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Sample records for sam levels gene

  1. Crystal structures of the SAM-III/S[subscript MK] riboswitch reveal the SAM-dependent translation inhibition mechanism

    Energy Technology Data Exchange (ETDEWEB)

    Lu, C.; Smith, A.M.; Fuchs, R.T.; Ding, F.; Rajashankar, K.; Henkin, T.M.; Ke, A. (Cornell); (OSU)

    2010-01-07

    Three distinct classes of S-adenosyl-L-methionine (SAM)-responsive riboswitches have been identified that regulate bacterial gene expression at the levels of transcription attenuation or translation inhibition. The SMK box (SAM-III) translational riboswitch has been identified in the SAM synthetase gene in members of the Lactobacillales. Here we report the 2.2-{angstrom} crystal structure of the Enterococcus faecalis SMK box riboswitch. The Y-shaped riboswitch organizes its conserved nucleotides around a three-way junction for SAM recognition. The Shine-Dalgarno sequence, which is sequestered by base-pairing with the anti-Shine-Dalgarno sequence in response to SAM binding, also directly participates in SAM recognition. The riboswitch makes extensive interactions with the adenosine and sulfonium moieties of SAM but does not appear to recognize the tail of the methionine moiety. We captured a structural snapshot of the SMK box riboswitch sampling the near-cognate ligand S-adenosyl-L-homocysteine (SAH) in which SAH was found to adopt an alternative conformation and fails to make several key interactions.

  2. SAM-VI RNAs selectively bind S-adenosylmethionine and exhibit similarities to SAM-III riboswitches.

    Science.gov (United States)

    Mirihana Arachchilage, Gayan; Sherlock, Madeline E; Weinberg, Zasha; Breaker, Ronald R

    2018-03-04

    Five distinct riboswitch classes that regulate gene expression in response to the cofactor S-adenosylmethionine (SAM) or its metabolic breakdown product S-adenosylhomocysteine (SAH) have been reported previously. Collectively, these SAM- or SAH-sensing RNAs constitute the most abundant collection of riboswitches, and are found in nearly every major bacterial lineage. Here, we report a potential sixth member of this pervasive riboswitch family, called SAM-VI, which is predominantly found in Bifidobacterium species. SAM-VI aptamers selectively bind the cofactor SAM and strongly discriminate against SAH. The consensus sequence and structural model for SAM-VI share some features with the consensus model for the SAM-III riboswitch class, whose members are mainly found in lactic acid bacteria. However, there are sufficient differences between the two classes such that current bioinformatics methods separately cluster representatives of the two motifs. These findings highlight the abundance of RNA structures that can form to selectively recognize SAM, and showcase the ability of RNA to utilize diverse strategies to perform similar biological functions.

  3. SAM Theory Manual

    Energy Technology Data Exchange (ETDEWEB)

    Hu, Rui [Argonne National Lab. (ANL), Argonne, IL (United States)

    2017-03-01

    The System Analysis Module (SAM) is an advanced and modern system analysis tool being developed at Argonne National Laboratory under the U.S. DOE Office of Nuclear Energy’s Nuclear Energy Advanced Modeling and Simulation (NEAMS) program. SAM development aims for advances in physical modeling, numerical methods, and software engineering to enhance its user experience and usability for reactor transient analyses. To facilitate the code development, SAM utilizes an object-oriented application framework (MOOSE), and its underlying meshing and finite-element library (libMesh) and linear and non-linear solvers (PETSc), to leverage modern advanced software environments and numerical methods. SAM focuses on modeling advanced reactor concepts such as SFRs (sodium fast reactors), LFRs (lead-cooled fast reactors), and FHRs (fluoride-salt-cooled high temperature reactors) or MSRs (molten salt reactors). These advanced concepts are distinguished from light-water reactors in their use of single-phase, low-pressure, high-temperature, and low Prandtl number (sodium and lead) coolants. As a new code development, the initial effort has been focused on modeling and simulation capabilities of heat transfer and single-phase fluid dynamics responses in Sodium-cooled Fast Reactor (SFR) systems. The system-level simulation capabilities of fluid flow and heat transfer in general engineering systems and typical SFRs have been verified and validated. This document provides the theoretical and technical basis of the code to help users understand the underlying physical models (such as governing equations, closure models, and component models), system modeling approaches, numerical discretization and solution methods, and the overall capabilities in SAM. As the code is still under ongoing development, this SAM Theory Manual will be updated periodically to keep it consistent with the state of the development.

  4. Identification of trans-acting factors regulating SamDC expression in Oryza sativa

    Energy Technology Data Exchange (ETDEWEB)

    Basu, Supratim, E-mail: supratim_genetics@yahoo.co.in [Department of Crop Soil and Environmental Sciences, University of Arkansas, Fayetteville, AR 72701 (United States); Division of Plant Biology, Bose Institute, Kolkata (India); Roychoudhury, Aryadeep [Post Graduate Department of Biotechnology, St. Xavier' s College (Autonomous), 30, Mother Teresa Sarani, Kolkata - 700016, West Bengal (India); Sengupta, Dibyendu N. [Division of Plant Biology, Bose Institute, Kolkata (India)

    2014-03-07

    Highlights: • Identification of cis elements responsible for SamDC expression by in silico analysis. • qPCR analysis of SamDC expression to abiotic and biotic stress treatments. • Detection of SamDC regulators using identified cis-elements as probe by EMSA. • Southwestern Blot analysis to predict the size of the trans-acting factors. - Abstract: Abiotic stress affects the growth and productivity of crop plants; to cope with the adverse environmental conditions, plants have developed efficient defense machinery comprising of antioxidants like phenolics and flavonoids, and osmolytes like polyamines. SamDC is a key enzyme in the polyamine biosynthesis pathway in plants. In our present communication we have done in silico analysis of the promoter region of SamDC to look for the presence of different cis-regulatory elements contributing to its expression. Based on the presence of different cis-regulatory elements we completed comparative analysis of SamDC gene expression in rice lamina of IR-29 and Nonabokra by qPCR in response to the abiotic stress treatments of salinity, drought, cold and the biotic stress treatments of ABA and light. Additionally, to explore the role of the cis-regulatory elements in regulating the expression of SamDC gene in plants we comparatively analyzed the binding of rice nuclear proteins prepared from IR-29 and Nonabokra undergoing various stress treatments. The intensity of the complex formed was low and inducible in IR-29 in contrast to Nonabokra. Southwestern blot analysis helped in predicting the size of the trans-acting factors binding to these cis-elements. To our knowledge this is the first report on the comprehensive analysis of SamDC gene expression in rice and identification of the trans-acting factors regulating its expression.

  5. Sam37 is crucial for formation of the mitochondrial TOM-SAM supercomplex, thereby promoting β-barrel biogenesis.

    Science.gov (United States)

    Wenz, Lena-Sophie; Ellenrieder, Lars; Qiu, Jian; Bohnert, Maria; Zufall, Nicole; van der Laan, Martin; Pfanner, Nikolaus; Wiedemann, Nils; Becker, Thomas

    2015-09-28

    Biogenesis of mitochondrial β-barrel proteins requires two preprotein translocases, the general translocase of the outer membrane (TOM) and the sorting and assembly machinery (SAM). TOM and SAM form a supercomplex that promotes transfer of β-barrel precursors. The SAM core complex contains the channel protein Sam50, which cooperates with Sam35 in precursor recognition, and the peripheral membrane protein Sam37. The molecular function of Sam37 has been unknown. We report that Sam37 is crucial for formation of the TOM-SAM supercomplex. Sam37 interacts with the receptor domain of Tom22 on the cytosolic side of the mitochondrial outer membrane and links TOM and SAM complexes. Sam37 thus promotes efficient transfer of β-barrel precursors to the SAM complex. We conclude that Sam37 functions as a coupling factor of the translocase supercomplex of the mitochondrial outer membrane. © 2015 Wenz et al.

  6. SAM Photovoltaic Model Technical Reference

    Energy Technology Data Exchange (ETDEWEB)

    Gilman, P. [National Renewable Energy Laboratory (NREL), Golden, CO (United States)

    2015-05-27

    This manual describes the photovoltaic performance model in the System Advisor Model (SAM). The U.S. Department of Energy’s National Renewable Energy Laboratory maintains and distributes SAM, which is available as a free download from https://sam.nrel.gov. These descriptions are based on SAM 2015.1.30 (SSC 41).

  7. Generation of induced pluripotent stem cells (iPSCs) stably expressing CRISPR-based synergistic activation mediator (SAM).

    Science.gov (United States)

    Xiong, Kai; Zhou, Yan; Hyttel, Poul; Bolund, Lars; Freude, Kristine Karla; Luo, Yonglun

    2016-11-01

    Human fibroblasts were engineered to express the CRISPR-based synergistic activation mediator (SAM) complex: dCas9-VP64 and MS2-P65-HSF1. Two induced pluripotent stem cells (iPSCs) clones expressing SAM were established by transducing these fibroblasts with lentivirus expressing OCT4, SOX2, KLF4 and C-MYC. We have validated that the reprogramming cassette is silenced in the SAM iPSC clones. Expression of pluripotency genes (OCT4, SOX2, LIN28A, NANOG, GDF3, SSEA4, and TRA-1-60), differentiation potential to all three germ layers, and normal karyotypes are validated. These SAM-iPSCs provide a novel, useful tool to investigate genetic regulation of stem cell proliferation and differentiation through CRISPR-mediated activation of endogenous genes. Copyright © 2016 Michael Boutros, German Cancer Research Center, Heidelberg, Germany. Published by Elsevier B.V. All rights reserved.

  8. Information System through ANIS at CeSAM

    Science.gov (United States)

    Moreau, C.; Agneray, F.; Gimenez, S.

    2015-09-01

    ANIS (AstroNomical Information System) is a web generic tool developed at CeSAM to facilitate and standardize the implementation of astronomical data of various kinds through private and/or public dedicated Information Systems. The architecture of ANIS is composed of a database server which contains the project data, a web user interface template which provides high level services (search, extract and display imaging and spectroscopic data using a combination of criteria, an object list, a sql query module or a cone search interfaces), a framework composed of several packages, and a metadata database managed by a web administration entity. The process to implement a new ANIS instance at CeSAM is easy and fast : the scientific project has to submit data or a data secure access, the CeSAM team installs the new instance (web interface template and the metadata database), and the project administrator can configure the instance with the web ANIS-administration entity. Currently, the CeSAM offers through ANIS a web access to VO compliant Information Systems for different projects (HeDaM, HST-COSMOS, CFHTLS-ZPhots, ExoDAT,...).

  9. The Sam-Sam interaction between Ship2 and the EphA2 receptor: design and analysis of peptide inhibitors.

    Science.gov (United States)

    Mercurio, Flavia Anna; Di Natale, Concetta; Pirone, Luciano; Iannitti, Roberta; Marasco, Daniela; Pedone, Emilia Maria; Palumbo, Rosanna; Leone, Marilisa

    2017-12-12

    The lipid phosphatase Ship2 represents a drug discovery target for the treatment of different diseases, including cancer. Its C-terminal sterile alpha motif domain (Ship2-Sam) associates with the Sam domain from the EphA2 receptor (EphA2-Sam). This interaction is expected to mainly induce pro-oncogenic effects in cells therefore, inhibition of the Ship2-Sam/EphA2-Sam complex may represent an innovative route to discover anti-cancer therapeutics. In the present work, we designed and analyzed several peptide sequences encompassing the interaction interface of EphA2-Sam for Ship2-Sam. Peptide conformational analyses and interaction assays with Ship2-Sam conducted through diverse techniques (CD, NMR, SPR and MST), identified a positively charged penta-amino acid native motif in EphA2-Sam, that once repeated three times in tandem, binds Ship2-Sam. NMR experiments show that the peptide targets the negatively charged binding site of Ship2-Sam for EphA2-Sam. Preliminary in vitro cell-based assays indicate that -at 50 µM concentration- it induces necrosis of PC-3 prostate cancer cells with more cytotoxic effect on cancer cells than on normal dermal fibroblasts. This work represents a pioneering study that opens further opportunities for the development of inhibitors of the Ship2-Sam/EphA2-Sam complex for therapeutic applications.

  10. Recent Updates to the System Advisor Model (SAM)

    Energy Technology Data Exchange (ETDEWEB)

    DiOrio, Nicholas A [National Renewable Energy Laboratory (NREL), Golden, CO (United States)

    2018-02-14

    The System Advisor Model (SAM) is a mature suite of techno-economic models for many renewable energy technologies that can be downloaded for free as a desktop application or software development kit. SAM is used for system-level modeling, including generating performance pro the release of the code as an open source project on GitHub. Other additions that will be covered include the ability to download data directly into SAM from the National Solar Radiation Database (NSRDB) and up- dates to a user-interface macro that assists with PV system sizing. A brief update on SAM's battery model and its integration with the detailed photovoltaic model will also be discussed. Finally, an outline of planned work for the next year will be presented, including the addition of a bifacial model, support for multiple MPPT inputs for detailed inverter modeling, and the addition of a model for inverter thermal behavior.

  11. SAM Photovoltaic Model Technical Reference 2016 Update

    Energy Technology Data Exchange (ETDEWEB)

    Gilman, Paul [National Renewable Energy Laboratory (NREL), Golden, CO (United States); DiOrio, Nicholas A [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Freeman, Janine M [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Janzou, Steven [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Dobos, Aron [No longer NREL employee; Ryberg, David [No longer NREL employee

    2018-03-19

    This manual describes the photovoltaic performance model in the System Advisor Model (SAM) software, Version 2016.3.14 Revision 4 (SSC Version 160). It is an update to the 2015 edition of the manual, which describes the photovoltaic model in SAM 2015.1.30 (SSC 41). This new edition includes corrections of errors in the 2015 edition and descriptions of new features introduced in SAM 2016.3.14, including: 3D shade calculator Battery storage model DC power optimizer loss inputs Snow loss model Plane-of-array irradiance input from weather file option Support for sub-hourly simulations Self-shading works with all four subarrays, and uses same algorithm for fixed arrays and one-axis tracking Linear self-shading algorithm for thin-film modules Loss percentages replace derate factors. The photovoltaic performance model is one of the modules in the SAM Simulation Core (SSC), which is part of both SAM and the SAM SDK. SAM is a user-friedly desktop application for analysis of renewable energy projects. The SAM SDK (Software Development Kit) is for developers writing their own renewable energy analysis software based on SSC. This manual is written for users of both SAM and the SAM SDK wanting to learn more about the details of SAM's photovoltaic model.

  12. Coastal lagoon sediments and benthic foraminifera as indicator for Holocene sea-level change: Samsø, southern Kattegat

    DEFF Research Database (Denmark)

    Sander, Lasse; Morigi, Caterina; Pejrup, Morten

    The island of Samsø is located in the southern Kattegat region of Denmark, a relatively sheltered micro-tidal environment. The area experienced a period of rapid transgression during the early Altantic period, reaching its maximum approx. 7,600 yr BP. Since then, isostatic uplift gradually caused....... Over time, an extensive beach ridge system formed, which eventually connected the islands, giving Samsø its characteristic shape. Ephemeral shallow-water lagoons evolved in topographic depressions along the shores of the island, most of which became inactive until today. A semi-enclosed coastal lagoon......-level and to investigate associated geomorphic responses in coastal lagoon and beach ridge systems. Vibracorings will be carried out in these sedimentary environments and will be supplemented with manual auger corings and ground penetrating radar (GPR) surveys to assess vertical variations in the deposited sediments...

  13. Redox Behavior of the S-Adenosylmethionine (SAM)-Binding Fe-S Cluster in Methylthiotransferase RimO, toward Understanding Dual SAM Activity.

    Science.gov (United States)

    Molle, Thibaut; Moreau, Yohann; Clemancey, Martin; Forouhar, Farhad; Ravanat, Jean-Luc; Duraffourg, Nicolas; Fourmond, Vincent; Latour, Jean-Marc; Gambarelli, Serge; Mulliez, Etienne; Atta, Mohamed

    2016-10-18

    RimO, a radical-S-adenosylmethionine (SAM) enzyme, catalyzes the specific C 3 methylthiolation of the D89 residue in the ribosomal S 12 protein. Two intact iron-sulfur clusters and two SAM cofactors both are required for catalysis. By using electron paramagnetic resonance, Mössbauer spectroscopies, and site-directed mutagenesis, we show how two SAM molecules sequentially bind to the unique iron site of the radical-SAM cluster for two distinct chemical reactions in RimO. Our data establish that the two SAM molecules bind the radical-SAM cluster to the unique iron site, and spectroscopic evidence obtained under strongly reducing conditions supports a mechanism in which the first molecule of SAM causes the reoxidation of the reduced radical-SAM cluster, impeding reductive cleavage of SAM to occur and allowing SAM to methylate a HS - ligand bound to the additional cluster. Furthermore, by using density functional theory-based methods, we provide a description of the reaction mechanism that predicts the attack of the carbon radical substrate on the methylthio group attached to the additional [4Fe-4S] cluster.

  14. CareSam

    DEFF Research Database (Denmark)

    Liveng, Anne; Christensen, Jonas

    2016-01-01

    negative cultural perceptions of help-needing elderly and the people who support them in everyday life? In answering these questions and thereby reflecting on our own work process we apply a caring, a learning and a political perspective. Hereby the article wishes to formulate a methodological point...... to maintain immediately conflicting dimensions in this kind of work.......This article presents findings and discussions generated on the basis of the Danish-Swedish development project CareSam. The article will on the one hand focus on how work in groups consisting of representatives from different levels in the elderly care sector at one time served as learning spaces...

  15. SAM International Case Studies: DPV Analysis in Mexico

    Energy Technology Data Exchange (ETDEWEB)

    McCall, James D [National Renewable Energy Laboratory (NREL), Golden, CO (United States)

    2018-03-28

    Presentation demonstrates the use of the System Advisor Model (SAM) in international analyses, specifically Mexico. Two analyses are discussed with relation to SAM modelling efforts: 1) Customer impacts from changes to net metering and billing agreements and 2) Potential benefits of PV for Mexican solar customers, the Mexican Treasury, and the environment. Along with the SAM analyses, integration of the International Utility Rate Database (I-URDB) with SAM and future international SAM work are discussed. Presentation was created for the International Solar Energy Society's (ISES) webinar titled 'International use of the NREL System Advisor Model (SAM) with case studies'.

  16. ASAMPSA-E guidance for level 2 PSA Volume 3. Verification and improvement of SAM strategies with L2 PSA

    International Nuclear Information System (INIS)

    Rahni, N.; Raimond, E.; Jan, P.; Lopez, J.; Loeffler, H.; Mildenberger, O.; Kubicek, J.; Vitazkova, J.; Ivanov, I.; Groudev, P.; Lajtha, G.; Serrano, C.; Zhabin, O.; Prosek, Andrej; Dirksen, G.; Yu, S.; Oury, L.; Hultqvist, G.

    2016-01-01

    For each NPP, severe accident management (SAM) strategies shall make use of components or systems and human resources to limit as far as possible the consequences of any severe accident on-site and off-site. L2 PSA is one of the tools that can be used to verify and improve these strategies. The present report (deliverable D40.5 of the project ASAMPSA-E) provides an opportunity for a comparison of objectives in the different countries in terms of SAM strategies verification and improvement. The report summarizes also experience of each partner (including potential deficiencies) involved in this activity, in order to derive some good practices and required progress, addressing: - SAM modeling in L2 PSA, - Positive and negative aspects in current SAM practices, - Discussion on possible criteria related to L2 PSA for verification and improvement: risk reduction (in relation with WP30 activities on risk metrics), reduction of uncertainties on the severe accident progression paths until NPP stabilization, reduction of human failure conditional probabilities (depending on the SAM strategy, the environmental conditions...), - Review with a perspective of verification and improvement of the main SAM strategies (corium cooling, RCS depressurization, control of flammable gases, reactivity control, containment function, containment pressure control, limitation of radioactive releases,...), - SAM strategies to be considered in the context of an extended L2 PSA (as far possible, depending on existing experience), taking into account all operating modes, accidents also occurring in the SFPs and long term and multi-unit accidents. The deliverable D40.5 is developed from the partners' experience. Many of the topics described here are beyond the common practices of L2 PSA applications: in some countries, L2 PSA application is limited to the calculations of frequencies of release categories with no formal requirement for SAM verification and improvement. (authors)

  17. Regulation of gene expression by low levels of ultraviolet-B radiation in Pisum sativum: Isolation of novel genes by suppression subtractive hybridisation

    International Nuclear Information System (INIS)

    Sävenstrand, H.; Brosché, M.; Strid, A.

    2002-01-01

    Suppression subtractive hybridisation was used to isolate genes differentially regulated by low levels (UV-B BE,300 0.13 W m -2 ) of ultraviolet-B radiation (UV-B; 290–320 nm) in Pisum sativum. Six genes were regulated, two of which were novel. The mRNA levels for these two (PsTSDC and PsUOS1) were increased and depressed by UV-B treatment, respectively. Domains in the PsTSDC translation product was similar to TIR (Toll-Interleukin-1 receptor-similar) domains and a NB-ARC domain (nucleotide-binding domain in APAF-1, R gene products and CED-4). The PsUOS1 translation product was similar to an open reading frame in Arabidopsis. Genes encoding embryo-abundant protein (PsEMB) and S-adenosyl-l-methionine synthase (PsSAMS) were induced by UV-B, whereas the transcript levels for genes encoding sucrose transport protein (PsSUT) or ribulose-5-phosphate 3-epimerase (PsR5P3E) were decreased. These regulation patterns are novel, and the PsEMB and PsR5P3E sequences are reported for the first time. The stress-specificity of regulation of these genes were tested by ozone fumigation (100 ppb O 3 ). Qualitatively, the similarity of expression after both UV-B and ozone exposure suggests that, for these genes, similar stress-response pathways are in action. (author)

  18. Automated one-loop calculations with GoSam

    International Nuclear Information System (INIS)

    Cullen, Gavin; Greiner, Nicolas; Heinrich, Gudrun; Reiter, Thomas; Luisoni, Gionata; Mastrolia, Pierpaolo; Ossola, Giovanni; Tramontano, Francesco

    2012-01-01

    We present the program package GoSam which is designed for the automated calculation of one-loop amplitudes for multi-particle processes in renormalisable quantum field theories. The amplitudes, which are generated in terms of Feynman diagrams, can be reduced using either D-dimensional integrand-level decomposition or tensor reduction. GoSam can be used to calculate one-loop QCD and/or electroweak corrections to Standard Model processes and offers the flexibility to link model files for theories Beyond the Standard Model. A standard interface to programs calculating real radiation is also implemented. We demonstrate the flexibility of the program by presenting examples of processes with up to six external legs attached to the loop. (orig.)

  19. Automated One-Loop Calculations with GoSam

    CERN Document Server

    Cullen, Gavin; Heinrich, Gudrun; Luisoni, Gionata; Mastrolia, Pierpaolo; Ossola, Giovanni; Reiter, Thomas; Tramontano, Francesco

    2012-01-01

    We present the program package GoSam which is designed for the automated calculation of one-loop amplitudes for multi-particle processes in renormalisable quantum field theories. The amplitudes, which are generated in terms of Feynman diagrams, can be reduced using either D-dimensional integrand-level decomposition or tensor reduction. GoSam can be used to calculate one-loop QCD and/or electroweak corrections to Standard Model processes and offers the flexibility to link model files for theories Beyond the Standard Model. A standard interface to programs calculating real radiation is also implemented. We demonstrate the flexibility of the program by presenting examples of processes with up to six external legs attached to the loop.

  20. Samsø Energy Vision 2030

    DEFF Research Database (Denmark)

    Mathiesen, Brian Vad; Hansen, Kenneth; Ridjan, Iva

    The purpose of this report is to investigate potential scenarios for converting Samsø into 100% renewable energy supply in 2030 with focus on local electricity and biomass resources. Firstly, a 2013 reference scenario is established to investigate whether Samsø is 100% renewable today. Next, scen...

  1. Generation of induced pluripotent stem cells (iPSCs) stably expressing CRISPR-based synergistic activation mediator (SAM)

    DEFF Research Database (Denmark)

    Xiong, Kai; Zhou, Yan; Hyttel, Poul

    2016-01-01

    Human fibroblasts were engineered to express the CRISPR-based synergistic activation mediator (SAM) complex: dCas9-VP64 and MS2-P65-HSF1. Two induced pluripotent stem cells (iPSCs) clones expressing SAM were established by transducing these fibroblasts with lentivirus expressing OCT4, SOX2, KLF4...... a novel, useful tool to investigate genetic regulation of stem cell proliferation and differentiation through CRISPR-mediated activation of endogenous genes....

  2. System for Award Management (SAM) API

    Data.gov (United States)

    General Services Administration — The SAM API is a RESTful method of retrieving public information about the businesses, organizations, or individuals (referred to as entities) within the SAM entity...

  3. 78 FR 62627 - Sam Rayburn Dam Rate

    Science.gov (United States)

    2013-10-22

    ..., Wholesale Rates for Hydro Power and Energy Sold to Sam Rayburn Dam Electric Cooperative, Inc. (Contract No... Schedule SRD-08, Wholesale Rates for Hydro Power and Energy Sold to Sam Rayburn Dam Electric Cooperative... ADMINISTRATION RATE SCHEDULE SRD-13 \\1\\ WHOLESALE RATES FOR HYDRO POWER AND ENERGY SOLD TO SAM RAYBURN DAM...

  4. System Advisor Model, SAM 2014.1.14: General Description

    Energy Technology Data Exchange (ETDEWEB)

    Blair, Nate [National Renewable Energy Lab. (NREL), Golden, CO (United States); Dobos, Aron P. [National Renewable Energy Lab. (NREL), Golden, CO (United States); Freeman, Janine [National Renewable Energy Lab. (NREL), Golden, CO (United States); Neises, Ty [National Renewable Energy Lab. (NREL), Golden, CO (United States); Wagner, Michael [National Renewable Energy Lab. (NREL), Golden, CO (United States); Ferguson, Tom [Global Resources, Northbrook, IL (United States); Gilman, Paul [National Renewable Energy Lab. (NREL), Golden, CO (United States); Janzou, Steven [Janzou Consulting, Idaho Springs, CO (United States)

    2014-02-01

    This document describes the capabilities of the U.S. Department of Energy and National Renewable Energy Laboratory's System Advisor Model (SAM), Version 2013.9.20, released on September 9, 2013. SAM is a computer model that calculates performance and financial metrics of renewable energy systems. Project developers, policy makers, equipment manufacturers, and researchers use graphs and tables of SAM results in the process of evaluating financial, technology, and incentive options for renewable energy projects. SAM simulates the performance of photovoltaic, concentrating solar power, solar water heating, wind, geothermal, biomass, and conventional power systems. The financial model can represent financial structures for projects that either buy and sell electricity at retail rates (residential and commercial) or sell electricity at a price determined in a power purchase agreement (utility). SAM's advanced simulation options facilitate parametric and sensitivity analyses, and statistical analysis capabilities are available for Monte Carlo simulation and weather variability (P50/P90) studies. SAM can also read input variables from Microsoft Excel worksheets. For software developers, the SAM software development kit (SDK) makes it possible to use SAM simulation modules in their applications written in C/C++, C#, Java, Python, and MATLAB. NREL provides both SAM and the SDK as free downloads at http://sam.nrel.gov. Technical support and more information about the software are available on the website.

  5. GoSam. A program for automated one-loop calculations

    Energy Technology Data Exchange (ETDEWEB)

    Cullen, G. [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany); Greiner, N.; Heinrich, G.; Reiter, T. [Max-Planck-Institut fuer Physik, Muenchen (Germany); Luisoni, G. [Durham Univ. (United Kingdom). Inst. for Particle Physics Phenomenology; Mastrolia, P. [Max-Planck-Institut fuer Physik, Muenchen (Germany); Padua Univ. (Italy). Dipt. di Fisica; Ossola, G. [City Univ. of New York, NY (United States). New York City College of Technology; Tramontano, F. [European Organization for Nuclear Research (CERN), Geneva (Switzerland)

    2011-11-15

    The program package GoSam is presented which aims at the automated calculation of one-loop amplitudes for multi-particle processes. The amplitudes are generated in terms of Feynman diagrams and can be reduced using either D-dimensional integrand-level decomposition or tensor reduction, or a combination of both. GoSam can be used to calculate one-loop corrections to both QCD and electroweak theory, and model files for theories Beyond the Standard Model can be linked as well. A standard interface to programs calculating real radiation is also included. The flexibility of the program is demonstrated by various examples. (orig.)

  6. GoSam. A program for automated one-loop calculations

    International Nuclear Information System (INIS)

    Cullen, G.; Greiner, N.; Heinrich, G.; Reiter, T.; Luisoni, G.

    2011-11-01

    The program package GoSam is presented which aims at the automated calculation of one-loop amplitudes for multi-particle processes. The amplitudes are generated in terms of Feynman diagrams and can be reduced using either D-dimensional integrand-level decomposition or tensor reduction, or a combination of both. GoSam can be used to calculate one-loop corrections to both QCD and electroweak theory, and model files for theories Beyond the Standard Model can be linked as well. A standard interface to programs calculating real radiation is also included. The flexibility of the program is demonstrated by various examples. (orig.)

  7. GoSam: A program for automated one-loop calculations

    International Nuclear Information System (INIS)

    Cullen, G; Greiner, N; Heinrich, G; Mastrolia, P; Reiter, T; Luisoni, G; Ossola, G; Tramontano, F

    2012-01-01

    The program package GoSam is presented which aims at the automated calculation of one-loop amplitudes for multi-particle processes. The amplitudes are generated in terms of Feynman diagrams and can be reduced using either D-dimensional integrand-level decomposition or tensor reduction, or a combination of both. GoSam can be used to calculate one-loop corrections to both QCD and electroweak theory, and model files for theories Beyond the Standard Model can be linked as well. A standard interface to programs calculating real radiation is also included. The flexibility of the program is demonstrated by various examples.

  8. 核蛋白Sam68的原核表达及鉴定%Prokaryotic Expression and Identification of Nuclear Protein Sam68

    Institute of Scientific and Technical Information of China (English)

    张华; 陈宁; 丁筠; 邹德华; 潘子夜; 李鹏飞; 李丽阳; 肖丽杰; 曹宏伟

    2017-01-01

    为了构建pGEX-4T-1-Sam68原核表达载体,表达并鉴定GST-Sam68融合蛋白,采用PCR扩增Sam68基因,插入pGEX-4T-1的EcoR I和Sal I位点,并转化Rosetta(DE3)大肠杆菌,IPTG诱导表达,SDS-PAGE和Western Blot验证蛋白表达,GST pull-down技术验证Sam68的结合活性.酶切和测序结果证实Sam68基因正确插入pGEX-4T-1载体中,载体能够在Rosetta(DE3)细胞中正确表达,且纯化的GST-Sam68蛋白具有与PI3K p85特异结合的活性,说明成功构建了原核表达载体pGEX-4T-1-Sam68.

  9. Storifying Samsøs Renewable Energy Transition

    DEFF Research Database (Denmark)

    Papazu, Irina

    2018-01-01

    Through a joint community effort Denmark’s Renewable Energy Island Samsø became self-sufficient with renewable energy over a period of 10 years from 1997 to 2007. Today, the story about Samsø’s successful energy transition has become a global export and a widely known model of community building...... the effects of such well-crafted transition narratives. This tendency toward the ‘storification’ of transition processes is not restricted to Samsø; it is employed as a tactics by environmental organizations operating globally....

  10. Experimental and computational investigation of graphene/SAMs/n-Si Schottky diodes

    Science.gov (United States)

    Aydin, H.; Bacaksiz, C.; Yagmurcukardes, N.; Karakaya, C.; Mermer, O.; Can, M.; Senger, R. T.; Sahin, H.; Selamet, Y.

    2018-01-01

    We have investigated the effect of two different self-assembled monolayers (SAMs) on electrical characteristics of bilayer graphene (BLG)/n-Si Schottky diodes. Novel 4″bis(diphenylamino)-1, 1‧:3″-terphenyl-5‧ carboxylic acids (TPA) and 4,4-di-9H-carbazol-9-yl-1,1‧:3‧1‧-terphenyl-5‧ carboxylic acid (CAR) aromatic SAMs have been used to modify n-Si surfaces. Cyclic voltammetry (CV) and Kelvin probe force microscopy (KPFM) results have been evaluated to verify the modification of n-Si surface. The current-voltage (I-V) characteristics of bare and SAMs modified devices show rectification behaviour verifying a Schottky junction at the interface. The ideality factors (n) from ln(I)-V dependences were determined as 2.13, 1.96 and 2.07 for BLG/n-Si, BLG/TPA/n-Si and BLG/CAR/n-Si Schottky diodes, respectively. In addition, Schottky barrier height (SBH) and series resistance (Rs) of SAMs modified diodes were decreased compared to bare diode due to the formation of a compatible interface between graphene and Si as well as π-π interaction between aromatic SAMs and graphene. The CAR-based device exhibits better diode characteristic compared to the TPA-based device. Computational simulations show that the BLG/CAR system exhibits smaller energy-level-differences than the BLG/TPA, which supports the experimental findings of a lower Schottky barrier and series resistance in BLG/CAR diode.

  11. The mthA mutation conferring low-level resistance to streptomycin enhances antibiotic production in Bacillus subtilis by increasing the S-adenosylmethionine pool size.

    Science.gov (United States)

    Tojo, Shigeo; Kim, Ji-Yun; Tanaka, Yukinori; Inaoka, Takashi; Hiraga, Yoshikazu; Ochi, Kozo

    2014-04-01

    Certain Str(r) mutations that confer low-level streptomycin resistance result in the overproduction of antibiotics by Bacillus subtilis. Using comparative genome-sequencing analysis, we successfully identified this novel mutation in B. subtilis as being located in the mthA gene, which encodes S-adenosylhomocysteine/methylthioadenosine nucleosidase, an enzyme involved in the S-adenosylmethionine (SAM)-recycling pathways. Transformation experiments showed that this mthA mutation was responsible for the acquisition of low-level streptomycin resistance and overproduction of bacilysin. The mthA mutant had an elevated level of intracellular SAM, apparently acquired by arresting SAM-recycling pathways. This increase in the SAM level was directly responsible for bacilysin overproduction, as confirmed by forced expression of the metK gene encoding SAM synthetase. The mthA mutation fully exerted its effect on antibiotic overproduction in the genetic background of rel(+) but not the rel mutant, as demonstrated using an mthA relA double mutant. Strikingly, the mthA mutation activated, at the transcription level, even the dormant ability to produce another antibiotic, neotrehalosadiamine, at concentrations of 150 to 200 μg/ml, an antibiotic not produced (antibiotic production, by introducing either the rsmG mutation to Streptomyces or the mthA mutation to eubacteria, since many eubacteria have mthA homologues.

  12. Samâ’ dalam Tradisi Tasawuf

    Directory of Open Access Journals (Sweden)

    Said Aqil Siradj

    2014-01-01

    Full Text Available Samâ‘ in Tasawuf has been a very important element in the dissemination of this spiritual dimension of Islam. Yet, it has received very little both from the practitioners of Tasawuf and its intellectuals. This paper tries to expose this simply in a hope to make it heard in the academic and popular circle. Here, samâ‘ is not only understood as a form of music, as many would do, but also as an art of listening of which music is certainly part. The paper will explore the meaning and definition of this term, putting emphasis on its many-faceted function in the formation and development of one’s soul and spirituality. It is argued that soul is musical and artistic. Using art and music to talk to soul is therefore the proper way and means. The paper will also try to show that samâ‘ is also an indispensable part of spiritual method to reach and know God. Knowledge of God in other words, can be gained through this practice. Hence, samâ‘ is treated not only as a form of entertainment, but also a kind of practical epistemology.

  13. Robust gene selection methods using weighting schemes for microarray data analysis.

    Science.gov (United States)

    Kang, Suyeon; Song, Jongwoo

    2017-09-02

    A common task in microarray data analysis is to identify informative genes that are differentially expressed between two different states. Owing to the high-dimensional nature of microarray data, identification of significant genes has been essential in analyzing the data. However, the performances of many gene selection techniques are highly dependent on the experimental conditions, such as the presence of measurement error or a limited number of sample replicates. We have proposed new filter-based gene selection techniques, by applying a simple modification to significance analysis of microarrays (SAM). To prove the effectiveness of the proposed method, we considered a series of synthetic datasets with different noise levels and sample sizes along with two real datasets. The following findings were made. First, our proposed methods outperform conventional methods for all simulation set-ups. In particular, our methods are much better when the given data are noisy and sample size is small. They showed relatively robust performance regardless of noise level and sample size, whereas the performance of SAM became significantly worse as the noise level became high or sample size decreased. When sufficient sample replicates were available, SAM and our methods showed similar performance. Finally, our proposed methods are competitive with traditional methods in classification tasks for microarrays. The results of simulation study and real data analysis have demonstrated that our proposed methods are effective for detecting significant genes and classification tasks, especially when the given data are noisy or have few sample replicates. By employing weighting schemes, we can obtain robust and reliable results for microarray data analysis.

  14. AhR and SHP regulate phosphatidylcholine and S-adenosylmethionine levels in the one-carbon cycle.

    Science.gov (United States)

    Kim, Young-Chae; Seok, Sunmi; Byun, Sangwon; Kong, Bo; Zhang, Yang; Guo, Grace; Xie, Wen; Ma, Jian; Kemper, Byron; Kemper, Jongsook Kim

    2018-02-07

    Phosphatidylcholines (PC) and S-adenosylmethionine (SAM) are critical determinants of hepatic lipid levels, but how their levels are regulated is unclear. Here, we show that Pemt and Gnmt, key one-carbon cycle genes regulating PC/SAM levels, are downregulated after feeding, leading to decreased PC and increased SAM levels, but these effects are blunted in small heterodimer partner (SHP)-null or FGF15-null mice. Further, aryl hydrocarbon receptor (AhR) is translocated into the nucleus by insulin/PKB signaling in the early fed state and induces Pemt and Gnmt expression. This induction is blocked by FGF15 signaling-activated SHP in the late fed state. Adenoviral-mediated expression of AhR in obese mice increases PC levels and exacerbates steatosis, effects that are blunted by SHP co-expression or Pemt downregulation. PEMT, AHR, and PC levels are elevated in simple steatosis patients, but PC levels are robustly reduced in steatohepatitis-fibrosis patients. This study identifies AhR and SHP as new physiological regulators of PC/SAM levels.

  15. Electronic patient self-assessment and management (SAM): a novel framework for cancer survivorship.

    Science.gov (United States)

    Vickers, Andrew J; Salz, Talya; Basch, Ethan; Cooperberg, Matthew R; Carroll, Peter R; Tighe, Foss; Eastham, James; Rosen, Raymond C

    2010-06-17

    We propose a novel framework for management of cancer survivorship: electronic patient Self-Assessment and Management (SAM). SAM is a framework for transfer of information to and from patients in such a way as to increase both the patient's and the health care provider's understanding of the patient's progress, and to help ensure that patient care follows best practice. Patients who participate in the SAM system are contacted by email at regular intervals and asked to complete validated questionnaires online. Patient responses on these questionnaires are then analyzed in order to provide patients with real-time, online information about their progress and to provide them with tailored and standardized medical advice. Patient-level data from the questionnaires are ported in real time to the patient's health care provider to be uploaded to clinic notes. An initial version of SAM has been developed at Memorial Sloan-Kettering Cancer Center (MSKCC) and the University of California, San Francisco (UCSF) for aiding the clinical management of patients after surgery for prostate cancer. Pilot testing at MSKCC and UCSF suggests that implementation of SAM systems are feasible, with no major problems with compliance (> 70% response rate) or security. SAM is a conceptually simple framework for passing information to and from patients in such a way as to increase both the patient's and the health care provider's understanding of the patient's progress, and to help ensure that patient care follows best practice.

  16. Electronic patient self-assessment and management (SAM: a novel framework for cancer survivorship

    Directory of Open Access Journals (Sweden)

    Tighe Foss

    2010-06-01

    Full Text Available Abstract Background We propose a novel framework for management of cancer survivorship: electronic patient Self-Assessment and Management (SAM. SAM is a framework for transfer of information to and from patients in such a way as to increase both the patient's and the health care provider's understanding of the patient's progress, and to help ensure that patient care follows best practice. Methods Patients who participate in the SAM system are contacted by email at regular intervals and asked to complete validated questionnaires online. Patient responses on these questionnaires are then analyzed in order to provide patients with real-time, online information about their progress and to provide them with tailored and standardized medical advice. Patient-level data from the questionnaires are ported in real time to the patient's health care provider to be uploaded to clinic notes. An initial version of SAM has been developed at Memorial Sloan-Kettering Cancer Center (MSKCC and the University of California, San Francisco (UCSF for aiding the clinical management of patients after surgery for prostate cancer. Results Pilot testing at MSKCC and UCSF suggests that implementation of SAM systems are feasible, with no major problems with compliance (> 70% response rate or security. Conclusion SAM is a conceptually simple framework for passing information to and from patients in such a way as to increase both the patient's and the health care provider's understanding of the patient's progress, and to help ensure that patient care follows best practice.

  17. Targeting EphA2-Sam and Its Interactome: Design and Evaluation of Helical Peptides Enriched in Charged Residues.

    Science.gov (United States)

    Mercurio, Flavia A; Marasco, Daniela; Di Natale, Concetta; Pirone, Luciano; Costantini, Susan; Pedone, Emilia M; Leone, Marilisa

    2016-11-17

    The EphA2 receptor controls diverse physiological and pathological conditions and its levels are often upregulated in cancer. Targeting receptor overexpression, through modulation of endocytosis and consequent degradation, appears to be an appealing strategy for attacking tumor malignancy. In this scenario, the Sam domain of EphA2 plays a pivotal role because it is the site where protein regulators of endocytosis and stability are recruited by means of heterotypic Sam-Sam interactions. Because EphA2-Sam heterotypic complexes are largely based on electrostatic contacts, we have investigated the possibility of attacking these interactions with helical peptides enriched in charged residues. Several peptide sequences with high predicted helical propensities were designed, and detailed conformational analyses were conducted by diverse techniques including NMR, CD, and molecular dynamics (MD) simulations. Interaction studies were also performed by NMR, surface plasmon resonance (SPR), and microscale thermophoresis (MST) and led to the identification of two peptides capable of binding to the first Sam domain of Odin. These molecules represent early candidates for the generation of efficient Sam domain binders and antagonists of Sam-Sam interactions involving EphA2. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. The nuclear protein Sam68 is cleaved by the FMDV 3C protease redistributing Sam68 to the cytoplasm during FMDV infection of host cells

    International Nuclear Information System (INIS)

    Lawrence, Paul; Schafer, Elizabeth A.; Rieder, Elizabeth

    2012-01-01

    Picornavirus infection can lead to disruption of nuclear pore traffic, shut-off of cell translation machinery, and cleavage of proteins involved in cellular signal transduction and the innate response to infection. Here, we demonstrated that the FMDV 3C pro induced the cleavage of nuclear RNA-binding protein Sam68 C-terminus containing the nuclear localization sequence (NLS). Consequently, it stimulated the redistribution of Sam68 to the cytoplasm. The siRNA knockdown of Sam68 resulted in a 1000-fold reduction in viral titers, which prompted us to study the effect of Sam68 on FMDV post-entry events. Interestingly, Sam68 interacts with the internal ribosomal entry site within the 5′ non-translated region of the FMDV genome, and Sam68 knockdown decreased FMDV IRES-driven activity in vitro suggesting that it could modulate translation of the viral genome. The results uncover a novel role for Sam68 in the context of picornaviruses and the proteolysis of a new cellular target of the FMDV 3C pro .

  19. Technical Manual for the SAM Physical Trough Model

    Energy Technology Data Exchange (ETDEWEB)

    Wagner, M. J.; Gilman, P.

    2011-06-01

    NREL, in conjunction with Sandia National Lab and the U.S Department of Energy, developed the System Advisor Model (SAM) analysis tool for renewable energy system performance and economic analysis. This paper documents the technical background and engineering formulation for one of SAM's two parabolic trough system models in SAM. The Physical Trough model calculates performance relationships based on physical first principles where possible, allowing the modeler to predict electricity production for a wider range of component geometries than is possible in the Empirical Trough model. This document describes the major parabolic trough plant subsystems in detail including the solar field, power block, thermal storage, piping, auxiliary heating, and control systems. This model makes use of both existing subsystem performance modeling approaches, and new approaches developed specifically for SAM.

  20. The two umuDC-like operons, samAB and umuDCST, in Salmonella typhimurium: The umuDCST operon may reduce UV-mutagenesis-promoting ability of the samAB operon

    International Nuclear Information System (INIS)

    Nohmi, Takehiko; Hakura, Atsushi; Watanabe, Masahiko; Yamada, Masami; Sofuni, Toshio; Nakai, Yasuharu; Murayama, Somay Y.

    1993-01-01

    Salmonella typhimurium, especially its derivatives containing pKM101 plasmid, has been widely used in the Ames test for the detection of environmental mutagens and carcinogens. It is known, however, that if the pKM101 plasmid is eliminated, S. typhimurium itself shows a much weaker mutagenic response to UV and some chemical mutagens than does Escherichia coli. In fact, certain potent base-change type mutagens, such as furylfuramide and aflatoxin B 1 , are nonmutagenic to S. typhimurium in the absence of pKM101, whereas they are strongly mutagenic to S. typhimurium in the presence of pKM101 plasmid as well as to E. coli. The low mutability can be restored to levels comparable to E. coli by introducing the plasmid carrying the E. coli umuDC operon or the pKM101 plasmid carrying mucAB operon. Salmonella typhimurium has an SOS regulatory system which resembles that of E. coli. Thus, it was suggested that S. typhimurium is deficient in the function of umuDC operon, which plays an essential role in UV and most chemical mutagenesis in E. coli. In order to clarify the implications of umuDC genes in mutagenesis and antimutagenesis in typhimurium, we have independently screened the umuDC-like genes of S. typhimurium TA1538. Consequently, we have cloned another umuDC-like operon which is 40% diverged from the aforementioned umuDC operon of S. typhimurium LT2 at the nucleotide level (16). We have termed the cloned DNA the samAB (Salmonella; mutagenesis) operon, and tentatively referred to the umuDC operon cloned from S. typhimurium LT2 (27,31) as the umuDC ST operon. Based on the results of the Southern hybridization experiment, we concluded that the two sets of umuDC-like operons reside in the same cells of S. typhimurium LT2 and TA1538. Our results also suggested that the umuDC ST operon reduces the UV-mutagenesis promoting ability of the samAB operon when the two operons are present on the same multi-copy number plasmid

  1. Structural basis of RNA recognition and dimerization by the STAR proteins T-STAR and Sam68

    Science.gov (United States)

    Feracci, Mikael; Foot, Jaelle N.; Grellscheid, Sushma N.; Danilenko, Marina; Stehle, Ralf; Gonchar, Oksana; Kang, Hyun-Seo; Dalgliesh, Caroline; Meyer, N. Helge; Liu, Yilei; Lahat, Albert; Sattler, Michael; Eperon, Ian C.; Elliott, David J.; Dominguez, Cyril

    2016-01-01

    Sam68 and T-STAR are members of the STAR family of proteins that directly link signal transduction with post-transcriptional gene regulation. Sam68 controls the alternative splicing of many oncogenic proteins. T-STAR is a tissue-specific paralogue that regulates the alternative splicing of neuronal pre-mRNAs. STAR proteins differ from most splicing factors, in that they contain a single RNA-binding domain. Their specificity of RNA recognition is thought to arise from their property to homodimerize, but how dimerization influences their function remains unknown. Here, we establish at atomic resolution how T-STAR and Sam68 bind to RNA, revealing an unexpected mode of dimerization different from other members of the STAR family. We further demonstrate that this unique dimerization interface is crucial for their biological activity in splicing regulation, and suggest that the increased RNA affinity through dimer formation is a crucial parameter enabling these proteins to select their functional targets within the transcriptome. PMID:26758068

  2. Bringing a Chemical Laboratory Named Sam to Mars on the 2011 Curiosity Rover

    Science.gov (United States)

    Mahaffy, P. R.; Bleacher, L.; Jones, A.; Atreya, S. K.; Manning, H. L.; Cabane, M.; Webster, C. R.; Sam Team

    2010-12-01

    Introduction: An important goal of upcoming missions to Mars is to understand if life could have developed there. The task of the Sample Analysis at Mars (SAM) suite of instruments [1] and the other Curiosity investigations [2] is to move us steadily toward that goal with an assessment of the habitability of our neighboring planet through a series of chemical and geological measurements. SAM is designed to search for organic compounds and inorganic volatiles and measure isotope ratios. Other instruments on Curiosity will provide elemental analysis and identify minerals. SAM will analyze both atmospheric samples and gases evolved from powdered rocks that may have formed billions of years ago with Curiosity providing access to interesting sites scouted by orbiting cameras and spectrometers. SAM Instrument Suite: SAM’s instruments are a Quadrupole Mass Spectrometer (QMS), a 6-column Gas Chromatograph (GC), and a 2-channel Tunable Laser Spectrometer (TLS). SAM can identify organic compounds in Mars rocks to sub-ppb sensitivity and secure precise isotope ratios for C, H, and O in carbon dioxide and water and measure trace levels of methane and its carbon 13 isotope. The SAM gas processing system consists of valves, heaters, pressure sensors, gas scrubbers and getters, traps, and gas tanks used for calibration or combustion experiments [2]. A variety of calibrant compounds interior and exterior to SAM will allow the science and engineering teams to assess SAM’s performance. SAM has been calibrated and tested in a Mars-like environment. Keeping Educators and the Public Informed: The Education and Public Outreach (EPO) goals of the SAM team are to make this complex chemical laboratory and its data widely available to educators, students, and the public. Formal education activities include developing templates for professional development workshops for educators to teach them about SAM and Curiosity, incorporating data into Mars Student Data Teams, and writing articles

  3. 78 FR 47695 - Sam Rayburn Dam Power Rate

    Science.gov (United States)

    2013-08-06

    ... DEPARTMENT OF ENERGY Southwestern Power Administration Sam Rayburn Dam Power Rate AGENCY: Southwestern Power Administration, DOE. ACTION: Notice of public review and comment. SUMMARY: The current Sam..., Southwestern Power Administration (Southwestern), has prepared Current and Revised 2013 Power Repayment Studies...

  4. Curiosity's Sample Analysis at Mars (SAM) Investigation: Overview of Results from the First 120 Sols on Mars

    Science.gov (United States)

    Mahaffy, P. R.; Cabane, M.; Webster, C. R.; Archer, P. D.; Atreya, S. K.; Benna, M.; Brinckerhoff, W. B.; Brunner, A. E.; Buch, A.; Coll, P.; hide

    2013-01-01

    During the first 120 sols of Curiosity s landed mission on Mars (8/6/2012 to 12/7/2012) SAM sampled the atmosphere 9 times and an eolian bedform named Rocknest 4 times. The atmospheric experiments utilized SAM s quadrupole mass spectrometer (QMS) and tunable laser spectrometer (TLS) while the solid sample experiments also utilized the gas chromatograph (GC). Although a number of core experiments were pre-programmed and stored in EEProm, a high level SAM scripting language enabled the team to optimize experiments based on prior runs.

  5. Serum estradiol levels associated with specific gene expression patterns in normal breast tissue and in breast carcinomas

    International Nuclear Information System (INIS)

    Haakensen, Vilde D; Børresen-Dale, Anne-Lise; Helland, Åslaug; Bjøro, Trine; Lüders, Torben; Riis, Margit; Bukholm, Ida K; Kristensen, Vessela N; Troester, Melissa A; Homen, Marit M; Ursin, Giske

    2011-01-01

    High serum levels of estradiol are associated with increased risk of postmenopausal breast cancer. Little is known about the gene expression in normal breast tissue in relation to levels of circulating serum estradiol. We compared whole genome expression data of breast tissue samples with serum hormone levels using data from 79 healthy women and 64 breast cancer patients. Significance analysis of microarrays (SAM) was used to identify differentially expressed genes and multivariate linear regression was used to identify independent associations. Six genes (SCGB3A1, RSPO1, TLN2, SLITRK4, DCLK1, PTGS1) were found differentially expressed according to serum estradiol levels (FDR = 0). Three of these independently predicted estradiol levels in a multivariate model, as SCGB3A1 (HIN1) and TLN2 were up-regulated and PTGS1 (COX1) was down-regulated in breast samples from women with high serum estradiol. Serum estradiol, but none of the differentially expressed genes were significantly associated with mammographic density, another strong breast cancer risk factor. In breast carcinomas, expression of GREB1 and AREG was associated with serum estradiol in all cancers and in the subgroup of estrogen receptor positive cases. We have identified genes associated with serum estradiol levels in normal breast tissue and in breast carcinomas. SCGB3A1 is a suggested tumor suppressor gene that inhibits cell growth and invasion and is methylated and down-regulated in many epithelial cancers. Our findings indicate this gene as an important inhibitor of breast cell proliferation in healthy women with high estradiol levels. In the breast, this gene is expressed in luminal cells only and is methylated in non-BRCA-related breast cancers. The possibility of a carcinogenic contribution of silencing of this gene for luminal, but not basal-like cancers should be further explored. PTGS1 induces prostaglandin E2 (PGE2) production which in turn stimulates aromatase expression and hence increases the

  6. Background of SAM atom-fraction profiles

    International Nuclear Information System (INIS)

    Ernst, Frank

    2017-01-01

    Atom-fraction profiles acquired by SAM (scanning Auger microprobe) have important applications, e.g. in the context of alloy surface engineering by infusion of carbon or nitrogen through the alloy surface. However, such profiles often exhibit an artifact in form of a background with a level that anti-correlates with the local atom fraction. This article presents a theory explaining this phenomenon as a consequence of the way in which random noise in the spectrum propagates into the discretized differentiated spectrum that is used for quantification. The resulting model of “energy channel statistics” leads to a useful semi-quantitative background reduction procedure, which is validated by applying it to simulated data. Subsequently, the procedure is applied to an example of experimental SAM data. The analysis leads to conclusions regarding optimum experimental acquisition conditions. The proposed method of background reduction is based on general principles and should be useful for a broad variety of applications. - Highlights: • Atom-fraction–depth profiles of carbon measured by scanning Auger microprobe • Strong background, varies with local carbon concentration. • Needs correction e.g. for quantitative comparison with simulations • Quantitative theory explains background. • Provides background removal strategy and practical advice for acquisition

  7. Background of SAM atom-fraction profiles

    Energy Technology Data Exchange (ETDEWEB)

    Ernst, Frank

    2017-03-15

    Atom-fraction profiles acquired by SAM (scanning Auger microprobe) have important applications, e.g. in the context of alloy surface engineering by infusion of carbon or nitrogen through the alloy surface. However, such profiles often exhibit an artifact in form of a background with a level that anti-correlates with the local atom fraction. This article presents a theory explaining this phenomenon as a consequence of the way in which random noise in the spectrum propagates into the discretized differentiated spectrum that is used for quantification. The resulting model of “energy channel statistics” leads to a useful semi-quantitative background reduction procedure, which is validated by applying it to simulated data. Subsequently, the procedure is applied to an example of experimental SAM data. The analysis leads to conclusions regarding optimum experimental acquisition conditions. The proposed method of background reduction is based on general principles and should be useful for a broad variety of applications. - Highlights: • Atom-fraction–depth profiles of carbon measured by scanning Auger microprobe • Strong background, varies with local carbon concentration. • Needs correction e.g. for quantitative comparison with simulations • Quantitative theory explains background. • Provides background removal strategy and practical advice for acquisition.

  8. Hybrid male sterility in rice controlled by interaction between divergent alleles of two adjacent genes.

    Science.gov (United States)

    Long, Yunming; Zhao, Lifeng; Niu, Baixiao; Su, Jing; Wu, Hao; Chen, Yuanling; Zhang, Qunyu; Guo, Jingxin; Zhuang, Chuxiong; Mei, Mantong; Xia, Jixing; Wang, Lan; Wu, Haibin; Liu, Yao-Guang

    2008-12-02

    Sterility is common in hybrids between divergent populations, such as the indica and japonica subspecies of Asian cultivated rice (Oryza sativa). Although multiple loci for plant hybrid sterility have been identified, it remains unknown how alleles of the loci interact at the molecular level. Here we show that a locus for indica-japonica hybrid male sterility, Sa, comprises two adjacent genes, SaM and SaF, encoding a small ubiquitin-like modifier E3 ligase-like protein and an F-box protein, respectively. Most indica cultivars contain a haplotype SaM(+)SaF(+), whereas all japonica cultivars have SaM(-)SaF(-) that diverged by nucleotide variations in wild rice. Male semi-sterility in this heterozygous complex locus is caused by abortion of pollen carrying SaM(-). This allele-specific gamete elimination results from a selective interaction of SaF(+) with SaM(-), a truncated protein, but not with SaM(+) because of the presence of an inhibitory domain, although SaM(+) is required for this male sterility. Lack of any one of the three alleles in recombinant plants does not produce male sterility. We propose a two-gene/three-component interaction model for this hybrid male sterility system. The findings have implications for overcoming male sterility in inter-subspecific hybrid rice breeding.

  9. Spirit Pluralisme dalam Klenteng Sam Po Kong Semarang

    Directory of Open Access Journals (Sweden)

    Edi Nurwahyu Julianto

    2015-07-01

    Full Text Available Klenteng Sam Po Kong has very deep meaning as a symbol of multi cultural; multi ethnic and multi religious. Klenteng Sam Po Kong has a different function, not only used by people with background religious Tri Dharma (Budha, Tao and Konghuchu, but also used by Javanese ethnic with different religious backgrounds. Between ethnic China and Java, mutual respect and tolerance run beliefs and rituals of each. More over, Klenteng Sam Po Kong is a form of pluralism which reflected the fact Sino Javanese Muslim Culture is preserved to date both of sightings physical culture and system cultural in the form of religious rites performed by ethnic China and Java.

  10. Study The Effect of 4 weeks of Special Aerobic Training on CBS and SAM Levels in Hippocampus of Rats with Alzheimer-induced Disease with Aβ1-42 Injection

    Directory of Open Access Journals (Sweden)

    Farhad Azimi

    2018-03-01

    Full Text Available Abstract Background: H2S plays a key role in the pathogenesis of the Alzheimer’s disease. The aim of the present study was to investigate the effects of 4 weeks of the special aerobic training after induction of Alzheimer’s disease by Aβ1-42 injection on CBS and SAM levels in hippocampus of Wistar male rats. Materials and Methods: Twenty male Wistar rats (8 weeks old and weight 195 ± 20 g were divided into four groups including: healthy control, Alzheimer’s control, Alzheimer’s + training and sham. To induce Alzheimer’s disease, Aβ1-42 was infused into the hippocampus of rats. Training group trained for 4-week. For data analysis, one-way ANOVA was used and Eta and Omega squared tests were used to determine the effect size (p<0.05. Results: Findings revealed that 4 weeks of special aerobic training increased significantly the CBS and SAM levels in hippocampus of Alzheimer’s rats compared to the control Alzheimer’s rats ( ES=53; p= 0.007, ES= 92.22; p= 0.001. Also, we showed 4 weeks of special aerobic training increased CBS level in hippocampus of Alzheimer’s rats compared to the healthy cotrol group (ES= 44.07; p= 0.014. Conclusion: It seems that the special aerobic training can be used as a useful non-pharmacologically effective therapeutic treatment for Alzheimer's patients through positive regulation of hydrogen sulfide via CBS and SAM enzymes.

  11. Cooperation between Magnesium and Metabolite Controls Collapse of the SAM-I Riboswitch.

    Science.gov (United States)

    Roy, Susmita; Onuchic, José N; Sanbonmatsu, Karissa Y

    2017-07-25

    The S-adenosylmethionine (SAM)-I riboswitch is a noncoding RNA that regulates the transcription termination process in response to metabolite (SAM) binding. The aptamer portion of the riboswitch may adopt an open or closed state depending on the presence of metabolite. Although the transition between the open and closed states is critical for the switching process, its atomistic details are not well understood. Using atomistic simulations, we calculate the effect of SAM and magnesium ions on the folding free energy landscape of the SAM-I riboswitch. These molecular simulation results are consistent with our previous wetlab experiments and aid in interpreting the SHAPE probing measurements. Here, molecular dynamics simulations explicitly identify target RNA motifs sensitive to magnesium ions and SAM. In the simulations, we observe that, whereas the metabolite mostly stabilizes the P1 and P3 helices, magnesium serves an important role in stabilizing a pseudoknot interaction between the P2 and P4 helices, even at high metabolite concentrations. The pseudoknot stabilization by magnesium, in combination with P1 stabilization by SAM, explains the requirement of both SAM and magnesium to form the fully collapsed metabolite-bound closed state of the SAM-I riboswitch. In the absence of SAM, frequent open-to-closed conformational transitions of the pseudoknot occur, akin to breathing. These pseudoknot fluctuations disrupt the binding site by facilitating fluctuations in the 5'-end of helix P1. Magnesium biases the landscape toward a collapsed state (preorganization) by coordinating pseudoknot and 5'-P1 fluctuations. The cooperation between SAM and magnesium in stabilizing important tertiary interactions elucidates their functional significance in transcription regulation. Published by Elsevier Inc.

  12. Selective translational repression of HIV-1 RNA by Sam68DeltaC occurs by altering PABP1 binding to unspliced viral RNA

    Directory of Open Access Journals (Sweden)

    Soros Vanessa

    2008-10-01

    Full Text Available Abstract HIV-1 structural proteins are translated from incompletely spliced 9 kb and 4 kb mRNAs, which are transported to the cytoplasm by Crm1. It has been assumed that once in the cytoplasm, translation of incompletely spliced HIV-1 mRNAs occurs in the same manner as host mRNAs. Previous analyses have demonstrated that Sam68 and a mutant thereof, Sam68ΔC, have dramatic effects on HIV gene expression, strongly enhancing and inhibiting viral structural protein synthesis, respectively. While investigating the inhibition of incompletely spliced HIV-1 mRNAs by Sam68ΔC, we determined that the effect was independent of the perinuclear bundling of the viral RNA. Inhibition was dependent upon the nuclear export pathway used, as translation of viral RNA exported via the Tap/CTE export pathway was not blocked by Sam68ΔC. We demonstrate that inhibition of HIV expression by Sam68ΔC is correlated with a loss of PABP1 binding with no attendant change in polyadenosine tail length of the affected RNAs. The capacity of Sam68ΔC to selectively inhibit translation of HIV-1 RNAs exported by Crm1 suggests that it is able to recognize unique characteristics of these viral RNPs, a property that could lead to new therapeutic approaches to controlling HIV-1 replication.

  13. SAMMate: a GUI tool for processing short read alignments in SAM/BAM format

    Directory of Open Access Journals (Sweden)

    Flemington Erik

    2011-01-01

    Full Text Available Abstract Background Next Generation Sequencing (NGS technology generates tens of millions of short reads for each DNA/RNA sample. A key step in NGS data analysis is the short read alignment of the generated sequences to a reference genome. Although storing alignment information in the Sequence Alignment/Map (SAM or Binary SAM (BAM format is now standard, biomedical researchers still have difficulty accessing this information. Results We have developed a Graphical User Interface (GUI software tool named SAMMate. SAMMate allows biomedical researchers to quickly process SAM/BAM files and is compatible with both single-end and paired-end sequencing technologies. SAMMate also automates some standard procedures in DNA-seq and RNA-seq data analysis. Using either standard or customized annotation files, SAMMate allows users to accurately calculate the short read coverage of genomic intervals. In particular, for RNA-seq data SAMMate can accurately calculate the gene expression abundance scores for customized genomic intervals using short reads originating from both exons and exon-exon junctions. Furthermore, SAMMate can quickly calculate a whole-genome signal map at base-wise resolution allowing researchers to solve an array of bioinformatics problems. Finally, SAMMate can export both a wiggle file for alignment visualization in the UCSC genome browser and an alignment statistics report. The biological impact of these features is demonstrated via several case studies that predict miRNA targets using short read alignment information files. Conclusions With just a few mouse clicks, SAMMate will provide biomedical researchers easy access to important alignment information stored in SAM/BAM files. Our software is constantly updated and will greatly facilitate the downstream analysis of NGS data. Both the source code and the GUI executable are freely available under the GNU General Public License at http://sammate.sourceforge.net.

  14. Supplementary Material for: A new mode of SAM domain mediated oligomerization observed in the CASKIN2 neuronal scaffolding protein

    KAUST Repository

    Smirnova, Ekaterina; Kwan, Jamie; Siu, Ryan; Gao, Xin; Zoidl, Georg; Demeler, Borries; Saridakis, Vivian; Donaldson, Logan

    2016-01-01

    Abstract Background CASKIN2 is a homolog of CASKIN1, a scaffolding protein that participates in a signaling network with CASK (calcium/calmodulin-dependent serine kinase). Despite a high level of homology between CASKIN2 and CASKIN1, CASKIN2 cannot bind CASK due to the absence of a CASK Interaction Domain and consequently, may have evolved undiscovered structural and functional distinctions. Results We demonstrate that the crystal structure of the Sterile Alpha Motif (SAM) domain tandem (SAM1-SAM2) oligomer from CASKIN2 is different than CASKIN1, with the minimal repeating unit being a dimer, rather than a monomer. Analytical ultracentrifugation sedimentation velocity methods revealed differences in monomer/dimer equilibria across a range of concentrations and ionic strengths for the wild type CASKIN2 SAM tandem and a structure-directed double mutant that could not oligomerize. Further distinguishing CASKIN2 from CASKIN1, EGFP-tagged SAM tandem proteins expressed in Neuro2a cells produced punctae that were distinct both in shape and size. Conclusions This study illustrates a new way in which neuronal SAM domains can assemble into large macromolecular assemblies that might concentrate and amplify synaptic responses.

  15. Coastal lagoon systems as indicator of Holocene sea-level development in a periglacial soft-sediment setting: Samsø, Denmark

    DEFF Research Database (Denmark)

    Sander, Lasse; Fruergaard, Mikkel; Johannessen, Peter N.

    2014-01-01

    . Stratigraphy, grain-size distribution, fossil and organic matter content of cores retrieved from the lagoons were analyzed and compared. Age control was established using radiocarbon and optically stimulated luminescence dating. Our data produced a surprisingly consistent pattern for the sedimentary......Confined shallow-water environments are encountered many places along the coast of the inner Danish waters. Despite their common occurrence, these environments have rarely been studied as sedimentary archives. In this study we set out to trace back changes in relative sea-level and associated...... geomorphological responses in sediment cores retrieved from coastal lagoon systems on the island of Samsø, central Denmark. In the mid-Atlantic period, the post-glacial sea-level rise reached what is today the southern Kattegat Sea. Waves, currents and tides began to erode the unconsolidated moraine material...

  16. Motor coordination defects in mice deficient for the Sam68 RNA-binding protein.

    Science.gov (United States)

    Lukong, Kiven E; Richard, Stéphane

    2008-06-03

    The role of RNA-binding proteins in the central nervous system and more specifically their role in motor coordination and learning are poorly understood. We previously reported that ablation of RNA-binding protein Sam68 in mice results in male sterility and delayed mammary gland development and protection against osteoporosis in females. Sam68 however is highly expressed in most regions of the brain especially the cerebellum and thus we investigated the cerebellar-related manifestations in Sam68-null mice. We analyzed the mice for motor function, sensory function, and learning and memory abilities. Herein, we report that Sam68-null mice have motor coordination defects as assessed by beam walking and rotorod performance. Forty-week-old Sam68-null mice (n=12) were compared to their wild-type littermates (n=12). The Sam68-null mice exhibited more hindpaw faults in beam walking tests and fell from the rotating drum at lower speeds and prematurely compared to the wild-type controls. The Sam68-null mice were, however, normal for forelimb strength, tail-hang reflex, balance test, grid walking, the Morris water task, recognition memory, visual discrimination, auditory stimulation and conditional taste aversion. Our findings support a role for Sam68 in the central nervous system in the regulation of motor coordination.

  17. Radiation streaming with SAM-CE

    International Nuclear Information System (INIS)

    De Gangi, N.; Cohen, M.O.; Waluschka, E.; Steinberg, H.A.

    1980-01-01

    The SAM-CE Monte Carlo code has been employed to calculate doses, due to neutron streaming, on the operating floor and other locations of the Millstone Unit II Nuclear Power Facility. Calculated results were compared against measured doses

  18. Report of Chinese family with severe dermatitis, multiple allergies and metabolic wasting syndrome caused by novel homozygous desmoglein-1 gene mutation.

    Science.gov (United States)

    Cheng, Ruhong; Yan, Ming; Ni, Cheng; Zhang, Jia; Li, Ming; Yao, Zhirong

    2016-10-01

    Recently, homozygous mutations in the desmoglein-1 (DSG1) gene and heterozygous mutation in the desmoplakin (DSP) gene have been demonstrated to be associated with severe dermatitis, multiple allergies and metabolic wasting (SAM) syndrome (Mendelian Inheritance in Man no. 615508). We aim to identify the molecular basis for a Chinese pedigree of SAM syndrome. A Chinese pedigree of SAM syndrome was subjected to mutation detection in the DSG1 gene. Sequence analysis of the DSG1 gene and quantitative reverse transcriptase polymerase chain reaction analysis for gene expression of DSG1 using cDNA derived from the epidermis of patients and controls were both performed. Skin biopsies were also taken from patients for pathological study and transmission electron microscopy observation. Novel homozygous splicing mutation c.1892-1delG in the exon-intron border of the DSG1 gene has been demonstrated to be associated with SAM syndrome. We report a new family of SAM syndrome of Asian decent and expand the spectrum of mutations in the DSG1 gene. © 2016 Japanese Dermatological Association.

  19. Improving discrimination of savanna tree species through a multiple endmember spectral-angle-mapper (SAM) approach: canopy level analysis

    CSIR Research Space (South Africa)

    Cho, Moses A

    2010-11-01

    Full Text Available sensing. The objectives of this paper were to (i) evaluate the classification performance of a multiple-endmember spectral angle mapper (SAM) classification approach (conventionally known as the nearest neighbour) in discriminating ten common African...

  20. On LAM's and SAM's for Halley's rotation

    Science.gov (United States)

    Peale, Stanton J.

    1992-01-01

    Non principal axis rotation for comet Halley is inferred from dual periodicities evident in the observations. The modes where the spin axis precesses around the axis of minimum moment of inertia (long axis mode or LAM) and where it precesses around the axis of maximum moment of inertia (short axis mode or SAM) are described from an inertial point of view. The currently favored LAM model for Halley's rotation state satisfies observational and dynamical constraints that apparently no SAM can satisfy. But it cannot reproduce the observed post perihelion brightening through seasonal illumination of localized sources on the nucleus, whereas a SAM can easily produce post or pre perihelion brightening by this mechanism. However, the likelihood of a LAM rotation for elongated nuclei of periodic comets such as Halley together with Halley's extreme post perihelion behavior far from the Sun suggest that Halley's post perihelion brightening may be due to effects other than seasonal illumination of localized sources, and therefore such brightening may not constrain its rotation state.

  1. Role of methionine on epigenetic modification of DNA methylation and gene expression in animals

    Directory of Open Access Journals (Sweden)

    Naifeng Zhang

    2018-03-01

    Full Text Available DNA methylation is one of the main epigenetic phenomena affecting gene expression. It is an important mechanism for the development of embryo, growth and health of animals. As a key nutritional factor limiting the synthesis of protein, methionine serves as the precursor of S-adenosylmethionine (SAM in the hepatic one-carbon metabolism. The dietary fluctuation of methionine content can alter the levels of metabolic substrates in one-carbon metabolism, e.g., the SAM, S-adenosylhomocysteine (SAH, and change the expression of genes related to the growth and health of animals by DNA methylation reactions. The ratio of SAM to SAH is called ‘methylation index’ but it should be carefully explained because the complexity of methylation reaction. Alterations of methylation in a specific cytosine-guanine (CpG site, rather than the whole promoter region, might be enough to change gene expression. Aberrant methionine cycle may provoke molecular changes of one-carbon metabolism that results in deregulation of cellular hemostasis and health problems. The importance of DNA methylation has been underscored but the mechanisms of methionine affecting DNA methylation are poorly understood. Nutritional epigenomics provides a promising insight into the targeting epigenetic changes in animals from a nutritional standpoint, which will deepen and expand our understanding of genes, molecules, tissues, and animals in which methionine alteration influences DNA methylation and gene expression. Keywords: Epigenetics, Methionine, DNA methylation, Gene expression, Epigenetic modification

  2. Surface adhesion and confinement variation of Staphylococcus aurius on SAM surfaces

    Science.gov (United States)

    Amroski, Alicia; Olsen, Morgan; Calabrese, Joseph; Senevirathne, Reshani; Senevirathne, Indrajith

    2012-02-01

    Controlled surface adhesion of non - pathogenic gram positive strain, Staphylococcus aureus is interesting as a model system due to possible development of respective biosensors for prevention and detection of the pathogenic strain methicillin resistant Staphylococcus aureus (MRSA) and further as a study for bio-machine interfacing. Self Assembled Monolayers (SAM) with engineered surfaces of linear thiols on Au(111) were used as the substrate. Sub cultured S. aureus were used for the analysis. The SAM layered surfaces were dipped in 2 -- 4 Log/ml S. aureus solution. Subsequent surface adhesion at different bacterial dilutions on surfaces will be discussed, and correlated with quantitative and qualitative adhesion properties of bacteria on the engineered SAM surfaces. The bacteria adhered SAM surfaces were investigated using intermittent contact, noncontact, lateral force and contact modes of Atomic Force Microscopy (AFM).

  3. Renewing Samsø

    DEFF Research Database (Denmark)

    Papazu, Irina

    2017-01-01

    and globally, I ask: if indeed such a process of renewal must be understood as a political process and the island’s energy transition as an inherently political event, what can Samsø teach us about the workings of politics and local democracy as enacted in practice? This is politics not as election result...... or ideological struggle over values, ideals and the distribution of goods, but as the down-to-earth but significant activity of creating something new together....

  4. A viral protein promotes host SAMS1 activity and ethylene production for the benefit of virus infection.

    Science.gov (United States)

    Zhao, Shanshan; Hong, Wei; Wu, Jianguo; Wang, Yu; Ji, Shaoyi; Zhu, Shuyi; Wei, Chunhong; Zhang, Jinsong; Li, Yi

    2017-10-10

    Ethylene plays critical roles in plant development and biotic stress response, but the mechanism of ethylene in host antiviral response remains unclear. Here, we report that Rice dwarf virus (RDV) triggers ethylene production by stimulating the activity of S-adenosyl-L-methionine synthetase (SAMS), a key component of the ethylene synthesis pathway, resulting in elevated susceptibility to RDV. RDV-encoded Pns11 protein specifically interacted with OsSAMS1 to enhance its enzymatic activity, leading to higher ethylene levels in both RDV-infected and Pns11-overexpressing rice. Consistent with a counter-defense role for ethylene, Pns11-overexpressing rice, as well as those overexpressing OsSAMS1 , were substantially more susceptible to RDV infection, and a similar effect was observed in rice plants treated with an ethylene precursor. Conversely, OsSAMS1- knockout mutants, as well as an osein2 mutant defective in ethylene signaling, resisted RDV infection more robustly. Our findings uncover a novel mechanism which RDV manipulates ethylene biosynthesis in the host plants to achieve efficient infection.

  5. Unanticipated coordination of tris buffer to the Radical SAM cluster of the RimO methylthiotransferase.

    Science.gov (United States)

    Molle, Thibaut; Clémancey, Martin; Latour, Jean-Marc; Kathirvelu, Velavan; Sicoli, Giuseppe; Forouhar, Farhad; Mulliez, Etienne; Gambarelli, Serge; Atta, Mohamed

    2016-07-01

    Radical SAM enzymes generally contain a [4Fe-4S](2+/1+) (RS cluster) cluster bound to the protein via the three cysteines of a canonical motif CxxxCxxC. The non-cysteinyl iron is used to coordinate SAM via its amino-carboxylate moiety. The coordination-induced proximity between the cluster acting as an electron donor and the adenosyl-sulfonium bond of SAM allows for the homolytic cleavage of the latter leading to the formation of the reactive 5'-deoxyadenosyl radical used for substrate activation. Most of the structures of Radical SAM enzymes have been obtained in the presence of SAM, and therefore, little is known about the situation when SAM is not present. In this report, we show that RimO, a methylthiotransferase belonging to the radical SAM superfamily, binds a Tris molecule in the absence of SAM leading to specific spectroscopic signatures both in Mössbauer and pulsed EPR spectroscopies. These data provide a cautionary note for researchers who work with coordinative unsaturated iron sulfur clusters.

  6. Study of radiation effects on the senescence accelerated mouse (SAM), 1

    International Nuclear Information System (INIS)

    Kishikawa, Masao; Iseki, Masachika; Kondo, Hisayoshi

    1989-01-01

    The study of age-related changes in the central nervous system due to irradiation is being carried out in our laboratory. The senescence accelerated mouse (SAM P/1, male) was used for this investigation concerning the one-trial passive avoidance reaction. The experimental group of SAM P/1 was irradiated with 4 Gy at 8 weeks old, and passive avoidance reaction (PAR) was measured for 180 seconds as a learning task. At the age of 7 months, statistical analysis of PAR was conducted using the life time analysis method. The passive avoidance reaction of the irradiated group was more impaired than that of the control group. The results of this investigation suggested that the learning and/or memory disturbance of irradiated SAM P/1 is similar to the changes of more aged SAM P/1. (author)

  7. Amine terminated SAMs: Investigating why oxygen is present in these films

    International Nuclear Information System (INIS)

    Baio, J.E.; Weidner, T.; Brison, J.; Graham, D.J.; Gamble, Lara J.; Castner, David G.

    2009-01-01

    Self-assembled monolayers (SAMs) on gold prepared from amine-terminated alkanethiols have long been employed as model positively charged surfaces. Yet in previous studies significant amounts of unexpected oxygen containing species are always detected in amine terminated SAMs. Thus, the goal of this investigation was to determine the source of these oxygen species and minimize their presence in the SAM. The surface composition, structure, and order of amine-terminated SAMs on Au were characterized by X-ray photoelectron spectroscopy (XPS), time-of-flight secondary ion mass spectroscopy (ToF-SIMS), sum frequency generation (SFG) and near edge X-ray absorption fine structure (NEXAFS) spectroscopy. XPS determined compositions of amine-terminated SAMs in the current study exhibited oxygen concentrations of 2.4 ± 0.4 atomic %, a substantially lower amount of oxygen than reported in previously published studies. High-resolution XPS results from the S 2p , C 1s and N 1s regions did not detect any oxidized species. Angle-resolved XPS indicated that the small amount of oxygen detected was located at or near the amine head group. Small amounts of oxidized nitrogen, carbon and sulfur secondary ions, as well as ions attributed to water, were detected in the ToF-SIMS data due to the higher sensitivity of ToF-SIMS. The lack of N-O, S-O, and C-O stretches in the SFG spectra are consistent with the XPS and ToF-SIMS results and together show that oxidation of the amine-terminated thiols alone can only account for, at most, a small fraction of the oxygen detected by XPS. Both the SFG and angle-dependent NEXAFS indicated the presence of gauche defects in the amine SAMs. However, the SFG spectral features near 2865 cm -1 , assigned to the stretch of the methylene group next to the terminal amine unit, demonstrate the SAM is reasonably ordered. The SFG results also show another broad feature near 3200 cm -1 related to hydrogen-bonded water. From this multi-technique investigation it is

  8. The SAMS: Smartphone Addiction Management System and verification.

    Science.gov (United States)

    Lee, Heyoung; Ahn, Heejune; Choi, Samwook; Choi, Wanbok

    2014-01-01

    While the popularity of smartphones has given enormous convenience to our lives, their pathological use has created a new mental health concern among the community. Hence, intensive research is being conducted on the etiology and treatment of the condition. However, the traditional clinical approach based surveys and interviews has serious limitations: health professionals cannot perform continual assessment and intervention for the affected group and the subjectivity of assessment is questionable. To cope with these limitations, a comprehensive ICT (Information and Communications Technology) system called SAMS (Smartphone Addiction Management System) is developed for objective assessment and intervention. The SAMS system consists of an Android smartphone application and a web application server. The SAMS client monitors the user's application usage together with GPS location and Internet access location, and transmits the data to the SAMS server. The SAMS server stores the usage data and performs key statistical data analysis and usage intervention according to the clinicians' decision. To verify the reliability and efficacy of the developed system, a comparison study with survey-based screening with the K-SAS (Korean Smartphone Addiction Scale) as well as self-field trials is performed. The comparison study is done using usage data from 14 users who are 19 to 50 year old adults that left at least 1 week usage logs and completed the survey questionnaires. The field trial fully verified the accuracy of the time, location, and Internet access information in the usage measurement and the reliability of the system operation over more than 2 weeks. The comparison study showed that daily use count has a strong correlation with K-SAS scores, whereas daily use times do not strongly correlate for potentially addicted users. The correlation coefficients of count and times with total K-SAS score are CC = 0.62 and CC =0.07, respectively, and the t-test analysis for the

  9. Nuclear Protein Sam68 Interacts with the Enterovirus 71 Internal Ribosome Entry Site and Positively Regulates Viral Protein Translation.

