript of the comments of more than 15 witnesses. These meetings were held to hear comments regarding the selection of a site for a second high-level nuclear waste repository

  15. DOE hearing on the draft area recommendation report for the Crystalline Repository Project, Lake Region High School, Bridgton, Maine: Volume 1, April 5, 1986: Transcript of proceedings

    International Nuclear Information System (INIS)

    1986-01-01

    This document contains a transcript of the comments of 26 witnesses. These meetings were held to hear public comments regarding the selection of a site for a second high-level nuclear waste repository

  16. DOE hearing on the Draft Area Recommendation Report for the Crystalline Repository Project, Lakes Region High School, Bridgton, Maine: Volume 4: Transcript of proceedings

    International Nuclear Information System (INIS)

    1986-01-01

    This document contains a transcript of the comments of 16 witnesses. These meetings were held to hear public comments regarding the selection of a site for a second high-level nuclear waste repository

  17. DOE hearing on the draft area recommendation report for the Crystalline Repository Project, Winthrop High School Gymnasium, Winthrop, Minnesota: Session 1, April 8, 1986: Transcript of proceedings

    International Nuclear Information System (INIS)

    1987-01-01

    This document contains a transcript of the comments of witnesses number 1 through 15. These meetings were held to hear comments regarding the selection of a site for a second high-level nuclear waste repository

  18. DOE hearing on the Draft Area Recommendation Report for the Crystalline Repository Project, Lakes Region High School, Bridgton, Maine: Volume 3: Transcript of proceedings

    International Nuclear Information System (INIS)

    1986-01-01

    This document contains a transcript of the comments of 22 witnesses. These meetings were held to hear public comments regarding the selection of a site for a second high-level nuclear waste repository

  19. DOE hearing on the draft area recommendation report for the Crystalline Repository Project, Asheville, North Carolina: Session 2: Transcript of proceedings

    International Nuclear Information System (INIS)

    1986-01-01

    This document contains a transcript of the comments of 79 witnesses. These meetings were held to hear public comments regarding the selection of a site for a second high-level nuclear waste repository

  20. DOE hearing on the draft area recommendation report for the Crystalline Repository Project, State House, Boston, Massachusetts, April 8, 1986: Transcript of proceedings

    International Nuclear Information System (INIS)

    1986-01-01

    This document contains a transcript of the comments of 48 witnesses. These meetings were held to hear public comments regarding the selection of a site for a second high-level nuclear waste repository

  1. DOE hearing on the draft area recommendation report for the Crystalline Repository Project, South Boston, Virginia: Session 1, March 26, 1986: Transcript of proceedings

    International Nuclear Information System (INIS)

    1986-01-01

    This document contains a transcript of the comments of 53 witnesses. These meetings were held to hear public comments regarding the selection of a site for a second high-level nuclear waste repository

  2. DOE hearing on the draft area recommendation report for the Crystalline Repository Project, Patrick Henry High School, Ashland, Virginia: Session 1, April 7, 1986: Transcript of proceedings

    International Nuclear Information System (INIS)

    1986-01-01

    This document contains a transcript of the comments of 35 witnesses. These meetings were held to hear public comments regarding the selection of a site for a second high-level nuclear waste repository

  3. DOE hearing on the draft area recommendation report for the Crystalline Repository Project, Ashland Public High School, Ashland, Wisconsin: Session 2, April 9, 1986: Transcript of proceedings

    International Nuclear Information System (INIS)

    1986-01-01

    This document contains a transcript of the comments of 111 witnesses. These meetings were held to hear the public's comments regarding the selection of a site for a second high-level radioactive waste repository

  4. DOE hearing on the draft area recommendation report for the Crystalline Repository Project, Capitol Hill Armory, St. Paul, Minnesota, April 15, 1986: Transcript of proceedings

    International Nuclear Information System (INIS)

    1986-01-01

    This document contains a transcript of the comments of over 23 witnesses. These meetings were held to hear public comments regarding the selection of a site for a second high-level nuclear waste repository

  5. DOE hearing on the draft area recommendation report for the Crystalline Repository Project, Ada High School Gymnasium, Ada, Minnesota, April 3, 1986: Transcript of proceedings

    International Nuclear Information System (INIS)

    1986-01-01

    This document contains a transcript of the comments of 64 witnesses. These meetings were held to hear public comments regarding the selection of a site for a second high-level nuclear waste repository

  6. DOE hearing on the draft area recommendation report for the Crystalline Repository Project, State House, Boston, Massachusetts, April 8, 1986: Transcript of proceedings

    International Nuclear Information System (INIS)

    1986-01-01

    This document contains a transcript of the comments of 48 witnesses. These meetings were held to hear public comments regarding the selection of a site for a second high-level nuclear waste repository. TAM

  7. DOE hearing on the draft area recommendation report for the Crystalline Repository Project, Providence, Rhode Island, April 10, 1986: Transcript of proceedings

    International Nuclear Information System (INIS)

    1986-01-01

    This document contains a transcript of the comments of 10 witnesses. These meetings were held to hear the public's comments regarding the selection of a site for a second high-level radioactive waste repository

  8. DOE hearing on the draft area recommendation report for the Crystalline Repository Project, Lakes Region High School, Bridgton, Maine: Volume 8, April 5, 1986: Transcript of proceedings

    International Nuclear Information System (INIS)

    1986-01-01

    This document contains a transcript of the comments of 10 witnesses. These meetings were held to hear public comments regarding the selection of a site for a second high-level nuclear waste repository

  9. DOE hearing on the Draft Area Recommendation Report for the Crystalline Repository Project, Lake Region High School, Bridgton, Maine: Volume 6: Transcript of proceedings

    International Nuclear Information System (INIS)

    1986-01-01

    This document contains a transcript of the comments of 18 witnesses. These meetings were held to hear public comments regarding the selection of a site for a second high-level nuclear waste repository

  10. DOE hearing on the draft area recommendation report for the Crystalline Repository Project, South Boston, Virginia: Session 2, March 26, 1986: Transcript of proceedings

    International Nuclear Information System (INIS)

    1986-01-01

    This document contains a transcript of the comments of 15 witnesses. These meetings were held to hear public comments regarding the selection of a site for a second high-level nuclear waste repository

  11. DOE hearing on the Draft Area Recommendation Report for the Crystalline Repository Project, Warren High School, Warren, Minnesota: Transcript of proceedings

    International Nuclear Information System (INIS)

    1986-01-01

    This document contains a transcript of the comments of over 30 witnesses. These meetings were held to hear public comments regarding the selection of a site for a second high-level nuclear waste repository

  12. DOE hearing on the Draft Area Recommendation Report for the Crystalline Repository Project, Liberty High School, Bedford, Virginia, Session 1: Transcript of proceedings

    International Nuclear Information System (INIS)

    1986-01-01

    This document contains a transcript of the comments of 52 witnesses. These meetings were held to hear public comments regarding the selection of a site for a second high-level nuclear waste repository

  13. DOE hearing on the draft area recommendation report for the Crystalline Repository Project, Springfield High School, Springfield, Vermont, April 15, 1986: Transcript of proceedings

    International Nuclear Information System (INIS)

    1986-01-01

    This document contains a transcript of the comments of 13 witnesses. These meetings were held to hear public comments regarding the selection of a site for a second high-level nuclear waste repository

  14. DOE hearing on the draft area recommendation report for the Crystalline Repository Project, Henniker, New Hampshire, April 1, 1986: Transcript of proceedings

    International Nuclear Information System (INIS)

    1986-01-01

    This document contains a transcript of the comments of 95 witnesses. These meetings were held to hear the public's comments regarding the selection of a site for a second high-level radioactive waste repository

  15. DOE hearing on the draft area recommendation report for the Crystalline Repository Project, Mattanawcook Academy, Lincoln, Maine, April 4, 1986: Volume 5: Transcript of proceedings

    International Nuclear Information System (INIS)

    1986-01-01

    This document contains a transcript of the comments of 14 witnesses. These meetings were held to hear public comments regarding the selection of a site for a second high-level nuclear waste repository

  16. DOE hearing on the draft area recommendation report for the Crystalline Repository Project, Lake Region High School, Bridgton, Maine, April 5, 1986: Volume 4: Transcript of proceedings

    International Nuclear Information System (INIS)

    1986-01-01

    This document contains a transcript of the comments of 14 witnesses. These meetings were held to hear public comments regarding the selection of a site for a second high-level nuclear waste repository

  17. DOE hearing on the draft area recommendation report for the Crystalline Repository Project, Concord City Auditorium, Concord, New Hampshire, April 3, 1986: Volume 2: Transcript of proceedings

    International Nuclear Information System (INIS)

    1986-01-01

    This document contains a transcript of the comments of 36 witnesses. These meetings were held to hear the public's comments regarding the selection of a site for a second high-level radioactive waste repository

  18. DOE hearing on the draft area recommendation report for the Crystalline Repository Project, Hilton Hotel, Hartford, Connecticut, April 14, 1986: Transcript of proceedings

    International Nuclear Information System (INIS)

    1986-01-01

    This document contains a transcript of the comments of 22 witnesses. These meetings were held to hear public comments regarding the selection of a site for a second high-level nuclear waste repository

  19. DOE hearing on the draft area recommendation report for the Crystalline Repository Project, Augusta Armory, Augusta, Maine: Volume 2, April 7, 1986: Transcript of proceedings

    International Nuclear Information System (INIS)

    1986-01-01

    This document contains a transcript of the comments of 9 witnesses. These meetings were held to hear the public's comments regarding the selection of a site for a second high-level radioactive waste repository

  20. Justification for Selecting Level A vs. Level B Personal Protective Equipment to Remediate a Room Containing Concentrated Acids, Bases and Radiological Constituents

    International Nuclear Information System (INIS)

    Hylko, J. M.; Thompson, A. L.; Walter, J. F.; Deecke, T. A.

    2002-01-01

    Selecting the appropriate personal protective equipment (PPE) is based on providing an adequate level of employee protection relative to the task-specific conditions and hazards. PPE is categorized into four ensembles, based on the degree of protection afforded; e.g., Levels A (most restrictive), B, C, and D (least restrictive). What is often overlooked in preparing an ensemble is that the PPE itself can create significant worker hazards; i.e., the greater the level of PPE, the greater the associated risks. Furthermore, there is confusion as to whether a more ''conservative approach'' should always be taken since Level B provides the same level of respiratory protection as Level A but less skin protection. This paper summarizes the Occupational Safety and Health Administration regulations addressing Level A versus Level B, and provides justification for selecting Level B over Level A without under-protecting the employee during a particular remediation scenario. The scenario consisted of an entry team performing (1) an initial entry into a room containing concentrated acids (e.g., hydrofluoric acid), bases, and radiological constituents; (2) sampling and characterizing container contents; and (3) retrieving characterized containers. The invasive nature of the hydrofluoric acid sampling and characterization scenario created a high potential for splash, immersion, and exposure to hazardous vapors, requiring additional skin protection. The hazards associated with this scenario and the chemical nature of hydrofluoric acid provided qualitative evidence to justify Level A. Once the hydrofluoric acid was removed from the room, PPE performance was evaluated against the remaining chemical inventory. If chemical breakthrough from direct contact was not expected to occur and instrument readings confirmed the absence of any hazardous vapors, additional skin protection afforded by wearing a vapor-tight, totally-encapsulated suit was not required. Therefore, PPE performance and

  1. The effect of aluminium-stress and exogenous spermidine on chlorophyll degradation, glutathione reductase activity and the photosystem II D1 protein gene (psbA) transcript level in lichen Xanthoria parietina.

    Science.gov (United States)

    Sen, Gulseren; Eryilmaz, Isil Ezgi; Ozakca, Dilek

    2014-02-01

    In this study, the effects of short-term aluminium toxicity and the application of spermidine on the lichen Xanthoria parietina were investigated at the physiological and transcriptional levels. Our results suggest that aluminium stress leads to physiological processes in a dose-dependent manner through differences in lipid peroxidation rate, chlorophyll content and glutathione reductase (EC 1.6.4.2) activity in aluminium and spermidine treated samples. The expression of the photosystem II D1 protein (psbA) gene was quantified using semi-quantitative RT-PCR. Increased glutathione reductase activity and psbA mRNA transcript levels were observed in the X. parietina thalli that were treated with spermidine before aluminium-stress. The results showed that the application of spermidine could mitigate aluminium-induced lipid peroxidation and chlorophyll degradation on lichen X. parietina thalli through an increase in psbA transcript levels and activity of glutathione reductase (GR) enzymes. Copyright © 2013 Elsevier Ltd. All rights reserved.

  2. Use of DOE site selection criteria for screening low-level waste disposal sites on the Oak Ridge Reservation

    International Nuclear Information System (INIS)

    Lee, D.W.; Ketelle, R.H.; Stinton, L.H.

    1983-09-01

    The proposed Department of Energy (DOE) site selection criteria were applied to the Oak Ridge Reservation, and the application was evaluated to determine the criteria's usefulness in the selection of a low-level waste disposal site. The application of the criteria required the development of a methodology to provide a framework for evaluation. The methodology is composed of site screening and site characterization stages. The site screening stage relies on reconnaissance data to identify a preferred site capable of satisfying the site selection criteria. The site characterization stage relies on a detailed site investigation to determine site acceptability. The site selection criteria were applied to the DOE Oak Ridge Reservation through the site screening stage. Results of this application were similar to those of a previous siting study on the Oak Ridge Reservation. The DOE site selection criteria when coupled with the methodology that was developed were easily applied and would be adaptable to any region of interest

  3. Transcriptional analysis of abdominal fat in chickens divergently selected on bodyweight at two ages reveals novel mechanisms controlling adiposity: validating visceral adipose tissue as a dynamic endocrine and metabolic organ.

    Science.gov (United States)

    Resnyk, C W; Carré, W; Wang, X; Porter, T E; Simon, J; Le Bihan-Duval, E; Duclos, M J; Aggrey, S E; Cogburn, L A

    2017-08-16

    Decades of intensive genetic selection in the domestic chicken (Gallus gallus domesticus) have enabled the remarkable rapid growth of today's broiler (meat-type) chickens. However, this enhanced growth rate was accompanied by several unfavorable traits (i.e., increased visceral fatness, leg weakness, and disorders of metabolism and reproduction). The present descriptive analysis of the abdominal fat transcriptome aimed to identify functional genes and biological pathways that likely contribute to an extreme difference in visceral fatness of divergently selected broiler chickens. We used the Del-Mar 14 K Chicken Integrated Systems microarray to take time-course snapshots of global gene transcription in abdominal fat of juvenile [1-11 weeks of age (wk)] chickens divergently selected on bodyweight at two ages (8 and 36 wk). Further, a RNA sequencing analysis was completed on the same abdominal fat samples taken from high-growth (HG) and low-growth (LG) cockerels at 7 wk, the age with the greatest divergence in body weight (3.2-fold) and visceral fatness (19.6-fold). Time-course microarray analysis revealed 312 differentially expressed genes (FDR ≤ 0.05) as the main effect of genotype (HG versus LG), 718 genes in the interaction of age and genotype, and 2918 genes as the main effect of age. The RNA sequencing analysis identified 2410 differentially expressed genes in abdominal fat of HG versus LG chickens at 7 wk. The HG chickens are fatter and over-express numerous genes that support higher rates of visceral adipogenesis and lipogenesis. In abdominal fat of LG chickens, we found higher expression of many genes involved in hemostasis, energy catabolism and endocrine signaling, which likely contribute to their leaner phenotype and slower growth. Many transcription factors and their direct target genes identified in HG and LG chickens could be involved in their divergence in adiposity and growth rate. The present analyses of the visceral fat transcriptome in

  4. Spatially resolved metabolic analysis reveals a central role for transcriptional control in carbon allocation to wood.

    Science.gov (United States)

    Roach, Melissa; Arrivault, Stéphanie; Mahboubi, Amir; Krohn, Nicole; Sulpice, Ronan; Stitt, Mark; Niittylä, Totte

    2017-06-15

    The contribution of transcriptional and post-transcriptional regulation to modifying carbon allocation to developing wood of trees is not well defined. To clarify the role of transcriptional regulation, the enzyme activity patterns of eight central primary metabolism enzymes across phloem, cambium, and developing wood of aspen (Populus tremula L.) were compared with transcript levels obtained by RNA sequencing of sequential stem sections from the same trees. Enzymes were selected on the basis of their importance in sugar metabolism and in linking primary metabolism to lignin biosynthesis. Existing enzyme assays were adapted to allow measurements from ~1 mm3 sections of dissected stem tissue. These experiments provided high spatial resolution of enzyme activity changes across different stages of wood development, and identified the gene transcripts probably responsible for these changes. In most cases, there was a clear positive relationship between transcripts and enzyme activity. During secondary cell wall formation, the increases in transcript levels and enzyme activities also matched with increased levels of glucose, fructose, hexose phosphates, and UDP-glucose, emphasizing an important role for transcriptional regulation in carbon allocation to developing aspen wood. These observations corroborate the efforts to increase carbon allocation to wood by engineering gene regulatory networks. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  5. TNF-α promotes nuclear enrichment of the transcription factor TonEBP/NFAT5 to selectively control inflammatory but not osmoregulatory responses in nucleus pulposus cells.

