WorldWideScience

Sample records for core macroautophagy genes

  1. The Role of Macroautophagy in Development of Filamentous Fungi

    NARCIS (Netherlands)

    Bartoszewska, Magdalena; Kiel, Jan A. K. W.

    Autophagy (macroautophagy) is a bulk degradative pathway by which cytoplasmic components are delivered to the vacuole for recycling. This process is conserved from yeast to human, where it is implicated in cancer and neurodegenerative diseases. During the last decade, many ATG genes involved in

  2. The role of macroautophagy in development of filamentous fungi.

    Science.gov (United States)

    Bartoszewska, Magdalena; Kiel, Jan A K W

    2011-06-01

    Autophagy (macroautophagy) is a bulk degradative pathway by which cytoplasmic components are delivered to the vacuole for recycling. This process is conserved from yeast to human, where it is implicated in cancer and neurodegenerative diseases. During the last decade, many ATG genes involved in autophagy have been identified, initially in Saccharomyces cerevisiae. This review summarizes the knowledge on the molecular mechanisms of autophagy using yeast as model system. Although many of the core components involved in autophagy are conserved from yeast to human, there are, nevertheless, significant differences between these organisms, for example, during autophagy initiation. Autophagy also plays an essential role in filamentous fungi especially during differentiation. Remarkably, in these species autophagy may reflect features of both yeast and mammals. This is exemplified by the finding that filamentous fungi lack the S. cerevisiae clade-specific Atg31 protein, but contain Atg101, which is absent in this clade. A reappraisal of genome data further suggests that, similar to yeast and mammals, filamentous fungi probably also contain two distinct phosphatidylinositol 3-kinase complexes. This review also summarizes the state of knowledge on the role of autophagy in filamentous fungi during differentiation, such as pathogenic development, programmed cell death during heteroincompatibility, and spore formation.

  3. Genetic ablation and short-duration inhibition of lipoxygenase results in increased macroautophagy

    Energy Technology Data Exchange (ETDEWEB)

    Jang, Insook; Park, Sujin; Cho, Jin Won [Department of Integrated OMICS for Biomedical Science, WCU Program of Graduate School, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-749 (Korea, Republic of); Yigitkanli, Kazim; Leyen, Klaus van [Neuroprotection Research Laboratory, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129 (United States); Roth, Jürgen, E-mail: jurgen.roth@bluewin.ch [Department of Integrated OMICS for Biomedical Science, WCU Program of Graduate School, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-749 (Korea, Republic of)

    2014-02-15

    12/15-lipoxygenase (12/15-LOX) is involved in organelle homeostasis by degrading mitochondria in maturing red blood cells and by eliminating excess peroxisomes in liver. Furthermore, 12/15-LOX contributes to diseases by exacerbating oxidative stress-related injury, notably in stroke. Nonetheless, it is unclear what the consequences are of abolishing 12/15-LOX activity. Mice in which the alox15 gene has been ablated do not show an obvious phenotype, and LOX enzyme inhibition is not overtly detrimental. We show here that liver histology is also unremarkable. However, electron microscopy demonstrated that 12/15-LOX knockout surprisingly leads to increased macroautophagy in the liver. Not only macroautophagy but also mitophagy and pexophagy were increased in hepatocytes, which otherwise showed unaltered fine structure and organelle morphology. These findings were substantiated by immunofluorescence showing significantly increased number of LC3 puncta and by Western blotting demonstrating a significant increase for LC3-II protein in both liver and brain homogenates of 12/15-LOX knockout mice. Inhibition of 12/15-LOX activity by treatment with four structurally different inhibitors had similar effects in cultured HepG2 hepatoma cells and SH-SY5Y neuroblastoma cells with significantly increased autophagy discernable already after 2 hours. Hence, our study reveals a link between ablation or inhibition of 12/15-LOX and stimulation of macroautophagy. The enhanced macroautophagy may be related to the known tissue-protective effects of LOX ablation or inhibition under various diseased conditions caused by oxidative stress and ischemia. This could provide an important cleaning mechanism of cells and tissues to prevent accumulation of damaged mitochondria and other cellular components. - Highlights: • A relationship between lipoxygenases and autophagy is disclosed. • 12/15-lipoxygenase knockout increases autophagy in mice liver and brain. • Lipoxygenase inhibition boosts

  4. The Phospholipase D1 Pathway Modulates Macroautophagy

    Science.gov (United States)

    Dall’Armi, Claudia; Hurtado-Lorenzo, Andres; Tian, Huasong; Morel, Etienne; Nezu, Akiko; Chan, Robin B.; Yu, W. Haung; Robinson, Kimberly S.; Yeku, Oladapo; Small, Scott A.; Duff, Karen; Frohman, Michael A.; Wenk, Markus R.; Yamamoto, Akitsugu; Di Paolo, Gilbert

    2012-01-01

    While macroautophagy is known to be an essential degradative process whereby autophagosomes mediate the engulfment and delivery of cytoplasmic components into lysosomes, the lipid changes underlying autophagosomal membrane dynamics are undetermined. Here we show that phospholipase D1 (PLD1), which is primarily associated with the endosomal system, partially relocalizes to the outer membrane of autophagosome-like structures upon nutrient starvation. The localization of PLD1, as well as the starvation-induced increase in PLD activity, are altered by wortmannin, a phosphatidylinositol 3-kinase inhibitor, suggesting PLD1 may act downstream of Vps34. Pharmacological inhibition of PLD and genetic ablation of PLD1 in the mouse decrease the starvation-induced expansion of LC3-positive compartments, consistent with a role of PLD1 in the regulation of autophagy. Furthermore, inhibition of PLD results in higher levels of tau and p62 aggregates in organotypic brain slices. Our in vitro and in vivo findings establish a novel role for PLD1 in autophagy. PMID:21266992

  5. Genomic variation in Salmonella enterica core genes for epidemiological typing

    DEFF Research Database (Denmark)

    Leekitcharoenphon, Pimlapas; Lukjancenko, Oksana; Rundsten, Carsten Friis

    2012-01-01

    time. The core genes-the genes that are conserved in all (or most) members of a genus or species-are potentially good candidates for investigating genomic variation in phylogeny and epidemiology. Results: We identify a set of 2,882 core genes clusters based on 73 publicly available Salmonella enterica...... confidence. The core genes can be divided into two categories: a few highly variable genes and a larger set of conserved core genes, with low variance. For the most variable core genes, the variance in amino acid sequences is higher than for the corresponding nucleotide sequences, suggesting...

  6. Macromusophagy: A solo piano musical representation of macroautophagy.

    Science.gov (United States)

    Lee, Wendy W-K; Klionsky, Daniel J

    2014-05-01

    Macroautophagy is a complex process involving dynamic membrane rearrangements in which parts of the cytoplasm are sequestered within double-membrane phagophores. Upon completion, these structures mature into autophagosomes that fuse with the yeast vacuole or mammalian lysosome, leading to degradation of the cargo and release of the resulting macromolecules back into the cytosol. How can the complexities of macroautophagy best be conveyed to an audience that is composed primarily of people who are not experts in this topic, and possibly not even scientists? The literature on learning is vast, and difficult to summarize, but there are certain themes that frequently appear. First, people learn in different ways. Thus, for example, while lectures are effective for conveying information to part of the audience, some will benefit tremendously from alternative methods of presentation. The latter can be visual (taking the form of illustrations, videos, or even physical movement), tactile or audible. Second, a line of research suggests that the engagement of more than one part of the brain (dual channels) improves learning. We decided to explore these concepts focusing on an audible format through a collaborative approach by combining a scientific explanation of macroautophagy with a musical score that was composed specifically to represent this process.

  7. A53T Human α-Synuclein Overexpression in Transgenic Mice Induces Pervasive Mitochondria Macroautophagy Defects Preceding Dopamine Neuron Degeneration

    Science.gov (United States)

    Xie, Zhiguo; Turkson, Susie

    2015-01-01

    In vitro evidence suggests that the inefficient removal of damaged mitochondria by macroautophagy contributes to Parkinson's disease (PD). Using a tissue-specific gene amplification strategy, we generated a transgenic mouse line with human α-synuclein A53T overexpression specifically in dopamine (DA) neurons. Transgenic mice showed profound early-onset mitochondria abnormalities, characterized by macroautophagy marker-positive cytoplasmic inclusions containing mainly mitochondrial remnants, which preceded the degeneration of DA neurons. Genetic deletion of either parkin or PINK1 in these transgenic mice significantly worsened mitochondrial pathologies, including drastically enlarged inclusions and loss of total mitochondria contents. These data suggest that mitochondria are the main targets of α-synuclein and their defective autophagic clearance plays a significant role during pathogenesis. Moreover, endogenous PINK1 or parkin is indispensable for the proper autophagic removal of damaged mitochondria. Our data for the first time establish an essential link between mitochondria macroautophagy impairments and DA neuron degeneration in an in vivo model based on known PD genetics. The model, its well-defined pathologies, and the demonstration of a main pathogenesis pathway in the present study have set the stage and direction of emphasis for future studies. PMID:25609609

  8. H1-antihistamines induce vacuolation in astrocytes through macroautophagy

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    Hu, Wei-Wei; Yang, Ying; Wang, Zhe; Shen, Zhe; Zhang, Xiang-Nan [Department of Pharmacology, Key Laboratory of Medical Neurobiology of the Ministry of Health of China, Zhejiang Province Key Laboratory of Neurobiology, School of Basic Medical Sciences, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058 (China); Wang, Guang-Hui [College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123 (China); Chen, Zhong, E-mail: chenzhong@zju.edu.cn [Department of Pharmacology, Key Laboratory of Medical Neurobiology of the Ministry of Health of China, Zhejiang Province Key Laboratory of Neurobiology, School of Basic Medical Sciences, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058 (China)

    2012-04-15

    H1-antihistamines induce vacuolation in vascular smooth muscle cells, which may contribute to their cardiovascular toxicity. The CNS toxicity of H1-antihistamines may also be related to their non-receptor-mediated activity. The aim of this study was to investigate whether H1-antihistamines induce vacuolation in astrocytes and the mechanism involved. The H1-antihistamines induced large numbers of giant vacuoles in astrocytes. Such vacuoles were marked with both the lysosome marker Lysotracker Red and the alkalescent fluorescence dye monodansylcadaverine, which indicated that these vacuoles were lysosome-like acidic vesicles. Quantitative analysis of monodansylcadaverine fluorescence showed that the effect of H1-antihistamines on vacuolation in astrocytes was dose-dependent, and was alleviated by extracellular acidification, but aggravated by extracellular alkalization. The order of potency to induce vacuolation at high concentrations of H1-antihistamines (diphenhydramine > pyrilamine > astemizole > triprolidine) corresponded to their pKa ranking. Co-treatment with histamine and the histamine receptor-1 agonist trifluoromethyl toluidide did not inhibit the vacuolation. Bafilomycin A1, a vacuolar (V)-ATPase inhibitor, which inhibits intracellular vacuole or vesicle acidification, clearly reversed the vacuolation and intracellular accumulation of diphenhydramine. The macroautophagy inhibitor 3-methyladenine largely reversed the percentage of LC3-positive astrocytes induced by diphenhydramine, while only partly reversing the number of monodansylcadaverine-labeled vesicles. In Atg5{sup −/−} mouse embryonic fibroblasts, which cannot form autophagosomes, the number of vacuoles induced by diphenhydramine was less than that in wild-type cells. These results indicated that H1-antihistamines induce V-ATPase-dependent acidic vacuole formation in astrocytes, and this is partly mediated by macroautophagy. The pKa and alkalescent characteristic of H1-antihistamines may be the

  9. A comprehensive siRNA screen for kinases that suppress macroautophagy in optimal growth conditions

    DEFF Research Database (Denmark)

    Szyniarowski, Piotr; Corcelle-Termeau, Elisabeth; Farkas, Thomas

    2011-01-01

    macroautophagy under optimal growth conditions. Therefore, we screened a human kinome siRNA library for siRNAs that increase the number of autophagosomes in normally growing MCF-7 human breast carcinoma cells, and identified 10 kinases as regulators of constitutive macroautophagy. Further analysis...

  10. Sequence comparison and phylogenetic analysis of core gene of ...

    African Journals Online (AJOL)

    In Pakistan, more than 10 million people are living with hepatitis C virus (HCV) with high morbidity and mortality. The aims of the present study are to report HCV core gene sequences from Pakistani population and perform their sequence comparison/phylogenetic analysis. The core gene of HCV has been cloned from six ...

  11. Sequence comparison and phylogenetic analysis of core gene of ...

    African Journals Online (AJOL)

    STORAGESEVER

    2010-07-19

    Jul 19, 2010 ... In Pakistan, more than 10 million people are living with hepatitis C virus (HCV) with high morbidity and mortality. The aims of the present study are to report HCV core gene sequences from Pakistani population and perform their sequence comparison/phylogenetic analysis. The core gene of HCV has.

  12. H1-antihistamines induce vacuolation in astrocytes through macroautophagy.

    Science.gov (United States)

    Hu, Wei-Wei; Yang, Ying; Wang, Zhe; Shen, Zhe; Zhang, Xiang-Nan; Wang, Guang-Hui; Chen, Zhong

    2012-04-15

    H1-antihistamines induce vacuolation in vascular smooth muscle cells, which may contribute to their cardiovascular toxicity. The CNS toxicity of H1-antihistamines may also be related to their non-receptor-mediated activity. The aim of this study was to investigate whether H1-antihistamines induce vacuolation in astrocytes and the mechanism involved. The H1-antihistamines induced large numbers of giant vacuoles in astrocytes. Such vacuoles were marked with both the lysosome marker Lysotracker Red and the alkalescent fluorescence dye monodansylcadaverine, which indicated that these vacuoles were lysosome-like acidic vesicles. Quantitative analysis of monodansylcadaverine fluorescence showed that the effect of H1-antihistamines on vacuolation in astrocytes was dose-dependent, and was alleviated by extracellular acidification, but aggravated by extracellular alkalization. The order of potency to induce vacuolation at high concentrations of H1-antihistamines (diphenhydramine>pyrilamine>astemizole>triprolidine) corresponded to their pKa ranking. Co-treatment with histamine and the histamine receptor-1 agonist trifluoromethyl toluidide did not inhibit the vacuolation. Bafilomycin A1, a vacuolar (V)-ATPase inhibitor, which inhibits intracellular vacuole or vesicle acidification, clearly reversed the vacuolation and intracellular accumulation of diphenhydramine. The macroautophagy inhibitor 3-methyladenine largely reversed the percentage of LC3-positive astrocytes induced by diphenhydramine, while only partly reversing the number of monodansylcadaverine-labeled vesicles. In Atg5⁻/⁻ mouse embryonic fibroblasts, which cannot form autophagosomes, the number of vacuoles induced by diphenhydramine was less than that in wild-type cells. These results indicated that H1-antihistamines induce V-ATPase-dependent acidic vacuole formation in astrocytes, and this is partly mediated by macroautophagy. The pKa and alkalescent characteristic of H1-antihistamines may be the major

  13. Core promoter functions in the regulation of gene expression of Drosophila dorsal target genes.

    Science.gov (United States)

    Zehavi, Yonathan; Kuznetsov, Olga; Ovadia-Shochat, Avital; Juven-Gershon, Tamar

    2014-04-25

    Developmental processes are highly dependent on transcriptional regulation by RNA polymerase II. The RNA polymerase II core promoter is the ultimate target of a multitude of transcription factors that control transcription initiation. Core promoters consist of core promoter motifs, e.g. the initiator, TATA box, and the downstream core promoter element (DPE), which confer specific properties to the core promoter. Here, we explored the importance of core promoter functions in the dorsal-ventral developmental gene regulatory network. This network includes multiple genes that are activated by different nuclear concentrations of Dorsal, an NFκB homolog transcription factor, along the dorsal-ventral axis. We show that over two-thirds of Dorsal target genes contain DPE sequence motifs, which is significantly higher than the proportion of DPE-containing promoters in Drosophila genes. We demonstrate that multiple Dorsal target genes are evolutionarily conserved and functionally dependent on the DPE. Furthermore, we have analyzed the activation of key Dorsal target genes by Dorsal, as well as by another Rel family transcription factor, Relish, and the dependence of their activation on the DPE motif. Using hybrid enhancer-promoter constructs in Drosophila cells and embryo extracts, we have demonstrated that the core promoter composition is an important determinant of transcriptional activity of Dorsal target genes. Taken together, our results provide evidence for the importance of core promoter composition in the regulation of Dorsal target genes.

  14. Macroautophagy and microautophagy in relation to vacuole formation in mesophyll cells of Dendrobium tepals.

    Science.gov (United States)

    van Doorn, Wouter G; Kirasak, Kanjana; Ketsa, Saichol

    2015-04-01

    Prior to flower opening, mesophyll cells at the vascular bundles of Dendrobium tepals showed a large increase in vacuolar volume, partially at the expense of the cytoplasm. Electron micrographs indicated that this increase in vacuolar volume was mainly due to vacuole fusion. Macroautophagous structures typical of plant cells were observed. Only a small part of the decrease in cytoplasmic volume seemed due to macroautophagy. The vacuoles contained vesicles of various types, including multilamellar bodies. It was not clear if these vacuolar inclusions were due to macroautophagy or microautophagy. Only a single structure was observed of a protruding vacuole, indicating microautophagy. It is concluded that macroautophagy occurs in these cells but its role in vacuole formation seems small, while a possible role of microautophagy in vacuole formation might be hypothesized. Careful labeling of organelle membranes seems required to advance our insight in plant macro- and microautophagy and their roles in vacuole formation. Copyright © 2015 Elsevier GmbH. All rights reserved.

  15. Core Gene Expression and Association of Genotypes with Viral ...

    African Journals Online (AJOL)

    Purpose: To determine genotypic distribution, ribonucleic acid (RNA) RNA viral load and express core gene from Hepatitis C Virus (HCV) infected patients in Punjab, Pakistan. Methods: A total of 1690 HCV RNA positive patients were included in the study. HCV genotyping was tested by type-specific genotyping assay, viral ...

  16. Oxidative stress induces macroautophagy of amyloid beta-protein and ensuing apoptosis

    DEFF Research Database (Denmark)

    Zheng, Lin; Kågedal, Katarina; Dehvari, Nodi

    2009-01-01

    There is increasing evidence for the toxicity of intracellular amyloid beta-protein (Abeta) to neurons and the involvement of lysosomes in this process in Alzheimer disease (AD). We have recently shown that oxidative stress, a recognized determinant of AD, enhances macroautophagy and leads...... to intralysosomal accumulation of Abeta in cultured neuroblastoma cells. We hypothesized that oxidative stress promotes AD by stimulating macroautophagy of Abeta that further may induce cell death by destabilizing lysosomal membranes. To investigate such possibility, we compared the effects of hyperoxia (40...

  17. Analysis of pan-genome to identify the core genes and essential genes of Brucella spp.

    Science.gov (United States)

    Yang, Xiaowen; Li, Yajie; Zang, Juan; Li, Yexia; Bie, Pengfei; Lu, Yanli; Wu, Qingmin

    2016-04-01

    Brucella spp. are facultative intracellular pathogens, that cause a contagious zoonotic disease, that can result in such outcomes as abortion or sterility in susceptible animal hosts and grave, debilitating illness in humans. For deciphering the survival mechanism of Brucella spp. in vivo, 42 Brucella complete genomes from NCBI were analyzed for the pan-genome and core genome by identification of their composition and function of Brucella genomes. The results showed that the total 132,143 protein-coding genes in these genomes were divided into 5369 clusters. Among these, 1710 clusters were associated with the core genome, 1182 clusters with strain-specific genes and 2477 clusters with dispensable genomes. COG analysis indicated that 44 % of the core genes were devoted to metabolism, which were mainly responsible for energy production and conversion (COG category C), and amino acid transport and metabolism (COG category E). Meanwhile, approximately 35 % of the core genes were in positive selection. In addition, 1252 potential essential genes were predicted in the core genome by comparison with a prokaryote database of essential genes. The results suggested that the core genes in Brucella genomes are relatively conservation, and the energy and amino acid metabolism play a more important role in the process of growth and reproduction in Brucella spp. This study might help us to better understand the mechanisms of Brucella persistent infection and provide some clues for further exploring the gene modules of the intracellular survival in Brucella spp.

  18. Methylene blue induces macroautophagy through 5′ adenosine monophosphate-activated protein kinase pathway to protect neurons from serum deprivation

    Science.gov (United States)

    Xie, Luokun; Li, Wenjun; Winters, Ali; Yuan, Fang; Jin, Kunlin; Yang, Shaohua

    2013-01-01

    Methylene blue has been shown to be neuroprotective in multiple experimental neurodegenerative disease models. However, the mechanisms underlying the neuroprotective effects have not been fully elucidated. Previous studies have shown that macroautophagy has multiple beneficial roles for maintaining normal cellular homeostasis and that induction of macroautophagy after myocardial ischemia is protective. In the present study we demonstrated that methylene blue could protect HT22 hippocampal cell death induced by serum deprivation, companied by induction of macroautophagy. We also found that methylene blue-mediated neuroprotection was abolished by macroautophagy inhibition. Interestingly, 5′ adenosine monophosphate-activated protein kinase (AMPK) signaling, but not inhibition of mammalian target of rapamycin signaling, was activated at 12 and 24 h after methylene blue treatment in a dose-dependent manner. Methylene blue-induced macroautophagy was blocked by AMPK inhibitor. Consistent with in vitro data, macroautophagy was induced in the cortex and hippocampus of mouse brains treated with methylene blue. Our findings suggest that methylene blue-induced neuroprotection is mediated, at least in part, by macroautophagy though activation of AMPK signaling. PMID:23653592

  19. Methylene blue induces macroautophagy through 5' adenosine monophosphate-activated protein kinase pathway to protect neurons from serum deprivation.

    Science.gov (United States)

    Xie, Luokun; Li, Wenjun; Winters, Ali; Yuan, Fang; Jin, Kunlin; Yang, Shaohua

    2013-01-01

    Methylene blue has been shown to be neuroprotective in multiple experimental neurodegenerative disease models. However, the mechanisms underlying the neuroprotective effects have not been fully elucidated. Previous studies have shown that macroautophagy has multiple beneficial roles for maintaining normal cellular homeostasis and that induction of macroautophagy after myocardial ischemia is protective. In the present study we demonstrated that methylene blue could protect HT22 hippocampal cell death induced by serum deprivation, companied by induction of macroautophagy. We also found that methylene blue-mediated neuroprotection was abolished by macroautophagy inhibition. Interestingly, 5' adenosine monophosphate-activated protein kinase (AMPK) signaling, but not inhibition of mammalian target of rapamycin signaling, was activated at 12 and 24 h after methylene blue treatment in a dose-dependent manner. Methylene blue-induced macroautophagy was blocked by AMPK inhibitor. Consistent with in vitro data, macroautophagy was induced in the cortex and hippocampus of mouse brains treated with methylene blue. Our findings suggest that methylene blue-induced neuroprotection is mediated, at least in part, by macroautophagy though activation of AMPK signaling.

  20. Functional gene pyrosequencing reveals core proteobacterial denitrifiers in boreal lakes

    Directory of Open Access Journals (Sweden)

    Jatta eSaarenheimo

    2015-07-01

    Full Text Available Denitrification is an important microbial process in aquatic ecosystems that can reduce the effects of eutrophication. Here, quantification and pyrosequencing of nirS, nirK and nosZ genes encoding for nitrite and nitrous oxide reductases was performed in sediment samples from four boreal lakes to determine the structure and seasonal stability of denitrifying microbial populations. Sediment quality and nitrate concentrations were linked to the quantity and diversity of denitrification genes, the abundance of denitrifying populations (nirS and nosZ genes correlated with coupled nitrification-denitrification (Dn, and the denitrification of the overlying water (Dw correlated with the nirS/nirK ratio. The number of core nirS, nirK and nosZ OTUs was low (6, 7 and 3, respectively, and most of these core OTUs were shared among the lakes. Dominant nirK sequences matched best with those of the order Rhizobiales, which was one of the main bacterial orders present in the sediment microbiomes, whereas the dominant nirS sequences were affiliated with the order Burkholderiales. Over half of the nosZ sequences belonged to a single OTU of the order Burkholderiales, but coupled nitrification-denitrification rate correlated with another dominant nosZ OTU assigned to the order Rhodospirillales. The study indicates that a few core proteobacterial clusters may drive denitrification in boreal lake sediments, as the same Alpha- and Betaproteobacteria denitrifier clusters were present in different lakes and seasons.

  1. Automated Identification of Core Regulatory Genes in Human Gene Regulatory Networks.

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    Vipin Narang

    Full Text Available Human gene regulatory networks (GRN can be difficult to interpret due to a tangle of edges interconnecting thousands of genes. We constructed a general human GRN from extensive transcription factor and microRNA target data obtained from public databases. In a subnetwork of this GRN that is active during estrogen stimulation of MCF-7 breast cancer cells, we benchmarked automated algorithms for identifying core regulatory genes (transcription factors and microRNAs. Among these algorithms, we identified K-core decomposition, pagerank and betweenness centrality algorithms as the most effective for discovering core regulatory genes in the network evaluated based on previously known roles of these genes in MCF-7 biology as well as in their ability to explain the up or down expression status of up to 70% of the remaining genes. Finally, we validated the use of K-core algorithm for organizing the GRN in an easier to interpret layered hierarchy where more influential regulatory genes percolate towards the inner layers. The integrated human gene and miRNA network and software used in this study are provided as supplementary materials (S1 Data accompanying this manuscript.

  2. Automated Identification of Core Regulatory Genes in Human Gene Regulatory Networks.

    Science.gov (United States)

    Narang, Vipin; Ramli, Muhamad Azfar; Singhal, Amit; Kumar, Pavanish; de Libero, Gennaro; Poidinger, Michael; Monterola, Christopher

    2015-01-01

    Human gene regulatory networks (GRN) can be difficult to interpret due to a tangle of edges interconnecting thousands of genes. We constructed a general human GRN from extensive transcription factor and microRNA target data obtained from public databases. In a subnetwork of this GRN that is active during estrogen stimulation of MCF-7 breast cancer cells, we benchmarked automated algorithms for identifying core regulatory genes (transcription factors and microRNAs). Among these algorithms, we identified K-core decomposition, pagerank and betweenness centrality algorithms as the most effective for discovering core regulatory genes in the network evaluated based on previously known roles of these genes in MCF-7 biology as well as in their ability to explain the up or down expression status of up to 70% of the remaining genes. Finally, we validated the use of K-core algorithm for organizing the GRN in an easier to interpret layered hierarchy where more influential regulatory genes percolate towards the inner layers. The integrated human gene and miRNA network and software used in this study are provided as supplementary materials (S1 Data) accompanying this manuscript.

  3. Evolution of a core gene network for skeletogenesis in chordates.

    Directory of Open Access Journals (Sweden)

    Jochen Hecht

    2008-03-01

    Full Text Available The skeleton is one of the most important features for the reconstruction of vertebrate phylogeny but few data are available to understand its molecular origin. In mammals the Runt genes are central regulators of skeletogenesis. Runx2 was shown to be essential for osteoblast differentiation, tooth development, and bone formation. Both Runx2 and Runx3 are essential for chondrocyte maturation. Furthermore, Runx2 directly regulates Indian hedgehog expression, a master coordinator of skeletal development. To clarify the correlation of Runt gene evolution and the emergence of cartilage and bone in vertebrates, we cloned the Runt genes from hagfish as representative of jawless fish (MgRunxA, MgRunxB and from dogfish as representative of jawed cartilaginous fish (ScRunx1-3. According to our phylogenetic reconstruction the stem species of chordates harboured a single Runt gene and thereafter Runt locus duplications occurred during early vertebrate evolution. All newly isolated Runt genes were expressed in cartilage according to quantitative PCR. In situ hybridisation confirmed high MgRunxA expression in hard cartilage of hagfish. In dogfish ScRunx2 and ScRunx3 were expressed in embryonal cartilage whereas all three Runt genes were detected in teeth and placoid scales. In cephalochordates (lancelets Runt, Hedgehog and SoxE were strongly expressed in the gill bars and expression of Runt and Hedgehog was found in endo- as well as ectodermal cells. Furthermore we demonstrate that the lancelet Runt protein binds to Runt binding sites in the lancelet Hedgehog promoter and regulates its activity. Together, these results suggest that Runt and Hedgehog were part of a core gene network for cartilage formation, which was already active in the gill bars of the common ancestor of cephalochordates and vertebrates and diversified after Runt duplications had occurred during vertebrate evolution. The similarities in expression patterns of Runt genes support the view

  4. Role of Macroautophagy in Nutrient Homeostasis During Fungal Development and Pathogenesis

    Directory of Open Access Journals (Sweden)

    Naweed I. Naqvi

    2012-08-01

    Full Text Available Macroautophagy is a non-selective, bulk degradation process conserved in eukaryotes. Response to starvation stress and/or regulation of nutrient breakdown/utilization is the major intracellular function of macroautophagy. Recent studies have revealed requirement for autophagy in diverse functions such as nutrient homeostasis, organelle degradation and programmed cell death in filamentous fungal pathogens, for proper morphogenesis and differentiation during critical steps of infection. In this review, we aim to summarize the physiological functions of autophagy in fungal virulence, with an emphasis on nutrient homeostasis in opportunistic human fungal pathogens and in the rice-blast fungus, Magnaporthe oryzae. We briefly summarize the role of autophagy on the host side: for resistance to, or subversion by, the pathogens.

  5. Gene Duplicability of Core Genes Is Highly Consistent across All Angiosperms.

    Science.gov (United States)

    Li, Zhen; Defoort, Jonas; Tasdighian, Setareh; Maere, Steven; Van de Peer, Yves; De Smet, Riet

    2016-02-01

    Gene duplication is an important mechanism for adding to genomic novelty. Hence, which genes undergo duplication and are preserved following duplication is an important question. It has been observed that gene duplicability, or the ability of genes to be retained following duplication, is a nonrandom process, with certain genes being more amenable to survive duplication events than others. Primarily, gene essentiality and the type of duplication (small-scale versus large-scale) have been shown in different species to influence the (long-term) survival of novel genes. However, an overarching view of "gene duplicability" is lacking, mainly due to the fact that previous studies usually focused on individual species and did not account for the influence of genomic context and the time of duplication. Here, we present a large-scale study in which we investigated duplicate retention for 9178 gene families shared between 37 flowering plant species, referred to as angiosperm core gene families. For most gene families, we observe a strikingly consistent pattern of gene duplicability across species, with gene families being either primarily single-copy or multicopy in all species. An intermediate class contains gene families that are often retained in duplicate for periods extending to tens of millions of years after whole-genome duplication, but ultimately appear to be largely restored to singleton status, suggesting that these genes may be dosage balance sensitive. The distinction between single-copy and multicopy gene families is reflected in their functional annotation, with single-copy genes being mainly involved in the maintenance of genome stability and organelle function and multicopy genes in signaling, transport, and metabolism. The intermediate class was overrepresented in regulatory genes, further suggesting that these represent putative dosage-balance-sensitive genes. © 2016 American Society of Plant Biologists. All rights reserved.

  6. Gene Duplicability of Core Genes Is Highly Consistent across All Angiosperms[OPEN

    Science.gov (United States)

    Li, Zhen; Van de Peer, Yves; De Smet, Riet

    2016-01-01

    Gene duplication is an important mechanism for adding to genomic novelty. Hence, which genes undergo duplication and are preserved following duplication is an important question. It has been observed that gene duplicability, or the ability of genes to be retained following duplication, is a nonrandom process, with certain genes being more amenable to survive duplication events than others. Primarily, gene essentiality and the type of duplication (small-scale versus large-scale) have been shown in different species to influence the (long-term) survival of novel genes. However, an overarching view of “gene duplicability” is lacking, mainly due to the fact that previous studies usually focused on individual species and did not account for the influence of genomic context and the time of duplication. Here, we present a large-scale study in which we investigated duplicate retention for 9178 gene families shared between 37 flowering plant species, referred to as angiosperm core gene families. For most gene families, we observe a strikingly consistent pattern of gene duplicability across species, with gene families being either primarily single-copy or multicopy in all species. An intermediate class contains gene families that are often retained in duplicate for periods extending to tens of millions of years after whole-genome duplication, but ultimately appear to be largely restored to singleton status, suggesting that these genes may be dosage balance sensitive. The distinction between single-copy and multicopy gene families is reflected in their functional annotation, with single-copy genes being mainly involved in the maintenance of genome stability and organelle function and multicopy genes in signaling, transport, and metabolism. The intermediate class was overrepresented in regulatory genes, further suggesting that these represent putative dosage-balance-sensitive genes. PMID:26744215

  7. A core program of gene expression characterizes cancer metastases.

    Science.gov (United States)

    Hartung, Franz; Wang, Yunguan; Aronow, Bruce; Weber, Georg F

    2017-11-24

    While aberrant expression or splicing of metastasis genes conveys to cancers the ability to break through tissue barriers and disseminate, the genetic basis for organ preference in metastasis formation has remained incompletely understood. Utilizing the gene expression profiles from 653 GEO datasets, we investigate whether the signatures by diverse cancers in various metastatic sites display common features. We corroborate the meta-analysis in a murine model. Metastases are generally characterized by a core program of gene expression that induces the oxidative metabolism, activates vascularization/tissue remodeling, silences extracellular matrix interactions, and alters ion homeostasis. This program distinguishes metastases from their originating primary tumors as well as from their target host tissues. Site-selectivity is accomplished through specific components that adjust to the target micro-environment. The same functional groups of gene expression programs are activated in the metastases of B16-F10 cells to various target organs. It remains to be investigated whether these genetic signatures precede implantation and thus determine organ preference or are shaped by the target site and are thus a consequence of implantation. Conceivably, chemotherapy of disseminated cancer might be more efficacious if selected to match the genetic makeup of the metastases rather than the organ of origin by the primary tumor.

  8. Strain-Dependent Effect of Macroautophagy on Abnormally Folded Prion Protein Degradation in Infected Neuronal Cells.

    Directory of Open Access Journals (Sweden)

    Daisuke Ishibashi

    Full Text Available Prion diseases are neurodegenerative disorders caused by the accumulation of abnormal prion protein (PrPSc in the central nervous system. With the aim of elucidating the mechanism underlying the accumulation and degradation of PrPSc, we investigated the role of autophagy in its degradation, using cultured cells stably infected with distinct prion strains. The effects of pharmacological compounds that inhibit or stimulate the cellular signal transduction pathways that mediate autophagy during PrPSc degradation were evaluated. The accumulation of PrPSc in cells persistently infected with the prion strain Fukuoka-1 (FK, derived from a patient with Gerstmann-Sträussler-Scheinker syndrome, was significantly increased in cultures treated with the macroautophagy inhibitor 3-methyladenine (3MA but substantially reduced in those treated with the macroautophagy inducer rapamycin. The decrease in FK-derived PrPSc levels was mediated, at least in part, by the phosphatidylinositol 3-kinase/MEK signalling pathway. By contrast, neither rapamycin nor 3MA had any apparently effect on PrPSc from either the 22L or the Chandler strain, indicating that the degradation of PrPSc in host cells might be strain-dependent.

  9. HO-1-mediated macroautophagy: a mechanism for unregulated iron deposition in aging and degenerating neural tissues.

    Science.gov (United States)

    Zukor, Hillel; Song, Wei; Liberman, Adrienne; Mui, Jeannie; Vali, Hojatollah; Fillebeen, Carine; Pantopoulos, Kostas; Wu, Ting-Di; Guerquin-Kern, Jean-Luc; Schipper, Hyman M

    2009-05-01

    Oxidative stress, deposition of non-transferrin iron, and mitochondrial insufficiency occur in the brains of patients with Alzheimer disease (AD) and Parkinson disease (PD). We previously demonstrated that heme oxygenase-1 (HO-1) is up-regulated in AD and PD brain and promotes the accumulation of non-transferrin iron in astroglial mitochondria. Herein, dynamic secondary ion mass spectrometry (SIMS) and other techniques were employed to ascertain (i) the impact of HO-1 over-expression on astroglial mitochondrial morphology in vitro, (ii) the topography of aberrant iron sequestration in astrocytes over-expressing HO-1, and (iii) the role of iron regulatory proteins (IRP) in HO-1-mediated iron deposition. Astroglial hHO-1 over-expression induced cytoplasmic vacuolation, mitochondrial membrane damage, and macroautophagy. HO-1 promoted trapping of redox-active iron and sulfur within many cytopathological profiles without impacting ferroportin, transferrin receptor, ferritin, and IRP2 protein levels or IRP1 activity. Thus, HO-1 activity promotes mitochondrial macroautophagy and sequestration of redox-active iron in astroglia independently of classical iron mobilization pathways. Glial HO-1 may be a rational therapeutic target in AD, PD, and other human CNS conditions characterized by the unregulated deposition of brain iron.

  10. Expression of core clock genes in colorectal tumour cells compared with normal mucosa

    DEFF Research Database (Denmark)

    Fonnes, S; Donatsky, A M; Gögenur, I

    2015-01-01

    AIM: Experimental studies have shown that some circadian core clock genes may act as tumour suppressors and have an important role in the response to oncological treatment. This study investigated the evidence regarding modified expression of core clock genes in colorectal cancer and its...... expression of colorectal cancer cells compared with healthy mucosa cells from specimens analysed by real-time or quantitative real-time polymer chain reaction. The expression of the core clock genes Period, Cryptochrome, Bmal1 and Clock in colorectal tumours were compared with healthy mucosa and correlated...... with clinicopathological features and survival. RESULTS: Seventy-four articles were identified and 11 studies were included. Overall, gene expression of Period was significantly decreased in colorectal cancer cells compared with healthy mucosa cells. This tendency was also seen in the gene expression of Clock. Other core...

  11. GLP-1 analogs reduce hepatocyte steatosis and improve survival by enhancing the unfolded protein response and promoting macroautophagy.

    Directory of Open Access Journals (Sweden)

    Shvetank Sharma

    Full Text Available Nonalcoholic fatty liver disease (NAFLD is a known outcome of hepatosteatosis. Free fatty acids (FFA induce the unfolded protein response (UPR or endoplasmic reticulum (ER stress that may induce apoptosis. Recent data indicate ER stress to be a major player in the progression of fatty liver to more aggressive lesions. Autophagy on the other hand has been demonstrated to be protective against ER stress-induced cell death. We hypothesized that exendin-4 (GLP-1 analog treatment of fat loaded hepatocytes can reduce steatosis by autophagy which leads to reduced ER stress-related hepatocyte apoptosis.Primary human hepatocytes were loaded with saturated, cis- and trans-unsaturated fatty acids (palmitic, oleic and elaidic acid respectively. Steatosis, induced with all three fatty acids, was significantly resolved after exendin-4 treatment. Exendin-4 sustained levels of GRP78 expression in fat-loaded cells when compared to untreated fat-loaded cells alone. In contrast, CHOP (C/EBP homologous protein; the penultimate protein that leads to ER stress-related cell death was significantly decreased by exendin-4 in hepatocytes loaded with fatty acids. Finally, exendin-4 in fat loaded hepatocytes clearly promoted gene products associated with macroautophagy as measured by enhanced production of both Beclin-1 and LC3B-II, markers for autophagy; and visualized by transmission electron microscopy (TEM. Similar observations were made in mouse liver lysates after mice were fed with high fat high fructose diet and treated with a long acting GLP-1 receptor agonist, liraglutide.GLP-1 proteins appear to protect hepatocytes from fatty acid-related death by prohibition of a dysfunctional ER stress response; and reduce fatty acid accumulation, by activation of both macro-and chaperone-mediated autophagy. These findings provide a novel role for GLP-1 proteins in halting the progression of more aggressive lesions from underlying steatosis in humans afflicted with NAFLD.

  12. Evolution of a core gene network for skeletogenesis in chordates

    National Research Council Canada - National Science Library

    Hecht, Jochen; Stricker, Sigmar; Wiecha, Ulrike; Stiege, Asita; Panopoulou, Georgia; Podsiadlowski, Lars; Poustka, Albert J; Dieterich, Christoph; Ehrich, Siegfried; Suvorova, Julia; Mundlos, Stefan; Seitz, Volkhard

    2008-01-01

    .... To clarify the correlation of Runt gene evolution and the emergence of cartilage and bone in vertebrates, we cloned the Runt genes from hagfish as representative of jawless fish (MgRunxA, MgRunxB...

  13. Enhancer-core-promoter specificity separates developmental and housekeeping gene regulation.

    Science.gov (United States)

    Zabidi, Muhammad A; Arnold, Cosmas D; Schernhuber, Katharina; Pagani, Michaela; Rath, Martina; Frank, Olga; Stark, Alexander

    2015-02-26

    Gene transcription in animals involves the assembly of RNA polymerase II at core promoters and its cell-type-specific activation by enhancers that can be located more distally. However, how ubiquitous expression of housekeeping genes is achieved has been less clear. In particular, it is unknown whether ubiquitously active enhancers exist and how developmental and housekeeping gene regulation is separated. An attractive hypothesis is that different core promoters might exhibit an intrinsic specificity to certain enhancers. This is conceivable, as various core promoter sequence elements are differentially distributed between genes of different functions, including elements that are predominantly found at either developmentally regulated or at housekeeping genes. Here we show that thousands of enhancers in Drosophila melanogaster S2 and ovarian somatic cells (OSCs) exhibit a marked specificity to one of two core promoters--one derived from a ubiquitously expressed ribosomal protein gene and another from a developmentally regulated transcription factor--and confirm the existence of these two classes for five additional core promoters from genes with diverse functions. Housekeeping enhancers are active across the two cell types, while developmental enhancers exhibit strong cell-type specificity. Both enhancer classes differ in their genomic distribution, the functions of neighbouring genes, and the core promoter elements of these neighbouring genes. In addition, we identify two transcription factors--Dref and Trl--that bind and activate housekeeping versus developmental enhancers, respectively. Our results provide evidence for a sequence-encoded enhancer-core-promoter specificity that separates developmental and housekeeping gene regulatory programs for thousands of enhancers and their target genes across the entire genome.

  14. Core Gene Expression and Association of Genotypes with Viral ...

    African Journals Online (AJOL)

    HP

    Lahore, Pakistan. 3Institute of Agricultural Sciences, 4Department of Microbiology and Molecular Genetics, University of the ... tested by type-specific genotyping assay, viral load, by real time polymerase chain reaction (PCR) and. HCV core protein was ... RT-PCR of HCV RNA was performed using Mini. OpticonTM System ...

  15. Sequence comparison and phylogenetic analysis of core gene of ...

    African Journals Online (AJOL)

    Nucleotides and deduced amino acid sequence comparison of six isolates was performed with each other and with two HCV genotype 3a type examples reported from Japan. Phylogenetic tree of HCV core sequences was constructed using CLC software. Nucleotides sequence comparison showed that our sequences ...

  16. Sequence comparison and phylogenetic analysis of core gene of ...

    African Journals Online (AJOL)

    STORAGESEVER

    2010-07-19

    Jul 19, 2010 ... Our sequences and sequences from Japan are grouped into same cluster in the phylogenetic tree. Sequence comparison and phylogenetic analysis showed that our isolates have high homology with Japanese isolates. Key words: Hepatitis C virus, core, phylogenetic analysis, Pakistan. INTRODUCTION.

  17. CORE

    DEFF Research Database (Denmark)

    Krigslund, Jeppe; Hansen, Jonas; Hundebøll, Martin

    2013-01-01

    different flows. Instead of maintaining these approaches separate, we propose a protocol (CORE) that brings together these coding mechanisms. Our protocol uses random linear network coding (RLNC) for intra- session coding but allows nodes in the network to setup inter- session coding regions where flows...... intersect. Routes for unicast sessions are agnostic to other sessions and setup beforehand, CORE will then discover and exploit intersecting routes. Our approach allows the inter-session regions to leverage RLNC to compensate for losses or failures in the overhearing or transmitting process. Thus, we...... increase the benefits of XORing by exploiting the underlying RLNC structure of individual flows. This goes beyond providing additional reliability to each individual session and beyond exploiting coding opportunistically. Our numerical results show that CORE outperforms both forwarding and COPE...

  18. Core histone genes of Giardia intestinalis: genomic organization, promoter structure, and expression

    Directory of Open Access Journals (Sweden)

    Adam Rodney D

    2007-04-01

    Full Text Available Abstract Background Giardia intestinalis is a protist found in freshwaters worldwide, and is the most common cause of parasitic diarrhea in humans. The phylogenetic position of this parasite is still much debated. Histones are small, highly conserved proteins that associate tightly with DNA to form chromatin within the nucleus. There are two classes of core histone genes in higher eukaryotes: DNA replication-independent histones and DNA replication-dependent ones. Results We identified two copies each of the core histone H2a, H2b and H3 genes, and three copies of the H4 gene, at separate locations on chromosomes 3, 4 and 5 within the genome of Giardia intestinalis, but no gene encoding a H1 linker histone could be recognized. The copies of each gene share extensive DNA sequence identities throughout their coding and 5' noncoding regions, which suggests these copies have arisen from relatively recent gene duplications or gene conversions. The transcription start sites are at triplet A sequences 1–27 nucleotides upstream of the translation start codon for each gene. We determined that a 50 bp region upstream from the start of the histone H4 coding region is the minimal promoter, and a highly conserved 15 bp sequence called the histone motif (him is essential for its activity. The Giardia core histone genes are constitutively expressed at approximately equivalent levels and their mRNAs are polyadenylated. Competition gel-shift experiments suggest that a factor within the protein complex that binds him may also be a part of the protein complexes that bind other promoter elements described previously in Giardia. Conclusion In contrast to other eukaryotes, the Giardia genome has only a single class of core histone genes that encode replication-independent histones. Our inability to locate a gene encoding the linker histone H1 leads us to speculate that the H1 protein may not be required for the compaction of Giardia's small and gene-rich genome.

  19. Inhibition of HCV 3a core gene through Silymarin and its fractions

    Directory of Open Access Journals (Sweden)

    Nawaz Zafar

    2011-04-01

    Full Text Available Abstract Hepatitis C is a major health problem affecting 270 million individuals in world including Pakistan. Current treatment regimen, interferon alpha and ribavirin only cure half of patients due to side effects and high cost. Results In the present study Silybum marianum (Milk thistle seeds were collected, extracted and analyzed against HCV 3a core gene by transiently transfecting the liver cells with HCV core plasmid. Our results demonstrated that Silymarin (SM dose dependently inhibit the expression or function of HCV core gene at a non toxic concentration while the GAPDH remained constant. To identify the active ingredient, SM was fractioned by thin layer chromatography (TLC, column chromatography and HPLC. Purified fractions were tested for HCV core gene and western blotting results showed that two factions of SM (S1 and S2 inhibit HCV 3a core expression or function in liver cells Conclusion Our results suggest SM and its fractions (S1 and S2 inhibit HCV core gene of 3a genotype and combination of SM and its fractions with interferon will be a better option to treat HCV infection

  20. Identification of a core set of genes that signifies pathways underlying cardiac hypertrophy

    DEFF Research Database (Denmark)

    Strom, C.C.; Kruhoffer, M.; Knudsen, Steen

    2004-01-01

    gene expression, using microarray technology in multiple models of cardiac hypertrophy, including aortic banding, myocardial infarction, an arteriovenous shunt and pharmacologically induced hypertrophy, would uncover networks of conserved hypertrophy-specific genes and identify novel genes involved...... in hypertrophic signalling. From gene expression analyses (8740 probe sets, n = 46) of rat ventricular RNA, we identified a core set of 139 genes with consistent differential expression in all hypertrophy models as compared to their controls, including 78 genes not previously associated with hypertrophy and 61...... genes whose altered expression had previously been reported. We identified a single common gene program underlying hypertrophic remodelling, regardless of how the hypertrophy was induced. These genes constitute the molecular basis for the existence of one main form of cardiac hypertrophy and may...

  1. Changes in macroautophagy, chaperone-mediated autophagy, and mitochondrial metabolism in murine skeletal and cardiac muscle during aging.

    Science.gov (United States)

    Zhou, Jin; Chong, Shu Yun; Lim, Andrea; Singh, Brijesh K; Sinha, Rohit A; Salmon, Adam B; Yen, Paul M

    2017-02-26

    Aging causes a general decline in cellular metabolic activity, and function in different tissues and whole body homeostasis. However, the understanding about the metabolomic and autophagy changes in skeletal muscle and heart during aging is still limited. We thus examined markers for macroautophagy, chaperone-mediated autophagy (CMA), mitochondrial quality control, as well as cellular metabolites in skeletal and cardiac muscle from young (5 months old) and aged (27 months old) mice. We found decreased autophagic degradation of p62 and increased ubiquitinated proteins in both tissues from aged mice, suggesting a decline in macroautophagy during aging. In skeletal muscle from aged mice, there also was a decline in LC3B-I conjugation to phosphatidylethanolamine (PE) possibly due to decreased protein levels of ATG3 and ATG12-ATG5. The CMA markers, LAMP-2A and Hsc70, and mitochondrial turnover markers, Drp1, PINK1 and PGC1α also were decreased. Metabolomics analysis showed impaired β-oxidation in heart of aged mice, whereas increased branched-chain amino acids (BCAAs) and ceramide levels were found in skeletal muscle of aged mice that in turn, may contribute to insulin resistance in muscle. Taken together, our studies showed similar declines in macroautophagy but distinct effects on CMA, mitochondrial turnover, and metabolic dysfunction in muscle vs. heart during aging.

  2. Differential regulation of horizontally acquired and core genome genes by the bacterial modulator H-NS.

    Directory of Open Access Journals (Sweden)

    Rosa C Baños

    2009-06-01

    Full Text Available Horizontal acquisition of DNA by bacteria dramatically increases genetic diversity and hence successful bacterial colonization of several niches, including the human host. A relevant issue is how this newly acquired DNA interacts and integrates in the regulatory networks of the bacterial cell. The global modulator H-NS targets both core genome and HGT genes and silences gene expression in response to external stimuli such as osmolarity and temperature. Here we provide evidence that H-NS discriminates and differentially modulates core and HGT DNA. As an example of this, plasmid R27-encoded H-NS protein has evolved to selectively silence HGT genes and does not interfere with core genome regulation. In turn, differential regulation of both gene lineages by resident chromosomal H-NS requires a helper protein: the Hha protein. Tight silencing of HGT DNA is accomplished by H-NS-Hha complexes. In contrast, core genes are modulated by H-NS homoligomers. Remarkably, the presence of Hha-like proteins is restricted to the Enterobacteriaceae. In addition, conjugative plasmids encoding H-NS variants have hitherto been isolated only from members of the family. Thus, the H-NS system in enteric bacteria presents unique evolutionary features. The capacity to selectively discriminate between core and HGT DNA may help to maintain horizontally transmitted DNA in silent form and may give these bacteria a competitive advantage in adapting to new environments, including host colonization.

  3. Identification of the Core Set of Carbon-Associated Genes in a Bioenergy Grassland Soil.

    Directory of Open Access Journals (Sweden)

    Adina Howe

    Full Text Available Despite the central role of soil microbial communities in global carbon (C cycling, little is known about soil microbial community structure and even less about their metabolic pathways. Efforts to characterize soil communities often focus on identifying differences in gene content across environmental gradients, but an alternative question is what genes are similar in soils. These genes may indicate critical species or potential functions that are required in all soils. Here we identified the "core" set of C cycling sequences widely present in multiple soil metagenomes from a fertilized prairie (FP. Of 226,887 sequences associated with known enzymes involved in the synthesis, metabolism, and transport of carbohydrates, 843 were identified to be consistently prevalent across four replicate soil metagenomes. This core metagenome was functionally and taxonomically diverse, representing five enzyme classes and 99 enzyme families within the CAZy database. Though it only comprised 0.4% of all CAZy-associated genes identified in FP metagenomes, the core was found to be comprised of functions similar to those within cumulative soils. The FP CAZy-associated core sequences were present in multiple publicly available soil metagenomes and most similar to soils sharing geographic proximity. In soil ecosystems, where high diversity remains a key challenge for metagenomic investigations, these core genes represent a subset of critical functions necessary for carbohydrate metabolism, which can be targeted to evaluate important C fluxes in these and other similar soils.

  4. Unravelling the relationship between macroautophagy and mitochondrial ROS in cancer therapy.

    Science.gov (United States)

    Zhao, Yuqian; Qu, Tiange; Wang, Peiqi; Li, Xinyi; Qiang, Jiayu; Xia, Zhaokun; Duan, Hangwu; Huang, Jian; Zhu, Lingjuan

    2016-05-01

    Macroautophagy (Autophagy), an evolutionarily conserved cellular self-digesting process implicated in various physiological and pathological processes, is activated by different stimuli including oxidative stress. Reactive oxygen species (ROS) are involved in autophagy modulation through multiple signaling pathways and transcription regulators. Accumulating data support both a positive and negative role of ROS-modulated autophagy in cancer. As a tumor suppressive mechanism, autophagy induces autophagic cell death and maintains genome stability. Conversely, autophagy may promote cancer development by limiting metabolic stress and supplying high-energetic nutrients. Mitochondrial ROS (mitoROS), the main source of endogenous ROS, serve as essential signal transducers that mediate autophagy, while autophagy can also regulate mitochondrial ROS generation in turn. Here, we untangle the knot between mitochondrial ROS and autophagy, which may be of great significance to solve the conundrum of the inter-conversion between cytoprotective and cytotoxic roles of autophagy; thus providing new insights for current cancer therapies. Whilst, we focus on anti-tumor agents that target mitoROS-regulated autophagy, in the hope of fueling the exploration of more potential novel anti-cancer drugs in the future.

  5. Transcription Factors Encoded on Core and Accessory Chromosomes of Fusarium oxysporum Induce Expression of Effector Genes.

    Directory of Open Access Journals (Sweden)

    H Charlotte van der Does

    2016-11-01

    Full Text Available Proteins secreted by pathogens during host colonization largely determine the outcome of pathogen-host interactions and are commonly called 'effectors'. In fungal plant pathogens, coordinated transcriptional up-regulation of effector genes is a key feature of pathogenesis and effectors are often encoded in genomic regions with distinct repeat content, histone code and rate of evolution. In the tomato pathogen Fusarium oxysporum f. sp. lycopersici (Fol, effector genes reside on one of four accessory chromosomes, known as the 'pathogenicity' chromosome, which can be exchanged between strains through horizontal transfer. The three other accessory chromosomes in the Fol reference strain may also be important for virulence towards tomato. Expression of effector genes in Fol is highly up-regulated upon infection and requires Sge1, a transcription factor encoded on the core genome. Interestingly, the pathogenicity chromosome itself contains 13 predicted transcription factor genes and for all except one, there is a homolog on the core genome. We determined DNA binding specificity for nine transcription factors using oligonucleotide arrays. The binding sites for homologous transcription factors were highly similar, suggesting that extensive neofunctionalization of DNA binding specificity has not occurred. Several DNA binding sites are enriched on accessory chromosomes, and expression of FTF1, its core homolog FTF2 and SGE1 from a constitutive promoter can induce expression of effector genes. The DNA binding sites of only these three transcription factors are enriched among genes up-regulated during infection. We further show that Ftf1, Ftf2 and Sge1 can activate transcription from their binding sites in yeast. RNAseq analysis revealed that in strains with constitutive expression of FTF1, FTF2 or SGE1, expression of a similar set of plant-responsive genes on the pathogenicity chromosome is induced, including most effector genes. We conclude that the Fol

  6. Transcription Factors Encoded on Core and Accessory Chromosomes of Fusarium oxysporum Induce Expression of Effector Genes.

    Science.gov (United States)

    van der Does, H Charlotte; Fokkens, Like; Yang, Ally; Schmidt, Sarah M; Langereis, Léon; Lukasiewicz, Joanna M; Hughes, Timothy R; Rep, Martijn

    2016-11-01

    Proteins secreted by pathogens during host colonization largely determine the outcome of pathogen-host interactions and are commonly called 'effectors'. In fungal plant pathogens, coordinated transcriptional up-regulation of effector genes is a key feature of pathogenesis and effectors are often encoded in genomic regions with distinct repeat content, histone code and rate of evolution. In the tomato pathogen Fusarium oxysporum f. sp. lycopersici (Fol), effector genes reside on one of four accessory chromosomes, known as the 'pathogenicity' chromosome, which can be exchanged between strains through horizontal transfer. The three other accessory chromosomes in the Fol reference strain may also be important for virulence towards tomato. Expression of effector genes in Fol is highly up-regulated upon infection and requires Sge1, a transcription factor encoded on the core genome. Interestingly, the pathogenicity chromosome itself contains 13 predicted transcription factor genes and for all except one, there is a homolog on the core genome. We determined DNA binding specificity for nine transcription factors using oligonucleotide arrays. The binding sites for homologous transcription factors were highly similar, suggesting that extensive neofunctionalization of DNA binding specificity has not occurred. Several DNA binding sites are enriched on accessory chromosomes, and expression of FTF1, its core homolog FTF2 and SGE1 from a constitutive promoter can induce expression of effector genes. The DNA binding sites of only these three transcription factors are enriched among genes up-regulated during infection. We further show that Ftf1, Ftf2 and Sge1 can activate transcription from their binding sites in yeast. RNAseq analysis revealed that in strains with constitutive expression of FTF1, FTF2 or SGE1, expression of a similar set of plant-responsive genes on the pathogenicity chromosome is induced, including most effector genes. We conclude that the Fol pathogenicity

  7. Autosomal dominant eccentric core disease caused by a heterozygous mutation in the MYH7 gene.

    Science.gov (United States)

    Romero, Norma B; Xie, Ting; Malfatti, Edoardo; Schaeffer, Ursula; Böhm, Johann; Wu, Bin; Xu, Fengping; Boucebci, Samy; Mathis, Stéphane; Neau, Jean-Philippe; Monnier, Nicole; Fardeau, Michel; Laporte, Jocelyn

    2014-10-01

    Autosomal dominant (AD) central core disease (CCD) is a congenital myopathy characterised by the presence of cores in the muscle fibres which correspond to broad areas of myofibrils disorganisation, Z-line streaming and lack of mitochondria. Heterozygous mutations in the RYR1 gene were observed in the large majority of AD-CCD families; however, this gene was excluded in some of AD-CCD families. To enlarge the genetic spectrum of AD-CCD demonstrating mutations in an additional gene. Four affected AD family members over three generations, three of whom were alive and participate in the study: the mother and two of three siblings. The symptoms began during the early childhood with mild delayed motor development. Later they developed mainly tibialis anterior weakness, hypertrophy of calves and significant weakness (amyotrophic) of quadriceps. No cardiac or ocular involvement was noted. The muscle biopsies sections showed a particular pattern: eccentric cores in type 1 fibres, associated with type 1 predominance. Most cores have abrupt borders. Electron microscopy confirmed the presence of both unstructured and structured cores. Exome sequencing analysis identified a novel heterozygous missense mutation p.Leu1723Pro in MYH7 segregating with the disease and affecting a conserved residue in the myosin tail domain. We describe MYH7 as an additional causative gene for AD-CCD. These findings have important implications for diagnosis and future investigations of AD-congenital myopathies with cores, without cardiomyopathy, but presenting a particular involvement of distal and quadriceps muscles. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

  8. Gene expression variation between distinct areas of breast cancer measured from paraffin-embedded tissue cores

    Directory of Open Access Journals (Sweden)

    Gugger Mathias

    2008-11-01

    Full Text Available Abstract Background Diagnosis and prognosis in breast cancer are mainly based on histology and immunohistochemistry of formalin-fixed, paraffin-embedded (FFPE material. Recently, gene expression analysis was shown to elucidate the biological variance between tumors and molecular markers were identified that led to new classification systems that provided better prognostic and predictive parameters. Archived FFPE samples represent an ideal source of tissue for translational research, as millions of tissue blocks exist from routine diagnostics and from clinical studies. These should be exploited to provide clinicians with more accurate prognostic and predictive information. Unfortunately, RNA derived from FFPE material is partially degraded and chemically modified and reliable gene expression measurement has only become successful after implementing novel and optimized procedures for RNA isolation, demodification and detection. Methods In this study we used tissue cylinders as known from the construction of tissue microarrays. RNA was isolated with a robust protocol recently developed for RNA derived from FFPE material. Gene expression was measured by quantitative reverse transcription PCR. Results Sixteen tissue blocks from 7 patients diagnosed with multiple histological subtypes of breast cancer were available for this study. After verification of appropriate localization, sufficient RNA yield and quality, 30 tissue cores were available for gene expression measurement on TaqMan® Low Density Arrays (16 invasive ductal carcinoma (IDC, 8 ductal carcinoma in situ (DCIS and 6 normal tissue, and 14 tissue cores were lost. Gene expression values were used to calculate scores representing the proliferation status (PRO, the estrogen receptor status and the HER2 status. The PRO scores measured from entire sections were similar to PRO scores determined from IDC tissue cores. Scores determined from normal tissue cores consistently revealed lower PRO scores

  9. GENIE: a software package for gene-gene interaction analysis in genetic association studies using multiple GPU or CPU cores.

    Science.gov (United States)

    Chikkagoudar, Satish; Wang, Kai; Li, Mingyao

    2011-05-26

    Gene-gene interaction in genetic association studies is computationally intensive when a large number of SNPs are involved. Most of the latest Central Processing Units (CPUs) have multiple cores, whereas Graphics Processing Units (GPUs) also have hundreds of cores and have been recently used to implement faster scientific software. However, currently there are no genetic analysis software packages that allow users to fully utilize the computing power of these multi-core devices for genetic interaction analysis for binary traits. Here we present a novel software package GENIE, which utilizes the power of multiple GPU or CPU processor cores to parallelize the interaction analysis. GENIE reads an entire genetic association study dataset into memory and partitions the dataset into fragments with non-overlapping sets of SNPs. For each fragment, GENIE analyzes: 1) the interaction of SNPs within it in parallel, and 2) the interaction between the SNPs of the current fragment and other fragments in parallel. We tested GENIE on a large-scale candidate gene study on high-density lipoprotein cholesterol. Using an NVIDIA Tesla C1060 graphics card, the GPU mode of GENIE achieves a speedup of 27 times over its single-core CPU mode run. GENIE is open-source, economical, user-friendly, and scalable. Since the computing power and memory capacity of graphics cards are increasing rapidly while their cost is going down, we anticipate that GENIE will achieve greater speedups with faster GPU cards. Documentation, source code, and precompiled binaries can be downloaded from http://www.cceb.upenn.edu/~mli/software/GENIE/.

  10. Data mining pathogen genomes using GeneOrder and CoreGenes and CGUG: gene order, synteny and in silico proteomes.

    Science.gov (United States)

    Mahadevan, Padmanabhan; King, John F; Seto, Donald

    2009-01-01

    Sequence databases are growing exponentially due to 'next generation' DNA analysers and applications of these data. Databases include multiple sequences of previously sequenced organisms, particularly ones of consequence to human health. Applications are limited by tools available to mine them, particularly user-friendly tools that are useful for bench researchers. GeneOrder, CoreGenes and CGUG are web-based 'on-the-fly' tools that examine gene order and synteny, as well as proteomes for comparative genomics and for drug discovery and design targets. CoreGenes (CGUG) now allows analysis of genomes ranging up to 1.9 megabases. Many of these small genome bacteria have impacts on human health.

  11. Fanconi anemia core complex gene promoters harbor conserved transcription regulatory elements.

    Directory of Open Access Journals (Sweden)

    Daniel Meier

    Full Text Available The Fanconi anemia (FA gene family is a recent addition to the complex network of proteins that respond to and repair certain types of DNA damage in the human genome. Since little is known about the regulation of this novel group of genes at the DNA level, we characterized the promoters of the eight genes (FANCA, B, C, E, F, G, L and M that compose the FA core complex. The promoters of these genes show the characteristic attributes of housekeeping genes, such as a high GC content and CpG islands, a lack of TATA boxes and a low conservation. The promoters functioned in a monodirectional way and were, in their most active regions, comparable in strength to the SV40 promoter in our reporter plasmids. They were also marked by a distinctive transcriptional start site (TSS. In the 5' region of each promoter, we identified a region that was able to negatively regulate the promoter activity in HeLa and HEK 293 cells in isolation. The central and 3' regions of the promoter sequences harbor binding sites for several common and rare transcription factors, including STAT, SMAD, E2F, AP1 and YY1, which indicates that there may be cross-connections to several established regulatory pathways. Electrophoretic mobility shift assays and siRNA experiments confirmed the shared regulatory responses between the prominent members of the TGF-β and JAK/STAT pathways and members of the FA core complex. Although the promoters are not well conserved, they share region and sequence specific regulatory motifs and transcription factor binding sites (TBFs, and we identified a bi-partite nature to these promoters. These results support a hypothesis based on the co-evolution of the FA core complex genes that was expanded to include their promoters.

  12. Identification and characterization of the genes encoding the core histones and histone variants of Neurospora crassa.

    OpenAIRE

    Hays, Shan M; Swanson, Johanna; Eric U Selker

    2002-01-01

    We have identified and characterized the complete complement of genes encoding the core histones of Neurospora crassa. In addition to the previously identified pair of genes that encode histones H3 and H4 (hH3 and hH4-1), we identified a second histone H4 gene (hH4-2), a divergently transcribed pair of genes that encode H2A and H2B (hH2A and hH2B), a homolog of the F/Z family of H2A variants (hH2Az), a homolog of the H3 variant CSE4 from Saccharomyces cerevisiae (hH3v), and a highly diverged ...