    Science.gov (United States)

    Zhang, Hua; Song, Lei; Cong, Haolong; Tien, Po

    2015-10-01

    enhance the translation of virus protein. To our knowledge, this is the first report that describes Sam68 actively participating in the life cycle of EV71 at a molecular level. These studies will not only improve our understanding of the replication of EV71 but also have the potential for aiding in developing a therapeutic strategy against EV71 infection. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  10. Teleconnection stationarity, variability and trends of the Southern Annular Mode (SAM) during the last millennium

    Science.gov (United States)

    Dätwyler, Christoph; Neukom, Raphael; Abram, Nerilie J.; Gallant, Ailie J. E.; Grosjean, Martin; Jacques-Coper, Martín; Karoly, David J.; Villalba, Ricardo

    2017-11-01

    The Southern Annular Mode (SAM) is the leading mode of atmospheric interannual variability in the Southern Hemisphere (SH) extra-tropics. Here, we assess the stationarity of SAM spatial correlations with instrumental and paleoclimate proxy data for the past millennium. The instrumental period shows that temporal non-stationarities in SAM teleconnections are not consistent across the SH land areas. This suggests that the influence of the SAM index is modulated by regional effects. However, within key-regions with good proxy data coverage (South America, Tasmania, New Zealand), teleconnections are mostly stationary over the instrumental period. Using different stationarity criteria for proxy record selection, we provide new austral summer and annual mean SAM index reconstructions over the last millennium. Our summer SAM reconstructions are very robust to changes in proxy record selection and the selection of the calibration period, particularly on the multi-decadal timescale. In contrast, the weaker performance and lower agreement in the annual mean SAM reconstructions point towards changing teleconnection patterns that may be particularly important outside the summer months. Our results clearly portend that the temporal stationarity of the proxy-climate relationships should be taken into account in the design of comprehensive regional and hemispherical climate reconstructions. The summer SAM reconstructions show no significant relationship to solar, greenhouse gas and volcanic forcing, with the exception of an extremely strong negative anomaly following the AD 1257 Samalas eruption. Furthermore, reconstructed pre-industrial summer SAM trends are very similar to trends obtained by model control simulations. We find that recent trends in the summer SAM lie outside the 5-95% range of pre-industrial natural variability.

  11. Evidence for Perchlorates and the Origin of Chlorinated Hydrocarbons Detected by SAM at the Rocknest Aeolian Deposit in Gale Crater

    Science.gov (United States)

    Glavin, Daniel P.; Freissinet, Caroline; Miller, Kristen E.; Eigenbrode, Jennifer L.; Brunner, Anna E.; Buch, Arnaud; Sutter, Brad; Archer, P. Douglas, Jr.; Atreya, Sushil K.; Brinckerhoff, William B.; hide

    2013-01-01

    A single scoop of the Rocknest aeolian deposit was sieved (less than 150 micrometers), and four separate sample portions, each with a mass of approximately 50 mg, were delivered to individual cups inside the Sample Analysis at Mars (SAM) instrument by the Mars Science Laboratory rover's sample acquisition system. The samples were analyzed separately by the SAM pyrolysis evolved gas and gas chromatograph mass spectrometer analysis modes. Several chlorinated hydrocarbons including chloromethane, dichloromethane, trichloromethane, a chloromethylpropene, and chlorobenzene were identified by SAM above background levels with abundances of approximately 0.01 to 2.3 nmol. The evolution of the chloromethanes observed during pyrolysis is coincident with the increase in O2 released from the Rocknest sample and the decomposition of a product of N-methyl-N-(tert-butyldimethylsilyl)-trifluoroacetamide (MTBSTFA), a chemical whose vapors were released from a derivatization cup inside SAM. The best candidate for the oxychlorine compounds in Rocknest is a hydrated calcium perchlorate (Ca(ClO4)2·nH2O), based on the temperature release of O2 that correlates with the release of the chlorinated hydrocarbons measured by SAM, although other chlorine-bearing phases are being considered. Laboratory analog experiments suggest that the reaction of Martian chlorine from perchlorate decomposition with terrestrial organic carbon from MTBSTFA during pyrolysis can explain the presence of three chloromethanes and a chloromethylpropene detected by SAM. Chlorobenzene may be attributed to reactions of Martian chlorine released during pyrolysis with terrestrial benzene or toluene derived from 2,6-diphenylphenylene oxide (Tenax) on the SAM hydrocarbon trap. At this time we do not have definitive evidence to support a nonterrestrial carbon source for these chlorinated hydrocarbons, nor do we exclude the possibility that future SAM analyses will reveal the presence of organic compounds native to the

  12. SAMS: The synchronization and monitoring system for ATF [Advanced Toroidal Facility] data acquisition

    International Nuclear Information System (INIS)

    Greenwood, D.E.

    1987-01-01

    SAMS performs much of the synchronization of the distributed data acquisition system for the Advanced Toroidal Facility (ATF). SAMS is responsible for propagating shot information and managing te data system directories and logical names. This paper describes how SAMS communicates with other processes, both within the VAX cluster that supports most of the ATF data acquisition and on VAXes that are connected to the cluster via DECnet. 3 refs

  13. Benchmark Simulation of Natural Circulation Cooling System with Salt Working Fluid Using SAM

    Energy Technology Data Exchange (ETDEWEB)

    Ahmed, K. K.; Scarlat, R. O.; Hu, R.

    2017-09-03

    Liquid salt-cooled reactors, such as the Fluoride Salt-Cooled High-Temperature Reactor (FHR), offer passive decay heat removal through natural circulation using Direct Reactor Auxiliary Cooling System (DRACS) loops. The behavior of such systems should be well-understood through performance analysis. The advanced system thermal-hydraulics tool System Analysis Module (SAM) from Argonne National Laboratory has been selected for this purpose. The work presented here is part of a larger study in which SAM modeling capabilities are being enhanced for the system analyses of FHR or Molten Salt Reactors (MSR). Liquid salt thermophysical properties have been implemented in SAM, as well as properties of Dowtherm A, which is used as a simulant fluid for scaled experiments, for future code validation studies. Additional physics modules to represent phenomena specific to salt-cooled reactors, such as freezing of coolant, are being implemented in SAM. This study presents a useful first benchmark for the applicability of SAM to liquid salt-cooled reactors: it provides steady-state and transient comparisons for a salt reactor system. A RELAP5-3D model of the Mark-1 Pebble-Bed FHR (Mk1 PB-FHR), and in particular its DRACS loop for emergency heat removal, provides steady state and transient results for flow rates and temperatures in the system that are used here for code-to-code comparison with SAM. The transient studied is a loss of forced circulation with SCRAM event. To the knowledge of the authors, this is the first application of SAM to FHR or any other molten salt reactors. While building these models in SAM, any gaps in the code’s capability to simulate such systems are identified and addressed immediately, or listed as future improvements to the code.

  14. Alternative function for the mitochondrial SAM complex in biogenesis of alpha-helical TOM proteins.

    Science.gov (United States)

    Stojanovski, Diana; Guiard, Bernard; Kozjak-Pavlovic, Vera; Pfanner, Nikolaus; Meisinger, Chris

    2007-12-03

    The mitochondrial outer membrane contains two preprotein translocases: the general translocase of outer membrane (TOM) and the beta-barrel-specific sorting and assembly machinery (SAM). TOM functions as the central entry gate for nuclear-encoded proteins. The channel-forming Tom40 is a beta-barrel protein, whereas all Tom receptors and small Tom proteins are membrane anchored by a transmembrane alpha-helical segment in their N- or C-terminal portion. Synthesis of Tom precursors takes place in the cytosol, and their import occurs via preexisting TOM complexes. The precursor of Tom40 is then transferred to SAM for membrane insertion and assembly. Unexpectedly, we find that the biogenesis of alpha-helical Tom proteins with a membrane anchor in the C-terminal portion is SAM dependent. Each SAM protein is necessary for efficient membrane integration of the receptor Tom22, whereas assembly of the small Tom proteins depends on Sam37. Thus, the substrate specificity of SAM is not restricted to beta-barrel proteins but also includes the majority of alpha-helical Tom proteins.

  15. A classification model of Hyperion image base on SAM combined decision tree

    Science.gov (United States)

    Wang, Zhenghai; Hu, Guangdao; Zhou, YongZhang; Liu, Xin

    2009-10-01

    Monitoring the Earth using imaging spectrometers has necessitated more accurate analyses and new applications to remote sensing. A very high dimensional input space requires an exponentially large amount of data to adequately and reliably represent the classes in that space. On the other hand, with increase in the input dimensionality the hypothesis space grows exponentially, which makes the classification performance highly unreliable. Traditional classification algorithms Classification of hyperspectral images is challenging. New algorithms have to be developed for hyperspectral data classification. The Spectral Angle Mapper (SAM) is a physically-based spectral classification that uses an ndimensional angle to match pixels to reference spectra. The algorithm determines the spectral similarity between two spectra by calculating the angle between the spectra, treating them as vectors in a space with dimensionality equal to the number of bands. The key and difficulty is that we should artificial defining the threshold of SAM. The classification precision depends on the rationality of the threshold of SAM. In order to resolve this problem, this paper proposes a new automatic classification model of remote sensing image using SAM combined with decision tree. It can automatic choose the appropriate threshold of SAM and improve the classify precision of SAM base on the analyze of field spectrum. The test area located in Heqing Yunnan was imaged by EO_1 Hyperion imaging spectrometer using 224 bands in visual and near infrared. The area included limestone areas, rock fields, soil and forests. The area was classified into four different vegetation and soil types. The results show that this method choose the appropriate threshold of SAM and eliminates the disturbance and influence of unwanted objects effectively, so as to improve the classification precision. Compared with the likelihood classification by field survey data, the classification precision of this model

  16. Quality Control Guidelines for SAM Biotoxin Methods

    Science.gov (United States)

    Learn more about quality control guidelines and recommendations for the analysis of samples using the pathogen methods listed in EPA's Selected Analytical Methods for Environmental Remediation and Recovery (SAM).

  17. Quality Control Guidelines for SAM Radiochemical Methods

    Science.gov (United States)

    Learn more about quality control guidelines and recommendations for the analysis of samples using the radiochemistry methods listed in EPA's Selected Analytical Methods for Environmental Remediation and Recovery (SAM).

  18. Quality Control Guidelines for SAM Pathogen Methods

    Science.gov (United States)

    Learn more about quality control guidelines and recommendations for the analysis of samples using the biotoxin methods listed in EPA's Selected Analytical Methods for Environmental Remediation and Recovery (SAM).

  19. Quality Control Guidelines for SAM Chemical Methods

    Science.gov (United States)

    Learn more about quality control guidelines and recommendations for the analysis of samples using the chemistry methods listed in EPA's Selected Analytical Methods for Environmental Remediation and Recovery (SAM).

  20. Non-Photolithographic Manufacturing Processes for Micro-Channels Functioned by Micro-Contact-Printed SAMs

    Science.gov (United States)

    Saigusa, Hiroki; Suga, Yasuo; Miki, Norihisa

    In this paper we propose non-photolithographic fabrication processes of micro-fluid channels with patterned SAMs (Self-Assembled-Monolayers). SAMs with a thiol group are micro-contact printed on a patterned Au/Ti layer, which is vapor-deposited through a shadow mask. Ti is an adhesion layer. Subsequently, the micro-channels are formed by bonding surface-activated PDMS onto the silicon substrate via a silanol group, producing a SAMs-functioned bottom wall of the micro-channel. No photolithographic processes are necessary and thus, the proposed processes are very simple, quick and low cost. The micro-reactors can have various functions associated with the micro-contact-printed SAMs. We demonstrate successful manufacturing of micro-reactors with two types of SAMs. The micro-reactor with patterned AUT (11-amino-1-undecanethiol) successfully trapped nano-particles with a carboxylic acid group, indicating that micro-contact-printed SAMs remain active after the manufacturing processes of the micro-reactor. AUT -functioned micro-channels are applicable to bioassay and to immobilize proteins for DNA arrays. ODT (1-octadecanethiol) makes surfaces hydrophobic with the methyl terminal group. When water was introduced into the micro-reactor with ODT-patterned surfaces, water droplets remained only in the hydrophilic areas where ODT was not patterned. ODT -functioned micro-channels are applicable to fluid handling.

  1. Data handling with SAM and art at the NOνA experiment

    International Nuclear Information System (INIS)

    Aurisano, A; Backhouse, C; Davies, G S; Illingworth, R; Mengel, M; Norman, A; Mayer, N; Rocco, D; Zirnstein, J

    2015-01-01

    During operations, NOvA produces between 5,000 and 7,000 raw files per day with peaks in excess of 12,000. These files must be processed in several stages to produce fully calibrated and reconstructed analysis files. In addition, many simulated neutrino interactions must be produced and processed through the same stages as data. To accommodate the large volume of data and Monte Carlo, production must be possible both on the Fermilab grid and on off-site farms, such as the ones accessible through the Open Science Grid. To handle the challenge of cataloging these files and to facilitate their off-line processing, we have adopted the SAM system developed at Fermilab. SAM indexes files according to metadata, keeps track of each file's physical locations, provides dataset management facilities, and facilitates data transfer to off-site grids. To integrate SAM with Fermilab's art software framework and the NOvA production workflow, we have developed methods to embed metadata into our configuration files, art files, and standalone ROOT files. A module in the art framework propagates the embedded information from configuration files into art files, and from input art files to output art files, allowing us to maintain a complete processing history within our files. Embedding metadata in configuration files also allows configuration files indexed in SAM to be used as inputs to Monte Carlo production jobs. Further, SAM keeps track of the input files used to create each output file. Parentage information enables the construction of self-draining datasets which have become the primary production paradigm used at NOvA. In this paper we will present an overview of SAM at NOvA and how it has transformed the file production framework used by the experiment. (paper)

  2. Surface barrier analysis of semi-insulating and n{sup +}-type GaAs(0 0 1) following passivation with n-alkanethiol SAMs

    Energy Technology Data Exchange (ETDEWEB)

    Marshall, Gregory M. [Laboratory for Quantum Semiconductors and Photon-Based BioNanotechnology, Department of Electrical and Computer Engineering, Universite de Sherbrooke, Sherbrooke, Quebec, J1K 2R1 (Canada); Institute for Chemical Process and Environmental Technology, National Research Council of Canada, Ottawa, Ontario, K1A 0R6 (Canada); Bensebaa, Farid [Institute for Chemical Process and Environmental Technology, National Research Council of Canada, Ottawa, Ontario, K1A 0R6 (Canada); Dubowski, Jan J., E-mail: jan.j.dubowski@usherbrooke.ca [Laboratory for Quantum Semiconductors and Photon-Based BioNanotechnology, Department of Electrical and Computer Engineering, Universite de Sherbrooke, Sherbrooke, Quebec, J1K 2R1 (Canada)

    2011-02-15

    The surface Fermi level of semi-insulating and n{sup +}-type GaAs(0 0 1) was determined before and after passivation with n-alkanethiol self-assembled monolayers (SAMs) by X-ray photoelectron spectroscopy. Fermi level positioning was achieved using Au calibration pads integrated directly onto the GaAs surface, prior to SAM deposition, in order to provide a surface equipotential binding energy reference. Fermi level pinning within 50 meV and surface barrier characteristics according to the Advanced Unified Defect Model were observed. Our results demonstrate the effectiveness of the Au integration technique for the determination of band-edge referenced Fermi level positions and are relevant to an understanding of emerging technologies based on the molecular-semiconductor junction.

  3. Winning Attitude & Dedication to Physical Therapy Keep Sam Schmidt on Track

    Science.gov (United States)

    Bosley, Nikki Prevenslik

    2006-01-01

    This article relates how Sam Schmidt returned to living a productive life after an accident left him with spinal cord injury. Schmidt was a former Indy Racing League driver who founded Sam Schmidt Motorsports after his accident in 2000. Schmidt's car hit the wall as he exited turn two during a practice session at Walt Disney World Speedway in…

  4. Technoeconomic Modeling of Battery Energy Storage in SAM

    Energy Technology Data Exchange (ETDEWEB)

    DiOrio, Nicholas [National Renewable Energy Lab. (NREL), Golden, CO (United States); Dobos, Aron [National Renewable Energy Lab. (NREL), Golden, CO (United States); Janzou, Steven [National Renewable Energy Lab. (NREL), Golden, CO (United States); Nelson, Austin [National Renewable Energy Lab. (NREL), Golden, CO (United States); Lundstrom, Blake [National Renewable Energy Lab. (NREL), Golden, CO (United States)

    2015-09-01

    Detailed comprehensive lead-acid and lithium-ion battery models have been integrated with photovoltaic models in an effort to allow System Advisor Model (SAM) to offer the ability to predict the performance and economic benefit of behind the meter storage. In a system with storage, excess PV energy can be saved until later in the day when PV production has fallen, or until times of peak demand when it is more valuable. Complex dispatch strategies can be developed to leverage storage to reduce energy consumption or power demand based on the utility rate structure. This document describes the details of the battery performance and economic models in SAM.

  5. Sam Wagstaffi unustatud kired / Ahto Külvet

    Index Scriptorium Estoniae

    Külvet, Ahto

    2008-01-01

    Dokumentaalfilm "Black, White & Gray: Sam Wagstaff and Robert Mapplethorpe" : autor ja režissöör James Crump : Ameerika Ühendriigid 2007. Filmi näidati filminädala "Art in America" raames Tallinnas

  6. Detection of Organics at Mars: How Wet Chemistry Onboard SAM Helps

    Science.gov (United States)

    Buch, A.; Freissinet, Caroline; Szopa, C.; Glavin, D.; Coll, P.; Cabane, M.; Eigenbrode, J.; Navarro-Gonzalez, R.; Coscia, D.; Teinturier, S.; hide

    2013-01-01

    For the first time in the history of space exploration, a mission of interest to astrobiology could be able to analyze refractory organic compounds in the soil of Mars. Wet chemistry experiment allow organic components to be altered in such a way that improves there detection either by releasing the compounds from sample matricies or by changing the chemical structure to be amenable to analytical conditions. The latter is particular important when polar compounds are present. Sample Analysis at Mars (SAM), on the Curiosity rover of the Mars Science Laboratory mission, has onboard two wet chemistry experiments: derivatization and thermochemolysis. Here we report on the nature of the MTBSTFA derivatization experiment on SAM, the detection of MTBSTFA in initial SAM results, and the implications of this detection.

  7. The Performance of CSAM SAM when Cycle Length is extended

    Energy Technology Data Exchange (ETDEWEB)

    Roh, Kyung-ho; Moon, Sang-rae [KHNP, Daejeon (Korea, Republic of)

    2016-10-15

    In order to verify validation of that, CPC Axial Power Distribution is compared with Axial Power Distribution based on ICI every week. The difference between CPC Axial Power Distribution and Axial Power Distribution based on ICI increases according as fuels are burned. It is called CPC Axial Power Distribution Root Mean Square Error (CPC RMS Error). SAM and calibration of ex-core detector are important factors influencing the magnitude of the difference. According to vendor, the difference is limited by 8%. Otherwise, CPC penalty increases as many as difference increase. Therefore, KHNP developed Constrained Simulated Annealing Method (CSAM), which has better performance than that of Least Square Method (LSM), to calculate SAM constant. The CSA SAM contributed largely to maintain CPC operating margin. Somewhat, KHNP is developing the technology to be able to operate nuclear power plants for 24 month to optimize their efficiency. This paper shows trends of CPC RMS Error in a case of 24 months operation. Trends are based on data of a few OPR1000s under operation. It is data of OPR1000s that CSA SAM is applied. KHNP is developing the technology to extend operation cycle length in order to optimize the operation efficiency of OPR1000. To verify effect of extended operation cycle length on CPC, CPC Axial Power Distribution RMS Error in a case of 24 months operation was expected using operation data of six cycles in OPR1000. In cases that CPC Axial Power Distribution RMS Error exceeds threshold, operation margin is decreased due to CPC penalty. To prevent CPC operation margin from being decreased, improved method to calculate SAM or to calibrate ex-core detector is required. KHNP will consider the way to maintain CPC operation margin along with 24 month operation technology development, hereafter.

  8. Celiac Disease in Children with Severe Acute Malnutrition (SAM): A Hospital Based Study.

    Science.gov (United States)

    Beniwal, Neetu; Ameta, Gaurav; Chahar, Chandra Kumar

    2017-05-01

    To evaluate the prevalence and clinical features of Celiac disease among children with severe acute malnutrition (SAM). This prospective observational study was conducted in PBM Children Hospital, Bikaner from July 2012 through December 2013. All consecutively admitted children with SAM were recruited. All subjects were screened for Celiac disease by serological test for IgA-anti tissue Transglutaminase (IgA tTG) antibodies. All seropositive children underwent upper gastrointestinal endoscopy for small bowel biopsy for the confirmation. Clinical features of patients with and without celiac disease were compared. The sero-prevalence (IgA tTg positivity) of Celiac disease was found to be 15.38% while prevalence of biopsy confirmed Celiac disease was 14.42% among SAM children. Abdominal distension, diarrhea, anorexia, constipation, pain in abdomen, vitamin deficiencies, edema, clubbing and mouth ulcers were more common in patients of Celiac disease compared to patients without Celiac disease but the difference was statistically significant only for abdominal distension and pain abdomen. There is a high prevalence of Celiac disease in SAM. Screening for Celiac disease (especially in presence of pain abdomen and abdominal distension) should be an essential part of work-up in all children with SAM.

  9. SAM-dependent enzyme-catalysed pericyclic reactions in natural product biosynthesis

    Science.gov (United States)

    Ohashi, Masao; Liu, Fang; Hai, Yang; Chen, Mengbin; Tang, Man-Cheng; Yang, Zhongyue; Sato, Michio; Watanabe, Kenji; Houk, K. N.; Tang, Yi

    2017-09-01

    Pericyclic reactions—which proceed in a concerted fashion through a cyclic transition state—are among the most powerful synthetic transformations used to make multiple regioselective and stereoselective carbon-carbon bonds. They have been widely applied to the synthesis of biologically active complex natural products containing contiguous stereogenic carbon centres. Despite the prominence of pericyclic reactions in total synthesis, only three naturally existing enzymatic examples (the intramolecular Diels-Alder reaction, and the Cope and the Claisen rearrangements) have been characterized. Here we report a versatile S-adenosyl-L-methionine (SAM)-dependent enzyme, LepI, that can catalyse stereoselective dehydration followed by three pericyclic transformations: intramolecular Diels-Alder and hetero-Diels-Alder reactions via a single ambimodal transition state, and a retro-Claisen rearrangement. Together, these transformations lead to the formation of the dihydropyran core of the fungal natural product, leporin. Combined in vitro enzymatic characterization and computational studies provide insight into how LepI regulates these bifurcating biosynthetic reaction pathways by using SAM as the cofactor. These pathways converge to the desired biosynthetic end product via the (SAM-dependent) retro-Claisen rearrangement catalysed by LepI. We expect that more pericyclic biosynthetic enzymatic transformations remain to be discovered in naturally occurring enzyme ‘toolboxes’. The new role of the versatile cofactor SAM is likely to be found in other examples of enzyme catalysis.

  10. Coastal lagoon sediments as a recorder of Holocene landscape evolution and sea-level development: Samsø, southern Kattegat Sea, Denmark

    DEFF Research Database (Denmark)

    Sander, Lasse; Fruergaard, Mikkel; Johannessen, Peter N.

    on the fine-grained (lagoonal) sections of the cores. Age control was facilitated using radiocarbon and optically stimulated luminescence dating. Our data produced a surprisingly consistent pattern for the sedimentary successions found in the lagoons. The initial transgression can be identified along...... with the onset of deposition of fine-grained, organic-rich lagoonal sediments. The subsequent truncation and partial erosion of the lagoon sediments can be related to a decreasing sea-level. Based on these findings, we suggest a conceptual model that allows inferring age and elevation of transgressive...... and regressive stages from the lagoon sediments. Indication of geomorphological developments occurring in proximity to the lagoons (barrier formation, overwashing, dune formation) is further recorded in the deposits. These data can be used to support the proposed reconstruction of Samsø’s landscape evolution...

  11. Multiple endmember spectral-angle-mapper (SAM) analysis improves discrimination of Savanna tree species

    CSIR Research Space (South Africa)

    Cho, Moses A

    2009-08-01

    Full Text Available of this paper was to evaluate the classification performance of a multiple-endmember spectral angle mapper (SAM) classification approach in discriminating seven common African savanna tree species and to compare the results with the traditional SAM classifier...

  12. General Quality Control (QC) Guidelines for SAM Methods

    Science.gov (United States)

    Learn more about quality control guidelines and recommendations for the analysis of samples using the methods listed in EPA's Selected Analytical Methods for Environmental Remediation and Recovery (SAM).

  13. The Porter-Whitesides Discrepancy: Revisiting Odd-Even Effects in Wetting Properties of n-Alkanethiolate SAMs

    Directory of Open Access Journals (Sweden)

    Zhengjia Wang

    2015-12-01

    Full Text Available This review discusses the Porter-Whitesides discrepancy in wetting properties of n-alkanethiolate self-assembled monolayers (SAMs. About 25 years ago, Whitesides and coworker failed to observe any odd-even effect in wetting, however, Porter and his coworker did, albeit in select cases. Most previous studies agreed with Whitesides’ results, suggesting the absence of the odd-even effect in hydrophobicity of n-alkanethiolate SAMs. Recent reports have, however, found the odd-even effect in hydrophobicity of n-alkanethiolate SAMs on smooth substrates, indicating that hydrophobicity, and analogous interfacial properties, of n-alkanethiolate SAMs significantly depends on the properties of substrate. Unfortunately, the Whitesides and Porter papers do not report on the quality of the surfaces used. Based on recent work, we inferred that the original discrepancy between Whitesides and Porter can be attributed to the quality of the surface. Odd-even effect of SAMs in charge transport, capacitance, friction, and SAM structure are also discussed in this review to inform the general discussion. The discrepancy between Porter's group and Whitesides’ group could be due to surface roughness, morphology, oxidation, and adventitious contaminants.

  14. Safety and Waste Management for SAM Pathogen Methods

    Science.gov (United States)

    The General Safety and Waste Management page offers section-specific safety and waste management details for the pathogens included in EPA's Selected Analytical Methods for Environmental Remediation and Recovery (SAM).

  15. Safety and Waste Management for SAM Biotoxin Methods

    Science.gov (United States)

    The General Safety and Waste Management page offers section-specific safety and waste management details for the biotoxins included in EPA's Selected Analytical Methods for Environmental Remediation and Recovery (SAM).

  16. ISO19770-1:2012 SAM process guidance

    CERN Document Server

    Canavan, Rory

    2012-01-01

    The pocket guide offers a concise summary of the principles of software asset management as conveyed by ISO 19770-1: 2012, and provides advice and guidance on how to kick-start your own SAM programme - something the Standard alone doesn't offer.

  17. Safety and Waste Management for SAM Chemistry Methods

    Science.gov (United States)

    The General Safety and Waste Management page offers section-specific safety and waste management details for the chemical analytes included in EPA's Selected Analytical Methods for Environmental Remediation and Recovery (SAM).

  18. Safety and Waste Management for SAM Radiochemical Methods

    Science.gov (United States)

    The General Safety and Waste Management page offers section-specific safety and waste management details for the radiochemical analytes included in EPA's Selected Analytical Methods for Environmental Remediation and Recovery (SAM).

  19. Necrosis-Driven Systemic Immune Response Alters SAM Metabolism through the FOXO-GNMT Axis

    Directory of Open Access Journals (Sweden)

    Fumiaki Obata

    2014-05-01

    Full Text Available Sterile inflammation triggered by endogenous factors is thought to contribute to the pathogenesis of acute and chronic inflammatory diseases. Here, we demonstrate that apoptosis-deficient mutants spontaneously develop a necrosis-driven systemic immune response in Drosophila and provide an in vivo model for studying the organismal response to sterile inflammation. Metabolomic analysis of hemolymph from apoptosis-deficient mutants revealed increased sarcosine and reduced S-adenosyl-methionine (SAM levels due to glycine N-methyltransferase (Gnmt upregulation. We showed that Gnmt was elevated in response to Toll activation induced by the local necrosis of wing epidermal cells. Necrosis-driven inflammatory conditions induced dFoxO hyperactivation, leading to an energy-wasting phenotype. Gnmt was cell-autonomously upregulated by dFoxO in the fat body as a possible rheostat for controlling energy loss, which functioned during fasting as well as inflammatory conditions. We propose that the dFoxO-Gnmt axis is essential for the maintenance of organismal SAM metabolism and energy homeostasis.

  20. SAM-CE, Time-Dependent 3-D Neutron Transport, Gamma Transport in Complex Geometry by Monte-Carlo

    International Nuclear Information System (INIS)

    2003-01-01

    1 - Nature of physical problem solved: The SAM-CE system comprises two Monte Carlo codes, SAM-F and SAM-A. SAM-F supersedes the forward Monte Carlo code, SAM-C. SAM-A is an adjoint Monte Carlo code designed to calculate the response due to fields of primary and secondary gamma radiation. The SAM-CE system is a FORTRAN Monte Carlo computer code designed to solve the time-dependent neutron and gamma-ray transport equations in complex three-dimensional geometries. SAM-CE is applicable for forward neutron calculations and for forward as well as adjoint primary gamma-ray calculations. In addition, SAM-CE is applicable for the gamma-ray stage of the coupled neutron-secondary gamma ray problem, which may be solved in either the forward or the adjoint mode. Time-dependent fluxes, and flux functionals such as dose, heating, count rates, etc., are calculated as functions of energy, time and position. Multiple scoring regions are permitted and these may be either finite volume regions or point detectors or both. Other scores of interest, e.g., collision and absorption densities, etc., are also made. 2 - Method of solution: A special feature of SAM-CE is its use of the 'combinatorial geometry' technique which affords the user geometric capabilities exceeding those available with other commonly used geometric packages. All nuclear interaction cross section data (derived from the ENDF for neutrons and from the UNC-format library for gamma-rays) are tabulated in point energy meshes. The energy meshes for neutrons are internally derived, based on built-in convergence criteria and user- supplied tolerances. Tabulated neutron data for each distinct nuclide are in unique and appropriate energy meshes. Both resolved and unresolved resonance parameters from ENDF data files are treated automatically, and extremely precise and detailed descriptions of cross section behaviour is permitted. Such treatment avoids the ambiguities usually associated with multi-group codes, which use flux

  1. Monovalent Cation Activation of the Radical SAM Enzyme Pyruvate Formate-Lyase Activating Enzyme.

    Science.gov (United States)

    Shisler, Krista A; Hutcheson, Rachel U; Horitani, Masaki; Duschene, Kaitlin S; Crain, Adam V; Byer, Amanda S; Shepard, Eric M; Rasmussen, Ashley; Yang, Jian; Broderick, William E; Vey, Jessica L; Drennan, Catherine L; Hoffman, Brian M; Broderick, Joan B

    2017-08-30

    Pyruvate formate-lyase activating enzyme (PFL-AE) is a radical S-adenosyl-l-methionine (SAM) enzyme that installs a catalytically essential glycyl radical on pyruvate formate-lyase. We show that PFL-AE binds a catalytically essential monovalent cation at its active site, yet another parallel with B 12 enzymes, and we characterize this cation site by a combination of structural, biochemical, and spectroscopic approaches. Refinement of the PFL-AE crystal structure reveals Na + as the most likely ion present in the solved structures, and pulsed electron nuclear double resonance (ENDOR) demonstrates that the same cation site is occupied by 23 Na in the solution state of the as-isolated enzyme. A SAM carboxylate-oxygen is an M + ligand, and EPR and circular dichroism spectroscopies reveal that both the site occupancy and the identity of the cation perturb the electronic properties of the SAM-chelated iron-sulfur cluster. ENDOR studies of the PFL-AE/[ 13 C-methyl]-SAM complex show that the target sulfonium positioning varies with the cation, while the observation of an isotropic hyperfine coupling to the cation by ENDOR measurements establishes its intimate, SAM-mediated interaction with the cluster. This monovalent cation site controls enzyme activity: (i) PFL-AE in the absence of any simple monovalent cations has little-no activity; and (ii) among monocations, going down Group 1 of the periodic table from Li + to Cs + , PFL-AE activity sharply maximizes at K + , with NH 4 + closely matching the efficacy of K + . PFL-AE is thus a type I M + -activated enzyme whose M + controls reactivity by interactions with the cosubstrate, SAM, which is bound to the catalytic iron-sulfur cluster.

  2. The ALICE Glance Shift Accounting Management System (SAMS)

    Science.gov (United States)

    Martins Silva, H.; Abreu Da Silva, I.; Ronchetti, F.; Telesca, A.; Maidantchik, C.

    2015-12-01

    ALICE (A Large Ion Collider Experiment) is an experiment at the CERN LHC (Large Hadron Collider) studying the physics of strongly interacting matter and the quark-gluon plasma. The experiment operation requires a 24 hours a day and 7 days a week shift crew at the experimental site, composed by the ALICE collaboration members. Shift duties are calculated for each institute according to their correlated members. In order to ensure the full coverage of the experiment operation as well as its good quality, the ALICE Shift Accounting Management System (SAMS) is used to manage the shift bookings as well as the needed training. ALICE SAMS is the result of a joint effort between the Federal University of Rio de Janeiro (UFRJ) and the ALICE Collaboration. The Glance technology, developed by the UFRJ and the ATLAS experiment, sits at the basis of the system as an intermediate layer isolating the particularities of the databases. In this paper, we describe the ALICE SAMS development process and functionalities. The database has been modelled according to the collaboration needs and is fully integrated with the ALICE Collaboration repository to access members information and respectively roles and activities. Run, period and training coordinators can manage their subsystem operation and ensure an efficient personnel management. Members of the ALICE collaboration can book shifts and on-call according to pre-defined rights. ALICE SAMS features a user profile containing all the statistics and user contact information as well as the Institutes profile. Both the user and institute profiles are public (within the scope of the collaboration) and show the credit balance in real time. A shift calendar allows the Run Coordinator to plan data taking periods in terms of which subsystems shifts are enabled or disabled and on-call responsible people and slots. An overview display presents the shift crew present in the control room and allows the Run Coordination team to confirm the presence

  3. Molten Salt Power Tower Cost Model for the System Advisor Model (SAM)

    Energy Technology Data Exchange (ETDEWEB)

    Turchi, C. S.; Heath, G. A.

    2013-02-01

    This report describes a component-based cost model developed for molten-salt power tower solar power plants. The cost model was developed by the National Renewable Energy Laboratory (NREL), using data from several prior studies, including a contracted analysis from WorleyParsons Group, which is included herein as an Appendix. The WorleyParsons' analysis also estimated material composition and mass for the plant to facilitate a life cycle analysis of the molten salt power tower technology. Details of the life cycle assessment have been published elsewhere. The cost model provides a reference plant that interfaces with NREL's System Advisor Model or SAM. The reference plant assumes a nominal 100-MWe (net) power tower running with a nitrate salt heat transfer fluid (HTF). Thermal energy storage is provided by direct storage of the HTF in a two-tank system. The design assumes dry-cooling. The model includes a spreadsheet that interfaces with SAM via the Excel Exchange option in SAM. The spreadsheet allows users to estimate the costs of different-size plants and to take into account changes in commodity prices. This report and the accompanying Excel spreadsheet can be downloaded at https://sam.nrel.gov/cost.

  4. RNA-Guided Activation of Pluripotency Genes in Human Fibroblasts

    DEFF Research Database (Denmark)

    Xiong, Kai; Zhou, Yan; Blichfeld, Kristian Aabo

    2017-01-01

    -associated protein 9 (dCas9)-VP64 (CRISPRa) alone, or a combination of dCas9-VP64 and MS2-P65-HSF1 [synergistic activation mediator (SAM) system] mediated activation of five pluripotency genes: KLF4 (K), LIN28 (L), MYC (M), OCT4 (O), and SOX2 (S) in human cells (HEK293T, HeLa, HepG2, and primary fibroblasts...... could be obtained from these SAM fibroblasts. In conclusion, our study showed that CRISPR/Cas9-based ATFs are potent to activate and maintain transcription of endogenous human pluripotent genes. However, future improvements of the system are still required to improve activation efficiency and cellular...

  5. Fabrication and tribological properties of self-assembled monolayer of n-alkyltrimethoxysilane on silicon: Effect of SAM alkyl chain length

    International Nuclear Information System (INIS)

    Huo, Lixia; Du, Pengcheng; Zhou, Hui; Zhang, Kaifeng; Liu, Peng

    2017-01-01

    Highlights: • n-Alkyltrimethoxysilanes with various chain lengths were self-assembled on silicon. • Effect of alkyl chain lengths (C6, C12, or C18) on the SAMs was investigated. • Surface roughness of the SAMs decreased with increasing the alkyl chain lengths. • The C 12 -SAM possessed superior friction reduction and wear resistance. - Abstract: It is well known that the self-assembled organic molecules on a solid surface exhibit the friction-reducing performance. However, the effect of the molecular size of the self-assembled organic molecules has not been established. In the present work, self-assembled monolayers (SAMs) of n-alkyltrimethoxysilanes with different alkyl chain lengths (C 6 , C 12 , or C 18 ) were fabricated on silicon substrate. The water contact angles of the SAMs increased from 26.8° of the hydroxylated silicon substrate to near 60° after self-assembly. The atomic force microscopy (AFM) analysis results showed that the mean roughness (R a ) of the SAMs decreased with increasing the alkyl chain length. The tribological properties of the SAMs sliding against Al 2 O 3 ball were evaluated on an UMT-2 tribometer, and the worn surfaces of the samples were analyzed by means of Nano Scratch Tester and surface profilometry. It was found that lowest friction coefficient and smallest width of wear were achieved with the SAMs of C 12 alkyl chain (C 12 -SAM). The superior friction reduction and wear resistance of the SAMs in comparison with the bare silicon substrate are attributed to good adhesion of the self-assembled films to the substrate, especially the C 12 -SAM with desirable alkyl chain length.

  6. Fabrication and Surface Properties of Composite Films of SAM/Pt/ZnO/SiO 2

    KAUST Repository

    Yao, Ke Xin

    2008-12-16

    Through synthetic architecture and functionalization with self-assembled monolayers (SAMs), complex nanocomposite films of SAM/Pt/ZnO/SiO2 have been facilely prepared in this work. The nanostructured films are highly uniform and porous, showing a wide range of tunable wettabilities from superhydrophilicity to superhydrophobicity (water contact angles: 0° to 170°). Our approach offers synthetic flexibility in controlling film architecture, surface topography, coating texture, crystallite size, and chemical composition of modifiers (e.g., SAMs derived from alkanethiols). For example, wettability properties of the nanocomposite films can be finely tuned with both inorganic phase (i.e., ZnO/SiO2 and Pt/ZnO/SiO2) and organic phase (i.e., SAMs on Pt/ZnO/SiO2). Due to the presence of catalytic components Pt/ZnO within the nanocomposites, surface reactions of the organic modifiers can further take place at room temperature and elevated temperatures, which provides a means for SAM formation and elimination. Because the Pt/ZnO forms an excellent pair of metal-semiconductors for photocatalysis, the anchored SAMs can also be modified or depleted by UV irradiation (i.e., the films possess self-cleaning ability). Potential applications of these nanocomposite films have been addressed. Our durability tests also confirm that the films are thermally stable and structurally robust in modification- regeneration cycles. © 2008 American Chemical Society.

  7. Bidirectional manipulation of gene expression in adipocytes using CRISPRa and siRNA

    DEFF Research Database (Denmark)

    Lundh, Morten; Pluciñska, Kaja; Isidor, Marie S

    2017-01-01

    OBJECTIVE: Functional investigation of novel gene/protein targets associated with adipocyte differentiation or function heavily relies on efficient and accessible tools to manipulate gene expression in adipocytes in vitro. Recent advances in gene-editing technologies such as CRISPR-Cas9 have...... not only eased gene editing but also greatly facilitated modulation of gene expression without altering the genome. Here, we aimed to develop and validate a competent in vitro adipocyte model of controllable functionality as well as multiplexed gene manipulation in adipocytes, using the CRISPRa "SAM......" system and siRNAs to simultaneously overexpress and silence selected genes in the same cell populations. METHODS: We introduced a stable expression of dCas9-VP64 and MS2-P65, the core components of the CRIPSRa SAM system, in mesenchymal C3H/10T1/2 cells through viral delivery and used guide RNAs...

  8. Agp2, a Member of the Yeast Amino Acid Permease Family, Positively Regulates Polyamine Transport at the Transcriptional Level

    KAUST Repository

    Aouida, Mustapha

    2013-06-03

    Agp2 is a plasma membrane protein of the Saccharomyces cerevisiae amino acid transporter family, involved in high-affinity uptake of various substrates including L-carnitine and polyamines. The discovery of two high affinity polyamine permeases, Dur3 and Sam3, prompted us to investigate whether Agp2 directly transports polyamines or acts instead as a regulator. Herein, we show that neither dur3? nor sam3? single mutant is defective in polyamine transport, while the dur3? sam3? double mutant exhibits a sharp decrease in polyamine uptake and an increased resistance to polyamine toxicity similar to the agp2? mutant. Studies of Agp2 localization indicate that in the double mutant dur3? sam3?, Agp2-GFP remains plasma membrane-localized, even though transport of polyamines is strongly reduced. We further demonstrate that Agp2 controls the expression of several transporter genes including DUR3 and SAM3, the carnitine transporter HNM1 and several hexose, nucleoside and vitamin permease genes, in addition to SKY1 encoding a SR kinase that positively regulates low-affinity polyamine uptake. Furthermore, gene expression analysis clearly suggests that Agp2 is a strong positive regulator of additional biological processes. Collectively, our data suggest that Agp2 might respond to environmental cues and thus regulate the expression of several genes including those involved in polyamine transport. © 2013 Aouida et al.

  9. Agp2, a Member of the Yeast Amino Acid Permease Family, Positively Regulates Polyamine Transport at the Transcriptional Level

    KAUST Repository

    Aouida, Mustapha; Texeira, Marta Rubio; Thevelein, Johan M.; Poulin, Richard; Ramotar, Dindial

    2013-01-01

    Agp2 is a plasma membrane protein of the Saccharomyces cerevisiae amino acid transporter family, involved in high-affinity uptake of various substrates including L-carnitine and polyamines. The discovery of two high affinity polyamine permeases, Dur3 and Sam3, prompted us to investigate whether Agp2 directly transports polyamines or acts instead as a regulator. Herein, we show that neither dur3? nor sam3? single mutant is defective in polyamine transport, while the dur3? sam3? double mutant exhibits a sharp decrease in polyamine uptake and an increased resistance to polyamine toxicity similar to the agp2? mutant. Studies of Agp2 localization indicate that in the double mutant dur3? sam3?, Agp2-GFP remains plasma membrane-localized, even though transport of polyamines is strongly reduced. We further demonstrate that Agp2 controls the expression of several transporter genes including DUR3 and SAM3, the carnitine transporter HNM1 and several hexose, nucleoside and vitamin permease genes, in addition to SKY1 encoding a SR kinase that positively regulates low-affinity polyamine uptake. Furthermore, gene expression analysis clearly suggests that Agp2 is a strong positive regulator of additional biological processes. Collectively, our data suggest that Agp2 might respond to environmental cues and thus regulate the expression of several genes including those involved in polyamine transport. © 2013 Aouida et al.

  10. Annals of SAM meeting `96. National meeting on precious metals; Anales de las jornadas SAM `96. Encuentro nacional de metales preciosos

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-12-31

    Works are presented at the SAM meeting `96 of the Argentine Materials Association. The papers can be grouped under the following main topics: physical metallurgy; ceramics; polymers; precious metals; extractive metallurgy; corrosion; powder metallurgy. refs., ills.

  11. Fabrication and tribological properties of self-assembled monolayer of n-alkyltrimethoxysilane on silicon: Effect of SAM alkyl chain length

    Energy Technology Data Exchange (ETDEWEB)

    Huo, Lixia [National Key Laboratory of Science and Technology on Vacuum Technology and Physics, Lanzhou Institute of Physics, Lanzhou, Gansu 730010 (China); Institute of Polymer Science and Engineering, College of Chemistry and Chemical Engineering, Lanzhou University, Gansu 730000 (China); Du, Pengcheng [Institute of Polymer Science and Engineering, College of Chemistry and Chemical Engineering, Lanzhou University, Gansu 730000 (China); Zhou, Hui; Zhang, Kaifeng [National Key Laboratory of Science and Technology on Vacuum Technology and Physics, Lanzhou Institute of Physics, Lanzhou, Gansu 730010 (China); Liu, Peng, E-mail: pliu@lzu.edu.cn [Institute of Polymer Science and Engineering, College of Chemistry and Chemical Engineering, Lanzhou University, Gansu 730000 (China)

    2017-02-28

    Highlights: • n-Alkyltrimethoxysilanes with various chain lengths were self-assembled on silicon. • Effect of alkyl chain lengths (C6, C12, or C18) on the SAMs was investigated. • Surface roughness of the SAMs decreased with increasing the alkyl chain lengths. • The C{sub 12}-SAM possessed superior friction reduction and wear resistance. - Abstract: It is well known that the self-assembled organic molecules on a solid surface exhibit the friction-reducing performance. However, the effect of the molecular size of the self-assembled organic molecules has not been established. In the present work, self-assembled monolayers (SAMs) of n-alkyltrimethoxysilanes with different alkyl chain lengths (C{sub 6}, C{sub 12}, or C{sub 18}) were fabricated on silicon substrate. The water contact angles of the SAMs increased from 26.8° of the hydroxylated silicon substrate to near 60° after self-assembly. The atomic force microscopy (AFM) analysis results showed that the mean roughness (R{sub a}) of the SAMs decreased with increasing the alkyl chain length. The tribological properties of the SAMs sliding against Al{sub 2}O{sub 3} ball were evaluated on an UMT-2 tribometer, and the worn surfaces of the samples were analyzed by means of Nano Scratch Tester and surface profilometry. It was found that lowest friction coefficient and smallest width of wear were achieved with the SAMs of C{sub 12} alkyl chain (C{sub 12}-SAM). The superior friction reduction and wear resistance of the SAMs in comparison with the bare silicon substrate are attributed to good adhesion of the self-assembled films to the substrate, especially the C{sub 12}-SAM with desirable alkyl chain length.

  12. The Combustion Experiment on the Sample Analysis at Mars (SAM) Instrument Suite on the Curiosity Rover

    Science.gov (United States)

    Stern, J. C.; Malespin, C. A.; Eigenbrode, J. L.; Graham, H. V.; Archer, P. D., Jr.; Brunner, A. E.; Freissinet, C.; Franz, H. B.; Fuentes, J.; Glavin, D. P.; hide

    2014-01-01

    The combustion experiment on the Sample Analysis at Mars (SAM) suite on Curiosity will heat a sample of Mars regolith in the presence of oxygen and measure composition of the evolved gases using quadrupole mass spectrometry (QMS) and tunable laser spectrometry (TLS). QMS will enable detection of combustion products such as CO, CO2, NO, and other oxidized species, while TLS will enable precise measurements of the abundance and carbon isotopic composition (delta(sup 13)C) of the evolved CO2 and hydrogen isotopic composition (deltaD) of H2O. SAM will perform a two-step combustion to isolate combustible materials below approx.550 C and above approx.550 C. The combustion experiment on SAM, if properly designed and executed, has the potential to answer multiple questions regarding the origins of volatiles seen thus far in SAM evolved gas analysis (EGA) on Mars. Constraints imposed by SAM and MSL time and power resources, as well as SAM consumables (oxygen gas), will limit the number of SAM combustion experiments, so it is imperative to design an experiment targeting the most pressing science questions. Low temperature combustion experiments will primarily target the quantification of carbon (and nitrogen) contributed by SAM wet chemistry reagants MTBSTFA (N-Methyl-N-tert-butyldimethylsilyltrifluoroacetamide) and DMF (Dimethylformamide), which have been identified in the background of blank and sample runs and may adsorb to the sample while the cup is in the Sample Manipulation System (SMS). In addition, differences between the sample and "blank" may yield information regarding abundance and delta(sup 13)C of bulk (both organic and inorganic) martian carbon. High temperature combustion experiments primarily aim to detect refractory organic matter, if present in Cumberland fines, as well as address the question of quantification and deltaD value of water evolution associated with hydroxyl hydrogen in clay minerals.

  13. Kuula. Kuu artist Sam Sparro. Kuu plaat / Mart Juur

    Index Scriptorium Estoniae

    Juur, Mart, 1964-

    2008-01-01

    Artistist Sam Sparrost. Heliplaatidest: "Sex And The City" Original Motion Picture Soundtrack, "Maestro: Blue Note Trip", Melvin/Soo/Remmel/Julm "Geografix", Alanis Morrisette "Flavors Of Entanglement", Guillemots "Red"

  14. Genes with stable DNA methylation levels show higher evolutionary conservation than genes with fluctuant DNA methylation levels.

    Science.gov (United States)

    Zhang, Ruijie; Lv, Wenhua; Luan, Meiwei; Zheng, Jiajia; Shi, Miao; Zhu, Hongjie; Li, Jin; Lv, Hongchao; Zhang, Mingming; Shang, Zhenwei; Duan, Lian; Jiang, Yongshuai

    2015-11-24

    Different human genes often exhibit different degrees of stability in their DNA methylation levels between tissues, samples or cell types. This may be related to the evolution of human genome. Thus, we compared the evolutionary conservation between two types of genes: genes with stable DNA methylation levels (SM genes) and genes with fluctuant DNA methylation levels (FM genes). For long-term evolutionary characteristics between species, we compared the percentage of the orthologous genes, evolutionary rate dn/ds and protein sequence identity. We found that the SM genes had greater percentages of the orthologous genes, lower dn/ds, and higher protein sequence identities in all the 21 species. These results indicated that the SM genes were more evolutionarily conserved than the FM genes. For short-term evolutionary characteristics among human populations, we compared the single nucleotide polymorphism (SNP) density, and the linkage disequilibrium (LD) degree in HapMap populations and 1000 genomes project populations. We observed that the SM genes had lower SNP densities, and higher degrees of LD in all the 11 HapMap populations and 13 1000 genomes project populations. These results mean that the SM genes had more stable chromosome genetic structures, and were more conserved than the FM genes.

  15. Fabrication and Surface Properties of Composite Films of SAM/Pt/ZnO/SiO 2

    KAUST Repository

    Yao, Ke Xin; Zeng, Hua Chun

    2008-01-01

    Through synthetic architecture and functionalization with self-assembled monolayers (SAMs), complex nanocomposite films of SAM/Pt/ZnO/SiO2 have been facilely prepared in this work. The nanostructured films are highly uniform and porous, showing a

  16. Fabrication and tribological properties of self-assembled monolayer of n-alkyltrimethoxysilane on silicon: Effect of SAM alkyl chain length

    Science.gov (United States)

    Huo, Lixia; Du, Pengcheng; Zhou, Hui; Zhang, Kaifeng; Liu, Peng

    2017-02-01

    It is well known that the self-assembled organic molecules on a solid surface exhibit the friction-reducing performance. However, the effect of the molecular size of the self-assembled organic molecules has not been established. In the present work, self-assembled monolayers (SAMs) of n-alkyltrimethoxysilanes with different alkyl chain lengths (C6, C12, or C18) were fabricated on silicon substrate. The water contact angles of the SAMs increased from 26.8° of the hydroxylated silicon substrate to near 60° after self-assembly. The atomic force microscopy (AFM) analysis results showed that the mean roughness (Ra) of the SAMs decreased with increasing the alkyl chain length. The tribological properties of the SAMs sliding against Al2O3 ball were evaluated on an UMT-2 tribometer, and the worn surfaces of the samples were analyzed by means of Nano Scratch Tester and surface profilometry. It was found that lowest friction coefficient and smallest width of wear were achieved with the SAMs of C12 alkyl chain (C12-SAM). The superior friction reduction and wear resistance of the SAMs in comparison with the bare silicon substrate are attributed to good adhesion of the self-assembled films to the substrate, especially the C12-SAM with desirable alkyl chain length.

  17. Optimization of pentacene double floating gate memories based on charge injection regulated by SAM functionalization

    Directory of Open Access Journals (Sweden)

    S. Li

    2018-02-01

    Full Text Available Pentacene based double nano-floating gate memories (NFGM by using gold nanoparticles (Au NPs and reduced graphene oxide (rGO sheets as charge trapping layers are prepared and demonstrated. Particularly, the NFGM chemically treated by 2,3,4,5,6-pentafluorobenzenethiol (PFBT self-assembled monolayers (SAM exhibits excellent memory performances, including high mobility of 0.23 cm2V-1s-1, the large memory window of 51 V, and the stable retention property more than 108 s. Comparing the performances of NFGM without treating with PFBT SAM, the improving performances of the memory devices by SAM modification are explained by the increase of charge injection, which could be further investigated by XPS and UPS. In particular, the results highlight the utility of SAM modulations and controlling of charge transport in the development of organic transistor memories.

  18. Optimization of pentacene double floating gate memories based on charge injection regulated by SAM functionalization

    Science.gov (United States)

    Li, S.; Guérin, D.; Lenfant, S.; Lmimouni, K.

    2018-02-01

    Pentacene based double nano-floating gate memories (NFGM) by using gold nanoparticles (Au NPs) and reduced graphene oxide (rGO) sheets as charge trapping layers are prepared and demonstrated. Particularly, the NFGM chemically treated by 2,3,4,5,6-pentafluorobenzenethiol (PFBT) self-assembled monolayers (SAM) exhibits excellent memory performances, including high mobility of 0.23 cm2V-1s-1, the large memory window of 51 V, and the stable retention property more than 108 s. Comparing the performances of NFGM without treating with PFBT SAM, the improving performances of the memory devices by SAM modification are explained by the increase of charge injection, which could be further investigated by XPS and UPS. In particular, the results highlight the utility of SAM modulations and controlling of charge transport in the development of organic transistor memories.

  19. Bringing a Chemical Laboratory Named Sam to Mars on the 2011 Curiosity Rover

    Science.gov (United States)

    Mahaffy, P. R.; Bleacher, L.; Jones, A.; Conrad, P. G.; Cabane, M.; Webster, C. R.; Atreya, S. A.; Manning, H.

    2010-01-01

    An important goal of upcoming missions to Mars is to understand if life could have developed there. The task of the Sample Analysis at Mars (SAM) suite of instruments [1] and the other Curiosity investigations [2] is to move us steadily toward that goal with an assessment of the habitability of our neighboring planet through a series of chemical and geological measurements. SAM is designed to search for organic compounds and inorganic volatiles and measure isotope ratios. Other instruments on Curiosity will provide elemental analysis and identify minerals. SAM will analyze both atmospheric samples and gases evolved from powdered rocks that may have formed billions of years ago with Curiosity providing access to interesting sites scouted by orbiting cameras and spectrometers.

  20. A magnesium-induced triplex pre-organizes the SAM-II riboswitch.

    Directory of Open Access Journals (Sweden)

    Susmita Roy

    2017-03-01

    Full Text Available Our 13C- and 1H-chemical exchange saturation transfer (CEST experiments previously revealed a dynamic exchange between partially closed and open conformations of the SAM-II riboswitch in the absence of ligand. Here, all-atom structure-based molecular simulations, with the electrostatic effects of Manning counter-ion condensation and explicit magnesium ions are employed to calculate the folding free energy landscape of the SAM-II riboswitch. We use this analysis to predict that magnesium ions remodel the landscape, shifting the equilibrium away from the extended, partially unfolded state towards a compact, pre-organized conformation that resembles the ligand-bound state. Our CEST and SAXS experiments, at different magnesium ion concentrations, quantitatively confirm our simulation results, demonstrating that magnesium ions induce collapse and pre-organization. Agreement between theory and experiment bolsters microscopic interpretation of our simulations, which shows that triplex formation between helix P2b and loop L1 is highly sensitive to magnesium and plays a key role in pre-organization. Pre-organization of the SAM-II riboswitch allows rapid detection of ligand with high selectivity, which is important for biological function.

  1. Simulated SAM A-scans on multilayer MEMS components

    DEFF Research Database (Denmark)

    Janting, Jakob; Petersen, Dirch Hjorth; Greisen, Christoffer

    2002-01-01

    A spreadsheet program for simulation of Scanning Acoustic Microscopy (SAM) A-scans on multilayer structures has been developed. Using this program, structure variations in samples can be analysed better. Further samples can be prepared to get optimal signal for enhanced failure and materials...

  2. Sam68 promotes Schwann cell proliferation by enhancing the PI3K/Akt pathway and acts on regeneration after sciatic nerve crush

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Weijie, E-mail: 459586768@qq.com; Liu, Yuxi, E-mail: 924013616@qq.com; Wang, Youhua, E-mail: wyouhua1516@163.com

    2016-05-13

    Sam68 (Src-associated in mitosis of 68 kD), a KH domain RNA-binding protein, is not only important in signaling transduction cascades, but crucial in a variety of cellular processes. Sam68 is reported to be involved in the phospoinositide3-kinase (PI3K) and nuclear factor-kappa B (NF-κB) signaling pathways, and it is closely associated with cell proliferation, RNA metabolism, and tumor progression. However, we know little about the role of Sam68 during peripheral nervous system injury and regeneration. In this study, we investigated the expression of Sam68 and its biological significances in sciatic nerve crush. Interestingly, we found Sam68 had a co-localization with S100 (Schwann cell marker). Moreover, after crush, Sam68 had a spatiotemporal protein expression, which was in parallel with proliferation cell nuclear antigen (PCNA). In vitro, we also observed increased expression of Sam68 during the process of TNF-α-induced Schwann cell proliferation model. Besides, flow cytometry analyses, CCK-8, and EDU were all performed with the purpose of investigating the role of Sam68 in the regulation of Schwann cell proliferation. Even more importantly, we discovered that Sam68 could enhance the phosphorylation of Akt while LY294002 (a PI3K inhibitor) obviously reversed Sam68-induced cell proliferation. Finally, we detected the variance during regeneration progress through the rat walk footprint test. In summary, all these evidences demonstrated that Sam68 might participate in Schwann cell proliferation partially via PI3K/Akt pathway and also regulate regeneration after sciatic nerve crush. -- Highlights: •The dynamic changes and location of Sam68 after sciatic nerve crush. •Sam68 promoted Schwann cell proliferation via PI3K/Akt pathway. •Sam68 modulated functional recovery after sciatic nerve crush.

  3. Sam68 promotes Schwann cell proliferation by enhancing the PI3K/Akt pathway and acts on regeneration after sciatic nerve crush

    International Nuclear Information System (INIS)

    Wu, Weijie; Liu, Yuxi; Wang, Youhua

    2016-01-01

    Sam68 (Src-associated in mitosis of 68 kD), a KH domain RNA-binding protein, is not only important in signaling transduction cascades, but crucial in a variety of cellular processes. Sam68 is reported to be involved in the phospoinositide3-kinase (PI3K) and nuclear factor-kappa B (NF-κB) signaling pathways, and it is closely associated with cell proliferation, RNA metabolism, and tumor progression. However, we know little about the role of Sam68 during peripheral nervous system injury and regeneration. In this study, we investigated the expression of Sam68 and its biological significances in sciatic nerve crush. Interestingly, we found Sam68 had a co-localization with S100 (Schwann cell marker). Moreover, after crush, Sam68 had a spatiotemporal protein expression, which was in parallel with proliferation cell nuclear antigen (PCNA). In vitro, we also observed increased expression of Sam68 during the process of TNF-α-induced Schwann cell proliferation model. Besides, flow cytometry analyses, CCK-8, and EDU were all performed with the purpose of investigating the role of Sam68 in the regulation of Schwann cell proliferation. Even more importantly, we discovered that Sam68 could enhance the phosphorylation of Akt while LY294002 (a PI3K inhibitor) obviously reversed Sam68-induced cell proliferation. Finally, we detected the variance during regeneration progress through the rat walk footprint test. In summary, all these evidences demonstrated that Sam68 might participate in Schwann cell proliferation partially via PI3K/Akt pathway and also regulate regeneration after sciatic nerve crush. -- Highlights: •The dynamic changes and location of Sam68 after sciatic nerve crush. •Sam68 promoted Schwann cell proliferation via PI3K/Akt pathway. •Sam68 modulated functional recovery after sciatic nerve crush.

  4. Rainfall declines over Queensland from 1951-2007 and links to the Subtropical Ridge and the SAM

    International Nuclear Information System (INIS)

    Cottrill, D A; Ribbe, J

    2010-01-01

    Much of southern and eastern Australia including Queensland have experienced rainfall declines over recent decades affecting agricultural production and accelerating water infrastructure development. Rainfall declines from southern Australia have now been directly related to changes in the Southern Annular Mode (SAM) and the subtropical ridge. In southern and coastal Queensland, the rainfall declines have occurred mostly in the austral summer and autumn. Observations from this region reveal the rainfall decline is correlated to an increase in the mean sea level pressure (MSLP) at many stations. The largest increases in MSLP are over southeast Queensland and coastal regions, where some of the largest rainfall declines occur. This study indicates the subtropical ridge as one of the main factors in the rainfall decline over this region. SAM is also likely to be important, although its seasonal influence, apart from winter, is harder to determine.

  5. Development of the criticality capability for the SAM-CE Monte Carlo System

    International Nuclear Information System (INIS)

    Lichtenstein, H.; Troubetzkoy, E.; Steinberg, H.; Cohen, M.O.

    1979-04-01

    A criticality capabilty has been developed and implemented in the SAM-CE Monte Carlo system. The data processing component, SAM-X, preserves, to any required accuracy, the data quality inherent in the ENDF/B library. The generated data is Doppler-broadened and includes (where applicable) probability tables for the unresolved resonance range, and thermal-scattering law data. Curves of several total and partial cross sections are generated and displayed. The Monte Carlo component, SAM-F, includes several eigenvalue estimators and variance reduction schemes. Stratification was found to effect significant improvement in calculational efficiency, but the usefulness of importance sampling is marginal in criticality problems. The entire system has been installed at BNL, for the analysis of TRX benchmarks. The TRX-1 and TRX-2 cell calculations have been performed, with estimated eigenvalues of 1.1751 +- 0.0016 and 1.1605 +- .0015, respectively. These results are shown to be statistically consistent with other sources

  6. Raman mapping and in situ SERS spectroelectrochemical studies of 6-mercaptopurine SAMs on the gold electrode.

    Science.gov (United States)

    Yang, Haifeng; Liu, Yanli; Liu, Zhimin; Yang, Yu; Jiang, Jianhui; Zhang, Zongrang; Shen, Guoli; Yu, Ruqin

    2005-02-24

    The self-assembled monolayers (SAMs) of 6-mercaptopurine (6MP) were formed at the roughened polycrystalline gold surfaces in acid and alkaline media. The time-dependent Raman mapping spectral analysis in conjunction with the quantum calculations for the vibrational modes using ab initio BLYP/6-31G method suggested that both of the resulted 6MP SAMs adopted the same adsorption mode through the S atom of pyrimidine moiety and the N7 atom of the imidazole moiety anchoring the gold surface in a vertical way. The in situ surface-enhanced Raman scattering spectroelectrochemical experiment was conducted to examine the stability of the SAMs at various bias potentials. It was found that the detaching process of the 6MP SAMs from the surface involved one electron reduction as the voltage was applied at ca. 0.7 V vs a standard calomel electrode.

  7. Orientation of 6-mercaptopurine SAMs at the silver electrode as studied by Raman mapping and in situ SERS.

    Science.gov (United States)

    Chu, Hui; Yang, Haifeng; Huan, Shuangyan; Shen, Guoli; Yu, Ruqin

    2006-03-23

    Self-assembled monolayers (SAMs) of 6-mercaptopurine (6MP) on a silver electrode in acid and alkaline media were investigated by a combination protocol of the SERS technique with Raman mapping, and it was found that the adsorption mode of 6MP SAMs changed with the pH value of the environment. Quantum calculations for the vibrational mode were performed by the BLYP/6-31G method. 6MP was adsorbed on the silver electrode with a tilted orientation via S, N1, and N7 atoms in acid medium, while the SAMs adopted head-on adsorption modes with the S atom and the N1 atom anchoring the silver surface in alkaline medium. However, 6MP SAMs turned to the same upright orientation on the electrode through the S and N7 atoms when either acid or basic solution was removed. Stability of 6MP SAMs was observed by in situ SERS spectroelectrochemical measurements. The results reveal that the desorption potentials of 6MP SAMs formed under acid and alkaline conditions from the Ag electrode were at ca. -1.3 V and -1.6 V vs SCE, respectively.

  8. Kualitas Udara Beberapa Ruang Perpustakaan Di Universitas Sam Ratulangi Manado Berdasarkan Uji Kualitas Fisika

    OpenAIRE

    Sahilatua, Josefine D

    2014-01-01

    : Air pollution not only comes from the outdoors but also indoors. Library is indoors that could potentially by polluted. Level of air quality that not complies the standard will cause symptoms such as sneezing, coughing, skin irritation, shortness of breathing, eye irritation and headache on library users. This research conducted on the five libraries at the Sam Ratulangi University using observational methods. Data collected was content of physical air quality. The variables were air temper...

  9. The SAM, not the electrodes, dominates charge transport in metal-monolayer//Ga2O3/gallium-indium eutectic junctions.

    Science.gov (United States)

    Reus, William F; Thuo, Martin M; Shapiro, Nathan D; Nijhuis, Christian A; Whitesides, George M

    2012-06-26

    The liquid-metal eutectic of gallium and indium (EGaIn) is a useful electrode for making soft electrical contacts to self-assembled monolayers (SAMs). This electrode has, however, one feature whose effect on charge transport has been incompletely understood: a thin (approximately 0.7 nm) film-consisting primarily of Ga(2)O(3)-that covers its surface when in contact with air. SAMs that rectify current have been measured using this electrode in Ag(TS)-SAM//Ga(2)O(3)/EGaIn (where Ag(TS) = template-stripped Ag surface) junctions. This paper organizes evidence, both published and unpublished, showing that the molecular structure of the SAM (specifically, the presence of an accessible molecular orbital asymmetrically located within the SAM), not the difference between the electrodes or the characteristics of the Ga(2)O(3) film, causes the observed rectification. By examining and ruling out potential mechanisms of rectification that rely either on the Ga(2)O(3) film or on the asymmetry of the electrodes, this paper demonstrates that the structure of the SAM dominates charge transport through Ag(TS)-SAM//Ga(2)O(3)/EGaIn junctions, and that the electrical characteristics of the Ga(2)O(3) film have a negligible effect on these measurements.

  10. In Situ Analysis of Martian Regolith with the SAM Experiment During the First Mars Year of the MSL Mission: Identification of Organic Molecules by Gas Chromatography from Laboratory Measurements

    Science.gov (United States)

    Millan, M.; Szopa, C.; Buch, A.; Coll, P.; Glavin, D. P.; Freissinet, C.; Navarro-Gonzalez, R.; Francois, P.; Coscia, D.; Bonnet, J. Y.; hide

    2016-01-01

    The Sample Analysis at Mars (SAM) instrument onboard the Curiosity rover, is specifically designed for in situ molecular and isotopic analyses of martian surface materials and atmosphere. It contributes to the Mars Science Laboratory (MSL) missions primary scientific goal to characterize the potential past, present or future habitability of Mars. In all of the analyses of solid samples delivered to SAM so far, chlorinated organic compounds have been detected above instrument background levels and identified by gas chromatography coupled to mass spectrometry (GC-MS) (Freissinet et al., 2015; Glavin et al., 2013). While some of these may originate from reactions between oxychlorines and terrestrial organic carbon present in the instrument background (Glavin et al., 2013), others have been demonstrated to originate from indigenous organic carbon present in samples (Freissinet et al., 2015). We present here laboratory calibrations that focused on the analyses performed with the MXT-CLP GC column (SAM GC-5 channel) used for nearly all of the GC-MS analyses of the martian soil samples carried out with SAM to date. Complementary to the mass spectrometric data, gas chromatography allows us to separate and identify the species analyzable in a nominal SAM-GC run time of about 21 min. To characterize the analytical capabilities of this channel within the SAM Flight Model (FM) operating conditions on Mars, and their implications on the detection of organic matter, it is required to perform laboratory experimental tests and calibrations on spare model components. This work assesses the SAM flight GC-5 column efficiency, confirms the identification of the molecules based on their retention time, and enables a better understanding of the behavior of the SAM injection trap (IT) and its release of organic molecules. This work will enable further optimization of the SAM-GC runs for additional samples to be analyzed during the MSL mission.

  11. CE-SAM: a conversational interface for ISR mission support

    Science.gov (United States)

    Pizzocaro, Diego; Parizas, Christos; Preece, Alun; Braines, Dave; Mott, David; Bakdash, Jonathan Z.

    2013-05-01

    There is considerable interest in natural language conversational interfaces. These allow for complex user interactions with systems, such as fulfilling information requirements in dynamic environments, without requiring extensive training or a technical background (e.g. in formal query languages or schemas). To leverage the advantages of conversational interactions we propose CE-SAM (Controlled English Sensor Assignment to Missions), a system that guides users through refining and satisfying their information needs in the context of Intelligence, Surveillance, and Reconnaissance (ISR) operations. The rapidly-increasing availability of sensing assets and other information sources poses substantial challenges to effective ISR resource management. In a coalition context, the problem is even more complex, because assets may be "owned" by different partners. We show how CE-SAM allows a user to refine and relate their ISR information needs to pre-existing concepts in an ISR knowledge base, via conversational interaction implemented on a tablet device. The knowledge base is represented using Controlled English (CE) - a form of controlled natural language that is both human-readable and machine processable (i.e. can be used to implement automated reasoning). Users interact with the CE-SAM conversational interface using natural language, which the system converts to CE for feeding-back to the user for confirmation (e.g. to reduce misunderstanding). We show that this process not only allows users to access the assets that can support their mission needs, but also assists them in extending the CE knowledge base with new concepts.

  12. TRX and UO2 criticality benchmarks with SAM-CE

    International Nuclear Information System (INIS)

    Beer, M.; Troubetzkoy, E.S.; Lichtenstein, H.; Rose, P.F.

    1980-01-01

    A set of thermal reactor benchmark calculations with SAM-CE which have been conducted at both MAGI and at BNL are described. Their purpose was both validation of the SAM-CE reactor eigenvalue capability developed by MAGI and a substantial contribution to the data testing of both ENDF/B-IV and ENDF/B-V libraries. This experience also resulted in increased calculational efficiency of the code and an example is given. The benchmark analysis included the TRX-1 infinite cell using both ENDF/B-IV and ENDF/B-V cross section sets and calculations using ENDF/B-IV of the TRX-1 full core and TRX-2 cell. BAPL-UO2-1 calculations were conducted for the cell using both ENDF/B-IV and ENDF/B-V and for the full core with ENDF/B-V

  13. Hemoglobin alpha 2 gene +861 G>A polymorphism in Turkish ...

    African Journals Online (AJOL)

    Dilay Ciglidag Dungul

    carrying individuals with intact beta globin gene. DNA was extracted from peripheral blood sam- ples of seven healthy carrier individuals who have abnormal hemoglobin variants and 16 control individuals from Turkey. Complete coding and intronic sequences of HBA1 and HBA2 genes were amplified by polymerase chain ...

  14. Produksi Bahasa Tertulis Mahasiswa Penderita Disgrafia Di Fakultas Ilmu Budaya Universitas Sam Ratulangi

    OpenAIRE

    TANGKE, RIMA APRILIANA

    2015-01-01

    This research is entitled “Written Language Production of Student with Disgraphia in Faculty of Humanity Sam Ratulangi University”. The objectives of this research are to describe dysgraphia itself and to analyze the influences of dysgraphia on the written language production of the student in Faculty of Humanity, Sam Ratulangi University. This research uses a descriptive method. There are three steps to finish this research, the first step is preparation. In this step, the writer reads the r...

  15. THE MYTH OF MATERIAL SUCCESS AS REFLECTED IN SAM WALTON: MADE IN AMERICA-MY STORY

    Directory of Open Access Journals (Sweden)

    Utut Kurniati

    2015-12-01

    Full Text Available American myth of material success had been orchestrated five basic beliefs that were reflected in Sam Walton’s biography, Sam Walton: Made in America-My Story. Those beliefs were: 1 Having a strong will to be successful man in America, Sam Walton was aware that the American democracy allowed its citizens to rise above any limitation in which they may have been born; 2 Then, he rose up from his limitation by hard work. His hard work successfully brought him to the riches and physical comforts; 3 He believed that those rewards came to those who were deserving of them (virtuous; 4 He also believed that those rewards came to those who had the drive and ambition to attain them. Therefore, he was optimistic to attain success in America; 5 Hard work to attain success made Sam Walton a lucky man who received good luck in his life. As a result, his dream of being a successful man in America came true. Keywords: the myth of material success, American dream, hard work

  16. Analysis of the in-vessel phase of SAM strategy for a Korean 1000 MWe PWR

    Energy Technology Data Exchange (ETDEWEB)

    Cho, Sung-Min; Oh, Seung-Jong [KEPCO International Nuclear Graduate School (KINGS), Ulsan (Korea, Republic of). Dept. of NPP Engineering; Diab, Aya [KEPCO International Nuclear Graduate School (KINGS), Ulsan (Korea, Republic of). Dept. of NPP Engineering; Ain Shams Univ., Cairo (Egypt). Mechanical Power Engineering Dept.

    2017-12-15

    This paper focuses on the in-vessel phase of Severe Accident Management (SAM) strategy for a Korean 1000 MWe Pressurized Water Reactor (PWR) with reference to ROAAM+ framework approach. To apply ROAAM+, it is needed to identify epistemic and aleatory uncertainties. The selected scenario is a station blackout (SBO) and the corresponding SAM strategy is RCS depressurization followed by water injection into the reactor pressure vessel (RPV). The analysis considers the depressurization timing and the flow rate and timing of in-vessel injection for scenario variations. For the phenomenological uncertainties, the core melting and relocation process is considered to be the most important phenomenon in the in-vessel phase of SAM strategy. Accordingly, a sensitivity analysis is carried out to assess the impact of the cut-off porosity below which the flow area of a core node is zero (EPSCUT), and the critical temperature for cladding rupture (TCLMAX) on the core melting and relocation process. In this paper, the SAM strategy for maintaining the integrity of RPV is derived after quantification of the scenario and phenomenological uncertainties.

  17. Novel gene sets improve set-level classification of prokaryotic gene expression data.

    Science.gov (United States)

    Holec, Matěj; Kuželka, Ondřej; Železný, Filip

    2015-10-28

    Set-level classification of gene expression data has received significant attention recently. In this setting, high-dimensional vectors of features corresponding to genes are converted into lower-dimensional vectors of features corresponding to biologically interpretable gene sets. The dimensionality reduction brings the promise of a decreased risk of overfitting, potentially resulting in improved accuracy of the learned classifiers. However, recent empirical research has not confirmed this expectation. Here we hypothesize that the reported unfavorable classification results in the set-level framework were due to the adoption of unsuitable gene sets defined typically on the basis of the Gene ontology and the KEGG database of metabolic networks. We explore an alternative approach to defining gene sets, based on regulatory interactions, which we expect to collect genes with more correlated expression. We hypothesize that such more correlated gene sets will enable to learn more accurate classifiers. We define two families of gene sets using information on regulatory interactions, and evaluate them on phenotype-classification tasks using public prokaryotic gene expression data sets. From each of the two gene-set families, we first select the best-performing subtype. The two selected subtypes are then evaluated on independent (testing) data sets against state-of-the-art gene sets and against the conventional gene-level approach. The novel gene sets are indeed more correlated than the conventional ones, and lead to significantly more accurate classifiers. The novel gene sets are indeed more correlated than the conventional ones, and lead to significantly more accurate classifiers. Novel gene sets defined on the basis of regulatory interactions improve set-level classification of gene expression data. The experimental scripts and other material needed to reproduce the experiments are available at http://ida.felk.cvut.cz/novelgenesets.tar.gz.

  18. 77 FR 67813 - Sam Rayburn Dam Project Power Rate

    Science.gov (United States)

    2012-11-14

    ... DEPARTMENT OF ENERGY Southwestern Power Administration Sam Rayburn Dam Project Power Rate AGENCY: Southwestern Power Administration, DOE. ACTION: Notice of Rate Order Approving an Extension of Power Rate on an.... James K. McDonald, Assistant Administrator, Southwestern Power Administration, Department of Energy...

  19. SAM : an experiment dedicated to the Carbon Quest at Mars

    Science.gov (United States)

    Coll, Patrice; Mahaffy, Paul; Webster, Chris; Cabane, Michel; Tan, F.; Coscia, D.; Nolan, T.; Rahen, E.; Teinturier, S.; Goutail, J. P.; Martin, D.; Montaron, C.; Galic, A.

    SAM is a suite of instruments that will be onboard the Mars Science Laboratory (MSL) rover. The SAM team consist of scientists and engineers at GSFC, U. Paris/CNRS, JPL, and Honeybee Robotics, along with many additional external partners. SAM's five science goals will address three of the most fundamental questions about the ability of Mars to support life -past, present, and future. Question 1: What does the inventory of carbon compounds near the surface of Mars tell us about its potential habitability? 1.Goal 1: Survey carbon compound sources and evaluate their possible mechanism of formation and destruction. 2.Goal 2: Search for organic compounds of biotic and prebiotic importance expecially methane. Question 2: What are the chemical and isotopic states of the lighter elements in the solids and atmosphere of Mars and what do they tell us about its potential habitability? 1.Goal 3: Reveal the chemical and isotopic state of elements (i.e., N, H, O, S and others) that are important for life as we know it. 2.Goal 4: Evaluate the habitability of Mars by studying its atmospheric chemistry and the composition of trace species that are evidence of interactions between the atmosphere and soil. Question 3: Were past habitability conditions different from today's? 1.Goal 5: Understand atmospheric and climatic evolution through measurements of noble gas and light element isotopes.

  20. The History of the Austin College Building and Old Main at Sam Houston State University

    Science.gov (United States)

    Singer, Erin; Shields, Samantha

    2017-01-01

    Austin Hall and Old Main serve as the heart of what is now Sam Houston State University. The buildings' rich histories help one to understand how Sam Houston State University and its proud teacher education heritage came to be. To begin with Austin Hall's story, the University's original building has a unique and interesting tale that journeys…

  1. A pilot study investigating the feasibility of symptom assessment manager (SAM), a Web-based real-time tool for monitoring challenging behaviors.

    Science.gov (United States)

    Loi, Samantha M; Wanasinghage, Sangeeth; Goh, Anita; Lautenschlager, Nicola T; Darby, David G; Velakoulis, Dennis

    2018-04-01

    Improving and minimizing challenging behaviors seen in psychiatric conditions, including behavioral and psychological symptoms of dementia are important in the care of people with these conditions. Yet there is a lack of systematic evaluation of these as a part of routine clinical care. The Neuropsychiatric Inventory is a validated and reliable tool for rating the severity and disruptiveness of challenging behaviors. We report on the evaluation of a Web-based symptom assessment manager (SAM), designed to address the limitation of previous tools using some of the Neuropsychiatric Inventory functions, to monitor behaviors by staff caring for people with dementia and other psychiatric conditions in inpatient and residential care settings. The SAM was piloted in an 8-bed inpatient neuropsychiatry unit over 5 months. Eleven nurses and 4 clinicians were trained in usage of SAM. Primary outcomes were usage of SAM and perceived usability, utility, and acceptance of SAM. Secondary outcomes were the frequencies of documented behavior. Usage data were analyzed using chi-square and logistic regression analyses. The SAM was used for all admitted patients regardless of diagnosis, with a usage rate of 64% for nurses regularly employed in the unit. Staff provided positive feedback regarding the utility of SAM. The SAM appeared to offer individualized behavior assessment by providing a quick, structured, and standardized platform for assessing behavior in a real-world setting. Further research would involve trialing SAM with more staff in alternative settings such as in home or residential care settings. Copyright © 2017 John Wiley & Sons, Ltd.