    Science.gov (United States)

    Johnson, Zariel I; Doolittle, Alexandra C; Snuggs, Joseph W; Shapiro, Irving M; Le Maitre, Christine L; Risbud, Makarand V

    2017-10-20

    Intervertebral disc degeneration (IDD) causes chronic back pain and is linked to production of proinflammatory molecules by nucleus pulposus (NP) and other disc cells. Activation of tonicity-responsive enhancer-binding protein (TonEBP)/NFAT5 by non-osmotic stimuli, including proinflammatory molecules, occurs in cells involved in immune response. However, whether inflammatory stimuli activate TonEBP in NP cells and whether TonEBP controls inflammation during IDD is unknown. We show that TNF-α, but not IL-1β or LPS, promoted nuclear enrichment of TonEBP protein. However, TNF-α-mediated activation of TonEBP did not cause induction of osmoregulatory genes. RNA sequencing showed that 8.5% of TNF-α transcriptional responses were TonEBP-dependent and identified genes regulated by both TNF-α and TonEBP. These genes were over-enriched in pathways and diseases related to inflammatory response and inhibition of matrix metalloproteases. Based on RNA-sequencing results, we further investigated regulation of novel TonEBP targets CXCL1 , CXCL2 , and CXCL3 TonEBP acted synergistically with TNF-α and LPS to induce CXCL1 -proximal promoter activity. Interestingly, this regulation required a highly conserved NF-κB-binding site but not a predicted TonE, suggesting cross-talk between these two members of the Rel family. Finally, analysis of human NP tissue showed that TonEBP expression correlated with canonical osmoregulatory targets TauT/SLC6A6 , SMIT/SLC5A3 , and AR/AKR1B1 , supporting in vitro findings that the inflammatory milieu during IDD does not interfere with TonEBP osmoregulation. In summary, whereas TonEBP participates in the proinflammatory response to TNF-α, therapeutic strategies targeting this transcription factor for treatment of disc disease must spare osmoprotective, prosurvival, and matrix homeostatic activities. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  6. Fatigue level estimation of monetary bills based on frequency band acoustic signals with feature selection by supervised SOM

    Science.gov (United States)

    Teranishi, Masaru; Omatu, Sigeru; Kosaka, Toshihisa

    Fatigued monetary bills adversely affect the daily operation of automated teller machines (ATMs). In order to make the classification of fatigued bills more efficient, the development of an automatic fatigued monetary bill classification method is desirable. We propose a new method by which to estimate the fatigue level of monetary bills from the feature-selected frequency band acoustic energy pattern of banking machines. By using a supervised self-organizing map (SOM), we effectively estimate the fatigue level using only the feature-selected frequency band acoustic energy pattern. Furthermore, the feature-selected frequency band acoustic energy pattern improves the estimation accuracy of the fatigue level of monetary bills by adding frequency domain information to the acoustic energy pattern. The experimental results with real monetary bill samples reveal the effectiveness of the proposed method.

  7. Regulatory hotspots in the malaria parasite genome dictate transcriptional variation.

    Directory of Open Access Journals (Sweden)

    Joseph M Gonzales

    2008-09-01

    Full Text Available The determinants of transcriptional regulation in malaria parasites remain elusive. The presence of a well-characterized gene expression cascade shared by different Plasmodium falciparum strains could imply that transcriptional regulation and its natural variation do not contribute significantly to the evolution of parasite drug resistance. To clarify the role of transcriptional variation as a source of stain-specific diversity in the most deadly malaria species and to find genetic loci that dictate variations in gene expression, we examined genome-wide expression level polymorphisms (ELPs in a genetic cross between phenotypically distinct parasite clones. Significant variation in gene expression is observed through direct co-hybridizations of RNA from different P. falciparum clones. Nearly 18% of genes were regulated by a significant expression quantitative trait locus. The genetic determinants of most of these ELPs resided in hotspots that are physically distant from their targets. The most prominent regulatory locus, influencing 269 transcripts, coincided with a Chromosome 5 amplification event carrying the drug resistance gene, pfmdr1, and 13 other genes. Drug selection pressure in the Dd2 parental clone lineage led not only to a copy number change in the pfmdr1 gene but also to an increased copy number of putative neighboring regulatory factors that, in turn, broadly influence the transcriptional network. Previously unrecognized transcriptional variation, controlled by polymorphic regulatory genes and possibly master regulators within large copy number variants, contributes to sweeping phenotypic evolution in drug-resistant malaria parasites.

  8. Enhancements to the CALIOP Aerosol Subtyping and Lidar Ratio Selection Algorithms for Level II Version 4

    Science.gov (United States)

    Omar, A. H.; Tackett, J. L.; Vaughan, M. A.; Kar, J.; Trepte, C. R.; Winker, D. M.

    2016-12-01

    This presentation describes several enhancements planned for the version 4 aerosol subtyping and lidar ratio selection algorithms of the Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP) instrument. The CALIOP subtyping algorithm determines the most likely aerosol type from CALIOP measurements (attenuated backscatter, estimated particulate depolarization ratios δe, layer altitude), and surface type. The aerosol type, so determined, is associated with a lidar ratio (LR) from a discrete set of values. Some of these lidar ratios have been updated in the version 4 algorithms. In particular, the dust and polluted dust will be adjusted to reflect the latest measurements and model studies of these types. Version 4 eliminates the confusion between smoke and clean marine aerosols seen in version 3 by modifications to the elevated layer flag definitions used to identify smoke aerosols over the ocean. In the subtyping algorithms pure dust is determined by high estimated particulate depolarization ratios [δe > 0.20]. Mixtures of dust and other aerosol types are determined by intermediate values of the estimated depolarization ratio [0.075limited to mixtures of dust and smoke, the so called polluted dust aerosol type. To differentiate between mixtures of dust and smoke, and dust and marine aerosols, a new aerosol type will be added in the version 4 data products. In the revised classification algorithms, polluted dust will still defined as dust + smoke/pollution but in the marine boundary layer instances of moderate depolarization will be typed as dusty marine aerosols with a lower lidar ratio than polluted dust. The dusty marine type introduced in version 4 is modeled as a mixture of dust + marine aerosol. To account for fringes, the version 4 Level 2 algorithms implement Subtype Coalescence Algorithm for AeRosol Fringes (SCAARF) routine to detect and classify fringe of aerosol plumes that are detected at 20 km or 80 km horizontal resolution at the plume base. These

  9. Study of a Country Level Facility LocationSelection for a Small Company

    OpenAIRE

    Eterovic, Mirko; Özgül, Simge

    2012-01-01

    Selection of an optimal facility location is a challenging decision for companies, since it would be costly and dicult to change the location after an installation has been already made. Existing numerical methods in the decision-making process help companies to perform their operations with minimum cost and maximum value based on their strategic objectives. Decision making process requires the selection of relative processes among several alternatives corresponding to a set of location facto...

  10. DNA-mediated cooperativity facilitates the co-selection of cryptic enhancer sequences by SOX2 and PAX6 transcription factors.

    Science.gov (United States)

    Narasimhan, Kamesh; Pillay, Shubhadra; Huang, Yong-Heng; Jayabal, Sriram; Udayasuryan, Barath; Veerapandian, Veeramohan; Kolatkar, Prasanna; Cojocaru, Vlad; Pervushin, Konstantin; Jauch, Ralf

    2015-02-18

    Sox2 and Pax6 are transcription factors that direct cell fate decision during neurogenesis, yet the mechanism behind how they cooperate on enhancer DNA elements and regulate gene expression is unclear. By systematically interrogating Sox2 and Pax6 interaction on minimal enhancer elements, we found that cooperative DNA recognition relies on combinatorial nucleotide switches and precisely spaced, but cryptic composite DNA motifs. Surprisingly, all tested Sox and Pax paralogs have the capacity to cooperate on such enhancer elements. NMR and molecular modeling reveal very few direct protein-protein interactions between Sox2 and Pax6, suggesting that cooperative binding is mediated by allosteric interactions propagating through DNA structure. Furthermore, we detected and validated several novel sites in the human genome targeted cooperatively by Sox2 and Pax6. Collectively, we demonstrate that Sox-Pax partnerships have the potential to substantially alter DNA target specificities and likely enable the pleiotropic and context-specific action of these cell-lineage specifiers. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  11. Longitudinal evaluation of leukocyte transcripts in killer whales (Orcinus Orca)

    Science.gov (United States)

    Sitt, Tatjana; Bowen, Lizabeth; Lee, Chia-Shan; Blanchard, Myra; McBain, James; Dold, Christopher; Stott, Jeffrey L.

    2016-01-01

    Early identification of illness and/or presence of environmental and/or social stressors in free-ranging and domestic cetaceans is a priority for marine mammal health care professionals. Incorporation of leukocyte gene transcript analysis into the diagnostic tool kit has the potential to augment classical diagnostics based upon ease of sample storage and shipment, inducible nature and well-defined roles of transcription and associated downstream actions. Development of biomarkers that could serve to identify “insults” and potentially differentiate disease etiology would be of great diagnostic value. To this end, a modest number of peripheral blood leukocyte gene transcripts were selected for application to a domestic killer whale population with a focus on broad representation of inducible immunologically relevant genes. Normalized leukocyte transcript values, longitudinally acquired from 232 blood samples derived from 26 clinically healthy whales, were not visibly influenced temporally nor by sex or the specific Park in which they resided. Stability in leukocyte transcript number during periods of health enhances their potential use in diagnostics through identification of outliers. Transcript levels of two cytokine genes, IL-4 and IL-17, were highly variable within the group as compared to the other transcripts. IL-4 transcripts were typically absent. Analysis of transcript levels on the other genes of interest, on an individual animal basis, identified more outliers than were visible when analyzed in the context of the entire population. The majority of outliers (9 samples) were low, though elevated transcripts were identified for IL-17 from 2 animals and one each for Cox-2 and IL-10. The low number of outliers was not unexpected as sample selection was intentionally directed towards animals that were clinically healthy at the time of collection. Outliers may reflect animals experiencing subclinical disease that is transient and self-limiting. The

  12. Development of the Teacher Candidates’ Level of being Affected from Public Personnel Selection Examination Scale

    Directory of Open Access Journals (Sweden)

    Fatma SUSAR KIRMIZI

    2015-07-01

    Full Text Available This study aimed to develop a scale to evaluate teacher candidates' level of being affected from the public personnel selection examination. The participants of the study consisted of the final year students at Pamukkale University Education Faculty. The participants were 207 teacher candidates, of whom 143 were female and 64 were male. The validity and reliability study of the scale was conducted on the data gathered from teacher candidates studying at Art Teaching, Music Teaching, Turkish Language Teaching, Social Studies Education, Science Teaching, Psychological Counseling and Guidance Education, Elementary Education and Preschool Education departments of Pamukkale University Education Faculty. The Lawshe technique was used in the evaluation of the scale by experts. To determine the construct validity, factor analysis was performed on the data, and two sub-scales were identified. The factor loading values of the items in the first sub-scale ranged between 0,65 and 0,35, and those in the second sub-scale between 0,75 and 0,39. As a result of the analyses, the "Teacher Candidates' Level of Being Affected From Public Personnel Selection Examination Scale" (TCLBAPPSES including 33 items, 23 negative and 10 positive, and two sub-scales was produced. The Cronbach's Alpha reliability coefficient was found as 0,86 for the first sub-dimension, 0,73 for the second sub-dimension, and 0,91 for the whole scale. As a result, it can be argued that the scale is reliable.-------------Öğretmen Adaylarının Kamu Personeli Seçme Sınavından Etkilenme Düzeyi Ölçeğinin GeliştirilmesiÖzet:Bu çalışmada, öğretmen adaylarının kamu personeli seçme sınavından etkilenme düzeylerini değerlendirmek için bir ölçek geliştirilmesi amaçlanmıştır. Araştırmanın çalışma grubunu Pamukkale Üniversitesi Eğitim Fakültesi son sınıf öğrencileri oluşturmuştur. Araştırmada 143 kız, 64 erkek olmak üzere toplam 207 öğretmen adayına ula

  13. Isoforms of elongation factor eEF1A may be differently regulated at post-transcriptional level in breast cancer progression

    Directory of Open Access Journals (Sweden)

    Vislovukh A. A.

    2013-01-01

    Full Text Available Eukaryotic translation elongation factor 1A exists as two 98 % homologous isoforms: eEF1A1 (A1 and eEF1A2 (A2 which are tissue and development specific. Despite high homology in an open reading frame (ORF region, mRNAs coding for eEF1A1 and eEF1A2 are different in their untranslated regions (UTR, suggesting a possibility of their dissimilar post-transcriptional regulation. Aim. To analyze the existence of cis-acting motifs in the UTRs of EEF1A1/A2 mRNAs, to confirm the possibility of post-transcriptional control of eEF1A1 and eEF1A2 expression. Methods. An ensemble of bioinformatic methods was applied to predict regulatory motifs in the UTRs of EEF1A1/A2 mRNAs. Dual-luciferase reporter assay was employed to detect post-transcriptional regulation of eEF1A1/A2 expression. Results. Numerous regulatory motifs in the UTR of EEF1A1/A2 mRNAs were found bioinformatically. The experimental evidence was obtained for the existence of negative regulation of EEF1A1 and positive regulation of EEF1A2 mRNA in the model of breast cancer development. Conclusions. EEF1A1 and EEF1A2 mRNAs contain distinct motifs in the UTRs and are differently regulated in cancer suggesting the possibility of their control by different cellular signals.

  14. Bioinformatic analysis of patient-derived ASPS gene expressions and ASPL-TFE3 fusion transcript levels identify potential therapeutic targets.

    Directory of Open Access Journals (Sweden)

    David G Covell

    Full Text Available Gene expression data, collected from ASPS tumors of seven different patients and from one immortalized ASPS cell line (ASPS-1, was analyzed jointly with patient ASPL-TFE3 (t(X;17(p11;q25 fusion transcript data to identify disease-specific pathways and their component genes. Data analysis of the pooled patient and ASPS-1 gene expression data, using conventional clustering methods, revealed a relatively small set of pathways and genes characterizing the biology of ASPS. These results could be largely recapitulated using only the gene expression data collected from patient tumor samples. The concordance between expression measures derived from ASPS-1 and both pooled and individual patient tumor data provided a rationale for extending the analysis to include patient ASPL-TFE3 fusion transcript data. A novel linear model was exploited to link gene expressions to fusion transcript data and used to identify a small set of ASPS-specific pathways and their gene expression. Cellular pathways that appear aberrantly regulated in response to the t(X;17(p11;q25 translocation include the cell cycle and cell adhesion. The identification of pathways and gene subsets characteristic of ASPS support current therapeutic strategies that target the FLT1 and MET, while also proposing additional targeting of genes found in pathways involved in the cell cycle (CHK1, cell adhesion (ARHGD1A, cell division (CDC6, control of meiosis (RAD51L3 and mitosis (BIRC5, and chemokine-related protein tyrosine kinase activity (CCL4.

  15. Do Current Recommendations for Upper Instrumented Vertebra Predict Shoulder Imbalance? An Attempted Validation of Level Selection for Adolescent Idiopathic Scoliosis.

    Science.gov (United States)

    Bjerke, Benjamin T; Cheung, Zoe B; Shifflett, Grant D; Iyer, Sravisht; Derman, Peter B; Cunningham, Matthew E

    2015-10-01

    Shoulder balance for adolescent idiopathic scoliosis (AIS) patients is associated with patient satisfaction and self-image. However, few validated systems exist for selecting the upper instrumented vertebra (UIV) post-surgical shoulder balance. The purpose is to examine the existing UIV selection criteria and correlate with post-surgical shoulder balance in AIS patients. Patients who underwent spinal fusion at age 10-18 years for AIS over a 6-year period were reviewed. All patients with a minimum of 1-year radiographic follow-up were included. Imbalance was determined to be radiographic shoulder height |RSH| ≥ 15 mm at latest follow-up. Three UIV selection methods were considered: Lenke, Ilharreborde, and Trobisch. A recommended UIV was determined using each method from pre-surgical radiographs. The recommended UIV for each method was compared to the actual UIV instrumented for all three methods; concordance between these levels was defined as "Correct" UIV selection, and discordance was defined as "Incorrect" selection. One hundred seventy-one patients were included with 2.3 ± 1.1 year follow-up. For all methods, "Correct" UIV selection resulted in more shoulder imbalance than "Incorrect" UIV selection. Overall shoulder imbalance incidence was improved from 31.0% (53/171) to 15.2% (26/171). New shoulder imbalance incidence for patients with previously level shoulders was 8.8%. We could not identify a set of UIV selection criteria that accurately predicted post-surgical shoulder balance. Further validated measures are needed in this area. The complexity of proximal thoracic curve correction is underscored in a case example, where shoulder imbalance occurred despite "Correct" UIV selection by all methods.

  16. Transcriptional profiles of hybrid Eucalyptus genotypes with contrasting lignin content reveal that monolignol biosynthesis-related genes regulate wood composition

    Directory of Open Access Journals (Sweden)

    Tomotaka eShinya

    2016-04-01

    Full Text Available Eucalyptus species constitutes the most widely planted hardwood trees in temperate and subtropical regions. In this study, we compared the transcript levels of genes involved in lignocellulose formation such as cellulose, hemicellulose and lignin biosynthesis in two selected three-year old hybrid Eucalyptus (Eucalyptus urophylla x E. grandis genotypes (AM063 and AM380 that have different lignin content. AM063 and AM380 had 20.2 and 35.5% of Klason lignin content and 59.0% and 48.2%, -cellulose contents, respectively. We investigated the correlation between wood properties and transcript levels of wood formation-related genes using RNA-seq with total RNAs extracted from developing xylem tissues at a breast height. Transcript levels of cell wall construction genes such as cellulose synthase (CesA and sucrose synthase (SUSY were almost the same in both genotypes. However, AM063 exhibited higher transcript levels of UDP-glucose pyrophosphorylase (UGP and xyloglucan endotransglucoxylase (XTH than those in AM380. Most monolignol biosynthesis- related isozyme genes showed higher transcript levels in AM380. These results indicate monolignol biosynthesis-related genes may regulate wood composition in Eucalyptus. Flavonoids contents were also observed at much higher levels in AM380 as a result of the elevated transcript levels of common phenylpropanoid pathway genes, phenylalanine ammonium lyase (PAL, cinnamate-4-hydroxylase (C4H and 4-coumarate-CoA ligase (4CL. Secondary plant cell wall formation is regulated by many transcription factors. We analyzed genes encoding NAC, WRKY, AP2/ERF and KNOX transcription factors and found higher transcript levels of these genes in AM380. We also observed increased transcription of some MYB and LIM domain transcription factors in AM380 compared to AM063. All these results show that genes related to monolignol biosynthesis may regulate the wood composition and help maintain the ratio of cellulose and lignin contents

  17. System and method for controlling ammonia levels in a selective catalytic reduction catalyst using a nitrogen oxide sensor

    Science.gov (United States)

    None

    2017-07-25

    A system according to the principles of the present disclosure includes an air/fuel ratio determination module and an emission level determination module. The air/fuel ratio determination module determines an air/fuel ratio based on input from an air/fuel ratio sensor positioned downstream from a three-way catalyst that is positioned upstream from a selective catalytic reduction (SCR) catalyst. The emission level determination module selects one of a predetermined value and an input based on the air/fuel ratio. The input is received from a nitrogen oxide sensor positioned downstream from the three-way catalyst. The emission level determination module determines an ammonia level based on the one of the predetermined value and the input received from the nitrogen oxide sensor.