  13. Hepatitis B viral core protein disrupts human host gene expression by binding to promoter regions

    Directory of Open Access Journals (Sweden)

    Guo Yanhai

    2012-10-01

    Full Text Available Abstract Background The core protein (HBc of hepatitis B virus (HBV has been implicated in the malignant transformation of chronically-infected hepatocytes and displays pleiotropic functions, including RNA- and DNA-binding activities. However, the mechanism by which HBc interacts with the human genome to exert effects on hepatocyte function remains unknown. This study investigated the distribution of HBc binding to promoters in the human genome and evaluated its effects on the related genes’ expression. Results Whole-genome chromatin immunoprecipitation microarray (ChIP-on-chip analysis was used to identify HBc-bound human gene promoters. Gene Ontology and pathway analyses were performed on related genes. The quantitative polymerase chain reaction assay was used to verify ChIP-on-chip results. Five novel genes were selected for luciferase reporter assay evaluation to assess the influence of HBc promoter binding. The HBc antibody immunoprecipitated approximately 3100 human gene promoters. Among these, 1993 are associated with known biological processes, and 2208 regulate genes with defined molecular functions. In total, 1286 of the related genes mediate primary metabolic processes, and 1398 encode proteins with binding activity. Sixty-four of the promoters regulate genes related to the mitogen-activated protein kinase (MAPK pathways, and 41 regulate Wnt/beta-catenin pathway genes. The reporter gene assay indicated that HBc binding up-regulates proto-oncogene tyrosine-protein kinase (SRC, type 1 insulin-like growth factor receptor (IGF1R, and neurotrophic tyrosine kinase receptor 2 (NTRK2, and down-regulates v-Ha-ras Harvey rat sarcoma viral oncogene (HRAS. Conclusion HBc has the ability to bind a large number of human gene promoters, and can disrupt normal host gene expression. Manipulation of the transcriptional profile in HBV-infected hepatocytes may represent a key pathogenic mechanism of HBV infection.

  14. A core filamentation response network in Candida albicans is restricted to eight genes.

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    Ronny Martin

    Full Text Available Although morphological plasticity is a central virulence trait of Candida albicans, the number of filament-associated genes and the interplay of mechanisms regulating their expression remain unknown. By correlation-based network modeling of the transcriptional response to different defined external stimuli for morphogenesis we identified a set of eight genes with highly correlated expression patterns, forming a core filamentation response. This group of genes included ALS3, ECE1, HGT2, HWP1, IHD1 and RBT1 which are known or supposed to encode for cell- wall associated proteins as well as the Rac1 guanine nucleotide exchange factor encoding gene DCK1 and the unknown function open reading frame orf19.2457. The validity of network modeling was confirmed using a dataset of advanced complexity that describes the transcriptional response of C. albicans during epithelial invasion as well as comparing our results with other previously published transcriptome studies. Although the set of core filamentation response genes was quite small, several transcriptional regulators are involved in the control of their expression, depending on the environmental condition.

  15. Testing the infinitely many genes model for the evolution of the bacterial core genome and pangenome.

    Science.gov (United States)

    Collins, R Eric; Higgs, Paul G

    2012-11-01

    When groups of related bacterial genomes are compared, the number of core genes found in all genomes is usually much less than the mean genome size, whereas the size of the pangenome (the set of genes found on at least one of the genomes) is much larger than the mean size of one genome. We analyze 172 complete genomes of Bacilli and compare the properties of the pangenomes and core genomes of monophyletic subsets taken from this group. We then assess the capabilities of several evolutionary models to predict these properties. The infinitely many genes (IMG) model is based on the assumption that each new gene can arise only once. The predictions of the model depend on the shape of the evolutionary tree that underlies the divergence of the genomes. We calculate results for coalescent trees, star trees, and arbitrary phylogenetic trees of predefined fixed branch length. On a star tree, the pangenome size increases linearly with the number of genomes, as has been suggested in some previous studies, whereas on a coalescent tree, it increases logarithmically. The coalescent tree gives a better fit to the data, for all the examples we consider. In some cases, a fixed phylogenetic tree proved better than the coalescent tree at reproducing structure in the gene frequency spectrum, but little improvement was gained in predictions of the core and pangenome sizes. Most of the data are well explained by a model with three classes of gene: an essential class that is found in all genomes, a slow class whose rate of origination and deletion is slow compared with the time of divergence of the genomes, and a fast class showing rapid origination and deletion. Although the majority of genes originating in a genome are in the fast class, these genes are not retained for long periods, and the majority of genes present in a genome are in the slow or essential classes. In general, we show that the IMG model is useful for comparison with experimental genome data both for species level and

  16. Plant Core Environmental Stress Response Genes Are Systemically Coordinated during Abiotic Stresses

    Science.gov (United States)

    Hahn, Achim; Kilian, Joachim; Mohrholz, Anne; Ladwig, Friederike; Peschke, Florian; Dautel, Rebecca; Harter, Klaus; Berendzen, Kenneth W.; Wanke, Dierk

    2013-01-01

    Studying plant stress responses is an important issue in a world threatened by global warming. Unfortunately, comparative analyses are hampered by varying experimental setups. In contrast, the AtGenExpress abiotic stress experiment displays intercomparability. Importantly, six of the nine stresses (wounding, genotoxic, oxidative, UV-B light, osmotic and salt) can be examined for their capacity to generate systemic signals between the shoot and root, which might be essential to regain homeostasis in Arabidopsis thaliana. We classified the systemic responses into two groups: genes that are regulated in the non-treated tissue only are defined as type I responsive and, accordingly, genes that react in both tissues are termed type II responsive. Analysis of type I and II systemic responses suggest distinct functionalities, but also significant overlap between different stresses. Comparison with salicylic acid (SA) and methyl-jasmonate (MeJA) responsive genes implies that MeJA is involved in the systemic stress response. Certain genes are predominantly responding in only one of the categories, e.g., WRKY genes respond mainly non-systemically. Instead, genes of the plant core environmental stress response (PCESR), e.g., ZAT10, ZAT12, ERD9 or MES9, are part of different response types. Moreover, several PCESR genes switch between the categories in a stress-specific manner. PMID:23567274

  17. Plant Core Environmental Stress Response Genes Are Systemically Coordinated during Abiotic Stresses

    Directory of Open Access Journals (Sweden)

    Kenneth W. Berendzen

    2013-04-01

    Full Text Available Studying plant stress responses is an important issue in a world threatened by global warming. Unfortunately, comparative analyses are hampered by varying experimental setups. In contrast, the AtGenExpress abiotic stress experiment displays intercomparability. Importantly, six of the nine stresses (wounding, genotoxic, oxidative, UV-B light, osmotic and salt can be examined for their capacity to generate systemic signals between the shoot and root, which might be essential to regain homeostasis in Arabidopsis thaliana. We classified the systemic responses into two groups: genes that are regulated in the non-treated tissue only are defined as type I responsive and, accordingly, genes that react in both tissues are termed type II responsive. Analysis of type I and II systemic responses suggest distinct functionalities, but also significant overlap between different stresses. Comparison with salicylic acid (SA and methyl-jasmonate (MeJA responsive genes implies that MeJA is involved in the systemic stress response. Certain genes are predominantly responding in only one of the categories, e.g., WRKY genes respond mainly non-systemically. Instead, genes of the plant core environmental stress response (PCESR, e.g., ZAT10, ZAT12, ERD9 or MES9, are part of different response types. Moreover, several PCESR genes switch between the categories in a stress-specific manner.

  18. The core clock gene Per1 phases molecular and electrical circadian rhythms in SCN neurons

    Directory of Open Access Journals (Sweden)

    Jeff R. Jones

    2016-08-01

    Full Text Available The brain’s biological clock, the suprachiasmatic nucleus (SCN, exhibits endogenous 24-hour rhythms in gene expression and spontaneous firing rate; however, the functional relationship between these neuronal rhythms is not fully understood. Here, we used a Per1::GFP transgenic mouse line that allows for the simultaneous quantification of molecular clock state and firing rate in SCN neurons to examine the relationship between these key components of the circadian clock. We find that there is a stable, phased relationship between E-box-driven clock gene expression and spontaneous firing rate in SCN neurons and that these relationships are independent of light input onto the system or of GABAA receptor-mediated synaptic activity. Importantly, the concordant phasing of gene and neural rhythms is disrupted in the absence of the homologous clock gene Per1, but persists in the absence of the core clock gene Per2. These results suggest that Per1 plays a unique, non-redundant role in phasing gene expression and firing rate rhythms in SCN neurons to increase the robustness of cellular timekeeping.

  19. The core clock gene Per1 phases molecular and electrical circadian rhythms in SCN neurons.

    Science.gov (United States)

    Jones, Jeff R; McMahon, Douglas G

    2016-01-01

    The brain's biological clock, the suprachiasmatic nucleus (SCN), exhibits endogenous 24-hour rhythms in gene expression and spontaneous firing rate; however, the functional relationship between these neuronal rhythms is not fully understood. Here, we used a Per1::GFP transgenic mouse line that allows for the simultaneous quantification of molecular clock state and firing rate in SCN neurons to examine the relationship between these key components of the circadian clock. We find that there is a stable, phased relationship between E-box-driven clock gene expression and spontaneous firing rate in SCN neurons and that these relationships are independent of light input onto the system or of GABAA receptor-mediated synaptic activity. Importantly, the concordant phasing of gene and neural rhythms is disrupted in the absence of the homologous clock gene Per1, but persists in the absence of the core clock gene Per2. These results suggest that Per1 plays a unique, non-redundant role in phasing gene expression and firing rate rhythms in SCN neurons to increase the robustness of cellular timekeeping.

  20. Core Gene Set As the Basis of Multilocus Sequence Analysis of the Subclass Actinobacteridae

    Science.gov (United States)

    Adékambi, Toïdi; Butler, Ray W.; Hanrahan, Finnian; Delcher, Arthur L.; Drancourt, Michel; Shinnick, Thomas M.

    2011-01-01

    Comparative genomic sequencing is shedding new light on bacterial identification, taxonomy and phylogeny. An in silico assessment of a core gene set necessary for cellular functioning was made to determine a consensus set of genes that would be useful for the identification, taxonomy and phylogeny of the species belonging to the subclass Actinobacteridae which contained two orders Actinomycetales and Bifidobacteriales. The subclass Actinobacteridae comprised about 85% of the actinobacteria families. The following recommended criteria were used to establish a comprehensive gene set; the gene should (i) be long enough to contain phylogenetically useful information, (ii) not be subject to horizontal gene transfer, (iii) be a single copy (iv) have at least two regions sufficiently conserved that allow the design of amplification and sequencing primers and (v) predict whole-genome relationships. We applied these constraints to 50 different Actinobacteridae genomes and made 1,224 pairwise comparisons of the genome conserved regions and gene fragments obtained by using Sequence VARiability Analysis Program (SVARAP), which allow designing the primers. Following a comparative statistical modeling phase, 3 gene fragments were selected, ychF, rpoB, and secY with R2>0.85. Selected sets of broad range primers were tested from the 3 gene fragments and were demonstrated to be useful for amplification and sequencing of 25 species belonging to 9 genera of Actinobacteridae. The intraspecies similarities were 96.3–100% for ychF, 97.8–100% for rpoB and 96.9–100% for secY among 73 strains belonging to 15 species of the subclass Actinobacteridae compare to 99.4–100% for 16S rRNA. The phylogenetic topology obtained from the combined datasets ychF+rpoB+secY was globally similar to that inferred from the 16S rRNA but with higher confidence. It was concluded that multi-locus sequence analysis using core gene set might represent the first consensus and valid approach for

  1. Analysis of the chondroitin sulfate proteoglycan core protein (CSPGCP) gene in achondroplasia and pseudoachondroplasia.

    Science.gov (United States)

    Finkelstein, J E; Doege, K; Yamada, Y; Pyeritz, R E; Graham, J M; Moeschler, J B; Pauli, R M; Hecht, J T; Francomano, C A

    1991-01-01

    Achondroplasia and pseudoachondroplasia are autosomal dominant skeletal dysplasias resulting in short-limbed dwarfism. Histologic and ultrastructural studies of the cartilage in pseudoachondroplasia and in homozygous achondroplasia have suggested a structural abnormality in chondroitin sulfate proteoglycan (CSPG), a major structural protein in the extra-cellular matrix. The gene encoding CSPG core protein (CSPGCP) is thus a logical "candidate gene" for analysis in these conditions. cDNA probes encoding CSPGCP were used to identify restriction fragment length polymorphisms (RFLPs) in DNA from a panel of control individuals. No gross alterations at the CSPGCP locus were noted in DNA from 37 individuals with achondroplasia and 5 individuals with pseudoachondroplasia. In addition, allelic frequencies of the RFLPs were not significantly different among controls and patients with either condition. In one three-generation family with achondroplasia, close linkage of the CSPGCP locus and the skeletal dysplasia was excluded using a Bgl II polymorphism. Similarly, in a three-generation family with pseudoachondroplasia, the CSPGCP gene was not tightly linked to the disease phenotype. These results indicate that mutations at the chondroitin sulfate proteoglycan core protein locus do not cause achondroplasia or pseudoachondroplasia in these families. Images Figure 1 Figure 2 Figure 3 Figure 4 PMID:1670752

  2. Phylogenetic analysis of the core histone doublet and DNA topo II genes of Marseilleviridae: evidence of proto-eukaryotic provenance.

    Science.gov (United States)

    Erives, Albert J

    2017-11-28

    While the genomes of eukaryotes and Archaea both encode the histone-fold domain, only eukaryotes encode the core histone paralogs H2A, H2B, H3, and H4. With DNA, these core histones assemble into the nucleosomal octamer underlying eukaryotic chromatin. Importantly, core histones for H2A and H3 are maintained as neofunctionalized paralogs adapted for general bulk chromatin (canonical H2 and H3) or specialized chromatin (H2A.Z enriched at gene promoters and cenH3s enriched at centromeres). In this context, the identification of core histone-like "doublets" in the cytoplasmic replication factories of the Marseilleviridae (MV) is a novel finding with possible relevance to understanding the origin of eukaryotic chromatin. Here, we analyze and compare the core histone doublet genes from all known MV genomes as well as other MV genes relevant to the origin of the eukaryotic replisome. Using different phylogenetic approaches, we show that MV histone domains encode obligate H2B-H2A and H4-H3 dimers of possible proto-eukaryotic origin. MV core histone moieties form sister clades to each of the four eukaryotic clades of canonical and variant core histones. This suggests that MV core histone moieties diverged prior to eukaryotic neofunctionalizations associated with paired linear chromosomes and variant histone octamer assembly. We also show that MV genomes encode a proto-eukaryotic DNA topoisomerase II enzyme that forms a sister clade to eukaryotes. This is a relevant finding given that DNA topo II influences histone deposition and chromatin compaction and is the second most abundant nuclear protein after histones. The combined domain architecture and phylogenomic analyses presented here suggest that a primitive origin for MV histone genes is a more parsimonious explanation than horizontal gene transfers + gene fusions + sufficient divergence to eliminate relatedness to eukaryotic neofunctionalizations within the H2A and H3 clades without loss of relatedness to each of

  3. Extensive horizontal transfer of core genome genes between two Lactobacillus species found in the gastrointestinal tract

    Directory of Open Access Journals (Sweden)

    Maguin Emmanuelle

    2007-08-01

    Full Text Available Abstract Background While genes that are conserved between related bacterial species are usually thought to have evolved along with the species, phylogenetic trees reconstructed for individual genes may contradict this picture and indicate horizontal gene transfer. Individual trees are often not resolved with high confidence, however, and in that case alternative trees are generally not considered as contradicting the species tree, although not confirming it either. Here we conduct an in-depth analysis of 401 protein phylogenetic trees inferred with varying levels of confidence for three lactobacilli from the acidophilus complex. At present the relationship between these bacteria, isolated from environments as diverse as the gastrointestinal tract (Lactobacillus acidophilus and Lactobacillus johnsonii and yogurt (Lactobacillus delbrueckii ssp. bulgaricus, is ambiguous due to contradictory phenotypical and 16S rRNA based classifications. Results Among the 401 phylogenetic trees, those that could be reconstructed with high confidence support the 16S-rRNA tree or one alternative topology in an astonishing 3:2 ratio, while the third possible topology is practically absent. Lowering the confidence threshold for trees to be taken into consideration does not significantly affect this ratio, and therefore suggests that gene transfer may have affected as much as 40% of the core genome genes. Gene function bias suggests that the 16S rRNA phylogeny of the acidophilus complex, which indicates that L. acidophilus and L. delbrueckii ssp. bulgaricus are the closest related of these three species, is correct. A novel approach of comparison of interspecies protein divergence data employed in this study allowed to determine that gene transfer most likely took place between the lineages of the two species found in the gastrointestinal tract. Conclusion This case-study reports an unprecedented level of phylogenetic incongruence, presumably resulting from extensive

  4. Quantitative detection of antibiotic resistance genes using magnetic/luminescent core-shell nanoparticles

    Science.gov (United States)

    Son, Ahjeong; Hristova, Krassimira R.; Dosev, Dosi; Kennedy, Ian M.

    2008-02-01

    Nanoscale magnetic/luminescent core-shell particles were used for DNA quantification in a hybridization-in-solution format. We demonstrated a simple, high-throughput, and non-PCR based DNA assay for quantifying antibiotic resistance gene tetQ. Fe 3O 4/Eu:Gd IIO 3 nanoparticles (NPs) synthesized by spray pyrolysis were biofunctionalized by passive adsorption of NeutrAvidin. Following immobilization of biotinylated probe DNA on the particles' surfaces, target dsDNA and signaling probe DNA labeled with Cy3 were hybridized with NPs-probe DNA. Hybridized DNA complexes were separated from solution by a magnet, while non-hybridized DNA remained in solution. A linear quantification (R2 = 0.99) of a target tetQ gene was achieved based on the normalized fluorescence (Cy3/NPs) of DNANP hybrids. A real-time qPCR assay was used for evaluation of the NPs assay sensitivity and range of quantification. The quantity of antibiotic resistance tetQ genes in activated sludge microcosms, with and without addition of tetracycline or triclosan has been determined, indicating the potential of the optimized assay for monitoring the level of antibiotic resistance in environmental samples. In addition, the tetQ gene copy numbers in microcosms determined by NPhybridization were well correlated with the numbers measured by real-time qPCR assay (R2 = 0.92).

  5. Role of HCV Core gene of genotype 1a and 3a and host gene Cox-2 in HCV-induced pathogenesis

    Directory of Open Access Journals (Sweden)

    Ahmad Waqar

    2011-04-01

    Full Text Available Abstract Background Hepatitis C virus (HCV Core protein is thought to trigger activation of multiple signaling pathways and play a significant role in the alteration of cellular gene expression responsible for HCV pathogenesis leading to hepatocellular carcinoma (HCC. However, the exact molecular mechanism of HCV genome specific pathogenesis remains unclear. We examined the in vitro effects of HCV Core protein of HCV genotype 3a and 1a on the cellular genes involved in oxidative stress and angiogenesis. We also studied the ability of HCV Core and Cox-2 siRNA either alone or in combination to inhibit viral replication and cell proliferation in HCV serum infected Huh-7 cells. Results Over expression of Core gene of HCV 3a genotype showed stronger effect in regulating RNA and protein levels of Cox-2, iNOS, VEGF, p-Akt as compared to HCV-1a Core in hepatocellular carcinoma cell line Huh-7 accompanied by enhanced PGE2 release and cell proliferation. We also observed higher expression levels of above genes in HCV 3a patient's blood and biopsy samples. Interestingly, the Core and Cox-2-specific siRNAs down regulated the Core 3a-enhanced expression of Cox-2, iNOS, VEGF, p-Akt. Furthermore, the combined siRNA treatment also showed a dramatic reduction in viral titer and expression of these genes in HCV serum-infected Huh-7 cells. Taken together, these results demonstrated a differential response by HCV 3a genotype in HCV-induced pathogenesis, which may be due to Core and host factor Cox-2 individually or in combination. Conclusions Collectively, these studies not only suggest a genotype-specific interaction between key players of HCV pathogenesis but also may represent combined viral and host gene silencing as a potential therapeutic strategy.

  6. Genome-Wide Temporal Expression Profiling in Caenorhabditis elegans Identifies a Core Gene Set Related to Long-Term Memory.

    Science.gov (United States)

    Freytag, Virginie; Probst, Sabine; Hadziselimovic, Nils; Boglari, Csaba; Hauser, Yannick; Peter, Fabian; Gabor Fenyves, Bank; Milnik, Annette; Demougin, Philippe; Vukojevic, Vanja; de Quervain, Dominique J-F; Papassotiropoulos, Andreas; Stetak, Attila

    2017-07-12

    The identification of genes related to encoding, storage, and retrieval of memories is a major interest in neuroscience. In the current study, we analyzed the temporal gene expression changes in a neuronal mRNA pool during an olfactory long-term associative memory (LTAM) in Caenorhabditis elegans hermaphrodites. Here, we identified a core set of 712 (538 upregulated and 174 downregulated) genes that follows three distinct temporal peaks demonstrating multiple gene regulation waves in LTAM. Compared with the previously published positive LTAM gene set (Lakhina et al., 2015), 50% of the identified upregulated genes here overlap with the previous dataset, possibly representing stimulus-independent memory-related genes. On the other hand, the remaining genes were not previously identified in positive associative memory and may specifically regulate aversive LTAM. Our results suggest a multistep gene activation process during the formation and retrieval of long-term memory and define general memory-implicated genes as well as conditioning-type-dependent gene sets.SIGNIFICANCE STATEMENT The identification of genes regulating different steps of memory is of major interest in neuroscience. Identification of common memory genes across different learning paradigms and the temporal activation of the genes are poorly studied. Here, we investigated the temporal aspects of Caenorhabditis elegans gene expression changes using aversive olfactory associative long-term memory (LTAM) and identified three major gene activation waves. Like in previous studies, aversive LTAM is also CREB dependent, and CREB activity is necessary immediately after training. Finally, we define a list of memory paradigm-independent core gene sets as well as conditioning-dependent genes. Copyright © 2017 the authors 0270-6474/17/376661-12$15.00/0.

  7. Architecture and Distribution of Introns in Core Genes of Four Fusarium Species

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    Mmatshepho M. Phasha

    2017-11-01

    Full Text Available Removal of introns from transcribed RNA represents a crucial step during the production of mRNA in eukaryotes. Available whole-genome sequences and expressed sequence tags (ESTs have increased our knowledge of this process and revealed various commonalities among eukaryotes. However, certain aspects of intron structure and diversity are taxon-specific, which can complicate the accuracy of in silico gene prediction methods. Using core genes, we evaluated the distribution and architecture of Fusarium circinatum spliceosomal introns, and linked these characteristics to the accuracy of the predicted gene models of the genome of this fungus. We also evaluated intron distribution and architecture in F. verticillioides, F. oxysporum, and F. graminearum, and made comparisons with F. circinatum. Results indicated that F. circinatum and the three other Fusarium species have canonical 5′ and 3′ splice sites, but with subtle differences that are apparently not shared with those of other fungal genera. The polypyrimidine tract of Fusarium introns was also found to be highly divergent among species and genes. Furthermore, the conserved adenosine nucleoside required during the first step of splicing is contained within unique branch site motifs in certain Fusarium introns. Data generated here show that introns of F. circinatum, as well as F. verticillioides, F. oxysporum, and F. graminearum, are characterized by a number of unique features such as the CTHAH and ACCAT motifs of the branch site. Incorporation of such information into genome annotation software will undoubtedly improve the accuracy of gene prediction methods used for Fusarium species and related fungi.

  8. Refactoring the six-gene photosystem II core in the chloroplast of the green algae Chlamydomonas reinhardtii

    DEFF Research Database (Denmark)

    Gimpel, Javier A.; Nour-Eldin, Hussam Hassan; Scranton, Melissa A.

    2016-01-01

    production, particularly under specific environmental conditions. PSII is a complex multisubunit enzyme with strong interdependence among its components. In this work, we have deleted the six core genes of PSII in the eukaryotic alga Chlamydomonas reinhardtii and refactored them in a single DNA construct....... Complementation of the knockout strain with the core PSII synthetic module from three different green algae resulted in reconstitution of photosynthetic activity to 85, 55, and 53% of that of the wild-type, demonstrating that the PSII core can be exchanged between algae species and retain function. The strains...

  9. Sequence analysis of the core gene of 14 hepatitis C virus genotypes.

    Science.gov (United States)

    Bukh, J; Purcell, R H; Miller, R H

    1994-01-01

    We previously sequenced the 5' noncoding region of 44 isolates of hepatitis C virus (HCV), as well as the envelope 1 (E1) gene of 51 HCV isolates, and provided evidence for the existence of at least 6 major genetic groups consisting of at least 12 minor genotypes of HCV (i.e., genotypes I/1a, II/1b, III/2a, IV/2b, 2c, V/3a, 4a-4d, 5a, and 6a). We now report the complete nucleotide sequence of the putative core (C) gene of 52 HCV isolates that represent all of these 12 genotypes as well as two additional genotypes provisionally designated 4e and 4f that we identified in this study. The phylogenetic analysis of the C gene sequences was in agreement with that of the E1 gene sequences. A major division in the genetic distance was observed between HCV isolates of genotype 2 and those of the other genotypes in analysis of both the E1 and C genes. The C gene sequences of 9 genotypes have not been reported previously (i.e., genotypes 2c, 4a-4f, 5a, and 6a). Our analysis indicates that the C gene-based methods currently used to determine the HCV genotype, such as PCR with genotype-specific primers, should be revised in light of these data. We found that the predicted C gene was exactly 573 nt long in all 52 HCV isolates, with an N-terminal start codon and no in-frame stop codons. The nucleotide and predicted amino acid identities of the C gene sequences were in the range of 79.4-99.0% and 85.3-100%, respectively. Furthermore, we mapped universally conserved, as well as genotype-specific, nucleotide and deduced amino acid sequences of the C gene. The predicted C proteins of the different HCV genotypes shared the following features: (i) high content of proline residues, (ii) high content of arginine and lysine residues located primarily in three domains with 10 such residues invariant at positions 39-62, (iii) a cluster of 5 conserved tryptophan residues, (iv) two nuclear localization signals and a DNA-binding motif, (v) a potential phosphorylation site with a serine

  10. Cationic niosomes an effective gene carrier composed of novel spermine-derivative cationic lipids: effect of central core structures.

    Science.gov (United States)

    Opanasopit, Praneet; Leksantikul, Lalita; Niyomtham, Nattisa; Rojanarata, Theerasak; Ngawhirunpat, Tanasait; Yingyongnarongkul, Boon-Ek

    2017-05-01

    Cationic niosomes formulated from Span 20, cholesterol (Chol) and novel spermine-based cationic lipids of multiple central core structures (di(oxyethyl)amino, di(oxyethyl)amino carboxy, 3-amino-1,2-dioxypropyl and 2-amino-1,3-dioxypropyl) were successfully prepared for improving transfection efficiency in vitro. The niosomes composed of spermine cationic lipid with central core structure of di(oxyethyl)amino revealed the highest gene transfection efficiency. To investigate the factors affecting gene transfection and cell viability including differences in the central core structures of cationic lipids, the composition of vesicles, molar ratio of cationic lipids in formulations and the weight ratio of niosomes to DNA. Cationic niosomes composed of nonionic surfactants (Span20), cholesterol and spermine-based cationic lipids of multiple central core structures were formulated. Gene transfection and cell viability were evaluated on a human cervical carcinoma cell line (HeLa cells) using pDNA encoding green fluorescent protein (pEGFP-C2). The morphology, size and charge were also characterized. High transfection efficiency was obtained from cationic niosomes composed of Span20:Chol:cationic lipid at the molar ratio of 2.5:2.5:0.5 mM. Cationic lipids with di(oxyethyl)amino as a central core structure exhibited highest transfection efficiency. In addition, there was also no serum effect on transfection efficiency. These novel cationic niosomes may constitute a good alternative carrier for gene transfection.

  11. Pangenome evidence for extensive interdomain horizontal transfer affecting lineage core and shell genes in uncultured planktonic thaumarchaeota and euryarchaeota.

    Science.gov (United States)

    Deschamps, Philippe; Zivanovic, Yvan; Moreira, David; Rodriguez-Valera, Francisco; López-García, Purificación

    2014-06-12

    Horizontal gene transfer (HGT) is an important force in evolution, which may lead, among other things, to the adaptation to new environments by the import of new metabolic functions. Recent studies based on phylogenetic analyses of a few genome fragments containing archaeal 16S rRNA genes and fosmid-end sequences from deep-sea metagenomic libraries have suggested that marine planktonic archaea could be affected by high HGT frequency. Likewise, a composite genome of an uncultured marine euryarchaeote showed high levels of gene sequence similarity to bacterial genes. In this work, we ask whether HGT is frequent and widespread in genomes of these marine archaea, and whether HGT is an ancient and/or recurrent phenomenon. To answer these questions, we sequenced 997 fosmid archaeal clones from metagenomic libraries of deep-Mediterranean waters (1,000 and 3,000 m depth) and built comprehensive pangenomes for planktonic Thaumarchaeota (Group I archaea) and Euryarchaeota belonging to the uncultured Groups II and III Euryarchaeota (GII/III-Euryarchaeota). Comparison with available reference genomes of Thaumarchaeota and a composite marine surface euryarchaeote genome allowed us to define sets of core, lineage-specific core, and shell gene ortholog clusters for the two archaeal lineages. Molecular phylogenetic analyses of all gene clusters showed that 23.9% of marine Thaumarchaeota genes and 29.7% of GII/III-Euryarchaeota genes had been horizontally acquired from bacteria. HGT is not only extensive and directional but also ongoing, with high HGT levels in lineage-specific core (ancient transfers) and shell (recent transfers) genes. Many of the acquired genes are related to metabolism and membrane biogenesis, suggesting an adaptive value for life in cold, oligotrophic oceans. We hypothesize that the acquisition of an important amount of foreign genes by the ancestors of these archaeal groups significantly contributed to their divergence and ecological success. © The Author

  12. Infection-associated nuclear degeneration in the rice blast fungus Magnaporthe oryzae requires non-selective macro-autophagy.

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    Min He

    Full Text Available The rice blast fungus Magnaporthe oryzae elaborates a specialized infection structure called an appressorium to breach the rice leaf surface and gain access to plant tissue. Appressorium development is controlled by cell cycle progression, and a single round of nuclear division occurs prior to appressorium formation. Mitosis is always followed by programmed cell death of the spore from which the appressorium develops. Nuclear degeneration in the spore is known to be essential for plant infection, but the precise mechanism by which it occurs is not known.In yeast, nuclear breakdown requires a specific form of autophagy, known as piecemeal microautophagy of the nucleus (PMN, and we therefore investigated whether this process occurs in the rice blast fungus. Here, we report that M. oryzae possesses two conserved components of a putative PMN pathway, MoVac8 and MoTsc13, but that both are dispensable for nuclear breakdown during plant infection. MoVAC8 encodes a vacuolar membrane protein and MoTSC13 a peri-nuclear and peripheral ER protein.We show that MoVAC8 is necessary for caffeine resistance, but dispensable for pathogenicity of M. oryzae, while MoTSC13 is involved in cell wall stress responses and is an important virulence determinant. By functional analysis of ΔMoatg1 and ΔMoatg4 mutants, we demonstrate that infection-associated nuclear degeneration in M. oryzae instead occurs by non-selective macroautophagy, which is necessary for rice blast disease.

  13. In vitro gene delivery using polyamidoamine dendrimers with a trimesyl core.

    Science.gov (United States)

    Zhang, Xue-Qing; Wang, Xu-Li; Huang, Shi-Wen; Zhuo, Ren-Xi; Liu, Zhi-Lan; Mao, Hai-Quan; Leong, Kam W

    2005-01-01

    Polyamidoamine (PAMAM) dendrimer represents one of the most efficient polymeric gene carriers. To investigate the effect of the core structure and generation of dendrimers on the complex formation and transfection efficiency, a series of PAMAM dendrimers with a trimesyl core (DT) at different generations (DT4 to DT8) were developed as gene carriers and compared with the PAMAM dendrimers derived from pentaerythritol (DP) and inositol (DI). The minimal generation number of DTs at which the dendrimer has enough amino group density to effectively condense DNA was higher (generation 6) than those of DPs and DIs (generation 5). DTs of generation 6 or higher condensed DNA into complexes with an average diameter ranging from 100 to 300 nm, but the 4th and 5th generations of DT (DT4 and DT5) formed only a severe aggregate with DNA. Interestingly, the DT6/pDNA complex was determined to be much smaller (100-300 nm) than those prepared with DP5 or DI5 (>600 nm) at N/P ratios higher than 15. The optimal generation numbers at which the dendrimers showed the highest transgene expression in COS-7 cells were 5 for DPs and DIs but 6 for DTs. The DT6/pDNAcomplex with smaller size mediated higher transgene expression in COS-7 cells than those prepared with DP5 or DI5. The in vitro transfection efficiency of the DT dendrimers as evaluated in HeLa cells, COS-7 cells, and primary hepatocytes decreased in the order of DT6 > DT7 > DT8 > DT5 > DT4. The transfection mediated by DT6 was significantly inhibited by bafilomycin A1. The acid-base titration curve for DT6 showed high buffer capacity in the pH range from 5.5 to 6.4 (pK(a) approximately 6). This permits dendrimers to buffer the pH change in the endosomal compartment. However, the transfection efficiency mediated by DT6 decreased significantly in the presence of serum in both HeLa cells and COS-7 cells. The cytotoxicity of DTs evaluated in HeLa cells using the 3-{4,5-dimethylthiazol-2-yl}-2,5-diphenyltetrazolium bromide assay showed a

  14. Functional Identification of Proteus mirabilis eptC Gene Encoding a Core Lipopolysaccharide Phosphoethanolamine Transferase

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    Eleonora Aquilini

    2014-04-01

    Full Text Available By comparison of the Proteus mirabilis HI4320 genome with known lipopolysaccharide (LPS phosphoethanolamine transferases, three putative candidates (PMI3040, PMI3576, and PMI3104 were identified. One of them, eptC (PMI3104 was able to modify the LPS of two defined non-polar core LPS mutants of Klebsiella pneumoniae that we use as surrogate substrates. Mass spectrometry and nuclear magnetic resonance showed that eptC directs the incorporation of phosphoethanolamine to the O-6 of l-glycero-d-mano-heptose II. The eptC gene is found in all the P. mirabilis strains analyzed in this study. Putative eptC homologues were found for only two additional genera of the Enterobacteriaceae family, Photobacterium and Providencia. The data obtained in this work supports the role of the eptC (PMI3104 product in the transfer of PEtN to the O-6 of l,d-HepII in P. mirabilis strains.

  15. A sequence-specific core promoter-binding transcription factor recruits TRF2 to coordinately transcribe ribosomal protein genes.

    Science.gov (United States)

    Baumann, Douglas G; Gilmour, David S

    2017-10-13

    Ribosomal protein (RP) genes must be coordinately expressed for proper assembly of the ribosome yet the mechanisms that control expression of RP genes in metazoans are poorly understood. Recently, TATA-binding protein-related factor 2 (TRF2) rather than the TATA-binding protein (TBP) was found to function in transcription of RP genes in Drosophila. Unlike TBP, TRF2 lacks sequence-specific DNA binding activity, so the mechanism by which TRF2 is recruited to promoters is unclear. We show that the transcription factor M1BP, which associates with the core promoter region, activates transcription of RP genes. Moreover, M1BP directly interacts with TRF2 to recruit it to the RP gene promoter. High resolution ChIP-exo was used to analyze in vivo the association of M1BP, TRF2 and TFIID subunit, TAF1. Despite recent work suggesting that TFIID does not associate with RP genes in Drosophila, we find that TAF1 is present at RP gene promoters and that its interaction might also be directed by M1BP. Although M1BP associates with thousands of genes, its colocalization with TRF2 is largely restricted to RP genes, suggesting that this combination is key to coordinately regulating transcription of the majority of RP genes in Drosophila. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  16. Inhibition of core gene of HCV 3a genotype using synthetic and vector derived siRNAs.

    Science.gov (United States)

    Khaliq, Saba; Jahan, Shah; Ijaz, Bushra; Ahmad, Waqar; Asad, Sultan; Pervaiz, Asim; Samreen, Baila; Khan, Mahwish; Hassan, Sajida

    2010-11-13

    Hepatitis C virus (HCV) is a major causative agent of liver associated diseases throughout the world, with genotype 3a responsible for most of the cases in Pakistan. Due to the limited efficiency of current therapy, RNA interference (RNAi) a novel regulatory and powerful silencing approach for molecular therapeutics through a sequence-specific RNA degradation process represents an alternative option. The current study was purposed to assess and explore the possibility of RNAi to silence the HCV-3a Core gene expression, which play complex role in regulation of cell growth and host genes expression essential for infectivity and disease progression. To identify the potent siRNA target sites, 5 small interfering RNAs (siRNAs) against Core gene were designed and in vitro transcribed after consensus sequence analysis of different HCV-3a isolates. Antiviral effects of siRNAs showed upto 80% inhibition of Core gene expression by different siRNAs into Huh-7 cells as compared with Mock transfected and control siRNAs treated cells. For long lasting effect of siRNAs, vector based short hairpin siRNAs (shRNAs) were designed and tested against HCV-3a Core which resulted in a similar pattern of inhibition on RNA and protein expression of HCV Core as synthetic siRNAs. Furthermore, the efficacy of cell culture tested siRNA and shRNA, were evaluated for inhibition of HCV replication in HCV infected serum inoculated Huh-7 cells and a significant decrease in HCV viral copy number was observed. Our results support the possibility of using consensus siRNA and shRNA-based molecular therapy as a promising strategy in effective inhibition of HCV-3a genotype.

  17. Altered expression patterns of lipid metabolism genes in an animal model of HCV core-related, nonobese, modest hepatic steatosis

    Directory of Open Access Journals (Sweden)

    Chang Ming-Ling

    2008-02-01

    Full Text Available Abstract Background Because the gene expression patterns of nonobese hepatic steatosis in affected patients remain unclear, we sought to explore these patterns using an animal model of nonobese hepatic steatosis. Methods We developed mice that conditionally express the hepatitis C virus (HCV core protein regulated by the tetracycline transactivator (tTA. Microarray analyses and reverse-transcription polymerase chain reaction were performed using liver samples of both the double transgenic mice (DTM, which express both the HCV core and tTA, and single transgenic mice (STM, which express tTA alone, at 2 months of age. Functional categories of genes with altered expression were classified using gene ontology programs. Serum glucose, lipid levels, and systemic blood pressure were also measured. Results Approximately 20–30% of hepatocytes from the DTM were steatotic. No significant differences were observed in the serum glucose, lipid content, or blood pressure levels between the DTM and STM. Gene expression analyses revealed Sterol-regulatory element-binding protein (SREBP pathway activation and dysregulation of the following genes involved in lipid metabolism: 3-hydroxy-3-methylglutaryl-coenzyme A synthase 1, Apolipoprotein AII, Apolipoprotein CI, acyl-CoA thioesterase I, and fatty acid binding protein 1; in mitochondrial function: solute carrier family 25 member 25 and cytochrome c oxidase subunit II; in immune reaction: complement component 3, lymphocyte antigen 6 complex, locus A, lymphocyte antigen 6 complex, locus C, lymphocyte antigen 6 complex, locus D, and lymphocyte antigen 6 complex, locus E. Conclusion Some genes of lipid metabolism, mitochondrial function, and immune reaction and the SREBP pathway are involved in HCV core-related, nonobese, modest hepatic steatosis.

  18. High expression of PI3K core complex genes is associated with poor prognosis in chronic lymphocytic leukemia

    DEFF Research Database (Denmark)

    Kristensen, Louise; Kielsgaard Kristensen, Thomas; Abildgaard, Niels

    2015-01-01

    Chronic lymphocytic leukemia (CLL) is the most common leukemia among adults in the Western world. Autophagy is a highly conserved process in eukaryotic cells. In CLL autophagy is involved in mediating the effect of chemotherapy but the role of autophagy in CLL pathogenesis remains unknown....... In the present study, we used real-time RT-PCR to analyze expression of the PIK3C3, PIK3R4, and BECN1 genes. These genes encode the components of the PI3K core complex, which is central to initiation of autophagy. A consecutive series of 149 well-characterized CLL cases from Region of Southern Denmark were...... included in the study. All three genes were observed to be independent markers of prognosis in CLL with high expression being associated with more aggressive disease. With this clear association with outcome in CLL, these genes thereby represent promising candidates for future functional studies...

  19. Comparison of automated and manual FISH for evaluation of HER2 gene status on breast carcinoma core biopsies

    OpenAIRE

    ?hlschlegel, Christian; Kradolfer, Doris; Hell, Margreth; Jochum, Wolfram

    2013-01-01

    Background Positive HER2 status identifies breast carcinomas that might respond to trastuzumab treatment. Manual HER2 fluorescent in situ hybridisation (FISH) is the most readily used method to detect HER2 gene amplification which defines positive HER2 status in addition to HER2 protein overexpression. Automation of HER2 FISH may improve HER2 gene testing. The aim of our study was to evaluate an automated HER2 FISH assay for assessing the HER2 genomic status. Methods Core biopsies of 100 inva...

  20. Alterations in ROS activity and lysosomal pH account for distinct patterns of macroautophagy in LINCL and JNCL fibroblasts.

    Science.gov (United States)

    Vidal-Donet, José Manuel; Cárcel-Trullols, Jaime; Casanova, Bonaventura; Aguado, Carmen; Knecht, Erwin

    2013-01-01

    Neuronal ceroid lipofuscinoses (NCL) are lysosomal storage disorders characterized by the accumulation of lipofuscin within lysosomes. Late infantile (LINCL) and juvenile (JNCL) are their most common forms and are caused by loss-of-function mutations in tripeptidyl peptidase 1 (TPP1), a lysosomal endopeptidase, and CLN3 protein (CLN3p), whose location and function is still controversial. LINCL patients suffer more severely from NCL consequences than JNCL patients, in spite of having in common an abnormal accumulation of material with a similar composition in the lysosomes. To identify distinctive characteristics that could explain the differences in the severity of LINCL and JNCL pathologies, we compared the protein degradation mechanisms in patientś fibroblasts. Pulse-chase experiments show a significant decrease in protein degradation by macroautophagy in fibroblasts bearing TPP1 (CLN2) and CLN3p (CLN3) mutations. In CLN2 fibroblasts, LC3-II levels and other procedures indicate an impaired formation of autophagosomes, which confirms the pulse-chase experiments. This defect is linked to an accumulation of reactive oxygen species (ROS), an upregulation of the Akt-mTOR signalling pathway and increased activities of the p38α and ERK1/2 MAPKs. In CLN3 fibroblasts, LC3-II analysis indicates impairment in autophagosome maturation and there is also a defect in fluid phase endocytosis, two alterations that can be related to an observed increase of 0.5 units in lysosomal pH. CLN3 fibroblasts also accumulate ROS but to a lower extent than CLN2. TPP1 activity is completely abrogated in CLN2 and partially diminished in CLN3 fibroblasts. TPP1 cleaves small hydrophobic proteins like subunit c of mitochondrial ATP synthase and the lack or a lower activity of this enzyme can contribute to lipofuscin accumulation. These alterations in TPP1 activity lead to an increased ROS production, especially in CLN2 in which it is aggravated by a decrease in catalase activity. This could

  1. Alterations in ROS activity and lysosomal pH account for distinct patterns of macroautophagy in LINCL and JNCL fibroblasts.

    Directory of Open Access Journals (Sweden)

    José Manuel Vidal-Donet

    Full Text Available Neuronal ceroid lipofuscinoses (NCL are lysosomal storage disorders characterized by the accumulation of lipofuscin within lysosomes. Late infantile (LINCL and juvenile (JNCL are their most common forms and are caused by loss-of-function mutations in tripeptidyl peptidase 1 (TPP1, a lysosomal endopeptidase, and CLN3 protein (CLN3p, whose location and function is still controversial. LINCL patients suffer more severely from NCL consequences than JNCL patients, in spite of having in common an abnormal accumulation of material with a similar composition in the lysosomes. To identify distinctive characteristics that could explain the differences in the severity of LINCL and JNCL pathologies, we compared the protein degradation mechanisms in patientś fibroblasts. Pulse-chase experiments show a significant decrease in protein degradation by macroautophagy in fibroblasts bearing TPP1 (CLN2 and CLN3p (CLN3 mutations. In CLN2 fibroblasts, LC3-II levels and other procedures indicate an impaired formation of autophagosomes, which confirms the pulse-chase experiments. This defect is linked to an accumulation of reactive oxygen species (ROS, an upregulation of the Akt-mTOR signalling pathway and increased activities of the p38α and ERK1/2 MAPKs. In CLN3 fibroblasts, LC3-II analysis indicates impairment in autophagosome maturation and there is also a defect in fluid phase endocytosis, two alterations that can be related to an observed increase of 0.5 units in lysosomal pH. CLN3 fibroblasts also accumulate ROS but to a lower extent than CLN2. TPP1 activity is completely abrogated in CLN2 and partially diminished in CLN3 fibroblasts. TPP1 cleaves small hydrophobic proteins like subunit c of mitochondrial ATP synthase and the lack or a lower activity of this enzyme can contribute to lipofuscin accumulation. These alterations in TPP1 activity lead to an increased ROS production, especially in CLN2 in which it is aggravated by a decrease in catalase activity

  2. Macroautophagy Proteins Control MHC Class I Levels on Dendritic Cells and Shape Anti-viral CD8+ T Cell Responses

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    Monica Loi

    2016-05-01

    Full Text Available The macroautophagy machinery has been implicated in MHC class II restricted antigen presentation. Here, we report that this machinery assists in the internalization of MHC class I molecules. In the absence of the autophagy factors Atg5 and Atg7, MHC class I surface levels are elevated due to decreased endocytosis and degradation. Internalization of MHC class I molecules occurs less efficiently if AAK1 cannot be recruited via Atg8/LC3B. In the absence of Atg-dependent MHC class I internalization, dendritic cells stimulate CD8+ T cell responses more efficiently in vitro and in vivo. During viral infections, lack of Atg5 results in enhanced influenza- and LCMV-specific CD8+ T cell responses in vivo. Elevated influenza-specific CD8+ T cell responses are associated with better immune control of this infection. Thus, the macroautophagy machinery orchestrates T cell immunity by supporting MHC class II but compromises MHC class I restricted antigen presentation.

  3. Mouse Skeletal Muscle Fiber-Type-Specific Macroautophagy and Muscle Wasting Are Regulated by a Fyn/STAT3/Vps34 Signaling Pathway

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    Eijiro Yamada

    2012-05-01

    Full Text Available Skeletal muscle atrophy induced by aging (sarcopenia, inactivity, and prolonged fasting states (starvation is predominantly restricted to glycolytic type II muscle fibers and typical spares oxidative type I fibers. However, the mechanisms accounting for muscle fiber-type specificity of atrophy have remained enigmatic. In the current study, although the Fyn tyrosine kinase activated the mTORC1 signaling complex, it also induced marked atrophy of glycolytic fibers with relatively less effect on oxidative muscle fibers. This was due to inhibition of macroautophagy via an mTORC1-independent but STAT3-dependent reduction in Vps34 protein levels and decreased Vps34/p150/Beclin1/Atg14 complex 1. Physiologically, in the fed state endogenous Fyn kinase activity was increased in glycolytic but not oxidative skeletal muscle. In parallel, Y705-STAT3 phosphorylation increased with decreased Vps34 protein levels. Moreover, fed/starved regulation of Y705-STAT3 phosphorylation and Vps34 protein levels was prevented in skeletal muscle of Fyn null mice. These data demonstrate a Fyn/STAT3/Vps34 pathway that is responsible for fiber-type-specific regulation of macroautophagy and skeletal muscle atrophy.

  4. Ancient exaptation of a CORE-SINE retroposon into a highly conserved mammalian neuronal enhancer of the proopiomelanocortin gene.

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    Andrea M Santangelo

    2007-10-01

    Full Text Available The proopiomelanocortin gene (POMC is expressed in the pituitary gland and the ventral hypothalamus of all jawed vertebrates, producing several bioactive peptides that function as peripheral hormones or central neuropeptides, respectively. We have recently determined that mouse and human POMC expression in the hypothalamus is conferred by the action of two 5' distal and unrelated enhancers, nPE1 and nPE2. To investigate the evolutionary origin of the neuronal enhancer nPE2, we searched available vertebrate genome databases and determined that nPE2 is a highly conserved element in placentals, marsupials, and monotremes, whereas it is absent in nonmammalian vertebrates. Following an in silico paleogenomic strategy based on genome-wide searches for paralog sequences, we discovered that opossum and wallaby nPE2 sequences are highly similar to members of the superfamily of CORE-short interspersed nucleotide element (SINE retroposons, in particular to MAR1 retroposons that are widely present in marsupial genomes. Thus, the neuronal enhancer nPE2 originated from the exaptation of a CORE-SINE retroposon in the lineage leading to mammals and remained under purifying selection in all mammalian orders for the last 170 million years. Expression studies performed in transgenic mice showed that two nonadjacent nPE2 subregions are essential to drive reporter gene expression into POMC hypothalamic neurons, providing the first functional example of an exapted enhancer derived from an ancient CORE-SINE retroposon. In addition, we found that this CORE-SINE family of retroposons is likely to still be active in American and Australian marsupial genomes and that several highly conserved exonic, intronic and intergenic sequences in the human genome originated from the exaptation of CORE-SINE retroposons. Together, our results provide clear evidence of the functional novelties that transposed elements contributed to their host genomes throughout evolution.

  5. Ancient exaptation of a CORE-SINE retroposon into a highly conserved mammalian neuronal enhancer of the proopiomelanocortin gene.

    Science.gov (United States)

    Santangelo, Andrea M; de Souza, Flávio S J; Franchini, Lucía F; Bumaschny, Viviana F; Low, Malcolm J; Rubinstein, Marcelo

    2007-10-01

    The proopiomelanocortin gene (POMC) is expressed in the pituitary gland and the ventral hypothalamus of all jawed vertebrates, producing several bioactive peptides that function as peripheral hormones or central neuropeptides, respectively. We have recently determined that mouse and human POMC expression in the hypothalamus is conferred by the action of two 5' distal and unrelated enhancers, nPE1 and nPE2. To investigate the evolutionary origin of the neuronal enhancer nPE2, we searched available vertebrate genome databases and determined that nPE2 is a highly conserved element in placentals, marsupials, and monotremes, whereas it is absent in nonmammalian vertebrates. Following an in silico paleogenomic strategy based on genome-wide searches for paralog sequences, we discovered that opossum and wallaby nPE2 sequences are highly similar to members of the superfamily of CORE-short interspersed nucleotide element (SINE) retroposons, in particular to MAR1 retroposons that are widely present in marsupial genomes. Thus, the neuronal enhancer nPE2 originated from the exaptation of a CORE-SINE retroposon in the lineage leading to mammals and remained under purifying selection in all mammalian orders for the last 170 million years. Expression studies performed in transgenic mice showed that two nonadjacent nPE2 subregions are essential to drive reporter gene expression into POMC hypothalamic neurons, providing the first functional example of an exapted enhancer derived from an ancient CORE-SINE retroposon. In addition, we found that this CORE-SINE family of retroposons is likely to still be active in American and Australian marsupial genomes and that several highly conserved exonic, intronic and intergenic sequences in the human genome originated from the exaptation of CORE-SINE retroposons. Together, our results provide clear evidence of the functional novelties that transposed elements contributed to their host genomes throughout evolution.

  6. Identification of a core set of genes that signifies pathways underlying cardiac hypertrophy

    DEFF Research Database (Denmark)

    Strøm, Claes C; Kruhøffer, Mogens; Knudsen, Steen

    2004-01-01

    Although the molecular signals underlying cardiac hypertrophy have been the subject of intense investigation, the extent of common and distinct gene regulation between different forms of cardiac hypertrophy remains unclear. We hypothesized that a general and comparative analysis of hypertrophic...... gene expression, using microarray technology in multiple models of cardiac hypertrophy, including aortic banding, myocardial infarction, an arteriovenous shunt and pharmacologically induced hypertrophy, would uncover networks of conserved hypertrophy-specific genes and identify novel genes involved...... genes whose altered expression had previously been reported. We identified a single common gene program underlying hypertrophic remodelling, regardless of how the hypertrophy was induced. These genes constitute the molecular basis for the existence of one main form of cardiac hypertrophy and may...

  7. Incidence and prognostic impact of c-Kit, FLT3, and Ras gene mutations in core binding factor acute myeloid leukemia (CBF-AML)

    National Research Council Canada - National Science Library

    Boissel, N; Leroy, H; Brethon, B; Philippe, N; de Botton, S; Auvrignon, A; Raffoux, E; Leblanc, T; Thomas, X; Hermine, O; Quesnel, B; Baruchel, A; Leverger, G; Dombret, H; Preudhomme, C

    2006-01-01

    In core binding factors (CBF) acute myeloid leukemia (AML), the disruption of CBFalpha/beta genes impairs normal hematopoietic differentiation and is supposed to cooperate with additional mutations promoting proliferation...

  8. Comparative genomics of four closely related Clostridium perfringens bacteriophages reveals variable evolution among core genes with therapeutic potential

    Directory of Open Access Journals (Sweden)

    Siragusa Gregory R

    2011-06-01

    Full Text Available Abstract Background Because biotechnological uses of bacteriophage gene products as alternatives to conventional antibiotics will require a thorough understanding of their genomic context, we sequenced and analyzed the genomes of four closely related phages isolated from Clostridium perfringens, an important agricultural and human pathogen. Results Phage whole-genome tetra-nucleotide signatures and proteomic tree topologies correlated closely with host phylogeny. Comparisons of our phage genomes to 26 others revealed three shared COGs; of particular interest within this core genome was an endolysin (PF01520, an N-acetylmuramoyl-L-alanine amidase and a holin (PF04531. Comparative analyses of the evolutionary history and genomic context of these common phage proteins revealed two important results: 1 strongly significant host-specific sequence variation within the endolysin, and 2 a protein domain architecture apparently unique to our phage genomes in which the endolysin is located upstream of its associated holin. Endolysin sequences from our phages were one of two very distinct genotypes distinguished by variability within the putative enzymatically-active domain. The shared or core genome was comprised of genes with multiple sequence types belonging to five pfam families, and genes belonging to 12 pfam families, including the holin genes, which were nearly identical. Conclusions Significant genomic diversity exists even among closely-related bacteriophages. Holins and endolysins represent conserved functions across divergent phage genomes and, as we demonstrate here, endolysins can have significant variability and host-specificity even among closely-related genomes. Endolysins in our phage genomes may be subject to different selective pressures than the rest of the genome. These findings may have important implications for potential biotechnological applications of phage gene products.

  9. Bayesian analysis of congruence of core genes in Prochlorococcus and Synechococcus and implications on horizontal gene transfer.

    Directory of Open Access Journals (Sweden)

    Nicholas J Matzke

    Full Text Available It is often suggested that horizontal gene transfer is so ubiquitous in microbes that the concept of a phylogenetic tree representing the pattern of vertical inheritance is oversimplified or even positively misleading. "Universal proteins" have been used to infer the organismal phylogeny, but have been criticized as being only the "tree of one percent." Currently, few options exist for those wishing to rigorously assess how well a universal protein phylogeny, based on a relative handful of well-conserved genes, represents the phylogenetic histories of hundreds of genes. Here, we address this problem by proposing a visualization method and a statistical test within a Bayesian framework. We use the genomes of marine cyanobacteria, a group thought to exhibit substantial amounts of HGT, as a test case. We take 379 orthologous gene families from 28 cyanobacteria genomes and estimate the Bayesian posterior distributions of trees - a "treecloud" - for each, as well as for a concatenated dataset based on putative "universal proteins." We then calculate the average distance between trees within and between all treeclouds on various metrics and visualize this high-dimensional space with non-metric multidimensional scaling (NMMDS. We show that the tree space is strongly clustered and that the universal protein treecloud is statistically significantly closer to the center of this tree space than any individual gene treecloud. We apply several commonly-used tests for incongruence/HGT and show that they agree HGT is rare in this dataset, but make different choices about which genes were subject to HGT. Our results show that the question of the representativeness of the "tree of one percent" is a quantitative empirical question, and that the phylogenetic central tendency is a meaningful observation even if many individual genes disagree due to the various sources of incongruence.

  10. Bayesian analysis of congruence of core genes in Prochlorococcus and Synechococcus and implications on horizontal gene transfer.

    Science.gov (United States)

    Matzke, Nicholas J; Shih, Patrick M; Kerfeld, Cheryl A

    2014-01-01

    It is often suggested that horizontal gene transfer is so ubiquitous in microbes that the concept of a phylogenetic tree representing the pattern of vertical inheritance is oversimplified or even positively misleading. "Universal proteins" have been used to infer the organismal phylogeny, but have been criticized as being only the "tree of one percent." Currently, few options exist for those wishing to rigorously assess how well a universal protein phylogeny, based on a relative handful of well-conserved genes, represents the phylogenetic histories of hundreds of genes. Here, we address this problem by proposing a visualization method and a statistical test within a Bayesian framework. We use the genomes of marine cyanobacteria, a group thought to exhibit substantial amounts of HGT, as a test case. We take 379 orthologous gene families from 28 cyanobacteria genomes and estimate the Bayesian posterior distributions of trees - a "treecloud" - for each, as well as for a concatenated dataset based on putative "universal proteins." We then calculate the average distance between trees within and between all treeclouds on various metrics and visualize this high-dimensional space with non-metric multidimensional scaling (NMMDS). We show that the tree space is strongly clustered and that the universal protein treecloud is statistically significantly closer to the center of this tree space than any individual gene treecloud. We apply several commonly-used tests for incongruence/HGT and show that they agree HGT is rare in this dataset, but make different choices about which genes were subject to HGT. Our results show that the question of the representativeness of the "tree of one percent" is a quantitative empirical question, and that the phylogenetic central tendency is a meaningful observation even if many individual genes disagree due to the various sources of incongruence.

  11. Acceleration of gene transfection efficiency in neuroblastoma cells through polyethyleneimine/poly(methyl methacrylate) core-shell magnetic nanoparticles

    Science.gov (United States)

    Tencomnao, Tewin; Klangthong, Kewalin; Pimpha, Nuttaporn; Chaleawlert-umpon, Saowaluk; Saesoo, Somsak; Woramongkolchai, Noppawan; Saengkrit, Nattika

    2012-01-01

    Background The purpose of this study was to demonstrate the potential of magnetic poly(methyl methacrylate) (PMMA) core/polyethyleneimine (PEI) shell (mag-PEI) nanoparticles, which possess high saturation magnetization for gene delivery. By using mag-PEI nanoparticles as a gene carrier, this study focused on evaluation of transfection efficiency under magnetic induction. The potential role of this newly synthesized nanosphere for therapeutic delivery of the tryptophan hydroxylase-2 (TPH-2) gene was also investigated in cultured neuronal LAN-5 cells. Methods The mag-PEI nanoparticles were prepared by one-step emulsifier-free emulsion polymerization, generating highly loaded and monodispersed magnetic polymeric nanoparticles bearing an amine group. The physicochemical properties of the mag-PEI nanoparticles and DNA-bound mag-PEI nanoparticles were investigated using the gel retardation assay, atomic force microscopy, and zeta size measurements. The gene transfection efficiencies of mag-PEI nanoparticles were evaluated at different transfection times. Confocal laser scanning microscopy confirmed intracellular uptake of the magnetoplex. The optimal conditions for transfection of TPH-2 were selected for therapeutic gene transfection. We isolated the TPH-2 gene from the total RNA of the human medulla oblongata and cloned it into an expression vector. The plasmid containing TPH-2 was subsequently bound onto the surfaces of the mag-PEI nanoparticles via electrostatic interaction. Finally, the mag-PEI nanoparticle magnetoplex was delivered into LAN-5 cells. Reverse-transcriptase polymerase chain reaction was performed to evaluate TPH-2 expression in a quantitative manner. Results The study demonstrated the role of newly synthesized high-magnetization mag-PEI nanoparticles for gene transfection in vitro. The expression signals of a model gene, luciferase, and a therapeutic gene, TPH-2, were enhanced under magnetic-assisted transfection. An in vitro study in neuronal cells

  12. Past climate change on Sky Islands drives novelty in a core developmental gene network and its phenotype.

    Science.gov (United States)

    Favé, Marie-Julie; Johnson, Robert A; Cover, Stefan; Handschuh, Stephan; Metscher, Brian D; Müller, Gerd B; Gopalan, Shyamalika; Abouheif, Ehab

    2015-09-04

    A fundamental and enduring problem in evolutionary biology is to understand how populations differentiate in the wild, yet little is known about what role organismal development plays in this process. Organismal development integrates environmental inputs with the action of gene regulatory networks to generate the phenotype. Core developmental gene networks have been highly conserved for millions of years across all animals, and therefore, organismal development may bias variation available for selection to work on. Biased variation may facilitate repeatable phenotypic responses when exposed to similar environmental inputs and ecological changes. To gain a more complete understanding of population differentiation in the wild, we integrated evolutionary developmental biology with population genetics, morphology, paleoecology and ecology. This integration was made possible by studying how populations of the ant species Monomorium emersoni respond to climatic and ecological changes across five 'Sky Islands' in Arizona, which are mountain ranges separated by vast 'seas' of desert. Sky Islands represent a replicated natural experiment allowing us to determine how repeatable is the response of M. emersoni populations to climate and ecological changes at the phenotypic, developmental, and gene network levels. We show that a core developmental gene network and its phenotype has kept pace with ecological and climate change on each Sky Island over the last ~90,000 years before present (BP). This response has produced two types of evolutionary change within an ant species: one type is unpredictable and contingent on the pattern of isolation of Sky lsland populations by climate warming, resulting in slight changes in gene expression, organ growth, and morphology. The other type is predictable and deterministic, resulting in the repeated evolution of a novel wingless queen phenotype and its underlying gene network in response to habitat changes induced by climate warming. Our

  13. [Differential display of messenger RNA and identification of selenocysteine lyase gene in hepatocellular carcinoma cells transiently expressing hepatitis C virus core protein].

    Science.gov (United States)

    Yepes, Jesús Orlando; Luz Gunturiz, María; Henao, Luis Felipe; Navas, María Cristina; Balcázar, Norman; Gómez, Luis Alberto

    2006-06-01

    Hepatitis C virus is associated with diverse liver diseases including acute and chronic hepatitis, steatosis, cirrhosis and hepatocellular carcinoma. Several studies have explored viral mechanisms involved in the establishment of persistent infection and oncogenic Hepatitis C virus. Expression assays of Hepatitis C virus core protein suggest that this protein has transforming and carcinogenic properties with multifunctional activities in host cells. Characterization of expressed genes in cells expressing Core protein is important in order to identify candidate genes responsible for these pathogenic alterations. To compare and identify gene expression profiles in the human hepatocarcinoma derived cell line, HepG2, with transient expression of Hepatitis C virus Core protein. We have used comparative PCR-mediated differential display of mRNA from HepG2 hepatocarcinoma with and without transient expression of HCV Core protein or green fluorescent protein, previously obtained using the Semliki Forest Virus-based expression, through transduction of recombinant particles, rSFV-Core and rSFV-GFP, respectively. We observed differences in band intensities of mRNA in HepG2 cells transduced with rSFV-Core compared with those detected in cells without transduction, and transduced with rSFV-GFP. Cloning and sequencing of a gene fragment (258 bp) that was expressed differentially in HepG2 cells transduced with rSFV-Core, was identified as selenocystein lyase. The results confirm that HCV Core protein expressed in HepG2 is associated with specific changes in mRNA expression, including the gene for selenocystein lyase. This gene may be involved in the pathophysiology of hepatocellular carcinoma.

  14. Planting increases the abundance and structure complexity of soil core functional genes relevant to carbon and nitrogen cycling.

    Science.gov (United States)

    Wang, Feng; Liang, Yuting; Jiang, Yuji; Yang, Yunfeng; Xue, Kai; Xiong, Jinbo; Zhou, Jizhong; Sun, Bo

    2015-09-23

    Plants have an important impact on soil microbial communities and their functions. However, how plants determine the microbial composition and network interactions is still poorly understood. During a four-year field experiment, we investigated the functional gene composition of three types of soils (Phaeozem, Cambisols and Acrisol) under maize planting and bare fallow regimes located in cold temperate, warm temperate and subtropical regions, respectively. The core genes were identified using high-throughput functional gene microarray (GeoChip 3.0), and functional molecular ecological networks (fMENs) were subsequently developed with the random matrix theory (RMT)-based conceptual framework. Our results demonstrated that planting significantly (P soils and 83.5% of microbial alpha-diversity can be explained by the plant factor. Moreover, planting had significant impacts on the microbial community structure and the network interactions of the microbial communities. The calculated network complexity was higher under maize planting than under bare fallow regimes. The increase of the functional genes led to an increase in both soil respiration and nitrification potential with maize planting, indicating that changes in the soil microbial communities and network interactions influenced ecological functioning.

  15. Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis.

    Directory of Open Access Journals (Sweden)

    Marcin J Skwark

    2017-02-01

    Full Text Available Recent advances in the scale and diversity of population genomic datasets for bacteria now provide the potential for genome-wide patterns of co-evolution to be studied at the resolution of individual bases. Here we describe a new statistical method, genomeDCA, which uses recent advances in computational structural biology to identify the polymorphic loci under the strongest co-evolutionary pressures. We apply genomeDCA to two large population data sets representing the major human pathogens Streptococcus pneumoniae (pneumococcus and Streptococcus pyogenes (group A Streptococcus. For pneumococcus we identified 5,199 putative epistatic interactions between 1,936 sites. Over three-quarters of the links were between sites within the pbp2x, pbp1a and pbp2b genes, the sequences of which are critical in determining non-susceptibility to beta-lactam antibiotics. A network-based analysis found these genes were also coupled to that encoding dihydrofolate reductase, changes to which underlie trimethoprim resistance. Distinct from these antibiotic resistance genes, a large network component of 384 protein coding sequences encompassed many genes critical in basic cellular functions, while another distinct component included genes associated with virulence. The group A Streptococcus (GAS data set population represents a clonal population with relatively little genetic variation and a high level of linkage disequilibrium across the genome. Despite this, we were able to pinpoint two RNA pseudouridine synthases, which were each strongly linked to a separate set of loci across the chromosome, representing biologically plausible targets of co-selection. The population genomic analysis method applied here identifies statistically significantly co-evolving locus pairs, potentially arising from fitness selection interdependence reflecting underlying protein-protein interactions, or genes whose product activities contribute to the same phenotype. This discovery

  16. Natural selection in a population of Drosophila melanogaster explained by changes in gene expression caused by sequence variation in core promoter regions.