  2. Parabolic Trough Collector Cost Update for the System Advisor Model (SAM)

    Energy Technology Data Exchange (ETDEWEB)

    Kurup, Parthiv [National Renewable Energy Lab. (NREL), Golden, CO (United States); Turchi, Craig S. [National Renewable Energy Lab. (NREL), Golden, CO (United States)

    2015-11-01

    This report updates the baseline cost for parabolic trough solar fields in the United States within NREL's System Advisor Model (SAM). SAM, available at no cost at https://sam.nrel.gov/, is a performance and financial model designed to facilitate decision making for people involved in the renewable energy industry. SAM is the primary tool used by NREL and the U.S. Department of Energy (DOE) for estimating the performance and cost of concentrating solar power (CSP) technologies and projects. The study performed a bottom-up build and cost estimate for two state-of-the-art parabolic trough designs -- the SkyTrough and the Ultimate Trough. The SkyTrough analysis estimated the potential installed cost for a solar field of 1500 SCAs as $170/m2 +/- $6/m2. The investigation found that SkyTrough installed costs were sensitive to factors such as raw aluminum alloy cost and production volume. For example, in the case of the SkyTrough, the installed cost would rise to nearly $210/m2 if the aluminum alloy cost was $1.70/lb instead of $1.03/lb. Accordingly, one must be aware of fluctuations in the relevant commodities markets to track system cost over time. The estimated installed cost for the Ultimate Trough was only slightly higher at $178/m2, which includes an assembly facility of $11.6 million amortized over the required production volume. Considering the size and overall cost of a 700 SCA Ultimate Trough solar field, two parallel production lines in a fully covered assembly facility, each with the specific torque box, module and mirror jigs, would be justified for a full CSP plant.

  3. Geometry modeling for SAM-CE Monte Carlo calculations

    International Nuclear Information System (INIS)

    Steinberg, H.A.; Troubetzkoy, E.S.

    1980-01-01

    Three geometry packages have been developed and incorporated into SAM-CE, for representing in three dimensions the transport medium. These are combinatorial geometry - a general (non-lattice) system, complex combinatorial geometry - a very general system with lattice capability, and special reactor geometry - a special purpose system for light water reactor geometries. Their different attributes are described

  4. Toposelective electrochemical desorption of thiol SAMs from neighboring polycrystalline gold surfaces.

    Science.gov (United States)

    Tencer, Michal; Berini, Pierre

    2008-11-04

    We describe a method for the selective desorption of thiol self-assembled monolayers from gold surfaces having micrometer-scale separations on a substrate. In an electrolyte solution, the electrical resistance between the adjacent areas can be much lower than the resistance between a surface and the counter electrode. Also, both reductive and oxidative thiol desorption may occur. Therefore, the potentials of the surfaces must be independently controlled with a multichannel potentiostat and operating windows for a given thiol/electrolyte system must be established. In this study operating windows were established for 1-dodecanethiol-based SAMs in phosphate buffer, phosphate-buffered saline, and sodium hydroxide solution, and selective SAM removal was successfully performed in a four-electrode configuration.

  5. Annals of SAM meeting '96. National meeting on precious metals

    International Nuclear Information System (INIS)

    1996-01-01

    Works are presented at the SAM meeting '96 of the Argentine Materials Association. The papers can be grouped under the following main topics: physical metallurgy; ceramics; polymers; precious metals; extractive metallurgy; corrosion; powder metallurgy. refs., ills

  6. Characterization of Timed Changes in Hepatic Copper Concentrations, Methionine Metabolism, Gene Expression, and Global DNA Methylation in the Jackson Toxic Milk Mouse Model of Wilson Disease

    Directory of Open Access Journals (Sweden)

    Anh Le

    2014-05-01

    Full Text Available Background: Wilson disease (WD is characterized by hepatic copper accumulation with progressive liver damage to cirrhosis. This study aimed to characterize the toxic milk mouse from The Jackson Laboratory (Bar Harbor, ME, USA (tx-j mouse model of WD according to changes over time in hepatic copper concentrations, methionine metabolism, global DNA methylation, and gene expression from gestational day 17 (fetal to adulthood (28 weeks. Methods: Included liver histology and relevant biochemical analyses including hepatic copper quantification, S-adenosylmethionine (SAM and S-adenosylhomocysteine (SAH liver levels, qPCR for transcript levels of genes relevant to methionine metabolism and liver damage, and DNA dot blot for global DNA methylation. Results: Hepatic copper was lower in tx-j fetuses but higher in weanling (three weeks and adult tx-j mice compared to controls. S-adenosylhomocysteinase transcript levels were significantly lower at all time points, except at three weeks, correlating negatively with copper levels and with consequent changes in the SAM:SAH methylation ratio and global DNA methylation. Conclusion: Compared to controls, methionine metabolism including S-adenosylhomocysteinase gene expression is persistently different in the tx-j mice with consequent alterations in global DNA methylation in more advanced stages of liver disease. The inhibitory effect of copper accumulation on S-adenosylhomocysteinase expression is associated with progressively abnormal methionine metabolism and decreased methylation capacity and DNA global methylation.

  7. Different level of population differentiation among human genes.

    Science.gov (United States)

    Wu, Dong-Dong; Zhang, Ya-Ping

    2011-01-14

    During the colonization of the world, after dispersal out of African, modern humans encountered changeable environments and substantial phenotypic variations that involve diverse behaviors, lifestyles and cultures, were generated among the different modern human populations. Here, we study the level of population differentiation among different populations of human genes. Intriguingly, genes involved in osteoblast development were identified as being enriched with higher FST SNPs, a result consistent with the proposed role of the skeletal system in accounting for variation among human populations. Genes involved in the development of hair follicles, where hair is produced, were also found to have higher levels of population differentiation, consistent with hair morphology being a distinctive trait among human populations. Other genes that showed higher levels of population differentiation include those involved in pigmentation, spermatid, nervous system and organ development, and some metabolic pathways, but few involved with the immune system. Disease-related genes demonstrate excessive SNPs with lower levels of population differentiation, probably due to purifying selection. Surprisingly, we find that Mendelian-disease genes appear to have a significant excessive of SNPs with high levels of population differentiation, possibly because the incidence and susceptibility of these diseases show differences among populations. As expected, microRNA regulated genes show lower levels of population differentiation due to purifying selection. Our analysis demonstrates different level of population differentiation among human populations for different gene groups.

  8. Vibrational Stark Effect of the Electric-Field Reporter 4-Mercaptobenzonitrile as a Tool for Investigating Electrostatics at Electrode/SAM/Solution Interfaces

    Directory of Open Access Journals (Sweden)

    Peter Hildebrandt

    2012-06-01

    Full Text Available 4-mercaptobenzonitrile (MBN in self-assembled monolayers (SAMs on Au and Ag electrodes was studied by surface enhanced infrared absorption and Raman spectroscopy, to correlate the nitrile stretching frequency with the local electric field exploiting the vibrational Stark effect (VSE. Using MBN SAMs in different metal/SAM interfaces, we sorted out the main factors controlling the nitrile stretching frequency, which comprise, in addition to external electric fields, the metal-MBN bond, the surface potential, and hydrogen bond interactions. On the basis of the linear relationships between the nitrile stretching and the electrode potential, an electrostatic description of the interfacial potential distribution is presented that allows for determining the electric field strengths on the SAM surface, as well as the effective potential of zero-charge of the SAM-coated metal. Comparing this latter quantity with calculated values derived from literature data, we note a very good agreement for Au/MBN but distinct deviations for Ag/MBN which may reflect either the approximations and simplifications of the model or the uncertainty in reported structural parameters for Ag/MBN. The present electrostatic model consistently explains the electric field strengths for MBN SAMs on Ag and Au as well as for thiophenol and mercaptohexanoic acid SAMs with MBN incorporated as a VSE reporter.

  9. Assessing the suitability of written stroke materials: an evaluation of the interrater reliability of the suitability assessment of materials (SAM) checklist.

    Science.gov (United States)

    Hoffmann, Tammy; Ladner, Yvette

    2012-01-01

    Written materials are frequently used to provide education to stroke patients and their carers. However, poor quality materials are a barrier to effective information provision. A quick and reliable method of evaluating material quality is needed. This study evaluated the interrater reliability of the Suitability Assessment of Materials (SAM) checklist in a sample of written stroke education materials. Two independent raters evaluated the materials (n = 25) using the SAM, and ratings were analyzed to reveal total percentage agreements and weighted kappa values for individual items and overall SAM rating. The majority of the individual SAM items had high interrater reliability, with 17 of the 22 items achieving substantial, almost perfect, or perfect weighted kappa value scores. The overall SAM rating achieved a weighted kappa value of 0.60, with a percentage total agreement of 96%. Health care professionals should evaluate the content and design characteristics of written education materials before using them with patients. A tool such as the SAM checklist can be used; however, raters should exercise caution when interpreting results from items with more subjective scoring criteria. Refinements to the scoring criteria for these items are recommended. The value of the SAM is that it can be used to identify specific elements that should be modified before education materials are provided to patients.

  10. Different level of population differentiation among human genes

    Directory of Open Access Journals (Sweden)

    Zhang Ya-Ping

    2011-01-01

    Full Text Available Abstract Background During the colonization of the world, after dispersal out of African, modern humans encountered changeable environments and substantial phenotypic variations that involve diverse behaviors, lifestyles and cultures, were generated among the different modern human populations. Results Here, we study the level of population differentiation among different populations of human genes. Intriguingly, genes involved in osteoblast development were identified as being enriched with higher FST SNPs, a result consistent with the proposed role of the skeletal system in accounting for variation among human populations. Genes involved in the development of hair follicles, where hair is produced, were also found to have higher levels of population differentiation, consistent with hair morphology being a distinctive trait among human populations. Other genes that showed higher levels of population differentiation include those involved in pigmentation, spermatid, nervous system and organ development, and some metabolic pathways, but few involved with the immune system. Disease-related genes demonstrate excessive SNPs with lower levels of population differentiation, probably due to purifying selection. Surprisingly, we find that Mendelian-disease genes appear to have a significant excessive of SNPs with high levels of population differentiation, possibly because the incidence and susceptibility of these diseases show differences among populations. As expected, microRNA regulated genes show lower levels of population differentiation due to purifying selection. Conclusion Our analysis demonstrates different level of population differentiation among human populations for different gene groups.

  11. Rhodium deposition onto a 4-mercaptopyridine SAM on Au(1 1 1)

    Energy Technology Data Exchange (ETDEWEB)

    Manolova, M. [Institute of Electrochemistry, University of Ulm, 89069 Ulm (Germany); Kayser, M. [Institute of Electrochemistry, University of Ulm, 89069 Ulm (Germany); Kolb, D.M. [Institute of Electrochemistry, University of Ulm, 89069 Ulm (Germany)]. E-mail: dieter.kolb@uni-ulm.de; Boyen, H.-G. [Institute of Solid State Physics, University of Ulm, 89069 Ulm (Germany); Ziemann, P. [Institute of Solid State Physics, University of Ulm, 89069 Ulm (Germany); Mayer, D. [BASF Electronic Materials GmbH, 67056 Ludwigshafen (Germany); Wirth, A. [BASF Electronic Materials GmbH, 67056 Ludwigshafen (Germany)

    2007-02-10

    The application of a recently developed method for the deposition of Pd and Pt on top of a SAM, has been successfully extended to Rh, thus proving the versatility of the new concept. Experimental evidence from cyclic voltammetry, in situ STM and ex situ X-ray photoemission spectroscopy is presented for the deposition of monoatomic high rhodium islands onto a 4-mercaptopyridine self-assembled monolayer on a Au(1 1 1) electrode. By repetitive complexation of the Rh ions to the ring-nitrogen and reduction in a Rh-ion free solution, an almost completely covered SAM is obtained. The consequences of making contacts for molecular electronics are briefly discussed.

  12. The Search for Organic Compounds of Martian Origin in Gale Crater by the Sample Analysis at Mars (SAM) Instrument on Curiosity

    Science.gov (United States)

    Glavin, Daniel; Freissinet, Caroline; Mahaffy, Paul; Miller, Kristen; Eigenbrode, Jennifer; Summons, Roger; Archer, Douglas, Jr.; Brunner, Anna; Martin, Mildred; Buch, Arrnaud; hide

    2014-01-01

    One of the key objectives of the Mars Science Laboratory rover and the Sample Analysis at Mars (SAM) instrument suite is to determine the inventory of organic and inorganic volatiles in the atmosphere and surface regolith and rocks to help assess the habitability potential of Gale Crater. The SAM instrument on the Curiosity rover can detect volatile organic compounds thermally evolved from solid samples using a combination of evolved gas analysis (EGA) and gas chromatography mass spectrometry (GCMS) (Mahaffy et al. 2012). The first solid samples analyzed by SAM, a scoop of windblown dust and sand at Rocknest, revealed several chloromethanes and a C4-chlorinated hydrocarbon derived primarily from reactions between a martian oxychlorine phase (e.g. perchlorate) and terrestrial carbon from N-methyl-N-(tertbutyldimethylsilyl)- trifluoroacetamide (MTBSTFA) vapor present in the SAM instrument background (Glavin et al. 2013). After the analyses at Rocknest, Curiosity traveled to Yellowknife Bay and drilled two separate holes in a fluvio-lacustrine sediment (the Sheepbed unit) designated John Klein and Cumberland. Analyses of the drilled materials by both SAM and the CheMin X-Ray Diffraction instrument revealed a mudstone consisting of 20 wt% smectite clays (Ming et al. 2013; Vaniman et al. 2013), which on Earth are known to aid the concentration and preservation of organic matter. Oxychlorine compounds were also detected in the Sheepbed mudstone during pyrolysis; however, in contrast to Rocknest, much higher levels of chloromethanes were released from the Sheepbed materials, suggesting an additional, possibly martian source of organic carbon (Ming et al. 2013). In addition, elevated abundances of chlorobenzene and a more diverse suite of chlorinated alkanes including dichloropropane and dichlorobutane detected in Cumberland compared to Rocknest suggest that martian or meteoritic organic carbon sources may be preserved in the mudstone (Freissinet et al. 2013

  13. Crystal Structure of Bicc1 SAM Polymer and Mapping of Interactions between the Ciliopathy-Associated Proteins Bicc1, ANKS3, and ANKS6.

    Science.gov (United States)

    Rothé, Benjamin; Leettola, Catherine N; Leal-Esteban, Lucia; Cascio, Duilio; Fortier, Simon; Isenschmid, Manuela; Bowie, James U; Constam, Daniel B

    2018-02-06

    Head-to-tail polymers of sterile alpha motifs (SAM) can scaffold large macromolecular complexes. Several SAM-domain proteins that bind each other are mutated in patients with cystic kidneys or laterality defects, including the Ankyrin (ANK) and SAM domain-containing proteins ANKS6 and ANKS3, and the RNA-binding protein Bicc1. To address how their interactions are regulated, we first determined a high-resolution crystal structure of a Bicc1-SAM polymer, revealing a canonical SAM polymer with a high degree of flexibility in the subunit interface orientations. We further mapped interactions between full-length and distinct domains of Bicc1, ANKS3, and ANKS6. Neither ANKS3 nor ANKS6 alone formed macroscopic homopolymers in vivo. However, ANKS3 recruited ANKS6 to Bicc1, and the three proteins together cooperatively generated giant macromolecular complexes. Thus, the giant assemblies are shaped by SAM domains, their flanking sequences, and SAM-independent protein-protein and protein-mRNA interactions. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. Potensi Tinggalan Arkeologis di Kawasan Bandar Udara Sam Ratulangi Manado: Upaya Pelestarian, Pemanfaatan, dan Pengembangan bagi Masyarakat

    Directory of Open Access Journals (Sweden)

    Irfanuddin W. Marzuki

    2016-08-01

    Full Text Available The area of Sam Ratulangi airport’s Manado has archaeological heritage which has been know as it is closed for public. This research used descriptive method, using inductive reasoning. Meanwhile, the analysis method used morphologyl, technology, and contextual analysis. This research aimed to find out the potential of archaeological heritage in Sam Ratulangi airport area of Manado. In addition to its strategy of preservation the haritage included veilbox, bungker, and waruga. The preservation can be conducted by doing protection, development, and utilization. The preservation both physical and non physical protection. The effort for its development and utilization was conducted for the purpose of science, education, culture, and tourism. Kawasan Bandar Udara Sam Ratulangi Manado mempunyai potensi tinggalan arkeologis yang selama ini tidak diketahui masyarakat luas, dikarenakan letak tinggalan yang berada dalam kawasan tertutup untuk umum. Penelitian menggunakan metode deskriptif dengan penalaran induktif. Metode analisis menggunakan analisis morfologi, teknologi dan kontekstual. Tujuan penelitian untuk mengetahui potensi tinggalan arkeologis yang terdapat di kawasan Bandar Udara Sam Ratulangi dan strategi pelestariannya. Tinggalan arkeologis yang terdapat di kawasan Bandar Udara Sam Ratulangi meliputi veilbox, bungker, dan waruga. Upaya pelestarian dapat dilakukan dengan cara perlindungan, pengembangan dan pemanfaatan. Upaya perlindungan meliputi perlindungan secara fisik dan non fisik. Upaya pengembangan dan pemanfaatan dilakukan untuk kepentingan ilmu pengetahuan, pendidikan, kebudayaan dan pariwisata.

  15. Carbon tax effects on the poor: a SAM-based approach

    Science.gov (United States)

    Chapa, Joana; Ortega, Araceli

    2017-09-01

    A SAM-based price model for Mexico is developed in order to assess the effects of the carbon tax, which was part of the fiscal reform approved in 2014. The model is formulated based on a social accounting matrix (SAM) that distinguishes households by the official poverty condition and geographical area. The main results are that the sector that includes coke, refined petroleum and nuclear fuel shows the highest price increase due to the direct impact of the carbon tax; in addition, air transport and inland transport are the most affected sectors, in an indirect manner, because both employ inputs from the former sector. Also, it is found that welfare diminishes more in the rural strata than in the urban one. In the urban area, the carbon tax is regressive: the negative impact of carbon tax on family welfare is greater on the poorest families.

  16. FIGURAL FORMS OF KNOWLEDGE: A STUDY OF THE SHORT PROSE OF SAM SHEPARD

    Directory of Open Access Journals (Sweden)

    RICARDO DA SILVA SOBREIRA

    2008-11-01

    Full Text Available ABSTRACTThe paratactical style and the indeterminacies are literary strategies that resistthe conventional impulse of totalizing the elements projected by the text, becauseinstead of selecting the aspects of reality and subordinating the images andperceptions into a hierarchy, the use of these techniques favors the juxtapositionof multiple perspectives and the frustration of narrative closure. Thus, the useof parataxis and indeterminacies in the collection of short stories Great Dreamof Heaven (2002, by the American author Sam Shepard, tends to challenge theprocess of meaning production through the progressive erasure of narrative“certainties”.KEY WORDS: Postmodern, indeterminacy, parataxis, narrative, Sam Shepard.  

  17. Structural investigation of a C-terminal EphA2 receptor mutant: Does mutation affect the structure and interaction properties of the Sam domain?

    Science.gov (United States)

    Mercurio, Flavia A; Costantini, Susan; Di Natale, Concetta; Pirone, Luciano; Guariniello, Stefano; Scognamiglio, Pasqualina L; Marasco, Daniela; Pedone, Emilia M; Leone, Marilisa

    2017-09-01

    Ephrin A2 receptor (EphA2) plays a key role in cancer, it is up-regulated in several types of tumors and the process of ligand-induced receptor endocytosis, followed by degradation, is considered as a potential path to diminish tumor malignancy. Protein modulators of this mechanism are recruited at the cytosolic Sterile alpha motif (Sam) domain of EphA2 (EphA2-Sam) through heterotypic Sam-Sam associations. These interactions engage the C-terminal helix of EphA2 and close loop regions (the so called End Helix side). In addition, several studies report on destabilizing mutations in EphA2 related to cataract formation and located in/or close to the Sam domain. Herein, we analyzed from a structural point of view, one of these mutants characterized by the insertion of a novel 39 residue long polypeptide at the C-terminus of EphA2-Sam. A 3D structural model was built by computational methods and revealed partial disorder in the acquired C-terminal tail and a few residues participating in an α-helix and two short β-strands. We investigated by CD and NMR studies the conformational properties in solution of two peptides encompassing the whole C-terminal tail and its predicted helical region, respectively. NMR binding experiments demonstrated that these peptides do not interact relevantly with either EphA2-Sam or its interactor Ship2-Sam. Molecular dynamics (MD) simulations further indicated that the EphA2 mutant could be represented only through a conformational ensemble and that the C-terminal tail should not largely wrap the EphA2-Sam End-Helix interface and affect binding to other Sam domains. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. A gene expression signature associated with survival in metastatic melanoma

    Science.gov (United States)

    Mandruzzato, Susanna; Callegaro, Andrea; Turcatel, Gianluca; Francescato, Samuela; Montesco, Maria C; Chiarion-Sileni, Vanna; Mocellin, Simone; Rossi, Carlo R; Bicciato, Silvio; Wang, Ena; Marincola, Francesco M; Zanovello, Paola

    2006-01-01

    Background Current clinical and histopathological criteria used to define the prognosis of melanoma patients are inadequate for accurate prediction of clinical outcome. We investigated whether genome screening by means of high-throughput gene microarray might provide clinically useful information on patient survival. Methods Forty-three tumor tissues from 38 patients with stage III and stage IV melanoma were profiled with a 17,500 element cDNA microarray. Expression data were analyzed using significance analysis of microarrays (SAM) to identify genes associated with patient survival, and supervised principal components (SPC) to determine survival prediction. Results SAM analysis revealed a set of 80 probes, corresponding to 70 genes, associated with survival, i.e. 45 probes characterizing longer and 35 shorter survival times, respectively. These transcripts were included in a survival prediction model designed using SPC and cross-validation which allowed identifying 30 predicting probes out of the 80 associated with survival. Conclusion The longer-survival group of genes included those expressed in immune cells, both innate and acquired, confirming the interplay between immunological mechanisms and the natural history of melanoma. Genes linked to immune cells were totally lacking in the poor-survival group, which was instead associated with a number of genes related to highly proliferative and invasive tumor cells. PMID:17129373

  19. A gene expression signature associated with survival in metastatic melanoma

    Directory of Open Access Journals (Sweden)

    Rossi Carlo R

    2006-11-01

    Full Text Available Abstract Background Current clinical and histopathological criteria used to define the prognosis of melanoma patients are inadequate for accurate prediction of clinical outcome. We investigated whether genome screening by means of high-throughput gene microarray might provide clinically useful information on patient survival. Methods Forty-three tumor tissues from 38 patients with stage III and stage IV melanoma were profiled with a 17,500 element cDNA microarray. Expression data were analyzed using significance analysis of microarrays (SAM to identify genes associated with patient survival, and supervised principal components (SPC to determine survival prediction. Results SAM analysis revealed a set of 80 probes, corresponding to 70 genes, associated with survival, i.e. 45 probes characterizing longer and 35 shorter survival times, respectively. These transcripts were included in a survival prediction model designed using SPC and cross-validation which allowed identifying 30 predicting probes out of the 80 associated with survival. Conclusion The longer-survival group of genes included those expressed in immune cells, both innate and acquired, confirming the interplay between immunological mechanisms and the natural history of melanoma. Genes linked to immune cells were totally lacking in the poor-survival group, which was instead associated with a number of genes related to highly proliferative and invasive tumor cells.

  20. Physical activity level among children recovering from severe acute malnutrition

    DEFF Research Database (Denmark)

    Babirekere-Iriso, Esther; Rytter, Maren Johanne Heilskov; Namusoke, Hanifa

    2018-01-01

    OBJECTIVE: To assess the level and predictors of physical activity at discharge among children recovering from severe acute malnutrition (SAM). METHODS: We conducted a prospective study among 69 children 6 - 59 months of age admitted with SAM for nutritional rehabilitation at Mulago National...

  1. DnaSAM: Software to perform neutrality testing for large datasets with complex null models.

    Science.gov (United States)

    Eckert, Andrew J; Liechty, John D; Tearse, Brandon R; Pande, Barnaly; Neale, David B

    2010-05-01

    Patterns of DNA sequence polymorphisms can be used to understand the processes of demography and adaptation within natural populations. High-throughput generation of DNA sequence data has historically been the bottleneck with respect to data processing and experimental inference. Advances in marker technologies have largely solved this problem. Currently, the limiting step is computational, with most molecular population genetic software allowing a gene-by-gene analysis through a graphical user interface. An easy-to-use analysis program that allows both high-throughput processing of multiple sequence alignments along with the flexibility to simulate data under complex demographic scenarios is currently lacking. We introduce a new program, named DnaSAM, which allows high-throughput estimation of DNA sequence diversity and neutrality statistics from experimental data along with the ability to test those statistics via Monte Carlo coalescent simulations. These simulations are conducted using the ms program, which is able to incorporate several genetic parameters (e.g. recombination) and demographic scenarios (e.g. population bottlenecks). The output is a set of diversity and neutrality statistics with associated probability values under a user-specified null model that are stored in easy to manipulate text file. © 2009 Blackwell Publishing Ltd.

  2. Solution structure of the receptor tyrosine kinase EphB2 SAM domain and identification of two distinct homotypic interaction sites.

    OpenAIRE

    Smalla, M.; Schmieder, P.; Kelly, M.; Ter Laak, A.; Krause, G.; Ball, L.; Wahl, M.; Bork, P.; Oschkinat, H.

    1999-01-01

    The sterile alpha motif (SAM) is a protein interaction domain of around 70 amino acids present predominantly in the N- and C-termini of more than 60 diverse proteins that participate in signal transduction and transcriptional repression. SAM domains have been shown to homo- and hetero-oligomerize and to mediate specific protein-protein interactions. A highly conserved subclass of SAM domains is present at the intracellular C-terminus of more than 40 Eph receptor tyrosine kinases that are invo...

  3. Smoking-Attributable Mortality, Morbidity, and Economic Costs (SAMMEC) - Smoking-Attributable Mortality (SAM)

    Data.gov (United States)

    U.S. Department of Health & Human Services — 2005-2009. SAMMEC - Smoking-Attributable Mortality, Morbidity, and Economic Costs. Smoking-attributable mortality (SAM) is the number of deaths caused by cigarette...

  4. SAMS--a systems architecture for developing intelligent health information systems.

    Science.gov (United States)

    Yılmaz, Özgün; Erdur, Rıza Cenk; Türksever, Mustafa

    2013-12-01

    In this paper, SAMS, a novel health information system architecture for developing intelligent health information systems is proposed and also some strategies for developing such systems are discussed. The systems fulfilling this architecture will be able to store electronic health records of the patients using OWL ontologies, share patient records among different hospitals and provide physicians expertise to assist them in making decisions. The system is intelligent because it is rule-based, makes use of rule-based reasoning and has the ability to learn and evolve itself. The learning capability is provided by extracting rules from previously given decisions by the physicians and then adding the extracted rules to the system. The proposed system is novel and original in all of these aspects. As a case study, a system is implemented conforming to SAMS architecture for use by dentists in the dental domain. The use of the developed system is described with a scenario. For evaluation, the developed dental information system will be used and tried by a group of dentists. The development of this system proves the applicability of SAMS architecture. By getting decision support from a system derived from this architecture, the cognitive gap between experienced and inexperienced physicians can be compensated. Thus, patient satisfaction can be achieved, inexperienced physicians are supported in decision making and the personnel can improve their knowledge. A physician can diagnose a case, which he/she has never diagnosed before, using this system. With the help of this system, it will be possible to store general domain knowledge in this system and the personnel's need to medical guideline documents will be reduced.

  5. Evolved Gas Analyses of the Murray Formation in Gale Crater, Mars: Results of the Curiosity Rover's Sample Analysis at Mars (SAM) Instrument

    Science.gov (United States)

    Sutter, B.; McAdam, A. C.; Rampe, E. B.; Thompson, L. M.; Ming, D. W.; Mahaffy, P. R.; Navarro-Gonzalez, R.; Stern, J. C.; Eigenbrode, J. L.; Archer, P. D.

    2017-01-01

    The Sample Analysis at Mars (SAM) instrument aboard the Mars Science Laboratory rover has analyzed 13 samples from Gale Crater. All SAM-evolved gas analyses have yielded a multitude of volatiles (e.g., H2O, SO2, H2S, CO2, CO, NO, O2, HCl) [1- 6]. The objectives of this work are to 1) Characterize recent evolved SO2, CO2, O2, and NO gas traces of the Murray formation mudstone, 2) Constrain sediment mineralogy/composition based on SAM evolved gas analysis (SAM-EGA), and 3) Discuss the implications of these results relative to understanding the geological history of Gale Crater.

  6. Integration, Validation, and Application of a PV Snow Coverage Model in SAM

    Energy Technology Data Exchange (ETDEWEB)

    Freeman, Janine M. [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Ryberg, David Severin [National Renewable Energy Laboratory (NREL), Golden, CO (United States)

    2017-08-01

    Due to the increasing deployment of PV systems in snowy climates, there is significant interest in a method capable of estimating PV losses resulting from snow coverage that has been verified for a variety of system designs and locations. Many independent snow coverage models have been developed over the last 15 years; however, there has been very little effort verifying these models beyond the system designs and locations on which they were based. Moreover, major PV modeling software products have not yet incorporated any of these models into their workflows. In response to this deficiency, we have integrated the methodology of the snow model developed in the paper by Marion et al. (2013) into the National Renewable Energy Laboratory's (NREL) System Advisor Model (SAM). In this work, we describe how the snow model is implemented in SAM and we discuss our demonstration of the model's effectiveness at reducing error in annual estimations for three PV arrays. Next, we use this new functionality in conjunction with a long term historical data set to estimate average snow losses across the United States for two typical PV system designs. The open availability of the snow loss estimation capability in SAM to the PV modeling community, coupled with our results of the nationwide study, will better equip the industry to accurately estimate PV energy production in areas affected by snowfall.

  7. Niedualna uważność a stan samādhi w kontekście badań neurofenomenologicznych

    Directory of Open Access Journals (Sweden)

    Piotr PŁANETA

    2016-12-01

    Full Text Available The aim of this paper is to compare various meditative states, such as Buddhist dhyāna‑s, yogic nirbīja samādhi and nondual awareness (Tib. gñis‑med. The primary source texts I refere to are Yogasūtras of Patañjali, Ānāpānasmṛtisūtra (MN 118, Samādhisūtra (AN 4.41, The Tibetan Yogas of Dream and Sleep. I also discuss some relevant claims of contemporary empirical studies. First, I define the key terms used in Eastern meditation studies as well as in neurophenomenology, a contemporary method applied to examining the meditative states of mind, such as samādhi, dhyāna, and śamatha. Inspired by Shinzen Young, I distinguish three groups of meditative states that might be identified with nondual awareness. These three groups are: (1 the second, the third and fourth Buddhist dhyāna being equivalent to nirvicāra samādhi and nirānanda samādhi in the classical Indian yoga; (2 nirbīja samādhi and (3 nondual awareness, typical to the Mahayāna contemplative traditions. I explain why we can recognize each of the above states as nondual awareness and how they differ from each other. Then, I make a comparison between meditation practice explained in Ānāpānasmṛtisūtra and nondual awareness presented in the Tibetan Buddhism. Besides, I discuss the above kinds of mental states in terms of recent neurophenomenological findings. While doing so, I am trying to demonstrate that our understanding of meditation can benefit from the empirical studies which help us to objectify this kind of subjective experience, to some degree, if they are given an adequate place in our study.

  8. Operationalizing Levels of Academic Mastery Based on Vygotsky's Theory: The Study of Mathematical Knowledge

    Science.gov (United States)

    Nezhnov, Peter; Kardanova, Elena; Vasilyeva, Marina; Ludlow, Larry

    2015-01-01

    The present study tested the possibility of operationalizing levels of knowledge acquisition based on Vygotsky's theory of cognitive growth. An assessment tool (SAM-Math) was developed to capture a hypothesized hierarchical structure of mathematical knowledge consisting of procedural, conceptual, and functional levels. In Study 1, SAM-Math was…

  9. Stool frequency recording in severe acute malnutrition ('StoolSAM'); an agreement study comparing maternal recall versus direct observation using diapers.

    Science.gov (United States)

    Voskuijl, Wieger; Potani, Isabel; Bandsma, Robert; Baan, Anne; White, Sarah; Bourdon, Celine; Kerac, Marko

    2017-06-07

    Approximately 50% of the deaths of children under the age of 5 can be attributed to undernutrition, which also encompasses severe acute malnutrition (SAM). Diarrhoea is strongly associated with these deaths and is commonly diagnosed solely based on stool frequency and consistency obtained through maternal recall. This trial aims to determine whether this approach is equivalent to a 'directly observed method' in which a health care worker directly observed stool frequency using diapers in hospitalised children with complicated SAM. This study was conducted at 'Moyo' Nutritional Rehabilitation Unit, Queen Elizabeth Central Hospital, Malawi. Participants were children aged 5-59 months admitted with SAM. We compared 2 days of stool frequency data obtained with next-day maternal-recall versus a 'gold standard' in which a health care worker observed stool frequency every 2 h using diapers. After study completion, guardians were asked their preferred method and their level of education. We found poor agreement between maternal recall and the 'gold standard' of directly observed diapers. The sensitivity to detect diarrhoea based on maternal recall was poor, with only 75 and 56% of diarrhoea cases identified on days 1 and 2, respectively. However, the specificity was higher with more than 80% of children correctly classified as not having diarrhoea. On day 1, the mean stool frequency difference between the two methods was -0.17 (SD; 1.68) with limits of agreement (of stool frequency) of -3.55 and 3.20 and, similarly on day 2, the mean difference was -0.2 (SD; 1.59) with limits of agreement of -3.38 and 2.98. These limits extend beyond the pre-specified 'acceptable' limits of agreement (±1.5 stool per day) and indicate that the 2 methods are non-equivalent. The higher the stool frequency, the more discrepant the two methods were. Most primary care givers strongly preferred using diapers. This study shows lack of agreement between the assessment of stool frequency in SAM

  10. Redox-based epigenetic status in drug addiction: a potential contributor to gene priming and a mechanistic rationale for metabolic intervention.

    Science.gov (United States)

    Trivedi, Malav S; Deth, Richard

    2014-01-01

    Alcohol and other drugs of abuse, including psychostimulants and opioids, can induce epigenetic changes: a contributing factor for drug addiction, tolerance, and associated withdrawal symptoms. DNA methylation is a major epigenetic mechanism and it is one of more than 200 methylation reactions supported by methyl donor S-adenosylmethionine (SAM). Levels of SAM are controlled by cellular redox status via the folate and vitamin B12-dependent enzyme methionine synthase (MS). For example, under oxidative conditions MS is inhibited, diverting its substrate homocysteine (HCY) to the trans sulfuration pathway. Alcohol, dopamine, and morphine, can alter intracellular levels of glutathione (GSH)-based cellular redox status, subsequently affecting SAM levels and DNA methylation status. Here, existing evidence is presented in a coherent manner to propose a novel hypothesis implicating the involvement of redox-based epigenetic changes in drug addiction. Further, we discuss how a "gene priming" phenomenon can contribute to the maintenance of redox and methylation status homeostasis under various stimuli including drugs of abuse. Additionally, a new mechanistic rationale for the use of metabolic interventions/redox-replenishers as symptomatic treatment of alcohol and other drug addiction and associated withdrawal symptoms is also provided. Hence, the current review article strengthens the hypothesis that neuronal metabolism has a critical bidirectional coupling with epigenetic changes in drug addiction exemplified by the link between redox-based metabolic changes and resultant epigenetic consequences under the effect of drugs of abuse.

  11. Atmospheric modeling of Mars CH4 subsurface clathrates releases mimicking SAM and 2003 Earth-based detections

    Science.gov (United States)

    Pla-García, J.; Rafkin, S. C.

    2017-12-01

    The aim of this work is to establish the amount of mixing during all martian seasons to test whether CH4 releases inside or outside of Gale crater are consistent with MSL-SAM observations. Several modeling scenarios were configured, including instantaneous and steady releases, both inside and outside the crater. A simulation to mimic the 2003 Earth-based detections (Mumma et al. 2009 or M09) was also performed. In the instantaneous release inside Gale experiments, Ls270 was shown to be the faster mixing season when air within and outside the crater was well mixed: all tracer mass inside the crater is diluted after just 8 hours. The mixing of near surface crater air with the external environment in the rest of the year is potentially rapid but slower than Ls270.In the instantaneous release outside Gale (NW) experiment, in just 12 hours the CH4 that makes it to the MSL landing location is diluted by six orders of magnitude. The timescale of mixing in MRAMS experiments is on the order of 1 sol regardless of season. The duration of the CH4 peak observed by SAM is 100 sols. Therefore there is a steady release inside the crater, or there is a very large magnitude steady release outside the crater. In the steady release Gale experiments, CH4 flux rate from ground is 1.8 kg m-2 s-1 (derived from Gloesener et al. 2017 clathrates fluxes) and it is not predictive. In these experiments, 200 times lower CH4 values detected by SAM are modeled around MSL location. There are CH4 concentration variations of orders of magnitude depending on the hour, so timing of SAM measurements is important. With a larger (but further away) outside crater release area compared to inside, similar CH4 values around MSL are modeled, so distance to source is important. In the steady experiments mimicking M09 detection release area, only 12 times lower CH4 values detected by SAM are modeled around MSL. The highest value in the M09 modeled scenario (0.6 ppbv) is reached in Ls270. This value is the

  12. The Au-S bond and SAM-protein contact in long-range electron transfer of pure and biomimetic metalloproteins via functionalized alkanethiol linkers

    DEFF Research Database (Denmark)

    Chi, Qijin; Ford, Michael J.; Halder, Arnab

    disentangled a wealth of data to identify the nature of the crucial Au-S contact, all suggesting prevalence of a Au(0)-thiyl radical unit. Molecular packing is further determined by the SAM molecular structure and involves binding either to Au-atoms mined out of the surface or directly to a flat surface. We...... functionalized alkanethiols have emerged as core linkers. We have studied molecular linking in the long-range ET (LRET) processes in detail using electrochemistry, in situ STM and AFM, and electronic structure computations. A focus is the electronic structure of the Au-S link and the SAM packing. We have...... is exceedingly sensitive to the structure of the thiol-based SAM molecules, testifying to the crucial importance of SAM packing and Au-S binding, and of the SAM link to the protein. Some of the subtleties are illustrated simpler by similar size (5-6 nm) nanoparticles (NPs). Biomimetic NPs must possess a certain...

  13. REPRESENTASI HOMOSEKSUALITAS DI YOUTUBE: (Studi Semiotika pada Video Pernikahan Sam Tsui

    Directory of Open Access Journals (Sweden)

    Lilis Rucirisyanti

    2017-12-01

    Full Text Available Abstract. Social media is instrumental in giving effect to nitizens, good effects or bad effect, then social media can be also represent a person. Diserve social media make it interesting for nitizens. One of social media is Youtube. Many a lot of video at there, strat from tips and trick videos, journey or vacation video, wedding video, and ect. Everyone can publish their video on Youtube. No exception of same sex enthusiast, in this study are homosexual or gay. One of is a wedding video Sam Tsui and Casey Braves. This research is a qualitative research and this research uses semiotcs analysus of Roland Barthes. By doing an analysis of video that have been published by Sam on Youtube, also do document search and literature. The author sees the existence of verbal and non vebal forms of representation from same sex merriage video of men and men.

  14. Application of the SAM Computer Program for Truckee River Stable Channel Analysis

    National Research Council Canada - National Science Library

    Scott, Stephen H

    2006-01-01

    The purpose of this Coastal and Hydraulics Engineering Technical Note (CHETN) is to demonstrate the utility of the SAM computer programs for evaluating the stability of a stream restoration design on the Truckee River...

  15. Parabolic Trough Reference Plant for Cost Modeling with the Solar Advisor Model (SAM)

    Energy Technology Data Exchange (ETDEWEB)

    Turchi, C.

    2010-07-01

    This report describes a component-based cost model developed for parabolic trough solar power plants. The cost model was developed by the National Renewable Energy Laboratory (NREL), assisted by WorleyParsons Group Inc., for use with NREL's Solar Advisor Model (SAM). This report includes an overview and explanation of the model, two summary contract reports from WorleyParsons, and an Excel spreadsheet for use with SAM. The cost study uses a reference plant with a 100-MWe capacity and six hours of thermal energy storage. Wet-cooling and dry-cooling configurations are considered. The spreadsheet includes capital and operating cost by component to allow users to estimate the impact of changes in component costs.

  16. HPA and SAM axis responses as correlates of self- vs parental ratings of anxiety in boys with an Autistic Disorder.

    Science.gov (United States)

    Bitsika, Vicki; Sharpley, Christopher F; Sweeney, John A; McFarlane, James R

    2014-03-29

    Anxiety and Autistic Disorder (AD) are both neurological conditions and both disorders share some features that make it difficult to precisely allocate specific symptoms to each disorder. HPA and SAM axis activities have been conclusively associated with anxiety, and may provide a method of validating anxiety rating scale assessments given by parents and their children with AD about those children. Data from HPA axis (salivary cortisol) and SAM axis (salivary alpha amylase) responses were collected from a sample of 32 high-functioning boys (M age=11yr) with an Autistic Disorder (AD) and were compared with the boys' and their mothers' ratings of the boys' anxiety. There was a significant difference between the self-ratings given by the boys and ratings given about them by their mothers. Further, only the boys' self-ratings of their anxiety significantly predicted the HPA axis responses and neither were significantly related to SAM axis responses. Some boys showed cortisol responses which were similar to that previously reported in children who had suffered chronic and severe anxiety arising from stressful social interactions. As well as suggesting that some boys with an AD can provide valid self-assessments of their anxiety, these data also point to the presence of very high levels of chronic HPA-axis arousal and consequent chronic anxiety in these boys. Copyright © 2014 Elsevier Inc. All rights reserved.

  17. The Seismic Aftershock Monitoring System (SAMS) for OSI - Experiences from IFE14

    Science.gov (United States)

    Gestermann, Nicolai; Sick, Benjamin; Häge, Martin; Blake, Thomas; Labak, Peter; Joswig, Manfred

    2016-04-01

    An on-site inspection (OSI) is the third of four elements of the verification regime of the Comprehensive Nuclear-Test-Ban Treaty (CTBT). The sole purpose of an OSI is to confirm whether a nuclear weapon test explosion or any other nuclear explosion has been carried out in violation of the treaty and to gather any facts which might assist in identifying any possible violator. It thus constitutes the final verification measure under the CTBT if all other available measures are not able to confirm the nature of a suspicious event. The Provisional Technical Secretariat (PTS) carried out the Integrated Field Exercise 2014 (IFE14) in the Dead Sea Area of Jordan from 3 November to 9. December 2014. It was a fictitious OSI whose aim was to test the inspection capabilities in an integrated manner. The technologies allowed during an OSI are listed in the Treaty. The aim of the Seismic Aftershock Monitoring System (SAMS) is to detect and localize aftershocks of low magnitudes of the triggering event or collapses of underground cavities. The locations of these events are expected in the vicinity of a possible previous explosion and help to narrow down the search area within an inspection area (IA) of an OSI. The success of SAMS depends on the main elements, hardware, software, deployment strategy, the search logic and not least the effective use of personnel. All elements of SAMS were tested and improved during the Built-Up Exercises (BUE) which took place in Austria and Hungary. IFE14 provided more realistic climatic and hazardous terrain conditions with limited resources. Significant variations in topography of the IA of IFE14 in the mountainous Dead Sea Area of Jordan led to considerable challenges which were not expected from experiences encountered during BUE. The SAMS uses mini arrays with an aperture of about 100 meters and with a total of 4 elements. The station network deployed during IFE14 and results of the data analysis will be presented. Possible aftershocks of

  18. Must, valge + hall : Sam Wagstaffi ja Robert Mapplethorpe'i portree / Madis Palm

    Index Scriptorium Estoniae

    Palm, Madis

    2008-01-01

    Dokumentaalfilm "Black, White & Gray: Sam Wagstaff and Robert Mapplethorpe" : autor ja režissöör James Crump : Ameerika Ühendriigid 2007. Filmi näidati filminädala "Art in America" raames Tallinnas

  19. Blood lead levels, iron metabolism gene polymorphisms and homocysteine: a gene-environment interaction study.

    Science.gov (United States)

    Kim, Kyoung-Nam; Lee, Mee-Ri; Lim, Youn-Hee; Hong, Yun-Chul

    2017-12-01

    Homocysteine has been causally associated with various adverse health outcomes. Evidence supporting the relationship between lead and homocysteine levels has been accumulating, but most prior studies have not focused on the interaction with genetic polymorphisms. From a community-based prospective cohort, we analysed 386 participants (aged 41-71 years) with information regarding blood lead and plasma homocysteine levels. Blood lead levels were measured between 2001 and 2003, and plasma homocysteine levels were measured in 2007. Interactions of lead levels with 42 genotyped single-nucleotide polymorphisms (SNPs) in five genes ( TF , HFE , CBS , BHMT and MTR ) were assessed via a 2-degree of freedom (df) joint test and a 1-df interaction test. In secondary analyses using imputation, we further assessed 58 imputed SNPs in the TF and MTHFR genes. Blood lead concentrations were positively associated with plasma homocysteine levels (p=0.0276). Six SNPs in the TF and MTR genes were screened using the 2-df joint test, and among them, three SNPs in the TF gene showed interactions with lead with respect to homocysteine levels through the 1-df interaction test (plead levels. Blood lead levels were positively associated with plasma homocysteine levels measured 4-6 years later, and three SNPs in the TF gene modified the association. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

  20. Folic Acid Supplementation Delays Atherosclerotic Lesion Development by Modulating MCP1 and VEGF DNA Methylation Levels In Vivo and In Vitro

    Science.gov (United States)

    Cui, Shanshan; Li, Wen; Lv, Xin; Wang, Pengyan; Gao, Yuxia; Huang, Guowei

    2017-01-01

    The pathogenesis of atherosclerosis has been partly acknowledged to result from aberrant epigenetic mechanisms. Accordingly, low folate levels are considered to be a contributing factor to promoting vascular disease because of deregulation of DNA methylation. We hypothesized that increasing the levels of folic acid may act via an epigenetic gene silencing mechanism to ameliorate atherosclerosis. Here, we investigated the atheroprotective effects of folic acid and the resultant methylation status in high-fat diet-fed ApoE knockout mice and in oxidized low-density lipoprotein-treated human umbilical vein endothelial cells. We analyzed atherosclerotic lesion histology, folate concentration, homocysteine concentration, S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH), and DNA methyltransferase activity, as well as monocyte chemotactic protein-1 (MCP1) and vascular endothelial growth factor (VEGF) expression and promoter methylation. Folic acid reduced atherosclerotic lesion size in ApoE knockout mice. The underlying folic acid protective mechanism appears to operate through regulating the normal homocysteine state, upregulating the SAM: SAH ratio, elevating DNA methyltransferase activity and expression, altering MCP1 and VEGF promoter methylation, and inhibiting MCP1 and VEGF expression. We conclude that folic acid supplementation effectively prevented atherosclerosis by modifying DNA methylation through the methionine cycle, improving DNA methyltransferase activity and expression, and thus changing the expression of atherosclerosis-related genes. PMID:28475147

  1. Congressmember Sam Farr: Five Decades of Public Service

    OpenAIRE

    Reti, Irene H.; Farr, Sam

    2017-01-01

    Congressmember Sam Farr (born July 4, 1941) represented California’s Central Coast in the United States House of Representatives for twenty-three years until his retirement from office in 2016.  Farr also served six years as a member of the Monterey County Board of Supervisors and twelve years in the California State Assembly. This oral history, a transcript of twenty-five hours of interviews conducted by Irene Reti, director of the UCSC Library’s Regional History Project, during the period i...

  2. Genome sequencing and annotation of Stenotrophomonas sp. SAM8

    Directory of Open Access Journals (Sweden)

    Samy Selim

    2015-12-01

    Full Text Available We report draft genome sequence of Stenotrophomonas sp. strain SAM8, isolated from environmental water. The draft genome size is 3,665,538 bp with a G + C content of 67.2% and contains 6 rRNA sequence (single copies of 5S, 16S & 23S rRNA. The genome sequence can be accessed at DDBJ/EMBL/GenBank under the accession no. LDAV00000000.

  3. Technical Manual for the SAM Biomass Power Generation Model

    Energy Technology Data Exchange (ETDEWEB)

    Jorgenson, J.; Gilman, P.; Dobos, A.

    2011-09-01

    This technical manual provides context for the implementation of the biomass electric power generation performance model in the National Renewable Energy Laboratory's (NREL's) System Advisor Model (SAM). Additionally, the report details the engineering and scientific principles behind the underlying calculations in the model. The framework established in this manual is designed to give users a complete understanding of behind-the-scenes calculations and the results generated.

  4. Reactions Involving Calcium and Magnesium Sulfates as Potential Sources of Sulfur Dioxide During MSL SAM Evolved Gas Analyses

    Science.gov (United States)

    McAdam, A. C.; Knudson, C. A.; Sutter, B.; Franz, H. B.; Archer, P. D., Jr.; Eigenbrode, J. L.; Ming, D. W.; Morris, R. V.; Hurowitz, J. A.; Mahaffy, P. R.; hide

    2016-01-01

    The Sample Analysis at Mars (SAM) and Chemistry and Mineralogy (CheMin) instruments on the Mars Science Laboratory (MSL) have analyzed several subsamples of 860 C). Sulfides or Fe sulfates were detected by CheMin (e.g., CB, MJ, BK) and could contribute to the high temperature SO2 evolution, but in most cases they are not present in enough abundance to account for all of the SO2. This additional SO2 could be largely associated with x-ray amorphous material, which comprises a significant portion of all samples. It can also be attributed to trace S phases present below the CheMin detection limit, or to reactions which lower the temperatures of SO2 evolution from sulfates that are typically expected to thermally decompose at temperatures outside the SAM temperature range (e.g., Ca and Mg sulfates). Here we discuss the results of SAM-like laboratory analyses targeted at understanding this last possibility, focused on understanding if reactions of HCl or an HCl evolving phase (oxychlorine phases, chlorides, etc.) and Ca and Mg sulfates can result in SO2 evolution in the SAM temperature range.

  5. Molecular tilt-dependent and tyrosine-enhanced electron transfer across ITO/SAM/[DPPC–Au NP–Tyrosine] Janus nanoparticle junction

    Energy Technology Data Exchange (ETDEWEB)

    Sarangi, Nirod Kumar; Patnaik, Archita, E-mail: archita59@yahoo.com [Indian Institute of Technology Madras, Department of Chemistry (India)

    2016-09-15

    Enhanced interfacial electron transfer (ET) across the otherwise insulating indium tin oxide/alkanethiol self-assembled monolayer (SAM)/redox molecule junction was accomplished when a Janus gold nanoparticle (JNP) protected by bioinspired phosphatidylcholine (DPPC) lipid and tyrosine amino acid ligands was anchored on it. In addition to the most theoretical and experimental investigations on the distance-dependent ET across Metal–Organic SAM–Nanoparticle (NP) architectures, the current results succinctly illustrate molecular tilt angle of the SAM and the characteristic of JNP as key factors in expediting the ET rate via electron tunneling. In the absence of JNP, electron tunneling with a tunneling factor β = 1.1 Å{sup −1} across the SAM was the rate-limiting step, evidenced from electrochemical impedance spectroscopy (EIS). The apparent electron transfer rate constant (k{sub app}{sup 0}) for anchored SAM was enhanced by at least one order of magnitude than the DPPC-only protected nanoparticle, suggesting the potential role of tyrosine towards the enhanced ET. The asymmetric and biogenic nature of the construct sheds light on a potential bioelectronic device for novel electronic attributes.Graphical abstractEntry of TOC .

  6. Non-invasive vibrational SFG spectroscopy reveals that bacterial adhesion can alter the conformation of grafted "brush" chains on SAM.

    Science.gov (United States)

    Bulard, Emilie; Guo, Ziang; Zheng, Wanquan; Dubost, Henri; Fontaine-Aupart, Marie-Pierre; Bellon-Fontaine, Marie-Noëlle; Herry, Jean-Marie; Briandet, Romain; Bourguignon, Bernard

    2011-04-19

    Understanding bacterial adhesion on a surface is a crucial step to design new materials with improved properties or to control biofilm formation and eradication. Sum Frequency Generation (SFG) vibrational spectroscopy has been employed to study in situ the conformational response of a self-assembled monolayer (SAM) of octadecanethiol (ODT) on a gold film to the adhesion of hydrophilic and hydrophobic ovococcoid model bacteria. The present work highlights vibrational SFG spectroscopy as a powerful and unique non-invasive biophysical technique to probe and control bacteria interaction with ordered surfaces. Indeed, the SFG vibrational spectral changes reveal different ODT SAM conformations in air and upon exposure to aqueous solution or bacterial adhesion. Furthermore, this effect depends on the bacterial cell surface properties. The SFG spectral modeling demonstrates that hydrophobic bacteria flatten the ODT SAM alkyl chain terminal part, whereas the hydrophilic ones raise this ODT SAM terminal part. Microorganism-induced alteration of grafted chains can thus affect the desired interfacial functionality, a result that should be considered for the design of new reactive materials. © 2011 American Chemical Society

  7. Evidence for Smectite Clays from MSL SAM Analyses of Mudstone at Yellowknife Bay, Gale Crater, Mars

    Science.gov (United States)

    McAdam, Amy; Franz, Heather; Mahaffy, Paul R.; Eigenbrode, Jennifer L.; Stern, Jennifer C.; Brunner, Anna; Archer, Paul Douglas; Ming, Douglas W.; Morris, Richard V.; Atreya, Sushil K.

    2013-01-01

    Drilled samples of mudstone from the Sheepbed unit at Yellowknife Bay were analyzed by MSL instruments including the Sample Analysis at Mars (SAM) and Chemistry and Mineralogy (CheMin) instruments in MSL's Analytical Laboratory. CheMin analyses revealed the first in situ X-ray diffraction based evidence of clay minerals on Mars, which are likely trioctahedral smectites (e.g., saponite) and comprise approx 20% of the mudstone sample (e.g., Bristow et al., this meeting). SAM analyses, which heated the mudstone samples to 1000 C and monitored volatiles evolved to perform in situ evolved gas analysis mass spectrometry (EGA-MS), resulted in a H2O trace exhibiting a wide evolution at temperatures smectite interlayer H2O, and structural H2O/OH from bassanite and akaganeite (identified by CheMin) and H2O/OH from amorphous phases in the sample. The high temperature H2O is consistent with the evolution of H2O from the dehydroxylation of the smectite clay mineral. Comparison to EGA-MS data collected under SAM-like conditions on a variety of clay mineral reference materials indicate that a trioctahedral smectite, such as saponite, is most consistent with the high temperature H2O evolution observed. There may also be SAM EGA-MS evidence for a small high temperature H2O evolution from scoop samples from the Yellowknife Bay Rocknest sand shadow bedform. As in the mudstone samples, this evolution may indicate the detection of smectite clays, and the idea that minor clays may be present in Rocknest materials that could be expected to be at least partially derived from local sources is reasonable. But, because smectite clays were not definitively observed in CheMin analyses of Rocknest materials, they must be present at much lower abundances than the approx 20% observed in the mudstone samples. This potential detection underscores the complementary nature of the MSL CheMin and SAM instruments for investigations of martian sample mineralogy. Information on the nature of Yellowknife

  8. Molecular junctions based on SAMs of cruciform oligo(phenylene ethynylene)s

    DEFF Research Database (Denmark)

    Wei, Zhongming; Li, Tao; Jennum, Karsten Stein

    2012-01-01

    Cruciform oligo(phenylene ethynylene)s (OPEs) with an extended tetrathiafulvalene (TTF) donor moiety (OPE5-TTF and OPE3-TTF) and their simple analogues (OPE5-S and OPE3) without conjugated substituents were used to form high quality self-assembled monolayers (SAMs) on ultra-flat gold substrates...

  9. Jo Ann Baumgartner and Sam Earnshaw: Organizers and Farmers

    OpenAIRE

    Rabkin, Sarah

    2010-01-01

    Jo Ann Baumgartner directs the Wild Farm Alliance, based in Watsonville, California. WFA’s mission, as described on the organization’s website, is “to promote agriculture that helps to protect and restore wild Nature.” Through research, publications, presentations, events, policy work, and consulting, the organization works to “connect food systems with ecosystems.” Sam Earnshaw is Central Coast regional coordinator of the Community Alliance with Family Farmers. Working with CAFF’s f...

  10. Reflections on Sam Harris' "Free Will"

    Directory of Open Access Journals (Sweden)

    Daniel C. Dennett

    2017-12-01

    Full Text Available In his book Free Will Sam Harris tries to persuade us to abandon the morally pernicious idea of free will. The following contribution articulates and defends a more sophisticated model of free will that is not only consistent with neuroscience and introspection but also grounds a variety of responsibility that justifies both praise and blame, reward and punishment. This begins with the long lasting parting of opinion between compatibilists (who argue that free will can live comfortably with determinism and incompatibilists (who deny this. While Harris dismisses compatibilism as a form of theology, this article aims at showing that Harris has underestimated and misinterpreted compatibilism and at defending a more sophisticated version of compatibilism that is imprevious to Harris’ criticism.

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

    Science.gov (United States)

    Osato, Naoki

    2018-01-19

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

  12. Methyl group balance in brain and liver: role of choline on increased S-adenosyl methionine (SAM) demand by chronic arsenic exposure.

    Science.gov (United States)

    Ríos, Rosalva; Santoyo, Martha E; Cruz, Daniela; Delgado, Juan Manuel; Zarazúa, Sergio; Jiménez-Capdeville, María E

    2012-11-30

    Arsenic toxicity has been related to its interference with one carbon metabolism, where a high demand of S-adenosylmethionine (SAM) for arsenic methylation as well as a failure of its regeneration would compromise the availability of methyl groups for diverse cellular functions. Since exposed animals show disturbances of methylated products such as methylated arginines, myelin and axon membranes, this work investigates whether alterations of SAM, choline and phosphatidylcholine (PC) in the brain of arsenic exposed rats are associated with myelin alterations and myelin basic protein (MBP) immunoreactivity. Also these metabolites, morphologic and biochemical markers of methyl group alterations were analyzed in the liver, the main site of arsenic methylation. In adult, life-long arsenic exposed rats through drinking water (3 ppm), no changes of SAM, choline and PC concentrations where found in the brain, but SAM and PC were severely decreased in liver accompanied by a significant increase of choline. These results suggest that choline plays an important role as methyl donor in arsenic exposure, which could underlie hepatic affections observed when arsenic exposure is combined with other environmental factors. Also, important myelin and nerve fiber alterations, accompanied by a 75% decrease of MBP immunoreactivity were not associated with a SAM deficit in the brain. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  13. Thermal and Evolved Gas Analysis of Calcite Under Reduced Operating Pressures: Implications for the 2011 MSL Sample Analysis at Mars (SAM) Instrument

    Science.gov (United States)

    Lauer, H. V. Jr.; Ming, D. W.; Sutter, B.; Mahaffy, P. R.

    2010-01-01

    The Mars Science Laboratory (MSL) is scheduled for launch in 2011. The science objectives for MSL are to assess the past or present biological potential, to characterize the geology, and to investigate other planetary processes that influence habitability at the landing site. The Sample Analysis at Mars (SAM) is a key instrument on the MSL payload that will explore the potential habitability at the landing site [1]. In addition to searching for organic compounds, SAM will have the capability to characterized evolved gases as a function of increasing temperature and provide information on the mineralogy of volatile-bearing phases such as carbonates, sulfates, phyllosilicates, and Fe-oxyhydroxides. The operating conditions in SAM ovens will be maintained at 30 mb pressure with a He carrier gas flowing at 1 sccm. We have previously characterized the thermal and evolved gas behaviors of volatile-bearing species under reduced pressure conditions that simulated operating conditions of the Thermal and Evolved Gas Analyzer (TEGA) that was onboard the 2007 Mars Phoenix Scout Mission [e.g., 2-8]. TEGA ovens operated at 12 mb pressure with a N2 carrier gas flowing at 0.04 sccm. Another key difference between SAM and TEGA is that TEGA was able to perform differential scanning calorimetry whereas SAM only has a pyrolysis oven. The operating conditions for TEGA and SAM have several key parameter differences including operating pressure (12 vs 30 mb), carrier gas (N2 vs. He), and carrier gas flow rate (0.04 vs 1 sccm). The objectives of this study are to characterize the thermal and evolved gas analysis of calcite under SAM operating conditions and then compare it to calcite thermal and evolved gas analysis under TEGA operating conditions.

  14. iSAM: An iPhone Stealth Airborne Malware

    OpenAIRE

    Damopoulos , Dimitrios; Kambourakis , Georgios; Gritzalis , Stefanos

    2011-01-01

    Part 2: Malware, Information Flow and DoS Attacks; International audience; Modern and powerful mobile devices comprise an attractive target for any potential intruder or malicious code. The usual goal of an attack is to acquire users’ sensitive data or compromise the device so as to use it as a stepping stone (or bot) to unleash a number of attacks to other targets. In this paper, we focus on the popular iPhone device.We create a new stealth and airborne malware namely iSAM able to wirelessly...

  15. Stealing the gold a celebration of the pioneering physics of Sam Edwards

    CERN Document Server

    Goldenfeld, Nigel; Sherrington, D C; Edwards, S F

    2004-01-01

    This title presents a survey of some of the most exciting topics in condensed matter physics today, from the perspective of the pioneering work of Sam Edwards. Original articles from leaders in the field highlight the historical development as well as new and emerging areas.

  16. Evolved Gas Analyses of Sedimentary Materials in Gale Crater, Mars: Results of the Curiosity Rover's Sample Analysis at Mars (SAM) Instrument from Yellowknife Bay to the Stimson Formation

    Science.gov (United States)

    Sutter, B.; McAdam, A. C.; Rampe, E. B.; Ming, D. W.; Mahaffy, P. R.; Navarro-Gonzalez, R.; Stern, J. C.; Eigenbrode, J. L.; Archer, P. D.

    2016-01-01

    The Sample Analysis at Mars (SAM) instrument aboard the Mars Science Laboratory rover has analyzed 10 samples from Gale Crater. All SAM evolved gas analyses have yielded a multitude of volatiles (e.g, H2O, SO2, H2S, CO2, CO, NO, O2, HC1). The objectives of this work are to 1) Characterize the evolved H2O, SO2, CO2, and O2 gas traces of sediments analyzed by SAM through sol 1178, 2) Constrain sediment mineralogy/composition based on SAM evolved gas analysis (SAM-EGA), and 3) Discuss the implications of these results releative to understanding the geochemical history of Gale Crater.

  17. Radiation-induced gene expression in human subcutaneous fibroblasts is predictive of radiation-induced fibrosis

    DEFF Research Database (Denmark)

    Rødningen, Olaug Kristin; Børresen-Dale, Anne-Lise; Alsner, Jan

    2008-01-01

    BACKGROUND AND PURPOSE: Breast cancer patients show a large variation in normal tissue reactions after ionizing radiation (IR) therapy. One of the most common long-term adverse effects of ionizing radiotherapy is radiation-induced fibrosis (RIF), and several attempts have been made over the last...... years to develop predictive assays for RIF. Our aim was to identify basal and radiation-induced transcriptional profiles in fibroblasts from breast cancer patients that might be related to the individual risk of RIF in these patients. MATERIALS AND METHODS: Fibroblast cell lines from 31 individuals......-treated fibroblasts. Transcriptional differences in basal and radiation-induced gene expression profiles were investigated using 15K cDNA microarrays, and results analyzed by both SAM and PAM. RESULTS: Sixty differentially expressed genes were identified by applying SAM on 10 patients with the highest risk of RIF...

  18. Radical SAM Enzymes in the Biosynthesis of Ribosomally Synthesized and Post-translationally Modified Peptides (RiPPs

    Directory of Open Access Journals (Sweden)

    Alhosna Benjdia

    2017-11-01

    Full Text Available Ribosomally-synthesized and post-translationally modified peptides (RiPPs are a large and diverse family of natural products. They possess interesting biological properties such as antibiotic or anticancer activities, making them attractive for therapeutic applications. In contrast to polyketides and non-ribosomal peptides, RiPPs derive from ribosomal peptides and are post-translationally modified by diverse enzyme families. Among them, the emerging superfamily of radical SAM enzymes has been shown to play a major role. These enzymes catalyze the formation of a wide range of post-translational modifications some of them having no counterparts in living systems or synthetic chemistry. The investigation of radical SAM enzymes has not only illuminated unprecedented strategies used by living systems to tailor peptides into complex natural products but has also allowed to uncover novel RiPP families. In this review, we summarize the current knowledge on radical SAM enzymes catalyzing RiPP post-translational modifications and discuss their mechanisms and growing importance notably in the context of the human microbiota.

  19. International ISOE Workshop - Direction Forward for the Finalization of the EG-SAM Report

    International Nuclear Information System (INIS)

    Okyar, H. Burcin

    2014-01-01

    The objective of the ISOE Expert Group on Occupational Radiation Protection in Severe Accident Management and Post-accident Recovery (EG-SAM) is to develop a report on best radiation protection management procedures for proper radiation protection job coverage during severe accident initial response and recovery efforts to identify good radiation protection practices and to organise and communicate radiation protection lessons learned from previous reactor accidents. The outcome of the work will be a new ISOE publication on Occupational Radiation Protection in severe accident management that will find broad use within the NPP radiation protection community. The EG-SAM has finalized an interim report which was presented at the Washington workshop. The interim report covered the following topics: RP Management and Organisation; RP Training and Exercises related to Severe Accident Management; Facility Configuration and Readiness; Overall Approach for Worker Protection; Monitoring and Managing the Radioactive Releases and Contamination; Key Lessons Learned from Past Accidents; Conclusions. Utilities and Regulatory Authorities have identified the factors and aspects which play key roles in achieving good practices on occupational radiation protection in severe accident management and post-accident recovery: knowledge, experience, technology, regulatory requirements and guidance, worker involvement, information exchange, training aspects, etc. They have analysed and quantified their impact on worker doses, and submitted recommendations for further work. The next step will be a final meeting of the EG-SAM for the finalization of the report with workshop inputs before its submission for approval

  20. The multi-state energy landscape of the SAM-I riboswitch: A single-molecule Förster resonance energy transfer spectroscopy study

    Science.gov (United States)

    Manz, Christoph; Kobitski, Andrei Yu.; Samanta, Ayan; Jäschke, Andres; Nienhaus, G. Ulrich

    2018-03-01

    RNA (ribonucleic acid) molecules are highly flexible biopolymers fluctuating at physiological temperatures among many different conformations that are represented by minima in a hierarchical conformational free energy landscape. Here we have employed single-molecule FRET (smFRET) to explore the energy landscape of the B. subtilis yitJ SAM-I riboswitch (RS). In this small RNA molecule, specific binding of an S-adenosyl-L-methionine (SAM) ligand in the aptamer domain regulates gene expression by inducing structural changes in another domain, the expression platform, causing transcription termination by the RNA polymerase. We have measured smFRET histograms over wide ranges of Mg2+ concentration for three RS variants that were specifically labeled with fluorescent dyes on different sites. In the analysis, different conformations are associated with discrete Gaussian model distributions, which are typically fairly broad on the FRET efficiency scale and thus can be extremely challenging to unravel due to their mutual overlap. Our earlier work on two SAM-I RS variants revealed four major conformations. By introducing a global fitting procedure which models both the Mg2+ concentration dependencies of the fractional populations and the average FRET efficiencies of the individual FRET distributions according to Mg2+ binding isotherms, we were able to consistently describe the histogram data of both variants at all studied Mg2+ concentrations. With the third FRET-labeled variant, however, we found significant deviations when applying the four-state model to the data. This can arise because the different FRET labeling of the new variant allows two states to be distinguished that were previously not separable due to overlap. Indeed, the resulting five-state model presented here consistently describes the smFRET histograms of all three variants as well as their variations with Mg2+ concentration. We also performed a triangulation of the donor position for two of the constructs

  1. SAM - Sistema Automatizado del Método MECAP para Especificar Casos de Prueba

    Directory of Open Access Journals (Sweden)

    Kenyer Domínguez

    2010-12-01

    Full Text Available Existen cuatro elementos que son relevantes al momento de definir las pruebas: Confiabilidad, Costo, Tiempo y Calidad. El tiempo de desarrollo y el costo del producto se incrementan cuando se desean pruebas confiables y un software de calidad. Pero ¿qué se puede hacer para que los involucrados comprendan que las pruebas deben ser vistas como una red de seguridad? Si la calidad no se contempla antes de comenzar las pruebas, entonces ella no estará cuando se éstas terminen. El objetivo de este artículo es presentar la herramienta, SAM – Sistema Automatizado del Método MECAP que permite especificar Casos de Prueba a partir de Casos de Uso incorporando elementos que promueven la verificación y validación de la trazabilidad entre la Gestión de Requerimientos, el Análisis y Diseño y las Pruebas. SAM soporta el proceso de pruebas de forma automatizada, mejorando la confiabilidad de las mismas

  2. Progress in the development of a reactivity capability in the SAM-CE system for validating fuel management codes. Interim report

    International Nuclear Information System (INIS)

    Lichtenstein, H.; Steinberg, H.; Troubetzkoy, E.; Cohen, M.O.; Chui, C.

    1978-02-01

    The SAM-CE Monte Carlo system (for three dimensional neutron, gamma ray and electron transport) has been expanded to include a reactivity capability. The implemented code modifications have effected the following improvements: (a) Doppler broadening of ENDF/B-IV based nuclear data (including fission); (b) probability table representation for the unresolved resonance range; (c) utilization of thermal scattering law data for the moderator; (d) free gas model in the absence of thermal scattering law data; (e) generalization of the nuclear element data tape structure to facilitate data management; (f) generalization of data management routines; (g) extension of the SAM-CE Complex Combinatorial Geometry capability to facilitate treatment of hexagonal lattices; (h) simultaneous use of 4 different eigenvalue estimators; (i) estimation of the eigenfunction in user prescribed spatial domains; and (j) variance reduction via stratification of source (position, energy, direction) and absorption (based on a quota sampling technique), as well as optional suppression of absorption. The new coding has undergone extensive testing, both specific (via drivers and idealized data) and integral (via comparison with previous computations). Base data have been examined for internal consistency and checked for reasonableness. A documented TRX-1 benchmark calculation has been performed. Agreement with other calculations, as well as with experiment, has served to validate the reactivity mode of SAM-CE. Further refinement of the cross section data processing component of SAM-CE (i.e., SAM-X) is suggested

  3. Detection of Reduced Nitrogen Compounds at Rocknest Using the Sample Analysis At Mars (SAM) Instrument on the Mars Science Laboratory (MSL)

    Science.gov (United States)

    Stern, J. C.; Steele, A.; Brunner, A.; Coll, P.; Eigenbrode, J.; Franz, H. B.; Freissinet, C.; Glavin, D.; Jones, J. H.; Navarro-Gonzalez, R.; hide

    2013-01-01

    The Sample Analysis at Mars (SAM) instrument suite on the Mars Science Laboratory (MSL) Curiosity Rover detected nitrogen-bearing compounds during the pyrolysis of Rocknest material at Gale Crater. Hydrogen cyanide and acetonitrile were identified by the quadrupole mass spectrometer (QMS) both in direct evolved gas analysis (EGA). SAM carried out four separate analyses from Rocknest Scoop 5. A significant low temperature release was present in Rocknest runs 1-4, while a smaller high temperature release was also seen in Rocknest runs 1-3. Here we evaluate whether these compounds are indigenous to Mars or a pyrolysis product resulting from known terrestrial materials that are part of the SAM derivatization.

  4. Theorizing the place of evil within Sam Ukala's Radical Theatre: A ...

    African Journals Online (AJOL)

    The perspectives of evil in this essay will be drawn mainly from the works of such thinkers as Paul Ricoeur, St Augustine, and Friedrich Nietzsche, yet not excluding occasional insights from thinkers like Immanuel Kant, Richard B. Sewall, and so on. Sam Ukala's Akpakaland, Break a Boil and Odour of Justice are the plays to ...

  5. Dosimetric comparison of the specific anthropomorphic mannequin (SAM) to 14 anatomical head models using a novel definition for the mobile phone positioning

    International Nuclear Information System (INIS)

    Kainz, Wolfgang; Christ, Andreas; Kellom, Tocher; Seidman, Seth; Nikoloski, Neviana; Beard, Brian; Kuster, Niels

    2005-01-01

    This paper presents new definitions for obtaining reproducible results in numerical phone dosimetry. Numerous numerical dosimetric studies have been published about the exposure of mobile phone users which concluded with conflicting results. However, many of these studies lack reproducibility due to shortcomings in the description of the phone positioning. The new approach was tested by two groups applying two different numerical program packages to compare the specific anthropomorphic mannequin (SAM) to 14 anatomically correct head models. A novel definition for the positioning of mobile phones next to anatomically correct head models is given along with other essential parameters to be reported. The definition is solely based on anatomical characteristics of the head. A simple up-to-date phone model was used to determine the peak spatial specific absorption rate (SAR) of mobile phones in SAM and in the anatomically correct head models. The results were validated by measurements. The study clearly shows that SAM gives a conservative estimate of the exposure in anatomically correct head models for head only tissue. Depending on frequency, phone position and head size the numerically calculated 10 g averaged SAR in the pinna can be up to 2.1 times greater than the peak spatial SAR in SAM. Measurements in small structures, such as the pinna, will significantly increase the uncertainty; therefore SAM was designed for SAR assessment in the head only. Whether SAM will provide a conservative value for the pinna depends on the pinna SAR limit of the safety standard considered

  6. Elp3 and RlmN: A tale of two mitochondrial tail-anchored radical SAM enzymes in Toxoplasma gondii.

    Science.gov (United States)

    Padgett, Leah R; Lentini, Jenna M; Holmes, Michael J; Stilger, Krista L; Fu, Dragony; Sullivan, William J

    2018-01-01

    Radical S-adenosylmethionine (rSAM) enzymes use a 5'-deoxyadensyl 5'-radical to methylate a wide array of diverse substrates including proteins, lipids and nucleic acids. One such enzyme, Elongator protein-3 (TgElp3), is an essential protein in Toxoplasma gondii, a protozoan parasite that can cause life-threatening opportunistic disease. Unlike Elp3 homologues which are present in all domains of life, TgElp3 localizes to the outer mitochondrial membrane (OMM) via a tail-anchored trafficking mechanism in Toxoplasma. Intriguingly, we identified a second tail-anchored rSAM domain containing protein (TgRlmN) that also localizes to the OMM. The transmembrane domain (TMD) on Toxoplasma Elp3 and RlmN homologues is required for OMM localization and has not been seen beyond the chromalveolates. Both TgElp3 and TgRlmN contain the canonical rSAM amino acid sequence motif (CxxxCxxC) necessary to form the 4Fe-4S cluster required for tRNA modifications. In E. coli, RlmN is responsible for the 2-methlyadenosine (m2A) synthesis at purine 37 in tRNA while in S. cerevisiae, Elp3 is necessary for the formation of 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U) at the wobble tRNA position. To investigate why these two rSAM enzymes localize to the mitochondrion in Toxoplasma, and whether or not TgRlmN and TgElp3 possess tRNA methyltransferase activity, a series of mutational and biochemical studies were performed. Overexpression of either TgElp3 or TgRlmN resulted in a significant parasite replication defect, but overexpression was tolerated if either the TMD or rSAM domain was mutated. Furthermore, we show the first evidence that Toxoplasma tRNAGlu contains the mcm5s2U modification, which is the putative downstream product generated by TgElp3 activity.

  7. Deposition of phospholipid layers on SiO{sub 2} surface modified by alkyl-SAM islands

    Energy Technology Data Exchange (ETDEWEB)

    Tero, R.; Takizawa, M.; Li, Y.J.; Yamazaki, M.; Urisu, T

    2004-11-15

    Formation of the supported planar bilayer of dipalmitoylphosphatidylcholine (DPPC) on SiO{sub 2} surfaces modified with the self-assembled monolayer (SAM) of octadecyltrichlorosilane (OTS) has been investigated by atomic force microscopy (AFM). DPPC was deposited by the fusion of vesicles on SiO{sub 2} surfaces with OTS-SAM islands of different sizes and densities. The DPPC bilayer membrane formed self-organizingly on the SiO{sub 2} surface with small and sparse OTS islands, while did not when the OTS islands were larger and denser. The relative size between the vesicles and the SiO{sub 2} regions is the critical factor for the formation of the DPPC bilayer membrane.

  8. Gene expression and functional studies of the optic nerve head astrocyte transcriptome from normal African Americans and Caucasian Americans donors.

    Directory of Open Access Journals (Sweden)

    Haixi Miao

    2008-08-01

    Full Text Available To determine whether optic nerve head (ONH astrocytes, a key cellular component of glaucomatous neuropathy, exhibit differential gene expression in primary cultures of astrocytes from normal African American (AA donors compared to astrocytes from normal Caucasian American (CA donors.We used oligonucleotide Affymetrix microarray (HG U133A & HG U133A 2.0 chips to compare gene expression levels in cultured ONH astrocytes from twelve CA and twelve AA normal age matched donor eyes. Chips were normalized with Robust Microarray Analysis (RMA in R using Bioconductor. Significant differential gene expression levels were detected using mixed effects modeling and Statistical Analysis of Microarray (SAM. Functional analysis and Gene Ontology were used to classify differentially expressed genes. Differential gene expression was validated by quantitative real time RT-PCR. Protein levels were detected by Western blots and ELISA. Cell adhesion and migration assays tested physiological responses. Glutathione (GSH assay detected levels of intracellular GSH.Multiple analyses selected 87 genes differentially expressed between normal AA and CA (P<0.01. The most relevant genes expressed in AA were categorized by function, including: signal transduction, response to stress, ECM genes, migration and cell adhesion.These data show that normal astrocytes from AA and CA normal donors display distinct expression profiles that impact astrocyte functions in the ONH. Our data suggests that differences in gene expression in ONH astrocytes may be specific to the development and/or progression of glaucoma in AA.

  9. Differential gene expression between African American and European American colorectal cancer patients.

    Directory of Open Access Journals (Sweden)

    Biljana Jovov

    Full Text Available The incidence and mortality of colorectal cancer (CRC is higher in African Americans (AAs than other ethnic groups in the U. S., but reasons for the disparities are unknown. We performed gene expression profiling of sporadic CRCs from AAs vs. European Americans (EAs to assess the contribution to CRC disparities. We evaluated the gene expression of 43 AA and 43 EA CRC tumors matched by stage and 40 matching normal colorectal tissues using the Agilent human whole genome 4x44K cDNA arrays. Gene and pathway analyses were performed using Significance Analysis of Microarrays (SAM, Ten-fold cross validation, and Ingenuity Pathway Analysis (IPA. SAM revealed that 95 genes were differentially expressed between AA and EA patients at a false discovery rate of ≤5%. Using IPA we determined that most prominent disease and pathway associations of differentially expressed genes were related to inflammation and immune response. Ten-fold cross validation demonstrated that following 10 genes can predict ethnicity with an accuracy of 94%: CRYBB2, PSPH, ADAL, VSIG10L, C17orf81, ANKRD36B, ZNF835, ARHGAP6, TRNT1 and WDR8. Expression of these 10 genes was validated by qRT-PCR in an independent test set of 28 patients (10 AA, 18 EA. Our results are the first to implicate differential gene expression in CRC racial disparities and indicate prominent difference in CRC inflammation between AA and EA patients. Differences in susceptibility to inflammation support the existence of distinct tumor microenvironments in these two patient populations.