  18. Tentative mapping of transcription-induced interchromosomal interaction using chimeric EST and mRNA data.

    Directory of Open Access Journals (Sweden)

    Per Unneberg

    Full Text Available Recent studies on chromosome conformation show that chromosomes colocalize in the nucleus, bringing together active genes in transcription factories. This spatial proximity of actively transcribing genes could provide a means for RNA interaction at the transcript level. We have screened public databases for chimeric EST and mRNA sequences with the intent of mapping transcription-induced interchromosomal interactions. We suggest that chimeric transcripts may be the result of close encounters of active genes, either as functional products or "noise" in the transcription process, and that they could be used as probes for chromosome interactions. We have found a total of 5,614 chimeric ESTs and 587 chimeric mRNAs that meet our selection criteria. Due to their higher quality, the mRNA findings are of particular interest and we hope that they may serve as food for thought for specialists in diverse areas of molecular biology.

  19. Hydrographs Showing Ground-Water Level Changes for Selected Wells in the Lower Skagit River Basin, Washington

    Science.gov (United States)

    Fasser, E.T.; Julich, R.J.

    2009-01-01

    Hydrographs for selected wells in the Lower Skagit River basin, Washington, are presented in an interactive web-based map to illustrate monthly and seasonal changes in ground-water levels in the study area. Ground-water level data and well information were collected by the U.S. Geological Survey using standard techniques and were stored in the USGS National Water Information System (NWIS), Ground-Water Site-Inventory (GWSI) System.

  20. Hydrographs showing groundwater levels for selected wells in the Puyallup River watershed and vicinity, Pierce and King Counties, Washington

    Science.gov (United States)

    Lane, R.C.; Julich, R.J.; Justin, G.B.

    2013-01-01

    Hydrographs of groundwater levels for selected wells in and adjacent to the Puyallup River watershed in Pierce and King Counties, Washington, are presented using an interactive Web-based map of the study area to illustrate changes in groundwater levels on a monthly and seasonal basis. The interactive map displays well locations that link to the hydrographs, which in turn link to the U.S. Geological Survey National Water Information System, Groundwater Site Inventory System.

  1. Use of magnesium silicate as a selective absorbent in radioimmunological method of determination of insulin level in human serum

    Energy Technology Data Exchange (ETDEWEB)

    Bogoniowska, Z; Stelmasiak, T [Wojskowy Instytut Higieny i Epidemiologii, Warsaw (Poland)

    1974-01-01

    The authors present a radioimmunological method for determination of insulin (IRI) level in the human serum using magnesium silicate (talc) as adsorbent. The method is based on the phenomenon of selective adsorption of the free radioactive hormone. The optimal parameters for the method were determined. The serum level of IRI in clinically healthy subjects after oral glucose loading was established. The obtained results were compared with the results obtained by the radioimmunological method of double antibodies in stochastically grouped samples.

  2. Technology needs for selecting and evaluating high-level waste repository sites in crystalline rock

    International Nuclear Information System (INIS)

    1988-12-01

    This report describes properties and processes that govern the performance of the geological barrier in a nuclear waste isolation system in crystalline rock and the state-of-the-art in the understanding of these properties and processes. Areas and topics that require further research and development as well as technology needs for investigating and selecting repository sites are presented. Experiences from the Swedish site selection program are discussed, and a general investigation strategy is presented for an area characterization phase of an exploratory program in crystalline rocks. 255 refs., 65 figs., 10 tabs

  3. Four novel FBN1 mutations: Significance for mutant transcript level and EGF-like domain calcium binding in the pathogenesis of Marfan syndrome

    Energy Technology Data Exchange (ETDEWEB)

    Dietz, H.C.; McIntosh, I.; Pyeritz, R.E.; Francomano, C.A. (Johns Hopkins Univ. School of Medicine, Baltimore, MD (United States)); Sakai, L.Y.; Corson, G.M.; Chalberg, S.C. (Oregon Health Sciences Univ., Portland (United States))

    1993-08-01

    Defects of fibrillin (FBN1), a glycoprotein component of the extracellular microfibril, cause Marfan syndrome. This disorder is characterized by marked inter- and intrafamilial variation in phenotypic severity. To understand the molecular basis for this clinical observation, the authors have screened the fibrillin gene (FBN1) on chromosome 15, including the newly cloned 5[prime] coding sequence, for disease-producing alterations in a panel of patients with a wide range of manifestations and clinical severity. All the missense mutations identified to date, including two novel mutations discussed here, are associated with classic and moderate to severe disease and occur at residues with putative significance for calcium binding to epidermal growth factor (EGF)-like domains. In contrast, two new mutations that create premature signals for termination of translation of mRNA and are associated with reduction in the amount of mutant allele transcript produce a range of phenotypic severity. The patient with the lowest amount of mutant transcript has the mildest disease. These data support a role for altered calcium binding to EGF-like domains in the pathogenesis of Marfan syndrome and suggest a dominant negative mechanism for the pathogenesis of this disorder. 26 refs., 6 figs., 1 tab.

  4. Nonsteroidal Selective Androgen Receptor Modulators and Selective Estrogen Receptor β Agonists Moderate Cognitive Deficits and Amyloid-β Levels in a Mouse Model of Alzheimer’s Disease

    Science.gov (United States)

    2013-01-01

    Decreases of the sex steroids, testosterone and estrogen, are associated with increased risk of Alzheimer’s disease. Testosterone and estrogen supplementation improves cognitive deficits in animal models of Alzheimer’s disease. Sex hormones play a role in the regulation of amyloid-β via induction of the amyloid-β degrading enzymes neprilysin and insulin-degrading enzyme. To mimic the effect of dihydrotestosterone (DHT), we administered a selective androgen receptor agonist, ACP-105, alone and in combination with the selective estrogen receptor β (ERβ) agonist AC-186 to male gonadectomized triple transgenic mice. We assessed long-term spatial memory in the Morris water maze, spontaneous locomotion, and anxiety-like behavior in the open field and in the elevated plus maze. We found that ACP-105 given alone decreases anxiety-like behavior. Furthermore, when ACP-105 is administered in combination with AC-186, they increase the amyloid-β degrading enzymes neprilysin and insulin-degrading enzyme and decrease amyloid-β levels in the brain as well as improve cognition. Interestingly, the androgen receptor level in the brain was increased by chronic treatment with the same combination treatment, ACP-105 and AC-186, not seen with DHT or ACP-105 alone. Based on these results, the beneficial effect of the selective ERβ agonist as a potential therapeutic for Alzheimer’s disease warrants further investigation. PMID:24020966

  5. Data analysis at the CMS level-1 trigger: migrating complex selection algorithms from offline analysis and high-level trigger to the trigger electronics

    CERN Document Server

    Wulz, Claudia

    2017-01-01

    With ever increasing luminosity at the LHC, optimum online data selection is becoming more and more important. While in the case of some experiments (LHCb and ALICE) this task is being completely transferred to computer farms, the others -- ATLAS and CMS -- will not be able to do this in the medium-term future for technological, detector-related reasons. Therefore, these experiments pursue the complementary approach of migrating more and more of the offline and high-level trigger intelligence into the trigger electronics. The presentation illustrates how the level-1 trigger of the CMS experiment and in particular its concluding stage, the so-called ``Global Trigger", take up this challenge.

  6. Quantitative profiling of housekeeping and Epstein-Barr virus gene transcription in Burkitt lymphoma cell lines using an oligonucleotide microarray

    Directory of Open Access Journals (Sweden)

    Niggli Felix K

    2006-06-01

    Full Text Available Abstract Background The Epstein-Barr virus (EBV is associated with lymphoid malignancies, including Burkitt's lymphoma (BL, and can transform human B cells in vitro. EBV-harboring cell lines are widely used to investigate lymphocyte transformation and oncogenesis. Qualitative EBV gene expression has been extensively described, but knowledge of quantitative transcription is lacking. We hypothesized that transcription levels of EBNA1, the gene essential for EBV persistence within an infected cell, are similar in BL cell lines. Results To compare quantitative gene transcription in the BL cell lines Namalwa, Raji, Akata, Jijoye, and P3HR1, we developed an oligonucleotide microarray chip, including 17 housekeeping genes, six latent EBV genes (EBNA1, EBNA2, EBNA3A, EBNA3C, LMP1, LMP2, and four lytic EBV genes (BZLF1, BXLF2, BKRF2, BZLF2, and used the cell line B95.8 as a reference for EBV gene transcription. Quantitative polymerase chain reaction assays were used to validate microarray results. We found that transcription levels of housekeeping genes differed considerably among BL cell lines. Using a selection of housekeeping genes with similar quantitative transcription in the tested cell lines to normalize EBV gene transcription data, we showed that transcription levels of EBNA1 were quite similar in very different BL cell lines, in contrast to transcription levels of other EBV genes. As demonstrated with Akata cells, the chip allowed us to accurately measure EBV gene transcription changes triggered by treatment interventions. Conclusion Our results suggest uniform EBNA1 transcription levels in BL and that microarray profiling can reveal novel insights on quantitative EBV gene transcription and its impact on lymphocyte biology.

  7. Optimal individual supervised hyperspectral band selection distinguishing savannah trees at leaf level

    CSIR Research Space (South Africa)

    Debba, Pravesh

    2009-08-01

    Full Text Available computer intensive search technique to find the bands optimizing the value of TSAM as a function of the bands, by continually updating this function at succes- sive steps. Band selection by means of minimizing the total accumulated correlation...

  8. Site suitability, selection and characterization: Branch technical position--Low-Level Waste Licensing Branch

    International Nuclear Information System (INIS)

    Siefken, D.; Pangburn, G.; Pennifill, R.; Starmer, R.J.

    1982-04-01

    The staff provides an expanded interpretation of the site suitability requirements in the proposed rule 10 CFR Part 61, a description of the anticipated site selection process, and a detailed discussion of the site characterization program needed to support a license application and environmental report. The paper provides early-on guidance to prospective applicants in these three subject areas

  9. Analysis artefacts of the INS-IGF2 fusion transcript

    DEFF Research Database (Denmark)

    Wernersson, Rasmus; Frogne, Thomas; Rescan, Claude

    2015-01-01

    Background: In gene expression analysis, overlapping genes, splice variants, and fusion transcripts are potential sources of data analysis artefacts, depending on how the observed intensity is assigned to one, or more genes. We here exemplify this by an in-depth analysis of the INS-IGF2 fusion...... transcript, which has recently been reported to be among the highest expressed transcripts in human pancreatic beta cells and its protein indicated as a novel autoantigen in Type 1 Diabetes. Results: Through RNA sequencing and variant specific qPCR analyses we demonstrate that the true abundance of INS-IGF2...... is >20,000 fold lower than INS in human beta cells, and we suggest an explanation to the nature of the artefacts which have previously led to overestimation of the gene expression level in selected studies. We reinvestigated the previous reported findings of detection of INS-IGF2 using antibodies both...

  10. Evaluation of levels of select toxic metals in commonly used herbal ...

    African Journals Online (AJOL)

    Even at low concentrations or levels of exposure, toxic metals have also been reported to pose health risks to man. Aim: To ... Materials/Methods :Herbal medicines (n=8) were purchased from on-the-street vendors and evaluated for levels of five toxic metals (Lead, Nickel, Mercury, Cadmium and Arsenic).Analysis of toxic ...

  11. The transcriptional landscape

    DEFF Research Database (Denmark)

    Nielsen, Henrik

    2011-01-01

    The application of new and less biased methods to study the transcriptional output from genomes, such as tiling arrays and deep sequencing, has revealed that most of the genome is transcribed and that there is substantial overlap of transcripts derived from the two strands of DNA. In protein coding...... regions, the map of transcripts is very complex due to small transcripts from the flanking ends of the transcription unit, the use of multiple start and stop sites for the main transcript, production of multiple functional RNA molecules from the same primary transcript, and RNA molecules made...... by independent transcription from within the unit. In genomic regions separating those that encode proteins or highly abundant RNA molecules with known function, transcripts are generally of low abundance and short-lived. In most of these cases, it is unclear to what extent a function is related to transcription...

  12. Hydrographs Showing Groundwater Level Changes for Selected Wells in the Chambers-Clover Creek Watershed and Vicinity, Pierce County, Washington

    Science.gov (United States)

    Justin, G.B.; Julich, R.; Payne, K.L.

    2009-01-01

    Selected groundwater level hydrographs for the Chambers-Clover Creek watershed (CCCW) and vicinity, Washington, are presented in an interactive web-based map to illustrate changes in groundwater levels in and near the CCCW on a monthly and seasonal basis. Hydrographs are linked to points corresponding to the well location on an interactive map of the study area. Groundwater level data and well information from Federal, State, and local agencies were obtained from the U.S. Geological Survey National Water Information System (NWIS), Groundwater Site Inventory (GWSI) System.

  13. Geological factors of disposal site selection for low-and intermediate-level solid radwastes in China

    International Nuclear Information System (INIS)

    Chen Zhangru

    1993-01-01

    For disposal of low- and intermediate-level solid radioactive wastes, shallow-ground disposal can provide adequate isolation of waste from human for a fairly long period of time. The objective of disposal site selection is to ensure that the natural properties of the site together with the engineered barrier site shall provide adequate isolation of radionuclides from the human beings and environment, so the whole disposal system can keep the radiological impact within an acceptable level. Since the early 1980's, complying with the national standards and the expert's conception as well as the related IAEA Criteria, geological selection of disposal sites for low-and intermediate-level solid radwastes has been carried out in East China, South China, Northwest China and Southwest China separately. Finally, 5 candidate sites were recommended to the CNNC

  14. Rapid determination of trace level copper in tea infusion samples by solid contact ion selective electrode

    Directory of Open Access Journals (Sweden)

    Aysenur Birinci

    2016-07-01

    Full Text Available A new solid contact copper selective electrode with a poly (vinyl chloride (PVC membrane consisting of o-xylylenebis(N,N-diisobutyldithiocarbamate as ionophore has been prepared. The main novelties of constructed ion selective electrode concept are the enhanced robustness, cheapness, and fastness due to the use of solid contacts. The electrode exhibits a rapid (< 10 seconds and near-Nernstian response to Cu2+ activity from 10−1 to 10−6 mol/L at the pH range of 4.0–6.0. No serious interference from common ions was found. The electrode characterizes by high potential stability, reproducibility, and full repeatability. The electrode was used as an indicator electrode in potentiometric titration of Cu(II ions with EDTA and for the direct assay of tea infusion samples by means of the calibration graph technique. The results compared favorably with those obtained by the atomic absorption spectroscopy (AAS.

  15. Implications of selection in common bean lines in contrasting environments concerning nitrogen levels

    Directory of Open Access Journals (Sweden)

    Isabela Volpi Furtini

    2014-10-01

    Full Text Available Grain productivities of 100 bean lines were evaluated in the presence and absence of nitrogen fertilizer in order to identify those with high nitrogen use efficiency (NUE and to determine the correlated response observed in a stressed environment following selection in a non-stressed environment. The genetic and phenotypic characteristics of the lines, as well as the response index to applied nitrogen, were determined. The average grain productivities at both locations were 39.5% higher in the presence of nitrogen fertilizer, with 8.3 kg of grain being produced per kg of nitrogen applied. NUE varied greatly between lines. Lines BP-16, CVII-85-11, BP-24, Ouro Negro and MA-IV-15-203 were the most efficient and responsive. The results showed that it is possible to select bean lines in stressed and non-stressed environments. It was inferred that common bean lines for environments with low nitrogen availability should preferably be selected under nitrogen stress.

  16. RNA Pol II promotes transcription of centromeric satellite DNA in beetles.

    Directory of Open Access Journals (Sweden)

    Zeljka Pezer

    Full Text Available Transcripts of centromeric satellite DNAs are known to play a role in heterochromatin formation as well as in establishment of the kinetochore. However, little is known about basic mechanisms of satellite DNA expression within constitutive heterochromatin and its regulation. Here we present comprehensive analysis of transcription of abundant centromeric satellite DNA, PRAT from beetle Palorus ratzeburgii (Coleoptera. This satellite is characterized by preservation and extreme sequence conservation among evolutionarily distant insect species. PRAT is expressed in all three developmental stages: larvae, pupae and adults at similar level. Transcripts are abundant comprising 0.033% of total RNA and are heterogeneous in size ranging from 0.5 kb up to more than 5 kb. Transcription proceeds from both strands but with 10 fold different expression intensity and transcripts are not processed into siRNAs. Most of the transcripts (80% are not polyadenylated and remain in the nucleus while a small portion is exported to the cytoplasm. Multiple, irregularly distributed transcription initiation sites as well as termination sites have been mapped within the PRAT sequence using primer extension and RLM-RACE. The presence of cap structure as well as poly(A tails in a portion of the transcripts indicate RNA polymerase II-dependent transcription and a putative polymerase II promoter site overlaps the most conserved part of the PRAT sequence. The treatment of larvae with alpha-amanitin decreases the level of PRAT transcripts at concentrations that selectively inhibit pol II activity. In conclusion, stable, RNA polymerase II dependant transcripts of abundant centromeric satellite DNA, not regulated by RNAi, have been identified and characterized. This study offers a basic understanding of expression of highly abundant heterochromatic DNA which in beetle species constitutes up to 50% of the genome.

