WorldWideScience

Sample records for model sumo substrates

  1. Sumo-dependent substrate targeting of the SUMO protease Ulp1

    Directory of Open Access Journals (Sweden)

    Westerbeck Jason W

    2011-10-01

    Full Text Available Abstract Background In the yeast Saccharomyces cerevisiae, the essential small ubiquitin-like modifier (SUMO protease Ulp1 is responsible for both removing SUMO/Smt3 from specific target proteins and for processing precursor SUMO into its conjugation-competent form. Ulp1 localizes predominantly to nuclear pore complexes but has also been shown to deconjugate sumoylated septins at the bud-neck of dividing cells. How Ulp1 is directed to bud-neck localized septins and other cytoplasmic deconjugation targets is not well understood. Results Using a structure/function approach, we set out to elucidate features of Ulp1 that are required for substrate targeting. To aid our studies, we took advantage of a catalytically inactive mutant of Ulp1 that is greatly enriched at the septin ring of dividing yeast cells. We found that the localization of Ulp1 to the septins requires both SUMO and specific structural features of Ulp1's catalytic domain. Our analysis identified a 218-amino acid, substrate-trapping mutant of the catalytic domain of Ulp1, Ulp1(3(C580S, that is necessary and sufficient for septin localization. We also used the targeting and SUMO-binding properties of Ulp1(3(C580S to purify Smt3-modified proteins from cell extracts. Conclusions Our study provides novel insights into how the Ulp1 SUMO protease is actively targeted to its substrates in vivo and in vitro. Furthermore, we found that a substrate-trapping Ulp1(3(C580S interacts robustly with human SUMO1, SUMO2 and SUMO2 chains, making it a potentially useful tool for the analysis and purification of SUMO-modified proteins.

  2. SUMO modification through rapamycin-mediated heterodimerization reveals a dual role for Ubc9 in targeting RanGAP1 to nuclear pore complexes

    International Nuclear Information System (INIS)

    Zhu Shanshan; Zhang Hong; Matunis, Michael J.

    2006-01-01

    SUMOs (small ubiquitin-related modifiers) are eukaryotic proteins that are covalently conjugated to other proteins and thereby regulate a wide range of important cellular processes. The molecular mechanisms by which SUMO modification influences the functions of most target proteins and cellular processes, however, remain poorly defined. A major obstacle to investigating the effects of SUMO modification is the availability of a system for selectively inducing the modification or demodification of an individual protein. To address this problem, we have developed a procedure using the rapamycin heterodimerizer system. This procedure involves co-expression of rapamycin-binding domain fusion proteins of SUMO and candidate SUMO substrates in living cells. Treating cells with rapamycin induces a tight association between SUMO and a single SUMO substrate, thereby allowing specific downstream effects to be analyzed. Using RanGAP1 as a model SUMO substrate, the heterodimerizer system was used to investigate the molecular mechanism by which SUMO modification targets RanGAP1 from the cytoplasm to nuclear pore complexes (NPCs). Our results revealed a dual role for Ubc9 in targeting RanGAP1 to NPCs: In addition to conjugating SUMO-1 to RanGAP1, Ubc9 is also required to form a stable ternary complex with SUMO-1 modified RanGAP1 and Nup358. As illustrated by our studies, the rapamycin heterodimerizer system represents a novel tool for studying the molecular effects of SUMO modification

  3. Modellering van begrazing in SUMO : verbetering van de vegetatiemodellering in de Natuurplanner

    NARCIS (Netherlands)

    Wamelink, G.W.W.; Wegman, R.M.A.; Slim, P.A.; Dirksen, J.; Mol-Dijkstra, J.P.; Dobben, van H.F.

    2001-01-01

    In samenwerking met het RIVM en WU wordt het vegetatievoorspellingsmodel SUMO ontwikkeld. Het model vormt een integraal onderdeel met SMART en wordt onder andere gebruikt in de natuurplanner van het RIVM. Om de modellering van de effecten van begrazing op de vegetatieontwikkeling en successie

  4. Identification of SUMO conjugation sites in the budding yeast proteome

    Directory of Open Access Journals (Sweden)

    Miguel Esteras

    2017-10-01

    Full Text Available Post-translational modification by the small ubiquitin-like modifier (SUMO is an important mechanism regulating protein function. Identification of SUMO conjugation sites on substrates is a challenging task. Here we employed a proteomic method to map SUMO acceptor lysines in budding yeast proteins. We report the identification of 257 lysine residues where SUMO is potentially attached. Amongst the hits, we identified already known SUMO substrates and sites, confirming the success of the approach. In addition, we tested several of the novel substrates using SUMO immunoprecipitation analysis and confirmed that the SUMO acceptor lysines identified in these proteins are indeed bona fide SUMOylation sites. We believe that the collection of SUMO sites presented here is an important resource for future functional studies of SUMOylation in yeast.

  5. SUMO, System performance assessment for a high-level nuclear waste repository: Mathematical models

    International Nuclear Information System (INIS)

    Eslinger, P.W.; Miley, T.B.; Engel, D.W.; Chamberlain, P.J. II.

    1992-09-01

    Following completion of the preliminary risk assessment of the potential Yucca Mountain Site by Pacific Northwest Laboratory (PNL) in 1988, the Office of Civilian Radioactive Waste Management (OCRWM) of the US Department of Energy (DOE) requested the Performance Assessment Scientific Support (PASS) Program at PNL to develop an integrated system model and computer code that provides performance and risk assessment analysis capabilities for a potential high-level nuclear waste repository. The system model that has been developed addresses the cumulative radionuclide release criteria established by the US Environmental Protection Agency (EPA) and estimates population risks in terms of dose to humans. The system model embodied in the SUMO (System Unsaturated Model) code will also allow benchmarking of other models being developed for the Yucca Mountain Project. The system model has three natural divisions: (1) source term, (2) far-field transport, and (3) dose to humans. This document gives a detailed description of the mathematics of each of these three divisions. Each of the governing equations employed is based on modeling assumptions that are widely accepted within the scientific community

  6. SUMO and Chromatin Remodeling.

    Science.gov (United States)

    Wotton, David; Pemberton, Lucy F; Merrill-Schools, Jacqueline

    2017-01-01

    Many of the known SUMO substrates are nuclear proteins, which regulate gene expression and chromatin dynamics. Sumoylation, in general, appears to correlate with decreased transcriptional activity, and in many cases modulation of the chromatin template is implicated. Sumoylation of the core histones is associated with transcriptional silencing, and transcription factor sumoylation can decrease gene expression by promoting recruitment of chromatin modifying enzymes. Additionally, sumoylation of transcriptional corepressors and chromatin remodeling enzymes can influence interactions with other transcriptional regulators, and alter their enzymatic activity. In some cases, proteins that are components of transcriptional corepressor complexes have been shown to be SUMO E3 ligases, further emphasizing the integration of sumoylation with the regulation of chromatin remodeling. Despite the evidence suggesting that sumoylation is primarily repressive for access to chromatin, recent analyses suggest that protein sumoylation on the chromatin template may play important roles at highly expressed genes. Elucidating the dynamic interplay of sumoylation with other post-translational modifications of histones and chromatin associated proteins will be key to fully understanding the regulation of access to the chromatin template.

  7. SUMO-targeted ubiquitin ligases.

    Science.gov (United States)

    Sriramachandran, Annie M; Dohmen, R Jürgen

    2014-01-01

    Covalent posttranslational modification with SUMO (small ubiquitin-related modifier) modulates functions of a wide range of proteins in eukaryotic cells. Sumoylation affects the activity, interaction properties, subcellular localization and the stability of its substrate proteins. The recent discovery of a novel class of ubiquitin ligases (E3), termed ULS (E3-S) or STUbL, that recognize sumoylated proteins, links SUMO modification to the ubiquitin/proteasome system. Here we review recent insights into the properties and function of these ligases and their roles in regulating sumoylated proteins. This article is part of a Special Issue entitled: Ubiquitin-Proteasome System. Guest Editors: Thomas Sommer and Dieter H. Wolf. © 2013. Published by Elsevier B.V. All rights reserved.

  8. SUMO and KSHV Replication

    Energy Technology Data Exchange (ETDEWEB)

    Chang, Pei-Ching [Institute of Microbiology and Immunology, National Yang-Ming University, Taipei 112, Taiwan (China); Kung, Hsing-Jien, E-mail: hkung@nhri.org.tw [Institute for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan (China); Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616 (United States); UC Davis Cancer Center, University of California, Davis, CA 95616 (United States); Division of Molecular and Genomic Medicine, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 35053, Taiwan (China)

    2014-09-29

    Small Ubiquitin-related MOdifier (SUMO) modification was initially identified as a reversible post-translational modification that affects the regulation of diverse cellular processes, including signal transduction, protein trafficking, chromosome segregation, and DNA repair. Increasing evidence suggests that the SUMO system also plays an important role in regulating chromatin organization and transcription. It is thus not surprising that double-stranded DNA viruses, such as Kaposi’s sarcoma-associated herpesvirus (KSHV), have exploited SUMO modification as a means of modulating viral chromatin remodeling during the latent-lytic switch. In addition, SUMO regulation allows the disassembly and assembly of promyelocytic leukemia protein-nuclear bodies (PML-NBs), an intrinsic antiviral host defense, during the viral replication cycle. Overcoming PML-NB-mediated cellular intrinsic immunity is essential to allow the initial transcription and replication of the herpesvirus genome after de novo infection. As a consequence, KSHV has evolved a way as to produce multiple SUMO regulatory viral proteins to modulate the cellular SUMO environment in a dynamic way during its life cycle. Remarkably, KSHV encodes one gene product (K-bZIP) with SUMO-ligase activities and one gene product (K-Rta) that exhibits SUMO-targeting ubiquitin ligase (STUbL) activity. In addition, at least two viral products are sumoylated that have functional importance. Furthermore, sumoylation can be modulated by other viral gene products, such as the viral protein kinase Orf36. Interference with the sumoylation of specific viral targets represents a potential therapeutic strategy when treating KSHV, as well as other oncogenic herpesviruses. Here, we summarize the different ways KSHV exploits and manipulates the cellular SUMO system and explore the multi-faceted functions of SUMO during KSHV’s life cycle and pathogenesis.

  9. Two SUMO Proteases SUMO PROTEASE RELATED TO FERTILITY1 and 2 Are Required for Fertility in Arabidopsis.

    Science.gov (United States)

    Liu, Linpo; Jiang, Ying; Zhang, Xiaomei; Wang, Xu; Wang, Yanbing; Han, Yuzhen; Coupland, George; Jin, Jing Bo; Searle, Iain; Fu, Yong-Fu; Chen, Fulu

    2017-12-01

    In plants, the posttranslational modification small ubiquitin-like modifier (SUMO) is involved in regulating several important developmental and cellular processes, including flowering time control and responses to biotic and abiotic stresses. Here, we report two proteases, SUMO PROTEASE RELATED TO FERTILITY1 (SPF1) and SPF2, that regulate male and female gamete and embryo development and remove SUMO from proteins in vitro and in vivo. spf1 mutants exhibit abnormal floral structures and embryo development, while spf2 mutants exhibit largely a wild-type phenotype. However, spf1 spf2 double mutants exhibit severe abnormalities in microgametogenesis, megagametogenesis, and embryo development, suggesting that the two genes are functionally redundant. Mutation of SPF1 and SPF2 genes also results in misexpression of generative- and embryo-specific genes. In vitro, SPF1 and SPF2 process SUMO1 precursors into a mature form, and as expected in vivo, spf1 and spf2 mutants accumulate SUMO conjugates. Using a yeast two-hybrid screen, we identified EMBRYO SAC DEVELOPMENT ARREST9 (EDA9) as an SPF1-interacting protein. In vivo, we demonstrate that EDA9 is sumolyated and that, in spf1 mutants, EDA9-SUMO conjugates increase in abundance, demonstrating that EDA9 is a substrate of SPF1. Together, our results demonstrate that SPF1 and SPF2 are two SUMO proteases important for plant development in Arabidopsis ( Arabidopsis thaliana ). © 2017 American Society of Plant Biologists. All Rights Reserved.

  10. Genetic and proteomic evidence for roles of Drosophila SUMO in cell cycle control, Ras signaling, and early pattern formation.

    Directory of Open Access Journals (Sweden)

    Minghua Nie

    2009-06-01

    Full Text Available SUMO is a protein modifier that is vital for multicellular development. Here we present the first system-wide analysis, combining multiple approaches, to correlate the sumoylated proteome (SUMO-ome in a multicellular organism with the developmental roles of SUMO. Using mass-spectrometry-based protein identification, we found over 140 largely novel SUMO conjugates in the early Drosophila embryo. Enriched functional groups include proteins involved in Ras signaling, cell cycle, and pattern formation. In support of the functional significance of these findings, sumo germline clone embryos exhibited phenotypes indicative of defects in these same three processes. Our cell culture and immunolocalization studies further substantiate roles for SUMO in Ras signaling and cell cycle regulation. For example, we found that SUMO is required for efficient Ras-mediated MAP kinase activation upstream or at the level of Ras activation. We further found that SUMO is dynamically localized during mitosis to the condensed chromosomes, and later also to the midbody. Polo kinase, a SUMO substrate found in our screen, partially colocalizes with SUMO at both sites. These studies show that SUMO coordinates multiple regulatory processes during oogenesis and early embryogenesis. In addition, our database of sumoylated proteins provides a valuable resource for those studying the roles of SUMO in development.

  11. Identification and molecular properties of SUMO-binding proteins in arabidopsis

    KAUST Repository

    Park, Hyeongcheol

    2011-05-20

    Reversible conjugation of the small ubiquitin modifier (SUMO) peptide to proteins (SUMOylation) plays important roles in cellular processes in animals and yeasts. However, little is known about plant SUMO targets. To identify SUMO substrates in Arabidopsis and to probe for biological functions of SUMO proteins, we constructed 6xHis-3xFLAG fused AtSUMO1 (HFAtSUMO1) controlled by the CaMV35S promoter for transformation into Arabidopsis Col-0. After heat treatment, an increased sumoylation pattern was detected in the transgenic plants. SUMO1-modified proteins were selected after two-dimensional gel electrophoresis (2-DE) image analysis and identified using matrix-assisted laser-desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). We identified 27 proteins involved in a variety of processes such as nucleic acid metabolism, signaling, metabolism, and including proteins of unknown functions. Binding and sumoylation patterns were confirmed independently. Surprisingly, MCM3 (At5G46280), a DNA replication licensing factor, only interacted with and became sumoylated by AtSUMO1, but not by SUMO1ΔGG or AtSUMO3. The results suggest specific interactions between sumoylation targets and particular sumoylation enzymes. ©2011 KSMCB.

  12. USP7 is a SUMO deubiquitinase essential for DNA replication

    DEFF Research Database (Denmark)

    Lecona, Emilio; Rodriguez-Acebes, Sara; Specks, Julia

    2016-01-01

    to the accumulation of Ub on SUMOylated proteins, which are displaced away from replisomes. Our findings provide a model explaining the differential accumulation of SUMO and Ub at replication forks and identify an essential role of USP7 in DNA replication that should be considered in the development of USP7...... is maintained at sites of DNA replication in mammalian cells remains unexplored. Here we identify USP7 as a replisome-enriched SUMO deubiquitinase that is essential for DNA replication. By acting on SUMO and SUMOylated proteins, USP7 counteracts their ubiquitination. Inhibition or genetic deletion of USP7 leads...

  13. SUMO regulation of cellular processes

    National Research Council Canada - National Science Library

    Wilson, Van Gene

    2009-01-01

    ... . . . . . . . . . . . . . . Christopher Ptak and Richard W. Wozniak 97 7 SUMO Modification of Ion Channels . . . . . . . . . . . . . . . . Mark Benson, Jorge A. Iñiguez-Lluhí, and Jeffrey Martens 117...

  14. SUMO regulation of cellular processes

    National Research Council Canada - National Science Library

    Wilson, Van Gene

    2009-01-01

    ... . . . . . . . . . . . . . . . . . . . . . . Vasupradha Vethantham and James L. Manley 41 4 SUMO and Chromatin Remodelling . . . . . . . . . . . . . . . . . David Wotton and Jacqueline C. Merrill 59 5 Functions...

  15. 2nd SUMO Conference

    CERN Document Server

    Weber, Melanie

    2015-01-01

    This contributed volume contains the conference proceedings of the Simulation of Urban Mobility (SUMO) conference 2014, Berlin. The included research papers cover a wide range of topics in traffic planning and simulation, including open data, vehicular communication, e-mobility, urban mobility, multimodal traffic as well as usage approaches. The target audience primarily comprises researchers and experts in the field, but the book may also be beneficial for graduate students.  

  16. Interplays between Sumoylation, SUMO-Targeted Ubiquitin Ligases, and the Ubiquitin-Adaptor Protein Ufd1 in Fission Yeast

    DEFF Research Database (Denmark)

    Køhler, Julie Bonne

    their conformation or interactions with other macromolecules. Though, whereas the downstream consequence of ubiquitin conjugation is often protein degradation, the functional outcomes of sumoylation are less unifiable. A class of ubiquitin E3 ligases able to target sumoylated proteins for degradation by the 26S...... proteasome mediates direct cross-talk between the two modification systems. By contributing to the dynamic turnover of SUMO conjugated species these SUMO-targeted ubiquitin ligases (STUbLs) fulfills essential roles in both yeast and man. However, the specific sumoylated proteins affected by STUbL activity...... and the specific molecular interactions and sequence of events linking sumoylation, ubiquitylation and substrate degradation, has been largely uncovered. Using the fission yeast model organism I here present evidence for a role of the Ufd1 (ubiquitinfusion degradation 1) protein, and by extension of the Cdc48-Ufd1...

  17. SUMO-2 and PIAS1 Modulate Insoluble Mutant Huntingtin Protein Accumulation

    Directory of Open Access Journals (Sweden)

    Jacqueline Gire O’Rourke

    2013-07-01

    Full Text Available A key feature in Huntington disease (HD is the accumulation of mutant Huntingtin (HTT protein, which may be regulated by posttranslational modifications. Here, we define the primary sites of SUMO modification in the amino-terminal domain of HTT, show modification downstream of this domain, and demonstrate that HTT is modified by the stress-inducible SUMO-2. A systematic study of E3 SUMO ligases demonstrates that PIAS1 is an E3 SUMO ligase for both HTT SUMO-1 and SUMO-2 modification and that reduction of dPIAS in a mutant HTT Drosophila model is protective. SUMO-2 modification regulates accumulation of insoluble HTT in HeLa cells in a manner that mimics proteasome inhibition and can be modulated by overexpression and acute knockdown of PIAS1. Finally, the accumulation of SUMO-2-modified proteins in the insoluble fraction of HD postmortem striata implicates SUMO-2 modification in the age-related pathogenic accumulation of mutant HTT and other cellular proteins that occurs during HD progression.

  18. The SUMO Pathway in Mitosis.

    Science.gov (United States)

    Mukhopadhyay, Debaditya; Dasso, Mary

    2017-01-01

    Mitosis is the stage of the cell cycle during which replicated chromosomes must be precisely divided to allow the formation of two daughter cells possessing equal genetic material. Much of the careful spatial and temporal organization of mitosis is maintained through post-translational modifications, such as phosphorylation and ubiquitination, of key cellular proteins. Here, we will review evidence that sumoylation, conjugation to the SUMO family of small ubiquitin-like modifiers, also serves essential regulatory roles during mitosis. We will discuss the basic biology of sumoylation, how the SUMO pathway has been implicated in particular mitotic functions, including chromosome condensation, centromere/kinetochore organization and cytokinesis, and what cellular proteins may be the targets underlying these phenomena.

  19. Thy1.2 driven expression of transgenic His₆-SUMO2 in the brain of mice alters a restricted set of genes.

    Science.gov (United States)

    Rossner, Moritz J; Tirard, Marilyn

    2014-08-05

    Protein SUMOylation is a post-translational protein modification with a key regulatory role in nerve cell development and function, but its function in mammals in vivo has only been studied cursorily. We generated two new transgenic mouse lines that express His6-tagged SUMO1 and SUMO2 driven by the Thy1.2 promoter. The brains of mice of the two lines express transgenic His6-SUMO peptides and conjugate them to substrates in vivo but cytoarchitecture and synaptic organization of adult transgenic mouse brains are indistinguishable from the wild-type situation. We investigated the impact of transgenic SUMO expression on gene transcription in the hippocampus by performing genome wide analyses using microarrays. Surprisingly, no changes were observed in Thy1.2::His6-SUMO1 transgenic mice and only a restricted set of genes were upregulated in Thy1.2::His6-SUMO2 mice. Among these, Penk1 (Preproenkephalin 1), which encodes Met-enkephalin neuropeptides, showed the highest degree of alteration. Accordingly, a significant increase in Met-enkephalin peptide levels in the hippocampus of Thy1.2::His6-SUMO2 was detected, but the expression levels and cellular localization of Met-enkephalin receptors were not changed. Thus, transgenic neuronal expression of His6-SUMO1 or His6-SUMO2 only induces very minor phenotypical changes in mice. Copyright © 2014 Elsevier B.V. All rights reserved.

  20. Enhanced SUMOylation of proteins containing a SUMO-interacting motif by SUMO-Ubc9 fusion

    International Nuclear Information System (INIS)

    Kim, Eui Tae; Kim, Kyeong Kyu; Matunis, Mike J.; Ahn, Jin-Hyun

    2009-01-01

    Identifying new targets for SUMO and understanding the function of protein SUMOylation are largely limited by low level of SUMOylation. It was found recently that Ubc9, the SUMO E2 conjugating enzyme, is covalently modified by SUMO at a lysine 14 in the N-terminal alpha helix, and that SUMO-modified Ubc9 has enhanced conjugation activity for certain target proteins containing a SUMO-interacting motif (SIM). Here, we show that, compared to intact Ubc9, the SUMO-Ubc9 fusion protein has higher conjugating activity for SIM-containing targets such as Sp100 and human cytomegalovirus IE2. Assays using an IE2 SIM mutant revealed the requirement of SIM for the enhanced IE2 SUMOylation by SUMO-Ubc9. In pull-down assays with cell extracts, the SUMO-Ubc9 fusion protein bound to more diverse cellular proteins and interacted with some SIM-containing proteins with higher affinities than Ubc9. Therefore, the devised SUMO-Ubc9 fusion will be useful for identifying SIM-containing SUMO targets and producing SUMO-modified proteins.

  1. Enhanced SUMOylation of proteins containing a SUMO-interacting motif by SUMO-Ubc9 fusion

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Eui Tae; Kim, Kyeong Kyu [Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, 300 Cheoncheondong Jangangu, Suwon, Gyeonggido 440-746 (Korea, Republic of); Matunis, Mike J. [Department of Biochemistry and Molecular Biology, Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD (United States); Ahn, Jin-Hyun, E-mail: jahn@med.skku.ac.kr [Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, 300 Cheoncheondong Jangangu, Suwon, Gyeonggido 440-746 (Korea, Republic of)

    2009-10-09

    Identifying new targets for SUMO and understanding the function of protein SUMOylation are largely limited by low level of SUMOylation. It was found recently that Ubc9, the SUMO E2 conjugating enzyme, is covalently modified by SUMO at a lysine 14 in the N-terminal alpha helix, and that SUMO-modified Ubc9 has enhanced conjugation activity for certain target proteins containing a SUMO-interacting motif (SIM). Here, we show that, compared to intact Ubc9, the SUMO-Ubc9 fusion protein has higher conjugating activity for SIM-containing targets such as Sp100 and human cytomegalovirus IE2. Assays using an IE2 SIM mutant revealed the requirement of SIM for the enhanced IE2 SUMOylation by SUMO-Ubc9. In pull-down assays with cell extracts, the SUMO-Ubc9 fusion protein bound to more diverse cellular proteins and interacted with some SIM-containing proteins with higher affinities than Ubc9. Therefore, the devised SUMO-Ubc9 fusion will be useful for identifying SIM-containing SUMO targets and producing SUMO-modified proteins.

  2. The STUbL RNF4 regulates protein group SUMOylation by targeting the SUMO conjugation machinery.

    Science.gov (United States)

    Kumar, Ramesh; González-Prieto, Román; Xiao, Zhenyu; Verlaan-de Vries, Matty; Vertegaal, Alfred C O

    2017-11-27

    SUMO-targeted ubiquitin ligases (STUbLs) mediate the ubiquitylation of SUMOylated proteins to modulate their functions. In search of direct targets for the STUbL RNF4, we have developed TULIP (targets for ubiquitin ligases identified by proteomics) to covalently trap targets for ubiquitin E3 ligases. TULIP methodology could be widely employed to delineate E3 substrate wiring. Here we report that the single SUMO E2 Ubc9 and the SUMO E3 ligases PIAS1, PIAS2, PIAS3, ZNF451, and NSMCE2 are direct RNF4 targets. We confirm PIAS1 as a key RNF4 substrate. Furthermore, we establish the ubiquitin E3 ligase BARD1, a tumor suppressor and partner of BRCA1, as an indirect RNF4 target, regulated by PIAS1. Interestingly, accumulation of BARD1 at local sites of DNA damage increases upon knockdown of RNF4. Combined, we provide an insight into the role of the STUbL RNF4 to balance the role of SUMO signaling by directly targeting Ubc9 and SUMO E3 ligases.

  3. SUMO: A small unmanned meteorological observer for atmospheric boundary layer research

    Energy Technology Data Exchange (ETDEWEB)

    Reuder, J; Jonassen, M; Mayer, S [Geophysical Institute, University of Bergen, Allegaten 70, 5009 Bergen (Norway); Brisset, P [Ecole Nationale de l' Aviation Civile (ENAC), 7 avenue Edouard Belin, 31055 Toulouse (France); Mueller, M [Orleansstrasse 26a, 31135 Hildesheim (Germany)], E-mail: joachim.reuder@gfi.uib.no, E-mail: pascal.brisset@enac.fr, E-mail: marius.jonassen@gfi.uib.no, E-mail: martin@pfump.org, E-mail: stephanie.mayer@gfi.uib.no

    2008-05-01

    A new system for atmospheric measurements in the lower troposphere has been developed and successfully tested. The presented Small Unmanned Meteorological Observer (SUMO) is based on a light-weighted commercially available model airplane, equipped with an autopilot and meteorological sensors for temperature, humidity and pressure. During the 5 week field campaign FLOHOF (Flow over and around HofsjoUkull) in Central Iceland the system has been successfully tested in July/August 2007. Atmospheric profiles of temperature, humidity, wind speed and wind direction have been determined up to 3500 m above ground. In addition the applicability of SUMO for horizontal surveys up to 4 km away from the launch site has been approved. During a 3 week campaign on and around Spitsbergen in February/March 2008 the SUMO system also proved its functionality under harsh polar conditions, reaching altitudes above 1500 m at ground temperatures of -20 deg. C and wind speeds up to 15 m s{sup -1}. With its wingspan of 80 cm, its length of 75 cm and its weight of below 600 g, SUMO is easy to transport and operate even in remote areas. The direct material costs for one SUMO unit, including airplane, autopilot and sensors are below 1200 Euro. Assuming at least several tenths of flights for each airframe, SUMO provides a cost-efficient measurement system with a large potential to close the existing observational gap of reasonable atmospheric measurement systems in between meteorological masts/towers and radiosondes.

  4. Functional characterization of a SUMO deconjugating protease of Plasmodium falciparum using newly identified small molecule inhibitors.

    Science.gov (United States)

    Ponder, Elizabeth L; Albrow, Victoria E; Leader, Brittany A; Békés, Miklós; Mikolajczyk, Jowita; Fonović, Urša Pečar; Shen, Aimee; Drag, Marcin; Xiao, Junpeng; Deu, Edgar; Campbell, Amy J; Powers, James C; Salvesen, Guy S; Bogyo, Matthew

    2011-06-24

    Small ubiquitin-related modifier (SUMO) is implicated in the regulation of numerous biological processes including transcription, protein localization, and cell cycle control. Protein modification by SUMO is found in Plasmodium falciparum; however, its role in the regulation of the parasite life cycle is poorly understood. Here we describe functional studies of a SUMO-specific protease (SENP) of P. falciparum, PfSENP1 (PFL1635w). Expression of the catalytic domain of PfSENP1 and biochemical profiling using a positional scanning substrate library demonstrated that this protease has unique cleavage sequence preference relative to the human SENPs. In addition, we describe a class of small molecule inhibitors of this protease. The most potent lead compound inhibited both recombinant PfSENP1 activity and P. falciparum replication in infected human blood. These studies provide valuable new tools for the study of SUMOylation in P. falciparum. Copyright © 2011 Elsevier Ltd. All rights reserved.

  5. Characterization of the loss of SUMO pathway function on cancer cells and tumor proliferation.

    Directory of Open Access Journals (Sweden)

    Xingyue He

    Full Text Available SUMOylation is a post-translational ubiquitin-like protein modification pathway that regulates important cellular processes including chromosome structure, kinetochore function, chromosome segregation, nuclear and sub-nuclear organization, transcription and DNA damage repair. There is increasing evidence that the SUMO pathway is dysregulated in cancer, raising the possibility that modulation of this pathway may have therapeutic potential. To investigate the importance of the SUMO pathway in the context of cancer cell proliferation and tumor growth, we applied lentivirus-based short hairpin RNAs (shRNA to knockdown SUMO pathway genes in human cancer cells. shRNAs for SAE2 and UBC9 reduced SUMO conjugation activity and inhibited proliferation of human cancer cells. To expand upon these observations, we generated doxycycline inducible conditional shRNA cell lines for SAE2 to achieve acute and reversible SAE2 knockdown. Conditional SAE2 knockdown in U2OS and HCT116 cells slowed cell growth in vitro, and SAE2 knockdown induced multiple terminal outcomes including apoptosis, endoreduplication and senescence. Multinucleated cells became senescent and stained positive for the senescence marker, SA-β Gal, and displayed elevated levels of p53 and p21. In an attempt to explain these phenotypes, we confirmed that loss of SUMO pathway activity leads to a loss of SUMOylated Topoisomerase IIα and the appearance of chromatin bridges which can impair proper cytokinesis and lead to multinucleation. Furthermore, knockdown of SAE2 induces disruption of PML nuclear bodies which may further promote apoptosis or senescence. In an in vivo HCT116 xenograft tumor model, conditional SAE2 knockdown strongly impaired tumor growth. These data demonstrate that the SUMO pathway is required for cancer cell proliferation in vitro and tumor growth in vivo, implicating the SUMO pathway as a potential cancer therapeutic target.

  6. Role of SUMO in RNF4-mediated promyelocytic leukemia protein (PML) degradation: sumoylation of PML and phospho-switch control of its SUMO binding domain dissected in living cells.

    Science.gov (United States)

    Percherancier, Yann; Germain-Desprez, Delphine; Galisson, Frédéric; Mascle, Xavier H; Dianoux, Laurent; Estephan, Patricia; Chelbi-Alix, Mounira K; Aubry, Muriel

    2009-06-12

    Promyelocytic leukemia protein (PML) is a tumor suppressor acting as the organizer of subnuclear structures called PML nuclear bodies (NBs). Both covalent modification of PML by the small ubiquitin-like modifier (SUMO) and non-covalent binding of SUMO to the PML SUMO binding domain (SBD) are necessary for PML NB formation and maturation. PML sumoylation and proteasome-dependent degradation induced by the E3 ubiquitin ligase, RNF4, are enhanced by the acute promyelocytic leukemia therapeutic agent, arsenic trioxide (As2O3). Here, we established a novel bioluminescence resonance energy transfer (BRET) assay to dissect and monitor PML/SUMO interactions dynamically in living cells upon addition of therapeutic agents. Using this sensitive and quantitative SUMO BRET assay that distinguishes PML sumoylation from SBD-mediated PML/SUMO non-covalent interactions, we probed the respective roles of covalent and non-covalent PML/SUMO interactions in PML degradation and interaction with RNF4. We found that, although dispensable for As2O3-enhanced PML sumoylation and RNF4 interaction, PML SBD core sequence was required for As2O3- and RNF4-induced PML degradation. As confirmed with a phosphomimetic mutant, phosphorylation of a stretch of serine residues, contained within PML SBD was needed for PML interaction with SUMO-modified protein partners and thus for NB maturation. However, mutation of these serine residues did not impair As2O3- and RNF4-induced PML degradation, contrasting with the known role of these phosphoserine residues for casein kinase 2-promoted PML degradation. Altogether, these data suggest a model whereby sumoylation- and SBD-dependent PML oligomerization within NBs is sufficient for RNF4-mediated PML degradation and does not require the phosphorylation-dependent association of PML with other sumoylated partners.

  7. A comprehensive compilation of SUMO proteomics

    DEFF Research Database (Denmark)

    Hendriks, Ivo A; Vertegaal, Alfred C O

    2016-01-01

    for identifying sumoylated proteins, with recent advances in detecting site-specific sumoylation. In this Analysis, we combined all human SUMO proteomics data currently available into one cohesive database. We provide proteomic evidence for sumoylation of 3,617 proteins at 7,327 sumoylation sites, and insight...... into SUMO group modification by clustering the sumoylated proteins into functional networks. The data support sumoylation being a frequent protein modification (on par with other major protein modifications) with multiple nuclear functions, including in transcription, mRNA processing, DNA replication...

  8. Cooperativity of the SUMO and Ubiquitin Pathways in Genome Stability

    Directory of Open Access Journals (Sweden)

    Minghua Nie

    2016-02-01

    Full Text Available Covalent attachment of ubiquitin (Ub or SUMO to DNA repair proteins plays critical roles in maintaining genome stability. These structurally related polypeptides can be viewed as distinct road signs, with each being read by specific protein interaction motifs. Therefore, via their interactions with selective readers in the proteome, ubiquitin and SUMO can elicit distinct cellular responses, such as directing DNA lesions into different repair pathways. On the other hand, through the action of the SUMO-targeted ubiquitin ligase (STUbL family proteins, ubiquitin and SUMO can cooperate in the form of a hybrid signal. These mixed SUMO-ubiquitin chains recruit “effector” proteins such as the AAA+ ATPase Cdc48/p97-Ufd1-Npl4 complex that contain both ubiquitin and SUMO interaction motifs. This review will summarize recent key findings on collaborative and distinct roles that ubiquitin and SUMO play in orchestrating DNA damage responses.

  9. The Sumo World through the gambling cases in 2010

    Directory of Open Access Journals (Sweden)

    Keiko Morita

    2012-07-01

    Full Text Available In summer, 2010, gambling cases of sumo wrestlers and bosses and the connection with the gangsters were reported day after day through mass media. This article chases the summary of a chain of these cases and the correspondence of the Sumo Association for it. The article looks at the present conditions of a unique competition called sumo from these a series of cases. At first, it examines the summary of the illegal gambling case of Ozeki Kotomitsuki, the top of Japanese sumo wrestlers, and the correspondence of Sumo Association and other social organs. It takes up a problem about holding the tournament at Nagoya this summer next. And it relates to dark customs of sumo world that a series of cases are able to happen and tries to explain such customs through the tradition of sumo. While writing this article, the news to ask the self-purification capacity of the Association and to suggest relations with the sumo world and the gangsters are reported every day. The darkness of the sumo world seems to be wide and deep.

  10. SUMO modulation of protein aggregation and degradation

    Directory of Open Access Journals (Sweden)

    Marco Feligioni

    2015-09-01

    Full Text Available Small ubiquitin-like modifier (SUMO conjugation and binding to target proteins regulate a wide variety of cellular pathways. The functional aspects of SUMOylation include changes in protein-protein interactions, intracellular trafficking as well as protein aggregation and degradation. SUMO has also been linked to specialized cellular pathways such as neuronal development and synaptic transmission. In addition, SUMOylation is associated with neurological diseases associated with abnormal protein accumulations. SUMOylation of the amyloid and tau proteins involved in Alzheimer's disease and other tauopathies may contribute to changes in protein solubility and proteolytic processing. Similar events have been reported for α-synuclein aggregates found in Parkinson's disease, polyglutamine disorders such as Huntington's disease as well as protein aggregates found in amyotrophic lateral sclerosis (ALS. This review provides a detailed overview of the impact SUMOylation has on the etiology and pathology of these related neurological diseases.

  11. The Small Unmanned Meteorological Observer SUMO. A new tool for atmospheric boundary layer research

    Energy Technology Data Exchange (ETDEWEB)

    Reuder, Joachim; Jonassen, Marius; Mayer, Stephanie [Bergen Univ. (Norway). Geophysical Inst.; Brisset, Pascal [Ecole Nationale de l' Aviation Civile (ENAC), Toulouse (France); Mueller, Martin [Martin Mueller Engineering, Hildesheim (Germany)

    2009-04-15

    The Small Unmanned Meteorological Observer SUMO has been developed as a cost-efficient measurement system with the aim to close the existing observational gap of atmospheric measurement systems in between meteorological masts/towers and radiosondes. The system is highly flexible and has the capability for in-situ ABL measurements with unique spatial and temporal resolution. SUMO is based on a light-weighted styrofoam model airplane, equipped with an autopilot system for autonomous flight missions and in its recent version with meteorological sensors for temperature, humidity and pressure. With its wingspan of 80 cm, its length of 75 cm and a total lift-off weight of 580 g, SUMO is easy to transport and operate even in remote areas with limited infrastructure. During several field campaigns in 2007 and 2008 the system has been successfully tested and operated. Atmospheric profiles of temperature, humidity, wind speed and wind direction have been determined up to 3500 m above ground during the FLOHOF (FLOw over and around HOFsjoekull) field campaign in Central Iceland in July/August 2007. During a 3 week campaign on and around Spitsbergen in February/March 2008 the SUMO system also proved its functionality under polar conditions, reaching altitudes above 1500 m even at ground temperatures of -20 C and wind speeds up to 15 m s{sup -1}. (orig.)

  12. The Small Unmanned Meteorological Observer SUMO: A new tool for atmospheric boundary layer research

    Directory of Open Access Journals (Sweden)

    Joachim Reuder

    2009-05-01

    Full Text Available The Small Unmanned Meteorological Observer SUMO has been developed as a cost-efficient measurement system with the aim to close the existing observational gap of atmospheric measurement systems in between meteorological masts/towers and radiosondes. The system is highly flexible and has the capability for in-situ ABL measurements with unique spatial and temporal resolution. SUMO is based on a light-weighted styrofoam model airplane, equipped with an autopilot system for autonomous flight missions and in its recent version with meteorological sensors for temperature, humidity and pressure. With its wingspan of 80 cm, its length of 75 cm and a total lift-off weight of 580 g, SUMO is easy to transport and operate even in remote areas with limited infrastructure. During several field campaigns in 2007 and 2008 the system has been successfully tested and operated. Atmospheric profiles of temperature, humidity, wind speed and wind direction have been determined up to 3500 m above ground during the FLOHOF (FLOw over and around HOFsjökull field campaign in Central Iceland in July/August 2007. During a 3 week campaign on and around Spitsbergen in February/March 2008 the SUMO system also proved its functionality under polar conditions, reaching altitudes above 1500 m even at ground temperatures of -20° C and wind speeds up to 15 m s-1.

  13. SUMO: Solar Ultraviolet Monitor and Ozone Nanosatellite

    Science.gov (United States)

    Damé, L.; Meftah, M.; Irbah, A.; Hauchecorne, A.; Keckhut, P.; Sarkissian, A.; Godin-Beekman, S.; Rogers, D. J.; Bove, P.; Lagage, P. O.; DeWitte, S.

    2014-12-01

    SUMO is an innovative proof-of-concept nanosatellite aiming to measure on the same platform the different components of the Earth radiation budget (ERB), the solar energy input and the energy reemitted at the top of the Earth atmosphere, with a particular focus on the far UV (FUV) part of the spectrum and on the ozone layer. The FUV is the only wavelength band with energy absorbed in the high atmosphere (stratosphere), in the ozone (Herzberg continuum, 200-220 nm) and oxygen bands, and its high variability is most probably at the origin of a climate influence (UV affects stratospheric dynamics and temperatures, altering interplanetary waves and weather patterns both poleward and downward to the lower stratosphere and tropopause). A simultaneous observation of incoming FUV and ozone production would bring an invaluable information on this process of solar-climate forcing. Space instruments have already measured the different components of the ERB but this is the first time that all instruments will operate on the same platform. This characteristic by itself guarantees original scientific results. SUMO is a 3.6 kg, 3W, 10x10x30 cm3 nanosatellite ("3U"), with a "1U" payload of nanosatellite program of Polytechnic School and CNES (following QB50) for a flight in 2018. Follow-up is 2 fold: on one part more complete measurements using SUMO miniaturized instruments on a larger satellite; on the other part, increase of the coverage in local time and latitude using a constellation of SUMO nanosatellites around the Earth to further geolocalize the Sun influence on our planet. Nanosatellites, with cost and risk limited, are also excellent platforms to evaluate technologies for future missions, e.g. nanotechnology ZnO protection barriers to limit contamination from solar panels in the UV and reduce reflection losses in the visible, or MgZnO solar blind detectors (R&D initiatives proposed to CNES).

  14. Fibroblast motility on substrates with different rigidities: modeling approach

    Science.gov (United States)

    Gracheva, Maria; Dokukina, Irina

    2009-03-01

    We develop a discrete model for cell locomotion on substrates with different rigidities and simulate experiments described in Lo, Wang, Dembo, Wang (2000) ``Cell movement is guided by the rigidity of the substrate'', Biophys. J. 79: 144-152. In these experiments fibroblasts were planted on a substrate with a step rigidity and showed preference for locomotion over stiffer side of the substrate when approaches the boundary between the soft and the stiff sides of the substrate. The model reproduces experimentally observed behavior of fibroblasts. In particular, we are able to show with our model how cell characteristics (such as cell length, shape, area and speed) change during cell crawling through the ``soft-stiff'' substrate boundary. Also, our model suggests the temporary increase of both cell speed and area in that very moment when cell leaves soft side of substrate.

  15. Puromycin induces SUMO and ubiquitin redistribution upon proteasome inhibition

    Energy Technology Data Exchange (ETDEWEB)

    Matsumoto, Hotaru [Course for Biological Sciences, Faculty of Science, Kumamoto University, Kumamoto (Japan); Saitoh, Hisato, E-mail: hisa@kumamoto-u.ac.jp [Course for Biological Sciences, Faculty of Science, Kumamoto University, Kumamoto (Japan); Department of Biological Sciences, Graduate School of Science and Technology, Kumamoto University, Kumamoto (Japan)

    2016-07-29

    We have previously reported the co-localization of O-propargyl-puromycin (OP-Puro) with SUMO-2/3 and ubiquitin at promyelocytic leukemia-nuclear bodies (PML-NBs) in the presence of the proteasome inhibitor MG132, implying a role for the ubiquitin family in sequestering OP-puromycylated immature polypeptides to the nucleus during impaired proteasome activity. Here, we found that as expected puromycin induced SUMO-1/2/3 accumulation with ubiquitin at multiple nuclear foci in HeLa cells when co-exposed to MG132. Co-administration of puromycin and MG132 also facilitated redistribution of PML and the SUMO-targeted ubiquitin ligase RNF4 concurrently with SUMO-2/3. As removal of the drugs from the medium led to disappearance of the SUMO-2/3-ubiquitin nuclear foci, our findings indicated that nuclear assembly/disassembly of SUMO-2/3 and ubiquitin was pharmacologically manipulable, supporting our previous observation on OP-Puro, which predicted the ubiquitin family function in sequestrating aberrant proteins to the nucleus. -- Highlights: •Puromycin exhibits the O-propargyl-puromycin effect. •Puromycin induces SUMO redistribution upon proteasome inhibition. •Ubiquitin and RNF4 accumulate at PML-nuclear bodies with SUMO-2/3. •The ubiquitin family may function in nuclear sequestration of immature proteins.

  16. Mutation in SUMO E3 ligase, SIZ1, disrupts the mature female gametophyte in Arabidopsis

    KAUST Repository

    Ling, Yu

    2012-01-09

    Female gametophyte is the multicellular haploid structure that can produce embryo and endosperm after fertilization, which has become an attractive model system for investigating molecular mechanisms in nuclei migration, cell specification, cell-to-cell communication and many other processes. Previous reports found that the small ubiquitin-like modifier (SUMO) E3 ligase, SIZ1, participated in many processes depending on particular target substrates and suppression of salicylic acid (SA) accumulation. Here, we report that SIZ1 mediates the reproductive process. SIZ1 showed enhanced expression in female organs, but was not detected in the anther or pollen. A defect in the siz1-2 maternal source resulted in reduced seed-set regardless of high SA concentration within the plant. Moreover, aniline blue staining and scanning electron microscopy revealed that funicular and micropylar pollen tube guidance was arrested in siz1-2 plants. Some of the embryo sacs of ovules in siz1-2 were also disrupted quickly after stage FG7. There was no significant affects of the siz1-2 mutation on expression of genes involved in female gametophyte development- or pollen tube guidance in ovaries. Together, our results suggest that SIZ1 sustains the stability and normal function of the mature female gametophyte which is necessary for pollen tube guidance. © 2012 Ling et al.

  17. An Analytical Model for Spectral Peak Frequency Prediction of Substrate Noise in CMOS Substrates

    DEFF Research Database (Denmark)

    Shen, Ming; Mikkelsen, Jan H.

    2013-01-01

    This paper proposes an analytical model describing the generation of switching current noise in CMOS substrates. The model eliminates the need for SPICE simulations in existing methods by conducting a transient analysis on a generic CMOS inverter and approximating the switching current waveform us......- ing a Modified Raised Cosine (MORAC) equation. The proposed model is scalable, easy to implement and capable of predicting the spectral peak frequency of the substrate noise. The validation has been done via simulations and measurements. Good agreement has been found between the modeled...

  18. Regulation of Plant Cellular and Organismal Development by SUMO.

    Science.gov (United States)

    Elrouby, Nabil

    2017-01-01

    This chapter clearly demonstrates the breadth and spectrum of the processes that SUMO regulates during plant development. The gross phenotypes observed in mutants of the SUMO conjugation and deconjugation enzymes reflect these essential roles, and detailed analyses of these mutants under different growth conditions revealed roles in biotic and abiotic stress responses, phosphate starvation, nitrate and sulphur metabolism, freezing and drought tolerance and response to excess copper. SUMO functions also intersect with those regulated by several hormones such as salicylic acid , abscisic acid , gibberellins and auxin, and detailed studies provide mechanistic clues of how sumoylation may regulate these processes. The regulation of COP1 and PhyB functions by sumoylation provides very strong evidence that SUMO is heavily involved in the regulation of light signaling in plants. At the cellular and subcellular levels, SUMO regulates meristem architecture, the switch from the mitotic cycle into the endocycle, meiosis, centromere decondensation and exit from mitosis, transcriptional control, and release from transcriptional silencing. Most of these advances in our understanding of SUMO functions during plant development emerged over the past 6-7 years, and they may only predict a prominent rise of SUMO as a major regulator of eukaryotic cellular and organismal growth and development.

  19. Modeling substrate-bacteria-grazer interactions coupled to substrate transport in groundwater

    Science.gov (United States)

    Bajracharya, Bijendra M.; Lu, Chuanhe; Cirpka, Olaf A.

    2014-05-01

    Models of microbial dynamics coupled to solute transport in aquifers typically require the introduction of a bacterial capacity term to prevent excessive microbial growth close to substrate-injection boundaries. The factors controlling this carrying capacity, however, are not fully understood. In this study, we propose that grazers or bacteriophages may control the density of bacterial biomass in continuously fed porous media. We conceptualize the flow-through porous medium as a series of retentostats, in which the dissolved substrate is advected with water flow whereas the biomasses of bacteria and grazers are considered essentially immobile. We first model a single retentostat with Monod kinetics of bacterial growth and a second-order grazing law, which shows that the system oscillates but approaches a stable steady state with nonzero concentrations of substrate, bacteria, and grazers. The steady state concentration of the bacteria biomass is independent of the substrate concentration in the inflow. When coupling several retentostats in a series to mimic a groundwater column, the steady state bacteria concentrations thus remain at a constant level over a significant travel distance. The one-dimensional reactive transport model also accounts for substrate dispersion and a random walk of grazers influenced by the bacteria concentration. These dispersive-diffusive terms affect the oscillations until steady state is reached, but hardly the steady state value itself. We conclude that grazing, or infection by bacteriophages, is a possible explanation of the maximum biomass concentration frequently needed in bioreactive transport models. Its value depends on parameters related to the grazers or bacteriophages and is independent of bacterial growth parameters or substrate concentration, provided that there is enough substrate to sustain bacteria and grazers.

  20. Desumoylation of the Endoplasmic Reticulum Membrane VAP Family Protein Scs2 by Ulp1 and SUMO Regulation of the Inositol Synthesis Pathway

    Science.gov (United States)

    Felberbaum, Rachael; Wilson, Nicole R.; Cheng, Dongmei; Peng, Junmin

    2012-01-01

    Posttranslational protein modification by the ubiquitin-like SUMO protein is critical to eukaryotic cell regulation, but much remains unknown regarding its operation and substrates. Here we report that specific mutations in the Saccharomyces cerevisiae Ulp1 SUMO protease, including its coiled-coil (CC) domain, lead to the accumulation of distinct sumoylated proteins in vivo. A prominent ∼50-kDa sumoylated protein accumulates in a Ulp1 CC mutant. The protein was identified as Scs2, an endoplasmic reticulum (ER) membrane protein that regulates phosphatidylinositol synthesis and lipid trafficking. Mutation of lysine 180 of Scs2 abolishes its sumoylation. Notably, impairment of either cellular sumoylation or cellular desumoylation mechanisms inhibits cell growth in the absence of inositol and exacerbates the inositol auxotrophy caused by deletion of SCS2. Mutants lacking the Ulp2 SUMO protease are the most severely affected, and this defect was traced to the mutants' impaired ability to induce transcription of INO1, which encodes the rate-limiting enzyme of inositol biosynthesis. Conversely, inositol starvation induces a striking change in the profiles of total cellular SUMO conjugates. These results provide the first evidence of cross-regulation between the SUMO and inositol pathways, including the sumoylation of an ER membrane protein central to phospholipid synthesis and phosphoinositide signaling. PMID:22025676

  1. Tools to Study SUMO Conjugation in Caenorhabditis elegans.

    Science.gov (United States)

    Pelisch, Federico; Hay, Ronald T

    2016-01-01

    The cell biology of sumoylation has mostly been studied using transformed cultured cells and yeast. In recent years, genetic analysis has demonstrated important roles for sumoylation in the biology of C. elegans. Here, we expand the existing set of tools making it possible to address the role of sumoylation in the nematode C. elegans using a combination of genetics, imaging, and biochemistry. Most importantly, the dynamics of SUMO conjugation and deconjugation can be followed very precisely both in space and time within living worms. Additionally, the biochemistry of SUMO conjugation and deconjugation can be addressed using recombinant purified components of the C. elegans sumoylation machinery, including E3 ligases and SUMO proteases. These tools and reagents will be useful to gain insights into the biological role of SUMO in the context of a multicellular organism.

  2. The Epstein-Barr virus miR-BHRF1-1 targets RNF4 during productive infection to promote the accumulation of SUMO conjugates and the release of infectious virus.

    Science.gov (United States)

    Li, Jinlin; Callegari, Simone; Masucci, Maria G

    2017-04-01

    Post-translational modification by the Small Ubiquitin-like Modifier (SUMO) regulates a variety of cellular functions, and is hijacked by viruses to remodel the host cell during latent and productive infection. Here we have monitored the activity of the SUMO conjugation machinery in cells productively infected with Epstein-Barr virus (EBV). We found that SUMO2/3 conjugates accumulate during the late phase of the productive virus cycle, and identified several viral proteins as bone fide SUMOylation substrates. Analysis of the mechanism involved in the accumulation of SUMOylated proteins revealed upregulation of several components of the SUMO-conjugation machinery and post-transcriptional downregulation of the SUMO-targeted ubiquitin ligase RNF4. The latter effect was mediated by selective inhibition of RNF4 protein expression by the viral miR-BHRF1-1. Reconstitution of RNF4 in cells expressing an inducible miR-BHRF1-1 sponge or a miR-BHRF1-1 resistant RNF4 was associated with reduced levels of early and late viral proteins and impaired virus release. These findings illustrate a novel strategy for viral interference with the SUMO pathway, and identify the EBV miR-BHRF1-1 and the cellular RNF4 as regulators of the productive virus cycle.

  3. Functional characterization of the SIZ/PIAS-type SUMO E3 ligases, OsSIZ1 and OsSIZ2 in rice

    KAUST Repository

    Park, Hyeongcheol

    2010-06-18

    Sumoylation is a post-translational regulatory process in diverse cellular processes in eukaryotes, involving conjugation/deconjugation of small ubiquitin-like modifier (SUMO) proteins to other proteins thus modifying their function. The PIAS [protein inhibitor of activated signal transducers and activators of transcription (STAT)] and SAP (scaffold attachment factor A/B/acinus/PIAS)/MIZ (SIZ) proteins exhibit SUMO E3-ligase activity that facilitates the conjugation of SUMO proteins to target substrates. Here, we report the isolation and molecular characterization of Oryza sativa SIZ1 (OsSIZ1) and SIZ2 (OsSIZ2), rice homologs of Arabidopsis SIZ1. The rice SIZ proteins are localized to the nucleus and showed sumoylation activities in a tobacco system. Our analysis showed increased amounts of SUMO conjugates associated with environmental stresses such as high and low temperature, NaCl and abscisic acid (ABA) in rice plants. The expression of OsSIZ1 and OsSIZ2 in siz1-2 Arabidopsis plants partially complemented the morphological mutant phenotype and enhanced levels of SUMO conjugates under heat shock conditions. In addition, ABA-hypersensitivity of siz1-2 seed germination was partially suppressed by OsSIZ1 and OsSIZ2. The results suggest that rice SIZ1 and SIZ2 are able to functionally complement Arabidopsis SIZ1 in the SUMO conjugation pathway. Their effects on the Arabidopsis mutant suggest a function for these genes related to stress responses and stress adaptation. © 2010 Blackwell Publishing Ltd.

  4. Modelling of Substrate Noise and Mitigation Schemes for UWB Systems

    DEFF Research Database (Denmark)

    Shen, Ming; Mikkelsen, Jan H.; Larsen, Torben

    2012-01-01

    -mode designs, digital switching noise is an ever-present problem that needs to be taken into consideration. This is of particular importance when low cost implementation technologies, e.g. lightly doped substrates, are aimed for. For traditional narrow-band designs much of the issue can be mitigated using...... tuned elements in the signal paths. However, for UWB designs this is not a viable option and other means are therefore required. Moreover, owing to the ultra-wideband nature and low power spectral density of the signal, UWB mixed-signal integrated circuits are more sensitive to substrate noise compared...... with narrow-band circuits. This chapter presents a study on the modeling and mitigation of substrate noise in mixed-signal integrated circuits (ICs), focusing on UWB system/circuit designs. Experimental impact evaluation of substrate noise on UWB circuits is presented. It shows how a wide-band circuit can...

  5. Kinetic models of cell growth, substrate utilization and bio ...

    African Journals Online (AJOL)

    Bio-decolorization kinetic studies of distillery effluent in a batch culture were conducted using Aspergillus fumigatus. A simple model was proposed using the Logistic Equation for the growth, Leudeking-Piret kinetics for bio-decolorization, and also for substrate utilization. The proposed models appeared to provide a suitable ...

  6. SUMO chain formation is required for response to replication arrest in S. pombe.

    Directory of Open Access Journals (Sweden)

    Andrew Skilton

    Full Text Available SUMO is a ubiquitin-like protein that is post-translationally attached to one or more lysine residues on target proteins. Despite having only 18% sequence identity with ubiquitin, SUMO contains the conserved betabetaalphabetabetaalphabeta fold present in ubiquitin. However, SUMO differs from ubiquitin in having an extended N-terminus. In S. pombe the N-terminus of SUMO/Pmt3 is significantly longer than those of SUMO in S. cerevisiae, human and Drosophila. Here we investigate the role of this N-terminal region. We have used two dimensional gel electrophoresis to demonstrate that S. pombe SUMO/Pmt3 is phosphorylated, and that this occurs on serine residues at the extreme N-terminus of the protein. Mutation of these residues (in pmt3-1 results in a dramatic reduction in both the levels of high Mr SUMO-containing species and of total SUMO/Pmt3, indicating that phosphorylation of SUMO/Pmt3 is required for its stability. Despite the significant reduction in high Mr SUMO-containing species, pmt3-1 cells do not display an aberrant cell morphology or sensitivity to genotoxins or stress. Additionally, we demonstrate that two lysine residues in the N-terminus of S. pombe SUMO/Pmt3 (K14 and K30 can act as acceptor sites for SUMO chain formation in vitro. Inability to form SUMO chains results in aberrant cell and nuclear morphologies, including stretched and fragmented chromatin. SUMO chain mutants are sensitive to the DNA synthesis inhibitor, hydroxyurea (HU, but not to other genotoxins, such as UV, MMS or CPT. This implies a role for SUMO chains in the response to replication arrest in S. pombe.

  7. Metabolic modeling of mixed substrate uptake for polyhydroxyalkanoate (PHA) production

    NARCIS (Netherlands)

    Jiang, Y.; Hebly, M.; Kleerebezem, R.; Muyzer, G.; van Loosdrecht, M.C.M.

    2011-01-01

    Polyhydroxyalkanoate (PHA) production by mixed microbial communities can be established in a two-stage process, consisting of a microbial enrichment step and a PHA accumulation step. In this study, a mathematical model was constructed for evaluating the influence of the carbon substrate composition

  8. Role of SUMO-specific protease 2 in reprogramming cellular glucose metabolism.

    Directory of Open Access Journals (Sweden)

    Shuang Tang

    Full Text Available Most cancer cells exhibit a shift in glucose metabolic strategy, displaying increased glycolysis even with adequate oxygen supply. SUMO-specific proteases (SENPs de-SUMOylate substrates including HIF1α and p53,two key regulators in cancer glucose metabolism, to regulate their activity, stability and subcellular localization. However, the role of SENPs in tumor glucose metabolism remains unclear. Here we report that SUMO-specific protease 2 (SENP2 negatively regulates aerobic glycolysis in MCF7 and MEF cells. Over-expression of SENP2 reduces the glucose uptake and lactate production, increasing the cellular ATP levels in MCF7 cells, while SENP2 knockout MEF cells show increased glucose uptake and lactate production along with the decreased ATP levels. Consistently, the MCF7 cells over-expressing SENP2 exhibit decreased expression levels of key glycolytic enzymes and an increased rate of glucose oxidation compared with control MCF7 cells, indicating inhibited glycolysis but enhanced oxidative mitochondrial respiration. Moreover, SENP2 over-expressing MCF7 cells demonstrated a reduced amount of phosphorylated AKT, whereas SENP2 knockout MEFs exhibit increased levels of phosphorylated AKT. Furthermore, inhibiting AKT phosphorylation by LY294002 rescued the phenotype induced by SENP2 deficiency in MEFs. In conclusion, SENP2 represses glycolysis and shifts glucose metabolic strategy, in part through inhibition of AKT phosphorylation. Our study reveals a novel function of SENP2 in regulating glucose metabolism.

  9. Kant e o sumo bem comunitário

    Directory of Open Access Journals (Sweden)

    Letícia Machado Spinelli

    2012-08-01

    Full Text Available http://dx.doi.org/10.5007/1677-2954.2012v11n1p37   O que aqui nos propomos fazer é explicitar o conceito de sumo bem enquanto bem comunitário, em que se evidencia um desdobramento da formulação do conceito de sumo bem sob a perspectiva de um bem coletivo. Esse conceito foi apresentado por Kant na terceira parte de A religião nos limites da simples razão, contexto no qual se dedicou a tratar da noção de um progresso moral nos termos de uma comunidade ética.

  10. The Comparison of a Roundabout Traffic Delay Estimation between SUMO and IHCM 1997 on Roundabout

    Directory of Open Access Journals (Sweden)

    Tina Andriyana

    2015-06-01

    The result showed the traffic delay in observation data is higher than delay in SUMO result and IHCM 1997 calculation. The statistical results showed that the traffic delay of SUMO, and IHCM 1997 have no similarities to the observation. Furthermore, from the linear regression result, only SUMO result has the highest value for determination coefficient (R2 compared to IHCM 1997 as shown in the West and South arms for SUMO result in the morning measurement. It means SUMO more representatives the observation compared to IHCM 1997. It is occurred because SUMO is developed in Europe and also the location for this research is in Sweden, Europe which has very different traffic condition from Indonesia. Keywords: Roundabout, traffic delay, SUMO, IHCM 1997.

  11. Modeling the Substrate Skin Effects in Mutual RL Characteristics.,

    Directory of Open Access Journals (Sweden)

    D. de Roest

    2003-12-01

    Full Text Available The goal of this work was to model the influence of the substrateskin effects on the distributed mutual impedance per unit lengthparameters of multiple coupled on-chip interconnects. The proposedanalytic model is based on the frequency-dependent distribution of thecurrent in the silicon substrate and the closed form integrationapproach. It is shown that the calculated frequency-dependentdistributed mutual inductance and the associated mutual resistance arein good agreement with the results obtained from CAD-oriented circuitmodeling technique.

  12. High Glucose Induces Sumoylation of Smad4 via SUMO2/3 in Mesangial Cells

    Directory of Open Access Journals (Sweden)

    Xueqin Zhou

    2014-01-01

    Full Text Available Recent studies have shown that sumoylation is a posttranslational modification involved in regulation of the transforming growth factor-β (TGF-β signaling pathway, which plays a critical role in renal fibrosis in diabetic nephropathy (DN. However, the role of sumoylation in the regulation of TGF-β signaling in DN is still unclear. In the present study, we investigated the expression of SUMO (SUMO1 and SUMO2/3 and Smad4 and the interaction between SUMO and Smad4 in cultured rat mesangial cells induced by high glucose. We found that SUMO1 and SUMO2/3 expression was significantly increased in the high glucose groups compared to the normal group P<0.05. Smad4 and fibronectin (FN levels were also increased in the high glucose groups in a dose-dependent manner. Coimmunoprecipitation and confocal laser scanning revealed that Smad4 interacted and colocalized with SUMO2/3, but not with SUMO1 in mesangial cells. Sumoylation (SUMO2/3 of Smad4 under high glucose condition was strongly enhanced compared to normal control P<0.05. These results suggest that high glucose may activate TGF-β/Smad signaling through sumoylation of Samd4 by SUMO2/3 in mesangial cells.

  13. Controlling DNA-End Resection: An Emerging Task for Ubiquitin and SUMO.

    Science.gov (United States)

    Himmels, Sarah-Felicitas; Sartori, Alessandro A

    2016-01-01

    DNA double-strand breaks (DSBs) are one of the most detrimental lesions, as their incorrect or incomplete repair can lead to genomic instability, a hallmark of cancer. Cells have evolved two major competing DSB repair mechanisms: Homologous recombination (HR) and non-homologous end joining (NHEJ). HR is initiated by DNA-end resection, an evolutionarily conserved process that generates stretches of single-stranded DNA tails that are no longer substrates for religation by the NHEJ machinery. Ubiquitylation and sumoylation, the covalent attachment of ubiquitin and SUMO moieties to target proteins, play multifaceted roles in DNA damage signaling and have been shown to regulate HR and NHEJ, thus ensuring appropriate DSB repair. Here, we give a comprehensive overview about the current knowledge of how ubiquitylation and sumoylation control DSB repair by modulating the DNA-end resection machinery.

  14. PIASxα Ligase Enhances SUMO1 Modification of PTEN Protein as a SUMO E3 Ligase*

    Science.gov (United States)

    Wang, Weibin; Chen, Yifan; Wang, Shuya; Hu, Ningguang; Cao, Zhengyi; Wang, Wengong; Tong, Tanjun; Zhang, Xiaowei

    2014-01-01

    The tumor suppressor PTEN plays a critical role in the regulation of multiple cellular processes that include survival, cell cycle, proliferation, and apoptosis. PTEN is frequently mutated or deleted in various human cancer cells to promote tumorigenesis. PTEN is regulated by SUMOylation, but the SUMO E3 ligase involved in the SUMOylation of PTEN remains unclear. Here, we demonstrated that PIASxα is a SUMO E3 ligase for PTEN. PIASxα physically interacted with PTEN both in vitro and in vivo. Their interaction depended on the integrity of phosphatase and C2 domains of PTEN and the region of PIASxα comprising residues 134–347. PIASxα enhanced PTEN protein stability by reducing PTEN ubiquitination, whereas the mutation of PTEN SUMO1 conjugation sites neutralized the effect of PIASxα on PTEN protein half-life. Functionally, PIASxα, as a potential tumor suppressor, negatively regulated the PI3K-Akt pathway through stabilizing PTEN protein. Overexpression of PIASxα led to G0/G1 cell cycle arrest, thus triggering cell proliferation inhibition and tumor suppression, whereas PIASxα knockdown or deficiency in catalytic activity abolished the inhibition. Together our studies suggest that PIASxα is a novel SUMO E3 ligase for PTEN, and it positively regulates PTEN protein level in tumor suppression. PMID:24344134

  15. PIASxα ligase enhances SUMO1 modification of PTEN protein as a SUMO E3 ligase.

    Science.gov (United States)

    Wang, Weibin; Chen, Yifan; Wang, Shuya; Hu, Ningguang; Cao, Zhengyi; Wang, Wengong; Tong, Tanjun; Zhang, Xiaowei

    2014-02-07

    The tumor suppressor PTEN plays a critical role in the regulation of multiple cellular processes that include survival, cell cycle, proliferation, and apoptosis. PTEN is frequently mutated or deleted in various human cancer cells to promote tumorigenesis. PTEN is regulated by SUMOylation, but the SUMO E3 ligase involved in the SUMOylation of PTEN remains unclear. Here, we demonstrated that PIASxα is a SUMO E3 ligase for PTEN. PIASxα physically interacted with PTEN both in vitro and in vivo. Their interaction depended on the integrity of phosphatase and C2 domains of PTEN and the region of PIASxα comprising residues 134-347. PIASxα enhanced PTEN protein stability by reducing PTEN ubiquitination, whereas the mutation of PTEN SUMO1 conjugation sites neutralized the effect of PIASxα on PTEN protein half-life. Functionally, PIASxα, as a potential tumor suppressor, negatively regulated the PI3K-Akt pathway through stabilizing PTEN protein. Overexpression of PIASxα led to G0/G1 cell cycle arrest, thus triggering cell proliferation inhibition and tumor suppression, whereas PIASxα knockdown or deficiency in catalytic activity abolished the inhibition. Together our studies suggest that PIASxα is a novel SUMO E3 ligase for PTEN, and it positively regulates PTEN protein level in tumor suppression.

  16. Rapid addition of unlabeled silent solubility tags to proteins using a new substrate-fused sortase reagent

    Energy Technology Data Exchange (ETDEWEB)

    Amer, Brendan R.; Macdonald, Ramsay; Jacobitz, Alex W.; Liauw, Brandon; Clubb, Robert T., E-mail: rclubb@mbi.ucla.edu [University of California, Los Angeles, Department of Chemistry and Biochemistry (United States)

    2016-03-15

    Many proteins can’t be studied using solution NMR methods because they have limited solubility. To overcome this problem, recalcitrant proteins can be fused to a more soluble protein that functions as a solubility tag. However, signals arising from the solubility tag hinder data analysis because they increase spectral complexity. We report a new method to rapidly and efficiently add a non-isotopically labeled Small Ubiquitin-like Modifier protein (SUMO) solubility tag to an isotopically labeled protein. The method makes use of a newly developed SUMO-Sortase tagging reagent in which SUMO and the Sortase A (SrtA) enzyme are present within the same polypeptide. The SUMO-Sortase reagent rapidly attaches SUMO to any protein that contains the sequence LPXTG at its C-terminus. It modifies proteins at least 15-times faster than previously described approaches, and does not require active dialysis or centrifugation during the reaction to increase product yields. In addition, silently tagged proteins are readily purified using the well-established SUMO expression and purification system. The utility of the SUMO-Sortase tagging reagent is demonstrated using PhoP and green fluorescent proteins, which are ~90 % modified with SUMO at room temperature within four hours. SrtA is widely used as a tool to construct bioconjugates. Significant rate enhancements in these procedures may also be achieved by fusing the sortase enzyme to its nucleophile substrate.

  17. A Critical SUMO1 Modification of LKB1 Regulates AMPK Activity during Energy Stress

    KAUST Repository

    Ritho, Joan

    2015-07-23

    SUMOylation has been implicated in cellular stress adaptation, but its role in regulating liver kinase B1 (LKB1), a major upstream kinase of the energy sensor AMP-activated protein kinase (AMPK), is unknown. Here, we show that energy stress triggers an increase in SUMO1 modification of LKB1, despite a global reduction in both SUMO1 and SUMO2/3 conjugates. During metabolic stress, SUMO1 modification of LKB1 lysine 178 is essential in promoting its interaction with AMPK via a SUMO-interacting motif (SIM) essential for AMPK activation. The LKB1 K178R SUMO mutant had defective AMPK signaling and mitochondrial function, inducing death in energy-deprived cells. These results provide additional insight into how LKB1-AMPK signaling is regulated during energy stress, and they highlight the critical role of SUMOylation in maintaining the cell’s energy equilibrium.

  18. Regulation of SUMO2 Target Proteins by the Proteasome in Human Cells Exposed to Replication Stress

    DEFF Research Database (Denmark)

    Bursomanno, Sara; McGouran, Joanna F; Kessler, Benedikt M

    2015-01-01

    In human cells, SUMO2 is predominantly conjugated to target proteins in response to cellular stress. Previous studies suggested that proteins conjugated to SUMO2, but not to SUMO1, could be regulated by the ubiquitin-mediated proteasome system. Hence, we set out to understand the role of the prot......In human cells, SUMO2 is predominantly conjugated to target proteins in response to cellular stress. Previous studies suggested that proteins conjugated to SUMO2, but not to SUMO1, could be regulated by the ubiquitin-mediated proteasome system. Hence, we set out to understand the role...... of genome instability, which is suggested to drive tumorigenesis and possibly aging, our data will facilitate future functional studies in the fields of DNA metabolism and cancer biology....

  19. Viral Mimicry to Usurp Ubiquitin and SUMO Host Pathways

    Directory of Open Access Journals (Sweden)

    Peter Wimmer

    2015-08-01

    Full Text Available Posttranslational modifications (PTMs of proteins include enzymatic changes by covalent addition of cellular regulatory determinants such as ubiquitin (Ub and small ubiquitin-like modifier (SUMO moieties. These modifications are widely used by eukaryotic cells to control the functional repertoire of proteins. Over the last decade, it became apparent that the repertoire of ubiquitiylation and SUMOylation regulating various biological functions is not restricted to eukaryotic cells, but is also a feature of human virus families, used to extensively exploit complex host-cell networks and homeostasis. Intriguingly, besides binding to host SUMO/Ub control proteins and interfering with the respective enzymatic cascade, many viral proteins mimic key regulatory factors to usurp this host machinery and promote efficient viral outcomes. Advanced detection methods and functional studies of ubiquitiylation and SUMOylation during virus-host interplay have revealed that human viruses have evolved a large arsenal of strategies to exploit these specific PTM processes. In this review, we highlight the known viral analogs orchestrating ubiquitin and SUMO conjugation events to subvert and utilize basic enzymatic pathways.

  20. Structural Analysis of a Complex between Small Ubiquitin-like Modifier 1 (SUMO1) and the ZZ Domain of CREB-binding Protein (CBP/p300) Reveals a New Interaction Surface on SUMO

    DEFF Research Database (Denmark)

    Diehl, Carl; Akke, Mikael; Bekker-Jensen, Simon

    2016-01-01

    We have recently discovered that the ZZ zinc finger domain represents a novel small ubiquitin-like modifier (SUMO) binding motif. In this study we identify the binding epitopes in the ZZ domain of CBP (CREB-binding protein) and SUMO1 using NMR spectroscopy. The binding site on SUMO1 represents a ...

  1. Thermodynamic modeling of algal cell–solid substrate interactions

    International Nuclear Information System (INIS)

    Cui, Yan; Yuan, Wenqiao

    2013-01-01

    Highlights: • A thermodynamic model was developed to simulate algal cell-substrate attachment. • The number of attached cells was positively correlated to work of attachment. • Algal cell attachment was determined by surface energies of cells and substrata. - Abstract: The process of microalgal cell attachment to solid-carrier surfaces was simulated through a thermodynamic model. The modeling results showed that, for most microbes, when the polar surface energy of the cell is smaller than that of water, cellular attachment would be more favorable on materials with higher dispersive surface energy but lower polar surface energy. If the polar surface energy of the cell is greater than that of water, more cell attachment would be expected on materials that are higher in both dispersive and polar surface energies. Modeling results qualitatively matched experimental data in the attachment of a freshwater alga, Scenedesmus dimorphus, and a marine alga, Nannochloropsis oculata, on five materials (nylon, stainless steel, polycarbonate, polypropylene, and glass). The model was also validated by published literature data on a wider variety of microbes and materials, indicating that the model developed can be applicable in designing, selecting, and matching algal strains and solid carrier materials to enhance cell attachment

  2. A predictive model for substrates of cytochrome P450-debrisoquine (2D6)

    NARCIS (Netherlands)

    Koymans, L.; Vermeulen, N P; van Acker, S.A.B.E.; te Koppele, J.M.; Heykants, J J; Lavrijsen, K; Meuldermans, W; Donné-Op den Kelder, G M

    1992-01-01

    Molecular modeling techniques were used to derive a predictive model for substrates of cytochrome P450 2D6, an isozyme known to metabolize only compounds with one or more basic nitrogen atoms. Sixteen substrates, accounting for 23 metabolic reactions, with a distance of either 5 A ("5-A substrates",

  3. Quantum Molecular Interaction Field Models of Substrate Enantioselection in Asymmetric Processes.

    Science.gov (United States)

    Kozlowski, Marisa C; Ianni, James C

    2010-06-01

    Computational models correlating substrate structure to enantioselection with asymmetric catalysts using the QMQSAR program are described. In addition to rapidly providing predictions that could be used to facilitate the screening of catalysts for novel substrates, the QMQSAR program identifies the portions of the substrate that most directly influence the enantioselectivity. The lack underlying relationship between all the substrates in one case, requires two quantitative structure selectivity relationships (QSSR) models to describe all of the experimental results.