  10. Wide Range Vacuum Pumps for the SAM Instrument on the MSL Curiosity Rover

    Science.gov (United States)

    Sorensen, Paul; Kline-Schoder, Robert; Farley, Rodger

    2014-01-01

    Creare Incorporated and NASA Goddard Space Flight Center developed and space qualified two wide range pumps (WRPs) that were included in the Sample Analysis at Mars (SAM) instrument. This instrument was subsequently integrated into the Mars Science Laboratory (MSL) "Curiosity Rover," launched aboard an Atlas V rocket in 2011, and landed on August 6, 2012, in the Gale Crater on Mars. The pumps have now operated for more than 18 months in the Gale Crater and have been evacuating the key components of the SAM instrument: a quadrupole mass spectrometer, a tunable laser spectrometer, and six gas chromatograph columns. In this paper, we describe the main design challenges and the ways in which they were solved. This includes the custom design of a miniaturized, high-speed motor to drive the turbo drag pump rotor, analysis of rotor dynamics for super critical operation, and bearing/lubricant design/selection.

  11. Non-functional genes repaired at the RNA level.

    Science.gov (United States)

    Burger, Gertraud

    2016-01-01

    Genomes and genes continuously evolve. Gene sequences undergo substitutions, deletions or nucleotide insertions; mobile genetic elements invade genomes and interleave in genes; chromosomes break, even within genes, and pieces reseal in reshuffled order. To maintain functional gene products and assure an organism's survival, two principal strategies are used - either repair of the gene itself or of its product. I will introduce common types of gene aberrations and how gene function is restored secondarily, and then focus on systematically fragmented genes found in a poorly studied protist group, the diplonemids. Expression of their broken genes involves restitching of pieces at the RNA-level, and substantial RNA editing, to compensate for point mutations. I will conclude with thoughts on how such a grotesquely unorthodox system may have evolved, and why this group of organisms persists and thrives since tens of millions of years. Copyright © 2016 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  12. Recoding painting? Repeated use of artwork in Cindy Sherman and Sam Taylor Wood

    Directory of Open Access Journals (Sweden)

    Dunja Radetic

    2012-12-01

    Through a theoretical analysis of two contemporary artworks by Cindy Sherman and Sam Taylor Wood, both based on earlier visual tradition, we will consider the effects of re-production of images as the re-production of deferred meaning. The intersystemic quotation such as painting - tableau vivant – coding by photographic and video technologies, works at different levels and creates high degree of ambiguity between the media and the images involved. This mediation produces disturbing effects on the viewer who has to recognize in the artwork an contaminated and elusive visual tradition, which displays a latent meanings and (reactivates memory images. In order to understand these complex layers it is necessary to consider the work and its subtext in terms of a shared temporality in which images, media and extratextual memories, interact.

  13. Franchising as a Potential Growth Strategy for a Small Business : A Case of Sam-Chi Fast Food Restaurant

    OpenAIRE

    Odunsi, Sadiq

    2015-01-01

    The purpose of this study was to find out whether Sam-Chi fast food restaurant can grow through franchising as well as to give the owners recommendations on how to effectively adopt the franchising business model as a means to grow their business. Sam-Chi restaurant is situated in Lagos, Nigeria and the restaurant is owned and operated by Samuel Okore and his wife Chichi Okore. The theoretical framework of this research is separated into two sections. The first section covers the growth of a ...

  14. Severe accident management (SAM), operator training and instrumentation capabilities - Summary and conclusions

    International Nuclear Information System (INIS)

    2002-01-01

    The Workshop on Operator Training for Severe Accident Management (SAM) and Instrumentation Capabilities During Severe Accidents was organised in collaboration with Electricite de France (Service Etudes et Projets Thermiques et Nucleaires). There were 34 participants, representing thirteen OECD Member countries, the Russian Federation and the OECD/NEA. Almost half the participants represented utilities. The second largest group was regulatory authorities and their technical support organisations. Basically, the Workshop was a follow-up to the 1997 Second Specialist Meeting on Operator Aids for Severe Accident Management (SAMOA-2) [Reports NEA/CSNI/R(97)10 and 27] and to the 1992 Specialist Meeting on Instrumentation to Manage Severe Accidents [Reports NEA/CSNI/R(92)11 and (93)3]. It was aimed at sharing and comparing progress made and experience gained from these two meetings, emphasizing practical lessons learnt during training or incidents as well as feedback from instrumentation capability assessment. The objectives of the Workshop were therefore: - to exchange information on recent and current activities in the area of operator training for SAM, and lessons learnt during the management of real incidents ('operator' is defined hear as all personnel involved in SAM); - to compare capabilities and use of instrumentation available during severe accidents; - to monitor progress made; - to identify and discuss differences between approaches relevant to reactor safety; - and to make recommendations to the Working Group on the Analysis and Management of Accidents and the CSNI (GAMA). The Workshop was organised into five sessions: - 1: Introduction; - 2: Tools and Methods; - 3: Training Programmes and Experience; - 4: SAM Organisation Efficiency; - 5: Instrumentation Capabilities. It was concluded by a Panel and General Discussion. This report presents the summary and conclusions: the meeting confirmed that only limited information is needed for making required decisions

  15. Low-level lasers alter mRNA levels from traditional reference genes used in breast cancer cells

    Science.gov (United States)

    Teixeira, A. F.; Canuto, K. S.; Rodrigues, J. A.; Fonseca, A. S.; Mencalha, A. L.

    2017-07-01

    Cancer is among the leading causes of mortality worldwide, increasing the importance of treatment development. Low-level lasers are used in several diseases, but some concerns remains on cancers. Reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) is a technique used to understand cellular behavior through quantification of mRNA levels. Output data from target genes are commonly relative to a reference that cannot vary according to treatment. This study evaluated reference genes levels from MDA-MB-231 cells exposed to red or infrared lasers at different fluences. Cultures were exposed to red and infrared lasers, incubated (4 h, 37 °C), total RNA was extracted and cDNA synthesis was performed to evaluate mRNA levels from ACTB, GUSB and TRFC genes by RT-qPCR. Specific amplification was verified by melting curves and agarose gel electrophoresis. RefFinder enabled data analysis by geNorm, NormFinder and BestKeeper. Specific amplifications were obtained and, although mRNA levels from ACTB, GUSB or TRFC genes presented no significant variation through traditional statistical analysis, Excel-based tools revealed that the use of these reference genes are dependent of laser characteristics. Our data showed that exposure to low-level red and infrared lasers at different fluences alter the mRNA levels from ACTB, GUSB and TRFC in MDA-MB-231 cells.

  16. Codon usage and amino acid usage influence genes expression level.

    Science.gov (United States)

    Paul, Prosenjit; Malakar, Arup Kumar; Chakraborty, Supriyo

    2018-02-01

    Highly expressed genes in any species differ in the usage frequency of synonymous codons. The relative recurrence of an event of the favored codon pair (amino acid pairs) varies between gene and genomes due to varying gene expression and different base composition. Here we propose a new measure for predicting the gene expression level, i.e., codon plus amino bias index (CABI). Our approach is based on the relative bias of the favored codon pair inclination among the genes, illustrated by analyzing the CABI score of the Medicago truncatula genes. CABI showed strong correlation with all other widely used measures (CAI, RCBS, SCUO) for gene expression analysis. Surprisingly, CABI outperforms all other measures by showing better correlation with the wet-lab data. This emphasizes the importance of the neighboring codons of the favored codon in a synonymous group while estimating the expression level of a gene.

  17. ISOE EG-SAM interim report - Report on behalf of the Sub expert Group

    International Nuclear Information System (INIS)

    Harris, Willie; Miller, David W.; Djeffal, Salah; Anderson, Ellen; Couasnon, Olivier; Hagemeyer, Derek; Sovijarvi, Jukka; Amaral, Marcos A.; Tarzia, J.P.; Schmidt, Claudia; Fritioff, Karin; Kaulard, Joerg; Lance, Benoit; Fritioff, Karin; Schieber, Caroline; Hayashida, Yoshihisa; Doty, Rick

    2014-01-01

    During its November 2012 meeting, the expert group decided to develop an interim (preliminary) report before the end of 2013 (with a general perspective and discussion of specific severe accident management worker dose issues), and to finalize the report by organizing the international workshop of 2014 to address national experiences, which will be incorporated to the report. The work of the EG-SAM focuses on radiation protection management and organization, radiation protection training and exercises related to severe accident management, facility configuration and readiness, worker protection, radioactive materials, contamination controls and logistics and key lessons learned especially from the TMI, Chernobyl and Fukushima Dai-ichi accidents. This interim report was completed through intensive work of all Group members nominated by the ISOE, and was accomplished during EG-SAM meetings through 2012-2013. This document gathers the different presentations given by the sub expert groups in charge of each chapter of the report

  18. Electrochemical characterization of a 1,8-octanedithiol self-assembled monolayer (ODT-SAM) on a Au(111) single crystal electrode

    Energy Technology Data Exchange (ETDEWEB)

    Garcia-Raya, Daniel; Madueno, Rafael; Sevilla, Jose Manuel; Blazquez, Manuel; Pineda, Teresa [Departamento de Quimica Fisica y Termodinamica Aplicada, Universidad de Cordoba, Campus de Rabanales, Cordoba (Spain)

    2008-11-15

    Recently, it has becoming increasingly important to control the organization of self-assembled monolayers (SAMs) of {omega}-functionalized thiols for its potential applications in the construction of more complex molecular architectures. In this paper, we report on the spontaneous formation of a SAM of octanedithiol (ODT) as a function of the modification time. Electrochemical techniques such as cyclic voltammetry, double layer capacitance and electrochemical impedance spectroscopy are used for the characterization of this monolayer. The increase in modification time brings about changes in the octanedithiol self-assembled monolayer (ODT-SAM) reductive desorption voltammograms that indicate an evolution toward a more ordered and compact monolayer. This trend has also been found by following the changes in the electron transfer processes of the redox probe K{sub 3}Fe(CN){sub 6}. In fact, the ODT-SAM formed at low-modification time does not significantly perturb the electrochemical response as it is typical of either a low coverage or of the presence of large defects in the layer. Upon increasing the modification time, the voltammograms of the redox probe adopt a sigmoidal shape indicating the existence of pinholes in the monolayer distributed as an array of microelectrodes. The surface coverage as well as the size and distribution of these pinholes have been determined by the impedance technique that gives a more reliable evaluation of these monolayer structural parameters. (author)

  19. The captain class : the hidden force that creates the world's greatest teams / Sam Walker

    Trove (Australia)

    Walker, Sam

    2017-01-01

    ... it is. It's not the coach. It's not the star. It's not chemistry. It's not a strategy. It's something else entirely. Several years ago, Sam Walker set out to answer one of the most hotly debated questions in sports ...

  20. Efficient degradation of sulfamethazine in simulated and real wastewater at slightly basic pH values using Co-SAM-SCS /H2O2 Fenton-like system.

    Science.gov (United States)

    Cheng, Min; Zeng, Guangming; Huang, Danlian; Lai, Cui; Liu, Yang; Zhang, Chen; Wan, Jia; Hu, Liang; Zhou, Chengyun; Xiong, Weiping

    2018-07-01

    The presence of antibiotics in aquatic environments has attracted global concern. Fenton process is an attractive yet challenging method for antibiotics degradation, especially when such a reaction can be conducted at neutral pH values. In this study, a novel composite Fe/Co catalyst was synthesized via the modification of steel converter slag (SCS) by salicylic acid-methanol (SAM) and cobalt nitrate (Co(NO 3 ) 2 ). The catalysts were characterized by N 2 -Brunauer-Emmett-Teller (BET), X-ray diffraction (XRD), Fourier transform infrared (FT-IR), X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM) and energy dispersive X-ray spectroscopy (EDS). The results indicated that the Co-SAM-SCS/H 2 O 2 Fenton-like system was very effective for sulfamethazine (SMZ) degradation at a wide pH range. At initial pH of 7.0, the degradation rate of SMZ in Co-SAM-SCS/H 2 O 2 system was 2.48, 3.20, 6.18, and 16.21 times of that in Fe-SAM-SCS/H 2 O 2 , SAM-SCS/H 2 O 2 , Co(NO 3 ) 2 /H 2 O 2 and SCS/H 2 O 2 system, respectively. The preliminary analysis suggested that high surface area of Co-SAM-SCS sample and synergistic effect between introduced Co and SAM-SCS are responsible for the efficient catalytic activity. During the degradation, three main intermediates were identified by high performance liquid chromatography-mass spectrometry (HPLC-MS) analysis. Based on this, a possible degradation pathway was proposed. The SEM images, XRD patterns and XPS spectra before and after the reactions demonstrate that the crystal and chemical structure of Co-SAM-SCS after five cycles are almost unchanged. Besides, the Co-SAM-SCS presented low iron and cobalt leaching (0.17 mg/L and 2.36 mg/L, respectively). The studied Fenton-like process also showed high degradation of SMZ in river water and municipal wastewater. The progress will bring valuable insights to develop high-performance heterogeneous Fenton-like catalysts for environmental remediation. Copyright © 2018

  1. A Study to Evaluate the Organization and the Operating Procedures of the Patient Assistance Function at Brooke Army Medical Center, Fort Sam Houston, Texas

    Science.gov (United States)

    1979-08-01

    15 March 1979. 59Interview with Wendy L. Farace , Head Nurse, Obstetrics/Gynecology Clinic, Brooke Army Medical Center, Fort Sam Houston, Texas, 8...6 February 1979. Farace , Wendy L. Head Nurse, Obstetrica/Gynecology Clinic, Brooke Army Medical Center, Fort Sam Houston, Texas. Interview, 8 January

  2. Redox-based Epigenetic status in Drug Addiction: Potential mediator of drug-induced gene priming phenomenon and use of metabolic intervention for symptomatic treatment in drug addiction.

    Directory of Open Access Journals (Sweden)

    Malav Suchin Trivedi

    2015-01-01

    Full Text Available Alcohol and other drugs of abuse, including psychostimulants and opioids, can induce epigenetic changes: a contributing factor for drug addiction, tolerance and associated withdrawal symptoms. DNA methylation is the major epigenetic mechanism and it is one of more than 200 methylation reactions supported by methyl donor S-adenosylmethionine (SAM. The levels of SAM are controlled by cellular redox status via the folate and vitamin B12-dependent enzyme methionine synthase (MS, for example; under oxidative conditions MS is inhibited, diverting its substrate homocysteine (HCY to the transsulfuration pathway. Alcohol, dopamine and morphine, can alter intracellular levels of glutathione (GSH-based cellular redox status, subsequently affecting S-adenosylmethionine (SAM levels and DNA methylation status. In this discussion, we compile this and other existing evidence in a coherent manner to present a novel hypothesis implicating the involvement of redox-based epigenetic changes in drug addiction. Next, we also discuss how gene priming phenomenon can contribute to maintenance of redox and methylation status homeostasis under various stimuli including drugs of abuse. Lastly, based on our hypothesis and some preliminary evidence, we discuss a mechanistic explanation for use of metabolic interventions / redox-replenishers as symptomatic treatment of alcohol addiction and associated withdrawal symptoms. Hence, the current review article strengthens the hypothesis that neuronal metabolism has a critical bidirectional coupling with epigenetic changes in drug addiction and we support this claim via exemplifying the link between redox-based metabolic changes and resultant epigenetic consequences under the effect of drugs of abuse.

  3. Effect of aromatic SAMs molecules on graphene/silicon schottky diode performance

    OpenAIRE

    Yağmurcukardeş, Nesli; Aydın, Hasan; Can, Mustafa; Yanılmaz, Alper; Mermer, Ömer; Okur, Salih; Selamet, Yusuf

    2016-01-01

    Au/n-Si/Graphene/Au Schottky diodes were fabricated by transferring atmospheric pressure chemical vapor deposited (APCVD) graphene on silicon substrates. Graphene/n-Si interface properties were improved by using 5-[(3-methylphenyl)(phenyl) amino]isophthalic acid (MePIFA) and 5-(diphenyl)amino]isophthalic acid (DPIFA) aromatic self-assembled monolayer (SAM) molecules. The surface morphologies of modified and non-modified films were investigated by atomic force microscopy and scanning electron ...

  4. GoSam-2.0. A tool for automated one-loop calculations within the Standard Model and beyond

    International Nuclear Information System (INIS)

    Cullen, Gavin; Deurzen, Hans van; Greiner, Nicolas

    2014-05-01

    We present the version 2.0 of the program package GoSam for the automated calculation of one-loop amplitudes. GoSam is devised to compute one-loop QCD and/or electroweak corrections to multi-particle processes within and beyond the Standard Model. The new code contains improvements in the generation and in the reduction of the amplitudes, performs better in computing time and numerical accuracy, and has an extended range of applicability. The extended version of the ''Binoth-Les-Houches-Accord'' interface to Monte Carlo programs is also implemented. We give a detailed description of installation and usage of the code, and illustrate the new features in dedicated examples.

  5. Observation of molecular level behavior in molecular electronic junction device

    Science.gov (United States)

    Maitani, Masato

    In this dissertation, I utilize AFM based scanning probe measurement and surface enhanced Raman scattering based vibrational spectroscopic analysis to directly characterize topographic, electronic, and chemical properties of molecules confined in the local area of M3 junction to elucidate the molecular level behavior of molecular junction electronic devices. In the introduction, the characterization of molecular electronic devices with different types of metal-molecule-metal (M3) structures based upon self-assembled monolayers (SAMs) is reviewed. A background of the characterization methods I use in this dissertation, conducting probe atomic force microscopy (cp-AFM) and surface enhanced Raman spectroscopy (SERS), is provided in chapter 1. Several attempts are performed to create the ideal top metal contacts on SAMs by metal vapor phase deposition in order to prevent the metal penetration inducing critical defects of the molecular electronic devices. The scanning probe microscopy (SPM), such as cp-AFM, contact mode (c-) AFM and non-contact mode (nc-) AFM, in ultra high vacuum conditions are utilized to study the process of the metal-SAM interface construction in terms of the correlation between the morphological and electrical properties including the metal nucleation and filament generation as a function of the functionalization of long-chain alkane thiolate SAMs on Au. In chapter 2, the nascent condensation process of vapor phase Al deposition on inert and reactive SAMs are studied by SPM. The results of top deposition, penetration, and filament generation of deposited Al are discussed and compared to the results previously observed by spectroscopic measurements. Cp-AFM was shown to provide new insights into Al filament formation which has not been observed by conventional spectroscopic analysis. Additionally, the electronic characteristics of individual Al filaments are measured. Chapter 3 reveals SPM characterization of Au deposition onto --COOH terminated SAMs

  6. Nonlinear Dynamics in Gene Regulation Promote Robustness and Evolvability of Gene Expression Levels.

    Science.gov (United States)

    Steinacher, Arno; Bates, Declan G; Akman, Ozgur E; Soyer, Orkun S

    2016-01-01

    Cellular phenotypes underpinned by regulatory networks need to respond to evolutionary pressures to allow adaptation, but at the same time be robust to perturbations. This creates a conflict in which mutations affecting regulatory networks must both generate variance but also be tolerated at the phenotype level. Here, we perform mathematical analyses and simulations of regulatory networks to better understand the potential trade-off between robustness and evolvability. Examining the phenotypic effects of mutations, we find an inverse correlation between robustness and evolvability that breaks only with nonlinearity in the network dynamics, through the creation of regions presenting sudden changes in phenotype with small changes in genotype. For genotypes embedding low levels of nonlinearity, robustness and evolvability correlate negatively and almost perfectly. By contrast, genotypes embedding nonlinear dynamics allow expression levels to be robust to small perturbations, while generating high diversity (evolvability) under larger perturbations. Thus, nonlinearity breaks the robustness-evolvability trade-off in gene expression levels by allowing disparate responses to different mutations. Using analytical derivations of robustness and system sensitivity, we show that these findings extend to a large class of gene regulatory network architectures and also hold for experimentally observed parameter regimes. Further, the effect of nonlinearity on the robustness-evolvability trade-off is ensured as long as key parameters of the system display specific relations irrespective of their absolute values. We find that within this parameter regime genotypes display low and noisy expression levels. Examining the phenotypic effects of mutations, we find an inverse correlation between robustness and evolvability that breaks only with nonlinearity in the network dynamics. Our results provide a possible solution to the robustness-evolvability trade-off, suggest an explanation for

  7. Nonlinear Dynamics in Gene Regulation Promote Robustness and Evolvability of Gene Expression Levels.

    Directory of Open Access Journals (Sweden)

    Arno Steinacher

    Full Text Available Cellular phenotypes underpinned by regulatory networks need to respond to evolutionary pressures to allow adaptation, but at the same time be robust to perturbations. This creates a conflict in which mutations affecting regulatory networks must both generate variance but also be tolerated at the phenotype level. Here, we perform mathematical analyses and simulations of regulatory networks to better understand the potential trade-off between robustness and evolvability. Examining the phenotypic effects of mutations, we find an inverse correlation between robustness and evolvability that breaks only with nonlinearity in the network dynamics, through the creation of regions presenting sudden changes in phenotype with small changes in genotype. For genotypes embedding low levels of nonlinearity, robustness and evolvability correlate negatively and almost perfectly. By contrast, genotypes embedding nonlinear dynamics allow expression levels to be robust to small perturbations, while generating high diversity (evolvability under larger perturbations. Thus, nonlinearity breaks the robustness-evolvability trade-off in gene expression levels by allowing disparate responses to different mutations. Using analytical derivations of robustness and system sensitivity, we show that these findings extend to a large class of gene regulatory network architectures and also hold for experimentally observed parameter regimes. Further, the effect of nonlinearity on the robustness-evolvability trade-off is ensured as long as key parameters of the system display specific relations irrespective of their absolute values. We find that within this parameter regime genotypes display low and noisy expression levels. Examining the phenotypic effects of mutations, we find an inverse correlation between robustness and evolvability that breaks only with nonlinearity in the network dynamics. Our results provide a possible solution to the robustness-evolvability trade-off, suggest

  8. A mammalianized synthetic nitroreductase gene for high-level expression

    International Nuclear Information System (INIS)

    Grohmann, Maik; Paulmann, Nils; Fleischhauer, Sebastian; Vowinckel, Jakob; Priller, Josef; Walther, Diego J

    2009-01-01

    The nitroreductase/5-(azaridin-1-yl)-2,4-dinitrobenzamide (NTR/CB1954) enzyme/prodrug system is considered as a promising candidate for anti-cancer strategies by gene-directed enzyme prodrug therapy (GDEPT) and has recently entered clinical trials. It requires the genetic modification of tumor cells to express the E. coli enzyme nitroreductase that bioactivates the prodrug CB1954 to a powerful cytotoxin. This metabolite causes apoptotic cell death by DNA interstrand crosslinking. Enhancing the enzymatic NTR activity for CB1954 should improve the therapeutical potential of this enzyme-prodrug combination in cancer gene therapy. We performed de novo synthesis of the bacterial nitroreductase gene adapting codon usage to mammalian preferences. The synthetic gene was investigated for its expression efficacy and ability to sensitize mammalian cells to CB1954 using western blotting analysis and cytotoxicity assays. In our study, we detected cytoplasmic protein aggregates by expressing GFP-tagged NTR in COS-7 cells, suggesting an impaired translation by divergent codon usage between prokaryotes and eukaryotes. Therefore, we generated a synthetic variant of the nitroreductase gene, called ntro, adapted for high-level expression in mammalian cells. A total of 144 silent base substitutions were made within the bacterial ntr gene to change its codon usage to mammalian preferences. The codon-optimized ntro either tagged to gfp or c-myc showed higher expression levels in mammalian cell lines. Furthermore, the ntro rendered several cell lines ten times more sensitive to the prodrug CB1954 and also resulted in an improved bystander effect. Our results show that codon optimization overcomes expression limitations of the bacterial ntr gene in mammalian cells, thereby improving the NTR/CB1954 system at translational level for cancer gene therapy in humans

  9. Mars Methane at Gale Crater Shows Strong Seasonal Cycle: Updated Results from TLS-SAM on Curiosity

    Science.gov (United States)

    Webster, C. R.; Mahaffy, P. R.; Atreya, S. K.; Flesch, G.; Malespin, C.; McKay, C.; Martinez, G.; Moores, J.; Smith, C. L.; Martin-Torres, F. J.; Gomez-Elvira, J.; Zorzano, M. P.; Wong, M. H.; Trainer, M. G.; Eigenbrode, J. L.; Glavin, D. P.; Steele, A.; Archer, D., Jr.; Sutter, B.; Coll, P. J.; Freissinet, C.; Meslin, P. Y.; Pavlov, A.; Keymeulen, D.; Christensen, L. E.; Gough, R. V.; Schwenzer, S. P.; Navarro-Gonzalez, R.; Pla-García, J.; Rafkin, S. C.; Vicente-Retortillo, Á.; Kahanpää, H.; Viudez-Moreiras, D.; Smith, M. D.; Harri, A. M.; Genzer, M.; Hassler, D.; Lemmon, M. T.; Crisp, J. A.; Zurek, R. W.; Vasavada, A. R.

    2017-12-01

    In situ measurements of atmospheric methane have been made over a 5-year period at Gale Crater on Mars using the Tunable Laser Spectrometer (TLS) instrument in the Sample Analysis at Mars (SAM) suite on the Curiosity rover. We report two important observations: (i) a background level of mean value of 0.41 ±0.11 (2sem) that is about 5 times lower than some model predictions based on generation from UV degradation of micro-meteorites or interplanetary dust delivered to the martian surface; (ii) "spikes" of elevated levels of 7 ppbv attributed to episodic releases from small local sources, probably to the north of Gale crater1. Reports of plumes, patches or episodic releases of methane in the Martian atmosphere have to date eluded explanation in part because of their lack of repeatability in time or location. Our in situ measurements of the background methane levels exhibit a strong, repeatable seasonal variability. The amplitude of the observed seasonal cycle is 3 times greater than both that expected from the annual sublimation and freezing of polar carbon dioxide and that expected from methane production from ultraviolet (UV) degradation of exogenously-delivered surface material. The observed large seasonal variation in the background, and sporadic observations of higher pulses of 7 ppbv appear consistent with localized small sources of methane release from Martian surface reservoirs that may be occurring throughout the planet. We will present our updated data set, correlations of Mars methane with various other measurements from SAM, REMS, RAD and ChemCam instruments on Curiosity, as well as empirical models of UV surface insolation, and provide preliminary interpretation of results. 1 "Mars Methane Detection and Variability at Gale Crater", C. R. Webster et al., Science, 347, 415-417 (2015) and references therein. The research described here was carried out in part at the Jet Propulsion Laboratory, California Institute of Technology, under a contract with the

  10. NORMAL NASAL GENE EXPRESSION LEVELS USING CDNA ARRAY TECHNOLOGY

    Science.gov (United States)

    Normal Nasal Gene Expression Levels Using cDNA Array Technology. The nasal epithelium is a target site for chemically-induced toxicity and carcinogenicity. To detect and analyze genetic events which contribute to nasal tumor development, we first defined the gene expressi...

  11. Influence of Oxychlorine Phases During the Pyrolysis of Organic Molecules: Implications for the Quest of Organics on Mars with the SAM Experiment Onboard the Curiosity Rover

    Science.gov (United States)

    Millan, M.; Szopa, C.; Buch, A.; Belmahdi, I.; Glavin, D. P.; Freissinet, C.; Eigenbrode, J. L.; Archer, P. D., Jr,; Sutter, B.; Mahaffy, P.

    2017-01-01

    One among the main objectives of the Sample Analysis at Mars (SAM) experiment is the in situ molecular analysis of gases evolving from solid samples heated up to approximately 850 degrees Centigrade, and collected by Curiosity on Mars surface/sub-surface in Gale crater. With this aim, SAM uses a gas-chromatograph coupled to a quadrupole mass spectrometer (GC-QMS) devoted to separate, detect and identify both volatile inorganic and organic compounds. SAM detected chlorinated organic molecules produced in evolved gas analysis (EGA) experiments. Several of these were also detected by the Viking experiments in 1976. SAM also detected oxychlorine compounds that were present at the Phoenix landing site. The oxychlorines may be prevelant over much of the martian surface. The C1 to C3 aliphatic chlorohydrocarbons (chloromethane and di- and trichloromethane) detected by SAM were attributed to reaction products occurring between the oxychlorines phases and the organic compounds coming from SAM instrument background. But SAM also showed the presence of a large excess of chlorobenzene and C2 to C4 dichloroalkanes among the volatile species released by the Cumberland sample of the Sheepbed mudstone. For the first time in the history of the Mars exploration, this proved the presence of Mars indigenous organic material at the Mars' surface. However, the identification of the precursor organic compounds of these chlorohydrocarbons is difficult due to the complexity of the reactions occurring during the sample pyrolysis. Laboratory pyrolysis experiments have demonstrated that oxychlorines phases such as perchlorates and chlorates, decomposed into dioxygen and volatile chlorine bearing molecules (HCl and/or Cl2) during the pyrolysis. These chemical species can then react with the organic molecules present in the martian solid samples through oxidation, chlorination and oxychlorination processes.

  12. miCLIP-MaPseq, a Substrate Identification Approach for Radical SAM RNA Methylating Enzymes.

    Science.gov (United States)

    Stojković, Vanja; Chu, Tongyue; Therizols, Gabriel; Weinberg, David E; Fujimori, Danica Galonić

    2018-06-13

    Although present across bacteria, the large family of radical SAM RNA methylating enzymes is largely uncharacterized. Escherichia coli RlmN, the founding member of the family, methylates an adenosine in 23S rRNA and several tRNAs to yield 2-methyladenosine (m 2 A). However, varied RNA substrate specificity among RlmN enzymes, combined with the ability of certain family members to generate 8-methyladenosine (m 8 A), makes functional predictions across this family challenging. Here, we present a method for unbiased substrate identification that exploits highly efficient, mechanism-based cross-linking between the enzyme and its RNA substrates. Additionally, by determining that the thermostable group II intron reverse transcriptase introduces mismatches at the site of the cross-link, we have identified the precise positions of RNA modification using mismatch profiling. These results illustrate the capability of our method to define enzyme-substrate pairs and determine modification sites of the largely uncharacterized radical SAM RNA methylating enzyme family.

  13. In situ analysis of Mars soil sample with the sam gcms instrumentation onboard Curiosity : interpretation and comparison of measurements done at Rocknest and Yelloknife bay sites

    Science.gov (United States)

    Szopa, Cyril; Coll, Patrice; Cabane, Michel; Coscia, David; Buch, Arnaud; Francois, Pascaline; Millan, Maeva; Teinturier, Sammy; Navarro-Gonzales, Rafael; Glavin, Daniel; Freissinet, Caro; Steele, Andrew; Eigenbrode, Jen; Mahaffy, Paul

    2014-05-01

    The characterisation of the chemical and mineralogical composition of regolith samples collected with the Curiosity rover is a primary objective of the SAM experiment. These data should provide essential clues on the past habitability of Gale crater. Amongst the SAM suite of instruments [1], SAM-GC (Gas Chromatograph) is devoted to identify and quantify volatiles evolved from the thermal (heating up to about 900°C)/chemical (derivatization procedure) treatment of any soil sample collected by the Curiosity rover. With the aim to search for potential organic molecules outgassed from the samples, a SAM-GC analytical channel composed of thermal-desorption injector and a MXT-CLP chromatographic column was chosen to achieve all the measurements done up today, as it was designed for the separation of a wide range of volatile organic molecules. Three solid samples have been analyzed with GCMS, one sand sample collected at the Rocknest site, and two rock samples (John Klein and Cumberland respectively) collected at the Yellowknife Bay site using the Curiosity driller. All the measurements were successful and they produced complex chromatograms with both detectors used for SAM GC, i.e. a thermal conductivity detector and the SAM quandrupole mass spectrometer. Their interpretation already revealed the presence of an oxychlorine phase present in the sample which is at the origin of chlorohydrocarbons clearly identified [2] but this represents only a fraction of the GCMS signal recorded [3,4]. This work presents a systematic comparison of the GCMS measurements done for the different samples collected, supported by reference data obtained in laboratory with different spare models of the gas chromatograph, with the aim to bring new elements of interpretation of the SAM measurements. References: [1] Mahaffy, P. et al. (2012) Space Sci Rev, 170, 401-478. [2] Glavin, D. et al. (2013), JGR. [3] Leshin L. et al. (2013), Science, [4] Ming D. et al. (2013), Science, 32, 64

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

    Science.gov (United States)

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

    2018-01-01

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

  15. Purification of 1-aminocyclopropane-1-carboxylate synthase from apple fruits using s-adenosyl [3,414C]-methionine (SAM) as a probe

    International Nuclear Information System (INIS)

    Yip, Wingkip; Dong, Jianguo; Yang, Shang Fa

    1989-01-01

    Tomato ACC synthase is inactivated by its substrate SAM, with the moiety of aminobutyrate being covalently linked to ACC synthase during the catalytic reactions. A partial purified ACC synthase (the catalytic activity 100 μmol/h·mg protein) from pellets of apple extract was incubated with [3,4 14 C] SAM. Only one radioactive peak was revealed in a C-4 reverse phase HPLC and one radioactive band on SDS-PAGE with an M.W. of 48 kDa. Apple ACC synthase in native form is resistant to V8, α-chromtrypsin and carboxylpeptidase A digestion, but effectively inactivated by trypsin and ficin, as demonstrated by both the activity assay and SAM labeling. The radioactive protein cut from the SDS-PAGE was injected to three mice, two of the mice showed responses to the protein in western blot analysis. The antibodies from mice is currently under characterization

  16. Substrates adoption methodology (SAM) to achieve “Fast, Flexible, Future (F3)” pharmaceutical production processes

    DEFF Research Database (Denmark)

    Singh, Ravendra; Rozada-Sanchez, Raquel; Wrate, Tim

    within the template. In this way the substrates adoption methodology helps to achieve “fast, flexible, future (F3)” pharmaceutical production processes by adapting a recently designed generic modular process-plant. The supporting tools for the substrate adoption are: (1) an ontological knowledge......There is a significant cost associated with process development of a portfolio of pharmaceutical products, few of which will reach the market. Continuous processing will increase the “chemical space” which can increase development efficiency. For example one, particularly attractive option...... is to develop manufacturing processes based on modular continuous systems; a flexible generic continuous modular plant which can be adapted for different substrates. In the work reported here, a substrates adoption methodology (SAM) has been developed. The proposed SAM identifies the necessary changes...

  17. Electrochemical characterization of a 1,8-octanedithiol self-assembled monolayer (ODT-SAM) on a Au(1 1 1) single crystal electrode

    Energy Technology Data Exchange (ETDEWEB)

    Garcia-Raya, Daniel; Madueno, Rafael; Sevilla, Jose Manuel; Blazquez, Manuel [Departamento de Quimica Fisica y Termodinamica Aplicada, Universidad de Cordoba, Campus de Rabanales, Ed. Marie Curie, E-14071 Cordoba (Spain); Pineda, Teresa [Departamento de Quimica Fisica y Termodinamica Aplicada, Universidad de Cordoba, Campus de Rabanales, Ed. Marie Curie, E-14071 Cordoba (Spain)], E-mail: tpineda@uco.es

    2008-11-15

    Recently, it has becoming increasingly important to control the organization of self-assembled monolayers (SAMs) of {omega}-functionalized thiols for its potential applications in the construction of more complex molecular architectures. In this paper, we report on the spontaneous formation of a SAM of octanedithiol (ODT) as a function of the modification time. Electrochemical techniques such as cyclic voltammetry, double layer capacitance and electrochemical impedance spectroscopy are used for the characterization of this monolayer. The increase in modification time brings about changes in the octanedithiol self-assembled monolayer (ODT-SAM) reductive desorption voltammograms that indicate an evolution toward a more ordered and compact monolayer. This trend has also been found by following the changes in the electron transfer processes of the redox probe K{sub 3}Fe(CN){sub 6}. In fact, the ODT-SAM formed at low-modification time does not significantly perturb the electrochemical response as it is typical of either a low coverage or of the presence of large defects in the layer. Upon increasing the modification time, the voltammograms of the redox probe adopt a sigmoidal shape indicating the existence of pinholes in the monolayer distributed as an array of microelectrodes. The surface coverage as well as the size and distribution of these pinholes have been determined by the impedance technique that gives a more reliable evaluation of these monolayer structural parameters.

  18. Regulation of homocysteine metabolism and methylation in human and mouse tissues

    Science.gov (United States)

    Chen, Natalie C.; Yang, Fan; Capecci, Louis M.; Gu, Ziyu; Schafer, Andrew I.; Durante, William; Yang, Xiao-Feng; Wang, Hong

    2010-01-01

    Hyperhomocysteinemia is an independent risk factor for cardiovascular disease. Homocysteine (Hcy) metabolism involves multiple enzymes; however, tissue Hcy metabolism and its relevance to methylation remain unknown. Here, we established gene expression profiles of 8 Hcy metabolic and 12 methylation enzymes in 20 human and 19 mouse tissues through bioinformatic analysis using expression sequence tag clone counts in tissue cDNA libraries. We analyzed correlations between gene expression, Hcy, S-adenosylhomocysteine (SAH), and S-adenosylmethionine (SAM) levels, and SAM/SAH ratios in mouse tissues. Hcy metabolic and methylation enzymes were classified into two types. The expression of Type 1 enzymes positively correlated with tissue Hcy and SAH levels. These include cystathionine β-synthase, cystathionine-γ-lyase, paraxonase 1, 5,10-methylenetetrahydrofolate reductase, betaine:homocysteine methyltransferase, methionine adenosyltransferase, phosphatidylethanolamine N-methyltransferases and glycine N-methyltransferase. Type 2 enzyme expressions correlate with neither tissue Hcy nor SAH levels. These include SAH hydrolase, methionyl-tRNA synthase, 5-methyltetrahydrofolate:Hcy methyltransferase, S-adenosylmethionine decarboxylase, DNA methyltransferase 1/3a, isoprenylcysteine carboxyl methyltransferases, and histone-lysine N-methyltransferase. SAH is the only Hcy metabolite significantly correlated with Hcy levels and methylation enzyme expression. We established equations expressing combined effects of methylation enzymes on tissue SAH, SAM, and SAM/SAH ratios. Our study is the first to provide panoramic tissue gene expression profiles and mathematical models of tissue methylation regulation.—Chen, N. C., Yang, F., Capecci, L. M., Gu, Z., Schafer, A. I., Durante, W., Yang, X.-F., Wang, H. Regulation of homocysteine metabolism and methylation in human and mouse tissues. PMID:20305127

  19. SAM II aerosol profile measurements, Poker Flat, Alaska; July 16-19, 1979

    Science.gov (United States)

    Mccormick, M. P.; Chu, W. P.; Mcmaster, L. R.; Grams, G. W.; Herman, B. M.; Pepin, T. J.; Russell, P. B.; Swissler, T. J.

    1981-01-01

    SAM II satellite measurements during the July 1979 Poker Flat mission, yielded an aerosol extinction coefficient of 0.0004/km at 1.0 micron wavelength, in the region of the stratospheric aerosol mixing ratio peak (12-16 km). The stratospheric aerosol optical depth for these data, calculated from the tropopause through 30 km, is approximately 0.001. These results are consistent with the average 1979 summertime values found throughout the Arctic.

  20. Why Nature Uses Radical SAM Enzymes so Widely: Electron Nuclear Double Resonance Studies of Lysine 2,3-Aminomutase Show the 5'-dAdo• "Free Radical" Is Never Free.

    Science.gov (United States)

    Horitani, Masaki; Byer, Amanda S; Shisler, Krista A; Chandra, Tilak; Broderick, Joan B; Hoffman, Brian M

    2015-06-10

    Lysine 2,3-aminomutase (LAM) is a radical S-adenosyl-L-methionine (SAM) enzyme and, like other members of this superfamily, LAM utilizes radical-generating machinery comprising SAM anchored to the unique Fe of a [4Fe-4S] cluster via a classical five-membered N,O chelate ring. Catalysis is initiated by reductive cleavage of the SAM S-C5' bond, which creates the highly reactive 5'-deoxyadenosyl radical (5'-dAdo•), the same radical generated by homolytic Co-C bond cleavage in B12 radical enzymes. The SAM surrogate S-3',4'-anhydroadenosyl-L-methionine (anSAM) can replace SAM as a cofactor in the isomerization of L-α-lysine to L-β-lysine by LAM, via the stable allylic anhydroadenosyl radical (anAdo•). Here electron nuclear double resonance (ENDOR) spectroscopy of the anAdo• radical in the presence of (13)C, (2)H, and (15)N-labeled lysine completes the picture of how the active site of LAM from Clostridium subterminale SB4 "tames" the 5'-dAdo• radical, preventing it from carrying out harmful side reactions: this "free radical" in LAM is never free. The low steric demands of the radical-generating [4Fe-4S]/SAM construct allow the substrate target to bind adjacent to the S-C5' bond, thereby enabling the 5'-dAdo• radical created by cleavage of this bond to react with its partners by undergoing small motions, ∼0.6 Å toward the target and ∼1.5 Å overall, that are controlled by tight van der Waals contact with its partners. We suggest that the accessibility to substrate and ready control of the reactive C5' radical, with "van der Waals control" of small motions throughout the catalytic cycle, is common within the radical SAM enzyme superfamily and is a major reason why these enzymes are the preferred means of initiating radical reactions in nature.

  1. SAM Technical Review Committee Final Report: Summary and Key Recommendations from the Onsite TRC Meeting Held April 22-23, 2013

    Energy Technology Data Exchange (ETDEWEB)

    Blair, N.; Dobos, S.; Janzou, S.; Gilman, P.; Freeman, J.; Kaffine, L.

    2013-08-01

    The System Advisor Model (SAM) is a broad and robust set of models and frameworks for analyzing both system performance and system financing. It does this across a range of technologies dominated by solar technologies including photovoltaics (PV) and concentrated solar power (CSP). The U.S. Department of Energy (DOE) Solar Energy Technology Program requested the SAM development team to review the photovoltaic performance modeling with the development community and specifically, with the independent engineering community. The report summarizes the major effort for this technical review committee (TRC).

  2. The Investigation of Perchlorate/Iron Phase Mixtures as A Possible Source of Oxygen Detected by the Sample Analysis at Mars (SAM) Instrument in Gale Crater, Mars

    Science.gov (United States)

    Sutter, B.; Heil, E.; Morris, R. V.; Archer, P. D.; Ming, D. W.; Niles, P. B.; Eigenbrode, J. L.; Franz, H.; Freissinet C.; Glavin, D. P.; hide

    2015-01-01

    The Sample Analysis at Mars (SAM) instrument onboard the Curiosity rover detected O2 and HCl gas releases from the Rocknest (RN) eolian bedform and the John Klein (JK) and Cumberland (CB) drill hole materials in Gale Crater. Chlorinated hydrocarbons have also been detected by the SAM quadrupole mass spectrometer (QMS) and gas chromatography/mass spectrometer (GCMS). These detections along with the detection of perchlorate (ClO4-) by the Mars Phoenix Lander's Wet Chemistry Laboratory (WCL) suggesting perchlorate is a possible candidate for evolved O2 and chlorine species. Laboratory thermal analysis of individual per-chlorates has yet to provide an unequivocal temperature match to the SAM O2 and HCl release data. These detections along with the detection of perchlorate (ClO4-) by the Mars Phoenix Lander's Wet Chemistry Laboratory suggested perchlorate is a possible candidate for evolved O2 and chlorine species. Laboratory thermal analysis of pure perchlorates has yet to provide an unequivocal temperature match to the SAM O2 and HCl release data. Analog laboratory analysis of iron mineralogy detected in Gale materials that was physically mixed with Ca- and Mg-perchlorate has been shown to catalyze lower O2 release temperatures and approach some SAM O2 release data. Instead of physical mixtures used in previous work, the work presented here utilized perchlorate solutions added to Fe phases. This technique allowed for perchlorate to come in closer contact with the Fe-phase and may more closely mimic Mars conditions where humidity can increase enough to cause deliquescence of the highly hygroscopic perchlorate phases. The objective of this work is to: 1) Utilize a laboratory SAM analog instrument to evaluate the O2 release temperatures from Mg- and Ca-perchlorates solutions applied to Fephases detetected in Gale Crate; and 2) Determine if perchlorate solutions can provide improved matches with the SAM O2 temperature release profiles.

  3. Influencia del Estado de Oxidación del Ión Cobalto en la Estabilidad de Electrodos Modificados con Monocapas SAM-TOA-ANTA-Con+-HRP-NHis.

    Directory of Open Access Journals (Sweden)

    Pedro R. Matheus*

    Full Text Available Influence of state oxidation of cobalt ion in the stability electrodes modified with monolayers SAM-TOA-ANTA-Con+-HRP-NHis. Quartz Crystal Microbalance (QCM was used to investigate the adsorption of the HRP-NHis enzyme (horseradish peroxidase, which was modified by the addition of a tail of six histidine on its extreme N-terminal. The QCM operating at flow of 0.025 mL min-1 on a crystal whose gold electrode was modified with monolayers of SAM-TOA-ANTA-Co2+ and SAM-TOA-ANTA -Co3+. The oxidize form was obtained from the electrochemical oxidation of a monolayer of SAM-TOA-ANTA-Co2+. The results suggest that the HRP-NHis is attached to both monolayers in a similar way; on the contrary, the desortion of the attached protein is dramatically different. Thus, whereas the ligand-Co2+ bonds are reversible, which allows that the anchored protein is easily replaced by imidazol molecules. The 3+ oxidation state of the metal does not allow the interchange of protein by the imidazol molecules.

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

    Directory of Open Access Journals (Sweden)

    Tu Kang

    2007-06-01

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

  5. Post-translational modification of ribosomally synthesized peptides by a radical SAM epimerase in Bacillus subtilis

    Science.gov (United States)

    Benjdia, Alhosna; Guillot, Alain; Ruffié, Pauline; Leprince, Jérôme; Berteau, Olivier

    2017-07-01

    Ribosomally synthesized peptides are built out of L-amino acids, whereas D-amino acids are generally the hallmark of non-ribosomal synthetic processes. Here we show that the model bacterium Bacillus subtilis is able to produce a novel type of ribosomally synthesized and post-translationally modified peptide that contains D-amino acids, and which we propose to call epipeptides. We demonstrate that a two [4Fe-4S]-cluster radical S-adenosyl-L-methionine (SAM) enzyme converts L-amino acids into their D-counterparts by catalysing Cα-hydrogen-atom abstraction and using a critical cysteine residue as the hydrogen-atom donor. Unexpectedly, these D-amino acid residues proved to be essential for the activity of a peptide that induces the expression of LiaRS, a major component of the bacterial cell envelope stress-response system. Present in B. subtilis and in several members of the human microbiome, these epipeptides and radical SAM epimerases broaden the landscape of peptidyl structures accessible to living organisms.

  6. Increasing the Fill Factor of Inverted P3HT:PCBM Solar Cells Through Surface Modification of Al-Doped ZnO via Phosphonic Acid-Anchored C60 SAMs

    DEFF Research Database (Denmark)

    Stubhan, Tobias; Salinas, Michael; Ebel, Alexander

    2012-01-01

    The influence of aluminum-doped zinc oxide (AZO) electron extraction layers modified with self-assembled monolayers (SAMs) on inverted polymer solar cells is investigated. It is found that AZO modification with phosphonic acid-anchored Fullerene–SAMs leads to a reduction of the series resistance,...

  7. Large scale study on the variation of RF energy absorption in the head & brain regions of adults and children and evaluation of the SAM phantom conservativeness

    Science.gov (United States)

    Keshvari, J.; Kivento, M.; Christ, A.; Bit-Babik, G.

    2016-04-01

    This paper presents the results of two computational large scale studies using highly realistic exposure scenarios, MRI based human head and hand models, and two mobile phone models. The objectives are (i) to study the relevance of age when people are exposed to RF by comparing adult and child heads and (ii) to analyze and discuss the conservativeness of the SAM phantom for all age groups. Representative use conditions were simulated using detailed CAD models of two mobile phones operating between 900 MHz and 1950 MHz including configurations with the hand holding the phone, which were not considered in most previous studies. The peak spatial-average specific absorption rate (psSAR) in the head and the pinna tissues is assessed using anatomically accurate head and hand models. The first of the two mentioned studies involved nine head-, four hand- and two phone-models, the second study included six head-, four hand- and three simplified phone-models (over 400 configurations in total). In addition, both studies also evaluated the exposure using the SAM phantom. Results show no systematic differences between psSAR induced in the adult and child heads. The exposure level and its variation for different age groups may be different for particular phones, but no correlation between psSAR and model age was found. The psSAR from all exposure conditions was compared to the corresponding configurations using SAM, which was found to be conservative in the large majority of cases.

  8. SAM: Support Vector Machine Based Active Queue Management

    International Nuclear Information System (INIS)

    Shah, M.S.

    2014-01-01

    Recent years have seen an increasing interest in the design of AQM (Active Queue Management) controllers. The purpose of these controllers is to manage the network congestion under varying loads, link delays and bandwidth. In this paper, a new AQM controller is proposed which is trained by using the SVM (Support Vector Machine) with the RBF (Radial Basis Function) kernal. The proposed controller is called the support vector based AQM (SAM) controller. The performance of the proposed controller has been compared with three conventional AQM controllers, namely the Random Early Detection, Blue and Proportional Plus Integral Controller. The preliminary simulation studies show that the performance of the proposed controller is comparable to the conventional controllers. However, the proposed controller is more efficient in controlling the queue size than the conventional controllers. (author)

  9. Correlation of gene expression and contaminat concentrations in wild largescale suckers: a field-based study

    Science.gov (United States)

    Christiansen, Helena E.; Mehinto, Alvine C.; Yu, Fahong; Perry, Russell W.; Denslow, Nancy D.; Maule, Alec G.; Mesa, Matthew G.

    2014-01-01

    Toxic compounds such as organochlorine pesticides (OCs), polychlorinated biphenyls (PCBs), and polybrominated diphenyl ether flame retardants (PBDEs) have been detected in fish, birds, and aquatic mammals that live in the Columbia River or use food resources from within the river. We developed a custom microarray for largescale suckers (Catostomus macrocheilus) and used it to investigate the molecular effects of contaminant exposure on wild fish in the Columbia River. Using Significance Analysis of Microarrays (SAM) we identified 72 probes representing 69 unique genes with expression patterns that correlated with hepatic tissue levels of OCs, PCBs, or PBDEs. These genes were involved in many biological processes previously shown to respond to contaminant exposure, including drug and lipid metabolism, apoptosis, cellular transport, oxidative stress, and cellular chaperone function. The relation between gene expression and contaminant concentration suggests that these genes may respond to environmental contaminant exposure and are promising candidates for further field and laboratory studies to develop biomarkers for monitoring exposure of wild fish to contaminant mixtures found in the Columbia River Basin. The array developed in this study could also be a useful tool for studies involving endangered sucker species and other sucker species used in contaminant research.

  10. Possible Detection of Perchlorates by the Sample Analysis at Mars (SAM) Instrument: Comparison with Previous Missions

    Science.gov (United States)

    Navarro-Gonzalex, Rafael; Sutter, Brad; Archer, Doug; Ming, Doug; Eigenbrode, Jennifer; Franz, Heather; Glavin, Daniel; McAdam, Amy; Stern, Jennifer; McKay, Christopher; hide

    2013-01-01

    The first chemical analysis of soluble salts in the soil was carried out by the Phoenix Lander in the Martian Arctic [1]. Surprisingly, chlorine was present as magnesium or calcium perchlorate at 0.4 to 0.6 percent. Additional support for the identification of perchlorate came from the evolved gas analysis which detected the release of molecular oxygen at 350-550C [1]. When Mars-like soils from the Atacama Desert were spiked with magnesium perchlorate (1 percent) and heated using the Viking GC-MS protocol, nearly all the organics were combusted but a small amount was chlorinated, forming chloromethane and dichloromethane [2]. These chlorohydrocarbons were detected by the Viking GC-MS experiments when the Martian soil was analyzed but they were considered to be terrestrial contaminants [3]. Reinterpretation of the Viking results suggests Analysis at Mars (SAM) instrument on board the Mars Science Laboratory (MSL) ran four samples from an aeolian bedform named Rocknest. The samples analyzed were portioned from the fifth scoop at this location. The samples were heated to 835C at 35C/min with a He flow. The SAM QMS detected a major oxygen release (300-500C) [5], coupled with the release of chlorinated hydrocarbons (chloromethane, dichloromethane, trichloromethane, and chloromethylpropene) detected both by SAM QMS and GC-MS derived from known Earth organic contaminants in the instrument [6]. Calcium perchlorate appears to be the best candidate for evolved O2 in the Rocknest samples at this time but other Cl species (e.g., chlorates) are possible and must be evaluated. The potential detection of perchlorates in Rocknest material adds weight to the argument that both Viking Landers measured signatures of perchlorates. Even if the source of the organic carbon detected is still unknown, the chlorine source was likely Martian. Two mechanisms have been hypothesized for the formation of soil perchlorate: (1) Atmospheric oxidation of chlorine; and (2) UV photooxidation of

  11. Autism and increased paternal age related changes in global levels of gene expression regulation.

    Directory of Open Access Journals (Sweden)

    Mark D Alter

    2011-02-01

    Full Text Available A causal role of mutations in multiple general transcription factors in neurodevelopmental disorders including autism suggested that alterations in global levels of gene expression regulation might also relate to disease risk in sporadic cases of autism. This premise can be tested by evaluating for changes in the overall distribution of gene expression levels. For instance, in mice, variability in hippocampal-dependent behaviors was associated with variability in the pattern of the overall distribution of gene expression levels, as assessed by variance in the distribution of gene expression levels in the hippocampus. We hypothesized that a similar change in variance might be found in children with autism. Gene expression microarrays covering greater than 47,000 unique RNA transcripts were done on RNA from peripheral blood lymphocytes (PBL of children with autism (n = 82 and controls (n = 64. Variance in the distribution of gene expression levels from each microarray was compared between groups of children. Also tested was whether a risk factor for autism, increased paternal age, was associated with variance. A decrease in the variance in the distribution of gene expression levels in PBL was associated with the diagnosis of autism and a risk factor for autism, increased paternal age. Traditional approaches to microarray analysis of gene expression suggested a possible mechanism for decreased variance in gene expression. Gene expression pathways involved in transcriptional regulation were down-regulated in the blood of children with autism and children of older fathers. Thus, results from global and gene specific approaches to studying microarray data were complimentary and supported the hypothesis that alterations at the global level of gene expression regulation are related to autism and increased paternal age. Global regulation of transcription, thus, represents a possible point of convergence for multiple etiologies of autism and other

  12. Why Nature Uses Radical SAM Enzymes so Widely: Electron Nuclear Double Resonance Studies of Lysine 2,3-Aminomutase Show the 5′-dAdo• “Free Radical” Is Never Free

    Science.gov (United States)

    Horitani, Masaki; Byer, Amanda S.; Shisler, Krista A.; Chandra, Tilak; Broderick, Joan B.; Hoffman, Brian M.

    2015-01-01

    Lysine 2,3-aminomutase (LAM) is a radical S-adenosyl-L-methionine (SAM) enzyme and, like other members of this superfamily, LAM utilizes radical-generating machinery comprising SAM anchored to the unique Fe of a [4Fe-4S] cluster via a classical five-membered N,O chelate ring. Catalysis is initiated by reductive cleavage of the SAM S–C5′ bond, which creates the highly reactive 5′-deoxyadenosyl radical (5′-dAdo•), the same radical generated by homolytic Co–C bond cleavage in B12 radical enzymes. The SAM surrogate S-3′,4′-anhydroadenosyl-L-methionine (anSAM) can replace SAM as a cofactor in the isomerization of L-α-lysine to L-β-lysine by LAM, via the stable allylic anhydroadenosyl radical (anAdo•). Here electron nuclear double resonance (ENDOR) spectroscopy of the anAdo• radical in the presence of 13C, 2H, and 15N-labeled lysine completes the picture of how the active site of LAM from Clostridium subterminale SB4 “tames” the 5′-dAdo• radical, preventing it from carrying out harmful side reactions: this “free radical” in LAM is never free. The low steric demands of the radical-generating [4Fe-4S]/SAM construct allow the substrate target to bind adjacent to the S–C5′ bond, thereby enabling the 5′-dAdo• radical created by cleavage of this bond to react with its partners by undergoing small motions, ~0.6 Å toward the target and ~1.5 Å overall, that are controlled by tight van der Waals contact with its partners. We suggest that the accessibility to substrate and ready control of the reactive C5′ radical, with “van der Waals control” of small motions throughout the catalytic cycle, is common within the radical SAM enzyme superfamily and is a major reason why these enzymes are the preferred means of initiating radical reactions in nature. PMID:25923449

  13. Copy Number Deletion Has Little Impact on Gene Expression Levels in Racehorses

    Directory of Open Access Journals (Sweden)

    Kyung-Do Park

    2014-09-01

    Full Text Available Copy number variations (CNVs, important genetic factors for study of human diseases, may have as large of an effect on phenotype as do single nucleotide polymorphisms. Indeed, it is widely accepted that CNVs are associated with differential disease susceptibility. However, the relationships between CNVs and gene expression have not been characterized in the horse. In this study, we investigated the effects of copy number deletion in the blood and muscle transcriptomes of Thoroughbred racing horses. We identified a total of 1,246 CNVs of deletion polymorphisms using DNA re-sequencing data from 18 Thoroughbred racing horses. To discover the tendencies between CNV status and gene expression levels, we extracted CNVs of four Thoroughbred racing horses of which RNA sequencing was available. We found that 252 pairs of CNVs and genes were associated in the four horse samples. We did not observe a clear and consistent relationship between the deletion status of CNVs and gene expression levels before and after exercise in blood and muscle. However, we found some pairs of CNVs and associated genes that indicated relationships with gene expression levels: a positive relationship with genes responsible for membrane structure or cytoskeleton and a negative relationship with genes involved in disease. This study will lead to conceptual advances in understanding the relationship between CNVs and global gene expression in the horse.

  14. Large scale study on the variation of RF energy absorption in the head and brain regions of adults and children and evaluation of the SAM phantom conservativeness

    International Nuclear Information System (INIS)

    Keshvari, J; Kivento, M; Christ, A; Bit-Babik, G

    2016-01-01

    This paper presents the results of two computational large scale studies using highly realistic exposure scenarios, MRI based human head and hand models, and two mobile phone models. The objectives are (i) to study the relevance of age when people are exposed to RF by comparing adult and child heads and (ii) to analyze and discuss the conservativeness of the SAM phantom for all age groups. Representative use conditions were simulated using detailed CAD models of two mobile phones operating between 900 MHz and 1950 MHz including configurations with the hand holding the phone, which were not considered in most previous studies. The peak spatial-average specific absorption rate (psSAR) in the head and the pinna tissues is assessed using anatomically accurate head and hand models. The first of the two mentioned studies involved nine head-, four hand- and two phone-models, the second study included six head-, four hand- and three simplified phone-models (over 400 configurations in total). In addition, both studies also evaluated the exposure using the SAM phantom. Results show no systematic differences between psSAR induced in the adult and child heads. The exposure level and its variation for different age groups may be different for particular phones, but no correlation between psSAR and model age was found. The psSAR from all exposure conditions was compared to the corresponding configurations using SAM, which was found to be conservative in the large majority of cases. (paper)

  15. Methylenetetrahydrofolate reductase deficiency alters levels of glutamate and γ-aminobutyric acid in brain tissue

    Directory of Open Access Journals (Sweden)

    N.M. Jadavji

    2015-06-01

    Full Text Available Methylenetetrahydrofolate reductase (MTHFR is an enzyme key regulator in folate metabolism. Deficiencies in MTHFR result in increased levels of homocysteine, which leads to reduced levels of S-adenosylmethionine (SAM. In the brain, SAM donates methyl groups to catechol-O-methyltransferase (COMT, which is involved in neurotransmitter analysis. Using the MTHFR-deficient mouse model the purpose of this study was to investigate levels of monoamine neurotransmitters and amino acid levels in brain tissue. MTHFR deficiency affected levels of both glutamate and γ-aminobutyric acid in within the cerebellum and hippocampus. Mthfr−/− mice had reduced levels of glutamate in the amygdala and γ-aminobutyric acid in the thalamus. The excitatory mechanisms of homocysteine through activation of the N-methyl-d-aspartate receptor in brain tissue might alter levels of glutamate and γ-aminobutyric acid.

  16. S-adenosylmethionine blocks osteosarcoma cells proliferation and invasion in vitro and tumor metastasis in vivo: therapeutic and diagnostic clinical applications

    International Nuclear Information System (INIS)

    Parashar, Surabhi; Cheishvili, David; Arakelian, Ani; Hussain, Zahid; Tanvir, Imrana; Khan, Haseeb Ahmed; Szyf, Moshe; Rabbani, Shafaat A

    2015-01-01

    Osteosarcoma (OS) is an aggressive and highly metastatic form of primary bone cancer affecting young children and adults. Previous studies have shown that hypomethylation of critical genes is driving metastasis. Here, we examine whether hypermethylation treatment can block OS growth and pulmonary metastasis. Human OS cells LM-7 and MG-63 were treated with the ubiquitous methyl donor S-adenosylmethionine (SAM) or its inactive analog S-adenosylhomocystine (SAH) as control. Treatment with SAM resulted in a dose-dependent inhibition of tumor cell proliferation, invasion, cell migration, and cell cycle characteristics. Inoculation of cells treated with 150 μmol/L SAM for 6 days into tibia or via intravenous route into Fox Chase severe combined immune deficient (SCID) mice resulted in the development of significantly smaller skeletal lesions and a marked reduction in pulmonary metastasis as compared to control groups. Epigenome wide association studies (EWAS) showed differential methylation of several genes involved in OS progression and prominent signaling pathways implicated in bone formation, wound healing, and tumor progression in SAM-treated LM-7 cells. Real-time polymerase chain reaction (qPCR) analysis confirmed that SAM treatment blocked the expression of several prometastatic genes and additional genes identified by EWAS analysis. Immunohistochemical analysis of normal human bone and tissue array from OS patients showed significantly high levels of expression of one of the identified gene platelet-derived growth factor alpha (PDGFA). These studies provide a possible mechanism for the role of DNA demethylation in the development and metastasis of OS to provide a rationale for the use of hypermethylation therapy for OS patients and identify new targets for monitoring OS development and progression

  17. Growth and Functionality of Cells Cultured on Conducting and Semi-Conducting Surfaces Modified with Self-Assembled Monolayers (SAMs

    Directory of Open Access Journals (Sweden)

    Rajendra K. Aithal

    2016-02-01

    Full Text Available Bioengineering of dermal and epidermal cells on surface modified substrates is an active area of research. The cytotoxicity, maintenance of cell phenotype and long-term functionality of human dermal fibroblast (HDF cells on conducting indium tin oxide (ITO and semi-conducting, silicon (Si and gallium arsenide (GaAs, surfaces modified with self-assembled monolayers (SAMs containing amino (–NH2 and methyl (–CH3 end groups have been investigated. Contact angle measurements and infrared spectroscopic studies show that the monolayers are conformal and preserve their functional end groups. Morphological analyses indicate that HDFs grow well on all substrates except GaAs, exhibiting their normal spindle-shaped morphology and exhibit no visible signs of stress or cytoplasmic vacuolation. Cell viability analyses indicate little cell death after one week in culture on all substrates except GaAs, where cells died within 6 h. Cells on all surfaces proliferate except on GaAs and GaAs-ODT. Cell growth is observed to be greater on SAM modified ITO and Si-substrates. Preservation of cellular phenotype assessed through type I collagen immunostaining and positive staining of HDF cells were observed on all modified surfaces except that on GaAs. These results suggest that conducting and semi-conducting SAM-modified surfaces support HDF growth and functionality and represent a promising area of bioengineering research.

  18. Fatty Acid Detection in Mars-Analogous Rock Samples with the TMAH Wet Chemistry Experiment on the Sample Analysis at Mars (SAM) Instrument

    Science.gov (United States)

    Williams, A. J.; Eigenbrode, J. L.; Wilhelm, M. B.; Johnson, S. S.; Craft, K.; O'Reilly, S.; Lewis, J. M. T.; Williams, R.; Summons, R. E.; Benison, K. C.; Mahaffy, P. R.

    2017-12-01

    The Curiosity rover is exploring sedimentary rock sequences in Gale Crater for evidence of habitability and searching for organic compounds using the Sample Analysis at Mars (SAM) instrument suite. SAM includes a gas chromatograph mass spectrometer (GC-MS) and pyrolysis ovens. SAM has the ability to perform wet chemistry experiments, one of which uses tetramethylammonium hydroxide (TMAH) thermochemolysis to liberate bound lipids, making them sufficiently volatile for detection by GC-MS. To determine the effectiveness of the SAM-like TMAH experiment on fatty acid methyl ester (FAME) biomarker identification, rock and sediment samples were collected from a variety of Mars analog environments including iron oxides from a modern mineral precipitate and older surface gossan at Iron Mountain, CA, as well as modern acid salt and neutral lake sediments with mixed iron oxides and clays from Western Australia; siliceous sinter from recently inactive and modern near-vent Icelandic hot springs deposits; modern carbonate ooids from The Bahamas, and organic-rich shale from Germany. Samples underwent pyrolysis with TMAH. Fatty acids were analyzed by pyro-GC-MS using a SAM-like heating ramp (35°C/min) as well as a 500°C flash on a Frontier pyrolyzer and Agilent GC-MS instrument. Results reveal that FAMEs were detectable with the TMAH experiment in nearly all samples. Low molecular weight (MW) C6:0-C10:0 FAMEs were present in all samples, medium MW C11:0-C18:2 FAMEs were present in select samples, and high MW (HMW) C20:0-C30:0 FAMEs were present in the shale sample. Many of these samples exhibited an even-over-odd carbon number preference, indicating biological production. These experiments demonstrate that TMAH thermochemolysis with SAM-like pyro-GC-MS is effective in fatty acid analysis from natural Mars-analog samples that vary in mineralogy, age, and microbial community input. HMW FAMEs are not detected in iron-dominated samples, and may not be detectable at low

  19. A paradigm shift for radical SAM reactions: The organometallic intermediate Ω is central to catalysis.

    Science.gov (United States)

    Byer, Amanda S; Yang, Hao; McDaniel, Elizabeth C; Kathiresan, Venkatesan; Impano, Stella; Pagnier, Adrien; Watts, Hope; Denler, Carly; Vagstad, Anna; Piel, Jörn; Duschene, Kaitlin S; Shepard, Eric M; Shields, Thomas P; Scott, Lincoln G; Lilla, Edward A; Yokoyama, Kenichi; Broderick, William E; Hoffman, Brian M; Broderick, Joan B

    2018-06-28

    Radical S-adenosyl-L-methionine (SAM) en-zymes comprise a vast superfamily catalyzing diverse reactions essential to all life through ho-molytic SAM cleavage to liberate the highly-reactive 5-deoxyadenosyl radical (5-dAdo•). Our recent observation of a catalytically compe-tent organometallic intermediate Ω that forms dur-ing reaction of the radical SAM (RS) enzyme py-ruvate formate-lyase activating-enzyme (PFL-AE) was therefore quite surprising, and led to the question of its broad relevance in the superfamily. We now show that Ω in PFL-AE forms as an in-termediate under a variety of mixing order condi-tions, suggesting it is central to catalysis in this enzyme. We further demonstrate that Ω forms in a suite of RS enzymes chosen to span the totality of superfamily reaction types, implicating Ω as essential in catalysis across the RS superfamily. Finally, EPR and electron nuclear double reso-nance spectroscopy establish that Ω involves an Fe-C5 bond between 5-dAdo• and the [4Fe-4S] cluster. An analogous organometallic bond is found in the well-known adenosylcobalamin (co-enzyme B12) cofactor used to initiate radical reac-tions via a 5'-dAdo• intermediate. Generation of a 5'-dAdo• intermediate via homolytic metal-carbon bond cleavage thus appears to be similar for Ω and coenzyme B12. However coenzyme B12 is involved in enzymes catalyzing of only a small number (~12) of distinct reactions, while the RS superfamily has more than 100,000 distinct se-quences and over 80 reaction types character-ized to date. The appearance of Ω across the RS superfamily therefore dramatically enlarges the sphere of bio-organometallic chemistry in Nature.

  20. GENE-counter: a computational pipeline for the analysis of RNA-Seq data for gene expression differences.

    Science.gov (United States)

    Cumbie, Jason S; Kimbrel, Jeffrey A; Di, Yanming; Schafer, Daniel W; Wilhelm, Larry J; Fox, Samuel E; Sullivan, Christopher M; Curzon, Aron D; Carrington, James C; Mockler, Todd C; Chang, Jeff H

    2011-01-01

    GENE-counter is a complete Perl-based computational pipeline for analyzing RNA-Sequencing (RNA-Seq) data for differential gene expression. In addition to its use in studying transcriptomes of eukaryotic model organisms, GENE-counter is applicable for prokaryotes and non-model organisms without an available genome reference sequence. For alignments, GENE-counter is configured for CASHX, Bowtie, and BWA, but an end user can use any Sequence Alignment/Map (SAM)-compliant program of preference. To analyze data for differential gene expression, GENE-counter can be run with any one of three statistics packages that are based on variations of the negative binomial distribution. The default method is a new and simple statistical test we developed based on an over-parameterized version of the negative binomial distribution. GENE-counter also includes three different methods for assessing differentially expressed features for enriched gene ontology (GO) terms. Results are transparent and data are systematically stored in a MySQL relational database to facilitate additional analyses as well as quality assessment. We used next generation sequencing to generate a small-scale RNA-Seq dataset derived from the heavily studied defense response of Arabidopsis thaliana and used GENE-counter to process the data. Collectively, the support from analysis of microarrays as well as the observed and substantial overlap in results from each of the three statistics packages demonstrates that GENE-counter is well suited for handling the unique characteristics of small sample sizes and high variability in gene counts.

  1. GENE-counter: a computational pipeline for the analysis of RNA-Seq data for gene expression differences.

    Directory of Open Access Journals (Sweden)

    Jason S Cumbie

    Full Text Available GENE-counter is a complete Perl-based computational pipeline for analyzing RNA-Sequencing (RNA-Seq data for differential gene expression. In addition to its use in studying transcriptomes of eukaryotic model organisms, GENE-counter is applicable for prokaryotes and non-model organisms without an available genome reference sequence. For alignments, GENE-counter is configured for CASHX, Bowtie, and BWA, but an end user can use any Sequence Alignment/Map (SAM-compliant program of preference. To analyze data for differential gene expression, GENE-counter can be run with any one of three statistics packages that are based on variations of the negative binomial distribution. The default method is a new and simple statistical test we developed based on an over-parameterized version of the negative binomial distribution. GENE-counter also includes three different methods for assessing differentially expressed features for enriched gene ontology (GO terms. Results are transparent and data are systematically stored in a MySQL relational database to facilitate additional analyses as well as quality assessment. We used next generation sequencing to generate a small-scale RNA-Seq dataset derived from the heavily studied defense response of Arabidopsis thaliana and used GENE-counter to process the data. Collectively, the support from analysis of microarrays as well as the observed and substantial overlap in results from each of the three statistics packages demonstrates that GENE-counter is well suited for handling the unique characteristics of small sample sizes and high variability in gene counts.

  2. Gene-level association analysis of systemic sclerosis: A comparison of African-Americans and White populations.

    Science.gov (United States)

    Gorlova, Olga Y; Li, Yafang; Gorlov, Ivan; Ying, Jun; Chen, Wei V; Assassi, Shervin; Reveille, John D; Arnett, Frank C; Zhou, Xiaodong; Bossini-Castillo, Lara; Lopez-Isac, Elena; Acosta-Herrera, Marialbert; Gregersen, Peter K; Lee, Annette T; Steen, Virginia D; Fessler, Barri J; Khanna, Dinesh; Schiopu, Elena; Silver, Richard M; Molitor, Jerry A; Furst, Daniel E; Kafaja, Suzanne; Simms, Robert W; Lafyatis, Robert A; Carreira, Patricia; Simeon, Carmen Pilar; Castellvi, Ivan; Beltran, Emma; Ortego, Norberto; Amos, Christopher I; Martin, Javier; Mayes, Maureen D

    2018-01-01

    Gene-level analysis of ImmunoChip or genome-wide association studies (GWAS) data has not been previously reported for systemic sclerosis (SSc, scleroderma). The objective of this study was to analyze genetic susceptibility loci in SSc at the gene level and to determine if the detected associations were shared in African-American and White populations, using data from ImmunoChip and GWAS genotyping studies. The White sample included 1833 cases and 3466 controls (956 cases and 2741 controls from the US and 877 cases and 725 controls from Spain) and the African American sample, 291 cases and 260 controls. In both Whites and African Americans, we performed a gene-level analysis that integrates association statistics in a gene possibly harboring multiple SNPs with weak effect on disease risk, using Versatile Gene-based Association Study (VEGAS) software. The SNP-level analysis was performed using PLINK v.1.07. We identified 4 novel candidate genes (STAT1, FCGR2C, NIPSNAP3B, and SCT) significantly associated and 4 genes (SERBP1, PINX1, TMEM175 and EXOC2) suggestively associated with SSc in the gene level analysis in White patients. As an exploratory analysis we compared the results on Whites with those from African Americans. Of previously established susceptibility genes identified in Whites, only TNFAIP3 was significant at the nominal level (p = 6.13x10-3) in African Americans in the gene-level analysis of the ImmunoChip data. Among the top suggestive novel genes identified in Whites based on the ImmunoChip data, FCGR2C and PINX1 were only nominally significant in African Americans (p = 0.016 and p = 0.028, respectively), while among the top novel genes identified in the gene-level analysis in African Americans, UNC5C (p = 5.57x10-4) and CLEC16A (p = 0.0463) were also nominally significant in Whites. We also present the gene-level analysis of SSc clinical and autoantibody phenotypes among Whites. Our findings need to be validated by independent studies, particularly

  3. Differential gene expression of wheat progeny with contrasting levels of transpiration efficiency.

    Science.gov (United States)

    Xue, Gang-Ping; McIntyre, C Lynne; Chapman, Scott; Bower, Neil I; Way, Heather; Reverter, Antonio; Clarke, Bryan; Shorter, Ray

    2006-08-01

    High water use efficiency or transpiration efficiency (TE) in wheat is a desirable physiological trait for increasing grain yield under water-limited environments. The identification of genes associated with this trait would facilitate the selection for genotypes with higher TE using molecular markers. We performed an expression profiling (microarray) analysis of approximately 16,000 unique wheat ESTs to identify genes that were differentially expressed between wheat progeny lines with contrasting TE levels from a cross between Quarrion (high TE) and Genaro 81 (low TE). We also conducted a second microarray analysis to identify genes responsive to drought stress in wheat leaves. Ninety-three genes that were differentially expressed between high and low TE progeny lines were identified. One fifth of these genes were markedly responsive to drought stress. Several potential growth-related regulatory genes, which were down-regulated by drought, were expressed at a higher level in the high TE lines than the low TE lines and are potentially associated with a biomass production component of the Quarrion-derived high TE trait. Eighteen of the TE differentially expressed genes were further analysed using quantitative RT-PCR on a separate set of plant samples from those used for microarray analysis. The expression levels of 11 of the 18 genes were positively correlated with the high TE trait, measured as carbon isotope discrimination (Delta(13)C). These data indicate that some of these TE differentially expressed genes are candidates for investigating processes that underlie the high TE trait or for use as expression quantitative trait loci (eQTLs) for TE.

  4. The Investigation of Chlorates as a Possible Source of Oxygen and Chlorine Detected by the Sample Analysis at Mars (SAM) Instrument in Gale Crater, Mars

    Science.gov (United States)

    Sutter, B.; Archer, D. P.; Ming, D. W.; Niles, P. B.; Eigenbrode, J. L.; Franz, H.; Glavin, D. P.; McAdam, A. C.; Mahaffy, P; Stern, J. C.; hide

    2014-01-01

    The Sample Analysis at Mars (SAM) instrument onboard the Curiosity rover detect-ed O2 and HCl gas releases from the Rocknest (RN) eolian bedform and the John Klein (JK) and Cumberland (CB) drill hole materials in Gale Crater. Chlorinated hydrocarbons have also been detected by the SAM quadrupole mass spectrometer (QMS) and gas chromatography/mass spectrometer (GCMS). These detections along with the detection of perchlorate (ClO4-) by the Mars Phoenix Lander’s Wet Chemistry Laboratory (WCL) suggesting perchlorate is a possible candidate for evolved O2 and chlorine species. Laboratory thermal analysis of perchlorates has yet to provide an unequivocal temperature match to the SAM O2 and HCl release data. Iron mineralogy found in the Rocknest materials when mixed with Ca-perchlorate does cause O2 release temperatures to be closer match to the SAM O2 release data but more work is required in evaluating the catalytic effects of Fe mineralogy on perchlorate decomposition. Chlorates (ClO3-) are relevant Mars materials and potential O2 and Cl sources. The objective of this work is to evaluate the thermal decomposition of select chlorate (ClO3-) salts as possible sources of the O2 and HCl releases in the Gale Crater materials.

  5. Surveillance and Measurement System (SAMS). Innovative Technology Summary Report

    International Nuclear Information System (INIS)

    2001-01-01

    The United States Department of Energy (DOE) continually seeks safer and more cost-effective technologies for the decontamination and decommissioning (D and D) of nuclear facilities. The Deactivation and Decommissioning Focus Area (DDFA) of the DOE's Office of Science and Technology sponsors large-scale demonstration and deployment projects (LSDDPs) to identify and demonstrate technologies that will be safer and more cost-effective. At these LSDDPs, developers and vendors of improved or innovative technologies showcase products that are potentially beneficial to the DOE's projects as well as others in the D and D community. Benefits sought include decreased health and safety risks to personnel and the environment, increased productivity, and decreased cost of operation. The Idaho National Engineering and Environmental Laboratory (INEEL) LSDDP generated a list of need statements defining specific needs or problems where improved technologies could be incorporated into ongoing D and D tasks. Advances in characterization technologies are continuously being sought to decrease the cost of sampling and increase the speed of obtaining results. Currently it can take as long as 90 days to receive isotopic analysis of radioactive samples from laboratories on soil, liquid, and paint samples. The cost to analyze these types of samples for radionuclides is about $150 per sample. This demonstration investigated the feasibility of using the Surveillance and Measurement System (SAMS) (innovative technology) to make in situ isotopic radiation measurements in paint and soil. Sample collection and on-site laboratory analysis (baseline technology) is currently being used on D and D sampling activities. Benefits expected from using the innovative technology include: Significant decrease in time to receive results on radiological samples; Decrease in cost associated with sample collection, preparation, analysis, and disposal; Equivalent data quality to laboratory analysis; and Fewer

  6. Exploration of the Habitability of Mars with the SAM Suite Investigation on the 2009 Mars Science Laboratory

    Science.gov (United States)

    Mahaffy, P. R.; Cabane, M.; Webster, C. R.

    2008-01-01

    The 2009 Mars Science Laboratory (MSL) with a substantially larger payload capability that any other Mars rover, to date, is designed to quantitatively assess a local region on Mars as a potential habitat for present or past life. Its goals are (1) to assess past or present biological potential of a target environment, (2) to characterize geology and geochemistry at the MSL landing site, and (3) to investigate planetary processes that influence habitability. The Sample Analysis at Mars (SAM) Suite, in its final stages of integration and test, enables a sensitive search for organic molecules and chemical and isotopic analysis of martian volatiles. MSL contact and remote surface and subsurface survey Instruments establish context for these measurements and facilitate sample identification and selection. The SAM instruments are a gas chromatograph (GC), a mass spectrometer (MS), and a tunable laser spectrometer (TLS). These together with supporting sample manipulation and gas processing devices are designed to analyze either the atmospheric composition or gases extracted from solid phase samples such as rocks and fines. For example, one of the core SAM experiment sequences heats a small powdered sample of a Mars rock or soil from ambient to -1300 K in a controlled manner while continuously monitoring evolved gases. This is followed by GCMS analysis of released organics. The general chemical survey is complemented by a specific search for molecular classes that may be relevant to life including atmospheric methane and its carbon isotope with the TLS and biomarkers with the GCMS.

