Sample records for a-to-i hyperediting substrates

  1. A genome-wide map of hyper-edited RNA reveals numerous new sites.

    PubMed

    Porath, Hagit T; Carmi, Shai; Levanon, Erez Y

    2014-08-27

    Adenosine-to-inosine editing is one of the most frequent post-transcriptional modifications, manifested as A-to-G mismatches when comparing RNA sequences with their source DNA. Recently, a number of RNA-seq data sets have been screened for the presence of A-to-G editing, and hundreds of thousands of editing sites identified. Here we show that existing screens missed the majority of sites by ignoring reads with excessive ('hyper') editing that do not easily align to the genome. We show that careful alignment and examination of the unmapped reads in RNA-seq studies reveal numerous new sites, usually many more than originally discovered, and in precisely those regions that are most heavily edited. Specifically, we discover 327,096 new editing sites in the heavily studied Illumina Human BodyMap data and more than double the number of detected sites in several published screens. We also identify thousands of new sites in mouse, rat, opossum and fly. Our results establish that hyper-editing events account for the majority of editing sites.

  2. Process for depositing I-125 onto a substrate used to manufacture I-125 sources

    DOEpatents

    McGovern, James J.; Olynyk, Joseph M.

    1988-01-01

    The invention relates to a process for depositing I-125 on a substrate which comprises contacting a predetermined surface area of substrate with Xe-125 gas, whereby the Xe-125 decays to I-125 and the I-125 in turn deposits as a solid on the surface of the substrate, the contact being for a time sufficient to deposit at least about 1 microcurie of I-125. I-125 is thereby deposited in a relatively uniform amount over the surface area of the substrate. The substrate is then assayed to determine how much I-125 has been deposited. The substrate is then divided into pieces of measured surface area, each piece therefore containing a measured amount of deposited I-125, and each piece can then be used in the manufacture of an I-125 source.

  3. Analysis of apolipoprotein A-I as a substrate for matrix metalloproteinase-14

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Park, Jun Hyoung; Park, Sung-Min; Park, Ki-Hoon

    2011-05-27

    Highlights: {yields} MMP-14 degrades apoA-I more efficiently than other tested MMPs. {yields} Lipid-free apoA-I is more susceptible to MMPs than lipid-bound apoA-I. {yields} MMP-14 cleavage sites on apoA-I have been determined. {yields} Cleavage of apoA-I by MMP-14 impairs its ability to form HDL. -- Abstract: Substrates for matrix metalloproteinase (MMP)-14 were previously identified in human plasma using proteomic techniques. One putative MMP-14 substrate was apolipoprotein A-I (apoA-I), a major component of high-density lipoprotein (HDL). In vitro cleavage assays showed that lipid-free apoA-I is a more accessible substrate for MMP-14 compared to lipid-bound apoA-I, and that MMP-14 is more prone tomore » digest apoA-I than MMP-3. The 28-kDa apoA-I was cleaved into smaller fragments of 27, 26, 25, 22, and 14-kDa by MMP-14. ApoA-I sites cleaved by MMP-14 were determined by isotope labeling of C-termini derived from the cleavage and analysis of the labeled peptides by mass spectrometry, along with N-terminal sequencing of the fragments. Cleavage of apoA-I by MMP-14 resulted in a loss of ability to form HDL. Our results suggest that cleavage of lipid-free apoA-I by MMP-14 may contribute to reduced HDL formation, and this may be occurring during the development of various vascular diseases as lipid metabolism is disrupted.« less

  4. Structure of the Fusarium oxysporum endoglucanase I with a nonhydrolyzable substrate analogue: substrate distortion gives rise to the preferred axial orientation for the leaving group.

    PubMed

    Sulzenbacher, G; Driguez, H; Henrissat, B; Schülein, M; Davies, G J

    1996-12-03

    Endoglucanase I (EG I) is a cellulase, from glycosyl hydrolase family 7, which cleaves the beta-1,4 linkages of cellulose with overall retention of configuration. The structure of the EG I from Fusarium oxysproum, complexed to a nonhydrolyzable thiooligosaccharide substrate analogue, has been determined by X-ray crystallography at a resolution of 2.7 A utilizing the 4-fold noncrystallographic symmetry present in the asymmetric unit. The electron density map clearly reveals the presence of three glucosyl units of the inhibitor, consistent with the known number of sugar-binding subsites, located at the active site of the enzyme in the -2, -1, and +1 subsites, i.e., actually spanning the point of enzymatic cleavage. The pyranose ring at the point of potential enzymatic cleavage is clearly distorted from the standard 4C1 chair as was originally suggested for beta-retaining enzymes by Phillips [Ford, L.O., Johnson, L.N., Machin, P. A., Phillips, D.C., & Tijan, T. (1974) J. Mol. Biol, 88, 349-371]. The distortion observed goes beyond the "sofa" conformation observed in previous studies and results in a conformation whose salient feature is the resulting quasi-axial orientation for the glycosidic bond and leaving group, as predicted by stereoelectronic theory. An almost identical conformation has recently been observed in a complex of chitobiase with its unhydrolyzed substrate [Tews, I., Perrakis, A., Oppenheim, A., Dauter, Z., Wilson, K. S., & Vorgias, C. E. (1996) Nat. Struct. Biol. 3, 638-648]. The striking similarity between these two complexes extends beyond the almost identical pyranose ring distortion. The overlap of the two respective sugars places the enzymatic nucleophile of endoglucanase I in coincidence with the C2 acetamido oxygen of N-acetylglucosamine in the catalytic site of the chitobiase, substantiating the involvement of this group in the catalytic mechanism of chitobiase and related chitinolytic enzymes. The endoglucanase I complex with the

  5. Structure of a [NiFe] hydrogenase maturation protease HycI provides insights into its substrate selectivity.

    PubMed

    Kwon, Sunghark; Nishitani, Yuichi; Hirao, Yoshinori; Kanai, Tamotsu; Atomi, Haruyuki; Miki, Kunio

    2018-04-15

    The immature large subunit of [NiFe] hydrogenases undergoes C-terminal cleavage by a specific protease in the final step of the post-translational process before assembly with other subunits. It has been reported that the [NiFe] hydrogenase maturation protease HycI from Thermococcus kodakarensis (TkHycI) has the catalytic ability to target the membrane-bound hydrogenase large subunit MbhL from T. kodakarensis. However, the detailed mechanism of its substrate recognition remains elusive. We determined the crystal structure of TkHycI at 1.59 Å resolution to clarify how TkHycI recognizes its own substrate MbhL. Although the overall structure of TkHycI is similar to that of its homologous protease TkHybD, TkHycI adopts a larger loop than TkHybD, thereby creating a broad and deep cleft. We analyzed the structural properties of the TkHycI cleft probably involved in its substrate recognition. Our findings provide novel and profound insights into the substrate selectivity of TkHycI. Copyright © 2018 Elsevier Inc. All rights reserved.

  6. Identification of a Degradation Signal Sequence within Substrates of the Mitochondrial i-AAA Protease.

    PubMed

    Rampello, Anthony J; Glynn, Steven E

    2017-03-24

    The i-AAA protease is a component of the mitochondrial quality control machinery that regulates respiration, mitochondrial dynamics, and protein import. The protease is required to select specific substrates for degradation from among the diverse complement of proteins present in mitochondria, yet the rules that govern this selection are unclear. Here, we reconstruct the yeast i-AAA protease, Yme1p, to examine the in vitro degradation of two intermembrane space chaperone subunits, Tim9 and Tim10. Yme1p degrades Tim10 more rapidly than Tim9 despite high sequence and structural similarity, and loss of Tim10 is accelerated by the disruption of conserved disulfide bonds within the substrate. An unstructured N-terminal region of Tim10 is necessary and sufficient to target the substrate to the protease through recognition of a short phenylalanine-rich motif, and the presence of similar motifs in other small Tim proteins predicts robust degradation by the protease. Together, these results identify the first specific degron sequence within a native i-AAA protease substrate. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. Detection of tripeptidyl peptidase I activity in living cells by fluorogenic substrates.

    PubMed

    Steinfeld, Robert; Fuhrmann, Jens C; Gärtner, Jutta

    2006-09-01

    Tripeptidyl peptidase I (TPP-I) is a lysosomal peptidase with unclear physiological function. TPP-I deficiency is associated with late-infantile neuronal ceroid lipofuscinosis (NCL), a fatal neurodegenerative disease of childhood that is characterized by loss of neurons and photoreceptor cells. We have developed two novel fluorogenic substrates, [Ala-Ala-Phe]2-rhodamine 110 and [Arg-Nle-Nle]2-rhodamine 110, that are cleaved by TPP-I in living cells. Fluorescence of liberated rhodamine 110 was detected by flow cytometry and was dependent on the level of TPP-I expression. Rhodamine-related fluorescence could be suppressed by preincubation with a specific inhibitor of TPP-I. When investigated by fluorescent confocal microscopy, rhodamine signals colocalized with lysosomal markers. Thus, cleavage of these rhodamide-derived substrates is a marker for mature enzymatically active TPP-I. In addition, TPP-I-induced cleavage of [Ala-Ala-Phe]2-rhodamine 110 could be visualized in primary neurons. We conclude that [Ala-Ala-Phe]2-rhodamine 110 and [Arg-Nle-Nle]2-rhodamine 110 are specific substrates for determining TPP-I activity and intracellular localization in living cells. Further, these substrates could be a valuable tool for studying the neuronal pathology underlying classical late-infantile NCL. This article contains online supplemental material at http://www.jhc.org. Please visit this article online to view these materials.

  8. Transcriptome-wide identification of A > I RNA editing sites by inosine specific cleavage

    PubMed Central

    Cattenoz, Pierre B.; Taft, Ryan J.; Westhof, Eric; Mattick, John S.

    2013-01-01

    Adenosine to inosine (A > I) RNA editing, which is catalyzed by the ADAR family of proteins, is one of the fundamental mechanisms by which transcriptomic diversity is generated. Indeed, a number of genome-wide analyses have shown that A > I editing is not limited to a few mRNAs, as originally thought, but occurs widely across the transcriptome, especially in the brain. Importantly, there is increasing evidence that A > I editing is essential for animal development and nervous system function. To more efficiently characterize the complete catalog of ADAR events in the mammalian transcriptome we developed a high-throughput protocol to identify A > I editing sites, which exploits the capacity of glyoxal to protect guanosine, but not inosine, from RNAse T1 treatment, thus facilitating extraction of RNA fragments with inosine bases at their termini for high-throughput sequencing. Using this method we identified 665 editing sites in mouse brain RNA, including most known sites and suite of novel sites that include nonsynonymous changes to protein-coding genes, hyperediting of genes known to regulate p53, and alterations to non-protein-coding RNAs. This method is applicable to any biological system for the de novo discovery of A > I editing sites, and avoids the complicated informatic and practical issues associated with editing site identification using traditional RNA sequencing data. This approach has the potential to substantially increase our understanding of the extent and function of RNA editing, and thereby to shed light on the role of transcriptional plasticity in evolution, development, and cognition. PMID:23264566

  9. Photosystem I assembly on chemically tailored SAM/ Au substrates for bio-hybrid device fabrication

    NASA Astrophysics Data System (ADS)

    Mukherjee, Dibyendu; Khomami, Bamin

    2011-03-01

    Photosystem I (PS I), a supra-molecular protein complex and a biological photodiode responsible for driving natural photosynthesis mechanism, charge separates upon exposure to light. Effective use of the photo-electrochemical activities of PS I for future bio-hybrid electronic devices requires controlled attachment of these proteins onto organic/ inorganic substrates. Our results indicate that various experimental parameters alter the surface topography of PS I deposited from colloidal aqueous buffer suspensions onto OH-terminated alkanethiolate SAM /Au substrates, thereby resulting in complex columnar structures that affect the electron capture pathway of PS I. Specifically, solution phase characterizations indicate that specific detergents used for PS I stabilization in buffer solutions drive the unique colloidal chemistry to tune protein-protein interactions and prevent aggregation, thereby allowing us to tailor the morphology of surface immobilized PS I. We present surface topographical, adsorption, and electrochemical characterizations of PSI /SAM/Au substrates to elucidate protein-surface attachment dynamics and its effect on the photo-activated electronic activities of surface immobilized PS I. Sustainable Energy Education and Research Center (SEERC).

  10. Specificity of Processing α-glucosidase I is guided by the substrate conformation: crystallographic and in silico studies.

    PubMed

    Barker, Megan K; Rose, David R

    2013-05-10

    The enzyme “GluI” is key to the synthesis of critical glycoproteins in the cell. We have determined the structure of GluI, and modeled binding with its unique sugar substrate. The specificity of this interaction derives from a unique conformation of the substrate. Understanding the mechanism of the enzyme is of basic importance and relevant to potential development of antiviral inhibitors. Processing α-glucosidase I (GluI) is a key member of the eukaryotic N-glycosylation processing pathway, selectively catalyzing the first glycoprotein trimming step in the endoplasmic reticulum. Inhibition of GluI activity impacts the infectivity of enveloped viruses; however, despite interest in this protein from a structural, enzymatic, and therapeutic standpoint, little is known about its structure and enzymatic mechanism in catalysis of the unique glycan substrate Glc3Man9GlcNAc2. The first structural model of eukaryotic GluI is here presented at 2-Å resolution. Two catalytic residues are proposed, mutations of which result in catalytically inactive, properly folded protein. Using Autodocking methods with the known substrate and inhibitors as ligands, including a novel inhibitor characterized in this work, the active site of GluI was mapped. From these results, a model of substrate binding has been formulated, which is most likely conserved in mammalian GluI.

  11. Saturation mutagenesis in selected amino acids to shift Pseudomonas sp. acidic lipase Lip I.3 substrate specificity and activity.

    PubMed

    Panizza, Paola; Cesarini, Silvia; Diaz, Pilar; Rodríguez Giordano, Sonia

    2015-01-25

    Several Pseudomonas sp. CR611 Lip I.3 mutants with overall increased activity and a shift towards longer chain substrates were constructed. Substitution of residues Y29 and W310 by smaller amino acids provided increased activity on C18-substrates. Residues G152 and S154, modified to study their influence on interfacial activation, displayed a five and eleven fold increased activity.

  12. Colorimetric determination of DNase I activity with a DNA-methyl green substrate.

    PubMed

    Sinicropi, D; Baker, D L; Prince, W S; Shiffer, K; Shak, S

    1994-11-01

    A simple, high throughput, and precise assay was developed for quantification of deoxyribonuclease I (DNase; IUB 3.1.21.1) activity. The method was adapted from the procedure devised by Kurnick which employs a substrate comprised of highly polymerized native DNA complexed with methyl green. Hydrolysis of the DNA produced unbound methyl green and a decrease in the absorbance of the solution at 620 nm. By adjusting the time and temperature of the reaction, the assay permits quantification of DNase activity over a wide concentration range (0.4 to 8900 ng/ml). Samples and standards were added to the substrate in microtiter plates and were incubated for 1-24 h at 25-37 degrees C to achieve the desired assay range. The DNase activity of the samples was interpolated from a standard curve generated with Pulmozyme recombinant human deoxyribonuclease I (rhDNase). Interassay precision was less than 12% CV and recovery was within 100 +/- 11%. Activity determination by the DNA-methyl green method correlated well with that determined by the widely used "hyperchromicity" method originated by Kunitz, which is based on the increase in absorbance at 260 nm upon hydrolysis of DNA. The DNA-methyl green assay was simpler and more versatile than the hyperchromicity method and was used to characterize the activity of rhDNase and DNase isolated from human urine.

  13. The I domain of the AAA+ HslUV protease coordinates substrate binding, ATP hydrolysis, and protein degradation

    PubMed Central

    Sundar, Shankar; Baker, Tania A; Sauer, Robert T

    2012-01-01

    In the AAA+ HslUV protease, substrates are bound and unfolded by a ring hexamer of HslU, before translocation through an axial pore and into the HslV degradation chamber. Here, we show that the N-terminal residues of an Arc substrate initially bind in the HslU axial pore, with key contacts mediated by a pore loop that is highly conserved in all AAA+ unfoldases. Disordered loops from the six intermediate domains of the HslU hexamer project into a funnel-shaped cavity above the pore and are positioned to contact protein substrates. Mutations in these I-domain loops increase KM and decrease Vmax for degradation, increase the mobility of bound substrates, and prevent substrate stimulation of ATP hydrolysis. HslU-ΔI has negligible ATPase activity. Thus, the I domain plays an active role in coordinating substrate binding, ATP hydrolysis, and protein degradation by the HslUV proteolytic machine. PMID:22102327

  14. A Conserved Surface Loop in Type I Dehydroquinate Dehydratases Positions an Active Site Arginine and Functions in Substrate Binding

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Light, Samuel H.; Minasov, George; Shuvalova, Ludmilla

    2012-04-18

    Dehydroquinate dehydratase (DHQD) catalyzes the third step in the biosynthetic shikimate pathway. We present three crystal structures of the Salmonella enterica type I DHQD that address the functionality of a surface loop that is observed to close over the active site following substrate binding. Two wild-type structures with differing loop conformations and kinetic and structural studies of a mutant provide evidence of both direct and indirect mechanisms of involvement of the loop in substrate binding. In addition to allowing amino acid side chains to establish a direct interaction with the substrate, closure of the loop necessitates a conformational change ofmore » a key active site arginine, which in turn positions the substrate productively. The absence of DHQD in humans and its essentiality in many pathogenic bacteria make the enzyme a target for the development of nontoxic antimicrobials. The structures and ligand binding insights presented here may inform the design of novel type I DHQD inhibiting molecules.« less

  15. Predominant nonproductive substrate binding by fungal cellobiohydrolase I and implications for activity improvement.

    PubMed

    Rabinovich, Mikhail L; Melnik, Maria S; Herner, Mikhail L; Voznyi, Yakov V; Vasilchenko, Lilia G

    2018-05-21

    Enzymatic conversion of the most abundant renewable source of organic compounds, cellulose to fermentable sugars is attractive for production of green fuels and chemicals. The major component of industrial enzyme systems, cellobiohydrolase I from Hypocrea jecorina (Trichoderma reesei) (HjCel7A) processively splits disaccharide units from the reducing ends of tightly packed cellulose chains. HjCel7A consists of a catalytic domain (CD) and a carbohydrate-binding module (CBM) separated by a linker peptide. A tunnel-shaped substrate-binding site in the CD includes 9 subsites for β-D-glucose units, 7 of which (-7 to -1) precede the catalytic center. Low catalytic activity of Cel7A is the bottleneck and the primary target for improvement. Here it is shown for the first time that, in spite of much lower apparent k cat of HjCel7A at the hydrolysis of β-1,4-glucosidic linkages in the fluorogenic cellotetra- and -pentaose compared to the structurally related endoglucanase I (HjCel7B), the specificity constants (catalytic efficiency) k cat /K m for both enzymes are almost equal in these reactions. The observed activity difference appears from strong nonproductive substrate binding by HjCel7A, particularly significant for MU-β-cellotetraose (MUG 4 ). Interaction of substrates with the subsites -6 and -5 proximal to the non-conserved Gln101 residue in HjCel7A decreases K m,ap by >1500 times. HjCel7A can be nonproductively bound onto cellulose surface with K d ∼2-9 nM via CBM and CD that captures 6 terminal glucose units of cellulose chain. Decomposition of this nonproductive complex can determine the rate of cellulose conversion. MUG 4 is a promising substrate to select active cellobiohydrolase I variants with reduced nonproductive substrate binding. This article is protected by copyright. All rights reserved.

  16. Insights into substrate binding and catalysis in bacterial type I dehydroquinase.

    PubMed

    Maneiro, María; Peón, Antonio; Lence, Emilio; Otero, José M; Van Raaij, Mark J; Thompson, Paul; Hawkins, Alastair R; González-Bello, Concepción

    2014-09-15

    Structural, biochemical and computational studies to study substrate binding and the role of the conserved residues of the DHQ1 (type I dehydroquinase) enzyme active site are reported in the present paper. The crystal structure of DHQ1 from Salmonella typhi in complex with (2R)-2-methyl-3-dehydroquinic acid, a substrate analogue, was solved at 1.5 Å. The present study reveals a previously unknown key role for conserved Glu46, Phe145 and Met205 and Gln236, Pro234 and Ala233 residues, with the latter three being located in the flexible substrate-covering loop. Gln236 was shown to be responsible for the folding of this loop and for the dramatic reduction of its flexibility, which triggers active site closure. Glu46 was found to be key in bringing the substrate close to the lysine/histidine catalytic pocket to initiate catalysis. The present study could be useful in the rational design of inhibitors of this challenging and recognized target for the development of novel herbicides and antimicrobial agents.

  17. IMPROVED EQUIPMENT CLEANING IN COATED AND LAMINATED SUBSTRATE MANUFACTURING FACILITIES (PHASE I)

    EPA Science Inventory

    The report gives results of a Phase I study to characterize current equipment cleaning practices in the coated and laminated substrate manufacturing industry, to identify alternative cleaning technologies, and to identify demonstrable technologies and estimate their emissions imp...

  18. Process for applying a superconductive powder to a wide variety of substrates

    NASA Astrophysics Data System (ADS)

    Hooker, Matthew W.; Wise, Stephanie A.; Tran, Sang Q.

    1992-12-01

    A fine superconducting powder such as YBa2Cu3O(7-x), wherein x is less than one, is blended into a liquid mixture comprising an epoxy resin and a thinner. This liquid mixture with the blended superconducting powder is coated onto a substrate. Next, the thinner is evaporated and the remaining coating cured, resulting in a coating of cured epoxy resin having superconducting powder suspended therein. This coating exhibits the Meissner effect, i.e., it expels a magnetic flux which protects the substrate from external magnetic interference. Since the coated substrate need only be heated for evaporation and curing at relatively low temperatures compared to firing, the superconducting coating can be applied to a wide variety of different materials.

  19. Dynamic hyper-editing underlies temperature adaptation in Drosophila

    PubMed Central

    Ashwal-Fluss, Reut; Pandey, Varun; Levanon, Erez Y.; Kadener, Sebastian

    2017-01-01

    In Drosophila, A-to-I editing is prevalent in the brain, and mutations in the editing enzyme ADAR correlate with specific behavioral defects. Here we demonstrate a role for ADAR in behavioral temperature adaptation in Drosophila. Although there is a higher level of editing at lower temperatures, at 29°C more sites are edited. These sites are less evolutionarily conserved, more disperse, less likely to be involved in secondary structures, and more likely to be located in exons. Interestingly, hypomorph mutants for ADAR display a weaker transcriptional response to temperature changes than wild-type flies and a highly abnormal behavioral response upon temperature increase. In sum, our data shows that ADAR is essential for proper temperature adaptation, a key behavior trait that is essential for survival of flies in the wild. Moreover, our results suggest a more general role of ADAR in regulating RNA secondary structures in vivo. PMID:28746393

  20. iHWG-μNIR: a miniaturised near-infrared gas sensor based on substrate-integrated hollow waveguides coupled to a micro-NIR-spectrophotometer.

    PubMed

    Rohwedder, J J R; Pasquini, C; Fortes, P R; Raimundo, I M; Wilk, A; Mizaikoff, B

    2014-07-21

    A miniaturised gas analyser is described and evaluated based on the use of a substrate-integrated hollow waveguide (iHWG) coupled to a microsized near-infrared spectrophotometer comprising a linear variable filter and an array of InGaAs detectors. This gas sensing system was applied to analyse surrogate samples of natural fuel gas containing methane, ethane, propane and butane, quantified by using multivariate regression models based on partial least square (PLS) algorithms and Savitzky-Golay 1(st) derivative data preprocessing. The external validation of the obtained models reveals root mean square errors of prediction of 0.37, 0.36, 0.67 and 0.37% (v/v), for methane, ethane, propane and butane, respectively. The developed sensing system provides particularly rapid response times upon composition changes of the gaseous sample (approximately 2 s) due the minute volume of the iHWG-based measurement cell. The sensing system developed in this study is fully portable with a hand-held sized analyser footprint, and thus ideally suited for field analysis. Last but not least, the obtained results corroborate the potential of NIR-iHWG analysers for monitoring the quality of natural gas and petrochemical gaseous products.

  1. Reconditioning of semiconductor substrates to remove photoresist during semiconductor device fabrication

    DOEpatents

    Farino, Anthony J.

    2004-01-27

    A method for reconditioning the surface of a semiconductor substrate to remove an unwanted (i.e. defective) layer of photoresist is disclosed. The method adapts a conventional automated spinner which is used to rotate the substrate at high speed while a stream of a first solvent (e.g. acetone) is used to dissolve the photoresist. A stream of a second solvent (e.g. methanol) is then used to clean the substrate at a lower speed, with the substrate being allowed to dry with continued rotation. The method of the present invention can be used within a photolithography track so that the substrates need never leave the track for reconditioning.

  2. Structure of Protein Geranylgeranyltransferase-I from the Human Pathogen Candida albicans Complexed with a Lipid Substrate

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Hast, Michael A.; Beese, Lorena S.

    2008-11-21

    Protein geranylgeranyltransferase-I (GGTase-I) catalyzes the transfer of a 20-carbon isoprenoid lipid to the sulfur of a cysteine residue located near the C terminus of numerous cellular proteins, including members of the Rho superfamily of small GTPases and other essential signal transduction proteins. In humans, GGTase-I and the homologous protein farnesyltransferase (FTase) are targets of anticancer therapeutics because of the role small GTPases play in oncogenesis. Protein prenyltransferases are also essential for many fungal and protozoan pathogens that infect humans, and have therefore become important targets for treating infectious diseases. Candida albicans, a causative agent of systemic fungal infections in immunocompromisedmore » individuals, is one pathogen for which protein prenylation is essential for survival. Here we present the crystal structure of GGTase-I from C. albicans (CaGGTase-I) in complex with its cognate lipid substrate, geranylgeranylpyrophosphate. This structure provides a high-resolution picture of a non-mammalian protein prenyltransferase. There are significant variations between species in critical areas of the active site, including the isoprenoid-binding pocket, as well as the putative product exit groove. These differences indicate the regions where specific protein prenyltransferase inhibitors with antifungal activity can be designed.« less

  3. Spectroscopic Ellipsometry Studies of Thin Film a-Si:H Solar Cell Fabrication by Multichamber Deposition in the n-i-p Substrate Configuration

    NASA Astrophysics Data System (ADS)

    Dahal, Lila Raj

    Real time spectroscopic ellipsometry (RTSE), and ex-situ mapping spectroscopic ellipsometry (SE) are powerful characterization techniques capable of performance optimization and scale-up evaluation of thin film solar cells used in various photovoltaics technologies. These non-invasive optical probes employ multichannel spectral detection for high speed and provide high precision parameters that describe (i) thin film structure, such as layer thicknesses, and (ii) thin film optical properties, such as oscillator variables in analytical expressions for the complex dielectric function. These parameters are critical for evaluating the electronic performance of materials in thin film solar cells and also can be used as inputs for simulating their multilayer optical performance. In this Thesis, the component layers of thin film hydrogenated silicon (Si:H) solar cells in the n-i-p or substrate configuration on rigid and flexible substrate materials have been studied by RTSE and ex-situ mapping SE. Depositions were performed by magnetron sputtering for the metal and transparent conducting oxide contacts and by plasma enhanced chemical vapor deposition (PECVD) for the semiconductor doped contacts and intrinsic absorber layers. The motivations are first to optimize the thin film Si:H solar cell in n-i-p substrate configuration for single-junction small-area dot cells and ultimately to scale-up the optimized process to larger areas with minimum loss in device performance. Deposition phase diagrams for both i- and p -layers on 2" x 2" rigid borosilicate glass substrate were developed as functions of the hydrogen-to-silane flow ratio in PECVD. These phase diagrams were correlated with the performance parameters of the corresponding solar cells, fabricated in the Cr/Ag/ZnO/n/i/ p/ITO structure. In both cases, optimization was achieved when the layers were deposited in the protocrystalline phase. Identical solar cell structures were fabricated on 6" x 6" borosilicate glass with

  4. Multiplex N-terminome analysis of MMP-2 and MMP-9 substrate degradomes by iTRAQ-TAILS quantitative proteomics.

    PubMed

    Prudova, Anna; auf dem Keller, Ulrich; Butler, Georgina S; Overall, Christopher M

    2010-05-01

    Proteolysis is a major protein posttranslational modification that, by altering protein structure, affects protein function and, by truncating the protein sequence, alters peptide signatures of proteins analyzed by proteomics. To identify such modified and shortened protease-generated neo-N-termini on a proteome-wide basis, we developed a whole protein isobaric tag for relative and absolute quantitation (iTRAQ) labeling method that simultaneously labels and blocks all primary amines including protein N- termini and lysine side chains. Blocking lysines limits trypsin cleavage to arginine, which effectively elongates the proteolytically truncated peptides for improved MS/MS analysis and peptide identification. Incorporating iTRAQ whole protein labeling with terminal amine isotopic labeling of substrates (iTRAQ-TAILS) to enrich the N-terminome by negative selection of the blocked mature original N-termini and neo-N-termini has many advantages. It enables simultaneous characterization of the natural N-termini of proteins, their N-terminal modifications, and proteolysis product and cleavage site identification. Furthermore, iTRAQ-TAILS also enables multiplex N-terminomics analysis of up to eight samples and allows for quantification in MS2 mode, thus preventing an increase in spectral complexity and extending proteome coverage by signal amplification of low abundance proteins. We compared the substrate degradomes of two closely related matrix metalloproteinases, MMP-2 (gelatinase A) and MMP-9 (gelatinase B), in fibroblast secreted proteins. Among 3,152 unique N-terminal peptides identified corresponding to 1,054 proteins, we detected 201 cleavage products for MMP-2 and unexpectedly only 19 for the homologous MMP-9 under identical conditions. Novel substrates identified and biochemically validated include insulin-like growth factor binding protein-4, complement C1r component A, galectin-1, dickkopf-related protein-3, and thrombospondin-2. Hence, N-terminomics analyses

  5. Multiplex N-terminome Analysis of MMP-2 and MMP-9 Substrate Degradomes by iTRAQ-TAILS Quantitative Proteomics*

    PubMed Central

    Prudova, Anna; auf dem Keller, Ulrich; Butler, Georgina S.; Overall, Christopher M.

    2010-01-01

    Proteolysis is a major protein posttranslational modification that, by altering protein structure, affects protein function and, by truncating the protein sequence, alters peptide signatures of proteins analyzed by proteomics. To identify such modified and shortened protease-generated neo-N-termini on a proteome-wide basis, we developed a whole protein isobaric tag for relative and absolute quantitation (iTRAQ) labeling method that simultaneously labels and blocks all primary amines including protein N- termini and lysine side chains. Blocking lysines limits trypsin cleavage to arginine, which effectively elongates the proteolytically truncated peptides for improved MS/MS analysis and peptide identification. Incorporating iTRAQ whole protein labeling with terminal amine isotopic labeling of substrates (iTRAQ-TAILS) to enrich the N-terminome by negative selection of the blocked mature original N-termini and neo-N-termini has many advantages. It enables simultaneous characterization of the natural N-termini of proteins, their N-terminal modifications, and proteolysis product and cleavage site identification. Furthermore, iTRAQ-TAILS also enables multiplex N-terminomics analysis of up to eight samples and allows for quantification in MS2 mode, thus preventing an increase in spectral complexity and extending proteome coverage by signal amplification of low abundance proteins. We compared the substrate degradomes of two closely related matrix metalloproteinases, MMP-2 (gelatinase A) and MMP-9 (gelatinase B), in fibroblast secreted proteins. Among 3,152 unique N-terminal peptides identified corresponding to 1,054 proteins, we detected 201 cleavage products for MMP-2 and unexpectedly only 19 for the homologous MMP-9 under identical conditions. Novel substrates identified and biochemically validated include insulin-like growth factor binding protein-4, complement C1r component A, galectin-1, dickkopf-related protein-3, and thrombospondin-2. Hence, N-terminomics analyses

  6. Substrate Topography Induces a Crossover from 2D to 3D Behavior in Fibroblast Migration

    PubMed Central

    Ghibaudo, Marion; Trichet, Léa; Le Digabel, Jimmy; Richert, Alain; Hersen, Pascal; Ladoux, Benoît

    2009-01-01

    Abstract In a three-dimensional environment, cells migrate through complex topographical features. Using microstructured substrates, we investigate the role of substrate topography in cell adhesion and migration. To do so, fibroblasts are plated on chemically identical substrates composed of microfabricated pillars. When the dimensions of the pillars (i.e., the diameter, length, and spacing) are varied, migrating cells encounter alternating flat and rough surfaces that depend on the spacing between the pillars. Consequently, we show that substrate topography affects cell shape and migration by modifying cell-to-substrate interactions. Cells on micropillar substrates exhibit more elongated and branched shapes with fewer actin stress fibers compared with cells on flat surfaces. By analyzing the migration paths in various environments, we observe different mechanisms of cell migration, including a persistent type of migration, that depend on the organization of the topographical features. These responses can be attributed to a spatial reorganization of the actin cytoskeleton due to physical constraints and a preferential formation of focal adhesions on the micropillars, with an increased lifetime compared to that observed on flat surfaces. By changing myosin II activity, we show that actomyosin contractility is essential in the cellular response to micron-scale topographic signals. Finally, the analysis of cell movements at the frontier between flat and micropillar substrates shows that cell transmigration through the micropillar substrates depends on the spacing between the pillars. PMID:19580774

  7. Method for adhering a coating to a substrate structure

    DOEpatents

    Taxacher, Glenn Curtis; Crespo, Andres Garcia; Roberts, III, Herbert Chidsey

    2015-02-17

    A method for adhering a coating to a substrate structure comprises selecting a substrate structure having an outer surface oriented substantially parallel to a direction of radial stress, modifying the outer surface to provide a textured region having steps to adhere a coating thereto, and applying a coating to extend over at least a portion of the textured region, wherein the steps are oriented substantially perpendicular to the direction of radial stress to resist deformation of the coating relative to the substrate structure. A rotating component comprises a substrate structure having an outer surface oriented substantially parallel to a direction of radial stress. The outer surface defines a textured region having steps to adhere a coating thereto, and a coating extends over at least a portion of the textured region. The steps are oriented substantially perpendicular to the direction of radial stress to resist creep.

  8. Impact of M36I polymorphism on the interaction of HIV-1 protease with its substrates: insights from molecular dynamics

    PubMed Central

    2014-01-01

    Background Over the last decades, a vast structural knowledge has been gathered on the HIV-1 protease (PR). Noticeably, most of the studies focused the B-subtype, which has the highest prevalence in developed countries. Accordingly, currently available anti-HIV drugs target this subtype, with considerable benefits for the corresponding patients. However, in developing countries, there is a wide variety of HIV-1 subtypes carrying PR polymorphisms related to reduced drug susceptibility. The non-active site mutation, M36I, is the most frequent polymorphism, and is considered as a non-B subtype marker. Yet, the structural impact of this substitution on the PR structure and on the interaction with natural substrates remains poorly documented. Results Herein, we used molecular dynamics simulations to investigate the role of this polymorphism on the interaction of PR with six of its natural cleavage-sites substrates. Free energy analyses by MMPB/SA calculations showed an affinity decrease of M36I-PR for the majority of its substrates. The only exceptions were the RT-RH, with equivalent affinity, and the RH-IN, for which an increased affinity was found. Furthermore, molecular simulations suggest that, unlike other peptides, RH-IN induced larger structural fluctuations in the wild-type enzyme than in the M36I variant. Conclusions With multiple approaches and analyses we identified structural and dynamical determinants associated with the changes found in the binding affinity of the M36I variant. This mutation influences the flexibility of both PR and its complexed substrate. The observed impact of M36I, suggest that combination with other non-B subtype polymorphisms, could lead to major effects on the interaction with the 12 known cleavage sites, which should impact the virion maturation. PMID:25573486

  9. Substrate Efflux Propensity Is the Key Determinant of Ca2+-independent Phospholipase A-β (iPLAβ)-mediated Glycerophospholipid Hydrolysis*

    PubMed Central

    Batchu, Krishna Chaithanya; Hokynar, Kati; Jeltsch, Michael; Mattonet, Kenny; Somerharju, Pentti

    2015-01-01

    The A-type phospholipases (PLAs) are key players in glycerophospholipid (GPL) homeostasis and in mammalian cells; Ca2+-independent PLA-β (iPLAβ) in particular has been implicated in this essential process. However, the regulation of this enzyme, which is necessary to avoid futile competition between synthesis and degradation, is not understood. Recently, we provided evidence that the efflux of the substrate molecules from the bilayer is the rate-limiting step in the hydrolysis of GPLs by some secretory (nonhomeostatic) PLAs. To study whether this is the case with iPLAβ as well, a mass spectrometric assay was employed to determine the rate of hydrolysis of multiple saturated and unsaturated GPL species in parallel using micelles or vesicle bilayers as the macrosubstrate. With micelles, the hydrolysis decreased with increasing acyl chain length independent of unsaturation, and modest discrimination between acyl positional isomers was observed, presumably due to the differences in the structure of the sn-1 and sn-2 acyl-binding sites of the protein. In striking contrast, no significant discrimination between positional isomers was observed with bilayers, and the rate of hydrolysis decreased with the acyl chain length logarithmically and far more than with micelles. These data provide compelling evidence that efflux of the substrate molecule from the bilayer, which also decreases monotonously with acyl chain length, is the rate-determining step in iPLAβ-mediated hydrolysis of GPLs in membranes. This finding is intriguing as it may help to understand how homeostatic PLAs are regulated and how degradation and biosynthesis are coordinated. PMID:25713085

  10. Application of a mixed metal oxide catalyst to a metallic substrate

    NASA Technical Reports Server (NTRS)

    Sevener, Kathleen M. (Inventor); Lohner, Kevin A. (Inventor); Mays, Jeffrey A. (Inventor); Wisner, Daniel L. (Inventor)

    2009-01-01

    A method for applying a mixed metal oxide catalyst to a metallic substrate for the creation of a robust, high temperature catalyst system for use in decomposing propellants, particularly hydrogen peroxide propellants, for use in propulsion systems. The method begins by forming a prepared substrate material consisting of a metallic inner substrate and a bound layer of a noble metal intermediate. Alternatively, a bound ceramic coating, or frit, may be introduced between the metallic inner substrate and noble metal intermediate when the metallic substrate is oxidation resistant. A high-activity catalyst slurry is applied to the surface of the prepared substrate and dried to remove the organic solvent. The catalyst layer is then heat treated to bind the catalyst layer to the surface. The bound catalyst layer is then activated using an activation treatment and calcinations to form the high-activity catalyst system.

  11. Highly flexible InSnO electrodes on thin colourless polyimide substrate for high-performance flexible CH3NH3PbI3 perovskite solar cells

    NASA Astrophysics Data System (ADS)

    Park, Jeong-Il; Heo, Jin Hyuck; Park, Sung-Hyun; Hong, Ki Il; Jeong, Hak Gee; Im, Sang Hyuk; Kim, Han-Ki

    2017-02-01

    We fabricated high-performance flexible CH3NH3PbI3 (MAPbI3) perovskite solar cells with a power conversion efficiency of 15.5% on roll-to-roll sputtered ITO films on 60 μm-thick colourless polyimide (CPI) substrate. Due to the thermal stability of the CPI substrate, an ITO/CPI sample subjected to rapid thermal annealing at 300 °C showed a low sheet resistance of 57.8 Ω/square and high transmittance of 83.6%, which are better values than those of an ITO/PET sample. Outer and inner bending tests demonstrated that the mechanical flexibility of the ITO/CPI was superior to that of the conventional ITO/PET sample owing to the thinness of the CPI substrate. In addition, due to its good mechanical flexibility, the ITO/CPI showed no change in resistance after 10,000 cycle outer and inner dynamic fatigue tests. Flexible perovskite solar cells with the structure of Au/PTAA/MAPbI3/ZnO/ITO/CPI showed a high power conversion efficiency of 15.5%. The successful operation of these flexible perovskite solar cells on ITO/CPI substrate indicated that the ITO film on thermally stable CPI substrate is a promising of flexible substrate for high-temperature processing, a finding likely to advance the commercialization of cost-efficient flexible perovskite solar cells.

  12. Graphene revisited: From orbital mapping to its impact as a substrate

    NASA Astrophysics Data System (ADS)

    Draxl, Claudia

    Graphene, the material of the 21st century, is without doubt one of the best characterized solids. Despite the enormous amount of investigations and related publications, it still it offers a variety of exciting aspects to explore, in particular in view of its excitations. Combining density-functional theory with many-body perturbation theory, as implemented in the all-electron full-potential package exciting, provides a powerful framework for this purpose. (i) The first example concerns the question, whether we can ``see'' orbitals in an electron microscope. Indeed, transmission electron microscopy can be used for mapping atomic orbitals, as demonstrated recently by a first-principles approach. For defected graphene, exhibiting either an isolated vacancy or a substitutional nitrogen atom different kinds of images are to be expected, depending on the orbital character. (ii) Graphene/BN heterostructures absorb light over a broad frequency range, from the near-infrared to the ultraviolet region, exhibiting novel features induced by the stacking. Peculiar features of their excitations are inter-layer excitons that can be modulated upon layer patterning. By choosing the stacking arrangement, the electronic coupling between the individual components can be tuned to enhance light-matter interaction. (iii) As demonstrated for azobenzene monolayers, graphene as a substrate strongly impacts the photo-switching behavior of molecules. Despite the weak hybridization, the photo-absorption of the molecules is remarkably modulated. While substrate polarization reduces the band-gap of the adsorbate, enhanced dielectric screening weakens the attractive interaction between electrons and holes. Furthermore, excitations corresponding to intermolecular electron-hole pairs, which are dark in the isolated monolayers, are activated by the presence of the substrate. (iv) Finally, we ask how first- and second-order Raman spectra of graphene are affected by strain that may be induced by an

  13. Characterization of a commercialized SERS-active substrate and its application to the identification of intact Bacillus endospores

    NASA Astrophysics Data System (ADS)

    Alexander, Troy A.; Le, Dianna M.

    2007-06-01

    Surface-enhanced-Raman-spectroscopy (SERS) can be made an attractive approach for the identification of Raman-active compounds and biological materials (i.e., toxins, viruses, or intact bacterial cells or spores) through development of reproducible, spatially uniform SERS-active substrates. Recently, reproducible (from substrate to substrate), spatially homogeneous (over large areas) SERS-active substrates have been commercialized and are now available in the marketplace. Scanning electron microscopy and high-resolution, tapping-mode atomic force microscopy have been used to analyze these novel plasmonic surfaces for topographical consistency. Additionally, we have assessed, by wavelength-tunable microreflectance spectrometry, the spatial distribution of the localized surface plasmon resonance (LSPR) across a single substrate surface as well as the LSPR λMAX variance from substrate to substrate. These analyses reveal that these surfaces are topologically uniform with small LSPR variance from substrate to substrate. Further, we have utilized these patterned surfaces to acquire SERS spectral signatures of four intact, genetically distinct Bacillus spore species cultivated under identical growth conditions. Salient spectral signature features make it possible to discriminate among these genetically distinct spores. Additionally, partial least squares, a multivariate calibration method, has been used to develop personal-computer-borne algorithms useful for classification of unknown spore samples based solely on SERS spectral signatures. To our knowledge, this is the first report detailing application of these commercially available SERS-active substrates to identification of intact Bacillus spores.

  14. Characterization of the IPEC-J2 MDR1 (iP-gp) cell line as a tool for identification of P-gp substrates.

    PubMed

    Ozgür, Burak; Saaby, Lasse; Langthaler, Kristine; Brodin, Birger

    2018-01-15

    Recently, we transfected the porcine intestinal cell line IPEC-J2, with human P-glycoprotein (P-gp, ABCB1). The resulting cell line, iP-gp, has a high expression of functional human P-gp in the apical membrane, and a low expression of nonhuman ATP-binding cassette (ABC) transporters. The aim of the present work was to investigate the usability of iP-gp cell line for determining transepithelial transport kinetics of the prototypical P-gp substrates digoxin and rhodamine 123. The cell line generated tight monolayers after 16days of culture, reflected by high transepithelial electrical resistance values (TEER>15,000Ω·cm 2 ), immunocytochemistry and low fluxes of the paracellular flux marker [ 14 C]-mannitol. Monolayer integrity was not affected the common solvents dimethyl sulfoxide (DMSO), methanol and ethanol in concentrations up to 2% (v/v). Transepithelial fluxes of [ 3 H]-labeled digoxin and rhodamine 123 were measured at varying donor concentrations, and kinetic parameters were estimated. K m and V max of P-gp mediated basolateral-to-apical (B-A) flux of rhodamine 123 were estimated to 332±124μM and 111±16pmol·cm -2 ·min -1 (n=3, total N=6), respectively. V max and K m of digoxin B-A flux could not be estimated due to the low aqueous solubility of digoxin. The half maximal inhibitory concentrations (IC 50 ) of the selective P-gp inhibitor, zosuquidar (LY-335979), were estimated to 0.05±0.01μM (n=3, total N=6) and 0.04±0.01μM (n=3, total N=6) in transport experiments with digoxin and rhodamine 123 as substrates, respectively. Bidirectional fluxes of digoxin and rhodamine 123 were measured in transfected Madin Darby canine kidney cells (MDCK II MDR1) and compared with the fluxes obtained with the iP-gp cell monolayers. Efflux ratios were highest in the iP-gp cells, due to a tighter paracellular pathway. In conclusion, both digoxin and rhodamine 123 could be used to obtain IC 50 values of inhibition, K i values were only possible to obtain using

  15. Automated cassette-to-cassette substrate handling system

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kraus, Joseph Arthur; Boyer, Jeremy James; Mack, Joseph

    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 amore » 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.« less

  16. Critical Casimir effect for colloids close to chemically patterned substrates.

    PubMed

    Tröndle, M; Kondrat, S; Gambassi, A; Harnau, L; Dietrich, S

    2010-08-21

    Colloids immersed in a critical or near-critical binary liquid mixture and close to a chemically patterned substrate are subject to normal and lateral critical Casimir forces of dominating strength. For a single colloid, we calculate these attractive or repulsive forces and the corresponding critical Casimir potentials within mean-field theory. Within this approach we also discuss the quality of the Derjaguin approximation and apply it to Monte Carlo simulation data available for the system under study. We find that the range of validity of the Derjaguin approximation is rather large and that it fails only for surface structures which are very small compared to the geometric mean of the size of the colloid and its distance from the substrate. For certain chemical structures of the substrate, the critical Casimir force acting on the colloid can change sign as a function of the distance between the particle and the substrate; this provides a mechanism for stable levitation at a certain distance which can be strongly tuned by temperature, i.e., with a sensitivity of more than 200 nm/K.

  17. Near single-crystalline, high-carrier-mobility silicon thin film on a polycrystalline/amorphous substrate

    DOEpatents

    Findikoglu, Alp T [Los Alamos, NM; Jia, Quanxi [Los Alamos, NM; Arendt, Paul N [Los Alamos, NM; Matias, Vladimir [Santa Fe, NM; Choi, Woong [Los Alamos, NM

    2009-10-27

    A template article including a base substrate including: (i) a base material selected from the group consisting of polycrystalline substrates and amorphous substrates, and (ii) at least one layer of a differing material upon the surface of the base material; and, a buffer material layer upon the base substrate, the buffer material layer characterized by: (a) low chemical reactivity with the base substrate, (b) stability at temperatures up to at least about 800.degree. C. under low vacuum conditions, and (c) a lattice crystal structure adapted for subsequent deposition of a semiconductor material; is provided, together with a semiconductor article including a base substrate including: (i) a base material selected from the group consisting of polycrystalline substrates and amorphous substrates, and (ii) at least one layer of a differing material upon the surface of the base material; and, a buffer material layer upon the base substrate, the buffer material layer characterized by: (a) low chemical reactivity with the base substrate, (b) stability at temperatures up to at least about 800.degree. C. under low vacuum conditions, and (c) a lattice crystal structure adapted for subsequent deposition of a semiconductor material, and, a top-layer of semiconductor material upon the buffer material layer.

  18. SOLVENT-BASED TO WATERBASED ADHESIVE-COATED SUBSTRATE RETROFIT - VOLUME I: COMPARATIVE ANALYSIS

    EPA Science Inventory

    This volume represents the analysis of case study facilities' experience with waterbased adhesive use and retrofit requirements. (NOTE: The coated and laminated substrate manufacturing industry was selected as part of NRMRL'S support of the 33/50 Program because of its significan...

  19. Tudor staphylococcal nuclease is a structure-specific ribonuclease that degrades RNA at unstructured regions during microRNA decay.

    PubMed

    Li, Chia-Lung; Yang, Wei-Zen; Shi, Zhonghao; Yuan, Hanna S

    2018-05-01

    Tudor staphylococcal nuclease (TSN) is an evolutionarily conserved ribonuclease in eukaryotes that is composed of five staphylococcal nuclease-like domains (SN1-SN5) and a Tudor domain. TSN degrades hyper-edited double-stranded RNA, including primary miRNA precursors containing multiple I•U and U•I pairs, and mature miRNA during miRNA decay. However, how TSN binds and degrades its RNA substrates remains unclear. Here, we show that the C. elegans TSN (cTSN) is a monomeric Ca 2+ -dependent ribonuclease, cleaving RNA chains at the 5'-side of the phosphodiester linkage to produce degraded fragments with 5'-hydroxyl and 3'-phosphate ends. cTSN degrades single-stranded RNA and double-stranded RNA containing mismatched base pairs, but is not restricted to those containing multiple I•U and U•I pairs. cTSN has at least two catalytic active sites located in the SN1 and SN3 domains, since mutations of the putative Ca 2+ -binding residues in these two domains strongly impaired its ribonuclease activity. We further show by small-angle X-ray scattering that rice osTSN has a flexible two-lobed structure with open to closed conformations, indicating that TSN may change its conformation upon RNA binding. We conclude that TSN is a structure-specific ribonuclease targeting not only single-stranded RNA, but also unstructured regions of double-stranded RNA. This study provides the molecular basis for how TSN cooperates with RNA editing to eliminate duplex RNA in cell defense, and how TSN selects and degrades RNA during microRNA decay. © 2018 Li et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  20. Halotolerant microbial consortia able to degrade highly recalcitrant plant biomass substrate.

    PubMed

    Cortes-Tolalpa, Larisa; Norder, Justin; van Elsas, Jan Dirk; Falcao Salles, Joana

    2018-03-01

    The microbial degradation of plant-derived compounds under salinity stress remains largely underexplored. The pretreatment of lignocellulose material, which is often needed to improve the production of lignocellulose monomers, leads to high salt levels, generating a saline environment that raises technical considerations that influence subsequent downstream processes. Here, we constructed halotolerant lignocellulose degrading microbial consortia by enriching a salt marsh soil microbiome on a recalcitrant carbon and energy source, i.e., wheat straw. The consortia were obtained after six cycles of growth on fresh substrate (adaptation phase), which was followed by four cycles on pre-digested (highly-recalcitrant) substrate (stabilization phase). The data indicated that typical salt-tolerant bacteria made up a large part of the selected consortia. These were "trained" to progressively perform better on fresh substrate, but a shift was observed when highly recalcitrant substrate was used. The most dominant bacteria in the consortia were Joostella marina, Flavobacterium beibuense, Algoriphagus ratkowskyi, Pseudomonas putida, and Halomonas meridiana. Interestingly, fungi were sparsely present and negatively affected by the change in the substrate composition. Sarocladium strictum was the single fungal strain recovered at the end of the adaptation phase, whereas it was deselected by the presence of recalcitrant substrate. Consortia selected in the latter substrate presented higher cellulose and lignin degradation than consortia selected on fresh substrate, indicating a specialization in transforming the recalcitrant regions of the substrate. Moreover, our results indicate that bacteria have a prime role in the degradation of recalcitrant lignocellulose under saline conditions, as compared to fungi. The final consortia constitute an interesting source of lignocellulolytic haloenzymes that can be used to increase the efficiency of the degradation process, while decreasing

  1. Determination of the order of substrate addition to MspI DNA methyltransferase using a novel mechanism-based inhibitor.

    PubMed Central

    Taylor, C; Ford, K; Connolly, B A; Hornby, D P

    1993-01-01

    The cloning and overexpression of the MspI DNA methyltransferase as a functional fusion with glutathione S-transferase is described. The fusion enzyme retains full biological activity and has been used to investigate the interaction of substrates and inhibitors with MspI DNA methyltransferase. The fusion enzyme has been purified to homogeneity in a single step on GSH-agarose and is free from contaminating exonuclease activity. The enzyme can be photolabelled with S-adenosyl-L-methionine and the level of incorporation of label is enhanced by the presence of a nonspecific DNA duplex. In the presence of a cognate oligodeoxynucleotide, no photolabelling was observed since methyl transfer occurs instead. The inclusion of a mechanism-based inhibitor of C-5 deoxycytidine DNA methylation (an oligodeoxynucleotide containing the base 2-pyrimidinone-1-beta-D-2'-deoxyribofuranoside in the position of the deoxycytidine to which methyl addition occurs), which is thought to form a covalent interaction with the reactive cysteine of such enzymes, led to an enhancement of S-adenosyl-L-methionine photolabelling which suggests that, in contrast with results obtained with EcoRII DNA methyltransferase [Som and Friedman (1991) J. Biol. Chem. 266, 2937-2945], methylcysteine is not the photolabelled product. The implications of the results obtained with this mechanism-based inhibitor are discussed with respect to other C-5-specific DNA methyltransferases. Gel-retardation assays in the presence of cognate oligodeoxynucleotides that contain the reactive pyrimidinone base in place of the deoxycytidine target base are described. These demonstrate that most probably a stable covalent bond is formed between the methyltransferase and this oligodeoxynucleotide. However, the alternative of extremely tight non-covalent binding cannot be rigorously excluded. Furthermore, the results from these experiments indicate that the reaction mechanism proceeds in a manner similar to that of HhaI DNA

  2. Bidirectional regulation of adenosine-to-inosine (A-to-I) RNA editing by DEAH box helicase 9 (DHX9) in cancer.

    PubMed

    Hong, HuiQi; An, Omer; Chan, Tim H M; Ng, Vanessa H E; Kwok, Hui Si; Lin, Jaymie S; Qi, Lihua; Han, Jian; Tay, Daryl J T; Tang, Sze Jing; Yang, Henry; Song, Yangyang; Bellido Molias, Fernando; Tenen, Daniel G; Chen, Leilei

    2018-05-18

    Adenosine-to-inosine (A-to-I) RNA editing entails the enzymatic deamination of adenosines to inosines by adenosine deaminases acting on RNA (ADARs). Dysregulated A-to-I editing has been implicated in various diseases, including cancers. However, the precise factors governing the A-to-I editing and their physiopathological implications remain as a long-standing question. Herein, we unravel that DEAH box helicase 9 (DHX9), at least partially dependent of its helicase activity, functions as a bidirectional regulator of A-to-I editing in cancer cells. Intriguingly, the ADAR substrate specificity determines the opposing effects of DHX9 on editing as DHX9 silencing preferentially represses editing of ADAR1-specific substrates, whereas augments ADAR2-specific substrate editing. Analysis of 11 cancer types from The Cancer Genome Atlas (TCGA) reveals a striking overexpression of DHX9 in tumors. Further, tumorigenicity studies demonstrate a helicase-dependent oncogenic role of DHX9 in cancer development. In sum, DHX9 constitutes a bidirectional regulatory mode in A-to-I editing, which is in part responsible for the dysregulated editome profile in cancer.

  3. System configured for applying a modifying agent to a non-equidimensional substrate

    DOEpatents

    Janikowski,; Stuart K. , Argyle; Mark D. , Fox; Robert V. , Propp; W Alan, Toth [Idaho Falls, ID; William J. , Ginosar; Daniel M. , Allen; Charles A. , Miller; David, L [Idaho Falls, ID

    2007-07-10

    The present invention is related to systems and methods for modifying various non-equidimensional substrates with modifying agents. The system comprises a processing chamber configured for passing the non-equidimensional substrate therethrough, wherein the processing chamber is further configured to accept a treatment mixture into the chamber during movement of the non-equidimensional substrate through the processing chamber. The treatment mixture can comprise of the modifying agent in a carrier medium, wherein the carrier medium is selected from the group consisting of a supercritical fluid, a near-critical fluid, a superheated fluid, a superheated liquid, and a liquefied gas. Thus, the modifying agent can be applied to the non-equidimensional substrate upon contact between the treatment mixture and the non-equidimensional substrate.

  4. System configured for applying a modifying agent to a non-equidimensional substrate

    DOEpatents

    Janikowski, Stuart K.; Toth, William J.; Ginosar, Daniel M.; Allen, Charles A.; Argyle, Mark D.; Fox, Robert V.; Propp, W. Alan; Miller, David L.

    2003-09-23

    The present invention is related to systems and methods for modifying various non-equidimensional substrates with modifying agents. The system comprises a processing chamber configured for passing the non-equidimensional substrate therethrough, wherein the processing chamber is further configured to accept a treatment mixture into the chamber during movement of the non-equidimensional substrate through the processing chamber. The treatment mixture can comprise of the modifying agent in a carrier medium, wherein the carrier medium is selected from the group consisting of a supercritical fluid, a near-critical fluid, a superheated fluid, a superheated liquid, and a liquefied gas. Thus, the modifying agent can be applied to the non-equidimensional substrate upon contact between the treatment mixture and the non-equidimensional substrate.

  5. Deformation of an Elastic Substrate Due to a Resting Sessile Droplet

    NASA Astrophysics Data System (ADS)

    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.

  6. Vacuum-assisted Fluid Flow in Microchannels to Pattern Substrates and Cells

    PubMed Central

    Shrirao, Anil B.; Kung, Frank H.; Yip, Derek; Cho, Cheul H.; Townes-Anderson, Ellen

    2014-01-01

    Substrate and cell patterning are widely used techniques in cell biology to study cell-to-cell and cell-to-substrate interactions. Conventional patterning techniques work well only with simple shapes, small areas and selected bio-materials. This paper describes a method to distribute cell suspensions as well as substrate solutions into complex, long, closed (dead-end) polydimethylsiloxane (PDMS) microchannels using negative pressure. Our method builds upon a previous vacuum-assisted method used for micromolding (Jeon, Choi et al. 1999) and successfully patterned collagen-I, fibronectin and Sal-1 substrates on glass and polystyrene surfaces, filling microchannels with lengths up to 120 mm and covering areas up to 13 × 10 mm2. Vacuum-patterned substrates were subsequently used to culture mammalian PC12 and fibroblast cells and amphibian neurons. Cells were also patterned directly by injecting cell suspensions into microchannels using vacuum. Fibroblast and neuronal cells patterned using vacuum showed normal growth and minimal cell death indicating no adverse effects of vacuum on cells. Our method fills reversibly sealed PDMS microchannels. This enables the user to remove the PDMS microchannel cast and access the patterned biomaterial or cells for further experimental purposes. Overall, this is a straightforward technique that has broad applicability for cell biology. PMID:24989641

  7. Vacuum-assisted fluid flow in microchannels to pattern substrates and cells.

    PubMed

    Shrirao, Anil B; Kung, Frank H; Yip, Derek; Cho, Cheul H; Townes-Anderson, Ellen

    2014-09-01

    Substrate and cell patterning are widely used techniques in cell biology to study cell-to-cell and cell-substrate interactions. Conventional patterning techniques work well only with simple shapes, small areas and selected bio-materials. This paper describes a method to distribute cell suspensions as well as substrate solutions into complex, long, closed (dead-end) polydimethylsiloxane (PDMS) microchannels using negative pressure. Our method builds upon a previous vacuum-assisted method used for micromolding (Jeon et al 1999 Adv. Mater 11 946) and successfully patterned collagen-I, fibronectin and Sal-1 substrates on glass and polystyrene surfaces, filling microchannels with lengths up to 120 mm and covering areas up to 13 × 10 mm(2). Vacuum-patterned substrates were subsequently used to culture mammalian PC12 and fibroblast cells and amphibian neurons. Cells were also patterned directly by injecting cell suspensions into microchannels using vacuum. Fibroblast and neuronal cells patterned using vacuum showed normal growth and minimal cell death indicating no adverse effects of vacuum on cells. Our method fills reversibly sealed PDMS microchannels. This enables the user to remove the PDMS microchannel cast and access the patterned biomaterial or cells for further experimental purposes. Overall, this is a straightforward technique that has broad applicability for cell biology.

  8. A Colloidal Route to Detection of Organic Molecules Based on Surface-Enhanced Raman Spectroscopy Using Nanostructured Substrate Derived from Aerosols

    NASA Astrophysics Data System (ADS)

    Gen, Masao; Kakuta, Hideo; Kamimoto, Yoshihito; Wuled Lenggoro, I.

    2011-06-01

    A detection method based on the surface-enhanced Raman spectroscopy (SERS)-active substrate derived from aerosol nanoparticles and a colloidal suspension for detecting organic molecules of a model analyte (a pesticide) is proposed. This approach can detect the molecules of the derived from its solution with the concentration levels of ppb. For substrate fabrication, a gas-phase method is used to directly deposit Ag nanoparticles on to a silicon substrate having pyramidal structures. By mixing the target analyte with a suspension of Ag colloids purchased in advance, clotianidin analyte on Ag colloid can exist in junctions of co-aggregated Ag colloids. Using (i) a nanostructured substrate made from aerosol nanoparticles and (ii) colloidal suspension can increase the number of activity spots.

  9. I-V Characteristics vs. Spatial Dissipation Maps in YBCO Grain Boundary on Bicrystal Substrates

    NASA Astrophysics Data System (ADS)

    Kwon, Chuhee; Yamamoto, Megumi; Pottish, Samuel; Haugan, Timothy; Barnes, Paul

    2008-03-01

    Grain boundary (GB) properties of YBCO films on SrTiO3 bicrystal substrates with 24 degree misorientations are examined by transport and scanning laser microscopy (SLM) techniques. Thermoelectric SLM clearly shows the location of grain boundaries, and variable temperature SLM confirms that GB has lower Tc. A series of I-V measured in superconducting states exhibit clear step-like features identified in earlier papers as sub-gap structures. The low temperature SLM shows a close relation between the step-like features and the local dissipation pattern in GB. We believe that the activation of Fiske steps is responsible for the step-like I-V, and SLM images show the spatial pattern of the self-excited resonance in GB. We will also discuss how Ca-doping and nanoparticle additions on YBCO affect the junction properties.

  10. Influence of substrate modification and C-terminal truncation on the active site structure of substrate-bound heme oxygenase from Neisseriae meningitidis; A 1H NMR study†

    PubMed Central

    Peng, Dungeng; Satterlee, James D.; Ma, Li-Hua; Dallas, Jerry L.; Smith, Kevin M.; Zhang, Xuhong; Sato, Michihiko; La Mar, Gerd N.

    2011-01-01

    Heme oxygenase, HO, from the pathogenic bacterium N. meningitidis, NmHO, which secures host iron, shares many properties with mammalian HOs, but also exhibits some key differences. The crystal structure appears more compact and the crystal-undetected C-terminus interacts with substrate in solution. The unique nature of substrate-protein, specifically pyrrole-I/II-helix-2, peripheral interactions in NmHO are probed by 2D 1H NMR to reveal unique structural features controlling substrate orientation. The thermodynamics of substrate orientational isomerism are mapped for substrates with individual vinyl → methyl → hydrogen substitutions and with enzyme C-terminal deletions. NmHO exhibits significantly stronger orientational preference, reflecting much stronger and selective pyrrole-I/II interactions with the protein matrix, than in mammalian HOs. Thus, replacing bulky vinyls with hydrogens results in a 180° rotation of substrate about the α,γ-meso axis in the active site. A "collapse" of the substrate pocket as substrate size decreases is reflected in movement of helix-2 toward the substrate as indicated by significant and selective increased NOESY cross peak intensity, increase in steric Fe-CN tilt reflected in the orientation of the major magnetic axis, and decrease in steric constraints controlling the rate of aromatic ring reorientation. The active site of NmHO appears "stressed" for native protohemin and its "collapse" upon replacing vinyls by hydrogen leads to a factor ~102 increase in substrate affinity. Interaction of the C-terminus with the active site destabilizes the crystallographic protohemin orientation by ~0.7 kcal/mol, which is consistent with optimizing the His207-Asp27 H-bond. Implications of the active site "stress" for product release are discussed. PMID:21870860

  11. Nitrification in a zeoponic substrate

    NASA Technical Reports Server (NTRS)

    McGilloway, R. L.; Weaver, R. W.; Ming, D. W.; Gruener, J. E.

    2003-01-01

    Clinoptilolite is a zeolite mineral with high cation exchange capacity used in zeoponic substrates that have been proposed as a solid medium for growing plants or as a fertilizer material. The kinetics of nitrification has not been measured for NH4+ saturated zeoponic substrate. Experiments were conducted to evaluate the production of NO2- and NO3-, and nitrifier populations in zeoponic substrates. Small columns were filled with zeoponic substrate inoculated with a commercial inoculum or soil enrichment culture of nitrifying bacteria. In addition to column studies, a growth chamber study was conducted to evaluate the kinetics of nitrification in zeoponic substrates used to grow radishes (Raphanus sativus L.). The zeoponic substrate provided a readily available source of NH4+, and nitrifying bacteria were active in the substrate. Ammonium oxidation rates in column studies ranged from 5 to 10 micrograms N g-1 substrate h-1, and NO2- oxidation rates were 2 to 9.5 micrograms N g-1 substrate h-1. Rates determined from the growth chamber study were approximately 1.2 micrograms N g-1 substrate h-1. Quantities of NH4+ oxidized to NO2- and NO3- in inoculated zeoponic substrate were in excess of plant up-take. Acidification as a result of NH4+ oxidation resulted in a pH decline, and the zeoponic substrate showed limited buffering capacity.