  17. Site selection factors for repositories of solid high-level and alpha-bearing wastes in geological formations

    International Nuclear Information System (INIS)

    1977-01-01

    The purpose of this report is to provide guidelines for the selection and evaluation of suitable areas and sites for the disposal of solid high-level and alpha-bearing wastes into geological formations. This report is also intended to provide summary information on many types of geological formations underlying the land masses that might be considered as well as guidance on the geological and hydrological factors that should be investigated to demonstrate the suitability of the formations. In addition, other factors that should be considered in selecting a site for a radioactive waste repository are discussed briefly. The information, as presented, was developed to the extent of current technology for application to the evaluation of deep (greater than about 300 metres below ground level) geological formations in the selection of suitable areas for the disposal of solid or solidified high-level and alpha-bearing wastes. The extreme complexity of many geological environments and of the rock features that govern the presence and circulation of groundwater does not make it feasible to derive strict criteria for the selection of a site for a radioactive waste repository in a geological formation. Each potential repository location must be evaluated according to its own unique geological and hydrological setting. Therefore, only general guidance is offered, and this is done through discussion of the many factors that need to be considered in order to obtain the necessary assurances that the radionuclides will be confined in the geological repository over the required period of time

  18. Site selection factors for repositories of solid high-level and alpha-bearing wastes in geological formations

    Energy Technology Data Exchange (ETDEWEB)

    1977-01-01

    The purpose of this report is to provide guidelines for the selection and evaluation of suitable areas and sites for the disposal of solid high-level and alpha-bearing wastes into geological formations. This report is also intended to provide summary information on many types of geological formations underlying the land masses that might be considered as well as guidance on the geological and hydrological factors that should be investigated to demonstrate the suitability of the formations. In addition, other factors that should be considered in selecting a site for a radioactive waste repository are discussed briefly. The information, as presented, was developed to the extent of current technology for application to the evaluation of deep (greater than about 300 meters below ground level) geological formations in the selection of suitable areas for the disposal of solid or solidified high-level and alpha-bearing wastes. The extreme complexity of many geological environments and of the rock features that govern the presence and circulation of groundwater does not make it feasible to derive strict criteria for the selection of a site for a radioactive waste repository in a geological formation. Each potential repository location must be evaluated according to its own unique geological and hydrological setting. Therefore, only general guidance is offered, and this is done through discussion of the many factors that need to be considered in order to obtain the necessary assurances that the radionuclides will be confined in the geological repository over the required period of time.

  19. Individual and Population Level Resource Selection Patterns of Mountain Lions Preying on Mule Deer along an Urban-Wildland Gradient.

    Directory of Open Access Journals (Sweden)

    John F Benson

    Full Text Available Understanding population and individual-level behavioral responses of large carnivores to human disturbance is important for conserving top predators in fragmented landscapes. However, previous research has not investigated resource selection at predation sites of mountain lions in highly urbanized areas. We quantified selection of natural and anthropogenic landscape features by mountain lions at sites where they consumed their primary prey, mule deer (Odocoileus hemionus, in and adjacent to urban, suburban, and rural areas in greater Los Angeles. We documented intersexual and individual-level variation in the environmental conditions present at mule deer feeding sites relative to their availability across home ranges. Males selected riparian woodlands and areas closer to water more than females, whereas females selected developed areas marginally more than males. Females fed on mule deer closer to developed areas and farther from riparian woodlands than expected based on the availability of these features across their home ranges. We suggest that mortality risk for females and their offspring associated with encounters with males may have influenced the different resource selection patterns between sexes. Males appeared to select mule deer feeding sites mainly in response to natural landscape features, while females may have made kills closer to developed areas in part because these are alternative sites where deer are abundant. Individual mountain lions of both sexes selected developed areas more strongly within home ranges where development occurred less frequently. Thus, areas near development may represent a trade-off for mountain lions such that they may benefit from foraging near development because of abundant prey, but as the landscape becomes highly urbanized these benefits may be outweighed by human disturbance.

  20. The impact of selected sea level rise scenarios in the vicinity of Cochin harbour, India

    Digital Repository Service at National Institute of Oceanography (India)

    DineshKumar, P.K.

    reconfiguration in response to different sea level rise scenarios, the method of empirical distribution of new shorelines using trend lines which accounts for the inherent variability in shoreline response based on differing coastal processes is employed...

  1. Selection of a radon level corresponding to 0.02 WL

    International Nuclear Information System (INIS)

    Haywood, L.R.

    1980-01-01

    The Atomic Energy Control Board requires that the concentration of radon daughters in occupied structures in communities associated with nuclear facilities be less than 0.02 working level. The AECB has been interested in using measurements of radon concentration rather than of working level for compliance at 0.02 WL. It has been found, however, that there is no radon concentration which corresponds to 0.02 WL over a typical range of field conditions. This is principally due to the range of physical characteristics of structures, heating methods, living habits and of outdoor temperatures that may be encountered. A radon level of 2.4 pCi/l would indicate 95 percent of the instances at the three towns studied when working level exceeded 0.02

  2. A case-control study on association of proteasome subunit beta 8 (PSMB8) and transporter associated with antigen processing 1 (TAP1) polymorphisms and their transcript levels in vitiligo from Gujarat.

    Science.gov (United States)

    Jadeja, Shahnawaz D; Mansuri, Mohmmad Shoab; Singh, Mala; Dwivedi, Mitesh; Laddha, Naresh C; Begum, Rasheedunnisa

    2017-01-01

    Autoimmunity has been implicated in the destruction of melanocytes from vitiligo skin. Major histocompatibility complex (MHC) class-II linked genes proteasome subunit beta 8 (PSMB8) and transporter associated with antigen processing 1 (TAP1), involved in antigen processing and presentation have been reported to be associated with several autoimmune diseases including vitiligo. To explore PSMB8 rs2071464 and TAP1 rs1135216 single nucleotide polymorphisms and to estimate the expression of PSMB8 and TAP1 in patients with vitiligo and unaffected controls from Gujarat. PSMB8 rs2071464 polymorphism was genotyped using polymerase chain reaction- restriction fragment length polymorphism (PCR-RFLP) and TAP1 rs1135216 polymorphism was genotyped by amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) in 378 patients with vitiligo and 509 controls. Transcript levels of PSMB8 and TAP1 were measured in the PBMCs of 91 patients and 96 controls by using qPCR. Protein levels of PSMB8 were also determined by Western blot analysis. The frequency of 'TT' genotype of PSMB8 polymorphism was significantly lowered in patients with generalized and active vitiligo (p = 0.019 and p = 0.005) as compared to controls suggesting its association with the activity of the disease. However, TAP1 polymorphism was not associated with vitiligo susceptibility. A significant decrease in expression of PSMB8 at both transcript level (p = 0.002) as well as protein level (p = 0.0460) was observed in vitiligo patients as compared to controls. No significant difference was observed between patients and controls for TAP1 transcripts (p = 0.553). Interestingly, individuals with the susceptible CC genotype of PSMB8 polymorphism showed significantly reduced PSMB8 transcript level as compared to that of CT and TT genotypes (p = 0.009 and p = 0.003 respectively). PSMB8 rs2071464 was associated with generalized and active vitiligo from Gujarat whereas TAP1 rs1135216 showed no association. The

  3. Guidelines for selecting codes for ground-water transport modeling of low-level waste burial sites. Executive summary

    International Nuclear Information System (INIS)

    Simmons, C.S.; Cole, C.R.

    1985-05-01

    This document was written to provide guidance to managers and site operators on how ground-water transport codes should be selected for assessing burial site performance. There is a need for a formal approach to selecting appropriate codes from the multitude of potentially useful ground-water transport codes that are currently available. Code selection is a problem that requires more than merely considering mathematical equation-solving methods. These guidelines are very general and flexible and are also meant for developing systems simulation models to be used to assess the environmental safety of low-level waste burial facilities. Code selection is only a single aspect of the overall objective of developing a systems simulation model for a burial site. The guidance given here is mainly directed toward applications-oriented users, but managers and site operators need to be familiar with this information to direct the development of scientifically credible and defensible transport assessment models. Some specific advice for managers and site operators on how to direct a modeling exercise is based on the following five steps: identify specific questions and study objectives; establish costs and schedules for achieving answers; enlist the aid of professional model applications group; decide on approach with applications group and guide code selection; and facilitate the availability of site-specific data. These five steps for managers/site operators are discussed in detail following an explanation of the nine systems model development steps, which are presented first to clarify what code selection entails

  4. Construction and characterization of stable, constitutively expressed, chromosomal green and red fluorescent transcriptional fusions in the select agents, Bacillus anthracis, Yersinia pestis, Burkholderia mallei, and Burkholderia pseudomallei.

    Science.gov (United States)

    Su, Shengchang; Bangar, Hansraj; Saldanha, Roland; Pemberton, Adin; Aronow, Bruce; Dean, Gary E; Lamkin, Thomas J; Hassett, Daniel J

    2014-10-01

    Here, we constructed stable, chromosomal, constitutively expressed, green and red fluorescent protein (GFP and RFP) as reporters in the select agents, Bacillus anthracis, Yersinia pestis, Burkholderia mallei, and Burkholderia pseudomallei. Using bioinformatic approaches and other experimental analyses, we identified P0253 and P1 as potent promoters that drive the optimal expression of fluorescent reporters in single copy in B. anthracis and Burkholderia spp. as well as their surrogate strains, respectively. In comparison, Y. pestis and its surrogate strain need two chromosomal copies of cysZK promoter (P2cysZK) for optimal fluorescence. The P0253-, P2cysZK-, and P1-driven GFP and RFP fusions were first cloned into the vectors pRP1028, pUC18R6KT-mini-Tn7T-Km, pmini-Tn7-gat, or their derivatives. The resultant constructs were delivered into the respective surrogates and subsequently into the select agent strains. The chromosomal GFP- and RFP-tagged strains exhibited bright fluorescence at an exposure time of less than 200 msec and displayed the same virulence traits as their wild-type parental strains. The utility of the tagged strains was proven by the macrophage infection assays and lactate dehydrogenase release analysis. Such strains will be extremely useful in high-throughput screens for novel compounds that could either kill these organisms, or interfere with critical virulence processes in these important bioweapon agents and during infection of alveolar macrophages. © 2014 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

  5. Automated detection of macular drusen using geometric background leveling and threshold selection.

    Science.gov (United States)

    Smith, R Theodore; Chan, Jackie K; Nagasaki, Takayuki; Ahmad, Umer F; Barbazetto, Irene; Sparrow, Janet; Figueroa, Marta; Merriam, Joanna

    2005-02-01

    Age-related macular degeneration (ARMD) is the most prevalent cause of visual loss in patients older than 60 years in the United States. Observation of drusen is the hallmark finding in the clinical evaluation of ARMD. To segment and quantify drusen found in patients with ARMD using image analysis and to compare the efficacy of image analysis segmentation with that of stereoscopic manual grading of drusen. Retrospective study. University referral center.Patients Photographs were randomly selected from an available database of patients with known ARMD in the ongoing Columbia University Macular Genetics Study. All patients were white and older than 60 years. Twenty images from 17 patients were selected as representative of common manifestations of drusen. Image preprocessing included automated color balancing and, where necessary, manual segmentation of confounding lesions such as geographic atrophy (3 images). The operator then chose among 3 automated processing options suggested by predominant drusen type. Automated processing consisted of elimination of background variability by a mathematical model and subsequent histogram-based threshold selection. A retinal specialist using a graphic tablet while viewing stereo pairs constructed digital drusen drawings for each image. The sensitivity and specificity of drusen segmentation using the automated method with respect to manual stereoscopic drusen drawings were calculated on a rigorous pixel-by-pixel basis. The median sensitivity and specificity of automated segmentation were 70% and 81%, respectively. After preprocessing and option choice, reproducibility of automated drusen segmentation was necessarily 100%. Automated drusen segmentation can be reliably performed on digital fundus photographs and result in successful quantification of drusen in a more precise manner than is traditionally possible with manual stereoscopic grading of drusen. With only minor preprocessing requirements, this automated detection

  6. Spontaneous sleep-wake cycle and sleep deprivation differently induce Bdnf1, Bdnf4 and Bdnf9a DNA methylation and transcripts levels in the basal forebrain and frontal cortex in rats.

    Science.gov (United States)

    Ventskovska, Olena; Porkka-Heiskanen, Tarja; Karpova, Nina N

    2015-04-01

    Brain-derived neurotrophic factor (Bdnf) regulates neuronal plasticity, slow wave activity and sleep homeostasis. Environmental stimuli control Bdnf expression through epigenetic mechanisms, but there are no data on epigenetic regulation of Bdnf by sleep or sleep deprivation. Here we investigated whether 5-methylcytosine (5mC) DNA modification at Bdnf promoters p1, p4 and p9 influences Bdnf1, Bdnf4 and Bdnf9a expression during the normal inactive phase or after sleep deprivation (SD) (3, 6 and 12 h, end-times being ZT3, ZT6 and ZT12) in rats in two brain areas involved in sleep regulation, the basal forebrain and cortex. We found a daytime variation in cortical Bdnf expression: Bdnf1 expression was highest at ZT6 and Bdnf4 lowest at ZT12. Such variation was not observed in the basal forebrain. Also Bdnf p1 and p9 methylation levels differed only in the cortex, while Bdnf p4 methylation did not vary in either area. Factorial analysis revealed that sleep deprivation significantly induced Bdnf1 and Bdnf4 with the similar pattern for Bdnf9a in both basal forebrain and cortex; 12 h of sleep deprivation decreased 5mC levels at the cortical Bdnf p4 and p9. Regression analysis between the 5mC promoter levels and the corresponding Bdnf transcript expression revealed significant negative correlations for the basal forebrain Bdnf1 and cortical Bdnf9a transcripts in only non-deprived rats, while these correlations were lost after sleep deprivation. Our results suggest that Bdnf transcription during the light phase of undisturbed sleep-wake cycle but not after SD is regulated at least partially by brain site-specific DNA methylation. © 2014 European Sleep Research Society.

  7. Infestation Level Influences Oviposition Site Selection in the Tomato Leafminer Tuta absoluta (Lepidoptera: Gelechiidae

    Directory of Open Access Journals (Sweden)

    Thomas Bawin

    2014-11-01

    Full Text Available The tomato leafminer, Tuta absoluta (Lepidoptera: Gelechiidae, is a devastating pest that develops principally on solanaceous plants throughout South and Central America and Europe. In this study, we tested the influence of three levels of T. absoluta infestations on the attraction and oviposition preference of adult T. absoluta. Three infestation levels (i.e., non-infested plants, plants infested with 10 T. absoluta larvae, and plants infested with 20 T. absoluta larvae were presented by pairs in a flying tunnel to groups of T. absoluta adults. We found no differences in terms of adult attraction for either level of infestations. However, female oviposition choice is influenced by larvae density on tomato plants. We discuss the underlying mechanisms and propose recommendations for further research.

  8. Selectivity in Postencoding Connectivity with High-Level Visual Cortex Is Associated with Reward-Motivated Memory.

    Science.gov (United States)

    Murty, Vishnu P; Tompary, Alexa; Adcock, R Alison; Davachi, Lila

    2017-01-18

    Reward motivation has been demonstrated to enhance declarative memory by facilitating systems-level consolidation. Although high-reward information is often intermixed with lower reward information during an experience, memory for high value information is prioritized. How is this selectivity achieved? One possibility is that postencoding consolidation processes bias memory strengthening to those representations associated with higher reward. To test this hypothesis, we investigated the influence of differential reward motivation on the selectivity of postencoding markers of systems-level memory consolidation. Human participants encoded intermixed, trial-unique memoranda that were associated with either high or low-value during fMRI acquisition. Encoding was interleaved with periods of rest, allowing us to investigate experience-dependent changes in connectivity as they related to later memory. Behaviorally, we found that reward motivation enhanced 24 h associative memory. Analysis of patterns of postencoding connectivity showed that, even though learning trials were intermixed, there was significantly greater connectivity with regions of high-level, category-selective visual cortex associated with high-reward trials. Specifically, increased connectivity of category-selective visual cortex with both the VTA and the anterior hippocampus predicted associative memory for high- but not low-reward memories. Critically, these results were independent of encoding-related connectivity and univariate activity measures. Thus, these findings support a model by which the selective stabilization of memories for salient events is supported by postencoding interactions with sensory cortex associated with reward. Reward motivation is thought to promote memory by supporting memory consolidation. Yet, little is known as to how brain selects relevant information for subsequent consolidation based on reward. We show that experience-dependent changes in connectivity of both the

  9. Trust Level and Routing Selection for Mobile Agents in a Smart Home

    NARCIS (Netherlands)

    Nasution, Sandy; Hartel, Pieter H.; Suryana, Nanna; Azman, Nur; Shahib, Shahrin

    The central security concern for systems where agents roam is how to establish trust in the agent. We present a Fuzzy Logic mechanism to calculate a level of trust and an optimal route for a mobile agent system in a smart home. The mechanism consists of two parts. The first part calculates a trust

  10. Levels of Some Selected (Essential-Mn, Zn and Toxic-Al, Sb) Metals in

    African Journals Online (AJOL)

    The fish were dissected, blood samples were obtained and the tissues were digested with standard methodsand assayed for levels of manganese, zinc, aluminum and antimony using inductively coupled plasma mass spectrophotometer (ICP-MS). Results obtained showed that the mean concentration of the elements ...

  11. Mild and selective labeling of malondialdehyde with 2-Aminoacridone: assessment of urinary malondialdehyde levels.

    NARCIS (Netherlands)

    Giera, M.; Kloos, D.-P.; Raaphorst, A.; Mayboroda, O.A.; Deelder, A.M.; Lingeman, H.; Niessen, W.M.A.