    Science.gov (United States)

    Sato, Mitsuhiko P; Makino, Takashi; Kawata, Masakado

    2016-02-09

    Understanding the evolutionary forces that influence variation in gene regulatory regions in natural populations is an important challenge for evolutionary biology because natural selection for such variations could promote adaptive phenotypic evolution. Recently, whole-genome sequence analyses have identified regulatory regions subject to natural selection. However, these studies could not identify the relationship between sequence variation in the detected regions and change in gene expression levels. We analyzed sequence variations in core promoter regions, which are critical regions for gene regulation in higher eukaryotes, in a natural population of Drosophila melanogaster, and identified core promoter sequence variations associated with differences in gene expression levels subjected to natural selection. Among the core promoter regions whose sequence variation could change transcription factor binding sites and explain differences in expression levels, three core promoter regions were detected as candidates associated with purifying selection or selective sweep and seven as candidates associated with balancing selection, excluding the possibility of linkage between these regions and core promoter regions. CHKov1, which confers resistance to the sigma virus and related insecticides, was identified as core promoter regions that has been subject to selective sweep, although it could not be denied that selection for variation in core promoter regions was due to linked single nucleotide polymorphisms in the regulatory region outside core promoter regions. Nucleotide changes in core promoter regions of CHKov1 caused the loss of two basal transcription factor binding sites and acquisition of one transcription factor binding site, resulting in decreased gene expression levels. Of nine core promoter regions regions associated with balancing selection, brat, and CG9044 are associated with neuromuscular junction development, and Nmda1 are associated with learning

  17. Comparative genomics of four Mycoplasma species of the human urogenital tract: Analysis of their core genomes and virulence genes.

    Science.gov (United States)

    Roachford, Orville St E; Nelson, Karen E; Mohapatra, Bidyut R

    2017-12-01

    The variation in Mycoplasma lipoproteins attributed to genome rearrangements and genetic insertions leads to phenotypic plasticity that allows for the evasion of the host's defence system and pathogenesis. This paper compared for the first time the genomes of four human urogenital Mycoplasma species (M. penetrans HF-2, M. fermentans JER, M. genitalium G37 and M. hominis PG21) to categorise the metabolic functions of the core genes and to assess the effects of tandem repeats, phage-like genetic elements and prophages on the virulence genes. The results of this comparative in silico genomic analysis revealed that the genes constituting their core genomes can be separated into three distinct categories: nuclear metabolism, protein metabolism and energy generation each making up 52%, 31% and 23%, respectively. The genomes have repeat sequences ranging from 3.7% in M. hominis PG21 to 9.5% in M. fermentans JER. Tandem repeats (mostly minisatellites) and phage-like proteins (including DNA gyrases/topoisomerases) were randomly distributed in the Mycoplasma genomes. Here, we identified a coiled-coil structure containing protein in M. penetrans HF-2 which is significantly similar to the Mem protein of M. fermentans ɸMFV1. Therefore, a Mycoplasma prophage seems to be embedded within M. penetrans HF-2 unannotated genome. To the best of our knowledge, no Mycoplasma phages or prophages have been detected in M. penetrans. This study is important not only in understanding the complex genetic factors involved in phenotypic plasticity and virulence in the relatively understudied Mycoplasma species but also in elucidating the effective arrangement of their redundant minimal genomes. Copyright © 2017 Elsevier GmbH. All rights reserved.

  18. Transcription Factors Encoded on Core and Accessory Chromosomes of Fusarium oxysporum Induce Expression of Effector Genes

    NARCIS (Netherlands)

    van der Does, H.C.; Fokkens, L.; Yang, A.; Schmidt, S.M.; Langereis, L.; Lukasiewicz, J.M.; Hughes, T.R.; Rep, M.

    2016-01-01

    Proteins secreted by pathogens during host colonization largely determine the outcome of pathogen-host interactions and are commonly called 'effectors'. In fungal plant pathogens, coordinated transcriptional up-regulation of effector genes is a key feature of pathogenesis and effectors are often

  19. Complete nucleomorph genome sequence of the nonphotosynthetic alga Cryptomonas paramecium reveals a core nucleomorph gene set.

    Science.gov (United States)

    Tanifuji, Goro; Onodera, Naoko T; Wheeler, Travis J; Dlutek, Marlena; Donaher, Natalie; Archibald, John M

    2011-01-01

    Nucleomorphs are the remnant nuclei of algal endosymbionts that were engulfed by nonphotosynthetic host eukaryotes. These peculiar organelles are found in cryptomonad and chlorarachniophyte algae, where they evolved from red and green algal endosymbionts, respectively. Despite their independent origins, cryptomonad and chlorarachniophyte nucleomorph genomes are similar in size and structure: they are both cryptomonad nucleomorph genomes known, that of the secondarily nonphotosynthetic cryptomonad Cryptomonas paramecium. The genome is 486 kbp in size and contains 518 predicted genes, 466 of which are protein coding. Although C. paramecium lacks photosynthetic ability, its nucleomorph genome still encodes 18 plastid-associated proteins. More than 90% of the "conserved" protein genes in C. paramecium (i.e., those with clear homologs in other eukaryotes) are also present in the nucleomorph genomes of the cryptomonads Guillardia theta and Hemiselmis andersenii. In contrast, 143 of 466 predicted C. paramecium proteins (30.7%) showed no obvious similarity to proteins encoded in any other genome, including G. theta and H. andersenii. Significantly, however, many of these "nucleomorph ORFans" are conserved in position and size between the three genomes, suggesting that they are in fact homologous to one another. Finally, our analyses reveal an unexpected degree of overlap in the genes present in the independently evolved chlorarachniophyte and cryptomonad nucleomorph genomes: ∼80% of a set of 120 conserved nucleomorph genes in the chlorarachniophyte Bigelowiella natans were also present in all three cryptomonad nucleomorph genomes. This result suggests that similar reductive processes have taken place in unrelated lineages of nucleomorph-containing algae.

  20. Mechanisms of Breast Cancer in Shift Workers: DNA Methylation in Five Core Circadian Genes in Nurses Working Night Shifts.

    Science.gov (United States)

    Samulin Erdem, Johanna; Skare, Øivind; Petersen-Øverleir, Marte; Notø, Heidi Ødegaard; Lie, Jenny-Anne S; Reszka, Edyta; Pepłońska, Beata; Zienolddiny, Shanbeh

    2017-01-01

    Shift work has been suggested to be associated with breast cancer risk, and circadian disruption in shift workers is hypothesized as one of the mechanisms of increased cancer risk. There is, however, insufficient molecular evidence supporting this hypothesis. Using the quantitative methodology of pyrosequencing, epigenetic changes in 5-methyl cytosine (5mC) in five circadian genes CLOCK, BMAL1, CRY1, PER1 and PER2 in female nurses working night shift work (278 breast cancer cases, 280 controls) were analyzed. In breast cancer cases, a medium exposure to night work was associated with increased methylation levels of the CLOCK (p=0.050), BMAL1 (p=0.001) and CRY1 (p=0.040) genes, compared with controls. Within the cases, analysis of the effects of shift work on the methylation patterns showed that methylation of CRY1 was lower in those who had worked night shift and had a high exposure (p=0.006) compared with cases that had worked only days. For cases with a medium exposure to night work, an increase in BMAL1 (p=0.003) and PER1 (p=0.035) methylation was observed compared with day working (unexposed) cases. The methylation levels of the five core circadian genes were also analyzed in relation to the estrogen and progesterone receptors status of the tumors in the cases, and no correlations were observed. Furthermore, nineteen polymorphisms in the five circadian genes were assessed for their effects on the methylation levels of the respective genes, but no associations were found. In summary, our data suggest that epigenetic regulation of CLOCK, BMAL1, CRY1 and PER1 may contribute to breast cancer in shift workers.

  1. Decorin protein core affects the global gene expression profile of the tumor microenvironment in a triple-negative orthotopic breast carcinoma xenograft model.

    Directory of Open Access Journals (Sweden)

    Simone Buraschi

    Full Text Available Decorin, a member of the small leucine-rich proteoglycan gene family, exists and functions wholly within the tumor microenvironment to suppress tumorigenesis by directly targeting and antagonizing multiple receptor tyrosine kinases, such as the EGFR and Met. This leads to potent and sustained signal attenuation, growth arrest, and angiostasis. We thus sought to evaluate the tumoricidal benefits of systemic decorin on a triple-negative orthotopic breast carcinoma xenograft model. To this end, we employed a novel high-density mixed expression array capable of differentiating and simultaneously measuring gene signatures of both Mus musculus (stromal and Homo sapiens (epithelial tissue origins. We found that decorin protein core modulated the differential expression of 374 genes within the stromal compartment of the tumor xenograft. Further, our top gene ontology classes strongly suggests an unexpected and preferential role for decorin protein core to inhibit genes necessary for immunomodulatory responses while simultaneously inducing expression of those possessing cellular adhesion and tumor suppressive gene properties. Rigorous verification of the top scoring candidates led to the discovery of three genes heretofore unlinked to malignant breast cancer that were reproducibly found to be induced in several models of tumor stroma. Collectively, our data provide highly novel and unexpected stromal gene signatures as a direct function of systemic administration of decorin protein core and reveals a fundamental basis of action for decorin to modulate the tumor stroma as a biological mechanism for the ascribed anti-tumorigenic properties.

  2. Shifting from a gene-centric to metabolite-centric strategy to determine the core gut microbiome.

    Science.gov (United States)

    Marchesi, Julian R

    2011-01-01

    A key challenge in the area of determining how the microbiome communicates with the host's karyome is deciding which microbial functions should be studied. Ideally we would wish to look at functions which are not only important to the microbial host, but which also play roles in host physiology. Selecting the key microbial functions is essential to developing robust strategies to either promote or demote them, with the aim to enhancing host health. This commentary argues that the bottom-up approach is not providing the necessary gene-set from which we can start to develop a robust core microbiome and in fact we should adopt a top-down strategy in order to indentify the functions that are important and need further study.

  3. A prospective comparison of ER, PR, Ki67 and gene expression in paired sequential core biopsies of primary, untreated breast cancer.

    Science.gov (United States)

    Hadad, Sirwan M; Jordan, Lee B; Roy, Pankaj G; Purdie, Colin A; Iwamoto, Takayuki; Pusztai, Lajos; Moulder-Thompson, Stacy L; Thompson, Alastair M

    2016-09-22

    Sequential biopsy of breast cancer is used to assess biomarker effects and drug efficacy. The preoperative "window of opportunity" setting is advantageous to test biomarker changes in response to therapeutic agents in previously untreated primary cancers. This study tested the consistency over time of paired, sequential biomarker measurements on primary, operable breast cancer in the absence of drug therapy. Immunohistochemistry was performed for ER, PR and Ki67 on paired preoperative/operative tumor samples taken from untreated patients within 2 weeks of each other. Microarray analysis on mRNA extracted from formalin fixed paraffin embedded cores was performed using Affymetrix based arrays on paired core biopsies analysed using Ingenuity Pathway Analysis (IPA) and Gene Set Analysis (GSA). In 41 core/resection pairs, the recognised trend to lower ER, PR and Ki67 score on resected material was confirmed. Concordance for ER, PR and Ki67 without changing biomarker status (e.g. ER+ to ER-) was 90, 74 and 80 % respectively. However, in 23 paired core samples (diagnostic core v on table core), Ki67 using a cut off of 13.25 % was concordant in 22/23 (96 %) and differences in ER and PR immunohistochemistry by Allred or Quickscore between the pairs did not impact hormone receptor status. IPA and GSA demonstrated substantial gene expression changes between paired cores at the mRNA level, including reduced expression of ER pathway analysis on the second core, despite the absence of drug intervention. Sequential core biopsies of primary breast cancer (but not core versus resection) was consistent and is appropriate to assess the effects of drug therapy in vivo on ER, PR and Ki67 using immunohistochemistry. Conversely, studies utilising mRNA expression may require non-treatment controls to distinguish therapeutic from biopsy differences.

  4. rapidGSEA: Speeding up gene set enrichment analysis on multi-core CPUs and CUDA-enabled GPUs.

    Science.gov (United States)

    Hundt, Christian; Hildebrandt, Andreas; Schmidt, Bertil

    2016-09-23

    Gene Set Enrichment Analysis (GSEA) is a popular method to reveal significant dependencies between predefined sets of gene symbols and observed phenotypes by evaluating the deviation of gene expression values between cases and controls. An established measure of inter-class deviation, the enrichment score, is usually computed using a weighted running sum statistic over the whole set of gene symbols. Due to the lack of analytic expressions the significance of enrichment scores is determined using a non-parametric estimation of their null distribution by permuting the phenotype labels of the probed patients. Accordingly, GSEA is a time-consuming task due to the large number of required permutations to accurately estimate the nominal p-value - a circumstance that is even more pronounced during multiple hypothesis testing since its estimate is lower-bounded by the inverse number of samples in permutation space. We present rapidGSEA - a software suite consisting of two tools for facilitating permutation-based GSEA: cudaGSEA and ompGSEA. cudaGSEA is a CUDA-accelerated tool using fine-grained parallelization schemes on massively parallel architectures while ompGSEA is a coarse-grained multi-threaded tool for multi-core CPUs. Nominal p-value estimation of 4,725 gene sets on a data set consisting of 20,639 unique gene symbols and 200 patients (183 cases + 17 controls) each probing one million permutations takes 19 hours on a Xeon CPU and less than one hour on a GeForce Titan X GPU while the established GSEA tool from the Broad Institute (broadGSEA) takes roughly 13 days. cudaGSEA outperforms broadGSEA by around two orders-of-magnitude on a single Tesla K40c or GeForce Titan X GPU. ompGSEA provides around one order-of-magnitude speedup to broadGSEA on a standard Xeon CPU. The rapidGSEA suite is open-source software and can be downloaded at https://github.com/gravitino/cudaGSEA as standalone application or package for the R framework.

  5. [Relationship between hepatitis B virus polymerase gene mutation patterns of rtM204I/V and pre-core/basal core promoter mutations].

    Science.gov (United States)

    Yan, Li; Wang, Jie-Fei; Wang, Zhan-Hui; Sun, Jian; Zhou, Bin; Hou, Jinlin

    2014-12-01

    To investigate the relationship between mutations of rtM204V/I (methionine to valine or isoleucine at position rt204 of reverse transcriptase domain) in the hepatitis B virus (HBV) polymerase gene and the G1896A and G1899A single mutations in the pre-eore (PC) region and the A1762T and G1764A double-mutations in the basal core promoter (BCP) region. A total of 2,849 hepatitis B complete genome sequences were retrieved from the GenBank/EMBL/DDBJ. The amino acid sequence of the of reverse transcriptase domain and genome sequences of the PC region and the BCP region were aligned using MEGA4 software. Data were calculated using Microsoft Excel and evaluated using SPSS 13.0 statistical software. Among the 2, 849 HBV complete genome sequences, 217 (8%) strains were identified with Y(I/V) DD and 120 of those had the YIDD mutation and 97 had the YVDD mutation. Of the 1543 strains (54.2%) with PC-BCP mutations, seven mutation patterns of G 1896A-G 1899A-G 1896A-G 1899A-A 1762T/G 1764A, A 1762T/G 1764AG 1896A, A 1762T/G 1764A-G 1899A, and A 1762T/G 1764A-G 1896A-G 1899A were identified. of YMDD and PC-BCP had a higher incidence than the single YMDD mutation (76% vs 24.0%, x2=45.283, P=0.000). The double-mutations of YIDD and PC-BCP had a higher incidence than the double-mutation of YVDD and PC-BCP (85% vs 64.9%, x2=11.836, P=0.000). The double-mutation for lamivudine resistance of YMDD and PC-BCP had a higher incidence than the double pre-existent YMDD and PC-BCP mutations (89.3% vs 58.9%, x2=27.084, P=0.000). The three mutation patterns of G1896A-G1899A (P=0.000, OR=7.573), A1762T/G1764A-G1899A (P=0.000, OR=6.539) and A1762T/G1764A-G1896A-G1899A (P=0.000, OR=6.596) were associated with a greater risk of developing the YIDD mutation, according to binary logistic analysis. There is a relationship between the HBV YI/VDD mutation and PC-BCP mutations. Different PC-BCP mutation patterns have different effects on the YI/VDD mutation.

  6. Sleep quality and methylation status of core circadian rhythm genes among nurses and midwives.

    Science.gov (United States)

    Bukowska-Damska, Agnieszka; Reszka, Edyta; Kaluzny, Pawel; Wieczorek, Edyta; Przybek, Monika; Zienolddiny, Shanbeh; Peplonska, Beata

    2017-01-01

    ABSTARCT Poor sleep quality or sleep restriction is associated with sleepiness and concentration problems. Moreover, chronic sleep restriction may affect metabolism, hormone secretion patterns and inflammatory responses. Limited recent reports suggest a potential link between sleep deprivation and epigenetic effects such as changes in DNA methylation profiles. The aim of the present study was to assess the potential association between poor sleep quality or sleep duration and the levels of 5-methylcytosine in the promoter regions of PER1, PER2, PER3, BMAL1, CLOCK, CRY1 CRY2 and NPAS2 genes, taking into account rotating night work and chronotype as potential confounders or modifiers. A cross-sectional study was conducted on 710 nurses and midwives (347 working on rotating nights and 363 working only during the day) aged 40-60 years. Data from in-person interviews about sleep quality, chronotype and potential confounders were used. Sleep quality and chronotype were assessed using Pittsburgh Sleep Quality Questionnaire (PSQI) and Morningness-Eveningness Questionnaire (MEQ), respectively. Morning blood samples were collected. The methylation status of the circadian rhythm genes was determined via quantitative methylation-specific real-time PCR assays (qMSP) reactions using DNA samples derived from leucocytes. The proportional odds regression model was fitted to quantify the relationship between methylation index (MI) as the dependent variable and sleep quality or sleep duration as the explanatory variable. Analyses were carried out for the total population as well as for subgroups of women stratified by the current system of work (rotating night shift/day work) and chronotype (morning type/intermediate type/evening type). A potential modifying effect of the system of work or the chronotype was examined using the likelihood ratio test. No significant findings were observed in the total study population. Subgroup analyses revealed two statistically significant

  7. CGUG: in silico proteome and genome parsing tool for the determination of "core" and unique genes in the analysis of genomes up to ca. 1.9 Mb.

    Science.gov (United States)

    Mahadevan, Padmanabhan; King, John F; Seto, Donald

    2009-08-25

    Viruses and small-genome bacteria (~2 megabases and smaller) comprise a considerable population in the biosphere and are of interest to many researchers. These genomes are now sequenced at an unprecedented rate and require complementary computational tools to analyze. "CoreGenesUniqueGenes" (CGUG) is an in silico genome data mining tool that determines a "core" set of genes from two to five organisms with genomes in this size range. Core and unique genes may reflect similar niches and needs, and may be used in classifying organisms. CGUG is available at http://binf.gmu.edu/geneorder.html as a web-based on-the-fly tool that performs iterative BLASTP analyses using a reference genome and up to four query genomes to provide a table of genes common to these genomes. The result is an in silico display of genomes and their proteomes, allowing for further analysis. CGUG can be used for "genome annotation by homology", as demonstrated with Chlamydophila and Francisella genomes. CGUG is used to reanalyze the ICTV-based classifications of bacteriophages, to reconfirm long-standing relationships and to explore new classifications. These genomes have been problematic in the past, due largely to horizontal gene transfers. CGUG is validated as a tool for reannotating small genome bacteria using more up-to-date annotations by similarity or homology. These serve as an entry point for wet-bench experiments to confirm the functions of these "hypothetical" and "unknown" proteins.

  8. CGUG: in silico proteome and genome parsing tool for the determination of "core" and unique genes in the analysis of genomes up to ca. 1.9 Mb

    Directory of Open Access Journals (Sweden)

    Mahadevan Padmanabhan

    2009-08-01

    Full Text Available Abstract Background Viruses and small-genome bacteria (~2 megabases and smaller comprise a considerable population in the biosphere and are of interest to many researchers. These genomes are now sequenced at an unprecedented rate and require complementary computational tools to analyze. "CoreGenesUniqueGenes" (CGUG is an in silico genome data mining tool that determines a "core" set of genes from two to five organisms with genomes in this size range. Core and unique genes may reflect similar niches and needs, and may be used in classifying organisms. Findings CGUG is available at http://binf.gmu.edu/geneorder.html as a web-based on-the-fly tool that performs iterative BLASTP analyses using a reference genome and up to four query genomes to provide a table of genes common to these genomes. The result is an in silico display of genomes and their proteomes, allowing for further analysis. CGUG can be used for "genome annotation by homology", as demonstrated with Chlamydophila and Francisella genomes. Conclusion CGUG is used to reanalyze the ICTV-based classifications of bacteriophages, to reconfirm long-standing relationships and to explore new classifications. These genomes have been problematic in the past, due largely to horizontal gene transfers. CGUG is validated as a tool for reannotating small genome bacteria using more up-to-date annotations by similarity or homology. These serve as an entry point for wet-bench experiments to confirm the functions of these "hypothetical" and "unknown" proteins.

  9. The effect of high fat diet on daily rhythm of the core clock genes and muscle functional genes in the skeletal muscle of Chinese soft-shelled turtle (Trionyx sinensis).

    Science.gov (United States)

    Liu, Li; Jiang, Guomin; Peng, Zhitao; Li, Yulong; Li, Jinlong; Zou, Li; He, Zhigang; Wang, Xiaoqing; Chu, Wuying

    2017-11-01

    In the present study, we sought to investigate the influence of high fat diet on the core clock genes and the muscle functional genes daily expression in the skeletal muscle of Chinese soft-shelled turtle. The turtles were fed by two diets including a control fat diet (the CON treatment, 7.98% lipid) and a high fat diet (the HFD treatment, 13.86% lipid) for six weeks and administrated by the photophase regimen of 24h light/dark (12L:12D) cycle. After the feeding trial experiment, we measured the daily expression levels of 17 core clock genes (Clock, Bmal1/2, NPAS2, Tim, Cry1/2, Per1/2, DBP, AANAT, NIFL3, BHLHE40, NR1D2, RORA, RORB, RORC) and 12 muscle functional genes (FBXO32, MBNL1, MSTN, Myf5, Myf6, MyoD, MyoG, MyoM1, PPARa, PDK4, Trim63, UCP3) in the skeletal muscle of the two treatments. The results showed that except for Bmal1, NPAS2, Per2 and RORB, the expression of the other 13 core clock genes exhibited circadian oscillation in the CON treatment. Among the 12 muscle functional genes, MBNL1, PDK4 and MyoM1 did not exhibit circadian oscillation in the CON treatment. In the HFD treatment, the circadian rhythms expressional patterns of the 8 core clock genes (Clock, Bmal2, Cry2, Per1, DBP, NFIL3, BHLHE40 and RORA) and 6 muscle functional genes (MSTN, Myf5, MyoD, MyoG, PPARa and Trim63) were disrupted. In addition, compared with the CON treatment, the circadian expression of the 5 core clock genes (Tim, Cry1, AANAT, NR1D2, RORC) and the 3 muscle functional genes (FBXO32, Myf6, UCP3) showed the advanced or delayed expression peaks in the HFD treatment. In CON treatment, the circadian expression of the MyoG, MyoD, Myf6, FBXO32 and PPARa showed positive or negative correlation with the transcription pattern of Clock, Bmal2, Cry1/2, Per1/2. However, only the FBXO32 and Myf6 presented positive or negative correlation with the circadian expression of Cry1, RORB, AANAT and Tim in HFD treatment. In summary, these results demonstrate that the disruption of the circadian

  10. The iron/heme regulated genes of Haemophilus influenzae: comparative transcriptional profiling as a tool to define the species core modulon

    Directory of Open Access Journals (Sweden)

    Morton Daniel J

    2009-01-01

    Full Text Available Abstract Background Haemophilus influenzae requires heme for aerobic growth and possesses multiple mechanisms to obtain this essential nutrient. Although an understanding of the heme acquisition mechanisms of H. influenzae is emerging, significant gaps in our knowledge remain. Unresolved issues include the identities of all genes exhibiting altered transcription in response to iron and heme availability, the fraction of such genes functioning in iron/heme acquisition, and the heterogeneity of this gene set among clinical isolates. Previously we utilized H. influenzae strain Rd KW20 to demonstrate the utility of transcriptional profiling in defining the genes exhibiting altered transcription in response to environmental iron and heme levels. The current study expands upon those observations by determining the iron/heme modulons of two clinical isolates, the type b isolate 10810 and the nontypeable isolate R2866. These data are used to begin to define the core iron/heme modulon of the species. Results Microarray studies were performed to compare gene expression on transition from iron/heme-restricted to iron/heme-replete conditions for each isolate. Of 1820 ORFs on the array corresponding to R2866 genes, 363 were significantly differentially expressed: 233 were maximally transcribed under iron/heme-replete conditions and 130 under iron/heme-restricted conditions. Of the 1883 ORFs representing genes of strain 10810, 353 were significantly differentially transcribed: 150 were preferentially transcribed under iron/heme-replete conditions and 203 under iron/heme-restricted conditions. Comparison of the data sets indicated that 163 genes exhibited similar regulation in both isolates and that 74 of these exhibited similar patterns of regulation in Rd KW20. These comprise the putative core iron/heme modulon. Conclusion This study provides evidence for a conserved core of H. influenzae genes the transcription of which is altered by the availability of

  11. The iron/heme regulated genes of Haemophilus influenzae: comparative transcriptional profiling as a tool to define the species core modulon.

    Science.gov (United States)

    Whitby, Paul W; Seale, Thomas W; VanWagoner, Timothy M; Morton, Daniel J; Stull, Terrence L

    2009-01-07

    Haemophilus influenzae requires heme for aerobic growth and possesses multiple mechanisms to obtain this essential nutrient. Although an understanding of the heme acquisition mechanisms of H. influenzae is emerging, significant gaps in our knowledge remain. Unresolved issues include the identities of all genes exhibiting altered transcription in response to iron and heme availability, the fraction of such genes functioning in iron/heme acquisition, and the heterogeneity of this gene set among clinical isolates. Previously we utilized H. influenzae strain Rd KW20 to demonstrate the utility of transcriptional profiling in defining the genes exhibiting altered transcription in response to environmental iron and heme levels. The current study expands upon those observations by determining the iron/heme modulons of two clinical isolates, the type b isolate 10810 and the nontypeable isolate R2866. These data are used to begin to define the core iron/heme modulon of the species. Microarray studies were performed to compare gene expression on transition from iron/heme-restricted to iron/heme-replete conditions for each isolate. Of 1820 ORFs on the array corresponding to R2866 genes, 363 were significantly differentially expressed: 233 were maximally transcribed under iron/heme-replete conditions and 130 under iron/heme-restricted conditions. Of the 1883 ORFs representing genes of strain 10810, 353 were significantly differentially transcribed: 150 were preferentially transcribed under iron/heme-replete conditions and 203 under iron/heme-restricted conditions. Comparison of the data sets indicated that 163 genes exhibited similar regulation in both isolates and that 74 of these exhibited similar patterns of regulation in Rd KW20. These comprise the putative core iron/heme modulon. This study provides evidence for a conserved core of H. influenzae genes the transcription of which is altered by the availability of iron and/or heme in the growth environment. Elucidation of

  12. Preparation by alkaline treatment and detailed characterisation of empty hepatitis B virus core particles for vaccine and gene therapy applications

    Science.gov (United States)

    Strods, Arnis; Ose, Velta; Bogans, Janis; Cielens, Indulis; Kalnins, Gints; Radovica, Ilze; Kazaks, Andris; Pumpens, Paul; Renhofa, Regina

    2015-06-01

    Hepatitis B virus (HBV) core (HBc) virus-like particles (VLPs) are one of the most powerful protein engineering tools utilised to expose immunological epitopes and/or cell-targeting signals and for the packaging of genetic material and immune stimulatory sequences. Although HBc VLPs and their numerous derivatives are produced in highly efficient bacterial and yeast expression systems, the existing purification and packaging protocols are not sufficiently optimised and standardised. Here, a simple alkaline treatment method was employed for the complete removal of internal RNA from bacteria- and yeast-produced HBc VLPs and for the conversion of these VLPs into empty particles, without any damage to the VLP structure. The empty HBc VLPs were able to effectively package the added DNA and RNA sequences. Furthermore, the alkaline hydrolysis technology appeared efficient for the purification and packaging of four different HBc variants carrying lysine residues on the HBc VLP spikes. Utilising the introduced lysine residues and the intrinsic aspartic and glutamic acid residues exposed on the tips of the HBc spikes for chemical coupling of the chosen peptide and/or nucleic acid sequences ensured a standard and easy protocol for the further development of versatile HBc VLP-based vaccine and gene therapy applications.

  13. Reference: -300CORE [PLACE

    Lifescience Database Archive (English)

    Full Text Available -300CORE Forde BG, Heyworth A, Pywell J, Kreis M Nucleotide sequence of a B1 hordein gene and the identifica...tion of possible upstream regulatory elements in endosperm storage protein genes fr

  14. D816 mutation of the KIT gene in core binding factor acute myeloid leukemia is associated with poorer prognosis than other KIT gene mutations.

    Science.gov (United States)

    Yui, Shunsuke; Kurosawa, Saiko; Yamaguchi, Hiroki; Kanamori, Heiwa; Ueki, Toshimitsu; Uoshima, Nobuhiko; Mizuno, Ishikazu; Shono, Katsuhiro; Usuki, Kensuke; Chiba, Shigeru; Nakamura, Yukinori; Yanada, Masamitsu; Kanda, Junya; Tajika, Kenji; Gomi, Seiji; Fukunaga, Keiko; Wakita, Satoshi; Ryotokuji, Takeshi; Fukuda, Takahiro; Inokuchi, Koiti

    2017-10-01

    The clinical impact of KIT mutations in core binding factor acute myeloid leukemia (CBF-AML) is still unclear. In the present study, we analyzed the prognostic significance of each KIT mutation (D816, N822K, and other mutations) in Japanese patients with CBF-AML. We retrospectively analyzed 136 cases of CBF-AML that had gone into complete remission (CR). KIT mutations were found in 61 (45%) of the patients with CBF-AML. D816, N822K, D816 and N822K, and other mutations of the KIT gene were detected in 29 cases (21%), 20 cases (15%), 7 cases (5%), and 5 cases (4%), respectively. The rate of relapse-free survival (RFS) and overall survival (OS) in patients with D816 and with both D816 and N822K mutations was significantly lower than in patients with other or with no KIT mutations (RFS: p mutation was associated with a significantly worse prognosis. In a further multivariate analysis of RFS and OS, D816 mutation was found to be an independent risk factor for significantly poorer prognosis. In the present study, we were able to establish that, of all KIT mutations, D816 mutation alone is an unfavorable prognostic factor.

  15. Fabrication of Core-Shell PEI/pBMP2-PLGA Electrospun Scaffold for Gene Delivery to Periodontal Ligament Stem Cells

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    Qiao Xie

    2016-01-01

    Full Text Available Bone tissue engineering is the most promising technology for enhancing bone regeneration. Scaffolds loaded with osteogenic factors improve the therapeutic effect. In this study, the bioactive PEI (polyethylenimine/pBMP2- (bone morphogenetic protein-2 plasmid- PLGA (poly(D, L-lactic-co-glycolic acid core-shell scaffolds were prepared using coaxial electrospinning for a controlled gene delivery to hPDLSCs (human periodontal ligament stem cells. The pBMP2 was encapsulated in the PEI phase as a core and PLGA was employed to control pBMP2 release as a shell. First, the scaffold characterization and mechanical properties were evaluated. Then the gene release behavior was analyzed. Our results showed that pBMP2 was released at high levels in the first few days, with a continuous release behavior in the next 28 days. At the same time, PEI/pBMP2 showed high transfection efficiency. Moreover, the core-shell electrospun scaffold showed BMP2 expression for a much longer time (more than 28 days compared with the single axial electrospun scaffold, as evaluated by qRT-PCR and western blot after culturing with hPDLSCs. These results suggested that the core-shell PEI/pBMP2-PLGA scaffold fabricated by coaxial electrospinning had a good gene release behavior and showed a prolonged expression time with a high transfection efficiency.

  16. PACAP38 differentially effects genes and CRMP2 protein expression in ischemic core and penumbra regions of permanent middle cerebral artery occlusion model mice brain.

    Science.gov (United States)

    Hori, Motohide; Nakamachi, Tomoya; Shibato, Junko; Rakwal, Randeep; Tsuchida, Masachi; Shioda, Seiji; Numazawa, Satoshi

    2014-09-23

    Pituitary adenylate-cyclase activating polypeptide (PACAP) has neuroprotective and axonal guidance functions, but the mechanisms behind such actions remain unclear. Previously we examined effects of PACAP (PACAP38, 1 pmol) injection intracerebroventrically in a mouse model of permanent middle cerebral artery occlusion (PMCAO) along with control saline (0.9% NaCl) injection. Transcriptomic and proteomic approaches using ischemic (ipsilateral) brain hemisphere revealed differentially regulated genes and proteins by PACAP38 at 6 and 24 h post-treatment. However, as the ischemic hemisphere consisted of infarct core, penumbra, and non-ischemic regions, specificity of expression and localization of these identified molecular factors remained incomplete. This led us to devise a new experimental strategy wherein, ischemic core and penumbra were carefully sampled and compared to the corresponding contralateral (healthy) core and penumbra regions at 6 and 24 h post PACAP38 or saline injections. Both reverse transcription-polymerase chain reaction (RT-PCR) and Western blotting were used to examine targeted gene expressions and the collapsin response mediator protein 2 (CRMP2) protein profiles, respectively. Clear differences in expression of genes and CRMP2 protein abundance and degradation product/short isoform was observed between ischemic core and penumbra and also compared to the contralateral healthy tissues after PACAP38 or saline treatment. Results indicate the importance of region-specific analyses to further identify, localize and functionally analyse target molecular factors for clarifying the neuroprotective function of PACAP38.

  17. PACAP38 Differentially Effects Genes and CRMP2 Protein Expression in Ischemic Core and Penumbra Regions of Permanent Middle Cerebral Artery Occlusion Model Mice Brain

    Directory of Open Access Journals (Sweden)

    Motohide Hori

    2014-09-01

    Full Text Available Pituitary adenylate-cyclase activating polypeptide (PACAP has neuroprotective and axonal guidance functions, but the mechanisms behind such actions remain unclear. Previously we examined effects of PACAP (PACAP38, 1 pmol injection intracerebroventrically in a mouse model of permanent middle cerebral artery occlusion (PMCAO along with control saline (0.9% NaCl injection. Transcriptomic and proteomic approaches using ischemic (ipsilateral brain hemisphere revealed differentially regulated genes and proteins by PACAP38 at 6 and 24 h post-treatment. However, as the ischemic hemisphere consisted of infarct core, penumbra, and non-ischemic regions, specificity of expression and localization of these identified molecular factors remained incomplete. This led us to devise a new experimental strategy wherein, ischemic core and penumbra were carefully sampled and compared to the corresponding contralateral (healthy core and penumbra regions at 6 and 24 h post PACAP38 or saline injections. Both reverse transcription-polymerase chain reaction (RT-PCR and Western blotting were used to examine targeted gene expressions and the collapsin response mediator protein 2 (CRMP2 protein profiles, respectively. Clear differences in expression of genes and CRMP2 protein abundance and degradation product/short isoform was observed between ischemic core and penumbra and also compared to the contralateral healthy tissues after PACAP38 or saline treatment. Results indicate the importance of region-specific analyses to further identify, localize and functionally analyse target molecular factors for clarifying the neuroprotective function of PACAP38.

  18. Independent evolution of the core and accessory gene sets in the genus Neisseria: insights gained from the genome of Neisseria lactamica isolate 020-06

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    White Brian

    2010-11-01

    Full Text Available Abstract Background The genus Neisseria contains two important yet very different pathogens, N. meningitidis and N. gonorrhoeae, in addition to non-pathogenic species, of which N. lactamica is the best characterized. Genomic comparisons of these three bacteria will provide insights into the mechanisms and evolution of pathogenesis in this group of organisms, which are applicable to understanding these processes more generally. Results Non-pathogenic N. lactamica exhibits very similar population structure and levels of diversity to the meningococcus, whilst gonococci are essentially recent descendents of a single clone. All three species share a common core gene set estimated to comprise around 1190 CDSs, corresponding to about 60% of the genome. However, some of the nucleotide sequence diversity within this core genome is particular to each group, indicating that cross-species recombination is rare in this shared core gene set. Other than the meningococcal cps region, which encodes the polysaccharide capsule, relatively few members of the large accessory gene pool are exclusive to one species group, and cross-species recombination within this accessory genome is frequent. Conclusion The three Neisseria species groups represent coherent biological and genetic groupings which appear to be maintained by low rates of inter-species horizontal genetic exchange within the core genome. There is extensive evidence for exchange among positively selected genes and the accessory genome and some evidence of hitch-hiking of housekeeping genes with other loci. It is not possible to define a 'pathogenome' for this group of organisms and the disease causing phenotypes are therefore likely to be complex, polygenic, and different among the various disease-associated phenotypes observed.

  19. Identification of a gene expression core signature for Duchenne Muscular Dystrophy (DMD) via integrative analysis reveals novel potential compounds for treatment

    KAUST Repository

    Ichim-Moreno, Norú

    2010-05-01

    Duchenne muscular dystrophy (DMD) is a recessive X-linked form of muscular dystrophy and one of the most prevalent genetic disorders of childhood. DMD is characterized by rapid progression of muscle degeneration, and ultimately death. Currently, glucocorticoids are the only available treatment for DMD, but they have been shown to result in serious side effects. The purpose of this research was to define a core signature of gene expression related to DMD via integrative analysis of mouse and human datasets. This core signature was subsequently used to screen for novel potential compounds that antagonistically affect the expression of signature genes. With this approach we were able to identify compounds that are 1) already used to treat DMD, 2) currently under investigation for treatment, and 3) so far unknown but promising candidates. Our study highlights the potential of meta-analyses through the combination of datasets to unravel previously unrecognized associations and reveal new relationships. © IEEE.

  20. Monitoring HSV-TK/ganciclovir cancer suicide gene therapy using CdTe/CdS core/shell quantum dots

    NARCIS (Netherlands)

    Shao, D.; Zeng, Q.; Fan, Z.; Li, J.; Zhang, M.; Zhang, Y.; Li, O.; Chen, L.; Kong, X.; Zhang, H.

    2012-01-01

    To be able to label a gene and monitor its migration are key important approaches for the clinical application of cancer suicide gene therapy. Photonic nanomaterials are introduced in this work. One of the most promised suicide genes - herpes simplex virus thymidine kinase (HSV-TK) gene - is

  1. Core Binding Factor β (CBFβ) and the Leukemogenic Fusion Protein CBFβ-Smooth Muscle Myosin Heavy Chain (SMMHC) Associate with Mitotic Chromosomes to Epigenetically Regulate Ribosomal Gene Expression*

    Science.gov (United States)

    Lopez-Camacho, Cesar; van Wijnen, Andre J.; Lian, Jane B.; Stein, Janet L.; Stein, Gary S.

    2014-01-01

    Mitotic bookmarking is an epigenetic control mechanism that sustains gene expression in progeny cells; it is often found in genes related to the maintenance of cellular phenotype and growth control. RUNX transcription factors regulate a broad spectrum of RNA Polymerase (Pol II) transcribed genes important for lineage commitment but also regulate RNA Polymerase I (Pol I) driven ribosomal gene expression, thus coordinating control of cellular identity and proliferation. In this study, using fluorescence microscopy and biochemical approaches we show that the principal RUNX co-factor, CBFβ, associates with nucleolar organizing regions (NORs) during mitosis to negatively regulate RUNX-dependent ribosomal gene expression. Of clinical relevance, we establish for the first time that the leukemogenic fusion protein CBFβ-SMMHC (smooth muscle myosin heavy chain) also associates with ribosomal genes in interphase chromatin and mitotic chromosomes to promote and epigenetically sustain regulation of ribosomal genes through RUNX factor interactions. Our results demonstrate that CBFβ contributes to the transcriptional regulation of ribosomal gene expression and provide further understanding of the epigenetic role of CBFβ-SMMHC in proliferation and maintenance of the leukemic phenotype. Background Runt-related transcription factors (RUNX) bookmark genes important for phenotype, but the mitotic behavior of RUNX cofactor, Core Binding Factor β (CBFβ) is unknown. Results CBFβ and leukemogenic fusion protein CBFβ-SMMHC associate with chromosomes during mitosis and regulate ribosomal genes. Conclusion CBFβ and CBFβ-SMMHC contribute to epigenetic control of ribosomal genes. Significance CBFβ-SMMHC alters regulation linking phenotypic control with cell growth, thereby promoting cancer. PMID:25079347

  2. Chronic Ethanol Consumption Disrupts the Core Molecular Clock and Diurnal Rhythms of Metabolic Genes in the Liver without Affecting the Suprachiasmatic Nucleus

    Science.gov (United States)

    Filiano, Ashley N.; Millender-Swain, Telisha; Johnson, Russell; Young, Martin E.; Gamble, Karen L.; Bailey, Shannon M.

    2013-01-01

    Chronic ethanol consumption disrupts several metabolic pathways including β-oxidation and lipid biosynthesis, facilitating the development of alcoholic fatty liver disease. Many of these same metabolic pathways are directly regulated by cell autonomous circadian clocks, and recent studies suggest that disruption of daily rhythms in metabolism contributes to multiple common cardiometabolic diseases (including non-alcoholic fatty liver disease). However, it is not known whether ethanol disrupts the core molecular clock in the liver, nor whether this, in turn, alters rhythms in lipid metabolism. Herein, we tested the hypothesis that chronic ethanol consumption disrupts the molecular circadian clock in the liver and potentially changes the diurnal expression patterns of lipid metabolism genes. Consistent with previous studies, male C57BL/6J mice fed an ethanol-containing diet exhibited higher levels of liver triglycerides compared to control mice, indicating hepatic steatosis. Further, the diurnal oscillations of core clock genes (Bmal1, Clock, Cry1, Cry2, Per1, and Per2) and clock-controlled genes (Dbp, Hlf, Nocturnin, Npas2, Rev-erbα, and Tef) were altered in livers from ethanol-fed mice. In contrast, ethanol had only minor effects on the expression of core clock genes in the suprachiasmatic nucleus (SCN). These results were confirmed in Per2Luciferase knock-in mice, in which ethanol induced a phase advance in PER2::LUC bioluminescence oscillations in liver, but not SCN. Further, there was greater variability in the phase of PER2::LUC oscillations in livers from ethanol-fed mice. Ethanol consumption also affected the diurnal oscillations of metabolic genes, including Adh1, Cpt1a, Cyp2e1, Pck1, Pdk4, Ppargc1a, Ppargc1b and Srebp1c, in the livers of C57BL/6J mice. In summary, chronic ethanol consumption alters the function of the circadian clock in liver. Importantly, these results suggest that chronic ethanol consumption, at levels sufficient to cause steatosis

  3. Photoenhanced gene transfection by a star-shaped polymer consisting of a porphyrin core and poly(L-lysine) dendron arms.

    Science.gov (United States)

    Ma, Dong; Zhao, Yi; Zhou, Xiao-Yan; Lin, Qian-Ming; Zhang, Yi; Lin, Jian-Tao; Xue, Wei

    2013-09-01

    A star-shaped polymer (PP-PLLD) consisting of a porphyrin (PP) core and poly(L-lysine) dendron arms (PLLD) is synthesized by the click reaction, and its ability to deliver pEGFP is investigated in this paper. It is found that PP-PLLD has a good buffer capacity and can form compact complexes with pEGFP. In vitro assay indicates that PP-PLLD shows photoenhanced gene transfection efficiency. PP-PLLD consisting of only third generation PLLD shows a higher transfected cell number than PEI under a Xe lamp at the N/P ratio of 20, and meanwhile shows a neglectable cytotoxicity to HeLa cells. Therefore, PP-PLLD with suited irradiation is a promising nontoxic and photoinducible effective gene delivery strategy, which should be encouraged in gene therapy. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Novel functional residues in the core domain of histone H2B regulate yeast gene expression and silencing and affect the response to DNA damage.

    Science.gov (United States)

    Kyriss, McKenna N M; Jin, Yi; Gallegos, Isaura J; Sanford, James A; Wyrick, John J

    2010-07-01

    Previous studies have identified novel modifications in the core fold domain of histone H2B, but relatively little is known about the function of these putative histone modification sites. We have mutated core modifiable residues that are conserved in Saccharomyces cerevisiae histone H2B and characterized the effects of the mutants on yeast silencing, gene expression, and the DNA damage response. We identified three histone H2B core modifiable residues as functionally important. We find that mutating H2B K49 in yeast confers a UV sensitivity phenotype, and we confirm that the homologous residue in human histone H2B is acetylated and methylated in human cells. Our results also indicate that mutating H2B K111 impairs the response to methyl methanesulfonate (MMS)-induced DNA lesions and disrupts telomeric silencing and Sir4 binding. In contrast, mutating H2B R102 enhances silencing at yeast telomeres and the HML silent mating loci and increases Sir4 binding to these regions. The H2B R102A mutant also represses the expression of endogenous genes adjacent to yeast telomeres, which is likely due to the ectopic spreading of the Sir complex in this mutant strain. We propose a structural model by which H2B R102 and K111 regulate the binding of the Sir complex to the nucleosome.

  5. Novel Functional Residues in the Core Domain of Histone H2B Regulate Yeast Gene Expression and Silencing and Affect the Response to DNA Damage ▿

    Science.gov (United States)

    Kyriss, McKenna N. M.; Jin, Yi; Gallegos, Isaura J.; Sanford, James A.; Wyrick, John J.

    2010-01-01

    Previous studies have identified novel modifications in the core fold domain of histone H2B, but relatively little is known about the function of these putative histone modification sites. We have mutated core modifiable residues that are conserved in Saccharomyces cerevisiae histone H2B and characterized the effects of the mutants on yeast silencing, gene expression, and the DNA damage response. We identified three histone H2B core modifiable residues as functionally important. We find that mutating H2B K49 in yeast confers a UV sensitivity phenotype, and we confirm that the homologous residue in human histone H2B is acetylated and methylated in human cells. Our results also indicate that mutating H2B K111 impairs the response to methyl methanesulfonate (MMS)-induced DNA lesions and disrupts telomeric silencing and Sir4 binding. In contrast, mutating H2B R102 enhances silencing at yeast telomeres and the HML silent mating loci and increases Sir4 binding to these regions. The H2B R102A mutant also represses the expression of endogenous genes adjacent to yeast telomeres, which is likely due to the ectopic spreading of the Sir complex in this mutant strain. We propose a structural model by which H2B R102 and K111 regulate the binding of the Sir complex to the nucleosome. PMID:20479120

  6. Lack of Association between Hepatitis C Virus core Gene Variation 70/91aa and Insulin Resistance

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    Letícia de Paula Scalioni

    2017-07-01

    Full Text Available The role of hepatitis C virus (HCV in insulin resistance (IR is not fully understood. The aim of this study was to determine the impact of amino acid (aa substitutions in the core region of HCV according to IR and to identify clinical and laboratory associations. Ninety-two treatment-naive HCV patients were recruited to determine laboratory data and blood cell count. IR was determined using Homeostasis Model Assessment (HOMA index where IR was defined as HOMA ≥2. HCV RNA load and genotype were determined by Abbott Real time HCV. HCV core region was determined by direct nucleotide sequencing. Bivariate analysis was conducted using HOMA IR ≥2 as a dependent factor. IR prevalence was 43.5% (n = 40, vitamin D sufficiency was found in 76.1% (n = 70 and 72.8% (n = 67 had advanced liver fibrosis. In the bivariate analyses, elevated values of γGT (p = 0.024 and fibrosis staging (p = 0.004 were associated with IR, but IR was not related to core mutations. The presence of glutamine in position 70 was associated with low vitamin D concentration (p = 0.005. In the multivariate analysis, no variable was independently associated with HOMA-IR. In conclusion, lack of association between IR and HCV core mutations in positions 70 and 91 suggests that genetic variability of this region has little impact on IR.

  7. Lack of Association between Hepatitis C Virus core Gene Variation 70/91aa and Insulin Resistance

    Science.gov (United States)

    Scalioni, Letícia de Paula; da Silva, Allan Peres; Miguel, Juliana Custódio; do Espírito Santo, Márcia Paschoal; Marques, Vanessa Alves; Brandão-Mello, Carlos Eduardo; Villela-Nogueira, Cristiane Alves; Lewis-Ximenez, Lia Laura; Lampe, Elisabeth; Villar, Livia Melo

    2017-01-01

    The role of hepatitis C virus (HCV) in insulin resistance (IR) is not fully understood. The aim of this study was to determine the impact of amino acid (aa) substitutions in the core region of HCV according to IR and to identify clinical and laboratory associations. Ninety-two treatment-naive HCV patients were recruited to determine laboratory data and blood cell count. IR was determined using Homeostasis Model Assessment (HOMA) index where IR was defined as HOMA ≥2. HCV RNA load and genotype were determined by Abbott Real time HCV. HCV core region was determined by direct nucleotide sequencing. Bivariate analysis was conducted using HOMA IR ≥2 as a dependent factor. IR prevalence was 43.5% (n = 40), vitamin D sufficiency was found in 76.1% (n = 70) and 72.8% (n = 67) had advanced liver fibrosis. In the bivariate analyses, elevated values of γGT (p = 0.024) and fibrosis staging (p = 0.004) were associated with IR, but IR was not related to core mutations. The presence of glutamine in position 70 was associated with low vitamin D concentration (p = 0.005). In the multivariate analysis, no variable was independently associated with HOMA-IR. In conclusion, lack of association between IR and HCV core mutations in positions 70 and 91 suggests that genetic variability of this region has little impact on IR. PMID:28753979

  8. Bioactive Core-Shell Nanofiber Hybrid Scaffold for Efficient Suicide Gene Transfection and Subsequent Time Resolved Delivery of Prodrug for Anticancer Therapy.

    Science.gov (United States)

    Sukumar, Uday Kumar; Packirisamy, Gopinath

    2015-08-26

    Nanofiber scaffold's ability to foster seemingly nonexistent interface with the cells enables them to effectively deliver various bioactive molecules to cells in the vicinity. Among such bioactive molecules, therapeutically active nucleic acid has been the most common candidate. In spite of such magnanimous efforts in this field, it remains a paradox that suicide gene delivery by nanofibers has never been sought for anticancer application. To investigate such a possibility, in the present work, a composite core-shell nanofiberous scaffold has been realized which could efficiently transfect suicide gene into cancer cells and simultaneously deliver prodrug, 5-Fluorocytosine (5-FC) in a controlled and sustained manner. The scaffold's ability to instigate apoptosis by suicide gene therapy in nonsmall lung cancer cells (A549) was ascertained at both phenotypic and genotypic levels. A cascade of events starting from suicide gene polyplex release from nanofibers, transfection, and expression of cytosine deaminase-uracil phosphoribosyltransferase (CD::UPRT) suicide gene by A549; subsequent prodrug release; and its metabolic conversion into toxic intermediates which finally culminates in host cells apoptosis has been monitored in a time-dependent manner. This work opens up new application avenues for nanofiber-based scaffolds which can effectively manage cancer prognosis.

  9. Comparative genomics defines the core genome of the growing N4-like phage genus and identifies N4-like Roseophage specific genes

    Directory of Open Access Journals (Sweden)

    Jacqueline Zoe-Munn Chan

    2014-10-01

    Full Text Available Two bacteriophages, RPP1 and RLP1, infecting members of the marine Roseobacter clade were isolated from seawater. Their linear genomes are 74.7 and 74.6 kb and encode 91 and 92 coding DNA sequences, respectively. Around 30% of these are homologous to genes found in Enterobacter phage N4. Comparative genomics of these two new Roseobacter phages and twenty-three other sequenced N4-like phages (three infecting members of the Roseobacter lineage and twenty infecting other Gammaproteobacteria revealed that N4-like phages share a core genome of 14 genes responsible for control of gene expression, replication and virion proteins. Phylogenetic analysis of these genes placed the five N4-like roseophages (RN4 into a distinct subclade. Analysis of the RN4 phage genomes revealed they share a further 19 genes of which nine are found exclusively in RN4 phages and four appear to have been acquired from their bacterial hosts. Proteomic analysis of the RPP1 and RLP1 virions identified a second structural module present in the RN4 phages similar to that found in the Pseudomonas N4-like phage LIT1. Searches of various metagenomic databases, included the GOS database, using CDS sequences from RPP1 suggests these phages are widely distributed in marine environments in particular in the open ocean environment.

  10. Genome-wide analysis of PHOSPHOLIPID:DIACYLGLYCEROL ACYLTRANSFERASE (PDAT) genes in plants reveals the eudicot-wide PDAT gene expansion and altered selective pressures acting on the core eudicot PDAT paralogs.

    Science.gov (United States)

    Pan, Xue; Peng, Fred Y; Weselake, Randall J

    2015-03-01

    PHOSPHOLIPID:DIACYLGLYCEROL ACYLTRANSFERASE (PDAT) is an enzyme that catalyzes the transfer of a fatty acyl moiety from the sn-2 position of a phospholipid to the sn-3-position of sn-1,2-diacylglyerol, thus forming triacylglycerol and a lysophospholipid. Although the importance of PDAT in triacylglycerol biosynthesis has been illustrated in some previous studies, the evolutionary relationship of plant PDATs has not been studied in detail. In this study, we investigated the evolutionary relationship of the PDAT gene family across the green plants using a comparative phylogenetic framework. We found that the PDAT candidate genes are present in all examined green plants, including algae, lowland plants (a moss and a lycophyte), monocots, and eudicots. Phylogenetic analysis revealed the evolutionary division of the PDAT gene family into seven major clades. The separation is supported by the conservation and variation in the gene structure, protein properties, motif patterns, and/or selection constraints. We further demonstrated that there is a eudicot-wide PDAT gene expansion, which appears to have been mainly caused by the eudicot-shared ancient gene duplication and subsequent species-specific segmental duplications. In addition, selection pressure analyses showed that different selection constraints have acted on three core eudicot clades, which might enable paleoduplicated PDAT paralogs to either become nonfunctionalized or develop divergent expression patterns during evolution. Overall, our study provides important insights into the evolution of the plant PDAT gene family and explores the evolutionary mechanism underlying the functional diversification among the core eudicot PDAT paralogs. © 2015 American Society of Plant Biologists. All Rights Reserved.

  11. HoxA-11 and FOXO1A cooperate to regulate decidual prolactin expression: towards inferring the core transcriptional regulators of decidual genes.

    Directory of Open Access Journals (Sweden)

    Vincent J Lynch

    Full Text Available BACKGROUND: During the menstrual cycle, the ovarian steroid hormones estrogen and progesterone control a dramatic transcriptional reprogramming of endometrial stromal cells (ESCs leading to a receptive state for blastocyst implantation and the establishment of pregnancy. A key marker gene of this decidualization process is the prolactin gene. Several transcriptional regulators have been identified that are essential for decidualization of ESCs, including the Hox genes HoxA-10 and HoxA-11, and the forkhead box gene FOXO1A. While previous studies have identified downstream target genes for HoxA-10 and FOXO1A, the role of HoxA-11 in decidualization has not been investigated. Here, we show that HoxA-11 is required for prolactin expression in decidualized ESC. While HoxA-11 alone is a repressor on the decidual prolactin promoter, it turns into an activator when combined with FOXO1A. Conversely, HoxA-10, which has been previously shown to associate with FOXO1A to upregulate decidual IGFBP-1 expression, is unable to upregulate PRL expression when co-expressed with FOXO1A. By co-immunoprecipitation and chromatin immunoprecipitation, we demonstrate physical association of HoxA-11 and FOXO1A, and binding of both factors to an enhancer region (-395 to -148 relative to the PRL transcriptional start site of the decidual prolactin promoter. Because FOXO1A is induced upon decidualization, it serves to assemble a decidual-specific transcriptional complex including HoxA-11. These data highlight cooperativity between numerous transcription factors to upregulate PRL in differentiating ESC, and suggest that this core set of transcription factors physically and functionally interact to drive the expression of a gene battery upregulated in differentiated ESC. In addition, the functional non-equivalence of HoxA-11 and HoxA-10 with respect to PRL regulation suggests that these transcription factors regulate distinct sets of target genes during decidualization.

  12. Proteomics Core

    Data.gov (United States)

    Federal Laboratory Consortium — Proteomics Core is the central resource for mass spectrometry based proteomics within the NHLBI. The Core staff help collaborators design proteomics experiments in a...

  13. The absence of core fucose up-regulates GnT-III and Wnt target genes: a possible mechanism for an adaptive response in terms of glycan function.

    Science.gov (United States)

    Kurimoto, Ayako; Kitazume, Shinobu; Kizuka, Yasuhiko; Nakajima, Kazuki; Oka, Ritsuko; Fujinawa, Reiko; Korekane, Hiroaki; Yamaguchi, Yoshiki; Wada, Yoshinao; Taniguchi, Naoyuki

    2014-04-25

    Glycans play key roles in a variety of protein functions under normal and pathological conditions, but several glycosyltransferase-deficient mice exhibit no or only mild phenotypes due to redundancy or compensation of glycan functions. However, we have only a limited understanding of the underlying mechanism for these observations. Our previous studies indicated that 70% of Fut8-deficient (Fut8(-/-)) mice that lack core fucose structure die within 3 days after birth, but the remainder survive for up to several weeks although they show growth retardation as well as emphysema. In this study, we show that, in mouse embryonic fibroblasts (MEFs) from Fut8(-/-) mice, another N-glycan branching structure, bisecting GlcNAc, is specifically up-regulated by enhanced gene expression of the responsible enzyme N-acetylglucosaminyltransferase III (GnT-III). As candidate target glycoproteins for bisecting GlcNAc modification, we confirmed that level of bisecting GlcNAc on β1-integrin and N-cadherin was increased in Fut8(-/-) MEFs. Moreover using mass spectrometry, glycan analysis of IgG1 in Fut8(-/-) mouse serum demonstrated that bisecting GlcNAc contents were also increased by Fut8 deficiency in vivo. As an underlying mechanism, we found that in Fut8(-/-) MEFs Wnt/β-catenin signaling is up-regulated, and an inhibitor against Wnt signaling was found to abrogate GnT-III expression, indicating that Wnt/β-catenin is involved in GnT-III up-regulation. Furthermore, various oxidative stress-related genes were also increased in Fut8(-/-) MEFs. These data suggest that Fut8(-/-) mice adapted to oxidative stress, both ex vivo and in vivo, by inducing various genes including GnT-III, which may compensate for the loss of core fucose functions.

  14. Inferring Gene Networks for Strains of Dehalococcoides Highlights Conserved Relationships between Genes Encoding Core Catabolic and Cell-Wall Structural Proteins.

    Directory of Open Access Journals (Sweden)

    Cresten B Mansfeldt

    Full Text Available The interpretation of high-throughput gene expression data for non-model microorganisms remains obscured because of the high fraction of hypothetical genes and the limited number of methods for the robust inference of gene networks. Therefore, to elucidate gene-gene and gene-condition linkages in the bioremediation-important genus Dehalococcoides, we applied a Bayesian inference strategy called Reverse Engineering/Forward Simulation (REFS™ on transcriptomic data collected from two organohalide-respiring communities containing different Dehalococcoides mccartyi strains: the Cornell University mixed community D2 and the commercially available KB-1® bioaugmentation culture. In total, 49 and 24 microarray datasets were included in the REFS™ analysis to generate an ensemble of 1,000 networks for the Dehalococcoides population in the Cornell D2 and KB-1® culture, respectively. Considering only linkages that appeared in the consensus network for each culture (exceeding the determined frequency cutoff of ≥ 60%, the resulting Cornell D2 and KB-1® consensus networks maintained 1,105 nodes (genes or conditions with 974 edges and 1,714 nodes with 1,455 edges, respectively. These consensus networks captured multiple strong and biologically informative relationships. One of the main highlighted relationships shared between these two cultures was a direct edge between the transcript encoding for the major reductive dehalogenase (tceA (D2 or vcrA (KB-1® and the transcript for the putative S-layer cell wall protein (DET1407 (D2 or KB1_1396 (KB-1®. Additionally, transcripts for two key oxidoreductases (a [Ni Fe] hydrogenase, Hup, and a protein with similarity to a formate dehydrogenase, "Fdh" were strongly linked, generalizing a strong relationship noted previously for Dehalococcoides mccartyi strain 195 to multiple strains of Dehalococcoides. Notably, the pangenome array utilized when monitoring the KB-1® culture was capable of resolving signals from

  15. Regulation of gene expression in the protozoan parasite Entamoeba invadens identification of core promoter elements and promoters with stage-specific expression patterns

    Science.gov (United States)

    Manna, Dipak; Ehrenkaufer, Gretchen M.; Singh, Upinder

    2014-01-01

    Developmental switching between life-cycle stages is a common feature among many pathogenic organisms. Entamoeba histolytica is an important human pathogen and is a leading parasitic cause of death globally. During its life cycle, Entamoeba converts between cysts (essential for disease transmission) and trophozoites (responsible for tissue invasion). Despite being central to its biology, the triggers that are involved in the developmental pathways of this parasite are not well understood. In order to define the transcriptional network associated with stage conversion we used Entamoeba invadens which serves as a model system for Entamoeba developmental biology, and performed RNA sequencing at different developmental time points . In this study RNA-Seq data was utilized to define basal transcriptional control elements as well as to identify promoters which regulate stage-specific gene expression patterns. We discovered that the 5’ and 3’ untranslated regions of E. invadens genes are short, a median of 20 nucleotides (nt) and 26 nt respectively. Bioinformatics analysis of DNA sequences proximate to the start and stop codons identified two conserved motifs: (i) E. invadens Core Promoter Motif - GAAC-Like (EiCPM-GL) (GAACTACAAA), and (ii) E. invadens 3’- U-Rich Motif (Ei3’-URM) (TTTGTT) in the 5’ and 3’ flanking regions, respectively. Electrophoretic mobility shift assays demonstrated that both motifs specifically bind nuclear protein(s) from E. invadens trophozoites. Additionally, we identified select genes with stage-specific expression patterns and analyzed the ability of each gene promoter to drive a luciferase reporter gene during the developmental cycle. This approach confirmed three trophozoite-specific, four encystation-specific and two excystation-specific promoters. This work lays the framework for use of stage-specific promoters to express proteins of interest in a particular life-cycle stage, adding to the molecular toolbox for genetic

  16. Regulation of gene expression in the protozoan parasite Entamoeba invadens: identification of core promoter elements and promoters with stage-specific expression patterns.

    Science.gov (United States)

    Manna, Dipak; Ehrenkaufer, Gretchen M; Singh, Upinder

    2014-10-01

    Developmental switching between life-cycle stages is a common feature among many pathogenic organisms. Entamoeba histolytica is an important human pathogen and is a leading parasitic cause of death globally. During its life cycle, Entamoeba converts between cysts (essential for disease transmission) and trophozoites (responsible for tissue invasion). Despite being central to its biology, the triggers that are involved in the developmental pathways of this parasite are not well understood. In order to define the transcriptional network associated with stage conversion we used Entamoeba invadens which serves as a model system for Entamoeba developmental biology, and performed RNA sequencing at different developmental time points. In this study RNA-Seq data was utilised to define basal transcriptional control elements as well as to identify promoters which regulate stage-specific gene expression patterns. We discovered that the 5' and 3' untranslated regions of E. invadens genes are short, a median of 20 nucleotides (nt) and 26 nt respectively. Bioinformatics analysis of DNA sequences proximate to the start and stop codons identified two conserved motifs: (i) E. invadens Core Promoter Motif - GAAC-Like (EiCPM-GL) (GAACTACAAA), and (ii) E. invadens 3'-U-Rich Motif (Ei3'-URM) (TTTGTT) in the 5' and 3' flanking regions, respectively. Electrophoretic mobility shift assays demonstrated that both motifs specifically bind nuclear protein(s) from E. invadens trophozoites. Additionally, we identified select genes with stage-specific expression patterns and analysed the ability of each gene promoter to drive a luciferase reporter gene during the developmental cycle. This approach confirmed three trophozoite-specific, four encystation-specific and two excystation-specific promoters. This work lays the framework for use of stage-specific promoters to express proteins of interest in a particular life-cycle stage, adding to the molecular toolbox for genetic manipulation of E

  17. Genome-Wide Transcriptional Profiling of Clostridium perfringens SM101 during Sporulation Extends the Core of Putative Sporulation Genes and Genes Determining Spore Properties and Germination Characteristics

    NARCIS (Netherlands)

    Xiao, Y.; Hijum, S.A.F.T. van; Abee, T.; Wells-Bennik, M.H.

    2015-01-01

    The formation of bacterial spores is a highly regulated process and the ultimate properties of the spores are determined during sporulation and subsequent maturation. A wide variety of genes that are expressed during sporulation determine spore properties such as resistance to heat and other adverse

  18. Genome-wide transcriptional profiling of Clostridium perfringens SM101 during sporulation extends the core of putative sporulation genes and genes determining spore properties and germination characteristics

    NARCIS (Netherlands)

    Xiao, Y.; Hijum, van S.A.F.T.; Abee, T.; Wells-Bennik, M.H.J.

    2015-01-01

    The formation of bacterial spores is a highly regulated process and the ultimate properties of the spores are determined during sporulation and subsequent maturation. A wide variety of genes that are expressed during sporulation determine spore properties such as resistance to heat and other adverse

  19. Influence of various stressors on the expression of core genes of the small interfering RNA pathway in the oriental fruit fly, Bactrocera dorsalis.

    Science.gov (United States)

    Xie, Yi-Fei; Niu, Jin-Zhi; Jiang, Xuan-Zhao; Yang, Wen-Jia; Shen, Guang-Mao; Wei, Dong; Smagghe, Guy; Wang, Jin-Jun

    2017-06-01

    RNA interference (RNAi)-based technology has emerged as a potential tool for controlling insect pests, however, previous studies found that the efficiency of RNAi in Bactrocera dorsalis was variable. In nature, insects often meet various challenges, such as pathogen infections, extreme temperatures, lack of nutrition and heavy metals. To better understand the association of the stressors with efficiency of RNAi, in the current study we tested the expression of three core genes, dicer2 (Bddcr2), r2d2 (Bdr2d2) and argonaute2 (Bdago2), of the small interfering RNA (siRNA) pathway of B. dorsalis upon various stressors. Our results showed that all three genes were upregulated by the infection of invertebrate iridescent virus 6, which suggested a function of the siRNA pathway against viral infection. The loading of FeCl3 could also increase the expression of Bddcr2. The treatments of Escherichia coli, extremely high (40°C) and low (0°C) temperatures, as well as starvation, could negatively influence the expression of Bddcr2 and/or Bdago2. In total, our results showed that various stressors could influence the expression of core components of B. dorsalis siRNA pathway. This highlights further speculation on the RNAi efficiency upon these stressors. Considering the complexity and variation of RNAi efficiency in different conditions, these results provide initial aspects in possible environmental stressors to influence the activity of the siRNA pathway, but the real impact of RNAi efficiency posed by these stressors requires further studies. © 2016 Institute of Zoology, Chinese Academy of Sciences.