  12. Imparting Icephobicity with Substrate Flexibility.

    PubMed

    Vasileiou, Thomas; Schutzius, Thomas M; Poulikakos, Dimos

    2017-07-11

    Ice accumulation hinders the performance of, and poses safety threats for, infrastructure both on the ground and in the air. Previously, rationally designed superhydrophobic surfaces have demonstrated some potential as a passive means to mitigate ice accretion; however, further studies on material solutions that reduce impalement and the contact time for impacting supercooled droplets (high viscosity) and can also repel droplets that freeze during surface contact are urgently needed. Here we demonstrate the collaborative effect of substrate flexibility and surface micro/nanotexture on enhancing both icephobicity and the repellency of viscous droplets (typical of supercooled water). We first investigate the influence of increased viscosity (spanning from 0.9 to 1078 mPa·s using water-glycerol mixtures) on impalement resistance and the droplet-substrate contact time after impact. Then we examine the effect of droplet partial solidification on recoil and simulate more challenging icing conditions by impacting supercooled water droplets (down to -15 °C) onto flexible and rigid surfaces containing ice nucleation promoters (AgI). We demonstrate a passive mechanism for shedding partially solidified (recalescent) droplets-under conditions where partial solidification occurs much faster than the natural droplet oscillation-which does not rely on converting droplet surface energy into kinetic energy (classic recoil mechanism). Using an energy-based model (kinetic-elastic-capillary), we identify a previously unexplored mechanism whereby the substrate oscillation and velocity govern the rebound process, with low areal density and moderately stiff substrates acting to efficiently absorb the incoming droplet kinetic energy and rectify it back, allowing droplets to overcome adhesion and gravitational forces, and recoil. This mechanism applies for a range of droplet viscosities, spanning from low- to high-viscosity fluids and even ice slurries, which do not rebound from rigid

  13. Universal Common Communication Substrate (UCCS) Specification; Universal Common Communication Substrate (UCCS) Implementation

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Universal Common Communication Substrate (UCCS) is a low-level communication substrate that exposes high-performance communication primitives, while providing network interoperability. It is intended to support multiple upper layer protocol (ULPs) or programming models including SHMEM,UPC,Titanium,Co-Array Fortran,Global Arrays,MPI,GASNet, and File I/O. it provides various communication operations including one-sided and two-sided point-to-point, collectives, and remote atomic operations. In addition to operations for ULPs, it provides an out-of-band communication channel required typically required to wire-up communication libraries.

  14. Analysis of substrate specificity of human DHHC protein acyltransferases using a yeast expression system

    PubMed Central

    Ohno, Yusuke; Kashio, Atsushi; Ogata, Ren; Ishitomi, Akihiro; Yamazaki, Yuki; Kihara, Akio

    2012-01-01

    Palmitoylation plays important roles in the regulation of protein localization, stability, and activity. The protein acyltransferases (PATs) have a common DHHC Cys-rich domain. Twenty-three DHHC proteins have been identified in humans. However, it is unclear whether all of these DHHC proteins function as PATs. In addition, their substrate specificities remain largely unknown. Here we develop a useful method to examine substrate specificities of PATs using a yeast expression system with six distinct model substrates. We identify 17 human DHHC proteins as PATs. Moreover, we classify 11 human and 5 yeast DHHC proteins into three classes (I, II, and III), based on the cellular localization of their respective substrates (class I, soluble proteins; class II, integral membrane proteins; class III, lipidated proteins). Our results may provide an important clue for understanding the function of individual DHHC proteins. PMID:23034182

  15. Structural Basis for Certain Naturally Occurring Bioflavonoids to Function as Reducing Co-Substrates of Cyclooxygenase I and II

    PubMed Central

    Zhu, Bao Ting

    2010-01-01

    Background Recent studies showed that some of the dietary bioflavonoids can strongly stimulate the catalytic activity of cyclooxygenase (COX) I and II in vitro and in vivo, presumably by facilitating enzyme re-activation. In this study, we sought to understand the structural basis of COX activation by these dietary compounds. Methodology/Principal Findings A combination of molecular modeling studies, biochemical analysis and site-directed mutagenesis assay was used as research tools. Three-dimensional quantitative structure-activity relationship analysis (QSAR/CoMFA) predicted that the ability of bioflavonoids to activate COX I and II depends heavily on their B-ring structure, a moiety known to be associated with strong antioxidant ability. Using the homology modeling and docking approaches, we identified the peroxidase active site of COX I and II as the binding site for bioflavonoids. Upon binding to this site, bioflavonoid can directly interact with hematin of the COX enzyme and facilitate the electron transfer from bioflavonoid to hematin. The docking results were verified by biochemical analysis, which reveals that when the cyclooxygenase activity of COXs is inhibited by covalent modification, myricetin can still stimulate the conversion of PGG2 to PGE2, a reaction selectively catalyzed by the peroxidase activity. Using the site-directed mutagenesis analysis, we confirmed that Q189 at the peroxidase site of COX II is essential for bioflavonoids to bind and re-activate its catalytic activity. Conclusions/Significance These findings provide the structural basis for bioflavonoids to function as high-affinity reducing co-substrates of COXs through binding to the peroxidase active site, facilitating electron transfer and enzyme re-activation. PMID:20808785

  16. Diffusion at the boundary between the film and substrate upon the electrocrystallization of zinc on a copper substrate

    NASA Astrophysics Data System (ADS)

    Shtapenko, E. Ph.; Zabludovsky, V. A.; Dudkina, V. V.

    2015-03-01

    In this paper, we present the results of experimental investigations of the diffusion layer formed at the film-substrate interface upon the electrodeposition of zinc films on a copper substrate. The investigations have shown that, in the transient layer, the deposited metal is diffused into the material of the substrate. The depth of the diffusion layer and, consequently, the concentrations of the incorporated zinc atoms depend strongly on the conditions of electrocrystallization, which vary from 1.5 μm when using direct current to 4 μm when using direct current in combination with laser-stimulated deposition (LSD). The X-ray diffraction investigations of the transient layer at the film-substrate interface have shown that, upon electrocrystallization using pulsed current in rigid regimes with the application of the LSD, a CuZn2 phase is formed in the diffusion layer. This indicates that the diffusion of zinc into copper occurs via two mechanisms, i.e., grainboundary and bulk. The obtained values of the coefficient of diffusion of zinc adatoms in polycrystalline copper are equal to 1.75 × 10-15 m2/s when using direct current and 1.74 × 10-13 m2/s when using LSD.

  17. High-performance Ge p-i-n photodetector on Si substrate

    NASA Astrophysics Data System (ADS)

    Chen, Li-qun; Huang, Xiang-ying; Li, Min; Huang, Yan-hua; Wang, Yue-yun; Yan, Guang-ming; Li, Cheng

    2015-05-01

    High-performance and tensile-strained germanium (Ge) p-i-n photodetector is demonstrated on Si substrate. The epitaxial Ge layers were prepared in an ultrahigh vacuum chemical vapor deposition (UHV-CVD) system using low temperature Ge buffer technique. The devices were fabricated by in situ doping and using Si as passivation layer between Ge and metal, which can improve the ohmic contact and realize the high doping. The results show that the dark current of the photodetector with diameter of 24 μm is about 2.5×10-7 μA at the bias voltage of -1 V, and the optical responsivity is 0.1 A/W at wavelength of 1.55 μm. The 3 dB bandwidth (BW) of 4 GHz is obtained for the photodetector with diameter of 24 μm at reverse bias voltage of 1 V. The long diffusion time of minority carrier in n-type Ge and the large contact resistance in metal/Ge contacts both affect the performance of Ge photodetectors.

  18. Quantification of Valleys of Randomly Textured Substrates as a Function of Opening Angle: Correlation to the Defect Density in Intrinsic nc-Si:H.

    PubMed

    Kim, Do Yun; Hänni, Simon; Schüttauf, Jan-Willem; van Swaaij, René A C M M; Zeman, Miro

    2016-08-17

    Optical and electrical properties of hydrogenated nanocrystalline silicon (nc-Si:H) solar cells are strongly influenced by the morphology of underlying substrates. By texturing the substrates, the photogenerated current of nc-Si:H solar cells can increase due to enhanced light scattering. These textured substrates are, however, often incompatible with defect-less nc-Si:H growth resulting in lower Voc and FF. In this study we investigate the correlation between the substrate morphology, the nc-Si:H solar-cell performance, and the defect density in the intrinsic layer of the solar cells (i-nc-Si:H). Statistical surface parameters representing the substrate morphology do not show a strong correlation with the solar-cell parameters. Thus, we first quantify the line density of potentially defective valleys of randomly textured ZnO substrates where the opening angle is smaller than 130° (ρ<130). This ρ<130 is subsequently compared with the solar-cell performance and the defect density of i-nc-Si:H (ρdefect), which is obtained by fitting external photovoltaic parameters from experimental results and simulations. We confirm that when ρ<130 increases the Voc and FF significantly drops. It is also observed that ρdefect increases following a power law dependence of ρ<130. This result is attributed to more frequently formed defective regions for substrates having higher ρ<130.

  19. Assessing Posidonia oceanica seedling substrate preference: an experimental determination of seedling anchorage success in rocky vs. sandy substrates.

    PubMed

    Alagna, Adriana; Fernández, Tomás Vega; Anna, Giovanni D; Magliola, Carlo; Mazzola, Salvatore; Badalamenti, Fabio

    2015-01-01

    In the last decades the growing awareness of the ecological importance of seagrass meadows has prompted increasing efforts to protect existing beds and restore degraded habitats. An in-depth knowledge of factors acting as major drivers of propagule settlement and recruitment is required in order to understand patterns of seagrass colonization and recovery and to inform appropriate management and conservation strategies. In this work Posidonia oceanica seedlings were reared for five months in a land-based culture facility under simulated natural hydrodynamic conditions to identify suitable substrates for seedling anchorage. Two main substrate features were investigated: firmness (i.e., sand vs. rock) and complexity (i.e., size of interstitial spaces between rocks). Seedlings were successfully grown in culture tanks, obtaining overall seedling survival of 93%. Anchorage was strongly influenced by substrate firmness and took place only on rocks, where it was as high as 89%. Anchorage occurred through adhesion by sticky root hairs. The minimum force required to dislodge plantlets attached to rocky substrates reached 23.830 N (equivalent to 2.43 kg), which would potentially allow many plantlets to overcome winter storms in the field. The ability of rocky substrates to retain seedlings increased with their complexity. The interstitial spaces between rocks provided appropriate microsites for seedling settlement, as seeds were successfully retained, and a suitable substrate for anchorage was available. In conclusion P. oceanica juveniles showed a clear-cut preference for hard substrates over the sandy one, due to the root system adhesive properties. In particular, firm and complex substrates allowed for propagule early and strong anchorage, enhancing persistence and establishment probabilities. Seedling substrate preference documented here leads to expect a more successful sexual recruitment on hard bottoms compared with soft ones. This feature could have influenced P

  20. Synthesis of iron composites on nano-pore substrates: identification and its application to removal of cyanide.

    PubMed

    Do, Si-Hyun; Jo, Young-Hoon; Park, Ho-Dong; Kong, Sung-Ho

    2012-11-01

    Two types of nano-pore substrates, waste-reclaimed (WR) and soil mineral (SM) with the relatively low density, were modified by the reaction with irons (i.e. Fe(II):Fe(III)=1:2) and the applicability of the modified substrates (i.e. Fe-WR and Fe-SM) on cyanide removal was investigated. Modification (i.e. Fe immobilization on substrate) decreased the BET surface area and PZC of the original substrates while it increased the pore diameter and the cation exchange capacity (CEC) of them. XRD analysis identified that maghemite (γ-Fe(2)O(3)) and iron silicate composite ((Mg, Fe)SiO(3)) existed on Fe-WR, while clinoferrosilite (FeSiO(3)) was identified on Fe-SM. Cyanide adsorption showed that WR adsorbed cyanide more favorably than SM. The adsorption ability of both original substrates was enhanced by the modification, which increased the negative charges of the surfaces. Without the pH adjustment, cyanide was removed as much as 97% by the only application of Fe-WR, but the undesirable transfer to hydrogen cyanide was possible because the pH was dropped to around 7.5. With a constant pH of 12, only 54% of cyanide was adsorbed on Fe-WR. On the other hand, the pH was kept as 12 without adjustment in Fe-WR/H(2)O(2) system and cyanide was effectively removed by not only adsorption but also the catalytic oxidation. The observed first-order rate constant (k(obs)) for cyanide removal were 0.49 (± 0.081) h(-1). Moreover, the more cyanate production with the modified substrates indicated the iron composites, especially maghemite, on substrates had the catalytic property to increase the reactivity of H(2)O(2). Copyright © 2012 Elsevier Ltd. All rights reserved.

  1. Formation and characterization of preferred oriented perovskite thin films on single-crystalline substrates

    NASA Astrophysics Data System (ADS)

    Chen, Lung-Chien; Chen, Cheng-Chiang; Hsiung Chang, Sheng; Lee, Kuan-Lin; Tseng, Zong-Liang; Chen, Sheng-Hui; Kuo, Hao-Chung

    2018-06-01

    Three single-crystalline (Al2O3, GaN/Al2O3 and InAs) substrates are used to assist the formation of crystallographically preferred oriented CH3NH3PbI3 (MAPbI3) thin films. The estimation of the lattice mismatch at the MAPbI3/substrate interface and water-droplet contact angle experiments indicate that the formation of a preferred oriented MAPbI3 thin film is induced by the single-crystalline substrate and is insensitive to the surface wettibility of the substrate. Moreover, the experimental results suggest that the lattice mismatch at the MAPbI3/single-crystalline semiconductor interface can strongly influence the photovoltaic performance of tandem solar cells.

  2. Flip Chip on Organic Substrates: A Feasibility Study for Space Applications

    DTIC Science & Technology

    2017-03-01

    scheme, a 1752 I/O land grid array (LGA) package with decoupling capacitors, heat sink and optional column attach [1] as shown in Figure 1...investigated the effect of moisture and current loading on the Class Y flip chip on ceramic reliability [ 2 ]. The UT1752FC Class Y technology has...chip assembly to ceramic test substrates, the FA10 die are assembled to build-up organic test substrates as shown in Figure 2 . These assemblies

  3. Substrate-biasing during plasma-assisted atomic layer deposition to tailor metal-oxide thin film growth

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Profijt, H. B.; Sanden, M. C. M. van de; Kessels, W. M. M.

    2013-01-15

    Two substrate-biasing techniques, i.e., substrate-tuned biasing and RF biasing, have been implemented in a remote plasma configuration, enabling control of the ion energy during plasma-assisted atomic layer deposition (ALD). With both techniques, substrate bias voltages up to -200 V have been reached, which allowed for ion energies up to 272 eV. Besides the bias voltage, the ion energy and the ion flux, also the electron temperature, the electron density, and the optical emission of the plasma have been measured. The effects of substrate biasing during plasma-assisted ALD have been investigated for Al{sub 2}O{sub 3}, Co{sub 3}O{sub 4}, and TiO{sub 2}more » thin films. The growth per cycle, the mass density, and the crystallinity have been investigated, and it was found that these process and material properties can be tailored using substrate biasing. Additionally, the residual stress in substrates coated with Al{sub 2}O{sub 3} films varied with the substrate bias voltage. The results reported in this article demonstrate that substrate biasing is a promising technique to tailor the material properties of thin films synthesized by plasma-assisted ALD.« less

  4. Modeling of substrate and inhibitor binding to phospholipase A2.

    PubMed

    Sessions, R B; Dauber-Osguthorpe, P; Campbell, M M; Osguthorpe, D J

    1992-09-01

    Molecular graphics and molecular mechanics techniques have been used to study the mode of ligand binding and mechanism of action of the enzyme phospholipase A2. A substrate-enzyme complex was constructed based on the crystal structure of the apoenzyme. The complex was minimized to relieve initial strain, and the structural and energetic features of the resultant complex analyzed in detail, at the molecular and residue level. The minimized complex was then used as a basis for examining the action of the enzyme on modified substrates, binding of inhibitors to the enzyme, and possible reaction intermediate complexes. The model is compatible with the suggested mechanism of hydrolysis and with experimental data about stereoselectivity, efficiency of hydrolysis of modified substrates, and inhibitor potency. In conclusion, the model can be used as a tool in evaluating new ligands as possible substrates and in the rational design of inhibitors, for the therapeutic treatment of diseases such as rheumatoid arthritis, atherosclerosis, and asthma.

  5. Substrate Creep on The Fatigue Life of A Model Dental Multilayer Structure

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Zhou, J; Huang, M; Niu, X

    In this paper, we investigated the effects of substrate creep on the fatigue behavior of a model dental multilayer structure, in which a top glass layer was bonded to a polycarbonate substrate through a dental adhesive. The top glass layers were ground using 120 grit or 600 grit sand papers before bonding to create different sub-surface crack sizes and morphologies. The multilayer structures were tested under cyclic Hertzian contact loading to study crack growth and obtain fatigue life curves. The experiment results showed that the fatigue lives of the multilayer structures were impaired by increasing crack sizes in the sub-surfaces.more » They were also significantly reduced by the substrate creep when tested at relatively low load levels i.e. P{sub m} < 60 N (Pm is the maximum magnitude of cyclic load). But at relatively high load levels i.e. P{sub m} > 65 N, slow crack growth (SCG) was the major failure mechanisms. A modeling study was then carried out to explore the possible failure mechanisms over a range of load levels. It is found that fatigue life at relatively low load levels can be better estimated by considering the substrate creep effect (SCE).« less

  6. Carbon nanotubes on a substrate

    DOEpatents

    Gao, Yufei [Kennewick, WA; Liu, Jun [West Richland, WA

    2002-03-26

    The present invention includes carbon nanotubes whose hollow cores are 100% filled with conductive filler. The carbon nanotubes are in uniform arrays on a conductive substrate and are well-aligned and can be densely packed. The uniformity of the carbon nanotube arrays is indicated by the uniform length and diameter of the carbon nanotubes, both which vary from nanotube to nanotube on a given array by no more than about 5%. The alignment of the carbon nanotubes is indicated by the perpendicular growth of the nanotubes from the substrates which is achieved in part by the simultaneous growth of the conductive filler within the hollow core of the nanotube and the densely packed growth of the nanotubes. The present invention provides a densely packed carbon nanotube growth where each nanotube is in contact with at least one nearest-neighbor nanotube. The substrate is a conductive substrate coated with a growth catalyst, and the conductive filler can be single crystals of carbide formed by a solid state reaction between the substrate material and the growth catalyst. The present invention further provides a method for making the filled carbon nanotubes on the conductive substrates. The method includes the steps of depositing a growth catalyst onto the conductive substrate as a prepared substrate, creating a vacuum within a vessel which contains the prepared substrate, flowing H2/inert (e.g. Ar) gas within the vessel to increase and maintain the pressure within the vessel, increasing the temperature of the prepared substrate, and changing the H2/Ar gas to ethylene gas such that the ethylene gas flows within the vessel. Additionally, varying the density and separation of the catalyst particles on the conductive substrate can be used to control the diameter of the nanotubes.

  7. Analysis of a Compressed Thin Film Bonded to a Compliant Substrate: The Energy Scaling Law

    NASA Astrophysics Data System (ADS)

    Kohn, Robert V.; Nguyen, Hoai-Minh

    2013-06-01

    We consider the deformation of a thin elastic film bonded to a thick compliant substrate, when the (compressive) misfit is far beyond critical. We take a variational viewpoint—focusing on the total elastic energy, i.e. the membrane and bending energy of the film plus the elastic energy of the substrate—viewing the buckling of the film as a problem of energy-driven pattern formation. We identify the scaling law of the minimum energy with respect to the physical parameters of the problem, and we prove that a herringbone pattern achieves the optimal scaling. These results complement previous numerical studies, which have shown that an optimized herringbone pattern has lower energy than a number of other patterns. Our results are different, because (i) we make the scaling law achieved by the herringbone pattern explicit, and (ii) we give an elementary, ansatz-free proof that no pattern can achieve a better law.

  8. Identification of cellular MMP substrates using quantitative proteomics: isotope-coded affinity tags (ICAT) and isobaric tags for relative and absolute quantification (iTRAQ).

    PubMed

    Butler, Georgina S; Dean, Richard A; Morrison, Charlotte J; Overall, Christopher M

    2010-01-01

    Identification of protease substrates is essential to understand the functional consequences of normal proteolytic processing and dysregulated proteolysis in disease. Quantitative proteomics and mass spectrometry can be used to identify protease substrates in the cellular context. Here we describe the use of two protein labeling techniques, Isotope-Coded Affinity Tags (ICAT and Isobaric Tags for Relative and Absolute Quantification (iTRAQ), which we have used successfully to identify novel matrix metalloproteinase (MMP) substrates in cell culture systems (1-4). ICAT and iTRAQ can label proteins and protease cleavage products of secreted proteins, protein domains shed from the cell membrane or pericellular matrix of protease-transfected cells that have accumulated in conditioned medium, or cell surface proteins in membrane preparations; isotopically distinct labels are used for control cells. Tryptic digestion and tandem mass spectrometry of the generated fragments enable sequencing of differentially labeled but otherwise identical pooled peptides. The isotopic tag, which is unique for each label, identifies the peptides originating from each sample, for instance, protease-transfected or control cells, and comparison of the peak areas enables relative quantification of the peptide in each sample. Thus proteins present in altered amounts between protease-expressing and null cells are implicated as protease substrates and can be further validated as such.

  9. Identification of ribozymes within a ribozyme library that efficiently cleave a long substrate RNA.

    PubMed Central

    Campbell, T B; Cech, T R

    1995-01-01

    Positions 2-6 of the substrate-binding internal guide sequence (IGS) of the L-21 Sca I form of the Tetrahymena thermophila intron were mutagenized to produce a GN5 IGS library. Ribozymes within the GN5 library capable of efficient cleavage of an 818-nt human immunodeficiency virus type 1 vif-vpr RNA, at 37 degrees C, were identified by ribozyme-catalyzed guanosine addition to the 3' cleavage product. Three ribozymes (IGS = GGGGCU, GGCUCC, and GUGGCU) within the GN5 library that actively cleaved the long substrate were characterized kinetically and compared to the wild-type ribozyme (GGAGGG) and two control ribozymes (GGAGUC and GGAGAU). The two control ribozymes have specific sites within the long substrate, but were not identified during screening of the library. Under single-turnover conditions, ribozymes GGGGCU, GGCUCC, and GUGGCU cleaved the 818-nt substrate 4- to 200-fold faster than control ribozymes. Short cognate substrates, which should be structureless and therefore accessible to ribozyme binding, were cleaved at similar rates by all ribozymes except GGGGCU, which showed a fourfold rate enhancement. The rate of cleavage of long relative to short substrate under single-turnover conditions suggests that GGCUCC and GUGGCU were identified because of accessibility to their specific cleavage sites within the long substrate (substrate-specific effects), whereas GGGGCU was identified because of an enhanced rate of substrate binding despite a less accessible site in the long substrate. Even though screening was performed with 100-fold excess substrate (relative to total ribozyme), the rate of multiple-turnover catalysis did not contribute to identification of trans-cleaving ribozymes in the GN5 library. PMID:7489519

  10. Urate as a Physiological Substrate for Myeloperoxidase

    PubMed Central

    Meotti, Flavia C.; Jameson, Guy N. L.; Turner, Rufus; Harwood, D. Tim; Stockwell, Samantha; Rees, Martin D.; Thomas, Shane R.; Kettle, Anthony J.

    2011-01-01

    Urate and myeloperoxidase (MPO) are associated with adverse outcomes in cardiovascular disease. In this study, we assessed whether urate is a likely physiological substrate for MPO and if the products of their interaction have the potential to exacerbate inflammation. Urate was readily oxidized by MPO and hydrogen peroxide to 5-hydroxyisourate, which decayed to predominantly allantoin. The redox intermediates of MPO were reduced by urate with rate constants of 4.6 × 105 m−1 s−1 for compound I and 1.7 × 104 m−1 s−1 for compound II. Urate competed with chloride for oxidation by MPO and at hyperuricemic levels is expected to be a substantive substrate for the enzyme. Oxidation of urate promoted super-stoichiometric consumption of glutathione, which indicates that it is converted to a free radical intermediate. In combination with superoxide and hydrogen peroxide, MPO oxidized urate to a reactive hydroperoxide. This would form by addition of superoxide to the urate radical. Urate also enhanced MPO-dependent consumption of nitric oxide. In human plasma, stimulated neutrophils produced allantoin in a reaction dependent on the NADPH oxidase, MPO and superoxide. We propose that urate is a physiological substrate for MPO that is oxidized to the urate radical. The reactions of this radical with superoxide and nitric oxide provide a plausible link between urate and MPO in cardiovascular disease. PMID:21266577

  11. The effect of the labile organic fraction in food waste and the substrate/inoculum ratio on anaerobic digestion for a reliable methane yield.

    PubMed

    Kawai, Minako; Nagao, Norio; Tajima, Nobuaki; Niwa, Chiaki; Matsuyama, Tatsushi; Toda, Tatsuki

    2014-04-01

    Influence of the labile organic fraction (LOF) on anaerobic digestion of food waste was investigated in different S/I ratio of 0.33, 0.5, 1.0, 2.0 and 4.0g-VSsubstrate/g-VSinoculum. Two types of substrate, standard food waste (Substrate 1) and standard food waste with the supernatant (containing LOF) removed (Substrate 2) were used. Highest methane yield of 435ml-CH4g-VS(-1) in Substrate 1 was observed in the lowest S/I ratio, while the methane yield of the other S/I ratios were 38-73% lower than the highest yield due to acidification. The methane yields in Substrate 2 were relatively stable in all S/I conditions, although the maximum methane yield was low compared with Substrate 1. These results showed that LOF in food waste causes acidification, but also contributes to high methane yields, suggesting that low S/I ratio (<0.33) is required to obtain a reliable methane yield from food waste compared to other organic substrates. Copyright © 2014 Elsevier Ltd. All rights reserved.

  12. Both Intrinsic Substrate Preference and Network Context Contribute to Substrate Selection of Classical Tyrosine Phosphatases*

    PubMed Central

    Tinti, Michele; Paoluzi, Serena; Santonico, Elena; Masch, Antonia; Schutkowski, Mike

    2017-01-01

    Reversible tyrosine phosphorylation is a widespread post-translational modification mechanism underlying cell physiology. Thus, understanding the mechanisms responsible for substrate selection by kinases and phosphatases is central to our ability to model signal transduction at a system level. Classical protein-tyrosine phosphatases can exhibit substrate specificity in vivo by combining intrinsic enzymatic specificity with the network of protein-protein interactions, which positions the enzymes in close proximity to their substrates. Here we use a high throughput approach, based on high density phosphopeptide chips, to determine the in vitro substrate preference of 16 members of the protein-tyrosine phosphatase family. This approach helped identify one residue in the substrate binding pocket of the phosphatase domain that confers specificity for phosphopeptides in a specific sequence context. We also present a Bayesian model that combines intrinsic enzymatic specificity and interaction information in the context of the human protein interaction network to infer new phosphatase substrates at the proteome level. PMID:28159843

  13. Method for applying a photoresist layer to a substrate having a preexisting topology

    DOEpatents

    Morales, Alfredo M.; Gonzales, Marcela

    2004-01-20

    The present invention describes a method for preventing a photoresist layer from delaminating, peeling, away from the surface of a substrate that already contains an etched three dimensional structure such as a hole or a trench. The process comprises establishing a saturated vapor phase of the solvent media used to formulate the photoresist layer, above the surface of the coated substrate as the applied photoresist is heated in order to "cure" or drive off the retained solvent constituent within the layer. By controlling the rate and manner in which solvent is removed from the photoresist layer the layer is stabilized and kept from differentially shrinking and peeling away from the substrate.

  14. Method of processing a substrate

    DOEpatents

    Babayan, Steven E [Huntington Beach, CA; Hicks, Robert F [Los Angeles, CA

    2008-02-12

    The invention is embodied in a plasma flow device or reactor having a housing that contains conductive electrodes with openings to allow gas to flow through or around them, where one or more of the electrodes are powered by an RF source and one or more are grounded, and a substrate or work piece is placed in the gas flow downstream of the electrodes, such that said substrate or work piece is substantially uniformly contacted across a large surface area with the reactive gases emanating therefrom. The invention is also embodied in a plasma flow device or reactor having a housing that contains conductive electrodes with openings to allow gas to flow through or around them, where one or more of the electrodes are powered by an RF source and one or more are grounded, and one of the grounded electrodes contains a means of mixing in other chemical precursors to combine with the plasma stream, and a substrate or work piece placed in the gas flow downstream of the electrodes, such that said substrate or work piece is contacted by the reactive gases emanating therefrom. In one embodiment, the plasma flow device removes organic materials from a substrate or work piece, and is a stripping or cleaning device. In another embodiment, the plasma flow device kills biological microorganisms on a substrate or work piece, and is a sterilization device. In another embodiment, the plasma flow device activates the surface of a substrate or work piece, and is a surface activation device. In another embodiment, the plasma flow device etches materials from a substrate or work piece, and is a plasma etcher. In another embodiment, the plasma flow device deposits thin films onto a substrate or work piece, and is a plasma-enhanced chemical vapor deposition device or reactor.

  15. Mapping protease substrates using a biotinylated phage substrate library.

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Scholle, M. D.; Kriplani, U.; Pabon, A.

    We describe a bacteriophage M13 substrate library encoding the AviTag (BirA substrate) and combinatorial heptamer peptides displayed at the N terminus of the mature form of capsid protein III. Phages are biotinylated efficiently (> or = 50%) when grown in E. coli cells coexpressing BirA, and such viral particles can be immobilized on a streptavidin-coated support and released by protease cleavage within the combinatorial peptide. We have used this library to map the specificity of human Factor Xa and a neuropeptidase, neurolysin (EC3.4.24.16). Validation by analysis of isolated peptide substrates has revealed that neurolysin recognizes the motif hydrophobic-X-Pro-Arg-hydrophobic, where Arg-hydrophobicmore » is the scissile bond.« less

  16. Decoding the Substrate Supply to Human Neuronal Nitric Oxide Synthase

    PubMed Central

    Habermeier, Alice; Closs, Ellen I.

    2013-01-01

    Nitric oxide, produced by the neuronal nitric oxide synthase (nNOS) from L-arginine is an important second messenger molecule in the central nervous system: It influences the synthesis and release of neurotransmitters and plays an important role in long-term potentiation, long-term depression and neuroendocrine secretion. However, under certain pathological conditions such as Alzheimer’s or Parkinson’s disease, stroke and multiple sclerosis, excessive NO production can lead to tissue damage. It is thus desirable to control NO production in these situations. So far, little is known about the substrate supply to human nNOS as a determinant of its activity. Measuring bioactive NO via cGMP formation in reporter cells, we demonstrate here that nNOS in both, human A673 neuroepithelioma and TGW-nu-I neuroblastoma cells can be fast and efficiently nourished by extracellular arginine that enters the cells via membrane transporters (pool I that is freely exchangeable with the extracellular space). When this pool was depleted, NO synthesis was partially sustained by intracellular arginine sources not freely exchangeable with the extracellular space (pool II). Protein breakdown made up by far the largest part of pool II in both cell types. In contrast, citrulline to arginine conversion maintained NO synthesis only in TGW-nu-I neuroblastoma, but not A673 neuroepithelioma cells. Histidine mimicked the effect of protease inhibitors causing an almost complete nNOS inhibition in cells incubated additionally in lysine that depletes the exchangeable arginine pool. Our results identify new ways to modulate nNOS activity by modifying its substrate supply. PMID:23874440

  17. Tensile cracking of a brittle conformal coating on a rough substrate

    DOE PAGES

    Reedy, Jr., E. D.

    2016-04-07

    This note examines the effect of interfacial roughness on the initiation and growth of channel cracks in a brittle film. A conformal film with cusp-like surface flaws that replicate the substrate roughness is investigated. This type of surface flaw is relatively severe in the sense that stress diverges as the cusp-tip is approached (i.e., there is a power-law stress singularity). For the geometry and range of film properties considered, the analysis suggests that smoothing the substrate could substantially increase the film’s resistance to the formation of the through-the-thickness cracks that precede channel cracking. Furthermore, smoothing the substrate’s surface has amore » relatively modest effect on the film stress needed to propagate a channel crack.« less

  18. An Acrobatic Substrate Metamorphosis Reveals a Requirement for Substrate Conformational Dynamics in Trypsin Proteolysis*

    PubMed Central

    Kayode, Olumide; Wang, Ruiying; Pendlebury, Devon F.; Cohen, Itay; Henin, Rachel D.; Hockla, Alexandra; Soares, Alexei S.; Papo, Niv; Caulfield, Thomas R.; Radisky, Evette S.

    2016-01-01

    The molecular basis of enzyme catalytic power and specificity derives from dynamic interactions between enzyme and substrate during catalysis. Although considerable effort has been devoted to understanding how conformational dynamics within enzymes affect catalysis, the role of conformational dynamics within protein substrates has not been addressed. Here, we examine the importance of substrate dynamics in the cleavage of Kunitz-bovine pancreatic trypsin inhibitor protease inhibitors by mesotrypsin, finding that the varied conformational dynamics of structurally similar substrates can profoundly impact the rate of catalysis. A 1.4-Å crystal structure of a mesotrypsin-product complex formed with a rapidly cleaved substrate reveals a dramatic conformational change in the substrate upon proteolysis. By using long all-atom molecular dynamics simulations of acyl-enzyme intermediates with proteolysis rates spanning 3 orders of magnitude, we identify global and local dynamic features of substrates on the nanosecond-microsecond time scale that correlate with enzymatic rates and explain differential susceptibility to proteolysis. By integrating multiple enhanced sampling methods for molecular dynamics, we model a viable conformational pathway between substrate-like and product-like states, linking substrate dynamics on the nanosecond-microsecond time scale with large collective substrate motions on the much slower time scale of catalysis. Our findings implicate substrate flexibility as a critical determinant of catalysis. PMID:27810896

  19. Better Back Contacts for Solar Cells on Flexible Substrates

    NASA Technical Reports Server (NTRS)

    Woods, Lawrence M.; Ribelin, Rosine M.

    2006-01-01

    Improved low-resistance, semitransparent back contacts, and a method of fabricating them, have been developed for solar photovoltaic cells that are made from thin films of I-III-VI2 semiconductor materials on flexible, high-temperatureresistant polyimide substrates or superstrates. The innovative aspect of the present development lies in the extension, to polyimide substrates or superstrates, of a similar prior development of improved low-resistance, semitransparent back contacts for I-III-VI2 solar cells on glass substrates or superstrates. A cell incorporating this innovation can be used either as a stand-alone photovoltaic device or as part of a monolithic stack containing another photovoltaic device that utilizes light of longer wavelengths.

  20. Differential growth responses of soil bacterial taxa to carbon substrates of varying chemical recalcitrance

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Goldfarb, K.C.; Karaoz, U.; Hanson, C.A.

    2011-04-18

    Soils are immensely diverse microbial habitats with thousands of co-existing bacterial, archaeal, and fungal species. Across broad spatial scales, factors such as pH and soil moisture appear to determine the diversity and structure of soil bacterial communities. Within any one site however, bacterial taxon diversity is high and factors maintaining this diversity are poorly resolved. Candidate factors include organic substrate availability and chemical recalcitrance, and given that they appear to structure bacterial communities at the phylum level, we examine whether these factors might structure bacterial communities at finer levels of taxonomic resolution. Analyzing 16S rRNA gene composition of nucleotide analog-labeledmore » DNA by PhyloChip microarrays, we compare relative growth rates on organic substrates of increasing chemical recalcitrance of >2,200 bacterial taxa across 43 divisions/phyla. Taxa that increase in relative abundance with labile organic substrates (i.e., glycine, sucrose) are numerous (>500), phylogenetically clustered, and occur predominantly in two phyla (Proteobacteria and Actinobacteria) including orders Actinomycetales, Enterobacteriales, Burkholderiales, Rhodocyclales, Alteromonadales, and Pseudomonadales. Taxa increasing in relative abundance with more chemically recalcitrant substrates (i.e., cellulose, lignin, or tannin-protein) are fewer (168) but more phylogenetically dispersed, occurring across eight phyla and including Clostridiales, Sphingomonadalaes, Desulfovibrionales. Just over 6% of detected taxa, including many Burkholderiales increase in relative abundance with both labile and chemically recalcitrant substrates. Estimates of median rRNA copy number per genome of responding taxa demonstrate that these patterns are broadly consistent with bacterial growth strategies. Taken together, these data suggest that changes in availability of intrinsically labile substrates may result in predictable shifts in soil bacterial

  1. An Acrobatic Substrate Metamorphosis Reveals a Requirement for Substrate Conformational Dynamics in Trypsin Proteolysis.

    PubMed

    Kayode, Olumide; Wang, Ruiying; Pendlebury, Devon F; Cohen, Itay; Henin, Rachel D; Hockla, Alexandra; Soares, Alexei S; Papo, Niv; Caulfield, Thomas R; Radisky, Evette S

    2016-12-16

    The molecular basis of enzyme catalytic power and specificity derives from dynamic interactions between enzyme and substrate during catalysis. Although considerable effort has been devoted to understanding how conformational dynamics within enzymes affect catalysis, the role of conformational dynamics within protein substrates has not been addressed. Here, we examine the importance of substrate dynamics in the cleavage of Kunitz-bovine pancreatic trypsin inhibitor protease inhibitors by mesotrypsin, finding that the varied conformational dynamics of structurally similar substrates can profoundly impact the rate of catalysis. A 1.4-Å crystal structure of a mesotrypsin-product complex formed with a rapidly cleaved substrate reveals a dramatic conformational change in the substrate upon proteolysis. By using long all-atom molecular dynamics simulations of acyl-enzyme intermediates with proteolysis rates spanning 3 orders of magnitude, we identify global and local dynamic features of substrates on the nanosecond-microsecond time scale that correlate with enzymatic rates and explain differential susceptibility to proteolysis. By integrating multiple enhanced sampling methods for molecular dynamics, we model a viable conformational pathway between substrate-like and product-like states, linking substrate dynamics on the nanosecond-microsecond time scale with large collective substrate motions on the much slower time scale of catalysis. Our findings implicate substrate flexibility as a critical determinant of catalysis. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  2. An Acrobatic Substrate Metamorphosis Reveals a Requirement for Substrate Conformational Dynamics in Trypsin Proteolysis

    DOE PAGES

    Kayode, Olumide; Wang, Ruiying; Pendlebury, Devon F.; ...

    2016-11-03

    The molecular basis of enzyme catalytic power and specificity derives from dynamic interactions between enzyme and substrate during catalysis. While considerable effort has been devoted to understanding how conformational dynamics within enzymes affect catalysis, the role of conformational dynamics within protein substrates has not been addressed. Here in this paper, we examine the importance of substrate dynamics in the cleavage of Kunitz-BPTI protease inhibitors by mesotrypsin, finding that the varied conformational dynamics of structurally similar substrates can profoundly impact the rate of catalysis. A 1.4 Å crystal structure of a mesotrypsin-product complex formed with a rapidly cleaved substrate reveals amore » dramatic conformational change in the substrate upon proteolysis. Using long all-atom molecular dynamics simulations of acyl-enzyme intermediates with proteolysis rates spanning three orders of magnitude, we identify global and local dynamic features of substrates on the ns-μs timescale that correlate with enzymatic rates and explain differential susceptibility to proteolysis. By integrating multiple enhanced sampling methods for molecular dynamics, we model a viable conformational pathway between substratelike and product-like states, linking substrate dynamics on the ns-μs timescale with large collective substrate motions on the much slower timescale of catalysis. Our findings implicate substrate flexibility as a critical determinant of catalysis.« less

  3. Hydrogenated amorphous silicon solar cells fabricated at low substrate temperature 110°C on flexible PET substrate

    NASA Astrophysics Data System (ADS)

    Ramakrishna, M.; Kumari, Juhi; Venkanna, K.; Agarwal, Pratima

    2018-05-01

    In this paper, we report a-Si:H solar cells fabricated on flexible Polyethylene terephthalate (PET) and corning glass. The a-Si:H thin films were prepared at low substrate temperature (110oC) on corning 1737 glass with different rf powers. The influence of rf power on structural and optoelectronic properties of i-a-Si:H were studied. The films deposited at rf power 50W show less broadening of <ɛ2> peak. This indicates these films are more ordered. With this optimized parameter for i-layer, solar cells fabricated on flexible PET substrate show best efficiency of 3.3% whereas on corning glass 3.82%.

  4. System Configured For Applying Multiple Modifying Agents To A Substrate.

    DOEpatents

    Propp, W. Alan; Argyle, Mark D.; Janikowski, Stuart K.; Fox, Robert V.; Toth, William J.; Ginosar, Daniel M.; Allen, Charles A.; Miller, David L.

    2005-11-08

    The present invention is related to the modifying of substrates with multiple modifying agents in a single continuous system. At least two processing chambers are configured for modifying the substrate in a continuous feed system. The processing chambers can be substantially isolated from one another by interstitial seals. Additionally, the two processing chambers can be substantially isolated from the surrounding atmosphere by end seals. Optionally, expansion chambers can be used to separate the seals from the processing chambers.

  5. System configured for applying multiple modifying agents to a substrate

    DOEpatents

    Propp, W. Alan; Argyle, Mark D.; Janikowski, Stuart K.; Fox, Robert V.; Toth, William J.; Ginosar, Daniel M.; Allen, Charles A.; Miller, David L.

    2003-11-25

    The present invention is related to the modifying of substrates with multiple modifying agents in a single continuous system. At least two processing chambers are configured for modifying the substrate in a continuous feed system. The processing chambers can be substantially isolated from one another by interstitial seals. Additionally, the two processing chambers can be substantially isolated from the surrounding atmosphere by end seals. Optionally, expansion chambers can be used to separate the seals from the processing chambers.

  6. Unmasking tandem site interaction in human acetylcholinesterase. Substrate activation with a cationic acetanilide substrate.

    PubMed

    Johnson, Joseph L; Cusack, Bernadette; Davies, Matthew P; Fauq, Abdul; Rosenberry, Terrone L

    2003-05-13

    Acetylcholinesterase (AChE) contains a narrow and deep active site gorge with two sites of ligand binding, an acylation site (or A-site) at the base of the gorge, and a peripheral site (or P-site) near the gorge entrance. The P-site contributes to catalytic efficiency by transiently binding substrates on their way to the acylation site, where a short-lived acyl enzyme intermediate is produced. A conformational interaction between the A- and P-sites has recently been found to modulate ligand affinities. We now demonstrate that this interaction is of functional importance by showing that the acetylation rate constant of a substrate bound to the A-site is increased by a factor a when a second molecule of substrate binds to the P-site. This demonstration became feasible through the introduction of a new acetanilide substrate analogue of acetylcholine, 3-(acetamido)-N,N,N-trimethylanilinium (ATMA), for which a = 4. This substrate has a low acetylation rate constant and equilibrates with the catalytic site, allowing a tractable algebraic solution to the rate equation for substrate hydrolysis. ATMA affinities for the A- and P-sites deduced from the kinetic analysis were confirmed by fluorescence titration with thioflavin T as a reporter ligand. Values of a >1 give rise to a hydrolysis profile called substrate activation, and the AChE site-specific mutant W86F, and to a lesser extent wild-type human AChE itself, showed substrate activation with acetylthiocholine as the substrate. Substrate activation was incorporated into a previous catalytic scheme for AChE in which a bound P-site ligand can also block product dissociation from the A-site, and two additional features of the AChE catalytic pathway were revealed. First, the ability of a bound P-site ligand to increase the substrate acetylation rate constant varied with the structure of the ligand: thioflavin T accelerated ATMA acetylation by a factor a(2) of 1.3, while propidium failed to accelerate. Second, catalytic rate

  7. EmrE, a multidrug transporter from Escherichia coli, transports monovalent and divalent substrates with the same stoichiometry.

    PubMed

    Rotem, Dvir; Schuldiner, Shimon

    2004-11-19

    Multidrug transporters recognize and transport substrates with apparently little common structural features. At times these substrates are neutral, negatively, or positively charged, and only limited information is available as to how these proteins deal with the energetic consequences of transport of substrates with different charges. Multidrug transporters and drug-specific efflux systems are responsible for clinically significant resistance to chemotherapeutic agents in pathogenic bacteria, fungi, parasites, and human cancer cells. Understanding how these efflux systems handle different substrates may also have practical implications in the development of strategies to overcome the resistance mechanisms mediated by these proteins. Here, we compare transport of monovalent and divalent substrates by EmrE, a multidrug transporter from Escherichia coli, in intact cells and in proteoliposomes reconstituted with the purified protein. The results demonstrated that whereas the transport of monovalent substrates involves charge movement (i.e. electrogenic), the transport of divalent substrate does not (i.e. electroneutral). Together with previous results, these findings suggest that an EmrE dimer exchanges two protons per substrate molecule during each transport cycle. In intact cells, under conditions where the only driving force is the electrical potential, EmrE confers resistance to monovalent substrates but not to divalent ones. In the presence of proton gradients, resistance to both types of substrates is detected. The finding that under some conditions EmrE does not remove certain types of drugs points out the importance of an in-depth understanding of mechanisms of action of multidrug transporters to devise strategies for coping with the problem of multidrug resistance.

  8. A trypanothione-dependent glyoxalase I with a prokaryotic ancestry in Leishmania major.

    PubMed

    Vickers, Tim J; Greig, Neil; Fairlamb, Alan H

    2004-09-07

    Glyoxalase I forms part of the glyoxalase pathway that detoxifies reactive aldehydes such as methylglyoxal, using the spontaneously formed glutathione hemithioacetal as substrate. All known eukaryotic enzymes contain zinc as their metal cofactor, whereas the Escherichia coli glyoxalase I contains nickel. Database mining and sequence analysis identified putative glyoxalase I genes in the eukaryotic human parasites Leishmania major, Leishmania infantum, and Trypanosoma cruzi, with highest similarity to the cyanobacterial enzymes. Characterization of recombinant L. major glyoxalase I showed it to be unique among the eukaryotic enzymes in sharing the dependence of the E. coli enzyme on nickel. The parasite enzyme showed little activity with glutathione hemithioacetal substrates but was 200-fold more active with hemithioacetals formed from the unique trypanosomatid thiol trypanothione. L. major glyoxalase I also was insensitive to glutathione derivatives that are potent inhibitors of all other characterized glyoxalase I enzymes. This substrate specificity is distinct from that of the human enzyme and is reflected in the modification in the L. major sequence of a region of the human protein that interacts with the glycyl-carboxyl moiety of glutathione, a group that is conjugated to spermidine in trypanothione. This trypanothione-dependent glyoxalase I is therefore an attractive focus for additional biochemical and genetic investigation as a possible target for rational drug design.

  9. Carbon Nanotube Patterning on a Metal Substrate

    NASA Technical Reports Server (NTRS)

    Nguyen, Cattien V. (Inventor)

    2016-01-01

    A CNT electron source, a method of manufacturing a CNT electron source, and a solar cell utilizing a CNT patterned sculptured substrate are disclosed. Embodiments utilize a metal substrate which enables CNTs to be grown directly from the substrate. An inhibitor may be applied to the metal substrate to inhibit growth of CNTs from the metal substrate. The inhibitor may be precisely applied to the metal substrate in any pattern, thereby enabling the positioning of the CNT groupings to be more precisely controlled. The surface roughness of the metal substrate may be varied to control the density of the CNTs within each CNT grouping. Further, an absorber layer and an acceptor layer may be applied to the CNT electron source to form a solar cell, where a voltage potential may be generated between the acceptor layer and the metal substrate in response to sunlight exposure.

  10. Heat Flux Analysis of a Reacting Thermite Spray Impingent on a Substrate

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Eric S. Collins; Michelle L. Pantoya; Michael A. Daniels

    2012-03-01

    Spray combustion from a thermite reaction is a new area of research relevant to localized energy generation applications, such as welding or cutting. In this study, we characterized the heat flux of combustion spray impinging on a target from a nozzle for three thermite mixtures. The reactions studied include aluminum (Al) with iron oxide (Fe2O3), Al with copper oxide (CuO), and Al with molybdenum oxide (MoO3). Several standoff distances (i.e., distance from the nozzle exit to the target) were analyzed. A fast response heat flux sensor was engineered for this purpose and is discussed in detail. Results correlated substrate damagemore » to a threshold heat flux of 4550 W/cm2 for a fixed-nozzle configuration. Also, higher gas-generating thermites were shown to produce a widely dispersed spray and be less effective at imparting kinetic energy damage to a target. These results provide an understanding of the role of thermal and physical properties (i.e., such as heat of combustion, gas generation, and particle size) on thermite spray combustion performance measured by damaging a target substrate.« less

  11. Substrate transport and anion permeation proceed through distinct pathways in glutamate transporters

    PubMed Central

    Cheng, Mary Hongying; Torres-Salazar, Delany; Gonzalez-Suarez, Aneysis D; Amara, Susan G; Bahar, Ivet

    2017-01-01

    Advances in structure-function analyses and computational biology have enabled a deeper understanding of how excitatory amino acid transporters (EAATs) mediate chloride permeation and substrate transport. However, the mechanism of structural coupling between these functions remains to be established. Using a combination of molecular modeling, substituted cysteine accessibility, electrophysiology and glutamate uptake assays, we identified a chloride-channeling conformer, iChS, transiently accessible as EAAT1 reconfigures from substrate/ion-loaded into a substrate-releasing conformer. Opening of the anion permeation path in this iChS is controlled by the elevator-like movement of the substrate-binding core, along with its wall that simultaneously lines the anion permeation path (global); and repacking of a cluster of hydrophobic residues near the extracellular vestibule (local). Moreover, our results demonstrate that stabilization of iChS by chemical modifications favors anion channeling at the expense of substrate transport, suggesting a mutually exclusive regulation mediated by the movement of the flexible wall lining the two regions. DOI: http://dx.doi.org/10.7554/eLife.25850.001 PMID:28569666

  12. Facile chemical routes to mesoporous silver substrates for SERS analysis

    PubMed Central

    Tastekova, Elina A; Polyakov, Alexander Yu; Goldt, Anastasia E; Sidorov, Alexander V; Oshmyanskaya, Alexandra A; Sukhorukova, Irina V; Shtansky, Dmitry V; Grünert, Wolgang

    2018-01-01

    Mesoporous silver nanoparticles were easily synthesized through the bulk reduction of crystalline silver(I) oxide and used for the preparation of highly porous surface-enhanced Raman scattering (SERS)-active substrates. An analogous procedure was successfully performed for the production of mesoporous silver films by chemical reduction of oxidized silver films. The sponge-like silver blocks with high surface area and the in-situ-prepared mesoporous silver films are efficient as both analyte adsorbents and Raman signal enhancement mediators. The efficiency of silver reduction was characterized by X-ray diffraction and X-ray photoelectron spectroscopy. The developed substrates were applied for SERS detection of rhodamine 6G (enhancement factor of about 1–5 × 105) and an anti-ischemic mildronate drug (meldonium; enhancement factor of ≈102) that is known for its ability to increase the endurance performance of athletes. PMID:29600149

  13. Application of I-structure though-glass interconnect filled with submicron gold particles to a hermetic sealing device

    NASA Astrophysics Data System (ADS)

    Nomura, Kazuya; Okada, Akiko; Shoji, Shuichi; Ogashiwa, Toshinori; Mizuno, Jun

    2016-10-01

    We propose hermetic sealing of a glass-to-glass structure with an I-structure through-glass interconnect via (TGV) filled with submicron Au particles. The top and bottom bumps and the TGV were formed by a simple filling process with a bump-patterned dry film resist. The sealing devices consisting of two glass substrates were bonded via Au interlayers. Vacuum ultraviolet irradiation in the presence of oxygen gas (VUV/O3) pretreatment was used for low-temperature Au-Au bonding at 200 °C. The bonded samples showed He leakage rates of less than 1.3  ×  10-9 Pa m3 s-1. The cross-sectional scanning electron microscope images of the fabricated I-structure TGV showed perfect adhesion between the I-structure TGV and glass substrate. These results indicate that the proposed I-structure TGV is suitable for hermetic sealing devices.

  14. Reel-to-reel substrate tape polishing system

    DOEpatents

    Selvamanickam, Venkat; Gardner, Michael T.; Judd, Raymond D.; Weloth, Martin; Qiao, Yunfei

    2005-06-21

    Disclosed is a reel-to-reel single-pass mechanical polishing system (100) suitable for polishing long lengths of metal substrate tape (124) used in the manufacture of high-temperature superconductor (HTS) coated tape, including multiple instantiations of a polishing station (114) in combination with a subsequent rinsing station (116) arranged along the axis of the metal substrate tape (124) that is translating between a payout spool (110a) and a take-up spool (110b). The metal substrate tape obtains a surface smoothness that is suitable for the subsequent deposition of a buffer layer.

  15. Designing interlayers to improve the mechanical reliability of transparent conductive oxide coatings on flexible substrates

    NASA Astrophysics Data System (ADS)

    Kim, Eun-Hye; Yang, Chan-Woo; Park, Jin-Woo

    2012-05-01

    In this study, we investigate the effect of interlayers on the mechanical properties of transparent conductive oxide (TCO) on flexible polymer substrates. Indium tin oxide (ITO), which is the most widely used TCO film, and Ti, which is the most widely used adhesive interlayer, are selected as the coating and the interlayer, respectively. These films are deposited on the polymer substrates using dc-magnetron sputtering to achieve varying thicknesses. The changes in the following critical factors for film cracking and delamination are analyzed: the internal stress (σi) induced in the coatings during deposition using a white light interferometer, the crystallinity using a transmission electron microscope, and the surface roughness of ITO caused by the interlayer using an atomic force microscope. The resistances to the cracking and delamination of ITO are evaluated using a fragmentation test. Our tests and analyses reveal the important role of the interlayers, which significantly reduce the compressive σi that is induced in the ITO and increase the resistance to the buckling delamination of the ITO. However, the relaxation of σi is not beneficial to cracking because there is less compensation for the external tension as σi further decreases. Based on these results, the microstructural control is revealed as a more influential factor than σi for improving crack resistance.

  16. Applying a biodeposition layer to increase the bond of a repair mortar on a mortar substrate.

    PubMed

    Snoeck, D; Wang, J; Bentz, D P; De Belie, N

    2018-02-01

    One of the major concerns in infrastructure repair is a sufficient bond between the substrate and the repair material, especially for the long-term performance and durability of the repaired structure. In this study, the bond of the repair material on the mortar substrate is promoted via the biodeposition of a calcium carbonate layer by a ureolytic bacterium. X-ray diffraction and scanning electron microscopy were used to examine the interfaces between the repair material and the substrate, as well as the polymorph of the deposited calcium carbonate. The approximately 50 μm thick biodeposition film on the mortar surface mostly consisted of calcite and vaterite. Both the repair material and the substrate tended to show a good adherence to that layer. The bond, as assessed by slant shear specimen testing, was improved by the presence of the biodeposition layer. A further increase was found when engineering the substrate surface using a structured pattern layer of biodeposition.

  17. Molecular modeling of lipase binding to a substrate-water interface.

    PubMed

    Gruber, Christian C; Pleiss, Jürgen

    2012-01-01

    Interactions of lipases with hydrophobic substrate-water interfaces are of great interest to design improved lipase variants and engineer reaction conditions. This chapter describes the necessary steps to carry out molecular dynamics simulations of Candida antarctica lipase B at tributyrin-water interface using the GROMACS simulation software. Special attention is drawn to the preparation of the protein and the substrate-water interface and to the analysis of the obtained trajectory.

  18. Probing the molecular determinants of aniline dioxygenase substrate specificity by saturation mutagenesis.

    PubMed

    Ang, Ee L; Obbard, Jeffrey P; Zhao, Huimin

    2007-02-01

    Aniline dioxygenase is a multicomponent Rieske nonheme-iron dioxygenase enzyme isolated from Acinetobacter sp. strain YAA. Saturation mutagenesis of the substrate-binding pocket residues, which were identified using a homology model of the alpha subunit of the terminal dioxygenase (AtdA3), was used to probe the molecular determinants of AtdA substrate specificity. The V205A mutation widened the substrate specificity of aniline dioxygenase to include 2-isopropylaniline, for which the wild-type enzyme has no activity. The V205A mutation also made 2-isopropylaniline a better substrate for the enzyme than 2,4-dimethylaniline, a native substrate of the wild-type enzyme. The I248L mutation improved the activity of aniline dioxygenase against aniline and 2,4-dimethylaniline approximately 1.7-fold and 2.1-fold, respectively. Thus, it is shown that the alpha subunit of the terminal dioxygenase indeed plays a part in the substrate specificity as well as the activity of aniline dioxygenase. Interestingly, the equivalent residues of V205 and I248 have not been previously reported to influence the substrate specificity of other Rieske dioxygenases. These results should facilitate future engineering of the enzyme for bioremediation and industrial applications.

  19. Identification of human flavin-containing monooxygenase 3 substrates by a colorimetric screening assay.

    PubMed

    Catucci, Gianluca; Polignano, Isabelle; Cusumano, Debora; Medana, Claudio; Gilardi, Gianfranco; Sadeghi, Sheila J

    2017-04-01

    Human hepatic flavin-containing monooxygenase 3 is a phase I drug-metabolizing enzyme that is responsible for the oxidation of a variety of drugs and xenobiotics. This work reports on a high throughput rapid colorimetric assay for the screening of substrates or inhibitors of this enzyme. The method is based on the competition of two substrates for access to the active site of hFMO3 whereby the enzymatic product of the first drug converts nitro-5-thiobenzoate (TNB, yellow) to 5,5'-dithiobis (2-nitrobenzoate) (DTNB, colourless). Upon addition of a competing substrate, the amount of detected DNTB is decreased. The assay is validated testing three known substrates of hFMO3, namely benzydamine, tozasertib and tamoxifen. The latter drugs resulted in 41%-55% inhibition. In addition, two other drugs also classified as doping drugs, selegiline and clomiphene, were selected based on their chemical structure similarity to known substrates of hFMO3. These drugs showed 21% and 60% inhibition in the colorimetric assay and therefore were proven to be hFMO3 substrates. LC-MS was used to confirm their N-oxide products. Further characterisation of these newly identified hFMO3 substrates was performed determining their K m and k cat values that resulted to be 314 μM and 1.4 min -1 for selegiline and, 18 μM and 0.1 min -1 for clomiphene. This method paves the way for a rapid automated high throughput screening of nitrogen-containing compounds as substrates/inhibitors of hFMO3. Copyright © 2017 Elsevier Inc. All rights reserved.

  20. Development of a templated approach to fabricate diamond patterns on various substrates.

    PubMed

    Shimoni, Olga; Cervenka, Jiri; Karle, Timothy J; Fox, Kate; Gibson, Brant C; Tomljenovic-Hanic, Snjezana; Greentree, Andrew D; Prawer, Steven

    2014-06-11

    We demonstrate a robust templated approach to pattern thin films of chemical vapor deposited nanocrystalline diamond grown from monodispersed nanodiamond (mdND) seeds. The method works on a range of substrates, and we herein demonstrate the method using silicon, aluminum nitride (AlN), and sapphire substrates. Patterns are defined using photo- and e-beam lithography, which are seeded with mdND colloids and subsequently introduced into microwave assisted chemical vapor deposition reactor to grow patterned nanocrystalline diamond films. In this study, we investigate various factors that affect the selective seeding of different substrates to create high quality diamond thin films, including mdND surface termination, zeta potential, surface treatment, and plasma cleaning. Although the electrostatic interaction between mdND colloids and substrates is the main process driving adherence, we found that chemical reaction (esterification) or hydrogen bonding can potentially dominate the seeding process. Leveraging the knowledge on these different interactions, we optimize fabrication protocols to eliminate unwanted diamond nucleation outside the patterned areas. Furthermore, we have achieved the deposition of patterned diamond films and arrays over a range of feature sizes. This study contributes to a comprehensive understanding of the mdND-substrate interaction that will enable the fabrication of integrated nanocrystalline diamond thin films for microelectronics, sensors, and tissue culturing applications.

  1. Method of Joining Graphite Fibers to a Substrate

    NASA Technical Reports Server (NTRS)

    Beringer, Durwood M. (Inventor); Caron, Mark E. (Inventor); Taddey, Edmund P. (Inventor); Gleason, Brian P. (Inventor)

    2014-01-01

    A method of assembling a metallic-graphite structure includes forming a wetted graphite subassembly by arranging one or more layers of graphite fiber material including a plurality of graphite fibers and applying a layer of metallization material to ends of the plurality of graphite fibers. At least one metallic substrate is secured to the wetted graphite subassembly via the layer of metallization material.

  2. Substrate specificity of human metallocarboxypeptidase D: Comparison of the two active carboxypeptidase domains

    PubMed Central

    Tanco, Sebastian; Díaz, Lucía; Dasgupta, Sayani; Fernandez-Recio, Juan; Lorenzo, Julia; Aviles, Francesc X.; Fricker, Lloyd D.

    2017-01-01

    Metallocarboxypeptidase D (CPD) is a membrane-bound component of the trans-Golgi network that cycles to the cell surface through exocytic and endocytic pathways. Unlike other members of the metallocarboxypeptidase family, CPD is a multicatalytic enzyme with three carboxypeptidase-like domains, although only the first two domains are predicted to be enzymatically active. To investigate the enzymatic properties of each domain in human CPD, a critical active site Glu in domain I and/or II was mutated to Gln and the protein expressed, purified, and assayed with a wide variety of peptide substrates. CPD with all three domains intact displays >50% activity from pH 5.0 to 7.5 with a maximum at pH 6.5, as does CPD with mutation of domain I. In contrast, the domain II mutant displayed >50% activity from pH 6.5–7.5. CPD with mutations in both domains I and II was completely inactive towards all substrates and at all pH values. A quantitative peptidomics approach was used to compare the activities of CPD domains I and II towards a large number of peptides. CPD cleaved C-terminal Lys or Arg from a subset of the peptides. Most of the identified substrates of domain I contained C-terminal Arg, whereas comparable numbers of Lys- and Arg-containing peptides were substrates of domain II. We also report that some peptides with C-terminal basic residues were not cleaved by either domain I or II, showing the importance of the P1 position for CPD activity. Finally, the preference of domain I for C-terminal Arg was validated through molecular docking experiments. Together with the differences in pH optima, the different substrate specificities of CPD domains I and II allow the enzyme to perform distinct functions in the various locations within the cell. PMID:29131831

  3. PrenDB, a Substrate Prediction Database to Enable Biocatalytic Use of Prenyltransferases.

    PubMed

    Gunera, Jakub; Kindinger, Florian; Li, Shu-Ming; Kolb, Peter

    2017-03-10

    Prenyltransferases of the dimethylallyltryptophan synthase (DMATS) superfamily catalyze the attachment of prenyl or prenyl-like moieties to diverse acceptor compounds. These acceptor molecules are generally aromatic in nature and mostly indole or indole-like. Their catalytic transformation represents a major skeletal diversification step in the biosynthesis of secondary metabolites, including the indole alkaloids. DMATS enzymes thus contribute significantly to the biological and pharmacological diversity of small molecule metabolites. Understanding the substrate specificity of these enzymes could create opportunities for their biocatalytic use in preparing complex synthetic scaffolds. However, there has been no framework to achieve this in a rational way. Here, we report a chemoinformatic pipeline to enable prenyltransferase substrate prediction. We systematically catalogued 32 unique prenyltransferases and 167 unique substrates to create possible reaction matrices and compiled these data into a browsable database named PrenDB. We then used a newly developed algorithm based on molecular fragmentation to automatically extract reactive chemical epitopes. The analysis of the collected data sheds light on the thus far explored substrate space of DMATS enzymes. To assess the predictive performance of our virtual reaction extraction tool, 38 potential substrates were tested as prenyl acceptors in assays with three prenyltransferases, and we were able to detect turnover in >55% of the cases. The database, PrenDB (www.kolblab.org/prendb.php), enables the prediction of potential substrates for chemoenzymatic synthesis through substructure similarity and virtual chemical transformation techniques. It aims at making prenyltransferases and their highly regio- and stereoselective reactions accessible to the research community for integration in synthetic work flows. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  4. Substrate Sorting by a Supercharged Nanoreactor

    PubMed Central

    2017-01-01

    Compartmentalization of proteases enables spatially and temporally controlled protein degradation in cells. Here we show that an engineered lumazine synthase protein cage, which possesses a negatively supercharged lumen, can exploit electrostatic effects to sort substrates for an encapsulated protease. This proteasome-like nanoreactor preferentially cleaves positively charged polypeptides over both anionic and zwitterionic substrates, inverting the inherent substrate specificity of the guest enzyme approximately 480 fold. Our results suggest that supercharged nanochambers could provide a simple and potentially general means of conferring substrate specificity to diverse encapsulated catalysts. PMID:29278496

  5. Spectroellipsometric detection of silicon substrate damage caused by radiofrequency sputtering of niobium oxide

    NASA Astrophysics Data System (ADS)

    Lohner, Tivadar; Serényi, Miklós; Szilágyi, Edit; Zolnai, Zsolt; Czigány, Zsolt; Khánh, Nguyen Quoc; Petrik, Péter; Fried, Miklós

    2017-11-01

    Substrate surface damage induced by deposition of metal atoms by radiofrequency (rf) sputtering or ion beam sputtering onto single-crystalline silicon (c-Si) surface has been characterized earlier by electrical measurements. The question arises whether it is possible to characterize surface damage using spectroscopic ellipsometry (SE). In our experiments niobium oxide layers were deposited by rf sputtering on c-Si substrates in gas mixture of oxygen and argon. Multiple angle of incidence spectroscopic ellipsometry measurements were performed, a four-layer optical model (surface roughness layer, niobium oxide layer, native silicon oxide layer and ion implantation-amorphized silicon [i-a-Si] layer on a c-Si substrate) was created in order to evaluate the spectra. The evaluations yielded thicknesses of several nm for the i-a-Si layer. Better agreement could be achieved between the measured and the generated spectra by inserting a mixed layer (with components of c-Si and i-a-Si applying the effective medium approximation) between the silicon oxide layer and the c-Si substrate. High depth resolution Rutherford backscattering (RBS) measurements were performed to investigate the interface disorder between the deposited niobium oxide layer and the c-Si substrate. Atomic resolution cross-sectional transmission electron microscopy investigation was applied to visualize the details of the damaged subsurface region of the substrate.

  6. Optimization of substrate preparation for oyster mushroom (Pleurotus ostreatus) cultivation by studying different raw materials and substrate preparation conditions (composting: phases I and II).

    PubMed

    Vieira, Fabrício Rocha; de Andrade, Meire Cristina Nogueira

    2016-11-01

    In recent years, oyster mushroom (Pleurotus ostreatus) has become one of the most cultivated mushrooms in the world, mainly in Brazil. Among many factors involved in a mushroom production, substrate preparation is the most critical step, which can be influenced by composting management techniques. Looking forward to optimizing the substrate preparation process, were tested different composting conditions (7 and 14 days of composting with or without conditioning), potential raw materials (decumbens grass, brizantha grass and sugarcane straw) and nitrogen supplementation (with or without wheat bran) on oyster mushroom yield and biological efficiency (BE). The substrate composted for 7 days with conditioning showed higher yield and biological efficiency of mushroom (24.04 and 100.54 %, respectively). Substrates without conditioning (7 and 14 days of composting) showed smaller mushroom yield and biological efficiency. Among the raw materials tested, brizantha grass showed higher mushroom yield followed by decumbens grass, sugarcane straw and wheat straw (28.5, 24.32, 23.5 and 19.27 %, respectively). Brizantha grass also showed higher biological efficiency followed by sugarcane straw, decumbens grass and wheat straw (123.95, 103.70, 96.90 and 86.44 %, respectively). Supplementation with wheat bran improved yield and biological efficiency in all substrate formulations tested; thus, oyster mushroom yield and biological efficiency were influenced by substrate formulation (raw materials), supplementation and composting conditions.