  4. SUMO and ubiquitin-dependent XPC exchange drives nucleotide excision repair

    DEFF Research Database (Denmark)

    Van Cuijk, Loes; Van Belle, Gijsbert J.; Turkyilmaz, Yasemin

    2015-01-01

    XPC recognizes UV-induced DNA lesions and initiates their removal by nucleotide excision repair (NER). Damage recognition in NER is tightly controlled by ubiquitin and SUMO modifications. Recent studies have shown that the SUMO-targeted ubiquitin ligase RNF111 promotes K63-linked ubiquitylation o...

  5. SUMO fusion technology for enhanced protein production in prokaryotic and eukaryotic expression systems.

    Science.gov (United States)

    Panavas, Tadas; Sanders, Carsten; Butt, Tauseef R

    2009-01-01

    In eukaryotic cells, the reversible attachment of small ubiquitin-like modifier (SUMO) protein is a post-translational modification that has been demonstrated to play an important role in various cellular processes. Moreover, it has been found that SUMO as an N-terminal fusion partner enhances functional protein production in prokaryotic and eukaryotic expression systems, based upon significantly improved protein stability and solubility. Following the expression and purification of the fusion protein, the SUMO-tag can be cleaved by specific (SUMO) proteases via their endopeptidase activity in vitro to generate the desired N-terminus of the released protein partner. In addition to its physiological relevance in eukaryotes, SUMO can, thus, be used as a powerful biotechnological tool for protein expression in prokaryotic and eukaryotic cell systems.In this chapter, we will describe the construction of a fusion protein with the SUMO-tag, its expression in Escherichia coli, and its purification followed by the removal of the SUMO-tag by a SUMO-specific protease in vitro.

  6. Comprehensive Identification of SUMO2/3 Targets and Their Dynamics during Mitosis

    DEFF Research Database (Denmark)

    Schou, Julie; Kelstrup, Christian D; Hayward, Daniel G

    2014-01-01

    During mitosis large alterations in cellular structures occur rapidly, which to a large extent is regulated by post-translational modification of proteins. Modification of proteins with the small ubiquitin-related protein SUMO2/3 regulates mitotic progression, but few mitotic targets have been...... identified so far. To deepen our understanding of SUMO2/3 during this window of the cell cycle, we undertook a comprehensive proteomic characterization of SUMO2/3 modified proteins in mitosis and upon mitotic exit. We developed an efficient tandem affinity purification strategy of SUMO2/3 modified proteins...... from mitotic cells. Combining this purification strategy with cell synchronization procedures and quantitative mass spectrometry allowed for the mapping of numerous novel targets and their dynamics as cells progressed out of mitosis. This identified RhoGDIα as a major SUMO2/3 modified protein...

  7. Analysis of Changes in SUMO-2/3 Modification during Breast Cancer Progression and Metastasis

    DEFF Research Database (Denmark)

    Subramonian, Divya; Raghunayakula, Sarita; Olsen, Jesper V

    2014-01-01

    up-regulated in metastatic breast cancer cells compared with nonmetastatic control cells. To identify proteins differentially modified by SUMO-2/3 between metastatic and nonmetastatic cells, we established a method in which endogenous SUMO-2/3 conjugates are labeled by stable isotope labeling......-regulation of PML SUMO-2/3 modification corresponds to an increased number of PML nuclear bodies (PML-NBs) in metastatic cells, whereas up-regulation of global SUMO-2/3 modification promotes 3D cell migration. Our findings provide a foundation for further investigating the effects of SUMOylation on breast cancer......SUMOylation is an essential posttranslational modification and regulates many cellular processes. Dysregulation of SUMOylation plays a critical role in metastasis, yet how its perturbation affects this lethal process of cancer is not well understood. We found that SUMO-2/3 modification is greatly...

  8. SUMO-interacting motifs of human TRIM5α are important for antiviral activity.

    Directory of Open Access Journals (Sweden)

    Gloria Arriagada

    2011-04-01

    Full Text Available Human TRIM5α potently restricts particular strains of murine leukemia viruses (the so-called N-tropic strains but not others (the B- or NB-tropic strains during early stages of infection. We show that overexpression of SUMO-1 in human 293T cells, but not in mouse MDTF cells, profoundly blocks N-MLV infection. This block is dependent on the tropism of the incoming virus, as neither B-, NB-, nor the mutant R110E of N-MLV CA (a B-tropic switch are affected by SUMO-1 overexpression. The block occurred prior to reverse transcription and could be abrogated by large amounts of restricted virus. Knockdown of TRIM5α in 293T SUMO-1-overexpressing cells resulted in ablation of the SUMO-1 antiviral effects, and this loss of restriction could be restored by expression of a human TRIM5α shRNA-resistant plasmid. Amino acid sequence analysis of human TRIM5α revealed a consensus SUMO conjugation site at the N-terminus and three putative SUMO interacting motifs (SIMs in the B30.2 domain. Mutations of the TRIM5α consensus SUMO conjugation site did not affect the antiviral activity of TRIM5α in any of the cell types tested. Mutation of the SIM consensus sequences, however, abolished TRIM5α antiviral activity against N-MLV. Mutation of lysines at a potential site of SUMOylation in the CA region of the Gag gene reduced the SUMO-1 block and the TRIM5α restriction of N-MLV. Our data suggest a novel aspect of TRIM5α-mediated restriction, in which the presence of intact SIMs in TRIM5α, and also the SUMO conjugation of CA, are required for restriction. We propose that at least a portion of the antiviral activity of TRIM5α is mediated through the binding of its SIMs to SUMO-conjugated CA.

  9. The Sumo-targeted ubiquitin ligase RNF4 regulates the localization and function of the HTLV-1 oncoprotein Tax

    Science.gov (United States)

    Fryrear, Kimberly A.; Guo, Xin

    2012-01-01

    The Really Interesting New Gene (RING) Finger Protein 4 (RNF4) represents a class of ubiquitin ligases that target Small Ubiquitin-like Modifier (SUMO)–modified proteins for ubiquitin modification. To date, the regulatory function of RNF4 appears to be ubiquitin-mediated degradation of sumoylated cellular proteins. In the present study, we show that the Human T-cell Leukemia Virus Type 1 (HTLV-1) oncoprotein Tax is a substrate for RNF4 both in vivo and in vitro. We mapped the RNF4-binding site to a region adjacent to the Tax ubiquitin/SUMO modification sites K280/K284. Interestingly, RNF4 modification of Tax protein results in relocalization of the oncoprotein from the nucleus to the cytoplasm. Overexpression of RNF4, but not the RNF4 RING mutant, resulted in cytoplasmic enrichment of Tax. The RNF4-induced nucleus-to-cytoplasm relocalization was associated with increased NF-κB–mediated and decreased cAMP Response Element-Binding (CREB)–mediated Tax activity. Finally, depletion of RNF4 by RNAi prevented the DNA damage–induced nuclear/cytoplasmic translocation of Tax. These results provide important new insight into STUbL-mediated pathways that regulate the subcellular localization and functional dynamics of viral oncogenes. PMID:22106342

  10. SUMO-2 Orchestrates Chromatin Modifiers in Response to DNA Damage

    DEFF Research Database (Denmark)

    Hendriks, Ivo A; Treffers, Louise W; Verlaan-de Vries, Matty

    2015-01-01

    dynamically SUMOylated interaction networks of chromatin modifiers, transcription factors, DNA repair factors, and nuclear body components. SUMOylated chromatin modifiers include JARID1B/KDM5B, JARID1C/KDM5C, p300, CBP, PARP1, SetDB1, and MBD1. Whereas SUMOylated JARID1B was ubiquitylated by the SUMO......-targeted ubiquitin ligase RNF4 and degraded by the proteasome in response to DNA damage, JARID1C was SUMOylated and recruited to the chromatin to demethylate histone H3K4....

  11. The p150 subunit of CAF-1 causes association of SUMO2/3 with the DNA replication foci

    Energy Technology Data Exchange (ETDEWEB)

    Uwada, Junsuke [Department of Biological Sciences, Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami, Kumamoto 860-8555 (Japan); Global COE (Centers of Excellence) Program, Global Initiative Center for Pulsed Power Engineering, Kumamoto University, 2-39-1 Kurokami, Kumamoto 860-8555 (Japan); Tanaka, Niina; Yamaguchi, Yutaro; Uchimura, Yasuhiro [Department of Biological Sciences, Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami, Kumamoto 860-8555 (Japan); Shibahara, Kei-ichi [Department of Integrated Genetics, National Institute of Genetics, Research Organization of Information and Systems, Mishima (Japan); Nakao, Mitsuyoshi [Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto (Japan); Saitoh, Hisato, E-mail: hisa@kumamoto-u.ac.jp [Department of Biological Sciences, Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami, Kumamoto 860-8555 (Japan); Global COE (Centers of Excellence) Program, Global Initiative Center for Pulsed Power Engineering, Kumamoto University, 2-39-1 Kurokami, Kumamoto 860-8555 (Japan)

    2010-01-01

    The small ubiquitin-related modifier 2/3 (SUMO2/3) can be post-translationally conjugated to a wide variety of proteins constituting chromatin, the platform for genetic and epigenetic regulation. Nevertheless, it is unclear how SUMO2/3 and SUMO2/3-modified proteins are delivered to the chromatin fibers. Here we report that the largest subunit of chromatin assembly factor 1 (CAF-1), human p150, interacts directly and preferentially with SUMO2/3. Amino acid residue of 98-105 in p150 is essential and sufficient for SUMO2/3 interaction. p150-SUMO2/3 interaction coincided with regions that replicate chromatin fibers, because accumulation of the proliferating cell nuclear antigen (PCNA), and incorporation of bromodeoxyuridine (BrdU) were detected at foci co-localized with both p150 and SUMO2/3 during the S-phase in a cell line expressing epitope-tagged p150. Although inhibition of SUMO2/3 expression had only a small effect on p150 deposition on the replication sites, depletion of p150 led to delocalization of SUMO2/3 from the replication foci. Furthermore, p150 mutants deficient in SUMO2/3 interaction, caused a major reduction of SUMO2/3 at the replication foci. Thus, our findings suggest an expanded role of p150 as a SUMO2/3-interacting factor, and raise the intriguing possibility that p150 plays a role in promoting delivery of SUMO2/3 or SUMO2/3-modified proteins (or both) on chromatin fibers during replication.

  12. Global (Q)SAR models on substrates for human Cytochrome P450 3A4

    DEFF Research Database (Denmark)

    Ringsted, Tine; Nikolov, Nikolai Georgiev; Wedebye, Eva Bay

    % of prescribed drugs. Literature on substrates and non-substrates primarily based on in vivo human data on the CYP 3A4 isoenzyme was collected and a training set of 863 chemicals was used to create (Q)SAR models. The modeling systems used were MultiCASE, Leadscope and MDL QSAR and the developed models cross...

  13. Sumo Puff: Tidal debris or disturbed ultra-diffuse galaxy?

    Science.gov (United States)

    Greco, Johnny P.; Greene, Jenny E.; Price-Whelan, Adrian M.; Leauthaud, Alexie; Huang, Song; Goulding, Andy D.; Strauss, Michael A.; Komiyama, Yutaka; Lupton, Robert H.; Miyazaki, Satoshi; Takada, Masahiro; Tanaka, Masayuki; Usuda, Tomonori

    2018-01-01

    We report the discovery of a diffuse stellar cloud with an angular extent ≳30″, which we term "Sumo Puff", in data from the Hyper Suprime-Cam Subaru Strategic Program (HSC-SSP). While we do not have a redshift for this object, it is in close angular proximity to a post-merger galaxy at redshift z = 0.0431 and is projected within a few virial radii (assuming similar redshifts) of two other ˜L⋆ galaxies, which we use to bracket a potential redshift range of 0.0055 population and similar to the nearby post-merger galaxy, and we may see tidal material connecting Sumo Puff with this galaxy. We offer two possible interpretations for the nature of this object: (1) it is an extreme, galaxy-sized tidal feature associated with a recent merger event, or (2) it is a foreground dwarf galaxy with properties consistent with a quenched, disturbed, ultra-diffuse galaxy. We present a qualitative comparison with simulations that demonstrates the feasibility of forming a structure similar to this object in a merger event. Follow-up spectroscopy and/or deeper imaging to confirm the presence of the bridge of tidal material will be necessary to reveal the true nature of this object.

  14. Kinetic models of cell growth, substrate utilization and bio ...

    African Journals Online (AJOL)

    STORAGESEVER

    2008-05-02

    May 2, 2008 ... Bio-decolorization kinetic studies of distillery effluent in a batch culture were conducted using. Aspergillus .... (2). Where X0 is inoculum's concentration and S0 is initial substrate concentration in g/l, respectively. Rearranging equation 2 gives: sx sx. Y. X. SY. X. S .... generation and biodecolorization.

  15. The SUMO Ship Detector Algorithm for Satellite Radar Images

    Directory of Open Access Journals (Sweden)

    Harm Greidanus

    2017-03-01

    Full Text Available Search for Unidentified Maritime Objects (SUMO is an algorithm for ship detection in satellite Synthetic Aperture Radar (SAR images. It has been developed over the course of more than 15 years, using a large amount of SAR images from almost all available SAR satellites operating in L-, C- and X-band. As validated by benchmark tests, it performs very well on a wide range of SAR image modes (from Spotlight to ScanSAR and resolutions (from 1–100 m and for all types and sizes of ships, within the physical limits imposed by the radar imaging. This paper describes, in detail, the algorithmic approach in all of the steps of the ship detection: land masking, clutter estimation, detection thresholding, target clustering, ship attribute estimation and false alarm suppression. SUMO is a pixel-based CFAR (Constant False Alarm Rate detector for multi-look radar images. It assumes a K distribution for the sea clutter, corrected however for deviations of the actual sea clutter from this distribution, implementing a fast and robust method for the clutter background estimation. The clustering of detected pixels into targets (ships uses several thresholds to deal with the typically irregular distribution of the radar backscatter over a ship. In a multi-polarization image, the different channels are fused. Azimuth ambiguities, a common source of false alarms in ship detection, are removed. A reliability indicator is computed for each target. In post-processing, using the results of a series of images, additional false alarms from recurrent (fixed targets including range ambiguities are also removed. SUMO can run in semi-automatic mode, where an operator can verify each detected target. It can also run in fully automatic mode, where batches of over 10,000 images have successfully been processed in less than two hours. The number of satellite SAR systems keeps increasing, as does their application to maritime surveillance. The open data policy of the EU

  16. Lamin A reassembly at the end of mitosis is regulated by its SUMO-interacting motif

    International Nuclear Information System (INIS)

    Moriuchi, Takanobu; Kuroda, Masaki; Kusumoto, Fumiya; Osumi, Takashi; Hirose, Fumiko

    2016-01-01

    Modification of proteins with small ubiquitin-related modifier (SUMO; SUMOylation) is involved in the regulation of various biological processes. Recent studies have demonstrated that noncovalent associations between SUMOylated proteins and co-operative proteins containing SUMO-interacting motifs (SIMs) are important for the spatiotemporal organization of many protein complexes. In this study, we demonstrate that interactions between lamin A, a major component of the nuclear lamina, and SUMO isoforms are dependent on one of the four SIMs (SIM3) resided in lamin A polypeptide in vitro. Live cell imaging and immunofluorescence staining showed that SIM3 is required for accumulation of lamin A on the chromosomes during telophase, and subsequent evaluation of a panel of deletion mutants determined that a 156-amino acid region spanning the carboxyl-terminal Ig-fold domain of lamin A is sufficient for this accumulation. Notably, mutation of SIM3 abrogated the dephosphorylation of mitosis-specific phosphorylation at Ser-22 of lamin A, which normally occurs during telophase, and the subsequent nuclear lamina reorganization. Furthermore, expression of a conjugation-defective SUMO2 mutant, which was previously shown to inhibit endogenous SUMOylation in a dominant-negative manner, also impaired the accumulation of wild type lamin A on telophase chromosomes. These findings suggest that interactions between SIM3 of lamin A and a putative SUMO2-modified protein plays an important role in the reorganization of the nuclear lamina at the end of mitosis. - Highlights: • Lamin A interacts with SUMO2 via a SUMO-interacting motif (SIM) in the Ig domain. • SIM3 of lamin A is responsible for chromosomal accumulation during telophase. • A 156-aa region spanning the Ig domain is sufficient for chromosomal accumulation. • Accumulation of lamin A is required for timely dephosphorylation on chromosomes. • A putative SUMO2-modified protein may mediate chromosomal accumulation of lamin

  17. A three-dimensional biomechanical analysis of sumo and conventional style deadlifts.

    Science.gov (United States)

    Escamilla, R F; Francisco, A C; Fleisig, G S; Barrentine, S W; Welch, C M; Kayes, A V; Speer, K P; Andrews, J R

    2000-07-01

    Strength athletes often employ the deadlift in their training or rehabilitation regimens. The purpose of this study was to quantify kinematic and kinetic parameters by employing a three-dimensional analysis during sumo and conventional style deadlifts. Two 60-Hz video cameras recorded 12 sumo and 12 conventional style lifters during a national powerlifting championship. Parameters were quantified at barbell liftoff (LO), at the instant the barbell passed the knees (KP), and at lift completion. Unpaired t-tests (P < 0.05) were used to compare all parameters. At LO and KP, thigh position was 11-16 degrees more horizontal for the sumo group, whereas the knees and hips extended approximately 12 degrees more for the conventional group. The sumo group had 5-10 degrees greater vertical trunk and thigh positions, employed a wider stance (70 +/- 11 cm vs 32 +/- 8 cm), turned their feet out more (42 +/- 8 vs 14 +/- 6 degrees). and gripped the bar with their hands closer together (47 +/- 4 cm vs 55 +/- 10 cm). Vertical bar distance, mechanical work, and predicted energy expenditure were approximately 25-40% greater in the conventional group. Hip extensor, knee extensor, and ankle dorsiflexor moments were generated for the sumo group, whereas hip extensor, knee extensor, knee flexor, and ankle plantar flexor moments were generated for the conventional group. Ankle and knee moments and moment arms were significantly different between the sumo and conventional groups, whereas hip moments and moments arms did not show any significantly differences. Three-dimensional calculations were more accurate and significantly different than two-dimensional calculations, especially for the sumo deadlift. Biomechanical differences between sumo and conventional deadlifts result from technique variations between these exercises. Understanding these differences will aid the strength coach or rehabilitation specialist in determining which deadlift style an athlete or patient should employ.

  18. Lamin A reassembly at the end of mitosis is regulated by its SUMO-interacting motif

    Energy Technology Data Exchange (ETDEWEB)

    Moriuchi, Takanobu; Kuroda, Masaki; Kusumoto, Fumiya; Osumi, Takashi; Hirose, Fumiko, E-mail: fhirose@sci.u-hyogo.ac.jp

    2016-03-01

    Modification of proteins with small ubiquitin-related modifier (SUMO; SUMOylation) is involved in the regulation of various biological processes. Recent studies have demonstrated that noncovalent associations between SUMOylated proteins and co-operative proteins containing SUMO-interacting motifs (SIMs) are important for the spatiotemporal organization of many protein complexes. In this study, we demonstrate that interactions between lamin A, a major component of the nuclear lamina, and SUMO isoforms are dependent on one of the four SIMs (SIM3) resided in lamin A polypeptide in vitro. Live cell imaging and immunofluorescence staining showed that SIM3 is required for accumulation of lamin A on the chromosomes during telophase, and subsequent evaluation of a panel of deletion mutants determined that a 156-amino acid region spanning the carboxyl-terminal Ig-fold domain of lamin A is sufficient for this accumulation. Notably, mutation of SIM3 abrogated the dephosphorylation of mitosis-specific phosphorylation at Ser-22 of lamin A, which normally occurs during telophase, and the subsequent nuclear lamina reorganization. Furthermore, expression of a conjugation-defective SUMO2 mutant, which was previously shown to inhibit endogenous SUMOylation in a dominant-negative manner, also impaired the accumulation of wild type lamin A on telophase chromosomes. These findings suggest that interactions between SIM3 of lamin A and a putative SUMO2-modified protein plays an important role in the reorganization of the nuclear lamina at the end of mitosis. - Highlights: • Lamin A interacts with SUMO2 via a SUMO-interacting motif (SIM) in the Ig domain. • SIM3 of lamin A is responsible for chromosomal accumulation during telophase. • A 156-aa region spanning the Ig domain is sufficient for chromosomal accumulation. • Accumulation of lamin A is required for timely dephosphorylation on chromosomes. • A putative SUMO2-modified protein may mediate chromosomal accumulation of lamin

  19. ATPase-dependent control of the Mms21 SUMO ligase during DNA repair.

    Directory of Open Access Journals (Sweden)

    Marcelino Bermúdez-López

    2015-03-01

    Full Text Available Modification of proteins by SUMO is essential for the maintenance of genome integrity. During DNA replication, the Mms21-branch of the SUMO pathway counteracts recombination intermediates at damaged replication forks, thus facilitating sister chromatid disjunction. The Mms21 SUMO ligase docks to the arm region of the Smc5 protein in the Smc5/6 complex; together, they cooperate during recombinational DNA repair. Yet how the activity of the SUMO ligase is controlled remains unknown. Here we show that the SUMO ligase and the chromosome disjunction functions of Mms21 depend on its docking to an intact and active Smc5/6 complex, indicating that the Smc5/6-Mms21 complex operates as a large SUMO ligase in vivo. In spite of the physical distance separating the E3 and the nucleotide-binding domains in Smc5/6, Mms21-dependent sumoylation requires binding of ATP to Smc5, a step that is part of the ligase mechanism that assists Ubc9 function. The communication is enabled by the presence of a conserved disruption in the coiled coil domain of Smc5, pointing to potential conformational changes for SUMO ligase activation. In accordance, scanning force microscopy of the Smc5-Mms21 heterodimer shows that the molecule is physically remodeled in an ATP-dependent manner. Our results demonstrate that the ATP-binding activity of the Smc5/6 complex is coordinated with its SUMO ligase, through the coiled coil domain of Smc5 and the physical remodeling of the molecule, to promote sumoylation and chromosome disjunction during DNA repair.

  20. QSAR Models for P-450 (2D6) Substrate Activity

    DEFF Research Database (Denmark)

    Ringsted, Tine; Nikolov, Nikolai Georgiev; Jensen, Gunde Egeskov

    2009-01-01

    Human Cytochrome P450 (CYP) is a large group of enzymes that possess an essential function in metabolising different exogenous and endogenous compounds. Humans have more than 50 different genes encoding CYP enzymes, among these a gene encoding for the CYP isoenzyme 2D6, a CYP able to metabolise d...... substrates. These chemicals are potentially present in the environment. The biological importance of the CYP 2D6 and the use of the software mentioned above were discussed....

  1. VP6-SUMO Self-Assembly as Nanocarriers for Gastrointestinal Delivery

    Directory of Open Access Journals (Sweden)

    V. Palmieri

    2015-01-01

    Full Text Available High proteolytic degradation and poor absorption through epithelial barriers are major challenges to successful oral delivery of therapeutics. Nanoparticle platforms can enhance drug stability and extend the residence time in gastrointestinal (GI tract. However, drug delivery systems are often inactivated in acidic environment of stomach or suffer poor absorption from intestinal cells due to the mucus layer. To overcome these issues we developed a drug delivery system constituted by a protein construct made by a Rotavirus capsid protein (VP6 and the small ubiquitin-like modifier SUMO. This chimeric construct allows specificity towards intestinal cells, the Rotavirus natural target, combined by an enhanced stability given by the eukaryotic protein transporter SUMO. Furthermore SUMO can act as a molecular switch that facilitates import/export of its ligand to the nucleus, the hypersensitive subcellular site target of many cell killing therapies. In this paper we show that SUMO-VP6 constructs self-assembly into stable nanocarriers. SUMO-VP6 nanocarriers display ideal features for drug delivery: a small size and high monodispersity, a high stability in different pH conditions and a high uptake in the nuclear and cytoplasmic compartment of intestinal cells. These features make SUMO-VP6 nanocarriers a promising novel system for oral delivery of poorly soluble drugs.

  2. Cell cycle-dependent SUMO-1 conjugation to nuclear mitotic apparatus protein (NuMA)

    International Nuclear Information System (INIS)

    Seo, Jae Sung; Kim, Ha Na; Kim, Sun-Jick; Bang, Jiyoung; Kim, Eun-A; Sung, Ki Sa; Yoon, Hyun-Joo; Yoo, Hae Yong; Choi, Cheol Yong

    2014-01-01

    Highlights: •NuMA is modified by SUMO-1 in a cell cycle-dependent manner. •NuMA lysine 1766 is the primary target site for SUMOylation. •SUMOylation-deficient NuMA induces multiple spindle poles during mitosis. •SUMOylated NuMA induces microtubule bundling. -- Abstract: Covalent conjugation of proteins with small ubiquitin-like modifier 1 (SUMO-1) plays a critical role in a variety of cellular functions including cell cycle control, replication, and transcriptional regulation. Nuclear mitotic apparatus protein (NuMA) localizes to spindle poles during mitosis, and is an essential component in the formation and maintenance of mitotic spindle poles. Here we show that NuMA is a target for covalent conjugation to SUMO-1. We find that the lysine 1766 residue is the primary NuMA acceptor site for SUMO-1 conjugation. Interestingly, SUMO modification of endogenous NuMA occurs at the entry into mitosis and this modification is reversed after exiting from mitosis. Knockdown of Ubc9 or forced expression of SENP1 results in impairment of the localization of NuMA to mitotic spindle poles during mitosis. The SUMOylation-deficient NuMA mutant is defective in microtubule bundling, and multiple spindles are induced during mitosis. The mitosis-dependent dynamic SUMO-1 modification of NuMA might contribute to NuMA-mediated formation and maintenance of mitotic spindle poles during mitosis

  3. Cell cycle-dependent SUMO-1 conjugation to nuclear mitotic apparatus protein (NuMA)

    Energy Technology Data Exchange (ETDEWEB)

    Seo, Jae Sung; Kim, Ha Na; Kim, Sun-Jick; Bang, Jiyoung; Kim, Eun-A; Sung, Ki Sa [Department of Biological Sciences, Sungkyunkwan University, Suwon 440-746 (Korea, Republic of); Yoon, Hyun-Joo [TissueGene Inc. 9605 Medical Center Dr., Rockville, MD 20850 (United States); Yoo, Hae Yong [Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Samsung Medical Center, Sungkyunkwan University, Seoul 135-710 (Korea, Republic of); Choi, Cheol Yong, E-mail: choicy@skku.ac.kr [Department of Biological Sciences, Sungkyunkwan University, Suwon 440-746 (Korea, Republic of)

    2014-01-03

    Highlights: •NuMA is modified by SUMO-1 in a cell cycle-dependent manner. •NuMA lysine 1766 is the primary target site for SUMOylation. •SUMOylation-deficient NuMA induces multiple spindle poles during mitosis. •SUMOylated NuMA induces microtubule bundling. -- Abstract: Covalent conjugation of proteins with small ubiquitin-like modifier 1 (SUMO-1) plays a critical role in a variety of cellular functions including cell cycle control, replication, and transcriptional regulation. Nuclear mitotic apparatus protein (NuMA) localizes to spindle poles during mitosis, and is an essential component in the formation and maintenance of mitotic spindle poles. Here we show that NuMA is a target for covalent conjugation to SUMO-1. We find that the lysine 1766 residue is the primary NuMA acceptor site for SUMO-1 conjugation. Interestingly, SUMO modification of endogenous NuMA occurs at the entry into mitosis and this modification is reversed after exiting from mitosis. Knockdown of Ubc9 or forced expression of SENP1 results in impairment of the localization of NuMA to mitotic spindle poles during mitosis. The SUMOylation-deficient NuMA mutant is defective in microtubule bundling, and multiple spindles are induced during mitosis. The mitosis-dependent dynamic SUMO-1 modification of NuMA might contribute to NuMA-mediated formation and maintenance of mitotic spindle poles during mitosis.

  4. Numerical Model to Quantify the Influence of the Cellulosic Substrate on the Ignition Propensity Tests

    Directory of Open Access Journals (Sweden)

    Guindos Pablo

    2016-07-01

    Full Text Available A numerical model based on the finite element method has been constructed to simulate the ignition propensity (IP tests. The objective of this mathematical model was to quantify the influence of different characteristics of the cellulosic substrate on the results of the IP-tests. The creation and validation of the model included the following steps: (I formulation of the model based on experimental thermodynamic characteristics of the cellulosic substrate; (ii calibration of the model according to cone calorimeter tests; (iii validation of the model through mass loss and temperature profiling during IP-testing. Once the model was validated, the influence of each isolated parameter of the cellulosic substrate was quantified via a parametric study. The results revealed that the substrate heat capacity, the cigarette temperature and the pyrolysis activation energy are the most influencing parameters on the thermodynamic response of the substrates, while other parameters like heat of the pyrolysis reaction, density and roughness of the substrate showed little influence. Also the results indicated that the thermodynamic mechanisms involved in the pyrolysis and combustion of the cellulosic substrate are complex and show low repeatability which might impair the reliability of the IP-tests.

  5. Experimental Results and Integrated Modeling of Bacterial Growth on an Insoluble Hydrophobic Substrate (Phenanthrene)

    DEFF Research Database (Denmark)

    Adam, Iris K. U.; Rein, Arno; Miltner, Anja

    2014-01-01

    Metabolism of a low-solubility substrate is limited by dissolution and availability and can hardly be determined. We developed a numerical model for simultaneously calculating dissolution kinetics of such substrates and their metabolism and microbial growth (Monod kinetics with decay) and tested ...

  6. Numerical Modeling of Ink-droplet Impact on Porous Substrate

    Science.gov (United States)

    Hosseini, Saman; Ashgriz, Nasser; Chandra, Sanjeev; Andrews, John; Droppel, Stephan; Xerox Corporation

    2011-11-01

    Solid ink is wax-resin based ink, which is solid at room temperature, and melts when heated. Impact of a solid ink droplet with different velocities and temperatures on paper is studied. Maximum spreading diameter of solid ink ``Colorstix8200'' on different papers has been evaluated. Increasing the temperature decreases the viscosity of the wax, which causes more spreading and penetration on the paper. Although lateral spreading is very rapid during the initial stages of impact, drop may penetrate inside the substrate too. Dynamically, wax penetration on paper is a function of inertia, surface tension and capillary pressure inside the paper. When a wax drop penetrates into the paper, it mechanically bonds to the paper through anchoring within the pores. After the impact, droplets are removed and remaining areas are measured for adhesion and cohesion characteristic. The adhesion of solid ink to paper has been studied qualitatively using scratch test and tape test techniques. The experimental setup consists of a pendent droplet generator which consists of heated cylinder for molten wax and a nozzle; imaging system, pull test system, and cutting system. Penetration, spreading and adhesion force have been studied for different temperatures and impact velocities on porous substrate.

  7. A functional SUMO-motif in the active site of PIM1 promotes its degradation via RNF4, and stimulates protein kinase activity.

    Science.gov (United States)

    Iyer, R Sumanth; Chatham, Lynsey; Sleigh, Roger; Meek, David W

    2017-06-15

    The PIM1 serine/threonine protein kinase mediates growth factor and survival signalling, and cooperates potently with c-MYC during tumorigenesis. PIM1 is overexpressed in many human cancers and is a promising target for drug development. PIM1 levels are regulated mainly through cytokine-induced transcription and protein degradation, but mechanisms regulating its activity and levels remain largely unexplored. Here, we show that PIM1 is modified in vitro and in cultured cells by the Small ubiquitin-like modifier (SUMO) on two independent sites: K169, within a consensus SUMOylation motif (IK 169 DE 171 ) in the active site of PIM1, and also at a second promiscuous site. Alanine substitution of E171 (within the consensus motif) abolished SUMOylation, significantly increased the half-life of PIM1, and markedly reduced its ubiquitylation. Mechanistically, SUMOylation promoted ubiquitin-mediated degradation of PIM1 via recruitment of the SUMO-targeted ubiquitin ligase, RNF4. Additionally, SUMOylated PIM1 showed enhanced protein kinase activity in vitro. Interestingly, the E171A mutant was active in vitro but displayed altered substrate specificity in cultured cells, consistent with the idea that SUMOylation may govern PIM1 substrate specificity under certain contexts. Taken together, these data demonstrate that the protein kinase activity and levels of PIM1 can be regulated by a covalent post-translational modification.

  8. Driven, underdamped Frenkel-Kontorova model on a quasiperiodic substrate

    International Nuclear Information System (INIS)

    Vanossi, A.; Ro''der, J.; Bishop, A. R.; Bortolani, V.

    2001-01-01

    We consider the underdamped dynamics of a chain of atoms subject to a dc driving force and a quasiperiodic substrate potential. The system has three inherent length scales which we take to be mutually incommensurate. We find that when the length scales are related by the spiral mean (a cubic irrational) there exists a value of the interparticle interaction strength above which the static friction is zero. When the length scales are related by the golden mean (a quadratic irrational) the static friction is always nonzero. >From considerations based on the connection of this problem to standard map theory, we postulate that zero static friction is generally possible for incommensurate ratios of the length scales involved. However, when the length scales are quadratic irrationals, or have some commensurability with each other, the static friction will be nonzero for all choices of interaction parameters. We also comment on the nature of the depinning mechanisms and the steady states achieved by the moving chain

  9. Asperity Interaction and Substrate Deformation in Statistical Summation Models of Contact Between Rough Surfaces

    NARCIS (Netherlands)

    Vakis, Antonis I.

    A method is proposed to account for asperity interaction and bulk substrate deformation in models that utilize statistical summation of asperity forces to characterize contact between rough surfaces. Interaction deformations of noncontacting asperities are calculated based on the probability that

  10. A Modeling Comparison of Methanogenesis from Noncompetitive vs Competitive Substrates in a Simulated Hypersaline Microbial Mat

    Science.gov (United States)

    Decker, K. L.; Potter, C.; Hoehler, T.

    2005-12-01

    The well-documented assumption about methanogens that co-occur in hypersaline mat communities with sulfate-reducing bacteria (SRB) is that they rely entirely on non-competitive substrates for methanogenesis. The reason for this is that during sulfate reduction, sulfur-reducing bacteria efficiently utilize H2, leaving a concentration too low for methanogenesis. Early results from recent work on a hypersaline microbial mat from salt evaporation ponds of Guerrero Negro, Baja, Mexico cast doubt that methanogenesis only occurs via non-competitive substrates, because it shows an excess of H2 in the mat rather than a paucity. We explore the use of our simulation model of the microbial biogeochemistry of a hypersaline mat (named MBGC) to compare methane production rates in a 1 cm thick mat when the methanogens use competitive substrates versus noncompetitive substrates. In the `non-competitive substrate' version of the model, methanogens rely exclusively on methylated amines that are accumulated as compatible solutes in cyanobacteria and released after lysis. In contrast, the `competitive substrate' models examine methanogen use of substrates (such as H2 + acetate) with different SRB population sizes (from absent to low). The comparison of these models of methane and sulfide biogeochemistry of a hypersaline mat has both ecological and geobiological significance, as one hypothesis of Archean microbial mats is that they existed in a low sulfate environment.

  11. Optimal Substrate Preheating Model for Thermal Spray Deposition of Thermosets onto Polymer Matrix Composites

    Science.gov (United States)

    Ivosevic, M.; Knight, R.; Kalidindi, S. R.; Palmese, G. R.; Tsurikov, A.; Sutter, J. K.

    2003-01-01

    High velocity oxy-fuel (HVOF) sprayed, functionally graded polyimide/WC-Co composite coatings on polymer matrix composites (PMC's) are being investigated for applications in turbine engine technologies. This requires that the polyimide, used as the matrix material, be fully crosslinked during deposition in order to maximize its engineering properties. The rapid heating and cooling nature of the HVOF spray process and the high heat flux through the coating into the substrate typically do not allow sufficient time at temperature for curing of the thermoset. It was hypothesized that external substrate preheating might enhance the deposition behavior and curing reaction during the thermal spraying of polyimide thermosets. A simple analytical process model for the deposition of thermosetting polyimide onto polymer matrix composites by HVOF thermal spray technology has been developed. The model incorporates various heat transfer mechanisms and enables surface temperature profiles of the coating to be simulated, primarily as a function of substrate preheating temperature. Four cases were modeled: (i) no substrate preheating; (ii) substrates electrically preheated from the rear; (iii) substrates preheated by hot air from the front face; and (iv) substrates electrically preheated from the rear and by hot air from the front.

  12. Kinetic characteristics and modelling of growth and substrate removal by Alcaligenes faecalis strain NR.

    Science.gov (United States)

    Chen, Jie; Zhao, Bin; An, Qiang; Wang, Xia; Zhang, Yi Xin

    2016-04-01

    Alcaligenes faecalis strain NR has the capability of simultaneous ammonium and organic carbon removal under sole aerobic conditions. The growth and substrate removal characteristics of A. faecalis strain NR were studied and appropriate kinetic models were developed. The maximum substrate removal rate of NH4 (+)-N and TOC were determined as 2.27 mg NH4 (+)-N/L/h and 30.00 mg TOC/L/h, respectively with initial NH4 (+)-N = 80 mg/L and TOC = 800 mg/L. Single-substrate models and double-substrate models based on Monod, Contois, Moser and Teissier were employed to describe the bioprocess kinetic coefficients. As a result, two double-substrate models, Teissier-Contois and Contois-Contois, were considered to be appropriate to model growth kinetics with both NH4 (+)-N and TOC as limiting substrates. The kinetic constants of maximum growth rate (μ max) and half-saturation constant (K S and B S) were obtained by solving multiple equations with regression. This work can be used to further understand and predict the performance of heterotrophic nitrifiers, and thus provides specific guidance of these functional strains in practical wastewater treatment process.

  13. Lamin A reassembly at the end of mitosis is regulated by its SUMO-interacting motif.

    Science.gov (United States)

    Moriuchi, Takanobu; Kuroda, Masaki; Kusumoto, Fumiya; Osumi, Takashi; Hirose, Fumiko

    2016-03-01

    Modification of proteins with small ubiquitin-related modifier (SUMO; SUMOylation) is involved in the regulation of various biological processes. Recent studies have demonstrated that noncovalent associations between SUMOylated proteins and co-operative proteins containing SUMO-interacting motifs (SIMs) are important for the spatiotemporal organization of many protein complexes. In this study, we demonstrate that interactions between lamin A, a major component of the nuclear lamina, and SUMO isoforms are dependent on one of the four SIMs (SIM3) resided in lamin A polypeptide in vitro. Live cell imaging and immunofluorescence staining showed that SIM3 is required for accumulation of lamin A on the chromosomes during telophase, and subsequent evaluation of a panel of deletion mutants determined that a 156-amino acid region spanning the carboxyl-terminal Ig-fold domain of lamin A is sufficient for this accumulation. Notably, mutation of SIM3 abrogated the dephosphorylation of mitosis-specific phosphorylation at Ser-22 of lamin A, which normally occurs during telophase, and the subsequent nuclear lamina reorganization. Furthermore, expression of a conjugation-defective SUMO2 mutant, which was previously shown to inhibit endogenous SUMOylation in a dominant-negative manner, also impaired the accumulation of wild type lamin A on telophase chromosomes. These findings suggest that interactions between SIM3 of lamin A and a putative SUMO2-modified protein plays an important role in the reorganization of the nuclear lamina at the end of mitosis. Copyright © 2016 Elsevier Inc. All rights reserved.

  14. Production of FMDV virus-like particles by a SUMO fusion protein approach in Escherichia coli

    Directory of Open Access Journals (Sweden)

    Liang Shu-Mei

    2009-08-01

    Full Text Available Abstract Virus-like particles (VLPs are formed by the self-assembly of envelope and/or capsid proteins from many viruses. Some VLPs have been proven successful as vaccines, and others have recently found applications as carriers for foreign antigens or as scaffolds in nanoparticle biotechnology. However, production of VLP was usually impeded due to low water-solubility of recombinant virus capsid proteins. Previous studies revealed that virus capsid and envelope proteins were often posttranslationally modified by SUMO in vivo, leading into a hypothesis that SUMO modification might be a common mechanism for virus proteins to retain water-solubility or prevent improper self-aggregation before virus assembly. We then propose a simple approach to produce VLPs of viruses, e.g., foot-and-mouth disease virus (FMDV. An improved SUMO fusion protein system we developed recently was applied to the simultaneous expression of three capsid proteins of FMDV in E. coli. The three SUMO fusion proteins formed a stable heterotrimeric complex. Proteolytic removal of SUMO moieties from the ternary complexes resulted in VLPs with size and shape resembling the authentic FMDV. The method described here can also apply to produce capsid/envelope protein complexes or VLPs of other disease-causing viruses.

  15. Cell cycle-dependent SUMO-1 conjugation to nuclear mitotic apparatus protein (NuMA).

    Science.gov (United States)

    Seo, Jae Sung; Kim, Ha Na; Kim, Sun-Jick; Bang, Jiyoung; Kim, Eun-A; Sung, Ki Sa; Yoon, Hyun-Joo; Yoo, Hae Yong; Choi, Cheol Yong

    2014-01-03

    Covalent conjugation of proteins with small ubiquitin-like modifier 1 (SUMO-1) plays a critical role in a variety of cellular functions including cell cycle control, replication, and transcriptional regulation. Nuclear mitotic apparatus protein (NuMA) localizes to spindle poles during mitosis, and is an essential component in the formation and maintenance of mitotic spindle poles. Here we show that NuMA is a target for covalent conjugation to SUMO-1. We find that the lysine 1766 residue is the primary NuMA acceptor site for SUMO-1 conjugation. Interestingly, SUMO modification of endogenous NuMA occurs at the entry into mitosis and this modification is reversed after exiting from mitosis. Knockdown of Ubc9 or forced expression of SENP1 results in impairment of the localization of NuMA to mitotic spindle poles during mitosis. The SUMOylation-deficient NuMA mutant is defective in microtubule bundling, and multiple spindles are induced during mitosis. The mitosis-dependent dynamic SUMO-1 modification of NuMA might contribute to NuMA-mediated formation and maintenance of mitotic spindle poles during mitosis. Copyright © 2013 Elsevier Inc. All rights reserved.

  16. Integration of statistical modeling and high-content microscopy to systematically investigate cell-substrate interactions.

    Science.gov (United States)

    Chen, Wen Li Kelly; Likhitpanichkul, Morakot; Ho, Anthony; Simmons, Craig A

    2010-03-01

    Cell-substrate interactions are multifaceted, involving the integration of various physical and biochemical signals. The interactions among these microenvironmental factors cannot be facilely elucidated and quantified by conventional experimentation, and necessitate multifactorial strategies. Here we describe an approach that integrates statistical design and analysis of experiments with automated microscopy to systematically investigate the combinatorial effects of substrate-derived stimuli (substrate stiffness and matrix protein concentration) on mesenchymal stem cell (MSC) spreading, proliferation and osteogenic differentiation. C3H10T1/2 cells were grown on type I collagen- or fibronectin-coated polyacrylamide hydrogels with tunable mechanical properties. Experimental conditions, which were defined according to central composite design, consisted of specific permutations of substrate stiffness (3-144 kPa) and adhesion protein concentration (7-520 microg/mL). Spreading area, BrdU incorporation and Runx2 nuclear translocation were quantified using high-content microscopy and modeled as mathematical functions of substrate stiffness and protein concentration. The resulting response surfaces revealed distinct patterns of protein-specific, substrate stiffness-dependent modulation of MSC proliferation and differentiation, demonstrating the advantage of statistical modeling in the detection and description of higher-order cellular responses. In a broader context, this approach can be adapted to study other types of cell-material interactions and can facilitate the efficient screening and optimization of substrate properties for applications involving cell-material interfaces. Copyright 2009 Elsevier Ltd. All rights reserved.

  17. Gas-Phase Enrichment of Multiply Charged Peptide Ions by Differential Ion Mobility Extend the Comprehensiveness of SUMO Proteome Analyses.

    Science.gov (United States)

    Pfammatter, Sibylle; Bonneil, Eric; McManus, Francis P; Thibault, Pierre

    2018-04-05

    The small ubiquitin-like modifier (SUMO) is a member of the family of ubiquitin-like modifiers (UBLs) and is involved in important cellular processes, including DNA damage response, meiosis and cellular trafficking. The large-scale identification of SUMO peptides in a site-specific manner is challenging not only because of the low abundance and dynamic nature of this modification, but also due to the branched structure of the corresponding peptides that further complicate their identification using conventional search engines. Here, we exploited the unusual structure of SUMO peptides to facilitate their separation by high-field asymmetric waveform ion mobility spectrometry (FAIMS) and increase the coverage of SUMO proteome analysis. Upon trypsin digestion, branched peptides contain a SUMO remnant side chain and predominantly form triply protonated ions that facilitate their gas-phase separation using FAIMS. We evaluated the mobility characteristics of synthetic SUMO peptides and further demonstrated the application of FAIMS to profile the changes in protein SUMOylation of HEK293 cells following heat shock, a condition known to affect this modification. FAIMS typically provided a 10-fold improvement of detection limit of SUMO peptides, and enabled a 36% increase in SUMO proteome coverage compared to the same LC-MS/MS analyses performed without FAIMS. Graphical Abstract ᅟ.

  18. SUMO expression shortens the lag phase of Saccharomyces cerevisiae yeast growth caused by complex interactive effects of major mixed fermentation inhibitors found in hot-compressed water-treated lignocellulosic hydrolysate.

    Science.gov (United States)

    Jayakody, Lahiru N; Kadowaki, Masafumi; Tsuge, Keisuke; Horie, Kenta; Suzuki, Akihiro; Hayashi, Nobuyuki; Kitagaki, Hiroshi

    2015-01-01

    The complex inhibitory effects of inhibitors present in lignocellulose hydrolysate suppress the ethanol fermentation of Saccharomyces cerevisiae. Although the interactive inhibitory effects play important roles in the actual hydrolysate, few studies have investigated glycolaldehyde, the key inhibitor of hot-compressed water-treated lignocellulose hydrolysate. Given this challenge, we investigated the interactive effects of mixed fermentation inhibitors, including glycolaldehyde. First, we confirmed that glycolaldehyde was the most potent inhibitor in the hydrolysate and exerted interactive inhibitory effects in combination with major inhibitors. Next, through genome-wide analysis and megavariate data modeling, we identified SUMOylation as a novel potential mechanism to overcome the combinational inhibitory effects of fermentation inhibitors. Indeed, overall SUMOylation was increased and Pgk1, which produces an ATP molecule in glycolysis by substrate-level phosphorylation, was SUMOylated and degraded in response to glycolaldehyde. Augmenting the SUMO-dependent ubiquitin system in the ADH1-expressing strain significantly shortened the lag phase of growth, released cells from G2/M arrest, and improved energy status and glucose uptake in the inhibitor-containing medium. In summary, our study was the first to establish SUMOylation as a novel platform for regulating the lag phase caused by complex fermentation inhibitors.

  19. A model for ink impression into a porous substrate

    Science.gov (United States)

    Megat Ahmed, M. M. H.; Gethin, D. T.; Claypole, T. C.; Roylance, B. J.

    1997-08-01

    This paper applies the physics of a squeezed film between porous surfaces to the impression of an ink dot into paper. The models developed are implemented numerically via the finite-element method. When compared with observations reported in the literature, the models are shown to be capable of representing the effects of process parameters such as the pressure, viscosity, permeability and film thickness on the dot gain which is used frequently as a characteristic to measure printing quality.

  20. Caspase recruitment domain of procaspase-2 could be a target for SUMO-1 modification through Ubc9

    International Nuclear Information System (INIS)

    Shirakura, Hiromi; Hayashi, Naoko; Ogino, Shin-ichi; Tsuruma, Kazuhiro; Uehara, Takashi; Nomura, Yasuyuki

    2005-01-01

    To identify the binding proteins that regulate the function of procaspase-2, we screened for proteins using the yeast two-hybrid method and isolated human Ubc9 and SUMO-1 as the candidates. Ubc9 and SUMO-1 interacted with the caspase recruitment domain of procaspase-2 in its N-terminal. We elucidated the covalent modification of procaspase-2 by SUMO-1 in mammalian cells by immunoprecipitation followed by Western blot analysis. Procaspase-2 and SUMO-1 were co-localized by dot-like structures in the nucleus that are related to promyelocytic leukemia bodies. Interestingly, a conjugation-deficient mutant (K60R) procaspase-2 resulted in a delay of its enzyme maturation (appearance of p12 subunit) compared to that of wild-type. Thus, the modification with SUMO-1 may play a critical role in the nuclear localization and the activation (maturation) of procaspase-2

  1. In Vivo Testing of Renilla Luciferase Substrate Analogs in an Orthotopic Murine Model of Human Glioblastoma

    Directory of Open Access Journals (Sweden)

    Maya Otto-Duessel

    2006-04-01

    Full Text Available In vivo bioluminescent imaging using cells expressing Renilla luciferase is becoming increasingly common. Hindrances to the more widespread use of Renilla luciferase are the high autoluminescence of its natural substrate, coelenterazine, in plasma; the relatively high absorbance by tissue of the light emitted by the enzyme–substrate reaction; rapid clearance of the substrate; and significant cost. These factors, save for the cost, which has its own limiting effect on use, can combine to reduce the sensitivity of in vivo assays utilizing this reporter system, and methods of increasing light output or decreasing autoluminescence could be of great benefit. A number of analogs of coelenterazine are being investigated that may accomplish one or both of these goals. In this study, we report on the testing of two new substrate analogs, EnduRen™ and ViviRen™, manufactured by Promega Corporation, in an orthotopic murine model of human glioblastoma expressing Renilla luciferase. We have tested these analogs in this cell line, both in vitro and in vivo, and find that the substrate ViviRen results in significantly greater light output than the natural substrate or the other analog EnduRen. This new substrate could be valuable for studies where greater sensitivity is important.

  2. Site-specific mapping of the human SUMO proteome reveals co-modification with phosphorylation

    DEFF Research Database (Denmark)

    Hendriks, Ivo A; Lyon, David; Young, Clifford

    2017-01-01

    -predictive analyses revealed that lysines residing in disordered regions are preferentially targeted by SUMO, in notable contrast to other widespread lysine modifications. In our data set, we identified 807 SUMOylated peptides that were co-modified by phosphorylation, along with dozens of SUMOylated peptides...... that were co-modified by ubiquitylation, acetylation and methylation. Notably, 9% of the identified SUMOylome occurred proximal to phosphorylation, and numerous SUMOylation sites were found to be fully dependent on prior phosphorylation events. SUMO-proximal phosphorylation occurred primarily in a proline......-directed manner, and inhibition of cyclin-dependent kinases dynamically affected co-modification. Collectively, we present a comprehensive analysis of the SUMOylated proteome, uncovering the structural preferences for SUMO and providing system-wide evidence for a remarkable degree of cross-talk between...

  3. Enhanced expression of rabies virus surface G-protein in Escherichia coli using SUMO fusion.

    Science.gov (United States)

    Singh, Ankit; Yadav, Dinesh; Rai, Krishan Mohan; Srivastava, Meenal; Verma, Praveen C; Singh, Pradhyumna K; Tuli, Rakesh

    2012-01-01

    Fusion systems are known to increase the expression of difficult to express recombinant proteins in soluble form to facilitate their purification. Rabies glycoprotein was also tough to express at sufficient level in soluble form in both E. coli and plant. The present work was aimed to over-express and purify this membrane protein from soluble extract of E. coli. Fusion of Small Ubiqutin like Modifier (SUMO) with rabies glycoprotein increased ~1.5 fold higher expression and ~3.0 fold solubility in comparison to non-fused in E. coli. The SUMO fusion also simplified the purification process. Previously engineered rabies glycoprotein gene in tobacco plants provides complete protection to mice, but the expression was very low for purification. Our finding demonstrated that the SUMO-fusion was useful for enhancing expression and solubility of the membrane protein and again proves to be a good alternative technology for applications in biomedical and pharmaceutical research.

  4. SUMO mediating fusion expression of antimicrobial peptide CM4 from two joined genes in Escherichia coli.

    Science.gov (United States)

    Li, Jian Feng; Zhang, Jie; Zhang, Zhen; Kang, Chun Tao; Zhang, Shuang Quan

    2011-01-01

    Antibacterial peptide CM4 (ABP-CM4) is a small cationic peptide with broad-spectrum activities against bacteria, fungi, and tumor cells, which may possibly be used as an antimicrobial agent. To improve the expression level of CM4 in Escherichia coli, two tandem repeats of CM4 genes were cloned into the vector pSUMO to construct an expression vector pSUMO-2CM4. The fusion protein SUMO-2CM4, purified by Ni(2+)-chelating chromatography, was cleaved by hydroxylamine hydrochloride to release recombinant CM4. After the cleaved sample was re-applied to a Ni-IDA column, finally, about 48 mg recombinant CM4 was obtained from 1 L bacterial culture with no less than 96% purity, which was the highest yield of CM4 reported so far.

  5. RNF111/Arkadia is a SUMO-targeted ubiquitin ligase that facilitates the DNA damage response

    DEFF Research Database (Denmark)

    Poulsen, Sara L; Hansen, Rebecca K; Wagner, Sebastian A

    2013-01-01

    Protein modifications by ubiquitin and small ubiquitin-like modifier (SUMO) play key roles in cellular signaling pathways. SUMO-targeted ubiquitin ligases (STUbLs) directly couple these modifications by selectively recognizing SUMOylated target proteins through SUMO-interacting motifs (SIMs...... nonproteolytic, K63-linked ubiquitylation of SUMOylated target proteins. We demonstrate that RNF111 promoted ubiquitylation of SUMOylated XPC (xeroderma pigmentosum C) protein, a central DNA damage recognition factor in nucleotide excision repair (NER) extensively regulated by ultraviolet (UV......)-induced SUMOylation and ubiquitylation. Moreover, we show that RNF111 facilitated NER by regulating the recruitment of XPC to UV-damaged DNA. Our findings establish RNF111 as a new STUbL that directly links nonproteolytic ubiquitylation and SUMOylation in the DNA damage response....

  6. Pro-recombination role of Srs2 protein requires SUMO (small ubiquitin-like modifier) but is independent of PCNA (proliferating cell nuclear antigen) interaction

    DEFF Research Database (Denmark)

    Kolesar, Peter; Altmannova, Veronika; Pinela da Silva, Sonia Cristina

    2016-01-01

    of SIM in asrs2ΔPIMstrain leads to a decrease in recombination, indicating a pro-recombination role of SUMO. Thus SIM has an ambivalent function in Srs2 regulation; it not only mediates interaction with SUMO-PCNA to promote the anti-recombination function but it also plays a PCNA-independent pro......Srs2 plays many roles in DNA repair, the proper regulation and coordination of which is essential. Post-translational modification by small ubiquitin-like modifier (SUMO) is one such possible mechanism. Here, we investigate the role of SUMO in Srs2 regulation and show that the SUMO...

  7. Modeling the microbial growth of two Escherichia coli strains in a multi-substrate environment

    Directory of Open Access Journals (Sweden)

    M. E. Poccia

    2014-06-01

    Full Text Available The microbial growth in multi-substrate environments may be viewed as an optimal resources allocation problem. The optimization aims at maximizing some biological objective like the biomass growth. The models developed using this hypothesis are called "cybernetic" and they represent the complex cell structure as an optimizing function that regulates the intracellular enzymatic machinery. In this work, a cybernetic model was developed to represent the growth of two E. coli strains (JM 109 and BL 21 -DE3- on a medium containing glucose and glycerol as carbon and energy sources. The model was able to accurately simulate the biomass growth, the substrates consumption and the growth-rate profiles.

  8. Mitigating the Goldilocks effect: the effects of different substrate models on track formation potential.

    Science.gov (United States)

    Falkingham, Peter L; Hage, Julian; Bäker, Martin

    2014-11-01

    In ichnology, the Goldilocks effect describes a scenario in which a substrate must be 'just right' in order for tracks to form-too soft, the animal will be unable to traverse the area, and too firm, the substrate will not deform. Any given substrate can therefore only preserve a range of tracks from those animals which exert an underfoot pressure at approximately the yield strength of the sediment. However, rarely are substrates vertically homogeneous for any great depth, varying either due to heterogeneity across sediment layers, or from mechanical behaviour such as strain hardening. Here, we explore the specificity of the Goldilocks effect in a number of virtual substrates simulated using finite-element analysis. We find that the inclusion of strain hardening into the model increases the potential range of trackmaker sizes somewhat, compared with a simple elastic-perfectly plastic model. The simulation of a vertically heterogeneous, strain hardening substrate showed a much larger range of potential trackmakers than strain hardening alone. We therefore show that the Goldilocks effect is lessened to varying degrees by the inclusion of more realistic soil parameters, though there still remains an upper and lower limit to the size of trackmaker able to traverse the area while leaving footprints.

  9. Integration of an external bicycle model in SUMO

    OpenAIRE

    Twaddle, Heather; Grigoropoulos, Georgios; Busch, Fritz

    2016-01-01

    Bicyclists are amongst the most flexible road users and can tactically choose their pathway across an intersection using available bicycle lanes, roadways and sidewalks, riding either with or against the direction of travel. This flexibility makes it difficult to accurately include the pathfinding behaviour of bicyclists in microscopic traffic simulation tools due to the limitations imposed by the internal design structure of the network elements. In this paper, a method for simul...

  10. Probing cellular mechanoadaptation using cell-substrate de-adhesion dynamics: experiments and model.

    Science.gov (United States)

    S S, Soumya; Sthanam, Lakshmi Kavitha; Padinhateeri, Ranjith; Inamdar, Mandar M; Sen, Shamik

    2014-01-01

    Physical properties of the extracellular matrix (ECM) are known to regulate cellular processes ranging from spreading to differentiation, with alterations in cell phenotype closely associated with changes in physical properties of cells themselves. When plated on substrates of varying stiffness, fibroblasts have been shown to exhibit stiffness matching property, wherein cell cortical stiffness increases in proportion to substrate stiffness up to 5 kPa, and subsequently saturates. Similar mechanoadaptation responses have also been observed in other cell types. Trypsin de-adhesion represents a simple experimental framework for probing the contractile mechanics of adherent cells, with de-adhesion timescales shown to scale inversely with cortical stiffness values. In this study, we combine experiments and computation in deciphering the influence of substrate properties in regulating de-adhesion dynamics of adherent cells. We first show that NIH 3T3 fibroblasts cultured on collagen-coated polyacrylamide hydrogels de-adhere faster on stiffer substrates. Using a simple computational model, we qualitatively show how substrate stiffness and cell-substrate bond breakage rate collectively influence de-adhesion timescales, and also obtain analytical expressions of de-adhesion timescales in certain regimes of the parameter space. Finally, by comparing stiffness-dependent experimental and computational de-adhesion responses, we show that faster de-adhesion on stiffer substrates arises due to force-dependent breakage of cell-matrix adhesions. In addition to illustrating the utility of employing trypsin de-adhesion as a biophysical tool for probing mechanoadaptation, our computational results highlight the collective interplay of substrate properties and bond breakage rate in setting de-adhesion timescales.

  11. Non-Smc element 5 (Nse5 of the Smc5/6 complex interacts with SUMO pathway components

    Directory of Open Access Journals (Sweden)

    Denise E. Bustard

    2016-06-01

    Full Text Available The Smc5/6 complex in Saccharomyces cerevisiae contains six essential non-Smc elements, Nse1-6. With the exception of Nse2 (also known as Mms21, which is an E3 small ubiquitin-like modifier (SUMO ligase, very little is understood about the role of these components or their contribution to Smc5/6 functionality. Our characterization of Nse5 establishes a previously unidentified relationship between the Smc5/6 complex and factors of the SUMO pathway. Nse5 physically associates with the E2 conjugating enzyme, Ubc9, where contacts are stabilized by non-covalent interactions with SUMO. SUMO also mediates the interactions between Nse5 and the two PIAS family E3 SUMO ligases, Siz1 and Siz2. Cells carrying the nse5-ts1 allele or lacking either SIZ1 or SIZ2 exhibit a reduction in Smc5 sumoylation upon MMS treatment and demonstrate functional redundancy for SUMO mediated events in the presence of DNA damage. Overall, given the extensive connection between Nse5 and components of the SUMO pathway, we speculate that one function of the Smc5/6 complex might be as a scaffold center to enable sumoylation events in budding yeast.

  12. Small ubiquitin-like modifier (SUMO) conjugation impedes transcriptional silencing by the polycomb group repressor Sex Comb on Midleg.

    Science.gov (United States)

    Smith, Matthew; Mallin, Daniel R; Simon, Jeffrey A; Courey, Albert J

    2011-04-01

    The Drosophila protein Sex Comb on Midleg (Scm) is a member of the Polycomb group (PcG), a set of transcriptional repressors that maintain silencing of homeotic genes during development. Recent findings have identified PcG proteins both as targets for modification by the small ubiquitin-like modifier (SUMO) protein and as catalytic components of the SUMO conjugation pathway. We have found that the SUMO-conjugating enzyme Ubc9 binds to Scm and that this interaction, which requires the Scm C-terminal sterile α motif (SAM) domain, is crucial for the efficient sumoylation of Scm. Scm is associated with the major Polycomb response element (PRE) of the homeotic gene Ultrabithorax (Ubx), and efficient PRE recruitment requires an intact Scm SAM domain. Global reduction of sumoylation augments binding of Scm to the PRE. This is likely to be a direct effect of Scm sumoylation because mutations in the SUMO acceptor sites in Scm enhance its recruitment to the PRE, whereas translational fusion of SUMO to the Scm N terminus interferes with this recruitment. In the metathorax, Ubx expression promotes haltere formation and suppresses wing development. When SUMO levels are reduced, we observe decreased expression of Ubx and partial haltere-to-wing transformation phenotypes. These observations suggest that SUMO negatively regulates Scm function by impeding its recruitment to the Ubx major PRE.

  13. Small Ubiquitin-like Modifier (SUMO) Conjugation Impedes Transcriptional Silencing by the Polycomb Group Repressor Sex Comb on Midleg*

    Science.gov (United States)

    Smith, Matthew; Mallin, Daniel R.; Simon, Jeffrey A.; Courey, Albert J.

    2011-01-01

    The Drosophila protein Sex Comb on Midleg (Scm) is a member of the Polycomb group (PcG), a set of transcriptional repressors that maintain silencing of homeotic genes during development. Recent findings have identified PcG proteins both as targets for modification by the small ubiquitin-like modifier (SUMO) protein and as catalytic components of the SUMO conjugation pathway. We have found that the SUMO-conjugating enzyme Ubc9 binds to Scm and that this interaction, which requires the Scm C-terminal sterile α motif (SAM) domain, is crucial for the efficient sumoylation of Scm. Scm is associated with the major Polycomb response element (PRE) of the homeotic gene Ultrabithorax (Ubx), and efficient PRE recruitment requires an intact Scm SAM domain. Global reduction of sumoylation augments binding of Scm to the PRE. This is likely to be a direct effect of Scm sumoylation because mutations in the SUMO acceptor sites in Scm enhance its recruitment to the PRE, whereas translational fusion of SUMO to the Scm N terminus interferes with this recruitment. In the metathorax, Ubx expression promotes haltere formation and suppresses wing development. When SUMO levels are reduced, we observe decreased expression of Ubx and partial haltere-to-wing transformation phenotypes. These observations suggest that SUMO negatively regulates Scm function by impeding its recruitment to the Ubx major PRE. PMID:21278366

  14. Two-dimensional modeling of water and heat fluxes in green roof substrates

    Science.gov (United States)

    Suarez, F. I.; Sandoval, V. P.

    2016-12-01

    Due to public concern towards sustainable development, greenhouse gas emissions and energy efficiency, green roofs have become popular in the last years. Green roofs integrate vegetation into infrastructures to reach additional benefits that minimize negative impacts of the urbanization. A properly designed green roof can reduce environmental pollution, noise levels, energetic requirements or surface runoff. The correct performance of green roofs depends on site-specific conditions and on each component of the roof. The substrate and the vegetation layers strongly influence water and heat fluxes on a green roof. The substrate is an artificial media that has an improved performance compared to natural soils as it provides critical resources for vegetation survival: water, nutrients, and a growing media. Hence, it is important to study the effects of substrate properties on green roof performance. The objective of this work is to investigate how the thermal and hydraulic properties affect the behavior of a green roof through numerical modeling. The substrates that were investigated are composed by: crushed bricks and organic soil (S1); peat with perlite (S2); crushed bricks (S3); mineral soil with tree leaves (S4); and a mixture of topsoil and mineral soil (S5). The numerical model utilizes summer-arid meteorological information to evaluate the performance of each substrate. Results show that the area below the water retention curve helps to define the substrate that retains more water. In addition, the non-linearity of the water retention curve can increment the water needed to irrigate the roof. The heat propagation through the roof depends strongly on the hydraulic behavior, meaning that a combination of a substrate with low thermal conductivity and more porosity can reduce the heat fluxes across the roof. Therefore, it can minimize the energy consumed of an air-conditioner system.

  15. An expert-based model for selecting the most suitable substrate material type for antenna circuits

    Science.gov (United States)

    AL-Oqla, Faris M.; Omar, Amjad A.

    2015-06-01

    Quality and properties of microwave circuits depend on all the circuit components. One of these components is the substrate. The process of substrate material selection is a decision-making problem that involves multicriteria with objectives that are diverse and conflicting. The aim of this work was to select the most suitable substrate material type to be used in antennas in the microwave frequency range that gives best performance and reliability of the substrate. For this purpose, a model was built to ease the decision-making that includes hierarchical alternatives and criteria. The substrate material type options considered were limited to fiberglass-reinforced epoxy laminates (FR4 εr = 4.8), aluminium (III) oxide (alumina εr = 9.6), gallium arsenide III-V compound (GaAs εr = 12.8) and PTFE composites reinforced with glass microfibers (Duroid εr = 2.2-2.3). To assist in building the model and making decisions, the analytical hierarchy process (AHP) was used. The decision-making process revealed that alumina substrate material type was the most suitable choice for the antennas in the microwave frequency range that yields best performance and reliability. In addition, both the size of the circuit and the loss tangent of the substrates were found to be the most contributing subfactors in the antenna circuit specifications criterion. Experimental assessments were conducted utilising The Expert Choice™ software. The judgments were tested and found to be precise, consistent and justifiable, and the marginal inconsistency values were found to be very narrow. A sensitivity analysis was also presented to demonstrate the confidence in the drawn conclusions.

  16. A comprehensive model of anaerobic bioconversion of complex substrates to biogas

    DEFF Research Database (Denmark)

    Angelidaki, Irini; Ellegaard, Lars; Ahring, Birgitte Kiær

    1999-01-01

    A dynamic model describing the anaerobic degradation of complex material, and codigestion of different types of wastes, was developed based on a model previously described (Angelidaki et al., 1993). in the model, the substrate is described by its composition of basic organic components, i.e., car...... wastewater and with bentonite-bound oil, which is a waste with high content of lipids. (C) 1999 John Wiley & Sons, Inc. Biotechnol Bioeng 63: 363-372, 1999....

  17. Functional expression and purification of recombinant Hepcidin25 production in Escherichia coli using SUMO fusion technology.

    Science.gov (United States)

    Sadr, Vahideh; Saffar, Behnaz; Emamzadeh, Rahman

    2017-04-30

    Hepcidin25 is a small cysteine-rich peptide hormone known as a new class of antimicrobial peptides. The purpose of the present study was to express, purify and investigate the antibacterial properties of recombinant human hepcidin25 protein production in Escherichia coli. Human hepcidin25 gene was optimized and fused to a small ubiquitin-related modifier (SUMO) gene for higher expression. Then SUMO-hepcidin25 was cloned into the pET-32a (+) vector and expressed in E. coli Origami. The fusion protein with a molecular weight of approximately 35kDa was analyzed on SDS-PAGE gel. The highest expression was observed after 6h induction and the fusion protein consisted approximately 47% of the total cellular protein. The purified SUMO-hepcidin25 purity was determined to be higher than 95%, with a final yield of 3.9mgl - 1 of media. The recombinant hepcidin25 showed antibacterial activity against both Gram negative (Klebsiella pneumonia) and Gram positive (Staphylococcus aureus and Bacillus cereus) bacteria with minimum inhibitory concentrations (MICs) of 150μgml -1 , 18.7μg/ml -1 and 37.5μg/ml -1 , respectively. These results indicated that thioredoxin and SUMO dual fusion system is an efficient production system for synthesis functional human hepcidin25. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. An Arabidopsis SUMO E3 Ligase, SIZ1, Negatively Regulates Photomorphogenesis by Promoting COP1 Activity

    KAUST Repository

    Lin, Xiao-Li

    2016-04-29

    COP1 (CONSTITUTIVE PHOTOMORPHOGENIC 1), a ubiquitin E3 ligase, is a central negative regulator of photomorphogenesis. However, how COP1 activity is regulated by post-translational modifications remains largely unknown. Here we show that SUMO (small ubiquitin-like modifier) modification enhances COP1 activity. Loss-of-function siz1 mutant seedlings exhibit a weak constitutive photomorphogenic phenotype. SIZ1 physically interacts with COP1 and mediates the sumoylation of COP1. A K193R substitution in COP1 blocks its SUMO modification and reduces COP1 activity in vitro and in planta. Consistently, COP1 activity is reduced in siz1 and the level of HY5, a COP1 target protein, is increased in siz1. Sumoylated COP1 may exhibits higher transubiquitination activity than does non-sumoylated COP1, but SIZ1-mediated SUMO modification does not affect COP1 dimerization, COP1-HY5 interaction, and nuclear accumulation of COP1. Interestingly, prolonged light exposure reduces the sumoylation level of COP1, and COP1 mediates the ubiquitination and degradation of SIZ1. These regulatory mechanisms may maintain the homeostasis of COP1 activity, ensuing proper photomorphogenic development in changing light environment. Our genetic and biochemical studies identify a function for SIZ1 in photomorphogenesis and reveal a novel SUMO-regulated ubiquitin ligase, COP1, in plants.

  19. Small Ubiquitin-like Modifier (SUMO) Conjugation Impedes Transcriptional Silencing by the Polycomb Group Repressor Sex Comb on Midleg*

    OpenAIRE

    Smith, Matthew; Mallin, Daniel R.; Simon, Jeffrey A.; Courey, Albert J.

    2011-01-01

    The Drosophila protein Sex Comb on Midleg (Scm) is a member of the Polycomb group (PcG), a set of transcriptional repressors that maintain silencing of homeotic genes during development. Recent findings have identified PcG proteins both as targets for modification by the small ubiquitin-like modifier (SUMO) protein and as catalytic components of the SUMO conjugation pathway. We have found that the SUMO-conjugating enzyme Ubc9 binds to Scm and that this interaction, which requires the Scm C-te...

  20. Efficient CAD Model to Analysis of High Tc Superconducting Circular Microstrip Antenna on Anisotropic Substrates

    Directory of Open Access Journals (Sweden)

    S. Bedra

    2017-05-01

    Full Text Available In this paper, an electromagnetic approach based on cavity model in conjunction with electromagnetic knowledge was developed. The cavity model combined with London’s equations and the Gorter-Casimir two-fluid model has been improved to investigate the resonant characteristics of high Tc superconducting circular microstrip patch in the case where the patch is printed on uniaxially anisotropic substrate materials.  Merits of our extended model include low computational cost and mathematical simplify. The numerical simulation of this modeling shows excellent agreement with experimental results available in the literature. Finally, numerical results for the dielectric anisotropic substrates effects on the operating frequencies for the case of superconducting circular patch are also presented.

  1. Modeling of InP HBTs in Transferred-Substrate Technology for Millimeter-Wave Applications

    DEFF Research Database (Denmark)

    Johansen, Tom Keinicke; Rudolph, Matthias; Jensen, Thomas

    2013-01-01

    In this paper, the modeling of InP heterojunction bipolar transistors (HBTs) in transferred substrate (TS) technology is investigated. At first, a direct parameter extraction methodology dedicated to III-V based HBTs is employed to determine the small-signal equivalent circuit parameters from...

  2. Thermodynamic network model for predicting effects of substrate addition and other perturbations on subsurface microbial communities

    Energy Technology Data Exchange (ETDEWEB)

    Jack Istok; Melora Park; James McKinley; Chongxuan Liu; Lee Krumholz; Anne Spain; Aaron Peacock; Brett Baldwin

    2007-04-19

    The overall goal of this project is to develop and test a thermodynamic network model for predicting the effects of substrate additions and environmental perturbations on microbial growth, community composition and system geochemistry. The hypothesis is that a thermodynamic analysis of the energy-yielding growth reactions performed by defined groups of microorganisms can be used to make quantitative and testable predictions of the change in microbial community composition that will occur when a substrate is added to the subsurface or when environmental conditions change.

  3. Global (Q)SAR models on substrates for human Cytochrome P450 3A4

    DEFF Research Database (Denmark)

    Ringsted, Tine; Nikolov, Nikolai Georgiev; Jensen, Gunde Egeskov

    domain. Domain coverage of EINECS chemicals and number of predicted substrates are discussed. Reference: C.W. Yap and Y.Z. Chen, Prediction of cytochrome p450 3A4, 2D6, and 2C9 inhibitors and substrates by using support vector machines, J. Chem. Inf. Model. 45 (2005), pp. 982–992.......The Cytochrome P450 (CYP) is a superfamily of enzymes which catalyze the metabolism of a wide range of endobiotics and xenobiotics. The latter category comprises drugs and about 75% of marketed drugs are metabolised by CYP enzymes. Besides drugs, CYP enzymes detoxify environmental compounds...

  4. A theoretical model describing the one-dimensional growth of single crystals on free sustained substrates

    Science.gov (United States)

    Ye, Ziran; Wang, Ke; Lu, Chenxi; Jin, Ying; Sui, Chenghua; Yan, Bo; Gao, Fan; Cai, Pinggen; Lv, Bin; Li, Yun; Chen, Naibo; Sun, Guofang; Xu, Fengyun; Ye, Gaoxiang

    2018-03-01

    We develop a theoretical model that interprets the growth mechanism of zinc (Zn) crystal nanorods on a liquid substrate by thermal evaporation. During deposition, Zn atoms diffuse randomly on an isotropic and quasi-free sustained substrate, the nucleation of the atoms results in the primary nanorod (or seed crystal) growth. Subsequently, a characteristic one-dimensional atomic aggregation is proposed, which leads to the accelerating growth of the crystal nanorod along its preferential growth direction until the growth terminates. The theoretical results are in good agreement with the experimental findings.