    2011-01-01

    Malondialdehyde (MDA) has become a well-established biomarker for oxidative stress. The most commonly used way to determine urinary MDA levels is the thiobarbituric acid (TBA) assay, which suffers from several drawbacks. In this manuscript, we describe a novel derivatization strategy for the highly

  12. Determining Intensity Levels of Selected Wii Fit Activities in College Aged Individuals

    Science.gov (United States)

    Grieser, Joshua D.; Gao, Yong; Ransdell, Lynda; Simonson, Shawn

    2012-01-01

    The purpose of this study was to determine the intensity of Nintendo Wii Fit games using indirect calorimetry. Twenty-five college students completed Wii Fit activity sessions at two difficulty levels within aerobics, strength, and yoga categories. Resting metabolic rate and exercise oxygen uptake were measured, and metabolic equivalents were…

  13. Interviews as a Selection Tool for Entry-Level Hospitality Employees.

    Science.gov (United States)

    Martin, Lynda

    2002-01-01

    Responses from human resource professionals in restaurants (n=85) and hotels (n=118) identified critical entry-level job behaviors that might be used in developing behavior-based interviews. The large variety of responses and lack of agreement suggest that clear identification of these behaviors may be an area of weakness in the hospitality…

  14. Age and gender differences in mate selection criteria for various involvement levels

    NARCIS (Netherlands)

    Buunk, Abraham (Bram); Dijkstra, Pieternel; Fetchenhauer, D.; Kenrick, D.T.

    The present study investigated mate preferences for five different levels of relationship involvement-marriage, serious relationship, falling in love, casual sex, and sexual fantasies-among individuals of 20, 30, 40, 50, and 60 years of age. Consistent with an evolutionary perspective, men preferred

  15. Trust Level and Routing Selection for Mobile Agents in a Smart Home (Extended version)

    NARCIS (Netherlands)

    Nasution, S.; Hartel, Pieter H.; Suryana, N.; Azman, N.; Shahib, S.

    The central security concern for systems where agents roam is how to establish trust in the agent. We present a Fuzzy Logic mechanism to calculate a level of trust and an optimal route for a mobile agent system in a smart home. The mechanism consists of two parts. The first part calculates a trust

  16. Low-level radioactive waste in the Midwest: an economic analysis of selected management options

    International Nuclear Information System (INIS)

    1983-06-01

    Possible economic scenarios for disposal of low-level radioactive waste generated in the Midwest are presented. Relative waste disposal site costs are estimated for each state separately, and for 5-state, 13-state, and 16-state regions. Costs for publicly and privately owned and operated sites are estimated as are incineration and transportation costs

  17. Select transition zone prostate cancers may be radiocurable despite markedly elevated prostate-specific antigen levels

    International Nuclear Information System (INIS)

    D'Amico, Anthony V.; Kaplan, Irving

    1996-01-01

    In 1993, three men with transition zone prostate cancers were described (Stamey et al., J. Urol. 149: 510-515, 1993) who despite high prostate-specific antigen (PSA) levels remained PSA failure-free at 22 months postoperatively. This report illustrates that prolonged PSA failure free survival may be achieved when external beam radiation therapy is used to treat similar patients

  18. Selected trace metal levels in common vegetables grown in NWFP, Pakistan

    International Nuclear Information System (INIS)

    Masud, K.; Jaffar, M.

    1998-01-01

    Seventeen vegetables procured from local markets of Peshawar and its suburbs were analyzed using wet digestion atomic absorption method for Fe, Pb, As, Hg, Cd, Cr, and Ni. The families investigated were: Cucurbitaceae, Solanaceae, Cruciferae, Liliaceae, Araceae, Leguminosae, Malvaceae, Umbelliferae and Zingiberaceae. The heavy metal data are reported at 99%(- + 2S) confidence level for triplicate measurements on sub samples of a given sample with an overall reproducibility of 2% compared with standard material samples. Comparison of averages through t-test indicates that each vegetable group is distinctly different from the other in terms of metal content. Maximum iron was present in garlic, at 4.585 mu g/g, dry weight (edible part-stem) of the Liliacease family. Arsenic was found to be below detection limit in all the vegetable groups. Lead levels were quite low, maximum concentration (0.0200 mu g/g, dry weight) was found in karaila (edible part-fruit). Mercury levels were relatively higher, with maximum concentration (2.590 mu g/g, dry weight) in gem (edible part-stem). The levels of nickel were moderately higher, being maximum (2.375 mu g/g dry weight) in karaila. The overall content of trace metals appeared to be within laid down internationally for safe human consumption, with only a few exceptions. (author)

  19. Student selection: are the school-leaving A-level grades in biology and chemistry important?

    Science.gov (United States)

    Green, A; Peters, T J; Webster, D J

    1993-01-01

    This study determined the relationships of grades in A-level biology and chemistry with examination success or failure during the medical course. By inspection of medical student records, A-level grades at entry to medical school and examination performance were obtained for 128 (91%) of the students who sat their final MBBCh examination at the University of Wales College of Medicine in June 1988. The majority, 92 (72%), completed their medical school careers with no professional examination failures; 15 failed examinations just in the period up to 2nd MB; 11 failed examinations in the clinical period only and 10 failed examinations in both periods. Whereas grade achieved in A-level chemistry was not associated with undergraduate examination performance, students with a grade A or B in A-level biology were less likely to have problems than the others (21% compared with 47%; the difference of 26% has a 95% confidence interval of 7% to 44%). Specifically, there appears to be a strong relationship between a low grade in biology and difficulties in the preclinical examinations. Moreover, for those who have difficulties at this stage, this association continues later in the course.

  20. Leveling the playing field : The selection and motivation effects of tournament prize spread information

    NARCIS (Netherlands)

    Cardinaels, Eddy; Chen, C.X.; Yin, Huaxiang

    Many companies administer wage policies based on tournaments or have different salaries attached to various promotion-based ranks within the company. Employees, however, do not always receive information about pay level differences at higher ranks prior to joining the company. While some companies

  1. Environmental Health Risk Communication: Assessing Levels of Fish-Consumption Literacy among Selected Southeast Asians

    Science.gov (United States)

    Ratnapradipa, Dhitinut; Getz, Thomas D.; Zarcadoolas, Christina; Panzara, Anthony D.; Esposito, Valerie; Wodika, Alicia B.; Caron, Colleen; Migliore, Beverly; Quilliam, Daniela N.

    2010-01-01

    Limited resources have led to a lack of comprehensive state outreach strategies that are geared for non-English speaking constituencies. The investigators worked with Southeast Asian communities in Rhode Island to determine perceptions and levels of trust with various health authorities providing health messaging about fish-consumption practices.…

  2. Wavenumber selection based analysis in Raman spectroscopy improves skin cancer diagnostic specificity at high sensitivity levels (Conference Presentation)

    Science.gov (United States)

    Zhao, Jianhua; Zeng, Haishan; Kalia, Sunil; Lui, Harvey

    2017-02-01

    Background: Raman spectroscopy is a non-invasive optical technique which can measure molecular vibrational modes within tissue. A large-scale clinical study (n = 518) has demonstrated that real-time Raman spectroscopy could distinguish malignant from benign skin lesions with good diagnostic accuracy; this was validated by a follow-up independent study (n = 127). Objective: Most of the previous diagnostic algorithms have typically been based on analyzing the full band of the Raman spectra, either in the fingerprint or high wavenumber regions. Our objective in this presentation is to explore wavenumber selection based analysis in Raman spectroscopy for skin cancer diagnosis. Methods: A wavenumber selection algorithm was implemented using variably-sized wavenumber windows, which were determined by the correlation coefficient between wavenumbers. Wavenumber windows were chosen based on accumulated frequency from leave-one-out cross-validated stepwise regression or least and shrinkage selection operator (LASSO). The diagnostic algorithms were then generated from the selected wavenumber windows using multivariate statistical analyses, including principal component and general discriminant analysis (PC-GDA) and partial least squares (PLS). A total cohort of 645 confirmed lesions from 573 patients encompassing skin cancers, precancers and benign skin lesions were included. Lesion measurements were divided into training cohort (n = 518) and testing cohort (n = 127) according to the measurement time. Result: The area under the receiver operating characteristic curve (ROC) improved from 0.861-0.891 to 0.891-0.911 and the diagnostic specificity for sensitivity levels of 0.99-0.90 increased respectively from 0.17-0.65 to 0.20-0.75 by selecting specific wavenumber windows for analysis. Conclusion: Wavenumber selection based analysis in Raman spectroscopy improves skin cancer diagnostic specificity at high sensitivity levels.

  3. Indoor radon levels in selected hot spring hotels in Guangdong, China

    Energy Technology Data Exchange (ETDEWEB)

    Song Gang [Guangzhou Institute of Geochemistry, Chinese Academy of Science, Guangzhou 510640 (China); Zhang Boyou [Guangzhou Institute of Geochemistry, Chinese Academy of Science, Guangzhou 510640 (China); Wang Xinming [Guangzhou Institute of Geochemistry, Chinese Academy of Science, Guangzhou 510640 (China)]. E-mail: wangxm@gig.ac.cn; Gong Jingping [Guangzhou Institute of Geochemistry, Chinese Academy of Science, Guangzhou 510640 (China); Chan, Daniel [Department of Building Services Engineering, Hong Kong Polytechnic University, Hong Kong (China); Bernett, John [Department of Building Services Engineering, Hong Kong Polytechnic University, Hong Kong (China); Lee, S.C. [Department of Civil and Structural Engineering, Hong Kong Polytechnic University, Hong Kong (China)

    2005-03-01

    Guangdong is one of the provinces that have most hot springs in China, and many hotels have been set up near hot springs, with spring water introduced into the bath inside each hotel room for hot spring bathing to attract tourists. In the present study, we measured radon in indoor and outdoor air, as well as in hot spring waters, in four hot spring hotels in Guangdong by using NR-667A (III) continuous radon detector. Radon concentrations ranged 53.4-292.5 Bq L{sup -1} in the hot spring water and 17.2-190.9 Bq m{sup -3} in outdoor air. Soil gas intrusion, indoor hot spring water use and inefficient ventilation all contributed to the elevated indoor radon levels in the hotel rooms. From the variation of radon levels in closed unoccupied hotel rooms, soil gas intrusion was found to be a very important source of indoor radon in hotel rooms with floors in contact with soils. When there was spring water bathing in the bathes, average radon levels were 10.9-813% higher in the hotel rooms and 13.8-489% higher in bathes compared to their corresponding average levels when there was no spring water use. Spring water use in the hotel rooms had radon transfer coefficients from 1.6x10{sup -4} to 5.0x10{sup -3}. Radon in some hotel rooms maintained in concentrations much higher than guideline levels might thus have potential health risks to the hotel workers, and technical and management measures should be taken to lower their exposure of radon through inhalation.

  4. Indoor radon levels in selected hot spring hotels in Guangdong, China.

    Science.gov (United States)

    Song, Gang; Zhang, Boyou; Wang, Xinming; Gong, Jingping; Chan, Daniel; Bernett, John; Lee, S C

    2005-03-01

    Guangdong is one of the provinces that have most hot springs in China, and many hotels have been set up near hot springs, with spring water introduced into the bath inside each hotel room for hot spring bathing to attract tourists. In the present study, we measured radon in indoor and outdoor air, as well as in hot spring waters, in four hot spring hotels in Guangdong by using NR-667A (III) continuous radon detector. Radon concentrations ranged 53.4-292.5 Bq L(-1) in the hot spring water and 17.2-190.9 Bq m(-3) in outdoor air. Soil gas intrusion, indoor hot spring water use and inefficient ventilation all contributed to the elevated indoor radon levels in the hotel rooms. From the variation of radon levels in closed unoccupied hotel rooms, soil gas intrusion was found to be a very important source of indoor radon in hotel rooms with floors in contact with soils. When there was spring water bathing in the bathes, average radon levels were 10.9-813% higher in the hotel rooms and 13.8-489% higher in bathes compared to their corresponding average levels when there was no spring water use. Spring water use in the hotel rooms had radon transfer coefficients from 1.6x10(-4) to 5.0x10(-3). Radon in some hotel rooms maintained in concentrations much higher than guideline levels might thus have potential health risks to the hotel workers, and technical and management measures should be taken to lower their exposure of radon through inhalation.

  5. Indoor radon levels in selected hot spring hotels in Guangdong, China

    International Nuclear Information System (INIS)

    Song Gang; Zhang Boyou; Wang Xinming; Gong Jingping; Chan, Daniel; Bernett, John; Lee, S.C.

    2005-01-01

    Guangdong is one of the provinces that have most hot springs in China, and many hotels have been set up near hot springs, with spring water introduced into the bath inside each hotel room for hot spring bathing to attract tourists. In the present study, we measured radon in indoor and outdoor air, as well as in hot spring waters, in four hot spring hotels in Guangdong by using NR-667A (III) continuous radon detector. Radon concentrations ranged 53.4-292.5 Bq L -1 in the hot spring water and 17.2-190.9 Bq m -3 in outdoor air. Soil gas intrusion, indoor hot spring water use and inefficient ventilation all contributed to the elevated indoor radon levels in the hotel rooms. From the variation of radon levels in closed unoccupied hotel rooms, soil gas intrusion was found to be a very important source of indoor radon in hotel rooms with floors in contact with soils. When there was spring water bathing in the bathes, average radon levels were 10.9-813% higher in the hotel rooms and 13.8-489% higher in bathes compared to their corresponding average levels when there was no spring water use. Spring water use in the hotel rooms had radon transfer coefficients from 1.6x10 -4 to 5.0x10 -3 . Radon in some hotel rooms maintained in concentrations much higher than guideline levels might thus have potential health risks to the hotel workers, and technical and management measures should be taken to lower their exposure of radon through inhalation

  6. Eukaryotic transcription factors

    DEFF Research Database (Denmark)

    Staby, Lasse; O'Shea, Charlotte; Willemoës, Martin

    2017-01-01

    Gene-specific transcription factors (TFs) are key regulatory components of signaling pathways, controlling, for example, cell growth, development, and stress responses. Their biological functions are determined by their molecular structures, as exemplified by their structured DNA-binding domains...... regions with function-related, short sequence motifs and molecular recognition features with structural propensities. This review focuses on molecular aspects of TFs, which represent paradigms of ID-related features. Through specific examples, we review how the ID-associated flexibility of TFs enables....... It is furthermore emphasized how classic biochemical concepts like allostery, conformational selection, induced fit, and feedback regulation are undergoing a revival with the appreciation of ID. The review also describes the most recent advances based on computational simulations of ID-based interaction mechanisms...

  7. The future of event-level information repositories, indexing, and selection in ATLAS

    CERN Document Server

    Barberis, D; The ATLAS collaboration; Dimitrov, G; Doherty, T; Gallas, E; Hrivnac, J; Malon, D; Nairz, A; Nowak, M; Quilty, D; Sorokoletov, R; Van Gemmeren, P; Zhang, Q

    2014-01-01

    ATLAS maintains a rich corpus of event-by-event information that provides a global view of virtually all of the billions of events the collaboration has seen or simulated, along with sufficient auxiliary information to navigate to and retrieve data for any event at any production processing stage. This unique resource has been employed for a range of purposes, from monitoring, statistics, anomaly detection, and integrity checking to event picking, subset selection, and sample extraction. Recent years of data-taking provide a foundation for assessment of how this resource has and has not been used in practice, of the uses for which it should be optimized, of how it should be deployed and provisioned for scalability to future data volumes, and of the areas in which enhancements to functionality would be most valuable. \

  8. A dynamic voltage restorer (DVR) with selective harmonic compensation at medium voltage level

    DEFF Research Database (Denmark)

    Newman, M.J.; Holmes, D.G.; Nielsen, J.G.

    2005-01-01

    Dynamic voltage restorers (DVRs) are now becoming more established in industry to reduce the impact of voltage sags to sensitive loads. However, DVRs spend most of their time in standby mode, since voltage sags occur very infrequently, and hence their utilization is low. In principle, it would...... be advantageous if the series-connected inverter of a DVR could also be used to compensate for any steady-state load voltage harmonics, since this would increase the power quality "value-added" benefits to the grid system. However, before this can be done, consideration must be given to the control of steady......-state power through the DVR, the increased losses, and the low modulation depths at which the scheme must operate to achieve acceptable harmonic compensation performance. This paper presents a selective harmonic feedback control strategy that can be easily added to medium-voltage DVR systems to provide...

  9. Selective and context-dependent effects of chemical stress across trophic levels at the basis of marine food webs.

    Science.gov (United States)

    Mensens, Christoph; De Laender, Frederik; Janssen, Colin R; Rivera, Frances Camille; Sabbe, Koen; De Troch, Marleen

    2018-04-26

    Human activities increasingly impact the functioning of marine food webs, but anthropogenic stressors are seldom included in ecological study designs. Diet quality, as distinct from just diet quantity, has moreover rarely been highlighted in food web studies in a stress context. We measured the effects of metal and pesticide stress (copper and atrazine) on the contribution of a benthic intertidal diatom community to two processes that are key to the functioning of intertidal systems: biomass (diet quantity) and lipid (diet quality) production. We then examined if stressors affected diatom functioning by selectively targeting the species contributing most to functioning (selective stress effects) or by changing the species' functional contribution (context-dependent effects). Finally, we tested if stress-induced changes in diet quality altered the energy flow to the diatoms' main grazers (harpacticoid copepods). Diatom diet quantity was reduced by metal stress but not by low pesticide levels due to the presence of an atrazine-tolerant, mixotrophic species. Selective effects of the pesticide reduced diatom diet quality by 60% and 75% at low and high pesticide levels respectively, by shifting diatom community structure from dominance by lipid-rich species toward dominance by an atrazine-tolerant, but lipid-poor, species. Context-dependent effects did not affect individual diatom lipid content at low levels of both stressors, but caused diatoms to lose 40% of their lipids at high copper stress. Stress-induced changes in diet quality predicted the energy flow from the diatoms to their copepod consumers, which lost half of their lipids when feeding on diatoms grown under low and high pesticide and high metal stress. Selective pesticide effects were a more important threat for trophic energy transfer than context-dependent effects of both stressors, with shifts in diatom community structure affecting the energy flow to their copepod grazers at stress levels where no

  10. Altered Circulating Levels of Serotonin and Immunological Changes in Laying Hens Divergently Selected for Feather Pecking Behavior

    DEFF Research Database (Denmark)

    Buitenhuis, Albert Johannes; Kjaer, Jørgen B.; Labouriau, Rodrigo

    2006-01-01

    The aim of this study was to investigate the changes in immunological parameters as well as changes with respect to plasma levels of serotonin and tryptophan in lines selected for and against feather pecking (FP) behavior [high FP (HP) line and low FP (LP) line] for 5 generations. The hens from...... response to infectious bursal disease virus vaccination after 1 wk post-vaccination compared with the control and LP lines. The number of white blood cells (P

  11. Selectivity in Postencoding Connectivity with High-Level Visual Cortex Is Associated with Reward-Motivated Memory

    OpenAIRE

    Murty, Vishnu P.; Tompary, Alexa; Adcock, R. Alison; Davachi, Lila

    2017-01-01

    Reward motivation has been demonstrated to enhance declarative memory by facilitating systems-level consolidation. Although high-reward information is often intermixed with lower reward information during an experience, memory for high value information is prioritized. How is this selectivity achieved? One possibility is that postencoding consolidation processes bias memory strengthening to those representations associated with higher reward. To test this hypothesis, we investigated the influ...

