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Sample records for integration chapter cis

  1. US/CIS integrated NTRE

    NASA Astrophysics Data System (ADS)

    Bulman, M. J.; Culver, D. W.; McIlwain, M. C.; Rochow, Richard; D'Yakov, E. K.; Smetannikov, V. P.

    1993-06-01

    The paper describes the Nuclear Thermal Energy (NTRE) engine, developed by taking advantage of mature fuel technology developed in the former Soviet Union, thus shortening the development schedule of this engine for moon and Mars explorations. The near-term NTRE engine has a number of features that provide safety, mission performance, cost, and risk benefits. These include: (1) high-temperature long-life CIS fuel, (2) high-pressure recuperated expander cycle, (3) assured restart, (4) long-life cooled nozzle with thin inner wall, (5) long-life turbopumps, (6) heat radiation and electrical power generation, and (7) component integration synergy. Diagrams of the reactor core, the recuperated bottoming cycle flow schematic, and the recuperated bottoming cycle engine schematic are presented.

  2. Chapter 1: Biomedical knowledge integration.

    PubMed

    Payne, Philip R O

    2012-01-01

    The modern biomedical research and healthcare delivery domains have seen an unparalleled increase in the rate of innovation and novel technologies over the past several decades. Catalyzed by paradigm-shifting public and private programs focusing upon the formation and delivery of genomic and personalized medicine, the need for high-throughput and integrative approaches to the collection, management, and analysis of heterogeneous data sets has become imperative. This need is particularly pressing in the translational bioinformatics domain, where many fundamental research questions require the integration of large scale, multi-dimensional clinical phenotype and bio-molecular data sets. Modern biomedical informatics theory and practice has demonstrated the distinct benefits associated with the use of knowledge-based systems in such contexts. A knowledge-based system can be defined as an intelligent agent that employs a computationally tractable knowledge base or repository in order to reason upon data in a targeted domain and reproduce expert performance relative to such reasoning operations. The ultimate goal of the design and use of such agents is to increase the reproducibility, scalability, and accessibility of complex reasoning tasks. Examples of the application of knowledge-based systems in biomedicine span a broad spectrum, from the execution of clinical decision support, to epidemiologic surveillance of public data sets for the purposes of detecting emerging infectious diseases, to the discovery of novel hypotheses in large-scale research data sets. In this chapter, we will review the basic theoretical frameworks that define core knowledge types and reasoning operations with particular emphasis on the applicability of such conceptual models within the biomedical domain, and then go on to introduce a number of prototypical data integration requirements and patterns relevant to the conduct of translational bioinformatics that can be addressed via the design and

  3. Chapter 1: Biomedical knowledge integration.

    PubMed

    Payne, Philip R O

    2012-01-01

    The modern biomedical research and healthcare delivery domains have seen an unparalleled increase in the rate of innovation and novel technologies over the past several decades. Catalyzed by paradigm-shifting public and private programs focusing upon the formation and delivery of genomic and personalized medicine, the need for high-throughput and integrative approaches to the collection, management, and analysis of heterogeneous data sets has become imperative. This need is particularly pressing in the translational bioinformatics domain, where many fundamental research questions require the integration of large scale, multi-dimensional clinical phenotype and bio-molecular data sets. Modern biomedical informatics theory and practice has demonstrated the distinct benefits associated with the use of knowledge-based systems in such contexts. A knowledge-based system can be defined as an intelligent agent that employs a computationally tractable knowledge base or repository in order to reason upon data in a targeted domain and reproduce expert performance relative to such reasoning operations. The ultimate goal of the design and use of such agents is to increase the reproducibility, scalability, and accessibility of complex reasoning tasks. Examples of the application of knowledge-based systems in biomedicine span a broad spectrum, from the execution of clinical decision support, to epidemiologic surveillance of public data sets for the purposes of detecting emerging infectious diseases, to the discovery of novel hypotheses in large-scale research data sets. In this chapter, we will review the basic theoretical frameworks that define core knowledge types and reasoning operations with particular emphasis on the applicability of such conceptual models within the biomedical domain, and then go on to introduce a number of prototypical data integration requirements and patterns relevant to the conduct of translational bioinformatics that can be addressed via the design and

  4. Chapter 1: Biomedical Knowledge Integration

    PubMed Central

    Payne, Philip R. O.

    2012-01-01

    The modern biomedical research and healthcare delivery domains have seen an unparalleled increase in the rate of innovation and novel technologies over the past several decades. Catalyzed by paradigm-shifting public and private programs focusing upon the formation and delivery of genomic and personalized medicine, the need for high-throughput and integrative approaches to the collection, management, and analysis of heterogeneous data sets has become imperative. This need is particularly pressing in the translational bioinformatics domain, where many fundamental research questions require the integration of large scale, multi-dimensional clinical phenotype and bio-molecular data sets. Modern biomedical informatics theory and practice has demonstrated the distinct benefits associated with the use of knowledge-based systems in such contexts. A knowledge-based system can be defined as an intelligent agent that employs a computationally tractable knowledge base or repository in order to reason upon data in a targeted domain and reproduce expert performance relative to such reasoning operations. The ultimate goal of the design and use of such agents is to increase the reproducibility, scalability, and accessibility of complex reasoning tasks. Examples of the application of knowledge-based systems in biomedicine span a broad spectrum, from the execution of clinical decision support, to epidemiologic surveillance of public data sets for the purposes of detecting emerging infectious diseases, to the discovery of novel hypotheses in large-scale research data sets. In this chapter, we will review the basic theoretical frameworks that define core knowledge types and reasoning operations with particular emphasis on the applicability of such conceptual models within the biomedical domain, and then go on to introduce a number of prototypical data integration requirements and patterns relevant to the conduct of translational bioinformatics that can be addressed via the design and

  5. US/CIS integrated NTRE concept

    SciTech Connect

    Bulman, M.J.; Culver, D.W.; McIlwain, M.C. ); D'yakov, E.K. ); Smetannikov, V.P. ); Rochow, R. )

    1993-01-10

    The team of Aerojet, Energopool and Babcock Wilcox has prepared a near-term Nuclear Thermal Rocket Engine (NTRE) concept that takes advantage of mature fuel technology developed in the former Soviet Union. This proven, advanced fuel appreciably shortens the development schedule of this engine for Moon and Mars exploration. Our near term engine has a number of features that provide safety, mission performance, cost and risk benefits, including: (1) High temperature, long life CIS fuel, (2) high pressure, recuperated topping cycle, (3) assured restart, (4) long life, cooled nozzle with thin inner wall, (5) long life turbopumps, (6) heat radiation and electrical power generation, and (7) component integration energy.

  6. US/CIS integrated NTRE concept

    NASA Astrophysics Data System (ADS)

    Bulman, Melvin J.; Culver, Donald W.; McIlwain, Melvin C.; D'Yakov, Evgeniy K.; Smetannikov, Vladimir P.; Rochow, Richard

    1993-01-01

    The team of Aerojet, Energopool and Babcock & Wilcox has prepared a near-term Nuclear Thermal Rocket Engine (NTRE) concept that takes advantage of mature fuel technology developed in the former Soviet Union. This proven, advanced fuel appreciably shortens the development schedule of this engine for Moon and Mars exploration. Our near term engine has a number of features that provide safety, mission performance, cost and risk benefits, including: (1) High temperature, long life CIS fuel, (2) high pressure, recuperated topping cycle, (3) assured restart, (4) long life, cooled nozzle with thin inner wall, (5) long life turbopumps, (6) heat radiation and electrical power generation, and (7) component integration energy.

  7. cisMEP: an integrated repository of genomic epigenetic profiles and cis-regulatory modules in Drosophila

    PubMed Central

    2014-01-01

    Background Cis-regulatory modules (CRMs), or the DNA sequences required for regulating gene expression, play the central role in biological researches on transcriptional regulation in metazoan species. Nowadays, the systematic understanding of CRMs still mainly resorts to computational methods due to the time-consuming and small-scale nature of experimental methods. But the accuracy and reliability of different CRM prediction tools are still unclear. Without comparative cross-analysis of the results and combinatorial consideration with extra experimental information, there is no easy way to assess the confidence of the predicted CRMs. This limits the genome-wide understanding of CRMs. Description It is known that transcription factor binding and epigenetic profiles tend to determine functions of CRMs in gene transcriptional regulation. Thus integration of the genome-wide epigenetic profiles with systematically predicted CRMs can greatly help researchers evaluate and decipher the prediction confidence and possible transcriptional regulatory functions of these potential CRMs. However, these data are still fragmentary in the literatures. Here we performed the computational genome-wide screening for potential CRMs using different prediction tools and constructed the pioneer database, cisMEP (cis-regulatory module epigenetic profile database), to integrate these computationally identified CRMs with genomic epigenetic profile data. cisMEP collects the literature-curated TFBS location data and nine genres of epigenetic data for assessing the confidence of these potential CRMs and deciphering the possible CRM functionality. Conclusions cisMEP aims to provide a user-friendly interface for researchers to assess the confidence of different potential CRMs and to understand the functions of CRMs through experimentally-identified epigenetic profiles. The deposited potential CRMs and experimental epigenetic profiles for confidence assessment provide experimentally testable

  8. Chapter 636, Voluntary Integration in Massachusetts. Successful Programs of Choice.

    ERIC Educational Resources Information Center

    Spier, Adele W.; And Others

    A statewide study was conducted to identify and describe successful voluntary school desegregation programs funded under Chapter 636, a 1974 amendment to Massachussets' Racial Imbalance Law. Programs selected were of four types: (1) school-based (elementary, middle, and high); (2) school system- or district-wide; (3) part-time and full-time…

  9. Testing of Cis-Regulatory Elements by Targeted Transgene Integration in Zebrafish Using PhiC31 Integrase.

    PubMed

    Hadzhiev, Yavor; Miguel-Escalada, Irene; Balciunas, Darius; Müller, Ferenc

    2016-01-01

    Herein we present several strategies for testing the function of cis-regulatory elements using the PhiC31 integrase system. Firstly, we present two different strategies to analyze the activity of candidate enhancer elements. Targeted integration of candidate enhancers into the same genomic location circumvents the variability-associated random integration and position effects. This method is suitable for testing of candidate enhancers identified through computational or other analyses a priori. Secondly, we present methodology for targeted integration of BACs into the same genomic location(s). By using additional reporters integrated into a BAC, this enables experimental testing whether cis-regulatory elements are functional in the sequence inserted in the BAC. PMID:27464802

  10. Integrating bioinformatic resources to predict transcription factors interacting with cis-sequences conserved in co-regulated genes

    PubMed Central

    2014-01-01

    Background Using motif detection programs it is fairly straightforward to identify conserved cis-sequences in promoters of co-regulated genes. In contrast, the identification of the transcription factors (TFs) interacting with these cis-sequences is much more elaborate. To facilitate this, we explore the possibility of using several bioinformatic and experimental approaches for TF identification. This starts with the selection of co-regulated gene sets and leads first to the prediction and then to the experimental validation of TFs interacting with cis-sequences conserved in the promoters of these co-regulated genes. Results Using the PathoPlant database, 32 up-regulated gene groups were identified with microarray data for drought-responsive gene expression from Arabidopsis thaliana. Application of the binding site estimation suite of tools (BEST) discovered 179 conserved sequence motifs within the corresponding promoters. Using the STAMP web-server, 49 sequence motifs were classified into 7 motif families for which similarities with known cis-regulatory sequences were identified. All motifs were subjected to a footprintDB analysis to predict interacting DNA binding domains from plant TF families. Predictions were confirmed by using a yeast-one-hybrid approach to select interacting TFs belonging to the predicted TF families. TF-DNA interactions were further experimentally validated in yeast and with a Physcomitrella patens transient expression system, leading to the discovery of several novel TF-DNA interactions. Conclusions The present work demonstrates the successful integration of several bioinformatic resources with experimental approaches to predict and validate TFs interacting with conserved sequence motifs in co-regulated genes. PMID:24773781

  11. Integration of bioinformatics and synthetic promoters leads to the discovery of novel elicitor-responsive cis-regulatory sequences in Arabidopsis.

    PubMed

    Koschmann, Jeannette; Machens, Fabian; Becker, Marlies; Niemeyer, Julia; Schulze, Jutta; Bülow, Lorenz; Stahl, Dietmar J; Hehl, Reinhard

    2012-09-01

    A combination of bioinformatic tools, high-throughput gene expression profiles, and the use of synthetic promoters is a powerful approach to discover and evaluate novel cis-sequences in response to specific stimuli. With Arabidopsis (Arabidopsis thaliana) microarray data annotated to the PathoPlant database, 732 different queries with a focus on fungal and oomycete pathogens were performed, leading to 510 up-regulated gene groups. Using the binding site estimation suite of tools, BEST, 407 conserved sequence motifs were identified in promoter regions of these coregulated gene sets. Motif similarities were determined with STAMP, classifying the 407 sequence motifs into 37 families. A comparative analysis of these 37 families with the AthaMap, PLACE, and AGRIS databases revealed similarities to known cis-elements but also led to the discovery of cis-sequences not yet implicated in pathogen response. Using a parsley (Petroselinum crispum) protoplast system and a modified reporter gene vector with an internal transformation control, 25 elicitor-responsive cis-sequences from 10 different motif families were identified. Many of the elicitor-responsive cis-sequences also drive reporter gene expression in an Agrobacterium tumefaciens infection assay in Nicotiana benthamiana. This work significantly increases the number of known elicitor-responsive cis-sequences and demonstrates the successful integration of a diverse set of bioinformatic resources combined with synthetic promoter analysis for data mining and functional screening in plant-pathogen interaction. PMID:22744985

  12. Integration of Bioinformatics and Synthetic Promoters Leads to the Discovery of Novel Elicitor-Responsive cis-Regulatory Sequences in Arabidopsis1[C][W][OA

    PubMed Central

    Koschmann, Jeannette; Machens, Fabian; Becker, Marlies; Niemeyer, Julia; Schulze, Jutta; Bülow, Lorenz; Stahl, Dietmar J.; Hehl, Reinhard

    2012-01-01

    A combination of bioinformatic tools, high-throughput gene expression profiles, and the use of synthetic promoters is a powerful approach to discover and evaluate novel cis-sequences in response to specific stimuli. With Arabidopsis (Arabidopsis thaliana) microarray data annotated to the PathoPlant database, 732 different queries with a focus on fungal and oomycete pathogens were performed, leading to 510 up-regulated gene groups. Using the binding site estimation suite of tools, BEST, 407 conserved sequence motifs were identified in promoter regions of these coregulated gene sets. Motif similarities were determined with STAMP, classifying the 407 sequence motifs into 37 families. A comparative analysis of these 37 families with the AthaMap, PLACE, and AGRIS databases revealed similarities to known cis-elements but also led to the discovery of cis-sequences not yet implicated in pathogen response. Using a parsley (Petroselinum crispum) protoplast system and a modified reporter gene vector with an internal transformation control, 25 elicitor-responsive cis-sequences from 10 different motif families were identified. Many of the elicitor-responsive cis-sequences also drive reporter gene expression in an Agrobacterium tumefaciens infection assay in Nicotiana benthamiana. This work significantly increases the number of known elicitor-responsive cis-sequences and demonstrates the successful integration of a diverse set of bioinformatic resources combined with synthetic promoter analysis for data mining and functional screening in plant-pathogen interaction. PMID:22744985

  13. PV Manufacturing R&D -- Integrated CIS Thin-Film Manufacturing Infrastructure: Phase I Technical Report, 2 August 2002--31 October 2003

    SciTech Connect

    Tarrant, D. E.; Gay, R. R.

    2004-06-01

    This subcontract report describes Shell Solar Industries (SSI), formerly Siemens Solar Industries, pursuing research and development of CuInSe2-based thin-film PV technology since 1980. In the 1980s, SSI demonstrated a 14.1%-efficient 3.4-cm2 active-area cell; unencapsulated integrated modules with aperture efficiencies of 11.2% on 940 cm2 and 9.1% on 3900 cm2; and an encapsulated module with 8.7% efficiency on 3883 cm2 (verified by NREL). Since these early achievements, SSI has made outstanding progress in the initial commercialization of high-performance thin-film CIS technology. Line yield has been increased from about 60% in 2000 to about 85% in 2002. This major accomplishment supports attractive cost projections for CIS. Recently, NREL confirmed a champion 12.8% aperture-area conversion efficiency for a large-area (3626 cm2) CIS module. Other than definition of the aperture area, this module is simply one module from the upper end of the production distribution for standard modules. Prerequisites for commitment to large-scale commercialization have been demonstrated at successive levels of CIS production. Remaining R&D challenges are to scale the processes to even larger areas, to reach higher production capacity, to demonstrate in-service durability over longer times, and to advance the fundamental understanding of CIS-based materials and devices with the goal of improvements for future products. SSI's thin-film CIS technology is poised to make very significant contributions to DOE/NREL/NCPV long-term goals of higher volume, lower-cost commercial products. The objective of this subcontract is to continue advancement of SSI's copper indium diselenide (CIS) technology through development and implementation of: high-throughput CIS absorber formation reactors; an XRF measurement system; a bar-code scribing system; a high-capacity ZnO monitoring system; a high-capacity continuous-light-source simulator; and integrated manufacturing infrastructure including

  14. Separate elements of the TERMINAL FLOWER 1 cis-regulatory region integrate pathways to control flowering time and shoot meristem identity.

    PubMed

    Serrano-Mislata, Antonio; Fernández-Nohales, Pedro; Doménech, María J; Hanzawa, Yoshie; Bradley, Desmond; Madueño, Francisco

    2016-09-15

    TERMINAL FLOWER 1 (TFL1) is a key regulator of Arabidopsis plant architecture that responds to developmental and environmental signals to control flowering time and the fate of shoot meristems. TFL1 expression is dynamic, being found in all shoot meristems, but not in floral meristems, with the level and distribution changing throughout development. Using a variety of experimental approaches we have analysed the TFL1 promoter to elucidate its functional structure. TFL1 expression is based on distinct cis-regulatory regions, the most important being located 3' of the coding sequence. Our results indicate that TFL1 expression in the shoot apical versus lateral inflorescence meristems is controlled through distinct cis-regulatory elements, suggesting that different signals control expression in these meristem types. Moreover, we identified a cis-regulatory region necessary for TFL1 expression in the vegetative shoot and required for a wild-type flowering time, supporting that TFL1 expression in the vegetative meristem controls flowering time. Our study provides a model for the functional organisation of TFL1 cis-regulatory regions, contributing to our understanding of how developmental pathways are integrated at the genomic level of a key regulator to control plant architecture. PMID:27385013

  15. Separate elements of the TERMINAL FLOWER 1 cis-regulatory region integrate pathways to control flowering time and shoot meristem identity.

    PubMed

    Serrano-Mislata, Antonio; Fernández-Nohales, Pedro; Doménech, María J; Hanzawa, Yoshie; Bradley, Desmond; Madueño, Francisco

    2016-09-15

    TERMINAL FLOWER 1 (TFL1) is a key regulator of Arabidopsis plant architecture that responds to developmental and environmental signals to control flowering time and the fate of shoot meristems. TFL1 expression is dynamic, being found in all shoot meristems, but not in floral meristems, with the level and distribution changing throughout development. Using a variety of experimental approaches we have analysed the TFL1 promoter to elucidate its functional structure. TFL1 expression is based on distinct cis-regulatory regions, the most important being located 3' of the coding sequence. Our results indicate that TFL1 expression in the shoot apical versus lateral inflorescence meristems is controlled through distinct cis-regulatory elements, suggesting that different signals control expression in these meristem types. Moreover, we identified a cis-regulatory region necessary for TFL1 expression in the vegetative shoot and required for a wild-type flowering time, supporting that TFL1 expression in the vegetative meristem controls flowering time. Our study provides a model for the functional organisation of TFL1 cis-regulatory regions, contributing to our understanding of how developmental pathways are integrated at the genomic level of a key regulator to control plant architecture.

  16. Designing Adaptive Low-Dissipative High Order Schemes for Long-Time Integrations. Chapter 1

    NASA Technical Reports Server (NTRS)

    Yee, Helen C.; Sjoegreen, B.; Mansour, Nagi N. (Technical Monitor)

    2001-01-01

    A general framework for the design of adaptive low-dissipative high order schemes is presented. It encompasses a rather complete treatment of the numerical approach based on four integrated design criteria: (1) For stability considerations, condition the governing equations before the application of the appropriate numerical scheme whenever it is possible; (2) For consistency, compatible schemes that possess stability properties, including physical and numerical boundary condition treatments, similar to those of the discrete analogue of the continuum are preferred; (3) For the minimization of numerical dissipation contamination, efficient and adaptive numerical dissipation control to further improve nonlinear stability and accuracy should be used; and (4) For practical considerations, the numerical approach should be efficient and applicable to general geometries, and an efficient and reliable dynamic grid adaptation should be used if necessary. These design criteria are, in general, very useful to a wide spectrum of flow simulations. However, the demand on the overall numerical approach for nonlinear stability and accuracy is much more stringent for long-time integration of complex multiscale viscous shock/shear/turbulence/acoustics interactions and numerical combustion. Robust classical numerical methods for less complex flow physics are not suitable or practical for such applications. The present approach is designed expressly to address such flow problems, especially unsteady flows. The minimization of employing very fine grids to overcome the production of spurious numerical solutions and/or instability due to under-resolved grids is also sought. The incremental studies to illustrate the performance of the approach are summarized. Extensive testing and full implementation of the approach is forthcoming. The results shown so far are very encouraging.

  17. Integration of coral reef ecosystem process studies and remote sensing: Chapter 5

    USGS Publications Warehouse

    Brook, John; Yates, Kimberly; Halley, Robert

    2006-01-01

    anthropogenic causes (Brown, 1988). Models of coral reef ecosystems, parameterized by process measurements and scaled in time-space using remote sensing, have the potential to address pressing research questions that are central to devising valid management strategies (Grigg el al., 1984; Hatcher, 1997b). To attain this goal, ecosystem-level models that integrate studies of physical and chemical forcing with observed biological and geological responses are required. This interdisciplinary approach to understanding reef biogeochemical dynamics can allow investigations that integrate the scales of time and space (Hatcher, 1997a), thereby enabling prediction of coral reef change (Andréfouët and Payri, 2001). In turn, prediction of holistic ecosystem function within various environmental focusing scenarios has substantial promise in mitigating future disturbance. Indeed, management of coral reefs at the ecosystem level has been suggested as the only meaningful approach to preserving coral reefs (Bohnsack and Ault, 1996; Christensen et al., 1996).

  18. Representative Agricultural Pathways and Scenarios for Regional Integrated Assessment of Climate Change Impacts, Vulnerability, and Adaptation. 5; Chapter

    NASA Technical Reports Server (NTRS)

    Valdivia, Roberto O.; Antle, John M.; Rosenzweig, Cynthia; Ruane, Alexander C.; Vervoort, Joost; Ashfaq, Muhammad; Hathie, Ibrahima; Tui, Sabine Homann-Kee; Mulwa, Richard; Nhemachena, Charles; Ponnusamy, Paramasivam; Rasnayaka, Herath; Singh, Harbir

    2015-01-01

    The global change research community has recognized that new pathway and scenario concepts are needed to implement impact and vulnerability assessment where precise prediction is not possible, and also that these scenarios need to be logically consistent across local, regional, and global scales. For global climate models, representative concentration pathways (RCPs) have been developed that provide a range of time-series of atmospheric greenhouse-gas concentrations into the future. For impact and vulnerability assessment, new socio-economic pathway and scenario concepts have also been developed, with leadership from the Integrated Assessment Modeling Consortium (IAMC).This chapter presents concepts and methods for development of regional representative agricultural pathways (RAOs) and scenarios that can be used for agricultural model intercomparison, improvement, and impact assessment in a manner consistent with the new global pathways and scenarios. The development of agriculture-specific pathways and scenarios is motivated by the need for a protocol-based approach to climate impact, vulnerability, and adaptation assessment. Until now, the various global and regional models used for agricultural-impact assessment have been implemented with individualized scenarios using various data and model structures, often without transparent documentation, public availability, and consistency across disciplines. These practices have reduced the credibility of assessments, and also hampered the advancement of the science through model intercomparison, improvement, and synthesis of model results across studies. The recognition of the need for better coordination among the agricultural modeling community, including the development of standard reference scenarios with adequate agriculture-specific detail led to the creation of the Agricultural Model Intercomparison and Improvement Project (AgMIP) in 2010. The development of RAPs is one of the cross-cutting themes in AgMIP's work

  19. Integrative Modeling of eQTLs and Cis-Regulatory Elements Suggests Mechanisms Underlying Cell Type Specificity of eQTLs

    PubMed Central

    Brown, Christopher D.; Mangravite, Lara M.; Engelhardt, Barbara E.

    2013-01-01

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

  20. Bioinformatic Identification of Conserved Cis-Sequences in Coregulated Genes.

    PubMed

    Bülow, Lorenz; Hehl, Reinhard

    2016-01-01

    Bioinformatics tools can be employed to identify conserved cis-sequences in sets of coregulated plant genes because more and more gene expression and genomic sequence data become available. Knowledge on the specific cis-sequences, their enrichment and arrangement within promoters, facilitates the design of functional synthetic plant promoters that are responsive to specific stresses. The present chapter illustrates an example for the bioinformatic identification of conserved Arabidopsis thaliana cis-sequences enriched in drought stress-responsive genes. This workflow can be applied for the identification of cis-sequences in any sets of coregulated genes. The workflow includes detailed protocols to determine sets of coregulated genes, to extract the corresponding promoter sequences, and how to install and run a software package to identify overrepresented motifs. Further bioinformatic analyses that can be performed with the results are discussed. PMID:27557771

  1. Diffusion of cis-5,8,11,14,17-eicosapentaenoic acid (1); carbon dioxide (2)

    NASA Astrophysics Data System (ADS)

    Winkelmann, J.

    This document is part of Subvolume A `Gases in Gases, Liquids and their Mixtures' of Volume 15 `Diffusion in Gases, Liquids and Electrolytes' of Landolt-Börnstein Group IV `Physical Chemistry'. It is part of the chapter of the chapter `Diffusion in Pure Gases' and contains data on diffusion of (1) cis-5,8,11,14,17-eicosapentaenoic acid; (2) carbon dioxide

  2. Status of flexible CIS research at ISET

    NASA Technical Reports Server (NTRS)

    Basol, B. M.; Kapur, V. K.; Minnick, A.; Halani, A.; Leidholm, C. R.

    1994-01-01

    Polycrystalline thin film solar cells fabricated on light-weight, flexible substrates are very attractive for space applications. In this work CulnSe2 (CIS) based thin film devices were processed on metallic foil substrates using the selenization technique. CIS deposition method involved reaction of electron-bean evaporated Cu-In precursor layers with a selenizing atmosphere at around 400 C. Several metallic foils such as Mo, Ti, Al, Ni, and Cu were evaluated as possible substrates for these devices. Solar cells with AM1.5 efficiencies of 9.0-9.34 percent and good mechanical integrity were demonstrated on Mo and Ti foils. Monolithic integration of these devices was also demonstrated up to 4 in x 4 in size.

  3. Cis-regulatory mutations in human disease

    PubMed Central

    2009-01-01

    Cis-acting regulatory sequences are required for the proper temporal and spatial control of gene expression. Variation in gene expression is highly heritable and a significant determinant of human disease susceptibility. The diversity of human genetic diseases attributed, in whole or in part, to mutations in non-coding regulatory sequences is on the rise. Improvements in genome-wide methods of associating genetic variation with human disease and predicting DNA with cis-regulatory potential are two of the major reasons for these recent advances. This review will highlight select examples from the literature that have successfully integrated genetic and genomic approaches to uncover the molecular basis by which cis-regulatory mutations alter gene expression and contribute to human disease. The fine mapping of disease-causing variants has led to the discovery of novel cis-acting regulatory elements that, in some instances, are located as far away as 1.5 Mb from the target gene. In other cases, the prior knowledge of the regulatory landscape surrounding the gene of interest aided in the selection of enhancers for mutation screening. The success of these studies should provide a framework for following up on the large number of genome-wide association studies that have identified common variants in non-coding regions of the genome that associate with increased risk of human diseases including, diabetes, autism, Crohn's, colorectal cancer, and asthma, to name a few. PMID:19641089

  4. Melt inclusions: Chapter 6

    USGS Publications Warehouse

    ,; Lowenstern, J. B.

    2014-01-01

    Melt inclusions are small droplets of silicate melt that are trapped in minerals during their growth in a magma. Once formed, they commonly retain much of their initial composition (with some exceptions) unless they are re-opened at some later stage. Melt inclusions thus offer several key advantages over whole rock samples: (i) they record pristine concentrations of volatiles and metals that are usually lost during magma solidification and degassing, (ii) they are snapshots in time whereas whole rocks are the time-integrated end products, thus allowing a more detailed, time-resolved view into magmatic processes (iii) they are largely unaffected by subsolidus alteration. Due to these characteristics, melt inclusions are an ideal tool to study the evolution of mineralized magma systems. This chapter first discusses general aspects of melt inclusions formation and methods for their investigation, before reviewing studies performed on mineralized magma systems.

  5. cis-regulatory region analysis using BEARR.

    PubMed

    Vega, Vinsensius Berlian

    2006-01-01

    Genome-wide studies are fast becoming the norm, partly fueled by the availability of genome sequences and the feasibility of high-throughput experimental platforms, e.g., microarrays. An important aspect in any genome-wide studies is determination of regulatory relationships, believed to be primarily transacted through transcription factor binding to DNA. Identification of specific transcription factor binding sites in the cis-regulatory regions of genes makes it possible to list direct targets of transcription factors, model transcriptional regulatory networks, and mine other associated datasets for relevant targets for experimental and clinical manipulation. We have developed a web-based tool to assist biologists in efficiently carrying out the analysis of genes from studies of specific transcription factors or otherwise. The batch extraction and analysis of cis-regulatory regions (BEARR) facilitates identification, extraction, and analysis of regulatory regions from the large amount of data that is typically generated in genome-wide studies. This chapter highlights features and serves as a tutorial for using this publicly available software. The URL is http://giscompute.gis.a-star.edu.sg/~vega/BEARR1.0/. PMID:16888354

  6. A Versatile Theranostic Delivery Platform Integrating Magnetic Resonance Imaging/Computed Tomography, pH/cis-Diol Controlled Release, and Targeted Therapy.

    PubMed

    Tseng, Yu-Jui; Chou, Shang-Wei; Shyue, Jing-Jong; Lin, Shih-Yao; Hsiao, Jong-Kai; Chou, Pi-Tai

    2016-06-28

    The functions of biomedical imaging, cancer targeting, and controlled release of therapeutic agents were integrated into a drug delivery platform to proof its diagnostic and therapeutic capabilities. This versatile nanocomposite is based on the strategic design of wormlike mesoporous silica nanocarriers that are decorated with extremely small iron oxide nanoparticles, having a prominent T1-weighted Magnetic Resonance Imaging (MRI) signal. The controlled release function was then achieved through the grafting of polyalcohol saccharide derivative ligands onto the surfaces of mesoporous silica nanoparticles to conjugate with boronic acid functionalized gold nanoparticles, which acted as the gate and the source of computed tomography (CT) signals. This versatile platform thus exhibited a MRI/CT dual imaging property drawing on the strong points to offset the weaknesses of each, rendering more accurate diagnosis. The capping of gold nanoparticles controlled with the hydrolysis of boronate ester bonds provides the reversible opening/closing process, avoiding further release of drug once the nanocomposite leaves the cell or tissue. To endow this platform with targeting ability, protocatechuic acid was utilized as a linker to connect folic acid with the boronic acid of the gold nanoparticles. The anchor of targeting moiety, folic acid, enriched this platform and enhanced the specific cellular uptake toward cells with folate receptor. This integrated drug delivery platform was then loaded with the antitumor agent doxorubicin, demonstrating its power for targeted delivery, bioimaging, and controlled release chemotherapy to reduce the undesired side effects of chemotherapy. PMID:27163375

  7. Gora Konder Crater, Yakutsk, CIS

    NASA Technical Reports Server (NTRS)

    1991-01-01

    Gora Konder Crater, Yakutsk, CIS (57.5N,134.5E) is located in a very remote region of the Republic of Yakutsk, CIS where little ground survey work has been done. It is not known for certain wether Gora Konder crater is the extinct caldera of an ancient volcano or an impact crater from a meteor strike since both occurrences may often exhibit similar visual appearances and only a ground survey can make a positive determination.

  8. Chapter Four: Discursive Resources

    ERIC Educational Resources Information Center

    Young, Richard F.

    2008-01-01

    In this chapter, the focus of attention moves from the contexts described in chapter 3 to the verbal, nonverbal, and interactional resources that participants employ in discursive practices. These resources are discussed within the frame of participation status and participation framework proposed by Goffman. Verbal resources employed by…

  9. Chapter 9: Electronics

    SciTech Connect

    Grupen, Claus; Shwartz, Boris A.

    2006-12-19

    Sophisticated front-end electronics are a key part of practically all modern radiation detector systems. This chapter introduces the basic principles and their implementation. Topics include signal acquisition, electronic noise, pulse shaping (analog and digital), and data readout techniques.

  10. DBMS UTILIZATION: A Corporate Information System (CIS) development approach

    NASA Technical Reports Server (NTRS)

    Rozett, P.

    1983-01-01

    The Corporate Information System (CIS), an integrated information system intended to tie the corporation together as a functioning entity, is described. In addition to being a major upgraded automated data processing system, the CIS is a management philosophy which recognizes data as a valuable corporate resource and which distinguishes between data and selected data, or information. It further recognizes that different users need different kinds of information. Plans for CIS development are discussed. It will offer its users not just after-the-fact data, but timely information in a format that is meaningful and useful to the particular user, so that the information can be applied in planning, controlling, and decision making by all levels of management. In effect, CIS will help the corporation itself to function as a total, integrated system by typing together administrative activities through information exchange. The CIS supports the operational, tactical control, and strategic planning functions of the corporation. Operational functions are the day-to-day processing necessary to support the corporation's work, such as purchasing and payroll.

  11. cis-1,2-Dichloroethylene

    Integrated Risk Information System (IRIS)

    cis - 1,2 - Dichloroethylene ; CASRN 156 - 59 - 2 Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health Hazard Assessments for Nonc

  12. COMPENDEX/TEXT-PAC: CIS.

    ERIC Educational Resources Information Center

    Standera, Oldrich

    This report evaluates the engineering information services provided by the University of Calgary since implementation of the COMPENDEX (tape service of Engineering Index, Inc.) service using the IBM TEXT-PAC system. Evaluation was made by a survey of the users of the Current Information Selection (CIS) service, the interaction between the system…

  13. Transfer of the EPA/NIH Chemical Information System (CIS) to Private Management.

    ERIC Educational Resources Information Center

    Kadec, Sarah T.; Jover, Antonio

    This paper discusses the programmatic concerns, the evaluation, and the ultimate decisions which led to the transfer of CIS (Chemical Information System) to the private sector. CIS is a complex, integrated system of some 20 chemical databases and data analysis programs which provide access to physical, toxicological, environmental effects, and…

  14. Cis-Lunar Base Camp

    NASA Technical Reports Server (NTRS)

    Merrill, Raymond G.; Goodliff, Kandyce E.; Mazanek, Daniel D.; Reeves, John D., Jr.

    2012-01-01

    Historically, when mounting expeditions into uncharted territories, explorers have established strategically positioned base camps to pre-position required equipment and consumables. These base camps are secure, safe positions from which expeditions can depart when conditions are favorable, at which technology and operations can be tested and validated, and facilitate timely access to more robust facilities in the event of an emergency. For human exploration missions into deep space, cis-lunar space is well suited to serve as such a base camp. The outer regions of cis-lunar space, such as the Earth-Moon Lagrange points, lie near the edge of Earth s gravity well, allowing equipment and consumables to be aggregated with easy access to deep space and to the lunar surface, as well as more distant destinations, such as near-Earth Asteroids (NEAs) and Mars and its moons. Several approaches to utilizing a cis-lunar base camp for sustainable human exploration, as well as some possible future applications are identified. The primary objective of the analysis presented in this paper is to identify options, show the macro trends, and provide information that can be used as a basis for more detailed mission development. Compared within are the high-level performance and cost of 15 preliminary cis-lunar exploration campaigns that establish the capability to conduct crewed missions of up to one year in duration, and then aggregate mass in cis-lunar space to facilitate an expedition from Cis-Lunar Base Camp. Launch vehicles, chemical propulsion stages, and electric propulsion stages are discussed and parametric sizing values are used to create architectures of in-space transportation elements that extend the existing in-space supply chain to cis-lunar space. The transportation options to cis-lunar space assessed vary in efficiency by almost 50%; from 0.16 to 0.68 kg of cargo in cis-lunar space for every kilogram of mass in Low Earth Orbit (LEO). For the 15 cases, 5-year campaign

  15. Thermal cis-trans isomerization of cis,cis-3,7-decadiene - A model for cis-1,4-polybutadiene

    NASA Technical Reports Server (NTRS)

    Golub, M. A.; Lee, W. M.

    1983-01-01

    The thermal cis-trans isomerization of cis,cis-3,7-decadiene (DD), a model compound for cis-PBD, is reported. It is demonstrated that the rather low E for the polyalkenamer isomerizations compared with that for the 2-olefins is not an artifact of the solid polymer structures, but rather is characteristic of both small and large molecules possessing pairs of nonconjugated vinylene double bonds in a suitable arrangement.

  16. Chapter 3: Energy Security

    SciTech Connect

    Foust, Thomas D.; Arent, Doug; de Carvalho Macedo, Isaias; Goldemberg, Jose; Hoysala, Chanakya; Filho, Rubens Maciel; Nigro, Francisco E. B.; Richard, Tom L.; Saddler, Jack; Samseth, Jon; Somerville, Chris R.

    2015-04-01

    This chapter considers the energy security implications and impacts of bioenergy. We provide an assessment to answer the following questions: What are the implications for bioenergy and energy security within the broader policy environment that includes food and water security, development, economic productivity, and multiple foreign policy aspects? What are the conditions under which bioenergy contributes positively to energy security?

  17. trans meets cis in MADS science.

    PubMed

    de Folter, Stefan; Angenent, Gerco C

    2006-05-01

    The interaction between a transcription factor and its binding site at the DNA is an integral part of transcriptional regulatory networks, which is fundamental for an understanding of biological processes. An example is the family of MADS domain transcription factors, which represent key regulators of processes in yeast, animals and plants. However, despite our extensive knowledge of these transcription factors, limited information is available on the cis-elements to which these proteins bind or how these elements are defined. Here, we discuss the current understanding of MADS protein binding sites and compare data from various organisms. This information can help us in developing algorithms to predict binding sites for MADS domain transcription factors, which would be a significant step forward in the identification of "down-stream" target genes and the elucidation of transcriptional networks. PMID:16616581

  18. IRIS Toxicological Review of Cis-& Trans-1,2-Dichloroethylene (External Review Draft)

    EPA Science Inventory

    EPA is conducting a peer review of the scientific basis supporting the human health hazard and dose-response assessment of cis- and trans-1,2-dichloroethylene that will appear in the Integrated Risk Information System (IRIS) database.

  19. Diagnostic and vaccine chapter.

    PubMed

    Wolfram, J H; Kokanov, S K; Verkhovsky, O A

    2010-10-01

    The first report in this chapter describes the development of a killed composite vaccine. This killed vaccine is non-infectious to humans, other animals, and the environment. The vaccine has low reactivity, is non-abortive, and does not induce pathomorphological alterations to the organs of vaccinated animals. The second report of this chapter describes the diagnostic value of a competitive enzyme-linked immunosorbent assay for detecting Brucella-specific antibodies and its ability to discriminate vaccinated cattle from infected cattle. The results indicated that the competitive enzyme-linked immunosorbent assay is more sensitive than traditional tests for detecting antibodies to Brucella abortus in naturally and experimentally infected cattle. PMID:20850688

  20. Recycling Of Cis Photovoltaic Waste

    DOEpatents

    Drinkard, Jr., William F.; Long, Mark O.; Goozner; Robert E.

    1998-07-14

    A method for extracting and reclaiming metals from scrap CIS photovoltaic cells and associated photovoltaic manufacturing waste by leaching the waste with dilute nitric acid, skimming any plastic material from the top of the leaching solution, separating glass substrate from the leachate, electrolyzing the leachate to plate a copper and selenium metal mixture onto a first cathode, replacing the cathode with a second cathode, re-electrolyzing the leachate to plate cadmium onto the second cathode, separating the copper from selenium, and evaporating the depleted leachate to yield a zinc and indium containing solid.

  1. Diffusion of cis-3-methyl-2-pent-2-enyl-cyclopent-2-enone (1); carbon dioxide (2)

    NASA Astrophysics Data System (ADS)

    Winkelmann, J.

    This document is part of Subvolume A `Gases in Gases, Liquids and their Mixtures' of Volume 15 `Diffusion in Gases, Liquids and Electrolytes' of Landolt-Börnstein Group IV `Physical Chemistry'. It is part of the chapter of the chapter `Diffusion in Pure Gases' and contains data on diffusion of (1) cis-3-methyl-2-pent-2-enyl-cyclopent-2-enone; (2) carbon dioxide

  2. Nutrient dynamics: Chapter 3

    USGS Publications Warehouse

    Likens, Gene E.; LaBaugh, James W.; Buso, Donald C.; Bade, Darren; Winter, Thomas C.; Likens, Gene E.

    2009-01-01

    This chapter focuses on the variability and trends in chemical concentrations and fluxes at Mirror Lake during the period 1981–2000. It examines the water and chemical budgets of Mirror Lake to identify and understand better long-term trends in the chemical characteristics of the lake. It also identifies the causes of changes in nutrient concentrations and examines the contribution of hydrologic pathways to the contamination of Mirror Lake by road salt. The role of groundwater and precipitation on water and chemical budgets of the lake are also examined.

  3. Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species

    PubMed Central

    Zhang, Yong; Liu, X. Shirley; Liu, Qing-Rong; Wei, Liping

    2006-01-01

    We developed a fast, integrative pipeline to identify cis natural antisense transcripts (cis-NATs) at genome scale. The pipeline mapped mRNAs and ESTs in UniGene to genome sequences in GoldenPath to find overlapping transcripts and combining information from coding sequence, poly(A) signal, poly(A) tail and splicing sites to deduce transcription orientation. We identified cis-NATs in 10 eukaryotic species, including 7830 candidate sense–antisense (SA) genes in 3915 SA pairs in human. The abundance of SA genes is remarkably low in worm and does not seem to be caused by the prevalence of operons. Hundreds of SA pairs are conserved across different species, even maintaining the same overlapping patterns. The convergent SA class is prevalent in fly, worm and sea squirt, but not in human or mouse as reported previously. The percentage of SA genes among imprinted genes in human and mouse is 24–47%, a range between the two previous reports. There is significant shortage of SA genes on Chromosome X in human and mouse but not in fly or worm, supporting X-inactivation in mammals as a possible cause. SA genes are over-represented in the catalytic activities and basic metabolism functions. All candidate cis-NATs can be downloaded from . PMID:16849434

  4. cis-Apa: a practical linker for the microwave-assisted preparation of cyclic pseudopeptides via RCM cyclative cleavage.

    PubMed

    Baron, Alice; Verdié, Pascal; Martinez, Jean; Lamaty, Frédéric

    2011-02-01

    A new linker cis-5-aminopent-3-enoic acid (cis-Apa) was prepared for the synthesis of cyclic pseudopeptides by cyclization-cleavage by using ring-closing methatesis (RCM). We developed a new synthetic pathway for the preparation of the cis-Apa linker that was tested in the cyclization-cleavage process of different RGD peptide sequences. Different macrocyclic peptidomimetics were prepared by using this integrated microwave-assisted method, showing that the readily available cis-Apa amino acid is well adapted as a linker in the cyclization-cleavage process.

  5. Modeling and Advanced Control for Sustainable Process Systems (chapter 5)

    EPA Science Inventory

    This book chapter introduces a novel process systems engineering framework that integrates process control with sustainability assessment tools for the simultaneous evaluation and optimization of process operations. The implemented control strategy consists of a biologically-insp...

  6. Toward an inclusive model of lesbian identity development: Outlining a common and nuanced model for cis and trans women.

    PubMed

    Tate, Charlotte Chucky; Pearson, Mercedes D

    2016-01-01

    This article proposes an integrative model of lesbian identity development that places cis and trans women together as equal contributors. Two of the most influential current models of female sexuality are reviewed, and we use their commonalities to build the foundation of our integrative model. We also use Tate's model of lesbian identity as a scaffolding to integrate trans women's experiences alongside cis women's. Finally, we provide the outline of the Inclusive Model of Female Sexuality and discuss the convergences and divergences that exist between cis women and trans women in the formation of lesbian identity. PMID:26701772

  7. Germinating the 2050 Cis-Lunar Econosphere

    NASA Technical Reports Server (NTRS)

    Scott, David W.; Curreri, Peter A.; Ferguson, Cynthia K.; Nall, Mark E.; Tinker, Michael L.; Wright, Gregory M.

    2015-01-01

    In early 2013, Marshall Space Flight Center's upper management chartered a diverse team for a six-week 'sprint' to speculate (in a disciplined manner) and paint (with broad brush strokes) a picture of how earth, space, and public/private entities might be operating and relating to each other... in the year 2100. Two 12-person groups of civil servants, one with members having 15 years or less of NASA experience and the other with more senior members, worked independently and then compared and integrated their conclusions. In 2014, the 'Space 2100' team, with some new team members and different group boundaries, ran a longer sprint to a) develop more detailed estimates of the operations and economics of space activities in the vicinity of the Earth and Moon in the 2050 time frame, b) identify evolutionary paths, barriers, and opportunities, and c) suggest actions and philosophies to enable and invigorate progress towards the vision. This paper explores Space 2100's first two sprints and their projections of NASA's role in what will likely be a highly networked, international space industry and cis-lunar infrastructure.

  8. Germinating the 2050 Cis-Lunar Econosphere

    NASA Technical Reports Server (NTRS)

    Scott, David W.; Tinker, Michael L.; Nall, Mark E.; Wright, Gregory M.

    2015-01-01

    In early 2013, the Marshall Space Flight Center (MSFC) Director and MSFC's Office of Strategic Analysis and Communications (OSAC) chartered a diverse team for a six-week "sprint" to speculate (in a disciplined manner) and paint (with broad brush strokes) a picture of how earth, space, and public/private entities might be operating and relating to each other...in the year 2100. Two 12-person groups of civil servants, one with members having 15 years or less of NASA experience and the other with more senior members, worked independently and then compared and integrated their conclusions. In 2014, the "Space 2100" team, with some new team members and different group boundaries, ran a longer sprint to a) develop more detailed estimates of the operations and economics of space activities in the vicinity of the Earth and Moon in the 2050 time frame, b) identify evolutionary steps and viable paths needed to make that a reality, and c) recommend actions to enable and invigorate those steps. This paper explores Space 2100's first two sprints and their projections of NASA's role in what will likely be a highly networked international space industry and cis-lunar infrastructure.

  9. Chapter 4: Solar Magnetism

    NASA Astrophysics Data System (ADS)

    Venkatakrishnan, P.; Gosain, Sanjay

    2008-10-01

    This chapter is basically divided into 2 parts. In the first part, the important properties of the solar magnetic field are summarized. The discussion begins with a simple introduction to solar magneto hydrodynamics. This introduction will be sufficient to understand the current status of the solar dynamo theory that follows. Some very curious and interesting results on force free fields are then presented in very basic terms. Finally, the application of this theoretical framework to the problems of coronal heating, solar flares and coronal mass ejections are developed in a simple unified scheme, based on a hierarchy of physical conditions. The second part consists of a tutorial on magnetographs. It begins with a description of polarization of light from very fundamental notions of coherence of light. This is followed by simple but comprehensive explanations of the Zeeman and Hanle effects along with the necessary basic ideas of quantum physics of scattering of light. Then the working of a few important magnetographs is outlined, with special emphasis on a solar vector magnetograph developed for USO, to provide a ''hands on" perspective. The article concludes with a few brief remarks on the possible future directions for research in the domain of solar magnetism...

  10. Chapter 20: Graphite

    SciTech Connect

    Burchell, Timothy D

    2012-01-01

    Graphite is truly a unique material. Its structure, from the nano- to the millimeter scale give it remarkable properties that lead to numerous and diverse applications. Graphite bond anisotropy, with strong in-plane covalent bonds and weak van der Waals type bonding between the planes, gives graphite its unique combination of properties. Easy shear of the crystal, facilitated by weak interplaner bonds allows graphite to be used as a dry lubricant, and is responsible for the substances name! The word graphite is derived from the Greek to write because of graphites ability to mark writing surfaces. Moreover, synthetic graphite contains within its structure, porosity spanning many orders of magnitude in size. The thermal closure of these pores profoundly affects the properties for example, graphite strength increases with temperature to temperatures in excess of 2200 C. Consequently, graphite is utilized in many high temperature applications. The basic physical properties of graphite are reviewed here. Graphite applications include metallurgical; (aluminum and steel production), single crystal silicon production, and metal casting; electrical (motor brushes and commutators); mechanical (seals, bearings and bushings); and nuclear applications, (see Chapter 91, Nuclear Graphite). Here we discuss the structure, manufacture, properties, and applications of Graphite.

  11. Synthesis: Chapter 19

    USGS Publications Warehouse

    Pardo, L.H.; Geiser, L.H.; Fenn, M.E.; Driscoll, C.T.; Goodale, C.L.; Allen, E.B.; Baron, J. S.; Bobbink, R.; Bowman, W.D.; Clark, C.M.; Emmett, B.; Gilliam, F.S.; Greaver, T.; Hall, S.J.; Lilleskov, E.A.; Liu, L.; Lynch, J.A.; Nadelhoffer, K.; Perakis, S.S.; Robin-Abbott, M. J.; Stoddard, J.L.; Weathers, K. C.

    2011-01-01

    Human activity in the last century has led to a substantial increase in nitrogen (N) emissions and deposition (Galloway et al. 2003). Because of past, and, in some regions, continuing increases in emissions (Lehmann et al. 2005, Nilles and Conley 2001), this N deposition has reached a level that has caused or is likely to cause alterations and damage in many ecosystems across the United States. In some ecoregions, the impact of N deposition has been severe and has changed the biotic community structure and composition of ecosystems. In the Mediterranean California ecoregion, for example (see Chapter 13), replacement of native by exotic invasive vegetation is accelerated because exotic species are often more productive under elevated N deposition than native species in some California grasslands, coastal sage scrub, and desert scrub (Fenn et al. 2010, Rao and Allen 2010, Rao et al. 2010, Weiss 1999, Yoshida and Allen 2004). Such shifts in plant community composition and species richness can have consequences beyond changes in ecosystem structure: shifts may lead to overall losses in biodiversity and further impair particular threatened or endangered species (Stevens et al. 2004). Th e extirpation of the endangered checkerspot butterfl y (Euphydryas editha bayensis), because the host plant for the larval stage disappears in N-enriched ecosystems (Fenn et al. 2010, Weiss 1999), is just one example of the detrimental impacts of elevated N deposition.

  12. Career development through local chapter involvement: perspectives from chapter members.

    PubMed

    Thomas, Melissa; Inniss-Richter, Zipporah; Mata, Holly; Cottrell, Randall R

    2013-07-01

    The importance of career development in professional organizations has been noted in the literature. Personal and professional benefits of membership regardless of discipline can be found across the career spectrum from student to executive. The benefits of professional membership with respect to career development in local chapter organizations have seldom been studied. Local chapter participation may offer significant career development opportunities for the practitioner, faculty member, and student. The purpose of this study was to explore the importance of local chapter involvement to the career development of health education practitioners. An 18-item questionnaire was disseminated to the membership of three local SOPHE (Society for Public Health Education) chapters that explored the level of local chapter involvement and the impact of how specific professional development activities impacted career development. The results of the survey highlighted the importance of continuing education programs, networking, and leadership experience in developing one's career that are offered by local SOPHE chapter involvement. Making a positive impact in the community and earning the respect of one's peers were most often reported as indicators of career success. These factors can directly impact local chapter participation. Career development can certainly be enhanced by active participation in the local chapter of a professional association.

  13. Career development through local chapter involvement: perspectives from chapter members.

    PubMed

    Thomas, Melissa; Inniss-Richter, Zipporah; Mata, Holly; Cottrell, Randall R

    2013-07-01

    The importance of career development in professional organizations has been noted in the literature. Personal and professional benefits of membership regardless of discipline can be found across the career spectrum from student to executive. The benefits of professional membership with respect to career development in local chapter organizations have seldom been studied. Local chapter participation may offer significant career development opportunities for the practitioner, faculty member, and student. The purpose of this study was to explore the importance of local chapter involvement to the career development of health education practitioners. An 18-item questionnaire was disseminated to the membership of three local SOPHE (Society for Public Health Education) chapters that explored the level of local chapter involvement and the impact of how specific professional development activities impacted career development. The results of the survey highlighted the importance of continuing education programs, networking, and leadership experience in developing one's career that are offered by local SOPHE chapter involvement. Making a positive impact in the community and earning the respect of one's peers were most often reported as indicators of career success. These factors can directly impact local chapter participation. Career development can certainly be enhanced by active participation in the local chapter of a professional association. PMID:23539263

  14. Plant growth inhibition by cis-cinnamoyl glucosides and cis-cinnamic acid.

    PubMed

    Hiradate, Syuntaro; Morita, Sayaka; Furubayashi, Akihiro; Fujii, Yoshiharu; Harada, Jiro

    2005-03-01

    Spiraea thunbergii Sieb. contains 1-O-cis-cinnamoyl-beta-D-glucopyranose (CG) and 6-O-(4'-hydroxy-2'-methylene-butyroyl)-1-O-cis-cinnamoyl-beta-D-glucopyranose (BCG) as major plant growth inhibiting constituents. In the present study, we determined the inhibitory activity of CG and BCG on root elongation of germinated seedlings of lettuce (Lactuca sativa), pigweed (Amaranthus retroflexus), red clover (Trifolium pratense), timothy (Phleum pratense), and bok choy (Brassica rapa var chinensis) in comparison with that of two well-known growth inhibitors, 2,4-dichlorophenoxyacetic acid (2,4-D) and (+)-2-cis-4-trans-abscisic acid (cis-ABA), as well as two related chemicals of CG and BCG, cis-cinnamic acid (cis-CA) and trans-cinnamic acid (trans-CA). The EC50 values for CG and BCG on lettuce were roughly one-half to one-quarter of the value for cis-ABA. cis-Cinnamic acid, which is a component of CG and BCG, possessed almost the same inhibitory activity of CG and BCG, suggesting that the essential chemical structure responsible for the inhibitory activity of CG and BCG is cis-CA. The cis-stereochemistry of the methylene moiety is apparently needed for high inhibitory activity, as trans-CA had an EC50 value roughly 100 times that of CG, BCG, and cis-CA. Growth inhibition by CG, BCG, and cis-CA was influenced by the nature of the soil in the growing medium: alluvial soil preserved the bioactivity, whereas volcanic ash and calcareous soils inhibited bioactivity. These findings indicate a potential role of cis-CA and its glucosides as allelochemicals for use as plant growth regulators in agricultural fields.

  15. Plant growth inhibition by cis-cinnamoyl glucosides and cis-cinnamic acid.

    PubMed

    Hiradate, Syuntaro; Morita, Sayaka; Furubayashi, Akihiro; Fujii, Yoshiharu; Harada, Jiro

    2005-03-01

    Spiraea thunbergii Sieb. contains 1-O-cis-cinnamoyl-beta-D-glucopyranose (CG) and 6-O-(4'-hydroxy-2'-methylene-butyroyl)-1-O-cis-cinnamoyl-beta-D-glucopyranose (BCG) as major plant growth inhibiting constituents. In the present study, we determined the inhibitory activity of CG and BCG on root elongation of germinated seedlings of lettuce (Lactuca sativa), pigweed (Amaranthus retroflexus), red clover (Trifolium pratense), timothy (Phleum pratense), and bok choy (Brassica rapa var chinensis) in comparison with that of two well-known growth inhibitors, 2,4-dichlorophenoxyacetic acid (2,4-D) and (+)-2-cis-4-trans-abscisic acid (cis-ABA), as well as two related chemicals of CG and BCG, cis-cinnamic acid (cis-CA) and trans-cinnamic acid (trans-CA). The EC50 values for CG and BCG on lettuce were roughly one-half to one-quarter of the value for cis-ABA. cis-Cinnamic acid, which is a component of CG and BCG, possessed almost the same inhibitory activity of CG and BCG, suggesting that the essential chemical structure responsible for the inhibitory activity of CG and BCG is cis-CA. The cis-stereochemistry of the methylene moiety is apparently needed for high inhibitory activity, as trans-CA had an EC50 value roughly 100 times that of CG, BCG, and cis-CA. Growth inhibition by CG, BCG, and cis-CA was influenced by the nature of the soil in the growing medium: alluvial soil preserved the bioactivity, whereas volcanic ash and calcareous soils inhibited bioactivity. These findings indicate a potential role of cis-CA and its glucosides as allelochemicals for use as plant growth regulators in agricultural fields. PMID:15898503

  16. Favorable genomic environments for cis-regulatory evolution: A novel theoretical framework.

    PubMed

    Maeso, Ignacio; Tena, Juan J

    2016-09-01

    Cis-regulatory changes are arguably the primary evolutionary source of animal morphological diversity. With the recent explosion of genome-wide comparisons of the cis-regulatory content in different animal species is now possible to infer general principles underlying enhancer evolution. However, these studies have also revealed numerous discrepancies and paradoxes, suggesting that the mechanistic causes and modes of cis-regulatory evolution are still not well understood and are probably much more complex than generally appreciated. Here, we argue that the mutational mechanisms and genomic regions generating new regulatory activities must comply with the constraints imposed by the molecular properties of cis-regulatory elements (CREs) and the organizational features of long-range chromatin interactions. Accordingly, we propose a new integrative evolutionary framework for cis-regulatory evolution based on two major premises for the origin of novel enhancer activity: (i) an accessible chromatin environment and (ii) compatibility with the 3D structure and interactions of pre-existing CREs. Mechanisms and DNA sequences not fulfilling these premises, will be less likely to have a measurable impact on gene expression and as such, will have a minor contribution to the evolution of gene regulation. Finally, we discuss current comparative cis-regulatory data under the light of this new evolutionary model, and propose that the two most prominent mechanisms for the evolution of cis-regulatory changes are the overprinting of ancestral CREs and the exaptation of transposable elements.

  17. Collective Intelligence. Chapter 17

    NASA Technical Reports Server (NTRS)

    Wolpert, David H.

    2003-01-01

    Many systems of self-interested agents have an associated performance criterion that rates the dynamic behavior of the overall system. This chapter presents an introduction to the science of such systems. Formally, collectives are defined as any system having the following two characteristics: First, the system must contain one or more agents each of which we view as trying to maximize an associated private utility; second, the system must have an associated world utility function that rates the possible behaviors of that overall system. In practice, collectives are often very large, distributed, and support little, if any, centralized communication and control, although those characteristics are not part of their formal definition. A naturally occurring example of a collective is a human economy. One can identify the agents and their private utilities as the human individuals in the economy and the associated personal rewards they are each trying to maximize. One could then identify the world utility as the time average of the gross domestic product. ("World utility" per se is not a construction internal to a human economy, but rather something defined from the outside.) To achieve high world utility it is necessary to avoid having the agents work at cross-purposes lest phenomena like liquidity traps or the Tragedy of the Commons (TOC) occur, in which agents' individually pursuing their private utilities lowers world utility. The obvious way to avoid such phenomena is by modifying the agents utility functions to be "aligned" with the world utility. This can be done via punitive legislation. A real-world example of an attempt to do this was the creation of antitrust regulations designed to prevent monopolistic practices.

  18. Explanatory chapter: PCR primer design.

    PubMed

    Álvarez-Fernández, Rubén

    2013-01-01

    This chapter is intended as a guide on polymerase chain reaction (PCR) primer design (for information on PCR, see General PCR and Explanatory Chapter: Troubleshooting PCR). In the next section, general guidelines will be provided, followed by a discussion on primer design for specific applications. A list of recommended software tools is shown at the end.

  19. Photoelectron Spectroscopy of cis-Nitrous Acid Anion (cis-HONO(-)).

    PubMed

    Oliveira, Allan M; Lehman, Julia H; McCoy, Anne B; Lineberger, W Carl

    2016-03-17

    We report photoelectron spectra of cis-HONO(-) formed from an association reaction of OH(-) and NO in a pulsed, plasma-entrainment ion source. The experimental data are assigned to the cis-HONO(-) isomer, which is predicted to be the global minimum on the anion potential energy surface. We do not find evidence for a significant contribution from trans-HONO(-). Electron photodetachment of cis-HONO(-) with 1613, 1064, 532, 355, and 301 nm photons accesses the ground X̃ (1)A' (S0) and excited ã (3)A″ (T1) states of neutral HONO. The photoelectron spectrum resulting from detachment forming cis-HONO (S0) exhibits a long vibrational progression, dominated by overtones and combination bands involving the central O-N stretching and ONO bending vibrations. This indicates that there is a significant change in the central O-N bond length between cis-HONO(-) and cis-HONO (S0). The electron affinity (EA) of cis-HONO is determined to be 0.356(8) eV. We also report the dissociation energy (D0) of cis-HONO(-), forming OH(-) + NO, as 0.594(9) eV, which is a factor of 4 decrease in the central O-N bond strength compared to neutral cis-HONO. The T1 state of cis-HONO is shown to be ∼2.3 eV higher in energy than cis-HONO (S0). Electron photodetachment to form cis-HONO (T1) accesses a transition state along the HO-NO bond dissociation coordinate. The resulting photoelectron spectrum exhibits broad peaks spaced by the terminal N═O stretching frequency. Electronic structure calculations and photoelectron spectrum simulations reported here show very good agreement with the experimental data. PMID:26886478

  20. Chapter 59: Web Services

    NASA Astrophysics Data System (ADS)

    Graham, M. J.