  5. Modeling Substrate Utilization, Metabolite Production, and Uranium Immobilization in Shewanella oneidensis Biofilms

    Directory of Open Access Journals (Sweden)

    Ryan S. Renslow

    2017-06-01

    Full Text Available In this study, we developed a two-dimensional mathematical model to predict substrate utilization and metabolite production rates in Shewanella oneidensis MR-1 biofilm in the presence and absence of uranium (U. In our model, lactate and fumarate are used as the electron donor and the electron acceptor, respectively. The model includes the production of extracellular polymeric substances (EPS. The EPS bound to the cell surface and distributed in the biofilm were considered bound EPS (bEPS and loosely associated EPS (laEPS, respectively. COMSOL® Multiphysics finite element analysis software was used to solve the model numerically (model file provided in the Supplementary Material. The input variables of the model were the lactate, fumarate, cell, and EPS concentrations, half saturation constant for fumarate, and diffusion coefficients of the substrates and metabolites. To estimate unknown parameters and calibrate the model, we used a custom designed biofilm reactor placed inside a nuclear magnetic resonance (NMR microimaging and spectroscopy system and measured substrate utilization and metabolite production rates. From these data we estimated the yield coefficients, maximum substrate utilization rate, half saturation constant for lactate, stoichiometric ratio of fumarate and acetate to lactate and stoichiometric ratio of succinate to fumarate. These parameters are critical to predicting the activity of biofilms and are not available in the literature. Lastly, the model was used to predict uranium immobilization in S. oneidensis MR-1 biofilms by considering reduction and adsorption processes in the cells and in the EPS. We found that the majority of immobilization was due to cells, and that EPS was less efficient at immobilizing U. Furthermore, most of the immobilization occurred within the top 10 μm of the biofilm. To the best of our knowledge, this research is one of the first biofilm immobilization mathematical models based on experimental

  6. El sumo bien kantiano: el objeto construído de la ley moral

    Directory of Open Access Journals (Sweden)

    Alonso Villarán

    2016-01-01

    Full Text Available El presente artículo tiene tres objetivos: a. compilar las críticas planteadas en contra del sumo bien kantiano (un mundo donde la virtud es premiada con felicidad; b. elaborar una revisión crítica de las respectivas defensas; y c. desarrollar una nueva defensa, con énfasis en el problema de derivación (según el cual el sumo bien no se deriva de la ley moral. Respecto al primero punto, el artículo muestra que son al menos cinco los problemas que amenazan la doctrina: heteronomía, derivación, imposibilidad, irrelevancia y dualismo. Respecto al segundo, el artículo revela que las múltiples defensas elaboradas en nombre del sumo bien son fuente, a su vez, de otros problemas, como los de incompletitud, ilusión, injusticia, deslealtad y escisión. Respecto al tercer y principal punto, y empezando por la derivación, el artículo propone ver al sumo bien como el objeto construido de la ley moral. Resuelto el problema de derivación, el artículo ofrece breves respuestas a los otros problemas en juego. El artículo también traduce por primera vez, del inglés al español, fragmentos de importantes publicaciones sobre el sumo bien.

  7. Proteome-wide analysis of SUMO2 targets in response to pathological DNA replication stress in human cells

    DEFF Research Database (Denmark)

    Bursomanno, Sara; Beli, Petra; Khan, Asif M

    2015-01-01

    subfamily. SUMO2/3, in contrast to SUMO1, are predominantly involved in the cellular response to certain stresses, including heat shock. Substantial evidence from studies in yeast has shown that SUMOylation plays an important role in the regulation of DNA replication and repair. Here, we report a proteomic...... analysis of proteins modified by SUMO2 in response to DNA replication stress in S phase in human cells. We have identified a panel of 22 SUMO2 targets with increased SUMOylation during DNA replication stress, many of which play key functions within the DNA replication machinery and/or in the cellular...... repair. We have also shown that deficiency of POLD3 leads to an increase in RPA-bound ssDNA when cells are under replication stress, suggesting that POLD3 plays a role in the cellular response to DNA replication stress. Considering that DNA replication stress is a source of genome instability...

  8. Development of Conformation Independent Computational Models for the Early Recognition of Breast Cancer Resistance Protein Substrates

    Science.gov (United States)

    Gantner, Melisa Edith; Di Ianni, Mauricio Emiliano; Ruiz, María Esperanza; Bruno-Blanch, Luis E.

    2013-01-01

    ABC efflux transporters are polyspecific members of the ABC superfamily that, acting as drug and metabolite carriers, provide a biochemical barrier against drug penetration and contribute to detoxification. Their overexpression is linked to multidrug resistance issues in a diversity of diseases. Breast cancer resistance protein (BCRP) is the most expressed ABC efflux transporter throughout the intestine and the blood-brain barrier, limiting oral absorption and brain bioavailability of its substrates. Early recognition of BCRP substrates is thus essential to optimize oral drug absorption, design of novel therapeutics for central nervous system conditions, and overcome BCRP-mediated cross-resistance issues. We present the development of an ensemble of ligand-based machine learning algorithms for the early recognition of BCRP substrates, from a database of 262 substrates and nonsubstrates compiled from the literature. Such dataset was rationally partitioned into training and test sets by application of a 2-step clustering procedure. The models were developed through application of linear discriminant analysis to random subsamples of Dragon molecular descriptors. Simple data fusion and statistical comparison of partial areas under the curve of ROC curves were applied to obtain the best 2-model combination, which presented 82% and 74.5% of overall accuracy in the training and test set, respectively. PMID:23984415

  9. The Effect of Substrate-Bulk Interaction on Hydrolysis Modeling in Anaerobic Digestion Process

    Directory of Open Access Journals (Sweden)

    Antonio Panico

    2014-11-01

    Full Text Available In an Anaerobic Digestion (AD process treating particulate substrates, the size of solids is expected to negatively affect the rate of hydrolysis step and consequently influence the performance of the whole process. To avoid any disadvantage due to size of solids, expensive pre-treatments aimed at disintegrating and solubilizing substrates are commonly conducted prior to AD. This practice is doubtlessly successful, but not always necessary, since some organic substrates, although particulate, once immersed in water, tend to solubilize immediately. This aspect, if properly considered, could result in saving money and time in the AD process, as well as refining the development and calibration of AD mathematical models. The present study is actually aimed at demonstrating, through experiments and mathematical simulations, different results deriving from the AD process performed, under the same operating conditions, on two different substrates, i.e. homemade pasta and carrot batons, having the same particle size, but different chemical composition and texture. Experimental outcomes highlighted the effect of particles size on bio-methane production only from the bio-methanation potential tests (BMP conducted on carrot batons. Similar results were obtained by mathematical model calibration, i.e., different kinetic constants for differently-sized carrot batons and same kinetic constant for differently-sized homemade pasta solids.

  10. Development of Conformation Independent Computational Models for the Early Recognition of Breast Cancer Resistance Protein Substrates

    Directory of Open Access Journals (Sweden)

    Melisa Edith Gantner

    2013-01-01

    Full Text Available ABC efflux transporters are polyspecific members of the ABC superfamily that, acting as drug and metabolite carriers, provide a biochemical barrier against drug penetration and contribute to detoxification. Their overexpression is linked to multidrug resistance issues in a diversity of diseases. Breast cancer resistance protein (BCRP is the most expressed ABC efflux transporter throughout the intestine and the blood-brain barrier, limiting oral absorption and brain bioavailability of its substrates. Early recognition of BCRP substrates is thus essential to optimize oral drug absorption, design of novel therapeutics for central nervous system conditions, and overcome BCRP-mediated cross-resistance issues. We present the development of an ensemble of ligand-based machine learning algorithms for the early recognition of BCRP substrates, from a database of 262 substrates and nonsubstrates compiled from the literature. Such dataset was rationally partitioned into training and test sets by application of a 2-step clustering procedure. The models were developed through application of linear discriminant analysis to random subsamples of Dragon molecular descriptors. Simple data fusion and statistical comparison of partial areas under the curve of ROC curves were applied to obtain the best 2-model combination, which presented 82% and 74.5% of overall accuracy in the training and test set, respectively.

  11. Towards the modeling of nanoindentation of virus shells: Do substrate adhesion and geometry matter?

    Science.gov (United States)

    Bousquet, Arthur; Dragnea, Bogdan; Tayachi, Manel; Temam, Roger

    2016-12-01

    Soft nanoparticles adsorbing at surfaces undergo deformation and buildup of elastic strain as a consequence of interfacial adhesion of similar magnitude with constitutive interactions. An example is the adsorption of virus particles at surfaces, a phenomenon of central importance for experiments in virus nanoindentation and for understanding of virus entry. The influence of adhesion forces and substrate corrugation on the mechanical response to indentation has not been studied. This is somewhat surprising considering that many single-stranded RNA icosahedral viruses are organized by soft intermolecular interactions while relatively strong adhesion forces are required for virus immobilization for nanoindentation. This article presents numerical simulations via finite elements discretization investigating the deformation of a thick shell in the context of slow evolution linear elasticity and in presence of adhesion interactions with the substrate. We study the influence of the adhesion forces in the deformation of the virus model under axial compression on a flat substrate by comparing the force-displacement curves for a shell having elastic constants relevant to virus capsids with and without adhesion forces derived from the Lennard-Jones potential. Finally, we study the influence of the geometry of the substrate in two-dimensions by comparing deformation of the virus model adsorbed at the cusp between two cylinders with that on a flat surface.

  12. Modeling of Rapid Solidification with Undercooling Effect During Droplet Flattening on a Substrate in Coating Formation

    Science.gov (United States)

    Shukla, Rajesh Kumar; Patel, Virendra; Kumar, Arvind

    2018-02-01

    The coating deposit on the substrate in thermal spray coating process develops by solidification of individual molten particle which impacts, flattens and solidifies on the surface of the substrate. Droplet flattening and solidification typically involves rapid cooling. In this paper, a model for non-equilibrium rapid solidification of a molten droplet spreading onto a substrate is presented. Transient flow during droplet impact and its subsequent spreading is considered using the volume of fluid surface tracking method which was fully coupled with the rapid solidification model. The rapid solidification model includes undercooling, nucleation, interface tracking, non-equilibrium solidification kinetics and combined heat transfer and fluid flow as required to treat a non-stagnant splat formed from droplet flattening. The model is validated with the literature results on stagnant splats. Subsequently, using the model the characteristics of the rapidly solidifying interface for non-stagnant splat, such as interface velocity and interface temperature, are described and the effect of undercooling and interfacial heat transfer coefficient are highlighted. In contrast to the stagnant splat, the non-stagnant splat considered in this study displays interesting features in the rapidly solidifying interface. These are attributed to droplet thinning and droplet recoiling that occur during the droplet spreading process.

  13. Gold Incorporated Mesoporous Silica Thin Film Model Surface as a Robust SERS and Catalytically Active Substrate

    Directory of Open Access Journals (Sweden)

    Anandakumari Chandrasekharan Sunil Sekhar

    2016-05-01

    Full Text Available Ultra-small gold nanoparticles incorporated in mesoporous silica thin films with accessible pore channels perpendicular to the substrate are prepared by a modified sol-gel method. The simple and easy spin coating technique is applied here to make homogeneous thin films. The surface characterization using FESEM shows crack-free films with a perpendicular pore arrangement. The applicability of these thin films as catalysts as well as a robust SERS active substrate for model catalysis study is tested. Compared to bare silica film our gold incorporated silica, GSM-23F gave an enhancement factor of 103 for RhB with a laser source 633 nm. The reduction reaction of p-nitrophenol with sodium borohydride from our thin films shows a decrease in peak intensity corresponding to –NO2 group as time proceeds, confirming the catalytic activity. Such model surfaces can potentially bridge the material gap between a real catalytic system and surface science studies.

  14. Computational Modelling of Catalytic Properties and Modified Substrates of Fungal B-N-Acetylhexosaminidases

    Czech Academy of Sciences Publication Activity Database

    Kulik, Natallia; Slámová, Kristýna

    2011-01-01

    Roč. 8, č. 3 (2011), s. 270-280 ISSN 1570-193X R&D Projects: GA ČR(CZ) GAP207/11/0629; GA ČR GD305/09/H008; GA MŠk(CZ) LC06010 Institutional research plan: CEZ:AV0Z50200510; CEZ:AV0Z60870520 Keywords : beta-N-Acetylhexosaminidase * computer modelling * modified substrate Subject RIV: CE - Biochemistry Impact factor: 2.406, year: 2011

  15. Global conservation model for a mushy region over a moving substrate

    Science.gov (United States)

    Kyselica, J.; Šimkanin, J.

    2018-03-01

    We study solidification over a cool substrate moving with a relative velocity with respect to the rest of the fluid. A mathematical model based on global conservation of solute is presented. The explicit solutions of the governing equations are found and analysed via the asymptotic methods. The assessment of how the boundary-layer flow influences the physical characteristics of the mushy region is given, together with the discussion of a possible connection with the solidification at the inner core boundary.

  16. Modeling of stable and metastable structures of Co, Cr, or Fe deposited on Ag(100) substrates

    Energy Technology Data Exchange (ETDEWEB)

    Canzian, A. [Grupo de Caracterizacion y Modelacion de Materiales, UTN, FRGP, H. Yrigoyen 288, (B1617FRP) Gral. Pacheco (Argentina); Bozzolo, G., E-mail: guille_bozzolo@yahoo.co [Loyola University of Maryland, 4501 N. Charles St, Baltimore, MD 21210 (United States); Mosca, H.O. [Gerencia de Investigacion y Aplicaciones, Comision Nacional de Energia Atomica, Av. Gral. Paz 1499 (B1650KNA), San Martin (Argentina)

    2011-01-31

    Atomistic modeling of the deposition of Co, Cr, or Fe on a Ag(100) substrate is performed using the Bozzolo-Ferrante-Smith method for alloys, in order to describe the similarities and differences between the three cases. An atom-by-atom description of the deposition process explains the growth patterns from an early stage, establishing a criterion for the determination of the ensuing growth modes.

  17. Modeling of air-droplet interaction, substrate melting and coating buildup in thermal spraying

    Science.gov (United States)

    Wei, Guanghua

    Among the many surface coating techniques now available, thermal spray is known to offer the most advantages. It can meet a wide range of technical and engineering requirements in a relatively inexpensive and easily controllable way with the capability of producing repeatable results. In the last few decades a lot of important strides have been made in the field of measurements and modelling of thermal spraying. However, due to the complex of the process and the lack of basic materials-based knowledge about the particle melting, spreading and deposition, the relationship between the process parameters and the coating properties still remains unclear. In thermal spraying, a particle is melted to form a droplet with morphology and thermal- and kinetic-energy status change by the interaction with the plasma/flame. In order to produce higher-quality coatings and expand the use of this versatile family of technologies, modelling of the particle behaviors during in-flight, spreading and deposition is essential. This thesis investigates the connections between particle characteristics and coating properties. Momentum, heat and mass transfer phenomena related to particle in-flight, droplet impacting, spreading, and splat layering are studied. Numerical models are developed to establish the quantitative relationships between spray parameters, particle and substrate properties and deposition characteristics. Most existing theoretical studies of in-flight particle assume that the particle is in a spherical shape without voids inside. The behavior of porous particles in thermal spray has not been well understood. However, the presence of voids in the feedstock powders may have a great impact on particle in-flight behaviors such as particle acceleration, melting and oxidation because a hollowed particle is also lighter than a densed one and this will affect the particle trajectory. The particle shape also needs to be taken into account because it influences the drag force and

  18. Swimming near the substrate: a simple robotic model of stingray locomotion.

    Science.gov (United States)

    Blevins, Erin; Lauder, George V

    2013-03-01

    Studies of aquatic locomotion typically assume that organisms move through unbounded fluid. However, benthic fishes swim close to the substrate and will experience significant ground effects, which will be greatest for fishes with wide spans such as benthic batoids and flatfishes. Ground effects on fixed-wing flight are well understood, but these models are insufficient to describe the dynamic interactions between substrates and undulating, oscillating fish. Live fish alter their swimming behavior in ground effect, complicating comparisons of near-ground and freestream swimming performance. In this study, a simple, stingray-inspired physical model offers insights into ground effects on undulatory swimmers, contrasting the self-propelled swimming speed, power requirements, and hydrodynamics of fins swimming with fixed kinematics near and far from a solid boundary. Contrary to findings for gliding birds and other fixed-wing fliers, ground effect does not necessarily enhance the performance of undulating fins. Under most kinematic conditions, fins do not swim faster in ground effect, power requirements increase, and the cost of transport can increase by up to 10%. The influence of ground effect varies with kinematics, suggesting that benthic fish might modulate their swimming behavior to minimize locomotor penalties and incur benefits from swimming near a substrate.

  19. Considerations in the selection of model substrates for microbiological effects research

    International Nuclear Information System (INIS)

    Francis, A.J.; Rose, A.W.

    1984-01-01

    The physical and chemical characteristics of several energy residues have been briefly reviewed in order to select a model or representative substrate of basic research to determine the significance of anaerobic microbial dissolution and mobilization or immobilization of toxic trace elements under subsurface environmental conditions. The major factors which influence the dissolution and mobilization of trace metals have been critically examined, e.g., (i) effects on pH of leachates (pyrite oxidation), soluble acid, and basic compounds; (ii) effects on oxidation state of leachates (oxidation state of Fe, presence of organics); (iii) concentration of toxic inorganic species, and chemical form; (iv) surface area of waste particles; and (v) physical strength and particle size, with resulting effects on permeability of the substrate. Several major physical and chemical characteristics are common to energy-related residues yet each of these materials has a unique set of physical and chemical properties. The pros and cons of selecting a single model substrate for microbiological research were discussed at the Geochemical and Biochemical Working Group Meeting and use of the end-member concept was suggested. From the abundance, distribution, forms of trace metals present, and volume of these metal-containing residues disposed of in the subsurface environments, microbiological studies can be performed with coal beneficiation and coal gasification residues under a variety of subsurface environmental conditions, and results can be validated in the field. The basic scientific information obtained from this research can be applied to other materials of similar composition. 18 references, 3 figures, 7 tables

  20. Considerations in the selection of model substrates for microbiological effects research

    Energy Technology Data Exchange (ETDEWEB)

    Francis, A.J.; Rose, A.W.

    1984-01-01

    The physical and chemical characteristics of several energy residues have been briefly reviewed in order to select a model or representative substrate of basic research to determine the significance of anaerobic microbial dissolution and mobilization or immobilization of toxic trace elements under subsurface environmental conditions. The major factors which influence the dissolution and mobilization of trace metals have been critically examined, e.g., (i) effects on pH of leachates (pyrite oxidation), soluble acid, and basic compounds; (ii) effects on oxidation state of leachates (oxidation state of Fe, presence of organics); (iii) concentration of toxic inorganic species, and chemical form; (iv) surface area of waste particles; and (v) physical strength and particle size, with resulting effects on permeability of the substrate. Several major physical and chemical characteristics are common to energy-related residues yet each of these materials has a unique set of physical and chemical properties. The pros and cons of selecting a single model substrate for microbiological research were discussed at the Geochemical and Biochemical Working Group Meeting and use of the end-member concept was suggested. From the abundance, distribution, forms of trace metals present, and volume of these metal-containing residues disposed of in the subsurface environments, microbiological studies can be performed with coal beneficiation and coal gasification residues under a variety of subsurface environmental conditions, and results can be validated in the field. The basic scientific information obtained from this research can be

  1. Nonstationary heat conduction in one-dimensional models with substrate potential

    Science.gov (United States)

    Gendelman, O. V.; Shvartsman, R.; Madar, B.; Savin, A. V.

    2012-01-01

    The paper investigates nonstationary heat conduction in one-dimensional models with substrate potential. To establish universal characteristic properties of the process, we explore three different models: Frenkel-Kontorova (FK), phi4+ (φ4+), and phi4- (φ4-). Direct numeric simulations reveal in all these models a crossover from oscillatory decay of short-wave perturbations of the temperature field to smooth diffusive decay of the long-wave perturbations. Such behavior is inconsistent with the parabolic Fourier equation of heat conduction and clearly demonstrates the necessity for hyperbolic corrections in the phenomenological description of the heat conduction process. The crossover wavelength decreases with an increase in the average temperature. The decay patterns of the temperature field almost do not depend on the amplitude of the perturbations, so the use of linear evolution equations for the temperature field is justified. In all models investigated, the relaxation of thermal perturbations is exponential, contrary to a linear chain, where it follows a power law. The most popular lowest-order hyperbolic generalization of the Fourier law, known as the Cattaneo-Vernotte or telegraph equation, is also not valid for the description of the observed behavior of the models with the substrate potential, since the characteristic relaxation time in an oscillatory regime strongly depends on the excitation wavelength. For some of the models, this dependence seems to obey a simple scaling law.

  2. Predictive modelling of the dielectric response of plasmonic substrates: application to the interpretation of ellipsometric spectra

    Science.gov (United States)

    Pugliara, A.; Bayle, M.; Bonafos, C.; Carles, R.; Respaud, M.; Makasheva, K.

    2018-03-01

    A predictive modelling of plasmonic substrates appropriate to read ellipsometric spectra is presented in this work. We focus on plasmonic substrates containing a single layer of silver nanoparticles (AgNPs) embedded in silica matrices. The model uses the Abeles matrix formalism and is based on the quasistatic approximation of the classical Maxwell-Garnett mixing rule, however accounting for the electronic confinement effect through the damping parameter. It is applied on samples elaborated by: (i) RF-diode sputtering followed by Plasma Enhanced Chemical Vapor Deposition (PECVD) and (ii) Low Energy Ion Beam Synthesis (LE-IBS), and represents situations with increasing degree of complexity that can be accounted for by the model. It allows extraction of the main characteristics of the AgNPs population: average size, volume fraction and distance of the AgNPs layer from the matrix free surface. Model validation is achieved through comparison with results obtained from transmission electron microscopy approving for its applicability. The advantages and limitations of the proposed model are discussed after eccentricity-based statistical analysis along with further developments related to the quality of comparison between the model-generated spectra and the experimentally-recorded ellipsometric spectra.

  3. Covalent conjugation of the equine infectious anemia virus Gag with SUMO.

    Science.gov (United States)

    Wang, Jinzhong; Wen, Shuping; Zhao, Rui; Qi, Jing; Liu, Zhao; Li, Weiwei; An, Jing; Wood, Charles; Wang, Ying

    2017-05-06

    The conjugation of small ubiquitin-like modifier (SUMO) to the target protein, namely, SUMOylation, is involved in the regulation of many important biological events including host-pathogen interaction. Some viruses have evolved to exploit the host SUMOylation machinery to modify their own protein. Retroviral Gag protein plays critical roles in the viral life cycle. The HIV-1 p6 and the Moloney murine leukemia virus CA have been reported to be conjugated with SUMO. In this study, we report for the first time, to our knowledge, the covalent conjugation of equine infectious anemia virus (EIAV) Gag with SUMO. The C-terminal p9 domain of Gag is a main target for SUMOylation and SUMO is attached to multiple sites of p9, including K30 whose mutation abolished p9 SUMOylation completely. The SUMOylation of p9, but not the p9-K30 mutant, was also detected in equine fibroblastic cells ATCC ® CCL-57™. Ubc9 and its C93 residue are indispensable for the SUMOylation of p9. Using confocal microscopy, it is found that EIAV Gag localizes primarily, if not exclusively, in the cytoplasm of the cell and the co-localization of EIAV Gag with Ubc9 was observed. Our findings that EIAV Gag is SUMOylated at p9-K30, together with previous findings on the defects of p9-K30 mutant in viral DNA translocation from cytoplasm to the nucleus, suggests that SUMOylation of Gag may be involved in such functions. Copyright © 2017 Elsevier Inc. All rights reserved.

  4. Expression of soluble and active interferon consensus in SUMO fusion expression system in E. coli.

    Science.gov (United States)

    Peciak, Karolina; Tommasi, Rita; Choi, Ji-won; Brocchini, Steve; Laurine, Emmanuelle

    2014-07-01

    Protein production can be improved if methods for soluble protein expression are developed. Interferon consensus (IFN-con) is used to treat hepatitis C. IFN-con has superior activity compared to other clinically used interferon α subtypes. However IFN-con is a challenging protein to produce in a soluble form using an Escherichia coli expression system. Here we describe the expression of soluble and active recombinant IFN-con in E. coli. The IFN-con gene sequence was optimised for expression in E. coli, which was then cloned into the Champion™ pET SUMO expression vector downstream of the SUMO fusion protein and under strong T7lac promoter. The SUMO-IFN-con fusion protein was efficiently expressed using the SHuffle™ E. coli strain and existed in soluble form as 86-88% of the total IFN-con. After removal of the SUMO fusion partner, approximately 50mg of recombinant IFN-con of at least 98% purity (by RP-HPLC) was obtained from a 1L fermentation culture. Using an A549/EMCV antiviral assay, the specific activity of the recombinant IFN-con was determined to be 960×10(6) IU/mg as calculated to NIBSC standard for IFN-con (3×10(5)pfu/mL virus titre). Comparison of the antiviral activity of the produced IFN-con to IFN α-2a showed that IFN-con displays 2.8 times greater activity, which is in good agreement with what has been reported in the literature for pure protein. IFN-con expression in a soluble form from E. coli allowed us to use a simple, two-step purification process to yield highly pure and active IFN-con which is more efficient than obtaining IFN-con from inclusion bodies. Copyright © 2014 Elsevier Inc. All rights reserved.

  5. EM simulation assisted parameter extraction for the modeling of transferred-substrate InP HBTs

    DEFF Research Database (Denmark)

    Johansen, Tom Keinicke; Weimann, Nils; Doerner, Ralf

    2017-01-01

    3D EM simulations up to 325 GHz. Following an on-wafer multi-line Through-Reflect-Line (TRL) calibration procedure, the external parasitic network is de-embedded from the transistor measurements and the active device parameters are extracted in a reliable way. The small-signal model structure......In this paper an electromagnetic (EM) simulation assisted parameters extraction procedure is demonstrated for accurate modeling of down-scaled transferred-substrate InP HBTs. The external parasitic network associated with via transitions and device electrodes is carefully extracted from calibrated...

  6. Molecular model of the specificity pocket of the hepatitis C virus protease: implications for substrate recognition.

    OpenAIRE

    Pizzi, E; Tramontano, A; Tomei, L; La Monica, N; Failla, C; Sardana, M; Wood, T; De Francesco, R

    1994-01-01

    We have built a model of the specificity pocket of the protease of hepatitis C virus on the basis of the known structures of trypsin-like serine proteases and of the conservation pattern of the protease sequences among various hepatitis C strains. The model allowed us to predict that the substrate of this protease should have a cysteine residue in position P1. This hypothesis was subsequently proved by N-terminal sequencing of two products of the protease. The success of this "blind" test inc...

  7. A unique SUMO-2-interacting motif within LANA is essential for KSHV latency.

    Directory of Open Access Journals (Sweden)

    Qiliang Cai

    Full Text Available Kaposi's sarcoma-associated herpesvirus (KSHV stabilizes hypoxia-inducible factor α (HIF-1α during latent infection, and HIF-1α reactivates lytic replication under hypoxic stress. However, the mechanism utilized by KSHV to block lytic reactivation with the accumulation of HIF-1α in latency remains unclear. Here, we report that LANA encoded by KSHV contains a unique SUMO-interacting motif (LANA(SIM which is specific for interaction with SUMO-2 and facilitates LANA SUMOylation at lysine 1140. Proteomic and co-immunoprecipitation analysis further reveal that the SUMO-2 modified transcription repressor KAP1 is a critical factor recruited by LANA(SIM. Deletion of LANA(SIM led to functional loss of both LANA-mediated viral episome maintenance and lytic gene silencing. Moreover, hypoxia reduced KAP1 SUMOylation and resulted in dissociation of both KAP1 and Sin3A repressors from LANA(SIM-associated complex. Therefore, the LANA(SIM motif plays an essential role in KSHV latency and is a potential drug target against KSHV-associated cancers.

  8. Tandem SUMO fusion vectors for improving soluble protein expression and purification.

    Science.gov (United States)

    Guerrero, Fernando; Ciragan, Annika; Iwaï, Hideo

    2015-12-01

    Availability of highly purified proteins in quantity is crucial for detailed biochemical and structural investigations. Fusion tags are versatile tools to facilitate efficient protein purification and to improve soluble overexpression of proteins. Various purification and fusion tags have been widely used for overexpression in Escherichia coli. However, these tags might interfere with biological functions and/or structural investigations of the protein of interest. Therefore, an additional purification step to remove fusion tags by proteolytic digestion might be required. Here, we describe a set of new vectors in which yeast SUMO (SMT3) was used as the highly specific recognition sequence of ubiquitin-like protease 1, together with other commonly used solubility enhancing proteins, such as glutathione S-transferase, maltose binding protein, thioredoxin and trigger factor for optimizing soluble expression of protein of interest. This tandem SUMO (T-SUMO) fusion system was tested for soluble expression of the C-terminal domain of TonB from different organisms and for the antiviral protein scytovirin. Copyright © 2015 Elsevier Inc. All rights reserved.

  9. Chromatin SUMOylation in heat stress: To protect, pause and organise?: SUMO stress response on chromatin.

    Science.gov (United States)

    Niskanen, Einari A; Palvimo, Jorma J

    2017-06-01

    Post-translational modifications, e.g. SUMO modifications (SUMOylation), provide a mechanism for swiftly changing a protein's activity. Various stress conditions trigger a SUMO stress response (SSR) - a stress-induced rapid change in the conjugation of SUMO to multiple proteins, which predominantly targets nuclear proteins. The SSR has been postulated to protect stressed cells by preserving the functionality of crucial proteins. However, it is unclear how it exerts its protective functions. Interestingly, heat stress (HS) increases SUMOylation of proteins at active promoters and enhancers. In promoters, HS-induced SUMOylation correlates with gene transcription and stress-induced RNA polymerase II (Pol2) pausing. Conversely, a disappearance of SUMOylation in HS occurs at chromatin anchor points that maintain chromatin-looping structures and the spatial organisation of chromatin. In reviewing the literature, we hypothesise that the SSR regulates Pol2 pausing by modulating the interactions of pausing-regulating proteins, whereas deSUMOylation alters the function of chromatin anchors. © 2017 WILEY Periodicals, Inc.

  10. Arabidopsis SUMO protease ASP1 positively regulates flowering time partially through regulating FLC stability 

    KAUST Repository

    Kong, Xiangxiong

    2016-12-07

    The initiation of flowering is tightly regulated by the endogenous and environment signals, which is crucial for the reproductive success of flowering plants. It is well known that autonomous and vernalization pathways repress transcription of FLOWERING LOCUS C (FLC), a focal floral repressor, but how its protein stability is regulated remains largely unknown. Here, we found that mutations in a novel Arabidopsis SUMO protease 1 (ASP1) resulted in a strong late-flowering phenotype under long-days, but to a lesser extent under short-days. ASP1 localizes in the nucleus and exhibited a SUMO protease activity in vitro and in vivo. The conserved Cys-577 in ASP1 is critical for its enzymatic activity, as well as its physiological function in the regulation of flowering time. Genetic and gene expression analyses demonstrated that ASP1 promotes transcription of positive regulators of flowering, such as FT, SOC1 and FD, and may function in both CO-dependent photoperiod pathway and FLC-dependent pathways. Although the transcription level of FLC was not affected in the loss-of-function asp1 mutant, the protein stability of FLC was increased in the asp1 mutant. Taken together, this study identified a novel bona fide SUMO protease, ASP1, which positively regulates transition to flowering at least partly by repressing FLC protein stability.

  11. Dynamic regulation of HIF1Α stability by SUMO2/3 and SENP3 in the human placenta.

    Science.gov (United States)

    Bhattacharjee, Jayonta; Alahari, Sruthi; Sallais, Julien; Tagliaferro, Andrea; Post, Martin; Caniggia, Isabella

    2016-04-01

    Hypoxia-inducible factor 1A (HIF1A) stability is tightly regulated by hydroxylation and ubiquitination. Emerging evidence indicates that HIF1A is also controlled by the interplay between SUMO-specific ligases, which execute protein SUMOylation, and Sentrin/SUMO-specific proteases that de-SUMOylate target proteins. Given the significance of HIF1A in the human placenta, we investigated whether placental HIF1A is subject to SUMOylation in physiological and pathological conditions. Placentae were obtained from normal and pregnancies complicated by preeclampsia. Human choriocarcinoma JEG3 cells were maintained at either 21% or 3% oxygen or exposed to sodium nitroprusside (SNP). Cells were transfected with SUMO2/3 constructs with and without Mg132, a proteasome inhibitor. Expression, distribution and associations of SUMO/SENPs and HIF1A were evaluated by Western blotting, immunohistochemistry and co-immunoprecipitation. HIF1A-SUMO2/3 associations peaked at 9-10 weeks, while its deSUMOylation by SENP3 was greatest at 10-12 weeks. In E-PE, HIF1A deSUMOylation by SENP3 was significantly elevated, while HIF1A-SUMO2/3 associations remained constant. In vitro, overexpression of SUMO2/3 de-stabilized HIF1A in hypoxia, and abrogated HIF1A expression following Mg132 treatment in normoxia. Hypoxia and SNP treatments promoted SENP3 nuclear redistribution from nucleoli to the nucleoplasm where it associates with HIF1A. During early placental development, SUMOylation events control HIF1A stability in an oxygen-dependent manner. In E-PE, enhanced deSUMOylation of HIF1A by SENP3 may in part contribute to increased HIF1A activity and stability found in this pathology. Copyright © 2016 Elsevier Ltd. All rights reserved.

  12. Modified kinetic-hydraulic UASB reactor model for treatment of wastewater containing biodegradable organic substrates.

    Science.gov (United States)

    El-Seddik, Mostafa M; Galal, Mona M; Radwan, A G; Abdel-Halim, Hisham S

    2016-01-01

    This paper addresses a modified kinetic-hydraulic model for up-flow anaerobic sludge blanket (UASB) reactor aimed to treat wastewater of biodegradable organic substrates as acetic acid based on Van der Meer model incorporated with biological granules inclusion. This dynamic model illustrates the biomass kinetic reaction rate for both direct and indirect growth of microorganisms coupled with the amount of biogas produced by methanogenic bacteria in bed and blanket zones of reactor. Moreover, the pH value required for substrate degradation at the peak specific growth rate of bacteria is discussed for Andrews' kinetics. The sensitivity analyses of biomass concentration with respect to fraction of volume of reactor occupied by granules and up-flow velocity are also demonstrated. Furthermore, the modified mass balance equations of reactor are applied during steady state using Newton Raphson technique to obtain a suitable degree of freedom for the modified model matching with the measured results of UASB Sanhour wastewater treatment plant in Fayoum, Egypt.

  13. Substrate storage concepts in modeling activated sludge systems for tannery wastewaters.

    Science.gov (United States)

    Dizdaroglu-Risvanoglu, Gülseda; Karahan, Ozlem; Cokgor, Emine Ubay; Orhon, Derin; Van Loosdrecht, Mark C M

    2007-12-01

    In spite of a variety of model structures proposed for activated sludge systems, calibration of these models for industrial wastewaters still stands untouched. In the scope of this study, a conceptual framework for the application of ASM1, ASM3 and 3 models, involving simultaneous growth and storage under dynamic conditions is presented and these models have been used for simulating biodegradation/tannery wastewaters. A comparative representation of the modeling results obtained with 5 different models is provided. The comparison of the simulation results showed that the possibility of describing the real case increases as the model gets more detailed. Although structured models are supposed to provide a better description of the dynamic behavior observed for tannery effluents, the insufficiency experienced in the experimental determination of all the storage products when complex substrate compositions are concerned, hindered the accurate determination of model coefficients. Furthermore, modeling results for different F/M ratios clearly emphasized the challenge in the definition of readily biodegradable COD. Process stoichiometry and wastewater fractionation should be defined cautiously with additional data in order to provide substantial basis for the evaluation of the respirometric response in batch tests for model calibration.

  14. A putative SUMO interacting motif in the B30.2/SPRY domain of rhesus macaque TRIM5α important for NF-κB/AP-1 signaling and HIV-1 restriction

    Directory of Open Access Journals (Sweden)

    Marie-Édith Nepveu-Traversy

    2016-01-01

    Full Text Available TRIM5α from the rhesus macaque (TRIM5αRh is a restriction factor that shows strong activity against HIV-1. TRIM5αRh binds specifically to HIV-1 capsid (CA through its B30.2/PRYSPRY domain shortly after entry of the virus into the cytoplasm. Recently, three putative SUMO interacting motifs (SIMs have been identified in the PRYSPRY domain of human and macaque TRIM5α. However, structural modeling of this domain suggested that two of them were buried in the hydrophobic core of the protein, implying that interaction with SUMO was implausible, while the third one was not relevant to restriction. In light of these results, we re-analyzed the TRIM5αRh PRYSPRY sequence and identified an additional putative SIM (435VIIC438 which we named SIM4. This motif is exposed at the surface of the PRYSPRY domain, allowing potential interactions with SUMO or SUMOylated proteins. Introducing a double mutation in SIM4 (V435K, I436K did not alter stability, unlike mutations in SIM1. SIM4-mutated TRIM5αRh failed to bind HIV-1CA and lost the ability to restrict this virus. Accordingly, SIM4 undergoes significant variation among primates and substituting this motif with naturally occurring SIM4 variants affected HIV-1 restriction by TRIM5αRh, suggesting a direct role in capsid recognition. Interestingly, SIM4-mutated TRIM5αRh also failed to activate NF-κB and AP-1-mediated transcription. Although there is no direct evidence that SIM4 is involved in direct interaction with SUMO or a SUMOylated protein, mutating this motif strongly reduced co-localization of TRIM5αRh with SUMO-1 and with PML, a SUMOylated nuclear protein. In conclusion, this new putative SIM is crucial for both direct interaction with incoming capsids and for NF-κB/AP-1 signaling. We speculate that the latter function is mediated by interactions of SIM4 with a SUMOylated protein involved in the NF-κB/AP-1 signaling pathways.

  15. A Compact P⁺ Contact Resistance Model for Characterization of Substrate Coupling in Modern Lightly Doped CMOS Processes

    DEFF Research Database (Denmark)

    Shen, Ming; Mikkelsen, Jan H.; Jensen, Ole Kiel

    2012-01-01

    Compact modeling of P+ contact resistances is important for characterization of substrate noise coupling in mixed-signal System on Chips (SoCs). Existing contact resistance models can handle uniformly doped bulk or epitaxial substrates. However, compact contact resistance models feasible for modern......, and it is scalable to layout/substrate parameters. The proposed model can also be used to predict noise coupling in terms of S-parameters. The model validation has been done by both EM simulations and measurements, and satisfactory agreement is found between the modeled and measured resistances as well as S-parameters....... lightly-doped CMOS processes with P-well layers are still unavailable. This paper presents a new compact resistance model aiming at solving this problem. A Conformal Mapping(CM) method was used to derive the closed-form expressions for the resistances in the model. The model requires no fitting factors...

  16. Towards a modeling synthesis of two or three-dimensional circuits through substrate coupling and interconnections

    CERN Document Server

    Gontrand, Christian

    2014-01-01

    The number of transistors in integrated circuits doubles every two years, as stipulated by Moore's law, and this has been the driving force for the huge development of the microelectronics industry in the past 50 years - currently advanced to the nanometric scale.This e-book is dedicated to electronic noises and parasites, accounting for issues involving substrate coupling and interconnections, in the perspective of the 3D integration: a second track for enhancing integration, also compatible with Moore's law. This reference explains the modeling of 3D circuits without delving into the latest

  17. Electrospun gelatin biopapers as substrate for in vitro bilayer models of blood-brain barrier tissue.

    Science.gov (United States)

    Bischel, Lauren L; Coneski, Peter N; Lundin, Jeffrey G; Wu, Peter K; Giller, Carl B; Wynne, James; Ringeisen, Brad R; Pirlo, Russell K

    2016-04-01

    Gaining a greater understanding of the blood-brain barrier (BBB) is critical for improvement in drug delivery, understanding pathologies that compromise the BBB, and developing therapies to protect the BBB. In vitro human tissue models are valuable tools for studying these issues. The standard in vitro BBB models use commercially available cell culture inserts to generate bilayer co-cultures of astrocytes and endothelial cells (EC). Electrospinning can be used to produce customized cell culture substrates with optimized material composition and mechanical properties with advantages over off-the-shelf materials. Electrospun gelatin is an ideal cell culture substrate because it is a natural polymer that can aid cell attachment and be modified and degraded by cells. Here, we have developed a method to produce cell culture inserts with electrospun gelatin "biopaper" membranes. The electrospun fiber diameter and cross-linking method were optimized for the growth of primary human endothelial cell and primary human astrocyte bilayer co-cultures to model human BBB tissue. BBB co-cultures on biopaper were characterized via cell morphology, trans-endothelial electrical resistance (TEER), and permeability to FITC-labeled dextran and compared to BBB co-cultures on standard cell culture inserts. Over longer culture periods (up to 21 days), cultures on the optimized electrospun gelatin biopapers were found to have improved TEER, decreased permeability, and permitted a smaller separation between co-cultured cells when compared to standard PET inserts. © 2016 Wiley Periodicals, Inc.

  18. Molecular model of the specificity pocket of the hepatitis C virus protease: implications for substrate recognition.

    Science.gov (United States)

    Pizzi, E; Tramontano, A; Tomei, L; La Monica, N; Failla, C; Sardana, M; Wood, T; De Francesco, R

    1994-02-01

    We have built a model of the specificity pocket of the protease of hepatitis C virus on the basis of the known structures of trypsin-like serine proteases and of the conservation pattern of the protease sequences among various hepatitis C strains. The model allowed us to predict that the substrate of this protease should have a cysteine residue in position P1. This hypothesis was subsequently proved by N-terminal sequencing of two products of the protease. The success of this "blind" test increases our confidence in the overall correctness of our proposed alignment of the enzyme sequence with those of other proteases of known structure and constitutes a first step in the construction of a complete model of the viral protease domain.

  19. Structural differences of matrix metalloproteinases. Homology modeling and energy minimization of enzyme-substrate complexes

    DEFF Research Database (Denmark)

    Terp, G E; Christensen, I T; Jørgensen, Flemming Steen

    2000-01-01

    to the homology modeling of matrix metalloproteinases, exemplified by the modeling of MMP2, MMP9, MMP12 and MMP14 is described. The models were refined using an energy minimization procedure developed for matrix metalloproteinases. This procedure includes incorporation of parameters for zinc and calcium ions......Matrix metalloproteinases are extracellular enzymes taking part in the remodeling of extracellular matrix. The structures of the catalytic domain of MMP1, MMP3, MMP7 and MMP8 are known, but structures of enzymes belonging to this family still remain to be determined. A general approach...... differences between the eight enzyme-substrate complexes were studied with particular emphasis on the active site, and possible sites for obtaining selectivity among the MMP's are discussed. Differences in the P1' pocket are well-documented and have been extensively exploited in inhibitor design. The present...

  20. Characterization of the SUMO-binding activity of the myeloproliferative and mental retardation (MYM-type zinc fingers in ZNF261 and ZNF198.

    Directory of Open Access Journals (Sweden)

    Catherine M Guzzo

    Full Text Available SUMO-binding proteins interact with SUMO modified proteins to mediate a wide range of functional consequences. Here, we report the identification of a new SUMO-binding protein, ZNF261. Four human proteins including ZNF261, ZNF198, ZNF262, and ZNF258 contain a stretch of tandem zinc fingers called myeloproliferative and mental retardation (MYM-type zinc fingers. We demonstrated that MYM-type zinc fingers from ZNF261 and ZNF198 are necessary and sufficient for SUMO-binding and that individual MYM-type zinc fingers function as SUMO-interacting motifs (SIMs. Our binding studies revealed that the MYM-type zinc fingers from ZNF261 and ZNF198 interact with the same surface on SUMO-2 recognized by the archetypal consensus SIM. We also present evidence that MYM-type zinc fingers in ZNF261 contain zinc, but that zinc is not required for SUMO-binding. Immunofluorescence microscopy studies using truncated fragments of ZNF198 revealed that MYM-type zinc fingers of ZNF198 are necessary for localization to PML-nuclear bodies (PML-NBs. In summary, our studies have identified and characterized the SUMO-binding activity of the MYM-type zinc fingers in ZNF261 and ZNF198.

  1. Age-related changes of protein SUMOylation balance in the AβPP Tg2576 mouse model of Alzheimer's disease

    Science.gov (United States)

    Nisticò, Robert; Ferraina, Caterina; Marconi, Veronica; Blandini, Fabio; Negri, Lucia; Egebjerg, Jan; Feligioni, Marco

    2014-01-01

    Alzheimer's disease (AD) is a complex disorder that affects the central nervous system causing a severe neurodegeneration. This pathology affects an increasing number of people worldwide due to the overall aging of the human population. In recent years SUMO protein modification has emerged as a possible cellular mechanism involved in AD. Some of the proteins engaged in the physiopathological process of AD, like BACE1, GSK3-β tau, AβPP, and JNK, are in fact subject to protein SUMO modifications or interactions. Here, we have investigated the SUMO/deSUMOylation balance and SUMO-related proteins during the onset and progression of the pathology in the Tg2576 mouse model of AD. We examined four age-stages (1.5, 3, 6, 17 months old) and observed shows an increase in SUMO-1 protein conjugation at 3 and 6 months in transgenic mice with respect to WT in both cortex and hippocampus. Interestingly this is paralleled by increased expression levels of Ubc9 and SENP1 in both brain regions. At 6 months of age also the SUMO-1 mRNA resulted augmented. SUMO-2-ylation was surprisingly decreased in old transgenic mice and was unaltered in the other time windows. The fact that alterations in SUMO/deSUMOylation equilibrium occur from the early phases of AD suggests that global posttranslational modifications may play an important role in the mechanisms underlying disease pathogenesis, thus providing potential targets for pharmacological interventions. PMID:24778618

  2. Age-related changes of protein SUMOylation balance in the AβPP Tg2576 mouse model of Alzheimer's disease

    Directory of Open Access Journals (Sweden)

    Robert eNisticò

    2014-04-01

    Full Text Available Alzheimer's disease (AD is a complex disorder that affects the central nervous system causing a severe neurodegeneration. This pathology affects an increasing number of people worldwide due to the overall aging of the human population. In recent years SUMO protein modification has emerged as a possible cellular mechanism involved in AD. Some of the proteins engaged in the physiopathological process of AD, like BACE1, GSK3-β tau, AβPP and JNK, are in fact subject to protein SUMO modifications or interactions. Here, we have investigated the SUMO/deSUMOylation balance and SUMO-related proteins during the onset and progression of the pathology in the Tg2576 mouse model of AD. We examined four age-stages (1.5; 3; 6; 17 months old and observed shows an increase in SUMO-1 protein conjugation at 3 and 6 months in transgenic mice with respect to WT in both cortex and hippocampus. Interestingly this is paralleled by increased expression levels of Ubc9 and SENP1 in both brain regions. At 6 months of age also the SUMO-1 mRNA resulted augmented. SUMO-2-ylation was surprisingly decreased in old transgenic mice and was unaltered in the other time windows. The fact that alterations in SUMO/deSUMOylation equilibrium occur from the early phases of AD suggests that global posttranslational modifications may play an important role in the mechanisms underlying disease pathogenesis, thus providing potential targets for pharmacological interventions.

  3. An Immunosensing System Using Stilbene Glycoside as a Fluorogenic Substrate for an Enzymatic Reaction Model

    Directory of Open Access Journals (Sweden)

    Ya-Fei Tan

    2008-09-01

    Full Text Available A natural product, stilbene glycoside (2,3,5,4’-tetrahydroxydiphenylethylene-2-O-glucoside, TBG, has been evaluated for the first time as a potential substrate for horseradish peroxidase (HRP-catalyzed fluorogenic reactions. The properties of TBG as a fluorogenic substrate for HRP and its application in a fluorometric enzyme-linked immunosensing system were compared with commercially available substrates such as p-hydroxyphenylpropionic acid (pHPPA, chavicol and Amplex red using Brucella melitensis antibody (BrAb as a model analyte. The immunosensing body based on HRP-BrAb was constructed by dispersing graphite, BrAg and paraffin wax at room temperature. In a competitive immunoassay procedure, the BrAb competed with HRP-BrAb to react with the immobilized BrAg. In the enzymatic reaction, the binding HRP-BrAb on the sensing body surface can catalyze the polymerization reaction of TBG by H2O2 forming fluorescent dimers and causing an increase in fluorescence intensity. TBG showed comparable ability for HRP detection and its enzyme-linked immunosensing reaction system, in a linear detection ranging of 3.5´10-8~7.6´10-6g/L and with a detection limit of 1.7´10-9 g/L. The immobilized biocomposite surface could be regenerated with excellent reproducibility (RSD=3.8% by simply polishing with an alumina paper. The proposed immunosensing system has been used to determine the BrAb in rabbit serum samples with satisfactory results.

  4. Component characterization and predictive modeling for green roof substrates optimized to adsorb P and improve runoff quality: A review.

    Science.gov (United States)

    Jennett, Tyson S; Zheng, Youbin

    2017-12-14

    This review is a synthesis of the current knowledge regarding the effects of green roof substrate components and their retentive capacity for nutrients, particularly phosphorus (P). Substrates may behave as either sources or sinks of P depending on the components they are formulated from, and to date, the total P-adsorbing capacity of a substrate has not been quantified as the sum of the contributions of its components. Few direct links have been established among substrate components and their physicochemical characteristics that would affect P-retention. A survey of recent literature presented herein highlights the trends within individual component selection (clays and clay-like material, organics, conventional soil and sands, lightweight inorganics, and industrial wastes and synthetics) for those most common during substrate formulation internationally. Component selection will vary with respect to ease of sourcing component materials, cost of components, nutrient-retention capacity, and environmental sustainability. However, the number of distinct components considered for inclusion in green roof substrates continues to expand, as the desires of growers, material suppliers, researchers and industry stakeholders are incorporated into decision-making. Furthermore, current attempts to characterize the most often used substrate components are also presented whereby runoff quality is correlated to entire substrate performance. With the use of well-described characterization (constant capacitance model) and modeling techniques (the soil assemblage model), it is proposed that substrates optimized for P adsorption may be developed through careful selection of components with prior knowledge of their chemical properties, that may increase retention of P in plant-available forms, thereby reducing green roof fertilizer requirements and P losses in roof runoff. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. Modelling of asymmetrical interconnect T-tree laminated on flexible substrate

    Science.gov (United States)

    Ravelo, Blaise

    2015-11-01

    A fast and accurate behavioral modelling of asymmetrical microstrip tree printed on plastic substrate is investigated. The methodology for extracting the asymmetrical tree transfer responses based on the ABCD-matrix analysis is presented. The elements of the interconnect T-tree are constituted by transmission lines (TLs) defined by their characteristic impedance and physical length. The distributed tree network can be assumed as a single input multiple output (SIMO) topology. By considering the circuit equivalent between the electrical path from the tree input and output, the single input single output (SISO) simplified circuit can be established. In order to determine the frequency response of the interconnect tree system, the elementary TLs constituting the tree branches are modelled with their equivalent frequency dependent RLCG network. The novelty of the present paper is the application of the model to the microstrip structure printed on the plastic substrate by analyzing the influence of the metallization conductivity. As proof of concept (POC), a single input and three output distributed interconnect T-tree having branches presented physical lengths from 3 cm to 20 cm was designed. The POC was printed on the Cu metal deposited plastic Kapton substrate. Then, the frequency dependent per unit length resistance, inductance, capacitance and conductance of the elementary branches of the T-tree from DC to 10 GHz were extracted. By implementing the behavioral model of the circuit, the frequency- and time-domain responses of the proposed asymmetrical T-tree are computed. Then, the analyses of the asymmetrical T-tree responses in function of the thin film conductivity of the microstrip interconnect lines were discussed. In addition, time domain analysis enabling to predict the influence of the deposited metallic ink conductivity on the signal integrity is realized by considering a mixed signal corresponding to the digital data "010110000" having 0.5 Gbps rate

  6. SIZ1-Dependent Post-Translational Modification by SUMO Modulates Sugar Signaling and Metabolism in Arabidopsis thaliana.

    Science.gov (United States)

    Castro, Pedro Humberto; Verde, Nuno; Lourenço, Tiago; Magalhães, Alexandre Papadopoulos; Tavares, Rui Manuel; Bejarano, Eduardo Rodríguez; Azevedo, Herlânder

    2015-12-01

    Post-translational modification mechanisms function as switches that mediate the balance between optimum growth and the response to environmental stimuli, by regulating the activity of key proteins. SUMO (small ubiquitin-like modifier) attachment, or sumoylation, is a post-translational modification that is essential for the plant stress response, also modulating hormonal circuits to co-ordinate developmental processes. The Arabidopsis SUMO E3 ligase SAP and Miz 1 (SIZ1) is the major SUMO conjugation enhancer in response to stress, and is implicated in several aspects of plant development. Here we report that known SUMO targets are over-represented in multiple carbohydrate-related proteins, suggesting a functional link between sumoylation and sugar metabolism and signaling in plants. We subsequently observed that SUMO-conjugated proteins accumulate in response to high doses of sugar in a SIZ1-dependent manner, and that the null siz1 mutant displays increased expression of sucrose and starch catabolic genes and shows reduced starch levels. We demonstrated that SIZ1 controls germination time and post-germination growth via osmotic and sugar-dependent signaling, respectively. Glucose was specifically linked to SUMO-sugar interplay, with high levels inducing root growth inhibition and aberrant root hair morphology in siz1. The use of sugar analogs and sugar marker gene expression analysis allowed us to implicate SIZ1 in a signaling pathway dependent on glucose metabolism, probably involving modulation of SNF1-related kinase 1 (SnRK1) activity. © The Author 2015. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  7. Applying multibeam sonar and mathematical modeling for mapping seabed substrate and biota of offshore shallows

    Science.gov (United States)

    Herkül, Kristjan; Peterson, Anneliis; Paekivi, Sander

    2017-06-01

    Both basic science and marine spatial planning are in a need of high resolution spatially continuous data on seabed habitats and biota. As conventional point-wise sampling is unable to cover large spatial extents in high detail, it must be supplemented with remote sensing and modeling in order to fulfill the scientific and management needs. The combined use of in situ sampling, sonar scanning, and mathematical modeling is becoming the main method for mapping both abiotic and biotic seabed features. Further development and testing of the methods in varying locations and environmental settings is essential for moving towards unified and generally accepted methodology. To fill the relevant research gap in the Baltic Sea, we used multibeam sonar and mathematical modeling methods - generalized additive models (GAM) and random forest (RF) - together with underwater video to map seabed substrate and epibenthos of offshore shallows. In addition to testing the general applicability of the proposed complex of techniques, the predictive power of different sonar-based variables and modeling algorithms were tested. Mean depth, followed by mean backscatter, were the most influential variables in most of the models. Generally, mean values of sonar-based variables had higher predictive power than their standard deviations. The predictive accuracy of RF was higher than that of GAM. To conclude, we found the method to be feasible and with predictive accuracy similar to previous studies of sonar-based mapping.

  8. [The oxenoid model of the mechanism of activating molecular oxygen by cytochrome p450: the role of substrate structure].

    Science.gov (United States)

    Kuznetsov, A V

    1990-01-01

    The arene oxides formation energy for about 30 benzene derivatives were calculated in frames of MO LCAO method. The benzene derivatives are typical substrates of cytochrome P-450 catalyzed aromatic oxidation. The relationship between the formation energy of tetrahedral type arene oxides and the relative reactivity of substrates toward microsomal hydroxylation was found. The formation energy of arene oxides correlates also with toxicity of benzene derivatives. Some limitations of the oxenoid model are discussed.

  9. Molecular modelling studies of substrate binding to the lipase from Rhizomucor miehei

    Science.gov (United States)

    Yagnik, Asutosh T.; Littlechild, Jennifer A.; Turner, Nicholas J.

    1997-05-01

    Lipase enzymes have found increasingly widespread use, especially in biotransformation reactions in organic synthesis. Due to their efficiency and high enantioselectivity, they can be employed in a variety of reactions to carry out asymmetric hydrolyses, esterifications and transesterifications. However, the reasons for their stereospecificity have not been fully correlated with the enzyme structure. Employing molecular modelling techniques and existing experimental data, a transesterification reaction using Rhizomucor miehei lipase was studied. The results indicate that the major controlling factor for this reaction is hydrophobic in nature, providing support for previous literature hypotheses. In addition, computational experiments suggest that the origin of enantioselectivity is the formation of essential hydrogen bonds in and around the catalytic triad of active site residues. Only one enantiomer of the substrate is able to form these hydrogen bonds during the formation of the first tetrahedral transition state.

  10. Design and synthesis of two new substrates for model ribosomal reactions

    International Nuclear Information System (INIS)

    Bayryamov, S.; Vassilev, N.; Petkov, D.

    2008-01-01

    2 ' /3 ' -O-[2-N-p-nitrobenzoyl, 5-N-tert-butyloxycarbonyl-L-ornithinyl] 5 ' -O- pivaloyladenosine :(2 ' /3 ' -O-[ Bz (NO 2 )-Orn (Boc )]-5 ' -O-Piv-Ado) 1and its deoxy analogue - 3 ' -O-[2-N-p-nitrobenzoyl , 5-N-tert-butyloxycarbonyl-L-ornithinyl] 5 ' -O- pivaloyl 2 ' -deoxyadenosine: (3 ' -O-[Bz(NO 2 )-Orn(Boc)]-5 ' -O-Piv-2 ' -dAdo) 2 were synthesized as substrates for a model ribosome reaction. They were used to demonstrate the crucial role of A76 2 ' -OH of peptidyl-tRNA in the rate acceleration of peptide bond formation during protein biosynthesis. The synthesis was carried out using suitable combinations of the methods of peptide, nucleoside and nucleotide synthesis. (authors)

  11. Modeling the behavioral substrates of associate learning and memory - Adaptive neural models

    Science.gov (United States)

    Lee, Chuen-Chien

    1991-01-01

    Three adaptive single-neuron models based on neural analogies of behavior modification episodes are proposed, which attempt to bridge the gap between psychology and neurophysiology. The proposed models capture the predictive nature of Pavlovian conditioning, which is essential to the theory of adaptive/learning systems. The models learn to anticipate the occurrence of a conditioned response before the presence of a reinforcing stimulus when training is complete. Furthermore, each model can find the most nonredundant and earliest predictor of reinforcement. The behavior of the models accounts for several aspects of basic animal learning phenomena in Pavlovian conditioning beyond previous related models. Computer simulations show how well the models fit empirical data from various animal learning paradigms.

  12. Substrate turnover at low carbon concentrations in a model drinking water distribution system

    DEFF Research Database (Denmark)

    Boe-Hansen, Rasmus; Albrechtsen, Hans-Jørgen; Arvin, Erik

    2002-01-01

    utilisation and bacterial growth at low nutrient conditions in a model distribution system. The model system consisted of two loops in series, where flow rate and retention time were controlled independently. Spiking the drinking water of the model system with two different environmentally realistic......-saturation constant of 2.6 μg C/L. Only 2–4% of the carbon being degraded was incorporated into the biofilm. The results from our study suggest that the cellspecific respiration of biofilm was much higher than for suspended bacteria, and that the growth rate of the bulk phase bacteria was approximately 10 times...... concentrations of carbon allowed for a close monitoring of the kinetics of substrate turnover (less than 10 μg C/L 14C-benzoic acid was added). The mineralisation of benzoic acid was rapid and could be modelled by a no-growth Monod expression using a maximum degradation rate of 0.59 μg C/L/h and a half...

  13. Substrate turnover at low carbon concentrations in a model drinking water distribution system

    DEFF Research Database (Denmark)

    Boe-Hansen, Rasmus; Albrechtsen, Hans-Jørgen; Arvin, Erik

    2002-01-01

    utilisation and bacterial growth at low nutrient conditions in a model distribution system. The model system consisted of two loops in series, where flow rate and retention time were controlled independently. Spiking the drinking water of the model system with two different environmentally realistic...... concentrations of carbon allowed for a close monitoring of the kinetics of substrate turnover (less than 10 μg C/L 14C-benzoic acid was added). The mineralisation of benzoic acid was rapid and could be modelled by a no-growth Monod expression using a maximum degradation rate of 0.59 μg C/L/h and a half......-saturation constant of 2.6 μg C/L. Only 2–4% of the carbon being degraded was incorporated into the biofilm. The results from our study suggest that the cellspecific respiration of biofilm was much higher than for suspended bacteria, and that the growth rate of the bulk phase bacteria was approximately 10 times...

  14. Myxococcus xanthus gliding motors are elastically coupled to the substrate as predicted by the focal adhesion model of gliding motility.

    Science.gov (United States)

    Balagam, Rajesh; Litwin, Douglas B; Czerwinski, Fabian; Sun, Mingzhai; Kaplan, Heidi B; Shaevitz, Joshua W; Igoshin, Oleg A

    2014-05-01

    Myxococcus xanthus is a model organism for studying bacterial social behaviors due to its ability to form complex multi-cellular structures. Knowledge of M. xanthus surface gliding motility and the mechanisms that coordinated it are critically important to our understanding of collective cell behaviors. Although the mechanism of gliding motility is still under investigation, recent experiments suggest that there are two possible mechanisms underlying force production for cell motility: the focal adhesion mechanism and the helical rotor mechanism, which differ in the biophysics of the cell-substrate interactions. Whereas the focal adhesion model predicts an elastic coupling, the helical rotor model predicts a viscous coupling. Using a combination of computational modeling, imaging, and force microscopy, we find evidence for elastic coupling in support of the focal adhesion model. Using a biophysical model of the M. xanthus cell, we investigated how the mechanical interactions between cells are affected by interactions with the substrate. Comparison of modeling results with experimental data for cell-cell collision events pointed to a strong, elastic attachment between the cell and substrate. These results are robust to variations in the mechanical and geometrical parameters of the model. We then directly measured the motor-substrate coupling by monitoring the motion of optically trapped beads and find that motor velocity decreases exponentially with opposing load. At high loads, motor velocity approaches zero velocity asymptotically and motors remain bound to beads indicating a strong, elastic attachment.

  15. Myxococcus xanthus gliding motors are elastically coupled to the substrate as predicted by the focal adhesion model of gliding motility.

    Directory of Open Access Journals (Sweden)

    Rajesh Balagam

    2014-05-01

    Full Text Available Myxococcus xanthus is a model organism for studying bacterial social behaviors due to its ability to form complex multi-cellular structures. Knowledge of M. xanthus surface gliding motility and the mechanisms that coordinated it are critically important to our understanding of collective cell behaviors. Although the mechanism of gliding motility is still under investigation, recent experiments suggest that there are two possible mechanisms underlying force production for cell motility: the focal adhesion mechanism and the helical rotor mechanism, which differ in the biophysics of the cell-substrate interactions. Whereas the focal adhesion model predicts an elastic coupling, the helical rotor model predicts a viscous coupling. Using a combination of computational modeling, imaging, and force microscopy, we find evidence for elastic coupling in support of the focal adhesion model. Using a biophysical model of the M. xanthus cell, we investigated how the mechanical interactions between cells are affected by interactions with the substrate. Comparison of modeling results with experimental data for cell-cell collision events pointed to a strong, elastic attachment between the cell and substrate. These results are robust to variations in the mechanical and geometrical parameters of the model. We then directly measured the motor-substrate coupling by monitoring the motion of optically trapped beads and find that motor velocity decreases exponentially with opposing load. At high loads, motor velocity approaches zero velocity asymptotically and motors remain bound to beads indicating a strong, elastic attachment.

  16. Cancer cell mechanics with altered cytoskeletal behavior and substrate effects: A 3D finite element modeling study.

    Science.gov (United States)

    Katti, Dinesh R; Katti, Kalpana S

    2017-12-01

    A robust computational model of a cancer cell is presented using finite element modeling. The model accurately captures nuances of the various components of the cellular substructure. The role of degradation of cytoskeleton on overall elastic properties of the cancer cell is reported. The motivation for degraded cancer cellular substructure, the cytoskeleton is the observation that the innate mechanics of cytoskeleton is disrupted by various anti-cancer drugs as therapeutic treatments for the destruction of the cancer tumors. We report a significant influence on the degradation of the cytoskeleton on the mechanics of cancer cell. Further, a simulations based study is reported where we evaluate mechanical properties of the cancer cell attached to a variety of substrates. The loading of the cancer cell is less influenced by nature of the substrate, but low modulus substrates such as osteoblasts and hydrogels indicate a significant change in unloading behavior and also the plastic deformation. Overall, softer substrates such as osteoblasts and other bone cells result in a much altered unloading response as well as significant plastic deformation. These substrates are relevant to metastasis wherein certain type of cancers such as prostate and breast cancer cells migrate to the bone and colonize through mesenchymal to epithelial transition. The modeling study presented here is an important first step in the development of strong predictive methodologies for cancer progression. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Substrate reduction augments the efficacy of enzyme therapy in a mouse model of Fabry disease.

    Directory of Open Access Journals (Sweden)

    John Marshall

    Full Text Available Fabry disease is an X-linked glycosphingolipid storage disorder caused by a deficiency in the activity of the lysosomal hydrolase α-galactosidase A (α-gal. This deficiency results in accumulation of the glycosphingolipid globotriaosylceramide (GL-3 in lysosomes. Endothelial cell storage of GL-3 frequently leads to kidney dysfunction, cardiac and cerebrovascular disease. The current treatment for Fabry disease is through infusions of recombinant α-gal (enzyme-replacement therapy; ERT. Although ERT can markedly reduce the lysosomal burden of GL-3 in endothelial cells, variability is seen in the clearance from several other cell types. This suggests that alternative and adjuvant therapies may be desirable. Use of glucosylceramide synthase inhibitors to abate the biosynthesis of glycosphingolipids (substrate reduction therapy, SRT has been shown to be effective at reducing substrate levels in the related glycosphingolipidosis, Gaucher disease. Here, we show that such an inhibitor (eliglustat tartrate, Genz-112638 was effective at lowering GL-3 accumulation in a mouse model of Fabry disease. Relative efficacy of SRT and ERT at reducing GL-3 levels in Fabry mouse tissues differed with SRT being more effective in the kidney, and ERT more efficacious in the heart and liver. Combination therapy with ERT and SRT provided the most complete clearance of GL-3 from all the tissues. Furthermore, treatment normalized urine volume and uromodulin levels and significantly delayed the loss of a nociceptive response. The differential efficacies of SRT and ERT in the different tissues indicate that the combination approach is both additive and complementary suggesting the possibility of an improved therapeutic paradigm in the management of Fabry disease.

  18. Ubiquitin/SUMO modification regulates VHL protein stability and nucleocytoplasmic localization.

    Directory of Open Access Journals (Sweden)

    Qiliang Cai

    Full Text Available Functional inactivation of the von Hippel-Lindau (VHL tumor suppressor protein is linked to the development of several forms of cancer as well as oncogenic progression like sporadic renal clear-cell carcinomas (RCC. Despite the critical role played by VHL in destruction of hypoxia-inducible factor α (HIFα via ubiquitin-mediated proteolysis, very little is known about the post-translational modification which regulates VHL activity. Our previous study showed that the SUMO E3 ligase PIASy interacts with VHL and induces VHL SUMOylation on lysine residue 171 (Cai et al, PLoS ONE, 2010, 5(3:e9720. Here we further report that VHL also undergoes ubiquitylation on both lysine residues 171 and 196, which is blocked by PIASy. Moreover, using a VHL-SUMO1 or ubiquitin fusion protein, we found that ubiquitylated VHL is localized predominantly in the cytoplasm, while SUMOylated VHL results in increased VHL protein stability and nuclear redistribution. Interestingly, substitution of lysine 171 and 196 to arginine of VHL abrogates its inhibitory function on the transcriptional activity of HIFα, and tube formation in vitro. This demonstrates that post-translational modifications like ubiquitylation and SUMOylation contributes to VHL protein stability and nucleocytoplasmic shuttling, and that the overall function of VHL in tumor suppression may require a precise and dynamically regulated process which involves protein modification.

  19. Elg1, the major subunit of an alternative RFC complex, interacts with SUMO-processing proteins.

    Science.gov (United States)

    Parnas, Oren; Amishay, Rona; Liefshitz, Batia; Zipin-Roitman, Adi; Kupiec, Martin

    2011-09-01

    PCNA is a homotrimeric ring with important roles in DNA replication and repair. PCNA is loaded and unloaded by the RFC complex, which is composed of five subunits (Rfc1-5). Three additional complexes that share with RFC the small subunits (Rfc2-5) and contain alternative large subunits were found in yeast and other eukaryotes. We have recently reported that one of these, the Elg1-RFC complex, interacts with SUMOylated PCNA and may play a role in its unloading during DNA repair. Here we report that a yeast-two-hybrid screen with the N terminus of Elg1(which interacts with SUMOylated PCNA) uncovered interactions with proteins that belong to the SUMO pathway, including Slx5 and Slx8, which form an E3 ubiquitin ligase that ubiquitinates SUMOylated proteins. Mutations in SLX5 result in a genomic instability phenotype similar to that of elg1 mutants. The physical interaction between the N terminus of Elg1 and Slx5 is mediated by poly-SUMO chains but not by PCNA modifications, and requires Siz2, but not Siz1, activity. Thus our results highlight the many important roles played by Elg1, some of which are PCNA-dependent and some PCNA-independent. © 2011 Landes Bioscience

  20. It takes two to tango: Ubiquitin and SUMO in the DNA damage response

    Science.gov (United States)

    Bologna, Serena; Ferrari, Stefano

    2013-01-01

    The complexity of living cells is primarily determined by the genetic information encoded in DNA and gets fully disclosed upon translation. A major determinant of complexity is the reversible post-translational modification (PTM) of proteins, which generates variants displaying distinct biological properties such as subcellular localization, enzymatic activity and the ability to assemble in complexes. Decades of work on phosphorylation have unambiguously proven this concept. In recent years, the covalent attachment of Ubiquitin or Small Ubiquitin-like Modifiers (SUMO) to amino acid residues of target proteins has been recognized as another crucial PTM, re-directing protein fate and protein-protein interactions. This review focuses on the role of ubiquitylation and sumoylation in the control of DNA damage response proteins. To lay the ground, we begin with a description of ubiquitylation and sumoylation, providing established examples of DNA damage response elements that are controlled through these PTMs. We then examine in detail the role of PTMs in the cellular response to DNA double-strand breaks illustrating hierarchy, cross-talk, synergism or antagonism between phosphorylation, ubiquitylation and sumoylation. We conclude offering a perspective on Ubiquitin and SUMO pathways as targets in cancer therapy. PMID:23781231

  1. PIAS proteins are involved in the SUMO-1 modification, intracellular translocation and transcriptional repressive activity of RET finger protein

    International Nuclear Information System (INIS)

    Matsuura, Tetsuo; Shimono, Yohei; Kawai, Kumi; Murakami, Hideki; Urano, Takeshi; Niwa, Yasumasa; Goto, Hidemi; Takahashi, Masahide

    2005-01-01

    Ret finger protein (RFP) is a nuclear protein that is highly expressed in testis and in various tumor cell lines. RFP functions as a transcriptional repressor and associates with Enhancer of Polycomb 1 (EPC1), a member of the Polycomb group proteins, and Mi-2β, a main component of the nucleosome remodeling and deacetylase (NuRD) complex. We show that RFP binds with PIAS (protein inhibitor of activated STAT) proteins, PIAS1, PIAS3, PIASxα and PIASy at their carboxyl-terminal region and is covalently modified by SUMO-1 (sumoylation). PIAS proteins enhance the sumoylation of RFP in a dose-dependent manner and induce the translocation of RFP into nuclear bodies reminiscent of the PML bodies. In addition, co-expression of PIAS proteins or SUMO-1 strengthened the transcriptional repressive activity of RFP. Finally, our immunohistochemical results show that RFP, SUMO-1 and PIASy localize in a characteristic nuclear structure juxtaposed with the inner nuclear membrane (XY body) of primary spermatocytes in mouse testis. These results demonstrate that the intracellular location and the transcriptional activity of RFP are modified by PIAS proteins which possess SUMO E3 ligase activities and suggest that they may play a co-operative role in spermatogenesis

  2. SUMO proteases ULP1c and ULP1d are required for development and osmotic stress responses in Arabidopsis thaliana.

    Science.gov (United States)

    Castro, Pedro Humberto; Couto, Daniel; Freitas, Sara; Verde, Nuno; Macho, Alberto P; Huguet, Stéphanie; Botella, Miguel Angel; Ruiz-Albert, Javier; Tavares, Rui Manuel; Bejarano, Eduardo Rodríguez; Azevedo, Herlânder

    2016-09-01

    Sumoylation is an essential post-translational regulator of plant development and the response to environmental stimuli. SUMO conjugation occurs via an E1-E2-E3 cascade, and can be removed by SUMO proteases (ULPs). ULPs are numerous and likely to function as sources of specificity within the pathway, yet most ULPs remain functionally unresolved. In this report we used loss-of-function reverse genetics and transcriptomics to functionally characterize Arabidopsis thaliana ULP1c and ULP1d SUMO proteases. GUS reporter assays implicated ULP1c/d in various developmental stages, and subsequent defects in growth and germination were uncovered using loss-of-function mutants. Microarray analysis evidenced not only a deregulation of genes involved in development, but also in genes controlled by various drought-associated transcriptional regulators. We demonstrated that ulp1c ulp1d displayed diminished in vitro root growth under low water potential and higher stomatal aperture, yet leaf transpirational water loss and whole drought tolerance were not significantly altered. Generation of a triple siz1 ulp1c ulp1d mutant suggests that ULP1c/d and the SUMO E3 ligase SIZ1 may display separate functions in development yet operate epistatically in response to water deficit. We provide experimental evidence that Arabidopsis ULP1c and ULP1d proteases act redundantly as positive regulators of growth, and operate mainly as isopeptidases downstream of SIZ1 in the control of water deficit responses.