  12. Alternatives generation and analysis for the phase 1 high-level waste pretreatment process selection

    International Nuclear Information System (INIS)

    Manuel, A.F.

    1997-01-01

    This report evaluates the effects of enhanced sludge washing and sludge washing without caustic leaching during the preparation of the Phase 1 high-level waste feeds. The pretreatment processing alternatives are evaluated against their ability to satisfy contractual, cost minimization, and other criteria. The information contained in this report is consistent with, and supplemental to, the Tank Waste Remediation System Operation and Utilization Plan (Kirkbride et al. 1997)

  13. Investigation of levels of organic pollutants in selected areas in the Philippines

    International Nuclear Information System (INIS)

    Cunanan, S.A.; Santos, F.L.; Solomero, S.S.

    1980-01-01

    Water and sediment samples from the Metro Manila, Camarines Sur and Iligan City were collected and analyzed for polychlorinated biphenyls (PCBs). Analysis was done by gas chromatography using an electron capture detector. No PCBs was detected in the 74 sediment samples analyzed at a minimum detection level of 40 ppb. Analysis of 44 water samples showed no PCB's at a detection limit of 1 ppb. (author)

  14. Selection of the best security controls for rapid development of enterprise-level cyber security

    OpenAIRE

    Tytarenko, Oleksandr

    2017-01-01

    Approved for public release; distribution is unlimited State-supported cyber attacks, cyber espionage campaigns, and hacktivist movements have forced many states to accelerate their cyber defense development in order to achieve at least a minimum level of protection against expanding threats of cyber space. As with any other development effort, cyber capability development requires resources of time, money, and people, which in most cases are very restricted. To rapidly build up the first ...

  15. Alternatives generation and analysis for the phase 1 high-level waste pretreatment process selection

    Energy Technology Data Exchange (ETDEWEB)

    Manuel, A.F.

    1997-10-02

    This report evaluates the effects of enhanced sludge washing and sludge washing without caustic leaching during the preparation of the Phase 1 high-level waste feeds. The pretreatment processing alternatives are evaluated against their ability to satisfy contractual, cost minimization, and other criteria. The information contained in this report is consistent with, and supplemental to, the Tank Waste Remediation System Operation and Utilization Plan (Kirkbride et al. 1997).

  16. Current R and D Status on High-Level Radioactive Waste Disposal in Selected Countries

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Youn Myoung; Hwang, Yong Soo

    2008-11-15

    Current R and D status of such countries moving forward as the United States, Sweden, France, Japan and a few other countries for high-level radioactive waste (HLW) disposal in deep geological formation has been reviewed. Even though no HLW repositories have not practically constructed nor operated yet, lots of related R and D are being proceeded in many countries as well as in Korea. Through this brief review further progress is anticipated in this related R and D area in Korea.

  17. Selection of candidate canister materials for high-level nuclear waste containment in a tuff repository

    International Nuclear Information System (INIS)

    McCright, R.D.; Weiss, H.; Juhas, M.C.; Logan, R.W.

    1983-11-01

    A repository located at Yucca Mountain at the Nevada Test Site is a potential site for permanent geological disposal of high-level nuclear waste. The repository can be located in a horizon in welded tuff, a volcanic rock, which is above the static water level at this site. The environmental conditions in this unsaturated zone are expected to be air and water vapor dominated for much of the containment period. Type 304L stainless steel is the reference material for fabricating canisters to contain the solid high-level wastes. Alternative stainless alloys are considered because of possible susceptibility of 304L to localized and stress forms of corrosion. For the reprocessed glass wastes, the canisters serve as the recipient for pouring the glass with the result that a sensitized microstructure may develop because of the times at elevated temperatures. Corrosion testing of the reference and alternative materials has begun in tuff-conditioned water and steam environments. 21 references, 8 figures, 8 tables

  18. QUALITY LEVEL-RELATED DIFFERENCES IN SELECTED MORPHOLOGICAL BODY CHARACTERISTICS AND MOTOR ABILITIES OF GOALKEEPERS IN TEAM HANDBALL

    Directory of Open Access Journals (Sweden)

    Marko Šibila

    2010-09-01

    Full Text Available The aim of the present study is to identify the quality level-related differences between two groups of team handball goalkeepers in selected morphological body characteristics and motor abilities. A group of 36 senior goalkeepers who were members of first and second Slovenian handball league clubs (age: 22,6 ± 5,4 yr, height: 185,8 ± 4,7 cm, body weight: 88,7 ± 9,1 kg, training experience: 11,8 ± 4,8 yr participated in the present study. The goalkeepers were divided in two groups, according to their competition level. The sample of variables consisted of age and competition experience data, four morphological body characteristics and of six motor ability tests. In order to determine differences between two groups of goalkeepers in selected morphologic and motor variables a one–way analysis of variance (one-way ANOVA was employed. Findings of the present study indicate existing of quality level-related differences between two groups of team handball goalkeepers in selected morphological body characteristics and motor abilities. Further individualization and careful planning of training process of the goalkeepers is essential if we want to improve for goalkeepers’ important motor abilities and morphological body characteristics.

  19. Large-scale integration of small molecule-induced genome-wide transcriptional responses, Kinome-wide binding affinities and cell-growth inhibition profiles reveal global trends characterizing systems-level drug action

    Directory of Open Access Journals (Sweden)

    Dusica eVidovic

    2014-09-01

    Full Text Available The Library of Integrated Network-based Cellular Signatures (LINCS project is a large-scale coordinated effort to build a comprehensive systems biology reference resource. The goals of the program include the generation of a very large multidimensional data matrix and informatics and computational tools to integrate, analyze, and make the data readily accessible. LINCS data include genome-wide transcriptional signatures, biochemical protein binding profiles, cellular phenotypic response profiles and various other datasets for a wide range of cell model systems and molecular and genetic perturbations. Here we present a partial survey of this data facilitated by data standards and in particular a robust compound standardization workflow; we integrated several types of LINCS signatures and analyzed the results with a focus on mechanism of action and chemical compounds. We illustrate how kinase targets can be related to disease models and relevant drugs. We identified some fundamental trends that appear to link Kinome binding profiles and transcriptional signatures to chemical information and biochemical binding profiles to transcriptional responses independent of chemical similarity. To fill gaps in the datasets we developed and applied predictive models. The results can be interpreted at the systems level as demonstrated based on a large number of signaling pathways. We can identify clear global relationships, suggesting robustness of cellular responses to chemical perturbation. Overall, the results suggest that chemical similarity is a useful measure at the systems level, which would support phenotypic drug optimization efforts. With this study we demonstrate the potential of such integrated analysis approaches and suggest prioritizing further experiments to fill the gaps in the current data.

  20. Transcript levels of members of the SLC2 and SLC5 families of glucose transport proteins in eel swimbladder tissue: the influence of silvering and the influence of a nematode infection.

    Science.gov (United States)

    Schneebauer, Gabriel; Mauracher, David; Fiechtner, Birgit; Pelster, Bernd

    2018-04-01

    The rate of glucose metabolism has been shown to be correlated to glucose uptake in swimbladder gas gland cells. Therefore, it is assumed that in the European eel silvering, i.e., the preparation of the eel for the spawning migration to the Sargasso Sea, coincides with an enhanced capacity for glucose uptake. To test this hypothesis expression of all known glucose transport proteins has been assessed at the transcript level in yellow and in silver eels, and we also included Anguillicola crassus infected swimbladders. Glucose uptake by rete mirabile endothelial cells could be crucial for the countercurrent exchange capacity of the rete. Therefore, this tissue was also included in our analysis. The results revealed expression of ten different members of the slc2 family of glucose transporters, of four slc5 family members, and of kiaa1919 in gas gland tissue. Glucose transporters of the slc2 family were expressed at very high level, and slc2a1b made up about 80% of all slc2 family members, irrespective of the developmental state or the infection status of the eel. Overall, the slc5 family contributed to only about 8% of all detected glucose transport transcripts in gas gland tissue, and the slc2 family to more than 85%. In rete capillaries, the contribution of sodium-dependent glucose transporters was significantly higher, leaving only 66% for the slc2 family of glucose transporters. Neither silvering nor the infection status had a significant effect on the expression of glucose transporters in swimbladder gas gland tissue, suggesting that glucose metabolism of eel gas gland cells may not be related to transcriptional changes of glucose transport proteins.

  1. Iron Loading Selectively Increases Hippocampal Levels of Ubiquitinated Proteins and Impairs Hippocampus-Dependent Memory.

    Science.gov (United States)

    Figueiredo, Luciana Silva; de Freitas, Betânia Souza; Garcia, Vanessa Athaíde; Dargél, Vinícius Ayub; Köbe, Luiza Machado; Kist, Luiza Wilges; Bogo, Maurício Reis; Schröder, Nadja

    2016-11-01

    Alterations of brain iron levels have been observed in a number of neurodegenerative disorders. We have previously demonstrated that iron overload in the neonatal period results in severe and persistent memory deficits in the adulthood. Protein degradation mediated by the ubiquitin-proteasome system (UPS) plays a central regulatory role in several cellular processes. Impairment of the UPS has been implicated in the pathogenesis of neurodegenerative disorders. Here, we examined the effects of iron exposure in the neonatal period (12th-14th day of postnatal life) on the expression of proteasome β-1, β-2, and β-5 subunits, and ubiquitinated proteins in brains of 15-day-old rats, to evaluate the immediate effect of the treatment, and in adulthood to assess long-lasting effects. Two different memory types, emotionally motivated conditioning and object recognition were assessed in adult animals. We found that iron administered in the neonatal period impairs both emotionally motivated and recognition memory. Polyubiquitinated protein levels were increased in the hippocampus, but not in the cortex, of adult animals treated with iron. Gene expression of subunits β1 and β5 was affected by age, being higher in the early stages of development in the hippocampus, accompanied by an age-related increase in polyubiquitinated protein levels in adults. In the cortex, gene expression of the three proteasome subunits was significantly higher in adulthood than in the neonatal period. These findings suggest that expression of proteasome subunits and activity are age-dependently regulated. Iron exposure in the neonatal period produces long-lasting harmful effects on the UPS functioning, which may be related with iron-induced memory impairment.

  2. Research for Preseismic Phenomena on the Underground Water Level and Temperature in Selected Areas of Greece

    Science.gov (United States)

    Contadakis, M. E.; Asteriadis, G.

    1997-08-01

    A comprehensive study of the tectonic activity require the contribution of a variety of methods, geological, seismic, geodetic, satellite etc., being currently available in our days. On the other hand, the risk evaluation in areas of high seismicity, like this one of the South Balkan Peninsula, is of vital importance. To this purpose an interdisciplinary following up of the tectonic activity in the area may provide the best provision to the administration for an effective confrontation and intervention for the elimination of the possible disastrous effects in human life cost, financial and social cost of the communities, to which may result a strong earthquake. Among the various methods of indirect monitoring of the tectonic activity in an area, which in addition is of a low cost, is that of the following up of the underground water level and temperature changes in the area of interest. This method is based on the fact that tectonic activity is expected to result to tectonic stresses producing alterations to the local water table which in its turn is expected is expected to be observed as variation of the underground water level and temperature. The method of the following up of the underground water and temperature changes has been applied, among others by the Department of Geodesy and Surveying of the University of Thessaloniki in two areas of high seismicity in Greece: (a) The seismic zone of the lake Volvi in North Greece (40.5 deg N and 23.5 deg E) for ten years (1983-1992) and (b) the area of South Thessaly (39.2 deg N and 21 deg E) for three years (1994-1996). The statistical analysis of the observations, shows that the low frequency constituent (Sa,Ssa,Mf,Mm) of the earth tides and the barometric pressure have a small influence on the water level measurements. The shallow underground water network of South Thessaly is more sensitive to the non tectonic factors than the network of Volvi. Tentative correlation of the underground wat! er and temperature

  3. On Usage of Pareto curves to Select Wind Turbine Controller Tunings to the Wind Turbulence Level

    DEFF Research Database (Denmark)

    Odgaard, Peter Fogh

    2015-01-01

    Model predictive control has in recently publications shown its potential for lowering of cost of energy of modern wind turbines. Pareto curves can be used to evaluate performance of these controllers with multiple conflicting objectives of power and fatigue loads. In this paper an approach...... to update an model predictive wind turbine controller tuning as the wind turbulence increases, as increased turbulence levels results in higher loads for the same controller tuning. In this paper the Pareto curves are computed using an industrial high fidelity aero-elastic model. Simulations show...

  4. On selection of geological medium for disposal of high-level radwaste

    International Nuclear Information System (INIS)

    Min Maozhong

    1991-01-01

    The present paper briefly reviews the suitability of some rocks as geological disposal repositories of high-level radwaste (HLW). The suitable rocks for geological ogi disposal of HLW are rock salt (salt diapir, bedded salt), granite, argillaceous rocks, tuff, basalt, gabbro, diabase, anhydrite, marine sedimentary rocks etc., especially, rock salt, granite, and argillaceous rocks. The data of principal hydraulic properties, mechanical-physical properties for various rocks in typical environment which might be considered for disposal purposes are also given in this paper. These data give a reference to China's geological disposal of HLW in the future

  5. Alternatives Generation and Analysis for Phase 1 High-Level Waste Feed Tanks Selection

    International Nuclear Information System (INIS)

    CRAWFORD, T.W.

    1999-01-01

    A recent revision of the US Department of Energy privatization contract for the immobilization of high-level waste (HLW) at Hanford necessitates the investigation of alternative waste feed sources to meet contractual feed requirements. This analysis identifies wastes to be considered as HLW feeds and develops and conducts alternative analyses to comply with established criteria. A total of 12,426 cases involving 72 waste streams are evaluated and ranked in three cost-based alternative models. Additional programmatic criteria are assessed against leading alternative options to yield an optimum blended waste feed stream

  6. Plasma metabolomics reveal alterations of sphingo- and glycerophospholipid levels in non-diabetic carriers of the transcription factor 7-like 2 polymorphism rs7903146.

    Science.gov (United States)

    Then, Cornelia; Wahl, Simone; Kirchhofer, Anna; Grallert, Harald; Krug, Susanne; Kastenmüller, Gabi; Römisch-Margl, Werner; Claussnitzer, Melina; Illig, Thomas; Heier, Margit; Meisinger, Christa; Adamski, Jerzy; Thorand, Barbara; Huth, Cornelia; Peters, Annette; Prehn, Cornelia; Heukamp, Ina; Laumen, Helmut; Lechner, Andreas; Hauner, Hans; Seissler, Jochen

    2013-01-01

    Polymorphisms in the transcription factor 7-like 2 (TCF7L2) gene have been shown to display a powerful association with type 2 diabetes. The aim of the present study was to evaluate metabolic alterations in carriers of a common TCF7L2 risk variant. Seventeen non-diabetic subjects carrying the T risk allele at the rs7903146 TCF7L2 locus and 24 subjects carrying no risk allele were submitted to intravenous glucose tolerance test and euglycemic-hyperinsulinemic clamp. Plasma samples were analysed for concentrations of 163 metabolites through targeted mass spectrometry. TCF7L2 risk allele carriers had a reduced first-phase insulin response and normal insulin sensitivity. Under fasting conditions, carriers of TCF7L2 rs7903146 exhibited a non-significant increase of plasma sphingomyelins (SMs), phosphatidylcholines (PCs) and lysophosphatidylcholines (lysoPCs) species. A significant genotype effect was detected in response to challenge tests in 6 SMs (C16:0, C16:1, C18:0, C18:1, C24:0, C24:1), 5 hydroxy-SMs (C14:1, C16:1, C22:1, C22:2, C24:1), 4 lysoPCs (C14:0, C16:0, C16:1, C17:0), 3 diacyl-PCs (C28:1, C36:6, C40:4) and 4 long-chain acyl-alkyl-PCs (C40:2, C40:5, C44:5, C44:6). Plasma metabolomic profiling identified alterations of phospholipid metabolism in response to challenge tests in subjects with TCF7L2 rs7903146 genotype. This may reflect a genotype-mediated link to early metabolic abnormalities prior to the development of disturbed glucose tolerance.

  7. A low-pH medium in vitro or the environment within a macrophage decreases the transcriptional levels of fimA, fimZ and lrp in Salmonella enterica serovar Typhimurium.