    Web services are a cornerstone of the distributed computing infrastructure that the VO is built upon yet to the newcomer, they can appear to be a black art. This perception is not helped by the miasma of technobabble that pervades the subject and the seemingly impenetrable high priesthood of actual users. In truth, however, there is nothing conceptually difficult about web services (unsurprisingly any complexities will lie in the implementation details) nor indeed anything particularly new. A web service is a piece of software available over a network with a formal description of how it is called and what it returns that a computer can understand. Note that entities such as web servers, ftp servers and database servers do not generally qualify as they lack the standardized description of their inputs and outputs. There are prior technologies, such as RMI, CORBA, and DCOM, that have employed a similar approach but the success of web services lies predominantly in its use of standardized XML to provide a language-neutral way for representing data. In fact, the standardization goes further as web services are traditionally (or as traditionally as five years will allow) tied to a specific set of technologies (WSDL and SOAP conveyed using HTTP with an XML serialization). Alternative implementations are becoming increasingly common and we will cover some of these here. One important thing to remember in all of this, though, is that web services are meant for use by computers and not humans (unlike web pages) and this is why so much of it seems incomprehensible gobbledegook. In this chapter, we will start with an overview of the web services current in the VO and present a short guide on how to use and deploy a web service. We will then review the different approaches to web services, particularly REST and SOAP, and alternatives to XML as a data format. We will consider how web services can be formally described and discuss how advanced features such as security, state

  1. Advanced Concepts. Chapter 21

    NASA Technical Reports Server (NTRS)

    Johnson, Les; Mulqueen, Jack

    2013-01-01

    Before there is a funded space mission, there must be a present need for the mission. Space science and exploration are expensive, and without a well-defined and justifiable need, no one is going to commit significant funding for any space endeavor. However, as discussed in Chapter 1, applications of space technology and many and broad, hence there are many ways to determine and establish a mission need. Robotic science missions are justified by their science return. To be selected for flight, questions like these must be addressed: What is the science question that needs answering, and will the proposed mission be the most cost-effective way to answer it? Why does answering the question require an expensive space flight, instead of some ground-based alternative? If the question can only be answered by flying in space, then why is this approach better than other potential approaches? How much will it cost? And is the technology required to answer the question in hand and ready to use? If not, then how much will it cost and how long will it take to mature the technology to a usable level? There are also many ways to justify human exploration missions, including science return, technology advancement, as well as intangible reasons, such as national pride. Nonetheless, many of the questions that need answering, are similar to those for robotic science missions: Where are the people going, why, and will the proposed mission be the most cost-effective way to get there? What is the safest method to achieve the goal? How much will it cost? And is the technology required to get there and keep the crew alive in hand and ready to use? If not, then how much will it cost and how long will it take to mature the technology to a usable level? Another reason for some groups sending spacecraft into space is for profit. Telecommunications, geospatial imaging, and tourism are examples of proven, market-driven space missions and applications. For this specific set of users, the

  2. CisSERS: Customizable In Silico Sequence Evaluation for Restriction Sites

    PubMed Central

    Sharpe, Richard M.; Koepke, Tyson; Harper, Artemus; Grimes, John; Galli, Marco; Satoh-Cruz, Mio; Kalyanaraman, Ananth; Evans, Katherine; Kramer, David; Dhingra, Amit

    2016-01-01

    High-throughput sequencing continues to produce an immense volume of information that is processed and assembled into mature sequence data. Data analysis tools are urgently needed that leverage the embedded DNA sequence polymorphisms and consequent changes to restriction sites or sequence motifs in a high-throughput manner to enable biological experimentation. CisSERS was developed as a standalone open source tool to analyze sequence datasets and provide biologists with individual or comparative genome organization information in terms of presence and frequency of patterns or motifs such as restriction enzymes. Predicted agarose gel visualization of the custom analyses results was also integrated to enhance the usefulness of the software. CisSERS offers several novel functionalities, such as handling of large and multiple datasets in parallel, multiple restriction enzyme site detection and custom motif detection features, which are seamlessly integrated with real time agarose gel visualization. Using a simple fasta-formatted file as input, CisSERS utilizes the REBASE enzyme database. Results from CisSERS enable the user to make decisions for designing genotyping by sequencing experiments, reduced representation sequencing, 3’UTR sequencing, and cleaved amplified polymorphic sequence (CAPS) molecular markers for large sample sets. CisSERS is a java based graphical user interface built around a perl backbone. Several of the applications of CisSERS including CAPS molecular marker development were successfully validated using wet-lab experimentation. Here, we present the tool CisSERS and results from in-silico and corresponding wet-lab analyses demonstrating that CisSERS is a technology platform solution that facilitates efficient data utilization in genomics and genetics studies. PMID:27071032

  3. CisSERS: Customizable in silico sequence evaluation for restriction sites

    DOE PAGES

    Sharpe, Richard M.; Koepke, Tyson; Harper, Artemus; Grimes, John; Galli, Marco; Satoh-Cruz, Mio; Kalyanaraman, Ananth; Evans, Katherine; Kramer, David; Dhingra, Amit; et al

    2016-04-12

    High-throughput sequencing continues to produce an immense volume of information that is processed and assembled into mature sequence data. Here, data analysis tools are urgently needed that leverage the embedded DNA sequence polymorphisms and consequent changes to restriction sites or sequence motifs in a high-throughput manner to enable biological experimentation. CisSERS was developed as a standalone open source tool to analyze sequence datasets and provide biologists with individual or comparative genome organization information in terms of presence and frequency of patterns or motifs such as restriction enzymes. Predicted agarose gel visualization of the custom analyses results was also integrated tomore » enhance the usefulness of the software. CisSERS offers several novel functionalities, such as handling of large and multiple datasets in parallel, multiple restriction enzyme site detection and custom motif detection features, which are seamlessly integrated with real time agarose gel visualization. Using a simple fasta-formatted file as input, CisSERS utilizes the REBASE enzyme database. Results from CisSERSenable the user to make decisions for designing genotyping by sequencing experiments, reduced representation sequencing, 3’UTR sequencing, and cleaved amplified polymorphic sequence (CAPS) molecular markers for large sample sets. CisSERS is a java based graphical user interface built around a perl backbone. Several of the applications of CisSERS including CAPS molecular marker development were successfully validated using wet-lab experimentation. Here, we present the tool CisSERSand results from in-silico and corresponding wet-lab analyses demonstrating that CisSERS is a technology platform solution that facilitates efficient data utilization in genomics and genetics studies.« less

  4. CisSERS: Customizable In Silico Sequence Evaluation for Restriction Sites.

    PubMed

    Sharpe, Richard M; Koepke, Tyson; Harper, Artemus; Grimes, John; Galli, Marco; Satoh-Cruz, Mio; Kalyanaraman, Ananth; Evans, Katherine; Kramer, David; Dhingra, Amit

    2016-01-01

    High-throughput sequencing continues to produce an immense volume of information that is processed and assembled into mature sequence data. Data analysis tools are urgently needed that leverage the embedded DNA sequence polymorphisms and consequent changes to restriction sites or sequence motifs in a high-throughput manner to enable biological experimentation. CisSERS was developed as a standalone open source tool to analyze sequence datasets and provide biologists with individual or comparative genome organization information in terms of presence and frequency of patterns or motifs such as restriction enzymes. Predicted agarose gel visualization of the custom analyses results was also integrated to enhance the usefulness of the software. CisSERS offers several novel functionalities, such as handling of large and multiple datasets in parallel, multiple restriction enzyme site detection and custom motif detection features, which are seamlessly integrated with real time agarose gel visualization. Using a simple fasta-formatted file as input, CisSERS utilizes the REBASE enzyme database. Results from CisSERS enable the user to make decisions for designing genotyping by sequencing experiments, reduced representation sequencing, 3'UTR sequencing, and cleaved amplified polymorphic sequence (CAPS) molecular markers for large sample sets. CisSERS is a java based graphical user interface built around a perl backbone. Several of the applications of CisSERS including CAPS molecular marker development were successfully validated using wet-lab experimentation. Here, we present the tool CisSERS and results from in-silico and corresponding wet-lab analyses demonstrating that CisSERS is a technology platform solution that facilitates efficient data utilization in genomics and genetics studies. PMID:27071032

  5. Promoting certification: the chapter's role.

    PubMed

    Staul, Luann

    2011-01-01

    The mission of the American Association of Critical-Care Nurses focuses on providing nurses with expert knowledge to promote delivery of excellent, safe, quality care to acutely and critically ill patients and their families. Chapters consist of professional leaders in a community who carry on the mission work of the American Association of Critical-Care Nurses at the local level. Chapters can emphasize the value of certification and continuing education, because they offer a wide spectrum of opportunities to meet the learning and developmental needs of nurses as they advance in their professional careers. This article will highlight strategies that can be implemented by local chapters to facilitate and promote certification.

  6. Cis-interactions between Notch and its ligands block ligand-independent Notch activity

    PubMed Central

    Palmer, William Hunt; Jia, Dongyu; Deng, Wu-Min

    2014-01-01

    The Notch pathway is integrated into numerous developmental processes and therefore is fine-tuned on many levels, including receptor production, endocytosis, and degradation. Notch is further characterized by a twofold relationship with its Delta-Serrate (DSL) ligands, as ligands from opposing cells (trans-ligands) activate Notch, whereas ligands expressed in the same cell (cis-ligands) inhibit signaling. We show that cells without both cis- and trans-ligands can mediate Notch-dependent developmental events during Drosophila oogenesis, indicating ligand-independent Notch activity occurs when the receptor is free of cis- and trans-ligands. Furthermore, cis-ligands can reduce Notch activity in endogenous and genetically induced situations of elevated trans-ligand-independent Notch signaling. We conclude that cis-expressed ligands exert their repressive effect on Notch signaling in cases of trans-ligand-independent activation, and propose a new function of cis-inhibition which buffers cells against accidental Notch activity. DOI: http://dx.doi.org/10.7554/eLife.04415.001 PMID:25486593

  7. Fragrance material review on cis-jasmone.

    PubMed

    Scognamiglio, J; Jones, L; Letizia, C S; Api, A M

    2012-10-01

    A toxicologic and dermatologic review of cis-jasmone when used as a fragrance ingredient is presented. cis-Jasmone is a member of the fragrance structural group ketones cyclopentanones and cyclopentenones. The common characteristic structural element of the group members is a cyclopentanone or cyclopentenone ring with a straight or branched chain alkane or alkene substituent. This review contains a detailed summary of all available toxicology and dermatology papers that are related to this individual fragrance ingredient and is not intended as a stand-alone document. Available data for cis-jasmone were evaluated then summarized and includes physical properties, acute toxicity, skin irritation, mucous membrane (eye) irritation, skin sensitization, phototoxicity, photoallergy, and genotoxicity data. A safety assessment of the entire ketones cyclopentanones and cyclopentenones will be published simultaneously with this document; please refer to Belsito et al. (2012) for an overall assessment of the safe use of this material and all ketones cyclopentanones and cyclopentenones in fragrances.

  8. Advances in the CIS research at NREL

    SciTech Connect

    Ramanathan, K.; Bhattacharya, R.N.; Granata, J.; Webb, J.; Niles, D.; Contreras, M.A.; Wiesner, H.; Hasoon, F.S.; Noufi, R.

    1997-12-31

    This paper summarizes the research of the CIS Team at NREL in three major areas: absorber deposition; understanding the role of chemical bath deposited (CBD) CdS in CIS junctions; and in the development of devices without CdS. Low cost, scaleable processes chosen for absorber fabrication include sputtering, electrodeposition (ED), and close spaced sublimation (CSS). The interaction between the CBD and the CIS has been investigated and the results show that Cd might be instrumental in shaping the interface. The authors have also developed a process to fabricate a 13.5% efficiency ZnO/CuInGaSe{sub 2} device without CdS or other buffer layers.

  9. 1H NMR titration and quantum calculation for the inclusion complexes of cis-cyclooctene, cis, cis-1, 3-cyclooctadiene and cis, cis-1, 5-cyclooctadiene with β-cyclodextrin

    NASA Astrophysics Data System (ADS)

    Yujuan, Cao; Runhua, Lu

    2009-08-01

    The inclusion behavior of cis-cyclooctene, cis, cis-1, 3-cyclooctadiene and cis, cis-1, 5-cyclooctadiene with β-cyclodextrin (β-CD) was studied by using 1H NMR method in D 2O/CD 3OD solution and PM3 quantum-chemical simulation in vacuum. The experimental results indicate that each guest molecule penetrates deeply into β-CD cavity and forms equimolecular inclusion complex with the host. The association constants of the complexes were determined by non-linear least-square method on the bases of the conversion-dependent chemical shift of two protons of the host molecule. The inclusion process and the most probable structure of the inclusion complexes were simulated using PM3 energy scanning and optimization. The trend of stability of the three inclusion complexes deduced from their calculated stabilization energies agrees well with the order of their association constants obtained from NMR experiments.

  10. 1H NMR titration and quantum calculation for the inclusion complexes of cis-cyclooctene, cis, cis-1, 3-cyclooctadiene and cis, cis-1, 5-cyclooctadiene with beta-cyclodextrin.

    PubMed

    Yujuan, Cao; Runhua, Lu

    2009-08-15

    The inclusion behavior of cis-cyclooctene, cis, cis-1, 3-cyclooctadiene and cis, cis-1, 5-cyclooctadiene with beta-cyclodextrin (beta-CD) was studied by using (1)H NMR method in D(2)O/CD(3)OD solution and PM3 quantum-chemical simulation in vacuum. The experimental results indicate that each guest molecule penetrates deeply into beta-CD cavity and forms equimolecular inclusion complex with the host. The association constants of the complexes were determined by non-linear least-square method on the bases of the conversion-dependent chemical shift of two protons of the host molecule. The inclusion process and the most probable structure of the inclusion complexes were simulated using PM3 energy scanning and optimization. The trend of stability of the three inclusion complexes deduced from their calculated stabilization energies agrees well with the order of their association constants obtained from NMR experiments.

  11. Methane Hydrates: Chapter 8

    USGS Publications Warehouse

    Boswell, Ray; Yamamoto, Koji; Lee, Sung-Rock; Collett, Timothy S.; Kumar, Pushpendra; Dallimore, Scott

    2008-01-01

    Gas hydrate is a solid, naturally occurring substance consisting predominantly of methane gas and water. Recent scientific drilling programs in Japan, Canada, the United States, Korea and India have demonstrated that gas hydrate occurs broadly and in a variety of forms in shallow sediments of the outer continental shelves and in Arctic regions. Field, laboratory and numerical modelling studies conducted to date indicate that gas can be extracted from gas hydrates with existing production technologies, particularly for those deposits in which the gas hydrate exists as pore-filling grains at high saturation in sand-rich reservoirs. A series of regional resource assessments indicate that substantial volumes of gas hydrate likely exist in sand-rich deposits. Recent field programs in Japan, Canada and in the United States have demonstrated the technical viability of methane extraction from gas-hydrate-bearing sand reservoirs and have investigated a range of potential production scenarios. At present, basic reservoir depressurisation shows the greatest promise and can be conducted using primarily standard industry equipment and procedures. Depressurisation is expected to be the foundation of future production systems; additional processes, such as thermal stimulation, mechanical stimulation and chemical injection, will likely also be integrated as dictated by local geological and other conditions. An innovative carbon dioxide and methane swapping technology is also being studied as a method to produce gas from select gas hydrate deposits. In addition, substantial additional volumes of gas hydrate have been found in dense arrays of grain-displacing veins and nodules in fine-grained, clay-dominated sediments; however, to date, no field tests, and very limited numerical modelling, have been conducted with regard to the production potential of such accumulations. Work remains to further refine: (1) the marine resource volumes within potential accumulations that can be

  12. Cis regius, a new species of Cis Latreille (Coleoptera: Ciidae) from Southern Africa.

    PubMed

    Orsetti, Artur; Lopes-Andrade, Cristiano

    2016-01-01

    Cis Latreille is the most diverse genus of Ciidae with 350 species and a worldwide distribution (Oliveira et al. 2013). It houses more than a half of the described ciid species, but the available phylogenetic analyses based on molecular data suggest that Cis is polyphyletic (Buder et al. 2008; Lopes-Andrade & Grebennikov 2015). Currently, there is no thoroughly accepted subgeneric classification for Cis and parts of the species are organized into artificial species-groups (Lawrence 1971; Lopes-Andrade et al. 2003; Lopes-Andrade 2008; Oliveira et al. 2013). PMID:27470794

  13. Cis-acting determinants of paramutation.

    PubMed

    Hövel, Iris; Pearson, Nigel A; Stam, Maike

    2015-08-01

    Paramutation is an epigenetic phenomenon whereby in trans communication between homologous sequences leads to meiotically heritable epigenetic changes at one of the alleles. Cis-acting determinants of paramutation are DNA sequences and associated epigenetic modifications that are required for paramutation. Here, we review how characteristics of the underlying DNA sequences determine whether paramutation can occur and how they affect the behavior displayed by the various paramutation phenomena. Paramutation is strongly associated with repeated sequences, especially tandemly repeated sequences. Cis-acting determinants consisting of repeated sequences are consistent with the involvement of RNA-directed DNA methylation (RdDM) in plants and the PIWI-interacting RNA (piRNA) pathway in animals. In the RdDM-based model, siRNAs produced by paramutagenic loci would reinforce the silenced state of paramutagenic loci in cis and initiate transcriptional silencing of paramutable loci in trans. In this review, we discuss how sequence characteristics and epigenetic modifications of cis-acting sequences can trigger the recruitment of silencing machineries. PMID:26321497

  14. Cis-acting determinants of paramutation.

    PubMed

    Hövel, Iris; Pearson, Nigel A; Stam, Maike

    2015-08-01

    Paramutation is an epigenetic phenomenon whereby in trans communication between homologous sequences leads to meiotically heritable epigenetic changes at one of the alleles. Cis-acting determinants of paramutation are DNA sequences and associated epigenetic modifications that are required for paramutation. Here, we review how characteristics of the underlying DNA sequences determine whether paramutation can occur and how they affect the behavior displayed by the various paramutation phenomena. Paramutation is strongly associated with repeated sequences, especially tandemly repeated sequences. Cis-acting determinants consisting of repeated sequences are consistent with the involvement of RNA-directed DNA methylation (RdDM) in plants and the PIWI-interacting RNA (piRNA) pathway in animals. In the RdDM-based model, siRNAs produced by paramutagenic loci would reinforce the silenced state of paramutagenic loci in cis and initiate transcriptional silencing of paramutable loci in trans. In this review, we discuss how sequence characteristics and epigenetic modifications of cis-acting sequences can trigger the recruitment of silencing machineries.

  15. Chapter A7. Biological Indicators

    USGS Publications Warehouse

    Myers, Donna N.; Wilde, Franceska D.

    2003-01-01

    The National Field Manual for the Collection of Water-Quality Data (National Field Manual) provides guidelines and standard procedures for U.S. Geological Survey (USGS) personnel who collect data used to assess the quality of the Nation's surface-water and ground-water resources. This chapter of the manual includes procedures for the (1) determination of biochemical oxygen demand using a 5-day bioassay test; (2) collection, identification, and enumeration of fecal indicator bacteria; (3) collection of samples and information on two laboratory methods for fecal indicator viruses (coliphages); and (4) collection of samples for protozoan pathogens. Each chapter of the National Field Manual is published separately and revised periodically. Newly published and revised chapters are posted on the World Wide Web on the USGS page 'National Field Manual for the Collection of Water-Quality Data.' The URL for this page is http://pubs.water.usgs.gov/twri9A/ (accessed November 25, 2003).

  16. "Unusually Successful": Pittsfield Chapter 1.

    ERIC Educational Resources Information Center

    Shiminski, James A.

    The United States Education Department recognizes projects that effectively meet the special needs of educationally deprived students. In 1992, the Pittsfield, Massachusetts, Chapter 1 preschool program earned national validation as an "unusually successful" compensatory education program. The program has served as a statewide model, and has…

  17. Sphingomyelin is synthesized in the cis Golgi.

    PubMed

    Jeckel, D; Karrenbauer, A; Birk, R; Schmidt, R R; Wieland, F

    1990-02-12

    We have employed in vitro a truncated ceramide analogue with 8 carbon atoms in the sphingosine and the fatty acyl residue, each, to investigate the activity of various membrane fractions to synthesize truncated sphingomyelin. This shortened ceramide readily diffuses through membranes and therefore can easily find access to the lumina of intact organelles. Sphingomyelin synthase activity resides in the Golgi apparatus, and after sucrose density gradient centrifugation of Golgi-enriched fractions sphingomyelin synthesis follows a cis Golgi marker enzyme. PMID:2155131

  18. PDSS/IMC CIS user's guide

    NASA Technical Reports Server (NTRS)

    1984-01-01

    The Spacelab Payload Development Support System PDSS Image Motion Compensator (IMC) computer interface simulation (CIS) user's manual is given. The software provides a real time interface simulation for the following IMC subsystems: the Dry Rotor Reference Unit, the Advanced Star/Target Reference Optical sensor, the Ultra Violet imaging telescope, the Wisconson Ultraviolet Photopolarimetry Experiment, the Cruciform Power distributor, and the Spacelab Experiment Computer Operating System.

  19. Venus 3 Book: Chapter 1

    NASA Astrophysics Data System (ADS)

    Taylor, F.; Svedhem, H.; Head, J.

    2014-04-01

    This will be the first chapter in the planned 'Venus 3' book, which will present the latest knowledge about all aspects of the planet Venus. Chapter 1 will include: 1. Brief history of Venus observations, from telescopic studies up to and including early space missions (Venera, Mariner) 2. Overview of key results from more recent groundbased observations and space missions, including Pioneer Venus, the later Veneras, Vega, Magellan, Akatsuki and Venus Express 3. Summary of current knowledge, in three main sections: a. Surface and interior b. Atmosphere and climate c. Thermosphere, exosphere and magnetosphere 4. Outstanding scientific questions remaining, and future mission concepts providing background, introduction and an overview to the rest of the book.

  20. Target Specific Tactics in Olefin Metathesis: Synthetic Approach to cis-syn-cis-Triquinanes and -Propellanes.

    PubMed

    Kotha, Sambasivarao; Aswar, Vikas R

    2016-04-15

    A concise and simple synthetic approach to cis-syn-cis-triquinanes and -propellanes has been demonstrated via olefin metathesis starting with exo-nadic anhydride. This approach involves a ring-opening and ring-closing metathesis sequence of norbornene derivatives using Grubb's catalyst. Early-stage diallylation of norbornene derivatives is demonstrated followed by ring-closing metathesis that delivers propellanes exclusively. Surprisingly, ring-opening metathesis, late-stage diallylation, followed by ring-closing metathesis delivers triquinane as well as propellane derivatives.

  1. Target Specific Tactics in Olefin Metathesis: Synthetic Approach to cis-syn-cis-Triquinanes and -Propellanes.

    PubMed

    Kotha, Sambasivarao; Aswar, Vikas R

    2016-04-15

    A concise and simple synthetic approach to cis-syn-cis-triquinanes and -propellanes has been demonstrated via olefin metathesis starting with exo-nadic anhydride. This approach involves a ring-opening and ring-closing metathesis sequence of norbornene derivatives using Grubb's catalyst. Early-stage diallylation of norbornene derivatives is demonstrated followed by ring-closing metathesis that delivers propellanes exclusively. Surprisingly, ring-opening metathesis, late-stage diallylation, followed by ring-closing metathesis delivers triquinane as well as propellane derivatives. PMID:27050839

  2. Phonons of the cis-polyacetylene chain

    NASA Astrophysics Data System (ADS)

    Faulques, Eric; Buisson, Jean-Pierre; Lefrant, Serge

    1995-12-01

    An investigation of the in-plane phonons of the cis-polyacetylene chain (CH)x and isotopic analogs (CD)x and (13CH)x is presented on the basis of a Fourier's dynamical D-matrix formalism. The conjugation is found to be similar to that of the trans-polyacetylene chain. Phonon dispersions have been calculated and follow the shapes predicted by Božović. Finally, the most interesting result is that phonon density of states exhibits van Hove singularities whose energies are close to those determined experimentally with incoherent inelastic neutron scattering.

  3. Environmental testing of CIS based modules

    SciTech Connect

    Willett, D.

    1995-11-01

    This report describes environmental testing of Siemen`s CIS modules. Charts and diagrams are presented on data concerning: temporary power loss of laminated mini-modules; the 50 thermal cycle test; the 10 humidity freeze cycle test; results after 1000 hours of exposure to damp heat; and interconnect test structures in damp heat testing. It is concluded that moisture ingress causes permanent increases in the series resistance of modules, and that improved packaging is needed for better high humidity reliability. Also, dry dark heat caused temporary power losses which were recovered in sunlight.

  4. Objectives and Overview. Chapter 1

    NASA Technical Reports Server (NTRS)

    Lamar, John E.; Hummel, Dietrich

    2009-01-01

    The RTO Task Group AVT-113 "Understanding and Modeling Vortical Flows to Improve the Technology Readiness Level for Military Aircraft" was established in April 2003. Two facets of the group, "Cranked Arrow Wing Aerodynamic Project International (CAWAPI)" and "Vortex Flow Experiment-2 (VFE-2)", worked closely together. However, because of the different requirements of each part, the CAWAPI facet concluded its work earlier (December 2006) than the VFE-2 facet (December 2007). In this first chapter of the Final Report of the Task Group an overview on its work is given, and the objectives for the Task Group are described.

  5. Chapter 3. Public health resources

    PubMed Central

    1973-01-01

    The resource requirements of the public health services are discussed in terms of their three main components: manpower, physical resources, and finances in relation to population. The observational data from the Republic of Korea provide an illustration of the problems of resource availability and utilization, with special reference to tuberculosis control. A calculation of resource and population constraints and estimates of the basic inputs required by tuberculosis control technology are presented. Data on the 1965 level of Korean health resources are given in the Annex to this chapter. PMID:20604424

  6. Earthquake ground motion: Chapter 3

    USGS Publications Warehouse

    Luco, Nicolas; Valley, Michael; Crouse, C.B.

    2012-01-01

    Most of the effort in seismic design of buildings and other structures is focused on structural design. This chapter addresses another key aspect of the design process—characterization of earthquake ground motion. Section 3.1 describes the basis of the earthquake ground motion maps in the Provisions and in ASCE 7. Section 3.2 has examples for the determination of ground motion parameters and spectra for use in design. Section 3.3 discusses and provides an example for the selection and scaling of ground motion records for use in response history analysis.

  7. 31 CFR Appendixes to Chapter V - Note

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 31 Money and Finance: Treasury 3 2010-07-01 2010-07-01 false Note Appendixes to Chapter V Money... CONTROL, DEPARTMENT OF THE TREASURY Ch. V, Nt. Appendixes to Chapter V—Note Notes: The alphabetical lists... blocked vessel in the underlying transaction. See § 501.604(b)(1) of this chapter. Financial...

  8. cis-Cinnamic acid selective suppressors distinct from auxin inhibitors.

    PubMed

    Okuda, Katsuhiro; Nishikawa, Keisuke; Fukuda, Hiroshi; Fujii, Yoshiharu; Shindo, Mitsuru

    2014-01-01

    The activity of cis-cinnamic acid (cis-CA), one of the allelochemicals, in plants is very similar to that of indole-3-acetic acid (IAA), a natural auxin, and thus cis-CA has long been believed to be an analog of auxin. We have reported some structure-activity relationships studies by synthesizing over 250 cis-CA derivatives and estimating their inhibitory activities on root growth inhibition in lettuce. In this study, the compounds that showed low- or no-activity on root growth inhibition were recruited as candidates suppressors against cis-CA and/or auxin and tested for their activity. In the presence of cis-CA, lettuce root growth was inhibited; however, the addition of some cis-CA derivatives restored control-level root growth. Four compounds, (Z)-3-(4-isopropylphenyl)acrylic acid, (Z)-3-(3-butoxyphenyl)acrylic acid, (Z)-3-[3-(pentyloxy)phenyl]acrylic acid, and (Z)-3-(naphthalen-1-yl)acrylic acid were selected as candidates for a cis-CA selective suppressor they allowed the recovery of root growth from inhibition by cis-CA treatment without any effects on the IAA-induced effect or elongating activity by themselves. Three candidates significantly ameliorated the root shortening by the potent inhibitor derived from cis-CA. In brief, we have found some cis-CA selective suppressors which have never been reported from inactive cis-CA derivatives for root growth inhibition. cis-CA selective suppressors will play an important role in elucidating the mechanism of plant growth regulation.

  9. Strand-specific RNA-seq reveals widespread occurrence of novel cis-natural antisense transcripts in rice

    PubMed Central

    2012-01-01

    Background Cis-natural antisense transcripts (cis-NATs) are RNAs transcribed from the antisense strand of a gene locus, and are complementary to the RNA transcribed from the sense strand. Common techniques including microarray approach and analysis of transcriptome databases are the major ways to globally identify cis-NATs in various eukaryotic organisms. Genome-wide in silico analysis has identified a large number of cis-NATs that may generate endogenous short interfering RNAs (nat-siRNAs), which participate in important biogenesis mechanisms for transcriptional and post-transcriptional regulation in rice. However, the transcriptomes are yet to be deeply sequenced to comprehensively investigate cis-NATs. Results We applied high-throughput strand-specific complementary DNA sequencing technology (ssRNA-seq) to deeply sequence mRNA for assessing sense and antisense transcripts that were derived under salt, drought and cold stresses, and normal conditions, in the model plant rice (Oryza sativa). Combined with RAP-DB genome annotation (the Rice Annotation Project Database build-5 data set), 76,013 transcripts corresponding to 45,844 unique gene loci were assembled, in which 4873 gene loci were newly identified. Of 3819 putative rice cis-NATs, 2292 were detected as expressed and giving rise to small RNAs from their overlapping regions through integrated analysis of ssRNA-seq data and small RNA data. Among them, 503 cis-NATs seemed to be associated with specific conditions. The deep sequence data from isolated epidermal cells of rice seedlings further showed that 54.0% of cis-NATs were expressed simultaneously in a population of homogenous cells. Nearly 9.7% of rice transcripts were involved in one-to-one or many-to-many cis-NATs formation. Furthermore, only 17.4-34.7% of 223 many-to-many cis-NAT groups were all expressed and generated nat-siRNAs, indicating that only some cis-NAT groups may be involved in complex regulatory networks. Conclusions Our study profiles an

  10. Teaching Integrity

    ERIC Educational Resources Information Center

    Saunders, Sue; Butts, Jennifer Lease

    2011-01-01

    Integrity is one of those essential yet highly ambiguous concepts. For the purpose of this chapter, integrity is defined as that combination of both attributes and actions that makes entities appear to be whole and ethical, as well as consistent. Like the concepts of leadership or wisdom or community or collaboration, integrity is a key element of…

  11. The twilight zone of cis element alignments.

    PubMed

    Sebastian, Alvaro; Contreras-Moreira, Bruno

    2013-02-01

    Sequence alignment of proteins and nucleic acids is a routine task in bioinformatics. Although the comparison of complete peptides, genes or genomes can be undertaken with a great variety of tools, the alignment of short DNA sequences and motifs entails pitfalls that have not been fully addressed yet. Here we confront the structural superposition of transcription factors with the sequence alignment of their recognized cis elements. Our goals are (i) to test TFcompare (http://floresta.eead.csic.es/tfcompare), a structural alignment method for protein-DNA complexes; (ii) to benchmark the pairwise alignment of regulatory elements; (iii) to define the confidence limits and the twilight zone of such alignments and (iv) to evaluate the relevance of these thresholds with elements obtained experimentally. We find that the structure of cis elements and protein-DNA interfaces is significantly more conserved than their sequence and measures how this correlates with alignment errors when only sequence information is considered. Our results confirm that DNA motifs in the form of matrices produce better alignments than individual sequences. Finally, we report that empirical and theoretically derived twilight thresholds are useful for estimating the natural plasticity of regulatory sequences, and hence for filtering out unreliable alignments.

  12. A cis-regulatory module activating transcription in the suspensor contains five cis-regulatory elements.

    PubMed

    Henry, Kelli F; Kawashima, Tomokazu; Goldberg, Robert B

    2015-06-01

    Little is known about the molecular mechanisms by which the embryo proper and suspensor of plant embryos activate specific gene sets shortly after fertilization. We analyzed the upstream region of the Scarlet Runner Bean (Phaseolus coccineus) G564 gene in order to understand how genes are activated specifically in the suspensor during early embryo development. Previously, we showed that a 54-bp fragment of the G564 upstream region is sufficient for suspensor transcription and contains at least three required cis-regulatory sequences, including the 10-bp motif (5'-GAAAAGCGAA-3'), the 10 bp-like motif (5'-GAAAAACGAA-3'), and Region 2 motif (partial sequence 5'-TTGGT-3'). Here, we use site-directed mutagenesis experiments in transgenic tobacco globular-stage embryos to identify two additional cis-regulatory elements within the 54-bp cis-regulatory module that are required for G564 suspensor transcription: the Fifth motif (5'-GAGTTA-3') and a third 10-bp-related sequence (5'-GAAAACCACA-3'). Further deletion of the 54-bp fragment revealed that a 47-bp fragment containing the five motifs (the 10-bp, 10-bp-like, 10-bp-related, Region 2 and Fifth motifs) is sufficient for suspensor transcription, and represents a cis-regulatory module. A consensus sequence for each type of motif was determined by comparing motif sequences shown to activate suspensor transcription. Phylogenetic analyses suggest that the regulation of G564 is evolutionarily conserved. A homologous cis-regulatory module was found upstream of the G564 ortholog in the Common Bean (Phaseolus vulgaris), indicating that the regulation of G564 is evolutionarily conserved in closely related bean species.

  13. Chapter 1 and Chapter 1 Migrant. Evaluation Findings, 1990-91. Executive Summary.

    ERIC Educational Resources Information Center

    Christner, Catherine; And Others

    This report describes an evaluation of the Austin (Texas) Independent School District's (AISD) Chapter 1 and Chapter 1 Migrant programs. Chapter 1 is a federally funded compensatory educational program that provided funding in 1990-91 to 25 AISD elementary schools with high concentrations of low-income students. Chapter 1 Migrant is also a…

  14. Secondary School Mathematics, Chapter 21, Rigid Motions and Vectors, Chapter 22, Computer and Programs. Teacher's Commentary.

    ERIC Educational Resources Information Center

    Stanford Univ., CA. School Mathematics Study Group.

    The teacher's guide for the eleventh unit in this SMSG series covers the chapter on rigid motions and vectors and the chapter on computers and programs. The overall purpose for each of the chapters is described, the prerequisite knowledge needed by students is specified, the mathematical development of each chapter is detailed, behavioral…

  15. The Role of cis Regulatory Evolution in Maize Domestication

    PubMed Central

    Lemmon, Zachary H.; Bukowski, Robert; Sun, Qi; Doebley, John F.

    2014-01-01

    Gene expression differences between divergent lineages caused by modification of cis regulatory elements are thought to be important in evolution. We assayed genome-wide cis and trans regulatory differences between maize and its wild progenitor, teosinte, using deep RNA sequencing in F1 hybrid and parent inbred lines for three tissue types (ear, leaf and stem). Pervasive regulatory variation was observed with approximately 70% of ∼17,000 genes showing evidence of regulatory divergence between maize and teosinte. However, many fewer genes (1,079 genes) show consistent cis differences with all sampled maize and teosinte lines. For ∼70% of these 1,079 genes, the cis differences are specific to a single tissue. The number of genes with cis regulatory differences is greatest for ear tissue, which underwent a drastic transformation in form during domestication. As expected from the domestication bottleneck, maize possesses less cis regulatory variation than teosinte with this deficit greatest for genes showing maize-teosinte cis regulatory divergence, suggesting selection on cis regulatory differences during domestication. Consistent with selection on cis regulatory elements, genes with cis effects correlated strongly with genes under positive selection during maize domestication and improvement, while genes with trans regulatory effects did not. We observed a directional bias such that genes with cis differences showed higher expression of the maize allele more often than the teosinte allele, suggesting domestication favored up-regulation of gene expression. Finally, this work documents the cis and trans regulatory changes between maize and teosinte in over 17,000 genes for three tissues. PMID:25375861

  16. The role of cis regulatory evolution in maize domestication.

    PubMed

    Lemmon, Zachary H; Bukowski, Robert; Sun, Qi; Doebley, John F

    2014-11-01

    Gene expression differences between divergent lineages caused by modification of cis regulatory elements are thought to be important in evolution. We assayed genome-wide cis and trans regulatory differences between maize and its wild progenitor, teosinte, using deep RNA sequencing in F1 hybrid and parent inbred lines for three tissue types (ear, leaf and stem). Pervasive regulatory variation was observed with approximately 70% of ∼17,000 genes showing evidence of regulatory divergence between maize and teosinte. However, many fewer genes (1,079 genes) show consistent cis differences with all sampled maize and teosinte lines. For ∼70% of these 1,079 genes, the cis differences are specific to a single tissue. The number of genes with cis regulatory differences is greatest for ear tissue, which underwent a drastic transformation in form during domestication. As expected from the domestication bottleneck, maize possesses less cis regulatory variation than teosinte with this deficit greatest for genes showing maize-teosinte cis regulatory divergence, suggesting selection on cis regulatory differences during domestication. Consistent with selection on cis regulatory elements, genes with cis effects correlated strongly with genes under positive selection during maize domestication and improvement, while genes with trans regulatory effects did not. We observed a directional bias such that genes with cis differences showed higher expression of the maize allele more often than the teosinte allele, suggesting domestication favored up-regulation of gene expression. Finally, this work documents the cis and trans regulatory changes between maize and teosinte in over 17,000 genes for three tissues.

  17. Crystal Structure and the Reaction Mechanism of cis-prenyltransferase

    NASA Astrophysics Data System (ADS)

    Fujihashi, Masahiro

    Over 23,000 isoprenoid compounds have been identified so far. They are known to play various important roles in cellular machinery, and all of them are synthesized through prenyldiphosphate compounds. These compounds are sub-classified into two families, cis- and trans-prenyldiphosphates, based on their geometric isomerism. Each isomer is synthesized by cis- and trans-prenyltransferases, respectively. This paper describes the structure and the reaction mechanism of a cis-prenyltransferase, undecaprenyl diphosphate synthase (UPP synthase), in comparison with those of trans-prenyltransferases. Despite the chemical similarity of the cis- and trans- reactions, the structures and the substrate recognition modes are quite different between each enzyme family.

  18. Beyond Chapter 4.7.

    PubMed

    Bandler, Lilon Gretl

    2015-12-01

    Chapter 4.7 of the National Statement on Ethical Conduct in Human Research refers specifically to Aboriginal and Torres Strait Islander Peoples. It lays out the points at which researchers working with Aboriginal and Torres Strait Islanders must consider their approach, and the engagement with individuals, communities or groups who are involved in or affected by their research. History, of Australia and of research involving Aboriginal and Torres Strait Islander Australians, has informed this approach. The response to that history has been a rational, institutionalised, systematic demand for a different perception of what should direct research and research processes to ensure engagement with and service to the community with whom the researchers wish to do the work. This paper considers whether these principles could inform the approach to other research work. PMID:27135116

  19. Chapter 14: Cancer Genome Analysis

    PubMed Central

    Vazquez, Miguel; de la Torre, Victor; Valencia, Alfonso

    2012-01-01

    Although there is great promise in the benefits to be obtained by analyzing cancer genomes, numerous challenges hinder different stages of the process, from the problem of sample preparation and the validation of the experimental techniques, to the interpretation of the results. This chapter specifically focuses on the technical issues associated with the bioinformatics analysis of cancer genome data. The main issues addressed are the use of database and software resources, the use of analysis workflows and the presentation of clinically relevant action items. We attempt to aid new developers in the field by describing the different stages of analysis and discussing current approaches, as well as by providing practical advice on how to access and use resources, and how to implement recommendations. Real cases from cancer genome projects are used as examples. PMID:23300415

  20. Defining groundwater age: Chapter 3

    USGS Publications Warehouse

    Torgersen, T.; Purtschert, R.; Phillips, F.M.; Plummer, L.N.; Sanford, W.E.; Suckow, A.

    2013-01-01

    This book investigates applications of selected chemical and isotopic substances that can be used to recognize and interpret age information pertaining to ‘old’ groundwater (defined as water that was recharged on a timescale from approximately 1000 to more than 1 000 000 a). However, as discussed below, only estimates of the ‘age’ of water extracted from wells can be inferred. These groundwater age estimates are interpreted from measured concentrations of chemical and isotopic substances in the groundwater. Even then, there are many complicating factors, as discussed in this book. In spite of these limitations, much can be learned about the physics of groundwater flow and about the temporal aspects of groundwater systems from age interpretations of measured concentrations of environmental tracers in groundwater systems. This chapter puts the concept of ‘age’ into context, including its meaning and interpretation, and attempts to provide a unifying usage for the rest of the book.

  1. Beyond Chapter 4.7.

    PubMed

    Bandler, Lilon Gretl

    2015-12-01

    Chapter 4.7 of the National Statement on Ethical Conduct in Human Research refers specifically to Aboriginal and Torres Strait Islander Peoples. It lays out the points at which researchers working with Aboriginal and Torres Strait Islanders must consider their approach, and the engagement with individuals, communities or groups who are involved in or affected by their research. History, of Australia and of research involving Aboriginal and Torres Strait Islander Australians, has informed this approach. The response to that history has been a rational, institutionalised, systematic demand for a different perception of what should direct research and research processes to ensure engagement with and service to the community with whom the researchers wish to do the work. This paper considers whether these principles could inform the approach to other research work.

  2. Conclusions and Recommendations. Chapter 37

    NASA Technical Reports Server (NTRS)

    Lamar, John E.; Hummel, Dietrich

    2009-01-01

    This chapter provides a brief wrap-up of the task group report and focuses on the overall conclusions and recommendations for future work for the CAWAPI and VFE-2 facets beyond the task group. The overall conclusion is that the Technology Readiness Level (TRL) of CFD solvers has been improved in predicting the flow-physics of vortex-dominated flows during the work of the task group, by having flight and wind-tunnel data available for comparison. Moreover, like all good scientific studies, this task group has identified flight conditions on the F-16XL airplane or wind-tunnel test conditions for a specific leading-edge radius on the 65 delta-wing model where the TRL still needs to be increased.

  3. A previously undescribed jasmonate compound in flowering Arabidopsis thaliana - The identification of cis-(+)-OPDA-Ile.

    PubMed

    Floková, Kristýna; Feussner, Kirstin; Herrfurth, Cornelia; Miersch, Otto; Mik, Václav; Tarkowská, Danuše; Strnad, Miroslav; Feussner, Ivo; Wasternack, Claus; Novák, Ondřej

    2016-02-01

    Jasmonates (JAs) are plant hormones that integrate external stress stimuli with physiological responses. (+)-7-iso-JA-L-Ile is the natural JA ligand of COI1, a component of a known JA receptor. The upstream JA biosynthetic precursor cis-(+)-12-oxo-phytodienoic acid (cis-(+)-OPDA) has been reported to act independently of COI1 as an essential signal in several stress-induced and developmental processes. Wound-induced increases in the endogenous levels of JA/JA-Ile are accompanied by two to tenfold increases in the concentration of OPDA, but its means of perception and metabolism are unknown. To screen for putative OPDA metabolites, vegetative tissues of flowering Arabidopsis thaliana were extracted with 25% aqueous methanol (v/v), purified by single-step reversed-phase polymer-based solid-phase extraction, and analyzed by high throughput mass spectrometry. This enabled the detection and quantitation of a low abundant OPDA analog of the biologically active (+)-7-iso-JA-L-Ile in plant tissue samples. Levels of the newly identified compound and the related phytohormones JA, JA-Ile and cis-(+)-OPDA were monitored in wounded leaves of flowering Arabidopsis lines (Col-0 and Ws) and compared to the levels observed in Arabidopsis mutants deficient in the biosynthesis of JA (dde2-2, opr3) and JA-Ile (jar1). The observed cis-(+)-OPDA-Ile levels varied widely, raising questions concerning its role in Arabidopsis stress responses.

  4. Evaluation of the genotoxicity of cis-bis(3-aminoflavone)dichloroplatinum(II) in comparison with cis-DDP.

    PubMed

    Kosmider, Beata; Wyszynska, Kalina; Janik-Spiechowicz, Ewa; Osiecka, Regina; Zyner, Elzbieta; Ochocki, Justyn; Ciesielska, Ewa; Wasowicz, Wojciech

    2004-03-14

    Short-term tests that detect genetic damage have provided information needed for evaluating carcinogenic risks of chemicals to man. The mutagenicity of cis-bis(3-aminoflavone)dichloroplatinum(II) (cis-[Pt(AF)2Cl2]) in comparison with cis-diamminedichloroplatinum(II) (cis-DDP) was evaluated in the standard plate-incorporation assay in four strains of Salmonella typhimurium: TA97a, TA98, TA100 and TA102, in experiments with and without metabolic activation. It was shown that cis-[Pt(AF)2Cl2] acts directly and is mutagenic for three strains of S. typhimurium: TA97a, TA98 and TA100. In comparison with cis-DDP this compound showed a weaker genotoxicity. Contrary to cis-DDP it has not shown toxic properties in the tester bacteria. The genotoxicity of both tested compounds was evaluated using chromosomal aberration, sister chromatid exchange and micronucleus assays, without and with metabolic activation, in human lymphocytes in vitro. The inhibitory effects of both compounds on mitotic activity, cell proliferation kinetics and nuclear division index were also compared. In all test systems applied, cis-[Pt(AF)2Cl2] was a less effective clastogen and a weaker inducer of both sister chromatid exchanges and micronuclei in comparison with cis-DDP, with and without metabolic activation. cis-[Pt(AF)2Cl2] has a direct mechanism of action and is less cytostatic and cytotoxic than the other compound. These results provide important data on the genotoxicity of cis-[Pt(AF)2Cl2] and indicate its beneficial properties as a potential anticancer drug, especially in comparison with cis-DDP. PMID:15036123

  5. Prepare dispersed CIS nano-scale particles and spray coating CIS absorber layers using nano-scale precursors

    NASA Astrophysics Data System (ADS)

    Liou, Jian-Chiun; Diao, Chien-Chen; Lin, Jing-Jenn; Chen, Yen-Lin; Yang, Cheng-Fu

    2014-01-01

    In this study, the Mo-electrode thin films were deposited by a two-stepped process, and the high-purity copper indium selenide-based powder (CuInSe2, CIS) was fabricated by hydrothermal process by Nanowin Technology Co. Ltd. From the X-ray pattern of the CIS precursor, the mainly crystalline phase was CIS, and the almost undetectable CuSe phase was observed. Because the CIS powder was aggregated into micro-scale particles and the average particle sizes were approximately 3 to 8 μm, the CIS power was ground into nano-scale particles, then the 6 wt.% CIS particles were dispersed into isopropyl alcohol to get the solution for spray coating method. Then, 0.1 ml CIS solution was sprayed on the 20 mm × 10 mm Mo/glass substrates, and the heat treatment for the nano-scale CIS solution under various parameters was carried out in a selenization furnace. The annealing temperature was set at 550°C, and the annealing time was changed from 5 to 30 min, without extra Se content was added in the furnace. The influences of annealing time on the densification, crystallization, resistivity ( ρ), hall mobility ( μ), and carrier concentration of the CIS absorber layers were well investigated in this study.

  6. Prepare dispersed CIS nano-scale particles and spray coating CIS absorber layers using nano-scale precursors

    PubMed Central

    2014-01-01

    In this study, the Mo-electrode thin films were deposited by a two-stepped process, and the high-purity copper indium selenide-based powder (CuInSe2, CIS) was fabricated by hydrothermal process by Nanowin Technology Co. Ltd. From the X-ray pattern of the CIS precursor, the mainly crystalline phase was CIS, and the almost undetectable CuSe phase was observed. Because the CIS powder was aggregated into micro-scale particles and the average particle sizes were approximately 3 to 8 μm, the CIS power was ground into nano-scale particles, then the 6 wt.% CIS particles were dispersed into isopropyl alcohol to get the solution for spray coating method. Then, 0.1 ml CIS solution was sprayed on the 20 mm × 10 mm Mo/glass substrates, and the heat treatment for the nano-scale CIS solution under various parameters was carried out in a selenization furnace. The annealing temperature was set at 550°C, and the annealing time was changed from 5 to 30 min, without extra Se content was added in the furnace. The influences of annealing time on the densification, crystallization, resistivity (ρ), hall mobility (μ), and carrier concentration of the CIS absorber layers were well investigated in this study. PMID:24380376

  7. PreCisIon: PREdiction of CIS-regulatory elements improved by gene's positION.

    PubMed

    Elati, Mohamed; Nicolle, Rémy; Junier, Ivan; Fernández, David; Fekih, Rim; Font, Julio; Képès, François

    2013-02-01

    Conventional approaches to predict transcriptional regulatory interactions usually rely on the definition of a shared motif sequence on the target genes of a transcription factor (TF). These efforts have been frustrated by the limited availability and accuracy of TF binding site motifs, usually represented as position-specific scoring matrices, which may match large numbers of sites and produce an unreliable list of target genes. To improve the prediction of binding sites, we propose to additionally use the unrelated knowledge of the genome layout. Indeed, it has been shown that co-regulated genes tend to be either neighbors or periodically spaced along the whole chromosome. This study demonstrates that respective gene positioning carries significant information. This novel type of information is combined with traditional sequence information by a machine learning algorithm called PreCisIon. To optimize this combination, PreCisIon builds a strong gene target classifier by adaptively combining weak classifiers based on either local binding sequence or global gene position. This strategy generically paves the way to the optimized incorporation of any future advances in gene target prediction based on local sequence, genome layout or on novel criteria. With the current state of the art, PreCisIon consistently improves methods based on sequence information only. This is shown by implementing a cross-validation analysis of the 20 major TFs from two phylogenetically remote model organisms. For Bacillus subtilis and Escherichia coli, respectively, PreCisIon achieves on average an area under the receiver operating characteristic curve of 70 and 60%, a sensitivity of 80 and 70% and a specificity of 60 and 56%. The newly predicted gene targets are demonstrated to be functionally consistent with previously known targets, as assessed by analysis of Gene Ontology enrichment or of the relevant literature and databases.

  8. Chapter 4: Geological Carbon Sequestration

    SciTech Connect

    Friedmann, J; Herzog, H

    2006-06-14

    Carbon sequestration is the long term isolation of carbon dioxide from the atmosphere through physical, chemical, biological, or engineered processes. The largest potential reservoirs for storing carbon are the deep oceans and geological reservoirs in the earth's upper crust. This chapter focuses on geological sequestration because it appears to be the most promising large-scale approach for the 2050 timeframe. It does not discuss ocean or terrestrial sequestration. In order to achieve substantial GHG reductions, geological storage needs to be deployed at a large scale. For example, 1 Gt C/yr (3.6 Gt CO{sub 2}/yr) abatement, requires carbon capture and storage (CCS) from 600 large pulverized coal plants ({approx}1000 MW each) or 3600 injection projects at the scale of Statoil's Sleipner project. At present, global carbon emissions from coal approximate 2.5 Gt C. However, given reasonable economic and demand growth projections in a business-as-usual context, global coal emissions could account for 9 Gt C. These volumes highlight the need to develop rapidly an understanding of typical crustal response to such large projects, and the magnitude of the effort prompts certain concerns regarding implementation, efficiency, and risk of the enterprise. The key questions of subsurface engineering and surface safety associated with carbon sequestration are: (1) Subsurface issues: (a) Is there enough capacity to store CO{sub 2} where needed? (b) Do we understand storage mechanisms well enough? (c) Could we establish a process to certify injection sites with our current level of understanding? (d) Once injected, can we monitor and verify the movement of subsurface CO{sub 2}? (2) Near surface issues: (a) How might the siting of new coal plants be influenced by the distribution of storage sites? (b) What is the probability of CO{sub 2} escaping from injection sites? What are the attendant risks? Can we detect leakage if it occurs? (3) Will surface leakage negate or reduce the

  9. Allergic contact dermatitis from octisalate and cis-3-hexenyl salicylate.

    PubMed

    Shaw, Daniel W

    2006-09-01

    A 62-year-old woman developed allergic contact dermatitis from sunscreens containing octisalate (octyl salicylate, 2-ethylhexyl salicylate) and from a fragrance containing cis-3-hexenyl salicylate. Results of patch testing and provocative use testing confirmed that she was allergic to octisalate. Provocative use testing indicated that she was also allergic to cis-3-hexenyl salicylate.

  10. U.S./CIS eye joint nuclear rocket venture

    NASA Astrophysics Data System (ADS)

    Clark, John S.; McIlwain, Melvin C.; Smetanikov, Vladimir; D'Yakov, Evgenij K.; Pavshuk, Vladimir A.

    1993-07-01

    An account is given of the significance for U.S. spacecraft development of a nuclear thermal rocket (NTR) reactor concept that has been developed in the (formerly Soviet) Commonwealth of Independent States (CIS). The CIS NTR reactor employs a hydrogen-cooled zirconium hydride moderator and ternary carbide fuels; the comparatively cool operating temperatures associated with this design promise overall robustness.

  11. U.S./CIS eye joint nuclear rocket venture

    NASA Technical Reports Server (NTRS)

    Clark, John S.; Mcilwain, Melvin C.; Smetanikov, Vladimir; D'Yakov, Evgenij K.; Pavshuk, Vladimir A.

    1993-01-01

    An account is given of the significance for U.S. spacecraft development of a nuclear thermal rocket (NTR) reactor concept that has been developed in the (formerly Soviet) Commonwealth of Independent States (CIS). The CIS NTR reactor employs a hydrogen-cooled zirconium hydride moderator and ternary carbide fuels; the comparatively cool operating temperatures associated with this design promise overall robustness.

  12. Sediment transport measurements: Chapter 5

    USGS Publications Warehouse

    Diplas, P.; Kuhnle, R.; Gray, J.; Glysson, D.; Edwards, T.; García, Marcelo H.

    2008-01-01

    Sediment erosion, transport, and deposition in fluvial systems are complex processes that are treated in detail in other sections of this book. Development of methods suitable for the collection of data that contribute to understanding these processes is a still-evolving science. Sediment and ancillary data are fundamental requirements for the proper management of river systems, including the design of structures, the determination of aspects of stream behavior, ascertaining the probable effect of removing an existing structure, estimation of bulk erosion, transport, and sediment delivery to the oceans, ascertaining the long-term usefulness of reservoirs and other public works, tracking movement of solid-phase contaminants, restoration of degraded or otherwise modified streams, and assistance in the calibration and validation of numerical models. This chapter presents techniques for measuring bed-material properties and suspended and bed-load discharges. Well-established and relatively recent, yet adequately tested, sampling equipment and methodologies, with designs that are guided by sound physical and statistical principles, are described. Where appropriate, the theory behind the development of the equipment and guidelines for its use are presented.

  13. Actively Controlled Components. Chapter 2

    NASA Technical Reports Server (NTRS)

    Horn, W.; Hiller, S.-J.; Pfoertner, H.; Schadow, K.; Rosenfeld, T.; Garg, S.

    2009-01-01

    Active Control can help to meet future engine requirements by an active improvement of the component characteristics. The concept is based on an intelligent control logic, which senses actual operating conditions and reacts with adequate actuator action. This approach can directly improve engine characteristics as performance, operability, durability and emissions on the one hand. On the other hand active control addresses the design constrains imposed by unsteady phenomena like inlet distortion, compressor surge, combustion instability, flow separations, vibration and noise, which only occur during exceptional operating conditions. The feasibility and effectiveness of active control technologies have been demonstrated in lab-scale tests. This chapter describes a broad range of promising applications for each engine component. Significant efforts in research and development remain to implement these technologies in engine rig and finally production engines and to demonstrate today s engine generation airworthiness, safety, reliability, and durability requirements. Active control applications are in particular limited by the gap between available and advanced sensors and actuators, which allow an operation in the harsh environment in an aero engine. The operating and performance requirements for actuators and sensors are outlined for each of the gas turbine sections from inlet to nozzle.

  14. Chapter 12: Human microbiome analysis.

    PubMed

    Morgan, Xochitl C; Huttenhower, Curtis

    2012-01-01

    Humans are essentially sterile during gestation, but during and after birth, every body surface, including the skin, mouth, and gut, becomes host to an enormous variety of microbes, bacterial, archaeal, fungal, and viral. Under normal circumstances, these microbes help us to digest our food and to maintain our immune systems, but dysfunction of the human microbiota has been linked to conditions ranging from inflammatory bowel disease to antibiotic-resistant infections. Modern high-throughput sequencing and bioinformatic tools provide a powerful means of understanding the contribution of the human microbiome to health and its potential as a target for therapeutic interventions. This chapter will first discuss the historical origins of microbiome studies and methods for determining the ecological diversity of a microbial community. Next, it will introduce shotgun sequencing technologies such as metagenomics and metatranscriptomics, the computational challenges and methods associated with these data, and how they enable microbiome analysis. Finally, it will conclude with examples of the functional genomics of the human microbiome and its influences upon health and disease.

  15. VUV thin films, chapter 7

    NASA Technical Reports Server (NTRS)

    Zukic, Muamer; Torr, Douglas G.

    1993-01-01

    The application of thin film technology to the vacuum ultraviolet (VUV) wavelength region from 120 nm to 230 nm has not been fully exploited in the past because of absorption effects which complicate the accurate determination of the optical functions of dielectric materials. The problem therefore reduces to that of determining the real and imaginary parts of a complex optical function, namely the frequency dependent refractive index n and extinction coefficient k. We discuss techniques for the inverse retrieval of n and k for dielectric materials at VUV wavelengths from measurements of their reflectance and transmittance. Suitable substrate and film materials are identified for application in the VUV. Such applications include coatings for the fabrication of narrow and broadband filters and beamsplitters. The availability of such devices open the VUV regime to high resolution photometry, interferometry and polarimetry both for space based and laboratory applications. This chapter deals with the optics of absorbing multilayers, the determination of the optical functions for several useful materials, and the design of VUV multilayer stacks as applied to the design of narrow and broadband reflection and transmission filters and beamsplitters. Experimental techniques are discussed briefly, and several examples of the optical functions derived for selected materials are presented.

  16. Chapter 12: Human Microbiome Analysis

    PubMed Central

    Morgan, Xochitl C.; Huttenhower, Curtis

    2012-01-01

    Humans are essentially sterile during gestation, but during and after birth, every body surface, including the skin, mouth, and gut, becomes host to an enormous variety of microbes, bacterial, archaeal, fungal, and viral. Under normal circumstances, these microbes help us to digest our food and to maintain our immune systems, but dysfunction of the human microbiota has been linked to conditions ranging from inflammatory bowel disease to antibiotic-resistant infections. Modern high-throughput sequencing and bioinformatic tools provide a powerful means of understanding the contribution of the human microbiome to health and its potential as a target for therapeutic interventions. This chapter will first discuss the historical origins of microbiome studies and methods for determining the ecological diversity of a microbial community. Next, it will introduce shotgun sequencing technologies such as metagenomics and metatranscriptomics, the computational challenges and methods associated with these data, and how they enable microbiome analysis. Finally, it will conclude with examples of the functional genomics of the human microbiome and its influences upon health and disease. PMID:23300406

  17. Evolution of cis-regulatory sequence and function in Diptera.

    PubMed

    Wittkopp, P J

    2006-09-01

    Cis-regulatory sequences direct patterns of gene expression essential for development and physiology. Evolutionary changes in these sequences contribute to phenotypic divergence. Despite their importance, cis-regulatory regions remain one of the most enigmatic features of the genome. Patterns of sequence evolution can be used to identify cis-regulatory elements, but the power of this approach depends upon the relationship between sequence and function. Comparative studies of gene regulation among Diptera reveal that divergent sequences can underlie conserved expression, and that expression differences can evolve despite largely similar sequences. This complex structure-function relationship is the primary impediment for computational identification and interpretation of cis-regulatory sequences. Biochemical characterization and in vivo assays of cis-regulatory sequences on a genomic-scale will relieve this barrier.

  18. Automated assembly of oligosaccharides containing multiple cis-glycosidic linkages

    NASA Astrophysics Data System (ADS)

    Hahm, Heung Sik; Hurevich, Mattan; Seeberger, Peter H.

    2016-09-01

    Automated glycan assembly (AGA) has advanced from a concept to a commercial technology that rapidly provides access to diverse oligosaccharide chains as long as 30-mers. To date, AGA was mainly employed to incorporate trans-glycosidic linkages, where C2 participating protecting groups ensure stereoselective couplings. Stereocontrol during the installation of cis-glycosidic linkages cannot rely on C2-participation and anomeric mixtures are typically formed. Here, we demonstrate that oligosaccharides containing multiple cis-glycosidic linkages can be prepared efficiently by AGA using monosaccharide building blocks equipped with remote participating protecting groups. The concept is illustrated by the automated syntheses of biologically relevant oligosaccharides bearing various cis-galactosidic and cis-glucosidic linkages. This work provides further proof that AGA facilitates the synthesis of complex oligosaccharides with multiple cis-linkages and other biologically important oligosaccharides.

  19. Automated assembly of oligosaccharides containing multiple cis-glycosidic linkages

    PubMed Central

    Hahm, Heung Sik; Hurevich, Mattan; Seeberger, Peter H

    2016-01-01

    Automated glycan assembly (AGA) has advanced from a concept to a commercial technology that rapidly provides access to diverse oligosaccharide chains as long as 30-mers. To date, AGA was mainly employed to incorporate trans-glycosidic linkages, where C2 participating protecting groups ensure stereoselective couplings. Stereocontrol during the installation of cis-glycosidic linkages cannot rely on C2-participation and anomeric mixtures are typically formed. Here, we demonstrate that oligosaccharides containing multiple cis-glycosidic linkages can be prepared efficiently by AGA using monosaccharide building blocks equipped with remote participating protecting groups. The concept is illustrated by the automated syntheses of biologically relevant oligosaccharides bearing various cis-galactosidic and cis-glucosidic linkages. This work provides further proof that AGA facilitates the synthesis of complex oligosaccharides with multiple cis-linkages and other biologically important oligosaccharides. PMID:27580973

  20. Automated assembly of oligosaccharides containing multiple cis-glycosidic linkages.

    PubMed

    Hahm, Heung Sik; Hurevich, Mattan; Seeberger, Peter H

    2016-01-01

    Automated glycan assembly (AGA) has advanced from a concept to a commercial technology that rapidly provides access to diverse oligosaccharide chains as long as 30-mers. To date, AGA was mainly employed to incorporate trans-glycosidic linkages, where C2 participating protecting groups ensure stereoselective couplings. Stereocontrol during the installation of cis-glycosidic linkages cannot rely on C2-participation and anomeric mixtures are typically formed. Here, we demonstrate that oligosaccharides containing multiple cis-glycosidic linkages can be prepared efficiently by AGA using monosaccharide building blocks equipped with remote participating protecting groups. The concept is illustrated by the automated syntheses of biologically relevant oligosaccharides bearing various cis-galactosidic and cis-glucosidic linkages. This work provides further proof that AGA facilitates the synthesis of complex oligosaccharides with multiple cis-linkages and other biologically important oligosaccharides. PMID:27580973

  1. Oxylipin Signaling: A Distinct Role for the Jasmonic Acid Precursor cis-(+)-12-Oxo-Phytodienoic Acid (cis-OPDA)

    PubMed Central

    Dave, Anuja; Graham, Ian A.

    2012-01-01

    Oxylipins are lipid-derived compounds, many of which act as signals in the plant response to biotic and abiotic stress. They include the phytohormone jasmonic acid (JA) and related jasmonate metabolites cis-(+)-12-oxo-phytodienoic acid (cis-OPDA), methyl jasmonate, and jasmonoyl-L-isoleucine (JA-Ile). Besides the defense response, jasmonates are involved in plant growth and development and regulate a range of processes including glandular trichome development, reproduction, root growth, and senescence. cis-OPDA is known to possess a signaling role distinct from JA-Ile. The non-enzymatically derived phytoprostanes are structurally similar to cis-OPDA and induce a common set of genes that are not responsive to JA in Arabidopsis thaliana. A novel role for cis-OPDA in seed germination regulation has recently been uncovered based on evidence from double mutants and feeding experiments showing that cis-OPDA interacts with abscisic acid (ABA), inhibits seed germination, and increases ABA INSENSITIVE5 (ABI5) protein abundance. Large amounts of cis-OPDA are esterified to galactolipids in A. thaliana and the resulting compounds, known as Arabidopsides, are thought to act as a rapidly available source of cis-OPDA. PMID:22645585

  2. Volcanism on Mars. Chapter 41

    NASA Technical Reports Server (NTRS)

    Zimbelman, J. R.; Garry, W. B.; Bleacher, J. E.; Crown, D. A.

    2015-01-01

    Spacecraft exploration has revealed abundant evidence that Mars possesses some of the most dramatic volcanic landforms found anywhere within the solar system. How did a planet half the size of Earth produce volcanoes like Olympus Mons, which is several times the size of the largest volcanoes on Earth? This question is an example of the kinds of issues currently being investigated as part of the space-age scientific endeavor called "comparative planetology." This chapter summarizes the basic information currently known about volcanism on Mars. The volcanoes on Mars appear to be broadly similar in overall morphology (although, often quite different in scale) to volcanic features on Earth, which suggests that Martian eruptive processes are not significantly different from the volcanic styles and processes on Earth. Martian volcanoes are found on terrains of different age, and Martian volcanic rocks are estimated to comprise more than 50% of the Martian surface. This is in contrast to volcanism on smaller bodies such as Earth's Moon, where volcanic activity was mainly confined to the first half of lunar history (see "Volcanism on the Moon"). Comparative planetology supports the concept that volcanism is the primary mechanism for a planetary body to get rid of its internal heat; smaller bodies tend to lose their internal heat more rapidly than larger bodies (although, Jupiter's moon Io appears to contradict this trend; Io's intense volcanic activity is powered by unique gravitational tidal forces within the Jovian system; see "Volcanism on Io"), so that volcanic activity on Mars would be expected to differ considerably from that found on Earth and the Moon.

  3. Comparative genomics-based identification and analysis of cis-regulatory elements.

    PubMed

    Ogino, Hajime; Ochi, Haruki; Uchiyama, Chihiro; Louie, Sarah; Grainger, Robert M

    2012-01-01

    Identification of cis-regulatory elements, such as enhancers and promoters, is very important not only for analysis of gene regulatory networks but also as a tool for targeted gene expression experiments. In this chapter, we introduce an easy but reliable approach to predict enhancers of a gene of interest by comparing mammalian and Xenopus genome sequences, and to examine their activity using a co-transgenesis technique in Xenopus embryos. Since the bioinformatics analysis utilizes publically available web tools, bench biologists can easily perform it without any need for special computing capability. The co-transgenesis assay, which directly uses polymerase chain reaction products, quickly screens for the activity of the candidate elements in a cloning-free manner.

  4. Fire as an ecosystem process: Chapter 3

    USGS Publications Warehouse

    Keeley, Jon E.; Safford, Hugh D.