  3. Modeling of metal nanocluster growth on patterned substrates and surface pattern formation under ion bombardment

    Energy Technology Data Exchange (ETDEWEB)

    Numazawa, Satoshi

    2012-11-01

    This work addresses the metal nanocluster growth process on prepatterned substrates, the development of atomistic simulation method with respect to an acceleration of the atomistic transition states, and the continuum model of the ion-beam inducing semiconductor surface pattern formation mechanism. Experimentally, highly ordered Ag nanocluster structures have been grown on pre-patterned amorphous SiO{sub 2} surfaces by oblique angle physical vapor deposition at room temperature. Despite the small undulation of the rippled surface, the stripe-like Ag nanoclusters are very pronounced, reproducible and well-separated. The first topic is the investigation of this growth process with a continuum theoretical approach to the surface gas condensation as well as an atomistic cluster growth model. The atomistic simulation model is a lattice-based kinetic Monte-Carlo (KMC) method using a combination of a simplified inter-atomic potential and experimental transition barriers taken from the literature. An effective transition event classification method is introduced which allows a boost factor of several thousand compared to a traditional KMC approach, thus allowing experimental time scales to be modeled. The simulation predicts a low sticking probability for the arriving atoms, millisecond order lifetimes for single Ag monomers and {approx}1 nm square surface migration ranges of Ag monomers. The simulations give excellent reproduction of the experimentally observed nanocluster growth patterns. The second topic specifies the acceleration scheme utilized in the metallic cluster growth model. Concerning the atomistic movements, a classical harmonic transition state theory is considered and applied in discrete lattice cells with hierarchical transition levels. The model results in an effective reduction of KMC simulation steps by utilizing a classification scheme of transition levels for thermally activated atomistic diffusion processes. Thermally activated atomistic movements

  4. Homology modeling of Homo sapiens lipoic acid synthase: Substrate docking and insights on its binding mode.

    Science.gov (United States)

    Krishnamoorthy, Ezhilarasi; Hassan, Sameer; Hanna, Luke Elizabeth; Padmalayam, Indira; Rajaram, Rama; Viswanathan, Vijay

    2017-05-07

    Lipoic acid synthase (LIAS) is an iron-sulfur cluster mitochondrial enzyme which catalyzes the final step in the de novo pathway for the biosynthesis of lipoic acid, a potent antioxidant. Recently there has been significant interest in its role in metabolic diseases and its deficiency in LIAS expression has been linked to conditions such as diabetes, atherosclerosis and neonatal-onset epilepsy, suggesting a strong inverse correlation between LIAS reduction and disease status. In this study we use a bioinformatics approach to predict its structure, which would be helpful to understanding its role. A homology model for LIAS protein was generated using X-ray crystallographic structure of Thermosynechococcus elongatus BP-1 (PDB ID: 4U0P). The predicted structure has 93% of the residues in the most favour region of Ramachandran plot. The active site of LIAS protein was mapped and docked with S-Adenosyl Methionine (SAM) using GOLD software. The LIAS-SAM complex was further refined using molecular dynamics simulation within the subsite 1 and subsite 3 of the active site. To the best of our knowledge, this is the first study to report a reliable homology model of LIAS protein. This study will facilitate a better understanding mode of action of the enzyme-substrate complex for future studies in designing drugs that can target LIAS protein. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. Fibrinogen adsorption mechanisms at the gold substrate revealed by QCM-D measurements and RSA modeling.

    Science.gov (United States)

    Kubiak, Katarzyna; Adamczyk, Zbigniew; Cieśla, Michał

    2016-03-01

    Adsorption kinetics of fibrinogen at a gold substrate at various pHs was thoroughly studied using the QCM-D method. The experimental were interpreted in terms of theoretical calculations performed according to the random sequential adsorption model (RSA). In this way, the hydration functions and water factors of fibrinogen monolayers were quantitatively evaluated at various pHs. It was revealed that for the lower range of fibrinogen coverage the hydration function were considerably lower than previously obtained for the silica sensor [33]. The lower hydration of fibrinogen monolayers on the gold sensor was attributed to its higher roughness. However, for higher fibrinogen coverage the hydration functions for both sensors became identical exhibiting an universal behavior. By using the hydration functions, the fibrinogen adsorption/desorption runs derived from QCM-D measurements were converted to the Γd vs. the time relationships. This allowed to precisely determine the maximum coverage that varied between 1.6mgm(-2) at pH 3.5 and 4.5mgm(-2) at pH 7.4 (for ionic strength of 0.15M). These results agree with theoretical eRSA modeling and previous experimental data derived by using ellipsometry, OWLS and TIRF. Various fibrinogen adsorption mechanisms were revealed by exploiting the maximum coverage data. These results allow one to develop a method for preparing fibrinogen monolayers of well-controlled coverage and molecule orientation. Copyright © 2015 Elsevier B.V. All rights reserved.

  6. Size Matters: Observed and Modeled Camouflage Response of European Cuttlefish (Sepia officinalis) to Different Substrate Patch Sizes during Movement.

    Science.gov (United States)

    Josef, Noam; Berenshtein, Igal; Rousseau, Meghan; Scata, Gabriella; Fiorito, Graziano; Shashar, Nadav

    2016-01-01

    Camouflage is common throughout the phylogenetic tree and is largely used to minimize detection by predator or prey. Cephalopods, and in particular Sepia officinalis cuttlefish, are common models for camouflage studies. Predator avoidance behavior is particularly important in this group of soft-bodied animals that lack significant physical defenses. While previous studies have suggested that immobile cephalopods selectively camouflage to objects in their immediate surroundings, the camouflage characteristics of cuttlefish during movement are largely unknown. In a heterogenic environment, the visual background and substrate feature changes quickly as the animal swim across it, wherein substrate patch is a distinctive and high contrast patch of substrate in the animal's trajectory. In the current study, we examine the effect of substrate patch size on cuttlefish camouflage, and specifically the minimal size of an object for eliciting intensity matching response while moving. Our results indicated that substrate patch size has a positive effect on animal's reflectance change, and that the threshold patch size resulting in camouflage response falls between 10 and 19 cm (width). These observations suggest that the animal's length (7.2-12.3 cm mantle length in our case) serves as a possible threshold filter below which objects are considered irrelevant for camouflage, reducing the frequency of reflectance changes-which may lead to detection. Accordingly, we have constructed a computational model capturing the main features of the observed camouflaging behavior, provided for cephalopod camouflage during movement.

  7. Predicting the influence of a p2-symmetric substrate on molecular self-organization with an interaction-site model.

    Science.gov (United States)

    Rohr, Carsten; Balbás Gambra, Marta; Gruber, Kathrin; Höhl, Cornelia; Malarek, Michael S; Scherer, Lukas J; Constable, Edwin C; Franosch, Thomas; Hermann, Bianca A

    2011-02-14

    An interaction-site model can a priori predict molecular self-organisation on a new substrate in Monte Carlo simulations. This is experimentally confirmed with scanning tunnelling microscopy on Fréchet dendrons of a pentacontane template. Local and global ordering motifs, inclusion molecules and a rotated unit cell are correctly predicted.

  8. Modeling gravity effects on water retention and gas transport characteristics in plant growth substrates

    DEFF Research Database (Denmark)

    Deepagoda Thuduwe Kankanamge Kelum, Chamindu; Jones, Scott B.; Tuller, Markus

    2014-01-01

    utilization to conserve energy and to limit transport costs, native materials mined on Moon or Mars are of primary interest for plant growth media in a future outpost, while terrestrial porous substrates with optimal growth media characteristics will be useful for onboard plant growth during space missions....... Due to limited experimental opportunities and prohibitive costs, liquid and gas behavior in porous substrates under reduced gravity conditions has been less studied and hence remains poorly understood. Based on ground-based measurements, this study examined water retention, oxygen diffusivity and air...... permeability characteristics of six plant growth substrates for potential applications in space, including two terrestrial analogs for lunar and Martian soils and four particulate substrates widely used in reduced gravity experiments. To simulate reduced gravity water characteristics, the predictions...

  9. Measurement and thermal modeling of sapphire substrate temperature at III-Nitride MOVPE conditions

    Science.gov (United States)

    Creighton, J. Randall; Coltrin, Michael E.; Figiel, Jeffrey J.

    2017-04-01

    Growth rates and alloy composition of AlGaN grown by MOVPE is often very temperature dependent due to the presence of gas-phase parasitic chemical processes. These processes make wafer temperature measurement highly important, but in fact such measurements are very difficult because of substrate transparency in the near-IR ( 900 nm) where conventional pyrometers detect radiation. The transparency problem can be solved by using a mid-IR pyrometer operating at a wavelength ( 7500 nm) where sapphire is opaque. We employ a mid-IR pyrometer to measure the sapphire wafer temperature and simultaneously a near-IR pyrometer to measure wafer pocket temperature, while varying reactor pressure in both a N2 and H2 ambient. Near 1300 °C, as the reactor pressure is lowered from 300 Torr to 10 Torr the wafer temperature drops dramatically, and the ΔT between the pocket and wafer increases from 20 °C to 250 °C. Without the mid-IR pyrometer the large wafer temperature change with pressure would not have been noted. In order to explain this behavior we have developed a quasi-2D thermal model that includes a proper accounting of the pressure-dependent thermal contact resistance, and also accounts for sapphire optical transmission. The model and experimental results demonstrate that at most growth conditions the majority of the heat is transported from the wafer pocket to the wafer via gas conduction, in the free molecular flow limit. In this limit gas conductivity is independent of gap size but first order in pressure, and can quantitatively explain results from 20 to 300 Torr. Further analysis yields a measure of the thermal accommodation coefficients; α(H2) =0.23, α(N2) =0.50, which are in the range typically measured.

  10. Modeling of Axially Loaded Nanowires Embedded in Elastic Substrate Media with Inclusion of Nonlocal and Surface Effects

    Directory of Open Access Journals (Sweden)

    Suchart Limkatanyu

    2013-01-01

    Full Text Available Nonlocal and surface effects are incorporated into a bar-elastic substrate element to account for small-scale and size-dependent effects on axial responses of nanowires embedded in elastic substrate media. The virtual displacement principle, employed to consistently derive the governing differential equation as well as the boundary conditions, forms the core of the displacement-based finite element formulation of the nanowire-elastic substrate element. The element displacement shape functions, analytically derived based on homogeneous solution to the governing differential equilibrium equation of the problem, result in the exact element stiffness matrix and equivalent load vector. Two numerical simulations employing the proposed model are performed to study characteristics and behavior of the nanowire-substrate system. The first simulation involves investigation of responses of the wire embedded in elastic substrate. The second examines influences of several system parameters on the contact stiffness and reveals the size-dependent effect on the effective Young's modulus of the system.

  11. To implicate the private sector in funding: The Kyoto mechanisms and SUMO policies

    International Nuclear Information System (INIS)

    Leguet, Benoit; Morel, Romain

    2015-01-01

    Internationally set objectives in the fight against climate change cannot be reached without funding from the private sector. Public money, a scarce resource, must be used as best possible, in particular when it has a leverage effect on private funding. In this respect, feedback from the Kyoto Protocol's clean development mechanism is of interest. On the eve of the 2015 Paris Climate Conference, we must ramp up the mobilization of private resources. Smart unconventional monetary (SUMO) policies could help us toward this goal. Several countries have adopted such policies to cope with macro-economic circumstances or systemic risks. Is the destabilization of the climate not a risk of this sort?

  12. Estudo da utilização de filmes de quitosana como conservante de sumos

    OpenAIRE

    Costa, Diana Barbosa

    2015-01-01

    A quitosana é um polissacarídeo linear constituído por resíduos de D-glucosamina e N-acetil-D-glucosamina que, devido às suas propriedades biológicas e físico-químicas, tem surgido como uma estratégia alternativa e segura aos conservantes de origem sintética utilizados pela indústria dos sumos. Apesar da utilização deste filmes de quitosana-genipina ser favorável em vinhos, a sua incorporação em refrigerantes, com alto teor de açúcares, levou à sua destruição. Neste estudo, filmes à base de q...

  13. Soluble expression and purification of the recombinant bioactive peptide precursor BPP-1 in Escherichia coli using a cELP-SUMO dual fusion system.

    Science.gov (United States)

    Rao, Shengqi; Zang, Xiangyu; Yang, Zhenquan; Gao, Lu; Yin, Yongqi; Fang, Weiming

    2016-02-01

    A bioactive peptide precursor (BPP-1, 14.3 kDa/115AA), a newly designed polypeptide that may exert a potential antihypertensive effect in vivo, is composed of many different ACE inhibitory peptides and antioxidant peptides tandemly linked according to the restriction sites of gastrointestinal proteases. In this report, we present a novel method to obtain soluble BPP-1 in Escherichia coli using cationic elastin-like polypeptide and SUMO (cELP-SUMO) tags. The cELP-SUMO-tagged fusion protein was expressed in soluble form at 20 °C for 20 h. After purification based on the inverse transition cycling (ITC) method, the purified cELP-SUMO-CFPP fusion protein was subsequently cleaved by a SUMO protease to release the mature BPP-1. After a subsequent simple salt precipitation process, approximately 167.2 mg of recombinant BPP-1 was obtained from 1 l of bacterial culture with at least 92% purity. The molecular mass (Mr) of the recombinant BPP-1 was confirmed by MALDI-TOF MS to equal 14,347. The purified BPP-1 was subjected to simulated gastrointestinal digestion, and the resulting hydrolysates exhibited notable ACE inhibitory and antioxidant activities in vitro. This report provides the first description of the soluble production of a bioactive peptide multimer with potential ACE inhibitory and antioxidant activities in E. coli using a cELP-SUMO tag. Copyright © 2015 Elsevier Inc. All rights reserved.

  14. Substrate stiffness and oxygen as regulators of stem cell differentiation during skeletal tissue regeneration: a mechanobiological model.

    Directory of Open Access Journals (Sweden)

    Darren Paul Burke

    Full Text Available Extrinsic mechanical signals have been implicated as key regulators of mesenchymal stem cell (MSC differentiation. It has been possible to test different hypotheses for mechano-regulated MSC differentiation by attempting to simulate regenerative events such as bone fracture repair, where repeatable spatial and temporal patterns of tissue differentiation occur. More recently, in vitro studies have identified other environmental cues such as substrate stiffness and oxygen tension as key regulators of MSC differentiation; however it remains unclear if and how such cues determine stem cell fate in vivo. As part of this study, a computational model was developed to test the hypothesis that substrate stiffness and oxygen tension regulate stem cell differentiation during fracture healing. Rather than assuming mechanical signals act directly on stem cells to determine their differentiation pathway, it is postulated that they act indirectly to regulate angiogenesis and hence partially determine the local oxygen environment within a regenerating tissue. Chondrogenesis of MSCs was hypothesized to occur in low oxygen regions, while in well vascularised regions of the regenerating tissue a soft local substrate was hypothesised to facilitate adipogenesis while a stiff substrate facilitated osteogenesis. Predictions from the model were compared to both experimental data and to predictions of a well established computational mechanobiological model where tissue differentiation is assumed to be regulated directly by the local mechanical environment. The model predicted all the major events of fracture repair, including cartilaginous bridging, endosteal and periosteal bony bridging and bone remodelling. It therefore provides support for the hypothesis that substrate stiffness and oxygen play a key role in regulating MSC fate during regenerative events such as fracture healing.

  15. COMPARISON OF NORMALIZED MAXIMUM AEROBIC CAPACITY AND BODY COMPOSITION OF SUMO WRESTLERS TO ATHLETES IN COMBAT AND OTHER SPORTS

    Directory of Open Access Journals (Sweden)

    Matthew D. Beekley

    2006-07-01

    Full Text Available Sumo wrestling is unique in combat sport, and in all of sport. We examined the maximum aerobic capacity and body composition of sumo wrestlers and compared them to untrained controls. We also compared "aerobic muscle quality", meaning VO2max normalized to predicted skeletal muscle mass (SMM (VO2max /SMM, between sumo wrestlers and controls and among previously published data for male athletes from combat, aerobic, and power sports. Sumo wrestlers, compared to untrained controls, had greater (p < 0.05 body mass (mean ± SD; 117.0 ± 4.9 vs. 56.1 ± 9.8 kg, percent fat (24.0 ± 1.4 vs. 13.3 ± 4.5, fat-free mass (88.9 ± 4.2 vs. 48.4 �� 6.8 kg, predicted SMM (48.2 ± 2.9 vs. 20.6 ± 4.7 kg and absolute VO2max (3.6 ± 1.3 vs. 2.5 ± 0.7 L·min-1. Mean VO2max /SMM (ml·kg SMM-1·min-1 was significantly different (p < 0.05 among aerobic athletes (164.8 ± 18.3, combat athletes (which was not different from untrained controls; 131.4 ± 9.3 and 128.6 ± 13.6, respectively, power athletes (96.5 ± 5.3, and sumo wrestlers (71.4 ± 5.3. There was a strong negative correlation (r = - 0.75 between percent body fat and VO2max /SMM (p < 0.05. We conclude that sumo wrestlers have some of the largest percent body fat and fat-free mass and the lowest "aerobic muscle quality" (VO2max /SMM, both in combat sport and compared to aerobic and power sport athletes. Additionally, it appears from analysis of the relationship between SMM and absolute VO2max for all sports that there is a "ceiling" at which increases in SMM do not result in additional increases in absolute VO2max

  16. Structural diversity in the dandelion (Taraxacum officinale polyphenol oxidase family results in different responses to model substrates.

    Directory of Open Access Journals (Sweden)

    Mareike E Dirks-Hofmeister

    Full Text Available Polyphenol oxidases (PPOs are ubiquitous type-3 copper enzymes that catalyze the oxygen-dependent conversion of o-diphenols to the corresponding quinones. In most plants, PPOs are present as multiple isoenzymes that probably serve distinct functions, although the precise relationship between sequence, structure and function has not been addressed in detail. We therefore compared the characteristics and activities of recombinant dandelion PPOs to gain insight into the structure-function relationships within the plant PPO family. Phylogenetic analysis resolved the 11 isoenzymes of dandelion into two evolutionary groups. More detailed in silico and in vitro analyses of four representative PPOs covering both phylogenetic groups were performed. Molecular modeling and docking predicted differences in enzyme-substrate interactions, providing a structure-based explanation for grouping. One amino acid side chain positioned at the entrance to the active site (position HB2+1 potentially acts as a "selector" for substrate binding. In vitro activity measurements with the recombinant, purified enzymes also revealed group-specific differences in kinetic parameters when the selected PPOs were presented with five model substrates. The combination of our enzyme kinetic measurements and the in silico docking studies therefore indicate that the physiological functions of individual PPOs might be defined by their specific interactions with different natural substrates.

  17. Structural diversity in the dandelion (Taraxacum officinale) polyphenol oxidase family results in different responses to model substrates.

    Science.gov (United States)

    Dirks-Hofmeister, Mareike E; Singh, Ratna; Leufken, Christine M; Inlow, Jennifer K; Moerschbacher, Bruno M

    2014-01-01

    Polyphenol oxidases (PPOs) are ubiquitous type-3 copper enzymes that catalyze the oxygen-dependent conversion of o-diphenols to the corresponding quinones. In most plants, PPOs are present as multiple isoenzymes that probably serve distinct functions, although the precise relationship between sequence, structure and function has not been addressed in detail. We therefore compared the characteristics and activities of recombinant dandelion PPOs to gain insight into the structure-function relationships within the plant PPO family. Phylogenetic analysis resolved the 11 isoenzymes of dandelion into two evolutionary groups. More detailed in silico and in vitro analyses of four representative PPOs covering both phylogenetic groups were performed. Molecular modeling and docking predicted differences in enzyme-substrate interactions, providing a structure-based explanation for grouping. One amino acid side chain positioned at the entrance to the active site (position HB2+1) potentially acts as a "selector" for substrate binding. In vitro activity measurements with the recombinant, purified enzymes also revealed group-specific differences in kinetic parameters when the selected PPOs were presented with five model substrates. The combination of our enzyme kinetic measurements and the in silico docking studies therefore indicate that the physiological functions of individual PPOs might be defined by their specific interactions with different natural substrates.

  18. Mechanism of the Quorum-Quenching Lactonase (AiiA) from Bacillus thuringiensis. 2. Substrate Modeling and Active Site Mutations

    Energy Technology Data Exchange (ETDEWEB)

    Momb, Jessica; Wang, Canhui; Liu, Dali; Thomas, Pei W.; Petsko, Gregory A.; Guo, Hua; Ringe, Dagmar; Fast, Walter (UNM); (Brandeis); (Texas)

    2008-12-02

    The N-acyl-l-homoserine lactone hydrolases (AHL lactonases) have attracted considerable attention because of their ability to quench AHL-mediated quorum-sensing pathways in Gram-negative bacteria and because of their relation to other enzymes in the metallo-{beta}-lactamase superfamily. To elucidate the detailed catalytic mechanism of AHL lactonase, mutations are made on residues that presumably contribute to substrate binding and catalysis. Steady-state kinetic studies are carried out on both the wild-type and mutant enzymes using a spectrum of substrates. Two mutations, Y194F and D108N, present significant effects on the overall catalysis. On the basis of a high-resolution structural model of the enzyme-product complex, a hybrid quantum mechanical/molecular mechanical method is used to model the substrate binding orientation and to probe the effect of the Y194F mutation. Combining all experimental and computational results, we propose a detailed mechanism for the ring-opening hydrolysis of AHL substrates as catalyzed by the AHL lactonase from Bacillus thuringiensis. Several features of the mechanism that are also found in related enzymes are discussed and may help to define an evolutionary thread that connects the hydrolytic enzymes of this mechanistically diverse superfamily.

  19. Surface morphology modelling for the resistivity analysis of low temperature sputtered indium tin oxide thin films on polymer substrates

    International Nuclear Information System (INIS)

    Yin Xuesong; Tang Wu; Weng Xiaolong; Deng Longjiang

    2009-01-01

    Amorphous or weakly crystalline indium tin oxide (ITO) thin film samples have been prepared on polymethylmethacrylate and polyethylene terephthalate substrates by RF-magnetron sputtering at a low substrate temperature. The surface morphological and electrical properties of the ITO layers were measured by atomic force microscopy (AFM) and a standard four-point probe measurement. The effect of surface morphology on the resistivity of ITO thin films was studied, which presented some different variations from crystalline films. Then, a simplified film system model, including the substrate, continuous ITO layer and ITO surface grain, was proposed to deal with these correlations. Based on this thin film model and the AFM images, a quadratic potential was introduced to simulate the characteristics of the ITO surface morphology, and the classical Kronig-Penney model, the semiconductor electrical theory and the modified Neugebauer-Webb model were used to expound the detailed experimental results. The modelling equation was highly in accord with the experimental variations of the resistivity on the characteristics of the surface morphology.

  20. Phase-field model for deposition process of platinum nanoparticles on carbon substrate

    International Nuclear Information System (INIS)

    Yamakawa, S; Hyodo, S; Okazaki-Maeda, K; Kohyama, M

    2008-01-01

    Platinum supported on a carbon carrier is widely used as a catalyst for polymer electrolyte membrane fuel cells. The catalytic activity is significantly affected by the size distribution and morphologies of the platinum particles. The objective of this study is to extend the phase-field approach to describe the formation process of platinum particles onto the substrate. The microstructural evolution of a nanoparticle was represented by the temporal evolution of the field variables related to the platinum concentration, long-range crystallographic ordering and phase transition. First-principles calculations were performed in order to estimate the interaction energies between several different types of platinum clusters and a graphene sheet. The platinum density profile concentrated over the substrate surface led to the formation of three-dimensional islands in accordance with the Volmer-Weber mode of growth. The size distributions of the platinum particles were sensitive to the heterogeneity of the substrate surface and to the competitive nucleation and growth processes

  1. Trojan horse strategies used by pathogens to influence the small ubiquitin-like modifier (SUMO) system of host eukaryotic cells.

    Science.gov (United States)

    Békés, Miklós; Drag, Marcin

    2012-01-01

    A remarkable feature of pathogenic organisms is their ability to utilize the cellular machinery of host cells to their advantage in facilitating their survival and propagation. Posttranslational modification of proteins offers a quick way to achieve changes in the localization, binding partners or functions of a target protein. It is no surprise then that pathogens have evolved multiple ways to interfere with host posttranslational modifications and hijack them for their own purposes. Recently, modification of proteins by small ubiquitin-like modifier has emerged as an important posttranslational modification regulating transcription, DNA repair and cell division, and literature has started to emerge documenting how it could be utilized by pathogenic bacteria and viruses during infection. In this brief review, we focus on the host small ubiquitin-like modifier (SUMO) system and how disease causing agents influence SUMO conjugation and deconjugation, highlighting the common theme of global hypoSUMOylation upon infection by pathogens. Copyright © 2012 S. Karger AG, Basel.

  2. Modeling osmotic salinity effects on yield characteristics of substrate-grown greenhouse crops

    NARCIS (Netherlands)

    Sonneveld, C.; Bos, van den A.L.; Voogt, W.

    2004-01-01

    In a series of experiments with different osmotic potentials in the root environment, various vegetables, and ornamentals were grown in a substrate system. The osmotic potential was varied by addition of nutrients. Yield characteristics of the crop were related to the osmotic potential of the

  3. Amylolytic activity in fruits: comparison of different substrates and methods using banana as model.

    Science.gov (United States)

    Bassinello, Priscila Z; Cordenunsi, Beatriz R; Lajolo, Franco M

    2002-10-09

    Several methodologies have been developed for cereal amylolytic activity estimation, but there is lack of information about the application of these methods for fruits. Mature green banana fruit can achieve 20% of starch content which is degraded during the ripening period in a complex process involving alpha- and beta-amylases and alpha-1,4 and alpha-1,6-glucosidases, besides phosphorylases that can compete for the same substrates. Methods used to determine total hydrolytic activity and individual activity of enzymes involved in starch breakdown were compared for banana extracts in several ripening stages. Total hydrolytic activity was measured by DNS and iodometric methods. Endoamylolytic activity on amylose-azure substrate was also evaluated. BPNPG7 and PNPG5 chromogenic substrates were used for alpha- and beta-amylase activities, respectively. The results showed that methods that depend on the use of thermal treatment or on inhibitors to inactivate one of the enzymes were not adequate. The use of p-nitrophenol derivatives seemed to be the most specific, reproducible, and easiest method employed for single alpha- and beta-amylases activities determination in complex tissues. The DNS and iodometric methods can be used only for initial screenings of total hydrolytic activity, because the nonspecific substrate used in these procedures allows the action of more than one enzyme simultaneously.

  4. High-level expression and purification of soluble recombinant FGF21 protein by SUMO fusion in Escherichia coli

    Directory of Open Access Journals (Sweden)

    Huang Yadong

    2010-02-01

    Full Text Available Abstract Background Fibroblast growth factor 21 (FGF21 is a promising drug candidate to combat metabolic diseases. However, high-level expression and purification of recombinant FGF21 (rFGF21 in Escherichia coli (E. coli is difficult because rFGF21 forms inclusion bodies in the bacteria making it difficult to purify and obtain high concentrations of bioactive rFGF21. To overcome this problem, we fused the FGF21 with SUMO (Small ubiquitin-related modifier by polymerase chain reaction (PCR, and expressed the fused gene in E. coli BL21(DE3. Results By inducing with IPTG, SUMO-FGF21 was expressed at a high level. Its concentration reached 30% of total protein, and exceeded 95% of all soluble proteins. The fused protein was purified by DEAE sepharose FF and Ni-NTA affinity chromatography. Once cleaved by the SUMO protease, the purity of rFGF21 by high performance liquid chromatography (HPLC was shown to be higher than 96% with low endotoxin level (in vivo animal experiments showed that rFGF21 produced by using this method, could decrease the concentration of plasma glucose in diabetic rats by streptozotocin (STZ injection. Conclusions This study demonstrated that SUMO, when fused with FGF21, was able to promote its soluble expression of the latter in E. coli, making it more convenient to purify rFGF21 than previously. This may be a better method to produce rFGF21 for pharmaceutical research and development.

  5. Real Estate in the DNA Damage Response: Ubiquitin and SUMO Ligases Home in on DNA Double-Strand Breaks.

    Science.gov (United States)

    Dantuma, Nico P; Pfeiffer, Annika

    2016-01-01

    Ubiquitin and the ubiquitin-like modifier SUMO are intimately connected with the cellular response to various types of DNA damage. A striking feature is the local accumulation of these proteinaceous post-translational modifications in the direct vicinity to DNA double-strand breaks, which plays a critical role in the formation of ionizing radiation-induced foci. The functional significance of these modifications is the coordinated recruitment and removal of proteins involved in DNA damage signaling and repair in a timely manner. The central orchestrators of these processes are the ubiquitin and SUMO ligases that are responsible for accurately tagging a broad array of chromatin and chromatin-associated proteins thereby changing their behavior or destination. Despite many differences in the mode of action of these enzymes, they share some striking features that are of direct relevance for their function in the DNA damage response. In this review, we outline the molecular mechanisms that are responsible for the recruitment of ubiquitin and SUMO ligases and discuss the importance of chromatin proximity in this process.

  6. Finite dipole model for extreme near-field thermal radiation between a tip and planar SiC substrate

    Science.gov (United States)

    Jarzembski, Amun; Park, Keunhan

    2017-04-01

    Recent experimental studies have measured the infrared (IR) spectrum of tip-scattered near-field thermal radiation for a SiC substrate and observed up to a 50cm-1 redshift of the surface phonon polariton (SPhP) resonance peak [1,2]. However, the observed spectral redshift cannot be explained by the conventional near-field thermal radiation model based on the point dipole approximation. In the present work, a heated tip is modeled as randomly fluctuating point charges (or fluctuating finite dipoles) aligned along the primary axis of a prolate spheroid, and quasistatic tip-substrate charge interactions are considered to formulate the effective polarizability and self-interaction Green's function. The finite dipole model (FDM), combined with fluctuational electrodynamics, allows the computation of tip-plane thermal radiation in the extreme near-field (i.e., H / R ≲ 1 , where H is the tip-substrate gap distance and R is the tip radius), which cannot be calculated with the point dipole approximation. The FDM provides the underlying physics on the spectral redshift of tip-scattered near-field thermal radiation as observed in experiments. In addition, the SPhP peak in the near-field thermal radiation spectrum may split into two peaks as the gap distance decreases into the extreme near-field regime. This observation suggests that scattering-type spectroscopic measurements may not convey the full spectral features of tip-plane extreme near-field thermal radiation.

  7. Salinosporamides A and B Inhibit Proteasome Activity and Delay the Degradation of N-end Rule Model Substrates

    Energy Technology Data Exchange (ETDEWEB)

    Shin, Seungkyun; Bang, Daein; Choi, Wonhoon; Lee, Minjae [Kyung Hee Univ., Yongin (Korea, Republic of); Kim, Seonghwan; Oh, Dongchan [Seoul National Univ., Seoul (Korea, Republic of)

    2013-05-15

    The proteasome, which is highly evolutionarily conserved, is responsible for the degradation of most short-lived proteins in cells. Small-molecule inhibitors targeting the proteasome's degradative activity have been extensively developed as lead compounds for various human diseases. An exemplified molecule is bortezomib, which was approved by FDA in 2003 for the treatment of multiple myeloma. Here, using transiently and stably expressed N-end rule model substrates in mammalian cells, we evaluated and identified that salinosporamide A and salinosporamide B effectively inhibited the proteasomal degradation. Considering that a variety of proteasome substrates are implicated in the pathogenesis of many diseases, they have the potential to be clinically applicable as therapeutic agents.

  8. Smart unconventional monetary (SUMO) policies: giving impetus to green investment. Climate Report no. 46

    International Nuclear Information System (INIS)

    Ferron, Camille; Morel, Romain

    2014-07-01

    Today, given the amount of investment needed to reach a 2-degree emissions reduction target and the tight budgetary constraints of governments worldwide, public spending alone will not be sufficient alone. Therefore, there is a double need to not only shift private financial flows from 'brown' sectors to 'green' sectors, but also to leverage new sources of financing. Addressing the second challenge, this study reviews three families of proposed funding mechanisms based on unconventional monetary policies targeting 'green' or 'climate' investments. These 'Smart Unconventional Monetary' (or SUMO) policies include: (i) the use of Special Drawing Rights (SDRs) issued by the International Monetary Fund (IMF), (ii) green quantitative easing and (iii) the issuance of Carbon Certificates. Proponents of these mechanisms assert that they have a strong potential to provide substantial low-cost financing for green projects and reduce the risks linked to green investments for private investors. Furthermore, they could have further macro-economic co-benefits in specific circumstances. For example, implemented jointly with appropriate 'demand-side' mechanisms, a SUMO policy mechanism, even if short-term, could help trigger investment, bank lending and growth in Europe and pave the way for a longer-term green policies' framework. Nevertheless, this analysis has identified that the implementation of such mechanisms has a number of challenges to overcome. The first challenge is to convince policy makers that these mechanisms, even if they resort to unconventional monetary policies, will not lead to inflation. The second challenge is the difficulty to reach multilateral agreements in the short run, because of geopolitical and institutional barriers. The third challenge is the necessity to involve the private sector. Furthermore, to facilitate their contribution to low-carbon investment, this analysis suggests that

  9. Quantitative SUMO-1 modification of a vaccinia virus protein is required for its specific localization and prevents its self-association.

    Science.gov (United States)

    Palacios, Silvia; Perez, Laurent H; Welsch, Sonja; Schleich, Sibylle; Chmielarska, Katarzyna; Melchior, Frauke; Locker, Jacomine Krijnse

    2005-06-01

    Vaccinia virus (VV), the prototype member of the Poxviridae, a family of large DNA viruses, carries out DNA replication in specialized cytoplasmic sites that are enclosed by the rough endoplasmic reticulum (ER). We show that the VV gene product of A40R is quantitatively modified by SUMO-1, which is required for its localization to the ER-enclosed replication sites. Expression of A40R lacking SUMO-1 induced the formation of rod-shaped cytoplasmic aggregates. The latter likely consisted of polymers of nonsumoylated protein, because unmodified A40R interacted with itself, but not with the SUMO-1-conjugated protein. Using a bacterial sumoylation system, we furthermore show that unmodified A40R is mostly insoluble, whereas the modified form is completely soluble. By electron microscopy, the A40R rods seen in cells were associated with the cytosolic side of the ER and induced the apposition of several ER cisternae. A40R is the first example of a poxvirus protein to acquire SUMO-1. Its quantitative SUMO-1 modification is required for its proper localization to the viral "mini-nuclei" and prevents its self-association. The ability of the nonsumoylated A40R to bring ER membranes close together could suggest a role in the fusion of ER cisternae when these coalesce to enclose the VV replication sites.

  10. Catalytic Cycle of Haloalkane Dehalogenases Toward Unnatural Substrates Explored by Computational Modeling.

    Science.gov (United States)

    Marques, Sérgio M; Dunajova, Zuzana; Prokop, Zbynek; Chaloupkova, Radka; Brezovsky, Jan; Damborsky, Jiri

    2017-08-28

    The anthropogenic toxic compound 1,2,3-trichloropropane is poorly degradable by natural enzymes. We have previously constructed the haloalkane dehalogenase DhaA31 by focused directed evolution ( Pavlova, M. et al. Nat. Chem. Biol. 2009 , 5 , 727 - 733 ), which is 32 times more active than the wild-type enzyme and is currently the most active variant known against that substrate. Recent evidence has shown that the structural basis responsible for the higher activity of DhaA31 was poorly understood. Here we have undertaken a comprehensive computational study of the main steps involved in the biocatalytic hydrolysis of 1,2,3-trichloropropane to decipher the structural basis for such enhancements. Using molecular dynamics and quantum mechanics approaches we have surveyed (i) the substrate binding, (ii) the formation of the reactive complex, (iii) the chemical step, and (iv) the release of the products. We showed that the binding of the substrate and its transport through the molecular tunnel to the active site is a relatively fast process. The cleavage of the carbon-halogen bond was previously identified as the rate-limiting step in the wild-type. Here we demonstrate that this step was enhanced in DhaA31 due to a significantly higher number of reactive configurations of the substrate and a decrease of the energy barrier to the S N 2 reaction. C176Y and V245F were identified as the key mutations responsible for most of those improvements. The release of the alcohol product was found to be the rate-limiting step in DhaA31 primarily due to the C176Y mutation. Mutational dissection of DhaA31 and kinetic analysis of the intermediate mutants confirmed the theoretical observations. Overall, our comprehensive computational approach has unveiled mechanistic details of the catalytic cycle which will enable a balanced design of more efficient enzymes. This approach is applicable to deepen the biochemical knowledge of a large number of other systems and may contribute to robust

  11. Droplet evaporation on a horizontal substrate under gravity field by mesoscopic modeling.

    Science.gov (United States)

    Xie, Chiyu; Zhang, Jianying; Bertola, Volfango; Wang, Moran

    2016-02-01

    The evaporation of water drop deposited on a horizontal substrate is investigated using a lattice Boltzmann method (LBM) for multiphase flows with a large-density ratio. To account for the variation of evaporation flux distribution along the drop interface, a novel evaporation scheme is introduced into the LBM framework, and validated by comparison with experimental data. We aim at discovering the effect of gravity on the evaporating drop in detail, and various evaporation conditions are considered as well as different wetting properties of the substrates. An effective diameter is introduced as an indicator of the critical drop size under which gravity is negligible. Our results show that such critical diameter is much smaller than the capillary length, which has been widely accepted as the critical size in previous and current works. The critical diameter is found to be almost independent of the evaporation conditions and the surface wettability. A correlation between this critical diameter and the capillary length is also proposed for easy use in applications. Copyright © 2015 Elsevier Inc. All rights reserved.

  12. Complex SUMO-1 regulation of cardiac transcription factor Nkx2-5.

    Directory of Open Access Journals (Sweden)

    Mauro W Costa

    Full Text Available Reversible post-translational protein modifications such as SUMOylation add complexity to cardiac transcriptional regulation. The homeodomain transcription factor Nkx2-5/Csx is essential for heart specification and morphogenesis. It has been previously suggested that SUMOylation of lysine 51 (K51 of Nkx2-5 is essential for its DNA binding and transcriptional activation. Here, we confirm that SUMOylation strongly enhances Nkx2-5 transcriptional activity and that residue K51 of Nkx2-5 is a SUMOylation target. However, in a range of cultured cell lines we find that a point mutation of K51 to arginine (K51R does not affect Nkx2-5 activity or DNA binding, suggesting the existence of additional Nkx2-5 SUMOylated residues. Using biochemical assays, we demonstrate that Nkx2-5 is SUMOylated on at least one additional site, and this is the predominant site in cardiac cells. The second site is either non-canonical or a "shifting" site, as mutation of predicted consensus sites and indeed every individual lysine in the context of the K51R mutation failed to impair Nkx2-5 transcriptional synergism with SUMO, or its nuclear localization and DNA binding. We also observe SUMOylation of Nkx2-5 cofactors, which may be critical to Nkx2-5 regulation. Our data reveal highly complex regulatory mechanisms driven by SUMOylation to modulate Nkx2-5 activity.

  13. Acid-denatured Green Fluorescent Protein (GFP) as model substrate to study the chaperone activity of protein disulfide isomerase.

    Science.gov (United States)

    Mares, Rosa E; Meléndez-López, Samuel G; Ramos, Marco A

    2011-01-01

    Green fluorescent protein (GFP) has been widely used in several molecular and cellular biology applications, since it is remarkably stable in vitro and in vivo. Interestingly, native GFP is resistant to the most common chemical denaturants; however, a low fluorescence signal has been observed after acid-induced denaturation. Furthermore, this acid-denatured GFP has been used as substrate in studies of the folding activity of some bacterial chaperones and other chaperone-like molecules. Protein disulfide isomerase enzymes, a family of eukaryotic oxidoreductases that catalyze the oxidation and isomerization of disulfide bonds in nascent polypeptides, play a key role in protein folding and it could display chaperone activity. However, contrasting results have been reported using different proteins as model substrates. Here, we report the further application of GFP as a model substrate to study the chaperone activity of protein disulfide isomerase (PDI) enzymes. Since refolding of acid-denatured GFP can be easily and directly monitored, a simple micro-assay was used to study the effect of the molecular participants in protein refolding assisted by PDI. Additionally, the effect of a well-known inhibitor of PDI chaperone activity was also analyzed. Because of the diversity their functional activities, PDI enzymes are potentially interesting drug targets. Since PDI may be implicated in the protection of cells against ER stress, including cancer cells, inhibitors of PDI might be able to enhance the efficacy of cancer chemotherapy; furthermore, it has been demonstrated that blocking the reductive cleavage of disulfide bonds of proteins associated with the cell surface markedly reduces the infectivity of the human immunodeficiency virus. Although several high-throughput screening (HTS) assays to test PDI reductase activity have been described, we report here a novel and simple micro-assay to test the chaperone activity of PDI enzymes, which is amenable for HTS of PDI

  14. A Mathematical Model for Dynamic Simulation of Anaerobic Digestion of Complex Substrates

    DEFF Research Database (Denmark)

    Angelidaki, Irini; Ellegaard, L.; Ahring, Birgitte Kiær

    1993-01-01

    A mathematical model for anaerobic degradation of complex organic material, such as manure, has been developed. The model includes an enzymatic hydrolytic step and four bacterial steps and involves 12 chemical compounds. The model focuses on ammonia inhibition and includes a detailed description...... of pH and temperature characteristics in order to accurately simulate free ammonia concentration. Free ammonia and acetate constitute the primary modulating factors in the model. The model has been applied for the simulation of digestion of cattle manure in continuously stirred tank reactors (CSTRs......), and results compare favorably with experimental data. 0 1993 John Wiley & Sons, Inc. Key words: anaerobic digestion ammonia inhibition manure mathematical model....

  15. A stress inducible SUMO conjugating enzyme gene (SaSce9 from a grass halophyte Spartina alterniflora enhances salinity and drought stress tolerance in Arabidopsis

    Directory of Open Access Journals (Sweden)

    Karan Ratna

    2012-10-01

    Full Text Available Abstract Background SUMO (Small Ubiquitin related Modifier conjugation is a post translational regulatory process found in all eukaryotes, mediated by SUMO activating enzyme, SUMO conjugating enzyme, and SUMO ligase for the attachment of SUMO to its target protein. Although the mechanism for regulation of SUMO conjugation pathway genes under abiotic stress has been studied to certain extent, the role of SUMO conjugating enzyme in improving abiotic stress tolerance to plant is largely unexplored. Here, we have characterized a SUMO conjugating enzyme gene ‘SaSce9’ from a halophytic grass Spartina alterniflora and investigated its role in imparting abiotic stress tolerance. Results SaSce9 gene encodes for a polypeptide of 162 amino acids with a molecular weight of ~18 kD and isoelectric point 8.43. Amino acid sequence comparisons of SaSce9 with its orthologs from other plant species showed high degree (~85-93% of structural conservation among each other. Complementation analysis using yeast SCE mutant, Ubc9, revealed functional conservation of SaSce9 between yeast and S. alterniflora. SaSce9 transcript was inducible by salinity, drought, cold, and exogenously supplied ABA both in leaves and roots of S. alterniflora. Constitutive overexpression of SaSce9 in Arabidopsis through Agrobacterium mediated transformation improved salinity and drought tolerance of Arabidopsis. SaSce9 overexpressing Arabidopsis plants retained more chlorophyll and proline both under salinity and drought stress. SaSce9 transgenic plants accumulated lower levels of reactive oxygen under salinity stress. Expression analysis of stress responsive genes in SaSce9 Arabidopsis plants revealed the increased expression of antioxidant genes, AtSOD and AtCAT, ion antiporter genes, AtNHX1 and AtSOS1, a gene involved in proline biosynthesis, AtP5CS, and a gene involved in ABA dependent signaling pathway, AtRD22. Conclusions These results highlight the prospect of improving abiotic

  16. Small- and large-signal modeling of InP HBTs in transferred-substrate technology

    DEFF Research Database (Denmark)

    Johansen, Tom Keinicke; Rudolph, Matthias; Jensen, Thomas

    2014-01-01

    a direct parameter extraction methodology dedicated to III–V based HBTs. It is shown that the modeling of measured S-parameters can be improved in the millimeter-wave frequency range by augmenting the small-signal model with a description of AC current crowding. The extracted elements of the small......-signal model structure are employed as a starting point for the extraction of a large-signal model. The developed large-signal model for the TS-HBTs accurately predicts the DC over temperature and small-signal performance over bias as well as the large-signal performance at millimeter-wave frequencies....

  17. Influence of dormancy on microbial competition under intermittent substrate supply: insights from model simulations.

    Science.gov (United States)

    Stolpovsky, Konstantin; Fetzer, Ingo; Van Cappellen, Philippe; Thullner, Martin

    2016-06-01

    Most natural environments are characterized by frequent changes of their abiotic conditions. Microorganisms can respond to such changes by switching their physiological state between activity and dormancy allowing them to endure periods of unfavorable abiotic conditions. As a consequence, the competitiveness of microbial species is not simply determined by their growth performance under favorable conditions but also by their ability and readiness to respond to periods of unfavorable environmental conditions. The present study investigates the relevance of factors controlling the abundance and activity of individual bacterial species competing for an intermittently supplied substrate. For this purpose, numerical experiments were performed addressing the response of microbial systems to regularly applied feeding pulses. Simulation results show that community dynamics may exhibit a non-trivial link to the frequency of the external constraints and that for a certain combination of these environmental conditions coexistence of species is possible. The ecological implication of our results is that even non-dominant, neglected species can have a strong influence on realized species composition of dominant key species, due to their invisible presence enable the coexistence between important key species and by this affecting provided function of the system. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  18. The Smc5-Smc6 complex and SUMO modification of Rad52 regulates recombinational repair at the ribosomal gene locus

    DEFF Research Database (Denmark)

    Torres-Rosell, Jordi; Sunjevaric, Ivana; De Piccoli, Giacomo

    2007-01-01

    at an extranucleolar site. The nucleolar exclusion of Rad52 recombination foci entails Mre11 and Smc5-Smc6 complexes and depends on Rad52 SUMO (small ubiquitin-related modifier) modification. Remarkably, mutations that abrogate these activities result in the formation of Rad52 foci within the nucleolus and cause r......DNA hyperrecombination and the excision of extrachromosomal rDNA circles. Our study also suggests a key role of sumoylation for nucleolar dynamics, perhaps in the compartmentalization of nuclear activities....

  19. DNA damage-inducible SUMOylation of HERC2 promotes RNF8 binding via a novel SUMO-binding Zinc finger

    DEFF Research Database (Denmark)

    Danielsen, Jannie Michaela Rendtlew; Povlsen, Lou Klitgaard; Villumsen, Bine Hare

    2012-01-01

    Nonproteolytic ubiquitylation of chromatin surrounding deoxyribonucleic acid (DNA) double-strand breaks (DSBs) by the RNF8/RNF168/HERC2 ubiquitin ligases facilitates restoration of genome integrity by licensing chromatin to concentrate genome caretaker proteins near the lesions. In parallel......, SUMOylation of so-far elusive upstream DSB regulators is also required for execution of this ubiquitin-dependent chromatin response. We show that HERC2 and RNF168 are novel DNA damage-dependent SUMOylation targets in human cells. In response to DSBs, both HERC2 and RNF168 were specifically modified with SUMO1...

  20. KAP1 Is a Host Restriction Factor That Promotes Human Adenovirus E1B-55K SUMO Modification.

    Science.gov (United States)

    Bürck, Carolin; Mund, Andreas; Berscheminski, Julia; Kieweg, Lisa; Müncheberg, Sarah; Dobner, Thomas; Schreiner, Sabrina

    2016-01-15

    Once transported to the replication sites, human adenoviruses (HAdVs) need to ensure decondensation and transcriptional activation of their viral genomes to synthesize viral proteins and initiate steps to reprogram the host cell for viral replication. These early stages during adenoviral infection are poorly characterized but represent a decisive moment in the establishment of a productive infection. Here, we identify a novel host viral restriction factor, KAP1. This heterochromatin-associated transcription factor regulates the dynamic organization of the host chromatin structure via its ability to influence epigenetic marks and chromatin compaction. In response to DNA damage, KAP1 is phosphorylated and functionally inactive, resulting in chromatin relaxation. We discovered that KAP1 posttranslational modification is dramatically altered during HAdV infection to limit the antiviral capacity of this host restriction factor, which represents an essential step required for efficient viral replication. Conversely, we also observed during infection an HAdV-mediated decrease of KAP1 SUMO moieties, known to promote chromatin decondensation events. Based on our findings, we provide evidence that HAdV induces KAP1 deSUMOylation to minimize epigenetic gene silencing and to promote SUMO modification of E1B-55K by a so far unknown mechanism. Here we describe a novel cellular restriction factor for human adenovirus (HAdV) that sheds light on very early modulation processes in viral infection. We reported that chromatin formation and cellular SWI/SNF chromatin remodeling play key roles in HAdV transcriptional regulation. We observed that the cellular chromatin-associated factor and epigenetic reader SPOC1 represses HAdV infection and gene expression. Here, we illustrate the role of the SPOC1-interacting factor KAP1 during productive HAdV growth. KAP1 binds to the viral E1B-55K protein, promoting its SUMO modification, therefore illustrating a crucial step for efficient viral

  1. Offshore Substrate

    Data.gov (United States)

    California Department of Resources — This shapefile displays the distribution of substrate types from Pt. Arena to Pt. Sal in central/northern California. Originally this data consisted of seven paper...

  2. Structural basis of regulation and substrate specificity of protein kinase CK2 deduced from the modeling of protein-protein interactions

    Directory of Open Access Journals (Sweden)

    Srinivasan N

    2003-05-01

    Full Text Available Abstract Background Protein Kinase Casein Kinase 2 (PKCK2 is an ubiquitous Ser/Thr kinase expressed in all eukaryotes. It phosphorylates a number of proteins involved in various cellular processes. PKCK2 holoenzyme is catalytically active tetramer, composed of two homologous or identical and constitutively active catalytic (α and two identical regulatory (β subunits. The tetramer cannot phosphorylate some substrates that can be phosphorylated by PKCK2α in isolation. The present work explores the structural basis of this feature using computational analysis and modeling. Results We have initially built a model of PKCK2α bound to a substrate peptide with a conformation identical to that of the substrates in the available crystal structures of other kinases complexed with the substrates/ pseudosubstrates. In this model however, the fourth acidic residue in the consensus pattern of the substrate, S/T-X-X-D/E where S/T is the phosphorylation site, did not result in interaction with the active form of PKCK2α and is highly solvent exposed. Interaction of the acidic residue is observed if the substrate peptide adopts conformations as seen in β turn, α helix, or 310 helices. This type of conformation is observed and accommodated well by PKCK2α in calmodulin where the phosphorylation site is at the central helix. PP2A carries sequence patterns for PKCK2α phosphorylation. While the possibility of PP2A being phosphorylated by PKCK2 has been raised in the literature we use the model of PP2A to generate a model of PP2A-PKCK2α complex. PKCK2β undergoes phosphorylation by holoenzyme at the N-terminal region, and is accommodated very well in the limited space available at the substrate-binding site of the holoenzyme while the space is insufficient to accommodate the binding of PP2A or calmodulin in the holoenzyme. Conclusion Charge and shape complimentarity seems to play a role in substrate recognition and binding to PKCK2α, along with the consensus

  3. The copper spoil heap Knappenberg, Austria, as a model for metal habitats – Vegetation, substrate and contamination

    Energy Technology Data Exchange (ETDEWEB)

    Adlassnig, Wolfram; Weiss, Yasmin S. [University of Vienna, Core Facility Cell Imaging and Ultrastructure Research, Althanstraße 14, A-1090 Vienna (Austria); Sassmann, Stefan [University of Vienna, Core Facility Cell Imaging and Ultrastructure Research, Althanstraße 14, A-1090 Vienna (Austria); University of Exeter, College of Life and Environmental Sciences, Biosciences, Stocker Road, Exeter EX4 4QD (United Kingdom); Steinhauser, Georg [Leibniz University Hannover, Institute of Radioecology and Radiation Protection, Herrenhäuser Straße 2, D30419 Hannover (Germany); Hofhansl, Florian [University of Vienna, Department of Microbiology and Ecosystem Science, Althanstraße 14, A-1090 Vienna (Austria); Instituto Nacional de Pesquisas da Amazônia, Coordenação de Dinâmica Ambiental, Manaus (Brazil); Baumann, Nils [Helmholtz-Zentrum Dresden-Rossendorf, Division of Biogeochemistry, Bautzner Landstraße 400, D-01328 Dresden (Germany); Lichtscheidl, Irene K. [University of Vienna, Core Facility Cell Imaging and Ultrastructure Research, Althanstraße 14, A-1090 Vienna (Austria); Lang, Ingeborg, E-mail: ingeborg.lang@univie.ac.at [University of Vienna, Core Facility Cell Imaging and Ultrastructure Research, Althanstraße 14, A-1090 Vienna (Austria)

    2016-09-01

    Historic mining in the Eastern Alps has left us with a legacy of numerous spoil heaps hosting specific, metal tolerant vegetation. Such habitats are characterized by elevated concentrations of toxic elements but also by high irradiation, a poorly developed substrate or extreme pH of the soil. This study investigates the distribution of vascular plants, mosses and lichens on a copper spoil heap on the ore bearing Knappenberg formed by Prebichl Layers and Werfener Schist in Lower Austria. It serves as a model for discriminating between various ecological traits and their effects on vegetation. Five distinct clusters were distinguished: (1) The bare, metal rich Central Spoil Heap was only colonised by highly resistant specialists. (2) The Northern and (3) Southern Peripheries contained less copper; the contrasting vegetation was best explained by the different microclimate. (4) A forest over acidic bedrock hosted a vegetation overlapping with the periphery of the spoil heap. (5) A forest over calcareous bedrock was similar to the spoil heap with regard to pH and humus content but hosted a vegetation differing strongly to all other habitats. Among the multiple toxic elements at the spoil heap, only Cu seems to exert a crucial influence on the vegetation pattern. Besides metal concentrations, irradiation, humidity, humus, pH and grain size distribution are important for the establishment of a metal tolerant vegetation. The difference between the species poor Northern and the diverse Southern Periphery can be explained by the microclimate rather than by the substrate. All plant species penetrating from the forest into the periphery of the spoil heap originate from the acidic but not from the calcareous bedrock. - Highlights: • Strong impact on plant diversity by isolation and extreme abiotic conditions • Both, microclimate and substrate explain species distribution. • Increased cellular metal tolerance of plants from the Central Spoil Heap • Among toxic elements

  4. The SUMO project I. A survey of multiple populations in globular clusters

    Science.gov (United States)

    Monelli, M.; Milone, A. P.; Stetson, P. B.; Marino, A. F.; Cassisi, S.; del Pino Molina, A.; Salaris, M.; Aparicio, A.; Asplund, M.; Grundahl, F.; Piotto, G.; Weiss, A.; Carrera, R.; Cebrián, M.; Murabito, S.; Pietrinferni, A.; Sbordone, L.

    2013-05-01

    We present a general overview and the first results of the SUMO project (a SUrvey of Multiple pOpulations in Globular Clusters). The objective of this survey is the study of multiple stellar populations in the largest sample of globular clusters homogeneously analysed to date. To this aim we obtained high signal-to-noise (S/N > 50) photometry for main sequence stars with mass down to ˜0.5 M⊙ in a large sample of clusters using both archival and proprietary U, B, V and I data from ground-based telescopes. In this paper, we focus on the occurrence of multiple stellar populations in 23 clusters. We define a new photometric index, cU, B, I = (U - B) - (B - I), which turns out to be very effective for identifying multiple sequences along the red giant branch (RGB). We found that in the V-cU, B, I diagram all clusters presented in this paper show broadened or multimodal RGBs, with the presence of two or more components. We found a direct connection with the chemical properties of different sequences, which display different abundances of light elements (O, Na, C, N and Al). The cU, B, I index is also a powerful tool for identifying distinct sequences of stars along the horizontal branch and, for the first time in the case of NGC 104 (47 Tuc), along the asymptotic giant branch. Our results demonstrate that (i) the presence of more than two stellar populations is a common feature amongst globular clusters, as already highlighted in previous work; (ii) multiple sequences with different chemical contents can be easily identified by using standard Johnson photometry obtained with ground-based facilities; (iii) in the study of globular cluster multiple stellar populations the cU, B, I index is an alternative to spectroscopy, and has the advantage of larger statistics.

  5. 8051 Mikrodenetleyicili Bir Sumo Robot Tasarımı ve Uygulaması

    Directory of Open Access Journals (Sweden)

    Mehmet ALBAYRAK

    2009-04-01

    Full Text Available Bu çalısmada, 8051 mikrodenetleyici kontrollü bir sumo robotun mekanik tasarımı, kontrol kartı ve yazılımı gerçeklestirilmistir. Robot, yarısma ve egitim amaçlı tasarlandıgı için hücum amaçlı strateji içeren yazılım gelistirilerek yüklenmistir. 8051 mikrodenetleyici içindeki kontrol yazılımı PC 'nin seri portuna baglı mikrodenetleyici programlama kartına takılıp, kolaylıkla güncellenebildigi için yazılım stratejisi her yarısma için degistirilebilir niteliktedir. Microdenetleyici yazılımı μVision Keil derleyicisinde C kodu kullanılarak hazırlanmıstır. Mekanik tasarım asamasında robot dıs yüzeyinin darbelere dayanıklı malzemeden seçilmesine ve tekerleklerin sürtünmesinin fazla (kaymaz olmasına özen gösterilmistir. Robotun gücünü belirlenen agırlık sınırları içinde en fazla hale getirebilmek için 4 ayrı disli DC motor ve 4 amperlik akü kullanılmıstır. Rakip algılama mesafe sensörü ve kontrast sensörü (beyaz algılama seçiminde cevap verme süresi çok az olan sensörler tercih edilmistir.

  6. The identification of new substrates of human DHRS7 by molecular modeling and in vitro testing

    Czech Academy of Sciences Publication Activity Database

    Zemanová, L.; Palani, Kirubakaran; Pato, I. H.; Štambergová, H.; Vondrášek, Jiří

    2017-01-01

    Roč. 105, č. 1 (2017), s. 171-182 ISSN 0141-8130 R&D Projects: GA MŠk(CZ) LM2015047 Institutional support: RVO:61388963 Keywords : DHRS7 * SDR superfamily * SDR34C1 * homology modeling * molecular modeling Subject RIV: CE - Biochemistry OBOR OECD: Biochemistry and molecular biology Impact factor: 3.671, year: 2016

  7. A whole-body model for glycogen regulation reveals a critical role for substrate cycling in maintaining blood glucose homeostasis.

    Directory of Open Access Journals (Sweden)

    Ke Xu

    2011-12-01

    Full Text Available Timely, and sometimes rapid, metabolic adaptation to changes in food supply is critical for survival as an organism moves from the fasted to the fed state, and vice versa. These transitions necessitate major metabolic changes to maintain energy homeostasis as the source of blood glucose moves away from ingested carbohydrates, through hepatic glycogen stores, towards gluconeogenesis. The integration of hepatic glycogen regulation with extra-hepatic energetics is a key aspect of these adaptive mechanisms. Here we use computational modeling to explore hepatic glycogen regulation under fed and fasting conditions in the context of a whole-body model. The model was validated against previous experimental results concerning glycogen phosphorylase a (active and glycogen synthase a dynamics. The model qualitatively reproduced physiological changes that occur during transition from the fed to the fasted state. Analysis of the model reveals a critical role for the inhibition of glycogen synthase phosphatase by glycogen phosphorylase a. This negative regulation leads to high levels of glycogen synthase activity during fasting conditions, which in turn increases substrate (futile cycling, priming the system for a rapid response once an external source of glucose is restored. This work demonstrates that a mechanistic understanding of the design principles used by metabolic control circuits to maintain homeostasis can benefit from the incorporation of mathematical descriptions of these networks into "whole-body" contextual models that mimic in vivo conditions.

  8. Modelling the anaerobic digestion of solid organic waste - Substrate characterisation method for ADM1 using a combined biochemical and kinetic parameter estimation approach.

    Science.gov (United States)

    Poggio, D; Walker, M; Nimmo, W; Ma, L; Pourkashanian, M

    2016-07-01

    This work proposes a novel and rigorous substrate characterisation methodology to be used with ADM1 to simulate the anaerobic digestion of solid organic waste. The proposed method uses data from both direct substrate analysis and the methane production from laboratory scale anaerobic digestion experiments and involves assessment of four substrate fractionation models. The models partition the organic matter into a mixture of particulate and soluble fractions with the decision on the most suitable model being made on quality of fit between experimental and simulated data and the uncertainty of the calibrated parameters. The method was tested using samples of domestic green and food waste and using experimental data from both short batch tests and longer semi-continuous trials. The results showed that in general an increased fractionation model complexity led to better fit but with increased uncertainty. When using batch test data the most suitable model for green waste included one particulate and one soluble fraction, whereas for food waste two particulate fractions were needed. With richer semi-continuous datasets, the parameter estimation resulted in less uncertainty therefore allowing the description of the substrate with a more complex model. The resulting substrate characterisations and fractionation models obtained from batch test data, for both waste samples, were used to validate the method using semi-continuous experimental data and showed good prediction of methane production, biogas composition, total and volatile solids, ammonia and alkalinity. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  9. MOLECULAR MODELLING OF HUMAN ALDEHYDE OXIDASE AND IDENTIFICATION OF THE KEY INTERACTIONS IN THE ENZYME-SUBSTRATE COMPLEX

    Directory of Open Access Journals (Sweden)

    Siavoush Dastmalchi

    2005-05-01

    Full Text Available Aldehyde oxidase (EC 1.2.3.1, a cytosolic enzyme containing FAD, molybdenum and iron-sulphur cluster, is a member of non-cytochrome P-450 enzymes called molybdenum hydroxylases which is involved in the metabolism of a wide range of endogenous compounds and many drug substances. Drug metabolism is one of the important characteristics which influences many aspects of a therapeutic agent such as routes of administration, drug interaction and toxicity and therefore, characterisation of the key interactions between enzymes and substrates is very important from drug development point of view. The aim of this study was to generate a three-dimensional model of human aldehyde oxidase (AO in order to assist us to identify the mode of interaction between enzyme and a set of phethalazine/quinazoline derivatives. Both sequence-based (BLAST and inverse protein fold recognition methods (THREADER were used to identify the crystal structure of bovine xanthine dehydrogenase (pdb code of 1FO4 as the suitable template for comparative modelling of human AO. Model structure was generated by aligning and then threading the sequence of human AO onto the template structure, incorporating the associated cofactors, and molecular dynamics simulations and energy minimization using GROMACS program. Different criteria which were measured by the PROCHECK, QPACK, VERIFY-3D were indicative of a proper fold for the predicted structural model of human AO. For example, 97.9 percentages of phi and psi angles were in the favoured and most favoured regions in the ramachandran plot, and all residues in the model are assigned environmentally positive compatibility scores. Further evaluation on the model quality was performed by investigation of AO-mediated oxidation of a set of phthalazine/quinazoline derivatives to develop QSAR model capable of describing the extent of the oxidation. Substrates were aligned by docking onto the active site of the enzyme using GOLD technology and then

  10. SUMO2/3 modification of activating transcription factor 5 (ATF5) controls its dynamic translocation at the centrosome.

    Science.gov (United States)

    Yuan, Yunsheng; Gaither, Kari; Kim, Eugene; Liu, Edward; Hu, Ming; Lengel, Kathy; Qian, Dongmeng; Xu, Yidi; Wang, Bin; Knipprath, Henning; Liu, David X

    2018-02-23

    Activating transcription factor 5 (ATF5) is a member of the ATF/cAMP response element-binding protein family of transcription factors. ATF5 regulates stress responses and cell survival, proliferation, and differentiation and also plays a role in viral infections, cancer, diabetes, schizophrenia, and the olfactory system. Moreover, it was found to also have a critical cell cycle-dependent structural function at the centrosome. However, the mechanism that controls the localization of ATF5 at the centrosome is unclear. Here we report that ATF5 is small ubiquitin-like modifier (SUMO) 2/3-modified at a conserved SUMO-targeting consensus site in various types of mammalian cells. We found that SUMOylation of ATF5 is elevated in the G 1 phase of the cell cycle and diminished in the G 2 /M phase. ATF5 SUMOylation disrupted the interaction of ATF5 with several centrosomal proteins and dislodged ATF5 from the centrosome at the end of the M phase. Of note, blockade of ATF5 SUMOylation deregulated the centrosome cycle, impeded ATF5 translocation from the centrosome, and caused genomic instability and G 2 /M arrest in HeLa cells. Our results indicate that ATF5 SUMOylation is an essential mechanism that regulates ATF5 localization and function at the centrosome. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

  11. Application of Thermal Network Model to Transient Thermal Analysis of Power Electronic Package Substrate

    Directory of Open Access Journals (Sweden)

    Masaru Ishizuka

    2011-01-01

    Full Text Available In recent years, there is a growing demand to have smaller and lighter electronic circuits which have greater complexity, multifunctionality, and reliability. High-density multichip packaging technology has been used in order to meet these requirements. The higher the density scale is, the larger the power dissipation per unit area becomes. Therefore, in the designing process, it has become very important to carry out the thermal analysis. However, the heat transport model in multichip modules is very complex, and its treatment is tedious and time consuming. This paper describes an application of the thermal network method to the transient thermal analysis of multichip modules and proposes a simple model for the thermal analysis of multichip modules as a preliminary thermal design tool. On the basis of the result of transient thermal analysis, the validity of the thermal network method and the simple thermal analysis model is confirmed.

  12. A model for the neuronal substrate of dead reckoning and memory in arthropods: a comparative computational and behavioral study.

    Science.gov (United States)

    Bernardet, Ulysses; Bermúdez I Badia, Sergi; Verschure, Paul F M J

    2008-06-01

    Returning to the point of departure after exploring the environment is a key capability for most animals. In the absence of landmarks, this task will be solved by integrating direction and distance traveled over time. This is referred to as path integration or dead reckoning. An important question is how the nervous systems of navigating animals such as the 1 mm(3) brain of ants can integrate local information in order to make global decision. In this article we propose a neurobiologically plausible system of storing and retrieving direction and distance information. The path memory of our model builds on the well established concept of population codes, moreover our system does not rely on trigonometric functions or other complex non-linear operations such as multiplication, but only uses biologically plausible operations such as integration and thresholding. We test our model in two paradigms; in the first paradigm the system receives input from a simulated compass, in the second paradigm, the model is tested against behavioral data recorded from 17 ants. We were able to show that our path memory system was able to reliably encode and compute the angle of the vector pointing to the start location, and that the system stores the total length of the trajectory in a dependable way. From the structure and behavior of our model, we derive testable predictions both at the level of observable behavior as well as on the anatomy and physiology of its underlying neuronal substrate.

  13. Heat and mass transfer models to understand the drying mechanisms of a porous substrate.

    Science.gov (United States)

    Songok, Joel; Bousfield, Douglas W; Gane, Patrick A C; Toivakka, Martti

    2016-02-01

    While drying of paper and paper coatings is expensive, with significant energy requirements, the rate controlling mechanisms are not currently fully understood. Two two-dimensional models are used as a first approximation to predict the heat transfer during hot air drying and to evaluate the role of various parameters on the drying rates of porous coatings. The models help determine the structural limiting factors during the drying process, while applying for the first time the recently known values of coating thermal diffusivity. The results indicate that the thermal conductivity of the coating structure is not the controlling factor, but the drying rate is rather determined by the thermal transfer process at the structure surface. This underlines the need for ensuring an efficient thermal transfer from hot air to coating surface during drying, before considering further measures to increase the thermal conductivity of porous coatings.

  14. Tautomerism of xanthine and alloxanthine: A model for substrate recognition by xanthine oxidase

    Science.gov (United States)

    Hernández, Regoña; Orozco, Modesto; Luque, Francisco J.

    1996-12-01

    Tautomerism of neutral xanthine and alloxanthine has been examined both in the gas phase and in aqueous solution. The tautomeric preference in the gas phase has been studied by means of semiempirical and ab initio quantum-mechanical computations with inclusion of correlation effects at the Møller-Plesset level, and from density-functional calculations. The influence of solvent on the relative stability between tautomers has been estimated from self-consistent reaction field calculations performed with different models. The results provide a detailed picture of tautomerism for these biologically relevant purine bases. The functional implications in the recognition by xanthine oxidase are analyzed from inspection of the interaction patterns of the most stable tautomeric forms. A model for the recognition of these purine derivatives in the enzyme binding site is discussed.

  15. A lattice Boltzmann model for substrates with regularly structured surface roughness

    Science.gov (United States)

    Yagub, A.; Farhat, H.; Kondaraju, S.; Singh, T.

    2015-11-01

    Superhydrophobic surface characteristics are important in many industrial applications, ranging from the textile to the military. It was observed that surfaces fabricated with nano/micro roughness can manipulate the droplet contact angle, thus providing an opportunity to control the droplet wetting characteristics. The Shan and Chen (SC) lattice Boltzmann model (LBM) is a good numerical tool, which holds strong potentials to qualify for simulating droplets wettability. This is due to its realistic nature of droplet contact angle (CA) prediction on flat smooth surfaces. But SC-LBM was not able to replicate the CA on rough surfaces because it lacks a real representation of the physics at work under these conditions. By using a correction factor to influence the interfacial tension within the asperities, the physical forces acting on the droplet at its contact lines were mimicked. This approach allowed the model to replicate some experimentally confirmed Wenzel and Cassie wetting cases. Regular roughness structures with different spacing were used to validate the study using the classical Wenzel and Cassie equations. The present work highlights the strength and weakness of the SC model and attempts to qualitatively conform it to the fundamental physics, which causes a change in the droplet apparent contact angle, when placed on nano/micro structured surfaces.

  16. Classification of the adenylation and acyl-transferase activity of NRPS and PKS systems using ensembles of substrate specific hidden Markov models.

    Directory of Open Access Journals (Sweden)

    Barzan I Khayatt

    Full Text Available There is a growing interest in the Non-ribosomal peptide synthetases (NRPSs and polyketide synthases (PKSs of microbes, fungi and plants because they can produce bioactive peptides such as antibiotics. The ability to identify the substrate specificity of the enzyme's adenylation (A and acyl-transferase (AT domains is essential to rationally deduce or engineer new products. We here report on a Hidden Markov Model (HMM-based ensemble method to predict the substrate specificity at high quality. We collected a new reference set of experimentally validated sequences. An initial classification based on alignment and Neighbor Joining was performed in line with most of the previously published prediction methods. We then created and tested single substrate specific HMMs and found that their use improved the correct identification significantly for A as well as for AT domains. A major advantage of the use of HMMs is that it abolishes the dependency on multiple sequence alignment and residue selection that is hampering the alignment-based clustering methods. Using our models we obtained a high prediction quality for the substrate specificity of the A domains similar to two recently published tools that make use of HMMs or Support Vector Machines (NRPSsp and NRPS predictor2, respectively. Moreover, replacement of the single substrate specific HMMs by ensembles of models caused a clear increase in prediction quality. We argue that the superiority of the ensemble over the single model is caused by the way substrate specificity evolves for the studied systems. It is likely that this also holds true for other protein domains. The ensemble predictor has been implemented in a simple web-based tool that is available at http://www.cmbi.ru.nl/NRPS-PKS-substrate-predictor/.

  17. Modified ADM1 for modelling an UASB reactor laboratory plant treating starch wastewater and synthetic substrate load tests.

    Science.gov (United States)

    Hinken, L; Huber, M; Weichgrebe, D; Rosenwinkel, K-H

    2014-11-01

    A laboratory plant consisting of two UASB reactors was used for the treatment of industrial wastewater from the wheat starch industry. Several load tests were carried out with starch wastewater and the synthetic substrates glucose, acetate, cellulose, butyrate and propionate to observe the impact of changing loads on gas yield and effluent quality. The measurement data sets were used for calibration and validation of the Anaerobic Digestion Model No. 1 (ADM1). For a precise simulation of the detected glucose degradation during load tests with starch wastewater and glucose, it was necessary to incorporate the complete lactic acid fermentation into the ADM1, which contains the formation and degradation of lactate and a non-competitive inhibition function. The modelling results of both reactors based on the modified ADM1 confirm an accurate calculation of the produced gas and the effluent concentrations. Especially, the modelled lactate effluent concentrations for the load cases are similar to the measurements and justified by literature. Copyright © 2014 Elsevier Ltd. All rights reserved.

  18. Microimaging studies of myocardial substrate utilization and perfusion in two models of non-coronary heart disease

    Energy Technology Data Exchange (ETDEWEB)

    Som, P.; Oster, Z.H.; Knapp, F.F. Jr.

    1987-01-01

    We have studied two animal models of non-coronary heart disease. The salt-sensitive Dahl strain hypertensive rats and their genetically matched normotensive controls and the cardiomyopathic BIO 53.58 (CM) strain Syrian hamsters with age and sex-matched RB strain controls. The CM strain hamster seems to be a very good model of human congestive cardiomyopathy and the Dahl strain hypertensive rats have also been found to be good models for studying the effects of hypertension on the myocardium. In our studies we compared the utilization of various metabolic substrates, viz., fatty acids, glucose analogs, and the early distribution of /sup 201/Tl, as an indicator of myocardial flow. The routine studies involving dissection of animals for assaying the radioactivity following the injection of radiopharmaceuticals is not suitable for assessing regional changes in metabolism and flow. The use of quantitative autoradiographic microimaging (ARG) enables the visualization of discrete regional as well as global changes from normal and to quantitate them. This paper describes the methodology and results of these investigations. 14 refs., 5 figs.

  19. Microimaging studies of myocardial substrate utilization and perfusion in two models of non-coronary heart disease

    International Nuclear Information System (INIS)

    Som, P.; Oster, Z.H.; Knapp, F.F. Jr.

    1987-01-01

    We have studied two animal models of non-coronary heart disease. The salt-sensitive Dahl strain hypertensive rats and their genetically matched normotensive controls and the cardiomyopathic BIO 53.58 (CM) strain Syrian hamsters with age and sex-matched RB strain controls. The CM strain hamster seems to be a very good model of human congestive cardiomyopathy and the Dahl strain hypertensive rats have also been found to be good models for studying the effects of hypertension on the myocardium. In our studies we compared the utilization of various metabolic substrates, viz., fatty acids, glucose analogs, and the early distribution of 201 Tl, as an indicator of myocardial flow. The routine studies involving dissection of animals for assaying the radioactivity following the injection of radiopharmaceuticals is not suitable for assessing regional changes in metabolism and flow. The use of quantitative autoradiographic microimaging (ARG) enables the visualization of discrete regional as well as global changes from normal and to quantitate them. This paper describes the methodology and results of these investigations. 14 refs., 5 figs

  20. Analysis of the diversity of substrate utilisation of soil bacteria exposed to Cd and earthworm activity using generalised additive models.