  20. The Chp1–Tas3 core is a multifunctional platform critical for gene silencing by RITS

    Energy Technology Data Exchange (ETDEWEB)

    Schalch, Thomas; Job, Godwin; Shanker, Sreenath; Partridge, Janet F.; Joshua-Tor, Leemor

    2011-11-13

    RNA interference (RNAi) is critical for the assembly of heterochromatin at Schizosaccharomyces pombe centromeres. Central to this process is the RNA-induced initiation of transcriptional gene silencing (RITS) complex, which physically anchors small noncoding RNAs to chromatin. RITS includes Ago1, the chromodomain protein Chp1, and Tas3, which forms a bridge between Chp1 and Ago1. Chp1 is a large protein with no recognizable domains, apart from its chromodomain. Here we describe how the structured C-terminal half of Chp1 binds the Tas3 N-terminal domain, revealing the tight association of Chp1 and Tas3. The structure also shows a PIN domain at the C-terminal tip of Chp1 that controls subtelomeric transcripts through a post-transcriptional mechanism. We suggest that the Chp1–Tas3 complex provides a solid and versatile platform to recruit both RNAi-dependent and RNAi-independent gene-silencing pathways for locus-specific regulation of heterochromatin.

  1. Hepatitis B virus infection in children, adolescents, and their relatives: genotype distribution and precore and core gene mutations

    Directory of Open Access Journals (Sweden)

    Adriana Parise Compri

    2012-06-01

    Full Text Available INTRODUCTION:The objectives of this study were evaluate hepatitis B virus (HBV serological markers in children and adolescents followed up at the Child Institute of the Hospital das Clínicas, Faculdade de Medicina de São Paulo, Universidade de São Paulo; identify chronic HBV carriers and susceptible individuals in the intrafamilial environment; characterize HBV genotypes; and identify mutations in the patients and household contacts. METHODS: Ninety-five hepatitis B surface antigen-positive children aged <19 years and 118 household contacts were enrolled in this study. Commercial kits were used for the detection of serological markers, and PCR was used for genotyping. RESULTS: Hepatitis B e antigen (HBeAg was detected in 66.3% (63/95 of cases. Three of the 30 HBeAg-negative and anti-HBeAg-positive patients presented with precore mutations and 11 presented with mutations in the basal core promoter (BCP. Genotype A was identified in 39 (43.8% patients, genotype D in 45 (50.6%, and genotype C in 5 (5.6%. Of the 118 relatives, 40 were chronic HBV carriers, 52 presented with the anti-HBc marker, 19 were vaccinated, and 7 were susceptible. Among the relatives, genotypes A, D, and C were the most frequent. One parent presented with a precore mutation and 4 presented with BCP mutations. CONCLUSIONS: Genotypes A and D were the most frequent among children, adolescents, and their relatives. The high prevalence of HBV in the families showed the possibility of its intrafamilial transmission.

  2. Ice cores

    DEFF Research Database (Denmark)

    Svensson, Anders

    2014-01-01

    Ice cores from Antarctica, from Greenland, and from a number of smaller glaciers around the world yield a wealth of information on past climates and environments. Ice cores offer unique records on past temperatures, atmospheric composition (including greenhouse gases), volcanism, solar activity......, dustiness, and biomass burning, among others. In Antarctica, ice cores extend back more than 800,000 years before present (Jouzel et al. 2007), whereas. Greenland ice cores cover the last 130,000 years...

  3. Core and symbiotic genes reveal nine Mesorhizobium genospecies and three symbiotic lineages among the rhizobia nodulating Cicer canariense in its natural habitat (La Palma, Canary Islands).

    Science.gov (United States)

    Armas-Capote, Natalia; Pérez-Yépez, Juan; Martínez-Hidalgo, Pilar; Garzón-Machado, Víctor; Del Arco-Aguilar, Marcelino; Velázquez, Encarna; León-Barrios, Milagros

    2014-03-01

    Cicer canariense is a threatened perennial wild chickpea endemic to the Canary Islands. In this study, rhizobia that nodulate this species in its natural habitats on La Palma (Canary Islands) were characterised. The genetic diversity and phylogeny were estimated by RAPD profiles, 16S-RFLP analysis and sequencing of the rrs, recA, glnII and nodC genes. 16S-RFLP grouped the isolates within the Mesorhizobium genus and distinguished nine different ribotypes. Four branches included minority ribotypes (3-5 isolates), whereas another five contained the predominant ribotypes that clustered with reference strains of M. tianshanense/M. gobiense/M. metallidurans, M. caraganae, M. opportunistum, M. ciceri and M. tamadayense. The sequences confirmed the RFLP groupings but resolved additional internal divergence within the M. caraganae group and outlined several potential novel species. The RAPD profiles showed a high diversity at the infraspecific level, except in the M. ciceri group. The nodC phylogeny resolved three symbiotic lineages. A small group of isolates had sequences identical to those of symbiovar ciceri and were only detected in M. ciceri isolates. Another group of sequences represented a novel symbiotic lineage that was associated with two particular chromosomal backgrounds. However, nodC sequences closely related to symbiovar loti predominated in most isolates, and they were detected in several chromosomal backgrounds corresponding to up to nine Mesorhizobium lineages. The results indicated that C. canariense is a promiscuous legume that can be nodulated by several rhizobial species and symbiotypes, which means it will be important to determine the combination of core and symbiotic genes that produce the most effective symbiosis. Copyright © 2013 Elsevier GmbH. All rights reserved.

  4. Transformer core

    NARCIS (Netherlands)

    Mehendale, A.; Hagedoorn, Wouter; Lötters, Joost Conrad

    2008-01-01

    A transformer core includes a stack of a plurality of planar core plates of a magnetically permeable material, which plates each consist of a first and a second sub-part that together enclose at least one opening. The sub-parts can be fitted together via contact faces that are located on either side

  5. Transformer core

    NARCIS (Netherlands)

    Mehendale, A.; Hagedoorn, Wouter; Lötters, Joost Conrad

    2010-01-01

    A transformer core includes a stack of a plurality of planar core plates of a magnetically permeable material, which plates each consist of a first and a second sub-part that together enclose at least one opening. The sub-parts can be fitted together via contact faces that are located on either side

  6. Shifting the circadian rhythm of feeding in mice induces gastrointestinal, metabolic and immune alterations which are influenced by ghrelin and the core clock gene Bmal1.

    Science.gov (United States)

    Laermans, Jorien; Broers, Charlotte; Beckers, Kelly; Vancleef, Laurien; Steensels, Sandra; Thijs, Theo; Tack, Jan; Depoortere, Inge

    2014-01-01

    In our 24-hour society, an increasing number of people are required to be awake and active at night. As a result, the circadian rhythm of feeding is seriously compromised. To mimic this, we subjected mice to restricted feeding (RF), a paradigm in which food availability is limited to short and unusual times of day. RF induces a food-anticipatory increase in the levels of the hunger hormone ghrelin. We aimed to investigate whether ghrelin triggers the changes in body weight and gastric emptying that occur during RF. Moreover, the effect of genetic deletion of the core clock gene Bmal1 on these physiological adaptations was studied. Wild-type, ghrelin receptor knockout and Bmal1 knockout mice were fed ad libitum or put on RF with a normal or high-fat diet (HFD). Plasma ghrelin levels were measured by radioimmunoassay. Gastric contractility was studied in vitro in muscle strips and in vivo (13C breath test). Cytokine mRNA expression was quantified and infiltration of immune cells was assessed histologically. The food-anticipatory increase in plasma ghrelin levels induced by RF with normal chow was abolished in HFD-fed mice. During RF, body weight restoration was facilitated by ghrelin and Bmal1. RF altered cytokine mRNA expression levels and triggered contractility changes resulting in an accelerated gastric emptying, independent from ghrelin signaling. During RF with a HFD, Bmal1 enhanced neutrophil recruitment to the stomach, increased gastric IL-1α expression and promoted gastric contractility changes. This is the first study demonstrating that ghrelin and Bmal1 regulate the extent of body weight restoration during RF, whereas Bmal1 controls the type of inflammatory infiltrate and contractility changes in the stomach. Disrupting the circadian rhythm of feeding induces a variety of diet-dependent metabolic, immune and gastrointestinal alterations, which may explain the higher prevalence of obesity and immune-related gastrointestinal disorders among shift workers.

  7. Shifting the circadian rhythm of feeding in mice induces gastrointestinal, metabolic and immune alterations which are influenced by ghrelin and the core clock gene Bmal1.

    Directory of Open Access Journals (Sweden)

    Jorien Laermans

    Full Text Available BACKGROUND: In our 24-hour society, an increasing number of people are required to be awake and active at night. As a result, the circadian rhythm of feeding is seriously compromised. To mimic this, we subjected mice to restricted feeding (RF, a paradigm in which food availability is limited to short and unusual times of day. RF induces a food-anticipatory increase in the levels of the hunger hormone ghrelin. We aimed to investigate whether ghrelin triggers the changes in body weight and gastric emptying that occur during RF. Moreover, the effect of genetic deletion of the core clock gene Bmal1 on these physiological adaptations was studied. METHODS: Wild-type, ghrelin receptor knockout and Bmal1 knockout mice were fed ad libitum or put on RF with a normal or high-fat diet (HFD. Plasma ghrelin levels were measured by radioimmunoassay. Gastric contractility was studied in vitro in muscle strips and in vivo (13C breath test. Cytokine mRNA expression was quantified and infiltration of immune cells was assessed histologically. RESULTS: The food-anticipatory increase in plasma ghrelin levels induced by RF with normal chow was abolished in HFD-fed mice. During RF, body weight restoration was facilitated by ghrelin and Bmal1. RF altered cytokine mRNA expression levels and triggered contractility changes resulting in an accelerated gastric emptying, independent from ghrelin signaling. During RF with a HFD, Bmal1 enhanced neutrophil recruitment to the stomach, increased gastric IL-1α expression and promoted gastric contractility changes. CONCLUSIONS: This is the first study demonstrating that ghrelin and Bmal1 regulate the extent of body weight restoration during RF, whereas Bmal1 controls the type of inflammatory infiltrate and contractility changes in the stomach. Disrupting the circadian rhythm of feeding induces a variety of diet-dependent metabolic, immune and gastrointestinal alterations, which may explain the higher prevalence of obesity and

  8. Core BPEL

    DEFF Research Database (Denmark)

    Hallwyl, Tim; Højsgaard, Espen

    extensions. Combined with the fact that the language definition does not provide a formal semantics, it is an arduous task to work formally with the language (e.g. to give an implementation). In this paper we identify a core subset of the language, called Core BPEL, which has fewer and simpler constructs......, does not allow omissions, and does not contain ignorable elements. We do so by identifying syntactic sugar, including default values, and ignorable elements in WS-BPEL. The analysis results in a translation from the full language to the core subset. Thus, we reduce the effort needed for working...... formally with WS-BPEL, as one, without loss of generality, need only consider the much simpler Core BPEL. This report may also be viewed as an addendum to the WS-BPEL standard specification, which clarifies the WS-BPEL syntax and presents the essential elements of the language in a more concise way...

  9. Ice Cores

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Records of past temperature, precipitation, atmospheric trace gases, and other aspects of climate and environment derived from ice cores drilled on glaciers and ice...

  10. Core benefits

    National Research Council Canada - National Science Library

    Keith, Brian W

    2010-01-01

    This SPEC Kit explores the core employment benefits of retirement, and life, health, and other insurance -benefits that are typically decided by the parent institution and often have significant governmental regulation...

  11. Hollow Core?

    Science.gov (United States)

    Qiao, G. J.; Liu, J. F.; Wang, Yang; Wu, X. J.; Han, J. L.

    We carried out the Gaussian fitting to the profile of PSR B1237+25 and found that six components rather than five are necessary to make a good fit. In the central part, we found that the core emission is not filled pencil beam but is a small hollow cone. This implies that the impact angle could be $\\beta<0.5^\\circ$. The ``hollow core'' is in agreement with Inverse Compton Scattering model of radio pulsars.

  12. Improving the Prediction of Prostate Cancer Overall Survival by Supplementing Readily Available Clinical Data with Gene Expression Levels of IGFBP3 and F3 in Formalin-Fixed Paraffin Embedded Core Needle Biopsy Material.

    Science.gov (United States)

    Peng, Zhuochun; Andersson, Karl; Lindholm, Johan; Dethlefsen, Olga; Pramana, Setia; Pawitan, Yudi; Nistér, Monica; Nilsson, Sten; Li, Chunde

    2016-01-01

    A previously reported expression signature of three genes (IGFBP3, F3 and VGLL3) was shown to have potential prognostic value in estimating overall and cancer-specific survivals at diagnosis of prostate cancer in a pilot cohort study using freshly frozen Fine Needle Aspiration (FNA) samples. We carried out a new cohort study with 241 prostate cancer patients diagnosed from 2004-2007 with a follow-up exceeding 6 years in order to verify the prognostic value of gene expression signature in formalin fixed paraffin embedded (FFPE) prostate core needle biopsy tissue samples. The cohort consisted of four patient groups with different survival times and death causes. A four multiplex one-step RT-qPCR test kit, designed and optimized for measuring the expression signature in FFPE core needle biopsy samples, was used. In archive FFPE biopsy samples the expression differences of two genes (IGFBP3 and F3) were measured. The survival time predictions using the current clinical parameters only, such as age at diagnosis, Gleason score, PSA value and tumor stage, and clinical parameters supplemented with the expression levels of IGFBP3 and F3, were compared. When combined with currently used clinical parameters, the gene expression levels of IGFBP3 and F3 are improving the prediction of survival time as compared to using clinical parameters alone. The assessment of IGFBP3 and F3 gene expression levels in FFPE prostate cancer tissue would provide an improved survival prediction for prostate cancer patients at the time of diagnosis.

  13. Gene

    Data.gov (United States)

    U.S. Department of Health & Human Services — Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes,...

  14. Chimeric hepatitis B virus core particles with parts or copies of the hepatitis C virus core protein.

    OpenAIRE

    Yoshikawa, A.; Tanaka, T.; Hoshi, Y.; Kato, N; Tachibana, K; Iizuka, H; Machida, A; Okamoto, H.; Yamasaki, M; Miyakawa, Y

    1993-01-01

    Either parts or multiple copies of the core gene of hepatitis C virus (HCV) were fused to the 3' terminus of the hepatitis B virus (HBV) core gene with 34 codons removed. As many as four copies of HCV core protein (720 amino acids) were fused to the carboxy terminus of truncated HBV core protein (149 amino acids) without preventing the assembly of HBV core particles. Chimeric core particles were sandwiched between monoclonal antibody to HBV core and that to HCV core, thereby indicating that a...

  15. Identification of Y-box binding protein 1 as a core regulator of MEK/ERK pathway-dependent gene signatures in colorectal cancer cells.

    Directory of Open Access Journals (Sweden)

    Karsten Jürchott

    2010-12-01

    Full Text Available Transcriptional signatures are an indispensible source of correlative information on disease-related molecular alterations on a genome-wide level. Numerous candidate genes involved in disease and in factors of predictive, as well as of prognostic, value have been deduced from such molecular portraits, e.g. in cancer. However, mechanistic insights into the regulatory principles governing global transcriptional changes are lagging behind extensive compilations of deregulated genes. To identify regulators of transcriptome alterations, we used an integrated approach combining transcriptional profiling of colorectal cancer cell lines treated with inhibitors targeting the receptor tyrosine kinase (RTK/RAS/mitogen-activated protein kinase pathway, computational prediction of regulatory elements in promoters of co-regulated genes, chromatin-based and functional cellular assays. We identified commonly co-regulated, proliferation-associated target genes that respond to the MAPK pathway. We recognized E2F and NFY transcription factor binding sites as prevalent motifs in those pathway-responsive genes and confirmed the predicted regulatory role of Y-box binding protein 1 (YBX1 by reporter gene, gel shift, and chromatin immunoprecipitation assays. We also validated the MAPK-dependent gene signature in colorectal cancers and provided evidence for the association of YBX1 with poor prognosis in colorectal cancer patients. This suggests that MEK/ERK-dependent, YBX1-regulated target genes are involved in executing malignant properties.

  16. Functional Screening of Core Promoter Activity.

    Science.gov (United States)

    Even, Dan Y; Kedmi, Adi; Ideses, Diana; Juven-Gershon, Tamar

    2017-01-01

    The core promoter is the DNA sequence that recruits the basal transcription machinery and directs accurate initiation of transcription. It is an active contributor to gene expression that can be rationally designed to manipulate the levels of expression. Core promoter function can be analyzed using different experimental approaches. Here, we describe the qualitative and quantitative analysis of engineered core promoter functions using the EGFP reporter gene that is driven by distinct core promoters. Expression plasmids are transfected into different mammalian cell lines, and the resulting fluorescence is monitored by live cell imaging , as well as by flow cytometry. In order to verify that the transcriptional activity of the examined core promoters is indeed a function of their activity, as opposed to differences in DNA uptake, real-time quantitative PCR analysis is performed. Importantly, the described methodology for functional screening of core promoter activity has enabled the analysis of engineered potent core promoters for extended time periods.

  17. Lipofuscin: formation, effects and role of macroautophagy

    Directory of Open Access Journals (Sweden)

    Annika Höhn

    2013-01-01

    Full Text Available Oxidative stress plays a crucial role in the development of the aging process and age dependent diseases. Both are closely connected to disturbances of proteostasis by protein oxidation and an impairment of the proteasomal system. The final consequence is the accumulation of highly cross-linked undegradable aggregates such as lipofuscin. These aggregates of damaged proteins are detrimental to normal cell functions. Here we provide an overview about effect of these aggregates on the proteasomal system, followed by transcription factor activation and loss of cell viability. Furthermore, findings on the mechanism of radical genesis, proteasomal inhibition and the required components of lipofuscin formation were resumed.

  18. Conserved and Divergent Rhythms of Crassulacean Acid Metabolism-Related and Core Clock Gene Expression in the Cactus Opuntia ficus-indica1[C][W

    Science.gov (United States)

    Mallona, Izaskun; Egea-Cortines, Marcos; Weiss, Julia

    2011-01-01

    The cactus Opuntia ficus-indica is a constitutive Crassulacean acid metabolism (CAM) species. Current knowledge of CAM metabolism suggests that the enzyme phosphoenolpyruvate carboxylase kinase (PPCK) is circadian regulated at the transcriptional level, whereas phosphoenolpyruvate carboxylase (PEPC), malate dehydrogenase (MDH), NADP-malic enzyme (NADP-ME), and pyruvate phosphate dikinase (PPDK) are posttranslationally controlled. As little transcriptomic data are available from obligate CAM plants, we created an expressed sequence tag database derived from different organs and developmental stages. Sequences were assembled, compared with sequences in the National Center for Biotechnology Information nonredundant database for identification of putative orthologs, and mapped using Kyoto Encyclopedia of Genes and Genomes Orthology and Gene Ontology. We identified genes involved in circadian regulation and CAM metabolism for transcriptomic analysis in plants grown in long days. We identified stable reference genes for quantitative polymerase chain reaction and found that OfiSAND, like its counterpart in Arabidopsis (Arabidopsis thaliana), and OfiTUB are generally appropriate standards for use in the quantification of gene expression in O. ficus-indica. Three kinds of expression profiles were found: transcripts of OfiPPCK oscillated with a 24-h periodicity; transcripts of the light-active OfiNADP-ME and OfiPPDK genes adapted to 12-h cycles, while transcript accumulation patterns of OfiPEPC and OfiMDH were arrhythmic. Expression of the circadian clock gene OfiTOC1, similar to Arabidopsis, oscillated with a 24-h periodicity, peaking at night. Expression of OfiCCA1 and OfiPRR9, unlike in Arabidopsis, adapted best to a 12-h rhythm, suggesting that circadian clock gene interactions differ from those of Arabidopsis. Our results indicate that the evolution of CAM metabolism could be the result of modified circadian regulation at both the transcriptional and posttranscriptional

  19. Conserved and divergent rhythms of crassulacean acid metabolism-related and core clock gene expression in the cactus Opuntia ficus-indica.

    Science.gov (United States)

    Mallona, Izaskun; Egea-Cortines, Marcos; Weiss, Julia

    2011-08-01

    The cactus Opuntia ficus-indica is a constitutive Crassulacean acid metabolism (CAM) species. Current knowledge of CAM metabolism suggests that the enzyme phosphoenolpyruvate carboxylase kinase (PPCK) is circadian regulated at the transcriptional level, whereas phosphoenolpyruvate carboxylase (PEPC), malate dehydrogenase (MDH), NADP-malic enzyme (NADP-ME), and pyruvate phosphate dikinase (PPDK) are posttranslationally controlled. As little transcriptomic data are available from obligate CAM plants, we created an expressed sequence tag database derived from different organs and developmental stages. Sequences were assembled, compared with sequences in the National Center for Biotechnology Information nonredundant database for identification of putative orthologs, and mapped using Kyoto Encyclopedia of Genes and Genomes Orthology and Gene Ontology. We identified genes involved in circadian regulation and CAM metabolism for transcriptomic analysis in plants grown in long days. We identified stable reference genes for quantitative polymerase chain reaction and found that OfiSAND, like its counterpart in Arabidopsis (Arabidopsis thaliana), and OfiTUB are generally appropriate standards for use in the quantification of gene expression in O. ficus-indica. Three kinds of expression profiles were found: transcripts of OfiPPCK oscillated with a 24-h periodicity; transcripts of the light-active OfiNADP-ME and OfiPPDK genes adapted to 12-h cycles, while transcript accumulation patterns of OfiPEPC and OfiMDH were arrhythmic. Expression of the circadian clock gene OfiTOC1, similar to Arabidopsis, oscillated with a 24-h periodicity, peaking at night. Expression of OfiCCA1 and OfiPRR9, unlike in Arabidopsis, adapted best to a 12-h rhythm, suggesting that circadian clock gene interactions differ from those of Arabidopsis. Our results indicate that the evolution of CAM metabolism could be the result of modified circadian regulation at both the transcriptional and posttranscriptional

  20. Aldosterone synthase gene polymorphism in alimentary obesity, metabolic syndrome components, some secondary forms of arterial hypertension, pathology of the adrenals glands core (literature review

    Directory of Open Access Journals (Sweden)

    S.N. Koval

    2017-08-01

    Full Text Available Hormonal factors of adrenal origin belong to the pathophysiological mechanisms of the formation and progression of arterial hypertension (AH and should be consi­dered while developing differentiated approaches to the treatment and prevention of hypertensive states, their primary, secondary and resistant forms. The first thing we should point up is aldosterone (AL, enzyme aldosterone synthase (AS, which takes a direct part in the formation of this hormone, as well as gene polymorphisms of AS, which have not only molecular genetic, but also differential diagnostic and therapeutic significance for secondary forms of arterial hypertension, abdominal obesity (AO, metabolic syndrome (MS, adrenal pathology and other endocrine disorders. AL is a steroid (mineralocorticoid hormone of the adrenal cortex, which is synthesized from cholesterol (CH, mainly in the glomerular zone of the adrenal glands, is released under the action of angiotensin II (A II and potassium ions (K+. AL acti­vity is mediated through the corresponding mineralocorticoid receptors (MKR. The particular importance in AH and MS development belongs to AL activation and MKR density in adipocytes, this phenomenon is accompanied by increased expression of pro-inflammatory cytokines, leptin, an adipogenic effect, and the inhibition of MCR activity is accompanied by increased production of adiponectin, which is more pronounced in patients with AH. Aldosterone synthase, a mitochondrial human enzyme encoded by the CYP11B2 gene (cytochrome P450, family 11, subfamily B, polypeptide 2 is located on the 8th chromosome. AS belongs to the superfamily of cytochrome P450 and regulates the synthesis of AL hormone. The CYP11B2 gene encodes the key enzyme for the synthesis of AL 18-hydroxylase. In scientific papers, single nucleotide polymorphism (SNP of AS gene is often studied, such as 5312T, Intron 2, Lys-173/Arg; T-344C, 3097 C/A. 227 SNP of the AS gene were identified in different

  1. The − 5 A/G single-nucleotide polymorphism in the core promoter region of MT2A and its effect on allele-specific gene expression and Cd, Zn and Cu levels in laryngeal cancer

    Energy Technology Data Exchange (ETDEWEB)

    Starska, Katarzyna, E-mail: katarzyna.starska@umed.lodz.pl [I Department of Otolaryngology and Laryngological Oncology, Medical University of Łódź, Kopcinskiego 22, 90-153 Łódź (Poland); Krześlak, Anna; Forma, Ewa [Department of Cytobiochemistry, University of Łódź, Pomorska 142/143, 90-236 Łódź (Poland); Olszewski, Jurek [II Department of Otolaryngology and Laryngological Oncology, Medical University of Łódź, Żeromskiego 113, 90-549 Łódź (Poland); Morawiec-Sztandera, Alina [Department of Head and Neck Surgery, Medical University of Łódź, Paderewskiego 4, 93-509 Łódź (Poland); Aleksandrowicz, Paweł [Department of Otolaryngology and Laryngological Oncology, Medical University of Lublin, Jaczewskiego 8, 20-954 Lublin (Poland); Lewy-Trenda, Iwona [Department of Pathology, Medical University of Łódź, Pomorska 251, 92-213 Łódź (Poland); and others

    2014-10-15

    Metallothioneins (MTs) are low molecular weight, cysteine-rich heavy metal-binding proteins which participate in the mechanisms of Zn homeostasis, and protect against toxic metals. MTs contain metal-thiolate cluster groups and suppress metal toxicity by binding to them. The aim of this study was to determine the − 5 A/G (rs28366003) single-nucleotide polymorphism (SNP) in the core promoter region of the MT2A gene and to investigate its effect on allele-specific gene expression and Cd, Zn and Cu content in squamous cell laryngeal cancer (SCC) and non-cancerous laryngeal mucosa (NCM) as a control. The MT2A promoter region − 5 A/G SNP was determined by restriction fragment length polymorphism using 323 SCC and 116 NCM. MT2A gene analysis was performed by quantitative real-time PCR. The frequency of A allele carriage was 94.2% and 91.8% in SCC and NCM, respectively, while G allele carriage was detected in 5.8% and 8.2% of SCC and NCM samples, respectively. As a result, a significant association was identified between the − 5 A/G SNP in the MT2A gene with mRNA expression in both groups. Metal levels were analyzed by flame atomic absorption spectrometry. The significant differences were identified between A/A and both the A/G and G/G genotypes, with regard to the concentration of the contaminating metal. The Spearman rank correlation results showed that the MT2A expression and Cd, Zn, Cu levels were negatively correlated. Results obtained in this study suggest that − 5 A/G SNP in MT2A gene may have an effect on allele-specific gene expression and accumulation of metal levels in laryngeal cancer. - Highlights: • MT2A gene expression and metal content in laryngeal cancer tissues • Association between SNP (rs28366003) and expression of MT2A • Significant associations between the SNP and Cd, Zn and Cu levels • Negative correlation between MT2A gene expression and Cd, Zn and Cu levels.

  2. The core regulatory network in human cells.

    Science.gov (United States)

    Kim, Man-Sun; Kim, Dongsan; Kang, Nam Sook; Kim, Jeong-Rae

    2017-03-04

    In order to discover the common characteristics of various cell types in the human body, many researches have been conducted to find the set of genes commonly expressed in various cell types and tissues. However, the functional characteristics of a cell is determined by the complex regulatory relationships among the genes rather than by expressed genes themselves. Therefore, it is more important to identify and analyze a core regulatory network where all regulatory relationship between genes are active across all cell types to uncover the common features of various cell types. Here, based on hundreds of tissue-specific gene regulatory networks constructed by recent genome-wide experimental data, we constructed the core regulatory network. Interestingly, we found that the core regulatory network is organized by simple cascade and has few complex regulations such as feedback or feed-forward loops. Moreover, we discovered that the regulatory links from genes in the core regulatory network to genes in the peripheral regulatory network are much more abundant than the reverse direction links. These results suggest that the core regulatory network locates at the top of regulatory network and plays a role as a 'hub' in terms of information flow, and the information that is common to all cells can be modified to achieve the tissue-specific characteristics through various types of feedback and feed-forward loops in the peripheral regulatory networks. We also found that the genes in the core regulatory network are evolutionary conserved, essential and non-disease, non-druggable genes compared to the peripheral genes. Overall, our study provides an insight into how all human cells share a common function and generate tissue-specific functional traits by transmitting and processing information through regulatory network. Copyright © 2017 Elsevier Inc. All rights reserved.

  3. Animal MRI Core

    Data.gov (United States)

    Federal Laboratory Consortium — The Animal Magnetic Resonance Imaging (MRI) Core develops and optimizes MRI methods for cardiovascular imaging of mice and rats. The Core provides imaging expertise,...

  4. Role of cardiotrophin-1 in the regulation of metabolic circadian rhythms and adipose core clock genes in mice and characterization of 24-h circulating CT-1 profiles in normal-weight and overweight/obese subjects.

    Science.gov (United States)

    López-Yoldi, Miguel; Stanhope, Kimber L; Garaulet, Marta; Chen, X Guoxia; Marcos-Gómez, Beatriz; Carrasco-Benso, María Paz; Santa Maria, Eva M; Escoté, Xavier; Lee, Vivien; Nunez, Marinelle V; Medici, Valentina; Martínez-Ansó, Eduardo; Sáinz, Neira; Huerta, Ana E; Laiglesia, Laura M; Prieto, Jesús; Martínez, J Alfredo; Bustos, Matilde; Havel, Peter J; Moreno-Aliaga, Maria J

    2017-04-01

    Cardiotrophin (CT)-1 is a regulator of glucose and lipid homeostasis. In the present study, we analyzed whether CT-1 also acts to peripherally regulate metabolic rhythms and adipose tissue core clock genes in mice. Moreover, the circadian pattern of plasma CT-1 levels was evaluated in normal-weight and overweight subjects. The circadian rhythmicity of oxygen consumption rate (Vo2) was disrupted in aged obese CT-1-deficient (CT-1(-/-)) mice (12 mo). Although circadian rhythms of Vo2 were conserved in young lean CT-1(-/-) mice (2 mo), CT-1 deficiency caused a phase shift of the acrophase. Most of the clock genes studied (Clock, Bmal1, and Per2) displayed a circadian rhythm in adipose tissue of both wild-type (WT) and CT-1(-/-) mice. However, the pattern was altered in CT-1(-/-) mice toward a lower percentage of the rhythm or lower amplitude, especially for Bmal1 and Clock. Moreover, CT-1 mRNA levels in adipose tissue showed significant circadian fluctuations in young WT mice. In humans, CT-1 plasma profile exhibited a 24-h circadian rhythm in normal-weight but not in overweight subjects. The 24-h pattern of CT-1 was characterized by a pronounced increase during the night (from 02:00 to 08:00). These observations suggest a potential role for CT-1 in the regulation of metabolic circadian rhythms.-López-Yoldi, M., Stanhope, K. L., Garaulet, M., Chen, X. G., Marcos-Gómez, B., Carrasco-Benso, M. P., Santa Maria, E. M., Escoté, X., Lee, V., Nunez, M. V., Medici, V., Martínez-Ansó, E., Sáinz, N., Huerta, A. E., Laiglesia, L. M., Prieto, J., Martínez, J. A., Bustos, M., Havel, P. J., Moreno-Aliaga, M. J. Role of cardiotrophin-1 in the regulation of metabolic circadian rhythms and adipose core clock genes in mice and characterization of 24-h circulating CT-1 profiles in normal-weight and overweight/obese subjects. © FASEB.

  5. Genome-Wide Mapping Targets of the Metazoan Chromatin Remodeling Factor NURF Reveals Nucleosome Remodeling at Enhancers, Core Promoters and Gene Insulators.

    Directory of Open Access Journals (Sweden)

    So Yeon Kwon

    2016-04-01

    Full Text Available NURF is a conserved higher eukaryotic ISWI-containing chromatin remodeling complex that catalyzes ATP-dependent nucleosome sliding. By sliding nucleosomes, NURF is able to alter chromatin dynamics to control transcription and genome organization. Previous biochemical and genetic analysis of the specificity-subunit of Drosophila NURF (Nurf301/Enhancer of Bithorax (E(bx has defined NURF as a critical regulator of homeotic, heat-shock and steroid-responsive gene transcription. It has been speculated that NURF controls pathway specific transcription by co-operating with sequence-specific transcription factors to remodel chromatin at dedicated enhancers. However, conclusive in vivo demonstration of this is lacking and precise regulatory elements targeted by NURF are poorly defined. To address this, we have generated a comprehensive map of in vivo NURF activity, using MNase-sequencing to determine at base pair resolution NURF target nucleosomes, and ChIP-sequencing to define sites of NURF recruitment. Our data show that, besides anticipated roles at enhancers, NURF interacts physically and functionally with the TRF2/DREF basal transcription factor to organize nucleosomes downstream of active promoters. Moreover, we detect NURF remodeling and recruitment at distal insulator sites, where NURF functionally interacts with and co-localizes with DREF and insulator proteins including CP190 to establish nucleosome-depleted domains. This insulator function of NURF is most apparent at subclasses of insulators that mark the boundaries of chromatin domains, where multiple insulator proteins co-associate. By visualizing the complete repertoire of in vivo NURF chromatin targets, our data provide new insights into how chromatin remodeling can control genome organization and regulatory interactions.

  6. k -core covers and the core

    NARCIS (Netherlands)

    Sanchez-Rodriguez, E.; Borm, P.; Estevez Fernandez, M.A.; Fiestras-Janeiro, M.G.; Mosquera, M.A.

    2015-01-01

    This paper extends the notion of individual minimal rights for a transferable utility game (TU-game) to coalitional minimal rights using minimal balanced families of a specific type, thus defining a corresponding minimal rights game. It is shown that the core of a TU-game coincides with the core of

  7. k-core covers and the core

    NARCIS (Netherlands)

    Sanchez-Rodriguez, E.; Borm, Peter; Estevez-Fernandez, A.; Fiestras-Janeiro, G.; Mosquera, M.A.

    This paper extends the notion of individual minimal rights for a transferable utility game (TU-game) to coalitional minimal rights using minimal balanced families of a specific type, thus defining a corresponding minimal rights game. It is shown that the core of a TU-game coincides with the core of

  8. Multi-core Microprocessors

    Indian Academy of Sciences (India)

    programming and computer fundamentals. His current research interests are parallel computing and history of computing. Multi-core microprocessor is an interconnected set of inde- pendent processors called cores integrated on a single sili- con chip. These processing cores communicate and cooperate with one another ...

  9. Core Competence and Education.

    Science.gov (United States)

    Holmes, Gary; Hooper, Nick

    2000-01-01

    Outlines the concept of core competence and applies it to postcompulsory education in the United Kingdom. Adopts an educational perspective that suggests accreditation as the core competence of universities. This economic approach suggests that the market trend toward lifetime learning might best be met by institutions developing a core competence…

  10. The Hepatitis C Virus Core Protein Inhibits Adipose Triglyceride Lipase (ATGL)-mediated Lipid Mobilization and Enhances the ATGL Interaction with Comparative Gene Identification 58 (CGI-58) and Lipid Droplets*

    Science.gov (United States)

    Camus, Gregory; Schweiger, Martina; Herker, Eva; Harris, Charles; Kondratowicz, Andrew S.; Tsou, Chia-Lin; Farese, Robert V.; Herath, Kithsiri; Previs, Stephen F.; Roddy, Thomas P.; Pinto, Shirly; Zechner, Rudolf; Ott, Melanie

    2014-01-01

    Liver steatosis is a common health problem associated with hepatitis C virus (HCV) and an important risk factor for the development of liver fibrosis and cancer. Steatosis is caused by triglycerides (TG) accumulating in lipid droplets (LDs), cellular organelles composed of neutral lipids surrounded by a monolayer of phospholipids. The HCV nucleocapsid core localizes to the surface of LDs and induces steatosis in cultured cells and mouse livers by decreasing intracellular TG degradation (lipolysis). Here we report that core at the surface of LDs interferes with the activity of adipose triglyceride lipase (ATGL), the key lipolytic enzyme in the first step of TG breakdown. Expressing core in livers or mouse embryonic fibroblasts of ATGL−/− mice no longer decreases TG degradation as observed in LDs from wild-type mice, supporting the model that core reduces lipolysis by engaging ATGL. Core must localize at LDs to inhibit lipolysis, as ex vivo TG hydrolysis is impaired in purified LDs coated with core but not when free core is added to LDs. Coimmunoprecipitation experiments revealed that core does not directly interact with the ATGL complex but, unexpectedly, increased the interaction between ATGL and its activator CGI-58 as well as the recruitment of both proteins to LDs. These data link the anti-lipolytic activity of the HCV core protein with altered ATGL binding to CGI-58 and the enhanced association of both proteins with LDs. PMID:25381252

  11. Core stability exercise principles.

    Science.gov (United States)

    Akuthota, Venu; Ferreiro, Andrea; Moore, Tamara; Fredericson, Michael

    2008-02-01

    Core stability is essential for proper load balance within the spine, pelvis, and kinetic chain. The so-called core is the group of trunk muscles that surround the spine and abdominal viscera. Abdominal, gluteal, hip girdle, paraspinal, and other muscles work in concert to provide spinal stability. Core stability and its motor control have been shown to be imperative for initiation of functional limb movements, as needed in athletics. Sports medicine practitioners use core strengthening techniques to improve performance and prevent injury. Core strengthening, often called lumbar stabilization, also has been used as a therapeutic exercise treatment regimen for low back pain conditions. This article summarizes the anatomy of the core, the progression of core strengthening, the available evidence for its theoretical construct, and its efficacy in musculoskeletal conditions.

  12. HYDRATE CORE DRILLING TESTS

    Energy Technology Data Exchange (ETDEWEB)

    John H. Cohen; Thomas E. Williams; Ali G. Kadaster; Bill V. Liddell

    2002-11-01

    The ''Methane Hydrate Production from Alaskan Permafrost'' project is a three-year endeavor being conducted by Maurer Technology Inc. (MTI), Noble, and Anadarko Petroleum, in partnership with the U.S. DOE National Energy Technology Laboratory (NETL). The project's goal is to build on previous and ongoing R&D in the area of onshore hydrate deposition. The project team plans to design and implement a program to safely and economically drill, core and produce gas from arctic hydrates. The current work scope includes drilling and coring one well on Anadarko leases in FY 2003 during the winter drilling season. A specially built on-site core analysis laboratory will be used to determine some of the physical characteristics of the hydrates and surrounding rock. Prior to going to the field, the project team designed and conducted a controlled series of coring tests for simulating coring of hydrate formations. A variety of equipment and procedures were tested and modified to develop a practical solution for this special application. This Topical Report summarizes these coring tests. A special facility was designed and installed at MTI's Drilling Research Center (DRC) in Houston and used to conduct coring tests. Equipment and procedures were tested by cutting cores from frozen mixtures of sand and water supported by casing and designed to simulate hydrate formations. Tests were conducted with chilled drilling fluids. Tests showed that frozen core can be washed out and reduced in size by the action of the drilling fluid. Washing of the core by the drilling fluid caused a reduction in core diameter, making core recovery very difficult (if not impossible). One successful solution was to drill the last 6 inches of core dry (without fluid circulation). These tests demonstrated that it will be difficult to capture core when drilling in permafrost or hydrates without implementing certain safeguards. Among the coring tests was a simulated hydrate

  13. Sediment Core Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — FUNCTION: Provides instrumentation and expertise for physical and geoacoustic characterization of marine sediments.DESCRIPTION: The multisensor core logger measures...

  14. Adaptive core simulation

    Science.gov (United States)

    Abdel-Khalik, Hany Samy

    The work presented in this thesis is a continuation of a master's thesis research project conducted by the author to gain insight into the applicability of inverse methods to developing adaptive simulation capabilities for core physics problems. Use of adaptive simulation is intended to improve the fidelity and robustness of important core attributes predictions such as core power distribution, thermal margins and core reactivity. Adaptive simulation utilizes a selected set of past and current reactor measurements of reactor observables, i.e. in-core instrumentations readings, to adapt the simulation in a meaningful way. A meaningful adaption will result in high fidelity and robust adapted core simulators models. To perform adaption, we propose an inverse theory approach in which the multitudes of input data to core simulators, i.e. reactor physics and thermal-hydraulic data, are to be adjusted to improve agreement with measured observables while keeping core simulators models unadapted. At a first glance, devising such adaption for typical core simulators models would render the approach impractical. This follows, since core simulators are based on very demanding computational models, i.e. based on complex physics models with millions of input data and output observables. This would spawn not only several prohibitive challenges but also numerous disparaging concerns. The challenges include the computational burdens of the sensitivity-type calculations required to construct Jacobian operators for the core simulators models. Also, the computational burdens of the uncertainty-type calculations required to estimate the uncertainty information of core simulators input data presents a demanding challenge. The concerns however are mainly related to the reliability of the adjusted input data. We demonstrate that the power of our proposed approach is mainly driven by taking advantage of this unfavorable situation. Our contribution begins with the realization that to obtain

  15. Core physics experiment of 100% MOX core: MISTRAL

    Energy Technology Data Exchange (ETDEWEB)

    Yamamoto, T.; Matsu-ura, H.; Ueji, M. [Nuclear Power Engineering Corp., Tokyo (Japan); Cathalau, S.; Cabrillat, J.C.; Chauvin, J.P.; Finck, P.J.; Fougeras, P.; Flamenbaum, G.

    1997-12-31

    An extensive experimental program, MISTRAL, was undertaken in the EOLE critical facility of CEA in order to measure the main core physics parameters of 100% MOX loaded cores of light water reactors. The experimental program comprises four core configurations with high moderator to fuel ratio, including three homogeneous cores and one PWR type mock-up core. This paper presents the experiment of the first homogeneous core of uranium fuel as a reference core of the MOX cores and a part of the experiment of the second core, a 100% MOX homogeneous core. (author)

  16. Can Psychiatric Rehabilitation Be Core to CORE?

    Science.gov (United States)

    Olney, Marjorie F.; Gill, Kenneth J.

    2016-01-01

    Purpose: In this article, we seek to determine whether psychiatric rehabilitation principles and practices have been more fully incorporated into the Council on Rehabilitation Education (CORE) standards, the extent to which they are covered in four rehabilitation counseling "foundations" textbooks, and how they are reflected in the…

  17. Core/shell nanoparticles in biomedical applications.

    Science.gov (United States)

    Chatterjee, Krishnendu; Sarkar, Sreerupa; Jagajjanani Rao, K; Paria, Santanu

    2014-07-01

    Nanoparticles have several exciting applications in different areas and biomedial field is not an exception of that because of their exciting performance in bioimaging, targeted drug and gene delivery, sensors, and so on. It has been found that among several classes of nanoparticles core/shell is most promising for different biomedical applications because of several advantages over simple nanoparticles. This review highlights the development of core/shell nanoparticles-based biomedical research during approximately past two decades. Applications of different types of core/shell nanoparticles are classified in terms of five major aspects such as bioimaging, biosensor, targeted drug delivery, DNA/RNA interaction, and targeted gene delivery. Copyright © 2013 Elsevier B.V. All rights reserved.

  18. Lunar Core and Tides

    Science.gov (United States)

    Williams, J. G.; Boggs, D. H.; Ratcliff, J. T.

    2004-01-01

    Variations in rotation and orientation of the Moon are sensitive to solid-body tidal dissipation, dissipation due to relative motion at the fluid-core/solid-mantle boundary, and tidal Love number k2 [1,2]. There is weaker sensitivity to flattening of the core-mantle boundary (CMB) [2,3,4] and fluid core moment of inertia [1]. Accurate Lunar Laser Ranging (LLR) measurements of the distance from observatories on the Earth to four retroreflector arrays on the Moon are sensitive to lunar rotation and orientation variations and tidal displacements. Past solutions using the LLR data have given results for dissipation due to solid-body tides and fluid core [1] plus Love number [1-5]. Detection of CMB flattening, which in the past has been marginal but improving [3,4,5], now seems significant. Direct detection of the core moment has not yet been achieved.

  19. The t-core of an s-core

    OpenAIRE

    Fayers, Matthew

    2011-01-01

    We consider the $t$-core of an $s$-core partition, when $s$ and $t$ are coprime positive integers. Olsson has shown that the $t$-core of an $s$-core is again an $s$-core, and we examine certain actions of the affine symmetric group on $s$-cores which preserve the $t$-core of an $s$-core. Along the way, we give a new proof of Olsson's result. We also give a new proof of a result of Vandehey, showing that there is a simultaneous $s$- and $t$-core which contains all others.

  20. Multifunction of autophagy-related genes in filamentous fungi.

    Science.gov (United States)

    Khan, Irshad Ali; Lu, Jian-Ping; Liu, Xiao-Hong; Rehman, Abdur; Lin, Fu-Cheng

    2012-06-20

    Autophagy (macroautophagy), a highly conserved eukaryotic mechanism, is a non-selective degradation process, helping to maintain a balance between the synthesis, degradation and subsequent recycling of macromolecules to overcome various stress conditions. The term autophagy denotes any cellular process which involves the delivery of cytoplasmic material to the lysosome for degradation. Autophagy, in filamentous fungi plays a critical role during cellular development and pathogenicity. Autophagy, like the mitogen-activated protein (MAP) kinase cascade and nutrient-sensing cyclic AMP (cAMP) pathway, is also an important process for appressorium turgor accumulation in order to penetrate the leaf surface of host plant and destroy the plant defense. Yeast, an autophagy model, has been used to compare the multi-valued functions of ATG (autophagy-related genes) in different filamentous fungi. The autophagy machinery in both yeast and filamentous fungi is controlled by Tor kinase and both contain two distinct phosphatidylinositol 3-kinase complexes. In this review, we focus on the functions of ATG genes during pathogenic development in filamentous fungi. Copyright © 2012 Elsevier GmbH. All rights reserved.

  1. Dependence of Core and Extended Flux on Core Dominance ...

    Indian Academy of Sciences (India)

    2016-01-27

    Jan 27, 2016 ... Based on two extragalactic radio source samples, the core dominance parameter is calculated, and the correlations between the core/extended flux density and core dominance parameter are investigated. When the core dominance parameter is lower than unity, it is linearly correlated with the core flux ...

  2. Earth's inner core: Innermost inner core or hemispherical variations?

    NARCIS (Netherlands)

    Lythgoe, K. H.; Deuss, A.; Rudge, J. F.; Neufeld, J. A.

    2014-01-01

    The structure of Earth's deep inner core has important implications for core evolution, since it is thought to be related to the early stages of core formation. Previous studies have suggested that there exists an innermost inner core with distinct anisotropy relative to the rest of the inner core.

  3. Dependence of Core and Extended Flux on Core Dominance ...

    Indian Academy of Sciences (India)

    Abstract. Based on two extragalactic radio source samples, the core dominance parameter is calculated, and the correlations between the core/extended flux density and core dominance parameter are investi- gated. When the core dominance parameter is lower than unity, it is linearly correlated with the core flux density, ...

  4. Korrelasjon mellom core styrke, core stabilitet og utholdende styrke i core

    OpenAIRE

    Berg-Olsen, Andrea Marie; Fugelsøy, Eivor; Maurstad, Ann-Louise

    2010-01-01

    Formålet med studien var å se hvilke korrelasjon det er mellom core styrke, core stabilitet og utholdende styrke i core. Testingen bestod av tre hoveddeler hvor vi testet core styrke, core stabilitet og utholdende styrke i core. Innenfor core styrke og utholdende styrke i core ble tre ulike tester utført. Ved måling av core stabilitet ble det gjennomført kun en test. I core styrke ble isometrisk abdominal fleksjon, isometrisk rygg ekstensjon og isometrisk lateral fleksjon testet. Sit-ups p...

  5. Core stability and bicycling.

    Science.gov (United States)

    Asplund, Chad; Ross, Michael

    2010-01-01

    Bicycling is a popular fitness activity in the United States and around the world. Because of the nature of the bicycling position, the neck and back are at risk for injury. One method to prevent these injuries is to ensure that the body's "core" is strong and stable. A strong and stable core also provides a platform to maximize power transfer, improving performance. Core exercises also may enhance recovery from intense bicycling efforts. Simple stability exercises can improve performance and may prevent injuries in bicyclists.

  6. IGCSE core mathematics

    CERN Document Server

    Wall, Terry

    2013-01-01

    Give your core level students the support and framework they require to get their best grades with this book dedicated to the core level content of the revised syllabus and written specifically to ensure a more appropriate pace. This title has been written for Core content of the revised Cambridge IGCSE Mathematics (0580) syllabus for first teaching from 2013. ? Gives students the practice they require to deepen their understanding through plenty of practice questions. ? Consolidates learning with unique digital resources on the CD, included free with every book. We are working with Cambridge

  7. Core shroud corner joints

    Science.gov (United States)

    Gilmore, Charles B.; Forsyth, David R.

    2013-09-10

    A core shroud is provided, which includes a number of planar members, a number of unitary corners, and a number of subassemblies each comprising a combination of the planar members and the unitary corners. Each unitary corner comprises a unitary extrusion including a first planar portion and a second planar portion disposed perpendicularly with respect to the first planar portion. At least one of the subassemblies comprises a plurality of the unitary corners disposed side-by-side in an alternating opposing relationship. A plurality of the subassemblies can be combined to form a quarter perimeter segment of the core shroud. Four quarter perimeter segments join together to form the core shroud.

  8. INTEGRAL core programme

    Science.gov (United States)

    Gehrels, N.; Schoenfelder, V.; Ubertini, P.; Winkler, C.

    1997-01-01

    The International Gamma Ray Astrophysics Laboratory (INTEGRAL) mission is described with emphasis on the INTEGRAL core program. The progress made in the planning activities for the core program is reported on. The INTEGRAL mission has a nominal lifetime of two years with a five year extension option. The observing time will be divided between the core program (between 30 and 35 percent during the first two years) and general observations. The core program consists of three main elements: the deep survey of the Galactic plane in the central radian of the Galaxy; frequent scans of the Galactic plane in the search for transient sources, and pointed observations of several selected sources. The allocation of the observation time is detailed and the sensitivities of the observations are outlined.

  9. The core helium flash

    Science.gov (United States)

    Cole, P. W.; Deupree, R. G.

    1980-12-01

    The role of convection in the core helium flash is simulated by two-dimensional eddies interacting with the thermonuclear runaway. These eddies are followed by the explicit solution of the two-dimensional conservation laws with a two-dimensional finite difference hydrodynamics code. Thus, no phenomenological theory of convection such as the local mixing length theory is required. The core helium flash is violent, producing a deflagration wave. This differs from the detonation wave (and subsequent disruption of the entire star) produced in previous spherically symmetric violent core helium flashes as the second dimension provides a degree of relief which allows the expansion wave to decouple itself from the burning front. The results predict that a considerable amount of helium in the core will be burned before the horizontal branch is reached and that some envelope mass loss is likely.

  10. Organizing Core Tasks

    DEFF Research Database (Denmark)

    Boll, Karen

    Civil servants conduct the work which makes welfare states functions on an everyday bases: Police men police, school teachers teach, and tax inspectors inspect. Focus in this paper is on the core tasks of tax inspectors. The paper argues that their core task of securing the collection of revenue...... has remained much the same within the last 10 years. However, how the core task has been organized has changed considerable under the influence of various “organizing devices”. The paper focusses on how organizing devices such as risk assessment, output-focus, effect orientation, and treatment...... projects influence the organization of core tasks within the tax administration. The paper shows that the organizational transformations based on the use of these devices have had consequences both for the overall collection of revenue and for the employees’ feeling of “making a difference”. All in all...

  11. iPSC Core

    Data.gov (United States)

    Federal Laboratory Consortium — The induced Pluripotent Stem Cells (iPSC) Core was created in 2011 to accelerate stem cell research in the NHLBI by providing investigators consultation, technical...

  12. The Core Knowledge System

    National Research Council Canada - National Science Library

    Strat, Thomas M; Smith, Grahame B

    1987-01-01

    This document contains an in-depth description of the Core Knowledge System (CKS)-an integrative environment for the many functions that must be performed by sensor-based autonomous and semi-autonomous systems...

  13. Double sequence core theorems

    Directory of Open Access Journals (Sweden)

    Richard F. Patterson

    1999-01-01

    Full Text Available In 1900, Pringsheim gave a definition of the convergence of double sequences. In this paper, that notion is extended by presenting definitions for the limit inferior and limit superior of double sequences. Also the core of a double sequence is defined. By using these definitions and the notion of regularity for 4-dimensional matrices, extensions, and variations of the Knopp Core theorem are proved.

  14. MCNP LWR Core Generator

    Energy Technology Data Exchange (ETDEWEB)

    Fischer, Noah A. [Los Alamos National Laboratory

    2012-08-14

    The reactor core input generator allows for MCNP input files to be tailored to design specifications and generated in seconds. Full reactor models can now easily be created by specifying a small set of parameters and generating an MCNP input for a full reactor core. Axial zoning of the core will allow for density variation in the fuel and moderator, with pin-by-pin fidelity, so that BWR cores can more accurately be modeled. LWR core work in progress: (1) Reflectivity option for specifying 1/4, 1/2, or full core simulation; (2) Axial zoning for moderator densities that vary with height; (3) Generating multiple types of assemblies for different fuel enrichments; and (4) Parameters for specifying BWR box walls. Fuel pin work in progress: (1) Radial and azimuthal zoning for generating further unique materials in fuel rods; (2) Options for specifying different types of fuel for MOX or multiple burn assemblies; (3) Additional options for replacing fuel rods with burnable poison rods; and (4) Control rod/blade modeling.

  15. Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data

    DEFF Research Database (Denmark)

    Yang, Laurence; Tan, Justin; O'Brien, Edward J.

    2015-01-01

    Finding the minimal set of gene functions needed to sustain life is of both fundamental and practical importance. Minimal gene lists have been proposed by using comparative genomics-based core proteome definitions. A definition of a core proteome that is supported by empirical data, is understood...... based on proteomics data. This systems biology core proteome includes 212 genes not found in previous comparative genomics-based core proteome definitions, accounts for 65% of known essential genes in E. coli, and has 78% gene function overlap with minimal genomes (Buchnera aphidicola and Mycoplasma...... genitalium). Based on transcriptomics data across environmental and genetic backgrounds, the systems biology core proteome is significantly enriched in nondifferentially expressed genes and depleted in differentially expressed genes. Compared with the noncore, core gene expression levels are also similar...

  16. Packing in protein cores

    Science.gov (United States)

    Gaines, J. C.; Clark, A. H.; Regan, L.; O'Hern, C. S.

    2017-07-01

    Proteins are biological polymers that underlie all cellular functions. The first high-resolution protein structures were determined by x-ray crystallography in the 1960s. Since then, there has been continued interest in understanding and predicting protein structure and stability. It is well-established that a large contribution to protein stability originates from the sequestration from solvent of hydrophobic residues in the protein core. How are such hydrophobic residues arranged in the core; how can one best model the packing of these residues, and are residues loosely packed with multiple allowed side chain conformations or densely packed with a single allowed side chain conformation? Here we show that to properly model the packing of residues in protein cores it is essential that amino acids are represented by appropriately calibrated atom sizes, and that hydrogen atoms are explicitly included. We show that protein cores possess a packing fraction of φ ≈ 0.56 , which is significantly less than the typically quoted value of 0.74 obtained using the extended atom representation. We also compare the results for the packing of amino acids in protein cores to results obtained for jammed packings from discrete element simulations of spheres, elongated particles, and composite particles with bumpy surfaces. We show that amino acids in protein cores pack as densely as disordered jammed packings of particles with similar values for the aspect ratio and bumpiness as found for amino acids. Knowing the structural properties of protein cores is of both fundamental and practical importance. Practically, it enables the assessment of changes in the structure and stability of proteins arising from amino acid mutations (such as those identified as a result of the massive human genome sequencing efforts) and the design of new folded, stable proteins and protein-protein interactions with tunable specificity and affinity.

  17. Bioinformatics Core Project Management

    Science.gov (United States)

    Vangala, Mahesh; Vincent, James; Driscoll, Heather

    2013-01-01

    Bioinformatics cores that provide fee for service style support encounter a wide variety of projects. The scope of projects varies greatly among investigators. Because of this variety, it is difficult to develop a set of predefined services that fit all project types. While our own core has developed a baseline set of services, we found in practice these often needed significant modification to meet the goals of particular investigator. To overcome this problem we factored common features of all projects and partitioned them into groups: workflow management, data management, user results, and tracking and reporting. We then implemented best practices for each group using commercial and open source software combined with our own management policies. Finally we linked these areas together to produce an overall integrated project management solution that combines workflow management, data management, user results management and reporting capabilities. This system solves the problem of developing well defined services that are trackable and repeatable while simultaneously enabling flexibility that is easily managed. The result improves the effectiveness and efficiency of the bioinformatics core for scientists working within the core, for investigators receiving core support and for external auditors and evaluators.

  18. Inner core structure behind the PKP core phase triplication

    NARCIS (Netherlands)

    Blom, Nienke A.; Deuss, Arwen; Paulssen, Hanneke; Waszek, Lauren

    The structure of the Earth's inner core is not well known between depths of ∼100–200 km beneath the inner core boundary. This is a result of the PKP core phase triplication and the existence of strong precursors to PKP phases, which hinder the measurement of inner core compressional PKIKP waves at

  19. GREEN CORE HOUSE

    Directory of Open Access Journals (Sweden)

    NECULAI Oana

    2017-05-01

    Full Text Available The Green Core House is a construction concept with low environmental impact, having as main central element a greenhouse. The greenhouse has the innovative role to use the biomass energy provided by plants to save energy. Although it is the central piece, the greenhouse is not the most innovative part of the Green Core House, but the whole building ensemble because it integrates many other sustainable systems as "waste purification systems", "transparent photovoltaic panels" or "double skin façades".

  20. Birefringent hollow core fibers

    DEFF Research Database (Denmark)

    Roberts, John

    2007-01-01

    Hollow core photonic crystal fiber (HC-PCF), fabricated according to a nominally non-birefringent design, shows a degree of un-controlled birefringence or polarization mode dispersion far in excess of conventional non polarization maintaining fibers. This can degrade the output pulse in many...... and an increased overlap between the polarization modes at the glass interfaces. The interplay between these effects leads to a wavelength for optimum polarization maintenance, lambda(PM), which is detuned from the wavelength of highest birefringence. By a suitable fiber design involving antiresonance of the core...

  1. CORE COMPONENT POT

    Energy Technology Data Exchange (ETDEWEB)

    MARTIN RL; OMBERG RP

    1975-12-19

    The core component pot is an open top vessel used to hold both new and irradiated core components for storage in the IDS and for holding the components submerged in sodium while being trasported inside CLEM. The top of the CCP is equipped with a grapple lip which is engaged by the hoisting grapples. Heat for maintaining the preheat of new components and dissipation of decay heat of irradiated fuel assemblies is conducted between the wall of the pot and the surrounding environment by thermal radiation and convection.

  2. Maximum stellar iron core mass

    Indian Academy of Sciences (India)

    An analytical method of estimating the mass of a stellar iron core, just prior to core collapse, is described in this paper. The method employed depends, in part, upon an estimate of the true relativistic mass increase experienced by electrons within a highly compressed iron core, just prior to core collapse, and is significantly ...

  3. Genome-wide functional profiling identifies genes and processes important for zinc-limited growth of Saccharomyces cerevisiae.

    Science.gov (United States)

    North, Matthew; Steffen, Janet; Loguinov, Alex V; Zimmerman, Ginelle R; Vulpe, Chris D; Eide, David J

    2012-01-01

    Zinc is an essential nutrient because it is a required cofactor for many enzymes and transcription factors. To discover genes and processes in yeast that are required for growth when zinc is limiting, we used genome-wide functional profiling. Mixed pools of ∼4,600 deletion mutants were inoculated into zinc-replete and zinc-limiting media. These cells were grown for several generations, and the prevalence of each mutant in the pool was then determined by microarray analysis. As a result, we identified more than 400 different genes required for optimal growth under zinc-limiting conditions. Among these were several targets of the Zap1 zinc-responsive transcription factor. Their importance is consistent with their up-regulation by Zap1 in low zinc. We also identified genes that implicate Zap1-independent processes as important. These include endoplasmic reticulum function, oxidative stress resistance, vesicular trafficking, peroxisome biogenesis, and chromatin modification. Our studies also indicated the critical role of macroautophagy in low zinc growth. Finally, as a result of our analysis, we discovered a previously unknown role for the ICE2 gene in maintaining ER zinc homeostasis. Thus, functional profiling has provided many new insights into genes and processes that are needed for cells to thrive under the stress of zinc deficiency.

  4. Inflation targeting and core inflation

    OpenAIRE

    Julie Smith

    2005-01-01

    This paper examines the interaction of core inflation and inflation targeting as a monetary policy regime. Interest in core inflation has grown because of inflation targeting. Core inflation is defined in numerous ways giving rise to many potential measures; this paper defines core inflation as the best forecaster of inflation. A cross-country study finds before the start of inflation targeting, but not after, core inflation differs between non-inflation targeters and inflation targeters. Thr...

  5. NUCLEAR REACTOR CORE DESIGN

    Science.gov (United States)

    Mahlmeister, J.E.; Peck, W.S.; Haberer, W.V.; Williams, A.C.

    1960-03-22

    An improved core design for a sodium-cooled, graphitemoderated nuclear reactor is described. The improved reactor core comprises a number of blocks of moderator material, each block being in the shape of a regular prism. A number of channels, extending the length of each block, are disposed around the periphery. When several blocks are placed in contact to form the reactor core, the channels in adjacent blocks correspond with each other to form closed conduits extending the length of the core. Fuel element clusters are disposed in these closed conduits, and liquid coolant is forced through the annulus between the fuel cluster and the inner surface of the conduit. In a preferred embodiment of the invention, the moderator blocks are in the form of hexagonal prisms with longitudinal channels cut into the corners of the hexagon. The main advantage of an "edge-loaded" moderator block is that fewer thermal neutrons are absorbed by the moderator cladding, as compared with a conventional centrally loaded moderator block.

  6. Schumpeter's core works revisited

    DEFF Research Database (Denmark)

    Andersen, Esben Sloth

    2012-01-01

    This paper organises Schumpeter’s core books in three groups: the programmatic duology,the evolutionaryeconomic duology,and the socioeconomic synthesis. By analysing these groups and their interconnections from the viewpoint of modern evolutionaryeconomics,the paper summarises resolved problems...

  7. Core Obstetrics and Gynaecology*

    African Journals Online (AJOL)

    Core Obstetrics and Gynaecology*. By J. T. Nel. Pp xvii + 992. Illustrated. Durban: Butterworths. 1995. ISBN 0-409-10134-6. For some years now, I have lamented the absence of a good, home-grown, comprehensive, student-centred textbook of obstetrics and gynaecology designed specifically for South African needs.

  8. Adult educators' core competences

    DEFF Research Database (Denmark)

    Wahlgren, Bjarne

    2016-01-01

    environment as well as the kind of adult education concerned (e.g. basic education, work-related education etc.). However, it seems that it is possible to identify certain competence requirements which transcend national, cultural and functional boundaries. This research note summarises these common or “core...

  9. The core and cosmopolitans

    DEFF Research Database (Denmark)

    Dahlander, Linus; Frederiksen, Lars

    2012-01-01

    Users often interact and help each other solve problems in communities, but few scholars have explored how these relationships provide opportunities to innovate. We analyze the extent to which people positioned within the core of a community as well as people that are cosmopolitans positioned...

  10. Looking for Core Values

    Science.gov (United States)

    Carter, Margie

    2010-01-01

    People who view themselves as leaders, not just managers or teachers, are innovators who focus on clarifying core values and aligning all aspects of the organization with these values to grow their vision. A vision for an organization can't be just one person's idea. Visions grow by involving people in activities that help them name and create…

  11. Some Core Contested Concepts

    Science.gov (United States)

    Chomsky, Noam

    2015-01-01

    Core concepts of language are highly contested. In some cases this is legitimate: real empirical and conceptual issues arise. In other cases, it seems that controversies are based on misunderstanding. A number of crucial cases are reviewed, and an approach to language is outlined that appears to have strong conceptual and empirical motivation, and…

  12. Modeling Core Collapse Supernovae

    Science.gov (United States)

    Mezzacappa, Anthony

    2017-01-01

    Core collapse supernovae, or the death throes of massive stars, are general relativistic, neutrino-magneto-hydrodynamic events. The core collapse supernova mechanism is still not in hand, though key components have been illuminated, and the potential for multiple mechanisms for different progenitors exists. Core collapse supernovae are the single most important source of elements in the Universe, and serve other critical roles in galactic chemical and thermal evolution, the birth of neutron stars, pulsars, and stellar mass black holes, the production of a subclass of gamma-ray bursts, and as potential cosmic laboratories for fundamental nuclear and particle physics. Given this, the so called ``supernova problem'' is one of the most important unsolved problems in astrophysics. It has been fifty years since the first numerical simulations of core collapse supernovae were performed. Progress in the past decade, and especially within the past five years, has been exponential, yet much work remains. Spherically symmetric simulations over nearly four decades laid the foundation for this progress. Two-dimensional modeling that assumes axial symmetry is maturing. And three-dimensional modeling, while in its infancy, has begun in earnest. I will present some of the recent work from the ``Oak Ridge'' group, and will discuss this work in the context of the broader work by other researchers in the field. I will then point to future requirements and challenges. Connections with other experimental, observational, and theoretical efforts will be discussed, as well.