  7. Séries temporais de NDVI do sensor SPOT Vegetation e algoritmo SAM aplicados ao mapeamento de cana‑de‑açúcar

    Directory of Open Access Journals (Sweden)

    Luiz Eduardo Vicente

    2012-09-01

    Full Text Available O objetivo deste trabalho foi avaliar o mapeamento de área de cana‑de‑açúcar por meio de série temporal, de seis anos de dados do índice de vegetação por diferença normalizada (NDVI, oriundos do sensor Vegetation, a bordo do satélite "système pour l'observation de la Terre" (SPOT. Três classes de cobertura do solo (cana‑de‑açúcar, pasto e floresta, do Estado de São Paulo, foram selecionadas como assinaturas espectro‑temporais de referência, que serviram como membros extremos ("endmembers" para classificação com o algoritmo "spectral angle mapper" (SAM. A partir desta classificação, o mapeamento da área de cana‑de‑açúcar foi realizado com uso de limiares na imagem-regra do SAM, gerados a partir dos valores dos espectros de referência. Os resultados mostram que o algoritmo SAM pode ser aplicado a séries de dados multitemporais de resolução moderada, o que permite eficiente mapeamento de alvo agrícola em escala mesorregional. Dados oficiais de áreas de cana‑de‑açúcar, para as microrregiões paulistas, apresentam boa correlação (r² = 0,8 com os dados obtidos pelo método avaliado. A aplicação do algoritmo SAM mostrou ser útil em análises temporais. As séries temporais de NDVI do sensor SPOT Vegetation podem ser utilizadas para mapeamento da área de cana‑de‑açúcar em baixa resolução.

  8. Highlight on the indigenous organic molecules detected on Mars by SAM and potential sources of artifacts and backgrounds generated by the sample preparation

    Science.gov (United States)

    Buch, A.; Belmahdi, I.; Szopa, C.; Freissinet, C.; Glavin, D. P.; Coll, P. J.; Cabane, M.; Millan, M.; Eigenbrode, J. L.; Navarro-Gonzalez, R.; Stern, J. C.; Pinnick, V. T.; Coscia, D.; Teinturier, S.; Stambouli, M.; Dequaire, T.; Mahaffy, P. R.

    2015-12-01

    Among the experiments which explore the martian soil aboard the Curiosity Rover, SAM experiment is mainly dedicated to the search for indigenous organic compounds. To reach its goals SAM can operate in different analysis modes: Pyrolysis-GC-MS and Pyrolysis-MS (EGA). In addition SAM includes wet chemistry experiments [1] to supports extraction of polar organic compounds from solid samples that improves their detection either by increasing the release of chemical species from solid sample matrices, or by changing their chemical structure to make compounds more amenable to gas chromatography mass spectrometry (GCMS). The two wet chemistry experimental capabilities of SAM provide alternatives to the nominal inert-thermal desorption/pyrolysis analytical protocol and are more aptly suited for polar components: MTBSTFA derivatization [2-3] and TMAH thermochemolysis [4-5]. Here we focus on the MTBSTFA derivatization experiment. In order to build a support used to help the interpretation of SAM results, we have investigated the artifacts and backgrounds sources generated by the all analysis process: Solid sample were heated up to approximately 840°C at a rate of 35°C/min under He flow. For GC analyses, the majority of the gas released was trapped on a hydrocarbon trap (Tenax®) over a specific temperature range. Adsorbed volatiles on the GC injection trap (IT) were then released into the GC column (CLP-MXT 30m x 0.25mm x 0.25μm) by rapidly heating the IT to 300°C. Then, in order better understand the part of compounds detected coming from internal reaction we have performed several lab experiments to mimic the SAM device: Among the sources of artifact, we test: (1) the thermal stability and the organic material released during the degradation of Tenax® and carbosieve, (2) the impact of MTBSTFA and a mixture of DMF and MTBSTFA on the adsorbent, (3) the reaction between the different adsorbents (Tenax® and Carbosieve) and calcium perchlorate and then (4) the sources

  9. Nano-indentation at the surface contact level: applying a harmonic frequency for measuring contact stiffness of self-assembled monolayers adsorbed on Au

    International Nuclear Information System (INIS)

    Chang, C.-W.; Liao, J.-D.

    2008-01-01

    In this study, the well-ordered alkanethiolate self-assembled monolayers (SAMs) of varied chain lengths and tail groups were employed as examples for nano-characterization on their mechanical properties. A novel nano-indentation technique with a constant harmonic frequency was applied on SAMs chemically adsorbed on Au to explore their contact mechanics, and furthermore to interpret how SAM molecules respond to an infinitesimal oscillation force without pressing them. Experimental results demonstrated that the harmonic contact stiffness along with the measured displacement of SAMs/Au was distinguishable using a dynamic contact modulus with the distinct feature of phase angles. Phase angles resulted from the relaxing continuation of an applied harmonic frequency and mostly influenced by the outermost tail group of SAM molecules. The harmonic contact stiffness of SAM molecules obviously increased with the densely packed alkyl chains and relatively intense agglomeration of the head group at the anchoring site. As a consequence, the result of this work is relevant to contact mechanics at the surface contact level for the distinction of molecular substances attached on a solid surface. Furthermore it is particularly anticipated to identify biological molecules of variable qualities under a fluid-like micro-environment

  10. Nano-indentation at the surface contact level: applying a harmonic frequency for measuring contact stiffness of self-assembled monolayers adsorbed on Au

    Energy Technology Data Exchange (ETDEWEB)

    Chang, C.-W.; Liao, J.-D. [Department of Materials Science and Engineering, National Cheng Kung University, No. 1, University Road, Tainan 70101, Taiwan (China)], E-mail: jdliao@mail.ncku.edu.tw

    2008-08-06

    In this study, the well-ordered alkanethiolate self-assembled monolayers (SAMs) of varied chain lengths and tail groups were employed as examples for nano-characterization on their mechanical properties. A novel nano-indentation technique with a constant harmonic frequency was applied on SAMs chemically adsorbed on Au to explore their contact mechanics, and furthermore to interpret how SAM molecules respond to an infinitesimal oscillation force without pressing them. Experimental results demonstrated that the harmonic contact stiffness along with the measured displacement of SAMs/Au was distinguishable using a dynamic contact modulus with the distinct feature of phase angles. Phase angles resulted from the relaxing continuation of an applied harmonic frequency and mostly influenced by the outermost tail group of SAM molecules. The harmonic contact stiffness of SAM molecules obviously increased with the densely packed alkyl chains and relatively intense agglomeration of the head group at the anchoring site. As a consequence, the result of this work is relevant to contact mechanics at the surface contact level for the distinction of molecular substances attached on a solid surface. Furthermore it is particularly anticipated to identify biological molecules of variable qualities under a fluid-like micro-environment.

  11. Systematic substrate adoption methodology (SAM) for future flexible, generic pharmaceutical production processes

    DEFF Research Database (Denmark)

    Singh, Ravendra; Godfrey, Andy; Gregertsen, Björn

    2013-01-01

    (APIs) for early delivery campaigns. Of these candidates only a few will be successful such that further development is required to scale-up the process. Systematic computer-aided methods and tools are required for faster manufacturing of these API candidates. In this work, a substrate adoption...... methodology (SAM) for a series of substrates with similar molecular functionality has been developed. The objective is to achieve “flexible, fast and future” pharmaceutical production processes by adapting a generic modular process template. Application of the methodology is illustrated through a case study...

  12. Free cortisol and salivary alpha-amylase levels during a six-hour-water immersion in healthy young men

    Science.gov (United States)

    Rohleder, N.; Wirth, D.; Fraßl, W.; Kowoll, R.; Schlemmer, M.; Vogler, S.; Kirsch, K. A.; Kirschbaum, C.; Gunga, H.-C.

    2005-08-01

    Limited data are available on the response of stress systems to microgravity. Increased activity of stress systems is reported during space flight, but unchanged or decreased activity during simulated microgravity. We here investigated the impact of head-out water immersion on the activity of the hypothalamus-pituitary-adrenal (HPA) axis and the sympathetic-adrenal-medullary (SAM) system.Eight healthy young men were exposed to a six-hour water immersion in a thermo neutral bath and a control condition. Saliva samples were taken before, during, and after interventions to assess cortisol as an index for HPA axis activity, and salivary α-amylase as an index for SAM system activity.Cortisol levels uniformly decreased during both conditions. Amylase levels increased during both conditions, but were significantly lower during the first half of water immersion compared to the control condition.In conclusion, the HPA axis is not influenced by simulated microgravity, while SAM system activity shows initial decreases during water immersion.

  13. In Situ Analysis of Mars Soil and Rocks Sample with the Sam Gcms Instrumentation Onboard Curiosity : Interpretation and Comparison of Measurements Done during the First Martian Year of Curiosity on Mars

    Science.gov (United States)

    Szopa, C.; Coll, P. J.; Cabane, M.; Buch, A.; Coscia, D.; Millan, M.; Francois, P.; Belmahadi, I.; Teinturier, S.; Navarro-Gonzalez, R.; Glavin, D. P.; Freissinet, C.; Steele, A.; Eigenbrode, J. L.; Mahaffy, P. R.

    2014-12-01

    The characterisation of the chemical and mineralogical composition of solid surface samples collected with the Curiosity rover is a primary objective of the SAM experiment. These data should provide essential clues on the past habitability of Gale crater. Amongst the SAM suite of instruments [1], SAM-GC (Gas Chromatograph) is devoted to identify and quantify volatiles evolved from the thermal (heating up to about 900°C)/chemical (derivatization procedure) treatment of any soil sample collected by the Curiosity rover. With the aim to search for potential organic molecules outgassed from the samples, SAM-GC analytical channels composed of thermal-desorption injector, and a MXT-CLP or a MXT-Q chromatographic column was chosen to achieve all the measurements done up today, with the aim to separate of a wide range of volatile inorganic and organic molecules. Four solid samples have been analyzed with GCMS, one sand sample collected at the Rocknest site, two rock samples (John Klein and Cumberland respectively) collected at the Yellowknife Bay site using the Curiosity driller, and one rock sample collected at the Kimberly site. All the measurements were successful and they produced complex chromatograms with both detectors used for SAM GC, i.e. a thermal conductivity detector and the SAM quandrupole mass spectrometer. Their interpretation already revealed the presence of an oxychlorine phase present in the sample which is at the origin of chlorohydrocarbons clearly identified [2] but this represents only a fraction of the GCMS signal recorded [3,4]. This work presents a systematic comparison of the GCMS measurements done for the different samples collected, supported by reference data obtained in laboratory with different spare models of the gas chromatograph, with the aim to bring new elements of interpretation of the SAM measurements. References: [1] Mahaffy, P. et al. (2012) Space Sci Rev, 170, 401-478. [2] Glavin, D. et al. (2013), JGR. [3] Leshin L. et al. (2013

  14. On the use of permutation in and the performance of a class of nonparametric methods to detect differential gene expression.

    Science.gov (United States)

    Pan, Wei

    2003-07-22

    Recently a class of nonparametric statistical methods, including the empirical Bayes (EB) method, the significance analysis of microarray (SAM) method and the mixture model method (MMM), have been proposed to detect differential gene expression for replicated microarray experiments conducted under two conditions. All the methods depend on constructing a test statistic Z and a so-called null statistic z. The null statistic z is used to provide some reference distribution for Z such that statistical inference can be accomplished. A common way of constructing z is to apply Z to randomly permuted data. Here we point our that the distribution of z may not approximate the null distribution of Z well, leading to possibly too conservative inference. This observation may apply to other permutation-based nonparametric methods. We propose a new method of constructing a null statistic that aims to estimate the null distribution of a test statistic directly. Using simulated data and real data, we assess and compare the performance of the existing method and our new method when applied in EB, SAM and MMM. Some interesting findings on operating characteristics of EB, SAM and MMM are also reported. Finally, by combining the idea of SAM and MMM, we outline a simple nonparametric method based on the direct use of a test statistic and a null statistic.

  15. PDS4 vs PDS3 - A Comparison of PDS Data for Two Mars Rovers - Existing Mars Curiosity Mission Mass Spectrometer (SAM) PDS3 Data vs Future ExoMars Rover Mass Spectrometer (MOMA) PDS4 Data

    Science.gov (United States)

    Lyness, E.; Franz, H. B.; Prats, B.

    2017-12-01

    The Sample Analysis at Mars (SAM) instrument is a suite of instruments on Mars aboard the Mars Science Laboratory rover. Centered on a mass spectrometer, SAM delivers its data to the PDS Atmosphere's node in PDS3 format. Over five years on Mars the process of operating SAM has evolved and extended significantly from the plan in place at the time the PDS3 delivery specification was written. For instance, SAM commonly receives double or even triple sample aliquots from the rover's drill. SAM also stores samples in spare cups for long periods of time for future analysis. These unanticipated operational changes mean that the PDS data deliveries are absent some valuable metadata without which the data can be confusing. The Mars Organic Molecule Analyzer (MOMA) instrument is another suite of instruments centered on a mass spectrometer bound for Mars. MOMA is part of the European ExoMars rover mission schedule to arrive on Mars in 2021. While SAM and MOMA differ in some important scientific ways - MOMA uses an linear ion trap compared to the SAM quadropole mass spectrometer and MOMA has a laser desorption experiment that SAM lacks - the data content from the PDS point of view is comparable. Both instruments produce data containing mass spectra acquired from solid samples collected on the surface of Mars. The MOMA PDS delivery will make use of PDS4 improvements to provide a metadata context to the data. The MOMA PDS4 specification makes few assumptions of the operational processes. Instead it provides a means for the MOMA operators to provide the important contextual metadata that was unanticipated during specification development. Further, the software tools being developed for instrument operators will provide a means for the operators to add this crucial metadata at the time it is best know - during operations.

  16. Design of chimeric expression elements that confer high-level gene activity in chromoplasts.

    Science.gov (United States)

    Caroca, Rodrigo; Howell, Katharine A; Hasse, Claudia; Ruf, Stephanie; Bock, Ralph

    2013-02-01

    Non-green plastids, such as chromoplasts, generally have much lower activity of gene expression than chloroplasts in photosynthetically active tissues. Suppression of plastid genes in non-green tissues occurs through a complex interplay of transcriptional and translational control, with the contribution of regulation of transcript abundance versus translational activity being highly variable between genes. Here, we have investigated whether the low expression of the plastid genome in chromoplasts results from inherent limitations in gene expression capacity, or can be overcome by designing appropriate combinations of promoters and translation initiation signals in the 5' untranslated region (5'-UTR). We constructed chimeric expression elements that combine promoters and 5'-UTRs from plastid genes, which are suppressed during chloroplast-to-chromoplast conversion in Solanum lycopersicum (tomato) fruit ripening, either just at the translational level or just at the level of mRNA accumulation. These chimeric expression elements were introduced into the tomato plastid genome by stable chloroplast transformation. We report the identification of promoter-UTR combinations that confer high-level gene expression in chromoplasts of ripe tomato fruits, resulting in the accumulation of reporter protein GFP to up to 1% of total cellular protein. Our work demonstrates that non-green plastids are capable of expressing genes to high levels. Moreover, the chimeric cis-elements for chromoplasts developed here are widely applicable in basic and applied research using transplastomic methods. © 2012 The Authors The Plant Journal © 2012 Blackwell Publishing Ltd.

  17. Crystallization and preliminary crystallographic analysis of nosiheptide-resistance methyltransferase from Streptomyces actuosus in complex with SAM

    International Nuclear Information System (INIS)

    Yang, Huirong; Wang, Ping; Dong, Zhenghong; Li, Xueyuan; Gong, Rui; Yang, Ying; Li, Ze; Xu, Youwei; Xu, Yanhui

    2010-01-01

    The expression, purification and crystallization of nosiheptide-resistance methyltransferase (NSR) from Streptomyces actuosus is described. Nosiheptide-resistance methyltransferase (NSR) methylates 23S rRNA at the nucleotide adenosine 1067 in Escherichia coli and thus contributes to resistance against nosiheptide, a sulfur-containing peptide antibiotic. Here, the expression, purification and crystallization of NSR from Streptomyces actuosus are reported. Diffracting crystals were grown by the hanging-drop vapour-diffusion method in reservoir solution consisting of 0.35 M ammonium chloride, 24%(w/v) PEG 3350, 0.1 M MES pH 5.7 at 293 K. Native data have been collected from the apo enzyme and a SAM complex, as well as apo SeMet SAD data. The diffraction patterns of the apo form of NSR, of NSR complexed with SAM and of SeMet-labelled NSR crystals extended to 1.90, 1.95 and 2.25 Å resolution, respectively, using synchrotron radiation. All crystals belonged to space group P2 1 , with approximate unit-cell parameters a = 64.6, b = 69.6, c = 64.9 Å, β = 117.8°

  18. Efecto bioestimulante de Trichoderma harzianum Rifai en posturas de Leucaena, Cedro y Samán

    Directory of Open Access Journals (Sweden)

    Leonides Castellanos González

    2018-01-01

    Full Text Available El presente artículo evaluó el efecto bioestimulante de Trichoderma harzianum Rifai en la producción de postura de Leucaena leucocephala (Lam de Wit., Cedrela odorata L. y Albizia saman (Jacq. Merr. Se desarrollaron tres experimentos en condiciones de vivero, uno para cada especie. Se empleó un diseño completamente aleatorio con cuatro parcelas por tratamiento. En cada experimento los tratamientos fueron: Trichoderma harzianum a razón de 20 g.L-1, 40 g.L-1 y un testigo. Se evaluó el porcentaje de germinación y las variables morfométricas diámetro y altura del tallo, así como biomasa seca en raíz y parte aérea de la planta. Los tratamientos con Trichoderma no incrementaron el porcentaje de germinación en cedro, samán y leucaena. T. harzianum incrementó la altura, el número de hojas y la biomasa seca del área foliar en las plántulas de cedro, mientras que en leucaena y samán solo provocó incrementos del diámetro basal de las plántulas.

  19. Orientational analysis of dodecanethiol and p-nitrothiophenol SAMs on metals with polarisation-dependent SFG spectroscopy.

    Science.gov (United States)

    Cecchet, Francesca; Lis, Dan; Guthmuller, Julien; Champagne, Benoît; Caudano, Yves; Silien, Christophe; Mani, Alaa Addin; Thiry, Paul A; Peremans, André

    2010-02-22

    Polarisation-dependent sum frequency generation (SFG) spectroscopy is used to investigate the orientation of molecules on metallic surfaces. In particular, self-assembled monolayers (SAMs) of dodecanethiol (DDT) and of p-nitrothiophenol (p-NTP), grown on Pt and on Au, have been chosen as models to highlight the ability of combining ppp and ssp polarisations sets (representing the polarisation of the involved beams in the conventional order of SFG, Vis and IR beam) to infer orientational information at metallic interfaces. Indeed, using only the ppp set of data, as it is usually done for metallic surfaces, is not sufficient to determine the full molecular orientation. We show here that simply combining ppp and ssp polarisations enables both the tilt and rotation angles of methyl groups in DDT SAMs to be determined. Moreover, for p-NTP, while the SFG active vibrations detected with the ppp polarisation alone provide no orientational information, however, the combination with ssp spectra enables to retrieve the tilt angle of the p-NTP 1,4 axis. Though orientational information obtained by polarisation-dependent measurements has been extensively used at insulating interfaces, we report here their first application to metallic surfaces.

  20. Orientational Analysis of Dodecanethiol and P-Nitrothiophenol SAMs on Metals with Polarisation - dependent SFG spectroscopy

    International Nuclear Information System (INIS)

    Manea, A.

    2011-01-01

    Polarisation-dependent sum frequency generation (SFG) spectroscopy is used to investigate the orientation of molecules on metallic surfaces. In particular, self-assembled monolayers (SAMs) of dodecanethiol (DDT) and of p-nitro thiophenol (p-NTP), grown on Pt and on Au, have been chosen as models to highlight the ability of combining ppp and ssp polarizations sets (representing the polarisation of the involved beams in the conventional order of SFG, Vis and IR beam) to infer orientational information at metallic interfaces. Indeed, using only the ppp set of data, as it is usually done for metallic surfaces, is not sufficient to determine the full molecular orientation. We show here that simply combining ppp and ssp polarizations enables both the tilt and rotation angles of methyl groups in DDT SAMs to be determined. Moreover, for p-NTP, while the SFG active vibrations detected with the ppp polarisation alone provide no orientational information, however, the combination with ssp spectra enables to retrieve the tilt angle of the p-NTP 1,4 axis. Though orientational information obtained by polarisation-dependent measurements has been extensively used at insulating interfaces, we report here their first application to metallic surfaces. (author)

  1. Supra-physiological folic acid concentrations induce aberrant DNA methylation in normal human cells in vitro.

    Science.gov (United States)

    Charles, Michelle A; Johnson, Ian T; Belshaw, Nigel J

    2012-07-01

    The micronutrients folate and selenium may modulate DNA methylation patterns by affecting intracellular levels of the methyl donor S-adenosylmethionine (SAM) and/or the product of methylation reactions S-adenosylhomocysteine (SAH). WI-38 fibroblasts and FHC colon epithelial cells were cultured in the presence of two forms of folate or four forms of selenium at physiologically-relevant doses, and their effects on LINE-1 methylation, gene-specific CpG island (CGI) methylation and intracellular SAM:SAH were determined. At physiologically-relevant doses the forms of folate or selenium had no effect on LINE-1 or CGI methylation, nor on intracellular SAM:SAH. However the commercial cell culture media used for the selenium studies, containing supra-physiological concentrations of folic acid, induced LINE-1 hypomethylation, CGI hypermethylation and decreased intracellular SAM:SAH in both cell lines. We conclude that the exposure of normal human cells to supra-physiological folic acid concentrations present in commercial cell culture media perturbs the intracellular SAM:SAH ratio and induces aberrant DNA methylation.

  2. Severe accident management at the Loviisa NPP - Application of integrated ROAAM and PSA level 2

    International Nuclear Information System (INIS)

    Siltanen, S.; Routamo, T.; Tuomisto, H.; Lundstrom, P.

    2007-01-01

    The Risk Oriented Accident Analysis Methodology (ROAAM) was developed for assessment and management of rare, high consequence hazards. The purpose of most ROAAM applications has been to solve major, isolated severe accident issues related to early containment failure such as Mark-I Liner Attack and Direct Containment Heating. In addition to ROAAM in the issue resolution context, the so called Integrated ROAAM approach can be used to provide an overall frame of safety evaluation that allows determination of whether an adequate level of safety has been achieved for a plant. Integrated ROAAM approach brings together quantifications of probabilistic elements based on statistical inference and treatment of deterministic elements based on identification of dominant physics, for severe accident phenomenology, in a well defined and clearly structured way. Fortum, as an owner of the Loviisa NPP, used the Integrated ROAAM approach when developing and implementing a comprehensive severe accident management (SAM) strategy for the Loviisa NPP. The SAM strategy is based on unique features of this VVER-440 plant with ice condenser containment and it includes hardware modifications at the plant, substantial new I and C qualified for severe accident conditions, new SAM guidelines, a SAM Handbook, revision of emergency preparedness organization, and versatile training approaches. It could be argued that the resolution of individual severe accident issues is not sufficient for assessing the overall safety of a nuclear power plant, and thus the ROAAM (in an issue resolution context) is not performing the same function as a PSA study (level 2 included). Actually the Integrated ROAAM approach takes on even a more ambitious task than the PSA, since it determines how a balance can be achieved between accident prevention and mitigation of containment-threatening physical phenomena. Thus it provides a tool for implementing a sound diverse defence-in-depth strategy at a plant. Integrated

  3. Effectivity System of Management Information in Information Tehcnology Center University of Sam Ratulangi Manado.

    OpenAIRE

    Kalalo, Intani Kirana; Mandey, Jantje; Pombengi, Jericho

    2015-01-01

    In accordance with Regulation of the Minister of Education and Culture of the Republic of Indonesia on the Organization and Work of Sam Ratulangi University of article 105, paragraph 1, which states that the Information and Communication Technology Unit is a unit of the technical implementation in the field of development and management of systems and information and communication technology. And Article 106, namely, Information and Communication Technology Unit has the t...

  4. Eldecalcitol improves mechanical strength of cortical bones by stimulating the periosteal bone formation in the senescence-accelerated SAM/P6 mice - a comparison with alfacalcidol.

    Science.gov (United States)

    Shiraishi, Ayako; Sakai, Sadaoki; Saito, Hitoshi; Takahashi, Fumiaki

    2014-10-01

    Eldecalcitol (ELD), a 2β-hydroxypropyloxy derivative of 1α,25(OH)2D3, is a potent inhibitor of bone resorption that has demonstrated a greater effect at reducing the risk of fracture in osteoporotic patients than alfacalcidol (ALF). In the present study, we used the senescence-accelerated mouse strain P6 (SAM/P6), which has low bone mass caused by osteoblast dysfunction, to evaluate the effect of ELD on cortical bone in comparison with ALF. Four-month-old SAM/P6 mice were given either ELD (0.025 or 0.05μg/kg) or ALF (0.2 or 0.4μg/kg) by oral gavage 5 times/week for 6 weeks. Both ELD and ALF increased serum calcium (Ca) in a dose-dependent manner. Serum Ca levels in the ELD 0.05μg/kg group were comparable to those of the ALF 0.2μg/kg group. ELD 0.05μg/kg significantly improved the bone biomechanical properties of the femur compared with the vehicle control group (pBone histomorphometry revealed that in the femoral endocortical surface, the suppression of bone resorption parameters (N.Oc/BS) and bone formation parameters (MS/BS) by ELD (0.05μg/kg) was greater than that by ALF (0.2μg/kg). In contrast, in the femoral periosteal surface, ELD 0.05μg/kg significantly increased bone formation parameters (BFR/BS, MS/BS) compared with the vehicle control group (pbone not only by inhibiting endocortical bone resorption but also by stimulating the periosteal bone formation in SAM/P6 mice. This article is part of a Special Issue entitled '16th Vitamin D Workshop'. Copyright © 2013 Elsevier Ltd. All rights reserved.

  5. Stress-induced gene expression and behavior are controlled by DNA methylation and methyl donor availability in the dentate gyrus

    Science.gov (United States)

    Saunderson, Emily A.; Spiers, Helen; Gutierrez-Mecinas, Maria; Trollope, Alexandra F.; Shaikh, Abeera; Mill, Jonathan; Reul, Johannes M. H. M.

    2016-01-01

    Stressful events evoke long-term changes in behavioral responses; however, the underlying mechanisms in the brain are not well understood. Previous work has shown that epigenetic changes and immediate-early gene (IEG) induction in stress-activated dentate gyrus (DG) granule neurons play a crucial role in these behavioral responses. Here, we show that an acute stressful challenge [i.e., forced swimming (FS)] results in DNA demethylation at specific CpG (5′-cytosine–phosphate–guanine-3′) sites close to the c-Fos (FBJ murine osteosarcoma viral oncogene homolog) transcriptional start site and within the gene promoter region of Egr-1 (early growth response protein 1) specifically in the DG. Administration of the (endogenous) methyl donor S-adenosyl methionine (SAM) did not affect CpG methylation and IEG gene expression at baseline. However, administration of SAM before the FS challenge resulted in an enhanced CpG methylation at the IEG loci and suppression of IEG induction specifically in the DG and an impaired behavioral immobility response 24 h later. The stressor also specifically increased the expression of the de novo DNA methyltransferase Dnmt3a [DNA (cytosine-5-)-methyltransferase 3 alpha] in this hippocampus region. Moreover, stress resulted in an increased association of Dnmt3a enzyme with the affected CpG loci within the IEG genes. No effects of SAM were observed on stress-evoked histone modifications, including H3S10p-K14ac (histone H3, phosphorylated serine 10 and acetylated lysine-14), H3K4me3 (histone H3, trimethylated lysine-4), H3K9me3 (histone H3, trimethylated lysine-9), and H3K27me3 (histone H3, trimethylated lysine-27). We conclude that the DNA methylation status of IEGs plays a crucial role in FS-induced IEG induction in DG granule neurons and associated behavioral responses. In addition, the concentration of available methyl donor, possibly in conjunction with Dnmt3a, is critical for the responsiveness of dentate neurons to environmental

  6. The Detection of Evolved Oxygen from the Rocknest Eolian Bedform Material by the Sample Analysis at Mars(SAM) instrument at the Mars Curiosity Landing Site

    Science.gov (United States)

    Sutter, B.; Archer, D.; Ming, D.; Eigenbrode, J. L.; Franz, H.; Glavin, D. P.; McAdam, A.; Mahaffy, P.; Stern, J.; Navarro-Gonzalex, R.; hide

    2013-01-01

    The Sample Analysis at Mars (SAM) instrument onboard the Curiosity rover detected an O2 gas release from the Rocknest eolain bedform (Fig. 1). The detection of perchlorate (ClO4-) by the Mars Phoenix Lander s Wet Chemistry Laboratory (WCL) [1] suggests that perchlorate is a possible candidate for evolved O2 release detected by SAM. The perchlorate would also serve as a source of chlorine in the chlorinated hydrocarbons detected by the SAM quadrupole mass spectrometer (QMS) and gas chromatography/mass spectrometer (GCMS) [2,3]. Chlorates (ClO3-) [4,5] and/or superoxides [6] may also be sources of evolved O2 from the Rocknest materials. The work objectives are to 1) evaluate the O2 release temperatures from Rocknest materials, 2) compare these O2 release temperatures with a series of perchlorates and chlorates, and 3) evaluate superoxide O2- sources and possible perchlorate interactions with other Rocknest phases during QMS analysis.

  7. Boron (B) deprivation increases plasma homocysteine and decreases liver S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH) in rats

    Science.gov (United States)

    The diverse effects of B deprivation suggest that B affects a biomolecule involved in a variety of biochemical reactions. An experiment was conducted to determine whether dietary B affects the liver concentration of SAM, a frequently used enzyme substrate, especially for methylation reactions that y...

  8. Serum TNF-α levels and Helicobacter pylori cagA and vacA genes

    Science.gov (United States)

    Siregar, G. A.; Halim, S.; Sitepu, R. R.; Darmadi

    2018-03-01

    Helicobacter pylori is associated with higher virulence. TNF-α has an important role in host defense against H. pylori infection. The aim of this study was to investigate the relationship between TNF-α serum levels with cagA and vacA genes in H. pylori infection. This was a cross-sectional study involving 80 patients that consecutively admitted to endoscopy unit. Diagnosis of H. pylori infection was based on rapid urease test. Serum samples werecollected to determine circulating TNF-α level. Polymerase chain reaction was done to examine H. pylori vacA and cagA genes. Data analysis was carriedout using SPSS version 22 with 95%CI and p<0.05 was considered statistically significant. About 45 (56.3%) patients infected with Helicobacter pylori. There were 33 (73.3%) patients with H. pylori cagA positive. Serum TNF-α levels in patients with the H. pylori positive were significantly higher compared to H. pylori negative. Serum level of TNF-α was significantly higher in cagA positive than negative. Subjects with H. pylori cagA gene positive were more likely to have ahigher level of serum TNF-α than H. pylori cagA gene negative.

  9. Improving the productivity of S-adenosyl-l-methionine by metabolic engineering in an industrial Saccharomyces cerevisiae strain.

    Science.gov (United States)

    Zhao, Weijun; Hang, Baojian; Zhu, Xiangcheng; Wang, Ri; Shen, Minjie; Huang, Lei; Xu, Zhinan

    2016-10-20

    S-Adenosyl-l-methionine (SAM) is an important metabolite having prominent roles in treating various diseases. In order to improve the production of SAM, the regulation of three metabolic pathways involved in SAM biosynthesis were investigated in an industrial yeast strain ZJU001. GLC3 encoded glycogen-branching enzyme (GBE), SPE2 encoded SAM decarboxylase, as well as ERG4 and ERG6 encoded key enzymes in ergosterol biosynthesis, were knocked out in ZJU001 accordingly. The results indicated that blocking of either glycogen pathway or SAM decarboxylation pathway could improve the SAM accumulation significantly in ZJU001, while single disruption of either ERG4 or ERG6 gene had no obvious effect on SAM production. Moreover, the double mutant ZJU001-GS with deletion of both GLC3 and SPE2 genes was also constructed, which showed further improvement of SAM accumulation. Finally, SAM2 was overexpressed in ZJU001-GS to give the best SAM-producing recombinant strain ZJU001-GS-SAM2, in which 12.47g/L SAM was produced by following our developed pseudo-exponential fed-batch cultivation strategy, about 81.0% increase comparing to its parent strain ZJU001. The present work laid a solid base for large-scale SAM production with the industrial Saccharomyces cerevisiae strain. Copyright © 2016 Elsevier B.V. All rights reserved.

  10. Increasing the fill factor of inverted P3HT:PCBM solar cells through surface modification of Al-doped ZnO via phosphonic acid-anchored C60 SAMs

    Energy Technology Data Exchange (ETDEWEB)

    Stubhan, Tobias [Institute of Materials for Electronics and Energy Technology (I-MEET), Friedrich-Alexander-University, Erlangen-Nuremberg, Erlangen (Germany); Salinas, Michael; Halik, Marcus [Organic Materials and Devices (OMD)-Institute of Polymer Materials, University Erlangen-Nuremberg, Erlangen (Germany); Ebel, Alexander; Hirsch, Andreas [Institute for Organic Chemistry II, Friedrich-Alexander-University, Erlangen-Nuremberg, Erlangen (Germany); Krebs, Frederick C. [Risoe National Laboratory for Sustainable Energy, Technical University of Denmark, Roskilde (Denmark); Brabec, Christoph J. [Institute of Materials for Electronics and Energy Technology (I-MEET), Friedrich-Alexander-University, Erlangen-Nuremberg, Erlangen (Germany); Bavarian Center for Applied Energy Research (ZAE Bayern), Erlangen (Germany)

    2012-05-15

    The influence of aluminum-doped zinc oxide (AZO) electron extraction layers modified with self-assembled monolayers (SAMs) on inverted polymer solar cells is investigated. It is found that AZO modification with phosphonic acid-anchored Fullerene-SAMs leads to a reduction of the series resistance, while increasing the parallel resistance. This results in an increased efficiency from 2.9 to 3.3%. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  11. Gene-specific correlation of RNA and protein levels in human cells and tissues

    DEFF Research Database (Denmark)

    Edfors, Fredrik; Danielsson, Frida; Hallström, Björn M.

    2016-01-01

    An important issue for molecular biology is to establish whether transcript levels of a given gene can be used as proxies for the corresponding protein levels. Here, we have developed a targeted proteomics approach for a set of human non-secreted proteins based on parallel reaction monitoring...... to measure, at steady-state conditions, absolute protein copy numbers across human tissues and cell lines and compared these levels with the corresponding mRNA levels using transcriptomics. The study shows that the transcript and protein levels do not correlate well unless a gene-specific RNA-to-protein (RTP...

  12. Kto samõi bogatõi v Estonii / Sten-Aleks Pihlak, Kärt Blumberg, Lemmi Kann

    Index Scriptorium Estoniae

    Pihlak, Sten-Aleks

    2008-01-01

    Eesti laevatranspordi kolmik - Ain Hanschmidt, Enn Pant ja Kalev Järvelill on Äripäeva rikaste edetabelis esimesed. Viimaste kuude suure aktsiahinnalanguse tõttu on paljud Äripäeva rikaste edetabelis olijad kaotanud igast kolmest kroonist kaks. Artiklis selgitatakse miks on Äripäeva Rikaste TOPis vähe naisi. Lisad: Iz TOP-500 samõhh bogatõhh ljudei v Estonii; Reitingi bogatshei za prezhnije godõ; Metodika

  13. A phase I study of a new polyamine biosynthesis inhibitor, SAM486A, in cancer patients with solid tumours

    NARCIS (Netherlands)

    Paridaens, R; Uges, DRA; Barbet, N; Choi, L; Seeghers, M; van der Graaf, WTA; Groen, HJM; Dumez, H; Van Buuren, [No Value; Muskiet, F; Capdeville, R; van Oosterom, AT; de Vries, EGE

    Because tumour cell proliferation is highly dependent upon up-regulation of de-novo polyamine synthesis, inhibition of the polyamine synthesis pathway represents a potential target for anticancer therapy. SAM486A (CGP 48664) is a new inhibitor of the polyamine biosynthetic enzyme

  14. Relationship of Serum Klotho Level With ACE Gene Polymorphism in Stable Kidney Allograft Recipients.

    Science.gov (United States)

    Zaare Nahandi, Maryam; Ardalan, Mohamad Reza; Banagozar Mohamadi, Ali; Ghorbani Haghjo, Amir; Jabbarpor Bonyadi, Morteza; Mohamadian, Tahere

    2017-03-01

    The kidney is the main source of serum Klotho production. Immunosuppressive agents could affect the kidney in this regard. The effect of the ACE gene polymorphism on Klotho production is a less studied area. This study aimed to assess serum Klotho and ACE gene in a group of stable kidney transplant recipients. In a cross-sectional study, 30 kidney transplant recipients with stable allograft function and 27 healthy young individuals were assessed for their serum Klotho levels. The ACE gene polymorphisms were studied in both groups. Klotho level was higher in kidney transplant recipients than the controls, but the difference was not significant (2.76 ± 2.41 ng/mL versus 2.01 ± 1.41 ng/mL, respectively). In both groups, serum Klotho level was higher in those with the I>I polymorphism, the men, those with higher glomerular filtration rate, and younger individuals, but the differences did not reach a significant level. Higher body mass index was significantly associated with lower serum Klotho level in both groups. Klotho level after kidney transplantation meets the range in healthy individuals, and it is not affected by the ACE gene polymorphism.

  15. Effects of Growth Hormone Gene Polymorphism on Lipogenic Gene Expression Levels in Diaphragm Tissues of Japanese Black Heifers

    Directory of Open Access Journals (Sweden)

    Astrid Ardiyanti

    2012-08-01

    Full Text Available Two SNPs, i.e. L127V and T172M, of bovine growth hormone (GH causing the presence of GH gene haplotypes A, B, and C was previously shown to alter intramuscular fatty acid (FA composition in Japanese Black (JB heifers. To determine the SNP effect on somatotropic hormone concentration and lipogenesis, we measured plasma GH, insulin, and insulin-like growth factor-1 (IGF-1 concentrations. We also measured mRNA levels of fatty acid synthase (FASN, stearoyl-coA desaturase (SCD, and sterol regulatory element binding proteins-1 (SREBP-1 and FA composition in diaphragm tissues. Heifers with genotype CC had the lowest plasma insulin concentration and FASN and SCD mRNA levels among genotypes. FASN mRNA levels in haplotype A tended to positively correlate with saturated FA (SFA content and negatively correlated with C18:2 and unsaturated FA (USFA contents. SCD mRNA levels in haplotype A positively correlated with monounsaturated FA (MUFA contents and negatively correlated with C18:0 content. They also tended to positively correlate with C16:1, C18:1, and USFA contents and USFA/SFA ratio and negatively correlate with SFA content. Taken together, GH gene polymorphism affects the lipogenic genes expression levels and their relationships with fatty acid compositions in diaphragm tissues of JB heifers at 31 months of age.

  16. Characterization of self-assembled monolayers (SAMs) on silicon substrate comparative with polymer substrate for Escherichia coli O157:H7 detection

    International Nuclear Information System (INIS)

    Moldovan, Carmen; Mihailescu, Carmen; Stan, Dana; Ruta, Lavinia; Iosub, Rodica; Gavrila, Raluca; Purica, Munizer; Vasilica, Schiopu

    2009-01-01

    This article presents the characterization of two substrates, silicon and polymer coated with gold, that are functionalized by mixed self-assembled monolayers (SAMs) in order to efficiently immobilize the anti-Escherichia coli O157:H7 polyclonal purified antibody. A biosurface functionalized by SAMs (self-assembled monolayers) technique has been developed. Immobilization of goat anti-E. coli O157:H7 antibody was performed by covalently bonding of thiolate mixed self-assembled monolayers (SAMs) realized on two substrates: polymer coated with gold and silicon coated with gold. The F(ab') 2 fragments of the antibodies have been used for eliminating nonspecific bindings between the Fc portions of antibodies and the Fc receptor on cells. The properties of the monolayers and the biofilm formatted with attached antibody molecules were analyzed at each step using infrared spectroscopy (FTIR-ATR), atomic force microscopy (AFM), scanning electron microscopy (SEM) and cyclic voltammetry (CV). In our study the gold-coated silicon substrates approach yielded the best results. These experimental results revealed the necessity to investigate each stage of the immobilization process taking into account in the same time the factors that influence the chemistry of the surface and the further interactions as well and also provide a solid basis for further studies aiming at elaborating sensitive and specific immunosensor or a microarray for the detection of E. coli O157:H7.

  17. Effect of assembled time on the corrosion behaviors of SAMs film on the AM60B alloy and its assembled mechanism

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Xianbin, E-mail: xbliu@imr.ac.cn; Shan, Dayong; Song, Yingwei; Han, En-hou

    2015-01-15

    The influence of assembled time on the corrosion behaviors of SAMs film on the AM60B alloy and its assembled mechanism have been investigated by electrochemical measurements, scanning electron microscopy (SEM) observation and X-ray photoelectron spectroscopy (XPS) analysis. The self-assembled experiment on the AM60B magnesium alloy indicates that the corrosion susceptibility decreases with increasing assembled time until 24 h on cast AM60B alloy and then increases with increase of the assembled time proved by EIS measurement and potentiodynamic curves. The self-assembled experiments on pure magnesium and various heat treated cast AM60B magnesium alloy illuminate that the dissolved aluminum in magnesium solid solution is the key factor for assembled efficiency and is hard to self-assemble on the pure magnesium without aluminum. The corrosion resistance of self-assembled film on AM60B magnesium alloy is monotonically increasing with the dissolved aluminum. The results of XPS analysis reveal the assembled mechanism on AM60B and corroborate the function of Al element. - Highlights: • It is hard to self-assemble on the pure magnesium. • 24 h assembled film has the low corrosion susceptibility by EIS and polarization. • The corrosion susceptibility of SAMs film lie on the Al atom state in AM60B. • The corrosion susceptibility of SAMs film is decreasing with the dissolved Al.

  18. Effect of assembled time on the corrosion behaviors of SAMs film on the AM60B alloy and its assembled mechanism

    International Nuclear Information System (INIS)

    Liu, Xianbin; Shan, Dayong; Song, Yingwei; Han, En-hou

    2015-01-01

    The influence of assembled time on the corrosion behaviors of SAMs film on the AM60B alloy and its assembled mechanism have been investigated by electrochemical measurements, scanning electron microscopy (SEM) observation and X-ray photoelectron spectroscopy (XPS) analysis. The self-assembled experiment on the AM60B magnesium alloy indicates that the corrosion susceptibility decreases with increasing assembled time until 24 h on cast AM60B alloy and then increases with increase of the assembled time proved by EIS measurement and potentiodynamic curves. The self-assembled experiments on pure magnesium and various heat treated cast AM60B magnesium alloy illuminate that the dissolved aluminum in magnesium solid solution is the key factor for assembled efficiency and is hard to self-assemble on the pure magnesium without aluminum. The corrosion resistance of self-assembled film on AM60B magnesium alloy is monotonically increasing with the dissolved aluminum. The results of XPS analysis reveal the assembled mechanism on AM60B and corroborate the function of Al element. - Highlights: • It is hard to self-assemble on the pure magnesium. • 24 h assembled film has the low corrosion susceptibility by EIS and polarization. • The corrosion susceptibility of SAMs film lie on the Al atom state in AM60B. • The corrosion susceptibility of SAMs film is decreasing with the dissolved Al

  19. Characterization of self-assembled monolayers (SAMs) on silicon substrate comparative with polymer substrate for Escherichia coli O157:H7 detection

    Energy Technology Data Exchange (ETDEWEB)

    Moldovan, Carmen, E-mail: carmen.moldovan@imt.ro [National Institute for R and D in Microtechnologies, IMT-Bucharest, 126A Erou Iancu Nicolae, 077190 Bucharest (Romania); Mihailescu, Carmen, E-mail: carmen_mihail28@yahoo.com [University of Bucharest, 90-92 Sos Panduri, Bucharest (Romania); Stan, Dana, E-mail: dana_stan2005@yahoo.com [DDS Diagnostic, 1 Segovia Street, Bucharest (Romania); Ruta, Lavinia, E-mail: laviniacoco@yahoo.com [University of Bucharest, 90-92 Sos Panduri, Bucharest (Romania); Iosub, Rodica, E-mail: rodica.iosub@imt.ro [National Institute for R and D in Microtechnologies, IMT-Bucharest, 126A Erou Iancu Nicolae, 077190 Bucharest (Romania); Gavrila, Raluca, E-mail: raluca.gavrila@imt.ro [National Institute for R and D in Microtechnologies, IMT-Bucharest, 126A Erou Iancu Nicolae, 077190 Bucharest (Romania); Purica, Munizer, E-mail: munizer.purica@imt.ro [National Institute for R and D in Microtechnologies, IMT-Bucharest, 126A Erou Iancu Nicolae, 077190 Bucharest (Romania); Vasilica, Schiopu, E-mail: vasilica.schiopu@imt.ro [National Institute for R and D in Microtechnologies, IMT-Bucharest, 126A Erou Iancu Nicolae, 077190 Bucharest (Romania)

    2009-08-30

    This article presents the characterization of two substrates, silicon and polymer coated with gold, that are functionalized by mixed self-assembled monolayers (SAMs) in order to efficiently immobilize the anti-Escherichia coli O157:H7 polyclonal purified antibody. A biosurface functionalized by SAMs (self-assembled monolayers) technique has been developed. Immobilization of goat anti-E. coli O157:H7 antibody was performed by covalently bonding of thiolate mixed self-assembled monolayers (SAMs) realized on two substrates: polymer coated with gold and silicon coated with gold. The F(ab'){sub 2} fragments of the antibodies have been used for eliminating nonspecific bindings between the Fc portions of antibodies and the Fc receptor on cells. The properties of the monolayers and the biofilm formatted with attached antibody molecules were analyzed at each step using infrared spectroscopy (FTIR-ATR), atomic force microscopy (AFM), scanning electron microscopy (SEM) and cyclic voltammetry (CV). In our study the gold-coated silicon substrates approach yielded the best results. These experimental results revealed the necessity to investigate each stage of the immobilization process taking into account in the same time the factors that influence the chemistry of the surface and the further interactions as well and also provide a solid basis for further studies aiming at elaborating sensitive and specific immunosensor or a microarray for the detection of E. coli O157:H7.

  20. Simultaneous determination of four active components in Alisma orientale (Sam. Juz. by HPLC–DAD using a single reference standard

    Directory of Open Access Journals (Sweden)

    Yao-Wen Zhang

    2015-04-01

    Full Text Available A rapid, simple and practical high-performance liquid chromatography method coupled with diode array detector (HPLC–DAD was developed to evaluate the quality of Alisma orientale (Sam. Juz. through a simultaneous determination of four major active triterpenes using a single standard to determine the multi-components (SSDMCs. Alisol B 23-acetate was selected as the reference compound for calculating the relative response factors. All calibration curves showed good linearity (R2>0.9998 within test ranges. RSDs for intra- and inter-day of four analytes were less than 3.6% and 2.3%; the overall recovery was 92.1–110.2% (SSDMC. The proposed method was successfully applied to quantify the four components in 20 samples from different localities in China. Moreover, significant variations were demonstrated in the content of these compounds. In addition, hierarchical clustering analysis (HCA and principal components analysis (PCA were performed to differentiate and classify the samples based on the contents of Alisol C 23-acetate, Alisol A, Alisol A 24-acetate and Alisol B 23-acetate. This simple, rapid, low-cost and reliable HPLC–DAD method using SSDMC is suitable for routine quantitative analysis and quality control of A. orientale (Sam. Juz. Keywords: SSDMC, Alisma orientale (Sam. Juz, Quality control, HCA, PCA

  1. Potential Precursor Compounds for Chlorohydrocarbons Detected in Gale Crater, Mars, by the SAM Instrument Suite on the Curiosity Rover

    Science.gov (United States)

    Miller, Kristen E.; Eigenbrode, Jennifer L.; Freissinet, Caroline; Glavin, Daniel P.; Kotrc, Benjamin; Francois, Pascaline; Summons, Roger E.

    2016-01-01

    The detection of chlorinated organic compounds in near-surface sedimentary rocks by the Sample Analysis at Mars (SAM) instrument suite aboard the Mars Science Laboratory Curiosity rover represents an important step toward characterizing habitable environments on Mars. However, this discovery also raises questions about the identity and source of their precursor compounds and the processes by which they become chlorinated. Here we present the results of analog experiments, conducted under conditions similar to SAM gas chromatography-mass spectrometry analyses, in which we pyrolyzed potential precursor compounds in the presence of various Cl salts and Fe oxides that have been identified in Martian sediments. While chloromethanes could not be unambiguously identified, 1,2-dichloropropane (1,2-DCP), which is one of the chlorinated compounds identified in SAM data, is formed from the chlorination of aliphatic precursors. Additionally, propanol produced more 1,2-DCP than nonfunctionalized aliphatics such as propane or hexanes. Chlorinated benzenes ranging from chlorobenzene to hexachlorobenzene were identified in experiments with benzene carboxylic acids but not with benzene or toluene. Lastly, the distribution of chlorinated benzenes depended on both the substrate species and the nature and concentration of the Cl salt. Ca and Mg perchlorate, both of which release O2 in addition to Cl2 and HCl upon pyrolysis, formed less chlorobenzene relative to the sum of all chlorinated benzenes than in experiments with ferric chloride. FeCl3, a Lewis acid, catalyzes chlorination but does not aid combustion. Accordingly, both the precursor chemistry and sample mineralogy exert important controls on the distribution of chlorinated organics.

  2. Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer

    Science.gov (United States)

    Pearson, T.; Giffard, P.; Beckstrom-Sternberg, S.; Auerbach, R.; Hornstra, H.; Tuanyok, A.; Price, E.P.; Glass, M.B.; Leadem, B.; Beckstrom-Sternberg, J. S.; Allan, G.J.; Foster, J.T.; Wagner, D.M.; Okinaka, R.T.; Sim, S.H.; Pearson, O.; Wu, Z.; Chang, J.; Kaul, R.; Hoffmaster, A.R.; Brettin, T.S.; Robison, R.A.; Mayo, M.; Gee, J.E.; Tan, P.; Currie, B.J.; Keim, P.

    2009-01-01

    Background: Phylogeographic reconstruction of some bacterial populations is hindered by low diversity coupled with high levels of lateral gene transfer. A comparison of recombination levels and diversity at seven housekeeping genes for eleven bacterial species, most of which are commonly cited as having high levels of lateral gene transfer shows that the relative contributions of homologous recombination versus mutation for Burkholderia pseudomallei is over two times higher than for Streptococcus pneumoniae and is thus the highest value yet reported in bacteria. Despite the potential for homologous recombination to increase diversity, B. pseudomallei exhibits a relative lack of diversity at these loci. In these situations, whole genome genotyping of orthologous shared single nucleotide polymorphism loci, discovered using next generation sequencing technologies, can provide very large data sets capable of estimating core phylogenetic relationships. We compared and searched 43 whole genome sequences of B. pseudomallei and its closest relatives for single nucleotide polymorphisms in orthologous shared regions to use in phylogenetic reconstruction. Results: Bayesian phylogenetic analyses of >14,000 single nucleotide polymorphisms yielded completely resolved trees for these 43 strains with high levels of statistical support. These results enable a better understanding of a separate analysis of population differentiation among >1,700 B. pseudomallei isolates as defined by sequence data from seven housekeeping genes. We analyzed this larger data set for population structure and allele sharing that can be attributed to lateral gene transfer. Our results suggest that despite an almost panmictic population, we can detect two distinct populations of B. pseudomallei that conform to biogeographic patterns found in many plant and animal species. That is, separation along Wallace's Line, a biogeographic boundary between Southeast Asia and Australia. Conclusion: We describe an

  3. Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer

    Directory of Open Access Journals (Sweden)

    Kaul Rajinder

    2009-11-01

    Full Text Available Abstract Background Phylogeographic reconstruction of some bacterial populations is hindered by low diversity coupled with high levels of lateral gene transfer. A comparison of recombination levels and diversity at seven housekeeping genes for eleven bacterial species, most of which are commonly cited as having high levels of lateral gene transfer shows that the relative contributions of homologous recombination versus mutation for Burkholderia pseudomallei is over two times higher than for Streptococcus pneumoniae and is thus the highest value yet reported in bacteria. Despite the potential for homologous recombination to increase diversity, B. pseudomallei exhibits a relative lack of diversity at these loci. In these situations, whole genome genotyping of orthologous shared single nucleotide polymorphism loci, discovered using next generation sequencing technologies, can provide very large data sets capable of estimating core phylogenetic relationships. We compared and searched 43 whole genome sequences of B. pseudomallei and its closest relatives for single nucleotide polymorphisms in orthologous shared regions to use in phylogenetic reconstruction. Results Bayesian phylogenetic analyses of >14,000 single nucleotide polymorphisms yielded completely resolved trees for these 43 strains with high levels of statistical support. These results enable a better understanding of a separate analysis of population differentiation among >1,700 B. pseudomallei isolates as defined by sequence data from seven housekeeping genes. We analyzed this larger data set for population structure and allele sharing that can be attributed to lateral gene transfer. Our results suggest that despite an almost panmictic population, we can detect two distinct populations of B. pseudomallei that conform to biogeographic patterns found in many plant and animal species. That is, separation along Wallace's Line, a biogeographic boundary between Southeast Asia and Australia

  4. Reflections on the individual–collective relation in change agency formation in the Samsø renewable energy island project

    DEFF Research Database (Denmark)

    Carlsson, Monica Susanne

    2018-01-01

    This paper offers reflections on change agency formation in the Renewable Energy Island (REI) project on Samsø, following a field visit to the island in June 2016. Both individual and collective agency are set out as central for the processes leading to the change in the REI project, spurring ref...

  5. High sequence variations in the region containing genes encoding a cellular morphogenesis protein and the repressor of sexual development help to reveal origins of Aspergillus oryzae.

    Science.gov (United States)

    Chang, Perng-Kuang; Scharfenstein, Leslie L; Solorzano, Cesar D; Abbas, Hamed K; Hua, Sui-Sheng T; Jones, Walker A; Zablotowicz, Robert M

    2015-05-04

    Aspergillus oryzae and Aspergillus flavus are closely related fungal species. The A. flavus morphotype that produces numerous small sclerotia (S strain) and aflatoxin has a unique 1.5 kb deletion in the norB-cypA region of the aflatoxin gene cluster (i.e. the S genotype). Phylogenetic studies have indicated that an isolate of the nonaflatoxigenic A. flavus with the S genotype is the ancestor of A. oryzae. Genome sequence comparison between A. flavus NRRL3357, which produces large sclerotia (L strain), and S-strain A. flavus 70S identified a region (samA-rosA) that was highly variable in the two morphotypes. A third type of samA-rosA region was found in A. oryzae RIB40. The three samA-rosA types were later revealed to be commonly present in A. flavus L-strain populations. Of the 182 L-strain A. flavus field isolates examined, 46%, 15% and 39% had the samA-rosA type of NRRL3357, 70S and RIB40, respectively. The three types also were found in 18 S-strain A. flavus isolates with different proportions. For A. oryzae, however, the majority (80%) of the 16 strains examined had the RIB40 type and none had the NRRL3357 type. The results suggested that A. oryzae strains in the current culture collections were mostly derived from the samA-rosA/RIB40 lineage of the nonaflatoxigenic A. flavus with the S genotype. Published by Elsevier B.V.

  6. Effect of the Presence of Chlorates and Perchlorates on the Pyrolysis of Organic Compounds: Implications for Measurements Done with the SAM Experiment Onboard the Curiosity Rover

    Science.gov (United States)

    Millan, M.; Szopa, C.; Buch, A.; Belmahdi, I.; Coll, P.; Glavin, D. P.; Freissinet, C.; Archer, P. D., Jr.; Sutter, B.; Summons, R. E.; hide

    2016-01-01

    The Mars Science Laboratory (MSL) Curiosity Rover carries a suite of instruments, one of which is the Sample Analysis at Mars (SAM) experiment. SAM is devoted to the in situ molecular analysis of gases evolving from solid samples collected by Curiosity on Mars surface/sub-surface. Among its three analytical devices, SAM has a gaschromatograph coupled to a quadrupole mass spectrometer (GC-QMS). The GC-QMS is devoted to the separation and identification of organic and inorganic material. Before proceeding to the GC-QMS analysis, the solid sample collected by Curiosity is subjected to a thermal treatment thanks to the pyrolysis oven to release the volatiles into the gas processing system. Depending on the sample, a derivatization method by wet chemistry: MTBSTFA of TMAH can also be applied to analyze the most refractory compounds. The GC is able to separate the organic molecules which are then detected and identified by the QMS (Figure 1). For the second time after the Viking landers in 1976, SAM detected chlorinated organic compounds with the pyrolysis GC-QMS experiment. The detection of perchlorates salts (ClO4-) in soil at the Phoenix Landing site suggests that the chlorohydrocarbons detected could come from the reaction of organics with oxychlorines. Indeed, laboratory pyrolysis experiments have demonstrated that oxychlorines decomposed into molecular oxygen and volatile chlorine (HCl and/or Cl2) when heated which then react with the organic matter in the solid samples by oxidation and/or chlorination processes.

  7. Microbial Habitability in Gale Crater: Sample Analysis at Mars (SAM) Instrument Detection of Microbial Essential Carbon and Nitrogen

    Science.gov (United States)

    Sutter, B.; Ming, D. W.; Eigenbrode, J. E.; Steele, A.; Stern, J. C.; Gonzalez, R. N.; McAdam, A. C.; Mahaffy, P. R.

    2016-01-01

    Chemical analyses of Mars soils and sediments from previous landed missions have demonstrated that Mars surface materials possessed major (e.g., P, K, Ca, Mg, S) and minor (e.g., Fe, Mn, Zn, Ni, Cl) elements essential to support microbial life. However, the detection of microbial essential organic-carbon (C) and nitrate have been more elusive until the Mars Science Laboratory (MSL) rover mission. Nitrate and organic-C in Gale Crater, Mars have been detected by the Sample Analysis at Mars (SAM) instrument onboard the MSL Curiosity rover. Eolian fines and drilled sedimentary rock samples were heated in the SAM oven from approximately 30 to 860 degrees Centigrade where evolved gases (e.g., nitrous oxide (NO) and CO2) were released and analyzed by SAM’s quadrupole mass spectrometer (MS). The temperatures of evolved NO was assigned to nitrate while evolved CO2 was assigned to organic-C and carbonate. The CO2 releases in several samples occurred below 450 degrees Centigrade suggesting organic-C dominated in those samples. As much as 7 micromoles NO3-N per gram and 200 micromoles CO2-C per gram have been detected in the Gale Crater materials. These N and C levels coupled with assumed microbial biomass (9 x 10 (sup -7) micrograms per cell) C (0.5 micrograms C per micrograms cell) and N (0.14 micrograms N per micrograms cell) requirements, suggests that less than 1 percent and less than 10 percent of Gale Crater C and N, respectively, would be required if available, to accommodate biomass requirements of 1 by 10 (sup 5) cells per gram sediment. While nitrogen is the limiting nutrient, the potential exists that sufficient N and organic-C were present to support limited heterotrophic microbial populations that may have existed on ancient Mars.

  8. Influence of the solution pH in the 6-mercaptopurine self-assembled monolayer (6MP-SAM) on a Au(111) single-crystal electrode.

    Science.gov (United States)

    Madueño, Rafael; García-Raya, Daniel; Viudez, Alfonso J; Sevilla, José M; Pineda, Teresa; Blázquez, Manuel

    2007-10-23

    Self-assembled monolayers (SAMs) of 6-mercaptopurine (6MP) have been prepared on a Au(111) single-crystal electrode by immersion of the metal surface in a 100 microM 6MP and 0.01 M HClO4 solution. The 6MP-SAM Au(111) single-crystal electrodes were transferred to the cell and allowed to equilibrate with the different aqueous working solutions before the electrochemical experiments. The influence of the solution pH was studied by cyclic voltammetry, double layer capacitance curves, and electrochemical impedance spectroscopy. The electrochemical behavior of the 6MP-SAM in acetic acid at pH 4 presents important differences in comparison to that obtained in 0.1 M KOH solutions. Cyclic voltammograms for the reductive desorption process in acid medium are broad and show some features that can be explained by a phase transition between a chemisorbed and a physisorbed state of the 6MP molecules. The low solubility of these molecules in acid medium could explain this phenomenon and the readsorption of the complete monolayer when the potential is scanned in the positive direction. The variation of the double-layer capacitance values in the potential range of monolayer stability with the pH suggests that the acid-base chemistry of the 6MP molecules is playing a role. This fact has been studied by following the variations of the electron-transfer rate constant of the highly charged redox probes as are Fe(CN)(6)-3/-4 and Ru(NH3)(6)+3/+2 as a function of solution pH. The apparent surface pKa value for the 6MP-SAM (pKa approximately 8) is explained by the total conversion of the different 6MP tautomers that exist in solution to the thiol species in the adsorbed state.

  9. Sample Analysis at Mars (SAM) and Mars Organic Molecule Analyzer (MOMA) as Critical In Situ Investigation for Targeting Mars Returned Samples

    Science.gov (United States)

    Freissinet, C.; Glavin, D. P.; Mahaffy, P. R.; Szopa, C.; Buch, A.; Goesmann, F.; Goetz, W.; Raulin, F.; SAM Science Team; MOMA Science Team

    2018-04-01

    SAM (Curiosity) and MOMA (ExoMars) Mars instruments, seeking for organics and biosignatures, are essential to establish taphonomic windows of preservation of molecules, in order to target the most interesting samples to return from Mars.

  10. Experimental Hyperthyroidism Decreases Gene Expression and Serum Levels of Adipokines in Obesity

    Directory of Open Access Journals (Sweden)

    Renata de Azevedo Melo Luvizotto

    2012-01-01

    Full Text Available Aims. To analyze the influence of hyperthyroidism on the gene expression and serum concentration of leptin, resistin, and adiponectin in obese animals. Main Methods. Male Wistar rats were randomly divided into two groups: control (C—fed with commercial chow ad libitum—and obese (OB—fed with a hypercaloric diet. After group characterization, the OB rats continued receiving a hypercaloric diet and were randomized into two groups: obese animals (OB and obese with 25 μg triiodothyronine (T3/100 BW (OT. The T3 dose was administered every day for the last 2 weeks of the study. After 30 weeks the animals were euthanized. Samples of blood and adipose tissue were collected for biochemical and hormonal analyses as well as gene expression of leptin, resistin, and adiponectin. Results. T3 treatment was effective, increasing fT3 levels and decreasing fT4 and TSH serum concentration. Administration of T3 promotes weight loss, decreases all fat deposits, and diminishes serum levels of leptin, resistin, and adiponectin by reducing their gene expression. Conclusions. Our results suggest that T3 modulate serum and gene expression levels of leptin, resistin, and adiponectin in experimental model of obesity, providing new insights regarding the relationship between T3 and adipokines in obesity.

  11. Experimental hyperthyroidism decreases gene expression and serum levels of adipokines in obesity.

    Science.gov (United States)

    Luvizotto, Renata de Azevedo Melo; do Nascimento, André Ferreira; de Síbio, Maria Teresa; Olímpio, Regiane Marques Castro; Conde, Sandro José; Lima-Leopoldo, Ana Paula; Leopoldo, André Soares; Cicogna, Antonio Carlos; Nogueira, Célia Regina

    2012-01-01

    To analyze the influence of hyperthyroidism on the gene expression and serum concentration of leptin, resistin, and adiponectin in obese animals. Male Wistar rats were randomly divided into two groups: control (C)-fed with commercial chow ad libitum-and obese (OB)-fed with a hypercaloric diet. After group characterization, the OB rats continued receiving a hypercaloric diet and were randomized into two groups: obese animals (OB) and obese with 25 μg triiodothyronine (T(3))/100 BW (OT). The T(3) dose was administered every day for the last 2 weeks of the study. After 30 weeks the animals were euthanized. Samples of blood and adipose tissue were collected for biochemical and hormonal analyses as well as gene expression of leptin, resistin, and adiponectin. T(3) treatment was effective, increasing fT(3) levels and decreasing fT(4) and TSH serum concentration. Administration of T(3) promotes weight loss, decreases all fat deposits, and diminishes serum levels of leptin, resistin, and adiponectin by reducing their gene expression. Our results suggest that T(3) modulate serum and gene expression levels of leptin, resistin, and adiponectin in experimental model of obesity, providing new insights regarding the relationship between T(3) and adipokines in obesity.

  12. Chemical imaging of structured SAMs with a novel SFG microscope

    Science.gov (United States)

    Hoffmann, Dominik M. P.; Kuhnke, Klaus; Kern, Klaus

    2002-11-01

    We present a newly developed microscope for sum frequency generation (SFG) imaging of opaque and reflecting interfaces. The sample is viewed at an angle of 60° with respect to the surface normal in order to increase the collected SFG intensity. Our setup is designed to keep the whole field of view (FOV) in focus and to compensate for the distortion usually related to oblique imaging by means of a blazed grating. The separation of the SFG intensity and the reflected visible beam is accomplished by a suitable combination of spectral filters. The sum frequency microscope (SFM) is capable of in-situ chemically selective imaging by tuning the IR-beam to vibrational transitions of the respective molecules. The SFM is applied to imaging of structured self-assembled monolayers (SAM) of thiol molecules on a gold surface.

  13. Stool frequency recording in severe acute malnutrition ('StoolSAM'); an agreement study comparing maternal recall versus direct observation using diapers

    NARCIS (Netherlands)

    Voskuijl, Wieger; Potani, Isabel; Bandsma, Robert; Baan, Anne; White, Sarah; Bourdon, Celine; Kerac, Marko

    2017-01-01

    Background: Approximately 50% of the deaths of children under the age of 5 can be attributed to undernutrition, which also encompasses severe acute malnutrition (SAM). Diarrhoea is strongly associated with these deaths and is commonly diagnosed solely based on stool frequency and consistency

  14. Serum Homocysteine, Vitamin B12, Folic Acid Levels and Methylenetetrahydrofolate Reductase (MTHFR) Gene Polymorphism in Vitiligo

    Science.gov (United States)

    Yasar, Ali; Gunduz, Kamer; Onur, Ece; Calkan, Mehmet

    2012-01-01

    The aim of this study was to determine serum vitamin B12, folic acid and homocysteine (Hcy) levels as well as MTHFR (C677, A1298C) gene polymorphisms in patients with vitiligo, and to compare the results with healthy controls. Forty patients with vitiligo and 40 age and sex matched healthy subjects were studied. Serum vitamin B12 and folate levels were determined by enzyme-linked immunosorbent assay. Plasma Hcy levels and MTHFR polymorphisms were determined by chemiluminescence and real time PCR methods, respectively. Mean serum vitamin B12 and Hcy levels were not significantly different while folic acid levels were significantly lower in the control group. There was no significant relationship between disease activity and vitamin B12, folic acid and homocystein levels. No significant difference in C677T gene polymorphism was detected. Heterozygote A1298C gene polymorphism in the patient group was statistically higher than the control group. There was no significant relationship between MTHFR gene polymorphisms and vitamin B12, folic acid and homocysteine levels. In conclusion, vitamin B12, folate and Hcy levels are not altered in vitiligo and MTHFR gene mutations (C677T and A1298C) do not seem to create susceptibility for vitiligo. PMID:22846211

  15. Serum Homocysteine, Vitamin B12, Folic Acid Levels and Methylenetetrahydrofolate Reductase (MTHFR Gene Polymorphism in Vitiligo

    Directory of Open Access Journals (Sweden)

    Ali Yasar

    2012-01-01

    Full Text Available The aim of this study was to determine serum vitamin B12, folic acid and homocysteine (Hcy levels as well as MTHFR (C677, A1298C gene polymorphisms in patients with vitiligo, and to compare the results with healthy controls. Forty patients with vitiligo and 40 age and sex matched healthy subjects were studied. Serum vitamin B12 and folate levels were determined by enzyme-linked immunosorbent assay. Plasma Hcy levels and MTHFR polymorphisms were determined by chemiluminescence and real time PCR methods, respectively. Mean serum vitamin B12 and Hcy levels were not significantly different while folic acid levels were significantly lower in the control group. There was no significant relationship between disease activity and vitamin B12, folic acid and homocystein levels. No significant difference in C677T gene polymorphism was detected. Heterozygote A1298C gene polymorphism in the patient group was statistically higher than the control group. There was no significant relationship between MTHFR gene polymorphisms and vitamin B12, folic acid and homocysteine levels. In conclusion, vitamin B12, folate and Hcy levels are not altered in vitiligo and MTHFR gene mutations (C677T and A1298C do not seem to create susceptibility for vitiligo.

  16. Efecto de la polietilenimina en la actividad catalítica de la peroxidasa de rábano (horseradish peroxidase inmovilizada en electrodos de oro modificados con monocapas autoensambladas de tioles (SAMs.

    Directory of Open Access Journals (Sweden)

    Pedro R. Matheus

    2009-05-01

    Full Text Available Effect of the Polyethyleneimine in the Activity Catalytic of the horseradish peroxidase Immobilized on Gold Electrodes Modified with a Self-assembled Monolayer of Thiols (SAMs. Studies were conducted bycyclic voltammetry (CV to investigate the effect of the polymer polyethyleneimine (PEI in the electrochemical reversibility of the mediator thionine and thus the catalytic activity of the enzyme horseradish peroxidase of recombinant HRP-NHis (horseradish peroxidase to the has been added to a chain of six histidine in the extreme N-terminal protein. This self produced monolayers of thiols (SAMS on gold electrodes, with chemical modifications obtained through successive stages in the solid phase of the electrode. The gold electrodes were modified with monolayer SAM-TOA-[ANTA/DADOO] -Co2+ [SAM: self-assembled monolayers of thiols, TOA: dithioctic acid, ANTA: nitrilotriacetic acid, DADOO: 1,8-diamino-3,6-dioxa octane]. The results showed that the presence of the polymer improves the electrochemical reversibility of the mediator to endure catalyticcurrents as high as those that are obtained with molar ratios ANTA:DADOO 10:1 in the absence of PEI, and improve the response voltammetric obtained.

  17. Diversity of the Genes Implicated in Algerian Patients Affected by Usher Syndrome.

    Science.gov (United States)

    Abdi, Samia; Bahloul, Amel; Behlouli, Asma; Hardelin, Jean-Pierre; Makrelouf, Mohamed; Boudjelida, Kamel; Louha, Malek; Cheknene, Ahmed; Belouni, Rachid; Rous, Yahia; Merad, Zahida; Selmane, Djamel; Hasbelaoui, Mokhtar; Bonnet, Crystel; Zenati, Akila; Petit, Christine

    2016-01-01

    Usher syndrome (USH) is an autosomal recessive disorder characterized by a dual sensory impairment affecting hearing and vision. USH is clinically and genetically heterogeneous. Ten different causal genes have been reported. We studied the molecular bases of the disease in 18 unrelated Algerian patients by targeted-exome sequencing, and identified the causal biallelic mutations in all of them: 16 patients carried the mutations at the homozygous state and 2 at the compound heterozygous state. Nine of the 17 different mutations detected in MYO7A (1 of 5 mutations), CDH23 (4 of 7 mutations), PCDH15 (1 mutation), USH1C (1 mutation), USH1G (1 mutation), and USH2A (1 of 2 mutations), had not been previously reported. The deleterious consequences of a missense mutation of CDH23 (p.Asp1501Asn) and the in-frame single codon deletion in USH1G (p.Ala397del) on the corresponding proteins were predicted from the solved 3D-structures of extracellular cadherin (EC) domains of cadherin-23 and the sterile alpha motif (SAM) domain of USH1G/sans, respectively. In addition, we were able to show that the USH1G mutation is likely to affect the binding interface between the SAM domain and USH1C/harmonin. This should spur the use of 3D-structures, not only of isolated protein domains, but also of protein-protein interaction interfaces, to predict the functional impact of mutations detected in the USH genes.

  18. Siðfræði og fagmennska í heimi fáránleikans: Um siðrof og útlaga í kvikmynd Sams Peckinpahs The Wild Bunch

    Directory of Open Access Journals (Sweden)

    Þórólfur Þórlíndsson

    2012-10-01

    Full Text Available Sam Peckinpah’s movie The Wild Bunch is a multilevel drama about an aging group of outlaws, trying to exist in a rapidly changing world. This paper analysis the movie from different sociological perspectives on three levels. First, it is argued that the movie provides an interesting example and an elaboration of Durkheim’s macrolevel theory of anomie. Second, at the micro level the movie describes the face to face interaction between gangmembers in terms of a symbolic interactionism in the tradition of Mead and Goffman. Third, at the individual level the gangmembers behave in many ways as existential heroes. These different levels of social science analysis come together to form a single coherent story line in Peckinpah’s complex portrayal of the Wild Bunch.

  19. GoSam 2.0. Automated one loop calculations within and beyond the standard model

    International Nuclear Information System (INIS)

    Greiner, Nicolas; Deutsches Elektronen-Synchrotron

    2014-10-01

    We present GoSam 2.0, a fully automated framework for the generation and evaluation of one loop amplitudes in multi leg processes. The new version offers numerous improvements both on generational aspects as well as on the reduction side. This leads to a faster and more stable code for calculations within and beyond the Standard Model. Furthermore it contains the extended version of the standardized interface to Monte Carlo programs which allows for an easy combination with other existing tools. We briefly describe the conceptual innovations and present some phenomenological results.

  20. Isolation and Molecular Characterization of Two Lectins from Dwarf Elder (Sambucus ebulus L. Blossoms Related to the Sam n1 Allergen

    Directory of Open Access Journals (Sweden)

    Tomas Girbes

    2013-10-01

    Full Text Available Sambucus species contain a number of lectins with and without antiribosomal activity. Here, we show that dwarf elder (Sambucus ebulus L. blossoms express two D-galactose-binding lectins that were isolated and purified by affinity chromatography and gel filtration. These proteins, which we named ebulin blo (A-B toxin and SELblo (B-B lectin—blo from blossoms—were subjected to molecular characterization and analysis by MALDI-TOF mass spectrometry and tryptic peptide fingerprinting. Both lectins share a high degree of amino acid sequence homology with Sambucus lectins related to the Sam n1 allergen. Ebulin blo, but not SELblo, was highly toxic by nasal instillation to mice. Overall, our results suggested that both lectins would belong to an allergen family exemplified by Sam n1 and could trigger allergy responses. Furthermore, they raise a concern about ebulin blo toxicity.

  1. Fluorocarbon Contamination from the Drill on the Mars Science Laboratory: Potential Science Impact on Detecting Martian Organics by Sample Analysis at Mars (SAM)

    Science.gov (United States)

    Eigenbrode, J. L.; McAdam, A.; Franz, H.; Freissinet, C.; Bower, H.; Floyd, M.; Conrad, P.; Mahaffy, P.; Feldman, J.; Hurowitz, J.; hide

    2013-01-01

    Polytetrafluoroethylene (PTFE or trade name: Teflon by Dupont Co.) has been detected in rocks drilled during terrestrial testing of the Mars Science Laboratory (MSL) drilling hardware. The PTFE in sediments is a wear product of the seals used in the Drill Bit Assemblies (DBAs). It is expected that the drill assembly on the MSL flight model will also shed Teflon particles into drilled samples. One of the primary goals of the Sample Analysis at Mars (SAM) instrument suite on MSL is to test for the presence of martian organics in samples. Complications introduced by the potential presence of PTFE in drilled samples to the SAM evolved gas analysis (EGA or pyrolysisquadrupole mass spectrometry, pyr-QMS) and pyrolysis- gas chromatography mass spectrometry (Pyr- GCMS) experiments was investigated.

  2. Granular statistical mechanics - Building on the legacy of Sir Sam Edwards

    Science.gov (United States)

    Blumenfeld, Raphael

    When Sir Sam Edwards laid down the foundations for the statistical mechanics of jammed granular materials he opened a new field in soft condensed matter and many followed. In this presentation we review briefly the Edwards formalism and some of its less discussed consequences. We point out that the formalism is useful for other classes of systems - cellular and porous materials. A certain shortcoming of the original formalism is then discussed and a modification to overcome it is proposed. Finally, a derivation of an equation of state with the new formalism is presented; the equation of state is analogous to the PVT relation for thermal gases, relating the volume, the boundary stress and measures of the structural and stress fluctuations. NUDT, Changsha, China, Imperial College London, UK, Cambridge University, UK.

  3. Radical SAM, A Novel Protein Superfamily Linking Unresolved Steps in Familiar Biosynthetic Pathways with Radical Mechanisms: Functional Characterization Using New Analysis and Information Visualization Methods

    Energy Technology Data Exchange (ETDEWEB)

    Sofia, Heidi J.; Chen, Guang; Hetzler, Elizabeth G.; Reyes Spindola, Jorge F.; Miller, Nancy E.

    2001-03-01

    A large protein superfamily with over 500 members has been discovered and analyzed using powerful new bioinformatics and information visualization methods. Evidence exists that these proteins generate a 5?-deoxyadenosyl radical by reductive cleavage of S-adenosylmethionine (SAM) through an unusual Fe-S center. Radical SAM superfamily proteins function in DNA precursor, vitamin, cofactor, antibiotic, and herbicide biosynthesis in a collection of basic and familiar pathways. One of the members is interferon-inducible and is considered a candidate drug target for osteoporosis. The identification of this superfamily suggests that radical-based catalysis is important in a number of previously well-studied but unresolved biochemical pathways.

  4. Genome-wide methylation analysis identifies a core set of hypermethylated genes in CIMP-H colorectal cancer.

    Science.gov (United States)

    McInnes, Tyler; Zou, Donghui; Rao, Dasari S; Munro, Francesca M; Phillips, Vicky L; McCall, John L; Black, Michael A; Reeve, Anthony E; Guilford, Parry J

    2017-03-28

    Aberrant DNA methylation profiles are a characteristic of all known cancer types, epitomized by the CpG island methylator phenotype (CIMP) in colorectal cancer (CRC). Hypermethylation has been observed at CpG islands throughout the genome, but it is unclear which factors determine whether an individual island becomes methylated in cancer. DNA methylation in CRC was analysed using the Illumina HumanMethylation450K array. Differentially methylated loci were identified using Significance Analysis of Microarrays (SAM) and the Wilcoxon Signed Rank (WSR) test. Unsupervised hierarchical clustering was used to identify methylation subtypes in CRC. In this study we characterized the DNA methylation profiles of 94 CRC tissues and their matched normal counterparts. Consistent with previous studies, unsupervized hierarchical clustering of genome-wide methylation data identified three subtypes within the tumour samples, designated CIMP-H, CIMP-L and CIMP-N, that showed high, low and very low methylation levels, respectively. Differential methylation between normal and tumour samples was analysed at the individual CpG level, and at the gene level. The distribution of hypermethylation in CIMP-N tumours showed high inter-tumour variability and appeared to be highly stochastic in nature, whereas CIMP-H tumours exhibited consistent hypermethylation at a subset of genes, in addition to a highly variable background of hypermethylated genes. EYA4, TFPI2 and TLX1 were hypermethylated in more than 90% of all tumours examined. One-hundred thirty-two genes were hypermethylated in 100% of CIMP-H tumours studied and these were highly enriched for functions relating to skeletal system development (Bonferroni adjusted p value =2.88E-15), segment specification (adjusted p value =9.62E-11), embryonic development (adjusted p value =1.52E-04), mesoderm development (adjusted p value =1.14E-20), and ectoderm development (adjusted p value =7.94E-16). Our genome-wide characterization of DNA

  5. The effects of laughter on post-prandial glucose levels and gene expression in type 2 diabetic patients.

    Science.gov (United States)

    Hayashi, Takashi; Murakami, Kazuo

    2009-07-31

    This report mainly summarizes the results of our study in which the physiological effects of laughter--as a positive emotional expression--were analyzed with respect to gene expression changes to demonstrate the hypothesis that the mind and genes mutually influence each other. We observed that laughter suppressed 2-h postprandial blood glucose level increase in patients with type 2 diabetes and analyzed gene expression changes. Some genes showed specific changes in their expression. In addition, we revealed that laughter decreased the levels of prorenin in blood; prorenin is involved in the onset of diabetic complications. Further, laughter normalized the expression of the prorenin receptor gene on peripheral blood leukocytes, which had been reduced in diabetic patients; this demonstrated that the inhibitory effects of laughter on the onset/deterioration of diabetic complications at the gene-expression level. In a subsequent study, we demonstrated the effects of laughter by discriminating 14 genes, related to natural killer (NK) cell activity, to exhibit continuous increases in expression as a result of laughter. Our results supported NK cell-mediated improvement in glucose tolerance at the gene-expression level. In this report, we also review other previous studies on laughter.