    Directory of Open Access Journals (Sweden)

    Selene Muñiz

    Full Text Available Biolog EcoPlates™ can be used to measure the carbon substrate utilisation patterns of microbial communities. This method results in a community-level physiological profile (CLPP, which yields a very large amount of data that may be difficult to interpret. In this work, we explore a combination of statistical techniques (particularly the use of generalised additive models [GAMs] to improve the exploitation of CLPP data. The strength of GAMs lies in their ability to address highly non-linear relationships between the response and the set of explanatory variables. We studied the impact of earthworms (Aporrectodea caliginosa Savigny 1826 and cadmium (Cd on the CLPP of soil bacteria. The results indicated that both Cd and earthworms modified the CLPP. GAMs were used to assess time-course changes in the diversity of substrate utilisation (DSU using the Shannon-Wiener index. GAMs revealed significant differences for all treatments (compared to control -S-. The Cd exposed microbial community presented very high metabolic capacities on a few substrata, resulting in an initial acute decrease of DSU (i.e. intense utilization of a few carbon substrata. After 54 h, and over the next 43 h the increase of the DSU suggest that other taxa, less dominant, reached high numbers in the wells containing sources that are less suitable for the Cd-tolerant taxa. Earthworms were a much more determining factor in explaining time course changes in DSU than Cd. Accordingly, Ew and EwCd soils presented similar trends, regardless the presence of Cd. Moreover, both treatments presented similar number of bacteria and higher than Cd-treated soils. This experimental approach, based on the use of DSU and GAMs allowed for a global and statistically relevant interpretation of the changes in carbon source utilisation, highlighting the key role of earthworms on the protection of microbial communities against the Cd.

  1. A coupled CFD and two-phase substrate kinetic model for enzymatic hydrolysis of lignocellulose

    Science.gov (United States)

    Danes, Nicholas; Sitaraman, Hariswaran; Stickel, Jonathan; Sprague, Michael

    2017-11-01

    Cost-effective production of fuels from lignocellulosic biomass is an important subject of research in order to meet the world's current and future energy demands. Enzymatic hydrolysis is one of the several steps in the biochemical conversion of biomass into fuels. This process involves the interplay of non-Newtonian fluid dynamics that happen over tens of seconds coupled with chemical reactions that happen over several hours. In this work, we present a coupled CFD-reaction model for conversion of cellulose to sugars in a benchtop mixer reactor. A subcycling approach is used to circumvent the large time scale disparity between fluid dynamics and reactions. We will present a validation study of our simulations with experiments for well-mixed and stratified reactor scenarios along with predictions for conversion rates and product concentrations at varying impeller speeds and in scaled-up reactors. This work is funded by the Bioenergy Technology Office of DOE and the NSF's Enriched Doctoral Training program (DMS-1551229).

  2. Date seed characterisation, substrate extraction and process modelling for the production of polyhydroxybutyrate by Cupriavidus necator.

    Science.gov (United States)

    Yousuf, R G; Winterburn, J B

    2016-12-01

    Poly-3-hydroxybutrate (PHB) is a biodegradable polymer synthesised via bacterial fermentation as a means of storing carbon and energy under unbalanced growth conditions. The production cost of petroleum-based plastics is currently lower than that for biopolymers, and the carbon source is the most significant contributor to biopolymer production cost. A feasibility study to assess the suitability of using a date seed derived media as an alternative for PHB production under various stress conditions was investigated. Results include fructose extraction from date seeds and a mass transfer model to describe the process, demonstrating that the high nutrient content of date seeds makes them a promising raw material for microbial growth and that a meaningful amount of PHB can be produced without supplementation. Maximum dry cell weight and PHB concentrations were 6.3g/l and 4.6g/l respectively, giving a PHB content of 73%, when an initial fructose concentration of 10.8g/l was used. Copyright © 2016 Elsevier Ltd. All rights reserved.

  3. Improvement of paracellular transport in the Caco-2 drug screening model using protein-engineered substrates.

    Science.gov (United States)

    DiMarco, Rebecca L; Hunt, Daniel R; Dewi, Ruby E; Heilshorn, Sarah C

    2017-06-01

    The Caco-2 assay has achieved wide popularity among pharmaceutical companies in the past two decades as an in vitro method for estimation of in vivo oral bioavailability of pharmaceutical compounds during preclinical characterization. Despite its popularity, this assay suffers from a severe underprediction of the transport of drugs which are absorbed paracellularly, that is, which pass through the cell-cell tight junctions of the absorptive cells of the small intestine. Here, we propose that simply replacing the collagen I matrix employed in the standard Caco-2 assay with an engineered matrix, we can control cell morphology and hence regulate the cell-cell junctions that dictate paracellular transport. Specifically, we use a biomimetic engineered extracellular matrix (eECM) that contains modular protein domains derived from two ECM proteins found in the small intestine, fibronectin and elastin. This eECM allows us to independently tune the density of cell-adhesive RGD ligands presented to Caco-2 cells as well as the mechanical stiffness of the eECM. We observe that lower amounts of RGD ligand presentation as well as decreased matrix stiffness results in Caco-2 morphologies that more closely resemble primary small intestinal epithelial cells than Caco-2 cells cultured on collagen. Additionally, these matrices result in Caco-2 monolayers with decreased recruitment of actin to the apical junctional complex and increased expression of claudin-2, a tight junction protein associated with higher paracellular permeability that is highly expressed throughout the small intestine. Consistent with these morphological differences, drugs known to be paracellularly transported in vivo exhibited significantly improved transport rates in this modified Caco-2 model. As expected, permeability of transcellularly transported drugs remained unaffected. Thus, we have demonstrated a method of improving the physiological accuracy of the Caco-2 assay that could be readily adopted by

  4. Experimental characterization and computational modeling of unimorph shape memory polymer actuators incorporating transverse curvature in the substrate

    Science.gov (United States)

    Cantrell, Jason T.

    This document outlines in detail the research performed by applying shape memory polymers in a generic unimorph actuator configuration. A set of experiments designed to investigate the influence of transverse curvature, the relative widths of shape memory polymer and composite substrates, and shape memory polymer thickness on actuator recoverability after multiple thermo-mechanical cycles is presented in detail. A theoretical model of the moment required to maintain shape fixity with minimal shape retention loss was developed and experimentally validated for unimorph composite actuators of varying cross-sectional areas. Theoretical models were also developed and evaluated to determine the relationship between the materials neutral axes and thermal stability during a thermo-mechanical cycle. Research was conducted on the incorporation of shape memory polymers on micro air vehicle wings to maximize shape fixity and shape recoverability while minimizing the volume of shape memory polymer on the wing surface. Applications based research also included experimentally evaluating the feasibility of shape memory polymers on deployable satellite antenna ribs both with and without resistance heaters which could be utilized to assist in antenna deployment.

  5. High Resolution X-ray Diffraction Dataset for Bacillus licheniformis Gamma Glutamyl Transpeptidase-acivicin complex: SUMO-Tag Renders High Expression and Solubility.

    Science.gov (United States)

    Kumari, Shobha; Pal, Ravi Kant; Gupta, Rani; Goel, Manisha

    2017-02-01

    Gamma glutamyl transpeptidase, (GGT) is a ubiquitous protein which plays a central role in glutathione metabolism and has myriad clinical implications. It has been shown to be a virulence factor for pathogenic bacteria, inhibition of which results in reduced colonization potential. However, existing inhibitors are effective but toxic and therefore search is on for novel inhibitors, which makes it imperative to understand the interactions of various inhibitors with the protein in substantial detail. High resolution structures of protein bound to different inhibitors can serve this purpose. Gamma glutamyl transpeptidase from Bacillus licheniformis is one of the model systems that have been used to understand the structure-function correlation of the protein. The structures of the native protein (PDB code 4OTT), of its complex with glutamate (PDB code 4OTU) and that of its precursor mimic (PDB code 4Y23) are available, although at moderate/low resolution. In the present study, we are reporting the preliminary analysis of, high resolution X-ray diffraction data collected for the co-crystals of B. licheniformis, Gamma glutamyl transpeptidase, with its inhibitor, Acivicin. Crystals belong to the orthorhombic space group P2 1 2 1 2 1 and diffract X-ray to 1.45 Å resolution. This is the highest resolution data reported for all GGT structures available till now. The use of SUMO fused expression system enhanced yield of the target protein in the soluble fraction, facilitating recovery of protein with high purity. The preliminary analysis of this data set shows clear density for the inhibitor, acivicin, in the protein active site.

  6. Theoretical development and validation of a Sharp Front model of the dewatering of a slurry by an absorbent substrate

    Science.gov (United States)

    Collier, N. C.; Wilson, M. A.; Carter, M. A.; Hoff, W. D.; Hall, Christopher; Ball, R. J.; El-Turki, A.; Allen, G. C.

    2007-07-01

    The absorption of water from a slurry into an absorbent substrate is analysed using Sharp Front theory. The analysis describes the relationship between the sorptivity S of the substrate, the desorptivity R of the slurry and the transfer sorptivity A between slurry and substrate, and leads to the relationship 1/A2 = 1/R2 + 1/S2. Experimental data are presented which validate this equation for the practically important case of the absorption of water from soft mortar mixes by fired clay bricks. A unique feature of the experimental work is the measurement of the desorptivity of the mortars at a pressure equal to the wetting front capillary pressure of the clay brick substrate. Analysis of the experimental data also enables, for the first time, the calculation of the capillary potential at the slurry/substrate interface. The analysis has relevance to many aspects of ceramic and mineral processing, industrial filtration and construction engineering.

  7. Characterization of a SUMO Ligase that is Essential for DNA Damage-Induced NF-Kappa B Activation

    Science.gov (United States)

    2008-03-01

    from pcDNA3.1(+) 2×HA–NEMO template. pcDNA3 2×HA–NEMO K277A and K309A mutants were generated through subcloning of pcDNA3 6×Myc–NEMO K277A and K309A...cloning are available on request. All constructs were verified by DNA sequencing. Xenopus pET28a–PIASy was subcloned into the pcDNA3–Myc3 vector...overexpression of Ubc9 or SUMO-1 inhibited NF-kB transcriptional activity induced by TNFa, IL-1 and okadaic acid as measured by an NF-kB- dependent HIV -LTR

  8. KAP1 Is a Host Restriction Factor That Promotes Human Adenovirus E1B-55K SUMO Modification

    DEFF Research Database (Denmark)

    Bürck, Carolin; Mund, Andreas; Berscheminski, Julia

    2016-01-01

    and chromatin compaction. In response to DNA damage, KAP1 is phosphorylated and functionally inactive, resulting in chromatin relaxation. We discovered that KAP1 posttranslational modification is dramatically altered during HAdV infection to limit the antiviral capacity of this host restriction factor, which...... epigenetic gene silencing and to promote SUMO modification of E1B-55K by a so far unknown mechanism. IMPORTANCE: Here we describe a novel cellular restriction factor for Human Adenovirus (HAdV) that sheds light on very early modulation processes in viral infection. We reported that chromatin formation...... characterized, but represent a decisive moment in establishing a productive infection. Here, we identify a novel host viral restriction factor, KAP1. This heterochromatin associated transcription factor regulates the dynamic organization of host chromatin structure via its ability to influence epigenetic marks...

  9. The SUMO protease SENP1 is required for cohesion maintenance and mitotic arrest following spindle poison treatment

    Energy Technology Data Exchange (ETDEWEB)

    Era, Saho [Fondazione IFOM, Istituto FIRC di Oncologia Molecolare, IFOM-IEO campus, Via Adamello 16, 20139 Milan (Italy); Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshida-Konoe, Sakyo-ku, Kyoto 606-8501 (Japan); Abe, Takuya; Arakawa, Hiroshi [Fondazione IFOM, Istituto FIRC di Oncologia Molecolare, IFOM-IEO campus, Via Adamello 16, 20139 Milan (Italy); Kobayashi, Shunsuke [Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshida-Konoe, Sakyo-ku, Kyoto 606-8501 (Japan); Szakal, Barnabas [Fondazione IFOM, Istituto FIRC di Oncologia Molecolare, IFOM-IEO campus, Via Adamello 16, 20139 Milan (Italy); Yoshikawa, Yusuke; Motegi, Akira; Takeda, Shunichi [Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshida-Konoe, Sakyo-ku, Kyoto 606-8501 (Japan); Branzei, Dana, E-mail: dana.branzei@ifom.eu [Fondazione IFOM, Istituto FIRC di Oncologia Molecolare, IFOM-IEO campus, Via Adamello 16, 20139 Milan (Italy)

    2012-09-28

    Highlights: Black-Right-Pointing-Pointer SENP1 knockout chicken DT40 cells are hypersensitive to spindle poisons. Black-Right-Pointing-Pointer Spindle poison treatment of SENP1{sup -/-} cells leads to increased mitotic slippage. Black-Right-Pointing-Pointer Mitotic slippage in SENP1{sup -/-} cells associates with apoptosis and endoreplication. Black-Right-Pointing-Pointer SENP1 counteracts sister chromatid separation during mitotic arrest. Black-Right-Pointing-Pointer Plk1-mediated cohesion down-regulation is involved in colcemid cytotoxicity. -- Abstract: SUMO conjugation is a reversible posttranslational modification that regulates protein function. SENP1 is one of the six SUMO-specific proteases present in vertebrate cells and its altered expression is observed in several carcinomas. To characterize SENP1 role in genome integrity, we generated Senp1 knockout chicken DT40 cells. SENP1{sup -/-} cells show normal proliferation, but are sensitive to spindle poisons. This hypersensitivity correlates with increased sister chromatid separation, mitotic slippage, and apoptosis. To test whether the cohesion defect had a causal relationship with the observed mitotic events, we restored the cohesive status of sister chromatids by introducing the TOP2{alpha}{sup +/-} mutation, which leads to increased catenation, or by inhibiting Plk1 and Aurora B kinases that promote cohesin release from chromosomes during prolonged mitotic arrest. Although TOP2{alpha} is SUMOylated during mitosis, the TOP2{alpha}{sup +/-} mutation had no obvious effect. By contrast, inhibition of Plk1 or Aurora B rescued the hypersensitivity of SENP1{sup -/-} cells to colcemid. In conclusion, we identify SENP1 as a novel factor required for mitotic arrest and cohesion maintenance during prolonged mitotic arrest induced by spindle poisons.

  10. A Novel Strategy for the Preparation of Codon-Optimized Truncated Ulp1 and its Simplified Application to Cleavage the SUMO Fusion Protein.

    Science.gov (United States)

    Wang, Xiaohua; Liu, Haifeng; Liu, Yawei; Li, Yuting; Yan, Lei; Yuan, Xiaohuan; Zhang, Yufei; Wu, Yan; Liu, Jieting; Zhang, Chunlei; Chu, Yanhui

    2016-04-01

    Ubiquitin-like protease 1 (Ulp1) of Saccharomyces cerevisiae emerges as a fundamental tool to obtain the natural N-terminal target protein by cleavage of the small ubiquitin-related modifier (SUMO) fusion protein. However, the costly commercial Ulp1 and its complicated procedures limit its application in the preparation of the target protein with natural N-terminal sequence. Here, we describe the preparation of bioactive codon-optimized recombinant truncated Ulp1 (Leu403-Lys621) (rtUlp1) of S. cerevisiae in Escherichia coli using only one-step with Ni-NTA affinity chromatograph, and the application of rtUlp1 to cleave the SUMO fusion protein by simply mixing the purified rtUlp1, SUMO fusion protein and DL-Dithiothreitol in Tris-HCl buffer. The optimal expression level of non-fusion protein rtUlp1 accounts for approximately 50 % of the total cellular protein and 36% of the soluble form by addition of isopropyl β-D-l-thiogalactopyranoside at a final concentration of 0.4 mM at 18 °C for 20 h. The purification of target protein rtUlp1 was conducted by Ni-NTA affinity chromatography. The final yield of rtUlp1 was 45 mg/l in flask fermentation with a purity up to 95%. Furthermore, the high purity of rtUlp1 could effectively cleave the SUMO-tTβRII fusion protein (SUMO gene fused to truncated transforming growth factor-beta receptor type II gene) with the above simplified approach, and the specific activity of the rtUlp1 reached up to 2.8 × 10(4) U/mg, which is comparable to the commercial Ulp1. The preparation and application strategy of the rtUlp1 with commonly available laboratory resources in this study will be convenient to the cleavage of the SUMO fusion protein to obtain the natural N-terminal target protein, which can be implemented in difficult-to-express protein functional analysis.

  11. Steady state kinetic model for the binding of substrates and allosteric effectors to Escherichia coli phosphoribosyl-diphosphate synthase

    DEFF Research Database (Denmark)

    Willemoës, Martin; Hove-Jensen, Bjarne; Larsen, Sine

    2000-01-01

    A steady state kinetic investigation of the Pi activation of 5-phospho-D-ribosyl α-1-diphosphate synthase from Escherichia coli suggests that Pi can bind randomly to the enzyme either before or after an ordered addition of free Mg2+ and substrates. Unsaturation with ribose 5-phosphate increased...... the apparent cooperativity of Pi activation. At unsaturating Pi concentrations partial substrate inhibition by ribose 5-phosphate was observed. Together these results suggest that saturation of the enzyme with Pi directs the subsequent ordered binding of Mg2+ and substrates via a fast pathway, whereas...... saturation with ribose 5-phosphate leads to the binding of Mg2+ and substrates via a slow pathway where Pi binds to the enzyme last. The random mechanism for Pi binding was further supported by studies with competitive inhibitors of Mg2+, MgATP, and ribose 5-phosphate that all appeared noncompetitive when...

  12. Investigation of the effects of misfit strain on barium strontium titanate thin films deposited on base metal substrates by a modified phenomenological model

    Science.gov (United States)

    Dong, Hanting; Li, Hongfang; Chen, Jianguo; Jin, Dengren; Cheng, Jinrong

    2017-10-01

    The Landau-Devonshire phenomenological model, which has been utilized to investigate epitaxial barium strontium titanate (BST) thin films, was modified to investigate the effects of misfit strain on the dielectric properties of polycrystalline BST thin films deposited on base metal substrates. The modification considers the relaxation of lattice misfit stress resulting from the formation of in-plane misfit dislocations. The modified lattice misfit strain was calculated by referring to the ferroelectric critical grain size. Moreover, the misfit strain and dielectric properties of BST thin films with different structures and substrates were investigated by the models. It was found that the measured dielectric constant and tunability of BST thin films on different metal substrates overall agreed with the computed data. In addition, the good agreement was also observed for sandwich-like structural BST thin films deposited on LNO buffered stainless steel plates. Our results indicated that the modified L-D models might be utilized to predict dielectric properties of polycrystalline BST thin films for varied substrates and multilayer structures.

  13. Adsorption mechanism of myelin basic protein on model substrates and its bridging interaction between the two surfaces.

    Science.gov (United States)

    Lee, Dong Woog; Banquy, Xavier; Kristiansen, Kai; Min, Younjin; Ramachandran, Arun; Boggs, Joan M; Israelachvili, Jacob N

    2015-03-17

    Myelin basic protein (MBP) is an intrinsically disordered (unstructured) protein known to play an important role in the stability of myelin's multilamellar membrane structure in the central nervous system. The adsorption of MBP and its capacity to interact with and bridge solid substrates has been studied using a surface forces apparatus (SFA) and a quartz crystal microbalance with dissipation (QCM-D). Adsorption experiments show that MBP molecules adsorb to the surfaces in a swollen state before undergoing a conformational change into a more compact structure with a thickness of ∼3 nm. Moreover, this compact structure is able to interact with nearby mica surfaces to form adhesive bridges. The measured adhesion force (energy) between two bridged surfaces is 1.0 ± 0.1 mN/m, (Ead = 0.21 ± 0.02 mJ/m(2)), which is slightly smaller than our previously reported adhesion force of 1.7 mN/m (Ead = 0.36 mJ/m(2)) for MBP adsorbed on two supported lipid bilayers (Lee et al., Proc. Natl. Acad. Sci. U.S.A. 2014, 111, E768-E775). The saturated surface concentration of compact MBP on a single SiO2 surface reaches a stable value of 310 ± 10 ng/cm(2) regardless of the bulk MBP concentration. A kinetic three-step adsorption model was developed that accurately fits the adsorption data. The developed model is a general model, not limited to intrinsically disordered proteins, that can be extended to the adsorption of various chemical compounds that undergo chemical reactions and/or conformational changes upon adsorbing to surfaces. Taken together with our previously published data (Lee et al., Proc. Natl. Acad. Sci. U.S.A. 2014, 111, E768-E775), the present results confirm that conformational changes of MBP upon adsorption are a key for strong adhesion, and that such conformational changes are strongly dependent on the nature of the surfaces.

  14. Increased oxidative stress and apoptosis in the hypothalamus of diabetic male mice in the insulin receptor substrate-2 knockout model.

    Science.gov (United States)

    Baquedano, Eva; Burgos-Ramos, Emma; Canelles, Sandra; González-Rodríguez, Agueda; Chowen, Julie A; Argente, Jesús; Barrios, Vicente; Valverde, Angela M; Frago, Laura M

    2016-05-01

    Insulin receptor substrate-2-deficient (IRS2(-/-)) mice are considered a good model to study the development of diabetes because IRS proteins mediate the pleiotropic effects of insulin-like growth factor-I (IGF-I) and insulin on metabolism, mitogenesis and cell survival. The hypothalamus might play a key role in the early onset of diabetes, owing to its involvement in the control of glucose homeostasis and energy balance. Because some inflammatory markers are elevated in the hypothalamus of diabetic IRS2(-/-) mice, our aim was to analyze whether the diabetes associated with the absence of IRS2 results in hypothalamic injury and to analyze the intracellular mechanisms involved. Only diabetic IRS2(-/-) mice showed increased cell death and activation of caspase-8 and -3 in the hypothalamus. Regulators of apoptosis such as FADD, Bcl-2, Bcl-xL and p53 were also increased, whereas p-IκB and c-FLIPL were decreased. This was accompanied by increased levels of Nox-4 and catalase, enzymes involved in oxidative stress. In summary, the hypothalamus of diabetic IRS2(-/-) mice showed an increase in oxidative stress and inflammatory markers that finally resulted in cell death via substantial activation of the extrinsic apoptotic pathway. Conversely, non-diabetic IRS2(-/-) mice did not show cell death in the hypothalamus, possibly owing to an increase in the levels of circulating IGF-I and in the enhanced hypothalamic IGF-IR phosphorylation that would lead to the stimulation of survival pathways. In conclusion, diabetes in IRS2-deficient male mice is associated with increased oxidative stress and apoptosis in the hypothalamus. © 2016. Published by The Company of Biologists Ltd.

  15. Comparing the effects of various fuel alcohols on the natural attenuation of benzene plumes using a general substrate interaction model.

    Science.gov (United States)

    Gomez, Diego E; Alvarez, Pedro J J

    2010-04-01

    The effects of five fuel alcohols (methanol, ethanol, 1-propanol, iso-butanol and n-butanol) on the natural attenuation of benzene were compared using a previously developed numerical model (General Substrate Interaction Module--GSIM) and a probabilistic sensitivity analysis. Simulations with a 30 gal dissolving LNAPL (light non-aqueous phase liquid) source consisting of a range of gasoline blends (10% and 85% v:v alcohol content) suggest that all fuel alcohols can hinder the natural attenuation of benzene, due mainly to accelerated depletion of dissolved oxygen and a decrease in the specific degradation rate for benzene (due to catabolite repression and metabolic flux dilution). Simulations for blends with 10% alcohol, assuming a homogeneous sandy aquifer, inferred maximum benzene plume elongations (relative to a regular gasoline release) of 26% for ethanol, 47% for iso-butanol, 147% for methanol, 188% for 1-propanol, and 265% for n-butanol. The corresponding elongation percentages for blends with 85% alcohol were generally smaller (i.e., 25%, 54%, 135%, 163%, and 181%, respectively), reflecting a lower content of benzene in the simulated release. Benzene plume elongation and longevity were more pronounced in the presence of alcohols that biodegrade slower (e.g., propanol and n-butanol), forming longer and more persistent alcohol plumes. Conversely, ethanol and iso-butanol exhibited the lowest potential to hinder the natural attenuation of benzene, illustrating the significant effect that a small difference in chemical structure (e.g., isomers) can have on biodegradation. Overall, simulations were highly sensitive to site-specific biokinetic coefficients for alcohol degradation, which forewarns against generalizations about the level of impact of specific fuel alcohols on benzene plume dynamics. 2010 Elsevier B.V. All rights reserved.

  16. Kinetics of bacterial phospholipase C activity at micellar interfaces: effect of substrate aggregate microstructure and a model for the kinetic parameters.

    Science.gov (United States)

    Singh, Jasmeet; Ranganathan, Radha; Hajdu, Joseph

    2008-12-25

    Activity at micellar interfaces of bacterial phospholipase C from Bacillus cereus on phospholipids solubilized in micelles was investigated with the goal of elucidating the role of the interface microstructure and developing further an existing kinetic model. Enzyme kinetics and physicochemical characterization of model substrate aggregates were combined, thus enabling the interpretation of kinetics in the context of the interface. Substrates were diacylphosphatidylcholine of different acyl chain lengths in the form of mixed micelles with dodecyldimethylammoniopropanesulfonate. An early kinetic model, reformulated to reflect the interfacial nature of the kinetics, was applied to the kinetic data. A better method of data treatment is proposed, use of which makes the presence of microstructure effects quite transparent. Models for enzyme-micelle binding and enzyme-lipid binding are developed, and expressions incorporating the microstructural properties are derived for the enzyme-micelle dissociation constant K(s) and the interface Michaelis-Menten constant, K(M). Use of these expressions in the interface kinetic model brings excellent agreement between the kinetic data and the model. Numerical values for the thermodynamic and kinetic parameters are determined. Enzyme-lipid binding is found to be an activated process with an acyl chain length dependent free energy of activation that decreases with micelle lipid molar fraction with a coefficient of about -15RT and correlates with the tightness of molecular packing in the substrate aggregate. Thus, the physical insight obtained includes a model for the kinetic parameters that shows that these parameters depend on the substrate concentration and acyl chain length of the lipid. Enzyme-micelle binding is indicated to be hydrophobic and solvent mediated with a dissociation constant of 1.2 mM.

  17. Small ubiquitin-like modifier 3-modified proteome regulated by brain ischemia in novel small ubiquitin-like modifier transgenic mice: putative protective proteins/pathways.

    Science.gov (United States)

    Yang, Wei; Sheng, Huaxin; Thompson, J Will; Zhao, Shengli; Wang, Liangli; Miao, Pei; Liu, Xiaozhi; Moseley, M Arthur; Paschen, Wulf

    2014-04-01

    Small ubiquitin-like modifier (SUMO) conjugation is a post-translational modification associated with many human diseases. Characterization of the SUMO-modified proteome is pivotal to define the mechanistic link between SUMO conjugation and such diseases. This is particularly evident for SUMO2/3 conjugation, which is massively activated after brain ischemia/stroke, and is believed to be a protective response. The purpose of this study was to perform a comprehensive analysis of the SUMO3-modified proteome regulated by brain ischemia using a novel SUMO transgenic mouse. To enable SUMO proteomics analysis in vivo, we generated transgenic mice conditionally expressing tagged SUMO1-3 paralogues. Transgenic mice were subjected to 10 minutes forebrain ischemia and 1 hour of reperfusion. SUMO3-conjugated proteins were enriched by anti-FLAG affinity purification and analyzed by liquid chromatography-tandem mass spectrometry. Characterization of SUMO transgenic mice demonstrated that all 3 tagged SUMO paralogues were functionally active, and expression of exogenous SUMOs did not modify the endogenous SUMOylation machinery. Proteomics analysis identified 112 putative SUMO3 substrates of which 91 candidates were more abundant in the ischemia group than the sham group. Data analysis revealed processes/pathways with putative neuroprotective functions, including glucocorticoid receptor signaling, RNA processing, and SUMOylation-dependent ubiquitin conjugation. The identified proteins/pathways modulated by SUMOylation could be the key to understand the mechanisms linking SUMOylation to neuroprotection, and thus provide new promising targets for therapeutic interventions. The new transgenic mouse will be an invaluable platform for analyzing the SUMO-modified proteome in models of human disorders and thereby help to mechanistically link SUMOylation to the pathological processes.

  18. SPR studies of the adsorption of silver/bovine serum albumin nanoparticles (Ag/BSA NPs) onto the model biological substrates.

    Science.gov (United States)

    Bhan, Chandra; Brower, Tina Louise; Raghavan, Dharmaraj

    2013-07-15

    The primary objective of this study is to investigate the interactive forces that promote the adsorption of bio-conjugated nanoparticles onto proteins. To elucidate the interactive forces, we demonstrate an approach using synthetic and model biological surfaces to study adsorption of bio-conjugated nanoparticles. Real-time adsorption of BSA conjugated silver nanoparticles (Ag/BSA NPs) on the immobilized substrates was followed by surface plasmon resonance (SPR). The extent of adsorption of the nanoparticles on the synthetic surface was found to be larger for self-assembled monolayers (SAMs) with ionizable terminal groups and lower for SAMs with unionizable terminal groups. For model biological substrate, the extent of nanoparticles adsorption was found to relate to the pKa of immobilized proteins. For collagen immobilized substrate, the adsorption of Ag/BSA nanoparticles showed a significantly higher SPR response than that of free BSA. The extent of nanoparticles adsorption on the collagen immobilized substrate was also influenced by the type and concentration of electrolyte used in dispersing nanoparticles. Our findings indicate that the adsorption of nanoparticles to immobilized surface has contributions from electrostatic interactions, hydrophobic, and/or hydrogen bonding. This work provides the framework to study interactions that may arise when bio-conjugated nanoparticles are transported in biological systems. Copyright © 2013 Elsevier Inc. All rights reserved.

  19. Recombinant scorpine produced using SUMO fusion partner in Escherichia coli has the activities against clinically isolated bacteria and inhibits the Plasmodium falciparum parasitemia in vitro.

    Directory of Open Access Journals (Sweden)

    Chao Zhang

    Full Text Available Scorpine, a small cationic peptide from the venom of Pandinus imperator, which has been shown to have anti-bacterial and anti-plasmodial activities, has potential important applications in the pharmaceutical industries. However, the isolation of scorpine from natural sources is inefficient and time-consuming. Here, we first report the expression and purification of recombinant scorpine in Escherichia coli, using small ubiquitin-related modifier (SUMO fusion partner. The fusion protein was expressed in soluble form in E. coli, and expression was verified by SDS-PAGE and western blotting analysis. The fusion protein was purified to 90% purity by nickel-nitrilotriacetic acid (Ni2+-NTA resin chromatography. After the SUMO-scorpine fusion protein was cleaved by the SUMO protease, the cleaved sample was reapplied to a Ni2+-NTA column. Tricine/SDS-PAGE gel results indicated that Scorpine had been purified successfully to more than 95% purity. The recombinantly expressed Scorpine showed anti-bacterial activity against two standard bacteria including Staphylococcus aureus ATCC 29213 and Acinetobacter baumannii ATCC 19606, and clinically isolated bacteria including S. aureus S, S. aureus R, A. baumannii S, and A. baumannii R. It also produced 100% reduction in Plasmodium falciparum parasitemia in vitro. Thus, the expression strategy presented in this study allowed convenient high yield and easy purification of recombinant Scorpine for pharmaceutical applications in the future.

  20. Role of the SUMO-interacting motif in HIPK2 targeting to the PML nuclear bodies and regulation of p53

    International Nuclear Information System (INIS)

    Sung, Ki Sa; Lee, Yun-Ah; Kim, Eui Tae; Lee, Seung-Rock; Ahn, Jin-Hyun; Choi, Cheol Yong

    2011-01-01

    Homeodomain-interacting protein kinase 2 (HIPK2) is a key regulator of various transcription factors including p53 and CtBP in the DNA damage signaling pathway. PML-nuclear body (NB) is required for HIPK2-mediated p53 phosphorylation at Ser46 and induction of apoptosis. Although PML-NB targeting of HIPK2 has been shown, much is not clear about the molecular mechanism of HIPK2 recruitment to PML-NBs. Here we show that HIPK2 colocalizes specifically with PML-I and PML-IV. Mutational analysis showed that HIPK2 recruitment to PML-IV-NBs is mediated by the SUMO-interaction motifs (SIMs) of both PML-IV and HIPK2. Wild-type HIPK2 associated with SUMO-conjugated PML-IV at a higher affinity than with un-conjugated PML-IV, while the association of a HIPK2 SIM mutant with SUMO-modified PML-IV was impaired. In colony formation assays, HIPK2 strongly suppressed cell proliferation, but HIPK2 SIM mutants did not. In addition, activation and phosphorylation of p53 at the Ser46 residue were impaired by HIPK2 SIM mutants. These results suggest that SIM-mediated HIPK2 targeting to PML-NBs is crucial for HIPK2-mediated p53 activation and induction of apoptosis.

  1. Steady state kinetic model for the binding of substrates and allosteric effectors to Escherichia coli phosphoribosyl-diphosphate synthase

    DEFF Research Database (Denmark)

    Willemoës, Martin; Hove-Jensen, Bjarne; Larsen, Sine

    2000-01-01

    the apparent cooperativity of Pi activation. At unsaturating Pi concentrations partial substrate inhibition by ribose 5-phosphate was observed. Together these results suggest that saturation of the enzyme with Pi directs the subsequent ordered binding of Mg2+ and substrates via a fast pathway, whereas...... saturation with ribose 5-phosphate leads to the binding of Mg2+ and substrates via a slow pathway where Pi binds to the enzyme last. The random mechanism for Pi binding was further supported by studies with competitive inhibitors of Mg2+, MgATP, and ribose 5-phosphate that all appeared noncompetitive when...... varying Pi at either saturating or unsaturating ribose 5-phosphate concentrations. Furthermore, none of the inhibitors induced inhibition at increasing Pi concentrations. Results from ADP inhibition of Pi activation suggest that these effectors compete for binding to a common regulatory site....

  2. Droplet dynamics on patterned substrates

    Indian Academy of Sciences (India)

    ... on a substrate comprising hydrophobic and hydrophilic stripes can depend sensitively on the dynamical pathway by which the state is reached. We also consider a substrate covered with micron-scale posts and investigate how this can lead to superhydrophobic behaviour. Finally we model how a Namibian desert beetle ...

  3. The Crystal Structure Analysis of Group B Streptococcus Sortase C1: A Model for the ;Lid; Movement upon Substrate Binding

    Energy Technology Data Exchange (ETDEWEB)

    Khare, Baldeep; Fu, Zheng-Qing; Huang, I-Hsiu; Ton-That, Hung; Narayana, Sthanam V.L. (UAB); (Georgia); (UTSMC)

    2012-02-07

    A unique feature of the class-C-type sortases, enzymes essential for Gram-positive pilus biogenesis, is the presence of a flexible 'lid' anchored in the active site. However, the mechanistic details of the 'lid' displacement, suggested to be a critical prelude for enzyme catalysis, are not yet known. This is partly due to the absence of enzyme-substrate and enzyme-inhibitor complex crystal structures. We have recently described the crystal structures of the Streptococcus agalactiae SAG2603 V/R sortase SrtC1 in two space groups (type II and type III) and that of its 'lid' mutant and proposed a role of the 'lid' as a protector of the active-site hydrophobic environment. Here, we report the crystal structures of SAG2603 V/R sortase C1 in a different space group (type I) and that of its complex with a small-molecule cysteine protease inhibitor. We observe that the catalytic Cys residue is covalently linked to the small-molecule inhibitor without lid displacement. However, the type I structure provides a view of the sortase SrtC1 lid displacement while having structural elements similar to a substrate sorting motif suitably positioned in the active site. We propose that these major conformational changes seen in the presence of a substrate mimic in the active site may represent universal features of class C sortase substrate recognition and enzyme activation.

  4. Class-conditional feature modeling for ignitable liquid classification with substantial substrate contribution in fire debris analysis

    NARCIS (Netherlands)

    Lopatka, M.; Sigman, M.E.; Sjerps, M.J.; Williams, M.R.; Vivó-Truyols, G.

    2015-01-01

    Forensic chemical analysis of fire debris addresses the question of whether ignitable liquid residue is present in a sample and, if so, what type. Evidence evaluation regarding this question is complicated by interference from pyrolysis products of the substrate materials present in a fire. A method

  5. Bone toughness at the molecular scale: A model for fracture toughness using crosslinked osteopontin on synthetic and biogenic mineral substrates.

    Science.gov (United States)

    Cavelier, S; Dastjerdi, A K; McKee, M D; Barthelat, F

    2018-02-24

    The most prominent structural components in bone are collagen and mineral. However, bone additionally contains a substantial amount of noncollagenous proteins (most notably of the SIBLING protein family), some of which may act as cohesive/adhesive "binders" for the composite hybrid collagen/mineral scaffolding, whether in the bulk phase of bone, or at its interfaces. One such noncollagenous protein - osteopontin (OPN) - appears to be critical to the deformability and fracture toughness of bone. In the present study, we used a reconstructed synthetic mineral-OPN-mineral interface, and a biogenic (natural tooth dentin) mineral/collagen-OPN-mineral/collagen interface, to measure the fracture toughness of OPN on mineralized substrates. We used this system to test the hypothesis that OPN crosslinking by the enzyme tissue transglutaminase 2 (TG2) that is found in bone enhances interfacial adhesion to increase the fracture toughness of bone. For this, we prepared double-cantilever beam substrates of synthetic pure hydroxyapatite mineral, and of narwhal dentin, and directly apposed them to one another under different intervening OPN/crosslinking conditions, and fracture toughness was tested using a miniaturized loading stage. The work-of-fracture of the OPN interface was measured for different OPN formulations (monomer vs. polymer), crosslinking states, and substrate composition. Noncrosslinked OPN provided negligible adhesion on pure hydroxyapatite, whereas OPN crosslinking (by the chemical crosslinker glutaraldehyde, and TG2 enzyme) provided strong interfacial adhesion for both hydroxyapatite and dentin using monomeric and polymeric OPN. Pre-coating of the substrate beams with monomeric OPN further improved the adhesive performance of the samples, likely by allowing effective binding of this nascent OPN form to mineral/matrix components, with this pre-attachment providing a protein layer for additional crosslinking between the substrates. Copyright © 2018. Published by

  6. Kinetic model for the coupling between allosteric transitions in GroEL and substrate protein folding and aggregation.

    Science.gov (United States)

    Tehver, Riina; Thirumalai, D

    2008-04-04

    The bacterial chaperonin GroEL and the co-chaperonin GroES assist in the folding of a number of structurally unrelated substrate proteins (SPs). In the absence of chaperonins, SP folds by the kinetic partitioning mechanism (KPM), according to which a fraction of unfolded molecules reaches the native state directly, while the remaining fraction gets trapped in a potentially aggregation-prone misfolded state. During the catalytic reaction cycle, GroEL undergoes a series of allosteric transitions (TR-->R"-->T) triggered by SP capture, ATP binding and hydrolysis, and GroES binding. We developed a general kinetic model that takes into account the coupling between the rates of the allosteric transitions and the folding and aggregation of the SP. Our model, in which the GroEL allosteric rates and SP-dependent folding and aggregation rates are independently varied without prior assumption, quantitatively fits the GroEL concentration-dependent data on the yield of native ribulose bisphosphate carboxylase/oxygenase (Rubisco) as a function of time. The extracted kinetic parameters for the GroEL reaction cycle are consistent with the available values from independent experiments. In addition, we also obtained physically reasonable parameters for the kinetic steps in the reaction cycle that are difficult to measure. If experimental values for GroEL allosteric rates are used, the time-dependent changes in native-state yield at eight GroEL concentrations can be quantitatively fit using only three SP-dependent parameters. The model predicts that the differences in the efficiencies (as measured by yields of the native state) of GroEL, single-ring mutant (SR1), and variants of SR1, in the rescue of mitochondrial malate dehydrogenase, citrate synthase, and Rubisco, are related to the large variations in the allosteric transition rates. We also show that GroEL/S mutants that efficiently fold one SP at the expense of all others are due to a decrease in the rate of a key step in the

  7. FEM Modeling of In-Plane Stress Distribution in Thick Brittle Coatings/Films on Ductile Substrates Subjected to Tensile Stress to Determine Interfacial Strength

    Directory of Open Access Journals (Sweden)

    Kaishi Wang

    2018-03-01

    Full Text Available The ceramic-metal interface is present in various material structures and devices that are vulnerable to failures, like cracking, which are typically due to their incompatible properties, e.g., thermal expansion mismatch. In failure of these multilayer systems, interfacial shear strength is a good measure of the robustness of interfaces, especially for planar films. There is a widely-used shear lag model and method by Agrawal and Raj to analyse and measure the interfacial shear strength of thin brittle film on ductile substrates. The use of this classical model for a type of polymer derived ceramic coatings (thickness ~18 μm on steel substrate leads to high values of interfacial shear strength. Here, we present finite element simulations for such a coating system when it is subjected to in-plane tension. Results show that the in-plane stresses in the coating are non-uniform, i.e., varying across the thickness of the film. Therefore, they do not meet one of the basic assumptions of the classical model: uniform in-plane stress. Furthermore, effects of three significant parameters, film thickness, crack spacing, and Young’s modulus, on the in-plane stress distribution have also been investigated. ‘Thickness-averaged In-plane Stress’ (TIS, a new failure criterion, is proposed for estimating the interfacial shear strength, which leads to a more realistic estimation of the tensile strength and interfacial shear strength of thick brittle films/coatings on ductile substrates.

  8. Explaining Ethnic Variability of Transporter Substrate Pharmacokinetics in Healthy Asian and Caucasian Subjects with Allele Frequencies of OATP1B1 and BCRP: A Mechanistic Modeling Analysis.

    Science.gov (United States)

    Li, Rui; Barton, Hugh A

    2018-04-01

    Ethnic variability in the pharmacokinetics of organic anion transporting polypeptide (OATP) 1B1 substrates has been observed, but its basis is unclear. A previous study hypothesizes that, without applying an intrinsic ethnic variability in transporter activity, allele frequencies of transporters cannot explain observed ethnic variability in pharmacokinetics. However, this hypothesis contradicts the data collected from compounds that are OATP1B1 substrates but not breast cancer resistance protein (BCRP) substrates. The objective of this study is to evaluate a hypothesis that is physiologically reasonable and more consistent with clinical observations. We evaluated if allele frequencies of two transporters (OATP1B1 and BCRP) are key contributors to ethnic variability. In this hypothesis, the same genotype leads to the same activity independent of ethnicity, in contrast to the previous hypothesis of intrinsic ethnic variability in OATP1B1 activity. As a validation, we perform mechanistic pharmacokinetic modeling for SLCO1B1 (encoding OATP1B1) and ABCG2 (encoding BCRP) genotyped pharmacokinetic data from 18 clinical studies with healthy Caucasian and/or Asian subjects. Simulations based on the current hypothesis reasonably describe SLCO1B1 and ABCG2 genotyped pharmacokinetic time course data for five transporter substrates (atorvastatin, pitavastatin, pravastatin, repaglinide, and rosuvastatin) in Caucasian and Asian populations. This hypothesis covers the observations that can (e.g., ethnic differences in rosuvastatin pharmacokinetics) or cannot (e.g., lack of differences for pitavastatin pharmacokinetics) be explained by the previous hypothesis. It helps to characterize sources of ethnic variability and provides a foundation for predicting ethnic variability in transporter substrate pharmacokinetics.

  9. Modelling the Effect of Different Substrates and Temperature on the Growth and Lactic Acid Production by Lactobacillus amylovorus DSM 20531T in Batch Process

    Directory of Open Access Journals (Sweden)

    Antonija Trontel

    2010-01-01

    Full Text Available Amylolytic lactic acid bacterium Lactobacillus amylovorus DSM 20531T utilised glucose, sucrose and starch as a sole carbon and energy source. The three substrates were completely depleted from MRS medium during batch cultivations carried out in a laboratory scale stirred tank bioreactor at constant temperature (40 °C and pH value (5.5. Under the tested conditions, the bacterium was capable of conducting simultaneously starch hydrolysis and fermentation. A mixture of two stereoisomers, D-(–- and L-(+-lactic acid, was produced in all cases by highly efficient homofermentative bioprocess with 0.93 to 1 g of lactate produced per g of total (consumed substrate. The effect of temperature on the kinetics of cell growth and lactic acid production by the amylolytic strain in the starch-containing medium was also investigated. Efficient simultaneous saccharification and fermentation (SSF was obtained at 35, 40 and 45 °C with completely degraded complex carbohydrate in 8 to 12 h and the product yield coefficient in the range from 0.91 to 0.93 g/g. Maximum values for substrate consumption rate (0.89 h^–1, maximum specific growth rate (0.87 h^–1, product formation rate (2.01 h^–1, and productivity of lactic acid (1.45 g/(L·h were obtained at 45 °C, while maximum biomass concentration (4.38 g/L was attained at 40 °C. The ratio of the two stereoisomeric forms of produced lactic acid was strongly affected by the temperature. Unstructured kinetic model was used to describe the consumption of the three substrates, bacterial biomass formation and lactic acid production by L. amylovorus DSM 20531T. The dependence of biokinetic parameters on temperature was described by cardinal temperature model. The applied models successfully predicted all experimental data.

  10. Mycobacterium tuberculosis RecG binds and unwinds model DNA substrates with a preference for Holliday junctions.

    Science.gov (United States)

    Zegeye, Ephrem Debebe; Balasingham, Seetha V; Laerdahl, Jon K; Homberset, Håvard; Tønjum, Tone

    2012-08-01

    The RecG enzyme, a superfamily 2 helicase, is present in nearly all bacteria. Here we report for the first time that the recG gene is also present in the genomes of most vascular plants as well as in green algae, but is not found in other eukaryotes or archaea. The precise function of RecG is poorly understood, although ample evidence shows that it plays critical roles in DNA repair, recombination and replication. We further demonstrate that Mycobacterium tuberculosis RecG (RecG(Mtb)) DNA binding activity had a broad substrate specificity, whereas it only unwound branched-DNA substrates such as Holliday junctions (HJs), replication forks, D-loops and R-loops, with a strong preference for the HJ as a helicase substrate. In addition, RecG(Mtb) preferentially bound relatively long (≥40 nt) ssDNA, exhibiting a higher affinity for the homopolymeric nucleotides poly(dT), poly(dG) and poly(dC) than for poly(dA). RecG(Mtb) helicase activity was supported by hydrolysis of ATP or dATP in the presence of Mg(2+), Mn(2+), Cu(2+) or Fe(2+). Like its Escherichia coli orthologue, RecG(Mtb) is also a strictly DNA-dependent ATPase.

  11. Hydrolysis of protein and model dipeptide substrated by attached and nonattached marine Pseudomonas sp. strain NCIMB 2021

    International Nuclear Information System (INIS)

    Griffith, P.C.; Fletcher, M.

    1991-01-01

    Rates of substrate hydrolysis by nonattached bacteria and by bacteria attached to particles derived from marine diatom frustules were estimated by using two substrates, a dipeptide analog and a protein. Adsorption of the two substrates onto the particles was also evaluated. Methyl-coumarinyl-amide-leucine (MCA-leucine) was used to estimate hydrolysis of dipeptides by measuring an increase in fluorescence as MCA-leucine was hydrolyzed to leucine and the fluorochrome methylcoumarin. To examine hydrolysis of a larger molecule, was prepared a radiolabeled protein by 14 C-methylation of bovine serum albumin. The rate of protein hydrolysis in samples of particle-attached or nonattached bacteria was estimated by precipitating all nonhydrolyzed protein with cold trichloroacetic acid and then determining the trichloroacetic acid-soluble radiolabeled material, which represented methyl- 14 C-peptides and -amino acids. About 25% of the MCA-leucine adsorbed to the particles. MCA-leucine was hydrolyzed faster by nonattached than attached bacteria, which was probably related to its tendency to remain dissolved in the liquid phase. In contrast, almost 100% of the labeled protein adsorbed to the particles. Accordingly, protein was much less available to nonattached bacteria but was rapidly hydrolyzed by attached bacteria

  12. Characterization of papillomavirus E1 helicase mutants defective for interaction with the SUMO-conjugating enzyme Ubc9

    International Nuclear Information System (INIS)

    Fradet-Turcotte, Amelie; Brault, Karine; Titolo, Steve; Howley, Peter M.; Archambault, Jacques

    2009-01-01

    The E1 helicase from BPV and HPV16 interacts with Ubc9 to facilitate viral genome replication. We report that HPV11 E1 also interacts with Ubc9 in vitro and in the yeast two-hybrid system. Residues in E1 involved in oligomerization (353-435) were sufficient for binding to Ubc9 in vitro, but the origin-binding and ATPase domains were additionally required in yeast. Nuclear accumulation of BPV E1 was shown previously to depend on its interaction with Ubc9 and sumoylation on lysine 514. In contrast, HPV11 and HPV16 E1 mutants defective for Ubc9 binding remained nuclear even when the SUMO pathway was inhibited. Furthermore, we found that K514 in BPV E1 and the analogous K559 in HPV11 E1 are not essential for nuclear accumulation of E1. These results suggest that the interaction of E1 with Ubc9 is not essential for its nuclear accumulation but, rather, depends on its oligomerization and binding to DNA and ATP.

  13. Simulation of green roof runoff under different substrate depths and vegetation covers by coupling a simple conceptual and a physically based hydrological model.

    Science.gov (United States)

    Soulis, Konstantinos X; Valiantzas, John D; Ntoulas, Nikolaos; Kargas, George; Nektarios, Panayiotis A

    2017-09-15

    In spite of the well-known green roof benefits, their widespread adoption in the management practices of urban drainage systems requires the use of adequate analytical and modelling tools. In the current study, green roof runoff modeling was accomplished by developing, testing, and jointly using a simple conceptual model and a physically based numerical simulation model utilizing HYDRUS-1D software. The use of such an approach combines the advantages of the conceptual model, namely simplicity, low computational requirements, and ability to be easily integrated in decision support tools with the capacity of the physically based simulation model to be easily transferred in conditions and locations other than those used for calibrating and validating it. The proposed approach was evaluated with an experimental dataset that included various green roof covers (either succulent plants - Sedum sediforme, or xerophytic plants - Origanum onites, or bare substrate without any vegetation) and two substrate depths (either 8 cm or 16 cm). Both the physically based and the conceptual models matched very closely the observed hydrographs. In general, the conceptual model performed better than the physically based simulation model but the overall performance of both models was sufficient in most cases as it is revealed by the Nash-Sutcliffe Efficiency index which was generally greater than 0.70. Finally, it was showcased how a physically based and a simple conceptual model can be jointly used to allow the use of the simple conceptual model for a wider set of conditions than the available experimental data and in order to support green roof design. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. Power electronics substrate for direct substrate cooling

    Science.gov (United States)

    Le, Khiet [Mission Viejo, CA; Ward, Terence G [Redondo Beach, CA; Mann, Brooks S [Redondo Beach, CA; Yankoski, Edward P [Corona, CA; Smith, Gregory S [Woodland Hills, CA

    2012-05-01

    Systems and apparatus are provided for power electronics substrates adapted for direct substrate cooling. A power electronics substrate comprises a first surface configured to have electrical circuitry disposed thereon, a second surface, and a plurality of physical features on the second surface. The physical features are configured to promote a turbulent boundary layer in a coolant impinged upon the second surface.

  15. Membrane-bound human orphan cytochrome P450 2U1: Sequence singularities, construction of a full 3D model, and substrate docking.

    Science.gov (United States)

    Ducassou, Lionel; Dhers, Laura; Jonasson, Gabriella; Pietrancosta, Nicolas; Boucher, Jean-Luc; Mansuy, Daniel; André, François

    2017-09-01

    Human cytochrome P450 2U1 (CYP2U1) is an orphan CYP that exhibits several distinctive characteristics among the 57 human CYPs with a highly conserved sequence in almost all living organisms. We compared its protein sequence with those of the 57 human CYPs and constructed a 3D structure of a full-length CYP2U1 model bound to a POPC membrane. We also performed docking experiments of arachidonic acid (AA) and N-arachidonoylserotonin (AS) in this model. The protein sequence of CYP2U1 displayed two unique characteristics when compared to those of the human CYPs, the presence of a longer N-terminal region upstream of the putative trans-membrane helix (TMH) containing 8 proline residues, and of an insert of about 20 amino acids containing 5 arginine residues between helices A' and A. Its N-terminal part upstream of TMH involved an additional short terminal helix, in a manner similar to what was reported in the crystal structure of Saccharomyces cerevisiae CYP51. Our model also showed a specific interaction between the charged residues of insert AA' and phosphate groups of lipid polar heads, suggesting a possible role of this insert in substrate recruitment. Docking of AA and AS in this model showed these substrates in channel 2ac, with the terminal alkyl chain of AA or the indole ring of AS close to the heme, in agreement with the reported CYP2U1-catalyzed AA and AS hydroxylation regioselectivities. This model should be useful to find new endogenous or exogenous CYP2U1 substrates and to interpret the regioselectivity of their hydroxylation. Copyright © 2017 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

  16. Mathematical modeling of the ethanol fermentation of cashew apple juice by a flocculent yeast: the effect of initial substrate concentration and temperature.

    Science.gov (United States)

    Pinheiro, Álvaro Daniel Teles; da Silva Pereira, Andréa; Barros, Emanuel Meneses; Antonini, Sandra Regina Ceccato; Cartaxo, Samuel Jorge Marques; Rocha, Maria Valderez Ponte; Gonçalves, Luciana Rocha B

    2017-08-01

    In this work, the effect of initial sugar concentration and temperature on the production of ethanol by Saccharomyces cerevisiae CCA008, a flocculent yeast, using cashew apple juice in a 1L-bioreactor was studied. The experimental results were used to develop a kinetic model relating biomass, ethanol production and total reducing sugar consumption. Monod, Andrews, Levenspiel and Ghose and Tyagi models were investigated to represent the specific growth rate without inhibition, with inhibition by substrate and with inhibition by product, respectively. Model validation was performed using a new set of experimental data obtained at 34 °C and using 100 g L -1 of initial substrate concentration. The model proposed by Ghose and Tyagi was able to accurately describe the dynamics of ethanol production by S. cerevisiae CCA008 growing on cashew apple juice, containing an initial reducing sugar concentration ranging from 70 to 170 g L -1 and temperature, from 26 to 42 °C. The model optimization was also accomplished based on the following parameters: percentage volume of ethanol per volume of solution (%V ethanol /V solution ), efficiency and reaction productivity. The optimal operational conditions were determined using response surface graphs constructed with simulated data, reaching an efficiency and a productivity of 93.5% and 5.45 g L -1  h -1 , respectively.

  17. Atrial Heterogeneity Generates Re-entrant Substrate during Atrial Fibrillation and Anti-arrhythmic Drug Action: Mechanistic Insights from Canine Atrial Models

    Science.gov (United States)

    Varela, Marta; Hancox, Jules C.; Aslanidi, Oleg V.

    2016-01-01

    Anti-arrhythmic drug therapy is a frontline treatment for atrial fibrillation (AF), but its success rates are highly variable. This is due to incomplete understanding of the mechanisms of action of specific drugs on the atrial substrate at different stages of AF progression. We aimed to elucidate the role of cellular, tissue and organ level atrial heterogeneities in the generation of a re-entrant substrate during AF progression, and their modulation by the acute action of selected anti-arrhythmic drugs. To explore the complex cell-to-organ mechanisms, a detailed biophysical models of the entire 3D canine atria was developed. The model incorporated atrial geometry and fibre orientation from high-resolution micro-computed tomography, region-specific atrial cell electrophysiology and the effects of progressive AF-induced remodelling. The actions of multi-channel class III anti-arrhythmic agents vernakalant and amiodarone were introduced in the model by inhibiting appropriate ionic channel currents according to experimentally reported concentration-response relationships. AF was initiated by applied ectopic pacing in the pulmonary veins, which led to the generation of localized sustained re-entrant waves (rotors), followed by progressive wave breakdown and rotor multiplication in both atria. The simulated AF scenarios were in agreement with observations in canine models and patients. The 3D atrial simulations revealed that a re-entrant substrate was typically provided by tissue regions of high heterogeneity of action potential duration (APD). Amiodarone increased atrial APD and reduced APD heterogeneity and was more effective in terminating AF than vernakalant, which increased both APD and APD dispersion. In summary, the initiation and sustenance of rotors in AF is linked to atrial APD heterogeneity and APD reduction due to progressive remodelling. Our results suggest that anti-arrhythmic strategies that increase atrial APD without increasing its dispersion are

  18. Structure-function relationship of a plant NCS1 member--homology modeling and mutagenesis identified residues critical for substrate specificity of PLUTO, a nucleobase transporter from Arabidopsis.

    Directory of Open Access Journals (Sweden)

    Sandra Witz

    Full Text Available Plastidic uracil salvage is essential for plant growth and development. So far, PLUTO, the plastidic nucleobase transporter from Arabidopsis thaliana is the only known uracil importer at the inner plastidic membrane which represents the permeability barrier of this organelle. We present the first homology model of PLUTO, the sole plant NCS1 member from Arabidopsis based on the crystal structure of the benzyl hydantoin transporter MHP1 from Microbacterium liquefaciens and validated by molecular dynamics simulations. Polar side chains of residues Glu-227 and backbones of Val-145, Gly-147 and Thr-425 are proposed to form the binding site for the three PLUTO substrates uracil, adenine and guanine. Mutational analysis and competition studies identified Glu-227 as an important residue for uracil and to a lesser extent for guanine transport. A differential response in substrate transport was apparent with PLUTO double mutants E227Q G147Q and E227Q T425A, both of which most strongly affected adenine transport, and in V145A G147Q, which markedly affected guanine transport. These differences could be explained by docking studies, showing that uracil and guanine exhibit a similar binding mode whereas adenine binds deep into the catalytic pocket of PLUTO. Furthermore, competition studies confirmed these results. The present study defines the molecular determinants for PLUTO substrate binding and demonstrates key differences in structure-function relations between PLUTO and other NCS1 family members.

  19. Structure-function relationship of a plant NCS1 member--homology modeling and mutagenesis identified residues critical for substrate specificity of PLUTO, a nucleobase transporter from Arabidopsis.

    Science.gov (United States)

    Witz, Sandra; Panwar, Pankaj; Schober, Markus; Deppe, Johannes; Pasha, Farhan Ahmad; Lemieux, M Joanne; Möhlmann, Torsten

    2014-01-01

    Plastidic uracil salvage is essential for plant growth and development. So far, PLUTO, the plastidic nucleobase transporter from Arabidopsis thaliana is the only known uracil importer at the inner plastidic membrane which represents the permeability barrier of this organelle. We present the first homology model of PLUTO, the sole plant NCS1 member from Arabidopsis based on the crystal structure of the benzyl hydantoin transporter MHP1 from Microbacterium liquefaciens and validated by molecular dynamics simulations. Polar side chains of residues Glu-227 and backbones of Val-145, Gly-147 and Thr-425 are proposed to form the binding site for the three PLUTO substrates uracil, adenine and guanine. Mutational analysis and competition studies identified Glu-227 as an important residue for uracil and to a lesser extent for guanine transport. A differential response in substrate transport was apparent with PLUTO double mutants E227Q G147Q and E227Q T425A, both of which most strongly affected adenine transport, and in V145A G147Q, which markedly affected guanine transport. These differences could be explained by docking studies, showing that uracil and guanine exhibit a similar binding mode whereas adenine binds deep into the catalytic pocket of PLUTO. Furthermore, competition studies confirmed these results. The present study defines the molecular determinants for PLUTO substrate binding and demonstrates key differences in structure-function relations between PLUTO and other NCS1 family members.

  20. Structure-Function Relationship of a Plant NCS1 Member – Homology Modeling and Mutagenesis Identified Residues Critical for Substrate Specificity of PLUTO, a Nucleobase Transporter from Arabidopsis

    Science.gov (United States)

    Witz, Sandra; Panwar, Pankaj; Schober, Markus; Deppe, Johannes; Pasha, Farhan Ahmad; Lemieux, M. Joanne; Möhlmann, Torsten

    2014-01-01

    Plastidic uracil salvage is essential for plant growth and development. So far, PLUTO, the plastidic nucleobase transporter from Arabidopsis thaliana is the only known uracil importer at the inner plastidic membrane which represents the permeability barrier of this organelle. We present the first homology model of PLUTO, the sole plant NCS1 member from Arabidopsis based on the crystal structure of the benzyl hydantoin transporter MHP1 from Microbacterium liquefaciens and validated by molecular dynamics simulations. Polar side chains of residues Glu-227 and backbones of Val-145, Gly-147 and Thr-425 are proposed to form the binding site for the three PLUTO substrates uracil, adenine and guanine. Mutational analysis and competition studies identified Glu-227 as an important residue for uracil and to a lesser extent for guanine transport. A differential response in substrate transport was apparent with PLUTO double mutants E227Q G147Q and E227Q T425A, both of which most strongly affected adenine transport, and in V145A G147Q, which markedly affected guanine transport. These differences could be explained by docking studies, showing that uracil and guanine exhibit a similar binding mode whereas adenine binds deep into the catalytic pocket of PLUTO. Furthermore, competition studies confirmed these results. The present study defines the molecular determinants for PLUTO substrate binding and demonstrates key differences in structure-function relations between PLUTO and other NCS1 family members. PMID:24621654

  1. Structure-function relationship of a plant NCS1 member - Homology modeling and mutagenesis identified residues critical for substrate specificity of PLUTO, a nucleobase transporter from arabidopsis

    KAUST Repository

    Witz, Sandra

    2014-03-12

    Plastidic uracil salvage is essential for plant growth and development. So far, PLUTO, the plastidic nucleobase transporter from Arabidopsis thaliana is the only known uracil importer at the inner plastidic membrane which represents the permeability barrier of this organelle. We present the first homology model of PLUTO, the sole plant NCS1 member from Arabidopsis based on the crystal structure of the benzyl hydantoin transporter MHP1 from Microbacterium liquefaciens and validated by molecular dynamics simulations. Polar side chains of residues Glu-227 and backbones of Val-145, Gly-147 and Thr-425 are proposed to form the binding site for the three PLUTO substrates uracil, adenine and guanine. Mutational analysis and competition studies identified Glu-227 as an important residue for uracil and to a lesser extent for guanine transport. A differential response in substrate transport was apparent with PLUTO double mutants E227Q G147Q and E227Q T425A, both of which most strongly affected adenine transport, and in V145A G147Q, which markedly affected guanine transport. These differences could be explained by docking studies, showing that uracil and guanine exhibit a similar binding mode whereas adenine binds deep into the catalytic pocket of PLUTO. Furthermore, competition studies confirmed these results. The present study defines the molecular determinants for PLUTO substrate binding and demonstrates key differences in structure-function relations between PLUTO and other NCS1 family members. 2014 Witz et al.

  2. The active site and substrate-binding mode of 1-aminocyclopropane-1-carboxylate oxidase determined by site-directed mutagenesis and comparative modelling studies.

    Science.gov (United States)

    Seo, Young Sam; Yoo, Ahrim; Jung, Jinwon; Sung, Soon-Kee; Yang, Dae Ryook; Kim, Woo Taek; Lee, Weontae

    2004-01-01

    The active site and substrate-binding mode of MD-ACO1 (Malus domestica Borkh. 1-aminocyclopropane-1-carboxylate oxidase) have been determined using site-directed mutagenesis and comparative modelling methods. The MD-ACO1 protein folds into a compact jelly-roll motif comprised of eight a-helices, 12 b-strands and several long loops. The active site is well defined as a wide cleft near the C-terminus. The co-substrate ascorbate is located in cofactor Fe2+-binding pocket, the so-called '2-His-1-carboxylate facial triad'. In addition, our results reveal that Arg244 and Ser246 are involved in generating the reaction product during enzyme catalysis. The structure agrees well with the biochemical and site-directed mutagenesis results. The three-dimensional structure together with the steady-state kinetics of both the wild-type and mutant MD-ACO1 proteins reveal how the substrate specificity of MD-ACO1 is involved in the catalytic mechanism, providing insights into understanding the fruit ripening process at atomic resolution. PMID:14972027

  3. Design of PEG-grafted-PLA nanoparticles as oral permeability enhancer for P-gp substrate drug model Famotidine.

    Science.gov (United States)

    Mokhtar, Mohamed; Gosselin, Patrick; Lacasse, François; Hildgen, Patrice

    2017-02-01

    Bioavailability of oral drugs can be limited by an intestinal excretion process mediated by P-glycoprotein (P-gp). Polyethylene glycol (PEG) is a known P-gp inhibitor. Dispersion of Famotidine (a P-gp substrate) within PEGylated nanoparticles (NPs) was used to improve its oral bioavailability. In this work, we evaluated the potential impact of NPs prepared from a grafted copolymer of polylactic acid and PEG on P-gp function by studying in vitro permeability of Famotidine across Caco-2 cells. Copolymers of PEG grafted on polylactic acid (PLA) backbone (PLA-g-PEG) were synthesised with 1 mol% and 5 mol% PEG vs. lactic acid monomer using PEG 750 and 2000 Da. The polymers were used to prepare Famotidine-loaded NPs and tested in vitro on Caco-2 cells. Significant decrease in basolateral-to-apical transport of Famotidine was observed when Famotidine was encapsulated in NPs prepared from PLA-g-PEG5%. NPs prepared from PLA-g-PEG5% are promising to improve oral bioavailability of P-gp substrates.

  4. Production of aggregation prone human interferon gamma and its mutant in highly soluble and biologically active form by SUMO fusion technology.

    Science.gov (United States)

    Tileva, M; Krachmarova, E; Ivanov, I; Maskos, K; Nacheva, G

    2016-01-01

    The Escherichia coli expression system is a preferable choice for production of recombinant proteins. A disadvantage of this system is the target protein aggregation in "inclusion bodies" (IBs) that further requires solubilisation and refolding, which is crucial for the properties and the yield of the final product. In order to prevent aggregation, SUMO fusion tag technology has been successfully applied for expression of eukaryotic proteins, including human interferon gamma (hIFNγ) that was reported, however, with no satisfactory biological activity. We modified this methodology for expression and purification of both the wild type hIFNγ and an extremely prone to aggregation mutant hIFNγ-K88Q, whose recovery from IBs showed to be ineffective upon numerous conditions. By expression of the N-terminal His-SUMO fusion proteins in the E. coli strain BL21(DE3)pG-KJE8, co-expressing two chaperone systems, at 24 °C a significant increase in solubility of both target proteins (1.5-fold for hIFNγ and 8-fold for K88Q) was achieved. Two-step chromatography (affinity and ion-exchange) with on-dialysis His-SUMO-tag cleavage was applied for protein purification that yielded 6.0-7.0mg/g wet biomass for both proteins with >95% purity and native N-termini. The optimised protocol led to increased yields from 5.5 times for hIFNγ up to 100 times for K88Q in comparison to their isolation from IBs. Purified hIFNγ showed preserved thermal stability and antiproliferative activity corresponding to that of the native reference sample (3 × 10(7)IU/mg). The developed methodology represents an optimised procedure that can be successfully applied for large scale expression and purification of aggregation-prone proteins in soluble native form. Copyright © 2015 Elsevier Inc. All rights reserved.

  5. Substrate noise coupling in RFICs

    CERN Document Server

    Helmy, Ahmed

    2008-01-01

    Substrate Noise Coupling in RFICs addresses substrate noise coupling in RF and mixed signal ICs when used in a system on chip (SoC) containing digital ICs as well. This trend of integrating RF, mixed signal ICs with large digital ICs is found in many of today's commercial ICs such as single chip Wi-Fi or Bluetooth solutions and is expected to grow rapidly in the future. The book reports modeling and simulation techniques for substrate noise coupling effects in RFICs and introduces isolation structures and design guides to mitigate such effects with the ultimate goal of enhancing the yield of R

  6. SUMO proteases ULP1c and ULP1d are required for development and osmotic stress responses in Arabidopsis thaliana

    DEFF Research Database (Denmark)

    Castro, Pedro Humberto Araújo R F; Couto, Daniel; Freitas, Sara

    2016-01-01

    defects in growth and germination were uncovered using loss-of-function mutants. Microarray analysis evidenced not only a deregulation of genes involved in development, but also in genes controlled by various drought-associated transcriptional regulators. We demonstrated that ulp1c ulp1d displayed...... diminished in vitro root growth under low water potential and higher stomatal aperture, yet leaf transpirational water loss and whole drought tolerance were not significantly altered. Generation of a triple siz1 ulp1c ulp1d mutant suggests that ULP1c/d and the SUMO E3 ligase SIZ1 may display separate...

  7. A Comuputerized DRBEM model for generalized magneto-thermo-visco-elastic stress waves in functionally graded anisotropic thin film/substrate structures

    Directory of Open Access Journals (Sweden)

    Mohamed Abdelsabour Fahmy

    Full Text Available A numerical computer model, based on the dual reciprocity boundary element method (DRBEM for studying the generalized magneto-thermo-visco-elastic stress waves in a rotating functionally graded anisotropic thin film/substrate structure under pulsed laser irradiation is established. An implicit-implicit staggered algorithm was proposed and implemented for use with the DRBEM to get the solution for the temperature, displacement components and thermal stress components through the structure thickness. A comparison of the results for different theories is presented in the presence and absence of rotation. Some numerical results that demonstrate the validity of the proposed method are also presented.

  8. Oxidation of dibenzothiophene as a model substrate for the removal of organic sulphur from fossil fuels by iron(III ions generated from pyrite by Acidithiobacillus ferrooxidans

    Directory of Open Access Journals (Sweden)

    VLADIMIR P. BESKOSKI

    2007-06-01

    Full Text Available Within this paper a new idea for the removal of organically bonded sulphur from fossil fuels is discussed. Dibenzothiophene (DBT was used as a model compound of organicmolecules containing sulphur. This form of (biodesulphurization was performed by an indirect mechanism in which iron(III ions generated from pyrite by Acidithiobacillus ferrooxidans performed the abiotic oxidation. The obtained reaction products, dibenzothiopene sulfoxide and dibenzothiophene sulfone, are more soluble in water than the basic substrate and the obtained results confirmed the basic hypothesis and give the posibility of continuing the experiments related to application of this (biodesulphurization process.

  9. Interaction of Pd with α-Al2O3(0001): A case study of modeling the metal-oxide interface on complex substrates

    OpenAIRE

    Gomes, J. R. B.; Illas, Francesc; Cruz Hernández, Norge; Márquez Cruz, Antonio Marcial; Fernández Sanz, Javier

    2002-01-01

    The Pd/α-Al2O3(0001) interface at low Pd coverage has been studied by a variety of theoretical methods and models at this metal-oxide interface. All results are consistent and predict a noticeable interaction dominated by the metal polarization in response to the presence of the substrate. A significant contribution of the charge transfer from the transition metal to the surface is also observed. The periodic fully relaxed calculations show that the most favorable adsorption site for the inte...

  10. Statistical evaluation and modeling of cheap substrate-based cultivation medium of Chlorella vulgaris to enhance microalgae lipid as new potential feedstock for biolubricant.

    Science.gov (United States)

    Mohammad Mirzaie, M A; Kalbasi, M; Mousavi, S M; Ghobadian, B

    2016-05-18

    Chlorella vulgaris (C. vulgaris) microalga was investigated as a new potential feedstock for the production of biodegradable lubricant. In order to enhance microalgae lipid for biolubricant production, mixotrophic growth of C. vulgaris was optimized using statistical analysis of Plackett-Burman (P-B) and response surface methodology (RSM). A cheap substrate-based medium of molasses and corn steep liquor (CSL) was used instead of expensive mineral salts to reduce the total cost of microalgae production. The effects of molasses and CSL concentration (cheap substrates) and light intensity on the growth of microalgae and their lipid content were analyzed and modeled. Designed models by RSM showed good compatibility with a 95% confidence level when compared to the cultivation system. According to the models, optimal cultivation conditions were obtained with biomass productivity of 0.123 g L(-1) day(-1) and lipid dry weight of 0.64 g L(-1) as 35% of dry weight of C. vulgaris. The extracted microalgae lipid presented useful fatty acid for biolubricant production with viscosities of 42.00 cSt at 40°C and 8.500 cSt at 100°C, viscosity index of 185, flash point of 185°C, and pour point of -6°C. These properties showed that microalgae lipid could be used as potential feedstock for biolubricant production.

  11. Electromagnetic modelling of Raman enhancement from nanoscale substrates: a route to estimation of the magnitude of the chemical enhancement mechanism in SERS.

    Science.gov (United States)

    Brown, Richard J C; Wang, Jian; Tantra, Ratna; Yardley, Rachel E; Milton, Martin J T

    2006-01-01

    Despite widespread use for more than two decades, the SERS phenomenon has defied accurate physical and chemical explanation. The relative contributions from electronic and chemical mechanisms are difficult to quantify and are often not reproduced under nominally similar experimental conditions. This work has used electromagnetic modelling to predict the Raman enhancement expected from three configurations: metal nanoparticles, structured metal surfaces, and sharp metal tips interacting with metal surfaces. In each case, parameters such as artefact size, artefact separation and incident radiation wavelength have been varied and the resulting electromagnetic field modelled. This has yielded an electromagnetic description of these configurations with predictions of the maximum expected Raman enhancement, and hence a prediction of the optimum substrate configuration for the SERS process. When combined with experimental observations of the dependence of Raman enhancement with changing ionic strength, the modelling results have allowed a novel estimate of the size of the chemical enhancement mechanism to be produced.

  12. BPD Following Preterm Birth: A Model for Chronic Lung Disease and a Substrate for ARDS in Childhood.

    Science.gov (United States)

    Bhandari, Anita; Carroll, Christopher; Bhandari, Vineet

    2016-01-01

    It has been suggested that pediatric acute respiratory distress syndrome (PARDS) may be a different entity, vis-à-vis adult acute respiratory distress syndrome (ARDS), based on its epidemiology and outcomes. A more pediatric-specific definition of PARDS to include the subgroup of patients with underlying lung (and heart) disease has been proposed. Epidemiological data suggest that up to 13% of the children with ARDS have a history of prematurity and/or underlying chronic lung disease. However, the specific contribution of bronchopulmonary dysplasia (BPD), the most common chronic lung disease in infants, to the development of PARDS is not known. BPD leads to damaged lungs with long-term consequences secondary to disordered growth and immune function. These damaged lungs could potentially act as a substrate, which given the appropriate noxious stimuli, can predispose a child to PARDS. Interestingly, similar biomarkers [KL-6, interleukin (IL)-6, IL-8, sICAM-1, angiopoietin-2, and matrix metalloproteinase-8 and -9] of pulmonary injury have been associated both with BPD and ARDS. Recognition of a unique pattern of clinical symptomatology and/or outcomes of PARDS, if present, could potentially be useful for investigating targeted therapeutic interventions.