  13. Core calculations of JMTR

    Energy Technology Data Exchange (ETDEWEB)

    Nagao, Yoshiharu [Japan Atomic Energy Research Inst., Oarai, Ibaraki (Japan). Oarai Research Establishment

    1998-03-01

    In material testing reactors like the JMTR (Japan Material Testing Reactor) of 50 MW in Japan Atomic Energy Research Institute, the neutron flux and neutron energy spectra of irradiated samples show complex distributions. It is necessary to assess the neutron flux and neutron energy spectra of an irradiation field by carrying out the nuclear calculation of the core for every operation cycle. In order to advance core calculation, in the JMTR, the application of MCNP to the assessment of core reactivity and neutron flux and spectra has been investigated. In this study, in order to reduce the time for calculation and variance, the comparison of the results of the calculations by the use of K code and fixed source and the use of Weight Window were investigated. As to the calculation method, the modeling of the total JMTR core, the conditions for calculation and the adopted variance reduction technique are explained. The results of calculation are shown. Significant difference was not observed in the results of neutron flux calculations according to the difference of the modeling of fuel region in the calculations by K code and fixed source. The method of assessing the results of neutron flux calculation is described. (K.I.)

  14. The Uncommon Core

    Science.gov (United States)

    Ohler, Jason

    2013-01-01

    This author contends that the United States neglects creativity in its education system. To see this, he states, one may look at the Common Core State Standards. If one searches the English Language Arts and Literacy standards for the words "creative," "innovative," and "original"--and any associated terms, one will…

  15. Genes and Gene Therapy

    Science.gov (United States)

    ... correctly, a child can have a genetic disorder. Gene therapy is an experimental technique that uses genes to ... or prevent disease. The most common form of gene therapy involves inserting a normal gene to replace an ...

  16. Measuring core stability.

    Science.gov (United States)

    Liemohn, Wendell P; Baumgartner, Ted A; Gagnon, Laura H

    2005-08-01

    In this study, a 4-item battery of core stability (CS) tests modeled on core stabilization activities used in training and rehabilitation research was developed, and a measurement schedule was established to maximize internal consistency and stability reliabilities. Specifically, we found that 4 test administrations on each of 4 days produced intraclass correlation coefficients that in most instances exceeded 0.90 and stability reliability coefficients on the third and fourth days of testing that exceeded 0.90 for 2 of the tests and 0.80 for the other 2. Thus, it is recommended that in future research, examiners administer the battery for at least 3 days and consider the data collected on day 3 as the best estimate of participant CS.

  17. Core Outlet Temperature Study

    Energy Technology Data Exchange (ETDEWEB)

    Moisseytsev, A. [Argonne National Laboratory (ANL), Argonne, IL (United States); Hoffman, E. [Argonne National Laboratory (ANL), Argonne, IL (United States); Majumdar, S. [Argonne National Laboratory (ANL), Argonne, IL (United States)

    2008-07-28

    It is a known fact that the power conversion plant efficiency increases with elevation of the heat addition temperature. The higher efficiency means better utilization of the available resources such that higher output in terms of electricity production can be achieved for the same size and power of the reactor core or, alternatively, a lower power core could be used to produce the same electrical output. Since any nuclear power plant, such as the Advanced Burner Reactor, is ultimately built to produce electricity, a higher electrical output is always desirable. However, the benefits of the higher efficiency and electricity production usually come at a price. Both the benefits and the disadvantages of higher reactor outlet temperatures are analyzed in this work.

  18. Ice Cores of the National Ice Core Laboratory

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — The U.S. National Ice Core Laboratory (NICL) is a facility for storing, curating, and studying ice cores recovered from the polar regions of the world. It provides...

  19. Core Exercises: Why You Should Strengthen Your Core Muscles

    Science.gov (United States)

    ... neglected. Still, it pays to get your core muscles — the muscles around your trunk and pelvis — in better shape. ... to find out why. Core exercises train the muscles in your pelvis, lower back, hips and abdomen ...

  20. USGS Core Research Center (CRC) Collection of Core

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — The Core Research Center (CRC) was established in 1974 by the U.S. Geological Survey (USGS) to preserve valuable rock cores for use by scientists and educators from...

  1. Leadership Core Competencies

    Science.gov (United States)

    2008-03-15

    different approaches led to a very similar understanding of what is required to develop leaders and achieve mission success. LEADERSHIP CORE... Leadership , the first principle, Know yourself and seek self-improvement performs the same function. Similar to the other services, Navy leaders evaluate... leadership styles. Like managers of today, those of tomorrow will also need to do more with less. They will have increased responsibilities and will

  2. Optimizing performance by improving core stability and core strength.

    Science.gov (United States)

    Hibbs, Angela E; Thompson, Kevin G; French, Duncan; Wrigley, Allan; Spears, Iain

    2008-01-01

    Core stability and core strength have been subject to research since the early 1980s. Research has highlighted benefits of training these processes for people with back pain and for carrying out everyday activities. However, less research has been performed on the benefits of core training for elite athletes and how this training should be carried out to optimize sporting performance. Many elite athletes undertake core stability and core strength training as part of their training programme, despite contradictory findings and conclusions as to their efficacy. This is mainly due to the lack of a gold standard method for measuring core stability and strength when performing everyday tasks and sporting movements. A further confounding factor is that because of the differing demands on the core musculature during everyday activities (low load, slow movements) and sporting activities (high load, resisted, dynamic movements), research performed in the rehabilitation sector cannot be applied to the sporting environment and, subsequently, data regarding core training programmes and their effectiveness on sporting performance are lacking. There are many articles in the literature that promote core training programmes and exercises for performance enhancement without providing a strong scientific rationale of their effectiveness, especially in the sporting sector. In the rehabilitation sector, improvements in lower back injuries have been reported by improving core stability. Few studies have observed any performance enhancement in sporting activities despite observing improvements in core stability and core strength following a core training programme. A clearer understanding of the roles that specific muscles have during core stability and core strength exercises would enable more functional training programmes to be implemented, which may result in a more effective transfer of these skills to actual sporting activities.

  3. Hollow-Core Fiber Lamp

    Science.gov (United States)

    Yi, Lin (Inventor); Tjoelker, Robert L. (Inventor); Burt, Eric A. (Inventor); Huang, Shouhua (Inventor)

    2016-01-01

    Hollow-core capillary discharge lamps on the millimeter or sub-millimeter scale are provided. The hollow-core capillary discharge lamps achieve an increased light intensity ratio between 194 millimeters (useful) and 254 millimeters (useless) light than conventional lamps. The capillary discharge lamps may include a cone to increase light output. Hollow-core photonic crystal fiber (HCPCF) may also be used.

  4. On core stability and extendability

    OpenAIRE

    Shellshear, Evan

    2011-01-01

    This paper investigates conditions under which the core of a TU cooperative game is stable. In particular the author extends the idea of extendability to find new conditions under which the core is stable. It is also shown that these new conditions are not necessary for core stability.

  5. Maximum stellar iron core mass

    Indian Academy of Sciences (India)

    Abstract. An analytical method of estimating the mass of a stellar iron core, just prior to core collapse, is .... approximately as an ideal gas, the mean kinetic energies of the free electrons and atomic nuclei will be equal. .... whose density varies from a maximum at the core's center to a minimum at its 'surface'. The dimensional ...

  6. Dual-core Itanium Processor

    CERN Multimedia

    2006-01-01

    Intel’s first dual-core Itanium processor, code-named "Montecito" is a major release of Intel's Itanium 2 Processor Family, which implements the Intel Itanium architecture on a dual-core processor with two cores per die (integrated circuit). Itanium 2 is much more powerful than its predecessor. It has lower power consumption and thermal dissipation.

  7. Drosophila TRF2 is a preferential core promoter regulator.

    Science.gov (United States)

    Kedmi, Adi; Zehavi, Yonathan; Glick, Yair; Orenstein, Yaron; Ideses, Diana; Wachtel, Chaim; Doniger, Tirza; Waldman Ben-Asher, Hiba; Muster, Nemone; Thompson, James; Anderson, Scott; Avrahami, Dorit; Yates, John R; Shamir, Ron; Gerber, Doron; Juven-Gershon, Tamar

    2014-10-01

    Transcription of protein-coding genes is highly dependent on the RNA polymerase II core promoter. Core promoters, generally defined as the regions that direct transcription initiation, consist of functional core promoter motifs (such as the TATA-box, initiator [Inr], and downstream core promoter element [DPE]) that confer specific properties to the core promoter. The known basal transcription factors that support TATA-dependent transcription are insufficient for in vitro transcription of DPE-dependent promoters. In search of a transcription factor that supports DPE-dependent transcription, we used a biochemical complementation approach and identified the Drosophila TBP (TATA-box-binding protein)-related factor 2 (TRF2) as an enriched factor in the fractions that support DPE-dependent transcription. We demonstrate that the short TRF2 isoform preferentially activates DPE-dependent promoters. DNA microarray analysis reveals the enrichment of DPE promoters among short TRF2 up-regulated genes. Using primer extension analysis and reporter assays, we show the importance of the DPE in transcriptional regulation of TRF2 target genes. It was previously shown that, unlike TBP, TRF2 fails to bind DNA containing TATA-boxes. Using microfluidic affinity analysis, we discovered that short TRF2-bound DNA oligos are enriched for Inr and DPE motifs. Taken together, our findings highlight the role of short TRF2 as a preferential core promoter regulator. © 2014 Kedmi et al.; Published by Cold Spring Harbor Laboratory Press.

  8. Perspectives for DNA studies on polar ice cores

    DEFF Research Database (Denmark)

    Hansen, Anders J.; Willerslev, E.

    2002-01-01

    cores as well. Here, we present some future perspectives for DNA studies on polar ice cores in regard to molecular ecology, DNA damage and degradation, anabiosis and antibiotic resistance genes. Finally, we address some of the methodological problems connected to ancient DNA research.......Recently amplifiable ancient DNA was obtained from a Greenland ice core. The DNA revealed a diversity of fungi, plants, algae and protists and has thereby expanded the range of detectable organic material in fossil glacier ice. The results suggest that ancient DNA can be obtained from other ice...

  9. Comparative analysis of the virulence characteristics of epidemic methicillin-resistant Staphylococcus aureus (MRSA) strains isolated from Chinese children: ST59 MRSA highly expresses core gene-encoded toxin.

    Science.gov (United States)

    Li, Shipeng; Sun, Jing; Zhang, Jianzhong; Li, Xiangmei; Tao, Xiaoxia; Wang, Lijuan; Sun, Mingjiao; Liu, Yingchao; Li, Juan; Qiao, Yanhong; Yu, Sangjie; Yao, Kaihu; Yang, Yonghong; Shen, Xuzhuang

    2014-02-01

    This study aims to investigate the prevalence of a novel cell wall-anchored protein gene, sasX, and to obtain information on the genetic basis for the pathogenic potential of the MRSA strains isolated from Chinese children. The molecular and virulence characteristics of the clinical strains were analyzed. Twenty-two sequence types (STs) were obtained, with six epidemic clones ST59, ST239, ST1, ST910, ST88, and ST338 accounting for 35.8, 22, 6.6, 6.6, 5.3, and 4.1% respectively. The expression levels of hla, psmα, and RNAIII were higher in ST59 than in other STs (p MRSA isolates. ST239-MRSA-SCCmecIII-t037 (61.5%) was the predominant sasX-positive MRSA clone. The expressions of PSMα and RNAIII were higher in sasX-positive ST239 isolates than in sasX-negative ST239 ones (p MRSA was higher than that by sasX-negative ST239 MRSA (p = 0.008). This study indicated that ST59 was the predominant clone in the MRSA isolates obtained from Chinese children and might have stronger pathogenic potential. The prevalence of the sasX gene in the MRSA isolates from children was relatively low. Furthermore, the sasX gene might be related to the expressions of PSMα and RNAIII and infection invasiveness. © 2013 APMIS Published by John Wiley & Sons Ltd.

  10. Differential Stoichiometry among Core Ribosomal Proteins

    Directory of Open Access Journals (Sweden)

    Nikolai Slavov

    2015-11-01

    Full Text Available Understanding the regulation and structure of ribosomes is essential to understanding protein synthesis and its dysregulation in disease. While ribosomes are believed to have a fixed stoichiometry among their core ribosomal proteins (RPs, some experiments suggest a more variable composition. Testing such variability requires direct and precise quantification of RPs. We used mass spectrometry to directly quantify RPs across monosomes and polysomes of mouse embryonic stem cells (ESC and budding yeast. Our data show that the stoichiometry among core RPs in wild-type yeast cells and ESC depends both on the growth conditions and on the number of ribosomes bound per mRNA. Furthermore, we find that the fitness of cells with a deleted RP-gene is inversely proportional to the enrichment of the corresponding RP in polysomes. Together, our findings support the existence of ribosomes with distinct protein composition and physiological function.

  11. Differential Stoichiometry among Core Ribosomal Proteins

    Science.gov (United States)

    Slavov, Nikolai; Semrau, Stefan; Airoldi, Edoardo; Budnik, Bogdan; van Oudenaarden, Alexander

    2015-01-01

    Summary Understanding the regulation and structure of ribosomes is essential to understanding protein synthesis and its dysregulation in disease. While ribosomes are believed to have a fixed stoichiometry among their core ribosomal proteins (RPs), some experiments suggest a more variable composition. Testing such variability requires direct and precise quantification of RPs. We used mass spectrometry to directly quantify RPs across monosomes and polysomes of mouse embryonic stem cells (ESC) and budding yeast. Our data show that the stoichiometry among core RPs in wild-type yeast cells and ESC depends both on the growth conditions and on the number of ribosomes bound per mRNA. Furthermore, we find that the fitness of cells with a deleted RP-gene is inversely proportional to the enrichment of the corresponding RP in polysomes. Together, our findings support the existence of ribosomes with distinct protein composition and physiological function. PMID:26565899

  12. Full MOX core for ABWR

    Energy Technology Data Exchange (ETDEWEB)

    Yamamoto, Yuki; Yoshioka, Ritsuo; Nagano, Mamoru [Toshiba Corp., Kawasaki, Kanagawa (Japan)

    1996-08-01

    The Japan Atomic Energy Commission has announced the construction plan for an advanced boiling-water reactor (ABWR) with a full MOX (mixed oxide) core instead of ATR. Increased MOX fuel utilization will result in greater savings of uranium ore. A full MOX core for a power plant requires flexibility in MOX fuel utilization, steadiness, and economical operation. We have proposed the optimum full MOX core design for an ABWR based on the MOX fuel and core technologies that we have developed over a period of many years, as well as our considerable experience in uranium fuel and cores. Our full MOX core design for an ABWR has good core characteristics and safety performance with no change in the basic design specifications of the current ABWR. (author)

  13. Proximity of Radiation Desiccation Response Motif to the core promoter is essential for basal repression as well as gamma radiation-induced gyrB gene expression in Deinococcus radiodurans.

    Science.gov (United States)

    Anaganti, Narasimha; Basu, Bhakti; Mukhopadhyaya, Rita; Apte, Shree Kumar

    2017-06-05

    The radioresistant D. radiodurans regulates its DNA damage regulon (DDR) through interaction between a 17bp palindromic cis-regulatory element called the Radiation Desiccation Response Motif (RDRM), the DdrO repressor and a protease IrrE. The role of RDRM in regulation of DDR was dissected by constructing RDRM sequence-, position- or deletion-variants of Deinococcal gyrB gene (DR0906) promoter and by RDRM insertion in the non-RDRM groESL gene (DR0606) promoter, and monitoring the effect of such modifications on the basal as well as gamma radiation inducible promoter activity by quantifying fluorescence of a GFP reporter. RDRM sequence-variants revealed that the conservation of sequence at the 5th and 13th position and the ends of RDRM is essential for basal repression by interaction with DdrO. RDRM position-variants showed that the sequence acts as a negative regulatory element only when located around transcription start site (TSS) and within the span of RNA polymerase (RNAP) binding region. RDRM deletion-variants indicated that the 5' sequence of RDRM possibly possesses an enhancer-like element responsible for higher expression yields upon repressor clearance post-irradiation. The results suggest that RDRM plays both a negative as well as a positive role in the regulation of DDR in D. radiodurans. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. NEUTRONIC REACTOR CORE INSTRUMENT

    Science.gov (United States)

    Mims, L.S.

    1961-08-22

    A multi-purpose instrument for measuring neutron flux, coolant flow rate, and coolant temperature in a nuclear reactor is described. The device consists essentially of a hollow thimble containing a heat conducting element protruding from the inner wall, the element containing on its innermost end an amount of fissionsble materinl to function as a heat source when subjected to neutron flux irradiation. Thermocouple type temperature sensing means are placed on the heat conducting element adjacent the fissionable material and at a point spaced therefrom, and at a point on the thimble which is in contact with the coolant fluid. The temperature differentials measured between the thermocouples are determinative of the neutron flux, coolant flow, and temperature being measured. The device may be utilized as a probe or may be incorporated in a reactor core. (AE C)

  15. Full MOX core in BWR

    Energy Technology Data Exchange (ETDEWEB)

    Aoyama, Motoo [Power and Industrial Systems R and D Laboratory, Hitachi Ltd., Hitachi, Ibaraki (Japan)

    1999-12-01

    Studies on the core design, the fuel rod thermal-mechanical design and the safety evaluation have been summarized for the Full MOX-ABWR, loaded with MOX fuels up to 100% of the core. Fuel bundle configuration for MOX fuels is identical to the STEP II fuel design and the discharge burnup is about 33 GWd/t. Core performance evaluations and fuel rod thermal-mechanical design analyses have been performed, and it has been confirmed that the design criteria are satisfied with enough margin like the UO{sub 2} fuel loaded core. Safety analyses on transients and accidents have also been performed by considering the MOX fuel and core characteristics adequately through selecting appropriate input data for each safety analysis. All safety criteria are satisfied like the UO{sub 2} core. (author)

  16. Wire core reactor for NTP

    Science.gov (United States)

    Harty, R. B.

    1991-01-01

    The development of the wire core system for Nuclear Thermal Propulsion (NTP) that took place from 1963 to 1965 is discussed. A wire core consists of a fuel wire with spacer wires. It's an annular flow core having a central control rod. There are actually four of these, with beryllium solid reflectors on both ends and all the way around. Much of the information on the concept is given in viewgraph form. Viewgraphs are presented on design details of the wire core, the engine design, engine weight vs. thrust, a technique used to fabricate the wire fuel element, and axial temperature distribution.

  17. Biochemistry Instrumentation Core Technology Center

    Data.gov (United States)

    Federal Laboratory Consortium — The UCLA-DOE Biochemistry Instrumentation Core Facility provides the UCLA biochemistry community with easy access to sophisticated instrumentation for a wide variety...

  18. Characterizing the Core via K-Core Covers

    NARCIS (Netherlands)

    Sanchez, S.M.; Borm, P.E.M.; Estevez, A.

    2013-01-01

    This paper extends the notion of individual minimal rights for a transferable utility game (TU-game) to coalitional minimal rights using minimal balanced families of a specific type, thus defining a corresponding minimal rights game. It is shown that the core of a TU-game coincides with the core of

  19. RUCS: Rapid identification of PCR primers for unique core sequences

    DEFF Research Database (Denmark)

    Thomsen, Martin Christen Frølund; Hasman, Henrik; Westh, Henrik

    2017-01-01

    in silico PCR simulation. We compared our method, which identifies the unique core sequences, against an existing tool called ssGeneFinder, and found that our method was 6.5-20 times more sensitive. We used RUCS to design primer pairs that would target a set of genomes known to contain the mcr-1 colistin...

  20. Sampling strategy to develop a primary core collection of apple ...

    African Journals Online (AJOL)

    PRECIOUS

    2010-01-11

    -483. Tanksley SD, McCouch SR ˜1997). Seedballkand molecular maps: Unlocking genetic Potential from the wild. Sci. 277: 1063-1066. Tohme J, Gonzalez D (1996). AFLP analysis of gene pools of a wild bean core collection ...

  1. Next Generation Sequencing at the University of Chicago Genomics Core

    Energy Technology Data Exchange (ETDEWEB)

    Faber, Pieter [University of Chicago

    2013-04-24

    The University of Chicago Genomics Core provides University of Chicago investigators (and external clients) access to State-of-the-Art genomics capabilities: next generation sequencing, Sanger sequencing / genotyping and micro-arrays (gene expression, genotyping, and methylation). The current presentation will highlight our capabilities in the area of ultra-high throughput sequencing analysis.

  2. Global Core Plasma Model

    Science.gov (United States)

    Gallagher, Dennis L.; Craven, Paul D.; Comfort, Richard H.

    1999-01-01

    Over 40 years of ground and spacecraft plasmaspheric measurements have resulted in many statistical descriptions of plasmaspheric properties. In some cases, these properties have been represented as analytical descriptions that are valid for specific regions or conditions. For the most part, what has not been done is to extend regional empirical descriptions or models to the plasmasphere as a whole. In contrast, many related investigations depend on the use of representative plasmaspheric conditions throughout the inner magnetosphere. Wave propagation, involving the transport of energy through the magnetosphere, is strongly affected by thermal plasma density and its composition. Ring current collisional and wave particle losses also strongly depend on these quantities. Plasmaspheric also plays a secondary role in influencing radio signals from the Global Positioning System satellites. The Global Core Plasma Model (GCPM) is an attempt to assimilate previous empirical evidence and regional models for plasmaspheric density into a continuous, smooth model of thermal plasma density in the inner magnetosphere. In that spirit, the International Reference Ionosphere is currently used to complete the low altitude description of density and composition in the model. The models and measurements on which the GCPM is currently based and its relationship to IRI will be discussed.

  3. Adult educators' core competences

    Science.gov (United States)

    Wahlgren, Bjarne

    2016-06-01

    Which competences do professional adult educators need? This research note discusses the topic from a comparative perspective, finding that adult educators' required competences are wide-ranging, heterogeneous and complex. They are subject to context in terms of national and cultural environment as well as the kind of adult education concerned (e.g. basic education, work-related education etc.). However, it seems that it is possible to identify certain competence requirements which transcend national, cultural and functional boundaries. This research note summarises these common or "core" requirements, organising them into four thematic subcategories: (1) communicating subject knowledge; (2) taking students' prior learning into account; (3) supporting a learning environment; and (4) the adult educator's reflection on his or her own performance. At the end of his analysis of different competence profiles, the author notes that adult educators' ability to train adult learners in a way which then enables them to apply and use what they have learned in practice (thus performing knowledge transfer) still seems to be overlooked.

  4. Espaço de cores

    OpenAIRE

    SANTANA, Claudia Feitosa; OIWA, Nestor Norio; COSTA, Marcelo Fernandes da; TIEDEMANN, Klaus Bruno; Silveira, Luiz Carlos de Lima; VENTURA, Dora Selma Fix

    2006-01-01

    O artigo apresenta definições para os termos espaço de cores e sistemas de cores; classifica, de acordo com David Brainard (2003), os sistemas de cores em dois grupos: aparência de cores e diferenças de cores. Dentre os diversos sistemas de cores existentes, o artigo descreve dois deles: o sistema de cores Munsell &– um dos mais utilizados entre os sistemas de aparência de cores &– e a descrição do sistema de cores CIE 1931 &– um dos mais utilizados dentre os sistemas de diferença de cores. F...

  5. The INTEGRAL Core Observing Programme

    DEFF Research Database (Denmark)

    Winkler, C.; Gehrels, N.; Lund, Niels

    1999-01-01

    The Core Programme of the INTEGRAL mission is defined as the portion of the scientific programme covering the guaranteed time observations for the INTEGRAL Science Working Team. This paper describes the current status of the Core Programme preparations and summarizes the key elements...... of the observing programme....

  6. Complicated Politics to the Core

    Science.gov (United States)

    McGuinn, Patrick

    2015-01-01

    People dislike the Common Core for several different reasons, and so it is important to disaggregate the sources of opposition and to assess and then to dispel some of the myths that have built up around it. It also is important to understand the unusual political alliances that have emerged in opposition to Common Core implementation and how they…

  7. Toward full MOX core design

    Energy Technology Data Exchange (ETDEWEB)

    Rouviere, G.; Guillet, J.L. [Cogema BCR/DSDP, 78 - Saint Quentin en Yvelines (France); Bruna, G.B.; Pelet, J. [FRAMATOME, 92 - Paris-La-Defense (France)

    1999-07-01

    This paper presents a selection of the main preliminary results of a study program sponsored by COGEMA and currently carried out by FRAMATOME. The objective of this study is to investigate the feasibility of full MOX core loading in a French 1300 MWe PWR, a recent and widespread standard nuclear power plant. The investigation includes core nuclear design, thermal hydraulic and systems aspects. (authors)

  8. Winning Cores in Parity Games

    DEFF Research Database (Denmark)

    Vester, Steen

    2016-01-01

    in their own right. In particular, we show that the winning core and the winning region for a player in a parity game are equivalently empty. Moreover, the winning core contains all fatal attractors but is not necessarily a dominion itself. Experimental results are very positive both with respect to quality...

  9. Anisotropic charged core envelope star

    Science.gov (United States)

    Mafa Takisa, P.; Maharaj, S. D.

    2016-08-01

    We study a charged compact object with anisotropic pressures in a core envelope setting. The equation of state is quadratic in the core and linear in the envelope. There is smooth matching between the three regions: the core, envelope and the Reissner-Nordström exterior. We show that the presence of the electric field affects the masses, radii and compactification factors of stellar objects with values which are in agreement with previous studies. We investigate in particular the effect of electric field on the physical features of the pulsar PSR J1614-2230 in the core envelope model. The gravitational potentials and the matter variables are well behaved within the stellar object. We demonstrate that the radius of the core and the envelope can vary by changing the parameters in the speed of sound.

  10. Waves in the core and mechanical core-mantle interactions

    DEFF Research Database (Denmark)

    Jault, D.; Finlay, Chris

    2015-01-01

    This Chapter focuses on time-dependent uid motions in the core interior, which can beconstrained by observations of the Earth's magnetic eld, on timescales which are shortcompared to the magnetic diusion time. This dynamics is strongly inuenced by the Earth's rapid rotation, which rigidies...... the motions in the direction parallel to the Earth'srotation axis. This property accounts for the signicance of the core-mantle topography.In addition, the stiening of the uid in the direction parallel to the rotation axis gives riseto a magnetic diusion layer attached to the core-mantle boundary, which would...

  11. Epistemology and ontology in core ontologies: FOLaw and LRI-Core, two core ontologies for law

    NARCIS (Netherlands)

    Breukers, J.A.P.J.; Hoekstra, R.J.

    2004-01-01

    For more than a decade constructing ontologies for legal domains, we, at the Leibniz Center for Law, felt really the need to develop a core ontology for law that would enable us to re-use the common denominator of the various legal domains. In this paper we present two core ontologies for law. The

  12. Polymorphisms in the hepatitis C virus core and its association with ...

    Indian Academy of Sciences (India)

    ). Some studies have focused on the roleof HCV viral proteins in hepatocyte transformation. In this work we have compiled and analysed current articles regardingthe impact of polymorphisms in the HCV core gene and protein on the ...

  13. Towards abolition of immunogenic structures in insect cells: characterization of a honey-bee (Apis mellifera) multi-gene family reveals both an allergy-related core α1,3-fucosyltransferase and the first insect Lewis-histo-blood-group-related antigen-synthesizing enzyme

    Science.gov (United States)

    Rendić, Dubravko; Klaudiny, Jaroslav; Stemmer, Ute; Schmidt, Julia; Paschinger, Katharina; Wilson, Iain B. H.

    2006-01-01

    Glycoproteins from honey-bee (Apis mellifera), such as phospholipase A2 and hyaluronidase, are well-known major bee-venom allergens. They carry N-linked oligosaccharide structures with two types of α1,3-fucosylation: the modification by α1,3-fucose of the innermost core GlcNAc, which constitutes an epitope recognized by IgE from some bee-venom-allergic patients, and an antennal Lewis-like GalNAcβ1,4(Fucα1,3)GlcNAc moiety. We now report the cloning and expression of two cDNAs encoding the relevant active α1,3-FucTs (α1,3-fucosyltransferases). The first sequence, closest to that of fruitfly (Drosophila melanogaster) FucTA, was found to be a core α1,3-FucT (EC 2.4.1.214), as judged by several enzyme and biochemical assays. The second cDNA encoded an enzyme, most related to Drosophila FucTC, that was shown to be capable of generating the Lex [Galβ1-4(Fucα1-3)GlcNAc] epitope in vitro and is the first Lewis-type α1,3-FucT (EC 2.4.1.152) to be described in insects. The transcription levels of these two genes in various tissues were examined: FucTA was found to be predominantly expressed in the brain tissue and venom glands, whereas FucTC transcripts were detected at highest levels in venom and hypopharyngeal glands. Very low expression of a third homologue of unknown function, FucTB, was also observed in various tissues. The characterization of these honey-bee gene products not only accounts for the observed α1,3-fucosylation of bee-venom glycoproteins, but is expected to aid the identification and subsequent down-regulation of the FucTs in insect cell lines of biotechnological importance. PMID:17029591

  14. Towards abolition of immunogenic structures in insect cells: characterization of a honey-bee (Apis mellifera) multi-gene family reveals both an allergy-related core alpha1,3-fucosyltransferase and the first insect Lewis-histo-blood-group-related antigen-synthesizing enzyme.

    Science.gov (United States)

    Rendić, Dubravko; Klaudiny, Jaroslav; Stemmer, Ute; Schmidt, Julia; Paschinger, Katharina; Wilson, Iain B H

    2007-02-15

    Glycoproteins from honey-bee (Apis mellifera), such as phospholipase A2 and hyaluronidase, are well-known major bee-venom allergens. They carry N-linked oligosaccharide structures with two types of alpha1,3-fucosylation: the modification by alpha1,3-fucose of the innermost core GlcNAc, which constitutes an epitope recognized by IgE from some bee-venom-allergic patients, and an antennal Lewis-like GalNAcbeta1,4(Fucalpha1,3)GlcNAc moiety. We now report the cloning and expression of two cDNAs encoding the relevant active alpha1,3-FucTs (alpha1,3-fucosyltransferases). The first sequence, closest to that of fruitfly (Drosophila melanogaster) FucTA, was found to be a core alpha1,3-FucT (EC 2.4.1.214), as judged by several enzyme and biochemical assays. The second cDNA encoded an enzyme, most related to Drosophila FucTC, that was shown to be capable of generating the Le(x) [Galbeta1-4(Fucalpha1-3)GlcNAc] epitope in vitro and is the first Lewis-type alpha1,3-FucT (EC 2.4.1.152) to be described in insects. The transcription levels of these two genes in various tissues were examined: FucTA was found to be predominantly expressed in the brain tissue and venom glands, whereas FucTC transcripts were detected at highest levels in venom and hypopharyngeal glands. Very low expression of a third homologue of unknown function, FucTB, was also observed in various tissues. The characterization of these honey-bee gene products not only accounts for the observed alpha1,3-fucosylation of bee-venom glycoproteins, but is expected to aid the identification and subsequent down-regulation of the FucTs in insect cell lines of biotechnological importance.

  15. ICF Core Sets for stroke.

    Science.gov (United States)

    Geyh, Szilvia; Cieza, Alarcos; Schouten, Jan; Dickson, Hugh; Frommelt, Peter; Omar, Zaliha; Kostanjsek, Nenad; Ring, Haim; Stucki, Gerold

    2004-07-01

    To report on the results of the consensus process integrating evidence from preliminary studies to develop the first version of the Comprehensive ICF Core Set and the Brief ICF Core Set for stroke. A formal decision-making and consensus process integrating evidence gathered from preliminary studies was followed. Preliminary studies included a Delphi exercise, a systematic review, and an empirical data collection. After training in the ICF and based on these preliminary studies relevant ICF categories were identified in a formal consensus process by international experts from different backgrounds. The preliminary studies identified a set of 448 ICF categories at the second, third and fourth ICF levels with 193 categories on body functions, 26 on body structures, 165 on activities and participation, and 64 on environmental factors. Thirty-nine experts from 12 different countries attended the consensus conference on stroke. Altogether 130 second-level categories were included in the Comprehensive ICF Core Set with 41 categories from the component body functions, 5 from body structures, 51 from activities and participation, and 33 from environmental factors. The Brief ICF Core Set included a total of 18 second-level categories (6 on body functions, 2 on body structures, 7 on activities and participation, and 3 on environmental factors). A formal consensus process integrating evidence and expert opinion based on the ICF framework and classification led to the definition of ICF Core Sets for stroke. Both the Comprehensive ICF Core Set and the Brief ICF Core Set were defined.

  16. Discovery of the Earth's core

    Science.gov (United States)

    Brush, Stephen G.

    1980-09-01

    In 1896 when Emil Wiechert proposed his model of the Earth with an iron core and stony shell, scientists generally believed that the entire earth was a solid as rigid as steel. R. D. Oldham's identification of P and S waves in seismological records allowed him to detect a discontinuity corresponding to a boundary between core and shell (mantle) in 1906, and Beno Gutenberg established the depth of this boundary as 2900 km. But failure to detect propagation of S waves through the core was not sufficient evidence to persuade seismologists that it is fluid (contrary to modern textbook statements). Not until 1926 did Harold Jeffreys refute the arguments for solidity and establish that the core is liquid. In 1936 Inge Lehmann discovered the small inner core. K. E. Bullen argued, on the basis of plausible assumptions about compressibility and density, that the inner core is solid. Attempts to find seismic signals that have passed through the inner core as S waves have so far failed (with one possible exception), but analysis of free oscillations provided fairly convincing evidence for its solidity.

  17. Core physics analysis of 100% MOX Core in IRIS

    Energy Technology Data Exchange (ETDEWEB)

    Franceschini, F.; Petrovic, B. [Westinghouse Electric Company LLC, Science and Technology Dept., 1344 Beulah Road, Pittsburgh, PA 15235 (United States)

    2006-07-01

    International Reactor Innovative and Secure (IRIS) is an advanced small-to-medium-size (1000 MWt) Pressurized Water Reactor (PWR), targeting deployment around 2015. Its reference core design is based on the current Westinghouse UO{sub 2} fuel with less than 5% {sup 235}U, and the analysis has been previously completed confirming good performance. The full MOX fuel core is currently under evaluation as one of the alternatives for the second wave of IRIS reactors. A full 3-D neutronic analysis has been performed to examine main core performance parameters, such as critical boron concentration, peaking factors, discharge burnup, etc. The enhanced moderation of the IRIS fuel lattice facilitates MOX core design, and all the obtained results are within the requirements, confirming viability of this option from the reactor physics standpoint. (authors)

  18. Unique core genomes of the bacterial family vibrionaceae: insights into niche adaptation and speciation

    Directory of Open Access Journals (Sweden)

    Kahlke Tim

    2012-05-01

    Full Text Available Abstract Background The criteria for defining bacterial species and even the concept of bacterial species itself are under debate, and the discussion is apparently intensifying as more genome sequence data is becoming available. However, it is still unclear how the new advances in genomics should be used most efficiently to address this question. In this study we identify genes that are common to any group of genomes in our dataset, to determine whether genes specific to a particular taxon exist and to investigate their potential role in adaptation of bacteria to their specific niche. These genes were named unique core genes. Additionally, we investigate the existence and importance of unique core genes that are found in isolates of phylogenetically non-coherent groups. These groups of isolates, that share a genetic feature without sharing a closest common ancestor, are termed genophyletic groups. Results The bacterial family Vibrionaceae was used as the model, and we compiled and compared genome sequences of 64 different isolates. Using the software orthoMCL we determined clusters of homologous genes among the investigated genome sequences. We used multilocus sequence analysis to build a host phylogeny and mapped the numbers of unique core genes of all distinct groups of isolates onto the tree. The results show that unique core genes are more likely to be found in monophyletic groups of isolates. Genophyletic groups of isolates, in contrast, are less common especially for large groups of isolate. The subsequent annotation of unique core genes that are present in genophyletic groups indicate a high degree of horizontally transferred genes. Finally, the annotation of the unique core genes of Vibrio cholerae revealed genes involved in aerotaxis and biosynthesis of the iron-chelator vibriobactin. Conclusion The presented work indicates that genes specific for any taxon inside the bacterial family Vibrionaceae exist. These unique core genes encode

  19. European core curriculum in neurorehabilitation

    NARCIS (Netherlands)

    Sandrini, G.; Binder, H.; Homberg, V.; Saltuari, L.; Tarkka, I.; Smania, N.; Corradini, C.; Giustini, A.; Katterer, C.; Picari, L.; Diserens, K.; Koenig, E.; Geurts, A.C.; Anghelescu, A.; Opara, J.; Tonin, P.; Kwakkel, G.; Golyk, V.; Onose, G.; Perennou, D.; Picelli, A.

    2017-01-01

    To date, medical education lacks Europe-wide standards on neurorehabilitation. To address this, the European Federation of NeuroRehabilitation Societies (EFNR) here proposes a postgraduate neurorehabilitation training scheme. In particular, the European medical core curriculum in neurorehabilitation

  20. Viral Evolution Core | FNLCR Staging

    Science.gov (United States)

    Brandon F. Keele, Ph.D. PI/Senior Principal Investigator, Retroviral Evolution Section Head, Viral Evolution Core Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research Frederick, MD 21702-1201 Tel: 301-846-173

  1. Nanoporous polymer liquid core waveguides

    DEFF Research Database (Denmark)

    Gopalakrishnan, Nimi; Christiansen, Mads Brøkner; Ndoni, Sokol

    2010-01-01

    We demonstrate liquid core waveguides defined by UV to enable selective water infiltration in nanoporous polymers, creating an effective refractive index shift Δn=0.13. The mode confinement and propagation loss in these waveguides are presented.......We demonstrate liquid core waveguides defined by UV to enable selective water infiltration in nanoporous polymers, creating an effective refractive index shift Δn=0.13. The mode confinement and propagation loss in these waveguides are presented....

  2. Core Benefits of Network Participation

    OpenAIRE

    Kheiri Pileh Roud, Ensieh

    2015-01-01

    This study deals with the core benefits of network participation from the maritime companies’ perspective. It mainly focuses on the area of innovation, network qualities and absorptive capacities. A single case study has been conducted to address two research questions; 1) what are the core benefits of network participation for a maritime company? 2) Which qualities of network events influence the benefits for the participants? The main findings show that, the networks are valuable communi...

  3. Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data.

    Science.gov (United States)

    Yang, Laurence; Tan, Justin; O'Brien, Edward J; Monk, Jonathan M; Kim, Donghyuk; Li, Howard J; Charusanti, Pep; Ebrahim, Ali; Lloyd, Colton J; Yurkovich, James T; Du, Bin; Dräger, Andreas; Thomas, Alex; Sun, Yuekai; Saunders, Michael A; Palsson, Bernhard O

    2015-08-25

    Finding the minimal set of gene functions needed to sustain life is of both fundamental and practical importance. Minimal gene lists have been proposed by using comparative genomics-based core proteome definitions. A definition of a core proteome that is supported by empirical data, is understood at the systems-level, and provides a basis for computing essential cell functions is lacking. Here, we use a systems biology-based genome-scale model of metabolism and expression to define a functional core proteome consisting of 356 gene products, accounting for 44% of the Escherichia coli proteome by mass based on proteomics data. This systems biology core proteome includes 212 genes not found in previous comparative genomics-based core proteome definitions, accounts for 65% of known essential genes in E. coli, and has 78% gene function overlap with minimal genomes (Buchnera aphidicola and Mycoplasma genitalium). Based on transcriptomics data across environmental and genetic backgrounds, the systems biology core proteome is significantly enriched in nondifferentially expressed genes and depleted in differentially expressed genes. Compared with the noncore, core gene expression levels are also similar across genetic backgrounds (two times higher Spearman rank correlation) and exhibit significantly more complex transcriptional and posttranscriptional regulatory features (40% more transcription start sites per gene, 22% longer 5'UTR). Thus, genome-scale systems biology approaches rigorously identify a functional core proteome needed to support growth. This framework, validated by using high-throughput datasets, facilitates a mechanistic understanding of systems-level core proteome function through in silico models; it de facto defines a paleome.

  4. Autism, will vitamin D treat core symptoms?

    Science.gov (United States)

    Cannell, John Jacob

    2013-08-01

    No medication exists to treat the core symptoms of autism. However, some children spontaneously improve and have optimal outcomes. Parents of autistic children who have access to swimming pool have reported summertime improvement in symptoms to me. A Japanese case report found the same summer times improvements. If the cause of that summertime improvement could be identified, it may lead to effective treatment. Vitamin D is highly seasonal with a summertime surfeit and a wintertime deficit. The hypotheses that the increased prevalence in the diagnosis of autism is due to better detection imply that parents, teachers and physicians of the 1950s, 60s, and 70s missed this non subtle diagnosis, an unlikely scenario. Recent research indicates that autism often first present itself during the second and third year of life. This is a time when most toddlers have no known sources of vitamin D. Vitamin D has remarkable antioxidant, anti-inflammatory, and anti-autoimmune properties. In vitro, in vivo, and animal experiments provide compelling data for vitamin D's role brain proliferation, differentiation, neurotrophism, neuroprotection, neurotransmission, and neuroplasticity. It also upregulates glutathione, upregulates a suit of genes involved in DNA repair and raises the seizure threshold. Adequate, perhaps pharmacological, doses of vitamin D may have a treatment effect in the core symptoms of autism. Copyright © 2013 Elsevier Ltd. All rights reserved.

  5. The infinitely many genes model with horizontal gene transfer

    OpenAIRE

    Baumdicker, Franz; Pfaffelhuber, Peter

    2013-01-01

    The genome of bacterial species is much more flexible than that of eukaryotes. Moreover, the distributed genome hypothesis for bacteria states that the total number of genes present in a bacterial population is greater than the genome of every single individual. The pangenome, i.e. the set of all genes of a bacterial species (or a sample), comprises the core genes which are present in all living individuals, and accessory genes, which are carried only by some individuals. In order to use acce...

  6. Core break-off mechanism

    Science.gov (United States)

    Myrick, Thomas M. (Inventor)

    2003-01-01

    A mechanism for breaking off and retaining a core sample of a drill drilled into a ground substrate has an outer drill tube and an inner core break-off tube sleeved inside the drill tube. The break-off tube breaks off and retains the core sample by a varying geometric relationship of inner and outer diameters with the drill tube. The inside diameter (ID) of the drill tube is offset by a given amount with respect to its outer diameter (OD). Similarly, the outside diameter (OD) of the break-off tube is offset by the same amount with respect to its inner diameter (ID). When the break-off tube and drill tube are in one rotational alignment, the two offsets cancel each other such that the drill can operate the two tubes together in alignment with the drill axis. When the tubes are rotated 180 degrees to another positional alignment, the two offsets add together causing the core sample in the break-off tube to be displaced from the drill axis and applying shear forces to break off the core sample.

  7. Viscosity of Earth's Outer Core

    CERN Document Server

    Smylie, D E

    2007-01-01

    A viscosity profile across the entire fluid outer core is found by interpolating between measured boundary values, using a differential form of the Arrhenius law governing pressure and temperature dependence. The discovery that both the retrograde and prograde free core nutations are in free decay (Palmer and Smylie, 2005) allows direct measures of viscosity at the top of the outer core, while the reduction in the rotational splitting of the two equatorial translational modes of the inner core allows it to be measured at the bottom. We find 2,371 plus/minus 1,530 Pa.s at the top and 1.247 plus/minus 0.035 x 10^11 Pa.s at the bottom. Following Brazhkin (1998) and Brazhkin and Lyapin (2000) who get 10^2 Pa.s at the top, 10^11 Pa.s at the bottom, by an Arrhenius extrapolation of laboratory experiments, we use a differential form of the Arrhenius law to interpolate along the melting temperature curve to find a viscosity profile across the outer core. We find the variation to be closely log-linear between the meas...

  8. Comprehensive genomic characterization defines human glioblastoma genes and core pathways

    NARCIS (Netherlands)

    Chin, L.; Meyerson, M.; Aldape, K.; Bigner, D.; Mikkelsen, T.; VandenBerg, S.; Kahn, A.; Penny, R.; Gerhard, D. S.; Getz, G.; Brennan, C.; Taylor, B. S.; Winckler, W.; Park, P.; Ladanyi, M.; Hoadley, K. A.; Verhaak, R. G. W.; Hayes, D. N.; Spellman, Paul T.; Absher, D.; Weir, B. A.; Ding, L.; Wheeler, D.; Lawrence, M. S.; Cibulskis, K.; Mardis, E.; Zhang, Jinghui; Wilson, R. K.; Donehower, L.; Wheeler, D. A.; Purdom, E.; Wallis, J.; Laird, P. W.; Herman, J. G.; Schuebel, K. E.; Weisenberger, D. J.; Baylin, S. B.; Schultz, N.; Yao, Jun; Wiedemeyer, R.; Weinstein, J.; Sander, C.; Gibbs, R. A.; Gray, J.; Kucherlapati, R.; Lander, E. S.; Myers, R. M.; Perou, C. M.; McLendon, Roger; Friedman, Allan; Van Meir, Erwin G; Brat, Daniel J; Mastrogianakis, Gena Marie; Olson, Jeffrey J; Lehman, Norman; Yung, W. K. Alfred; Bogler, Oliver; Berger, Mitchel; Prados, Michael; Muzny, Donna; Morgan, Margaret; Scherer, Steve; Sabo, Aniko; Nazareth, Lynn; Lewis, Lora; Hall, Otis; Zhu, Yiming; Ren, Yanru; Alvi, Omar; Yao, Jiqiang; Hawes, Alicia; Jhangiani, Shalini; Fowler, Gerald; San Lucas, Anthony; Kovar, Christie; Cree, Andrew; Dinh, Huyen; Santibanez, Jireh; Joshi, Vandita; Gonzalez-Garay, Manuel L.; Miller, Christopher A.; Milosavljevic, Aleksandar; Sougnez, Carrie; Fennell, Tim; Mahan, Scott; Wilkinson, Jane; Ziaugra, Liuda; Onofrio, Robert; Bloom, Toby; Nicol, Rob; Ardlie, Kristin; Baldwin, Jennifer; Gabriel, Stacey; Fulton, Robert S.; McLellan, Michael D.; Larson, David E.; Shi, Xiaoqi; Abbott, Rachel; Fulton, Lucinda; Chen, Ken; Koboldt, Daniel C.; Wendl, Michael C.; Meyer, Rick; Tang, Yuzhu; Lin, Ling; Osborne, John R.; Dunford-Shore, Brian H.; Miner, Tracie L.; Delehaunty, Kim; Markovic, Chris; Swift, Gary; Courtney, William; Pohl, Craig; Abbott, Scott; Hawkins, Amy; Leong, Shin; Haipek, Carrie; Schmidt, Heather; Wiechert, Maddy; Vickery, Tammi; Scott, Sacha; Dooling, David J.; Chinwalla, Asif; Weinstock, George M.; O'Kelly, Michael; Robinson, Jim; Alexe, Gabriele; Beroukhim, Rameen; Carter, Scott; Chiang, Derek; Gould, Josh; Gupta, Supriya; Korn, Josh; Mermel, Craig; Mesirov, Jill; Monti, Stefano; Nguyen, Huy; Parkin, Melissa; Reich, Michael; Stransky, Nicolas; Garraway, Levi; Golub, Todd; Protopopov, Alexei; Perna, Ilana; Aronson, Sandy; Sathiamoorthy, Narayan; Ren, Georgia; Kim, Hyunsoo; Kong, Sek Won; Xiao, Yonghong; Kohane, Isaac S.; Seidman, Jon; Cope, Leslie; Pan, Fei; Van Den Berg, David; Van Neste, Leander; Yi, Joo Mi; Li, Jun Z.; Southwick, Audrey; Brady, Shannon; Aggarwal, Amita; Chung, Tisha; Sherlock, Gavin; Brooks, James D.; Jakkula, Lakshmi R.; Lapuk, Anna V.; Marr, Henry; Dorton, Shannon; Choi, Yoon Gi; Han, Ju; Ray, Amrita; Wang, Victoria; Durinck, Steffen; Robinson, Mark; Wang, Nicholas J.; Vranizan, Karen; Peng, Vivian; Van Name, Eric; Fontenay, Gerald V.; Ngai, John; Conboy, John G.; Parvin, Bahram; Feiler, Heidi S.; Speed, Terence P.; Socci, Nicholas D.; Olshen, Adam; Lash, Alex; Reva, Boris; Antipin, Yevgeniy; Stukalov, Alexey; Gross, Benjamin; Cerami, Ethan; Wang, Wei Qing; Qin, Li-Xuan; Seshan, Venkatraman E.; Villafania, Liliana; Cavatore, Magali; Borsu, Laetitia; Viale, Agnes; Gerald, William; Topal, Michael D.; Qi, Yuan; Balu, Sai; Shi, Yan; Wu, George; Bittner, Michael; Shelton, Troy; Lenkiewicz, Elizabeth; Morris, Scott; Beasley, Debbie; Sanders, Sheri; Sfeir, Robert; Chen, Jessica; Nassau, David; Feng, Larry; Hickey, Erin; Schaefer, Carl; Madhavan, Subha; Buetow, Ken; Barker, Anna; Vockley, Joseph; Compton, Carolyn; Vaught, Jim; Fielding, Peter; Collins, Francis; Good, Peter; Guyer, Mark; Ozenberger, Brad; Peterson, Jane; Thomson, Elizabeth

    2008-01-01

    Human cancer cells typically harbour multiple chromosomal aberrations, nucleotide substitutions and epigenetic modifications that drive malignant transformation. The Cancer Genome Atlas ( TCGA) pilot project aims to assess the value of large- scale multi- dimensional analysis of these molecular

  9. Full MOX core for PWRs

    Energy Technology Data Exchange (ETDEWEB)

    Puill, A.; Aniel-Buchheit, S. [CEA Centre d`Etudes de Saclay, 91 - Gif-sur-Yvette (France). Direction des Reacteurs Nucleaires

    1997-12-31

    Plutonium management is a major problem of the back end of the fuel cycle. Fabrication costs must be reduced and plant operation simplified. The design of a full MOX PWR core would enable the number of reactors devoted to plutonium recycling to be reduced and fuel zoning to be eliminated. This paper is a contribution to the feasibility studies for achieving such a core without fundamental modification of the current design. In view of the differences observed between uranium and plutonium characteristics it seems necessary to reconsider the safety of a MOX-fuelled PWR. Reduction of the control worth and modification of the moderator density coefficient are the main consequences of using MOX fuel in a PWR. The core reactivity change during a draining or a cooling is thus of prime interest. The study of core global draining leads to the following conclusion: only plutonium fuels of very poor quality (i.e. with low fissile content) cannot be used in a 900 MWe PWR because of a positive global voiding reactivity effect. During a cooling accident, like an spurious opening of a secondary-side valve, the hypothetical return to criticality of a 100% MOX core controlled by means of 57 control rod clusters (made of hafnium-clad B{sub 4}C rods with a 90% {sup 10}B content) depends on the isotopic plutonium composition. But safety criteria can be complied with for all isotopic compositions provided the {sup 10}B content of the soluble boron is increased to a value of 40%. Core global draining and cooling accidents do not present any major obstacle to the feasibility of a 100% MOX PWR, only minor hardware modifications will be required. (author)

  10. The core and unique proteins of haloarchaea

    Directory of Open Access Journals (Sweden)

    Capes Melinda D

    2012-01-01

    Full Text Available Abstract Background Since the first genome of a halophilic archaeon was sequenced in 2000, biologists have been advancing the understanding of genomic characteristics that allow for survival in the harsh natural environments of these organisms. An increase in protein acidity and GC-bias in the genome have been implicated as factors in tolerance to extreme salinity, desiccation, and high solar radiation. However, few previous attempts have been made to identify novel genes that would permit survival in such extreme conditions. Results With the recent release of several new complete haloarchaeal genome sequences, we have conducted a comprehensive comparative genomic analysis focusing on the identification of unique haloarchaeal conserved proteins that likely play key roles in environmental adaptation. Using bioinformatic methods, we have clustered 31,312 predicted proteins from nine haloarchaeal genomes into 4,455 haloarchaeal orthologous groups (HOGs. We assigned likely functions by association with established COG and KOG databases in NCBI. After identifying homologs in four additional haloarchaeal genomes, we determined that there were 784 core haloarchaeal protein clusters (cHOGs, of which 83 clusters were found primarily in haloarchaea. Further analysis found that 55 clusters were truly unique (tucHOGs to haloarchaea and qualify as signature proteins while 28 were nearly unique (nucHOGs, the vast majority of which were coded for on the haloarchaeal chromosomes. Of the signature proteins, only one example with any predicted function, Ral, involved in desiccation/radiation tolerance in Halobacterium sp. NRC-1, was identified. Among the core clusters, 33% was predicted to function in metabolism, 25% in information transfer and storage, 10% in cell processes and signaling, and 22% belong to poorly characterized or general function groups. Conclusion Our studies have established conserved groups of nearly 800 protein clusters present in all

  11. Ice Core Dating Software for Interactive Dating of Ice Cores

    Science.gov (United States)

    Kurbatov, A. V.; Mayewski, P. A.; Abdul Jawad, B. S.

    2005-12-01

    Scientists involved in ice core dating are well familiar with the problem of identification and recording the depth of annual signals using stable isotopes, glaciochemistry, ECM (electrical conductivity), DEP (dielectric properties) and particle counter data. Traditionally all parameters used for ice core dating were plotted as a function of depth, printed and after years were marked on the paper, converted to depth vs. age time scale. To expedite this tedious and manual process we developed interactive computer software, Ice core Dating (ICD) program. ICD is written in Java programming language, and uses GPL and GPL site licensed graphic libraries. The same 3.5 Mb in size pre-compiled single jar file, that includes all libraries and application code, was successfully tested on WinOS, Mac OSX, Linux, and Solaris operating systems running Java VM version 1.4. We have followed the modular design philosophy in our source code so potential integration with other software modules, data bases and server side distributed computer environments can be easily implemented. We expect to continue development of new suites of tools for easy integration of ice core data with other available time proxies. ICD is thoroughly documented and comes with a technical reference and cookbook that explains the purpose of the software and its many features, and provides examples to help new users quickly become familiar with the operation and philosophy of the software. ICD is available as a free download from the Climate Change Institute web site ( under the terms of GNU GPL public license.

  12. Core physics analysis of 100% MOX core in IRIS

    Energy Technology Data Exchange (ETDEWEB)

    Franceschini, Fausto [Westinghouse Electric Company LLC, Science and Technology Department, Pittsburgh, PA 15235 (United States)], E-mail: FranceF@westinghouse.com; Petrovic, Bojan [Georgia Institute of Technology, Nuclear and Radiological Engineering, G.W. Woodruff School, Atlanta, GA 30332-0405 (United States)

    2008-09-15

    International Reactor Innovative and Secure (IRIS) is an advanced small-to-medium-size (1000 MWt) Pressurized Water Reactor (PWR), targeting deployment around 2015. Its reference core design is based on the current Westinghouse UO{sub 2} fuel with less than 5% {sup 235}U, and the analysis has been previously completed confirming good performance for that case. The full MOX fuel core is currently under evaluation as one of the alternatives for the second wave of IRIS reactors. A full 3-D neutronic analysis has been performed to examine main core performance and safety parameters, such as critical boron concentration, peaking factors, discharge burnup, reactivity coefficients, shut-down margin, etc. In addition, the basis to perform load follow maneuvers via the Westinghouse innovative strategy MSHIM has been established. The enhanced moderation of the IRIS fuel lattice facilitates MOX core design, and all the obtained results are within the operational and safety limits considered thus confirming viability of this option from the reactor physics standpoint.

  13. The myth of core stability.

    Science.gov (United States)

    Lederman, Eyal

    2010-01-01

    The principle of core stability has gained wide acceptance in training for the prevention of injury and as a treatment modality for rehabilitation of various musculoskeletal conditions in particular of the lower back. There has been surprisingly little criticism of this approach up to date. This article re-examines the original findings and the principles of core stability/spinal stabilisation approaches and how well they fare within the wider knowledge of motor control, prevention of injury and rehabilitation of neuromuscular and musculoskeletal systems following injury.

  14. Core-shell nanostructured catalysts.

    Science.gov (United States)

    Zhang, Qiao; Lee, Ilkeun; Joo, Ji Bong; Zaera, Francisco; Yin, Yadong

    2013-08-20

    Novel nanotechnologies have allowed great improvements in the syn-thesis of catalysts with well-controlled size, shape, and surface properties. Transition metal nanostructures with specific sizes and shapes, for instance, have shown great promise as catalysts with high selectivities and relative ease of recycling. Researchers have already demonstrated new selective catalysis with solution-dispersed or supported-metal nanocatalysts, in some cases applied to new types of reactions. Several challenges remain, however, particularly in improving the structural stability of the catalytic active phase. Core-shell nanostructures are nanoparticles encapsulated and protected by an outer shell that isolates the nanoparticles and prevents their migration and coalescence during the catalytic reactions. The synthesis and characterization of effective core-shell catalysts has been at the center of our research efforts and is the focus of this Account. Efficient core-shell catalysts require porous shells that allow free access of chemical species from the outside to the surface of nanocatalysts. For this purpose, we have developed a surface-protected etching process to prepare mesoporous silica and titania shells with controllable porosity. In certain cases, we can tune catalytic reaction rates by adjusting the porosity of the outer shell. We also designed and successfully applied a silica-protected calcination method to prepare crystalline shells with high surface area, using anatase titania as a model system. We achieved a high degree of control over the crystallinity and porosity of the anatase shells, allowing for the systematic optimization of their photocatalytic activity. Core-shell nanostructures also provide a great opportunity for controlling the interaction among the different components in ways that might boost structural stability or catalytic activity. For example, we fabricated a SiO₂/Au/N-doped TiO₂ core-shell photocatalyst with a sandwich structure that showed

  15. Core Task and Organizational Reality

    DEFF Research Database (Denmark)

    Vikkelsø, Signe

    2015-01-01

    of core objects such as ‘task’ and ‘coordination,’ contemporary organization studies emphasize, much like other social science disciplines, broader topics such as ‘network,’ ‘identity,’ and ‘change.’ The paper argues that this altered focus and vocabulary is accompanied by a diminished ability to specify...... and intervene into the practical reality of organizations. It further argues that a discipline's core objects are not anachronisms to be discarded with, but crucial for specifying reality in ways that have proven practically relevant and still are....

  16. Regulatory Enhancer-Core-Promoter Communication via Transcription Factors and Cofactors.

    Science.gov (United States)

    Zabidi, Muhammad A; Stark, Alexander

    2016-12-01

    Gene expression is regulated by genomic enhancers that recruit transcription factors and cofactors to activate transcription from target core promoters. Over the past years, thousands of enhancers and core promoters in animal genomes have been annotated, and we have learned much about the domain structure in which regulatory genomes are organized in animals. Enhancer-core-promoter targeting occurs at several levels, including regulatory domains, DNA accessibility, and sequence-encoded core-promoter specificities that are likely mediated by different regulatory proteins. We review here current knowledge about enhancer-core-promoter targeting, regulatory communication between enhancers and core promoters, and the protein factors involved. We conclude with an outlook on open questions that we find particularly interesting and that will likely lead to additional insights in the upcoming years. Copyright © 2016 Elsevier Ltd. All rights reserved.

  17. Gelcasting Alumina Cores for Investment Casting

    Energy Technology Data Exchange (ETDEWEB)

    Janney, M A; Klug, F J

    2001-01-01

    General Electric currently uses silica investment casting cores for making superalloy turbine blades. The silica core technology does not provide the degree of dimensional control needed for advanced turbine system manufacture. The sum of the various process variables in silica core manufacturing produces cores that have more variability than is allowed for in advanced, power-generation gas turbine airfoils.

  18. Core Stability Training for Injury Prevention

    OpenAIRE

    Huxel Bliven, Kellie C.; Anderson, Barton E.

    2013-01-01

    Context: Enhancing core stability through exercise is common to musculoskeletal injury prevention programs. Definitive evidence demonstrating an association between core instability and injury is lacking; however, multifaceted prevention programs including core stabilization exercises appear to be effective at reducing lower extremity injury rates. Evidence Acquisition: PubMed was searched for epidemiologic, biomechanic, and clinical studies of core stability for injury prevention (keywords: ...

  19. Gene Therapy

    Science.gov (United States)

    Gene therapy Overview Gene therapy involves altering the genes inside your body's cells in an effort to treat or stop disease. Genes contain your ... that don't work properly can cause disease. Gene therapy replaces a faulty gene or adds a new ...

  20. One Health Core Competency Domains

    Directory of Open Access Journals (Sweden)

    Rebekah Frankson

    2016-09-01

    Full Text Available The emergence of complex global challenges at the convergence of human, animal, and environmental health has catalyzed a movement supporting ‘One Health’ approaches. Despite recognition of the importance of One Health approaches to address these complex challenges, little effort has been directed at identifying the seminal knowledge, skills and attitudes necessary for individuals to successfully contribute to One Health efforts. Between 2008 and 2011, three groups independently embarked on separate initiatives to identify core competencies for professionals involved with One Health approaches. Core competencies were considered critically important for guiding curriculum development and continuing professional education as they describe the knowledge, skills and attitudes required to be effective. A workshop was convened in 2012 to synthesize the various strands of work on One Health competencies. Despite having different mandates, participants, and approaches, all of these initiatives identified similar core competency domains: management; communication and informatics; values and ethics; leadership; teams and collaboration; roles and responsibilities; and systems thinking. These core competency domains have been used to develop new continuing professional education programs for One Health professionals and help university curricula prepare new graduates to be able to contribute more effectively to One Health approaches.

  1. Stability of Molten Core Materials

    Energy Technology Data Exchange (ETDEWEB)

    Layne Pincock; Wendell Hintze

    2013-01-01

    The purpose of this report is to document a literature and data search for data and information pertaining to the stability of nuclear reactor molten core materials. This includes data and analysis from TMI-2 fuel and INL’s LOFT (Loss of Fluid Test) reactor project and other sources.

  2. Core shift effect in blazars

    Science.gov (United States)

    Agarwal, A.; Mohan, P.; Gupta, Alok C.; Mangalam, A.; Volvach, A. E.; Aller, M. F.; Aller, H. D.; Gu, M. F.; Lähteenmäki, A.; Tornikoski, M.; Volvach, L. N.

    2017-07-01

    We studied the pc-scale core shift effect using radio light curves for three blazars, S5 0716+714, 3C 279 and BL Lacertae, which were monitored at five frequencies (ν) between 4.8 and 36.8 GHz using the University of Michigan Radio Astronomical Observatory (UMRAO), the Crimean Astrophysical Observatory (CrAO) and Metsähovi Radio Observatory for over 40 yr. Flares were Gaussian fitted to derive time delays between observed frequencies for each flare (Δt), peak amplitude (A) and their half width. Using A ∝ να, we infer α in the range of -16.67-2.41 and using Δ t ∝ ν ^{1/k_r}, we infer kr ∼ 1, employed in the context of equipartition between magnetic and kinetic energy density for parameter estimation. From the estimated core position offset (Ωrν) and the core radius (rcore), we infer that opacity model may not be valid in all cases. The mean magnetic field strengths at 1 pc (B1) and at the core (Bcore) are in agreement with previous estimates. We apply the magnetically arrested disc model to estimate black hole spins in the range of 0.15-0.9 for these blazars, indicating that the model is consistent with expected accretion mode in such sources. The power-law-shaped power spectral density has slopes -1.3 to -2.3 and is interpreted in terms of multiple shocks or magnetic instabilities.

  3. Fuzzy Cores and Fuzzy Balancedness

    NARCIS (Netherlands)

    van Gulick, G.; Norde, H.W.

    2011-01-01

    We study the relation between the fuzzy core and balancedness for fuzzy games. For regular games, this relation has been studied by Bondareva (1963) and Shapley (1967). First, we gain insight in this relation when we analyse situations where the fuzzy game is continuous. Our main result shows that

  4. Fuzzy cores and fuzzy balancedness

    NARCIS (Netherlands)

    van Gulick, G.; Norde, H.W.

    2013-01-01

    We study the relation between the fuzzy core and balancedness for fuzzy games. For regular games, this relation has been studied by Bondareva (Problemy Kibernet 10:119–139, 1963) and Shapley (Naval Res Logist Q 14: 453–460, 1967). First, we gain insight in this relation when we analyse situations

  5. Common Core: Fact vs. Fiction

    Science.gov (United States)

    Greene, Kim

    2012-01-01

    Despite students' interest in informational text, it has played second fiddle in literacy instruction for years. Now, though, nonfiction is getting its turn in the spotlight. The Common Core State Standards require that students become thoughtful consumers of complex, informative texts--taking them beyond the realm of dry textbooks and…

  6. Epistemology and ontology in core ontologies: FOLaw and LRI-Core, two core ontologies for law

    OpenAIRE

    Breukers, J.A.P.J.; Hoekstra, R.J.

    2004-01-01

    For more than a decade constructing ontologies for legal domains, we, at the Leibniz Center for Law, felt really the need to develop a core ontology for law that would enable us to re-use the common denominator of the various legal domains. In this paper we present two core ontologies for law. The first one was the result of a PhD thesis by [Valente, 1995], called FOLaw. FOLaw speci- fies functional dependencies between types of knowledge involved in legal reasoning. Despite the fact that FOL...

  7. Cores to the rescue: how old cores enable new science

    Science.gov (United States)

    Ito, E.; Noren, A. J.; Brady, K.

    2016-12-01

    The value of archiving scientific specimens and collections for the purpose of enabling further research using new analytical techniques, resolving conflicting results, or repurposing them for entirely new research, is often discussed in abstract terms. We all agree that samples with adequate metadata ought to be archived systematically for easy access, for a long time and stored under optimal conditions. And yet, as storage space fills, there is a temptation to cull the collection, or when a researcher retires, to discard the collection unless the researcher manages to make his or her own arrangement for the collection to be accessioned elsewhere. Nobody has done anything with these samples in over 20 years! Who would want them? It turns out that plenty of us do want them, if we know how to find them and if they have sufficient metadata to assess past work and suitability for new analyses. The LacCore collection holds over 33 km of core from >6700 sites in diverse geographic locations worldwide with samples collected as early as 1950s. From these materials, there are many examples to illustrate the scientific value of archiving geologic samples. One example that benefitted Ito personally were cores from Lakes Mirabad and Zeribar, Iran, acquired in 1963 by Herb Wright and his associates. Several doctoral and postdoctoral students generated and published paleoecological reconstructions based on cladocerans, diatoms, pollen or plant macrofossils, mostly between 1963 and 1967. The cores were resampled in 1990s by a student being jointly advised by Wright and Ito for oxygen isotope analysis of endogenic calcite. The results were profitably compared with pollen and the results published in 2001 and 2006. From 1979 until very recently, visiting Iran for fieldwork was not pallowed for US scientists. Other examples will be given to further illustrate the power of archived samples to advance science.