    2016-01-01

    This long-anticipated reference and sourcebook for California’s remarkable ecological abundance provides an integrated assessment of each major ecosystem type—its distribution, structure, function, and management. A comprehensive synthesis of our knowledge about this biologically diverse state, Ecosystems of California covers the state from oceans to mountaintops using multiple lenses: past and present, flora and fauna, aquatic and terrestrial, natural and managed. Each chapter evaluates natural processes for a specific ecosystem, describes drivers of change, and discusses how that ecosystem may be altered in the future. This book also explores the drivers of California’s ecological patterns and the history of the state’s various ecosystems, outlining how the challenges of climate change and invasive species and opportunities for regulation and stewardship could potentially affect the state’s ecosystems. The text explicitly incorporates both human impacts and conservation and restoration efforts and shows how ecosystems support human well-being. Edited by two esteemed ecosystem ecologists and with overviews by leading experts on each ecosystem, this definitive work will be indispensable for natural resource management and conservation professionals as well as for undergraduate or graduate students of California’s environment and curious naturalists.

  5. Integrity in Transactional Leadership

    ERIC Educational Resources Information Center

    Miller, Thomas

    2011-01-01

    This chapter begins with a discussion of the impact of limited resources on the integrity of transactions between students and student affairs administrators. A framework and guiding principles for maintaining integrity are offered, and then some general principles for transactions with students are presented. Next, the chapter involves integrity…

  6. National ESEA Chapter 1 Schoolwide Projects Conference.

    ERIC Educational Resources Information Center

    Cleveland Public Schools, OH.

    This document is a collection of schoolwide compensatory education project plans for 22 elementary schools in the Cleveland (Ohio) Public Schools system, with funding provided by Chapter 1 of the Education Consolidation and Improvement Act. Chapter 1 project plans are included for the following schools: (1) Alfred A. Benesch; (2) Andrew J.…

  7. Chapter 6: Selenium Toxicity to Aquatic Organisms

    EPA Science Inventory

    This chapter addresses the characteristics and nature of organic selenium (Se) toxicity to aquatic organisms, based on the most current state of scientific knowledge. As such, the information contained in this chapter relates to the 'toxicity assessment' phase of aquatic ecologi...

  8. Comprehensively evaluating cis-regulatory variation in the human prostate transcriptome by using gene-level allele-specific expression.

    PubMed

    Larson, Nicholas B; McDonnell, Shannon; French, Amy J; Fogarty, Zach; Cheville, John; Middha, Sumit; Riska, Shaun; Baheti, Saurabh; Nair, Asha A; Wang, Liang; Schaid, Daniel J; Thibodeau, Stephen N

    2015-06-01

    The identification of cis-acting regulatory variation in primary tissues has the potential to elucidate the genetic basis of complex traits and further our understanding of transcriptomic diversity across cell types. Expression quantitative trait locus (eQTL) association analysis using RNA sequencing (RNA-seq) data can improve upon the detection of cis-acting regulatory variation by leveraging allele-specific expression (ASE) patterns in association analysis. Here, we present a comprehensive evaluation of cis-acting eQTLs by analyzing RNA-seq gene-expression data and genome-wide high-density genotypes from 471 samples of normal primary prostate tissue. Using statistical models that integrate ASE information, we identified extensive cis-eQTLs across the prostate transcriptome and found that approximately 70% of expressed genes corresponded to a significant eQTL at a gene-level false-discovery rate of 0.05. Overall, cis-eQTLs were heavily concentrated near the transcription start and stop sites of affected genes, and effects were negatively correlated with distance. We identified multiple instances of cis-acting co-regulation by using phased genotype data and discovered 233 SNPs as the most strongly associated eQTLs for more than one gene. We also noted significant enrichment (25/50, p = 2E-5) of previously reported prostate cancer risk SNPs in prostate eQTLs. Our results illustrate the benefit of assessing ASE data in cis-eQTL analyses by showing better reproducibility of prior eQTL findings than of eQTL mapping based on total expression alone. Altogether, our analysis provides extensive functional context of thousands of SNPs in prostate tissue, and these results will be of critical value in guiding studies examining disease of the human prostate.

  9. Effects of Cd{sup 2+} on cis-dimer structure of E-cadherin in living cells

    SciTech Connect

    Takeda, Hiroshi

    2014-02-21

    Highlights: • The effects of Cd on the dimer of cadherin in living cells was analyzed. • Cd induced cadherin dimer formation was not detected in living cell with low Ca. • Ca mediated structural cooperativity and allostery in the native cadherin. • Ca concentration-dependent competitive displacement of Cd from cadherin is proposed. - Abstract: E-cadherin, a calcium (Ca{sup 2+})-dependent cell–cell adhesion molecule, plays a key role in the maintenance of tissue integrity. We have previously demonstrated that E-cadherin functions in vivo as a cis-dimer through chemical cross-linking reagents. Ca{sup 2+} plays an important role in the cis-dimer formation of cadherin. However, the molecular mechanisms by which Ca{sup 2+} interacts with the binding sites that regulate cis-dimer structures have not been completely elucidated. As expected for a Ca{sup 2+} antagonist, cadmium (Cd{sup 2+}) disrupts cadherin function by displacing Ca{sup 2+} from its binding sites on the cadherin molecules. We used Cd{sup 2+} as a probe for investigating the role of Ca{sup 2+} in the dynamics of the E-cadherin extracellular region that involve cis-dimer formation and adhesion. While cell–cell adhesion assembly was completely disrupted in the presence of Cd{sup 2+}, the amount of cis-dimers of E-cadherin that formed at the cell surface was not affected. In our “Cd{sup 2+}-switch” experiments, we did not find that Cd{sup 2+}-induced E-cadherin cis-dimer formation in EL cells when they were incubated in low-Ca{sup 2+} medium. In the present study, we demonstrated for the first time the effects of Cd{sup 2+} on the cis-dimer structure of E-cadherin in living cells using a chemical cross-link analysis.

  10. Chapter 17: Estimating Net Savings: Common Practices

    SciTech Connect

    Violette, D. M.; Rathbun, P.

    2014-09-01

    This chapter focuses on the methods used to estimate net energy savings in evaluation, measurement, and verification (EM&V) studies for energy efficiency (EE) programs. The chapter provides a definition of net savings, which remains an unsettled topic both within the EE evaluation community and across the broader public policy evaluation community, particularly in the context of attribution of savings to particular program. The chapter differs from the measure-specific Uniform Methods Project (UMP) chapters in both its approach and work product. Unlike other UMP resources that provide recommended protocols for determining gross energy savings, this chapter describes and compares the current industry practices for determining net energy savings, but does not prescribe particular methods.

  11. 26 CFR 31.3503-1 - Tax under chapter 21 or 22 paid under wrong chapter.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 26 Internal Revenue 15 2010-04-01 2010-04-01 false Tax under chapter 21 or 22 paid under wrong chapter. 31.3503-1 Section 31.3503-1 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY... TAX AT SOURCE General Provisions Relating to Employment Taxes (Chapter 25, Internal Revenue Code...

  12. Multi-phase back contacts for CIS solar cells

    DOEpatents

    Rockett, A.A.; Yang, L.C.

    1995-12-19

    Multi-phase, single layer, non-interdiffusing M-Mo back contact metallized films, where M is selected from Cu, Ga, or mixtures thereof, for CIS cells are deposited by a sputtering process on suitable substrates, preferably glass or alumina, to prevent delamination of the CIS from the back contact layer. Typical CIS compositions include CuXSe{sub 2} where X is In or/and Ga. The multi-phase mixture is deposited on the substrate in a manner to provide a columnar microstructure, with micro-vein Cu or/and Ga regions which partially or fully vertically penetrate the entire back contact layer. The CIS semiconductor layer is then deposited by hybrid sputtering and evaporation process. The Cu/Ga-Mo deposition is controlled to produce the single layer two-phase columnar morphology with controllable Cu or Ga vein size less than about 0.01 microns in width. During the subsequent deposition of the CIS layer, the columnar Cu/Ga regions within the molybdenum of the Cu/Ga-Mo back layer tend to partially leach out, and are replaced by columns of CIS. Narrower Cu and/or Ga regions, and those with fewer inner connections between regions, leach out more slowly during the subsequent CIS deposition. This gives a good mechanical and electrical interlock of the CIS layer into the Cu/Ga-Mo back layer. Solar cells employing In-rich CIS semiconductors bonded to the multi-phase columnar microstructure back layer of this invention exhibit vastly improved photo-electrical conversion on the order of 17% greater than Mo alone, improved uniformity of output across the face of the cell, and greater Fill Factor. 15 figs.

  13. Multi-phase back contacts for CIS solar cells

    DOEpatents

    Rockett, Angus A.; Yang, Li-Chung

    1995-01-01

    Multi-phase, single layer, non-interdiffusing M-Mo back contact metallized films, where M is selected from Cu, Ga, or mixtures thereof, for CIS cells are deposited by a sputtering process on suitable substrates, preferably glass or alumina, to prevent delamination of the CIS from the back contact layer. Typical CIS compositions include CuXSe.sub.2 where X is In or/and Ga. The multi-phase mixture is deposited on the substrate in a manner to provide a columnar microstructure, with micro-vein Cu or/and Ga regions which partially or fully vertically penetrate the entire back contact layer. The CIS semiconductor layer is then deposited by hybrid sputtering and evaporation process. The Cu/Ga-Mo deposition is controlled to produce the single layer two-phase columnar morphology with controllable Cu or Ga vein size less than about 0.01 microns in width. During the subsequent deposition of the CIS layer, the columnar Cu/Ga regions within the molybdenum of the Cu/Ga-Mo back layer tend to partially leach out, and are replaced by columns of CIS. Narrower Cu and/or Ga regions, and those with fewer inner connections between regions, leach out more slowly during the subsequent CIS deposition. This gives a good mechanical and electrical interlock of the CIS layer into the Cu/Ga-Mo back layer. Solar cells employing In-rich CIS semiconductors bonded to the multi-phase columnar microstructure back layer of this invention exhibit vastly improved photo-electrical conversion on the order of 17% greater than Mo alone, improved uniformity of output across the face of the cell, and greater Fill Factor.

  14. Closeout of CRADA JSA 2012S004: Chapter 5, Integrated Control System, of the document of the ESS Conceptual Design Report, publicly available at https://europeanspallationsource.se/accelerator-documents

    SciTech Connect

    Satogata, Todd

    2013-04-22

    The integrated control system (ICS) is responsible for the whole ESS machine and facility: accelerator, target, neutron scattering instruments and conventional facilities. This unified approach keeps the costs of development, maintenance and support relatively low. ESS has selected a standardised, field-proven controls framework, the Experimental Physics and Industrial Control System (EPICS), which was originally developed jointly by Argonne and Los Alamos National Laboratories. Complementing this selection are best practices and experience from similar facilities regarding platform standardisation, control system development and device integration and commissioning. The components of ICS include the control system core, the control boxes, the BLED database management system, and the human machine interface. The control system core is a set of systems and tools that make it possible for the control system to provide required data, information and services to engineers, operators, physicists and the facility itself. The core components are the timing system that makes possible clock synchronisation across the facility, the machine protection system (MPS) and the personnel protection system (PPS) that prevent damage to the machine and personnel, and a set of control system services. Control boxes are servers that control a collection of equipment (for example a radio frequency cavity). The integrated control system will include many control boxes that can be assigned to one supplier, such as an internal team, a collaborating institute or a commercial vendor. This approach facilitates a clear division of responsibilities and makes integration much easier. A control box is composed of a standardised hardware platform, components, development tools and services. On the top level, it interfaces with the core control system components (timing, MPS, PPS) and with the human-machine interface. At the bottom, it interfaces with the equipment and parts of the facility through

  15. Two new species and nomenclatural changes in the Cis castaneus species group (Coleoptera, Ciidae).

    PubMed

    Królik, Roman

    2016-01-01

    Cis hanseni A. Strand, 1965 is a junior synonym of Cis matchanus Reitter, 1915 stat. nov. The lectotype for Cis matchanus Reitter, 1915 is designated and illustrated, together with its original data labels. Two new species-Cis lasoni sp. nov. and Cis lugowoji sp. nov. from the Talysh and Alborz Mts. (Azerbaijan, Iran)-are described. The body and terminalia of males are illustrated in detail. The definition of the Cis castaneus species group is discussed. PMID:27395144

  16. Competition in Notch Signaling with Cis Enriches Cell Fate Decisions

    PubMed Central

    Formosa-Jordan, Pau; Ibañes, Marta

    2014-01-01

    Notch signaling is involved in cell fate choices during the embryonic development of Metazoa. Commonly, Notch signaling arises from the binding of the Notch receptor to its ligands in adjacent cells driving cell-to-cell communication. Yet, cell-autonomous control of Notch signaling through both ligand-dependent and ligand-independent mechanisms is known to occur as well. Examples include Notch signaling arising in the absence of ligand binding, and cis-inhibition of Notch signaling by titration of the Notch receptor upon binding to its ligands within a single cell. Increasing experimental evidences support that the binding of the Notch receptor with its ligands within a cell (cis-interactions) can also trigger a cell-autonomous Notch signal (cis-signaling), whose potential effects on cell fate decisions and patterning remain poorly understood. To address this question, herein we mathematically and computationally investigate the cell states arising from the combination of cis-signaling with additional Notch signaling sources, which are either cell-autonomous or involve cell-to-cell communication. Our study shows that cis-signaling can switch from driving cis-activation to effectively perform cis-inhibition and identifies under which conditions this switch occurs. This switch relies on the competition between Notch signaling sources, which share the same receptor but differ in their signaling efficiency. We propose that the role of cis-interactions and their signaling on fine-grained patterning and cell fate decisions is dependent on whether they drive cis-inhibition or cis-activation, which could be controlled during development. Specifically, cis-inhibition and not cis-activation facilitates patterning and enriches it by modulating the ratio of cells in the high-ligand expression state, by enabling additional periodic patterns like stripes and by allowing localized patterning highly sensitive to the precursor state and cell-autonomous bistability. Our study

  17. i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly

    PubMed Central

    Imrichová, Hana; Hulselmans, Gert; Kalender Atak, Zeynep; Potier, Delphine; Aerts, Stein

    2015-01-01

    i-cisTarget is a web tool to predict regulators of a set of genomic regions, such as ChIP-seq peaks or co-regulated/similar enhancers. i-cisTarget can also be used to identify upstream regulators and their target enhancers starting from a set of co-expressed genes. Whereas the original version of i-cisTarget was focused on Drosophila data, the 2015 update also provides support for human and mouse data. i-cisTarget detects transcription factor motifs (position weight matrices) and experimental data tracks (e.g. from ENCODE, Roadmap Epigenomics) that are enriched in the input set of regions. As experimental data tracks we include transcription factor ChIP-seq data, histone modification ChIP-seq data and open chromatin data. The underlying processing method is based on a ranking-and-recovery procedure, allowing accurate determination of enrichment across heterogeneous datasets, while also discriminating direct from indirect target regions through a ‘leading edge’ analysis. We illustrate i-cisTarget on various Ewing sarcoma datasets to identify EWS-FLI1 targets starting from ChIP-seq, differential ATAC-seq, differential H3K27ac and differential gene expression data. Use of i-cisTarget is free and open to all, and there is no login requirement. Address: http://gbiomed.kuleuven.be/apps/lcb/i-cisTarget. PMID:25925574

  18. i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly.

    PubMed

    Imrichová, Hana; Hulselmans, Gert; Atak, Zeynep Kalender; Potier, Delphine; Aerts, Stein

    2015-07-01

    i-cisTarget is a web tool to predict regulators of a set of genomic regions, such as ChIP-seq peaks or co-regulated/similar enhancers. i-cisTarget can also be used to identify upstream regulators and their target enhancers starting from a set of co-expressed genes. Whereas the original version of i-cisTarget was focused on Drosophila data, the 2015 update also provides support for human and mouse data. i-cisTarget detects transcription factor motifs (position weight matrices) and experimental data tracks (e.g. from ENCODE, Roadmap Epigenomics) that are enriched in the input set of regions. As experimental data tracks we include transcription factor ChIP-seq data, histone modification ChIP-seq data and open chromatin data. The underlying processing method is based on a ranking-and-recovery procedure, allowing accurate determination of enrichment across heterogeneous datasets, while also discriminating direct from indirect target regions through a 'leading edge' analysis. We illustrate i-cisTarget on various Ewing sarcoma datasets to identify EWS-FLI1 targets starting from ChIP-seq, differential ATAC-seq, differential H3K27ac and differential gene expression data. Use of i-cisTarget is free and open to all, and there is no login requirement. Address: http://gbiomed.kuleuven.be/apps/lcb/i-cisTarget.

  19. Misinterpretations of United States pharmacopeia chapter <797>.

    PubMed

    McElhiney, Linda F

    2012-01-01

    By now, all compounding pharmacists should be aware that United States Pharmacopeia Chapter <797> has been revised. However, the revisions are tedious to read and may be misinterpreted. This article discusses some of the misinterpreted revisions of United States Pharmacopeia Chapter <797> and clarifies the revisions on the topics of Terminology, The Compounder, Facilities and Environment, Personnel Cleansing and Garbing, Assigning Beyond-use Dates, and Testing. Compounders need to take a firm stand with these misinterpretations of United States Pharmacopeia Chapter <797> and educate those who are not thoroughly familiar with the document. Compounders need to be diligent in following these standards to prevent harm to the patients.

  20. Structured decision making: Chapter 5

    USGS Publications Warehouse

    Runge, Michael C.; Grand, James B.; Mitchell, Michael S.; Krausman, Paul R.; Cain, James W. III

    2013-01-01

    Wildlife management is a decision-focused discipline. It needs to integrate traditional wildlife science and social science to identify actions that are most likely to achieve the array of desires society has surrounding wildlife populations. Decision science, a vast field with roots in economics, operations research, and psychology, offers a rich set of tools to help wildlife managers frame, decompose, analyze, and synthesize their decisions. The nature of wildlife management as a decision science has been recognized since the inception of the field, but formal methods of decision analysis have been underused. There is tremendous potential for wildlife management to grow further through the use of formal decision analysis. First, the wildlife science and human dimensions of wildlife disciplines can be readily integrated. Second, decisions can become more efficient. Third, decisions makers can communicate more clearly with stakeholders and the public. Fourth, good, intuitive wildlife managers, by explicitly examining how they make decisions, can translate their art into a science that is readily used by the next generation.

  1. Workstation Designs for a Cis-Lunar Deep Space Habitat

    NASA Technical Reports Server (NTRS)

    Howe, A. Scott

    2014-01-01

    Using the International Standard Payload Rack (ISPR) system, a suite of workstations required for deep space missions have been proposed to fill out habitation functions in an International Space Station (ISS) derived Cis-lunar Deep Space Habitat. This paper introduces the functional layout of the Cis-lunar habitat design, and describes conceptual designs for modular deployable work surfaces, General Maintenance Workstation (GMWS), In-Space Manufacturing Workstation (ISMW), Intra-Vehicular Activity Telerobotics Work Station (IVA-TRWS), and Galley / Wardroom.

  2. Elongin B/C recruitment regulates substrate binding by CIS.

    PubMed

    Piessevaux, Julie; De Ceuninck, Leentje; Catteeuw, Dominiek; Peelman, Frank; Tavernier, Jan

    2008-08-01

    SOCS proteins play a major role in the regulation of cytokine signaling. They are recruited to activated receptors and can suppress signaling by different mechanisms including targeting of the receptor complex for proteasomal degradation. The activity of SOCS proteins is regulated at different levels including transcriptional control and posttranslational modification. We describe here a novel regulatory mechanism for CIS, one of the members of this protein family. A CIS mutant deficient in recruitment of the Elongin B/C complex completely failed to suppress STAT5 activation. This deficiency was not caused by altered turnover of CIS but by loss of cytokine receptor interaction. Intriguingly, no such effect was seen for binding to MyD88. The interaction between CIS and the Elongin B/C complex, which depends on the levels of uncomplexed Elongin B/C, was easily disrupted. This regulatory mechanism may be unique for CIS, as similar mutations in SOCS1, -2, -3, -6, and -7 had no functional impact. Our findings indicate that the SOCS box not only plays a role in the formation of E3 ligase complexes but, at least for CIS, can also regulate the binding modus of SOCS box-containing proteins. PMID:18508766

  3. Chapter 42. Waterborne and Foodborne Parasites

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This chapter identifies the most prominent parasites in North America that are acquired through contaminated food and water including protozoa (Acanthamoeba, Naegleria, Entamoeba, Giardia, Cryptosporidium, Cystoisospora, Cyclospora, Toxoplasma, and Balantidium), nematodes (Trichinella, Angiostrongyl...

  4. How to write a medical book chapter?

    PubMed

    Kendirci, Muammer

    2013-09-01

    Invited medical book chapters are usually requested by editors from experienced authors who have made significant contributions to the literature in certain fields requested by an editor from an experienced. Before the start of the writing process a consensus should be established between the editor and the author with regard to the title, deadline, specific instructions and content of the manuscript. Certain issues concerning a chapter can be negotiated by the parties beforehand, but some issues cannot. As writing a medical book chapter is seen as an honor in its own right, the assignment needs to be treated with sincerity by elucidating the topic in detail, and maximal effort should be made to keep in mind that the chapter will reach a large target audience. The purpose of this review article is to provide guidance to residents and junior specialists in the field of urology to improve their writing skills.

  5. AIR POLLUTION CONTROL TECHNOLOGIES (CHAPTER 65)

    EPA Science Inventory

    The chapter discusses the use of technologies for reducing air pollution emissions from stationary sources, with emphasis on the control of combustion gen-erated air pollution. Major stationary sources include utility power boilers, industrial boilers and heaters, metal smelting ...

  6. AMPLIFICATION OF RIBOSOMAL RNA SEQUENCES - Book Chapter

    EPA Science Inventory

    This book chapter contains the following headings and subheadings: Introduction; Experimental Approach - Precautions, Template, Primers, Reaction Conditions, Enhancers, Post Amplification; Procedures - Template DNA, Basic PCR, Thermal Cycle Parameters, Enzyme Addition, Agarose Ge...

  7. MORPH: probabilistic alignment combined with hidden Markov models of cis-regulatory modules.

    PubMed

    Sinha, Saurabh; He, Xin

    2007-11-01

    The discovery and analysis of cis-regulatory modules (CRMs) in metazoan genomes is crucial for understanding the transcriptional control of development and many other biological processes. Cross-species sequence comparison holds much promise for improving computational prediction of CRMs, for elucidating their binding site composition, and for understanding how they evolve. Current methods for analyzing orthologous CRMs from multiple species rely upon sequence alignments produced by off-the-shelf alignment algorithms, which do not exploit the presence of binding sites in the sequences. We present here a unified probabilistic framework, called MORPH, that integrates the alignment task with binding site predictions, allowing more robust CRM analysis in two species. The framework sums over all possible alignments of two sequences, thus accounting for alignment ambiguities in a natural way. We perform extensive tests on orthologous CRMs from two moderately diverged species Drosophila melanogaster and D. mojavensis, to demonstrate the advantages of the new approach. We show that it can overcome certain computational artifacts of traditional alignment tools and provide a different, likely more accurate, picture of cis-regulatory evolution than that obtained from existing methods. The burgeoning field of cis-regulatory evolution, which is amply supported by the availability of many related genomes, is currently thwarted by the lack of accurate alignments of regulatory regions. Our work will fill in this void and enable more reliable analysis of CRM evolution.

  8. MORPH: probabilistic alignment combined with hidden Markov models of cis-regulatory modules.

    PubMed

    Sinha, Saurabh; He, Xin

    2007-11-01

    The discovery and analysis of cis-regulatory modules (CRMs) in metazoan genomes is crucial for understanding the transcriptional control of development and many other biological processes. Cross-species sequence comparison holds much promise for improving computational prediction of CRMs, for elucidating their binding site composition, and for understanding how they evolve. Current methods for analyzing orthologous CRMs from multiple species rely upon sequence alignments produced by off-the-shelf alignment algorithms, which do not exploit the presence of binding sites in the sequences. We present here a unified probabilistic framework, called MORPH, that integrates the alignment task with binding site predictions, allowing more robust CRM analysis in two species. The framework sums over all possible alignments of two sequences, thus accounting for alignment ambiguities in a natural way. We perform extensive tests on orthologous CRMs from two moderately diverged species Drosophila melanogaster and D. mojavensis, to demonstrate the advantages of the new approach. We show that it can overcome certain computational artifacts of traditional alignment tools and provide a different, likely more accurate, picture of cis-regulatory evolution than that obtained from existing methods. The burgeoning field of cis-regulatory evolution, which is amply supported by the availability of many related genomes, is currently thwarted by the lack of accurate alignments of regulatory regions. Our work will fill in this void and enable more reliable analysis of CRM evolution. PMID:17997594

  9. Control of carotenoid biosynthesis through a heme-based cis-trans isomerase.

    PubMed

    Beltrán, Jesús; Kloss, Brian; Hosler, Jonathan P; Geng, Jiafeng; Liu, Aimin; Modi, Anuja; Dawson, John H; Sono, Masanori; Shumskaya, Maria; Ampomah-Dwamena, Charles; Love, James D; Wurtzel, Eleanore T

    2015-08-01

    Plants synthesize carotenoids, which are essential for plant development and survival. These metabolites also serve as essential nutrients for human health. The biosynthetic pathway for all plant carotenoids occurs in chloroplasts and other plastids and requires 15-cis-ζ-carotene isomerase (Z-ISO). It was not known whether Z-ISO catalyzes isomerization alone or in combination with other enzymes. Here we show that Z-ISO is a bona fide enzyme and integral membrane protein. Z-ISO independently catalyzes the cis-trans isomerization of the 15-15' carbon-carbon double bond in 9,15,9'-cis-ζ-carotene to produce the substrate required by the subsequent biosynthetic-pathway enzyme. We discovered that isomerization depends upon a ferrous heme b cofactor that undergoes redox-regulated ligand switching between the heme iron and alternate Z-ISO amino acid residues. Heme b-dependent isomerization of a large hydrophobic compound in a membrane was previously undescribed. As an isomerase, Z-ISO represents a new prototype for heme b proteins and potentially uses a new chemical mechanism.

  10. Control of carotenoid biosynthesis through a heme-based cis-trans isomerase

    PubMed Central

    Beltrán, Jesús; Kloss, Brian; Hosler, Jonathan P.; Geng, Jiafeng; Liu, Aimin; Modi, Anuja; Dawson, John H.; Sono, Masanori; Shumskaya, Maria; Ampomah-Dwamena, Charles; Love, James D.; Wurtzel, Eleanore T.

    2015-01-01

    Plants synthesize carotenoids essential for plant development and survival. These metabolites also serve as essential nutrients for human health. The biosynthetic pathway leading to all plant carotenoids occurs in chloroplasts and other plastids and requires 15-cis-ζ-carotene isomerase (Z-ISO). It was not certain whether isomerization was achieved by Z-ISO alone or in combination with other enzymes. Here we show that Z-ISO is a bona fide enzyme and integral membrane protein. Z-ISO independently catalyzes the cis-to-trans isomerization of the 15–15′ C=C bond in 9,15,9′-cis-ζ-carotene to produce the substrate required by the following biosynthetic pathway enzyme. We discovered that isomerization depends upon a ferrous heme b cofactor that undergoes redox-regulated ligand-switching between the heme iron and alternate Z-ISO amino acid residues. Heme b-dependent isomerization of a large, hydrophobic compound in a membrane is unprecedented. As an isomerase, Z-ISO represents a new prototype for heme b proteins and potentially utilizes a novel chemical mechanism. PMID:26075523

  11. Predominant contribution of cis-regulatory divergence in the evolution of mouse alternative splicing

    PubMed Central

    Gao, Qingsong; Sun, Wei; Ballegeer, Marlies; Libert, Claude; Chen, Wei

    2015-01-01

    Divergence of alternative splicing represents one of the major driving forces to shape phenotypic diversity during evolution. However, the extent to which these divergences could be explained by the evolving cis-regulatory versus trans-acting factors remains unresolved. To globally investigate the relative contributions of the two factors for the first time in mammals, we measured splicing difference between C57BL/6J and SPRET/EiJ mouse strains and allele-specific splicing pattern in their F1 hybrid. Out of 11,818 alternative splicing events expressed in the cultured fibroblast cells, we identified 796 with significant difference between the parental strains. After integrating allele-specific data from F1 hybrid, we demonstrated that these events could be predominately attributed to cis-regulatory variants, including those residing at and beyond canonical splicing sites. Contrary to previous observations in Drosophila, such predominant contribution was consistently observed across different types of alternative splicing. Further analysis of liver tissues from the same mouse strains and reanalysis of published datasets on other strains showed similar trends, implying in general the predominant contribution of cis-regulatory changes in the evolution of mouse alternative splicing. PMID:26134616

  12. Where Social and Professional Networking Meet: The Virtual Association Chapter

    ERIC Educational Resources Information Center

    Noxon, Rose

    2011-01-01

    Online Capella University wanted to sponsor an International Society for Performance Improvement (ISPI) chapter. Using social networking platforms, a new type of chapter was designed. The virtual chapter breaks new ground on more than the chapter's platform; it is also the first university-sponsored chapter and has a unique approach to…

  13. 48 CFR 9900.000 - Scope of chapter.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 48 Federal Acquisition Regulations System 7 2010-10-01 2010-10-01 false Scope of chapter. 9900.000... PROCUREMENT POLICY, OFFICE OF MANAGEMENT AND BUDGET SCOPE OF CHAPTER 9900.000 Scope of chapter. This chapter... and subcontracts. This chapter does not apply to sealed bid contracts or to any contract with a...

  14. 1 CFR 21.8 - Chapters and subchapters.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 1 General Provisions 1 2010-01-01 2010-01-01 false Chapters and subchapters. 21.8 Section 21.8... Chapters and subchapters. (a) The normal divisions of a title are chapters, assigned to the various...) Subchapters may be used to group related parts within a chapter. (c) Chapter and subchapter assignments...

  15. Chapter IV - Safety During Payload Ground Processing

    NASA Technical Reports Server (NTRS)

    Kirkpatrick, Paul; Dollberg, John; Trinchero, Jean-Pierre

    2012-01-01

    This chapter describes the typical hazards that can be expected to be encountered when processing payloads on the ground. Also described are some of the more common controls for these hazards. Many of these controls are based on hard requirements but they are also based on specific lessons learned. This chapter uses the term Flight Hardware (F/H) for all payloads regardless of size.

  16. Nozomi Cis-Lunar Phase Orbit Determination

    NASA Technical Reports Server (NTRS)

    Ryne, Mark; Criddle, Kevin

    2000-01-01

    Japan's Institute of Space and Astronautical Science (ISAS) launched Nozomi, its first mission to the planet Mars using the newly developed M-V launch vehicle on July 3, 1998. Scientific objectives of the mission are to study the structure and dynamics of the Martian upper atmosphere and its interaction with the solar wind. Nozomi is a cooperative mission between ISAS and the National Aeronautics and Space Administration (NASA). The NASA contribution includes navigation and tracking services provided by the Jet Propulsion Laboratory (JPL). The spacecraft also serves as an engineering demonstration of basic technology for planetary exploration. One of the new technologies was a unique trajectory, developed by ISAS, which used solar gravitational perturbations at the weak stability boundary as an aid to achieve an Earth-Mars transfer orbit. This trajectory saves approximately 120 m/s of Delta V compared to direct hyperbolic insertion and is considered an enabling technology for the mission. Nozomi was the first spacecraft to employ this trajectory and provided on-orbit validation of the technique. The trajectory was achieved by initially placing the spacecraft in a highly elliptical cis-lunar phasing orbit. Six maneuvers were performed during this period to correct injection errors and target an outbound lunar swingby in September 1998. The gravity assist from the lunar swingby raised apogee to the vicinity of the weak stability boundary. After three more targeting maneuvers, Nozomi performed an inbound lunar swingby followed immediately by a powered Earth swingby in late December 1998. A 420 m/s Trans Mars Insertion (TMI) burn at the final Earth periapsis was intended to place the spacecraft on a heliocentric trajectory leading to Mars orbit insertion in October 1999. Orbit determination for Nozomi is performed in parallel by both ISAS and the Multi-Mission Navigation (MMNAV) group at JPL. This was an advantage for the mission because each group would generate

  17. Modeling DNA sequence-based cis-regulatory gene networks.

    PubMed

    Bolouri, Hamid; Davidson, Eric H

    2002-06-01

    Gene network analysis requires computationally based models which represent the functional architecture of regulatory interactions, and which provide directly testable predictions. The type of model that is useful is constrained by the particular features of developmentally active cis-regulatory systems. These systems function by processing diverse regulatory inputs, generating novel regulatory outputs. A computational model which explicitly accommodates this basic concept was developed earlier for the cis-regulatory system of the endo16 gene of the sea urchin. This model represents the genetically mandated logic functions that the system executes, but also shows how time-varying kinetic inputs are processed in different circumstances into particular kinetic outputs. The same basic design features can be utilized to construct models that connect the large number of cis-regulatory elements constituting developmental gene networks. The ultimate aim of the network models discussed here is to represent the regulatory relationships among the genomic control systems of the genes in the network, and to state their functional meaning. The target site sequences of the cis-regulatory elements of these genes constitute the physical basis of the network architecture. Useful models for developmental regulatory networks must represent the genetic logic by which the system operates, but must also be capable of explaining the real time dynamics of cis-regulatory response as kinetic input and output data become available. Most importantly, however, such models must display in a direct and transparent manner fundamental network design features such as intra- and intercellular feedback circuitry; the sources of parallel inputs into each cis-regulatory element; gene battery organization; and use of repressive spatial inputs in specification and boundary formation. Successful network models lead to direct tests of key architectural features by targeted cis-regulatory analysis. PMID

  18. Evaluating cis-2,6-Dimethylpiperidide (cis-DMP) as a Base Component in Lithium-Mediated Zincation Chemistry

    PubMed Central

    Armstrong, David R; Garden, Jennifer A; Kennedy, Alan R; Leenhouts, Sarah M; Mulvey, Robert E; O'Keefe, Philip; O'Hara, Charles T; Steven, Alan

    2013-01-01

    Most recent advances in metallation chemistry have centred on the bulky secondary amide 2,2,6,6-tetramethylpiperidide (TMP) within mixed metal, often ate, compositions. However, the precursor amine TMP(H) is rather expensive so a cheaper substitute would be welcome. Thus this study was aimed towards developing cheaper non-TMP based mixed-metal bases and, as cis-2,6-dimethylpiperidide (cis-DMP) was chosen as the alternative amide, developing cis-DMP zincate chemistry which has received meagre attention compared to that of its methyl-rich counterpart TMP. A new lithium diethylzincate, [(TMEDA)LiZn(cis-DMP)Et2] (TMEDA=N,N,N′,N′-tetramethylethylenediamine) has been synthesised by co-complexation of Li(cis-DMP), Et2Zn and TMEDA, and characterised by NMR (including DOSY) spectroscopy and X-ray crystallography, which revealed a dinuclear contact ion pair arrangement. By using N,N-diisopropylbenzamide as a test aromatic substrate, the deprotonative reactivity of [(TMEDA)LiZn(cis-DMP)Et2] has been probed and contrasted with that of the known but previously uninvestigated di-tert-butylzincate, [(TMEDA)LiZn(cis-DMP)tBu2]. The former was found to be the superior base (for example, producing the ortho-deuteriated product in respective yields of 78 % and 48 % following D2O quenching of zincated benzamide intermediates). An 88 % yield of 2-iodo-N,N-diisopropylbenzamide was obtained on reaction of two equivalents of the diethylzincate with the benzamide followed by iodination. Comparisons are also drawn using 1,1,1,3,3,3-hexamethyldisilazide (HMDS), diisopropylamide and TMP as the amide component in the lithium amide, Et2Zn and TMEDA system. Under certain conditions, the cis-DMP base system was found to give improved results in comparison to HMDS and diisopropylamide (DA), and comparable results to a TMP system. Two novel complexes isolated from reactions of the di-tert-butylzincate and crystallographically characterised, namely the pre-metallation complex [{(iPr)2N(Ph)C=O}LiZn(cis

  19. CisMiner: Genome-Wide In-Silico Cis-Regulatory Module Prediction by Fuzzy Itemset Mining

    PubMed Central

    Navarro, Carmen; Lopez, Francisco J.; Cano, Carlos; Garcia-Alcalde, Fernando; Blanco, Armando

    2014-01-01

    Eukaryotic gene control regions are known to be spread throughout non-coding DNA sequences which may appear distant from the gene promoter. Transcription factors are proteins that coordinately bind to these regions at transcription factor binding sites to regulate gene expression. Several tools allow to detect significant co-occurrences of closely located binding sites (cis-regulatory modules, CRMs). However, these tools present at least one of the following limitations: 1) scope limited to promoter or conserved regions of the genome; 2) do not allow to identify combinations involving more than two motifs; 3) require prior information about target motifs. In this work we present CisMiner, a novel methodology to detect putative CRMs by means of a fuzzy itemset mining approach able to operate at genome-wide scale. CisMiner allows to perform a blind search of CRMs without any prior information about target CRMs nor limitation in the number of motifs. CisMiner tackles the combinatorial complexity of genome-wide cis-regulatory module extraction using a natural representation of motif combinations as itemsets and applying the Top-Down Fuzzy Frequent- Pattern Tree algorithm to identify significant itemsets. Fuzzy technology allows CisMiner to better handle the imprecision and noise inherent to regulatory processes. Results obtained for a set of well-known binding sites in the S. cerevisiae genome show that our method yields highly reliable predictions. Furthermore, CisMiner was also applied to putative in-silico predicted transcription factor binding sites to identify significant combinations in S. cerevisiae and D. melanogaster, proving that our approach can be further applied genome-wide to more complex genomes. CisMiner is freely accesible at: http://genome2.ugr.es/cisminer. CisMiner can be queried for the results presented in this work and can also perform a customized cis-regulatory module prediction on a query set of transcription factor binding sites provided by

  20. Evaluating cis-2,6-dimethylpiperidide (cis-DMP) as a base component in lithium-mediated zincation chemistry.

    PubMed

    Armstrong, David R; Garden, Jennifer A; Kennedy, Alan R; Leenhouts, Sarah M; Mulvey, Robert E; O'Keefe, Philip; O'Hara, Charles T; Steven, Alan

    2013-09-27

    Most recent advances in metallation chemistry have centred on the bulky secondary amide 2,2,6,6-tetramethylpiperidide (TMP) within mixed metal, often ate, compositions. However, the precursor amine TMP(H) is rather expensive so a cheaper substitute would be welcome. Thus this study was aimed towards developing cheaper non-TMP based mixed-metal bases and, as cis-2,6-dimethylpiperidide (cis-DMP) was chosen as the alternative amide, developing cis-DMP zincate chemistry which has received meagre attention compared to that of its methyl-rich counterpart TMP. A new lithium diethylzincate, [(TMEDA)LiZn(cis-DMP)Et2] (TMEDA=N,N,N',N'-tetramethylethylenediamine) has been synthesised by co-complexation of Li(cis-DMP), Et2Zn and TMEDA, and characterised by NMR (including DOSY) spectroscopy and X-ray crystallography, which revealed a dinuclear contact ion pair arrangement. By using N,N-diisopropylbenzamide as a test aromatic substrate, the deprotonative reactivity of [(TMEDA)LiZn(cis-DMP)Et2] has been probed and contrasted with that of the known but previously uninvestigated di-tert-butylzincate, [(TMEDA)LiZn(cis-DMP)tBu2]. The former was found to be the superior base (for example, producing the ortho-deuteriated product in respective yields of 78% and 48% following D2O quenching of zincated benzamide intermediates). An 88% yield of 2-iodo-N,N-diisopropylbenzamide was obtained on reaction of two equivalents of the diethylzincate with the benzamide followed by iodination. Comparisons are also drawn using 1,1,1,3,3,3-hexamethyldisilazide (HMDS), diisopropylamide and TMP as the amide component in the lithium amide, Et2Zn and TMEDA system. Under certain conditions, the cis-DMP base system was found to give improved results in comparison to HMDS and diisopropylamide (DA), and comparable results to a TMP system. Two novel complexes isolated from reactions of the di-tert-butylzincate and crystallographically characterised, namely the pre-metallation complex [{(iPr)2N(Ph)C=O}LiZn(cis

  1. Thermodynamic and kinetic properties of cis-diammineglycolatoplatinum in different water solvents

    NASA Astrophysics Data System (ADS)

    Li, Z. X.; Zhao, W. W.; Gou, X. X.; Pu, X. H.

    2016-05-01

    The dissolution behavior of cis-diammineglycolatoplatinum (nedaplatin) in saline, water and glucose were studied by a microcalorimetric method. The integral heats and differential heats of the dissolution were measured to establish the equation for the solute and the heats. The corresponding half-life, kinetic and thermodynamic properties of the nedaplatin solutions were determined. The results show that hydrogen bonds could be generated and the dissolution entropy of nedaplatin in different solvents is negative during the dissolution process, so as to enhance the drug stability, but there is an obvious difference in stability in different solvents.

  2. Geological Survey Research 1966, Chapter A

    USGS Publications Warehouse

    ,

    1966-01-01

    'Geological Survey Research 1966' is the seventh annual review of the econamic and scientific work of the U.S. Geological Survey. As in previous years the purpose of the volume is to make available promptly to the public the highlights of Survey investigations. This year the volume consists of 4 chapters (A through D) of Professional Paper 550. Chapter A contains a summary of significant results, and the remaining chapters are made up of collections of short technical papers. Many of the results summarized in chapter A are discussed in greater detail in the short papers or in reports listed in 'Publications in Fiscal Year 1966,' beginning on page A265. The tables of contents for chapters B through D are listed on pages A259-A264. Numerous Federal, State, county, and municipal agencies listed on pages A211-A215 cooperated financially with the Geological Survey during fiscal 1966 and have contributed significantly to the results reported here. They are identified where appropriate in the short technical papers that have appeared in Geological Survey Research and in papers published cooperatively, but generally are not identified in the brief statements in chapter A. Many individuals on the staff of the Geological Survey have contributed to 'Geological Survey Research 1966.' Reference is made to only a few. Frank W. Trainer, Water Resources Division, was responsible for organizing and assembling chapter A and for critical review of papers in chapters B-D, assisted by Louis Pavlides, Geologic Division. Marston S. Chase, Publications Division, was in charge of production aspects of the series, assisted by Jesse R. Upperco in technical editing, and William H. Elliott and James R. Hamilton in planning and preparing illustrations. The volume for next year, 'Geological Survey Research 1967,' will be published as chapters af Professional Paper 5715. Previous volumes are listed below, with their series designations. Gealagical Survey Research 1960-Prof. Paper 400 Gealagical

  3. Cis-regulatory mechanisms governing stem and progenitor cell transitions

    PubMed Central

    Johnson, Kirby D.; Kong, Guangyao; Gao, Xin; Chang, Yuan-I; Hewitt, Kyle J.; Sanalkumar, Rajendran; Prathibha, Rajalekshmi; Ranheim, Erik A.; Dewey, Colin N.; Zhang, Jing; Bresnick, Emery H.

    2015-01-01

    Cis-element encyclopedias provide information on phenotypic diversity and disease mechanisms. Although cis-element polymorphisms and mutations are instructive, deciphering function remains challenging. Mutation of an intronic GATA motif (+9.5) in GATA2, encoding a master regulator of hematopoiesis, underlies an immunodeficiency associated with myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). Whereas an inversion relocalizes another GATA2 cis-element (−77) to the proto-oncogene EVI1, inducing EVI1 expression and AML, whether this reflects ectopic or physiological activity is unknown. We describe a mouse strain that decouples −77 function from proto-oncogene deregulation. The −77−/− mice exhibited a novel phenotypic constellation including late embryonic lethality and anemia. The −77 established a vital sector of the myeloid progenitor transcriptome, conferring multipotentiality. Unlike the +9.5−/− embryos, hematopoietic stem cell genesis was unaffected in −77−/− embryos. These results illustrate a paradigm in which cis-elements in a locus differentially control stem and progenitor cell transitions, and therefore the individual cis-element alterations cause unique and overlapping disease phenotypes. PMID:26601269

  4. Influence of the cis-9, cis-12 and cis-15 double bond position in octadecenoic acid (18:1) isomers on the rat FADS2-catalyzed Δ6-desaturation.

    PubMed

    Rioux, Vincent; Choque, Benjamin; Ezanno, Hélène; Duby, Cécile; Catheline, Daniel; Legrand, Philippe

    2015-04-01

    Oleic (cis9-18:1), linoleic (cis9,cis12-18:2) and α-linolenic (cis9,cis12,cis15-18:3) acids are well described substrates of the Δ6-desaturase encoded by the mammalian fatty acid desaturase 2 (FADS2) gene. In addition, at least 9 other very structurally different fatty acids have been shown to be Δ6- or even Δ8-desaturated by the FADS2 protein. A better characterization of the substrate specificity of this enzyme is therefore needed. By using commercial cis9-18:1 and chemically synthesized cis12- and cis15-18:1 (sharing the n-6 double bond with 18:2 n-6 and the n-3 double bond with 18:3 n-3, respectively), we tried to decrypt the fatty acid structure driving the FADS2 substrate affinity. We first showed that both recombinant and native rat FADS2 were able to Δ6-desaturate not only the cis9- but also the cis12- and cis15-18:1 isomers. Next, the inhibitory effect of increasing concentrations of each 18:1 isomer was investigated in vitro on the Δ6-desaturation of α-linolenic acid. At equimolar inhibitor/substrate ratio (60 μM), the cis9-18:1 exhibited a significantly higher inhibition (25%) than the cis12- (8%) and cis15-18:1 (5%). This study shows that a single cis double bond in 12- or 15-position in 18:1 is enough to make them low Δ6-desaturable substrates. If a preexisting cis9-double bond is not absolutely required for the Δ6-desaturation of octadecenoic acids, its presence is however crucial to explain the higher enzyme affinity. Compared with oleic acid, the additional presence of a cis12-double bond in linoleic acid increased its inhibitory effect on the Δ6-desaturation of α-linolenic acid at low concentration (30 μM) but not at higher concentrations (60 and 120 μM). In this classification of the decreasing impact of the double bond when it comes closer to the methyl end of octadecenoic acids, the cis11-18:1 (cis-vaccenic acid) should be considered apart since it is itself not Δ6-desaturated but still a good competitive inhibitor of the

  5. Chapter A5. Processing of Water Samples

    USGS Publications Warehouse

    Wilde, Franceska D.; Radtke, Dean B.; Gibs, Jacob; Iwatsubo, Rick T.

    1999-01-01

    The National Field Manual for the Collection of Water-Quality Data (National Field Manual) describes protocols and provides guidelines for U.S. Geological Survey (USGS) personnel who collect data used to assess the quality of the Nation's surface-water and ground-water resources. This chapter addresses methods to be used in processing water samples to be analyzed for inorganic and organic chemical substances, including the bottling of composite, pumped, and bailed samples and subsamples; sample filtration; solid-phase extraction for pesticide analyses; sample preservation; and sample handling and shipping. Each chapter of the National Field Manual is published separately and revised periodically. Newly published and revised chapters will be announced on the USGS Home Page on the World Wide Web under 'New Publications of the U.S. Geological Survey.' The URL for this page is http:/ /water.usgs.gov/lookup/get?newpubs.

  6. Marine West Coast Forests, Chapter 9

    USGS Publications Warehouse

    Perakis, Steven S.; Geiser, Linda H.; Lilleskov, Erik A.; Pardo, Linda H.; Robin-Abbott, Molly J.; Driscoll, Charles T.

    2011-01-01

    Human activities have greatly increased nitrogen emissions and deposition across large areas of Earth. Although nitrogen is an essential nutrient for plant growth, too much nitrogen in excess of critical loads leads to losses of biodiversity, soil and stream acidification, nutrient imbalances, and other deleterious effects. In a new report quantifying critical loads of nitrogen deposition across the United States, USGS scientist Steve Perakis and co-authors provided a chapter about responses of marine west coast forests. Much of this region is understudied with respect to nitrogen deposition, and in this chapter the authors identify known adverse effects and estimate critical loads of nitrogen deposition for western Oregon and Washington and southeast Alaska forests. Perakis also contributed to the synthesis chapter, which includes background, objectives, advantages and uncertainties of critical loads, an overview of critical loads across U.S. ecoregions, and other topics.

  7. Identification of altered cis-regulatory elements in human disease.

    PubMed

    Mathelier, Anthony; Shi, Wenqiang; Wasserman, Wyeth W

    2015-02-01

    It has long been appreciated that variations in regulatory regions of genes can impact gene expression. With the advent of whole-genome sequencing (WGS), it has become possible to begin cataloging these noncoding variants. Evidence continues to accumulate linking clinical cases with cis-regulatory element disruption in a wide range of diseases. Identifying variants is becoming routine, but assessing their impact on regulation remains challenging. Bioinformatics approaches that identify variations functionally altering transcription factor (TF) binding are increasingly important for meeting this challenge. We present the current state of computational tools and resources for identifying the genomic regulatory components (cis-regulatory regions and TF binding sites, TFBSs) controlling gene transcriptional regulation. We review how such approaches can be used to interpret the potential disease causality of point mutations and small insertions or deletions. We hope this will motivate further the development of methods enabling the identification of etiological cis-regulatory variations.

  8. Secondary School Mathematics, Chapter 21, Rigid Motions and Vectors, Chapter 22, Computers and Programs. Student's Text.

    ERIC Educational Resources Information Center

    Stanford Univ., CA. School Mathematics Study Group.

    Transformation geometry topics are covered in one chapter of Unit 11 of this SMSG series. Work with translations, reflections, rotations, and composition of motions is included; vectors are briefly discussed. The chapter on computers and programming deals with recent history and uses of of the computer, organization of a digital computer, an…

  9. [Biennial Survey of Education, 1926-1928. Bulletin, 1930, No. 16. Chapter I - Chapter XX

    ERIC Educational Resources Information Center

    Office of Education, United States Department of the Interior, 1930

    1930-01-01

    This document contains the first twenty chapters of the Biennial Survey of Education document, covering the years 1926-1928. The following chapters are included in this document: (1) Higher education (Arthur J. Klein); (2) Medical education (N. P. Colwell); (3) Legal education (Alfred Z. Reed); (4) Significant movements in city school systems (W.…

  10. Report of the Chapter 1 Sustained Effects Study. Elementary and Secondary Education Act--Chapter 1.

    ERIC Educational Resources Information Center

    Donaldson, William S.

    School districts receiving Chapter 1 funds are to conduct a study of sustained effects once every 3 years and to use the results for planning future Chapter 1 programs. As part of this effort, the Columbus (Ohio) public schools conducted pretest-to-posttest, posttest-to-sustained effect, and pretest-to-sustained effect studies of 4,031 students in…

  11. Secondary School Mathematics, Chapter 13, Perpendiculars and Parallels (I), Chapter 14, Similarity. Student's Text.

    ERIC Educational Resources Information Center

    Stanford Univ., CA. School Mathematics Study Group.

    The first chapter of the seventh unit in this SMSG series discusses perpendiculars and parallels; topics covered include the relationship between parallelism and perpendicularity, rectangles, transversals, parallelograms, general triangles, and measurement of the circumference of the earth. The second chapter, on similarity, discusses scale…

  12. Secondary School Mathematics, Chapter 27, Logic, Chapter 28, Applications of Probability and Statistics. Student's Text.

    ERIC Educational Resources Information Center

    Stanford Univ., CA. School Mathematics Study Group.

    One chapter in the fourteenth unit of this SMSG series deals with logic; simple and compound statements, truth tables, logical equivalence, rules of a logical argument, proof, quantifiers, and negations are the topics covered. The second chapter of the unit discusses applications of probability and statistics, including random sampling,…

  13. Secondary School Mathematics, Chapter 17, Perpendiculars and Parallels (II), Chapter 18, Coordinate Geometry. Student's Text.

    ERIC Educational Resources Information Center

    Stanford Univ., CA. School Mathematics Study Group.

    The first chapter, Perpendiculars and Parallels (II), of the ninth unit in this SMSG series includes a discussion of the properties of triangles, circles and perpendiculars, parallels in space, perpendicular lines and planes, and parallel planes. The next chapter, on coordinate geometry, covers distance; midpoints; algebraic descriptions of…

  14. Interactions of Molecules with cis and trans Double Bonds: A Theoretical Study of cis- and trans-2-Butene.

    PubMed

    Zarić, Milana M; Bugarski, Branko; Kijevčanin, Mirjana Lj

    2016-01-18

    Noncovalent interactions of cis- and trans-2-butene, as the smallest model systems of molecules with cis and trans double bonds, were studied to find potential differences in interactions of these molecules. The study was performed using quantum chemical methods including very accurate CCSD(T)/CBS method. We studied parallel and displaced parallel interactions in 2-butene dimers, in butane dimers, and between 2-butene and saturated butane. The results show the trend that interactions of 2-butene with butane are the strongest, followed by interactions in butane dimers, whereas the interaction in 2-butene dimers are the weakest. The strongest calculated interaction energy is between trans-2-butene and butane, with a CCSD(T)/CBS energy of -2.80 kcal mol(-1) . Interactions in cis-2-butene dimers are stronger than interactions in trans-2-butene dimers. Interestingly, some of the interactions involving 2-butene are as strong as interactions in a benzene dimer. These insights into interactions of cis- and trans-2-butene can improve understanding of the properties and processes that involve molecules with cis and trans double bonds, such as fatty acids and polymers.

  15. Conditional gene vectors regulated in cis

    PubMed Central

    Pich, Dagmar; Humme, Sibille; Spindler, Mark-Peter; Schepers, Aloys; Hammerschmidt, Wolfgang

    2008-01-01

    Non-integrating gene vectors, which are stably and extrachromosomally maintained in transduced cells would be perfect tools to support long-term expression of therapeutic genes but preserve the genomic integrity of the cellular host. Small extrachromosomal plasmids share some of these ideal characteristics but are primarily based on virus blueprints. These plasmids are dependent on viral trans-acting factors but they can replicate their DNA molecules in synchrony with the chromosome of the cellular host and segregate to daughter cells in an autonomous fashion. On the basis of the concept of the latent origin of DNA replication of Epstein-Barr virus, oriP, we devised novel derivatives, which exclusively rely on an artificial replication factor for both nuclear retention and replication of plasmid DNA. In addition, an allosteric switch regulates the fate of the plasmid molecules, which are rapidly lost upon addition of doxycycline. Conditional maintenance of these novel plasmid vectors allows the reversible transfer of genetic information into target cells for the first time. PMID:18566006

  16. From Cis-Regulatory Elements to Complex RNPs and Back

    PubMed Central

    Gebauer, Fátima; Preiss, Thomas; Hentze, Matthias W.

    2012-01-01

    Messenger RNAs (mRNAs), the templates for translation, have evolved to harbor abundant cis-acting sequences that affect their posttranscriptional fates. These elements are frequently located in the untranslated regions and serve as binding sites for trans-acting factors, RNA-binding proteins, and/or small non-coding RNAs. This article provides a systematic synopsis of cis-acting elements, trans-acting factors, and the mechanisms by which they affect translation. It also highlights recent technical advances that have ushered in the era of transcriptome-wide studies of the ribonucleoprotein complexes formed by mRNAs and their trans-acting factors. PMID:22751153

  17. Studies on the s-cis-trans isomerism for some furan derivatives through IR and NMR spectroscopies and theoretical calculations.

    PubMed

    Rittner, Roberto; Ducati, Lucas C; Tormena, Cláudio F; Cormanich, Rodrigo A; Fiorin, Barbara C; Braga, Carolyne B; Abraham, Raymond J

    2013-02-15

    The s-cis-trans isomerism of two furan derivatives [2-acetyl- (AF) and 2-acetyl-5-methylfuran, (AMF)] was analyzed, using data from the deconvolution of their carbonyl absorption band in two solvents (CH(2)Cl(2) and CH(3)CN). These infrared data showed that the O,O-trans conformers predominate in the less polar solvent (CH(2)Cl(2)), but these equilibria change in a more polar solvent (CH(3)CN) leading to a slight predominance of the O,O-cis conformers, in agreement with the theoretical calculations. The later results were obtained using B3LYP-IEFPCM/6-31++g(3df,3p) level of theory, which taking into account the solvent effects at IEFPCM (Integral Equation Formalism Polarizable Continuum Model). Low temperature (13)CNMR spectra in CD(2)Cl(2) (ca. -75 °C) showed pairs of signals for each carbon, due to the known high energy barrier for the cis-trans interconversion leading to a large predominance of the trans isomers, which decreases in acetone-d(6). This was confirmed by their (1)HNMR spectra at the same temperatures. Moreover, despite the larger hyperconjugative interactions for the O,O-cis isomers, obtained from NBO data, these isomers are destabilized by the their Lewis energy.

  18. INDOOR AIR QUALITY MODELING (CHAPTER 58)

    EPA Science Inventory

    The chapter discussses indoor air quality (IAQ) modeling. Such modeling provides a way to investigate many IAQ problems without the expense of large field experiments. Where experiments are planned, IAQ models can be used to help design experiments by providing information on exp...

  19. Chapter 4. Students' Attitudes toward Computer Games

    ERIC Educational Resources Information Center

    Russian Education and Society, 2004

    2004-01-01

    In this chapter, the authors attempt not only to discern aspects that relate to age, place, and the amount of time devoted to playing computer games in adolescence, but also to study content characteristics of their attitudes such as: the developmental dynamic in the change of their genre preferences in computer games, changes in factors that…

  20. Chapter 8: Youth, Technology, and Media Cultures

    ERIC Educational Resources Information Center

    Sefton-Green, Julian

    2006-01-01

    This chapter begins with a scenario contrasting two seemingly different images of child and media from before and after the "digital revolution." The author argues that there is much greater continuity in how this relationship has been conceptualized over the period than is commonly imagined. While not offering a comprehensive study of recent…

  1. Chapter 12: spatial or area repellents

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Spatial repellents a three-dimensional zone of protection around a host from attacks by biting arthropods. This chapter reviews current knowledge and outlines future directions for utilization of spatial repellents. Current knowledge includes the kinds of products, both active and passive devices,...

  2. The Chapter I Challenge: Colorado's Contribution 1995.

    ERIC Educational Resources Information Center

    Petro, Janice Rose

    Chapter I of the Elementary and Secondary Education Act (ESEA) is the largest federally-funded program designed to provide services to elementary and secondary students to meet the special needs of educationally deprived students who reside in areas with high concentrations of low-income families. The 1994-95 school year is the last year of…

  3. Recommended Research on Artificial Gravity. Chapter 13

    NASA Technical Reports Server (NTRS)

    Vernikos, Joan; Paloski, William; Fuller, Charles; Clement, Gilles

    2006-01-01

    Based on the summaries presented in the above sections of what is still to be learned on the effects of artificial gravity on human functions, this chapter will discuss the short- and long-term steps of research required to understand fundamentals and to validate operational aspects of using artificial gravity as an effective countermeasure for long-duration space travel.

  4. Chapter Five: Language Learning and Discursive Practice

    ERIC Educational Resources Information Center

    Young, Richard F.

    2008-01-01

    This chapter is framed by the three questions related to learning in Practice Theory posed by Johannes Wagner (2008): (1) What is learned?; (2) Who is learning?; and (3) Who is participating in the learning? These questions are addressed in two learning theories: Language Socialization and Situated Learning theory. In Language Socialization, the…

  5. Chapter 7: Principles of Professional Development

    ERIC Educational Resources Information Center

    O'Sullivan, Mary; Deglau, Dena

    2006-01-01

    This chapter summarizes the 4-year-long PEP professional development (PD) initiative in terms of current perspectives on teacher learning and PD, shares lessons learned about the design and delivery of high-quality PD, and presents some principles to guide the development of future PD efforts. The first section reviews the definition and…

  6. Systematic identification of cis-silenced genes by trans complementation

    PubMed Central

    Lee, Jae Hyun; Bugarija, Branimir; Millan, Enrique J.; Walton, Noah M.; Gaetz, Jedidiah; Fernandes, Croydon J.; Yu, Wei-Hua; Mekel-Bobrov, Nitzan; Vallender, Tammy W.; Snyder, Gregory E.; Xiang, Andy Peng; Lahn, Bruce T.

    2009-01-01

    A gene’s transcriptional output is the combined product of two inputs: diffusible factors in the cellular milieu acting in trans, and chromatin state acting in cis. Here, we describe a strategy for dissecting the relative contribution of cis versus trans mechanisms to gene regulation. Referred to as trans complementation, it entails fusing two disparate cell types and searching for genes differentially expressed between the two genomes of fused cells. Any differential expression can be causally attributed to cis mechanisms because the two genomes of fused cells share a single homogenized milieu in trans. This assay uncovered a state of transcriptional competency that we termed ‘occluded’ whereby affected genes are silenced by cis-acting mechanisms in a manner that blocks them from responding to the trans-acting milieu of the cell. Importantly, occluded genes in a given cell type tend to include master triggers of alternative cell fates. Furthermore, the occluded state is maintained during cell division and is extraordinarily stable under a wide range of physiological conditions. These results support the model that the occlusion of lineage-inappropriate genes is a key mechanism of cell fate restriction. The identification of occluded genes by our assay provides a hitherto unavailable functional readout of chromatin state that is distinct from and complementary to gene expression status. PMID:19050040

  7. Cis and trans activation of adenovirus IVa2 gene transcription.

    PubMed Central

    Natarajan, V; Salzman, N P

    1985-01-01

    The transcriptional control region of the adenovirus IVa2 promoter was analyzed by cloning this promoter in front of a gene coding for bacterial chloramphenicol acetyl transferase (CATase) and estimating levels of CATase and IVa2 promoter specific RNA synthesized after transfection. To produce detectable amounts of CATase with the IVa2 promoter, an enhancer has to be present in cis. In the absence of enhancer sequences, the adenovirus E1A gene can not stimulate CATase synthesis. When cells were transfected with plasmids containing enhancer sequences and various IVa2 mutant promoters upstream of the CAT gene, we observed that CATase activity was not reduced significantly even after deletion of all sequences upstream of the RNA initiation site. Synthesis of IVa2 specific RNA was dependent on plasmids containing an enhancer (SV40 72 bp repeat) that was present in cis. In the absence of enhancer sequences, co-transfection to provide the adenovirus E1A gene in trans also stimulated IVa2 RNA synthesis. When HeLa cells were transfected with various deletion mutants with an enhancer in cis it was seen that sequences -38 to -64 base pairs upstream of the RNA initiation site are necessary for efficient transcription. The E1A gene in trans and an enhancer in cis have an additive effect on RNA synthesis from both IVa2 and major late promoters. The basis for the conflicting results between transcription and CATase synthesis is discussed. Images PMID:2989786

  8. 7 CFR 272.10 - ADP/CIS Model Plan.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 4 2014-01-01 2014-01-01 false ADP/CIS Model Plan. 272.10 Section 272.10 Agriculture Regulations of the Department of Agriculture (Continued) FOOD AND NUTRITION SERVICE, DEPARTMENT OF AGRICULTURE... other State agencies that have similar characteristics such as whether they are urban or rural,...

  9. Peer Tutoring in the CIS Sandbox: Does It Work?

    ERIC Educational Resources Information Center

    Frydenberg, Mark

    2013-01-01

    This paper reports on a student-created and facilitated peer-tutoring activity to assist first-year students in preparing for their final exam in an introductory information technology course. Tutors at the CIS Sandbox, a collaborative learning lab at an American university, offered a series of "Crunch Sessions" to their peers. This…

  10. Creating a Collaborative Learning Community in the CIS Sandbox

    ERIC Educational Resources Information Center

    Frydenberg, Mark

    2013-01-01

    Purpose: The purpose of this paper is to investigate the impact of transforming a traditional university computer lab to create a collaborative learning community known as the CIS Sandbox, by remodeling a physical space and supporting it with a virtual presence through the use of social media tools. The discussion applies Selander's "designs for…

  11. Epistatic Interactions in the Arabinose Cis-Regulatory Element.

    PubMed

    Lagator, Mato; Igler, Claudia; Moreno, Anaísa B; Guet, Călin C; Bollback, Jonathan P

    2016-03-01

    Changes in gene expression are an important mode of evolution; however, the proximate mechanism of these changes is poorly understood. In particular, little is known about the effects of mutations within cis binding sites for transcription factors, or the nature of epistatic interactions between these mutations. Here, we tested the effects of single and double mutants in two cis binding sites involved in the transcriptional regulation of the Escherichia coli araBAD operon, a component of arabinose metabolism, using a synthetic system. This system decouples transcriptional control from any posttranslational effects on fitness, allowing a precise estimate of the effect of single and double mutations, and hence epistasis, on gene expression. We found that epistatic interactions between mutations in the araBAD cis-regulatory element are common, and that the predominant form of epistasis is negative. The magnitude of the interactions depended on whether the mutations are located in the same or in different operator sites. Importantly, these epistatic interactions were dependent on the presence of arabinose, a native inducer of the araBAD operon in vivo, with some interactions changing in sign (e.g., from negative to positive) in its presence. This study thus reveals that mutations in even relatively simple cis-regulatory elements interact in complex ways such that selection on the level of gene expression in one environment might perturb regulation in the other environment in an unpredictable and uncorrelated manner.