  13. Substrate compositional variation with tissue/region and Gba1 mutations in mouse models--implications for Gaucher disease.

    Directory of Open Access Journals (Sweden)

    Ying Sun

    Full Text Available Gaucher disease results from GBA1 mutations that lead to defective acid β-glucosidase (GCase mediated cleavage of glucosylceramide (GC and glucosylsphingosine as well as heterogeneous manifestations in the viscera and CNS. The mutation, tissue, and age-dependent accumulations of different GC species were characterized in mice with Gba1 missense mutations alone or in combination with isolated saposin C deficiency (C*. Gba1 heteroallelism for D409V and null alleles (9V/null led to GC excesses primarily in the visceral tissues with preferential accumulations of lung GC24∶0, but not in liver, spleen, or brain. Age-dependent increases of different GC species were observed. The combined saposin C deficiency (C* with V394L homozygosity (4L;C* showed major GC18:0 degradation defects in the brain, whereas the analogous mice with D409H homozygosity and C* (9H;C* led to all GC species accumulating in visceral tissues. Glucosylsphingosine was poorly degraded in brain by V394L and D409H GCases and in visceral tissues by D409V GCase. The neonatal lethal N370S/N370S genotype had insignificant substrate accumulations in any tissue. These results demonstrate age, organ, and mutation-specific quantitative differences in GC species and glucosylsphingosine accumulations that can have influence in the tissue/regional expression of Gaucher disease phenotypes.

  14. Detection of O-propargyl-puromycin with SUMO and ubiquitin by click chemistry at PML-nuclear bodies during abortive proteasome activities

    Energy Technology Data Exchange (ETDEWEB)

    Uozumi, Naoki; Matsumoto, Hotaru [Course for Biological Sciences, Faculty of Science, Kumamoto University, Kumamoto (Japan); Saitoh, Hisato, E-mail: hisa@kumamoto-u.ac.jp [Course for Biological Sciences, Faculty of Science, Kumamoto University, Kumamoto (Japan); Department of Biological Sciences, Graduate School of Science and Technology, Kumamoto University, Kumamoto (Japan)

    2016-05-27

    The amino-nucleoside antibiotic, puromycin, acts by covalently linking to elongating polypeptide chains on ribosomes to generate prematurely terminated immature polypeptides. The trafficking of puromycin-conjugated (puromycylated) immature polypeptides within cell has, however, remained elusive. In this study, using O-propargyl-puromycin (OP-Puro), the distribution of puromycylated polypeptides was assessed in HeLa cells by click chemistry. Under standard culture conditions, OP-Puro signals were detected in the cytoplasm and nucleus with the highest concentrations in the nucleolus. Intriguingly, when proteasome activities were aborted using MG132, OP-Puro signals began to accumulate at promyelocytic leukemia nuclear bodies (PML-NBs) in addition to the nucleolus. We also found promiscuous association of OP-Puro signals with SUMO-2/3 and ubiquitin at PML-NBs, but not at the nucleolus, during abortive proteasome activities. This study reveals a previously unknown distribution of OP-Puro that argues for a nuclear function in regulating immature protein homeostasis. -- Highlights: •Click chemistry detects O-propargyl-puromycin (OP-Puro) signals in the nucleus. •OP-Puro accumulates at PML-NBs during abortive proteasome activities. •SUMO and ubiquitin are promiscuously associated with OP-Puro at PML-NBs. •The nucleus may function in immature protein homeostasis.

  15. Detection of O-propargyl-puromycin with SUMO and ubiquitin by click chemistry at PML-nuclear bodies during abortive proteasome activities

    International Nuclear Information System (INIS)

    Uozumi, Naoki; Matsumoto, Hotaru; Saitoh, Hisato

    2016-01-01

    The amino-nucleoside antibiotic, puromycin, acts by covalently linking to elongating polypeptide chains on ribosomes to generate prematurely terminated immature polypeptides. The trafficking of puromycin-conjugated (puromycylated) immature polypeptides within cell has, however, remained elusive. In this study, using O-propargyl-puromycin (OP-Puro), the distribution of puromycylated polypeptides was assessed in HeLa cells by click chemistry. Under standard culture conditions, OP-Puro signals were detected in the cytoplasm and nucleus with the highest concentrations in the nucleolus. Intriguingly, when proteasome activities were aborted using MG132, OP-Puro signals began to accumulate at promyelocytic leukemia nuclear bodies (PML-NBs) in addition to the nucleolus. We also found promiscuous association of OP-Puro signals with SUMO-2/3 and ubiquitin at PML-NBs, but not at the nucleolus, during abortive proteasome activities. This study reveals a previously unknown distribution of OP-Puro that argues for a nuclear function in regulating immature protein homeostasis. -- Highlights: •Click chemistry detects O-propargyl-puromycin (OP-Puro) signals in the nucleus. •OP-Puro accumulates at PML-NBs during abortive proteasome activities. •SUMO and ubiquitin are promiscuously associated with OP-Puro at PML-NBs. •The nucleus may function in immature protein homeostasis.

  16. Modeling Geometric Arrangements of TiO2-Based Catalyst Substrates and Isotropic Light Sources to Enhance the Efficiency of a Photocatalystic Oxidation (PCO) Reactor

    Science.gov (United States)

    Richards, Jeffrey T.; Levine, Lanfang H.; Husk, Geoffrey K.

    2011-01-01

    The closed confined environments of the ISS, as well as in future spacecraft for exploration beyond LEO, provide many challenges to crew health. One such challenge is the availability of a robust, energy efficient, and re-generable air revitalization system that controls trace volatile organic contaminants (VOCs) to levels below a specified spacecraft maximum allowable concentration (SMAC). Photocatalytic oxidation (PCO), which is capable of mineralizing VOCs at room temperature and of accommodating a high volumetric flow, is being evaluated as an alternative trace contaminant control technology. In an architecture of a combined air and water management system, placing a PCO unit before a condensing heat exchanger for humidity control will greatly reduce the organic load into the humidity condensate loop ofthe water processing assembly (WPA) thereby enhancing the life cycle economics ofthe WPA. This targeted application dictates a single pass efficiency of greater than 90% for polar VOCs. Although this target was met in laboratory bench-scaled reactors, no commercial or SBIR-developed prototype PCO units examined to date have achieved this goal. Furthermore, the formation of partial oxidation products (e.g., acetaldehyde) was not eliminated. It is known that single pass efficiency and partial oxidation are strongly dependent upon the contact time and catalyst illumination, hence the requirement for an efficient reactor design. The objective of this study is to maximize the apparent contact time and illuminated catalyst surface area at a given reactor volume and volumetric flow. In this study, a Ti02-based photocatalyst is assumed to be immobilized on porous substrate panels and illumination derived from linear isotropic light sources. Mathematical modeling using computational fluid dynamics (CFD) analyses were performed to investigate the effect of: 1) the geometry and configuration of catalyst-coated substrate panels, 2) porosity of the supporting substrate, and 3

  17. Iron deposition following chronic myocardial infarction as a substrate for cardiac electrical anomalies: initial findings in a canine model.

    Directory of Open Access Journals (Sweden)

    Ivan Cokic

    evolve as an arrhythmogenic substrate in the post MI period.

  18. Consumption and release of dissolved organic carbon by marine bacteria in a pulsed-substrate environment: from experiments to modelling.

    NARCIS (Netherlands)

    Eichinger, M.; Kooijman, S.A.L.M.; Sempere, R.; Poggiale, J.C.

    2009-01-01

    To investigate the effects of episodic occurrence of dissolved organic carbon(DOC) in the natural environment, bacterial degradation of labile DOC was studied under laboratory-controlled conditions followed by modelling. A single labile DOC compound was periodically added to the experimental culture

  19. Reduced tract integrity of the model for social communication is a neural substrate of social communication deficits in autism spectrum disorder.

    Science.gov (United States)

    Lo, Yu-Chun; Chen, Yu-Jen; Hsu, Yung-Chin; Tseng, Wen-Yih Isaac; Gau, Susan Shur-Fen

    2017-05-01

    Autism spectrum disorder (ASD) is a neurodevelopmental disorder with social communication deficits as one of the core symptoms. Recently, a five-level model for the social communication has been proposed in which white matter tracts corresponding to each level of the model are identified. Given that the model for social communication subserves social language functions, we hypothesized that the tract integrity of the model for social communication may be reduced in ASD, and the reduction may be related to social communication deficits. Sixty-two right-handed boys with ASD and 55 typically developing (TD) boys received clinical evaluations, intelligence tests, the Social Communication Questionnaire (SCQ), and MRI scans. Generalized fractional anisotropy (GFA) was measured by diffusion spectrum imaging to indicate the microstructural integrity of the tracts for each level of the social communication model. Group difference in the tract integrity and its relationship with the SCQ subscales of social communication and social interaction were investigated. We found that the GFA values of the superior longitudinal fasciculus III (SLF III, level 1) and the frontal aslant tracts (FAT, level 2) were decreased in ASD compared to TD. Moreover, the GFA values of the SLF III and the FAT were associated with the social interaction subscale in ASD. The tract integrity of the model for social communication is reduced in ASD, and the reduction is associated with impaired social interaction. Our results support that reduced tract integrity of the model for social communication might be a neural substrate of social communication deficits in ASD. © 2016 Association for Child and Adolescent Mental Health.

  20. Droplet dynamics on patterned substrates

    Indian Academy of Sciences (India)

    tens of microns and it is important to understand how their spreading depends on the properties of the substrate onto which they are printed. Experimental work on such mesoscopic drops is difficult and expensive because of the length and time scales involved. Therefore there is a need for numerical modelling both to ...

  1. Quantum chemical modeling of the reaction path of chorismate mutase based on the experimental substrate/product complex.

    Science.gov (United States)

    Burschowsky, Daniel; Krengel, Ute; Uggerud, Einar; Balcells, David

    2017-06-01

    Chorismate mutase is a well-known model enzyme, catalyzing the Claisen rearrangement of chorismate to prephenate. Recent high-resolution crystal structures along the reaction coordinate of this enzyme enabled computational analyses at unprecedented detail. Using quantum chemical simulations, we investigated how the catalytic reaction mechanism is affected by electrostatic and hydrogen-bond interactions. Our calculations showed that the transition state (TS) was mainly stabilized electrostatically, with Arg90 playing the leading role. The effect was augmented by selective hydrogen-bond formation to the TS in the wild-type enzyme, facilitated by a small-scale local induced fit. We further identified a previously underappreciated water molecule, which separates the negative charges during the reaction. The analysis includes the wild-type enzyme and a non-natural enzyme variant, where the catalytic arginine was replaced with an isosteric citrulline residue.

  2. AMPK activation through mitochondrial regulation results in increased substrate oxidation and improved metabolic parameters in models of diabetes.

    Directory of Open Access Journals (Sweden)

    Yonchu Jenkins

    Full Text Available Modulation of mitochondrial function through inhibiting respiratory complex I activates a key sensor of cellular energy status, the 5'-AMP-activated protein kinase (AMPK. Activation of AMPK results in the mobilization of nutrient uptake and catabolism for mitochondrial ATP generation to restore energy homeostasis. How these nutrient pathways are affected in the presence of a potent modulator of mitochondrial function and the role of AMPK activation in these effects remain unclear. We have identified a molecule, named R419, that activates AMPK in vitro via complex I inhibition at much lower concentrations than metformin (IC50 100 nM vs 27 mM, respectively. R419 potently increased myocyte glucose uptake that was dependent on AMPK activation, while its ability to suppress hepatic glucose production in vitro was not. In addition, R419 treatment of mouse primary hepatocytes increased fatty acid oxidation and inhibited lipogenesis in an AMPK-dependent fashion. We have performed an extensive metabolic characterization of its effects in the db/db mouse diabetes model. In vivo metabolite profiling of R419-treated db/db mice showed a clear upregulation of fatty acid oxidation and catabolism of branched chain amino acids. Additionally, analyses performed using both (13C-palmitate and (13C-glucose tracers revealed that R419 induces complete oxidation of both glucose and palmitate to CO2 in skeletal muscle, liver, and adipose tissue, confirming that the compound increases mitochondrial function in vivo. Taken together, our results show that R419 is a potent inhibitor of complex I and modulates mitochondrial function in vitro and in diabetic animals in vivo. R419 may serve as a valuable molecular tool for investigating the impact of modulating mitochondrial function on nutrient metabolism in multiple tissues and on glucose and lipid homeostasis in diabetic animal models.

  3. Substrate curvature regulates cell migration.

    Science.gov (United States)

    He, Xiuxiu; Jiang, Yi

    2017-05-23

    Cell migration is essential in many aspects of biology. Many basic migration processes, including adhesion, membrane protrusion and tension, cytoskeletal polymerization, and contraction, have to act in concert to regulate cell migration. At the same time, substrate topography modulates these processes. In this work, we study how substrate curvature at micrometer scale regulates cell motility. We have developed a 3D mechanical model of single cell migration and simulated migration on curved substrates with different curvatures. The simulation results show that cell migration is more persistent on concave surfaces than on convex surfaces. We have further calculated analytically the cell shape and protrusion force for cells on curved substrates. We have shown that while cells spread out more on convex surfaces than on concave ones, the protrusion force magnitude in the direction of migration is larger on concave surfaces than on convex ones. These results offer a novel biomechanical explanation to substrate curvature regulation of cell migration: geometric constrains bias the direction of the protrusion force and facilitates persistent migration on concave surfaces.

  4. New approach to characterise physicochemical properties of solid substrates by inverse gas chromatography at infinite dilution. III. Determination of the acid-base properties of some solid substrates (polymers, oxides and carbon fibres): a new model.

    Science.gov (United States)

    Hamieh, Tayssir; Fadlallah, Mohamed-Baker; Schultz, Jacques

    2002-09-06

    In this paper, the inverse gas chromatography (IGC) technique was used to calculate the acid-base superficial characteristics of some solid substrates such as oxides, polymer and polymer adsorbed on oxide. The acid-base constants were calculated for many solids: Monogal, MgO, ZnO, SiO2 and Al2O3, four different carbon fibres and polymers such as poly(methyl methacrylate) (PMMA) at various tacticities adsorbed on alumina or silica. The determination, by IGC, of the specific free enthalpy deltaG(a)sp of adsorption corresponding to the specific interactions of polar molecules with the solid, as a function of the temperature, allowed to obtain the specific enthalpy deltaH(a)sp and specific entropy deltaS(a)sp. Knowing deltaH(a)sp of the various polar molecules, we were able to determine the acidic constant K(A) and basic constant K(D), the two constants characterizing solid substrates like PMMA, PMMA-SiO2 or PMMA-Al2O3, using the following classical expression: - deltaH(a)sp = K(A)DN + K(D)AN where DN and AN are respectively the electron donor and acceptor numbers of the solid substrates. This study showed an important effect of the tacticity on the acid-base properties. On the other hand, we proved that the previous relation was not correct in many cases and especially for some oxides (as MgO, ZnO and Monogal) and carbon fibres. We proposed a new relationship by adding a third parameter K reflecting the amphoteric character of the solid according to: - deltaH(a)sp = K(A)DN + K(D)AN - KDN x AN.

  5. P-glycoprotein Mediated Efflux Limits Substrate and Drug Uptake in a Preclinical Brain Metastases of Breast Cancer Model

    Directory of Open Access Journals (Sweden)

    Chris E Adkins

    2013-11-01

    Full Text Available The blood-brain barrier (BBB is a specialized vascular interface that restricts the entry of many compounds into brain. This is accomplished through the sealing of vascular endothelial cells together with tight junction proteins to prevent paracellular diffusion. In addition, the BBB has a high degree of expression of numerous efflux transporters which actively extrude compounds back into blood. However, when a metastatic lesion develops in brain the vasculature is typically compromised with increases in passive permeability (blood-tumor barrier; BTB. What is not well documented is to what degree active efflux retains function at the BTB despite the changes observed in passive permeability. In addition, there have been previous reports documenting both increased and decreased expression of P-gp in lesion vasculature. Herein, we simultaneously administer a passive diffusion marker (14C-AIB and a tracer subject to P-gp efflux (rhodamine 123 into a murine preclinical model of brain metastases of breast cancer. We observed that the metastatic lesions had similar expression (p>0.05; n=756-1214 vessels evaluated at the BBB and the BTB. Moreover, tissue distribution of R123 was not significantly (p>0.05 different between normal brain and the metastatic lesion. It is possible that the similar expression of P-gp on the BBB and the BTB contribute to this phenomenon. Additionally we observed P-gp expression at the metastatic cancer cells adjacent to the vasculature which may also contribute to reduced R123 uptake into the lesion. The data suggest that despite the disrupted integrity of the BTB, efflux mechanisms appear to be intact, and may be functionally comparable to the normal BBB. The BTB is a significant hurdle to delivering drugs to brain metastasis.

  6. Designing specificity of protein-substrate interactions

    NARCIS (Netherlands)

    Coluzza, I.; Frenkel, D.

    2004-01-01

    One of the key properties of biological molecules is that they can bind strongly to certain substrates yet interact only weakly with the very large number of other molecules that they encounter. Using a simple lattice model, we test several methods to design molecule-substrate binding specificity.

  7. Relationships between the catechol substrate binding site and amphetamine, cocaine, and mazindol binding sites in a kinetic model of the striatal transporter of dopamine in vitro.

    Science.gov (United States)

    Wayment, H; Meiergerd, S M; Schenk, J O

    1998-05-01

    Experiments were conducted to determine how (-)-cocaine and S(+)-amphetamine binding sites relate to each other and to the catechol substrate site on the striatal dopamine transporter (sDAT). In controls, m-tyramine and S(+)-amphetamine caused release of dopamine from intracellular stores at concentrations > or = 12-fold those observed to inhibit inwardly directed sDAT activity for dopamine. In preparations from animals pretreated with reserpine, m-tyramine and S(+)-amphetamine caused release of preloaded dopamine at concentrations similar to those that inhibit inwardly directed sDAT activity. S(+)-Amphetamine and m-tyramine inhibited sDAT activity for dopamine by competing for a common binding site with dopamine and each other, suggesting that phenethylamines are substrate analogues at the plasmalemmal sDAT. (-)-Cocaine inhibited sDAT at a site separate from that for substrate analogues. This site is mutually interactive with the substrate site (K(int) = 583 nM). Mazindol competitively inhibited sDAT at the substrate analogue binding site. The results with (-)-cocaine suggest that the (-)-cocaine binding site on sDAT is distinct from that of hydroxyphenethylamine substrates, reinforcing the notion that an antagonist for (-)-cocaine binding may be developed to block (-)-cocaine binding with minimal effects on dopamine transporter activity. However, a strategy of how to antagonize drugs of abuse acting as substrate analogues is still elusive.

  8. Evaluation of silicon nitride as a substrate for culture of PC12 cells: an interfacial model for functional studies in neurons.

    Directory of Open Access Journals (Sweden)

    Johan Jaime Medina Benavente

    Full Text Available Silicon nitride is a biocompatible material that is currently used as an interfacial surface between cells and large-scale integration devices incorporating ion-sensitive field-effect transistor technology. Here, we investigated whether a poly-L-lysine coated silicon nitride surface is suitable for the culture of PC12 cells, which are widely used as a model for neural differentiation, and we characterized their interaction based on cell behavior when seeded on the tested material. The coated surface was first examined in terms of wettability and topography using contact angle measurements and atomic force microscopy and then, conditioned silicon nitride surface was used as the substrate for the study of PC12 cell culture properties. We found that coating silicon nitride with poly-L-lysine increased surface hydrophilicity and that exposing this coated surface to an extracellular aqueous environment gradually decreased its roughness. When PC12 cells were cultured on a coated silicon nitride surface, adhesion and spreading were facilitated, and the cells showed enhanced morphological differentiation compared to those cultured on a plastic culture dish. A bromodeoxyuridine assay demonstrated that, on the coated silicon nitride surface, higher proportions of cells left the cell cycle, remained in a quiescent state and had longer survival times. Therefore, our study of the interaction of the silicon nitride surface with PC12 cells provides important information for the production of devices that need to have optimal cell culture-supporting properties in order to be used in the study of neuronal functions.

  9. Evaluation of Silicon Nitride as a Substrate for Culture of PC12 Cells: An Interfacial Model for Functional Studies in Neurons

    Science.gov (United States)

    Medina Benavente, Johan Jaime; Mogami, Hideo; Sakurai, Takashi; Sawada, Kazuaki

    2014-01-01

    Silicon nitride is a biocompatible material that is currently used as an interfacial surface between cells and large-scale integration devices incorporating ion-sensitive field-effect transistor technology. Here, we investigated whether a poly-L-lysine coated silicon nitride surface is suitable for the culture of PC12 cells, which are widely used as a model for neural differentiation, and we characterized their interaction based on cell behavior when seeded on the tested material. The coated surface was first examined in terms of wettability and topography using contact angle measurements and atomic force microscopy and then, conditioned silicon nitride surface was used as the substrate for the study of PC12 cell culture properties. We found that coating silicon nitride with poly-L-lysine increased surface hydrophilicity and that exposing this coated surface to an extracellular aqueous environment gradually decreased its roughness. When PC12 cells were cultured on a coated silicon nitride surface, adhesion and spreading were facilitated, and the cells showed enhanced morphological differentiation compared to those cultured on a plastic culture dish. A bromodeoxyuridine assay demonstrated that, on the coated silicon nitride surface, higher proportions of cells left the cell cycle, remained in a quiescent state and had longer survival times. Therefore, our study of the interaction of the silicon nitride surface with PC12 cells provides important information for the production of devices that need to have optimal cell culture-supporting properties in order to be used in the study of neuronal functions. PMID:24587271

  10. alpha-Bromoisovalerylurea as model substrate for studies on pharmacokinetics of glutathione conjugation in the rat. II. Pharmacokinetics and stereoselectivity of metabolism and excretion in vivo and in the perfused liver

    NARCIS (Netherlands)

    te Koppele, J.M.; Dogterom, P; Vermeulen, N P; Meijer, D K; van der Gen, A.; Mulder, G J

    1986-01-01

    The hypnotic drug alpha-bromoisovalerylurea (BIU) has been studied in the rat with respect to its potential use as model substrate to investigate the pharmacokinetics of glutathione conjugation in vivo. The major metabolites of racemic BIU are the diastereomeric glutathione conjugates (bile) and

  11. Imparting Icephobicity with Substrate Flexibility

    Science.gov (United States)

    Schutzius, Thomas; Vasileiou, Thomas; Poulikakos, Dimos

    2017-11-01

    Ice accumulation poses serious safety and performance issues for modern infrastructure. Rationally designed superhydrophobic surfaces have demonstrated potential as a passive means to mitigate ice accretion; however, further studies on solutions that reduce impalement and contact time for impacting supercooled droplets are urgently needed. Here we demonstrate the collaborative effect of substrate flexibility and surface texture on enhancing icephobicity and repelling viscous droplets. We first investigate the influence of increased viscosity on impalement resistance and droplet-substrate contact time. Then we examine the effect of droplet partial solidification on recoil by impacting supercooled water droplets onto surfaces containing ice nucleation promoters. We demonstrate a passive method for shedding partially solidified droplets that does not rely on the classic recoil mechanism. Using an energy-based model, we identify a previously unexplored mechanism whereby the substrate oscillation governs the rebound process by efficiently absorbing the droplet kinetic energy and rectifying it back, allowing for droplet recoil. This mechanism applies for a range of droplet viscosities and ice slurries, which do not rebound from rigid superhydrophobic substrates. Partial support of the Swiss National Science Foundation under Grant No. 162565 and the European Research Council under Advanced Grant No. 669908 (INTICE) is acknowledged.

  12. An Electrically Tight In Vitro Blood-Brain Barrier Model Displays Net Brain-to-Blood Efflux of Substrates for the ABC Transporters, P-gp, Bcrp and Mrp-1

    DEFF Research Database (Denmark)

    Helms, Hans Christian; Hersom, Maria; Kuhlmann, Louise Borella

    2014-01-01

    if a bovine endothelial/rat astrocyte in vitro BBB co-culture model displayed polarized transport of known efflux transporter substrates. The co-culture model displayed low mannitol permeabilities of 0.95 ± 0.1 · 10(-6) cm·s(-1) and high transendothelial electrical resistances of 1,177 ± 101 Ω·cm(2...

  13. Sensor Substrate Development

    Data.gov (United States)

    National Aeronautics and Space Administration — Novel substrates, such as aerogels and porous, low density ceramics may increase the sensitivities of chemical reaction-based sensors for toxic vapors. These sensors...

  14. Electric cell-substrate impedance sensing (ECIS) based real-time measurement of titer dependent cytotoxicity induced by adenoviral vectors in an IPI-2I cell culture model.

    Science.gov (United States)

    Müller, Jakob; Thirion, Christian; Pfaffl, Michael W

    2011-01-15

    Recombinant viral vectors are widespread tools for transfer of genetic material in various modern biotechnological applications like for example RNA interference (RNAi). However, an accurate and reproducible titer assignment represents the basic step for most downstream applications regarding a precise multiplicity of infection (MOI) adjustment. As necessary scaffold for the studies described in this work we introduce a quantitative real-time PCR (qPCR) based approach for viral particle measurement. Still an implicated problem concerning physiological effects is that the appliance of viral vectors is often attended by toxic effects on the individual target. To determine the critical viral dose leading to cell death we developed an electric cell-substrate impedance sensing (ECIS) based assay. With ECIS technology the impedance change of a current flow through the cell culture medium in an array plate is measured in a non-invasive manner, visualizing effects like cell attachment, cell-cell contacts or proliferation. Here we describe the potential of this online measurement technique in an in vitro model using the porcine ileal epithelial cell line IPI-2I in combination with an adenoviral transfection vector (Ad5-derivate). This approach shows a clear dose-depending toxic effect, as the amount of applied virus highly correlates (p<0.001) with the level of cell death. Thus this assay offers the possibility to discriminate the minimal non-toxic dose of the individual transfection method. In addition this work suggests that the ECIS-device bears the feasibility to transfer this assay to multiple other cytotoxicological questions. Copyright © 2010 Elsevier B.V. All rights reserved.

  15. Sodium/myo-Inositol Transporters: Substrate Transport Requirements and Regional Brain Expression in the TgCRND8 Mouse Model of Amyloid Pathology

    Science.gov (United States)

    Fenili, Daniela; Weng, Ying-Qi; Aubert, Isabelle; Nitz, Mark; McLaurin, JoAnne

    2011-01-01

    Inositol stereoisomers, myo- and scyllo-inositol, are known to enter the brain and are significantly elevated following oral administration. Elevations in brain inositol levels occur across a concentration gradient as a result of active transport from the periphery. There are two sodium/myo-inositol transporters (SMIT1, SMIT2) that may be responsible for regulating brain inositol levels. The goals of this study were to determine the effects of aging and Alzheimer's disease (AD)-like amyloid pathology on transporter expression, to compare regional expression and to analyze substrate requirements of the inositol transporters. QPCR was used to examine expression of the two transporters in the cortex, hippocampus and cerebellum of TgCRND8 mice, a mouse model of amyloid pathology, in comparison to non-transgenic littermates. In addition, we examined the structural features of inositol required for active transport, utilizing a cell-based competitive uptake assay. Disease pathology did not alter transporter expression in the cortex or hippocampus (p>0.005), with only minimal effects of aging observed in the cerebellum (SMIT1: F2,26 = 12.62; p = 0.0002; SMIT2: F2,26 = 8.71; p = 0.0015). Overall, brain SMIT1 levels were higher than SMIT2, however, regional differences were observed. For SMIT1, at 4 and 6 months cerebellar SMIT1 levels were significantly higher than cortical and hippocampal levels (pInositol transporter levels are stably expressed as a function of age, and expression is unaltered with disease pathology in the TgCRND8 mouse. Given the fact that scyllo-inositol is currently in clinical trials for the treatment of AD, the stable expression of inositol transporters regardless of disease pathology is an important finding. PMID:21887366

  16. Over-accumulation of nuclear IGF-1 receptor in tumor cells requires elevated expression of the receptor and the SUMO-conjugating enzyme Ubc9

    Energy Technology Data Exchange (ETDEWEB)

    Deng, Hua; Lin, Yingbo; Badin, Margherita; Vasilcanu, Daiana; Stroemberg, Thomas [Department of Oncology and Pathology, The Karolinska Institute, Cancer Center Karolinska, SE-17176 Stockholm (Sweden); Jernberg-Wiklund, Helena [Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala (Sweden); Sehat, Bita [Department of Oncology and Pathology, The Karolinska Institute, Cancer Center Karolinska, SE-17176 Stockholm (Sweden); Larsson, Olle, E-mail: olle.larsson@ki.se [Department of Oncology and Pathology, The Karolinska Institute, Cancer Center Karolinska, SE-17176 Stockholm (Sweden)

    2011-01-14

    Research highlights: {yields} SUMOylation mediates nuclear translocation of IGF-1R which activates transcription. {yields} Here we show that nuclear IGF-1R over-accumulates in tumor cells. {yields} This requires overexpression of the receptor that is a common feature in tumor cells. {yields} An increased expression of the SUMO ligase Ubc9 seems to be an involved mechanism too. -- Abstract: The insulin-like growth factor 1 receptor (IGF-1R) plays crucial roles in tumor cell growth and is overexpressed in many cancers. IGF-1R's trans-membrane kinase signaling pathways have been well characterized. Very recently, we showed that SUMOylation mediates nuclear translocation of the IGF-1R, and that nuclear IGF-1R (nIGF-1R) binds to enhancer regions and activates transcription. We identified three lysine residues in the {beta}-subunit of the receptor and that mutation of these blocks nuclear translocation and gene activation. Furthermore, accumulation of nIGF-1R was proven strongly dependent on the specific SUMO-conjugating enzyme Ubc9. Here we show that nIGF-1R originates solely from the cell membrane and that phosphorylation of the core tyrosine residues of the receptor kinase is crucial for nuclear accumulation. We also compared the levels of nIGF-1R, measured as nuclear/membrane ratios, in tumor and normal cells. We found that the breast cancer cell line MCF-7 has 13-fold higher amounts of nIGF-1R than breast epithelial cells (IME) which showed only a small amount of nIGF-1R. In comparison, the total expression of IGF-1R was only 3.7- higher in MCF-7. Comparison of several other tumor and normal cell lines showed similar tumor cell over-accumulation of nIGF-1R, exceeding the total receptor expression substantially. Ectopic overexpression (>10-fold) of the receptor increased nIGF-1R in IME cells but not to that high level as in wild type MCF-7. The levels of Ubc9 were higher in all tumor cell lines, compared to the normal cells, and this probably contributes to over

  17. Over-accumulation of nuclear IGF-1 receptor in tumor cells requires elevated expression of the receptor and the SUMO-conjugating enzyme Ubc9

    International Nuclear Information System (INIS)

    Deng, Hua; Lin, Yingbo; Badin, Margherita; Vasilcanu, Daiana; Stroemberg, Thomas; Jernberg-Wiklund, Helena; Sehat, Bita; Larsson, Olle

    2011-01-01

    Research highlights: → SUMOylation mediates nuclear translocation of IGF-1R which activates transcription. → Here we show that nuclear IGF-1R over-accumulates in tumor cells. → This requires overexpression of the receptor that is a common feature in tumor cells. → An increased expression of the SUMO ligase Ubc9 seems to be an involved mechanism too. -- Abstract: The insulin-like growth factor 1 receptor (IGF-1R) plays crucial roles in tumor cell growth and is overexpressed in many cancers. IGF-1R's trans-membrane kinase signaling pathways have been well characterized. Very recently, we showed that SUMOylation mediates nuclear translocation of the IGF-1R, and that nuclear IGF-1R (nIGF-1R) binds to enhancer regions and activates transcription. We identified three lysine residues in the β-subunit of the receptor and that mutation of these blocks nuclear translocation and gene activation. Furthermore, accumulation of nIGF-1R was proven strongly dependent on the specific SUMO-conjugating enzyme Ubc9. Here we show that nIGF-1R originates solely from the cell membrane and that phosphorylation of the core tyrosine residues of the receptor kinase is crucial for nuclear accumulation. We also compared the levels of nIGF-1R, measured as nuclear/membrane ratios, in tumor and normal cells. We found that the breast cancer cell line MCF-7 has 13-fold higher amounts of nIGF-1R than breast epithelial cells (IME) which showed only a small amount of nIGF-1R. In comparison, the total expression of IGF-1R was only 3.7- higher in MCF-7. Comparison of several other tumor and normal cell lines showed similar tumor cell over-accumulation of nIGF-1R, exceeding the total receptor expression substantially. Ectopic overexpression (>10-fold) of the receptor increased nIGF-1R in IME cells but not to that high level as in wild type MCF-7. The levels of Ubc9 were higher in all tumor cell lines, compared to the normal cells, and this probably contributes to over-accumulation of nIGF-1R

  18. Both conditional ablation and overexpression of E2 SUMO-conjugating enzyme (UBC9) in mouse pancreatic beta cells result in impaired beta cell function.

    Science.gov (United States)

    He, Xiaoyu; Lai, Qiaohong; Chen, Cai; Li, Na; Sun, Fei; Huang, Wenting; Zhang, Shu; Yu, Qilin; Yang, Ping; Xiong, Fei; Chen, Zhishui; Gong, Quan; Ren, Boxu; Weng, Jianping; Eizirik, Décio L; Zhou, Zhiguang; Wang, Cong-Yi

    2018-04-01

    Post-translational attachment of a small ubiquitin-like modifier (SUMO) to the lysine (K) residue(s) of target proteins (SUMOylation) is an evolutionary conserved regulatory mechanism. This modification has previously been demonstrated to be implicated in the control of a remarkably versatile regulatory mechanism of cellular processes. However, the exact regulatory role and biological actions of the E2 SUMO-conjugating enzyme (UBC9)-mediated SUMOylation function in pancreatic beta cells has remained elusive. Inducible beta cell-specific Ubc9 (also known as Ube2i) knockout (KO; Ubc9 Δbeta ) and transgenic (Ubc9 Tg ) mice were employed to address the impact of SUMOylation on beta cell viability and functionality. Ubc9 deficiency or overexpression was induced at 8 weeks of age using tamoxifen. To study the mechanism involved, we closely examined the regulation of the transcription factor nuclear factor erythroid 2-related factor 2 (NRF2) through SUMOylation in beta cells. Upon induction of Ubc9 deficiency, Ubc9 Δbeta islets exhibited a 3.5-fold higher accumulation of reactive oxygen species (ROS) than Ubc9 f/f control islets. Islets from Ubc9 Δbeta mice also had decreased insulin content and loss of beta cell mass after tamoxifen treatment. Specifically, at day 45 after Ubc9 deletion only 40% of beta cell mass remained in Ubc9 Δbeta mice, while 90% of beta cell mass was lost by day 75. Diabetes onset was noted in some Ubc9 Δbeta mice 8 weeks after induction of Ubc9 deficiency and all mice developed diabetes by 10 weeks following tamoxifen treatment. In contrast, Ubc9 Tg beta cells displayed an increased antioxidant ability but impaired insulin secretion. Unlike Ubc9 Δbeta mice, which spontaneously developed diabetes, Ubc9 Tg mice preserved normal non-fasting blood glucose levels without developing diabetes. It was noted that SUMOylation of NRF2 promoted its nuclear expression along with enhanced transcriptional activity, thereby preventing ROS accumulation in

  19. PREFACE: Cell-substrate interactions Cell-substrate interactions

    Science.gov (United States)

    Gardel, Margaret; Schwarz, Ulrich

    2010-05-01

    not on the amount of ligand for adhesion receptors, but on its spatial distribution [1]. New protocols for the preparation of soft elastic substrates were essential to show that adhesion structures and cytoskeleton of adherent cells strongly adapt to substrate stiffness [2], with dramatic effects for cellular decision making. For example, it has been shown recently that differentiation of mesenchymal stem cells is strongly influenced by substrate stiffness [3]. Thus, physical factors appear to be equally important as biochemical ones in determining the cellular response to its substrate [4]. The introduction of novel physical techniques not only opened up completely new perspectives regarding biological function, it also introduced a new quantitative element into this field. For example, the availability of soft elastic substrates with controlled stiffness allows us to reconstruct cellular traction forces and to correlate them with other cellular features. This development enables modeling approaches to work in close contact with experimental data, thus opening up the perspective that the field of cell-substrate interactions will become a quantitative and predictive science in the future. Because physical research into cell-substrate interactions has become one of the fastest growing research areas in cellular biophysics and materials science, we believe that it is very timely that this special issue gathers some of the on-going research effort in this field. In contrast to the non-living world, cellular systems usually interact with their environment through specific adhesion, mainly based on adhesion receptors from the integrin family. During recent years, force spectroscopy has emerged as one of the main methods to study the physics of specific adhesion. In this special issue, single cell force spectroscopy is used by Boettiger and Wehrle-Haller to characterize the strength of cell-matrix adhesion and how it is modulated by the glycocalyx [5], while Chirasatitsin

  20. Monte Carlo studies of effects of substrate size on water endash substrate interaction energy and water structure

    International Nuclear Information System (INIS)

    Fang, J.X.; Marlow, W.H.; Lu, J.X.; Lucchese, R.R.

    1997-01-01

    Water on a planar substrate and on spherical substrates of radii r=10, 15, and 20 Angstrom are studied at temperatures of 200, 240, 270, and 290 K by Monte Carlo simulations. The average water endash water potential energies and the average water endash substrate interaction energies are obtained by use of the single point charge model for the water endash water interaction and the nonsingular van der Waals potential plus the Born-type repulsive potential for the water endash substrate interaction. Water structure and water endash substrate interaction energy are shown to be sensitive to substrate size. copyright 1997 American Institute of Physics

  1. An Efficient and Accurate Method of Estimating Substrate Noise Coupling in Heavily Doped Substrates

    Science.gov (United States)

    2005-08-24

    substrate resistances in large circuits,” in Proc. European Design and Test Conference, March 1996, pp. 560-565. [5] E. Charbon , R. Gharpurey, P. Miliozzi...and E. Charbon , “Substrate coupling: modeling, simulation and design perspectives,” in Proc. of Quality Electronic Design, March 2004, pp. 283-290. [8

  2. Substrate-induced instability in gas microstrip detectors

    International Nuclear Information System (INIS)

    Bateman, J.E.; Connolly, J.F.

    1992-12-01

    The results of a programme of research into substrate-induced gain instability in gas microstrip detectors are reported. Information has been collected on a wide range of substrates including many commonly available glasses and ceramics. A theoretical model of the gain instability is proposed. While we have not yet found an acceptable substrate for the construction of high flux detectors our experience points to electronically conductive glasses as the most promising source of a stable substrate. (Author)

  3. Coating of substrates

    International Nuclear Information System (INIS)

    Cairns, J.A.; Nelson, R.L.; Woodhead, J.L.

    1979-01-01

    The process is concerned with providing substrates with coatings obtainable from sols, for example to protect the substrate (such as in nuclear reactors or hydrocarbon cracking plant) or to provide a carrier for catalytically active material. Hitherto, coatings obtained from sols have had a high porosity and high surface area so that they have not been entirely satisfactory for the above applications. In the process described, dense, low-porosity coatings are provided by contacting the substrate with a sol of refractory material (e.g. CeO 2 or SiO 2 ) convertible to a gel of density at least 40% of the theoretical density of the refractory material, and converting the sol to the gel. Optionally, the gel may be converted to a ceramic coating by firing. (author)

  4. PHD finger of the SUMO ligase Siz/PIAS family in rice reveals specific binding for methylated histone H3 at lysine 4 and arginine 2.

    Science.gov (United States)

    Shindo, Heisaburo; Suzuki, Rintaro; Tsuchiya, Wataru; Taichi, Misako; Nishiuchi, Yuji; Yamazaki, Toshimasa

    2012-06-21

    We determined the three-dimensional structure of the PHD finger of the rice Siz/PIAS-type SUMO ligase, OsSiz1, by NMR spectroscopy and investigated binding ability for a variety of methylated histone H3 tails, showing that OsSiz1-PHD primarily recognizes dimethylated Arg2 of the histone H3 and that methylations at Arg2 and Lys4 reveal synergy effect on binding to OsSiz1-PHD. The K4 cage of OsSiz1-PHD for trimethylated Lys4 of H3K4me3 was similar to that of the BPTF-PHD finger, while the R2 pocket for Arg2 was different. It is intriguing that the PHD module of Siz/PIAS plays an important role, with collaboration with the DNA binding domain SAP, in gene regulation through SUMOylation of a variety of effectors associated with the methylated arginine-riched chromatin domains. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  5. Robust plasmonic substrates

    DEFF Research Database (Denmark)

    Kostiučenko, Oksana; Fiutowski, Jacek; Tamulevicius, Tomas

    2014-01-01

    Robustness is a key issue for the applications of plasmonic substrates such as tip-enhanced Raman spectroscopy, surface-enhanced spectroscopies, enhanced optical biosensing, optical and optoelectronic plasmonic nanosensors and others. A novel approach for the fabrication of robust plasmonic...... substrates is presented, which relies on the coverage of gold nanostructures with diamond-like carbon (DLC) thin films of thicknesses 25, 55 and 105 nm. DLC thin films were grown by direct hydrocarbon ion beam deposition. In order to find the optimum balance between optical and mechanical properties...

  6. Evaluation of organ-specific glucose metabolism by 18F-FDG in insulin receptor substrate-1 (IRS-1) knockout mice as a model of insulin resistance

    International Nuclear Information System (INIS)

    Cheng, Chao; Nakamura, Akinobu; Minamimoto, Ryogo; Shinoda, Kazuaki; Tateishi, Ukihide; Terauchi, Yasuo; Inoue, Tomio; Goto, Atsuhi; Kadowaki, Takashi

    2011-01-01

    Insulin resistance (IR) is a physiological condition in which the body produces insulin but does not result in a sufficient biological effect. Insulin resistance is usually asymptomatic but is associated with health problems and is a factor in the metabolic syndrome. The aim of the present study is to clarify organ-specific insulin resistance in normal daily conditions using [ 18 F]-2-fluoro-2-deoxy-D-glucose ([ 18 F]-FDG). The biodistribution of [ 18 F]-FDG was examined in insulin receptor substrate-1 (IRS-1) knockout mice, an animal model of skeletal muscle insulin resistance, and C57BL/6J (wild-type) mice with and without insulin loading. Mice received 0.5 MBq of [ 18 F]-FDG injected into the tail vein, immediately followed by nothing (control cohorts) or an intraperitoneal injection of 1.5 mU/g body weight of human insulin as an insulin loading test. Blood glucose concentrations for all of the experimental animals were assessed at 0, 20, 40, and 60 min post-injection. The mice were subsequently killed, and tissue was collected for evaluation of [ 18 F]-FDG biodistribution. The radioactivity of each organ was measured using a gamma counter. In the absence of insulin, the blood glucose concentrations of wild-type mice (132±26 mg/dl) and IRS-1 knockout mice (134±18 mg/dl) were not significantly different. Blood glucose concentrations decreased following insulin administration, with lower concentrations in wild-type mice than in knockout mice at 20, 40, and 60 min. A statistically significant difference in [ 18 F]-FDG uptake between wild-type mice and IRS-1 knockout mice was confirmed in the heart, abdominal muscle, and femoral muscle. With insulin loading, [ 18 F]-FDG uptake in the heart, back muscle, and abdominal muscle was significantly increased compared to without insulin loading in both wild-type mice and knockout mice. Our results showed that IR significantly affected [ 18 F]-FDG uptake in the heart in normal daily conditions. IR was associated with

  7. Multiple alternative substrate kinetics.

    Science.gov (United States)

    Anderson, Vernon E

    2015-11-01

    The specificity of enzymes for their respective substrates has been a focal point of enzyme kinetics since the initial characterization of metabolic chemistry. Various processes to quantify an enzyme's specificity using kinetics have been utilized over the decades. Fersht's definition of the ratio kcat/Km for two different substrates as the "specificity constant" (ref [7]), based on the premise that the important specificity existed when the substrates were competing in the same reaction, has become a consensus standard for enzymes obeying Michaelis-Menten kinetics. The expansion of the theory for the determination of the relative specificity constants for a very large number of competing substrates, e.g. those present in a combinatorial library, in a single reaction mixture has been developed in this contribution. The ratio of kcat/Km for isotopologs has also become a standard in mechanistic enzymology where kinetic isotope effects have been measured by the development of internal competition experiments with extreme precision. This contribution extends the theory of kinetic isotope effects to internal competition between three isotopologs present at non-tracer concentrations in the same reaction mix. This article is part of a special issue titled: Enzyme Transition States from Theory and Experiment. Published by Elsevier B.V.

  8. Aplicação de quitosano na redução do escurecimento enzimático em sumo de maçã não pasteurizado (estabilizado por hiperpressão)

    OpenAIRE

    Bértolo, Diana Fernandes Quitério

    2011-01-01

    Dissertação para obtenção do Grau de Mestre em Tecnologia e Segurança Alimentar A maçã, sendo um dos frutos com maior produção em Portugal, detentor de elevado valor nutricional, apresenta um potencial comercial e industrial elevado. O consumo de sumo de maçã natural, não pasteurizado e estabilizado por hiperpressão, está em franca expansão, sendo muito apreciado pelo consumidor. No entanto, o seu tempo de prateleira é consideravelmente curto, apresentando um escurecimento enzimático ac...

  9. Experimental analysis of green roof substrate detention characteristics.

    Science.gov (United States)

    Yio, Marcus H N; Stovin, Virginia; Werdin, Jörg; Vesuviano, Gianni

    2013-01-01

    Green roofs may make an important contribution to urban stormwater management. Rainfall-runoff models are required to evaluate green roof responses to specific rainfall inputs. The roof's hydrological response is a function of its configuration, with the substrate - or growing media - providing both retention and detention of rainfall. The objective of the research described here is to quantify the detention effects due to green roof substrates, and to propose a suitable hydrological modelling approach. Laboratory results from experimental detention tests on green roof substrates are presented. It is shown that detention increases with substrate depth and as a result of increasing substrate organic content. Model structures based on reservoir routing are evaluated, and it is found that a one-parameter reservoir routing model coupled with a parameter that describes the delay to start of runoff best fits the observed data. Preliminary findings support the hypothesis that the reservoir routing parameter values can be defined from the substrate's physical characteristics.

  10. SOI MESFETs on high-resistivity, trap-rich substrates

    Science.gov (United States)

    Mehr, Payam; Zhang, Xiong; Lepkowski, William; Li, Chaojiang; Thornton, Trevor J.

    2018-04-01

    The DC and RF characteristics of metal-semiconductor field-effect-transistors (MESFETs) on conventional CMOS silicon-on-insulator (SOI) substrates are compared to nominally identical devices on high-resistivity, trap-rich SOI substrates. While the DC transfer characteristics are statistically identical on either substrate, the maximum available gain at GHz frequencies is enhanced by ∼2 dB when using the trap-rich substrates, with maximum operating frequencies, fmax, that are approximately 5-10% higher. The increased fmax is explained by the reduced substrate conduction at GHz frequencies using a lumped-element, small-signal model.

  11. Nanomechanics of hard films on compliant substrates.

    Energy Technology Data Exchange (ETDEWEB)

    Reedy, Earl David, Jr. (Sandia National Laboratories, Albuquerque, NM); Emerson, John Allen (Sandia National Laboratories, Albuquerque, NM); Bahr, David F. (Washington State University, Pullman, WA); Moody, Neville Reid; Zhou, Xiao Wang; Hales, Lucas (University of Minnesota, Minneapolis, MN); Adams, David Price (Sandia National Laboratories, Albuquerque, NM); Yeager,John (Washington State University, Pullman, WA); Nyugen, Thao D. (Johns Hopkins University, Baltimore, MD); Corona, Edmundo (Sandia National Laboratories, Albuquerque, NM); Kennedy, Marian S. (Clemson University, Clemson, SC); Cordill, Megan J. (Erich Schmid Institute, Leoben, Austria)

    2009-09-01

    a result, our understanding of the critical relationship between adhesion, properties, and fracture for hard films on compliant substrates is limited. To address this issue, we integrated nanomechanical testing and mechanics-based modeling in a program to define the critical relationship between deformation and fracture of nanoscale films on compliant substrates. The approach involved designing model film systems and employing nano-scale experimental characterization techniques to isolate effects of compliance, viscoelasticity, and plasticity on deformation and fracture of thin hard films on substrates that spanned more than two orders of compliance magnitude exhibit different interface structures, have different adhesion strengths, and function differently under stress. The results of this work are described in six chapters. Chapter 1 provides the motivation for this work. Chapter 2 presents experimental results covering film system design, sample preparation, indentation response, and fracture including discussion on the effects of substrate compliance on fracture energies and buckle formation from existing models. Chapter 3 describes the use of analytical and finite element simulations to define the role of substrate compliance and film geometry on the indentation response of thin hard films on compliant substrates. Chapter 4 describes the development and application of cohesive zone model based finite element simulations to determine how substrate compliance affects debond growth. Chapter 5 describes the use of molecular dynamics simulations to define the effects of substrate compliance on interfacial fracture of thin hard tungsten films on silicon substrates. Chapter 6 describes the Workshops sponsored through this program to advance understanding of material and system behavior.

  12. Evaluation of a SUMO E2 conjugating enzyme involved in resistance to Clavibacter michiganensis subsp. michiganensis in Solanum peruvianum, through a tomato mottle virus VIGS assay

    Directory of Open Access Journals (Sweden)

    Mayra Janeth Esparza-Araiza

    2015-12-01

    Full Text Available Clavibacter michiganensis subsp. michiganensis (Cmm causes bacterial wilt and canker of tomato. Currently, no Solanum lycopersicum resistant varieties are commercially available, but some degree of Cmm resistance has been identified in Solanum peruvianum. Previous research showed up-regulation of a SUMO E2 conjugating enzyme (SCEI transcript in resistant S. peruvianum compared to susceptible S. lycopersicum following infection by Cmm. In order to test the role of SCEI in resistance to Cmm, a fragment of the gene from S. peruvianum was cloned into a novel virus-induced gene-silencing (VIGS vector based on the geminivirus Tomato Mottle Virus (ToMoV. Using biolistic inoculation, the ToMoV-based VIGS vector was shown to be effective in S. peruvianum by silencing the magnesium chelatase gene, which resulted in leaf bleaching. The ToMoV_SCEI construct resulted in approx. 61% silencing of SCEI in leaves of S. peruvianum as determined by quantitative RT-PCR. VIGS of SCEI in S. peruvianum resulted in unilateral wilting (15 dpi and subsequent death (20 dpi of the entire plant after Cmm inoculation, whereas empty vector-treated plants only showed wilting in the Cmm-inoculated leaf. SCEI-silenced plants also showed higher Cmm colonization with an average of 4.5 times more damaged tissue compared to the empty vector control plants. SCEI appears to play an important role in the innate immunity of S. peruvianum against Cmm, perhaps through the regulation of WRKY transcription factors, which may lead to expression of proteins involved in salicylic acid-dependent defense responses.

  13. Evaluation of a SUMO E2 Conjugating Enzyme Involved in Resistance to Clavibacter michiganensis Subsp. michiganensis in Solanum peruvianum, Through a Tomato Mottle Virus VIGS Assay

    Science.gov (United States)

    Esparza-Araiza, Mayra J.; Bañuelos-Hernández, Bernardo; Argüello-Astorga, Gerardo R.; Lara-Ávila, José P.; Goodwin, Paul H.; Isordia-Jasso, María I.; Castillo-Collazo, Rosalba; Rougon-Cardoso, Alejandra; Alpuche-Solís, Ángel G.

    2015-01-01

    Clavibacter michiganensis subsp. michiganensis (Cmm) causes bacterial wilt and canker of tomato. Currently, no Solanum lycopersicum resistant varieties are commercially available, but some degree of Cmm resistance has been identified in Solanum peruvianum. Previous research showed up-regulation of a SUMO E2 conjugating enzyme (SCEI) transcript in S. peruvianum compared to S. lycopersicum following infection with Cmm. In order to test the role of SCEI in resistance to Cmm, a fragment of SCEI from S. peruvianum was cloned into a novel virus-induced gene-silencing (VIGS) vector based on the geminivirus, Tomato Mottle Virus (ToMoV). Using biolistic inoculation, the ToMoV-based VIGS vector was shown to be effective in S. peruvianum by silencing the magnesium chelatase gene, resulting in leaf bleaching. VIGS with the ToMoV_SCEI construct resulted in ~61% silencing of SCEI in leaves of S. peruvianum as determined by quantitative RT-PCR. The SCEI-silenced plants showed unilateral wilting (15 dpi) and subsequent death (20 dpi) of the entire plant after Cmm inoculation, whereas the empty vector-treated plants only showed wilting in the Cmm-inoculated leaf. The SCEI-silenced plants showed higher Cmm colonization and an average of 4.5 times more damaged tissue compared to the empty vector control plants. SCEI appears to play an important role in the innate immunity of S. peruvianum against Cmm, perhaps through the regulation of transcription factors, leading to expression of proteins involved in salicylic acid-dependent defense responses. PMID:26734014

  14. A Generic Protocol for Purifying Disulfide-Bonded Domains and Random Protein Fragments Using Fusion Proteins with SUMO3 and Cleavage by SenP2 Protease.

    Science.gov (United States)

    Besir, Hüseyin

    2017-01-01

    Recombinant expression of heterologous proteins in E. coli is well established for a wide range of proteins, although in many cases, purifying soluble and properly folded proteins remains challenging (Sorensen and Mortensen, J Biotechnol 115:113-128, 2005; Correa and Oppezzo, Methods Mol Biol 1258:27-44, 2015). Proteins that contain disulfide bonds (e.g., cytokines, growth factors) are often particularly difficult to purify in soluble form and still need optimizing of protocols in almost every step of the process (Berkmen, Protein Expr Purif 82:240-251, 2012; de Marco, Microb Cell Fact 11:129, 2012). Expression of disulfide bonded proteins in the periplasm of E. coli is one approach that can help to obtain soluble protein with the correct disulfide bridges forming in the periplasm. This offers the appropriate conditions for disulfide formation although periplasmic expression can also result in low expression levels and incorrect folding of the target protein (Schlapschy and Skerra, Methods Mol Biol 705:211-224, 2011). Generation of specific antibodies often requires a specific antigenic sequence of a protein in order to get an efficient immune response and minimize cross-reactivity of antibodies. Larger proteins like GST (Glutathione-S-transferase) or MBP (maltose binding protein) as solubilizing fusion partners are frequently used to keep antigens soluble and immunize animals. This approach has the disadvantage that the immune response against the fusion partner leads to additional antibodies that need to be separated from the antigen-specific antibodies. For both classes of proteins mentioned above, a protocol has been developed and optimized using the human version of small ubiquitin-like modifier 3 (SUMO3) protein and its corresponding protease SenP2. This chapter describes the experimental steps for expression, purification, refolding, and cleavage that are applicable to both disulfide-bonded proteins with a defined structure and random protein fragments for

  15. Crystal structure of Mycobacterium tuberculosis ClpP1P2 suggests a model for peptidase activation by AAA+ partner binding and substrate delivery.

    Science.gov (United States)

    Schmitz, Karl R; Carney, Daniel W; Sello, Jason K; Sauer, Robert T

    2014-10-28

    Caseinolytic peptidase P (ClpP), a double-ring peptidase with 14 subunits, collaborates with ATPases associated with diverse activities (AAA+) partners to execute ATP-dependent protein degradation. Although many ClpP enzymes self-assemble into catalytically active homo-tetradecamers able to cleave small peptides, the Mycobacterium tuberculosis enzyme consists of discrete ClpP1 and ClpP2 heptamers that require a AAA+ partner and protein-substrate delivery or a peptide agonist to stabilize assembly of the active tetradecamer. Here, we show that cyclic acyldepsipeptides (ADEPs) and agonist peptides synergistically activate ClpP1P2 by mimicking AAA+ partners and substrates, respectively, and determine the structure of the activated complex. Our studies establish the basis of heteromeric ClpP1P2 assembly and function, reveal tight coupling between the conformations of each ring, show that ADEPs bind only to one ring but appear to open the axial pores of both rings, provide a foundation for rational drug development, and suggest strategies for studying the roles of individual ClpP1 and ClpP2 rings in Clp-family proteolysis.

  16. Substrate mediated enzyme prodrug therapy.

    Directory of Open Access Journals (Sweden)

    Betina Fejerskov

    Full Text Available In this report, we detail Substrate Mediated Enzyme Prodrug Therapy (SMEPT as a novel approach in drug delivery which relies on enzyme-functionalized cell culture substrates to achieve a localized conversion of benign prodrug(s into active therapeutics with subsequent delivery to adhering cells or adjacent tissues. For proof-of-concept SMEPT, we use surface adhered micro-structured physical hydrogels based on poly(vinyl alcohol, β-glucuronidase enzyme and glucuronide prodrugs. We demonstrate enzymatic activity mediated by the assembled hydrogel samples and illustrate arms of control over rate of release of model fluorescent cargo. SMEPT was not impaired by adhering cells and afforded facile time - and dose - dependent uptake of the in situ generated fluorescent cargo by hepatic cells, HepG2. With the use of a glucuronide derivative of an anticancer drug, SN-38, SMEPT afforded a decrease in cell viability to a level similar to that achieved using parent drug. Finally, dose response was achieved using SMEPT and administration of judiciously chosen concentration of SN-38 glucuronide prodrug thus revealing external control over drug delivery using drug eluting surface. We believe that this highly adaptable concept will find use in diverse biomedical applications, specifically surface mediated drug delivery and tissue engineering.

  17. Overexpression of the Rice SUMO E3 Ligase Gene OsSIZ1 in Cotton Enhances Drought and Heat Tolerance, and Substantially Improves Fiber Yields in the Field under Reduced Irrigation and Rainfed Conditions

    Science.gov (United States)

    Mishra, Neelam; Sun, Li; Zhu, Xunlu; Smith, Jennifer; Prakash Srivastava, Anurag; Yang, Xiaojie; Pehlivan, Necla; Esmaeili, Nardana; Luo, Hong; Shen, Guoxin; Jones, Don; Auld, Dick; Burke, John

    2017-01-01

    The Arabidopsis SUMO E3 ligase gene AtSIZ1 plays important roles in plant response to abiotic stresses as loss of function in AtSIZ1 leads to increased sensitivity to drought, heat and salt stresses. Overexpression of the AtSIZ1 rice homolog, OsSIZ1, leads to increased heat and drought tolerance in bentgrass, suggesting that the function of the E3 ligase SIZ1 is highly conserved in plants and it plays a critical role in abiotic stress responses. To test the possibility that the SUMO E3 ligase could be used to engineer drought- and heat-tolerant crops, the rice gene OsSIZ1 was overexpressed in cotton. We report here that overexpression of OsSIZ1 in cotton results in higher net photosynthesis and better growth than wild-type cotton under drought and thermal stresses in growth chamber and greenhouse conditions. Additionally, this tolerance to abiotic stresses was correlated with higher fiber yield in both controlled-environment and field trials carried out under reduced irrigation and rainfed conditions. These results suggest that OsSIZ1 is a viable candidate gene to improve crop yields under water-limited and rainfed agricultural production systems. PMID:28340002

  18. Kinetic characterization, optimum conditions for catalysis and substrate preference of secretory phospholipase A2 from Glycine max in model membrane systems.

    Science.gov (United States)

    Mariani, María Elisa; Madoery, Ricardo Román; Fidelio, Gerardo Daniel

    2015-01-01

    Two secretory phospholipase A2 (sPLA2s) from Glycine max, GmsPLA2-IXA-1 and GmsPLA2-XIB-2, have been purified as recombinant proteins and the activity was evaluated in order to obtain the optimum conditions for catalysis using mixed micelles and lipid monolayers as substrate. Both sPLA2s showed a maximum enzyme activity at pH 7 and a requirement of Ca(2+) in the micromolar range. These parameters were similar to those found for animal sPLA2s but a surprising optimum temperature for catalysis at 60 °C was observed. The effect of negative interfacial charges on the hydrolysis of organized substrates was evaluated through initial rate measurements using short chain phospholipids with different head groups. The enzymes showed subtle differences in the specificity for phospholipids with different head groups (DLPC, DLPG, DLPE, DLPA) in presence or absence of NaCl. Both recombinant enzymes showed lower activity toward anionic phospholipids and a preference for the zwitterionic ones. The values of the apparent kinetic parameters (Vmax and KM) demonstrated that these enzymes have more affinity for phosphatidylcholine compared with phosphatidylglycerol, in contrast with the results observed for pancreatic sPLA2. A hopping mode of catalysis was proposed for the action of these sPLA2 on mixed phospholipid/triton micelles. On the other hand, Langmuir-monolayers assays indicated an optimum lateral surface pressure for activity in between 13 and 16 mN/m for both recombinant enzymes. Copyright © 2014 Elsevier B.V. and Société française de biochimie et biologie Moléculaire (SFBBM). All rights reserved.

  19. Spectroscopic investigation of new water soluble Mn(II)(2) and Mg(II)(2) complexes for the substrate binding models of xylose/glucose isomerases.

    Science.gov (United States)

    Patra, Ayan; Bera, Manindranath

    2014-01-30

    In methanol, the reaction of stoichiometric amounts of Mn(OAc)(2)·4H(2)O and the ligand H(3)hpnbpda [H(3)hpnbpda=N,N'-bis(2-pyridylmethyl)-2-hydroxy-1,3-propanediamine-N,N'-diacetic acid] in the presence of NaOH, afforded a new water soluble dinuclear manganese(II) complex, [Mn2(hpnbpda)(μ-OAc)] (1). Similarly, the reaction of Mg(OAc)(2)·4H(2)O and the ligand H3hpnbpda in the presence of NaOH, in methanol, yielded a new water soluble dinuclear magnesium(II) complex, [Mg2(hpnbpda)(μ-OAc)(H2O)2] (2). DFT calculations have been performed for the structural optimization of complexes 1 and 2. The DFT optimized structure of complex 1 shows that two manganese(II) centers are in a distorted square pyramidal geometry, whereas the DFT optimized structure of complex 2 reveals that two magnesium(II) centers adopt a six-coordinate distorted octahedral geometry. To understand the mode of substrate binding and the mechanistic details of the active site metals in xylose/glucose isomerases (XGI), we have investigated the binding interactions of biologically important monosaccharides d-glucose and d-xylose with complexes 1 and 2, in aqueous alkaline solution by a combined approach of FTIR, UV-vis, fluorescence, and (13)C NMR spectroscopic techniques. Fluorescence spectra show the binding-induced gradual decrease in emission of complexes 1 and 2 accompanied by a significant blue shift upon increasing the concentration of sugar substrates. The binding modes of d-glucose and d-xylose with complex 2 are indicated by their characteristic coordination induced shift (CIS) values in (13)C NMR spectra for C1 and C2 carbon atoms. Copyright © 2013 Elsevier Ltd. All rights reserved.

  20. The Hydra small ubiquitin-like modifier.

    Science.gov (United States)

    Khan, Umair; Mehere, Prajwalini; Deivasigamani, Senthilkumar; Ratnaparkhi, Girish S

    2013-09-01

    SUMO is a protein posttranslational modifier. SUMO cycle components are believed to be conserved in all eukaryotes. Proteomic analyses have lead to the identification a wealth of SUMO targets that are involved in almost every cellular function in eukaryotes. In this article, we describe the characterization of SUMO Cycle components in Hydra, a Cnidarian with an ability to regenerate body parts. In cells, the translated SUMO polypeptide cannot conjugate to a substrate protein unless the C-terminal tail is cleaved, exposing the di-Glycine motif. This critical task is done by SUMO proteases that in addition to SUMO maturation are also involved in deconjugating SUMO from its substrate. We describe the identification, bioinformatics analysis, cloning, and biochemical characterization of Hydra SUMO cycle components, with a focus on SUMO and SUMO proteases. We demonstrate that the ability of SUMO proteases to process immature SUMO is conserved from Hydra to flies. A transgenic Hydra, expressing a SUMO-GFP fusion protein under a constitutive actin promoter, is generated in an attempt to monitor the SUMO Cycle in vivo as also to purify and identify SUMO targets in Hydra. Copyright © 2013 Wiley Periodicals, Inc.

  1. Reduced Tract Integrity of the Model for Social Communication Is a Neural Substrate of Social Communication Deficits in Autism Spectrum Disorder

    Science.gov (United States)

    Lo, Yu-Chun; Chen, Yu-Jen; Hsu, Yung-Chin; Tseng, Wen-Yih Isaac; Gau, Susan Shur-Fen

    2017-01-01

    Background: Autism spectrum disorder (ASD) is a neurodevelopmental disorder with social communication deficits as one of the core symptoms. Recently, a five-level model for the social communication has been proposed in which white matter tracts corresponding to each level of the model are identified. Given that the model for social communication…

  2. Substrate utilization and VSS relations in activated sludge processes

    Energy Technology Data Exchange (ETDEWEB)

    Droste, R.L.; Fernandes, L.; Sun, X. [Ottawa Univ., ON (Canada). Dept. of Civil Engineering

    1993-12-31

    A new empirical substrate removal model for activated sludge in continuous flow stirred tank reactor (CFSTR) and sequencing batch reactor (SBR) was developed in this study. This model includes an exponential function of volatile suspended solids to express the active biomass which is actually involved in substrate utilization. Results indicate that the proposed exponential models predict more accurately effluent COD in CFSTR and SBR systems than the first or zero order models. (author). 7 refs., 1 fig., 4 tabs.

  3. An empirical-statistical model for laser cladding of Ti-6Al-4V powder on Ti-6Al-4V substrate

    Science.gov (United States)

    Nabhani, Mohammad; Razavi, Reza Shoja; Barekat, Masoud

    2018-03-01

    In this article, Ti-6Al-4V powder alloy was directly deposited on Ti-6Al-4V substrate using laser cladding process. In this process, some key parameters such as laser power (P), laser scanning rate (V) and powder feeding rate (F) play important roles. Using linear regression analysis, this paper develops the empirical-statistical relation between these key parameters and geometrical characteristics of single clad tracks (i.e. clad height, clad width, penetration depth, wetting angle, and dilution) as a combined parameter (PαVβFγ). The results indicated that the clad width linearly depended on PV-1/3 and powder feeding rate had no effect on it. The dilution controlled by a combined parameter as VF-1/2 and laser power was a dispensable factor. However, laser power was the dominant factor for the clad height, penetration depth, and wetting angle so that they were proportional to PV-1F1/4, PVF-1/8, and P3/4V-1F-1/4, respectively. Based on the results of correlation coefficient (R > 0.9) and analysis of residuals, it was confirmed that these empirical-statistical relations were in good agreement with the measured values of single clad tracks. Finally, these relations led to the design of a processing map that can predict the geometrical characteristics of the single clad tracks based on the key parameters.

  4. PLZT capacitor on glass substrate

    Science.gov (United States)

    Fairchild, M. Ray; Taylor, Ralph S.; Berlin, Carl W.; Wong, Celine W. K.; Ma, Beihai; Balachandran, Uthamalingam

    2016-01-05

    A lead-lanthanum-zirconium-titanate (PLZT) capacitor on a substrate formed of glass. The first metallization layer is deposited on a top side of the substrate to form a first electrode. The dielectric layer of PLZT is deposited over the first metallization layer. The second metallization layer deposited over the dielectric layer to form a second electrode. The glass substrate is advantageous as glass is compatible with an annealing process used to form the capacitor.

  5. Biomechanics of the endothelium substrate influences leukocyte transmigration

    Science.gov (United States)

    Stroka, Kimberly; Aranda-Espinoza, Helim

    2012-02-01

    The effects of shear flow and cytokines on leukocyte transmigration are well understood. However, the effects of substrate stiffness on transmigration remain unexplored. We have developed an in vitro model that allows us to study leukocyte transmigration as a function of varying physiological substrate stiffness. Interestingly, leukocyte transmigration increased with increasing substrate stiffness below the endothelium. intercellular adhesion molecule-1 expression, stiffness, cytoskeletal arrangement, morphology, and cell-substrate adhesion could not account for the dependence of transmigration on substrate stiffness. We also explored the role of cell contraction and observed that (1) neutrophil transmigration caused large hole formation in monolayers on stiff substrates. (2) Neutrophil transmigration on soft substrates was increased by decreasing cell-cell adhesion. (3) Inhibition of myosin light chain kinase normalized the effects of substrate stiffness by reducing cell contraction on stiff substrates. These results demonstrate that neutrophil transmigration is regulated by MLCK-mediated generation of gaps at cell borders through substrate stiffness-dependent endothelial cell contraction.

  6. The effect of mineral substrates on the crystallization of lysozyme

    Science.gov (United States)

    Kimble, W. L.; Paxton, T. E.; Rousseau, R. W.; Sambanis, A.

    1998-05-01

    The effects of exogenous mineral substrates on the induction time for nucleation, and on the number, morphology and purity of protein crystals were investigated in a series of experiments using chicken egg-white lysozyme (CEWL) as a model protein. CEWL was crystallized using the vapor-diffusion technique in the absence of substrates (control) and in the presence of mineral substrates exhibiting various degrees of crystalline lattice match to CEWL (experiments). Results indicate that mineral substrates with a close lattice match to CEWL had a greater influence on the induction time for nucleation and crystal properties.

  7. Substrate-induced bulk alignment of liquid crystals

    DEFF Research Database (Denmark)

    Zhang, Zhengping; Chakrabarti, A.; Mouritsen, Ole G.

    1996-01-01

    The Gay-Berne model for liquid crystals in the presence of a substrate surface is studied using the hybrid Monte Carlo method. A simple non-mean-field substrate-molecule potential is proposed to describe the effects of rubbed polymer-coated substrates on the liquid crystals. Effects...... of the substrate surface on the bulk alignment of the liquid crystals are studied. It is found that the bulk pretilt angle is controlled by the surface through the orientation of the adsorbed liquid crystal monolayer. This is consistent with the results of recent experimental studies....

  8. FEM for modelling 193 nm excimer laser treatment of SiO{sub 2}/Si/Si{sub (1-x)}Ge{sub x} heterostructures on SOI substrates

    Energy Technology Data Exchange (ETDEWEB)

    Conde, J.C.; Chiussi, S.; Gontad, F.; Gonzalez, P. [Dpto. Fisica Aplicada, E.T.S.I.I. University of Vigo, Campus Universitario, Rua Maxwell s/n, 36310 Vigo (Spain); Martin, E. [Dpto. de Mecanica, Maquinas, Motores Termicos y Fluidos, E.T.S.I.I. University of Vigo, Campus Universitario, Rua Maxwell s/n, 36310 Vigo (Spain)

    2011-03-15

    Research on epitaxial crystalline silicon (c-Si) and silicon-germanium (Si{sub 1-x}Ge{sub x}) alloys growth and annealing for microelectronic purposes, such as Micro- or Nano-Electro-Mechanical Systems (MEMS or NEMS) and Silicon-On-Nothing (SON) devices is continuously in progress. Laser assisted annealing techniques using commercial ArF Excimer Laser sources are based on ultra-rapid heating and cooling cycles induced by the 193 nm pulses of 20 ns, which are absorbed in the near surface region of the heterostructures. During and after the absorption of these laser pulses, complex physical processes appear that strongly depend on sample structure and applied laser pulse energy densities. The control of the experimental parameters is therefore a key task for obtaining high quality alloys. The Finite ElementsMethod (FEM) is a powerful tool for the optimization of such treatments, because it provides the spatial and temporal temperature fields that are produced by the laser pulses. In this work, we have used a FEM commercial software, to predict the temperatures gradients induced by ArF excimer laser over a wide energy densities range, 0.1<{phi}<0.4 J/cm{sup 2}, on different SiO{sub 2}/Si/Si{sub (1-x)}Ge{sub (x)} thin films deposited on SOI substrate. These numerical results allow us to predict the threshold energies needed to reach the melting point (MP) of the Si and SiGe alloy without oxidation of the thin films system. Therefore, it is possible to optimize the conditions to achieve high quality epitaxy films. (copyright 2011 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  9. SERS substrate and a method of providing a SERS substrate

    DEFF Research Database (Denmark)

    2011-01-01

    Source: US2011116089A A substrate primarily for SERS determination, the substrate has a number of elongate elements with a density of at least 1x108 elongate elements per cm2 and having metal coated tips. When the elements may be made to lean toward each other, such as by providing a drop...

  10. Substrate Effects in Wideband SiGe HBT Mixer Circuits

    DEFF Research Database (Denmark)

    Johansen, Tom Keinicke; Vidkjær, Jens; Krozer, Viktor

    2005-01-01

    In this paper, the influence from substrate effects on the performance of wideband SiGe HBT mixer circuits is investigated. Equivalent circuit models including substrate networks are extracted from on-wafer test structures and compared with electromagnetic simulations. Electromagnetic simulations...

  11. Evidence for Substrate Influence on Artificial Substrate Invertebrate Communities.

    Science.gov (United States)

    Phillips, Iain D; Prestie, Kate S

    2017-08-01

    Cobble baskets are frequently used as a tool to measure differences in benthic macroinvertebrate communities between waterbodies; however, underlying differences in substrate type may influence the resultant colonization of baskets, misrepresenting communities. This study tests the hypothesis that cobble basket placement influences the resulting benthic macroinvertebrate community. Cobble basket arrays (n = 4) were deployed in Dog Lake, Saskatchewan, in 2011 (97 d) and 2012 (95 d) on cobble habitats and soft or sandy substrates ∼100 m apart. Baskets placed on cobble substrate had significantly higher Shannon-Weaver diversity relative to those placed on soft substrate in both years, and higher % EPT (Ephemeroptera Plecoptera Trichoptera) in 2011, but total density was not significantly different. Nonmetric multidimensional scaling revealed that the community was different between both treatments, characterized by higher densities of Gammarus lacustris Sars in baskets placed on soft sediment in both years, higher densities of Aeshna sp. and Mystacides sp. on cobble substrate in 2011, and higher densities of Helobdella stagnalis (L.) and Glossophinia complanata (L.) on cobble substrate in 2012. The results were consistent with the hypothesis that baskets placed on cobble substrate versus soft substrate will result in differing community colonization. The resulting recommendation for monitoring and assessment using cobble baskets in lakes is that baskets be placed on comparable substrate type when comparing between lakes, and that cobble beds be chosen as a more appropriate substrate for deployment, as the added habitat complexity of baskets on soft sediment may act as an attractant and not reflect the true community composition of that habitat. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  12. Substrate reduction therapy for glycosphingolipid storage disorders.

