WorldWideScience

Sample records for model sumo substrates

  1. Purification of SUMO conjugating enzymes and kinetic analysis of substrate conjugation

    Science.gov (United States)

    Yunus, Ali A.; Lima, Christopher D.

    2009-01-01

    SUMO conjugation to protein substrates requires the concerted action of a dedicated E2 ubiquitin conjugation enzyme (Ubc9) and associated E3 ligases. Although Ubc9 can directly recognize and modify substrate lysine residues that occur within a consensus site for SUMO modification, E3 ligases can redirect specificity and enhance conjugation rates during SUMO conjugation in vitro and in vivo. In this chapter, we will describe methods utilized to purify SUMO conjugating enzymes and model substrates which can be used for analysis of SUMO conjugation in vitro. We will also describe methods to extract kinetic parameters during E3-dependent or E3-independent substrate conjugation. PMID:19107417

  2. 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.

  3. Targeting of SUMO substrates to a Cdc48-Ufd1-Npl4 segregase and STUbL pathway in fission yeast

    DEFF Research Database (Denmark)

    Køhler, Julie Bonne; Tammsalu, Triin; Jørgensen, Maria Louise Mønster

    2015-01-01

    48/p97-Ufd1-Npl4 facilitates this process. However, the extent to which the two pathways overlap, and how substrates are selected, remains unknown. Here we address these questions in fission yeast through proteome-wide analyses of SUMO modification sites. We identify over a thousand sumoylated...... lysines in a total of 468 proteins and quantify changes occurring in the SUMO modification status when the STUbL or Ufd1 pathways are compromised by mutations. The data suggest the coordinated processing of several classes of SUMO conjugates, many dynamically associated with centromeres or telomeres...

  4. 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

  5. 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

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. Structural analysis of poly-SUMO chain recognition by the RNF4-SIMs domain.

    Science.gov (United States)

    Kung, Camy C-H; Naik, Mandar T; Wang, Szu-Huan; Shih, Hsiu-Ming; Chang, Che-Chang; Lin, Li-Ying; Chen, Chia-Lin; Ma, Che; Chang, Chi-Fon; Huang, Tai-Huang

    2014-08-15

    The E3 ubiquitin ligase RNF4 (RING finger protein 4) contains four tandem SIM [SUMO (small ubiquitin-like modifier)-interaction motif] repeats for selective interaction with poly-SUMO-modified proteins, which it targets for degradation. We employed a multi-faceted approach to characterize the structure of the RNF4-SIMs domain and the tetra-SUMO2 chain to elucidate the interaction between them. In solution, the SIM domain was intrinsically disordered and the linkers of the tetra-SUMO2 were highly flexible. Individual SIMs of the RNF4-SIMs domains bind to SUMO2 in the groove between the β2-strand and the α1-helix parallel to the β2-strand. SIM2 and SIM3 bound to SUMO with a high affinity and together constituted the recognition module necessary for SUMO binding. SIM4 alone bound to SUMO with low affinity; however, its contribution to tetra-SUMO2 binding avidity is comparable with that of SIM3 when in the RNF4-SIMs domain. The SAXS data of the tetra-SUMO2-RNF4-SIMs domain complex indicate that it exists as an ordered structure. The HADDOCK model showed that the tandem RNF4-SIMs domain bound antiparallel to the tetra-SUMO2 chain orientation and wrapped around the SUMO protamers in a superhelical turn without imposing steric hindrance on either molecule.

  11. USP7 is a SUMO deubiquitinase essential for DNA replication

    DEFF Research Database (Denmark)

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

    2016-01-01

    Post-translational modification of proteins by ubiquitin (Ub) and Ub-like modifiers regulates DNA replication. We have previously shown that chromatin around replisomes is rich in SUMO and poor in Ub, whereas mature chromatin exhibits an opposite pattern. How this SUMO-rich, Ub-poor environment...... 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...... 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...

  12. 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.

  13. 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.

  14. Meiosis and SUMO

    DEFF Research Database (Denmark)

    Holm, Lærke Rebekka

    to target proteins can be catalyzed by the SUMO E3 ligase Pli1. In this study we investigate the role of Pli1 and Pmt3 during meiotic differentiation and at repetitive DNA during mitotic growth. Target proteins for Pmt3 are many; however, Pli1 has a meiosis-specic function regulating meiotic recombination...

  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

    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...... 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...... either in STUbL or Ufd1 function. In addition to identifying more than 900 unique sumoylated sites, these efforts revealed a number of proteins with upregulated sumoylation either in STUbL and/or Ufd1 mutant cells. These findings propose specific candidate substrates through which STUbL and Cdc48-Ufd1...

  17. SUMO Signaling by Hypoxic Inactivation of SUMO-Specific Isopeptidases

    Directory of Open Access Journals (Sweden)

    Kathrin Kunz

    2016-09-01

    Full Text Available Post-translational modification of proteins with ubiquitin-like SUMO modifiers is a tightly regulated and highly dynamic process. The SENP family of SUMO-specific isopeptidases comprises six cysteine proteases. They are instrumental in counterbalancing SUMO conjugation, but their regulation is not well understood. We demonstrate that in hypoxic cell extracts, the catalytic activity of SENP family members, in particular SENP1 and SENP3, is inhibited in a rapid and fully reversible process. Comparative mass spectrometry from normoxic and hypoxic cells defines a subset of hypoxia-induced SUMO1 targets, including SUMO ligases RanBP2 and PIAS2, glucose transporter 1, and transcriptional regulators. Among the most strongly induced targets, we identified the transcriptional co-repressor BHLHE40, which controls hypoxic gene expression programs. We provide evidence that SUMOylation of BHLHE40 is reversed by SENP1 and contributes to transcriptional repression of the metabolic master regulator gene PGC-1α. We propose a pathway that connects oxygen-controlled SENP activity to hypoxic reprogramming of metabolism.

  18. SUMO-1 is associated with a subset of lysosomes in glial protein aggregate diseases.

    Science.gov (United States)

    Wong, Mathew B; Goodwin, Jacob; Norazit, Anwar; Meedeniya, Adrian C B; Richter-Landsberg, Christiane; Gai, Wei Ping; Pountney, Dean L

    2013-01-01

    Oligodendroglial inclusion bodies characterize a subset of neurodegenerative diseases. Multiple system atrophy (MSA) is characterized by α-synuclein glial cytoplasmic inclusions and progressive supranuclear palsy (PSP) is associated with glial tau inclusions. The ubiquitin homologue, SUMO-1, has been identified in inclusion bodies in MSA, located in discrete sub-domains in α-synuclein-positive inclusions. We investigated SUMO-1 associated with oligodendroglial inclusion bodies in brain tissue from MSA and PSP and in glial cell models. We examined MSA and PSP cases and compared to age-matched normal controls. Fluorescence immunohistochemistry revealed frequent SUMO-1 sub-domains within and surrounding inclusions bodies in both diseases and showed punctate co-localization of SUMO-1 and the lysosomal marker, cathepsin D, in affected brain regions. Cell counting data revealed that 70-75 % of lysosomes in inclusion body-positive oligodendrocytes were SUMO-1-positive consistently across MSA and PSP cases, compared to 20 % in neighbouring inclusion body negative oligodendrocytes and 10 % in normal brain tissue. Hsp90 co-localized with some SUMO-1 puncta. We examined the SUMO-1 status of lysosomes in 1321N1 human glioma cells over-expressing α-synuclein and in immortalized rat oligodendrocyte cells over-expressing the four repeat form of tau following treatment with the proteasome inhibitor, MG132. We also transfected 1321N1 cells with the inherently aggregation-prone huntingtin exon 1 mutant, HttQ74-GFP. Each cell model showed the association of SUMO-1-positive lysosomes around focal cytoplasmic accumulations of α-synuclein, tau or HttQ74-GFP, respectively. Association of SUMO-1 with lysosomes was also detected in glial cells bearing α-synuclein aggregates in a rotenone-lesioned rat model. SUMO-1 labelling of lysosomes showed a major increase between 24 and 48 h post-incubation of 1321N1 cells with MG132 resulting in an increase in a 90 kDa SUMO-1-positive band

  19. USP7 is a SUMO deubiquitinase essential for DNA replication

    Science.gov (United States)

    Lecona, Emilio; Rodriguez-Acebes, Sara; Specks, Julia; Lopez-Contreras, Andres J; Ruppen, Isabel; Murga, Matilde; Muñoz, Javier; Mendez, Juan; Fernandez-Capetillo, Oscar

    2016-01-01

    Post-translational modification of proteins by ubiquitin (Ub) and Ub-like modifiers regulates various aspects of DNA replication. We previously showed that the chromatin around replisomes is rich in SUMO and depleted in Ub, whereas an opposite pattern is observed in mature chromatin. How this SUMO-rich/Ub-low environment is maintained at sites of DNA replication is not known. 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. Chemical inhibition or genetic deletion of USP7 leads to the accumulation of Ub on SUMOylated proteins, which are displaced to chromatin away from replisomes. Our findings provide a model to explain the differential accumulation of SUMO and Ub at replication forks, and identify an essential role of USP7 in DNA replication that should be taken into account for the use of USP7 inhibitors as anticancer agents. PMID:26950370

  20. 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.

  1. SUMO-fusion, purification, and characterization of a (+)-zizaene synthase from Chrysopogon zizanioides

    International Nuclear Information System (INIS)

    Hartwig, S.; Frister, T.; Alemdar, S.; Li, Z.; Scheper, T.; Beutel, S.

    2015-01-01

    An uncharacterized plant cDNA coding for a polypeptide presumably having sesquiterpene synthase activity, was expressed in soluble and active form. Two expression strategies were evaluated in Escherichia coli. The enzyme was fused to a highly soluble SUMO domain, in addition to being produced in an unfused form by a cold-shock expression system. Yields up to ∼325 mg/L −1 were achieved in batch cultivations. The 6x-His-tagged enzyme was purified employing an Ni 2+ -IMAC-based procedure. Identity of the protein was established by Western Blot analysis as well as peptide mass fingerprinting. A molecular mass of 64 kDa and an isoelectric point of pI 4.95 were determined by 2D gel electrophoresis. Cleavage of the fusion domain was possible by digestion with specific SUMO protease. The synthase was active in Mg 2+ containing buffer and catalyzed the production of (+)-zizaene (syn. khusimene), a precursor of khusimol, from farnesyl diphosphate. Product identity was confirmed by GC–MS and comparison of retention indices. Enzyme kinetics were determined by measuring initial reaction rates for the product, using varying substrate concentrations. By assuming a Michaelis–Menten model, kinetic parameters of K M  = 1.111 μM (±0.113), v max  = 0.3245 μM min −1 (±0.0035), k cat  = 2.95 min −1 , as well as a catalytic efficiency k cat /K M  = 4.43 × 10 4  M −1 s −1 were calculated. Fusion to a SUMO moiety can substantially increase soluble expression levels of certain hard to express terpene synthases in E. coli. The kinetic data determined for the recombinant synthase are comparable to other described plant sesquiterpene synthases and in the typical range of enzymes belonging to the secondary metabolism. This leaves potential for optimizing catalytic parameters through methods like directed evolution. - Highlights: • Uncharacterized (+)-zizaene synthase from C. zizanoides was cloned and expressed. • Fusion to SUMO and cold-shock induction

  2. SUMO-fusion, purification, and characterization of a (+)-zizaene synthase from Chrysopogon zizanioides

    Energy Technology Data Exchange (ETDEWEB)

    Hartwig, S.; Frister, T.; Alemdar, S.; Li, Z.; Scheper, T.; Beutel, S., E-mail: beutel@iftc.uni-hannover.de

    2015-03-20

    An uncharacterized plant cDNA coding for a polypeptide presumably having sesquiterpene synthase activity, was expressed in soluble and active form. Two expression strategies were evaluated in Escherichia coli. The enzyme was fused to a highly soluble SUMO domain, in addition to being produced in an unfused form by a cold-shock expression system. Yields up to ∼325 mg/L{sup −1} were achieved in batch cultivations. The 6x-His-tagged enzyme was purified employing an Ni{sup 2+}-IMAC-based procedure. Identity of the protein was established by Western Blot analysis as well as peptide mass fingerprinting. A molecular mass of 64 kDa and an isoelectric point of pI 4.95 were determined by 2D gel electrophoresis. Cleavage of the fusion domain was possible by digestion with specific SUMO protease. The synthase was active in Mg{sup 2+} containing buffer and catalyzed the production of (+)-zizaene (syn. khusimene), a precursor of khusimol, from farnesyl diphosphate. Product identity was confirmed by GC–MS and comparison of retention indices. Enzyme kinetics were determined by measuring initial reaction rates for the product, using varying substrate concentrations. By assuming a Michaelis–Menten model, kinetic parameters of K{sub M} = 1.111 μM (±0.113), v{sub max} = 0.3245 μM min{sup −1} (±0.0035), k{sub cat} = 2.95 min{sup −1}, as well as a catalytic efficiency k{sub cat}/K{sub M} = 4.43 × 10{sup 4} M{sup −1} s{sup −1} were calculated. Fusion to a SUMO moiety can substantially increase soluble expression levels of certain hard to express terpene synthases in E. coli. The kinetic data determined for the recombinant synthase are comparable to other described plant sesquiterpene synthases and in the typical range of enzymes belonging to the secondary metabolism. This leaves potential for optimizing catalytic parameters through methods like directed evolution. - Highlights: • Uncharacterized (+)-zizaene synthase from C. zizanoides was cloned

  3. 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.

  4. 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.

  5. 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.

  6. Evolution of SUMO Function and Chain Formation in Insects.

    Science.gov (United States)

    Ureña, Enric; Pirone, Lucia; Chafino, Silvia; Pérez, Coralia; Sutherland, James D; Lang, Valérie; Rodriguez, Manuel S; Lopitz-Otsoa, Fernando; Blanco, Francisco J; Barrio, Rosa; Martín, David

    2016-02-01

    SUMOylation, the covalent binding of Small Ubiquitin-like Modifier (SUMO) to target proteins, is a posttranslational modification that regulates critical cellular processes in eukaryotes. In insects, SUMOylation has been studied in holometabolous species, particularly in the dipteran Drosophila melanogaster, which contains a single SUMO gene (smt3). This has led to the assumption that insects contain a single SUMO gene. However, the analysis of insect genomes shows that basal insects contain two SUMO genes, orthologous to vertebrate SUMO1 and SUMO2/3. Our phylogenetical analysis reveals that the SUMO gene has been duplicated giving rise to SUMO1 and SUMO2/3 families early in Metazoan evolution, and that later in insect evolution the SUMO1 gene has been lost after the Hymenoptera divergence. To explore the consequences of this loss, we have examined the characteristics and different biological functions of the two SUMO genes (SUMO1 and SUMO3) in the hemimetabolous cockroach Blattella germanica and compared them with those of Drosophila Smt3. Here, we show that the metamorphic role of the SUMO genes is evolutionary conserved in insects, although there has been a regulatory switch from SUMO1 in basal insects to SUMO3 in more derived ones. We also show that, unlike vertebrates, insect SUMO3 proteins cannot form polySUMO chains due to the loss of critical lysine residues within the N-terminal part of the protein. Furthermore, the formation of polySUMO chains by expression of ectopic human SUMO3 has a deleterious effect in Drosophila. These findings contribute to the understanding of the functional consequences of the evolution of SUMO genes. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  7. Senp1 Is Essential for Desumoylating Sumo1-Modified Proteins but Dispensable for Sumo2 and Sumo3 Deconjugation in the Mouse Embryo

    Directory of Open Access Journals (Sweden)

    Prashant Sharma

    2013-05-01

    Full Text Available Posttranslational modification with small ubiquitin-like modifier (Sumo regulates numerous cellular and developmental processes. Sumoylation is dynamic with deconjugation by Sumo-specific proteases (Senps regulating steady-state levels. Different Senps are found in distinct subcellular domains, which may limit their deconjugation activity to colocalizing Sumo-modified proteins. In vitro, Senps can discriminate between the different Sumo paralogs: Sumo1 versus the highly related Sumo2 and Sumo3 (Sumo2/3, which can form poly-Sumo chains. However, a full understanding of Senp specificity in vivo is still lacking. Here, using biochemical and genetic approaches, we establish that Senp1 has an essential, nonredundant function to desumoylate Sumo1-modified proteins during mouse embryonic development. Senp1 specificity for Sumo1 conjugates represents an intrinsic function and not simply a product of colocalization. In contrast, Senp1 has only a limited role in Sumo2/3 desumoylation, although it may regulate Sumo1-mediated termination of poly-Sumo2/3 chains.

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

    International Nuclear Information System (INIS)

    Reuder, J; Jonassen, M; Mayer, S; Brisset, P; Mueller, M

    2008-01-01

    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 -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

  9. 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.

  10. Analysis of the SUMO2 Proteome during HSV-1 Infection.

    Directory of Open Access Journals (Sweden)

    Elizabeth Sloan

    2015-07-01

    Full Text Available Covalent linkage to members of the small ubiquitin-like (SUMO family of proteins is an important mechanism by which the functions of many cellular proteins are regulated. Sumoylation has roles in the control of protein stability, activity and localization, and is involved in the regulation of transcription, gene expression, chromatin structure, nuclear transport and RNA metabolism. Sumoylation is also linked, both positively and negatively, with the replication of many different viruses both in terms of modification of viral proteins and modulation of sumoylated cellular proteins that influence the efficiency of infection. One prominent example of the latter is the widespread reduction in the levels of cellular sumoylated species induced by herpes simplex virus type 1 (HSV-1 ubiquitin ligase ICP0. This activity correlates with relief from intrinsic immunity antiviral defence mechanisms. Previous work has shown that ICP0 is selective in substrate choice, with some sumoylated proteins such the promyelocytic leukemia protein PML being extremely sensitive, while RanGAP is completely resistant. Here we present a comprehensive proteomic analysis of changes in the cellular SUMO2 proteome during HSV-1 infection. Amongst the 877 potentially sumoylated species detected, we identified 124 whose abundance was decreased by a factor of 3 or more by the virus, several of which were validated by western blot and expression analysis. We found many previously undescribed substrates of ICP0 whose degradation occurs by a range of mechanisms, influenced or not by sumoylation and/or the SUMO2 interaction motif within ICP0. Many of these proteins are known or are predicted to be involved in the regulation of transcription, chromatin assembly or modification. These results present novel insights into mechanisms and host cell proteins that might influence the efficiency of HSV-1 infection.

  11. 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.

  12. 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.

  13. 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.

  14. Functional characterization of DnSIZ1, a SIZ/PIAS-type SUMO E3 ligase from Dendrobium.

    Science.gov (United States)

    Liu, Feng; Wang, Xiao; Su, Mengying; Yu, Mengyuan; Zhang, Shengchun; Lai, Jianbin; Yang, Chengwei; Wang, Yaqin

    2015-09-17

    SUMOylation is an important post-translational modification of eukaryotic proteins that involves the reversible conjugation of a small ubiquitin-related modifier (SUMO) polypeptide to its specific protein substrates, thereby regulating numerous complex cellular processes. The PIAS (protein inhibitor of activated signal transducers and activators of transcription [STAT]) and SIZ (scaffold attachment factor A/B/acinus/PIAS [SAP] and MIZ) proteins are SUMO E3 ligases that modulate SUMO conjugation. The characteristic features and SUMOylation mechanisms of SIZ1 protein in monocotyledon are poorly understood. Here, we examined the functions of a homolog of Arabidopsis SIZ1, a functional SIZ/PIAS-type SUMO E3 ligase from Dendrobium. In Dendrobium, the predicted DnSIZ1 protein has domains that are highly conserved among SIZ/PIAS-type proteins. DnSIZ1 is widely expressed in Dendrobium organs and has a up-regulated trend by treatment with cold, high temperature and wounding. The DnSIZ1 protein localizes to the nucleus and shows SUMO E3 ligase activity when expressed in an Escherichia coli reconstitution system. Moreover, ectopic expression of DnSIZ1 in the Arabidopsis siz1-2 mutant partially complements several phenotypes and results in enhanced levels of SUMO conjugates in plants exposed to heat shock conditions. We observed that DnSIZ1 acts as a negative regulator of flowering transition which may be via a vernalization-induced pathway. In addition, ABA-hypersensitivity of siz1-2 seed germination can be partially suppressed by DnSIZ1. Our results suggest that DnSIZ1 is a functional homolog of the Arabidopsis SIZ1 with SUMO E3 ligase activity and may play an important role in the regulation of Dendrobium stress responses, flowering and development.

  15. A comprehensive compilation of SUMO proteomics

    DEFF Research Database (Denmark)

    Hendriks, Ivo A; Vertegaal, Alfred C O

    2016-01-01

    Small ubiquitin-like modifiers (SUMOs) are essential for the regulation of several cellular processes and are potential therapeutic targets owing to their involvement in diseases such as cancer and Alzheimer disease. In the past decade, we have witnessed a rapid expansion of proteomic approaches ...

  16. Modelling substrate specificity and enantioselectivity for lipases and esterases by substrate-imprinted docking

    Directory of Open Access Journals (Sweden)

    Tyagi Sadhna

    2009-06-01

    Full Text Available Abstract Background Previously, ways to adapt docking programs that were developed for modelling inhibitor-receptor interaction have been explored. Two main issues were discussed. First, when trying to model catalysis a reaction intermediate of the substrate is expected to provide more valid information than the ground state of the substrate. Second, the incorporation of protein flexibility is essential for reliable predictions. Results Here we present a predictive and robust method to model substrate specificity and enantioselectivity of lipases and esterases that uses reaction intermediates and incorporates protein flexibility. Substrate-imprinted docking starts with covalent docking of reaction intermediates, followed by geometry optimisation of the resulting enzyme-substrate complex. After a second round of docking the same substrate into the geometry-optimised structures, productive poses are identified by geometric filter criteria and ranked by their docking scores. Substrate-imprinted docking was applied in order to model (i enantioselectivity of Candida antarctica lipase B and a W104A mutant, (ii enantioselectivity and substrate specificity of Candida rugosa lipase and Burkholderia cepacia lipase, and (iii substrate specificity of an acetyl- and a butyrylcholine esterase toward the substrates acetyl- and butyrylcholine. Conclusion The experimentally observed differences in selectivity and specificity of the enzymes were reproduced with an accuracy of 81%. The method was robust toward small differences in initial structures (different crystallisation conditions or a co-crystallised ligand, although large displacements of catalytic residues often resulted in substrate poses that did not pass the geometric filter criteria.

  17. Analysis list: SUMO2 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available SUMO2 Blood,Prostate + hg19 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/target/...SUMO2.1.tsv http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/target/SUMO2.5.tsv http://dbarchive.biosciencedb...c.jp/kyushu-u/hg19/target/SUMO2.10.tsv http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/colo/SUMO2.Blood.tsv,http://dbarchive.bioscien...cedbc.jp/kyushu-u/hg19/colo/SUMO2.Prostate.tsv http://dbarchive.bioscience...dbc.jp/kyushu-u/hg19/colo/Blood.gml,http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/colo/Prostate.gml ...

  18. 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.)

  19. 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 definition has been completed (platform and payload AIT are possible in 24 months). SUMO is proposed for the 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

  20. 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.

  1. Puromycin induces SUMO and ubiquitin redistribution upon proteasome inhibition

    International Nuclear Information System (INIS)

    Matsumoto, Hotaru; Saitoh, Hisato

    2016-01-01

    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.

  2. 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.

  3. Structure of the Siz/PIAS SUMO E3 Ligase Siz1 and Determinants Required for SUMO Modification of PCNA

    Energy Technology Data Exchange (ETDEWEB)

    Yunus, Ali A.; Lima, Christopher D.; (SKI)

    2010-01-12

    Siz1 is a founding member of the Siz/PIAS RING family of SUMO E3 ligases. The X-ray structure of an active Siz1 ligase revealed an elongated tripartite architecture comprised of an N-terminal PINIT domain, a central zinc-containing RING-like SP-RING domain, and a C-terminal domain we term the SP-CTD. Structure-based mutational analysis and biochemical studies show that the SP-RING and SP-CTD are required for activation of the E2SUMO thioester, while the PINIT domain is essential for redirecting SUMO conjugation to the proliferating cell nuclear antigen (PCNA) at lysine 164, a nonconsensus lysine residue that is not modified by the SUMO E2 in the absence of Siz1. Mutational analysis of Siz1 and PCNA revealed surfaces on both proteins that are required for efficient SUMO modification of PCNA in vitro and in vivo.

  4. 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...

  5. 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.

    Directory of Open Access Journals (Sweden)

    Jinlin Li

    2017-04-01

    Full Text Available 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.

  6. 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.

  7. Modeling of anaerobic digestion of complex substrates

    International Nuclear Information System (INIS)

    Keshtkar, A. R.; Abolhamd, G.; Meyssami, B.; Ghaforian, H.

    2003-01-01

    A structured mathematical model of anaerobic conversion of complex organic materials in non-ideally cyclic-batch reactors for biogas production has been developed. The model is based on multiple-reaction stoichiometry (enzymatic hydrolysis, acidogenesis, aceto genesis and methano genesis), microbial growth kinetics, conventional material balances in the liquid and gas phases for a cyclic-batch reactor, liquid-gas interactions, liquid-phase equilibrium reactions and a simple mixing model which considers the reactor volume in two separate sections: the flow-through and the retention regions. The dynamic model describes the effects of reactant's distribution resulting from the mixing conditions, time interval of feeding, hydraulic retention time and mixing parameters on the process performance. The model is applied in the simulation of anaerobic digestion of cattle manure under different operating conditions. The model is compared with experimental data and good correlations are obtained

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

    KAUST Repository

    Park, Hyeongcheol; Kim, Hun; Koo, Sungcheol; Park, Heejin; Cheong, Misun; Hong, Hyewon; Baek, Dongwon; Chung, Woosik; Kim, Dohhoon; Bressan, Ray Anthony; Lee, Sangyeol; Bohnert, Hans Jü rgen; Yun, Daejin

    2010-01-01

    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.

  9. 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.

  10. 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 proteasome in determining the fate of proteins conjugated to SUMO2 when cells are treated with DNA replication stress conditions. We conducted a quantitative proteomic analysis in a U2OS cell line stably expressing SUMO2(Q87R) tagged with StrepHA in the presence or absence of epoxomicin (EPOX), a proteasome...... inhibitor. We identified subgroups of putative SUMO2 targets that were either degraded or stabilized by EPOX upon SUMO2 conjugation in response to replication stress. Interestingly, the subgroup of proteins degraded upon SUMO2 conjugation was enriched in proteins playing roles in DNA damage repair...

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

    DEFF Research Database (Denmark)

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

    2012-01-01

    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......The last chapter of this first part of the book, chapter seven, is devoted to Modeling of Substrate Noise and Mitigation Schemes for Ultrawideband (UWB) systems, and is written by Ming Shen, Jan H. Mikkelsen, and Torben Larsen from Aalborg University, Denmark. In highly integrated mixed...

  12. Design and modeling of Faraday cages for substrate noise isolation

    Science.gov (United States)

    Wu, Joyce H.; del Alamo, Jesús A.

    2013-07-01

    A Faraday cage structure using through-substrate vias is an effective strategy to suppress substrate crosstalk, particularly at high frequencies. Faraday cages can reduce substrate noise by 32 dB at 10 GHz, and 26 dB at 50 GHz. We have developed lumped-element, equivalent circuit models of the Faraday cages and test structures to better understand the performance of the Faraday cages. These models compare well to measured results and show that the vias of the Faraday cage act as an RLC shunt to ground that draws substrate current. Designing a Faraday cage to achieve optimum isolation requires low via impedance and mitigation of via sidewall capacitance. The Faraday cage inductance is correlated to the number of vias and via spacing of the cage and can be optimized for the frequency of operation.

  13. Global SUMO proteome responses guide gene regulation, mRNA biogenesis, and plant stress responses

    Directory of Open Access Journals (Sweden)

    Magdalena eMazur

    2012-09-01

    Full Text Available Small-ubiquitin-like MOdifier (SUMO is a key regulator of abiotic stress, disease resistance and development in plants. The identification of >350 plant SUMO targets has revealed many processes modulated by SUMO and potential consequences of SUMO on its targets. Importantly, highly related proteins are SUMO-modified in plants, yeast, and metazoans. Overlapping SUMO targets include heat-shock proteins, transcription regulators, histones, histone-modifying enzymes, proteins involved in DNA damage repair, but also proteins involved in mRNA biogenesis and nucleo-cytoplasmic transport. Proteomics studies indicate key roles for SUMO in gene repression by controlling histone (deacetylation activity at genomic loci. The responsible heavily sumoylated transcriptional repressor complexes are recruited by EAR (Ethylene-responsive element binding factor [ERF]-associated Amphiphilic Repression-motif containing transcription factors in plants. These transcription factors are not necessarily themselves a SUMO target. Conversely, SUMO acetylation prevents binding of downstream partners by preventing binding of SIMs (SUMO-interaction peptide motifs presents in these partners, while SUMO acetylation has emerged as mechanism to recruit specifically bromodomains; bromodomain are generally linked with gene activation. These findings strengthen the idea of a bidirectional sumo-/acetylation switch in gene regulation. Quantitative proteomics has highlighted that global sumoylation provides a dynamic response to protein damage involving SUMO chain-mediated protein degradation, but also SUMO E3 ligase-dependent transcription of HSP (Heat-shock protein genes. With these insights in SUMO function and novel technical advancements, we can now study SUMO dynamics in responses to (abiotic stress in plants.

  14. Association of donor and recipient SUMO4 rs237025 genetic variant with new-onset diabetes mellitus after liver transplantation in a Chinese population.

    Science.gov (United States)

    Zhang, Tao; Liu, Yuan; Hu, Yibo; Zhang, Xiaoqing; Zhong, Lin; Fan, Junwei; Peng, Zhihai

    2017-09-05

    New-onset diabetes mellitus (NODM) is a common complication after liver transplantation (LT). The small ubiquitin-like modifier 4 (SUMO4) rs237025 polymorphism has been reported to be associated with type 2 diabetes mellitus (T2DM). In this study, we aimed to evaluate the association of donor and recipient SUMO4 rs237025 polymorphisms with NODM and the long-term consequences of NODM after LT. A total of 126 liver transplant patients were enrolled in the study. One single nucleotide polymorphism, SUMO4 rs237025, was genotyped in both donors and recipients. Both donor and recipient SUMO4 rs237025 polymorphisms were found to be significantly associated with NODM after LT. In multivariate analysis, recipient age>50 years, tacrolimus trough concentrations>10ng/mL at 1month after LT, donor and recipient rs237025 genetic variant, and the combined donor and recipient rs237025 genetic variant were independent predictive factors of NODM. Area under the receiver operating characteristic curve (AUROC) analysis indicated the higher predictive ability of the model containing combined donor and recipient rs237025 polymorphisms than the clinical model (p=0.046). Furthermore, Kaplan-Meier survival analysis demonstrated that NODM was related to significantly poorer patient survival in comparison with non-NODM patients (p=0.041). Both donor and recipient SUMO4 rs237025 polymorphisms contribute to the development of NODM after LT and NODM is a frequent complication that negatively affects patient survival. Copyright © 2017. Published by Elsevier B.V.

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

    KAUST Repository

    Park, Hyeongcheol; Choi, Wonkyun; Park, Heejin; Cheong, Misun; Koo, Yoonduck; Shin, Gilok; Chung, Woosik; Kim, Woeyeon; Kim, Mingab; Bressan, Ray Anthony; Bohnert, Hans Jü rgen; Lee, Sangyeol; Yun, Daejin

    2011-01-01

    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

  16. 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 ...

  17. SUMO: operation and maintenance management web tool for astronomical observatories

    Science.gov (United States)

    Mujica-Alvarez, Emma; Pérez-Calpena, Ana; García-Vargas, María. Luisa

    2014-08-01

    SUMO is an Operation and Maintenance Management web tool, which allows managing the operation and maintenance activities and resources required for the exploitation of a complex facility. SUMO main capabilities are: information repository, assets and stock control, tasks scheduler, executed tasks archive, configuration and anomalies control and notification and users management. The information needed to operate and maintain the system must be initially stored at the tool database. SUMO shall automatically schedule the periodical tasks and facilitates the searching and programming of the non-periodical tasks. Tasks planning can be visualized in different formats and dynamically edited to be adjusted to the available resources, anomalies, dates and other constrains that can arise during daily operation. SUMO shall provide warnings to the users notifying potential conflicts related to the required personal availability or the spare stock for the scheduled tasks. To conclude, SUMO has been designed as a tool to help during the operation management of a scientific facility, and in particular an astronomical observatory. This is done by controlling all operating parameters: personal, assets, spare and supply stocks, tasks and time constrains.

  18. Structure of the Siz/PIAS SUMO E3 ligase Siz1 and determinants required for SUMO modification of PCNA

    Science.gov (United States)

    Yunus, Ali A.; Lima, Christopher D.

    2009-01-01

    Summary Siz1 is a founding member of the Siz/PIAS RING family of SUMO E3 ligases. The x-ray structure of an active Siz1 ligase revealed an elongated tripartite architecture comprised of an N-terminal PINIT domain, a central zinc-containing RING-like SP-RING domain, and a C-terminal domain we term the SP-CTD. Structure-based mutational analysis and biochemical studies show that the SP-RING and SP-CTD are required for activation of the E2~SUMO thioester while the PINIT domain is essential for redirecting SUMO conjugation to the proliferating cell nuclear antigen (PCNA) at lysine 164, a non-consensus lysine residue that is not modified by the SUMO E2 in the absence of Siz1. Mutational analysis of Siz1 and PCNA revealed surfaces on both proteins that are required for efficient SUMO modification of PCNA in vitro and in vivo. PMID:19748360

  19. 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.

  20. Modelling of Amperometric Biosensor Used for Synergistic Substrates Determination

    Directory of Open Access Journals (Sweden)

    Dainius Simelevicius

    2012-04-01

    Full Text Available In this paper the operation of an amperometric biosensor producing a chemically amplified signal is modelled numerically. The chemical amplification is achieved by using synergistic substrates. The model is based on non-stationary reaction-diffusion equations. The model involves three layers (compartments: a layer of enzyme solution entrapped on the electrode surface, a dialysis membrane covering the enzyme layer and an outer diffusion layer which is modelled by the Nernst approach. The equation system is solved numerically by using the finite difference technique. The biosensor response and sensitivity are investigated by altering the model parameters influencing the enzyme kinetics as well as the mass transport by diffusion. The biosensor action was analyzed with a special emphasis to the effect of the chemical amplification. The simulation results qualitatively explain and confirm the experimentally observed effect of the synergistic substrates conversion on the biosensor response.

  1. 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.

  2. 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

  3. 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.

  4. The Sumo World through the gambling cases in 2010 The Sumo World as Seen Through the Gambling Cases of 2010

    Directory of Open Access Journals (Sweden)

    Keiko Morita

    2012-11-01

    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.This article is in Japanese. In summer 2010, a scandal in gambling on baseball matches implicating sumo wrestlers and their bosses was reported day after day by Japanese mass media. This scandal revealed the connections between the sumo world and criminal organizations and lead to unprecedented actions, such as the dismissal of the active Ozeki Kotomitsuki, one of the top Japanese sumo wrestlers, and the suspension of live television broadcasting of the sumo tournament. The reason why the Japanese public instigated mass public debates may relate to the notion that sumo has an intimate association with the gods, reinforced with its special position in Japanese tradition and culture. This article first presents a brief history of sumo and explains its particular characteristics. Then it provides a summary of the chain of events in the baseball gambling scandal and the responses from the Japan Sumo Association. In conjunction with

  5. Modeling universal dynamics of cell spreading on elastic substrates.

    Science.gov (United States)

    Fan, Houfu; Li, Shaofan

    2015-11-01

    A three-dimensional (3D) multiscale moving contact line model is combined with a soft matter cell model to study the universal dynamics of cell spreading over elastic substrates. We have studied both the early stage and the late stage cell spreading by taking into account the actin tension effect. In this work, the cell is modeled as an active nematic droplet, and the substrate is modeled as a St. Venant Kirchhoff elastic medium. A complete 3D simulation of cell spreading has been carried out. The simulation results show that the spreading area versus spreading time at different stages obeys specific power laws, which is in good agreement with experimental data and theoretical prediction reported in the literature. Moreover, the simulation results show that the substrate elasticity may affect force dipole distribution inside the cell. The advantage of this approach is that it combines the hydrodynamics of actin retrograde flow with moving contact line model so that it can naturally include actin tension effect resulting from actin polymerization and actomyosin contraction, and thus it might be capable of simulating complex cellular scale phenomenon, such as cell spreading or even crawling.

  6. Principles of ubiquitin and SUMO modifications in DNA repair

    NARCIS (Netherlands)

    Bergink, Steven; Jentsch, Stefan

    2009-01-01

    With the discovery in the late 1980s that the DNA-repair gene RAD6 encodes a ubiquitin-conjugating enzyme, it became clear that protein modification by ubiquitin conjugation has a much broader significance than had previously been assumed. Now, two decades later, ubiquitin and its cousin SUMO are

  7. Binding properties of SUMO-interacting motifs (SIMs) in yeast.

    Science.gov (United States)

    Jardin, Christophe; Horn, Anselm H C; Sticht, Heinrich

    2015-03-01

    Small ubiquitin-like modifier (SUMO) conjugation and interaction play an essential role in many cellular processes. A large number of yeast proteins is known to interact non-covalently with SUMO via short SUMO-interacting motifs (SIMs), but the structural details of this interaction are yet poorly characterized. In the present work, sequence analysis of a large dataset of 148 yeast SIMs revealed the existence of a hydrophobic core binding motif and a preference for acidic residues either within or adjacent to the core motif. Thus the sequence properties of yeast SIMs are highly similar to those described for human. Molecular dynamics simulations were performed to investigate the binding preferences for four representative SIM peptides differing in the number and distribution of acidic residues. Furthermore, the relative stability of two previously observed alternative binding orientations (parallel, antiparallel) was assessed. For all SIMs investigated, the antiparallel binding mode remained stable in the simulations and the SIMs were tightly bound via their hydrophobic core residues supplemented by polar interactions of the acidic residues. In contrary, the stability of the parallel binding mode is more dependent on the sequence features of the SIM motif like the number and position of acidic residues or the presence of additional adjacent interaction motifs. This information should be helpful to enhance the prediction of SIMs and their binding properties in different organisms to facilitate the reconstruction of the SUMO interactome.