  12. cis- and trans-Stilbenes: Chromatographic Separation and Photochemical Isomerization.

    ERIC Educational Resources Information Center

    Levine, Samuel G.; And Others

    1988-01-01

    Describes an experiment that is to be performed midway in the first semester of an undergraduate organic chemistry laboratory coinciding with the students' introduction to cis-trans isomerism in the study of alkenes. Discusses the apparatus, materials, experimental procedure, historical significance, and results. (CW)

  13. Commercial Off-the-Shelf (COTS) Components and Enterprise Component Information System (eCIS)

    SciTech Connect

    John Minihan; Ed Schmidt; Greg Enserro; Melissa Thompson

    2008-06-30

    The purpose of the project was to develop the processes for using commercial off-the-shelf (COTS) parts for WR production and to put in place a system for implementing the data management tools required to disseminate, store, track procurement, and qualify vendors. Much of the effort was devoted to determining if the use of COTS parts was possible. A basic question: How does the Nuclear Weapons Complex (NWC) begin to use COTS in the weapon Stockpile Life Extension Programs with high reliability, affordability, while managing risk at acceptable levels? In FY00, it was determined that a certain weapon refurbishment program could not be accomplished without the use of COTS components. The elements driving the use of COTS components included decreased cost, greater availability, and shorter delivery time. Key factors that required implementation included identifying the best suppliers and components, defining life cycles and predictions of obsolescence, testing the feasibility of using COTS components with a test contractor to ensure capability, as well as quality and reliability, and implementing the data management tools required to disseminate, store, track procurement, and qualify vendors. The primary effort of this project then was to concentrate on the risks involved in the use of COTS and address the issues of part and vendor selection, procurement and acceptance processes, and qualification of the parts via part and sample testing. The Enterprise Component Information System (eCIS) was used to manage the information generated by the COTS process. eCIS is a common interface for both the design and production of NWC components and systems integrating information between SNL National Laboratory (SNL) and the Kansas City Plant (KCP). The implementation of COTS components utilizes eCIS from part selection through qualification release. All part related data is linked across an unclassified network for access by both SNL and KCP personnel. The system includes not

  14. Metrology of Large Parts. Chapter 5

    NASA Technical Reports Server (NTRS)

    Stahl, H. Philip

    2012-01-01

    As discussed in the first chapter of this book, there are many different methods to measure a part using optical technology. Chapter 2 discussed the use of machine vision to measure macroscopic features such as length and position, which was extended to the use of interferometry as a linear measurement tool in chapter 3, and laser or other trackers to find the relation of key points on large parts in chapter 4. This chapter looks at measuring large parts to optical tolerances in the sub-micron range using interferometry, ranging, and optical tools discussed in the previous chapters. The purpose of this chapter is not to discuss specific metrology tools (such as interferometers or gauges), but to describe a systems engineering approach to testing large parts. Issues such as material warpage and temperature drifts that may be insignificant when measuring a part to micron levels under a microscope, as will be discussed in later chapters, can prove to be very important when making the same measurement over a larger part. In this chapter, we will define a set of guiding principles for successfully overcoming these challenges and illustrate the application of these principles with real world examples. While these examples are drawn from specific large optical testing applications, they inform the problems associated with testing any large part to optical tolerances. Manufacturing today relies on micrometer level part performance. Fields such as energy and transportation are demanding higher tolerances to provide increased efficiencies and fuel savings. By looking at how the optics industry approaches sub-micrometer metrology, one can gain a better understanding of the metrology challenges for any larger part specified to micrometer tolerances. Testing large parts, whether optical components or precision structures, to optical tolerances is just like testing small parts, only harder. Identical with what one does for small parts, a metrologist tests large parts and optics

  15. Functional cis-regulatory genomics for systems biology

    PubMed Central

    Nam, Jongmin; Dong, Ping; Tarpine, Ryan; Istrail, Sorin; Davidson, Eric H.

    2010-01-01

    Gene expression is controlled by interactions between trans-regulatory factors and cis-regulatory DNA sequences, and these interactions constitute the essential functional linkages of gene regulatory networks (GRNs). Validation of GRN models requires experimental cis-regulatory tests of predicted linkages to authenticate their identities and proposed functions. However, cis-regulatory analysis is, at present, at a severe bottleneck in genomic system biology because of the demanding experimental methodologies currently in use for discovering cis-regulatory modules (CRMs), in the genome, and for measuring their activities. Here we demonstrate a high-throughput approach to both discovery and quantitative characterization of CRMs. The unique aspect is use of DNA sequence tags to “barcode” CRM expression constructs, which can then be mixed, injected together into sea urchin eggs, and subsequently deconvolved. This method has increased the rate of cis-regulatory analysis by >100-fold compared with conventional one-by-one reporter assays. The utility of the DNA-tag reporters was demonstrated by the rapid discovery of 81 active CRMs from 37 previously unexplored sea urchin genes. We then obtained simultaneous high-resolution temporal characterization of the regulatory activities of more than 80 CRMs. On average 2–3 CRMs were discovered per gene. Comparison of endogenous gene expression profiles with those of the CRMs recovered from each gene showed that, for most cases, at least one CRM is active in each phase of endogenous expression, suggesting that CRM recovery was comprehensive. This approach will qualitatively alter the practice of GRN construction as well as validation, and will impact many additional areas of regulatory system biology. PMID:20142491

  16. Abundant raw material for cis-regulatory evolution in humans

    NASA Technical Reports Server (NTRS)

    Rockman, Matthew V.; Wray, Gregory A.

    2002-01-01

    Changes in gene expression and regulation--due in particular to the evolution of cis-regulatory DNA sequences--may underlie many evolutionary changes in phenotypes, yet little is known about the distribution of such variation in populations. We present in this study the first survey of experimentally validated functional cis-regulatory polymorphism. These data are derived from more than 140 polymorphisms involved in the regulation of 107 genes in Homo sapiens, the eukaryote species with the most available data. We find that functional cis-regulatory variation is widespread in the human genome and that the consequent variation in gene expression is twofold or greater for 63% of the genes surveyed. Transcription factor-DNA interactions are highly polymorphic, and regulatory interactions have been gained and lost within human populations. On average, humans are heterozygous at more functional cis-regulatory sites (>16,000) than at amino acid positions (<13,000), in part because of an overrepresentation among the former in multiallelic tandem repeat variation, especially (AC)(n) dinucleotide microsatellites. The role of microsatellites in gene expression variation may provide a larger store of heritable phenotypic variation, and a more rapid mutational input of such variation, than has been realized. Finally, we outline the distinctive consequences of cis-regulatory variation for the genotype-phenotype relationship, including ubiquitous epistasis and genotype-by-environment interactions, as well as underappreciated modes of pleiotropy and overdominance. Ordinary small-scale mutations contribute to pervasive variation in transcription rates and consequently to patterns of human phenotypic variation.

  17. Structural Brain Network Characteristics Can Differentiate CIS from Early RRMS

    PubMed Central

    Muthuraman, Muthuraman; Fleischer, Vinzenz; Kolber, Pierre; Luessi, Felix; Zipp, Frauke; Groppa, Sergiu

    2016-01-01

    Focal demyelinated lesions, diffuse white matter (WM) damage, and gray matter (GM) atrophy influence directly the disease progression in patients with multiple sclerosis. The aim of this study was to identify specific characteristics of GM and WM structural networks in subjects with clinically isolated syndrome (CIS) in comparison to patients with early relapsing-remitting multiple sclerosis (RRMS). Twenty patients with CIS, 33 with RRMS, and 40 healthy subjects were investigated using 3 T-MRI. Diffusion tensor imaging was applied, together with probabilistic tractography and fractional anisotropy (FA) maps for WM and cortical thickness correlation analysis for GM, to determine the structural connectivity patterns. A network topology analysis with the aid of graph theoretical approaches was used to characterize the network at different community levels (modularity, clustering coefficient, global, and local efficiencies). Finally, we applied support vector machines (SVM) to automatically discriminate the two groups. In comparison to CIS subjects, patients with RRMS were found to have increased modular connectivity and higher local clustering, highlighting increased local processing in both GM and WM. Both groups presented increased modularity and clustering coefficients in comparison to healthy controls. SVM algorithms achieved 97% accuracy using the clustering coefficient as classifier derived from GM and 65% using WM from probabilistic tractography and 67% from modularity of FA maps to differentiate between CIS and RRMS patients. We demonstrate a clear increase of modular and local connectivity in patients with early RRMS in comparison to CIS and healthy subjects. Based only on a single anatomic scan and without a priori information, we developed an automated and investigator-independent paradigm that can accurately discriminate between patients with these clinically similar disease entities, and could thus complement the current dissemination-in-time criteria for

  18. Use of a Drosophila Genome-Wide Conserved Sequence Database to Identify Functionally Related cis-Regulatory Enhancers

    PubMed Central

    Brody, Thomas; Yavatkar, Amarendra S; Kuzin, Alexander; Kundu, Mukta; Tyson, Leonard J; Ross, Jermaine; Lin, Tzu-Yang; Lee, Chi-Hon; Awasaki, Takeshi; Lee, Tzumin; Odenwald, Ward F

    2012-01-01

    Background: Phylogenetic footprinting has revealed that cis-regulatory enhancers consist of conserved DNA sequence clusters (CSCs). Currently, there is no systematic approach for enhancer discovery and analysis that takes full-advantage of the sequence information within enhancer CSCs. Results: We have generated a Drosophila genome-wide database of conserved DNA consisting of >100,000 CSCs derived from EvoPrints spanning over 90% of the genome. cis-Decoder database search and alignment algorithms enable the discovery of functionally related enhancers. The program first identifies conserved repeat elements within an input enhancer and then searches the database for CSCs that score highly against the input CSC. Scoring is based on shared repeats as well as uniquely shared matches, and includes measures of the balance of shared elements, a diagnostic that has proven to be useful in predicting cis-regulatory function. To demonstrate the utility of these tools, a temporally-restricted CNS neuroblast enhancer was used to identify other functionally related enhancers and analyze their structural organization. Conclusions: cis-Decoder reveals that co-regulating enhancers consist of combinations of overlapping shared sequence elements, providing insights into the mode of integration of multiple regulating transcription factors. The database and accompanying algorithms should prove useful in the discovery and analysis of enhancers involved in any developmental process. Developmental Dynamics 241:169–189, 2012. © 2011 Wiley Periodicals, Inc. Key findings A genome-wide catalog of Drosophila conserved DNA sequence clusters. cis-Decoder discovers functionally related enhancers. Functionally related enhancers share balanced sequence element copy numbers. Many enhancers function during multiple phases of development. PMID:22174086

  19. Volumetric Properties of the Mixture Cyclooctane C8H16 + C10H18 cis-Bicyclo[4.4.0]decane (VMSD1111, LB3903_V)

    NASA Astrophysics Data System (ADS)

    Cibulka, I.; Fontaine, J.-C.; Sosnkowska-Kehiaian, K.; Kehiaian, H. V.

    This document is part of Subvolume B 'Binary Liquid Systems of Nonelectrolytes II' of Volume 26 'Heats of Mixing, Vapor-Liquid Equilibrium, and Volumetric Properties of Mixtures and Solutions' of Landolt-Börnstein Group IV 'Physical Chemistry'. It contains the Chapter 'Volumetric Properties of the Mixture Cyclooctane C8H16 + C10H18 cis-Bicyclo[4.4.0]decane (VMSD1111, LB3903_V)' providing data from direct low-pressure measurement of mass density at variable mole fraction and constant temperature, in the single-phase region(s).

  20. Volumetric Properties of the Mixture Cyclooctane C8H16 + C10H18 cis-Bicyclo[4.4.0]decane (VMSD1212, LB3897_V)

    NASA Astrophysics Data System (ADS)

    Cibulka, I.; Fontaine, J.-C.; Sosnkowska-Kehiaian, K.; Kehiaian, H. V.

    This document is part of Subvolume B 'Binary Liquid Systems of Nonelectrolytes II' of Volume 26 'Heats of Mixing, Vapor-Liquid Equilibrium, and Volumetric Properties of Mixtures and Solutions' of Landolt-Börnstein Group IV 'Physical Chemistry'. It contains the Chapter 'Volumetric Properties of the Mixture Cyclooctane C8H16 + C10H18 cis-Bicyclo[4.4.0]decane (VMSD1212, LB3897_V)' providing data by calculation of molar excess volume from low-pressure density measurements at variable mole fraction and constant temperature.

  1. Volumetric Properties of the Mixture cis-1,4-Dimethylcyclohexane C8H16 + C14H30 Tetradecane (VMSD1111, LB4202_V)

    NASA Astrophysics Data System (ADS)

    Cibulka, I.; Fontaine, J.-C.; Sosnkowska-Kehiaian, K.; Kehiaian, H. V.

    This document is part of Subvolume B 'Binary Liquid Systems of Nonelectrolytes II' of Volume 26 'Heats of Mixing, Vapor-Liquid Equilibrium, and Volumetric Properties of Mixtures and Solutions' of Landolt-Börnstein Group IV 'Physical Chemistry'. It contains the Chapter 'Volumetric Properties of the Mixture cis-1,4-Dimethylcyclohexane C8H16 + C14H30 Tetradecane (VMSD1111, LB4202_V)' providing data from direct low-pressure measurement of mass density at variable mole fraction and constant temperature, in the single-phase region(s).

  2. Volumetric Properties of the Mixture cis-1,4-Dimethylcyclohexane C8H16 + C14H30 Tetradecane (VMSD1212, LB4208_V)

    NASA Astrophysics Data System (ADS)

    Cibulka, I.; Fontaine, J.-C.; Sosnkowska-Kehiaian, K.; Kehiaian, H. V.

    This document is part of Subvolume B 'Binary Liquid Systems of Nonelectrolytes II' of Volume 26 'Heats of Mixing, Vapor-Liquid Equilibrium, and Volumetric Properties of Mixtures and Solutions' of Landolt-Börnstein Group IV 'Physical Chemistry'. It contains the Chapter 'Volumetric Properties of the Mixture cis-1,4-Dimethylcyclohexane C8H16 + C14H30 Tetradecane (VMSD1212, LB4208_V)' providing data by calculation of molar excess volume from low-pressure density measurements at variable mole fraction and constant temperature.

  3. Generation of a catR deficient mutant of P. putida KT2440 that produces cis, cis-muconate from benzoate at high rate and yield.

    PubMed

    van Duuren, J B J H; Wijte, D; Leprince, A; Karge, B; Puchałka, J; Wery, J; Dos Santos, V A P Martins; Eggink, G; Mars, A E

    2011-12-10

    Pseudomonas putida KT2440-JD1 was derived from P. putida KT2440 after N-methyl-N'-nitro-N-nitrosoguanidine (NTG)-mutagenesis and exposure to 3-fluorobenzoate (3-FB). The mutant was no longer able to grow using benzoate as a sole carbon source, but co-metabolized benzoate to cis, cis-muconate during growth on glucose, which accumulated in the growth medium. The specific production rate (q(pm)) was 0.18±0.03 g cis, cis-muconate/(g(DCW) h) in continuous cultures, and increased to 1.4 g cis, cis-muconate/(g(DCW) h) during wash-out cultivation. Transcriptome analysis showed that the cat operon was not induced in P. putida KT2440-JD1 in the presence of 5mM benzoate, due to a point mutation in the highly conserved DNA binding domain of the transcriptional regulator (catR) of the cat operon. The ben operon was highly expressed in the presence of benzoate in the mutant and its parental strain. This operon contains PP_3166 (catA2), which was shown to be a second catechol 1,2-dioxygenase besides catA. P. putida KT2440-JD1 is the first cis, cis-muconate-accumulating mutant that was characterized at the genetic level. The specific production rate achieved is at least eight times higher than those reported for other cis, cis-muconate-producing strains.

  4. Vaccination against bacterial kidney disease: Chapter 22

    USGS Publications Warehouse

    Elliott, Diane G.; Wiens, Gregory D.; Hammell, K. Larry; Rhodes, Linda D.; Edited by Gudding, Roar; Lillehaug, Atle; Evensen, Øystein

    2014-01-01

    Bacterial kidney disease (BKD) of salmonid fishes, caused by Renibacterium salmoninarum, has been recognized as a serious disease in salmonid fishes since the 1930s. This chapter discusses the occurrence and significance, etiology, and pathogenesis of BKD. It then describes the different vaccination procedures and the effects and side-effects of vaccination. Despite years of research, however, only a single vaccine has been licensed for prevention of BKD, and has demonstrated variable efficacy. Therefore, in addition to a presentation of the current status of BKD vaccination, a discussion of potential future directions for BKD vaccine development is included in the chapter. This discussion is focused on the unique characteristics of R. salmoninarum and its biology, as well as aspects of the salmonid immune system that might be explored specifically to develop more effective vaccines for BKD prevention.

  5. Fundamentals of Physics, Part 1 (Chapters 1-11)

    NASA Astrophysics Data System (ADS)

    Halliday, David; Resnick, Robert; Walker, Jearl

    2003-12-01

    Chapter 1.Measurement. How does the appearance of a new type of cloud signal changes in Earth's atmosphere? 1-1 What Is Physics? 1-2 Measuring Things. 1-3 The International System of Units. 1-4 Changing Units. 1-5 Length. 1-6 Time. 1-7 Mass. Review & Summary. Problems. Chapter 2.Motion Along a Straight Line. What causes whiplash injury in rear-end collisions of cars? 2-1 What Is Physics? 2-2 Motion. 2-3 Position and Displacement. 2-4 Average Velocity and Average Speed. 2-5 Instantaneous Velocity and Speed. 2-6 Acceleration. 2-7 Constant Acceleration: A Special Case. 2-8 Another Look at Constant Acceleration. 2-9 Free-Fall Acceleration. 2-10 Graphical Integration in Motion Analysis. Review & Summary. Questions. Problems. Chapter 3.Vectors. How does an ant know the way home with no guiding clues on the deser t plains? 3-2 Vectors and Scalars. 3-3 Adding Vectors Geometrically. 3-4 Components of Vectors. 3-5 Unit Vectors. 3-6 Adding Vectors by Components. 3-7 Vectors and the Laws of Physics. 3-8 Multiplying Vectors. Review & Summary. Questions. Problems. Chapter 4.Motion in Two and Three Dimensions. In a motorcycle jump for record distance, where does the jumper put the second ramp? 4-1 What Is Physics? 4-2 Position and Displacement. 4-3 Average Velocity and Instantaneous Velocity. 4-4 Average Acceleration and Instantaneous Acceleration. 4-5 Projectile Motion. 4-6 Projectile Motion Analyzed. 4-7 Uniform Circular Motion. 4-8 Relative Motion in One Dimension. 4-9 Relative Motion in Two Dimensions. Review & Summary. Questions. Problems. Chapter 5.Force and Motion-I. When a pilot takes off from an aircraft carrier, what causes the compulsion to fly the plane into the ocean? 5-1 What Is Physics? 5-2 Newtonian Mechanics. 5-3 Newton's First Law. 5-4 Force. 5-5 Mass. 5-6 Newton's Second Law. 5-7 Some Particular Forces. 5-8 Newton's Third Law. 5-9 Applying Newton's Laws. Review & Summary. Questions. Problems. Chapter 6.Force and Motion-II. Can a Grand Prix race car be driven

  6. Dust and human health: Chapter 15

    USGS Publications Warehouse

    Morman, Suzette A.; Plumlee, Geoffrey S.; Knippertz, Peter; Stuut, Jan-Berend W.

    2013-01-01

    It is generally accepted that exposure to fine particulate matter may increase risk for human morbidity and mortality. Until recently, population health related studies examining the effects of particulate matter on human health generally examined anthropogenic (industry and combustion by-products) sources with few studies considering contributions from natural sources. This chapter provides an overview of naturally occurring inorganic mineral dust research and associated human health ailments and some of the challenges in elucidating the etiological mechanisms responsible.

  7. Managing atypical hemolytic uremic syndrome: chapter 2.

    PubMed

    Nester, Carla M

    2015-05-01

    Licht et al. present the 2-year follow-up data of the landmark trials studying the efficacy of eculizumab in the treatment of atypical hemolytic uremic syndrome (aHUS). They report sustained improvements in hematologic parameters, continued safety, and additional improvements in kidney function with extended treatment. This report adds a layer of comfort to our care of patients with this rare disease; however, it is unlikely to be the final chapter in the treatment of aHUS.

  8. Chapter A9. Safety in Field Activities

    USGS Publications Warehouse

    Lane, Susan L.; Ray, Ronald G.

    1998-01-01

    The National Field Manual for the Collection of Water-Quality Data (National Field Manual) describes protocols (requirements and recommendations) and provides guidelines for U.S. Geological Survey (USGS) personnel who collect data used to assess the quality of the Nation's surface-water and ground-water resources. This chapter of the manual addresses topics related to personal safety to be used in the collection of water-quality data, including: policies and general regulations on field safety; transportation of people and equipment; implementation of surface-water and ground-water activities; procedures for handling chemicals; and information on potentially hazardous environmental conditions, animals, and plants. Each chapter of the National Field Manual is published separately and revised periodically. Newly published and revised chapters will be announced on the USGS Home Page on the World Wide Web under 'New Publications of the U.S. Geological Survey.' The URL for this page is http://pubs.usgs.gov/publications/ index.html.

  9. Solid Lubrication Fundamentals and Applications. Chapter 6

    NASA Technical Reports Server (NTRS)

    Miyoshi, Kazuhisa

    2000-01-01

    This chapter focuses attention on the friction and wear properties of selected solid lubricating films to aid users in choosing the best lubricant, deposition conditions, and operational variables. For simplicity, discussion of the tribological properties of concern is separated into two parts. The first part of the chapter discusses the different solid lubricating films selected for study including commercially developed solid film lubricants: (1) bonded molybdenum disulfide (MoS2), (2) magnetron-sputtered MoS2, (3) ion-plated silver, (4) ion-plated lead, (5) magnetron-sputtered diamondlike carbon (MS DLC), and (6) plasma-assisted, chemical-vapor-deposited diamondlike carbon (PACVD DEC) films. Marked differences in the friction and wear properties of the different films resulted from the different environmental conditions (ultrahigh vacuum, humid air, and dry nitrogen) and the solid film lubricant materials. The second part of the chapter discusses the physical and chemical characteristics, friction behavior, and endurance life of the magnetron-sputtered MoS2 films. The role of interface species and the effects of applied load, film thickness, oxygen pressure, environment, and temperature on the friction and wear properties are considered.

  10. A Survey of Geologic Resources. Chapter 11

    NASA Technical Reports Server (NTRS)

    Edmonson, Jennifer; Rickman, Doug

    2012-01-01

    This chapter focuses on the resources available from the Moon itself: regolith, geologically concentrated materials, and lunar physical features that will enable habitation and generation of power on the surface. This chapter briefly covers the formation of the Moon and thus the formation of the crust of the Moon, as well as the evolution of the regolith. The characteristics of the regolith are provided in some detail, including its mineralogy and lithology. The location of high concentrations of specific minerals or rocks is noted. Other ideal locations for in situ resource utilization technology and lunar habitation are presented. This chapter is intended to be a brief review of current knowledge, and to serve as a foundational source for further study. Each concept presented here has a wealth of literature associated with it; the reader is therefore directed to that literature with each discussion. With great interest in possible manned lunar landings and continued study of the Moon by multiple satellites, the available information changes regularly.

  11. Water, water quality and health (Chapter 3 in Book entitled: Environmental Tracking for Public Health Surveillance).

    EPA Science Inventory

    This chapter identifies the role environmental tracking plays in identifying public health water hazard and water quality issues. It outlines public health issues to be examined and provides an integrated overview of water and diseases by combining knowledge of the hydrological ...

  12. Proper Use of Allele-Specific Expression Improves Statistical Power for cis-eQTL Mapping with RNA-Seq Data

    PubMed Central

    HU, Yi-Juan; SUN, Wei; TZENG, Jung-Ying; PEROU, Charles M.

    2015-01-01

    Studies of expression quantitative trait loci (eQTLs) offer insight into the molecular mechanisms of loci that were found to be associated with complex diseases and the mechanisms can be classified into cis- and trans-acting regulation. At present, high-throughput RNA sequencing (RNA-seq) is rapidly replacing expression microarrays to assess gene expression abundance. Unlike microarrays that only measure the total expression of each gene, RNA-seq also provides information on allele-specific expression (ASE), which can be used to distinguish cis-eQTLs from trans-eQTLs and, more importantly, enhance cis-eQTL mapping. However, assessing the cis-effect of a candidate eQTL on a gene requires knowledge of the haplotypes connecting the candidate eQTL and the gene, which cannot be inferred with certainty. The existing two-stage approach that first phases the candidate eQTL against the gene and then treats the inferred phase as observed in the association analysis tends to attenuate the estimated cis-effect and reduce the power for detecting a cis-eQTL. In this article, we provide a maximum-likelihood framework for cis-eQTL mapping with RNA-seq data. Our approach integrates the inference of haplotypes and the association analysis into a single stage, and is thus unbiased and statistically powerful. We also develop a pipeline for performing a comprehensive scan of all local eQTLs for all genes in the genome by controlling for false discovery rate, and implement the methods in a computationally efficient software program. The advantages of the proposed methods over the existing ones are demonstrated through realistic simulation studies and an application to empirical breast cancer data from The Cancer Genome Atlas project. PMID:26568645

  13. FootprintDB: Analysis of Plant Cis-Regulatory Elements, Transcription Factors, and Binding Interfaces.

    PubMed

    Contreras-Moreira, Bruno; Sebastian, Alvaro

    2016-01-01

    FootprintDB is a database and search engine that compiles regulatory sequences from open access libraries of curated DNA cis-elements and motifs, and their associated transcription factors (TFs). It systematically annotates the binding interfaces of the TFs by exploiting protein-DNA complexes deposited in the Protein Data Bank. Each entry in footprintDB is thus a DNA motif linked to the protein sequence of the TF(s) known to recognize it, and in most cases, the set of predicted interface residues involved in specific recognition. This chapter explains step-by-step how to search for DNA motifs and protein sequences in footprintDB and how to focus the search to a particular organism. Two real-world examples are shown where this software was used to analyze transcriptional regulation in plants. Results are described with the aim of guiding users on their interpretation, and special attention is given to the choices users might face when performing similar analyses. PMID:27557773

  14. Overview of NATO Background on Scramjet Technology. Chapter 1

    NASA Technical Reports Server (NTRS)

    Drummond, J. Philip; Bouchez, Marc; McClinton, Charles R.

    2006-01-01

    The purpose of the present overview is to summarize the current knowledge of the NATO contributors. All the topics will be addressed in this chapter, with references and some examples. This background enhances the level of knowledge of the NATO scramjet community, which will be used for writing the specific chapters of the Report. Some previous overviews have been published on scramjet technology worldwide. NASA, DOD, the U.S. industry and global community have studied scramjet-powered hypersonic vehicles for over 40 years. Within the U.S. alone, NASA, DOD (DARPA, U.S. Navy and USAF), and industry have participated in hypersonic technology development. Over this time NASA Langley Research Center continuously studied hypersonic system design, aerothermodynamics, scramjet propulsion, propulsion-airframe integration, high temperature materials and structural architectures, and associated facilities, instrumentation and test methods. These modestly funded programs were substantially augmented during the National Aero-Space Plane (X-30) Program, which spent more than $3B between 1984 and 1995, and brought the DOD and other NASA Centers, universities and industry back into hypersonics. In addition, significant progress was achieved in all technologies required for hypersonic flight, and much of that technology was transferred into other programs, such as X-33, DC-X, X-37, X-43, etc. In addition, technology transfer impacted numerous other industries, including automotive, medical, sports and aerospace.

  15. Fundamentals of Physics, Volume 1, (Chapters 1 - 21)

    NASA Astrophysics Data System (ADS)

    Walker, Jearl

    2004-01-01

    Chapter 1. Measurement 1. How does the appearance of a new type of cloud signal changes in Earth's atmosphere? 1-1 What Is Physics? 1-2 Measuring Things. 1-3 The International System of Units. 1-4 Changing Units. 1-5 Length. 1-6 Time. 1-7 Mass. Review & Summary. Problems. Chapter 2. Motion Along a Straight Line. What causes whiplash injury in rear-end collisions of cars? 2-1 What Is Physics? 2-2 Motion. 2-3 Position and Displacement. 2-4 Average Velocity and Average Speed. 2-5 Instantaneous Velocity and Speed. 2-6 Acceleration. 2-7 Constant Acceleration: A Special Case. 2-8 Another Look at Constant Acceleration. 2-9 Free-Fall Acceleration. 2-10 Graphical Integration in Motion Analysis. 2 Review & Summary. Questions. Problems. Chapter 3. Vectors. How does an ant know the way home with no guiding clues on the desert plains? 3-1 What Is Physics? 3-2 Vectors and Scalars. 3-3 Adding Vectors Geometrically. 3-4 Components of Vectors. 3-5 Unit Vectors. 3-6 Adding Vectors by Components. 3-7 Vectors and the Laws of Physics. 3-8 Multiplying Vectors. Review & Summary. Questions. Problems. Chapter 4. Motion in Two and Three Dimensions. In a motorcycle jump for record distance, where does the jumper put the second ramp? 4-1 What Is Physics? 4-2 Position and Displacement. 4-3 Average Velocity and Instantaneous Velocity. 4-4 Average Acceleration and Instantaneous Acceleration. 4-5 Projectile Motion. 4-6 Projectile Motion Analyzed. 4-7 Uniform Circular Motion. 4-8 Relative Motion in One Dimension. 4-9 Relative Motion in Two Dimensions. Review & Summary. Questions. Problems. Chapter 5. Force and Motion--I. When a pilot takes off from an aircraft carrier, what causes the compulsion to .y the plane into the ocean? 5-1 What Is Physics? 5-2 Newtonian Mechanics. 5-3 Newton's First Law. 5-4 Force. 5-5 Mass. 5-6 Newton's Second Law. 5-7 Some Particular Forces. 5-8 Newton's Third Law. 5-9 Applying Newton's Laws. Review & Summary. Questions. Problems. Chapter 6. Force and Motion--II. Can a

  16. Near-UV absorption cross sections and trans/cis equilibrium of nitrous acid

    SciTech Connect

    Bongartz, A.; Kames, J.; Welter, F.; Schurath, U. )

    1991-02-07

    The A {sup 1}A{double prime} {l arrow} X {sup 1}A{prime} absorption spectrum of gaseous nitrous acid has been measured in the 300-400-nm range. Absolute cross sections were determined by a combination of gas-phase and wet chemical analysis. The cross sections of prominent bands are 25% larger than the recommended values of Stockwell and Calvert. The influence of spectral resolution on absolute and differential absorption cross sections was also investigated. The integrated band area of the n{pi}* transition yields an oscillator strength f = (8.90 {plus minus} 0.36) {times} 10{sup {minus}4}, less than the reported liquid phase value of 2 {times} 10{sup {minus}3}. The equilibrium constant K = p{sub trans}/p{sub cis}, based on the assumption that the oscillator strength of the n{pi}* transition is the same for both rotamers, was found to be 3.25 {plus minus} 0.30 at 277 K. This yields an energy difference {Delta}E between trans- and cis-HONO of -2,700 J mol{sup {minus}1} in the electronic ground state, and -6,000 J mol{sup {minus}1} in the excited state.

  17. Absorption of CIS Immigrants into Israeli Schools: A Semipermeable Enclave Model.

    ERIC Educational Resources Information Center

    Resnik, Julia; Sabar, Naama; Shoham, Edna; Shapira, Rina

    2001-01-01

    Examined how immigrants from the Commonwealth of Independent States (CIS) assimilated into Israeli society and schools. Data from observations, interviews, and surveys indicated that educational policies and school arrangements, and CIS immigrants' high self-esteem, produced a semipermeable enclave. CIS students acquired the Hebrew language and…

  18. Functional evolution of a cis-regulatory module.

    PubMed

    Ludwig, Michael Z; Palsson, Arnar; Alekseeva, Elena; Bergman, Casey M; Nathan, Janaki; Kreitman, Martin

    2005-04-01

    Lack of knowledge about how regulatory regions evolve in relation to their structure-function may limit the utility of comparative sequence analysis in deciphering cis-regulatory sequences. To address this we applied reverse genetics to carry out a functional genetic complementation analysis of a eukaryotic cis-regulatory module-the even-skipped stripe 2 enhancer-from four Drosophila species. The evolution of this enhancer is non-clock-like, with important functional differences between closely related species and functional convergence between distantly related species. Functional divergence is attributable to differences in activation levels rather than spatiotemporal control of gene expression. Our findings have implications for understanding enhancer structure-function, mechanisms of speciation and computational identification of regulatory modules.

  19. [Transsexual wish and and cis-sexual defense].

    PubMed

    Sigusch, V

    1995-01-01

    The desire of trans-sexual patients to appropriate the physical attributes of the opposite sex via hormone treatment or surgery confronts psychoanalysis and sex research with problems that are not only psychological in nature. Sigusch uses the term "defence" here not only in a technical sense but also in an epistemological, discourse-analytic and disposition-analytic register. The general dispositions determining the reality of gender and gender difference are "cis-sexual" in nature. The polarity they display extends to the physical and manifests itself in the form of sexual binarism. The author coins the consciously neologistic term "cis-sexual" to describe individuals where physical gender and gender identity are completely and "naturally" co-extensive. Only the realization that "second-nature" is in reality primary can trigger the detotalization of so-called trans-sexuality that Sigusch is concerned to call into question. PMID:7480808

  20. Multicomponent reactions of methyl substituted all-cis tetrafluorocyclohexane aldehydes.

    PubMed

    Bykova, Tetiana; Al-Maharik, Nawaf; Slawin, Alexandra M Z; O'Hagan, David

    2016-01-21

    This paper reports the preparation of methyl substituted all-cis tetrafluorocyclohexanes prepared from a Birch reduction of benzoic acid, worked up with a methyl iodide quench. The resultant methylcyclohexadiene carboxylic acid was reduced to the alcohol, protected as an ether and then a sequence of functional group manipulations carried out to introduce four fluorines. The cyclohexadienyl ring was then epoxidised and the C-O bonds sequentially converted through deoxyfluorination reactions to two sets of isomers of all-cis tetrafluorocyclohexane isomers. The blocking methyl group renders the ring safe to hydrogen fluoride elimination. Deprotection of the benzylic ether and then oxidation gave aldehydes which were then used in Ugi and Passerini multicomponent reactions, allowing this facially polarised cyclohexane to be incorporated into peptidic structural motifs. PMID:26646211

  1. Different reaction mechanisms for cis- and trans-prenyltransferases

    SciTech Connect

    Lu Yenpin; Liu Hunge; Liang, P-H.

    2009-02-06

    Octaprenyl diphosphate synthase (OPPs) and undecaprenyl diphosphate synthases (UPPs) catalyze consecutive condensation reactions of farnesyl diphosphate (FPP) with 5 and 8 isopentenyl diphosphate (IPP) to generate C{sub 40} and C{sub 55} products with trans- and cis-double bonds, respectively. In this study, we used IPP analogue, 3-bromo-3-butenyl diphosphate (Br-IPP), in conjunction with radiolabeled FPP, to probe the reaction mechanisms of the two prenyltransferases. Using this alternative substrate with electron-withdrawing bromo group at the C3 position to slow down the condensation step, trapping of farnesol in the OPPs reaction from radiolabeled FPP under basic condition was observed, consistent with a sequential mechanism. In contrast, UPPs reaction yielded no farnesyl carbocation intermediate under the same condition with radiolabeled FPP and Br-IPP, indicating a concerted mechanism. Our data demonstrate the different reaction mechanisms for cis- and tran-prenyltransferases although they share the same substrates.

  2. Different reaction mechanisms for cis- and trans-prenyltransferases.

    PubMed

    Lu, Yen-Pin; Liu, Hun-Ge; Liang, Po-Huang

    2009-02-01

    Octaprenyl diphosphate synthase (OPPs) and undecaprenyl diphosphate synthases (UPPs) catalyze consecutive condensation reactions of farnesyl diphosphate (FPP) with 5 and 8 isopentenyl diphosphate (IPP) to generate C(40) and C(55) products with trans- and cis-double bonds, respectively. In this study, we used IPP analogue, 3-bromo-3-butenyl diphosphate (Br-IPP), in conjunction with radiolabeled FPP, to probe the reaction mechanisms of the two prenyltransferases. Using this alternative substrate with electron-withdrawing bromo group at the C3 position to slow down the condensation step, trapping of farnesol in the OPPs reaction from radiolabeled FPP under basic condition was observed, consistent with a sequential mechanism. In contrast, UPPs reaction yielded no farnesyl carbocation intermediate under the same condition with radiolabeled FPP and Br-IPP, indicating a concerted mechanism. Our data demonstrate the different reaction mechanisms for cis- and tran-prenyltransferases although they share the same substrates.

  3. BEARR: Batch Extraction and Analysis of cis-Regulatory Regions.

    PubMed

    Vega, Vinsensius B; Bangarusamy, Dhinoth Kumar; Miller, Lance D; Liu, Edison T; Lin, Chin-Yo

    2004-07-01

    Transcription factors play important roles in regulating biological and disease processes. Microarray technology has enabled researchers to simultaneously monitor changes in the expression of thousands of transcripts. By identifying specific transcription factor binding sites in the cis-regulatory regions of differentially expressed genes, it is then possible to identify direct targets of transcription factors, model transcriptional regulatory networks and mine the dataset for relevant targets for experimental and clinical manipulation. We have developed web-based software to assist biologists in efficiently carrying out the analysis of microarray data from studies of specific transcription factors. Batch Extraction and Analysis of cis-Regulatory Regions, or BEARR, accepts gene identifier lists from microarray data analysis tools and facilitates identification, extraction and analysis of regulatory regions from the large amount of data that is typically generated in these types of studies. The software is publicly available at http://giscompute.gis.a-star.edu.sg/~vega/BEARR1.0/. PMID:15215391

  4. pH-stat fed-batch process to enhance the production of cis, cis-muconate from benzoate by Pseudomonas putida KT2440-JD1.

    PubMed

    van Duuren, Jozef B J H; Wijte, Dorien; Karge, Bianka; dos Santos, Vítor A P Martins; Yang, Yu; Mars, Astrid E; Eggink, Gerrit

    2012-01-01

    Pseudomonas putida KT2440-JD1 is able to cometabolize benzoate to cis, cis-muconate in the presence of glucose as growth substrate. P. putida KT2440-JD1 was unable to grow in the presence of concentrations above 50 mM benzoate or 600 mM cis, cis-muconate. The inhibitory effects of both compounds were cumulative. The maximum specific uptake rate of benzoate was higher than the specific production rate of cis, cis-muconate during growth on glucose in the presence of benzoate, indicating that a benzoate derivative accumulated in the cells, which is likely to be catechol. Catechol was shown to reduce the expression level of the ben operon, which encodes the conversion of benzoate to cis, cis-muconate. To prevent overdoses of benzoate, a pH-stat fed-batch process for the production of cis, cis-muconate from benzoate was developed, in which the addition of benzoate was coupled to the acidification of the medium. The maximum specific production rate during the pH-stat fed-batch process was 0.6 g (4.3 mmol) g dry cell weight(-1) h(-1), whereas 18.5 g L(-1) cis, cis-muconate accumulated in the culture medium with a molar product yield of close to 100%. Proteome analysis revealed that the outer membrane protein H1 was upregulated during the pH-stat fed-batch process, whereas the expression of 10 other proteins was reduced. The identified proteins are involved in energy household, transport, translation of RNA, and motility.

  5. Fundamentals of Physics, Volume 1, (Chapters 1 - 21)

    NASA Astrophysics Data System (ADS)

    Walker, Jearl

    2004-01-01

    Chapter 1. Measurement 1. How does the appearance of a new type of cloud signal changes in Earth's atmosphere? 1-1 What Is Physics? 1-2 Measuring Things. 1-3 The International System of Units. 1-4 Changing Units. 1-5 Length. 1-6 Time. 1-7 Mass. Review & Summary. Problems. Chapter 2. Motion Along a Straight Line. What causes whiplash injury in rear-end collisions of cars? 2-1 What Is Physics? 2-2 Motion. 2-3 Position and Displacement. 2-4 Average Velocity and Average Speed. 2-5 Instantaneous Velocity and Speed. 2-6 Acceleration. 2-7 Constant Acceleration: A Special Case. 2-8 Another Look at Constant Acceleration. 2-9 Free-Fall Acceleration. 2-10 Graphical Integration in Motion Analysis. 2 Review & Summary. Questions. Problems. Chapter 3. Vectors. How does an ant know the way home with no guiding clues on the desert plains? 3-1 What Is Physics? 3-2 Vectors and Scalars. 3-3 Adding Vectors Geometrically. 3-4 Components of Vectors. 3-5 Unit Vectors. 3-6 Adding Vectors by Components. 3-7 Vectors and the Laws of Physics. 3-8 Multiplying Vectors. Review & Summary. Questions. Problems. Chapter 4. Motion in Two and Three Dimensions. In a motorcycle jump for record distance, where does the jumper put the second ramp? 4-1 What Is Physics? 4-2 Position and Displacement. 4-3 Average Velocity and Instantaneous Velocity. 4-4 Average Acceleration and Instantaneous Acceleration. 4-5 Projectile Motion. 4-6 Projectile Motion Analyzed. 4-7 Uniform Circular Motion. 4-8 Relative Motion in One Dimension. 4-9 Relative Motion in Two Dimensions. Review & Summary. Questions. Problems. Chapter 5. Force and Motion--I. When a pilot takes off from an aircraft carrier, what causes the compulsion to .y the plane into the ocean? 5-1 What Is Physics? 5-2 Newtonian Mechanics. 5-3 Newton's First Law. 5-4 Force. 5-5 Mass. 5-6 Newton's Second Law. 5-7 Some Particular Forces. 5-8 Newton's Third Law. 5-9 Applying Newton's Laws. Review & Summary. Questions. Problems. Chapter 6. Force and Motion--II. Can a

  6. Fundamentals of Physics, Part 1 (Chapters 1-11)

    NASA Astrophysics Data System (ADS)

    Halliday, David; Resnick, Robert; Walker, Jearl

    2003-12-01

    Chapter 1.Measurement. How does the appearance of a new type of cloud signal changes in Earth's atmosphere? 1-1 What Is Physics? 1-2 Measuring Things. 1-3 The International System of Units. 1-4 Changing Units. 1-5 Length. 1-6 Time. 1-7 Mass. Review & Summary. Problems. Chapter 2.Motion Along a Straight Line. What causes whiplash injury in rear-end collisions of cars? 2-1 What Is Physics? 2-2 Motion. 2-3 Position and Displacement. 2-4 Average Velocity and Average Speed. 2-5 Instantaneous Velocity and Speed. 2-6 Acceleration. 2-7 Constant Acceleration: A Special Case. 2-8 Another Look at Constant Acceleration. 2-9 Free-Fall Acceleration. 2-10 Graphical Integration in Motion Analysis. Review & Summary. Questions. Problems. Chapter 3.Vectors. How does an ant know the way home with no guiding clues on the deser t plains? 3-2 Vectors and Scalars. 3-3 Adding Vectors Geometrically. 3-4 Components of Vectors. 3-5 Unit Vectors. 3-6 Adding Vectors by Components. 3-7 Vectors and the Laws of Physics. 3-8 Multiplying Vectors. Review & Summary. Questions. Problems. Chapter 4.Motion in Two and Three Dimensions. In a motorcycle jump for record distance, where does the jumper put the second ramp? 4-1 What Is Physics? 4-2 Position and Displacement. 4-3 Average Velocity and Instantaneous Velocity. 4-4 Average Acceleration and Instantaneous Acceleration. 4-5 Projectile Motion. 4-6 Projectile Motion Analyzed. 4-7 Uniform Circular Motion. 4-8 Relative Motion in One Dimension. 4-9 Relative Motion in Two Dimensions. Review & Summary. Questions. Problems. Chapter 5.Force and Motion-I. When a pilot takes off from an aircraft carrier, what causes the compulsion to fly the plane into the ocean? 5-1 What Is Physics? 5-2 Newtonian Mechanics. 5-3 Newton's First Law. 5-4 Force. 5-5 Mass. 5-6 Newton's Second Law. 5-7 Some Particular Forces. 5-8 Newton's Third Law. 5-9 Applying Newton's Laws. Review & Summary. Questions. Problems. Chapter 6.Force and Motion-II. Can a Grand Prix race car be driven

  7. Cluster Ion Spectrometry (CIS) Data Archiving in the CAA

    NASA Astrophysics Data System (ADS)

    Dandouras, I. S.; Barthe, A.; Penou, E.; Brunato, S.; Reme, H.; Kistler, L. M.; Blagau, A.; Facsko, G.; Kronberg, E.; Laakso, H. E.

    2009-12-01

    The Cluster Active Archive (CAA) aims at preserving the four Cluster spacecraft data, so that they are usable in the long-term by the scientific community as well as by the instrument team PIs and Co-Is. This implies that the data are filed together with the descriptive and documentary elements making it possible to select and interpret them. The CIS (Cluster Ion Spectrometry) experiment is a comprehensive ionic plasma spectrometry package onboard the four Cluster spacecraft, capable of obtaining full three-dimensional ion distributions (about 0 to 40 keV/e) with a time resolution of one spacecraft spin (4 sec) and with mass-per-charge composition determination. The CIS package consists of two different instruments, a Hot Ion Analyser (HIA) and a time-of-flight ion Composition Distribution Function (CODIF) analyser. For the archival of the CIS data a multi-level approach has been adopted. The CAA archival includes processed raw data (Level 1 data), moments of the ion distribution functions (Level 2 data), and calibrated high-resolution data in a variety of physical units (Level 3 data). The latter are 3-D ion distribution functions and 2-D pitch-angle distributions. In addition, a software package has been developed to allow the CAA user to interactively calculate partial or total moments of the ion distributions. Instrument cross-calibration has been an important activity in preparing the data for archival. The CIS data archive includes also experiment documentation, graphical products for browsing through the data, and data caveats. In addition, data quality indexes are under preparation, to help the user. Given the complexity of an ion spectrometer, and the variety of its operational modes, each one being optimised for a different magnetospheric region or measurement objective, consultation of the data caveats by the end user will always be a necessary step in the data analysis.

  8. City of Troitsk and Sooty Snow, Chelyabinsk, CIS

    NASA Technical Reports Server (NTRS)

    1992-01-01

    This view shows the industrial pollution around the Siberian city of Troitsk (54.0N, 61.0E). Troitsk is the smallest of a group of three heavy industrial cities east of the Urals, the others being Magnitogorsk and Chelyabinsk. All have been cited as being some of the worst industrial polluted cities in the CIS. Despite being the smallest of the three, Troitsk has the largest area of soot blackened snow. Respiratory diseases among the citizens are chronic.

  9. History and Status of the CIS Customs Union

    SciTech Connect

    Lawson, T.M.; Erickson, S.A.

    1999-08-31

    This report explores the history of the CIS Customs Union and the major obstacles the Union faces in its implementation. Investigation of the Customs Union is necessary as its implementation could effect the Second Line of Defense (SLD) Program. Russian Customs contends that radiation detectors should not be installed along the Customs Union members borders of as the borders will be dissolved when the Union is implemented.

  10. Proton irradiation of the CIS115 for the JUICE mission

    NASA Astrophysics Data System (ADS)

    Soman, M. R.; Allanwood, E. A. H.; Holland, A. D.; Winstone, G. P.; Gow, J. P. D.; Stefanov, K.; Leese, M.

    2015-09-01

    The CIS115 is one of the latest CMOS Imaging Sensors designed by e2v technologies, with 1504x2000 pixels on a 7 μm pitch. Each pixel in the array is a pinned photodiode with a 4T architecture, achieving an average dark current of 22 electrons pixel-1 s-1 at 21°C measured in a front-faced device. The sensor aims for high optical sensitivity by utilising e2v's back-thinning and processing capabilities, providing a sensitive silicon thickness approximately 9 μm to 12 μm thick with a tuned anti-reflective coating. The sensor operates in a rolling shutter mode incorporating reset level subtraction resulting in a mean pixel readout noise of 4.25 electrons rms. The full well has been measured to be 34000 electrons in a previous study, resulting in a dynamic range of up to 8000. These performance characteristics have led to the CIS115 being chosen for JANUS, the high-resolution and wide-angle optical camera on the JUpiter ICy moon Explorer (JUICE). The three year science phase of JUICE is in the harsh radiation environment of the Jovian magnetosphere, primarily studying Jupiter and its icy moons. Analysis of the expected radiation environment and shielding levels from the spacecraft and instrument design predict the End Of Life (EOL) displacement and ionising damage for the CIS115 to be equivalent to 1010 10 MeV protons cm-2 and 100 krad(Si) respectively. Dark current and image lag characterisation results following initial proton irradiations are presented, detailing the initial phase of space qualification of the CIS115. Results are compared to the pre-irradiation performance and the instrument specifications and further qualification plans are outlined.

  11. Anatomy and physiology of plant conductive systems. Book chapter

    SciTech Connect

    McFarlane, C.

    1993-01-01

    Mathematical models considered in the book are representations of the physical features and chemical reactions that define interactions between plants and their environment. By centering attention on equations, it is easy to lose sight of the intricate and complex nature of the problem. The particular chapter describes the anatomy of important plant features and briefly discuss some physiological principles that will help to visualize and perceive the conditions which are represented in the models. Because of the many competing interactions, the fate of chemicals in the soil/plant/air environment is not obvious. Models were thus developed to intelligently integrate available knowledge, to increase understanding of the complex interactions, to aid in presentation of plant functions, and to help make predictions about chemical fate.

  12. CREME: Cis-Regulatory Module Explorer for the Human Genome

    SciTech Connect

    Loots, G G; Sharan, R; Ovcharenko, I; Ben-Hur, A

    2004-02-11

    The binding of transcription factors to specific regulatory sequence elements is a primary mechanism for controlling gene transcription. Eukaryotic genes are often regulated by several transcription factors, whose binding sites are tightly clustered and form cis-regulatory modules. In this paper we present a web-server, CREME, for identifying and visualizing cis-regulatory modules in the promoter regions of a given set of potentially co-regulated genes. CREME relies on a database of putative transcription factor binding sites that have been annotated across the human genome using a library of position weight matrices and evolutionary conservation with the mouse and rat genomes. A search algorithm is applied to this dataset to identify combinations of transcription factors whose binding sites tend to co-occur in close proximity in the promoter regions of the input gene set. The identified cis-regulatory modules are statistically scored and significant combinations are reported and graphically visualized. Our web-server is available at http://creme.dcode.org/.

  13. Cis-elements governing trinucleotide repeat instability in Saccharomyces cerevisiae.

    PubMed Central

    Rolfsmeier, M L; Dixon, M J; Pessoa-Brandão, L; Pelletier, R; Miret, J J; Lahue, R S

    2001-01-01

    Trinucleotide repeat (TNR) instability in humans is governed by unique cis-elements. One element is a threshold, or minimal repeat length, conferring frequent mutations. Since thresholds have not been directly demonstrated in model systems, their molecular nature remains uncertain. Another element is sequence specificity. Unstable TNR sequences are almost always CNG, whose hairpin-forming ability is thought to promote instability by inhibiting DNA repair. To understand these cis-elements further, TNR expansions and contractions were monitored by yeast genetic assays. A threshold of approximately 15--17 repeats was observed for CTG expansions and contractions, indicating that thresholds function in organisms besides humans. Mutants lacking the flap endonuclease Rad27p showed little change in the expansion threshold, suggesting that this element is not altered by the presence or absence of flap processing. CNG or GNC sequences yielded frequent mutations, whereas A-T rich sequences were substantially more stable. This sequence analysis further supports a hairpin-mediated mechanism of TNR instability. Expansions and contractions occurred at comparable rates for CTG tract lengths between 15 and 25 repeats, indicating that expansions can comprise a significant fraction of mutations in yeast. These results indicate that several unique cis-elements of human TNR instability are functional in yeast. PMID:11290713

  14. Molecular characterization of the cis-prenyltransferase of Giardia lamblia.

    PubMed

    Grabińska, Kariona A; Cui, Jike; Chatterjee, Aparajita; Guan, Ziqiang; Raetz, Christian R H; Robbins, Phillips W; Samuelson, John

    2010-07-01

    Giardia lamblia, the protist that causes diarrhea, makes an Asn-linked-glycan (N-glycan) precursor that contains just two sugars (GlcNAc(2)) attached by a pyrophosphate linkage to a polyprenol lipid. Because the candidate cis-prenyltransferase of Giardia appears to be more similar to bacterial enzymes than to those of most eukaryotes and because Giardia is missing a candidate dolichol kinase (ortholog to Saccharomyces cerevisiae SEC59 gene product), we wondered how Giardia synthesizes dolichol phosphate (Dol-P), which is used to make N-glycans and glycosylphosphatidylinositol (GPI) anchors. Here we show that cultured Giardia makes an unsaturated polyprenyl pyrophosphate (dehydrodolichol), which contains 11 and 12 isoprene units and is reduced to dolichol. The Giardia cis-prenyltransferase that we have named Gl-UPPS because the enzyme primarily synthesizes undecaprenol pyrophosphate is phylogenetically related to those of bacteria and Trypanosoma rather than to those of other protists, metazoans and fungi. In transformed Saccharomyces, the Giardia cis-prenyltransferase also makes a polyprenol containing 11 and 12 isoprene units and supports normal growth, N-glycosylation and GPI anchor synthesis of a rer2Delta, srt1Delta double-deletion mutant. Finally, despite the absence of an ortholog to SEC59, Giardia has cytidine triphosphate-dependent dolichol kinase activity. These results suggest that the synthetic pathway for Dol-P is conserved in Giardia, even if some of the important enzymes are different from those of higher eukaryotes or remain unidentified.

  15. Ready access to functionally embellished cis-hydrindanes and cis-decalins: protecting group-free total syntheses of (±)-Nootkatone and (±)-Noreremophilane.

    PubMed

    Handore, Kishor L; Seetharamsingh, B; Reddy, D Srinivasa

    2013-08-16

    A simple and efficient synthesis of functionalized cis-hydrindanes and cis-decalins was achieved using a sequential Diels-Alder/aldol approach in a highly diastereoselective manner. The scope of this method was tested with a variety of substrates and was successfully applied to the synthesis of two natural products in racemic form. The highlights of the present work provide ready access to 13 new cis-hydrindanes/cis-decalins, a protecting group-free total synthesis of an insect repellent Nootkatone, and the first synthesis of a Noreremophilane using the shortest sequence. PMID:23855542

  16. Structure and function of the 3-carboxy-cis,cis-muconate lactonizing enzyme from the protocatechuate degradative pathway of Agrobacterium radiobacter S2.

    PubMed

    Halak, Sad; Lehtiö, Lari; Basta, Tamara; Bürger, Sibylle; Contzen, Matthias; Stolz, Andreas; Goldman, Adrian

    2006-11-01

    3-carboxy-cis,cis-muconate lactonizing enzymes participate in the protocatechuate branch of the 3-oxoadipate pathway of various aerobic bacteria. The gene encoding a 3-carboxy-cis,cis-muconate lactonizing enzyme (pcaB1S2) was cloned from a gene cluster involved in protocatechuate degradation by Agrobacterium radiobacter strain S2. This gene encoded for a 3-carboxy-cis,cis-muconate lactonizing enzyme of 353 amino acids - significantly smaller than all previously studied 3-carboxy-cis,cis-muconate lactonizing enzymes. This enzyme, ArCMLE1, was produced in Escherichia coli and shown to convert not only 3-carboxy-cis,cis-muconate but also 3-sulfomuconate. ArCMLE1 was purified as a His-tagged enzyme variant, and the basic catalytic constants for the conversion of 3-carboxy-cis,cis-muconate and 3-sulfomuconate were determined. In contrast, Agrobacterium tumefaciens 3-carboxy-cis,cis-muconate lactonizing enzyme 1 could not, despite 87% sequence identity to ArCMLE1, use 3-sulfomuconate as substrate. The crystal structure of ArCMLE1 was determined at 2.2 A resolution. Consistent with the sequence, it showed that the C-terminal domain, present in all other members of the fumarase II family, is missing in ArCMLE1. Nonetheless, both the tertiary and quaternary structures, and the structure of the active site, are similar to those of Pseudomonas putida 3-carboxy-cis,cis-muconate lactonizing enzyme. One principal difference is that ArCMLE1 contains an Arg, as opposed to a Trp, in the active site. This indicates that activation of the carboxylic nucleophile by a hydrophobic environment is not required for lactonization, unlike earlier proposals [Yang J, Wang Y, Woolridge EM, Arora V, Petsko GA, Kozarich JW & Ringe D (2004) Biochemistry43, 10424-10434]. We identified citrate and isocitrate as noncompetitive inhibitors of ArCMLE1, and found a potential binding pocket for them on the enzyme outside the active site.

  17. Retention of configuration in nucleophilic vinylic halide substitution - Proton magnetic resonance spectra of cis- and trans- beta-styryldiphenylphosphine oxides.

    NASA Technical Reports Server (NTRS)

    Aguiar, A. M.; Daigle, D.

    1965-01-01

    Cis- and trans-beta-bromostyrene reaction with lithium diphenylphosphide in tetrahydrofuran producing cis- and trans-beta- styryldiphenylphosphine, discussing proton magnetic resonance and configuration retention

  18. 48 CFR Appendix E to Chapter 7 - [Reserved

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 48 Federal Acquisition Regulations System 5 2013-10-01 2013-10-01 false E Appendix E to Chapter 7 Federal Acquisition Regulations System AGENCY FOR INTERNATIONAL DEVELOPMENT Appendix E to Chapter 7...

  19. 48 CFR Appendix E to Chapter 7 - [Reserved

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 48 Federal Acquisition Regulations System 5 2014-10-01 2014-10-01 false E Appendix E to Chapter 7 Federal Acquisition Regulations System AGENCY FOR INTERNATIONAL DEVELOPMENT Appendix E to Chapter 7...

  20. 48 CFR Appendix E to Chapter 7 - [Reserved

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 48 Federal Acquisition Regulations System 5 2012-10-01 2012-10-01 false E Appendix E to Chapter 7 Federal Acquisition Regulations System AGENCY FOR INTERNATIONAL DEVELOPMENT Appendix E to Chapter 7...

  1. 48 CFR Appendixes A-C to Chapter 7 - [Reserved

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 48 Federal Acquisition Regulations System 5 2014-10-01 2014-10-01 false A Appendixes A-C to Chapter 7 Federal Acquisition Regulations System AGENCY FOR INTERNATIONAL DEVELOPMENT Appendixes A-C to Chapter 7...

  2. 48 CFR Appendix E to Chapter 7 - [Reserved

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false E Appendix E to Chapter 7 Federal Acquisition Regulations System AGENCY FOR INTERNATIONAL DEVELOPMENT Appendix E to Chapter 7...

  3. 48 CFR Appendix G to Chapter 2 - [Reserved

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 48 Federal Acquisition Regulations System 3 2010-10-01 2010-10-01 false G Appendix G to Chapter 2 Federal Acquisition Regulations System DEFENSE ACQUISITION REGULATIONS SYSTEM, DEPARTMENT OF DEFENSE Appendix G to Chapter 2...

  4. 48 CFR Appendixes G-H to Chapter 7 - [Reserved

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false G Appendixes G-H to Chapter 7 Federal Acquisition Regulations System AGENCY FOR INTERNATIONAL DEVELOPMENT Appendixes G-H to Chapter 7...

  5. 48 CFR Appendixes A-C to Chapter 7 - [Reserved

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false A Appendixes A-C to Chapter 7 Federal Acquisition Regulations System AGENCY FOR INTERNATIONAL DEVELOPMENT Appendixes A-C to Chapter 7...

  6. 48 CFR Appendix E to Chapter 7 - [Reserved

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 48 Federal Acquisition Regulations System 5 2011-10-01 2011-10-01 false E Appendix E to Chapter 7 Federal Acquisition Regulations System AGENCY FOR INTERNATIONAL DEVELOPMENT Appendix E to Chapter 7...

  7. 48 CFR Appendixes G-H to Chapter 7 - [Reserved

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 48 Federal Acquisition Regulations System 5 2011-10-01 2011-10-01 false G Appendixes G-H to Chapter 7 Federal Acquisition Regulations System AGENCY FOR INTERNATIONAL DEVELOPMENT Appendixes G-H to Chapter 7...

  8. Binding affinities of CRBPI and CRBPII for 9-cis-retinoids

    PubMed Central

    Kane, Maureen A.; Bright, Frank V.; Napoli, Joseph L.

    2014-01-01

    Background Cellular retinol binding-protein I (CRBPI) and cellular retinol binding-protein II (CRBPII) serve as intracellular retinoid chaperones that bind retinol and retinal with high affinity and facilitate substrate delivery to select enzymes that catalyze retinoic acid (RA) and retinyl ester biosynthesis. Recently, 9-cis-RA has been identified in vivo in the pancreas, where it contributes to regulating glucose-stimulated insulin secretion. In vitro, 9-cis-RA activates RXR (retinoid×receptors), which serve as therapeutic targets for treating cancer and metabolic diseases. Binding affinities and structure–function relationships have been well characterized for CRBPI and CRBPII with all-trans-retinoids, but not for 9-cis-retinoids. This study extended current knowledge by establishing binding affinities for CRBPI and CRBPII with 9-cis-retinoids. Methods We have determined apparent dissociation constants, Kd′, through monitoring binding of 9-cis-retinol, 9-cis-retinal, and 9-cis-RA with CRBPI and CRBPII by fluorescence spectroscopy, and analyzing the data with non-linear regression. We compared these data to the data we obtained for all-trans- and 13-cis-retinoids under identical conditions. Results CRBPI and CRBPII, respectively, bind 9-cis-retinol ( Kd′, 11 nM and 68 nM) and 9-cis-retinal ( Kd′, 8 nM and 5 nM) with high affinity. No significant 9-cis-RA binding was observed with CRBPI or CRBPII. Conclusions CRBPI and CRBPII bind 9-cis-retinol and 9-cis-retinal with high affinities, albeit with affinities somewhat lower than for all-trans-retinol and all-trans-retinal. General significance These data provide further insight into structure–binding relationships of cellular retinol binding-proteins and are consistent with a model of 9-cis-RA biosynthesis that involves chaperoned delivery of 9-cis-retinoids to enzymes that recognize retinoid binding-proteins. PMID:21382444

  9. Space Applications of Mass Spectrometry. Chapter 31

    NASA Technical Reports Server (NTRS)

    Hoffman, John H.; Griffin, Timothy P.; Limero, Thomas; Arkin, C. Richard

    2010-01-01

    Mass spectrometers have been involved in essentially all aspects of space exploration. This chapter outlines some of these many uses. Mass spectrometers have not only helped to expand our knowledge and understanding of the world and solar system around us, they have helped to put man safely in space and expand our frontier. Mass spectrometry continues to prove to be a very reliable, robust, and flexible analytical instrument, ensuring that its use will continue to help aid our investigation of the universe and this small planet that we call home.

  10. Solid Lubrication Fundamentals and Applications. Chapter 2

    NASA Technical Reports Server (NTRS)

    Miyoshi, Kazuhisa

    1998-01-01

    This chapter describes powerful analytical techniques capable of sampling tribological surfaces and solid-film lubricants. Some of these techniques may also be used to determine the locus of failure in a bonded structure or coated substrate; such information is important when seeking improved adhesion between a solid-film lubricant and a substrate and when seeking improved performance and long life expectancy of solid lubricants. Many examples are given here and through-out the book on the nature and character of solid surfaces and their significance in lubrication, friction, and wear. The analytical techniques used include the late spectroscopic methods.

  11. Columbia: The Economic Foundation of Peace. Chapters 21-28.

    ERIC Educational Resources Information Center

    Giugale, Marcelo M., Ed.; Lafourcade, Olivier, Ed.; Luff, Connie, Ed.