  6. Modulation of DNA methylation levels sensitizes doxorubicin-resistant breast adenocarcinoma cells to radiation-induced apoptosis

    Energy Technology Data Exchange (ETDEWEB)

    Luzhna, Lidia [Department of Biological Sciences, University of Lethbridge, AB, Canada T1K 3M4 (Canada); Kovalchuk, Olga, E-mail: olga.kovalchuk@uleth.ca [Department of Biological Sciences, University of Lethbridge, AB, Canada T1K 3M4 (Canada)

    2010-02-05

    Chemoresistant tumors often fail to respond to other cytotoxic treatments such as radiation therapy. The mechanisms of chemo- and radiotherapy cross resistance are not fully understood and are believed to be epigenetic in nature. We hypothesize that MCF-7 cells and their doxorubicin-resistant variant MCF-7/DOX cells may exhibit different responses to ionizing radiation due to their dissimilar epigenetic status. Similar to previous studies, we found that MCF-7/DOX cells harbor much lower levels of global DNA methylation than MCF-7 cells. Furthermore, we found that MCF-7/DOX cells had lower background apoptosis levels and were less responsive to radiation than MCF-7 cells. Decreased radiation responsiveness correlated to significant global DNA hypomethylation in MCF-7/DOX cells. Here, for the first time, we show that the radiation resistance of MCF-7/DOX cells can be reversed by an epigenetic treatment - the application of methyl-donor SAM. SAM-mediated reversal of DNA methylation led to elevated radiation sensitivity in MCF-7/DOX cells. Contrarily, application of SAM on the radiation sensitive and higher methylated MCF-7 cells resulted in a decrease in their radiation responsiveness. This data suggests that a fine balance of DNA methylation is needed to insure proper radiation and drug responsiveness.

  7. Detailed assessment of gene activation levels by multiple hypoxia-responsive elements under various hypoxic conditions.

    Science.gov (United States)

    Takeuchi, Yasuto; Inubushi, Masayuki; Jin, Yong-Nan; Murai, Chika; Tsuji, Atsushi B; Hata, Hironobu; Kitagawa, Yoshimasa; Saga, Tsuneo

    2014-12-01

    HIF-1/HRE pathway is a promising target for the imaging and the treatment of intractable malignancy (HIF-1; hypoxia-inducible factor 1, HRE; hypoxia-responsive element). The purposes of our study are: (1) to assess the gene activation levels resulting from various numbers of HREs under various hypoxic conditions, (2) to evaluate the bidirectional activity of multiple HREs, and (3) to confirm whether multiple HREs can induce gene expression in vivo. Human colon carcinoma HCT116 cells were transiently transfected by the constructs containing a firefly luciferase reporter gene and various numbers (2, 4, 6, 8, 10, and 12) of HREs (nHRE+, nHRE-). The relative luciferase activities were measured under various durations of hypoxia (6, 12, 18, and 24 h), O2 concentrations (1, 2, 4, 8, and 16 %), and various concentrations of deferoxamine mesylate (20, 40, 80, 160, and 320 µg/mL growth medium). The bidirectional gene activation levels by HREs were examined in the constructs (dual-luc-nHREs) containing firefly and Renilla luciferase reporter genes at each side of nHREs. Finally, to test whether the construct containing 12HRE and the NIS reporter gene (12HRE-NIS) can induce gene expression in vivo, SPECT imaging was performed in a mouse xenograft model. (1) gene activation levels by HREs tended to increase with increasing HRE copy number, but a saturation effect was observed in constructs with more than 6 or 8 copies of an HRE, (2) gene activation levels by HREs increased remarkably during 6-12 h of hypoxia, but not beyond 12 h, (3) gene activation levels by HREs decreased with increasing O2 concentrations, but could be detected even under mild hypoxia at 16 % O2, (4) the bidirectionally proportional activity of the HRE was confirmed regardless of the hypoxic severity, and (5) NIS expression driven by 12 tandem copies of an HRE in response to hypoxia could be visualized on in vivo SPECT imaging. The results of this study will help in the understanding and assessment of

  8. High-level transfer and long-term expression of the human beta-globin gene in a mouse transplant model.

    Science.gov (United States)

    Raftopoulos, H; Ward, M; Bank, A

    1998-06-30

    Insertion of a normally functioning human beta-globin gene into the hematopoietic stem cells (HSC) of patients with beta-thalassemia may be an effective approach to the therapy of this disorder. Safe, efficient gene transfer and long-term, high-level expression of the transferred human beta-globin gene in animal models are prerequisites for HSC somatic gene therapy. We have recently shown for the first time that, using a modified beta-globin retroviral vector in a mouse transplant model, long-term, high-level expression of a transferred human beta-globin gene is possible. The human beta-globin gene continues to be detected up to eight months post-transplantation of beta-globin-transduced hematopoietic cells into lethally irradiated mice. The transferred human beta-globin gene is detected in three of five mice surviving long-term (> 4 months) transplanted with bone marrow cells transduced with high-titer virus. The unrearranged 5.1 kb human beta-globin gene-containing provirus is seen by Southern blotting in two of these mice. More importantly, long-term expression of the transferred gene is seen in two mice at levels of 5% and 20% that of endogenous murine beta-globin. We document stem cell transduction by showing continued high-level expression of the human beta-globin gene in secondarily transplanted recipient mice. These results provide evidence of HSC transduction with a human beta-globin gene in animals and demonstrate that retroviral-mediated unrearranged human beta-globin gene transfer leads to a high level of human beta-globin gene expression in the long term for the first time. A gene therapy strategy may be a feasible therapeutic approach to the beta-thalassemias if consistent human beta-globin gene transfer and expression into HSC can be achieved.

  9. A New Structural Form in the SAM/Metal-Dependent O;#8209;Methyltransferase Family: MycE from the Mycinamicin Biosynthetic Pathway

    Energy Technology Data Exchange (ETDEWEB)

    Akey, David L.; Li, Shengying; Konwerski, Jamie R.; Confer, Laura A.; Bernard, Steffen M.; Anzai, Yojiro; Kato, Fumio; Sherman, David H.; Smith, Janet L. (Michigan); (Toho)

    2012-08-01

    O-linked methylation of sugar substituents is a common modification in the biosynthesis of many natural products and is catalyzed by multiple families of S-adenosyl-l-methionine (SAM or AdoMet)-dependent methyltransferases (MTs). Mycinamicins, potent antibiotics from Micromonospora griseorubida, can be methylated at two positions on a 6-deoxyallose substituent. The first methylation is catalyzed by MycE, a SAM- and metal-dependent MT. Crystal structures were determined for MycE bound to the product S-adenosyl-l-homocysteine (AdoHcy) and magnesium, both with and without the natural substrate mycinamicin VI. This represents the first structure of a natural product sugar MT in complex with its natural substrate. MycE is a tetramer of a two-domain polypeptide, comprising a C-terminal catalytic MT domain and an N-terminal auxiliary domain, which is important for quaternary assembly and for substrate binding. The symmetric MycE tetramer has a novel MT organization in which each of the four active sites is formed at the junction of three monomers within the tetramer. The active-site structure supports a mechanism in which a conserved histidine acts as a general base, and the metal ion helps to position the methyl acceptor and to stabilize a hydroxylate intermediate. A conserved tyrosine is suggested to support activity through interactions with the transferred methyl group from the SAM methyl donor. The structure of the free enzyme reveals a dramatic order-disorder transition in the active site relative to the S-adenosyl-L-homocysteine complexes, suggesting a mechanism for product/substrate exchange through concerted movement of five loops and the polypeptide C-terminus.

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

    Science.gov (United States)

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

    2015-08-01

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

  11. Replacing -CH2CH2- with -CONH- does not significantly change rates of charge transport through Ag(TS)-SAM//Ga2O3/EGaIn junctions.

    Science.gov (United States)

    Thuo, Martin M; Reus, William F; Simeone, Felice C; Kim, Choongik; Schulz, Michael D; Yoon, Hyo Jae; Whitesides, George M

    2012-07-04

    This paper describes physical-organic studies of charge transport by tunneling through self-assembled monolayers (SAMs), based on systematic variations of the structure of the molecules constituting the SAM. Replacing a -CH(2)CH(2)- group with a -CONH- group changes the dipole moment and polarizability of a portion of the molecule and has, in principle, the potential to change the rate of charge transport through the SAM. In practice, this substitution produces no significant change in the rate of charge transport across junctions of the structure Ag(TS)-S(CH(2))(m)X(CH(2))(n)H//Ga(2)O(3)/EGaIn (TS = template stripped, X = -CH(2)CH(2)- or -CONH-, and EGaIn = eutectic alloy of gallium and indium). Incorporation of the amide group does, however, increase the yields of working (non-shorting) junctions (when compared to n-alkanethiolates of the same length). These results suggest that synthetic schemes that combine a thiol group on one end of a molecule with a group, R, to be tested, on the other (e.g., HS~CONH~R) using an amide-based coupling provide practical routes to molecules useful in studies of molecular electronics.

  12. Biodistribution of samarium-153-EDTMP in rats treated with docetaxel Biodistribuição de EDTMP-153-samário em ratos tratados com docetaxel

    Directory of Open Access Journals (Sweden)

    Arthur Villarim Neto

    2009-02-01

    Full Text Available PURPOSE: Many patients with metastatic bone disease have to use radiopharmaceuticals associated with chemotherapy to relieve bone pain. The aim of this study was to assess the influence of docetaxel on the biodistribution of samarium-153-EDTMP in bones and other organs of rats. METHODS: Wistar male rats were randomly allocated into 2 groups of 6 rats each. The DS (docetaxel/samarium group received docetaxel (15 mg/kg intraperitoneally in two cycles 11 days apart. The S (samarium/control group rats were not treated with docetaxel. Nine days after chemotherapy, all the rats were injected with 0.1ml of samarium-153-EDTMP via orbital plexus (25µCi. After 2 hours, the animals were killed and samples of the brain, thyroid, lung, heart, stomach, colon, liver, kidney and both femurs were removed. The percentage radioactivity of each sample (% ATI/g was determined in an automatic gamma-counter (Wizard-1470, Perkin-Elmer, Finland. RESULTS: On the 9th day after the administration of the 2nd chemotherapy cycle, the rats had a significant weight loss (314.50±22.09g compared (pOBJETIVO: Muitos pacientes com metástases ósseas são tratados com radiofármacos associados com quimioterapia para alívio da dor óssea. O objetivo do trabalho foi estudar a influência do docetaxel na biodistribuição do EDTMP-153-samário nos ossos e outros órgãos de ratos. MÉTODOS: Ratos Wistar foram aleatoriamente alocados em 2 grupos de 6 animais cada. O grupo DS (docetaxel/samário recebeu docetaxel (15 mg/kg intraperitoneal em dois ciclos com 11 dias de intervalo. Os ratos do grupo S (samário/controle não foram tratados com docetaxel. Nove dias após a quimioterapia, todos os animais receberam 0,1ml de EDTMP-153-samário via plexo orbital (25µCi. Após 2 horas, os animais foram mortos e feitas biópsias de cérebro, tireóide, pulmão, coração, estômago, cólon, fígado, rim e fêmures. O percentual de radioatividade por grama (%ATI/g de tecido de cada bi

  13. Growth dynamics of L-cysteine SAMs on single-crystal gold surfaces: a metastable deexcitation spectroscopy study

    Science.gov (United States)

    Canepa, M.; Lavagnino, L.; Pasquali, L.; Moroni, R.; Bisio, F.; DeRenzi, V.; Terreni, S.; Mattera, L.

    2009-07-01

    We report on a metastable deexcitation spectroscopy investigation of the growth of L-cysteine layers deposited under UHV conditions on well-defined Au(110)- (1 × 2) and Au(111) surfaces. The interaction of He* with molecular orbitals gave rise to well-defined UPS-like Penning spectra which provided information on the SAM assembly dynamics and adsorption configurations. Penning spectra have been interpreted through comparison with molecular orbital DFT calculations of the free molecule and have been compared with XPS results of previous works. Regarding adsorption of first-layer molecules at room temperature (RT), two different growth regimes were observed. On Au(110), the absence of spectral features related to orbitals associated with SH groups indicated the formation of a compact SAM of thiolate molecules. On Au(111), the data demonstrated the simultaneous presence, since the early stages of growth, of strongly and weakly bound molecules, the latter showing intact SH groups. The different growth mode was tentatively assigned to the added rows of the reconstructed Au(110) surface which behave as extended defects effectively promoting the formation of the S-Au bond. The growth of the second molecular layer was instead observed to proceed similarly for both substrates. Second-layer molecules preferably adopt an adsorption configuration in which the SH group protrudes into the vacuum side.

  14. Growth dynamics of L-cysteine SAMs on single-crystal gold surfaces: a metastable deexcitation spectroscopy study

    International Nuclear Information System (INIS)

    Canepa, M; Lavagnino, L; Moroni, R; Bisio, F; Terreni, S; Mattera, L; Pasquali, L; De Renzi, V

    2009-01-01

    We report on a metastable deexcitation spectroscopy investigation of the growth of L-cysteine layers deposited under UHV conditions on well-defined Au(110)- (1 x 2) and Au(111) surfaces. The interaction of He* with molecular orbitals gave rise to well-defined UPS-like Penning spectra which provided information on the SAM assembly dynamics and adsorption configurations. Penning spectra have been interpreted through comparison with molecular orbital DFT calculations of the free molecule and have been compared with XPS results of previous works. Regarding adsorption of first-layer molecules at room temperature (RT), two different growth regimes were observed. On Au(110), the absence of spectral features related to orbitals associated with SH groups indicated the formation of a compact SAM of thiolate molecules. On Au(111), the data demonstrated the simultaneous presence, since the early stages of growth, of strongly and weakly bound molecules, the latter showing intact SH groups. The different growth mode was tentatively assigned to the added rows of the reconstructed Au(110) surface which behave as extended defects effectively promoting the formation of the S-Au bond. The growth of the second molecular layer was instead observed to proceed similarly for both substrates. Second-layer molecules preferably adopt an adsorption configuration in which the SH group protrudes into the vacuum side.

  15. Identification of a novel set of genes reflecting different in vivo invasive patterns of human GBM cells

    International Nuclear Information System (INIS)

    Monticone, Massimiliano; Giaretti, Walter; Pfeffer, Ulrich; Daga, Antonio; Candiani, Simona; Romeo, Francesco; Mirisola, Valentina; Viaggi, Silvia; Melloni, Ilaria; Pedemonte, Simona; Zona, Gianluigi

    2012-01-01

    Most patients affected by Glioblastoma multiforme (GBM, grade IV glioma) experience a recurrence of the disease because of the spreading of tumor cells beyond surgical boundaries. Unveiling mechanisms causing this process is a logic goal to impair the killing capacity of GBM cells by molecular targeting. We noticed that our long-term GBM cultures, established from different patients, may display two categories/types of growth behavior in an orthotopic xenograft model: expansion of the tumor mass and formation of tumor branches/nodules (nodular like, NL-type) or highly diffuse single tumor cell infiltration (HD-type). We determined by DNA microarrays the gene expression profiles of three NL-type and three HD-type long-term GBM cultures. Subsequently, individual genes with different expression levels between the two groups were identified using Significance Analysis of Microarrays (SAM). Real time RT-PCR, immunofluorescence and immunoblot analyses, were performed for a selected subgroup of regulated gene products to confirm the results obtained by the expression analysis. Here, we report the identification of a set of 34 differentially expressed genes in the two types of GBM cultures. Twenty-three of these genes encode for proteins localized to the plasma membrane and 9 of these for proteins are involved in the process of cell adhesion. This study suggests the participation in the diffuse infiltrative/invasive process of GBM cells within the CNS of a novel set of genes coding for membrane-associated proteins, which should be thus susceptible to an inhibition strategy by specific targeting. Massimiliano Monticone and Antonio Daga contributed equally to this work

  16. Identification of a novel set of genes reflecting different in vivo invasive patterns of human GBM cells.

    Science.gov (United States)

    Monticone, Massimiliano; Daga, Antonio; Candiani, Simona; Romeo, Francesco; Mirisola, Valentina; Viaggi, Silvia; Melloni, Ilaria; Pedemonte, Simona; Zona, Gianluigi; Giaretti, Walter; Pfeffer, Ulrich; Castagnola, Patrizio

    2012-08-17

    Most patients affected by Glioblastoma multiforme (GBM, grade IV glioma) experience a recurrence of the disease because of the spreading of tumor cells beyond surgical boundaries. Unveiling mechanisms causing this process is a logic goal to impair the killing capacity of GBM cells by molecular targeting.We noticed that our long-term GBM cultures, established from different patients, may display two categories/types of growth behavior in an orthotopic xenograft model: expansion of the tumor mass and formation of tumor branches/nodules (nodular like, NL-type) or highly diffuse single tumor cell infiltration (HD-type). We determined by DNA microarrays the gene expression profiles of three NL-type and three HD-type long-term GBM cultures. Subsequently, individual genes with different expression levels between the two groups were identified using Significance Analysis of Microarrays (SAM). Real time RT-PCR, immunofluorescence and immunoblot analyses, were performed for a selected subgroup of regulated gene products to confirm the results obtained by the expression analysis. Here, we report the identification of a set of 34 differentially expressed genes in the two types of GBM cultures. Twenty-three of these genes encode for proteins localized to the plasma membrane and 9 of these for proteins are involved in the process of cell adhesion. This study suggests the participation in the diffuse infiltrative/invasive process of GBM cells within the CNS of a novel set of genes coding for membrane-associated proteins, which should be thus susceptible to an inhibition strategy by specific targeting.Massimiliano Monticone and Antonio Daga contributed equally to this work.

  17. The constrained maximal expression level owing to haploidy shapes gene content on the mammalian X chromosome

    DEFF Research Database (Denmark)

    Hurst, Laurence D.; Ghanbarian, Avazeh T.; Forrest, Alistair R R

    2015-01-01

    that the trend is shaped by the maximal expression level not the breadth of expression per se. Importantly, a limit to the maximal expression level explains biased tissue of expression profiles of X-linked genes. Tissues whose tissue-specific genes are very highly expressed (e.g., secretory tissues, tissues...... abundant in structural proteins) are also tissues in which gene expression is relatively rare on the X chromosome. These trends cannot be fully accounted for in terms of alternative models of biased expression. In conclusion, the notion that it is hard for genes on the Therian X to be highly expressed...

  18. Optimisation and Characterisation of Anti-Fouling Ternary SAM Layers for Impedance-Based Aptasensors

    Directory of Open Access Journals (Sweden)

    Anna Miodek

    2015-09-01

    Full Text Available An aptasensor with enhanced anti-fouling properties has been developed. As a case study, the aptasensor was designed with specificity for human thrombin. The sensing platform was developed on screen printed electrodes and is composed of a self-assembled monolayer made from a ternary mixture of 15-base thiolated DNA aptamers specific for human thrombin co-immobilised with 1,6-hexanedithiol (HDT and further passivated with 1-mercapto-6-hexanol (MCH. HDT binds to the surface by two of its thiol groups forming alkyl chain bridges and this architecture protects from non-specific attachment of molecules to the electrode surface. Using Electrochemical Impedance Spectroscopy (EIS, the aptasensor is able to detect human thrombin as variations in charge transfer resistance (Rct upon protein binding. After exposure to a high concentration of non-specific Bovine Serum Albumin (BSA solution, no changes in the Rct value were observed, highlighting the bio-fouling resistance of the surface generated. In this paper, we present the optimisation and characterisation of the aptasensor based on the ternary self-assembled monolayer (SAM layer. We show that anti-fouling properties depend on the type of gold surface used for biosensor construction, which was also confirmed by contact angle measurements. We further studied the ratio between aptamers and HDT, which can determine the specificity and selectivity of the sensing layer. We also report the influence of buffer pH and temperature used for incubation of electrodes with proteins on detection and anti-fouling properties. Finally, the stability of the aptasensor was studied by storage of modified electrodes for up to 28 days in different buffers and atmospheric conditions. Aptasensors based on ternary SAM layers are highly promising for clinical applications for detection of a range of proteins in real biological samples.

  19. Diversity of the Genes Implicated in Algerian Patients Affected by Usher Syndrome.

    Directory of Open Access Journals (Sweden)

    Samia Abdi

    Full Text Available Usher syndrome (USH is an autosomal recessive disorder characterized by a dual sensory impairment affecting hearing and vision. USH is clinically and genetically heterogeneous. Ten different causal genes have been reported. We studied the molecular bases of the disease in 18 unrelated Algerian patients by targeted-exome sequencing, and identified the causal biallelic mutations in all of them: 16 patients carried the mutations at the homozygous state and 2 at the compound heterozygous state. Nine of the 17 different mutations detected in MYO7A (1 of 5 mutations, CDH23 (4 of 7 mutations, PCDH15 (1 mutation, USH1C (1 mutation, USH1G (1 mutation, and USH2A (1 of 2 mutations, had not been previously reported. The deleterious consequences of a missense mutation of CDH23 (p.Asp1501Asn and the in-frame single codon deletion in USH1G (p.Ala397del on the corresponding proteins were predicted from the solved 3D-structures of extracellular cadherin (EC domains of cadherin-23 and the sterile alpha motif (SAM domain of USH1G/sans, respectively. In addition, we were able to show that the USH1G mutation is likely to affect the binding interface between the SAM domain and USH1C/harmonin. This should spur the use of 3D-structures, not only of isolated protein domains, but also of protein-protein interaction interfaces, to predict the functional impact of mutations detected in the USH genes.

  20. Development of library preparation method able to correct gene expression levels in rice anther and isolate a trace expression gene mediated in cold-resistance

    Energy Technology Data Exchange (ETDEWEB)

    Yamaguchi, Tomoya; Koike, Setsuo [Tohoku National Agricultural Experiment Station, Morioka (Japan)

    2000-02-01

    When cDNA library is prepared by a previously developed method, genes of which expression level is high are apt to be cloned at a high frequency, whereas genes of which expression level are low, are difficult to be cloned. A low-expression gene has been cloned at very low frequency. Therefore, the gene encoding the key enzyme that is involved in growth disturbance of rice pollen has not been identified. In this study, development of a library preparing method able to correct the expression level was attempted using highly sensitive detection method with radioisotope and some genes related to cold-resistance of rice were isolated. Double strand DNAs were synthesized using mRNA extract from rice anthers and annealed following heat-denaturation. It has been known that single strand DNA molecules abundantly existing in DNA solution can easily aggregate to form double strand DNA, but single stranded DNA molecules poor in the solution are apt to still remain as single strand after annealing. Thus, the amount of single strand DNA would be balanced in the solution between abundant DNA and poor DNA species. The authors succeeded to prepare a gene library including low and high expression genes at similar proportions. Moreover, spin trap method that allows RI labeling of DNA bound to latex particle, was developed to detect with high sensitivity, especially for genes that are expressed at low level. The present method could be used for recovery, detection and quantitative analysis of radiolabeled single strand DNA. Thus, it was demonstrated that the stage from tetrad sperm to small sperm might be easily affected by cold stress. The present results suggest that the expressions of {beta}-1 and {beta}-3 glucanase, which are involved in the release of small sperms following meiosis in the pollen formation, might be easily affected by cold stress. (M.N.)

  1. Development of library preparation method able to correct gene expression levels in rice anther and isolate a trace expression gene mediated in cold-resistance

    International Nuclear Information System (INIS)

    Yamaguchi, Tomoya; Koike, Setsuo

    2000-01-01

    When cDNA library is prepared by a previously developed method, genes of which expression level is high are apt to be cloned at a high frequency, whereas genes of which expression level are low, are difficult to be cloned. A low-expression gene has been cloned at very low frequency. Therefore, the gene encoding the key enzyme that is involved in growth disturbance of rice pollen has not been identified. In this study, development of a library preparing method able to correct the expression level was attempted using highly sensitive detection method with radioisotope and some genes related to cold-resistance of rice were isolated. Double strand DNAs were synthesized using mRNA extract from rice anthers and annealed following heat-denaturation. It has been known that single strand DNA molecules abundantly existing in DNA solution can easily aggregate to form double strand DNA, but single stranded DNA molecules poor in the solution are apt to still remain as single strand after annealing. Thus, the amount of single strand DNA would be balanced in the solution between abundant DNA and poor DNA species. The authors succeeded to prepare a gene library including low and high expression genes at similar proportions. Moreover, spin trap method that allows RI labeling of DNA bound to latex particle, was developed to detect with high sensitivity, especially for genes that are expressed at low level. The present method could be used for recovery, detection and quantitative analysis of radiolabeled single strand DNA. Thus, it was demonstrated that the stage from tetrad sperm to small sperm might be easily affected by cold stress. The present results suggest that the expressions of β-1 and β-3 glucanase, which are involved in the release of small sperms following meiosis in the pollen formation, might be easily affected by cold stress. (M.N.)

  2. Selection of Reference Genes for qRT-PCR Analysis of Gene Expression in Stipa grandis during Environmental Stresses.

    Directory of Open Access Journals (Sweden)

    Dongli Wan

    Full Text Available Stipa grandis P. Smirn. is a dominant plant species in the typical steppe of the Xilingole Plateau of Inner Mongolia. Selection of suitable reference genes for the quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR is important for gene expression analysis and research into the molecular mechanisms underlying the stress responses of S. grandis. In the present study, 15 candidate reference genes (EF1 beta, ACT, GAPDH, SamDC, CUL4, CAP, SNF2, SKIP1, SKIP5, SKIP11, UBC2, UBC15, UBC17, UCH, and HERC2 were evaluated for their stability as potential reference genes for qRT-PCR under different stresses. Four algorithms were used: GeNorm, NormFinder, BestKeeper, and RefFinder. The results showed that the most stable reference genes were different under different stress conditions: EF1beta and UBC15 during drought and salt stresses; ACT and GAPDH under heat stress; SKIP5 and UBC17 under cold stress; UBC15 and HERC2 under high pH stress; UBC2 and UBC15 under wounding stress; EF1beta and UBC17 under jasmonic acid treatment; UBC15 and CUL4 under abscisic acid treatment; and HERC2 and UBC17 under salicylic acid treatment. EF1beta and HERC2 were the most suitable genes for the global analysis of all samples. Furthermore, six target genes, SgPOD, SgPAL, SgLEA, SgLOX, SgHSP90 and SgPR1, were selected to validate the most and least stable reference genes under different treatments. Our results provide guidelines for reference gene selection for more accurate qRT-PCR quantification and will promote studies of gene expression in S. grandis subjected to environmental stress.

  3. Interaction between LRP5 and periostin gene polymorphisms on serum periostin levels and cortical bone microstructure.

    Science.gov (United States)

    Pepe, J; Bonnet, N; Herrmann, F R; Biver, E; Rizzoli, R; Chevalley, T; Ferrari, S L

    2018-02-01

    We investigated the interaction between periostin SNPs and the SNPs of the genes assumed to modulate serum periostin levels and bone microstructure in a cohort of postmenopausal women. We identified an interaction between LRP5 SNP rs648438 and periostin SNP rs9547970 on serum periostin levels and on radial cortical porosity. The purpose of this study is to investigate the interaction between periostin gene polymorphisms (SNPs) and other genes potentially responsible for modulating serum periostin levels and bone microstructure in a cohort of postmenopausal women. In 648 postmenopausal women from the Geneva Retirees Cohort, we analyzed 6 periostin SNPs and another 149 SNPs in 14 genes, namely BMP2, CTNNB1, ESR1, ESR2, LRP5, LRP6, PTH, SPTBN1, SOST, TGFb1, TNFRSF11A, TNFSF11, TNFRSF11B and WNT16. Volumetric BMD and bone microstructure were measured by high-resolution peripheral quantitative computed tomography at the distal radius and tibia. Serum periostin levels were associated with radial cortical porosity, including after adjustment for age, BMI, and years since menopause (p = 0.036). Sixteen SNPs in the ESR1, LRP5, TNFRSF11A, SOST, SPTBN1, TNFRSF11B and TNFSF11 genes were associated with serum periostin levels (p range 0.03-0.001) whereas 26 SNPs in 9 genes were associated with cortical porosity at the radius and/or at the tibia. WNT 16 was the gene with the highest number of SNPs associated with both trabecular and cortical microstructure. The periostin SNP rs9547970 was also associated with cortical porosity (p = 0.04). In particular, SNPs in LRP5, ESR1 and near the TNFRSF11A gene were associated with both cortical porosity and serum periostin levels. Eventually, we identified an interaction between LRP5 SNP rs648438 and periostin SNP rs9547970 on serum periostin levels (interaction p = 0.01) and on radial cortical porosity (interaction p = 0.005). These results suggest that periostin expression is genetically modulated, particularly by polymorphisms

  4. Mice heterozygous for the Mdr2 gene demonstrate decreased PEMT activity and diminished steatohepatitis on the MCD diet.

    Science.gov (United States)

    Igolnikov, Alexander C; Green, Richard M

    2006-03-01

    The administration of a methionine and choline deficient (MCD) diet to mice serves as an animal model of NASH. The multidrug resistant 2 (Mdr2) P-glycoprotein encodes for the canalicular phospholipid transporter, and Mdr2 (+/-) mice secrete 40% less phosphatidylcholine than wild-type mice. We have hypothesized that phosphatidylethanolamine-N-methyl transferase (PEMT) up-regulation is a consequence of MCD diet administration, and is important for the pathogenesis of steatohepatitis in this model. However, the effect of decreased phosphatidylcholine secretion and modulation of PEMT on the development of diet-induced steatohepatitis in Mdr2 (+/-) mice has not been explored. Thus, the purpose of the study is to examine the effects of the MCD diet on Mdr2 (+/-) mice. Mdr2 (+/-) and Mdr2 (+/+) mice were treated with an MCD or control diet for up to 30 days, and the severity of steatohepatitis, PEMT activity and hepatic S-adenosylmethionine (SAM), and S-adenosylhomocysteine (SAH) levels were measured. Serum ALT levels, hepatic inflammation, and PEMT activity were significantly lower, and hepatic SAM:SAH ratios were significantly higher in Mdr2 (+/-) mice at 7 and 30 days on the MCD diet. Mdr2 (+/-) mice have diminished susceptibility to MCD diet-induced NASH, which is associated with a relative decrease in PEMT activity and increased SAM:SAH ratios.

  5. Involvements of PCD and changes in gene expression profile during self-pruning of spring shoots in sweet orange (Citrus sinensis).

    Science.gov (United States)

    Zhang, Jin-Zhi; Zhao, Kun; Ai, Xiao-Yan; Hu, Chun-Gen

    2014-10-13

    Citrus shoot tips abscise at an anatomically distinct abscission zone (AZ) that separates the top part of the shoots into basal and apical portions (citrus self-pruning). Cell separation occurs only at the AZ, which suggests its cells have distinctive molecular regulation. Although several studies have looked into the morphological aspects of self-pruning process, the underlying molecular mechanisms remain unknown. In this study, the hallmarks of programmed cell death (PCD) were identified by TUNEL experiments, transmission electron microscopy (TEM) and histochemical staining for reactive oxygen species (ROS) during self-pruning of the spring shoots in sweet orange. Our results indicated that PCD occurred systematically and progressively and may play an important role in the control of self-pruning of citrus. Microarray analysis was used to examine transcriptome changes at three stages of self-pruning, and 1,378 differentially expressed genes were identified. Some genes were related to PCD, while others were associated with cell wall biosynthesis or metabolism. These results strongly suggest that abscission layers activate both catabolic and anabolic wall modification pathways during the self-pruning process. In addition, a strong correlation was observed between self-pruning and the expression of hormone-related genes. Self-pruning plays an important role in citrus floral bud initiation. Therefore, several key flowering homologs of Arabidopsis and tomato shoot apical meristem (SAM) activity genes were investigated in sweet orange by real-time PCR and in situ hybridization, and the results indicated that these genes were preferentially expressed in SAM as well as axillary meristem. Based on these findings, a model for sweet orange spring shoot self-pruning is proposed, which will enable us to better understand the mechanism of self-pruning and abscission.

  6. Interspecies Systems Biology Uncovers Metabolites Affecting C. elegans Gene Expression and Life History Traits

    Science.gov (United States)

    Watson, Emma; MacNeil, Lesley T.; Ritter, Ashlyn D.; Yilmaz, L. Safak; Rosebrock, Adam P.; Caudy, Amy A.; Walhout, Albertha J. M.

    2014-01-01

    SUMMARY Diet greatly influences gene expression and physiology. In mammals, elucidating the effects and mechanisms of individual nutrients is challenging due to the complexity of both the animal and its diet. Here we used an interspecies systems biology approach with Caenorhabditis elegans and two if its bacterial diets, Escherichia coli and Comamonas aquatica, to identify metabolites that affect the animal’s gene expression and physiology. We identify vitamin B12 as the major dilutable metabolite provided by Comamonas aq. that regulates gene expression, accelerates development and reduces fertility, but does not affect lifespan. We find that vitamin B12 has a dual role in the animal: it affects development and fertility via the methionine/S-Adenosylmethionine (SAM) cycle and breaks down the short-chain fatty acid propionic acid preventing its toxic buildup. Our interspecies systems biology approach provides a paradigm for understanding complex interactions between diet and physiology. PMID:24529378

  7. Detecting Organic Compounds Released from Iron Oxidizing Bacteria using Sample Analysis at Mars (SAM) Like Instrument Protocols

    Science.gov (United States)

    Glavin, D. P.; Popa, R.; Martin, M. G.; Freissinet, C.; Fisk, M. R.; Dworkin, J. P.; Mahaffy, P. R.

    2012-01-01

    Mars is a planet of great interest for Astrobiology since its past environmental conditions are thought to have been favourable for the emergence life. At present, the Red Planet is extremely cold and dry and the surface is exposed to intense UV and ionizing radiation, conditions generally considered to be incompatible with life as we know it on Earth. It was proposed that the shallow subsurface of Mars, where temperatures can be above freezing and liquid water can exist on rock surfaces, could harbor chemolithoautotrophic bacteria such as the iron oxidizing microorganism Pseudomonas sp. HerB. The Mars Science Laboratory (MSL) mission will provide the next opportunity to carry out in situ measurements for organic compounds of possible biological origin on Mars. One instrument onboard MSL, called the Sample Analysis at Mars (SAM) instrument suite, will carry out a broad and sensitive search for organic compounds in surface samples using either high temperature pyrolysis or chemical extraction followed by gas chromatography mass spectrometry. We present gas chromatograph mass spectrometer (GC/MS) data on crushed olivine rock powders that have been inoculated with Pseudomonas sp. HerB at different concentrations ranging from approx 10(exp 2) to 10(exp 7) cells per gram. The inoculated olivine samples were heated under helium carrier gas flow at 500 C and the pyrolysis products concentrated using a SAM-like hydrocarbon trap set at -20 C followed by trap heating and analysis by GC/Ms. In addition, the samples were also extracted using a low temperature "one-pot" chemical extraction technique using N-methyl, N-(tert-butyldimethylsilyl) trifluoroacetamide (MTBSTFA) as the silylating agent prior to GC/MS analysis. We identified several aldehydes, thiols, and alkene nitriles after pyrolysis GC/MS analysis of the bacteria that were not found in the olivine control samples that had not been inoculated with bacteria. The distribution of pyrolysis products extracted from the

  8. Sulphur-bearing Compounds Detected by MSL SAM Evolved Gas Analysis of Materials from Yellowknife Bay, Gale Crater, Mars

    Science.gov (United States)

    McAdam, A. C.; Franz, H. B.; Archer, P. D. Jr.; Sutter, B.; Eigenbrode, J. L.; Freissinet, C.; Atreya, S. K.; Bish, D. L.; Blake, D. F.; Brunner, A.; hide

    2014-01-01

    The Sample Analysis at Mars (SAM) and Chemistry and Mineralogy (CheMin) instruments on the Mars Science Laboratory (MSL) analysed several subsamples of sample fines (bearing phases present below the CheMin detection limit or difficult to characterize with XRD (e.g., X-ray amorphous phases). Here, we focus on potential constraints on phases that evolved SO2, H2S, OCS, and CS2 during thermal analysis.

  9. Progress Report on SAM Reduced-Order Model Development for Thermal Stratification and Mixing during Reactor Transients

    Energy Technology Data Exchange (ETDEWEB)

    Hu, R. [Argonne National Lab. (ANL), Argonne, IL (United States)

    2017-09-01

    This report documents the initial progress on the reduced-order flow model developments in SAM for thermal stratification and mixing modeling. Two different modeling approaches are pursued. The first one is based on one-dimensional fluid equations with additional terms accounting for the thermal mixing from both flow circulations and turbulent mixing. The second approach is based on three-dimensional coarse-grid CFD approach, in which the full three-dimensional fluid conservation equations are modeled with closure models to account for the effects of turbulence.

  10. Timecourse microarray analyses reveal global changes in gene expression of susceptible Glycine max (soybean) roots during infection by Heterodera glycines (soybean cyst nematode).

    Science.gov (United States)

    Alkharouf, Nadim W; Klink, Vincent P; Chouikha, Imed B; Beard, Hunter S; MacDonald, Margaret H; Meyer, Susan; Knap, Halina T; Khan, Rana; Matthews, Benjamin F

    2006-09-01

    Changes in gene expression within roots of Glycine max (soybean), cv. Kent, susceptible to infection by Heterodera glycines (the soybean cyst nematode [SCN]), at 6, 12, and 24 h, and 2, 4, 6, and 8 days post-inoculation were monitored using microarrays containing more than 6,000 cDNA inserts. Replicate, independent biological samples were examined at each time point. Gene expression was analyzed statistically using T-tests, ANOVA, clustering algorithms, and online analytical processing (OLAP). These analyses allow the user to query the data in several ways without importing the data into third-party software. RT-PCR confirmed that WRKY6 transcription factor, trehalose phosphate synthase, EIF4a, Skp1, and CLB1 were differentially induced across most time-points. Other genes induced across most timepoints included lipoxygenase, calmodulin, phospholipase C, metallothionein-like protein, and chalcone reductase. RT-PCR demonstrated enhanced expression during the first 12 h of infection for Kunitz trypsin inhibitor and sucrose synthase. The stress-related gene, SAM-22, phospholipase D and 12-oxophytodienoate reductase were also induced at the early time-points. At 6 and 8 dpi there was an abundance of transcripts expressed that encoded genes involved in transcription and protein synthesis. Some of those genes included ribosomal proteins, and initiation and elongation factors. Several genes involved in carbon metabolism and transport were also more abundant. Those genes included glyceraldehyde 3-phosphate dehydrogenase, fructose-bisphosphate aldolase and sucrose synthase. These results identified specific changes in gene transcript levels triggered by infection of susceptible soybean roots by SCN.

  11. Gene expression profiles in testis of pigs with extreme high and low levels of androstenone

    Directory of Open Access Journals (Sweden)

    Bendixen Christian

    2007-11-01

    Full Text Available Abstract Background: Boar taint is a major obstacle when using uncastrated male pigs for swine production. One of the main compounds causing this taint is androstenone, a pheromone produced in porcine testis. Here we use microarrays to study the expression of thousands of genes simultaneously in testis of high and low androstenone boars. The study allows identification of genes and pathways associated with elevated androstenone levels, which is essential for recognising potential molecular markers for breeding purposes. Results: Testicular tissue was collected from 60 boars, 30 with extreme high and 30 with extreme low levels of androstenone, from each of the two breeds Duroc and Norwegian Landrace. The samples were hybridised to porcine arrays containing 26,877 cDNA clones, detecting 563 and 160 genes that were differentially expressed (p Conclusion: This study contributes to the understanding of the complex genetic system controlling and responding to androstenone levels in pig testis. The identification of new pathways and genes involved in the biosynthesis and metabolism of androstenone is an important first step towards finding molecular markers to reduce boar taint.

  12. Whole-genome transcription and DNA methylation analysis of peripheral blood mononuclear cells identified aberrant gene regulation pathways in systemic lupus erythematosus.

    Science.gov (United States)

    Zhu, Honglin; Mi, Wentao; Luo, Hui; Chen, Tao; Liu, Shengxi; Raman, Indu; Zuo, Xiaoxia; Li, Quan-Zhen

    2016-07-13

    Recent achievement in genetics and epigenetics has led to the exploration of the pathogenesis of systemic lupus erythematosus (SLE). Identification of differentially expressed genes and their regulatory mechanism(s) at whole-genome level will provide a comprehensive understanding of the development of SLE and its devastating complications, lupus nephritis (LN). We performed whole-genome transcription and DNA methylation analysis in PBMC of 30 SLE patients, including 15 with LN (SLE LN(+)) and 15 without LN (SLE LN(-)), and 25 normal controls (NC) using HumanHT-12 Beadchips and Illumina Human Methy450 chips. The serum proinflammatory cytokines were quantified using Bio-plex Human Cytokine 27-plex assay. Differentially expressed genes and differentially methylated CpG were analyzed with GenomeStudio, R, and SAM software. The association between DNA methylation and gene expression were tested. Gene interaction pathways of the differentially expressed genes were analyzed by IPA software. We identified 552 upregulated genes and 550 downregulated genes in PBMC of SLE. Integration of DNA methylation and gene expression profiling showed that 334 upregulated genes were hypomethylated, and 479 downregulated genes were hypermethylated. Pathway analysis on the differential genes in SLE revealed significant enrichment in interferon (IFN) signaling and toll-like receptor (TLR) signaling pathways. Nine IFN- and seven TLR-related genes were identified and displayed step-wise increase in SLE LN(-) and SLE LN(+). Hypomethylated CpG sites were detected on these genes. The gene expressions for MX1, GPR84, and E2F2 were increased in SLE LN(+) as compared to SLE LN(-) patients. The serum levels of inflammatory cytokines, including IL17A, IP-10, bFGF, TNF-α, IL-6, IL-15, GM-CSF, IL-1RA, IL-5, and IL-12p70, were significantly elevated in SLE compared with NC. The levels of IL-15 and IL1RA correlated with their mRNA expression. The upregulation of IL-15 may be regulated by hypomethylated

  13. The Investigation of Chlorate and Perchlorate/Saponite Mixtures as a Possible Source of Oxygen and Chlorine Detected by the Sample Analysis at Mars (SAM) Instrument in Gale Crater

    Science.gov (United States)

    Clark, J.; Sutter, B.; Min, D. W.; Mahaffy, P.

    2016-01-01

    The Sample Analysis at Mars (SAM) instrument on board the Curiosity Rover has detected O2 and HCl gas releases from all analyzed Gale Crater sediments, which are attributed to the presence of perchlorates and/or chlorates in martian sediment. Previous SAM analog laboratory analyses found that most pure perchlorates and chlorates release O2 and HCl at different temperatures than those observed in the SAM data. Subsequent studies examined the effects of perchlorate and chlorate mixtures with Gale Crater analog iron phases, which are known to catalyze oxychlorine decomposition. Several mixtures produced O2 releases at similar temperatures as Gale Crater materials, but most of these mixtures did not produce significant HCl releases comparable to those detected by the SAM instrument. In order to better explain the Gale Crater HCl releases, perchlorates and chlorates were mixed with Gale Crater analog saponite, which is found at abundances from 8 to 20 wt % in the John Klein and Cumberland drill samples. Mixtures of chlorates or perchlorates with calcium-saponite or ferrian-saponite were heated to 1000 deg C in a Labsys EVO differential scanning calorimeter/mass spectrometer configured to operate similarly to the SAM oven/quadrupole mass spectrometer system. Our results demonstrate that all chlorate and perchlorate mixtures produce significant HCl releases below 1000 deg C as well as depressed oxygen peak release temperatures when mixed with saponite. The type of saponite (calcium or ferrian saponite) did not affect the evolved gas results significantly. Saponite/Mg-perchlorate mixtures produced two HCl releases similar to the Cumberland drilled sample. Mg-chlorate mixed with saponite produced HCl releases similar to the Big Sky drilled sample in an eolian sandstone. A mixture of Ca-perchlorate and saponite produced HCl and oxygen releases similar to the Buckskin mudstone drilled sample and the Gobabeb 2 eolian dune material. Ca-chlorate mixed with saponite produced both

  14. Importance of correlation between gene expression levels: application to the type I interferon signature in rheumatoid arthritis.

    Science.gov (United States)

    Reynier, Frédéric; Petit, Fabien; Paye, Malick; Turrel-Davin, Fanny; Imbert, Pierre-Emmanuel; Hot, Arnaud; Mougin, Bruno; Miossec, Pierre

    2011-01-01

    The analysis of gene expression data shows that many genes display similarity in their expression profiles suggesting some co-regulation. Here, we investigated the co-expression patterns in gene expression data and proposed a correlation-based research method to stratify individuals. Using blood from rheumatoid arthritis (RA) patients, we investigated the gene expression profiles from whole blood using Affymetrix microarray technology. Co-expressed genes were analyzed by a biclustering method, followed by gene ontology analysis of the relevant biclusters. Taking the type I interferon (IFN) pathway as an example, a classification algorithm was developed from the 102 RA patients and extended to 10 systemic lupus erythematosus (SLE) patients and 100 healthy volunteers to further characterize individuals. We developed a correlation-based algorithm referred to as Classification Algorithm Based on a Biological Signature (CABS), an alternative to other approaches focused specifically on the expression levels. This algorithm applied to the expression of 35 IFN-related genes showed that the IFN signature presented a heterogeneous expression between RA, SLE and healthy controls which could reflect the level of global IFN signature activation. Moreover, the monitoring of the IFN-related genes during the anti-TNF treatment identified changes in type I IFN gene activity induced in RA patients. In conclusion, we have proposed an original method to analyze genes sharing an expression pattern and a biological function showing that the activation levels of a biological signature could be characterized by its overall state of correlation.

  15. Konsep Kehidupan Dalam Ruang Pada Kelenteng Sam Kouw Di Surakarta Studi Kasus : Kelenteng T’ien Kok Sie, Kelenteng Poo An Kiong Dan Cetiya Ksiti Garbha

    Directory of Open Access Journals (Sweden)

    Dyah Susilowati Pradnya Paramita

    2008-09-01

    Full Text Available The kelenteng was used by three traditional religions brought by Chinese traders, namely Tao, Khonghucu and Buddhism which then together named Sam Kouw (Tri Darma The kelenteng Sam Kouw had many worshiped sculptures to which their worship ritualwas based. The kelenteng was taken care by a suhu acted as a mediator during the worship. Due to his role in worship, the Suhu and his family also stayed in the kelenteng.Based on that phenomenon, this research is focused on the rooms usage in kelenteng as a place of interaction of both worship and household routines. This research applies naturalistic qualitative methodology. The researcher played as the main instrument in collecting the data by observation, interview. The data gained during the research was formulated to some topics analyzed inductively before the researcher conducted an inter -topic dialog.. Thi s researched was conducted in three objects with cross sectional method to strengthen the data and sharpen the focus of observation. The three objects are: 1 Kelenteng T’ien Kok Sie in Ketandan; 2 Kelenteng Poo An Kiong in Coyudan, and 3 Cetiya Ksiti Garbha in Srambatan  The result of the research shows that kelenteng Sam Kouw has a public worship room in front of kelenteng , has a particular worship room in behind of kelenteng , and always has a meditation room that has always perpendicular a prominent god altar.

  16. Transgene-induced gene silencing is not affected by a change in ploidy level.

    Directory of Open Access Journals (Sweden)

    Daniela Pignatta

    Full Text Available BACKGROUND: Whole genome duplication, which results in polyploidy, is a common feature of plant populations and a recurring event in the evolution of flowering plants. Polyploidy can result in changes to gene expression and epigenetic instability. Several epigenetic phenomena, occurring at the transcriptional or post-transcriptional level, have been documented in allopolyploids (polyploids derived from species hybrids of Arabidopsis thaliana, yet findings in autopolyploids (polyploids derived from the duplication of the genome of a single species are limited. Here, we tested the hypothesis that an increase in ploidy enhances transgene-induced post-transcriptional gene silencing using autopolyploids of A. thaliana. METHODOLOGY/PRINCIPAL FINDINGS: Diploid and tetraploid individuals of four independent homozygous transgenic lines of A. thaliana transformed with chalcone synthase (CHS inverted repeat (hairpin constructs were generated. For each line diploids and tetraploids were compared for efficiency in post-transcriptional silencing of the endogenous CHS gene. The four lines differed substantially in their silencing efficiency. Yet, diploid and tetraploid plants derived from these plants and containing therefore identical transgene insertions showed no difference in the efficiency silencing CHS as assayed by visual scoring, anthocyanin assays and quantification of CHS mRNA. CONCLUSIONS/SIGNIFICANCE: Our results in A. thaliana indicated that there is no effect of ploidy level on transgene-induced post-transcriptional gene silencing. Our findings that post-transcriptional mechanisms were equally effective in diploids and tetraploids supports the use of transgene-driven post-transcriptional gene silencing as a useful mechanism to modify gene expression in polyploid species.

  17. Effects of nutritional level of concentrate-based diets on meat quality and expression levels of genes related to meat quality in Hainan black goats.

    Science.gov (United States)

    Wang, Dingfa; Zhou, Luli; Zhou, Hanlin; Hou, Guanyu; Shi, Liguang; Li, Mao; Huang, Xianzhou; Guan, Song

    2015-02-01

    The present study investigated the effects of the nutritional levels of diets on meat quality and related gene expression in Hainan black goat. Twenty-four goats were divided into six dietary treatments and were fed a concentrate-based diet with two levels of crude protein (CP) (15% or 17%) and three levels of digestive energy (DE) (11.72, 12.55 or 13.39 MJ/kg DM) for 90 days. Goats fed the concentrate-based diet with 17% CP had significantly (P meat quality and expression levels of genes associated with meat quality in Hainan black goats. © 2014 Japanese Society of Animal Science.

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

    International Nuclear Information System (INIS)

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

    1997-01-01

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

  19. From fundamental supramolecular chemistry to self-assembled nanomaterials and medicines and back again - how Sam inspired SAMul.

    Science.gov (United States)

    Smith, David K

    2018-05-08

    This feature article provides a personal insight into the research from my group over the past 10 years. In particular, the article explains how, inspired in 2005 by meeting my now-husband, Sam, who had cystic fibrosis, and who in 2011 went on to have a double lung transplant, I took an active decision to follow a more applied approach to some of our research, attempting to use fundamental supramolecular chemistry to address problems of medical interest. In particular, our strategy uses self-assembly to fabricate biologically-active nanosystems from simple low-molecular-weight building blocks. These systems can bind biological polyanions in highly competitive conditions, allowing us to approach applications in gene delivery and coagulation control. In the process, however, we have also developed new fundamental principles such as self-assembled multivalency (SAMul), temporary 'on-off' multivalency, and adaptive/shape-persistent multivalent binding. By targeting materials with applications in drug formulation and tissue engineering, we have discovered novel self-assembling low-molecular-weight hydrogelators based on the industrially-relevant dibenzylidenesorbitol framework and developed innovative approaches to spatially-resolved gels and functional multicomponent hybrid hydrogels. In this way, taking an application-led approach to research has also delivered significant academic value and conceptual advances. Furthermore, beginning to translate fundamental supramolecular chemistry into real-world applications, starts to demonstrate the power of this approach, and its potential to transform the world around us for the better.

  20. OAHG: an integrated resource for annotating human genes with multi-level ontologies.

    Science.gov (United States)

    Cheng, Liang; Sun, Jie; Xu, Wanying; Dong, Lixiang; Hu, Yang; Zhou, Meng

    2016-10-05

    OAHG, an integrated resource, aims to establish a comprehensive functional annotation resource for human protein-coding genes (PCGs), miRNAs, and lncRNAs by multi-level ontologies involving Gene Ontology (GO), Disease Ontology (DO), and Human Phenotype Ontology (HPO). Many previous studies have focused on inferring putative properties and biological functions of PCGs and non-coding RNA genes from different perspectives. During the past several decades, a few of databases have been designed to annotate the functions of PCGs, miRNAs, and lncRNAs, respectively. A part of functional descriptions in these databases were mapped to standardize terminologies, such as GO, which could be helpful to do further analysis. Despite these developments, there is no comprehensive resource recording the function of these three important types of genes. The current version of OAHG, release 1.0 (Jun 2016), integrates three ontologies involving GO, DO, and HPO, six gene functional databases and two interaction databases. Currently, OAHG contains 1,434,694 entries involving 16,929 PCGs, 637 miRNAs, 193 lncRNAs, and 24,894 terms of ontologies. During the performance evaluation, OAHG shows the consistencies with existing gene interactions and the structure of ontology. For example, terms with more similar structure could be associated with more associated genes (Pearson correlation γ 2  = 0.2428, p < 2.2e-16).

  1. Identification of a novel set of genes reflecting different in vivo invasive patterns of human GBM cells

    Directory of Open Access Journals (Sweden)

    Monticone Massimiliano

    2012-08-01

    Full Text Available Abstract Background Most patients affected by Glioblastoma multiforme (GBM, grade IV glioma experience a recurrence of the disease because of the spreading of tumor cells beyond surgical boundaries. Unveiling mechanisms causing this process is a logic goal to impair the killing capacity of GBM cells by molecular targeting. We noticed that our long-term GBM cultures, established from different patients, may display two categories/types of growth behavior in an orthotopic xenograft model: expansion of the tumor mass and formation of tumor branches/nodules (nodular like, NL-type or highly diffuse single tumor cell infiltration (HD-type. Methods We determined by DNA microarrays the gene expression profiles of three NL-type and three HD-type long-term GBM cultures. Subsequently, individual genes with different expression levels between the two groups were identified using Significance Analysis of Microarrays (SAM. Real time RT-PCR, immunofluorescence and immunoblot analyses, were performed for a selected subgroup of regulated gene products to confirm the results obtained by the expression analysis. Results Here, we report the identification of a set of 34 differentially expressed genes in the two types of GBM cultures. Twenty-three of these genes encode for proteins localized to the plasma membrane and 9 of these for proteins are involved in the process of cell adhesion. Conclusions This study suggests the participation in the diffuse infiltrative/invasive process of GBM cells within the CNS of a novel set of genes coding for membrane-associated proteins, which should be thus susceptible to an inhibition strategy by specific targeting. Massimiliano Monticone and Antonio Daga contributed equally to this work

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

    International Nuclear Information System (INIS)

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

    2013-01-01

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

  3. Synergistic and Antagonistic Interplay between Myostatin Gene Expression and Physical Activity Levels on Gene Expression Patterns in Triceps Brachii Muscles of C57/BL6 Mice

    Science.gov (United States)

    Caetano-Anollés, Kelsey; Mishra, Sanjibita; Rodriguez-Zas, Sandra L.

    2015-01-01

    Levels of myostatin expression and physical activity have both been associated with transcriptome dysregulation and skeletal muscle hypertrophy. The transcriptome of triceps brachii muscles from male C57/BL6 mice corresponding to two genotypes (wild-type and myostatin-reduced) under two conditions (high and low physical activity) was characterized using RNA-Seq. Synergistic and antagonistic interaction and ortholog modes of action of myostatin genotype and activity level on genes and gene pathways in this skeletal muscle were uncovered; 1,836, 238, and 399 genes exhibited significant (FDR-adjusted P-value myostatin-reduced relative to active and inactive wild-type, (ii) inactive myostatin-reduced and active wild-type, and (iii) inactive myostatin-reduced and inactive wild-type. Several remarkable genes and gene pathways were identified. The expression profile of nascent polypeptide-associated complex alpha subunit (Naca) supports a synergistic interaction between activity level and myostatin genotype, while Gremlin 2 (Grem2) displayed an antagonistic interaction. Comparison between activity levels revealed expression changes in genes encoding for structural proteins important for muscle function (including troponin, tropomyosin and myoglobin) and for fatty acid metabolism (some linked to diabetes and obesity, DNA-repair, stem cell renewal, and various forms of cancer). Conversely, comparison between genotype groups revealed changes in genes associated with G1-to-S-phase transition of the cell cycle of myoblasts and the expression of Grem2 proteins that modulate the cleavage of the myostatin propeptide. A number of myostatin-feedback regulated gene products that are primarily regulatory were uncovered, including microRNA impacting central functions and Piezo proteins that make cationic current-controlling mechanosensitive ion channels. These important findings extend hypotheses of myostatin and physical activity master regulation of genes and gene pathways

  4. Apolipoprotein A5: A newly identified gene impacting plasmatriglyceride levels in humans and mice

    Energy Technology Data Exchange (ETDEWEB)

    Pennacchio, Len A.; Rubin, Edward M.

    2002-09-15

    Apolipoprotein A5 (APOA5) is a newly described member of theapolipoprotein gene family whose initial discovery arose from comparativesequence analysis of the mammalian APOA1/C3/A4 gene cluster. Functionalstudies in mice indicated that alteration in the level of APOA5significantly impacted plasma triglyceride concentrations. Miceover-expressing human APOA5 displayed significantly reducedtriglycerides, while mice lacking apoA5 had a large increase in thislipid parameter. Studies in humans have also suggested an important rolefor APOA5 in determining plasma triglyceride concentrations. In theseexperiments, polymorphisms in the human gene were found to define severalcommon haplotypes that were associated with significant changes intriglyceride concentrations in multiple populations. Several separateclinical studies have provided consistent and strong support for theeffect with 24 percent of Caucasians, 35 percent of African-Americans and53 percent of Hispanics carrying APOA5 haplotypes associated withincreased plasma triglyceride levels. In summary, APOA5 represents anewly discovered gene involved in triglyceride metabolism in both humansand mice whose mechanism of action remains to be deciphered.

  5. Association Between Human Hair Loss and the Expression Levels of Nucleolin, Nucleophosmin, and UBTF Genes.

    Science.gov (United States)

    Tasdemir, Sener; Eroz, Recep; Dogan, Hasan; Erdem, Haktan Bagis; Sahin, Ibrahim; Kara, Murat; Engin, Ragip Ismail; Turkez, Hasan

    2016-04-01

    Nucleolar organizer regions, also known as argyrophilic nucleolar organizer regions, are associated with ribosomal genes. The main function of the nucleolus is the rapid production of ribosomal subunits, a process that must be highly regulated to provide the appropriate levels for cellular proliferation and cell growth. There are no studies in the literature addressing the expression and function of nucleolar component proteins, including nucleophosmin, nucleolin and the upstream binding transcription factor (UBTF), in human follicular hair cells. Nineteen healthy males who had normal and sufficient hair follicles on the back of the head, but exhibited hair loss on the frontal/vertex portions of the head and 14 healthy males without hair loss were included in the current study. Gene expression levels were measured by relative quantitative real time polymerase chain reaction. In the individuals suffering from alopecia, the total expression levels of nucleolin, nucleophosmin, and UBTF were lower in normal sites than in hair loss sites. Strong expression level correlations were detected between: nucleophosmin and nucleolin; nucleophosmin and UBTF, and nucleolin and UBTF for both groups. There was an association between human hair loss and the expression levels of nucleolin, nucleophosmin, and UBTF genes.

  6. Interspecies systems biology uncovers metabolites affecting C. elegans gene expression and life history traits.

    Science.gov (United States)

    Watson, Emma; MacNeil, Lesley T; Ritter, Ashlyn D; Yilmaz, L Safak; Rosebrock, Adam P; Caudy, Amy A; Walhout, Albertha J M

    2014-02-13

    Diet greatly influences gene expression and physiology. In mammals, elucidating the effects and mechanisms of individual nutrients is challenging due to the complexity of both the animal and its diet. Here, we used an interspecies systems biology approach with Caenorhabditis elegans and two of its bacterial diets, Escherichia coli and Comamonas aquatica, to identify metabolites that affect the animal's gene expression and physiology. We identify vitamin B12 as the major dilutable metabolite provided by Comamonas aq. that regulates gene expression, accelerates development, and reduces fertility but does not affect lifespan. We find that vitamin B12 has a dual role in the animal: it affects development and fertility via the methionine/S-Adenosylmethionine (SAM) cycle and breaks down the short-chain fatty acid propionic acid, preventing its toxic buildup. Our interspecies systems biology approach provides a paradigm for understanding complex interactions between diet and physiology. Copyright © 2014 Elsevier Inc. All rights reserved.

  7. Determination of low levels of cadmium ions by the under potential deposition on a self-assembled monolayer on gold electrode

    Energy Technology Data Exchange (ETDEWEB)

    Noyhouzer, Tomer [Institute of Chemistry, Hebrew University of Jerusalem, Jerusalem 91904 (Israel); Mandler, Daniel, E-mail: mandler@vms.huji.ac.il [Institute of Chemistry, Hebrew University of Jerusalem, Jerusalem 91904 (Israel)

    2011-01-17

    The electrochemical determination of low levels of Cd using a self-assembled monolayer (SAM) modified Au electrode is reported. Determination was based on the stripping of Cd, which was deposited by under potential deposition (UPD). A series of short alkanethiol SAMs bearing different end groups, i.e., sulfonate, carboxylate and ammonium, were examined. Lowest level of detection (ca. 50 ng L{sup -1}) was achieved with a 3-mercaptopropionic acid (MPA) monolayer using subtractive anodic square wave voltammetry (SASV). Additional surface methods, namely, reductive desorption and X-ray photoelectron spectroscopy, were applied to determine the interfacial structure of the electrodeposited Cd on the modified electrodes. We conclude that the deposited Cd forms a monoatomic layer, which bridges between the gold surface and the alkanethiol monolayer associating with both the gold and the sulfur atoms.

  8. Intra and Interspecific Variations of Gene Expression Levels in Yeast Are Largely Neutral: (Nei Lecture, SMBE 2016, Gold Coast).

    Science.gov (United States)

    Yang, Jian-Rong; Maclean, Calum J; Park, Chungoo; Zhao, Huabin; Zhang, Jianzhi

    2017-09-01

    It is commonly, although not universally, accepted that most intra and interspecific genome sequence variations are more or less neutral, whereas a large fraction of organism-level phenotypic variations are adaptive. Gene expression levels are molecular phenotypes that bridge the gap between genotypes and corresponding organism-level phenotypes. Yet, it is unknown whether natural variations in gene expression levels are mostly neutral or adaptive. Here we address this fundamental question by genome-wide profiling and comparison of gene expression levels in nine yeast strains belonging to three closely related Saccharomyces species and originating from five different ecological environments. We find that the transcriptome-based clustering of the nine strains approximates the genome sequence-based phylogeny irrespective of their ecological environments. Remarkably, only ∼0.5% of genes exhibit similar expression levels among strains from a common ecological environment, no greater than that among strains with comparable phylogenetic relationships but different environments. These and other observations strongly suggest that most intra and interspecific variations in yeast gene expression levels result from the accumulation of random mutations rather than environmental adaptations. This finding has profound implications for understanding the driving force of gene expression evolution, genetic basis of phenotypic adaptation, and general role of stochasticity in evolution. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  9. Electrical properties of SAM-modified ITO surface using aromatic small molecules with double bond carboxylic acid groups for OLED applications

    Energy Technology Data Exchange (ETDEWEB)

    Can, Mustafa [Izmir Katip Celebi University, Faculty of Engineering, Department of Engineering Sciences, Çiğli, Izmir (Turkey); Havare, Ali Kemal [Toros University, Faculty of Engineering, Electric and Electronic Department, Mersin (Turkey); Aydın, Hasan; Yagmurcukardes, Nesli [Izmir Institute of Technology, Material Science and Engineering, Izmir (Turkey); Demic, Serafettin [Izmir Katip Celebi University, Faculty of Engineering, Department of Material Science and Engineering, Çiğli, Izmir (Turkey); Icli, Sıddık [Ege University, Solar Energy Institute, Izmir (Turkey); Okur, Salih, E-mail: salih.okur@ikc.edu.tr [Izmir Katip Celebi University, Faculty of Engineering, Department of Material Science and Engineering, Çiğli, Izmir (Turkey)

    2014-09-30

    Graphical abstract: - Highlights: • We report that the performance of OLED consist of aromatic small molecules with double bond carboxylic acid groups on ITO surface. • The OLED devices were tested in terms of electrical and optical characteristics. • The I–V results show that OLEDs with SAM-modified ITO surface have lower turn on voltages than OLED configurations without SAMs. - Abstract: 5-[(3-Methylphenyl)(phenyl)amino]isophthalic acid (5-MePIFA) and 5-(diphenyl)amino]isophthalic acid (5-DPIFA) organic molecules were synthesized to form self-assembled monolayer on indium tin oxide (ITO) anode to enhance hole transport from ITO to organic hole transport layers such as TPD. The modified surface was characterized by scanning tunneling microscopy (STM). The change in the surface potential was measured by Kelvin probe force microscopy (KPFM). Our Kelvin probe force microscopy (KPFM) measurements showed that the surface potentials increased more than 100 mV with reference to bare indium tin-oxide. The results show that the threshold voltage on OLEDs with modified ITO is lowered significantly compared to OLEDs with unmodified ITO. The hole mobility of TPD has been estimated using space–charge-limited current measurements (SCLC)

  10. Electrical properties of SAM-modified ITO surface using aromatic small molecules with double bond carboxylic acid groups for OLED applications

    International Nuclear Information System (INIS)

    Can, Mustafa; Havare, Ali Kemal; Aydın, Hasan; Yagmurcukardes, Nesli; Demic, Serafettin; Icli, Sıddık; Okur, Salih

    2014-01-01

    Graphical abstract: - Highlights: • We report that the performance of OLED consist of aromatic small molecules with double bond carboxylic acid groups on ITO surface. • The OLED devices were tested in terms of electrical and optical characteristics. • The I–V results show that OLEDs with SAM-modified ITO surface have lower turn on voltages than OLED configurations without SAMs. - Abstract: 5-[(3-Methylphenyl)(phenyl)amino]isophthalic acid (5-MePIFA) and 5-(diphenyl)amino]isophthalic acid (5-DPIFA) organic molecules were synthesized to form self-assembled monolayer on indium tin oxide (ITO) anode to enhance hole transport from ITO to organic hole transport layers such as TPD. The modified surface was characterized by scanning tunneling microscopy (STM). The change in the surface potential was measured by Kelvin probe force microscopy (KPFM). Our Kelvin probe force microscopy (KPFM) measurements showed that the surface potentials increased more than 100 mV with reference to bare indium tin-oxide. The results show that the threshold voltage on OLEDs with modified ITO is lowered significantly compared to OLEDs with unmodified ITO. The hole mobility of TPD has been estimated using space–charge-limited current measurements (SCLC)

  11. Characterization of a SAM-dependent fluorinase from a latent biosynthetic pathway for fluoroacetate and 4-fluorothreonine formation in Nocardia brasiliensis.

    Science.gov (United States)

    Wang, Yaya; Deng, Zixin; Qu, Xudong

    2014-01-01

    Fluorination has been widely used in chemical synthesis, but is rare in nature. The only known biological fluorination scope is represented by the fl pathway from Streptomyces cattleya that produces fluoroacetate (FAc) and 4-fluorothreonine (4-FT). Here we report the identification of a novel pathway for FAc and 4-FT biosynthesis from the actinomycetoma-causing pathogen Nocardia brasiliensis ATCC 700358. The new pathway shares overall conservation with the fl pathway in S. cattleya. Biochemical characterization of the conserved domains revealed a novel fluorinase NobA that can biosynthesize 5'-fluoro-5'-deoxyadenosine (5'-FDA) from inorganic fluoride and S-adenosyl-l-methionine (SAM). The NobA shows similar halide specificity and characteristics to the fluorination enzyme FlA of the fl pathway. Kinetic parameters for fluoride ( K m 4153 μM, k cat 0.073 min (-1)) and SAM ( K m 416 μM, k cat 0.139 min (-1)) have been determined, revealing that NobA is slightly (2.3 fold) slower than FlA. Upon sequence comparison, we finally identified a distinct loop region in the fluorinases that probably accounts for the disparity of fluorination activity.

  12. Fabrication of an a-IGZO thin film transistor using selective deposition of cobalt by the self-assembly monolayer (SAM) process.

    Science.gov (United States)

    Cho, Young-Je; Kim, HyunHo; Park, Kyoung-Yun; Lee, Jaegab; Bobade, Santosh M; Wu, Fu-Chung; Choi, Duck-Kyun

    2011-01-01

    Interest in transparent oxide thin film transistors utilizing ZnO material has been on the rise for many years. Recently, however, IGZO has begun to draw more attention due to its higher stability and superior electric field mobility when compared to ZnO. In this work, we address an improved method for patterning an a-IGZO film using the SAM process, which employs a cost-efficient micro-contact printing method instead of the conventional lithography process. After a-IGZO film deposition on the surface of a SiO2-layered Si wafer, the wafer was illuminated with UV light; sources and drains were then patterned using n-octadecyltrichlorosilane (OTS) molecules by a printing method. Due to the low surface energy of OTS, cobalt was selectively deposited on the OTS-free a-IGZO surface. The selective deposition of cobalt electrodes was successful, as confirmed by an optical microscope. The a-IZGO TFT fabricated using the SAM process exhibited good transistor performance: electric field mobility (micro(FE)), threshold voltage (V(th)), subthreshold slope (SS) and on/off ratio were 2.1 cm2/Vs, 2.4 V, 0.35 V/dec and 2.9 x 10(6), respectively.

  13. Low-level lasers affect uncoupling protein gene expression in skin and skeletal muscle tissues

    International Nuclear Information System (INIS)

    Canuto, K S; Sergio, L P S; Mencalha, A L; Fonseca, A S; Paoli, F

    2016-01-01

    Wavelength, frequency, power, fluence, and emission mode determine the photophysical, photochemical, and photobiological responses of biological tissues to low-level lasers. Free radicals are involved in these responses acting as second messengers in intracellular signaling processes. Irradiated cells present defenses against these chemical species to avoid unwanted effects, such as uncoupling proteins (UCPs), which are part of protective mechanisms and minimize the effects of free radical generation in mitochondria. In this work UCP2 and UCP3 mRNA gene relative expression in the skin and skeletal muscle tissues of Wistar rats exposed to low-level red and infrared lasers was evaluated. Samples of the skin and skeletal muscle tissue of Wistar rats exposed to low-level red and infrared lasers were withdrawn for total RNA extraction, cDNA synthesis, and the evaluation of gene expression by quantitative polymerase chain reaction. UCP2 and UCP3 mRNA expression was differently altered in skin and skeletal muscle tissues exposed to lasers in a wavelength-dependent effect, with the UCP3 mRNA expression dose-dependent. Alteration on UCP gene expression could be part of the biostimulation effect and is necessary to make cells exposed to red and infrared low-level lasers more resistant or capable of adapting in damaged tissues or diseases. (paper)

  14. Molecular Evolution and Expression Divergence of HMT Gene Family in Plants

    Directory of Open Access Journals (Sweden)

    Man Zhao

    2018-04-01

    Full Text Available Homocysteine methyltransferase (HMT converts homocysteine to methionine using S-methylmethionine (SMM or S-adenosylmethionine (SAM as methyl donors in organisms, playing an important role in supplying methionine for the growth and the development of plants. To better understand the functions of the HMT genes in plants, we conducted a wide evolution and expression analysis of these genes. Reconstruction of the phylogenetic relationship showed that the HMT gene family was divided into Class 1 and Class 2. In Class 1, HMTs were only found in seed plants, while Class 2 presented in all land plants, which hinted that the HMT genes might have diverged in seed plants. The analysis of gene structures and selection pressures showed that they were relatively conserved during evolution. However, type I functional divergence had been detected in the HMTs. Furthermore, the expression profiles of HMTs showed their distinct expression patterns in different tissues, in which some HMTs were widely expressed in various organs, whereas the others were highly expressed in some specific organs, such as seeds or leaves. Therefore, according to our results in the evolution, functional divergence, and expression, the HMT genes might have diverged during evolution. Further analysis in the expression patterns of AthHMTs with their methyl donors suggested that the diverged HMTs might be related to supply methionine for the development of plant seeds.

  15. The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome

    KAUST Repository

    Hurst, Laurence D.

    2015-12-18

    X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functionally biased gene content may more profoundly be shaped by limits imposed on gene expression owing to haploid expression of the X chromosome. Notably, if the X, as in primates, is transcribed at rates comparable to the ancestral rate (per promoter) prior to the X chromosome formation, then the X is not a tolerable environment for genes with very high maximal net levels of expression, owing to transcriptional traffic jams. We test this hypothesis using The Encyclopedia of DNA Elements (ENCODE) and data from the Functional Annotation of the Mammalian Genome (FANTOM5) project. As predicted, the maximal expression of human X-linked genes is much lower than that of genes on autosomes: on average, maximal expression is three times lower on the X chromosome than on autosomes. Similarly, autosome-to-X retroposition events are associated with lower maximal expression of retrogenes on the X than seen for X-to-autosome retrogenes on autosomes. Also as expected, X-linked genes have a lesser degree of increase in gene expression than autosomal ones (compared to the human/Chimpanzee common ancestor) if highly expressed, but not if lowly expressed. The traffic jam model also explains the known lower breadth of expression for genes on the X (and the Z of birds), as genes with broad expression are, on average, those with high maximal expression. As then further predicted, highly expressed tissue-specific genes are also rare on the X and broadly expressed genes on the X tend to be lowly expressed, both indicating that the trend is shaped by the maximal expression level not the breadth of expression per se. Importantly, a limit to the maximal expression level explains biased tissue of expression

  16. The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome.

    Directory of Open Access Journals (Sweden)

    Laurence D Hurst

    2015-12-01

    Full Text Available X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functionally biased gene content may more profoundly be shaped by limits imposed on gene expression owing to haploid expression of the X chromosome. Notably, if the X, as in primates, is transcribed at rates comparable to the ancestral rate (per promoter prior to the X chromosome formation, then the X is not a tolerable environment for genes with very high maximal net levels of expression, owing to transcriptional traffic jams. We test this hypothesis using The Encyclopedia of DNA Elements (ENCODE and data from the Functional Annotation of the Mammalian Genome (FANTOM5 project. As predicted, the maximal expression of human X-linked genes is much lower than that of genes on autosomes: on average, maximal expression is three times lower on the X chromosome than on autosomes. Similarly, autosome-to-X retroposition events are associated with lower maximal expression of retrogenes on the X than seen for X-to-autosome retrogenes on autosomes. Also as expected, X-linked genes have a lesser degree of increase in gene expression than autosomal ones (compared to the human/Chimpanzee common ancestor if highly expressed, but not if lowly expressed. The traffic jam model also explains the known lower breadth of expression for genes on the X (and the Z of birds, as genes with broad expression are, on average, those with high maximal expression. As then further predicted, highly expressed tissue-specific genes are also rare on the X and broadly expressed genes on the X tend to be lowly expressed, both indicating that the trend is shaped by the maximal expression level not the breadth of expression per se. Importantly, a limit to the maximal expression level explains biased

  17. Identification and molecular characterization of the nicotianamine synthase gene family in bread wheat.

    Science.gov (United States)

    Bonneau, Julien; Baumann, Ute; Beasley, Jesse; Li, Yuan; Johnson, Alexander A T

    2016-12-01

    Nicotianamine (NA) is a non-protein amino acid involved in fundamental aspects of metal uptake, transport and homeostasis in all plants and constitutes the biosynthetic precursor of mugineic acid family phytosiderophores (MAs) in graminaceous plant species. Nicotianamine synthase (NAS) genes, which encode enzymes that synthesize NA from S-adenosyl-L-methionine (SAM), are differentially regulated by iron (Fe) status in most plant species and plant genomes have been found to contain anywhere from 1 to 9 NAS genes. This study describes the identification of 21 NAS genes in the hexaploid bread wheat (Triticum aestivum L.) genome and their phylogenetic classification into two distinct clades. The TaNAS genes are highly expressed during germination, seedling growth and reproductive development. Fourteen of the clade I NAS genes were up-regulated in root tissues under conditions of Fe deficiency. Protein sequence analyses revealed the presence of endocytosis motifs in all of the wheat NAS proteins as well as chloroplast, mitochondrial and secretory transit peptide signals in four proteins. These results greatly expand our knowledge of NAS gene families in graminaceous plant species as well as the genetics underlying Fe nutrition in bread wheat. © 2016 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

  18. HC-Pro silencing suppressor significantly alters the gene expression profile in tobacco leaves and flowers

    Directory of Open Access Journals (Sweden)

    Lehto Kirsi

    2011-04-01

    Full Text Available Abstract Background RNA silencing is used in plants as a major defence mechanism against invasive nucleic acids, such as viruses. Accordingly, plant viruses have evolved to produce counter defensive RNA-silencing suppressors (RSSs. These factors interfere in various ways with the RNA silencing machinery in cells, and thereby disturb the microRNA (miRNA mediated endogene regulation and induce developmental and morphological changes in plants. In this study we have explored these effects using previously characterized transgenic tobacco plants which constitutively express (under CaMV 35S promoter the helper component-proteinase (HC-Pro derived from a potyviral genome. The transcript levels of leaves and flowers of these plants were analysed using microarray techniques (Tobacco 4 × 44 k, Agilent. Results Over expression of HC-Pro RSS induced clear phenotypic changes both in growth rate and in leaf and flower morphology of the tobacco plants. The expression of 748 and 332 genes was significantly changed in the leaves and flowers, respectively, in the HC-Pro expressing transgenic plants. Interestingly, these transcriptome alterations in the HC-Pro expressing tobacco plants were similar as those previously detected in plants infected with ssRNA-viruses. Particularly, many defense-related and hormone-responsive genes (e.g. ethylene responsive transcription factor 1, ERF1 were differentially regulated in these plants. Also the expression of several stress-related genes, and genes related to cell wall modifications, protein processing, transcriptional regulation and photosynthesis were strongly altered. Moreover, genes regulating circadian cycle and flowering time were significantly altered, which may have induced a late flowering phenotype in HC-Pro expressing plants. The results also suggest that photosynthetic oxygen evolution, sugar metabolism and energy levels were significantly changed in these transgenic plants. Transcript levels of S

  19. Determination of ploidy level and isolation of genes encoding acetyl-CoA carboxylase in Japanese Foxtail (Alopecurus japonicus.

    Directory of Open Access Journals (Sweden)

    Hongle Xu

    Full Text Available Ploidy level is important in biodiversity studies and in developing strategies for isolating important plant genes. Many herbicide-resistant weed species are polyploids, but our understanding of these polyploid weeds is limited. Japanese foxtail, a noxious agricultural grass weed, has evolved herbicide resistance. However, most studies on this weed have ignored the fact that there are multiple copies of target genes. This may complicate the study of resistance mechanisms. Japanese foxtail was found to be a tetraploid by flow cytometer and chromosome counting, two commonly used methods in the determination of ploidy levels. We found that there are two copies of the gene encoding plastidic acetyl-CoA carboxylase (ACCase in Japanese foxtail and all the homologous genes are expressed. Additionally, no difference in ploidy levels or ACCase gene copy numbers was observed between an ACCase-inhibiting herbicide-resistant and a herbicide-sensitive population in this study.

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

    DEFF Research Database (Denmark)

    Farajzadeh, Leila; Hornshøj, Henrik; Momeni, Jamal

    2013-01-01

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

  1. Coordinated Regulation of Anthocyanin Biosynthesis Genes Confers Varied Phenotypic and Spatial-Temporal Anthocyanin Accumulation in Radish (Raphanus sativus L.