  7. Method and system for evaluating integrity of adherence of a conductor bond to a mating surface of a substrate

    DOEpatents

    Telschow, K.L.; Siu, B.K.

    1996-07-09

    A method of evaluating integrity of adherence of a conductor bond to a substrate includes: (a) impinging a plurality of light sources onto a substrate; (b) detecting optical reflective signatures emanating from the substrate from the impinged light; (c) determining location of a selected conductor bond on the substrate from the detected reflective signatures; (d) determining a target site on the selected conductor bond from the detected reflective signatures; (e) optically imparting an elastic wave at the target site through the selected conductor bond and into the substrate; (f) optically detecting an elastic wave signature emanating from the substrate resulting from the optically imparting step; and (g) determining integrity of adherence of the selected conductor bond to the substrate from the detected elastic wave signature emanating from the substrate. A system is disclosed which is capable of conducting the method. 13 figs.

  8. Method and system for evaluating integrity of adherence of a conductor bond to a mating surface of a substrate

    DOEpatents

    Telschow, Kenneth L.; Siu, Bernard K.

    1996-01-01

    A method of evaluating integrity of adherence of a conductor bond to a substrate includes: a) impinging a plurality of light sources onto a substrate; b) detecting optical reflective signatures emanating from the substrate from the impinged light; c) determining location of a selected conductor bond on the substrate from the detected reflective signatures; d) determining a target site on the selected conductor bond from the detected reflective signatures; e) optically imparting an elastic wave at the target site through the selected conductor bond and into the substrate; f) optically detecting an elastic wave signature emanating from the substrate resulting from the optically imparting step; and g) determining integrity of adherence of the selected conductor bond to the substrate from the detected elastic wave signature emanating from the substrate. A system is disclosed which is capable of conducting the method.

  9. Substrate inhibition kinetics of phenol biodegradation

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Goudar, C.T.; Ganji, S.H.; Pujar, B.G.

    Phenol biodegradation was studied in batch experiments using an acclimated inoculum and initial phenol concentrations ranging from 0.1 to 1.3 g/L. Phenol depletion an associated microbial growth were monitored over time to provide information that was used to estimate the kinetics of phenol biodegradation. Phenol inhibited biodegradation at high concentrations, and a generalized substrate inhibition model based on statistical thermodynamics was used to describe the dynamics of microbial growth in phenol. For experimental data obtained in this study, the generalized substrate inhibition model reduced to a form that is analogous to the Andrews equation, and the biokinetic parameters {micro}{sub max},more » maximum specific growth; K{sub s}, saturation constant; and K{sub i}, inhibition constant were estimated as 0.251 h{sup {minus}1}, 0.011 g/L, and 0.348 g/L, respectively, using a nonlinear least squares technique. Given the wide variability in substrate inhibition models used to describe phenol biodegradation, an attempt was made to justify selection of particular model based on theoretical considerations. Phenol biodegradation data from nine previously published studies were used in the generalized substrate inhibition model to determine the appropriate form of the substrate inhibition model. In all nine cases, the generalized substrate inhibition model reduced to a form analogous to the Andrews equation suggesting the suitability of the Andrews equation to describe phenol biodegradation data.« less

  10. Cuboidal-to-pyramidal shape transition of a strained island on a substrate

    NASA Astrophysics Data System (ADS)

    Abbes, Fatima Z.; Durinck, Julien; Talea, Mohamed; Grilhé, Jean; Colin, Jérôme

    2017-10-01

    The stability of a strained cuboidal island deposited on a substrate has been numerically investigated by means of finite element simulations in the case where the structure is submitted to misfit strain resulting from the lattice mismatch between the island and the substrate. In the hypothesis where the surface energy is isotropic, it is found that, depending on the island volume, the formation of a truncated or inverted truncated pyramid can be favored by the misfit strain with respect to the cuboidal shape. A shape diagram is finally provided as a function of the misfit strain and island volume.

  11. Response of nematode-trapping fungi to organic substrates in a coastal grassland soil.

    PubMed

    Nguyen, Vi L; Bastow, Justin L; Jaffee, Bruce A; Strong, Don R

    2007-07-01

    To understand why Arthrobotrys oligospora and other nematode-trapping fungi are common and sometimes abundant in the coastal grassland soils of the Bodega Marine Reserve (BMR, Sonoma County, CA), we examined how resident trapping fungi responded to the addition of eight organic substrates (lupine leaves, grass leaves, dead isopods, dead moth larvae, isopod faeces, deer faeces, shrimp shells, and powdered chitin). We were especially interested in the effects of dead isopods because isopods are abundant at BMR and because previous studies had documented strong responses of A. oligospora to other arthropods (dead moth larvae). Soil from BMR was packed into vials (40 g dry mass equivalent per vial with water potential at -230 kPa and bulk density at 0.9 gcm(-3)), and one substrate or no substrate was added to the soil surface. After 30 d at 20 degrees C, trapping fungi were quantified by dilution plating and most probable number procedures. The response of A. oligospora was inversely related to substrate carbon:nitrogen (C:N) ratio: substrates with low C:N ratios (dead isopods, lupine leaves, dead moth larvae) usually caused large increases in A. oligospora whereas those with higher C:N ratios (isopod faeces, deer faeces, grass leaves) did not. An exception was chitin powder, which had a low C:N ratio, but which did not cause A. oligospora to proliferate. Responses of A. oligospora were directly related to the quantity of nitrogen added with each substrate, and those substrates that caused large increases in resident nematodes usually caused large increases in A. oligospora. Other trapping fungi did not respond as strongly as A. oligospora.

  12. Composite Pillars with a Tunable Interface for Adhesion to Rough Substrates

    PubMed Central

    2016-01-01

    The benefits of synthetic fibrillar dry adhesives for temporary and reversible attachment to hard objects with smooth surfaces have been successfully demonstrated in previous studies. However, surface roughness induces a dramatic reduction in pull-off stresses and necessarily requires revised design concepts. Toward this aim, we introduce cylindrical two-phase single pillars, which are composed of a mechanically stiff stalk and a soft tip layer. Adhesion to smooth and rough substrates is shown to exceed that of conventional pillar structures. The adhesion characteristics can be tuned by varying the thickness of the soft tip layer, the ratio of the Young’s moduli and the curvature of the interface between the two phases. For rough substrates, adhesion values similar to those obtained on smooth substrates were achieved. Our concept of composite pillars overcomes current practical limitations caused by surface roughness and opens up fields of application where roughness is omnipresent. PMID:27997118

  13. Crystal structures of the structure-selective nuclease Mus81-Eme1 bound to flap DNA substrates

    PubMed Central

    Gwon, Gwang Hyeon; Jo, Aera; Baek, Kyuwon; Jin, Kyeong Sik; Fu, Yaoyao; Lee, Jong-Bong; Kim, YoungChang; Cho, Yunje

    2014-01-01

    The Mus81-Eme1 complex is a structure-selective endonuclease with a critical role in the resolution of recombination intermediates during DNA repair after interstrand cross-links, replication fork collapse, or double-strand breaks. To explain the molecular basis of 3′ flap substrate recognition and cleavage mechanism by Mus81-Eme1, we determined crystal structures of human Mus81-Eme1 bound to various flap DNA substrates. Mus81-Eme1 undergoes gross substrate-induced conformational changes that reveal two key features: (i) a hydrophobic wedge of Mus81 that separates pre- and post-nick duplex DNA and (ii) a “5′ end binding pocket” that hosts the 5′ nicked end of post-nick DNA. These features are crucial for comprehensive protein-DNA interaction, sharp bending of the 3′ flap DNA substrate, and incision strand placement at the active site. While Mus81-Eme1 unexpectedly shares several common features with members of the 5′ flap nuclease family, the combined structural, biochemical, and biophysical analyses explain why Mus81-Eme1 preferentially cleaves 3′ flap DNA substrates with 5′ nicked ends. PMID:24733841

  14. GaAs Photovoltaics on Polycrystalline Ge Substrates

    NASA Technical Reports Server (NTRS)

    Wilt, David M.; Pal, AnnaMaria T.; McNatt, Jeremiah S.; Wolford, David S.; Landis, Geoffrey A.; Smith, Mark A.; Scheiman, David; Jenkins, Phillip P.; McElroy Bruce

    2007-01-01

    High efficiency III-V multijunction solar cells deposited on metal foil or even polymer substrates can provide tremendous advantages in mass and stowage, particularly for planetary missions. As a first step towards that goal, poly-crystalline p/i/n GaAs solar cells are under development on polycrystalline Ge substrates. Organo Metallic Vapor Phase Epitaxy (OMVPE) parameters for pre-growth bake, nucleation and deposition have been examined. Single junction p/i/n GaAs photovoltaic devices, incorporating InGaP front and back window layers, have been grown and processed. Device performance has shown a dependence upon the thickness of a GaAs buffer layer deposited between the Ge substrate and the active device structure. A thick (2 m) GaAs buffer provides for both increased average device performance as well as reduced sensitivity to variations in grain size and orientation. Illumination under IR light (lambda > 1 micron), the cells showed a Voc, demonstrating the presence of an unintended photoactive junction at the GaAs/Ge interface. The presence of this junction limited the efficiency to approx.13% (estimated with an anti-refection coating) due to the current mismatch and lack of tunnel junction interconnect.

  15. Process Of Bonding A Metal Brush Structure To A Planar Surface Of A Metal Substrate

    DOEpatents

    Slattery, Kevin T.; Driemeyer, Daniel E.; Wille; Gerald W.

    1999-11-02

    Process for bonding a metal brush structure to a planar surface of a metal substrate in which an array of metal rods are retained and immobilized at their tips by a common retention layer formed of metal, and the brush structure is then joined to a planar surface of a metal substrate via the retention layer.

  16. Hybrid solar cell based on a-Si/polymer flat heterojunction on flexible substrates

    NASA Astrophysics Data System (ADS)

    Olivares Vargas, A. J.; Mansurova, S.; Cosme, I.; Kosarev, A.; Ospina Ocampo, C. A.; Martinez Mateo, H. E.

    2017-08-01

    In this work, we present the results of investigation of thin film hybrid organic-inorganic photovoltaic structures based on flat heterojunction hydrogenated silicon (a-Si:H) and poly(3,4 ethylene dioxythiophene):poly(4-styrenesulfonate) (PEDOT:PSS) fabricated on polyethylene naphthalate (PEN). Different thicknesses of transparent AL doped Zn:O (AZO) electrodes have been tested on PEN substrate and studied by atomic force microscopy (AFM). The AZO films on PEN substrate were statistically processed to obtain surface morphological characteristics, such as root mean square roughness RQ, skewness SK and kurtosis KU. Performance characteristics of fabricated photovoltaic structures have been measured and analyzed for different thicknesses of the transparent electrodes under standard illumination (AM 1.5 I0= 100mW/cm2). Structures on flexible substrates show reproducible performance characteristic as their glass substrate counterpart with values of JSC= 6 mA/cm2, VOC= 0.535 V, FF= 43 % and PCE= 1.41%.

  17. PREFACE: Cell-substrate interactions Cell-substrate interactions

    NASA Astrophysics Data System (ADS)

    Gardel, Margaret; Schwarz, Ulrich

    2010-05-01

    cytoskeleton-bound microbeads—the effect of bead-receptor binding dynamics J. Phys.: Condens. Matter 22 194105 [10] Ryzhkov P, Prass M, Gummich M, Kühn J-S, Oettmeier C and Döbereiner H-G 2010 Adhesion patterns in early cell spreading J. Phys.: Condens. Matter 22 194106 [11] Cretel E, Touchard D, Benoliel A M, Bongrand P and Pierres A 2010 Early contacts between T lymphocytes and activating surfaces J. Phys.: Condens. Matter 22 194107 [12] Heil P and Spatz J P 2010 Lateral shear forces applied to cells with single elastic micropillars to influence focal adhesion dynamics J. Phys.: Condens. Matter 22 194108 [13] Kirchenbüchler D, Born S, Kirchgeßner N, Houben S, Hoffmann B and Merkel R 2010 Substrate, focal adhesions, and actin filaments: a mechanical unit with a weak spot for mechanosensitive proteins J. Phys.: Condens. Matter 22 194109 [14] Zemel A, Rehfeldt F, Brown A E X, Discher D E and Safran S A 2010 Cell shape, spreading symmetry, and the polarization of stress-fibers in cells J. Phys.: Condens. Matter 22 194110 [15] Biton Y Y and Safran S A 2010 Theory of the mechanical response of focal adhesions to shear flow J. Phys.: Condens. Matter 22 194111 [16] Sabass B and Schwarz U S 2010 Modeling cytoskeletal flow over adhesion sites: competition between stochastic bond dynamics and intracellular relaxation J. Phys.: Condens. Matter 22 194112 [17] Li Y, Bhimalapuram P and Dinner A R 2010 Model for how retrograde actin flow regulates adhesion traction stresses J. Phys.: Condens. Matter 22 194113 [18] Moshayedi P, da F Costa L, Christ A, Lacour S P, Fawcett J, Guck J and Franze K 2010 Mechanosensitivity of astrocytes on optimized polyacrylamide gels analyzed by quantitative morphometry J. Phys.: Condens. Matter 22 194114 [19] Lee S, Zeiger A, Maloney J M, Kotecki M, Van Vliet K J and Herman I M 2010 Pericyte contraction at the cell-material interface can modulate the microvascular niche J. Phys.: Condens. Matter 22 194115 [20] Buxboim A, Rajagopal K, Brown A E X and

  18. Two distinct domains contribute to the substrate acyl chain length selectivity of plant acyl-ACP thioesterase.

    PubMed

    Jing, Fuyuan; Zhao, Le; Yandeau-Nelson, Marna D; Nikolau, Basil J

    2018-02-28

    The substrate specificity of acyl-ACP thioesterase (TE) plays an essential role in controlling the fatty acid profile produced by type II fatty acid synthases. Here we identify two groups of residues that synergistically determine different substrate specificities of two acyl-ACP TEs from Cuphea viscosissima (CvFatB1 and CvFatB2). One group (V194, V217, N223, R226, R227, and I268 in CvFatB2) is critical in determining the structure and depth of a hydrophobic cavity in the N-terminal hotdog domain that binds the substrate's acyl moiety. The other group (255-RKLSKI-260 and 285-RKLPKL-289 in CvFatB2) defines positively charged surface patches that may facilitate binding of the ACP moiety. Mutagenesis of residues within these two groups results in distinct synthetic acyl-ACP TEs that efficiently hydrolyze substrates with even shorter chains (C4- to C8-ACPs). These insights into structural determinants of acyl-ACP TE substrate specificity are useful in modifying this enzyme for tailored fatty acid production in engineered organisms.

  19. Bonding strength of glass-ceramic trabecular-like coatings to ceramic substrates for prosthetic applications.

    PubMed

    Chen, Qiang; Baino, Francesco; Pugno, Nicola M; Vitale-Brovarone, Chiara

    2013-04-01

    A new approach based on the concepts of quantized fracture mechanics (QFM) is presented and discussed in this paper to estimate the bonding strength of trabecular-like coatings, i.e. glass-ceramic scaffolds mimicking the architecture of cancellous bone, to ceramic substrates. The innovative application of glass-derived scaffolds as trabecular-like coatings is proposed in order to enhance the osteointegration of prosthetic ceramic devices. The scaffolds, prepared by polymeric sponge replication, are joined to alumina substrates by a dense glass-ceramic coating (interlayer) and the so-obtained 3-layer constructs are investigated from micro-structural, morphological and mechanical viewpoints. In particular, the fracture strengths of three different crack propagation modes, i.e. glass-derived scaffold fracture, interface delamination or mixed fracture, are predicted in agreement with those of experimental mechanical tests. The approach proposed in this work could have interesting applications towards an ever more rational design of bone tissue engineering biomaterials and coatings, in view of the optimization of their mechanical properties for making them actually suitable for clinical applications. Copyright © 2012 Elsevier B.V. All rights reserved.

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

    PubMed

    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.

  1. A new buckwheat dihydroflavonol 4-reductase (DFR), with a unique substrate binding structure, has altered substrate specificity.

    PubMed

    Katsu, Kenjiro; Suzuki, Rintaro; Tsuchiya, Wataru; Inagaki, Noritoshi; Yamazaki, Toshimasa; Hisano, Tomomi; Yasui, Yasuo; Komori, Toshiyuki; Koshio, Motoyuki; Kubota, Seiji; Walker, Amanda R; Furukawa, Kiyoshi; Matsui, Katsuhiro

    2017-12-11

    Dihydroflavonol 4-reductase (DFR) is the key enzyme committed to anthocyanin and proanthocyanidin biosynthesis in the flavonoid biosynthetic pathway. DFR proteins can catalyse mainly the three substrates (dihydrokaempferol, dihydroquercetin, and dihydromyricetin), and show different substrate preferences. Although relationships between the substrate preference and amino acids in the region responsible for substrate specificity have been investigated in several plant species, the molecular basis of the substrate preference of DFR is not yet fully understood. By using degenerate primers in a PCR, we isolated two cDNA clones that encoded DFR in buckwheat (Fagopyrum esculentum). Based on sequence similarity, one cDNA clone (FeDFR1a) was identical to the FeDFR in DNA databases (DDBJ/Gen Bank/EMBL). The other cDNA clone, FeDFR2, had a similar sequence to FeDFR1a, but a different exon-intron structure. Linkage analysis in an F 2 segregating population showed that the two loci were linked. Unlike common DFR proteins in other plant species, FeDFR2 contained a valine instead of the typical asparagine at the third position and an extra glycine between sites 6 and 7 in the region that determines substrate specificity, and showed less activity against dihydrokaempferol than did FeDFR1a with an asparagine at the third position. Our 3D model suggested that the third residue and its neighbouring residues contribute to substrate specificity. FeDFR1a was expressed in all organs that we investigated, whereas FeDFR2 was preferentially expressed in roots and seeds. We isolated two buckwheat cDNA clones of DFR genes. FeDFR2 has unique structural and functional features that differ from those of previously reported DFRs in other plants. The 3D model suggested that not only the amino acid at the third position but also its neighbouring residues that are involved in the formation of the substrate-binding pocket play important roles in determining substrate preferences. The unique

  2. Power electronics substrate for direct substrate cooling

    DOEpatents

    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.

  3. From wrinkling to global buckling of a ring on a curved substrate

    NASA Astrophysics Data System (ADS)

    Lagrange, R.; López Jiménez, F.; Terwagne, D.; Brojan, M.; Reis, P. M.

    2016-04-01

    We present a combined analytical approach and numerical study on the stability of a ring bound to an annular elastic substrate, which contains a circular cavity. The system is loaded by depressurizing the inner cavity. The ring is modeled as an Euler-Bernoulli beam and its equilibrium equations are derived from the mechanical energy which takes into account both stretching and bending contributions. The curvature of the substrate is considered explicitly to model the work done by its reaction force on the ring. We distinguish two different instabilities: periodic wrinkling of the ring or global buckling of the structure. Our model provides an expression for the critical pressure, as well as a phase diagram that rationalizes the transition between instability modes. Towards assessing the role of curvature, we compare our results for the critical stress and the wrinkling wavelength to their planar counterparts. We show that the critical stress is insensitive to the curvature of the substrate, while the wavelength is only affected due to the permissible discrete values of the azimuthal wavenumber imposed by the geometry of the problem. Throughout, we contrast our analytical predictions against finite element simulations.

  4. Shape-engineering substrate-based plasmonic nanomaterials

    NASA Astrophysics Data System (ADS)

    Gilroy, Kyle D.

    The advancement of next generation technologies is reliant on our ability to engineer matter at the nanoscale. Since the morphological features of nanomaterials dictate their chemical and physical properties, a significant effort has been put forth to develop syntheses aimed at fine tuning their size, shape and composition. This massive effort has resulted in a maturing colloidal chemistry containing an extensive collection of morphologies with compositions nearly spanning the entire transition of the periodic table. While colloidal nanoparticles have opened the door to promising applications in fields such as cancer theranostics, drug delivery, catalysis and sensing; the synthetic protocols for the placement of nanomaterials on surfaces, a requisite for chip-based devices, are ill-developed. This dissertation serves to address this limitation by highlighting a series of syntheses related to the design of substrate-based nanoparticles whose size, shape and composition are controllably engineered to a desired endpoint. The experimental methods are based on a template-mediated approach which sees chemical modifications made to prepositioned thermally assembled metal nanostructures which are well bonded to a sapphire substrate. The first series of investigations will highlight synthetic routes utilizing galvanic replacement reactions, where the prepositioned templates are chemically transformed into hollow nanoshells. Detailed studies are provided highlighting discoveries related to (i) hollowing, (ii) defect transfer, (iii) strain induction, (iv) interdiffusion, (v) crystal structure and (vi) the localized surface plasmon resonance (LSPR). The second series of investigations, based on heterogeneous nucleation, have Au templates serve as nucleation sites for metal atoms arriving in either the solution- or vapor phase. The solution-phase heterogeneous nucleation of Ag on Au reveals that chemical kinetics (injection rate & precursor concentration) can be used to control

  5. A VCP inhibitor substrate trapping approach (VISTA) enables proteomic profiling of endogenous ERAD substrates.

    PubMed

    Huang, Edmond Y; To, Milton; Tran, Erica; Dionisio, Lorraine T Ador; Cho, Hyejin J; Baney, Katherine L M; Pataki, Camille I; Olzmann, James A

    2018-05-01

    Endoplasmic reticulum (ER)-associated degradation (ERAD) mediates the proteasomal clearance of proteins from the early secretory pathway. In this process, ubiquitinated substrates are extracted from membrane-embedded dislocation complexes by the AAA ATPase VCP and targeted to the cytosolic 26S proteasome. In addition to its well-established role in the degradation of misfolded proteins, ERAD also regulates the abundance of key proteins such as enzymes involved in cholesterol synthesis. However, due to the lack of generalizable methods, our understanding of the scope of proteins targeted by ERAD remains limited. To overcome this obstacle, we developed a VCP inhibitor substrate trapping approach (VISTA) to identify endogenous ERAD substrates. VISTA exploits the small-molecule VCP inhibitor CB5083 to trap ERAD substrates in a membrane-associated, ubiquitinated form. This strategy, coupled with quantitative ubiquitin proteomics, identified previously validated (e.g., ApoB100, Insig2, and DHCR7) and novel (e.g., SCD1 and RNF5) ERAD substrates in cultured human hepatocellular carcinoma cells. Moreover, our results indicate that RNF5 autoubiquitination on multiple lysine residues targets it for ubiquitin and VCP--dependent clearance. Thus, VISTA provides a generalizable discovery method that expands the available toolbox of strategies to elucidate the ERAD substrate landscape.

  6. Identification of amino acids important for substrate specificity in sucrose transporters using gene shuffling.

    PubMed

    Reinders, Anke; Sun, Ye; Karvonen, Kayla L; Ward, John M

    2012-08-31

    Plant sucrose transporters (SUTs) are H(+)-coupled uptake transporters. Type I and II (SUTs) are phylogenetically related but have different substrate specificities. Type I SUTs transport sucrose, maltose, and a wide range of natural and synthetic α- and β-glucosides. Type II SUTs are more selective for sucrose and maltose. Here, we investigated the structural basis for this difference in substrate specificity. We used a novel gene shuffling method called synthetic template shuffling to introduce 62 differentially conserved amino acid residues from type I SUTs into OsSUT1, a type II SUT from rice. The OsSUT1 variants were tested for their ability to transport the fluorescent coumarin β-glucoside esculin when expressed in yeast. Fluorescent yeast cells were selected using fluorescence-activated cell sorting (FACS). Substitution of five amino acids present in type I SUTs in OsSUT1 was found to be sufficient to confer esculin uptake activity. The changes clustered in two areas of the OsSUT1 protein: in the first loop and the top of TMS2 (T80L and A86K) and in TMS5 (S220A, S221A, and T224Y). The substrate specificity of this OsSUT1 variant was almost identical to that of type I SUTs. Corresponding changes in the sugarcane type II transporter ShSUT1 also changed substrate specificity, indicating that these residues contribute to substrate specificity in type II SUTs in general.

  7. Identification of Amino Acids Important for Substrate Specificity in Sucrose Transporters Using Gene Shuffling*

    PubMed Central

    Reinders, Anke; Sun, Ye; Karvonen, Kayla L.; Ward, John M.

    2012-01-01

    Plant sucrose transporters (SUTs) are H+-coupled uptake transporters. Type I and II (SUTs) are phylogenetically related but have different substrate specificities. Type I SUTs transport sucrose, maltose, and a wide range of natural and synthetic α- and β-glucosides. Type II SUTs are more selective for sucrose and maltose. Here, we investigated the structural basis for this difference in substrate specificity. We used a novel gene shuffling method called synthetic template shuffling to introduce 62 differentially conserved amino acid residues from type I SUTs into OsSUT1, a type II SUT from rice. The OsSUT1 variants were tested for their ability to transport the fluorescent coumarin β-glucoside esculin when expressed in yeast. Fluorescent yeast cells were selected using fluorescence-activated cell sorting (FACS). Substitution of five amino acids present in type I SUTs in OsSUT1 was found to be sufficient to confer esculin uptake activity. The changes clustered in two areas of the OsSUT1 protein: in the first loop and the top of TMS2 (T80L and A86K) and in TMS5 (S220A, S221A, and T224Y). The substrate specificity of this OsSUT1 variant was almost identical to that of type I SUTs. Corresponding changes in the sugarcane type II transporter ShSUT1 also changed substrate specificity, indicating that these residues contribute to substrate specificity in type II SUTs in general. PMID:22807445

  8. Depth and type of substrate influence the ability of Nasonia vitripennis to locate a host

    PubMed Central

    Frederickx, Christine; Dekeirsschieter, Jessica; Verheggen, François J.; Haubruge, Eric

    2014-01-01

    Abstract The foraging behaviour of a parasitoid insect species includes the host’s habitat and subsequent location of the host. Habitats substrate, substrate moisture, and light levels can affect the host searching of different species of parasitoids. However, the depth at which parasitoids concentrate their search effort is another important ecological characteristic and plays an important role in locating a host. Here, we investigated the ability of a pupal parasitoid, Nasonia vitripennis Walker (Hymenoptera: Pteromalidae), to penetrate and kill fly pupae located at different depths of the substrate. Three different types of substrate were tested: loam soil, compost, and vermiculite substrate. In both loam soil and compost, all of the parasitism activity was restricted to pupae placed directly on the surface. Parasitism activity in vermiculite showed that the average number of pupae parasitized decreased with depth of substrate. These results suggest that fly pupae situated deeper in the substrate are less subjected to parasitism by N. vitripennis . PMID:25373205

  9. Conformational Properties of Seven Toac-Labeled Angiotensin I Analogues Correlate with Their Muscle Contraction Activity and Their Ability to Act as ACE Substrates.

    PubMed

    Teixeira, Luis Gustavo D; Malavolta, Luciana; Bersanetti, Patrícia A; Schreier, Shirley; Carmona, Adriana K; Nakaie, Clovis R

    2015-01-01

    Conformational properties of the angiotensin II precursor, angiotensin I (AngI) and analogues containing the paramagnetic amino acid TOAC (2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid) at positions 0, 1, 3, 5, 8, 9, and 10, were examined by EPR, CD, and fluorescence. The conformational data were correlated to their activity in muscle contraction experiments and to their properties as substrates of the angiotensin I-converting enzyme (ACE). Biological activity studies indicated that TOAC0-AngI and TOAC1-AngI maintained partial potency in guinea pig ileum and rat uterus. Kinetic parameters revealed that only derivatives labeled closer to the N-terminus (positions 0, 1, 3, and 5) were hydrolyzed by ACE, indicating that peptides bearing the TOAC moiety far from the ACE cleavage site (Phe8-His9 peptide bond) were susceptible to hydrolysis, albeit less effectively than the parent compound. CD spectra indicated that AngI exhibited a flexible structure resulting from equilibrium between different conformers. While the conformation of N-terminally-labeled derivatives was similar to that of the native peptide, a greater propensity to acquire folded structures was observed for internally-labeled, as well as C-terminally labeled, analogues. These structures were stabilized in secondary structure-inducing agent, TFE. Different analogues gave rise to different β-turns. EPR spectra in aqueous solution also distinguished between N-terminally, internally-, and C-terminally labeled peptides, yielding narrower lines, indicative of greater mobility for the former. Interestingly, the spectra of peptides labeled at, or close, to the C-terminus, showed that the motion in this part of the peptides was intermediate between that of N-terminally and internally-labeled peptides, in agreement with the suggestion of turn formation provided by the CD spectra. Quenching of the Tyr4 fluorescence by the differently positioned TOAC residues corroborated the data obtained by the

  10. Conformational Properties of Seven Toac-Labeled Angiotensin I Analogues Correlate with Their Muscle Contraction Activity and Their Ability to Act as ACE Substrates

    PubMed Central

    Teixeira, Luis Gustavo D.; Malavolta, Luciana; Bersanetti, Patrícia A.; Schreier, Shirley; Carmona, Adriana K.; Nakaie, Clovis R.

    2015-01-01

    Conformational properties of the angiotensin II precursor, angiotensin I (AngI) and analogues containing the paramagnetic amino acid TOAC (2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid) at positions 0, 1, 3, 5, 8, 9, and 10, were examined by EPR, CD, and fluorescence. The conformational data were correlated to their activity in muscle contraction experiments and to their properties as substrates of the angiotensin I-converting enzyme (ACE). Biological activity studies indicated that TOAC0-AngI and TOAC1-AngI maintained partial potency in guinea pig ileum and rat uterus. Kinetic parameters revealed that only derivatives labeled closer to the N-terminus (positions 0, 1, 3, and 5) were hydrolyzed by ACE, indicating that peptides bearing the TOAC moiety far from the ACE cleavage site (Phe8-His9 peptide bond) were susceptible to hydrolysis, albeit less effectively than the parent compound. CD spectra indicated that AngI exhibited a flexible structure resulting from equilibrium between different conformers. While the conformation of N-terminally-labeled derivatives was similar to that of the native peptide, a greater propensity to acquire folded structures was observed for internally-labeled, as well as C-terminally labeled, analogues. These structures were stabilized in secondary structure-inducing agent, TFE. Different analogues gave rise to different β-turns. EPR spectra in aqueous solution also distinguished between N-terminally, internally-, and C-terminally labeled peptides, yielding narrower lines, indicative of greater mobility for the former. Interestingly, the spectra of peptides labeled at, or close, to the C-terminus, showed that the motion in this part of the peptides was intermediate between that of N-terminally and internally-labeled peptides, in agreement with the suggestion of turn formation provided by the CD spectra. Quenching of the Tyr4 fluorescence by the differently positioned TOAC residues corroborated the data obtained by the

  11. Effect of substrate dislocations on the Hg in-diffusion in CdZnTe substrates used for HgCdTe epilayer growth

    NASA Astrophysics Data System (ADS)

    Kumar, Shiv; Kapoor, A. K.; Nagpal, A.; Sharma, S.; Verma, D.; Kumar, A.; Raman, R.; Basu, P. K.

    2006-12-01

    Chemical-etched HgCdTe epilayers grown onto CdZnTe substrates have been studied using defect etching and EDS on cleaved (1 1 0) face. Formation of etch pits and mercury (Hg) in-diffusion into CZT substrate has been correlated with the substrate quality i.e. the presence of dislocations around second phase inclusions. That the Hg in-diffusion takes place through these dislocations is authenticated by the presence of Te-inclusions in substrates where large density of etch pits are revealed after chemical etching. X-ray rocking curve measurements were carried out to reveal crystalline quality of the substrates. FTIR spectroscopy indicates low transmission values and absence of interference fringes in MCT epilayers with large Hg diffusion. Hg diffusion into CZT substrate upto 25 μm in samples with low FWHM values and upto 250 μm in samples with multiple peaks and high FWHM values was observed.

  12. Strong room temperature electroluminescence from lateral p-SiGe/i-Ge/n-SiGe heterojunction diodes on silicon-on-insulator substrate

    NASA Astrophysics Data System (ADS)

    Lin, Guangyang; Yi, Xiaohui; Li, Cheng; Chen, Ningli; Zhang, Lu; Chen, Songyan; Huang, Wei; Wang, Jianyuan; Xiong, Xihuan; Sun, Jiaming

    2016-10-01

    A lateral p-Si0.05Ge0.95/i-Ge/n-Si0.05Ge0.95 heterojunction light emitting diode on a silicon-on-insulator (SOI) substrate was proposed, which is profitable to achieve higher luminous extraction compared to vertical junctions. Due to the high carrier injection ratio of heterostructures and optical reflection at the SiO2/Si interface of the SOI, strong room temperature electroluminescence (EL) at around 1600 nm from the direct bandgap of i-Ge with 0.30% tensile strain was observed. The EL peak intensity of the lateral heterojunction is enhanced by ˜4 folds with a larger peak energy than that of the vertical Ge p-i-n homojunction, suggesting that the light emitting efficiency of the lateral heterojunction is effectively improved. The EL peak intensity of the lateral heterojunction, which increases quadratically with injection current density, becomes stronger for diodes with a wider i-Ge region. The CMOS compatible fabrication process of the lateral heterojunctions paves the way for the integration of the light source with the Ge metal-oxide-semiconductor field-effect-transistor.

  13. The Type of Forage Substrate Preparation Included as Substrate in a RUSITEC System Affects the Ruminal Microbiota and Fermentation Characteristics

    PubMed Central

    Duarte, Andrea C.; Holman, Devin B.; Alexander, Trevor W.; Durmic, Zoey; Vercoe, Philip E.; Chaves, Alexandre V.

    2017-01-01

    In vitro fermentation systems such as the rumen simulation technique (RUSITEC) are frequently used to assess dietary manipulations in livestock, thereby limiting the use of live animals. Despite being in use for nearly 40 years, improvements are continually sought in these systems to better reflect and mimic natural processes in ruminants. The aim of this study was to evaluate the effect of forage preparation, i.e., frozen minced (FM) and freeze-dried and ground (FDG), on the ruminal microbiota and on fermentation characteristics when included as a substrate in a RUSITEC system. A completely randomized design experiment was performed over a 15-day period, with 7 days of adaptation and an 8-day experimental period. Fermentation parameters (total gas, CH4, and volatile fatty acid production) were analyzed on a daily basis over the experimental period and the archaeal and bacterial microbiota (liquid-associated microbes [LAM] and solid-associated microbes [SAM] was assessed at 0, 5, 10, and 15 days using high-throughput sequencing of the 16S rRNA gene. Results from this study suggested a tendency (P = 0.09) of FM treatment to increase daily CH4 (mg/d) production by 16.7% when compared with FDG treatment. Of the major volatile fatty acids (acetate, propionate, and butyrate), only butyrate production was greater (P = 0.01) with FM treatment compared with FDG substrate. The archaeal and bacterial diversity and richness did not differ between the forage preparations, although feed particle size of the forage had a significant effect on microbial community structure in the SAM and LAM samples. The Bacteroidetes phylum was more relatively abundant in the FM substrate treatment, while Proteobacteria was enriched in the FDG treatment. At the genus-level, Butyrivibrio, Prevotella, and Roseburia were enriched in the FM substrate treatment and Campylobacter and Lactobacillus in the FDG substrate treatment. Evidence from this study suggests that forage preparation affects CH4

  14. SUPECA kinetics for scaling redox reactions in networks of mixed substrates and consumers and an example application to aerobic soil respiration

    NASA Astrophysics Data System (ADS)

    Tang, Jin-Yun; Riley, William J.

    2017-09-01

    Several land biogeochemical models used for studying carbon-climate feedbacks have begun explicitly representing microbial dynamics. However, to our knowledge, there has been no theoretical work on how to achieve a consistent scaling of the complex biogeochemical reactions from microbial individuals to populations, communities, and interactions with plants and mineral soils. We focus here on developing a mathematical formulation of the substrate-consumer relationships for consumer-mediated redox reactions of the form A + BE→<i style=" margin-left:-.7em"> products, where products could be, e.g., microbial biomass or bioproducts. Under the quasi-steady-state approximation, these substrate-consumer relationships can be formulated as the computationally difficult full equilibrium chemistry problem or approximated analytically with the dual Monod (DM) or synthesizing unit (SU) kinetics. We find that DM kinetics is scaling inconsistently for reaction networks because (1) substrate limitations are not considered, (2) contradictory assumptions are made regarding the substrate processing rate when transitioning from single- to multi-substrate redox reactions, and (3) the product generation rate cannot be scaled from one to multiple substrates. In contrast, SU kinetics consistently scales the product generation rate from one to multiple substrates but predicts unrealistic results as consumer abundances reach large values with respect to their substrates. We attribute this deficit to SU's failure to incorporate substrate limitation in its derivation. To address these issues, we propose SUPECA (SU plus the equilibrium chemistry approximation - ECA) kinetics, which consistently imposes substrate and consumer mass balance constraints. We show that SUPECA kinetics satisfies the partition principle, i.e., scaling invariance across a network of an arbitrary number of reactions (e.g., as in Newton's law of motion and

  15. Profiling RNA editing in human tissues: towards the inosinome Atlas

    PubMed Central

    Picardi, Ernesto; Manzari, Caterina; Mastropasqua, Francesca; Aiello, Italia; D’Erchia, Anna Maria; Pesole, Graziano

    2015-01-01

    Adenine to Inosine RNA editing is a widespread co- and post-transcriptional mechanism mediated by ADAR enzymes acting on double stranded RNA. It has a plethora of biological effects, appears to be particularly pervasive in humans with respect to other mammals, and is implicated in a number of diverse human pathologies. Here we present the first human inosinome atlas comprising 3,041,422 A-to-I events identified in six tissues from three healthy individuals. Matched directional total-RNA-Seq and whole genome sequence datasets were generated and analysed within a dedicated computational framework, also capable of detecting hyper-edited reads. Inosinome profiles are tissue specific and edited gene sets consistently show enrichment of genes involved in neurological disorders and cancer. Overall frequency of editing also varies, but is strongly correlated with ADAR expression levels. The inosinome database is available at: http://srv00.ibbe.cnr.it/editing/. PMID:26449202

  16. Adhesion strength of a living cell to various substrates measured using a cup-attached atomic force microscopy chip

    NASA Astrophysics Data System (ADS)

    Kim, Hyonchol; Ishibashi, Kenta; Matsuo, Kosuke; Kira, Atsushi; Onomura, Yui; Okada, Tomoko; Nakamura, Chikashi

    2018-03-01

    Cell adhesion strengths to various substrates were quantitatively measured using atomic force microscopy (AFM). A cup-shaped metal hemisphere was attached to the apex of the AFM cantilever, the “cup-chip” approached a cell (FP10SC2) to pick it up, the captured cell approached any one of six different substrates [gold (Au), nickel (Ni), bovine serum albumin (BSA), an amino group (NH2), poly(tetrafluoroethylene) (PTFE), and structured PTFE (sPTFE)], and the cell adhesion strength at the initial contact period was evaluated by detaching the cell from the substrate. The results obtained showed that the force needed to detach the cell from the NH2 substrate was more than 3-fold larger than that of metal substrates (Au and Ni), more than 15-fold larger than that of biochemically treated substrates (BSA), and more than 20-fold larger than that of hydrophobic substrates (PTFE and sPTFE). Using differences in adhesion strengths, a cell on a sPTFE substrate was picked up using a BSA-coated cup-chip, placed on a NH2 substrate, repeating this cell manipulation five times, and line patterning of cells was achieved. These results indicate that measurements of cell adhesion strength are fundamental to fabricate desired cell networks and the cup-chip is a useful tool for achieving easy cell manipulation.

  17. A systemic study on key parameters affecting nanocomposite coatings on magnesium substrates.

    PubMed

    Johnson, Ian; Wang, Sebo Michelle; Silken, Christine; Liu, Huinan

    2016-05-01

    Nanocomposite coatings offer multiple functions simultaneously to improve the interfacial properties of magnesium (Mg) alloys for skeletal implant applications, e.g., controlling the degradation rate of Mg substrates, improving bone cell functions, and providing drug delivery capability. However, the effective service time of nanocomposite coatings may be limited due to their early delamination from the Mg-based substrates. Therefore, the objective of this study was to address the delamination issue of nanocomposite coatings, improve the coating properties for reducing the degradation of Mg-based substrates, and thus improve their cytocompatibility with bone marrow derived mesenchymal stem cells (BMSCs). The surface conditions of the substrates, polymer component type of the nanocomposite coatings, and post-deposition processing are the key parameters that contribute to the efficacy of the nanocomposite coatings in regulating substrate degradation and bone cell responses. Specifically, the effects of metallic surface versus alkaline heat-treated hydroxide surface of the substrates on coating quality were investigated. For the nanocomposite coatings, nanophase hydroxyapatite (nHA) was dispersed in three types of biodegradable polymers, i.e., poly(lactic-co-glycolic acid) (PLGA), poly(l-lactic acid) (PLLA), or poly(caprolactone) (PCL) to determine which polymer component could provide integrated properties for slowest Mg degradation. The nanocomposite coatings with or without post-deposition processing, i.e., melting, annealing, were compared to determine which processing route improved the properties of the nanocomposite coatings most significantly. The results showed that optimizing the coating processes addressed the delamination issue. The melted then annealed nHA/PCL coating on the metallic Mg substrates showed the slowest degradation and the best coating adhesion, among all the combinations of conditions studied; and, it improved the adhesion density of BMSCs

  18. PLASMA POLYMER FILMS AS ADHESION PROMOTING PRIMERS FOR ALUMINUM SUBSTRATES. PART I: CHARACTERIZATION OF FILMS AND FILM/SUBSTRATE INTERFACES

    EPA Science Inventory

    Plasma polymerized hexamethyldisiloxane (HMDSO) films (~800 Å in thickness) were deposited onto aluminum substrates (6111-T4 alloy) in radio frequency (RF) and microwave (MW) powered reactors to be used as primers for structural adhesive bonding. Processing variables such as sub...

  19. The proto-oncogene product c-Crk associates with insulin receptor substrate-1 and 4PS. Modulation by insulin growth factor-I (IGF) and enhanced IGF-I signaling.

    PubMed

    Beitner-Johnson, D; Blakesley, V A; Shen-Orr, Z; Jimenez, M; Stannard, B; Wang, L M; Pierce, J; LeRoith, D

    1996-04-19

    The Crk proto-oncogene product is an SH2 and SH3 domain-containing adaptor protein which we have previously shown to become rapidly tyrosine phosphorylated in response to stimulation with insulin-like growth factor I (IGF-I) in NIH-3T3 cells. In order to further characterize the role of Crk in the IGF-I signaling pathway, NIH-3T3 and 293 cells were stably transfected with an expression vector containing the Crk cDNA. The various resultant 3T3-Crk clones expressed Crk at approximately 2-15-fold higher levels than parental 3T3 cells. In 3T3-Crk cells, Crk immunoreactivity was detected in insulin receptor substrate-1 (IRS-1) immunoprecipitates. Stimulation with IGF-I resulted in a dissociation of Crk protein from IRS-1. In contrast, the association of the related adaptor protein Grb2 with IRS-1 was enhanced by IGF-I stimulation. Similar results were obtained in stably transfected 293-Crk cells, which express both IRS-1 and the IRS-1-related signaling protein 4PS. In these cells, IRS-1 and 4PS both associated with Crk, and this association was also decreased by IGF-I treatment, whereas the association of Grb2 with IRS-1 and 4PS was enhanced by IGF-I. Overexpression of Crk also enhanced IGF-I-induced mitogenesis of NIH-3T3 cells, as measured by [3H]thymidine incorporation. The levels of IGF-I-induced mitogenesis were proportional to the level of Crk expression. These results suggest that Crk is a positive effector of IGF-I signaling, and may mediate its effects via interaction with IRS-1 and/or 4PS.

  20. Lactate Dehydrogenase Undergoes a Substantial Structural Change to Bind its Substrate

    PubMed Central

    Qiu, Linlin; Gulotta, Miriam; Callender, Robert

    2007-01-01

    Employing temperature-jump relaxation spectroscopy, we investigate the kinetics and thermodynamics of the formation of a very early ternary binding intermediate formed when lactate dehydrogenase (LDH) binds a substrate mimic on its way to forming the productive LDH/NADH·substrate Michaelis complex. Temperature-jump scans show two distinct submillisecond processes are involved in the formation of this ternary binding intermediate, called the encounter complex here. The on-rate of the formation of the encounter complex from LDH/NADH with oxamate (a substrate mimic) is determined as a function of temperature and in the presence of small concentrations of a protein destabilizer (urea) and protein stabilizer (TMAO). It shows a strong temperature dependence with inverse Arrhenius behavior and a temperature-dependent enthalpy (heat capacity of 610 ± 84 cal/Mol K), is slowed in the presence of TMAO and speeded up in the presence of urea. These results suggest that LDH/NADH occupies a range of conformations, some competent to bind substrate (open structure; a minority population) and others noncompetent (closed), in fast equilibrium with each other in accord with a select fit model of binding. From the thermodynamic results, the two species differ in the rearrangement of low energy hydrogen bonds as would arise from changes in internal hydrogen bonding and/or increases in the solvation of the protein structure. The binding-competent species can bind ligand at or very near diffusion-limited speeds, suggesting that the binding pocket is substantially exposed to solvent in these species. This would be in contrast to the putative closed structure where the binding pocket resides deep within the protein interior. PMID:17483169

  1. Substrate texture affects female cricket walking response to male calling song

    NASA Astrophysics Data System (ADS)

    Sarmiento-Ponce, E. J.; Sutcliffe, M. P. F.; Hedwig, B.

    2018-03-01

    Field crickets are extensively used as a model organism to study female phonotactic walking behaviour, i.e. their attraction to the male calling song. Laboratory-based phonotaxis experiments generally rely on arena or trackball-based settings; however, no attention has been paid to the effect of substrate texture on the response. Here, we tested phonotaxis in female Gryllus bimaculatus, walking on trackballs machined from methyl-methacrylate foam with different cell sizes. Surface height variations of the trackballs, due to the cellular composition of the material, were measured with profilometry and characterized as smooth, medium or rough, with roughness amplitudes of 7.3, 16 and 180 µm. Female phonotaxis was best on a rough and medium trackball surface, a smooth surface resulted in a significant lower phonotactic response. Claws of the cricket foot were crucial for effective walking. Females insert their claws into the surface pores to allow mechanical interlocking with the substrate texture and a high degree of attachment, which cannot be established on smooth surfaces. These findings provide insight to the biomechanical basis of insect walking and may inform behavioural studies that the surface texture on which walking insects are tested is crucial for the resulting behavioural response.

  2. Aptamer Recognition of Multiplexed Small-Molecule-Functionalized Substrates.

    PubMed

    Nakatsuka, Nako; Cao, Huan H; Deshayes, Stephanie; Melkonian, Arin Lucy; Kasko, Andrea M; Weiss, Paul S; Andrews, Anne M

    2018-05-31

    Aptamers are chemically synthesized oligonucleotides or peptides with molecular recognition capabilities. We investigated recognition of substrate-tethered small-molecule targets, using neurotransmitters as examples, and fluorescently labeled DNA aptamers. Substrate regions patterned via microfluidic channels with dopamine or L-tryptophan were selectively recognized by previously identified dopamine or L-tryptophan aptamers, respectively. The on-substrate dissociation constant determined for the dopamine aptamer was comparable to, though slightly greater than the previously determined solution dissociation constant. Using pre-functionalized neurotransmitter-conjugated oligo(ethylene glycol) alkanethiols and microfluidics patterning, we produced multiplexed substrates to capture and to sort aptamers. Substrates patterned with L-DOPA, L-DOPS, and L-5-HTP enabled comparison of the selectivity of the dopamine aptamer for different targets via simultaneous determination of in situ binding constants. Thus, beyond our previous demonstrations of recognition by protein binding partners (i.e., antibodies and G-protein-coupled receptors), strategically optimized small-molecule-functionalized substrates show selective recognition of nucleic acid binding partners. These substrates are useful for side-by-side target comparisons, and future identification and characterization of novel aptamers targeting neurotransmitters or other important small-molecules.

  3. The C-Terminal Amino Acid of the MHC-I Heavy Chain Is Critical for Binding to Derlin-1 in Human Cytomegalovirus US11-Induced MHC-I Degradation

    PubMed Central

    Cho, Sunglim; Kim, Bo Young; Ahn, Kwangseog; Jun, Youngsoo

    2013-01-01

    Derlin-1 plays a critical role in endoplasmic reticulum-associated protein degradation (ERAD) of a particular subset of proteins. Although it is generally accepted that Derlin-1 mediates the export of ERAD substrates from the ER to the cytosol, little is known about how Derlin-1 interacts with these substrates. Human cytomegalovirus (HCMV) US11 exploits Derlin-1-dependent ERAD to degrade major histocompatibility complex class I (MHC-I) molecules and evade immune surveillance. US11 requires the cytosolic tail of the MHC-I heavy chain to divert MHC-I molecules into the ERAD pathway for degradation; however, the underlying mechanisms remain unknown. Here, we show that the cytosolic tail of the MHC-I heavy chain, although not required for interaction with US11, is required for tight binding to Derlin-1 and thus for US11-induced dislocation of the MHC-I heavy chain to the cytosol for proteasomal degradation. Surprisingly, deletion of a single C-terminal amino acid from the cytosolic tail disrupted the interaction between MHC-I molecules and Derlin-1, rendering mutant MHC-I molecules resistant to US11-induced degradation. Consistently, deleting the C-terminal cytosolic region of Derlin-1 prevented it from binding to MHC-I molecules. Taken together, these results suggest that the cytosolic region of Derlin-1 is involved in ERAD substrate binding and that this interaction is critical for the Derlin-1-mediated dislocation of the MHC-I heavy chain to the cytosol during US11-induced MHC-I degradation. PMID:23951315

  4. The C-terminal amino acid of the MHC-I heavy chain is critical for binding to Derlin-1 in human cytomegalovirus US11-induced MHC-I degradation.

    PubMed

    Cho, Sunglim; Kim, Bo Young; Ahn, Kwangseog; Jun, Youngsoo

    2013-01-01

    Derlin-1 plays a critical role in endoplasmic reticulum-associated protein degradation (ERAD) of a particular subset of proteins. Although it is generally accepted that Derlin-1 mediates the export of ERAD substrates from the ER to the cytosol, little is known about how Derlin-1 interacts with these substrates. Human cytomegalovirus (HCMV) US11 exploits Derlin-1-dependent ERAD to degrade major histocompatibility complex class I (MHC-I) molecules and evade immune surveillance. US11 requires the cytosolic tail of the MHC-I heavy chain to divert MHC-I molecules into the ERAD pathway for degradation; however, the underlying mechanisms remain unknown. Here, we show that the cytosolic tail of the MHC-I heavy chain, although not required for interaction with US11, is required for tight binding to Derlin-1 and thus for US11-induced dislocation of the MHC-I heavy chain to the cytosol for proteasomal degradation. Surprisingly, deletion of a single C-terminal amino acid from the cytosolic tail disrupted the interaction between MHC-I molecules and Derlin-1, rendering mutant MHC-I molecules resistant to US11-induced degradation. Consistently, deleting the C-terminal cytosolic region of Derlin-1 prevented it from binding to MHC-I molecules. Taken together, these results suggest that the cytosolic region of Derlin-1 is involved in ERAD substrate binding and that this interaction is critical for the Derlin-1-mediated dislocation of the MHC-I heavy chain to the cytosol during US11-induced MHC-I degradation.

  5. Method for forming a nano-textured substrate

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Jeong, Sangmoo; Hu, Liangbing; Cui, Yi

    A method for forming a nano-textured surface on a substrate is disclosed. An illustrative embodiment of the present invention comprises dispensing of a nanoparticle ink of nanoparticles and solvent onto the surface of a substrate, distributing the ink to form substantially uniform, liquid nascent layer of the ink, and enabling the solvent to evaporate from the nanoparticle ink thereby inducing the nanoparticles to assemble into an texture layer. Methods in accordance with the present invention enable rapid formation of large-area substrates having a nano-textured surface. Embodiments of the present invention are well suited for texturing substrates using high-speed, large scale,more » roll-to-roll coating equipment, such as that used in office product, film coating, and flexible packaging applications. Further, embodiments of the present invention are well suited for use with rigid or flexible substrates.« less

  6. Methods to introduce sub-micrometer, symmetry-breaking surface corrugation to silicon substrates to increase light trapping

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Han, Sang Eon; Hoard, Brittany R.; Han, Sang M.

    Provided is a method for fabricating a nanopatterned surface. The method includes forming a mask on a substrate, patterning the substrate to include a plurality of symmetry-breaking surface corrugations, and removing the mask. The mask includes a pattern defined by mask material portions that cover first surface portions of the substrate and a plurality of mask space portions that expose second surface portions of the substrate, wherein the plurality of mask space portions are arranged in a lattice arrangement having a row and column, and the row is not oriented parallel to a [110] direction of the substrate. The patterningmore » the substrate includes anisotropically removing portions of the substrate exposed by the plurality of spaces.« less

  7. Reassessing SERS enhancement factors: using thermodynamics to drive substrate design.

    PubMed

    Guicheteau, J A; Tripathi, A; Emmons, E D; Christesen, S D; Fountain, Augustus W

    2017-12-04

    Over the past 40 years fundamental and application research into Surface-Enhanced Raman Scattering (SERS) has been explored by academia, industry, and government laboratories. To date however, SERS has achieved little commercial success as an analytical technique. Researchers are tackling a variety of paths to help break through the commercial barrier by addressing the reproducibility in both the SERS substrates and SERS signals as well as continuing to explore the underlying mechanisms. To this end, investigators use a variety of methodologies, typically studying strongly binding analytes such as aromatic thiols and azarenes, and report SERS enhancement factor calculations. However a drawback of the traditional SERS enhancement factor calculation is that it does not yield enough information to understand substrate reproducibility, application potential with another analyte, or the driving factors behind the molecule-metal interaction. Our work at the US Army Edgewood Chemical Biological Center has focused on these questions and we have shown that thermodynamic principles play a key role in the SERS response and are an essential factor in future designs of substrates and applications. This work will discuss the advantages and disadvantages of various experimental techniques used to report SERS enhancement with planar SERS substrates and present our alternative SERS enhancement value. We will report on three types of analysis scenarios that all yield different information concerning the effectiveness of the SERS substrate, practical application of the substrate, and finally the thermodynamic properties of the substrate. We believe that through this work a greater understanding for designing substrates will be achieved, one that is based on both thermodynamic and plasmonic properties as opposed to just plasmonic properties. This new understanding and potential change in substrate design will enable more applications for SERS based methodologies including targeting

  8. Rectification of Ion Current in Nanopipettes by External Substrates

    PubMed Central

    Shi, Wenqing; Baker, Lane A.

    2014-01-01

    We describe ion distribution and the current-voltage (i-V) response of nanopipettes at different probe-to-substrate distances (Dps) as simulated by finite-element methods. Results suggest electrostatic interactions between a charged substrate and the nanopipette dominate electrophoretic ion transport through the nanopipette when Dps is within one order of magnitude of the Debye length (~10 nm for a 1 mM solution as employed in the simulation). Ion current rectification (ICR) and permselectivity associated with a neutral or charged nanopipette can be reversibly enhanced or reduced dependent on Dps, charge polarity and charge density (σ) of the substrate. Regulation of nanopipette current is a consequence of the enrichment or depletion of ions within the nanopipette interior which influences conductivity of the nanopipette. When the external substrate is less negatively charged than the nanopipette, the substrate first reduces, and then enhances the ICR as Dps decreases. Surprisingly, both experimental and simulated data show that a neutral substrate was also able to reduce and reverse the ICR of a slightly negatively charged nanopipette. Simulated results ascribe such effects to the elimination of ion depletion within the nanopipette at positive potentials. PMID:24200344

  9. Rectification of ion current in nanopipettes by external substrates.

    PubMed

    Sa, Niya; Lan, Wen-Jie; Shi, Wenqing; Baker, Lane A

    2013-12-23

    We describe ion distribution and the current-voltage (i-V) response of nanopipettes at different probe-to-substrate distances (Dps) as simulated by finite-element methods. Results suggest electrostatic interactions between a charged substrate and the nanopipette dominate electrophoretic ion transport through the nanopipette when Dps is within 1 order of magnitude of the Debye length (∼10 nm for a 1 mM solution as employed in the simulation). Ion current rectification (ICR) and permselectivity associated with a neutral or charged nanopipette can be reversibly enhanced or reduced dependent on Dps, charge polarity, and charge density (σ) of the substrate. Regulation of nanopipette current is a consequence of the enrichment or depletion of ions within the nanopipette interior, which influences conductivity of the nanopipette. When the external substrate is less negatively charged than the nanopipette, the substrate first reduces, and then enhances the ICR as Dps decreases. Surprisingly, both experimental and simulated data show that a neutral substrate was also able to reduce and reverse the ICR of a slightly negatively charged nanopipette. Simulated results ascribe such effects to the elimination of ion depletion within the nanopipette at positive potentials.

  10. Structure of tropinone reductase-II complexed with NADP+ and pseudotropine at 1.9 A resolution: implication for stereospecific substrate binding and catalysis.

    PubMed

    Yamashita, A; Kato, H; Wakatsuki, S; Tomizaki, T; Nakatsu, T; Nakajima, K; Hashimoto, T; Yamada, Y; Oda, J

    1999-06-15

    Tropinone reductase-II (TR-II) catalyzes the NADPH-dependent reduction of the carbonyl group of tropinone to a beta-hydroxyl group. The crystal structure of TR-II complexed with NADP+ and pseudotropine (psi-tropine) has been determined at 1.9 A resolution. A seven-residue peptide near the active site, disordered in the unliganded structure, is fixed in the ternary complex by participation of the cofactor and substrate binding. The psi-tropine molecule is bound in an orientation which satisfies the product configuration and the stereochemical arrangement toward the cofactor. The substrate binding site displays a complementarity to the bound substrate (psi-tropine) in its correct orientation. In addition, electrostatic interactions between the substrate and Glu156 seem to specify the binding position and orientation of the substrate. A comparison between the active sites in TR-II and TR-I shows that they provide different van der Waals surfaces and electrostatic features. These differences likely contribute to the correct binding mode of the substrates, which are in opposite orientations in TR-II and TR-I, and to different reaction stereospecificities. The active site structure in the TR-II ternary complex also suggests that the arrangement of the substrate, cofactor, and catalytic residues is stereoelectronically favorable for the reaction.

  11. A Xylenol Orange-Based Screening Assay for the Substrate Specificity of Flavin-Dependent para-Phenol Oxidases.

    PubMed

    Ewing, Tom A; van Noord, Aster; Paul, Caroline E; van Berkel, Willem J H

    2018-01-14

    Vanillyl alcohol oxidase (VAO) and eugenol oxidase (EUGO) are flavin-dependent enzymes that catalyse the oxidation of para -substituted phenols. This makes them potentially interesting biocatalysts for the conversion of lignin-derived aromatic monomers to value-added compounds. To facilitate their biocatalytic exploitation, it is important to develop methods by which variants of the enzymes can be rapidly screened for increased activity towards substrates of interest. Here, we present the development of a screening assay for the substrate specificity of para -phenol oxidases based on the detection of hydrogen peroxide using the ferric-xylenol orange complex method. The assay was used to screen the activity of VAO and EUGO towards a set of twenty-four potential substrates. This led to the identification of 4-cyclopentylphenol as a new substrate of VAO and EUGO and 4-cyclohexylphenol as a new substrate of VAO. Screening of a small library of VAO and EUGO active-site variants for alterations in their substrate specificity led to the identification of a VAO variant (T457Q) with increased activity towards vanillyl alcohol (4-hydroxy-3-methoxybenzyl alcohol) and a EUGO variant (V436I) with increased activity towards chavicol (4-allylphenol) and 4-cyclopentylphenol. This assay provides a quick and efficient method to screen the substrate specificity of para -phenol oxidases, facilitating the enzyme engineering of known para- phenol oxidases and the evaluation of the substrate specificity of novel para -phenol oxidases.

  12. Ribbed electrode substrates

    DOEpatents

    Breault, Richard D.; Goller, Glen J.

    1983-01-01

    A ribbed substrate for an electrochemical cell electrode is made from a mixture of carbon fibers and carbonizable resin and has a mean pore size in the ribs which is 60-75% of the mean pore size of the web portions of the substrate which interconnect the ribs. Preferably the mean pore size of the web portion is 25-45 microns; and, if the substrate includes edge seals parallel to the ribs, the edge seals preferably have a mean pore size no greater than about ten microns. Most preferably the substrate has the same ratio of carbon fibers to polymeric carbon in all areas, including the ribs, webs, and edge seals. A substrate according to the present invention will have better overall performance than prior art substrates and minimizes the substrate thickness required for the substrate to perform all its functions well.

  13. Interactions between Casein Kinase Iε (CKIε) and Two Substrates from Disparate Signaling Pathways Reveal Mechanisms for Substrate-Kinase Specificity

    PubMed Central

    Dahlberg, Caroline Lund; Nguyen, Elizabeth Z.; Goodlett, David; Kimelman, David

    2009-01-01

    Background 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 CKIε and two substrates from different signaling pathways. Methodology/Principal Findings CKIε, but not CKIα, 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 CKIα's kinase domain prevent Disheveled and Period from binding. We also show that the unique C-terminus of CKIε does not determine Dishevelled's and Period's preference for CKIε nor is it essential for binding, but instead plays an auxillary role in stabilizing the interactions of CKIε with its substrates. We demonstrate that autophosphorylation of CKIε'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. Conclusions/Significance The biochemical interactions between CKIε and Disheveled, Period, and its own C-terminus lead to models that explain CKIε's specificity and regulation. PMID:19274088

  14. Hsl7 is a substrate-specific type II protein arginine methyltransferase in yeast

    PubMed Central

    Sayegh, Joyce; Clarke, Steven G.

    2008-01-01

    The Saccharomyces cerevisiae protein Hsl7 is a regulator of the Swe1 protein kinase in cell cycle checkpoint control. Hsl7 has been previously described as a type III protein arginine methyltransferase, catalyzing the formation of ω-monomethylarginine residues on non-physiological substrates. However, we show here that Hsl7 can also display type II activity, generating symmetric dimethylarginine residues on calf thymus histone H2A. Symmetric dimethylation is only observed when enzyme and the methyl-accepting substrate were incubated for extended times. We confirmed the Hsl7-dependent formation of symmetric dimethylarginine by amino acid analysis and thin layer chromatography with wild type and mutant recombinant enzymes expressed from both bacteria and yeast. This result is significant because no type II activity has been previously demonstrated in S. cerevisiae. We also show that Hsl7 has little or no activity on GST-GAR, a commonly used substrate for protein arginine methyltransferases, and only minimal activity on myelin basic protein. This enzyme thus may only recognize only a small subset of potential substrate proteins in yeast, in contrast to the situation with Rmt1, the major type I methyltransferase. PMID:18515076

  15. Method of making carbon nanotubes on a substrate

    DOEpatents

    Gao, Yufei; Liu, Jun

    2006-03-14

    The present invention includes carbon nanotubes whose hollow cores are 100% filled with conductive filler. The carbon nanotubes are in uniform arrays on a conductive substrate and are well-aligned and can be densely packed. The uniformity of the carbon nanotube arrays is indicated by the uniform length and diameter of the carbon nanotubes, both which vary from nanotube to nanotube on a given array by no more than about 5%. The alignment of the carbon nanotubes is indicated by the perpendicular growth of the nanotubes from the substrates which is achieved in part by the simultaneous growth of the conductive filler within the hollow core of the nanotube and the densely packed growth of the nanotubes. The present invention provides a densely packed carbon nanotube growth where each nanotube is in contact with at least one nearest-neighbor nanotube. The substrate is a conductive substrate coated with a growth catalyst, and the conductive filler can be single crystals of carbide formed by a solid state reaction between the substrate material and the growth catalyst. The present invention further provides a method for making the filled carbon nanotubes on the conductive substrates. The method includes the steps of depositing a growth catalyst onto the conductive substrate as a prepared substrate, creating a vacuum within a vessel which contains the prepared substrate, flowing H2/inert (e.g. Ar) gas within the vessel to increase and maintain the pressure within the vessel, increasing the temperature of the prepared substrate, and changing the H2/Ar gas to ethylene gas such that the ethylene gas flows within the vessel. Additionally, varying the density and separation of the catalyst particles on the conductive substrate can be used to control the diameter of the nanotubes.

  16. Functional visual sensitivity to ultraviolet wavelengths in the Pileated Woodpecker (Dryocopus pileatus), and its influence on foraging substrate selection

    USGS Publications Warehouse

    O'Daniels, Sean T.; Kesler, Dylan C.; Mihail, Jeanne D.; Webb, Elisabeth B.; Werner, Scott J.

    2017-01-01

    Most diurnal birds are presumed visually sensitive to near ultraviolet (UV) wavelengths, however, controlled behavioral studies investigating UV sensitivity remain few. Although woodpeckers are important as primary cavity excavators and nuisance animals, published work on their visual systems is limited. We developed a novel foraging-based behavioral assay designed to test UV sensitivity in the Pileated Woodpecker (Dryocopus pileatus). We acclimated 21 wild-caught woodpeckers to foraging for frozen mealworms within 1.2 m sections of peeled cedar (Thuja spp.) poles. We then tested the functional significance of UV cues by placing frozen mealworms behind UV-reflective covers, UV-absorptive covers, or decayed red pine substrates within the same 1.2 m poles in independent experiments. Behavioral responses were greater toward both UV-reflective and UV-absorptive substrates in three experiments. Study subjects therefore reliably differentiated and attended to two distinct UV conditions of a foraging substrate. Cue-naïve subjects showed a preference for UV-absorptive substrates, suggesting that woodpeckers may be pre-disposed to foraging from such substrates. Behavioral responses were greater toward decayed pine substrates (UV-reflective) than sound pine substrates suggesting that decayed pine can be a useful foraging cue. The finding that cue-naïve subjects selected UV-absorbing foraging substrates has implications for ecological interactions of woodpeckers with fungi. Woodpeckers transport fungal spores, and communication methods analogous to those of plant-pollinator mutualisms (i.e. UV-absorbing patterns) may have evolved to support woodpecker-fungus mutualisms.