    This document contains 8 chapters of a 35-chapter book that presents a comprehensive diagnosis of current economic, social, and educational conditions in Colombia and their importance to development prospects and the quest for peace. The eight chapters covered here are part of a section titled "Sharing the Fruits of Growth with All Colombians."…

  12. 38 CFR 21.6380 - Additional applicable Chapter 31 regulations.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Chapter 31 regulations. 21.6380 Section 21.6380 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF... applicable Chapter 31 regulations. The following regulations are applicable to veterans pursuing the vocational training under this program in the same manner as they apply to 38 U.S.C. chapter 31: §...

  13. 24 CFR 300.1 - Scope of chapter.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 24 Housing and Urban Development 2 2010-04-01 2010-04-01 false Scope of chapter. 300.1 Section 300.1 Housing and Urban Development Regulations Relating to Housing and Urban Development (Continued... of chapter. This chapter consists of general information and does not purport to set forth all of...

  14. Using Kolb's Experiential Learning Cycle in Chapter Presentations

    ERIC Educational Resources Information Center

    Stokes-Eley, Stephanie

    2007-01-01

    Student-led chapter presentations provide an excellent opportunity for instructors to evaluate a student's comprehension of the assigned chapter, as well as the student's ability to present and convey information in a public forum. Although several instructors realize the benefits of requiring students to complete chapter presentations either as…

  15. Methods of assessing responses of trees, stands, and ecosystems to air pollution (Chapter 7). Book chapter

    SciTech Connect

    Stolte, K.W.; Duriscoe, D.M.; Cook, E.R.; Cline, S.P.

    1992-01-01

    The chapter focuses on three main types of assessments of pollution effects used in the case studies chronicled in Chapter 8 through 12 (Regional Studies of conifer forests in the west). These are measures of crown condition of individual trees; impacts on populations and communities; and temporal patterns in radial growth. The concepts behind the development of each approach are introduced with references to previous work, leading to a discussion of the state of science. The importance of quality assurance techniques to the success of any assessment of air pollution effects is also discussed.

  16. Modulation of multiple sclerosis by sunlight exposure: role of cis-urocanic acid.

    PubMed

    Correale, Jorge; Farez, Mauricio F

    2013-08-15

    The role of cis-urocanic acid (UCA) as a UV-mediated immunomodulator in MS patients was investigated. Plasma levels of cis-UCA were significantly lower in MS patients compared to controls. Stimulation of MBP- and MOG-specific T cells in the presence of cis-UCA, significantly increased IL-10, and inhibited IFN-γ production. PBMCs cultured in the presence of cis-UCA increased CD4(+)CD25(+)FoxP3(+) regulatory T cell percentages. Dendritic cells cultured in the presence of cis-UCA significantly reduced Ag presentation capacity. Finally, cis-UCA activated the 5-HT2A receptor, inducing the increase in phosphorylated forms of ERK 1/2 and JNK2. Thus, in addition to vitamin D, cis-UCA also appears to be an additional UV-mediated immunomodulator. PMID:23800457

  17. Universal Sensor and Actuator Requirements. Chapter 5

    NASA Technical Reports Server (NTRS)

    Rosenfeld, Taylor; Webster, John; Garg, Sanjay

    2009-01-01

    The previous chapters have focused on the requirements for sensors and actuators for "More Intelligent Gas Turbine Engines" from the perspective of performance and operating environment. Even if a technology is available, which meets these performance requirements, there are still various hurdles to be overcome for the technology to transition into a real engine. Such requirements relate to TRL (Technology Readiness Level), durability, reliability, volume, weight, cost, etc. This chapter provides an overview of such universal requirements which any sensor or actuator technology will have to meet before it can be implemented on a product. The objective here is to help educate the researchers or technology developers on the extensive process that the technology has to go through beyond just meeting performance requirements. The hope is that such knowledge will help the technology developers as well as decision makers to prevent wasteful investment in developing solutions to performance requirements, which have no potential to meet the "universal" requirements. These "universal" requirements can be divided into 2 broad areas: 1) Technology value proposition; and 2) Technology maturation. These requirements are briefly discussed in the following.

  18. Volatile hydrocarbons and fuel oxygenates: Chapter 12

    USGS Publications Warehouse

    Cozzarelli, Isabelle M.

    2014-01-01

    Petroleum hydrocarbons and fuel oxygenates are among the most commonly occurring and widely distributed contaminants in the environment. This chapter presents a summary of the sources, transport, fate, and remediation of volatile fuel hydrocarbons and fuel additives in the environment. Much research has focused on the transport and transformation processes of petroleum hydrocarbons and fuel oxygenates, such as benzene, toluene, ethylbenzene, and xylenes and methyl tert‐butyl ether, in groundwater following release from underground storage tanks. Natural attenuation from biodegradation limits the movement of these contaminants and has received considerable attention as an environmental restoration option. This chapter summarizes approaches to environmental restoration, including those that rely on natural attenuation, and also engineered or enhanced remediation. Researchers are increasingly combining several microbial and molecular-based methods to give a complete picture of biodegradation potential and occurrence at contaminated field sites. New insights into the fate of petroleum hydrocarbons and fuel additives have been gained by recent advances in analytical tools and approaches, including stable isotope fractionation, analysis of metabolic intermediates, and direct microbial evidence. However, development of long-term detailed monitoring programs is required to further develop conceptual models of natural attenuation and increase our understanding of the behavior of contaminant mixtures in the subsurface.

  19. Functional conservation of cis-regulatory elements of heat-shock genes over long evolutionary distances.

    PubMed

    He, Zhengying; Eichel, Kelsie; Ruvinsky, Ilya

    2011-01-01

    Transcriptional control of gene regulation is an intricate process that requires precise orchestration of a number of molecular components. Studying its evolution can serve as a useful model for understanding how complex molecular machines evolve. One way to investigate evolution of transcriptional regulation is to test the functions of cis-elements from one species in a distant relative. Previous results suggested that few, if any, tissue-specific promoters from Drosophila are faithfully expressed in C. elegans. Here we show that, in contrast, promoters of fly and human heat-shock genes are upregulated in C. elegans upon exposure to heat. Inducibility under conditions of heat shock may represent a relatively simple "on-off" response, whereas complex expression patterns require integration of multiple signals. Our results suggest that simpler aspects of regulatory logic may be retained over longer periods of evolutionary time, while more complex ones may be diverging more rapidly.

  20. Enantioselective disruption of the endocrine system by Cis-Bifenthrin in the male mice.

    PubMed

    Jin, Yuanxiang; Wang, Jiangcong; Pan, Xiuhong; Miao, Wenyu; Lin, Xiaojian; Wang, Linggang; Fu, Zhengwei

    2015-07-01

    Bifenthrin (BF), as a chiral pyrethroid, is widely used to control field and household pests in China. At present, the commercial BF is a mixed compound containing cis isomers (cis-BF) including two enantiomers of 1R-cis-BF and 1S-cis-BF. In the present study, the two individual cis-BF enantiomers were separated by a preparative supercritical fluid chromatography. Then, four week-old adolescent male ICR mice were orally administered 1R-cis-BF and 1S-cis-BF separately daily for 3 weeks at doses of 0, 7.5 and 15 mg/kg/day, respectively. Results showed that the transcription status of some genes involved in cholesterol synthesis and transport as well as testosterone (T) synthesis in the testes were influenced by cis-BF enantiomers. Especially, we observed that the transcription status of key genes on the pathway of T synthesis including cytochrome P450 cholesterol side-chain cleavage enzyme (P450scc) and cytochrome P450 17α-hydroxysteroid dehydrogenase (P45017α)) were selectively altered in the testis of mice when treated with 1S-cis-BF, suggesting that it is the possible reason to explain why the lower serum T concentration in 1S-cis-BF treated group. Taken together, it concluded that both of the cis-BF enantiomers have the endocrine disruption activities, while 1S-cis-BF was higher than 1R-cis-BF in mice when exposed during the puberty. The data was helpful to understand the toxicity of cis-BF in mammals under enantiomeric level.

  1. Integrity in Student Affairs Organizations

    ERIC Educational Resources Information Center

    Baird, Leonard

    2011-01-01

    "Integrity" is a term that is intuitively appealing, but hard to define and implement. This chapter discusses those conceptual complexities as well as an ideal portrait of organizations with integrity, a description of the challenges to the integrity of organizations, a discussion of the enhancement of integrity through compliance programs and…

  2. Chapter 2: Stand-alone Applications - TOPCAT

    NASA Astrophysics Data System (ADS)

    Miller, C. J.

    Tool for OPerations on Catalogues And Tables or TOPCAT is a graphical viewer for table data. It offers a variety of ways to work with data tables, including a browser for the cell data, viewers for information about table and column metadata, dataset visualization, and even analysis. We discuss a small subset of TOPCAT's functionalities in this chapter. TOPCAT was originally developed as part of the Starlink program in the United Kingdom. It is now maintained by AstroGrid. The program is written in pure Java and available under the GNU General Public License. It is available for download and a version is included in the software distribution accompanying this book. TOPCAT is a GUI interface on top of the STIL library. A command line interface to this library, STILTS, described in Chapter 21 provides scriptable access to many of the capabilities described here. The purpose of this tutorial is to provide an overview of TOPCAT to the novice user. The best place to look for and learn about TOPCAT is the web page maintained by Mark B. Taylor. There, TOPCAT documentation is provided in HTML, PDF, via screen shots, etc. In this chapter we take the user through a few examples that give the general idea of how TOPCAT works. The majority of the functionality of TOPCAT is not included in this short tutorial. Our goal in this tutorial is to lead the reader through an exercise that would result in a publication quality figure (e.g. for a journal article). Specifically, we will use TOPCAT to show how the color-magnitude relation of a galaxy cluster compares to that of all galaxies in the Sloan Digital Sky Survey (York et al. 2000). This diagnostic is used not only in cluster finding, but its linear fit can provide insight into the age and/or metallicity of the oldest galaxies in galaxy clusters (which are some of the oldest galaxies in the Universe). The data we need for this exercise are: 1) the entire spectroscopic galaxy catalog from the SDSS, with galaxy positions, galaxy

  3. Reaction engineering and precursor film deposition for CIS synthesis

    NASA Astrophysics Data System (ADS)

    Stanbery, B. J.; Davydov, A.; Chang, C. H.; Anderson, T. J.

    1997-02-01

    We present an analysis of alternative reaction pathways for the synthesis of CuInSe2-based films for photovoltaic applications based on our recent and ongoing investigations of the thermochemistry in the Cu-In-Se ternary, Na-Cu-In-Se quaternary, and constituent unary and binary systems. We also describe our efforts to determine the relationship between film growth conditions in our novel rotating-disc system and resultant phase constitution of precursor reactant films intended for subsequent ex-situ rapid thermal processing. A model for the phase chemistry of sodium in CIS films is presented.

  4. Adriamycin and cis-platinum in advanced ovarian cancer.

    PubMed

    de Gramont, A; Drolet, Y; Lavoie, A; Painchaud, M; Blouin, R; Tessier, C; Ouellet, P

    1985-06-01

    Forty-eight patients with stage III and IV ovarian epithelial carcinoma were treated with single doses of adriamycin (ADM) 50 mg/m2 and cis-platinum (DDP) 50 mg/m2 every month for nine courses. The pathologically proven response rate was 52.2%, with 22.7% complete response and 29.5% partial response. Median survival was 22 months for all patients, 25 months in stage III and 15 months in stage IV. This study confirms that ADM-DDP is a valuable drug regimen in advanced ovarian carcinoma but further progress is needed to improve the cure rate, which remains low.

  5. cis-clerodane diterpenes from the liverwort Scapania ciliata.

    PubMed

    Liu, Na; Zhu, Rong-Xiu; Wang, Song; Zhang, Jiao-Zhen; Lin, Zhao-Min; Li, Rui-Juan; Lou, Hong-Xiang

    2013-09-01

    Chemical investigation of the Chinese liverwort Scapania ciliata led to the isolation of four new cis-clerodane lactones, named ciliatolides A-D (1-4, resp.), among which compound 1 was found to be a tetranorclerodanoid. Their structures were determined by extensive analysis of spectroscopic data, and, in the case of compound 1, together with a single-crystal X-ray diffraction analysis. The absolute configurations were established by analysis of the CD spectra and by quantum-chemical CD calculations. The cytotoxicities of compounds 1-4 were preliminarily tested against the PC3 and MCF-7 cell lines.

  6. History of Artificial Gravity. Chapter 3

    NASA Technical Reports Server (NTRS)

    Clement, Gilles; Bukley, Angie; Paloski, William

    2006-01-01

    This chapter reviews the past and current projects on artificial gravity during space missions. The idea of a rotating wheel-like space station providing artificial gravity goes back in the writings of Tsiolkovsky, Noordung, and Wernher von Braun. Its most famous fictional representation is in the film 2001: A Space Odyssey, which also depicts spin-generated artificial gravity aboard a space station and a spaceship bound for Jupiter. The O Neill-type space colony provides another classic illustration of this technique. A more realistic approach to rotating the space station is to provide astronauts with a smaller centrifuge contained within a spacecraft. The astronauts would go into it for a workout, and get their gravity therapeutic dose for a certain period of time, daily or a few times a week. This simpler concept is current being tested during ground-based studies in several laboratories around the world.

  7. New training building heralds new chapter.

    PubMed

    Baillie, Jonathan

    2014-09-01

    Established in 1969 by the Department of Health as the National Centre for Hospital Engineering, Eastwood Park is today acknowledged as one of the UK's leading providers of specialist technical, engineering, estates, and facilities management training to the healthcare sector. Having celebrated 40 years in business in 2009, and with the breadth of its portfolio growing year-on-year, the training provider has recently entered a particularly exciting new chapter, as plans for a new 3,000 m2 training centre, due to open late next year, and equipped with facilities which Eastwood Park's management say will be 'unrivalled anywhere else in the world', come to fruition. HEJ editor, Jonathan Baillie reports.

  8. Coldwater fish in wadeable streams: chapter 8

    USGS Publications Warehouse

    Dunham, Jason B.; Rosenberger, Amanda E.; Thurow, Russell F.; Dolloff, C. Andrew; Howell, Philip J.

    2009-01-01

    Standardizing sampling methods for fish populations across large regions is important for consistent measurement of large-scale effects of climate or geography. In addition, pooling samples creates larger sample sizes and can facilitate data sharing among scientists and land managers. Sampling freshwater fish has largely not been standardized due to the diversity of fish and habitats. USGS aquatic ecologist Jason Dunham and co-authors contributed a chapter about sampling coldwater fish in wadeable streams to a new book that details common methods, protocols, and guidelines for sampling fish across North America. Topics include three common sampling methods: electrofishing, snorkeling, and nest counts. Each method provides complementary information about different species and life stages. The information will be useful for initiating new or fine-tuning ongoing sampling programs.

  9. Mercury and halogens in coal: Chapter 2

    USGS Publications Warehouse

    Kolker, Allan; Quick, Jeffrey C.; Granite, Evan J.; Pennline, Henry W.; Senior, Constance L.

    2014-01-01

    Apart from mercury itself, coal rank and halogen content are among the most important factors inherent in coal that determine the proportion of mercury captured by conventional controls during coal combustion. This chapter reviews how mercury in coal occurs, gives available concentration data for mercury in U.S. and international commercial coals, and provides an overview of the natural variation in halogens that influence mercury capture. Three databases, the U.S. Geological Survey coal quality (USGS COALQUAL) database for in-ground coals, and the 1999 and 2010 U.S. Environmental Protection Agency (EPA) Information Collection Request (ICR) databases for coals delivered to power stations, provide extensive results for mercury and other parameters that are compared in this chapter. In addition to the United States, detailed characterization of mercury is available on a nationwide basis for China, whose mean values in recent compilations are very similar to the United States in-ground mean of 0.17 ppm mercury. Available data for the next five largest producers (India, Australia, South Africa, the Russian Federation, and Indonesia) are more limited and with the possible exceptions of Australia and the Russian Federation, do not allow nationwide means for mercury in coal to be calculated. Chlorine in coal varies as a function of rank and correspondingly, depth of burial. As discussed elsewhere in this volume, on a proportional basis, bromine is more effective than chlorine in promoting mercury oxidation in flue gas and capture by conventional controls. The ratio of bromine to chlorine in coal is indicative of the proportion of halogens present in formation waters within a coal basin. This ratio is relatively constant except in coals that have interacted with deep-basin brines that have reached halite saturation, enriching residual fluids in bromine. Results presented here help optimize mercury capture by conventional controls and provide a starting point for

  10. Substituent effects of cis-cinnamic acid analogues as plant growh inhibitors.

    PubMed

    Nishikawa, Keisuke; Fukuda, Hiroshi; Abe, Masato; Nakanishi, Kazunari; Taniguchi, Tomoya; Nomura, Takashi; Yamaguchi, Chihiro; Hiradate, Syuntaro; Fujii, Yoshiharu; Okuda, Katsuhiro; Shindo, Mitsuru

    2013-12-01

    1-O-cis-Cinnamoyl-β-D-glucopyranose is one of the most potent allelochemicals that has been isolated from Spiraea thunbergii Sieb by Hiradate et al. It derives its strong inhibitory activity from cis-cinnamic acid (cis-CA), which is crucial for phytotoxicity. By preparing and assaying a series of cis-CA analogues, it was previously found that the key features of cis-CA for lettuce root growth inhibition are a phenyl ring, cis-configuration of the alkene moiety, and carboxylic acid. On the basis of a structure-activity relationship study, the substituent effects on the aromatic ring of cis-CA were examined by systematic synthesis and the lettuce root growth inhibition assay of a series of cis-CA analogues having substituents on the aromatic ring. While ortho- and para-substituted analogues exhibited low potency in most cases, meta-substitution was not critical for potency, and analogues having a hydrophobic and sterically small substituent were more likely to be potent. Finally, several cis-CA analogues were found to be more potent root growth inhibitors than cis-CA.

  11. Kinetics of trans-cis isomerization in azobenzene dimers at an air-water interface

    SciTech Connect

    Kumar, Bharat; Suresh, K. A.

    2009-08-15

    We have studied the kinetics of trans to cis isomerization under the illumination of ultraviolet light, in the Langmuir monolayer of mesogenic azobenzene dimer, bis-[5-(4{sup '}-n-dodecyloxy benzoyloxy)-2-(4{sup ''}-methylphenylazo)phenyl] adipate, at an air-water interface. We find that the trans to cis isomerization reaction of the molecules in the monolayer shows deviation from the first-order kinetics unlike those reported on Langmuir monolayers of azobenzene molecules. We attribute the deviation from first-order kinetics to the simultaneous photoisomerization of trans isomers to form cis isomers and the reverse thermal isomerization of cis isomers to form trans isomers. Our analysis of the rate of change of mole fraction of trans isomers to form cis isomers indicates a first-order kinetics for trans to cis photoisomerization reaction and a second-order kinetics for cis to trans thermal isomerization reaction. This second-order kinetics mechanism is similar to the Lindemann-Hinshelwood mechanism for the unimolecular reactions at low concentration of reactants. The formation of the activated cis isomer by collisions is a slow process as compared to the decay of the activated cis isomer to trans isomer in the liquid expanded phase. This results in the second-order kinetics for the thermal isomerization of cis isomers.

  12. Integrity in Student Development

    ERIC Educational Resources Information Center

    Roberts, Dennis C.; Banta, Trudy W.

    2011-01-01

    The quest for integrity in practice and theory has been part of the evolution of student personnel work all the way back to the turn of the 20th century. This chapter seeks to take stock of the question of integrity in relation to one of the core knowledge bases used by those engaged in student affairs work today--student development. The authors…

  13. Latex Clearing Protein—an Oxygenase Cleaving Poly(cis-1,4-Isoprene) Rubber at the cis Double Bonds

    PubMed Central

    Hiessl, Sebastian; Böse, Dietrich; Oetermann, Sylvia; Eggers, Jessica; Pietruszka, Jörg

    2014-01-01

    Gordonia polyisoprenivorans strain VH2, a potent rubber-degrading actinomycete, harbors two latex clearing proteins (Lcps), which are known to be essential for the microbial degradation of rubber. However, biochemical information on the exact role of this protein in the degradation of polyisoprene was lacking. In this study, the gene encoding Lcp1VH2 was heterologously expressed in strains of Escherichia coli, the corresponding protein was purified, and its role in rubber degradation was examined by measurement of oxygen consumption as well as by chromatographic and spectroscopic methods. It turned out that active Lcp1VH2 is a monomer and is responsible for the oxidative cleavage of poly(cis-1,4-isoprene) in synthetic as well as in natural rubber by the addition of oxygen (O2) to the cis double bonds. The resulting oligomers possess repetitive isoprene units with aldehyde (CHO-CH2—) and ketone (—CH2-CO-CH3) functional groups at the termini. Two fractions with average isoprene contents of 18 and 10, respectively, were isolated, thus indicating an endocleavage mechanism. The activity of Lcp1VH2 was determined by applying a polarographic assay. Alkenes, acyclic terpenes, or other rubber-like polymers, such as poly(cis-1,4-butadiene) or poly(trans-1,4-isoprene), are not oxidatively cleaved by Lcp1VH2. The pH and temperature optima of the enzyme are at pH 7 and 30°C, respectively. Furthermore, it was demonstrated that active Lcp1VH2 is a Cu(II)-containing oxygenase that exhibits a conserved domain of unknown function which cannot be detected in any other hitherto-characterized enzyme. The results presented here indicate that this domain might represent a new protein family of oxygenases. PMID:24928880

  14. Latex clearing protein-an oxygenase cleaving poly(cis-1,4-isoprene) rubber at the cis double bonds.

    PubMed

    Hiessl, Sebastian; Böse, Dietrich; Oetermann, Sylvia; Eggers, Jessica; Pietruszka, Jörg; Steinbüchel, Alexander

    2014-09-01

    Gordonia polyisoprenivorans strain VH2, a potent rubber-degrading actinomycete, harbors two latex clearing proteins (Lcps), which are known to be essential for the microbial degradation of rubber. However, biochemical information on the exact role of this protein in the degradation of polyisoprene was lacking. In this study, the gene encoding Lcp1VH2 was heterologously expressed in strains of Escherichia coli, the corresponding protein was purified, and its role in rubber degradation was examined by measurement of oxygen consumption as well as by chromatographic and spectroscopic methods. It turned out that active Lcp1VH2 is a monomer and is responsible for the oxidative cleavage of poly(cis-1,4-isoprene) in synthetic as well as in natural rubber by the addition of oxygen (O2) to the cis double bonds. The resulting oligomers possess repetitive isoprene units with aldehyde (CHO-CH2-) and ketone (-CH2-CO-CH3) functional groups at the termini. Two fractions with average isoprene contents of 18 and 10, respectively, were isolated, thus indicating an endocleavage mechanism. The activity of Lcp1VH2 was determined by applying a polarographic assay. Alkenes, acyclic terpenes, or other rubber-like polymers, such as poly(cis-1,4-butadiene) or poly(trans-1,4-isoprene), are not oxidatively cleaved by Lcp1VH2. The pH and temperature optima of the enzyme are at pH 7 and 30°C, respectively. Furthermore, it was demonstrated that active Lcp1VH2 is a Cu(II)-containing oxygenase that exhibits a conserved domain of unknown function which cannot be detected in any other hitherto-characterized enzyme. The results presented here indicate that this domain might represent a new protein family of oxygenases.

  15. Cis-trans photoisomerization of fluorescent-protein chromophores.

    PubMed

    Voliani, Valerio; Bizzarri, Ranieri; Nifosì, Riccardo; Abbruzzetti, Stefania; Grandi, Elena; Viappiani, Cristiano; Beltram, Fabio

    2008-08-28

    Photochromic variants of fluorescent proteins are opening the way to a number of opportunities for high-sensitivity regioselective studies in the cellular environment and may even lead to applications in information and communication technology. Yet, the detailed photophysical processes at the basis of photoswitching have not been fully clarified. In this paper, we used synthetic FP chromophores to clarify the photophysical processes associated with the photochromic behavior. In particular, we investigated the spectral modification of synthetic chromophore analogues of wild-type green fluorescent protein (GFP), Y66F GFP (BFPF), and Y66W GFP (CFP) upon irradiation in solutions of different polarities. We found that the cis-trans photoisomerization mechanism can be induced in all the chromophores. The structural assignments were carried out both by NMR measurements and DFT calculations. Remarkably, we determined for the first time the spectra of neutral trans isomers in different solvents. Finally, we calculated the photoconversion quantum yields by absorption measurements under continuous illumination at different times and by a nanosecond laser-flash photolysis method. Our results indicate that cis-trans photoisomerization is a general mechanism of FP chromophores whose efficiency is modulated by the detailed mutant-specific protein environment. PMID:18671358

  16. The C-terminus of CIS defines its interaction pattern.

    PubMed

    Lavens, Delphine; Ulrichts, Peter; Catteeuw, Dominiek; Gevaert, Kris; Vandekerckhove, Joël; Peelman, Frank; Eyckerman, Sven; Tavernier, Jan

    2007-01-01

    Proteins of the SOCS (suppressors of cytokine signalling) family are characterized by a conserved modular structure with pre-SH2 (Src homology 2), SH2 and SOCS-box domains. Several members, including CIS (cytokine-inducible SH2 protein), SOCS1 and SOCS3, are induced rapidly upon cytokine receptor activation and function in a negative-feedback loop, attenuating signalling at the receptor level. We used a recently developed mammalian two-hybrid system [MAPPIT (mammalian protein-protein interaction trap)] to analyse SOCS protein-interaction patterns in intact cells, allowing direct comparison with biological function. We find that, besides the SH2 domain, the C-terminal part of the CIS SOCS-box is required for functional interaction with the cytokine receptor motifs examined, but not with the N-terminal death domain of the TLR (Toll-like receptor) adaptor MyD88. Mutagenesis revealed that one single tyrosine residue at position 253 is a critical binding determinant. In contrast, substrate binding by the highly related SOCS2 protein, and also by SOCS1 and SOCS3, does not require their SOCS-box. PMID:16961462

  17. The C-terminus of CIS defines its interaction pattern

    PubMed Central

    Lavens, Delphine; Ulrichts, Peter; Catteeuw, Dominiek; Gevaert, Kris; Vandekerckhove, Joël; Peelman, Frank; Eyckerman, Sven; Tavernier, Jan

    2006-01-01

    Proteins of the SOCS (suppressors of cytokine signalling) family are characterized by a conserved modular structure with pre-SH2 (Src homology 2), SH2 and SOCS-box domains. Several members, including CIS (cytokine-inducible SH2 protein), SOCS1 and SOCS3, are induced rapidly upon cytokine receptor activation and function in a negative-feedback loop, attenuating signalling at the receptor level. We used a recently developed mammalian two-hybrid system [MAPPIT (mammalian protein–protein interaction trap)] to analyse SOCS protein-interaction patterns in intact cells, allowing direct comparison with biological function. We find that, besides the SH2 domain, the C-terminal part of the CIS SOCS-box is required for functional interaction with the cytokine receptor motifs examined, but not with the N-terminal death domain of the TLR (Toll-like receptor) adaptor MyD88. Mutagenesis revealed that one single tyrosine residue at position 253 is a critical binding determinant. In contrast, substrate binding by the highly related SOCS2 protein, and also by SOCS1 and SOCS3, does not require their SOCS-box. PMID:16961462

  18. NMR relaxation study of crosslinked cis-1,4-polybutadiene

    SciTech Connect

    Munie, G.C.; Jonas, J.; Rowland, T.J.

    1980-01-01

    Proton relaxation measurements have been used to investigate the effects of crosslinking on the segmental motion in cis-1,4-polybutadiene samples. The temperature dependence of proton spin-lattice relaxation time T/sub 1/ and spin-spin relaxation time T/sub 2/ at 60 and 24.3 MHz is reported in cis-1,4-polybutadiene (PB) samples with different crosslink density including uncrosslinked PB and samples with 140, 40, and 14 repeat units between crosslinks. In addition, spin-lattice relaxation times in rotating coordinate frame, T/sub 1p/, have also been determined. The relaxation data are interpreted in terms of the effects of crosslinks on segmental chain motions. Because of their sensitivity to low-frequency motion, T/sub 2/ data are of major interest. At temperatures well above the T/sub 1/ minimum the small T/sub 2/ temperature dependence resembles solidlike behavior reflecting the nonzero averaging of dipolar interactions due to anisotropic motion of the chain segments between crosslinks. The magnitude of T/sub 2/ at 60/sup 0/C is found to be proportional to the average mass between crosslinks.

  19. Wavelength dependent cis-trans isomerization in vision.

    PubMed

    Kim, J E; Tauber, M J; Mathies, R A

    2001-11-20

    The primary event in vision is the light-driven cis-trans isomerization of the 11-cis-retinal chromophore in the G-protein coupled receptor rhodopsin. Early measurements showed that this photoisomerization has a reaction quantum yield phi of approximately 0.67 [Dartnall (1936) Proc. R. Soc. A 156, 158-170; Dartnall (1968) Vision Res. 8, 339-358] and suggested that the quantum yield was wavelength independent [Schneider (1939) Proc. Natl. Acad. Sci. U.S.A. 170, 102-112]. Here we more accurately determine phi(500) = 0.65 +/- 0.01 and reveal that phi surprisingly depends on the wavelength of the incident light. Although there is no difference in the quantum yield between 450 and 480 nm, the quantum yield falls significantly as the photon energy is reduced below 20 000 cm(-1) (500 nm). At the reddest wavelength measured (570 nm), the quantum yield is reduced by 5 +/- 1% relative to the 500 nm value. These experiments correct the long-held presumption that the quantum yield in vision is wavelength independent, and support the hypothesis that the 200 fs photoisomerization reaction that initiates vision is dictated by nonstationary excited-state vibrational wave packet dynamics. PMID:11705366

  20. Wavelength Dependent Cis-Trans Isomerization in Vision†

    PubMed Central

    Kim, Judy E.; Tauber, Michael J.; Mathies, Richard A.

    2005-01-01

    The primary event in vision is the light-driven cis-trans isomerization of the 11-cis-retinal chromophore in the G-protein coupled receptor rhodopsin. Early measurements showed that this photoisomerization has a reaction quantum yield Φ of ∼0.67 [Dartnall (1936) Proc. R. Soc. A 156, 158-170; Dartnall (1968) Vision Res. 8, 339-358] and suggested that the quantum yield was wavelength independent [Schneider (1939) Proc. Natl. Acad. Sci. U.S.A. 170, 102-112]. Here we more accurately determine Φ 500) = 0.65 ± 0.01 and reveal that Φ surprisingly depends on the wavelength of the incident light. Although there is no difference in the quantum yield between 450 and 480 nm, the quantum yield falls significantly as the photon energy is reduced below 20 000 cm-1 (500 nm). At the reddest wavelength measured (570 nm), the quantum yield is reduced by 5 ± 1% relative to the 500 nm value. These experiments correct the long-held presumption that the quantum yield in vision is wavelength independent, and support the hypothesis that the 200 fs photoisomerization reaction that initiates vision is dictated by nonstationary excited-state vibrational wave packet dynamics. PMID:11705366

  1. Active Ageing in CIS Countries: Semantics, Challenges, and Responses

    PubMed Central

    Sidorenko, Alexandre; Zaidi, Asghar

    2013-01-01

    Although the CIS countries are connected together by the legacy of breaking away from the Soviet Union, they have had a distinctive transition course and are rather diverse in terms of the population ageing challenges and policy responses in place. The commonality is that a comprehensive national strategy on ageing is lacking, and many of necessary reforms were put aside owing to political uncertainties, lack of societal consensus, and financial instability. The notion of active ageing is associated with the term “accelerated ageing,” which is understood to be an individual living a life under harsh living conditions or a society experiencing rapid increases in the relative number of older persons, and therefore it carries a negative connotation. Yet, in the same spirit as the European Year for Active Ageing and Solidarity between Generations 2012, the CIS countries have initiated sectoral programmes towards enhancing employment of older workers, social participation of older people in the society in a wider sense and also measures promoting health and independent living of older persons. PMID:23346109

  2. A primer on regression methods for decoding cis-regulatory logic

    SciTech Connect

    Das, Debopriya; Pellegrini, Matteo; Gray, Joe W.

    2009-03-03

    The rapidly emerging field of systems biology is helping us to understand the molecular determinants of phenotype on a genomic scale [1]. Cis-regulatory elements are major sequence-based determinants of biological processes in cells and tissues [2]. For instance, during transcriptional regulation, transcription factors (TFs) bind to very specific regions on the promoter DNA [2,3] and recruit the basal transcriptional machinery, which ultimately initiates mRNA transcription (Figure 1A). Learning cis-Regulatory Elements from Omics Data A vast amount of work over the past decade has shown that omics data can be used to learn cis-regulatory logic on a genome-wide scale [4-6]--in particular, by integrating sequence data with mRNA expression profiles. The most popular approach has been to identify over-represented motifs in promoters of genes that are coexpressed [4,7,8]. Though widely used, such an approach can be limiting for a variety of reasons. First, the combinatorial nature of gene regulation is difficult to explicitly model in this framework. Moreover, in many applications of this approach, expression data from multiple conditions are necessary to obtain reliable predictions. This can potentially limit the use of this method to only large data sets [9]. Although these methods can be adapted to analyze mRNA expression data from a pair of biological conditions, such comparisons are often confounded by the fact that primary and secondary response genes are clustered together--whereas only the primary response genes are expected to contain the functional motifs [10]. A set of approaches based on regression has been developed to overcome the above limitations [11-32]. These approaches have their foundations in certain biophysical aspects of gene regulation [26,33-35]. That is, the models are motivated by the expected transcriptional response of genes due to the binding of TFs to their promoters. While such methods have gathered popularity in the computational domain

  3. Chapter 24: Programmatic Interfaces - IDL VOlib

    NASA Astrophysics Data System (ADS)

    Miller, C. J.

    In this chapter, we describe a library for working with the VO using IDL (the Interactive Data Language). IDL is a software environment for data analysis, visualization, and cross-platform application development. It has wide-usage in astronomy, including NASA (e.g. http://seadas.gsfc.nasa.gov/), the Sloan Digital Sky Survey (http://www.sdss.org), and the Spitzer Infrared Spectrograph Instrument (http://ssc.spitzer.caltech.edu/archanaly/contributed/smart/). David Stern, the founder of Research Systems, Inc. (RSI), began the development of IDL while working with NASA's Mars Mariner 7 and 9 data at the Laboratory for Atmospheric and Space Physics at the University of Colorado. In 1981, IDL was rewritten in assembly language and FORTRAN for VAX/VMS. IDL's usage has expanded over the last decade into the fields of medical imaging and engineering, among many others. IDL's programming style carries over much of this FORTRAN-legacy, and has a familiar feel to many astronomers who learned their trade using FORTRAN. The spread of IDL-usage amongst astronomers can in part be attributed to the wealth of publicly astronomical libraries. The Goddard Space Flight Center (GSFC) maintains a list of astronomy-related IDL libraries, including the well known Astronomy User's Library (hereafter ASTROLIB2). We will use some of these GSFC IDL libraries. We note that while IDL is a licensed-software product, the source code of user-written procedures are typically freely available to the community. To make the most out of this section as a reader, it is important that many of the data discovery, access, and analysis protocols are understood before reading this chapter. In the next section, we provide an overview of some of the NVO terminology with which the reader should be familiar. The IDL library discussed here is specifically for use with the Virtual Observatory and is named VOlib. IDL's VOlib is available at http://nvo.noao.edu and is included with the software distrubution for this

  4. Numerical Prediction of Dust. Chapter 10

    NASA Technical Reports Server (NTRS)

    Benedetti, Angela; Baldasano, J. M.; Basart, S.; Benincasa, F.; Boucher, O.; Brooks, M.; Chen, J. P.; Colarco, P. R.; Gong, S.; Huneeus, N.; Jones, L; Lu, S.; Menut, L.; Mulcahy, J.; Nickovic, S.; Morcrette, J.-J.; Perez, C.; Reid, J. S.; Sekiyama, T. T.; Tanaka, T.; Terradellas, E.; Westphal, D. L.; Zhang, X.-Y.; Zhou, C.-H.

    2013-01-01

    Covers the whole breadth of mineral dust research, from a scientific perspective Presents interdisciplinary work including results from field campaigns, satellite observations, laboratory studies, computer modelling and theoretical studies Explores the role of dust as a player and recorder of environmental change This volume presents state-of-the-art research about mineral dust, including results from field campaigns, satellite observations, laboratory studies, computer modelling and theoretical studies. Dust research is a new, dynamic and fast-growing area of science and due to its multiple roles in the Earth system, dust has become a fascinating topic for many scientific disciplines. Aspects of dust research covered in this book reach from timescales of minutes (as with dust devils, cloud processes, and radiation) to millennia (as with loess formation and oceanic sediments), making dust both a player and recorder of environmental change. The book is structured in four main parts that explore characteristics of dust, the global dust cycle, impacts of dust on the Earth system, and dust as a climate indicator. The chapters in these parts provide a comprehensive, detailed overview of this highly interdisciplinary subject. The contributions presented here cover dust from source to sink and describe all the processes dust particles undergo while travelling through the atmosphere. Chapters explore how dust is lifted and transported, how it affects radiation, clouds, regional circulations, precipitation and chemical processes in the atmosphere, and how it deteriorates air quality. The book explores how dust is removed from the atmosphere by gravitational settling, turbulence or precipitation, how iron contained in dust fertilizes terrestrial and marine ecosystems, and about the role that dust plays in human health. We learn how dust is observed, simulated using computer models and forecast. The book also details the role of dust deposits for climate reconstructions

  5. Organisational culture matters for system integration in health care.

    PubMed

    Munir, Samina K; Kay, Stephen

    2003-01-01

    This paper illustrates the importance of organisational culture for Clinical Information Systems (CIS) integration. The study is based on data collected in intensive care units in the UK and Denmark. Data were collected using qualitative methods, i.e., observations, interviews and shadowing of health care providers, together with a questionnaire at each site. The data are analysed to extract salient variables for CIS integration, and it is shown that these variables can be separated into two categories that describe the 'Actual Usefulness' of the system and the 'Organisational Culture'. This model is then extended to show that CIS integration directly affects the work processes of the organisation, forming an iterative process of change as a CIS is introduced and integrated. PMID:14728220

  6. Effect of dimethyl sulfoxide (DMSO) on cis-Pt induced changes in renal microvillar enzymes

    SciTech Connect

    Noordewier, B.; Reeves, P.G.; Saari, J.T. )

    1989-02-09

    Cis-diamminedichloroplatinum (cis-Pt) is an antitumor agent with known nephrotoxic effects. We studied cis-Pt effects on five renal microvillar enzymes. Further, because the nephrotoxic effects of cis-Pt have been associated with O{sub 2}-derived free radicals, we studied the effect of the hydroxyl radical scavenger DMSO on observed enzyme changes. Male, weanling Sprague-Dawley rats were fed a purified diet and water with or without DMSO (4.75%). After 35 days they were given (iv) either cis-Pt (7.5 mg/kg) or saline in a 2{times}2 design. Rats were killed 4 days post-injection. Compared to saline-treated rats, Pt-treated animals showed increased blood urea nitrogen (BUN), plasma creatinine (Cr), liver and kidney minerals (including Zn) and increased activity of renal microvillar angiotensin converting enzyme (ACE). Cis-Pt decreased the activity of gamma glutamyl transferase (GGT), alkaline phosphatase (AP) and endopeptidase (EP) and had no effect on aminopeptidase (AMP). DMSO attenuated cis-pt-mediated BUN and Cr changes, independently increased ACE activity, showed significant inhibition of cis-Pt effects on GGT and AP and had no effect on EP or AP activities. We conclude that cis-Pt-mediated microvillar enzyme changes may be related, in some cases, to renal Zn levels and, in others, to damage by hydroxyl radical.

  7. Small RNAs and the regulation of cis-natural antisense transcripts in Arabidopsis

    PubMed Central

    Jin, Hailing; Vacic, Vladimir; Girke, Thomas; Lonardi, Stefano; Zhu, Jian-Kang

    2008-01-01

    Background In spite of large intergenic spaces in plant and animal genomes, 7% to 30% of genes in the genomes encode overlapping cis-natural antisense transcripts (cis-NATs). The widespread occurrence of cis-NATs suggests an evolutionary advantage for this type of genomic arrangement. Experimental evidence for the regulation of two cis-NAT gene pairs by natural antisense transcripts-generated small interfering RNAs (nat-siRNAs) via the RNA interference (RNAi) pathway has been reported in Arabidopsis. However, the extent of siRNA-mediated regulation of cis-NAT genes is still unclear in any genome. Results The hallmarks of RNAi regulation of NATs are 1) inverse regulation of two genes in a cis-NAT pair by environmental and developmental cues and 2) generation of siRNAs by cis-NAT genes. We examined Arabidopsis transcript profiling data from public microarray databases to identify cis-NAT pairs whose sense and antisense transcripts show opposite expression changes. A subset of the cis-NAT genes displayed negatively correlated expression profiles as well as inverse differential expression changes under at least one of the examined developmental stages or treatment conditions. By searching the Arabidopsis Small RNA Project (ASRP) and Massively Parallel Signature Sequencing (MPSS) small RNA databases as well as our stress-treated small RNA dataset, we found small RNAs that matched at least one gene in 646 pairs out of 1008 (64%) protein-coding cis-NAT pairs, which suggests that siRNAs may regulate the expression of many cis-NAT genes. 209 putative siRNAs have the potential to target more than one gene and half of these small RNAs could target multiple members of a gene family. Furthermore, the majority of the putative siRNAs within the overlapping regions tend to target only one transcript of a given NAT pair, which is consistent with our previous finding on salt- and bacteria-induced nat-siRNAs. In addition, we found that genes encoding plastid- or mitochondrion

  8. Formation of cis-coniferin in cell-free extracts of Fagus grandifolia Ehrh bark

    NASA Technical Reports Server (NTRS)

    Yamamoto, E.; Inciong, E. J.; Davin, L. B.; Lewis, N. G.

    1990-01-01

    American beech (Fagus grandifolia Ehrh) bark exclusively accumulates cis-monolignols and their glucosidic conjugates; no evidence for the accumulation of trans-monolignols has been found. The glucosyltransferase from this source exhibits a very unusual substrate specificity for cis, and not trans, monolignols. This is further evidence that cis monolignols are involved in lignin formation in these plant tissues. Preliminary evidence for the existence of a novel trans-cis monolignol isomerase was obtained, in agreement with our contention that this isomerization is not photochemically mediated.

  9. Anti-tumor Properties of cis-Resveratrol Methylated Analogues in Metastatic Mouse Melanoma Cells

    PubMed Central

    Morris, Valery L.; Toseef, Tayyaba; Nazumudeen, Fathima B.; Rivoira, Christian; Spatafora, Carmela; Tringali, Corrado; Rotenberg, Susan A.

    2015-01-01

    Resveratrol (E-3,5,4’-trihydroxystilbene) is a polyphenol found in red wine that has been shown to have multiple anti-cancer properties. Although cis (Z) and trans (E) isomers of resveratrol occur in nature, the cis form is not biologically active. However, methylation at key positions of the cis form results in more potent anti-cancer properties. This study determined that synthetic cis-polymethoxystilbenes (methylated analogues of cis-resveratrol) inhibited cancer-related phenotypes of metastatic B16 F10 and non-metastatic B16 F1 mouse melanoma cells. In contrast with cis or trans-resveratrol and trans-polymethoxystilbene which were ineffective at 10 μM, cis-polymethoxystilbenes inhibited motility and proliferation of melanoma cells with low micromolar specificity (IC50 <10 μM). Inhibitory effects by cis-polymethoxystilbenes were significantly stronger with B16 F10 cells and were accompanied by decreased expression of β-tubulin and pleckstrin homology domain-interacting protein, a marker of metastatic B16 cells. Thus, cis-polymethoxystilbenes have potential as chemotherapeutic agents for metastatic melanoma. PMID:25567208

  10. Abiotic reductive dechlorination of cis-DCE by ferrous monosulfide mackinawite.

    PubMed

    Hyun, Sung Pil; Hayes, Kim F

    2015-11-01

    Cis-1,2,-dichloroethylene (cis-DCE) is a toxic, persistent contaminant occurring mainly as a daughter product of incomplete degradation of perchloroethylene (PCE) and trichloroethylene (TCE). This paper reports on abiotic reductive dechlorination of cis-DCE by mackinawite (FeS1-x), a ferrous monosulfide, under variable geochemical conditions. To assess in situ abiotic cis-DCE dechlorination by mackinawite in the field, mackinawite suspensions prepared in a field groundwater sample collected from a cis-DCE contaminated field site were used for dechlorination experiments. The effects of geochemical variables on the dechlorination rates were monitored. A set of dechlorination experiments were also carried out in the presence of aquifer sediment from the site over a range of pH conditions to better simulate the actual field situations. The results showed that the suspensions of freshly prepared mackinawite reductively transformed cis-DCE to acetylene, whereas the conventionally prepared powder form of mackinawite had practically no reactivity with cis-DCE under the same experimental conditions. Significant cis-DCE degradation by mackinawite has not been reported prior to this study, although mackinawite has been shown to reductively transform PCE and TCE. This study suggests feasibility of using mackinawite for in situ remediation of cis-DCE-contaminated sites with high S levels such as estuaries under naturally achieved or stimulated sulfate-reducing conditions.

  11. Cloning and functional analysis of novel short-chain cis-prenyltransferases.

    PubMed

    Ambo, Takanori; Noike, Motoyoshi; Kurokawa, Hirofumi; Koyama, Tanetoshi

    2008-10-31

    cis-Prenyltransferase catalyzes the synthesis of Z,E-mixed prenyl diphosphates by sequential condensation of isopentenyl diphosphate with allylic diphosphate. cis-Prenyltransferases can be classified into three subgroups: short-, medium-, and long-chain cis-prenyltransferase, according to their product chain lengths. cis-Farnesyl diphosphate synthase from Mycobacterium tuberculosis has been the only example as short-chain cis-prenyltransferase so far characterized. In this study, we cloned the novel short-chain cis-prenyltransferases from three different bacteria, and characterized their enzymatic activities to compare and elucidate a common feature of the short-chain cis-prenyltransferases. Furthermore, we identified a specific isoleucine that is conserved in short-chain cis-prenyltransferases and located in close proximity of the omega-end of the geranyl diphosphate. Several site-directed mutants with respect to the isoleucine residue synthesized longer prenyl chain products and showed broader allylic substrate specificity. These results suggested that the isoleucine plays an important role in the substrate specificity and chain length determination mechanism of cis-prenyltransferase.

  12. Enantioselective synthesis of cis-decalins using organocatalysis and sulfonyl Nazarov reagents.

    PubMed

    Peña, Javier; Silveira-Dorta, Gastón; Moro, Rosalina F; Garrido, Narciso M; Marcos, Isidro S; Sanz, Francisca; Díez, David

    2015-04-10

    The first organocatalytic synthesis of cis-decalins using sulfonyl Nazarov reagents is reported. The Jørgensen's catalyst directs this highly enantioselective synthesis using different cyclohexenal derivatives.

  13. Dealing with Processing Chapter 10 Files from Multiple Vendors

    NASA Technical Reports Server (NTRS)

    Knudtson, Kevin Mark

    2011-01-01

    This presentation discusses the experiences of the NASA Dryden Flight Research Center's (DFRC) Western Aeronautical Test Range (WATR) in dealing with the problems encountered while performing post flight data processing using the WATR's data collection/processing system on Chapter 10 files from different Chapter 10 recorders. The transition to Chapter 10 recorders has brought Vvith it an assortment of issues that must be addressed: the ambiguities of language in the Chapter 10 standard, the unrealistic near-term expectations of the Chapter 10 standard, the incompatibility of data products generated from Chapter 10 recorders, and the unavailability of mature Chapter 10 applications. Some of these issues properly belong to the users of Chapter 10 recorders, some to the manufacturers, and some to the flight test community at large. The goal of this presentation is to share the WATR's lesson learned in processing data products from various Chapter 10 recorder vendors. The WATR could benefit greatly in the open forum Vvith lessons learned discussions with other members of the flight test community.

  14. Carbon cycling in terrestrial environments: Chapter 17

    USGS Publications Warehouse

    Wang, Yang; Huntington, Thomas G.; Osher, Laurie J.; Wassenaar, Leonard I; Trumbore, Susan E.; Amundson, Ronald; Harden, Jennifer W.; McKnight, Diane M.; Schiff, Sherry L.; Aiken, George R.; Lyons, W. Berry; Aravena, Ramon O.; Baron, Jill S.

    1998-01-01

    This chapter reviews a number of applications of isotopic techniques for the investigation of carbon cycling processes. Carbon dioxide (C02) is an important greenhouse gas. Its concentration in the atmosphere has increased from an estimated 270 ppm at the beginning of the industrial revolution to ∼ 360 ppm at present. Climatic conditions and atmospheric C02 concentration also influence isotopic discrimination during photosynthesis. Natural and anthropogenically induced variations in the carbon isotopic abundance can be exploited to investigate carbon transformations between pools on various time scales. It also discusses one of the isotopes of carbon, the 14C, that is produced in the atmosphere by interactions of cosmic-ray produced neutrons with stable isotopes of nitrogen (N), oxygen (O), and carbon (C), and has a natural abundance in the atmosphere of ∼1 atom 14 C per 1012 atoms 12C. The most important factor affecting the measured 14C ages of soil organic matter is the rate of organic carbon cycling in soils. Differences in the dynamics of soil carbon among different soils or soil horizons will result in different soil organic 14C signatures. As a result, the deviation of the measured 14C age from the true age could differ significantly among different soils or soil horizons.

  15. Chapter 19: visual images and neurological illustration.

    PubMed

    Ione, Amy

    2010-01-01

    This chapter examines the importance of visual materials for studying the brain in health and in disease. Surveying historical representations, this research confirms that images of the brain's form and function have long served as teaching tools and as historical reference points for neurological events. The research is divided into five sections: the first section, Early History to Printing Technology considers prehistoric and ancient imagery, pre-Renaissance thinking about the brain, and the impact of printing and printmaking on neurological research. The second section, Renaissance Illustration, focuses on Leonardo da Vinci, Andreas Vesalius, and other contributors who produced images of the brain as dissection restrictions eased. The third section, which turns to Early Modern and Modern Illustration, highlights the work of Thomas Willis, Charles Bell, and other scientists (throughout the 19th century) who demonstrated the value of a visual component within brain studies. The fourth section presents examples of Neurologically-Descriptive Illustrations, with the final section considering Historical Illustration and Contemporary Research. PMID:19892122

  16. Chapter 1: Epidemiology of Type 1 Diabetes

    PubMed Central

    Maahs, David M; West, Nancy A; Lawrence, Jean M.; Mayer-Davis, Elizabeth J

    2010-01-01

    Synopsis This chapter describes the epidemiology of type 1 diabetes mellitus (T1D) around the world and across the lifespan. Epidemiologic patterns of T1D by demographic, geographic, biologic, cultural and other factors in populations are presented to gain insight about the etiology, natural history, risks, and complications of T1D. Data from large epidemiologic studies worldwide indicate that the incidence of T1D has been increasing by 2–5% worldwide and that the prevalence of T1D is approximately 1 in 300 in the US by 18 years of age. Research on risk factors for T1D is an active area of research to identify genetic and environmental triggers that could potentially be targeted for intervention. While significant advances have been made in the clinical care of T1D with resultant improvements in quality of life and clinical outcomes, much more needs to be done to improve care of, and ultimately find a cure for T1D. Epidemiologic studies have an important on-going role to investigate the complex causes, clinical care, prevention, and cure of T1D. PMID:20723815

  17. CIS-TRANS ISOMERS OF VITAMIN A AND RETINENE IN THE RHODOPSIN SYSTEM

    PubMed Central

    Hubbard, Ruth; Wald, George

    1952-01-01

    Vitamin A and retinene, the carotenoid precursors of rhodopsin, occur in a variety of molecular shapes, cis-trans isomers of one another. For the synthesis of rhodopsin a specific cis isomer of vitamin A is needed. Ordinary crystalline vitamin A, as also the commercial synthetic product, both primarily all-trans, are ineffective. The main site of isomer specificity is the coupling of retinene with opsin. It is this reaction that requires a specific cis isomer of retinene. The oxidation of vitamin A to retinene by the alcohol dehydrogenase-cozymase system displays only a low degree of isomer specificity. Five isomers of retinene have been isolated in crystalline condition: all-trans; three apparently mono-cis forms, neoretinenes a and b and isoretinene a; and one apparently di-cis isomer, isoretinene b. Neoretinenes a and b were first isolated in our laboratory, and isoretinenes a and b in the Organic Research Laboratory of Distillation Products Industries. Each of these substances is converted to an equilibrium mixture of stereoisomers on simple exposure to light. For this reaction, light is required which retinene can absorb; i.e., blue, violet, or ultraviolet light. Yellow, orange, or red light has little effect. The single geometrical isomers of retinene must therefore be protected from low wave length radiation if their isomerization is to be avoided. By incubation with opsin in the dark, the capacity of each of the retinene isomers to synthesize rhodopsin was examined. All-trans retinene and neoretinene a are inactive. Neoretinene b yields rhodopsin indistinguishable from that extracted from the dark-adapted retina (λmax· 500 mµ). Isoretinene a yields a similar light-sensitive pigment, isorhodopsin, the absorption spectrum of which is displaced toward shorter wave lengths (λmax· 487 mµ). Isoretinene b appears to be inactive, but isomerizes preferentially to isoretinene a, which in the presence of opsin is removed to form isorhodopsin before the

  18. Construction of cis-regulatory input functions of yeast promoters.

    PubMed

    Ratna, Prasuna; Becskei, Attila

    2011-01-01

    Promoters contain a large number of binding sites for transcriptional factors transmitting signals from a variety of cellular pathways. The promoter processes these input signals and sets the level of gene expression, the output of the gene. Here, we describe how to design genetic constructs and measure gene expression to deliver data suitable for quantitative analysis. Synthetic genetic constructs are well suited to precisely control and measure gene expression to construct cis-regulatory input functions. These functions can be used to predict gene expression based on signal intensities transmitted to activators and repressors in the gene regulatory region. Simple models of gene expression are presented for competitive and noncompetitive repressions. Complex phenomena, exemplified by synergistic silencing, are modeled by reaction-diffusion equations.

  19. Options for Staging Orbits in Cis-Lunar Space

    NASA Technical Reports Server (NTRS)

    Martinez, Roland; Whitley, Ryan

    2016-01-01

    NASA has been studying options to conduct missions beyond Low Earth Orbit, but within the Earth-Moon system, in preparation for deep space exploration including human missions to Mars. Referred to as the Proving Ground, this arena of exploration activities will enable the development of human spaceflight systems and operations to satisfy future exploration objectives beyond the cis-lunar environment. One option being considered includes the deployment of a habitable element or elements, which could be used as a central location for aggregation of supplies and resources for human missions in cis-lunar space and beyond. Characterizing candidate orbit locations for this asset and the impacts on system design and mission operations is important in the overall assessment of the options being considered. The orbits described in this paper were initially selected by taking advantage of previous studies conducted by NASA and the work of other authors. In this paper orbits are assessed for their relative attractiveness based on various factors. A set of constraints related to the capability of the combined Orion and SLS system to deliver humans and cargo to and from the orbit are evaluated. Deployed assets intended to spend multiple years in the Proving Ground would ideally require minimal station keeping costs to reduce the mass budget allocated to this function. Additional mission design drivers include eclipse frequency, potential for uninterrupted communication with deployed assets, thermal, attitude control, communications, and other operational implications. Also the ability to support potential lunar surface activities and excursion missions beyond Earth-Moon space is considered. The results of the characterization and evaluation of the selected orbits indicate a Near Rectilinear Orbit (NRO) is an attractive candidate as an aggregation point or staging location for operations. In this paper, the NRO is further described in terms which balance a number of key

  20. Options for Staging Orbits in Cis-Lunar Space

    NASA Technical Reports Server (NTRS)

    Whitley, Ryan; Martinez, Roland

    2015-01-01

    NASA has been studying options to conduct missions beyond Low Earth Orbit, but within the Earth-Moon system, in preparation for deep space exploration including human missions to Mars. Referred to as the Proving Ground, this arena of exploration activities will enable the development of human spaceflight systems and operations to satisfy future exploration objectives beyond the cis-lunar environment. One option being considered includes the deployment of a habitable element or elements, which could be used as a central location for aggregation of supplies and resources for human missions in cis-lunar space and beyond. Characterizing candidate orbit locations for this asset and the impacts on system design and mission operations is important in the overall assessment of the options being considered. The orbits described in this paper were initially selected by taking advantage of previous studies conducted by NASA and the work of other authors. In this paper orbits are assessed for their relative attractiveness based on various factors. First, a set of constraints related to the capability of the combined Orion and SLS system to deliver humans and cargo to and from the orbit are evaluated. Second, the ability to support potential lunar surface activities is considered. Finally, deployed assets intended to spend multiple years in the Proving Ground would ideally require minimal station keeping costs to reduce the mass budget allocated to this function. Additional mission design drivers include potential for uninterrupted communication with deployed assets, thermal, communications, and other operational implications. The results of the characterization and evaluation of the selected orbits indicate a Near Rectilinear Orbit (NRO) is an attractive candidate as an aggregation point or staging location for operations. In this paper, the NRO is further described in terms which balance a number of key attributes that favor a variety of mission classes to meet multiple

  1. Ecological consequences of manipulative parasites: chapter 9

    USGS Publications Warehouse

    Lafferty, Kevin D.; Kuris, A. M.

    2012-01-01

    phrases such as “may ultimately infl uence community structure” (Kiesecker and Blaustein 1999), yet few demonstrate ecological effects. Here, we consider the conditions under which manipulative parasites might have a substantial ecological effect in nature and highlight those for which evidence exists (see also Chapter 10).

  2. Introduction to MODIS Cloud Products. Chapter 5

    NASA Technical Reports Server (NTRS)

    Baum, Bryan A.; Platnick, Steven

    2006-01-01

    derived from heritage instruments. This chapter provides an overview of the MODIS Level-2 and -3 operational cloud products.

  3. Synthesis of palmyrolide A and its cis-isomer and mechanistic insight into trans-cis isomerisation of the enamide macrocycle.

    PubMed

    Philkhana, Satish Chandra; Seetharamsingh, B; Dangat, Yuvraj B; Vanka, Kumar; Reddy, D Srinivasa

    2013-04-25

    Concise and protecting-group free synthesis of ent-palmyrolide A and (-)-cis-palmyrolide A were achieved starting from commercially available (S)-citronellal. The key fragment of palmyrolide A, "(5S,7S)-7-hydroxy-5,8,8-trimethylnonanamide", which makes up the most challenging part of the target molecule, was prepared in just three steps. A plausible mechanism for the trans-cis isomerization of the double bond in the macrocycle has been investigated.

  4. Chapter 23: history of neuroendocrinology "the spring of primitive existence".

    PubMed

    Kreier, Felix; Swaab, Dick F

    2010-01-01

    The history of neuroendocrinology is intimately related to one of the key questions, i.e. how does the brain manage to keep us alive and let our species survive? Neuroendocrinology, part of the answer to this question, is the discipline that studies hormone production by neurons, the sensitivity of neurons to hormones, and the dynamic, bidirectional interactions between neurons and endocrine glands. These interactions do not only occur through hormones, but are partly executed by the autonomic system that is regulated by the hypothalamus and that innervates not only the endocrine glands, but all our organs. The hypothalamus acts as a central integrator for endocrine, autonomic, and higher brain functions. The history of neuroendocrinology begins in 200 AD, with Galenus, who postulated that the brain excreted a residue from animal spirits (pituita), and continues into the last century, when researchers from different disciplines tried to understand how the brain regulates the vital functions of the body. Thanks to massive recent electronic publications of English and German scientific journals from the early 20th century we were able to rediscover fascinating articles, written in Europe before World War II, which showed that some of our most recent "innovative" concepts had in fact already been thought up some 50-100 years earlier. Apparently, World War II and the migration and exile of many researchers interrupted the development of concepts in this field and made rediscovery necessary. Our chapter gives an overview of the developments, both new and newly discovered. PMID:19892126

  5. Chapter 23: history of neuroendocrinology "the spring of primitive existence".

    PubMed

    Kreier, Felix; Swaab, Dick F

    2010-01-01

    The history of neuroendocrinology is intimately related to one of the key questions, i.e. how does the brain manage to keep us alive and let our species survive? Neuroendocrinology, part of the answer to this question, is the discipline that studies hormone production by neurons, the sensitivity of neurons to hormones, and the dynamic, bidirectional interactions between neurons and endocrine glands. These interactions do not only occur through hormones, but are partly executed by the autonomic system that is regulated by the hypothalamus and that innervates not only the endocrine glands, but all our organs. The hypothalamus acts as a central integrator for endocrine, autonomic, and higher brain functions. The history of neuroendocrinology begins in 200 AD, with Galenus, who postulated that the brain excreted a residue from animal spirits (pituita), and continues into the last century, when researchers from different disciplines tried to understand how the brain regulates the vital functions of the body. Thanks to massive recent electronic publications of English and German scientific journals from the early 20th century we were able to rediscover fascinating articles, written in Europe before World War II, which showed that some of our most recent "innovative" concepts had in fact already been thought up some 50-100 years earlier. Apparently, World War II and the migration and exile of many researchers interrupted the development of concepts in this field and made rediscovery necessary. Our chapter gives an overview of the developments, both new and newly discovered.

  6. Chapter 6: Essential Orientations and Practices

    ERIC Educational Resources Information Center

    Roholt, Ross VeLure; Hildreth, R. W.; Baizerman, Michael

    2007-01-01

    In civic youth work program staff focus on larger outcomes and do not often attend to the importance of seemingly mundane and simple tasks. Young people talk about how these simple tasks have powerful meaning for them and their work even as adult volunteers talked about the challenges of working democratically with young people. To integrate these…

  7. 48 CFR Appendixes B-E to Chapter 2 - [Reserved

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 48 Federal Acquisition Regulations System 3 2011-10-01 2011-10-01 false B Appendixes B-E to Chapter 2 Federal Acquisition Regulations System DEFENSE ACQUISITION REGULATIONS SYSTEM, DEPARTMENT OF DEFENSE Appendixes B-E to Chapter 2...

  8. 48 CFR Appendixes B-E to Chapter 2 - [Reserved

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 48 Federal Acquisition Regulations System 3 2012-10-01 2012-10-01 false B Appendixes B-E to Chapter 2 Federal Acquisition Regulations System DEFENSE ACQUISITION REGULATIONS SYSTEM, DEPARTMENT OF DEFENSE Appendixes B-E to Chapter 2...

  9. 48 CFR Appendixes B-E to Chapter 2 - [Reserved

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 48 Federal Acquisition Regulations System 3 2014-10-01 2014-10-01 false B Appendixes B-E to Chapter 2 Federal Acquisition Regulations System DEFENSE ACQUISITION REGULATIONS SYSTEM, DEPARTMENT OF DEFENSE Appendixes B-E to Chapter 2...

  10. Report of Evaluation, Chapter I Mathematics Program, 1982-83.

    ERIC Educational Resources Information Center

    Tompkins, John F.

    The Des Moines Chapter I math program served 1110 students in grades 1-8 during school year 1982-83. The total population of Chapter I students attained the established criteria for achievement gains but the gains for grades 7 and 8, taken alone, were lower than the goals. The same was true for mastery of math objectives. All parent contact…

  11. Chapter I Mathematics Program, 1982-83. Report of Evaluation.

    ERIC Educational Resources Information Center

    Tompkins, John F.

    The Des Moines (Iowa) Independent Community School District Chapter I Mathematics Program served 1,110 students in grades 2-8. Chapter I Math students in grades two through six achieved gains on the Iowa Tests of Basic Skills from pre to posttesting. Scores on these tests are reported using a metric known as the Normal Curve Equivalent (NCE). The…

  12. Chapter 2: Optical Properties of the Water Column

    NASA Technical Reports Server (NTRS)

    Kiefer, D. A.; Collins, D. J.

    1994-01-01

    In this chapter, and in chapter 29, the basic inter-relationship between the flux of radiant energy through the water column and the fixation of carbon by the phytoplankton in the ocean through processes of photosynthesis or primary production will be discussed.

  13. 48 CFR Appendixes B-E to Chapter 2 - [Reserved

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 48 Federal Acquisition Regulations System 3 2010-10-01 2010-10-01 false B Appendixes B-E to Chapter 2 Federal Acquisition Regulations System DEFENSE ACQUISITION REGULATIONS SYSTEM, DEPARTMENT OF DEFENSE Appendixes B-E to Chapter 2...