    Directory of Open Access Journals (Sweden)

    Everlyne M'mbone Muleke

    2017-07-01

    Full Text Available Anthocyanins are natural pigments that have important functions in plant growth and development. Radish taproots are rich in anthocyanins which confer different taproot colors and are potentially beneficial to human health. The crop differentially accumulates anthocyanin during various stages of growth, yet molecular mechanisms underlying this differential anthocyanin accumulation remains unknown. In the present study, transcriptome analysis was used to concisely identify putative genes involved in anthocyanin biosynthesis in radish. Spatial-temporal transcript expressions were then profiled in four color variant radish cultivars. From the total transcript sequences obtained through illumina sequencing, 102 assembled unigenes, and 20 candidate genes were identified to be involved in anthocyanin biosynthesis. Fifteen genomic sequences were isolated and sequenced from radish taproot. The length of these sequences was between 900 and 1,579 bp, and the unigene coverage to all of the corresponding cloned sequences was more than 93%. Gene structure analysis revealed that RsF3′H is intronless and anthocyanin biosynthesis genes (ABGs bear asymmetrical exons, except RsSAM. Anthocyanin accumulation showed a gradual increase in the leaf of the red radish and the taproot of colored cultivars during development, with a rapid increase at 30 days after sowing (DAS, and the highest content at maturity. Spatial-temporal transcriptional analysis of 14 genes revealed detectable expressions of 12 ABGs in various tissues at different growth levels. The investigation of anthocyanin accumulation and gene expression in four color variant radish cultivars, at different stages of development, indicated that total anthocyanin correlated with transcript levels of ABGs, particularly RsUFGT, RsF3H, RsANS, RsCHS3 and RsF3′H1. Our results suggest that these candidate genes play key roles in phenotypic and spatial-temporal anthocyanin accumulation in radish through

  2. Molecular Level Manipulation of Interfacial Charge Transport

    Science.gov (United States)

    Song, Charles Kiseok

    The bulk-heterojunction organic (BHJ) photovoltaics (OPVs) and lithium ion battery (LiB) have been extensively studied. Power conversion efficiency (PCE) of an OPV greater than 10% and utilizing group 4 elements as the anode to accommodate high capacity for LiBs are the goals of many studies. However, the currently ubiquitous hole-collecting layer of OPVs limit device performance and durability, and group 4 elements are unstable and brittle to be commercially produced. Thus, my thesis has focused on developing functional and durable interfacial layers (IFLs) for OPVs and characterizing flexible artificial solid-electrolyte interphase (SEI) for LiBs. In Chapter 2, a series of robust organosilane-based dipolar self-assembled monolayer (SAM) IFLs on the tin-doped indium oxide (ITO) anodes of OPVs are developed. These hydrophobic and amorphous IFLs modify anode work functions from 4.66 to 5.27 eV. Two series of Glass/ITO/SAM IFL/Active Layer/LiF/Al BHJ OPVs are fabricated, and a strong positive correlation between the electrochemically-derived heterogeneous electron transport rate constants (ks) and OPV PCEs are observed due to enhanced anode carrier extraction. In Chapter 3, a series of unusually denser organosilane-based SAM IFLs on ITO anodes of OPVs are developed. Precursor mixtures having short and long tail groups were simultaneously deposited to minimize sterical encumbrance and denser SAM IFLs are achieved. These heterogeneous supersaturated SAMs (SHSAMs), with PCE (7.62%) exceeding that of PEDOT:PSS IFL, are found to be 17% denser and enhances PCE by 54% versus comparable devices with homogeneous SAM IFLs due to enhanced charge selectivity and collection. In Chapter 4, libraries of electron affinities (EAs) of widely used conductive polymers are constructed by cyclic voltammetry (CV) in conventional and LiB media. The EAs of the conductive polymer films measured via CV in conventional (EAC) and Li+ battery (EAB) media could be linearly correlated by EAB = (1

  3. Cerebrospinal fluid Aβ42 levels and APP processing pathway genes in Parkinson's disease.

    Science.gov (United States)

    Bekris, Lynn M; Tsuang, Debby W; Peskind, Elaine R; Yu, Chang E; Montine, Thomas J; Zhang, Jing; Zabetian, Cyrus P; Leverenz, James B

    2015-06-01

    Of recent interest is the finding that certain cerebrospinal fluid (CSF) biomarkers traditionally linked to Alzheimer's disease (AD), specifically amyloid beta protein (Aβ), are abnormal in PD CSF. The aim of this exploratory investigation was to determine whether genetic variation within the amyloid precursor protein (APP) processing pathway genes correlates with CSF Aβ42 levels in Parkinson's disease (PD). Parkinson's disease (n = 86) and control (n = 161) DNA were genotyped for 19 regulatory region tagging single-nucleotide polymorphisms (SNPs) within nine genes (APP, ADAM10, BACE1, BACE2, PSEN1, PSEN2, PEN2, NCSTN, and APH1B) involved in the cleavage of APP. The SNP genotypes were tested for their association with CSF biomarkers and PD risk while adjusting for age, sex, and APOE ɛ4 status. Significant correlation with CSF Aβ42 levels in PD was observed for two SNPs, (APP rs466448 and APH1B rs2068143). Conversely, significant correlation with CSF Aβ42 levels in controls was observed for three SNPs (APP rs214484, rs2040273, and PSEN1 rs362344). In addition, results of this exploratory investigation suggest that an APP SNP and an APH1B SNP are marginally associated with PD CSF Aβ42 levels in APOE ɛ4 noncarriers. Further hypotheses generated include that decreased CSF Aβ42 levels are in part driven by genetic variation in APP processing genes. Additional investigation into the relationship between these findings and clinical characteristics of PD, including cognitive impairment, compared with other neurodegenerative diseases, such as AD, are warranted. © 2015 International Parkinson and Movement Disorder Society. © 2015 International Parkinson and Movement Disorder Society.

  4. Synergistic Effects of SAM and Selenium Compounds on Proliferation, Migration and Adhesion of HeLa Cells.

    Science.gov (United States)

    Sun, Licui; Zhang, Jianxin; Yang, Qiu; Si, Yang; Liu, Yiqun; Wang, Qin; Han, Feng; Huang, Zhenwu

    2017-08-01

    To determine the antitumor activities and molecular mechanism of selenium compounds in HeLa cells. Western blotting was used to detect ERK and AKT activation in HeLa cells induced by selenium compounds selenomethionine (SeMet), methylselenocysteine (MeSeCys) and methylseleninic acids (MeSeA). Using MTT, wound-healing and Matrigel adhesion assays, the antitumor effects of SAM and selenium compounds were evaluated in HeLa cells. MeSeA inhibited ERK and AKT signaling pathways and suppressed the proliferation (peffects compared to the other treatments. Copyright© 2017, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

  5. [Association between serum aluminium level and methylation of amyloid precursor protein gene in workers engaged in aluminium electrolysis].

    Science.gov (United States)

    Yang, X J; Yuan, Y Z; Niu, Q

    2016-04-20

    To investigate the association between serum aluminium level and methylation of the promoter region of amyloid precursor protein (APP)gene in workers engaged in aluminium electrolysis. In 2012, 366 electrolysis workers in an aluminium factory were enrolled as exposure group (working years >10 and age >40 years)and divided into low-exposure group and high-exposure group based on the median serum aluminium level. Meanwhile, 102 workers in a cement plant not exposed to aluminium were enrolled as control group. Graphite furnace atomic absorption spectrometry was used to measure serum aluminium level, methylation specific PCR was used to measure the methylation rate of the promoter region of APP gene, and ELI-SA was used to measure the protein expression of APP in lymphocytes in peripheral blood. The exposure group had a significantly higher serum aluminium level than the control group (45.07 μg/L vs 30.51 μg/L, P0.05). The multivariate logistic regression analysis showed that with reference to the control group, low aluminium exposure (OR=1.86, 95% CI 1.67~3.52)and high aluminium exposure (OR=2.98, 95% CI 1.97~4.15)were risk factors for a reduced methylation rate of the promoter region of APP gene. Reduced methylation of the promoter region of APP gene may be associated with increased serum aluminium level, and downregulated methylation of the promoter region of APP gene may accelerate APP gene transcription.

  6. The Ability of Different Imputation Methods to Preserve the Significant Genes and Pathways in Cancer

    Directory of Open Access Journals (Sweden)

    Rosa Aghdam

    2017-12-01

    Full Text Available Deciphering important genes and pathways from incomplete gene expression data could facilitate a better understanding of cancer. Different imputation methods can be applied to estimate the missing values. In our study, we evaluated various imputation methods for their performance in preserving significant genes and pathways. In the first step, 5% genes are considered in random for two types of ignorable and non-ignorable missingness mechanisms with various missing rates. Next, 10 well-known imputation methods were applied to the complete datasets. The significance analysis of microarrays (SAM method was applied to detect the significant genes in rectal and lung cancers to showcase the utility of imputation approaches in preserving significant genes. To determine the impact of different imputation methods on the identification of important genes, the chi-squared test was used to compare the proportions of overlaps between significant genes detected from original data and those detected from the imputed datasets. Additionally, the significant genes are tested for their enrichment in important pathways, using the ConsensusPathDB. Our results showed that almost all the significant genes and pathways of the original dataset can be detected in all imputed datasets, indicating that there is no significant difference in the performance of various imputation methods tested. The source code and selected datasets are available on http://profiles.bs.ipm.ir/softwares/imputation_methods/.

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

    Science.gov (United States)

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

    2014-01-01

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

  8. A comparison of brain gene expression levels in domesticated and wild animals.

    Directory of Open Access Journals (Sweden)

    Frank W Albert

    2012-09-01

    Full Text Available Domestication has led to similar changes in morphology and behavior in several animal species, raising the question whether similarities between different domestication events also exist at the molecular level. We used mRNA sequencing to analyze genome-wide gene expression patterns in brain frontal cortex in three pairs of domesticated and wild species (dogs and wolves, pigs and wild boars, and domesticated and wild rabbits. We compared the expression differences with those between domesticated guinea pigs and a distant wild relative (Cavia aperea as well as between two lines of rats selected for tameness or aggression towards humans. There were few gene expression differences between domesticated and wild dogs, pigs, and rabbits (30-75 genes (less than 1% of expressed genes were differentially expressed, while guinea pigs and C. aperea differed more strongly. Almost no overlap was found between the genes with differential expression in the different domestication events. In addition, joint analyses of all domesticated and wild samples provided only suggestive evidence for the existence of a small group of genes that changed their expression in a similar fashion in different domesticated species. The most extreme of these shared expression changes include up-regulation in domesticates of SOX6 and PROM1, two modulators of brain development. There was almost no overlap between gene expression in domesticated animals and the tame and aggressive rats. However, two of the genes with the strongest expression differences between the rats (DLL3 and DHDH were located in a genomic region associated with tameness and aggression, suggesting a role in influencing tameness. In summary, the majority of brain gene expression changes in domesticated animals are specific to the given domestication event, suggesting that the causative variants of behavioral domestication traits may likewise be different.

  9. Plasma ghrelin levels and polymorphisms of ghrelin gene in Chinese obese children and adolescents.

    Science.gov (United States)

    Zhu, J F; Liang, L; Zou, C C; Fu, J F

    2010-09-01

    To evaluate the role of fasting plasma ghrelin levels [ln(ghrelin)] and polymorphisms of ghrelin gene in Chinese obese children. Genotyping for ghrelin polymorphism was performed in 230 obese and 100 normal weight children. Among them, plasma ghrelin levels were measured in 91 obese and 23 health subjects. (1) Bivariate correlation analysis showed the ln(ghrelin) was inversely correlated with abnormality of glucose metabolism (r = -0.240, P = 0.023). Stepwise multiple regression analysis showed that abnormality of glucose metabolism was an independent determinant of plasma ghrelin levels (P = 0.023). (2) There was no difference in frequency of Leu72Met polymorphisms between obese and control groups (36.09 vs. 41.00%). Ghrelin is associated with obesity in childhood, especially associated with the glucose homeostasis. Lower ghrelin levels might be a result of obesity, but not a cause of obesity. The Leu72Met polymorphism of ghrelin gene is not associated with obesity and metabolic syndrome in Chinese children.

  10. Striking similarity in the gene expression levels of individual Myc module members among ESCs, EpiSCs, and partial iPSCs.

    Directory of Open Access Journals (Sweden)

    Masataka Hirasaki

    Full Text Available Predominant transcriptional subnetworks called Core, Myc, and PRC modules have been shown to participate in preservation of the pluripotency and self-renewality of embryonic stem cells (ESCs. Epiblast stem cells (EpiSCs are another cell type that possesses pluripotency and self-renewality. However, the roles of these modules in EpiSCs have not been systematically examined to date. Here, we compared the average expression levels of Core, Myc, and PRC module genes between ESCs and EpiSCs. EpiSCs showed substantially higher and lower expression levels of PRC and Core module genes, respectively, compared with those in ESCs, while Myc module members showed almost equivalent levels of average gene expression. Subsequent analyses revealed that the similarity in gene expression levels of the Myc module between these two cell types was not just overall, but striking similarities were evident even when comparing the expression of individual genes. We also observed equivalent levels of similarity in the expression of individual Myc module genes between induced pluripotent stem cells (iPSCs and partial iPSCs that are an unwanted byproduct generated during iPSC induction. Moreover, our data demonstrate that partial iPSCs depend on a high level of c-Myc expression for their self-renewal properties.

  11. Gene expression and plant hormone levels in two contrasting rice genotypes responding to brown planthopper infestation.

    Science.gov (United States)

    Li, Changyan; Luo, Chao; Zhou, Zaihui; Wang, Rui; Ling, Fei; Xiao, Langtao; Lin, Yongjun; Chen, Hao

    2017-02-28

    The brown planthopper (BPH; Nilaparvata lugens Stål) is a destructive piercing-sucking insect pest of rice. The plant hormones salicylic acid (SA) and jasmonic acid (JA) play important roles in plant-pest interactions. Many isolated rice genes that modulate BPH resistance are involved in the metabolism or signaling pathways of SA, JA and ethylene. 'Rathu Heenati' (RH) is a rice cultivar with a high-level, broad-spectrum resistance to all BPH biotypes. Here, RH was used as the research material, while a BPH-susceptible rice cultivar 'Taichung Native 1' (TN1) was the control. A cDNA microarray analysis illuminated the resistance response at the genome level of RH under BPH infestation. The levels of SA and JA in RH and TN1 seedlings after BPH infestation were also determined. The expression pattern clustering indicated that 1467 differential probe sets may be associated with constitutive resistance and 67 with the BPH infestation-responsive resistance of RH. A Venn diagram analysis revealed 192 RH-specific and BPH-inducible probe sets. Finally, 23 BPH resistance-related gene candidates were selected based on the expression pattern clustering and Venn diagram analysis. In RH, the SA content significantly increased and the JA content significantly decreased after BPH infestation, with the former occurring prior to the latter. In RH, the differential genes in the SA pathway were synthesis-related and were up-regulated after BPH infestation. The differential genes in the JA pathway were also up-regulated. They were jasmonate ZIM-domain transcription factors, which are important negative regulators of the JA pathway. Comparatively, genes involved in the ET pathway were less affected by a BPH infestation in RH. DNA sequence analysis revealed that most BPH infestation-inducible genes may be regulated by the genetic background in a trans-acting manner, instead of by their promoters. We profiled the analysis of the global gene expression in RH and TN1 under BPH infestation

  12. The Sample at Mars Analysis (SAM) Detections of CO2 and CO in Sedimentary Material from Gale Crater, Mars: Implications for the Presence of Organic Carbon and Microbial Habitability on Mars

    Science.gov (United States)

    Sutter, Brad; Eigenbrode, Jennifer L.; Steele, Andrew; Ming, Douglas W.

    2016-01-01

    Sedimentary rock samples heated to 860 degrees Centigrade in the SAM (Sample at Mars) instrument evolved CO2 and CO indicating the presence of organic-carbon(C) in Gale Crater materials. Martian or exogenous (meteoritic, interplanetary dust) CO2 and CO could be derived from combustion of simple organics (less than 300 degrees Centigrade), complex refractory organics/amorphous carbon (300-600 degrees Centigrade), and/or magmatic carbon (greater than 600 degrees Centigrade) as result of thermal decomposition of Gale Crater perchlorates, and sulfates present that produce O2. Oxidized organic compounds could also evolve CO2 and CO over broad temperature range (150 to 800 degrees Centigrade) and such organics are expected on Mars via exogenous sources. Alternatively, organic-C could also have been oxidized to carboxylic acids [e.g, mellitic acid (RCOOH), acetate (CH3CO2-), and oxalates (C2O42-)] by oxidative radiolytic weathering, or other oxidation processes. The presence of oxidized organics is consistent with the limited detection of reduced organic-C phases by the SAM-gas chromatography. Organic-C content as determined by CO2 and CO contents could range between 800 and 2400 parts per million C indicating that substantial organic-C component is present in Gale Crater. There are contributions from SAM background however, even in worst-case scenarios, this would only account for as much as half of the detected CO2 and CO. Nevertheless, if organic-C levels were assumed to have existed in a reduced form on ancient Mars and this was bioavailable C, then less than 1 percent of C in Gale Crater sediments could have supported an exclusively heterotrophic microbial population of 1 by 10 (sup 5) cells per gram sediment (assumes 9 by 10 (sup -7) microgram per cell and 0.5 micrograms C per microgram cell). While other essential nutrients (e.g., S and P) could be limiting, organic-C contents, may have been sufficient to support limited heterotrophic microbial populations on

  13. Changes in Holocene relative sea-level and coastal morphology

    DEFF Research Database (Denmark)

    Hede, Mikkel Ulfeldt; Sander, Lasse; Clemmensen, Lars B

    2015-01-01

    Changes in relative sea-level (RSL) during the Holocene are reconstructed based on ground-penetrating radar (GPR) data collected across a raised beach ridge system on the island of Samsø, Denmark. The internal architecture of the beach ridge and swale deposits is divided into characteristic radar...... ridge progradation through time. The vertical levels of identified downlap points are combined with an age model based on optically stimulated luminescence-dated samples to reconstruct RSL for the past c. 5000 years. Overall, the reconstruction shows that the period between c. 4800 and 3800 yr BP...

  14. Structure-related clustering of gene expression fingerprints of thp-1 cells exposed to smaller polycyclic aromatic hydrocarbons.

    Science.gov (United States)

    Wan, B; Yarbrough, J W; Schultz, T W

    2008-01-01

    This study was undertaken to test the hypothesis that structurally similar PAHs induce similar gene expression profiles. THP-1 cells were exposed to a series of 12 selected PAHs at 50 microM for 24 hours and gene expressions profiles were analyzed using both unsupervised and supervised methods. Clustering analysis of gene expression profiles revealed that the 12 tested chemicals were grouped into five clusters. Within each cluster, the gene expression profiles are more similar to each other than to the ones outside the cluster. One-methylanthracene and 1-methylfluorene were found to have the most similar profiles; dibenzothiophene and dibenzofuran were found to share common profiles with fluorine. As expression pattern comparisons were expanded, similarity in genomic fingerprint dropped off dramatically. Prediction analysis of microarrays (PAM) based on the clustering pattern generated 49 predictor genes that can be used for sample discrimination. Moreover, a significant analysis of Microarrays (SAM) identified 598 genes being modulated by tested chemicals with a variety of biological processes, such as cell cycle, metabolism, and protein binding and KEGG pathways being significantly (p < 0.05) affected. It is feasible to distinguish structurally different PAHs based on their genomic fingerprints, which are mechanism based.

  15. NUCB2 gene polymorphism and its relationship with nesfatin-1 levels in polycystic ovary syndrome.

    Science.gov (United States)

    Taskin, Mine Islimye; Eser, Betul; Adali, Ertan; Kara, Hayrettin; Cuce, Coskun; Hismiogulları, Adnan Adil

    2016-01-01

    Nesfatin-1, encoded by the nucleobindin-2 (NUCB2) gene, is an anorexigenic protein related to energy metabolism, obesity, and insulin resistance. The aim of this study was to evaluate NUCB2 gene polymorphism (rs757081) and its association with serum levels of nesfatin-1 in obese and non-obese women with polycystic ovary syndrome (PCOS). In the study population, we analyzed 60 patients with PCOS and 26 age-matched healthy women as controls. The patients with PCOS were divided into two groups based on body mass index (BMI): obese group (n = 28) or non-obese group (n = 32). NUCB2 was genotyped using the polymerase chain reaction-restriction (PCR) technique. Serum nesfatin-1 level was measured by enzyme-linked immunosorbent assay (ELISA). Nesfatin-1 levels in the obese PCOS group were significantly lower than those in the non-obese PCOS and control groups (p  0.05), whereas nesfatin-1 levels in the CC and CG genotypes were lower than those in the GG genotype. Nesfatin-1 decreases in PCOS, especially in obese women, and is negatively correlated with cardiometabolic risk factors. Although genotype disturbances of NUCB2 were similar among the groups, CC and CG genotypes accompanied lower nesfatin-1 levels. C allele of NUCB2 gene polymorphism and nesfatin-1 may play a role in the pathophysiology of PCOS.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-04-15

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

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

    International Nuclear Information System (INIS)

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

    2015-01-01

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

  18. Gene-specific DNA methylation association with serum levels of C-reactive protein in African Americans.

    Directory of Open Access Journals (Sweden)

    Yan V Sun

    Full Text Available A more thorough understanding of the differences in DNA methylation (DNAm profiles in populations may hold promise for identifying molecular mechanisms through which genetic and environmental factors jointly contribute to human diseases. Inflammation is a key molecular mechanism underlying several chronic diseases including cardiovascular disease, and it affects DNAm profile on both global and locus-specific levels. To understand the impact of inflammation on the DNAm of the human genome, we investigated DNAm profiles of peripheral blood leukocytes from 966 African American participants in the Genetic Epidemiology Network of Arteriopathy (GENOA study. By testing the association of DNAm sites on CpG islands of over 14,000 genes with C-reactive protein (CRP, an inflammatory biomarker of cardiovascular disease, we identified 257 DNAm sites in 240 genes significantly associated with serum levels of CRP adjusted for age, sex, body mass index and smoking status, and corrected for multiple testing. Of the significantly associated DNAm sites, 80.5% were hypomethylated with higher CRP levels. The most significant Gene Ontology terms enriched in the genes associated with the CRP levels were immune system process, immune response, defense response, response to stimulus, and response to stress, which are all linked to the functions of leukocytes. While the CRP-associated DNAm may be cell-type specific, understanding the DNAm association with CRP in peripheral blood leukocytes of multi-ethnic populations can assist in unveiling the molecular mechanism of how the process of inflammation affects the risks of developing common disease through epigenetic modifications.

  19. Association of a Human FABP1 Gene Promoter Region Polymorphism with Altered Serum Triglyceride Levels.

    Directory of Open Access Journals (Sweden)

    Xian-E Peng

    Full Text Available Liver fatty acid-binding protein (L-FABP, also known as fatty acid-binding protein 1 (FABP1, is a key regulator of hepatic lipid metabolism. Elevated FABP1 levels are associated with an increased risk of cardiovascular disease (CVD and metabolic syndromes. In this study, we examine the association of FABP1 gene promoter variants with serum FABP1 and lipid levels in a Chinese population. Four promoter single-nucleotide polymorphisms (SNPs of FABP1 gene were genotyped in a cross-sectional survey of healthy volunteers (n = 1,182 from Fuzhou city of China. Results showed that only the rs2919872 G>A variant was significantly associated with serum TG concentration(P = 0.032.Compared with the rs2919872 G allele, rs2919872 A allele contributed significantly to reduced serum TG concentration, and this allele dramatically decreased the FABP1 promoter activity(P < 0.05. The rs2919872 A allele carriers had considerably lower serum FABP1 levels than G allele carriers (P < 0.01. In the multivariable linear regression analysis, the rs2919872 A allele was negatively associated with serum FABP1 levels (β = -0.320, P = 0.003, while serum TG levels were positively associated with serum FABP1 levels (β = 0.487, P = 0.014. Our data suggest that compared with the rs2919872 G allele, the rs2919872 A allele reduces the transcriptional activity of FABP1 promoter, and thereby may link FABP1 gene variation to TG level in humans.

  20. Nicotinamide N-Methyltransferase Suppression Participates in Nickel-Induced Histone H3 Lysine9 Dimethylation in BEAS-2B Cells

    Directory of Open Access Journals (Sweden)

    Qian Li

    2017-04-01

    Full Text Available Background: Nickel compounds are well-established human carcinogens with weak mutagenic activity. Histone methylation has been proposed to play an important role in nickel-induced carcinogenesis. Nicotinamide N-methyltransferase (NNMT decreases histone methylation in several cancer cells by altering the cellular ratio of S-adenosylmethionine (SAM to S-adenosylhomocysteine (SAH. However, the role of NNMT in nickel-induced histone methylation remains unclear. Methods: BEAS-2B cells were exposed to different concentrations of nickel chloride (NiCl2 for 72 h or 200 μM NiCl2 for different time periods. Histone H3 on lysine 9 (H3K9 mono-, di-, and trimethylation and NNMT protein levels were measured by western blot analysis. Expressions of NNMT mRNA and the H3k9me2-associated genes, mitogen-activated protein kinase 3 (MAP2K3 and dickkopf1 (DKK1, were determined by qPCR analysis. The cellular ratio of nicotinamide adenine dinucleotide (NAD+ to reduced NAD (NADH and SAM/SAH ratio were determined. Results: Exposure of BEAS-2B cells to nickel increased H3K9 dimethylation (H3K9me2, suppressed the expressions of H3K9me2-associated genes (MAP2K3 and DKK1, and induced NNMT repression at both the protein and mRNA levels. Furthermore, over-expression of NNMT inhibited nickel-induced H3K9me2 and altered the cellular SAM/SAH ratio. Additionally, the NADH oxidant phenazine methosulfate (PMS not only reversed the nickel-induced reduction in NAD+/NADH but also inhibited the increase in H3K9me2. Conclusions: These findings indicate that the repression of NNMT may underlie nickel-induced H3K9 dimethylation by altering the cellular SAM/SAH ratio.

  1. Analysis of gene expression levels in individual bacterial cells without image segmentation

    International Nuclear Information System (INIS)

    Kwak, In Hae; Son, Minjun; Hagen, Stephen J.

    2012-01-01

    Highlights: ► We present a method for extracting gene expression data from images of bacterial cells. ► The method does not employ cell segmentation and does not require high magnification. ► Fluorescence and phase contrast images of the cells are correlated through the physics of phase contrast. ► We demonstrate the method by characterizing noisy expression of comX in Streptococcus mutans. -- Abstract: Studies of stochasticity in gene expression typically make use of fluorescent protein reporters, which permit the measurement of expression levels within individual cells by fluorescence microscopy. Analysis of such microscopy images is almost invariably based on a segmentation algorithm, where the image of a cell or cluster is analyzed mathematically to delineate individual cell boundaries. However segmentation can be ineffective for studying bacterial cells or clusters, especially at lower magnification, where outlines of individual cells are poorly resolved. Here we demonstrate an alternative method for analyzing such images without segmentation. The method employs a comparison between the pixel brightness in phase contrast vs fluorescence microscopy images. By fitting the correlation between phase contrast and fluorescence intensity to a physical model, we obtain well-defined estimates for the different levels of gene expression that are present in the cell or cluster. The method reveals the boundaries of the individual cells, even if the source images lack the resolution to show these boundaries clearly.

  2. Integron types, gene cassettes and antimicrobial resistance profile of Acinetobacter baumannii isolated from BAL samples in Babol, north of Iran.

    Science.gov (United States)

    Akrami, Fariba; Shahandashti, Elaheh Ferdosi; Yahyapour, Yousef; Sadeghi, Mohsen; Khafri, Soraya; Pournajaf, Abazar; Rajabnia, Ramazan

    2017-08-01

    Multi-drug resistant isolates of Acinetobacter baumannii have created therapeutic problems worldwide. This current study was intended to determine the Integron types, gene cassettes and antimicrobial resistance profile of A. baumannii isolated from BAL samples in Babol, north of Iran. During a 15-month period, 35 A. baumannii isolates were studied. Different classes of antimicrobial agents were used to determine the resistance ratios. Multiplex-PCR was used to detect different types of integrons and associated gene cassettes. The resistance rates to GM, FEP, AK, TOB, CP, PIP, SAM, IPM, SXT, CTX, CAZ, CL, TIM, MEM, and TZP were 85.7%, 100%, 91.4%, 68.5%, 94.3%, 88.5%, 97.1%, 94.3%, 100%, 100%, 100%, 0.0%, 91.4%, 94.3% and 91.4%, respectively. The distribution analysis of int genes showed that 25.7%, 88.6% and 28.6% of isolates carried the intI, intII and intIII genes, respectively. The prevalence of aadB, dfrA1, bla-OXA 30 and aadA1 genes were 94.3%, 77.1%, 40% and 5.7%, respectively. The current study showed that a high level of A. baumannii isolates harbor integrons in our therapeutic center, which may lead to distribution of multiple antimicrobial resistance. The different types of gene cassette arrays in the present study highlight the important role of geographical features in MDR isolates dissemination which could be credited to different profiles of drug consumption in different areas. The findings emphasized that the need for continuous surveillance to prevent distribution of multidrug resistance among A. baumannii strains in Iran. Copyright © 2017. Published by Elsevier Ltd.

  3. The effect of thiopurine drugs on DNA methylation in relation to TPMT expression.

    Science.gov (United States)

    Hogarth, L A; Redfern, C P F; Teodoridis, J M; Hall, A G; Anderson, H; Case, M C; Coulthard, S A

    2008-10-15

    The thiopurine drugs 6-mercaptopurine (6-MP) and 6-thioguanine (6-TG) are well-established agents for the treatment of leukaemia but their main modes of action are controversial. Thiopurine methyltransferase (TPMT) metabolises thiopurine drugs and influences their cytotoxic activity. TPMT, like DNA methyltransferases (DNMTs), transfers methyl groups from S-adenosylmethionine (SAM) and generates S-adenosylhomocysteine (SAH). Since SAM levels are dependent on de novo purine synthesis (DNPS) and the metabolic products of 6-TG and 6-MP differ in their ability to inhibit DNPS, we postulated that 6-TG compared to 6-MP would have differential effects on changes in SAM and SAH levels and global DNA methylation, depending on TPMT status. To test this hypothesis, we used a human embryonic kidney cell line with inducible TPMT. Although changes in SAM and SAH levels occurred with each drug, decrease in global DNA methylation more closely reflected a decrease in DNMT activity. Inhibition was influenced by TPMT for 6-TG, but not 6-MP. The decrease in global methylation and DNMT activity with 6-MP, or with 6-TG when TPMT expression was low, were comparable to 5-aza-2'-deoxycytidine. However, this was not reflected in changes in methylation at the level of an individual marker gene (MAGE1A). The results suggest that a non-TPMT metabolised metabolite of 6-MP and 6-TG and the TPMT-metabolised 6-MP metabolite 6-methylthioguanosine 5'-monophosphate, contribute to a decrease in DNMT levels and global DNA methylation. As demethylating agents have shown promise in leukaemia treatment, inhibition of DNA methylation by the thiopurine drugs may contribute to their cytotoxic affects.

  4. Coastal lagoons and beach ridges as complementary sedimentary archives for the reconstruction of Holocene relative sea-level changes

    DEFF Research Database (Denmark)

    Sander, Lasse; Hede, Mikkel Ulfeldt; Fruergaard, Mikkel

    2016-01-01

    Coastal lagoons and beach ridges are genetically independent, though non-continuous, sedimentary archives. We here combine the results from two recently published studies in order to produce an 8000-year-long record of Holocene relative sea-level changes on the island of Samsø, southern Kattegat,...

  5. Probe-level linear model fitting and mixture modeling results in high accuracy detection of differential gene expression

    Directory of Open Access Journals (Sweden)

    Lemieux Sébastien

    2006-08-01

    Full Text Available Abstract Background The identification of differentially expressed genes (DEGs from Affymetrix GeneChips arrays is currently done by first computing expression levels from the low-level probe intensities, then deriving significance by comparing these expression levels between conditions. The proposed PL-LM (Probe-Level Linear Model method implements a linear model applied on the probe-level data to directly estimate the treatment effect. A finite mixture of Gaussian components is then used to identify DEGs using the coefficients estimated by the linear model. This approach can readily be applied to experimental design with or without replication. Results On a wholly defined dataset, the PL-LM method was able to identify 75% of the differentially expressed genes within 10% of false positives. This accuracy was achieved both using the three replicates per conditions available in the dataset and using only one replicate per condition. Conclusion The method achieves, on this dataset, a higher accuracy than the best set of tools identified by the authors of the dataset, and does so using only one replicate per condition.

  6. Molecular cloning and characterization of juvenile hormone acid methyltransferase in the honey bee, Apis mellifera, and its differential expression during caste differentiation.

    Directory of Open Access Journals (Sweden)

    Wenfeng Li

    Full Text Available Juvenile hormone acid methyltransferase (JHAMT is an enzyme involved in one of the final steps of juvenile hormone biosynthesis in insects. It transfers a methyl group from S-adenosyl-L-methionine (SAM to the carboxyl group of either farnesoic acid (FA or JH acid (JHA. Several genes coding for JHAMT have been cloned and characterized from insects from different orders, and they have been shown to play critical roles in metamorphosis and reproduction. However, the significance of JHAMT in Hymenopteran insects is unknown. We used RACE amplification method to clone JHAMT cDNA from the honey bee, Apis mellifera (AmJHAMT. The full length cDNA of AmJHAMT that we cloned is 1253bp long and encodes a 278-aa protein that shares 32-36% identity with known JHAMTs. A SAM-binding motif, conserved in the SAM-dependent methyltransferase (SAM-MT superfamily, is present in AmJHAMT. Its secondary structure also contains a typical SAM-MT fold. Most of the active sites bound with SAM and substrates (JHA or FA are conserved in AmJHAMT as in other JHAMT orthologs. Phylogenetic analysis clustered AmJHAMT with the other orthologs from Hymenoptera to form a major clade in the phylogenetic tree. Purified recombinant AmJHAMT protein expressed in E. coli was used to produce polyclonal antibodies and to verify the identity of AmJHAMT by immunoblotting and mass spectrometry. Quantitative RT-PCR and immunoblotting analyses revealed that queen larvae contained significantly higher levels of AmJHAMT mRNA and protein than worker larvae during the periods of caste development. The temporal profiles of both AmJHAMT mRNA and protein in queens and workers showed a similar pattern as the JH biosynthesis. These results suggest that the gene that we cloned codes for a functional JHAMT that catalyzes the final reactions of JH biosynthesis in honey bees. In addition, AmJHAMT may play an important role in honey bee caste differentiation.

  7. Identification of distal regulatory regions in the human alpha IIb gene locus necessary for consistent, high-level megakaryocyte expression.

    Science.gov (United States)

    Thornton, Michael A; Zhang, Chunyan; Kowalska, Maria A; Poncz, Mortimer

    2002-11-15

    The alphaIIb/beta3-integrin receptor is present at high levels only in megakaryocytes and platelets. Its presence on platelets is critical for hemostasis. The tissue-specific nature of this receptor's expression is secondary to the restricted expression of alphaIIb, and studies of the alphaIIb proximal promoter have served as a model of a megakaryocyte-specific promoter. We have examined the alphaIIb gene locus for distal regulatory elements. Sequence comparison between the human (h) and murine (m) alphaIIb loci revealed high levels of conservation at intergenic regions both 5' and 3' to the alphaIIb gene. Additionally, deoxyribonuclease (DNase) I sensitivity mapping defined tissue-specific hypersensitive (HS) sites that coincide, in part, with these conserved regions. Transgenic mice containing various lengths of the h(alpha)IIb gene locus, which included or excluded the various conserved/HS regions, demonstrated that the proximal promoter was sufficient for tissue specificity, but that a region 2.5 to 7.1 kb upstream of the h(alpha)IIb gene was necessary for consistent expression. Another region 2.2 to 7.4 kb downstream of the gene enhanced expression 1000-fold and led to levels of h(alpha)IIb mRNA that were about 30% of the native m(alpha)IIb mRNA level. These constructs also resulted in detectable h(alpha)IIb/m(beta)3 on the platelet surface. This work not only confirms the importance of the proximal promoter of the alphaIIb gene for tissue specificity, but also characterizes the distal organization of the alphaIIb gene locus and provides an initial localization of 2 important regulatory regions needed for the expression of the alphaIIb gene at high levels during megakaryopoiesis.

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

    Science.gov (United States)

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

    2009-09-01

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

  9. The Influence of Mineralogy on Recovering Organic Acids from Mars Analogue Materials Using the One-Pot Derivatization Experiment on the Sample Analysis at Mars(SAM) Instrument Suite

    Science.gov (United States)

    Stalport, Fabien; Glavin, Daniel P.; Eigenbrode, J. L.; Bish, D.; Blake, D.; Coll, P.; Szopa, C.; Buch, A.; McAdam, A.; Dworkin, J. P.; hide

    2012-01-01

    The search for complex organic molecules on Mars, including important biomolecules such as amino acids and carboxylic acids, will require a chemical extraction and a derivatization step to transform these organic compounds into species that are sufficiently volatile to be detected by gas chromatography mass spectrometry (GCMS). We have developed a ''one-pot'' extraction and chemical derivatization protocol using N-methyl-N-(tert-butyldimethylsilyl) trifluoroacetamide (MTBSTFA) and dimethylformamide (DMF) for the Sample Analysis at Mars (SAM) experiment instrument suite on NASA's the Mars Science Laboratory (MSL) mission. The temperature and duration of the derivatization reaction, pre-concentration of chemical derivatives, and gas chromatographic separation parameters have been optimized under SAM instrument design constraints. MTBSTFA/DMF extraction and derivatization at 300 1C for several minutes of a variety of terrestrial Mars analog materials facilitated the detection of amino acids and carboxylic acids in a surface soil sample collected from the Atacama Desert and a carbonate-rich stromatolite sample from Svalbard. However, the rapid reaction of MTBSTFA with water in several analog materials that contained high abundances of hydrated minerals, and the possible deactivation of derivatized compounds by iron oxides, as detected by XRD/XRF using the CheMin field unit Terra, proved to be highly problematic for the direct extraction of organics using MTBSTFA. The combination of pyrolysis and two different wet-chemical derivatization methods employed by SAM should enable a wide range of organic compounds to be detected by GCMS if present on Mars.

  10. Cloned Bacillus subtilis alkaline protease (aprA) gene showing high level of keratinolytic activity.

    Science.gov (United States)

    Zaghloul, T I

    1998-01-01

    The Bacillus subtilis alkaline protease(aprA) gene was previously cloned on a pUBHO-derivative plasmid. High levels of expression and gene stability were demonstrated when B. subtilis cells were grown on the laboratory medium 2XSG. B. subtilis cells harboring the multicopy aprA gene were grown on basal medium, supplemented with 1 % chicken feather as a source of energy, carbon, and nitrogen. Proteolytic and keratinolytic activities were monitored throughout the cultivation time. A high level of keratinolytic activity was obtained, and this indicates that alkaline protease is acting as a keratinase. Furthermore, considerable amounts of soluble proteins and free amino acids were obtained as a result of the enzymatic hydrolysis of feather. Biodegradation of feather waste using these cells represents an alternative way to improve the nutritional value of feather, since feather waste is currently utilized on a limited basis as a dietary protein supplement for animal feedstuffs. Moreover, the release of free amino acids from feather and the secreted keratinase enzyme would promote industries based on feather waste.

  11. Impact analysis of side door of a car and bullet proof vest with material ‘SAM2X5-630’ using finite element analysis

    Science.gov (United States)

    Dhode, Trushant; Patil, Girish; Rajkumar, E.

    2017-11-01

    The components which are bound to impact are subjected to deformation even though it may be for a small scale. The efforts are always on for finding the best material to take impact that has no failure or moreover, less plastic deformation. A newly found material which is glass matrix steel named as ‘SAM2X5-630’ has astounding high elastic limit of 12.5GPa. Thus it can take powerful impact & regain its original shape avoiding the deformation of component under impact. The paper is focused on performing the Finite element analysis to assess the behaviour of ‘SAM2X5-630’ steel under impact loading of side door of car as well as impact of bullet on bulletproof jacket on which the material is assigned. The displacement or deformation occurred during impact is found to be lesser than known materials like Kevlar in bulletproof vest and Aluminium alloy in car door.

  12. Distinct gene expression signatures in human embryonic stem cells differentiated towards definitive endoderm at single-cell level

    DEFF Research Database (Denmark)

    Norrman, Karin; Strömbeck, Anna; Semb, Henrik

    2013-01-01

    for the three activin A based protocols applied. Our data provide novel insights in DE gene expression at the cellular level of in vitro differentiated human embryonic stem cells, and illustrate the power of using single-cell gene expression profiling to study differentiation heterogeneity and to characterize...... of anterior definitive endoderm (DE). Here, we differentiated human embryonic stem cells towards DE using three different activin A based treatments. Differentiation efficiencies were evaluated by gene expression profiling over time at cell population level. A panel of key markers was used to study DE...... formation. Final DE differentiation was also analyzed with immunocytochemistry and single-cell gene expression profiling. We found that cells treated with activin A in combination with sodium butyrate and B27 serum-free supplement medium generated the most mature DE cells. Cell population studies were...

  13. A felkelés éghajlata: Sam White környezettörténeti elmélete az Oszmán Birodalom hanyatlásáról - The Climate of Rebellion: Sam White’s Environmental Theory about the Decline of the Ottoman Empire

    Directory of Open Access Journals (Sweden)

    RÁCZ, Lajos

    2014-09-01

    Full Text Available The book of Sam White has offered a new interpretation of Ottoman history from the 16th to the 18th centuries. The American author has argued that historians have to consider the ecological conditions of the early modern Near East and the profound impacts and repercussions of the Little Ice Age in order to understand the empire’s successes, crises and transformations. White’s study presents the expansive ‘imperial ecology’ underlying the rapid expansion in the classical age which made the empire increasingly vulnerable to war and natural disasters as the population pressure set in in the late 1500s. Sam White examined the impact of Little Ice Age and climatic fluctuation from the late 16th through the early 18th centuries, demonstrating the strong links between extreme climatic events and the outbreak of the Celali Rebellion and the recurring disorders of the 1600s. Finally, the author argued that transformations in human ecology – particularly the spread of nomadic pastoralism, migration to urban areas, and a shift to new crops for commerce and exports – slowed the demographic recovery of Ottoman lands, leaving the empire relatively depopulated by the mid-19th century.

  14. Investigation of Surface Pre-Treatment Methods for Wafer-Level Cu-Cu Thermo-Compression Bonding

    Directory of Open Access Journals (Sweden)

    Koki Tanaka

    2016-12-01

    Full Text Available To increase the yield of the wafer-level Cu-Cu thermo-compression bonding method, certain surface pre-treatment methods for Cu are studied which can be exposed to the atmosphere before bonding. To inhibit re-oxidation under atmospheric conditions, the reduced pure Cu surface is treated by H2/Ar plasma, NH3 plasma and thiol solution, respectively, and is covered by Cu hydride, Cu nitride and a self-assembled monolayer (SAM accordingly. A pair of the treated wafers is then bonded by the thermo-compression bonding method, and evaluated by the tensile test. Results show that the bond strengths of the wafers treated by NH3 plasma and SAM are not sufficient due to the remaining surface protection layers such as Cu nitride and SAMs resulting from the pre-treatment. In contrast, the H2/Ar plasma–treated wafer showed the same strength as the one with formic acid vapor treatment, even when exposed to the atmosphere for 30 min. In the thermal desorption spectroscopy (TDS measurement of the H2/Ar plasma–treated Cu sample, the total number of the detected H2 was 3.1 times more than the citric acid–treated one. Results of the TDS measurement indicate that the modified Cu surface is terminated by chemisorbed hydrogen atoms, which leads to high bonding strength.

  15. The Ability of Different Imputation Methods to Preserve the Significant Genes and Pathways in Cancer.

    Science.gov (United States)

    Aghdam, Rosa; Baghfalaki, Taban; Khosravi, Pegah; Saberi Ansari, Elnaz

    2017-12-01

    Deciphering important genes and pathways from incomplete gene expression data could facilitate a better understanding of cancer. Different imputation methods can be applied to estimate the missing values. In our study, we evaluated various imputation methods for their performance in preserving significant genes and pathways. In the first step, 5% genes are considered in random for two types of ignorable and non-ignorable missingness mechanisms with various missing rates. Next, 10 well-known imputation methods were applied to the complete datasets. The significance analysis of microarrays (SAM) method was applied to detect the significant genes in rectal and lung cancers to showcase the utility of imputation approaches in preserving significant genes. To determine the impact of different imputation methods on the identification of important genes, the chi-squared test was used to compare the proportions of overlaps between significant genes detected from original data and those detected from the imputed datasets. Additionally, the significant genes are tested for their enrichment in important pathways, using the ConsensusPathDB. Our results showed that almost all the significant genes and pathways of the original dataset can be detected in all imputed datasets, indicating that there is no significant difference in the performance of various imputation methods tested. The source code and selected datasets are available on http://profiles.bs.ipm.ir/softwares/imputation_methods/. Copyright © 2017. Production and hosting by Elsevier B.V.

  16. Upregulation of biotransformation genes in gills of oyster Crassostrea brasiliana exposed in situ to urban effluents, Florianópolis Bay, Southern Brazil.

    Science.gov (United States)

    Pessatti, Tomás B; Lüchmann, Karim H; Flores-Nunes, Fabrício; Mattos, Jacó J; Sasaki, Sílvio T; Taniguchi, Satie; Bícego, Márcia C; Dias Bainy, Afonso Celso

    2016-09-01

    The release of untreated sanitary sewage, combined with unplanned urban growth, are major factors contributing to degradation of coastal ecosystems in developing countries, including Brazil. Sanitary sewage is a complex mixture of chemicals that can negatively affect aquatic organisms. The use of molecular biomarkers can help to understand and to monitor the biological effects elicited by contaminants. The aim of this study was to evaluate changes in transcript levels of genes related to xenobiotic biotransformation in the gills of oysters Crassostrea brasiliana transplanted and kept for 24h at three areas potentially contaminated by sanitary sewage (Bücheller river, BUC; Biguaçu river, BIG; and Ratones island, RAT), one farming area (Sambaqui beach, SAM) and at one reference site (Forte beach, FOR) in the North Bay of Santa Catarina Island (Florianópolis, Brazil). Transcript levels of four cytochrome P450 isoforms (CYP2AU1, CYP3A-like, CYP356A1-like and CYP20A1-like), three glutathione S-transferase (GST alpha-like, GST pi-like and GST microsomal 3-like) and one sulfotransferase gene (SULT-like) were evaluated by means of quantitative reverse transcription PCR (qRT-PCR). Chemical analysis of the sediment from each site were performed and revealed the presence of aliphatic and polycyclic aromatic hydrocarbons, linear alkylbenzenes and fecal sterols in the contaminated areas (BUC and BIG). Water quality analysis showed that these sites had the highest levels of fecal coliforms and other parameters evidencing the presence of urban sewage discharges. Among the results for gene transcription, CYP2AU1 and SULT-like levels were upregulated by 20 and 50-fold, respectively, in the oysters kept for 24h at the most contaminated site (BUC), suggesting a role of these genes in the detoxification of organic pollutants. These data reinforce that gills possibly have an important role in xenobiotic metabolism and highlight the use of C. brasiliana as a sentinel for monitoring

  17. Analysis of gene expression levels in individual bacterial cells without image segmentation.

    Science.gov (United States)

    Kwak, In Hae; Son, Minjun; Hagen, Stephen J

    2012-05-11

    Studies of stochasticity in gene expression typically make use of fluorescent protein reporters, which permit the measurement of expression levels within individual cells by fluorescence microscopy. Analysis of such microscopy images is almost invariably based on a segmentation algorithm, where the image of a cell or cluster is analyzed mathematically to delineate individual cell boundaries. However segmentation can be ineffective for studying bacterial cells or clusters, especially at lower magnification, where outlines of individual cells are poorly resolved. Here we demonstrate an alternative method for analyzing such images without segmentation. The method employs a comparison between the pixel brightness in phase contrast vs fluorescence microscopy images. By fitting the correlation between phase contrast and fluorescence intensity to a physical model, we obtain well-defined estimates for the different levels of gene expression that are present in the cell or cluster. The method reveals the boundaries of the individual cells, even if the source images lack the resolution to show these boundaries clearly. Copyright © 2012 Elsevier Inc. All rights reserved.

  18. Analysis of gene expression levels in individual bacterial cells without image segmentation

    Energy Technology Data Exchange (ETDEWEB)

    Kwak, In Hae; Son, Minjun [Physics Department, University of Florida, P.O. Box 118440, Gainesville, FL 32611-8440 (United States); Hagen, Stephen J., E-mail: sjhagen@ufl.edu [Physics Department, University of Florida, P.O. Box 118440, Gainesville, FL 32611-8440 (United States)

    2012-05-11

    Highlights: Black-Right-Pointing-Pointer We present a method for extracting gene expression data from images of bacterial cells. Black-Right-Pointing-Pointer The method does not employ cell segmentation and does not require high magnification. Black-Right-Pointing-Pointer Fluorescence and phase contrast images of the cells are correlated through the physics of phase contrast. Black-Right-Pointing-Pointer We demonstrate the method by characterizing noisy expression of comX in Streptococcus mutans. -- Abstract: Studies of stochasticity in gene expression typically make use of fluorescent protein reporters, which permit the measurement of expression levels within individual cells by fluorescence microscopy. Analysis of such microscopy images is almost invariably based on a segmentation algorithm, where the image of a cell or cluster is analyzed mathematically to delineate individual cell boundaries. However segmentation can be ineffective for studying bacterial cells or clusters, especially at lower magnification, where outlines of individual cells are poorly resolved. Here we demonstrate an alternative method for analyzing such images without segmentation. The method employs a comparison between the pixel brightness in phase contrast vs fluorescence microscopy images. By fitting the correlation between phase contrast and fluorescence intensity to a physical model, we obtain well-defined estimates for the different levels of gene expression that are present in the cell or cluster. The method reveals the boundaries of the individual cells, even if the source images lack the resolution to show these boundaries clearly.

  19. Role of Renin-Angiotensin-converting Enzyme Level and ACE Gene Polymorphism in Patients with Nonalcoholic Fatty Liver Disease.

    Science.gov (United States)

    Tekatas, Demet D; Bahcecioglu, Ibrahim H; Ispiroglu, Murat; Sahin, Abdurrahman; Ilhan, Necip; Yalniz, Mehmet; Demirel, Ulvi

    2016-01-01

    In this study, we aimed to investigate the histological and clinical effect of angiotensin-converting enzyme (ACE) and ACE gene polymorphism in nonalcoholic fatty liver disease (NAFLD) and their roles in the progression of the disease. Liver function tests, body mass index, waist circumference, lipid parameters, fasting blood glucose (FBG), hemoglobin A1c (HbA1c), homeostasis model assessment-IR (HOMA-IR), ACE, and ACE gene polymorphism were evaluated in the NAFLD group and control group. The study group was evaluated by dividing the group into four subgroups by ACE gene polymorphism (D/D homozygous, I/I homozygous, D/I heterozygous, I/D heterozygous). Liver biopsies were evaluated according to Brunt Classification. A total of 31 patients who were diagnosed with NAFLD and 40 healthy individuals were included in the study. The ACE level was found to be 11.69 ± 1.99 in the NAFLD group and 11.52 ± 1.72 in the control group (p = 0.70). There was a negative correlation between ACE levels and HOMA-IR levels (p = 0.008, r= -0.512). Biochemical parameters were not different among ACE gene polimorphism subgroups, except FBG (between D/D, I/D and D/I, I/D; p = 0.02). When the ACE levels were compared in terms of grade and stage, no significant difference was found (for stage and grade p = 0.68). The ACE gene polymorphism subgroups did not differ by histopathologic findings; grade and stage (for grade p = 0.42, for stage p = 0.92). In this study, we could not find a correlation of ACE and ACE gene polymorphism with metabolic risk factors and the disease severity in NAFLD. Tekatas DD, Bahcecioglu IH, Ispiroglu M, Sahin A, Ilhan N, Yalniz M, Demirel U. Role of Renin-Angiotensin-converting Enzyme Level and ACE Gene Polymorphism in Patients with Nonalcoholic Fatty Liver Disease. Euroasian J Hepato-Gastroenterol 2016;6(2):137-142.

  20. Improved score statistics for meta-analysis in single-variant and gene-level association studies.

    Science.gov (United States)

    Yang, Jingjing; Chen, Sai; Abecasis, Gonçalo

    2018-06-01

    Meta-analysis is now an essential tool for genetic association studies, allowing them to combine large studies and greatly accelerating the pace of genetic discovery. Although the standard meta-analysis methods perform equivalently as the more cumbersome joint analysis under ideal settings, they result in substantial power loss under unbalanced settings with various case-control ratios. Here, we investigate the power loss problem by the standard meta-analysis methods for unbalanced studies, and further propose novel meta-analysis methods performing equivalently to the joint analysis under both balanced and unbalanced settings. We derive improved meta-score-statistics that can accurately approximate the joint-score-statistics with combined individual-level data, for both linear and logistic regression models, with and without covariates. In addition, we propose a novel approach to adjust for population stratification by correcting for known population structures through minor allele frequencies. In the simulated gene-level association studies under unbalanced settings, our method recovered up to 85% power loss caused by the standard methods. We further showed the power gain of our methods in gene-level tests with 26 unbalanced studies of age-related macular degeneration . In addition, we took the meta-analysis of three unbalanced studies of type 2 diabetes as an example to discuss the challenges of meta-analyzing multi-ethnic samples. In summary, our improved meta-score-statistics with corrections for population stratification can be used to construct both single-variant and gene-level association studies, providing a useful framework for ensuring well-powered, convenient, cross-study analyses. © 2018 WILEY PERIODICALS, INC.

  1. Detection of Evolved Carbon Dioxide in the Rocknest Eolian Bedform by the Sample Analysis at Mars(SAM) Instrument at the Mars Curiosity Landing Site

    Science.gov (United States)

    Sutter, B.; Archer, D.; McAdam, A.; Franz, H.; Ming, D. W.; Eigenbrode, J. L.; Glavin, D. P.; Mahaffy, P.; Stern, J.; Navarro-Gonzalez, R.

    2013-01-01

    The Sample Analysis at Mars (SAM) instrument detected four releases of carbon dioxide (CO2) that ranged from 100 to 700 C from the Rocknest eolian bedform material (Fig. 1). Candidate sources of CO2 include adsorbed CO2, carbonate(s), combusted organics that are either derived from terrestrial contamination and/or of martian origin, occluded or trapped CO2, and other sources that have yet to be determined. The Phoenix Lander s Thermal Evolved Gas Analyzer (TEGA) detected two CO2 releases (400-600, 700-840 C) [1,2]. The low temperature release was attributed to Fe- and/or Mg carbonates [1,2], per-chlorate interactions with carbonates [3], nanophase carbonates [4] and/or combusted organics [1]. The high temperature CO2 release was attributed to a calcium bearing carbonate [1,2]. No evidence of a high temperature CO2 release similar to the Phoenix material was detected in the Rocknest materials by SAM. The objectives of this work are to evaluate the temperature and total contribution of each Rocknest CO2 release and their possible sources. Four CO2 releases from the Rocknest material were detected by SAM. Potential sources of CO2 are adsorbed CO2, (peak 1) and Fe/Mg carbonates (peak 4). Only a fraction of peaks 2 and 3 (0.01 C wt.%) may be partially attributed to combustion of organic contamination. Meteoritic organics mixed in the Rocknest bedform could be present, but the peak 2 and 3 C concentration (approx.0.21 C wt. %) is likely too high to be attributed solely to meteoritic organic C. Other inorganic sources of C such as interactions of perchlorates and carbonates and sources yet to be identified will be evaluated to account for CO2 released from the thermal decomposition of Rocknest material.

  2. A genome-wide study of DNA methylation patterns and gene expression levels in multiple human and chimpanzee tissues.

    Directory of Open Access Journals (Sweden)

    Athma A Pai

    2011-02-01

    Full Text Available The modification of DNA by methylation is an important epigenetic mechanism that affects the spatial and temporal regulation of gene expression. Methylation patterns have been described in many contexts within and across a range of species. However, the extent to which changes in methylation might underlie inter-species differences in gene regulation, in particular between humans and other primates, has not yet been studied. To this end, we studied DNA methylation patterns in livers, hearts, and kidneys from multiple humans and chimpanzees, using tissue samples for which genome-wide gene expression data were also available. Using the multi-species gene expression and methylation data for 7,723 genes, we were able to study the role of promoter DNA methylation in the evolution of gene regulation across tissues and species. We found that inter-tissue methylation patterns are often conserved between humans and chimpanzees. However, we also found a large number of gene expression differences between species that might be explained, at least in part, by corresponding differences in methylation levels. In particular, we estimate that, in the tissues we studied, inter-species differences in promoter methylation might underlie as much as 12%-18% of differences in gene expression levels between humans and chimpanzees.

  3. Stabilization of Ag nanostructures by tuning their Fermi levels

    Science.gov (United States)

    Tani, Tadaaki; Kan, Ryota; Yamano, Yuka; Uchida, Takayuki

    2018-05-01

    The oxidation of Ag nanostructures has been studied as a key step for their degradation under the guiding principle in the previous paper that they are stable when their Fermi level is lower than those of their surroundings. The drop of the Fermi level of a thin Ag layer was caused by the formation of self-assembled monolayers (SAMs) of certain organic compounds including those of photographic interest and a monolayer of AgI, and attributed to the formation of dielectric layers, whose positive charges were closer to the Ag layer than negative charges. A consideration is given on further examinations needed to realize the above guiding principle in individual devices.

  4. Electrochemistry of 2-dimethylaminoethanethiol SAM on gold electrode: Interaction with SWCNT-poly(m-aminobenzene sulphonic acid), electric field-induced protonation-deprotonation, and surface pKa

    CSIR Research Space (South Africa)

    Pillay, J

    2009-06-01

    Full Text Available -called electric field induced protonation-deprotonation process, hitherto observed for the -COOH terminated SAMs, is also observed for the -N(H)+(CH3)2 terminated. The surface pKa of DMAET was estimated as 7.6, smaller than its solution pKa of 10.8. It is also...

  5. Analysis of genes that influence sheep follicular development by different nutrition levels during the luteal phase using expression profiling.

    Science.gov (United States)

    Luo, F; Jia, R; Ying, S; Wang, Z; Wang, F

    2016-06-01

    Nutrition is an important factor that regulates reproductive performance of sheep and affects follicle development. However, the correlation between nutrition and follicle development is poorly understood at the molecular level. To study its possible molecular mechanisms, we performed expression profiling of granulosa cells isolated from sheep that were fed different levels of nutrition levels during the luteal phase. To do this, ewes received a maintenance diet (M), and their estrus was synchronized by intravaginal progestogen sponges for 12 days. Ewes were randomly divided into the short-term dietary-restricted group (R; 0.5 × M) and the nutrient-supplemented group (S; 1.5 × M). RNA samples were extracted from granulosa cells. Transcriptome libraries from each group were constructed by Illumina sequencing. Among 18 468 detected genes, 170 genes were significantly differentially expressed, of which 140 genes were upregulated and 30 genes were downregulated in group S relative to group R. These genes could be candidates regulating follicular development in sheep. Gene Ontology, KEGG and clustering analyses were performed. Genes related to oocyte meiosis, such as ADCY7, were upregulated. We identified two important groups of related genes that were upregulated with improved nutrition: one group comprising the genes PTGS2, UCP2 and steroidogenic acute regulatory protein and the other group comprising interleukin-1A and interleukin-1B. The genes within each group showed similar expression patterns. Additionally, all five genes are involved in the reproduction process. Quantitative real-time PCR was performed to validate the results of expression profiling. These data in our study are an abundant genomic resource to expand the understanding of the molecular and cellular events underlying follicle development. © 2016 Stichting International Foundation for Animal Genetics.

  6. Neuropeptide S and BDNF gene expression in the amygdala are influenced by social decision-making under stress

    Directory of Open Access Journals (Sweden)

    Justin P. Smith

    2014-04-01

    Full Text Available In a newly developed conceptual model of stressful social decision making, the Stress-Alternatives Model (SAM; used for the 1st time in mice elicits two types of response: escape or remain submissively. Daily (4d aggressive social interaction in a neutral arena between a C57BL6/N test mouse and a larger, novel aggressive CD1 mouse, begin after an audible tone (conditioned stimulus; CS. Although escape holes (only large enough for smaller test animals are available, and the aggressor is unremittingly antagonistic, only half of the mice tested utilize the possibility of escape. During training, for mice that choose to leave the arena and social interaction, latency to escape dramatically decreases over time; this is also true for control C57BL6/N mice which experienced no aggression. Therefore, the open field of the SAM apparatus is intrinsically anxiogenic. It also means that submission to the aggressor is chosen despite this anxiety and the high intensity of the aggressive attacks and defeat. While both groups that received aggression displayed stress responsiveness, corticosterone levels were significantly higher in animals that chose submissive coexistence. Although both escaping and non-escaping groups of animals experienced aggression and defeat, submissive animals also exhibited classic fear conditioning, freezing in response to the CS alone, while escaping animals did not. In the basolateral amygdala, gene expression of BDNF was diminished, but NPS expression was significantly elevated, but only in submissive animals. This increase in submission-evoked NPS mRNA expression was greatest in the central amygdala, which coincided with decreased BDNF expression. Reduced expression of BDNF is only in submissive animals that also exhibit elevated NPS expression, despite elevated corticosterone in all socially interacting animals. The results suggest an interwoven relationship, linked by social context, between amygdalar BDNF, NPS and plasma

  7. Endostatin gene variation and protein levels in breast cancer susceptibility and severity

    International Nuclear Information System (INIS)

    Balasubramanian, Sabapathy P; Cross, Simon S; Globe, Jenny; Cox, Angela; Brown, Nicola J; Reed, Malcolm W

    2007-01-01

    Endostatin is a potent endogenous anti-angiogenic agent which inhibits tumour growth. A non-synonymous coding polymorphism in the Endostatin gene is thought to affect Endostatin activity. We aimed to determine the role of this Endostatin polymorphism in breast cancer pathogenesis and any influence on serum Endostatin levels in healthy volunteers. Endostatin protein expression on a breast cancer micro array was also studied to determine any relationship to genotype and to breast cancer prognosis. The 4349G > A (coding non-synonymous) polymorphism in exon 42 of the Endostatin gene was genotyped in approximately 846 breast cancer cases and 707 appropriate controls. In a separate healthy cohort of 57 individuals, in addition to genotyping, serum Endostatin levels were measured using enzyme linked immunosorbant assay (ELISA). A semi-quantitative assessment of Endostatin protein expression on immunostained tissue micro arrays (TMA) constructed from breast cancer samples of patients with genotype data was performed. The rare allele (A) was significantly associated with invasive breast cancers compared to non-invasive tumours (p = 0.03), but there was no association with tumour grade, nodal status, vascular invasion or overall survival. There was no association with breast cancer susceptibility. Serum Endostatin levels and Endostatin protein expression on the tissue micro array were not associated with genotype. The Endostatin 4349A allele is associated with invasive breast cancer. The Endostatin 4349G > A polymorphism however does not appear to be associated with breast cancer susceptibility or severity in invasive disease. By studying circulating levels and tumour Endostatin protein expression, we have shown that any influence of this polymorphism is unlikely to be through an effect on the levels of protein produced

  8. Progranulin gene variation affects serum progranulin levels differently in Danish bipolar individuals compared with healthy controls.

    Science.gov (United States)

    Buttenschøn, Henriette N; Nielsen, Marit N; Thotakura, Gangadaar; Lee, Chris W; Nykjær, Anders; Mors, Ole; Glerup, Simon

    2017-06-01

    The identification of peripheral biomarkers for bipolar disorder is of great importance and has the potential to improve diagnosis, treatment and prognosis. Recent studies have reported lower plasma progranulin levels in bipolar individuals compared with controls and association with single nucleotide polymorphisms (SNPs) within the progranulin gene (GRN). In the present study, we investigated the effect of GRN and sortilin (SORT1) gene variation on serum progranulin levels in bipolar individuals and controls. In a Danish cohort of individuals with bipolar disorder and controls, we analysed the serum progranulin level (nbipolar=80, ncontrols=76) and five SNPs located within GRN and two SNPs near the SORT1 gene encoding sortilin, a progranulin scavenger receptor known to affect circulating progranulin levels (nbipolar=166, ncontrols=186). We observed no significant difference in the serum progranulin level between cases and controls and none of the analysed SNPs located within GRN or close to SORT1 were associated with bipolar disorder. Crude and adjusted (adjusted for case-control status, sex and age) linear regression analyses showed no effect of any SNPs on the serum progranulin level. However, we observed that the mean serum progranulin level in cases and controls is affected differently depending on the genotypes of two SNPs within GRN (rs2879096 and rs4792938). The sample size is relatively small and detailed information on medication and polarity of the disorder is not available. No correction for multiple testing was performed. Our study suggests that the potential of progranulin as a biomarker for bipolar disorder is genotype dependent.

  9. Photobiomodulation effects on mRNA levels from genomic and chromosome stabilization genes in injured muscle.

    Science.gov (United States)

    da Silva Neto Trajano, Larissa Alexsandra; Trajano, Eduardo Tavares Lima; da Silva Sergio, Luiz Philippe; Teixeira, Adilson Fonseca; Mencalha, Andre Luiz; Stumbo, Ana Carolina; de Souza da Fonseca, Adenilson

    2018-04-26

    Muscle injuries are the most prevalent type of injury in sports. A great number of athletes have relapsed in muscle injuries not being treated properly. Photobiomodulation therapy is an inexpensive and safe technique with many benefits in muscle injury treatment. However, little has been explored about the infrared laser effects on DNA and telomeres in muscle injuries. Thus, the aim of this study was to evaluate photobiomodulation effects on mRNA relative levels from genes related to telomere and genomic stabilization in injured muscle. Wistar male rats were randomly divided into six groups: control, laser 25 mW, laser 75 mW, injury, injury laser 25 mW, and injury laser 75 mW. Photobiomodulation was performed with 904 nm, 3 J/cm 2 at 25 or 75 mW. Cryoinjury was induced by two applications of a metal probe cooled in liquid nitrogen directly on the tibialis anterior muscle. After euthanasia, skeletal muscle samples were withdrawn and total RNA extracted for evaluation of mRNA levels from genomic (ATM and p53) and chromosome stabilization (TRF1 and TRF2) genes by real-time quantitative polymerization chain reaction. Data show that photobiomodulation reduces the mRNA levels from ATM and p53, as well reduces mRNA levels from TRF1 and TRF2 at 25 and 75 mW in injured skeletal muscle. In conclusion, photobiomodulation alters mRNA relative levels from genes related to genomic and telomere stabilization in injured skeletal muscle.

  10. RNA deep sequencing reveals novel candidate genes and polymorphisms in boar testis and liver tissues with divergent androstenone levels.

    Directory of Open Access Journals (Sweden)

    Asep Gunawan

    Full Text Available Boar taint is an unpleasant smell and taste of pork meat derived from some entire male pigs. The main causes of boar taint are the two compounds androstenone (5α-androst-16-en-3-one and skatole (3-methylindole. It is crucial to understand the genetic mechanism of boar taint to select pigs for lower androstenone levels and thus reduce boar taint. The aim of the present study was to investigate transcriptome differences in boar testis and liver tissues with divergent androstenone levels using RNA deep sequencing (RNA-Seq. The total number of reads produced for each testis and liver sample ranged from 13,221,550 to 33,206,723 and 12,755,487 to 46,050,468, respectively. In testis samples 46 genes were differentially regulated whereas 25 genes showed differential expression in the liver. The fold change values ranged from -4.68 to 2.90 in testis samples and -2.86 to 3.89 in liver samples. Differentially regulated genes in high androstenone testis and liver samples were enriched in metabolic processes such as lipid metabolism, small molecule biochemistry and molecular transport. This study provides evidence for transcriptome profile and gene polymorphisms of boars with divergent androstenone level using RNA-Seq technology. Digital gene expression analysis identified candidate genes in flavin monooxygenease family, cytochrome P450 family and hydroxysteroid dehydrogenase family. Moreover, polymorphism and association analysis revealed mutation in IRG6, MX1, IFIT2, CYP7A1, FMO5 and KRT18 genes could be potential candidate markers for androstenone levels in boars. Further studies are required for proving the role of candidate genes to be used in genomic selection against boar taint in pig breeding programs.

  11. Beyond reading level: a systematic review of the suitability of cancer education print and Web-based materials.

    Science.gov (United States)

    Finnie, Ramona K C; Felder, Tisha M; Linder, Suzanne Kneuper; Mullen, Patricia Dolan

    2010-12-01

    Consideration of categories related to reading comprehension--beyond reading level--is imperative to reach low literacy populations effectively. "Suitability" has been proposed as a term to encompass six categories of such factors: content, literacy demand graphics, layout/typography, learning stimulation, and cultural appropriateness. Our purpose was to describe instruments used to evaluate categories of suitability in cancer education materials in published reports and their findings. We searched databases and reference lists for evaluations of print and Web-based cancer education materials to identify and describe measures of these categories. Studies had to evaluate reading level and at least one category of suitability. Eleven studies met our criteria. Seven studies reported inter-rater reliability. Cultural appropriateness was most often assessed; four instruments assessed only surface aspects of cultural appropriateness. Only two of seven instruments used, the suitability assessment of materials (SAM) and the comprehensibility assessment of materials (SAM + CAM), were described as having any evidence of validity. Studies using Simplified Measure of Goobledygook (SMOG) and Fry reported higher average reading level scores than those using Flesh-Kincaid. Most materials failed criteria for reading level and cultural appropriateness. We recommend more emphasis on the categories of suitability for those developing cancer education materials and more study of these categories and reliability and validity testing of instruments.

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

    Science.gov (United States)

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

    2012-01-01

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

  13. Correlation of mRNA and protein levels: Cell type-specific gene expression of cluster designation antigens in the prostate

    Directory of Open Access Journals (Sweden)

    Deutsch Eric W

    2008-05-01

    Full Text Available Abstract Background: Expression levels of mRNA and protein by cell types exhibit a range of correlations for different genes. In this study, we compared levels of mRNA abundance for several cluster designation (CD genes determined by gene arrays using magnetic sorted and laser-capture microdissected human prostate cells with levels of expression of the respective CD proteins determined by immunohistochemical staining in the major cell types of the prostate – basal epithelial, luminal epithelial, stromal fibromuscular, and endothelial – and for prostate precursor/stem cells and prostate carcinoma cells. Immunohistochemical stains of prostate tissues from more than 50 patients were scored for informative CD antigen expression and compared with cell-type specific transcriptomes. Results: Concordance between gene and protein expression findings based on 'present' vs. 'absent' calls ranged from 46 to 68%. Correlation of expression levels was poor to moderate (Pearson correlations ranged from 0 to 0.63. Divergence between the two data types was most frequently seen for genes whose array signals exceeded background (> 50 but lacked immunoreactivity by immunostaining. This could be due to multiple factors, e.g. low levels of protein expression, technological sensitivities, sample processing, probe set definition or anatomical origin of tissue and actual biological differences between transcript and protein abundance. Conclusion: Agreement between these two very different methodologies has great implications for their respective use in both molecular studies and clinical trials employing molecular biomarkers.

  14. Peatland succession induces a shift in the community composition of Sphagnum-associated active methanotrophs.

    Science.gov (United States)

    Putkinen, Anuliina; Larmola, Tuula; Tuomivirta, Tero; Siljanen, Henri M P; Bodrossy, Levente; Tuittila, Eeva-Stiina; Fritze, Hannu

    2014-06-01

    Sphagnum-associated methanotrophs (SAM) are an important sink for the methane (CH4) formed in boreal peatlands. We aimed to reveal how peatland succession, which entails a directional change in several environmental variables, affects SAM and their activity. Based on the pmoA microarray results, SAM community structure changes when a peatland develops from a minerotrophic fen to an ombrotrophic bog. Methanotroph subtypes Ia, Ib, and II showed slightly contrasting patterns during succession, suggesting differences in their ecological niche adaptation. Although the direct DNA-based analysis revealed a high diversity of type Ib and II methanotrophs throughout the studied peatland chronosequence, stable isotope probing (SIP) of the pmoA gene indicated they were active mainly during the later stages of succession. In contrast, type Ia methanotrophs showed active CH4 consumption in all analyzed samples. SIP-derived (13)C-labeled 16S rRNA gene clone libraries revealed a high diversity of SAM in every succession stage including some putative Methylocella/Methyloferula methanotrophs that are not detectable with the pmoA-based approach. In addition, a high diversity of 16S rRNA gene sequences likely representing cross-labeled nonmethanotrophs was discovered, including a significant proportion of Verrucomicrobia-related sequences. These results help to predict the effects of changing environmental conditions on SAM communities and activity. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  15. Finding differentially expressed genes in high dimensional data: Rank based test statistic via a distance measure.

    Science.gov (United States)

    Mathur, Sunil; Sadana, Ajit

    2015-12-01

    We present a rank-based test statistic for the identification of differentially expressed genes using a distance measure. The proposed test statistic is highly robust against extreme values and does not assume the distribution of parent population. Simulation studies show that the proposed test is more powerful than some of the commonly used methods, such as paired t-test, Wilcoxon signed rank test, and significance analysis of microarray (SAM) under certain non-normal distributions. The asymptotic distribution of the test statistic, and the p-value function are discussed. The application of proposed method is shown using a real-life data set. © The Author(s) 2011.

  16. Calpain-5 gene variants are associated with diastolic blood pressure and cholesterol levels

    Directory of Open Access Journals (Sweden)

    Morón Francisco J

    2007-01-01

    Full Text Available Abstract Background Genes implicated in common complex disorders such as obesity, type 2 diabetes mellitus (T2DM or cardiovascular diseases are not disease specific, since clinically related disorders also share genetic components. Cysteine protease Calpain 10 (CAPN10 has been associated with T2DM, hypertension, hypercholesterolemia, increased body mass index (BMI and polycystic ovary syndrome (PCOS, a reproductive disorder of women in which isunlin resistance seems to play a pathogenic role. The calpain 5 gene (CAPN5 encodes a protein homologue of CAPN10. CAPN5 has been previously associated with PCOS by our group. In this new study, we have analysed the association of four CAPN5 gene variants(rs948976A>G, rs4945140G>A, rs2233546C>T and rs2233549G>A with several cardiovascular risk factors related to metabolic syndrome in general population. Methods Anthropometric measurements, blood pressure, insulin, glucose and lipid profiles were determined in 606 individuals randomly chosen from a cross-sectional population-based epidemiological survey in the province of Segovia in Central Spain (Castille, recruited to investigate the prevalence of anthropometric and physiological parameters related to obesity and other components of the metabolic syndrome. Genotypes at the four polymorphic loci in CAPN5 gene were detected by polymerase chain reaction (PCR. Results Genotype association analysis was significant for BMI (p ≤ 0.041, diastolic blood pressure (p = 0.015 and HDL-cholesterol levels (p = 0.025. Different CAPN5 haplotypes were also associated with diastolic blood pressure (DBP (0.0005 ≤ p ≤ 0.006 and total cholesterol levels (0.001 ≤ p ≤ 0.029. In addition, the AACA haplotype, over-represented in obese individuals, is also more frequent in individuals with metabolic syndrome defined by ATPIII criteria (p = 0.029. Conclusion As its homologue CAPN10, CAPN5 seems to influence traits related to increased risk for cardiovascular diseases. Our

  17. PathMAPA: a tool for displaying gene expression and performing statistical tests on metabolic pathways at multiple levels for Arabidopsis

    Directory of Open Access Journals (Sweden)

    Ma Ligeng

    2003-11-01

    Full Text Available Abstract Background To date, many genomic and pathway-related tools and databases have been developed to analyze microarray data. In published web-based applications to date, however, complex pathways have been displayed with static image files that may not be up-to-date or are time-consuming to rebuild. In addition, gene expression analyses focus on individual probes and genes with little or no consideration of pathways. These approaches reveal little information about pathways that are key to a full understanding of the building blocks of biological systems. Therefore, there is a need to provide useful tools that can generate pathways without manually building images and allow gene expression data to be integrated and analyzed at pathway levels for such experimental organisms as Arabidopsis. Results We have developed PathMAPA, a web-based application written in Java that can be easily accessed over the Internet. An Oracle database is used to store, query, and manipulate the large amounts of data that are involved. PathMAPA allows its users to (i upload and populate microarray data into a database; (ii integrate gene expression with enzymes of the pathways; (iii generate pathway diagrams without building image files manually; (iv visualize gene expressions for each pathway at enzyme, locus, and probe levels; and (v perform statistical tests at pathway, enzyme and gene levels. PathMAPA can be used to examine Arabidopsis thaliana gene expression patterns associated with metabolic pathways. Conclusion PathMAPA provides two unique features for the gene expression analysis of Arabidopsis thaliana: (i automatic generation of pathways associated with gene expression and (ii statistical tests at pathway level. The first feature allows for the periodical updating of genomic data for pathways, while the second feature can provide insight into how treatments affect relevant pathways for the selected experiment(s.

  18. In Silico Gene-Level Evolution Explains Microbial Population Diversity through Differential Gene Mobility

    NARCIS (Netherlands)

    van Dijk, Bram; Hogeweg, P.

    2016-01-01

    Microbial communities can show astonishing ecological and phylogenetic diversity. What is the role of pervasive horizontal gene transfer (HGT) in shaping this diversity in the presence of clonally expanding "killer strains"? Does HGT of antibiotic production and resistance genes erase phylogenetic

  19. Depletion of cellular brassinolide decreases embryo production and disrupts the architecture of the apical meristems in Brassica napus microspore-derived embryos.

    Science.gov (United States)

    Belmonte, Mark; Elhiti, Mohamed; Waldner, Blaine; Stasolla, Claudio

    2010-06-01

    Exogenous applications of brassinolide (BL) increased the number and quality of microspore-derived embryos (MDEs) whereas treatments with brassinazole (BrZ), a BL biosynthetic inhibitor, had the opposite effect. At the optimal concentration (4x10(-6) M) BrZ decreased both embryo yield and conversion to less than half the value of control embryos. Metabolic studies revealed that BL levels had profound effects on glutathione and ascorbate metabolism by altering the amounts of their reduced forms (ASC and GSH) and oxidized forms [dehydroascorbate (DHA), ascorbate free radicals (AFRs), and GSSG]. Applications of BL switched the glutathione and ascorbate pools towards the oxidized forms, thereby lowering the ASC/ASC+DHA+AFR and GSH/GSH+GSSG ratios. These changes were ascribed to the ability of BL to increase the activity of ascorbate peroxidase (APX) and decrease that of glutathione reductase (GR). This trend was reversed in a BL-depleted environment, effected by BrZ applications. These metabolic alterations were associated with changes in embryo structure and performance. BL-treated MDEs developed zygotic-like shoot apical meristems (SAMs) whereas embryos treated with BrZ developed abnormal meristems. In the presence of BrZ, embryos either lacked a visible SAM, or formed SAMs in which the meristematic cells showed signs of differentiation, such as vacuolation and storage product accumulation. These abnormalities were accompanied by the lack or misexpression of three meristem marker genes isolated from Brassica napus (denoted as BnSTM, BnCLV1, and BnZLL-1) homologous to the Arabidopsis SHOOTMERISTEMLESS (STM), CLAVATA 1 (CLV1), and ZWILLE (ZLL). The expression of BnSTM and BnCLV1 increased after a few days in cultures in embryos treated with BL whereas an opposite tendency was observed with applications of BrZ. Compared with control embryos where these two genes exhibited abnormal localization patterns, BnSTM and BnCLV1 always localized throughout the subapical domains

  20. [Selection and construction of cell line stably expressing survivin gene in lower level through eukaryotic plasmid vector of shRNA].

    Science.gov (United States)

    Wang, Wen-Xia; Sun, Shan-Zhen; Song, Ying

    2008-06-01

    To construct a short hairpin RNA(shRNA) interference expression plasmid vector of survivin gene, transfect tongue squamous cell carcinoma line Tca8113 which expressed survivin gene in a high level, and choose the cells whose survivin gene were suppressed significantly. Two pairs of oligonucleotide sequences specific for survivin gene were designed and synthesized, and cloned into pSilencer-2.1U6-neo plasmid. The recombinant plasmids (named PS1 and PS2) were amplified in Ecoli. DH5alpha was identified by restriction digestion, PCR and sequencing. The vectors were transfected into Tca8113 cells with lipofectamine 2000. After selection with G418, the stable cell clones were attained. Survivn expression was assayed with real-time quantitative PCR and Western blotting. SAS8.0 software package was used for Student t test. Two vectors were constructed successfully and stable cell clones with PS1 or PS2 plasmid were obtained. As compared with those of control, survivin expression of transfected cell with PS1 or PS2 in mRNA level was significantly suppressed (P<0.05). In protein level, only those of transfected cell with PS2 was significantly suppressed (P<0.01). The shRNA interference expression plasmid vectors of survivin gene are successfully constructed, and Tca8113 cells which express survivin gene in a stable lower level are attained, which enable us to carry out further research on gene therapy of oral squamous cell carcinoma. Supported by National Natural Science Foundation of China (Grant No.30572056).

  1. Re-engineering SAM or Changing the Engine in the Train While it is Running

    Science.gov (United States)

    Illingworth, R.; Mengel, M.; Norman, A.

    2015-12-01

    In the last few years at Fermilab we re-architect-ed our SAM1[1] family of data catalog and file transfer tools - including major changes - while continuing to transfer over 1 Pb/month of data to multiple existing experiments and bring new experiments on board. This work was done with less than 3 FTE-years of effort, and the changes made include major ones, such as changing interprocess communication protocols, migrating database back-ends, removing and replacing major components, and supporting new file delivery methods. This paper will summarize the approaches we have used to do this, including using design patterns like the Facade, Adapter, and Command patterns, and assisting experiments one at a time with client migration. This process has allowed us to modernize our infrastructure with reasonable costs in both calendar time and developer effort, while continuing to provide the operating service to our customers with minimal interruptions.