  8. 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

    SUMOylation is a form of post-translational modification involving covalent attachment of SUMO (Small Ubiquitin-like Modifier) polypeptides to specific lysine residues in the target protein. In human cells, there are four SUMO proteins, SUMO1-4, with SUMO2 and SUMO3 forming a closely related subf......, and that excessive replication stress is a hallmark of pre-neoplastic and tumor cells, our characterization of SUMO2 targets during a perturbed S-phase should provide a valuable resource for future functional studies in the fields of DNA metabolism and cancer biology....

  9. 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.

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

    KAUST Repository

    Ritho, Joan; Arold, Stefan T.; Yeh, Edward  T.H.

    2015-01-01

    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.

  11. The Small Unmanned Meteorological Observer SUMO: Recent developments and applications of a Micro-UAS for atmospheric boundary layer research

    Science.gov (United States)

    Reuder, J.; Jonassen, M. O.; Ólafsson, H.

    2012-04-01

    During the last 5 years, the Small Unmanned Meteorological Observer SUMO has been developed as a new and flexible tool for atmospheric boundary layer (ABL) research to be operated as controllable and recoverable atmospheric sounding system for the lowest 4 km above the Earth's surface. In the year 2011 two main technical improvements of the system have been accomplished. The integration of an inertial measurement unit (IMU) into the Paparazzi autopilot system has expanded the environmental conditions for SUMO operation to now even allowing incloud flights. In the field of sensor technology the implementation of a 5-hole probe for the determination of the 3 dimensional flow vector impinging the aircraft with a 100 Hz resolution and of a faster Pt1000 based temperature sensor have distinctly enhanced the meteorological measurement capabilities. The extended SUMO version has recently been operated during two field campaigns. The first one in a wind farm close to Vindeby on Lolland, Denmark, was dedicated to the investigation of the effects of wind turbines on boundary layer turbulence. In spite of a few pitfalls related to configuration and synchronisation of the corresponding data logging systems, this campaign provided promising results indicating the capability and future potential of small UAS for turbulence characterization in and around wind farms. The second one, the international BLLAST (Boundary Layer Late Afternoon and Sunset Transition) field campaign at the foothills of the Pyrenees in Lannemezan, France was focussing on processes related to the afternoon transition of the convective boundary layer. On a calm sunny day during this experiment, the SUMO soundings revealed an unexpected 2°C cooling in the ABL during morning hours. By a comparison with model simulations this cooling can be associated with thermally-driven upslope winds and the subsequent advection of relatively cool air from the lowlands north of the Pyrenees.

  12. 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.

  13. Implication of SUMO E3 ligases in nucleotide excision repair.

    Science.gov (United States)

    Tsuge, Maasa; Kaneoka, Hidenori; Masuda, Yusuke; Ito, Hiroki; Miyake, Katsuhide; Iijima, Shinji

    2015-08-01

    Post-translational modifications alter protein function to mediate complex hierarchical regulatory processes that are crucial to eukaryotic cellular function. The small ubiquitin-like modifier (SUMO) is an important post-translational modification that affects transcriptional regulation, nuclear localization, and the maintenance of genome stability. Nucleotide excision repair (NER) is a very versatile DNA repair system that is essential for protection against ultraviolet (UV) irradiation. The deficiencies in NER function remarkably increase the risk of skin cancer. Recent studies have shown that several NER factors are SUMOylated, which influences repair efficiency. However, how SUMOylation modulates NER has not yet been elucidated. In the present study, we performed RNAi knockdown of SUMO E3 ligases and found that, in addition to PIASy, the polycomb protein Pc2 affected the repair of cyclobutane pyrimidine dimers. PIAS1 affected both the removal of 6-4 pyrimidine pyrimidone photoproducts and cyclobutane pyrimidine dimers, whereas other SUMO E3 ligases did not affect the removal of either UV lesion.

  14. Arabidopsis TCP Transcription Factors Interact with the SUMO Conjugating Machinery in Nuclear Foci

    Directory of Open Access Journals (Sweden)

    Magdalena J. Mazur

    2017-11-01

    Full Text Available In Arabidopsis more than 400 proteins have been identified as SUMO targets, both in vivo and in vitro. Among others, transcription factors (TFs are common targets for SUMO conjugation. Here we aimed to exhaustively screen for TFs that interact with the SUMO machinery using an arrayed yeast two-hybrid library containing more than 1,100 TFs. We identified 76 interactors that foremost interact with the SUMO conjugation enzyme SCE1 and/or the SUMO E3 ligase SIZ1. These interactors belong to various TF families, which control a wide range of processes in plant development and stress signaling. Amongst these interactors, the TCP family was overrepresented with several TCPs interacting with different proteins of the SUMO conjugation cycle. For a subset of these TCPs we confirmed that the catalytic site of SCE1 is essential for this interaction. In agreement, TCP1, TCP3, TCP8, TCP14, and TCP15 were readily SUMO modified in an E. coli sumoylation assay. Strikingly, these TCP-SCE1 interactions were found to redistribute these TCPs into nuclear foci/speckles, suggesting that these TCP foci represent sites for SUMO (conjugation activity.

  15. 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...

  16. 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...

  17. 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.

  18. 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

  19. 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....

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

    International Nuclear Information System (INIS)

    Uwada, Junsuke; Tanaka, Niina; Yamaguchi, Yutaro; Uchimura, Yasuhiro; Shibahara, Kei-ichi; Nakao, Mitsuyoshi; Saitoh, Hisato

    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.

  1. 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

    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...... in metastatic cells. Targets with altered SUMOylation are involved in cell cycle, migration, inflammation, glycolysis, gene expression, and SUMO/ubiquitin pathways, suggesting that perturbations of SUMO-2/3 modification might contribute to metastasis by affecting these processes. Consistent with this, up...... progression and metastasis....

  2. A role for non-covalent SUMO interaction motifs in Pc2/CBX4 E3 activity.

    Directory of Open Access Journals (Sweden)

    Jacqueline C Merrill

    2010-01-01

    Full Text Available Modification of proteins by the small ubiquitin like modifier (SUMO is an essential process in mammalian cells. SUMO is covalently attached to lysines in target proteins via an enzymatic cascade which consists of E1 and E2, SUMO activating and conjugating enzymes. There is also a variable requirement for non-enzymatic E3 adapter like proteins, which can increase the efficiency and specificity of the sumoylation process. In addition to covalent attachment of SUMO to target proteins, specific non-covalent SUMO interaction motifs (SIMs that are generally short hydrophobic peptide motifs have been identified.Intriguingly, consensus SIMs are present in most SUMO E3s, including the polycomb protein, Pc2/Cbx4. However, a role for SIMs in SUMO E3 activity remains to be shown. We show that Pc2 contains two functional SIMs, both of which contribute to full E3 activity in mammalian cells, and are also required for sumoylation of Pc2 itself. Pc2 forms distinct sub-nuclear foci, termed polycomb bodies, and can recruit partner proteins, such as the corepressor CtBP. We demonstrate that mutation of the SIMs in Pc2 prevents Pc2-dependent CtBP sumoylation, and decreases enrichment of SUMO1 and SUMO2 at polycomb foci. Furthermore, mutational analysis of both SUMO1 and SUMO2 reveals that the SIM-interacting residues of both SUMO isoforms are required for Pc2-mediated sumoylation and localization to polycomb foci.This work provides the first clear evidence for a role for SIMs in SUMO E3 activity.

  3. Mathematical model of organic substrate degradation in solid waste windrow composting.

    Science.gov (United States)

    Seng, Bunrith; Kristanti, Risky Ayu; Hadibarata, Tony; Hirayama, Kimiaki; Katayama-Hirayama, Keiko; Kaneko, Hidehiro

    2016-01-01

    Organic solid waste composting is a complex process that involves many coupled physical, chemical and biological mechanisms. To understand this complexity and to ease in planning, design and management of the composting plant, mathematical model for simulation is usually applied. The aim of this paper is to develop a mathematical model of organic substrate degradation and its performance evaluation in solid waste windrow composting system. The present model is a biomass-dependent model, considering biological growth processes under the limitation of moisture, oxygen and substrate contents, and temperature. The main output of this model is substrate content which was divided into two categories: slowly and rapidly degradable substrates. To validate the model, it was applied to a laboratory scale windrow composting of a mixture of wood chips and dog food. The wastes were filled into a cylindrical reactor of 6 cm diameter and 1 m height. The simulation program was run for 3 weeks with 1 s stepwise. The simulated results were in reasonably good agreement with the experimental results. The MC and temperature of model simulation were found to be matched with those of experiment, but limited for rapidly degradable substrates. Under anaerobic zone, the degradation of rapidly degradable substrate needs to be incorporated into the model to achieve full simulation of a long period static pile composting. This model is a useful tool to estimate the changes of substrate content during composting period, and acts as a basic model for further development of a sophisticated model.

  4. 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

  5. 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

  6. 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

  7. 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.

  8. 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.

  9. SUMO-1 promotes association of SNURF (RNF4) with PML nuclear bodies

    International Nuclear Information System (INIS)

    Haekli, Marika; Karvonen, Ulla; Jaenne, Olli A.; Palvimo, Jorma J.

    2005-01-01

    Small nuclear RING finger protein SNURF (RNF4) is involved in transcriptional and cell growth regulation. We show here that a significant portion of endogenous SNURF localizes to nuclear bodies (NBs) that overlap with or are adjacent to domains containing endogenous promyelocytic leukemia (PML) protein and small ubiquitin-like modifier-1 (SUMO-1). In biochemical assays, SNURF efficiently binds SUMO-1 in a noncovalent fashion. SNURF is also covalently modified by SUMO-1 at nonconsensus attachment sites. Ectopic expression of SUMO-1 markedly enhances the interaction between PML3 (PML IV) and SNURF, but covalent attachment of SUMO-1 to neither protein is required. Moreover, overexpression of PML3, but not PML-L (PML III), abolishes the coactivation function of SNURF in transactivation assays, which parallels the ability of PML3 to recruit SNURF to nuclear bodies. In sum, we have identified SNURF as a novel component in PML bodies and suggest that SUMO-1-facilitated sequestration into these nuclear domains regulates the transcriptional activity of SNURF

  10. Wrestling with Chromosomes: The Roles of SUMO During Meiosis.

    Science.gov (United States)

    Nottke, Amanda C; Kim, Hyun-Min; Colaiácovo, Monica P

    2017-01-01

    Meiosis is a specialized form of cell division required for the formation of haploid gametes and therefore is essential for successful sexual reproduction. Various steps are exquisitely coordinated to ensure accurate chromosome segregation during meiosis, thereby promoting the formation of haploid gametes from diploid cells. Recent studies are demonstrating that an important form of regulation during meiosis is exerted by the post-translational protein modification known as sumoylation. Here, we review and discuss the various critical steps of meiosis in which SUMO-mediated regulation has been implicated thus far. These include the maintenance of meiotic centromeric heterochromatin , meiotic DNA double-strand break repair and homologous recombination, centromeric coupling, and the assembly of a proteinaceous scaffold between homologous chromosomes known as the synaptonemal complex.

  11. Cytosolic expression of functional Fab fragments in Escherichia coli using a novel combination of dual SUMO expression cassette and EnBase® cultivation mode.

    Science.gov (United States)

    Rezaie, F; Davami, F; Mansouri, K; Agha Amiri, S; Fazel, R; Mahdian, R; Davoudi, N; Enayati, S; Azizi, M; Khalaj, V

    2017-05-08

    The Escherichia coli expression system is highly effective in producing recombinant proteins. However, there are some limitations in this system, especially in obtaining correctly folded forms of some complex proteins such as Fab fragments. To improve the solubility and folding quality of Fab fragments, we have examined the effect of simultaneous application of a SUMO fusion tag, EnBase ® cultivation mode and a redox mutant strain in the E. coli expression system. A bicistronic gene construct was designed to express an antivascular endothelial growth factor (VEGF) Fab fragment as a model system. The construct contained a dual SUMO fusion gene fragment to encode SUMO-tagged heavy and light chains. While the expression of the construct in batch cultures of BL21 or SHuffle ® transformants produced insoluble and unfolded products, the induction of the transformants in EnBase ® medium resulted in soluble and correctly folded Fab fragment, reaching as high as 19% of the total protein in shuffle strain. The functional assays indicated that the biological activity of the target Fab is similar to the commercial anti-VEGF, Lucentis ® . This study demonstrated that the combination of SUMO fusion technology, EnBase ® cultivation system and recruiting a redox mutant of E. coli can efficiently enhance the solubility and productivity of recombinant Fab fragments. The presented strategy provides not only a novel method to produce soluble and active form of an anti-VEGF Fab but also may use in the efficient production of other antibody fragments. © 2017 The Society for Applied Microbiology.

  12. Modeling of the Bacillus subtilis Bacterial Biofilm Growing on an Agar Substrate.

    Science.gov (United States)

    Wang, Xiaoling; Wang, Guoqing; Hao, Mudong

    2015-01-01

    Bacterial biofilms are organized communities composed of millions of microorganisms that accumulate on almost any kinds of surfaces. In this paper, a biofilm growth model on an agar substrate is developed based on mass conservation principles, Fick's first law, and Monod's kinetic reaction, by considering nutrient diffusion between biofilm and agar substrate. Our results show biofilm growth evolution characteristics such as biofilm thickness, active biomass, and nutrient concentration in the agar substrate. We quantitatively obtain biofilm growth dependence on different parameters. We provide an alternative mathematical method to describe other kinds of biofilm growth such as multiple bacterial species biofilm and also biofilm growth on various complex substrates.

  13. 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.

  14. 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 ...

  15. 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

  16. 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.

  17. Logistic growth models of China pinks, cultivated on seven substrates, as a function of degree days

    Directory of Open Access Journals (Sweden)

    Marília Milani

    Full Text Available ABSTRACT: The objective of this study was to characterize the height (H and leaf number (LN of China pinks, grown in seven substrates, as a function of degree days, using the logistic growth model. H and LN were measured from 56 plants per substrate, for 392 plants in total. Plants that were grown on substrates formed of 50% soil with 50% rice husk ash (50% S + 50% RH and 80% rice husk ash with 20% worm castings (80% RH + 20% W had the longest vegetative growth period (74d, corresponding to 1317.9ºCd. The logistic growth model, adjusted for H, showed differences in the estimation of maximum expected height (α between the substrates, with values between 10.47cm for 50% S + 50% RH and 35.75cm for Mecplant(r. When α was estimated as LN, variation was also observed between the different substrates, from approximately 30 leaves on plants growing on 50% S + 50% RH to 34 leaves on the plants growing on the substrate formed of 80% RH + 20% W. Growth of China pinks can be characterized using H or LN in the logistic growth model as a function of degree days, being the provided plants adequately fertilized. The best substrates in terms of maximum height and leaf number were 80% soil + 20% worm castings and Mecplant(r. However, users must recalibrate the model with the estimated parameters before applying it to different growing conditions.

  18. A phenomenological model of coating/substrate adhesion and interfacial bimetallic peeling stress in composite mirrors

    Science.gov (United States)

    Mcelroy, Paul M.; Lawson, Daniel D.

    1990-01-01

    Adhesion and interfacial stress between metal films and structural composite material substrates is discussed. A theoretical and conceptual basis for selecting coating materials for composite mirror substrates is described. A phenomenological model that interrelates cohesive tensile strength of thin film coatings and interfacial peeling stresses is presented. The model serves as a basis in determining gradiated materials response and compatibility of composite substrate and coating combinations. Parametric evaluation of material properties and geometrical factors such as coating thickness are used to determine the threshold stress levels for maintaining adhesion at the different interfaces.

  19. 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.

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

    African Journals Online (AJOL)

    STORAGESEVER

    2008-05-02

    May 2, 2008 ... Aspergillus fumigatus. A simple model was proposed using the Logistic Equation for the growth, ... costs and also involved in less sophisticated fermentation ... apply and they are accurately proved that the model can express ...

  1. 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.

  2. Expression, Localization of SUMO-1, and Analyses of Potential SUMOylated Proteins in Bubalus bubalis Spermatozoa.

    Science.gov (United States)

    Brohi, Rahim Dad; Wang, Li; Hassine, Najla Ben; Cao, Jing; Talpur, Hira Sajjad; Wu, Di; Huang, Chun-Jie; Rehman, Zia-Ur; Bhattarai, Dinesh; Huo, Li-Jun

    2017-01-01

    Mature spermatozoa have highly condensed DNA that is essentially silent both transcriptionally and translationally. Therefore, post translational modifications are very important for regulating sperm motility, morphology, and for male fertility in general. Protein sumoylation was recently demonstrated in human and rodent spermatozoa, with potential consequences for sperm motility and DNA integrity. We examined the expression and localization of small ubiquitin-related modifier-1 (SUMO-1) in the sperm of water buffalo ( Bubalus bubalis ) using immunofluorescence analysis. We confirmed the expression of SUMO-1 in the acrosome. We further found that SUMO-1 was lost if the acrosome reaction was induced by calcium ionophore A23187. Proteins modified or conjugated by SUMO-1 in water buffalo sperm were pulled down and analyzed by mass spectrometry. Sixty proteins were identified, including proteins important for sperm morphology and motility, such as relaxin receptors and cytoskeletal proteins, including tubulin chains, actins, and dyneins. Forty-six proteins were predicted as potential sumoylation targets. The expression of SUMO-1 in the acrosome region of water buffalo sperm and the identification of potentially SUMOylated proteins important for sperm function implicates sumoylation as a crucial PTM related to sperm function.

  3. Expression, Localization of SUMO-1, and Analyses of Potential SUMOylated Proteins in Bubalus bubalis Spermatozoa

    Directory of Open Access Journals (Sweden)

    Rahim Dad Brohi

    2017-06-01

    Full Text Available Mature spermatozoa have highly condensed DNA that is essentially silent both transcriptionally and translationally. Therefore, post translational modifications are very important for regulating sperm motility, morphology, and for male fertility in general. Protein sumoylation was recently demonstrated in human and rodent spermatozoa, with potential consequences for sperm motility and DNA integrity. We examined the expression and localization of small ubiquitin-related modifier-1 (SUMO-1 in the sperm of water buffalo (Bubalus bubalis using immunofluorescence analysis. We confirmed the expression of SUMO-1 in the acrosome. We further found that SUMO-1 was lost if the acrosome reaction was induced by calcium ionophore A23187. Proteins modified or conjugated by SUMO-1 in water buffalo sperm were pulled down and analyzed by mass spectrometry. Sixty proteins were identified, including proteins important for sperm morphology and motility, such as relaxin receptors and cytoskeletal proteins, including tubulin chains, actins, and dyneins. Forty-six proteins were predicted as potential sumoylation targets. The expression of SUMO-1 in the acrosome region of water buffalo sperm and the identification of potentially SUMOylated proteins important for sperm function implicates sumoylation as a crucial PTM related to sperm function.

  4. 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

    2018-04-01

    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. [Figure not available: see fulltext.

  5. 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.

  6. 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.

  7. 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

  8. Surface structures of equilibrium restricted curvature model on two fractal substrates

    International Nuclear Information System (INIS)

    Song Li-Jian; Tang Gang; Zhang Yong-Wei; Han Kui; Xun Zhi-Peng; Xia Hui; Hao Da-Peng; Li Yan

    2014-01-01

    With the aim to probe the effects of the microscopic details of fractal substrates on the scaling of discrete growth models, the surface structures of the equilibrium restricted curvature (ERC) model on Sierpinski arrowhead and crab substrates are analyzed by means of Monte Carlo simulations. These two fractal substrates have the same fractal dimension d f , but possess different dynamic exponents of random walk z rw . The results show that the surface structure of the ERC model on fractal substrates are related to not only the fractal dimension d f , but also to the microscopic structures of the substrates expressed by the dynamic exponent of random walk z rw . The ERC model growing on the two substrates follows the well-known Family—Vicsek scaling law and satisfies the scaling relations 2α + d f ≍ z ≍ 2z rw . In addition, the values of the scaling exponents are in good agreement with the analytical prediction of the fractional Mullins—Herring equation. (general)

  9. 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...

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

    Science.gov (United States)

    Bursomanno, Sara; Beli, Petra; Khan, Asif M; Minocherhomji, Sheroy; Wagner, Sebastian A; Bekker-Jensen, Simon; Mailand, Niels; Choudhary, Chunaram; Hickson, Ian D; Liu, Ying

    2015-01-01

    SUMOylation is a form of post-translational modification involving covalent attachment of SUMO (Small Ubiquitin-like Modifier) polypeptides to specific lysine residues in the target protein. In human cells, there are four SUMO proteins, SUMO1-4, with SUMO2 and SUMO3 forming a closely related 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 response to DNA damage. Interestingly, POLD3 was found modified most significantly in response to a low dose aphidicolin treatment protocol that promotes common fragile site (CFS) breakage. POLD3 is the human ortholog of POL32 in budding yeast, and has been shown to act during break-induced recombinational 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, and that excessive replication stress is a hallmark of pre-neoplastic and tumor cells, our characterization of SUMO2 targets during a perturbed S-phase should provide a valuable resource for future functional studies in the fields of DNA metabolism and cancer biology. Copyright © 2014 Elsevier B.V. All rights reserved.

  11. Inhibition of DNA binding of Sox2 by the SUMO conjugation

    International Nuclear Information System (INIS)

    Tsuruzoe, Shu; Ishihara, Ko; Uchimura, Yasuhiro; Watanabe, Sugiko; Sekita, Yoko; Aoto, Takahiro; Saitoh, Hisato; Yuasa, Yasuhito; Niwa, Hitoshi; Kawasuji, Michio; Baba, Hideo; Nakao, Mitsuyoshi

    2006-01-01

    Sox2 is a member of the high mobility group (HMG) domain DNA-binding proteins for transcriptional control and chromatin architecture. The HMG domain of Sox2 binds the DNA to facilitate transactivation by the cooperative transcription factors such as Oct3/4. We report that mouse Sox2 is modified by SUMO at lysine 247. Substitution of the target lysine to arginine lost the sumoylation but little affected transcriptional potential or nuclear localization of Sox2. By contrast with the unmodified form, Sox2 fused to SUMO-1 did not augment transcription via the Fgf4 enhancer in the presence of Oct3/4. Further, SUMO-1-conjugated Sox2 at the lysine 247 or at the carboxyl terminus reduced the binding to the Fgf4 enhancer. These indicate that Sox2 sumoylation negatively regulates its transcriptional role through impairing the DNA binding

  12. 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

    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...

  13. Modeling of the Bacillus subtilis Bacterial Biofilm Growing on an Agar Substrate

    Directory of Open Access Journals (Sweden)

    Xiaoling Wang

    2015-01-01

    Full Text Available Bacterial biofilms are organized communities composed of millions of microorganisms that accumulate on almost any kinds of surfaces. In this paper, a biofilm growth model on an agar substrate is developed based on mass conservation principles, Fick’s first law, and Monod’s kinetic reaction, by considering nutrient diffusion between biofilm and agar substrate. Our results show biofilm growth evolution characteristics such as biofilm thickness, active biomass, and nutrient concentration in the agar substrate. We quantitatively obtain biofilm growth dependence on different parameters. We provide an alternative mathematical method to describe other kinds of biofilm growth such as multiple bacterial species biofilm and also biofilm growth on various complex substrates.

  14. Heterologous SUMO-2/3-ubiquitin chains optimize IκBα degradation and NF-κB activity.

    Directory of Open Access Journals (Sweden)

    Fabienne Aillet

    Full Text Available The NF-κB pathway is regulated by SUMOylation at least at three levels: the inhibitory molecule IκBα, the IKK subunit γ/NEMO and the p52 precursor p100. Here we investigate the role of SUMO-2/3 in the degradation of IκBα and activation of NF-κB mediated by TNFα. We found that under conditions of deficient SUMOylation, an important delay in both TNFα-mediated proteolysis of IκBα and NF-κB dependent transcription occurs. In vitro and ex vivo approaches, including the use of ubiquitin-traps (TUBEs, revealed the formation of chains on IκBα containing SUMO-2/3 and ubiquitin after TNFα stimulation. The integration of SUMO-2/3 appears to promote the formation of ubiquitin chains on IκBα after activation of the TNFα signalling pathway. Furthermore, heterologous chains of SUMO-2/3 and ubiquitin promote a more efficient degradation of IκBα by the 26S proteasome in vitro compared to chains of either SUMO-2/3 or ubiquitin alone. Consistently, Ubc9 silencing reduced the capture of IκBα modified with SUMO-ubiquitin hybrid chains that display a defective proteasome-mediated degradation. Thus, hybrid SUMO-2/3-ubiquitin chains increase the susceptibility of modified IκBα to the action of 26S proteasome, contributing to the optimal control of NF-κB activity after TNFα-stimulation.

  15. 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.

  16. 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

  17. Modeling the electrical resistance of gold film conductors on uniaxially stretched elastomeric substrates

    Science.gov (United States)

    Cao, Wenzhe; Görrn, Patrick; Wagner, Sigurd

    2011-05-01

    The electrical resistance of gold film conductors on polydimethyl siloxane substrates at stages of uniaxial stretching is measured and modeled. The surface area of a gold conductor is assumed constant during stretching so that the exposed substrate takes up all strain. Sheet resistances are calculated from frames of scanning electron micrographs by numerically solving for the electrical potentials of all pixels in a frame. These sheet resistances agree sufficiently well with values measured on the same conductors to give credence to the model of a stretchable network of gold links defined by microcracks.

  18. A discrete model on Sierpinski gasket substrate for a conserved current equation with a conservative noise

    Science.gov (United States)

    Kim, Dae Ho; Kim, Jin Min

    2012-09-01

    A conserved discrete model on the Sierpinski gasket substrate is studied. The interface width W in the model follows the Family-Vicsek dynamic scaling form with growth exponent β ≈ 0.0542, roughness exponent α ≈ 0.240 and dynamic exponent z ≈ 4.42. They satisfy a scaling relation α + z = 2zrw, where zrw is the random walk exponent of the fractal substrate. Also, they are in a good agreement with the predicted values of a fractional Langevin equation \\frac{\\partial h}{\\partial t}={\

  19. A discrete model on Sierpinski gasket substrate for a conserved current equation with a conservative noise

    International Nuclear Information System (INIS)

    Kim, Dae Ho; Kim, Jin Min

    2012-01-01

    A conserved discrete model on the Sierpinski gasket substrate is studied. The interface width W in the model follows the Family–Vicsek dynamic scaling form with growth exponent β ≈ 0.0542, roughness exponent α ≈ 0.240 and dynamic exponent z ≈ 4.42. They satisfy a scaling relation α + z = 2z rw , where z rw is the random walk exponent of the fractal substrate. Also, they are in a good agreement with the predicted values of a fractional Langevin equation where η c is a conservative noise. (paper)

  20. 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.

  1. Modeling of the rough spherical nanoparticles manipulation on a substrate based on the AFM nanorobot

    Science.gov (United States)

    Zakeri, M.; Faraji, J.

    2014-12-01

    In this paper, dynamic behavior of the rough spherical micro/nanoparticles during pulling/pushing on the flat substrate has been investigated and analyzed. For this purpose, at first, two hexagonal roughness models (George and Cooper) were studied and then evaluations for adhesion force were determined for rough particle manipulation on flat substrate. These two models were then changed by using of the Rabinovich theory. Evaluations were determined for contact adhesion force between rough particle and flat substrate; depth of penetration evaluations were determined by the Johnson-Kendall-Roberts contact mechanic theory and the Schwartz method and according to Cooper and George roughness models. Then, the novel contact theory was used to determine a dynamic model for rough micro/nanoparticle manipulation on flat substrate. Finally, simulation of particle dynamic behavior was implemented during pushing of rough spherical gold particles with radii of 50, 150, 400, 600, and 1,000 nm. Results derived from simulations of particles with several rates of roughness on flat substrate indicated that compared to results for flat particles, inherent roughness on particles might reduce the rate of critical force needed for sliding and rolling given particles. Given a fixed radius for roughness value and increased roughness height, evaluations for sliding and rolling critical forces showed greater reduction. Alternately, the rate of critical force was shown to reduce relative to an increased roughness radius. With respect to both models, based on the George roughness model, the predicted rate of adhesion force was greater than that determined in the Cooper roughness model, and as a result, the predicted rate of critical force based on the George roughness model was closer to the critical force value of flat particle.

  2. 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.

  3. 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...

  4. 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.

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

    KAUST Repository

    Lin, Xiao-Li; Niu, De; Hu, Zi-Liang; Kim, Dae Heon; Jin, Yin Hua; Cai, Bin; Liu, Peng; Miura, Kenji; Yun, Dae-Jin; Kim, Woe-Yeon; Lin, Rongcheng; Jin, Jing Bo

    2016-01-01

    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.

  6. Growth and substrate consumption of Nitrobacter agilis cells immobilized in carrageenan: part 1. Dynamic modeling.

    Science.gov (United States)

    de Gooijer, C D; Wijffels, R H; Tramper, J

    1991-07-01

    The modeling of the growth of Nitrobacter agilis cell immobilized in kappa-carrageenan is presented. A detailed description is given of the modeling of internal diffusion and growth of cells in the support matrix in addition to external mass transfer resistance. The model predicts the substrate and biomass profiles in the support as well as the macroscopic oxygen consumption rate of the immobilized biocatalyst in time. The model is tested by experiments with continuously operated airlift loop reactors containing cells immobilized in kappa-carrageenan. The model describes experimental data very well. It is clearly shown that external mass transfer may not be neglected. Furthermore, a sensitivity analysis of the parameters at their values during the experiments revealed that apart from the radius of the spheres and the substrate bulk concentration, the external mass transfer resistance coefficient is the most sensitive parameter for our case.

  7. 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

    In this paper, the small- and large-signal modeling of InP heterojunction bipolar transistors (HBTs) in transferred substrate (TS) technology is investigated. The small-signal equivalent circuit parameters for TS-HBTs in two-terminal and three-terminal configurations are determined by employing...

  8. 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...

  9. 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

    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 calibrate...

  10. How can cells sense the elasticity of a substrate? An analysis using a cell tensegrity model

    Directory of Open Access Journals (Sweden)

    G De Santis

    2011-10-01

    Full Text Available A eukaryotic cell attaches and spreads on substrates, whether it is the extracellular matrix naturally produced by the cell itself, or artificial materials, such as tissue-engineered scaffolds. Attachment and spreading require the cell to apply forces in the nN range to the substrate via adhesion sites, and these forces are balanced by the elastic response of the substrate. This mechanical interaction is one determinant of cell morphology and, ultimately, cell phenotype. In this paper we use a finite element model of a cell, with a tensegrity structure to model the cytoskeleton of actin filaments and microtubules, to explore the way cells sense the stiffness of the substrate and thereby adapt to it. To support the computational results, an analytical 1D model is developed for comparison. We find that (i the tensegrity hypothesis of the cytoskeleton is sufficient to explain the matrix-elasticity sensing, (ii cell sensitivity is not constant but has a bell-shaped distribution over the physiological matrix-elasticity range, and (iii the position of the sensitivity peak over the matrix-elasticity range depends on the cytoskeletal structure and in particular on the F-actin organisation. Our model suggests that F-actin reorganisation observed in mesenchymal stem cells (MSCs in response to change of matrix elasticity is a structural-remodelling process that shifts the sensitivity peak towards the new value of matrix elasticity. This finding discloses a potential regulatory role of scaffold stiffness for cell differentiation.

  11. 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.

  12. 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

  13. Molecular Modeling of Peroxidase and Polyphenol Oxidase: Substrate Specificity and Active Site Comparison

    Directory of Open Access Journals (Sweden)

    Lalida Shank

    2010-09-01

    Full Text Available Peroxidases (POD and polyphenol oxidase (PPO are enzymes that are well known to be involved in the enzymatic browning reaction of fruits and vegetables with different catalytic mechanisms. Both enzymes have some common substrates, but each also has its specific substrates. In our computational study, the amino acid sequence of grape peroxidase (ABX was used for the construction of models employing homology modeling method based on the X-ray structure of cytosolic ascorbate peroxidase from pea (PDB ID:1APX, whereas the model of grape polyphenol oxidase was obtained directly from the available X-ray structure (PDB ID:2P3X. Molecular docking of common substrates of these two enzymes was subsequently studied. It was found that epicatechin and catechin exhibited high affinity with both enzymes, even though POD and PPO have different binding pockets regarding the size and the key amino acids involved in binding. Predicted binding modes of substrates with both enzymes were also compared. The calculated docking interaction energy of trihydroxybenzoic acid related compounds shows high affinity, suggesting specificity and potential use as common inhibitor to grape ascorbate peroxidase and polyphenol oxidase.

  14. 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.

  15. 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.

  16. The ROS/SUMO Axis Contributes to the Response of Acute Myeloid Leukemia Cells to Chemotherapeutic Drugs

    Directory of Open Access Journals (Sweden)

    Guillaume Bossis

    2014-06-01

    Full Text Available Chemotherapeutic drugs used in the treatment of acute myeloid leukemias (AMLs are thought to induce cancer cell death through the generation of DNA double-strand breaks. Here, we report that one of their early effects is the loss of conjugation of the ubiquitin-like protein SUMO from its targets via reactive oxygen species (ROS-dependent inhibition of the SUMO-conjugating enzymes. Desumoylation regulates the expression of specific genes, such as the proapoptotic gene DDIT3, and helps induce apoptosis in chemosensitive AMLs. In contrast, chemotherapeutics do not activate the ROS/SUMO axis in chemoresistant cells. However, pro-oxidants or inhibition of the SUMO pathway by anacardic acid restores DDIT3 expression and apoptosis in chemoresistant cell lines and patient samples, including leukemic stem cells. Finally, inhibition of the SUMO pathway decreases tumor growth in mice xenografted with AML cells. Thus, targeting the ROS/SUMO axis might constitute a therapeutic strategy for AML patients resistant to conventional chemotherapies.

  17. Deterministic three-half-order kinetic model for microbial degradation of added carbon substrates in soil

    International Nuclear Information System (INIS)

    Brunner, W.; Focht, D.D.

    1984-01-01

    The kinetics of mineralization of carbonaceous substrates has been explained by a deterministic model which is applicable to either growth or nongrowth conditions in soils. The mixed-order nature of the model does not require a priori decisions about reaction order, discontinuity period of lag or stationary phase, or correction for endogenous mineralization rates. The integrated equation is simpler than the integrated form of the Monod equation because of the following: (i) only two, rather than four, interdependent constants have to be determined by nonlinear regression analysis, (ii) substrate or product formation can be expressed explicitly as a function of time, (iii) biomass concentration does not have to be known, and (iv) the required initial estimate for the nonlinear regression analysis can be easily obtained from a linearized form rather than from an interval estimate of a differential equation. 14 CO 2 evolution data from soil have been fitted to the model equation. All data except those from irradiated soil gave us better fits by residual sum of squares (RSS) by assuming growth in soil was linear (RSS =0.71) as opposed to exponential (RSS = 2.87). The underlying reasons for growth (exponential versus linear), no growth, and relative degradation rates of substrates are consistent with the basic mechanisms from which the model is derived. 21 references

  18. Electromagnetic Modelling of Raman Enhancement from Nanoscale Structures as a Means to Predict the Efficacy of SERS Substrates

    Directory of Open Access Journals (Sweden)

    Richard J. C. Brown

    2007-01-01

    Full Text Available The requirement to optimise the balance between signal enhancement and reproducibility in surface enhanced Raman spectroscopy (SERS is stimulating the development of novel substrates for enhancing Raman signals. This paper describes the application of finite element electromagnetic modelling to predict the Raman enhancement produced from a variety of SERS substrates with differently sized, spaced and shaped morphologies with nanometre dimensions. For the first time, a theoretical comparison between four major generic types of SERS substrate (including metal nanoparticles, structured surfaces, and sharp tips has been performed and the results are presented and discussed. The results of the modelling are consistent with published experimental data from similar substrates.

  19. Modeling cell-substrate de-adhesion dynamics under fluid shear

    Science.gov (United States)

    Maan, Renu; Rani, Garima; Menon, Gautam I.; Pullarkat, Pramod A.

    2018-07-01

    Changes in cell-substrate adhesion are believed to signal the onset of cancer metastasis, but such changes must be quantified against background levels of intrinsic heterogeneity between cells. Variations in cell-substrate adhesion strengths can be probed through biophysical measurements of cell detachment from substrates upon the application of an external force. Here, we investigate, theoretically and experimentally, the detachment of cells adhered to substrates when these cells are subjected to fluid shear. We present a theoretical framework within which we calculate the fraction of detached cells as a function of shear stress for fast ramps as well as the decay in this fraction at fixed shear stress as a function of time. Using HEK and 3T3 fibroblast cells as experimental model systems, we extract characteristic force scales for cell adhesion as well as characteristic detachment times. We estimate force-scales of  ∼500 pN associated to a single focal contact, and characteristic time-scales of s representing cell-spread-area dependent mean first passage times to the detached state at intermediate values of the shear stress. Variations in adhesion across cell types are especially prominent when cell detachment is probed by applying a time-varying shear stress. These methods can be applied to characterizing changes in cell adhesion in a variety of contexts, including metastasis.

  20. 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.

  1. Low-order modelling of a drop on a highly-hydrophobic substrate: statics and dynamics

    Science.gov (United States)

    Wray, Alexander W.; Matar, Omar K.; Davis, Stephen H.