    Science.gov (United States)

    Wang, Ke-Chuan; Hsu, Yuan-Hsun; Huang, Yi-Ning; Chen, Ter-Hsin; Lin, Jiunn-Horng; Hsuan, Shih-Ling; Chien, Maw-Sheng; Lee, Wei-Cheng; Yeh, Kuang-Sheng

    2013-09-01

    Many Salmonella Typhimurium isolates produce type 1 fimbriae and exhibit fimbrial phase variation in vitro. Static broth culture favours the production of fimbriae, while solid agar medium inhibits the generation of these appendages. Little information is available regarding whether S. Typhimurium continues to produce type 1 fimbriae during in vivo growth. We used a type 1 fimbrial phase-variable strain S. Typhimurium LB5010 and its derivatives to infect RAW 264.7 macrophages. Following entry into macrophages, S. Typhimurium LB5010 gradually decreased the transcript levels of fimbrial subunit gene fimA, positive regulatory gene fimZ, and global regulatory gene lrp. A similar decrease in transcript levels was detected by RT-PCRwhen the pH of static brothmediumwas shifted frompH 7 to amore acidic pH 4. A fimA-deleted strain continued to multiply within macrophages as did the parental strain. An lrp deletion strain was unimpaired for in vitro growth at pH 7 or pH 4, while a strain harboring an lrp-containing plasmid exhibited impaired in vitro growth at pH 4. We propose that acidic medium, which resembles one aspect of the intracellular environment in a macrophage, inhibits type 1 fimbrial production by down-regulation of the expression of lrp, fimZ and fimA.

  8. Assessment of DDT levels in selected environmental media and biological samples from Mexico and Central America.

    Science.gov (United States)

    Pérez-Maldonado, Iván N; Trejo, Antonio; Ruepert, Clemens; Jovel, Reyna del Carmen; Méndez, Mónica Patricia; Ferrari, Mirtha; Saballos-Sobalvarro, Emilio; Alexander, Carlos; Yáñez-Estrada, Leticia; Lopez, Dania; Henao, Samuel; Pinto, Emilio R; Díaz-Barriga, Fernando

    2010-03-01

    Taking into account the environmental persistence and the toxicity of DDT, the Pan American Health Organization (PAHO) organized a surveillance program in Mesoamerica which included the detection of residual DDT in environmental (soil) and biological samples (fish tissue and children's blood). This program was carried out in communities from Mexico, Guatemala, El Salvador, Honduras, Nicaragua, Costa Rica and Panama. This paper presents the first report of that program. As expected, the results show that the levels for [summation operator] DDT in soil (outdoor or indoor) and fish samples in the majority of the locations studied are below guidelines. However, in some locations, we found children with high concentrations of DDT as in Mexico (mean level 50.2 ng/mL). Furthermore, in some communities and for some matrices, the DDT/DDE quotient is higher than one and this may reflect a recent DDT exposure. Therefore, more efforts are needed to avoid exposure and to prevent the reintroduction of DDT into the region. In this regard it is important to know that under the surveillance of PAHO and with the support of UNEP, a regional program in Mesoamerica for the collection and disposal of DDT and other POPs stockpiles is in progress. Copyright (c) 2009 Elsevier Ltd. All rights reserved.

  9. [Level of selected antibacterial tear proteins in children with diabetes type 1].

    Science.gov (United States)

    Moll, Agnieszka; Wyka, Krystyna; Młynarski, Wojciech; Niwald, Anna

    2011-01-01

    Antibacterial immunity in diabetes is impaired, which increases the risk of general and local infections. The aim of the study was to evaluate non-specific local antibacterial immunity based on lactoferrin and lysozyme concentration in tears in children with diabetes type 1. Children at the age of 10-18 years old were studied. Group 1. consisted of children without diabetes, group 2. included patients with new onset of diabetes and group 3. consisted of children with decade-long diabetes. Among all patients tears were collected from inferior coniunctival fornix with hematocrit glass capillaries in purpose to measure lactoferrin and lysozyme concentration. ELISA method was used in laboratory testing. Level of lactoferrin did not differ significantly among all groups. Concentration of lysozyme was statistically lower in group with decade-long diabetes (group 3.) compared to patients without diabetes. Mild correlation between lactoferrin and lysozyme levels was seen in individual patients in whole group of probands together. Diabetes type 1 in children is associated with significant changes in concentration of tear proteins, which contribute to antibacterial immunity.

  10. Research in the selection of very low level radioactive waste disposal site in southwest China

    International Nuclear Information System (INIS)

    Tuo, Xianguo; Long, Qiong; Zhong, Hongmei; Xu, Zhengqi; Mu, Keliang; Gao, Lan

    2008-01-01

    The ultimate goal of Chinese Radioactive Nuclear Waste Management and Disposal Security is that must use proper and optimized ways to manage radioactive waste and make sure human beings and the environment either at the present or in the future can be free from any unacceptable risks. According to the goal, this paper presents an overview of comprehensive site characterization work that comprises investigations of physical geography, climatology, geology and hydrogeology, as well as geological hazard on two candidate Very Low Level Radioactive Waste (VLLW) disposal sites (Site 1 and Site 2) which are both located in the south west of China. The results showed that there are many similarities in the regional extent of the two sites, but many distinct differences are found in terrain and topographic features, granule stratum, hydraulic gradient, and so on. On the whole, the two alternative sites are in line with the requirements for very low level radioactive waste disposal, and Site 1 is superior to Site 2. (author)

  11. Between “design” and “bricolage”: Genetic networks, levels of selection, and adaptive evolution

    Science.gov (United States)

    Wilkins, Adam S.

    2007-01-01

    The extent to which “developmental constraints” in complex organisms restrict evolutionary directions remains contentious. Yet, other forms of internal constraint, which have received less attention, may also exist. It will be argued here that a set of partial constraints below the level of phenotypes, those involving genes and molecules, influences and channels the set of possible evolutionary trajectories. At the top-most organizational level there are the genetic network modules, whose operations directly underlie complex morphological traits. The properties of these network modules, however, have themselves been set by the evolutionary history of the component genes and their interactions. Characterization of the components, structures, and operational dynamics of specific genetic networks should lead to a better understanding not only of the morphological traits they underlie but of the biases that influence the directions of evolutionary change. Furthermore, such knowledge may permit assessment of the relative degrees of probability of short evolutionary trajectories, those on the microevolutionary scale. In effect, a “network perspective” may help transform evolutionary biology into a scientific enterprise with greater predictive capability than it has hitherto possessed. PMID:17494754

  12. Between "design" and "bricolage": genetic networks, levels of selection, and adaptive evolution.

    Science.gov (United States)

    Wilkins, Adam S

    2007-05-15

    The extent to which "developmental constraints" in complex organisms restrict evolutionary directions remains contentious. Yet, other forms of internal constraint, which have received less attention, may also exist. It will be argued here that a set of partial constraints below the level of phenotypes, those involving genes and molecules, influences and channels the set of possible evolutionary trajectories. At the top-most organizational level there are the genetic network modules, whose operations directly underlie complex morphological traits. The properties of these network modules, however, have themselves been set by the evolutionary history of the component genes and their interactions. Characterization of the components, structures, and operational dynamics of specific genetic networks should lead to a better understanding not only of the morphological traits they underlie but of the biases that influence the directions of evolutionary change. Furthermore, such knowledge may permit assessment of the relative degrees of probability of short evolutionary trajectories, those on the microevolutionary scale. In effect, a "network perspective" may help transform evolutionary biology into a scientific enterprise with greater predictive capability than it has hitherto possessed.

  13. Atlas(®) Listeria monocytogenes LmG2 Detection Assay Using Transcription Mediated Amplification to Detect Listeria monocytogenes in Selected Foods and Stainless Steel Surface.

    Science.gov (United States)

    Bres, Vanessa; Yang, Hua; Hsu, Ernie; Ren, Yan; Cheng, Ying; Wisniewski, Michele; Hanhan, Maesa; Zaslavsky, Polina; Noll, Nathan; Weaver, Brett; Campbell, Paul; Reshatoff, Michael; Becker, Michael

    2014-01-01

    The Atlas Listeria monocytogenes LmG2 Detection Assay, developed by Roka Bioscience Inc., was compared to a reference culture method for seven food types (hot dogs, cured ham, deli turkey, chicken salad, vanilla ice cream, frozen chocolate cream pie, and frozen cheese pizza) and one surface (stainless steel, grade 316). A 125 g portion of deli turkey was tested using a 1:4 food:media dilution ratio, and a 25 g portion for all other foods was tested using 1:9 food:media dilution ratio. The enrichment time and media for Roka's method was 24 to 28 h for 25 g food samples and environmental surfaces, and 44 to 48 h for 125 g at 35 ± 2°C in PALCAM broth containing 0.02 g/L nalidixic acid. Comparison of the Atlas Listeria monocytogenes LmG2 Detection Assay to the reference method required an unpaired approach. For each matrix, 20 samples inoculated at a fractional level and five samples inoculated at a high level with a different strain of Listeria monocytogenes were tested by each method. The Atlas Listeria monocytogenes LmG2 Detection Assay was compared to the Official Methods of Analysis of AOAC INTERNATIONAL 993.12 method for dairy products, the U.S. Department of Agriculture, Food Safety and Inspection Service, Microbiology Laboratory Guidebook 8.08 method for ready-to-eat meat and environmental samples, and the U.S. Food and Drug Administration Bacteriological Analytical Manual, Chapter 10 method for frozen foods. In the method developer studies, Roka's method, at 24 h (or 44 h for 125 g food samples), had 126 positives out of 200 total inoculated samples, compared to 102 positives for the reference methods at 48 h. In the independent laboratory studies, vanilla ice cream, deli turkey and stainless steel grade 316 were evaluated. Roka's method, at 24 h (or 44 h for 125 g food samples), had 64 positives out of 75 total inoculated samples compared to 54 positives for the reference methods at 48 h. The Atlas Listeria monocytogenes LmG2 Detection Assay detected all 50

  14. Matching Level between Professors’ Selected Media and Emotional-Perception Preferences of Students

    Directory of Open Access Journals (Sweden)

    Hedayati N

    2015-12-01

    Full Text Available Aims: Considering individual differences and different learning styles in the learners is necessary in more effective learning. If the used learning style may be fully correspond with the students’ preffered style, there is a better learning performance. The aim of this study was to assess the conformity of the students’ learning styles with educational media and technologies used by the teachers at Isfahan University of Medical Sciences. Instrument & Methods: In the descriptive-correlational study, 90 medicine and dentistry students of Isfahan University were randomly selected via Stratified Sampling method in 2014-15 academic year. The study tool was a researcher-made questionnaire to investigate the learning styles and technologies used by the teachers. Data was analyzed in SPSS 22 software using Hotelling’s T test, and Somers’, Kendall’s, and Gamma Agreement Coefficients. Findings: From the students’ viewpoints, visual and auditory styles were the most and the least preffered styles, respectively. A combination of the technologies was used by the teachers. In addition, visual and kinesthetic/motion mediae were the most and the least used technologies by the teachers, respectively. There was no significant conformity between read/write, aural, and kinesthetic/motion styles of the students and the technologies used by the teachers (p>0.05. Neverheless, there was a significant conformity between the students’ visual style and the visual technologies used by the teachers (p<0.05. Conclusion: There is conformity between the technologies used by the teachers of Isfahan University of Medical Sciences and the students’ viual learning style. However, the technologies are not compatible with read/write, aural, and kinesthetic/motion styles of the students.

  15. The effect of base image window level selection on the dimensional measurement accuracy of resultant three-dimensional image displays

    International Nuclear Information System (INIS)

    Kurmis, A.P.; Hearn, T.C.; Reynolds, K.J.

    2003-01-01

    Purpose: The aim of this study was to determine the effect of base image window level selection on direct linear measurement of knee structures displayed using new magnetic resonance (MR)-based three-dimensional reconstructed computer imaging techniques. Methods: A prospective comparative study was performed using a series of three-dimensional knee images, generated from conventional MR imaging (MRI) sections. Thirty distinct anatomical structural features were identified within the image series of which repeated measurements were compared at 10 different window grey scale levels. Results: Statistical analysis demonstrated an excellent raw correlation between measurements and suggested no significant difference between measurements made at each of the 10 window level settings (P>0.05). Conclusions: The findings of this study suggest that unlike conventional MR or CT applications, grey scale window level selection at the time of imaging does not significantly affect the visual quality of resultant three-dimensional reconstructed images and hence the accuracy of subsequent direct linear measurement. The diagnostic potential of clinical progression from routine two-dimensional to advanced three-dimensional reconstructed imaging techniques may therefore be less likely to be degraded by inappropriate MR technician image windowing during the capturing of image series

  16. A Novel Variant with Positive Natural Selection Influenced Hb A2 Levels in Chinese Individuals with β-Thalassemia.

    Science.gov (United States)

    Yu, Shanjuan; Chen, Yang; Lai, Ketong; Dewan, Roma Kajal; He, Yunyan

    2017-05-01

    β-Thalassemia (β-thal) is the most common inherited hemolytic anemia worldwide. Elevated Hb A 2 is a mark of β-thal carriers. The aim of this study was to identify the pathogenic variants associated with the Hb A 2 levels. One thousand and thirty β-thal carriers were recruited for this study. Using positive natural expression quantitative trait loci (eQTL) analysis, a significant variant was selected. Genotyping for the rs231841 polymorphism was performed by the Sequenom MassARRAY IPLEX platform. All genetic association analyses were performed with the PLINK program. The linear regression analysis showed that rs231841 in the intron region of the potassium voltage-gated channel subfamily Q member 1 (KCNQ1) gene on chromosome 11p15 was significantly associated with Hb A 2 levels. The presence of the C allele was associated with elevated Hb A 2 levels. Our results suggest that rs231841 on the KCNQ1 gene with positive natural selection is related to Hb A 2 levels in Chinese β-thal carriers, and KCNQ1 is probably associated with the expression of the β-like globin gene cluster.

  17. DOE hearing on the draft area recommendation report for the Crystalline Repository Project, Civic Center Arena, Asheville, North Carolina: Session 1, Volume 4, April 4, 1986: Transcript of proceedings

    International Nuclear Information System (INIS)

    1986-01-01

    This document contains a transcript of the comments of 15 witnesses. These meetings were held to hear public comments regarding the selection of a site for a second high-level nuclear waste repository

  18. Selection of low-level radioactive waste disposal sites using screening models versus more complex methodologies

    International Nuclear Information System (INIS)

    Uslu, I.; Fields, D.E.

    1993-01-01

    The task of choosing a waste-disposal site from a set of candidate sites requires an approach capable of objectively handling many environmental variables for each site. Several computer methodologies have been developed to assist in the process of choosing a site for the disposal of low-level radioactive waste; however, most of these models are costly to apply, in terms of computer resources and the time and effort required by professional modelers, geologists, and waste-disposal experts. The authors describe how the relatively simple DRASTIC methodology (a standardized system for evaluating groundwater pollution potential using hydrogeologic settings) may be used for open-quotes pre-screeningclose quotes of sites to determine which subset of candidate sites is worthy of more detailed screening. Results of site comparisons made with DRASTIC are compared with results obtained using PRESTO-II methodology, which is representative of the more complex release-transport-human exposure methodologies. 6 refs., 1 fig., 1 tab

  19. Shallow land burial of low-level radioactive wastes. A selected, annotated bibliography

    International Nuclear Information System (INIS)

    Fore, C.S.; Vaughan, N.D.; Tappen, J.

    1978-06-01

    The data file was built to provide information support to DOE researchers in the field of low-level radioactive waste disposal and management. The scope of the data base emphasizes studies which deal with the ''old'' Manhattan sites, commercial disposal sites, and the specific parameters which affect the soil and geologic migration of radionuclides. Specialized data fields have been incorporated into the data base to improve the ease and accuracy of locating pertinent references. Specific radionuclides for which data are presented are listed in the ''Measured Radionuclides'' field, and specific parameters which affect the migration of these radionuclides are presented in the ''Measured Parameters'' field. The 504 references are rated indicating applicability to shallow land burial technology and whether interpretation is required. Indexes are provided for author, geographic location, title, measured parameters, measured radionuclides, keywords, subject categories, and publication description

  20. Selection of a computer code for Hanford low-level waste engineered-system performance assessment

    International Nuclear Information System (INIS)

    McGrail, B.P.; Mahoney, L.A.

    1995-10-01

    Planned performance assessments for the proposed disposal of low-level waste (LLW) glass produced from remediation of wastes stored in underground tanks at Hanford, Washington will require calculations of radionuclide release rates from the subsurface disposal facility. These calculations will be done with the aid of computer codes. Currently available computer codes were ranked in terms of the feature sets implemented in the code that match a set of physical, chemical, numerical, and functional capabilities needed to assess release rates from the engineered system. The needed capabilities were identified from an analysis of the important physical and chemical process expected to affect LLW glass corrosion and the mobility of radionuclides. The highest ranked computer code was found to be the ARES-CT code developed at PNL for the US Department of Energy for evaluation of and land disposal sites

  1. Quality assurance program preparation - review of requirements and plant systems - selection of program levels

    International Nuclear Information System (INIS)

    Asmuss, G.

    1980-01-01

    The establishment and implementation for a practicable quality assurance program for a nuclear power plant demands a detailed background in the field of engineering, manufacturing, organization and quality assurance. It will be demonstrated with examples to define and control the achievement of quality related activities during the phases of design, procurement, manufactoring, commissioning and operation. In general the quality assurance program applies to all items, processes and services important to safety of nuclear power plant. The classification for safety related and non-safety related items and services demonstrate the levels of quality assurance requirements. The lecture gives an introduction of QA Program preparation under the following topics: -Basic criteria and international requirements - Interaction of QA activities - Modular and product oriented QA programs - Structuring of organization for the QA program - Identification of the main quality assurance functions and required actions - Quality Assurance Program documentation - Documentation of planning of activities - Control of program documents - Definitions. (orig./RW)

  2. Component-Level Selection and Qualification for the Global Ecosystem Dynamics Investigation (GEDI) Laser Altimeter Transmitter

    Science.gov (United States)

    Frese, Erich A.; Chiragh, Furqan L.; Switzer, Robert; Vasilyev, Aleksey A.; Thomes, Joe; Coyle, D. Barry; Stysley, Paul R.