  17. Cell-Imprinted Substrates Modulate Differentiation, Redifferentiation, and Transdifferentiation.

    PubMed

    Bonakdar, Shahin; Mahmoudi, Morteza; Montazeri, Leila; Taghipoor, Mojtaba; Bertsch, Arnaud; Shokrgozar, Mohammad Ali; Sharifi, Shahriar; Majidi, Mohammad; Mashinchian, Omid; Hamrang Sekachaei, Mohammad; Zolfaghari, Pegah; Renaud, Philippe

    2016-06-08

    Differentiation of stem cells into mature cells through the use of physical approaches is of great interest. Here, we prepared smart nanoenvironments by cell-imprinted substrates based on chondrocytes, tenocytes, and semifibroblasts as templates and demonstrated their potential for differentiation, redifferentiation, and transdifferentiation. Analysis of shape and upregulation/downregulation of specific genes of stem cells, which were seeded on these cell-imprinted substrates, confirmed that imprinted substrates have the capability to induce specific shapes and molecular characteristics of the cell types that were used as templates for cell-imprinting. Interestingly, immunofluorescent staining of a specific protein in chondrocytes (i.e., collagen type II) confirmed that adipose-derived stem cells, semifibroblasts, and tenocytes can acquire the chondrocyte phenotype after a 14 day culture on chondrocyte-imprinted substrates. In summary, we propose that common polystyrene tissue culture plates can be replaced by this imprinting technique as an effective and promising way to regulate any cell phenotype in vitro with significant potential applications in regenerative medicine and cell-based therapies.

  18. Screening method for selecting semiconductor substrates having defects below a predetermined level in an oxide layer

    DOEpatents

    Warren, William L.; Vanheusden, Karel J. R.; Schwank, James R.; Fleetwood, Daniel M.; Shaneyfelt, Marty R.; Winokur, Peter S.; Devine, Roderick A. B.

    1998-01-01

    A method for screening or qualifying semiconductor substrates for integrated circuit fabrication. The method comprises the steps of annealing at least one semiconductor substrate at a first temperature in a defect-activating ambient (e.g. hydrogen, forming gas, or ammonia) for sufficient time for activating any defects within on oxide layer of the substrate; measuring a defect-revealing electrical characteristic of at least a portion of the oxide layer for determining a quantity of activated defects therein; and selecting substrates for which the quantity of activated defects is below a predetermined level. The defect-revealing electrical characteristic may be a capacitance-versus-voltage (C-V) characteristic or a current-versus-voltage (I-V) characteristic that is dependent on an electrical charge in the oxide layer generated by the activated defects. Embodiments of the present invention may be applied for screening any type of semiconductor substrate or wafer having an oxide layer formed thereon or therein. This includes silicon-on-insulator substrates formed by a separation by the implantation of oxygen (SIMOX) process or the bond and etch back silicon-on-insulator (BESOI) process, as well as silicon substrates having a thermal oxide layer or a deposited oxide layer.

  19. Charged/Polar-Residue Scanning of the Hydrophobic Face of Transmembrane Domain 9 of the Yeast Glutathione Transporter, Hgt1p, Reveals a Conformationally Critical Region for Substrate Transport

    PubMed Central

    Thakur, Anil; Bachhawat, Anand K.

    2015-01-01

    Unraveling the mechanistic workings of membrane transporters has remained a challenging task. We describe a novel strategy that involves subjecting the residues of the hydrophobic face of a transmembrane helix to a charged/polar scanning mutagenesis. TMD9 of the yeast glutathione transporter, Hgt1p, has been identified as being important in substrate binding, and two residues, F523 and Q526, are expected to line the substrate translocation channel while the other face is hydrophobic. The hydrophobic face of TMD9 helix consists of residues A509, V513, L517, L520, I524, and I528, and these were mutated to lysine, glutamine, and glutamic acid. Among the 16 charged mutants created, six were nonfunctional, revealing a surprising tolerance of charged residues in the hydrophobic part of TM helices. Furthermore, the only position that did not tolerate any charged residue was I524, proximal to the substrate binding residues. However, P525, also proximal to the substrate binding residues, did tolerate charged/polar residues, suggesting that mere proximity to the substrate binding residues was not the only factor. The I524K/E/Q mutants expressed well and localized correctly despite lacking any glutathione uptake capability. Isolation of suppressors for all nonfunctional mutants yielded second-site suppressors only for I524K and I524Q, and suppressors for these mutations appeared at G202K/I and G202K/Q, respectively. G202 is in the hydrophilic loop between TMD3 and TMD4. The results suggest that I524 in the hydrophobic face interacts with this region and is also in a conformationally critical region for substrate translocation. PMID:25784163

  20. A simple and efficient feeder-free culture system to up-scale iPSCs on polymeric material surface for use in 3D bioprinting.

    PubMed

    Wong, Chui-Wei; Chen, You-Tzung; Chien, Chung-Liang; Yu, Tien-Yu; Rwei, Syang-Peng; Hsu, Shan-Hui

    2018-01-01

    The 3D bioprinting and cell/tissue printing techniques open new possibilities for future applications. To facilitate the 3D bioprinting process, a large amount of living cells are required. Induced pluripotent stem cells (iPSCs) represent a promising cell source for bioprinting. However, the maintenance and expansion of undifferentiated iPSCs are expensive and time consuming. Therefore, in this study a culture method to obtain a sufficient amount of healthy and undifferentiated iPSCs in a short-term period was established. The iPSCs could be passaged for twice on tissue culture polystyrene (TCPS) dish with the conditional medium and could adapt to the feeder-free environment. Feeder-free dishes were further prepared from chitosan, chitosan-hyaluronan, silk fibroin, and polyurethane (PU1 and PU2) two-dimensional substrates. The iPSCs cultured on the chitosan substrates showed a higher proliferation rate without losing the stemness feature. Among the different materials, PU2 could be prepared as a thermoresponsive hydrogel, which was a potential ink for 3D bioprinting. The iPSCs cultured on PU2 substrates well survived when further embedded in PU2 hydrogel. Moreover, PU2 hydrogel printed with iPSCs remained structural integrity. The use of PU2 hydrogel to embed iPSCs reduced the injury to iPSCs by shear stress. These results indicate that iPSCs could be expanded on chitosan or PU2 membranes without the feeder layer and then printed in PU2 hydrogel. The combination of these steps could offer a new possibility for future applications of iPSC-based 3D bioprinting in tissue engineering. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Coral settlement onto Halimeda opuntia: a fatal attraction to an ephemeral substrate?

    NASA Astrophysics Data System (ADS)

    Nugues, Maggy M.; Szmant, Alina M.

    2006-11-01

    Degraded reefs with a high abundance of macroalgae usually also have low densities of coral recruits. Few studies, however, have examined whether these algae affect coral larval settlement. This study demonstrates, experimentally, that larvae of the Caribbean coral Favia fragrum can settle on the green alga Halimeda opuntia even when another substrate more suitable for settlement is present. Larval settlement onto experimental substrates was quantified under three treatments: rubble only, rubble plus plastic algal mimic, and rubble plus live H. opuntia. Similar total larval settlement was observed in all treatments. No larvae settled on the algal mimic, but total settlement was similar on the rubble in the first two treatments, showing that the rubble alone offered sufficient substrate for high settlement success. About half the larvae in the live algal treatment settled on H. opuntia instead of on the rubble, showing that larvae did not reject this substrate as they did the algal mimic. This result raises the possibility that corals will settle on some macroalgae when their abundance is high. Most macroalgae, including H. opuntia, are ephemeral substrates unsuitable for post-settlement survival. Such unexpected settlement may therefore have significant consequences for coral recruitment success on algal-dominated reefs.

  2. A combined cell based approach to identify P-glycoprotein substrates and inhibitors in a single assay.

    PubMed

    Balimane, Praveen V; Chong, Saeho

    2005-09-14

    The objective of this project was to develop a cell based in vitro experimental procedure that can differentiate P-glycoprotein (P-gp) substrates from inhibitors in a single assay. Caco-2 cells grown to confluency on 12-well Transwell were used for this study. The efflux permeability (B to A) of P-gp specific probe (viz., digoxin) in the presence of test compounds (e.g. substrates, inhibitors and non-substrates of P-gp) was monitored, and the influx permeability (A to B) of test compounds was evaluated after complete P-gp blockade. Radiolabelled digoxin was added on the basolateral side with buffer on the apical side. The digoxin concentration appearing on the apical side represents digoxin efflux permeability during the control phase (0-1 h period). After 1 h, a test compound (10 microM) was added on the apical side. The reduced efflux permeability of digoxin suggests that the added test compound is an inhibitor. The influx permeability of test compound is also determined during the 1-2 h study period by measuring the concentration of the test compound in the basolateral side. At the end of 2 h, a potent P-gp inhibitor (GF120918) was added. The increased influx permeability of test compound during the 2-3 h incubation period indicates that the added test compound is a substrate. Samples were taken from both sides at the end of 1-3 h and the concentrations of the test compounds and digoxin were quantitated. Digoxin efflux permeability remained unchanged when incubated with P-gp substrates (e.g., etoposide, rhodamine123, taxol). However, when a P-gp inhibitor was added to the apical side, the digoxin efflux (B to A permeability) was significantly reduced (ketoconazole=51% reduction) as expected. The influx permeability of substrates increased significantly (rhodamine123=70%, taxol=220%, digoxin=290%) after the P-gp inhibitor (GF120918) was introduced, whereas the influx permeability of P-gp inhibitor and non-substrates was not affected by GF120918. Thus, this

  3. The Use of Arbuscular Mycorrhizal Fungi to Improve Strawberry Production in Coir Substrate

    PubMed Central

    Robinson Boyer, Louisa; Feng, Wei; Gulbis, Natallia; Hajdu, Klara; Harrison, Richard J.; Jeffries, Peter; Xu, Xiangming

    2016-01-01

    Strawberry is an important fruit crop within the UK. To reduce the impact of soil-borne diseases and extend the production season, more than half of the UK strawberry production is now in substrate (predominantly coir) under protection. Substrates such as coir are usually depleted of microbes including arbuscular mycorrhizal fungi (AMF) and consequently the introduction of beneficial microbes is likely to benefit commercial cropping systems. Inoculating strawberry plants in substrate other than coir has been shown to increase plants tolerance to soil-borne pathogens and water stress. We carried out studies to investigate whether AMF could improve strawberry production in coir under low nitrogen input and regulated deficit irrigation. Application of AMF led to an appreciable increase in the size and number of class I fruit, especially under either deficient irrigation or low nitrogen input condition. However, root length colonization by AMF was reduced in strawberry grown in coir compared to soil and Terragreen. Furthermore, the appearance of AMF colonizing strawberry and maize roots grown in coir showed some physical differences from the structure in colonized roots in soil and Terragreen: the colonization structure appeared to be more compact and smaller in coir. PMID:27594859

  4. A facile method to align carbon nanotubes on polymeric membrane substrate

    PubMed Central

    Zhao, Haiyang; Zhou, Zhijun; Dong, Hang; Zhang, Lin; Chen, Huanlin; Hou, Lian

    2013-01-01

    The alignment of carbon nanotubes (CNT) is the fundamental requirement to ensure their excellent functions but seems to be desolated in recent years. A facile method, hot-press combined with peel-off (HPPO), is introduced here, through which CNT can be successfully vertically aligned on the polymeric membrane substrate. Shear force and mechanical stretch are proposed to be the main forces to align the tubes perpendicular to the substrate surface during the peel-off process. The alignment of CNT keeps its orientation in a thin hybrid membrane by dip-coating cellulose acetate dope solution. It is expected that the stable alignment of CNT by HPPO would contribute to the realization of its potential applications. PMID:24326297

  5. Forest litter crickets prefer higher substrate moisture for oviposition: Evidence from field and lab experiments

    PubMed Central

    Sperber, Carlos Frankl; Albeny-Simões, Daniel; Breaux, Jennifer Ann; Fianco, Marcos; Szinwelski, Neucir

    2017-01-01

    For insects, choosing a favorable oviposition site is a type of parental care, as far as it increases the fitness of its offspring. Niche theory predicts that crickets should show a bell-shaped oviposition response to substrate moisture. However, lab experiments with mole crickets showed a linear oviposition response to substrate moisture. Studies with the house cricket Acheta domesticus also showed a linear juvenile body growth response to water availability, thus adult ovipositing females should respond positively to substrate moisture. We used a field experiment to evaluate the relationship between oviposition preference and substrate moisture in forest litter-dwelling cricket species. We also evaluated oviposition responses to substrate moisture level in Ubiquepuella telytokous, the most abundant litter cricket species in our study area, using a laboratory study. We offered cotton substrate for oviposition which varied in substrate moisture level from zero (i.e., dry) to maximum water absorption capacity. We used two complementary metrics to evaluate oviposition preference: (i) presence or absence of eggs in each sampling unit as binary response variable, and (ii) number of eggs oviposited per sampling unit as count response variable. To test for non-linear responses, we adjusted generalized additive models (GAMM) with mixed effects. We found that both cricket oviposition probability and effort (i.e., number of eggs laid) increased linearly with substrate moisture in the field experiment, and for U. telytokous in the lab experiment. We discarded any non-linear responses. Our results demonstrate the importance of substrate moisture as an ecological niche dimension for litter crickets. This work bolsters knowledge of litter cricket life history association with moisture, and suggests that litter crickets may be particularly threatened by changes in climate that favor habitat drying. PMID:28977023

  6. Forest litter crickets prefer higher substrate moisture for oviposition: Evidence from field and lab experiments.

    PubMed

    de Farias-Martins, Fernando; Sperber, Carlos Frankl; Albeny-Simões, Daniel; Breaux, Jennifer Ann; Fianco, Marcos; Szinwelski, Neucir

    2017-01-01

    For insects, choosing a favorable oviposition site is a type of parental care, as far as it increases the fitness of its offspring. Niche theory predicts that crickets should show a bell-shaped oviposition response to substrate moisture. However, lab experiments with mole crickets showed a linear oviposition response to substrate moisture. Studies with the house cricket Acheta domesticus also showed a linear juvenile body growth response to water availability, thus adult ovipositing females should respond positively to substrate moisture. We used a field experiment to evaluate the relationship between oviposition preference and substrate moisture in forest litter-dwelling cricket species. We also evaluated oviposition responses to substrate moisture level in Ubiquepuella telytokous, the most abundant litter cricket species in our study area, using a laboratory study. We offered cotton substrate for oviposition which varied in substrate moisture level from zero (i.e., dry) to maximum water absorption capacity. We used two complementary metrics to evaluate oviposition preference: (i) presence or absence of eggs in each sampling unit as binary response variable, and (ii) number of eggs oviposited per sampling unit as count response variable. To test for non-linear responses, we adjusted generalized additive models (GAMM) with mixed effects. We found that both cricket oviposition probability and effort (i.e., number of eggs laid) increased linearly with substrate moisture in the field experiment, and for U. telytokous in the lab experiment. We discarded any non-linear responses. Our results demonstrate the importance of substrate moisture as an ecological niche dimension for litter crickets. This work bolsters knowledge of litter cricket life history association with moisture, and suggests that litter crickets may be particularly threatened by changes in climate that favor habitat drying.

  7. Measuring specificity in multi-substrate/product systems as a tool to investigate selectivity in vivo.

    PubMed

    Kuo, Yin-Ming; Henry, Ryan A; Andrews, Andrew J

    2016-01-01

    Multiple substrate enzymes present a particular challenge when it comes to understanding their activity in a complex system. Although a single target may be easy to model, it does not always present an accurate representation of what that enzyme will do in the presence of multiple substrates simultaneously. Therefore, there is a need to find better ways to both study these enzymes in complicated systems, as well as accurately describe the interactions through kinetic parameters. This review looks at different methods for studying multiple substrate enzymes, as well as explores options on how to most accurately describe an enzyme's activity within these multi-substrate systems. Identifying and defining this enzymatic activity should help clear the way to using in vitro systems to accurately predicting the behavior of multi-substrate enzymes in vivo. This article is part of a Special Issue entitled: Physiological Enzymology and Protein Functions. Copyright © 2015. Published by Elsevier B.V.

  8. A practical method to fabricate gold substrates for surface-enhanced Raman spectroscopy.

    PubMed

    Tantra, Ratna; Brown, Richard J C; Milton, Martin J T; Gohil, Dipak

    2008-09-01

    We describe a practical method of fabricating surface-enhanced Raman spectroscopy (SERS) substrates based on dip-coating poly-L-lysine derivatized microscope slides in a gold colloidal suspension. The use of only commercially available starting materials in this preparation is particularly advantageous, aimed at both reducing time and the inconsistency associated with surface modification of substrates. The success of colloid deposition has been demonstrated by scanning electron microscopy (SEM) and the corresponding SERS response (giving performance comparable to the corresponding traditional colloidal SERS substrates). Reproducibility was evaluated by conducting replicate measurements across six different locations on the substrate and assessing the extent of the variability (standard deviation values of spectral parameters: peak width and height), in response to either Rhodamine 6G or Isoniazid. Of particular interest is the observation of how some peaks in a given spectrum are more susceptible to data variability than others. For example, in a Rhodamine 6G SERS spectrum, spectral parameters of the peak at 775 cm(-1) were shown to have a relative standard deviation (RSD) % of <10%, while the peak at 1573 cm(-1) has a RSD of >or=10%. This observation is best explained by taking into account spectral variations that arise from the effect of a chemisorption process and the local nature of chemical enhancement mechanisms, which affects the enhancement of some spectral peaks but not others (analogous to resonant Raman phenomenon).

  9. Alteration of Substrate and Inhibitor Specificity of Feline Immunodeficiency Virus Protease

    PubMed Central

    Lin, Ying-Chuan; Beck, Zachary; Lee, Taekyu; Le, Van-Duc; Morris, Garrett M.; Olson, Arthur J.; Wong, Chi-Huey; Elder, John H.

    2000-01-01

    Feline immunodeficiency virus (FIV) protease is structurally very similar to human immunodeficiency virus (HIV) protease but exhibits distinct substrate and inhibitor specificities. We performed mutagenesis of subsite residues of FIV protease in order to define interactions that dictate this specificity. The I37V, N55M, M56I, V59I, and Q99V mutants yielded full activity. The I37V, N55M, V59I, and Q99V mutants showed a significant increase in activity against the HIV-1 reverse transcriptase/integrase and P2/nucleocapsid junction peptides compared with wild-type (wt) FIV protease. The I37V, V59I, and Q99V mutants also showed an increase in activity against two rapidly cleaved peptides selected by cleavage of a phage display library with HIV-1 protease. Mutations at Q54K, I98P, and L101I dramatically reduced activity. Mutants containing a I35D or I57G substitution showed no activity against either FIV or HIV substrates. FIV proteases all failed to cut HIV-1 matrix/capsid, P1/P6, P6/protease, and protease/reverse transcriptase junctions, indicating that none of the substitutions were sufficient to change the specificity completely. The I37V, N55M, M56I, V59I, and Q99V mutants, compared with wt FIV protease, all showed inhibitor specificity more similar to that of HIV-1 protease. The data also suggest that FIV protease prefers a hydrophobic P2/P2′ residue like Val over Asn or Glu, which are utilized by HIV-1 protease, and that S2/S2′ might play a critical role in distinguishing FIV and HIV-1 protease by specificity. The findings extend our observations regarding the interactions involved in substrate binding and aid in the development of broad-based inhibitors. PMID:10775609

  10. Removing bonded skin from a substrate

    NASA Technical Reports Server (NTRS)

    Chartier, E. N.

    1980-01-01

    Metal skin is peeled off like sardine-can cover with key. Method is useful in removing bonded skins from any substrate where substrate is strong enough not to buckle or tear when bonded skin is rolled free. Also, it is useful for removing sections of damaged skin where bladders of other equipment below substrate might be damaged if saw or router were used to cut completely through skin.

  11. Electric field induced microstructures in thin films on physicochemically heterogeneous and patterned substrates.

    PubMed

    Srivastava, Samanvaya; Reddy, P Dinesh Sankar; Wang, Cindy; Bandyopadhyay, Dipankar; Sharma, Ashutosh

    2010-05-07

    We study by nonlinear simulations the electric field induced pattern formation in a thin viscous film resting on a topographically or chemically patterned substrate. The thin film microstructures can be aligned to the substrate patterns within a window of parameters where the spinodal length scale of the field induced instability is close to the substrate periodicity. We investigate systematically the change in the film morphology and order when (i) the substrate pattern periodicity is varied at a constant film thickness and (ii) the film thickness is varied at a constant substrate periodicity. Simulations show two distinct pathway of evolution when the substrate-topography changes from protrusions to cavities. The isolated substrate defects generate locally ordered ripplelike structures distinct from the structures on a periodically patterned substrate. In the latter case, film morphology is governed by a competition between the pattern periodicity and the length scale of instability. Relating the thin film morphologies to the underlying substrate pattern has implications for field induced patterning and robustness of inter-interface pattern transfer, e.g., coding-decoding of information printed on a substrate.

  12. BIOMASS, OLEATE, AND OTHER POSSIBLE SUBSTRATES FOR CHLOROETHENE REDUCTIVE DEHALOGENATION. (R825689C084)

    EPA Science Inventory

    Abstract

    Comparative studies were conducted with benzoate, propionate, oleate, tetrabutyl orthosilicate (TBOS), and biomass as substrates for dehalogenation of <i>cis>-1,2-dichloroethene (cDCE). All five substrates supported dehalogenation. Sufficient calcium was re...

  13. Life-history, substrate choice and Cytochrome Oxidase I variations in sandy beach peracaridans along the Rio de la Plata estuary

    NASA Astrophysics Data System (ADS)

    Fanini, L.; Zampicinini, G.; Tsigenopoulos, C. S.; Barboza, F. R.; Lozoya, J. P.; Gómez, J.; Celentano, E.; Lercari, D.; Marchetti, G. M.; Defeo, O.

    2017-03-01

    Life-history, substrate choice and Cytochrome Oxidase I (COI) sequences were analysed in populations of two peracaridans, the supralittoral talitrid Atlantorchestoidea brasiliensis and the intertidal cirolanid Excirolana armata. Three populations of each species, from beaches with similar grain size and located at different points along the natural gradient generated by the Rio de la Plata estuary were analysed. Abundance of E. armata increased with distance from the estuary, while the opposite trend was observed for A. brasiliensis. The proportion of females decreased towards high salinities for both species, significantly for E. armata. A test on substrate salinity preference revealed the absence of patterns due to active choice in E. armata. By contrast, A. brasiliensis showed no preference for the population closer to the estuary, while individuals from the other two sites significantly preferred high salinity substrates. Mitochondrial COI sequences were obtained from A. brasiliensis specimens tested for behaviour. Sequence analysis showed the population from the intermediate site to differ significantly from the other two. No significant genetic differentiation was instead found between populations from the two most distant sites, nor between individuals that expressed different salinity preference. Results showed that diverse sets of traits at the population level enable sandy beach species to cope with local environmental changes: life-history and behavioural traits appear to change in response to different ecological conditions, and, in the case of A brasiliensis, independently of the population structure inferred from COI sequence variation. Information from multiple traits allowed detection of population profiles, highlighting the relevance of multidisciplinary information and the concurrent analysis of field data and laboratory experiments, to detect responses of resident biota to environmental changes.

  14. A potent peptidomimetic inhibitor of botulinum neurotoxin serotype A has a very different conformation than SNAP-25 substrate.

    PubMed

    Zuniga, Jorge E; Schmidt, James J; Fenn, Timothy; Burnett, James C; Araç, Demet; Gussio, Rick; Stafford, Robert G; Badie, Shirin S; Bavari, Sina; Brunger, Axel T

    2008-10-08

    Botulinum neurotoxin serotype A is the most lethal of all known toxins. Here, we report the crystal structure, along with SAR data, of the zinc metalloprotease domain of BoNT/A bound to a potent peptidomimetic inhibitor (K(i)=41 nM) that resembles the local sequence of the SNAP-25 substrate. Surprisingly, the inhibitor adopts a helical conformation around the cleavage site, in contrast to the extended conformation of the native substrate. The backbone of the inhibitor's P1 residue displaces the putative catalytic water molecule and concomitantly interacts with the "proton shuttle" E224. This mechanism of inhibition is aided by residue contacts in the conserved S1' pocket of the substrate binding cleft and by the induction of new hydrophobic pockets, which are not present in the apo form, especially for the P2' residue of the inhibitor. Our inhibitor is specific for BoNT/A as it does not inhibit other BoNT serotypes or thermolysin.

  15. Evaluation of Fluorine-18-Labeled α1(I)-N-Telopeptide Analogs as Substrate-Based Radiotracers for PET Imaging of Melanoma-Associated Lysyl Oxidase.

    PubMed

    Kuchar, Manuela; Neuber, Christin; Belter, Birgit; Bergmann, Ralf; Lenk, Jens; Wodtke, Robert; Kniess, Torsten; Steinbach, Jörg; Pietzsch, Jens; Löser, Reik

    2018-01-01

    Accumulating evidence suggests an unequivocal role of lysyl oxidases as key players of tumor progression and metastasis, which renders this enzyme family highly attractive for targeted non-invasive functional imaging of tumors. Considering their function in matrix remodeling, malignant melanoma appears as particularly interesting neoplasia in this respect. For the development of radiotracers that enable PET imaging of the melanoma-associated lysyl oxidase activity, substrates derived from the type I collagen α1 N-telopeptide were labeled with fluorine-18 using N -succinimidyl 4-[ 18 F]fluorobenzoate ([ 18 F]SFB) as prosthetic reagent. With regards to potential crosslinking to tumor-associated collagen in vivo , their interaction with triple-helical type I collagen was studied by SPR. A mouse model of human melanoma was established on the basis of the A375 cell line, for which the expression of the oncologically relevant lysyl oxidase isoforms LOX and LOXL2 was demonstrated in Western blot and immunohistochemical experiments. The radiopharmacological profiles of the peptidic radiotracers were evaluated in normal rats and A375 melanoma-bearing mice by ex vivo metabolite analysis, whole-body biodistribution studies and dynamic PET imaging. Out of three 18 F-labeled telopeptide analogs, the one with the most favorable substrate properties has shown favorable tumor uptake and tumor-to-muscle ratio. Lysyl oxidase-mediated tumor uptake was proven by pharmacological inhibition using β-aminopropionitrile and by employing negative-control analogs of impeded or abolished targeting capability. The latter were obtained by substituting the lysine residue by ornithine and norleucine, respectively. Comparing the tumor uptake of the lysine-containing peptide with that of the non-functional analogs indicate the feasibility of lysyl oxidase imaging in melanoma using substrate-based radiotracers.

  16. Evaluation of Fluorine-18-Labeled α1(I)-N-Telopeptide Analogs as Substrate-Based Radiotracers for PET Imaging of Melanoma-Associated Lysyl Oxidase

    PubMed Central

    Kuchar, Manuela; Neuber, Christin; Belter, Birgit; Bergmann, Ralf; Lenk, Jens; Wodtke, Robert; Kniess, Torsten; Steinbach, Jörg; Pietzsch, Jens; Löser, Reik

    2018-01-01

    Accumulating evidence suggests an unequivocal role of lysyl oxidases as key players of tumor progression and metastasis, which renders this enzyme family highly attractive for targeted non-invasive functional imaging of tumors. Considering their function in matrix remodeling, malignant melanoma appears as particularly interesting neoplasia in this respect. For the development of radiotracers that enable PET imaging of the melanoma-associated lysyl oxidase activity, substrates derived from the type I collagen α1 N-telopeptide were labeled with fluorine-18 using N-succinimidyl 4-[18F]fluorobenzoate ([18F]SFB) as prosthetic reagent. With regards to potential crosslinking to tumor-associated collagen in vivo, their interaction with triple-helical type I collagen was studied by SPR. A mouse model of human melanoma was established on the basis of the A375 cell line, for which the expression of the oncologically relevant lysyl oxidase isoforms LOX and LOXL2 was demonstrated in Western blot and immunohistochemical experiments. The radiopharmacological profiles of the peptidic radiotracers were evaluated in normal rats and A375 melanoma-bearing mice by ex vivo metabolite analysis, whole-body biodistribution studies and dynamic PET imaging. Out of three 18F-labeled telopeptide analogs, the one with the most favorable substrate properties has shown favorable tumor uptake and tumor-to-muscle ratio. Lysyl oxidase-mediated tumor uptake was proven by pharmacological inhibition using β-aminopropionitrile and by employing negative-control analogs of impeded or abolished targeting capability. The latter were obtained by substituting the lysine residue by ornithine and norleucine, respectively. Comparing the tumor uptake of the lysine-containing peptide with that of the non-functional analogs indicate the feasibility of lysyl oxidase imaging in melanoma using substrate-based radiotracers.

  17. Assembly of synthetic cellulose I.

    PubMed

    Lee, J H; Brown, R M; Kuga, S; Shoda, S; Kobayashi, S

    1994-08-02

    Cellulose microfibrils with an electron diffraction pattern characteristic of crystalline native cellulose I have been assembled abiotically by means of a cellulase-catalyzed polymerization of beta-cellobiosyl fluoride substrate monomer in acetonitrile/acetate buffer. Substantial purification of the Trichoderma viride cellulase enzyme was found to be essential for the formation of the synthetic cellulose I allomorph. Assembly of synthetic cellulose I appears to be a result of a micellar aggregation of the partially purified enzyme and the substrate in an organic/aqueous solvent system favoring the alignment of glucan chains with the same polarity and extended chain conformation, resulting in crystallization to form the metastable cellulose I allomorph.

  18. The Effect of Substrate Microstructure on the Heat-Affected Zone Size in Sn-Zn Alloys Due to Adjoining Ni-Al Reactive Multilayer Foil Reaction

    DOE PAGES

    Hooper, R. J.; Adams, D. P.; Hirschfeld, D.; ...

    2015-08-05

    The rapid release of energy from reactive multilayer foils can create extreme local temperature gradients near substrate materials. To fully exploit the potential of these materials, a better understanding of the interaction between the substrate or filler material and the foil is needed. In particular, this work investigates how variations in local properties within the substrate (i.e. differences between properties in constituent phases) can affect heat transport into the substrate. Furthermore, this can affect the microstructural evolution observed within the substrate, which may affect the final joint properties. The effect of the initial substrate microstructure on microstructural evolution within themore » heat-affected zone is evaluated experimentally in two Sn-Zn alloys and numerical techniques are utilized to inform the analysis.« less

  19. The Effect of Substrate Topography on Direct Reprogramming of Fibroblasts to Induced Neurons

    PubMed Central

    Kulangara, Karina; Adler, Andrew F.; Wang, Hong; Chellappan, Malathi; Hammett, Ellen; Yasuda, Ryohei; Leong, Kam W.

    2014-01-01

    Cellular reprogramming holds tremendous potential for cell therapy and regenerative medicine. Recently, fibroblasts have been directly converted into induced neurons (iNs) by overexpression of the neuronal transcription factors Ascl1, Brn2 and Myt1L. Hypothesizing that cell-topography interactions could influence the fibroblast-to-neuron reprogramming process, we investigated the effects of various topographies on iNs produced by direct reprogramming. Final iN purity and conversion efficiency were increased on micrograting substrates. Neurite branching was increased on microposts and decreased on microgratings, with a simplified dendritic arbor characterized by the reduction of MAP2+ neurites. Neurite outgrowth increased significantly on various topographies. DNA microarray analysis detected 20 differentially expressed genes in iNs reprogrammed on smooth versus microgratings, and quantitative PCR (qPCR) confirmed the upregulation of Vip and downregulation of Thy1 and Bmp5 on microgratings. Electrophysiology and calcium imaging verified the functionality of these iNs. This study demonstrates the potential of applying topographical cues to optimize cellular reprogramming. PMID:24709523

  20. Design of a cylindrical LED substrate without radiator

    NASA Astrophysics Data System (ADS)

    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.

  1. Human and rat liver phenol sulfotransferase: structure-activity relationships for phenolic substrates.

    PubMed

    Campbell, N R; Van Loon, J A; Sundaram, R S; Ames, M M; Hansch, C; Weinshilboum, R

    1987-12-01

    Phenol sulfotransferase (PST) catalyzes the sulfate conjugation of many phenolic drugs. Human liver contains thermostable (TS) and thermolabile forms of PST. Ion exchange chromatography shows that two isozymes of TS PST (peaks I and II) are present in human liver preparations. Rat liver contains four forms of PST that can be separated by ion exchange chromatography. Quantitative structure-activity relationship (QSAR) analysis was used to study phenolic substrates for both human and rat liver PST. Thirty-six substituted phenols were tested as substrates for partially purified human liver TS PST peak I. QSAR analysis resulted in derivation of the following equation: log 1/Km = 0.92 (+/- 0.18)log P - 1.48 (+/- 0.38)MR'4 - 0.64 (+/- 0.41)MR3 + 1.04 (+/- 0.63)MR2 + 0.67(+/- 0.44) sigma- + 4.03 (+/- 0.42). In this equation Km is the Michaelis constant, P is the octanol-water partition coefficient, MR is the molar refractivity of substituents at the 2-, 3-, and 4-positions, and sigma- is the Hammett constant. Values of log 1/Km calculated with this equation were highly correlated with log 1/Km values (r = 0.950) that were observed experimentally. Nine phenols were also tested as substrates for partially purified human liver TS PST peak II. Log 1/Km values for these compounds were significantly correlated for the two isozymes of TS PST (r = 0.992, p less than 0.001). QSAR analysis was also used to derive equations that described the behavior of phenolic substrates for rat liver PST forms I and II. These equations differed substantially from the equation derived for compounds tested with human liver TS PST peak I. Therefore, the characteristics of the active sites of human liver TS PST peak I and rat liver PST forms I and II appear to differ. Application of these equations may make it possible to predict Km values of phenolic substrates for human liver TS PST and for rat liver PST forms I and II.

  2. Single crystalline CH 3NH 3PbI 3 self-grown on FTO/TiO 2 substrate for high efficiency perovskite solar cells

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Zhao, Jinjin; Kong, Guoli; Chen, Shulin

    In this work, we developed an innovative approach to self-grow single crystalline CH 3NH 3PbI 3 directly on polycrystalline FTO/TiO 2 substrate, with which n-i-p type of perovskite solar cells were fabricated. The single crystalline nature of CH 3NH 3PbI 3 has been confirmed by X-ray diffraction and high resolution transmission electron microscopy, and it is observed that they possess smaller optic band gap and longer carrier life time. Highly efficient charge extractions occur at the interface between electron collecting TiO 2 and photo-harvesting CH 3NH 3PbI 3, resulting in a maximum short-circuit current density of 24.40 mA/cm 2. Themore » champion cell possesses a photovoltaic conversion efficiency of 8.78%, and there are still substantial room for further improvement, making it promising for the perovskite solar cell applications.« less

  3. Single crystalline CH 3NH 3PbI 3 self-grown on FTO/TiO 2 substrate for high efficiency perovskite solar cells

    DOE PAGES

    Zhao, Jinjin; Kong, Guoli; Chen, Shulin; ...

    2017-08-21

    In this work, we developed an innovative approach to self-grow single crystalline CH 3NH 3PbI 3 directly on polycrystalline FTO/TiO 2 substrate, with which n-i-p type of perovskite solar cells were fabricated. The single crystalline nature of CH 3NH 3PbI 3 has been confirmed by X-ray diffraction and high resolution transmission electron microscopy, and it is observed that they possess smaller optic band gap and longer carrier life time. Highly efficient charge extractions occur at the interface between electron collecting TiO 2 and photo-harvesting CH 3NH 3PbI 3, resulting in a maximum short-circuit current density of 24.40 mA/cm 2. Themore » champion cell possesses a photovoltaic conversion efficiency of 8.78%, and there are still substantial room for further improvement, making it promising for the perovskite solar cell applications.« less

  4. Optically controlled electrophoresis with a photoconductive substrate

    NASA Astrophysics Data System (ADS)

    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.

  5. Functional visual sensitivity to ultraviolet wavelengths in the Pileated Woodpecker (Dryocopus pileatus), and its influence on foraging substrate selection.

    PubMed

    O'Daniels, Sean T; Kesler, Dylan C; Mihail, Jeanne D; Webb, Elisabeth B; Werner, Scott J

    2017-05-15

    Most diurnal birds are presumed visually sensitive to near ultraviolet (UV) wavelengths, however, controlled behavioral studies investigating UV sensitivity remain few. Although woodpeckers are important as primary cavity excavators and nuisance animals, published work on their visual systems is limited. We developed a novel foraging-based behavioral assay designed to test UV sensitivity in the Pileated Woodpecker (Dryocopus pileatus). We acclimated 21 wild-caught woodpeckers to foraging for frozen mealworms within 1.2m sections of peeled cedar (Thuja spp.) poles. We then tested the functional significance of UV cues by placing frozen mealworms behind UV-reflective covers, UV-absorptive covers, or decayed red pine substrates within the same 1.2m poles in independent experiments. Behavioral responses were greater toward both UV-reflective and UV-absorptive substrates in three experiments. Study subjects therefore reliably differentiated and attended to two distinct UV conditions of a foraging substrate. Cue-naïve subjects showed a preference for UV-absorptive substrates, suggesting that woodpeckers may be pre-disposed to foraging from such substrates. Behavioral responses were greater toward decayed pine substrates (UV-reflective) than sound pine substrates suggesting that decayed pine can be a useful foraging cue. The finding that cue-naïve subjects selected UV-absorbing foraging substrates has implications for ecological interactions of woodpeckers with fungi. Woodpeckers transport fungal spores, and communication methods analogous to those of plant-pollinator mutualisms (i.e. UV-absorbing patterns) may have evolved to support woodpecker-fungus mutualisms. Published by Elsevier Inc.

  6. Extracted sweet corn tassels as a renewable alternative to peat in greenhouse substrates

    USDA-ARS?s Scientific Manuscript database

    Soilless substrates are primarily used in the production of containerized greenhouse and nursery crops. Sphagnum peat moss is a primary constituent of these substrates and its harvest from endangered ecosystems has become a worldwide concern. Ethanol-extracted, coarse-ground corn (Zea mays L. ‘Sil...

  7. Method and apparatus for coating substrates using a laser

    NASA Technical Reports Server (NTRS)

    Zaplatynsky, I. (Inventor)

    1984-01-01

    Metal substrates, preferably of titanium and titanium alloys, are coated by alloying or forming TiN on a substrate surface. A laser beam strikes the surface of a moving substrate in the presence of purified nitrogen gas. A small area of the substrate surface is quickly heated without melting. This heated area reacts with the nitrogen to form a solid solution. The alloying or formation of TiN occurs by diffusion of nitrogen into the titanium. Only the surface layer of the substrate is heated because of the high power density of the laser beam and short exposure time. The bulk of the substrate is not affected, and melting of the substrate is avoided because it would be detrimental.

  8. Effects of magnetic flux density and substrate bias voltage on Ni films prepared on a flexible substrate material using unbalanced magnetron sputtering assisted by inductively coupled plasma

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Koda, Tatsunori; Toyota, Hiroshi, E-mail: h.toyota.za@it-hiroshima.ac.jp

    The authors fabricated Ni films on a flexible substrate material using unbalanced magnetron sputtering assisted by inductively coupled plasma. The effects of magnetic flux density B{sub C} and substrate DC bias voltage V{sub S} on the Ni film structures were investigated. For V{sub S} = −40 V, the average surface grain size D{sub G} measured by atomic force microscopy for B{sub C} = 0, 3, and 5 mT was 88.2, 95.4, and 104.4 nm, respectively. In addition, D{sub G} increased with V{sub S}. From x-ray diffraction measurements, the (111) and (200) peaks were clearly visible for the fabricated Ni films. The ratio of the integrated intensities ofmore » I(111)/I(200) increased with V{sub S}. For V{sub S} = −40 V and B{sub C} = 3 mT, a film resistivity ρ of 8.96 × 10{sup −6} Ω cm was observed, which is close to the Ni bulk value of 6.84 × 10{sup −6} Ω cm. From these results, the authors determined that the structure of the fabricated Ni films on the flexible substrate material was affected by the values of B{sub C} and V{sub S}.« less

  9. The effect of grooves in amorphous substrates on the orientation of metal deposits. I - Carbon substrates

    NASA Technical Reports Server (NTRS)

    Anton, R.; Poppa, H.; Flanders, D. C.

    1982-01-01

    The graphoepitaxial alignment of vapor-deposited discrete metal crystallites is investigated in the nucleation and growth stages and during annealing by in situ UHV/TEM techniques. Various stages of nucleation, growth and coalescence of vapor deposits of Au, Ag, Pb, Sn, and Bi on amorphous, topographically structured C substrates are analyzed by advanced dark-field techniques to detect preferred local orientations. It is found that the topography-induced orientation of metal crystallites depends strongly on their mobility and their respective tendency to develop pronounced crystallographic shapes. Lowering of the average surface free energies and increasing the crystallographic surface energy anisotropies cause generally improved graphoepitaxial alignments.

  10. Screening method for selecting semiconductor substrates having defects below a predetermined level in an oxide layer

    DOEpatents

    Warren, W.L.; Vanheusden, K.J.R.; Schwank, J.R.; Fleetwood, D.M.; Shaneyfelt, M.R.; Winokur, P.S.; Devine, R.A.B.

    1998-07-28

    A method is disclosed for screening or qualifying semiconductor substrates for integrated circuit fabrication. The method comprises the steps of annealing at least one semiconductor substrate at a first temperature in a defect-activating ambient (e.g. hydrogen, forming gas, or ammonia) for sufficient time for activating any defects within on oxide layer of the substrate; measuring a defect-revealing electrical characteristic of at least a portion of the oxide layer for determining a quantity of activated defects therein; and selecting substrates for which the quantity of activated defects is below a predetermined level. The defect-revealing electrical characteristic may be a capacitance-versus voltage (C-V) characteristic or a current-versus-voltage (I-V) characteristic that is dependent on an electrical charge in the oxide layer generated by the activated defects. Embodiments of the present invention may be applied for screening any type of semiconductor substrate or wafer having an oxide layer formed thereon or therein. This includes silicon-on-insulator substrates formed by a separation by the implantation of oxygen (SIMOX) process or the bond and etch back silicon-on-insulator (BESOI) process, as well as silicon substrates having a thermal oxide layer or a deposited oxide layer. 5 figs.

  11. Method for masking selected regions of a substrate

    DOEpatents

    Fusaro, Jr., Robert Anthony; Bethel, Timothy Francis

    2010-05-04

    Described herein is a method for providing a clean edge at the interface of a portion of a substrate coated with a coating system and an adjacent portion of the substrate which is uncoated. The method includes the step of forming a zone of non-adherence on the substrate portion which is to be uncoated, prior to application of the coating system. The zone of non-adherence is adjacent the interface, so that the coating system will not adhere to the zone of non-adherence, but will adhere to the portion of the substrate which is to be coated with the coating system.

  12. Method For Making Selected Regions Of A Substrate

    DOEpatents

    Fusaro, Jr., Robert Anthony; Bethel, Timothy Francis

    2003-07-15

    Described herein is a method for providing a clean edge at the interface of a portion of a substrate coated with a coating system and an adjacent portion of the substrate which is uncoated. The method includes the step of forming a zone of non-adherence on the substrate portion which is to be uncoated, prior to application of the coating system. The zone of non-adherence is adjacent the interface, so that the coating system will not adhere to the zone of non-adherence, but will adhere to the portion of the substrate which is to be coated with the coating system.

  13. Complementary and partially complementary DNA duplexes tethered to a functionalized substrate: a molecular dynamics approach to biosensing.

    PubMed

    Monti, Susanna; Cacelli, Ivo; Ferretti, Alessandro; Prampolini, Giacomo; Barone, Vincenzo

    2011-07-21

    Molecular dynamics simulations (90 ns) of different DNA complexes attached to a functionalized substrate in solution were performed in order to clarify the behavior of mismatched DNA sequences captured by a tethered DNA probe (biochip). Examination of the trajectories revealed that the substrate influence and a series of cooperative events, including recognition, reorientation and reorganization of the bases, could induce the formation of stable duplexes having non-canonical arrangements. Major adjustment of the structures was observed when the mutated base was located in the end region of the chain close to the surface. This journal is © the Owner Societies 2011

  14. Substrate inhibition: Oxidation of D-sorbitol and D-mannitol by potassium periodate in alkaline medium

    NASA Astrophysics Data System (ADS)

    Lakshman Kumar, Y.; Venkata Nadh, R.; Radhakrishnamurti, P. S.

    2014-05-01

    In the oxidation of D-sorbitol and D-mannitol by potassium periodate in alkaline media, substrate inhibition was observed with both substrates, i.e., a decrease in the rate of the reaction was observed with an increase in the concentration of substrate. The substrate inhibition was attributed to the formation of stable complex between the substrate and periodate. The reactions were found to be first order in case of periodate and a positive fractional order with hydroxide ions. Arrhenius parameters were calculated for the oxidation of sorbitol and mannitol by potassium periodate in alkali media.

  15. Transmembrane domain I contributes to the permeation pathway for serotonin and ions in the serotonin transporter.

    PubMed

    Barker, E L; Moore, K R; Rakhshan, F; Blakely, R D

    1999-06-15

    Mutation of a conserved Asp (D98) in the rat serotonin (5HT) transporter (rSERT) to Glu (D98E) led to decreased 5HT transport capacity, diminished coupling to extracellular Na+ and Cl-, and a selective loss of antagonist potencies (cocaine, imipramine, and citalopram but not paroxetine or mazindol) with no change in 5HT Km value. D98E, which extends the acidic side chain by one carbon, affected the rank-order potency of substrate analogs for inhibition of 5HT transport, selectively increasing the potency of two analogs with shorter alkylamine side chains, gramine, and dihydroxybenzylamine. D98E also increased the efficacy of gramine relative to 5HT for inducing substrate-activated currents in Xenopus laevis oocytes, but these currents were noticeably dependent on extracellular medium acidification. I-V profiles for substrate-independent and -dependent currents indicated that the mutation selectively impacts ion permeation coupled to 5HT occupancy. The ability of the D98E mutant to modulate selective aspects of substrate recognition, to perturb ion dependence as well as modify substrate-induced currents, suggests that transmembrane domain I plays a critical role in defining the permeation pathway of biogenic amine transporters.

  16. Nemesia Root Hair Response to Paper Pulp Substrate for Micropropagation

    PubMed Central

    Labrousse, Pascal; Delmail, David; Decou, Raphaël; Carlué, Michel; Lhernould, Sabine; Krausz, Pierre

    2012-01-01

    Agar substrates for in vitro culture are well adapted to plant micropropagation, but not to plant rooting and acclimatization. Conversely, paper-pulp-based substrates appear as potentially well adapted for in vitro culture and functional root production. To reinforce this hypothesis, this study compares in vitro development of nemesia on several substrates. Strong differences between nemesia roots growing in agar or in paper-pulp substrates were evidenced through scanning electron microscopy. Roots developed in agar have shorter hairs, larger rhizodermal cells, and less organized root caps than those growing on paper pulp. In conclusion, it should be noted that in this study, in vitro microporous substrates such as paper pulp lead to the production of similar root hairs to those found in greenhouse peat substrates. Consequently, if agar could be used for micropropagation, rooting, and plant acclimatization, enhancement could be achieved if rooting stage was performed on micro-porous substrates such as paper pulp. PMID:22312323

  17. Nemesia root hair response to paper pulp substrate for micropropagation.

    PubMed

    Labrousse, Pascal; Delmail, David; Decou, Raphaël; Carlué, Michel; Lhernould, Sabine; Krausz, Pierre

    2012-01-01

    Agar substrates for in vitro culture are well adapted to plant micropropagation, but not to plant rooting and acclimatization. Conversely, paper-pulp-based substrates appear as potentially well adapted for in vitro culture and functional root production. To reinforce this hypothesis, this study compares in vitro development of nemesia on several substrates. Strong differences between nemesia roots growing in agar or in paper-pulp substrates were evidenced through scanning electron microscopy. Roots developed in agar have shorter hairs, larger rhizodermal cells, and less organized root caps than those growing on paper pulp. In conclusion, it should be noted that in this study, in vitro microporous substrates such as paper pulp lead to the production of similar root hairs to those found in greenhouse peat substrates. Consequently, if agar could be used for micropropagation, rooting, and plant acclimatization, enhancement could be achieved if rooting stage was performed on micro-porous substrates such as paper pulp.

  18. Colloidal chitin stained with Remazol Brilliant Blue R, a useful substrate to select chitinolytic microorganisms and to evaluate chitinases.

    PubMed

    Gómez Ramírez, M; Rojas Avelizapa, L I; Rojas Avelizapa, N G; Cruz Camarillo, R

    2004-02-01

    A simple and sensitive method based on the use of colloidal chitin stained with Remazol Brilliant Blue R (RBB) is proposed to evaluate chitinase activity. If this colloidal-stained substrate is included as a carbon source in a liquid medium, this technique allows the selection or the comparison of chitinolytic microorganisms. The colloidal substrate is proportionally solubilized and the dye released is spectrophotometrically quantified at 595 nm. The procedures used for the staining and fixing of RBB in the colloidal chitin, and a comparison with the commercial substrate chitin-azure, are presented. The influence of several physicochemical and enzymatic parameters on the release of dyes is also shown. Both stained substrates were used for studying the effect of pH, substrate concentration, temperature and time on the chitinase reaction of Bacillus thuringiensis Bt-107.

  19. Electrostatic measures for a piezoelectric thin film with an embedded crack in the substrate: II. Mode II

    NASA Astrophysics Data System (ADS)

    Ali, Rizwaan; Mahapatra, D. Roy; Gopalakrishnan, S.

    2008-04-01

    This paper is a successor to the previous paper by Ali et al (2008 Smart Mater. Struct. 17 025037); it presents the analysis for sensing an embedded mode-II crack in a substrate. The displacement field kinematics for the film-substrate system is extended to the problem of applied surface shear stress. This extension requires modifying the model presented in the previous paper to include the differences due to changes in boundary and excitation conditions. The film response in terms of voltage pattern over the film area—peculiar to the presence of a mode-II crack in the substrate—is illustrated here through the results of numerical simulations. Our analysis shows that the proposed electrostatic measures of the voltage and its gradients are useful in identifying the axial and depth-wise location, as well as the crack-face area of a planar mode-II crack. There is a marked difference in the pattern of results presented in this paper with the results in part I of this work for a mode-I crack. This distinction is of utmost importance, for it singularly suffices to identify the mode of crack in a substrate for a given set of boundary conditions.

  20. Substrate inhibition kinetic model for West Nile virus NS2B-NS3 protease.

    PubMed

    Tomlinson, Suzanne M; Watowich, Stanley J

    2008-11-11

    West Nile virus (WNV) has recently emerged in North America as a significant disease threat to humans and animals. Unfortunately, no approved antiviral drugs exist to combat WNV or other members of the genus Flavivirus in humans. The WNV NS2B-NS3 protease has been one of the primary targets for anti-WNV drug discovery and design since it is required for virus replication. As part of our efforts to develop effective WNV inhibitors, we reexamined the reaction kinetics of the NS2B-NS3 protease and the inhibition mechanisms of newly discovered inhibitors. The WNV protease showed substrate inhibition in assays utilizing fluorophore-linked peptide substrates GRR, GKR, and DFASGKR. Moreover, a substrate inhibition reaction step was required to accurately model kinetic data generated from protease assays with a peptide inhibitor. The substrate inhibition model suggested that peptide substrates could bind to two binding sites on the protease. Reaction product analogues also showed inhibition of the protease, demonstrating product inhibition in addition to and distinct from substrate inhibition. We propose that small peptide substrates and inhibitors may interact with protease residues that form either the P3-P1 binding surface (i.e., the S3-S1 sites) or the P1'-P3' interaction surface (i.e., the S1'-S3' sites). Optimization of substrate analogue inhibitors that target these two independent sites may lead to novel anti-WNV drugs.

  1. Phosphatidylinositol 3-Kinase (PI3K) Activity Bound to Insulin-like Growth Factor-I (IGF-I) Receptor, which Is Continuously Sustained by IGF-I Stimulation, Is Required for IGF-I-induced Cell Proliferation*

    PubMed Central

    Fukushima, Toshiaki; Nakamura, Yusaku; Yamanaka, Daisuke; Shibano, Takashi; Chida, Kazuhiro; Minami, Shiro; Asano, Tomoichiro; Hakuno, Fumihiko; Takahashi, Shin-Ichiro

    2012-01-01

    Continuous stimulation of cells with insulin-like growth factors (IGFs) in G1 phase is a well established requirement for IGF-induced cell proliferation; however, the molecular components of this prolonged signaling pathway that is essential for cell cycle progression from G1 to S phase are unclear. IGF-I activates IGF-I receptor (IGF-IR) tyrosine kinase, followed by phosphorylation of substrates such as insulin receptor substrates (IRS) leading to binding of signaling molecules containing SH2 domains, including phosphatidylinositol 3-kinase (PI3K) to IRS and activation of the downstream signaling pathways. In this study, we found prolonged (>9 h) association of PI3K with IGF-IR induced by IGF-I stimulation. PI3K activity was present in this complex in thyrocytes and fibroblasts, although tyrosine phosphorylation of IRS was not yet evident after 9 h of IGF-I stimulation. IGF-I withdrawal in mid-G1 phase impaired the association of PI3K with IGF-IR and suppressed DNA synthesis the same as when PI3K inhibitor was added. Furthermore, we demonstrated that Tyr1316-X-X-Met of IGF-IR functioned as a PI3K binding sequence when this tyrosine is phosphorylated. We then analyzed IGF signaling and proliferation of IGF-IR−/− fibroblasts expressing exogenous mutant IGF-IR in which Tyr1316 was substituted with Phe (Y1316F). In these cells, IGF-I stimulation induced tyrosine phosphorylation of IGF-IR and IRS-1/2, but mutated IGF-IR failed to bind PI3K and to induce maximal phosphorylation of GSK3β and cell proliferation in response to IGF-I. Based on these results, we concluded that PI3K activity bound to IGF-IR, which is continuously sustained by IGF-I stimulation, is required for IGF-I-induced cell proliferation. PMID:22767591

  2. Low-Temperature Growth of Amorphous Silicon Films and Direct Fabrication of Solar Cells on Flexible Polyimide and Photo-Paper Substrates

    NASA Astrophysics Data System (ADS)

    Madaka, Ramakrishna; Kanneboina, Venkanna; Agarwal, Pratima

    2018-05-01

    Direct deposition of hydrogenated amorphous silicon (a-Si:H) thin films and fabrication of solar cells on polyimide (PI) and photo-paper (PP) substrates using a rf-plasma-enhanced chemical vapor deposition technique is reported. Intrinsic amorphous silicon films were deposited on PI and PP substrates by varying the substrate temperature (T s) over 70-150°C to optimize the deposition parameters for best quality films. The films deposited on both PI and PP substrates at a temperature as low as 70°C showed a photosensitivity (σ ph/σ d) of nearly 4 orders of magnitude which increased to 5-6 orders of magnitude when the substrate temperature was increased to 130-150°C. The increase in σ ph/σ d is due to the presence of a few nanometer-sized crystallites embedded in the film. Solar cells (n-i-p) were fabricated directly on PI, PP and Corning 1737 glass (Corning) at 150°C for different thicknesses of an intrinsic amorphous silicon layer (i-layer). With the increase in i-layer thickness from 330 nm to 700 nm, the solar cell efficiency was found to increase from 3.81% to 5.02% on the Corning substrate whereas on the flexible PI substrate an increase from 3.38% to 4.38% was observed. On the other hand, in the case of cells on PP, the i-layer thickness was varied from 200 nm to 700 nm and the best cell efficiency 1.54% was obtained for the 200-nm-thick i-layer. The fabrication of a-Si (n-i-p) solar cells on photo-paper is presented for the first time.

  3. A Bottom-Up Proteomic Approach to Identify Substrate Specificity of Outer-Membrane Protease OmpT.

    PubMed

    Wood, Sarah E; Sinsinbar, Gaurav; Gudlur, Sushanth; Nallani, Madhavan; Huang, Che-Fan; Liedberg, Bo; Mrksich, Milan

    2017-12-22

    Identifying peptide substrates that are efficiently cleaved by proteases gives insights into substrate recognition and specificity, guides development of inhibitors, and improves assay sensitivity. Peptide arrays and SAMDI mass spectrometry were used to identify a tetrapeptide substrate exhibiting high activity for the bacterial outer-membrane protease (OmpT). Analysis of protease activity for the preferred residues at the cleavage site (P1, P1') and nearest-neighbor positions (P2, P2') and their positional interdependence revealed FRRV as the optimal peptide with the highest OmpT activity. Substituting FRRV into a fragment of LL37, a natural substrate of OmpT, led to a greater than 400-fold improvement in OmpT catalytic efficiency, with a k cat /K m value of 6.1×10 6  L mol -1  s -1 . Wild-type and mutant OmpT displayed significant differences in their substrate specificities, demonstrating that even modest mutants may not be suitable substitutes for the native enzyme. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Substrate and inhibitor specificity of kynurenine monooxygenase from Cytophaga hutchinsonii.

    PubMed

    Phillips, Robert S; Anderson, Andrew D; Gentry, Harvey G; Güner, Osman F; Bowen, J Phillip

    2017-04-15

    Kynurenine monooxygenase (KMO) is a potential drug target for treatment of neurodegenerative disorders such as Huntington's and Alzheimer's diseases. We have evaluated substituted kynurenines as substrates or inhibitors of KMO from Cytophaga hutchinsonii. Kynurenines substituted with a halogen at the 5-position are excellent substrates, with values of k cat and k cat /K m comparable to or higher than kynurenine. However, kynurenines substituted in the 3-position are competitive inhibitors, with K I values lower than the K m for kynurenine. Bromination also enhances inhibition, and 3,5-dibromokynurenine is a potent competitive inhibitor with a K I value of 1.5μM. A pharmacophore model of KMO was developed, and predicted that 3,4-dichlorohippuric acid would be an inhibitor. The K I for this compound was found to be 34μM, thus validating the pharmacophore model. We are using these results and our model to design more potent inhibitors of KMO. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. A new lime material for container substrates

    USDA-ARS?s Scientific Manuscript database

    The primary component in greenhouse potting substrates is sphagnum peatmoss. Substrate solution pH of non-amended peatmoss ranges from 4.0 to 4.5. Ideal pH for most greenhouse floriculture crops ranges from 5.8 to 6.2. Dolomitic lime is most often used to elevate substrate pH in peatmoss-based me...

  6. Hydrophobic properties of a wavy rough substrate.

    PubMed

    Carbone, G; Mangialardi, L

    2005-01-01

    The wetting/non-wetting properties of a liquid drop in contact with a chemically hydrophobic rough surface (thermodynamic contact angle theta(e)>pi/2) are studied for the case of an extremely idealized rough profile: the liquid drop is considered to lie on a simple sinusoidal profile. Depending on surface geometry and pressure values, it is found that the Cassie and Wenzel states can coexist. But if the amplitude h of the substrate is sufficiently large the only possible stable state is the Cassie one, whereas if h is below a certain critical value hcr a transition to the Wenzel state occurs. Since in many potential applications of such super-hydrophobic surfaces, liquid drops often collide with the substrate (e.g. vehicle windscreens), in the paper the critical drop pressure pW is calculated at which the Cassie state is no longer stable and the liquid jumps into full contact with the substrate (Wenzel state). By analyzing the asymptotic behavior of the systems in the limiting case of a large substrate corrugation, a simple criterion is also proposed to calculate the minimum height asperity h necessary to prevent the Wenzel state from being formed, to preserve the super-hydrophobic properties of the substrate, and, hence, to design a robust super-hydrophobic surface.

  7. Using ALD To Bond CNTs to Substrates and Matrices

    NASA Technical Reports Server (NTRS)

    Wong, Eric W.; Bronikowski, Michael J.; Kowalczyk, Robert S.

    2008-01-01

    Atomic-layer deposition (ALD) has been shown to be effective as a means of coating carbon nanotubes (CNTs) with layers of Al2O3 that form strong bonds between the CNTs and the substrates on which the CNTs are grown. ALD is a previously developed vaporphase thin-film-growth technique. ALD differs from conventional chemical vapor deposition, in which material is deposited continually by thermal decomposition of a precursor gas. In ALD, material is deposited one layer of atoms at a time because the deposition process is self-limiting and driven by chemical reactions between the precursor gas and the surface of the substrate or the previously deposited layer.

  8. Microgrooved Polymer Substrates Promote Collective Cell Migration To Accelerate Fracture Healing in an in Vitro Model.

    PubMed

    Zhang, Qing; Dong, Hua; Li, Yuli; Zhu, Ye; Zeng, Lei; Gao, Huichang; Yuan, Bo; Chen, Xiaofeng; Mao, Chuanbin

    2015-10-21

    Surface topography can affect cell adhesion, morphology, polarity, cytoskeleton organization, and osteogenesis. However, little is known about the effect of topography on the fracture healing in repairing nonunion and large bone defects. Microgrooved topography on the surface of bone implants may promote cell migration into the fracture gap to accelerate fracture healing. To prove this hypothesis, we used an in vitro fracture (wound) healing assay on the microgrooved polycaprolactone substrates to study the effect of microgroove widths and depths on the osteoblast-like cell (MG-63) migration and the subsequent healing. We found that the microgrooved substrates promoted MG-63 cells to migrate collectively into the wound gap, which serves as a fracture model, along the grooves and ridges as compared with the flat substrates. Moreover, the groove widths did not show obvious influence on the wound healing whereas the smaller groove depths tended to favor the collective cell migration and thus subsequent healing. The microgrooved substrates accelerated the wound healing by facilitating the collective cell migration into the wound gaps but not by promoting the cell proliferation. Furthermore, microgrooves were also found to promote the migration of human mesenchymal stem cells (hMSCs) to heal the fracture model. Though osteogenic differentiation of hMSCs was not improved on the microgrooved substrate, collagen I and minerals deposited by hMSCs were organized in a way similar to those in the extracellular matrix of natural bone. These findings suggest the necessity in using microgrooved implants in enhancing fracture healing in bone repair.

  9. Process for metallization of a substrate by curing a catalyst applied thereto

    DOEpatents

    Chen, Ken S.; Morgan, William P.; Zich, John L.

    2002-10-08

    An improved additive process for metallization of substrates is described whereby a catalyst solution is applied to a surface of a substrate. Metallic catalytic clusters can be formed in the catalyst solution on the substrate surface by heating the substrate. Electroless plating can then deposit metal onto the portion of the substrate surface coated with catalyst solution. Additional metallization thickness can be obtained by electrolytically plating the substrate surface after the electroless plating step.

  10. Coated substrates and process

    DOEpatents

    Chu, Wei-kan; Childs, Charles B.

    1991-01-01

    Disclosed herein is a coated substrate and a process for forming films on substrates and for providing a particularly smooth film on a substrate. The method of this invention involves subjecting a surface of a substrate to contact with a stream of ions of an inert gas having sufficient force and energy to substantially change the surface characteristics of said substrate, and then exposing a film-forming material to a stream of ions of an inert gas having sufficient energy to vaporize the atoms of said film-forming material and to transmit the vaporized atoms to the substrate surface with sufficient force to form a film bonded to the substrate. This process is particularly useful commercially because it forms strong bonds at room temperature. This invention is particularly useful for adhering a gold film to diamond and forming ohmic electrodes on diamond, but also can be used to bond other films to substrates.

  11. PEGylated substrates of NSP4 protease: A tool to study protease specificity

    NASA Astrophysics Data System (ADS)

    Wysocka, Magdalena; Gruba, Natalia; Grzywa, Renata; Giełdoń, Artur; Bąchor, Remigiusz; Brzozowski, Krzysztof; Sieńczyk, Marcin; Dieter, Jenne; Szewczuk, Zbigniew; Rolka, Krzysztof; Lesner, Adam

    2016-03-01

    Herein we present the synthesis of a novel type of peptidomimetics composed of repeating diaminopropionic acid residues modified with structurally diverse heterobifunctional polyethylene glycol chains (abbreviated as DAPEG). Based on the developed compounds, a library of fluorogenic substrates was synthesized. Further library deconvolution towards human neutrophil serine protease 4 (NSP4) yielded highly sensitive and selective internally quenched peptidomimetic substrates. In silico analysis of the obtained peptidomimetics revealed the presence of an interaction network with distant subsites located on the enzyme surface.

  12. Re-engineering of CYP2C9 to probe acid-base substrate selectivity.

    PubMed

    Tai, Guoying; Dickmann, Leslie J; Matovic, Nicholas; DeVoss, James J; Gillam, Elizabeth M J; Rettie, Allan E

    2008-10-01

    A common feature of many CYP2C9 ligands is their weak acidity. As revealed by crystallography, the structural basis for this behavior involves a charge-pairing interaction between an anionic moiety on the substrate and an active site R108 residue. In the present study we attempted to re-engineer CYP2C9 to better accept basic ligands by charge reversal at this key residue. We expressed and purified the R108E and R108E/D293N mutants and compared their ability with that of native CYP2C9 to interact with (S)-warfarin, diclofenac, pyrene, propranolol, and ibuprofen amine. As expected, the R108E mutant maintained all the native enzyme's pyrene 1-hydroxylation activity, but catalytic activity toward diclofenac and (S)-warfarin was abrogated. In contrast, the double mutant displayed much less selectivity in its behavior toward these control ligands. Neither of the mutants displayed significant enhancement of propranolol metabolism, and all three preparations exhibited a type II (inhibitor) rather than type I (substrate) spectrum with ibuprofen amine, although binding became progressively weaker with the single and double mutants. Collectively, these data underscore the importance of the amino acid at position 108 in the acid substrate selectivity of CYP2C9, highlight the accommodating nature of the CYP2C9 active site, and provide a cautionary note regarding facile re-engineering of these complex cytochrome P450 active sites.

  13. Re-engineering of CYP2C9 to Probe Acid-Base Substrate Selectivity

    PubMed Central

    Tai, Guoying; Dickmann, Leslie J.; Matovic, Nicholas; DeVoss, James J.; Gillam, Elizabeth M. J.; Rettie, Allan E.