  8. Separated core turbofan engine; Core bunrigata turbofan engine

    Energy Technology Data Exchange (ETDEWEB)

    Saito, Y.; Endo, M.; Matsuda, Y.; Sugiyama, N.; Sugahara, N.; Yamamoto, K. [National Aerospace Laboratory, Tokyo (Japan)

    1996-04-01

    This report outlines the separated core turbofan engine. This engine is featured by parallel separated arrangement of a fan and core engine which are integrated into one unit in the conventional turbofan engine. In general, cruising efficiency improvement and noise reduction are achieved by low fan pressure ratio and low exhaust speed due to high bypass ratio, however, it causes various problems such as large fan and nacelle weight due to large air flow rate of a fan, and shift of an operating point affected by flight speed. The parallel separated arrangement is thus adopted. The stable operation of a fan and core engine is easily retained by independently operating air inlet unaffected by fan. The large degree of freedom of combustion control is also obtained by independent combustor. Fast response, simple structure and optimum aerodynamic design are easily achieved. This arrangement is also featured by flexibility of development and easy maintenance, and by various merits superior to conventional turbofan engines. It has no technological problems difficult to be overcome, and is also suitable for high-speed VTOL transport aircraft. 4 refs., 5 figs.

  9. Espaço de cores

    Directory of Open Access Journals (Sweden)

    Claudia Feitosa-Santana

    2006-01-01

    Full Text Available O artigo apresenta definições para os termos espaço de cores e sistemas de cores; classifica, de acordo com David Brainard (2003, os sistemas de cores em dois grupos: aparência de cores e diferenças de cores. Dentre os diversos sistemas de cores existentes, o artigo descreve dois deles: o sistema de cores Munsell &– um dos mais utilizados entre os sistemas de aparência de cores &– e a descrição do sistema de cores CIE 1931 &– um dos mais utilizados dentre os sistemas de diferença de cores. Faz-se uma retrospectiva histórica da busca por espaços de cores que representem a percepção de cores humana assim como as diversas reconstruções de espaços de cores por métodos eletrofisiológicos ou psicofísicos. Muitas dessas reconstruções utilizam a escala multidimensional (mds. O artigo também introduz a possibilidade da reconstrução dos espaços de cores de pacientes com discromatopsia adquirida como uma distorção do espaço de indivíduos tricromatas normais.

  10. Conceptual study of advanced PWR core design

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Young Jin; Chang, Moon Hee; Kim, Keung Ku; Joo, Hyung Kuk; Kim, Young Il; Noh, Jae Man; Hwang, Dae Hyun; Kim, Taek Kyum; Yoo, Yon Jong

    1997-09-01

    The purpose of this project is for developing and verifying the core design concepts with enhanced safety and economy, and associated methodologies for core analyses. From the study of the sate-of-art of foreign advanced reactor cores, we developed core concepts such as soluble boron free, high convertible and enhanced safety core loaded semi-tight lattice hexagonal fuel assemblies. To analyze this hexagonal core, we have developed and verified some neutronic and T/H analysis methodologies. HELIOS code was adopted as the assembly code and HEXFEM code was developed for hexagonal core analysis. Based on experimental data in hexagonal lattices and the COBRA-IV-I code, we developed a thermal-hydraulic analysis code for hexagonal lattices. Using the core analysis code systems developed in this project, we designed a 600 MWe core and studied the feasibility of the core concepts. Two additional scopes were performed in this project : study on the operational strategies of soluble boron free core and conceptual design of large scale passive core. By using the axial BP zoning concept and suitable design of control rods, this project showed that it was possible to design a soluble boron free core in 600 MWe PWR. The results of large scale core design showed that passive concepts and daily load follow operation could be practiced. (author). 15 refs., 52 tabs., 101 figs.

  11. Whole Core Transport Calculation Methodology for a Hexagonal Core

    Energy Technology Data Exchange (ETDEWEB)

    Cho, J. Y.; Kim, K. S.; Lee, C. C.; Zee, S. Q.; Joo, H. G

    2007-07-15

    This report discusses the hexagonal module implemented to the DeCART code and the performance of them. The implemented hexagonal module includes the hexagonal ray tracing and the CMFD acceleration modules. The performance of the implemented hexagonal module is examined for 4 tests of: (1) CMFD acceleration test, (2) the accuracy test of the hexagonal module, (3) the performance test for 2-D NGNP problem and (4) the applicability test for 3-D NGNP problem. The features of the implemented hexagonal modules are: (1) The Modular ray tracing scheme based on a hexagonal assembly and a path linking scheme between the modular rays. (2) Segment generation based on the structure unit. (3) Cell ray approximation: This feature is developed to reduce the memory required to store the segment information. (4) Modified cycle ray scheme that begins the ray tracing at a given surface and finishes if the reflected ray meets the starting surface. This feature is developed to reduce the memory required for the angular flux at the core boundary. (5) Fixed assembly geometry. The pin geometry of the single pin per assembly problem is different from that of the multi-pin problem. The core geometry of a single assembly problem is also different from that of the multi-assembly problem. (6) CMFD module based on unstructured cell. This feature is to deal with the irregular gap cells that are positioned at the assembly boundaries. The examination results of the 4 tests can be summarized as: (1) The CMFD acceleration test shows that the CMFD module speedups about greater than 200 for the core problem. (2) The accuracy test shows that the hexagonal MOC module produces an accurate solution of less than 60 pcm of eigenvalue and less than 2 % of local pin power errors. (3) The performance test for 2-D NGNP problem shows that the implemented hexagonal module works soundly and produces a reasonable solution by cooperating with the existing DeCART library and the other modules. (4) The applicability

  12. Evolution of Hemoglobin and Its Genes

    Science.gov (United States)

    Hardison, Ross C.

    2012-01-01

    Insights into the evolution of hemoglobins and their genes are an abundant source of ideas regarding hemoglobin function and regulation of globin gene expression. This article presents the multiple genes and gene families encoding human globins, summarizes major events in the evolution of the hemoglobin gene clusters, and discusses how these studies provide insights into regulation of globin genes. Although the genes in and around the α-like globin gene complex are relatively stable, the β-like globin gene clusters are more dynamic, showing evidence of transposition to a new locus and frequent lineage-specific expansions and deletions. The cis-regulatory modules controlling levels and timing of gene expression are a mix of conserved and lineage-specific DNA, perhaps reflecting evolutionary constraint on core regulatory functions shared broadly in mammals and adaptive fine-tuning in different orders of mammals. PMID:23209182

  13. Continuous Chemistry in Ice Cores

    DEFF Research Database (Denmark)

    Kjær, Helle Astrid

    corrections. Further the method successfully identified volcanic eruptions as well as the underlying anthropogenic signal related to the industrial pollution peaking in the 1970’s. The pH method was also applied on the Antarctic RICE ice core and proved useful, contrary to both the ECM and melt water......Ice cores provide high resolution records of past climate and environment. In recent years the use of continuous flow analysis (CFA) systems has increased the measurement throughput, while simultaneously decreasing the risk of contaminating the ice samples. CFA measurements of high temporal...... for the continuous determination of dissolved reactive phosphorus (DRP) by means of a reaction with molybdenum blue. The concentration of DRP in polar ice is low and thus the method relies on enhancing the limit of detection by increasing the absorption length by means of a 2.5 metre LiquidWaveguide Capillary Cell...

  14. Early Evolution of Prestellar Cores

    Science.gov (United States)

    Horedt, G. P.

    2013-08-01

    Prestellar cores are approximated by singular polytropic spheres. Their early evolution is studied analytically with a Bondi-like scheme. The considered approximation is meaningful for polytropic exponents γ between 0 and 6/5, implying radial power-law density profiles between r -1 and r -2.5. Gravitationally unstable Jeans and Bonnor-Ebert masses differ at most by a factor of 3.25. Tidally stable prestellar cores must have a mean density contrast >~ 8 with respect to the external parent cloud medium. The mass-accretion rate relates to the cube of equivalent sound speed, as in Shu's seminal paper. The prestellar masses accreted over 105 years cover the whole stellar mass spectrum; they are derived in simple closed form, depending only on the polytropic equation of state. The stellar masses that can be formed via strict conservation of angular momentum are at most of the order of a brown dwarf.

  15. Accelerator driven sub-critical core

    Science.gov (United States)

    McIntyre, Peter M; Sattarov, Akhdiyor

    2015-03-17

    Systems and methods for operating an accelerator driven sub-critical core. In one embodiment, a fission power generator includes a sub-critical core and a plurality of proton beam generators. Each of the proton beam generators is configured to concurrently provide a proton beam into a different area of the sub-critical core. Each proton beam scatters neutrons within the sub-critical core. The plurality of proton beam generators provides aggregate power to the sub-critical core, via the proton beams, to scatter neutrons sufficient to initiate fission in the sub-critical core.

  16. Divergent Chemoenzymatic Synthesis of Asymmetrical-Core-Fucosylated and Core-Unmodified N-Glycans

    NARCIS (Netherlands)

    Li, Tiehai; Huang, Min; Liu, Lin; Wang, Shuo; Moremen, Kelley W; Boons, Geert-Jan|info:eu-repo/dai/nl/088245489

    2016-01-01

    A divergent chemoenzymaytic approach for the preparation of core-fucosylated and core-unmodified asymmetrical N-glycans from a common advances precursor is described. An undecasaccharide was synthesized by sequential chemical glycosylations of an orthogonally protected core fucosylated

  17. Superconducting Vortex with Antiferromagnetic Core

    Energy Technology Data Exchange (ETDEWEB)

    Arovas, D.P. [Department of Physics, University of California at San Diego, La Jolla, California 92093 (United States); Berlinsky, A.J.; Kallin, C.; Zhang, S. [Department of Physics, Stanford University, Stanford, California 94305 (United States)

    1997-10-01

    We show that a superconducting vortex in underdoped high T{sub c} superconductors could have an antiferromagnetic core. This type of vortex configuration arises as a topological solution in the recently constructed SO(5) nonlinear {sigma} model and in Landau-Ginzburg theory with competing antiferromagnetic and superconducting order parameters. Experimental detection of this type of vortex by muon spin resonance and neutron scattering is proposed. {copyright} {ital 1997} {ital The American Physical Society}

  18. Core curriculum illustration: rib fractures.

    Science.gov (United States)

    Dunham, Gregor M; Perez-Girbes, Alexandre; Linnau, Ken F

    2017-06-01

    This is the 24th installment of a series that will highlight one case per publication issue from the bank of cases available online as part of the American Society of Emergency Radiology (ASER) educational resources. Our goal is to generate more interest in and use of our online materials. To view more cases online, please visit the ASER Core Curriculum and Recommendations for Study online at http://www.aseronline.org/curriculum/toc.htm .

  19. Core curriculum illustration: epiploic appendagitis.

    Science.gov (United States)

    Perez-Girbes, Alexandre; Alegre, Alberto; Linnau, Ken F

    2017-10-12

    This is the 45th installment of a series that will highlight one case per publication issue from the bank of cases available online as part of the American Society of Emergency Radiology (ASER) educational resources. Our goal is to generate more interest in and use of our online materials. To view more cases online, please visit the ASER Core Curriculum and Recommendations for Study online at: http://www.erad.org/page/CCIP_TOC .

  20. Core curriculum illustration: pulmonary laceration.

    Science.gov (United States)

    Carson, Daniel; Edwards, Rachael

    2017-09-05

    This is the 44th installment of a series that will highlight one case per publication issue from the bank of cases available online as part of the American Society of Emergency Radiology (ASER) educational resources. Our goal is to generate more interest in and use of our online materials. To view more cases online, please visit the ASER Core Curriculum and Recommendations for Study online at: http://www.erad.org/page/CCIP_TOC .

  1. Rich-cores in networks

    CERN Document Server

    Ma, Athen

    2014-01-01

    A core is said to be a group of central and densely connected nodes which governs the overall behavior of a network. Profiling this meso--scale structure currently relies on a limited number of methods which are often complex, and have scalability issues when dealing with very large networks. As a result, we are yet to fully understand its impact on network properties and dynamics. Here we introduce a simple method to profile this structure by combining the concepts of core/periphery and rich-club. The key challenge in addressing such association of the two concepts is to establish a way to define the membership of the core. The notion of a "rich-club" describes nodes which are essentially the hub of a network, as they play a dominating role in structural and functional properties. Interestingly, the definition of a rich-club naturally emphasizes high degree nodes and divides a network into two subgroups. Our approach theoretically couples the underlying principle of a rich-club with the escape time of a rand...

  2. Coring in deep hardrock formations

    Energy Technology Data Exchange (ETDEWEB)

    Drumheller, D.S.

    1988-08-01

    The United States Department of Energy is involved in a variety of scientific and engineering feasibility studies requiring extensive drilling in hard crystalline rock. In many cases well depths extend from 6000 to 20,000 feet in high-temperature, granitic formations. Examples of such projects are the Hot Dry Rock well system at Fenton Hill, New Mexico and the planned exploratory magma well near Mammoth Lakes, California. In addition to these programs, there is also continuing interest in supporting programs to reduce drilling costs associated with the production of geothermal energy from underground sources such as the Geysers area near San Francisco, California. The overall progression in these efforts is to drill deeper holes in higher temperature, harder formations. In conjunction with this trend is a desire to improve the capability to recover geological information. Spot coring and continuous coring are important elements in this effort. It is the purpose of this report to examine the current methods used to obtain core from deep wells and to suggest projects which will improve existing capabilities. 28 refs., 8 figs., 2 tabs.

  3. Core stability training for injury prevention.

    Science.gov (United States)

    Huxel Bliven, Kellie C; Anderson, Barton E

    2013-11-01

    Enhancing core stability through exercise is common to musculoskeletal injury prevention programs. Definitive evidence demonstrating an association between core instability and injury is lacking; however, multifaceted prevention programs including core stabilization exercises appear to be effective at reducing lower extremity injury rates. PUBMED WAS SEARCHED FOR EPIDEMIOLOGIC, BIOMECHANIC, AND CLINICAL STUDIES OF CORE STABILITY FOR INJURY PREVENTION (KEYWORDS: "core OR trunk" AND "training OR prevention OR exercise OR rehabilitation" AND "risk OR prevalence") published between January 1980 and October 2012. Articles with relevance to core stability risk factors, assessment, and training were reviewed. Relevant sources from articles were also retrieved and reviewed. Stabilizer, mobilizer, and load transfer core muscles assist in understanding injury risk, assessing core muscle function, and developing injury prevention programs. Moderate evidence of alterations in core muscle recruitment and injury risk exists. Assessment tools to identify deficits in volitional muscle contraction, isometric muscle endurance, stabilization, and movement patterns are available. Exercise programs to improve core stability should focus on muscle activation, neuromuscular control, static stabilization, and dynamic stability. Core stabilization relies on instantaneous integration among passive, active, and neural control subsystems. Core muscles are often categorized functionally on the basis of stabilizing or mobilizing roles. Neuromuscular control is critical in coordinating this complex system for dynamic stabilization. Comprehensive assessment and training require a multifaceted approach to address core muscle strength, endurance, and recruitment requirements for functional demands associated with daily activities, exercise, and sport.

  4. CORE SHAPES AND ORIENTATIONS OF CORE-SÉRSIC GALAXIES

    Energy Technology Data Exchange (ETDEWEB)

    Dullo, Bililign T.; Graham, Alister W., E-mail: Bdullo@astro.swin.edu.au [Centre for Astrophysics and Supercomputing, Swinburne University of Technology, Hawthorn, Victoria 3122 (Australia)

    2015-01-01

    The inner and outer shapes and orientations of core-Sérsic galaxies may hold important clues to their formation and evolution. We have therefore measured the central and outer ellipticities and position angles for a sample of 24 core-Sérsic galaxies using archival Hubble Space Telescope (HST) images and data. By selecting galaxies with core-Sérsic break radii R{sub b} —a measure of the size of their partially depleted core—that are ≳ 0.''2, we find that the ellipticities and position angles are quite robust against HST seeing. For the bulk of the galaxies, there is a good agreement between the ellipticities and position angles at the break radii and the average outer ellipticities and position angles determined over R {sub e}/2 < R < R {sub e}, where R {sub e} is the spheroids' effective half light radius. However there are some interesting differences. We find a median ''inner'' ellipticity at R{sub b} of ε{sub med} = 0.13 ± 0.01, rounder than the median ellipticity of the ''outer'' regions ε{sub med} = 0.20 ± 0.01, which is thought to reflect the influence of the central supermassive black hole at small radii. In addition, for the first time we find a trend, albeit weak (2σ significance), such that galaxies with larger (stellar deficit-to-supermassive black hole) mass ratios—thought to be a measure of the number of major dry merger events—tend to have rounder inner and outer isophotes, suggesting a connection between the galaxy shapes and their merger histories. We show that this finding is not simply reflecting the well known result that more luminous galaxies are rounder, but it is no doubt related.

  5. Expression of core antigen of HCV genotype 3a and its evaluation as screening agent for HCV infection in Pakistan

    OpenAIRE

    Yousaf, Muhammad Z; Idrees, Muhammad; Saleem, Zafar; Rehman, Irshad U; Ali, Muhammad

    2011-01-01

    Abstract Background Pakistan is facing a threat from hepatitis C infection which is increasing at an alarming rate throughout the country. More specific and sensitive screening assays are needed to timely and correctly diagnose this infection. Methods After RNA extraction from specimen (HCV-3a), cDNA was synthesized that was used to amplify full length core gene of HCV 3a. After verification through PCR, DNA sequencing and BLAST, a properly oriented positive recombinant plasmid for core gene ...

  6. Decorin-evoked paternally expressed gene 3 (PEG3) is an upstream regulator of the transcription factor EB (TFEB) in endothelial cell autophagy.

    Science.gov (United States)

    Neill, Thomas; Sharpe, Catherine; Owens, Rick T; Iozzo, Renato V

    2017-09-29

    Macroautophagy is a fundamental and evolutionarily conserved catabolic process that eradicates damaged and aging macromolecules and organelles in eukaryotic cells. Decorin, an archetypical small leucine-rich proteoglycan, initiates a protracted autophagic program downstream of VEGF receptor 2 (VEGFR2) signaling that requires paternally expressed gene 3 (PEG3). We have discovered that PEG3 is an upstream transcriptional regulator of transcription factor EB (TFEB), a master transcription factor of lysosomal biogenesis, for decorin-evoked endothelial cell autophagy. We found a functional requirement of PEG3 for TFEB transcriptional induction and nuclear translocation in human umbilical vein endothelial and PAER2 cells. Mechanistically, inhibiting VEGFR2 or AMP-activated protein kinase (AMPK), a major decorin-activated energy sensor kinase, prevented decorin-evoked TFEB induction and nuclear localization. In conclusion, our findings indicate a non-canonical (nutrient- and energy-independent) mechanism underlying the pro-autophagic bioactivity of decorin via PEG3 and TFEB. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  7. Molecular cloning and characterization of autophagy-related gene TmATG8 in Listeria-invaded hemocytes of Tenebrio molitor.

    Science.gov (United States)

    Tindwa, Hamisi; Jo, Yong Hun; Patnaik, Bharat Bhusan; Lee, Yong Seok; Kang, Sang Sun; Han, Yeon Soo

    2015-07-01

    Macroautophagy (hereinafter called autophagy) is a highly regulated process used by eukaryotic cells to digest portions of the cytoplasm that remodels and recycles nutrients and disposes of unwanted cytoplasmic constituents. Currently 36 autophagy-related genes (ATG) and their homologs have been characterized in yeast and higher eukaryotes, including insects. In the present study, we identified and functionally characterized the immune function of an ATG8 homolog in a coleopteran insect, Tenebrio molitor (TmATG8). The cDNA of TmATG8 comprises of an ORF of 363 bp that encodes a protein of 120 amino acid residues. TmATG8 transcripts are detected in all the developmental stages analyzed. TmAtg8 protein contains a highly conserved C-terminal glycine residue (Gly116) and shows high amino acid sequence identity (98%) to its Tribolium castaneum homolog, TcAtg8. Loss of function of TmATG8 by RNAi led to a significant increase in the mortality rates of T. molitor larvae against Listeria monocytogenes. Unlike dsEGFP-treated control larvae, TmATG8-silenced larvae failed to turn-on autophagy in hemocytes after injection with L. monocytogenes. These data suggest that TmATG8 play a role in mediating autophagy-based clearance of Listeria in T. molitor. Copyright © 2015 Elsevier Ltd. All rights reserved.

  8. High Efficiency Solar Furnace Core Project

    Data.gov (United States)

    National Aeronautics and Space Administration — It is proposed to develop a high efficiency solar furnace core that greatly lessens the heat losses from the furnace core, either greatly reducing the amount of...

  9. BWR MOX core monitoring at Kernkraftwerk Gundremmingen

    Energy Technology Data Exchange (ETDEWEB)

    Noel, Alejandro [Studsvik Scandpower (Suisse) GmbH, Nussbaumen AG (Switzerland); Holzer, Robert [NIS Ingenieurgesellschaft GmbH, Alzenau (Germany); Anton, Gerd [Studsvik Scandpower GmbH, Norderstedt (Germany); Smith, Kord [Studsvik Scandpower Inc., Idaho Falls (United States)

    2008-07-01

    The replacement of the core monitoring system for twin KWU Boiling Water Reactors (BWR) is presented. The reactors, Kernkraftwerk Gundremmingen B and C (KGG), are located in Germany. Core monitoring for KGG is more challenging than for most BWR reactors due to its core composition with about 30% MOX fuel assemblies. The objectives of this paper are to discuss the specific MOX modelling aspects in CASMO-4/Simulate-3, the impact of the MOX fuel on several core monitoring aspects like the LPRM detector modelling and to present some core monitoring results since the beginning of GARDEL's operation. The available core monitoring results confirm the accuracy of the underlying physical methods. The core monitoring system replacement att KGG was a common project of Studsvik Scandpower and NIS Ingenieurgesellschaft GmbH, where Studsvik Scandpower supplied its standard core monitoring system GARDEL and NIS was responsible for the computer hardware, system integration and plant specific add-ons. (authors)

  10. Optimized Cellular Core for Rotorcraft Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Patz Materials and Technologies has developed, produced and tested, as part of the Phase-I SBIR, a new form of composite cellular core material, named Interply Core,...

  11. Exploration of the core metabolism of symbiotic bacteria

    Directory of Open Access Journals (Sweden)

    Klein Cecilia Coimbra

    2012-08-01

    Full Text Available Abstract Background A large number of genome-scale metabolic networks is now available for many organisms, mostly bacteria. Previous works on minimal gene sets, when analysing host-dependent bacteria, found small common sets of metabolic genes. When such analyses are restricted to bacteria with similar lifestyles, larger portions of metabolism are expected to be shared and their composition is worth investigating. Here we report a comparative analysis of the small molecule metabolism of symbiotic bacteria, exploring common and variable portions as well as the contribution of different lifestyle groups to the reduction of a common set of metabolic capabilities. Results We found no reaction shared by all the bacteria analysed. Disregarding those with the smallest genomes, we still do not find a reaction core, however we did find a core of biochemical capabilities. While obligate intracellular symbionts have no core of reactions within their group, extracellular and cell-associated symbionts do have a small core composed of disconnected fragments. In agreement with previous findings in Escherichia coli, their cores are enriched in biosynthetic processes whereas the variable metabolisms have similar ratios of biosynthetic and degradation reactions. Conversely, the variable metabolism of obligate intracellular symbionts is enriched in anabolism. Conclusion Even when removing the symbionts with the most reduced genomes, there is no core of reactions common to the analysed symbiotic bacteria. The main reason is the very high specialisation of obligate intracellular symbionts, however, host-dependence alone is not an explanation for such absence. The composition of the metabolism of cell-associated and extracellular bacteria shows that while they have similar needs in terms of the building blocks of their cells, they have to adapt to very distinct environments. On the other hand, in obligate intracellular bacteria, catabolism has largely disappeared

  12. Core Stability of Vertex Cover Games

    OpenAIRE

    Fang, Qizhi; Kong, Liang; Zhao, Jia

    2008-01-01

    In this paper, we focus on the core stability of vertex cover games, which arise from vertex cover problems on graphs. Based on duality theory of linear programming, we prove that a balanced vertex cover game has a stable core if and only if every edge belongs to a maximum matching in the underlying graph. We also prove that for a totally balanced vertex cover game, the core largeness, extendability, and exactness are all equivalent, which implies core stability. Furtherm...

  13. Core Processes: Earth's eccentric magnetic field

    DEFF Research Database (Denmark)

    Finlay, Chris

    2012-01-01

    Earth’s magnetic field is characterized by a puzzling hemispheric asymmetry. Calculations of core dynamo processes suggest that lopsided growth of the planet’s inner core may be part of the cause.......Earth’s magnetic field is characterized by a puzzling hemispheric asymmetry. Calculations of core dynamo processes suggest that lopsided growth of the planet’s inner core may be part of the cause....

  14. Characterizing core stability with fuzzy games

    OpenAIRE

    Shellshear, Evan

    2009-01-01

    This paper investigates core stability of cooperative, TU games via a fuzzy extension of the totally balanced cover of a TU game. The stability of the core of the fuzzy extension of a game, the concave extension, is shown to reflect the core stability of the original game and vice versa. Stability of the core is then shown to be equivalent to the existence of an equilibrium of a certain correspondence.

  15. Core trénink ve florbale

    OpenAIRE

    Mašková, Alžběta

    2014-01-01

    Title: Use of core training in floorball Objectives: Present an overview of research papers regarding core training and its possible use in floorball Tasks: First aim of this thesis is to provide description and explanation of the core training by using available literature, research papers, bachelor or magister thesis and also thesis of the coaching school. Second aim is to analyze the necessary components of floorball player's performance relative to the core training. This is followed by a...

  16. Origin of a novel protein-coding gene family with similar signal sequence in Schistosoma japonicum

    National Research Council Canada - National Science Library

    Mbanefo, Evaristus Chibunna; Chuanxin, Yu; Kikuchi, Mihoko; Shuaibu, Mohammed Nasir; Boamah, Daniel; Kirinoki, Masashi; Hayashi, Naoko; Chigusa, Yuichi; Osada, Yoshio; Hamano, Shinjiro; Hirayama, Kenji

    2012-01-01

    ...). To find the mechanism underlying the origination of these genes with similar core promoter regions and signal sequence, we adopted an integrated approach utilizing whole genome, transcriptome...

  17. Influence of core electrons on plasmon oscillations

    Science.gov (United States)

    Lipparini, E.; Pederiva, Francesco

    1993-09-01

    Core electrons constitute a polarizable background which tends to screen the plasma oscillations. The influence of core electrons on plasmon dispersion is studied with sum rule techniques. Analytical expressions are derived for the surface plasmon of flat surfaces and of small metal particles. Core polarization explains semiquantitatively the blue-shift of the surface plasmon recently observed in silver systems.

  18. Mars: a new core-crystallization regime

    NARCIS (Netherlands)

    Stewart, A.J.; Schmidt, M.W.; van Westrenen, W.; Liebske, C.

    2007-01-01

    The evolution of the martian core is widely assumed to mirror the characteristics observed for Earth's core. Data from experiments performed on iron-sulfur and iron-nickel-sulfur systems at pressures corresponding to the center of Mars indicate that its core is presently completely liquid and that

  19. Common Core: Teaching Optimum Topic Exploration (TOTE)

    Science.gov (United States)

    Karge, Belinda Dunnick; Moore, Roxane Kushner

    2015-01-01

    The Common Core has become a household term and yet many educators do not understand what it means. This article explains the historical perspectives of the Common Core and gives guidance to teachers in application of Teaching Optimum Topic Exploration (TOTE) necessary for full implementation of the Common Core State Standards. An effective…

  20. Simplifying the ELA Common Core; Demystifying Curriculum

    Science.gov (United States)

    Schmoker, Mike; Jago, Carol

    2013-01-01

    The English Language Arts (ELA) Common Core State Standards ([CCSS], 2010) could have a transformational effect on American education. Though the process seems daunting, one can begin immediately integrating the essence of the ELA Common Core in every subject area. This article shows how one could implement the Common Core and create coherent,…

  1. Improving Core Strength to Prevent Injury

    Science.gov (United States)

    Oliver, Gretchen D.; Adams-Blair, Heather R.

    2010-01-01

    Regardless of the sport or skill, it is essential to have correct biomechanical positioning, or postural control, in order to maximize energy transfer. Correct postural control requires a strong, stable core. A strong and stable core allows one to transfer energy effectively as well as reduce undue stress. An unstable or weak core, on the other…

  2. Full MOX core design for PWR

    Energy Technology Data Exchange (ETDEWEB)

    Komano, Y.; Tochihara, H.; Ishida, M. [Mitsubishi Heavy Industries Ltd., Tokyo (Japan)

    1999-12-01

    Full MOX core design for APWR was analyzed in nuclear design, fuel integrity analysis, thermal hydraulic design and safety analysis et. al. Feasibility of Full MOX core was confirmed from these analyses without any large modifications. Full MOX PWR core has very good characteristics in which single Pu content in an assembly, burnable poison free, higher burnup and longer cycle operation are feasible. (author)

  3. Reinforcement core facilitates O-ring installation

    Science.gov (United States)

    1965-01-01

    Reinforcement core holds O-ring in place within a structure while adjacent parts are being assembled. The core in the O-ring adds circumferential rigidity to the O-ring material. This inner core does not appreciably affect the sectional elasticity or gland-sealing characteristics of the O-ring.

  4. Heterogeneity and anisotropy of Earth's inner core

    NARCIS (Netherlands)

    Deuss, Arwen|info:eu-repo/dai/nl/412396610

    2014-01-01

    Seismic observations provide strong evidence that Earth's inner core is anisotropic, with larger velocity in the polar than in the equatorial direction. The top 60-80 km of the inner core is isotropic; evidence for an innermost inner core is less compelling. The anisotropy is most likely due to

  5. Identifying Core vs. Non-Core Activities of Household Members

    Directory of Open Access Journals (Sweden)

    Mahdieh Allahviranloo

    2016-02-01

    Full Text Available Understanding scheduling behavior of households has been the focus of research for nearly half a century. Presumably activity engagement is being impacted by the importance of the activity to household members as well as time and cost constraints. Depending on the level of time budget, household members would eliminates some activities from the agenda or replace them with higher priority ones. In this paper, in order to capture the importance of different activities, we propose a methodology to schedule household activities under different levels of uncertainty about the importance of the activity. In this approach we combine discrete choice models and concepts of Fuzzy logic to identify core versus non-core activities in the agenda. The possibility of inclusion of an activity is the agenda is computed by estimating the expected importance of the activity and mapping to a set of fuzzy graphs. Activity scheduling and selection is then modeled as the outcome of a mixed integer optimization problem, in which the objective function is maximizing the expected desirability gained from activities and total saved time, subject to network connectivity, time windows, time budget and cost budget constraints.

  6. Identifying gene expression modules that define human cell fates

    OpenAIRE

    Germanguz, I; Listgarten, J; Cinkornpumin, J.; Solomon, A; Gaeta, X.; Lowry, W. E.

    2016-01-01

    Using a compendium of cell-state-specific gene expression data, we identified genes that uniquely define cell states, including those thought to represent various developmental stages. Our analysis sheds light on human cell fate through the identification of core genes that are altered over several developmental milestones, and across regional specification. Here we present cell-type specific gene expression data for 17 distinct cell states and demonstrate that these modules of genes can in f...

  7. ARTEMISTM Core Simulator: Latest Developments

    Science.gov (United States)

    Hobson, Greg; Bolloni, Hans-Wilhelm; Breith, Karl-Albert; Dall'Osso, Aldo; van Geemert, René; Haase, Hartmut; Hartmann, Bettina; Leberig, Mario; Porsch, Dieter; Pothet, Baptiste; Riedmann, Michael; Sieber, Galina; Tomatis, Daniele

    2014-06-01

    AREVA has developed a new coupled neutronics/thermal-hydraulics code system, ARCADIA®. It makes use of modern computing resources to enable more realistic reactor analysis as improved understanding of nuclear reactor behavior is the basis for efficient margin management, i.e. optimization of safety and performance. One of the principal components of this new system is the core simulator, ARTEMIS™. The purpose of this paper is to recall its features, present the latest developments and give a summary of the validation tests.

  8. HPLWR fine mesh core analysis

    Energy Technology Data Exchange (ETDEWEB)

    Temesvari, E.; Maraczy, C.; Hegyi, G.; Hordosy, G.; Molnar, A. [Hungarian Academy of Sciences, Budapest (Hungary). Centre for Energy Research

    2014-08-15

    The European version of Supercritical Water Reactors (SCWR), the High Performance Light Water Reactor (HPLWR) operates in the thermodynamically supercritical region of water. Our basic objective was to elaborate a stationary coupled neutronic-thermohydraulic code capable for the calculation of the actual 3-pass core design with fuel assembly clusters. The calculations covered the neutronic transport calculations of HPLWR fuel assemblies, the coupled neutronic-thermohydraulic global calculations and the pin-wise analysis. Applying conservative assumptions, the relation to the linear heat rate and maximum cladding temperature limits was checked for the equilibrium cycle of HPLWR with this new code system.

  9. Inner Core Anisotropy in Attenuation

    Science.gov (United States)

    Yu, W.; Wen, L.

    2004-12-01

    It is now well established that the compressional velocity in the Earth's inner core varies in both direction and geographic location. The compressional waves travel faster along the polar directions than along the equatorial directions. Such polar-equatorial difference is interpreted as a result of inner core anisotropy in velocity (with a magnitude of about 3%) and such anisotropy appears to be stronger in the ``western hemisphere" (180oW -40oE) than in the ``eastern hemisphere" (40oE-180oE). Along the equatorial paths, the compressional velocity also exhibits a hemispheric pattern with the eastern hemisphere being about 1% higher than the western hemisphere. Possible explanations for the causes of the velocity in anisotropy and the hemispheric difference in velocity along the equatorial paths include different geometric inclusions of melt or different alignments of iron crystals which are known to be anisotropic in velocities. Here, we report an observation of ubiquitous correlation between small (large) amplitude and fast (slow) travel time of the PKIKP waves sampling the top 300 km of the inner core. We study this correlation by jointly analyzing the differential travel times and amplitude ratios of the PKiKP-PKIKP and the PKPbc-PKIKP phases recorded by the Global Seismographic Network (1990-2001), various regional seismic networks (BANJO, BLSP, FREESIA, GEOFON, GEOSCOPE, Kazakhstan, Kyrgyz, MEDNET, and OHP), and several PASSCAL Networks deployed in Alaska and Antarctica (XE: 1999-2001, XF: 1995-1996, and YI: 1998-1999). Our dataset consists of 310 PKiKP-PKIKP and 240 PKPbc-PKIKP phases, selected from a total of more than 16,000 observations. PKIKP waves exhibit relatively smaller amplitudes for those sampling the eastern hemisphere along the equatorial paths and even smaller amplitudes for those sampling the polar paths in the western hemisphere. One simple explanation for the velocity-attenuation relation is that the inner core is anisotropic in attenuation

  10. gene structure, gene expression

    Indian Academy of Sciences (India)

    Primer 5.0 software. To adjust for RNA quality and diffe- rences in cDNA concentration, we amplified actin as an internal control with the following primers: PtActin-F (5′-TG. AAGGAGAAACTTGCGTAT-3′) and PtActin-R (5′-GCA. CAATGTTACCGTACAGAT-3′). These genes were ampli- fied from first-strand cDNA using ...

  11. Double U-Core Switched Reluctance Machine

    DEFF Research Database (Denmark)

    2016-01-01

    The present invention relates to an electrical machine stator comprising a plurality of stator segments (131,132,133), each segment comprises a first U-core and a second U-core wound with a winding, where the winding being arranged with at least one coil turn, each coil turn comprises a first axial......(s), wherein the first U-core and the second U-core are located adjacent to each other, whereby the winding spans the first and second U-cores. The invention also relates to a SRM machine with a stator mentioned above and a rotor....

  12. Hydrophilic-Core Microcapsules and Their Formation

    Science.gov (United States)

    Calle, Luz M. (Inventor); Li, Wenyan (Inventor); Buhrow, Jerry W. (Inventor); Jolley, Scott T. (Inventor)

    2016-01-01

    Hydrophilic-core microcapsules and methods of their formation are provided. A hydrophilic-core microcapsule may include a shell that encapsulates water with the core substance dissolved or dispersed therein. The hydrophilic-core microcapsules may be formed from an emulsion having hydrophilic-phase droplets dispersed in a hydrophobic phase, with shell-forming compound contained in the hydrophilic phase or the hydrophobic phase and the core substance contained in the hydrophilic phase. The shells of the microcapsules may be capable of being broken down in response to being contacted by an alkali, e.g., produced during corrosion, contacting the shell.

  13. Hydrophobic-Core Microcapsules and Their Formation

    Science.gov (United States)

    Calle, Luz M. (Inventor); Li, Wenyan (Inventor); Buhrow, Jerry W. (Inventor); Jolley, Scott T. (Inventor)

    2016-01-01

    Hydrophobic-core microcapsules and methods of their formation are provided. A hydrophobic-core microcapsule may include a shell that encapsulates a hydrophobic substance with a core substance, such as dye, corrosion indicator, corrosion inhibitor, and/or healing agent, dissolved or dispersed therein. The hydrophobic-core microcapsules may be formed from an emulsion having hydrophobic-phase droplets, e.g., containing the core substance and shell-forming compound, dispersed in a hydrophilic phase. The shells of the microcapsules may be capable of being broken down in response to being contacted by an alkali, e.g., produced during corrosion, contacting the shell.

  14. Nitride stabilized core/shell nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Kuttiyiel, Kurian Abraham; Sasaki, Kotaro; Adzic, Radoslav R.

    2018-01-30

    Nitride stabilized metal nanoparticles and methods for their manufacture are disclosed. In one embodiment the metal nanoparticles have a continuous and nonporous noble metal shell with a nitride-stabilized non-noble metal core. The nitride-stabilized core provides a stabilizing effect under high oxidizing conditions suppressing the noble metal dissolution during potential cycling. The nitride stabilized nanoparticles may be fabricated by a process in which a core is coated with a shell layer that encapsulates the entire core. Introduction of nitrogen into the core by annealing produces metal nitride(s) that are less susceptible to dissolution during potential cycling under high oxidizing conditions.

  15. Comparison of gravity-resisted and gym-based core training on core ...

    African Journals Online (AJOL)

    Conditioning specialists have been incorporating concepts of gravity-resisted core training, both on stable and unstable surfaces, to enhance core endurance despite limited empirical evidence. The purpose of this study was to compare the effects of gravity-resisted and gym-based core training on core endurance.

  16. 77 FR 30435 - In-core Thermocouples at Different Elevations and Radial Positions in Reactor Core

    Science.gov (United States)

    2012-05-23

    ... COMMISSION 10 CFR Part 50 In-core Thermocouples at Different Elevations and Radial Positions in Reactor Core... ``require all holders of operating licenses for nuclear power plants (``NPP'') to operate NPPs with in-core thermocouples at different elevations and radial positions throughout the reactor core.'' DATES: Submit comments...

  17. Characterization and identification of microRNA core promoters in four model species.

    Directory of Open Access Journals (Sweden)

    Xuefeng Zhou

    2007-03-01

    Full Text Available MicroRNAs are short, noncoding RNAs that play important roles in post-transcriptional gene regulation. Although many functions of microRNAs in plants and animals have been revealed in recent years, the transcriptional mechanism of microRNA genes is not well-understood. To elucidate the transcriptional regulation of microRNA genes, we study and characterize, in a genome scale, the promoters of intergenic microRNA genes in Caenorhabditis elegans, Homo sapiens, Arabidopsis thaliana, and Oryza sativa. We show that most known microRNA genes in these four species have the same type of promoters as protein-coding genes have. To further characterize the promoters of microRNA genes, we developed a novel promoter prediction method, called common query voting (CoVote, which is more effective than available promoter prediction methods. Using this new method, we identify putative core promoters of most known microRNA genes in the four model species. Moreover, we characterize the promoters of microRNA genes in these four species. We discover many significant, characteristic sequence motifs in these core promoters, several of which match or resemble the known cis-acting elements for transcription initiation. Among these motifs, some are conserved across different species while some are specific to microRNA genes of individual species.

  18. Research on plasma core reactors

    Science.gov (United States)

    Jarvis, G. A.; Barton, D. M.; Helmick, H. H.; Bernard, W.; White, R. H.

    1976-01-01

    Experiments and theoretical studies are being conducted for NASA on critical assemblies with one-meter diameter by one-meter long low-density cores surrounded by a thick beryllium reflector. These assemblies make extensive use of existing nuclear propulsion reactor components, facilities, and instrumentation. Due to excessive porosity in the reflector, the initial critical mass was 19 kg U(93.2). Addition of a 17 cm thick by 89 cm diameter beryllium flux trap in the cavity reduced the critical mass to 7 kg when all the uranium was in the zone just outside the flux trap. A mockup aluminum UF6 container was placed inside the flux trap and fueled with uranium-graphite elements. Fission distributions and reactivity worths of fuel and structural materials were measured. Finally, an 85,000 cu cm aluminum canister in the central region was fueled with UF6 gas and fission density distributions determined. These results are to be used to guide the design of a prototype plasma core reactor which will test energy removal by optical radiation.

  19. Drilling history core hole DC-8

    Energy Technology Data Exchange (ETDEWEB)

    1978-10-01

    Core hole DC-8 was completed in August, 1978 by Boyles Brothers Drilling Company, Spokane, Washington, under subcontract to Fenix and Scission, Inc. The hole was cored for the US Department of Energy and the Rockwell Hanford Operations' Basalt Waste Isolation Program. Fenix and Scisson, Inc. furnished the engineering, daily supervision of the core drilling activities, and geologic core logging for hole DC-8. Core hole DC-8 is located on the Hanford Site near the Wye Barricade and 50 feet northwest of rotary hole DC-7. The Hanford Site vation coordinates for DC-8 are North 14,955.94 feet and West 14,861.92 coordinates for DC-8 are North 14,955.94 feet and West 14,861.92 mean sea level. The purpose of core hole DC-8 was to core drill vertically through the basalt and interbed units for stratigraphic depth determination and core collection, and to provide a borehole for hydrologic testing and cross-hole seismic shear and pressure wave velocity studies with rotary hole DC-7. The total depth of core hole DC-8 was 4100.5 feet. Core recovery exceeded 97 percent of the total footage cored.

  20. Reconstruction of the biosynthetic pathway for the core fungal polyketide scaffold rubrofusarin in Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Rugbjerg, Peter; Naesby, Michael; Mortensen, Uffe Hasbro

    2013-01-01

    intermediate was converted into nor-rubrofusarin upon expression of the dehydratase gene aurZ from the aurofusarin gene cluster of F. graminearum. Final conversion into rubrofusarin was achieved by expression of the O-methyltransferase encoding gene aurJ, also obtained from the aurofusarin gene cluster....... CONCLUSIONS: The reconstructed pathway for rubrofusarin in S. cerevisiae allows the production of a core scaffold molecule with a branch-point role in several fungal polyketide pathways, thus paving the way for production of further natural pigments and bioactive molecules. Furthermore, the reconstruction...

  1. Circadian expression of clock genes and clock-controlled genes in the rat retina

    NARCIS (Netherlands)

    Kamphuis, Willem; Cailotto, Cathy; Dijk, Frederike; Bergen, Arthur; Buijs, Ruud M.

    2005-01-01

    The circadian expression patterns of genes encoding for proteins that make up the core of the circadian clock were measured in rat retina using real-time quantitative PCR (qPCR). Transcript levels of several genes previously used for normalization of qPCR assays were determined and the effect of

  2. High prevalence of antibodies to core+1/ARF protein in HCV-infected patients with advanced cirrhosis.

    Science.gov (United States)

    Kassela, Katerina; Karakasiliotis, Ioannis; Charpantidis, Stefanos; Koskinas, John; Mylopoulou, Theodora; Mimidis, Konstantinos; Sarrazin, Christoph; Grammatikos, Georgios; Mavromara, Penelope

    2017-07-01

    Hepatitis C virus (HCV) possesses a second open reading frame (ORF) within the core gene encoding an additional protein, known as the alternative reading frame protein (ARFP), F or core+1. The biological significance of the core+1/ARF protein remains elusive. However, several independent studies have shown the presence of core+1/ARFP antibodies in chronically HCV-infected patients. Furthermore, a higher prevalence of core+1/ARFP antibodies was detected in patients with HCV-associated hepatocellular carcinoma (HCC). Here, we investigated the incidence of core+1/ARFPantibodies in chronically HCV-infected patients at different stages of cirrhosis in comparison to chronically HCV-infected patients at earlier stages of disease. Using ELISA, we assessed the prevalence of anti-core+1 antibodies in 30 patients with advanced cirrhosis [model for end-stage liver disease (MELD) ≥15] in comparison with 50 patients with mild cirrhosis (MELD core+1 antibodies, in contrast with 16.5 % of non-cirrhotic HCV patients. Moreover, there was significantly higher positivity for anti-core+1 antibodies in HCV patients with advanced cirrhosis (36.7 %) compared to those with early cirrhosis (24 %) (Pcore+1 antibodies in HCV patients with HCC, suggest that core+1 protein may have a role in virus-associated pathogenesis, and provide evidence to suggest that the levels of anti-core+1 antibodies may serve as a marker for disease progression.

  3. A missense change in the ATG4D gene links aberrant autophagy to a neurodegenerative vacuolar storage disease.

    Science.gov (United States)

    Kyöstilä, Kaisa; Syrjä, Pernilla; Jagannathan, Vidhya; Chandrasekar, Gayathri; Jokinen, Tarja S; Seppälä, Eija H; Becker, Doreen; Drögemüller, Michaela; Dietschi, Elisabeth; Drögemüller, Cord; Lang, Johann; Steffen, Frank; Rohdin, Cecilia; Jäderlund, Karin H; Lappalainen, Anu K; Hahn, Kerstin; Wohlsein, Peter; Baumgärtner, Wolfgang; Henke, Diana; Oevermann, Anna; Kere, Juha; Lohi, Hannes; Leeb, Tosso

    2015-04-01

    Inherited neurodegenerative disorders are debilitating diseases that occur across different species. We have performed clinical, pathological and genetic studies to characterize a novel canine neurodegenerative disease present in the Lagotto Romagnolo dog breed. Affected dogs suffer from progressive cerebellar ataxia, sometimes accompanied by episodic nystagmus and behavioral changes. Histological examination revealed unique pathological changes, including profound neuronal cytoplasmic vacuolization in the nervous system, as well as spheroid formation and cytoplasmic aggregation of vacuoles in secretory epithelial tissues and mesenchymal cells. Genetic analyses uncovered a missense change, c.1288G>A; p.A430T, in the autophagy-related ATG4D gene on canine chromosome 20 with a highly significant disease association (p = 3.8 x 10-136) in a cohort of more than 2300 Lagotto Romagnolo dogs. ATG4D encodes a poorly characterized cysteine protease belonging to the macroautophagy pathway. Accordingly, our histological analyses indicated altered autophagic flux in affected tissues. The knockdown of the zebrafish homologue atg4da resulted in a widespread developmental disturbance and neurodegeneration in the central nervous system. Our study describes a previously unknown canine neurological disease with particular pathological features and implicates the ATG4D protein as an important autophagy mediator in neuronal homeostasis. The canine phenotype serves as a model to delineate the disease-causing pathological mechanism(s) and ATG4D function, and can also be used to explore treatment options. Furthermore, our results reveal a novel candidate gene for human neurodegeneration and enable the development of a genetic test for veterinary diagnostic and breeding purposes.

  4. A Missense Change in the ATG4D Gene Links Aberrant Autophagy to a Neurodegenerative Vacuolar Storage Disease

    Science.gov (United States)

    Kyöstilä, Kaisa; Syrjä, Pernilla; Jagannathan, Vidhya; Chandrasekar, Gayathri; Jokinen, Tarja S.; Seppälä, Eija H.; Becker, Doreen; Drögemüller, Michaela; Dietschi, Elisabeth; Drögemüller, Cord; Lang, Johann; Steffen, Frank; Rohdin, Cecilia; Jäderlund, Karin H.; Lappalainen, Anu K.; Hahn, Kerstin; Wohlsein, Peter; Baumgärtner, Wolfgang; Henke, Diana; Oevermann, Anna; Kere, Juha; Lohi, Hannes; Leeb, Tosso

    2015-01-01

    Inherited neurodegenerative disorders are debilitating diseases that occur across different species. We have performed clinical, pathological and genetic studies to characterize a novel canine neurodegenerative disease present in the Lagotto Romagnolo dog breed. Affected dogs suffer from progressive cerebellar ataxia, sometimes accompanied by episodic nystagmus and behavioral changes. Histological examination revealed unique pathological changes, including profound neuronal cytoplasmic vacuolization in the nervous system, as well as spheroid formation and cytoplasmic aggregation of vacuoles in secretory epithelial tissues and mesenchymal cells. Genetic analyses uncovered a missense change, c.1288G>A; p.A430T, in the autophagy-related ATG4D gene on canine chromosome 20 with a highly significant disease association (p = 3.8 x 10-136) in a cohort of more than 2300 Lagotto Romagnolo dogs. ATG4D encodes a poorly characterized cysteine protease belonging to the macroautophagy pathway. Accordingly, our histological analyses indicated altered autophagic flux in affected tissues. The knockdown of the zebrafish homologue atg4da resulted in a widespread developmental disturbance and neurodegeneration in the central nervous system. Our study describes a previously unknown canine neurological disease with particular pathological features and implicates the ATG4D protein as an important autophagy mediator in neuronal homeostasis. The canine phenotype serves as a model to delineate the disease-causing pathological mechanism(s) and ATG4D function, and can also be used to explore treatment options. Furthermore, our results reveal a novel candidate gene for human neurodegeneration and enable the development of a genetic test for veterinary diagnostic and breeding purposes. PMID:25875846

  5. A missense change in the ATG4D gene links aberrant autophagy to a neurodegenerative vacuolar storage disease.

    Directory of Open Access Journals (Sweden)

    Kaisa Kyöstilä

    2015-04-01

    Full Text Available Inherited neurodegenerative disorders are debilitating diseases that occur across different species. We have performed clinical, pathological and genetic studies to characterize a novel canine neurodegenerative disease present in the Lagotto Romagnolo dog breed. Affected dogs suffer from progressive cerebellar ataxia, sometimes accompanied by episodic nystagmus and behavioral changes. Histological examination revealed unique pathological changes, including profound neuronal cytoplasmic vacuolization in the nervous system, as well as spheroid formation and cytoplasmic aggregation of vacuoles in secretory epithelial tissues and mesenchymal cells. Genetic analyses uncovered a missense change, c.1288G>A; p.A430T, in the autophagy-related ATG4D gene on canine chromosome 20 with a highly significant disease association (p = 3.8 x 10-136 in a cohort of more than 2300 Lagotto Romagnolo dogs. ATG4D encodes a poorly characterized cysteine protease belonging to the macroautophagy pathway. Accordingly, our histological analyses indicated altered autophagic flux in affected tissues. The knockdown of the zebrafish homologue atg4da resulted in a widespread developmental disturbance and neurodegeneration in the central nervous system. Our study describes a previously unknown canine neurological disease with particular pathological features and implicates the ATG4D protein as an important autophagy mediator in neuronal homeostasis. The canine phenotype serves as a model to delineate the disease-causing pathological mechanism(s and ATG4D function, and can also be used to explore treatment options. Furthermore, our results reveal a novel candidate gene for human neurodegeneration and enable the development of a genetic test for veterinary diagnostic and breeding purposes.

  6. Transport Properties of Earth's Core

    Science.gov (United States)

    Cohen, R. E.; Zhang, P.; Xu, J.

    2016-12-01

    One of the most important parameters governing the original heat that drives all processes in the Earth is the thermal conductivity of Earth's core. Heat is transferred through the core by convection and conduction, and the convective component provides energy to drive the geodynamo. Sha and Cohen (2011) found that the electrical conductivity of solid hcp-iron was much higher than had been assumed by geophysicists, based on electronic structure computations for electron-phonon scattering (e-p) within density functional theory [1]. Thermal conductivity is related to electrical conductivity through the empirical Wiedmann-Franz law of 1853 [2]. Pozzo et al. [3] found that the high electrical conductivity of liquid iron alloys was too high for conventional dynamo models to work—there simply is not enough energy, so O'Rourke and Stevenson proposed a model driven by participation of Mg from the core [4], supported by recent experients [5]. Recent measurements by Ohta et al. show even lower resistivities than predicted by DFT e-p, and invoked a saturation model to account for this, [6] whereas, Konopkova et al. found thermal conductivities consistent with earlier geophysical estimates. [7] We are using first-principles methods, including dynamical mean field theory for electron-electron scattering, and highly converged e-p computations, and find evidence for strong anisotropy in solid hcp-Fe that may help explain some experimental results. The current status of the field will be discussed along with our recent results. This work is supported by the ERC Advanced grant ToMCaT, the NSF, and the Carnegie Institution for Science.[1] X. Sha and R. E. Cohen, J.Phys.: Condens.Matter 23, 075401 (2011).[2] R. Franz and G. Wiedemann, Annalen Physik 165, 497 (1853).[3] M. Pozzo, C. Davies, D. Gubbins, and D. Alfe, Nature 485, 355 (2012).[4] J. G. O'Rourke and D. J. Stevenson, Nature 529, 387 (2016).[5] J. Badro, J. Siebert, and F. Nimmo, Nature (2016).[6] K. Ohta, Y. Kuwayama, K

  7. ElemeNT: a computational tool for detecting core promoter elements

    Science.gov (United States)

    Sloutskin, Anna; Danino, Yehuda M; Orenstein, Yaron; Zehavi, Yonathan; Doniger, Tirza; Shamir, Ron; Juven-Gershon, Tamar

    2015-01-01

    Core promoter elements play a pivotal role in the transcriptional output, yet they are often detected manually within sequences of interest. Here, we present 2 contributions to the detection and curation of core promoter elements within given sequences. First, the Elements Navigation Tool (ElemeNT) is a user-friendly web-based, interactive tool for prediction and display of putative core promoter elements and their biologically-relevant combinations. Second, the CORE database summarizes ElemeNT-predicted core promoter elements near CAGE and RNA-seq-defined Drosophila melanogaster transcription start sites (TSSs). ElemeNT's predictions are based on biologically-functional core promoter elements, and can be used to infer core promoter compositions. ElemeNT does not assume prior knowledge of the actual TSS position, and can therefore assist in annotation of any given sequence. These resources, freely accessible at http://lifefaculty.biu.ac.il/gershon-tamar/index.php/resources, facilitate the identification of core promoter elements as active contributors to gene expression. PMID:26226151

  8. Two independent transcription initiation codes overlap on vertebrate core promoters

    Science.gov (United States)

    Haberle, Vanja; Li, Nan; Hadzhiev, Yavor; Plessy, Charles; Previti, Christopher; Nepal, Chirag; Gehrig, Jochen; Dong, Xianjun; Akalin, Altuna; Suzuki, Ana Maria; van Ijcken, Wilfred F. J.; Armant, Olivier; Ferg, Marco; Strähle, Uwe; Carninci, Piero; Müller, Ferenc; Lenhard, Boris

    2014-03-01

    A core promoter is a stretch of DNA surrounding the transcription start site (TSS) that integrates regulatory inputs and recruits general transcription factors to initiate transcription. The nature and causative relationship of the DNA sequence and chromatin signals that govern the selection of most TSSs by RNA polymerase II remain unresolved. Maternal to zygotic transition represents the most marked change of the transcriptome repertoire in the vertebrate life cycle. Early embryonic development in zebrafish is characterized by a series of transcriptionally silent cell cycles regulated by inherited maternal gene products: zygotic genome activation commences at the tenth cell cycle, marking the mid-blastula transition. This transition provides a unique opportunity to study the rules of TSS selection and the hierarchy of events linking transcription initiation with key chromatin modifications. We analysed TSS usage during zebrafish early embryonic development at high resolution using cap analysis of gene expression, and determined the positions of H3K4me3-marked promoter-associated nucleosomes. Here we show that the transition from the maternal to zygotic transcriptome is characterized by a switch between two fundamentally different modes of defining transcription initiation, which drive the dynamic change of TSS usage and promoter shape. A maternal-specific TSS selection, which requires an A/T-rich (W-box) motif, is replaced with a zygotic TSS selection grammar characterized by broader patterns of dinucleotide enrichments, precisely aligned with the first downstream (+1) nucleosome. The developmental dynamics of the H3K4me3-marked nucleosomes reveal their DNA-sequence-associated positioning at promoters before zygotic transcription and subsequent transcription-independent adjustment to the final position downstream of the zygotic TSS. The two TSS-defining grammars coexist, often physically overlapping, in core promoters of constitutively expressed genes to enable

  9. The Transcendental Core of Correlationism

    Directory of Open Access Journals (Sweden)

    Paul J. Ennis

    2011-06-01

    Full Text Available In this paper I read Quentin Meillassoux’s critique of correlationism as truly a critique of transcendentalism and the transcendental method. I do so by considering the two correlationist rejoinders that occur in the English edition of Meillassoux’s After Finitude. The first rejoinder is from an idealist and relies on adumbrations for its defence. This reliance on adumbrations will be shown to be itself transcendentally implicated through Edmund Husserl’s Crisis of the European Sciences and Transcendental Phenomenology. I then turn to the explicit engagement with the transcendental method that arises from the transcendentalist’s rejoinder. Considered together I hope to convince the reader that the core of correlationism is transcendentalism.

  10. Shuttle Spacelab Core Equipment Freezer

    Science.gov (United States)

    Copeland, R. J.

    1977-01-01

    This paper describes the preliminary design of a Shuttle Spacelab Core Equipment Freezer. The unit will provide the capability to freeze and store many experiment specimens. Two models of the unit are planned. One model provides storage at -70 C; the other model will provide -70 C storage, a freeze dry capability, storage at a selectable temperature in the range of 0 C to -70 C, and means of maintaining close temperature tolerances. In addition an exchanger loop will be available at 4 C for cooling of a centrifuge and a remote storage compartment. A test tube holder, a dish holder and thermal capacitors for rapid freezing of large specimens will also be provided. A Stirling Cycle was selected as the active refrigerator for minimum cost and weight.

  11. Methodology for embedded transport core calculation

    Science.gov (United States)

    Ivanov, Boyan D.

    The progress in the Nuclear Engineering field leads to developing new generations of Nuclear Power Plants (NPP) with complex rector core designs, such as cores loaded partially with mixed-oxide (MOX) fuel, high burn-up loadings, and cores with advanced designs of fuel assemblies and control rods. Such heterogeneous cores introduce challenges for the diffusion theory that has been used for several decades for calculations of the current Pressurized Water Rector (PWR) cores. To address the difficulties the diffusion approximation encounters new core calculation methodologies need to be developed by improving accuracy, while preserving efficiency of the current reactor core calculations. In this thesis, an advanced core calculation methodology is introduced, based on embedded transport calculations. Two different approaches are investigated. The first approach is based on embedded finite element (FEM), simplified P3 approximation (SP3), fuel assembly (FA) homogenization calculation within the framework of the diffusion core calculation with NEM code (Nodal Expansion Method). The second approach involves embedded FA lattice physics eigenvalue calculation based on collision probability method (CPM) again within the framework of the NEM diffusion core calculation. The second approach is superior to the first because most of the uncertainties introduced by the off-line cross-section generation are eliminated.

  12. Analysis of MOX core physics experiments MISTRAL

    Energy Technology Data Exchange (ETDEWEB)

    Ishii, Kazuya [Hitachi, Ltd., Tokyo (Japan); Tatsumi, Masahiro [Nuclear Fuel Industries Ltd., Tokyo (Japan); Kan, Taro [Mitsubishi Heavy Industries Ltd., Tokyo (Japan); Ando, Yoshihira [Toshiba Corp., Tokyo (Japan); Yamamoto, Toru; Iwata, Yutaka; Umano, Takuya; Kanda, Ryoji [Nuclear Power Engineering Corp., Tokyo (Japan)

    2003-03-01

    Nuclear Power Engineering Corporation (NUPEC) has been performing conceptual design studies of high moderation full MOX LWR cores that aim for increasing fissile Pu consumption rate and reducing residual Pu in discharged MOX fuel. As part of these studies, NUPEC, French Atomic Energy Commission (CEA) and their industrial partners implemented an experimental program, MISTRAL, that was devoted to measuring the core physics parameters of such advanced cores. The program consists of one reference UO{sub 2} core, two homogeneous full MOX cores and one full MOX PWR mock-up core that have higher moderation ratio than the conventional lattice. NUPEC has been analyzing the experimental results with the diffusion and the transport calculations by the SRAC code system and the continuous energy Monte Carlo calculations by the MVP code with the common nuclear data file, JENDL-3.2. The calculation results well reproduce the experimental data approximately within the same range of the experimental uncertainty. This indicates that these applied analysis methods give the same accuracy for the UO{sub 2} core and MOX cores, for the different moderation MOX cores, and for the homogeneous and the mock-up MOX cores. (author)

  13. The core protein of classical Swine Fever virus is dispensable for virus propagation in vitro.

    Directory of Open Access Journals (Sweden)

    Christiane Riedel

    Full Text Available Core protein of Flaviviridae is regarded as essential factor for nucleocapsid formation. Yet, core protein is not encoded by all isolates (GBV- A and GBV- C. Pestiviruses are a genus within the family Flaviviridae that affect cloven-hoofed animals, causing economically important diseases like classical swine fever (CSF and bovine viral diarrhea (BVD. Recent findings describe the ability of NS3 of classical swine fever virus (CSFV to compensate for disabling size increase of core protein (Riedel et al., 2010. NS3 is a nonstructural protein possessing protease, helicase and NTPase activity and a key player in virus replication. A role of NS3 in particle morphogenesis has also been described for other members of the Flaviviridae (Patkar et al., 2008; Ma et al., 2008. These findings raise questions about the necessity and function of core protein and the role of NS3 in particle assembly. A reverse genetic system for CSFV was employed to generate poorly growing CSFVs by modification of the core gene. After passaging, rescued viruses had acquired single amino acid substitutions (SAAS within NS3 helicase subdomain 3. Upon introduction of these SAAS in a nonviable CSFV with deletion of almost the entire core gene (Vp447(Δc, virus could be rescued. Further characterization of this virus with regard to its physical properties, morphology and behavior in cell culture did not reveal major differences between wildtype (Vp447 and Vp447(Δc. Upon infection of the natural host, Vp447(Δc was attenuated. Hence we conclude that core protein is not essential for particle assembly of a core-encoding member of the Flaviviridae, but important for its virulence. This raises questions about capsid structure and necessity, the role of NS3 in particle assembly and the function of core protein in general.

  14. Synthetic Core Promoters as Universal Parts for Fine-Tuning Expression in Different Yeast Species.

    Science.gov (United States)

    Portela, Rui M C; Vogl, Thomas; Kniely, Claudia; Fischer, Jasmin E; Oliveira, Rui; Glieder, Anton

    2017-03-17

    Synthetic biology and metabolic engineering experiments frequently require the fine-tuning of gene expression to balance and optimize protein levels of regulators or metabolic enzymes. A key concept of synthetic biology is the development of modular parts that can be used in different contexts. Here, we have applied a computational multifactor design approach to generate de novo synthetic core promoters and 5' untranslated regions (UTRs) for yeast cells. In contrast to upstream cis-regulatory modules (CRMs), core promoters are typically not subject to specific regulation, making them ideal engineering targets for gene expression fine-tuning. 112 synthetic core promoter sequences were designed on the basis of the sequence/function relationship of natural core promoters, nucleosome occupancy and the presence of short motifs. The synthetic core promoters were fused to the Pichia pastoris AOX1 CRM, and the resulting activity spanned more than a 200-fold range (0.3% to 70.6% of the wild type AOX1 level). The top-ten synthetic core promoters with highest activity were fused to six additional CRMs (three in P. pastoris and three in Saccharomyces cerevisiae). Inducible CRM constructs showed significantly higher activity than constitutive CRMs, reaching up to 176% of natural core promoters. Comparing the activity of the same synthetic core promoters fused to different CRMs revealed high correlations only for CRMs within the same organism. These data suggest that modularity is maintained to some extent but only within the same organism. Due to the conserved role of eukaryotic core promoters, this rational design concept may be transferred to other organisms as a generic engineering tool.

  15. On-line core axial power distribution synthesis method from in-core and ex-core neutron detectors

    Energy Technology Data Exchange (ETDEWEB)

    In, Wang Kee; Cho, Byung Oh [Korea Atomic Energy Research Institute, Taejon (Korea)

    1999-10-01

    This document describes the methodology in detail and the synthesis coefficients of the Fourier series expansion and the cubic spline synthesis techniques. A computer program was developed to generate the synthesis coefficients and the core power distribution. For the illustration, various axial power shapes for YGN 3 Cycle 1 and SMART were synthesized using the simulated in-core and/or ex-core detector signals. The results of this study will be useful to select the best synthesis method for the SMART core monitoring and protection systems and to evaluate the accuracy of the synthesized power shape. 4 refs., 13 figs., 5 tabs. (Author)

  16. Synchronizing ice cores from the Renland and Agassiz ice caps to the Greenland Ice Core Chronology

    DEFF Research Database (Denmark)

    Vinther, Bo Møllesøe; Clausen, Henrik Brink; Fischer, D. A.

    2008-01-01

    Four ice cores from the Agassiz ice cap in the Canadian high arctic and one ice core from the Renland ice cap in eastern Greenland have been synchronized to the Greenland Ice Core Chronology 2005 (GICC05) which is based on annual layer counts in the DYE-3, GRIP and NGRIP ice cores. Volcanic....... Annual layer thicknesses in the Agassiz ice cores point to a well-developed Raymond bump in the Agassiz ice cap....... reference horizons, seen in electrical conductivity measurements (ECM) have been used to carry out the synchronization throughout the Holocene. The Agassiz ice cores have been matched to the NGRIP ice core ECM signal, while the Renland core has been matched to the GRIP ice core ECM signal, thus tying...