    2018-01-01

    Flight quality solid-state lasers require a unique and extensive set of testing and qualification processes, both at the system and component levels to insure the laser's promised performance. As important as the overall laser transmitter design is, the quality and performance of individual subassemblies, optics, and electro-optics dictate the final laser unit's quality. The Global Ecosystem Dynamics Investigation (GEDI) laser transmitters employ all the usual components typical for a diode-pumped, solid-state laser, yet must each go through their own individual process of specification, modeling, performance demonstration, inspection, and destructive testing. These qualification processes and results for the laser crystals, laser diode arrays, electro-optics, and optics, will be reviewed as well as the relevant critical issues encountered, prior to their installation in the GEDI flight laser units.

  3. The analysis of the sustainable mobility level in selected European cities

    Energy Technology Data Exchange (ETDEWEB)

    Ciaston-Ciulkin, A.

    2016-07-01

    Transport needs have to be met through efficient and integrated usage of existing transport infrastructure and urban space together with actions taken in order to reduce traffic congestion by reducing the number and length of travels by car and reducing the demand for the travelling. The expected effect of these actions is the less noise, air pollution and greenhouse gas emissions. The article presents the proposal of the indicator for measuring the degree of sustainable mobility based on the example of European Union cities. The presented method for determining the level of sustainable mobility has been inspired by different researches and it is based on a study of different sub-indicators used for measuring the degree of sustainability of the modal split. (Author)

  4. Shallow land burial of low-level radioactive wastes. A selected, annotated bibliography

    Energy Technology Data Exchange (ETDEWEB)

    Fore, C.S.; Vaughan, N.D.; Tappen, J. (comps.)

    1978-06-01

    The data file was built to provide information support to DOE researchers in the field of low-level radioactive waste disposal and management. The scope of the data base emphasizes studies which deal with the ''old'' Manhattan sites, commercial disposal sites, and the specific parameters which affect the soil and geologic migration of radionuclides. Specialized data fields have been incorporated into the data base to improve the ease and accuracy of locating pertinent references. Specific radionuclides for which data are presented are listed in the ''Measured Radionuclides'' field, and specific parameters which affect the migration of these radionuclides are presented in the ''Measured Parameters'' field. The 504 references are rated indicating applicability to shallow land burial technology and whether interpretation is required. Indexes are provided for author, geographic location, title, measured parameters, measured radionuclides, keywords, subject categories, and publication description. (DLC)

  5. The importance of considering community-level effects when selecting insecticidal malaria vector products

    Directory of Open Access Journals (Sweden)

    Coosemans Marc

    2011-08-01

    Full Text Available Abstract Background Insecticide treatment of nets, curtains or walls and ceilings of houses represent the primary means for malaria prevention worldwide. Direct personal protection of individuals and households arises from deterrent and insecticidal activities which divert or kill mosquitoes before they can feed. However, at high coverage, community-level reductions of mosquito density and survival prevent more transmission exposure than the personal protection acquired by using a net or living in a sprayed house. Methods A process-explicit simulation of malaria transmission was applied to results of 4 recent Phase II experimental hut trials comparing a new mosaic long-lasting insecticidal net (LLIN which combines deltamethrin and piperonyl butoxide with another LLIN product by the same manufacturer relying on deltamethrin alone. Results Direct estimates of mean personal protection against insecticide-resistant vectors in Vietnam, Cameroon, Burkina Faso and Benin revealed no clear advantage for combination LLINs over deltamethrin-only LLINs (P = 0.973 unless both types of nets were extensively washed (Relative mean entomologic inoculation rate (EIR ± standard error of the mean (SEM for users of combination nets compared to users of deltamethrin only nets = 0.853 ± 0.056, P = 0.008. However, simulations of impact at high coverage (80% use predicted consistently better impact for the combination net across all four sites (Relative mean EIR ± SEM in communities with combination nets, compared with those using deltamethrin only nets = 0.613 ± 0.076, P Conclusion Process-explicit simulations of community-level protection, parameterized using locally-relevant experimental hut studies, should be explicitly considered when choosing vector control products for large-scale epidemiological trials or public health programme procurement, particularly as growing insecticide resistance necessitates the use of multiple active ingredients.

  6. Survey of peanut levels in selected Irish food products bearing peanut allergen advisory labels.

    Science.gov (United States)

    Robertson, Orla N; Hourihane, Jonathan O'B; Remington, Benjamin C; Baumert, Joseph L; Taylor, Steve L

    2013-01-01

    Peanut allergy affects up to 2% of consumers and is responsible for the majority of fatalities caused by food-induced anaphylaxis. Peanut-containing products must be clearly labelled. Manufacturers are not legally required to label peanut if its inclusion resulted from unintentional cross contact with foods manufactured in the same facility. However, the use of allergen advisory statements alerting consumers of the potential presence of peanut allergen has increased in recent years. In previous studies, the vast majority of foods with precautionary allergen statements did not contain detectable levels of peanut, but no data are available on Irish food products. Thirty-eight food products bearing peanut/nut allergen-related statements were purchased from multiple locations in the Republic of Ireland and analysed for the presence of peanut. Peanut was detected in at least one lot in 5.3% (2 of 38) of the products tested. The doses of peanut detected ranged from 0.14 mg to 0.52 mg per suggested serving size (0.035-0.13 mg peanut protein). No detectable levels of peanut were found in the products that indicated peanut/nuts as a minor ingredient. Quantitative risk assessment, based on the known distribution of individual threshold doses for peanut, indicates that only a very small percentage of the peanut-allergic population would be likely to experience an allergic reaction to those products while the majority of products with advisory labels appear safe for the peanut-allergic population. Food manufacturers should be encouraged to analyse products manufactured in shared facilities and even on shared equipment with peanuts for peanut residues to determine whether sufficient risk exists to warrant the use of advisory labelling. Although it appears that the majority of food products bearing advisory nut statements are in fact free of peanut contamination, advice to peanut allergy sufferers to avoid said foods should continue in Ireland and therefore in the wider European

  7. Assessing the levels of mercury in selected mining communities in the East Akim Municipality of Ghana

    International Nuclear Information System (INIS)

    Kwateng, I.K.

    2010-01-01

    Mercury concentrations in tailings, soil, sediment and water from one active and one non-active (abandoned) mine site each from Agyapoma, Kibi and Tete Asikam were studied together with water from the Birim River. The concentrations were measured using Instrumental Neutron Activation Analysis - a 30 kW tank-in-pool Ghana Research Reactor-1 (GHARR - 1) operating at a thermal flux of 5 x 10 1 1' ns -1 cm -2 . The samples were irradiated and counted without any chemical treatment. Atomic Absorption Spectrometry was used for full analysis of all the water samples to measure the concentrations of Hg, Cd, Pb, Fe, Mn, Cu, Zn, and As. Ultra violet visible spectrophotometer was used to measure the concentrations of SO 4 2- , PO 4 3- and NO 3- . Elevated levels of Hg were found in the tailings at all the active sites which ranged from 3.45-5.09 mg/kg. The non-active sites had concentrations ranging from 0.02-0.24 mg/kg. Soil, sediment and water samples analysed for Hg were below detection limit. The difference in Hg concentrations in tailings from one site to another is significant as it ranged from 0.02-5.09 mg/kg. Levels of mercury in drinking water, soil and sediments were below detection limit. The Birim river and dam water showed a wide range of characteristics in terms of physciochemical parameters and elemental concentrations. The temperature ranged from 26.5-56.7 degrees Celsius with a pH range of 5.85-7.18. The electrical conductivity values were in the range 53.8-192.4 μS/cm and TDS values in the range of 23.2-82.2mg/L. the water samples varied largely in total hardness from 21.95-76.8mg/L. Concentrations of Pb and Fe were all above the guidance values of 0.01 mg/L and 0.3 mg/L respectively. The concentration of Pb ranged from 0.067-0.127 mg/L and that of Fe ranged from 0.653-2.1 mg/L. Arsenic concentrations were also above the WHO guidance values of 0.01 mg/L except for samples from the Birim River. The concentration of SO 4 2- ranges from 7.424-57.26 mg/L which

  8. Levels and patterns of nucleotide variation in domestication QTL regions on rice chromosome 3 suggest lineage-specific selection.

    Directory of Open Access Journals (Sweden)

    Xianfa Xie

    Full Text Available Oryza sativa or Asian cultivated rice is one of the major cereal grass species domesticated for human food use during the Neolithic. Domestication of this species from the wild grass Oryza rufipogon was accompanied by changes in several traits, including seed shattering, percent seed set, tillering, grain weight, and flowering time. Quantitative trait locus (QTL mapping has identified three genomic regions in chromosome 3 that appear to be associated with these traits. We would like to study whether these regions show signatures of selection and whether the same genetic basis underlies the domestication of different rice varieties. Fragments of 88 genes spanning these three genomic regions were sequenced from multiple accessions of two major varietal groups in O. sativa--indica and tropical japonica--as well as the ancestral wild rice species O. rufipogon. In tropical japonica, the levels of nucleotide variation in these three QTL regions are significantly lower compared to genome-wide levels, and coalescent simulations based on a complex demographic model of rice domestication indicate that these patterns are consistent with selection. In contrast, there is no significant reduction in nucleotide diversity in the homologous regions in indica rice. These results suggest that there are differences in the genetic and selective basis for domestication between these two Asian rice varietal groups.

  9. Selection and Basic Properties of the Buffer Material for High-Level Radioactive Waste Repository in China

    Institute of Scientific and Technical Information of China (English)

    WEN Zhijian

    2008-01-01

    Radioactive wastes arising from a wide range of human activities are in many different physical and chemical forms, contaminated with varying radioactivity. Their common features are the potential hazard associated with their radioactivity and the need to manage them in such a way as to protect the human environment. The geological disposal is regarded as the most reasonable and effective way to safely disposing high-level radioactive wastes in the world. The conceptual model of geological disposal in China is based on a multi-barrier system that combines an isolating geological environment with an engineered barrier system. The buffer is one of the main engineered barriers for HLW repository. It is expected to maintain its low water permeability, self-sealing property, radio nuclides adsorption and retardation properties, thermal conductivity, chemical buffering property,canister supporting property, and stress buffering property over a long period of time. Bentonite is selected as the main content of buffer material that can satisfy the above requirements. The Gaomiaozi deposit is selected as the candidate supplier for China's buffer material of high level radioactive waste repository. This paper presents the geological features of the GMZ deposit and basic properties of the GMZ Na-bentonite. It is a super-large deposit with a high content of montmorillonite (about 75%), and GMZ-1, which is Na-bentonite produced from GMZ deposit is selected as the reference material for China's buffer material study.

  10. Method for selective detection of explosives in mass spectrometer or ion mobility spectrometer at parts-per-quadrillion level

    Science.gov (United States)

    Ewing, Robert G.; Atkinson, David A.; Clowers, Brian H.

    2015-09-01

    A method for selective detection of volatile and non-volatile explosives in a mass spectrometer or ion mobility spectrometer at a parts-per-quadrillion level without preconcentration is disclosed. The method comprises the steps of ionizing a carrier gas with an ionization source to form reactant ions or reactant adduct ions comprising nitrate ions (NO.sub.3.sup.-); selectively reacting the reactant ions or reactant adduct ions with at least one volatile or non-volatile explosive analyte at a carrier gas pressure of at least about 100 Ton in a reaction region disposed between the ionization source and an ion detector, the reaction region having a length which provides a residence time (tr) for reactant ions therein of at least about 0.10 seconds, wherein the selective reaction yields product ions comprising reactant ions or reactant adduct ions that are selectively bound to the at least one explosive analyte when present therein; and detecting product ions with the ion detector to determine presence or absence of the at least one explosive analyte.

  11. Polychlorinated terphenyl patterns and levels in selected marine mammals and a river fish from different continents.

    Science.gov (United States)

    Rosenfelder, Natalie; Vetter, Walter

    2014-01-01

    Polychlorinated terphenyls (PCTs) are a class of persistent organic pollutants which have been used from the 1920s to the 1980s for similar purposes as polychlorinated biphenyls (PCBs). Comparably little data was available on the PCT distribution in the environment mainly due to analytical difficulties in their determination. By means of a calculation algorithm recently developed we now studied the PCT pattern in individual marine mammal samples and one fish sample from different continents. Altogether, 97 PCTs were detected in eight samples and twelve to 66 tetra- to nonachloroterphenyl (tetra- to nonaCT) congeners were detected in individual samples. PCTs were present in all marine mammal samples which originated from four continents, but the PCT pattern was varied. TetraCTs were dominant in the sample from Africa, Australia, Spitsbergen (European Arctic) and in a sample from the Baltic Sea, heptaCTs in samples from the North Sea and octaCTs in a sample from Iceland. The abundance of sumPCTs relative to PCB 153, estimated from the GC/ECNI-MS response corrected for the degree of chlorination, ranged from 0.9 to 8.8%, corresponding with ~0.22-2.2% of the total PCB content. The highest PCT level detected was 980 mg/kg lipid in a harbour seal from the North Sea, Germany. The results from this study indicated that samples from certain areas, e.g. the North Sea may still be polluted with PCTs. © 2013.

  12. High level radioactive waste management policies and reflections of citizens' opinions in selected European countries

    International Nuclear Information System (INIS)

    Nagano, Koji

    2002-01-01

    This report considered on policy decision aiming at practice of landfill disposal and process at disposal site forward practice of high level radioactive wastes (HLWs) disposal by adopting Finland and Sweden, for examples among European countries showing their own efforts, to attempt to absorb some instructions for Japan planning to promote practice of unique process in future. As a result performing information collection and analysis at a center of surveys at sites, conclusion shown as follows were obtained: (1) Characteristics of nuclear policy decision making at Finland are confirmation of decision making based on decision in principle (DiP) procedure, participation of nations, especially congress, and high reliability of citizens to social systems. (2) At Oskarshamn in Sweden, positive efforts and decision making on disposal site problem are progressed as results of leading by local assembly, construction planning on decision making competence on HLWs, and planning preparation on presence of troubles and decision with responsibility to citizens. (3) As when promoting disposal site process, failure of loss on reliability relation brings large time and economical losses, for its success conditions, it was proposed that psychological refusal feelings of residents at sites on nuclear energy were small, the sites had some capacities and well-informed capable of understanding and judging on nuclear troubles, and decision not only present facility and trouble proposing construction, but also through discussion on future images for local society. (G.K.)

  13. Potent and Selective BACE-1 Peptide Inhibitors Lower Brain Aβ Levels Mediated by Brain Shuttle Transport

    Directory of Open Access Journals (Sweden)

    Nadine Ruderisch

    2017-10-01

    Full Text Available Therapeutic approaches to fight Alzheimer's disease include anti-Amyloidβ (Aβ antibodies and secretase inhibitors. However, the blood-brain barrier (BBB limits the brain exposure of biologics and the chemical space for small molecules to be BBB permeable. The Brain Shuttle (BS technology is capable of shuttling large molecules into the brain. This allows for new types of therapeutic modalities engineered for optimal efficacy on the molecular target in the brain independent of brain penetrating properties. To this end, we designed BACE1 peptide inhibitors with varying lipid modifications with single-digit picomolar cellular potency. Secondly, we generated active-exosite peptides with structurally confirmed dual binding mode and improved potency. When fused to the BS via sortase coupling, these BACE1 inhibitors significantly reduced brain Aβ levels in mice after intravenous administration. In plasma, both BS and non-BS BACE1 inhibitor peptides induced a significant time- and dose-dependent decrease of Aβ. Our results demonstrate that the BS is essential for BACE1 peptide inhibitors to be efficacious in the brain and active-exosite design of BACE1 peptide inhibitors together with lipid modification may be of therapeutic relevance.

  14. Selection of non-Saccharomyces yeast strains for reducing alcohol levels in wine by sugar respiration.

    Science.gov (United States)

    Quirós, Manuel; Rojas, Virginia; Gonzalez, Ramon; Morales, Pilar

    2014-07-02

    Respiration of sugars by non-Saccharomyces yeasts has been recently proposed for lowering alcohol levels in wine. Development of industrial fermentation processes based on such an approach requires, amongst other steps, the identification of yeast strains which are able to grow and respire under the relatively harsh conditions found in grape must. This work describes the characterization of a collection of non-Saccharomyces yeast strains in order to identify candidate yeast strains for this specific application. It involved the estimation of respiratory quotient (RQ) values under aerated conditions, at low pH and high sugar concentrations, calculation of yields of ethanol and other relevant metabolites, and characterization of growth responses to the main stress factors found during the first stages of alcoholic fermentation. Physiological features of some strains of Metschnikowia pulcherrima or two species of Kluyveromyces, suggest they are suitable for lowering ethanol yields by respiration. The unsuitability of Saccharomyces cerevisiae strains for this purpose was not due to ethanol yields (under aerated conditions they are low enough for a significant reduction in final ethanol content), but to the high acetic acid yields under these growth conditions. According to results from controlled aeration fermentations with one strain of M. pulcherrima, design of an aeration regime allowing for lowering ethanol yields though preserving grape must components from excessive oxidation, would be conceivable. Copyright © 2014. Published by Elsevier B.V.

  15. A successful case site selection for low-and intermediate-level radioactive waste disposal facility

    International Nuclear Information System (INIS)

    Lee, Bongwoo

    2007-01-01

    Korea decided on Gyeongju-si as the site of low-and intermediate-level radioactive waste disposal facility by referendum in November, 2005. Five success factors are considered; 1) the mayor and municipal assembly leaded the public opinion of inhabitants, 2) an invitation group was formed by citizen, social and religious group, 3) Gyeongju-si has operated the nuclear power plant since 20 years ago, and this radioactive waste disposal facility brings large financial support, 4) many kinds of public information means were used for invitation agreement and 5) the preconception, a nuclear facility is danger, was removed by visiting citizen, social group and local inhabitants at the nuclear power plant facility. Promotion process of the project, invitation process of Gyeongju-si and success factors, construction of an invitation promotion group and development of public information activities, publicity of financial effects and safety of radioactive waste disposal facility, increase of general acceptance among inhabitants by many kinds of public information means, and P.R. of safety of nuclear power plant facility by visiting leadership layers are reported. (S.Y.)

  16. Hydrogeologic factors in t