    2017-11-01

    We analyse the behaviour of droplets resting on highly-hydrophobic substrates. This problem is of practical interest due to its appearance in many physical contexts involving the spreading, wetting, and dewetting of fluids on solid substrates. In mathematical terms, it exhibits an interesting challenge as the interface is multi-valued as a function of the natural Cartesian co-ordinates, presenting a stumbling block to typical low-order modelling techniques. Nonetheless, we show that in the static case, the interfacial shape is governed by the Young-Laplace equation, which may be solved explicitly in terms of elliptic functions. We present simple low-order expressions that faithfully reproduce the shapes. We then consider the dynamic case, showing that the predictions of our low-order model compare favourably with those obtained from direct numerical simulations. We also examine the characteristic flow regimes of interest. EPSRC, UK, MEMPHIS program Grant (EP/K003976/1), RAEng Research Chair (OKM).

  2. 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

  3. 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.

  4. Modeling and Design Guidelines for P⁺ Guard Rings in Lightly Doped CMOS Substrates

    DEFF Research Database (Denmark)

    Shen, Ming; Mikkelsen, Jan H.; Zhang, Ke

    2013-01-01

    of ${rm P}^{+}$ guard rings in terms of S-parameters, which is useful for substrate noise mitigation in mixed-signal system-on-chips. Validation of the model has been done by both electromagnetic simulation and experimental results from guard rings implemented using a standard 0.18-$mu{rm m}$ CMOS process....... In addition, design guidelines have been drawn for minimizing the guard ring size while maintaining the noise suppression performance....

  5. Model-based confirmation of alternative substrates of mitochondrial electron transport chain.

    Science.gov (United States)

    Kleessen, Sabrina; Araújo, Wagner L; Fernie, Alisdair R; Nikoloski, Zoran

    2012-03-30

    Discrimination of metabolic models based on high throughput metabolomics data, reflecting various internal and external perturbations, is essential for identifying the components that contribute to the emerging behavior of metabolic processes. Here, we investigate 12 different models of the mitochondrial electron transport chain (ETC) in Arabidopsis thaliana during dark-induced senescence in order to elucidate the alternative substrates to this metabolic pathway. Our findings demonstrate that the coupling of the proposed computational approach, based on dynamic flux balance analysis, with time-resolved metabolomics data results in model-based confirmations of the hypotheses that, during dark-induced senescence in Arabidopsis, (i) under conditions where the main substrate for the ETC are not fully available, isovaleryl-CoA dehydrogenase and 2-hydroxyglutarate dehydrogenase are able to donate electrons to the ETC, (ii) phytanoyl-CoA does not act even as an indirect substrate of the electron transfer flavoprotein/electron-transfer flavoprotein:ubiquinone oxidoreductase complex, and (iii) the mitochondrial γ-aminobutyric acid transporter has functional significance in maintaining mitochondrial metabolism. Our study provides a basic framework for future in silico studies of alternative pathways in mitochondrial metabolism under extended darkness whereby the role of its components can be computationally discriminated based on available molecular profile data.

  6. USP7/HAUSP: A SUMO deubiquitinase at the heart of DNA replication.

    Science.gov (United States)

    Smits, Veronique A J; Freire, Raimundo

    2016-09-01

    DNA replication is both highly conserved and controlled. Problematic DNA replication can lead to genomic instability and therefore carcinogenesis. Numerous mechanisms work together to achieve this tight control and increasing evidence suggests that post-translational modifications (phosphorylation, ubiquitination, SUMOylation) of DNA replication proteins play a pivotal role in this process. Here we discuss such modifications in the light of a recent article that describes a novel role for the deubiquitinase (DUB) USP7/HAUSP in the control of DNA replication. USP7 achieves this function by an unusual and novel mechanism, namely deubiquitination of SUMOylated proteins at the replication fork, making USP7 also a SUMO DUB (SDUB). This work extends previous observations of increased levels of SUMO and low levels of ubiquitin at the on-going replication fork. Here, we discuss this novel study, its contribution to the DNA replication and genomic stability field and what questions arise from this work. © 2016 WILEY Periodicals, Inc.

  7. Scavenger receptors mediate the role of SUMO and Ftz-f1 in Drosophila steroidogenesis.

    Directory of Open Access Journals (Sweden)

    Ana Talamillo

    2013-04-01

    Full Text Available SUMOylation participates in ecdysteroid biosynthesis at the onset of metamorphosis in Drosophila melanogaster. Silencing the Drosophila SUMO homologue smt3 in the prothoracic gland leads to reduced lipid content, low ecdysone titers, and a block in the larval-pupal transition. Here we show that the SR-BI family of Scavenger Receptors mediates SUMO functions. Reduced levels of Snmp1 compromise lipid uptake in the prothoracic gland. In addition, overexpression of Snmp1 is able to recover lipid droplet levels in the smt3 knockdown prothoracic gland cells. Snmp1 expression depends on Ftz-f1 (an NR5A-type orphan nuclear receptor, the expression of which, in turn, depends on SUMO. Furthermore, we show by in vitro and in vivo experiments that Ftz-f1 is SUMOylated. RNAi-mediated knockdown of ftz-f1 phenocopies that of smt3 at the larval to pupal transition, thus Ftz-f1 is an interesting candidate to mediate some of the functions of SUMO at the onset of metamorphosis. Additionally, we demonstrate that the role of SUMOylation, Ftz-f1, and the Scavenger Receptors in lipid capture and mobilization is conserved in other steroidogenic tissues such as the follicle cells of the ovary. smt3 knockdown, as well as ftz-f1 or Scavenger knockdown, depleted the lipid content of the follicle cells, which could be rescued by Snmp1 overexpression. Therefore, our data provide new insights into the regulation of metamorphosis via lipid homeostasis, showing that Drosophila Smt3, Ftz-f1, and SR-BIs are part of a general mechanism for uptake of lipids such as cholesterol, required during development in steroidogenic tissues.

  8. 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

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

    International Nuclear Information System (INIS)

    Blevins, Erin; Lauder, George V

    2013-01-01

    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. (paper)

  10. Dynamic Modelling Reveals 'Hotspots' on the Pathway to Enzyme-Substrate Complex Formation.

    Directory of Open Access Journals (Sweden)

    Shane E Gordon

    2016-03-01

    Full Text Available Dihydrodipicolinate synthase (DHDPS catalyzes the first committed step in the diaminopimelate pathway of bacteria, yielding amino acids required for cell wall and protein biosyntheses. The essentiality of the enzyme to bacteria, coupled with its absence in humans, validates DHDPS as an antibacterial drug target. Conventional drug design efforts have thus far been unsuccessful in identifying potent DHDPS inhibitors. Here, we make use of contemporary molecular dynamics simulation and Markov state models to explore the interactions between DHDPS from the human pathogen Staphylococcus aureus and its cognate substrate, pyruvate. Our simulations recover the crystallographic DHDPS-pyruvate complex without a priori knowledge of the final bound structure. The highly conserved residue Arg140 was found to have a pivotal role in coordinating the entry of pyruvate into the active site from bulk solvent, consistent with previous kinetic reports, indicating an indirect role for the residue in DHDPS catalysis. A metastable binding intermediate characterized by multiple points of intermolecular interaction between pyruvate and key DHDPS residue Arg140 was found to be a highly conserved feature of the binding trajectory when comparing alternative binding pathways. By means of umbrella sampling we show that these binding intermediates are thermodynamically metastable, consistent with both the available experimental data and the substrate binding model presented in this study. Our results provide insight into an important enzyme-substrate interaction in atomistic detail that offers the potential to be exploited for the discovery of more effective DHDPS inhibitors and, in a broader sense, dynamic protein-drug interactions.

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

    KAUST Repository

    Kong, Xiangxiong; Luo, Xi; Qu, Gao Ping; Liu, Peng; Jin, Jing Bo

    2016-01-01

    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.

  12. Interplay between Ubiquitin, SUMO, and Poly(ADP-Ribose) in the Cellular Response to Genotoxic Stress

    Science.gov (United States)

    Pellegrino, Stefania; Altmeyer, Matthias

    2016-01-01

    Cells employ a complex network of molecular pathways to cope with endogenous and exogenous genotoxic stress. This multilayered response ensures that genomic lesions are efficiently detected and faithfully repaired in order to safeguard genome integrity. The molecular choreography at sites of DNA damage relies heavily on post-translational modifications (PTMs). Protein modifications with ubiquitin and the small ubiquitin-like modifier SUMO have recently emerged as important regulatory means to coordinate DNA damage signaling and repair. Both ubiquitylation and SUMOylation can lead to extensive chain-like protein modifications, a feature that is shared with yet another DNA damage-induced PTM, the modification of proteins with poly(ADP-ribose) (PAR). Chains of ubiquitin, SUMO, and PAR all contribute to the multi-protein assemblies found at sites of DNA damage and regulate their spatio-temporal dynamics. Here, we review recent advancements in our understanding of how ubiquitin, SUMO, and PAR coordinate the DNA damage response and highlight emerging examples of an intricate interplay between these chain-like modifications during the cellular response to genotoxic stress. PMID:27148359

  13. 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.

  14. 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.

  15. Quantitative Analysis of Subcellular Distribution of the SUMO Conjugation System by Confocal Microscopy Imaging.

    Science.gov (United States)

    Mas, Abraham; Amenós, Montse; Lois, L Maria

    2016-01-01

    Different studies point to an enrichment in SUMO conjugation in the cell nucleus, although non-nuclear SUMO targets also exist. In general, the study of subcellular localization of proteins is essential for understanding their function within a cell. Fluorescence microscopy is a powerful tool for studying subcellular protein partitioning in living cells, since fluorescent proteins can be fused to proteins of interest to determine their localization. Subcellular distribution of proteins can be influenced by binding to other biomolecules and by posttranslational modifications. Sometimes these changes affect only a portion of the protein pool or have a partial effect, and a quantitative evaluation of fluorescence images is required to identify protein redistribution among subcellular compartments. In order to obtain accurate data about the relative subcellular distribution of SUMO conjugation machinery members, and to identify the molecular determinants involved in their localization, we have applied quantitative confocal microscopy imaging. In this chapter, we will describe the fluorescent protein fusions used in these experiments, and how to measure, evaluate, and compare average fluorescence intensities in cellular compartments by image-based analysis. We show the distribution of some components of the Arabidopsis SUMOylation machinery in epidermal onion cells and how they change their distribution in the presence of interacting partners or even when its activity is affected.

  16. 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.

  17. 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...... that estimates the gas percolation threshold based on the pore size distribution. The model successfully captured measured data for all investigated media and demonstrated the implications of the poorly-understood shift in gas percolation threshold with improved gas percolation in reduced gravity. Finally, using...

  18. Two-dimensional discrete dislocation models of deformation in polycrystalline thin metal films on substrates

    International Nuclear Information System (INIS)

    Hartmaier, Alexander; Buehler, Markus J.; Gao, Huajian

    2005-01-01

    The time-dependent irreversible deformation of polycrystalline thin metal films on substrates is investigated using two-dimensional discrete dislocation dynamics models incorporating essential parameters determined from atomistic studies. The work is focused on the mechanical properties of uncapped films, where diffusive processes play an important role. The simulations incorporate dislocation climb along the grain boundary as well as conservative glide. Despite of severe limitations of the two-dimensional dislocation models, the simulation results are found to largely corroborate experimental findings on different dominant deformation mechanisms at different film thicknesses

  19. Computational modelling of multi-cell migration in a multi-signalling substrate

    International Nuclear Information System (INIS)

    Mousavi, Seyed Jamaleddin; Doblaré, Manuel; Doweidar, Mohamed Hamdy

    2014-01-01

    Cell migration is a vital process in many biological phenomena ranging from wound healing to tissue regeneration. Over the past few years, it has been proven that in addition to cell–cell and cell-substrate mechanical interactions (mechanotaxis), cells can be driven by thermal, chemical and/or electrical stimuli. A numerical model was recently presented by the authors to analyse single cell migration in a multi-signalling substrate. That work is here extended to include multi-cell migration due to cell–cell interaction in a multi-signalling substrate under different conditions. This model is based on balancing the forces that act on the cell population in the presence of different guiding cues. Several numerical experiments are presented to illustrate the effect of different stimuli on the trajectory and final location of the cell population within a 3D heterogeneous multi-signalling substrate. Our findings indicate that although multi-cell migration is relatively similar to single cell migration in some aspects, the associated behaviour is very different. For instance, cell–cell interaction may delay single cell migration towards effective cues while increasing the magnitude of the average net cell traction force as well as the local velocity. Besides, the random movement of a cell within a cell population is slightly greater than that of single cell migration. Moreover, higher electrical field strength causes the cell slug to flatten near the cathode. On the other hand, as with single cell migration, the existence of electrotaxis dominates mechanotaxis, moving the cells to the cathode or anode pole located at the free surface. The numerical results here obtained are qualitatively consistent with related experimental works. (paper)

  20. 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.

  1. Accessory enzymes influence cellulase hydrolysis of the model substrate and the realistic lignocellulosic biomass.

    Science.gov (United States)

    Sun, Fubao Fuebiol; Hong, Jiapeng; Hu, Jinguang; Saddler, Jack N; Fang, Xu; Zhang, Zhenyu; Shen, Song

    2015-11-01

    The potential of cellulase enzymes in the developing and ongoing "biorefinery" industry has provided a great motivation to develop an efficient cellulase mixture. Recent work has shown how important the role that the so-called accessory enzymes can play in an effective enzymatic hydrolysis. In this study, three newest Novozymes Cellic CTec cellulase preparations (CTec 1/2/3) were compared to hydrolyze steam pretreated lignocellulosic substrates and model substances at an identical FPA loading. These cellulase preparations were found to display significantly different hydrolytic performances irrelevant with the FPA. And this difference was even observed on the filter paper itself when the FPA based assay was revisited. The analysis of specific enzyme activity in cellulase preparations demonstrated that different accessory enzymes were mainly responsible for the discrepancy of enzymatic hydrolysis between diversified substrates and various cellulases. Such the active role of accessory enzymes present in cellulase preparations was finally verified by supplementation with β-glucosidase, xylanase and lytic polysaccharide monooxygenases AA9. This paper provides new insights into the role of accessory enzymes, which can further provide a useful reference for the rational customization of cellulase cocktails in order to realize an efficient conversion of natural lignocellulosic substrates. Copyright © 2015 Elsevier Inc. All rights reserved.

  2. 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.

  3. Nuclear pool of phosphatidylinositol 4 phosphate 5 kinase 1α is modified by polySUMO-2 during apoptosis

    Energy Technology Data Exchange (ETDEWEB)

    Chakrabarti, Rajarshi; Bhowmick, Debajit; Bhargava, Varsha; Bhar, Kaushik; Siddhanta, Anirban, E-mail: asiddhanto@yahoo.com

    2013-09-20

    Highlights: •Nuclear pool of PIP5K is SUMOylated. •Enhancement of SUMOylated nuclear PIP5K during apoptosis. •Nuclear PIP5K is modified by polySUMO-1 during apoptosis. •Nuclear PIP5K is modified by polySUMO-2 chain during apoptosis. -- Abstract: Phosphatidylinositol 4 phosphate 5 kinase 1α (PIP5K) is mainly localized in the cytosol and plasma membrane. Studies have also indicated its prominent association with nuclear speckles. The exact nature of this nuclear pool of PIP5K is not clear. Using biochemical and microscopic techniques, we have demonstrated that the nuclear pool of PIP5K is modified by SUMO-1 in HEK-293 cells stably expressing PIP5K. Moreover, this SUMOylated pool of PIP5K increased during apoptosis. PolySUMO-2 chain conjugated PIP5K was detected by pull-down experiment using affinity-tagged RNF4, a polySUMO-2 binding protein, during late apoptosis.

  4. Intense Resistance Exercise Promotes the Acute and Transient Nuclear Translocation of Small Ubiquitin-Related Modifier (SUMO-1 in Human Myofibres

    Directory of Open Access Journals (Sweden)

    Sebastian Gehlert

    2016-04-01

    Full Text Available Protein sumoylation is a posttranslational modification triggered by cellular stress. Because general information concerning the role of small ubiquitin-related modifier (SUMO proteins in adult skeletal muscle is sparse, we investigated whether SUMO-1 proteins will be subjected to time-dependent changes in their subcellular localization in sarcoplasmic and nuclear compartments of human type I and II skeletal muscle fibers in response to acute stimulation by resistance exercise (RE. Skeletal muscle biopsies were taken at baseline (PRE, 15, 30, 60, 240 min and 24 h post RE from 6 male subjects subjected to a single bout of one-legged knee extensions. SUMO-1 localization was determined via immunohistochemistry and confocal laser microscopy. At baseline SUMO-1 was localized in perinuclear regions of myonuclei. Within 15 and up to 60 min post exercise, nuclear SUMO-1 localization was significantly increased (p < 0.01, declining towards baseline levels within 240 min post exercise. Sarcoplasmic SUMO-1 localization was increased at 15 min post exercise in type I and up to 30 min post RE in type II myofibres. The changing localization of SUMO-1 proteins acutely after intense muscle contractions points to a role for SUMO proteins in the acute regulation of the skeletal muscle proteome after exercise.

  5. Ubiquitin-specific Protease 11 (USP11) Deubiquitinates Hybrid Small Ubiquitin-like Modifier (SUMO)-Ubiquitin Chains to Counteract RING Finger Protein 4 (RNF4)

    DEFF Research Database (Denmark)

    Hendriks, Ivo A; Schimmel, Joost; Eifler, Karolin

    2015-01-01

    of RNF4 as a counterbalancing factor. In response to DNA damage induced by methyl methanesulfonate, USP11 could counteract RNF4 to inhibit the dissolution of nuclear bodies. Thus, we provide novel insight into cross-talk between ubiquitin and SUMO and uncover USP11 and RNF4 as a balanced SUMO...

  6. 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.

  7. 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

  8. 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.

  9. Dynamic modelling of substrate degradation for urban wastewater treatment by sequencing batch reactor

    International Nuclear Information System (INIS)

    Dere, T.; Demirci, Y.; Cekim, M.

    2014-01-01

    This paper presents the dynamic modelling of substrate degradation for urban wastewater treatment by a pilot-scaled sequencing batch reactor including experimental data of a long-term experimental work performed at different operation conditions. During the study, pH, chemical oxygen demand (COD), total nitrogen (TN) and total phosphorus (TP) were measured to investigate SBR treatment performance. Optimum operation times were determined and kinetic constant (k) was calculated (0.60 h-1) with using experimental results for urban wastewater. The Model Simulation estimates were very good fit with the experimental data under organic loading degradation conditions model simulation predictions well match with the experimental results under disturbed organic loading conditions. (author)

  10. 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

    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...... 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...... in the AMBER 4.1 force field, applying a non-bonded approach and a full ion charge representation. Energy minimization of the apoenzymes yielded structures with distorted active sites, while reliable three-dimensional structures of the enzymes containing a substrate in active site were obtained. The structural...

  11. Functional Crosstalk between the PP2A and SUMO Pathways Revealed by Analysis of STUbL Suppressor, razor 1-1.

    Directory of Open Access Journals (Sweden)

    Minghua Nie

    2016-07-01

    Full Text Available Posttranslational modifications (PTMs provide dynamic regulation of the cellular proteome, which is critical for both normal cell growth and for orchestrating rapid responses to environmental stresses, e.g. genotoxins. Key PTMs include ubiquitin, the Small Ubiquitin-like MOdifier SUMO, and phosphorylation. Recently, SUMO-targeted ubiquitin ligases (STUbLs were found to integrate signaling through the SUMO and ubiquitin pathways. In general, STUbLs are recruited to target proteins decorated with poly-SUMO chains to ubiquitinate them and drive either their extraction from protein complexes, and/or their degradation at the proteasome. In fission yeast, reducing or preventing the formation of SUMO chains can circumvent the essential and DNA damage response functions of STUbL. This result indicates that whilst some STUbL "targets" have been identified, the crucial function of STUbL is to antagonize SUMO chain formation. Herein, by screening for additional STUbL suppressors, we reveal crosstalk between the serine/threonine phosphatase PP2A-Pab1B55 and the SUMO pathway. A hypomorphic Pab1B55 mutant not only suppresses STUbL dysfunction, but also mitigates the phenotypes associated with deletion of the SUMO protease Ulp2, or mutation of the STUbL cofactor Rad60. Together, our results reveal a novel role for PP2A-Pab1B55 in modulating SUMO pathway output, acting in parallel to known critical regulators of SUMOylation homeostasis. Given the broad evolutionary functional conservation of the PP2A and SUMO pathways, our results could be relevant to the ongoing attempts to therapeutically target these factors.

  12. SUMO regulates p21Cip1 intracellular distribution and with p21Cip1 facilitates multiprotein complex formation in the nucleolus upon DNA damage.

    Science.gov (United States)

    Brun, Sonia; Abella, Neus; Berciano, Maria T; Tapia, Olga; Jaumot, Montserrat; Freire, Raimundo; Lafarga, Miguel; Agell, Neus

    2017-01-01

    We previously showed that p21Cip1 transits through the nucleolus on its way from the nucleus to the cytoplasm and that DNA damage inhibits this transit and induces the formation of p21Cip1-containing intranucleolar bodies (INoBs). Here, we demonstrate that these INoBs also contain SUMO-1 and UBC9, the E2 SUMO-conjugating enzyme. Furthermore, whereas wild type SUMO-1 localized in INoBs, a SUMO-1 mutant, which is unable to conjugate with proteins, does not, suggesting the presence of SUMOylated proteins at INoBs. Moreover, depletion of the SUMO-conjugating enzyme UBC9 or the sumo hydrolase SENP2 changed p21Cip1 intracellular distribution. In addition to SUMO-1 and p21Cip1, cell cycle regulators and DNA damage checkpoint proteins, including Cdk2, Cyclin E, PCNA, p53 and Mdm2, and PML were also detected in INoBs. Importantly, depletion of UBC9 or p21Cip1 impacted INoB biogenesis and the nucleolar accumulation of the cell cycle regulators and DNA damage checkpoint proteins following DNA damage. The impact of p21Cip1 and SUMO-1 on the accumulation of proteins in INoBs extends also to CRM1, a nuclear exportin that is also important for protein translocation from the cytoplasm to the nucleolus. Thus, SUMO and p21Cip1 regulate the transit of proteins through the nucleolus, and that disruption of nucleolar export by DNA damage induces SUMO and p21Cip1 to act as hub proteins to form a multiprotein complex in the nucleolus.

  13. 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.

  14. Numerical modelling of adsorption of metallic particles on graphite substrate via molecular dynamics simulation

    International Nuclear Information System (INIS)

    Rafii-Tabar, H.

    1998-01-01

    A computer-based numerical modelling of the adsorption process of gas phase metallic particles on the surface of a graphite substrate has been performed via the application of molecular dynamics simulation method. The simulation related to an extensive STM-based experiment performed in this field, and reproduces part of the experimental results. Both two-body and many-body inter-atomic potentials have been employed. A Morse-type potential describing the metal-carbon interactions at the interface was specially formulated for this modelling. Intercalation of silver in graphite has been observed as well as the correct alignments of monomers, dimers and two-dimensional islands on the surface. (author)

  15. 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

    2018-06-01

    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.

  16. Diamond-like carbon films deposited on three-dimensional shape substrate model by liquid electrochemical technique

    International Nuclear Information System (INIS)

    He, Y.Y.; Zhang, G.F.; Zhao, Y.; Liu, D.D.; Cong, Y.; Buck, V.

    2015-01-01

    Diamond-like carbon (DLC) films were deposited on three-dimensional (3D) shape substrate model by electrolysis of 2-propanol solution at low temperature (60 °C). This 3D shape model was composed of a horizontally aligned stainless steel wafer and vertically aligned stainless steel rods. Morphology and microstructure of the films were analyzed by scanning electron microscopy (SEM), atomic force microscopy (AFM) and Raman spectroscopy, respectively. The results suggested there were only differences in film uniformity and thickness for two kinds of samples. The hydrogenated amorphous carbon films deposited on horizontally aligned substrate were smooth and homogeneous. And the film thickness of DLC films gained on the vertical substrates decreased along vertical direction. It is believed that bubble formation could enhance nucleation on the wetted capillary area. This experiment shows that deposition of DLC films by liquid phase deposition on 3D shape conductive substrates is possible. - Highlights: • DLC film is expected to be deposited on complex surface/shape substrate. • DLC film is deposited on 3D shape substrate by liquid electrochemical method. • Horizontal substrate is covered by smooth and homogeneous DLC films. • Film thickness decreases along vertical direction due to boiling effect

  17. Diamond-like carbon films deposited on three-dimensional shape substrate model by liquid electrochemical technique

    Energy Technology Data Exchange (ETDEWEB)

    He, Y.Y. [Institute of Nano-photonics, School of Physics and Materials Engineering, Dalian Nationalities University, 116600 Dalian (China); Zhang, G.F. [School of Materials Science and Engineering, Dalian University of Technology, 116024, Dalian China (China); Zhao, Y.; Liu, D.D. [Institute of Nano-photonics, School of Physics and Materials Engineering, Dalian Nationalities University, 116600 Dalian (China); Cong, Y., E-mail: congyan@ciomp.ac.cn [Institute of Nano-photonics, School of Physics and Materials Engineering, Dalian Nationalities University, 116600 Dalian (China); Buck, V. [Thin Film Technology Group, Faculty of Physics, University Duisburg-Essen and CeNIDE, 47057 Duisburg (Germany)

    2015-09-01

    Diamond-like carbon (DLC) films were deposited on three-dimensional (3D) shape substrate model by electrolysis of 2-propanol solution at low temperature (60 °C). This 3D shape model was composed of a horizontally aligned stainless steel wafer and vertically aligned stainless steel rods. Morphology and microstructure of the films were analyzed by scanning electron microscopy (SEM), atomic force microscopy (AFM) and Raman spectroscopy, respectively. The results suggested there were only differences in film uniformity and thickness for two kinds of samples. The hydrogenated amorphous carbon films deposited on horizontally aligned substrate were smooth and homogeneous. And the film thickness of DLC films gained on the vertical substrates decreased along vertical direction. It is believed that bubble formation could enhance nucleation on the wetted capillary area. This experiment shows that deposition of DLC films by liquid phase deposition on 3D shape conductive substrates is possible. - Highlights: • DLC film is expected to be deposited on complex surface/shape substrate. • DLC film is deposited on 3D shape substrate by liquid electrochemical method. • Horizontal substrate is covered by smooth and homogeneous DLC films. • Film thickness decreases along vertical direction due to boiling effect.

  18. 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.

  19. Proof of concept for turbulence measurements with the RPAS SUMO during the BLLAST campaign

    Science.gov (United States)

    Båserud, Line; Reuder, Joachim; Jonassen, Marius O.; Kral, Stephan T.; Paskyabi, Mostafa B.; Lothon, Marie

    2016-10-01

    The micro-RPAS (remotely piloted aircraft system) SUMO (Small Unmanned Meteorological Observer) equipped with a five-hole-probe (5HP) system for turbulent flow measurements was operated in 49 flight missions during the BLLAST (Boundary-Layer Late Afternoon and Sunset Turbulence) field campaign in 2011. Based on data sets from these flights, we investigate the potential and limitations of airborne velocity variance and TKE (turbulent kinetic energy) estimations by an RPAS with a take-off weight below 1 kg. The integration of the turbulence probe in the SUMO system was still in an early prototype stage during this campaign, and therefore extensive post-processing of the data was required. In order to be able to calculate the three-dimensional wind vector, flow probe measurements were first synchronized with the autopilot's attitude and velocity data. Clearly visible oscillations were detected in the resulting vertical velocity, w, even after correcting for the aircraft motion. The oscillations in w were identified as the result of an internal time shift between the inertial measurement unit (IMU) and the GPS sensors, leading to insufficient motion correction, especially for the vertical wind component, causing large values of σw. Shifting the IMU 1-1.5 s forward in time with respect to the GPS yields a minimum for σw and maximum covariance between the IMU pitch angle and the GPS climb angle. The SUMO data show a good agreement to sonic anemometer data from a 60 m tower for σu, but show slightly higher values for σv and σw. Vertical TKE profiles, obtained from consecutive flight legs at different altitudes, show reasonable results, both with respect to the overall TKE level and the temporal variation. A thorough discussion of the methods used and the identified uncertainties and limitations of the system for turbulence measurements is included and should help the developers and users of other systems with similar problems.

  20. 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?

  1. 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

    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...

  2. 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.

  3. Temporal and SUMO-specific SUMOylation contribute to the dynamics of Polo-like kinase 1 (PLK1) and spindle integrity during mouse oocyte meiosis.

    Science.gov (United States)

    Feitosa, Weber Beringui; Hwang, KeumSil; Morris, Patricia L

    2018-02-15

    During mammalian meiosis, Polo-like kinase 1 (PLK1) is essential during cell cycle progression. In oocyte maturation, PLK1 expression is well characterized but timing of posttranslational modifications regulating its activity and subcellular localization are less clear. Small ubiquitin-related modifier (SUMO) posttranslational modifier proteins have been detected in mammalian gametes but their precise function during gametogenesis is largely unknown. In the present paper we report for mouse oocytes that both PLK1 and phosphorylated PLK1 undergo SUMOylation in meiosis II (MII) oocytes using immunocytochemistry, immunoprecipitation and in vitro SUMOylation assays. At MII, PLK1 is phosphorylated at threonine-210 and serine-137. MII oocyte PLK1 and phosphorylated PLK1 undergo SUMOylation by SUMO-1, -2 and -3 as shown by individual in vitro assays. Using these assays, forms of phosphorylated PLK1 normalized to PLK1 increased significantly and correlated with SUMOylated PLK1 levels. During meiotic progression and maturation, SUMO-1-SUMOylation of PLK1 is involved in spindle formation whereas SUMO-2/3-SUMOylation may regulate PLK1 activity at kinetochore-spindle attachment sites. Microtubule integrity is required for PLK1 localization with SUMO-1 but not with SUMO-2/3. Inhibition of SUMOylation disrupts proper meiotic bipolar spindle organization and spindle-kinetochore attachment. The data show that both temporal and SUMO-specific-SUMOylation play important roles in orchestrating functional dynamics of PLK1 during mouse oocyte meiosis, including subcellular compartmentalization. Copyright © 2018 Elsevier Inc. All rights reserved.

  4. Modeling enzymatic hydrolysis of lignocellulosic substrates using confocal fluorescence microscopy I: filter paper cellulose.

    Science.gov (United States)

    Luterbacher, Jeremy S; Moran-Mirabal, Jose M; Burkholder, Eric W; Walker, Larry P

    2015-01-01

    Enzymatic hydrolysis is one of the critical steps in depolymerizing lignocellulosic biomass into fermentable sugars for further upgrading into fuels and/or chemicals. However, many studies still rely on empirical trends to optimize enzymatic reactions. An improved understanding of enzymatic hydrolysis could allow research efforts to follow a rational design guided by an appropriate theoretical framework. In this study, we present a method to image cellulosic substrates with complex three-dimensional structure, such as filter paper, undergoing hydrolysis under conditions relevant to industrial saccharification processes (i.e., temperature of 50°C, using commercial cellulolytic cocktails). Fluorescence intensities resulting from confocal images were used to estimate parameters for a diffusion and reaction model. Furthermore, the observation of a relatively constant bound enzyme fluorescence signal throughout hydrolysis supported our modeling assumption regarding the structure of biomass during hydrolysis. The observed behavior suggests that pore evolution can be modeled as widening of infinitely long slits. The resulting model accurately predicts the concentrations of soluble carbohydrates obtained from independent saccharification experiments conducted in bulk, demonstrating its relevance to biomass conversion work. © 2014 Wiley Periodicals, Inc.

  5. Heterogeneous nucleation on convex spherical substrate surfaces: A rigorous thermodynamic formulation of Fletcher's classical model and the new perspectives derived.

    Science.gov (United States)

    Qian, Ma; Ma, Jie

    2009-06-07

    Fletcher's spherical substrate model [J. Chem. Phys. 29, 572 (1958)] is a basic model for understanding the heterogeneous nucleation phenomena in nature. However, a rigorous thermodynamic formulation of the model has been missing due to the significant complexities involved. This has not only left the classical model deficient but also likely obscured its other important features, which would otherwise have helped to better understand and control heterogeneous nucleation on spherical substrates. This work presents a rigorous thermodynamic formulation of Fletcher's model using a novel analytical approach and discusses the new perspectives derived. In particular, it is shown that the use of an intermediate variable, a selected geometrical angle or pseudocontact angle between the embryo and spherical substrate, revealed extraordinary similarities between the first derivatives of the free energy change with respect to embryo radius for nucleation on spherical and flat substrates. Enlightened by the discovery, it was found that there exists a local maximum in the difference between the equivalent contact angles for nucleation on spherical and flat substrates due to the existence of a local maximum in the difference between the shape factors for nucleation on spherical and flat substrate surfaces. This helps to understand the complexity of the heterogeneous nucleation phenomena in a practical system. Also, it was found that the unfavorable size effect occurs primarily when R<5r( *) (R: radius of substrate and r( *): critical embryo radius) and diminishes rapidly with increasing value of R/r( *) beyond R/r( *)=5. This finding provides a baseline for controlling the size effects in heterogeneous nucleation.

  6. Uranium sorption to natural substrates-insights provided by isotope exchange, selective extraction and surface complexation modelling approaches

    International Nuclear Information System (INIS)

    Waite, T.D.; Payne T.E.; Davis, J.A.

    1993-01-01

    An extensive experimental program has been conducted over the last three years into the interaction of U(VI) with both single oxides and clays and complex natural substrates from the weathered zone in the vicinity of a uranium ore body in northern Australia. While iron oxides have frequently been considered to account for much of the uptake on such natural substrates, the results of laboratory open-quotes pH edgeclose quotes studies and of isotope exchange and selective extraction studies suggest that other phases must also play a significant role in controlling the partitioning of U(VI) between solid and solution phases. Supporting studies on kaolinite, the dominant clay in this system, provide insight into the most appropriate method of modelling the interaction of U(VI) with these natural substrates. The problems still remaining in adequately describing sorption of radionuclides and trace elements to complex natural substrates are discussed

  7. 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

  8. MEL-18 interacts with HSF2 and the SUMO E2 UBC9 to inhibit HSF2 sumoylation.

    Science.gov (United States)

    Zhang, Jie; Goodson, Michael L; Hong, Yiling; Sarge, Kevin D

    2008-03-21

    In a previous study we found that sumoylation of the DNA-binding protein heat shock factor 2 (HSF2) is up-regulated during mitosis, but the mechanism that mediates this regulation was unknown. Here we show that HSF2 interacts with the polycomb protein MEL-18, that this interaction decreases during mitosis, and that overexpression and RNA interference-mediated reduction of MEL-18 result in decreased and increased HSF2 sumoylation, respectively. Other results suggest that MEL-18 may also function to inhibit the sumoylation of other cellular proteins. The results also show that MEL-18 is able to interact with the small ubiquitin-like modifier (SUMO) ubiquitin carrier protein (E2) enzyme UBC9 and that MEL-18 inhibits the ability of UBC9 to transfer the SUMO protein to target proteins. Together, the results in this work suggest a mechanism in which MEL-18 bound to HSF2 inhibits its sumoylation by binding to and inhibiting the activity of UBC9 enzymes in the vicinity of HSF2. These results provide an explanation for how mitotic HSF2 sumoylation is regulated and suggest that MEL-18, in contrast to the sumoylation-stimulating activities of the polycomb protein PC2, actually functions like an anti-SUMO ubiquitin-protein isopeptide ligase (E3), interacting both with HSF2 and the SUMO E2 UBC9 but acting to inhibit UBC9 activity to decrease sumoylation of a target protein, in this case that of HSF2.

  9. 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...

  10. 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.

  11. 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

  12. 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

  13. 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.

  14. 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.

  15. A preliminary study of the relation between adsorption and CP-MAS-NMR characteristics of fused silica model substrates

    NARCIS (Netherlands)

    Scholten, A.B.; Janssen, J.G.M.; Haan, de J.W.; Cramers, C.A.M.G.; Sandra, P.J.F.; Devos, G.; Sandra, P.

    1993-01-01

    The fumed silica model substrate Aerosil was trimethylsilylated to different extents and studied by the combination of IGC and 29Si CP-MAS-NMR. Dihydroxydisiloxane groups were shown to be chemically more reactive than monohydroxytrisiloxane groups. Chromatographic experiments showed that these

  16. Structure of a SUMO-binding-motif mimic bound to Smt3p–Ubc9p: conservation of a noncovalent Ubiquitin-like protein–E2 complex as a platform for selective interactions within a SUMO pathway

    Science.gov (United States)

    Duda, David M.; van Waardenburg, Robert C. A. M.; Borg, Laura A.; McGarity, Sierra; Nourse, Amanda; Waddell, M. Brett; Bjornsti, Mary-Ann; Schulman, Brenda A.

    2007-01-01

    Summary The SUMO ubiquitin-like proteins play regulatory roles in cell division, transcription, DNA repair, and protein subcellular localization. Paralleling other ubiquitin-like proteins, SUMO proteins are proteolytically processed to maturity, conjugated to targets by E1-E2-E3 cascades, and subsequently recognized by specific downstream effectors containing a SUMO-binding motif (SBM). SUMO and its E2 from the budding yeast S. cerevisiae, Smt3p and Ubc9p, are encoded by essential genes. Here we describe the 1.9 Å resolution crystal structure of a noncovalent Smt3p–Ubc9p complex. Unexpectedly, a heterologous portion of the crystallized complex derived from the expression construct mimics an SBM, and binds Smt3p in a manner resembling SBM binding to human SUMO family members. In the complex, Smt3p binds a surface distal from Ubc9's catalytic cysteine. The structure implies that a single molecule of Smt3p cannot bind concurrently to both the noncovalent binding site and the catalytic cysteine of a single Ubc9p molecule. However, formation of higher-order complexes can occur, where a single Smt3p covalently linked to one Ubc9p's catalytic cysteine also binds noncovalently to another molecule of Ubc9p. Comparison with other structures from the SUMO pathway suggests that formation of the noncovalent Smt3p–Ubc9p complex occurs mutually exclusively with many other Smt3p and Ubc9p interactions in the conjugation cascade. By contrast, high-resolution insights into how Smt3p–Ubc9p can also interact with downstream recognition machineries come from contacts with the SBM mimic. Interestingly, the overall architecture of the Smt3p–Ubc9p complex is strikingly similar to recent structures from the ubiquitin pathway. The results imply that noncovalent ubiquitin-like protein–E2 complexes are conserved platforms, which function as parts of larger assemblies involved many protein post-translational regulatory pathways. PMID:17475278

  17. 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.