  2. Nitrogenase activity of Herbaspirillum seropedicae grown under low iron levels requires the products of nifXorf1 genes.

    Science.gov (United States)

    Klassen, Giseli; de Oliveira Pedrosa, Fábio; de Souza, Emanuel M; Yates, M Geoffrey; Rigo, Liu Un

    2003-07-29

    Herbaspirillum seropedicae strains mutated in the nifX or orf1 genes showed 90% or 50% reduction in nitrogenase activity under low levels of iron or molybdenum respectively. Mutations in nifX or orf1 genes did not affect nif gene expression since a nifH::lacZ fusion was fully active in both mutants. nifX and the contiguous gene orf1 are essential for maximum nitrogen fixation under iron limitation and are probably involved in synthesis of nitrogenase iron or iron-molybdenum clusters.

  3. An Idea of 20% test of the Initial Core Reactor Physics

    International Nuclear Information System (INIS)

    Roh, Kyung Ho; Yang, Sung Tae; Jung, Ji Eun

    2012-01-01

    Many tests have been performed on the OPR1000 and APR1400 before commercial operation. Some of these tests were performed at reactor power levels of 20% and 50%. The CPC (Core Protection Calculator) power distribution test is one of these tests. It is performed to assure the reliability of the Core Protection Calculator System (CPCS). Through this test, SAM1 is calculated using the snapshots2. The test takes about nine hours at a reactor power level of 20% and about thirty hours at a reactor power level of 50%. SAM used at each reactor power level is as follows: 1. Reactor power of 0% ∼ 20%: Designed SAM (DSAM) 2. Reactor power of 20% ∼ 50%: SAM calculated (C-SAM) at a reactor power of 20% 3. Reactor power 50% ∼ End of Cycle : SAM calculated at a reactor power of 50% As mentioned earlier, SAM is calculated and punched into CPC to assure the reliability of CPCS. Therefore, CPC is operated having penalties with D-SAM until3 reaching a reactor power of 20%. That is, the penalty of CPC will be removed when SAM is calculated and punched into the CPC at a reactor power of 20%. But these penalties are considered to be removed after a reactor power of 50% test in order to maintain the conservatism of the CPC. This is done because the final values calculated using C-SAM, in contrast to those calculated using SAM, a reactor power of 50%, are not correct. This paper began from an idea, 'If so, what would happen if we removed the CPC power distribution test at a reactor power of 20%?'

  4. Did life exist on Mars? Search for organic and inorganic signatures, one of the goals for ``SAM'' (sample analysis at Mars)

    Science.gov (United States)

    Cabane, M.; Coll, P.; Szopa, C.; Israël, G.; Raulin, F.; Sternberg, R.; Mahaffy, P.; Person, A.; Rodier, C.; Navarro-Gonzàlez, R.; Niemann, H.; Harpold, D.; Brinckerhoff, W.

    2004-01-01

    Observation of Mars shows signs of a past Earth-like climate, and, in that case, there is no objection to the possible development of life, in the underground or at the surface, as in the terrestrial primitive biosphere. Sample analysis at Mars (SAM) is an experiment which may be proposed for atmospheric, ground and underground in situ measurements. One of its goals is to bring direct or indirect information on the possibility for life to have developed on Mars, and to detect traces of past or present biological activity. With this aim, it focuses on the detection of organic molecules: volatile organics are extracted from the sample by simple heating, whereas refractory molecules are made analyzable (i.e. volatile), using derivatization technique or fragmentation by pyrolysis. Gaseous mixtures thus obtained are analyzed by gas chromatography associated to mass spectrometry. Beyond organics, carbonates and other salts are associated to the dense and moist atmosphere necessary to the development of life, and might have formed and accumulated in some places on Mars. They represent another target for SAM. Heating of the samples allows the analysis of structural gases of these minerals (CO2 from carbonates, etc.), enabling to identify them. We also show, in this paper, that it may be possible to discriminate between abiotic minerals, and minerals (shells, etc.) created by living organisms.

  5. Polyunsaturated Fatty Acid Status and Physical Activity Level in Children Admitted with Severe Acute Malnutrition

    DEFF Research Database (Denmark)

    Babirekere-Iriso, Esther

    Severe acute malnutrition (SAM) is a worldwide problem although it commonly occurs in children living in low-income countries. SAM may be associated with reduced relative contribution of whole-blood polyunsaturated fatty acids (PUFA) yet PUFA play very important roles in the body such as immune...

  6. Analysis of baseline gene expression levels from ...

    Science.gov (United States)

    The use of gene expression profiling to predict chemical mode of action would be enhanced by better characterization of variance due to individual, environmental, and technical factors. Meta-analysis of microarray data from untreated or vehicle-treated animals within the control arm of toxicogenomics studies has yielded useful information on baseline fluctuations in gene expression. A dataset of control animal microarray expression data was assembled by a working group of the Health and Environmental Sciences Institute's Technical Committee on the Application of Genomics in Mechanism Based Risk Assessment in order to provide a public resource for assessments of variability in baseline gene expression. Data from over 500 Affymetrix microarrays from control rat liver and kidney were collected from 16 different institutions. Thirty-five biological and technical factors were obtained for each animal, describing a wide range of study characteristics, and a subset were evaluated in detail for their contribution to total variability using multivariate statistical and graphical techniques. The study factors that emerged as key sources of variability included gender, organ section, strain, and fasting state. These and other study factors were identified as key descriptors that should be included in the minimal information about a toxicogenomics study needed for interpretation of results by an independent source. Genes that are the most and least variable, gender-selectiv

  7. Codon Optimization Significantly Improves the Expression Level of α-Amylase Gene from Bacillus licheniformis in Pichia pastoris

    Directory of Open Access Journals (Sweden)

    Jian-Rong Wang

    2015-01-01

    Full Text Available α-Amylase as an important industrial enzyme has been widely used in starch processing, detergent, and paper industries. To improve expression efficiency of recombinant α-amylase from Bacillus licheniformis (B. licheniformis, the α-amylase gene from B. licheniformis was optimized according to the codon usage of Pichia pastoris (P. pastoris and expressed in P. pastoris. Totally, the codons encoding 305 amino acids were optimized in which a total of 328 nucleotides were changed and the G+C content was increased from 47.6 to 49.2%. The recombinants were cultured in 96-deep-well microplates and screened by a new plate assay method. Compared with the wild-type gene, the optimized gene is expressed at a significantly higher level in P. pastoris after methanol induction for 168 h in 5- and 50-L bioreactor with the maximum activity of 8100 and 11000 U/mL, which was 2.31- and 2.62-fold higher than that by wild-type gene. The improved expression level makes the enzyme a good candidate for α-amylase production in industrial use.

  8. Verticillium dahliae-Arabidopsis Interaction Causes Changes in Gene Expression Profiles and Jasmonate Levels on Different Time Scales

    Directory of Open Access Journals (Sweden)

    Sandra S. Scholz

    2018-02-01

    Full Text Available Verticillium dahliae is a soil-borne vascular pathogen that causes severe wilt symptoms in a wide range of plants. Co-culture of the fungus with Arabidopsis roots for 24 h induces many changes in the gene expression profiles of both partners, even before defense-related phytohormone levels are induced in the plant. Both partners reprogram sugar and amino acid metabolism, activate genes for signal perception and transduction, and induce defense- and stress-responsive genes. Furthermore, analysis of Arabidopsis expression profiles suggests a redirection from growth to defense. After 3 weeks, severe disease symptoms can be detected for wild-type plants while mutants impaired in jasmonate synthesis and perception perform much better. Thus, plant jasmonates have an important influence on the interaction, which is already visible at the mRNA level before hormone changes occur. The plant and fungal genes that rapidly respond to the presence of the partner might be crucial for early recognition steps and the future development of the interaction. Thus they are potential targets for the control of V. dahliae-induced wilt diseases.

  9. On sulfur core level binding energies in thiol self-assembly and alternative adsorption sites: An experimental and theoretical study

    International Nuclear Information System (INIS)

    Jia, Juanjuan; Kara, Abdelkader; Pasquali, Luca; Bendounan, Azzedine; Sirotti, Fausto; Esaulov, Vladimir A.

    2015-01-01

    Characteristic core level binding energies (CLBEs) are regularly used to infer the modes of molecular adsorption: orientation, organization, and dissociation processes. Here, we focus on a largely debated situation regarding CLBEs in the case of chalcogen atom bearing molecules. For a thiol, this concerns the case when the CLBE of a thiolate sulfur at an adsorption site can be interpreted alternatively as due to atomic adsorption of a S atom, resulting from dissociation. Results of an investigation of the characteristics of thiol self-assembled monolayers (SAMs) obtained by vacuum evaporative adsorption are presented along with core level binding energy calculations. Thiol ended SAMs of 1,4-benzenedimethanethiol (BDMT) obtained by evaporation on Au display an unconventional CLBE structure at about 161.25 eV, which is close to a known CLBE of a S atom on Au. Adsorption and CLBE calculations for sulfur atoms and BDMT molecules are reported and allow delineating trends as a function of chemisorption on hollow, bridge, and atop sites and including the presence of adatoms. These calculations suggest that the 161.25 eV peak is due to an alternative adsorption site, which could be associated to an atop configuration. Therefore, this may be an alternative interpretation, different from the one involving the adsorption of atomic sulfur resulting from the dissociation process of the S–C bond. Calculated differences in S(2p) CLBEs for free BDMT molecules, SH group sulfur on top of the SAM, and disulfide are also reported to clarify possible errors in assignments

  10. On sulfur core level binding energies in thiol self-assembly and alternative adsorption sites: An experimental and theoretical study

    Energy Technology Data Exchange (ETDEWEB)

    Jia, Juanjuan [Institut des Sciences Moléculaires d’Orsay, Université-Paris Sud, 91405 Orsay (France); CNRS, UMR 8214, Institut des Sciences Moléculaires d’Orsay, Orsay ISMO, Bâtiment 351, Université Paris Sud, 91405 Orsay (France); Kara, Abdelkader, E-mail: abdelkader.kara@ucf.edu, E-mail: vladimir.esaulov@u-psud.fr [Department of Physics, University of Central Florida, Orlando, Florida 32816 (United States); Pasquali, Luca [Dipartimento di Ingegneria “E. Ferrari,” Università di Modena e Reggio Emilia, Via Vignolese 905, 41125 Modena (Italy); IOM-CNR, s.s. 14, Km. 163.5 in AREA Science Park, 34149 Basovizza, Trieste (Italy); Department of Physics, University of Johannesburg, P.O. Box 524, Auckland Park 2006 (South Africa); Bendounan, Azzedine; Sirotti, Fausto [Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin, BP 48, F-91192 Gif-sur-Yvette Cedex (France); Esaulov, Vladimir A., E-mail: abdelkader.kara@ucf.edu, E-mail: vladimir.esaulov@u-psud.fr [Institut des Sciences Moléculaires d’Orsay, Université-Paris Sud, 91405 Orsay (France); CNRS, UMR 8214, Institut des Sciences Moléculaires d’Orsay, Orsay ISMO, Bâtiment 351, Université Paris Sud, 91405 Orsay (France); IOM-CNR, s.s. 14, Km. 163.5 in AREA Science Park, 34149 Basovizza, Trieste (Italy)

    2015-09-14

    Characteristic core level binding energies (CLBEs) are regularly used to infer the modes of molecular adsorption: orientation, organization, and dissociation processes. Here, we focus on a largely debated situation regarding CLBEs in the case of chalcogen atom bearing molecules. For a thiol, this concerns the case when the CLBE of a thiolate sulfur at an adsorption site can be interpreted alternatively as due to atomic adsorption of a S atom, resulting from dissociation. Results of an investigation of the characteristics of thiol self-assembled monolayers (SAMs) obtained by vacuum evaporative adsorption are presented along with core level binding energy calculations. Thiol ended SAMs of 1,4-benzenedimethanethiol (BDMT) obtained by evaporation on Au display an unconventional CLBE structure at about 161.25 eV, which is close to a known CLBE of a S atom on Au. Adsorption and CLBE calculations for sulfur atoms and BDMT molecules are reported and allow delineating trends as a function of chemisorption on hollow, bridge, and atop sites and including the presence of adatoms. These calculations suggest that the 161.25 eV peak is due to an alternative adsorption site, which could be associated to an atop configuration. Therefore, this may be an alternative interpretation, different from the one involving the adsorption of atomic sulfur resulting from the dissociation process of the S–C bond. Calculated differences in S(2p) CLBEs for free BDMT molecules, SH group sulfur on top of the SAM, and disulfide are also reported to clarify possible errors in assignments.

  11. Watt-level passively Q-switched double-cladding fiber laser based on graphene oxide saturable absorber.

    Science.gov (United States)

    Yu, Zhenhua; Song, Yanrong; Dong, Xinzheng; Li, Yanlin; Tian, Jinrong; Wang, Yonggang

    2013-10-10

    A watt-level passively Q-switched ytterbium-doped double-cladding fiber laser with a graphene oxide (GO) absorber was demonstrated. The structure of the GO saturable absorber mirror (GO-SAM) was of the sandwich type. A maximum output power of 1.8 W was obtained around a wavelength of 1044 nm. To the best of our knowledge, this is the highest output power in Q-switched fiber lasers based on a GO saturable absorber. The pure GO was protected from the oxygen in the air so that the damage threshold of the GO-SAM was effectively raised. The gain fiber was a D-shaped ytterbium-doped double-cladding fiber. The pulse repetition rates were tuned from 120 to 215 kHz with pump powers from 3.89 to 7.8 W. The maximum pulse energy was 8.37 μJ at a pulse width of 1.7 μs.

  12. Stoichiometric Representation of Gene–Protein–Reaction Associations Leverages Constraint-Based Analysis from Reaction to Gene-Level Phenotype Prediction

    DEFF Research Database (Denmark)

    Machado, Daniel; Herrgard, Markus; Rocha, Isabel

    2016-01-01

    only describe the metabolic phenotype at the reaction level, understanding the mechanistic link between genotype and phenotype is still hampered by the complexity of gene-protein-reaction associations. We implement a model transformation that enables constraint-based methods to be applied at the gene...... design methods are not actually feasible, and show how our approach allows using the same methods to obtain feasible gene-based designs. We also show, by extensive comparison with experimental 13C-flux data, how simple reformulations of different simulation methods with gene-wise objective functions...

  13. [Clinical significance of calcitonin gene-related peptide level before and after treatment in patients with chronic periodontitis].

    Science.gov (United States)

    Yan, Ying; Xiang, Xue-Rong; Wang, Chun; Ye, Guo; Fan, Xiao-Ping

    2016-08-01

    To explore the clinical significance of calcitonin gene-related peptide (CGRP) levels in patients with chronic periodontitis before and after treatment, and to detect the calcitonin gene-related peptide content in human venous blood. Thirty healthy controls and thirty patients with mild, moderate, severe periodontitis were enrolled from August 2014 to June 2015.CGRP level in the patients' peripheral blood was detected by ELISA. Three months after periodontal treatment, CGRP level in mild, moderate, severe periodontitis patients' peripheral blood was re-examined by ELISA. Then the correlation between calcitonin gene-related peptide and inflammation of chronic periodontitis was analyzed with SPSS 22.0 software package. The content of CGRP in healthy controls was significantly higher than that in patients with periodontitis. With the aggravation of periodontal inflammation, blood level of CGRP decreased gradually, and the lowest was in patients with severe periodontitis (Pperiodontal treatment, CGRP content was significantly higher compared with that before treatment (Pperiodontitis (P>0.05). The level of CGRP in venous blood decreased with the increasing severity of chronic periodontitis, and CGRP was negatively correlated with the degree of inflammation of chronic periodontitis. CGRP may be involved in the occurrence and development of chronic periodontitis. CGRP content in serum of patients with chronic periodontitis after treatment was significantly increased, CGRP may be used as the basis for clinical detection of chronic periodontitis.

  14. Neighboring Genes Show Correlated Evolution in Gene Expression

    Science.gov (United States)

    Ghanbarian, Avazeh T.; Hurst, Laurence D.

    2015-01-01

    When considering the evolution of a gene’s expression profile, we commonly assume that this is unaffected by its genomic neighborhood. This is, however, in contrast to what we know about the lack of autonomy between neighboring genes in gene expression profiles in extant taxa. Indeed, in all eukaryotic genomes genes of similar expression-profile tend to cluster, reflecting chromatin level dynamics. Does it follow that if a gene increases expression in a particular lineage then the genomic neighbors will also increase in their expression or is gene expression evolution autonomous? To address this here we consider evolution of human gene expression since the human-chimp common ancestor, allowing for both variation in estimation of current expression level and error in Bayesian estimation of the ancestral state. We find that in all tissues and both sexes, the change in gene expression of a focal gene on average predicts the change in gene expression of neighbors. The effect is highly pronounced in the immediate vicinity (genes increasing their expression in humans tend to avoid nuclear lamina domains and be enriched for the gene activator 5-hydroxymethylcytosine, we conclude that, most probably owing to chromatin level control of gene expression, a change in gene expression of one gene likely affects the expression evolution of neighbors, what we term expression piggybacking, an analog of hitchhiking. PMID:25743543

  15. Immunohistochemical expression of EGFR in colorectal carcinoma correlates with high but not low level gene amplification, as demonstrated by CISH.

    Science.gov (United States)

    Hemmings, Chris; Broomfield, Amy; Bean, Elaine; Whitehead, Martin; Yip, Desmond

    2009-01-01

    To assess and compare immunohistochemical expression of epidermal growth factor receptor (EGFR) with gene amplification as demonstrated by chromogenic in situ hybridisation (CISH), in colorectal adenocarcinoma. Sections from 100 consecutive colorectal cancer resection specimens were stained for EGFR using immunohistochemistry and CISH. Immunohistochemical assessment was independently performed at two laboratories, using the same antibody and protocols. With immunohistochemistry, strong circumferential membrane staining (3+ staining) was demonstrated in only 5% of cases, and this was only focal in three of five cases. At one laboratory, weak or incomplete staining (1+ or 2+) was observed in five further cases (5%), which had been negative at the other laboratory. CISH demonstrated high level gene amplification (>10 copies/nucleus) in the same five cases which had demonstrated 3+ staining with immunohistochemistry, and in those cases where the staining was focal, the amplification was demonstrated in the same foci of the tumour. Five further cases (5%) had low level amplification (5-10 copies per nucleus); these cases did not exhibit significant positive staining with immunohistochemistry. All the cases which demonstrated gene amplification (high or low level) arose in the distal colon. There was no correlation between gene amplification status and a variety of other variables, including stage at diagnosis, mucinous differentiation, neuroendocrine differentiation, or loss of expression of mismatch repair proteins. Immunohistochemical expression of EGFR is variable between laboratories, even using standardised protocols. 3+ staining is predictive of high level gene amplification, but correlates very poorly with low level amplification, which may still be clinically significant. In some cases gene amplification was only focal, offering a potential explanation for poor response to targeted therapy in patients with EGFR positive tumours.

  16. Tracking the MSL-SAM methane detection source location Through Mars Regional Atmospheric Modeling System (MRAMS)

    Science.gov (United States)

    Pla-García, Jorge

    2016-04-01

    1. Introduction: The putative in situ detection of methane by Sample Analysis at Mars (SAM) instrument suite on Curiosi-ty at Gale crater has garnered significant attention because of the potential implications for the presence of geological methane sources or indigenous Martian organisms [1, 2]. SAM reported detection of back-ground levels of atmospheric methane of mean value 0.69±0.25 parts per billion by volume (ppbv) at the 95% confidence interval (CI). Additionally, in four sequential measurements spanning a 60-sol period, SAM observed elevated levels of methane of 7.2±2.1 ppbv (95% CI), implying that Mars is episodically producing methane from an additional unknown source. There are many major unresolved questions regard-ing this detection: 1) What are the potential sources of the methane release? 2) What causes the rapid decrease in concentration? and 3) Where is the re-lease location? 4) How spatially extensive is the re-lease? 5) For how long is CH4 released? Regarding the first question, the source of methane, is so far not identified. It could be related with geo-logical process like methane release from clathrates [3], serpentinisation [4] and volcanism [5]; or due to biological activity from methanogenesis [6]. To answer the second question, the rapid decrease in concentration, it is important to note that the photo-chemical lifetime of methane is of order 100 years, much longer than the atmospheric mixing time scale, and thus the gas should tend to be well mixed except near a source or shortly after an episodic release. The observed spike of 7 ppb from the background of System (MRAMS). The model was focused on rover locations using nested grids with a spacing of 330 meters on the in-nermost grid that is centered over the landing [8, 9]. MRAMS is ideally suited for this investigation; the model is explicitly designed to simulate Mars' at-mospheric circulations at the mesoscale and smaller with realistic, high-resolution surface properties [10, 11

  17. Identification of 8-methyladenosine as the modification catalyzed by the radical SAM methyltransferase Cfr that confers antibiotic resistance in bacteria

    DEFF Research Database (Denmark)

    Giessing, Anders; Jensen, Søren Skov; Rasmussen, Anette

    2009-01-01

    The Cfr methyltransferase confers combined resistance to five different classes of antibiotics that bind to the peptidyl transferase center of bacterial ribosomes. The Cfr-mediated modification has previously been shown to occur on nucleotide A2503 of 23S rRNA and has a mass corresponding......,8-dimethyladenosine. The mutation of single conserved cysteine residues in the radical SAM motif CxxxCxxC of Cfr abolishes its activity, lending support to the notion that the Cfr modification reaction occurs via a radical-based mechanism. Antibiotic susceptibility data confirm that the antibiotic resistance...

  18. Feature level fusion for enhanced geological mapping of ophiolile complex using ASTER and Landsat TM data

    International Nuclear Information System (INIS)

    Pournamdari, M; Hashim, M

    2014-01-01

    Chromite ore deposit occurrence is related to ophiolite complexes as a part of the oceanic crust and provides a good opportunity for lithological mapping using remote sensing data. The main contribution of this paper is a novel approaches to discriminate different rock units associated with ophiolite complex using the Feature Level Fusion technique on ASTER and Landsat TM satellite data at regional scale. In addition this study has applied spectral transform approaches, consisting of Spectral Angle Mapper (SAM) to distinguish the concentration of high-potential areas of chromite and also for determining the boundary between different rock units. Results indicated both approaches show superior outputs compared to other methods and can produce a geological map for ophiolite complex rock units in the arid and the semi-arid region. The novel technique including feature level fusion and Spectral Angle Mapper (SAM) discriminated ophiolitic rock units and produced detailed geological maps of the study area. As a case study, Sikhoran ophiolite complex located in SE, Iran has been selected for image processing techniques. In conclusion, a suitable approach for lithological mapping of ophiolite complexes is demonstrated, this technique contributes meaningfully towards economic geology in terms of identifying new prospects

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

    Science.gov (United States)

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

    2013-01-04

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

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

    Science.gov (United States)

    Dill, Kariena K; Amacher, Sharon L

    2005-11-15

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

  1. Evaluation of the effect of divalent metal transporter 1 gene polymorphism on blood iron, lead and cadmium levels

    Energy Technology Data Exchange (ETDEWEB)

    Kayaaltı, Zeliha, E-mail: kayaalti@ankara.edu.tr; Akyüzlü, Dilek Kaya; Söylemezoğlu, Tülin

    2015-02-15

    Divalent metal transporter 1 (DMT1), a member of the proton-coupled metal ion transporter family, mediates transport of ferrous iron from the lumen of the intestine into the enterocyte and export of iron from endocytic vesicles. It has an affinity not only for iron but also for other divalent cations including manganese, cobalt, nickel, cadmium, lead, copper, and zinc. DMT1 is encoded by the SLC11a2 gene that is located on chromosome 12q13 in humans and express four major mammalian isoforms (1A/+IRE, 1A/-IRE, 2/+IRE and 2/-IRE). Mutations or polymorphisms of DMT1 gene may have an impact on human health by disturbing metal trafficking. To study the possible association of DMT1 gene with the blood levels of some divalent cations such as iron, lead and cadmium, a single nucleotide polymorphism (SNP) (IVS4+44C/A) in DMT1 gene was investigated in 486 unrelated and healthy individuals in a Turkish population by method of polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP). The genotype frequencies were found as 49.8% homozygote typical (CC), 38.3% heterozygote (CA) and 11.9% homozygote atypical (AA). Metal levels were analyzed by dual atomic absorption spectrometer system and the average levels of iron, lead and cadmium in the blood samples were 446.01±81.87 ppm, 35.59±17.72 ppb and 1.25±0.87 ppb, respectively. Individuals with the CC genotype had higher blood iron, lead and cadmium levels than those with AA and CA genotypes. Highly statistically significant associations were detected between IVS4+44 C/A polymorphism in the DMT1 gene and iron and lead levels (p=0.001 and p=0.036, respectively), but no association was found with cadmium level (p=0.344). This study suggested that DMT1 IVS4+44 C/A polymorphism is associated with inter-individual variations in blood iron, lead and cadmium levels. - Highlights: • DMT1 IVS4+44 C/A polymorphism is associated with inter-individual variations in blood iron, cadmium and lead levels.

  2. Evaluation of the effect of divalent metal transporter 1 gene polymorphism on blood iron, lead and cadmium levels

    International Nuclear Information System (INIS)

    Kayaaltı, Zeliha; Akyüzlü, Dilek Kaya; Söylemezoğlu, Tülin

    2015-01-01

    Divalent metal transporter 1 (DMT1), a member of the proton-coupled metal ion transporter family, mediates transport of ferrous iron from the lumen of the intestine into the enterocyte and export of iron from endocytic vesicles. It has an affinity not only for iron but also for other divalent cations including manganese, cobalt, nickel, cadmium, lead, copper, and zinc. DMT1 is encoded by the SLC11a2 gene that is located on chromosome 12q13 in humans and express four major mammalian isoforms (1A/+IRE, 1A/-IRE, 2/+IRE and 2/-IRE). Mutations or polymorphisms of DMT1 gene may have an impact on human health by disturbing metal trafficking. To study the possible association of DMT1 gene with the blood levels of some divalent cations such as iron, lead and cadmium, a single nucleotide polymorphism (SNP) (IVS4+44C/A) in DMT1 gene was investigated in 486 unrelated and healthy individuals in a Turkish population by method of polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP). The genotype frequencies were found as 49.8% homozygote typical (CC), 38.3% heterozygote (CA) and 11.9% homozygote atypical (AA). Metal levels were analyzed by dual atomic absorption spectrometer system and the average levels of iron, lead and cadmium in the blood samples were 446.01±81.87 ppm, 35.59±17.72 ppb and 1.25±0.87 ppb, respectively. Individuals with the CC genotype had higher blood iron, lead and cadmium levels than those with AA and CA genotypes. Highly statistically significant associations were detected between IVS4+44 C/A polymorphism in the DMT1 gene and iron and lead levels (p=0.001 and p=0.036, respectively), but no association was found with cadmium level (p=0.344). This study suggested that DMT1 IVS4+44 C/A polymorphism is associated with inter-individual variations in blood iron, lead and cadmium levels. - Highlights: • DMT1 IVS4+44 C/A polymorphism is associated with inter-individual variations in blood iron, cadmium and lead levels.

  3. Gene expression levels of elastin and fibulin-5 according to differences between carotid plaque regions.

    Science.gov (United States)

    Sivrikoz, Emre; Timirci-Kahraman, Özlem; Ergen, Arzu; Zeybek, Ümit; Aksoy, Murat; Yanar, Fatih; İsbir, Turgay; Kurtoğlu, Mehmet

    2015-01-01

    The purpose of this study was to investigate the gene expression levels of elastin and fibulin-5 according to differences between carotid plaque regions and to correlate it with clinical features of plaque destabilization. The study included 44 endarterectomy specimens available from operated symptomatic carotid artery stenoses. The specimens were separated according to anatomic location: internal carotid artery (ICA), external carotid artery (ECA) and common carotid artery (CCA), and then stored in liquid nitrogen. The amounts of cDNA for elastin and fibulin-5 were determined by Quantitative real-time PCR (Q-RT-PCR). Target gene copy numbers were normalized using hypoxanthine-guanine phosphoribosyltransferase (HPRT1) gene. The delta-delta CT method was applied for relative quantification. Q-RT-PCR data showed that relative fibulin-5 gene expression was increased in ICA plaque regions when compared to CCA regions but not reaching significance (p=0.061). At the same time, no differences were observed in elastin mRNA level between different anatomic plaque regions (p>0.05). Moreover, elastin and fibulin-5 mRNA expression and clinical parameters were compared in ICA plaques versus CCA and ECA regions, respectively. Up-regulation of elastin and fibulin-5 mRNA levels in ICA were strongly correlated with family history of cardiovascular disease when compared to CCA (p<0.05). Up-regulation of fibulin-5 in ICA was significantly associated with diabetes, and elevated triglycerides and very low density lipoprotein (VLDL) when compared to ECA (p<0.05). The clinical significance is the differences between the proximal and distal regions of the lesion, associated with the ICA, CCA and ECA respectively, with increased fibulin-5 in the ICA region. Copyright © 2015 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

  4. A polymorphism in the IGF-I gene influences the age-related decline in circulating total IGF-I levels

    NARCIS (Netherlands)

    I. Rietveld (Ingrid); J.A.M.J.L. Janssen (Joseph); A. Hofman (Albert); C.M. van Duijn (Cornelia); S.W.J. Lamberts (Steven); H.A.P. Pols (Huib)

    2003-01-01

    markdownabstractOBJECTIVE: Recent studies have demonstrated an association between a 192 bp polymorphism of the IGF-I gene and total IGF-I serum levels, birth weight, body height and the risk of developing diabetes and cardiovascular diseases later on in life. This IGF-I gene polymorphism in the

  5. Genetic interaction analysis of point mutations enables interrogation of gene function at a residue-level resolution

    Science.gov (United States)

    Braberg, Hannes; Moehle, Erica A.; Shales, Michael; Guthrie, Christine; Krogan, Nevan J.

    2014-01-01

    We have achieved a residue-level resolution of genetic interaction mapping – a technique that measures how the function of one gene is affected by the alteration of a second gene – by analyzing point mutations. Here, we describe how to interpret point mutant genetic interactions, and outline key applications for the approach, including interrogation of protein interaction interfaces and active sites, and examination of post-translational modifications. Genetic interaction analysis has proven effective for characterizing cellular processes; however, to date, systematic high-throughput genetic interaction screens have relied on gene deletions or knockdowns, which limits the resolution of gene function analysis and poses problems for multifunctional genes. Our point mutant approach addresses these issues, and further provides a tool for in vivo structure-function analysis that complements traditional biophysical methods. We also discuss the potential for genetic interaction mapping of point mutations in human cells and its application to personalized medicine. PMID:24842270

  6. Reduction of lns-1 gene expression and tissue insulin levels in n5-STZ rats

    Directory of Open Access Journals (Sweden)

    Belinda Vargas Guerrero

    2013-01-01

    Full Text Available Objective: The high global incidence of type 2 diabetes has challenged researchers to establish animal models that resemble the chronic stage observed in type 2 diabetes patients. One such model is induced by neonatal streptozotocin (n-STZ administration to rat pups at 0, 2, or 5 days after birth. In this study, we assessed lns-1 gene expression and tissue insulin levels as well as serum concentration of glucose and insulin, insulin resistance, and histological changes of the islets of Langerhans in n5-STZ rats after 20-weeks post-induction. Methods: Wistar rat pups were randomly distributed into a control group and a streptozotocin-induced group. Experimental induction involved a single intraperitoneal injection of streptozotocin (150 mg/kg into neonates at five days after birth. Results: At 20 weeks post-induction, streptozotocin-induced rats exhibited increased serum glucose levels, reduced serum insulin levels, impaired glucose metabolism and insulin resistance compared to control rats. Histologically, streptozotocin-induced rats exhibited atrophic islets, vacuolization, and significantly fewer insulin-positive cells. lns-1 gene expression was significantly decreased in n5-STZ rats in comparison to the control group. Conclusion: Our findings support that the n5-STZ model 20 weeks post-induction represents an appropriate experimental tool to study T2D and to evaluate novel therapeutic agents and targets that involve insulin gene expression and secretion, as well as complications caused by chronic diabetes.

  7. ribB and ribBA genes from Acidithiobacillus ferrooxidans: expression levels under different growth conditions and phylogenetic analysis.

    Science.gov (United States)

    Knegt, Fábio H P; Mello, Luciane V; Reis, Fernanda C; Santos, Marcos T; Vicentini, Renato; Ferraz, Lúcio F C; Ottoboni, Laura M M

    2008-01-01

    Acidithiobacillus ferrooxidans is a Gram-negative, chemolithoautotrophic bacterium involved in metal bioleaching. Using the RNA arbitrarily primed polymerase chain reaction (RAP-PCR), we have identified several cDNAs that were differentially expressed when A. ferrooxidans LR was submitted to potassium- and phosphate-limiting conditions. One of these cDNAs showed similarity with ribB. An analysis of the A. ferrooxidans ATCC 23270 genome, made available by The Institute for Genomic Research, showed that the ribB gene was not located in the rib operon, but a ribBA gene was present in this operon instead. The ribBA gene was isolated from A. ferrooxidans LR and expression of both ribB and ribBA was investigated. Transcript levels of both genes were enhanced in cells grown in the absence of K2HPO4, in the presence of zinc and copper sulfate and in different pHs. Transcript levels decreased upon exposure to a temperature higher than the ideal 30 degrees C and at pH 1.2. A comparative genomic analysis using the A. ferrooxidans ATCC 23270 genome revealed similar putative regulatory elements for both genes. Moreover, an RFN element was identified upstream from the ribB gene. Phylogenetic analysis of the distribution of RibB and RibBA in bacteria showed six different combinations. We suggest that the presence of duplicated riboflavin synthesis genes in bacteria must provide their host with some benefit in certain stressful situations.

  8. CBrowse: a SAM/BAM-based contig browser for transcriptome assembly visualization and analysis.

    Science.gov (United States)

    Li, Pei; Ji, Guoli; Dong, Min; Schmidt, Emily; Lenox, Douglas; Chen, Liangliang; Liu, Qi; Liu, Lin; Zhang, Jie; Liang, Chun

    2012-09-15

    To address the impending need for exploring rapidly increased transcriptomics data generated for non-model organisms, we developed CBrowse, an AJAX-based web browser for visualizing and analyzing transcriptome assemblies and contigs. Designed in a standard three-tier architecture with a data pre-processing pipeline, CBrowse is essentially a Rich Internet Application that offers many seamlessly integrated web interfaces and allows users to navigate, sort, filter, search and visualize data smoothly. The pre-processing pipeline takes the contig sequence file in FASTA format and its relevant SAM/BAM file as the input; detects putative polymorphisms, simple sequence repeats and sequencing errors in contigs and generates image, JSON and database-compatible CSV text files that are directly utilized by different web interfaces. CBowse is a generic visualization and analysis tool that facilitates close examination of assembly quality, genetic polymorphisms, sequence repeats and/or sequencing errors in transcriptome sequencing projects. CBrowse is distributed under the GNU General Public License, available at http://bioinfolab.muohio.edu/CBrowse/ liangc@muohio.edu or liangc.mu@gmail.com; glji@xmu.edu.cn Supplementary data are available at Bioinformatics online.

  9. Increased plasma orexin-A levels in patients with insomnia disorder are not associated with prepro-orexin or orexin receptor gene polymorphisms.

    Science.gov (United States)

    Tang, Shi; Huang, Weiwei; Lu, Shanshan; Lu, Lili; Li, Guohua; Chen, Xu; Liu, Xiaomin; Lv, Xin; Zhao, Zhangning; Duan, Ruisheng; Du, Yifeng; Tang, Jiyou

    2017-02-01

    Orexins, also known as hypocretins, play a regulatory role in the sleep-wake cycle by activating orexin receptors. Previous animal studies have shown that sleep deprivation can elevate orexinergic peptide levels. However, the relationship between insomnia disorder and orexin-A levels in humans has not been explored. In the current study, we examined plasma orexin-A levels in patients with insomnia disorder and in normal sleepers. We also studied the possible mechanisms underlying changes in orexin-A levels between the study groups; this included investigations of prepro-orexin and orexin receptor gene polymorphisms as well as exploration of other variables. We measured plasma orexin-A levels in 228 patients with insomnia disorder and 282 normal sleepers. The results indicated that the patients with insomnia disorder had significantly higher orexin-A levels than normal sleepers (63.42±37.56 vs. 54.84±23.95pg/ml). A positive relationship was detected between orexin-A level and age in patients with insomnia disorder. Orexin-A levels were elevated in relation to course of insomnia, as well as in relation to increased Insomnia Severity Index score. None of the evaluated prepro-orexin gene single nucleotide polymorphisms were informative between the two study populations. After sequencing all orexin receptor exons, one variation (rs2271933) in the OX1R gene and one variation (rs2653349) in the OX2R gene were found. However, no significant differences were found in either genotypic or allelic frequency distributions between the two study groups. It is suggested that the increased plasma orexin-A levels in patients with insomnia disorder are associated with the course and severity of insomnia, but not with prepro-orexin and orexin receptor gene polymorphisms. Copyright © 2016 Elsevier Inc. All rights reserved.

  10. Occupational Radiation Protection in Severe Accident Management. EG-SAM Interim Report

    International Nuclear Information System (INIS)

    2014-01-01

    As an early response to the Fukushima NPP accident, the ISOE Bureau decided to focus on the following issues as an initial response of the joint program after having direct communications with the Japanese official participants in April 2011; - Management of high radiation area worker doses: It has been decided to make available the experience and information from the Chernobyl accident in terms of how emergency worker / responder doses were legally and practically managed, - Personal protective equipment for highly-contaminated areas: It was agreed to collect information about the types of personnel protective equipment and other equipment (e.g. air bottles, respirators, air-hoods or plastic suits, etc.), as well as high-radiation area worker dosimetry use (e.g. type, number and placement of dosimetry) for different types of emergency and high-radiation work situations. Detailed information was collected on dose criteria which are used for emergency workers/responders and their basis, dose management criteria for high dose/dose rate areas, protective equipment which is recommended for emergency workers / responders, recommended individual monitoring procedures, and any special requirement for assessment from the ISOE participating nuclear utilities and regulatory authorities and made available for Japanese utilities. With this positive response of the ISOE actors and interest in the situation in Fukushima, the Expert Group on Occupational Radiation Protection in Severe Accident Management (EG-SAM) was established by the ISOE Management Board in May 2011. The overall objective of the EG-SAM is to contribute to occupational exposure management (providing a view on management of high radiation area worker doses) within the Fukushima plant boundary with the ISOE participants and to develop a state-of-the- art ISOE report on best radiation protection management practices for proper radiation protection job coverage during severe accident initial response and recovery

  11. WDR1 and CLNK gene polymorphisms correlate with serum glucose and high-density lipoprotein levels in Tibetan gout patients.

    Science.gov (United States)

    Lan, Bing; Chen, Peng; Jiri, Mutu; He, Na; Feng, Tian; Liu, Kai; Jin, Tianbo; Kang, Longli

    2016-03-01

    Current evidence suggests heredity and metabolic syndrome contributes to gout progression. Specifically, the WDR1 and CLNK genes may play a role in gout progression in European ancestry populations. However, no studies have focused on Chinese populations, especially Tibetan individuals. This study aims to determine whether variations in these two genes correlate with gout-related indices in Chinese-Tibetan gout patients. Eleven single-nucleotide polymorphisms in the WDR1 and CLNK genes were detected in 319 Chinese-Tibetan gout patients and 318 controls. We used one-way analysis of variance to evaluate the polymorphisms' effects on gout based on mean serum levels of metabolism indicators, such as albumin, glucose (GLU), triglycerides, cholesterol, high-density lipoproteins (HDL-C), creatinine, and uric acid, from fasting venous blood samples. All p values were Bonferroni corrected. Polymorphisms of the WDR1 and CLNK genes affected multiple risk factors for gout development. Significant differences in serum GLU levels were detected between different genotypic groups with WDRI polymorphisms rs4604059 (p = 0.005) and rs12498927 (p = 0.005). In addition, significant differences in serum HDL-C levels were detected between different genotypic groups with the CLNK polymorphism rs2041215 (p = 0.001). Polymorphisms of CLNK also affected levels of albumin, triglycerides, and creatinine. This study is the first to investigate and identify positive correlations between WDR1 and CLNK gene polymorphisms in Chinese-Tibetan populations. Our findings provide significant evidence for the effect of genetic polymorphisms on gout-related factors in Chinese-Tibetan populations.

  12. Analysis of polymorphisms in the promoter region and protein levels of interleukin-6 gene among gout patients.

    Science.gov (United States)

    Tsai, P-C; Chen, C-J; Lai, H-M; Chang, S-J

    2008-01-01

    To explore the associations between the polymorphisms and protein levels of interleukin-6 (IL-6) gene and gout disease. A total of 120 male gout patients and 184 healthy controls were enrolled. Each patient was matched with 1-2 gout-free controls by age within three years. Four polymorphisms in the promoter of IL-6 gene, including -597G/A, -572C/G, -373A(m)T(n), and -174G/C, and the IL-6 levels were analyzed. The clinical characteristics and biochemical markers in plasma were measured, including age of gout onset, duration of gout history, tophus number, gout attack frequency, uric acid, total cholesterol, triglycerides and creatinine. The mean IL-6 level for gout patients was 9.80 (+/-11.76 pg/ml) which showed no significant difference from the controls (7.06+/-7.58 pg/ml, p=0.230). When the IL-6 levels were dichotomized according to the median value (5 pg/ml), there were significantly higher proportions of the gout patients (59.66%) than controls (44%) with high IL-6 levels (OR=1.88, 95% CI=1.17-3.02, p=0.008). Unique genotype was found at polymorphisms -174G/C and -597G/A. Neither the polymorphisms -572C/G nor -373A(m)T(n) in the genotype or allele distributions showed a significant association related to clinical characteristics, biochemical markers, IL-6 levels or gout disease (all p>0.05). Those with gout disease have greater proportions of high IL-6 levels in plasma than controls, and there is no significant association between the four polymorphisms in the promoter region of IL-6 gene and gout disease.

  13. GSHR, a Web-Based Platform Provides Gene Set-Level Analyses of Hormone Responses in Arabidopsis

    Directory of Open Access Journals (Sweden)

    Xiaojuan Ran

    2018-01-01

    Full Text Available Phytohormones regulate diverse aspects of plant growth and environmental responses. Recent high-throughput technologies have promoted a more comprehensive profiling of genes regulated by different hormones. However, these omics data generally result in large gene lists that make it challenging to interpret the data and extract insights into biological significance. With the rapid accumulation of theses large-scale experiments, especially the transcriptomic data available in public databases, a means of using this information to explore the transcriptional networks is needed. Different platforms have different architectures and designs, and even similar studies using the same platform may obtain data with large variances because of the highly dynamic and flexible effects of plant hormones; this makes it difficult to make comparisons across different studies and platforms. Here, we present a web server providing gene set-level analyses of Arabidopsis thaliana hormone responses. GSHR collected 333 RNA-seq and 1,205 microarray datasets from the Gene Expression Omnibus, characterizing transcriptomic changes in Arabidopsis in response to phytohormones including abscisic acid, auxin, brassinosteroids, cytokinins, ethylene, gibberellins, jasmonic acid, salicylic acid, and strigolactones. These data were further processed and organized into 1,368 gene sets regulated by different hormones or hormone-related factors. By comparing input gene lists to these gene sets, GSHR helped to identify gene sets from the input gene list regulated by different phytohormones or related factors. Together, GSHR links prior information regarding transcriptomic changes induced by hormones and related factors to newly generated data and facilities cross-study and cross-platform comparisons; this helps facilitate the mining of biologically significant information from large-scale datasets. The GSHR is freely available at http://bioinfo.sibs.ac.cn/GSHR/.

  14. High folic acid consumption leads to pseudo-MTHFR deficiency, altered lipid metabolism, and liver injury in mice12345

    Science.gov (United States)

    Christensen, Karen E; Mikael, Leonie G; Leung, Kit-Yi; Lévesque, Nancy; Deng, Liyuan; Wu, Qing; Malysheva, Olga V; Best, Ana; Caudill, Marie A; Greene, Nicholas DE

    2015-01-01

    Background: Increased consumption of folic acid is prevalent, leading to concerns about negative consequences. The effects of folic acid on the liver, the primary organ for folate metabolism, are largely unknown. Methylenetetrahydrofolate reductase (MTHFR) provides methyl donors for S-adenosylmethionine (SAM) synthesis and methylation reactions. Objective: Our goal was to investigate the impact of high folic acid intake on liver disease and methyl metabolism. Design: Folic acid–supplemented diet (FASD, 10-fold higher than recommended) and control diet were fed to male Mthfr+/+ and Mthfr+/− mice for 6 mo to assess gene-nutrient interactions. Liver pathology, folate and choline metabolites, and gene expression in folate and lipid pathways were examined. Results: Liver and spleen weights were higher and hematologic profiles were altered in FASD-fed mice. Liver histology revealed unusually large, degenerating cells in FASD Mthfr+/− mice, consistent with nonalcoholic fatty liver disease. High folic acid inhibited MTHFR activity in vitro, and MTHFR protein was reduced in FASD-fed mice. 5-Methyltetrahydrofolate, SAM, and SAM/S-adenosylhomocysteine ratios were lower in FASD and Mthfr+/− livers. Choline metabolites, including phosphatidylcholine, were reduced due to genotype and/or diet in an attempt to restore methylation capacity through choline/betaine-dependent SAM synthesis. Expression changes in genes of one-carbon and lipid metabolism were particularly significant in FASD Mthfr+/− mice. The latter changes, which included higher nuclear sterol regulatory element-binding protein 1, higher Srepb2 messenger RNA (mRNA), lower farnesoid X receptor (Nr1h4) mRNA, and lower Cyp7a1 mRNA, would lead to greater lipogenesis and reduced cholesterol catabolism into bile. Conclusions: We suggest that high folic acid consumption reduces MTHFR protein and activity levels, creating a pseudo-MTHFR deficiency. This deficiency results in hepatocyte degeneration, suggesting a 2

  15. High folic acid consumption leads to pseudo-MTHFR deficiency, altered lipid metabolism, and liver injury in mice.

    Science.gov (United States)

    Christensen, Karen E; Mikael, Leonie G; Leung, Kit-Yi; Lévesque, Nancy; Deng, Liyuan; Wu, Qing; Malysheva, Olga V; Best, Ana; Caudill, Marie A; Greene, Nicholas D E; Rozen, Rima

    2015-03-01

    Increased consumption of folic acid is prevalent, leading to concerns about negative consequences. The effects of folic acid on the liver, the primary organ for folate metabolism, are largely unknown. Methylenetetrahydrofolate reductase (MTHFR) provides methyl donors for S-adenosylmethionine (SAM) synthesis and methylation reactions. Our goal was to investigate the impact of high folic acid intake on liver disease and methyl metabolism. Folic acid-supplemented diet (FASD, 10-fold higher than recommended) and control diet were fed to male Mthfr(+/+) and Mthfr(+/-) mice for 6 mo to assess gene-nutrient interactions. Liver pathology, folate and choline metabolites, and gene expression in folate and lipid pathways were examined. Liver and spleen weights were higher and hematologic profiles were altered in FASD-fed mice. Liver histology revealed unusually large, degenerating cells in FASD Mthfr(+/-) mice, consistent with nonalcoholic fatty liver disease. High folic acid inhibited MTHFR activity in vitro, and MTHFR protein was reduced in FASD-fed mice. 5-Methyltetrahydrofolate, SAM, and SAM/S-adenosylhomocysteine ratios were lower in FASD and Mthfr(+/-) livers. Choline metabolites, including phosphatidylcholine, were reduced due to genotype and/or diet in an attempt to restore methylation capacity through choline/betaine-dependent SAM synthesis. Expression changes in genes of one-carbon and lipid metabolism were particularly significant in FASD Mthfr(+/-) mice. The latter changes, which included higher nuclear sterol regulatory element-binding protein 1, higher Srepb2 messenger RNA (mRNA), lower farnesoid X receptor (Nr1h4) mRNA, and lower Cyp7a1 mRNA, would lead to greater lipogenesis and reduced cholesterol catabolism into bile. We suggest that high folic acid consumption reduces MTHFR protein and activity levels, creating a pseudo-MTHFR deficiency. This deficiency results in hepatocyte degeneration, suggesting a 2-hit mechanism whereby mutant hepatocytes cannot

  16. p53 Gene (NY-CO-13 Levels in Patients with Chronic Myeloid Leukemia: The Role of Imatinib and Nilotinib

    Directory of Open Access Journals (Sweden)

    Hayder M. Al-kuraishy

    2018-01-01

    Full Text Available The p53 gene is also known as tumor suppressor p53. The main functions of the p53 gene are an anticancer effect and cellular genomic stability via various pathways including activation of DNA repair, induction of apoptosis, and arresting of cell growth at the G1/S phase. Normally, the p53 gene is inactivated by mouse double minute 2 proteins (mdm2, but it is activated in chronic myeloid leukemia (CML. Tyrosine kinase inhibitors are effective chemotherapeutic agents in the management of CML. The purpose of the present study was to evaluate the differential effect of imatinib and nilotinib on p53 gene serum levels in patients with CML. A total number of 60 patients with chronic myeloid leukemia with ages ranging from 47 to 59 years were recruited from the Iraqi Hematology Center. They started with tyrosine kinase inhibitors as first-line chemotherapy. They were divided into two groups—Group A, 29 patients treated with imatinib and Group B, 31 patients treated with nilotinib—and compared with 28 healthy subjects for evaluation p53 serum levels regarding the selective effect of either imatinib or nilotinib. There were significantly (p < 0.01 high p53 gene serum levels in patients with CML (2.135 ± 1.44 ng/mL compared to the control (0.142 ± 0.11 ng/mL. Patients with CML that were treated with either imatinib or nilotinib showed insignificant differences in most of the hematological profile (p > 0.05 whereas, p53 serum levels were high (3.22 ± 1.99 ng/mL in nilotinib-treated patients and relatively low (1.18 ± 0.19 ng/mL in imatinib-treated patients (p = 0.0001. Conclusions: Nilotinib is more effective than imatinib in raising p53 serum levels in patients with chronic myeloid leukemia.

  17. Evaluation of the hormonal state of columnar apple trees (Malus x domestica) based on high throughput gene expression studies.

    Science.gov (United States)

    Krost, Clemens; Petersen, Romina; Lokan, Stefanie; Brauksiepe, Bastienne; Braun, Peter; Schmidt, Erwin R

    2013-02-01

    The columnar phenotype of apple trees (Malus x domestica) is characterized by a compact growth habit with fruit spurs instead of lateral branches. These properties provide significant economic advantages by enabling high density plantings. The columnar growth results from the presence of a dominant allele of the gene Columnar (Co) located on chromosome 10 which can appear in a heterozygous (Co/co) or homozygous (Co/Co) state. Although two deep sequencing approaches could shed some light on the transcriptome of columnar shoot apical meristems (SAMs), the molecular mechanisms of columnar growth are not yet elaborated. Since the influence of phytohormones is believed to have a pivotal role in the establishment of the phenotype, we performed RNA-Seq experiments to study genes associated with hormone homeostasis and clearly affected by the presence of Co. Our results provide a molecular explanation for earlier findings on the hormonal state of columnar apple trees. Additionally, they allow hypotheses on how the columnar phenotype might develop. Furthermore, we show a statistically approved enrichment of differentially regulated genes on chromosome 10 in the course of validating RNA-Seq results using additional gene expression studies.

  18. Co-Cultures of Pseudomonas aeruginosa and Roseobacter denitrificans Reveal Shifts in Gene Expression Levels Compared to Solo Cultures

    Directory of Open Access Journals (Sweden)

    Crystal A. Conway

    2012-01-01

    Full Text Available Consistent biosynthesis of desired secondary metabolites (SMs from pure microbial cultures is often unreliable. In a proof-of-principle study to induce SM gene expression and production, we describe mixed “co-culturing” conditions and monitoring of messages via quantitative real-time PCR (qPCR. Gene expression of model bacterial strains (Pseudomonas aeruginosa PAO1 and Roseobacter denitrificans Och114 was analyzed in pure solo and mixed cocultures to infer the effects of interspecies interactions on gene expression in vitro, Two P. aeruginosa genes (PhzH coding for portions of the phenazine antibiotic pathway leading to pyocyanin (PCN and the RhdA gene for thiosulfate: cyanide sulfurtransferase (Rhodanese and two R. denitrificans genes (BetaLact for metallo-beta-lactamase and the DMSP gene for dimethylpropiothetin dethiomethylase were assessed for differential expression. Results showed that R. denitrificans DMSP and BetaLact gene expression became elevated in a mixed culture. In contrast, P. aeruginosa co-cultures with R. denitrificans or a third species did not increase target gene expression above control levels. This paper provides insight for better control of target SM gene expression in vitro and bypass complex genetic engineering manipulations.

  19. Inadequate Dietary Phosphorus Levels Cause Skeletal Anomalies and Alter Osteocalcin Gene Expression in Zebrafish

    Directory of Open Access Journals (Sweden)

    Juliana M. Costa

    2018-01-01

    Full Text Available Phosphorus (P is an essential mineral for the development and maintenance of the vertebrate skeletal system. Modulation of P levels is believed to influence metabolism and the physiological responses of gene expression. In this study, we investigated the influence of dietary P on skeletal deformities and osteocalcin gene expression in zebrafish (Danio rerio, and sought to determine appropriate levels in a diet. We analyzed a total of 450 zebrafish within 31 days of hatching. Animals were distributed in a completely randomized experimental design that consisted of five replications. After an eight-week experiment, fish were diaphanized to evaluate cranial and spinal bone deformities. Increases in dietary phosphorus were inversely proportional to the occurrence of partial spine fusions, the absence of spine fusions, absence of parallelism between spines, intervertebral spacing, vertebral compression, scoliosis, lordosis, ankylosis, fin caudal insertion, and craniofacial deformities. Additionally, osteocalcin expression was inversely correlated to P levels, suggesting a physiological recovery response for bone mineralization deficiency. Our data showed that dietary P concentration was a critical factor in the occurrence of zebrafish skeletal abnormalities. We concluded that 1.55% P in the diet significantly reduces the appearance of skeletal deformities and favors adequate bone mineralization through the adjustment of osteocalcin expression.

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

    Science.gov (United States)

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

    2015-04-01

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

  1. Survivin gene levels in the peripheral blood of patients with gastric cancer independently predict survival

    Directory of Open Access Journals (Sweden)

    Scalerta Romano

    2009-12-01

    Full Text Available Abstract Background The detection of circulating tumor cells (CTC is considered a promising tool for improving risk stratification in patients with solid tumors. We investigated on whether the expression of CTC related genes adds any prognostic power to the TNM staging system in patients with gastric carcinoma. Methods Seventy patients with TNM stage I to IV gastric carcinoma were retrospectively enrolled. Peripheral blood samples were tested by means of quantitative real time PCR (qrtPCR for the expression of four CTC related genes: carcinoembryonic antigen (CEA, cytokeratin-19 (CK19, vascular endothelial growth factor (VEGF and Survivin (BIRC5. Results Gene expression of Survivin, CK19, CEA and VEGF was higher than in normal controls in 98.6%, 97.1%, 42.9% and 38.6% of cases, respectively, suggesting a potential diagnostic value of both Survivin and CK19. At multivariable survival analysis, TNM staging and Survivin mRNA levels were retained as independent prognostic factors, demonstrating that Survivin expression in the peripheral blood adds prognostic information to the TNM system. In contrast with previously published data, the transcript abundance of CEA, CK19 and VEGF was not associated with patients' clinical outcome. Conclusions Gene expression levels of Survivin add significant prognostic value to the current TNM staging system. The validation of these findings in larger prospective and multicentric series might lead to the implementation of this biomarker in the routine clinical setting in order to optimize risk stratification and ultimately personalize the therapeutic management of these patients.

  2. High resolution XPS of the S 2p core level region of the L-cysteine/gold interface

    International Nuclear Information System (INIS)

    Cavalleri, O; Gonella, G; Terreni, S; Vignolo, M; Pelori, P; Floreano, L; Morgante, A; Canepa, M; Rolandi, R

    2004-01-01

    L-cysteine self-assembled monolayers (SAMs) have been deposited on gold from the liquid and vapour phase. Synchrotron based high resolution x-ray photoemission spectroscopy has been used to characterize the sulfur chemical states at the SAM/gold interface. Results obtained from pristine and x-ray irradiated samples, prepared with both as-received and purified L-cysteine, are reported. Pristine samples prepared with purified cysteine are characterized by an intense, largely dominant S 2p state at a binding energy around 162 eV (2p 3/2 level) assigned to thiolates. A second doublet around 161 eV develops during irradiation. By comparison with the literature, this doublet is assigned to atomic sulfur present either as impurity or generated by S-C bond scission. Comparative measurements performed, under similar experimental conditions, on pristine 3-mercaptopropionic acid [HS(CH 2 ) 2 COOH] layers deposited from the liquid phase are also presented and discussed

  3. Arabidopsis thaliana gonidialess A/Zuotin related factors (GlsA/ZRF) are essential for maintenance of meristem integrity.

    Science.gov (United States)

    Guzmán-López, José Alfredo; Abraham-Juárez, María Jazmín; Lozano-Sotomayor, Paulina; de Folter, Stefan; Simpson, June

    2016-05-01

    Observation of a differential expression pattern, including strong expression in meristematic tissue of an Agave tequilana GlsA/ZRF ortholog suggested an important role for this gene during bulbil formation and developmental changes in this species. In order to better understand this role, the two GlsA/ZFR orthologs present in the genome of Arabidopsis thaliana were functionally characterized by analyzing expression patterns, double mutant phenotypes, promoter-GUS fusions and expression of hormone related or meristem marker genes. Patterns of expression for A. thaliana show that GlsA/ZFR genes are strongly expressed in SAMs and RAMs in mature plants and developing embryos and double mutants showed multiple changes in morphology related to both SAM and RAM tissues. Typical double mutants showed stunted growth of aerial and root tissue, formation of multiple ectopic meristems and effects on cotyledons, leaves and flowers. The KNOX genes STM and BP were overexpressed in double mutants whereas CLV3, WUSCHEL and AS1 were repressed and lack of AtGlsA expression was also associated with changes in localization of auxin and cytokinin. These results suggest that GlsA/ZFR is an essential component of the machinery that maintains the integrity of SAM and RAM tissue and underline the potential to identify new genes or gene functions based on observations in non-model plants.

  4. Importance of stress-response genes to the survival of airborne Escherichia coli under different levels of relative humidity.

    Science.gov (United States)

    Ng, Tsz Wai; Chan, Wing Lam; Lai, Ka Man

    2017-12-01

    Other than the needs for infection control to investigate the survival and inactivation of airborne bacterial pathogens, there has been a growing interest in exploring bacterial communities in the air and the effect of environmental variables on them. However, the innate biological mechanism influencing the bacterial viability is still unclear. In this study, a mutant-based approach, using Escherichia coli as a model, was used to prove the concept that common stress-response genes are important for airborne survival of bacteria. Mutants with a single gene knockout that are known to respond to general stress (rpoS) and oxidative stress (oxyR, soxR) were selected in the study. Low relative humidity (RH), 30-40% was more detrimental to the bacteria than high RH, >90%. The log reduction of ∆rpoS was always higher than that of the parental strain at all RH levels but the ∆oxyR had a higher log reduction than the parental strain at intermediate RH only. ∆soxR had the same viability compared to the parental strain at all RH levels. The results hint that although different types and levels of stress are produced under different RH conditions, stress-response genes always play a role in the bacterial viability. This study is the first reporting the association between stress-response genes and viability of airborne bacteria.

  5. Correlation Analysis Between Expression Levels of Hepatic Growth Hormone Receptor, Janus Kinase 2, Insulin-Like Growth Factor-I Genes and Dwarfism Phenotype in Bama Minipig.

    Science.gov (United States)

    Yang, Haowen; Jiang, Qinyang; Wu, Dan; Lan, Ganqiu; Fan, Jing; Guo, Yafen; Chen, Baojian; Yang, Xiurong; Jiang, Hesheng

    2015-02-01

    Animal growth and development are complex and sophisticated biological metabolic processes, in which genes plays an important role. In this paper, we employed real-time quantitative PCR (RT-qPCR) to analyze the expression levels of hepatic GHR, JAK2 and IGF-I genes in 1, 30, 180 day of Bama minipig and Landrace with attempt to verify the correlation between the expression of these growth-associated genes and the dwarfism phenotype of Bama minipig. The results showed that the expression levels of these 3 genes in Bama minipigs were down-regulated expressed from 1 day to 30 day, and which was up-regulated expressed in Landrace. The expression levels of the 3 genes on 1, 30, 180 day were prominently higher in Landrace than in Bama minipigs. The significant differences of the 3 genes expression levels on 1 day between this two breeds indicate that different expressions of these genes might occur before birth. It is speculated that the down-regulated expression of the 3 genes may have a close correlation with the dwarfism phenotype of Bama minipig. More investigations in depth of this study is under progress with the help of biochip nanotechnology.

  6. Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression

    Directory of Open Access Journals (Sweden)

    Vining Kelly J

    2012-01-01

    Full Text Available Abstract Background DNA cytosine methylation is an epigenetic modification that has been implicated in many biological processes. However, large-scale epigenomic studies have been applied to very few plant species, and variability in methylation among specialized tissues and its relationship to gene expression is poorly understood. Results We surveyed DNA methylation from seven distinct tissue types (vegetative bud, male inflorescence [catkin], female catkin, leaf, root, xylem, phloem in the reference tree species black cottonwood (Populus trichocarpa. Using 5-methyl-cytosine DNA immunoprecipitation followed by Illumina sequencing (MeDIP-seq, we mapped a total of 129,360,151 36- or 32-mer reads to the P. trichocarpa reference genome. We validated MeDIP-seq results by bisulfite sequencing, and compared methylation and gene expression using published microarray data. Qualitative DNA methylation differences among tissues were obvious on a chromosome scale. Methylated genes had lower expression than unmethylated genes, but genes with methylation in transcribed regions ("gene body methylation" had even lower expression than genes with promoter methylation. Promoter methylation was more frequent than gene body methylation in all tissues except male catkins. Male catkins differed in demethylation of particular transposable element categories, in level of gene body methylation, and in expression range of genes with methylated transcribed regions. Tissue-specific gene expression patterns were correlated with both gene body and promoter methylation. Conclusions We found striking differences among tissues in methylation, which were apparent at the chromosomal scale and when genes and transposable elements were examined. In contrast to other studies in plants, gene body methylation had a more repressive effect on transcription than promoter methylation.

  7. Assembly of Highly Standardized Gene Fragments for High-Level Production of Porphyrins in E. coli

    DEFF Research Database (Denmark)

    Nielsen, Morten Thrane; Madsen, Karina Marie; Seppala, Susanna

    2015-01-01

    to formulate a molecular cloning pipeline and iteratively assemble and optimize a six-gene pathway for protoporphyrin IX synthesis in Escherichia coli. State of the art production levels were achieved through two simple cycles of engineering and screening. The principles defined here are generally applicable...

  8. Heterogeneity at the CETP gene locus. Influence on plasma CETP concentrations and HDL cholesterol levels

    NARCIS (Netherlands)

    Kuivenhoven, J.A.; de Knijff, P.; Boer, J M; Smalheer, H A; Botma, G.J.; Seidell, J C; Kastelein, J.J.; Pritchard, P H

    This study was designed to investigate the association(s) between heterogeneity at the cholesteryl ester transfer protein (CETP) gene locus, CETP plasma concentrations, and HDL cholesterol levels. Healthy men with the lowest, median, and highest deciles of HDL cholesterol were selected from a large

  9. The evolution of gene expression levels in mammalian organs

    DEFF Research Database (Denmark)

    Brawand, David; Soumillon, Magali; Necsulea, Anamaria

    2011-01-01

    and chromosomes, owing to differences in selective pressures: transcriptome change was slow in nervous tissues and rapid in testes, slower in rodents than in apes and monotremes, and rapid for the X chromosome right after its formation. Although gene expression evolution in mammals was strongly shaped......Changes in gene expression are thought to underlie many of the phenotypic differences between species. However, large-scale analyses of gene expression evolution were until recently prevented by technological limitations. Here we report the sequencing of polyadenylated RNA from six organs across...... ten species that represent all major mammalian lineages (placentals, marsupials and monotremes) and birds (the evolutionary outgroup), with the goal of understanding the dynamics of mammalian transcriptome evolution. We show that the rate of gene expression evolution varies among organs, lineages...

  10. Expression of DNA repair genes in burned skin exposed to low-level red laser.

    Science.gov (United States)

    Trajano, Eduardo Tavares Lima; Mencalha, Andre Luiz; Monte-Alto-Costa, Andréa; Pôrto, Luís Cristóvão; de Souza da Fonseca, Adenilson

    2014-11-01

    Although red laser lights lie in the region of non-ionizing radiations in the electromagnetic spectrum, there are doubts whether absorption of these radiations causes lesions in the DNA molecule. Our aim was to investigate the expression of the genes involved with base excision and nucleotide excision repair pathways in skin tissue submitted to burn injury and exposed to low-level red laser. Wistar rats were divided as follows: control group-rats burned and not irradiated, laser group-rats burned and irradiated 1 day after injury for five consecutive days, and later laser group-rats injured and treated 4 days after injury for five consecutive days. Irradiation was performed according to a clinical protocol (20 J/cm(2), 100 mW, continuous wave emission mode). The animals were sacrificed on day 10, and scarred tissue samples were withdrawn for total RNA extraction, complementary DNA (cDNA) synthesis, and evaluation of gene expression by quantitative polymerase chain reaction. Low-level red laser exposure (1) reduces the expression of APE1 messenger (mRNA), (2) increases the expression of OGG1 mRNA, (3) reduces the expression of XPC mRNA, and (4) increases the expression of XPA mRNA both in laser and later laser groups. Red laser exposure at therapeutic fluences alters the expression of genes related to base excision and nucleotide excision pathways of DNA repair during wound healing of burned skin.

  11. GSEH: A Novel Approach to Select Prostate Cancer-Associated Genes Using Gene Expression Heterogeneity.

    Science.gov (United States)

    Kim, Hyunjin; Choi, Sang-Min; Park, Sanghyun

    2018-01-01

    When a gene shows varying levels of expression among normal people but similar levels in disease patients or shows similar levels of expression among normal people but different levels in disease patients, we can assume that the gene is associated with the disease. By utilizing this gene expression heterogeneity, we can obtain additional information that abets discovery of disease-associated genes. In this study, we used collaborative filtering to calculate the degree of gene expression heterogeneity between classes and then scored the genes on the basis of the degree of gene expression heterogeneity to find "differentially predicted" genes. Through the proposed method, we discovered more prostate cancer-associated genes than 10 comparable methods. The genes prioritized by the proposed method are potentially significant to biological processes of a disease and can provide insight into them.

  12. Mutations in the gene for lipoprotein lipase. A cause for low HDL cholesterol levels in individuals heterozygous for familial hypercholesterolemia

    NARCIS (Netherlands)

    Pimstone, S. N.; Gagné, S. E.; Gagné, C.; Lupien, P. J.; Gaudet, D.; Williams, R. R.; Kotze, M.; Reymer, P. W.; Defesche, J. C.; Kastelein, J. J.

    1995-01-01

    Familial hypercholesterolemia (FH) is characterized by elevated plasma concentrations of LDL cholesterol resulting from mutations in the gene for the LDL receptor. Low HDL cholesterol levels are seen frequently in patients both heterozygous and homozygous for mutations in this gene. Suggested

  13. miRNA and Degradome Sequencing Reveal miRNA and Their Target Genes That May Mediate Shoot Growth in Spur Type Mutant “Yanfu 6”

    Science.gov (United States)

    Song, Chunhui; Zhang, Dong; Zheng, Liwei; Zhang, Jie; Zhang, Baojuan; Luo, Wenwen; Li, Youmei; Li, Guangfang; Ma, Juanjuan; Han, Mingyu

    2017-01-01

    The spur-type growth habit in apple trees is characterized by short internodes, increased number of fruiting spurs, and compact growth that promotes flowering and facilitates management practices, such as pruning. The molecular mechanisms responsible for regulating spur-type growth have not been elucidated. In the present study, miRNAs and the expression of their potential target genes were evaluated in shoot tips of “Nagafu 2” (CF) and spur-type bud mutation “Yanfu 6” (YF). A total of 700 mature miRNAs were identified, including 202 known apple miRNAs and 498 potential novel miRNA candidates. A comparison of miRNA expression in CF and YF revealed 135 differentially expressed genes, most of which were downregulated in YF. YF also had lower levels of GA, ZR, IAA, and ABA hormones, relative to CF. Exogenous applications of GA promoted YF shoot growth. Based on the obtained results, a regulatory network involving plant hormones, miRNA, and their potential target genes is proposed for the molecular mechanism regulating the growth of YF. miRNA164, miRNA166, miRNA171, and their potential targets, and associated plant hormones, appear to regulate shoot apical meristem (SAM) growth. miRNA159, miRNA167, miRNA396, and their potential targets, and associated plant hormones appear to regulate cell division and internode length. This study provides a foundation for further studies designed to elucidate the mechanism underlying spur-type apple architecture. PMID:28424721

  14. Serum hepcidin levels, iron status, and HFE gene alterations during the first year of life in healthy Spanish infants.

    Science.gov (United States)

    Aranda, Nuria; Bedmar, Cristina; Arija, Victoria; Jardí, Cristina; Jimenez-Feijoo, Rosa; Ferré, Natalia; Tous, Monica

    2018-06-01

    The aims of this study were to describe hepcidin levels and to assess their associations with iron status and the main variants in the HFE gene in healthy and full-term newborns during the first year of life, as a longitudinal study conducted on 140 infants. Anthropometric and biochemical parameters, hepcidin, hemoglobin (Hb), serum ferritin (SF), transferrin saturation (TS), mean corpuscular volume (MCV), and C-reactive protein (CRP), were assessed in 6- and 12-month-olds. Infants were genotyped for the three main HFE variants: C282Y, H63D, and S65C. Hepcidin levels increased from 6 to 12 months of age (43.7 ± 1.5 to 52.0 ± 1.5 ng/mL; p HFE gene (p = 0.046 and p = 0.048 in 6- and 12-month-olds, respectively). However, this association was not found in HFE-alteration-carrying infants. Hepcidin levels increased in healthy infants during the first year of life and were positively associated with iron levels only in infants with wild-type HFE gene, a situation that requires further investigation.

  15. Normal uniform mixture differential gene expression detection for cDNA microarrays

    Directory of Open Access Journals (Sweden)

    Raftery Adrian E

    2005-07-01

    Full Text Available Abstract Background One of the primary tasks in analysing gene expression data is finding genes that are differentially expressed in different samples. Multiple testing issues due to the thousands of tests run make some of the more popular methods for doing this problematic. Results We propose a simple method, Normal Uniform Differential Gene Expression (NUDGE detection for finding differentially expressed genes in cDNA microarrays. The method uses a simple univariate normal-uniform mixture model, in combination with new normalization methods for spread as well as mean that extend the lowess normalization of Dudoit, Yang, Callow and Speed (2002 1. It takes account of multiple testing, and gives probabilities of differential expression as part of its output. It can be applied to either single-slide or replicated experiments, and it is very fast. Three datasets are analyzed using NUDGE, and the results are compared to those given by other popular methods: unadjusted and Bonferroni-adjusted t tests, Significance Analysis of Microarrays (SAM, and Empirical Bayes for microarrays (EBarrays with both Gamma-Gamma and Lognormal-Normal models. Conclusion The method gives a high probability of differential expression to genes known/suspected a priori to be differentially expressed and a low probability to the others. In terms of known false positives and false negatives, the method outperforms all multiple-replicate methods except for the Gamma-Gamma EBarrays method to which it offers comparable results with the added advantages of greater simplicity, speed, fewer assumptions and applicability to the single replicate case. An R package called nudge to implement the methods in this paper will be made available soon at http://www.bioconductor.org.

  16. Large-scale event extraction from literature with multi-level gene normalization.

    Directory of Open Access Journals (Sweden)

    Sofie Van Landeghem

    Full Text Available Text mining for the life sciences aims to aid database curation, knowledge summarization and information retrieval through the automated processing of biomedical texts. To provide comprehensive coverage and enable full integration with existing biomolecular database records, it is crucial that text mining tools scale up to millions of articles and that their analyses can be unambiguously linked to information recorded in resources such as UniProt, KEGG, BioGRID and NCBI databases. In this study, we investigate how fully automated text mining of complex biomolecular events can be augmented with a normalization strategy that identifies biological concepts in text, mapping them to identifiers at varying levels of granularity, ranging from canonicalized symbols to unique gene and proteins and broad gene families. To this end, we have combined two state-of-the-art text mining components, previously evaluated on two community-wide challenges, and have extended and improved upon these methods by exploiting their complementary nature. Using these systems, we perform normalization and event extraction to create a large-scale resource that is publicly available, unique in semantic scope, and covers all 21.9 million PubMed abstracts and 460 thousand PubMed Central open access full-text articles. This dataset contains 40 million biomolecular events involving 76 million gene/protein mentions, linked to 122 thousand distinct genes from 5032 species across the full taxonomic tree. Detailed evaluations and analyses reveal promising results for application of this data in database and pathway curation efforts. The main software components used in this study are released under an open-source license. Further, the resulting dataset is freely accessible through a novel API, providing programmatic and customized access (http://www.evexdb.org/api/v001/. Finally, to allow for large-scale bioinformatic analyses, the entire resource is available for bulk download from

  17. Low density lipoprotein receptor gene Ava II polymorphism and serum lipid levels in the Guangxi Bai Ku Yao and Han populations

    Directory of Open Access Journals (Sweden)

    Wu Dong-Feng

    2011-02-01

    Full Text Available Abstract Background Several common genetic polymorphisms in the low density lipoprotein receptor (LDL-R gene have associated with modifications of serum total cholesterol (TC and low density lipoprotein cholesterol (LDL-C levels, but the results are not consistent in different populations. Bai Ku Yao is a special subgroup of the Yao minority in China. The present study was undertaken to detect the association of LDL-R gene Ava Ⅱ polymorphism and serum lipid levels in the Guangxi Bai Ku Yao and Han populations. Methods A total of 1024 subjects of Bai Ku Yao and 792 participants of Han Chinese were randomly selected from our previous stratified randomized cluster samples. Genotyping of the LDL-R gene Ava Ⅱ polymorphism was performed by polymerase chain reaction and restriction fragment length polymorphism combined with gel electrophoresis, and then confirmed by direct sequencing. Results The levels of serum TC, high density lipoprotein cholesterol (HDL-C, LDL-C, apolipoprotein (Apo A1 and the ratio of ApoA1 to ApoB were lower in Bai Ku Yao than in Han (P - and A+ alleles was 65.5% and 34.5% in Bai Ku Yao, and 80.7% and 19.3% in Han (P -A-, A-A+ and A+A+ genotypes was 42.6%, 45.9% and 11.5% in Bai Ku Yao, and 64.9%, 31.6% and 3.5% in Han (P P 3.20 mmol/L subgroups in Bai Ku Yao (P P P P +A+ genotype had higher serum LDL-C, TC, HDL-C or ApoA1 levels than the subjects with A-A+ and A-A- genotypes. Spearman rank correlation analysis revealed that the levels of LDL-C in Bai Ku Yao and HDL-C in Han were correlated with genotypes (P P Conclusions The association of LDL-R gene Ava Ⅱ polymorphism and serum lipid levels is different between the Bai Ku Yao and Han populations. The discrepancy might partly result from different LDL-R gene Ava Ⅱ polymorphism or LDL-R gene-enviromental interactions.

  18. Identification of a radiosensitivity signature using integrative metaanalysis of published microarray data for NCI-60 cancer cells

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    Kim Han

    2012-07-01

    Full Text Available Abstract Background In the postgenome era, a prediction of response to treatment could lead to better dose selection for patients in radiotherapy. To identify a radiosensitive gene signature and elucidate related signaling pathways, four different microarray experiments were reanalyzed before radiotherapy. Results Radiosensitivity profiling data using clonogenic assay and gene expression profiling data from four published microarray platforms applied to NCI-60 cancer cell panel were used. The survival fraction at 2 Gy (SF2, range from 0 to 1 was calculated as a measure of radiosensitivity and a linear regression model was applied to identify genes or a gene set with a correlation between expression and radiosensitivity (SF2. Radiosensitivity signature genes were identified using significant analysis of microarrays (SAM and gene set analysis was performed using a global test using linear regression model. Using the radiation-related signaling pathway and identified genes, a genetic network was generated. According to SAM, 31 genes were identified as common to all the microarray platforms and therefore a common radiosensitivity signature. In gene set analysis, functions in the cell cycle, DNA replication, and cell junction, including adherence and gap junctions were related to radiosensitivity. The integrin, VEGF, MAPK, p53, JAK-STAT and Wnt signaling pathways were overrepresented in radiosensitivity. Significant genes including ACTN1, CCND1, HCLS1, ITGB5, PFN2, PTPRC, RAB13, and WAS, which are adhesion-related molecules that were identified by both SAM and gene set analysis, and showed interaction in the genetic network with the integrin signaling pathway. Conclusions Integration of four different microarray experiments and gene selection using gene set analysis discovered possible target genes and pathways relevant to radiosensitivity. Our results suggested that the identified genes are candidates for radiosensitivity biomarkers and that

  19. Analysis of Hyperspectral Imagery for Oil Spill Detection Using SAM Unmixing Algorithm Techniques

    Directory of Open Access Journals (Sweden)

    Ahmad Keshavarz

    2017-04-01

    Full Text Available Oil spill is one of major marine environmental challenges. The main impacts of this phenomenon are preventing light transmission into the deep water and oxygen absorption, which can disturb the photosynthesis process of water plants. In this research, we utilize SpecTIR airborne sensor data to extract and classify oils spill for the Gulf of Mexico Deepwater Horizon (DWH happened in 2010. For this purpose, by using FLAASH algorithm atmospheric correction is first performed. Then, total 360 spectral bands from 183 to 198 and from 255 to 279 have been excluded by applying the atmospheric correction algorithm due to low signal to noise ratio (SNR. After that, bands 1 to 119 have been eliminated for their irrelevancy to extracting oil spill spectral endmembers. In the next step, by using MATLAB hyperspectral toolbox, six spectral endmembers according to the ratio of oil to water have been extracted. Finally, by using extracted endmembers and SAM classification algorithm, the image has been classified into 6 classes. The classes are 100% oil, 80% oil and 20% water, 60% oil and 40% water, 40% oil and 60% water, 20% oil and 80% water, and 100% water.

  20. Dissecting miRNA gene repression on single cell level with an advanced fluorescent reporter system

    Science.gov (United States)

    Lemus-Diaz, Nicolas; Böker, Kai O.; Rodriguez-Polo, Ignacio; Mitter, Michael; Preis, Jasmin; Arlt, Maximilian; Gruber, Jens

    2017-01-01

    Despite major advances on miRNA profiling and target predictions, functional readouts for endogenous miRNAs are limited and frequently lead to contradicting conclusions. Numerous approaches including functional high-throughput and miRISC complex evaluations suggest that the functional miRNAome differs from the predictions based on quantitative sRNA profiling. To resolve the apparent contradiction of expression versus function, we generated and applied a fluorescence reporter gene assay enabling single cell analysis. This approach integrates and adapts a mathematical model for miRNA-driven gene repression. This model predicts three distinct miRNA-groups with unique repression activities (low, mid and high) governed not just by expression levels but also by miRNA/target-binding capability. Here, we demonstrate the feasibility of the system by applying controlled concentrations of synthetic siRNAs and in parallel, altering target-binding capability on corresponding reporter-constructs. Furthermore, we compared miRNA-profiles with the modeled predictions of 29 individual candidates. We demonstrate that expression levels only partially reflect the miRNA function, fitting to the model-projected groups of different activities. Furthermore, we demonstrate that subcellular localization of miRNAs impacts functionality. Our results imply that miRNA profiling alone cannot define their repression activity. The gene regulatory function is a dynamic and complex process beyond a minimalistic conception of “highly expressed equals high repression”. PMID:28338079