    2009-01-01

    A common feature of many CYP2C9 ligands is their weak acidity. As revealed by crystallography, the structural basis for this behavior involves a charge-pairing interaction between an anionic moiety on the substrate and an active site R108 residue. In the present study we attempted to re-engineer CYP2C9 to better accept basic ligands by charge reversal at this key residue. We expressed and purified the R108E and R108E/D293N mutants and compared their ability with that of native CYP2C9 to interact with (S)-warfarin, diclofenac, pyrene, propranolol, and ibuprofen amine. As expected, the R108E mutant maintained all the native enzyme's pyrene 1-hydroxylation activity, but catalytic activity toward diclofenac and (S)-warfarin was abrogated. In contrast, the double mutant displayed much less selectivity in its behavior toward these control ligands. Neither of the mutants displayed significant enhancement of propranolol metabolism, and all three preparations exhibited a type II (inhibitor) rather than type I (substrate) spectrum with ibuprofen amine, although binding became progressively weaker with the single and double mutants. Collectively, these data underscore the importance of the amino acid at position 108 in the acid substrate selectivity of CYP2C9, highlight the accommodating nature of the CYP2C9 active site, and provide a cautionary note regarding facile re-engineering of these complex cytochrome P450 active sites. PMID:18606741

  14. High current densities enable exoelectrogens to outcompete aerobic heterotrophs for substrate.

    PubMed

    Ren, Lijiao; Zhang, Xiaoyuan; He, Weihua; Logan, Bruce E

    2014-11-01

    In mixed-culture microbial fuel cells (MFCs), exoelectrogens and other microorganisms compete for substrate. It has previously been assumed that substrate losses to other terminal electron acceptors over a fed-batch cycle, such as dissolved oxygen, are constant. However, a constant rate of substrate loss would only explain small increases in coulombic efficiencies (CEs, the fraction of substrate recovered as electrical current) with shorter cycle times, but not the large increases in CE that are usually observed with higher current densities and reduced cycle times. To better understand changes in CEs, COD concentrations were measured over time in fed-batch, single-chamber, air-cathode MFCs at different current densities (external resistances). COD degradation rates were all found to be first-order with respect to COD concentration, even under open circuit conditions with no current generation (first-order rate constant of 0.14 ± 0.01 h(-1) ). The rate of COD removal increased when there was current generation, with the highest rate constant (0.33 ± 0.02 h(-1) ) obtained at the lowest external resistance (100 Ω). Therefore, as the substrate concentration was reduced more quickly due to current generation, the rate of loss of substrate to non-exoelectrogens decreased due to this first-order substrate-concentration dependence. As a result, coulombic efficiencies rapidly increased due to decreased, and not constant, removal rates of substrate by non-exoelectrogens. These results show that higher current densities (lower resistances) redirect a greater percentage of substrate into current generation, enabling large increase in CEs with increased current densities. Biotechnol. Bioeng. 2014;111: 2163-2169. © 2014 Wiley Periodicals, Inc. © 2014 Wiley Periodicals, Inc.

  15. Method of forming fluorine-bearing diamond layer on substrates, including tool substrates

    DOEpatents

    Chang, R. P. H.; Grannen, Kevin J.

    2002-01-01

    A method of forming a fluorine-bearing diamond layer on non-diamond substrates, especially on tool substrates comprising a metal matrix and hard particles, such as tungsten carbide particles, in the metal matrix. The substrate and a fluorine-bearing plasma or other gas are then contacted under temperature and pressure conditions effective to nucleate fluorine-bearing diamond on the substrate. A tool insert substrate is treated prior to the diamond nucleation and growth operation by etching both the metal matrix and the hard particles using suitable etchants.

  16. Hysteresis in the Cell Response to Time-Dependent Substrate Stiffness

    PubMed Central

    Besser, Achim; Schwarz, Ulrich S.

    2010-01-01

    Abstract Mechanical cues like the rigidity of the substrate are main determinants for the decision-making of adherent cells. Here we use a mechano-chemical model to predict the cellular response to varying substrate stiffnesses. The model equations combine the mechanics of contractile actin filament bundles with a model for the Rho-signaling pathway triggered by forces at cell-matrix contacts. A bifurcation analysis of cellular contractility as a function of substrate stiffness reveals a bistable response, thus defining a lower threshold of stiffness, below which cells are not able to build up contractile forces, and an upper threshold of stiffness, above which cells are always in a strongly contracted state. Using the full dynamical model, we predict that rate-dependent hysteresis will occur in the cellular traction forces when cells are exposed to substrates of time-dependent stiffness. PMID:20655823

  17. Structural insights into conserved L-arabinose metabolic enzymes reveal the substrate binding site of a thermophilic L-arabinose isomerase.

    PubMed

    Lee, Yong-Jik; Lee, Sang-Jae; Kim, Seong-Bo; Lee, Sang Jun; Lee, Sung Haeng; Lee, Dong-Woo

    2014-03-18

    Structural genomics demonstrates that despite low levels of structural similarity of proteins comprising a metabolic pathway, their substrate binding regions are likely to be conserved. Herein based on the 3D-structures of the α/β-fold proteins involved in the ara operon, we attempted to predict the substrate binding residues of thermophilic Geobacillus stearothermophilus L-arabinose isomerase (GSAI) with no 3D-structure available. Comparison of the structures of L-arabinose catabolic enzymes revealed a conserved feature to form the substrate-binding modules, which can be extended to predict the substrate binding site of GSAI (i.e., D195, E261 and E333). Moreover, these data implicated that proteins in the l-arabinose metabolic pathway might retain their substrate binding niches as the modular structure through conserved molecular evolution even with totally different structural scaffolds. Copyright © 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  18. Substrate system for spray forming

    DOEpatents

    Chu, Men G.; Chernicoff, William P.

    2000-01-01

    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.

  19. Substrate system for spray forming

    DOEpatents

    Chu, Men G.; Chernicoff, William P.

    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.

  20. Measuring the Global Substrate Specificity of Mycobacterial Serine Hydrolases Using a Library of Fluorogenic Ester Substrates.

    PubMed

    Bassett, Braden; Waibel, Brent; White, Alex; Hansen, Heather; Stephens, Dominique; Koelper, Andrew; Larsen, Erik M; Kim, Charles; Glanzer, Adam; Lavis, Luke D; Hoops, Geoffrey C; Johnson, R Jeremy

    2018-04-16

    Among the proteins required for lipid metabolism in Mycobacterium tuberculosis are a significant number of uncharacterized serine hydrolases, especially lipases and esterases. Using a streamlined synthetic method, a library of immolative fluorogenic ester substrates was expanded to better represent the natural lipidomic diversity of Mycobacterium. This expanded fluorogenic library was then used to rapidly characterize the global structure activity relationship (SAR) of mycobacterial serine hydrolases in M. smegmatis under different growth conditions. Confirmation of fluorogenic substrate activation by mycobacterial serine hydrolases was performed using nonspecific serine hydrolase inhibitors and reinforced the biological significance of the SAR. The hydrolases responsible for the global SAR were then assigned using gel-resolved activity measurements, and these assignments were used to rapidly identify the relative substrate specificity of previously uncharacterized mycobacterial hydrolases. These measurements provide a global SAR of mycobacterial hydrolase activity, a picture of cycling hydrolase activity, and a detailed substrate specificity profile for previously uncharacterized hydrolases.

  1. Low Friction Droplet Transportation on a Substrate with a Selective Leidenfrost Effect.

    PubMed

    Dodd, Linzi E; Wood, David; Geraldi, Nicasio R; Wells, Gary G; McHale, Glen; Xu, Ben B; Stuart-Cole, Simone; Martin, James; Newton, Michael I

    2016-08-31

    An energy saving Leidenfrost levitation method is introduced to transport microdroplets with virtually frictionless contact between the liquid and solid substrate. Through microengineering of the heating units, selective areas of the whole substrate can be electrothermally activated. A droplet can be levitated as a result of the Leidenfrost effect and further transported when the substrate is tilted slightly. Selective electroheating produces a uniform temperature distribution on the heating units within 1 s in response to a triggering voltage. Alongside these experimental observations, finite element simulations were conducted to understand the role of substrate thermal conductivity on the temperature profile of the selectively heated substrate. We also generated phase diagrams to verify the Leidenfrost regime for different substrate materials. Finally, we demonstrated the possibility of controlling low friction high speed droplet transportation (∼65 mm/s) when the substrate is tilted (∼7°) by structurally designing the substrate. This work establishes the basis for an entirely new approach to droplet microfluidics.

  2. Equilibrium Droplets on Deformable Substrates: Equilibrium Conditions.

    PubMed

    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.

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

    PubMed Central

    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. Protein NMR Studies of Substrate Binding to Human Blood Group A and B Glycosyltransferases.

    PubMed

    Grimm, Lena Lisbeth; Weissbach, Sophie; Flügge, Friedemann; Begemann, Nora; Palcic, Monica M; Peters, Thomas

    2017-07-04

    Donor and acceptor substrate binding to human blood group A and B glycosyltransferases (GTA, GTB) has been studied by a variety of protein NMR experiments. Prior crystallographic studies had shown these enzymes to adopt an open conformation in the absence of substrates. Binding either of the donor substrate UDP-Gal or of UDP induces a semiclosed conformation. In the presence of both donor and acceptor substrates, the enzymes shift towards a closed conformation with ordering of an internal loop and the C-terminal residues, which then completely cover the donor-binding pocket. Chemical-shift titrations of uniformly 2 H, 15 N-labeled GTA or GTB with UDP affected about 20 % of all crosspeaks in 1 H, 15 N TROSY-HSQC spectra, reflecting substantial plasticity of the enzymes. On the other hand, it is this conformational flexibility that impedes NH backbone assignments. Chemical-shift-perturbation experiments with δ1-[ 13 C]methyl-Ile-labeled samples revealed two Ile residues-Ile123 at the bottom of the UDP binding pocket, and Ile192 as part of the internal loop-that were significantly disturbed upon stepwise addition of UDP and H-disaccharide, also revealing long-range perturbations. Finally, methyl TROSY-based relaxation dispersion experiments do not reveal micro- to millisecond timescale motions. Although this study reveals substantial conformational plasticity of GTA and GTB, the matter of how binding of substrates shifts the enzymes into catalytically competent states remains enigmatic. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. 2G HTS wires made on 30 μm thick Hastelloy substrate

    NASA Astrophysics Data System (ADS)

    Sundaram, A.; Zhang, Y.; Knoll, A. R.; Abraimov, D.; Brownsey, P.; Kasahara, M.; Carota, G. M.; Nakasaki, R.; Cameron, J. B.; Schwab, G.; Hope, L. V.; Schmidt, R. M.; Kuraseko, H.; Fukushima, T.; Hazelton, D. W.

    2016-10-01

    REBCO (RE = rare earth) based high temperature superconducting (HTS) wires are now being utilized for the development of electric and electromagnetic devices for various industrial, scientific and medical applications. In the last several years, the increasing efforts in using the so-called second generation (2G) HTS wires for some of the applications require a further increase in their engineering current density (J e). The applications are those typically related to high magnetic fields where the higher J e of a REBCO wire, in addition to its higher irreversibility fields and higher mechanical strength, is already a major advantage over other superconducting wires. An effective way to increase the J e is to decrease the total thickness of a wire, for which using a thinner substrate becomes an obvious and attractive approach. By using our IBAD-MOCVD (ion beam assisted deposition-metal organic chemical vapor deposition) technology we have successfully made 2G HTS wires using a Hastelloy® C276 substrate that is only 30 μm in thickness. By using this thinner substrate instead of the typical 50 μm thick substrate and with a same critical current (I c), the J e of a wire can be increased by 30% to 45% depending on the copper stabilizer thickness. In this paper, we report the fabrication and characterization of the 2G HTS wires made on the 30 μm thick Hastelloy® C276 substrate. It was shown that with the optimization in the processing protocol, the surface of the thinner Hastelloy® C276 substrate can be readily electropolished to the quality needed for the deposition of the buffer stack. Same in the architecture as that on the standard 50 μm thick substrate, the buffer stack made on the 30 μm thick substrate showed an in-plane texture with a Δϕ of around 6.7° in the LaMnO3 cap layer. Low-temperature in-field transport measurement results suggest that the wires on the thinner substrate had achieved equivalent superconducting performance, most importantly the I

  6. Methylene blue improves mitochondrial respiration and decreases oxidative stress in a substrate-dependent manner in diabetic rat hearts.

    PubMed

    Duicu, Oana M; Privistirescu, Andreea; Wolf, Adrian; Petruş, Alexandra; Dănilă, Maria D; Raţiu, Corina D; Muntean, Danina M; Sturza, Adrian

    2017-11-01

    Diabetic cardiomyopathy has been systematically associated with compromised mitochondrial energetics and increased generation of reactive oxygen species (ROS) that underlie its progression to heart failure. Methylene blue is a redox drug with reported protective effects mainly on brain mitochondria. The purpose of the present study was to characterize the effects of acute administration of methylene blue on mitochondrial respiration, H 2 O 2 production, and calcium sensitivity in rat heart mitochondria isolated from healthy and 2 months (streptozotocin-induced) diabetic rats. Mitochondrial respiratory function was assessed by high-resolution respirometry. H 2 O 2 production and calcium retention capacity were measured spectrofluorimetrically. The addition of methylene blue (0.1 μmol·L -1 ) elicited an increase in oxygen consumption of mitochondria energized with complex I and II substrates in both normal and diseased mitochondria. Interestingly, methylene blue elicited a significant increase in H 2 O 2 release in the presence of complex I substrates (glutamate and malate), but had an opposite effect in mitochondria energized with complex II substrate (succinate). No changes in the calcium retention capacity of healthy or diabetic mitochondria were found in the presence of methylene blue. In conclusion, in cardiac mitochondria isolated from diabetic and nondiabetic rat hearts, methylene blue improved respiratory function and elicited a dichotomic, substrate-dependent effect on ROS production.

  7. Critical Determinants of Substrate Recognition by Cyclin-Dependent Kinase-like 5 (CDKL5).

    PubMed

    Katayama, Syouichi; Sueyoshi, Noriyuki; Kameshita, Isamu

    2015-05-19

    Cyclin-dependent kinase-like 5 (CDKL5) is a Ser/Thr protein kinase known to be associated with X-linked neurodevelopmental disorders. In a previous study, we identified amphiphysin 1 (Amph1) as a potential substrate for CDKL5 and identified a single phosphorylation site at Ser-293. In this study, we investigated the molecular mechanisms of substrate recognition by CDKL5 using Amph1 as a model substrate. Amph1 served as an efficient CDKL5 substrate, whereas Amph2, a structurally related homologue of Amph1, was not phosphorylated by CDKL5. The sequence around the Amph1 phosphorylation site is RPR(293)SPSQ, while the corresponding sequence in Amph2 is IPK(332)SPSQ. To define the amino acid sequence specificity of the substrate, various point mutants of Amph1 and Amph2 were prepared and phosphorylated by CDKL5. Both Amph2(I329R) and Amph1 served as efficient CDKL5 substrates, but Amph1(R290I) did not, indicating that the arginyl residue at the P -3 position is critical for substrate recognition. With regard to prolyl residues around the phosphorylation site of Amph1, Pro-291 at the P -2 position, but not Pro-294 at the P +1 position, is indispensable for phosphorylation by CDKL5. Phosphorylation experiments using various deletion mutants of Amph1 revealed that the proline-rich domain (PRD) (amino acids 247-315) alone was not phosphorylated by CDKL5. In contrast, Amph1(247-385), which comprised the PRD and CLAP domains, served as an efficient CDKL5 substrate. These results, taken together, suggest that both the phosphorylation site sequence (RPXSX) and the CLAP domain structure in Amph1 play crucial roles in recognition and phosphorylation by CDKL5.

  8. Human dermatosparaxis: a form of Ehlers-Danlos syndrome that results from failure to remove the amino-terminal propeptide of type I procollagen.

    PubMed

    Smith, L T; Wertelecki, W; Milstone, L M; Petty, E M; Seashore, M R; Braverman, I M; Jenkins, T G; Byers, P H

    1992-08-01

    Dermatosparaxis is a recessively inherited connective-tissue disorder that results from lack of the activity of type I procollagen N-proteinase, the enzyme that removes the amino-terminal propeptides from type I procollagen. Initially identified in cattle more than 20 years ago, the disorder was subsequently characterized in sheep, cats, and dogs. Affected animals have fragile skin, lax joints, and often die prematurely because of sepsis following avulsion of portions of skin. We recently identified two children with soft, lax, and fragile skin, which, when examined by transmission electron microscopy, contained the twisted, ribbon-like collagen fibrils characteristic of dermatosparaxis. Skin extracts from one child contained collagen precursors with amino-terminal extensions. Cultured fibroblasts from both children failed to cleave the amino-terminal propeptides from the pro alpha 1(I) and pro alpha 2(I) chains in type I procollagen molecules. Extracts of normal cells cleaved to collagen, the type I procollagen synthesized by cells from both children, demonstrating that the enzyme, not the substrate, was defective. These findings distinguish dermatosparaxis from Ehlers-Danlos syndrome type VII, which results from substrate mutations that prevent proteolytic processing of type I procollagen molecules.

  9. Method of forming through substrate vias (TSVs) and singulating and releasing die having the TSVs from a mechanical support substrate

    DOEpatents

    Okandan, Murat; Nielson, Gregory N

    2014-12-09

    Accessing a workpiece object in semiconductor processing is disclosed. The workpiece object includes a mechanical support substrate, a release layer over the mechanical support substrate, and an integrated circuit substrate coupled over the release layer. The integrated circuit substrate includes a device layer having semiconductor devices. The method also includes etching through-substrate via (TSV) openings through the integrated circuit substrate that have buried ends at or within the release layer including using the release layer as an etch stop. TSVs are formed by introducing one or more conductive materials into the TSV openings. A die singulation trench is etched at least substantially through the integrated circuit substrate around a perimeter of an integrated circuit die. The integrated circuit die is at least substantially released from the mechanical support substrate.

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

    NASA Astrophysics Data System (ADS)

    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.

  11. Study of adhesion of vertically aligned carbon nanotubes to a substrate by atomic-force microscopy

    NASA Astrophysics Data System (ADS)

    Ageev, O. A.; Blinov, Yu. F.; Il'ina, M. V.; Il'in, O. I.; Smirnov, V. A.; Tsukanova, O. G.

    2016-02-01

    The adhesion to a substrate of vertically aligned carbon nanotubes (VA CNT) produced by plasmaenhanced chemical vapor deposition has been experimentally studied by atomic-force microscopy in the current spectroscopy mode. The longitudinal deformation of VA CNT by applying an external electric field has been simulated. Based on the results, a technique of determining VA CNT adhesion to a substrate has been developed that is used to measure the adhesion strength of connecting VA CNT to a substrate. The adhesion to a substrate of VA CNT 70-120 nm in diameter varies from 0.55 to 1.19 mJ/m2, and the adhesion force from 92.5 to 226.1 nN. When applying a mechanical load, the adhesion strength of the connecting VA CNT to a substrate is 714.1 ± 138.4 MPa, and the corresponding detachment force increases from 1.93 to 10.33 μN with an increase in the VA CNT diameter. As an external electric field is applied, the adhesion strength is almost doubled and is 1.43 ± 0.29 GPa, and the corresponding detachment force is changed from 3.83 to 20.02 μN. The results can be used in the design of technological processes of formation of emission structures, VA CNT-based elements for vacuum microelectronics and micro- and nanosystem engineering, and also the methods of probe nanodiagnostics of VA CNT.

  12. Cuttlefish dynamic camouflage: responses to substrate choice and integration of multiple visual cues.

    PubMed

    Allen, Justine J; Mäthger, Lydia M; Barbosa, Alexandra; Buresch, Kendra C; Sogin, Emilia; Schwartz, Jillian; Chubb, Charles; Hanlon, Roger T

    2010-04-07

    Prey camouflage is an evolutionary response to predation pressure. Cephalopods have extensive camouflage capabilities and studying them can offer insight into effective camouflage design. Here, we examine whether cuttlefish, Sepia officinalis, show substrate or camouflage pattern preferences. In the first two experiments, cuttlefish were presented with a choice between different artificial substrates or between different natural substrates. First, the ability of cuttlefish to show substrate preference on artificial and natural substrates was established. Next, cuttlefish were offered substrates known to evoke three main camouflage body pattern types these animals show: Uniform or Mottle (function by background matching); or Disruptive. In a third experiment, cuttlefish were presented with conflicting visual cues on their left and right sides to assess their camouflage response. Given a choice between substrates they might encounter in nature, we found no strong substrate preference except when cuttlefish could bury themselves. Additionally, cuttlefish responded to conflicting visual cues with mixed body patterns in both the substrate preference and split substrate experiments. These results suggest that differences in energy costs for different camouflage body patterns may be minor and that pattern mixing and symmetry may play important roles in camouflage.

  13. High-content profiling of cell responsiveness to graded substrates based on combinyatorially variant polymers.

    PubMed

    Liu, Er; Treiser, Matthew D; Patel, Hiral; Sung, Hak-Joon; Roskov, Kristen E; Kohn, Joachim; Becker, Matthew L; Moghe, Prabhas V

    2009-08-01

    We have developed a novel approach combining high information and high throughput analysis to characterize cell adhesive responses to biomaterial substrates possessing gradients in surface topography. These gradients were fabricated by subjecting thin film blends of tyrosine-derived polycarbonates, i.e. poly(DTE carbonate) and poly(DTO carbonate) to a gradient temperature annealing protocol. Saos-2 cells engineered with a green fluorescent protein (GFP) reporter for farnesylation (GFP-f) were cultured on the gradient substrates to assess the effects of nanoscale surface topology and roughness that arise during the phase separation process on cell attachment and adhesion strength. The high throughput imaging approach allowed us to rapidly identify the "global" and "high content" structure-property relationships between cell adhesion and biomaterial properties such as polymer chemistry and topography. This study found that cell attachment and spreading increased monotonically with DTE content and were significantly elevated at the position with intermediate regions corresponding to the highest "gradient" of surface roughness, while GFP-f farnesylation intensity descriptors were sensitively altered by surface roughness, even in cells with comparable levels of spreading.

  14. Substrate quality alters microbial mineralization of added substrate and soil organic carbon

    NASA Astrophysics Data System (ADS)

    Jagadamma, S.; Mayes, M. A.; Steinweg, J. M.; Schaeffer, S. M.

    2014-03-01

    The rate and extent of decomposition of soil organic carbon (SOC) is dependent on substrate chemistry and microbial dynamics. Our objectives were to understand the influence of substrate chemistry on microbial processing of carbon (C), and to use model fitting to quantify differences in pool sizes and mineralization rates. We conducted an incubation experiment for 270 days using four uniformly-labeled 14C substrates (glucose, starch, cinnamic acid and stearic acid) on four different soils (a temperate Mollisol, a tropical Ultisol, a sub-arctic Andisol, and an arctic Gelisol). The 14C labeling enabled us to separate CO2 respired from added substrates and from native SOC. Microbial gene copy numbers were quantified at days 4, 30 and 270 using quantitative polymerase chain reaction (qPCR). Substrate C respiration was always higher for glucose than other substrates. Soils with cinnamic and stearic acid lost more native SOC than glucose- and starch-amended soils, despite an initial delay in respiration. Cinnamic and stearic acid amendments also exhibited higher fungal gene copy numbers at the end of incubation compared to unamended soils. We found that 270 days was sufficient to model decomposition of simple substrates (glucose and starch) with three pools, but was insufficient for more complex substrates (cinnamic and stearic acid) and native SOC. This study reveals that substrate quality imparts considerable control on microbial decomposition of newly added and native SOC, and demonstrates the need for multi-year incubation experiments to constrain decomposition parameters for the most recalcitrant fractions of SOC and added substrates.

  15. Interaction of Substrate Mechanics with Dental Pulp Stem Cells (DPSCs) differentiation to generate a scaffold for Bone regeneration

    NASA Astrophysics Data System (ADS)

    Rafailovich, Miriam; Bhatnagar, Divya; Bherwani, Aneel; Simon, Marcia

    2012-02-01

    This work investigates the interaction of the substrate mechanics with the differentiation in the absence of chemical induction and only resulting from the stimuli of the substrate mechanics and chemistry. We chose enzymatically cross-linked gelatin hydrogels substrates of different stiffness varying from 8KPa to 100Pa. DPSCs were cultured and differentiated on the substrates for 7, 14 and 21 days with and without dexamethasone induction media. SEM and EDX analysis after 21 days indicate that cells produced a sheet of biomineralized deposits, several tenths of mm thick on the hard substrate irrespective of chemical induction. Modulli of the cells was independent of the induction and stiffness of the hydrogels. RT-PCR assays indicated that cells expressed more osteocalcin when cultured in non-induction media and harder substrate. The shape of the deposits was more uniform and in close packing on the harder substrate with a higher Ca:P ratio. On soft substrate the deposits were more flat with less Ca:P ratio. Further experiments indicated that conformational change due to the crosslinking of gelatin could be the reason for biomineralization.

  16. An improved continuous compositional-spread technique based on pulsed-laser deposition and applicable to large substrate areas

    NASA Astrophysics Data System (ADS)

    Christen, H. M.; Rouleau, C. M.; Ohkubo, I.; Zhai, H. Y.; Lee, H. N.; Sathyamurthy, S.; Lowndes, D. H.

    2003-09-01

    A method for continuous compositional-spread (CCS) thin-film fabrication based on pulsed-laser deposition (PLD) is introduced. This approach is based on a translation of the substrate heater and the synchronized firing of the excimer laser, with the deposition occurring through a slit-shaped aperture. Alloying is achieved during film growth (possible at elevated temperature) by the repeated sequential deposition of submonolayer amounts. Our approach overcomes serious shortcomings in previous in situ implementation of CCS based on sputtering or PLD, in particular the variation of thickness across the compositional spread and the differing deposition energetics as a function of position. While moving-shutter techniques are appropriate for PLD approaches yielding complete spreads on small substrates (i.e., small as compared to distances over which the deposition parameters in PLD vary, typically ≈1 cm), our method can be used to fabricate samples that are large enough for individual compositions to be analyzed by conventional techniques, including temperature-dependent measurements of resistivity and dielectric and magnetic properties (i.e., superconducting quantum interference device magnetometry). Initial results are shown for spreads of (Sr1-xCax)RuO3.

  17. Colloidal diffusion over a quasicrystalline-patterned substrate

    NASA Astrophysics Data System (ADS)

    Su, Yun; Lai, Pik-Yin; Ackerson, Bruce; Tong, Penger

    We report a systematic study of colloidal diffusion over a quasicrystalline-patterned substrate. The sample substrate is made of a flat thin layer of photoresist and contains identical cylindrical holes of diameter dh, which are arranged on a quasicrystal lattice. A monolayer of silica spheres of diameter comparable to dh diffuse over the rugged quasicrystalline-patterned substrate and experience a gravitational potential U (x , y) . With optical microscopy and the particle tracking method, we measure U (x , y) and particle's diffusion trajectories, which are found to undergo two distinct states: a trapped state when the particles are inside the holes and a free diffusion state when they are over the flat portion of the substrate. The dynamic properties of the diffusing particle, such as its mean dwell time, mean square displacement, and long-time diffusion coefficient DL are obtained from the particle trajectories. The measured DL is found to be in good agreement with the prediction of two theoretical models proposed for diffusion over a quasicrystal lattice. The experiment demonstrates the applications of this newly constructed colloidal potential landscape. This work was supported by the Research Grants Council of Hong Kong SAR.

  18. Basis for substrate recognition and distinction by matrix metalloproteinases

    PubMed Central

    Ratnikov, Boris I.; Cieplak, Piotr; Gramatikoff, Kosi; Pierce, James; Eroshkin, Alexey; Igarashi, Yoshinobu; Kazanov, Marat; Sun, Qing; Godzik, Adam; Osterman, Andrei; Stec, Boguslaw; Strongin, Alex; Smith, Jeffrey W.

    2014-01-01

    Genomic sequencing and structural genomics produced a vast amount of sequence and structural data, creating an opportunity for structure–function analysis in silico [Radivojac P, et al. (2013) Nat Methods 10(3):221–227]. Unfortunately, only a few large experimental datasets exist to serve as benchmarks for function-related predictions. Furthermore, currently there are no reliable means to predict the extent of functional similarity among proteins. Here, we quantify structure–function relationships among three phylogenetic branches of the matrix metalloproteinase (MMP) family by comparing their cleavage efficiencies toward an extended set of phage peptide substrates that were selected from ∼64 million peptide sequences (i.e., a large unbiased representation of substrate space). The observed second-order rate constants [k(obs)] across the substrate space provide a distance measure of functional similarity among the MMPs. These functional distances directly correlate with MMP phylogenetic distance. There is also a remarkable and near-perfect correlation between the MMP substrate preference and sequence identity of 50–57 discontinuous residues surrounding the catalytic groove. We conclude that these residues represent the specificity-determining positions (SDPs) that allowed for the expansion of MMP proteolytic function during evolution. A transmutation of only a few selected SDPs proximal to the bound substrate peptide, and contributing the most to selectivity among the MMPs, is sufficient to enact a global change in the substrate preference of one MMP to that of another, indicating the potential for the rational and focused redesign of cleavage specificity in MMPs. PMID:25246591

  19. The use of agricultural substrates to improve methane yield in anaerobic co-digestion with pig slurry: effect of substrate type and inclusion level.

    PubMed

    Ferrer, Pablo; Cambra-López, María; Cerisuelo, Alba; Peñaranda, David S; Moset, Verónica

    2014-01-01

    Anaerobic co-digestion of pig slurry with four agricultural substrates (tomato, pepper, persimmon and peach) was investigated. Each agricultural substrate was tested in co-digestion with pig slurry at four inclusion levels: 0%, 15%, 30% and 50%. Inclusion levels consisted in the replacement of the volatile solids (VS) from the pig slurry with the VS from the agricultural substrate. The effect of substrate type and inclusion level on the biochemical methane potential (BMP) was evaluated in a batch assay performed at 35 °C for 100 days. Agricultural substrate's chemical composition was also analyzed and related with BMP. Additionally, Bacteria and Archaea domains together with the four main methanogenic archaeal orders were quantified using quantitative real-time TaqMan polymerase chain reaction (qPCR) at the end of the experiment to determine the influence of agricultural substrate on sludge's microbial composition. Results showed that vegetable substrates (pepper and tomato) had higher lipid and protein content and lower carbohydrates than fruit substrates (persimmon and peach). Among substrates, vegetable substrates showed higher BMP than fruit substrates. Higher BMP values were obtained with increasing addition of agricultural substrate. The replacement of 50% of VS from pig slurry by tomato and pepper increased BMP in 41% and 44%, respectively compared with pig slurry only. Lower increments in BMP were achieved with lower inclusion levels. Results from qPCR showed that total bacteria and total archaea gene concentrations were similar in all combinations tested. Methanomicrobiales gene concentrations dominated over the rest of individual archaeal orders. Copyright © 2013 Elsevier Ltd. All rights reserved.

  20. The ZnO-FET Biosensor for Cardiac Troponin I

    NASA Astrophysics Data System (ADS)

    Fathil, M. F. M.; Arshad, M. K. Md; Nuzaihan, M. N. M.; Gopinath, Subash C. B.; Ruslinda, A. R.; Hashim, U.

    2018-03-01

    This paper investigates the influence of substrate-gate coupling on the ZnO-FET biosensor’s sensitivity for detection of cardiac troponin I (cTnI), a ‘gold standard’ biomarker for acute myocardial infarction (AMI). The FET-based device with introduction of substrate-gate coupling on p-type silicon-on-insulator (SOI) substrate is fabricated using conventional lithography processes. An n-type zinc oxide (ZnO) thin film deposited via electron-beam evaporator is used as transducer for bridging the source and drain regions. Surface modifications via functionalization with 3-aminopropyltriethoxysilane (APTES) and glutaraldehyde (GA) as chemical linkers, followed by immobilization of cTnI monoclonal antibody (MAb-cTnI) as bio-receptor on the ZnO thin film allow different concentration of cTnI detection with high selectivity. The device’s sensitivity increases up to 9 %·(g/ml)-1 with the increase of the substrate-gate voltage (VSG) up to -10 V at very low limit of detection (LOD) down to 1.6 fg/ml.

  1. Structural and evolutionary relationships of "AT-less" type I polyketide synthase ketosynthases.

    PubMed

    Lohman, Jeremy R; Ma, Ming; Osipiuk, Jerzy; Nocek, Boguslaw; Kim, Youngchang; Chang, Changsoo; Cuff, Marianne; Mack, Jamey; Bigelow, Lance; Li, Hui; Endres, Michael; Babnigg, Gyorgy; Joachimiak, Andrzej; Phillips, George N; Shen, Ben

    2015-10-13

    Acyltransferase (AT)-less type I polyketide synthases (PKSs) break the type I PKS paradigm. They lack the integrated AT domains within their modules and instead use a discrete AT that acts in trans, whereas a type I PKS module minimally contains AT, acyl carrier protein (ACP), and ketosynthase (KS) domains. Structures of canonical type I PKS KS-AT didomains reveal structured linkers that connect the two domains. AT-less type I PKS KSs have remnants of these linkers, which have been hypothesized to be AT docking domains. Natural products produced by AT-less type I PKSs are very complex because of an increased representation of unique modifying domains. AT-less type I PKS KSs possess substrate specificity and fall into phylogenetic clades that correlate with their substrates, whereas canonical type I PKS KSs are monophyletic. We have solved crystal structures of seven AT-less type I PKS KS domains that represent various sequence clusters, revealing insight into the large structural and subtle amino acid residue differences that lead to unique active site topologies and substrate specificities. One set of structures represents a larger group of KS domains from both canonical and AT-less type I PKSs that accept amino acid-containing substrates. One structure has a partial AT-domain, revealing the structural consequences of a type I PKS KS evolving into an AT-less type I PKS KS. These structures highlight the structural diversity within the AT-less type I PKS KS family, and most important, provide a unique opportunity to study the molecular evolution of substrate specificity within the type I PKSs.

  2. Sorption characteristics of pesticides on matrix substrates used in biopurification systems.

    PubMed

    De Wilde, Tineke; Spanoghe, Pieter; Ryckeboer, Jaak; Jaeken, Peter; Springael, Dirk

    2009-03-01

    On-farm biopurification systems were developed to remove pesticides from contaminated water generated at the farmyard. An important process in the system's efficiency is the sorption of pesticides to the substrates used in the biopurification systems. The composition and type of material present in the biobed are crucial for retention of chemicals. This study investigated the sorption of linuron, isoproturon, metalaxyl, isoxaben, bentazon and lenacil on substrates commonly used in a biopurification system, i.e. cow manure, straw, willow chopping, soil, coconut chips, garden waste compost, and peat mix. Linear, Freundlich, and Langmuir sorption isotherms were fitted to the obtained data. The best fit was obtained with the Freundlich model. More immobile pesticides (i.e. linuron and isoxaben) tended to associate with the organic substrate, while more mobile pesticides partition in the water (i.e. bentazon). According to sorption capacity, the substrates could be classified as peat mix > compost, coco chips, straw > cow manure, willow chopping > sandy loam soil. Sorption capacity was positively correlated with the organic carbon content, CaO and the cation exchange capacity. Furthermore, no significant differences in sorption could be found between technical and formulated isoproturon and bentazon. Moreover, the individual sorption coefficient K(d) was additive, which means that individual sorption coefficients can be used to calculate the sorption coefficients of a mixture of substrates. What concerns the mutual interaction of pesticides it could be observed that the sorption of linuron and metalaxyl was significantly lower in combination with isoproturon and bentazon, while the latter pesticides were not influenced by the presence of linuron and metalaxyl. As guidelines, firstly, it could be stated that using the most sorbing materials such as peat mix, might significantly increase the biopurification systems efficiency. Secondly, the treatment of very mobile

  3. Development of pyrethroid-like fluorescent substrates for glutathione S-transferase

    PubMed Central

    Huang, Huazhang; Yao, Hongwei; Liu, Jun-Yan; Samra, Aman I.; Kamita, Shizuo G.; Cornel, Anthony J.; Hammock, Bruce D.

    2012-01-01

    The availability of highly sensitive substrates is critical for the development of precise and rapid assays for detecting changes in glutathione S-transferase (GST) activity that are associated with GST-mediated metabolism of insecticides. In this study, six pyrethroid-like compounds were synthesized and characterized as substrates for insect and mammalian GSTs. All of the substrates were esters composed of the same alcohol moiety, 7-hydroxy-4-methylcoumarin, and acid moieties that structurally mimic some commonly used pyrethroid insecticides including cypermethrin and cyhalothrin. CpGSTD1, a recombinant Delta class GST from the mosquito Culex pipiens, metabolized our pyrethroid-like substrates with both chemical and geometric (i.e., the cis-isomers were metabolized at 2- to 5-fold higher rates than the corresponding trans-isomers) preference. A GST preparation from mouse liver also metabolized most of our pyrethroid-like substrates with both chemical and geometric preference but at 10- to 170-fold lower rates. CpGSTD1 and mouse GSTs metabolized CDNB, a general GST substrate, at more than 200-fold higher rates than our novel pyrethroid-like substrates. There was a 10-fold difference in the specificity constant (kcat/KM ratio) of CpGSTD1 for CDNB and those of CpGSTD1 for cis-DCVC and cis-TFMCVC suggesting that cis-DCVC and cis-TFMCVC may be useful for the detection of GST-based metabolism of pyrethroids in mosquitoes. PMID:23000005

  4. Substrate specificity of platypus venom L-to-D-peptide isomerase.

    PubMed

    Bansal, Paramjit S; Torres, Allan M; Crossett, Ben; Wong, Karen K Y; Koh, Jennifer M S; Geraghty, Dominic P; Vandenberg, Jamie I; Kuchel, Philip W

    2008-04-04

    The L-to-D-peptide isomerase from the venom of the platypus (Ornithorhyncus anatinus) is the first such enzyme to be reported for a mammal. In delineating its catalytic mechanism and broader roles in the animal, its substrate specificity was explored. We used N-terminal segments of defensin-like peptides DLP-2 and DLP-4 and natriuretic peptide OvCNP from the venom as substrates. The DLP analogues IMFsrs and ImFsrs (srs is a solubilizing chain; lowercase letters denote D-amino acid) were effective substrates for the isomerase; it appears to recognize the N-terminal tripeptide sequence Ile-Xaa-Phe-. A suite of 26 mutants of these hexapeptides was synthesized by replacing the second residue (Met) with another amino acid, viz. Ala, alpha-aminobutyric acid, Ile, Leu, Lys, norleucine, Phe, Tyr, and Val. It was shown that mutant peptides incorporating norleucine and Phe are substrates and exhibit L- or D-amino acid isomerization, but mutant peptides that contain residues with shorter, beta-branched or long side chains with polar terminal groups, viz. Ala, alpha-aminobutyric acid, Ile, Val, Leu, Lys, and Tyr, respectively, are not substrates. It was demonstrated that at least three N-terminal amino acid residues are absolutely essential for L-to-D-isomerization; furthermore, the third amino acid must be a Phe residue. None of the hexapeptides based on LLH, the first three residues of OvCNP, were substrates. A consistent 2-base mechanism is proposed for the isomerization; abstraction of a proton by 1 base is concomitant with delivery of a proton by the conjugate acid of a second base.

  5. Evaporation of liquid droplets on solid substrates. I. Flat substrate with pinned or moving contact line

    NASA Astrophysics Data System (ADS)

    Amini, Amirhossein; Homsy, G. M.

    2017-04-01

    We study the evolution of the profile of a two-dimensional volatile liquid droplet that is evaporating on a flat heated substrate. We adopt a one-sided model with thermal control that, together with the lubrication approximation, results in an evolution equation for the local height of the droplet. Without requiring any presumption for the shape of the drop, the problem is formulated for the two modes of evaporation: a pinned contact line and a moving contact line with fixed contact angle. Numerical solutions are provided for each case. For the pinned contact line case, we observe that after a time interval the contact angle dynamics become nonlinear and, interestingly, the local contact angle goes to zero in advance of total evaporation of the drop. For the case of a moving contact line, in which the singularity at the contact line is treated by a numerical slip model, we find that the droplet nearly keeps its initial circular shape and that the contact line recedes with constant speed.

  6. Thin-film solar cell fabricated on a flexible metallic substrate

    DOEpatents

    Tuttle, John R.; Noufi, Rommel; Hasoon, Falah S.

    2006-05-30

    A thin-film solar cell (10) is provided. The thin-film solar cell (10) comprises a flexible metallic substrate (12) having a first surface and a second surface. A back metal contact layer (16) is deposited on the first surface of the flexible metallic substrate (12). A semiconductor absorber layer (14) is deposited on the back metal contact. A photoactive film deposited on the semiconductor absorber layer (14) forms a heterojunction structure and a grid contact (24) deposited on the heterjunction structure. The flexible metal substrate (12) can be constructed of either aluminium or stainless steel. Furthermore, a method of constructing a solar cell is provided. The method comprises providing an aluminum substrate (12), depositing a semiconductor absorber layer (14) on the aluminum substrate (12), and insulating the aluminum substrate (12) from the semiconductor absorber layer (14) to inhibit reaction between the aluminum substrate (12) and the semiconductor absorber layer (14).

  7. Thin-Film Solar Cell Fabricated on a Flexible Metallic Substrate

    DOEpatents

    Tuttle, J. R.; Noufi, R.; Hasoon, F. S.

    2006-05-30

    A thin-film solar cell (10) is provided. The thin-film solar cell (10) comprises a flexible metallic substrate (12) having a first surface and a second surface. A back metal contact layer (16) is deposited on the first surface of the flexible metallic substrate (12). A semiconductor absorber layer (14) is deposited on the back metal contact. A photoactive film deposited on the semiconductor absorber layer (14) forms a heterojunction structure and a grid contact (24) deposited on the heterjunction structure. The flexible metal substrate (12) can be constructed of either aluminium or stainless steel. Furthermore, a method of constructing a solar cell is provided. The method comprises providing an aluminum substrate (12), depositing a semiconductor absorber layer (14) on the aluminum substrate (12), and insulating the aluminum substrate (12) from the semiconductor absorber layer (14) to inhibit reaction between the aluminum substrate (12) and the semiconductor absorber layer (14).

  8. Type II Secretion Substrates of Legionella pneumophila Translocate Out of the Pathogen-Occupied Vacuole via a Semipermeable Membrane.

    PubMed

    Truchan, Hilary K; Christman, Harry D; White, Richard C; Rutledge, Nakisha S; Cianciotto, Nicholas P

    2017-06-20

    Legionella pneumophila replicates in macrophages in a host-derived phagosome, termed the Legionella- containing vacuole (LCV). While the translocation of type IV secretion (T4S) effectors into the macrophage cytosol is well established, the location of type II secretion (T2S) substrates in the infected host cell is unknown. Here, we show that the T2S substrate ProA, a metalloprotease, translocates into the cytosol of human macrophages, where it associates with the LCV membrane (LCVM). Translocation is detected as early as 10 h postinoculation (p.i.), which is approximately the midpoint of the intracellular life cycle. However, it is detected as early as 6 h p.i. if ProA is hyperexpressed, indicating that translocation depends on the timing of ProA expression and that any other factors necessary for translocation are in place by that time point. Translocation occurs with all L. pneumophila strains tested and in amoebae, natural hosts for L. pneumophila It was absent in murine bone marrow-derived macrophages and murine macrophage cell lines. The ChiA chitinase also associated with the cytoplasmic face of the LCVM at 6 h p.i. and in a T2S-dependent manner. Galectin-3 and galectin-8, eukaryotic proteins whose localization is influenced by damage to host membranes, appeared within the LCV of infected human but not murine macrophages beginning at 6 h p.i. Thus, we hypothesize that ProA and ChiA are first secreted into the vacuolar lumen by the activity of the T2S and subsequently traffic into the macrophage cytosol via a novel mechanism that involves a semipermeable LCVM. IMPORTANCE Infection of macrophages and amoebae plays a central role in the pathogenesis of L. pneumophila , the agent of Legionnaires' disease. We have previously demonstrated that the T2S system of L. pneumophila greatly contributes to intracellular infection. However, the location of T2S substrates within the infected host cell is unknown. This report presents the first evidence of a L

  9. Substrate comprising a nanometer-scale projection array

    DOEpatents

    Cui, Yi; Zhu, Jia; Hsu, Ching-Mei; Connor, Stephen T; Yu, Zongfu; Fan, Shanhui; Burkhard, George

    2012-11-27

    A method for forming a substrate comprising nanometer-scale pillars or cones that project from the surface of the substrate is disclosed. The method enables control over physical characteristics of the projections including diameter, sidewall angle, and tip shape. The method further enables control over the arrangement of the projections including characteristics such as center-to-center spacing and separation distance.

  10. Liquid-Vapor Coexistence at a Mesoporous Substrate

    NASA Astrophysics Data System (ADS)

    Kityk, A. V.; Hofmann, T.; Knorr, K.

    2008-01-01

    The condensation of hexane vapor onto a mesoporous Si substrate with a pore radius of 3.5 nm has been studied by means of volumetry and ellipsometry. The filling fraction of the pores and the coverage of the substrate have been determined. The coverage of the regime after the completion of capillary condensation has been compared to recent theoretical work.

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

    PubMed Central

    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

  12. Methods for both coating a substrate with aluminum oxide and infusing the substrate with elemental aluminum

    DOEpatents

    Choi, Jung-Pyung; Weil, Kenneth Scott

    2016-11-01

    Methods of aluminizing the surface of a metal substrate. The methods of the present invention do not require establishment of a vacuum or a reducing atmosphere, as is typically necessary. Accordingly, aluminization can occur in the presence of oxygen, which greatly simplifies and reduces processing costs by allowing deposition of the aluminum coating to be performed, for example, in air. Embodiments of the present invention can be characterized by applying a slurry that includes a binder and powder granules containing aluminum to the metal substrate surface. Then, in a combined step, a portion of the aluminum is diffused into the substrate and a portion of the aluminum is oxidized by heating the slurry to a temperature greater than the melting point of the aluminum in an oxygen-containing atmosphere.

  13. Polished polymide substrate

    DOEpatents

    Farah, John; Sudarshanam, Venkatapuram S.

    2003-05-13

    Polymer substrates, in particular polyimide substrates, and polymer laminates for optical applications are described. Polyimide substrates are polished on one or both sides depending on their thickness, and single-layer or multi-layer waveguide structures are deposited on the polished polyimide substrates. Optical waveguide devices are machined by laser ablation using a combination of IR and UV lasers. A waveguide-fiber coupler with a laser-machined groove for retaining the fiber is also disclosed.

  14. Response of reef corals on a fringing reef flat to elevated suspended-sediment concentrations: Moloka‘i, Hawai‘i

    USGS Publications Warehouse

    Jokiel, Paul L.; Rodgers, Ku'ulei S.; Storlazzi, Curt D.; Field, Michael E.; Lager, Claire V.; Lager, Dan

    2014-01-01

    A long-term (10 month exposure) experiment on effects of suspended sediment on the mortality, growth, and recruitment of the reef corals Montipora capitata and Porites compressa was conducted on the shallow reef flat off south Molokaʻi, Hawaiʻi. Corals were grown on wire platforms with attached coral recruitment tiles along a suspended solid concentration (SSC) gradient that ranged from 37 mg l−1 (inshore) to 3 mg l−1(offshore). Natural coral reef development on the reef flat is limited to areas with SSCs less than 10 mg l−1 as previously suggested in the scientific literature. However, the experimental corals held at much higher levels of turbidity showed surprisingly good survivorship and growth. High SSCs encountered on the reef flat reduced coral recruitment by one to three orders of magnitude compared to other sites throughout Hawaiʻi. There was a significant correlation between the biomass of macroalgae attached to the wire growth platforms at the end of the experiment and percentage of the corals showing mortality. We conclude that lack of suitable hard substrate, macroalgal competition, and blockage of recruitment on available substratum are major factors accounting for the low natural coral coverage in areas of high turbidity. The direct impact of high turbidity on growth and mortality is of lesser importance.

  15. Guanosine 5'-triphosphate binding protein (G/sub i/) and two additional pertussis toxin substrates associated with muscarinic receptors in rat heart myocytes: characterization and age dependency

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Moscona-Amir, E.; Henis, Y.I.; Sokolovsky, M.

    1988-07-12

    The coupling of muscarinic receptors with G-proteins was investigated in cultured myocytes prepared from the hearts of newborn rats. The coupling was investigated in both young (5 days after plating) and aged (14 days after plating) cultures, in view of the completely different effects of 5'-guanylyl imidodiphosphate (Gpp(NH)p) on muscarinic agonist binding to homogenates from young vs aged cultures. Pretreatment of cultures from both ages by Bordetella pertussis toxin (IAP) was found to eliminate any Gpp(NH)p effect on carbamylcholine binding. IAP by itself induced a rightward shift in the carbamylcholine competition curve in homogenates from aged cultures, but no suchmore » effect was observed in homogenates from young cultures. IAP-catalyzed (/sup 32/P)ADP-ribosylation of membrane preparations from young and aged cultures revealed major differences between them. Young cultures exhibited a major IAP substrate at 40 kDa, which was also recognized by anti-..cap alpha../sub i/ antibodies, and two novel IAP substrates at 28 and 42 kDa, which were weakly ADP-ribosylated by the toxin and were not recognized with either anti-..cap alpha../sub i/ or anti-..cap alpha../sub 0/ antibodies. In aged cultures, only the 40-kDa band (ribosylated to a lower degree) was detected. The parallel age-dependent changes in the three IAP substrates (28, 40, and 42 kDa) and in the interactions of the G-protein(s) with the muscarinic receptors strongly suggest close association between the two phenomena. All of these age-dependent changes in the G-protein related parameters were prevented by phosphatidylcholine-liposome treatment of the aged cultures. The role of the membrane lipid composition in these phenomena is discussed.« less

  16. Holocene Substrate Influences on Plant and Fire Response to Climate Change

    NASA Astrophysics Data System (ADS)

    Briles, C.; Whitlock, C. L.

    2011-12-01

    The role of substrates in facilitating plant responses to climate change in the past has received little attention. Ecological studies, documenting the relative role of fertile and infertile substrates in mediating the effects of climate change, lack the temporal information that paleoecological lake studies provide on how plants have responded under equal, larger and more rapid past climate events than today. In this paper, pollen and macroscopic charcoal preserved in the sediments of eight lakes surrounded by infertile ultramafic soils and more fertile soils in the Klamath Mountains of northern California were analyzed. Comparison of late-Quaternary paleoecological sites suggests that infertile and fertile substrates supported distinctly different plant communities. Trees and shrubs on infertile substrates were less responsive to climate change than those on fertile substrates, with the only major compositional change occurring at the glacial/interglacial transition (~11.5ka), when temperature rose 5oC. Trees and shrubs on fertile substrates were more responsive to climate changes, and tracked climate by moving along elevational gradients, including during more recent climate events such as the Little Ice Age and Medieval Climate Anomaly. Fire regimes were similar until 4ka on both substrate types. After 4ka, understory fuels on infertile substrates became sparse and fire activity decreased, while on fertile substrates forests became increasingly denser and fire activity increased. The complacency of plant communities on infertile sites to climate change contrasts with the individualistic and rapid adjustments of species on fertile sites. The findings differ from observations on shorter time scales that show the most change in herb cover and richness in the last 60 years on infertile substrates. Thus, the paleorecord provides unique long-term ecological data necessary to evaluate the response of plants to future climate change under different levels of soil

  17. Method for electrostatic deposition of graphene on a substrate

    NASA Technical Reports Server (NTRS)

    Sumanasekera, Gamini (Inventor); Sidorov, Anton N. (Inventor); Ouseph, P. John (Inventor); Yazdanpanah, Mehdi M. (Inventor); Cohn, Robert W. (Inventor); Jalilian, Romaneh (Inventor)

    2010-01-01

    A method for electrostatic deposition of graphene on a substrate comprises the steps of securing a graphite sample to a first electrode; electrically connecting the first electrode to a positive terminal of a power source; electrically connecting a second electrode to a ground terminal of the power source; placing the substrate over the second electrode; and using the power source to apply a voltage, such that graphene is removed from the graphite sample and deposited on the substrate.

  18. Mechanistic Insight on the Activity and Substrate Selectivity of Nonheme Iron Dioxygenases.

    PubMed

    de Visser, Sam P

    2018-06-07

    Nonheme iron dioxygenases catalyze vital reactions for human health particularly related to aging processes. They are involved in the biosynthesis of amino acids, but also the biodegradation of toxic compounds. Typically they react with their substrate(s) through oxygen atom transfer, although often with the assistance of a co-substrate like α-ketoglutarate that is converted to succinate and CO 2 . Many reaction processes catalyzed by the nonheme iron dioxygenases are stereoselective or regiospecific and hence understanding the mechanism and protein involvement in the selectivity is important for the design of biotechnological applications of these enzymes. To this end, I will review recent work of our group on nonheme iron dioxygenases and include background information on their general structure and catalytic cycle. Examples of stereoselective and regiospecific reaction mechanisms we elucidated are for the AlkB repair enzyme, prolyl-4-hydroxylase and the ergothioneine biosynthesis enzyme. Finally, I cover an example where we bioengineered S-p-hydroxymandelate synthase into the R-p-hydroxymandelate synthase. © 2018 The Chemical Society of Japan & Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Human dermatosparaxis: a form of Ehlers-Danlos syndrome that results from failure to remove the amino-terminal propeptide of type I procollagen.

    PubMed Central

    Smith, L T; Wertelecki, W; Milstone, L M; Petty, E M; Seashore, M R; Braverman, I M; Jenkins, T G; Byers, P H

    1992-01-01

    Dermatosparaxis is a recessively inherited connective-tissue disorder that results from lack of the activity of type I procollagen N-proteinase, the enzyme that removes the amino-terminal propeptides from type I procollagen. Initially identified in cattle more than 20 years ago, the disorder was subsequently characterized in sheep, cats, and dogs. Affected animals have fragile skin, lax joints, and often die prematurely because of sepsis following avulsion of portions of skin. We recently identified two children with soft, lax, and fragile skin, which, when examined by transmission electron microscopy, contained the twisted, ribbon-like collagen fibrils characteristic of dermatosparaxis. Skin extracts from one child contained collagen precursors with amino-terminal extensions. Cultured fibroblasts from both children failed to cleave the amino-terminal propeptides from the pro alpha 1(I) and pro alpha 2(I) chains in type I procollagen molecules. Extracts of normal cells cleaved to collagen, the type I procollagen synthesized by cells from both children, demonstrating that the enzyme, not the substrate, was defective. These findings distinguish dermatosparaxis from Ehlers-Danlos syndrome type VII, which results from substrate mutations that prevent proteolytic processing of type I procollagen molecules. Images Figure 5 Figure 2 Figure 3 Figure 1 Figure 4 Figure 6 PMID:1642226

  20. Cocaine action on peripheral, non-monoamine neural substrates as a trigger of electroencephalographic desynchronization and electromyographic activation following i.v. administration in freely moving rats.

    PubMed

    Smirnov, M S; Kiyatkin, E A

    2010-01-20

    Many important physiological, behavioral and subjective effects of i.v. cocaine (COC) are exceptionally rapid and transient, suggesting a possible involvement of peripheral neural substrates in their triggering. In the present study, we used high-speed electroencephalographic (EEG) and electromyographic (EMG) recordings (4-s resolution) in freely moving rats to characterize the central electrophysiological effects of i.v. COC at low doses within a self-administration range (0.25-1.0 mg/kg). We found that COC induces rapid, strong, and prolonged desynchronization of cortical EEG (decrease in alpha and increase in beta and gamma activity) and activation of the neck EMG that begin within 2-6 s following the start of a 10-s injection; immediate components of both effects were dose-independent. The rapid effects of COC were mimicked by i.v. COC methiodide (COC-MET), a derivative that cannot cross the blood-brain barrier. At equimolar doses (0.33-1.33 mg/kg), COC-MET had equally fast and strong effects on EEG and EMG total powers, decreasing alpha and increasing beta and gamma activities. Rapid EEG desynchronization and EMG activation was also induced by i.v. procaine, a structurally similar, short-acting local anesthetic with virtually no effects on monoamine uptake; at equipotential doses (1.25-5.0 mg/kg), these effects were weaker and shorter in duration than those of COC. Surprisingly, i.v. saline injection delivered during slow-wave sleep (but not during quiet wakefulness) also induced a transient EEG desynchronization but without changes in EMG and motor activity; these effects were significantly weaker and much shorter than those induced by all tested drugs. These data suggest that in awake animals, i.v. COC induces rapid cortical activation and a subsequent motor response via its action on peripheral non-monoamine neural elements, involving neural transmission via visceral sensory pathways. By providing a rapid neural signal and triggering neural activation, such

  1. Substrate utilization profiles of bacterial strains in plankton from the River Warnow, a humic and eutrophic river in north Germany.

    PubMed

    Freese, Heike M; Eggert, Anja; Garland, Jay L; Schumann, Rhena

    2010-01-01

    Bacteria are very important degraders of organic substances in aquatic environments. Despite their influential role in the carbon (and many other element) cycle(s), the specific genetic identity of active bacteria is mostly unknown, although contributing phylogenetic groups had been investigated. Moreover, the degree to which phenotypic potential (i. e., utilization of environmentally relevant carbon substrates) is related to the genomic identity of bacteria or bacterial groups is unclear. The present study compared the genomic fingerprints of 27 bacterial isolates from the humic River Warnow with their ability to utilize 14 environmentally relevant substrates. Acetate was the only substrate utilized by all bacterial strains. Only 60% of the strains respired glucose, but this substrate always stimulated the highest bacterial activity (respiration and growth). Two isolates, both closely related to the same Pseudomonas sp., also had very similar substrate utilization patterns. However, similar substrate utilization profiles commonly belonged to genetically different strains (e.g., the substrate profile of Janthinobacterium lividum OW6/RT-3 and Flavobacterium sp. OW3/15-5 differed by only three substrates). Substrate consumption was sometimes totally different for genetically related isolates. Thus, the genomic profiles of bacterial strains were not congruent with their different substrate utilization profiles. Additionally, changes in pre-incubation conditions strongly influenced substrate utilization. Therefore, it is problematic to infer substrate utilization and especially microbial dissolved organic matter transformation in aquatic systems from bacterial molecular taxonomy.

  2. Self-assembled nanospheres with multiple endohedral binding sites pre-organize catalysts and substrates for highly efficient reactions

    NASA Astrophysics Data System (ADS)

    Wang, Qi-Qiang; Gonell, Sergio; Leenders, Stefan H. A. M.; Dürr, Maximilian; Ivanović-Burmazović, Ivana; Reek, Joost N. H.

    2016-03-01

    Tuning reagent and catalyst concentrations is crucial in the development of efficient catalytic transformations. In enzyme-catalysed reactions the substrate is bound—often by multiple non-covalent interactions—in a well-defined pocket close to the active site of the enzyme; this pre-organization facilitates highly efficient transformations. Here we report an artificial system that co-encapsulates multiple catalysts and substrates within the confined space defined by an M12L24 nanosphere that contains 24 endohedral guanidinium-binding sites. Cooperative binding means that sulfonate guests are bound much more strongly than carboxylates. This difference has been used to fix gold-based catalysts firmly, with the remaining binding sites left to pre-organize substrates. This strategy was applied to a Au(I)-catalysed cyclization of acetylenic acid to enol lactone in which the pre-organization resulted in much higher reaction rates. We also found that the encapsulated sulfonate-containing Au(I) catalysts did not convert neutral (acid) substrates, and so could have potential in the development of substrate-selective catalysis and base-triggered on/off switching of catalysis.

  3. Retuning Rieske-type Oxygenases to Expand Substrate Range

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Mohammadi, Mahmood; Viger, Jean-François; Kumar, Pravindra

    2012-09-17

    Rieske-type oxygenases are promising biocatalysts for the destruction of persistent pollutants or for the synthesis of fine chemicals. In this work, we explored pathways through which Rieske-type oxygenases evolve to expand their substrate range. BphAE{sub p4}, a variant biphenyl dioxygenase generated from Burkholderia xenovorans LB400 BphAE{sub LB400} by the double substitution T335A/F336M, and BphAE{sub RR41}, obtained by changing Asn{sup 338}, Ile{sup 341}, and Leu{sup 409} of BphAE{sub p4} to Gln{sup 338}, Val{sup 341}, and Phe{sup 409}, metabolize dibenzofuran two and three times faster than BphAE{sub LB400}, respectively. Steady-state kinetic measurements of single- and multiple-substitution mutants of BphAE{sub LB400} showed thatmore » the single T335A and the double N338Q/L409F substitutions contribute significantly to enhanced catalytic activity toward dibenzofuran. Analysis of crystal structures showed that the T335A substitution relieves constraints on a segment lining the catalytic cavity, allowing a significant displacement in response to dibenzofuran binding. The combined N338Q/L409F substitutions alter substrate-induced conformational changes of protein groups involved in subunit assembly and in the chemical steps of the reaction. This suggests a responsive induced fit mechanism that retunes the alignment of protein atoms involved in the chemical steps of the reaction. These enzymes can thus expand their substrate range through mutations that alter the constraints or plasticity of the catalytic cavity to accommodate new substrates or that alter the induced fit mechanism required to achieve proper alignment of reaction-critical atoms or groups.« less

  4. Substrate quality alters the microbial mineralization of added substrate and soil organic carbon

    NASA Astrophysics Data System (ADS)

    Jagadamma, S.; Mayes, M. A.; Steinweg, J. M.; Schaeffer, S. M.

    2014-09-01

    The rate and extent of decomposition of soil organic carbon (SOC) is dependent, among other factors, on substrate chemistry and microbial dynamics. Our objectives were to understand the influence of substrate chemistry on microbial decomposition of carbon (C), and to use model fitting to quantify differences in pool sizes and mineralization rates. We conducted an incubation experiment for 270 days using four uniformly labeled 14C substrates (glucose, starch, cinnamic acid and stearic acid) on four different soils (a temperate Mollisol, a tropical Ultisol, a sub-arctic Andisol, and an arctic Gelisol). The 14C labeling enabled us to separate CO2 respired from added substrates and from native SOC. Microbial gene copy numbers were quantified at days 4, 30 and 270 using quantitative polymerase chain reaction (qPCR). Substrate C respiration was always higher for glucose than other substrates. Soils with cinnamic and stearic acid lost more native SOC than glucose- and starch-amended soils. Cinnamic and stearic acid amendments also exhibited higher fungal gene copy numbers at the end of incubation compared to unamended soils. We found that 270 days were sufficient to model the decomposition of simple substrates (glucose and starch) with three pools, but were insufficient for more complex substrates (cinnamic and stearic acid) and native SOC. This study reveals that substrate quality exerts considerable control on the microbial decomposition of newly added and native SOC, and demonstrates the need for multi-year incubation experiments to constrain decomposition parameters for the most recalcitrant fractions of SOC and complex substrates.

  5. Structural and evolutionary relationships of "AT-less" type I polyketide synthase ketosynthases

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Lohman, Jeremy; Ma, Ming; Osipiuk, Jerzy

    2015-10-13

    Acyltransferase (AT)-less type I polyketide synthases (PKSs) break the type I PKS paradigm. They lack the integrated AT domains within their modules and instead use a discrete AT that acts in trans, whereas a type I PKS module minimally contains AT, acyl carrier protein (ACP), and ketosynthase (KS) domains. Structures of canonical type I PKS KS-AT didomains reveal structured linkers that connect the two domains. AT-less type I PKS KSs have remnants of these linkers, which have been hypothesized to be AT docking domains. Natural products produced by AT-less type I PKSs are very complex because of an increased representationmore » of unique modifying domains. AT-less type I PKS KSs possess substrate specificity and fall into phylogenetic clades that correlate with their substrates, whereas canonical type I PKS KSs are monophyletic. We have solved crystal structures of seven AT-less type I PKS KS domains that represent various sequence clusters, revealing insight into the large structural and subtle amino acid residue differences that lead to unique active site topologies and substrate specificities. One set of structures represents a larger group of KS domains from both canonical and AT-less type I PKSs that accept amino acid-containing substrates. One structure has a partial AT-domain, revealing the structural consequences of a type I PKS KS evolving into an AT-less type I PKS KS. These structures highlight the structural diversity within the AT-less type I PKS KS family, and most important, provide a unique opportunity to study the molecular evolution of substrate specificity within the type I PKSs.« less

  6. Pedestal substrate for coated optics

    DOEpatents

    Hale, Layton C.; Malsbury, Terry N.; Patterson, Steven R.

    2001-01-01

    A pedestal optical substrate that simultaneously provides high substrate dynamic stiffness, provides low surface figure sensitivity to mechanical mounting hardware inputs, and constrains surface figure changes caused by optical coatings to be primarily spherical in nature. The pedestal optical substrate includes a disk-like optic or substrate section having a top surface that is coated, a disk-like base section that provides location at which the substrate can be mounted, and a connecting cylindrical section between the base and optics or substrate sections. The connecting cylindrical section may be attached via three spaced legs or members. However, the pedestal optical substrate can be manufactured from a solid piece of material to form a monolith, thus avoiding joints between the sections, or the disk-like base can be formed separately and connected to the connecting section. By way of example, the pedestal optical substrate may be utilized in the fabrication of optics for an extreme ultraviolet (EUV) lithography imaging system, or in any optical system requiring coated optics and substrates with reduced sensitivity to mechanical mounts.

  7. Computational approaches to substrate-based cell motility

    DOE PAGES

    Ziebert, Falko; Aranson, Igor S.

    2016-07-15

    Substrate-based crawling motility of eukaryotic cells is essential for many biological functions, both in developing and mature organisms. Motility dysfunctions are involved in several life-threatening pathologies such as cancer and metastasis. Motile cells are also a natural realization of active, self-propelled ‘particles’, a popular research topic in nonequilibrium physics. Finally, from the materials perspective, assemblies of motile cells and evolving tissues constitute a class of adaptive self-healing materials that respond to the topography, elasticity, and surface chemistry of the environment and react to external stimuli. Although a comprehensive understanding of substrate-based cell motility remains elusive, progress has been achieved recentlymore » in its modeling on the whole cell level. Furthermore we survey the most recent advances in computational approaches to cell movement and demonstrate how these models improve our understanding of complex self-organized systems such as living cells.« less

  8. Rational design of a carboxylic esterase RhEst1 based on computational analysis of substrate binding

    DOE PAGES

    Chen, Qi; Luan, Zheng -Jiao; Yu, Hui -Lei; ...