    Science.gov (United States)

    Lachmann, R H; Platt, F M

    2001-03-01

    Substrate reduction therapy is a novel approach to treating glycosphingolipid (GSL) lysosomal storage disorders. These diseases are caused by mutations in the genes coding for enzymes involved in GSL catabolism and are characterised by the accumulation of GSL substrates within the lysosomes of cells. The aim of substrate reduction therapy is to inhibit the rate of synthesis of GSLs to levels where the residual activity of the mutant catabolic enzyme is sufficient to prevent pathological storage. In this review we discuss the development of N-butyldeoxynojirimycin (NB-DNJ), an imino sugar that inhibits the ceramide-specific glucosyltransferase which catalyses the first committed step of GSL synthesis. This agent has been shown to slow accumulation of stored glycolipid in an in vitro model of Gaucher's disease and in knockout mouse models of Tay-Sachs and Sandhoff diseases. Furthermore, administration of NB-DNJ to Sandhoff mice delays the onset of neurological disease and also slows its progression. We discuss safety and efficacy data from the clinical trial of substrate reduction with NB-DNJ which has been undertaken in patients with Type 1 Gaucher's disease. This trial provides a proof-of-principle for the use of this approach in a wide range of GSL lysosomal storage diseases.

  13. Dancing drops over vibrating substrates

    Science.gov (United States)

    Borcia, Rodica; Borcia, Ion Dan; Helbig, Markus; Meier, Martin; Egbers, Christoph; Bestehorn, Michael

    2017-04-01

    We study the motion of a liquid drop on a solid plate simultaneously submitted to horizontal and vertical harmonic vibrations. The investigation is done via a phase field model earlier developed for describing static and dynamic contact angles. The density field is nearly constant in every bulk region (ρ = 1 in the liquid phase, ρ ≈ 0 in the vapor phase) and varies continuously from one phase to the other with a rapid but smooth variation across the interfaces. Complicated explicit boundary conditions along the interface are avoided and captured implicitly by gradient terms of ρ in the hydrodynamic basic equations. The contact angle θ is controlled through the density at the solid substrate ρ S , a free parameter varying between 0 and 1 [R. Borcia, I.D. Borcia, M. Bestehorn, Phys. Rev. E 78, 066307 (2008)]. We emphasize the swaying and the spreading modes, earlier theoretically identified by Benilov and Billingham via a shallow-water model for drops climbing uphill along an inclined plane oscillating vertically [E.S. Benilov, J. Billingham, J. Fluid Mech. 674, 93 (2011)]. The numerical phase field simulations will be completed by experiments. Some ways to prevent the release of the dancing drops along a hydrophobic surface into the gas atmosphere are also discussed in this paper.

  14. Composite substrate for bipolar electrodes

    Science.gov (United States)

    Tekkanat, Bora; Bolstad, James J.

    1992-12-22

    Substrates for electrode systems, particularly those to be used for bipolar electrodes in zinc-bromine batteries, are disclosed. The substrates preferably include carbon-black as a conductive filler in a polymeric matrix, with reinforcing materials such as glass fibers. Warpage of the zinc-bromine electrodes which was experienced in the prior art and which was believed to be caused by physical expansion of the electrodes due to bromine absorption by the carbon-black, is substantially eliminated when new substrate fabrication techniques are employed. In the pesent invention, substrates are prepared using a lamination process known as glass mat reinforced thermoplastics technology or, in an alternate embodiment, the substrate is made using a slurry process.

  15. A full-coordinate model of the polymerase domain of HIV-1 reverse transcriptase and its interaction with a nucleic acid substrate

    Science.gov (United States)

    Setlik, R. F.; Meyer, D. J.; Shibata, M.; Roskwitalski, R.; Ornstein, R. L.; Rein, R.

    1994-01-01

    We present a full-coordinate model of residues 1-319 of the polymerase domain of HIV-I reverse transcriptase. This model was constructed from the x-ray crystallographic structure of Jacobo-Molina et al. (Jacobo-Molina et al., P.N.A.S. USA 90, 6320-6324 (1993)) which is currently available to the degree of C-coordinates. The backbone and side-chain atoms were constructed using the MAXSPROUT suite of programs (L. Holm and C. Sander, J. Mol. Biol. 218, 183-194 (1991)) and refined through molecular modeling. A seven base pair A-form dsDNA was positioned in the nucleic acid binding cleft to represent the template-primer complex. The orientation of the template-primer complex in the nucleic acid binding cleft was guided by the positions of phosphorus atoms in the crystal structure.

  16. Using a Large-scale Neural Model of Cortical Object Processing to Investigate the Neural Substrate for Managing Multiple Items in Short-term Memory.

    Science.gov (United States)

    Liu, Qin; Ulloa, Antonio; Horwitz, Barry

    2017-11-01

    Many cognitive and computational models have been proposed to help understand working memory. In this article, we present a simulation study of cortical processing of visual objects during several working memory tasks using an extended version of a previously constructed large-scale neural model [Tagamets, M. A., & Horwitz, B. Integrating electrophysiological and anatomical experimental data to create a large-scale model that simulates a delayed match-to-sample human brain imaging study. Cerebral Cortex, 8, 310-320, 1998]. The original model consisted of arrays of Wilson-Cowan type of neuronal populations representing primary and secondary visual cortices, inferotemporal (IT) cortex, and pFC. We added a module representing entorhinal cortex, which functions as a gating module. We successfully implemented multiple working memory tasks using the same model and produced neuronal patterns in visual cortex, IT cortex, and pFC that match experimental findings. These working memory tasks can include distractor stimuli or can require that multiple items be retained in mind during a delay period (Sternberg's task). Besides electrophysiology data and behavioral data, we also generated fMRI BOLD time series from our simulation. Our results support the involvement of IT cortex in working memory maintenance and suggest the cortical architecture underlying the neural mechanisms mediating particular working memory tasks. Furthermore, we noticed that, during simulations of memorizing a list of objects, the first and last items in the sequence were recalled best, which may implicate the neural mechanism behind this important psychological effect (i.e., the primacy and recency effect).

  17. Model-based characterisation of growth performance and l-lactic acid production with high optical purity by thermophilic Bacillus coagulans in a lignin-supplemented mixed substrate medium.

    Science.gov (United States)

    Glaser, Robert; Venus, Joachim

    2017-07-25

    Three Bacillus coagulans strains were characterised in terms of their ability to grow in lignin-containing fermentation media and to consume the lignocellulose-related sugars glucose, xylose, and arabinose. An optical-density high-throughput screening was used for precharacterisation by means of different mathematical models for comparison (Logistic, Gompertz, Baranyi, Richards & Stannard, and Schnute). The growth response was characterised by the maximum growth rate and lag time. For a comparison of the screening and fermentation results, an unstructured mathematical model was proposed to characterise the lactate production, bacterial growth and substrate consumption. The growth model was then applied to fermentation procedures using wheat straw hydrolysates. The results indicated that the unstructured growth model can be used to evaluate lactate producing fermentation. Under the experimental fermentation conditions, one strain showed the ability to tolerate a high lignin concentration (2.5g/L) but lacked the capacity for sufficient pentose uptake. The lactate yield of the strains that were able to consume all sugar fractions of glucose, xylose and arabinose was ∼83.4%. A photometric measurement at 280nm revealed a dynamic change in alkali-lignin concentrations during lactate producing fermentation. A test of decolourisation of vanillin, ferulic acid, and alkali-lignin samples also showed the decolourisation performance of the B. coagulans strains under study. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.

  18. Enhanced 3D fluorescence live cell imaging on nanoplasmonic substrate

    Energy Technology Data Exchange (ETDEWEB)

    Gartia, Manas Ranjan [Department of Nuclear, Plasma and Radiological Engineering, University of Illinois, Urbana, IL 61801 (United States); Hsiao, Austin; Logan Liu, G [Department of Bioengineering, University of Illinois, Urbana, IL 61801 (United States); Sivaguru, Mayandi [Institute for Genomic Biology, University of Illinois, Urbana, IL 61801 (United States); Chen Yi, E-mail: loganliu@illinois.edu [Department of Electrical and Computer Engineering, University of Illinois, Urbana, IL 61801 (United States)

    2011-09-07

    We have created a randomly distributed nanocone substrate on silicon coated with silver for surface-plasmon-enhanced fluorescence detection and 3D cell imaging. Optical characterization of the nanocone substrate showed it can support several plasmonic modes (in the 300-800 nm wavelength range) that can be coupled to a fluorophore on the surface of the substrate, which gives rise to the enhanced fluorescence. Spectral analysis suggests that a nanocone substrate can create more excitons and shorter lifetime in the model fluorophore Rhodamine 6G (R6G) due to plasmon resonance energy transfer from the nanocone substrate to the nearby fluorophore. We observed three-dimensional fluorescence enhancement on our substrate shown from the confocal fluorescence imaging of chinese hamster ovary (CHO) cells grown on the substrate. The fluorescence intensity from the fluorophores bound on the cell membrane was amplified more than 100-fold as compared to that on a glass substrate. We believe that strong scattering within the nanostructured area coupled with random scattering inside the cell resulted in the observed three-dimensional enhancement in fluorescence with higher photostability on the substrate surface.

  19. Enhanced 3D fluorescence live cell imaging on nanoplasmonic substrate

    International Nuclear Information System (INIS)

    Gartia, Manas Ranjan; Hsiao, Austin; Logan Liu, G; Sivaguru, Mayandi; Chen Yi

    2011-01-01

    We have created a randomly distributed nanocone substrate on silicon coated with silver for surface-plasmon-enhanced fluorescence detection and 3D cell imaging. Optical characterization of the nanocone substrate showed it can support several plasmonic modes (in the 300-800 nm wavelength range) that can be coupled to a fluorophore on the surface of the substrate, which gives rise to the enhanced fluorescence. Spectral analysis suggests that a nanocone substrate can create more excitons and shorter lifetime in the model fluorophore Rhodamine 6G (R6G) due to plasmon resonance energy transfer from the nanocone substrate to the nearby fluorophore. We observed three-dimensional fluorescence enhancement on our substrate shown from the confocal fluorescence imaging of chinese hamster ovary (CHO) cells grown on the substrate. The fluorescence intensity from the fluorophores bound on the cell membrane was amplified more than 100-fold as compared to that on a glass substrate. We believe that strong scattering within the nanostructured area coupled with random scattering inside the cell resulted in the observed three-dimensional enhancement in fluorescence with higher photostability on the substrate surface.

  20. Kinetic Modeling of Ethanol Batch Fermentation by Escherichia Coli FBWHR Using Hot-Water Sugar Maple Wood Extract Hydrolyzate as Substrate

    Directory of Open Access Journals (Sweden)

    Yang Wang

    2014-12-01

    Full Text Available A recombinant strain of Escherichia coli FBWHR was used for ethanol fermentation from hot-water sugar maple wood extract hydrolyzate in batch experiments. Kinetic studies of cell growth, sugar utilization and ethanol production were investigated at different initial total sugar concentrations of wood extract hydrolyzate. The highest ethanol concentration of 24.05 g/L was obtained using an initial total sugar concentration of 70.30 g/L. Unstructured models were developed to describe cell growth, sugar utilization and ethanol production and validated by comparing the predictions of model and experimental data. The results from this study could be expected to provide insights into the process performance, optimize the process and aid in the design of processes for large-scale production of ethanol fermentation from woody biomass.

  1. A model framework to describe growth-linked biodegradation of trace-level pesticides in the presence of coincidental carbon substrates and microbes

    DEFF Research Database (Denmark)

    Liu, Li; Helbling, Damian E.; Kohler, Hans-Peter E.

    2014-01-01

    , challenges remain in developing engineered remediation strategies for pesticide-contaminated environments because the fundamental processes that regulate growth-linked biodegradation of pesticides in natural environments remain poorly understood. In this research, we developed a model framework to describe......Pollutants such as pesticides and their degradation products occur ubiquitously in natural aquatic environments at trace concentrations (μg L–1 and lower). Microbial biodegradation processes have long been known to contribute to the attenuation of pesticides in contaminated environments. However...... growth-linked biodegradation of pesticides at trace concentrations. We used experimental data reported in the literature or novel simulations to explore three fundamental kinetic processes in isolation. We then combine these kinetic processes into a unified model framework. The three kinetic processes...

  2. Culture in the mind's mirror: how anthropology and neuroscience can inform a model of the neural substrate for cultural imitative learning.

    Science.gov (United States)

    Losin, Elizabeth A Reynolds; Dapretto, Mirella; Iacoboni, Marco

    2009-01-01

    Cultural neuroscience, the study of how cultural experience shapes the brain, is an emerging subdiscipline in the neurosciences. Yet, a foundational question to the study of culture and the brain remains neglected by neuroscientific inquiry: "How does cultural information get into the brain in the first place?" Fortunately, the tools needed to explore the neural architecture of cultural learning - anthropological theories and cognitive neuroscience methodologies - already exist; they are merely separated by disciplinary boundaries. Here we review anthropological theories of cultural learning derived from fieldwork and modeling; since cultural learning theory suggests that sophisticated imitation abilities are at the core of human cultural learning, we focus our review on cultural imitative learning. Accordingly we proceed to discuss the neural underpinnings of imitation and other mechanisms important for cultural learning: learning biases, mental state attribution, and reinforcement learning. Using cultural neuroscience theory and cognitive neuroscience research as our guides, we then propose a preliminary model of the neural architecture of cultural learning. Finally, we discuss future studies needed to test this model and fully explore and explain the neural underpinnings of cultural imitative learning.

  3. Direct cooled power electronics substrate

    Science.gov (United States)

    Wiles, Randy H [Powell, TN; Wereszczak, Andrew A [Oak Ridge, TN; Ayers, Curtis W [Kingston, TN; Lowe, Kirk T [Knoxville, TN

    2010-09-14

    The disclosure describes directly cooling a three-dimensional, direct metallization (DM) layer in a power electronics device. To enable sufficient cooling, coolant flow channels are formed within the ceramic substrate. The direct metallization layer (typically copper) may be bonded to the ceramic substrate, and semiconductor chips (such as IGBT and diodes) may be soldered or sintered onto the direct metallization layer to form a power electronics module. Multiple modules may be attached to cooling headers that provide in-flow and out-flow of coolant through the channels in the ceramic substrate. The modules and cooling header assembly are preferably sized to fit inside the core of a toroidal shaped capacitor.

  4. Sensitivity of reentrant driver localization to electrophysiological parameter variability in image-based computational models of persistent atrial fibrillation sustained by a fibrotic substrate

    Science.gov (United States)

    Deng, Dongdong; Murphy, Michael J.; Hakim, Joe B.; Franceschi, William H.; Zahid, Sohail; Pashakhanloo, Farhad; Trayanova, Natalia A.; Boyle, Patrick M.

    2017-09-01

    Atrial fibrillation (AF) is the most common sustained cardiac arrhythmia, causing morbidity and mortality in millions worldwide. The atria of patients with persistent AF (PsAF) are characterized by the presence of extensive and distributed atrial fibrosis, which facilitates the formation of persistent reentrant drivers (RDs, i.e., spiral waves), which promote fibrillatory activity. Targeted catheter ablation of RD-harboring tissues has shown promise as a clinical treatment for PsAF, but the outcomes remain sub-par. Personalized computational modeling has been proposed as a means of non-invasively predicting optimal ablation targets in individual PsAF patients, but it remains unclear how RD localization dynamics are influenced by inter-patient variability in the spatial distribution of atrial fibrosis, action potential duration (APD), and conduction velocity (CV). Here, we conduct simulations in computational models of fibrotic atria derived from the clinical imaging of PsAF patients to characterize the sensitivity of RD locations to these three factors. We show that RDs consistently anchor to boundaries between fibrotic and non-fibrotic tissues, as delineated by late gadolinium-enhanced magnetic resonance imaging, but those changes in APD/CV can enhance or attenuate the likelihood that an RD will anchor to a specific site. These findings show that the level of uncertainty present in patient-specific atrial models reconstructed without any invasive measurements (i.e., incorporating each individual's unique distribution of fibrotic tissue from medical imaging alongside an average representation of AF-remodeled electrophysiology) is sufficiently high that a personalized ablation strategy based on targeting simulation-predicted RD trajectories alone may not produce the desired result.

  5. Impact of bacterial activity on turnover of insoluble hydrophobic substrates (phenanthrene and pyrene)—Model simulations for prediction of bioremediation success

    DEFF Research Database (Denmark)

    Rein, Arno; Adam, Iris K.U.; Miltner, Anja

    2016-01-01

    Many attempts for bioremediation of polycyclic aromatic hydrocarbon (PAH) contaminated sites failed in the past, but the reasons for this failure are not well understood. Here we apply and improve a model for integrated assessment of mass transfer, biodegradation and residual concentrations...... for predicting the success of remediation actions. First, we provide growth parameters for Mycobacterium rutilum and Mycobacterium pallens growing on phenanthrene (PHE) or pyrene (PYR) degraded the PAH completely at all investigated concentrations. Maximum metabolic rates vmax and growth rates μ were similar...

  6. Analytical model for subthreshold current and subthreshold swing of short-channel double-material-gate MOSFETs with strained-silicon channel on silicon—germanium substrates

    International Nuclear Information System (INIS)

    Tiwari Pramod Kumar; Saramekala Gopi Krishna; Mukhopadhyay Anand Kumar; Dubey Sarvesh

    2014-01-01

    The present work gives some insight into the subthreshold behaviour of short-channel double-material-gate strained-silicon on silicon—germanium MOSFETs in terms of subthreshold swing and off-current. The formulation of subthreshold current and, thereupon, the subthreshold swing have been done by exploiting the expression of potential distribution in the channel region of the device. The dependence of the subthreshold characteristics on the device parameters, such as Ge mole fraction, gate length ratio, work function of control gate metal and gate length, has been tested in detail. The analytical models have been validated by the numerical simulation results that were obtained from the device simulation software ATLAS™ by Silvaco Inc. (semiconductor devices)

  7. Laboratory Tests of Substrate Physical Properties May Not Represent the Retention Capacity of Green Roof Substrates In Situ

    Directory of Open Access Journals (Sweden)

    Christopher Szota

    2017-11-01

    Full Text Available Green roofs can be used to reduce the volume of polluted stormwater that is generated by cities. Modelling rainfall retention is critical, but green roof water balance models often rely on the physical properties of substrates. In these models, substrate water holding capacity (WHC determines the depth of water which can be stored before runoff is generated; whereas, the permanent wilting point (PWP limits evapotranspiration. The WHC and PWP, as well as plant available water (PAW; where PAW = WHC − PWP, as determined from laboratory tests, may not truly reflect how substrates perform on green roofs. We therefore ran a simulated rainfall experiment on green roof modules to (i compare the rainfall retention of vegetated and non-vegetated substrates with different WHC and PAW, and (ii relate retention to substrate storage capacity, as calculated from laboratory measures of WHC and PAW. We found that the PAW of a substrate is a better indicator of evapotranspiration and retention when compared with WHC. However, we also found that substrates always retained less water than their calculated storage capacity would suggest, most likely being due to their high permeability. Our results indicate that using laboratory-derived measures of WHC and PAW in green roof models may be over-estimating both evapotranspiration and rainfall retention.

  8. Coated substrate apparatus and method

    Energy Technology Data Exchange (ETDEWEB)

    Bao, Zhenan; Diao, Ying; Mannsfeld, Stefan Christian Bernhardt; Tee, Chee-Keong; Becerril-Garcia, Hector A.; Zhou, Yan

    2018-01-09

    A coated substrate is formed with aligned objects such as small molecules, macromolecules and nanoscale particulates, such as inorganic, organic or inorganic/organic hybrid materials. In accordance with one or more embodiments, an apparatus or method involves an applicator having at least one surface patterned with protruded or indented features, and a coated substrate including a solution-based layer of objects having features and morphology attributes arranged as a function of the protruded or indented features.

  9. Substrate channeling in proline metabolism

    Science.gov (United States)

    Arentson, Benjamin W.; Sanyal, Nikhilesh; Becker, Donald F.

    2012-01-01

    Proline metabolism is an important pathway that has relevance in several cellular functions such as redox balance, apoptosis, and cell survival. Results from different groups have indicated that substrate channeling of proline metabolic intermediates may be a critical mechanism. One intermediate is pyrroline-5-carboxylate (P5C), which upon hydrolysis opens to glutamic semialdehyde (GSA). Recent structural and kinetic evidence indicate substrate channeling of P5C/GSA occurs in the proline catabolic pathway between the proline dehydrogenase and P5C dehydrogenase active sites of bifunctional proline utilization A (PutA). Substrate channeling in PutA is proposed to facilitate the hydrolysis of P5C to GSA which is unfavorable at physiological pH. The second intermediate, gamma-glutamyl phosphate, is part of the proline biosynthetic pathway and is extremely labile. Substrate channeling of gamma-glutamyl phosphate is thought to be necessary to protect it from bulk solvent. Because of the unfavorable equilibrium of P5C/GSA and the reactivity of gamma-glutamyl phosphate, substrate channeling likely improves the efficiency of proline metabolism. Here, we outline general strategies for testing substrate channeling and review the evidence for channeling in proline metabolism. PMID:22201749

  10. Curvature and bow of bulk GaN substrates

    Energy Technology Data Exchange (ETDEWEB)

    Foronda, Humberto M.; Young, Erin C.; Robertson, Christian A.; Speck, James S. [Materials Department, UCSB, Santa Barbara, California 93106 (United States); Romanov, Alexey E. [Materials Department, UCSB, Santa Barbara, California 93106 (United States); Ioffe Physico-Technical Institute RAS, St. Petersburg 194021 (Russian Federation); ITMO University, St. Petersburg 197101 (Russian Federation); Beltz, Glenn E. [Mechanical Engineering Department, UCSB, Santa Barbara, California 93106 (United States)

    2016-07-21

    We investigate the bow of free standing (0001) oriented hydride vapor phase epitaxy grown GaN substrates and demonstrate that their curvature is consistent with a compressive to tensile stress gradient (bottom to top) present in the substrates. The origin of the stress gradient and the curvature is attributed to the correlated inclination of edge threading dislocation (TD) lines away from the [0001] direction. A model is proposed and a relation is derived for bulk GaN substrate curvature dependence on the inclination angle and the density of TDs. The model is used to analyze the curvature for commercially available GaN substrates as determined by high resolution x-ray diffraction. The results show a close correlation between the experimentally determined parameters and those predicted from theoretical model.

  11. The effect of substrate morphological structure on photoelectrical conversion performance of silicon solar cell

    Science.gov (United States)

    Li, Yongtao; Sun, Xiaomeng; Xia, Yang

    2017-03-01

    A novel method is proposed to evaluate electrical characteristics of silicon solar cell at real operating conditions. Silicon solar cells with different substrate morphological structures have various photoelectrical performances. The effect of substrate morphological structure on photoelectrical conversation performance of silicon solar cell has been investigated by illustration analysis, mathematical model and I-V test system. Results show that the solar cell with the porous-sponge like substrate has better electrical characteristics than those with conical like substrate morphological structure. The output power of porous substrate solar cell can exceed by 11% at 40 degree incident angle of sunlight compared to conical substrate solar cell.

  12. Mapping protease substrates using a biotinylated phage substrate library.

    Energy Technology Data Exchange (ETDEWEB)

    Scholle, M. D.; Kriplani, U.; Pabon, A.; Sishtla, K.; Glucksman, M. J.; Kay, B. K.; Biosciences Division; Chicago Medical School

    2005-05-05

    We describe a bacteriophage M13 substrate library encoding the AviTag (BirA substrate) and combinatorial heptamer peptides displayed at the N terminus of the mature form of capsid protein III. Phages are biotinylated efficiently (> or = 50%) when grown in E. coli cells coexpressing BirA, and such viral particles can be immobilized on a streptavidin-coated support and released by protease cleavage within the combinatorial peptide. We have used this library to map the specificity of human Factor Xa and a neuropeptidase, neurolysin (EC3.4.24.16). Validation by analysis of isolated peptide substrates has revealed that neurolysin recognizes the motif hydrophobic-X-Pro-Arg-hydrophobic, where Arg-hydrophobic is the scissile bond.

  13. Neurobiological substrates of dread.

    Science.gov (United States)

    Berns, Gregory S; Chappelow, Jonathan; Cekic, Milos; Zink, Caroline F; Pagnoni, Giuseppe; Martin-Skurski, Megan E

    2006-05-05

    Given the choice of waiting for an adverse outcome or getting it over with quickly, many people choose the latter. Theoretical models of decision-making have assumed that this occurs because there is a cost to waiting-i.e., dread. Using functional magnetic resonance imaging, we measured the neural responses to waiting for a cutaneous electric shock. Some individuals dreaded the outcome so much that, when given a choice, they preferred to receive more voltage rather than wait. Even when no decision was required, these extreme dreaders were distinguishable from those who dreaded mildly by the rate of increase of neural activity in the posterior elements of the cortical pain matrix. This suggests that dread derives, in part, from the attention devoted to the expected physical response and not simply from fear or anxiety. Although these differences were observed during a passive waiting procedure, they correlated with individual behavior in a subsequent choice paradigm, providing evidence for a neurobiological link between the experienced disutility of dread and subsequent decisions about unpleasant outcomes.

  14. Cell In Situ Zymography: Imaging Enzyme-Substrate Interactions.

    Science.gov (United States)

    Chhabra, Aastha; Rani, Vibha

    2017-01-01

    Zymography has long been used for the detection of substrate-specific enzyme activity. In situ zymography (ISZ), an adaptation from the conventional substrate zymography, is a widely employed technique useful for the detection, localization, and estimation of enzyme-substrate interactions in tissues. Here, we describe a protocol to detect 'in position' matrix metalloproteinase (MMP) activity in cells utilizing H9c2 cardiomyoblasts as a model. This technique is primarily adopted from the method used for histological sections and is termed as 'Cell in situ Zymography'. It is a simple, sensitive, and quantifiable methodology to assess the functional activity of an enzyme 'on site/in position' in cell culture.

  15. Substrate Channel Flexibility in Pseudomonas aeruginosa MurB Accommodates Two Distinct Substrates.

    Directory of Open Access Journals (Sweden)

    Ming Wei Chen

    Full Text Available Biosynthesis of UDP-N-acetylmuramic acid in bacteria is a committed step towards peptidoglycan production. In an NADPH- and FAD-dependent reaction, the UDP-N-acetylglucosamine-enolpyruvate reductase (MurB reduces UDP-N-acetylglucosamine-enolpyruvate to UDP-N-acetylmuramic acid. We determined the three-dimensional structures of the ternary complex of Pseudomonas aeruginosa MurB with FAD and NADP(+ in two crystal forms to resolutions of 2.2 and 2.1 Å, respectively, to investigate the structural basis of the first half-reaction, hydride transfer from NADPH to FAD. The nicotinamide ring of NADP(+ stacks against the si face of the isoalloxazine ring of FAD, suggesting an unusual mode of hydride transfer to flavin. Comparison with the structure of the Escherichia coli MurB complex with UDP-N-acetylglucosamine-enolpyruvate shows that both substrates share the binding site located between two lobes of the substrate-binding domain III, consistent with a ping pong mechanism with sequential substrate binding. The nicotinamide and the enolpyruvyl moieties are strikingly well-aligned upon superimposition, both positioned for hydride transfer to and from FAD. However, flexibility of the substrate channel allows the non-reactive parts of the two substrates to bind in different conformations. A potassium ion in the active site may assist in substrate orientation and binding. These structural models should help in structure-aided drug design against MurB, which is essential for cell wall biogenesis and hence bacterial survival.

  16. Porous substrates filled with nanomaterials

    Science.gov (United States)

    Worsley, Marcus A.; Baumann, Theodore F.; Satcher, Jr., Joe H.; Stadermann, Michael

    2014-08-19

    A composition comprising: at least one porous carbon monolith, such as a carbon aerogel, comprising internal pores, and at least one nanomaterial, such as carbon nanotubes, disposed uniformly throughout the internal pores. The nanomaterial can be disposed in the middle of the monolith. In addition, a method for making a monolithic solid with both high surface area and good bulk electrical conductivity is provided. A porous substrate having a thickness of 100 microns or more and comprising macropores throughout its thickness is prepared. At least one catalyst is deposited inside the porous substrate. Subsequently, chemical vapor deposition is used to uniformly deposit a nanomaterial in the macropores throughout the thickness of the porous substrate. Applications include electrical energy storage, such as batteries and capacitors, and hydrogen storage.

  17. Methods of etching a substrate

    International Nuclear Information System (INIS)

    Cosmo, J.J.; Gambino, R.J.; Harper, J.M.E.

    1979-01-01

    The invention relates to a method of etching a substrate. The substrate is located opposite a target electrode in a vacuum chamber, and the surface of the target electrode is bombarded with energetic particles of atomic dimensions. The target electrode is an intermetallic composition (compound, alloy or finely divided homogeneous mixture) of two metals A and B such that upon bombardment the electrode emits negative ions of metal B which have sufficient energy to produce etching of the substrate. Many target materials are exemplified. Typically the metal A has an electronegativity XA and metal B has an electronegativity XB such that Xb - Xa is greater than about 2.55 electron volts, with the exception of combinations of metals having a fractional ionicity Q less than about 0.314. The source of the energetic particles may be an ionised gas in the vacuum chamber. The apparatus and its mode of operation are described in detail. (U.K.)

  18. Porous substrates filled with nanomaterials

    Energy Technology Data Exchange (ETDEWEB)

    Worsley, Marcus A.; Baumann, Theodore F.; Satcher, Jr., Joe H.; Stadermann, Michael

    2018-04-03

    A composition comprising: at least one porous carbon monolith, such as a carbon aerogel, comprising internal pores, and at least one nanomaterial, such as carbon nanotubes, disposed uniformly throughout the internal pores. The nanomaterial can be disposed in the middle of the monolith. In addition, a method for making a monolithic solid with both high surface area and good bulk electrical conductivity is provided. A porous substrate having a thickness of 100 microns or more and comprising macropores throughout its thickness is prepared. At least one catalyst is deposited inside the porous substrate. Subsequently, chemical vapor deposition is used to uniformly deposit a nanomaterial in the macropores throughout the thickness of the porous substrate. Applications include electrical energy storage, such as batteries and capacitors, and hydrogen storage.

  19. Optical measurement of microroughness of pigment coatings on rough substrates

    Science.gov (United States)

    Elton, N. J.

    2009-02-01

    The optical determination of rms roughness at the sub-wavelength scale by measurement of specular intensity as a function of wavelength or angle of incidence is well known. The method is normally used for specimens that are macroscopically flat. However, important industrial materials such as coated paper and paint consist of microscopically rough pigment coatings on a macroscopically rough substrate. Numerical modelling is used to assess the applicability and limitations of optical measurement of microroughness for such materials. Experimental results are presented for a range of paints on substrates of various macroroughness. Model and data are in fair agreement and show that the presence of substrate macroroughness always leads to an underestimation of microroughness. Generally, optical measurements of microroughness are only comparable for substrates of similar macroroughness and a limiting value exists above which measurements may not be meaningful.

  20. Optical measurement of microroughness of pigment coatings on rough substrates

    International Nuclear Information System (INIS)

    Elton, N J

    2009-01-01

    The optical determination of rms roughness at the sub-wavelength scale by measurement of specular intensity as a function of wavelength or angle of incidence is well known. The method is normally used for specimens that are macroscopically flat. However, important industrial materials such as coated paper and paint consist of microscopically rough pigment coatings on a macroscopically rough substrate. Numerical modelling is used to assess the applicability and limitations of optical measurement of microroughness for such materials. Experimental results are presented for a range of paints on substrates of various macroroughness. Model and data are in fair agreement and show that the presence of substrate macroroughness always leads to an underestimation of microroughness. Generally, optical measurements of microroughness are only comparable for substrates of similar macroroughness and a limiting value exists above which measurements may not be meaningful

  1. Substrate mediated enzyme prodrug therapy

    DEFF Research Database (Denmark)

    Fejerskov, Betina; Jarlstad Olesen, Morten T; Zelikin, Alexander N

    2017-01-01

    Substrate mediated enzyme prodrug therapy (SMEPT) is a biomedical platform developed to perform a localized synthesis of drugs mediated by implantable biomaterials. This approach combines the benefits and at the same time offers to overcome the drawbacks for traditional pill-based drug administra......Substrate mediated enzyme prodrug therapy (SMEPT) is a biomedical platform developed to perform a localized synthesis of drugs mediated by implantable biomaterials. This approach combines the benefits and at the same time offers to overcome the drawbacks for traditional pill-based drug...

  2. The sensitivity of graphene “snap-through” to substrate geometry

    KAUST Repository

    Wagner, Till J. W.

    2012-01-01

    We study theoretically the deposition of few layer graphene sheets onto a grooved substrate incorporating adhesion between substrate and sheet. We develop a model to understand the equilibrium of the sheet allowing for partial conformation of sheet to substrate. This model gives physical insight into recent observations of snap-through from flat to conforming states and emphasizes the crucial role of substrate shape in determining the nature of this transition. Our analytical results are consistent with numerical simulations using a van der Waals-like interaction. Finally, we propose a substrate shape that should exhibit a continuous, rather than snap-through, transition. © 2012 American Institute of Physics.

  3. Phonon scattering in graphene over substrate steps

    DEFF Research Database (Denmark)

    Sevincli, Haldun; Brandbyge, Mads

    2014-01-01

    We calculate the effect on phonon transport of substrate-induced bends in graphene. We consider bending induced by an abrupt kink in the substrate, and provide results for different step-heights and substrate interaction strengths. We find that individual substrate steps reduce thermal conductance...

  4. Neuronal substrate of eating disorders

    OpenAIRE

    Timofeeva, Elena; Calvez, Juliane

    2014-01-01

    Eating disorders are devastating and life-threatening psychiatric diseases. Although clinical and experimental investigations have significantly progressed in discovering the neuronal causes of eating disorders, the exact neuronal and molecular mechanisms of the development and maintenance of these pathologies are not fully understood. The complexity of the neuronal substrate of eating disorders hampers progress in revealing the precise mechanisms. The present re...

  5. Neurobiological Substrates of Tourette's Disorder

    NARCIS (Netherlands)

    Leckman, James F.; Bloch, Michael H.; Smith, Megan E.; Larabi, Daouia; Hampson, Michelle

    Objective: This article reviews the available scientific literature concerning the neurobiological substrates of Tourette's disorder (TD). Methods: The electronic databases of PubMed, ScienceDirect, and PsycINFO were searched for relevant studies using relevant search terms. Results:

  6. Sensor Technologies on Flexible Substrates

    Science.gov (United States)

    Koehne, Jessica

    2016-01-01

    NASA Ames has developed sensor technologies on flexible substrates integrated into textiles for personalized environment monitoring and human performance evaluation. Current technologies include chemical sensing for gas leak and event monitoring and biological sensors for human health and performance monitoring. Targeted integration include next generation EVA suits and flexible habitats.

  7. Electrostatic Suppression of the Leidenfrost State on Liquid Substrates.

    Science.gov (United States)

    Shahriari, Arjang; Ozkan, Onur; Bahadur, Vaibhav

    2017-11-21

    An applied electric field can fundamentally eliminate the Leidenfrost effect (formation of a vapor layer at the solid-liquid interface at high temperatures). This study analyzes electrostatic suppression of the Leidenfrost state on liquid substrates. Electrostatic suppression on silicone oil and Wood's metal (liquid alloy) is studied via experimentation, high-speed imaging, and analyses. It is seen that the nature of electrostatic suppression can be drastically different from that on a solid substrate. First, the Leidenfrost droplet completely penetrates into the silicone oil substrate and converts to a thin film under an electric field. This is due to the existence of an electric field inside the substrate and the deformability of the silicone oil interface. A completely different type of suppression is observed for Wood's metal and solid substrates, which have low deformability and lack an electric field in the substrate. Second, the minimum voltage to trigger suppression is significantly lower on silicone oil when compared to Wood's metal and solid substrates. Fundamental differences between these transitions are analyzed, and a multiphysics analytical model is developed to predict the vapor layer thickness on deformable liquids. Overall, this study lays the foundation for further studies on electrostatic manipulation of the Leidenfrost state on liquids.

  8. Molybdenum protective coatings adhesion to steel substrate

    Science.gov (United States)

    Blesman, A. I.; Postnikov, D. V.; Polonyankin, D. A.; Teplouhov, A. A.; Tyukin, A. V.; Tkachenko, E. A.

    2017-06-01

    Protection of the critical parts, components and assemblies from corrosion is an urgent engineering problem and many other industries. Protective coatings’ forming on surface of metal products is a promising way of corrosionprevention. The adhesion force is one of the main characteristics of coatings’ durability. The paper presents theoretical and experimental adhesion force assessment for coatings formed by molybdenum magnetron sputtering ontoa steel substrate. Validity and reliability of results obtained by simulation and sclerometry method allow applying the developed model for adhesion force evaluation in binary «steel-coating» systems.

  9. Substrate Curvature Regulates Cell Migration -A Computational Study

    Science.gov (United States)

    He, Xiuxiu; Jiang, Yi

    Cell migration in host microenvironment is essential to cancer etiology, progression and metastasis. Cellular processes of adhesion, cytoskeletal polymerization, contraction, and matrix remodeling act in concert to regulate cell migration, while local extracellular matrix architecture modulate these processes. In this work we study how stromal microenvironment with native and cell-derived curvature at micron-meter scale regulate cell motility pattern. We developed a 3D model of single cell migration on a curved substrate. Mathematical analysis of cell morphological adaption to the cell-substrate interface shows that cell migration on convex surfaces deforms more than on concave surfaces. Both analytical and simulation results show that curved surfaces regulate the cell motile force for cell's protruding front through force balance with focal adhesion and cell contraction. We also found that cell migration on concave substrates is more persistent. These results offer a novel biomechanical explanation to substrate curvature regulation of cell migration. NIH 1U01CA143069.

  10. Ketone Bodies as Brain Substrates

    OpenAIRE

    Silva, Paula Sofia Valente da

    2015-01-01

    SILVA, Paula Sofia Valente da - Ketone Bodies as Brain Substrates. Coimbra : [s.n.], 2015. Dissertação de Mestrado em Bioquimica. Since their discovery as a marker for diabetic ketoacidosis, ketone bodies have become known for their therapeutic role as effective agents in refractory epilepsy and a diet specifically designed to increase ketone bodies’ levels in circulation has been often prescribed as treatment. In the classical ketogenic diet, intake of even small additional amounts of car...

  11. Substrate analogues for isoprenoid enzymes

    Energy Technology Data Exchange (ETDEWEB)

    Stremler, K.E.

    1987-01-01

    Diphosphonate analogues of geranyl diphosphate, resistant to degradation by phosphatases, were found to be alternate substrates for the reaction with farnesyl diphosphate synthetase isolated from avian liver. The difluoromethane analogue was shown to be the better alternate substrate, in agreement with solvolysis results which indicate that the electronegativity of the difluoromethylene unit more closely approximates that of the normal bridging oxygen. The usefulness of the C/sub 10/ difluoro analogue, for detecting low levels of isoprenoid enzymes in the presence of high levels of phosphatase activity, was demonstrated with a cell-free preparation from lemon peel. A series of C/sub 5/ through C/sub 15/ homoallylic and allylic diphosphonates, as well as two 5'-nucleotide diphosphonates, was prepared in high overall yield using the activation-displacement sequence. Radiolabeled samples of several of the allylic diphosphonates were prepared with tritium located at C1. A series of geraniols, stereospecifically deuterated at C1, was prepared. The enantiomeric purities and absolute configurations were determined by derivatization as the mandelate esters for analysis by /sup 1/H NMR. The stereochemistry of the activation-displacement sequence was examined using C1-deuterated substrates.

  12. Real-time sensing of epithelial cell-cell and cell-substrate interactions by impedance spectroscopy on porous substrates

    International Nuclear Information System (INIS)

    Mondal, D.; RoyChaudhuri, C.; Pal, D.

    2015-01-01

    Oxidized porous silicon (PS) is a common topographical biocompatible substrate that potentially provides a distinct in vitro environment for better understanding of in vivo behavior. But in the reported studies on oxidized PS, cell-cell and cell-substrate interactions have been detected only by fluorescent labeling. This paper is the first attempt to investigate real-time sensing of these interactions on HaCaT cells by label-free impedance spectroscopy on oxidized PS of two pore diameters (50 and 500 nm). One of the major requirements for successful impedance spectroscopy measurement is to restrict the channeling of electric field lines through the pores. To satisfy this criterion, we have designed the pore depths after analyzing the penetration of the medium by using computational fluid dynamics simulation. A distributed electrical model was also developed for estimating the various cellular attributes by considering a pseudorandom distribution of pores. It is observed from the impedance measurements and from the model that the proliferation rate increases for 50 nm pores but decreases for 500 nm pores compared to that for planar substrates. The rate of decrease in cell substrate separation (h) in the initial stage is more than the rate of increase in cell-cell junction resistance (R b ) corresponding to the initial adhesion phase of cells. It is observed that R b and h are higher for 50 nm pores than those for planar substrates, corresponding to the fact that substrates more conducive toward cell adhesion encourage cell-cell interactions than direct cell-substrate interactions. Thus, the impedance spectroscopy coupled with the proposed theoretical framework for PS substrates can sense and quantify the cellular interactions

  13. SIMULATION OF HEAT TRANSFER BY COOLING CHANNELS IN LTCC SUBSTRATE

    Directory of Open Access Journals (Sweden)

    Tomas GIRASEK

    2017-06-01

    Full Text Available The thermal resistance, flow analysis, pressure drop and distribution of coolant inside multilayer LTCC (Low Temperature Co-fired Ceramics substrate are detailed investigated in this paper. For this reason four various structures of internal channels in the multilayer LTCC substrates were designed and simulated. The simulation 3D model consist of 6 LTCC of DuPont 951® layer with cooling microchannel in middle of substrate, power chips paced on top of LTCC and silver sintered joints under power chips. The impact of the structure of channels, volume flow and power loss of die was simulated, calculated and analyzed by using the simulation software Mentor Graphics FloEFDTM. The structure and size of channels have the significant impact on thermal resistance, pressure of coolant as well as the effectivity of cooling power components which can be placed on LTCC substrate. The thermal resistance was calculated from the temperature gradient among chip junction, the inlet fluid and the thermal load of chip. Optimizing and comparison of cooling channels structure inside LTCC substrates and analyzing the effect of volume flow for achieving the least thermal resistance of LTCC multilayer substrate is the main contribution of this paper.

  14. Characterizing Protease Specificity: How Many Substrates Do We Need?

    Directory of Open Access Journals (Sweden)

    Michael Schauperl

    Full Text Available Calculation of cleavage entropies allows to quantify, map and compare protease substrate specificity by an information entropy based approach. The metric intrinsically depends on the number of experimentally determined substrates (data points. Thus a statistical analysis of its numerical stability is crucial to estimate the systematic error made by estimating specificity based on a limited number of substrates. In this contribution, we show the mathematical basis for estimating the uncertainty in cleavage entropies. Sets of cleavage entropies are calculated using experimental cleavage data and modeled extreme cases. By analyzing the underlying mathematics and applying statistical tools, a linear dependence of the metric in respect to 1/n was found. This allows us to extrapolate the values to an infinite number of samples and to estimate the errors. Analyzing the errors, a minimum number of 30 substrates was found to be necessary to characterize substrate specificity, in terms of amino acid variability, for a protease (S4-S4' with an uncertainty of 5 percent. Therefore, we encourage experimental researchers in the protease field to record specificity profiles of novel proteases aiming to identify at least 30 peptide substrates of maximum sequence diversity. We expect a full characterization of protease specificity helpful to rationalize biological functions of proteases and to assist rational drug design.

  15. Carbon Nanotube Patterning on a Metal Substrate

    Science.gov (United States)

    Nguyen, Cattien V. (Inventor)

    2016-01-01

    A CNT electron source, a method of manufacturing a CNT electron source, and a solar cell utilizing a CNT patterned sculptured substrate are disclosed. Embodiments utilize a metal substrate which enables CNTs to be grown directly from the substrate. An inhibitor may be applied to the metal substrate to inhibit growth of CNTs from the metal substrate. The inhibitor may be precisely applied to the metal substrate in any pattern, thereby enabling the positioning of the CNT groupings to be more precisely controlled. The surface roughness of the metal substrate may be varied to control the density of the CNTs within each CNT grouping. Further, an absorber layer and an acceptor layer may be applied to the CNT electron source to form a solar cell, where a voltage potential may be generated between the acceptor layer and the metal substrate in response to sunlight exposure.

  16. Enzyme Substrate Specificity Conferred by Distinct Conformational Pathways.

    Science.gov (United States)

    Rago, Florencia; Saltzberg, Daniel; Allen, Karen N; Tolan, Dean R

    2015-11-04

    Substrate recognition is one of the hallmarks of enzyme catalysis. Enzyme conformational changes have been linked to selectivity between substrates with little direct evidence. Aldolase, a glycolytic enzyme, must distinguish between two physiologically important substrates, fructose 1-phosphate and fructose 1,6-bisphosphate, and provides an excellent model system for the study of this question. Previous work has shown that isozyme specific residues (ISRs) distant from the active site are responsible for kinetic distinction between these substrates. Notably, most of the ISRs reside in a cluster of five surface α-helices, and the carboxyl-terminal region (CTR), and cooperative interactions among these helices have been demonstrated. To test the hypothesis that conformational changes are at the root of these changes, single surface-cysteine variants were created with the cysteine located on helices of the cluster and CTR. This allowed for site-specific labeling with an environmentally sensitive fluorophore, and subsequent monitoring of conformational changes by fluorescence emission spectrophotometry. These labeled variants revealed different spectra in the presence of saturating amounts of each substrate, which suggested the occurrence of different conformations. Emission spectra collected at various substrate concentrations showed a concentration dependence of the fluorescence spectra, consistent with binding events. Lastly, stopped-flow fluorescence spectrophotometry showed that the rate of these fluorescence changes was on the same time-scale as catalysis, thus suggesting a link between the different fluorescence changes and events during catalysis. On the basis of these results, we propose that different conformational changes may be a common mechanism for dictating substrate specificity in other enzymes with multiple substrates.

  17. Verfahren zum Herstellen einer Beschichtung eines Substrats

    OpenAIRE

    Wilke, Martin; Töpper, Michael

    2013-01-01

    The method involves applying coating material (7) on surface (2) of recess (3) formed in substrate (1). A liquid auxiliary agent (6) is applied on substrate surface, such that recess is filled with auxiliary agent. The coating material is subsequently applied to auxiliary agent on substrate. A coating material portion in auxiliary agent is transported by coating material diffusion. The agent is subsequently separated from coating material, such that coating material on substrate surface is le...

  18. Förpackning av keramiska substrat

    OpenAIRE

    Karlsson, Jan

    2008-01-01

    Detta examensarbete handlar om forpackning av keramiska substrat. Canning ar det universella namnet pa forpackning av keramiska substrat. Keramiska substrat kan vara katalysatorer eller partikelfilter som anvands som ett efterbehandlingssystem i bensin och Diesel applikationer. Examensarbetet genomfordes hos Scania CV AB. I installationsprocessen sveps en keramisk fibermatta runt det keramiska substratet. Substratet inkapslas sedan med ett metalholje. Rapporten inleds med att beskriva olika i...

  19. SUPPLEMENTARY INFORMATION Indicators for suicide substrate ...

    Indian Academy of Sciences (India)

    Jatinder

    The usual trend is to apply QSSA to a system with high substrate concentration. But, QSSA, i.e., steadiness in intermediate concentration, may even be achieved at high and even comparable enzyme-substrate ratio. Whether a system will attain a steady state depends not only on the high substrate concentration, but also on ...

  20. Method for coating substrates and mask holder

    NARCIS (Netherlands)

    Bijkerk, Frederik; Yakshin, Andrey; Louis, Eric; Kessels, M.J.H.; Maas, Edward Lambertus Gerardus; Bruineman, Caspar

    2004-01-01

    When coating substrates it is frequently desired that the layer thickness should be a certain function of the position on the substrate to be coated. To control the layer thickness a mask is conventionally arranged between the coating particle source and the substrate. This leads to undesirable

  1. Method For Producing Mechanically Flexible Silicon Substrate

    KAUST Repository

    Hussain, Muhammad Mustafa

    2014-08-28

    A method for making a mechanically flexible silicon substrate is disclosed. In one embodiment, the method includes providing a silicon substrate. The method further includes forming a first etch stop layer in the silicon substrate and forming a second etch stop layer in the silicon substrate. The method also includes forming one or more trenches over the first etch stop layer and the second etch stop layer. The method further includes removing the silicon substrate between the first etch stop layer and the second etch stop layer.

  2. Heat transfer simulation in solid substrate fermentation.

    Science.gov (United States)

    Saucedo-Castañeda, G; Gutiérrez-Rojas, M; Bacquet, G; Raimbault, M; Viniegra-González, G

    1990-04-05

    A mathematical model was developed and tested to simulate the generation and transfer of heat in solid substrate fermentation (SSF). The experimental studies were realized in a 1-L static bioreactor packed with cassava wet meal and inoculated with Aspergillus niger. A simplified pseudohomogeneous monodimensional dynamic model was used for the energy balance. Kinetic equations taking into account biomass formation (logistic), sugar consumption (with maintenance), and carbon dioxide formation were used. Model verification was achieved by comparison of calculated and experimental temperatures. Heat transfer was evaluated by the estimation of Biot and Peclet heat dimensionless numbers 5-10 and 2550-2750, respectively. It was shown that conduction through the fermentation fixed bed was the main heat transfer resistance. This model intends to reach a better understanding of transport phenomena in SSF, a fact which could be used to evaluate various alternatives for temperature control of SSF, i.e., changing air flow rates and increasing water content. Dimensionless numbers could be used as scale-up criteria of large fermentors, since in those ratios are described the operating conditions, geometry, and size of the bioreactor. It could lead to improved solid reactor systems. The model can be used as a basis for automatic control of SSF for the production of valuable metabolites in static fermentors.

  3. Substrate heater for thin film deposition

    Science.gov (United States)

    Foltyn, Steve R.

    1996-01-01

    A substrate heater for thin film deposition of metallic oxides upon a target substrate configured as a disk including means for supporting in a predetermined location a target substrate configured as a disk, means for rotating the target substrate within the support means, means for heating the target substrate within the support means, the heating means about the support means and including a pair of heating elements with one heater element situated on each side of the predetermined location for the target substrate, with one heater element defining an opening through which desired coating material can enter for thin film deposition and with the heating means including an opening slot through which the target substrate can be entered into the support means, and, optionally a means for thermal shielding of the heating means from surrounding environment is disclosed.

  4. Substrate Integrated Evanescent Filters Employing Coaxial Stubs

    DEFF Research Database (Denmark)

    Zhurbenko, Vitaliy

    2015-01-01

    is designed, fabricated, and tested. The filter exhibits a transmission zero due to the implemented stubs. The problem of evanescent mode filter analysis is formulated in terms of conventional network concepts. This formulation is then used for modelling of the filters. Strategies to further miniaturization...... and small height of the waveguide. In this work, one of the realization methods of evanescent mode waveguides using a single layer substrate is considered. The method is based on the use of coaxial stubs as capacitive susceptances externally connected to a SIW. A microwave filter based on these principles...... of the microwave filter are discussed. The approach is useful in applications where a sharp roll-off at the upper stop-band is required....

  5. Mechanics of patterned helical Si springs on Si substrate.

    Science.gov (United States)

    Liu, D L; Ye, D X; Khan, F; Tang, F; Lim, B K; Picu, R C; Wang, G C; Lu, T M

    2003-12-01

    The elastic response, including the spring constant, of individual Si helical-shape submicron springs, was measured using a tip-cantilever assembly attached to a conventional atomic force microscope. The isolated, four-turn Si springs were fabricated using oblique angle deposition with substrate rotation, also known as the glancing angle deposition, on a templated Si substrate. The response of the structures was modeled using finite elements, and it was shown that the conventional formulae for the spring constant required modifications before they could be used for the loading scheme used in the present experiment.

  6. Adhesion mechanisms of nanoparticle silver to substrate materials: identification

    International Nuclear Information System (INIS)

    Joo, Sungchul; Baldwin, Daniel F

    2010-01-01

    Nanoparticle silver (NPS) conductors are increasingly being investigated for printed electronics applications. However, the adhesion mechanism of the nanoparticle silver to substrate materials has not been identified yet. In particular, the adhesion of NPS to organic materials such as the widely used polyimide Kapton HN and Kapton FPC dry films is concerned with low adhesion strength because the processed polymer surface is chemically inert. Moreover, its adhesion to substrate materials such as benzocyclobutene (BCB), copper and aluminum was found to be very weak. Therefore, in this paper, the mechanisms of NPS adhesion to organic and inorganic materials are identified as the first step in improving NPS adhesion strength. Improving the adhesion strength of NPS will be the key issue for printed electronics applications. The adhesion of NPS to substrate materials was found to be mainly attributed to van der Waals forces based on particle adhesion mechanisms. This finding provides the initiative of developing an adhesion prediction model of NPS to substrate materials in order to provide guidelines for improving the NPS adhesion strength to the substrate materials used in printed electronics.

  7. Effects of substrate binding site residue substitutions of xynA from Bacillus amyloliquefaciens on substrate specificity.

    Science.gov (United States)

    Prajapati, Anil S; Pawar, Vishakha A; Panchal, Ketankumar J; Sudhir, Ankit P; Dave, Bhaumik R; Patel, Darshan H; Subramanian, R B

    2018-02-13

    The aromatic residues of xylanase enzyme, W187, Y124, W144, Y128 and W63 of substrate binding pocket from Bacillus amyloliquefaciens were investigated for their role in substrate binding by homology modelling and sequence analysis. These residues are highly conserved and play an important role in substrate binding through steric hindrance. The substitution of these residues with alanine allows the enzyme to accommodate nonspecific substrates. Wild type and mutated genes were cloned and overexpressed in BL21. Optimum pH and temperature of rBAxn exhibited pH 9.0 and 50 °C respectively and it was stable up to 215 h. Along with the physical properties of rBAxn, kinetic parameters (K m 19.34 ± 0.72 mg/ml; k cat 6449.12 ± 155.37 min - 1 and k cat /K m 333.83 ± 6.78 ml min - 1  mg - 1 ) were also compared with engineered enzymes. Out of five mutations, W63A, Y128A and W144A lost almost 90% activity and Y124A and W187A retained almost 40-45% xylanase activity. The site-specific single mutation, led to alteration in substrate specificity from xylan to CMC while in case of double mutant the substrate specificity was altered from xylan to CMC, FP and avicel, indicating the role of aromatic residues on substrate binding, catalytic process and overall catalytic efficiency.

  8. Towards a formal design model based on a genetic design model system

    DEFF Research Database (Denmark)

    Storga, Mario; Andreasen, Mogens Myrup; Marjanovic, Dorian

    2005-01-01

    developed by N.H. Mortensen was chosen. In order to achieve the useful formalization of the GDMS structure we have followed modelling procedure on the four levels: epistemological, generic, domain and project level. As an epistemological foundation, The Suggested Upper Merged Ontology (SUMO) proposed....... In this article, we briefly summarize our experience of converting informal definitions of the concepts from the product development domain based on the existing theoretical background into formal design model. As a main data source for extracting the content of a design ontology, Genetic Design Model System...... by IEEE, provides us definitions for the most general and universal concepts, that we used in our research for derivation of terms definitions and axioms in the Design Ontology. The Design Ontology was evaluated using the OntoEdit® ontology engineering environment, on a real product example, and based...

  9. Substrate and inhibitor studies on proteinase 3

    NARCIS (Netherlands)

    Kam, C. M.; Kerrigan, J. E.; Dolman, K. M.; Goldschmeding, R.; von dem Borne, A. E.; Powers, J. C.

    1992-01-01

    Various amino acid and peptide thioesters were tested as substrates for human proteinase 3 and the best substrate is Boc-Ala-Ala-Nva-SBzl with a kcat/Km value of 1.0 x 10(6) M-1.s-1. Boc-Ala-Ala-AA-SBzl (AA = Val, Ala, or Met) are also good substrates with kcat/Km values of (1-4) x 10(5) M-1.s-1.

  10. Adhesion of rhodium films on metallic substrates

    International Nuclear Information System (INIS)

    Marot, L.; Covarel, G.; Tuilier, M.-H.; Steiner, R.; Oelhafen, P.

    2008-01-01

    Rhodium coated metallic films were prepared by magnetron sputtering on metallic substrates. All films were elaborated in same conditions on copper, molybdenum and stainless steel. Adhesion strength tests were carried out by scratch test. The results reveal that the adhesion strength between the film and the substrate is influenced by the hardness of the substrate. Increase of deposition temperature improves the adhesion of the coating. In addition, pre-treatment of substrates by a filtered cathodic vacuum arc and the layer thickness have has some effects on the final adhesion strength

  11. Thin glass substrates for mobile applications

    Science.gov (United States)

    Mauch, Reiner H.; Wegener, Holger; Kruse, Anke; Hildebrand, Norbert

    2000-10-01

    Flat panel displays play an important role as the visual interface for today's electronic devices (Notebook computers, PDA's, pagers, mobile phones, etc.). Liquid Crystal Display's are dominating the market. While for higher resolution displays active matrix displays like Thin Film Transistor LCD's are used, portable devices are mainly using Super Twisted Nematic (STN) displays. Based on the application, STN displays for mobile applications require thinner glass substrates with improved surface quality at a lower cost. The requirements and trends for STN glass substrates are identified and discussed. Different glass manufacturing processes are used today for the manufacture of these substrates. Advantages and disadvantages of the different glass substrate types are presented and discussed.

  12. Optical properties of thin Cu films as a function of substrate temperature

    CERN Document Server

    Savaloni, H

    2003-01-01

    Copper films (250 nm) deposited on glass substrates, at different substrate temperatures. Their optical properties were measured by ellipsometry (single wavelength of 589.3 nm) and spectrophotometry in the spectral range of 200-2600 nm. Kramers Kronig method was used for the analysis of the reflectivity curves of Cu films to obtain the optical constants of the films, while ellipsometry measurement was carried out as an independent method. The influence of substrate temperature on the microstructure of thin metallic films [Structure Zone Model ] is well established. The Effective Medium Approximation analysis was used to establish the relationship between the Structure Zone Model and Effective Medium Approximation predictions. Good agreements between Structure Zone Model as a function of substrate temperature and the values of volume fraction of voids obtained from Effective Medium Temperature analysis, are obtained; by increasing the substrate temperature the separation of the metallic grains decrease hence t...

  13. A proteomic approach for comprehensively screening substrates of protein kinases such as Rho-kinase.

    Directory of Open Access Journals (Sweden)

    Mutsuki Amano

    Full Text Available BACKGROUND: Protein kinases are major components of signal transduction pathways in multiple cellular processes. Kinases directly interact with and phosphorylate downstream substrates, thus modulating their functions. Despite the importance of identifying substrates in order to more fully understand the signaling network of respective kinases, efficient methods to search for substrates remain poorly explored. METHODOLOGY/PRINCIPAL FINDINGS: We combined mass spectrometry and affinity column chromatography of the catalytic domain of protein kinases to screen potential substrates. Using the active catalytic fragment of Rho-kinase/ROCK/ROK as the model bait, we obtained about 300 interacting proteins from the rat brain cytosol fraction, which included the proteins previously reported as Rho-kinase substrates. Several novel interacting proteins, including doublecortin, were phosphorylated by Rho-kinase both in vitro and in vivo. CONCLUSIONS/SIGNIFICANCE: This method would enable identification of novel specific substrates for kinases such as Rho-kinase with high sensitivity.

  14. Modellierung und Simulation des Substrat-Rauschens in integrierten RF CMOS-Schaltungen

    Science.gov (United States)

    Lin, L.; Xiong, J.; Mathis, W.

    2009-05-01

    Im integrierten CMOS-Schaltungsentwurf kann das Substrat-Rauschen, das vom digitalen Teil entsteht, die Funktionalität des analogen Teils stark beeinflussen. Es wird daher immer wichtiger, das Substrat als ein Medium der Rauschen-Propagation genau zu modellieren. Im vorliegenden Artikel wird ein auf der Finite Elemente Methode (FEM) und Modellordnungsreduktion (MOR) basiertes Modellierungsverfahren zur Admittanzen-Extraktion im Halbleitersubstrat vorgestellt. Nach der Diskretisierung mit FEM wird das Substrat im Allgemeinen als ein resistives/kapazitives Netz angesehen. Durch Bestimmung der Admittanz-Matrix und MOR ist es möglich ein äquivalentes Dreipol-Modell zwischen digitalem und analogem Teil über das Substrat zu bilden. Das Ergebnis der Modellierung wird dargestellt und mit numerischer Simulation des Substrat-Rauschens verglichen. Die Modellierung ermöglicht es, die Einflüsse des Substrat-Rauschens im Schaltungsentwurf zu berücksichtigen und so bestehende CMOS-Schaltungsarchitekturen zu optimieren.

  15. Determining the Elastic Modulus of Compliant Thin Films Supported on Substrates from Flat Punch Indentation Measurements

    Science.gov (United States)

    M.J. Wald; J.M. Considine; K.T. Turner

    2013-01-01

    Instrumented indentation is a technique that can be used to measure the elastic properties of soft thin films supported on stiffer substrates, including polymer films, cellulosic sheets, and thin layers of biological materials. When measuring thin film properties using indentation, the effect of the substrate must be considered. Most existing models for determining the...

  16. Composition of agarose substrate affects behavioral output of Drosophila larvae

    Directory of Open Access Journals (Sweden)

    Anthi Aristomenis Apostolopoulou

    2014-01-01

    Full Text Available In the last decade the Drosophila larva has evolved into a simple model organism offering the opportunity to integrate molecular genetics with systems neuroscience. This led to a detailed understanding of the functional neuronal networks for a number of sensory functions and behaviors including olfaction, vision, gustation and learning and memory. Typically, behavioral assays in use exploit simple Petri dish setups with either agarose or agar as a substrate. However, neither the quality nor the concentration of the substrate is generally standardized across these experiments and there is no data available on how larval behavior is affected by such different substrates. Here, we have investigated the effects of different agarose concentrations on several larval behaviors. We demonstrate that agarose concentration is an important parameter, which affects all behaviors tested: preference, feeding, learning and locomotion. Larvae can discriminate between different agarose concentrations, they feed differently on them, they can learn to associate an agarose concentration with an odor stimulus and crawl faster on a substrate of higher agarose concentration. Additionally, we have investigated the effect of agarose concentration on three quinine based behaviors: preference, feeding and learning. We show that in all cases examined the behavioral output changes in an agarose concentration-dependent manner. Our results suggest that comparisons between experiments performed on substrates differing in agarose concentration should be done with caution. It should be taken into consideration that the agarose concentration can affect the behavioral output and thereby the experimental outcomes per se potentially due to an increased escape response on more rigid substrates.

  17. Polarimetric studies of polyethylene terephtalate flexible substrates

    Science.gov (United States)

    Stchakovsky, M.; Garcia-Caurel, E.; Warenghem, M.

    2008-12-01

    Polymer sheets are currently used worldwide in a wide range of applications. The manufacturing process of these sheets involves extruding machines that stretch the material in both lateral and longitudinal directions with respect to the machine direction, thus inducing birefringence. In most cases, the film obtained is optically biaxial. Polarimetric spectroscopy (Ellipsometry and Mueller Matrix) combined with conoscopic observation are the methods of choice to study these properties. In this work we report an analysis of commercially available polyethylene terephtalate (PET) films used as substrate for food packaging as well as for embedded electronic devices such as solar cells or flexible displays. Initial observation of these films through polarizing microscope in conoscopic mode reveals first the trace of optical axis plane with respect to the film surface and second, whether the optical axis is acute or not. This preliminary study allows optimal sample positioning for further polarimetric studies. The measurements and modelling are done in both reflection and transmission mode on several spectroscopic polarimetric setups from UV to NIR. The models give as a main result, the dielectric tensor of the film as well as its orientation with respect to the laboratory reference frame.

  18. A multidisciplinary approach to study the functional properties of neuron-like cell models constituting a living bio-hybrid system: SH-SY5Y cells adhering to PANI substrate

    Directory of Open Access Journals (Sweden)

    S. Caponi

    2016-11-01

    Full Text Available A living bio-hybrid system has been successfully implemented. It is constituted by neuroblastic cells, the SH-SY5Y human neuroblastoma cells, adhering to a poly-anyline (PANI a semiconductor polymer with memristive properties. By a multidisciplinary approach, the biocompatibility of the substrate has been analyzed and the functionality of the adhering cells has been investigated. We found that the PANI films can support the cell adhesion. Moreover, the SH-SY5Y cells were successfully differentiated into neuron-like cells for in vitro applications demonstrating that PANI can also promote cell differentiation. In order to deeply characterize the modifications of the bio-functionality induced by the cell-substrate interaction, the functional properties of the cells have been characterized by electrophysiology and Raman spectroscopy. Our results confirm that the PANI films do not strongly affect the general properties of the cells, ensuring their viability without toxic effects on their physiology. Ascribed to the adhesion process, however, a slight increase of the markers of the cell suffering has been evidenced by Raman spectroscopy and accordingly the electrophysiology shows a reduction at positive stimulations in the cells excitability.

  19. AFM plough YBCO micro bridges: substrate effects

    CSIR Research Space (South Africa)

    Elkaseh, A

    2009-04-01

    Full Text Available AFM nanolithography was used as a novel cutting technique to define micro-size YBCO superconducting constrictions. Researchers studied the substrate effects on MgO and STO substrates and showed that the observed Shapiro steps from the bridges on STO...

  20. Substrate tolerant direct block copolymer nanolithography

    DEFF Research Database (Denmark)

    Li, Tao; Wang, Zhongli; Schulte, Lars

    2016-01-01

    Block copolymer (BC) self-assembly constitutes a powerful platform for nanolithography. However, there is a need for a general approach to BC lithography that critically considers all the steps from substrate preparation to the final pattern transfer. We present a procedure that significantly...... plasma treatment enables formation of the oxidized PDMS hard mask, PS block removal and polymer or graphene substrate patterning....

  1. Transformation kinetics of mixed polymeric substrates under ...

    African Journals Online (AJOL)

    Transformation kinetics of mixed polymeric substrates under transitory conditions by Aspergillus niger. ... Abstract. A mixture of polymeric substrates (simulating a complex wastewater) was transformed under sewer conditions and aerobiosis by Aspergillus niger in a tanks-in-series reactor at a hydraulic retention time of 14 h.

  2. Metal oxide nanorod arrays on monolithic substrates

    Energy Technology Data Exchange (ETDEWEB)

    Gao, Pu-Xian; Guo, Yanbing; Ren, Zheng

    2018-01-02

    A metal oxide nanorod array structure according to embodiments disclosed herein includes a monolithic substrate having a surface and multiple channels, an interface layer bonded to the surface of the substrate, and a metal oxide nanorod array coupled to the substrate surface via the interface layer. The metal oxide can include ceria, zinc oxide, tin oxide, alumina, zirconia, cobalt oxide, and gallium oxide. The substrate can include a glass substrate, a plastic substrate, a silicon substrate, a ceramic monolith, and a stainless steel monolith. The ceramic can include cordierite, alumina, tin oxide, and titania. The nanorod array structure can include a perovskite shell, such as a lanthanum-based transition metal oxide, or a metal oxide shell, such as ceria, zinc oxide, tin oxide, alumina, zirconia, cobalt oxide, and gallium oxide, or a coating of metal particles, such as platinum, gold, palladium, rhodium, and ruthenium, over each metal oxide nanorod. Structures can be bonded to the surface of a substrate and resist erosion if exposed to high velocity flow rates.

  3. Cellulose Nanofiber Composite Substrates for Flexible Electronics

    Science.gov (United States)

    Ronald Sabo; Jung-Hun Seo; Zhenqiang Ma

    2012-01-01

    Flexible electronics have a large number of potential applications including malleable displays and wearable computers. The current research into high-speed, flexible electronic substrates employs the use of plastics for the flexible substrate, but these plastics typically have drawbacks, such as high thermal expansion coefficients. Transparent films made from...

  4. Microbial growth and substrate utilization kinetics | Okpokwasili ...

    African Journals Online (AJOL)

    Microbial growth on and utilization of environmental contaminants as substrates have been studied by many researchers. Most times, substrate utilization results in removal of chemical contaminant, increase in microbial biomass and subsequent biodegradation of the contaminant. These are all aimed at detoxification of the ...

  5. Alternative substrates for cultivating oyster mushrooms ( Pleurotus ...

    African Journals Online (AJOL)

    Wheat straw has generally been used as the main substrate for cultivating oyster mushrooms (Pleurotus ostreatus); however, in South Africa it is becoming expensive for small-scale farmers to utilise. Therefore, the main objective of the study was to investigate the use of alternative, but suitable substrates for planting oyster ...

  6. Direct transfer of graphene onto flexible substrates

    Science.gov (United States)

    Pimenta, Luiz Gustavo; Song, Yi; Zeng, Tingying; Dresselhaus, Mildred; Kong, Jing; Araujo, Paulo

    2014-03-01

    We explore the direct transfer via lamination of chemical vapor deposition graphene onto different flexible substrates. The transfer method investigated here is fast, simple, and does not require an intermediate transfer membrane, such as polymethylmethacrylate. Various substrates of general interest in research and industry were studied including polytetrafluoroethylene filter membranes, PVC, cellulose nitrate/cellulose acetate filter membranes, polycarbonate, paraffin, polyethylene terephthalate, paper, and cloth. By comparing the properties of these substrates, two critical factors to ensure a successful transfer on bare substrates were identified: the substrate's hydrophobicity and good contact between the substrate and graphene. For substrates that do not satisfy those requirements, polymethylmethacrylate can be used as a surface modifier or glue to ensure successful transfer. Our results can be applied to facilitate present processes and open up directions for applications of chemical vapor deposition (CVD) graphene on flexible substrates. A broad range of applications of CVD graphene can be envisioned, including fabrication of graphene devices for opto/organic electronics, graphene membranes for gas/liquid separation, and ubiquitous electronics with graphene.

  7. Is substrate composition a suitable predictor for deep-water coral occurrence on fine scales?

    Science.gov (United States)

    Bennecke, Swaantje; Metaxas, Anna

    2017-06-01

    Species distribution modelling can be applied to identify potentially suitable habitat for species with largely unknown distributions, such as many deep-water corals. Important variables influencing species occurrence in the deep sea, e.g. substrate composition, are often not included in these modelling approaches because high-resolution data are unavailable. We investigated the relationship between substrate composition and the occurrence of the two deep-water octocoral species Primnoa resedaeformis and Paragorgia arborea, which require hard substrate for attachment. On a scale of 10s of metres, we analysed images of the seafloor taken at two locations inside the Northeast Channel Coral Conservation Area in the Northwest Atlantic. We interpolated substrate composition over the sampling areas and determined the contribution of substrate classes, depth and slope to describe habitat suitability using maximum entropy modelling (Maxent). Substrate composition was similar at both sites - dominated by pebbles in a matrix of sand (>80%) with low percentages of suitable substrate for coral occurrence. Coral abundance was low at site 1 (0.9 colonies of P. resedaeformis per 100 m2) and high at site 2 (63 colonies of P. resedaeformis per 100 m2) indicating that substrate alone is not sufficient to explain varying patterns in coral occurrence. Spatial interpolations of substrate classes revealed the difficulty to accurately resolve sparsely distributed boulders (3-5% of substrate). Boulders were by far the most important variable in the habitat suitability model (HSM) for P. resedaeformis at site 1, indicating the fundamental influence of a substrate class that is the least abundant. At site 2, HSMs identified cobbles and sand/pebble as the most important variables for habitat suitability. However, substrate classes were correlated making it difficult to determine the influence of individual variables. To provide accurate information on habitat suitability for the two coral

  8. Butyrate as preferred substrate for polyhydroxybutyrate production.

    Science.gov (United States)

    Marang, Leonie; Jiang, Yang; van Loosdrecht, Mark C M; Kleerebezem, Robbert

    2013-08-01

    In this study, the suitability of butyrate as substrate for polyhydroxyalkanoate (PHA) production by microbial enrichment cultures was assessed. Two sequencing batch reactors were operated under feast-famine conditions: one fed with butyrate, and another with mixed acetate and butyrate. The obtained results were compared to previous results with acetate as sole substrate. In all three reactors Plasticicumulans acidivorans dominated the enrichment culture. The carbon uptake rate and PHA yield were significantly higher on butyrate than on acetate, resulting in a higher PHA production rate. When both substrates were available the bacteria strongly preferred the uptake of butyrate. Only after butyrate depletion acetate was taken up at a high rate. The molar substrate uptake rate remained the same, suggesting that substrate uptake is the rate-limiting step. The results show that for optimized waste-based PHA production the pre-fermentation process should be directed towards butyrate production. Copyright © 2013 Elsevier Ltd. All rights reserved.

  9. A signal-substrate match in the substrate-borne component of a multimodal courtship display

    Directory of Open Access Journals (Sweden)

    Damian O. ELIAS, Andrew C. MASON, Eileen A. HEBETS

    2010-06-01

    Full Text Available The environment can impose strong limitations on the efficacy of signal transmission. In particular, for vibratory communication, the signaling environment is often extremely heterogeneous at very small scales. Nevertheless, natural selection is expected to select for signals well-suited to effective transmission. Here, we test for substrate-dependent signal efficacy in the wolf spider Schizocosa stridulans Stratton 1991. We first explore the transmission characteristics of this important signaling modality by playing recorded substrate-borne signals through three different substrates (leaf litter, pine litter, and red clay and measuring the propagated signal. We found that the substrate-borne signal of S. stridulans attenuates the least on leaf litter, the substrate upon which the species is naturally found. Next, by assessing mating success with artificially muted and non-muted males across different signaling substrates (leaf litter, pine litter, and sand, we explored the relationship between substrate-borne signaling and substrate for mating success. We found that muted males were unsuccessful in obtaining copulations regardless of substrate, while mating success was dependent on the signaling substrate for non-muted males. For non-muted males, more males copulated on leaf litter than any other substrate. Taken together, these results confirm the importance of substrate-borne signaling in S. stridulans and suggest a match between signal properties and signal efficacy – leaf litter transmits the signal most effectively and males are most successful in obtaining copulations on leaf litter [Current Zoology 56 (3: 370–378, 2010].