  18. Coxsackievirus B5 induced apoptosis of HeLa cells: Effects on p53 and SUMO

    International Nuclear Information System (INIS)

    Gomes, Rogerio; Guerra-Sa, Renata; Arruda, Eurico

    2010-01-01

    Coxsackievirus B5 (CVB5), a human enterovirus of the family Picornaviridae, is a frequent cause of acute and chronic human diseases. The pathogenesis of enteroviral infections is not completely understood, and the fate of the CVB5-infected cell has a pivotal role in this process. We have investigated the CVB5-induced apoptosis of HeLa cells and found that it happens by the intrinsic pathway by a mechanism dependent on the ubiquitin-proteasome system, associated with nuclear aggregation of p53. Striking redistribution of both SUMO and UBC9 was noted at 4 h post-infection, simultaneously with a reduction in the levels of the ubiquitin-ligase HDM2. Taken together, these results suggest that CVB5 infection of HeLa cells elicit the intrinsic pathway of apoptosis by MDM2 degradation and p53 activation, destabilizing protein sumoylation, by a mechanism that is dependent on a functional ubiquitin-proteasome system.

  19. 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

  20. Functions of Ubiquitin and SUMO in DNA Replication and Replication Stress

    Science.gov (United States)

    García-Rodríguez, Néstor; Wong, Ronald P.; Ulrich, Helle D.

    2016-01-01

    Complete and faithful duplication of its entire genetic material is one of the essential prerequisites for a proliferating cell to maintain genome stability. Yet, during replication DNA is particularly vulnerable to insults. On the one hand, lesions in replicating DNA frequently cause a stalling of the replication machinery, as most DNA polymerases cannot cope with defective templates. This situation is aggravated by the fact that strand separation in preparation for DNA synthesis prevents common repair mechanisms relying on strand complementarity, such as base and nucleotide excision repair, from working properly. On the other hand, the replication process itself subjects the DNA to a series of hazardous transformations, ranging from the exposure of single-stranded DNA to topological contortions and the generation of nicks and fragments, which all bear the risk of inducing genomic instability. Dealing with these problems requires rapid and flexible responses, for which posttranslational protein modifications that act independently of protein synthesis are particularly well suited. Hence, it is not surprising that members of the ubiquitin family, particularly ubiquitin itself and SUMO, feature prominently in controlling many of the defensive and restorative measures involved in the protection of DNA during replication. In this review we will discuss the contributions of ubiquitin and SUMO to genome maintenance specifically as they relate to DNA replication. We will consider cases where the modifiers act during regular, i.e., unperturbed stages of replication, such as initiation, fork progression, and termination, but also give an account of their functions in dealing with lesions, replication stalling and fork collapse. PMID:27242895

  1. Ebola Zaire virus blocks type I interferon production by exploiting the host SUMO modification machinery.

    Directory of Open Access Journals (Sweden)

    Tsung-Hsien Chang

    2009-06-01

    Full Text Available Ebola Zaire virus is highly pathogenic for humans, with case fatality rates approaching 90% in large outbreaks in Africa. The virus replicates in macrophages and dendritic cells (DCs, suppressing production of type I interferons (IFNs while inducing the release of large quantities of proinflammatory cytokines. Although the viral VP35 protein has been shown to inhibit IFN responses, the mechanism by which it blocks IFN production has not been fully elucidated. We expressed VP35 from a mouse-adapted variant of Ebola Zaire virus in murine DCs by retroviral gene transfer, and tested for IFN transcription upon Newcastle Disease virus (NDV infection and toll-like receptor signaling. We found that VP35 inhibited IFN transcription in DCs following these stimuli by disabling the activity of IRF7, a transcription factor required for IFN transcription. By yeast two-hybrid screens and coimmunoprecipitation assays, we found that VP35 interacted with IRF7, Ubc9 and PIAS1. The latter two are the host SUMO E2 enzyme and E3 ligase, respectively. VP35, while not itself a SUMO ligase, increased PIAS1-mediated SUMOylation of IRF7, and repressed Ifn transcription. In contrast, VP35 did not interfere with the activation of NF-kappaB, which is required for induction of many proinflammatory cytokines. Our findings indicate that Ebola Zaire virus exploits the cellular SUMOylation machinery for its advantage and help to explain how the virus overcomes host innate defenses, causing rapidly overwhelming infection to produce a syndrome resembling fulminant septic shock.

  2. 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.

  3. Molecular and neurochemical substrates of the audiogenic seizure strains: The GASH:Sal model.

    Science.gov (United States)

    Prieto-Martín, Ana I; Aroca-Aguilar, J Daniel; Sánchez-Sánchez, Francisco; Muñoz, Luis J; López, Dolores E; Escribano, Julio; de Cabo, Carlos

    2017-06-01

    Animal models of audiogenic epilepsy are useful tools to understand the mechanisms underlying human reflex epilepsies. There is accumulating evidence regarding behavioral, anatomical, electrophysiological, and genetic substrates of audiogenic seizure strains, but there are still aspects concerning their neurochemical basis that remain to be elucidated. Previous studies have shown the involved of γ-amino butyric acid (GABA) in audiogenic seizures. The aim of our research was to clarify the role of the GABAergic system in the generation of epileptic seizures in the genetic audiogenic seizure-prone hamster (GASH:Sal) strain. We studied the K + /Cl - cotransporter KCC2 and β2-GABAA-type receptor (GABAAR) and β3-GABAAR subunit expressions in the GASH:Sal both at rest and after repeated sound-induced seizures in different brain regions using the Western blot technique. We also sequenced the coding region for the KCC2 gene both in wild- type and GASH:Sal hamsters. Lower expression of KCC2 protein was found in GASH:Sal when compared with controls at rest in several brain areas: hippocampus, cortex, cerebellum, hypothalamus, pons-medulla, and mesencephalon. Repeated induction of seizures caused a decrease in KCC2 protein content in the inferior colliculus and hippocampus and an increase in the pons-medulla. When compared to controls, the basal β 2 -GABA A R subunit in the GASH:Sal was overexpressed in the inferior colliculus, rest of the mesencephalon, and cerebellum, whereas basal β 3 subunit levels were lower in the inferior colliculus and rest of the mesencephalon. Repeated seizures increased β2 both in the inferior colliculus and in the hypothalamus and β 3 in the hypothalamus. No differences in the KCC2 gene-coding region were found between GASH:Sal and wild-type hamsters. These data indicate that GABAergic system functioning is impaired in the GASH:Sal strain, and repeated seizures seem to aggravate this dysfunction. These results have potential clinical

  4. 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.

  5. 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.

  6. 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

  7. Numerical modeling of the destruction of steel plates with a gradient substrate

    Science.gov (United States)

    Orlov, M. Yu.; Glazyrin, V. P.; Orlov, Yu. N.

    2017-10-01

    The paper presents the results of numerical simulation of the shock loading process of steel barriers with a gradient substrate. In an elastic plastic axisymmetric statement, a shock is simulated along the normal in the range of initial velocities up to 300 m / s. A range of initial velocities was revealed, in which the presence of a substrate "saved" the obstacle from spallation. New tasks were announced to deepen scientific knowledge about the behavior of unidirectional gradient barriers at impact. The results of calculations are obtained in the form of graphs, calculated configurations of the "impact - barrier" and tables.

  8. Uncovering SUMOylation Dynamics during Cell-Cycle Progression Reveals FoxM1 as a Key Mitotic SUMO Target Protein

    DEFF Research Database (Denmark)

    Schimmel, Joost; Eifler, Karolin; Sigurdsson, Jón Otti

    2014-01-01

    Loss of small ubiquitin-like modification (SUMOylation) in mice causes genomic instability due to the missegregation of chromosomes. Currently, little is known about the identity of relevant SUMO target proteins that are involved in this process and about global SUMOylation dynamics during cell......-cycle progression. We performed a large-scale quantitative proteomics screen to address this and identified 593 proteins to be SUMO-2 modified, including the Forkhead box transcription factor M1 (FoxM1), a key regulator of cell-cycle progression and chromosome segregation. SUMOylation of FoxM1 peaks during G2 and M...... relieving FoxM1 autorepression. Cells deficient for FoxM1 SUMOylation showed increased levels of polyploidy. Our findings contribute to understanding the role of SUMOylation during cell-cycle progression....

  9. 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.

  10. Modelling of passive heating for replication of sub-micron patterns in optical disk substrates

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Youngmin; Bae, Jaecheol; Kim, Hongmin; Kang, Shinill [School of Mechanical Engineering, Yonsei University, 134 Shinchon-dong, Seodaemoon-ku, Seoul (Korea, Republic of)

    2004-05-07

    The transcribability of pit or land groove structures in replicating an optical disk substrate greatly affects the performance of a high-density optical disk. However, a solidified layer generated during the polymer filling worsens transcribability because the solidified layer prevents the polymer melt from filling the sub-micron patterns. Therefore, the development of the solidified layer during the filling stage of injection moulding must be delayed. For this delay, passive heating through an insulation layer has been used. In the present study, to examine the development of the solidified layer, delayed by passive heating, the flow of the polymer melt with passive heating was analysed. Passive heating delayed markedly the development of the solidified layer, reduced the viscosity of the polymer melt, and increased the fluidity of the polymer melt in the vicinity of the stamper surface with the sub-micron patterns. As a result, we predict that passive heating can improve the transcribability of an optical disk substrate. To verify our prediction, we fabricated an optical disk substrate by using passive heating of a mould and measured the transcribability of an optical disk substrate.

  11. Modelling of passive heating for replication of sub-micron patterns in optical disk substrates

    International Nuclear Information System (INIS)

    Kim, Youngmin; Bae, Jaecheol; Kim, Hongmin; Kang, Shinill

    2004-01-01

    The transcribability of pit or land groove structures in replicating an optical disk substrate greatly affects the performance of a high-density optical disk. However, a solidified layer generated during the polymer filling worsens transcribability because the solidified layer prevents the polymer melt from filling the sub-micron patterns. Therefore, the development of the solidified layer during the filling stage of injection moulding must be delayed. For this delay, passive heating through an insulation layer has been used. In the present study, to examine the development of the solidified layer, delayed by passive heating, the flow of the polymer melt with passive heating was analysed. Passive heating delayed markedly the development of the solidified layer, reduced the viscosity of the polymer melt, and increased the fluidity of the polymer melt in the vicinity of the stamper surface with the sub-micron patterns. As a result, we predict that passive heating can improve the transcribability of an optical disk substrate. To verify our prediction, we fabricated an optical disk substrate by using passive heating of a mould and measured the transcribability of an optical disk substrate

  12. 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

  13. 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.

  14. End-joining inhibition at telomeres requires the translocase and polySUMO-dependent ubiquitin ligase Uls1.

    Science.gov (United States)

    Lescasse, Rachel; Pobiega, Sabrina; Callebaut, Isabelle; Marcand, Stéphane

    2013-03-20

    In eukaryotes, permanent inhibition of the non-homologous end joining (NHEJ) repair pathway at telomeres ensures that chromosome ends do not fuse. In budding yeast, binding of Rap1 to telomere repeats establishes NHEJ inhibition. Here, we show that the Uls1 protein is required for the maintenance of NHEJ inhibition at telomeres. Uls1 protein is a non-essential Swi2/Snf2-related translocase and a Small Ubiquitin-related Modifier (SUMO)-Targeted Ubiquitin Ligase (STUbL) with unknown targets. Loss of Uls1 results in telomere-telomere fusions. Uls1 requirement is alleviated by the absence of poly-SUMO chains and by rap1 alleles lacking SUMOylation sites. Furthermore, Uls1 limits the accumulation of Rap1 poly-SUMO conjugates. We propose that one of Uls1 functions is to clear non-functional poly-SUMOylated Rap1 molecules from telomeres to ensure the continuous efficiency of NHEJ inhibition. Since Uls1 is the only known STUbL with a translocase activity, it can be the general molecular sweeper for the clearance of poly-SUMOylated proteins on DNA in eukaryotes.

  15. The effect of the physical properties of the substrate on the kinetics of cell adhesion and crawling studied by an axisymmetric diffusion-energy balance coupled model.

    Science.gov (United States)

    Samadi-Dooki, Aref; Shodja, Hossein M; Malekmotiei, Leila

    2015-05-14

    In this paper an analytical approach to study the effect of the substrate physical properties on the kinetics of adhesion and motility behavior of cells is presented. Cell adhesion is mediated by the binding of cell wall receptors and substrate's complementary ligands, and tight adhesion is accomplished by the recruitment of the cell wall binders to the adhesion zone. The binders' movement is modeled as their axisymmetric diffusion in the fluid-like cell membrane. In order to preserve the thermodynamic consistency, the energy balance for the cell-substrate interaction is imposed on the diffusion equation. Solving the axisymmetric diffusion-energy balance coupled equations, it turns out that the physical properties of the substrate (substrate's ligand spacing and stiffness) have considerable effects on the cell adhesion and motility kinetics. For a rigid substrate with uniform distribution of immobile ligands, the maximum ligand spacing which does not interrupt adhesion growth is found to be about 57 nm. It is also found that as a consequence of the reduction in the energy dissipation in the isolated adhesion system, cell adhesion is facilitated by increasing substrate's stiffness. Moreover, the directional movement of cells on a substrate with gradients in mechanical compliance is explored with an extension of the adhesion formulation. It is shown that cells tend to move from soft to stiff regions of the substrate, but their movement is decelerated as the stiffness of the substrate increases. These findings based on the proposed theoretical model are in excellent agreement with the previous experimental observations.

  16. Nanostructure Formation by controlled dewetting on patterned substrates: A combined theoretical, modeling and experimental study.

    Science.gov (United States)

    Lu, Liang-Xing; Wang, Ying-Min; Srinivasan, Bharathi Madurai; Asbahi, Mohamed; Yang, Joel K W; Zhang, Yong-Wei

    2016-09-01

    We perform systematic two-dimensional energetic analysis to study the stability of various nanostructures formed by dewetting solid films deposited on patterned substrates. Our analytical results show that by controlling system parameters such as the substrate surface pattern, film thickness and wetting angle, a variety of equilibrium nanostructures can be obtained. Phase diagrams are presented to show the complex relations between these system parameters and various nanostructure morphologies. We further carry out both phase field simulations and dewetting experiments to validate the analytically derived phase diagrams. Good agreements between the results from our energetic analyses and those from our phase field simulations and experiments verify our analysis. Hence, the phase diagrams presented here provide guidelines for using solid-state dewetting as a tool to achieve various nanostructures.

  17. 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

  18. Substrate and metabolite diffusion within model medium for soft cheese in relation to growth of Penicillium camembertii.

    Science.gov (United States)

    Aldarf, Mazen; Fourcade, Florence; Amrane, Abdeltif; Prigent, Yves

    2006-08-01

    Penicillium camembertii was cultivated on a jellified peptone-lactate based medium to simulate the composition of Camembert cheese. Diffusional limitations due to substrate consumption were not involved in the linear growth recorded during culture, while nitrogen (peptone) limitation accounted for growth cessation. Examination of gradients confirmed that medium neutralization was the consequence of lactate consumption and ammonium production. The diffusion of the lactate assimilated from the core to the rind and that of the ammonium produced from the rind to the core was described by means of a diffusion/reaction model involving a partial linking of consumption or production to growth. The model matched experimental data throughout growth.

  19. 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

    described were: the growth-linked biodegradation of micropollutant at environmentally relevant concentrations; the effect of coincidental assimilable organic carbon substrates; and the effect of coincidental microbes that compete for assimilable organic carbon substrates. We used Monod kinetic models...... to describe substrate utilization and microbial growth rates for specific pesticide and degrader pairs. We then extended the model to include terms for utilization of assimilable organic carbon substrates by the specific degrader and coincidental microbes, growth on assimilable organic carbon substrates......, 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...

  20. 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

  1. Modeling of the substrate and product transfer coefficients for ethanol fermentation

    International Nuclear Information System (INIS)

    Zerajic, S.; Grbavcic, Z.; Savkovic-Stevanovic, J.

    2008-01-01

    The transfer phenomena of the substrate and product for ethanol fermentation with immobilized biocatalyst were investigated. Fermentation was carried out with a biocatalyst consisting of Ca-alginate gel in the form of two-layer spherical beads in anaerobic conditions. The determination of kinetic parameters was achieved by fitting bioreaction progress curves to the experimental data. The calculation of the diffusion coefficients was performed by numerical methods for experimental conditions. Finally, the glucose and ethanol transfer coefficients are defined and determined, using the effective diffusion coefficients. (Abstract Copyright [2008], Wiley Periodicals, Inc.)

  2. SUMO E3 ligase Mms21 prevents spontaneous DNA damage induced genome rearrangements.

    Directory of Open Access Journals (Sweden)

    Jason Liang

    2018-03-01

    Full Text Available Mms21, a subunit of the Smc5/6 complex, possesses an E3 ligase activity for the Small Ubiquitin-like MOdifier (SUMO. Here we show that the mms21-CH mutation, which inactivates Mms21 ligase activity, causes increased accumulation of gross chromosomal rearrangements (GCRs selected in the dGCR assay. These dGCRs are formed by non-allelic homologous recombination between divergent DNA sequences mediated by Rad52-, Rrm3- and Pol32-dependent break-induced replication. Combining mms21-CH with sgs1Δ caused a synergistic increase in GCRs rates, indicating the distinct roles of Mms21 and Sgs1 in suppressing GCRs. The mms21-CH mutation also caused increased rates of accumulating uGCRs mediated by breakpoints in unique sequences as revealed by whole genome sequencing. Consistent with the accumulation of endogenous DNA lesions, mms21-CH mutants accumulate increased levels of spontaneous Rad52 and Ddc2 foci and had a hyper-activated DNA damage checkpoint. Together, these findings support that Mms21 prevents the accumulation of spontaneous DNA lesions that cause diverse GCRs.

  3. Srs2 mediates PCNA-SUMO-dependent inhibition of DNA repair synthesis

    International Nuclear Information System (INIS)

    Burkovics, Peter; Sebesta, Marek; Kolesar, Peter; Sisakova, Alexandra; Marini, Victoria; Plault, Nicolas; Szukacsov, Valeria; Pinter, Lajos; Haracska, Lajos; Robert, Thomas; Kolesar, Peter; Gangloff, Serge; Krejci, Lumir

    2013-01-01

    Completion of DNA replication needs to be ensured even when challenged with fork progression problems or DNA damage. PCNA and its modifications constitute a molecular switch to control distinct repair pathways. In yeast, SUMOylated PCNA (S-PCNA) recruits Srs2 to sites of replication where Srs2 can disrupt Rad51 filaments and prevent homologous recombination (HR). We report here an unexpected additional mechanism by which S-PCNA and Srs2 block the synthesis-dependent extension of a recombination intermediate, thus limiting its potentially hazardous resolution in association with a cross-over. This new Srs2 activity requires the SUMO interaction motif at its C-terminus, but neither its translocase activity nor its interaction with Rad51. Srs2 binding to S-PCNA dissociates Polδ and Polη from the repair synthesis machinery, thus revealing a novel regulatory mechanism controlling spontaneous genome rearrangements. Our results suggest that cycling cells use the Siz1-dependent SUMOylation of PCNA to limit the extension of repair synthesis during template switch or HR and attenuate reciprocal DNA strand exchanges to maintain genome stability. (authors)

  4. Global-genome Nucleotide Excision Repair Controlled by Ubiquitin/Sumo Modifiers

    Directory of Open Access Journals (Sweden)

    Peter eRuethemann

    2016-04-01

    Full Text Available Global-genome nucleotide excision repair (GG-NER prevents genome instability by excising a wide range of structurally unrelated DNA base adducts and crosslinks induced by chemical carcinogens, ultraviolet (UV radiation or intracellular metabolic by-products. As a versatile damage sensor, xeroderma pigmentosum group C (XPC protein initiates this generic defense reaction by locating the damage and recruiting the subunits of a large lesion demarcation complex that, in turn, triggers the excision of aberrant DNA by endonucleases. In the very special case of a DNA repair response to UV radiation, the function of this XPC initiator is tightly controlled by the dual action of cullin-type CRL4DDB2 and sumo-targeted RNF111 ubiquitin ligases. This twofold protein ubiquitination system promotes GG-NER reactions by spatially and temporally regulating the interaction of XPC protein with damaged DNA across the nucleosome landscape of chromatin. In the absence of either CRL4DDB2 or RNF111, the DNA excision repair of UV lesions is inefficient, indicating that these two ubiquitin ligases play a critical role in mitigating the adverse biological effects of UV light in the exposed skin.

  5. 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.

  6. The modeling of ethanol production by Kluyveromyces marxianus using whey as substrate in continuous A-Stat bioreactors.

    Science.gov (United States)

    Gabardo, Sabrina; Pereira, Gabriela Feix; Rech, Rosane; Ayub, Marco Antônio Záchia

    2015-09-01

    We investigated the kinetics of whey bioconversion into ethanol by Kluyveromyces marxianus in continuous bioreactors using the "accelerostat technique" (A-stat). Cultivations using free and Ca-alginate immobilized cells were evaluated using two different acceleration rates (a). The kinetic profiles of these systems were modeled using four different unstructured models, differing in the expressions for the specific growth (μ) and substrate consumption rates (r s), taking into account substrate limitation and product inhibition. Experimental data showed that the dilution rate (D) directly affected cell physiology and metabolism. The specific growth rate followed the dilution rate (μ≈D) for the lowest acceleration rate (a = 0.0015 h(-2)), condition in which the highest ethanol yield (0.52 g g(-1)) was obtained. The highest acceleration rate (a = 0.00667 h(-2)) led to a lower ethanol yield (0.40 g g(-1)) in the system where free cells were used, whereas with immobilized cells ethanol yields increased by 23 % (0.49 g g(-1)). Among the evaluated models, Monod and Levenspiel combined with Ghose and Tyagi models were found to be more appropriate for describing the kinetics of whey bioconversion into ethanol. These results may be useful in scaling up the process for ethanol production from whey.

  7. Optimization of the selection process of the co-substrates for chicken manure fermentation using neural modeling

    Directory of Open Access Journals (Sweden)

    Lewicki Andrzej

    2016-01-01

    Full Text Available Intense development of research equipment leads directly to increasing cognitive abilities. However, along with the raising amount of data generated, the development of the techniques allowing the analysis is also essential. Currently, one of the most dynamically developing branch of computer science and mathematics are the Artificial Neural Networks (ANN. Their main advantage is very high ability to solve the regression and approximation issues. This paper presents the possibility of application of artificial intelligence methods to optimize the selection of co-substrates intended for methane fermentation of chicken manure. 4-layer MLP network has proven to be the optimal structure modeling the obtained empirical data.

  8. Systemic Delivery of a Glucosylceramide Synthase Inhibitor Reduces CNS Substrates and Increases Lifespan in a Mouse Model of Type 2 Gaucher Disease

    OpenAIRE

    Cabrera-Salazar, Mario A.; DeRiso, Matthew; Bercury, Scott D.; Li, Lingyun; Lydon, John T.; Weber, William; Pande, Nilesh; Cromwell, Mandy A.; Copeland, Diane; Leonard, John; Cheng, Seng H.; Scheule, Ronald K.

    2012-01-01

    Neuropathic Gaucher disease (nGD), also known as type 2 or type 3 Gaucher disease, is caused by a deficiency of the enzyme glucocerebrosidase (GC). This deficiency impairs the degradation of glucosylceramide (GluCer) and glucosylsphingosine (GluSph), leading to their accumulation in the brains of patients and mouse models of the disease. These accumulated substrates have been thought to cause the severe neuropathology and early death observed in patients with nGD and mouse models. Substrate a...

  9. 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......-recombination role, probably by stimulating the formation of recombination complexes. The fact that deletion of PIM suppresses the phenotypes of Srs2 lacking SIM suggests that proper balance between the anti-recombination PCNA-bound and pro-recombination pools of Srs2 is crucial. Notably, sumoylation of Srs2 itself...

  10. Multi-scale modeling for prediction of distributed cellular properties in response to substrate spatial gradients in a continuously run microreactor

    DEFF Research Database (Denmark)

    Lencastre Fernandes, Rita; Krühne, Ulrich; Nopens, Ingmar

    2012-01-01

    microbioreactor is simulated. A multiscale model consisting of the coupling of a population balance model, a kinetic model and a flow model was developed in order to predict simultaneously local concentrations of substrate (glucose), product (ethanol) and biomass, as well as the local cell size distributions....

  11. SUMO-modified insulin-like growth factor 1 receptor (IGF-1R) increases cell cycle progression and cell proliferation.

    Science.gov (United States)

    Lin, Yingbo; Liu, Hongyu; Waraky, Ahmed; Haglund, Felix; Agarwal, Prasoon; Jernberg-Wiklund, Helena; Warsito, Dudi; Larsson, Olle

    2017-10-01

    Increasing number of studies have shown nuclear localization of the insulin-like growth factor 1 receptor (nIGF-1R) in tumor cells and its links to adverse clinical outcome in various cancers. Any obvious cell physiological roles of nIGF-1R have, however, still not been disclosed. Previously, we reported that IGF-1R translocates to cell nucleus and modulates gene expression by binding to enhancers, provided that the receptor is SUMOylated. In this study, we constructed stable transfectants of wild type IGF1R (WT) and triple-SUMO-site-mutated IGF1R (TSM) using igf1r knockout mouse fibroblasts (R-). Cell clones (R-WT and R-TSM) expressing equal amounts of IGF-1R were selected for experiments. Phosphorylation of IGF-1R, Akt, and Erk upon IGF-1 stimulation was equal in R-WT and R-TSM. WT was confirmed to enter nuclei. TSM did also undergo nuclear translocation, although to a lesser extent. This may be explained by that TSM heterodimerizes with insulin receptor, which is known to translocate to cell nuclei. R-WT proliferated substantially faster than R-TSM, which did not differ significantly from the empty vector control. Upon IGF-1 stimulation G1-S-phase progression of R-WT increased from 12 to 38%, compared to 13 to 20% of R-TSM. The G1-S progression of R-WT correlated with increased expression of cyclin D1, A, and CDK2, as well as downregulation of p27. This suggests that SUMO-IGF-1R affects upstream mechanisms that control and coordinate expression of cell cycle regulators. Further studies to identify such SUMO-IGF-1R dependent mechanisms seem important. © 2017 The Authors. Journal of Cellular Physiology Published by Wiley Periodicals Inc.

  12. Bulk substrate porosity verification by applying Monte Carlo modeling and Castaing's formula using energy-dispersive x-rays

    Science.gov (United States)

    Yung, Lai Chin; Fei, Cheong Choke; Mandeep, Jit Singh; Amin, Nowshad; Lai, Khin Wee

    2015-11-01

    The leadframe fabrication process normally involves additional thin-metal layer plating on the bulk copper substrate surface for wire bonding purposes. Silver, tin, and copper flakes are commonly adopted as plating materials. It is critical to assess the density of the plated metal layer, and in particular to look for porosity or voids underneath the layer, which may reduce the reliability during high-temperature stress. A fast, reliable inspection technique is needed to assess the porosity or void weakness. To this end, the characteristics of x-rays generated from bulk samples were examined using an energy-dispersive x-ray (EDX) detector to examine the porosity percentage. Monte Carlo modeling was integrated with Castaing's formula to verify the integrity of the experimental data. Samples with different porosity percentages were considered to test the correlation between the intensity of the collected x-ray signal and the material density. To further verify the integrity of the model, conventional cross-sectional samples were also taken to observe the porosity percentage using Image J software measurement. A breakthrough in bulk substrate assessment was achieved by applying EDX for the first time to nonelemental analysis. The experimental data showed that the EDX features were not only useful for elemental analysis, but also applicable to thin-film metal layer thickness measurement and bulk material density determination. A detailed experiment was conducted using EDX to assess the plating metal layer and bulk material porosity.

  13. A simple, single-substrate model to interpret intra-annual stable isotope signals in tree-ring cellulose

    Science.gov (United States)

    Ogée, J.; Barbour, M. M.; Wingate, L.; Bert, D.; Bosc, A.; Stievenard, M.; Lambrot, C.; Pierre, M.; Bariac, T.; Dewar, R. C.

    2009-04-01

    High-resolution intra-annual measurements of the carbon and oxygen stable isotope composition of cellulose in annual tree rings (δ13Ccellulose and δ18Ocellulose, respectively) reveal well-defined seasonal patterns that could contain valuable records of past climate and tree function. Interpreting these signals is nonetheless complex because they not only record the signature of current assimilates, but also depend on carbon allocation dynamics within the trees. Here, we present a simple, single-substrate model for wood growth containing only 12 main parameters. The model is used to interpret an isotopic intra-annual chronology collected in an even-aged maritime pine plantation growing in the South-West of France, where climate, soil and flux variables were also monitored. The empirical δ13Ccellulose and δ18Ocellulose exhibit dynamic seasonal patterns, with clear differences between years and individuals, that are mostly captured by the model. In particular, the amplitude of both signals is reproduced satisfactorily as well as the sharp 18O enrichment at the beginning of 1997 and the less pronounced 13C and 18O depletion observed at the end of the latewood. Our results suggest that the single-substrate hypothesis is a good approximation for tree ring studies on Pinus pinaster, at least for the environmental conditions covered by this study. A sensitivity analysis revealed that, in the early wood, the model was particularly sensitive to the date when cell wall thickening begins (twt). We therefore propose to use the model to reconstruct time series of twt and explore how climate influences this key parameter of xylogenesis.

  14. Offshore Substrate

    Data.gov (United States)

    California Natural Resource Agency — 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...

  15. 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.

  16. 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

  17. 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

  18. 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

    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...

  19. 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.

  20. 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

  1. SUMO modification of Stra13 is required for repression of cyclin D1 expression and cellular growth arrest.

    Directory of Open Access Journals (Sweden)

    Yaju Wang

    Full Text Available Stra13, a basic helix-loop-helix (bHLH transcription factor is involved in myriad biological functions including cellular growth arrest, differentiation and senescence. However, the mechanisms by which its transcriptional activity and function are regulated remain unclear. In this study, we provide evidence that post-translational modification of Stra13 by Small Ubiquitin-like Modifier (SUMO dramatically potentiates its ability to transcriptionally repress cyclin D1 and mediate G(1 cell cycle arrest in fibroblast cells. Mutation of SUMO acceptor lysines 159 and 279 located in the C-terminal repression domain has no impact on nuclear localization; however, it abrogates association with the co-repressor histone deacetylase 1 (HDAC1, attenuates repression of cyclin D1, and prevents Stra13-mediated growth suppression. HDAC1, which promotes cellular proliferation and cell cycle progression, antagonizes Stra13 sumoylation-dependent growth arrest. Our results uncover an unidentified regulatory axis between Stra13 and HDAC1 in progression through the G(1/S phase of the cell cycle, and provide new mechanistic insights into regulation of Stra13-mediated transcriptional repression by sumoylation.

  2. SENP7 Potentiates cGAS Activation by Relieving SUMO-Mediated Inhibition of Cytosolic DNA Sensing.

    Directory of Open Access Journals (Sweden)

    Ye Cui

    2017-01-01

    Full Text Available Cyclic GMP-AMP (cGAMP synthase (cGAS, a.k.a. MB21D1, a cytosolic DNA sensor, catalyzes formation of the second messenger 2'3'-cGAMP that activates the stimulator of interferon genes (STING signaling. How the cGAS activity is modulated remains largely unknown. Here, we demonstrate that sentrin/SUMO-specific protease 7 (SENP7 interacted with and potentiated cGAS activation. The small ubiquitin-like modifier (SUMO was conjugated onto the lysine residues 335, 372 and 382 of cGAS, which suppressed its DNA-binding, oligomerization and nucleotidyl-transferase activities. SENP7 reversed this inhibition via catalyzing the cGAS de-SUMOylation. Consistently, silencing of SENP7 markedly impaired the IRF3-responsive gene expression induced by cGAS-STING axis. SENP7-knockdown mice were more susceptible to herpes simplex virus 1 (HSV-1 infection. SENP7 was significantly up-regulated in patients with SLE. Our study highlights the temporal modulation of the cGAS activity via dynamic SUMOylation, uncovering a novel mechanism for fine-tuning the STING signaling in innate immunity.

  3. SUMO-Modification of the La Protein Facilitates Binding to mRNA In Vitro and in Cells.

    Science.gov (United States)

    Kota, Venkatesh; Sommer, Gunhild; Durette, Chantal; Thibault, Pierre; van Niekerk, Erna A; Twiss, Jeffery L; Heise, Tilman

    2016-01-01

    The RNA-binding protein La is involved in several aspects of RNA metabolism including the translational regulation of mRNAs and processing of pre-tRNAs. Besides its well-described phosphorylation by Casein kinase 2, the La protein is also posttranslationally modified by the Small Ubiquitin-like MOdifier (SUMO), but the functional outcome of this modification has not been defined. The objective of this study was to test whether sumoylation changes the RNA-binding activity of La. Therefore, we established an in vitro sumoylation assay for recombinant human La and analyzed its RNA-binding activity by electrophoretic mobility shift assays. We identified two novel SUMO-acceptor sites within the La protein located between the RNA recognition motif 1 and 2 and we demonstrate for the first time that sumoylation facilitates the RNA-binding of La to small RNA oligonucleotides representing the oligopyrimidine tract (TOP) elements from the 5' untranslated regions (UTR) of mRNAs encoding ribosomal protein L22 and L37 and to a longer RNA element from the 5' UTR of cyclin D1 (CCND1) mRNA in vitro. Furthermore, we show by RNA immunoprecipitation experiments that a La mutant deficient in sumoylation has impaired RNA-binding activity in cells. These data suggest that modulating the RNA-binding activity of La by sumoylation has important consequences on its functionality.

  4. SUMO-Modification of the La Protein Facilitates Binding to mRNA In Vitro and in Cells.

    Directory of Open Access Journals (Sweden)

    Venkatesh Kota

    Full Text Available The RNA-binding protein La is involved in several aspects of RNA metabolism including the translational regulation of mRNAs and processing of pre-tRNAs. Besides its well-described phosphorylation by Casein kinase 2, the La protein is also posttranslationally modified by the Small Ubiquitin-like MOdifier (SUMO, but the functional outcome of this modification has not been defined. The objective of this study was to test whether sumoylation changes the RNA-binding activity of La. Therefore, we established an in vitro sumoylation assay for recombinant human La and analyzed its RNA-binding activity by electrophoretic mobility shift assays. We identified two novel SUMO-acceptor sites within the La protein located between the RNA recognition motif 1 and 2 and we demonstrate for the first time that sumoylation facilitates the RNA-binding of La to small RNA oligonucleotides representing the oligopyrimidine tract (TOP elements from the 5' untranslated regions (UTR of mRNAs encoding ribosomal protein L22 and L37 and to a longer RNA element from the 5' UTR of cyclin D1 (CCND1 mRNA in vitro. Furthermore, we show by RNA immunoprecipitation experiments that a La mutant deficient in sumoylation has impaired RNA-binding activity in cells. These data suggest that modulating the RNA-binding activity of La by sumoylation has important consequences on its functionality.

  5. Modeling the transport of chemical warfare agents and simulants in polymeric substrates for reactive decontamination

    Science.gov (United States)

    Pearl, Thomas; Mantooth, Brent; Varady, Mark; Willis, Matthew

    2014-03-01

    Chemical warfare agent simulants are often used for environmental testing in place of highly toxic agents. This work sets the foundation for modeling decontamination of absorbing polymeric materials with the focus on determining relationships between agents and simulants. The correlations of agents to simulants must consider the three way interactions in the chemical-material-decontaminant system where transport and reaction occur in polymer materials. To this end, diffusion modeling of the subsurface transport of simulants and live chemical warfare agents was conducted for various polymer systems (e.g., paint coatings) with and without reaction pathways with applied decontamination. The models utilized 1D and 2D finite difference diffusion and reaction models to simulate absorption and reaction in the polymers, and subsequent flux of the chemicals out of the polymers. Experimental data including vapor flux measurements and dynamic contact angle measurements were used to determine model input parameters. Through modeling, an understanding of the relationship of simulant to live chemical warfare agent was established, focusing on vapor emission of agents and simulants from materials.

  6. 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.

  7. Growth and lipid production of Umbelopsis isabellina on a solid substrate - Mechanistic modeling and validation

    NARCIS (Netherlands)

    Meeuwse, P.; Klok, A.J.; Haemers, S.; Tramper, J.; Rinzema, A.

    2012-01-01

    Microbial lipids are an interesting feedstock for biodiesel. Their production from agricultural waste streams by fungi cultivated in solid-state fermentation may be attractive, but the yield of this process is still quite low. In this article, a mechanistic model is presented that describes growth,

  8. 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.

  9. Translational rodent models of Korsakoff syndrome reveal the critical neuroanatomical substrates of memory dysfunction and recovery.

    Science.gov (United States)

    Savage, Lisa M; Hall, Joseph M; Resende, Leticia S

    2012-06-01

    Investigation of the amnesic disorder Korsakoff Syndrome (KS) has been vital in elucidating the critical brain regions involved in learning and memory. Although the thalamus and mammillary bodies are the primary sites of neuropathology in KS, functional deactivation of the hippocampus and certain cortical regions also contributes to the chronic cognitive dysfunction reported in KS. The rodent pyrithiamine-induced thiamine deficiency (PTD) model has been used to study the extent of hippocampal and cortical neuroadaptations in KS. In the PTD model, the hippocampus, frontal and retrosplenial cortical regions display loss of cholinergic innervation, decreases in behaviorally stimulated acetylcholine release and reductions in neurotrophins. While PTD treatment results in significant impairment in measures of spatial learning and memory, other cognitive processes are left intact and may be recruited to improve cognitive outcome. In addition, behavioral recovery can be stimulated in the PTD model by increasing acetylcholine levels in the medial septum, hippocampus and frontal cortex, but not in the retrosplenial cortex. These data indicate that although the hippocampus and frontal cortex are involved in the pathogenesis of KS, these regions retain neuroplasticity and may be critical targets for improving cognitive outcome in KS.