    2015-10-31

    A new carboxylic esterase RhEst1 which catalyzes the hydrolysis of (S)-(+)-2,2-dimethylcyclopropanecarboxylate (S-DmCpCe), the key chiral building block of cilastatin, was identified and subsequently crystallized in our previous work. Mutant RhEst 1A147I/V148F/G254A was found to show a 5-fold increase in the catalytic activity. In this work, molecular dynamic simulations were performed to elucidate the molecular determinant of the enzyme activity. Our simulations show that the substrate binds much more strongly in the A147I/V148F/G254A mutant than in wild type, with more hydrogen bonds formed between the substrate and the catalytic triad and the oxyanion hole. The OH group of the catalytic residuemore » Ser101 in the mutant is better positioned to initiate the nucleophilic attack on S-DmCpCe. Interestingly, the "170-179" loop which is involved in shaping the catalytic sites and facilitating the product release shows remarkable dynamic differences in the two systems. Based on the simulation results, six residues were identified as potential "hot-spots" for further experimental testing. Consequently, the G126S and R133L mutants show higher catalytic efficiency as compared with the wild type. In conclusion, this work provides molecular-level insights into the substrate binding mechanism of carboxylic esterase RhEst1, facilitating future experimental efforts toward developing more efficient RhEst1 variants for industrial applications.« less

  9. Metallic coatings on silicon substrates, and methods of forming metallic coatings on silicon substrates

    DOEpatents

    Branagan, Daniel J [Idaho Falls, ID; Hyde, Timothy A [Idaho Falls, ID; Fincke, James R [Los Alamos, NM

    2008-03-11

    The invention includes methods of forming a metallic coating on a substrate which contains silicon. A metallic glass layer is formed over a silicon surface of the substrate. The invention includes methods of protecting a silicon substrate. The substrate is provided within a deposition chamber along with a deposition target. Material from the deposition target is deposited over at least a portion of the silicon substrate to form a protective layer or structure which contains metallic glass. The metallic glass comprises iron and one or more of B, Si, P and C. The invention includes structures which have a substrate containing silicon and a metallic layer over the substrate. The metallic layer contains less than or equal to about 2 weight % carbon and has a hardness of at least 9.2 GPa. The metallic layer can have an amorphous microstructure or can be devitrified to have a nanocrystalline microstructure.

  10. RING E3 mechanism for ubiquitin ligation to a disordered substrate visualized for human anaphase-promoting complex

    DOE PAGES

    Brown, Nicholas G.; VanderLinden, Ryan; Watson, Edmond R.; ...

    2015-03-30

    For many E3 ligases, a mobile RING (Really Interesting New Gene) domain stimulates ubiquitin (Ub) transfer from a thioester-linked E2~Ub intermediate to a lysine on a remotely bound disordered substrate. One such E3 is the gigantic, multisubunit 1.2-MDa anaphase-promoting complex/cyclosome (APC), which controls cell division by ubiquitinating cell cycle regulators to drive their timely degradation. Intrinsically disordered substrates are typically recruited via their KEN-box, D-box, and/or other motifs binding to APC and a coactivator such as CDH1. On the opposite side of the APC, the dynamic catalytic core contains the cullin-like subunit APC2 and its RING partner APC11, which collaboratesmore » with the E2 UBCH10 (UBE2C) to ubiquitinate substrates. However, how dynamic RING–E2~Ub catalytic modules such as APC11–UBCH10~Ub collide with distally tethered disordered substrates remains poorly understood. In this paper, we report structural mechanisms of UBCH10 recruitment to APC CDH1 and substrate ubiquitination. Unexpectedly, in addition to binding APC11’s RING, UBCH10 is corecruited via interactions with APC2, which we visualized in a trapped complex representing an APC CDH1–UBCH10~Ub–substrate intermediate by cryo-electron microscopy, and in isolation by X-ray crystallography. To our knowledge, this is the first structural view of APC, or any cullin–RING E3, with E2 and substrate juxtaposed, and it reveals how tripartite cullin–RING–E2 interactions establish APC’s specificity for UBCH10 and harness a flexible catalytic module to drive ubiquitination of lysines within an accessible zone. Finally, we propose that multisite interactions reduce the degrees of freedom available to dynamic RING E3–E2~Ub catalytic modules, condense the search radius for target lysines, increase the chance of active-site collision with conformationally fluctuating substrates, and enable regulation.« less

  11. 4PS/insulin receptor substrate (IRS)-2 is the alternative substrate of the insulin receptor in IRS-1-deficient mice.

    PubMed

    Patti, M E; Sun, X J; Bruening, J C; Araki, E; Lipes, M A; White, M F; Kahn, C R

    1995-10-20

    Insulin receptor substrate-1 (IRS-1) is the major cytoplasmic substrate of the insulin and insulin-like growth factor (IGF)-1 receptors. Transgenic mice lacking IRS-1 are resistant to insulin and IGF-1, but exhibit significant residual insulin action which corresponds to the presence of an alternative high molecular weight substrate in liver and muscle. Recently, Sun et al. (Sun, X.-J., Wang, L.-M., Zhang, Y., Yenush, L. P., Myers, M. G., Jr., Glasheen, E., Lane, W.S., Pierce, J. H., and White, M. F. (1995) Nature 377, 173-177) purified and cloned 4PS, the major substrate of the IL-4 receptor-associated tyrosine kinase in myeloid cells, which has significant structural similarity to IRS-1. To determine if 4PS is the alternative substrate of the insulin receptor in IRS-1-deficient mice, we performed immunoprecipitation, immunoblotting, and phosphatidylinositol (PI) 3-kinase assays using specific antibodies to 4PS. Following insulin stimulation, 4PS is rapidly phosphorylated in liver and muscle, binds to the p85 subunit of PI 3-kinase, and activates the enzyme. Insulin stimulation also results in the association of 4PS with Grb 2 in both liver and muscle. In IRS-1-deficient mice, both the phosphorylation of 4PS and associated PI 3-kinase activity are enhanced, without an increase in protein expression. Immunodepletion of 4PS from liver and muscle homogenates removes most of the phosphotyrosine-associated PI 3-kinase activity in IRS-1-deficient mice. Thus, 4PS is the primary alternative substrate, i.e. IRS-2, which plays a major role in physiologic insulin signal transduction via both PI 3-kinase activation and Grb 2/Sos association. In IRS-1-deficient mice, 4PS/IRS-2 provides signal transduction to these two major pathways of insulin signaling.

  12. Surface-enhanced infrared spectroscopic studies of the catalytic behavior of silver nanoparticles on a germanium substrate.

    PubMed

    Liou, Yen-Chen Maggie; Yang, Jyisy; Fasasi, Ayuba; Griffiths, Peter R

    2011-05-01

    The catalytic activity of silver nanoparticles (AgNPs) on a germanium substrate is reported. Para-nitrothiophenol (pNTP) that had been adsorbed on this substrate is converted to p-aminothiophenol (pATP) under very mild reaction conditions, such as simply soaking in water. The AgNPs may be formed either by physical vapor deposition or by electroless deposition from a solution of silver nitrate. Analogous reactions were not observed on copper nanoparticles on germanium or AgNPs on silicon or zinc selenide even though very slow conversion of pNTP to pATP was observed with Au nanoparticles (AuNPs) on Ge under controlled reaction conditions. The effects of factors that could influence the catalytic reaction were examined; these included the particle size of the AgNPs, reaction temperature, concentration and chemical nature of other ions present in the solution, the pH of the water, and the nature of the substrate. The reaction rate was approximately independent of the particle size for AgNPs between 50 and 150 nm in diameter. Increasing the temperature accelerates the reaction significantly; at temperatures above 40 °C, the adsorbed pNTP is completely converted by water within five minutes. Not surprisingly, the reaction rate was increased as the pH of the solution was decreased, as the reduction of each nitro group to an amino group requires six protons. The presence of Br(-) and I(-) ions accelerated the reaction to the point that even at 4 °C, the conversion of the nitro group was still observable, while solutions containing chloride ions had to be heated to 40 °C before their effect became apparent. Apparently, Br(-) and I(-) ions remove the oxide layer from the surface of the germanium substrate, facilitating transfer of electrons from the germanium to the nitro group of the pNTP.

  13. Depth profiling and morphological characterization of AlN thin films deposited on Si substrates using a reactive sputter magnetron

    NASA Astrophysics Data System (ADS)

    Macchi, Carlos; Bürgi, Juan; García Molleja, Javier; Mariazzi, Sebastiano; Piccoli, Mattia; Bemporad, Edoardo; Feugeas, Jorge; Sennen Brusa, Roberto; Somoza, Alberto

    2014-08-01

    It is well-known that the characteristics of aluminum nitride thin films mainly depend on their morphologies, the quality of the film-substrate interfaces and the open volume defects. A study of the depth profiling and morphological characterization of AlN thin films deposited on two types of Si substrates is presented. Thin films of thicknesses between 200 and 400 nm were deposited during two deposition times using a reactive sputter magnetron. These films were characterized by means of X-ray diffraction and imaging techniques (SEM and TEM). To analyze the composition of the films, energy dispersive X-ray spectroscopy was applied. Positron annihilation spectroscopy, specifically Doppler broadening spectroscopy, was used to gather information on the depth profiling of open volume defects inside the films and the AlN films-Si substrate interfaces. The results are interpreted in terms of the structural changes induced in the films as a consequence of changes in the deposition time (i.e., thicknesses) and of the orientation of the substrates.

  14. Biohydrogen production from rotten orange with immobilized mixed culture: Effect of immobilization media for various composition of substrates

    NASA Astrophysics Data System (ADS)

    Damayanti, Astrilia; Sarto, Syamsiah, Siti; Sediawan, Wahyudi B.

    2015-12-01

    Enriched-immobilized mixed culture was utilized to produce biohydrogen in mesophilic condition under anaerobic condition using rotten orange as substrate. The process was conducted in batch reactors for 100 hours. Microbial cultures from three different sources were subject to a series of enrichment and immobilized in two different types of media, i.e. calcium alginate (CA, 2%) and mixture of alginate and activated carbon (CAC, 1:1). The performance of immobilized culture in each media was tested for biohydrogen production using four different substrate compositions, namely orange meat (OM), orange meat added with peel (OMP), orange meat added with limonene (OML), and mixture of orange meat and peel added with limonene (OMPL). The results show that, with immobilized culture in CA, the variation of substrate composition gave significant effect on the production of biohydrogen. The highest production of biohydrogen was detected for substrate containing only orange meet, i.e. 2.5%, which was about 3-5 times higher than biohydrogen production from other compositions of substrate. The use of immobilized culture in CAC in general has increased the hydrogen production by 2-7 times depending on the composition of substrate, i.e. 5.4%, 4.8%, 5.1%, and 4.4% for OM, OMP, OML, and OMPL, respectively. The addition of activated carbon has eliminated the effect of inhibitory compounds in the substrate. The major soluble metabolites were acetic acid, propionic acid, and butyric acid.

  15. Biohydrogen production from rotten orange with immobilized mixed culture: Effect of immobilization media for various composition of substrates

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Damayanti, Astrilia, E-mail: liasholehasd@gmail.com; Department of Chemical Engineering, Faculty of Engineering, Gadjah Mada University, Jl. Grafika No. 2, Kampus UGM, Yogyakarta 55281; Sarto,

    Enriched–immobilized mixed culture was utilized to produce biohydrogen in mesophilic condition under anaerobic condition using rotten orange as substrate. The process was conducted in batch reactors for 100 hours. Microbial cultures from three different sources were subject to a series of enrichment and immobilized in two different types of media, i.e. calcium alginate (CA, 2%) and mixture of alginate and activated carbon (CAC, 1:1). The performance of immobilized culture in each media was tested for biohydrogen production using four different substrate compositions, namely orange meat (OM), orange meat added with peel (OMP), orange meat added with limonene (OML), and mixturemore » of orange meat and peel added with limonene (OMPL). The results show that, with immobilized culture in CA, the variation of substrate composition gave significant effect on the production of biohydrogen. The highest production of biohydrogen was detected for substrate containing only orange meet, i.e. 2.5%, which was about 3-5 times higher than biohydrogen production from other compositions of substrate. The use of immobilized culture in CAC in general has increased the hydrogen production by 2-7 times depending on the composition of substrate, i.e. 5.4%, 4.8%, 5.1%, and 4.4% for OM, OMP, OML, and OMPL, respectively. The addition of activated carbon has eliminated the effect of inhibitory compounds in the substrate. The major soluble metabolites were acetic acid, propionic acid, and butyric acid.« less

  16. Exosites in the substrate specificity of blood coagulation reactions.

    PubMed

    Bock, P E; Panizzi, P; Verhamme, I M A

    2007-07-01

    The specificity of blood coagulation proteinases for substrate, inhibitor, and effector recognition is mediated by exosites on the surfaces of the catalytic domains, physically separated from the catalytic site. Some thrombin ligands bind specifically to either exosite I or II, while others engage both exosites. The involvement of different, overlapping constellations of exosite residues enables binding of structurally diverse ligands. The flexibility of the thrombin structure is central to the mechanism of complex formation and the specificity of exosite interactions. Encounter complex formation is driven by electrostatic ligand-exosite interactions, followed by conformational rearrangement to a stable complex. Exosites on some zymogens are in low affinity proexosite states and are expressed concomitant with catalytic site activation. The requirement for exosite expression controls the specificity of assembly of catalytic complexes on the coagulation pathway, such as the membrane-bound factor Xa*factor Va (prothrombinase) complex, and prevents premature assembly. Substrate recognition by prothrombinase involves a two-step mechanism with initial docking of prothrombin to exosites, followed by a conformational change to engage the FXa catalytic site. Prothrombin and its activation intermediates bind prothrombinase in two alternative conformations determined by the zymogen to proteinase transition that are hypothesized to involve prothrombin (pro)exosite I interactions with FVa, which underpin the sequential activation pathway. The role of exosites as the major source of substrate specificity has stimulated development of exosite-targeted anticoagulants for treatment of thrombosis.

  17. Winter colonisation and succession of filamentous macroalgae on artificial substrates and possible relationships to Fucus vesiculosus settlement in early summer

    NASA Astrophysics Data System (ADS)

    Kraufvelin, Patrik; Ruuskanen, Ari T.; Nappu, Niko; Kiirikki, Mikko

    2007-05-01

    During the reproduction period of Fucus vesiculosus, which occurs only once a year (in May-June) along the Finnish coast of the northern Baltic Sea, a thick carpet of filamentous algae often covers hard substrates suitable for zygote settlement. By placing out artificial substrates into the field, monthly over a period of eight months prior to F. vesiculosus settlement (October 2001-June 2002), we investigated the autumn/winter/spring colonisation and succession of filamentous algae and their possible relationships with the settlement success of F. vesiculosus under naturally variable field conditions. The substrates exposed in October 2001 became covered by filamentous brown algal Pilayella littoralis mats, which persisted over the settlement period of F. vesiculosus, but now also were accompanied by large amounts of the filamentous green alga Cladophora glomerata. The substrates exposed from November 2001 onwards hosted smaller amounts of P. littoralis during the winter and different filamentous algal communities at the time of F. vesiculosus settlement, i.e. less P. littoralis and C. glomerata, but Dictyosiphon foeniculaceus, Ceramium tenuicorne and Ulva intestinalis instead. We observed recruits of F. vesiculosus on all substrates, except on the ones placed out in October 2001. Significantly more P. littoralis and C. glomerata on the October substrates may explain the failed F. vesiculosus recruitment, although we could not establish direct causal or correlational relationships between filamentous algae and F. vesiculosus settlement. We compared the results with a previous un-replicated pilot study in the same area demonstrating similar response patterns.

  18. Batch kinetics of Pseudomonas sp. growth on benzene. Modeling of product and substrate inhibitions.

    PubMed

    Monero, Alessandra; Lanza, Luca; Zilli, Mario; Sene, Luciane; Converti, Attilio

    2003-01-01

    Batch tests of benzene degradation were performed in liquid phase at 30 degrees C, pH 6.8 +/- 0.2, and 200 rpm in two 3-L stirred tank bioreactors, using the benzene-degrading bacterium Pseudomonas sp. NCIMB 9688. A relatively high starting biomass level (220-270 mg(X)/L) and starting benzene concentration ranging from 20 to 200 mg(S)/L were selected as conditions to investigate possible inhibition phenomena. Volumetric as well as specific rates of biomass formation and substrate consumption were calculated from experimental data of both growth and benzene degradation and used to propose and check a new overall kinetic model for cell growth simultaneously accounting for both product and substrate inhibitions. The results of the present study evidenced the occurrence of a competitive-type product inhibition due to 2-hydroxymuconic semialdehyde (K(iP)' = 0.902 mg(S)/L), which was stronger than the uncompetitive-type inhibition exerted by substrate (K(iS) = 7.69 mg(S)/L).

  19. A microarray of ubiquitylated proteins for profiling deubiquitylase activity reveals the critical roles of both chain and substrate.

    PubMed

    Loch, Christian M; Strickler, James E

    2012-11-01

    Substrate ubiquitylation is a reversible process critical to cellular homeostasis that is often dysregulated in many human pathologies including cancer and neurodegeneration. Elucidating the mechanistic details of this pathway could unlock a large store of information useful to the design of diagnostic and therapeutic interventions. Proteomic approaches to the questions at hand have generally utilized mass spectrometry (MS), which has been successful in identifying both ubiquitylation substrates and profiling pan-cellular chain linkages, but is generally unable to connect the two. Interacting partners of the deubiquitylating enzymes (DUBs) have also been reported by MS, although substrates of catalytically competent DUBs generally cannot be. Where they have been used towards the study of ubiquitylation, protein microarrays have usually functioned as platforms for the identification of substrates for specific E3 ubiquitin ligases. Here, we report on the first use of protein microarrays to identify substrates of DUBs, and in so doing demonstrate the first example of microarray proteomics involving multiple (i.e., distinct, sequential and opposing) enzymatic activities. This technique demonstrates the selectivity of DUBs for both substrate and type (mono- versus poly-) of ubiquitylation. This work shows that the vast majority of DUBs are monoubiquitylated in vitro, and are incapable of removing this modification from themselves. This work also underscores the critical role of utilizing both ubiquitin chains and substrates when attempting to characterize DUBs. This article is part of a Special Issue entitled: Ubiquitin Drug Discovery and Diagnostics. Copyright © 2012 Elsevier B.V. All rights reserved.

  20. Efficient, flexible and mechanically robust perovskite solar cells on inverted nanocone plastic substrates.

    PubMed

    Tavakoli, Mohammad Mahdi; Lin, Qingfeng; Leung, Siu-Fung; Lui, Ga Ching; Lu, Hao; Li, Liang; Xiang, Bin; Fan, Zhiyong

    2016-02-21

    Utilization of nanostructures on photovoltaic devices can significantly improve the device energy conversion efficiency by enhancing the device light harvesting capability as well as carrier collection efficiency. However, improvements in device mechanical robustness and reliability, particularly for flexible devices, have rarely been reported with in-depth understanding. In this work, we fabricated efficient, flexible and mechanically robust organometallic perovskite solar cells on plastic substrates with inverted nanocone (i-cone) structures. Compared with the reference cell that was fabricated on a flat substrate, it was shown that the device power conversion efficiency could be improved by 37%, and reached up to 11.29% on i-cone substrates. More interestingly, it was discovered that the performance of an i-cone device remained more than 90% of the initial value even after 200 mechanical bending cycles, which is remarkably better than for the flat reference device, which degraded down to only 60% in the same test. Our experiments, coupled with mechanical simulation, demonstrated that a nanostructured template can greatly help in relaxing stress and strain upon device bending, which suppresses crack nucleation in different layers of a perovskite solar cell. This essentially leads to much improved device reliability and robustness and will have significant impact on practical applications.

  1. Use of aluminum oxide as a permeation barrier for producing thin films on aluminum substrates

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Provo, James L., E-mail: jlprovo@verizon.net

    2016-07-15

    Aluminum has desirable characteristics of good thermal properties, good electrical characteristics, good optical properties, and the characteristic of being nonmagnetic and having a low atomic weight (26.98 g atoms), but because of its low melting point (660 °C) and ability as a reactive metal to alloy with most common metals in use, it has been ignored as a substrate material for use in processing thin films. The author developed a simple solution to this problem, by putting a permeation barrier of alumina (Al{sub 2}O{sub 3}) onto the surface of pure Al substrates by using a standard chemical oxidation process of the surfacemore » (i.e., anodization), before additional film deposition of reactive metals at temperatures up to 500 °C for 1-h, without the formation of alloys or intermetallic compounds to affect the good properties of Al substrates. The chromic acid anodization process used (MIL-A-8625) produced a film barrier of ∼(500–1000) nm of alumina. The fact that refractory Al{sub 2}O{sub 3} can inhibit the reaction of metals with Al at temperatures below 500 °C suggests that Al is a satisfactory substrate if properly oxidized prior to film deposition. To prove this concept, thin film samples of Cr, Mo, Er, Sc, Ti, and Zr were prepared on anodized Al substrates and studied by x-ray diffraction, Rutherford ion back scattering, and Auger/argon sputter surface profile analysis to determine any film substrate interactions. In addition, a major purpose of our study was to determine if ErD{sub 2} thin films could be produced on Al substrates with fully hydrided Er films. Thus, a thin film of ErD{sub 2} on an anodized Al substrate was prepared and studied, with and without the alumina permeation barrier. Films for study were prepared on 1.27 cm diameter Al substrates with ∼500 nm of the metals studied after anodization. Substrates were weighed, cleaned, and vacuum fired at 500 °C prior to use. The Al substrates were deposited using standard

  2. Access channels to the buried active site control substrate specificity in CYP1A P450 enzymes.

    PubMed

    Urban, Philippe; Truan, Gilles; Pompon, Denis

    2015-04-01

    A cytochrome P450 active site is buried within the protein molecule and several channels connect the catalytic cavity to the protein surface. Their role in P450 catalysis is still matter of debate. The aim of this study was to understand the possible relations existing between channels and substrate specificity. Time course studies were carried out with a collection of polycyclic substrates of increasing sizes assayed with a library of wild-type and chimeric CYP1A enzymes. This resulted in a matrix of activities sufficiently large to allow statistical analysis. Multivariate statistical tools were used to decipher the correlation between observed activity shifts and sequence segment swaps. The global kinetic behavior of CYP1A enzymes toward polycyclic substrates is significantly different depending on the size of the substrate. Mutations which are close or lining the P450 channels significantly affect this discrimination, whereas mutations distant from the P450 channels do not. Size discrimination is taking place for polycyclic substrates at the entrance of the different P450 access channels. It is thus hypothesized that channels differentiate small from large substrates in CYP1A enzymes, implying that residues located at the surface of the protein may be implied in this differential recognition. Catalysis thus occurs after a two-step recognition process, one at the surface of the protein and the second within the catalytic cavity in enzymes with a buried active site. Copyright © 2014 Elsevier B.V. All rights reserved.

  3. Process for forming a metal compound coating on a substrate

    DOEpatents

    Sharp, D.J.; Vernon, M.E.; Wright, S.A.

    1988-06-29

    A method of coating a substrate with a thin layer of a metal compound by forming a dispersion of an electrophoretically active organic colloid and a precursor of the metal compound in an electrolytic cell in which the substrate is an electrode. Upon application of an electric potential, the electrode is coated with a mixture of the organic colloid and the precursor to the metal compound, and the coated substrate is then heated in the presence of an atmosphere or vacuum to decompose the organic colloid and form a coating of either a combination of metal compound and carbon, or optionally forming a porous metal compound coating by heating to a temperature high enough to chemically react the carbon.

  4. Strain Multiplexed Metasurface Holograms on a Stretchable Substrate.

    PubMed

    Malek, Stephanie C; Ee, Ho-Seok; Agarwal, Ritesh

    2017-06-14

    We demonstrate reconfigurable phase-only computer-generated metasurface holograms with up to three image planes operating in the visible regime fabricated with gold nanorods on a stretchable polydimethylsiloxane substrate. Stretching the substrate enlarges the hologram image and changes the location of the image plane. Upon stretching, these devices can switch the displayed holographic image between multiple distinct images. This work opens up the possibilities for stretchable metasurface holograms as flat devices for dynamically reconfigurable optical communication and display. It also confirms that metasurfaces on stretchable substrates can serve as platform for a variety of reconfigurable optical devices.

  5. Evaporation of liquid droplets on solid substrates. II. Periodic substrates with moving contact lines

    NASA Astrophysics Data System (ADS)

    Amini, Amirhossein; Homsy, G. M.

    2017-04-01

    Experiments on evaporating droplets on structured surfaces have shown that the contact line does not move with constant speed, but rather in a steplike "stick-slip" fashion. As a first step in understanding such behavior, we study the evaporation of a two-dimensional volatile liquid droplet on a nonplanar heated solid substrate with a moving contact line and fixed contact angle. The model for the flat case is adapted to include curved substrates, numerical solutions are achieved for various periodic and quasiperiodic substrate profiles, and the dynamics of the contact line and the apparent contact angle are studied. In contrast with our results for a flat substrate, for which the contact line recedes in a nearly constant speed, we observe that the contact line speed and position show significant time variation and that the contact line moves in an approximate steplike fashion on relatively steep substrates. For the simplest case of a periodic substrate, we find that the apparent contact angle is periodic in time. For doubly periodic substrates, we find that the apparent contact angle is periodic and that the problem exhibits a phase-locking behavior. For multimode quasiperiodic substrates, we find the contact line behavior to be temporally complex and not only limited to a stick-slip motion. In all cases, we find that the overall evaporation is increased relative to the flat substrate.

  6. Probing photo-carrier collection efficiencies of individual silicon nanowire diodes on a wafer substrate.

    PubMed

    Schmitt, S W; Brönstrup, G; Shalev, G; Srivastava, S K; Bashouti, M Y; Döhler, G H; Christiansen, S H

    2014-07-21

    Vertically aligned silicon nanowire (SiNW) diodes are promising candidates for the integration into various opto-electronic device concepts for e.g. sensing or solar energy conversion. Individual SiNW p-n diodes have intensively been studied, but to date an assessment of their device performance once integrated on a silicon substrate has not been made. We show that using a scanning electron microscope (SEM) equipped with a nano-manipulator and an optical fiber feed-through for tunable (wavelength, power using a tunable laser source) sample illumination, the dark and illuminated current-voltage (I-V) curve of individual SiNW diodes on the substrate wafer can be measured. Surprisingly, the I-V-curve of the serially coupled system composed of SiNW/wafers is accurately described by an equivalent circuit model of a single diode and diode parameters like series and shunting resistivity, diode ideality factor and photocurrent can be retrieved from a fit. We show that the photo-carrier collection efficiency (PCE) of the integrated diode illuminated with variable wavelength and intensity light directly gives insight into the quality of the device design at the nanoscale. We find that the PCE decreases for high light intensities and photocurrent densities, due to the fact that considerable amounts of photo-excited carriers generated within the substrate lead to a decrease in shunting resistivity of the SiNW diode and deteriorate its rectification. The PCE decreases systematically for smaller wavelengths of visible light, showing the possibility of monitoring the effectiveness of the SiNW device surface passivation using the shown measurement technique. The integrated device was pre-characterized using secondary ion mass spectrometry (SIMS), TCAD simulations and electron beam induced current (EBIC) measurements to validate the properties of the characterized material at the single SiNW diode level.

  7. Substrate degradation by the proteasome: a single-molecule kinetic analysis

    PubMed Central

    Lu, Ying; Lee, Byung-hoon; King, Randall W; Finley, Daniel; Kirschner, Marc W

    2015-01-01

    To address how the configuration of conjugated ubiquitins determines the recognition of substrates by the proteasome, we analyzed the degradation kinetics of substrates with chemically defined ubiquitin configurations. Contrary to the view that a tetraubiquitin chain is the minimal signal for efficient degradation, we find that distributing the ubiquitins as diubiquitin chains provides a more efficient signal. To understand how the proteasome actually discriminates among ubiquitin configurations, we developed single-molecule assays that distinguished intermediate steps of degradation kinetically. The level of ubiquitin on a substrate drives proteasome-substrate interaction, whereas the chain structure of ubiquitin affects translocation into the axial channel on the proteasome. Together these two features largely determine the susceptibility of substrates for proteasomal degradation. PMID:25859050

  8. A Consecutive Spray Printing Strategy to Construct and Integrate Diverse Supercapacitors on Various Substrates.

    PubMed

    Wang, Xinyu; Lu, Qiongqiong; Chen, Chen; Han, Mo; Wang, Qingrong; Li, Haixia; Niu, Zhiqiang; Chen, Jun

    2017-08-30

    The rapid development of printable electronic devices with flexible and wearable characteristics requires supercapacitor devices to be printable, light, thin, integrated macro- and micro-devices with flexibility. Herein, we developed a consecutive spray printing strategy to controllably construct and integrate diverse supercapacitors on various substrates. In such a strategy, all supercapacitor components are fully printable, and their thicknesses and shapes are well controlled. As a result, supercapacitors obtained by this strategy achieve diverse structures and shapes. In addition, different nanocarbon and pseudocapacitive materials are applicable for the fabrication of these diverse supercapacitors. Furthermore, the diverse supercapacitors can be readily constructed on various objects with planar, curved, or even rough surfaces (e.g., plastic film, glass, cloth, and paper). More importantly, the consecutive spray printing process can integrate several supercapacitors together in the perpendicular and parallel directions of one substrate by designing the structure of electrodes and separators. This enlightens the construction and integration of fully printable supercapacitors with diverse configurations to be compatible with fully printable electronics on various substrates.

  9. Inoculation of sphagnum-based soil substrate with entomopathogenic fungus Isaria fumosorosea (Hypocreales: Cordycipitaceae)

    NASA Astrophysics Data System (ADS)

    Zemek, Rostislav; Konopická, Jana; Bohatá, Andrea

    2018-04-01

    Convenient ecological alternative to broad-spectrum chemical pesticides is the utilization of natural enemies, like predators, parasitoids and microorganisms. A substantial number of microbial biopesticides based on entomopathogenic fungi have been developed worldwide since 1960s. Beauveria bassiana (Balsamo-Crivelli) Vuillemin, Metarhizium anisopliae (Metchnikoff) Sorokin, Isaria fumosorosea (Wize), and B. brongniartii (Saccardo) Petch are the most common species used in commercially produced mycopesticides. Besides direct biological pest control, these fungi could be also used in preventive application programs, particularly in ornamental or nursery plants to provide better control against pests. The aim of the present study was to investigate potential of pre-colonization of sphagnum-based soil substrate with I. fumosorosea strain CCM 8367 which was found earlier to be highly virulent against several pest species. We developed simple laboratory apparatus for application of fungal spore suspension into the substrate. Suspension was prepared from blastospores obtained by submerged cultivation on potato dextrose broth (PDB) medium using an orbital shaker. Inoculated substrate was placed into plastic bags and stored at constant temperature for six months. Every month, samples were analyzed for concentration of colony forming units (CFU) by elution and selective medium technique. The results showed that at 20°C the fungus successfully colonized the soil substrate and persisted there although the mean concentration slightly decreased from 5.89×104 to 2.76×104 CFU per milliliter of substrate during the experiment. Temperature 30°C had negative effect on survival of the fungus and is not recommended for long-term storage of pre-inoculated substrate. We can conclude that I. fumosorosea-colonized substrate can be convenient for preventive and permanent protection of various plants against soil-dwelling pests.

  10. Process for metallization of a substrate by irradiative curing of a catalyst applied thereto

    DOEpatents

    Chen, Ken S.; Morgan, William P.; Zich, John L.

    1999-01-01

    An improved additive process for metallization of substrates is described whereby a catalyst solution is applied to a surface of a substrate. Metallic catalytic clusters can be formed in the catalyst solution on the substrate surface by irradiating the substrate. Electroless plating can then deposit metal onto the portion of the substrate surface having metallic clusters. Additional metallization thickness can be obtained by electrolytically plating the substrate surface after the electroless plating step.

  11. Arabidopsis ATG4 cysteine proteases specificity toward ATG8 substrates

    PubMed Central

    Park, Eunsook; Woo, Jongchan; Dinesh-Kumar, SP

    2014-01-01

    Macroautophagy (hereafter autophagy) is a regulated intracellular process during which cytoplasmic cargo engulfed by double-membrane autophagosomes is delivered to the vacuole or lysosome for degradation and recycling. Atg8 that is conjugated to phosphatidylethanolamine (PE) during autophagy plays an important role not only in autophagosome biogenesis but also in cargo recruitment. Conjugation of PE to Atg8 requires processing of the C-terminal conserved glycine residue in Atg8 by the Atg4 cysteine protease. The Arabidopsis plant genome contains 9 Atg8 (AtATG8a to AtATG8i) and 2 Atg4 (AtATG4a and AtATG4b) family members. To understand AtATG4’s specificity toward different AtATG8 substrates, we generated a unique synthetic substrate C-AtATG8-ShR (citrine-AtATG8-Renilla luciferase SuperhRLUC). In vitro analyses indicated that AtATG4a is catalytically more active and has broad AtATG8 substrate specificity compared with AtATG4b. Arabidopsis transgenic plants expressing the synthetic substrate C-AtAtg8a-ShR is efficiently processed by endogenous AtATG4s and targeted to the vacuole during nitrogen starvation. These results indicate that the synthetic substrate mimics endogenous AtATG8, and its processing can be monitored in vivo by a bioluminescence resonance energy transfer (BRET) assay. The synthetic Atg8 substrates provide an easy and versatile method to study plant autophagy during different biological processes. PMID:24658121

  12. Arbuscular Mycorrhiza Alleviates Restrictions to Substrate Water Flow and Delays Transpiration Limitation to Stronger Drought in Tomato.

    PubMed

    Bitterlich, Michael; Sandmann, Martin; Graefe, Jan

    2018-01-01

    Arbuscular mycorrhizal fungi (AMF) proliferate in soil pores, on the surface of soil particles and affect soil structure. Although modifications in substrate moisture retention depend on structure and could influence plant water extraction, mycorrhizal impacts on water retention and hydraulic conductivity were rarely quantified. Hence, we asked whether inoculation with AMF affects substrate water retention, water transport properties and at which drought intensity those factors become limiting for plant transpiration. Solanum lycopersicum plants were set up in the glasshouse, inoculated or not with Funneliformis mosseae , and grown for 35 days under ample water supply. After mycorrhizal establishment, we harvested three sets of plants, one before (36 days after inoculation) and the second (day 42) and third (day 47) within a sequential drying episode. Sampling cores were introduced into pots before planting. After harvest, moisture retention and substrate conductivity properties were assessed and water retention and hydraulic conductivity models were fitted. A root water uptake model was adopted in order to identify the critical substrate moisture that induces soil derived transpiration limitation. Neither substrate porosity nor saturated water contents were affected by inoculation, but both declined after substrates dried. Drying also caused a decline in pot water capacity and hydraulic conductivity. Plant available water contents under wet (pF 1.8-4.2) and dry (pF 2.5-4.2) conditions increased in mycorrhizal substrates and were conserved after drying. Substrate hydraulic conductivity was higher in mycorrhizal pots before and during drought exposure. After withholding water from pots, higher substrate drying rates and lower substrate water potentials were found in mycorrhizal substrates. Mycorrhiza neither affected leaf area nor root weight or length. Consistently with higher substrate drying rates, AMF restored the plant hydraulic status, and increased plant

  13. Arbuscular Mycorrhiza Alleviates Restrictions to Substrate Water Flow and Delays Transpiration Limitation to Stronger Drought in Tomato

    PubMed Central

    Bitterlich, Michael; Sandmann, Martin; Graefe, Jan

    2018-01-01

    Arbuscular mycorrhizal fungi (AMF) proliferate in soil pores, on the surface of soil particles and affect soil structure. Although modifications in substrate moisture retention depend on structure and could influence plant water extraction, mycorrhizal impacts on water retention and hydraulic conductivity were rarely quantified. Hence, we asked whether inoculation with AMF affects substrate water retention, water transport properties and at which drought intensity those factors become limiting for plant transpiration. Solanum lycopersicum plants were set up in the glasshouse, inoculated or not with Funneliformis mosseae, and grown for 35 days under ample water supply. After mycorrhizal establishment, we harvested three sets of plants, one before (36 days after inoculation) and the second (day 42) and third (day 47) within a sequential drying episode. Sampling cores were introduced into pots before planting. After harvest, moisture retention and substrate conductivity properties were assessed and water retention and hydraulic conductivity models were fitted. A root water uptake model was adopted in order to identify the critical substrate moisture that induces soil derived transpiration limitation. Neither substrate porosity nor saturated water contents were affected by inoculation, but both declined after substrates dried. Drying also caused a decline in pot water capacity and hydraulic conductivity. Plant available water contents under wet (pF 1.8–4.2) and dry (pF 2.5–4.2) conditions increased in mycorrhizal substrates and were conserved after drying. Substrate hydraulic conductivity was higher in mycorrhizal pots before and during drought exposure. After withholding water from pots, higher substrate drying rates and lower substrate water potentials were found in mycorrhizal substrates. Mycorrhiza neither affected leaf area nor root weight or length. Consistently with higher substrate drying rates, AMF restored the plant hydraulic status, and increased plant

  14. A platelet-to-pyramid shape transition under the influence of the adsorbate substrate interfacial energy

    NASA Astrophysics Data System (ADS)

    Lin, Cheng-Hsiao; Tsai, Yan-Chr

    2002-07-01

    Within the Tersoff approximation, we obtain an analytic expression for the elastic self-energy of a truncated hut which is more general than that of a truncated pyramid [C. Duport, C. Priester, J. Villain, in: Morphological Organization in Epitaxial Growth and Removal, World Scientific Series on Directions in Condensed Matter Physics, 1997, p. 73]. A pyramidal cluster studied previously can be treated as a square-based hut within the present formalism. The previous results [C. Duport, C. Priester, J. Villain, in: Morphological Organization in Epitaxial Growth and Removal, World Scientific Series on Directions in Condensed Matter Physics, 1997, p. 73; C. Duport, Université de Grenoble, Juin 1996; Phys. Rep. 324 (2000) 271] were obtained on the assumptions of neglecting the adsorbate-substrate interfacial energy and the equilibrium cluster forming with a square base. They predicted that when the volume of a cluster is above some critical value, it preferably forms as a pyramid rather than a platelet in the absence of other strained clusters. Instead, in this paper, we take the interfacial energy into account, based on the work by Korutcheva et al. [I. Markov, Crystal Growth for Beginners, Fundamentals of Nucleation, Crystal Growth Epitaxy, World Scientific, Singapore, 1995; Phys. Rev. B 61 (2000) 16890]. Besides, we start with the consideration of a hut cluster probably forming with a rectangular base instead of a square one [C. Duport, C. Priester, J. Villain, in: Morphological Organization in Epitaxial Growth and Removal, World Scientific Series on Directions in Condensed Matter Physics, 1997, p. 73; C. Duport, Université de Grenoble, Juin 1996]. By employing the derived analytic expression of the surface and elastic energies, we find that the two- to three- dimensional (2D-3D) transition with the inclusion of the adsorbate-substrate interfacial energy is quantitatively modified. It should provide more accurate predicted values of the critical volume in 2D-3D

  15. How do animals use substrate-borne vibrations as an information source?

    NASA Astrophysics Data System (ADS)

    Hill, Peggy S. M.

    2009-12-01

    Animal communication is a dynamic field that promotes cross-disciplinary study of the complex mechanisms of sending and receiving signals, the neurobiology of signal detection and processing, and the behaviors of animals creating and responding to encoded messages. Alongside visual signals, songs, or pheromones exists another major communication channel that has been rather neglected until recent decades: substrate-borne vibration. Vibrations carried in the substrate are considered to provide a very old and apparently ubiquitous communication channel that is used alone or in combination with other information channels in multimodal signaling. The substrate could be ‘the ground’, or a plant leaf or stem, or the surface of water, or a spider’s web, or a honeybee’s honeycomb. Animals moving on these substrates typically create incidental vibrations that can alert others to their presence. They also may use behaviors to create vibrational waves that are employed in the contexts of mate location and identification, courtship and mating, maternal care and sibling interactions, predation, predator avoidance, foraging, and general recruitment of family members to work. In fact, animals use substrate-borne vibrations to signal in the same contexts that they use vision, hearing, touch, taste, or smell. Study of vibrational communication across animal taxa provides more than just a more complete story. Communication through substrate-borne vibration has its own constraints and opportunities not found in other signaling modalities. Here, I review the state of our understanding of information acquisition via substrate-borne vibrations with special attention to the most recent literature.

  16. Substrate channel in nitrogenase revealed by a molecular dynamics approach.

    PubMed

    Smith, Dayle; Danyal, Karamatullah; Raugei, Simone; Seefeldt, Lance C

    2014-04-15

    Mo-dependent nitrogenase catalyzes the biological reduction of N2 to two NH3 molecules at FeMo-cofactor buried deep inside the MoFe protein. Access of substrates, such as N2, to the active site is likely restricted by the surrounding protein, requiring substrate channels that lead from the surface to the active site. Earlier studies on crystallographic structures of the MoFe protein have suggested three putative substrate channels. Here, we have utilized submicrosecond atomistic molecular dynamics simulations to allow the nitrogenase MoFe protein to explore its conformational space in an aqueous solution at physiological ionic strength, revealing a putative substrate channel. The viability of this observed channel was tested by examining the free energy of passage of N2 from the surface through the channel to FeMo-cofactor, resulting in the discovery of a very low energy barrier. These studies point to a viable substrate channel in nitrogenase that appears during thermal motions of the protein in an aqueous environment and that approaches a face of FeMo-cofactor earlier implicated in substrate binding.

  17. Proteolytic Activity of Prostate-Specific Antigen (PSA) towards Protein Substrates and Effect of Peptides Stimulating PSA Activity

    PubMed Central

    Mattsson, Johanna M.; Ravela, Suvi; Hekim, Can; Jonsson, Magnus; Malm, Johan; Närvänen, Ale; Stenman, Ulf-Håkan; Koistinen, Hannu

    2014-01-01

    Prostate-specific antigen (PSA or kallikrein-related peptidase-3, KLK3) exerts chymotrypsin-like proteolytic activity. The main biological function of PSA is the liquefaction of the clot formed after ejaculation by cleavage of semenogelins I and II in seminal fluid. PSA also cleaves several other substrates, which may explain its putative functions in prostate cancer and its antiangiogenic activity. We compared the proteolytic efficiency of PSA towards several protein and peptide substrates and studied the effect of peptides stimulating the activity of PSA with these substrates. An endothelial cell tube formation model was used to analyze the effect of PSA-degraded protein fragments on angiogenesis. We showed that PSA degrades semenogelins I and II much more efficiently than other previously identified protein substrates, e.g., fibronectin, galectin-3 and IGFBP-3. We identified nidogen-1 as a new substrate for PSA. Peptides B2 and C4 that stimulate the activity of PSA towards small peptide substrates also enhanced the proteolytic activity of PSA towards protein substrates. Nidogen-1, galectin-3 or their fragments produced by PSA did not have any effect on endothelial cell tube formation. Although PSA cleaves several other protein substrates, in addition to semenogelins, the physiological importance of this activity remains speculative. The PSA levels in prostate are very high, but several other highly active proteases, such as hK2 and trypsin, are also expressed in the prostate and may cleave protein substrates that are weakly cleaved by PSA. PMID:25237904

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Khare, Baldeep; Fu, Zheng-Qing; Huang, I-Hsiu

    2012-02-07

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

  19. Purification and substrate specificities of a fructanase from Kluyveromyces marxianus isolated from the fermentation process of Mezcal.

    PubMed

    Arrizon, Javier; Morel, Sandrine; Gschaedler, Anne; Monsan, Pierre

    2011-02-01

    A fructanase, produced by a Kluyveromyces marxianus strain isolated during the fermentation step of the elaboration process of "Mezcal de Guerrero" was purified and biochemically characterized. The active protein was a glycosylated dimer with a molecular weight of approximately 250 kDa. The specific enzymatic activity of the protein was determined for different substrates: sucrose, inulin, Agave tequilana fructan, levan and Actilight® and compared with the activity of Fructozyme®. The hydrolysis profile of the different substrates analyzed by HPAEC-PAD showed that the enzyme has different affinities over the substrates tested with a sucrose/inulin enzymatic activity ratio (S/I) of 125. For the hydrolysis of Agave tequilana fructans, the enzyme also showed a higher enzymatic activity and specificity than Fructozyme®, which is important for its potential application in the tequila industry. Copyright © 2010 Elsevier Ltd. All rights reserved.

  20. Mechanics of hard films on soft substrates

    NASA Astrophysics Data System (ADS)

    Lu, Nanshu

    2009-12-01

    strain they are subject to. Instead of using blanket films that fail at strains less than i%, we have patterned ceramic films into a lattice of periodic, isolated islands. Failure modes such as channel cracking, debonding, and wrinkling have been identified. Island behaviors are controlled by factors such as island size, thickness, and elastic mismatch with the substrate. A very soft interlayer between the islands and the underlying polyimide substrate reduces strains in the islands by orders of magnitude. Using this approach, substrates with arrays of 200 x 200 mum2 large SiNx islands were stretched beyond 20% without cracking or debonding the islands. In summary, highly stretchable thin metal films and ceramic island arrays supported by polymer substrates have been achieved, along with mechanistic understandings of their deformation and failure mechanisms.

  1. Group I-III-VI.sub.2 semiconductor films for solar cell application

    DOEpatents

    Basol, Bulent M.; Kapur, Vijay K.

    1991-01-01

    This invention relates to an improved thin film solar cell with excellent electrical and mechanical integrity. The device comprises a substrate, a Group I-III-VI.sub.2 semiconductor absorber layer and a transparent window layer. The mechanical bond between the substrate and the Group I-III-VI.sub.2 semiconductor layer is enhanced by an intermediate layer between the substrate and the Group I-III-VI.sub.2 semiconductor film being grown. The intermediate layer contains tellurium or substitutes therefor, such as Se, Sn, or Pb. The intermediate layer improves the morphology and electrical characteristics of the Group I-III-VI.sub.2 semiconductor layer.

  2. Engineering Klebsiella sp. 601 multicopper oxidase enhances the catalytic efficiency towards phenolic substrates.

    PubMed

    Li, Yadong; Gong, Zijun; Li, Xin; Li, Yang; Wang, Xing-Guo

    2011-05-31

    Structural comparison between bacterial CueO and fungal laccases has suggested that a charged residue Glu (E106) in CueO replaces the corresponding residue Phe in fungal laccases at the gate of the tunnel connecting type II copper to the protein surface and an extra α-helix (L351-G378) near the type I copper site covers the substrate binding pocket and might compromise the electron transfer from substrate to type I copper. To test this hypothesis, several mutants were made in Klebsiella sp. 601 multicopper oxidase, which is highly homologous to E. coli CueO with a similarity of 90% and an identity of 78%. The E106F mutant gave smaller K(m) (2.4-7 fold) and k(cat) (1-4.4 fold) values for all three substrates DMP, ABTS and SGZ as compared with those for the wild-type enzyme. Its slightly larger k(cat)/K(m) values for three substrates mainly come from the decreased K(m). Deleting α-helix (L351-G378) resulted in the formation of inactive inclusion body when the mutant (Δ)α351-378 was expressed in E. coli. Another mutant α351-380M was then made via substitution of seven amino acid residues in the α-helix (L351-G378) region. The α351-380M mutant was active, and displayed a far-UV CD spectrum markedly different from that for wild-type enzyme. Kinetic studies showed the α351-380M mutant gave very low K(m) values for DMP, ABTS and SGZ, 4.5-, 1.9- and 7-fold less than those for the wild type. In addition, k(cat)/K(m) values were increased, 9.4-fold for DMP, similar for ABTS and 3-fold for SGZ. The Glu residue at position 106 appears not to be the only factor affecting the copper binding, and it may also play a role in maintaining enzyme conformation. The α-helix (L351-G378) may not only block access to the type I copper site but also play a role in substrate specificities of bacterial MCOs. The α351-380M mutant catalyzing oxidation of the phenolic substrate DMP effectively would be very useful in green chemistry.

  3. Fabrication of a superhydrophobic coating with high adhesive effect to substrates and tunable wettability

    NASA Astrophysics Data System (ADS)

    Li, Yuan; Zhang, Zhaozhu; Zhu, Xiaotao; Men, Xuehu; Ge, Bo; Zhou, Xiaoyan

    2015-02-01

    In this paper, a new superhydrophobic coating was successfully prefabricated by a facile sol-gel process which was made up of first the surface chemical reaction of (3-Glycidyloxypropyl) trimethoxysilane (A-187) and SiO2 particles and subsequent spray-coating onto the substrate. Further hardening treatment and surface fluorination allowed the SiO2 coating with the optimum mass ratio of 2.0:1 to exhibit nice superhydrophobic property and high adhesive effect to substrates. Our researches indicated that the mass ratio of A-187 and SiO2 particles could significantly control the surface morphology (or the wettability) and affect adhesion force of the superhydrophobic coating to substrates. In the process, hardening temperature was quite important for rapid evaporation of the solvent and then fast hardening of the coating despite the absence of the similar effect to the mass ratio of A-187 and SiO2 particles on the superhydrophobic coating, and moreover, a higher hardening temperature could also highly improve transparency of the superhydrophobic coating. These findings suggest that the superhydrophobic coating should have promising commercial applications as a self-cleaning product.

  4. The silicon on dust substrate path to make solar cells directly from a gaseous feedstock

    NASA Astrophysics Data System (ADS)

    Serra, J M; Pinto, C R; Silva, J A; Brito, M C; Maia Alves, J; Vallêra, A M

    2009-04-01

    In this paper, we present a silicon on dust substrate (SDS) process, a new method for the growth of silicon ribbons. As a demonstration of the concept, we also present results on solar cells made of these new silicon ribbons. SDS ribbons were obtained directly from a gaseous feedstock by a fast CVD step using silane. The resulting self-supported intrinsic ribbons were microcrystalline and porous. To make these ribbon films suitable for photovoltaic applications, a novel recrystallization with an in situ doping step was developed. To this purpose, the ribbons were sprayed with boric acid and then recrystallized by float zone melting. Simple solar cells were prepared by employing: aluminium back contacts, Ti/Pd/Ag front grid contacts, with no anti-reflective coating, doping optimization, passivation or gettering. The 1-sun I-V characteristics of the cells were: Voc ~ 530 mV and Jsc ~ 24 mA cm-2. The minority carrier diffusion length obtained from a spectral response at long wavelengths gave values of Ln ~ 70 µm.

  5. A kinetic and thermodynamic framework for the Azoarcus group I ribozyme reaction

    PubMed Central

    Gleitsman, Kristin R.

    2014-01-01

    Determination of quantitative thermodynamic and kinetic frameworks for ribozymes derived from the Azoarcus group I intron and comparisons to their well-studied analogs from the Tetrahymena group I intron reveal similarities and differences between these RNAs. The guanosine (G) substrate binds to the Azoarcus and Tetrahymena ribozymes with similar equilibrium binding constants and similar very slow association rate constants. These and additional literature observations support a model in which the free ribozyme is not conformationally competent to bind G and in which the probability of assuming the binding-competent state is determined by tertiary interactions of peripheral elements. As proposed previously, the slow binding of guanosine may play a role in the specificity of group I intron self-splicing, and slow binding may be used analogously in other biological processes. The internal equilibrium between ribozyme-bound substrates and products is similar for these ribozymes, but the Azoarcus ribozyme does not display the coupling in the binding of substrates that is observed with the Tetrahymena ribozyme, suggesting that local preorganization of the active site and rearrangements within the active site upon substrate binding are different for these ribozymes. Our results also confirm the much greater tertiary binding energy of the 5′-splice site analog with the Azoarcus ribozyme, binding energy that presumably compensates for the fewer base-pairing interactions to allow the 5′-exon intermediate in self splicing to remain bound subsequent to 5′-exon cleavage and prior to exon ligation. Most generally, these frameworks provide a foundation for design and interpretation of experiments investigating fundamental properties of these and other structured RNAs. PMID:25246656

  6. Structural and evolutionary relationships of “AT-less” type I polyketide synthase ketosynthases

    PubMed Central

    Lohman, Jeremy R.; Ma, Ming; Osipiuk, Jerzy; Nocek, Boguslaw; Kim, Youngchang; Chang, Changsoo; Cuff, Marianne; Mack, Jamey; Bigelow, Lance; Li, Hui; Endres, Michael; Babnigg, Gyorgy; Joachimiak, Andrzej; Phillips, George N.; Shen, Ben

    2015-01-01

    Acyltransferase (AT)-less type I polyketide synthases (PKSs) break the type I PKS paradigm. They lack the integrated AT domains within their modules and instead use a discrete AT that acts in trans, whereas a type I PKS module minimally contains AT, acyl carrier protein (ACP), and ketosynthase (KS) domains. Structures of canonical type I PKS KS-AT didomains reveal structured linkers that connect the two domains. AT-less type I PKS KSs have remnants of these linkers, which have been hypothesized to be AT docking domains. Natural products produced by AT-less type I PKSs are very complex because of an increased representation of unique modifying domains. AT-less type I PKS KSs possess substrate specificity and fall into phylogenetic clades that correlate with their substrates, whereas canonical type I PKS KSs are monophyletic. We have solved crystal structures of seven AT-less type I PKS KS domains that represent various sequence clusters, revealing insight into the large structural and subtle amino acid residue differences that lead to unique active site topologies and substrate specificities. One set of structures represents a larger group of KS domains from both canonical and AT-less type I PKSs that accept amino acid-containing substrates. One structure has a partial AT-domain, revealing the structural consequences of a type I PKS KS evolving into an AT-less type I PKS KS. These structures highlight the structural diversity within the AT-less type I PKS KS family, and most important, provide a unique opportunity to study the molecular evolution of substrate specificity within the type I PKSs. PMID:26420866

  7. Substrates coated with silver nanoparticles as a neuronal regenerative material

    PubMed Central

    Alon, Noa; Miroshnikov, Yana; Perkas, Nina; Nissan, Ifat; Gedanken, Aharon; Shefi, Orit

    2014-01-01

    Much effort has been devoted to the design of effective biomaterials for nerve regeneration. Here, we report the novel use of silver nanoparticles (AgNPs) as regenerative agents to promote neuronal growth. We grew neuroblastoma cells on surfaces coated with AgNPs and studied the effect on the development of the neurites during the initiation and the elongation growth phases. We find that the AgNPs function as favorable anchoring sites, and the growth on the AgNP-coated substrates leads to a significantly enhanced neurite outgrowth. Cells grown on substrates coated with AgNPs have initiated three times more neurites than cells grown on uncoated substrates, and two times more than cells grown on substrates sputtered with a plain homogenous layer of silver. The growth of neurites on AgNPs in the elongation phase was enhanced as well. A comparison with substrates coated with gold nanoparticles (AuNPs) and zinc oxide nanoparticles (ZnONPs) demonstrated a clear silver material-driven promoting effect, in addition to the nanotopography. The growth on substrates coated with AgNPs has led to a significantly higher number of initiating neurites when compared to substrates coated with AuNPs or ZnONPs. All nanoparticle-coated substrates affected and promoted the elongation of neurites, with a significant positive maximal effect for the AgNPs. Our results, combined with the well-known antibacterial effect of AgNPs, suggest the use of AgNPs as an attractive nanomaterial – with dual activity – for neuronal repair studies. PMID:24872701

  8. A cellular glass substrate solar concentrator

    NASA Technical Reports Server (NTRS)

    Bedard, R.; Bell, D.

    1980-01-01

    The design of a second generation point focusing solar concentration is discussed. The design is based on reflective gores fabricated of thin glass mirror bonded continuously to a contoured substrate of cellular glass. The concentrator aperture and structural stiffness was optimized for minimum concentrator cost given the performance requirement of delivering 56 kWth to a 22 cm diameter receiver aperture with a direct normal insolation of 845 watts sq m and an operating wind of 50 kmph. The reflective panel, support structure, drives, foundation and instrumentation and control subsystem designs, optimized for minimum cost, are summarized. The use of cellular glass as a reflective panel substrate material is shown to offer significant weight and cost advantages compared to existing technology materials.

  9. A study of substrate-liquid crystal interaction

    NASA Astrophysics Data System (ADS)

    Zhang, Baoshe

    This thesis concerns the study of substrate-liquid crystal interaction from two different angles. In one approach, we used the IPS (in-plane switching) technique to investigate the liquid crystal alignment by rubbed polyimide films. The IPS mode of liquid crystal cell operation is facilitated through comb electrodes capable of producing planar electric field. We have fabricated comb electrodes with a periodicity of 2 mum in order to confine the planar electric field close to the liquid crystal-substrate interface. Through optical transmittance measurements and comparison with theoretical predictions based on the Ladau-de Gennes formalism, we found the experimental data to be consistent with the physical picture of soft anchoring, in which the liquid crystal director at the substrate interface is rotated azimuthally under the planar electric field. As a result, we were able to obtain the azimuthal anchoring strength as a fitting parameter of the theory. This part of the thesis thus presents evidence(s) for director switching at the liquid crystal-substrate interface, as well as a method for measuring the azimuthal anchoring strength through optical means. In the second approach, we used nano-lithographic technique to fabricate textured two dimensional periodic patterns on silicon wafers, and examined the resulting liquid crystal alignment effect of such textured substrates. It was found that with decreasing periodicity, there exists an orientational transition from a state in which the liquid crystal alignment copies the substrate pattern at larger periodicity, to a state of uniform alignment at smaller periodicity. In our system, this transition occurs at a periodicity between 0.4 mum and 0.8 mum. Through theoretical simulations based on the model of competition between the elastic distortion energy and the interfacial anchoring potential, it was found that there is indeed a first-order abrupt transition when the periodicity is decreased. This is due to the fact

  10. Angiotensin-converting enzyme: I. New strategies for assay

    PubMed Central

    Ryan, James W.; Chung, Alfred; Ryan, Una S.

    1980-01-01

    The disposition of converting enzyme (kininase II) on the luminal surface of pulmonary endothelial cells is well established. Further, it is known that there is a net conversion of angiotensin I into angiotensin II as blood passes through the lungs. However, little is known about modulations of converting enzyme activity that may arise through, e.g., changes in the quality of inhalants, blood flow, or blood oxygenation. There are few data on the effects of lung disease. A major barrier to studies to examine for pathophysiologic modulations of converting enzyme is that of assay. The enzyme can be measured in terms of the rate of formation of angiotensin II from a known quantity of angiotensin I. However, both peptides are biologically active, and lungs contain other enzymes capable of degrading them. We have developed a series of radiolabeled, acylated tripeptides to improve our ability to examine for changes in the net converting enzyme of intact lungs. The enzyme, a dipeptidyl carboxypeptidase, is capable of removing C-terminal dipeptides from a variety of oligopeptides. We have prepared benzoyl-Gly-Gly-Gly (I), benzoyl-Pro-Phe-Arg (II), benzoyl-Gly-His-Leu (III), benzoyl-Phe-Ala-Pro (IV), and benzoyl-Phe-His-Leu (V), each containing a 3H-atom in the para position of the benzoyl moiety. Substrates I and III have been used previously in photometric assays of low sensitivity. II is the acylated C-terminal tripeptide of bradykinin, IV is an acylated tripeptide analog of BPP5a (I. These substrates can be used in vitro or in vivo to measure converting enzyme. The 3H-labeled product is separable by partitioning between an organic solvent and acidified aqueous solution. The product is quantified by scintillation counting of the organic phase. The choice of substrate depends on the goals of the experiment: substrate I or III when wide variations in substrate concentrations are needed but high

  11. Apparatus for thermally evolving chemical analytes from a removable substrate

    DOEpatents

    Linker, Kevin L.; Hannum, David W.

    2003-06-03

    Method and apparatus suited to convenient field use for heating a porous metallic substrate swiped on the surface of an article possibly bearing residue of contraband or other target chemical substances. The preferred embodiment of the device includes means for holding the swiped substrate between electrodes bearing opposite electrical charges, thereby completing an electrical circuit in which current can flow through the porous metallic substrate. Resistance causes the substrate to heat, thus driving adherent target chemicals, if present, into a space from which they are carried via gas flow into a detector such as a portable IMS for analysis.

  12. Effects of different substrates on the sprint performance of lizards.

    PubMed

    Tulli, Maria Jose; Abdala, Virginia; Cruz, Felix B

    2012-03-01

    The variation in substrate structure is one of the most important determinants of the locomotor abilities of lizards. Lizards are found across a range of habitats, from large rocks to loose sand, each of them with conflicting mechanical demands on locomotion. We examined the relationships among sprint speed, morphology and different types of substrate surfaces in species of lizards that exploit different structural habitats (arboreal, saxicolous, terrestrial and arenicolous) in a phylogenetic context. Our main goals were to assess which processes drive variability in morphology (i.e. phylogeny or adaptation to habitat) in order to understand how substrate structure affects sprint speed in species occupying different habitats and to determine the relationship between morphology and performance. Liolaemini lizards show that most morphological traits are constrained by phylogeny, particularly toe 3, the femur and foot. All ecological groups showed significant differences on rocky surfaces. Surprisingly, no ecological group performed better on the surface resembling its own habitat. Moreover, all groups exhibited significant differences in sprint speed among the three different types of experimental substrates and showed the best performance on sand, with the exception of the arboreal group. Despite the fact that species use different types of habitats, the highly conservative morphology of Liolaemini species and the similar levels of performance on different types of substrates suggest that they confer to the 'jack of all trades and master of none' principle.

  13. The potential of organic substrates based on mushroom substrate and straw to dissipate fungicides contained in effluents from the fruit-packaging industry - Is there a role for Pleurotus ostreatus?

    PubMed

    Karas, Panagiotis A; Makri, Sotirina; Papadopoulou, Evangelia S; Ehaliotis, Constantinos; Menkissoglu-Spiroudi, Urania; Karpouzas, Dimitrios G

    2016-02-01

    Citrus fruit-packaging plants (FPP) produce large wastewater volumes with high loads of fungicides like ortho-phenylphenol (OPP) and imazalil (IMZ). No methods are in place for the treatment of those effluents and biobeds appear as a viable alternative. We employed a column study to investigate the potential of spent mushroom substrate (SMS) of Pleurotus ostreatus, either alone or in mixture with straw and soil plus a mixture of straw /soil to retain and dissipate IMZ and OPP. The role of P. ostreatus on fungicides dissipation was also investigated by studying in parallel the performance of fresh mushroom substrate of P. ostreatus (FMS) and measuring lignolytic enzymatic activity in the leachates. All substrates effectively reduced the leaching of OPP and IMZ which corresponded to 0.014-1.1% and 0.120-0.420% of their initial amounts respectively. Mass balance analysis revealed that FMS and SMS/Straw/Soil (50/25/25 by vol) offered the most efficient removal of OPP and IMZ from wastewaters respectively. Regardless of the substrate, OPP was restricted in the top 0-20cm of the columns and was bioavailable (extractable with water), compared to IMZ which was less bioavailable (extractable with acetonitrile) but diffused at deeper layers (20-50, 50-80cm) in the SMS- and Straw/Soil-columns. PLFAs showed that fungal abundance was significantly lower in the top layer of all substrates from where the highest pesticide amounts were recovered suggesting an inhibitory effect of fungicides on total fungi in the substrates tested. Our data suggest that biobeds packed with SMS-rich substrates could ensure the efficient removal of IMZ and OPP from wastewaters of citrus FPP. Copyright © 2015 Elsevier Inc. All rights reserved.

  14. Effective medium model for a granular monolayer on an elastic substrate

    NASA Astrophysics Data System (ADS)

    Maznev, Alexei

    Effective medium models have been shown to work well in describing experimental observations of the interaction of surface Rayleigh waves with contact vibrations of a monolayer of microspheres . However, these models contain intrinsic conceptual problems: for example, the local displacement of the substrate at the contact point is equated to the effective medium average value of the surface displacement. I will present a rigorous derivation of the effective medium model for a random arrangement of mass-spring oscillators on an elastic half-space using elastodynamic surface Green's function formalism. We will see that the model equating the local surface displacement to the effective medium displacement is indeed valid if the spring constant of the oscillators is modified to include the stiffness of the contact calculated in the quasistatic approximation. In the case of contact vibrations of microspheres, this means using the spring constant calculated using the Hertzian contact model. Thus the results obtained in the prior work were correct despite the apparent inconsistencies in the model. The presented analysis will provide a solid foundation for effective medium models used to describe dynamics of microparticle arrays adhered to a solid substrate. This work was supported by the U. S. Army Research Office through the Institute for Soldier Nanotechnologies under Grant W911NF-13-D-0001.

  15. Mechanically dynamic PDMS substrates to investigate changing cell environments

    PubMed Central

    Yeh, Yi-Cheun; Corbin, Elise A.; Caliari, Steven R.; Ouyang, Liu; Vega, Sebastián L.; Truitt, Rachel; Han, Lin; Margulies, Kenneth B.; Burdick, Jason A.

    2018-01-01

    Mechanics of the extracellular matrix (ECM) play a pivotal role in governing cell behavior, such as cell spreading and differentiation. ECM mechanics have been recapitulated primarily in elastic hydrogels, including with dynamic properties to mimic complex behaviors (e.g., fibrosis); however, these dynamic hydrogels fail to introduce the viscoelastic nature of many tissues. Here, we developed a two-step crosslinking strategy to first form (via platinum-catalyzed crosslinking) networks of polydimethylsiloxane (PDMS) and then to increase PDMS crosslinking (via thiol-ene click reaction) in a temporally-controlled manner. This photoinitiated reaction increased the compressive modulus of PDMS up to 10-fold within minutes and was conducted under cytocompatible conditions. With stiffening, cells displayed increased spreading, changing from ~1300 to 1900 μm2 and from ~2700 to 4600 μm2 for fibroblasts and mesenchymal stem cells, respectively. In addition, higher myofibroblast activation (from ~2 to 20%) for cardiac fibroblasts was observed with increasing PDMS substrate stiffness. These results indicate a cellular response to changes in PDMS substrate mechanics, along with a demonstration of a mechanically dynamic and photoresponsive PDMS substrate platform to model the dynamic behavior of ECM. PMID:28843064

  16. Adenosine-to-inosine RNA editing by ADAR1 is essential for normal murine erythropoiesis

    PubMed Central

    Liddicoat, Brian J.; Hartner, Jochen C.; Piskol, Robert; Ramaswami, Gokul; Chalk, Alistair M.; Kingsley, Paul D.; Sankaran, Vijay G.; Wall, Meaghan; Purton, Louise E.; Seeburg, Peter H.; Palis, James; Orkin, Stuart H.; Lu, Jun; Li, Jin Billy; Walkley, Carl R.