  17. Progressive Curation of IODP Core Material at Kochi Core Center, Japan

    Science.gov (United States)

    Gupta, L. P.; Hisamitsu, T.; Ahagon, N.; Kuramoto, T.; Tokuyama, H.; Kinoshita, M.

    2014-12-01

    Kochi Core Center (KCC) is one of the 3 IODP core repositories in the world, and is in-charge of curating core materials collected/to be collected from most of the Indian Ocean, west Pacific Ocean and Bering Sea. Curation of IODP core material in the KCC began in 2007 as it started receiving 83 km of Legacy cores from the other IODP core repositories. Since then the KCC has not only maintained curatorial standards of the IODP, but also added many services for convenience of the IODP researchers that include curation of cuttings and deep frozen aliquots of cores, open access to logging equipment in the KCC for core measurements, virtual core library to provide quick online access to 3-D XCT images of the cores collected by the D/V Chikyu, online summary of the cores being curated in the KCC, and up-to-date online images of working half to show status of samples available for prospective users. With its existing stock of 104 km of the IODP & Legacy cores and cores to be recovered from the Indian Ocean in near future by the JOIDES Resolution, and a huge new reefer building with storage capacity of ca. 150 km core becoming part of the KCC this August, the KCC is bound to play a significant role in promoting earth and biogeo-sciences throughout the world, especially in neighboring Asian countries.

  18. Inner Core Rotation from Geomagnetic Westward Drift and a Stationary Spherical Vortex in Earth's Core

    Science.gov (United States)

    Voorhies, C. V.

    1999-01-01

    The idea that geomagnetic westward drift indicates convective leveling of the planetary momentum gradient within Earth's core is pursued in search of a differentially rotating mean state, upon which various oscillations and secular effects might be superimposed. The desired state conforms to roughly spherical boundary conditions, minimizes dissipative interference with convective cooling in the bulk of the core, yet may aide core cooling by depositing heat in the uppermost core and lower mantle. The variational calculus of stationary dissipation applied to a spherical vortex within the core yields an interesting differential rotation profile akin to spherical Couette flow bounded by thin Hartmann layers. Four boundary conditions are required. To concentrate shear induced dissipation near the core-mantle boundary, these are taken to be: (i) no-slip at the core-mantle interface; (ii) geomagnetically estimated bulk westward flow at the base of the core-mantle boundary layer; (iii) no-slip at the inner-outer core interface; and, to describe magnetic locking of the inner core to the deep outer core, (iv) hydrodynamically stress-free at the inner-outer core boundary. By boldly assuming the axial core angular momentum anomaly to be zero, the super-rotation of the inner core is calculated to be at most 1.5 degrees per year.

  19. Core strengthening exercises for low back pain.

    Science.gov (United States)

    Baerga-Varela, Luis; Abréu Ramos, Antonio M

    2006-01-01

    Core strengthening concepts have gained increased popularity in low back rehabilitation. Traditional low back pain rehabilitation is based on a static spine stability model and is composed mostly of modalities, stretching and strengthening exercises. More recent theories, however, include newer concepts of dynamic spinal stability, coordination and neuromuscular control. Core strengthening exercises incorporate these new concepts. Although more research is necessary, the best available evidence suggests that a core strengthening program may be beneficial in reducing pain scores, functional disability and recurrences of acute low back pain episodes. This article reviews "core" anatomy, physiologic models of spinal stability, effects, of low back pain on spinal stability, evidence-based reasoning behind core strengthening and the basic concepts involved in designing a core strengthening program.

  20. Investigating the translation of Earth's inner core

    DEFF Research Database (Denmark)

    Day, Elizabeth A; Cormier, Vernon F; Geballe, Zachary M

    2012-01-01

    The Earth’s inner core provides unique insights into processes that are occurring deep within our Earth today, as well as processes that occurred in the past. The seismic structure of the inner core is complex, and is dominated by anisotropic and isotropic differences between the Eastern......; and a complex hemispherical and radial dependence of anisotropy, attenuation, and scattering in the uppermost inner core. We explore the compatibility of geodynamic models of a translating inner core with seismic observations. Using a relatively simple set of translation models we map the age of material...... times consisting of paths that sample the core near to the proposed hemisphere boundaries. This combination of body wave data samples a range of depths (and consequently ages) in the inner core, and provides an insight into the nature of hemispheres and their compatibility with our predictions...

  1. BN-600 full MOX core benchmark analysis.

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Y. I.; Hill, R. N.; Grimm, K.; Rimpault, G.; Newton, T.; Li, Z. H.; Rineiski, A.; Mohanakrishan, P.; Ishikawa, M.; Lee, K. B.; Danilytchev, A.; Stogov, V.; Nuclear Engineering Division; International Atomic Energy Agency; CEA/Cadarache; SERCO Assurance; China Inst. of Atomic Energy; Forschnungszentrum Karlsruhe; Indira Gandhi Centre for Atomic Research; Japan Nuclear Cycle Development Inst.; Korea Atomic Energy Research Inst.; Inst. of Physics and Power Engineering

    2004-01-01

    As a follow-up of the BN-600 hybrid core benchmark, a full MOX core benchmark was performed within the framework of the IAEA co-ordinated research project. Discrepancies between the values of main reactivity coefficients obtained by the participants for the BN-600 full MOX core benchmark appear to be larger than those in the previous hybrid core benchmarks on traditional core configurations. This arises due to uncertainties in the proper modelling of the axial sodium plenum above the core. It was recognized that the sodium density coefficient strongly depends on the core model configuration of interest (hybrid core vs. fully MOX fuelled core with sodium plenum above the core) in conjunction with the calculation method (diffusion vs. transport theory). The effects of the discrepancies revealed between the participants results on the ULOF and UTOP transient behaviours of the BN-600 full MOX core were investigated in simplified transient analyses. Generally the diffusion approximation predicts more benign consequences for the ULOF accident but more hazardous ones for the UTOP accident when compared with the transport theory results. The heterogeneity effect does not have any significant effect on the simulation of the transient. The comparison of the transient analyses results concluded that the fuel Doppler coefficient and the sodium density coefficient are the two most important coefficients in understanding the ULOF transient behaviour. In particular, the uncertainty in evaluating the sodium density coefficient distribution has the largest impact on the description of reactor dynamics. This is because the maximum sodium temperature rise takes place at the top of the core and in the sodium plenum.

  2. The effect of HCV Core protein on the expression of miR-150

    Directory of Open Access Journals (Sweden)

    Sayad Khanizadeh

    2016-09-01

    Full Text Available Background : Hepatitis C virus (HCV is considered as one of the major pathogenic agents of chronic liver diseases. Previous studies have shown that HCV proteins can interaction with gene regulatory networks such as microRNAs. The aim of this study was to investigate the effect of HCV core protein on the expression of miR-150 in a cell culture model. Materials and Methods: Plasmids expressing full HCV core protein was transfected into Huh7 cell lines while a GFP expressing plasmid employed as negative control. Subsequently, total RNA extracted and Real-Time PCR performed to measure the expression level of miR-150 expression. Moreover, trypan blue exclusion assay was performed to investigate the effect of core protein on cell viability. Results: The gene expression analysis of miR-150 in Huh7 cells showed that endogenous HCV core protein could significantly down regulation of miR-150 when compared to GFP control plasmid and normal cells (P<0.01. Beside, core protein induced no significant proliferative or cytotoxic effects on hepatic cells as determined by trypan blue exclusion assay (P<0.05. Conclusion: Our study suggests that HCV core protein can led to down regulation of miR-150 expression. This data revealed that HCV protein interactions with cell regulatory machinery may contribute to pathogenesis of chronic liver diseases.

  3. [Structure and dynamic of the nucleosome core particle].

    Science.gov (United States)

    Bertin, Aurélie; Mangenot, Stéphanie

    2008-01-01

    In eukaryotic cell, a few meters of DNA are compacted in nuclear compartment of a few microns. This high level of compaction is an important way to regulate gene expression. In the present paper, we present a description of the organization of DNA into its first level of compaction: the nucleosome core particle. The structure of the nucleosome has been described at an atomic resolution more than 10 years ago, where DNA is wrapped around an octamer of histones. Post-translational modifications affecting histone tails have been shown to regulate the chromatin degree of compaction and thus the gene expression and regulation. The structure of the NCP is far from being frozen and is highly dynamic. Remodeling factors can induce DNA sliding around the histones, DNA transaction processes such as transcription and replication.

  4. Relationship between cycling mechanics and core stability.

    Science.gov (United States)

    Abt, John P; Smoliga, James M; Brick, Matthew J; Jolly, John T; Lephart, Scott M; Fu, Freddie H

    2007-11-01

    Core stability has received considerable attention with regards to functional training in sports. Core stability provides the foundation from which power is generated in cycling. No research has described the relationship between core stability and cycling mechanics of the lower extremity. The purpose of this study was to determine the relationship between cycling mechanics and core stability. Hip, knee, and ankle joint kinematic and pedal force data were collected on 15 competitive cyclists while cycling untethered on a high-speed treadmill. The exhaustive cycling protocol consisted of cycling at 25.8 km x h(-1) while the grade was increased 1% every 3 minutes. A core fatigue workout was performed before the second treadmill test. Total frontal plane knee motion (test 1: 15.1 +/- 6.0 degrees ; test 2: 23.3 +/- 12.5 degrees), sagittal plane knee motion (test 1: 69.9 +/- 4.9 degrees ; test 2: 79.3 +/- 10.1 degrees), and sagittal plane ankle motion (test 1: 29.0 +/- 8.5 degrees ; test 2: 43.0 +/- 22.9 degrees) increased after the core fatigue protocol. No significant differences were demonstrated for pedaling forces. Core fatigue resulted in altered cycling mechanics that might increase the risk of injury because the knee joint is potentially exposed to greater stress. Improved core stability and endurance could promote greater alignment of the lower extremity when riding for extended durations as the core is more resistant to fatigue.

  5. Optimized Cellular Core for Rotorcraft Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Patz Materials and Technologies proposes to develop a unique structural cellular core material to improve mechanical performance, reduce platform weight and lower...

  6. Material with core-shell structure

    Science.gov (United States)

    Luhrs, Claudia [Rio Rancho, NM; Richard, Monique N [Ann Arbor, MI; Dehne, Aaron [Maumee, OH; Phillips, Jonathan [Rio Rancho, NM; Stamm, Kimber L [Ann Arbor, MI; Fanson, Paul T [Brighton, MI

    2011-11-15

    Disclosed is a material having a composite particle, the composite particle including an outer shell and a core. The core is made from a lithium alloying material and the outer shell has an inner volume that is greater in size than the core of the lithium alloying material. In some instances, the outer mean diameter of the outer shell is less than 500 nanometers and the core occupies between 5 and 99% of the inner volume. In addition, the outer shell can have an average wall thickness of less than 100 nanometers.

  7. Challenges Regarding IP Core Functional Reliability

    Science.gov (United States)

    Berg, Melanie D.; LaBel, Kenneth A.

    2017-01-01

    For many years, intellectual property (IP) cores have been incorporated into field programmable gate array (FPGA) and application specific integrated circuit (ASIC) design flows. However, the usage of large complex IP cores were limited within products that required a high level of reliability. This is no longer the case. IP core insertion has become mainstream including their use in highly reliable products. Due to limited visibility and control, challenges exist when using IP cores and subsequently compromise product reliability. We discuss challenges and suggest potential solutions to critical application IP insertion.

  8. Full MOX core design for advanced PWR

    Energy Technology Data Exchange (ETDEWEB)

    Tochihara, H.; Komano, Y.; Ishida, M.; Mukai, H. [Mitsubishi Heavy Industries, Ltd., Yokohama (Japan)

    1995-12-31

    A full MOX core is an attractive option for large consumption of the recycled plutonium from reprocessed LWR fuel. The feasibility is verified of a full MOX core in a PWR with only small hardware modifications. The advanced PWR has been selected for this purpose. The full MOX core is feasible by increasing the number of control rods and adopting the enriched {sup 10}B in the soluble boron of reactor coolant system. The full MOX cores can be designed using one Pu` content per assembly and without any burnable absorbers. (author) 2 refs.

  9. Core Training and Rehabilitation in Horses.

    Science.gov (United States)

    Clayton, Hilary M

    2016-04-01

    The central body axis or core is a key component in controlling body posture and providing a stable platform for limb movements and generation of locomotor forces. Persistent dysfunction of the deep stabilizing muscles seems to be common in horses indicating a need for core training exercises to restore normal function. Core training should be performed throughout the horse's athletic career to maintain a healthy back and used therapeutically when back pain is identified. This article reviews the structure and function of the equine thoracolumbar spine with special reference to function, dysfunction, conditioning, and rehabilitation of the core musculature. Copyright © 2016 Elsevier Inc. All rights reserved.

  10. Design Principles for Synthesizable Processor Cores

    DEFF Research Database (Denmark)

    Schleuniger, Pascal; McKee, Sally A.; Karlsson, Sven

    2012-01-01

    As FPGAs get more competitive, synthesizable processor cores become an attractive choice for embedded computing. Currently popular commercial processor cores do not fully exploit current FPGA architectures. In this paper, we propose general design principles to increase instruction throughput...... on FPGA-based processor cores: first, superpipelining enables higher-frequency system clocks, and second, predicated instructions circumvent costly pipeline stalls due to branches. To evaluate their effects, we develop Tinuso, a processor architecture optimized for FPGA implementation. We demonstrate...... through the use of micro-benchmarks that our principles guide the design of a processor core that improves performance by an average of 38% over a similar Xilinx MicroBlaze configuration....

  11. Nuclear reactor core modelling in multifunctional simulators

    Energy Technology Data Exchange (ETDEWEB)

    Puska, E.K. [VTT Energy, Nuclear Energy, Espoo (Finland)

    1999-06-01

    The thesis concentrates on the development of nuclear reactor core models for the APROS multifunctional simulation environment and the use of the core models in various kinds of applications. The work was started in 1986 as a part of the development of the entire APROS simulation system. The aim was to create core models that would serve in a reliable manner in an interactive, modular and multifunctional simulator/plant analyser environment. One-dimensional and three-dimensional core neutronics models have been developed. Both models have two energy groups and six delayed neutron groups. The three-dimensional finite difference type core model is able to describe both BWR- and PWR-type cores with quadratic fuel assemblies and VVER-type cores with hexagonal fuel assemblies. The one- and three-dimensional core neutronics models can be connected with the homogeneous, the five-equation or the six-equation thermal hydraulic models of APROS. The key feature of APROS is that the same physical models can be used in various applications. The nuclear reactor core models of APROS have been built in such a manner that the same models can be used in simulator and plant analyser applications, as well as in safety analysis. In the APROS environment the user can select the number of flow channels in the three-dimensional reactor core and either the homogeneous, the five- or the six-equation thermal hydraulic model for these channels. The thermal hydraulic model and the number of flow channels have a decisive effect on the calculation time of the three-dimensional core model and thus, at present, these particular selections make the major difference between a safety analysis core model and a training simulator core model. The emphasis on this thesis is on the three-dimensional core model and its capability to analyse symmetric and asymmetric events in the core. The factors affecting the calculation times of various three-dimensional BWR, PWR and WWER-type APROS core models have been

  12. Synergistic recognition of an epigenetic DNA element by Pleiohomeotic and a Polycomb core complex.

    NARCIS (Netherlands)

    A.B. Mohd Sarip; F. Cleard (Fabienne); R.K. Mishra (Rakesh); F. Karch (Francois); C.P. Verrijzer (Peter)

    2005-01-01

    textabstractPolycomb response elements (PREs) are cis-acting DNA elements that mediate epigenetic gene silencing by Polycomb group (PcG) proteins. Here, we report that Pleiohomeotic (PHO) and a multiprotein Polycomb core complex (PCC) bind highly cooperatively to PREs. We identified a conserved

  13. Gene Locater

    DEFF Research Database (Denmark)

    Anwar, Muhammad Zohaib; Sehar, Anoosha; Rehman, Inayat-Ur

    2012-01-01

    UNLABELLED: Locating genes on a chromosome is important for understanding the gene function and its linkage and recombination. Knowledge of gene positions on chromosomes is necessary for annotation. The study is essential for disease genetics and genomics, among other aspects. Currently available...... software's for calculating recombination frequency is mostly limited to the range and flexibility of this type of analysis. GENE LOCATER is a fully customizable program for calculating recombination frequency, written in JAVA. Through an easy-to-use interface, GENE LOCATOR allows users a high degree...

  14. Cytotoxic T lymphocytes and CD4 epitope mutations in the pre-core/core region of hepatitis B virus in chronic hepatitis B carriers in Northeast Iran.

    Science.gov (United States)

    Zhand, Sareh; Tabarraei, Alijan; Nazari, Amineh; Moradi, Abdolvahab

    2017-07-01

    Hepatitis B virus (HBV) is vulnerable to many various mutations. Those within epitopes recognized by sensitized T cells may influence the re-emergence of the virus. This study was designed to investigate the mutation in immune epitope regions of HBV pre-core/core among chronic HBV patients of Golestan province, Northeast Iran. In 120 chronic HBV carriers, HBV DNA was extracted from blood plasma samples and PCR was done using specific primers. Direct sequencing and alignment of the pre-core/core region were applied using reference sequence from Gene Bank database (Accession Number AB033559). The study showed 27 inferred amino acid substitutions, 9 of which (33.3%) were in CD4 and 2 (7.4%) in cytotoxic T lymphocytes' (CTL) epitopes and 16 other mutations (59.2%) were observed in other regions. CTL escape mutations were not commonly observed in pre-core/core sequences of chronic HBV carriers in the locale of study. It can be concluded that most of the inferred amino acid substitutions occur in different immune epitopes other than CTL and CD4.

  15. Iron snow in the Martian core?

    Science.gov (United States)

    Davies, Christopher J.; Pommier, Anne

    2018-01-01

    The decline of Mars' global magnetic field some 3.8-4.1 billion years ago is thought to reflect the demise of the dynamo that operated in its liquid core. The dynamo was probably powered by planetary cooling and so its termination is intimately tied to the thermochemical evolution and present-day physical state of the Martian core. Bottom-up growth of a solid inner core, the crystallization regime for Earth's core, has been found to produce a long-lived dynamo leading to the suggestion that the Martian core remains entirely liquid to this day. Motivated by the experimentally-determined increase in the Fe-S liquidus temperature with decreasing pressure at Martian core conditions, we investigate whether Mars' core could crystallize from the top down. We focus on the "iron snow" regime, where newly-formed solid consists of pure Fe and is therefore heavier than the liquid. We derive global energy and entropy equations that describe the long-timescale thermal and magnetic history of the core from a general theory for two-phase, two-component liquid mixtures, assuming that the snow zone is in phase equilibrium and that all solid falls out of the layer and remelts at each timestep. Formation of snow zones occurs for a wide range of interior and thermal properties and depends critically on the initial sulfur concentration, ξ0. Release of gravitational energy and latent heat during growth of the snow zone do not generate sufficient entropy to restart the dynamo unless the snow zone occupies at least 400 km of the core. Snow zones can be 1.5-2 Gyrs old, though thermal stratification of the uppermost core, not included in our model, likely delays onset. Models that match the available magnetic and geodetic constraints have ξ0 ≈ 10% and snow zones that occupy approximately the top 100 km of the present-day Martian core.

  16. Magnetic Properties of Electrical Steel, Power Transformer Core Losses and Core Design Concepts

    OpenAIRE

    Freitag, Christian

    2017-01-01

    The work presented in this PhD-thesis includes the measurement of electrical steel's properties as well as the simulation of power transformer core losses and leads to the investigation of new core design methods.

  17. Magnetic field generation in the lunar core: The role of inner core growth

    Science.gov (United States)

    Scheinberg, A.; Soderlund, K. M.; Schubert, G.

    2015-07-01

    The source of the magnetic field recorded in the lunar crust remains an unresolved problem. The field was most likely produced by a self-sustaining dynamo in the Moon's electrically conducting metal core, but heat flux across the core-mantle boundary was probably insufficient to power a dynamo for the field's currently known duration from 4.2 to 3.56 Ga. Since seismic measurements indicate the existence of a solid iron inner core in addition to a still-liquid iron alloy outer core, inner core solidification and its associated thermochemically driven convection in the outer core could have been responsible for extending the dynamo's lifetime even in the absence of superadiabatic heat flux. Here we present a coupled mantle-core thermal evolution model of the Moon and show that core solidification could explain the onset and shutoff of the lunar dynamo consistent with the global magnetic field inferred from the paleomagnetic record.

  18. Continuous core photographs of sediment cores collected in 2009 offshore from Palos Verdes, California

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This part of the data release includes continuous core photographs in bmp format of sediment cores collected in 2009 offshore of Palos Verdes, California. It is one...

  19. Core and Shell Song Systems Unique to the Parrot Brain

    Science.gov (United States)

    Chakraborty, Mukta; Walløe, Solveig; Nedergaard, Signe; Fridel, Emma E.; Dabelsteen, Torben; Pakkenberg, Bente; Bertelsen, Mads F.; Dorrestein, Gerry M.; Brauth, Steven E.; Durand, Sarah E.; Jarvis, Erich D.

    2015-01-01

    The ability to imitate complex sounds is rare, and among birds has been found only in parrots, songbirds, and hummingbirds. Parrots exhibit the most advanced vocal mimicry among non-human animals. A few studies have noted differences in connectivity, brain position and shape in the vocal learning systems of parrots relative to songbirds and hummingbirds. However, only one parrot species, the budgerigar, has been examined and no differences in the presence of song system structures were found with other avian vocal learners. Motivated by questions of whether there are important differences in the vocal systems of parrots relative to other vocal learners, we used specialized constitutive gene expression, singing-driven gene expression, and neural connectivity tracing experiments to further characterize the song system of budgerigars and/or other parrots. We found that the parrot brain uniquely contains a song system within a song system. The parrot “core” song system is similar to the song systems of songbirds and hummingbirds, whereas the “shell” song system is unique to parrots. The core with only rudimentary shell regions were found in the New Zealand kea, representing one of the only living species at a basal divergence with all other parrots, implying that parrots evolved vocal learning systems at least 29 million years ago. Relative size differences in the core and shell regions occur among species, which we suggest could be related to species differences in vocal and cognitive abilities. PMID:26107173

  20. Evolutionary and Topological Properties of Genes and Community Structures in Human Gene Regulatory Networks.

    Science.gov (United States)

    Szedlak, Anthony; Smith, Nicholas; Liu, Li; Paternostro, Giovanni; Piermarocchi, Carlo

    2016-06-01

    The diverse, specialized genes present in today's lifeforms evolved from a common core of ancient, elementary genes. However, these genes did not evolve individually: gene expression is controlled by a complex network of interactions, and alterations in one gene may drive reciprocal changes in its proteins' binding partners. Like many complex networks, these gene regulatory networks (GRNs) are composed of communities, or clusters of genes with relatively high connectivity. A deep understanding of the relationship between the evolutionary history of single genes and the topological properties of the underlying GRN is integral to evolutionary genetics. Here, we show that the topological properties of an acute myeloid leukemia GRN and a general human GRN are strongly coupled with its genes' evolutionary properties. Slowly evolving ("cold"), old genes tend to interact with each other, as do rapidly evolving ("hot"), young genes. This naturally causes genes to segregate into community structures with relatively homogeneous evolutionary histories. We argue that gene duplication placed old, cold genes and communities at the center of the networks, and young, hot genes and communities at the periphery. We demonstrate this with single-node centrality measures and two new measures of efficiency, the set efficiency and the interset efficiency. We conclude that these methods for studying the relationships between a GRN's community structures and its genes' evolutionary properties provide new perspectives for understanding evolutionary genetics.

  1. Core Concepts in Introductory Physical Geography.

    Science.gov (United States)

    Bacon, Robert S.; Green, Jerry E.

    1981-01-01

    An analysis of 14 introductory physical geography textbooks yielded 121 core concepts (basic concepts appearing in 7-10 books). The authors suggest that the trend toward overspecialization in introductory geography classes can be reversed if teachers agree to stress core concepts and their relationships to geography as a whole. (AM)

  2. Moving core beam energy absorber and converter

    Science.gov (United States)

    Degtiarenko, Pavel V.

    2012-12-18

    A method and apparatus for the prevention of overheating of laser or particle beam impact zones through the use of a moving-in-the-coolant-flow arrangement for the energy absorbing core of the device. Moving of the core spreads the energy deposition in it in 1, 2, or 3 dimensions, thus increasing the effective cooling area of the device.

  3. Observations of exotic inner core waves

    NARCIS (Netherlands)

    Waszek, Lauren; Deuss, A.F.

    2015-01-01

    The seismic structure of Earth’s inner core is highly complex, displaying strong anisotropy and further regional variations. However, few seismic waves are sensitive to the inner core and fundamental questions regarding the origin of the observed seismic features remain unanswered. Thus, new

  4. Common Core in the Real World

    Science.gov (United States)

    Hess, Frederick M.; McShane, Michael Q.

    2013-01-01

    There are at least four key places where the Common Core intersects with current efforts to improve education in the United States--testing, professional development, expectations, and accountability. Understanding them can help educators, parents, and policymakers maximize the chance that the Common Core is helpful to these efforts and, perhaps…

  5. UV Defined Nanoporous Liquid Core Waveguides

    DEFF Research Database (Denmark)

    Christiansen, Mads Brøkner; Gopalakrishnan, Nimi; Ndoni, Sokol

    2011-01-01

    Nanoporous liquid core waveguides, where both core and cladding are made from the same material, are presented. The nanoporous polymer used is intrinsically hydrophobic, but selective UV exposure enables it to infiltrate with an aqueous solution, thus raising the refractive index from 1.26 to 1...

  6. Review of oil water core annular flow

    Energy Technology Data Exchange (ETDEWEB)

    Ghosh, S.; Mandal, T.K.; Das, G. [Department of Chemical Engineering, Indian Institute of Technology, Kharagpur 721302 (India); Das, P.K. [Department of Mechanical Engineering, Indian Institute of Technology, Kharagpur 721302 (India)

    2009-10-15

    The emerging energy efficient technology in the field of high viscous oil transportation is water-lubricated transport of heavy oil, known as core annular flow or CAF. This paper provides a brief review of the past studies on oil-water core annular flows - including studies on hydrodynamics as well as stability of flow. (author)

  7. Reinventing the Core: Community, Dialogue, and Change

    Science.gov (United States)

    Pittendrigh, Adele

    2007-01-01

    This article examines a six-year process of reforming the core curriculum at a midsize public research university, showing how a seminar for first-year students, a lengthy campus-wide dialogue, and a multidisciplinary community of faculty produced a new core curriculum focused on inquiry, communication, and undergraduate research. (Contains 1…

  8. Time: Assessing Understanding of Core Ideas

    Science.gov (United States)

    Thomas, Margaret; McDonough, Andrea; Clarkson, Philip; Clarke, Doug

    2016-01-01

    Although an understanding of time is crucial in our society, curriculum documents have an undue emphasis on reading time and little emphasis on core underlying ideas. Given this context, a one-to-one assessment interview, based on a new framework, was developed and administered to investigate students' understanding of core ideas undergirding the…

  9. Reinventing the Platform Core Through Acquisition

    DEFF Research Database (Denmark)

    Toppenberg, Gustav; Henningsson, Stefan; Eaton, Ben

    2016-01-01

    Digital platform leaders need to continuously innovate the platform core to drive the technological trajectory of the overall architecture and business system, of which the platform is a core element. This papers analyses the potential of and challenges to completing this task through the acquisi...

  10. Development of core design technology for LMR

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Young Jin; Kim Young In; Kim, Young Il; Kim, Y. G.; Kim, S. J.; Song, H.; Kim, T. K.; Kim, W. S.; Hwang, W.; Lee, B. O.; Park, C. K.; Joo, H. K.; Yoo, J. W.; Kang, H. Y.; Park, W. S

    2000-05-01

    For the development of KALIMER (150 MWe) core conceptual design, design evolution and optimization for improved economics and safety enhancement was performed in the uranium metallic fueled equilibrium core design which uses U-Zr binary fuel not in excess of 20 percent enrichment. Utilizing results of the uranium ,metallic fueled core design, the breeder equilibrium core design with breeding ratio being over 1.1 was developed. In addition, utilizing LMR's excellent neutron economy, various core concepts for minor actinide burnup, inherent safety, economics and non-proliferation were realized and its optimization studies were performed. A code system for the LMR core conceptual design has been established through the implementation of needed functions into the existing codes and development of codes. To improve the accuracy of the core design, a multi-dimensional nodal transport code SOLTRAN, a three-dimensional transient code analysis code STEP, MATRA-LMR and ASSY-P for T/H analysis are under development. Through the automation of design calculations for efficient core design, an input generator and several interface codes have been developed. (author)

  11. The Core-Collapse Supernova Explosion Mechanism

    Science.gov (United States)

    Müller, Bernhard

    2017-11-01

    The explosion mechanism of core-collapse supernovae is a long-standing problem in stellar astrophysics. We briefly outline the main contenders for a solution and review recent efforts to model core-collapse supernova explosions by means of multi-dimensional simulations. Focusing on the neutrino-driven mechanism, we summarize currents efforts to predict supernova explosion and remnant properties.

  12. Go Figure: Math and the Common Core

    Science.gov (United States)

    Burns, Marilyn

    2013-01-01

    In this article about the Common Core State Standards and mathematics, the author wanted to point out what's familiar in these standards and to give teachers clear access to what's different about them. She wanted to emphasize what has made her passionate about the Common Core standards--which is their two-part structure: Standards for…

  13. The Core Journal Concept in Black Studies

    Science.gov (United States)

    Weissinger, Thomas

    2010-01-01

    Black Studies scholars have shown interest in the core journal concept. Indeed, the idea of core journals for the study of the Black experience has changed several times since 1940. While Black Studies scholars are citing Black Studies journals with frequency, they also cite traditional disciplinary journals a great deal of the time. However,…

  14. The modelling of infrared dark cloud cores

    NARCIS (Netherlands)

    Ormel, CW; Shipman, RF; Ossenkopf, [No Value; Helmich, FP

    This paper presents results from modelling 450 mu m and 850 mu m continuum and HCO+ line observations of three distinct cores of an infrared dark cloud (IRDC) directed toward the W51 GMC. In the sub-mm continuum these cores appear as bright, isolated emission features. One of them coincides with the

  15. Lateral restraint assembly for reactor core

    Science.gov (United States)

    Gorholt, Wilhelm; Luci, Raymond K.

    1986-01-01

    A restraint assembly for use in restraining lateral movement of a reactor core relative to a reactor vessel wherein a plurality of restraint assemblies are interposed between the reactor core and the reactor vessel in circumferentially spaced relation about the core. Each lateral restraint assembly includes a face plate urged against the outer periphery of the core by a plurality of compression springs which enable radial preloading of outer reflector blocks about the core and resist low-level lateral motion of the core. A fixed radial key member cooperates with each face plate in a manner enabling vertical movement of the face plate relative to the key member but restraining movement of the face plate transverse to the key member in a plane transverse to the center axis of the core. In this manner, the key members which have their axes transverse to or subtending acute angles with the direction of a high energy force tending to move the core laterally relative to the reactor vessel restrain such lateral movement.

  16. Kinematically Decoupled Cores in Dwarf (Elliptical) Galaxies

    NARCIS (Netherlands)

    Toloba, E.; Peletier, R. F.; Guhathakurta, P.; van de Ven, G.; Boissier, S.; Boselli, A.; Brok, M. d.; Falcón-Barroso, J.; Hensler, G.; Janz, J.; Laurikainen, E.; Lisker, T.; Paudel, S.; Ryś, A.; Salo, H.

    An overview is given of what we know about the frequency of kinematically decoupled cores in dwarf elliptical galaxies. New observations show that kinematically decoupled cores happen just as often in dwarf elliptical as in ordinary early-type galaxies. This has important consequences for the

  17. Genome-wide analysis of core promoter structures in Schizosaccharomyces pombe with DeepCAGE

    Science.gov (United States)

    Li, Hua; Hou, Jingyi; Bai, Ling; Hu, Chuansheng; Tong, Pan; Kang, Yani; Zhao, Xiaodong; Shao, Zhifeng

    2015-01-01

    The core promoter, which immediately flanks the transcription start site (TSS), plays a critical role in transcriptional regulation of eukaryotes. Recent studies on higher eukaryotes have revealed an unprecedented complexity of core promoter structures that underscores diverse regulatory mechanisms of gene expression. For unicellular eukaryotes, however, the structures of core promoters have not been investigated in detail. As an important model organism, Schizosaccharomyces pombe still lacks the precise annotation for TSSs, thus hampering the analysis of core promoter structures and their relationship to higher eukaryotes. Here we used a deep sequencing-based approach (DeepCAGE) to generate 16 million uniquely mapped tags, corresponding to 93,736 positions in the S. pombe genome. The high-resolution TSS landscape enabled identification of over 8,000 core promoters, characterization of 4 promoter classes and observation of widespread alternative promoters. The landscape also allowed precise determination of the representative TSSs within core promoters, thus redefining the 5' UTR for 82.8% of S. pombe genes. We further identified the consensus initiator (Inr) sequence – PyPyPuN(A/C)(C/A), the TATA-enriched region (between position −25 and −37) and an Inr immediate downstream motif – CC(T/A)(T/C)(T/C/A)(A/G)CCA(A/T/C), all of which were associated with highly expressed promoters. In conclusion, the detailed analysis of core promoters not only significantly improves the genome annotation of S. pombe, but also reveals that this unicellular eukaryote shares a highly similar organization in the core promoters with higher eukaryotes. These findings lend additional evidence for the power of this model system in delineating complex regulatory processes in multicellular organisms, despite its perceived simplicity. PMID:25747261

  18. Genome-wide analysis of core promoter structures in Schizosaccharomyces pombe with DeepCAGE.

    Science.gov (United States)

    Li, Hua; Hou, Jingyi; Bai, Ling; Hu, Chuansheng; Tong, Pan; Kang, Yani; Zhao, Xiaodong; Shao, Zhifeng

    2015-01-01

    The core promoter, which immediately flanks the transcription start site (TSS), plays a critical role in transcriptional regulation of eukaryotes. Recent studies on higher eukaryotes have revealed an unprecedented complexity of core promoter structures that underscores diverse regulatory mechanisms of gene expression. For unicellular eukaryotes, however, the structures of core promoters have not been investigated in detail. As an important model organism, Schizosaccharomyces pombe still lacks the precise annotation for TSSs, thus hampering the analysis of core promoter structures and their relationship to higher eukaryotes. Here we used a deep sequencing-based approach (DeepCAGE) to generate 16 million uniquely mapped tags, corresponding to 93,736 positions in the S. pombe genome. The high-resolution TSS landscape enabled identification of over 8,000 core promoters, characterization of 4 promoter classes and observation of widespread alternative promoters. The landscape also allowed precise determination of the representative TSSs within core promoters, thus redefining the 5' UTR for 82.8% of S. pombe genes. We further identified the consensus initiator (Inr) sequence--PyPyPuN(A/C)(C/A), the TATA-enriched region (between position -25 and -37) and an Inr immediate downstream motif--CC(T/A)(T/C)(T/C/A)(A/G)CCA(A/T/C), all of which were associated with highly expressed promoters. In conclusion, the detailed analysis of core promoters not only significantly improves the genome annotation of S. pombe, but also reveals that this unicellular eukaryote shares a highly similar organization in the core promoters with higher eukaryotes. These findings lend additional evidence for the power of this model system in delineating complex regulatory processes in multicellular organisms, despite its perceived simplicity.

  19. Core-annular flow through a horizontal pipe : Hydrodynamic counterbalancing of buoyancy force on core

    NARCIS (Netherlands)

    Ooms, G.; Vuik, C.; Poesio, P.

    2007-01-01

    A theoretical investigation has been made of core-annular flow: the flow of a high-viscosity liquid core surrounded by a low-viscosity liquid annular layer through a horizontal pipe. Special attention is paid to the question of how the buoyancy force on the core, caused by a density difference

  20. Beyond the Core: Peer Observation Brings Common Core to Vocational and Electives Classes

    Science.gov (United States)

    Thurber Rasmussen, Harriette

    2014-01-01

    This article describes how a Washington State School District increased professional learning around the Common Core State Standards. The challenge was how to establish a way for career and technical education and electives teachers to learn and apply Common Core in their classes. Weaving Common Core literacy standards into vocational and…

  1. The EPOS Integrated Core Services

    Science.gov (United States)

    Jeffery, Keith; Michelini, Alberto; Bailo, Daniele

    2013-04-01

    EPOS also including other work packages in EPOS such as those concerned with legalistics and financing; (c) a prototype based on the woodman architecture in one domain (seismology) to provide assurance that the architecture is valid. The key aspect is the metadata catalog. In one dimension this is described in 3 levels: (1) discovery metadata using well-known and commonly used standards such as DC (Dublin Core) to enable users (via an intelligent user interface) to search for objects within the EPOS environment relevant to their needs; (2) contextual metadata providing the context of the object described in the catalog to enable a user or the system to determine the relevance of the discovered object(s) to their requirement - the context includes projects, funding, organisations involved, persons involved, related publications, facilities, equipment etc and utilises CERIF (Common European Research Information Format) see www.eurocris.org ; (3) detailed metadata which is specific to a domain or to a particular object and includes the schema describing the object to processing software. The other dimension of the metadata concerns the objects described. These are classified into users, services (including software), data and resources (computing, data storage, instruments and scientific equipment). The core services include not only user access to data, software, services, equipment and associated processing but also facilities for interaction and cooperative working between users and storage of history and experience. EPOS will operate a full e-Science environment including metadata and persistent identifiers.

  2. HBV Core Protein Enhances Cytokine Production

    Directory of Open Access Journals (Sweden)

    Tatsuo Kanda

    2015-09-01

    Full Text Available Hepatitis B virus (HBV infection, a cause of hepatocellular carcinoma (HCC, remains a serious global health concern. HCC development and human hepatocarcinogenesis are associated with hepatic inflammation caused by host interferons and cytokines. This article focused on the association between the HBV core protein, which is one of the HBV-encoding proteins, and cytokine production. The HBV core protein induced the production of interferons and cytokines in human hepatoma cells and in a mouse model. These factors may be responsible for persistent HBV infection and hepatocarcinogenesis. Inhibitors of programmed death (PD-1 and HBV core and therapeutic vaccines including HBV core might be useful for the treatment of patients with chronic HBV infection. Inhibitors of HBV core, which is important for hepatic inflammation, could be helpful in preventing the progression of liver diseases in HBV-infected patients.

  3. Core design and fuel management studies

    Energy Technology Data Exchange (ETDEWEB)

    Min, Byung Joo [Korea Atomic Energy Research Institute, Taejon (Korea, Republic of); Chan, P. [Atomic Energy of Canada Ltd., Chalk River, ON (Canada)

    1997-06-01

    The design target for the CANDU 9 requires a 20% increase in electrical power output from an existing 480-channel CANDU core. Assuming a net electrical output of 861 MW(e) for a natural uranium fuelled Bruce-B/Darlington reactor in a warm water site, the net electrical output of the reference CANDU 9 reactor would be 1033 MW(e). This report documents the result of the physics studies for the design of the CANDU 9 480/SEU core. The results of the core design and fuel management studies of the CANDU 9 480/SEU reactor indicated that up to 1033 MW(e) output can be achieved in a 480-channel CANDU core by using SEU core can easily be maintained indefinitely using an automated refuelling program. Fuel performance evaluation based on the data of the 500 FPDs refuelling simulation concluded that SEU fuel failure is not expected. (author). 2 tabs., 38 figs., 5 refs.

  4. Core of communities in bipartite networks

    Science.gov (United States)

    Bongiorno, Christian; London, András; Miccichè, Salvatore; Mantegna, Rosario N.

    2017-08-01

    We use the information present in a bipartite network to detect cores of communities of each set of the bipartite system. Cores of communities are found by investigating statistically validated projected networks obtained using information present in the bipartite network. Cores of communities are highly informative and robust with respect to the presence of errors or missing entries in the bipartite network. We assess the statistical robustness of cores by investigating an artificial benchmark network, the coauthorship network, and the actor-movie network. The accuracy and precision of the partition obtained with respect to the reference partition are measured in terms of the adjusted Rand index and the adjusted Wallace index, respectively. The detection of cores is highly precise, although the accuracy of the methodology can be limited in some cases.

  5. FAST FOSSIL ROTATION OF NEUTRON STAR CORES

    Energy Technology Data Exchange (ETDEWEB)

    Melatos, A., E-mail: amelatos@unimelb.edu.au [School of Physics, University of Melbourne, Parkville, VIC 3010 (Australia)

    2012-12-10

    It is argued that the superfluid core of a neutron star super-rotates relative to the crust, because stratification prevents the core from responding to the electromagnetic braking torque, until the relevant dissipative (viscous or Eddington-Sweet) timescale, which can exceed {approx}10{sup 3} yr and is much longer than the Ekman timescale, has elapsed. Hence, in some young pulsars, the rotation of the core today is a fossil record of its rotation at birth, provided that magnetic crust-core coupling is inhibited, e.g., by buoyancy, field-line topology, or the presence of uncondensed neutral components in the superfluid. Persistent core super-rotation alters our picture of neutron stars in several ways, allowing for magnetic field generation by ongoing dynamo action and enhanced gravitational wave emission from hydrodynamic instabilities.

  6. Fast Fossil Rotation of Neutron Star Cores

    Science.gov (United States)

    Melatos, A.

    2012-12-01

    It is argued that the superfluid core of a neutron star super-rotates relative to the crust, because stratification prevents the core from responding to the electromagnetic braking torque, until the relevant dissipative (viscous or Eddington-Sweet) timescale, which can exceed ~103 yr and is much longer than the Ekman timescale, has elapsed. Hence, in some young pulsars, the rotation of the core today is a fossil record of its rotation at birth, provided that magnetic crust-core coupling is inhibited, e.g., by buoyancy, field-line topology, or the presence of uncondensed neutral components in the superfluid. Persistent core super-rotation alters our picture of neutron stars in several ways, allowing for magnetic field generation by ongoing dynamo action and enhanced gravitational wave emission from hydrodynamic instabilities.

  7. Evidence of Historical Supernovae in Ice Cores

    Science.gov (United States)

    Young, Donna

    2011-05-01

    Within the framework of the U.S. Greenland Ice Core Science Project (GISP2), an ice core, known as the GISP H-Core, was collected in June, 1992 adjacent to the GISP2 summit drill site. The project scientists, Gisela A.M. Dreschhoff and Edward J. Zeller, were interested in dating solar proton events with volcanic eruptions. The GISP2-H 122-meter firn and ice core is a record of 415 years of liquid electrical conductivity (LEC) and nitrate concentrations, spanning the years 1992 at the surface through 1577 at the bottom. At the National Ice Core Laboratory in Denver, Colorado, the core (beneath the 12-meter firn) was sliced into 1.5 cm sections and analyzed. The resulting data set consisted of 7,776 individual analyses. The ultrahigh resolution sampling technique resulted in a time resolution of one week near the surface and one month at depth. The liquid electrical conductivity (LEC) sequence contains signals from a number of known volcanic eruptions and provides a dating system at specific locations along the core. The terrestrial and solar background nitrate records show seasonal and annual variations, respectively. However, major nitrate anomalies within the record do not correspond to any known terrestrial or solar events. There is evidence that these nitrate anomalies could be a record of supernovae events. Cosmic X-rays ionize atmospheric nitrogen, producing excess nitrate that is then deposited in the Polar Regions. The GISP2-H ice core has revealed nitrate anomalies at the times of the Tycho and Kepler supernovae. The Cassiopeia A supernova event may be documented in the core as well. We have developed a classroom activity for high school and college students, in which they examine several lines of evidence in the Greenland ice core, discriminating among nearby and mid-latitude volcanic activity, solar proton events, and supernovae. Students infer the date of the Cassiopeia A supernova.

  8. Core-annular flow through a horizontal pipe: hydrodynamic counterbalancing of buoyancy force on core

    OpenAIRE

    Ooms, G.; Vuik, C.; Poesio, P.

    2008-01-01

    A theoretical investigation has been made of core-annular flow: the flow of a high-viscosity liquid core surrounded by a low-viscosity liquid annular layer through a horizontal pipe. Special attention is paid to the question of how the buoyancy force on the core, caused by a density difference between the core and the annular layer, is counterbalanced. From earlier studies it is known that at the interface between the annular layer and the core waves are present that move with respect to the ...

  9. A study on the recriticality possibilities of fast reactor cores after a hypothetical core meltdown accident

    Energy Technology Data Exchange (ETDEWEB)

    Na, Byung Chan; Han, Do Hee; Kim, Young Cheol

    1997-04-01

    The preliminary and parametric sensitivity study on recriticality risk of fast reactor cores after a hypothetical total core meltdown accident was performed. Only the neutronic aspects of the accident was considered for this study, independent of the accident scenario. Estimation was made for the quantities of molten fuel which must be ejected out of the core in order to assure a sub-critical state. Diverse parameters were examined: molten pool type (homogenized or stratified), fuel temperature, conditions of the reactor core, core size (small or large), and fuel type (oxide, nitride, metal) (author). 7 refs.

  10. Transcriptome Profiling of Pediatric Core Binding Factor AML.

    Directory of Open Access Journals (Sweden)

    Chih-Hao Hsu

    Full Text Available The t(8;21 and Inv(16 translocations disrupt the normal function of core binding factors alpha (CBFA and beta (CBFB, respectively. These translocations represent two of the most common genomic abnormalities in acute myeloid leukemia (AML patients, occurring in approximately 25% pediatric and 15% of adult with this malignancy. Both translocations are associated with favorable clinical outcomes after intensive chemotherapy, and given the perceived mechanistic similarities, patients with these translocations are frequently referred to as having CBF-AML. It remains uncertain as to whether, collectively, these translocations are mechanistically the same or impact different pathways in subtle ways that have both biological and clinical significance. Therefore, we used transcriptome sequencing (RNA-seq to investigate the similarities and differences in genes and pathways between these subtypes of pediatric AMLs. Diagnostic RNA from patients with t(8;21 (N = 17, Inv(16 (N = 14, and normal karyotype (NK, N = 33 were subjected to RNA-seq. Analyses compared the transcriptomes across these three cytogenetic subtypes, using the NK cohort as the control. A total of 1291 genes in t(8;21 and 474 genes in Inv(16 were differentially expressed relative to the NK controls, with 198 genes differentially expressed in both subtypes. The majority of these genes (175/198; binomial test p-value < 10(-30 are consistent in expression changes among the two subtypes suggesting the expression profiles are more similar between the CBF cohorts than in the NK cohort. Our analysis also revealed alternative splicing events (ASEs differentially expressed across subtypes, with 337 t(8;21-specific and 407 Inv(16-specific ASEs detected, the majority of which were acetylated proteins (p = 1.5 x 10(-51 and p = 1.8 x 10(-54 for the two subsets. In addition to known fusions, we identified and verified 16 de novo fusions in 43 patients, including three fusions involving NUP98 in six

  11. The Fuzziness of Giant Planets’ Cores

    Science.gov (United States)

    Helled, Ravit; Stevenson, David

    2017-05-01

    Giant planets are thought to have cores in their deep interiors, and the division into a heavy-element core and hydrogen-helium envelope is applied in both formation and structure models. We show that the primordial internal structure depends on the planetary growth rate, in particular, the ratio of heavy elements accretion to gas accretion. For a wide range of likely conditions, this ratio is in one-to-one correspondence with the resulting post-accretion profile of heavy elements within the planet. This flux ratio depends sensitively on the assumed solid-surface density in the surrounding nebula. We suggest that giant planets’ cores might not be distinct from the envelope and includes some hydrogen and helium, and the deep interior can have a gradual heavy-element structure. Accordingly, Jupiter’s core may not be well defined. Accurate measurements of Jupiter’s gravitational field by Juno could put constraints on Jupiter’s core mass. However, as we suggest here, the definition of Jupiter’s core is complex, and the core’s physical properties (mass, density) depend on the actual definition of the core and on the planet’s growth history.

  12. The Fuzziness of Giant Planets’ Cores

    Energy Technology Data Exchange (ETDEWEB)

    Helled, Ravit [Institute for Computational Science, University of Zurich, Zurich (Switzerland); Stevenson, David [Division of Geological and Planetary Sciences, Caltech, Pasadena, CA (United States)

    2017-05-01

    Giant planets are thought to have cores in their deep interiors, and the division into a heavy-element core and hydrogen–helium envelope is applied in both formation and structure models. We show that the primordial internal structure depends on the planetary growth rate, in particular, the ratio of heavy elements accretion to gas accretion. For a wide range of likely conditions, this ratio is in one-to-one correspondence with the resulting post-accretion profile of heavy elements within the planet. This flux ratio depends sensitively on the assumed solid-surface density in the surrounding nebula. We suggest that giant planets’ cores might not be distinct from the envelope and includes some hydrogen and helium, and the deep interior can have a gradual heavy-element structure. Accordingly, Jupiter’s core may not be well defined. Accurate measurements of Jupiter’s gravitational field by Juno could put constraints on Jupiter’s core mass. However, as we suggest here, the definition of Jupiter’s core is complex, and the core’s physical properties (mass, density) depend on the actual definition of the core and on the planet’s growth history.

  13. Core muscle activity during suspension exercises.

    Science.gov (United States)

    Mok, Nicola W; Yeung, Ella W; Cho, Jeran C; Hui, Samson C; Liu, Kimee C; Pang, Coleman H

    2015-03-01

    Suspension exercise has been advocated as an effective means to improve core stability among healthy individuals and those with musculoskeletal complaints. However, the activity of core muscles during suspension exercises has not been reported. In this study, we investigated the level of activation of core muscles during suspension exercises within young and healthy adults. The study was conducted in a controlled laboratory setting. Surface electromyographic (sEMG) activity of core muscles (rectus abdominis, external oblique, internal oblique/transversus abdominis, and superficial lumbar multifidus) during four suspension workouts (hip abduction in plank, hamstring curl, chest press, and 45° row) was investigated. Muscle activity during a 5-s hold period of the workouts was measured by sEMG and normalized to the individual's maximal voluntary isometric contraction (MVIC). Different levels of muscle activation were observed during the hip abduction in plank, hamstring curl, and chest press. Hip abduction in plank generated the highest activation of most abdominal muscles. The 45° row exercise generated the lowest muscle activation. Among the four workouts investigated, the hip abduction in plank with suspension was found to have the strongest potential strengthening effect on core muscles. Also, suspension training was found to generate relatively high levels of core muscle activation when compared with that among previous studies of core exercises on stable and unstable support surfaces. Copyright © 2014 Sports Medicine Australia. Published by Elsevier Ltd. All rights reserved.

  14. Primordial Stratification of the Earth's Core (Invited)

    Science.gov (United States)

    Hernlund, J. W.; Rubie, D. C.; Labrosse, S. J.

    2013-12-01

    A variety of diverse approaches have been used to assess the formation of Earth's core by silicate-metal equilibration in magma oceans formed by energetic impacts during accretion, all of which invariably yield increasing temperatures and impurity concentrations in the downgoing metal as planetary growth progresses. If one builds the core incrementally with metal equilibrated in magma oceans from the center-up, this gives rise to a gravitationally stratified core with a cool iron-rich central region surrounded by a hot impurity-enriched veneer. The kinetic energy of infalling metal leads to mixing that could moderate such stratification, however, in detail the energetic barriers are difficult to overcome. Regardless of the mechanism of downward metal transport from a magma ocean, the fastest possible descent rate of metal into the core is limited by hard turbulence, for which scaling arguments show that the kinetic energy is much smaller than the expected stabilizing gravitational potential energy. This presents a paradox because the bulk of Earth's present day outer core exhibits density fluctuations of order ppb, apart from stratified regions in the uppermost and lowermost ~100 km. The required degree of mixing seems likely to have been achieved by additional kinetic energy from the direct merging of the cores of large differentiated planetesimal-sized bodies, thus metal transport and merging was not entirely determined by processes such as gravity-driven descent through the mantle from a magma ocean. It is unknown whether the mixing was complete, or whether stratified regions such as the F-layer represent the residue of early stratification. It is possible that Earth's inner core has been growing inside an impurity depleted region of Earth's central core since its birth, which carries implications for the age of the inner core as well as the mechanism of its growth.

  15. Muscle activation of different core exercises.

    Science.gov (United States)

    Oliver, Gretchen D; Dwelly, Priscilla M; Sarantis, Nicholas D; Helmer, Rachael A; Bonacci, Jeffery A

    2010-11-01

    Sport health care professionals are always trying to increase muscle activation while instructing exercises that are functional to the sport performance. However, the traditional core exercises are the ones typically performed. This study examined the muscle activation of the lumbopelvic hip complex during traditional core stability exercises and that of the sports performance movements using the CORE X. Fourteen healthy, college-age men (mean age 20.8 ± 3.9 years; mean height, 177.8 ± 10.9 cm; mean weight, 67.3 ± 9.9 kg) participated. Electromyographic (EMG) data were collected on the following muscles: dominant gluteus maximus, dominant gluteus medius, rectus abdomonis (bilateral), external oblique (bilateral), and multifidis (bilateral). Results revealed a significant difference between the 2 different exercise programs for all muscles investigated except the external obliques (p CORE X showed increased mean muscle activation for the dominant (57.8% maximum voluntary isometric contraction [MVIC]) and nondominant multifidus (56.4% MVIC) and the dominant gluteus maximus (48.3% MVIC) and medius (65.3% MVIC), whereas the traditional core exercises showed greater mean muscle activation for the dominant (45.1% MVIC) and nondominant rectus abdominis (47.4% MVIC) and external oblique (45.8% MVIC and 47.8% MVIC). The investigators were able to determine that while performing movements that mimicked more sports-related activities with the CORE X, there is a greater activation of the core musculature. Coaches, trainers, and athletic trainers should focus on training a core neutral while performing sports-specific movements that can be done with the CORE X.

  16. Oak Ridge National Laboratory Core Competencies

    Energy Technology Data Exchange (ETDEWEB)

    Roberto, J.B.; Anderson, T.D.; Berven, B.A.; Hildebrand, S.G.; Hartman, F.C.; Honea, R.B.; Jones, J.E. Jr.; Moon, R.M. Jr.; Saltmarsh, M.J.; Shelton, R.B. [and others

    1994-12-01

    A core competency is a distinguishing integration of capabilities which enables an organization to deliver mission results. Core competencies represent the collective learning of an organization and provide the capacity to perform present and future missions. Core competencies are distinguishing characteristics which offer comparative advantage and are difficult to reproduce. They exhibit customer focus, mission relevance, and vertical integration from research through applications. They are demonstrable by metrics such as level of investment, uniqueness of facilities and expertise, and national impact. The Oak Ridge National Laboratory (ORNL) has identified four core competencies which satisfy the above criteria. Each core competency represents an annual investment of at least $100M and is characterized by an integration of Laboratory technical foundations in physical, chemical, and materials sciences; biological, environmental, and social sciences; engineering sciences; and computational sciences and informatics. The ability to integrate broad technical foundations to develop and sustain core competencies in support of national R&D goals is a distinguishing strength of the national laboratories. The ORNL core competencies are: 9 Energy Production and End-Use Technologies o Biological and Environmental Sciences and Technology o Advanced Materials Synthesis, Processing, and Characterization & Neutron-Based Science and Technology. The distinguishing characteristics of each ORNL core competency are described. In addition, written material is provided for two emerging competencies: Manufacturing Technologies and Computational Science and Advanced Computing. Distinguishing institutional competencies in the Development and Operation of National Research Facilities, R&D Integration and Partnerships, Technology Transfer, and Science Education are also described. Finally, financial data for the ORNL core competencies are summarized in the appendices.

  17. Spatial Indexing of Datasets for CoreWall: CoreNavigator

    Science.gov (United States)

    Morin, P.; Jenkins, C.; Rao, A.; Kamp, B.; Higgins, S.; Ito, E.; Johnson, A.

    2006-12-01

    Corewall is a community computing facility for logging ice, lake, sediment and hard rock cores. It is described as a Collaborative Interactive Core Analysis Environment, allowing dispersed (even international and ship-side / in-the-field) logging and interpretation on sections of core representing Earth history. Many institutions support Corewall, including NSF. CoreNavigator is a 3D Visual Indexer of core and stratigraphic datasets, necessary because GIS systems available to researchers do not adequately display the vertical stratigraphic structure, or let users browse at will through the stratigraphy. CoreNavigator including its Google Earth extension, is likely to be a primary point of entry for the community into CoreWall. By a combination of 3D VRML and KML visualization technologies CoreNavigator indexes thousands of cores for user selection leading to a variety of actions. By clicking on visual 3D elements of CoreNavigator, users can obtain tables of integrated ready-to-use data (e.g., from dbSEABED, see web). They can also drill down into the original field notes, core photos, equipment types, lab analysis files, calibrations, etc. They can launch applications including the Corelyzer part of Corewall. [CoreNavigator 3D VRML displays are also editable and publishable, and can have seismic, oceanography, culture objects inserted. In the Geowall environment they are a resource for education.] CoreNavigator will be demonstrated as part of Corewall. By adopting a single spatial - global approach in this way to all types of cored stratigraphic data - ice, sediment, rock sea and lake - researchers will be able to transfer their enquiries and validation exercises in questions of environmental change, across the whole Earth surface.

  18. Depletion of autophagy-related genes ATG3 and ATG5 in Tenebrio molitor leads to decreased survivability against an intracellular pathogen, Listeria monocytogenes.

    Science.gov (United States)

    Tindwa, Hamisi; Jo, Yong Hun; Patnaik, Bharat Bhusan; Noh, Mi Young; Kim, Dong Hyun; Kim, Iksoo; Han, Yeon Soo; Lee, Yong Seok; Lee, Bok Luel; Kim, Nam Jung

    2015-01-01

    Macroautophagy (autophagy) is an evolutionarily conserved catabolic process involved in physiological and developmental processes including cell survival, death, and innate immunity. Homologues of most of 36 originally discovered autophagy-related (ATG) genes in yeast have been characterized in higher eukaryotes including insects. In this study, the homologues of ATG3 (TmATG3) and ATG5 (TmATG5) were isolated from the coleopteran beetle, Tenebrio molitor by expressed sequence tag and RNAseq approaches. The cDNA of TmATG3 and TmATG5 comprise open-reading frame sizes of 963 and 792 bp encoding polypeptides of 320 and 263 amino acid residues, respectively. TmATG3 and TmATG5 mRNA are expressed in all developmental stages, and mainly in fat body and hemocytes of larvae. TmATG3 and TmATG5 showed an overall sequence identity of 58-95% to other insect Atg proteins. There exist clear one-to-one orthologs of TmATG3 and TmATG5 in Tribolium and that they clustered together in the gene tree. Depletion of TmATG3 and TmATG5 by RNA interference led to a significant reduction in survival ability of T. molitor larvae against an intracellular pathogen, Listeria monocytogenes. Six days post-Listeria challenge, the survival rate in the dsEGFP-injected (where EGFP is enhanced green fluorescent protein) control larvae was significantly higher (55%) compared to 4 and 3% for TmATG3 and TmATG5 double-stranded RNA injected larvae, respectively. These data suggested that TmATG3 and TmATG5 may play putative role in mediating autophagy-based clearance of Listeria in T. molitor model. © 2014 Wiley Periodicals, Inc.

  19. Impact response of balsa core sandwiches

    Directory of Open Access Journals (Sweden)

    Nurdane Mortas

    2014-10-01

    Full Text Available The benefits of resins nano-enhanced on the impact response of sandwich composites made by fiber glass/epoxy skins and balsa wood core were studied. Afterwards, the influence of the core's discontinuity was analyzed in terms of impact strength. For better dispersion and interface adhesion matrix/clay nanoclays were previously subjected to a silane treatment appropriate to the epoxy resin. Resins enhanced by nanoclays promote higher maximum impact loads, lower displacements and the best performance in terms of elastic recuperation. The core's discontinuity decreases the impact strength, but the resin enhanced by nanoclays promotes significant benefits.

  20. Hollow Core, Whispering Gallery Resonator Sensors

    CERN Document Server

    Ward, Jonathan M; Chormaic, Síle Nic

    2014-01-01

    A review of hollow core whispering gallery resonators (WGRs)is given. After a short introduction to the topic of whispering gallery resonators we provide a description of whispering gallery modes in hollow or liquid core WGRs. Next, whispering gallery mode (WGM) sensing mechanisms are outlined and some fabrication methods for microbubbles, microcapillaries and other tubular WGM devices are discussed. We then focus on the most common applications of hollow core WGRs, namely refractive index and temperature sensing, gas sensing, force sensing, biosensing, and lasing. The review highlights some of the key papers in this field and gives the reader a general overview of the current state-of-the-art.

  1. Petrographic Analysis of Cores from Plant 42

    Science.gov (United States)

    2016-10-01

    ER D C TR -X X- D R AF T Petrographic Analysis of Cores from Plant 42 E n gi n ee r R es ea rc h a n d D ev el op m en t C en te r...Air Force Plant 42, were logged in as CMB No. 160143-1 to 160143-13, were subjected to an in-depth analysis consisting of visual and petrographic...Struc- tures Laboratory was requested to perform an analysis on concrete core samples extracted from Air Force Plant 42. A total of 13 cores were

  2. Identification of a core TP53 transcriptional program with highly distributed tumor suppressive activity.

    Science.gov (United States)

    Andrysik, Zdenek; Galbraith, Matthew D; Guarnieri, Anna L; Zaccara, Sara; Sullivan, Kelly D; Pandey, Ahwan; MacBeth, Morgan; Inga, Alberto; Espinosa, Joaquín M

    2017-10-01

    The tumor suppressor TP53 is the most frequently mutated gene product in human cancer. Close to half of all solid tumors carry inactivating mutations in the TP53 gene, while in the remaining cases, TP53 activity is abrogated by other oncogenic events, such as hyperactivation of its endogenous repressors MDM2 or MDM4. Despite identification of hundreds of genes regulated by this transcription factor, it remains unclear which direct target genes and downstream pathways are essential for the tumor suppressive function of TP53. We set out to address this problem by generating multiple genomic data sets for three different cancer cell lines, allowing the identification of distinct sets of TP53-regulated genes, from early transcriptional targets through to late targets controlled at the translational level. We found that although TP53 elicits vastly divergent signaling cascades across cell lines, it directly activates a core transcriptional program of ∼100 genes with diverse biological functions, regardless of cell type or cellular response to TP53 activation. This core program is associated with high-occupancy TP53 enhancers, high levels of paused RNA polymerases, and accessible chromatin. Interestingly, two different shRNA screens failed to identify a single TP53 target gene required for the anti-proliferative effects of TP53 during pharmacological activation in vitro. Furthermore, bioinformatics analysis of thousands of cancer genomes revealed that none of these core target genes are frequently inactivated in tumors expressing wild-type TP53. These results support the hypothesis that TP53 activates a genetically robust transcriptional program with highly distributed tumor suppressive functions acting in diverse cellular contexts. © 2017 Andrysik et al.; Published by Cold Spring Harbor Laboratory Press.

  3. Preliminaries on core image analysis using fault drilling samples; Core image kaiseki kotohajime (danso kussaku core kaisekirei)

    Energy Technology Data Exchange (ETDEWEB)

    Miyazaki, T.; Ito, H. [Geological Survey of Japan, Tsukuba (Japan)

    1996-05-01

    This paper introduces examples of image data analysis on fault drilling samples. The paper describes the following matters: core samples used in the analysis are those obtained from wells drilled piercing the Nojima fault which has moved in the Hygoken-Nanbu Earthquake; the CORESCAN system made by DMT Corporation, Germany, used in acquiring the image data consists of a CCD camera, a light source and core rotation mechanism, and a personal computer, its resolution being about 5 pixels/mm in both axial and circumferential directions, and 24-bit full color; with respect to the opening fractures in core samples collected by using a constant azimuth coring, it was possible to derive values of the opening width, inclination angle, and travel from the image data by using a commercially available software for the personal computer; and comparison of this core image with the BHTV record and the hydrophone VSP record (travel and inclination obtained from the BHTV record agree well with those obtained from the core image). 4 refs., 4 figs.

  4. Trichoderma genes

    Science.gov (United States)

    Foreman, Pamela [Los Altos, CA; Goedegebuur, Frits [Vlaardingen, NL; Van Solingen, Pieter [Naaldwijk, NL; Ward, Michael [San Francisco, CA

    2012-06-19

    Described herein are novel gene sequences isolated from Trichoderma reesei. Two genes encoding proteins comprising a cellulose binding domain, one encoding an arabionfuranosidase and one encoding an acetylxylanesterase are described. The sequences, CIP1 and CIP2, contain a cellulose binding domain. These proteins are especially useful in the textile and detergent industry and in pulp and paper industry.

  5. Network topology reveals key cardiovascular disease genes.

    Directory of Open Access Journals (Sweden)

    Anida Sarajlić

    Full Text Available The structure of protein-protein interaction (PPI networks has already been successfully used as a source of new biological information. Even though cardiovascular diseases (CVDs are a major global cause of death, many CVD genes still await discovery. We explore ways to utilize the structure of the human PPI network to find important genes for CVDs that should be targeted by drugs. The hope is to use the properties of such important genes to predict new ones, which would in turn improve a choice of therapy. We propose a methodology that examines the PPI network wiring around genes involved in CVDs. We use the methodology to identify a subset of CVD-related genes that are statistically significantly enriched in drug targets and "driver genes." We seek such genes, since driver genes have been proposed to drive onset and progression of a disease. Our identified subset of CVD genes has a large overlap with the Core Diseasome, which has been postulated to be the key to disease formation and hence should be the primary object of therapeutic intervention. This indicates that our methodology identifies "key" genes responsible for CVDs. Thus, we use it to predict new CVD genes and we validate over 70% of our predictions in the literature. Finally, we show that our predicted genes are functionally similar to currently known CVD drug targets, which confirms a potential utility of our methodology towards improving therapy for CVDs.

  6. Scaling of a Fast Fourier Transform and a pseudo-spectral fluid solver up to 196608 cores

    KAUST Repository

    Chatterjee, Anando G.