  10. 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.

  11. Mechanism-based population pharmacokinetic modelling in diabetes: vildagliptin as a tight binding inhibitor and substrate of dipeptidyl peptidase IV

    Science.gov (United States)

    Landersdorfer, Cornelia B; He, Yan-Ling; Jusko, William J

    2012-01-01

    AIMS To assess the pharmacokinetics of vildagliptin at different doses and build a mechanism-based population model that simultaneously describes vildagliptin pharmacokinetics and its effects on DPP-4 activity based on underlying physiology and biology. METHODS Vildagliptin concentrations and DPP-4 activity vs. time from 13 type 2 diabetic patients after oral vildagliptin 10, 25 or 100 mg and placebo twice daily for 28 days were co-modelled. NONMEM VI and S-ADAPT were utilized for population modelling. RESULTS A target-mediated drug disposition (TMDD) model accounting for capacity-limited high affinity binding of vildagliptin to DPP-4 in plasma and tissues had good predictive performance. Modelling the full time course of the vildagliptin-DPP-4 interaction suggested parallel vildagliptin dissociation from DPP-4 by a slow first-order process and hydrolysis by DPP-4 to an inactive metabolite as a disposition mechanism. Due to limited amounts of DPP-4, vildagliptin concentrations increased slightly more than dose proportionally. This newly proposed model and the parameter estimates are supported by published in vitro studies. Mean parameter estimates (inter-individual coefficient of variation) were: non-saturable clearance 36 l h−1 (25%), central volume of distribution 22 l (37%), half-life of dissociation from DPP-4 1.1 h (94%) and half-life of hydrolysis 6.3 h (81%). CONCLUSIONS Vildagliptin is both an inhibitor and substrate for DPP-4. By utilizing the TMDD approach, slow dissociation of vildagliptin from DPP-4 was found in patients and the half-life of hydrolysis by DPP-4 estimated. This model can be used to predict DPP-4 inhibition effects of other dosage regimens and be modified for other DPP-4 inhibitors to differentiate their properties. PMID:22442826

  12. Optical modelling of thin-film silicon solar cells deposited on textured substrates

    International Nuclear Information System (INIS)

    Krc, J.; Zeman, M.; Smole, F.; Topic, M.

    2004-01-01

    Optical modelling is used to investigate effects of light scattering in amorphous silicon and microcrystalline silicon solar cells. The role of enhanced haze parameter and different angular distribution function of scattered light is analyzed. Results of optical simulation show that enhanced haze parameter compared to that of Asahi U-type SnO 2 :F does not improve external quantum efficiency and short-circuit current density of amorphous silicon solar cell significantly, whereas for microcrystalline silicon solar cell the improvement is larger. Angular distribution function affects the external quantum efficiency and the short-circuit current density significantly

  13. 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).

  14. 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.

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

    International Nuclear Information System (INIS)

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

    2007-01-01

    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/A 2 = 1/R 2 + 1/S 2 . 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

  16. Shaping meiotic chromosomes with SUMO: a feedback loop controls the assembly of the synaptonemal complex in budding yeast

    Directory of Open Access Journals (Sweden)

    Hideo Tsubouchi

    2016-02-01

    Full Text Available The synaptonemal complex (SC is a meiosis-specific chromosomal structure in which homologous chromosomes are intimately linked through arrays of specialized proteins called transverse filaments (TF. Widely conserved in eukaryote meiosis, the SC forms during prophase I and is essential for accurate segregation of homologous chromosomes at meiosis I. However, the basic mechanism overlooking formation and regulation of the SC has been poorly understood. By using the budding yeast Saccharomyces cerevisiae, we recently showed that SC formation is controlled through the attachment of multiple molecules of small ubiquitin-like modifier (SUMO to a regulator of TF assembly. Intriguingly, this SUMOylation is activated by TF, implicating the involvement of a positive feedback loop in the control of SC assembly. We discuss the implication of this finding and possible involvement of a similar mechanism in regulating other processes.

  17. 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.

  18. A study of the adsorption activities of silanol surface structures on a fused silica model substrate by combining 29Si CP MAS NMR and inverse gas chromatographic data

    NARCIS (Netherlands)

    Scholten, A.B.; Janssen, J.G.M.; Haan, de J.W.; Cramers, C.A.

    1994-01-01

    The possibilities of inverse gas-solid chromatog. (IGC) in obtaining chromatog. data on fumed silica were examd. Aerosil A-200, a fused silica model substrate in 29Si NMR anal., was trimethylsilylated to different degrees. IGC was used to vary reproducibly det. the free specific energies of

  19. A model framework to describe growth-linked biodegradation of trace-level pollutants in the presence of coincidental carbon substrates and microbes.

    Science.gov (United States)

    Liu, Li; Helbling, Damian E; Kohler, Hans-Peter E; Smets, Barth F

    2014-11-18

    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, 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 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 described were: the growth-linked biodegradation of micropollutant at environmentally relevant concentrations; the effect of coincidental assimilable organic carbon substrates; and the effect of coincidental microbes that compete for assimilable organic carbon substrates. We used Monod kinetic models to describe substrate utilization and microbial growth rates for specific pesticide and degrader pairs. We then extended the model to include terms for utilization of assimilable organic carbon substrates by the specific degrader and coincidental microbes, growth on assimilable organic carbon substrates by the specific degrader and coincidental microbes, and endogenous metabolism. The proposed model framework enables interpretation and description of a range of experimental observations on micropollutant biodegradation. The model provides a useful tool to identify environmental conditions with respect to the occurrence of assimilable organic carbon and coincidental microbes that may result in enhanced or reduced micropollutant biodegradation.

  20. The tight binding model study of the role of band filling on the charge gap in graphene-on-substrate in paramagnetic state

    Science.gov (United States)

    Panda, Rudrashish; Sahu, Sivabrata; Rout, G. C.

    2017-05-01

    We communicate here a tight binding theoretical model study of the band filling effect on the charge gap in graphene-on-substrate. The Hamiltonian consists of nearest neighbor electron hopping and substrate induced gap. Besides this the Coulomb interaction is considered here within mean-field approximation in the paramagnetic limit. The electron occupancies at two sublattices are calculated by Green's function technique and are solved self consistently. Finally the charge gap i.e. Δ ¯=U [ - ] is calculated and computed numerically. The results are reported.

  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

    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...

  2. High-level SUMO-mediated fusion expression of ABP-dHC-cecropin A from multiple joined genes in Escherichia coli.

    Science.gov (United States)

    Zhang, Jiaxin; Movahedi, Ali; Wei, Zhiheng; Sang, Ming; Wu, Xiaolong; Wang, Mengyang; Wei, Hui; Pan, Huixin; Yin, Tongming; Zhuge, Qiang

    2016-09-15

    The antimicrobial peptide ABP-dHC-cecropin A is a small cationic peptide with potent activity against a wide range of bacterial species. Evidence of antifungal activity has also been suggested; however, evaluation of this peptide has been limited due to the low expression of cecropin proteins in Escherichia coli. To improve the expression level of ABP-dHC-cecropin A in E. coli, tandem repeats of the ABP-dHC-cecropin A gene were constructed and expressed as fusion proteins (SUMO-nABP-dHC-cecropin, n = 1, 2, 3, 4) via pSUMO-nABP-dHC-cecropin A vectors (n = 1, 2, 3, 4). Comparison of the expression levels of soluble SUMO-nABP-dHC-cecropin A fusion proteins (n = 1, 2, 3, 4) suggested that BL21 (DE3)/pSUMO-3ABP-dHC-cecropin A is an ideal recombinant strain for ABP-dHC-cecropin A production. Under the selected conditions of cultivation and isopropylthiogalactoside (IPTG) induction, the expression level of ABP-dHC-cecropin A was as high as 65 mg/L, with ∼21.3% of the fusion protein in soluble form. By large-scale fermentation, protein production reached nearly 300 mg/L, which is the highest yield of ABP-dHC-cecropin A reported to date. In antibacterial experiments, the efficacy was approximately the same as that of synthetic ABP-dHC-cecropin A. This method provides a novel and effective means of producing large amounts of ABP-dHC-cecropin A. Copyright © 2016 Elsevier Inc. All rights reserved.

  3. The nucleolar SUMO-specific protease SMT3IP1/SENP3 attenuates Mdm2-mediated p53 ubiquitination and degradation

    Energy Technology Data Exchange (ETDEWEB)

    Nishida, Tamotsu, E-mail: nishida@gene.mie-u.ac.jp [Department of Human Functional Genomics, Life Science Research Center, Mie University, 1577 Kurima-machiya, Tsu 514-8507 (Japan); Yamada, Yoshiji [Department of Human Functional Genomics, Life Science Research Center, Mie University, 1577 Kurima-machiya, Tsu 514-8507 (Japan)

    2011-03-11

    Research highlights: {yields} SMT3IP1 interacts with p53 and Mdm2, and desumoylates both proteins. {yields} SMT3IP1 competes with p53 for binding to the central acidic domain of Mdm2. {yields} SMT3IP1 binding to Mdm2 inhibits Mdm2-mediated p53 ubiquitination and degradation. {yields} We postulate that SMT3IP1 acts as a new regulator of the p53-Mdm2 pathway. -- Abstract: SUMO (small ubiquitin-like modifier) modification plays multiple roles in several cellular processes. Sumoylation is reversibly regulated by SUMO-specific proteases. SUMO-specific proteases have recently been implicated in cell proliferation and early embryogenesis, but the underlying mechanisms remain unknown. Here, we show that a nucleolar SUMO-specific protease, SMT3IP1/SENP3, controls the p53-Mdm2 pathway. We found that SMT3IP1 interacts with p53 and Mdm2, and desumoylates both proteins. Overexpression of SMT3IP1 in cells resulted in the accumulation of Mdm2 in the nucleolus and increased stability of the p53 protein. In addition, SMT3IP1 bound to the acidic domain of Mdm2, which also mediates the p53 interaction, and competed with p53 for binding. Increasing expression of SMT3IP1 suppressed Mdm2-mediated p53 ubiquitination and subsequent proteasomal degradation. Interestingly, the desumoylation activity of SMT3IP1 was not necessary for p53 stabilization. These results suggest that SMT3IP1 is a new regulator of the p53-Mdm2 pathway.

  4. The nucleolar SUMO-specific protease SMT3IP1/SENP3 attenuates Mdm2-mediated p53 ubiquitination and degradation

    International Nuclear Information System (INIS)

    Nishida, Tamotsu; Yamada, Yoshiji

    2011-01-01

    Research highlights: → SMT3IP1 interacts with p53 and Mdm2, and desumoylates both proteins. → SMT3IP1 competes with p53 for binding to the central acidic domain of Mdm2. → SMT3IP1 binding to Mdm2 inhibits Mdm2-mediated p53 ubiquitination and degradation. → We postulate that SMT3IP1 acts as a new regulator of the p53-Mdm2 pathway. -- Abstract: SUMO (small ubiquitin-like modifier) modification plays multiple roles in several cellular processes. Sumoylation is reversibly regulated by SUMO-specific proteases. SUMO-specific proteases have recently been implicated in cell proliferation and early embryogenesis, but the underlying mechanisms remain unknown. Here, we show that a nucleolar SUMO-specific protease, SMT3IP1/SENP3, controls the p53-Mdm2 pathway. We found that SMT3IP1 interacts with p53 and Mdm2, and desumoylates both proteins. Overexpression of SMT3IP1 in cells resulted in the accumulation of Mdm2 in the nucleolus and increased stability of the p53 protein. In addition, SMT3IP1 bound to the acidic domain of Mdm2, which also mediates the p53 interaction, and competed with p53 for binding. Increasing expression of SMT3IP1 suppressed Mdm2-mediated p53 ubiquitination and subsequent proteasomal degradation. Interestingly, the desumoylation activity of SMT3IP1 was not necessary for p53 stabilization. These results suggest that SMT3IP1 is a new regulator of the p53-Mdm2 pathway.

  5. 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.

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

    Science.gov (United States)

    Canelles, Sandra; Argente, Jesús; Barrios, Vicente

    2016-01-01

    ABSTRACT 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. PMID:27013528

  7. Evaluation of a biomimetic 3D substrate based on the Human Elastin-like Polypeptides (HELPs) model system for elastolytic activity detection.

    Science.gov (United States)

    Corich, Lucia; Busetti, Marina; Petix, Vincenzo; Passamonti, Sabina; Bandiera, Antonella

    2017-08-10

    Elastin is a fibrous protein that confers elasticity to tissues such as skin, arteries and lung. It is extensively cross-linked, highly hydrophobic and insoluble. Nevertheless, elastin can be hydrolysed by bacterial proteases in infectious diseases, resulting in more or less severe tissue damage. Thus, development of substrates able to reliably and specifically detect pathogen-secreted elastolytic activity is needed to improve the in vitro evaluation of the injury that bacterial proteases may provoke. In this work, two human biomimetic elastin polypeptides, HELP and HELP1, as well as the matrices derived from HELP, have been probed as substrates for elastolytic activity detection. Thirty strains of Pseudomonas aeruginosa isolated from cystic fibrosis patients were analyzed in parallel with standard substrates, to detect proteolytic and elastolytic activity. Results point to the HELP-based 3D matrix as an interesting biomimetic model of elastin to assess bacterial elastolytic activity in vitro. Moreover, this model substrate enables to further elucidate the mechanism underlying elastin degradation at molecular level, as well as to develop biomimetic material-based devices responsive to external stimuli. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. Wetting on structured substrates

    International Nuclear Information System (INIS)

    Dietrich, S; Popescu, M N; Rauscher, M

    2005-01-01

    Chemically patterned surfaces are of significant interest in the context of microfluidic applications, and miniaturization of such devices aims at generating structures on the nano-scale. Whereas on the micron scale purely macroscopic descriptions of liquid flow are valid, on the nanometre scale long-ranged inter-molecular interactions, thermal fluctuations such as capillary waves, and finally the molecular structure of the liquid become important. We discuss the most important conceptual differences between flow on chemically patterned substrates on the micron scale and on the nanometre scale, and formulate four design issues for nanofluidics related to channel width, channel separation, and channel bending radius. As a specific example of nano-scale transport we present a microscopic model for the dynamics of spreading of monolayers on homogeneous substrates. Kinetic Monte Carlo simulations of this model on a homogeneous substrate reveal a complex spatio-temporal structure of the extracted monolayer, which includes the emergence of interfaces and of scaling properties of density profiles. These features are discussed and rationalized within the corresponding continuum limit derived from the microscopic dynamics. The corresponding spreading behaviour on a patterned substrate is briefly addressed

  9. Systemic delivery of a glucosylceramide synthase inhibitor reduces CNS substrates and increases lifespan in a mouse model of type 2 Gaucher disease.

    Directory of Open Access Journals (Sweden)

    Mario A Cabrera-Salazar

    Full Text Available Neuropathic Gaucher disease (nGD, also known as type 2 or type 3 Gaucher disease, is caused by a deficiency of the enzyme glucocerebrosidase (GC. This deficiency impairs the degradation of glucosylceramide (GluCer and glucosylsphingosine (GluSph, leading to their accumulation in the brains of patients and mouse models of the disease. These accumulated substrates have been thought to cause the severe neuropathology and early death observed in patients with nGD and mouse models. Substrate accumulation is evident at birth in both nGD mouse models and humans affected with the most severe type of the disease. Current treatment of non-nGD relies on the intravenous delivery of recombinant human glucocerebrosidase to replace the missing enzyme or the administration of glucosylceramide synthase inhibitors to attenuate GluCer production. However, the currently approved drugs that use these mechanisms do not cross the blood brain barrier, and thus are not expected to provide a benefit for the neurological complications in nGD patients. Here we report the successful reduction of substrate accumulation and CNS pathology together with a significant increase in lifespan after systemic administration of a novel glucosylceramide synthase inhibitor to a mouse model of nGD. To our knowledge this is the first compound shown to cross the blood brain barrier and reduce substrates in this animal model while significantly enhancing its lifespan. These results reinforce the concept that systemically administered glucosylceramide synthase inhibitors could hold enhanced therapeutic promise for patients afflicted with neuropathic lysosomal storage diseases.

  10. Systemic delivery of a glucosylceramide synthase inhibitor reduces CNS substrates and increases lifespan in a mouse model of type 2 Gaucher disease.

    Science.gov (United States)

    Cabrera-Salazar, Mario A; Deriso, Matthew; Bercury, Scott D; Li, Lingyun; Lydon, John T; Weber, William; Pande, Nilesh; Cromwell, Mandy A; Copeland, Diane; Leonard, John; Cheng, Seng H; Scheule, Ronald K

    2012-01-01

    Neuropathic Gaucher disease (nGD), also known as type 2 or type 3 Gaucher disease, is caused by a deficiency of the enzyme glucocerebrosidase (GC). This deficiency impairs the degradation of glucosylceramide (GluCer) and glucosylsphingosine (GluSph), leading to their accumulation in the brains of patients and mouse models of the disease. These accumulated substrates have been thought to cause the severe neuropathology and early death observed in patients with nGD and mouse models. Substrate accumulation is evident at birth in both nGD mouse models and humans affected with the most severe type of the disease. Current treatment of non-nGD relies on the intravenous delivery of recombinant human glucocerebrosidase to replace the missing enzyme or the administration of glucosylceramide synthase inhibitors to attenuate GluCer production. However, the currently approved drugs that use these mechanisms do not cross the blood brain barrier, and thus are not expected to provide a benefit for the neurological complications in nGD patients. Here we report the successful reduction of substrate accumulation and CNS pathology together with a significant increase in lifespan after systemic administration of a novel glucosylceramide synthase inhibitor to a mouse model of nGD. To our knowledge this is the first compound shown to cross the blood brain barrier and reduce substrates in this animal model while significantly enhancing its lifespan. These results reinforce the concept that systemically administered glucosylceramide synthase inhibitors could hold enhanced therapeutic promise for patients afflicted with neuropathic lysosomal storage diseases.

  11. 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

    2018-05-01

    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 Elsevier Inc

  12. 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.

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

    Science.gov (United States)

    Wang, Kaishi; Zhang, Fangzhou; Bordia, Rajendra K

    2018-03-27

    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.

  14. 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.

  15. 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.

  16. 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.

  17. 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

  18. 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.

  19. 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.

  20. Dynamic mechanistic modeling of the multienzymatic one-pot reduction of dehydrocholic acid to 12-keto ursodeoxycholic acid with competing substrates and cofactors.

    Science.gov (United States)

    Sun, Boqiao; Hartl, Florian; Castiglione, Kathrin; Weuster-Botz, Dirk

    2015-01-01

    Ursodeoxycholic acid (UDCA) is a bile acid which is used as pharmaceutical for the treatment of several diseases, such as cholesterol gallstones, primary sclerosing cholangitis or primary biliary cirrhosis. A potential chemoenzymatic synthesis route of UDCA comprises the two-step reduction of dehydrocholic acid to 12-keto-ursodeoxycholic acid (12-keto-UDCA), which can be conducted in a multienzymatic one-pot process using 3α-hydroxysteroid dehydrogenase (3α-HSDH), 7β-hydroxysteroid dehydrogenase (7β-HSDH), and glucose dehydrogenase (GDH) with glucose as cosubstrate for the regeneration of cofactor. Here, we present a dynamic mechanistic model of this one-pot reduction which involves three enzymes, four different bile acids, and two different cofactors, each with different oxidation states. In addition, every enzyme faces two competing substrates, whereas each bile acid and cofactor is formed or converted by two different enzymes. First, the kinetic mechanisms of both HSDH were identified to follow an ordered bi-bi mechanism with EBQ-type uncompetitive substrate inhibition. Rate equations were then derived for this mechanism and for mechanisms describing competing substrates. After the estimation of the model parameters of each enzyme independently by progress curve analyses, the full process model of a simple batch-process was established by coupling rate equations and mass balances. Validation experiments of the one-pot multienzymatic batch process revealed high prediction accuracy of the process model and a model analysis offered important insight to the identification of optimum reaction conditions. © 2015 American Institute of Chemical Engineers.

  1. 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.

  2. 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.

  3. Mutually exclusive STAT1 modifications identified by Ubc9/substrate dimerization-dependent SUMOylation.

    Science.gov (United States)

    Zimnik, Susan; Gaestel, Matthias; Niedenthal, Rainer

    2009-03-01

    Post-translational modifications control the physiological activity of the signal transducer and activator of transcription STAT1. While phosphorylation at tyrosine Y701 is a prerequisite for STAT1 dimerization, its SUMOylation represses the transcriptional activity. Recently, we have demonstrated that SUMOylation at lysine K703 inhibits the phosphorylation of nearby localized Y701 of STAT1. Here, we analysed the influence of phosphorylation of Y701 on SUMOylation of K703 in vivo. For that reason, an Ubc9/substrate dimerization-dependent SUMOylation (USDDS) system was developed, which consists of fusions of the SUMOylation substrate and of the SUMO-conjugating enzyme Ubc9 to the chemically activatable heterodimerization domains FKBP and FRB, respectively. When FKBP fusion proteins of STAT1, p53, CRSP9, FOS, CSNK2B, HES1, TCF21 and MYF6 are coexpressed with Ubc9-FRB, treatment of HEK293 cells with the rapamycin-related dimerizer compound AP21967 induces SUMOylation of these proteins in vivo. For STAT1-FKBP and p53-FKBP we show that this SUMOylation takes place at their specific SUMOylation sites in vivo. Using USDDS, we then demonstrate that STAT1 phosphorylation at Y701 induced by interferon-beta treatment inhibits SUMOylation of K703 in vivo. Thus, pY701 and SUMO-K703 of STAT1 represent mutually exclusive modifications, which prevent signal integration at this molecule and probably ensure the existence of differentially modified subpopulations of STAT1 necessary for its regulated nuclear cytoplasmic activation/inactivation cycle.

  4. SUMO Ligase Protein Inhibitor of Activated STAT1 (PIAS1) Is a Constituent Promyelocytic Leukemia Nuclear Body Protein That Contributes to the Intrinsic Antiviral Immune Response to Herpes Simplex Virus 1.

    Science.gov (United States)

    Brown, James R; Conn, Kristen L; Wasson, Peter; Charman, Matthew; Tong, Lily; Grant, Kyle; McFarlane, Steven; Boutell, Chris

    2016-07-01

    Aspects of intrinsic antiviral immunity are mediated by promyelocytic leukemia nuclear body (PML-NB) constituent proteins. During herpesvirus infection, these antiviral proteins are independently recruited to nuclear domains that contain infecting viral genomes to cooperatively promote viral genome silencing. Central to the execution of this particular antiviral response is the small ubiquitin-like modifier (SUMO) signaling pathway. However, the participating SUMOylation enzymes are not fully characterized. We identify the SUMO ligase protein inhibitor of activated STAT1 (PIAS1) as a constituent PML-NB protein. We show that PIAS1 localizes at PML-NBs in a SUMO interaction motif (SIM)-dependent manner that requires SUMOylated or SUMOylation-competent PML. Following infection with herpes simplex virus 1 (HSV-1), PIAS1 is recruited to nuclear sites associated with viral genome entry in a SIM-dependent manner, consistent with the SIM-dependent recruitment mechanisms of other well-characterized PML-NB proteins. In contrast to that of Daxx and Sp100, however, the recruitment of PIAS1 is enhanced by PML. PIAS1 promotes the stable accumulation of SUMO1 at nuclear sites associated with HSV-1 genome entry, whereas the accumulation of other evaluated PML-NB proteins occurs independently of PIAS1. We show that PIAS1 cooperatively contributes to HSV-1 restriction through mechanisms that are additive to those of PML and cooperative with those of PIAS4. The antiviral mechanisms of PIAS1 are counteracted by ICP0, the HSV-1 SUMO-targeted ubiquitin ligase, which disrupts the recruitment of PIAS1 to nuclear domains that contain infecting HSV-1 genomes through mechanisms that do not directly result in PIAS1 degradation. Adaptive, innate, and intrinsic immunity cooperatively and efficiently restrict the propagation of viral pathogens. Intrinsic immunity mediated by constitutively expressed cellular proteins represents the first line of intracellular defense against infection. PML

  5. 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

  6. 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.

  7. Re-investigation of slip rate along the southern part of the Sumatran Fault Zone using SuMo GPS network

    Science.gov (United States)

    Hermawan, I.; Lubis, A. M.; Sahputra, R.; Hill, E.; Sieh, K.; Feng, L.; Salman, R.; Hananto, N.

    2015-12-01

    The Sumatran Fault Zone (SFZ) accommodates a significant component of the strike-slip motion of oblique convergence along the Sumatra subduction zone. Previous studies have suggested that the slip rates of the SFZ increase from south to north. However, recent work shows that the slip rates may not vary along the SFZ [Bradley et al., 2015]. New data are needed to help confirm these results, and to assess slip-rate variability and fault segmentation in more detail. This information is vital for seismic hazard assessment for the region. We have therefore installed and operated the SuMo (Sumatran Fault Monitoring) network, a dense GPS campaign network focused around the SFZ. From 2013-2015 we selected and installed 32 GPS monuments over the southern part of the SFZ. The network comprises of three transects. The first transect is around the location of the great 1900 earthquake, at the Musi segment. Two transects cover the Manna segment, which saw its last great earthquake in 1893, and the Kumering segment, which saw two great earthquakes in 1933 (M 7.5) and 1994 (M 7.0). We have now conducted three GPS campaign surveys for these stations (3-4 days of measurement for each occupation site), and established 5 semi-permanent cGPS stations in the area. The processed data show that the campaigns sites are still too premature to be used for estimating slip rates, but from the preliminary results for the semi-permanent stations we may see our first signal of deformation. More data from future survey campaigns will help us to estimated revised slip rates. In addition to the science goals for our project, we are this year starting a project called "SuMo Goes to School," which will aim to disseminate information on our science to the schools that house the SuMo GPS stations. The SuMo project also achieves capacity building by training students from Bengkulu University in geodesy and campaign GPS survey techniques.

  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. 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.

  10. The use of LeuT as a model in elucidating binding sites for substrates and inhibitors in neurotransmitter transporters

    DEFF Research Database (Denmark)

    Løland, Claus Juul

    2015-01-01

    Background: The mammalian neurotransmitter transporters are complex proteins playing a central role in synaptic transmission between neurons by rapid reuptake of neurotransmitters. The proteins which transport dopamine, noradrenaline and serotonin belong to the Neurotransmitter:Sodium Symporters...... (NSS). Due to their important role, dysfunctions are associated with several psychiatric and neurological diseases and they also serve as targets for a wide range of therapeutic and illicit drugs. Despite the central physiological and pharmacological importance, direct evidence on structure......–function relationships on mammalian NSS proteins has so far been unsuccessful. The crystal structure of the bacterial NSS protein, LeuT, has been a turning point in structural investigations. Scope of review: To provide an update on what is known about the binding sites for substrates and inhibitors in the Leu...

  11. Real-time optical modelling and investigation of inorganic nano-layer growth onto flexible polymeric substrates

    International Nuclear Information System (INIS)

    Laskarakis, A.; Georgiou, D.; Logothetidis, S.

    2010-01-01

    A major factor for the achievement of the desirable performance, efficiency and lifetime of flexible organic electronic devices is the optimization of the encapsulation layers that protect the device active layers by atmospheric gas molecule permeation. The active layers consisted of small molecule and/or polymer organic semiconductors as well as the organic conductors need to be encapsulated into a transparent medium that will provide the necessary protection and maintain their charge generation and transport characteristics. The encapsulation layers are generally consisted of inorganic thin films (silicon oxide-SiO x and aluminium oxide-AlO x ) deposited onto the polymeric substrates, such as PolyEthylene Terephthalate (PET). In this work, in situ and real-time Spectroscopic Ellipsometry in the ultraviolet spectral region has been implemented in order to investigate the growth of inorganic SiO x and AlO x nano-layers onto PET flexible polymeric substrates as well as the PET/inorganic interface effects during the early stages of growth. The analysis of the pseudodielectric function that was measured in real-time in very short time scales (in the order of hundreds of ms) has provided detailed information on the time evolution of the thickness and deposition rate of the inorganic nano-layers during their growth process as well as on their optical and electronic properties. This work proposes a methodology for using real-time optical monitoring technique with the aim to tailor and control the functionality of these materials for application in flexible electronic devices.

  12. Evaluation of a hierarchy of models reveals importance of substrate limitation for predicting carbon dioxide and methane exchange in restored wetlands

    Science.gov (United States)

    Oikawa, P. Y.; Jenerette, G. D.; Knox, S. H.; Sturtevant, C.; Verfaillie, J.; Dronova, I.; Poindexter, C. M.; Eichelmann, E.; Baldocchi, D. D.

    2017-01-01

    Wetlands and flooded peatlands can sequester large amounts of carbon (C) and have high greenhouse gas mitigation potential. There is growing interest in financing wetland restoration using C markets; however, this requires careful accounting of both CO2 and CH4 exchange at the ecosystem scale. Here we present a new model, the PEPRMT model (Peatland Ecosystem Photosynthesis Respiration and Methane Transport), which consists of a hierarchy of biogeochemical models designed to estimate CO2 and CH4 exchange in restored managed wetlands. Empirical models using temperature and/or photosynthesis to predict respiration and CH4 production were contrasted with a more process-based model that simulated substrate-limited respiration and CH4 production using multiple carbon pools. Models were parameterized by using a model-data fusion approach with multiple years of eddy covariance data collected in a recently restored wetland and a mature restored wetland. A third recently restored wetland site was used for model validation. During model validation, the process-based model explained 70% of the variance in net ecosystem exchange of CO2 (NEE) and 50% of the variance in CH4 exchange. Not accounting for high respiration following restoration led to empirical models overestimating annual NEE by 33-51%. By employing a model-data fusion approach we provide rigorous estimates of uncertainty in model predictions, accounting for uncertainty in data, model parameters, and model structure. The PEPRMT model is a valuable tool for understanding carbon cycling in restored wetlands and for application in carbon market-funded wetland restoration, thereby advancing opportunity to counteract the vast degradation of wetlands and flooded peatlands.

  13. 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.

  14. Predicting the effect of cytochrome P450 inhibitors on substrate drugs: analysis of physiologically based pharmacokinetic modeling submissions to the US Food and Drug Administration.

    Science.gov (United States)

    Wagner, Christian; Pan, Yuzhuo; Hsu, Vicky; Grillo, Joseph A; Zhang, Lei; Reynolds, Kellie S; Sinha, Vikram; Zhao, Ping

    2015-01-01

    The US Food and Drug Administration (FDA) has seen a recent increase in the application of physiologically based pharmacokinetic (PBPK) modeling towards assessing the potential of drug-drug interactions (DDI) in clinically relevant scenarios. To continue our assessment of such approaches, we evaluated the predictive performance of PBPK modeling in predicting cytochrome P450 (CYP)-mediated DDI. This evaluation was based on 15 substrate PBPK models submitted by nine sponsors between 2009 and 2013. For these 15 models, a total of 26 DDI studies (cases) with various CYP inhibitors were available. Sponsors developed the PBPK models, reportedly without considering clinical DDI data. Inhibitor models were either developed by sponsors or provided by PBPK software developers and applied with minimal or no modification. The metric for assessing predictive performance of the sponsors' PBPK approach was the R predicted/observed value (R predicted/observed = [predicted mean exposure ratio]/[observed mean exposure ratio], with the exposure ratio defined as [C max (maximum plasma concentration) or AUC (area under the plasma concentration-time curve) in the presence of CYP inhibition]/[C max or AUC in the absence of CYP inhibition]). In 81 % (21/26) and 77 % (20/26) of cases, respectively, the R predicted/observed values for AUC and C max ratios were within a pre-defined threshold of 1.25-fold of the observed data. For all cases, the R predicted/observed values for AUC and C max were within a 2-fold range. These results suggest that, based on the submissions to the FDA to date, there is a high degree of concordance between PBPK-predicted and observed effects of CYP inhibition, especially CYP3A-based, on the exposure of drug substrates.

  15. Signal sensitivity of alternating current potential drop measurement for crack detection of conductive substrate with tunable coating materials through finite element modeling

    International Nuclear Information System (INIS)

    Rao, Simha Sandeep; Zhao, Huijuan; Liu, Ming; Peng, Fei; Zhang, Bo

    2016-01-01

    We adopt a finite element numerical modeling approach to investigate the electromagnetic coupling effect of two parallel electric conductors with tunable electric conductivity σ and magnetic permeability μ . For two parallel conductors C and S ( μ C   ⋅  σ C   ≤  μ S   ⋅  σ S ), we find that the shape of current density profile of conductor S is dependent on the product of μ C   ⋅  σ C , while the magnitude is determined by the AC current frequency f . On the other hand, the frequency f affects not only the shape but also the magnitude of the current density profile of conductor C. We further adopt a coplanar model to investigate the signal sensitivity of alternating current potential drop (ACPD) measurement for both surface crack and inner crack detection. We find that with modified coating materials (lower electric conductivity and higher magnetic permeability, compared with the substrate material properties), the crack detection signal sensitivity can be greatly enhanced for both the cracks within the coating and at the coating/substrate interface, where cracks are most commonly encountered in real situations. (paper)

  16. 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.

  17. 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.

  18. EXTRAÇÃO DO SUMO DA BETA VULGARIS COMO ALTERNATIVA SUSTENTÁVEL NA PRODUÇÃO DE TINTAS

    Directory of Open Access Journals (Sweden)

    Gabriela Camila Ribeiro

    2017-04-01

    Full Text Available O trabalho apresenta a extração do sumo da beterraba a partir de um método simples ao mais complexo, sendo utilizado apenas a pigmentação arrocheada para a fabricação de tinta natural, sem corantes para que não deteriore o material. Teremos a infusão da beterraba, deixando que aconteça naturalmente por minutos, dias ou semanas, para que possamos obter um pigmento completamente natural, utilizando também um aparelho, cujo nome é soxhlet, tendo a propriedade de extrair o sumo de lipídios em apenas algumas horas, dependendo do tamanho que seja o lipídio utilizado. Após a pigmentação fez necessário a adição de um aglutinante com objetivo de formar uma liga. Tento como resultado uma tinta sem corantes e não prejudicial ao meio ambiente.

  19. 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.

  20. 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

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

    KAUST Repository

    Ling, Yu; Zhang, Chunyu; Chen, Tong; Hao, Huaiqing; Liu, Peng; Bressan, Ray A.; Hasegawa, Paul M.; Jin, Jing Bo; Lin, Jinxing

    2012-01-01

    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

  2. Improved management of lysosomal glucosylceramide levels in a mouse model of type 1 Gaucher disease using enzyme and substrate reduction therapy.

    Science.gov (United States)

    Marshall, John; McEachern, Kerry Anne; Chuang, Wei-Lien; Hutto, Elizabeth; Siegel, Craig S; Shayman, James A; Grabowski, Greg A; Scheule, Ronald K; Copeland, Diane P; Cheng, Seng H

    2010-06-01

    Gaucher disease is caused by a deficiency of the lysosomal enzyme glucocerebrosidase (acid beta-glucosidase), with consequent cellular accumulation of glucosylceramide (GL-1). The disease is managed by intravenous administrations of recombinant glucocerebrosidase (imiglucerase), although symptomatic patients with mild to moderate type 1 Gaucher disease for whom enzyme replacement therapy (ERT) is not an option may also be treated by substrate reduction therapy (SRT) with miglustat. To determine whether the sequential use of both ERT and SRT may provide additional benefits, we compared the relative pharmacodynamic efficacies of separate and sequential therapies in a murine model of Gaucher disease (D409V/null). As expected, ERT with recombinant glucocerebrosidase was effective in reducing the burden of GL-1 storage in the liver, spleen, and lung of 3-month-old Gaucher mice. SRT using a novel inhibitor of glucosylceramide synthase (Genz-112638) was also effective, albeit to a lesser degree than ERT. Animals administered recombinant glucocerebrosidase and then Genz-112638 showed the lowest levels of GL-1 in all the visceral organs and a reduced number of Gaucher cells in the liver. This was likely because the additional deployment of SRT following enzyme therapy slowed the rate of reaccumulation of GL-1 in the affected organs. Hence, in patients whose disease has been stabilized by intravenously administered recombinant glucocerebrosidase, orally administered SRT with Genz-112638 could potentially be used as a convenient maintenance therapy. In patients naïve to treatment, ERT followed by SRT could potentially accelerate clearance of the offending substrate.

  3. The influence of a brittle Cr interlayer on the deformation behavior of thin Cu films on flexible substrates: Experiment and model

    International Nuclear Information System (INIS)

    Marx, Vera M.; Toth, Florian; Wiesinger, Andreas; Berger, Julia; Kirchlechner, Christoph; Cordill, Megan J.; Fischer, Franz D.; Rammerstorfer, Franz G.; Dehm, Gerhard

    2015-01-01

    Thin metal films deposited on polymer substrates are used in flexible electronic devices such as flexible displays or printed memories. They are often fabricated as complicated multilayer structures. Understanding the mechanical behavior of the interface between the metal film and the substrate as well as the process of crack formation under global tension is important for producing reliable devices. In the present work, the deformation behavior of copper films (50–200 nm thick), bonded to polyimide directly or via a 10 nm chromium interlayer, is investigated by experimental analysis and computational simulations. The influence of the various copper film thicknesses and the usage of a brittle interlayer on the crack density as well as on the stress magnitude in the copper after saturation of the cracking process are studied with in situ tensile tests in a synchrotron and under an atomic force microscope. From the computational point of view, the evolution of the crack pattern is modeled as a stochastic process via finite element based cohesive zone simulations. Both, experiments and simulations show that the chromium interlayer dominates the deformation behavior. The interlayer forms cracks that induce a stress concentration in the overlying copper film. This behavior is more pronounced in the 50 nm than in the 200 nm copper films

  4. Nonergodic dynamics of the two-dimensional random-phase sine-Gordon model: Applications to vortex-glass arrays and disordered-substrate surfaces

    International Nuclear Information System (INIS)

    Cule, D.; Shapir, Y.