  14. Technology and Chapter 1: Solutions for Catholic School Participation.

    ERIC Educational Resources Information Center

    National Catholic Educational Association, Washington, DC.

    This booklet is designed to provide pertinent information about Chapter 1 (Elementary and Secondary Education Act), explaining what it is, who can participate, how funds are spent, and how technology can be used in a non-public school to meet the needs of students. Chapter 1 channels federal funds to school districts with high concentrations of…

  15. Chapter 2 Formula: Evaluation Report 1990-91.

    ERIC Educational Resources Information Center

    Bliss, Kristen M.

    Chapter 2 Formula provides federal funds to the states through the Elementary and Secondary Education Act of 1965 (ESEA) as amended by P.L. 100-297 in 1988. Chapter 2 funds can support one or more programs that do the following: meet the educational needs of students with special needs (at-risk and high-cost students); acquire curricular…

  16. Chapter 1 Support for Instructional Development, 1986-87.

    ERIC Educational Resources Information Center

    Kaemper, Jack; Morse, Kathy

    Six of the 39 Albuquerque (New Mexico) Public Schools' Chapter 1 participating schools, as part of the school-based budgeting process, allocated a portion of their Chapter 1 resource allocation for on-site intensive staff development activities. Three schools--Alamosa, Chaparral, and Duranes--agreed to utilize the time of a Support for…

  17. Chromophore switch from 11-cis-dehydroretinal (A2) to 11-cis-retinal (A1) decreases dark noise in salamander red rods

    PubMed Central

    Ala-Laurila, Petri; Donner, Kristian; Crouch, Rosalie K; Cornwall, M Carter

    2007-01-01

    Dark noise, light-induced noise and responses to brief flashes of light were recorded in the membrane current of isolated rods from larval tiger salamander retina before and after bleaching most of the native visual pigment, which mainly has the 11-cis-3,4-dehydroretinal (A2) chromophore, and regenerating with the 11-cis-retinal (A1) chromophore in the same isolated rods. The purpose was to test the hypothesis that blue-shifting the pigment by switching from A2 to A1 will decrease the rate of spontaneous thermal activations and thus intrinsic light-like noise in the rod. Complete recordings were obtained in five cells (21°C). Based on the wavelength of maximum absorbance, λmax,A1 = 502 nm and λmax,A2 = 528 nm, the average A2 : A1 ratio determined from rod spectral sensitivities and absorbances was ∼0.74 : 0.26 in the native state and ∼0.09 : 0.91 in the final state. In the native (A2) state, the single-quantum response (SQR) had an amplitude of 0.41 ± 0.03 pA and an integration time of 3.16 ± 0.15 s (mean ± s.e.m.). The low-frequency branch of the dark noise power spectrum was consistent with discrete SQR-like events occurring at a rate of 0.238 ± 0.026 rod−1 s−1. The corresponding values in the final state were 0.57 ± 0.07 pA (SQR amplitude), 3.47 ± 0.26 s (SQR integration time), and 0.030 ± 0.006 rod−1 s−1 (rate of dark events). Thus the rate of dark events per rod and the fraction of A2 pigment both changed by ca 8-fold between the native and final states, indicating that the dark events originated mainly in A2 molecules even in the final state. By extrapolating the linear relation between event rates and A2 fraction to 0% A2 (100% A1) and 100% A2 (0% A1), we estimated that the A1 pigment is at least 36 times more stable than the A2 pigment. The noise component attributed to discrete dark events accounted for 73% of the total dark current variance in the native (A2) state and 46% in the final state. The power spectrum of the remaining

  18. Chromophore switch from 11-cis-dehydroretinal (A2) to 11-cis-retinal (A1) decreases dark noise in salamander red rods.

    PubMed

    Ala-Laurila, Petri; Donner, Kristian; Crouch, Rosalie K; Cornwall, M Carter

    2007-11-15

    Dark noise, light-induced noise and responses to brief flashes of light were recorded in the membrane current of isolated rods from larval tiger salamander retina before and after bleaching most of the native visual pigment, which mainly has the 11-cis-3,4-dehydroretinal (A2) chromophore, and regenerating with the 11-cis-retinal (A1) chromophore in the same isolated rods. The purpose was to test the hypothesis that blue-shifting the pigment by switching from A2 to A1 will decrease the rate of spontaneous thermal activations and thus intrinsic light-like noise in the rod. Complete recordings were obtained in five cells (21 degrees C). Based on the wavelength of maximum absorbance, lambda max,A1 = 502 nm and lambda max,A2 = 528 nm, the average A2 : A1 ratio determined from rod spectral sensitivities and absorbances was approximately 0.74 : 0.26 in the native state and approximately 0.09 : 0.91 in the final state. In the native (A2) state, the single-quantum response (SQR) had an amplitude of 0.41 +/- 0.03 pA and an integration time of 3.16 +/- 0.15 s (mean +/- s.e.m.). The low-frequency branch of the dark noise power spectrum was consistent with discrete SQR-like events occurring at a rate of 0.238 +/- 0.026 rod(-1) s(-1). The corresponding values in the final state were 0.57 +/- 0.07 pA (SQR amplitude), 3.47 +/- 0.26 s (SQR integration time), and 0.030 +/- 0.006 rod(-1) s(-1) (rate of dark events). Thus the rate of dark events per rod and the fraction of A2 pigment both changed by ca 8-fold between the native and final states, indicating that the dark events originated mainly in A2 molecules even in the final state. By extrapolating the linear relation between event rates and A2 fraction to 0% A2 (100% A1) and 100% A2 (0% A1), we estimated that the A1 pigment is at least 36 times more stable than the A2 pigment. The noise component attributed to discrete dark events accounted for 73% of the total dark current variance in the native (A2) state and 46% in the final

  19. Biological effects: Marine mammals and sea turtles (chapter 14). Book chapter

    SciTech Connect

    Haebler, R.

    1994-01-01

    All spills are different, varying in type and amount of oil spilled, species exposed, and geographic and atmospheric conditions. It is important to understand as much as possible about both the natural history and characteristics of various species and the specific effects oil has on wildlife. Doing so improves the ability to extrapolate from one spill to another and improves prediction of types and severity of effects to wildlife. This chapter presents an overview of the biological effects of oil on marine mammals and sea turtles.

  20. Chapter A3. Cleaning of Equipment for Water Sampling

    USGS Publications Warehouse

    Wilde, Franceska D.; Radtke, Dean B.; Gibs, Jacob; Iwatsubo, Rick T.

    1998-01-01

    The National Field Manual for the Collection of Water-Quality Data (National Field Manual) describes protocols and provides guidelines for U.S. Geological Survey (USGS) personnel who collect data used to assess the quality of the Nation's surface-water and ground-water resources. Chapter A3 describes procedures for cleaning the equipment used to collect and process samples of surface water and ground water and procedures for assessing the efficacy of the equipment-cleaning process. This chapter is designed for use with the other chapters of this field manual. Each chapter of the National Field Manual is published separately and revised periodically. Newly published and revised chapters will be posted on the USGS page 'National Field Manual for the Collection of Water-Quality Data.' The URL for this page is http://pubs.water.usgs.gov/twri9A/ (accessed September 20, 2004).

  1. A CIS (Clinical Information System) Quality Evaluation Tool for Nursing Care Services

    ERIC Educational Resources Information Center

    Lee, Seon Ah

    2010-01-01

    The purpose of this study was to develop a tool to evaluate the quality of a clinical information system (CIS) conceived by nurses and conduct a pilot test with the developed tool as an initial assessment. CIS quality is required for successful implementation in information technology (IT) environments. The study started with the realization that…

  2. Columbia River Coordinated Information System (CIS), 1992-1993 Annual Report.

    SciTech Connect

    Rowe, Mike; Roger, Phillip B.; O'Connor, Dick

    1993-11-01

    The purposes of this report are to: (1) describe the project to date; (2) to document the work and accomplishments of the (CIS) project for Fiscal Year 1993; and (3) to provide a glimpse of future project direction. The concept of a Coordinated Information System (CIS) as an approach to meeting the growing needs for regionally standardized anadromous fish information.

  3. IRIS Toxicological Review of cis- & trans-1,2-Dichloroethylene (2010 Final)

    EPA Science Inventory

    The final Toxicological Review of cis- & trans-1,2-Dichloroethylene provides scientific support and rationale for the hazard and dose-response assessment pertaining to chronic exposure to cis- and trans-1,2-dichloroethylene. 1,2-Dichloroethylene is used as a solvent for wa...

  4. The Influence of 13-cis Retinoic Acid on Human Meibomian Gland Epithelial Cells

    PubMed Central

    Ding, Juan; Kam, Wendy R.; Dieckow, Julia; Sullivan, David A.

    2013-01-01

    Purpose. Meibomian gland dysfunction (MGD) is a primary cause of dry eye disease. One of the risk factors for MGD is exposure to 13-cis retinoic acid (13-cis RA), a metabolite of vitamin A. However, the mechanism is not well understood. We hypothesize that 13-cis RA inhibits cell proliferation, promotes cell death, alters gene and protein expressions, and attenuates cell survival pathways in human meibomian gland epithelial cells. Methods. To test our hypotheses, immortalized human meibomian gland epithelial cells were cultured with or without 13-cis RA for varying doses and time. Cell proliferation, cell death, gene expression, and proteins involved in proliferation/survival and inflammation were evaluated. Results. We found that 13-cis RA inhibited cell proliferation, induced cell death, and significantly altered the expression of 6726 genes, including those involved in cell proliferation, cell death, differentiation, keratinization, and inflammation, in human meibomian gland epithelial cells. Further, 13-cis RA also reduced the phosphorylation of Akt and increased the generation of interleukin-1β and matrix metallopeptidase 9. Conclusions. Exposure to 13-cis RA inhibits cell proliferation, increases cell death, alters gene expression, changes signaling pathways, and promotes inflammatory mediator and protease expression in meibomian gland epithelial cells. These effects may be responsible, at least in part, for the 13-cis RA–related induction of MGD. PMID:23722388

  5. Ethical Challenges of Educational Leadership in the Countries of the CIS

    ERIC Educational Resources Information Center

    Zagoumennov, Iouri

    2010-01-01

    There is no school administrators' pre-service training in the CIS (Former USSR) countries. As for the in-service training, it has been traditionally focused on educational management. As a result, schools in the CIS countries are run as well-oiled machines but there is a big question mark over whether these machines are running in the right…

  6. Planning "and" Sprinting: Use of a Hybrid Project Management Methodology within a CIS Capstone Course

    ERIC Educational Resources Information Center

    Baird, Aaron; Riggins, Frederick J.

    2012-01-01

    An increasing number of information systems projects in industry are managed using hybrid project management methodologies, but this shift in project management methods is not fully represented in our CIS curriculums. CIS capstone courses often include an applied project that is managed with traditional project management methods (plan first,…

  7. cis-Prenyltransferase: New Insights into Protein Glycosylation, Rubber Synthesis, and Human Diseases.

    PubMed

    Grabińska, Kariona A; Park, Eon Joo; Sessa, William C

    2016-08-26

    cis-Prenyltransferases (cis-PTs) constitute a large family of enzymes conserved during evolution and present in all domains of life. cis-PTs catalyze consecutive condensation reactions of allylic diphosphate acceptor with isopentenyl diphosphate (IPP) in the cis (Z) configuration to generate linear polyprenyl diphosphate. The chain lengths of isoprenoid carbon skeletons vary widely from neryl pyrophosphate (C10) to natural rubber (C>10,000). The homo-dimeric bacterial enzyme, undecaprenyl diphosphate synthase (UPPS), has been structurally and mechanistically characterized in great detail and serves as a model for understanding the mode of action of eukaryotic cis-PTs. However, recent experiments have revealed that mammals, fungal, and long-chain plant cis-PTs are heteromeric enzymes composed of two distantly related subunits. In this review, the classification, function, and evolution of cis-PTs will be discussed with a special emphasis on the role of the newly described NgBR/Nus1 subunit and its plants' orthologs as essential, structural components of the cis-PTs activity. PMID:27402831

  8. Nanoporous Materials in Atmosphere Revitalization. Chapter 1

    NASA Technical Reports Server (NTRS)

    Hernandez-Maldonado, J.; Ishikawa, Yasuyuki; Luna, Bernadette; Junaedi, Christian; Mulloth, Lila; Perry, Jay L.; Raptis, Raphael G.; Roychoudhury, Subir

    2012-01-01

    lowering cabin levels of CO2 and NH3 as well as reducing power requirements and increasing reliability. This chapter summarizes the challenges faced by ECLS system engineers in pursuing these goals, and the promising materials developments that may be part of the technical solution for challenges of crewed space exploration beyond LEO.

  9. Chapter 9: Analyses Using Disease Ontologies

    PubMed Central

    Shah, Nigam H.; Cole, Tyler; Musen, Mark A.

    2012-01-01

    Advanced statistical methods used to analyze high-throughput data such as gene-expression assays result in long lists of “significant genes.” One way to gain insight into the significance of altered expression levels is to determine whether Gene Ontology (GO) terms associated with a particular biological process, molecular function, or cellular component are over- or under-represented in the set of genes deemed significant. This process, referred to as enrichment analysis, profiles a gene-set, and is widely used to makes sense of the results of high-throughput experiments. The canonical example of enrichment analysis is when the output dataset is a list of genes differentially expressed in some condition. To determine the biological relevance of a lengthy gene list, the usual solution is to perform enrichment analysis with the GO. We can aggregate the annotating GO concepts for each gene in this list, and arrive at a profile of the biological processes or mechanisms affected by the condition under study. While GO has been the principal target for enrichment analysis, the methods of enrichment analysis are generalizable. We can conduct the same sort of profiling along other ontologies of interest. Just as scientists can ask “Which biological process is over-represented in my set of interesting genes or proteins?” we can also ask “Which disease (or class of diseases) is over-represented in my set of interesting genes or proteins?“. For example, by annotating known protein mutations with disease terms from the ontologies in BioPortal, Mort et al. recently identified a class of diseases—blood coagulation disorders—that were associated with a 14-fold depletion in substitutions at O-linked glycosylation sites. With the availability of tools for automatic annotation of datasets with terms from disease ontologies, there is no reason to restrict enrichment analyses to the GO. In this chapter, we will discuss methods to perform enrichment analysis using any

  10. Quantitative comparison of cis-regulatory element (CRE) activities in transgenic Drosophila melanogaster.

    PubMed

    Rogers, William A; Williams, Thomas M

    2011-01-01

    Gene expression patterns are specified by cis-regulatory element (CRE) sequences, which are also called enhancers or cis-regulatory modules. A typical CRE possesses an arrangement of binding sites for several transcription factor proteins that confer a regulatory logic specifying when, where, and at what level the regulated gene(s) is expressed. The full set of CREs within an animal genome encodes the organism's program for development, and empirical as well as theoretical studies indicate that mutations in CREs played a prominent role in morphological evolution. Moreover, human genome wide association studies indicate that genetic variation in CREs contribute substantially to phenotypic variation. Thus, understanding regulatory logic and how mutations affect such logic is a central goal of genetics. Reporter transgenes provide a powerful method to study the in vivo function of CREs. Here a known or suspected CRE sequence is coupled to heterologous promoter and coding sequences for a reporter gene encoding an easily observable protein product. When a reporter transgene is inserted into a host organism, the CRE's activity becomes visible in the form of the encoded reporter protein. P-element mediated transgenesis in the fruit fly species Drosophila (D.) melanogaster has been used for decades to introduce reporter transgenes into this model organism, though the genomic placement of transgenes is random. Hence, reporter gene activity is strongly influenced by the local chromatin and gene environment, limiting CRE comparisons to being qualitative. In recent years, the phiC31 based integration system was adapted for use in D. melanogaster to insert transgenes into specific genome landing sites. This capability has made the quantitative measurement of gene and, relevant here, CRE activity feasible. The production of transgenic fruit flies can be outsourced, including phiC31-based integration, eliminating the need to purchase expensive equipment and/or have proficiency at

  11. Induction of chromosome aberrations by cis-platinum(II)diamminodichloride in Drosophila melanogaster

    SciTech Connect

    Brodberg, R.K.; Lyman, R.F.; Woodruff, R.C.

    1983-01-01

    The authors have determined the in vivo effects of cis-platinum(II)diamminodichloride (cis-PDD) treatment on the induction of chromosome aberrations in Drosophila melanogaster germ cells. cis-PDD treatment induces significant increases in chromosome breakage in all stages of spermatogenesis in a battery of test systems using ring or rod-X males and repair-proficient or deficient females. Since no increase in nondisjunction was induced by cis-PDD in either male or female germ cells, any aneuploidy inducing effects of this compound should result from its clastogenic action. They also find that mei-9 excision repair function is involved in the repair of cis-PDD-induced DNA lesions in a manner that provides additional evidence that partital and ring chromosome losses are not completely homologous.

  12. Single-Molecule Observation of a Mechanically Activated Cis-to-Trans Cyclopropane Isomerization.

    PubMed

    Wang, Junpeng; Kouznetsova, Tatiana B; Craig, Stephen L

    2016-08-24

    The mechanochemical activation of cis-gem-difluorocyclopropane (cis-gDFC) mechanophore in toluene was characterized with single-molecule force spectroscopy. Unlike previously reported behavior in methyl benzoate (MB), two transitions are observed in the force vs extension curves of cis-gDFC polymers in toluene. The first transition occurs at the same force of ∼1300 pN observed previously in MB, but a second transition is observed at forces of ∼1800 pN that reveal the partial formation of the trans-gDFC isomer. The behavior is attributed to competing reactions of the cis-gDFC at the 1300 pN plateau: addition of oxygen to a ring-opened diradicaloid intermediate, and isomerization of cis-gDFC to its trans isomer. PMID:27500711

  13. Getting the Most from Pi Sigma Alpha Chapters: Exploring the Chapter Activity Grant Program and Its Multiplier Effects

    ERIC Educational Resources Information Center

    Alexander, Robert M.

    2009-01-01

    The political science honor society, Pi Sigma Alpha, has chapters in nearly 700 institutions across the United States. The organization sponsors many programs that can contribute a great deal to students of political science; however, many students are unaware of these opportunities. This article encourages chapter advisors to make use of these…

  14. Cis-9, trans-11 and trans-10, cis-12 CLA mixture does not change body composition, induces insulin resistance and increases serum HDL cholesterol level in rats.

    PubMed

    de Almeida, Mariana Macedo; de Souza, Yamara Oliveira; Dutra Luquetti, Sheila Cristina Potente; Sabarense, Céphora Maria; do Amaral Corrêa, José Otávio; da Conceição, Ellen Paula Santos; Lisboa, Patrícia Cristina; de Moura, Egberto Gaspar; Andrade Soares, Sara Malaguti; Moura Gualberto, Ana Cristina; Gameiro, Jacy; da Gama, Marco Antônio Sundfeld; Ferraz Lopes, Fernando César; González Garcia, Raúl Marcel

    2015-01-01

    Synthetic supplements of conjugated linoleic acid (CLA) containing 50:50 mixture of cis-9, trans-11 and trans-10, cis-12 CLA isomers have been commercialized in some places for reducing body fat. However the safety of this CLA mixture is controversial and in some countries the CLA usage as food supplement is not authorized. Changes in insulinemic control and serum lipids profile are potential negative effects related to consumption of CLA mixture. The present study aimed to evaluate the effects of a diet containing mixture of cis-9, trans-11 and trans-10, cis-12 CLA on prevention of obesity risk as well as on potential side effects such as insulin resistance and dyslipidemia in Wistar rats. Thirty male Wistar rats were randomly assigned to the following dietary treatments (n=10/group), for 60 days: Normolipidic Control (NC), diet containing 4.0% soybean oil (SO); High Fat-Control (HF-C), diet containing 24.0% SO; High Fat-synthetic CLA (HF-CLA), diet containing 1.5% of an isomeric CLA mixture (Luta-CLA 60) and 22.5% SO. Luta-CLA 60 (BASF) contained nearly 60% of CLA (cis-9, trans-11 and trans-10, cis-12 CLA at 50:50 ratio). The HF-CLA diet contained 0.3% of each CLA isomer. HF-CLA diet had no effect on dietary intake and body composition. HF-CLA-fed rats had lower levels of PPARγ protein in retroperitoneal adipose tissue, hyperinsulinemia compared to HF-C-fed rats, hyperglycemia compared to NC-fed rats while no differences in glycemia were observed between NC and HF-C groups, increased HOMA index and higher levels of serum HDL cholesterol. Thus, feeding rats with a high fat diet containing equal parts of cis-9, trans-11 and trans-10, cis-12 CLA isomers had no effect on body composition and induced insulin resistance. Despite HF-CLA-fed rats had increased serum HDL cholesterol levels, caution should be taken before synthetic supplements containing cis-9, trans-11 and trans-10, cis-12 CLA are recommended as a nutritional strategy for weight management.

  15. Chapter 9: Pedagogical Content Knowing for Model-Based Instruction in Physical Education and Future Directions for Research

    ERIC Educational Resources Information Center

    Lund, Jacalyn L.; Metzler, Michael W.; Gurvitch, Rachel

    2008-01-01

    The purpose of this chapter is to advance the concept of pedagogical content knowledge in a manner that would better align it with the integrative type of knowledge needed by teachers at all three stages (preservice teachers, induction teachers, and cooperating teachers), allowing them to use model-based instruction (MBI) most effectively in…

  16. Application of CIS to high-efficiency PV module fabrication. Phase 3 final technical report

    SciTech Connect

    Basol, B M; Kapur, V K; Leidholm, C R; Halani, A; Roe, R; Norsworthy, G

    1998-08-01

    During this research period, researchers at International Solar Electric Technology (ISET) concentrated their efforts on three different areas of research. Within the National CIS R and D Team, ISET participated in the substrate/Mo interactions working group and investigated issues such as Na diffusion from the soda-lime glass substrate into the Mo layers and CIS films. Researchers determined that the Na content within the Mo layers was not a strong function of the nature of the Mo film. However, they found that diffusion through the Mo layers was a function of the Mo film characteristics as well as a very strong function of the CIS growth process itself. Researchers showed conclusively that the Na resided on the grain boundaries of CIS layers. Another team activity involved evaluation of CdS-free CIS solar cells. ZnO/CIS junctions prepared by the two-stage process showed light-soaking effects. Cells left under illumination improved in efficiency and were similar to the CdS/CIS junctions. After storage in the dark, however, efficiency deteriorated greatly for the ZnO/CIS device, most of the decline coming from the open-circuit voltage values. Much of the effort during this period was spent on developing a low-cost, non-vacuum CIS deposition technique. The method developed involves particulate deposition and formation of precursor layers followed by the conversion of these layers into CIS. Test modules of 40--60 cm{sup 2} were adapted to understand the issues involved in this novel technology. At the present time, the submodule efficiencies are 6--7%. Single-cell efficiencies are in the 10--13% range.

  17. Cis and trans effects of human genomic variants on gene expression.

    PubMed

    Bryois, Julien; Buil, Alfonso; Evans, David M; Kemp, John P; Montgomery, Stephen B; Conrad, Donald F; Ho, Karen M; Ring, Susan; Hurles, Matthew; Deloukas, Panos; Davey Smith, George; Dermitzakis, Emmanouil T

    2014-07-01

    Gene expression is a heritable cellular phenotype that defines the function of a cell and can lead to diseases in case of misregulation. In order to detect genetic variations affecting gene expression, we performed association analysis of single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) with gene expression measured in 869 lymphoblastoid cell lines of the Avon Longitudinal Study of Parents and Children (ALSPAC) cohort in cis and in trans. We discovered that 3,534 genes (false discovery rate (FDR) = 5%) are affected by an expression quantitative trait locus (eQTL) in cis and 48 genes are affected in trans. We observed that CNVs are more likely to be eQTLs than SNPs. In addition, we found that variants associated to complex traits and diseases are enriched for trans-eQTLs and that trans-eQTLs are enriched for cis-eQTLs. As a variant affecting both a gene in cis and in trans suggests that the cis gene is functionally linked to the trans gene expression, we looked specifically for trans effects of cis-eQTLs. We discovered that 26 cis-eQTLs are associated to 92 genes in trans with the cis-eQTLs of the transcriptions factors BATF3 and HMX2 affecting the most genes. We then explored if the variation of the level of expression of the cis genes were causally affecting the level of expression of the trans genes and discovered several causal relationships between variation in the level of expression of the cis gene and variation of the level of expression of the trans gene. This analysis shows that a large sample size allows the discovery of secondary effects of human variations on gene expression that can be used to construct short directed gene regulatory networks.

  18. Cis and Trans Effects of Human Genomic Variants on Gene Expression

    PubMed Central

    Bryois, Julien; Buil, Alfonso; Evans, David M.; Kemp, John P.; Montgomery, Stephen B.; Conrad, Donald F.; Ho, Karen M.; Ring, Susan; Hurles, Matthew; Deloukas, Panos; Davey Smith, George; Dermitzakis, Emmanouil T.

    2014-01-01

    Gene expression is a heritable cellular phenotype that defines the function of a cell and can lead to diseases in case of misregulation. In order to detect genetic variations affecting gene expression, we performed association analysis of single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) with gene expression measured in 869 lymphoblastoid cell lines of the Avon Longitudinal Study of Parents and Children (ALSPAC) cohort in cis and in trans. We discovered that 3,534 genes (false discovery rate (FDR) = 5%) are affected by an expression quantitative trait locus (eQTL) in cis and 48 genes are affected in trans. We observed that CNVs are more likely to be eQTLs than SNPs. In addition, we found that variants associated to complex traits and diseases are enriched for trans-eQTLs and that trans-eQTLs are enriched for cis-eQTLs. As a variant affecting both a gene in cis and in trans suggests that the cis gene is functionally linked to the trans gene expression, we looked specifically for trans effects of cis-eQTLs. We discovered that 26 cis-eQTLs are associated to 92 genes in trans with the cis-eQTLs of the transcriptions factors BATF3 and HMX2 affecting the most genes. We then explored if the variation of the level of expression of the cis genes were causally affecting the level of expression of the trans genes and discovered several causal relationships between variation in the level of expression of the cis gene and variation of the level of expression of the trans gene. This analysis shows that a large sample size allows the discovery of secondary effects of human variations on gene expression that can be used to construct short directed gene regulatory networks. PMID:25010687

  19. 9-cis β-Carotene Increased Cholesterol Efflux to HDL in Macrophages.

    PubMed

    Bechor, Sapir; Zolberg Relevy, Noa; Harari, Ayelet; Almog, Tal; Kamari, Yehuda; Ben-Amotz, Ami; Harats, Dror; Shaish, Aviv

    2016-01-01

    Cholesterol efflux from macrophages is a key process in reverse cholesterol transport and, therefore, might inhibit atherogenesis. 9-cis-β-carotene (9-cis-βc) is a precursor for 9-cis-retinoic-acid (9-cis-RA), which regulates macrophage cholesterol efflux. Our objective was to assess whether 9-cis-βc increases macrophage cholesterol efflux and induces the expression of cholesterol transporters. Enrichment of a mouse diet with βc from the alga Dunaliella led to βc accumulation in peritoneal macrophages. 9-cis-βc increased the mRNA levels of CYP26B1, an enzyme that regulates RA cellular levels, indicating the formation of RA from βc in RAW264.7 macrophages. Furthermore, 9-cis-βc, as well as all-trans-βc, significantly increased cholesterol efflux to high-density lipoprotein (HDL) by 50% in RAW264.7 macrophages. Likewise, food fortification with 9-cis-βc augmented cholesterol efflux from macrophages ex vivo. 9-cis-βc increased both the mRNA and protein levels of ABCA1 and apolipoprotein E (APOE) and the mRNA level of ABCG1. Our study shows, for the first time, that 9-cis-βc from the diet accumulates in peritoneal macrophages and increases cholesterol efflux to HDL. These effects might be ascribed to transcriptional induction of ABCA1, ABCG1, and APOE. These results highlight the beneficial effect of βc in inhibition of atherosclerosis by improving cholesterol efflux from macrophages. PMID:27447665

  20. Pharmacokinetics and effects on plasma retinol concentrations of 13-cis-retinoic acid in melanoma patients.

    PubMed Central

    Formelli, F.; Cavadini, E.; Mascheroni, L.; Belli, F.; Cascinelli, N.

    1997-01-01

    The pharmacokinetics of 13-cis-retinoic acid (13cisRA) and its effects on retinol plasma levels were investigated after the first and the last doses in melanoma patients, who participated in a study run to assess tolerance over a long period of a treatment schedule of 13cisRA associated with recombinant interferon alpha2a (rIFN-alpha2a). Melanoma patients with regional node metastases after radical surgery were randomized to be treated for 3 months with rIFN-alpha2a, 3 x 10(6) IU s.c. every other day, associated with oral 13cisRA at doses of 20 mg day(-1) (five patients) or 40 mg every other day (seven patients). Maximum 13cisRA blood concentrations usually occurred 4 h after drug administration, with average values of 406 and 633 ng ml(-1) (i.e. 1.3 and 2.1 microM) after the 20 and 40 mg dose respectively. The average half-life (t(1/2)) was approximately 30 h. The maximum concentration, the t(1/2) and the area under the concentration-time curves from 0 to 48 h (AUC(0-48)) of 13cisRA did not change after multiple dosing, whereas the AUC(0-48) of its major blood metabolite, 4-oxo-13-cis-retinoic acid, increased. Immediately after 13cisRA treatment, retinol plasma levels started to decline and they reached the lowest values (approximately 20% reduction) shortly after the time of maximum 13cisRA concentrations (i.e. 4-12 h after drug intake). Afterwards, values returned to baseline. The amount of retinol reduction in time was correlated with 13cisRA maximum concentrations. PMID:9413958

  1. Cis-Golgi cisternal assembly and biosynthetic activation occur sequentially in plants and algae

    PubMed Central

    Donohoe, Bryon S.; Kang, Byung-Ho; Gerl, Mathias J.; Gergely, Zachary R.; McMichael, Colleen M.; Bednarek, Sebastian Y.; Staehelin, L. Andrew

    2013-01-01

    The cisternal progression/maturation model of Golgi trafficking predicts that cis-Golgi cisternae are formed de novo on the cis-side of the Golgi. Here we describe structural and functional intermediates of the cis cisterna assembly process in high-pressure frozen algae (Scherffelia dubia, Chlamydomonas reinhardtii) and plants (Arabidopsis thaliana, Dionaea muscipula; Venus Flytrap) as determined by electron microscopy, electron tomography and immuno-electron microscopy techniques. Our findings are as follows: (1) The cis-most (C1) Golgi cisternae are generated de novo from cisterna initiators produced by the fusion of 3–5 COPII vesicles in contact with a C2 cis cisterna. (2) COPII vesicles fuel the growth of the initiators, which then merge into a coherent C1 cisterna. (3) When a C1 cisterna nucleates its first cisterna initiator it becomes a C2 cisterna. (4) C2-Cn cis cisternae grow through COPII vesicle fusion. (5) ER-resident proteins are recycled from cis cisternae to the ER via COPIa-type vesicles. (6) In S. dubia the C2 cisternae are capable of mediating the self-assembly of scale protein complexes. (7) In plants, ~90% of native α-mannosidase I localizes to medial Golgi cisternae. (8) Biochemical activation of cis cisternae appears to coincide with their conversion to medial cisternae via recycling of medial cisterna enzymes. We propose how the different cis cisterna assembly intermediates of plants and algae may actually be related to those present in the ERGIC and in the pre-cis Golgi cisterna layer in mammalian cells. PMID:23369235

  2. Cis-Golgi cisternal assembly and biosynthetic activation occur sequentially in plants and algae.

    PubMed

    Donohoe, Bryon S; Kang, Byung-Ho; Gerl, Mathias J; Gergely, Zachary R; McMichael, Colleen M; Bednarek, Sebastian Y; Staehelin, L Andrew

    2013-05-01

    The cisternal progression/maturation model of Golgi trafficking predicts that cis-Golgi cisternae are formed de novo on the cis-side of the Golgi. Here we describe structural and functional intermediates of the cis cisterna assembly process in high-pressure frozen algae (Scherffelia dubia, Chlamydomonas reinhardtii) and plants (Arabidopsis thaliana, Dionaea muscipula; Venus flytrap) as determined by electron microscopy, electron tomography and immuno-electron microscopy techniques. Our findings are as follows: (i) The cis-most (C1) Golgi cisternae are generated de novo from cisterna initiators produced by the fusion of 3-5 COPII vesicles in contact with a C2 cis cisterna. (ii) COPII vesicles fuel the growth of the initiators, which then merge into a coherent C1 cisterna. (iii) When a C1 cisterna nucleates its first cisterna initiator it becomes a C2 cisterna. (iv) C2-Cn cis cisternae grow through COPII vesicle fusion. (v) ER-resident proteins are recycled from cis cisternae to the ER via COPIa-type vesicles. (vi) In S. dubia the C2 cisternae are capable of mediating the self-assembly of scale protein complexes. (vii) In plants, ∼90% of native α-mannosidase I localizes to medial Golgi cisternae. (viii) Biochemical activation of cis cisternae appears to coincide with their conversion to medial cisternae via recycling of medial cisterna enzymes. We propose how the different cis cisterna assembly intermediates of plants and algae may actually be related to those present in the ERGIC and in the pre-cis Golgi cisterna layer in mammalian cells.

  3. cis-Isomers of Cytokinins Predominate in Chickpea Seeds throughout Their Development1

    PubMed Central

    Emery, Robert Joseph Neil; Leport, Laurent; Barton, Joanne Edith; Turner, Neil Clifford; Atkins, Craig Anthony

    1998-01-01

    Trans-isomers of cytokinins (CK) are thought to predominate and have greater biological activity than corresponding cis-isomers in higher plants. However, this study demonstrates a system within which the predominant CK are cis-isomers. CK were measured at four developmental stages in developing chickpea (Cicer arietinum L. cultivar Kaniva) seeds by gas chromatography-mass spectrometry. Concentrations were highest at an early endospermic fluid stage and fell considerably when the cotyledons expanded. The cis-isomers of zeatin nucleotide ([9R-MP]Z), zeatin riboside ([9R]Z), and zeatin (Z) were present in greater concentrations than those of corresponding trans-isomers: (trans)[9R-MP]Z, (trans)[9R]Z, (trans)Z, or dihydrozeatin riboside. Dihydrozeatin, dihydrozeatin nucleotide, and the isopentenyl-type CK concentrations were either low or not detectable. Root xylem exudates also contained predominantly cis-isomers of [9R-MP]Z and [9R]Z. Identities of (cis)[9R]Z and (cis)Z were confirmed by comparison of ion ratios and retention indices, and a full spectrum was obtained for (cis)[9R]Z. Tissues were extracted under conditions that minimized the possibility of RNase hydrolysis of tRNA following tissue disruption, being a significant source of the cis-CK. Since no isomerization of (trans)[2H]CK internal standards occurred, it is unlikely that the cis-CK resulted from enzymic or nonenzymic isomerization during extraction. Although quantities of total CK varied, similar CK profiles were found among three different chickpea cultivars and between adequately watered and water-stressed plants. Developing chickpea seeds will be a useful system for investigating the activity of cis-CK or determining the origin and metabolism of free CK. PMID:9701607

  4. 9-cis β-Carotene Increased Cholesterol Efflux to HDL in Macrophages

    PubMed Central

    Bechor, Sapir; Zolberg Relevy, Noa; Harari, Ayelet; Almog, Tal; Kamari, Yehuda; Ben-Amotz, Ami; Harats, Dror; Shaish, Aviv

    2016-01-01

    Cholesterol efflux from macrophages is a key process in reverse cholesterol transport and, therefore, might inhibit atherogenesis. 9-cis-β-carotene (9-cis-βc) is a precursor for 9-cis-retinoic-acid (9-cis-RA), which regulates macrophage cholesterol efflux. Our objective was to assess whether 9-cis-βc increases macrophage cholesterol efflux and induces the expression of cholesterol transporters. Enrichment of a mouse diet with βc from the alga Dunaliella led to βc accumulation in peritoneal macrophages. 9-cis-βc increased the mRNA levels of CYP26B1, an enzyme that regulates RA cellular levels, indicating the formation of RA from βc in RAW264.7 macrophages. Furthermore, 9-cis-βc, as well as all-trans-βc, significantly increased cholesterol efflux to high-density lipoprotein (HDL) by 50% in RAW264.7 macrophages. Likewise, food fortification with 9-cis-βc augmented cholesterol efflux from macrophages ex vivo. 9-cis-βc increased both the mRNA and protein levels of ABCA1 and apolipoprotein E (APOE) and the mRNA level of ABCG1. Our study shows, for the first time, that 9-cis-βc from the diet accumulates in peritoneal macrophages and increases cholesterol efflux to HDL. These effects might be ascribed to transcriptional induction of ABCA1, ABCG1, and APOE. These results highlight the beneficial effect of βc in inhibition of atherosclerosis by improving cholesterol efflux from macrophages. PMID:27447665

  5. Stock Summary Reports for Columbia River Anadromous Salmonids, Volume 1; Oregon Subbasins Below Bonneville Dam, 1992 CIS Summary Report.

    SciTech Connect

    Olsen, Eric; Pierce, Paige; Hatch, Keith

    1993-05-01

    An essential component of the effort to rebuild the Columbia Basin's anadromous fish resources is that available information and experience be organized and shared among numerous organizations and individuals. Past experience and knowledge must form the basis for actions into the future. Much of this knowledge exists only in unpublished form in agency and individual files. Even that information which is published in the form of technical and contract reports receives only limited distribution and is often out of print and unavailable after a few years. Only a small fraction of the basin's collective knowledge is captured in permanent and readily available databases (such as the Northwest Environmental Database) or in recognized journals. State, tribal, and federal fishery managers have recognized these information management problems and have committed to a program, the Coordinated Information System Project, to capture and share more easily the core data and other information upon which management decisions are based. That project has completed scoping and identification of key information needs and development of a project plan. Work performed under the CIS project will be coordinated with and extend information contained in the Northwest Environmental Database. Construction of prototype systems will begin in Phase 3. This report is one in a series of seven describing the results of the Coordinated Information System scoping and needs identification phase. A brief description of each of these reports follows. This report (Roger 1992) summarizes and integrates the results of the next five reports and relates them to deliverables identified in the Phase II cooperative agreement. Broader issues of organization and operation which are not appropriate for the more focused reports are also discussed. This report should be viewed as an executive summary for the CIS project to date. If one wants a quick overview of the CIS project, this report and the project plan will

  6. Characterization of a putative cis-regulatory element that controls transcriptional activity of the pig uroplakin II gene promoter

    SciTech Connect

    Kwon, Deug-Nam; Park, Mi-Ryung; Park, Jong-Yi; Cho, Ssang-Goo; Park, Chankyu; Oh, Jae-Wook; Song, Hyuk; Kim, Jae-Hwan; Kim, Jin-Hoi

    2011-07-01

    Highlights: {yields} The sequences of -604 to -84 bp of the pUPII promoter contained the region of a putative negative cis-regulatory element. {yields} The core promoter was located in the 5F-1. {yields} Transcription factor HNF4 can directly bind in the pUPII core promoter region, which plays a critical role in controlling promoter activity. {yields} These features of the pUPII promoter are fundamental to development of a target-specific vector. -- Abstract: Uroplakin II (UPII) is a one of the integral membrane proteins synthesized as a major differentiation product of mammalian urothelium. UPII gene expression is bladder specific and differentiation dependent, but little is known about its transcription response elements and molecular mechanism. To identify the cis-regulatory elements in the pig UPII (pUPII) gene promoter region, we constructed pUPII 5' upstream region deletion mutants and demonstrated that each of the deletion mutants participates in controlling the expression of the pUPII gene in human bladder carcinoma RT4 cells. We also identified a new core promoter region and putative negative cis-regulatory element within a minimal promoter region. In addition, we showed that hepatocyte nuclear factor 4 (HNF4) can directly bind in the pUPII core promoter (5F-1) region, which plays a critical role in controlling promoter activity. Transient cotransfection experiments showed that HNF4 positively regulates pUPII gene promoter activity. Thus, the binding element and its binding protein, HNF4 transcription factor, may be involved in the mechanism that specifically regulates pUPII gene transcription.

  7. A clinical information system strategic planning model for integrated healthcare delivery networks.

    PubMed

    Snyder-Halpern, R; Chervany, N L

    2000-12-01

    As healthcare organizations are transformed into consolidated healthcare delivery networks, their success is increasingly dependent on the integration and effectiveness of their clinical information systems (CIS). Greater financial investments are being made in CIS products and services to support processes related to clinical care oversight, direct care delivery, and ancillary clinical services. To make good investment decisions, these enterprises must engage in a comprehensive strategic planning process that tightly links their healthcare delivery network clinical strategy, CIS strategic vision, and specific CIS investments. The authors illustrate the linkages among these three strategic planning stages through the application of a clinical information system strategic planning model to a case example.

  8. Synthesis of natural fragrant molecules cis-3-methyl-4-decanolide and aerangis lactone. General enantioselective routes to beta,gamma-cis-disubstituted gamma-lactones and gamma,delta-cis-disubstituted delta-lactones.

    PubMed

    Wu, Yikang; Shen, Xin; Tang, Chao-Jun; Chen, Zhi-Long; Hu, Qi; Shi, Wei

    2002-05-31

    General enantioselective routes to 3,4-cis-dialkyl substituted gamma-lactones and 4,5-cis-dialkyl substituted delta-lactones using TiCl(4)-mediated Evans asymmetric aldolization as the key step are reported. The syntheses are exemplified with two natural fragrant molecules, cis-3-methyl-4-decanolide (1) and aerangis lactone (2). The (R,R) steroegenic centers were established using (S)-phenylalanine-derived 2-oxazolidinone or thiazolidinethione as chiral auxiliary, whereas the (S,S) ones were constructed with auxiliary prepared from (R)-phenylglycine. NaBH(4)/CaCl(2)/THF in the presence of a small amount of EtOH was introduced as a new effective method for reductive cleavage of chiral oxazolidinone auxiliaries. Previously unknown, tricky concentration effects were observed during the monotosylation of diol 7 and BOM protection of Evans aldol 23.

  9. BMC{trademark}: Baseline report; Greenbook (chapter)

    SciTech Connect

    1997-07-31

    Barrier Membrane Containment (BMC){trademark} is a high-density polyethylene membrane (HDPE) groundwater barrier and pass-through system, with applications ranging from plume control and containment to groundwater manipulation coupled with in-site treatment. BMC{trademark} system can function as a permeable or impermeable reaction wall, a cut-off wall, interceptor trenches, a barrier with collection and/or monitoring system, and a pass-through in a funnel and gate configuration. BMC{trademark} can be inspected with a down-hole video camera, producing a permanent VHS format tape, insuring the integrity of the wall and the interlocking joints.

  10. Annual Report of the Integrated Status and Effectiveness Monitoring Program: Fiscal Year 2008

    SciTech Connect

    Terraqua, Inc.

    2009-07-20

    This document was created as an annual report detailing the accomplishments of the Integrated Status and Effectiveness Monitoring Program (ISEMP) in the Upper Columbia Basin in fiscal year 2008. The report consists of sub-chapters that reflect the various components of the program. Chapter 1 presents a report on programmatic coordination and accomplishments, and Chapters 2 through 4 provide a review of how ISEMP has progressed during the 2008 fiscal year in each of the pilot project subbasins: the John Day (Chapter 2), Wenatchee/Entiat (Chapter 3) and Salmon River (Chapter 4). Chapter 5 presents a report on the data management accomplishments in 2008.

  11. Chapter 8: Plasma operation and control

    NASA Astrophysics Data System (ADS)

    ITER Physics Expert Group on Disruptions, Control, Plasma, and MHD; ITER Physics Expert Group on Energetic Particles, Heating, Current and Drive; ITER Physics Expert Group on Diagnostics; ITER Physics Basis Editors

    1999-12-01

    well as in plasma periphery and divertor. The planned diagnostics (Chapter 7) serve as sensors for kinetic control, while gas and pellet fuelling, auxiliary power and angular momentum input, impurity injection, and non-inductive current drive constitute the control actuators. For example, in an ignited plasma, core density controls fusion power output. Kinetic control algorithms vary according to the plasma state, e.g. H- or L-mode. Generally, present facilities have demonstrated the kinetic control methods required for a reactor scale device. Plasma initiation - breakdown, burnthrough and initial current ramp - in reactor scale tokamaks will not involve physics differing from that found in present day devices. For ITER, the induced electric field in the chamber will be ~0.3V· m-1 - comparable to that required by breakdown theory but somewhat smaller than in present devices. Thus, a start-up 3MW electron cyclotron heating system will be employed to assure burnthrough. Simulations show that plasma current ramp up and termination in a reactor scale device can follow procedures developed to avoid disruption in present devices. In particular, simulations remain in the stable area of the li-q plane. For design purposes, the resistive V·s consumed during initiation is found, by experiments, to follow the Ejima expression, 0.45μ0 RIp. Advanced tokamak control has two distinct goals. First, control of density, auxiliary power, and inductive current ramping to attain reverse shear q profiles and internal transport barriers, which persist until dissipated by magnetic flux diffusion. Such internal transport barriers can lead to transient ignition. Second, combined use poloidal field shape control with non-inductive current drive and NBI angular momentum injection to create and control steady state, high bootstrap fraction, reverse shear discharges. Active n = 1 magnetic feedback and/or driven rotation will be required to suppress resistive wall modes for steady state plasmas

  12. Cis-Suppression to Arrest Protein Aggregation in Mammalian Cells

    PubMed Central

    Gregoire, Simpson; Zhang, Shaojie; Costanzo, Joseph; Wilson, Kelly; Fernandez, Erik J.; Kwon, Inchan

    2015-01-01

    Protein misfolding and aggregation are implicated in numerous human diseases and significantly lower production yield of proteins expressed in mammalian cells. Despite the importance of understanding and suppressing protein aggregation in mammalian cells, a protein design and selection strategy to modulate protein misfolding/aggregation in mammalian cells has not yet been reported. In this work, we address the particular challenge presented by mutation-induced protein aggregation in mammalian cells. We hypothesize that an additional mutation(s) can be introduced in an aggregation-prone protein variant, spatially near the original mutation, to suppress misfolding and aggregation (cis-suppression). As a model protein, we chose human copper, zinc superoxide dismutase mutant (SOD1A4V) containing an alanine to valine mutation at residue 4, associated with the familial form of amyotrophic lateral sclerosis. We used the program RosettaDesign to identify Phe20 in SOD1A4V as a key residue responsible for SOD1A4V conformational destabilization. This information was used to rationally develop a pool of candidate mutations at the Phe20 site. After two rounds of mammalian-cell based screening of the variants, three novel SOD1A4V variants with a significantly reduced aggregation propensity inside cells were selected. The enhanced stability and reduced aggregation propensity of the three novel SOD1A4V variants were verified using cell fractionation and in vitro stability assays. PMID:24114411

  13. Photoinduced trans-to-cis isomerization of cyclocurcumin.

    PubMed

    Adhikary, Ramkrishna; Barnes, Charles A; Trampel, Rachel L; Wallace, Samuel J; Kee, Tak W; Petrich, Jacob W

    2011-09-15

    The photophysical properties of cyclocurcumin in various solvents are studied for the first time to shed light on the nonradiative processes of the parent compound, curcumin, which has a range of medicinal properties. Steady-state fluorescence and fluorescence-excitation spectra of cyclocurcumin in polar aprotic solvents are strongly dependent on excitation (λ(ex)) and emission (λ(em)) wavelength, respectively. The fluorescence quantum yield also depends on λ(ex) and increases with the viscosity of the medium. Time-resolved studies show nonexponential fluorescence decay in all solvents studied. The two fluorescence decay components of cyclocurcumin in alcohols exhibit a strong dependence on viscosity and temperature. NMR spectroscopy indicates that cyclocurcumin is entirely in the trans form with respect to the C6-C7 double bond in methanol, chloroform, and acetone. It is suggested that at least two conformational isomers about another single bond (C5-C6 or C7-C1″ or both) and that trans-to-cis isomerization about the C6-C7 double bond of these isomers provide the most likely means of rationalizing the steady-state spectra and the nonradiative decay mechanisms in both protic and aprotic polar solvents.

  14. Toucan: deciphering the cis-regulatory logic of coregulated genes

    PubMed Central

    Aerts, Stein; Thijs, Gert; Coessens, Bert; Staes, Mik; Moreau, Yves; De Moor, Bart

    2003-01-01

    TOUCAN is a Java application for the rapid discovery of significant cis-regulatory elements from sets of coexpressed or coregulated genes. Biologists can automatically (i) retrieve genes and intergenic regions, (ii) identify putative regulatory regions, (iii) score sequences for known transcription factor binding sites, (iv) identify candidate motifs for unknown binding sites, and (v) detect those statistically over-represented sites that are characteristic for a gene set. Genes or intergenic regions are retrieved from Ensembl or EMBL, together with orthologs and supporting information. Orthologs are aligned and syntenic regions are selected as candidate regulatory regions. Putative sites for known transcription factors are detected using our MotifScanner, which scores position weight matrices using a probabilistic model. New motifs are detected using our MotifSampler based on Gibbs sampling. Binding sites characteristic for a gene set—and thus statistically over-represented with respect to a reference sequence set—are found using a binomial test. We have validated Toucan by analyzing muscle-specific genes, liver-specific genes and E2F target genes; we have easily detected many known binding sites within intergenic DNA and identified new biologically plausible sites for known and unknown transcription factors. Software available at http://www.esat.kuleuven.ac.be/∼dna/BioI/Software.html. PMID:12626717

  15. Mechanism of cis-prenyltransferase reaction probed by substrate analogues

    SciTech Connect

    Lu, Yen-Pin; Liu, Hon-Ge; Teng, Kuo-Hsun; Liang, Po-Huang

    2010-10-01

    Research highlights: {yields} The extremely slow trans-OPPS reaction using 2-Fluoro-FPP supports the sequential mechanism with the carbocation intermediate. {yields} The similar UPPS reaction rate under single turnover supports the concerted mechanism, without the carbocation intermediate. {yields} The secondary kinetic isotope effect also supports associate transition state for UPPS reaction, without the carbocation intermediate. -- Abstract: Undecaprenyl pyrophosphate synthase (UPPS) is a cis-type prenyltransferases which catalyzes condensation reactions of farnesyl diphosphate (FPP) with eight isopentenyl pyrophosphate (IPP) units to generate C{sub 55} product. In this study, we used two analogues of FPP, 2-fluoro-FPP and [1,1-{sup 2}H{sub 2}]FPP, to probe the reaction mechanism of Escherichia coli UPPS. The reaction rate of 2-fluoro-FPP with IPP under single-turnover condition is similar to that of FPP, consistent with the mechanism without forming a farnesyl carbocation intermediate. Moreover, the deuterium secondary KIE of 0.985 {+-} 0.022 measured for UPPS reaction using [1,1-{sup 2}H{sub 2}]FPP supports the associative transition state. Unlike the sequential mechanism used by trans-prenyltransferases, our data demonstrate E. coli UPPS utilizes the concerted mechanism.

  16. L-methionine antagonism of cis-platinum nephrotoxicity.

    PubMed

    Basinger, M A; Jones, M M; Holscher, M A

    1990-03-15

    L-Methionine administered simultaneously with cis-platinum (CDDP) iv results in a significant reduction of the nephrotoxicity normally associated with CDDP without any apparent effect on the antineoplastic activity for rats bearing the Walker 256 carcinosarcoma. CDDP given with L-methionine at a 1:20 mole ratio can be administered to rats at doses up to 35 mg/kg iv with the survival of all treated animals (3/3) and up to 56 mg/kg iv (bolus injection) with the survival of 3/6 animals, while CDDP administered alone at these levels is lethal. A reduced level of protection against the nephrotoxicity was also achieved at lower mole ratios of L-methionine to CDDP. Renal function was monitored using BUN and serum creatinine levels, and gastrointestinal toxicity by weight changes during the course of the experiments. A histopathological examination of the kidneys was also performed to evaluate the protection provided by L-methionine. Under the conditions used, the reaction between L-methionine and CDDP does not appear to proceed so rapidly as to interfere with the antitumor activity of the CDDP. The examination of structural analogs as agents for the control of CDDP-induced nephrotoxicity revealed that the C-S-C-group is the essential group for the protective action in these structures. Although L-methionine can provide renal protection in rats given high doses of CDDP, it does not prevent the accumulation of platinum in the kidney.

  17. Low aqueous solubility of 11-cis-retinal limits the rate of pigment formation and dark adaptation in salamander rods.

    PubMed

    Frederiksen, Rikard; Boyer, Nicholas P; Nickle, Benjamin; Chakrabarti, Kalyan S; Koutalos, Yiannis; Crouch, Rosalie K; Oprian, Daniel; Cornwall, M Carter

    2012-06-01

    We report experiments designed to test the hypothesis that the aqueous solubility of 11-cis-retinoids plays a significant role in the rate of visual pigment regeneration. Therefore, we have compared the aqueous solubility and the partition coefficients in photoreceptor membranes of native 11-cis-retinal and an analogue retinoid, 11-cis 4-OH retinal, which has a significantly higher solubility in aqueous medium. We have then correlated these parameters with the rates of pigment regeneration and sensitivity recovery that are observed when bleached intact salamander rod photoreceptors are treated with physiological solutions containing these retinoids. We report the following results: (a) 11-cis 4-OH retinal is more soluble in aqueous buffer than 11-cis-retinal. (b) Both 11-cis-retinal and 11-cis 4-OH retinal have extremely high partition coefficients in photoreceptor membranes, though the partition coefficient of 11-cis-retinal is roughly 50-fold greater than that of 11-cis 4-OH retinal. (c) Intact bleached isolated rods treated with solutions containing equimolar amounts of 11-cis-retinal or 11-cis 4-OH retinal form functional visual pigments that promote full recovery of dark current, sensitivity, and response kinetics. However, rods treated with 11-cis 4-OH retinal regenerated on average fivefold faster than rods treated with 11-cis-retinal. (d) Pigment regeneration from recombinant and wild-type opsin in solution is slower when treated with 11-cis 4-OH retinal than with 11-cis-retinal. Based on these observations, we propose a model in which aqueous solubility of cis-retinoids within the photoreceptor cytosol can place a limit on the rate of visual pigment regeneration in vertebrate photoreceptors. We conclude that the cytosolic gap between the plasma membrane and the disk membranes presents a bottleneck for retinoid flux that results in slowed pigment regeneration and dark adaptation in rod photoreceptors.

  18. Organic Compounds in the C3H6O3 Family: Microwave Spectrum of cis-cis Dimethyl Carbonate

    NASA Astrophysics Data System (ADS)

    McGuire, B. A.; Widicus Weaver, S. L.; Lovas, F. J.; Plusquellic, D. F.; Blake, G. A.

    2011-05-01

    A number of recent spectroscopic and observational efforts have focused on simple sugars and sugar alcohols because of their importance in prebiotic astro- chemistry. The simplest sugar-related species, glycolaldehyde, has been detected in Sgr B2(N), as have its C2H4O2 structural isomers acetic acid and methyl formate. Additional studies of the C3-sugars with empirical formula C3H6O3, glyceraldehyde and dihydroxyacetone, resulted in no clear interstellar detection. Structural isomerism is extensive in interstellar clouds, and there is a high level of correlation between the relative energies of isomers and their relative abundances, with the lowest energy isomers detected in greatest abundance. The detected members of the C2H4O2 family, however, defy this trend, having relative abundances of (acetic acid):(glycolaldehyde):(methyl formate) of about 2:1:52, despite acetic acid being the lowest energy isomer. These puzzling abundance ratios and the lack of detection of the C3H6O3 sugars gives rise to the question: "Which is the most likely isomer in the C3H6O3 family to be detectable in inter- stellar clouds?" In an attempt to answer this question, we carried out geometry optimization calculations to determine the relative binding energies of the 13 members of the C3H6O3 family. Of the four lowest- energy isomers, only lactic acid [CH3CH(OH)COOH] and dimethyl carbonate [(CH3)2CO3] are commercially available, and lactic acid has been previously investigated spectroscopically. We have therefore conducted a laboratory study of dimethyl carbonate, measuring its rotational spectrum from 8.4 - 25.3 GHz using a Fourier-Transform microwave spectrometer, and from 227 - 350 GHz using a direct absorption spectrometer. We report on the theoretical calculations performed on the C3H6O3 family of isomers, the experimental studies of cis-cis dimethyl carbonate, and the implica- tions of these results for interstellar chemistry. The details of this work are also reported in Lovas et

  19. cis,cis-Muconic acid: separation and catalysis to bio-adipic acid for nylon-6,6 polymerization

    SciTech Connect

    Vardon, Derek R.; Rorrer, Nicholas A.; Salvachúa, Davinia; Settle, Amy E.; Johnson, Christopher W.; Menart, Martin J.; Cleveland, Nicholas S.; Ciesielski, Peter N.; Steirer, K. Xerxes; Dorgan, John R.; Beckham, Gregg T.

    2016-01-01

    cis,cis-Muconic acid is a polyunsaturated dicarboxylic acid that can be produced renewably via the biological conversion of sugars and lignin-derived aromatic compounds. Subsequently, muconic acid can be catalytically converted to adipic acid -- the most commercially significant dicarboxylic acid manufactured from petroleum. Nylon-6,6 is the major industrial application for adipic acid, consuming 85% of market demand; however, high purity adipic acid (99.8%) is required for polymer synthesis. As such, process technologies are needed to effectively separate and catalytically transform biologically derived muconic acid to adipic acid in high purity over stable catalytic materials. To that end, this study: (1) demonstrates bioreactor production of muconate at 34.5 g L-1 in an engineered strain of Pseudomonas putida KT2440, (2) examines the staged recovery of muconic acid from culture media, (3) screens platinum group metals (e.g., Pd, Pt, Rh, Ru) for activity and leaching stability on activated carbon (AC) and silica supports, (4) evaluates the time-on-stream performance of Rh/AC in a trickle bed reactor, and (5) demonstrates the polymerization of bio-adipic acid to nylon-6,6. Separation experiments confirmed AC effectively removed broth color compounds, but subsequent pH/temperature shift crystallization resulted in significant levels of Na, P, K, S and N in the crystallized product. Ethanol dissolution of muconic acid precipitated bulk salts, achieving a purity of 99.8%. Batch catalysis screening reactions determined that Rh and Pd were both highly active compared to Pt and Ru, but Pd leached significantly (1-9%) from both AC and silica supports. Testing of Rh/AC in a continuous trickle bed reactor for 100 h confirmed stable performance after 24 h, although organic adsorption resulted in reduced steady-state activity. Lastly, polymerization of bio-adipic acid with hexamethyldiamine produced nylon-6,6 with comparable properties to its petrochemical counterpart

  20. Isomerization of all-trans-retinoids to 11-cis-retinoids in vitro

    SciTech Connect

    Bernstein, P.S.; Law, W.C.; Rando, R.R.

    1987-04-01

    The key biochemical process of the vertebrate visual cycle required for rhodopsin regeneration, 11-cis-retinoid production from all-trans-retinoids, is shown to occur in vitro. A 600 X g supernatant from a frog retina/pigment epithelium homogenate transforms added all-trans-(/sup 3/H)retinol, in a time-dependent fashion, to a mixture of 11-cis-retinol, 11-cis-retinal, and 11-cis-retinyl palmitate. 13-cis-Retinoids are formed in only minor amounts by nonspecific processes. Studies using washed particulate fractions of the 600 X g supernatant indicate that all-trans-(/sup 3/H)retinol is isomerized to 11-cis-retinoids much more effectively than is all-trans-(/sup 3/H)retinal or all-trans-(/sup 3/H)retinyl palmitate. The 11-cis-retinoid biosynthetic activity is heat-labile, sedimentable by high-speed centrifugation, and largely found in the pigment epithelium rather than in the neural retina.

  1. Thermal processing differentially affects lycopene and other carotenoids in cis-lycopene containing, tangerine tomatoes.

    PubMed

    Cooperstone, Jessica L; Francis, David M; Schwartz, Steven J

    2016-11-01

    Tangerine tomatoes, unlike red tomatoes, accumulate cis-lycopenes instead of the all-trans isomer. cis-Lycopene is the predominating isomeric form of lycopene found in blood and tissues. Our objective was to understand how thermal processing and lipid concentration affect carotenoid isomerisation and degradation in tangerine tomatoes. We conducted duplicated factorial designed experiments producing tangerine tomato juice and sauce, varying both processing time and lipid concentration. Carotenoids were extracted and analysed using high-performance liquid chromatography with photodiode array detection. Phytoene, phytofluene, ζ-carotene, neurosporene, tetra-cis-lycopene, all-trans-lycopene and other-cis-lycopenes were quantified. Tetra-cis-lycopene decreased with increasing heating time and reached 80% of the original level in sauce after processing times of 180min. All-trans-lycopene and other-cis-lycopenes increased with longer processing times. Total carotenoids and total lycopene decreased with increased heating times while phytoene and phytofluene were unchanged. These data suggest limiting thermal processing of tangerine tomato products if delivery of tetra-cis-lycopene is desirable.

  2. Bactericidal activity of the human skin fatty acid cis-6-hexadecanoic acid on Staphylococcus aureus.

    PubMed

    Cartron, Michaël L; England, Simon R; Chiriac, Alina Iulia; Josten, Michaele; Turner, Robert; Rauter, Yvonne; Hurd, Alexander; Sahl, Hans-Georg; Jones, Simon; Foster, Simon J

    2014-07-01

    Human skin fatty acids are a potent aspect of our innate defenses, giving surface protection against potentially invasive organisms. They provide an important parameter in determining the ecology of the skin microflora, and alterations can lead to increased colonization by pathogens such as Staphylococcus aureus. Harnessing skin fatty acids may also give a new avenue of exploration in the generation of control measures against drug-resistant organisms. Despite their importance, the mechanism(s) whereby skin fatty acids kill bacteria has remained largely elusive. Here, we describe an analysis of the bactericidal effects of the major human skin fatty acid cis-6-hexadecenoic acid (C6H) on the human commensal and pathogen S. aureus. Several C6H concentration-dependent mechanisms were found. At high concentrations, C6H swiftly kills cells associated with a general loss of membrane integrity. However, C6H still kills at lower concentrations, acting through disruption of the proton motive force, an increase in membrane fluidity, and its effects on electron transfer. The design of analogues with altered bactericidal effects has begun to determine the structural constraints on activity and paves the way for the rational design of new antistaphylococcal agents.

  3. Bactericidal Activity of the Human Skin Fatty Acid cis-6-Hexadecanoic Acid on Staphylococcus aureus

    PubMed Central

    Cartron, Michaël L.; England, Simon R.; Chiriac, Alina Iulia; Josten, Michaele; Turner, Robert; Rauter, Yvonne; Hurd, Alexander; Sahl, Hans-Georg; Jones, Simon

    2014-01-01

    Human skin fatty acids are a potent aspect of our innate defenses, giving surface protection against potentially invasive organisms. They provide an important parameter in determining the ecology of the skin microflora, and alterations can lead to increased colonization by pathogens such as Staphylococcus aureus. Harnessing skin fatty acids may also give a new avenue of exploration in the generation of control measures against drug-resistant organisms. Despite their importance, the mechanism(s) whereby skin fatty acids kill bacteria has remained largely elusive. Here, we describe an analysis of the bactericidal effects of the major human skin fatty acid cis-6-hexadecenoic acid (C6H) on the human commensal and pathogen S. aureus. Several C6H concentration-dependent mechanisms were found. At high concentrations, C6H swiftly kills cells associated with a general loss of membrane integrity. However, C6H still kills at lower concentrations, acting through disruption of the proton motive force, an increase in membrane fluidity, and its effects on electron transfer. The design of analogues with altered bactericidal effects has begun to determine the structural constraints on activity and paves the way for the rational design of new antistaphylococcal agents. PMID:24709265

  4. Bacterial regulon modeling and prediction based on systematic cis regulatory motif analyses

    NASA Astrophysics Data System (ADS)

    Liu, Bingqiang; Zhou, Chuan; Li, Guojun; Zhang, Hanyuan; Zeng, Erliang; Liu, Qi; Ma, Qin

    2016-03-01

    Regulons are the basic units of the response system in a bacterial cell, and each consists of a set of transcriptionally co-regulated operons. Regulon elucidation is the basis for studying the bacterial global transcriptional regulation network. In this study, we designed a novel co-regulation score between a pair of operons based on accurate operon identification and cis regulatory motif analyses, which can capture their co-regulation relationship much better than other scores. Taking full advantage of this discovery, we developed a new computational framework and built a novel graph model for regulon prediction. This model integrates the motif comparison and clustering and makes the regulon prediction problem substantially more solvable and accurate. To evaluate our prediction, a regulon coverage score was designed based on the documented regulons and their overlap with our prediction; and a modified Fisher Exact test was implemented to measure how well our predictions match the co-expressed modules derived from E. coli microarray gene-expression datasets collected under 466 conditions. The results indicate that our program consistently performed better than others in terms of the prediction accuracy. This suggests that our algorithms substantially improve the state-of-the-art, leading to a computational capability to reliably predict regulons for any bacteria.