    2016-01-01

    Adenosine deaminases that act on RNA (ADARs) convert adenosine residues to inosine in double-stranded RNA. In vivo, ADAR1 is essential for the maintenance of hematopoietic stem/progenitors. Whether other hematopoietic cell types also require ADAR1 has not been assessed. Using erythroid- and myeloid-restricted deletion of Adar1, we demonstrate that ADAR1 is dispensable for myelopoiesis but is essential for normal erythropoiesis. Adar1-deficient erythroid cells display a profound activation of innate immune signaling and high levels of cell death. No changes in microRNA levels were found in ADAR1-deficient erythroid cells. Using an editing-deficient allele, we demonstrate that RNA editing is the essential function of ADAR1 during erythropoiesis. Mapping of adenosine-to-inosine editing in purified erythroid cells identified clusters of hyperedited adenosines located in long 3’-untranslated regions of erythroid-specific transcripts and these are ADAR1-specific editing events. ADAR1-mediated RNA editing is essential for normal erythropoiesis. PMID:27373493

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

    PubMed

    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.

  18. Rational design of a carboxylic esterase RhEst1 based on computational analysis of substrate binding.

    PubMed

    Chen, Qi; Luan, Zheng-Jiao; Yu, Hui-Lei; Cheng, Xiaolin; Xu, Jian-He

    2015-11-01

    A new carboxylic esterase RhEst1 which catalyzes the hydrolysis of (S)-(+)-2,2-dimethylcyclopropanecarboxylate (S-DmCpCe), the key chiral building block of cilastatin, was identified and subsequently crystallized in our previous work. Mutant RhEst1A147I/V148F/G254A was found to show a 5-fold increase in the catalytic activity. In this work, molecular dynamic simulations were performed to elucidate the molecular determinant of the enzyme activity. Our simulations show that the substrate binds much more strongly in the A147I/V148F/G254A mutant than in wild type, with more hydrogen bonds formed between the substrate and the catalytic triad and the oxyanion hole. The OH group of the catalytic residue Ser101 in the mutant is better positioned to initiate the nucleophilic attack on S-DmCpCe. Interestingly, the "170-179" loop which is involved in shaping the catalytic sites and facilitating the product release shows remarkable dynamic differences in the two systems. Based on the simulation results, six residues were identified as potential "hot-spots" for further experimental testing. Consequently, the G126S and R133L mutants show higher catalytic efficiency as compared with the wild type. This work provides molecular-level insights into the substrate binding mechanism of carboxylic esterase RhEst1, facilitating future experimental efforts toward developing more efficient RhEst1 variants for industrial applications. Copyright © 2015 Elsevier Inc. All rights reserved.

  19. Maintainable substrate carrier for electroplating

    DOEpatents

    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.

  20. Maintainable substrate carrier for electroplating

    DOEpatents

    Chen, Chen-An; Abas, Emmanuel Chua; Divino, Edmundo Anida; Ermita, Jake Randal G.; Capulong, Jose Francisco S.; Castillo, Arnold Villamor; Ma, Diana Xiaobing

    2016-08-02

    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.

  1. Methods of repairing a substrate

    NASA Technical Reports Server (NTRS)

    Riedell, James A. (Inventor); Easler, Timothy E. (Inventor)

    2011-01-01

    A precursor of a ceramic adhesive suitable for use in a vacuum, thermal, and microgravity environment. The precursor of the ceramic adhesive includes a silicon-based, preceramic polymer and at least one ceramic powder selected from the group consisting of aluminum oxide, aluminum nitride, boron carbide, boron oxide, boron nitride, hafnium boride, hafnium carbide, hafnium oxide, lithium aluminate, molybdenum silicide, niobium carbide, niobium nitride, silicon boride, silicon carbide, silicon oxide, silicon nitride, tin oxide, tantalum boride, tantalum carbide, tantalum oxide, tantalum nitride, titanium boride, titanium carbide, titanium oxide, titanium nitride, yttrium oxide, zirconium boride, zirconium carbide, zirconium oxide, and zirconium silicate. Methods of forming the ceramic adhesive and of repairing a substrate in a vacuum and microgravity environment are also disclosed, as is a substrate repaired with the ceramic adhesive.

  2. Laser desorption/ionization mass spectrometry of lipids using etched silver substrates.

    PubMed

    Schnapp, Andreas; Niehoff, Ann-Christin; Koch, Annika; Dreisewerd, Klaus

    2016-07-15

    Silver-assisted laser desorption/ionization mass spectrometry can be used for the analysis of small molecules. For example, adduct formation with silver cations enables the molecular analysis of long-chain hydrocarbons, which are difficult to ionize via conventional matrix-assisted laser desorption ionization (MALDI). Here we used highly porous silver foils, produced by etching with nitric acid, as sample substrates for LDI mass spectrometry. As model system for the analysis of complex lipid mixtures, cuticular extracts of fruit flies (Drosophila melanogaster) and worker bees (Apis mellifera) were investigated. The mass spectra obtained by spotting extract onto the etched silver substrates demonstrate the sensitive detection of numerous lipid classes such as long-chain saturated and unsaturated hydrocarbons, fatty acyl alcohols, wax esters, and triacylglycerols. MS imaging of cuticular surfaces with a lateral resolution of a few tens of micrometers became possible after blotting, i.e., after transferring lipids by physical contact with the substrate. The examples of pheromone-producing male hindwings of the squinting bush brown butterfly (Bicyclus anynana) and a fingermark are shown. Because the substrates are also easy to produce, they provide a viable alternative to colloidal silver nanoparticles and other so far described silver substrates. Copyright © 2016 Elsevier Inc. All rights reserved.

  3. Bioaugmentation as a solution to increase methane production from an ammonia-rich substrate.

    PubMed

    Fotidis, Ioannis A; Wang, Han; Fiedel, Nicolai R; Luo, Gang; Karakashev, Dimitar B; Angelidaki, Irini

    2014-07-01

    Ammonia-rich substrates inhibit the anaerobic digestion (AD) process and constitute the main reason for low energy recovery in full-scale reactors. It is estimated that many full-scale AD reactors are operating in ammonia induced "inhibited steady-state" with significant losses of the potential biogas production yield. To date there are not any reliable methods to alleviate the ammonia toxicity effect or to efficiently digest ammonia-rich waste. In the current study, bioaugmentation as a possible method to alleviate ammonia toxicity effect in a mesophilic continuously stirred-tank reactor (CSTR) operating under "inhibited steady state" was tested. A fast growing hydrogenotrophic methanogen (i.e., Methanoculleus bourgensis MS2(T)) was bioaugmented in the CSTR reactor at high ammonia levels (5 g NH4(+)-N L(-1)). A second CSTR reactor was used as control with no bioaugmentation. The results derived from this study clearly demonstrated a 31.3% increase in methane production yield in the CSTR reactor, at steady-state, after bioaugmentation. Additionally, high-throughput 16S rRNA gene sequencing analysis showed a 5-fold increase in relative abundance of Methanoculleus spp. after bioaugmentation. On the contrary to all methods used today to alleviate ammonia toxicity effect, the tested bioaugmentation process performed without interrupting the continuous operation of the reactor and without replacing the ammonia-rich feedstock.

  4. Plant Growth Experiments in Zeoponic Substrates: Applications for Advanced Life Support Systems

    NASA Technical Reports Server (NTRS)

    Ming, Douglas W.; Gruener, J. E.; Henderson, K. E.; Steinberg, S. L.; Barta, D. J.; Galindo, C.; Henninger, D. L.

    2001-01-01

    A zeoponic plant-growth system is defined as the cultivation of plants in artificial soils, which have zeolites as a major component (Allen and Ming, 1995). Zeolites are crystalline, hydrated aluminosilicate minerals that have the ability to exchange constituent cations without major change of the mineral structure. Recently, zeoponic systems developed at the National Aeronautics and Space Administration (NASA) slowly release some (Allen et at., 1995) or all of the essential plant-growth nutrients (Ming et at., 1995). These systems have NH4- and K-exchanged clinoptilolite (a natural zeolite) and either natural or synthetic apatite (a calcium phosphate mineral). For the natural apatite system, Ca and P were made available to the plant by the dissolution of apatite. Potassium and NH4-N were made available by ion-exchange reactions involving Ca(2+) from apatite dissolution and K(+) and NH4(+) on zeolitic exchange sites. In addition to NH4-N, K, Ca, and P, the synthetic apatite system also supplied Mg, S, and other micronutrients during dissolution (Figure 1). The overall objective of this research task is to develop zeoponic substrates wherein all plant growth nutrients are supplied by the plant growth medium for several growth seasons with only the addition of water. The substrate is being developed for plant growth in Advanced Life Support (ALS) testbeds (i.e., BioPLEX) and microgravity plant growth experiments. Zeoponic substrates have been used for plant growth experiments on two Space Shuttle flight experiments (STS-60; STS-63; Morrow et aI., 1995). These substrates may be ideally suited for plant growth experiments on the International Space Station and applications in ALS testbeds. However, there are several issues that need to be resolved before zeoponics will be the choice substrate for plant growth experiments in space. The objective of this paper is to provide an overview on recent research directed toward the refinement of zeoponic plant growth substrates.

  5. Properties of Silica-Based Aerogel Substrates and Application to C-Band Circular Patch Antenna

    NASA Astrophysics Data System (ADS)

    Abdel-Rahman, Mohamed; Haraz, Osama M.; Ashraf, Nadeem; Zia, Muhammad Fakhar; Khaled, Usama; Elsahfiey, Ibrahim; Alshebeili, Saleh; Sebak, Abdel Razik

    2018-03-01

    Silica aerogel is a lightweight and low-permittivity dielectric material that possesses attractive features for use as an antenna substrate. In this paper, we characterize the radio frequency and microwave dielectric permittivity properties of substrates composed of silica aerogel encapsulated in polymer aerogel in the frequency range from 10 MHz to 8.5 GHz. Characterized silica-based aerogel substrates show relative permittivity values varying between 1.055 and 1.25 and loss tangent values ranging from 5.08 × 10-4 to 0.0206. Silica-based aerogel substrates thus have the potential of use in designing antennas with high gain and large bandwidth. Validation is presented by characterizing the performance of a manufactured C-band circular patch antenna on silica-based aerogel substrate. The performance is also compared to a design that uses Rogers Duroid RT5880 substrate. The results reveal that the silica aerogel substrate antenna at 7.2 GHz provides 1.5 dB increase in gain, 88% enhancement in bandwidth and 68.5% reduction in mass, in comparison with the antenna on RT5880 substrate.

  6. Charged Substrate and Product Together Contribute Like a Nonreactive Species to the Overall Electrostatic Steering in Diffusion-Reaction Processes.

    PubMed

    Xu, Jingjie; Xie, Yan; Lu, Benzhuo; Zhang, Linbo

    2016-08-25

    The Debye-Hückel limiting law is used to study the binding kinetics of substrate-enzyme system as well as to estimate the reaction rate of a electrostatically steered diffusion-controlled reaction process. It is based on a linearized Poisson-Boltzmann model and known for its accurate predictions in dilute solutions. However, the substrate and product particles are in nonequilibrium states and are possibly charged, and their contributions to the total electrostatic field cannot be explicitly studied in the Poisson-Boltzmann model. Hence the influences of substrate and product on reaction rate coefficient were not known. In this work, we consider all the charged species, including the charged substrate, product, and mobile salt ions in a Poisson-Nernst-Planck model, and then compare the results with previous work. The results indicate that both the charged substrate and product can significantly influence the reaction rate coefficient with different behaviors under different setups of computational conditions. It is interesting to find that when substrate and product are both considered, under an overall neutral boundary condition for all the bulk charged species, the computed reaction rate kinetics recovers a similar Debye-Hückel limiting law again. This phenomenon implies that the charged product counteracts the influence of charged substrate on reaction rate coefficient. Our analysis discloses the fact that the total charge concentration of substrate and product, though in a nonequilibrium state individually, obeys an equilibrium Boltzmann distribution, and therefore contributes as a normal charged ion species to ionic strength. This explains why the Debye-Hückel limiting law still works in a considerable range of conditions even though the effects of charged substrate and product particles are not specifically and explicitly considered in the theory.

  7. Charge-free method of forming nanostructures on a substrate

    DOEpatents

    Hoffbauer; Mark , Akhadov; Elshan

    2010-07-20

    A charge-free method of forming a nanostructure at low temperatures on a substrate. A substrate that is reactive with one of atomic oxygen and nitrogen is provided. A flux of neutral atoms of least one of oxygen and nitrogen is generated within a laser-sustained-discharge plasma source and a collimated beam of energetic neutral atoms and molecules is directed from the plasma source onto a surface of the substrate to form the nanostructure. The energetic neutral atoms and molecules in the beam have an average kinetic energy in a range from about 1 eV to about 5 eV.

  8. Pt skin on AuCu intermetallic substrate: a strategy to maximize Pt utilization for fuel cells.

    PubMed

    Wang, Gongwei; Huang, Bing; Xiao, Li; Ren, Zhandong; Chen, Hao; Wang, Deli; Abruña, Héctor D; Lu, Juntao; Zhuang, Lin

    2014-07-09

    The dependence on Pt catalysts has been a major issue of proton-exchange membrane (PEM) fuel cells. Strategies to maximize the Pt utilization in catalysts include two main approaches: to put Pt atoms only at the catalyst surface and to further enhance the surface-specific catalytic activity (SA) of Pt. Thus far there has been no practical design that combines these two features into one single catalyst. Here we report a combined computational and experimental study on the design and implementation of Pt-skin catalysts with significantly improved SA toward the oxygen reduction reaction (ORR). Through screening, using density functional theory (DFT) calculations, a Pt-skin structure on AuCu(111) substrate, consisting of 1.5 monolayers of Pt, is found to have an appropriately weakened oxygen affinity, in comparison to that on Pt(111), which would be ideal for ORR catalysis. Such a structure is then realized by substituting the Cu atoms in three surface layers of AuCu intermetallic nanoparticles (AuCu iNPs) with Pt. The resulting Pt-skinned catalyst (denoted as Pt(S)AuCu iNPs) has been characterized in depth using synchrotron XRD, XPS, HRTEM, and HAADF-STEM/EDX, such that the Pt-skin structure is unambiguously identified. The thickness of the Pt skin was determined to be less than two atomic layers. Finally the catalytic activity of Pt(S)AuCu iNPs toward the ORR was measured via rotating disk electrode (RDE) voltammetry through which it was established that the SA was more than 2 times that of a commercial Pt/C catalyst. Taking into account the ultralow Pt loading in Pt(S)AuCu iNPs, the mass-specific catalytic activity (MA) was determined to be 0.56 A/mg(Pt)@0.9 V, a value that is well beyond the DOE 2017 target for ORR catalysts (0.44 A/mg(Pt)@0.9 V). These findings provide a strategic design and a realizable approach to high-performance and Pt-efficient catalysts for fuel cells.

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

    PubMed

    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.

  10. Delineation of xenobiotic substrate sites in rat glutathione S-transferase M1-1.

    PubMed

    Hearne, Jennifer L; Colman, Roberta F

    2005-10-01

    Glutathione S-transferases catalyze the conjugation of glutathione with endogenous and exogenous xenobiotics. Hu and Colman (1995) proposed that there are two distinct substrate sites in rat GST M1-1, a 1-chloro-2,4-dintrobenzene (CDNB) substrate site located in the vicinity of tyrosine-115, and a monobromobimane (mBBr) substrate site. To determine whether the mBBr substrate site is distinguishable from the CDNB substrate site, we tested S-(hydroxyethyl)bimane, a nonreactive derivative of mBBr, for its ability to compete kinetically with the substrates. We find that S-(hydroxyethyl)bimane is a competitive inhibitor (K(I) = 0.36 microM) when mBBr is used as substrate, but not when CDNB is used as substrate, demonstrating that these two sites are distinct. Using site-directed mutagenesis, we have localized the mBBr substrate site to an area midway through alpha-helix 4 (residues 90-114) and have identified residues that are important in the enzymatic reaction. Substitution of alanine at positions along alpha-helix 4 reveals that mutations at positions 103, 104, and 109 exhibit a greater perturbation of the enzymatic reaction with mBBr than with CDNB as substrate. Various other substitutions at positions 103 and 104 reveal that a hydrophobic residue is necessary at each of these positions to maintain optimal affinity of the enzyme for mBBr and preserve the secondary structure of the enzyme. Substitutions at position 109 indicate that this residue is important in the enzyme's affinity for mBBr but has a minimal effect on Vmax. These results demonstrate that the promiscuity of rat GST M1-1 is in part due to at least two distinct substrate sites.

  11. Carbon nanotube substrates and catalyzed hot stamp for polishing and patterning the substrates

    DOEpatents

    Wang, Yuhuang [Evanston, IL; Hauge, Robert H [Houston, TX; Schmidt, Howard K [Houston, TX; Kim, Myung Jong [Houston, TX; Kittrell, W Carter [Houston, TX

    2009-09-08

    The present invention is generally directed to catalyzed hot stamp methods for polishing and/or patterning carbon nanotube-containing substrates. In some embodiments, the substrate, as a carbon nanotube fiber end, is brought into contact with a hot stamp (typically at 200-800.degree. C.), and is kept in contact with the hot stamp until the morphology/patterns on the hot stamp have been transferred to the substrate. In some embodiments, the hot stamp is made of material comprising one or more transition metals (Fe, Ni, Co, Pt, Ag, Au, etc.), which can catalyze the etching reaction of carbon with H.sub.2, CO.sub.2, H.sub.2O, and/or O.sub.2. Such methods can (1) polish the carbon nanotube-containing substrate with a microscopically smooth finish, and/or (2) transfer pre-defined patterns from the hot stamp to the substrate. Such polished or patterned carbon nanotube substrates can find application as carbon nanotube electrodes, field emitters, and field emitter arrays for displays and electron sources.

  12. Gallium phosphide nanowires as a substrate for cultured neurons.

    PubMed

    Hällström, Waldemar; Mårtensson, Thomas; Prinz, Christelle; Gustavsson, Per; Montelius, Lars; Samuelson, Lars; Kanje, Martin

    2007-10-01

    Dissociated sensory neurons were cultured on epitaxial gallium phosphide (GaP) nanowires grown vertically from a gallium phosphide surface. Substrates covered by 2.5 microm long, 50 nm wide nanowires supported cell adhesion and axonal outgrowth. Cell survival was better on nanowire substrates than on planar control substrates. The cells interacted closely with the nanostructures, and cells penetrated by hundreds of wires were observed as well as wire bending due to forces exerted by the cells.

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

    NASA Technical Reports Server (NTRS)

    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.

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

    PubMed

    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.

  15. A Substrate Pharmacophore for the Human Sodium Taurocholate Co-transporting Polypeptide

    PubMed Central

    Dong, Zhongqi; Ekins, Sean; Polli, James E.

    2014-01-01

    Human Sodium Taurocholate Co-transporting Polypeptide (NTCP) is the main bile acid uptake transporter in the liver with the capability to translocate xenobiotics. While its inhibitor requirements have been recently characterized, its substrate requirements have not. The objectives of this study were a) to elucidate NTCP substrate requirements using native bile acids and bile acid analogs, b) to develop the first pharmacophore for NTCP substrates and compare it with the inhibitor pharmacophores, and c) to identify additional NTCP novel substrates. Thus, 18 native bile acids and two bile acid conjugates were initially assessed for NTCP inhibition and/or uptake, which suggested a role of hydroxyl pattern and steric interaction in NTCP binding and translocation. A common feature pharmacophore for NTCP substrate uptake was developed, using 14 native bile acids and bile acid conjugates, yielding a model which featured three hydrophobes, one hydrogen bond donor, one negative ionizable feature and three excluded volumes. This model was used to search a database of FDA approved drugs and retrieved the majority of the known NTCP substrates. Among the retrieved drugs, irbesartan and losartan were identified as novel NTCP substrates, suggesting a potential role of NTCP in drug disposition. PMID:25448570

  16. Substrates of Peltigera Lichens as a Potential Source of Cyanobionts.

    PubMed

    Zúñiga, Catalina; Leiva, Diego; Carú, Margarita; Orlando, Julieta

    2017-10-01

    Photobiont availability is one of the main factors determining the success of the lichenization process. Although multiple sources of photobionts have been proposed, there is no substantial evidence confirming that the substrates on which lichens grow are one of them. In this work, we obtained cyanobacterial 16S ribosomal RNA gene sequences from the substrates underlying 186 terricolous Peltigera cyanolichens from localities in Southern Chile and maritime Antarctica and compared them with the sequences of the cyanobionts of these lichens, in order to determine if cyanobacteria potentially available for lichenization were present in the substrates. A phylogenetic analysis of the sequences showed that Nostoc phylotypes dominated the cyanobacterial communities of the substrates in all sites. Among them, an overlap was observed between the phylotypes of the lichen cyanobionts and those of the cyanobacteria present in their substrates, suggesting that they could be a possible source of lichen photobionts. Also, in most cases, higher Nostoc diversity was observed in the lichens than in the substrates from each site. A better understanding of cyanobacterial diversity in lichen substrates and their relatives in the lichens would bring insights into mycobiont selection and the distribution patterns of lichens, providing a background for hypothesis testing and theory development for future studies of the lichenization process.

  17. Response of reef corals on a fringing reef flat to elevated suspended-sediment concentrations: Molokaʻi, Hawaiʻi

    PubMed Central

    Jokiel, Paul L.; Storlazzi, Curt D.; Field, Michael E.; Lager, Claire V.; Lager, Dan

    2014-01-01

    A long-term (10 month exposure) experiment on effects of suspended sediment on the mortality, growth, and recruitment of the reef corals Montipora capitata and Porites compressa was conducted on the shallow reef flat off south Molokaʻi, Hawaiʻi. Corals were grown on wire platforms with attached coral recruitment tiles along a suspended solid concentration (SSC) gradient that ranged from 37 mg l−1 (inshore) to 3 mg l−1 (offshore). Natural coral reef development on the reef flat is limited to areas with SSCs less than 10 mg l−1 as previously suggested in the scientific literature. However, the experimental corals held at much higher levels of turbidity showed surprisingly good survivorship and growth. High SSCs encountered on the reef flat reduced coral recruitment by one to three orders of magnitude compared to other sites throughout Hawaiʻi. There was a significant correlation between the biomass of macroalgae attached to the wire growth platforms at the end of the experiment and percentage of the corals showing mortality. We conclude that lack of suitable hard substrate, macroalgal competition, and blockage of recruitment on available substratum are major factors accounting for the low natural coral coverage in areas of high turbidity. The direct impact of high turbidity on growth and mortality is of lesser importance. PMID:25653896

  18. Direct in Situ Conversion of Metals into Metal-Organic Frameworks: A Strategy for the Rapid Growth of MOF Films on Metal Substrates.

    PubMed

    Ji, Hoon; Hwang, Sunhyun; Kim, Keonmok; Kim, CheolGi; Jeong, Nak Cheon

    2016-11-30

    The fabrication of metal-organic framework (MOF) films on conducting substrates has demonstrated great potential in applications such as electronic conduction and sensing. For these applications, direct contact of the film to the conducting substrate without a self-assembled monolayer (SAM) is a desired step that must be achieved prior to the use of MOF films. In this report, we propose an in situ strategy for the rapid one-step conversion of Cu metal into HKUST-1 films on conducting Cu substrates. The Cu substrate acts both as a conducting substrate and a source of Cu 2+ ions during the synthesis of HKUST-1. This synthesis is possible because of the simultaneous reaction of an oxidizing agent and a deprotonating agent, in which the former agent dissolves the metal substrate to form Cu 2+ ions while the latter agent deprotonates the ligand. Using this strategy, the HKUST-1 film could not only be rapidly synthesized within 5 min but also be directly attached to the Cu substrate. Based on microscopic studies, we propose a plausible mechanism for the growth reaction. Furthermore, we show the versatility of this in situ conversion methodology, applying it to ZIF-8, which comprises Zn 2+ ions and imidazole-based ligands. Using an I 2 -filled HKUST-1 film, we further demonstrate that the direct contact of the MOF film to the conducting substrate makes the material more suitable for use as a sensor or electronic conductor.

  19. Mechanically dynamic PDMS substrates to investigate changing cell environments.

    PubMed

    Yeh, Yi-Cheun; Corbin, Elise A; Caliari, Steven R; Ouyang, Liu; Vega, Sebastián L; Truitt, Rachel; Han, Lin; Margulies, Kenneth B; Burdick, Jason A

    2017-11-01

    Mechanics of the extracellular matrix (ECM) play a pivotal role in governing cell behavior, such as cell spreading and differentiation. ECM mechanics have been recapitulated primarily in elastic hydrogels, including with dynamic properties to mimic complex behaviors (e.g., fibrosis); however, these dynamic hydrogels fail to introduce the viscoelastic nature of many tissues. Here, we developed a two-step crosslinking strategy to first form (via platinum-catalyzed crosslinking) networks of polydimethylsiloxane (PDMS) and then to increase PDMS crosslinking (via thiol-ene click reaction) in a temporally-controlled manner. This photoinitiated reaction increased the compressive modulus of PDMS up to 10-fold within minutes and was conducted under cytocompatible conditions. With stiffening, cells displayed increased spreading, changing from ∼1300 to 1900 μm 2 and from ∼2700 to 4600 μm 2 for fibroblasts and mesenchymal stem cells, respectively. In addition, higher myofibroblast activation (from ∼2 to 20%) for cardiac fibroblasts was observed with increasing PDMS substrate stiffness. These results indicate a cellular response to changes in PDMS substrate mechanics, along with a demonstration of a mechanically dynamic and photoresponsive PDMS substrate platform to model the dynamic behavior of ECM. Copyright © 2017 Elsevier Ltd. All rights reserved.

  20. Chemistry of Sulfur-Contaminated Soil Substrate from a Former Frasch Extraction Method Sulfur Mine Leachate with Various Forms of Litter in a Controlled Experiment.

    PubMed

    Likus-Cieślik, Justyna; Pietrzykowski, Marcin; Chodak, Marcin

    2018-01-01

    The impact of tree litter on soil chemistry leachate and sulfurous substrates of mine soils from former Jeziórko sulfur mine was investigated. Composites were used: soil substrate (less contaminated at mean 5090 mg kg -1  S or high contaminated at 42,500 mg kg -1  S) + birch or pine litter and control substrate (no litter). The composites were rinsed with distilled water over 12 weeks. In the obtained leachate, pH, EC, dissolved organic carbon, N, Ca, Mg, Al, and S were determined. Physicochemical parameters of the substrates and their basal respiration rate were determined. Rinsing and litter application lowered sulfur concentration in high contamination substrates. Pine litter application decreased EC and increased pH of the low-contaminated substrate. The substrate pH remained at low phytotoxic level (i.e., below 3.0), resulting in the low biological activity of the composites. Birch litter application increased leaching of N and Mg, indicating the possibility of an intensification of soil-forming processes in contaminated sites.

  1. Substrate attributes determine gait in a terrestrial gastropod.

    PubMed

    McKee, Amberle; Voltzow, Janice; Pernet, Bruno

    2013-02-01

    Some terrestrial gastropods are able to move using two gaits: adhesive crawling, where the entire foot is separated from the substrate only by a thin layer of mucus and the snail leaves a continuous mucus trail; and loping, where regions of the foot arch above the substrate and the snail leaves a discontinuous mucus trail. Loping has been interpreted as a means of rapidly escaping predators. We found that the pulmonate Cornu aspersum moved using adhesive crawling on dry acrylic or glass substrates, but loped on dry concrete or wood. Loping snails did not move more rapidly than snails using adhesive crawling. Snails moving on concrete secreted a greater volume of pedal mucus per area of trail than those moving on acrylic; locomotion on concrete thus requires greater expenditure of mucus than does locomotion on acrylic. Because loping snails deposit a smaller area of mucus per distance traveled than do snails using adhesive crawling, loping may conserve mucus when moving on porous, absorbent substrates. Members of several other terrestrial pulmonate taxa can also lope on concrete, suggesting that this plasticity in gait is widespread among terrestrial snails.

  2. Cell movement is guided by the rigidity of the substrate

    NASA Technical Reports Server (NTRS)

    Lo, C. M.; Wang, H. B.; Dembo, M.; Wang, Y. L.

    2000-01-01

    Directional cell locomotion is critical in many physiological processes, including morphogenesis, the immune response, and wound healing. It is well known that in these processes cell movements can be guided by gradients of various chemical signals. In this study, we demonstrate that cell movement can also be guided by purely physical interactions at the cell-substrate interface. We cultured National Institutes of Health 3T3 fibroblasts on flexible polyacrylamide sheets coated with type I collagen. A transition in rigidity was introduced in the central region of the sheet by a discontinuity in the concentration of the bis-acrylamide cross-linker. Cells approaching the transition region from the soft side could easily migrate across the boundary, with a concurrent increase in spreading area and traction forces. In contrast, cells migrating from the stiff side turned around or retracted as they reached the boundary. We call this apparent preference for a stiff substrate "durotaxis." In addition to substrate rigidity, we discovered that cell movement could also be guided by manipulating the flexible substrate to produce mechanical strains in the front or rear of a polarized cell. We conclude that changes in tissue rigidity and strain could play an important controlling role in a number of normal and pathological processes involving cell locomotion.

  3. Substrate binding ability of chemically inactivated pectinase for the substrate pectic acid.

    PubMed

    Chiba, Y; Kobayashi, M

    1995-07-01

    Pectinase (polygalacturonase) was purified from a commercial pectinase preparation from a mold. Substrate binding of pectinase was measured by centrifugal affinity chromatography using an immobilized substrate, pectic acid. Desorption of pectinase from the affinity matrix with the substrate pectin and pectic acid gave Kd values of 5.3 and 8.5 mg/ml, respectively. Chemical modification of pectinase by 1-ethyl-3-(3-dimethyl-aminopropyl)carbodiimide (EDC) and diethyl pyrocarbonate (DEP) caused a loss of most of the enzyme activity, but the substrate binding ability was not impaired. Thus, the pectinase preparation was digested with lysyl endopeptidase and the resulting peptides were treated with pectic acid-affinity gel. Three peptide fragments, which were recovered from the affinity column and sequenced, were identical to sequences in the second pectinase gene from Aspergillus niger. The first peptide contained 17 amino acids, Asp101-Ser117, and the second and third peptides corresponded to 18 amino acids of Asn152-Asp169. These results indicate that the inactivated pectinase retained substrate binding ability and would function as an acidic polysaccharide recognizing protein.

  4. A non-modular type B feruloyl esterase from Neurospora crassa exhibits concentration-dependent substrate inhibition.

    PubMed Central

    Crepin, Valerie F; Faulds, Craig B; Connerton, Ian F

    2003-01-01

    Feruloyl esterases, a subclass of the carboxylic acid esterases (EC 3.1.1.1), are able to hydrolyse the ester bond between the hydroxycinnamic acids and sugars present in the plant cell wall. The enzymes have been classified as type A or type B, based on their substrate specificity for aromatic moieties. We show that Neurospora crassa has the ability to produce multiple ferulic acid esterase activities depending upon the length of fermentation with either sugar beet pulp or wheat bran substrates. A gene identified on the basis of its expression on sugar beet pulp has been cloned and overexpressed in Pichia pastoris. The gene encodes a single-domain ferulic acid esterase, which represents the first report of a non-modular type B enzyme (fae-1 gene; GenBank accession no. AJ293029). The purified recombinant protein has been shown to exhibit concentration-dependent substrate inhibition (K(m) 0.048 mM, K (i) 2.5 mM and V(max) 8.2 units/mg against methyl 3,4-dihydroxycinnamate). The kinetic behaviour of the non-modular enzyme is discussed in terms of the diversity in the roles of the feruloyl esterases in the mobilization of plant cell wall materials and their respective modes of action. PMID:12435269

  5. Composite substrate for bipolar electrodes

    DOEpatents

    Tekkanat, B.; Bolstad, J.J.

    1992-12-22

    Substrates for electrode systems, particularly those to be used for bipolar electrodes in zinc-bromine batteries, are disclosed. The substrates preferably include carbon-black as a conductive filler in a polymeric matrix, with reinforcing materials such as glass fibers. Warpage of the zinc-bromine electrodes which was experienced in the prior art and which was believed to be caused by physical expansion of the electrodes due to bromine absorption by the carbon-black, is substantially eliminated when new substrate fabrication techniques are employed. In the present invention, substrates are prepared using a lamination process known as glass mat reinforced thermoplastics technology or, in an alternate embodiment, the substrate is made using a slurry process. 4 figs.

  6. Composite substrate for bipolar electrodes

    DOEpatents

    Tekkanat, Bora; Bolstad, James J.

    1992-12-22

    Substrates for electrode systems, particularly those to be used for bipolar electrodes in zinc-bromine batteries, are disclosed. The substrates preferably include carbon-black as a conductive filler in a polymeric matrix, with reinforcing materials such as glass fibers. Warpage of the zinc-bromine electrodes which was experienced in the prior art and which was believed to be caused by physical expansion of the electrodes due to bromine absorption by the carbon-black, is substantially eliminated when new substrate fabrication techniques are employed. In the pesent invention, substrates are prepared using a lamination process known as glass mat reinforced thermoplastics technology or, in an alternate embodiment, the substrate is made using a slurry process.

  7. Systematic study for DNA recovery and profiling from common IED substrates: From laboratory to casework.

    PubMed

    Phetpeng, Sukanya; Kitpipit, Thitika; Thanakiatkrai, Phuvadol

    2015-07-01

    Improvised explosive devices (IEDs) made from household items are encountered in terrorist attacks worldwide. Assembling an IED leaves trace DNA on its components, but deflagration degrades DNA. To maximize the amount of DNA recovered, a systematic evaluation of DNA collection methods was carried out and the most efficient methods were implemented with IED casework evidence as a validation exercise. Six swab types and six moistening agents were used to collect dried buffy coat stains on four common IED substrates. The most efficient swab/moistening agent combinations were then compared with tape-lifting using three brands of adhesive tape and also with direct DNA extraction from evidence. The most efficient collection methods for different IED substrates (post-study protocol) were then implemented for IED casework and compared with the pre-study protocol using 195 pieces of IED evidence. There was no single best swab type or moistening agent. Swab type had the largest effect on DNA recovery percentages, but moistening agents, substrates, and the interactions between factors all affected DNA recovery. The most efficient swab/moistening agent combinations performed equally well when compared with the best adhesive tape and direct extraction. The post-study protocol significantly improved STR profiles obtained from IED evidence. This paper outlines a comprehensive study of DNA collection methods for trace DNA and the validation of the most efficient collection methods with IED evidence. The findings from both parts of this study emphasize the need to continuously re-evaluate standard operating protocols with empirical studies. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  8. P-glycoprotein substrate transport assessed by comparing cellular and vesicular ATPase activity.

    PubMed

    Nervi, Pierluigi; Li-Blatter, Xiaochun; Aänismaa, Päivi; Seelig, Anna

    2010-03-01

    We compared the P-glycoprotein ATPase activity in inside-out plasma membrane vesicles and living NIH-MDR1-G185 cells with the aim to detect substrate transport. To this purpose we used six substrates which differ significantly in their passive influx through the plasma membrane. In cells, the cytosolic membrane leaflet harboring the substrate binding site of P-glycoprotein has to be approached by passive diffusion through the lipid membrane, whereas in inside-out plasma membrane vesicles, it is accessible directly from the aqueous phase. Compounds exhibiting fast passive influx compared to active efflux by P-glycoprotein induced similar ATPase activity profiles in cells and inside-out plasma membrane vesicles, because their concentrations in the cytosolic leaflets were similar. Compounds exhibiting similar influx as efflux induced in contrast different ATPase activity profiles in cells and inside-out vesicles. Their concentration was significantly lower in the cytosolic leaflet of cells than in the cytosolic leaflet of inside-out membrane vesicles, indicating that P-glycoprotein could cope with passive influx. P-glycoprotein thus transported all compounds at a rate proportional to ATP hydrolysis (i.e. all compounds were substrates). However, it prevented substrate entry into the cytosol only if passive influx of substrates across the lipid bilayer was in a similar range as active efflux. Copyright 2009 Elsevier B.V. All rights reserved.

  9. Graphene-Mesoporous Si Nanocomposite as a Compliant Substrate for Heteroepitaxy.

    PubMed

    Boucherif, Abderrahim Rahim; Boucherif, Abderraouf; Kolhatkar, Gitanjali; Ruediger, Andreas; Arès, Richard

    2017-05-01

    The ultimate performance of a solid state device is limited by the restricted number of crystalline substrates that are available for epitaxial growth. As a result, only a small fraction of semiconductors are usable. This study describes a novel concept for a tunable compliant substrate for epitaxy, based on a graphene-porous silicon nanocomposite, which extends the range of available lattice constants for epitaxial semiconductor alloys. The presence of graphene and its effect on the strain of the porous layer lattice parameter are discussed in detail and new remarkable properties are demonstrated. These include thermal stability up to 900 °C, lattice tuning up to 0.9 % mismatch, and compliance under stress for virtual substrate thicknesses of several micrometers. A theoretical model is proposed to define the compliant substrate design rules. These advances lay the foundation for the fabrication of a compliant substrate that could unlock the lattice constant restrictions for defect-free new epitaxial semiconductor alloys and devices. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Yeast hexokinase. A fluorescence temperature-jump study of the kinetics of the binding of glucose to the monomer forms of hexokinases P-I and P-II.

    PubMed

    Hoggett, J G; Kellett, G L

    1976-09-15

    The binding of glucose to the monomeric forms of hexokinases P-I and P-II in Tris and phosphate buffers at pH 8.0 in the presence of 1 mol l-1 KCl has been studied using the fluorescence temperature-jump technique. For both isozymes only one relaxation time was observed; values of tau-1 increased linearly with increasing concentration of free reacting partners. The apparent second-order rate constant for association was about 2 X 10(6) 1 mol-1 s-1 for both isozymes; the differences in the stabilities of the complexes with P-I and P-II are entirely attributable to the fact that glucose dissociates more slowly from its complex with P-I than P-II (approximately 300 s-1 and 1100 s-1 respectively). Although the kinetic data are compatible with a single-step mechanism for glucose binding the association rate constant was much lower than that expected for a diffusion-limited rate of encounter. Other mechanisms for describing an induced-fit are discussed. It is shown that the data are incompatible with a slow 'prior-isomerization' pathway of substrate binding, but are consistent with a 'substrate-guided' pathway involving isomerization of the enzyme-substrate complex.

  11. Growth of CH3NH3PbI3 Perovskite on Stainless Steel Substrate Layered by ZnO Nanoparticles Using One-Step Spin Coating Route

    NASA Astrophysics Data System (ADS)

    Fuad, A.; Fibriyanti, A. A.; Mufti, N.; Taufiq, A.; Maryam, S.; Hidayat, N.

    2018-04-01

    In this work, we report the preparation of CH3NH3PbI3 perovskite using one-step spin coating route for solar cell application. CH3NH3I• PbI2•DMF•DMSO complexes were coated on stainless steel as a subtrate layered by ZnO nanoparticles as an electron transport layer. To obtain samples with a special performance, we annealed the samples at a temperature of 100, 120, and 140°C for 10 minutes. The samples were then characterized by means of XRD, SEM/EDX, and Spectroscopic Ellipsometry. The analysis of XRD data presented that the CH3NH3PbI3 perovskites were successfully prepared and crystallized in tetragonal structure confirming from crystalline planes (110) and (220). Meanwhile, the particle size of the samples prepared at a temperature of 100, 120, and 140°C presented 42.96, 54.73, and 55.19 nm, respectively with coincide with the SEM images. The results indicated that the increase in temperature during synthesis influenced the particle growth. Furthermore, the characterization using Spectroscopic Ellipsometry exhibited that the CH3NH3PbI3 successfully layered on the substrate sizing nano metric scale that open high opportunity to be applied to solar cells with high performance.

  12. Non-permeable substrate carrier for electroplating

    DOEpatents

    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.

  13. Non-permeable substrate carrier for electroplating

    DOEpatents

    Abas, Emmanuel Chua; Chen, Chen-an; Ma, Diana Xiaobing; Ganti, Kalyana; Divino, Edmundo Anida; Ermita, Jake Randal G.; Capulong, Jose Francisco S.; Castillo, Arnold Villamor

    2015-12-29

    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.

  14. Bicarbonate is a recycling substrate for cyanase.

    PubMed

    Johnson, W V; Anderson, P M

    1987-07-05

    Cyanase is an inducible enzyme in Escherichia coli that catalyzes bicarbonate-dependent decomposition of cyanate to ammonia and bicarbonate. Previous studies provided evidence that carbamate is an initial product and that the kinetic mechanism is rapid equilibrium random (bicarbonate serving as substrate as opposed to activator); the following mechanism was proposed (Anderson, P. M. (1980) Biochemistry 19, 2282-2888; Anderson, P. M., and Little, R. M. (1986) Biochemistry 25, 1621-1626). (formula; see text) Direct evidence for this mechanism was obtained in this study by 1) determining whether CO2 or HCO3- serves as substrate and is formed as product, 2) identifying the products formed from [14C]HCO3- and [14C] OCN-, 3) identifying the products formed from [13C] HCO3- and [12C]OCN- in the presence of [18O]H2O, and 4) determining whether 18O from [18O]HCO3- is incorporated into CO2 derived from OCN-. Bicarbonate (not CO2) is the substrate. Carbon dioxide (not HCO3-) is produced in stoichiometric amounts from both HCO3- and OCN-. 18O from [18O]H2O is not incorporated into CO2 formed from either HCO3- or OCN-. Oxygen-18 from [18O]HCO3- is incorporated into CO2 derived from OCN-. These results support the above mechanism, indicating that decomposition of cyanate catalyzed by cyanase is not a hydrolysis reaction and that bicarbonate functions as a recycling substrate.

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

    PubMed

    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.

  16. Silicon nanowire-based tunneling field-effect transistors on flexible plastic substrates.

    PubMed

    Lee, Myeongwon; Koo, Jamin; Chung, Eun-Ae; Jeong, Dong-Young; Koo, Yong-Seo; Kim, Sangsig

    2009-11-11

    A technique to implement silicon nanowire (SiNW)-based tunneling field-effect transistors (TFETs) on flexible plastic substrates is developed for the first time. The p-i-n configured Si NWs are obtained from an Si wafer using a conventional top-down CMOS-compatible technology, and they are then transferred onto the plastic substrate. Based on gate-controlled band-to-band tunneling (BTBT) as their working principle, the SiNW-based TFETs show normal p-channel switching behavior with a threshold voltage of -1.86 V and a subthreshold swing of 827 mV/dec. In addition, ambipolar conduction is observed due to the presence of the BTBT between the heavily doped p+ drain and n+ channel regions, indicating that our TFETs can operate in the n-channel mode as well. Furthermore, the BTBT generation rates for both the p-channel and n-channel operating modes are nearly independent of the bending state (strain = 0.8%) of the plastic substrate.

  17. Effect of graphene oxide ratio on the cell adhesion and growth behavior on a graphene oxide-coated silicon substrate

    NASA Astrophysics Data System (ADS)

    Jeong, Jin-Tak; Choi, Mun-Ki; Sim, Yumin; Lim, Jung-Taek; Kim, Gil-Sung; Seong, Maeng-Je; Hyung, Jung-Hwan; Kim, Keun Soo; Umar, Ahmad; Lee, Sang-Kwon

    2016-09-01

    Control of living cells on biocompatible materials or on modified substrates is important for the development of bio-applications, including biosensors and implant biomaterials. The topography and hydrophobicity of substrates highly affect cell adhesion, growth, and cell growth kinetics, which is of great importance in bio-applications. Herein, we investigate the adhesion, growth, and morphology of cultured breast cancer cells on a silicon substrate, on which graphene oxides (GO) was partially formed. By minimizing the size and amount of the GO-containing solution and the further annealing process, GO-coated Si samples were prepared which partially covered the Si substrates. The coverage of GO on Si samples decreases upon annealing. The behaviors of cells cultured on two samples have been observed, i.e. partially GO-coated Si (P-GO) and annealed partially GO-coated Si (Annealed p-GO), with a different coverage of GO. Indeed, the spreading area covered by the cells and the number of cells for a given culture period in the incubator were highly dependent on the hydrophobicity and the presence of oxygenated groups on GO and Si substrates, suggesting hydrophobicity-driven cell growth. Thus, the presented method can be used to control the cell growth via an appropriate surface modification.

  18. Active Site Metal Identity Alters Histone Deacetylase 8 Substrate Selectivity: A Potential Novel Regulatory Mechanism.

    PubMed

    Castaneda, Carol Ann; Lopez, Jeffrey E; Joseph, Caleb G; Scholle, Michael D; Mrksich, Milan; Fierke, Carol A

    2017-10-24

    Histone deacetylase 8 (HDAC8) is a well-characterized member of the class I acetyl-lysine deacetylase (HDAC) family. Previous work has shown that the efficiency of HDAC8-catalyzed deacetylation of a methylcoumarin peptide varies depending on the identity of the divalent metal ion in the HDAC8 active site. Here we demonstrate that both HDAC8 activity and substrate selectivity for a diverse range of peptide substrates depend on the identity of the active site metal ion. Varied deacetylase activities of Fe(II)- and Zn(II)-HDAC8 toward an array of peptide substrates were identified using self-assembled monolayers for matrix-assisted laser desorption ionization (SAMDI) mass spectrometry. Subsequently, the metal dependence of deacetylation of peptides of biological interest was measured using an in vitro peptide assay. While Fe(II)-HDAC8 is generally more active than Zn(II)-HDAC8, the Fe(II)/Zn(II) HDAC8 activity ratio varies widely (from 2 to 150) among the peptides tested. These data provide support for the hypothesis that HDAC8 may undergo metal switching in vivo that, in turn, may regulate its activity. However, future studies are needed to explore the identity of the metal ion bound to HDAC8 in cells under varied conditions.

  19. Low Substrate Loading Limits Methanogenesis and Leads to High Coulombic Efficiency in Bioelectrochemical Systems

    PubMed Central

    Sleutels, Tom H. J. A.; Molenaar, Sam D.; Heijne, Annemiek Ter; Buisman, Cees J. N.

    2016-01-01

    A crucial aspect for the application of bioelectrochemical systems (BESs) as a wastewater treatment technology is the efficient oxidation of complex substrates by the bioanode, which is reflected in high Coulombic efficiency (CE). To achieve high CE, it is essential to give a competitive advantage to electrogens over methanogens. Factors that affect CE in bioanodes are, amongst others, the type of wastewater, anode potential, substrate concentration and pH. In this paper, we focus on acetate as a substrate and analyze the competition between methanogens and electrogens from a thermodynamic and kinetic point of view. We reviewed experimental data from earlier studies and propose that low substrate loading in combination with a sufficiently high anode overpotential plays a key-role in achieving high CE. Low substrate loading is a proven strategy against methanogenic activity in large-scale reactors for sulfate reduction. The combination of low substrate loading with sufficiently high overpotential is essential because it results in favorable growth kinetics of electrogens compared to methanogens. To achieve high current density in combination with low substrate concentrations, it is essential to have a high specific anode surface area. New reactor designs with these features are essential for BESs to be successful in wastewater treatment in the future. PMID:27681899

  20. Low Substrate Loading Limits Methanogenesis and Leads to High Coulombic Efficiency in Bioelectrochemical Systems.

    PubMed

    Sleutels, Tom H J A; Molenaar, Sam D; Heijne, Annemiek Ter; Buisman, Cees J N

    2016-01-05

    A crucial aspect for the application of bioelectrochemical systems (BESs) as a wastewater treatment technology is the efficient oxidation of complex substrates by the bioanode, which is reflected in high Coulombic efficiency (CE). To achieve high CE, it is essential to give a competitive advantage to electrogens over methanogens. Factors that affect CE in bioanodes are, amongst others, the type of wastewater, anode potential, substrate concentration and pH. In this paper, we focus on acetate as a substrate and analyze the competition between methanogens and electrogens from a thermodynamic and kinetic point of view. We reviewed experimental data from earlier studies and propose that low substrate loading in combination with a sufficiently high anode overpotential plays a key-role in achieving high CE. Low substrate loading is a proven strategy against methanogenic activity in large-scale reactors for sulfate reduction. The combination of low substrate loading with sufficiently high overpotential is essential because it results in favorable growth kinetics of electrogens compared to methanogens. To achieve high current density in combination with low substrate concentrations, it is essential to have a high specific anode surface area. New reactor designs with these features are essential for BESs to be successful in wastewater treatment in the future.

  1. Piezoelectric biosensor with a ladder polymer substrate coating

    DOEpatents

    Renschler, Clifford L.; White, Christine A.; Carter, Robert M.

    1998-01-01

    A piezoelectric biosensor substrate useful for immobilizing biomolecules in an oriented manner on the surface of a piezoelectric sensor has a ladder polymer of polyacrylonitrile. To make the substrate, a solution of an organic polymer, preferably polyacrylonitrile, is applied to the surface of a piezoelectric sensor. The organic polymer is modifying by heating the polymer in a controlled fashion in air such that a ladder polymer is produced which, in turn, forms the attachment point for the biomolecules comprising the piezoelectric biosensor.

  2. Adaptation of continuous biogas reactors operating under wet fermentation conditions to dry conditions with corn stover as substrate.

    PubMed

    Kakuk, Balázs; Kovács, Kornél L; Szuhaj, Márk; Rákhely, Gábor; Bagi, Zoltán

    2017-08-01

    Corn stover (CS) is the agricultural by-product of maize cultivation. Due to its high abundance and high energy content it is a promising substrate for the bioenergy sector. However, it is currently neglected in industrial scale biogas plants, because of its slow decomposition and hydrophobic character. To assess the maximum biomethane potential of CS, long-term batch fermentations were carried out with various substrate concentrations and particle sizes for 72 days. In separate experiments we adapted the biogas producing microbial community in wet fermentation arrangement first to the lignocellulosic substrate, in Continuous Stirred Tank Reactor (CSTR), then subsequently, by continuously elevating the feed-in concentration, to dry conditions in solid state fermenters (SS-AD). In the batch tests, the <10 mm fraction of the grinded and sieved CS was amenable for biogasification, but it required 10% more time to produce 90% of the total biomethane yield than the <2 mm sized fraction, although in the total yields there was no significant difference between the two size ranges. We also observed that increasing amount of substrate added to the fermentation lowered the specific methane yield. In the CSTR experiment, the daily substrate loading was gradually increased from 1 to 2 g vs /L/day until the system produced signs of overloading. Then the biomass was transferred to SS-AD reactors and the adaptation process was studied. Although the specific methane yields were lower in the SS-AD arrangement (177 mL CH 4 /g vs in CSTR vs. 105 mL in SS-AD), the benefits of process operational parameters, i.e. lower energy consumption, smaller reactor volume, digestate amount generated and simpler configuration, may compensate the somewhat lower yield. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  3. Bile acids and their oxo derivatives: Potential inhibitors of carbonic anhydrase I and II, androgen receptor antagonists and CYP3A4 substrates.

    PubMed

    Trifunović, Jovana; Borčić, Vladan; Mikov, Momir

    2017-05-01

    Some biological properties of bile acids and their oxo derivatives have not been sufficiently investigated, although the interest in bile acids as signaling molecules is rising. The aim of this work was to evaluate physico-chemical parametar b (slope) that represents the lipophilicity of the examined molecules and to investigate interactions of bile acids with carbonic anhydrase I, II, androgen receptor and CYP450s. Thirteen candidates were investigated using normal-phase thin-layer chromatography in two solvent systems. Retention parameters were used in further quantitative structure-activity relationship analysis and docking studies to predict interactions and binding affinities of examined molecules with enzymes and receptors. Prediction of activity on androgen receptor showed that compounds 3α-hydroxy-12-oxo-5β-cholanoic and 3α-hydroxy-7-oxo-5β-cholanoic acid have stronger antiandrogen activity than natural bile acids. The inhibitory potential for carbonic anhydrase I and II was tested and it was concluded that molecules 3α-hydroxy-12-oxo-5β-cholanoic, 3α-hydroxy-7-oxo-5β-cholanoic, 3,7,12-trioxo-5β-cholanoic acid and hyodeoxycholic acid show the best results. Substrate behavior for CYP3A4 was confirmed for all investigated compounds. Oxo derivatives of bile acids show stronger interactions with enzymes and receptors as classical bile acids and lower membranolytic activity compared with them. These significant observations could be valuable in consideration of oxo derivatives as building blocks in medicinal chemistry. Copyright © 2016 John Wiley & Sons, Ltd.

  4. Substrate-Assisted Catalysis in the Reaction Catalyzed by Salicylic Acid Binding Protein 2 (SABP2), a Potential Mechanism of Substrate Discrimination for Some Promiscuous Enzymes.

    PubMed

    Yao, Jianzhuang; Guo, Haobo; Chaiprasongsuk, Minta; Zhao, Nan; Chen, Feng; Yang, Xiaohan; Guo, Hong

    2015-09-01

    Although one of an enzyme's hallmarks is the high specificity for their natural substrates, substrate promiscuity has been reported more frequently. It is known that promiscuous enzymes generally show different catalytic efficiencies to different substrates, but our understanding of the origin of such differences is still lacking. Here we report the results of quantum mechanical/molecular mechanical simulations and an experimental study of salicylic acid binding protein 2 (SABP2). SABP2 has promiscuous esterase activity toward a series of substrates but shows a high activity toward its natural substrate, methyl salicylate (MeSA). Our results demonstrate that this enzyme may use substrate-assisted catalysis involving the hydroxyl group from MeSA to enhance the activity and achieve substrate discrimination.

  5. Substrate-Assisted Catalysis in the Reaction Catalyzed by Salicylic Acid Binding Protein 2 (SABP2), a Potential Mechanism of Substrate Discrimination for Some Promiscuous Enzymes

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Yao, Jianzhuang; Guo, Haobo; Chaiprasongsuk, Minta

    Although one of an enzyme’s hallmarks is the high specificity for their natural substrates, substrate promiscuity has been reported more frequently. We know that promiscuous enzymes generally show different catalytic efficiencies to different substrates, but our understanding of the origin of such differences is still lacking. We report the results of quantum mechanical/molecular mechanical simulations and an experimental study of salicylic acid binding protein 2 (SABP2). SABP2 has promiscuous esterase activity toward a series of substrates but shows a high activity toward its natural substrate, methyl salicylate (MeSA). Finally, our results demonstrate that this enzyme may use substrate-assisted catalysis involvingmore » the hydroxyl group from MeSA to enhance the activity and achieve substrate discrimination.« less

  6. Substrate-Assisted Catalysis in the Reaction Catalyzed by Salicylic Acid Binding Protein 2 (SABP2), a Potential Mechanism of Substrate Discrimination for Some Promiscuous Enzymes

    DOE PAGES

    Yao, Jianzhuang; Guo, Haobo; Chaiprasongsuk, Minta; ...

    2015-08-05

    Although one of an enzyme’s hallmarks is the high specificity for their natural substrates, substrate promiscuity has been reported more frequently. We know that promiscuous enzymes generally show different catalytic efficiencies to different substrates, but our understanding of the origin of such differences is still lacking. We report the results of quantum mechanical/molecular mechanical simulations and an experimental study of salicylic acid binding protein 2 (SABP2). SABP2 has promiscuous esterase activity toward a series of substrates but shows a high activity toward its natural substrate, methyl salicylate (MeSA). Finally, our results demonstrate that this enzyme may use substrate-assisted catalysis involvingmore » the hydroxyl group from MeSA to enhance the activity and achieve substrate discrimination.« less

  7. Process for selectively patterning epitaxial film growth on a semiconductor substrate

    DOEpatents

    Sheldon, Peter; Hayes, Russell E.

    1986-01-01

    A process is disclosed for selectively patterning epitaxial film growth on a semiconductor substrate. The process includes forming a masking member on the surface of the substrate, the masking member having at least two layers including a first layer disposed on the substrate and the second layer covering the first layer. A window is then opened in a selected portion of the second layer by removing that portion to expose the first layer thereunder. The first layer is then subjected to an etchant introduced through the window to dissolve a sufficient amount of the first layer to expose the substrate surface directly beneath the window, the first layer being adapted to preferentially dissolve at a substantially greater rate than the second layer so as to create an overhanging ledge portion with the second layer by undercutting the edges thereof adjacent to the window. The epitaxial film is then deposited on the exposed substrate surface directly beneath the window. Finally, an etchant is introduced through the window to dissolve the remainder of the first layer so as to lift-off the second layer and materials deposited thereon to fully expose the balance of the substrate surface.

  8. Understanding Substrate Selectivity of Human UDP-glucuronosyltransferases through QSAR modeling and analysis of homologous enzymes

    PubMed Central

    Dong, Dong; Ako, Roland; Hu, Ming; Wu, Baojian

    2015-01-01

    The UDP-glucuronosyltransferase (UGT) enzyme catalyzes the glucuronidation reaction which is a major metabolic and detoxification pathway in humans. Understanding the mechanisms for substrate recognition by UGT assumes great importance in an attempt to predict its contribution to xenobiotic/drug disposition in vivo. Spurred on by this interest, 2D/3D-quantitative structure activity relationships (QSAR) and pharmacophore models have been established in the absence of a complete mammalian UGT crystal structure. This review discusses the recent progress in modeling human UGT substrates including those with multiple sites of glucuronidation. A better understanding of UGT active site contributing to substrate selectivity (and regioselectivity) from the homologous enzymes (i.e., plant and bacterial UGTs, all belong to family 1 of glycosyltransferase (GT1)) is also highlighted, as these enzymes share a common catalytic mechanism and/or overlapping substrate selectivity. PMID:22385482

  9. Identification of a Second Substrate-binding Site in Solute-Sodium Symporters*

    PubMed Central

    Li, Zheng; Lee, Ashley S. E.; Bracher, Susanne; Jung, Heinrich; Paz, Aviv; Kumar, Jay P.; Abramson, Jeff; Quick, Matthias; Shi, Lei

    2015-01-01

    The structure of the sodium/galactose transporter (vSGLT), a solute-sodium symporter (SSS) from Vibrio parahaemolyticus, shares a common structural fold with LeuT of the neurotransmitter-sodium symporter family. Structural alignments between LeuT and vSGLT reveal that the crystallographically identified galactose-binding site in vSGLT is located in a more extracellular location relative to the central substrate-binding site (S1) in LeuT. Our computational analyses suggest the existence of an additional galactose-binding site in vSGLT that aligns to the S1 site of LeuT. Radiolabeled galactose saturation binding experiments indicate that, like LeuT, vSGLT can simultaneously bind two substrate molecules under equilibrium conditions. Mutating key residues in the individual substrate-binding sites reduced the molar substrate-to-protein binding stoichiometry to ∼1. In addition, the related and more experimentally tractable SSS member PutP (the Na+/proline transporter) also exhibits a binding stoichiometry of 2. Targeting residues in the proposed sites with mutations results in the reduction of the binding stoichiometry and is accompanied by severely impaired translocation of proline. Our data suggest that substrate transport by SSS members requires both substrate-binding sites, thereby implying that SSSs and neurotransmitter-sodium symporters share common mechanistic elements in substrate transport. PMID:25398883

  10. Process for selectively patterning epitaxial film growth on a semiconductor substrate

    DOEpatents

    Sheldon, P.; Hayes, R.E.

    1984-12-04

    Disclosed is a process for selectively patterning epitaxial film growth on a semiconductor substrate. The process includes forming a masking member on the surface of the substrate, the masking member having at least two layers including a first layer disposed on the substrate and the second layer covering the first layer. A window is then opened in a selected portion of the second layer by removing that portion to expose the first layer thereunder. The first layer is then subjected to an etchant introduced through the window to dissolve the first layer a sufficient amount to expose the substrate surface directly beneath the window, the first layer being adapted to preferentially dissolve at a substantially greater rate than the second layer so as to create an overhanging ledge portion with the second layer by undercutting the edges thereof adjacent the window. The epitaxial film is then deposited on the exposed substrate surface directly beneath the window. Finally, an etchant is introduced through the window to dissolve the remainder of the first layer so as to lift-off the second layer and materials deposited thereon to fully expose the balance of the substrate surface.

  11. Effect of Substrate and Process Parameters on the Gas-Substrate Convective Heat Transfer Coefficient During Cold Spraying

    NASA Astrophysics Data System (ADS)

    Mahdavi, Amirhossein; McDonald, André

    2018-02-01

    The final quality of cold-sprayed coatings can be significantly influenced by gas-substrate heat exchange, due to the dependence of the deposition efficiency of the particles on the substrate temperature distribution. In this study, the effect of the air temperature and pressure, as process parameters, and surface roughness and thickness, as substrate parameters, on the convective heat transfer coefficient of the impinging air jet was investigated. A low-pressure cold spraying unit was used to generate a compressed air jet that impinged on a flat substrate. A comprehensive mathematical model was developed and coupled with experimental data to estimate the heat transfer coefficient and the surface temperature of the substrate. The effect of the air total temperature and pressure on the heat transfer coefficient was studied. It was found that increasing the total pressure would increase the Nusselt number of the impinging air jet, while total temperature of the air jet had negligible effect on the Nusslet number. It was further found that increasing the roughness of the substrate enhanced the heat exchange between the impinging air jet and the substrate. As a result, higher surface temperatures on the rough substrate were measured. The study of the effect of the substrate thickness on the heat transfer coefficient showed that the Nusselt number that was predicted by the model was independent of the thickness of the substrate. The surface temperature profile, however, decreased in increasing radial distances from the stagnation point of the impinging jet as the thickness of the substrate increased. The results of the current study were aimed to inform on the influence and effect of substrate and process parameters on the gas-substrate heat exchange and the surface temperature of the substrate on the final quality of cold-sprayed coatings.

  12. A process for preparing an ultra-thin, adhesiveless, multi-layered, patterned polymer substrate

    NASA Technical Reports Server (NTRS)

    Bryant, Robert G. (Inventor); Kruse, Nancy H. M. (Inventor); Fox, Robert L. (Inventor); Tran, Sang Q. (Inventor)

    1995-01-01

    A process for preparing an ultra-thin, adhesiveless, multi-layered, patterned polymer substrate is disclosed. The process may be used to prepare both rigid and flexible cables and circuit boards. A substrate is provided and a polymeric solution comprising a self-bonding, soluble polymer and a solvent is applied to the substrate. Next, the polymer solution is dried to form a polymer coated substrate. The polymer coated substrate is metallized and patterned. At least one additional coating of the polymeric solution is applied to the metallized, patterned, polymer coated substrate and the steps of metallizing and patterning are repeated. Lastly, a cover coat is applied. When preparing a flexible cable and flexible circuit board, the polymer coating is removed from the substrate.

  13. Cryo-EM structures of the eukaryotic replicative helicase bound to a translocation substrate

    NASA Astrophysics Data System (ADS)

    Abid Ali, Ferdos; Renault, Ludovic; Gannon, Julian; Gahlon, Hailey L.; Kotecha, Abhay; Zhou, Jin Chuan; Rueda, David; Costa, Alessandro

    2016-02-01

    The Cdc45-MCM-GINS (CMG) helicase unwinds DNA during the elongation step of eukaryotic genome duplication and this process depends on the MCM ATPase function. Whether CMG translocation occurs on single- or double-stranded DNA and how ATP hydrolysis drives DNA unwinding remain open questions. Here we use cryo-electron microscopy to describe two subnanometre resolution structures of the CMG helicase trapped on a DNA fork. In the predominant state, the ring-shaped C-terminal ATPase of MCM is compact and contacts single-stranded DNA, via a set of pre-sensor 1 hairpins that spiral around the translocation substrate. In the second state, the ATPase module is relaxed and apparently substrate free, while DNA intimately contacts the downstream amino-terminal tier of the MCM motor ring. These results, supported by single-molecule FRET measurements, lead us to suggest a replication fork unwinding mechanism whereby the N-terminal and AAA+ tiers of the MCM work in concert to translocate on single-stranded DNA.

  14. Concurrent Cooperativity and Substrate Inhibition in the Epoxidation of Carbamazepine by Cytochrome P450 3A4 Active Site Mutants Inspired by Molecular Dynamics Simulations

    PubMed Central

    2015-01-01

    Cytochrome P450 3A4 (CYP3A4) is the major human P450 responsible for the metabolism of carbamazepine (CBZ). To explore the mechanisms of interactions of CYP3A4 with this anticonvulsive drug, we carried out multiple molecular dynamics (MD) simulations, starting with the complex of CYP3A4 manually docked with CBZ. On the basis of these simulations, we engineered CYP3A4 mutants I369F, I369L, A370V, and A370L, in which the productive binding orientation was expected to be stabilized, thus leading to increased turnover of CBZ to the 10,11-epoxide product. In addition, we generated CYP3A4 mutant S119A as a control construct with putative destabilization of the productive binding pose. Evaluation of the kinetics profiles of CBZ epoxidation demonstrate that CYP3A4-containing bacterial membranes (bactosomes) as well as purified CYP3A4 (wild-type and mutants I369L/F) exhibit substrate inhibition in reconstituted systems. In contrast, mutants S119A and A370V/L exhibit S-shaped profiles that are indicative of homotropic cooperativity. MD simulations with two to four CBZ molecules provide evidence that the substrate-binding pocket of CYP3A4 can accommodate more than one molecule of CBZ. Analysis of the kinetics profiles of CBZ metabolism with a model that combines the formalism of the Hill equation with an allowance for substrate inhibition demonstrates that the mechanism of interactions of CBZ with CYP3A4 involves multiple substrate-binding events (most likely three). Despite the retention of the multisite binding mechanism in the mutants, functional manifestations reveal an exquisite sensitivity to even minor structural changes in the binding pocket that are introduced by conservative substitutions such as I369F, I369L, and A370V. PMID:25545162

  15. Concurrent cooperativity and substrate inhibition in the epoxidation of carbamazepine by cytochrome P450 3A4 active site mutants inspired by molecular dynamics simulations.

    PubMed

    Müller, Christian S; Knehans, Tim; Davydov, Dmitri R; Bounds, Patricia L; von Mandach, Ursula; Halpert, James R; Caflisch, Amedeo; Koppenol, Willem H

    2015-01-27

    Cytochrome P450 3A4 (CYP3A4) is the major human P450 responsible for the metabolism of carbamazepine (CBZ). To explore the mechanisms of interactions of CYP3A4 with this anticonvulsive drug, we carried out multiple molecular dynamics (MD) simulations, starting with the complex of CYP3A4 manually docked with CBZ. On the basis of these simulations, we engineered CYP3A4 mutants I369F, I369L, A370V, and A370L, in which the productive binding orientation was expected to be stabilized, thus leading to increased turnover of CBZ to the 10,11-epoxide product. In addition, we generated CYP3A4 mutant S119A as a control construct with putative destabilization of the productive binding pose. Evaluation of the kinetics profiles of CBZ epoxidation demonstrate that CYP3A4-containing bacterial membranes (bactosomes) as well as purified CYP3A4 (wild-type and mutants I369L/F) exhibit substrate inhibition in reconstituted systems. In contrast, mutants S119A and A370V/L exhibit S-shaped profiles that are indicative of homotropic cooperativity. MD simulations with two to four CBZ molecules provide evidence that the substrate-binding pocket of CYP3A4 can accommodate more than one molecule of CBZ. Analysis of the kinetics profiles of CBZ metabolism with a model that combines the formalism of the Hill equation with an allowance for substrate inhibition demonstrates that the mechanism of interactions of CBZ with CYP3A4 involves multiple substrate-binding events (most likely three). Despite the retention of the multisite binding mechanism in the mutants, functional manifestations reveal an exquisite sensitivity to even minor structural changes in the binding pocket that are introduced by conservative substitutions such as I369F, I369L, and A370V.