    1995-01-01

    The dynamics of the random-phase sine-Gordon model, which describes two-dimensional vortex-glass arrays and crystalline surfaces on disordered substrates, is investigated using the self-consistent Hartree approximation. The fluctuation-dissipation theorem is violated below the critical temperature T c for large time t>t * where t * diverges in the thermodynamic limit. While above T c the averaged autocorrelation function diverges as Tln(t), for T c it approaches a finite value q * ∼1/(T c -T) as q(t)=q * -c(t/t * ) -ν (for t→t * ) where ν is a temperature-dependent exponent. On larger time scales t>t * the dynamics becomes nonergodic. The static correlations behave as ∼Tln|rvec x| for T>T c and for T c when x * with ξ * ∼exp{A/(T c -T)}. For scales x>ξ * , they behave as ∼m -1 Tln|rvec x| where m∼T/T c near T c , in general agreement with the variational replica-symmetry breaking approach and with recent simulations of the disordered-substrate surface. For strong coupling the transition becomes first order

  5. Bayesian inference of substrate properties from film behavior

    International Nuclear Information System (INIS)

    Aggarwal, R; Demkowicz, M J; Marzouk, Y M

    2015-01-01

    We demonstrate that by observing the behavior of a film deposited on a substrate, certain features of the substrate may be inferred with quantified uncertainty using Bayesian methods. We carry out this demonstration on an illustrative film/substrate model where the substrate is a Gaussian random field and the film is a two-component mixture that obeys the Cahn–Hilliard equation. We construct a stochastic reduced order model to describe the film/substrate interaction and use it to infer substrate properties from film behavior. This quantitative inference strategy may be adapted to other film/substrate systems. (paper)

  6. 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

  7. 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.

  8. Intracerebroventricular delivery of glucocerebrosidase reduces substrates and increases lifespan in a mouse model of neuronopathic Gaucher disease.

    Science.gov (United States)

    Cabrera-Salazar, M A; Bercury, S D; Ziegler, R J; Marshall, J; Hodges, B L; Chuang, W-L; Pacheco, J; Li, L; Cheng, S H; Scheule, R K

    2010-10-01

    Gaucher disease is caused by a deficit in the enzyme glucocerebrosidase. As a consequence, degradation of the glycolipids glucosylceramide (GluCer) and glucosylsphingosine (GluSph) is impaired, and their subsequent buildup can lead to significant pathology and early death. Type 1 Gaucher patients can be treated successfully with intravenous replacement enzyme, but this enzyme does not reach the CNS and thus does not ameliorate the neurological involvement in types 2 and 3 Gaucher disease. As one potential approach to treating these latter patients, we have evaluated intracerebroventricular (ICV) administration of recombinant human glucocerebrosidase (rhGC) in a mouse model of neuronopathic Gaucher disease. ICV administration resulted in enzyme distribution throughout the brain and alleviated neuropathology in multiple brain regions of this mouse model. Treatment also resulted in dose-dependent decreases in GluCer and GluSph and significantly extended survival. To evaluate the potential of continuous enzyme delivery, a group of animals was treated ICV with an adeno-associated viral vector encoding hGC and resulted in a further extension of survival. These data suggest that ICV administration of rhGC may represent a potential therapeutic approach for type 2/3 Gaucher patients. Preclinical evaluation in larger animals will be needed to ascertain the translatability of this approach to the clinic. Copyright © 2010 Elsevier Inc. All rights reserved.

  9. Electrokinetic properties of tantalum oxide deposited on model substrate in NaCl and LiCl solutions

    International Nuclear Information System (INIS)

    Sidorova, M.P.; Bogdanova, N.F.; Ermakova, L.Eh.; Bobrov, P.V.

    1997-01-01

    Electrokinetic characteristics of tantalum oxide have been studied using a model system - a plane-parallel capillary in chloride solutions containing monocharge (H + , Na + , Li + ) counterions in a wide range of pH and concentrations. It is shown that position of isoelectric point (IEP) of Ta 2 O 5 depends on concentration and type of counterion, moreover, the dependence is not explained in the framework of classical notions of the influence of counterion specific adsorption on IEP position. Electrokinetic potential of Ta 2 O-5 surface at the background of diluted LiCl solutions is higher in its absolute value, than at the background of NaCl solutions according to direct lyotropic series. The results of measurements of the capillary resistance dependence on pH at the background of NaCl and LiCl solutions 10 -3 -10 -1 M are used for the calculation of efficiency and specific surface conductivity factors

  10. 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.

  11. Nanowires and nanoneedles nucleation on vicinal substrate

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Xu, E-mail: zhangxubetter@gmail.com [Henan Key Laboratory of Laser and Opto-electric Information Technology, School of Information Engineering, Zhengzhou University, Zhengzhou 450052 (China); Xie, Dan; Huang, Genling [Zhengzhou Railway Vocational and Technical College, Zhengzhou 450052 (China); Sun, Xiao-Hong [Henan Key Laboratory of Laser and Opto-electric Information Technology, School of Information Engineering, Zhengzhou University, Zhengzhou 450052 (China)

    2015-01-01

    An analytic stress-driven nucleation model of nanowires (NWs) and nanoneedles (NNs) growing on a mismatched vicinal substrate is proposed. It is demonstrated that the formation enthalpy of NWs and NNs is a function of three independent variables, the base radius, aspect ratio and miscut angle of the vicinal surface. Theoretical analysis shows that the minimum nucleation barrier of an island decreases with increment of substrate misorientation, which means the nucleation of islands on a vicinal substrate is more favorable than that on a flat substrate.

  12. Impact of bacterial activity on turnover of insoluble hydrophobic substrates (phenanthrene and pyrene)-Model simulations for prediction of bioremediation success.

    Science.gov (United States)

    Rein, Arno; Adam, Iris K U; Miltner, Anja; Brumme, Katja; Kästner, Matthias; Trapp, Stefan

    2016-04-05

    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 for the substrates PHE and PYR and for both strains. The investigated Mycobacterium species were not superior in PHE degradation to strains investigated earlier with this method. Real-world degradation scenario simulations including diffusive flux to the microbial cells indicate: that (i) bioaugmentation only has a small, short-lived effect; (ii) Increasing sorption shifts the remaining PAH to the adsorbed/sequestered PAH pool; (iii) mobilizing by solvents or surfactants resulted in a significant decrease of the sequestered PAH, and (iv) co-metabolization e.g. by compost addition can contribute significantly to the reduction of PAH, because active biomass is maintained at a high level by the compost. The model therefore is a valuable contribution to the assessment of potential remediation action at PAH-polluted sites. Copyright © 2015 Elsevier B.V. All rights reserved.

  13. In vitro generation of three-dimensional substrate-adherent embryonic stem cell-derived neural aggregates for application in animal models of neurological disorders.

    Science.gov (United States)

    Hargus, Gunnar; Cui, Yi-Fang; Dihné, Marcel; Bernreuther, Christian; Schachner, Melitta

    2012-05-01

    In vitro-differentiated embryonic stem (ES) cells comprise a useful source for cell replacement therapy, but the efficiency and safety of a translational approach are highly dependent on optimized protocols for directed differentiation of ES cells into the desired cell types in vitro. Furthermore, the transplantation of three-dimensional ES cell-derived structures instead of a single-cell suspension may improve graft survival and function by providing a beneficial microenvironment for implanted cells. To this end, we have developed a new method to efficiently differentiate mouse ES cells into neural aggregates that consist predominantly (>90%) of postmitotic neurons, neural progenitor cells, and radial glia-like cells. When transplanted into the excitotoxically lesioned striatum of adult mice, these substrate-adherent embryonic stem cell-derived neural aggregates (SENAs) showed significant advantages over transplanted single-cell suspensions of ES cell-derived neural cells, including improved survival of GABAergic neurons, increased cell migration, and significantly decreased risk of teratoma formation. Furthermore, SENAs mediated functional improvement after transplantation into animal models of Parkinson's disease and spinal cord injury. This unit describes in detail how SENAs are efficiently derived from mouse ES cells in vitro and how SENAs are isolated for transplantation. Furthermore, methods are presented for successful implantation of SENAs into animal models of Huntington's disease, Parkinson's disease, and spinal cord injury to study the effects of stem cell-derived neural aggregates in a disease context in vivo.

  14. Application of the relative activity factor approach in scaling from heterologously expressed cytochromes p450 to human liver microsomes: studies on amitriptyline as a model substrate.

    Science.gov (United States)

    Venkatakrishnan, K; von Moltke, L L; Greenblatt, D J

    2001-04-01

    The relative activity factor (RAF) approach is being increasingly used in the quantitative phenotyping of multienzyme drug biotransformations. Using lymphoblast-expressed cytochromes P450 (CYPs) and the tricyclic antidepressant amitriptyline as a model substrate, we have tested the hypothesis that the human liver microsomal rates of a biotransformation mediated by multiple CYP isoforms can be mathematically reconstructed from the rates of the biotransformation catalyzed by individual recombinant CYPs using the RAF approach, and that the RAF approach can be used for the in vitro-in vivo scaling of pharmacokinetic clearance from in vitro intrinsic clearance measurements in heterologous expression systems. In addition, we have compared the results of two widely used methods of quantitative reaction phenotyping, namely, chemical inhibition studies and the prediction of relative contributions of individual CYP isoforms using the RAF approach. For the pathways of N-demethylation (mediated by CYPs 1A2, 2B6, 2C8, 2C9, 2C19, 2D6, and 3A4) and E-10 hydroxylation (mediated by CYPs 2B6, 2D6, and 3A4), the model-predicted biotransformation rates in microsomes from a panel of 12 human livers determined from enzyme kinetic parameters of the recombinant CYPs were similar to, and correlated with the observed rates. The model-predicted clearance via N-demethylation was 53% lower than the previously reported in vivo pharmacokinetic estimates. Model-predicted relative contributions of individual CYP isoforms to the net biotransformation rate were similar to, and correlated with the fractional decrement in human liver microsomal reaction rates by chemical inhibitors of the respective CYPs, provided the chemical inhibitors used were specific to their target CYP isoforms.

  15. Produtividade do tomateiro em diferentes substratos e modelos de casas de vegetação Tomato crop production under different substrates and greenhouse models

    Directory of Open Access Journals (Sweden)

    Osmar A. Carrijo

    2004-03-01

    Full Text Available Um experimento com a cultura do tomate, foi instalado na Embrapa Hortaliças em Brasília, durante os anos de 2000 e 2001, para avaliar a produção do tomateiro em diferentes substratos e casas de vegetação. Os substratos utilizados foram casca de arroz, casca de arroz parcialmente carbonizada, fibra de coco verde, lã de rocha, maravalha, serragem e substrato para produção de mudas utilizado na Embrapa Hortaliças (150 L de terra de subsolo, 50 L de casca de arroz parcialmente carbonizada e 17 L de esterco de galinha. Os modelos de casas de vegetação utilizados foram teto em arco, arco com teto convectivo e capela. Não foi verificada diferença estatística significativa quanto a produção de frutos comerciais entre os substratos fibra de coco (10,4 kg m-2, serragem (9,3 kg m-2, casca de arroz carbonizada (9,3 kg m-2 e maravalha (9,0 kg m-2. A menor produção foi obtida com o substrato lã de rocha (6,4 kg m-2. Houve redução da produção entre os anos de cultivo, em torno de 33%, em decorrência de um intenso ataque de traça do tomateiro (Tuta absoluta em todas as casas de vegetação, prejudicando a produtividade. O maior peso médio dos frutos foi obtido sobre a fibra de coco (128 g m-2 e casca de arroz carbonizada (123 g m-2, independente do modelo de casa de vegetação utilizado.The trial was carried out at Embrapa Hortaliças, in Brasilia, Brazil, to evaluate the performance of tomato crop production during two years (2000 and 2001, under three greenhouse models and different types of substrates. The greenhouse models were arch roof; even span and an arch roof with upper convective aperture. The substrates were rice husk, carbonized rice husk, coconut fiber, sawdust, coarsed sawdust, rockwool and a substrate for seedling production used at Embrapa Hortaliças. No significant statistical difference was verified for tomatoes cultivated in coconut fiber (10,4 kg m-2, sawdust (9,9 kg m-2, carbonized rice husk (9,3 kg m-2 and

  16. 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.

  17. Foot-and-mouth disease virus-like particles produced by a SUMO fusion protein system in Escherichia coli induce potent protective immune responses in guinea pigs, swine and cattle

    Science.gov (United States)

    2013-01-01

    Foot-and-mouth disease virus (FMDV) causes a highly contagious infection in cloven-hoofed animals. The format of FMD virus-like particles (VLP) as a non-replicating particulate vaccine candidate is a promising alternative to conventional inactivated FMDV vaccines. In this study, we explored a prokaryotic system to express and assemble the FMD VLP and validated the potential of VLP as an FMDV vaccine candidate. VLP composed entirely of FMDV (Asia1/Jiangsu/China/2005) capsid proteins (VP0, VP1 and VP3) were simultaneously produced as SUMO fusion proteins by an improved SUMO fusion protein system in E. coli. Proteolytic removal of the SUMO moiety from the fusion proteins resulted in the assembly of VLP with size and shape resembling the authentic FMDV. Immunization of guinea pigs, swine and cattle with FMD VLP by intramuscular inoculation stimulated the FMDV-specific antibody response, neutralizing antibody response, T-cell proliferation response and secretion of cytokine IFN-γ. In addition, immunization with one dose of the VLP resulted in complete protection of these animals from homologous FMDV challenge. The 50% protection dose (PD50) of FMD VLP in cattle is up to 6.34. These results suggest that FMD VLP expressed in E. coli are an effective vaccine in guinea pigs, swine and cattle and support further development of these VLP as a vaccine candidate for protection against FMDV. PMID:23826638

  18. Satellite cell senescence underlies myopathy in a mouse model of limb-girdle muscular dystrophy 2H

    Science.gov (United States)

    Kudryashova, Elena; Kramerova, Irina; Spencer, Melissa J.

    2012-01-01

    Mutations in the E3 ubiquitin ligase tripartite motif-containing 32 (TRIM32) are responsible for the disease limb-girdle muscular dystrophy 2H (LGMD2H). Previously, we generated Trim32 knockout mice (Trim32–/– mice) and showed that they display a myopathic phenotype accompanied by neurogenic features. Here, we used these mice to investigate the muscle-specific defects arising from the absence of TRIM32, which underlie the myopathic phenotype. Using 2 models of induced atrophy, we showed that TRIM32 is dispensable for muscle atrophy. Conversely, TRIM32 was necessary for muscle regrowth after atrophy. Furthermore, TRIM32-deficient primary myoblasts underwent premature senescence and impaired myogenesis due to accumulation of PIAS4, an E3 SUMO ligase and TRIM32 substrate that was previously shown to be associated with senescence. Premature senescence of myoblasts was also observed in vivo in an atrophy/regrowth model. Trim32–/– muscles had substantially fewer activated satellite cells, increased PIAS4 levels, and growth failure compared with wild-type muscles. Moreover, Trim32–/– muscles exhibited features of premature sarcopenia, such as selective type II fast fiber atrophy. These results imply that premature senescence of muscle satellite cells is an underlying pathogenic feature of LGMD2H and reveal what we believe to be a new mechanism of muscular dystrophy associated with reductions in available satellite cells and premature sarcopenia. PMID:22505452

  19. 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.

  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

    KAUST Repository

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

    2014-01-01

    . 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

  1. Moving college students to a better understanding of substrate specificity of enzymes through utilizing multimedia pre-training and an interactive enzyme model

    Science.gov (United States)

    Saleh, Mounir R.

    Scientists' progress in understanding enzyme specificity uncovered a complex natural phenomenon. However, not all of the currently available biology textbooks seem to be up to date on this progress. Students' understanding of how enzymes work is a core requirement in biochemistry and biology tertiary education. Nevertheless, current pre-college science education does not provide students with enough biochemical background to enable them to understand complex material such as this. To bridge this gap, a multimedia pre-training presentation was prepared to fuel the learner's prior knowledge with discrete facts necessary to understand the presented concept. This treatment is also known to manage intrinsic cognitive load during the learning process. An interactive instructional enzyme model was also built to motivate students to learn about substrate specificity of enzymes. Upon testing the effect of this combined treatment on 111 college students, desirable learning outcomes were found in terms of cognitive load, motivation, and achievement. The multimedia pre-training group reported significantly less intrinsic cognitive load, higher motivation, and demonstrated higher transfer performance than the control and post-training groups. In this study, a statistical mediation model is also proposed to explain how cognitive load and motivation work in concert to foster learning from multimedia pre-training. This type of research goes beyond simple forms of "what works" to a deeper understanding of "how it works", thus enabling informed decisions for multimedia instructional design. Multimedia learning plays multiple roles in science education. Therefore, science learners would be some of the first to benefit from improving multimedia instructional design. Accordingly, complex scientific phenomena can be introduced to college students in a motivating, informative, and cognitively efficient learning environment.

  2. Extrapolation of Inter Domain Communications and Substrate Binding Cavity of Camel HSP70 1A: A Molecular Modeling and Dynamics Simulation Study.

    Directory of Open Access Journals (Sweden)

    Saurabh Gupta

    Full Text Available Heat shock protein 70 (HSP70 is an important chaperone, involved in protein folding, refolding, translocation and complex remodeling reactions under normal as well as stress conditions. However, expression of HSPA1A gene in heat and cold stress conditions associates with other chaperons and perform its function. Experimental structure for Camel HSP70 protein (cHSP70 has not been reported so far. Hence, we constructed 3D models of cHSP70 through multi- template comparative modeling with HSP110 protein of S. cerevisiae (open state and with HSP70 protein of E. coli 70kDa DnaK (close state and relaxed them for 100 nanoseconds (ns using all-atom Molecular Dynamics (MD Simulation. Two stable conformations of cHSP70 with Substrate Binding Domain (SBD in open and close states were obtained. The collective mode analysis of different transitions of open state to close state and vice versa was examined via Principal Component Analysis (PCA and Minimum Distance Matrix (MDM. The results provide mechanistic representation of the communication between Nucleotide Binding Domain (NBD and SBD to identify the role of sub domains in conformational change mechanism, which leads the chaperone cycle of cHSP70. Further, residues present in the chaperon functioning site were also identified through protein-peptide docking. This study provides an overall insight into the inter domain communication mechanism and identification of the chaperon binding cavity, which explains the underlying mechanism involved during heat and cold stress conditions in camel.

  3. Dynamics of Preferential Substrate Recognition in HIV-1 Protease: Redefining the Substrate Envelope

    Science.gov (United States)

    Özen, Ayşegül; Haliloğlu, Türkan; Schiffer, Celia A.

    2011-01-01

    HIV-1 protease (PR) permits viral maturation by processing the Gag and Gag-Pro-Pol polyproteins. Though HIV-1 PR inhibitors (PIs) are used in combination antiviral therapy, the emergence of drug resistance has limited their efficacy. The rapid evolution of HIV-1 necessitates the consideration of drug resistance in novel drug-design strategies. Drug-resistant HIV-1 PR variants, while no longer efficiently inhibited, continue to efficiently hydrolyze the natural viral substrates. Though highly diverse in sequence, the HIV-1 PR substrates bind in a conserved three-dimensional shape we defined as the “substrate envelope”. We previously showed that resistance mutations arise where PIs protrude beyond the substrate envelope, as these regions are crucial for drug binding but not for substrate recognition. Here, we extend this model by considering the role of protein dynamics in the interaction of HIV-1 PR with its substrates. Seven molecular dynamics simulations of PR-substrate complexes were performed to estimate the conformational flexibility of substrates in their complexes. Interdependency of the substrate-protease interactions may compensate for the variations in cleavage-site sequences, and explain how a diverse set of sequences can be recognized as substrates by the same enzyme. This diversity may be essential for regulating sequential processing of substrates. We also define a dynamic substrate envelope as a more accurate representation of PR-substrate interactions. This dynamic substrate envelope, described by a probability distribution function, is a powerful tool for drug design efforts targeting ensembles of resistant HIV-1 PR variants with the aim of developing drugs that are less susceptible to resistance. PMID:21762811

  4. 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...

  5. 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

  6. 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

  7. 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.

  8. Dewetting of thin polymer film on rough substrate: II. Experiment

    International Nuclear Information System (INIS)

    Volodin, Pylyp; Kondyurin, Alexey

    2008-01-01

    The theory of the dewetting process developed for a model of substrate-film interaction forces was examined by an experimental investigation of the dewetting process of thin polystyrene (PS) films on chemically etched silicon substrates. In the dependence on PS films thickness and silicon roughness, various situations of dewetting were observed as follows: (i) if the wavelength of the substrate roughness is much larger than the critical spinodal wavelength of a film, then spinodal dewetting of the film is observed; (ii) if the wavelength of the substrate roughness is smaller than the critical wavelength of the film and the substrate roughness is larger in comparison with film thickness, then the dewetting due to substrate roughness is observed and the dewetted film patterns repeat the rough substrate structure; (iii) if the wavelength of the substrate roughness is smaller than the critical wavelength of the film and the substrate roughness is small in comparison with the film thickness, then spinodal dewetting proceeds

  9. 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

  10. 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)

  11. 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)

  12. 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...

  13. 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

  14. Substrate system for spray forming

    Energy Technology Data Exchange (ETDEWEB)

    Chu, Men G. (Export, PA); Chernicoff, William P. (Harrisburg, PA)

    2002-01-01

    A substrate system for receiving a deposit of sprayed metal droplets including a movable outer substrate on which the sprayed metal droplets are deposited. The substrate system also includes an inner substrate disposed adjacent the outer substrate where the sprayed metal droplets are deposited on the outer substrate. The inner substrate includes zones of differing thermal conductivity to resist substrate layer porosity and to resist formation of large grains and coarse constituent particles in a bulk layer of the metal droplets which have accumulated on the outer substrate. A spray forming apparatus and associated method of spray forming a molten metal to form a metal product using the substrate system of the invention is also provided.

  15. Quantitative framework for ordered degradation of APC/C substrates.

    Science.gov (United States)

    Lu, Dan; Girard, Juliet R; Li, Weihan; Mizrak, Arda; Morgan, David O

    2015-11-16

    During cell-cycle progression, substrates of a single master regulatory enzyme can be modified in a specific order. Here, we used experimental and computational approaches to dissect the quantitative mechanisms underlying the ordered degradation of the substrates of the ubiquitin ligase APC/C(Cdc20), a key regulator of chromosome segregation in mitosis. We show experimentally that the rate of catalysis varies with different substrates of APC/C(Cdc20). Using a computational model based on multi-step ubiquitination, we then show how changes in the interaction between a single substrate and APC/C(Cdc20) can alter the timing of degradation onset relative to APC/C(Cdc20) activation, while ensuring a fast degradation rate. Degradation timing and dynamics depend on substrate affinity for the enzyme as well as the catalytic rate at which the substrate is modified. When two substrates share the same pool of APC/C(Cdc20), their relative enzyme affinities and rates of catalysis influence the partitioning of APC/C(Cdc20) among substrates, resulting in substrate competition. Depending on how APC/C(Cdc20) is partitioned among its substrates, competition can have minor or major effects on the degradation of certain substrates. We show experimentally that increased expression of the early APC/C(Cdc20) substrate Clb5 does not delay the degradation of the later substrate securin, arguing against a role for competition with Clb5 in establishing securin degradation timing. The degradation timing of APC/C(Cdc20) substrates depends on the multi-step nature of ubiquitination, differences in substrate-APC/C(Cdc20) interactions, and competition among substrates. Our studies provide a conceptual framework for understanding how ordered modification can be established among substrates of the same regulatory enzyme, and facilitate our understanding of how precise temporal control is achieved by a small number of master regulators to ensure a successful cell division cycle.

  16. Toward a Molecular Understanding of the Interaction of Dual Specificity Phosphatases with Substrates: Insights from Structure-Based Modeling and High Throughput Screening

    OpenAIRE

    Bakan, Ahmet; Lazo, John S; Wipf, Peter; Brummond, Kay M; Bahar, Ivet

    2008-01-01

    Dual-specificity phosphatases (DSPs) are important, but poorly understood, cell signaling enzymes that remove phosphate groups from tyrosine and serine/threonine residues on their substrate. Deregulation of DSPs has been implicated in cancer, obesity, diabetes, inflammation, and Alzheimer’s disease. Due to their biological and biomedical significance, DSPs have increasingly become the subject of drug discovery high-throughput screening (HTS) and focused compound library development efforts. P...

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. Chemometrics approach to substrate development, case: semisyntetic cheese

    DEFF Research Database (Denmark)

    Nielsen, Per Væggemose; Hansen, Birgitte Vedel

    1998-01-01

    from food production facilities.The Chemometrics approach to substrate development is illustrated by the development of a semisyntetic cheese substrate. Growth, colour formation and mycotoxin production of 6 cheese related fungi were studied on 9 types of natural cheeses and 24 synthetic cheese......, the most frequently occurring contaminant on semi-hard cheese. Growth experiments on the substrate were repeatable and reproducible. The substrate was also suitable for the starter P. camemberti. Mineral elements in cheese were shown to have strong effect on growth, mycotoxin production and colour...... formation of fungi. For P. roqueforti, P. discolor, P. verrucosum and Aspergillus versicolor the substrate was less suitable as a model cheese substrate, which indicates great variation in nutritional demands of the fungi. Substrates suitable for studies of specific cheese types was found for P. roqueforti...

  2. 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.

  3. Fusion of the SUMO/Sentrin-specific protease 1 gene SENP1 and the embryonic polarity-related mesoderm development gene MESDC2 in a patient with an infantile teratoma and a constitutional t(12;15)(q13;q25).

    NARCIS (Netherlands)

    Veltman, I.M.; Basten-Vreede, L.A.J.; Cheng, J.; Looijenga, L.H.J.; Janssen, H.A.P.; Schoenmakers, E.F.P.M.; Yeh, E.T.; Geurts van Kessel, A.H.M.

    2005-01-01

    Recently, we identified a patient with an infantile sacrococcygeal teratoma and a constitutional t(12;15)(q13;q25). Here, we show that, as a result of this chromosomal translocation, the SUMO/Sentrin-specific protease 1 gene (SENP1) on chromosome 12 and the embryonic polarity-related mesoderm

  4. Substrate Effects in Wideband SiGe HBT Mixer Circuits

    DEFF Research Database (Denmark)

    Johansen, Tom Keinicke; Vidkjær, Jens; Krozer, Viktor

    2005-01-01

    are also applied to predict short distance substrate coupling effects. Simulation results using extracted equivalent circuit models and substrate coupling networks are compared with experimental results obtained on a wideband mixer circuit implemented in a 0.35 μm, 60 GHz ft SiGe HBT BiCMOS process.......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...

  5. Solid substrate fermentation

    Energy Technology Data Exchange (ETDEWEB)

    Tengerdy, R P

    1985-04-01

    Solid Substrate Fermentation (SSF) describes the microbiological tranformation of biological materials in their natural state, in contrast with liquid or submerged fermentations which are carried out in dilute solutions or slurries. The most important industrial microorganisms used in SSF are filamentous fungi and the critical factors in their growth are the control of the moisture level and the temperature. Traditionally, most SSFs are conducted in shallow trays (so that heat build up is avoided) and stacked in a moist chamber, however, the modern SSF should be able to mix large amounts of substrate for a uniform fermentation, maximum automization scale-up of the process, continuous operation and fermentation control and a promising new design is the Helical screw fermenter. At the present time SSF is used in the production of foods (e.g. mushrooms and oriental foods) in municipal, agricultural and industrial solid waste disposal and in the production of enzymes and speciality chemicals but it does not seem likely that it will replace prevalent liquid fermentation technologies. 29 references.

  6. Maintainable substrate carrier for electroplating

    Science.gov (United States)

    Chen, Chen-An [Milpitas, CA; Abas, Emmanuel Chua [Laguna, PH; Divino, Edmundo Anida [Cavite, PH; Ermita, Jake Randal G [Laguna, PH; Capulong, Jose Francisco S [Laguna, PH; Castillo, Arnold Villamor [Batangas, PH; Ma,; Xiaobing, Diana [Saratoga, CA

    2012-07-17

    One embodiment relates to a substrate carrier for use in electroplating a plurality of substrates. The carrier includes a non-conductive carrier body on which the substrates are placed and conductive lines embedded within the carrier body. A plurality of conductive clip attachment parts are attached in a permanent manner to the conductive lines embedded within the carrier body. A plurality of contact clips are attached in a removable manner to the clip attachment parts. The contact clips hold the substrates in place and conductively connecting the substrates with the conductive lines. Other embodiments, aspects and features are also disclosed.

  7. 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.

  8. Model experiments on growth modes and interface electronics of CuInS{sub 2}: Ultrathin epitaxial films on GaAs(100) substrates

    Energy Technology Data Exchange (ETDEWEB)

    Calvet, Wolfram [Institute for Heterogeneous Materials Systems, Helmholtz-Zentrum Berlin, Hahn-Meitner-Platz 1, 14109, Berlin (Germany); Lewerenz, Hans-Joachim [Joint Center for Artificial Photosynthesis, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA, 91101 (United States); Pettenkofer, Christian [Institute Silicon Photovoltaics, Helmholtz-Zentrum Berlin, Kekulestrasse 5, 12489, Berlin (Germany)

    2014-09-15

    The heterojunction formation between GaAs(100) and CuInS{sub 2} is investigated using ultraviolet photoelectron spectroscopy (UPS), X-ray photoelectron spectroscopy (XPS), and low energy electron diffraction (LEED). Thin layers of CuInS{sub 2} films were deposited in a step-by-step process on wet chemically pre-treated GaAs(100) surfaces by molecular beam epitaxy (MBE) with a total upper thickness limit of the films of 60 nm. The film growth starts from a sulfur-rich GaAs(100) surface. XPS core level analysis of the substrate and film reveals initially a transitory growth regime with the formation of a Ga containing chalcopyrite phase. With increasing film thickness, a change in stoichiometry from Cu-poor to Cu-rich composition is observed. The evaluation of the LEED data shows the occurrence of a recrystallization process where the film orientation follows that of the substrate with the epitaxial relation GaAs{100} parallel CuInS{sub 2}{001}. On the completed junction with a CuInS{sub 2} film thickness of 60 nm, the band discontinuities of the GaAs(100)/CuInS{sub 2} structure measured with XPS and UPS were determined as ΔE{sub V} = 0.1 ± 0.1 eV and ΔE{sub C} = 0.0 ± 0.1 eV, thus showing a type II band alignment. (copyright 2014 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  9. Estrogen receptor alpha and nuclear factor Y coordinately regulate the transcription of the SUMO-conjugating UBC9 gene in MCF-7 breast cancer cells.

    Directory of Open Access Journals (Sweden)

    Shibo Ying

    Full Text Available UBC9 encodes a protein that conjugates small ubiquitin-related modifier (SUMO to target proteins thereby changing their functions. Recently, it was noted that UBC9 expression and activity play a role in breast tumorigenesis and response to anticancer drugs. However, the underlying mechanism is poorly understood. To investigate the transcriptional regulation of the UBC9 gene, we identified and characterized its promoter and cis-elements. Promoter activity was tested using luciferase reporter assays. The binding of transcription factors to the promoter was detected by chromatin immunoprecipitation (ChIP, and their functional role was confirmed by siRNA knockdown. UBC9 mRNA and protein levels were measured by quantitative reverse transcription PCR and Western blot analysis, respectively. An increased expression of UBC9 mRNA and protein was found in MCF-7 breast cancer cells treated with 17β-estradiol (E2. Analysis of various deletion mutants revealed a 137 bp fragment upstream of the transcription initiation site to be sufficient for reporter gene transcription. Mutations of putative estrogen receptor α (ER-α (one imperfect estrogen response element, ERE and/or nuclear factor Y (NF-Y binding sites (two CCAAT boxes markedly reduced promoter activity. Similar results were obtained in ER-negative MDA-MB-231 cells except that the ERE mutation did not affect promoter activity. Additionally, promoter activity was stimulated upon E2 treatment and overexpression of ER-α or NF-YA in MCF-7 cells. ChIP confirmed direct binding of both transcription factors to the UBC9 promoter in vivo. Furthermore, UBC9 expression was diminished by ER-α and NF-Y siRNAs on the mRNA and protein levels. In conclusion, we identified the proximal UBC9 promoter and provided evidence that ER-α and NF-Y regulate UBC9 expression on the transcriptional level in response to E2 in MCF-7 cells. These findings may contribute to a better understanding of the regulation of UBC9 in ER

  10. Estrogen receptor alpha and nuclear factor Y coordinately regulate the transcription of the SUMO-conjugating UBC9 gene in MCF-7 breast cancer cells.

    Science.gov (United States)

    Ying, Shibo; Dünnebier, Thomas; Si, Jing; Hamann, Ute

    2013-01-01

    UBC9 encodes a protein that conjugates small ubiquitin-related modifier (SUMO) to target proteins thereby changing their functions. Recently, it was noted that UBC9 expression and activity play a role in breast tumorigenesis and response to anticancer drugs. However, the underlying mechanism is poorly understood. To investigate the transcriptional regulation of the UBC9 gene, we identified and characterized its promoter and cis-elements. Promoter activity was tested using luciferase reporter assays. The binding of transcription factors to the promoter was detected by chromatin immunoprecipitation (ChIP), and their functional role was confirmed by siRNA knockdown. UBC9 mRNA and protein levels were measured by quantitative reverse transcription PCR and Western blot analysis, respectively. An increased expression of UBC9 mRNA and protein was found in MCF-7 breast cancer cells treated with 17β-estradiol (E2). Analysis of various deletion mutants revealed a 137 bp fragment upstream of the transcription initiation site to be sufficient for reporter gene transcription. Mutations of putative estrogen receptor α (ER-α) (one imperfect estrogen response element, ERE) and/or nuclear factor Y (NF-Y) binding sites (two CCAAT boxes) markedly reduced promoter activity. Similar results were obtained in ER-negative MDA-MB-231 cells except that the ERE mutation did not affect promoter activity. Additionally, promoter activity was stimulated upon E2 treatment and overexpression of ER-α or NF-YA in MCF-7 cells. ChIP confirmed direct binding of both transcription factors to the UBC9 promoter in vivo. Furthermore, UBC9 expression was diminished by ER-α and NF-Y siRNAs on the mRNA and protein levels. In conclusion, we identified the proximal UBC9 promoter and provided evidence that ER-α and NF-Y regulate UBC9 expression on the transcriptional level in response to E2 in MCF-7 cells. These findings may contribute to a better understanding of the regulation of UBC9 in ER

  11. 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.

  12. 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

    1994-12-31

    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.

  13. 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…

  14. 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.

  15. Equilibrium Droplets on Deformable Substrates: Equilibrium Conditions.

    Science.gov (United States)

    Koursari, Nektaria; Ahmed, Gulraiz; Starov, Victor M

    2018-05-15

    Equilibrium conditions of droplets on deformable substrates are investigated, and it is proven using Jacobi's sufficient condition that the obtained solutions really provide equilibrium profiles of both the droplet and the deformed support. At the equilibrium, the excess free energy of the system should have a minimum value, which means that both necessary and sufficient conditions of the minimum should be fulfilled. Only in this case, the obtained profiles provide the minimum of the excess free energy. The necessary condition of the equilibrium means that the first variation of the excess free energy should vanish, and the second variation should be positive. Unfortunately, the mentioned two conditions are not the proof that the obtained profiles correspond to the minimum of the excess free energy and they could not be. It is necessary to check whether the sufficient condition of the equilibrium (Jacobi's condition) is satisfied. To the best of our knowledge Jacobi's condition has never been verified for any already published equilibrium profiles of both the droplet and the deformable substrate. A simple model of the equilibrium droplet on the deformable substrate is considered, and it is shown that the deduced profiles of the equilibrium droplet and deformable substrate satisfy the Jacobi's condition, that is, really provide the minimum to the excess free energy of the system. To simplify calculations, a simplified linear disjoining/conjoining pressure isotherm is adopted for the calculations. It is shown that both necessary and sufficient conditions for equilibrium are satisfied. For the first time, validity of the Jacobi's condition is verified. The latter proves that the developed model really provides (i) the minimum of the excess free energy of the system droplet/deformable substrate and (ii) equilibrium profiles of both the droplet and the deformable substrate.

  16. 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.

  17. Sealed substrate carrier for electroplating

    Science.gov (United States)

    Ganti, Kalyana Bhargava [Fremont, CA

    2012-07-17

    One embodiment relates to a substrate carrier for use in electroplating a plurality of substrates. The substrate carrier includes a non-conductive carrier body on which the substrates are held, and conductive lines are embedded within the carrier body. A conductive bus bar is embedded into a top side of the carrier body and is conductively coupled to the conductive lines. A thermoplastic overmold covers a portion of the bus bar, and there is a plastic-to-plastic bond between the thermoplastic overmold and the non-conductive carrier body. Other embodiments, aspects and features are also disclosed.

  18. 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.)

  19. Michaelis - Menten equation for degradation of insoluble substrate

    DEFF Research Database (Denmark)

    Andersen, Morten; Kari, Jeppe; Borch, Kim

    2017-01-01

    substrate it is difficult to assess whether the requirement of the MM equation is met. In this paper we study a simple kinetic model, where removal of attack sites expose new ones which preserve the total accessible substrate, and denote this approach the substrate conserving model. The kinetic equations...... are solved in closed form, both steady states and progress curves, for any admissible values of initial conditions and rate constants. The model is shown to merge with the MM equation and the reverse MM equation when these are valid. The relation between available molar concentration of attack sites and mass...

  20. 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.

  1. 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.

  2. Study on the influence of package parasitics and substrate resistance on the Charged Device Model(CDM) failure levels - possible protection methodology

    NARCIS (Netherlands)

    Sowariraj, M.S.B.; Smedes, Theo; Salm, Cora; Mouthaan, A.J.; Kuper, F.G.