  10. Effect of continuous addition of an organic substrate to the anoxic phase on biological phosphorus removal

    DEFF Research Database (Denmark)

    Meinhold, Jens; Pedersen, Heinz; Arnold, Eva

    1998-01-01

    The continuous introduction of a biological phosphorus removal (BPR) promoting organic substrate to the denitrifying reactor of a BPR process is examined through a series of batch experiments using acetate as model organic substrate. Several observations are made regarding the influence of substr......The continuous introduction of a biological phosphorus removal (BPR) promoting organic substrate to the denitrifying reactor of a BPR process is examined through a series of batch experiments using acetate as model organic substrate. Several observations are made regarding the influence...... of substrate availability on PHA storage/utilization and phosphate uptake/release. Under anoxic conditions PHB is utilized and phosphate is taken up, indicating that at least a fraction of the PAO can denitrify. The rates of anoxic P-uptake, PHB utilization and denitrification are found to increase...

  11. The effect of clay amendment on substrate properties and growth of woody plants

    Directory of Open Access Journals (Sweden)

    Tomáš Meisl

    2012-01-01

    Full Text Available This work deals with the effect of two clay products differing in particle size distribution on properties of growing substrate and on growth of containerized woody plants in substrates amended with these clay products. Fine and coarse clay were added to a peat substrate, each at two rates. The peat substrate without clay was used as a control. The substrates were tested in experiments with two woody ornamentals (Thuja occidentalis ’Smaragd’ and Prunus cistena. Chemical and physical properties of the substrates were measured according to European Standards before planting. Proportion of water categories differing in availability to the plants were calculated from retention curves measured on the sand box. Properties of substrates in containers with and without plants were evaluated in the same way at the end of the culture. Clay addition changed chemical and physical properties of the tested substrates in terms: available nutrients content, particle density, bulk density, total pore volume, easy available water, water buffering capacity, air capacity, and shrinkage. The effect of fine clay was much stronger. In comparison with the clear effect of clay addition on the substrate chemical and physical properties, the effect on the growth and quality of model woody plants was not so explicit.

  12. Liquid crystal polymer substrate based wideband tapered step antenna

    Directory of Open Access Journals (Sweden)

    Boddapati Taraka Phani MADHAV

    2015-05-01

    Full Text Available Performance study of wideband tapered step antenna on liquid crystal polymer substrate material is presented. Bandwidth enhancement is achieved by adding step serrated ground on the front side of the model along with the radiating patch. The radiating patch seems to be the intersection of two half circles connected back to back. The lower half circle radius is more than upper half circle radius. Wideband tapered step antenna is designed on the liquid crystal polymer substrate (Ultralam 3850, εr = 2.9 with dimensions of 20×20×0.5 mm. Coplanar waveguide feeding is used in this model with feed line width of 2.6 mm and gap between feed line to ground plane of 0.5 mm.

  13. Additive Manufacturing of Catalyst Substrates for Steam-Methane Reforming

    Science.gov (United States)

    Kramer, Michelle; McKelvie, Millie; Watson, Matthew

    2018-01-01

    Steam-methane reforming is a highly endothermic reaction, which is carried out at temperatures up to 1100 °C and pressures up to 3000 kPa, typically with a Ni-based catalyst distributed over a substrate of discrete alumina pellets or beads. Standard pellet geometries (spheres, hollow cylinders) limit the degree of mass transfer between gaseous reactants and catalyst. Further, heat is supplied to the exterior of the reactor wall, and heat transfer is limited due to the nature of point contacts between the reactor wall and the substrate pellets. This limits the degree to which the process can be intensified, as well as limiting the diameter of the reactor wall. Additive manufacturing now gives us the capability to design structures with tailored heat and mass transfer properties, not only within the packed bed of the reactor, but also at the interface between the reactor wall and the packed bed. In this work, the use of additive manufacturing to produce monolithic-structured catalyst substrate models, made from acrylonitrile-butadiene-styrene, with enhanced conductive heat transfer is described. By integrating the reactor wall into the catalyst substrate structure, the effective thermal conductivity increased by 34% from 0.122 to 0.164 W/(m K).

  14. Bacterial protease uses distinct thermodynamic signatures for substrate recognition.

    Science.gov (United States)

    Bezerra, Gustavo Arruda; Ohara-Nemoto, Yuko; Cornaciu, Irina; Fedosyuk, Sofiya; Hoffmann, Guillaume; Round, Adam; Márquez, José A; Nemoto, Takayuki K; Djinović-Carugo, Kristina

    2017-06-06

    Porphyromonas gingivalis and Porphyromonas endodontalis are important bacteria related to periodontitis, the most common chronic inflammatory disease in humans worldwide. Its comorbidity with systemic diseases, such as type 2 diabetes, oral cancers and cardiovascular diseases, continues to generate considerable interest. Surprisingly, these two microorganisms do not ferment carbohydrates; rather they use proteinaceous substrates as carbon and energy sources. However, the underlying biochemical mechanisms of their energy metabolism remain unknown. Here, we show that dipeptidyl peptidase 11 (DPP11), a central metabolic enzyme in these bacteria, undergoes a conformational change upon peptide binding to distinguish substrates from end products. It binds substrates through an entropy-driven process and end products in an enthalpy-driven fashion. We show that increase in protein conformational entropy is the main-driving force for substrate binding via the unfolding of specific regions of the enzyme ("entropy reservoirs"). The relationship between our structural and thermodynamics data yields a distinct model for protein-protein interactions where protein conformational entropy modulates the binding free-energy. Further, our findings provide a framework for the structure-based design of specific DPP11 inhibitors.

  15. Elastocapillary levelling of thin viscous films on soft substrates

    Science.gov (United States)

    Rivetti, Marco; Bertin, Vincent; Salez, Thomas; Hui, Chung-Yuen; Linne, Christine; Arutkin, Maxence; Wu, Haibin; Raphaël, Elie; Bäumchen, Oliver

    2017-09-01

    A thin liquid film with nonzero curvature at its free surface spontaneously flows to reach a flat configuration, a process driven by Laplace pressure gradients and resisted by the liquid's viscosity. Inspired by recent progresses on the dynamics of liquid droplets on soft substrates, we here study the relaxation of a viscous film supported by an elastic foundation. Experiments involve thin polymer films on elastomeric substrates, where the dynamics of the liquid-air interface is monitored using atomic force microscopy. A theoretical model that describes the coupled evolution of the solid-liquid and the liquid-air interfaces is also provided. In this soft-levelling configuration, Laplace pressure gradients not only drive the flow, but they also induce elastic deformations on the substrate that affect the flow and the shape of the liquid-air interface itself. This process represents an original example of elastocapillarity that is not mediated by the presence of a contact line. We discuss the impact of the elastic contribution on the levelling dynamics and show the departure from the classical self-similarities and power laws observed for capillary levelling on rigid substrates.

  16. Direct transfer of graphene onto flexible substrates

    Science.gov (United States)

    Martins, Luiz G. P.; Song, Yi; Zeng, Tingying; Dresselhaus, Mildred S.; Kong, Jing; Araujo, Paulo T.

    2013-01-01

    In this paper we explore the direct transfer via lamination of chemical vapor deposition graphene onto different flexible substrates. The transfer method investigated here is fast, simple, and does not require an intermediate transfer membrane, such as polymethylmethacrylate, which needs to be removed afterward. Various substrates of general interest in research and industry were studied in this work, including polytetrafluoroethylene filter membranes, PVC, cellulose nitrate/cellulose acetate filter membranes, polycarbonate, paraffin, polyethylene terephthalate, paper, and cloth. By comparing the properties of these substrates, two critical factors to ensure a successful transfer on bare substrates were identified: the substrate’s hydrophobicity and good contact between the substrate and graphene. For substrates that do not satisfy those requirements, polymethylmethacrylate can be used as a surface modifier or glue to ensure successful transfer. Our results can be applied to facilitate current processes and open up directions for applications of chemical vapor deposition graphene on flexible substrates. A broad range of applications can be envisioned, including fabrication of graphene devices for opto/organic electronics, graphene membranes for gas/liquid separation, and ubiquitous electronics with graphene. PMID:24127582

  17. Method of beryllium implantation in germanium substrate

    International Nuclear Information System (INIS)

    Kagawa, S.; Baba, Y.; Kaneda, T.; Shirai, T.

    1983-01-01

    A semiconductor device is disclosed, as well as a method for manufacturing it in which ions of beryllium are implanted into a germanium substrate to form a layer containing p-type impurity material. There after the substrate is heated at a temperature in the range of 400 0 C. to 700 0 C. to diffuse the beryllium ions into the substrate so that the concentration of beryllium at the surface of the impurity layer is in the order of 10 17 cm- 3 or more. In one embodiment, a p-type channel stopper is formed locally in a p-type germanium substrate and an n-type active layer is formed in a region surrounded by, and isolated from, the channel stopper region. In another embodiment, a relatively shallow p-type active layer is formed at one part of an n-type germanium substrate and p-type guard ring regions are formed surrounding, and partly overlapping said p-type active layer. In a further embodiment, a p-type island region is formed at one part of an n-type germanium substrate, and an n-type region is formed within said p-type region. In these embodiments, the p-type channel stopper region, p-type guard ring regions and the p-type island region are all formed by implanting ions of beryllium into the germanium substrate

  18. Induction of mesenchymal stem cell chondrogenesis by polyacrylate substrates

    OpenAIRE

    Glennon-Alty, Laurence; Williams, Rachel; Dixon, Simon; Murray, Patricia

    2013-01-01

    Mesenchymal stem cells (MSCs) can generate chondrocytes in vitro, but typically need to be cultured as aggregates in the presence of transforming growth factor beta (TGF-?), which makes scale-up difficult. Here we investigated if polyacrylate substrates modelled on the functional group composition and distribution of the Arg-Gly-Asp (RGD) integrin-binding site could induce MSCs to undergo chondrogenesis in the absence of exogenous TGF-?. Within a few days of culture on the biomimetic polyacry...

  19. Study of Carbon Nanotube-Substrate Interaction

    Directory of Open Access Journals (Sweden)

    Jaqueline S. Soares

    2012-01-01

    Full Text Available Environmental effects are very important in nanoscience and nanotechnology. This work reviews the importance of the substrate in single-wall carbon nanotube properties. Contact with a substrate can modify the nanotube properties, and such interactions have been broadly studied as either a negative aspect or a solution for developing carbon nanotube-based nanotechnologies. This paper discusses both theoretical and experimental studies where the interaction between the carbon nanotubes and the substrate affects the structural, electronic, and vibrational properties of the tubes.

  20. Mass spectrometry-assisted protease substrate screening

    DEFF Research Database (Denmark)

    Schlüter, Hartmut; Rykl, Jana; Thiemann, Joachim

    2007-01-01

    Since sequencing of the human genome was completed, more than 500 genes have been annotated as proteases. Exploring the physiological role of each protease requires the identification of their natural substrates. However, the endogenous substrates of many of the human proteases are as yet unknown....... Here we describe a new assay that addresses this problem. The assay, which easily can be automated, is based on the incubation of immobilized protein fractions, which may contain the natural substrate, with a defined protease. After concentrating the proteolytically released peptides by reversed...

  1. Animal deoxyribonucleoside kinases: 'forward' and 'retrograde' evolution of their substrate specificity

    DEFF Research Database (Denmark)

    Piskur, Jure; Sandrini, Michael P; Knecht, Wolfgang

    2004-01-01

    Deoxyribonucleoside kinases, which catalyse the phosphorylation of deoxyribonucleosides, are present in several copies in most multicellular organisms and therefore represent an excellent model to study gene duplication and specialisation of the duplicated copies through partitioning of substrate...

  2. Substrate and product inhibition of hydrogen production by the extreme thermophile, Caldicellulosiruptor saccharolyticus

    NARCIS (Netherlands)

    Niel, van E.W.J.; Claassen, P.A.M.; Stams, A.J.M.

    2003-01-01

    Substrate and product inhibition of hydrogen production during sucrose fermentation by the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus was studied. The inhibition kinetics were analyzed with a noncompetitive, nonlinear inhibition model. Hydrogen was the most severe

  3. Deformation of an Elastic Substrate Due to a Resting Sessile Droplet

    Science.gov (United States)

    Bardall, Aaron; Daniels, Karen; Shearer, Michael

    2017-11-01

    On a sufficiently soft substrate, a resting fluid droplet will cause significant deformation of the substrate. This deformation is driven by a combination of capillary forces at the contact line and the fluid pressure at the solid surface. These forces are balanced at the surface by the solid traction stress induced by the substrate deformation. Young's Law, which predicts the equilibrium contact angle of the droplet, also indicates an a priori radial force balance for rigid substrates, but not necessarily for soft substrates which deform under loading. It remains an open question whether the contact line transmits a non-zero force tangent to the substrate surface in addition to the conventional normal force. This talk will present a model for the static deformation of the substrate that includes a non-zero tangential contact line force as well as general interfacial energy conditions governing the angle of a two-dimensional droplet. We discuss extensions of this model to non-symmetric droplets and their effect on the static configuration of the droplet/substrate system. NSF #DMS-1517291.

  4. Cell-substrate interaction with cell-membrane-stress dependent adhesion.

    Science.gov (United States)

    Jiang, H; Yang, B

    2012-01-10

    Cell-substrate interaction is examined in a two-dimensional mechanics model. The cell and substrate are treated as a shell and an elastic solid, respectively. Their interaction through adhesion is treated using nonlinear springs. Compared to previous cell mechanics models, the present model introduces a cohesive force law that is dependent not only on cell-substrate distance but also on internal cell-membrane stress. It is postulated that a living cell would establish focal adhesion sites with density dependent on the cell-membrane stress. The formulated mechanics problem is numerically solved using coupled finite elements and boundary elements for the cell and the substrate, respectively. The nodes in the adhesion zone from either side are linked by the cohesive springs. The specific cases of a cell adhering to a homogeneous substrate and a heterogeneous bimaterial substrate are examined. The analyses show that the substrate stiffness affects the adhesion behavior significantly and regulates the direction of cell adhesion, in good agreement with the experimental results in the literature. By introducing a reactive parameter (i.e., cell-membrane stress) linking biological responses of a living cell to a mechanical environment, the present model offers a unified mechanistic vehicle for characterization and prediction of living cell responses to various kinds of mechanical stimuli including local extracellular matrix and neighboring cells. Copyright © 2011 Elsevier Ltd. All rights reserved.

  5. Surface enhanced Raman optical activity of molecules on orientationally averaged substrates: theory of electromagnetic effects.

    Science.gov (United States)

    Janesko, Benjamin G; Scuseria, Gustavo E

    2006-09-28

    We present a model for electromagnetic enhancements in surface enhanced Raman optical activity (SEROA) spectroscopy. The model extends previous treatments of SEROA to substrates, such as metal nanoparticles in solution, that are orientationally averaged with respect to the laboratory frame. Our theoretical treatment combines analytical expressions for unenhanced Raman optical activity with molecular polarizability tensors that are dressed by the substrate's electromagnetic enhancements. We evaluate enhancements from model substrates to determine preliminary scaling laws and selection rules for SEROA. We find that dipolar substrates enhance Raman optical activity (ROA) scattering less than Raman scattering. Evanescent gradient contributions to orientationally averaged ROA scale to first or higher orders in the gradient of the incident plane-wave field. These evanescent gradient contributions may be large for substrates with quadrupolar responses to the plane-wave field gradient. Some substrates may also show a ROA contribution that depends only on the molecular electric dipole-electric dipole polarizability. These conclusions are illustrated via numerical calculations of surface enhanced Raman and ROA spectra from (R)-(-)-bromochlorofluoromethane on various model substrates.

  6. Contact of a spherical probe with a stretched rubber substrate

    Science.gov (United States)

    Frétigny, Christian; Chateauminois, Antoine

    2017-07-01

    We report on a theoretical and experimental investigation of the normal contact of stretched neo-Hookean substrates with rigid spherical probes. Starting from a published formulation of surface Green's function for incremental displacements on a prestretched, neo-Hookean, substrate [J. Mech. Phys. Solids 56, 2957 (2008), 10.1016/j.jmps.2008.07.002], a model is derived for both adhesive and nonadhesive contacts. The shape of the elliptical contact area together with the contact load and the contact stiffness are predicted as a function of the in-plane stretch ratios λx and λy of the substrate. The validity of this model is assessed by contact experiments carried out using an uniaxally stretched silicone rubber. For stretch ratio below about 1.25, a good agreement is observed between theory and experiments. Above this threshold, some deviations from the theoretical predictions are induced as a result of the departure of the mechanical response of the silicone rubber from the neo-Hokeean description embedded in the model.

  7. Flexible and foldable paper-substrate thermoelectric generator (teg)

    KAUST Repository

    Rojas, Jhonathan Prieto

    2017-08-24

    Flexible and foldable paper-substrate thermoelectric generators (TEGs) and methods for making the paper-substrate TEGs are disclosed. A method includes depositing a plurality of thermocouples in series on a paper substrate to create a paper-substrate TEG, wherein the plurality of thermocouples is deposited between two contact points of the paper-substrate TEG. The method may also include setting the power density and maximum achievable temperature gradient of the paper-substrate TEG by folding the paper-substrate TEG. A paper-substrate TEG apparatus may include a paper substrate and a plurality of thermocouples deposited in series on the paper substrate between two contact points of the paper-substrate TEG, wherein the power density and maximum achievable temperature gradient of the paper-substrate TEG is set by folding the paper-substrate TEG.

  8. Prediction of membrane transport proteins and their substrate specificities using primary sequence information.

    Directory of Open Access Journals (Sweden)

    Nitish K Mishra

    Full Text Available Membrane transport proteins (transporters move hydrophilic substrates across hydrophobic membranes and play vital roles in most cellular functions. Transporters represent a diverse group of proteins that differ in topology, energy coupling mechanism, and substrate specificity as well as sequence similarity. Among the functional annotations of transporters, information about their transporting substrates is especially important. The experimental identification and characterization of transporters is currently costly and time-consuming. The development of robust bioinformatics-based methods for the prediction of membrane transport proteins and their substrate specificities is therefore an important and urgent task.Support vector machine (SVM-based computational models, which comprehensively utilize integrative protein sequence features such as amino acid composition, dipeptide composition, physico-chemical composition, biochemical composition, and position-specific scoring matrices (PSSM, were developed to predict the substrate specificity of seven transporter classes: amino acid, anion, cation, electron, protein/mRNA, sugar, and other transporters. An additional model to differentiate transporters from non-transporters was also developed. Among the developed models, the biochemical composition and PSSM hybrid model outperformed other models and achieved an overall average prediction accuracy of 76.69% with a Mathews correlation coefficient (MCC of 0.49 and a receiver operating characteristic area under the curve (AUC of 0.833 on our main dataset. This model also achieved an overall average prediction accuracy of 78.88% and MCC of 0.41 on an independent dataset.Our analyses suggest that evolutionary information (i.e., the PSSM and the AAIndex are key features for the substrate specificity prediction of transport proteins. In comparison, similarity-based methods such as BLAST, PSI-BLAST, and hidden Markov models do not provide accurate predictions

  9. Prediction of membrane transport proteins and their substrate specificities using primary sequence information.

    Science.gov (United States)

    Mishra, Nitish K; Chang, Junil; Zhao, Patrick X

    2014-01-01

    Membrane transport proteins (transporters) move hydrophilic substrates across hydrophobic membranes and play vital roles in most cellular functions. Transporters represent a diverse group of proteins that differ in topology, energy coupling mechanism, and substrate specificity as well as sequence similarity. Among the functional annotations of transporters, information about their transporting substrates is especially important. The experimental identification and characterization of transporters is currently costly and time-consuming. The development of robust bioinformatics-based methods for the prediction of membrane transport proteins and their substrate specificities is therefore an important and urgent task. Support vector machine (SVM)-based computational models, which comprehensively utilize integrative protein sequence features such as amino acid composition, dipeptide composition, physico-chemical composition, biochemical composition, and position-specific scoring matrices (PSSM), were developed to predict the substrate specificity of seven transporter classes: amino acid, anion, cation, electron, protein/mRNA, sugar, and other transporters. An additional model to differentiate transporters from non-transporters was also developed. Among the developed models, the biochemical composition and PSSM hybrid model outperformed other models and achieved an overall average prediction accuracy of 76.69% with a Mathews correlation coefficient (MCC) of 0.49 and a receiver operating characteristic area under the curve (AUC) of 0.833 on our main dataset. This model also achieved an overall average prediction accuracy of 78.88% and MCC of 0.41 on an independent dataset. Our analyses suggest that evolutionary information (i.e., the PSSM) and the AAIndex are key features for the substrate specificity prediction of transport proteins. In comparison, similarity-based methods such as BLAST, PSI-BLAST, and hidden Markov models do not provide accurate predictions for the

  10. Substrate curvature gradient drives rapid droplet motion.

    Science.gov (United States)

    Lv, Cunjing; Chen, Chao; Chuang, Yin-Chuan; Tseng, Fan-Gang; Yin, Yajun; Grey, Francois; Zheng, Quanshui

    2014-07-11

    Making small liquid droplets move spontaneously on solid surfaces is a key challenge in lab-on-chip and heat exchanger technologies. Here, we report that a substrate curvature gradient can accelerate micro- and nanodroplets to high speeds on both hydrophilic and hydrophobic substrates. Experiments for microscale water droplets on tapered surfaces show a maximum speed of 0.42  m/s, 2 orders of magnitude higher than with a wettability gradient. We show that the total free energy and driving force exerted on a droplet are determined by the substrate curvature and substrate curvature gradient, respectively. Using molecular dynamics simulations, we predict nanoscale droplets moving spontaneously at over 100  m/s on tapered surfaces.

  11. Pressure-Sensitive Paint: Effect of Substrate

    Science.gov (United States)

    Quinn, Mark Kenneth; Yang, Leichao; Kontis, Konstantinos

    2011-01-01

    There are numerous ways in which pressure-sensitive paint can be applied to a surface. The choice of substrate and application method can greatly affect the results obtained. The current study examines the different methods of applying pressure-sensitive paint to a surface. One polymer-based and two porous substrates (anodized aluminum and thin-layer chromatography plates) are investigated and compared for luminescent output, pressure sensitivity, temperature sensitivity and photodegradation. Two luminophores [tris-Bathophenanthroline Ruthenium(II) Perchlorate and Platinum-tetrakis (pentafluorophenyl) Porphyrin] will also be compared in all three of the substrates. The results show the applicability of the different substrates and luminophores to different testing environments. PMID:22247685

  12. The substrate specificity of phospholipase A

    NARCIS (Netherlands)

    Deenen, L.L.M. van; Haas, Gerard H. de

    1963-01-01

    Investigations on variously modified analogues of phospholipids elucidated the following substrate characteristics for phospholipase A (Crotalus adamanteus). 1. 1. Within the class of α-phosphoglycerides -isomers are readily hydrolysed, while -α-phospholipids appeared not to be attacked. 2.

  13. Transformation kinetics of mixed polymeric substrates under ...

    African Journals Online (AJOL)

    bglucosidase and a-mannosidase were abundantly secreted in the growth medium. This research is the first report on mixed polymeric substrate biodegradation under sewer condition by A. niger, and could be considered as an open window on ...

  14. Biochemicalmethane potential (BMP) of solid organic substrates

    DEFF Research Database (Denmark)

    Raposo, F.; Fernández-Cegrí, V.; de la Rubia, M.A.

    2011-01-01

    and experimental conditions were investigated. The study was performed using four substrates: three positive control substrates (starch, cellulose and gelatine), and one raw biomassmaterial (mung bean) at two different inoculum to substrate ratios (ISR). RESULTS: The average methane yields for starch, cellulose......, gelatine and mung bean at ISR of 2 and 1 were 350 ± 33, 350 ± 29, 380 ± 42, 370 ± 36 and 370 ± 35 mL CH4 g−1 VSadded, respectively. The percentages of biotransformation of these substrates into methane were 85 ± 8, 85 ± 7, 88 ± 9, 85 ± 8 and 85 ± 8%, respectively. On the other hand, the first-order rate...

  15. Transferring substrates to the 26S proteasome

    DEFF Research Database (Denmark)

    Hartmann-Petersen, Rasmus; Seeger, Michael; Gordon, Colin

    2003-01-01

    Ubiquitin-dependent protein degradation is not only involved in the recycling of amino acids from damaged or misfolded proteins but also represents an essential and deftly controlled mechanism for modulating the levels of key regulatory proteins. Chains of ubiquitin conjugated to a substrate...... protein specifically target it for degradation by the 26S proteasome, a huge multi-subunit protein complex found in all eukaryotic cells. Recent reports have clarified some of the molecular mechanisms involved in the transfer of ubiquitinated substrates from the ubiquitination machinery to the proteasome....... This novel substrate transportation step in the ubiquitin-proteasome pathway seems to occur either directly or indirectly via certain substrate-recruiting proteins and appears to involve chaperones....

  16. Substrates and method for determining enzymes

    Science.gov (United States)

    Smith, R.E.; Bissell, E.R.

    1981-10-13

    A method is disclosed for determining the presence of an enzyme in a biological fluid, which includes the steps of contacting the fluid with a synthetic chromogenic substrate, which is an amino acid derivative of 7-amino-4-trifluoromethylcoumarin; incubating the substrate-containing fluid to effect enzymatic hydrolysis; and fluorometrically determining the presence of the free 7-amino-4-trifluoromethylcoumarin chromophore in the hydrolyzate. No Drawings

  17. Micromechanics of substrate-supported thin films

    Science.gov (United States)

    He, Wei; Han, Meidong; Wang, Shibin; Li, Lin-An; Xue, Xiuli

    2017-09-01

    The mechanical properties of metallic thin films deposited on a substrate play a crucial role in the performance of micro/nano-electromechanical systems (MEMS/NEMS) and flexible electronics. This article reviews ongoing study on the mechanics of substrate-supported thin films, with emphasis on the experimental characterization techniques, such as the rule of mixture and X-ray tensile testing. In particular, the determination of interfacial adhesion energy, film deformation, elastic properties and Bauschinger effect are discussed.

  18. Alternative substrates for higher mushrooms mycelia cultivation

    Directory of Open Access Journals (Sweden)

    TETIANA KRUPODOROVA

    2015-12-01

    Full Text Available Cultivation of 29 species of higher mushroom mycelia on alternative substrates – wastes of Ukrainian oil-fat industry, has been investigated. The amount of mushroom mycelia obtaining on 12 investigated substrates varied significantly, from 1.0 g/L to 22.9 g/L on the 14th day of cultivation. The superficial cultivation adopted in this study allows for easy to choose appropriate medium (substrate for mycelia production. Alternative substrates (compared to glucose-peptone-yeast medium were selected for all studied species, from soybean cake – most suitable for the mycelial growth of 24 species, to walnut cake − suitable only for 2 species. The utilization of substrates has been evaluated by biological efficiency. The best index of biological efficiency varied from 19.0% to 41.6% depending on the mushroom species. It was established high biological efficiency of mycelia cultivation on substrates: wheat seed cake – Pleurotus djamor, Lyophyllum shimeji, Crinipellis schevczenkovi, Phellinus igniarius, Spongipellis litschaueri; oat seed cake – Ganoderma applanatum and G. lucidum; soybean cake – Hohenbuehelia myxotricha, Trametes versicolor, Morchella esculenta, Cordyceps sinensis, C. militaris, and Agrocybe aegerita; rape seed cake – Auriporia aurea; camelina seed cake – Fomes fomentarius. The cultivation of these species are perspective as a biotechnological process of agricultural wastes converted into mycelia, which could be used in different forms of products with therapeutic action: powder or tablets nutraceuticals or ingredients for functional foods.

  19. Manufacturing Process for OLED Integrated Substrate

    Energy Technology Data Exchange (ETDEWEB)

    Hung, Cheng-Hung [Vitro Flat Glass LLC, Cheswick, PA (United States). Glass Technology Center

    2017-03-31

    The main objective of this project was to develop a low-cost integrated substrate for rigid OLED solid-state lighting produced at a manufacturing scale. The integrated substrates could include combinations of soda lime glass substrate, light extraction layer, and an anode layer (i.e., Transparent Conductive Oxide, TCO). Over the 3+ year course of the project, the scope of work was revised to focus on the development of a glass substrates with an internal light extraction (IEL) layer. A manufacturing-scale float glass on-line particle embedding process capable of producing an IEL glass substrate having a thickness of less than 1.7mm and an area larger than 500mm x 400mm was demonstrated. Substrates measuring 470mm x 370mm were used in the OLED manufacturing process for fabricating OLED lighting panels in single pixel devices as large as 120.5mm x 120.5mm. The measured light extraction efficiency (calculated as external quantum efficiency, EQE) for on-line produced IEL samples (>50%) met the project’s initial goal.

  20. Temperature effects on kinetic parameters and substrate affinity of Cel7A cellobiohydrolases

    DEFF Research Database (Denmark)

    Sørensen, Trine Holst; Cruys-Bagger, Nicolaj; Windahl, Michael Skovbo

    2015-01-01

    We measured hydrolytic rates of four purified cellulases in small increments of temperature (10–50 °C) and substrate loads (0–100 g/liter) and analyzed the data by a steady state kinetic model that accounts for the processive mechanism. We used wild type cellobiohydrolases (Cel7A) from mesophilic...... Hypocrea jecorina and thermophilic Rasamsonia emersonii and two variants of these enzymes designed to elucidate the role of the carbohydrate binding module (CBM). We consistently found that the maximal rate increased strongly with temperature, whereas the affinity for the insoluble substrate decreased......, and as a result, the effect of temperature depended strongly on the substrate load. Thus, temperature had little or no effect on the hydrolytic rate in dilute substrate suspensions, whereas strong temperature activation (Q10 values up to 2.6) was observed at saturating substrate loads. The CBM had a dual effect...

  1. Substrate-bound structure of the E. coli multidrug resistance transporter MdfA.

    Science.gov (United States)

    Heng, Jie; Zhao, Yan; Liu, Ming; Liu, Yue; Fan, Junping; Wang, Xianping; Zhao, Yongfang; Zhang, Xuejun C

    2015-09-01

    Multidrug resistance is a serious threat to public health. Proton motive force-driven antiporters from the major facilitator superfamily (MFS) constitute a major group of multidrug-resistance transporters. Currently, no reports on crystal structures of MFS antiporters in complex with their substrates exist. The E. coli MdfA transporter is a well-studied model system for biochemical analyses of multidrug-resistance MFS antiporters. Here, we report three crystal structures of MdfA-ligand complexes at resolutions up to 2.0 Å, all in the inward-facing conformation. The substrate-binding site sits proximal to the conserved acidic residue, D34. Our mutagenesis studies support the structural observations of the substrate-binding mode and the notion that D34 responds to substrate binding by adjusting its protonation status. Taken together, our data unveil the substrate-binding mode of MFS antiporters and suggest a mechanism of transport via this group of transporters.

  2. Cell density overrides the effect of substrate stiffness on human mesenchymal stem cells' morphology and proliferation.

    Science.gov (United States)

    Venugopal, Balu; Mogha, Pankaj; Dhawan, Jyotsna; Majumder, Abhijit

    2018-03-12

    The effect of substrate stiffness on the cellular morphology, proliferation, and differentiation of human mesenchymal stem cells (hMSCs) has been extensively researched and well established. However, the majority of these studies are done with a low seeding density where cell to cell interactions do not play a significant role. While these conditions permit an analysis of cell-substratum interactions at the single cell level, such a model system fails to capture a critical aspect of the cellular micro-environment in vivo, i.e. the cell-cell interaction via matrix deformation (i.e., strain). To address this question, we seeded hMSCs on soft poly-acrylamide (PAA) gels, at a seeding density that permits cells to be mechanically interacting via the underlying substrate. We found that as the intercellular distance decreases with the increasing seeding density, cellular sensitivity towards the substrate rigidity becomes significantly diminished. With the increasing seeding density, the cell spread area increased on a soft substrate (500 Pa) but reduced on an even slightly stiffer substrate (2 kPa) as well as on glass making them indistinguishable at a high seeding density. Not only in terms of cell spread area but also at a high seeding density, cells formed mature focal adhesions and prominent stress fibres on a soft substrate similar to that of the cells being cultured on a stiff substrate. The decreased intercellular distance also influenced the proliferation rate of the cells: higher seeding density on the soft substrate showed cell cycle progression similar to that of the cells on glass substrates. In summary, this paper demonstrates how the effect of substrate rigidity on the cell morphology and fate is a function of inter-cellular distance when seeded on a soft substrate. Our AFM data suggest that such changes happen due to local strain stiffening of the soft PAA gel, an effect that has been rarely reported in the literature so far.

  3. Influence of the laser pre-quenched substrate on an electroplated chromium coating/steel substrate

    Science.gov (United States)

    Chen, Xuejun; Yan, Qian; Ma, Qian

    2017-05-01

    The chromium coatings were electroplated onto a laser pre-quenched steel substrate to improve the interfacial adhesion properties of chromium coating/steel substrate system. The influence of laser pre-treatment on the substrate, coating as well as interface was investigated by using microstructure characterization, hardness testing, tensile testing and finite element analysis. An apparent boundary line instead of an interlayer was identified between chromium coating/pre-quenched steel substrate. The Vickers hardness and yield strength of steel substrate were significantly improved after laser pre-quenching. The fracture toughness of chromium coating was increased by about 28.6% compared to the un-treated counterpart. The energy release rate for an interfacial crack in the chromium coating/laser-quenched substrate was smaller than that in the untreated specimen. These results may help understand the life prolongation mechanism for the laser pre-quenched chromium/coated steel parts.

  4. Structure formation in bis(terpyridine) derivative adlayers: molecule-substrate versus molecule-molecule interactions.

    Science.gov (United States)

    Hoster, Harry E; Roos, Matthias; Breitruck, Achim; Meier, Christoph; Tonigold, Katrin; Waldmann, Thomas; Ziener, Ulrich; Landfester, Katharina; Behm, R Jürgen

    2007-11-06

    The influence of the substrate and the deposition conditions-vapor deposition versus deposition from solution-on the structures formed upon self-assembly of deposited bis(terpyridine) derivative (2,4'-BTP) monolayers on different hexagonal substrates, including highly oriented pyrolytic graphite (HOPG), Au(111), and (111)-oriented Ag thin films, was investigated by high-resolution scanning tunneling microscopy and by model calculations of the intermolecular energies and the lateral corrugation of the substrate-adsorbate interaction. Similar quasi-quadratic network structures with almost the same lattice constants obtained on all substrates are essentially identical to the optimum configuration expected from an optimization of the adlayer structure with C-H...N-type bridging bonds as a structure-determining factor, which underlines a key role of the intermolecular interactions in adlayer order. Slight distortions from the optimum values to form commensurate adlayer structures on the metal substrates and the preferential orientation of the adlayer with respect to the substrate are attributed to the substrate-adsorbate interactions, specifically, the lateral corrugation in the substrate-adsorbate interaction upon lateral displacement and rotation of the adsorbed BTP molecules. The fact that similar adlayer structures are obtained on HOPG under ultrahigh vacuum conditions (solid|gas interface) and on HOPG in trichlorobenzene (solid|liquid interface) indicates that the intermolecular interactions are not severely affected by the solvent.

  5. Cellular contractility and substrate elasticity: a numerical investigation of the actin cytoskeleton and cell adhesion.

    Science.gov (United States)

    Ronan, William; Deshpande, Vikram S; McMeeking, Robert M; McGarry, J Patrick

    2014-04-01

    Numerous experimental studies have established that cells can sense the stiffness of underlying substrates and have quantified the effect of substrate stiffness on stress fibre formation, focal adhesion area, cell traction, and cell shape. In order to capture such behaviour, the current study couples a mixed mode thermodynamic and mechanical framework that predicts focal adhesion formation and growth with a material model that predicts stress fibre formation, contractility, and dissociation in a fully 3D implementation. Simulations reveal that SF contractility plays a critical role in the substrate-dependent response of cells. Compliant substrates do not provide sufficient tension for stress fibre persistence, causing dissociation of stress fibres and lower focal adhesion formation. In contrast, cells on stiffer substrates are predicted to contain large amounts of dominant stress fibres. Different levels of cellular contractility representative of different cell phenotypes are found to alter the range of substrate stiffness that cause the most significant changes in stress fibre and focal adhesion formation. Furthermore, stress fibre and focal adhesion formation evolve as a cell spreads on a substrate and leading to the formation of bands of fibres leading from the cell periphery over the nucleus. Inhibiting the formation of FAs during cell spreading is found to limit stress fibre formation. The predictions of this mutually dependent material-interface framework are strongly supported by experimental observations of cells adhered to elastic substrates and offer insight into the inter-dependent biomechanical processes regulating stress fibre and focal adhesion formation.

  6. Mechanical Buckling of Individual Silicon Nanoribbons on a Compliant Substrate

    Science.gov (United States)

    Chang, Siang Yee

    About a decade ago, mechanical buckling evolves as a promising metrology to rapidly measure the elastic moduli of thin films and one-dimensional (1D) nanostructures. This form of metrology translates the geometrical measurements of the buckling profile into material property value. The strategy applied in the mechanical buckling-based metrology consists of three steps: i) applying pre-strain to the compliant substrate, ii) depositing or transferring 1D nanostructures onto the surface of the pre-strained compliant substrate, and iii) releasing the pre-strain of the compliant substrate so as to allow it to return to its original dimensions. The release of the pre-strain on the compliant substrate induces a compressive stress on the strain-free 1D nanostructures which later buckle spontaneously into sinusoidal shape in order to relieve the compressive stress. Using the Newtonian mechanics model, previous researchers developed a relation to identify the elastic properties of the 1D nanostructures by correlating the buckling wavelength with materials and geometric parameters of the system. However, previous work mainly emphasized on application of small strain (less than 40%), and single material system of relatively long and having equal moment of inertia (e.g. circular or hexagon). Without acknowledging the existence of the native sheath layer surrounding the nanostructures could lead to measurement error of 15% or more. In this dissertation work, silicon nanoribbons of variable aspect ratios (width B ranging 40, 60, 80, 100 and 200 nm, and constant thickness H of 30 nm) were individually deposited on a 100% pre-strained elastomeric (polydimethylsiloxane, PDMS) substrate. Since the as-fabricated Si nanoribbons consist of native oxide layer of 5 nm, the core-sheath structure had to be accounted for the property measurement where the effective modulus was being considered. Upon relaxing the 100% pre-strain on the pristine substrate, Si nanoribbons showed increased

  7. Patchy silica-coated silver nanowires as SERS substrates

    Energy Technology Data Exchange (ETDEWEB)

    Hunyadi Murph, Simona E.; Murphy, Catherine J.

    2013-05-08

    We report a class of core-shell nanomaterials that can be used as efficient surface-enhancement Raman scattering (SERS) substrates. The core consists of silver nanowires, prepared through a chemical reduction process, that are used to capture 4- mercaptobenzoic acid (4-MBA), a model analyte. The shell was prepared through a modified Stöber method and consists of patchy or full silica coats. The formation of silica coats was monitored via transmission electron microscopy, UV-visible spectroscopy and phase-analysis light scattering for measuring effective surface charge. Surprisingly, the patchy silica coated silver nanowires are better SERS substrate than silver nanowires; nanomolar concentration of 4-MBA can be detected. In addition, “nano-matryoshka” configurations were used to quantitate/explore the effect of the electromagnetic field at the tips of the nanowire (“hot spots”) in the Raman scattering experiment.

  8. Monte Carlo simulation of ramified aggregates on hetero-substrates

    International Nuclear Information System (INIS)

    Chang-Ji, Qian; Hong, Li; Rui, Zhong; Meng-Bo, Luo; Gao-Xiang, Ye

    2009-01-01

    We have studied the aggregation of particles on a hetero-substrate consisting of two different substrates A and B with finite surface barriers E AB and E BA between the AB and BA boundaries, respectively. With the diffusion energy limited aggregation (DELA) model, we find that the number of clusters and the mean radius of gyration of the clusters are dependent on the surface barriers E AB and E BA . For the case with a constant of E BA , a series of minima are summarized as E AB = (E 0 – k BA E BA )/k AB with k AB and k BA being two integers, for main minima (k BA = k AB − 1) and two local minima (k BA = k AB and k BA = k AB + 1) between two neighbouring main minima

  9. Kovar Micro Heat Pipe Substrates for Microelectronic Cooling

    Energy Technology Data Exchange (ETDEWEB)

    Benson, David A.; Burchett, Steven N.; Kravitz, Stanley H.; Robino, Charles V.; Schmidt, Carrie; Tigges, Chris P.

    1999-04-01

    We describe the development of a new technology for cooling microelectronics. This report documents the design, fabrication, and prototype testing of micro scale heat pipes embedded in a flat plate substrate or heat spreader. A thermal model tuned to the test results enables us to describe heat transfer in the prototype, as well as evaluate the use of this technology in other applications. The substrate walls are Kovar alloy, which has a coefficient of thermal expansion close to that of microelectronic die. The prototype designs integrating micro heat pipes with Kovar enhance thermal conductivity by more than a factor of two over that of Kovar alone, thus improving the cooling of micro-electronic die.

  10. Neural substrates of opiate withdrawal.

    Science.gov (United States)

    Koob, G F; Maldonado, R; Stinus, L

    1992-05-01

    Drug withdrawal is an integral part of most types of dependence and, to a large extent, opiate withdrawal has been considered the prototypic, classic measure of opiate dependence. The opiate withdrawal syndrome is characterized by multiple behavioral and physiological signs such as behavioral activation, ptosis, diarrhea, 'wet dog' shakes and motivational dysfunction, which may be represented in the CNS at multiple sites. It seems that the activating effects associated with the opiate withdrawal syndrome may be mediated by the nucleus locus coeruleus. Other signs such as wet dog shakes may involve sites in the hypothalamus important for temperature regulation. Certain other signs such as diarrhea and lacrimation may be dependent on peripheral opiate receptors. The motivational aspects of opiate withdrawal as demonstrated by the aversive stimulus effects or negative reinforcing effects (e.g. disrupted lever-pressing for food and place aversions) may involve those elements of the nucleus accumbens that are known to be important for the acute reinforcing effects of opiates in nondependent rats. Evidence exists at the cellular and molecular level for both 'within-system' and 'between-system' adaptations to dependence. Elucidation of the neural networks, cellular mechanisms and molecular elements involved in opiate withdrawal may provide not only a model for our understanding of the adaptive processes associated with drug dependence but also of those associated with other chronic insults to CNS function.

  11. Atomically flat single terminated oxide substrate surfaces

    Science.gov (United States)

    Biswas, Abhijit; Yang, Chan-Ho; Ramesh, Ramamoorthy; Jeong, Yoon H.

    2017-05-01

    Scientific interest in atomically controlled layer-by-layer fabrication of transition metal oxide thin films and heterostructures has increased intensely in recent decades for basic physics reasons as well as for technological applications. This trend has to do, in part, with the coming post-Moore era, and functional oxide electronics could be regarded as a viable alternative for the current semiconductor electronics. Furthermore, the interface of transition metal oxides is exposing many new emergent phenomena and is increasingly becoming a playground for testing new ideas in condensed matter physics. To achieve high quality epitaxial thin films and heterostructures of transition metal oxides with atomically controlled interfaces, one critical requirement is the use of atomically flat single terminated oxide substrates since the atomic arrangements and the reaction chemistry of the topmost surface layer of substrates determine the growth and consequent properties of the overlying films. Achieving the atomically flat and chemically single terminated surface state of commercially available substrates, however, requires judicious efforts because the surface of as-received substrates is of chemically mixed nature and also often polar. In this review, we summarize the surface treatment procedures to accomplish atomically flat surfaces with single terminating layer for various metal oxide substrates. We particularly focus on the substrates with lattice constant ranging from 4.00 Å to 3.70 Å, as the lattice constant of most perovskite materials falls into this range. For materials outside the range, one can utilize the substrates to induce compressive or tensile strain on the films and explore new states not available in bulk. The substrates covered in this review, which have been chosen with commercial availability and, most importantly, experimental practicality as a criterion, are KTaO3, REScO3 (RE = Rare-earth elements), SrTiO3, La0.18Sr0.82Al0.59Ta0.41O3 (LSAT), Nd

  12. Multistructural biomimetic substrates for controlled cellular differentiation

    International Nuclear Information System (INIS)

    Orza, Anamaria I; Kanarpardy, Ganesh K; Biris, Alexandru S; Mihu, Carmen; Soritau, Olga; Diudea, Mircea; Florea, Adrian; Matei, Horea; Balici, Stefana; Mudalige, Thilak

    2014-01-01

    Multidimensional scaffolds are considered to be ideal candidates for regenerative medicine and tissue engineering based on their potential to provide an excellent microenvironment and direct the fate of the cultured cells. More recently, the use of stem cells in medicine has opened a new technological opportunity for controlled tissue formation. However, the mechanism through which the substrate directs the differentiation of stem cells is still rather unclear. Data concerning its specific surface chemistry, topology, and its signaling ability need to be further understood and analyzed. In our study, atomic force microscopy was used to study the stiffness, roughness, and topology of the collagen (Coll) and metallized collagen (MC) substrates, proposed as an excellent substrate for regenerative medicine. The importance of signaling molecules was studied by constructing a new hybrid signaling substrate that contains both collagen and laminin extracellular matrix (ECM) proteins. The cellular response—such as attachment capability, proliferation and cardiac and neuronal phenotype expression on the metallized and non-metallized hybrid substrates (collagen + laminin)—was studied using MTT viability assay and immunohistochemistry studies. Our findings indicate that such hybrid materials could play an important role in the regeneration of complex tissues. (paper)

  13. Substrate morphology repetition in 'thick' polymer films

    International Nuclear Information System (INIS)

    Pietsch, Ullrich; Panzner, Tobias; Pfeiffer, Franz; Robinson, Ian K.

    2005-01-01

    Using Grazing-incidence small-angle scattering (GISAXS) technique we investigated the surface morphology of polymer films spin-coated on different silicon substrates. As substrates we used either technologically smooth silicon wafers or the same silicon wafer coated with thin aluminium or gold films which show a granular structure at the surface. Although the polymer thickness exceeds 300nm the GISAXS pattern of the film shows the same in-plane angle distribution Δ2Θ as the underlying substrate. Annealing the polymer films at a temperature above its glass transition temperature Δ2Θ changed from a broad to a narrow distribution as it is typically for films on pure silicon. The experiment can be interpreted by roughness replication and density fluctuation within the polymer film created while spin-coating at room temperature. Due to the low segment mobility there are density fluctuations which repeat the surface morphology of the substrate. Above the glass temperature the polymer density can be homogenized independently from the morphology of the substrate

  14. Radiolabelled substrates for angiotensin converting enzyme

    International Nuclear Information System (INIS)

    Chung, A.Y.; Ryan, J.W.; Ryan, J.P.; Ryan, U.S.

    1986-01-01

    Six [3H]benzoyl-tripeptides were prepared and tested as substrates for angiotensin converting enzyme. Each was prepared first as its [4-iodo]-benzoyl-analog, and an atom of 3H per molecule was introduced by catalytic dehalogenation in 3H2-gas. Kinetic parameters were measured at 37 degrees C using as buffer 0.05 M Hepes, pH 8.0 containing 0.1 M NaCl and 0.6 M Na2SO4. When the substrates were used at concentrations far below their respective Km values, fractional rates of substrate utilization per unit time for constant enzyme concentration were direct function of respective second order rate constants (Kc/Km). Although absolute values of Kc/Km differed for human enzyme as opposed to rabbit enzyme, relative values of Kc/Km were virtually identical. Similarly, relative rates of substrates utilization during passage through lungs of anesthetized rats were similar to relative values of Kc/Km measured in vitro. Thus, there is now a range of ACE substrates usable, in vitro and in vivo, under conditions of first order enzyme kinetics, conditions under which values of V/Km and Ki can be measured directly

  15. Decoding P4-ATPase substrate interactions.

    Science.gov (United States)

    Roland, Bartholomew P; Graham, Todd R

    Cellular membranes display a diversity of functions that are conferred by the unique composition and organization of their proteins and lipids. One important aspect of lipid organization is the asymmetric distribution of phospholipids (PLs) across the plasma membrane. The unequal distribution of key PLs between the cytofacial and exofacial leaflets of the bilayer creates physical surface tension that can be used to bend the membrane; and like Ca 2+ , a chemical gradient that can be used to transduce biochemical signals. PL flippases in the type IV P-type ATPase (P4-ATPase) family are the principle transporters used to set and repair this PL gradient and the asymmetric organization of these membranes are encoded by the substrate specificity of these enzymes. Thus, understanding the mechanisms of P4-ATPase substrate specificity will help reveal their role in membrane organization and cell biology. Further, decoding the structural determinants of substrate specificity provides investigators the opportunity to mutationally tune this specificity to explore the role of particular PL substrates in P4-ATPase cellular functions. This work reviews the role of P4-ATPases in membrane biology, presents our current understanding of P4-ATPase substrate specificity, and discusses how these fundamental aspects of P4-ATPase enzymology may be used to enhance our knowledge of cellular membrane biology.

  16. Substrate-Directed Catalytic Selective Chemical Reactions.

    Science.gov (United States)

    Sawano, Takahiro; Yamamoto, Hisashi

    2018-03-06

    The development of highly efficient reactions at only the desired position is one of the most important subjects in organic chemistry. Most of the reactions in current organic chemistry are reagent- or catalyst-controlled reactions, and the regio- and stereoselectivity of the reactions are determined by the inherent nature of the reagent or catalyst. In sharp contrast, substrate-directed reaction determines the selectivity of the reactions by the functional group on the substrate and can strictly distinguish sterically and electronically similar multiple reaction sites in the substrate. In this Perspective, three topics of substrate-directed reaction are mainly reviewed: (1) directing group-assisted epoxidation of alkenes, (2) ring-opening reactions of epoxides by various nucleophiles, and (3) catalytic peptide synthesis. Our newly developed synthetic methods with new ligands including hydroxamic acid derived ligands realized not only highly efficient reactions but also pinpointed reactions at the expected position, demonstrating the substrate-directed reaction as a powerful method to achieve the desired regio- and stereoselective functionalization of molecules from different viewpoints of reagent- or catalyst-controlled reactions.

  17. Nucleation of wetting films on cylindrical and spherical substrates: A numerical study by the string method

    KAUST Repository

    Qiu, Chunyin

    2009-09-25

    Using the mean-field diffuse-interface model for liquid-vapor system and employing the numerical string method, we study the critical nuclei involved in the prewetting transitions on curved substrates. We first introduce three distinct kinds of critical nuclei, namely, the disklike, bandlike, and layerlike ones, which respectively correspond to three possible growth modes of wettingfilms. We show the disklike growth mode to be the only mode for infinite planar substrates. We then turn to cylindrical and spherical substrates, the two simplest but most important geometries in the real world. We focus on the critical nuclei of finite size, through which the wettingfilms may be formed with finite thermodynamic probabilities. It is shown that the disklike growth mode is always the most probable for wettingfilmnucleation and growth as long as a disklike critical nucleus exists. It is also shown that on a cylindrical substrate, the disklike critical nucleus can no longer exist if the substrate radius is smaller than some critical value, comparable to the radius of the disklike critical nucleus on planar substrate. We find that on a cylindrical substrate whose radius is below the critical value, the nucleation and growth of a wettingfilm can only occur through the bandlike critical nucleus. It is worth emphasizing that the results concerning the bandlike and layerlike growth modes can only be obtained from the diffuse-interface model, beyond the macroscopic description based on the line and surface tensions.

  18. Influence of metal substrates on the detection of explosive residues with laser-induced breakdown spectroscopy.

    Science.gov (United States)

    Gottfried, Jennifer L

    2013-02-01

    Laser-induced breakdown spectroscopy is a promising approach for explosive residue detection, but several limitations to its widespread use remain. One issue is that the emission spectra of the residues are dependent on the substrate composition because some of the substrate is usually entrained in the laser-induced plasma and the laser-material interaction can be significantly affected by the substrate type. Here, we have demonstrated that despite the strong spectral variation in cyclotrimethylenetrinitramine (RDX) residues applied to various metal substrates, classification of the RDX residue independent of substrate type is feasible. Several approaches to improving the chemometric models based on partial least squares discriminant analysis (PLS-DA) have been described: classifying the RDX residue spectra together in one class independent of substrate, using selected emission intensities and ratios to increase the true positive rate (TPR) and decrease the false positive rate (FPR), and fusing the results from two PLS-DA models generated using the full broadband spectra and selected intensities and ratios. The combination of these approaches resulted in a TPR of 97.5% and a FPR of 1.0% for RDX classification on metal substrates.

  19. Effect of flow velocity, substrate concentration and hydraulic cleaning on biofouling of reverse osmosis feed channels

    KAUST Repository

    Radu, Andrea I.

    2012-04-01

    A two-dimensional mathematical model coupling fluid dynamics, salt and substrate transport and biofilm development in time was used to investigate the effects of cross-flow velocity and substrate availability on biofouling in reverse osmosis (RO)/nanofiltration (NF) feed channels. Simulations performed in channels with or without spacer filaments describe how higher liquid velocities lead to less overall biomass amount in the channel by increasing the shear stress. In all studied cases at constant feed flow rate, biomass accumulation in the channel reached a steady state. Replicate simulation runs prove that the stochastic biomass attachment model does not affect the stationary biomass level achieved and has only a slight influence on the dynamics of biomass accumulation. Biofilm removal strategies based on velocity variations are evaluated. Numerical results indicate that sudden velocity increase could lead to biomass sloughing, followed however by biomass re-growth when returning to initial operating conditions. Simulations show particularities of substrate availability in membrane devices used for water treatment, e.g., the accumulation of rejected substrates at the membrane surface due to concentration polarization. Interestingly, with an increased biofilm thickness, the overall substrate consumption rate dominates over accumulation due to substrate concentration polarization, eventually leading to decreased substrate concentrations in the biofilm compared to bulk liquid. © 2012 Elsevier B.V.

  20. Multifunctionality is affected by interactions between green roof plant species, substrate depth, and substrate type.

    Science.gov (United States)

    Dusza, Yann; Barot, Sébastien; Kraepiel, Yvan; Lata, Jean-Christophe; Abbadie, Luc; Raynaud, Xavier

    2017-04-01

    Green roofs provide ecosystem services through evapotranspiration and nutrient cycling that depend, among others, on plant species, substrate type, and substrate depth. However, no study has assessed thoroughly how interactions between these factors alter ecosystem functions and multifunctionality of green roofs. We simulated some green roof conditions in a pot experiment. We planted 20 plant species from 10 genera and five families (Asteraceae, Caryophyllaceae, Crassulaceae, Fabaceae, and Poaceae) on two substrate types (natural vs. artificial) and two substrate depths (10 cm vs. 30 cm). As indicators of major ecosystem functions, we measured aboveground and belowground biomasses, foliar nitrogen and carbon content, foliar transpiration, substrate water retention, and dissolved organic carbon and nitrates in leachates. Interactions between substrate type and depth strongly affected ecosystem functions. Biomass production was increased in the artificial substrate and deeper substrates, as was water retention in most cases. In contrast, dissolved organic carbon leaching was higher in the artificial substrates. Except for the Fabaceae species, nitrate leaching was reduced in deep, natural soils. The highest transpiration rates were associated with natural soils. All functions were modulated by plant families or species. Plant effects differed according to the observed function and the type and depth of the substrate. Fabaceae species grown on natural soils had the most noticeable patterns, allowing high biomass production and high water retention but also high nitrate leaching from deep pots. No single combination of factors enhanced simultaneously all studied ecosystem functions, highlighting that soil-plant interactions induce trade-offs between ecosystem functions. Substrate type and depth interactions are major drivers for green roof multifunctionality.

  1. Domain nucleation in the contact layer at an interface of water and a polarizable substrate

    Science.gov (United States)

    Shevkunov, S. V.

    2013-10-01

    The growth of a molecular water film on the basic plane of a silver iodide monocrystal is studied through computer simulation. Decomposition into domains with spontaneous polarization is observed in the contact layer of the film at the interface with the substrate. The formation of domains is found to be sharply enhanced on a model substrate with the double polarizability of iodine ions; heteropolarization interactions caused by the formation of domain structures increase the film's coupling with the substrate. It is demonstrated that the vapor pressure needed for molecular film growth is reduced appreciably via heteropolarization interactions.

  2. Rice Seedling Substrate Produced by Coal Gangue

    Directory of Open Access Journals (Sweden)

    SHAO Yu-fei

    2017-10-01

    Full Text Available Peats are the mostly used material in making rice seedling substrate. However, mining peats could cause environmental problems. In order to reduce or replace peats in rice seedling substrate industry, this paper studied suitable way to configure rice seedling. The coal gangue was used to experiment cultivating rice. Four rice seeding experiments were carried out based on physical and chemical properties of materials attributes. The results showed:(1 Coal gangue was feasible for rice seedling; (2 The maximum adding amount of coal gangue was 80%(volume ratio though the coal gangue need to be activated; (3 In the case of no activated treatment only 38%(volume ratio of coal gangue could be added to the substrate.

  3. Plasma jet printing for flexible substrates

    Energy Technology Data Exchange (ETDEWEB)

    Gandhiraman, Ram P.; Singh, Eric; Diaz-Cartagena, Diana C.; Koehne, Jessica; Meyyappan, M. [Center for Nanotechnology, NASA Ames Research Center, Moffett Field, California 94035 (United States); Nordlund, Dennis [Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025 (United States)

    2016-03-21

    Recent interest in flexible electronics and wearable devices has created a demand for fast and highly repeatable printing processes suitable for device manufacturing. Robust printing technology is critical for the integration of sensors and other devices on flexible substrates such as paper and textile. An atmospheric pressure plasma-based printing process has been developed to deposit different types of nanomaterials on flexible substrates. Multiwalled carbon nanotubes were deposited on paper to demonstrate site-selective deposition as well as direct printing without any type of patterning. Plasma-printed nanotubes were compared with non-plasma-printed samples under similar gas flow and other experimental conditions and found to be denser with higher conductivity. The utility of the nanotubes on the paper substrate as a biosensor and chemical sensor was demonstrated by the detection of dopamine, a neurotransmitter, and ammonia, respectively.

  4. Growth of lettuce seedlings in different substrates

    Directory of Open Access Journals (Sweden)

    Milene Rodrigues Peres

    2007-12-01

    Full Text Available This research studied the growth of lettuce seedlings (Lactuca sativa L. cv. Veronica cultivated under greenhouse conditions, using polystyrene trays with 128 cells and three different commercial substrates: Golden Mix, Plantmax and Plugmix. The statistical design was in the form of randomized blocks, with eight (8 replications. Fifteen days after sowing the seeds, samples (five in total of plants were taken to evaluate the height, number of leaves, leaf area, leaf specific area, leaf specific weight, absolute and relative growth rates and net assimilation rates. The evaluated growth indexes showed that seedlings produced with the Plantmax and Plugmix substrates could be planted 25 days after sowing, since they have at least four definitive leaves. The Plantmax substrate showed, at the end of the evaluation, the best results in height, dry weight, leaf specific area, absolute growth rates and net assimilation rates.

  5. Substrate recognition by ribonucleoprotein ribonuclease MRP.

    Science.gov (United States)

    Esakova, Olga; Perederina, Anna; Quan, Chao; Berezin, Igor; Krasilnikov, Andrey S

    2011-02-01

    The ribonucleoprotein complex ribonuclease (RNase) MRP is a site-specific endoribonuclease essential for the survival of the eukaryotic cell. RNase MRP closely resembles RNase P (a universal endoribonuclease responsible for the maturation of the 5' ends of tRNA) but recognizes distinct substrates including pre-rRNA and mRNA. Here we report the results of an in vitro selection of Saccharomyces cerevisiae RNase MRP substrates starting from a pool of random sequences. The results indicate that RNase MRP cleaves single-stranded RNA and is sensitive to sequences in the immediate vicinity of the cleavage site requiring a cytosine at the position +4 relative to the cleavage site. Structural implications of the differences in substrate recognition by RNases P and MRP are discussed.

  6. Anisotropic dewetting on stretched elastomeric substrates.

    Science.gov (United States)

    Qiao, L; He, L H

    2008-08-01

    We study the instability of a very thin liquid film resting on a uniformly stretched soft elastomeric substrate driven by van der Waals forces. A linear stability analysis shows that the critical fluctuation wavelength in the tensile direction is larger than those in the other directions. The magnitudes of the critical wavelengths are adjustable in the sense that they depend on the principal stretch of the substrate. For example, when the principal stretch of the substrate varies from 1.0 (unstretched) to 3.0, the range of the critical wavelength in the tensile direction increases by 7.0% while that normal to the tensile direction decreases by 8.7%. Therefore, the phenomenon may find potential applications in creating tunable topographically patterned surfaces with nano- to microscale features.

  7. Michaelis constants of non-chromogenic substrates may be determined using chromogenic substrates

    Energy Technology Data Exchange (ETDEWEB)

    Blake, D.A.; Vassall, R.F.; Blake, R.C. II

    1987-05-01

    The object of these experiments was to demonstrate a means of determining the Michaelis constants (Km and Vmax) of a non-chromogenic substrate in a three-part experimental system containing a non-chromogenic substrate, the corresponding enzyme, and an appropriate chromogenic substrate. Two experimental systems were examined, one in which the enzyme activity was subject to product inhibition (alkaline phosphatase) and one in which the activity was not (..beta..-lactamase). In both systems, the initial experimental goal was to quantify the area defined by the entire kinetic trace (absorbance versus time) obtained with the chromogenic substrate in the absence or presence of the non-chromogenic substrate. The difference between these two areas was directly proportional to the concentration of the non-chromogenic substrate and inversely proportional to the Vmax of the non-chromogenic substrate. The value of Vmax thus obtained could then be used with the appropriate integrated Michaelis-Menten rate equation to extract the value of the Km for the non-chromogenic substrate. This method yielded values of kinetic constants that were in good agreement with those obtained directly and/or those available from the literature. It is anticipated that this method may be extended to enzymes with more complicated kinetic mechanisms.

  8. Integration substrate with a ultra-high-density capacitor and a through-substrate via

    NARCIS (Netherlands)

    Klootwijk, J.H.; Roozeboom, F.; Ruigrok, J.J.M.; Reefman, D.

    2014-01-01

    An integration substrate for a system in package comprises a through-substrate via and a trench capacitor wherein with a trench filling that includes at least four electrically conductive capacitor-electrode layers in an alternating arrangement with dielectric layers. --The capacitor-electrode

  9. Formation and dynamics of supported phospholipid membranes on a periodic nanotextured substrate

    Energy Technology Data Exchange (ETDEWEB)

    Werner, James H [Los Alamos National Laboratory; Montano, Gabriel M [Los Alamos National Laboratory; Shreve, Andrew P [Los Alamos National Laboratory

    2008-01-01

    We have studied and modeled the morphology and dynamics of planar lipid bilayer assemblies supported on a textured silicon substrate that contains nano-structured features perpendicular to the plane of observation. Using a combination of characterization methods, including atomic force microscopy and quantitative fluorescence microscopy, we have discovered the bilayer assemblies are conformal to the underlying nanostructured substrate. As far as the dynamics are concnerned, the lipids freely diffuse in and out of the plane of observation while supported by the nanotextured material. In a microscopic sense, diffusion is isotropic along the patterned substrate. Macroscopically, when observed over length scales exceeding the dimensions of the nano-structured features, the diffusion appears anisotropic. The observed macroscopic anisotropy is well simulated using models of diffusion on the nanostructured surface that assume the lipids diffuse homogeneously and isotropically on the supporting nanotextured substrate.

  10. The effect of substrate microstructure on high temperature oxidation of Zr alloy

    International Nuclear Information System (INIS)

    Li, H.; Lin, J.; Szpunar, J.

    2005-01-01

    'Full text:' Specimens with various substrate microstructures of Zr-2.5Nb, Zircaloy 4 and pure Zr have been oxidized at 500C in air. Oxidation kinetics is measured and the microstructures of both oxide and substrate are analyzed. The difference in oxidation kinetics among various specimens is significant. This difference is explained by the distribution of oxide grain size, grain shape and grain boundary, which are controlled by substrate grain size and β phase distribution. The previously proposed model of Zr oxidation is used to predict oxidation kinetics and oxide microstructure from substrate microstructure. Computer simulation based on the model is performed and simulation results are compared with the experimental results. (author)

  11. Buckling of a stiff thin film on an elastic graded compliant substrate

    Science.gov (United States)

    Chen, Zhou; Chen, Weiqiu; Song, Jizhou

    2017-12-01

    The buckling of a stiff film on a compliant substrate has attracted much attention due to its wide applications such as thin-film metrology, surface patterning and stretchable electronics. An analytical model is established for the buckling of a stiff thin film on a semi-infinite elastic graded compliant substrate subjected to in-plane compression. The critical compressive strain and buckling wavelength for the sinusoidal mode are obtained analytically for the case with the substrate modulus decaying exponentially. The rigorous finite element analysis (FEA) is performed to validate the analytical model and investigate the postbuckling behaviour of the system. The critical buckling strain for the period-doubling mode is obtained numerically. The influences of various material parameters on the results are investigated. These results are helpful to provide physical insights on the buckling of elastic graded substrate-supported thin film.

  12. High alcohol production by solid substrate fermentation from starchy substrates using thermotolerant Saccharomyces cerevisiae

    Energy Technology Data Exchange (ETDEWEB)

    Sree, N.K.; Sridhar, M.; Suresh, K.; Rao, L.V. [Department of Microbiology, Osmania University, Hyderabad 500007, Andhra Pradesh (India)

    1999-06-01

    Solid Substrate Fermentation system (SSF) was used to produce ethanol from various starchy substrates like sweet sorghum, sweet potato, wheat flour, rice starch, soluble starch and potato starch using thermotolerant yeast isolate (VS{sub 3}) by simultaneous saccharification and fermentation process. Alcohol produced was estimated by gas chromatography after an incubation time of 96 hrs at 37 C and 42 C. More ethanol was produced from rice starch and sweet sorghum. The maximum amount of ethanol produced from these substrates using VS{sub 3} was 10 g/100 g and 3.5 g/100 g substrate (rice starch) and 8.2 g and 7.5 g/100 g substrate (sweet sorghum) at 37 C and 42 C respectively. (orig.) With 2 figs., 1 tab., 12 refs.

  13. Ferromagnetic film on a superconducting substrate

    Energy Technology Data Exchange (ETDEWEB)

    Bulaevskii, L. N.; Chudnovsky, E. M.

    2001-01-01

    We study the equilibrium domain structure and magnetic flux around a ferromagnetic film with perpendicular magnetization M{sub 0} on a superconducting (SC) substrate. At 4{pi}M{sub 0}substrate, l{sub N}/4{pi}{lambda}{sub L}>>1; {lambda}{sub L} being the London penetration length.

  14. Ferromagnetic film on a superconducting substrate

    International Nuclear Information System (INIS)

    Bulaevskii, L. N.; Chudnovsky, E. M.

    2001-01-01

    We study the equilibrium domain structure and magnetic flux around a ferromagnetic film with perpendicular magnetization M 0 on a superconducting (SC) substrate. At 4πM 0 c1 the SC is in the Meissner state and the equilibrium domain width in the film, l, scales as (l/4πλ L )=(l N /4πλ L ) 2/3 with the domain width on a normal (nonsuperconducting) substrate, l N /4πλ L >>1; λ L being the London penetration length

  15. Induction of mesenchymal stem cell chondrogenesis by polyacrylate substrates.

    Science.gov (United States)

    Glennon-Alty, Laurence; Williams, Rachel; Dixon, Simon; Murray, Patricia

    2013-04-01

    Mesenchymal stem cells (MSCs) can generate chondrocytes in vitro, but typically need to be cultured as aggregates in the presence of transforming growth factor beta (TGF-β), which makes scale-up difficult. Here we investigated if polyacrylate substrates modelled on the functional group composition and distribution of the Arg-Gly-Asp (RGD) integrin-binding site could induce MSCs to undergo chondrogenesis in the absence of exogenous TGF-β. Within a few days of culture on the biomimetic polyacrylates, both mouse and human MSCs, and a mesenchymal-like mouse-kidney-derived stem cell line, began to form multi-layered aggregates and started to express the chondrocyte-specific markers, Sox9, collagen II and aggrecan. Moreover, collagen II tended to be expressed in the centre of the aggregates, similarly to developing limb buds in vivo. Surface analysis of the substrates indicated that those with the highest surface amine content were most effective at promoting MSC chondrogenesis. These results highlight the importance of surface group functionality and the distribution of those groups in the design of substrates to induce MSC chondrogenesis. Copyright © 2012 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

  16. Computing Generalized Matrix Inverse on Spiking Neural Substrate

    Directory of Open Access Journals (Sweden)

    Rohit Shukla

    2018-03-01

    Full Text Available Emerging neural hardware substrates, such as IBM's TrueNorth Neurosynaptic System, can provide an appealing platform for deploying numerical algorithms. For example, a recurrent Hopfield neural network can be used to find the Moore-Penrose generalized inverse of a matrix, thus enabling a broad class of linear optimizations to be solved efficiently, at low energy cost. However, deploying numerical algorithms on hardware platforms that severely limit the range and precision of representation for numeric quantities can be quite challenging. This paper discusses these challenges and proposes a rigorous mathematical framework for reasoning about range and precision on such substrates. The paper derives techniques for normalizing inputs and properly quantizing synaptic weights originating from arbitrary systems of linear equations, so that solvers for those systems can be implemented in a provably correct manner on hardware-constrained neural substrates. The analytical model is empirically validated on the IBM TrueNorth platform, and results show that the guarantees provided by the framework for range and precision hold under experimental conditions. Experiments with optical flow demonstrate the energy benefits of deploying a reduced-precision and energy-efficient generalized matrix inverse engine on the IBM TrueNorth platform, reflecting 10× to 100× improvement over FPGA and ARM core baselines.

  17. Metabolic flux prediction in cancer cells with altered substrate uptake.

    Science.gov (United States)

    Schwartz, Jean-Marc; Barber, Michael; Soons, Zita

    2015-12-01

    Proliferating cells, such as cancer cells, are known to have an unusual metabolism, characterized by an increased rate of glycolysis and amino acid metabolism. Our understanding of this phenomenon is limited but could potentially be used in order to develop new therapies. Computational modelling techniques, such as flux balance analysis (FBA), have been used to predict fluxes in various cell types, but remain of limited use to explain the unusual metabolic shifts and altered substrate uptake in human cancer cells. We implemented a new flux prediction method based on elementary modes (EMs) and structural flux (StruF) analysis and tested them against experimentally measured flux data obtained from (13)C-labelling in a cancer cell line. We assessed the quality of predictions using different objective functions along with different techniques in normalizing a metabolic network with more than one substrate input. Results show a good correlation between predicted and experimental values and indicate that the choice of cellular objective critically affects the quality of predictions. In particular, lactate gives an excellent correlation and correctly predicts the high flux through glycolysis, matching the observed characteristics of cancer cells. In contrast with FBA, which requires a priori definition of all uptake rates, often hard to measure, atomic StruFs (aStruFs) are able to predict uptake rates of multiple substrates. © 2015 Authors; published by Portland Press Limited.

  18. Optically transparent frequency selective surfaces on flexible thin plastic substrates

    Directory of Open Access Journals (Sweden)

    Aliya A. Dewani

    2015-02-01

    Full Text Available A novel 2D simple low cost frequency selective surface was screen printed on thin (0.21 mm, flexible transparent plastic substrate (relative permittivity 3.2. It was designed, fabricated and tested in the frequency range 10-20 GHz. The plane wave transmission and reflection coefficients agreed with numerical modelling. The effective permittivity and thickness of the backing sheet has a significant effect on the frequency characteristics. The stop band frequency reduced from 15GHz (no backing to 12.5GHz with polycarbonate. The plastic substrate thickness beyond 1.8mm has minimal effect on the resonant frequency. While the inner element spacing controls the stop-band frequency, the substrate thickness controls the bandwidth. The screen printing technique provided a simple, low cost FSS fabrication method to produce flexible, conformal, optically transparent and bio-degradable FSS structures which can find their use in electromagnetic shielding and filtering applications in radomes, reflector antennas, beam splitters and polarizers.

  19. Substrate specificity of microbial transglutaminase as revealed by three-dimensional docking simulation and mutagenesis

    OpenAIRE

    Tagami, Uno; Shimba, Nobuhisa; Nakamura, Mina; Yokoyama, Kei-ichi; Suzuki, Ei-ichiro; Hirokawa, Takatsugu

    2009-01-01

    Transglutaminases (TGases) are used in fields such as food and pharmaceuticals. Unlike other TGases, microbial transglutaminase (MTG) activity is Ca2+-independent, broadening its application. Here, a three-dimensional docking model of MTG binding to a peptide substrate, CBZ-Gln-Gly, was simulated. The data reveal CBZ-Gln-Gly to be stretched along the MTG active site cleft with hydrophobic and/or aromatic residues interacting directly with the substrate. Moreover, an oxyanion binding site for ...

  20. Molecular dynamics investigation of nanoscale substrate topography and its interaction with liquids

    Science.gov (United States)

    Cordeiro Rodrigues, Jhonatam

    Nanotechnology has been presenting successful applications in several areas. However, experimentation with nanoscale materials is costly and limited in analysis capability. This research investigates the use of molecular dynamics (MD) simulations to model and study nanomaterials and manufacturing processes. MD simulations are employed to reduce cost, optimize design, increase productivity and allow for the investigation of material interactions not yet observable through experimentation. This work investigates the interaction of water with substrates at the nanoscale. The effect of temperature, droplet impingement velocities and size, as well as substrate material, are investigated at the nanoscale. Several substrate topography designs were modeled to reveal their influence on the wettability of the substrate. Nanoscale gold and silicon substrates are more hydrophilic at higher temperatures than at room temperature. The reduction in droplet diameter increases its wettability. High impingement velocity of droplets does not influence final wettability of substrates but induces higher diffusion rates of droplets in a heated environment. Droplets deposited over a gradient of surface exposure presents spontaneous movement. The Leidenfrost effect was investigated at the nanoscale. Droplets of 4 and 10nm in diameter presented behaviors pertinent to the Leidenfrost effect at 373K, significantly lower than at micro scale and of potential impact to the field. Topographical features were manipulated using superhydrophobic coating resulting in micro whiskers. Nanoimprint lithography (NIL) was used to manufacture substrate topographies at the nanoscale. Water droplets were deposited on the substrates and their wettability was measured using droplet contact angles. Lower surface area exposure resulted in higher contact angles. The experimental relationships between surface topography and substrate wettability were used to validate the insights gained from MD simulations for