    2017-11-04

    In this paper we present scaling results of a FFT library, FFTK, and a pseudospectral code, Tarang, on grid resolutions up to 81923 grid using 65536 cores of Blue Gene/P and 196608 cores of Cray XC40 supercomputers. We observe that communication dominates computation, more so on the Cray XC40. The computation time scales as Tcomp∼p−1, and the communication time as Tcomm∼n−γ2 with γ2 ranging from 0.7 to 0.9 for Blue Gene/P, and from 0.43 to 0.73 for Cray XC40. FFTK, and the fluid and convection solvers of Tarang exhibit weak as well as strong scaling nearly up to 196608 cores of Cray XC40. We perform a comparative study of the performance on the Blue Gene/P and Cray XC40 clusters.

  7. Massive Quiescent Cores in Orion: Dichotomy in the Dynamical Status of Cores

    Science.gov (United States)

    Velusamy, Thangasamy; Goldsmith, P. F.; Li, D.; Langer, W. D.; Pineda, J. L.; Peng, R.

    2009-01-01

    To study the evolution of high mass cores we have searched for evidence of collapse motions in a large sample of starless cores in the Orion molecular cloud. We used the Caltech Submillimeter Observatory telescope to obtain spectra of the optically thin (H13CO+) and optically thick (HCO+) high density tracer molecules in 27 cores with masses > 1 MO. The red- and blue-asymmetries seen in the line profiles of the optically thick line with respect to the optically thin line indicate that 2/3 of these cores are not static and we interpret these as evidence for inward or outward motions in 19 cores. We present RATRAN radiative transfer models of these cores that support the interpretation of inward and outward motion consistent with the observed spectral asymmetries. Thus we detect infall (inward motions) in 9 cores and outward motions for 10 cores, suggesting a dichotomy in the kinematic state in this sample. This population of massive molecular cloud cores is in general likely to be dynamic, out-of-equilibrium structures, rather than quasi-hydro/magneto-static structures. Our results provide an important observational constraint on the fraction of collapsing (inward motions) versus non-collapsing (re-expanding) cores for comparison with model simulations. This work was performed by the Jet Propulsion Laboratory, California Institute of Technology, under contract with the National Aeronautics and Space Administration. Research at the Caltech Submillimeter Observatory is supported by NSF grant AST-0229008.

  8. Assessment of the HPLWR thermal core design

    Energy Technology Data Exchange (ETDEWEB)

    Schulenberg, T. [Karlsruhe Inst. of Tech., Karlsruhe (Germany); Maraczy, C. [Hungarian Academy of Sciences KFKI, Budapest (Hungary); Bernnat, W.; Starflinger, J. [Univ. of Stuttgart, IKE (Germany)

    2011-07-01

    The core design concept of the High Performance Light Water Reactor features a thermal neutron spectrum, provided by additional moderator water in water boxes and in gaps between assembly boxes, and a heat-up of the coolant in three steps from 280{sup o}C to 500{sup o}C. Intermediate coolant mixing has been foreseen by mixing chambers underneath and above the core to overcome the hot channel issue of a core design with a large enthalpy rise. The paper summarizes the various analyses performed within the project HPLWR-Phase 2 with respect to this core design and assesses how far the initial design target has been met. (author)

  9. NICHD Microscopy and Imaging Core (MIC)

    Data.gov (United States)

    Federal Laboratory Consortium — The NICHD Microscopy and Imaging Core (MIC) is designed as a multi-user research facility providing training and instrumentation for high resolution microscopy and...

  10. Bioinformatics and Computational Core Technology Center

    Data.gov (United States)

    Federal Laboratory Consortium — SERVICES PROVIDED BY THE COMPUTER CORE FACILITYEvaluation, purchase, set up, and maintenance of the computer hardware and network for the 170 users in the research...

  11. Inquiry, New Literacies, and the Common Core

    Science.gov (United States)

    Stegman, Bridget

    2014-01-01

    For 21st century learning, students need to be well versed in techniques for inquiry using new literacies. Developing these skills also will meet the rigorous expectations of the Common Core State Standards.

  12. Pilates: Build Strength in Your Core Muscles

    Science.gov (United States)

    ... in the 1920s. A Pilates routine generally includes exercises that promote core strength and stability, muscle control and endurance, including exercises that stress proper posture and movement patterns and ...

  13. Core inflation indicators for Saudi Arabia

    Directory of Open Access Journals (Sweden)

    Alkhareif Ryadh M.

    2015-01-01

    Full Text Available This paper constructs and analyzes core inflation indicators for Saudi Arabia for the period of March 2012 to May 2014 using two alternative approaches: the exclusion method (ex food and housing/rent and the statistical method. The findings of the analysis suggest that the ex food and housing/ rent inflation is more volatile than the overall CPI inflation over the sample period. In contrast, the statistical core inflation is relatively more stable and less volatile. Moreover, the ex food and housing/rent inflation is only weakly correlated with headline inflation, whereas the statistical core inflation exhibits a stronger correlation. This combination of lower volatility and higher correlation with headline inflation makes the statistical method a much better choice for policymakers. From a monetary policy standpoint, using a bundle of core inflation measures, including both properly constructed exclusion and statistical methods, is more desirable, especially when variation across measures is widespread, as is the case in Saudi Arabia.

  14. Data from Devils Hole Core DH-11

    Science.gov (United States)

    Landwehr, Jurate Maciunas; Coplen, T.B.; Ludwig, K. R.; Winograd, I.J.; Riggs, A.C.

    1997-01-01

    This report presents the stable isotope values measured in Devils Hole Core DH-11 and interpolated ages at the depth the samples were taken, as analyzed in a recent publication by Winograd and others (1997).

  15. Perception Management: A Core IO Capability

    National Research Council Canada - National Science Library

    Zaman, Khyber

    2007-01-01

    This thesis postulates that in today's media environment, with adversaries skillfully using propaganda to skirt nations' resolve, Perception Management is key to military success and should be an Information Operations (IO) Core Capability...

  16. Chamber Core Structures for Fairing Acoustic Mitigation

    National Research Council Canada - National Science Library

    Lane, Steven A; Henderson, Kyle; Williams, Andrew; Ardelean, Emil

    2007-01-01

    .... A composite chamber core fairing consists of many axial tubes sandwiched between face sheets, tubes that can be used as acoustic dampers to reduce low-frequency interior noise with virtually no added mass...

  17. Wire core reactor for nuclear thermal propulsion

    Science.gov (United States)

    Harty, Richard B.; Brengle, Robert G.

    1993-01-01

    Studies have been performed of a compact high-performance nuclear rocket reactor that incorporates a tungsten alloy wire fuel element. This reactor, termed the wire core reactor, can deliver a specific impulse of 1,000 s using an expander cycle and a nozzle expansion ratio of 500 to 1. The core is constructed of layers of 0.8-mm-dia fueled tungsten wires wound over alternate layers of spacer wires, which forms a rugged annular lattice. Hydrogen flow in the core is annular, flowing from inside to outside. In addition to the concepts compact size and good heat transfer, the core has excellent power-flow matching features and can resist vibration and thermal stresses during star-up and shutdown.

  18. Multi-core fiber undersea transmission systems

    DEFF Research Database (Denmark)

    Nooruzzaman, Md; Morioka, Toshio

    2017-01-01

    Various potential architectures of branching units for multi-core fiber undersea transmission systems are presented. It is also investigated how different architectures of branching unit influence the number of fibers and those of inline components....

  19. Core Stabilization Exercise Prescription, Part I

    Science.gov (United States)

    Brumitt, Jason; Matheson, J. W.; Meira, Erik P.

    2013-01-01

    Context: Injury to the low back can cause significant pain and dysfunction, which can affect an athlete’s performance and result in time lost from sport. A common conservative treatment is therapeutic core stabilization exercises, which can address pain and musculoskeletal dysfunction in patients with low back pathology. Evidence Acquisition: MEDLINE and CINAHL were searched (from 1966 to March 2013) to identify relevant research. Keywords and keyword combinations searched included motor control exercise, segmental stabilization, core stabilization, transversus abdominis, multifidi, and low back pain. Results: There are 2 popular rehabilitation strategies to assess core function and promote core stabilization. Each has been developed based on biomechanical models of lumbar segmental stability and observed motor control dysfunction in patients with low back pain. Conclusion: Controversy exists among clinical and research groups as to the optimal strategy for an athlete with low back pain. PMID:24427424

  20. NICHD Biomedical Mass Spectrometry Core Facility

    Data.gov (United States)

    Federal Laboratory Consortium — The NICHD Biomedical Mass Spectrometry Core Facility was created under the auspices of the Office of the Scientific Director to provide high-end mass-spectrometric...

  1. Satcom access in the evolved packet core

    NARCIS (Netherlands)

    Cano, M.D.; Norp, A.H.J.; Popova, M.P.

    2012-01-01

    Satellite communications (Satcom) networks are increasingly integrating with terrestrial communications networks, namely Next Generation Networks (NGN). In the area of NGN the Evolved Packet Core (EPC) is a new network architecture that can support multiple access technologies. When Satcom is

  2. Multiple network interface core apparatus and method

    Science.gov (United States)

    Underwood, Keith D [Albuquerque, NM; Hemmert, Karl Scott [Albuquerque, NM

    2011-04-26

    A network interface controller and network interface control method comprising providing a single integrated circuit as a network interface controller and employing a plurality of network interface cores on the single integrated circuit.

  3. Design, synthesis and applications of core-shell, hollow core, and nanorattle multifunctional nanostructures

    Science.gov (United States)

    El-Toni, Ahmed Mohamed; Habila, Mohamed A.; Labis, Joselito Puzon; Alothman, Zeid A.; Alhoshan, Mansour; Elzatahry, Ahmed A.; Zhang, Fan

    2016-01-01

    With the evolution of nanoscience and nanotechnology, studies have been focused on manipulating nanoparticle properties through the control of their size, composition, and morphology. As nanomaterial research has progressed, the foremost focus has gradually shifted from synthesis, morphology control, and characterization of properties to the investigation of function and the utility of integrating these materials and chemical sciences with the physical, biological, and medical fields, which therefore necessitates the development of novel materials that are capable of performing multiple tasks and functions. The construction of multifunctional nanomaterials that integrate two or more functions into a single geometry has been achieved through the surface-coating technique, which created a new class of substances designated as core-shell nanoparticles. Core-shell materials have growing and expanding applications due to the multifunctionality that is achieved through the formation of multiple shells as well as the manipulation of core/shell materials. Moreover, core removal from core-shell-based structures offers excellent opportunities to construct multifunctional hollow core architectures that possess huge storage capacities, low densities, and tunable optical properties. Furthermore, the fabrication of nanomaterials that have the combined properties of a core-shell structure with that of a hollow one has resulted in the creation of a new and important class of substances, known as the rattle core-shell nanoparticles, or nanorattles. The design strategies of these new multifunctional nanostructures (core-shell, hollow core, and nanorattle) are discussed in the first part of this review. In the second part, different synthesis and fabrication approaches for multifunctional core-shell, hollow core-shell and rattle core-shell architectures are highlighted. Finally, in the last part of the article, the versatile and diverse applications of these nanoarchitectures in

  4. Core Muscle Activation in Suspension Training Exercises

    OpenAIRE

    Cugliari, Giovanni; Boccia, Gennaro

    2017-01-01

    Abstract A quantitative observational laboratory study was conducted to characterize and classify core training exercises executed in a suspension modality on the base of muscle activation. In a prospective single-group repeated measures design, seventeen active male participants performed four suspension exercises typically associated with core training (roll-out, bodysaw, pike and knee-tuck). Surface electromyographic signals were recorded from lower and upper parts of rectus abdominis, ext...

  5. Retention Models on Core-Shell Columns.

    Science.gov (United States)

    Jandera, Pavel; Hájek, Tomáš; Růžičková, Marie

    2017-07-13

    A thin, active shell layer on core-shell columns provides high efficiency in HPLC at moderately high pressures. We revisited three models of mobile phase effects on retention for core-shell columns in mixed aqueous-organic mobile phases: linear solvent strength and Snyder-Soczewiński two-parameter models and a three-parameter model. For some compounds, two-parameter models show minor deviations from linearity due to neglect of possible minor retention in pure weak solvent, which is compensated for in the three-parameter model, which does not explicitly assume either the adsorption or the partition retention mechanism in normal- or reversed-phase systems. The model retention equation can be formulated as a function of solute retention factors of nonionic compounds in pure organic solvent and in pure water (or aqueous buffer) and of the volume fraction of an either aqueous or organic solvent component in a two-component mobile phase. With core-shell columns, the impervious solid core does not participate in the retention process. Hence, the thermodynamic retention factors, defined as the ratio of the mass of the analyte mass contained in the stationary phase to its mass in the mobile phase in the column, should not include the particle core volume. The values of the thermodynamic factors are lower than the retention factors determined using a convention including the inert core in the stationary phase. However, both conventions produce correct results if consistently used to predict the effects of changing mobile phase composition on retention. We compared three types of core-shell columns with C18-, phenyl-hexyl-, and biphenyl-bonded phases. The core-shell columns with phenyl-hexyl- and biphenyl-bonded ligands provided lower errors in two-parameter model predictions for alkylbenzenes, phenolic acids, and flavonoid compounds in comparison with C18-bonded ligands.

  6. Impact response of balsa core sandwiches

    OpenAIRE

    Nurdane Mortas; Paulo N.B. Reis; José A.M. Ferreira

    2014-01-01

    The benefits of resins nano-enhanced on the impact response of sandwich composites made by fiber glass/epoxy skins and balsa wood core were studied. Afterwards, the influence of the core's discontinuity was analyzed in terms of impact strength. For better dispersion and interface adhesion matrix/clay nanoclays were previously subjected to a silane treatment appropriate to the epoxy resin. Resins enhanced by nanoclays promote higher maximum impact loads, lower displacements and the...

  7. Distributed Memory Programming on Many-Cores

    DEFF Research Database (Denmark)

    Berthold, Jost; Dieterle, Mischa; Lobachev, Oleg

    2009-01-01

    is tailored to networks of workstations. Recent work has shown that this implementation shows surprisingly competitive performance on many-core machines, compared to dedicated shared-memory implementations of parallel Haskell. In the paper we describe a case study with different Eden divide......-and-conquer skeletons. We analyse their performance comparing example applications implemented using these Eden skeletons against parallel Haskell implementations using shared memory on many-core machines...

  8. Validation of Core Temperature Estimation Algorithm

    Science.gov (United States)

    2016-01-20

    and risk of heat injury. An algorithm for estimating core temperature based on heart rate has been developed by others in order to avoid standard... risk of heat injury. Accepted standards for measuring core temperature include probes in the pulmonary artery, rectum, or esophagus, and an ingestible...temperature estimation from heart rate for first responders wearing different levels of personal protective equipment," Ergonomics , 2015. 8. J.M

  9. Porous-core honeycomb bandgap THz fiber

    DEFF Research Database (Denmark)

    Nielsen, Kristian; Rasmussen, Henrik K.; Jepsen, Peter Uhd

    2011-01-01

    In this Letter we propose a novel (to our knowledge) porous-core honeycomb bandgap design. The holes of the porous core are the same size as the holes in the surrounding cladding, thereby giving the proposed fiber important manufacturing benefits. The fiber is shown to have a 0:35-THz......-wide fundamental bandgap centered at 1:05 THz. The calculated minimum loss of the fiber is 0:25 dB=cm....

  10. Hepatitis B virus core antigen: synthesis in Escherichia coli and application in diagnosis.

    Science.gov (United States)

    Stahl, S; MacKay, P; Magazin, M; Bruce, S A; Murray, K

    1982-01-01

    Fragments of hepatitis B virus DNA cloned in plasmid pBR322 carrying the gene for the viral core antigen have been placed under the control of the lac promoter of Escherichia coli. Several of the new recombinants direct higher levels of synthesis of the antigen, but the degree of enhancement varies with the different structures of the plasmids and hence the mRNAs produced. The antigen in crude bacterial lysates is a satisfactory diagnostic reagent for antibodies to the core antigen in serum samples. Images PMID:7041126

  11. Core-Shell Structured Magnetic Ternary Nanocubes

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Lingyan; Wang, Xin; Luo, Jin; Wanjala, Bridgid N.; Wang, Chong M.; Chernova, Natalya; Engelhard, Mark H.; Liu, Yao; Bae, In-Tae; Zhong, Chuan-Jian

    2010-12-01

    While transition metal-doped ferrite nanoparticles constitute an important class of soft magnetic nanomaterials with spinel structures, the ability to control the shape and composition would enable a wide range of applications in homogeneous or heterogeneous reactions such as catalysis and magnetic separation of biomolecules. This report describes novel findings of an investigation of core-shell structured MnZn ferrite nanocubes synthesized in organic solvents by manipulating the reaction temperature and capping agent composition in the absence of the conventionally-used reducing agents. The core-shell structure of the highly-monodispersed nanocubes (~20 nm) are shown to consist of an Fe3O4 core and an (Mn0.5Zn0.5)(Fe0.9, Mn1.1)O4 shell. In comparison with Fe3O4 and other binary ferrite nanoparticles, the core-shell structured nanocubes were shown to display magnetic properties regulated by a combination of the core-shell composition, leading to a higher coercivity (~350 Oe) and field-cool/zero-field-cool characteristics drastically different from many regular MnZn ferrite nanoparticles. The findings are discussed in terms of the unique core-shell composition, the understanding of which has important implication to the exploration of this class of soft magnetic nanomaterials in many potential applications such as magnetic resonance imaging, fuel cells, and batteries.

  12. Photon upconversion in core-shell nanoparticles.

    Science.gov (United States)

    Chen, Xian; Peng, Denfeng; Ju, Qiang; Wang, Feng

    2015-03-21

    Photon upconversion generally results from a series of successive electronic transitions within complex energy levels of lanthanide ions that are embedded in the lattice of a crystalline solid. In conventional lanthanide-doped upconversion nanoparticles, the dopant ions homogeneously distributed in the host lattice are readily accessible to surface quenchers and lose their excitation energy, giving rise to weak and susceptible emissions. Therefore, present studies on upconversion are mainly focused on core-shell nanoparticles comprising spatially confined dopant ions. By doping upconverting lanthanide ions in the interior of a core-shell nanoparticle, the upconversion emission can be substantially enhanced, and the optical integrity of the nanoparticles can be largely preserved. Optically active shells are also frequently employed to impart multiple functionalities to upconversion nanoparticles. Intriguingly, the core-shell design introduces the possibility of constructing novel upconversion nanoparticles by exploiting the energy exchange interactions across the core-shell interface. In this tutorial review, we highlight recent advances in the development of upconversion core-shell nanoparticles, with particular emphasis on the emerging strategies for regulating the interplay of dopant interactions through core-shell nanostructural engineering that leads to unprecedented upconversion properties. The improved control over photon energy conversion will open up new opportunities for biological and energy applications.

  13. Subannual layer variability in Greenland firn cores

    Science.gov (United States)

    Kjær, Helle Astrid; Vallelonga, Paul; Vinther, Bo; Winstrup, Mai; Simonsen, Marius; Maffezzoli, Niccoló; Jensen, Camilla Marie

    2017-04-01

    Ice cores are used to infer information about the past and modern techniques allow for high resolution (CFA) of the ice. Such analysis is often used to inform on annual layers to constrain dating of ice cores, but can also be extended to provide information on sub-annual deposition patterns. In this study we use available high resolution data from multiple shallow cores around Greenland to investigate the seasonality and trends in the most often continuously measured components sodium, insoluble dust, calcium, ammonium and conductivity (or acidity) from 1800 AD to today. We evaluate the similarities and differences between the records and discuss the causes from different sources and transport to deposition and post-deposition effects over differences in measurement set up. Further we add to the array of cores already published with measurements from the newly drilled ReCAP ice core from a coastal ice cap in eastern Greenland and from a shallow core drilled at the high accumulation site at the Greenland South Dome.

  14. A highly efficient multi-core algorithm for clustering extremely large datasets

    Directory of Open Access Journals (Sweden)

    Kraus Johann M

    2010-04-01

    Full Text Available Abstract Background In recent years, the demand for computational power in computational biology has increased due to rapidly growing data sets from microarray and other high-throughput technologies. This demand is likely to increase. Standard algorithms for analyzing data, such as cluster algorithms, need to be parallelized for fast processing. Unfortunately, most approaches for parallelizing algorithms largely rely on network communication protocols connecting and requiring multiple computers. One answer to this problem is to utilize the intrinsic capabilities in current multi-core hardware to distribute the tasks among the different cores of one computer. Results We introduce a multi-core parallelization of the k-means and k-modes cluster algorithms based on the design principles of transactional memory for clustering gene expression microarray type data and categorial SNP data. Our new shared memory parallel algorithms show to be highly efficient. We demonstrate their computational power and show their utility in cluster stability and sensitivity analysis employing repeated runs with slightly changed parameters. Computation speed of our Java based algorithm was increased by a factor of 10 for large data sets while preserving computational accuracy compared to single-core implementations and a recently published network based parallelization. Conclusions Most desktop computers and even notebooks provide at least dual-core processors. Our multi-core algorithms show that using modern algorithmic concepts, parallelization makes it possible to perform even such laborious tasks as cluster sensitivity and cluster number estimation on the laboratory computer.

  15. Saturation current spikes eliminated in saturable core transformers

    Science.gov (United States)

    Schwarz, F. C.

    1971-01-01

    Unsaturating composite magnetic core transformer, consisting of two separate parallel cores designed so impending core saturation causes signal generation, terminates high current spike in converter primary circuit. Simplified waveform, demonstrates transformer effectiveness in eliminating current spikes.

  16. Development of Toroidal Core Transformers

    Energy Technology Data Exchange (ETDEWEB)

    de Leon, Francisco [New York Univ. (NYU), Brooklyn, NY (United States). Dept. of Electrical and Computer Engineering

    2014-08-01

    The original objective of this project was to design, build and test a few prototypes of single-phase dry-type distribution transformers of 25 kVA, 2.4 kV primary to 120 V transformers using cores made of a continuous steel strip shaped like a doughnut (toroid). At different points during the development of the project, the scope was enhanced to include the more practical case of a 25 kVA transformer for a 13.8 kV primary system voltage. Later, the scope was further expanded to design and build a 50 kVA unit to transformer voltage from 7.62 kV to 2x120 V. This is a common transformer used by Con Edison of New York and they are willing to test it in the field. The project officially started in September 2009 and ended in May 2014. The progress was reported periodically to DOE in eighteen quarterly reports. A Continuation Application was submitted to DOE in June 2010. In May 2011 we have requested a non-cost extension of the project. In December 2011, the Statement of Project Objectives (SOPO) was updated to reflect the real conditions and situation of the project as of 2011. A second Continuation Application was made and funding was approved in 2013 by DOE and the end date was extended to May 2014. The technical challenges that were overcome in this project include: the development of the technology to pass the impulse tests, derive a model for the thermal performance, produce a sound mechanical design, and estimate the inrush current. However, the greatest challenge that we faced during the development of the project was the complications of procuring the necessary parts and materials to build the transformers. The actual manufacturing process is relatively fast, but getting all parts together is a very lengthy process. The main products of this project are two prototypes of toroidal distribution transformers of 7.62 kV (to be used in a 13.8 kV system) to 2x120 V secondary (standard utilization voltage); one is rated at 25 kVA and the other at 50 kVA. The 25 k

  17. Effects of Core-valence and Core-core Correlation On the Line-strength of the Resonance Lines In Li-i and Na-i

    OpenAIRE

    Brage, Tomas; Fischer, C.F.; Jonsson, P

    1994-01-01

    The resonance lines in Li I and Na I both exhibit a puzzling discrepancy between experiment and accurate ab initio calculations. Only results from a semiempirical method, that in principal neglects core-core correlation, agree with the experiments. The agreement with a multiconfiguration Hartree-Fock calculation, including only core-valence correlation, shows that this might be fortuitous. A method for including some core-core correlation is designed and gives results in excellent agreement w...

  18. NEPHTIS: Core depletion validation relying on 2D transport core calculations with the APOLLO2 code

    Energy Technology Data Exchange (ETDEWEB)

    Damian, F.; Raepsaet, X.; Groizard, M.; Poinot, C. [DEN/DM2S/SERMA/LCA, CEA Saclay, 91191 Gif-sur-Yvette Cedex (France)

    2006-07-01

    The CEA, in collaboration with EDF and AREVA-NP, is developing a core modelling tool called NEPHTIS, for Neutronic Process for HTGR Innovating Systems and dedicated at present day to the prismatic block-type HTGR (High Temperature Gas-Cooled Reactors). Due to the lack of usable HTGR experimental results, the confidence in this neutronic computational tool relies essentially on comparisons to reference or best-estimate calculations. In the present analysis, the Aleppo deterministic transport code has been selected as reference for validating core depletion simulations carried out within NEPHTIS. These reference calculations were performed on fully detailed 2D core configurations using the Method of Characteristics. The latter has been validated versus Monte Carlo method for different static core configurations [1], [2] and [3]. All the presented results come from an annular HTGR core loaded with uranium-based fuel (15% enrichment). During the core depletion validation, reactivity, reaction rates distributions and nuclei concentrations have been compared. In addition, the impact of various physical and geometrical parameters such as the core loading (one-through or batch-wise reloading) and the amount of burnable poison has been investigated during the validation phases. The results confirm that NEPHTIS is able to predict the core reactivity with uncertainties of {+-}350 pcm. At the end of the core irradiation, the U-235 consumption is calculated within {+-} 0, 7 % while the plutonium mass discharged from the core is calculated within {+-}1 %. As far as the core power distributions are concerned, small discrepancies ( and < 2.3 %) can be observed on the fuel block-averaged power distribution in the core. (authors)

  19. Study of hepatitis B virus gene mutations with enzymatic colorimetry-based DNA microarray.

    Science.gov (United States)

    Mao, Hailei; Wang, Huimin; Zhang, Donglei; Mao, Hongju; Zhao, Jianlong; Shi, Jian; Cui, Zhichu

    2006-01-01

    To establish a modified microarray method for detecting HBV gene mutations in the clinic. Site-specific oligonucleotide probes were immobilized to microarray slides and hybridized to biotin-labeled HBV gene fragments amplified from two-step PCR. Hybridized targets were transferred to nitrocellulose membranes, followed by intensity measurement using BCIP/NBT colorimetry. HBV genes from 99 Hepatitis B patients and 40 healthy blood donors were analyzed. Mutation frequencies of HBV pre-core/core and basic core promoter (BCP) regions were found to be significantly higher in the patient group (42%, 40% versus 2.5%, 5%, P colorimetry method exhibited the same level of sensitivity and reproducibility. An enzymatic colorimetry-based DNA microarray assay was successfully established to monitor HBV mutations. Pre-core/core and BCP mutations of HBV genes could be major causes of HBV infection in HBeAg-negative patients and could also be relevant to chronicity and aggravation of hepatitis B.

  20. Top coalitions, common rankings, and semistrict core stability

    OpenAIRE

    Dinko Dimitrov

    2006-01-01

    The top coalition property of Banerjee et al. (2001) and the common ranking property of Farrell and Scotchmer (1988) are sufficient conditions for core stability in hedonic games. We introduce the semistrict core as a stronger stability concept than the core, and show that the top coalition property guarantees the existence of semistrictly core stable coalition structures. Moreover, for each game satisfying the common ranking property, the core and the semistrict core coincide.

  1. Modulation of RANTES expression by HCV core protein in liver derived cell lines

    Directory of Open Access Journals (Sweden)

    Rapicetta Maria

    2007-06-01

    Full Text Available Abstract Background Hepatitis C virus (HCV infection is associated with high percentage of chronicity which implies the ability of the virus to evade or modulate host cell immune system. Modulation of chemokines, such as RANTES may be part of the virus induced pathogenicity. We examined the effect of core and structural proteins of HCV on RANTES expression in two liver derived cell lines, HepG2 and Chang Liver (CHL. Methods HepG2 and Chang Liver (CHL cell lines were established and selected for constitutive expression of HCV core and structural genes. Flow cytometry and quantitative RT-PCR analysis were performed to examine the effect of HCV core protein on RANTES expression. Luciferase analysis after RANTES-Luc-promoter transfection of established cell lines was assayed by luminometer measurements (RLU of RANTES promoter activity. IRF-1 and IRF-7 expression was then examined by immunoblotting analysis. Results Results of flow cytometry and RT-PCR analysis indicated that RANTES is differentially regulated by HCV core protein in the two cell lines examined as its expression was inhibited in HepG2 cells, by a reduction of RANTES promoter activity. Conversely, RANTES protein and mRNA were induced by the core protein in CHL cells, through the induction of the promoter. Since HCV genome modulates IRF-1 and IRF-7 in replicon system and IRF-1, IRF-3 and IRF-7 have been reported to regulate RANTES promoter in various cell systems, analysis of the mechanism underlying RANTES modulation by the core protein revealed that IRF-1 expression was induced in HepG2 cells by the core protein, whereas in CHL cells it was expressed at a very low level that was not influenced by transfection with the core protein construct. This suggested that IRF-1 level may mediate the expression of RANTES in cell lines of liver origin. The effect of the core protein on RANTES promoter was countered by co-transfection with NF90, a double-stranded-RNA binding protein that activates

  2. Gene Therapy

    Science.gov (United States)

    ... or improve your body's ability to fight disease. Gene therapy holds promise for treating a wide range of diseases, such as cancer, cystic fibrosis, heart disease, diabetes, hemophilia and AIDS. Researchers are still studying how and ...

  3. ICF Core Sets for rheumatoid arthritis.

    Science.gov (United States)

    Stucki, Gerold; Cieza, Alarcos; Geyh, Szilvia; Battistella, Linamara; Lloyd, Jill; Symmons, Deborah; Kostanjsek, Nenad; Schouten, Jan

    2004-07-01

    To report on the results of the consensus process integrating evidence from preliminary studies to develop the first version of a Comprehensive ICF Core Set and a Brief ICF Core Set for rheumatoid arthritis. A formal decision-making and consensus process integrating evidence gathered from preliminary studies was followed. Preliminary studies included a Delphi exercise, a systematic review, and an empirical data collection. After training in the ICF, and based on these preliminary studies, relevant ICF categories were identified in a formal consensus process by international experts from different backgrounds. The preliminary studies identified a set of 530 ICF categories at the second, third and fourth ICF levels with 203 categories on body functions, 76 on body structures, 188 on activities and participation, and 63 on environmental factors. Seventeen experts from 12 different countries attended the consensus conference on rheumatoid arthritis (7 physicians with at least a specialization in physical and rehabilitation medicine, 7 rheumatologists, one nurse, one occupational therapist, and one physical therapist). Altogether 96 categories (76 second-level and 20 third-, and fourth-level categories) were included in the Comprehensive ICF Core Set with 25 categories from the component body functions, 18 from body structures, 32 from activities and participation, and 21 from environmental factors. The Brief ICF Core Set included a total of 39 second-level categories, with 8 on body functions, 7 on body structures, 14 on activities and participation, and 10 on environmental factors. A formal consensus process integrating evidence and expert opinion based on the ICF framework and classification led to the definition of ICF Core Sets for rheumatoid arthritis. Both the Comprehensive ICF Core Set and the Brief ICF Core Set were defined.

  4. Overview on Hydrate Coring, Handling and Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Jon Burger; Deepak Gupta; Patrick Jacobs; John Shillinglaw

    2003-06-30

    Gas hydrates are crystalline, ice-like compounds of gas and water molecules that are formed under certain thermodynamic conditions. Hydrate deposits occur naturally within ocean sediments just below the sea floor at temperatures and pressures existing below about 500 meters water depth. Gas hydrate is also stable in conjunction with the permafrost in the Arctic. Most marine gas hydrate is formed of microbially generated gas. It binds huge amounts of methane into the sediments. Worldwide, gas hydrate is estimated to hold about 1016 kg of organic carbon in the form of methane (Kvenvolden et al., 1993). Gas hydrate is one of the fossil fuel resources that is yet untapped, but may play a major role in meeting the energy challenge of this century. In June 2002, Westport Technology Center was requested by the Department of Energy (DOE) to prepare a ''Best Practices Manual on Gas Hydrate Coring, Handling and Analysis'' under Award No. DE-FC26-02NT41327. The scope of the task was specifically targeted for coring sediments with hydrates in Alaska, the Gulf of Mexico (GOM) and from the present Ocean Drilling Program (ODP) drillship. The specific subjects under this scope were defined in 3 stages as follows: Stage 1: Collect information on coring sediments with hydrates, core handling, core preservation, sample transportation, analysis of the core, and long term preservation. Stage 2: Provide copies of the first draft to a list of experts and stakeholders designated by DOE. Stage 3: Produce a second draft of the manual with benefit of input from external review for delivery. The manual provides an overview of existing information available in the published literature and reports on coring, analysis, preservation and transport of gas hydrates for laboratory analysis as of June 2003. The manual was delivered as draft version 3 to the DOE Project Manager for distribution in July 2003. This Final Report is provided for records purposes.

  5. Embedded binaries and their dense cores

    Science.gov (United States)

    Sadavoy, Sarah I.; Stahler, Steven W.

    2017-08-01

    We explore the relationship between young, embedded binaries and their parent cores, using observations within the Perseus Molecular Cloud. We combine recently published Very Large Array observations of young stars with core properties obtained from Submillimetre Common-User Bolometer Array 2 observations at 850 μm. Most embedded binary systems are found towards the centres of their parent cores, although several systems have components closer to the core edge. Wide binaries, defined as those systems with physical separations greater than 500 au, show a tendency to be aligned with the long axes of their parent cores, whereas tight binaries show no preferred orientation. We test a number of simple, evolutionary models to account for the observed populations of Class 0 and I sources, both single and binary. In the model that best explains the observations, all stars form initially as wide binaries. These binaries either break up into separate stars or else shrink into tighter orbits. Under the assumption that both stars remain embedded following binary break-up, we find a total star formation rate of 168 Myr-1. Alternatively, one star may be ejected from the dense core due to binary break-up. This latter assumption results in a star formation rate of 247 Myr-1. Both production rates are in satisfactory agreement with current estimates from other studies of Perseus. Future observations should be able to distinguish between these two possibilities. If our model continues to provide a good fit to other star-forming regions, then the mass fraction of dense cores that becomes stars is double what is currently believed.

  6. Himalayan Ice Core Analyses With Snow Algae

    Science.gov (United States)

    Yoshimura, Y.; Kohshima, S.; Takeuchi, N.; Seko, K.; Fujita, K.

    2004-12-01

    Snow algae in a shallow ice core (7 m in length) from the Yala Glacier, Langtang region of Nepal, were examined for potential use in ice core analyses. Ice core samples taken at 5350 m a.s.l. in 1994, contained more than 7 species of snow algae. In a vertical profile of the algal biomass, 11 distinct algal layers were observed. Seasonal observation in 1996 at the coring site indicated most algal growth to occur from late spring to late summer. Pit observation in 1991, 1992 and 1994 indicated algal layer formation to take place annually. Delta 18O, chemical ions (Na+, Cl-, SO42-, and NO3-) and microparticles failed to show any clear seasonal variation, particularly so at depths exceeding 2 m, possibly due to heavy melt-water percolation. Snow algae in the ice core would thus be accurate boundary markers of annual layers in the ice cores of this region. Algal biomass in each annual layer was noted to be quite closely correlated with the following two environmental indices calculated from air temperature and precipitation at Kyangjing (3,920 m a.s.l.), the village nearest the Yala Glacier: estimated mean snow cover thickness (MST) and estimated summer mass balance (SMB) (n = 6, r = -0.975, P snow cover thickness on algal layers, which would be a major determinant of light available for algal growth on the glacier. The algal biomass was also found to be roughly correlated with air temperature (n = 7, r = 0.773, P snow algae. Snow algal biomass in an ice core should prove a good environmental marker for indicating summer mass balance which is important for understanding summer-accumulation-type glaciers in this region.

  7. Theoretical Investigation of Inter-core Crosstalk Properties in Homogeneous Trench-Assisted Multi-Core Fibers

    DEFF Research Database (Denmark)

    Ye, Feihong; Morioka, Toshio; Tu, Jiajing

    2014-01-01

    We derive analytical expressions for inter-core crosstalk, its dependence on core pitch and wavelength in homogeneous trench-assisted multi-core fibers. They are in excellent agreement with numerical simulation results.......We derive analytical expressions for inter-core crosstalk, its dependence on core pitch and wavelength in homogeneous trench-assisted multi-core fibers. They are in excellent agreement with numerical simulation results....

  8. RUCS: rapid identification of PCR primers for unique core sequences.

    Science.gov (United States)

    Thomsen, Martin Christen Frølund; Hasman, Henrik; Westh, Henrik; Kaya, Hülya; Lund, Ole

    2017-12-15

    Designing PCR primers to target a specific selection of whole genome sequenced strains can be a long, arduous and sometimes impractical task. Such tasks would benefit greatly from an automated tool to both identify unique targets, and to validate the vast number of potential primer pairs for the targets in silico. Here we present RUCS, a program that will find PCR primer pairs and probes for the unique core sequences of a positive genome dataset complement to a negative genome dataset. The resulting primer pairs and probes are in addition to simple selection also validated through a complex in silico PCR simulation. We compared our method, which identifies the unique core sequences, against an existing tool called ssGeneFinder, and found that our method was 6.5-20 times more sensitive. We used RUCS to design primer pairs that would target a set of genomes known to contain the mcr-1 colistin resistance gene. Three of the predicted pairs were chosen for experimental validation using PCR and gel electrophoresis. All three pairs successfully produced an amplicon with the target length for the samples containing mcr-1 and no amplification products were produced for the negative samples. The novel methods presented in this manuscript can reduce the time needed to identify target sequences, and provide a quick virtual PCR validation to eliminate time wasted on ambiguously binding primers. Source code is freely available on https://bitbucket.org/genomicepidemiology/rucs. Web service is freely available on https://cge.cbs.dtu.dk/services/RUCS. mcft@cbs.dtu.dk. Supplementary data are available at Bioinformatics online.

  9. Hepatitis C virus core+1/ARFP modulates Cyclin D1/pRb pathway and promotes carcinogenesis.

    Science.gov (United States)

    Moustafa, Savvina; Karakasiliotis, Ioannis; Mavromara, Penelope

    2018-02-14

    Viruses often encompass overlapping reading frames and unconventional translation mechanisms in order to maximize the output from a minimum genome and to orchestrate timely their gene expression. HCV possesses such an unconventional open reading frame (ORF) within the core-coding region, encoding an additional protein designated initially as ARFP or F or core+1. Two predominant isoforms of core+1/ARFP have been reported, core+1/L initiating from codon 26 and core+1/S initiating from codons 85/87 of the polyprotein coding region, respectively. The biological significance of core+1/ARFP expression remains elusive. The aim of the present study was to gain insight into the functional and pathological properties of core+1/ARFP through its interaction with the host cell combining in vitro and in vivo approaches. Our data provide strong evidence that the core+1/ARFP of HCV-1a stimulates cell proliferation in Huh7-based cell lines expressing either core+1/S or core+1/L isoforms and in transgenic liver disease mouse models expressing core+1/S protein in a liver-specific manner. Both isoforms of core+1/ARFP increase the levels of cyclin D1 and phosphorylated Rb, thus promoting the cell cycle. In addition, core+1/S was found to enhance liver regeneration and oncogenesis in transgenic mice. The induction of the cell cycle together with increased mRNA levels of cell proliferation-related oncogenes in cells expressing the core+1/ARFP proteins argue for an oncogenic potential of these proteins and an important role in HCV-associated pathogenesis. IMPORTANCE This study sheds light on the biological importance of a unique HCV protein. We show here that core+1/ARFP of HCV-1a interacts with the host machinery leading to acceleration of cell cycle and enhancement of liver carcinogenesis. This pathological mechanism(s) may complement the action of other viral proteins with oncogenic properties leading to the development of hepatocellular carcinoma. In addition, given that immunological

  10. HANARO core channel flow-rate measurement

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Heon Il; Chae, Hee Tae; Im, Don Soon; Kim, Seon Duk [Korea Atomic Energy Research Institute, Taejon (Korea, Republic of)

    1996-06-01

    HANARO core consists of 23 hexagonal flow tubes and 16 cylindrical flow tubes. To get the core flow distribution, we used 6 flow-rate measuring dummy fuel assemblies (instrumented dummy fuel assemblies). The differential pressures were measured and converted to flow-rates using the predetermined relationship between AP and flow-rate for each instrumented dummy fuel assemblies. The flow-rate for the cylindrical flow channels shows +-7% relative errors and that for the hexagonal flow channels shows +-3.5% relative errors. Generally the flow-rates of outer core channels show smaller values compared to those of inner core. The channels near to the core inlet pipe and outlet pipes also show somewhat lower flow-rates. For the lower flow channels, the thermal margin was checked by considering complete linear power histories. From the experimental results, the gap flow-rate was estimated to be 49.4 kg/s (cf. design flow of 50 kg/s). 15 tabs., 9 figs., 10 refs. (Author) .new.

  11. Development of full MOX core in ABWR

    Energy Technology Data Exchange (ETDEWEB)

    Aoyama, Motoo; Bessho, Yasunori; Izutsu, Sadayuki; Uchikawa, Sadao [Hitachi Ltd., Tokyo (Japan)

    1995-10-01

    In the long term plan on the research, development and utilization of nuclear power, the plan of processing the plutonium extracted by reprocessing spent fuel into MOX fuel and utilizing it for light water reactors was shown. According to this plan, it is considered appropriate that the utilization of MOX fuel will be started in the latter half of 1990s in small number of BWRs and PWRs, and it will be expanded flexibly along the plan to about 10 plants by around 2000. The project of verifying a small number of MOX fuel assemblies has been carried out in Japan, and the experience of the design and operation of MOX fuel has been accumulated independently. In addition to this experience, reflecting the knowledge resulted from utilizing MOX fuel for the advanced thermal reactor, Hitachi Ltd. has exerted efforts positively for the research and development toward the full scale use of MOX fuel for BWRs. The core of advanced BWR has the excellent characteristics suitable to the use of Mox fuel, in which plutonium can absorb neutrons more easily than uranium. In ABWRs, the volume ratio of water to fuel was increased. As to the full MOX core of ABWRs, equilibrium core characteristics, the characteristics of initial charge and converted cores, and core management are described. (K.I.).

  12. Managing water addition to a degraded core

    Energy Technology Data Exchange (ETDEWEB)

    Kuan, P.; Hanson, D.J. [EG and G Idaho, Inc., Idaho Falls, ID (United States); Odar, F. [Nuclear Regulatory Commission, Washington, DC (United States)

    1991-12-31

    In this paper we present information that can be used in severe accident management by providing an improved understanding of the effects of water addition to a degraded core. This improved understanding is developed using a diagram showing a sequence of core damage states. Whenever possible, a temperature and a time after accident initiation are estimated for each damage state in the sequence diagram. This diagram can be used to anticipate the evolution of events during an accident. Possible responses of plant instruments are described to identify these damage states and the effects of water addition. The rate and amount of water addition needed (1) to remove energy from the core, (2) to stabilize the core or (3) to not adversely affect the damage progression, are estimated. Analysis of the capability to remove energy from large cohesive and particulate debris beds indicates that these beds may not be stabilized in the core region and they may partially relocate to the lower plenum of the reactor vessel.

  13. THE RIGIDITY OF THE EARTH'S INNER CORE

    Directory of Open Access Journals (Sweden)

    K. E. BULLEN

    1953-06-01

    Full Text Available The purpose of this paper is to examine and assess, in the
    light of recent evidence, the theory lliat the Earth's inner core has
    a significant rigidity.
    The presenee of an inner core in the Earth is revealed from
    observations of the seismie pliase PKP in the « sliadow zone » for
    which the epicentral distance A lies in the range 105" < A < 143".
    Miss I. Lehmann (r in 1936, followed by Gutenberg and Richter (2
    in 1938, atlrihuted these observations to tlie presence of an inner
    core; and Jeffreys (3 in 1939 applied Airy's theory of diffraetion
    near a caustic to sliow that the alternative theory of diffraetion
    round the outer boundary of the centrai core was not capable of
    explaining tlie observations in the shadow zone. The existence of the
    inner core has been fairly generallv accepted sinee tliis ealculation
    of Jeffreys.

  14. Data-mining the FlyAtlas online resource to identify core functional motifs across transporting epithelia.

    Science.gov (United States)

    Chintapalli, Venkateswara R; Wang, Jing; Herzyk, Pawel; Davies, Shireen A; Dow, Julian A T

    2013-07-30

    Comparative analysis of tissue-specific transcriptomes is a powerful technique to uncover tissue functions. Our FlyAtlas.org provides authoritative gene expression levels for multiple tissues of Drosophila melanogaster (1). Although the main use of such resources is single gene lookup, there is the potential for powerful meta-analysis to address questions that could not easily be framed otherwise. Here, we illustrate the power of data-mining of FlyAtlas data by comparing epithelial transcriptomes to identify a core set of highly-expressed genes, across the four major epithelial tissues (salivary glands, Malpighian tubules, midgut and hindgut) of both adults and larvae. Parallel hypothesis-led and hypothesis-free approaches were adopted to identify core genes that underpin insect epithelial function. In the former, gene lists were created from transport processes identified in the literature, and their expression profiles mapped from the flyatlas.org online dataset. In the latter, gene enrichment lists were prepared for each epithelium, and genes (both transport related and unrelated) consistently enriched in transporting epithelia identified. A key set of transport genes, comprising V-ATPases, cation exchangers, aquaporins, potassium and chloride channels, and carbonic anhydrase, was found to be highly enriched across the epithelial tissues, compared with the whole fly. Additionally, a further set of genes that had not been predicted to have epithelial roles, were co-expressed with the core transporters, extending our view of what makes a transporting epithelium work. Further insights were obtained by studying the genes uniquely overexpressed in each epithelium; for example, the salivary gland expresses lipases, the midgut organic solute transporters, the tubules specialize for purine metabolism and the hindgut overexpresses still unknown genes. Taken together, these data provide a unique insight into epithelial function in this key model insect, and a framework

  15. Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes

    DEFF Research Database (Denmark)

    Kaas, Rolf Sommer; Rundsten, Carsten Friis; Ussery, David

    2012-01-01

    for creating better phylogenies, for determination of molecular clocks and for improved typing techniques. Results We find 3,051 gene clusters/families present in at least 95% of the genomes and 1,702 gene clusters present in 100% of the genomes. The former 'soft core' of about 3,000 gene families is perhaps...... more biologically relevant, especially considering that many of these genome sequences are draft quality. The E. coli pan-genome for this set of isolates contains 16,373 gene clusters. A core-gene tree, based on alignment and a pan-genome tree based on gene presence/absence, maps the relatedness...... of the 186 sequenced E. coli genomes. The core-gene tree displays high confidence and divides the E. coli strains into the observed MLST type clades and also separates defined phylotypes. Conclusion The results of comparing a large and diverse E. coli dataset support the theory that reliable and good...

  16. Scaling gysela code beyond 32K-cores on bluegene/Q***

    Directory of Open Access Journals (Sweden)

    Bigot J.

    2013-12-01

    Full Text Available Gyrokinetic simulations lead to huge computational needs. Up to now, the semi- Lagrangian code Gysela performed large simulations using a few thousands cores (8k cores typically. Simulation with finer resolutions and with kinetic electrons are expected to increase those needs by a huge factor, providing a good example of applications requiring Exascale machines. This paper presents our work to improve Gysela in order to target an architecture that presents one possible way towards Exascale: the Blue Gene/Q. After analyzing the limitations of the code on this architecture, we have implemented three kinds of improvement: computational performance improvements, memory consumption improvements and disk i/o improvements. As a result, we show that the code now scales beyond 32k cores with much improved performances. This will make it possible to target the most powerful machines available and thus handle much larger physical cases.

  17. Optimal core acquisition and remanufacturing policies under uncertain core quality fractions

    NARCIS (Netherlands)

    Teunter, Ruud H.; Flapper, Simme Douwe P.

    2011-01-01

    Cores acquired by a remanufacturer are typically highly variable in quality. Even if the expected fractions of the various quality levels are known, then the exact fractions when acquiring cores are still uncertain. Our model incorporates this uncertainty in determining optimal acquisition decisions

  18. Verification of Cell-Homogenized Whole-Core Transport Calculations in Actual PWR Core Geometry

    Energy Technology Data Exchange (ETDEWEB)

    Akio Yamamoto; Masahiro Tatsumi; Tatsuya Kimoto; Shinya Kosaka; Etsuro Saji

    2000-11-12

    In this paper, a cell-homogenized whole-core transport calculation is applied to a pressurized water reactor (PWR) core and its prediction accuracy on reactivity and power distribution is verified in comparison with cell-heterogeneous whole-core transport calculation results obtained by the method of characteristics. Recent progress in common computer hardware promotes continuous improvements on core calculation methods. Among several different approaches, a three-dimensional pin-by-pin (fine-mesh) core calculation is considered as one of the candidates of advanced methods. In general, although the fine-mesh core calculation explicitly treats each individual pin, it still has three approximations: cell-homogenization, low-level transport theory (usually the SPN or the diffusion approximation) and few-group treatment. Therefore, the impact of these approximations on core characteristics should be evaluated to confirm the feasibility of the three-dimensional fine-mesh core calculation method. This paper focuses on two former approximations, and the impact of these approximations is evaluated.

  19. Wavelength-Dependence of Inter-Core Crosstalk in Homogeneous Multi-Core Fibers

    DEFF Research Database (Denmark)

    Ye, Feihong; Saitoh, Kunimasa; Takenaga, Katsuhiro

    2016-01-01

    The wavelength dependence of inter-core crosstalk in homogeneous multi-core fibers (MCFs) is investigated, and the corresponding analytical expressions are derived. The derived analytical expressions can be used to determine the crosstalk at any wavelength necessary for designing future MCF wavel...

  20. Preserving Social Studies as Core Curricula in an Era of Common Core Reform

    Science.gov (United States)

    Denton, David W.; Sink, Cindy

    2015-01-01

    Education reform over the last two decades has changed perceptions of core curricula. Although social studies has traditionally been part of the core, emphasis on standards-based teaching and learning, along with elaborate accountability schemes, is causing unbalanced treatment of subjects. While the research literature indicates teachers are…

  1. Continuous greenhouse gas measurements from ice cores

    DEFF Research Database (Denmark)

    Stowasser, Christopher

    -consuming and labor-intensive. This PhD thesis presents the development of a new method for measurements of greenhouse gas mixing ratios from ice cores based on a melting device of a continuous flow analysis (CFA) system. The coupling to a CFA melting device enables time-efficient measurements of high resolution......Ice cores offer the unique possibility to study the history of past atmospheric greenhouse gases over the last 800,000 years, since past atmospheric air is trapped in bubbles in the ice. Since the 1950s, paleo-scientists have developed a variety of techniques to extract the trapped air from...... individual ice core samples, and to measure the mixing ratio of greenhouse gases such as carbon dioxide, methane and nitrous oxide in the extracted air. The discrete measurements have become highly accurate and reproducible, but require relatively large amounts of ice per measured species and are both time...

  2. From DeepCore to PINGU

    Directory of Open Access Journals (Sweden)

    Yáñez J.P.

    2016-01-01

    Full Text Available Very large volume neutrino telescopes (VLVNTs observe atmospheric neutrinos over a wide energy range (GeV to TeV, after they travel distances as large as the Earth's diameter. DeepCore, the low energy extension of IceCube, has started making meaningful measurements of the neutrino oscillation parameters θ23 and | Δm232| by analyzing the atmospheric flux at energies above 10 GeV. PINGU, a proposed project to lower DeepCore's energy threshold, aims to use the same flux to further increase the precision with which these parameters are known, and eventually determine the sign of Δm232. The latest results from DeepCore, and the planned transition to PINGU, are discussed here.

  3. Core Graduate Courses: A Missed Learning Opportunity?

    CERN Document Server

    Singh, Chandralekha

    2016-01-01

    An important goal of graduate physics core courses is to help students develop expertise in problem solving and improve their reasoning and meta-cognitive skills. We explore the conceptual difficulties of physics graduate students by administering conceptual problems on topics covered in undergraduate physics courses before and after instruction in related first year core graduate courses. Here, we focus on physics graduate students' difficulties manifested by their performance on two qualitative problems involving diagrammatic representation of vector fields. Some graduate students had great difficulty in recognizing whether the diagrams of the vector fields had divergence and/or curl but they had no difficulty computing the divergence and curl of the vector fields mathematically. We also conducted individual discussions with various faculty members who regularly teach first year graduate physics core courses about the goals of these courses and the performance of graduate students on the conceptual problems...

  4. Stretchable inductor with liquid magnetic core

    Science.gov (United States)

    Lazarus, N.; Meyer, C. D.

    2016-03-01

    Adding magnetic materials is a well-established method for improving performance of inductors. However, traditional magnetic cores are rigid and poorly suited for the emerging field of stretchable electronics, where highly deformable inductors are used to wirelessly couple power and data signals. In this work, stretchable inductors are demonstrated based on the use of ferrofluids, magnetic liquids based on distributed magnetic particles, to create a compliant magnetic core. Using a silicone molding technique to create multi-layer fluidic channels, a liquid metal solenoid is fabricated around a ferrofluid channel. An analytical model is developed for the effects of mechanical strain, followed by experimental verification using two different ferrofluids with different permeabilities. Adding ferrofluid was found to increase the unstrained inductance by up to 280% relative to a similar inductor with a non-magnetic silicone core, while retaining the ability to survive uniaxial strains up to 100%.

  5. Geomagnetic Core Field Secular Variation Models

    DEFF Research Database (Denmark)

    Gillet, N.; Lesur, V.; Olsen, Nils

    2010-01-01

    We analyse models describing time changes of the Earth’s core magnetic field (secular variation) covering the historical period (several centuries) and the more recent satellite era (previous decade), and we illustrate how both the information contained in the data and the a priori information...... (regularisation) affect the result of the ill-posed geomagnetic inverse problem. We show how data quality, frequency and selection procedures govern part of the temporal changes in the secular variation norms and spectra, which are sometimes difficult to dissociate from true changes of the core state. We...... in artificial changes in the model norms and spectra. Model users should keep in mind that such features can be mis-interpreted as the signature of physical mechanisms (e.g. diffusion). Finally, we present perspectives concerning core field modelling: imposing dynamical constraints (e.g. by means of data...

  6. Uncertainties in Core Collapse Supernovae Simulations

    Science.gov (United States)

    Duggan, Jefferson; Cunningham, J.; Kuhlmann, S.; Biswas, R.; Kovacs, E.; Spinka, H.

    2013-01-01

    We present the results of a study of selection criteria to identify Type Ia supernovae photometrically in a simulated mixed sample of Type Ia supernovae and core collapse supernovae. The simulated sample is a mockup of the expected results of the Dark Energy Survey (DES) using the supernovae simulation and fitting package of SNANA [Kessler et al. arXiv:0908.4280]. This is an extension of a previous analysis, [Gjergo et al. arXiv:1205.1480], with updated core collapse templates that are used to simulate the supernovae. We have also studied how systematic variations in the input parameters of the core collapse supernovae, such as absolute brightness and brightness smearing, affect the measured purity of the Type Ia supernova sample.

  7. Free core nutation and geomagnetic jerks

    Science.gov (United States)

    Malkin, Z.

    2013-12-01

    Variations in free core nutation (FCN) are associated with different processes in the Earth's fluid core and core-mantle coupling. The same processes are generally caused the variations in the geomagnetic field (GMF) particularly the geomagnetic jerks (GMJs), which are rapid changes in GMF secular variations. Therefore, the joint investigation of variations in FCN and GMF can elucidate the Earth's interior and dynamics. In this paper, we investigated the FCN amplitude and phase variations derived from VLBI observations. Comparison of the epochs of the changes in the FCN amplitude and phase with the epochs of the GMJs indicated that the observed extremes in the FCN amplitude and phase variations were closely related to the GMJ epochs. In particular, the FCN amplitude begins to grow one to three years after the GMJs. Thus, processes that cause GMJs are assumed as sources of FCN excitation.

  8. Core-shell fuel cell electrodes

    Energy Technology Data Exchange (ETDEWEB)

    Adzic, Radoslav; Bliznakov, Stoyan; Vukmirovic, Miomir

    2017-07-25

    Embodiments of the disclosure relate to electrocatalysts. The electrocatalyst may include at least one gas-diffusion layer having a first side and a second side, and particle cores adhered to at least one of the first and second sides of the at least one gas-diffusion layer. The particle cores includes surfaces adhered to the at least one of the first and second sides of the at least one gas-diffusion layer and surfaces not in contact with the at least one gas-diffusion layer. Furthermore, a thin layer of catalytically atoms may be adhered to the surfaces of the particle cores not in contact with the at least one gas-diffusion layer.

  9. Spin wave mediated magnetic vortex core reversal

    Science.gov (United States)

    Stoll, Hermann

    2012-10-01

    The magnetic vortex is the simplest, non-trivial ground state configuration of micron and sub-micron sized soft magnetic thin film platelets and therefore an interesting subject for the study of micro magnetism. Essential progress in the understanding of nonlinear vortex dynamics was achieved when low-field core toggling was discovered by excitation of the gyrotropic eigenmode at sub-GHz frequencies. At frequencies more than an order of magnitude higher vortex state structures possess spin wave eigenmodes arising from the magneto-static interaction. We demonstrated, experimentally and by micromagnetic simulations, that the unidirectional vortex core reversal process also occurs when azimuthal spin wave modes are excited in the multi-GHz frequency range. This finding highlights the importance of spin wave - vortex interaction and boosts vortex core reversal to much higher frequencies, which may offer new routes for GHz spintronics applications.

  10. Arms Trafficking: Aiding and Abetting Core Crimes

    Directory of Open Access Journals (Sweden)

    Sabina Zgaga

    2015-11-01

    Full Text Available The provision of arms for the commission of crimes is one of the typical forms of aiding and abetting. This article discusses arms trafficking as a form of aiding and abetting the commission of core crimes. It opens with a discussion of aiding and abetting as a form of complicity in the Rome Statute and the case law of the International Criminal Court. Furthermore, the article also analyses the regulation of legal arms trafficking in international and European law. Accordingly, the international criminal law further regulates illegal arms trafficking as an international crime and as complicity to core crimes. Therefore, the article first presents arms trafficking as an international crime and subsequently discusses arms trafficking as complicity in core crimes. The article concludes with a discussion on the regulation of arms trafficking in Slovene law, beginning with legal arms trafficking according to the Firearms Act-1 and ending with illegal arms trafficking as a crime.

  11. Feasibility study on ABWR full MOX core

    Energy Technology Data Exchange (ETDEWEB)

    Yagi, Makoto; Nagano, Mamoru; Sakurai, Shungo [Toshiba Corp., Yokohama (Japan)

    1996-12-31

    Mixed-oxide (MOX) fuels will be utilized as reload fuels in some existing commercial boiling water reactors (BWRs) in Japan around the year 2000. The first step MOX fuel is expected to have an average discharge exposure of 33 GWd/t and to be loaded within one-third of all fuel rods in a core. On the other hand, it becomes necessary to minimize the number of MOX fuels and plants utilizing MOX fuel, mainly because of fuel economy, handling, and site inspection costs. Under these situations, it is important to develop higher burnup MOX fuel containing more plutonium and a core with a larger amount of MOX fuel. The purpose of this study is to clarify the feasibility of high-burnup MOX fuel and core through the evaluation of nuclear characteristics.

  12. NEUTRONIC REACTOR FUEL ELEMENT AND CORE SYSTEM

    Science.gov (United States)

    Moore, W.T.

    1958-09-01

    This patent relates to neutronic reactors and in particular to an improved fuel element and a novel reactor core system for facilitating removal of contaminating fission products, as they are fermed, from association with the flssionable fuel, so as to mitigate the interferent effects of such fission products during reactor operation. The fuel elements are comprised of tubular members impervious to fluid and contatning on their interior surfaces a thin layer of fissionable material providing a central void. The core structure is comprised of a plurality of the tubular fuel elements arranged in parallel and a closed manifold connected to their ends. In the reactor the core structure is dispersed in a water moderator and coolant within a pressure vessel, and a means connected to said manifuld is provided for withdrawing and disposing of mobile fission product contamination from the interior of the feel tubes and manifold.

  13. Core-shell fuel cell electrodes

    Energy Technology Data Exchange (ETDEWEB)

    Adzic, Radoslav; Bliznakov, Stoyan; Vukmirovic, Miomir

    2017-12-26

    Embodiments of the disclosure relate to membrane electrode assemblies. The membrane electrode assembly may include at least one gas-diffusion layer having a first side and a second side, and particle cores adhered to at least one of the first and second sides of the at least one gas-diffusion layer. The particle cores includes surfaces adhered to the at least one of the first and second sides of the at least one gas-diffusion layer and surfaces not in contact with the at least one gas-diffusion layer. Furthermore, a thin layer of catalytically atoms may be adhered to the surfaces of the particle cores not in contact with the at least one gas-diffusion layer.

  14. Identifying gene expression modules that define human cell fates.

    Science.gov (United States)

    Germanguz, I; Listgarten, J; Cinkornpumin, J; Solomon, A; Gaeta, X; Lowry, W E

    2016-05-01

    Using a compendium of cell-state-specific gene expression data, we identified genes that uniquely define cell states, including those thought to represent various developmental stages. Our analysis sheds light on human cell fate through the identification of core genes that are altered over several developmental milestones, and across regional specification. Here we present cell-type specific gene expression data for 17 distinct cell states and demonstrate that these modules of genes can in fact define cell fate. Lastly, we introduce a web-based database to disseminate the results. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

  15. Peroxisome degradation in Saccharomyces cerevisiae is dependent on machinery of macroautophagy and the Cvt pathway

    NARCIS (Netherlands)

    Hutchins, Maria U.; Veenhuis, Marten; Klionsky, Daniel J.

    1999-01-01

    Organelle biogenesis and turnover are necessary to maintain biochemical processes that are appropriate to the needs of the eukaryotic cell. Specific degradation of organelles in response to changing environmental cues is one aspect of achieving proper metabolic function. For example, the yeast

  16. ICE CHEMISTRY IN STARLESS MOLECULAR CORES

    Energy Technology Data Exchange (ETDEWEB)

    Kalvans, J., E-mail: juris.kalvans@venta.lv [Engineering Research Institute “Ventspils International Radio Astronomy Center” of Ventspils University College, Inzenieru 101, Ventspils, LV-3601 (Latvia)

    2015-06-20

    Starless molecular cores are natural laboratories for interstellar molecular chemistry research. The chemistry of ices in such objects was investigated with a three-phase (gas, surface, and mantle) model. We considered the center part of five starless cores, with their physical conditions derived from observations. The ice chemistry of oxygen, nitrogen, sulfur, and complex organic molecules (COMs) was analyzed. We found that an ice-depth dimension, measured, e.g., in monolayers, is essential for modeling of chemistry in interstellar ices. Particularly, the H{sub 2}O:CO:CO{sub 2}:N{sub 2}:NH{sub 3} ice abundance ratio regulates the production and destruction of minor species. It is suggested that photodesorption during the core-collapse period is responsible for the high abundance of interstellar H{sub 2}O{sub 2} and O{sub 2}H and other species synthesized on the surface. The calculated abundances of COMs in ice were compared to observed gas-phase values. Smaller activation barriers for CO and H{sub 2}CO hydrogenation may help explain the production of a number of COMs. The observed abundance of methyl formate HCOOCH{sub 3} could be reproduced with a 1 kyr, 20 K temperature spike. Possible desorption mechanisms, relevant for COMs, are gas turbulence (ice exposure to interstellar photons) or a weak shock within the cloud core (grain collisions). To reproduce the observed COM abundances with the present 0D model, 1%–10% of ice mass needs to be sublimated. We estimate that the lifetime for starless cores likely does not exceed 1 Myr. Taurus cores are likely to be younger than their counterparts in most other clouds.

  17. Superrotation of Earth’s Inner Core, Extraterrestrial Impacts, and the Effective Viscosity of Outer Core

    Directory of Open Access Journals (Sweden)

    Pirooz Mohazzabi

    2015-01-01

    Full Text Available The recently verified superrotation of Earth’s inner core is examined and a new model is presented which is based on the tidal despinning of the mantle and the viscosity of the outer core. The model also takes into account other damping mechanisms arising from the inner core superrotation such as magnetic and gravitational coupling as well as contribution from eddy viscosity in the outer core. The effective viscosity obtained in this model confirms a previously well constrained value of about 103 Pa s. In addition, the model shows that the currently measured superrotation of the inner core must be almost exactly equal to its asymptotic or steady-state value. The effect of extraterrestrial impacts is also investigated, and it is shown that perturbations due to such impacts can only persist over a short geological time.

  18. Hole fluids for deep ice core drilling

    OpenAIRE

    Talalay, P.G.; Gundestrup, N.S.

    2002-01-01

    This paper is based on the data published in research report of P. G. Talalay and N. S. Gundestrup; Hole fluids for deep ice core drilling : A review. Copenhagen University, Copenhagen, 1999,120p. In the practice of deep ice core drilling only three types of bore-hole fluids have been used : 1) petroleum oil products (fuels or solvents) containing densifier, 2) aqueous ethylene glycol or ethanol solutions, 3) n-butyl acetate. The main parameters of drilling fluids are 1) density and fluid top...

  19. SproutCore web application development

    CERN Document Server

    Keating, Tyler

    2013-01-01

    Written as a practical, step-by-step tutorial, Creating HTML5 Apps with SproutCore is full of engaging examples to help you learn in a practical context.This book is for any person looking to write software for the Web or already writing software for the Web. Whether your background is in web development or in software development, Creating HTML5 Apps with SproutCore will help you expand your skills so that you will be ready to apply the software development principles in the web development space.

  20. Neural simulations on multi-core architectures

    Directory of Open Access Journals (Sweden)

    Hubert Eichner

    2009-07-01

    Full Text Available Neuroscience is witnessing increasing knowledge about the anatomy and electrophysiological properties of neurons and their connectivity, leading to an ever increasing computational complexity of neural simulations. At the same time, a rather radical change in personal computer technology emerges with the establishment of multi-cores: high-density, explicitly parallel processor architectures for both high performance as well as standard desktop computers. This work introduces strategies for the parallelization of biophysically realistic neural simulations based on the compartmental modeling technique and results of such an implementation, with a strong focus on multi-core architectures and automation, i. e. user-transparent load balancing.