    2003-01-01

    Charged Device Model (CDM) type of Electrostatic Discharge (ESD) stress events are becoming the major reason for field returns in the Integrated Circuit (IC) industry especially with downscaling of device dimensions and increased usage of automated handlers. In the case of CDM stress, the IC is both

  3. A 'Big leaf, big fruit, big substrate' model for experiments on receding horizon optimal control of nutrient supply to greenhouse tomato

    NARCIS (Netherlands)

    Straten, van G.; Vanthoor, B.H.E.; Willigenburg, van L.G.; Elings, A.

    2006-01-01

    A dynamic model was set up to describe the mineral content, fruit dry matter content, and biomass of greenhouse tomato, for use in an experiment aiming at controlling the fertigation so as to reach the best compromise between disinfection costs of the recycled water and income from fruit fresh

  4. 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...

  5. 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.

  6. Efficient Substrate Noise Coupling Verification and Failure Analysis Methodology for Smart Power ICs in Automotive Applications

    OpenAIRE

    Moursy , Yasser; Zou , Hao; Khalil , Raouf; Iskander , Ramy; Tisserand , Pierre; Ton , Dieu-My; Pasetti , Giuseppe; Louërat , Marie-Minerve

    2016-01-01

    International audience; This paper presents a methodology to analyze the substrate noise coupling and reduce their effects in smart power integrated circuits. This methodology considers the propagation of minority carriers in the substrate. Hence, it models the lateral bipolar junction transistors that are layout dependent and are not modeled in conventional substrate extraction tools. It allows the designer to simulate substrate currents and check their effects on circuits functionality. The...

  7. 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.

  8. Design of a cylindrical LED substrate without radiator

    Science.gov (United States)

    Tang, Fan; Guo, Zhenning

    2017-12-01

    To reduce the weight and production costs of light-emitting diode (LED) lamps, we applied the principle of the chimney effect to design a cylindrical LED substrate without a radiator. We built a 3D model by using Solidworks software and applied the flow simulation plug-in to conduct model simulation, thereby optimizing the heat source distribution and substrate thickness. The results indicate that the design achieved optimal cooling with a substrate with an upper extension length of 35 mm, a lower extension length of 8 mm, and a thickness of 1 mm. For a substrate of those dimensions, the highest LED chip temperature was 64.78 °C, the weight of the substrate was 35.09 g, and R jb = 7.00 K/W. If the substrate is powered at 8, 10, and 12 W, its temperature meets LED safety requirements. In physical tests, the highest temperature for a physical 8 W cylindrical LED substrate was 66 °C, which differed by only 1.22 °C from the simulation results, verifying the validity of the simulation. The designed cylindrical LED substrate can be used in high-power LED lamps that do not require radiators. This design is not only excellent for heat dissipation, but also for its low weight, low cost, and simplicity of manufacture.

  9. Modeling the Phase Behavior of PEO-PPO-PEO Surfactants in Carbon Dioxide Using the PC-SAFT Equation of State: Application to Dry Decontamination of Solid Substrates

    International Nuclear Information System (INIS)

    Kleiner, M.; Sadowski, G.; Stoychev, I.; Galy, J.; Fournel, B.; Lacroix-Desmazes, P.

    2009-01-01

    The phase behavior of several commercially available poly(ethylene oxide)-b-poly(propylene oxide)-b-poly(ethylene oxide) block copolymers (PEO-PPO-PEO or Pluronics L) in compressed carbon dioxide has been investigated within the framework of dry nuclear decontamination. For this purpose, cloud points have been measured in the pressure and temperature range from P = (10 to 40) MPa and from T = (293 to 338) K, respectively. To find a reliable method for surfactant selection, the perturbed-chain statistical association fluid theory (PC-SAFT) equation of state (EoS) has been applied to model the experimental data. The pure-component and the respective homopolymer + CO 2 binary interaction parameters have been fitted to liquid densities and to homopolymer + CO 2 binary equilibrium data. The phase behavior of Pluronics L copolymers as a function of concentration, molar mass, and copolymer composition has been predicted very accurately using a constant PEO-PPO binary interaction parameter k(PEO-PPO) = 0.007. The P and SAFT model was also successfully applied to Pluronics R copolymers (PPO-PEO-PPO), although a different k(PEO-PPO) = -0.018 was required to match the experimental data. The model predictions have shown that Pluronics L copolymers with molar mass M ≤ 2750 g.mol -1 and a PEO mass fraction in the copolymer of less than 30 % have sufficiently low cloud-point pressures and are therefore the most suitable for the decontamination process. (authors)

  10. 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.

  11. 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.

  12. 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.

  13. Evaluation of substrate noise suppression method to mitigate crosstalk among trough-silicon vias

    Science.gov (United States)

    Araga, Yuuki; Kikuchi, Katsuya; Aoyagi, Masahiro

    2018-04-01

    Substrate noise from a single through-silicon via (TSV) and the noise attenuation by a substrate tap and a guard ring are clarified. A CMOS test vehicle is designed, and 6-µm-diameter TSVs are manufactured on a 20-µm-thick silicon substrate by the via-last method. An on-chip waveform-capturing circuitry is embedded in the test vehicle to capture transient waveforms of substrate noise. The embedded waveform-capturing circuitry demonstrates small and local noise propagation. Experimental results show increased substrate noise level induced by TSVs and the effectiveness of the substrate tap and guard ring for mitigating the crosstalk among TSVs. An analytical model to explain substrate noise propagation is developed to validate experimental results. Results obtained using the substrate model with a multilayer mesh shows good consistency with experimental results, indicating that the model can be used for examination of noise suppression methods.

  14. Dielectric coatings on metal substrates

    International Nuclear Information System (INIS)

    Glaros, S.S.; Baker, P.; Milam, D.

    1976-01-01

    Large aperture, beryllium substrate-based mirrors have been used to focus high intensity pulsed laser beams. Finished surfaces have high reflectivity, low wavefront distortion, and high laser damage thresholds. This paper describes the development of a series of metallic coatings, surface finishing techniques, and dielectric overcoatings to meet specified performance requirements. Beryllium substrates were coated with copper, diamond-machined to within 5 micro-inches to final contour, nickel plated, and abrasively figured to final contour. Bond strengths for several bonding processes are presented. Dielectric overcoatings were deposited on finished multimetallic substrates to increase both reflectivity and the damage thresholds. Coatings were deposited using both high and low temperature processes which induce varying stresses in the finished coating substrate system. Data are presented to show the evolution of wavefront distortion, reflectivity, and damage thresholds throughout the many steps involved in fabrication

  15. Probing protein phosphatase substrate binding

    DEFF Research Database (Denmark)

    Højlys-Larsen, Kim B.; Sørensen, Kasper Kildegaard; Jensen, Knud Jørgen

    2012-01-01

    Proteomics and high throughput analysis for systems biology can benefit significantly from solid-phase chemical tools for affinity pull-down of proteins from complex mixtures. Here we report the application of solid-phase synthesis of phosphopeptides for pull-down and analysis of the affinity...... profile of the integrin-linked kinase associated phosphatase (ILKAP), a member of the protein phosphatase 2C (PP2C) family. Phosphatases can potentially dephosphorylate these phosphopeptide substrates but, interestingly, performing the binding studies at 4 °C allowed efficient binding to phosphopeptides......, without the need for phosphopeptide mimics or phosphatase inhibitors. As no proven ILKAP substrates were available, we selected phosphopeptide substrates among known PP2Cδ substrates including the protein kinases: p38, ATM, Chk1, Chk2 and RSK2 and synthesized directly on PEGA solid supports through a BAL...

  16. 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.

  17. 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)

  18. Graphene on insulating crystalline substrates

    International Nuclear Information System (INIS)

    Akcoeltekin, S; El Kharrazi, M; Koehler, B; Lorke, A; Schleberger, M

    2009-01-01

    We show that it is possible to prepare and identify ultra-thin sheets of graphene on crystalline substrates such as SrTiO 3 , TiO 2 , Al 2 O 3 and CaF 2 by standard techniques (mechanical exfoliation, optical and atomic force microscopy). On the substrates under consideration we find a similar distribution of single layer, bilayer and few-layer graphene and graphite flakes as with conventional SiO 2 substrates. The optical contrast C of a single graphene layer on any of those substrates is determined by calculating the optical properties of a two-dimensional metallic sheet on the surface of a dielectric, which yields values between C = -1.5% (G/TiO 2 ) and C = -8.8% (G/CaF 2 ). This contrast is in reasonable agreement with experimental data and is sufficient to make identification by an optical microscope possible. The graphene layers cover the crystalline substrate in a carpet-like mode and the height of single layer graphene on any of the crystalline substrates as determined by atomic force microscopy is d SLG = 0.34 nm and thus much smaller than on SiO 2 .

  19. Warpage behavior analysis in package processes of embedded copper substrates

    Directory of Open Access Journals (Sweden)

    Hwang Yeong-Maw

    2017-01-01

    Full Text Available With the advance of the semiconductor industry and in response to the demands of ultra-thin products, packaging technology has been continuously developed. Thermal bonding process of copper pillar flip chip packages is a new bonding process in packaging technology, especially for substrates with embedded copper trace. During the packaging process, the substrate usually warps because of the heating process. In this paper, a finite element software ANSYS is used to model the embedded copper trace substrate and simulate the thermal and deformation behaviors of the substrate during the heating package process. A fixed geometric configuration equivalent to the real structure is duplicated to make the simulation of the warpage behavior of the substrate feasible. An empirical formula for predicting the warpage displacements is also established.

  20. 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.

  1. Methods of etching a substrate

    Energy Technology Data Exchange (ETDEWEB)

    Cosmo, J J; Gambino, R J; Harper, J M.E.

    1979-05-16

    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.

  2. 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.)

  3. Porous substrates filled with nanomaterials

    Science.gov (United States)

    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.

  4. 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.

  5. 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

  6. 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.

  7. 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...

  8. Effects of Dioscorea esculenta and Eubacterium rectale on insulin receptor substrate 1 (Irs1 Expression in skeletal muscle and homeostatic model assessment-insulin resistance (HOMA-IR in diabetic rats

    Directory of Open Access Journals (Sweden)

    . Sunarti

    2017-01-01

    Full Text Available Low expression of insulin receptor substrate 1 (Irs1 is associated with insulin resistance and type 2 diabetes mellitus (type 2 DM. This study was performed to evaluate the effects of Dioscorea esculenta and Eubacterium rectale on the Irs1 expression in the skeletal muscle and the homeostatic model assessment-insulin resistance (HOMA-IR of diabetic rats. Twenty-five male Wistar rats were divided into five groups i.e. non diabetic rats Group 1; diabetic rats as Group 2; diabetic rats + D. esculenta as Group 3; diabetic rats + E.rectale as Group 4 and diabetic rats + both E. rectale and D. esculenta as Group 5. Rats were made diabetic with induction of intraperitoneally injection of nicotinamide and streptozotocin. After four weeks of the interventions, the blood and skeletal muscles were taken. The Irs1 expression was analyzed with immunohistochemical staining, plasma glucose levels was analyzed using a spectrophotometer, and insulin was analyzed using ELISA methods. All intervention groups reduced plasma glucose levels and HOMA-IRs (p<0.001 and increased Irs1 expression. The greatest reduction of  plasma glucose levels and increase of Irs1 expression in the skeletal muscle were found in Group 4, however, the lowest of HOMA-IR was seen in Group 5. These results suggested that D.esculenta, E.rectale, and the combination reduced plasma glucose levels and HOMA-IR by increasing Irs1 expression in skeletal muscle.

  9. 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...

  10. 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:

  11. 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.

  12. 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.

  13. Substrate vibrations during courtship in three Drosophila species.

    Directory of Open Access Journals (Sweden)

    Valerio Mazzoni

    Full Text Available While a plethora of studies have focused on the role of visual, chemical and near-field airborne signals in courtship of Drosophila fruit flies, the existence of substrate-borne vibrational signals has been almost completely overlooked. Here we describe substrate vibrations generated during courtship in three species of the D. melanogaster group, from the allegedly mute species D. suzukii, its sister species D. biarmipes, and from D. melanogaster. In all species, we recorded several types of substrate vibrations which were generated by locomotion, abdominal vibrations and most likely through the activity of thoracic wing muscles. In D. melanogaster and D. suzukii, all substrate vibrations described in intact males were also recorded in males with amputated wings. Evidence suggests that vibrational signalling may be widespread among Drosophila species, and fruit flies may provide an ideal model to study various aspects of this widespread form of animal communication.

  14. 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.

  15. Ultrasensitivity in phosphorylation-dephosphorylation cycles with little substrate.

    Directory of Open Access Journals (Sweden)

    Bruno M C Martins

    Full Text Available Cellular decision-making is driven by dynamic behaviours, such as the preparations for sunrise enabled by circadian rhythms and the choice of cell fates enabled by positive feedback. Such behaviours are often built upon ultrasensitive responses where a linear change in input generates a sigmoidal change in output. Phosphorylation-dephosphorylation cycles are one means to generate ultrasensitivity. Using bioinformatics, we show that in vivo levels of kinases and phosphatases frequently exceed the levels of their corresponding substrates in budding yeast. This result is in contrast to the conditions often required by zero-order ultrasensitivity, perhaps the most well known means for how such cycles become ultrasensitive. We therefore introduce a mechanism to generate ultrasensitivity when numbers of enzymes are higher than numbers of substrates. Our model combines distributive and non-distributive actions of the enzymes with two-stage binding and concerted allosteric transitions of the substrate. We use analytical and numerical methods to calculate the Hill number of the response. For a substrate with [Formula: see text] phosphosites, we find an upper bound of the Hill number of [Formula: see text], and so even systems with a single phosphosite can be ultrasensitive. Two-stage binding, where an enzyme must first bind to a binding site on the substrate before it can access the substrate's phosphosites, allows the enzymes to sequester the substrate. Such sequestration combined with competition for each phosphosite provides an intuitive explanation for the sigmoidal shifts in levels of phosphorylated substrate. Additionally, we find cases for which the response is not monotonic, but shows instead a peak at intermediate levels of input. Given its generality, we expect the mechanism described by our model to often underlay decision-making circuits in eukaryotic cells.

  16. Deposition on disordered substrates with precursor layer diffusion

    Science.gov (United States)

    Filipe, J. A. N.; Rodgers, G. J.; Tavassoli, Z.

    1998-09-01

    Recently we introduced a one-dimensional accelerated random sequential adsorption process as a model for chemisorption with precursor layer diffusion. In this paper we consider this deposition process on disordered or impure substrates. The problem is solved exactly on both the lattice and continuum and for various impurity distributions. The results are compared with those from the standard random sequential adsorption model.

  17. An improved method to unravel phosphoacceptors in Ser/Thr protein kinase-phosphorylated substrates.

    Science.gov (United States)

    Molle, Virginie; Leiba, Jade; Zanella-Cléon, Isabelle; Becchi, Michel; Kremer, Laurent

    2010-11-01

    Identification of the phosphorylated residues of bacterial Ser/Thr protein kinase (STPK) substrates still represents a challenging task. Herein, we present a new strategy allowing the rapid determination of phosphoacceptors in kinase substrates, essentially based on the dual expression of the kinase with its substrate in the surrogate E. coli, followed by MS analysis in a single-step procedure. The performance of this strategy is illustrated using two distinct proteins from Mycobacterium tuberculosis as model substrates, the GroEL2 and HspX chaperones. A comparative analysis with a standard method that includes mass spectrometry analysis of in vitro phosphorylated substrates is also addressed.

  18. Design, fabrication and characterisation of advanced substrate crosstalk suppression structures in silicon on insulator substrates with buried ground planes (GPSOI)

    International Nuclear Information System (INIS)

    Stefanou, Stefanos

    2002-07-01

    Substrate crosstalk or coupling has been acknowledged to be a limiting factor in mixed signal RF integration. Although high levels of integration and high frequencies of operation are desirable for mixed mode RF and microwave circuits, they make substrate crosstalk more pronounced and may lead to circuit performance degradation. High signal isolation is dictated by requirements for low power dissipation, reduced number of components and lower integration costs for feasible system-on-chip (SoC) solutions. Substrate crosstalk suppression in ground plane silicon-on-insulator (GPSOI) substrates is investigated in this thesis. Test structures are designed and fabricated on SOI substrates with a buried WSi 2 plane that is connected to ground; hence it is called a ground plane. A Faraday cage structure that exhibits very high degrees of signal isolation is presented and compared to other SOI isolation schemes. The Faraday cage structure is shown to achieve 20 dB increased isolation in the frequency range of 0.5-50 GHz compared to published data for high resistivity (200 Ωcm) thin film SOI substrates with no ground planes, but where capacitive guard rings were used. The measurement results are analysed with the aid of planar electromagnetic simulators and compact lumped element models of all the fabricated test structures are developed. The accuracy of the lumped models is validated against experimental measurements. (author)

  19. 8-band and 14-band kp modeling of electronic band structure and material gain in Ga(In)AsBi quantum wells grown on GaAs and InP substrates

    Energy Technology Data Exchange (ETDEWEB)

    Gladysiewicz, M.; Wartak, M. S. [Faculty of Fundamental Problems of Technology, Wroclaw University of Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw (Poland); Department of Physics and Computer Science, Wilfrid Laurier University, Waterloo, Ontario N2L 3C5 (Canada); Kudrawiec, R. [Faculty of Fundamental Problems of Technology, Wroclaw University of Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw (Poland)

    2015-08-07

    The electronic band structure and material gain have been calculated for GaAsBi/GaAs quantum wells (QWs) with various bismuth concentrations (Bi ≤ 15%) within the 8-band and 14-band kp models. The 14-band kp model was obtained by extending the standard 8-band kp Hamiltonian by the valence band anticrossing (VBAC) Hamiltonian, which is widely used to describe Bi-related changes in the electronic band structure of dilute bismides. It has been shown that in the range of low carrier concentrations n < 5 × 10{sup 18 }cm{sup −3}, material gain spectra calculated within 8- and 14-band kp Hamiltonians are similar. It means that the 8-band kp model can be used to calculate material gain in dilute bismides QWs. Therefore, it can be applied to analyze QWs containing new dilute bismides for which the VBAC parameters are unknown. Thus, the energy gap and electron effective mass for Bi-containing materials are used instead of VBAC parameters. The electronic band structure and material gain have been calculated for 8 nm wide GaInAsBi QWs on GaAs and InP substrates with various compositions. In these QWs, Bi concentration was varied from 0% to 5% and indium concentration was tuned in order to keep the same compressive strain (ε = 2%) in QW region. For GaInAsBi/GaAs QW with 5% Bi, gain peak was determined to be at about 1.5 μm. It means that it can be possible to achieve emission at telecommunication windows (i.e., 1.3 μm and 1.55 μm) for GaAs-based lasers containing GaInAsBi/GaAs QWs. For GaInAsBi/Ga{sub 0.47}In{sub 0.53}As/InP QWs with 5% Bi, gain peak is predicted to be at about 4.0 μm, i.e., at the wavelengths that are not available in current InP-based lasers.

  20. Real-time sensing of epithelial cell-cell and cell-substrate interactions by impedance spectroscopy on porous substrates

    Energy Technology Data Exchange (ETDEWEB)

    Mondal, D.; RoyChaudhuri, C., E-mail: chirosreepram@yahoo.com [Department of Electronics and Telecommunication Engineering, Indian Institute of Engineering Science and Technology, Shibpur, Howrah 711103 (India); Pal, D. [Department of Aerospace Engineering and Applied Mechanics, Indian Institute of Engineering Science and Technology, Shibpur, Howrah 711103 (India)

    2015-07-28

    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{sub b}) corresponding to the initial adhesion phase of cells. It is observed that R{sub 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.

  1. 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

  2. Molecular docking simulations provide insights in the substrate binding sites and possible substrates of the ABCC6 transporter.

    Directory of Open Access Journals (Sweden)

    Mohammad Jakir Hosen

    Full Text Available The human ATP-binding cassette family C member 6 (ABCC6 gene encodes an ABC transporter protein (ABCC6, primarily expressed in liver and kidney. Mutations in the ABCC6 gene cause pseudoxanthoma elasticum (PXE, an autosomal recessive connective tissue disease characterized by ectopic mineralization of the elastic fibers. The pathophysiology underlying PXE is incompletely understood, which can at least partly be explained by the undetermined nature of the ABCC6 substrates as well as the unknown substrate recognition and binding sites. Several compounds, including anionic glutathione conjugates (N-ethylmaleimide; NEM-GS and leukotriene C4 (LTC4 were shown to be modestly transported in vitro; conversely, vitamin K3 (VK3 was demonstrated not to be transported by ABCC6. To predict the possible substrate binding pockets of the ABCC6 transporter, we generated a 3D homology model of ABCC6 in both open and closed conformation, qualified for molecular docking and virtual screening approaches. By docking 10 reported in vitro substrates in our ABCC6 3D homology models, we were able to predict the substrate binding residues of ABCC6. Further, virtual screening of 4651 metabolites from the Human Serum Metabolome Database against our open conformation model disclosed possible substrates for ABCC6, which are mostly lipid and biliary secretion compounds, some of which are found to be involved in mineralization. Docking of these possible substrates in the closed conformation model also showed high affinity. Virtual screening expands this possibility to explore more compounds that can interact with ABCC6, and may aid in understanding the mechanisms leading to PXE.

  3. 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.

  4. 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...

  5. Interrogating the Molecular Basis for Substrate Recognition in Serotonin and Dopamine Transporters with High-Affinity Substrate-Based Bivalent Ligands

    DEFF Research Database (Denmark)

    Andersen, Jacob; Ladefoged, Lucy Kate; Kristensen, Trine N. Bjerre

    2016-01-01

    insight into substrate recognition in SERT and DAT. An optimized bivalent ligand comprising two serotonin moieties binds SERT with 3,800-fold increased affinity compared to that of serotonin, suggesting that the human transporters have two distinct substrate binding sites. We show that the bivalent...... ligands are inhibitors of SERT and an experimentally validated docking model suggests that the bivalent compounds bind with one substrate moiety in the central binding site (the S1 site), whereas the other substrate moiety binds in a distinct binding site (the S2 site). A systematic study of nonconserved...

  6. 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 ...

  7. 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

  8. Interactions between Casein kinase Iepsilon (CKIepsilon and two substrates from disparate signaling pathways reveal mechanisms for substrate-kinase specificity.

    Directory of Open Access Journals (Sweden)

    Caroline Lund Dahlberg

    Full Text Available Members of the Casein Kinase I (CKI family of serine/threonine kinases regulate diverse biological pathways. The seven mammalian CKI isoforms contain a highly conserved kinase domain and divergent amino- and carboxy-termini. Although they share a preferred target recognition sequence and have overlapping expression patterns, individual isoforms often have specific substrates. In an effort to determine how substrates recognize differences between CKI isoforms, we have examined the interaction between CKIepsilon and two substrates from different signaling pathways.CKIepsilon, but not CKIalpha, binds to and phosphorylates two proteins: Period, a transcriptional regulator of the circadian rhythms pathway, and Disheveled, an activator of the planar cell polarity pathway. We use GST-pull-down assays data to show that two key residues in CKIalpha's kinase domain prevent Disheveled and Period from binding. We also show that the unique C-terminus of CKIepsilon does not determine Dishevelled's and Period's preference for CKIepsilon nor is it essential for binding, but instead plays an auxillary role in stabilizing the interactions of CKIepsilon with its substrates. We demonstrate that autophosphorylation of CKIepsilon's C-terminal tail prevents substrate binding, and use mass spectrometry and chemical crosslinking to reveal how a phosphorylation-dependent interaction between the C-terminal tail and the kinase domain prevents substrate phosphorylation and binding.The biochemical interactions between CKIepsilon and Disheveled, Period, and its own C-terminus lead to models that explain CKIepsilon's specificity and regulation.

  9. Memory Consolidation and Neural Substrate of Reward

    Directory of Open Access Journals (Sweden)

    Redolar-Ripoll, Diego

    2012-08-01

    Full Text Available The aim of this report is to analyze the relationships between reward and learning and memory processes. Different studies have described how information about rewards influences behavior and how the brain uses this reward information to control learning and memory processes. Reward nature seems to be processed in different ways by neurons in different brain structures, ranging from the detection and perception of rewards to the use of information about predicted rewards for the control of goal-directed behavior. The neural substrate underling this processing of reward information is a reliable way of improving learning and memory processes. Evidence from several studies indicates that this neural system can facilitate memory consolidation in a wide variety of learning tasks. From a molecular perspective, certain cardinal features of reward have been described as forms of memory. Studies of human addicts and studies in animal models of addiction show that chronic drug exposure produces stable changes in the brain at the cellular and molecular levels that underlie the long-lasting behavioral plasticity associated with addiction. These molecular and cellular adaptations involved in addiction are also implicated in learning and memory processes. Dopamine seems to be a critical common signal to activate different genetic mechanisms that ultimately remodel synapses and circuits. Despite memory is an active and complex process mediated by different brain areas, the neural substrate of reward is able to improve memory consolidation in a several paradigms. We believe that there are many equivalent traits between reward and learning and memory processes.

  10. Superhydrophobicity enhancement through substrate flexibility

    Science.gov (United States)

    Vasileiou, Thomas; Gerber, Julia; Prautzsch, Jana; Schutzius, Thomas; Poulikakos, Dimos

    2017-11-01

    Inspired by manifestations in nature, micro/nanoengineering superhydrophobic surfaces has been the focus of much work. Generally, hydrophobicity is increased through the combined effects of surface texturing and chemistry; being durable, rigid substrate materials are the norm. However, many natural and technical materials are flexible, and the resulting effect on hydrophobicity has been largely unexplored. Here, we show that the rational tuning of flexibility can work collaboratively with the surface micro/nanotexture to enhance liquid repellency performance, defined by impalement and breakup resistance, contact time reduction, and restitution coefficient increase. Reduction in substrate stiffness and areal density imparts immediate acceleration and intrinsic responsiveness to impacting droplets, mitigating the collision and lowering the impalement probability by 60 % without the need for active actuation. We demonstrate the above discoveries with materials ranging from thin steel or polymer sheets to butterfly wings. Partial support of the Swiss National Science Foundation under Grant 162565 and the European Research Council under Advanced Grant 669908 (INTICE) is acknowledged.

  11. Quartz substrate infrared photonic crystal

    Science.gov (United States)

    Ghadiri, Khosrow; Rejeb, Jalel; Vitchev, Vladimir N.

    2003-01-01

    This paper presents the fabrication of a planar photonic crystal (p2c) made of a square array of dielectric rods embedded in air, operating in the infrared spectrum. A quartz substrate is employed instead of the commonly used silicon or column III-V substrate. Our square structure has a normalized cylinder radius-to-pitch ratio of r/a = 0.248 and dielectric material contrast ɛr of 4.5. We choose a Z-cut synthetic quartz for its cut (geometry), and etching properties. Then a particular Z-axis etching process is employed in order to ensure the sharp-edged verticality of the rods and fast etching speed. We also present the computer simulations that allowed the establishment of the photonic band gaps (PBG) of our photonic crystal, as well as the actual measurements. An experimental measurement have been carried out and compared with different simulations. It was found that experimental results are in good agreement with different simulation results. Finally, a frequency selective device for optical communication based on the introduction of impurity sites in the photonic crystal is presented. With our proposed structure Optical System on a Chip (OsoC) with micro-cavity based active devices such as lasers, diodes, modulators, couplers, frequency selective emitters, add-drop filters, detectors, mux/demuxes and polarizers connected by passive waveguide links can be realized.

  12. Automated cassette-to-cassette substrate handling system

    Science.gov (United States)

    Kraus, Joseph Arthur; Boyer, Jeremy James; Mack, Joseph; DeChellis, Michael; Koo, Michael

    2014-03-18

    An automated cassette-to-cassette substrate handling system includes a cassette storage module for storing a plurality of substrates in cassettes before and after processing. A substrate carrier storage module stores a plurality of substrate carriers. A substrate carrier loading/unloading module loads substrates from the cassette storage module onto the plurality of substrate carriers and unloads substrates from the plurality of substrate carriers to the cassette storage module. A transport mechanism transports the plurality of substrates between the cassette storage module and the plurality of substrate carriers and transports the plurality of substrate carriers between the substrate carrier loading/unloading module and a processing chamber. A vision system recognizes recesses in the plurality of substrate carriers corresponding to empty substrate positions in the substrate carrier. A processor receives data from the vision system and instructs the transport mechanism to transport substrates to positions on the substrate carrier in response to the received data.

  13. 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.

  14. Phonon scattering in graphene over substrate steps

    International Nuclear Information System (INIS)

    Sevinçli, H.; Brandbyge, M.

    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 in the range between 5% and 47%. We also consider the transmission across linear kinks formed by adsorption of atomic hydrogen at the bends and find that individual kinks suppress thermal conduction substantially, especially at high temperatures. Our analysis show that substrate irregularities can be detrimental for thermal conduction even for small step heights.

  15. Method For Producing Mechanically Flexible Silicon Substrate

    KAUST Repository

    Hussain, Muhammad Mustafa; Rojas, Jhonathan Prieto

    2014-01-01

    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.

  16. Evaluation of different substrates for inkjet printing of rasagiline mesylate

    DEFF Research Database (Denmark)

    Genina, Natalja; Janßen, Eva Maria; Breitenbach, Armin

    2013-01-01

    The main goal of the present study was to evaluate applicability of the different model substrates, namely orodispersible films (ODFs), porous copy paper sheets, and water impermeable transparency films (TFs) in preparation of the inkjet-printed drug-delivery systems. Rasagiline mesylate (RM...

  17. 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.

  18. Ductile film delamination from compliant substrates using hard overlayers.

    Science.gov (United States)

    Cordill, M J; Marx, V M; Kirchlechner, C

    2014-11-28

    Flexible electronic devices call for copper and gold metal films to adhere well to polymer substrates. Measuring the interfacial adhesion of these material systems is often challenging, requiring the formulation of different techniques and models. Presented here is a strategy to induce well defined areas of delamination to measure the adhesion of copper films on polyimide substrates. The technique utilizes a stressed overlayer and tensile straining to cause buckle formation. The described method allows one to examine the effects of thin adhesion layers used to improve the adhesion of flexible systems.

  19. Optically transparent frequency selective surfaces on flexible thin plastic substrates

    Energy Technology Data Exchange (ETDEWEB)

    Dewani, Aliya A., E-mail: a.ashraf@griffith.edu.au; O’Keefe, Steven G.; Thiel, David V.; Galehdar, Amir [School Of Electrical Engineering, Griffith University, Brisbane, 4111 (Australia)

    2015-02-15

    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.

  20. Optically transparent frequency selective surfaces on flexible thin plastic substrates

    Science.gov (United States)

    Dewani, Aliya A.; O'Keefe, Steven G.; Thiel, David V.; Galehdar, Amir

    2015-02-01

    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.

  1. A pentacene monolayer trapped between graphene and a substrate.

    Science.gov (United States)

    Zhang, Qicheng; Peng, Boyu; Chan, Paddy Kwok Leung; Luo, Zhengtang

    2015-09-21

    A self-assembled pentacene monolayer can be fabricated between the solid-solid interface of few-layered graphene (FLG) and the mica substrate, through a diffusion-spreading method. By utilizing a transfer method that allows us to sandwich pentacene between graphene and mica, followed by controlled annealing, we enabled the diffused pentacene to be trapped in the interfaces and led to the formation of a stable monolayer. We found that the formation of a monolayer is kinetically favored by using a 2D Ising lattice gas model for pentacene trapped between the graphene-substrate interfaces. This kinetic Monte Carlo simulation results indicate that, due to the graphene substrate enclosure, the spreading of the first layer proceeds faster than the second layer, as the kinetics favors the filling of voids by molecules from the second layer. This graphene assisted monolayer assembly method provides a new avenue for the fabrication of two-dimensional monolayer structures.

  2. 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.

  3. Chemical vapor deposition of yttria stabilized zirconia in porous substrates

    International Nuclear Information System (INIS)

    Carolan, M.F.; Michaels, J.N.

    1987-01-01

    Electrochemical vapor deposition (EVD) of yttria stabilized zirconia (YSZ) is the preferred route to the production of thin films of YSZ on porous substrates. This process has been used in the construction of both fuel cells and steam electrolyzers. A critical aspect of the EVD process is an initial chemical vapor deposition phase in which the pores of a porous substrate are plugged by YSZ. In this process, water vapor and a mixture of gaseous zirconium chloride and yttrium chloride diffuse into the porous substrate from opposite sides and react to form YSZ and HCl ga. During the second stage of the process a continuous dense film of electrolyte is formed by a tarnishing-type process. Experimentally it is observed that the pores plug within a few pore diameters of the metal chloride face of the substrate. A kinetic rate expression that is first order in metal chloride but zero order in water is best able to explain this phenomenon. With this rate expression, the pores always plug near the metal chloride face. The model predicts less pore narrowing to occur as the ratio of the reaction rate to the diffusion rate of the metal chloride is increased. A kinetic rate expression that is first order in both water and metal chloride predicts that the pores plug much deeper in the substrate

  4. A liquid aluminum corrosion resistance surface on steel substrate

    International Nuclear Information System (INIS)

    Wang Deqing; Shi Ziyuan; Zou Longjiang

    2003-01-01

    The process of hot dipping pure aluminum on a steel substrate followed by oxidation was studied to form a surface layer of aluminum oxide resistant to the corrosion of aluminum melt. The thickness of the pure aluminum layer on the steel substrate is reduced with the increase in temperature and time in initial aluminizing, and the thickness of the aluminum layer does not increase with time at given temperature when identical temperature and complete wetting occur between liquid aluminum and the substrate surface. The thickness of the Fe-Al intermetallic layer on the steel base is increased with increasing bath temperature and time. Based on the experimental data and the mathematics model developed by the study, a maximum exists in the thickness of the Fe-Al intermetallic at certain dipping temperature. X-ray diffraction (XRD) and energy dispersive X-ray (EDX) analysis reveals that the top portion of the steel substrate is composed of a thin layer of α-Al 2 O 3 , followed by a thinner layer of FeAl 3 , and then a much thicker one of Fe 2 Al 5 on the steel base side. In addition, there is a carbon enrichment zone in diffusion front. The aluminum oxide surface formed on the steel substrate is in perfect condition after corrosion test in liquid aluminum at 750 deg. C for 240 h, showing extremely good resistance to aluminum melt corrosion

  5. Computational Approach for Epitaxial Polymorph Stabilization through Substrate Selection

    Energy Technology Data Exchange (ETDEWEB)

    Ding, Hong; Dwaraknath, Shyam S.; Garten, Lauren; Ndione, Paul; Ginley, David; Persson, Kristin A.

    2016-05-25

    With the ultimate goal of finding new polymorphs through targeted synthesis conditions and techniques, we outline a computational framework to select optimal substrates for epitaxial growth using first principle calculations of formation energies, elastic strain energy, and topological information. To demonstrate the approach, we study the stabilization of metastable VO2 compounds which provides a rich chemical and structural polymorph space. We find that common polymorph statistics, lattice matching, and energy above hull considerations recommends homostructural growth on TiO2 substrates, where the VO2 brookite phase would be preferentially grown on the a-c TiO2 brookite plane while the columbite and anatase structures favor the a-b plane on the respective TiO2 phases. Overall, we find that a model which incorporates a geometric unit cell area matching between the substrate and the target film as well as the resulting strain energy density of the film provide qualitative agreement with experimental observations for the heterostructural growth of known VO2 polymorphs: rutile, A and B phases. The minimal interfacial geometry matching and estimated strain energy criteria provide several suggestions for substrates and substrate-film orientations for the heterostructural growth of the hitherto hypothetical anatase, brookite, and columbite polymorphs. These criteria serve as a preliminary guidance for the experimental efforts stabilizing new materials and/or polymorphs through epitaxy. The current screening algorithm is being integrated within the Materials Project online framework and data and hence publicly available.

  6. Non-permeable substrate carrier for electroplating

    Science.gov (United States)

    Abas, Emmanuel Chua; Chen, Chen-An; Ma, Diana Xiaobing; Ganti, Kalyana Bhargava

    2012-11-27

    One embodiment relates to a substrate carrier for use in electroplating a plurality of substrates. The substrate carrier comprises a non-conductive carrier body on which the substrates are to be held. Electrically-conductive lines are embedded within the carrier body, and a plurality of contact clips are coupled to the electrically-conductive lines embedded within the carrier body. The contact clips hold the substrates in place and electrically couple the substrates to the electrically-conductive lines. The non-conductive carrier body is continuous so as to be impermeable to flow of electroplating solution through the non-conductive carrier body. Other embodiments, aspects and features are also disclosed.

  7. Optically controlled electrophoresis with a photoconductive substrate

    Science.gov (United States)

    Inami, Wataru; Nagashima, Taiki; Kawata, Yoshimasa

    2018-05-01

    A photoconductive substrate is used to perform electrophoresis. Light-induced micro-particle flow manipulation is demonstrated without using a fabricated flow channel. The path along which the particles were moved was formed by an illuminated light pattern on the substrate. Because the substrate conductivity and electric field distribution can be modified by light illumination, the forces acting on the particles can be controlled. This technique has potential applications as a high functionality analytical device.

  8. Substrate optimization for integrated circuit antennas

    OpenAIRE

    Alexopoulos, N. G.; Katehi, P. B.; Rutledge, D. B.

    1982-01-01

    Imaging systems in microwaves, millimeter and submillimeter wave applications employ printed circuit antenna elements. The effect of substrate properties is analyzed in this paper by both reciprocity theorem as well as integral equation approach for infinitesimally short as well as finite length dipole and slot elements. Radiation efficiency and substrate surface wave guidance is studied for practical substrate materials as GaAs, Silicon, Quartz and Duroid.

  9. Identification of putative substrates for cynomolgus monkey cytochrome P450 2C8 by substrate depletion assays with 22 human P450 substrates and inhibitors.