  5. Isolation and characterization of tetrachloroethylene- and cis-1,2-dichloroethylene-dechlorinating propionibacteria.

    PubMed

    Chang, Young-Cheol; Ikeutsu, Kaori; Toyama, Tadashi; Choi, Dubok; Kikuchi, Shintaro

    2011-10-01

    Two rapidly growing propionibacteria that could reductively dechlorinate tetrachloroethylene (PCE) and cis-1,2-dichloroethylene (cis-DCE) to ethylene were isolated from environmental sediments. Metabolic characterization and partial sequence analysis of their 16S rRNA genes showed that the new isolates, designated as strains Propionibacterium sp. HK-1 and Propionibacterium sp. HK-3, did not match any known PCE- or cis-DCE-degrading bacteria. Both strains dechlorinated relatively high concentrations of PCE (0.3 mM) and cis-DCE (0.52 mM) under anaerobic conditions without accumulating toxic intermediates during incubation. Cell-free extracts of both strains catalyzed PCE and cis-DCE dechlorination; degradation was accelerated by the addition of various electron donors. PCE dehalogenase from strain HK-1 was mediated by a corrinoid protein, since the dehalogenase was inactivated by propyl iodide only after reduction by titanium citrate. The amounts of chloride ions (0.094 and 0.103 mM) released after PCE (0.026 mM) and cis-DCE (0.05 mM) dehalogenation using the cell-free enzyme extracts of both strains, HK-1 and HK-3, were stoichiometrically similar (91 and 100%), indicating that PCE and cis-DCE were fully dechlorinated. Radiotracer studies with [1,2-¹⁴C] PCE and [1,2-¹⁴C] cis-DCE indicated that ethylene was the terminal product; partial conversion to ethylene was observed. Various chlorinated aliphatic compounds (PCE, trichloroethylene, cis-DCE, trans-1,2-dichloroethylene, 1,1-dichloroethylene, 1,1-dichloroethane, 1,2-dichloroethane, 1,2-dichloropropane, 1,1,2-trichloroethane, and vinyl chloride) were degraded by cell-free extracts of strain HK-1.

  6. The cis-effect using the topology of the electronic charge density

    NASA Astrophysics Data System (ADS)

    Jenkins, Samantha; Kirk, Steven R.; Rong, Chunying; Yin, Dulin

    2013-03-01

    We provide a physics-inspired coupling mechanism explaining the cis-effect in terms of electronic and nuclear degrees of freedom and explore the implications for three families of molecules. The cis- or trans-effect is related to the tendency of electronic charge density to move away from the bond critical point (BCP) and towards the associated nuclear attractors. A quantitative measure of this effect is given by the λ 3 eigenvalue of the Hessian matrix of the electronic charge density. The physical origin of the cis-effect is tied to the observation that the central X=X, X=C or N bond-paths of the cis-isomers are more bent (they are up to 1.5% longer than the internuclear distance) than the bond-paths of the corresponding trans-isomers. Greater bond-path bending is associated with a stronger cis-effect; the direction of bond deformation can in all cases be predicted by the most facile (least compressible) mode of the electronic stress tensor. Further to this, the ellipticity ε of the X=X BCPs of a molecule displaying the cis-effect is lower in the cis-isomer than for the corresponding trans-isomer, suggesting that the cis-effect is less counterintuitive than previously thought. The molecules that exhibit the greatest cis-effect are those with fluorinated double bonds; this is because the most facile modes of the C-F bond couple with the highest-symmetry normal mode of vibration. Qualitative agreement is found with existing experimental data and predictions are made where experimental data is lacking.

  7. Solid Lubrication Fundamentals and Applications. Chapter 1; Introduction and Background

    NASA Technical Reports Server (NTRS)

    Miyoshi, Kazuhisa

    1996-01-01

    This chapter presents an introduction and historical background to the field of tribology, especially solid lubrication and lubricants and sets them in the perspective of techniques and materials in lubrication. Also, solid and liquid lubrication films are defined and described.

  8. Transverse section through the Grand Lodge and Grand Chapter rooms ...

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

    Transverse section through the Grand Lodge and Grand Chapter rooms of James H. Windrim and George Summers’s neoclassical competition design for the New Masonic Temple, Philadelphia, 1867 - Masonic Temple, 1 North Broad Street, Philadelphia, Philadelphia County, PA

  9. Row erupts over axed chapter from Newt Gingrich book

    NASA Astrophysics Data System (ADS)

    Gwynne, Peter

    2012-02-01

    A chapter written by a respected climate scientist for a book co-edited by Republican presidential candidate Newt Gingrich has been canned because its author asserts that humans are responsible for climate change.

  10. Standardizing electrofishing power for boat electrofishing: chapter 14

    USGS Publications Warehouse

    Miranda, L.E. (Steve); Bonar, Scott A.; Hubert, Wayne A.; Willis, David W.

    2009-01-01

    Standardizing boat electrofishing entails achieving an accepted level of collection consistency by managing various brand factors, including (1) the temporal and spatial distribution of sampling effort, (2) boat operation, (3) equipment configuration, (4) characteristics of the waveform and energized field, and (5) power transferred to fish. This chapter focuses exclusively on factor 5:L factors 1-4 have been addressed in earlier chapters. Additionally, while the concepts covered in this chapter address boat electrofishing in general, the power settings discussed were developed from tests with primarily warmwater fish communities. Others (see Chapter 9) recommend lower power settings for communities consisting of primarily coldwater fishes. For reviews of basic concepts of electricity, electrofishing theory and systems, fish behavior relative to diverse waveforms, and injury matter, the reader is referred to Novotny (1990), Reynold (1996), and Snyder (2003).

  11. United States Parmacopeia Chapter <797> timeline: 1989 to 2013.

    PubMed

    Newton, David W

    2013-01-01

    This article features a tabular chronology of events deemed relevant to the creation and revision of United States Pharmacopeia General Chapter <797> Pharmaceutical Compounding--Sterile Preparations, which premiered in 2004.

  12. Implications of climate and land use change: Chapter 4

    USGS Publications Warehouse

    Hall, Jefferson S.; Murgueitio, Enrique; Calle, Zoraida; Raudsepp-Hearne, Ciara; Stallard, Robert F.; Balvanera, Patricia; Hall, Jefferson S.; Kirn, Vanessa; Yanguas-Fernandez, Estrella

    2015-01-01

    This chapter relates ecosystem services to climate change and land use. The bulk of the chapter focuses on ecosystem services and steepland land use in the humid Neotropics – what is lost with land-cover changed, and what is gained with various types of restoration that are sustainable given private ownership. Many case studies are presented later in the white paper. The USGS contribution relates to climate change and the role of extreme weather events in land-use planning.

  13. In vitro cytokinetic response of human colon cancer cells to cis-dichlorodiammineplatinum(II).

    PubMed

    Bergerat, J P; Barlogie, B; Göhde, W; Johnston, D A; Drewinko, B

    1979-11-01

    The cytokinetic response of a human colon carcinoma cell line to cis-dichlorodiammineplatinum(II) was investigated using flow cytometry of DNA content, autoradiography after pulse and continuous tritiated thymidine exposure, and mitotic accumulation after continuous Colcemid treatment. With increasing concentration and exposure time, cis-dichlorodiammineplatinum(II) delayed and then blocked cycle traverse in S and G2 phases. After prolonged treatment with high concentrations of cis-dichlorodiammineplatinum(II), an additional block in G1 or at the G1-S boundary was established. Irreversibility of cell cycle distribution changes after prolonged observation periods suggests cell death in G2, S, and G1 compartments.

  14. cis-trans-Isomerization of unsaturated fatty acids during /γ-irradiation of barley grains

    NASA Astrophysics Data System (ADS)

    Geißler, Christian; Brede, Ortwin; Reinhardt, Jürgen

    2003-06-01

    Gamma-irradiating barley grains with doses of 10-100 kGy, a dose dependent isomerization of the naturally occurring cis-unsaturated fatty acids such as oleic, cis-vaccenic, linoleic and also of linolenic acid was found. Whereas the effect was negligible up to 10 kGy, at 50 kGy the trans-fatty acid level became comparable to that of other natural products like butter fat which means that there is no essential nutrition danger. The cis-trans-isomerization found in barley grains is explained mainly by a thiyl radical driven process rather than direct isomerization.

  15. Commercialization of CIS-Based Thin-Film PV: Final Technical Report, August 1998--November 2001

    SciTech Connect

    Tarrant, D. E.; Gay, R. R.

    2002-09-01

    This report describes the primary objectives of this subcontract, which are to scale up substrate size and to scale up production capacity of the baseline Siemens Solar Industries (SSI) CIS-based module process while introducing CIS-based products. The primary goals are to scale the substrate size from about 900 cm2 (1 ft2) to approximately 4000 cm2 by the middle of Phase II, and to achieve pilot production rates of 500 kW per year by the end of Phase III. Deliverables for the subcontract include CIS-based products and representative modules delivered to the NREL Module Testing Team for outdoor testing and evaluation.

  16. Designing CIS to improve decisions in depression disease management: a discourse analysis of front line practice.

    PubMed

    Mirel, Barbara; Ackerman, Mark S; Kerber, Kevin; Klinkman, Michael

    2006-01-01

    Clinical care management promises to help diminish the major health problem of depression. To realize this promise, front line clinicians must know which care management interventions are best for which patients and act accordingly. Unfortunately, the detailed intervention data required for such differentiated assessments are missing in most clinical information systems (CIS). To determine frontline clinicians' needs for these data and to identify the data that CIS should keep, we conducted an 18 month ethnographic study and discourse analysis of telehealth depression care management. Results show care managers need data-based evidence to choose best options, and discourse analysis suggests some personalized interventions that CIS should and can feasibly capture for evidence.

  17. Taking Action: Ideas To Promote Technology Integration [and] Administrator's Desk Reference: Readings To Promote Technology Integration. Technology Integration: A Thematic Focus.

    ERIC Educational Resources Information Center

    Thormann, Joan, Ed.; And Others

    This guide for school administrators interested in technology integration in the curriculum was developed from discussions at the Technology Integration Seminar held in March, 1991. The guide is divided into five chapters covering various administrative responsibilities and action steps. The first chapter presents an overview and identifies…

  18. Atmospheric chemistry of cis-CF3CHdbnd CHCl (HCFO-1233zd(Z)): Kinetics of the gas-phase reactions with Cl atoms, OH radicals, and O3

    NASA Astrophysics Data System (ADS)

    Andersen, Lene Løffler; Østerstrøm, Freja From; Sulbaek Andersen, Mads P.; Nielsen, Ole John; Wallington, Timothy J.

    2015-10-01

    FTIR smog chamber techniques were used to measure the rate coefficients k(Cl + cis-CF3CHdbnd CHCl) = (6.26 ± 0.84) × 10-11, k(OH + cis-CF3CHdbnd CHCl) = (8.45 ± 1.52) × 10-13, and k(O3 + cis-CF3CHdbnd CHCl) = (1.53 ± 0.12) × 10-21 cm3 molecule-1 s-1. The atmospheric lifetime of cis-CF3CHdbnd CHCl is determined by reaction with OH radicals and is estimated to be 14 days. The infrared spectrum of cis-CF3CHdbnd CHCl was recorded and the integrated absorption over the range 600-2000 cm-1 was measured to be (1.48 ± 0.07) × 10-16 cm molecule-1. Accounting for non-uniform horizontal and vertical mixing leads to a GWP100 value of essentially zero. Correction to account for unwanted Cl atom chemistry in our previous relative rate study of the kinetics of the reaction of OH with trans-CF3CHdbnd CHCl gives k(OH + trans-CF3CHdbnd CHCl) = (3.61 ± 0.37) × 10-13 cm3 molecule-1 s-1.

  19. A Mutational Analysis of the Active Site Loop Residues in cis-3-Chloroacrylic Acid Dehalogenase

    PubMed Central

    Schroeder, Gottfried K.; Huddleston, Jamison P.; Johnson, William H.; Whitman, Christian P.

    2013-01-01

    cis -3-Chloroacrylic acid dehalogenase (cis-CaaD) from Pseudomonas pavonaceae 170 and a homologue from Corynebacterium glutamicum designated Cg10062 share 34% sequence identity (54% similarity). The former catalyzes a key step in a bacterial catabolic pathway for the nematocide 1,3-dichloropropene, whereas the latter has no known biological activity. Although Cg10062 has the six active site residues (Pro-1, His-28, Arg-70, Arg-73, Tyr-103, Glu-114) that are critical for cis-CaaD activity, it shows only a low level cis-CaaD activity and lacks the specificity of cis-CaaD: Cg10062 processes both isomers of 3-chloroacrylate with a preference for the cis-isomer. Although the basis for these differences is unknown, a comparison of the crystal structures of the enzymes covalently modified by an adduct resulting from their incubation with the same inhibitor offers a possible explanation. A 6-residue active site loop in cis-CaaD shows a strikingly different conformation from that observed in Cg10062: the loop closes down on the active site of cis-CaaD, but not on that of Cg10062. In order to examine what this loop might contribute to cis-CaaD catalysis and specificity, the residues were changed individually to those found in Cg10062. Subsequent kinetic and mechanistic analysis suggests that the T34A mutant of cis-CaaD is more Cg10062-like. The mutant enzyme shows a 4-fold increase in Km (using cis-3-bromoacrylate), but not to the degree observed for Cg10062 (687-fold). The mutation also causes a 4-fold decrease in the burst rate (compared to the wild type cis-CaaD), whereas Cg10062 shows no burst rate. More telling is the reaction of the T34A mutant of cis-CaaD with the alternate substrate, 2,3-butadienoate. In the presence of NaBH4 and the allene, cis-CaaD is completely inactivated after one turnover due to the covalent modification of Pro-1. The same experiment with Cg10062 does not result in the covalent modification of Pro-1. The different outcomes are attributed to

  20. CIS-lunar space infrastructure lunar technologies: Executive summary

    NASA Technical Reports Server (NTRS)

    Faller, W.; Hoehn, A.; Johnson, S.; Moos, P.; Wiltberger, N.

    1989-01-01

    Technologies necessary for the creation of a cis-Lunar infrastructure, namely: (1) automation and robotics; (2) life support systems; (3) fluid management; (4) propulsion; and (5) rotating technologies, are explored. The technological focal point is on the development of automated and robotic systems for the implementation of a Lunar Oasis produced by Automation and Robotics (LOAR). Under direction from the NASA Office of Exploration, automation and robotics were extensively utilized as an initiating stage in the return to the Moon. A pair of autonomous rovers, modular in design and built from interchangeable and specialized components, is proposed. Utilizing a buddy system, these rovers will be able to support each other and to enhance their individual capabilities. One rover primarily explores and maps while the second rover tests the feasibility of various materials-processing techniques. The automated missions emphasize availability and potential uses of Lunar resources, and the deployment and operations of the LOAR program. An experimental bio-volume is put into place as the precursor to a Lunar environmentally controlled life support system. The bio-volume will determine the reproduction, growth and production characteristics of various life forms housed on the Lunar surface. Physicochemical regenerative technologies and stored resources will be used to buffer biological disturbances of the bio-volume environment. The in situ Lunar resources will be both tested and used within this bio-volume. Second phase development on the Lunar surface calls for manned operations. Repairs and re-configuration of the initial framework will ensue. An autonomously-initiated manned Lunar oasis can become an essential component of the United States space program.

  1. Précis of Neural organization: structure, function, and dynamics.

    PubMed

    Arbib, M A; Erdi, P

    2000-08-01

    NEURAL ORGANIZATION: Structure, function, and dynamics shows how theory and experiment can supplement each other in an integrated, evolving account of the brain's structure, function, and dynamics. (1) STRUCTURE: Studies of brain function and dynamics build on and contribute to an understanding of many brain regions, the neural circuits that constitute them, and their spatial relations. We emphasize Szentágothai's modular architectonics principle, but also stress the importance of the microcomplexes of cerebellar circuitry and the lamellae of hippocampus. (2) FUNCTION: Control of eye movements, reaching and grasping, cognitive maps, and the roles of vision receive a functional decomposition in terms of schemas. Hypotheses as to how each schema is implemented through the interaction of specific brain regions provide the basis for modeling the overall function by neural networks constrained by neural data. Synthetic PET integrates modeling of primate circuitry with data from human brain imaging. (3) DYNAMICS: Dynamic system theory analyzes spatiotemporal neural phenomena, such as oscillatory and chaotic activity in both single neurons and (often synchronized) neural networks, the self-organizing development and plasticity of ordered neural structures, and learning and memory phenomena associated with synaptic modification. Rhythm generation involves multiple levels of analysis, from intrinsic cellular processes to loops involving multiple brain regions. A variety of rhythms are related to memory functions. The Précis presents a multifaceted case study of the hippocampus. We conclude with the claim that language and other cognitive processes can be fruitfully studied within the framework of neural organization that the authors have charted with John Szentágothai.

  2. Chapter 9: MEMS Applications in Spacecraft Thermal Control and Chapter 13: Handling and Contamination Control Considerations for Critical Space Applications

    NASA Technical Reports Server (NTRS)

    Osiander, Robert; Darin, Ann; Chen, Philip

    2004-01-01

    Thermal control systems (TCS) are an integral part of all spacecraft and instruments. To operate properly all spacecraft components must be maintained within a specified temperature band, which in some instances can be quite tight (less than 1 degree C). Traditionally this is accomplished by "passive" designs, but with modem spacecraft and instruments it is increasingly necessary to use active thermal control technologies. Microelectromechanical System (MEMS) can be useful in developing an active TCS, and may be especially useful for small spacecraft. As the MEMS knowledge matures, the applications of MEMS in spacecraft thermal control emerges as a viable technology for thermal engineers. Potential applications include specialized thermal control coatings, thermal switches, and specialized filters for instruments. Although MEMS technology demonstrates benefits, it also poses challenges for thermal en,oineers due to the lack of in-flight MEMS data. As a consequence, in order to design a MEMS thermal control device and receive the full advantage, it is important to understand the potential impact of the space environment on MEMS devices and the design/operational constraints imposed in their use. An entire chapter is devoted to handling and contamination controls for Micro Electro Mechanical Systems (MEMS) in space applications due to the importance of the topic area to final mission success. Handling and contamination control is discussed relative to the full life cycle from the very basic wafer level processing up through on orbit deployment. MEMS packaging will drive the need to tailor the Handling and Contamination Control Plan in order to assure adequacy of the overall program on a program by program basis. Plan elements are discussed at length to assist the user in preparing and implementing effective plans for both handling and contamination control to prevent deleterious effects.

  3. Implementing an ICU-CIS integrated to a HIS in Latin America.

    PubMed

    Espinosa, A

    2000-01-01

    The hospital has been the main target for Medical Informatics since the beginning of its development. Ancillary and clinical systems entered into the scene first when the financial issues were covered. From those kind of applications the Intensive Care Unit (ICU) represents perhaps the most important challenge to achieve where there is a representative subset of the organization with most variables under control to show the performance of the institution. At the ICU, information technology defines many of the tasks which are performed and enable the professionals to process and interpret the great quantities of data that is generated about the patients and the system in which they receive their treatment and quality assurance (QA) is now almost completely dependent upon information technology in pretty much facets of medical care. In this paper, a clinical information system developed for the ICU is presented where the use of validated severity illness scoring systems and standardized definitions for events and outcomes the care delivered can be analysed comparing clinical outcomes and resource utilization. Cost containment can be also applied and observations simultaneously with quality improvement standards can be undergone. Clinical research regarding medical and nursing practice is also very helpful. PMID:11187688

  4. Microwave Spectrum and Molecular Structure of the ARGON-CIS-1,2-DICHLOROETHYLENE Complex

    NASA Astrophysics Data System (ADS)

    Marshall, Mark D.; Leung, Helen O.; Nelson, Craig J.; Yoon, Leonard H.

    2016-06-01

    The non-planar molecular structure of the complex formed between the argon atom and cis-1,2-dichloroethylene is determined via analysis of its microwave spectrum. Spectra of the 35Cl and 37Cl isotopologues are observed in natural abundance and the nuclear quadrupole splitting due to the two chlorine nuclei is fully resolved. In addition, the complete quadrupole coupling tensor for the cis-1,2-dichloroethylene molecule, including the single non-zero off-diagonal element, has been determined. Unlike the argon-cis-1,2-difluoroethylene and the argon-vinyl chloride complexes, tunneling between the two equivalent non-planar configurations of argon-cis-1,2-dichloroethylene is not observed.

  5. Cis-Lunar Synergies with Human Missions to the Martian Moons

    NASA Astrophysics Data System (ADS)

    Lupisella, M. L.; Mazanek, D. D.; Antol, J.; Bass, D.; Beaty, D.; Daugherty, K.; Graham, L.; Lewis, R.

    2012-06-01

    This presentation will a review recent work from the Human Spaceflight Architecture Team outlining a number of promising activities to conduct in cis-lunar space to help prepare for a human mission to the Martian system.

  6. cis-3-Chloroacrylic Acid: A New Cotton Defoliant and Crop Desiccant.

    PubMed

    Herrett, R A; Kurtz, A N

    1963-09-20

    cis-3-Chloroacrylic acid is a potent cotton defoliant and a crop desiccant. Relationships between structure and activity indicate a relatively high degree of specificity, since minor modifications in structure result in loss of activity. PMID:17751800

  7. cis-3-Chloroacrylic Acid: A New Cotton Defoliant and Crop Desiccant.

    PubMed

    Herrett, R A; Kurtz, A N

    1963-09-20

    cis-3-Chloroacrylic acid is a potent cotton defoliant and a crop desiccant. Relationships between structure and activity indicate a relatively high degree of specificity, since minor modifications in structure result in loss of activity.

  8. Enantioselective synthesis of cis-decalins using organocatalysis and sulfonyl Nazarov reagents.

    PubMed

    Peña, Javier; Silveira-Dorta, Gastón; Moro, Rosalina F; Garrido, Narciso M; Marcos, Isidro S; Sanz, Francisca; Díez, David

    2015-01-01

    The first organocatalytic synthesis of cis-decalins using sulfonyl Nazarov reagents is reported. The Jørgensen's catalyst directs this highly enantioselective synthesis using different cyclohexenal derivatives. PMID:25867826

  9. Entry and Exit Mechanisms at the cis-Face of the Golgi Complex

    PubMed Central

    Lorente-Rodríguez, Andrés; Barlowe, Charles

    2011-01-01

    Vesicular transport of protein and lipid cargo from the endoplasmic reticulum (ER) to cis-Golgi compartments depends on coat protein complexes, Rab GTPases, tethering factors, and membrane fusion catalysts. ER-derived vesicles deliver cargo to an ER-Golgi intermediate compartment (ERGIC) that then fuses with and/or matures into cis-Golgi compartments. The forward transport pathway to cis-Golgi compartments is balanced by a retrograde directed pathway that recycles transport machinery back to the ER. How trafficking through the ERGIC and cis-Golgi is coordinated to maintain organelle structure and function is poorly understood and highlights central questions regarding trafficking routes and organization of the early secretory pathway. PMID:21482742

  10. Isolation and characteristics analysis of a novel high bacterial cellulose producing strain Gluconacetobacter intermedius CIs26.

    PubMed

    Yang, Ying; Jia, Jingjing; Xing, Jianrong; Chen, Jianbing; Lu, Shengmin

    2013-02-15

    A strain producing bacterial cellulose (BC) screened from rotten mandarin fruit was identified as Gluconacetobacter intermedius CIs26 by the examination of general taxonomical characteristics and 16S rDNA sequence analysis. Furthermore, Fourier transform infrared (FT-IR) spectrum showed that pellicle produced by strain CIs26 was composed of glucan, and had the same functional group as a typical BC. X-ray diffractometry (XRD) analysis indicated that the BC was type I in structure with crystallinity index of 75%. BC yields of strain CIs26 in Hestrin-Schramn (HS), citrus waste modified HS (CMHS) and citrus waste solution (CWS) mediums were 2.1 g/L, 5.7 g/L, and 7.2 g/L, respectively. It was shown that citrus waste could stimulate BC production of strain CIs26 efficiently. Based on the ability of utilization of citrus waste, this strain appeared to have potential in BC manufacture on an industrial scale.

  11. Integrating the Curricula: A Collection.

    ERIC Educational Resources Information Center

    Fogarty, Robin, Ed.

    In response to the search for ways to create forms of schooling that are more holistic and natural, and more integrated and interwoven, this collection of articles pulls together elements of the multifaceted concept of curriculum integration. Divided into six sections, the chapters explore the reasons and rationale for moving toward more holistic…

  12. Regulation of cytokine-inducible SH2-containing protein (CIS) by ubiquitination and Elongin B/C interaction.

    PubMed

    Jensik, Philip J; Arbogast, Lydia A

    2015-02-01

    Cytokine-inducible SH2-containing protein (CIS) inhibits prolactin receptor (PRLR) signaling and acts as part of an E3 ubiquitin ligase complex through interactions with Elongin B/C proteins. This study aimed to identify CIS lysine ubiquitination sites and determine roles of ubiquitination and Elongin B/C interactions on CIS protein stability and PRLR signaling inhibition. Site-directed mutations revealed that CIS can be ubiquitinated on all six lysine residues. Elongin B/C interaction box mutation had no influence on CIS ubiquitination. CIS stability was increased by mutation of lysine residues and further enhanced by co-mutation of Elongin B/C interaction domain. CIS inhibition of STAT5B phosphorylation and casein promoter activation was dependent on CIS interactions with Elongin B/C, but not on CIS ubiquitination. These data indicate CIS protein stability is regulated through multiple mechanisms, including ubiquitination and interaction with Elongin B/C proteins, whereas CIS functional inhibition of PRLR signaling is dependent on the Elongin B/C interaction.

  13. Synthesis of Conjugated Polymers Containing cis-Phenylenevinylenes by Titanium Mediated Reductions

    PubMed Central

    Moslin, Ryan M.; Espino, Christine G.; Swager, Timothy M.

    2009-01-01

    The utility of Sato's titanium-mediated reduction of alkynes towards the synthesis of all cis-poly(phenylenevinylene)s (PPVs) is demonstrated by the syn-selective reduction of a variety of model diynes as well as a tetrayne. This technique was then applied to the reduction of a poly(phenyleneethynylene) (PPE) to provide the corresponding all-cis PPV polymer. PMID:20827441

  14. Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs

    PubMed Central

    Ivan, Andra; Halfon, Marc S; Sinha, Saurabh

    2008-01-01

    We consider the problem of predicting cis-regulatory modules without knowledge of motifs. We formulate this problem in a pragmatic setting, and create over 30 new data sets, using Drosophila modules, to use as a 'benchmark'. We propose two new methods for the problem, and evaluate these, as well as two existing methods, on our benchmark. We find that the challenge of predicting cis-regulatory modules ab initio, without any input of relevant motifs, is a realizable goal. PMID:18226245

  15. Torquoselective Ring Opening of Fused Cyclobutenamides: Evidence for a Cis,Trans-Cyclooctadienone Intermediate

    PubMed Central

    2015-01-01

    Electrocyclic ring opening of 4,6-fused cyclobutenamides 1 under thermal conditions leads to cis,trans-cyclooctadienones 2-E,E as transient intermediates, en route to 5,5-bicyclic products 3. Theoretical calculations predict that 4,5-fused cyclobutenamides should likewise undergo thermal ring opening, giving cis,trans-cycloheptadienones, but in this case conversion to 5,4-bicyclic products is thermodynamically disfavored, and these cyclobutenamides instead rearrange to vinyl cyclopentenones. PMID:24992255

  16. Air cleaners for indoor-air-pollution control (Chapter 10). Book chapter, Feb 89-Jul 90

    SciTech Connect

    Viner, A.S.; Ramanathan, K.; Hanley, J.T.; Smith, D.D.; Ensor, D.S.

    1991-01-01

    The chapter describes an experimental study to evaluate performance characteristics of currently available controls for indoor air pollutants, including both particles and gases. The study evaluated the particle-size-dependent collection efficiency of seven commercially available devices for particulate control: a common furnace filter, four industrial filters, and two electronic air cleaners (EACs). The furnance filter had negligible effect on particles with diameters between 0.1 and 1 micrometer. The industrial filters, with ASHRAE ratings of 95, 85, 65, and 40% showed minimum efficiency at about 0.1 micrometer, which was substantially less than the ASHRAE efficiency. One EAC, essentially a furnance filter with a high-voltage electrode, reached a maximum efficiency of 30% at low flowrates (7 cu m/min); however, it had a negligible effect at higher flowrates. The other EAC, similar to an industrial ESP, showed efficiencies of 80-90% over the entire size range at low to moderate flowrates. At the highest flowrate, a minimum efficiency was detected at 0.35 micrometer. The study also evaluated the suitability of commerically available carbon-based sorbents (wood, coal, and coconut) for removing low concentrations of volatile organic compounds (benzene, acetaldehyde, and 1,1,1-trichloroethane).

  17. Current Status and Future Development of Structuring and Modeling Intelligent Appearing Motion. Chapter 11

    NASA Technical Reports Server (NTRS)

    Alexander, Thomas; Ellis, Stephen R.

    2007-01-01

    The two topics covered by this symposium were intelligent appearing motion and Virtual Environments (VE). Both of these are broad research areas with enough content to fill large conferences. Their intersection has become important due to conceptual and technological advances enabling the introduction of intelligent appearing motion into Virtual Environments. This union brings new integration challenges and opportunities, some of which were examined at this symposium. This chapter was inspired by the contributions of several of the conference participants, but is not a complete review of all presentations. It will hopefully serve as a basis for formulating a new approach to the understanding of motion within VE

  18. Key structural features of cis-cinnamic acid as an allelochemical.

    PubMed

    Abe, Masato; Nishikawa, Keisuke; Fukuda, Hiroshi; Nakanishi, Kazunari; Tazawa, Yuta; Taniguchi, Tomoya; Park, So-Young; Hiradate, Syuntaro; Fujii, Yoshiharu; Okuda, Katsuhiro; Shindo, Mitsuru

    2012-12-01

    1-O-cis-cinnamoyl-β-D-glucopyranose is one of the most potent allelochemicals isolated from Spiraea thunbergii Sieb. It is suggested that it derives its strong inhibitory activity from cis-cinnamic acid, which is crucial for phytotoxicity. It was synthesized to confirm its structure and bioactivity, and also a series of cis-cinnamic acid analogues were prepared to elucidate the key features of cis-cinnamic acid for lettuce root growth inhibition. The cis-cyclopropyl analogue showed potent inhibitory activity while the saturated and alkyne analogues proved to be inactive, demonstrating the importance of the cis-double bond. Moreover, the aromatic ring could not be replaced with a saturated ring. However, the 1,3-dienylcyclohexene analogue showed strong activity. These results suggest that the geometry of the C-C double bond between the carboxyl group and the aromatic ring is essential for potent inhibitory activity. In addition, using several light sources, the photostability of the cinnamic acid derivatives and the role of the C-C double bond were also investigated.

  19. Single d(ApG)/cis-diamminedichloroplatinum(II) adduct-induced mutagenesis in Escherichia coli

    SciTech Connect

    Burnouf, D.; Fuchs, R.P.P. ); Gauthier, C.; Chottard, J.C. )

    1990-08-01

    The mutation spectrum induced by the widely used antitumor drug cis-diamminedichloroplatinum(II) (cis-DDP) showed that cisDDP(d(ApG)) adducts, although they account for only 25% of the lesions formed are {approx}5 times more mutagenic than the major GG adduct. The authors report the construction of vectors bearing a single cisDDP(d(ApG)) lesion and their use in mutagenesis experiments in Escherichia coli. The mutagenic processing of the lesion is found to depend strictly on induction of the SOS system of the bacterial host cells. In SOS-induced cells, mutation frequencies of 1-2% were detected. All these mutations are targeted to the 5{prime} base of the adduct. Single A {yields} T transversions are mainly observed (80%), whereas A {yields} G transitions account for 10% of the total mutations. Tandem base-pair substitutions involving the adenine residue and the thymine residue immediately 5{prime} to the adduct occur at a comparable frequency (10%). No selective loss of the strand bearing the platinum adduct was seen, suggesting that, in vivo, cisDDP(d(ApG)) adducts are not blocking lesions. The high mutation specificity of cisDDP-(d(ApG))-induced mutagenesis is discussed in relation to structural data.

  20. Conformational Preferences in Small Peptide Models: The Relevance of cis/trans-Conformations.

    PubMed

    Jangra, Harish; Haindl, Michael H; Achrainer, Florian; Hioe, Johnny; Gschwind, Ruth M; Zipse, Hendrik

    2016-09-01

    The accurate description of cis/trans peptide structures is of fundamental relevance for the field of protein modeling and protein structure determination. A comprehensive conformational analysis of dipeptide model Ace-Gly-NMe (1) has been carried out by using a combination of theoretical calculations and experimental ((1) H and (13) C NMR and NOESY) spectroscopic measurements to assess the relevance of cis-peptide conformers. NMR measurements in dimethyl sulfoxide (DMSO) solution and calculations employing a continuum solvation model both point to the extended trans,trans conformer C5_tt as the global minimum. The cis-peptide structures C5_ct and C5_tc, with the N- or C-terminal amide group in cis-conformation, are observed separately and located 13.0±2 kJ mol(-1) higher in energy. This is in close agreement with the theoretical prediction of around 12 kJ mol(-1) in DMSO. The ability of common protein force fields to reproduce the energies of the cis-amide conformers C5_ct and C5_tc in 1 is limited, making these methods unsuitable for the description of cis-peptide structures in protein simulations. PMID:27535479

  1. Photochemical trans-/cis-isomerization and quantitation of zearalenone in edible oils.

    PubMed

    Köppen, Robert; Riedel, Juliane; Proske, Matthias; Drzymala, Sarah; Rasenko, Tatjana; Durmaz, Vedat; Weber, Marcus; Koch, Matthias

    2012-11-28

    The emphasis of the present work was to investigate the photochemical conversion of trans- to cis-zearalenone in edible oils under real-life conditions. For quantitation purposes a cis-zearalenone standard was synthesized and characterized for its identity and purity (≥95%) by (1)H NMR, X-ray crystallography, HPLC fluorescence and mass spectrometric detection. In a sample survey of 12 edible oils (9 corn oils, 3 hempseed oils) from local supermarkets all corn oils contained trans-zearalenone (median 194 μg/kg), but no cis-zearalenone was detected. For alteration studies trans-zearalenone contaminated corn oils were exposed to sunlight over 4 and 30 weeks, revealing an obvious shift toward cis-zearalenone up to a cis/trans ratio of 9:1 by storage in colorless glass bottles. Irradiation experiments of trans-zearalenone in different organic solvents confirmed the preferred formation of cis-zearalenone possibly caused by entropic effects rather than by enthalpic entities as investigated by quantum chemical and classical force field simulations.

  2. Enhancer choice in cis and in trans in Drosophila melanogaster: role of the promoter.

    PubMed Central

    Morris, James R; Petrov, Dmitri A; Lee, Anne M; Wu, Chao-Ting

    2004-01-01

    Eukaryotic enhancers act over very long distances, yet still show remarkable specificity for their own promoter. To better understand mechanisms underlying this enhancer-promoter specificity, we used transvection to analyze enhancer choice between two promoters, one located in cis to the enhancer and the other in trans to the enhancer, at the yellow gene of Drosophila melanogaster. Previously, we demonstrated that enhancers at yellow prefer to act on the cis-linked promoter, but that mutation of core promoter elements in the cis-linked promoter releases enhancers to act in trans. Here, we address the mechanism by which these elements affect enhancer choice. We consider and explicitly test three models that are based on promoter competency, promoter pairing, and promoter identity. Through targeted gene replacement of the endogenous yellow gene, we show that competency of the cis-linked promoter is a key parameter in the cis-trans choice of an enhancer. In fact, complete replacement of the yellow promoter with both TATA-containing and TATA-less heterologous promoters maintains enhancer action in cis. PMID:15342512

  3. Précis of The brain and emotion.

    PubMed

    Rolls, E T

    2000-04-01

    The topics treated in The brain and emotion include the definition, nature, and functions of emotion (Ch. 3); the neural bases of emotion (Ch. 4); reward, punishment, and emotion in brain design (Ch. 10); a theory of consciousness and its application to understanding emotion and pleasure (Ch. 9); and neural networks and emotion-related learning (Appendix). The approach is that emotions can be considered as states elicited by reinforcers (rewards and punishers). This approach helps with understanding the functions of emotion, with classifying different emotions, and in understanding what information-processing systems in the brain are involved in emotion, and how they are involved. The hypothesis is developed that brains are designed around reward- and punishment-evaluation systems, because this is the way that genes can build a complex system that will produce appropriate but flexible behavior to increase fitness (Ch. 10). By specifying goals rather than particular behavioral patterns of responses, genes leave much more open the possible behavioral strategies that might be required to increase fitness. The importance of reward and punishment systems in brain design also provides a basis for understanding the brain mechanisms of motivation, as described in Chapters 2 for appetite and feeding, 5 for brain-stimulation reward, 6 for addiction, 7 for thirst, and 8 for sexual behavior.

  4. Two splice variants of Golgi-microtubule-associated protein of 210 kDa (GMAP-210) differ in their binding to the cis-Golgi network.

    PubMed Central

    Ramos-Morales, F; Vime, C; Bornens, M; Fedriani, C; Rios, R M

    2001-01-01

    GMAP-210 (Golgi-microtubule-associated protein of 210 kDa) is a peripheral Golgi protein that interacts with the minus end of microtubules through its C-terminus and with cis-Golgi network membranes through its N-terminus; it participates in the maintenance of the structural integrity of the Golgi apparatus [Infante, Ramos-Morales, Fedriani, Bornens and Rios (1999) J. Cell Biol. 145, 83--98]. We report here the cloning of a new isoform of GMAP-210 that lacks amino acid residues 105--196. On the basis of the analysis of the gmap-210 genomic sequence, we propose that the small isoform, GMAP-200, arises from alternative splicing of exon 4 of the primary transcript. Overexpression of GMAP-200 induces perturbations in both the Golgi apparatus and the microtubule network that are similar to those previously reported for GMAP-210 overexpression. We show that both isoforms are able to oligomerize under overexpression conditions. Analysis in vitro and in vivo, with the green fluorescent protein as a marker, reveals that the binding of the N-terminal domain of GMAP-200 to the cis-Golgi network membranes is lower than that of the N-terminal domain of GMAP-210. Implications for the regulation of interaction between the cis-Golgi network and microtubules are discussed. PMID:11463340

  5. Positive regulation of phenolic catabolism in Agrobacterium tumefaciens by the pcaQ gene in response to beta-carboxy-cis,cis-muconate.

    PubMed Central

    Parke, D

    1993-01-01

    An Escherichia coli system for generating a commercially unavailable catabolite in vivo was developed and was used to facilitate molecular genetic studies of phenolic catabolism. Introduction of the plasmid-borne Acinetobacter pcaHG genes, encoding the 3,4-dioxygenase which acts on protocatechuate, into E. coli resulted in bioconversion of exogenously supplied protocatechuate into beta-carboxy-cis,cis-muconate. This compound has been shown to be an inducer of the protocatechuate (pca) genes required for catabolism of protocatechuate to tricarboxylic acid cycle intermediates in Rhizobium leguminosarum biovar trifolii. The E. coli bioconversion system was used to explore regulation of the pca genes in a related bacterium, Agrobacterium tumefaciens. The pcaD gene, which encodes beta-ketoadipate enol-lactone hydrolase, from A. tumefaciens A348 was cloned and was shown to be adjacent to a regulatory region which responds strongly to beta-carboxy-cis,cis-muconate in E. coli. Site-specific insertional mutagenesis of the regulatory region eliminated expression of the pcaD gene in E. coli. When the mutation was incorporated into the A. tumefaciens chromosome, it eliminated expression of the pcaD gene and at least three other pca genes as well. The regulatory region was shown to activate gene expression in trans. The novel regulatory gene was termed pcaQ to differentiate it from pca regulatory genes identified in other microbes, which bind different metabolites. PMID:8501056

  6. Rotational Analysis of Bands in the High-Resolution Infrared Spectra of cis,cis- and trans,trans-1,4-difluorobutadiene-2-d1

    SciTech Connect

    Craig, Norman C.; Easterday, Clay C.; Nemchick, Deacon J.; Williamson, Drew; Sams, Robert L.

    2012-02-01

    Pure samples of cis,cis- and trans,trans-1,4-difluorobutadiene-2-d1 have been synthesized, and high-resolution (0.0015 cm-1) infrared spectra have been recorded for these nonpolar molecules in the gas phase. For the cis,cis isomer, the rotational structure in two C-type bands at 775 and 666 cm-1 and one A-type band at 866 cm-1 has been analyzed to yield a combined set of 2020 ground state combination differences (GSCDs). Ground state rotational constants fit to these GSCDs are A0 = 0.4195790(4), B0 = 0.0536508(8), and C0 = 0.0475802(9) cm-1. For the trans,trans isomer, three Ctype bands at 856, 839, and 709 cm-1 have been investigated to give a combined set of 1624 GSCDs. Resulting ground state rotational constants for this isomer are A0 = 0.9390117(8), B0 = 0.0389225(4), and C0 = 0.0373778(3) cm-1. Small inertial defects confirm the planarity of both isomers in the ground state. Upper state rotational constants have been determined for most of the transitions. The ground state rotational constants for the two isotopologues will contribute to the data set needed for determining semiexperimental equilibrium structures for the nonpolar isomers of 1,4- difluorobutadiene.

  7. 21 CFR 573.637 - Methyl esters of conjugated linoleic acid (cis-9, trans-11 and trans-10, cis-12-octadecadienoic...

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... RELATED PRODUCTS FOOD ADDITIVES PERMITTED IN FEED AND DRINKING WATER OF ANIMALS Food Additive Listing...-octadecadienoic acids). The food additive, methyl esters of conjugated linoleic acid (cis-9, trans-11 and trans-10... conditions: (a) The food additive is manufactured by the reaction of refined sunflower oil with methanol...

  8. 21 CFR 573.637 - Methyl esters of conjugated linoleic acid (cis-9, trans-11 and trans-10, cis-12-octadecadienoic...

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... RELATED PRODUCTS FOOD ADDITIVES PERMITTED IN FEED AND DRINKING WATER OF ANIMALS Food Additive Listing...-octadecadienoic acids). The food additive, methyl esters of conjugated linoleic acid (cis-9, trans-11 and trans-10... conditions: (a) The food additive is manufactured by the reaction of refined sunflower oil with methanol...

  9. 21 CFR 573.637 - Methyl esters of conjugated linoleic acid (cis-9, trans-11 and trans-10, cis-12-octadecadienoic...

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... RELATED PRODUCTS FOOD ADDITIVES PERMITTED IN FEED AND DRINKING WATER OF ANIMALS Food Additive Listing...-octadecadienoic acids). The food additive, methyl esters of conjugated linoleic acid (cis-9, trans-11 and trans-10... conditions: (a) The food additive is manufactured by the reaction of refined sunflower oil with methanol...

  10. 21 CFR 573.637 - Methyl esters of conjugated linoleic acid (cis-9, trans-11 and trans-10, cis-12-octadecadienoic...

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... RELATED PRODUCTS FOOD ADDITIVES PERMITTED IN FEED AND DRINKING WATER OF ANIMALS Food Additive Listing...-octadecadienoic acids). The food additive, methyl esters of conjugated linoleic acid (cis-9, trans-11 and trans-10... conditions: (a) The food additive is manufactured by the reaction of refined sunflower oil with methanol...

  11. 21 CFR 573.637 - Methyl esters of conjugated linoleic acid (cis-9, trans-11 and trans-10, cis-12-octadecadienoic...

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... RELATED PRODUCTS FOOD ADDITIVES PERMITTED IN FEED AND DRINKING WATER OF ANIMALS Food Additive Listing...-octadecadienoic acids). The food additive, methyl esters of conjugated linoleic acid (cis-9, trans-11 and trans-10... conditions: (a) The food additive is manufactured by the reaction of refined sunflower oil with methanol...

  12. Mirror Lake: Past, present and future: Chapter 6

    USGS Publications Warehouse

    Likens, Gene E.; LaBaugh, James W.; Winter, Thomas C.; Likens, Gene E.

    2009-01-01

    This chapter discusses the hydrological and biogeochemical characteristics of Mirror Lake and the changes that resulted from air-land-water interactions and human activities. Since the formation of Mirror Lake, both the watershed and the lake have undergone many changes, such as vegetation development and basin filling. These changes are ongoing, and Mirror Lake is continuing along an aging pathway and ultimately, it will fill with sediment and no longer be a lake. The chapter also identifies major factors that affected the hydrology and biogeochemistry of Mirror Lake: acid rain, atmospheric deposition of lead and other heavy metals, increased human settlement around the lake, the construction of an interstate highway through the watershed of the Northeast Tributary, the construction of an access road through the West and Northeast watersheds to the lake, and climate change. The chapter also offers future recommendations for management and protection of Mirror Lake.

  13. The Western Aeronautical Test Range. Chapter 10 Tools

    NASA Technical Reports Server (NTRS)

    Knudtson, Kevin; Park, Alice; Downing, Robert; Sheldon, Jack; Harvey, Robert; Norcross, April

    2011-01-01

    The Western Aeronautical Test Range (WATR) staff at the NASA Dryden Flight Research Center is developing a translation software called Chapter 10 Tools in response to challenges posed by post-flight processing data files originating from various on-board digital recorders that follow the Range Commanders Council Inter-Range Instrumentation Group (IRIG) 106 Chapter 10 Digital Recording Standard but use differing interpretations of the Standard. The software will read the date files regardless of the vendor implementation of the source recorder, displaying data, identifying and correcting errors, and producing a data file that can be successfully processed post-flight

  14. Measurement and modeling of unsaturated hydraulic conductivity: Chapter 21

    USGS Publications Warehouse

    Perkins, Kim S.; Elango, Lakshmanan

    2011-01-01

    This chapter will discuss, by way of examples, various techniques used to measure and model hydraulic conductivity as a function of water content, K(). The parameters that describe the K() curve obtained by different methods are used directly in Richards’ equation-based numerical models, which have some degree of sensitivity to those parameters. This chapter will explore the complications of using laboratory measured or estimated properties for field scale investigations to shed light on how adequately the processes are represented. Additionally, some more recent concepts for representing unsaturated-zone flow processes will be discussed.

  15. CHAPTER 7. BERYLLIUM ANALYSIS BY NON-PLASMA BASED METHODS

    SciTech Connect

    Ekechukwu, A

    2009-04-20

    The most common method of analysis for beryllium is inductively coupled plasma atomic emission spectrometry (ICP-AES). This method, along with inductively coupled plasma mass spectrometry (ICP-MS), is discussed in Chapter 6. However, other methods exist and have been used for different applications. These methods include spectroscopic, chromatographic, colorimetric, and electrochemical. This chapter provides an overview of beryllium analysis methods other than plasma spectrometry (inductively coupled plasma atomic emission spectrometry or mass spectrometry). The basic methods, detection limits and interferences are described. Specific applications from the literature are also presented.

  16. Molecular mechanism of 9-cis-retinoic acid inhibition of adipogenesis in 3T3-L1 cells

    SciTech Connect

    Sagara, Chiaki; Takahashi, Katsuhiko; Kagechika, Hiroyuki; Takahashi, Noriko

    2013-03-29

    Highlights: ► We examined the effects of 9-cis-RA on adipogenesis in mouse preadipocyte 3T3-L1. ► 9-cis-RA inhibited lipid accumulation in adipogenetically-induced 3T3-L1 cells. ► A RXR pan-antagonist suppressed the inhibitory effects of 9-cis-RA on adipogenesis. ► This antagonist had no effects on RXRα and PPARγ levels in 9-cis-RA-treated cells. ► 9-cis-RA-induced decrease in both RXRα and PPARγ was independent of RXR activation. -- Abstract: Retinoic acid (RA) signaling is mediated by specific nuclear hormone receptors. Here we examined the effects of 9-cis-RA on adipogenesis in mouse preadipocyte 3T3-L1 cells. 9-cis-RA inhibits the lipid accumulation of adipogenetically induced 3T3-L1 cells. The complex of retinoid X receptor α (RXRα) with peroxisome proliferator-activated receptor γ (PPARγ) is a major transcription factor in the process of adipogenesis, and the levels of these molecules were decreased by 9-cis-RA treatment. A RXR pan-antagonist suppressed 9-cis-RA’s inhibitory effects on adipogenesis, but not on the intracellular levels of both RXRα and PPARγ. These results suggest that 9-cis-RA could inhibit adipogenesis by activating RXR, and decrease both RXR and PPARγs levels in a RXR activation-independent manner.

  17. Hazard identification of cis/trans-zearalenone through the looking-glass.

    PubMed

    Dellafiora, Luca; Galaverna, Gianni; Dall'Asta, Chiara; Cozzini, Pietro

    2015-12-01

    Among the food-related health issues, the presence of contaminants has a prominent role, due to the wide range of exogenous compounds that can occur in food commodities and to their large differences in structure and biological activity. A comprehensive assessment of the related risk is thus actually demanding in terms of time and facilities involved. In this context, the use of computational strategies can be an effective choice for supporting the hazard identification procedure at the early stage. In this work, we focused on the food contaminant zearalenone by comparing the trans and cis isomers, respectively the well-known mycoestrogen and its still largely understudied isomer. We estimated the possible effects exerted by human metabolism on the xenoestrogenicity of cis-ZEN by using a validated in silico strategy based on docking simulations and rescoring procedures. Similarly, the exploitation of the most promising enzymatic detoxifying routes designed for trans-ZEN - which relies on the enzyme lactono hydrolase from Clonostachys rosea - has been assessed for the cis-isomer as well. Our results showed that both isomers can act as functional analogues with respect to xenoestrogenic activity, and several cis-ZEN metabolites with high biological potential have been identified. On the contrary, in spite of the high degree of structural analogy, the cis isomer showed a pattern of interaction with the degrading enzyme in stark contrast with that observed for trans-ZEN. For these reasons, the outcomes presented herein strongly support the inclusion of cis-ZEN in further studies of occurrence, metabolism and bioactivity assessment, and suggest the need for a dedicated handling for the cis isomer in risk assessment studies. PMID:26391124

  18. Extensive compensatory cis-trans regulation in the evolution of mouse gene expression

    PubMed Central

    Goncalves, Angela; Leigh-Brown, Sarah; Thybert, David; Stefflova, Klara; Turro, Ernest; Flicek, Paul; Brazma, Alvis; Odom, Duncan T.; Marioni, John C.

    2012-01-01

    Gene expression levels are thought to diverge primarily via regulatory mutations in trans within species, and in cis between species. To test this hypothesis in mammals we used RNA-sequencing to measure gene expression divergence between C57BL/6J and CAST/EiJ mouse strains and allele-specific expression in their F1 progeny. We identified 535 genes with parent-of-origin specific expression patterns, although few of these showed full allelic silencing. This suggests that the number of imprinted genes in a typical mouse somatic tissue is relatively small. In the set of nonimprinted genes, 32% showed evidence of divergent expression between the two strains. Of these, 2% could be attributed purely to variants acting in trans, while 43% were attributable only to variants acting in cis. The genes with expression divergence driven by changes in trans showed significantly higher sequence constraint than genes where the divergence was explained by variants acting in cis. The remaining genes with divergent patterns of expression (55%) were regulated by a combination of variants acting in cis and variants acting in trans. Intriguingly, the changes in expression induced by the cis and trans variants were in opposite directions more frequently than expected by chance, implying that compensatory regulation to stabilize gene expression levels is widespread. We propose that expression levels of genes regulated by this mechanism are fine-tuned by cis variants that arise following regulatory changes in trans, suggesting that many cis variants are not the primary targets of natural selection. PMID:22919075

  19. Cationic iridium(III) complexes with two carbene-based cyclometalating ligands: cis versus trans isomers.

    PubMed

    Monti, Filippo; La Placa, Maria Grazia I; Armaroli, Nicola; Scopelliti, Rosario; Grätzel, Michael; Nazeeruddin, Mohammad Khaja; Kessler, Florian

    2015-03-16

    A series of cationic iridium(III) complexes with two carbene-based cyclometalating ligands and five different N^N bipyridine and 1,10-phenanthroline ancillary ligands is presented. For the first time--in the frame of a rarely studied class of bis(heteroleptic) iridium complexes with two carbene-based cyclometalating ligands--a pair of cis and trans isomers has been isolated. All complexes (trans-1-5 and cis-3) were characterized by (1)H NMR, (13)C NMR, (31)P NMR, and HRMS (ESI-TOF); in addition, crystal structures of cis-3 and trans-4 are reported and discussed. Cyclic voltammetric studies show that the whole series exhibits highly reversible oxidation and reduction processes, suggesting promising potential for optoelectronic applications. Ground-state DFT and TD-DFT calculations nicely predict the blue shift experimentally observed in the room-temperature absorption and emission spectra of cis-3, compared to the trans complexes. In CH3CN, cis-3 displays a 4-fold increase in photoluminescence quantum yield (PLQY) with respect to trans-3, as a consequence of drastically slower nonradiative rate constant. By contrast, at 77 K, the emission properties of all the compounds, including the cis isomer, are much more similar, with a pronounced hypsochromic shift for the trans complexes. A similar behavior is found in solid state (1% w/w poly(methyl methacrylate) matrix), with all complexes displaying PLQY of ∼70-80%, comparable emission lifetimes (τ ≈ 1.3 μs), and a remarkable rigidochromic shift. To rationalize the more pronounced nonradiative deactivation (and smaller PLQY) observed for photoexcited trans complexes, comparative temperature-dependent emission studies in the range of 77-450 K for cis-3 and trans-3 were made in propylene glycol, showing that solvation effects are primarily responsible for the observed behavior.

  20. Hazard identification of cis/trans-zearalenone through the looking-glass.

    PubMed

    Dellafiora, Luca; Galaverna, Gianni; Dall'Asta, Chiara; Cozzini, Pietro

    2015-12-01

    Among the food-related health issues, the presence of contaminants has a prominent role, due to the wide range of exogenous compounds that can occur in food commodities and to their large differences in structure and biological activity. A comprehensive assessment of the related risk is thus actually demanding in terms of time and facilities involved. In this context, the use of computational strategies can be an effective choice for supporting the hazard identification procedure at the early stage. In this work, we focused on the food contaminant zearalenone by comparing the trans and cis isomers, respectively the well-known mycoestrogen and its still largely understudied isomer. We estimated the possible effects exerted by human metabolism on the xenoestrogenicity of cis-ZEN by using a validated in silico strategy based on docking simulations and rescoring procedures. Similarly, the exploitation of the most promising enzymatic detoxifying routes designed for trans-ZEN - which relies on the enzyme lactono hydrolase from Clonostachys rosea - has been assessed for the cis-isomer as well. Our results showed that both isomers can act as functional analogues with respect to xenoestrogenic activity, and several cis-ZEN metabolites with high biological potential have been identified. On the contrary, in spite of the high degree of structural analogy, the cis isomer showed a pattern of interaction with the degrading enzyme in stark contrast with that observed for trans-ZEN. For these reasons, the outcomes presented herein strongly support the inclusion of cis-ZEN in further studies of occurrence, metabolism and bioactivity assessment, and suggest the need for a dedicated handling for the cis isomer in risk assessment studies.

  1. cis-trans isomerization of carbon double bonds in monounsaturated triacylglycerols via generation of free radicals.

    PubMed

    Tsuzuki, Wakako

    2010-09-01

    We investigated the heat-induced cis/trans isomerization of double bonds in monounsaturated lipids. When triolein (9-cis, 18:1) was heated around 180 degrees C, small amounts of isomerization products were obtained depending on the heating period. The heat-induced isomerization of triolein was considerably suppressed by the addition of different antioxidants or under nitrogen stream, and these additives simultaneously inhibited the thermal oxidation of double bonds in triolein. Therefore, an intermediate of the thermal oxidation reaction might be responsible for the heat-induced isomerization of the double bonds in triolein. The thermodynamics of the heat-induced isomerization of triolein (9-cis, 18:1) and trielaidin (9-trans, 18:1) were investigated using Arrhenius plot. The Arrhenius activation energies of cis double bonds in triolein and trans double bonds in trielaidin were 106 kJ/mol and 137 kJ/mol, respectively. The calculated internal rotational barrier heights of these double bonds were similar to those of the double bond of 2-butene radical and significantly lower than those of non-radicalized double bonds in 2-butene. These results suggest that heat-induced cis/trans isomerization of triolein and trielaidin occurs mainly through the formation of radical species, which are the intermediates produced during thermal oxidation. The activation energy difference between the two forms suggests that trans trielaidin radicals are more stable than cis triolein radicals. The high thermodynamic stability of the trans double bonds in lipid radicals would influence the population of cis and trans isomers in edible oils and contribute to slight accumulation of trans-18:1 isomers during heating or industrial processing.

  2. Preparation and characterization of cis-{Lambda}-[Ru(bpy){sub 2}(py)(O)]{sup 2+}

    SciTech Connect

    Hua, Xiao; Lappin, A.G.

    1995-02-15

    High-oxidation-state oxo complexes of ruthenium with polypyridine ligands such as cis-[Ru(bpy){sub 2}(py)O]{sup 2+} (bpy = 2,2{prime}-bipyridine, py = pyridine) are efficient stoichiometric and catalytic oxidants in a variety of organic and inorganic oxidation reactions. Recently, it was also reported that cis-[Ru(bpy){sub 2}(py)O]{sup 2+} is an efficient DNA cleavage agent. The results of mechanistic studies involving cis-[Ru(bpy){sub 2}(py)(O)]{sup 2+} suggest that oxidation of PPh{sub 3} to Ph{sub 3}PO or (CH{sub 3}){sub 2}S to (CH{sub 3}){sub 2}SO occurs by O atom transfer in oxidation of alcohols to aldehydes may occur by hydride transfer and oxidation of hydroquinones occurs by proton-coupled electron transfer. The complex cis-[Ru(bpy){sub 2}(py)(O)]{sup 2+} and its reduced form, cis-[Ru(bpy){sub 2}(py)(H{sub 2}O)]{sup 2+}, are chiral at the metal center. Stereoselective oxygen atom transfer from the chiral oxidant to an organic substrate is a possibility. Most well-studied asymmetric oxidation reactions of this sort are dependent on the selectivity of chiral ligands. Stereoselective oxidation directly involving the chiral metal center has not been studied extensively although the topic has been addressed. In this paper, the preparation and characterization of optically active cis-[Ru(bpy){sub 2}(py)(O)]{sup 2+} from optically active cis-[Ru(bpy){sub 2}(py)(H{sub 2}O)]{sup 2+} and the asymmetric oxidation of methyl p-tolyl sulfide by this chiral oxidant to chiral sulfoxide are reported.

  3. Manipulation of prenyl chain length determination mechanism of cis-prenyltransferases.

    PubMed

    Kharel, Yugesh; Takahashi, Seiji; Yamashita, Satoshi; Koyama, Tanetoshi

    2006-02-01

    The carbon backbones of Z,E-mixed isoprenoids are synthesized by sequential cis-condensation of isopentenyl diphosphate (IPP) and an allylic diphosphate through actions of a series of enzymes called cis-prenyltransferases. Recent molecular analyses of Micrococcus luteus B-P 26 undecaprenyl diphosphate (UPP, C55) synthase [Fujihashi M, Zhang Y-W, Higuchi Y, Li X-Y, Koyama T & Miki K (2001) Proc Natl Acad Sci USA98, 4337-4342.] showed that not only the primary structure but also the crystal structure of cis-prenyltransferases were totally different from those of trans-prenyltransferases. Although many studies on structure-function relationships of cis-prenyltransferases have been reported, regulation mechanisms for the ultimate prenyl chain length have not yet been elucidated. We report here that the ultimate chain length of prenyl products can be controlled through structural manipulation of UPP synthase of M. luteus B-P 26, based on comparisons between structures of various cis-prenyltransferases. Replacements of Ala72, Phe73, and Trp78, which are located in the proximity of the substrate binding site, with Leu--as in Z,E-farnesyl diphosphate (C15) synthase--resulted in shorter ultimate products with C(20-35). Additional mutation of F223H resulted in even shorter products. On the other hand, insertion of charged residues originating from long-chain cis-prenyltransferases into helix-3, which participates in constitution of the large hydrophobic cleft, resulted in lengthening of the ultimate product chain length, leading to C(60-75). These results helped us understand reaction mechanisms of cis-prenyltransferase including regulation of the ultimate prenyl chain-length.

  4. On the Concept of Cis-regulatory Information: From Sequence Motifs to Logic Functions

    NASA Astrophysics Data System (ADS)

    Tarpine, Ryan; Istrail, Sorin

    The regulatory genome is about the “system level organization of the core genomic regulatory apparatus, and how this is the locus of causality underlying the twin phenomena of animal development and animal evolution” (E.H. Davidson. The Regulatory Genome: Gene Regulatory Networks in Development and Evolution, Academic Press, 2006). Information processing in the regulatory genome is done through regulatory states, defined as sets of transcription factors (sequence-specific DNA binding proteins which determine gene expression) that are expressed and active at the same time. The core information processing machinery consists of modular DNA sequence elements, called cis-modules, that interact with transcription factors. The cis-modules “read” the information contained in the regulatory state of the cell through transcription factor binding, “process” it, and directly or indirectly communicate with the basal transcription apparatus to determine gene expression. This endowment of each gene with the information-receiving capacity through their cis-regulatory modules is essential for the response to every possible regulatory state to which it might be exposed during all phases of the life cycle and in all cell types. We present here a set of challenges addressed by our CYRENE research project aimed at studying the cis-regulatory code of the regulatory genome. The CYRENE Project is devoted to (1) the construction of a database, the cis-Lexicon, containing comprehensive information across species about experimentally validated cis-regulatory modules; and (2) the software development of a next-generation genome browser, the cis-Browser, specialized for the regulatory genome. The presentation is anchored on three main computational challenges: the Gene Naming Problem, the Consensus Sequence Bottleneck Problem, and the Logic Function Inference Problem.

  5. Transiently-Evoked Otoacoustic Emissions (teoaes) in Monitoring Adult Cis-Platin Patients.

    NASA Astrophysics Data System (ADS)

    Ribera, John Everett

    1995-01-01

    There is evidence to suggest that otoacoustic emissions (OAEs) reflect the integrity of cochlear outer hair cell (OHC) function. Cis-platin (CDDP) is a potent ototoxic chemotherapeutic agent that tends to destroy or disable OHCs. Therefore, this study was designed to answer the following questions: (1) Can TEOAEs be used in monitoring for ototoxicity in adult VA oncology patients receiving CDDP treatment? (2) If so, how sensitive are TEOAEs in detecting significant changes when compared to Audiometry in a VA population? and (3) Which of several TEOAE measures is the most sensitive to changes in hearing due to CDDP ototoxicity in a VA population?. In Experiment I, VA Medical Center patients were recruited (control group) and tested using a conventional audiometer and the ILO88 Otoacoustic Analyzer on three separate days. Data from this experiment were used to develop change criteria in each of four TEOAE measures (Reproducibility, Compare, 1 kHz Band Analysis, and OAE Response) for Experiment II. Experiment II was of similar design with the exception that the subjects (experimental group) were patients enrolled from the oncology ward and were administered CDDP after the first and second test sessions. Data from both groups and all test measures revealed (1) that there was no ear effect in any of the test conditions, (2) there was a group (drug) effect, and (3) there was a frequency effect at 2 kHz. Audiometry detected changes in 56% of the experimental subjects, while the number of changes varied among the TEOAE measures studied. Compare agreed with Audiometry more often and performed better than any other TEOAE measure in detecting change. Based on these findings, incorporation of Compare into an audiometric test battery to monitor for ototoxicity in the VA population is feasible. There is evidence to suggest that as measurement techniques are refined TEOAE analysis will become a valid test for monitoring of adult CDDP patients.