    Science.gov (United States)

    Hosaka, Shinya; Murayama, Norie; Satsukawa, Masahiro; Uehara, Shotaro; Shimizu, Makiko; Iwasaki, Kazuhide; Iwano, Shunsuke; Uno, Yasuhiro; Yamazaki, Hiroshi

    2016-07-01

    Cynomolgus monkeys are widely used in drug developmental stages as non-human primate models. Previous studies used 89 compounds to investigate species differences associated with cytochrome P450 (P450 or CYP) function that reported monkey specific CYP2C76 cleared 19 chemicals, and homologous CYP2C9 and CYP2C19 metabolized 17 and 30 human CYP2C9 and/or CYP2C19 substrates/inhibitors, respectively. In the present study, 22 compounds selected from viewpoints of global drug interaction guidances and guidelines were further evaluated to seek potential substrates for monkey CYP2C8, which is highly homologous to human CYP2C8 (92%). Amodiaquine, montelukast, quercetin and rosiglitazone, known as substrates or competitive inhibitors of human CYP2C8, were metabolically depleted by recombinant monkey CYP2C8 at relatively high rates. Taken together with our reported findings of the slow eliminations of amodiaquine and montelukast by monkey CYP2C9, CYP2C19 and CYP2C76, the present results suggest that these at least four chemicals may be good marker substrates for monkey CYP2C8. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

  10. Seneca Valley Virus 3Cpro Substrate Optimization Yields Efficient Substrates for Use in Peptide-Prodrug Therapy.

    Directory of Open Access Journals (Sweden)

    Linde A Miles

    Full Text Available The oncolytic picornavirus Seneca Valley Virus (SVV-001 demonstrates anti-tumor activity in models of small cell lung cancer (SCLC, but may ultimately need to be combined with cytotoxic therapies to improve responses observed in patients. Combining SVV-001 virotherapy with a peptide prodrug activated by the viral protease 3Cpro is a novel strategy that may increase the therapeutic potential of SVV-001. Using recombinant SVV-001 3Cpro, we measured cleavage kinetics of predicted SVV-001 3Cpro substrates. An efficient substrate, L/VP4 (kcat/KM = 1932 ± 183 M(-1s(-1, was further optimized by a P2' N→P substitution yielding L/VP4.1 (kcat/KM = 17446 ± 2203 M(-1s(-1. We also determined essential substrate amino acids by sequential N-terminal deletion and substitution of amino acids found in other picornavirus genera. A peptide corresponding to the L/VP4.1 substrate was selectively cleaved by SVV-001 3Cpro in vitro and was stable in human plasma. These data define an optimized peptide substrate for SVV-001 3Cpro, with direct implications for anti-cancer therapeutic development.

  11. 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

  12. Adhesion of rhodium films on metallic substrates

    Energy Technology Data Exchange (ETDEWEB)

    Marot, L. [Department of Physics, University of Basel, Klingelbergstrasse 82, CH-4056 Basel (Switzerland)], E-mail: laurent.marot@unibas.ch; Covarel, G.; Tuilier, M.-H. [Laboratoire Mecanique, Materiaux et Procedes de Fabrication, Pole STIC-SPI-Math 61 rue Albert Camus, Universite de Haute-Alsace, F-68093 - Mulhouse Cedex (France); Steiner, R.; Oelhafen, P. [Department of Physics, University of Basel, Klingelbergstrasse 82, CH-4056 Basel (Switzerland)

    2008-09-01

    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.

  13. 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...

  14. Experimental and numerical study of a YBCO pancake coil with a magnetic substrate

    International Nuclear Information System (INIS)

    Zhang Min; Coombs, T A; Kvitkovic, J; Pamidi, S V

    2012-01-01

    A finite element model for a YBCO pancake coil with a magnetic substrate is developed in this paper. An axial symmetrical H formulation and the E–J power law are used to construct the model, with the magnetic substrate considered by introducing an extra time-dependent term in the formula. A pancake coil is made and tested. The measurement of critical current and transport loss is compared to the model result, showing good consistency. The influence of magnetic substrate in the condition of AC and DC current is studied. The AC loss decreases without a magnetic substrate. It is observed that when the applied DC current approaches the critical current the coil turn loss profile changes completely in the presence of magnetic substrate due to the change of magnetic field distribution. (paper)

  15. 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.

  16. 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...

  17. 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.

  18. Analyses of edge effects on residual stresses in film strip/substrate systems

    International Nuclear Information System (INIS)

    Hsueh, Chun-Hway

    2000-01-01

    The residual stress distribution in a thin-film strip overlaid on a substrate is influenced by the edges of the strip. An analytical model is developed to derive a closed-form solution for the stress distribution along the film width. Because the film is much thinner than the substrate, the stress variation through the film thickness is ignored; however, the stress variation through the substrate thickness is considered in the analysis. Compared to the existing analytical models, the present model is more rigorous and the analytical results agree better with both finite element results and experimental measurements. (c) 2000 American Institute of Physics

  19. 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.

  20. 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.

  1. Organism-substrate relationships in lowland streams

    NARCIS (Netherlands)

    Tolkamp, H.H.

    1980-01-01

    A field and laboratory study on the microdistribution of bottom dwelling macroinvertebrates to investigate the role of the stream substrate In the development and preservation of the macroinvertebrate communities in natural, undisturbed lowland streams is described. Field data on bottom substrates

  2. 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...

  3. 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

    2013-10-29

    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.

  4. 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.

  5. 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 ...

  6. 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...

  7. 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 sim...... plasma treatment enables formation of the oxidized PDMS hard mask, PS block removal and polymer or graphene substrate patterning....

  8. 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].

  9. Alternative Substrate Metabolism in Yarrowia lipolytica

    Directory of Open Access Journals (Sweden)

    Michael Spagnuolo

    2018-05-01

    Full Text Available Recent advances in genetic engineering capabilities have enabled the development of oleochemical producing strains of Yarrowia lipolytica. Much of the metabolic engineering effort has focused on pathway engineering of the product using glucose as the feedstock; however, alternative substrates, including various other hexose and pentose sugars, glycerol, lipids, acetate, and less-refined carbon feedstocks, have not received the same attention. In this review, we discuss recent work leading to better utilization of alternative substrates. This review aims to provide a comprehensive understanding of the current state of knowledge for alternative substrate utilization, suggest potential pathways identified through homology in the absence of prior characterization, discuss recent work that either identifies, endogenous or cryptic metabolism, and describe metabolic engineering to improve alternative substrate utilization. Finally, we describe the critical questions and challenges that remain for engineering Y. lipolytica for better alternative substrate utilization.

  10. 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.

  11. Consequences of elastic anisotropy in patterned substrate heteroepitaxy.

    Science.gov (United States)

    Dixit, Gopal Krishna; Ranganathan, Madhav

    2018-06-13

    The role of elastic anisotropy on quantum dot formation and evolution on a pre-patterned substrate is evaluated within the framework of a continuum model. We first extend the formulation for surface evolution to take elastic anisotropy into account. Using a small slope approximation, we derive the evolution equation and show how it can be numerically implemented up to linear and second order for stripe and egg-carton patterned substrates using an accurate and efficient procedure. The semi--infinite nature of the substrate is used to solve the elasticity problem subject to other boundary conditions at the free surface and at the film--substrate interface. The positioning of the quantum dots with respect to the peaks and valleys of the pattern is explained by a competition between the length scale of the pattern and the wavelength of the Asaro--Tiller--Grinfeld instability, which is also affected by the elastic anisotropy. The alignment of dots is affected by a competition between the elastic anisotropy of the film and the pattern orientation. A domain of pattern inversion, wherein the quantum dots form exclusively in the valleys of the patterns is identified as a function of the average film thickness and the elastic anisotropy, and the time--scale for this inversion as function of height is analyzed. © 2018 IOP Publishing Ltd.

  12. Cellulase biosynthesis by trichoderma viride on soluble substrates

    Energy Technology Data Exchange (ETDEWEB)

    Shin, S B; Kitagawa, Y; Suga, K; Ichikawa, K

    1978-01-01

    Batch and continuous cultures of Trichoderma viride QM 6a were carried out using either glucose or cellobiose as the sole carbon source. From the data obtained in the continuous culture with glucose as substrate, growth parameters of this fungus ..mu../sub m/, K/sub s/, m and Y were identified. In the case of glucose as substrate, there were extremely low levels of cellobiase and no detectable cellulase activity in both batch and continuous cultures. The inducible cellobiase was an intracellular enzyme, produced in association with cell growth in batch culture on cellobiose as substrate. A kinetic model for cellobiose degradation and cell growth is proposed. A significant increase in the extracellular cellulase productivity was obtained in the range of low dilution rates from 0.025 h/sup -1/ to 0.2 h/sup -1/ in the continuous culture on cellobiose. From the results of these experiments, it was concluded that in continuous culture on cellobiose as substrate the cellulase activity was determined by the balance between induction and catabolite repression.

  13. 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.

  14. 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

  15. 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

  16. Transport ac loss studies of YBCO coated conductors with nickel alloy substrates

    International Nuclear Information System (INIS)

    Duckworth, R C; Thompson, J R; Gouge, M J; Lue, J W; Ijaduola, A O; Yu, D; Verebelyi, D T

    2003-01-01

    Transport alternating current (ac) loss measurements were performed on a series of rolling-assisted biaxially textured substrate (RABiTS) processed YBa 2 Cu 3 O x (YBCO) coated conductors at 77 K. While each sample possessed a 1 μm layer of YBCO and a 3 μm silver cap layer, two different nickel alloy substrates were used and their impact on the ac loss was examined. Both substrates possessed a 75 μm Ni-5 at%W base, but one substrate also had a 2 μm nickel overlayer as part of the buffer layer architecture. The ac losses, which were determined by thermal and electrical measurements, contained two dominant contributions: superconductive hysteresis in the YBCO and ferromagnetic hysteresis in the substrates. The superconductive component followed the Norris elliptic model for the substrate with the nickel overlayer and the Norris thin strip model for the substrate without the nickel overlayer. The substrates' ferromagnetic loss was determined separately through magnetization measurements, which showed that this loss contribution was independent of the presence of the nickel overlayer for effective ac currents less than 50 A. While the overall loss was lower for the thin-strip-like conductor with no nickel overlayer, further research is necessary to strengthen this connection

  17. 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.

  18. Targeting Biological Sensing with Commercial SERS Substrates

    Science.gov (United States)

    2012-09-01

    substrate substrate. Sl x 4 mm waf urement to re ossible contam substrates, fiv resented as an e being used f tigated, and nam eived in an ac cations...targeted nanotechnology-based inhalation co-delivery of anticancer drugs and siRNA," Journal of Drug Targeting, 900-914 (2011). [35] Jong , H.J., Na...J.H., Jin, B.S., Lee, W.K., Lee, W.H., Jung, H.J., Kim , S.C., Lim, S.H., Yu, Y.G., "Identification of Dinitrotoluene Selective Peptides by Phage

  19. Ion implantation methods for semiconductor substrates

    International Nuclear Information System (INIS)

    Matsushita, T.; Mamine, T.; Hayashi, H.; Nishiyama, K.

    1980-01-01

    A method of ion implantation for controlling the life time of minority carriers in a semiconductor substrate and hence to reduce the temperature dependency of the life time, comprises implanting iron ions into an N type semiconductor substrate with a dosage of 10 10 to 10 15 ions cm -2 , and then heat-treating the implanted substrate at 850 0 to 1250 0 C. The method is applicable to the production of diodes, transistors, Si controlled rectifiers and gate controlled switching devices. (author)

  20. 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...

  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. 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.

  4. 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.

  5. Na+/substrate Coupling in the Multidrug Antiporter NorM Probed with a Spin-labeled Substrate

    Science.gov (United States)

    Steed, P. Ryan; Stein, Richard A.; Mishra, Smriti; Goodman, Michael C.; Mchaourab, Hassane S.

    2013-01-01

    NorM of the multidrug and toxic compound extrusion (MATE) family of transporters couples the efflux of a broad range of hydrophobic molecules to an inward Na+ gradient across the cell membrane. Several crystal structures of MATE transporters revealed distinct substrate binding sites leading to differing models of the mechanism of ion-coupled substrate extrusion. In the experiments reported here, we observed that a spin-labeled derivative of daunorubicin, Ruboxyl, is transported by NorM from Vibrio cholerae. It is therefore ideal to characterize mechanistically relevant binding interactions with NorM and to directly address the coupling of ion and drug binding. Fluorescence and EPR experiments revealed that Ruboxyl binds to NorM with micromolar affinity and becomes immobilized upon binding, even in the presence of Na+. Using double electron-electron resonance (DEER) spectroscopy, we determined that Ruboxyl binds to a single site on the periplasmic side of the protein. The presence of Na+ did not translocate the substrate to a second site as previously proposed. These experiments surprisingly show that Na+ does not affect the affinity or location of the substrate binding site on detergent-solubilized NorM, thus suggesting that additional factors beyond simple mutual exclusivity of binding, such as the presence of a Na+ gradient across the native membrane, govern Na+/drug coupling during antiport. PMID:23902581

  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. 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

  8. 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.

  9. Iron films deposited on porous alumina substrates

    Energy Technology Data Exchange (ETDEWEB)

    Yamada, Yasuhiro, E-mail: yyasu@rs.kagu.tus.ac.jp; Tanabe, Kenichi; Nishida, Naoki [Tokyo University of Science (Japan); Kobayashi, Yoshio [The University of Electro-Communications (Japan)

    2016-12-15

    Iron films were deposited on porous alumina substrates using an arc plasma gun. The pore sizes (120 – 250 nm) of the substrates were controlled by changing the temperature during the anodic oxidation of aluminum plates. Iron atoms penetrated into pores with diameters of less than 160 nm, and were stabilized by forming γ-Fe, whereas α-Fe was produced as a flat plane covering the pores. For porous alumina substrates with pore sizes larger than 200 nm, the deposited iron films contained many defects and the resulting α-Fe had smaller hyperfine magnetic fields. In addition, only a very small amount of γ-Fe was obtained. It was demonstrated that the composition and structure of an iron film can be affected by the surface morphology of the porous alumina substrate on which the film is grown.

  10. 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 ...

  11. Palladium clusters deposited on the heterogeneous substrates

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Kun, E-mail: cqdxwk@126.com [College of Power Engineering, Chongqing University, Chongqing 400044 (China); Key Laboratory of Low-grade Energy Utilization Technologies and Systems, Ministry of Education of PRC, Chongqing 400044 (China); Liu, Juanfang, E-mail: juanfang@cqu.edu.cn [College of Power Engineering, Chongqing University, Chongqing 400044 (China); Key Laboratory of Low-grade Energy Utilization Technologies and Systems, Ministry of Education of PRC, Chongqing 400044 (China); Chen, Qinghua, E-mail: qhchen@cqu.edu.cn [College of Power Engineering, Chongqing University, Chongqing 400044 (China); Key Laboratory of Low-grade Energy Utilization Technologies and Systems, Ministry of Education of PRC, Chongqing 400044 (China)

    2016-07-15

    Graphical abstract: The site-exchange between the substrate and cluster atoms can result in the formation of the surface alloys and the reconstruction of the cluster structure before the collision system approaching the thermal equilibrium. The deposited cluster adjusted the atom arrangement as possibly as to match the substrate lattice arrangement from bottom to up. The structural reconstruction is accompanied by the system potential energy minimization. - Highlights: • The deposition process can divide explicitly into three stages: adsorption, collision, relaxation. • The local melt does not emerge inside the substrate during the deposition process. • Surface alloys are formed by the site-exchange between the cluster and substrate atoms. • The cluster reconstructs the atom arrangement following as the substrate lattice arrangement from bottom to up. • The structural reconstruction ability and scope depend on the cluster size and incident energy. - Abstract: To improve the performance of the Pd composite membrane prepared by the cold spraying technology, it is extremely essential to give insights into the deposition process of the cluster and the heterogeneous deposition of the big Pd cluster at the different incident velocities on the atomic level. The deposition behavior, morphologies, energetic and interfacial configuration were examined by the molecular dynamic simulation and characterized by the cluster flattening ratio, the substrate maximum local temperature, the atom-embedded layer number and the surface-alloy formation. According to the morphology evolution, three deposition stages and the corresponding structural and energy evolution were clearly identified. The cluster deformation and penetrating depth increased with the enhancement of the incident velocity, but the increase degree also depended on the substrate hardness. The interfacial interaction between the cluster and the substrate can be improved by the higher substrate local temperature

  12. Substrate-dependent cell elasticity measured by optical tweezers indentation

    Science.gov (United States)

    Yousafzai, Muhammad S.; Ndoye, Fatou; Coceano, Giovanna; Niemela, Joseph; Bonin, Serena; Scoles, Giacinto; Cojoc, Dan

    2016-01-01

    In the last decade, cell elasticity has been widely investigated as a potential label free indicator for cellular alteration in different diseases, cancer included. Cell elasticity can be locally measured by pulling membrane tethers, stretching or indenting the cell using optical tweezers. In this paper, we propose a simple approach to perform cell indentation at pN forces by axially moving the cell against a trapped microbead. The elastic modulus is calculated using the Hertz-model. Besides the axial component, the setup also allows us to examine the lateral cell-bead interaction. This technique has been applied to measure the local elasticity of HBL-100 cells, an immortalized human cell line, originally derived from the milk of a woman with no evidence of breast cancer lesions. In addition, we have studied the influence of substrate stiffness on cell elasticity by performing experiments on cells cultured on two substrates, bare and collagen-coated, having different stiffness. The mean value of the cell elastic modulus measured during indentation was 26±9 Pa for the bare substrate, while for the collagen-coated substrate it diminished to 19±7 Pa. The same trend was obtained for the elastic modulus measured during the retraction of the cell: 23±10 Pa and 13±7 Pa, respectively. These results show the cells adapt their stiffness to that of the substrate and demonstrate the potential of this setup for low-force probing of modifications to cell mechanics induced by the surrounding environment (e.g. extracellular matrix or other cells).

  13. Fermentative hydrogen production from agroindustrial lignocellulosic substrates

    Science.gov (United States)

    Reginatto, Valeria; Antônio, Regina Vasconcellos

    2015-01-01

    To achieve economically competitive biological hydrogen production, it is crucial to consider inexpensive materials such as lignocellulosic substrate residues derived from agroindustrial activities. It is possible to use (1) lignocellulosic materials without any type of pretreatment, (2) lignocellulosic materials after a pretreatment step, and (3) lignocellulosic materials hydrolysates originating from a pretreatment step followed by enzymatic hydrolysis. According to the current literature data on fermentative H2 production presented in this review, thermophilic conditions produce H2 in yields approximately 75% higher than those obtained in mesophilic conditions using untreated lignocellulosic substrates. The average H2 production from pretreated material is 3.17 ± 1.79 mmol of H2/g of substrate, which is approximately 50% higher compared with the average yield achieved using untreated materials (2.17 ± 1.84 mmol of H2/g of substrate). Biological pretreatment affords the highest average yield 4.54 ± 1.78 mmol of H2/g of substrate compared with the acid and basic pretreatment - average yields of 2.94 ± 1.85 and 2.41 ± 1.52 mmol of H2/g of substrate, respectively. The average H2 yield from hydrolysates, obtained from a pretreatment step and enzymatic hydrolysis (3.78 ± 1.92 mmol of H2/g), was lower compared with the yield of substrates pretreated by biological methods only, demonstrating that it is important to avoid the formation of inhibitors generated by chemical pretreatments. Based on this review, exploring other microorganisms and optimizing the pretreatment and hydrolysis conditions can make the use of lignocellulosic substrates a sustainable way to produce H2. PMID:26273246

  14. Enhanced substrate conversion effiency of fermentation processes

    OpenAIRE

    Sanders, J.P.M.; Weusthuis, R.A.; Mooibroek, H.

    2008-01-01

    The present invention relates to the field of fermentation technology. In particular the invention relates to fermentation processes for the production of a first and a second fermentation product by a single production organism wherein the first product is in a more reduced state than the substrate and the second fermentation product is in a more oxidised state than the substrate yet in a less oxidised state than the final oxidation product CO2, such that the concurrent synthesis of the firs...

  15. 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

  16. 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.

  17. Spectrophotometric determination of substrate-borne polyacrylamide.

    Science.gov (United States)

    Lu, Jianhang; Wu, Laosheng

    2002-08-28

    Polyacrylamides (PAMs) have wide application in many industries and in agriculture. Scientific research and industrial applications manifested a need for a method that can quantify substrate-borne PAM. The N-bromination method (a PAM analytical technique based on N-bromination of amide groups and spectrophotometric determination of the formed starch-triiodide complex), which was originally developed for determining PAM in aqueous solutions, was modified to quantify substrate-borne PAM. In the modified method, the quantity of substrate-borne PAM was converted to a concentration of starch-triiodide complex in aqueous solution that was then measured by spectrophotometry. The method sensitivity varied with substrates due to sorption of reagents and reaction intermediates on the substrates. Therefore, separate calibration for each substrate was required. Results from PAM samples in sand, cellulose, organic matter burnt soils, and clay minerals showed that this method had good accuracy and reproducibility. The PAM recoveries ranged from 95.8% to 103.7%, and the relative standard deviations (n = 4) were application and facilitating PAM-related research.

  18. 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.

  19. Use of waste material in cultivation substrates

    Directory of Open Access Journals (Sweden)

    Petr Salaš

    2004-01-01

    Full Text Available Gardeners' practical experience and experimental work prove the affirmation that the used substrate is a very important base for the production of quality nursery products. It is important to emphasis the complexity and synergy of all factors influencing the ecosystem and there mutual relations. Physical, chemical and biological properties do not separately affect the growth and development of plants. In addition, the relations are not statical but differ in relation with other factors changes. This article is dealing with the possibility to use waste material from timber processing in cultivation substrates. The large scale use of such substrates would enable people to reach a relative independence from peat substrates, of which the global reserve is gradually decreasing.Our research activities focus on the use of bark. The basic problems of a bark substrate are easy dehydration and unbalanced nutrition of trees and shrubs. The suggested and experimented cultivation technology solves these problems. It is based on the cultivation of woody species in bark substrates, using modern irrigation systems, slow release fertilisers (Silvamix Forte and special soil conditioners (TerraCottem. This technology was tested on the following species of trees and shrubs: Malus and Buxus.

  20. Mechanisms of Deformation and Fracture of Thin Coatings on Different Substrates in Instrumented Indentation

    Science.gov (United States)

    Eremina, G. M.; Smolin, A. Yu.; Psakhie, S. G.

    2018-04-01

    Mechanical properties of thin surface layers and coatings are commonly studied using instrumented indentation and scratch testing, where the mechanical response of the coating - substrate system essentially depends on the substrate material. It is quite difficult to distinguish this dependence and take it into account in the course of full-scale experiments due to a multivariative and nonlinear character of the influence. In this study the process of instrumented indentation of a hardening coating formed on different substrates is investigated numerically by the method of movable cellular automata. As a result of modeling, we identified the features of the substrate material influence on the derived mechanical characteristics of the coating - substrate systems and the processes of their deformation and fracture.

  1. Growth, Plastochron, and the Final Number of Nodes of China Pink Seedlings Grown on Different Substrates

    Directory of Open Access Journals (Sweden)

    Marília Milani

    Full Text Available ABSTRACT The objective of this work was to plot the growth curves and determine the plastochron and the final number of nodes of China pink seedlings grown on different substrates. Thus, 392 China pink seedlings were grown on seven substrates under greenhouse conditions, in Santa Maria in the state of Rio Grande do Sul, Brazil. The growth curves were plotted using the logistic model. The plastochron was estimated by the inverse of the angular coefficient of the simple linear regression between the number of accumulated nodes and accumulated thermal sum from the subsampling of the seedlings. In all substrates, the logistic model fit better for the variable number of leaves than for the plant height. The plants in substrates with 50% of soil plus 50% of rice husk ash, and 80% of rice husk ash plus 20% earthworm humus had the longest cycles with 74 and 65 days, respectively. They completed the cycles with a thermal sum of 1317.9 ºC day for number of leaves and plant height. The growth curves that were plotted by the logistic model and the plastochron of the China pink seedlings are dependent on the type of substrate used. The commercial substrate Mecplant® had the best results. The average final number of nodes of the main stem of the plants was 14 for all substrates.

  2. Biochemistry students' ideas about how an enzyme interacts with a substrate.

    Science.gov (United States)

    Linenberger, Kimberly J; Bretz, Stacey Lowery

    2015-01-01

    Enzyme-substrate interactions are a fundamental concept of biochemistry that is built upon throughout multiple biochemistry courses. Central to understanding enzyme-substrate interactions is specific knowledge of exactly how an enzyme and substrate interact. Within this narrower topic, students must understand the various binding sites on an enzyme and be able to reason from simplistic lock and key or induced fit models to the more complex energetics model of transition state theory. Learning to understand these many facets of enzyme-substrate interactions and reasoning from multiple models present challenges where students incorrectly make connections between concepts or make no connection at all. This study investigated biochemistry students' understanding of enzyme-substrate interactions through the use of clinical interviews and a national administration (N = 707) of the Enzyme-Substrate Interactions Concept Inventory. Findings include misconceptions regarding the nature of enzyme-substrate interactions, naïve ideas about the active site, a lack of energetically driven interactions, and an incomplete understanding of the specificity pocket. © 2015 by the International Union of Biochemistry and Molecular Biology.

  3. Surface-enhanced Raman spectroscopy based on conical holed enhancing substrates

    International Nuclear Information System (INIS)

    Chen, Yao; Chen, Zeng-Ping; Zuo, Qi; Shi, Cai-Xia; Yu, Ru-Qin

    2015-01-01

    In this contribution, surface-enhanced Raman spectroscopy (SERS) based on conical holed glass substrates deposited with silver colloids was reported for the first time. It combines the advantages of both dry SERS assays based on plane films deposited with silver colloids and wet SERS assays utilizing cuvettes or capillary tubes. Compared with plane glass substrates deposited with silver colloids, the conical holed glass substrates deposited with silver colloids exhibited five-to ten-folds of increase in the rate of signal enhancement, due to the internal multiple reflections of both the excitation laser beam and the Raman scattering photons within conical holes. The application of conical holed glass substrates could also yield significantly stronger and more reproducible SERS signals than SERS assays utilizing capillary tubes to sample the mixture of silver colloids and the solution of the analyte of interest. The conical holed glass substrates in combination with the multiplicative effects model for surface-enhanced Raman spectroscopy (MEM SERS ) achieved quite sensitive and precise quantification of 6-mercaptopurine in complex plasma samples with an average relative prediction error of about 4% and a limit of detection of about 0.02 μM using a portable i-Raman 785H spectrometer. It is reasonable to expect that SERS technique based on conical holed enhancing substrates in combination with MEM SERS model can be developed and extended to other application areas such as drug detection, environmental monitoring, and clinic analysis, etc. - Highlights: • A novel conical holed SERS enhancing substrate was designed and manufactured. • The optimal conical holed glass substrates can produce stronger SERS signal. • The novel substrates can overcome the shortcomings of both dry and wet methods. • The novel substrates coupled with MEM SERS can realize quantitative SERS assays

  4. Extensions of the Stoney formula for substrate curvature to configurations with thin substrates or large deformations

    International Nuclear Information System (INIS)

    Freund, L.B.; Floro, J.A.; Chason, E.

    1999-01-01

    Two main assumptions which underlie the Stoney formula relating substrate curvature to mismatch strain in a bonded thin film are that the film is very thin compared to the substrate, and the deformations are infinitesimally small. Expressions for the curvature - strain relationship are derived for cases in which these assumptions are relaxed, thereby providing a basis for interpretation of experimental observations for a broader class of film - substrate configurations. copyright 1999 American Institute of Physics

  5. Influence of substrate temperature on properties of MgF2 coatings

    International Nuclear Information System (INIS)

    Yu Hua; Qi Hongji; Cui Yun; Shen Yanming; Shao Jianda; Fan Zhengxiu

    2007-01-01

    Thermal boat evaporation was employed to prepare MgF 2 single-layer coatings upon both JGS1 and UBK7 substrates at different substrate temperatures. Microstructure, transmittance and residual stress of these coatings were measured by X-ray diffraction, spectrophotometer, and optical interferometer, respectively. Measurement of laser induced damage threshold (LIDT) of the samples was performed at 355 nm, 8 ns pulses. The results showed that high substrate temperature was beneficial to crystallization of the film. Above 244 deg. C, the refractive index increased gradually with the substrate temperature rising. Whereas, it was exceptional at 210 deg. C that the refractive index was higher than those deposited at 244 and 277 deg. C. The tensile residual stresses were exhibited in all MgF 2 films, but not well correlated with the substrate temperature. In addition, the stresses were comparatively smaller upon JGS1 substrates. A tendency could be seen that the LIDTs reached the highest values at about 244 deg. C, and the films upon JGS1 had higher LIDTs than those upon UBK7 substrates at the same temperature. Meanwhile, the damage morphologies showed that the laser damage of the coating resulted from an absorbing center at the film-substrate interface. The features of the damages were displayed by an absorbing center dominated model. Furthermore, the reason of the difference in LIDT values was discussed in detail

  6. 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.

  7. Empirical evaluation of inhibitory product, substrate, and enzyme effects during the enzymatic saccharification of lignocellulosic biomass.

    Science.gov (United States)

    Smith, Benjamin T; Knutsen, Jeffrey S; Davis, Robert H

    2010-05-01

    The cellulose hydrolysis kinetics during batch enzymatic saccharification are typified by a rapid initial rate that subsequently decays, resulting in incomplete conversion. Previous studies suggest that changes associated with the solution, substrate, or enzymes may be responsible. In this work, kinetic experiments were conducted to determine the relative magnitude of these effects. Pretreated corn stover (PCS) was used as a lignocellulosic substrate likely to be found in a commercial saccharification process, while Avicel and Kraft lignin were used to create model substrates. Glucose inhibition was observed by spiking the reaction slurry with glucose during initial-rate experiments. Increasing the glucose concentration from 7 to 48 g/L reduced the cellulose conversion rate by 94%. When product sugars were removed using ultrafiltration with a 10 kDa membrane, the glucose-based conversion increased by 9.5%. Reductions in substrate reactivity with conversion were compared directly by saccharifying PCS and Avicel substrates that had been pre-reacted to different conversions. Reaction of substrate with a pre-conversion of 40% resulted in about 40% reduction in the initial rate of saccharification, relative to fresh substrate with identical cellulose concentration. Overall, glucose inhibition and reduced substrate reactivity appear to be dominant factors, whereas minimal reductions of enzyme activity were observed.

  8. 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.

  9. Impact of the substrate on the efficiency of thin film thermoelectric technology

    International Nuclear Information System (INIS)

    Alvarez-Quintana, J.

    2015-01-01

    Thermoelectricity is one of the simplest technologies for thermal energy conversion. Moreover, because of their relatively low efficiency, bulk thermoelectric materials are generally used in environments where their solid state nature outweighs their poor efficiency. Nevertheless, low dimensional thermoelectric materials shed a light in order to achieve higher thermoelectric performance than their bulk counterparts via quantum and spatial confinement of energy carriers. The Thermoelectric figure of merit ZT is the basic criterion for estimating the performance of thermoelectric materials. In this work, by way of an extension of the Harman method to thin films onto substrate to evaluate ZT it is shown that the solely presence of a substrate affects significantly the intrinsic value of the ZT independently of the electrical and thermal nature of the substrate. Furthermore, the model unveils that as the thickness ratio between substrate and thin film increases, the parameter ZT sharply tends to zero; this effect opens a serious problem to overcome by the thin film thermoelectric technology, especially at nanoscale. In this sense, challenges in order to engineering planar thermoelectric devices at micro/nanoscale are properly identified. - Highlights: • Extended Harman method to evaluate ZT of thin films onto substrate is presented. • ZT of thermoelectric thin films is strongly affected by substrate's nature. • Thin dielectric substrates are desirable to hold ZT in in-plane configuration. • Film/substrate thickness ratio play important role on the device performance. • Challenges to engineering planar thermoelectric devices are properly identified

  10. Structural pathway of regulated substrate transfer and threading through an Hsp100 disaggregase.

    Science.gov (United States)

    Deville, Célia; Carroni, Marta; Franke, Kamila B; Topf, Maya; Bukau, Bernd; Mogk, Axel; Saibil, Helen R

    2017-08-01

    Refolding aggregated proteins is essential in combating cellular proteotoxic stress. Together with Hsp70, Hsp100 chaperones, including Escherichia coli ClpB, form a powerful disaggregation machine that threads aggregated polypeptides through the central pore of tandem adenosine triphosphatase (ATPase) rings. To visualize protein disaggregation, we determined cryo-electron microscopy structures of inactive and substrate-bound ClpB in the presence of adenosine 5'- O -(3-thiotriphosphate), revealing closed AAA+ rings with a pronounced seam. In the substrate-free state, a marked gradient of resolution, likely corresponding to mobility, spans across the AAA+ rings with a dynamic hotspot at the seam. On the seam side, the coiled-coil regulatory domains are locked in a horizontal, inactive orientation. On the opposite side, the regulatory domains are accessible for Hsp70 binding, substrate targeting, and activation. In the presence of the model substrate casein, the polypeptide threads through the entire pore channel and increased nucleotide occupancy correlates with higher ATPase activity. Substrate-induced domain displacements indicate a pathway of regulated substrate transfer from Hsp70 to the ClpB pore, inside which a spiral of loops contacts the substrate. The seam pore loops undergo marked displacements, along with ordering of the regulatory domains. These asymmetric movements suggest a mechanism for ATPase activation and substrate threading during disaggregation.

  11. Inducing morphological changes in lipid bilayer membranes with microfabricated substrates

    Science.gov (United States)

    Liu, Fangjie; Collins, Liam F.; Ashkar, Rana; Heberle, Frederick A.; Srijanto, Bernadeta R.; Collier, C. Patrick

    2016-11-01

    Lateral organization of lipids and proteins into distinct domains and anchoring to a cytoskeleton are two important strategies employed by biological membranes to carry out many cellular functions. However, these interactions are difficult to emulate with model systems. Here we use the physical architecture of substrates consisting of arrays of micropillars to systematically control the behavior of supported lipid bilayers - an important step in engineering model lipid membrane systems with well-defined functionalities. Competition between attractive interactions of supported lipid bilayers with the underlying substrate versus the energy cost associated with membrane bending at pillar edges can be systematically investigated as functions of pillar height and pitch, chemical functionalization of the microstructured substrate, and the type of unilamellar vesicles used for assembling the supported bilayer. Confocal fluorescent imaging and AFM measurements highlight correlations that exist between topological and mechanical properties of lipid bilayers and lateral lipid mobility in these confined environments. This study provides a baseline for future investigations into lipid domain reorganization on structured solid surfaces and scaffolds for cell growth.

  12. Substrate uptake, phosphorus repression, and effect of seed culture on glycopeptide antibiotic production

    DEFF Research Database (Denmark)

    Maiti, Soumen K.; Singh, Kamaleshwar P.; Eliasson Lantz, Anna

    2010-01-01

    may experience catabolite repression by one or more of the substrates. Availability of reliable process models is a key bottleneck in optimization of such processes. Here we present a structured kinetic model to describe the growth, substrate uptake and product formation for the glycopeptide....... The model is also able to predict key phenomena such as simultaneous uptake of glucose and glycerol but with different specific uptake rates, and inhibition of glycopeptide production by high intracellular phosphate levels. The model is successfully applied to both production and seed medium with varying....... The model may have applications in optimizing seed transfer, medium composition, and feeding strategy for maximizing production....

  13. 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.

  14. Patchy silica-coated silver nanowires as SERS substrates

    International Nuclear Information System (INIS)

    Hunyadi Murph, Simona E.; Murphy, Catherine J.

    2013-01-01

    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.

  15. 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.

  16. Equilibrium stability of strained epitaxial layers on a rigid substrate

    International Nuclear Information System (INIS)

    Granato, E.; Kosterlitz, J.M.; Ying, S.C.

    1987-07-01

    A simple theory of the equilibrium stability of an strained epitaxial layer on a rigid substrate is presented. We generalise the Frankvan der Merwe model of a single layer and consider N layers of adsorbate on a substrate. Continuum elasticity theory is used to describe each layer, but the coupling between layers is treated ina discrete fashion. Our method interpolates between a few layers and the thick film limit of standard dislocation theory, and in this limit the standard results are obtained. In addition, we developed a variational approach which agrees well with our exact calculations. The advantage of our method over previous ores is that it allows to perform stability analyses of arbitrary superlattice configurations. (author) [pt

  17. 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.

  18. Holocene footprints in Namibia: the influence of substrate on footprint variability.

    Science.gov (United States)

    Morse, Sarita A; Bennett, Matthew R; Liutkus-Pierce, Cynthia; Thackeray, Francis; McClymont, Juliet; Savage, Russell; Crompton, Robin H

    2013-06-01

    We report a Holocene human and animal footprint site from the Namib Sand Sea, south of Walvis Bay, Namibia. Using these data, we explore intratrail footprint variability associated with small variations in substrate properties using a "whole foot" analytical technique developed for the studies in human ichnology. We demonstrate high levels of intratrail variability as a result of variations in grain size, depositional moisture content, and the degree of sediment disturbance, all of which determine the bearing capacity of the substrate. The two principal trails were examined, which had consistent stride and step lengths, and as such variations in print typology were primarily controlled by substrate rather than locomotor mechanics. Footprint typology varies with bearing capacity such that firm substrates show limited impressions associated with areas of peak plantar pressure, whereas softer substrates are associated with deep prints with narrow heels and reduced medial longitudinal arches. Substrates of medium bearing capacity give displacement rims and proximal movement of sediment, which obscures the true form of the medial longitudinal arch. A simple conceptual model is offered which summarizes these conclusions and is presented as a basis for further investigation into the control of substrate on footprint typology. The method, model, and results presented here are essential in the interpretation of any sites of greater paleoanthropological significance, such as recently reported from Ileret (1.5 Ma, Kenya; Bennett et al.: Science 323 (2009) 1197-1201). Copyright © 2013 Wiley Periodicals, Inc.

  19. 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