  6. Identification of a cis-acting replication element within the poliovirus coding region.

    PubMed

    Goodfellow, I; Chaudhry, Y; Richardson, A; Meredith, J; Almond, J W; Barclay, W; Evans, D J

    2000-05-01

    The replication of poliovirus, a positive-stranded RNA virus, requires translation of the infecting genome followed by virus-encoded VPg and 3D polymerase-primed synthesis of a negative-stranded template. RNA sequences involved in the latter process are poorly defined. Since many sequences involved in picornavirus replication form RNA structures, we searched the genome, other than the untranslated regions, for predicted local secondary structural elements and identified a 61-nucleotide (nt) stem-loop in the region encoding the 2C protein. Covariance analysis suggested the structure was well conserved in the Enterovirus genus of the Picornaviridae. Site-directed mutagenesis, disrupting the structure without affecting the 2C product, destroyed genome viability and suggested that the structure was required in the positive sense for function. Recovery of revertant viruses suggested that integrity of the structure was critical for function, and analysis of replication demonstrated that nonviable mutants did not synthesize negative strands. Our conclusion, that this RNA secondary structure constitutes a novel poliovirus cis-acting replication element (CRE), is supported by the demonstration that subgenomic replicons bearing lethal mutations in the native structure can be restored to replication competence by the addition of a second copy of the 61-nt wild-type sequence at another location within the genome. This poliovirus CRE functionally resembles an element identified in rhinovirus type 14 (K. L. McKnight and S. M. Lemon, RNA 4:1569-1584, 1998) and the cardioviruses (P. E. Lobert, N. Escriou, J. Ruelle, and T. Michiels, Proc. Natl. Acad. Sci. USA 96:11560-11565, 1999) but differs in sequence, structure, and location. The functional role and evolutionary significance of CREs in the replication of positive-sense RNA viruses is discussed.

  7. The effects of conjugated linoleic acid isomers cis-9,trans-11 and trans-10,cis-12 on in vitro bovine embryo production and cryopreservation.

    PubMed

    Absalón-Medina, V A; Bedford-Guaus, S J; Gilbert, R O; Siqueira, L C; Esposito, G; Schneider, A; Cheong, S H; Butler, W R

    2014-10-01

    Conjugated linoleic acid (CLA) isomers can affect the lipid profile and signaling of cells and thereby alter their function. A total of 5,700 bovine oocytes were used in a structured series of experiments to test the effects of CLA cis-9,trans-11 and CLA trans-10,cis-12 in vitro. In experiment 1, high doses of each CLA isomer during in vitro maturation (IVM) were compared with high or low doses during the entire in vitro culture (IVC) of parthenogenetic embryos. High doses of the CLA isomers ranged from 50 to 200 μM and low doses were 15 and 25 μM. In experiment 2, the low doses of each CLA isomer were tested during IVM/IVC on embryos produced by in vitro fertilization (IVF). Experiment 3 compared the effects of 15 μM doses of each CLA isomer during IVM or IVC of IVF embryos. In experiment 4, post-rewarming survival rates and blastomere counts were assessed for embryos supplemented with each CLA isomer during IVM or for 36 h before vitrification. In experiment 1, when either CLA isomer was provided only during IVM, we observed no effects on overall rates of maturation, cleavage, or blastocysts (92.2 ± 1.6%, 78.3 ± 4.1%, and 28.9 ± 5.1%, respectively). However, high doses of each CLA isomer, but not low doses, during the entire embryo culture period decreased blastocyst rates (5-20%) in a dose-dependent manner. Cleavage rates improved with 15 or 50 μM CLA trans-10,cis-12. Progesterone concentrations in maturation media were significantly increased by high doses of each CLA isomer compared with control, but low doses of CLA isomers had no effect. In experiment 2 with IVF embryos, low doses of each CLA isomer did not alter cleavage rates (average 84.9 ± 1.9%) and only 25 μM CLA trans-10,cis-12 during IVC reduced blastocyst rates below those of controls (25.5 ± 2.1 vs. 38.2 ± 2.3%). The lipid content of embryos was increased and relative expression of the BIRC5 (baculoviral IAP repeat containing 5) gene was depressed by CLA trans-10,cis-12. In experiment 3

  8. 38 CFR 21.7044 - Persons with eligibility under 38 U.S.C. chapter 34.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... under 38 U.S.C. chapter 34. 21.7044 Section 21.7044 Pensions, Bonuses, and Veterans' Relief DEPARTMENT... under 38 U.S.C. chapter 34. Certain individuals with 38 U.S.C. chapter 34 eligibility may establish eligibility for educational assistance under 38 U.S.C. chapter 30. This section requires an individual...

  9. 38 CFR 21.82 - Completing the plan under Chapter 31.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Chapter 31. 21.82 Section 21.82 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS.... Chapter 31 Individualized Written Rehabilitation Plan § 21.82 Completing the plan under Chapter 31. (a... completion of the program provided by the plan under Chapter 31. The provisions of § 21.70 and § 21.78(c)...

  10. 2 CFR 1.200 - Purpose of chapters I and II.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 2 Grants and Agreements 1 2010-01-01 2010-01-01 false Purpose of chapters I and II. 1.200 Section... Introduction toSubtitle A § 1.200 Purpose of chapters I and II. (a) Chapters I and II of subtitle A provide OMB... procedures for management of the agencies' grants and agreements. (b) There are two chapters for...

  11. 24 CFR 1720.205 - Suspension notice under § 1710.45(a) of this chapter.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ...(a) of this chapter. 1720.205 Section 1720.205 Housing and Urban Development Regulations Relating to....45(a) of this chapter. A suspension pursuant to § 1710.45(a) of this chapter shall be effected by... fee tender which constitute the grounds under § 1710.45(a) of this chapter, of the suspension, and...

  12. 41 CFR 304-2.1 - What definitions apply to this chapter?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... to this chapter? 304-2.1 Section 304-2.1 Public Contracts and Property Management Federal Travel... chapter? The following definitions apply to this chapter: Employee means an appointed officer or employee... defined in this chapter does not include a meeting or other event required to carry out an...

  13. 47 CFR 2.811 - Transmitters operated under part 73 of this chapter.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... chapter. 2.811 Section 2.811 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL FREQUENCY....811 Transmitters operated under part 73 of this chapter. Section 2.803(a) through (d) shall not be... chapter, provided the conditions set out in part 73 of this chapter for the acceptability of...

  14. 38 CFR 21.79 - Determining entitlement usage under Chapter 31.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... usage under Chapter 31. 21.79 Section 21.79 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF... Employment Under 38 U.S.C. Chapter 31 Duration of Rehabilitation Programs § 21.79 Determining entitlement usage under Chapter 31. (a) General. The determination of entitlement usage for chapter 31...

  15. Biotic and abiotic anaerobic transformations of trichloroethene and cis-1,2-dichloroethene in fractured sandstone.

    PubMed

    Darlington, Ramona; Lehmicke, Leo; Andrachek, Richard G; Freedman, David L

    2008-06-15

    A fractured sandstone aquifer at an industrial site in southern California is contaminated with trichloroethene (TCE) and cis-1,2-dichloroethene (cis-DCE) to depths in excess of 244 m. Field monitoring data suggest that TCE is undergoing reduction to cis-DCE and that additional attenuation is occurring. However, vinyl chloride (VC) and ethene have not been detected in significant amounts, so that if transformation is occurring, a process other than reductive dechlorination must be responsible. The objective of this study was to evaluate the occurrence of biotic and abiotic transformation processes at this site for TCE, cis-DCE, and VC. Anaerobic microcosms were constructed with site groundwater and sandstone core samples. 14C-labeled compounds were used to detect transformation products (e.g., CO2 and soluble products) that are not readily identifiable by headspace analysis. The microcosms confirmed the occurrence of biotic reduction of TCE to cis-DCE, driven by electron donor in the groundwater and/or sandstone. VC and ethene were not detected. Following incubation periods up to 22 months, the distribution of 14C indicated statistically significant transformation of [14C]TCE and [14C]cis-DCE in live microcosms, to as high as 10% 14CO2 from TCE and 20% 14CO2 from cis-DCE. In autoclaved microcosms, significant transformation of [14C]TCE and [14C]cis-DCE also occurred; although some 14CO2 accumulated, the predominant 14C product was soluble and could not be stripped by N2 from an acidic solution (referred to as nonstrippable residue, or NSR). Characterization of the NSR by high-performance liquid and ion chromatography identified glycolate, acetate, and formate as significant components. These results suggest that a combination of abiotic and biotic transformation processes is responsible for attenuation of TCE and cis-DCE in the fractured sandstone aquifer. Tracking the distribution of 14C during the microcosm study was essential for observing these phenomena.

  16. Ethical & Legal Issues in School Counseling. Chapter 1: Ethical Standards.

    ERIC Educational Resources Information Center

    Huey, Wayne C.; And Others

    This document contains chapter 1 (8 articles) from a collection of 35 articles primarily from American Association for Counseling and Development (AACD) publications on the most important legal and ethical topics about which all school counselors need to be informed. "Ethical Standards for School Counselors: Test Your Knowledge" (Wayne C. Huey)…

  17. Chapter 1 Early Literacy Summer School. Final Evaluation Report.

    ERIC Educational Resources Information Center

    Pollock, John S.

    A study examined the effectiveness of the Chapter 1 Early Literacy Summer School program. The program provided additional reading instruction to underachieving first-grade pupils at five schools located throughout the Columbus, Ohio public school district. The program featured group instruction (with many of the activities modelled after the…

  18. Chapter 1 Early Literacy Summer School, 1993. Final Evaluation Report.

    ERIC Educational Resources Information Center

    Pollock, John S.

    A study examined the effectiveness of the Chapter 1 Early Literacy Summer School program. The program provided additional reading instruction to underachieving first-grade pupils at six schools located throughout the Columbus, Ohio public school district. The program featured group instruction (with many of the activities modeled after the Reading…

  19. 48 CFR 9900.000 - Scope of chapter.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 48 Federal Acquisition Regulations System 7 2011-10-01 2011-10-01 false Scope of chapter. 9900.000 Section 9900.000 Federal Acquisition Regulations System COST ACCOUNTING STANDARDS BOARD, OFFICE OF FEDERAL... describes policies and procedures for applying the Cost Accounting Standards (CAS) to negotiated...

  20. Elements of Mathematics, Book O: Intuitive Background. Chapter 5, Mappings.

    ERIC Educational Resources Information Center

    Exner, Robert; And Others

    The sixteen chapters of this book provide the core material for the Elements of Mathematics Program, a secondary sequence developed for highly motivated students with strong verbal abilities. The sequence is based on a functional-relational approach to mathematics teaching, and emphasizes teaching by analysis of real-life situations. This text is…

  1. Chapter 1: Redefining Disciplinary Learning in Classroom Contexts

    ERIC Educational Resources Information Center

    Ford, Michael J.; Forman, Ellice A.

    2006-01-01

    In this chapter, the authors aim to review recent, sociocultural studies of classroom-based research in science education in light of a sample of practice-based research within the field of science studies. They provide a framework for examining the discipline of science that can also be useful for assessing its impact on students. The framework…

  2. Ethical & Legal Issues in School Counseling. Chapter 6: Special Issues.

    ERIC Educational Resources Information Center

    Sampson, James P., Jr.; And Others

    This document contains chapter 6 (5 articles) of a collection of 35 articles primarily from American Association for Counseling and Development (AACD) publications on the most important legal and ethical topics about which all school counselors need to be informed. "Ethical Issues Involved With the Use of Computer-Assisted Counseling, Testing, and…

  3. Chapter 2 Forumula. 1988-89 Final Technical Report.

    ERIC Educational Resources Information Center

    Austin Independent School District, TX. Office of Research and Evaluation.

    Presented is the final technical report on the evaluation of the 1988-89 supplementary education programs of the Austin (Texas) Independent School District funded under Chapter 2 of the Education Consolidation and Improvement Act. The following major findings are reported: (1) extracurricular transportation costs, which had been reduced by…

  4. 24 CFR 300.1 - Scope of chapter.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 24 Housing and Urban Development 2 2011-04-01 2011-04-01 false Scope of chapter. 300.1 Section 300.1 Housing and Urban Development Regulations Relating to Housing and Urban Development (Continued) GOVERNMENT NATIONAL MORTGAGE ASSOCIATION, DEPARTMENT OF HOUSING AND URBAN DEVELOPMENT GENERAL § 300.1...

  5. Chapter 11. Quality evaluation of apple by computer vision

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Apple is one of the most consumed fruits in the world, and there is a critical need for enhanced computer vision technology for quality assessment of apples. This chapter gives a comprehensive review on recent advances in various computer vision techniques for detecting surface and internal defects ...

  6. Missing Chapters II: West Virginia Women in History.

    ERIC Educational Resources Information Center

    Hensley, Frances S., Ed.

    This collection of essays chronicles the contributions of 14 West Virginia women active in individual and group endeavors from 1824 to the present. Because the achievements of these women are absent from previous histories of West Virginia, their stories constitute missing chapters in the state's history. Some of these women made contributions in…

  7. Chapter Two: Foundations for the Study of Practice

    ERIC Educational Resources Information Center

    Young, Richard F.

    2008-01-01

    In this chapter, the historical roots of contemporary Practice Theory are unearthed in the work of semioticians, philosophers, and anthropologists. Saussure's semiotic theory is contrasted with that of Peirce, and the importance of Peirce's work for understanding the context of signs is stressed. The philosophy of language in the writings of…

  8. Economic and Societal Benefits of Soil Carbon Management (Chapter 1).

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Many papers and books on soil carbon management have addressed specific ecosystems such as agricultural lands, rangelands, forestlands, etc. This paper introduces a book within which each chapter begins by addressing a particular concern and potential options to manage it, along with their real and...

  9. From Literacy Activities to Entrepreneurship in Siete Pilas. Chapter 6.

    ERIC Educational Resources Information Center

    Chacon, Antonio; Polo, Angel

    This chapter describes a community development project in Siete Pilas (Spain), a village whose economy is based primarily on small family farms and unskilled labor. The project grew out of the Sierra Education Program, which in 1980 sent adult-education teachers to five villages in the Sierra de Ronda region. The goal was to stimulate a socially…

  10. Evaluation of the 1985 Chapter 1 Citywide Summer School Program.

    ERIC Educational Resources Information Center

    Detroit Public Schools, MI. Dept. of Evaluation and Testing.

    Described are aspects of the evaluation of the Detroit (Michigan) Public Schools' 1985 Chapter 1 Citywide Summer School program, a program implemented to improve the reading and mathematics skills of students from pre-kindergarten classes through grade 8. A random sample of 18 schools, including elementary and middle schools, was selected for…

  11. Chapter 13. Exploring Use of the Reserved Core

    SciTech Connect

    Holmen, John; Humphrey, Alan; Berzins, Martin

    2015-07-29

    In this chapter, we illustrate benefits of thinking in terms of thread management techniques when using a centralized scheduler model along with interoperability of MPI and PThread. This is facilitated through an exploration of thread placement strategies for an algorithm modeling radiative heat transfer with special attention to the 61st core. This algorithm plays a key role within the Uintah Computational Framework (UCF) and current efforts taking place at the University of Utah to model next-generation, large-scale clean coal boilers. In such simulations, this algorithm models the dominant form of heat transfer and consumes a large portion of compute time. Exemplified by a real-world example, this chapter presents our early efforts in porting a key portion of a scalability-centric codebase to the Intel Xeon Phi coprocessor. Specifically, this chapter presents results from our experiments profiling the native execution of a reverse Monte-Carlo ray tracing-based radiation model on a single coprocessor. These results demonstrate that our fastest run configurations utilized the 61st core and that performance was not profoundly impacted when explicitly oversubscribing the coprocessor operating system thread. Additionally, this chapter presents a portion of radiation model source code, a MIC-centric UCF cross-compilation example, and less conventional thread management technique for developers utilizing the PThreads threading model.

  12. "Preescolar Na Casa": Teaching Parents To Teach Children. Chapter 3.

    ERIC Educational Resources Information Center

    Fernandez, Ermitas

    This chapter describes a school readiness program that has been implemented in rural Galicia (Spain) since 1977. Data reveal that 70 percent of Galicia's population lives in rural areas, the economy remains primarily agricultural, Galicians earn less than the national average and have the largest number of public assistance recipients, and there…

  13. Television & Literacy Development in the Czech Republic. Chapter 14.

    ERIC Educational Resources Information Center

    Hubik, Stanislav

    This chapter begins by explaining that cultural literacy is the ability of a community to create relationships, processes, and institutions aimed at multifaceted community development using indigenous resources (natural, human, social, and cultural). Literacy development in a rural community involves three equally important dimensions--social,…

  14. Chapter 688 Implementation Guidelines and Instructions for Local School Districts.

    ERIC Educational Resources Information Center

    Massachusetts State Executive Office of Human Services, Boston.

    The booklet presents guidelines for implementing Massachusetts Chapter 688, which provides for a 2-year transitional process to plan for habilitative services for severely disabled young adults who will lose their entitlement to special education upon graduation or reaching the age of 22. The law is intended to serve individuals who traditionally…

  15. Reading Recovery and ESEA Chapter 1: Issues and Possibilities.

    ERIC Educational Resources Information Center

    Zajano, Nancy C.

    The simultaneous implementation of Reading Recovery (an early intervention program designed to help children "at risk" of failure in their first year of reading instruction) and Chapter 1 programs in schools raises a number of issues as educators attempt to provide effective reading instruction within the policies and guidelines of both programs.…

  16. Chapter 5: Long-term benefits analysis of EERE's Programs

    SciTech Connect

    None, None

    2009-01-18

    This chapter provides an overview of the modeling approach used in MARKAL-GPRA05 to evaluate the benefits of EERE R&D programs and technologies. The program benefits reported in this section result from comparisons of each Program Case to the Baseline Case, as modeled in MARKAL-GPRA05.

  17. Chapter 5: Long-term benefits analysis of EERE's programs

    SciTech Connect

    None, None

    2009-01-18

    This chapter provides an overview of the modeling approach used in MARKAL-GPRA06 to evaluate the benefits of EERE R&D programs and technologies. The program benefits reported in this section result from comparisons of each Program Case to the Baseline Case, as modeled in MARKAL-GPRA06.

  18. Chapter 2 Formula. 1992-93 Final Report.

    ERIC Educational Resources Information Center

    Marable, Paula; And Others

    The Chapter 2 Formula provides federal funds to states through the Elementary and Secondary Education Act of 1965 (ESEA). These funds are used to help students at risk of academic failure or dropping out, support purchases and programs, and develop teachers' professional skills. In 1992-93, the Austin Independent School District (AISD) received…

  19. Chapter 2 Formula Final Report, 1993-94.

    ERIC Educational Resources Information Center

    Griffith, Julia E.

    Chapter 2 Formula funds provide federal aid to states through the Elementary and Secondary Education Act (ESEA) of 1965 as amended in 1988 by PL 100-297. Funds can support programs for students at risk of failure or dropping out, or students for whom providing an education entails higher than average costs. Funds can also support programs for…

  20. Chapter 2 Formula: 1991-92. Final Report.

    ERIC Educational Resources Information Center

    Moede, Lauren Hall

    Education Consolidation and Improvement Act (ECIA) Chapter 2 Formula has provided funding to the Austin (Texas) Independent School District (AISD) in order to expand existing programs and implement new programs, including the addition of staff and the acquisition of materials and equipment that would not otherwise be available from state or local…

  1. Ethical & Legal Issues in School Counseling. Chapter 3: Legal Issues.

    ERIC Educational Resources Information Center

    Remley, Theodore P., Jr.; And Others

    This document contains chapter 3 (7 articles) of a collection of 35 articles primarily from American Association for Counseling and Development (AACD) publications on the most important legal and ethical topics about which all school counselors need to be informed. "The Law and Ethical Practices in Elementary and Middle Schools" (Theodore P.…

  2. Endocrine and exocrine function of the bovine testis. Chapter 2

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This chapter is devoted to the endocrine and exocrine function of the normal bovine male testes. The discussion begins with a historical review of the literature dating back to Aristotle’s (300 BC) initial description of the anatomy of the mammalian testes. The first microscopic examination of the t...

  3. Extensive cis-Regulatory Variation Robust to Environmental Perturbation in Arabidopsis[W

    PubMed Central

    Cubillos, Francisco A.; Stegle, Oliver; Grondin, Cécile; Canut, Matthieu; Tisné, Sébastien; Gy, Isabelle

    2014-01-01

    cis- and trans-acting factors affect gene expression and responses to environmental conditions. However, for most plant systems, we lack a comprehensive map of these factors and their interaction with environmental variation. Here, we examined allele-specific expression (ASE) in an F1 hybrid to study how alleles from two Arabidopsis thaliana accessions affect gene expression. To investigate the effect of the environment, we used drought stress and developed a variance component model to estimate the combined genetic contributions of cis- and trans-regulatory polymorphisms, environmental factors, and their interactions. We quantified ASE for 11,003 genes, identifying 3318 genes with consistent ASE in control and stress conditions, demonstrating that cis-acting genetic effects are essentially robust to changes in the environment. Moreover, we found 1618 genes with genotype x environment (GxE) interactions, mostly cis x E interactions with magnitude changes in ASE. We found fewer trans x E interactions, but these effects were relatively less robust across conditions, showing more changes in the direction of the effect between environments; this confirms that trans-regulation plays an important role in the response to environmental conditions. Our data provide a detailed map of cis- and trans-regulation and GxE interactions in A. thaliana, laying the ground for mechanistic investigations and studies in other plants and environments. PMID:25428981

  4. Antibody against early driver of neurodegeneration cis P-tau blocks brain injury and tauopathy.

    PubMed

    Kondo, Asami; Shahpasand, Koorosh; Mannix, Rebekah; Qiu, Jianhua; Moncaster, Juliet; Chen, Chun-Hau; Yao, Yandan; Lin, Yu-Min; Driver, Jane A; Sun, Yan; Wei, Shuo; Luo, Man-Li; Albayram, Onder; Huang, Pengyu; Rotenberg, Alexander; Ryo, Akihide; Goldstein, Lee E; Pascual-Leone, Alvaro; McKee, Ann C; Meehan, William; Zhou, Xiao Zhen; Lu, Kun Ping

    2015-07-23

    Traumatic brain injury (TBI), characterized by acute neurological dysfunction, is one of the best known environmental risk factors for chronic traumatic encephalopathy and Alzheimer's disease, the defining pathologic features of which include tauopathy made of phosphorylated tau protein (P-tau). However, tauopathy has not been detected in the early stages after TBI, and how TBI leads to tauopathy is unknown. Here we find robust cis P-tau pathology after TBI in humans and mice. After TBI in mice and stress in vitro, neurons acutely produce cis P-tau, which disrupts axonal microtubule networks and mitochondrial transport, spreads to other neurons, and leads to apoptosis. This process, which we term 'cistauosis', appears long before other tauopathy. Treating TBI mice with cis antibody blocks cistauosis, prevents tauopathy development and spread, and restores many TBI-related structural and functional sequelae. Thus, cis P-tau is a major early driver of disease after TBI and leads to tauopathy in chronic traumatic encephalopathy and Alzheimer's disease. The cis antibody may be further developed to detect and treat TBI, and prevent progressive neurodegeneration after injury. PMID:26176913

  5. cis p-tau: early driver of brain injury and tauopathy blocked by antibody

    PubMed Central

    Mannix, Rebekah; Qiu, Jianhua; Moncaster, Juliet; Chen, Chun-Hau; Yao, Yandan; Lin, Yu-Min; Driver, Jane A; Sun, Yan; Wei, Shuo; Luo, Man-Li; Albayram, Onder; Huang, Pengyu; Rotenberg, Alexander; Ryo, Akihide; Goldstein, Lee E; Pascual-Leone, Alvaro; McKee, Ann C.; Meehan, William; Zhou, Xiao Zhen; Lu, Kun Ping

    2015-01-01

    Traumatic brain injury (TBI), characterized by acute neurological dysfunction, is one of the best known environmental risk factors for chronic traumatic encephalopathy (CTE) and Alzheimer's disease (AD), whose defining pathologic features include tauopathy made of phosphorylated tau (p-tau). However, tauopathy has not been detected in early stages after TBI and how TBI leads to tauopathy is unknown. Here we find robust cis p-tau pathology after sport- and military-related TBI in humans and mice. Acutely after TBI in mice and stress in vitro, neurons prominently produce cis p-tau, which disrupts axonal microtubule network and mitochondrial transport, spreads to other neurons, and leads to apoptosis. This process, termed “cistauosis”, appears long before other tauopathy. Treating TBI mice with cis antibody blocks cistauosis, prevents tauopathy development and spread, and restores many TBI-related structural and functional sequelae. Thus, cis p-tau is a major early driver after TBI and leads to tauopathy in CTE and AD, and cis antibody may be further developed to detect and treat TBI, and prevent progressive neurodegeneration after injury. PMID:26176913

  6. Discovery of cis-elements between sorghum and rice using co-expression and evolutionary conservation

    PubMed Central

    Wang, Xi; Haberer, Georg; Mayer, Klaus FX

    2009-01-01

    Background The spatiotemporal regulation of gene expression largely depends on the presence and absence of cis-regulatory sites in the promoter. In the economically highly important grass family, our knowledge of transcription factor binding sites and transcriptional networks is still very limited. With the completion of the sorghum genome and the available rice genome sequence, comparative promoter analyses now allow genome-scale detection of conserved cis-elements. Results In this study, we identified thousands of phylogenetic footprints conserved between orthologous rice and sorghum upstream regions that are supported by co-expression information derived from three different rice expression data sets. In a complementary approach, cis-motifs were discovered by their highly conserved co-occurrence in syntenic promoter pairs. Sequence conservation and matches to known plant motifs support our findings. Expression similarities of gene pairs positively correlate with the number of motifs that are shared by gene pairs and corroborate the importance of similar promoter architectures for concerted regulation. This strongly suggests that these motifs function in the regulation of transcript levels in rice and, presumably also in sorghum. Conclusion Our work provides the first large-scale collection of cis-elements for rice and sorghum and can serve as a paradigm for cis-element analysis through comparative genomics in grasses in general. PMID:19558665

  7. Fgf3-Fgf4-cis: A new mouse line for studying Fgf functions during mouse development.

    PubMed

    Anderson, Matthew J; Southon, Eileen; Tessarollo, Lino; Lewandoski, Mark

    2016-02-01

    The fibroblast growth factor (FGF) family consists of 22 ligands in mice and humans. FGF signaling is vital for embryogenesis and, when dysregulated, can cause disease. Loss-of-function genetic analysis in the mouse has been crucial for understanding FGF function. Such analysis has revealed that multiple Fgfs sometimes function redundantly. Exploring such redundancy between Fgf3 and Fgf4 is currently impossible because both genes are located on chromosome 7, about 18.5 kb apart, making the frequency of interallelic cross-over between existing mutant alleles too infrequent to be practicable. Therefore, we retargeted Fgf3 and Fgf4 in cis, generating an Fgf3 null allele and a conditional Fgf4 allele, subject to Cre inactivation. To increase the frequency of cis targeting, we used an F1 embryonic stem cell line that contained 129/SvJae (129) and C57BL/6J (B6) chromosomes and targeting constructs isogenic to the 129 chromosome. We confirmed cis targeting by assaying for B6/129 allele-specific single-nucleotide polymorphisms. We demonstrated the utility of the Fgf3(Δ)-Fgf4(flox)-cis mouse line by showing that the caudal axis extension defects found in the Fgf3 mutants worsen when Fgf4 is also inactivated. This Fgf3(Δ)-Fgf4(flox)-cis line will be useful to study redundancy of these genes in a variety of tissues and stages in development.

  8. Vision for Micro Technology Space Missions. Chapter 2

    NASA Technical Reports Server (NTRS)

    Dennehy, Neil

    2005-01-01

    It is exciting to contemplate the various space mission applications that Micro Electro Mechanical Systems (MEMS) technology could enable in the next 10-20 years. The primary objective of this chapter is to both stimulate ideas for MEMS technology infusion on future NASA space missions and to spur adoption of the MEMS technology in the minds of mission designers. This chapter is also intended to inform non-space oriented MEMS technologists, researchers and decision makers about the rich potential application set that future NASA Science and Exploration missions will provide. The motivation for this chapter is therefore to lead the reader down a path to identify and it is exciting to contemplate the various space mission applications that Micro Electro Mechanical Systems (MEMS) technology could enable in the next 10-20 years. The primary objective of this chapter is to both stimulate ideas for MEMS technology infusion on future NASA space missions and to spur adoption of the MEMS technology in the minds of mission designers. This chapter is also intended to inform non-space oriented MEMS technologists, researchers and decision makers about the rich potential application set that future NASA Science and Exploration missions will provide. The motivation for this chapter is therefore to lead the reader down a path to identify and consider potential long-term, perhaps disruptive or revolutionary, impacts that MEMS technology may have for future civilian space applications. A general discussion of the potential for MEMS in space applications is followed by a brief showcasing of a few selected examples of recent MEMS technology developments for future space missions. Using these recent developments as a point of departure, a vision is then presented of several areas where MEMS technology might eventually be exploited in future Science and Exploration mission applications. Lastly, as a stimulus for future research and development, this chapter summarizes a set of barriers

  9. The Arabidopsis CORI3 promoter contains two cis-acting regulatory regions required for transcriptional activity in companion cells.

    PubMed

    Tsuwamoto, Ryo; Harada, Takeo

    2011-09-01

    Companion cells are metabolically active and functionally specialized cells that behave as terminals for the transport of materials between phloem and the surrounding tissue. Although previous research has clarified the distinct function of companion cells, it is still largely unknown how plants establish and maintain the special identity of these cells. To shed further light on this issue, we carried out expressed sequence tag (EST) analysis. To minimize the difficulty of dissociating and gathering intact companion cells, vascular strings with an abundant content of companion cells were excised from the petioles of Brassica napus. By random sequencing with a string-specific cDNA library derived by suppression subtractive hybridization between the string itself and the petiole from which it had been removed, we identified 377 ESTs and assembled them into 247 EST groups. The most frequent EST was ExBdl-102 (15 of 377 ESTs), which showed the highest sequence similarity to the Arabidopsis CORI3 (CORONATINE INDUCED 3) gene. The CORI3 promoter:GUS showed predominant expression in the vascular tissue of Arabidopsis. Through transient expression assay using Brassica vasculature and gene-gun-mediated transient assay, we found two integrated cis-regulatory regions of the CORI3 promoter. This work has provided not only string-specific EST information and shown that two novel cis-regulatory regions sustain transcriptional activity in companion cells, but also a series of procedures for efficiently examining the transcriptional framework of companion cells by exploiting the histochemical advantage of B. napus as an experimental material. PMID:21559970

  10. Global analysis of cis-natural antisense transcripts and their heat-responsive nat-siRNAs in Brassica rapa

    PubMed Central

    2013-01-01

    Background Brassica rapa includes several important leaf vegetable crops whose production is often damaged by high temperature. Cis-natural antisense transcripts (cis-NATs) and cis-NATs-derived small interfering RNAs (nat-siRNAs) play important roles in plant development and stress responses. However, genome-wide cis-NATs in B. rapa are not known. The NATs and nat-siRNAs that respond to heat stress have never been well studied in B. rapa. Here, we took advantage of RNA-seq and small RNA (sRNA) deep sequencing technology to identify cis-NATs and heat responsive nat-siRNAs in B. rapa. Results Analyses of four RNA sequencing datasets revealed 1031 cis-NATs B. rapa ssp. chinensis cv Wut and B. rapa ssp. pekinensis cv. Bre. Based on sequence homology between Arabidopsis thaliana and B. rapa, 303 conserved cis-NATs in B. rapa were found to correspond to 280 cis-NATs in Arabidopsis; the remaining 728 novel cis-NATs were identified as Brassica-specific ones. Using six sRNA libraries, 4846 nat-siRNAs derived from 150 cis-NATs were detected. Differential expression analysis revealed that nat-siRNAs derived from 12 cis-NATs were responsive to heat stress, and most of them showed strand bias. Real-time PCR indicated that most of the transcripts generating heat-responsive nat-siRNAs were upregulated under heat stress, while the transcripts from the opposite strands of the same loci were downregulated. Conclusions Our results provide the first subsets of genome-wide cis-NATs and heat-responsive nat-siRNAs in B. rapa; these sRNAs are potentially useful for the genetic improvement of heat tolerance in B. rapa and other crops. PMID:24320882

  11. Implementing United States Pharmacopeia chapter <1163> quality assurance in pharmaceutical compounding, Part 1.

    PubMed

    Allen, Loyd V

    2012-01-01

    Compounding pharmacists must be familiar with and participate in the appropriate standards set forth in each chapter of the United States Pharmacopeia. Pharmacists should also be aware of any revisions to these standards. This article discusses the revisions to United States Pharmacopeia Chapter <1163> Quality Assurance in Pharmaceutical Compounding, a chapter which has been compared with other chapters, discusses some of those other chapters, and discusses the components of a reasonable quality-assurance program.

  12. Chapter 1 Reading Program. Final Evaluation Report 1994-95. Elementary and Secondary Education Act--Chapter 1.

    ERIC Educational Resources Information Center

    Lore, Rosemary

    A study evaluated the Chapter 1 Reading Program that served 5,914 underachieving pupils in grades 1 through 8 in the Columbus, Ohio, public schools. The program provided service to 84 public elementary schools, 26 public middle schools, and 11 nonpublic schools. These students appeared unlikely to learn to read successfully without additional…

  13. Chapter I: Impacting Excellence in Basic Skills since 1965. Initiative to Improve the Quality of Chapter I Projects.

    ERIC Educational Resources Information Center

    Bailey, Billie; And Others

    The overall goal of the sections of Mercer County's Chapter 1 project described in this profile was to provide a low-risk environment for the development of writing, reading, and related language arts skills in first, second, and third grade children. This goal was implemented within the broader sphere of the total school community. Communication,…

  14. Siemens solar CIS photovoltaic module and system performance at the National Renewable Energy Laboratory

    SciTech Connect

    Strand, T.; Kroposki, B.; Hansen, R.; Willett, D.

    1996-05-01

    This paper evaluates the individual module and array performance of Siemens Solar Industries copper indium diselenide (CIS) polycrystalline thin-film technology. This is accomplished by studying module and array performance over time. Preliminary temperature coefficients for maximum power, maximum-power voltage, maximum-power current, open-circuit voltage, short-circuit current, and fill factor are determined at both the module and array level. These coefficients are used to correct module/array performance to 25{degrees}C to evaluate stability. The authors show that CIS exhibits a strong inverse correlation between array power and back-of-module temperature. This is due mainly to the narrow bandgap of the CIS material, which results in a strong inverse correlation between voltage and temperature. They also show that the temperature-corrected module and array performance has been relatively stable over the evaluation interval ({approx}2 years).

  15. Barcoded DNA-Tag Reporters for Multiplex Cis-Regulatory Analysis

    PubMed Central

    Nam, Jongmin; Davidson, Eric H.

    2012-01-01

    Cis-regulatory DNA sequences causally mediate patterns of gene expression, but efficient experimental analysis of these control systems has remained challenging. Here we develop a new version of “barcoded" DNA-tag reporters, “Nanotags" that permit simultaneous quantitative analysis of up to 130 distinct cis-regulatory modules (CRMs). The activities of these reporters are measured in single experiments by the NanoString RNA counting method and other quantitative procedures. We demonstrate the efficiency of the Nanotag method by simultaneously measuring hourly temporal activities of 126 CRMs from 46 genes in the developing sea urchin embryo, otherwise a virtually impossible task. Nanotags are also used in gene perturbation experiments to reveal cis-regulatory responses of many CRMs at once. Nanotag methodology can be applied to many research areas, ranging from gene regulatory networks to functional and evolutionary genomics. PMID:22563420

  16. Analysis of rat cytosolic 9-cis-retinol dehydrogenase activity and enzymatic characterization of rat ADHII.

    PubMed

    Popescu, G; Napoli, J L

    2000-01-01

    We report the characterization of two enzymes that catalyze NAD(+)-dependent 9-cis-retinol dehydrogenase activity in rat liver cystol. Alcohol dehydrogenase class I (ADHI) contributes > 80% of the NA D+-dependent 9-cis-retinol dehydrogenase activity recovered, whereas alcohol dehydrogenase class II (ADHII), not identified previously at the protein level, nor characterized enzymatically in rat, accounts for approximately 2% of the activity. Rat ADHII exhibits properties different from those described for human ADHII. Moreover, rat ADHII-catalyzed rates of ethanol dehydrogenation are markedly lower than octanol or retinoid dehydrogenation rates. Neither ethanol nor 4-methylpyrazole inhibits the 9-cis-retinol dehydrogenase activity of rat ADHII. We propose that ADHII represents the previously observed additional retinoid oxidation activity of rat liver cytosol which occurred in the presence of either ethanol or 4-methylpyrazole. We also show that human and rat ADHII differ considerably in enzymatic properties. PMID:10606766

  17. Separation of cis/trans isomers of a prolyl peptide bond by capillary zone electrophoresis.

    PubMed

    Meyer, S; Jabs, A; Schutkowski, M; Fischer, G

    1994-01-01

    On capillary electrophoresis of the chemically pure thioxo peptide Ala-Phe-psi[CS-N]-Pro-Phe-4-nitroanilide a peak splitting was observed at a capillary temperature of 25 degrees C. By contrast, the oxo peptide analogue exhibits a single, sharp peak under these conditions. Both peaks of the thioxo compound coincided gradually when the temperature was increased to 60 degrees C. Peak fusion was reverted by cooling down the heated sample. This behavior could be attributed to the electrophoresis-mediated separation of the cis/trans prolyl bond isomers of the thioxo peptide, allowing data of this conformational equilibrium to be determined. Derived from computational data about molecular volume and the hydration energy of low-energy cis and trans isomeric structures, the more rapid migration of the cis form in comparison to trans may be explained by structural parameters.

  18. Identification of cis-regulatory sequence variations in individual genome sequences.

    PubMed

    Worsley-Hunt, Rebecca; Bernard, Virginie; Wasserman, Wyeth W

    2011-01-01

    Functional contributions of cis-regulatory sequence variations to human genetic disease are numerous. For instance, disrupting variations in a HNF4A transcription factor binding site upstream of the Factor IX gene contributes causally to hemophilia B Leyden. Although clinical genome sequence analysis currently focuses on the identification of protein-altering variation, the impact of cis-regulatory mutations can be similarly strong. New technologies are now enabling genome sequencing beyond exomes, revealing variation across the non-coding 98% of the genome responsible for developmental and physiological patterns of gene activity. The capacity to identify causal regulatory mutations is improving, but predicting functional changes in regulatory DNA sequences remains a great challenge. Here we explore the existing methods and software for prediction of functional variation situated in the cis-regulatory sequences governing gene transcription and RNA processing.

  19. Identification of cis-regulatory sequence variations in individual genome sequences

    PubMed Central

    2011-01-01

    Functional contributions of cis-regulatory sequence variations to human genetic disease are numerous. For instance, disrupting variations in a HNF4A transcription factor binding site upstream of the Factor IX gene contributes causally to hemophilia B Leyden. Although clinical genome sequence analysis currently focuses on the identification of protein-altering variation, the impact of cis-regulatory mutations can be similarly strong. New technologies are now enabling genome sequencing beyond exomes, revealing variation across the non-coding 98% of the genome responsible for developmental and physiological patterns of gene activity. The capacity to identify causal regulatory mutations is improving, but predicting functional changes in regulatory DNA sequences remains a great challenge. Here we explore the existing methods and software for prediction of functional variation situated in the cis-regulatory sequences governing gene transcription and RNA processing. PMID:21989199

  20. WebCIS: large scale deployment of a Web-based clinical information system.

    PubMed

    Hripcsak, G; Cimino, J J; Sengupta, S

    1999-01-01

    WebCIS is a Web-based clinical information system. It sits atop the existing Columbia University clinical information system architecture, which includes a clinical repository, the Medical Entities Dictionary, an HL7 interface engine, and an Arden Syntax based clinical event monitor. WebCIS security features include authentication with secure tokens, authorization maintained in an LDAP server, SSL encryption, permanent audit logs, and application time outs. WebCIS is currently used by 810 physicians at the Columbia-Presbyterian center of New York Presbyterian Healthcare to review and enter data into the electronic medical record. Current deployment challenges include maintaining adequate database performance despite complex queries, replacing large numbers of computers that cannot run modern Web browsers, and training users that have never logged onto the Web. Although the raised expectations and higher goals have increased deployment costs, the end result is a far more functional, far more available system. PMID:10566471

  1. A saturation screen for cis-acting regulatory DNA in the Hox genes of Ciona intestinalis

    SciTech Connect

    Keys, David N.; Lee, Byung-in; Di Gregorio, Anna; Harafuji, Naoe; Detter, Chris; Wang, Mei; Kahsai, Orsalem; Ahn, Sylvia; Arellano, Andre; Zhang, Quin; Trong, Stephan; Doyle, Sharon A.; Satoh, Noriyuki; Satou, Yutaka; Saiga, Hidetoshi; Christian, Allen; Rokhsar, Dan; Hawkins, Trevor L.; Levine, Mike; Richardson, Paul

    2005-01-05

    A screen for the systematic identification of cis-regulatory elements within large (>100 kb) genomic domains containing Hox genes was performed by using the basal chordate Ciona intestinalis. Randomly generated DNA fragments from bacterial artificial chromosomes containing two clusters of Hox genes were inserted into a vector upstream of a minimal promoter and lacZ reporter gene. A total of 222 resultant fusion genes were separately electroporated into fertilized eggs, and their regulatory activities were monitored in larvae. In sum, 21 separable cis-regulatory elements were found. These include eight Hox linked domains that drive expression in nested anterior-posterior domains of ectodermally derived tissues. In addition to vertebrate-like CNS regulation, the discovery of cis-regulatory domains that drive epidermal transcription suggests that C. intestinalis has arthropod-like Hox patterning in the epidermis.

  2. Detection of trans–cis flips and peptide-plane flips in protein structures

    SciTech Connect

    Touw, Wouter G.; Joosten, Robbie P.; Vriend, Gert

    2015-07-28

    A method is presented to detect peptide bonds that need either a trans–cis flip or a peptide-plane flip. A coordinate-based method is presented to detect peptide bonds that need correction either by a peptide-plane flip or by a trans–cis inversion of the peptide bond. When applied to the whole Protein Data Bank, the method predicts 4617 trans–cis flips and many thousands of hitherto unknown peptide-plane flips. A few examples are highlighted for which a correction of the peptide-plane geometry leads to a correction of the understanding of the structure–function relation. All data, including 1088 manually validated cases, are freely available and the method is available from a web server, a web-service interface and through WHAT-CHECK.

  3. Trajectory Design Tools for Libration and Cis-Lunar Environments

    NASA Technical Reports Server (NTRS)

    Folta, David C.; Webster, Cassandra M.; Bosanac, Natasha; Cox, Andrew; Guzzetti, Davide; Howell, Kathleen C.

    2016-01-01

    Innovative trajectory design tools are required to support challenging multi-body regimes with complex dynamics, uncertain perturbations, and the integration of propulsion influences. Two distinctive tools, Adaptive Trajectory Design and the General Mission Analysis Tool have been developed and certified to provide the astrodynamics community with the ability to design multi-body trajectories. In this paper we discuss the multi-body design process and the capabilities of both tools. Demonstrable applications to confirmed missions, the Lunar IceCube Cubesat lunar mission and the Wide-Field Infrared Survey Telescope (WFIRST) Sun-Earth L2 mission, are presented.

  4. Interleukin-6 inhibits hepatic growth hormone signaling via upregulation of Cis and Socs-3.

    PubMed

    Denson, Lee A; Held, Matthew A; Menon, Ram K; Frank, Stuart J; Parlow, Albert F; Arnold, Dodie L

    2003-04-01

    Cytokines may cause an acquired growth hormone (GH) resistance in patients with inflammatory diseases. Anabolic effects of GH are mediated through activation of STAT5 transcription factors. We have reported that TNF-alpha suppresses hepatic GH receptor (GHR) gene expression, whereas the cytokine-inducible SH2-containing protein 1 (Cis)/suppressors of cytokine signaling (Socs) genes are upregulated by TNF-alpha and IL-6 and inhibit GH activation of STAT5. However, the relative importance of these mechanisms in inflammatory GH resistance was not known. We hypothesized that IL-6 would prevent GH activation of STAT5 and that this would involve Cis/Socs protein upregulation. GH +/- LPS was administered to TNF receptor 1 (TNFR1) or IL-6 null mice and wild-type (WT) controls. STAT5, STAT3, GHR, Socs 1-3, and Cis phosphorylation and abundance were assessed by using immunoblots, EMSA, and/or real time RT-PCR. TNF-alpha and IL-6 abundance were assessed by using ELISA. GH activated STAT5 in WT and TNFR1 or IL-6 null mice. LPS pretreatment prevented STAT5 activation in WT and TNFR1 null mice; however, STAT5 activation was preserved in IL-6 null mice. GHR abundance did not change with LPS administration. Inhibition of STAT5 activation by LPS was temporally associated with phosphorylation of STAT3 and upregulation of Cis and Socs-3 protein in WT and TNFR1 null mice; STAT3, Cis, and Socs-3 were not induced in IL-6 null mice. IL-6 inhibits hepatic GH signaling by upregulating Cis and Socs-3, which may involve activation of STAT3. Therapies that block IL-6 may enhance GH signaling in inflammatory diseases.

  5. Locust retinoid X receptors: 9-Cis-retinoic acid in embryos from a primitive insect.

    PubMed

    Nowickyj, Shaun M; Chithalen, James V; Cameron, Don; Tyshenko, Michael G; Petkovich, Martin; Wyatt, Gerard R; Jones, Glenville; Walker, Virginia K

    2008-07-15

    The retinoid X receptor (RXR) is activated by its often elusive cognate ligand, 9-cis-retinoic acid (9-cis-RA). In flies and moths, molting is mediated by a heterodimer ecdysone receptor consisting of the ecdysone monomer (EcR) and an RXR homolog, ultraspiracle (USP); the latter is believed to have diverged from its RXR origin. In the more primitive insect, Locusta migratoria (Lm), RXR is more similar to human RXRs than to USPs. LmRXR was detected in early embryos when EcR transcripts were absent, suggesting another role apart from ecdysone signaling. Recombinant LmRXRs bound 9-cis-RA and all-trans-RA with high affinity (IC(50) = 61.2-107.7 nM; K(d) = 3 nM), similar to human RXR. To determine whether specific binding had functional significance, the presence of endogenous retinoids was assessed. Embryos were extracted by using modified Bligh and Dyer and solid-phase protocols to avoid the oily precipitate that makes this material unsuitable for assay. These extracts contained retinoids (5.4 nM) as assessed by RA-inducible Cyp26A1-promoter luciferase reporter cell lines. Furthermore, the use of HPLC and MS confirmed the presence of retinoids and identified in any embryo, 9-cis-RA, in addition to all-trans-RA. We estimate that whole embryos contain 3 nM RA, including 9-cis-RA at a concentration of 1.6 nM. These findings strongly argue for a functional role for retinoids in primitive insects and favor a model where signaling through the binding of 9-cis-RA to its RXR is established relatively early in evolution and embryonic development.

  6. cis-Jasmone induces accumulation of defence compounds in wheat, Triticum aestivum.

    PubMed

    Moraes, Maria C Blassioli; Birkett, Michael A; Gordon-Weeks, Ruth; Smart, Lesley E; Martin, Janet L; Pye, Barry J; Bromilow, Richard; Pickett, John A

    2008-01-01

    Liquid phase extraction (LPE) and vapor phase extraction (VPE) methodologies were used to evaluate the impact of the plant activator, cis-jasmone, on the secondary metabolism of wheat, Triticum aestivum, var. Solstice. LPE allowed the measurement of benzoxazinoids, i.e. 2,4-dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one (DIMBOA), 2-hydroxy-7-methoxy-1,4-benzoxazin-3-one (HMBOA) and 6-methoxy-benzoxazolin-2-one (MBOA), and phenolic acids such as trans-p-coumaric acid, syringic acid, p-hydroxybenzoic acid, vanillic acid and cis- and trans-ferulic acid. Using LPE, a significantly higher level of DIMBOA was found in aerial parts and roots of T. aestivum following treatment with cis-jasmone, when compared with untreated plants. Similar results were obtained for phenolic acids, such as trans-ferulic acid and vanillic acid in roots. Using VPE, it was possible to measure levels of 2-hydroxy-7-methoxy-(2H)-1,4-benzoxazin-3(4H)-one (HBOA), benzoxazolin-2(3H)-one (BOA), ferulic acid, syringic acid and coumaric acid. The levels of HBOA in aerial parts and roots were significantly greater in cis-jasmone treated plants compared to untreated plants. cis-Jasmone is known to be a plant activator in terms of production of defence-related volatile semiochemicals that repel aphids and increase the foraging activity of aphid parasitoids. These results show, for the first time, that cis-jasmone also induces selective production of secondary metabolites that are capable of directly reducing development of pests, diseases and weeds.

  7. The effect of CIS hydroxyproline on ventral prostatic growth in rats.

    PubMed

    Uke, E; Lee, C; Grayhack, J T

    1983-01-01

    Changes in prostatic collagen were measured in Sprague-Dawley rats to gain further insight into the relationship between this stromal component and androgen mediated prostatic growth. Regulation of prostatic collagen by other endocrine factors was also studied. Collagen content per prostate was estimated by determination of tissue levels of hydroxyproline. The 1st experiment examined changes in the content of hydroxyproline in the prostate during pre- and post-pubertal growth with the use of rats between 21 and 80 days of age. As the animals grew, their prostatic weights and hydroxyproline contents increased in a parallel fashion (correlation coefficient R = 0.977, p less than 0.01). In the 2nd experiment, rats were castrated for a period up to 28 days. The hydroxyproline content in the prostate did not change significantly by castration despite a marked decrease in prostatic weights. Results of the 3rd experiment indicated that castration-hypophysectomy or castration-hypophysectomy plus estrogen treatment did not significantly change the content of prostatic hydroxyproline from that in the untreated intact animals. The 4th experiment studied the effect of the collagen synthesis inhibitor, cis-4-hydroxyproline, on prostatic growth. Subcutaneous injection of cis-4-hydroxyproline to castrated testosterone treated rats caused a significantly slower increase in total ventral prostatic weights and contents of protein, DNA and hydroxyproline than those of saline treated controls. This inhibition in prostatic growth is unlikely to be related to any antiandrogenic effect of cis hydroxyproline as the protein/DNA ratio in the prostate was the same for both saline and cis-4-hydroxyproline treated groups. Electron microscopic studies revealed that cis-4-hydroxyproline treatment resulted in a derangement of the basement membrane in the ventral prostate. The above results suggest that collagen plays an important role in limiting prostatic growth since inhibition of collagen

  8. Nonadiabatic ab initio dynamics of a model protonated Schiff base of 9-cis retinal.

    PubMed

    Chung, Wilfredo Credo; Nanbu, Shinkoh; Ishida, Toshimasa

    2010-08-19

    The dynamics of the photoisomerization of a model protonated Schiff base of 9-cis retinal in isorhodopsin is investigated using nonadiabatic molecular dynamics simulation combined with ab initio quantum chemical calculations on-the-fly. The quantum chemical part is treated at the complete-active space self-consistent field level for six electrons in six active pi orbitals with the 6-31G basis set (CASSCF(6,6)/6-31G). The probabilities of nonadiabatic transitions between the S(1) ((1)pipi*) and S(0) states are estimated in light of the Zhu-Nakamura theory. The photoinduced cis-trans isomerization of 9-cis retinal proceeds slower than that of its 11-cis analogue and at a lower quantum yield, confirming experimental observations. An energetic barrier in the excited state impedes the elongation and twist of the C(9)=C(10) stretch and torsion coordinates, respectively, resulting in the trapping of trajectories before transition. Consequently, the isomerization takes longer time and the transition more often occurs at smaller twist angle of =C(8)-C(9)=C(10)-C(11)=, which leads to regeneration of the 9-cis reactant. Thus, neither the smaller twist observed in the X-ray crystal nor the slower movement of nuclei in the transition region would be the main reason for the longer reaction time and lower yield. A well-known space-saving asynchronous bicycle pedal or crankshaft photoisomerization mechanism is found to be operational in 9-cis retinal. The simulation in vacuo suggests that the excited-state barrier and the photoisomerization itself are intrinsic properties of the visual chromophore and not triggered mainly by the protein environment that surrounds the chromophore. PMID:20666503

  9. Comparative toxicity of cis-cypermethrin in rainbow trout, frog, mouse, and quail.

    PubMed

    Edwards, R; Millburn, P; Hutson, D H

    1986-07-01

    The synthetic alpha-cyano-phenoxybenzyl-containing pyrethroid insecticides act on the CNS of vertebrates and show a species-selective toxicity in the order fish greater than amphibians much greater than mammals greater than birds. Concentrations of [14C]cis-cypermethrin in the brains of representative members of each of these classes of chordates were measured at toxic signs (an onset of hyperactivity followed by seizures and loss of balance/equilibrium) as an indicator of target organ sensitivity. The concentration of cis-cypermethrin in brain, associated with toxic signs, in micrograms per gram (mean +/- SE) as determined by high-performance liquid chromatography was 0.08 +/- 0.03 (frog), 0.23 +/- 0.05 (trout), 1.71 +/- 0.33 (mouse), and 3.94 +/- 0.88 (quail). Trout brain was equally sensitive to the cis and trans isomers of cypermethrin. In both mouse and quail, some 90% of the radioactivity in the brain was parent pyrethroid. Trout and frog, however, afforded only 56 and 32%, respectively, of the brain 14C as cypermethrin, with the remaining radioactivity in both extractable and nonextractable metabolites, including 4'-hydroxy-cis-cypermethrin, which is potentially neuroactive. Following oral administration, cis-cypermethrin was readily absorbed and metabolized by quail. Intestinal uptake was far less rapid in trout and mouse, with unchanged cypermethrin dispersed in secreted bile, being readily eliminated from the intestines of fish. The uptake and metabolism of cis-cypermethrin and the brain sensitivities of these animals to the pyrethroid account for the observed differences in acute toxicity.

  10. 9-Cis Retinoic Acid Promotes Lymphangiogenesis and Enhances Lymphatic Vessel Regeneration: Therapeutic Implications of 9-Cis Retinoic Acid for Secondary Lymphedema

    PubMed Central

    Choi, Inho; Lee, Sunju; Chung, Hee Kyoung; Lee, Yong Suk; Kim, Kyu Eui; Choi, Dongwon; Park, Eun Kyung; Yang, Dongyun; Ecoiffier, Tatiana; Monahan, John; Chen, Wen; Aguilar, Berenice; Lee, Ha Neul; Yoo, Jaehyuk; Koh, Chester J.; Chen, Lu; Wong, Alex K.; Hong, Young-Kwon

    2012-01-01

    Background The lymphatic system plays a key role in tissue fluid homeostasis and lymphatic dysfunction due to genetic defects or lymphatic vessel obstruction can cause lymphedema, disfiguring tissue swellings often associated with fibrosis and recurrent infections without available cures to date. In this study, retinoic acids (RAs) were determined to be a potent therapeutic agent that is immediately applicable to reduce secondary lymphedema. Methods and Results We report that RAs promote proliferation, migration and tube formation of cultured lymphatic endothelial cells (LECs) by activating FGF-receptor signaling. Moreover, RAs control the expression of cell-cycle checkpoint regulators such as p27Kip1, p57Kip2 and the aurora kinases through both an Akt-mediated non-genomic action and a transcription-dependent genomic action that is mediated by Prox1, a master regulator of lymphatic development. Moreover, 9-cisRA was found to activate in vivo lymphangiogenesis in animals based on mouse trachea, matrigel plug and cornea pocket assays. Finally, we demonstrate that 9-cisRA can provide a strong therapeutic efficacy in ameliorating the experimental mouse tail lymphedema by enhancing lymphatic vessel regeneration. Conclusions These in vitro and animal studies demonstrate that 9-cisRA potently activates lymphangiogenesis and promotes lymphatic regeneration in an experimental lymphedema model, presenting it as a promising novel therapeutic agent to treat human lymphedema patients. PMID:22275501

  11. Evolutionary computation method for pattern recognition of cis-acting sites.

    PubMed

    Howard, Daniel; Benson, Karl

    2003-11-01

    This paper develops an evolutionary method that learns inductively to recognize the makeup and the position of very short consensus sequences, cis-acting sites, which are a typical feature of promoters in genomes. The method combines a Finite State Automata (FSA) and Genetic Programming (GP) to discover candidate promoter sequences in primary sequence data. An experiment measures the success of the method for promoter prediction in the human genome. This class of method can take large base pair jumps and this may enable it to process very long genomic sequences to discover gene specific cis-acting sites, and genes which are regulated together. PMID:14642656

  12. cis-Regulatory Mutations Are a Genetic Cause of Human Limb Malformations

    PubMed Central

    VanderMeer, Julia E.; Ahituv, Nadav

    2011-01-01

    The underlying mutations that cause human limb malformations are often difficult to determine, particularly for limb malformations that occur as isolated traits. Evidence from a variety of studies shows that cis-regulatory mutations, specifically in enhancers, can lead to some of these isolated limb malformations. Here, we provide a review of human limb malformations that have been shown to be caused by enhancer mutations and propose that cis-regulatory mutations will continue to be identified as the cause of additional human malformations as our understanding of regulatory sequences improves. PMID:21509892

  13. Separation of cis and trans Isomers of Polyproline by FAIMS Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Creese, Andrew J.; Cooper, Helen J.

    2016-10-01

    High field asymmetric waveform ion mobility spectrometry (FAIMS) is well-established as a tool for separating peptide isomers (sequence inversions and post-translationally modified localization variants). Here, we demonstrate the FAIMS is able to differentiate cis and trans isomers of polyproline. Polyproline assumes an all-cis conformation—the PPI helix—in 1-propanol, and an all-trans conformation—the PPII helix—in aqueous solutions. Differentiation of these conformers may be achieved both through use of a cylindrical FAIMS device and a miniaturized ultrahigh field planar FAIMS device.

  14. Large area low cost processing for CIS photovoltaics. Final technical report

    SciTech Connect

    B. Basol; G. Norsworthy; C. Leidholm; A. Halani; R. Roe; V. Kapur

    1999-07-22

    An ink coating method was developed for CIS absorber deposition. The technique involves four processing steps: (1) preparation of a Cu-In alloy powder, (2) preparation of an ink using this powder, (3) deposition of the ink on a substrate in the form of a precursor layer, and (4) selenization to convert the Cu-In precursor into a fused CIS film. Absorbers grown by this low-cost, large-area method were used in the fabrication of 10.5% efficient solar cells.

  15. The Role of Cis-Lunar Space in Future Global Space Exploration

    NASA Technical Reports Server (NTRS)

    Bobskill, Marianne R.; Lupisella, Mark L.

    2012-01-01

    Cis-lunar space offers affordable near-term opportunities to help pave the way for future global human exploration of deep space, acting as a bridge between present missions and future deep space missions. While missions in cis-lunar space have value unto themselves, they can also play an important role in enabling and reducing risk for future human missions to the Moon, Near-Earth Asteroids (NEAs), Mars, and other deep space destinations. The Cis-Lunar Destination Team of NASA's Human Spaceflight Architecture Team (HAT) has been analyzing cis-lunar destination activities and developing notional missions (or "destination Design Reference Missions" [DRMs]) for cis-lunar locations to inform roadmap and architecture development, transportation and destination elements definition, operations, and strategic knowledge gaps. The cis-lunar domain is defined as that area of deep space under the gravitational influence of the earth-moon system. This includes a set of earth-centered orbital locations in low earth orbit (LEO), geosynchronous earth orbit (GEO), highly elliptical and high earth orbits (HEO), earth-moon libration or "Lagrange" points (E-ML1 through E-ML5, and in particular, E-ML1 and E-ML2), and low lunar orbit (LLO). To help explore this large possibility space, we developed a set of high level cis-lunar mission concepts in the form of a large mission tree, defined primarily by mission duration, pre-deployment, type of mission, and location. The mission tree has provided an overall analytical context and has helped in developing more detailed design reference missions that are then intended to inform capabilities, operations, and architectures. With the mission tree as context, we will describe two destination DRMs to LEO and GEO, based on present human space exploration architectural considerations, as well as our recent work on defining mission activities that could be conducted with an EML1 or EML2 facility, the latter of which will be an emphasis of this

  16. trans and cis Chromophore structures in the kindling fluorescent protein asFP595

    NASA Astrophysics Data System (ADS)

    Grigorenko, Bella; Savitsky, Alexander; Topol, Igor; Burt, Stanley; Nemukhin, Alexander

    2006-06-01

    The ab initio QM/MM calculations are used to optimize geometry configurations of the chromophore and surrounding residues for the kindling protein asFP595. The time-dependent DFT method is applied to estimate parameters of the S 0-S 1 vertical transition of the chromophore at the protein geometry taking into account effects from the nearest residues. The results of simulations provide a theoretical support to the hypothesis on the possibility of trans-cis izomerization of the chromophore in the mechanism of kindling. The system can absorb light in the trans anion form of the chromophore and emit at longer wavelength in the cis anion form.

  17. Ultrafast studies of solvent effects in the isomerization of cis-stilbene

    SciTech Connect

    Rice, J.K.; Baronavski, A.P.

    1992-04-16

    Using a femtosecond pump-probe laser system, the excited-state lifetimes of cis-stilbene in n-hexane, tetradecane, methanol, 1,4-dioxane, and cyclohexane are measured and correlated with solvent bulk viscosity. The measured lifetimes in n-hexane and tetradecane correlate well to solvent bulk viscosity, but methanol, 1,4-dioxane, and cyclohexane do not. Polarity-influenced solvent-solute interactions occur in methanol and 1,4-dioxane and a slow isomerization rate in cyclohexane occurs with cis-stilbene. 39 refs., 7 figs., 2 tabs.

  18. Premature physeal closure following 13-cis-retinoic acid and prolonged fenretinide administration in neuroblastoma.

    PubMed

    Steineck, Angela; MacKenzie, John D; Twist, Clare J

    2016-11-01

    Retinoid therapy has contributed to improved outcomes in neuroblastoma. Clinical trials of fenretinide report favorable toxicity and disease stabilization in patients with high risk (HR) neuroblastoma. Skeletal effects have been described with other retinoids, but not with fenretinide to date. Two patients with HR, metastatic, refractory neuroblastoma received protracted courses of oral fenretinide for more than 5 years' duration. Both developed premature long bone physeal closure, causing limb length discrepancies; their neuroblastoma remains in remission. The radiographic and clinical findings reported suggest these skeletal abnormalities may be a consequence of treatment with 13-cis-retinoic acid (13cisRA) followed by prolonged oral fenretinide exposure.

  19. Structures, mechanisms and inhibitors of undecaprenyl diphosphate synthase: a cis-prenyltransferase for bacterial peptidoglycan biosynthesis.

    PubMed

    Teng, Kuo-Hsun; Liang, Po-Huang

    2012-08-01

    Isoprenoids are an intensive group of compounds made from isopentenyl diphosphate (IPP), catalyzed by prenyltransferases such as farnesyl diphosphate (FPP) cyclases, squalene synthase, protein farnesyltransferases and geranylgeranyltransferases, aromatic prenyltransferases as well as a group of prenyltransferases (cis- and trans-types) catalyzing consecutive condensation reactions of FPP with specific numbers of IPP to generate linear products with designate chain lengths. These prenyltransferases play significant biological functions and some of them are drug targets. In this review, structures, mechanisms, and inhibitors of a cis-prenyltransferase, undecaprenyl diphosphate synthase (UPPS) that mediates bacterial peptidoglycan biosynthesis, are summarized for comparison with the most related trans-prenyltransferases and other prenyltransferases.

  20. Silica sol assisted chromatographic NMR spectroscopy for resolution of trans- and cis-isomers

    NASA Astrophysics Data System (ADS)

    Yang, Ying; Wu, Rui; Huang, Shaohua; Bai, Zhengwu

    2016-04-01

    Chromatographic NMR spectroscopy can separate the mixtures of species with significantly different molecular size, but generally fails for isomeric species. Herein, we reported the resolution of trans- and cis-isomers and their structural analogue, which are different in molecular shapes, but similar in mass, were greatly enhanced in the presence of silica sol. The mixtures of maleic acid, fumaric acid and succinic acid, and the mixtures of trans- and cis-1,2-cyclohexanedicarboxylic acids, were distinguished by virtue of their different degrees of interaction with silica sol. Moreover, we found mixed solvents could improve the spectral resolution of DOSY spectra of mixtures.