  16. Sealed substrate carrier for electroplating

    DOEpatents

    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.

  17. Biochemistry Students' Ideas about How an Enzyme Interacts with a Substrate

    ERIC Educational Resources Information Center

    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…

  18. Piezoelectric biosensor with a ladder polymer substrate coating

    DOEpatents

    Renschler, C.L.; White, C.A.; Carter, R.M.

    1998-09-29

    A piezoelectric biosensor substrate useful for immobilizing biomolecules in an oriented manner on the surface of a piezoelectric sensor has a ladder polymer of polyacrylonitrile. To make the substrate, a solution of an organic polymer, preferably polyacrylonitrile, is applied to the surface of a piezoelectric sensor. The organic polymer is modifying by heating the polymer in a controlled fashion in air such that a ladder polymer is produced which, in turn, forms the attachment point for the biomolecules comprising the piezoelectric biosensor. 3 figs.

  19. Precise impurity analysis of Cu films by GDMS: relation between negative substrate bias voltage and impurity ionization potentials

    NASA Astrophysics Data System (ADS)

    Lim, J. W.; Mimura, K.; Isshiki, M.

    2005-02-01

    Cu films were deposited on Si(100) substrates by applying a negative substrate bias voltage using the non-mass-separated ion beam deposition method. Glow-discharge mass spectrometry was used to determine the impurity concentrations of the deposited Cu films and the 6N Cu target. It was found that the Cu film deposited at the substrate bias voltage of -50 V showed lower impurity contents than the Cu film deposited without the substrate bias voltage, although both the Cu films were contaminated during the deposition. The purification effect might result from the following reasons: (i) the Penning ionization and an ionization mechanism proposed in the present study, (ii) a difference in the kinetic energy of accelerated Cu+ ions toward the substrate with/without the negative substrate bias voltage.

  20. Development of a bacterial screen for novel hypoxanthine-guanine phosphoribosyltransferase substrates.

    PubMed

    Shivashankar, K; Subbayya, I N; Balaram, H

    2001-10-01

    The lack of de novo purine biosynthesis in many parasitic protozoans makes the enzymes in the salvage of purines attractive chemotherapeutic targets. Hypoxanthine-guanine phosphoribosyltransferase (HGPRT) is a key enzyme for purine salvage and bacterial complementation screens for HGPRT inhibitors are known. The low KMS for purine bases makes purine analogs unattractive as competitive inhibitors for this enzyme. Despite the availability of many crystal structures of HGPRTs, it is only recently that selective inhibitors of the enzyme have been developed. Therefore, novel purine analogs which act as substrates for the HGPRT reaction and thereby inhibit downstream enzymes or get incorporated into the nucleotide pool are an attractive altenative for drug design. We have used a combination of two E. coli strains Sphi606 (ara, deltapro-gpt-lac, thi, hpt) and Sphi609 (ara, deltapro-gpt-lac, thi, hpt, pup, purH,J, strA) to identify inhibitors and substrates of HGPRT. E. coli Sphi609 is deficient in both de novo synthesis as well as salvage enzymes of purine nucleotide synthesis, while E. coli Sphi606 is deficient in salvage enzymes only. Hence, expression of functional HGPRTs in E. coli Sphi606 grown in minimal medium makes it susceptible to HGPRT substrates, which inhibit downstream processes. Growth of E. coli Sphi609 in minimal medium can be made conditional for the expression of a functional HGPRT and this growth would be susceptible to both HGPRT substrate analogs and inhibitors. A substance that strictly acts as an inhibitor will affect growth of transformed E. coli Sphi609 only. For this purpose, we compared the human and P. falciparum enzymes with known HGPRT substrate analogs. Our data with 6-mercaptopurine, 6-thioguanine and allopurinol show that these compounds act by being substrates for HGPRT. Our results with allopurinol suggest that it is a better substrate for P. falciparum HGXPRT than the human enzyme. Therefore, species-specific substrates can be tested

  1. Mapping the Substrate Binding Site of Phenylacetone Monooxygenase from Thermobifida fusca by Mutational Analysis▿†

    PubMed Central

    Dudek, Hanna M.; de Gonzalo, Gonzalo; Torres Pazmiño, Daniel E.; Stępniak, Piotr; Wyrwicz, Lucjan S.; Rychlewski, Leszek; Fraaije, Marco W.

    2011-01-01

    Baeyer-Villiger monooxygenases catalyze oxidations that are of interest for biocatalytic applications. Among these enzymes, phenylacetone monooxygenase (PAMO) from Thermobifida fusca is the only protein showing remarkable stability. While related enzymes often present a broad substrate scope, PAMO accepts only a limited number of substrates. Due to the absence of a substrate in the elucidated crystal structure of PAMO, the substrate binding site of this protein has not yet been defined. In this study, a structural model of cyclopentanone monooxygenase, which acts on a broad range of compounds, has been prepared and compared with the structure of PAMO. This revealed 15 amino acid positions in the active site of PAMO that may account for its relatively narrow substrate specificity. We designed and analyzed 30 single and multiple mutants in order to verify the role of these positions. Extensive substrate screening revealed several mutants that displayed increased activity and altered regio- or enantioselectivity in Baeyer-Villiger reactions and sulfoxidations. Further substrate profiling resulted in the identification of mutants with improved catalytic properties toward synthetically attractive compounds. Moreover, the thermostability of the mutants was not compromised in comparison to that of the wild-type enzyme. Our data demonstrate that the positions identified within the active site of PAMO, namely, V54, I67, Q152, and A435, contribute to the substrate specificity of this enzyme. These findings will aid in more dedicated and effective redesign of PAMO and related monooxygenases toward an expanded substrate scope. PMID:21724896

  2. Pinus sylvestris switches respiration substrates under shading but not during drought

    NASA Astrophysics Data System (ADS)

    Hartmann, Henrik; Fischer, Sarah; Hanf, Stefan; Frosch, Torsten; Poppp, Jürgen; Trumbore, Susan

    2015-04-01

    Reduced carbon assimilation during prolonged drought forces trees to rely on stored carbon to maintain vital processes like respiration. It has been shown, however, that the use of carbohydrates, a major carbon storage pool and main respiratory substrate in plants, strongly declines with deceasing plant hydration. Yet, no empirical evidence has been produced to what degree other carbon storage compounds like lipids and proteins may fuel respiration during drought. We exposed young scots pine trees to carbon limitation using either drought or shading and assessed respiratory substrate use by monitoring the respiratory quotient, δ13C of respired CO2and concentrations of the major storage compounds, i.e. carbohydrates (COH), lipids and amino acids. Generally, respiration was dominated by the most abundant substrate. Only shaded trees shifted from carbohydrate-dominated to lipid-dominated respiration and showed progressive carbohydrate depletion. In drought trees respiration was strongly reduced and fueled with carbohydrates from also strongly reduced carbon assimilation. Initial COH content was maintained during drought probably due to reduced COH mobilization and use and the maintained COH content may have prevented lipid catabolism via sugar signaling. Our results suggest that respiratory substrates other than carbohydrates are used under carbohydrate limitation but not during drought. Thus, respiratory substrate change cannot provide an efficient means to counterbalance carbon limitation under natural drought.

  3. Strain-Engineered Nanomembrane Substrates for Si/SiGe Heterostructures

    NASA Astrophysics Data System (ADS)

    Sookchoo, Pornsatit

    For Group IV materials, including silicon, germanium, and their alloys, although they are most widely used in the electronics industry, the development of photonic devices is hindered by indirect band gaps and large lattice mismatches. Thus, any heterostructures involving Si and Ge (4.17% lattice mismatch) are subject to plastic relaxation by dislocation formation in the heterolayers. These defects make many devices impossible and at minimum degrade the performance of those that are possible. Fabrication using elastic strain engineering in Si/SiGe nanomembranes (NMs) is an approach that is showing promise to overcome this limitation. A key advantage of such NM substrates over conventional bulk substrates is that they are relaxed elastically and therefore free of dislocations that occur in the conventional fabrication of SiGe substrates, which are transferred to the epilayers and roughen film interfaces. In this thesis, I use the strain engineering of NMs or NM stacks to fabricate substrates for the epitaxial growth of many repeating units of Si/SiGe heterostructure, known as a 'superlattice', by the elastic strain sharing of a few periods of the repeating unit of Si/SiGe heterolayers or a Si/SiGe/Si tri-layer structure. In both cases, the process begins with the epitaxial growth of Si/SiGe heterolayers on silicon-on-insulator (SOI), where each layer thickness is designed to stay below its kinetic critical thickness for the formation of dislocations. The heterostructure NMs are then released by etching of the SiO2 sacrificial layer in hydrofluoric acid. The resulting freestanding NMs are elastically relaxed by the sharing of strain between the heterolayers. The NMs can be bonded in-place to their host substrate or transferred to another host substrate for the subsequent growth of many periods of superlattice film. The magnitude of strain sharing in these freestanding NMs is influenced by their layer thicknesses and layer compositions. As illustrated in this

  4. Damage to the Silicon Substrate by Reactive Ion Etching Detected by a Slow Positron Beam

    NASA Astrophysics Data System (ADS)

    Wei, Long; Tabuki, Yasushi; Tanigawa, Shoichiro

    1993-01-01

    Defects in reactive ion-etched Si have been investigated by means of a slow positron beam. A thin carbon-containing film (<30 Å) was formed on the Si surface after reactive ion etching (RIE). Vacancy-type defects, which were estimated to distribute over 1200 Å in depth by numerical fitting using the positron trapping model, were observed in the damaged subsurface region of Si. Aside from ion bombardment, ultraviolet radiation is also presumed to affect the formation of vacancies, interstitials in oxide and the formation of vacancies in Si substrate. The ionization-enhanced diffusion (IED) mechanism is expected to promote the diffusion of vacancies and interstitials into Si substrate.

  5. In situ elasticity modulation with dynamic substrates to direct cell phenotype

    PubMed Central

    Kloxin, April M.; Benton, Julie A.; Anseth, Kristi S.

    2009-01-01

    Microenvironment elasticity influences critical cell functions such as differentiation, cytoskeletal organization, and process extension. Unfortunately, few materials allow elasticity modulation in real-time to probe its direct effect on these dynamic cellular processes. Here, a new approach is presented for the photochemical modulation of elasticity within the cell's microenvironment at any point in time. A photodegradable hydrogel was irradiated and degraded under cytocompatible conditions to generate a wide range of elastic moduli similar to soft tissues and characterized using rheometry and atomic force microscopy (AFM). The effect of the elastic modulus on valvular interstitial cell (VIC) activation into myofibroblasts was explored. In these studies, gradient samples were used to identify moduli that either promote or suppress VIC myofibroblastic activation. With this knowledge, VICs were cultured on a high modulus, activating hydrogel substrate, and uniquely, results show that decreasing the substrate modulus with irradiation reverses this activation, demonstrating that myofibroblasts can be de-activated solely by changing the modulus of the underlying substrate. This finding is important for the rational design of biomaterials for tissue regeneration and offers insight into fibrotic disease progression. These photodegradable hydrogels demonstrate the capability to both probe and direct cell function through dynamic changes in substrate elasticity. PMID:19788947

  6. Reductive trapping of substrate to bovine plasma amine oxidase

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Hartmann, C.; Klinman, J.P.

    1987-01-25

    Plasma amine oxidases catalyze the oxidative deamination of amines to aldehydes, followed by a 2e- reduction of O/sub 2/ to H/sub 2/O/sub 2/. Pyrroloquinoline quinone (PQQ), previously believed to be restricted to prokaryotes, has recently been proposed to be the cofactor undergoing reduction in the first half-reaction of bovine plasma amine oxidase (Ameyama, M., Hayashi, U., Matsushita, K., Shinagawa, E., and Adachi, O. (1984) Agric. Biol. Chem. 48, 561-565; Lobenstein-Verbeek, C. L., Jongejan, J. A., Frank, J., and Duine, J. A. (1984) FEBS Lett. 170, 305-309). This result is unexpected, since model studies with PQQ implicate Schiff's base formation betweenmore » a reactive carbonyl and substrates, whereas experiments with bovine plasma amine oxidase have failed to provide evidence for a carbonyl cofactor. We have, therefore, re-examined putative adducts between substrate and enzyme-bound cofactor, employing a combination of (/sup 14/C)benzylamine and (/sup 3/H)NaCNBH/sub 3/. The use of the relatively weak reductant, NaCNBH/sub 3/, affords Schiff's base specificity and permits the study of enzyme below pH 7.0. As we show, enzyme can only be inactivated by NaCNBH/sub 3/ in the presence of substrate, leading to the incorporation of 1 mol of (/sup 14/C)benzylamine/mol of enzyme subunit at complete inactivation. By contrast, we are unable to detect any labeling with (/sup 3/H)NaCNBH/sub 3/, analogous to an earlier study with (/sup 3/H)NaCNBH/sub 4/ (Suva, R. H., and Abeles, R. H. (1978) Biochemistry 17, 3538-3545). We conclude, first, that our inability to obtain adducts containing both carbon 14 and tritium rules out the reductive trapping either of amine substrate with pyridoxal phosphate or of aldehyde product with a lysyl side chain and, second, that the observed pattern of labeling is fully consistent with the presence of PQQ at the active site of bovine plasma amine oxidase.« less

  7. Substrate for thin silicon solar cells

    DOEpatents

    Ciszek, Theodore F.

    1998-01-01

    A substrate for a photovoltaic device wherein the substrate is the base upon which photosensitive material is to be grown and the substrate comprises an alloy having boron in a range from 0.1 atomic % of the alloy to 1.3 atomic % of the alloy and the substrate has a resistivity less than 3.times.10.sup.-3 ohm-cm.

  8. Silicon-based hot electron emitting substrate with double tunneling

    NASA Astrophysics Data System (ADS)

    Chen, Fei; Zhan, Xinghua; Salcic, Zoran; Wong, Chee Cheong; Gao, Wei

    2017-07-01

    We propose a novel silicon structure, Hot Electron Emitting Substrate (HEES), which exhibits important effect of repeated tunneling at two different voltage ranges, which we refer to as double tunneling. In ambient atmosphere and room temperature, the I-V characteristic of HEES shows two current peaks during voltage sweep from 2 to 15 V. These two peaks are formed by the Fowler-Nordheim (FN) tunneling effect and tunneling diode mechanism, respectively.

  9. SUPECA kinetics for scaling redox reactions in networks of mixed substrates and consumers and an example application to aerobic soil respiration

    DOE PAGES

    Tang, Jin-Yun; Riley, William J.

    2017-09-05

    Several land biogeochemical models used for studying carbon–climate feedbacks have begun explicitly representing microbial dynamics. However, to our knowledge, there has been no theoretical work on how to achieve a consistent scaling of the complex biogeochemical reactions from microbial individuals to populations, communities, and interactions with plants and mineral soils. We focus here on developing a mathematical formulation of the substrate–consumer relationships for consumer-mediated redox reactions of the form A +  B E→  products, where products could be, e.g., microbial biomass or bioproducts. Under the quasi-steady-state approximation, these substrate–consumer relationships can be formulated as the computationally difficult full equilibrium chemistrymore » problem or approximated analytically with the dual Monod (DM) or synthesizing unit (SU) kinetics. We find that DM kinetics is scaling inconsistently for reaction networks because (1) substrate limitations are not considered, (2) contradictory assumptions are made regarding the substrate processing rate when transitioning from single- to multi-substrate redox reactions, and (3) the product generation rate cannot be scaled from one to multiple substrates. In contrast, SU kinetics consistently scales the product generation rate from one to multiple substrates but predicts unrealistic results as consumer abundances reach large values with respect to their substrates. We attribute this deficit to SU's failure to incorporate substrate limitation in its derivation. To address these issues, we propose SUPECA (SU plus the equilibrium chemistry approximation – ECA) kinetics, which consistently imposes substrate and consumer mass balance constraints. We show that SUPECA kinetics satisfies the partition principle, i.e., scaling invariance across a network of an arbitrary number of reactions (e.g., as in Newton's law of motion and Dalton's law of partial pressures). We tested SUPECA kinetics with

  10. SUPECA kinetics for scaling redox reactions in networks of mixed substrates and consumers and an example application to aerobic soil respiration

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Tang, Jin-Yun; Riley, William J.

    Several land biogeochemical models used for studying carbon–climate feedbacks have begun explicitly representing microbial dynamics. However, to our knowledge, there has been no theoretical work on how to achieve a consistent scaling of the complex biogeochemical reactions from microbial individuals to populations, communities, and interactions with plants and mineral soils. We focus here on developing a mathematical formulation of the substrate–consumer relationships for consumer-mediated redox reactions of the form A +  B E→  products, where products could be, e.g., microbial biomass or bioproducts. Under the quasi-steady-state approximation, these substrate–consumer relationships can be formulated as the computationally difficult full equilibrium chemistrymore » problem or approximated analytically with the dual Monod (DM) or synthesizing unit (SU) kinetics. We find that DM kinetics is scaling inconsistently for reaction networks because (1) substrate limitations are not considered, (2) contradictory assumptions are made regarding the substrate processing rate when transitioning from single- to multi-substrate redox reactions, and (3) the product generation rate cannot be scaled from one to multiple substrates. In contrast, SU kinetics consistently scales the product generation rate from one to multiple substrates but predicts unrealistic results as consumer abundances reach large values with respect to their substrates. We attribute this deficit to SU's failure to incorporate substrate limitation in its derivation. To address these issues, we propose SUPECA (SU plus the equilibrium chemistry approximation – ECA) kinetics, which consistently imposes substrate and consumer mass balance constraints. We show that SUPECA kinetics satisfies the partition principle, i.e., scaling invariance across a network of an arbitrary number of reactions (e.g., as in Newton's law of motion and Dalton's law of partial pressures). We tested SUPECA kinetics with

  11. Molecular dynamics study of interfacial thermal transport between silicene and substrates.

    PubMed

    Zhang, Jingchao; Hong, Yang; Tong, Zhen; Xiao, Zhihuai; Bao, Hua; Yue, Yanan

    2015-10-07

    In this work, the interfacial thermal transport across silicene and various substrates, i.e., crystalline silicon (c-Si), amorphous silicon (a-Si), crystalline silica (c-SiO2) and amorphous silica (a-SiO2) are explored by classical molecular dynamics (MD) simulations. A transient pulsed heating technique is applied in this work to characterize the interfacial thermal resistance in all hybrid systems. It is reported that the interfacial thermal resistances between silicene and all substrates decrease nearly 40% with temperature from 100 K to 400 K, which is due to the enhanced phonon couplings from the anharmonicity effect. Analysis of phonon power spectra of all systems is performed to interpret simulation results. Contradictory to the traditional thought that amorphous structures tend to have poor thermal transport capabilities due to the disordered atomic configurations, it is calculated that amorphous silicon and silica substrates facilitate the interfacial thermal transport compared with their crystalline structures. Besides, the coupling effect from substrates can improve the interface thermal transport up to 43.5% for coupling strengths χ from 1.0 to 2.0. Our results provide fundamental knowledge and rational guidelines for the design and development of the next-generation silicene-based nanoelectronics and thermal interface materials.

  12. Common Ion Effects In Zeoponic Substrates: Dissolution And Cation Exchange Variations Due to Additions of Calcite, Dolomite and Wollastonite

    NASA Technical Reports Server (NTRS)

    Beiersdorfer, R. E.; Ming, D. W.; Galindo, C., Jr.

    2003-01-01

    c1inoptilolite-rich tuff-hydroxyapatite mixture (zeoponic substrate) has the potential to serve as a synthetic soil-additive for plant growth. Essential plant macro-nutrients such as calcium, phosphorous, magnesium, ammonium and potassium are released into solution via dissolution of the hydroxyapatite and cation exchange on zeolite charged sites. Plant growth experiments resulting in low yield for wheat have been attributed to a Ca deficiency caused by a high degree of cation exchange by the zeolite. Batch-equilibration experiments were performed in order to determine if the Ca deficiency can be remedied by the addition of a second Ca-bearing, soluble, mineral such as calcite, dolomite or wollastonite. Variations in the amount of calcite, dolomite or wollastonite resulted in systematic changes in the concentrations of Ca and P. The addition of calcite, dolomite or wollastonite to the zeoponic substrate resulted in an exponential decrease in the phosphorous concentration in solution. The exponential rate of decay was greatest for calcite (5.60 wt. % -I), intermediate for wollastonite (2.85 wt.% -I) and least for dolomite (1.58 wt.% -I). Additions of the three minerals resulted in linear increases in the calcium concentration in solution. The rate of increase was greatest for calcite (3.64), intermediate for wollastonite (2.41) and least for dolomite (0.61). The observed changes in P and Ca concentration are consistent with the solubilities of calcite, dolomite and wollastonite and with changes expected from a common ion effect with Ca. Keywords: zeolite, zeoponics, common-ion effect, clinoptilolite, hydroxyapatite

  13. PDMS substrate stiffness affects the morphology and growth profiles of cancerous prostate and melanoma cells.

    PubMed

    Prauzner-Bechcicki, Szymon; Raczkowska, Joanna; Madej, Ewelina; Pabijan, Joanna; Lukes, Jaroslav; Sepitka, Josef; Rysz, Jakub; Awsiuk, Kamil; Bernasik, Andrzej; Budkowski, Andrzej; Lekka, Małgorzata

    2015-01-01

    A deep understanding of the interaction between cancerous cells and surfaces is particularly important for the design of lab-on-chip devices involving the use of polydimethylsiloxane (PDMS). In our studies, the effect of PDMS substrate stiffness on mechanical properties of cancerous cells was investigated in conditions where the PDMS substrate is not covered with any of extracellular matrix proteins. Two human prostate cancer (Du145 and PC-3) and two melanoma (WM115 and WM266-4) cell lines were cultured on two groups of PDMS substrates that were characterized by distinct stiffness, i.e. 0.75 ± 0.06 MPa and 2.92 ± 0.12 MPa. The results showed the strong effect on cellular behavior and morphology. The detailed analysis of chemical and physical properties of substrates revealed that cellular behavior occurs only due to substrate elasticity. Copyright © 2014 Elsevier Ltd. All rights reserved.

  14. Arginine Kinase. Joint Crystallographic & NMR RDC Analyses link Substrate-Associated Motions to Intrinsic Flexibility

    PubMed Central

    Niu, Xiaogang; Brüschweiler-Li, Lei; Davulcu, Omar; Skalicky, Jack J.; Brüschweiler, Rafael; Chapman, Michael S.

    2010-01-01

    The phosphagen kinase family, including creatine and arginine kinases, catalyze the reversible transfer of a “high energy” phosphate between ATP and a phospho-guanidino substrate. They have become a model for the study of both substrate-induced conformational change and intrinsic protein dynamics. Prior crystallographic studies indicated large substrate-induced domain rotations, but differences among a recent set of arginine kinase structures was interpreted as a plastic deformation. Here, the structure of Limulus substrate-free arginine kinase is refined against high resolution crystallographic data and compared quantitatively with NMR chemical shifts and residual dipolar couplings (RDCs). This demonstrates the feasibility of this type of RDC analysis of proteins that are large by NMR standards (42 kDa), and illuminates the solution structure, free from crystal-packing constraints. Detailed comparison of the 1.7 Å resolution substrate-free crystal structure against the 1.2 Å transition state analog complex shows large substrate-induced domain motions which can be broken down into movements of smaller quasi-rigid bodies. The solution state structure of substrate-free arginine kinase is most consistent with an equilibrium of substrate-free and –bound structures, with the substrate-free form dominating, but with varying displacements of the quasi-rigid groups. Rigid-group rotations evident from the crystal structures are about axes previously associated with intrinsic millisecond dynamics using NMR relaxation dispersion. Thus, “substrate-induced” motions are along modes that are intrinsically flexible in the substrate-free enzyme, and likely involve some degree of conformational selection. PMID:21075117

  15. Adsorbates in a Box: Titration of Substrate Electronic States

    NASA Astrophysics Data System (ADS)

    Cheng, Zhihai; Wyrick, Jonathan; Luo, Miaomiao; Sun, Dezheng; Kim, Daeho; Zhu, Yeming; Lu, Wenhao; Kim, Kwangmoo; Einstein, T. L.; Bartels, Ludwig

    2010-08-01

    Nanoscale confinement of adsorbed CO molecules in an anthraquinone network on Cu(111) with a pore size of ≈4nm arranges the CO molecules in a shell structure that coincides with the distribution of substrate confined electronic states. Molecules occupy the states approximately in the sequence of rising electron energy. Despite the sixfold symmetry of the pore boundary itself, the adsorbate distribution adopts the threefold symmetry of the network-substrate system, highlighting the importance of the substrate even for such quasi-free-electron systems.

  16. Pretreatment process for forming a smooth surface diamond film on a carbon-coated substrate

    DOEpatents

    Feng, Zhu; Brewer, Marilee; Brown, Ian; Komvopoulos, Kyriakos

    1994-01-01

    A process is disclosed for the pretreatment of a carbon-coated substrate to provide a uniform high density of nucleation sites thereon for the subsequent deposition of a continuous diamond film without the application of a bias voltage to the substrate. The process comprises exposing the carbon-coated substrate, in a microwave plasma enhanced chemical vapor deposition system, to a mixture of hydrogen-methane gases, having a methane gas concentration of at least about 4% (as measured by partial pressure), while maintaining the substrate at a pressure of about 10 to about 30 Torr during the pretreatment.

  17. Pretreatment process for forming a smooth surface diamond film on a carbon-coated substrate

    DOEpatents

    Feng, Z.; Brewer, M.; Brown, I.; Komvopoulos, K.

    1994-05-03

    A process is disclosed for the pretreatment of a carbon-coated substrate to provide a uniform high density of nucleation sites thereon for the subsequent deposition of a continuous diamond film without the application of a bias voltage to the substrate. The process comprises exposing the carbon-coated substrate, in a microwave plasma enhanced chemical vapor deposition system, to a mixture of hydrogen-methane gases, having a methane gas concentration of at least about 4% (as measured by partial pressure), while maintaining the substrate at a pressure of about 10 to about 30 Torr during the pretreatment. 6 figures.

  18. Recovery of EUVL substrates

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Vernon, S.P.; Baker, S.L.

    1995-01-19

    Mo/Si multilayers, were removed from superpolished zerodur and fused silica substrates with a dry etching process that, under suitable processing conditions, produces negligible change in either the substrate surface figure or surface roughness. Full recovery of the initial normal incidence extreme ultra-violet (EUV) reflectance response has been demonstrated on reprocessed substrates.

  19. In vitro characterization of pol I*, an SOS inducible, error-prone from of Escherichia coli DNA polymerase I

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Hodes, C.S.

    E. coli strains carrying mutations in the SOS regulon were screened for the presence of pol I*. Use of pol I* in assays of polymerase fidelity and selectivity has been limited by the low concentration and purity of the enzyme. Therefore, attempts were made to further concentrate and purify pol I*. The template selectivity of pol I* was compared to that of pol I using three models of damaged DNA. UV-irradiated M13 DNA was used in a two-stage termination reaction to determine if pol I* could bypass putative pyrimidine dimers to a greater extent than pol I. In the gelmore » system no reproducibly significant bypass could be detected by either pol I* or pol I. However, the degree of replication by pol I* utilizing UV-irradiated M13 DNA template, was up to 5-fold greater than for pol I. OsO{sub 4}-oxidized M13 DNA was used as a model substrate for oxidative DNA damage. Opposite this substrate incorporation by pol I* is less inhibited than incorporation by pol I. However, in a test of nucleotide selectivity neither pol I*, pol I, nor terminal deoxyribonucleotidyl transferase will incorporate ({alpha}-{sup 32}P)thymine glycol deoxyribonucleotide. The activity of pol I* was compared to that of pol I on the synthetic templates, poly (dA) and poly((dA)+2-AP). Pol I* misincorporated both dCMP and dGMP to a greater extent than pol I when utilizing templates containing 2-aminopurine deoxyribonucleotide.« less

  20. The effects of substrate pre-treatment on anaerobic digestion systems: a review.

    PubMed

    Carlsson, My; Lagerkvist, Anders; Morgan-Sagastume, Fernando

    2012-09-01

    Focus is placed on substrate pre-treatment in anaerobic digestion (AD) as a means of increasing biogas yields using today's diversified substrate sources. Current pre-treatment methods to improve AD are being examined with regard to their effects on different substrate types, highlighting approaches and associated challenges in evaluating substrate pre-treatment in AD systems and its influence on the overall system of evaluation. WWTP residues represent the substrate type that is most frequently assessed in pre-treatment studies, followed by energy crops/harvesting residues, organic fraction of municipal solid waste, organic waste from food industry and manure. The pre-treatment effects are complex and generally linked to substrate characteristics and pre-treatment mechanisms. Overall, substrates containing lignin or bacterial cells appear to be the most amendable to pre-treatment for enhancing AD. Approaches used to evaluate AD enhancement in different systems is further reviewed and challenges and opportunities for improved evaluations are identified. Copyright © 2012 Elsevier Ltd. All rights reserved.

  1. Method of producing an electronic unit having a polydimethylsiloxane substrate and circuit lines

    DOEpatents

    Davidson, James Courtney [Livermore, CA; Krulevitch, Peter A [Pleasanton, CA; Maghribi, Mariam N [Livermore, CA; Benett, William J [Livermore, CA; Hamilton, Julie K [Tracy, CA; Tovar, Armando R [San Antonio, TX

    2012-06-19

    A system of metalization in an integrated polymer microsystem. A flexible polymer substrate is provided and conductive ink is applied to the substrate. In one embodiment the flexible polymer substrate is silicone. In another embodiment the flexible polymer substrate comprises poly(dimethylsiloxane).

  2. A multicomponent complex is required for the AAUAAA-dependent cross-linking of a 64-kilodalton protein to polyadenylation substrates.

    PubMed Central

    Wilusz, J; Shenk, T; Takagaki, Y; Manley, J L

    1990-01-01

    A 64-kilodalton (kDa) polypeptide that is cross-linked by UV light specifically to polyadenylation substrate RNAs containing a functional AAUAAA element has been identified previously. Fractionated HeLa nuclear components that can be combined to regenerate efficient and accurate polyadenylation in vitro have now been screened for the presence of the 64-kDa protein. None of the individual components contained an activity which could generate the 64-kDa species upon UV cross-linking in the presence of substrate RNA. It was necessary to mix two components, cleavage stimulation factor and specificity factor, to reconstitute 64-kDa protein-RNA cross-linking. The addition of cleavage factors to this mixture very efficiently reconstituted the AAUAAA-specific 64-kDa protein-RNA interaction. The 64-kDa protein, therefore, is present in highly purified, reconstituted polyadenylation reactions. However, it is necessary to form a multicomponent complex to efficiently cross-link the protein to a substrate RNA. Images PMID:2304466

  3. [Biogas production from cellulose-containing substrates: a review].

    PubMed

    Tsavkelova, E A; Netrusov, A I

    2012-01-01

    Anaerobic microbial conversion of organic substrates to various biofuels is one of the alternative energy sources attracting the greatest attention of scientists. The advantages of biogas production over other technologies are the ability of methanogenic communities to degrade a broad range of substrates and concomitant benefits: neutralization of organic waste, reduction of greenhouse gas emission, and fertilizer production. Cellulose-containing materials are a good substrate, but their full-scale utilization encounters a number of problems, including improvement of the quality and amount ofbiogas produced and maintenance of the stability and high efficiency of microbial communities. We review data on microorganisms that form methanogenic cellulolytic communities, enzyme complexes of anaerobes essential for cellulose fiber degradation, and feedstock pretreatment, as biodegradation is hindered in the presence of lignin. Methods for improving biogas production by optimization of microbial growth conditions are considered on the examples of biogas formation from various types of plant and paper materials: writing paper and cardboard.

  4. Membrane protease degradomics: proteomic identification and quantification of cell surface protease substrates.

    PubMed

    Butler, Georgina S; Dean, Richard A; Smith, Derek; Overall, Christopher M

    2009-01-01

    The modification of cell surface proteins by plasma membrane and soluble proteases is important for physiological and pathological processes. Methods to identify shed and soluble substrates are crucial to further define the substrate repertoire, termed the substrate degradome, of individual proteases. Identifying protease substrates is essential to elucidate protease function and involvement in different homeostatic and disease pathways. This characterisation is also crucial for drug target identification and validation, which would then allow the rational design of specific targeted inhibitors for therapeutic intervention. We describe two methods for identifying and quantifying shed cell surface protease targets in cultured cells utilising Isotope-Coded Affinity Tags (ICAT) and Isobaric Tags for Relative and Absolute Quantification (iTRAQ). As a model system to develop these techniques, we chose a cell-membrane expressed matrix metalloproteinase, MMP-14, but the concepts can be applied to proteases of other classes. By over-expression, or conversely inhibition, of a particular protease with careful selection of control conditions (e.g. vector or inactive protease) and differential labelling, shed proteins can be identified and quantified by mass spectrometry (MS), MS/MS fragmentation and database searching.

  5. Ultrafast time-resolved photoemission of a metallic tip/substrate junction

    NASA Astrophysics Data System (ADS)

    Meng, Xiang; Jin, Wencan; Yang, Hao; Dadap, Jerry; Osgood, Richard; Camillone, Nicholas, III

    The strong near-field enhancement of metallic-tip nanostructures has attracted great interest in scanning microscopy techniques, such as surface-enhanced Raman scattering, near-field scanning optical microscopy and tip-enhanced nonlinear imaging. In this talk, we use a full vectorial 3D-FDTD method to investigate the spatial characteristics of the optical field confinement and localization between a tungsten nanoprobe and an infinite planar silver substrate, with two-color ultrafast laser excitation scheme. The degree of two-color excited field enhancement, geometry dependence, the exact mechanism of optical tip-substrate coupling and tip-substrate plasmon resonances are significant in understanding the electrodynamical responses at tip-substrate junction. The demonstrated measurements with subpicosecond time and subnanometer spatial resolution suggest a new approach to ultrafast time-resolved measurements of surface electron dynamics. DE-FG 02-90-ER-14104; DE-FG 02-04-ER-46157.

  6. Identifying 8-hydroxynaringenin as a suicide substrate of mushroom tyrosinase.

    PubMed

    Chang, Te-Sheng; Lin, Meng-Yi; Lin, Hsuan-Jung

    2010-01-01

    A biotransformed metabolite of naringenin was isolated from the fermentation broth of Aspergillus oryzae, fed with naringenin, and identified as 8-hydroxynaringenin based on the mass and (1)H- and (13)C-NMR spectral data. The compound showed characteristics of both an irreversible inhibitor and a substrate of mushroom tyrosinase in preincubation and HPLC analysis. These results demonstrate that 8-hydroxynaringenin belongs to a suicide substrate of mushroom tyrosinase. The partition ratio between the compound's molecules in the formation of product and in the inactivation of the enzyme was determined to be 283 +/- 21. The present study's results, together with our previous findings, which proved that both 8-hydroxydaidzein and 8-hydroxygenistein are suicide substrates of mushroom tyrosinase, show that 7,8,4'-trihydroxyl functional groups on flavonoids' skeletons play important roles in producing suicide substrate properties toward mushroom tyrosinase.

  7. Effect of substrate RNA sequence on the cleavage reaction by a short ribozyme.

    PubMed Central

    Ohmichi, T; Okumoto, Y; Sugimoto, N

    1998-01-01

    Leadzyme is a ribozyme that requires Pb2+. The catalytic sequence, CUGGGAGUCC, binds to an RNA substrate, GGACC downward arrowGAGCCAG, cleaving the RNA substrate at one site. We have investigated the effect of the substrate sequence on the cleavage activity of leadzyme using mutant substrates in order to structurally understand the RNA catalysis. The results showed that leadzyme acted as a catalyst for single site cleavage of a C5 deletion mutant substrate, GGAC downward arrowGAGCCAG, as well as the wild-type substrate. However, a mutant substrate GGACCGACCAG, which had G8 deleted from the wild-type substrate, was not cleaved. Kinetic studies by surface plasmon resonance indicated that the difference between active and inactive structures reflected the slow association and dissociation rate constants of complex formation induced by Pb2+rather than differences in complex stability. CD spectra showed that the active form of the substrate-leadzyme complex was rearranged by Pb2+binding. The G8 of the wild-type substrate, which was absent in the inactive complex, is not near the cleavage site. Thus, these results show that the active substrate-leadzyme complex has a Pb2+binding site at the junction between the unpaired region (asymmetric internal loop) and the stem region, which is distal to the cleavage site. Pb2+may play a role in rearranging the bases in the asymmetric internal loop to the correct position for catalysis. PMID:9837996

  8. Copper(I)-catalyzed aryl bromides to form intermolecular and intramolecular carbon-oxygen bonds.

    PubMed

    Niu, Jiajia; Guo, Pengran; Kang, Juntao; Li, Zhigang; Xu, Jingwei; Hu, Shaojing

    2009-07-17

    A highly efficient Cu-catalyzed C-O bond-forming reaction of alcohol and aryl bromides has been developed. This transformation was realized through the use of copper(I) iodide as a catalyst, 8-hydroxyquinoline as a ligand, and K(3)PO(4) as a base. A variety of functionalized substrates were found to react under these reaction conditions to provide products in good to excellent yields.

  9. Substrate-Based Noble-Metal Nanomaterials: Shape Engineering and Applications

    NASA Astrophysics Data System (ADS)

    Hajfathalian, Maryam

    Nanostructures have potential for use in state-of-the-art applications such as sensing, imaging, therapeutics, drug delivery, and electronics. The ability to fabricate and engineer these nanoscale materials is essential for the continued development of such devices. Because the morphological features of nanomaterials play a key role in determining chemical and physical properties, there is great interest in developing and improving methods capable of controlling their size, shape, and composition. While noble nanoparticles have opened the door to promising applications in fields such as imaging, cancer targeting, photothermal treatment, drug delivery, catalysis and sensing, the synthetic processes required to form these nanoparticles on surfaces are not well-developed. Herein is a detailed account on efforts for adapting established solution-based seed-mediated synthetic protocols to structure in a substrate-based platform. These syntheses start by (i) defining heteroepitaxially oriented nanostructured seeds at site-specific locations using lithographic or directed-assembly techniques, and then (ii) transforming the seeds using either a solution or vapor phase processing route to activate kinetically- or thermodynamically-driven growth modes, to arrive at nanocrystals with complex and useful geometries. The first series of investigations highlight synthesis-routes based on heterogeneous nucleation, where templates serve as nucleation sites for metal atoms arriving in the vapor phase. In the first research direction, the vapor-phase heterogeneous nucleation of Ag on Au was carried out at high temperatures, where the Ag vapor was sourced from a sublimating foil onto adjacent Au templates. This process transformed both the composition and morphology of the initial Au Wulff-shaped nanocrystals to a homogeneous AuAg nanoprism. In the second case, the vapor-phase heterogeneous nucleation of Cu atoms on Au nanocrystal templates was investigated by placing a Cu foil next

  10. Design and isolation of ribozyme-substrate pairs using RNase P-based ribozymes containing altered substrate binding sites.

    PubMed Central

    Mobley, E M; Pan, T

    1999-01-01

    Substrate recognition and cleavage by the bacterial RNase P RNA requires two domains, a specificity domain, or S-domain, and a catalytic domain, or C-domain. The S-domain binds the T stem-loop region in a pre-tRNA substrate to confer specificity for tRNA substrates. In this work, the entire S-domain of the Bacillus subtilis RNase P RNA is replaced with an artificial substrate binding module. New RNA substrates are isolated by in vitro selection using two libraries containing random regions of 60 nt. At the end of the selection, the cleavage rates of the substrate library are approximately 0.7 min(-1)in 10 mM MgCl(2)at 37 degrees C, approximately 4-fold better than the cleavage of a pre-tRNA substrate by the wild-type RNase P RNA under the same conditions. The contribution of the S-domain replacement to the catalytic efficiency is from 6- to 22 000-fold. Chemical and nuclease mapping of two ribozyme-product complexes shows that this contribution correlates with direct interactions between the S-domain replacement and the selected substrate. These results demonstrate the feasibility of design and isolation of RNase P-based, matching ribozyme-substrate pairs without prior knowledge of the sequence or structure of the interactive modules in the ribozyme or substrate. PMID:10518624

  11. A simple method using two-step hot embossing technique with shrinking for fabrication of cross microchannels on PMMA substrate and its application to electrophoretic separation of amino acids in functional drinks.

    PubMed

    Wiriyakun, Natta; Nacapricha, Duangjai; Chantiwas, Rattikan

    2016-12-01

    This work presents a simple hot embossing method with a shrinking procedure to produce cross-shape microchannels on poly(methyl methacrylate) (PMMA) substrate for the fabrication of an electrophoresis chip. The proposed method employed a simple two-step hot embossing technique, carried out consecutively on the same piece of substrate to make the crossing channels. Studies of embossing conditions, i.e. temperature, pressure and time, were carried out to investigate their effects on the dimension of the microchannels. Applying a simple shrinking procedure reduced the size of the channels from 700±20µm wide×150±5µm deep to 250±10µm wide×30±2µm deep, i.e. 80% and 64% reduction in the depth and width, respectively. Thermal fusion was employed to bond the PMMA substrate with a PMMA cover plate to produce the microfluidic device. Replication of microchip was achieved by precise control of conditions in the fabrication process (pressure, temperature and time), resulting in lower than 7% RSD of channel dimension, width and depth (n =10 devices). The method was simple and robust without the use of expensive equipment to construct the microstructure on a thermoplastic substrate. The PMMA microchip was used for demonstration of amine functionalization on the PMMA surface, measurement of electroosmotic flow and for electrophoretic separation of amino acids in functional drink samples. The precision of migration time and peak area of the amino acids, Lys, Ile and Phe at 125μM to 500μM, were in the range 3.2-4.2% RSD (n=9 devices) and 4.5-5.3% RSD (n=9 devices), respectively. Copyright © 2016 Elsevier B.V. All rights reserved.

  12. On the use of copper-based substrates for YBCO coated conductors

    NASA Astrophysics Data System (ADS)

    Vannozzi, A.; Fabbri, F.; Augieri, A.; Angrisani Armenio, A.; Galluzzi, V.; Mancini, A.; Rizzo, F.; Rufoloni, A.; Padilla, J. A.; Xuriguera, E.; De Felicis, D.; Bemporad, E.; Celentano, G.

    2014-05-01

    It is well known that the recrystallization texture of heavily cold-rolled pure copper is almost completely cubic. However, one of the main drawbacks concerning the use of pure copper cube-textured substrates for YBCO coated conductor is the reduced secondary recrystallization temperature. The onset of secondary recrystallization (i.e., the occurrence of abnormal grains with unpredictable orientation) in pure copper substrate was observed within the typical temperature range required for buffer layer and YBCO processing (600-850 °C). To avoid the formation of abnormal grains the effect of both grain size adjustment (GSA) and recrystallization annealing was analyzed. The combined use of a small initial grain size and a recrystallization two-step annealing (TSA) drastically reduced the presence of abnormal grains in pure copper tapes. Another way to overcome the limitation imposed by the formation of abnormal grains is to deposit a buffer layer at temperatures where secondary recrystallization does not occur. For example, La2Zr2O7 (LZO) film with a high degree of epitaxy was grown by metal-organic decomposition (MOD) at 1000 °C on pure copper substrate. In several samples the substrate underwent secondary recrystallization. Our experiments indicate that the motion of grain boundaries occurring during secondary recrystallization process does not affect the quality of LZO film.

  13. Efficiency of vibrational sounding in parasitoid host location depends on substrate density.

    PubMed

    Fischer, S; Samietz, J; Dorn, S

    2003-10-01

    Parasitoids of concealed hosts have to drill through a substrate with their ovipositor for successful parasitization. Hymenopteran species in this drill-and-sting guild locate immobile pupal hosts by vibrational sounding, i.e., echolocation on solid substrate. Although this host location strategy is assumed to be common among the Orussidae and Ichneumonidae there is no information yet whether it is adapted to characteristics of the host microhabitat. This study examined the effect of substrate density on responsiveness and host location efficiency in two pupal parasitoids, Pimpla turionellae and Xanthopimpla stemmator (Hymenoptera: Ichneumonidae), with different host-niche specialization and corresponding ovipositor morphology. Location and frequency of ovipositor insertions were scored on cylindrical plant stem models of various densities. Substrate density had a significant negative effect on responsiveness, number of ovipositor insertions, and host location precision in both species. The more niche-specific species X. stemmator showed a higher host location precision and insertion activity. We could show that vibrational sounding is obviously adapted to the host microhabitat of the parasitoid species using this host location strategy. We suggest the attenuation of pulses during vibrational sounding as the energetically costly limiting factor for this adaptation.

  14. SERS substrates for in-situ biosensing (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Venugopalan, Priyamvada; Quilis, Nestor; Jakub, Dostalek; Wolfgang, Knoll

    2017-06-01

    Abstract: Recent years have seen a rapid progress in the field of surface-enhanced Raman spectroscopy (SERS) which is attributed to the thriving field of plasmonics [1]. SERS is a susceptible technique that can address basic scientific questions and technological problems. In both cases, it is highly dependent upon the plasmonic substrate, where excitation of the localized surface plasmon resonance enhances the vibrational scattering signal of the analyte molecules adsorbed on to the surface [2]. In this work, using finite difference time domain (FDTD) method we investigate the optical properties of plasmonic nanostructures with tuned plasmonic resonances as a function of dielectric environment and geometric parameters. An optimized geometry will be discussed based on the plasmonic resonant position and the SERS intensity. These SERS substrates will be employed for the detection of changes in conformation caused by interactions between an aptamer and analyte molecules. This will be done by using a microfluidic channel designed within the configuration of the lab-on-a-chip concept based on the intensity changes of the SERS signal. More efficient and reproducible results are obtained for such a quantitative measurement of analytes at low concentration levels. We will also demonstrate that the plasmonic substrates fabricated by top down approach such as e-beam lithography (EBL) and laser interference lithography (LIL) are highly reproducible, robust and can result in high electric field enhancement. Our results demonstrate the potential to use SERS substrates for highly sensitive detection schemes opening up the window for a wide range of applications including biomedical diagnostics, forensic investigation etc. Acknowledgement: This work was supported by the Austrian Science Fund (FWF), project NANOBIOSENSOR (I 2647). References: [1] J. N. Anker, W. P. Hall, O. Lyandres, N. C. Shah, J. Zhao and R. P. V. Duyne., " Biosensing with plasmonic nanosensors," Nature

  15. Wetting Transition of Nonpolar Neutral Molecule System on a Neutral and Atomic Length Scale Roughness Substrate

    NASA Astrophysics Data System (ADS)

    Zhou, Shiqi

    2018-03-01

    One recently proposed new method for accurately determining wetting temperature is applied to the wetting transition occurring in a single component nonpolar neutral molecule system near a neutral planar substrate with roughness produced by cosinusoidal modulation(s). New observations are summarized into five points: (i) for a planar substrate superimposed with one cosinusoidal modulation, with increasing of the periodicity length or the surface attraction force field, or decreasing of the amplitude, wetting temperature T_W drops accordingly and the three parameters show multiplication effect; moreover, both the periodicity length and amplitude effect curves display pole phenomena and saturation phenomena, and the T_W saturation occurs at small (for case of large amplitude) or large (for case of small amplitude) periodicity length side, respectively. (ii) In the case of the planar substrate superimposed with two cosinusoidal modulations with equal periodicity length, the initial phase difference is critical issue that influences the T_W, which decreases with the initial phase difference. (iii) In the case of the planar substrate superimposed with two cosinusoidal modulations with zero phase difference, change of the T_W with one periodicity length under the condition of another periodicity length unchanged is non-monotonous. (iv) When the parameters are chosen such that the T_W draws ever closer to the bulk critical temperature, wetting transition on the roughness substrate eventually does not occur. (v) The present microscopic calculation challenges traditional macroscopic theory by confirming that the atomic length scale roughness always renders the surface less hydrophilic and whereas the mesoscopical roughness renders the surface more hydrophilic. All of these observations summarized can be reasonably explained by the relative strength of the attraction actually enjoyed by the surface gas molecules to the attraction the gas molecules can get when in bulk.

  16. A two-layer structured PbI2 thin film for efficient planar perovskite solar cells.

    PubMed

    Ying, Chao; Shi, Chengwu; Wu, Ni; Zhang, Jincheng; Wang, Mao

    2015-07-28

    In this paper, a two-layer structured PbI2 thin film was constructed by the spin-coating procedure using a 0.80 M PbI2 solution in DMF and subsequent close-spaced vacuum thermal evaporation using PbI2 powder as a source. The bottom PbI2 thin film was compact with a sheet-like appearance, parallel to the FTO substrate, and can be easily converted to a compact perovskite thin film to suppress the charge recombination of the electrons of the TiO2 conduction band and the holes of the spiro-OMeTAD valence band. The top PbI2 thin film was porous with nano-sheet arrays, perpendicular to the FTO substrate, and can be easily converted to a porous perovskite thin film to improve the hole migration from the perovskite to spiro-OMeTAD and the charge separation at the perovskite/spiro-OMeTAD interface. The planar perovskite solar cells based on the two-layer structured PbI2 thin film exhibited a photoelectric conversion efficiency of 11.64%, along with an open-circuit voltage of 0.90 V, a short-circuit photocurrent density of 19.29 mA cm(-2) and a fill factor of 0.67.

  17. A flexible and transparent graphene/ZnO nanorod hybrid structure fabricated by exfoliating a graphite substrate

    NASA Astrophysics Data System (ADS)

    Nam, Gwang-Hee; Baek, Seong-Ho; Cho, Chang-Hee; Park, Il-Kyu

    2014-09-01

    We demonstrate the fabrication of a graphene/ZnO nanorod (NR) hybrid structure by mechanical exfoliation of ZnO NRs grown on a graphite substrate. We confirmed the existence of graphene sheets on the hybrid structure by analyzing the Raman spectra and current-voltage (I-V) characteristics. The Raman spectra of the exfoliated graphene/ZnO NR hybrid structure show G and 2D band peaks that are shifted to lower wavenumbers, indicating that the exfoliated graphene layer exists under a significant amount of strain. The I-V characteristics of the graphene/ZnO NR hybrid structure show current flow through the graphene layer, while no current flow is observed on the ZnO NR/polydimethylsiloxane (PDMS) composite without graphene, thereby indicating that the few-layer graphene was successfully transferred onto the hybrid structure. A piezoelectric nanogenerator is demonstrated by using the fabricated graphene/ZnO NR hybrid structure. The nanogenerator exhibits stable output voltage up to 3.04 V with alternating current output characteristics.We demonstrate the fabrication of a graphene/ZnO nanorod (NR) hybrid structure by mechanical exfoliation of ZnO NRs grown on a graphite substrate. We confirmed the existence of graphene sheets on the hybrid structure by analyzing the Raman spectra and current-voltage (I-V) characteristics. The Raman spectra of the exfoliated graphene/ZnO NR hybrid structure show G and 2D band peaks that are shifted to lower wavenumbers, indicating that the exfoliated graphene layer exists under a significant amount of strain. The I-V characteristics of the graphene/ZnO NR hybrid structure show current flow through the graphene layer, while no current flow is observed on the ZnO NR/polydimethylsiloxane (PDMS) composite without graphene, thereby indicating that the few-layer graphene was successfully transferred onto the hybrid structure. A piezoelectric nanogenerator is demonstrated by using the fabricated graphene/ZnO NR hybrid structure. The nanogenerator

  18. GaN-based light-emitting diodes on various substrates: a critical review.

    PubMed

    Li, Guoqiang; Wang, Wenliang; Yang, Weijia; Lin, Yunhao; Wang, Haiyan; Lin, Zhiting; Zhou, Shizhong

    2016-05-01

    GaN and related III-nitrides have attracted considerable attention as promising materials for application in optoelectronic devices, in particular, light-emitting diodes (LEDs). At present, sapphire is still the most popular commercial substrate for epitaxial growth of GaN-based LEDs. However, due to its relatively large lattice mismatch with GaN and low thermal conductivity, sapphire is not the most ideal substrate for GaN-based LEDs. Therefore, in order to obtain high-performance and high-power LEDs with relatively low cost, unconventional substrates, which are of low lattice mismatch with GaN, high thermal conductivity and low cost, have been tried as substitutes for sapphire. As a matter of fact, it is not easy to obtain high-quality III-nitride films on those substrates for various reasons. However, by developing a variety of techniques, distincts progress has been made during the past decade, with high-performance LEDs being successfully achieved on these unconventional substrates. This review focuses on state-of-the-art high-performance GaN-based LED materials and devices on unconventional substrates. The issues involved in the growth of GaN-based LED structures on each type of unconventional substrate are outlined, and the fundamental physics behind these issues is detailed. The corresponding solutions for III-nitride growth, defect control, and chip processing for each type of unconventional substrate are discussed in depth, together with a brief introduction to some newly developed techniques in order to realize LED structures on unconventional substrates. This is very useful for understanding the progress in this field of physics. In this review, we also speculate on the prospects for LEDs on unconventional substrates.

  19. Expression and Characterization of a PNPLA3 Protein Isoform (I148M) Associated with Nonalcoholic Fatty Liver Disease*

    PubMed Central

    Huang, Yongcheng; Cohen, Jonathan C.; Hobbs, Helen H.

    2011-01-01

    A genetic variant of PNPLA3 (patatin-like phospholipase domain-containing 3; PNPLA3-I148M), a serine protease of unknown function, is associated with accumulation of triacylglycerol (TAG) in the liver. To determine the biological substrates of PNPLA3 and the effect of the I148M substitution on enzymatic activity and substrate specificity, we purified and characterized recombinant human PNPLA3 and PNPLA3-I148M. Maximal hydrolytic activity of PNPLA3 was observed against the three major glycerolipids, TAG, diacylglycerol, and monoacylglycerol, with a strong preference for oleic acid as the acyl moiety. Substitution of methionine for isoleucine at position 148 markedly decreased the Vmax of the enzyme for glycerolipids but had only a modest effect on the Km. Purified PNPLA3 also catalyzed the hydrolysis of oleoyl-CoA, but the Vmax was 100-fold lower for oleoyl-CoA than for triolein. The thioesterase activity required the catalytic serine but was only modestly decreased by the I148M substitution. The enzyme had little or no hydrolytic activity against the other lipid substrates tested, including phospholipids, cholesteryl ester, and retinyl esters. Neither the wild-type nor mutant enzyme catalyzed transfer of oleic acid from oleoyl-CoA to glycerophosphate, lysophosphatidic acid, or diacylglycerol, suggesting that the enzyme does not promote de novo TAG synthesis. Taken together, our results are consistent with the notion that PNPLA3 plays a role in the hydrolysis of glycerolipids and that the I148M substitution causes a loss of function, although we cannot exclude the possibility that the enzyme has additional substrates or activities. PMID:21878620

  20. Light-Emitting GaAs Nanowires on a Flexible Substrate.

    PubMed

    Valente, João; Godde, Tillmann; Zhang, Yunyan; Mowbray, David J; Liu, Huiyun

    2018-06-18

    Semiconductor nanowire-based devices are among the most promising structures used to meet the current challenges of electronics, optics and photonics. Due to their high surface-to-volume ratio and excellent optical and electrical properties, devices with low power, high efficiency and high density can be created. This is of major importance for environmental issues and economic impact. Semiconductor nanowires have been used to fabricate high performance devices, including detectors, solar cells and transistors. Here, we demonstrate a technique for transferring large-area nanowire arrays to flexible substrates while retaining their excellent quantum efficiency in emission. Starting with a defect-free self-catalyzed molecular beam epitaxy (MBE) sample grown on a Si substrate, GaAs core-shell nanowires are embedded in a dielectric, removed by reactive ion etching and transferred to a plastic substrate. The original structural and optical properties, including the vertical orientation, of the nanowires are retained in the final plastic substrate structure. Nanowire emission is observed for all stages of the fabrication process, with a higher emission intensity observed for the final transferred structure, consistent with a reduction in nonradiative recombination via the modification of surface states. This transfer process could form the first critical step in the development of flexible nanowire-based light-emitting devices.

  1. Textured substrate tape and devices thereof

    DOEpatents

    Goyal, Amit

    2006-08-08

    A method for forming a sharply biaxially textured substrate, such as a single crystal substrate, includes the steps of providing a deformed metal substrate, followed by heating above the secondary recrystallization temperature of the deformed substrate, and controlling the secondary recrystallization texture by either using thermal gradients and/or seeding. The seed is selected to shave a stable texture below a predetermined temperature. The sharply biaxially textured substrate can be formed as a tape having a length of 1 km, or more. Epitaxial articles can be formed from the tapes to include an epitaxial electromagnetically active layer. The electromagnetically active layer can be a superconducting layer.

  2. Thin film with oriented cracks on a flexible substrate

    DOEpatents

    Feng, Bao; McGilvray, Andrew; Shi, Bo

    2010-07-27

    A thermoelectric film is disclosed. The thermoelectric film includes a substrate that is substantially electrically non-conductive and flexible and a thermoelectric material that is deposited on at least one surface of the substrate. The thermoelectric film also includes multiple cracks oriented in a predetermined direction.

  3. Effects of substrate to inoculum ratio on the biochemical methane potential of piggery slaughterhouse wastes.

    PubMed

    Yoon, Young-Man; Kim, Seung-Hwan; Shin, Kook-Sik; Kim, Chang-Hyun

    2014-04-01

    The aim of this study was to assess the effect of substrate to inoculum ratio (S/I ratio) on the biochemical methane potential (BMP) and anaerobic biodegradability (Ddeg) of different piggery slaughterhouse wastes, such as piggery blood, intestine residue, and digestive tract content. These wastes were sampled from a piggery slaughterhouse located in Kimje, South Korea. Cumulative methane production curves for the wastes were obtained from the anaerobic batch fermentation having different S/I ratios of 0.1, 0.5, 1.0, and 1.5. BMP and anaerobic biodegradabilities (Ddeg) of the wastes were calculated from cumulative methane production data for the tested conditions. At the lowest S/I ration of 0.1, BMPs of piggery blood, intestine residue, and digestive tract content were determined to be 0.799, 0.848, and 1.076 Nm(3) kg(-1)-VSadded, respectively, which were above the theoretical methane potentials of 0.539, 0.644, and 0.517 Nm(3) kg(-1)-VSadded for blood, intestine residue, and digestive tract content, respectively. However, BMPs obtained from the higher S/I ratios of 0.5, 1.0, and 1.5 were within the theoretical range for all three types of waste and were not significantly different for the different S/I ratios tested. Anaerobic biodegradabilities calculated from BMP data showed a similar tendency. These results imply that, for BMP assay in an anaerobic reactor, the S/I ratio of anaerobic reactor should be above 0.1 and the inoculum should be sufficiently stabilized to avoid further degradation during the assay.

  4. Effects of Substrate to Inoculum Ratio on the Biochemical Methane Potential of Piggery Slaughterhouse Wastes

    PubMed Central

    Yoon, Young-Man; Kim, Seung-Hwan; Shin, Kook-Sik; Kim, Chang-Hyun

    2014-01-01

    The aim of this study was to assess the effect of substrate to inoculum ratio (S/I ratio) on the biochemical methane potential (BMP) and anaerobic biodegradability (Ddeg) of different piggery slaughterhouse wastes, such as piggery blood, intestine residue, and digestive tract content. These wastes were sampled from a piggery slaughterhouse located in Kimje, South Korea. Cumulative methane production curves for the wastes were obtained from the anaerobic batch fermentation having different S/I ratios of 0.1, 0.5, 1.0, and 1.5. BMP and anaerobic biodegradabilities (Ddeg) of the wastes were calculated from cumulative methane production data for the tested conditions. At the lowest S/I ration of 0.1, BMPs of piggery blood, intestine residue, and digestive tract content were determined to be 0.799, 0.848, and 1.076 Nm3 kg−1-VSadded, respectively, which were above the theoretical methane potentials of 0.539, 0.644, and 0.517 Nm3 kg−1-VSadded for blood, intestine residue, and digestive tract content, respectively. However, BMPs obtained from the higher S/I ratios of 0.5, 1.0, and 1.5 were within the theoretical range for all three types of waste and were not significantly different for the different S/I ratios tested. Anaerobic biodegradabilities calculated from BMP data showed a similar tendency. These results imply that, for BMP assay in an anaerobic reactor, the S/I ratio of anaerobic reactor should be above 0.1 and the inoculum should be sufficiently stabilized to avoid further degradation during the assay. PMID:25049994

  5. PLZT capacitor on glass substrate

    DOEpatents

    Fairchild, Manuel Ray; Taylor, Ralph S.; Berlin, Carl W.; Wong, Celine Wk; Ma, Beihai; Balachandran, Uthamalingam

    2016-03-29

    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.

  6. PLZT capacitor on glass substrate

    DOEpatents

    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.

  7. Investigating mycobacterial topoisomerase I mechanism from the analysis of metal and DNA substrate interactions at the active site.

    PubMed

    Cao, Nan; Tan, Kemin; Annamalai, Thirunavukkarasu; Joachimiak, Andrzej; Tse-Dinh, Yuk-Ching

    2018-06-14

    We have obtained new crystal structures of Mycobacterium tuberculosis topoisomerase I, including structures with ssDNA substrate bound to the active site, with and without Mg2+ ion present. Significant enzyme conformational changes upon DNA binding place the catalytic tyrosine in a pre-transition state position for cleavage of a specific phosphodiester linkage. Meanwhile, the enzyme/DNA complex with bound Mg2+ ion may represent the post-transition state for religation in the enzyme's multiple-step DNA relaxation catalytic cycle. The first observation of Mg2+ ion coordinated with the TOPRIM residues and DNA phosphate in a type IA topoisomerase active site allows assignment of likely catalytic role for the metal and draws a comparison to the proposed mechanism for type IIA topoisomerases. The critical function of a strictly conserved glutamic acid in the DNA cleavage step was assessed through site-directed mutagenesis. The functions assigned to the observed Mg2+ ion can account for the metal requirement for DNA rejoining but not DNA cleavage by type IA topoisomerases. This work provides new structural insights into a more stringent requirement for DNA rejoining versus cleavage in the catalytic cycle of this essential enzyme, and further establishes the potential for selective interference of DNA rejoining by this validated TB drug target.

  8. Method of coating a substrate with a calcium phosphate compound

    DOEpatents

    Gao, Yufei; Campbell, Allison A.

    2000-01-01

    The present invention is a method of coating a substrate with a calcium phosphate compound using plasma enhanced MOCVD. The substrate is a solid material that may be porous or non-porous, including but not limited to metal, ceramic, glass and combinations thereof. The coated substrate is preferably used as an implant, including but not limited to orthopaedic, dental and combinations thereof. Calcium phosphate compound includes but is not limited to tricalcium phosphate (TCP), hydroxyapatite (HA) and combinations thereof. TCP is preferred on a titanium implant when implant resorbability is desired. HA is preferred when the bone bonding of new bone tissue into the structure of the implant is desired. Either or both of TCP and/or HA coated implants may be placed into a solution with an agent selected from the group of protein, antibiotic, antimicrobial, growth factor and combinations thereof that can be adsorbed into the coating before implantation. Once implanted, the release of TCP will also release the agent to improve growth of new bone tissues and/or to prevent infection.

  9. Multifunctionality is affected by interactions between green roof plant species, substrate depth, and substrate type.

    PubMed

    Dusza, Yann; Barot, Sébastien; Kraepiel, Yvan; Lata, Jean-Christophe; Abbadie, Luc; Raynaud, Xavier

    2017-04-01

    Green roofs provide ecosystem services through evapotranspiration and nutrient cycling that depend, among others, on plant species, substrate type, and substrate depth. However, no study has assessed thoroughly how interactions between these factors alter ecosystem functions and multifunctionality of green roofs. We simulated some green roof conditions in a pot experiment. We planted 20 plant species from 10 genera and five families (Asteraceae, Caryophyllaceae, Crassulaceae, Fabaceae, and Poaceae) on two substrate types (natural vs. artificial) and two substrate depths (10 cm vs. 30 cm). As indicators of major ecosystem functions, we measured aboveground and belowground biomasses, foliar nitrogen and carbon content, foliar transpiration, substrate water retention, and dissolved organic carbon and nitrates in leachates. Interactions between substrate type and depth strongly affected ecosystem functions. Biomass production was increased in the artificial substrate and deeper substrates, as was water retention in most cases. In contrast, dissolved organic carbon leaching was higher in the artificial substrates. Except for the Fabaceae species, nitrate leaching was reduced in deep, natural soils. The highest transpiration rates were associated with natural soils. All functions were modulated by plant families or species. Plant effects differed according to the observed function and the type and depth of the substrate. Fabaceae species grown on natural soils had the most noticeable patterns, allowing high biomass production and high water retention but also high nitrate leaching from deep pots. No single combination of factors enhanced simultaneously all studied ecosystem functions, highlighting that soil-plant interactions induce trade-offs between ecosystem functions. Substrate type and depth interactions are major drivers for green roof multifunctionality.

  10. Structure of a AAA+ unfoldase in the process of unfolding substrate

    PubMed Central

    Ripstein, Zev A; Huang, Rui; Augustyniak, Rafal; Kay, Lewis E; Rubinstein, John L

    2017-01-01

    AAA+ unfoldases are thought to unfold substrate through the central pore of their hexameric structures, but how this process occurs is not known. VAT, the Thermoplasma acidophilum homologue of eukaryotic CDC48/p97, works in conjunction with the proteasome to degrade misfolded or damaged proteins. We show that in the presence of ATP, VAT with its regulatory N-terminal domains removed unfolds other VAT complexes as substrate. We captured images of this transient process by electron cryomicroscopy (cryo-EM) to reveal the structure of the substrate-bound intermediate. Substrate binding breaks the six-fold symmetry of the complex, allowing five of the six VAT subunits to constrict into a tight helix that grips an ~80 Å stretch of unfolded protein. The structure suggests a processive hand-over-hand unfolding mechanism, where each VAT subunit releases the substrate in turn before re-engaging further along the target protein, thereby unfolding it. DOI: http://dx.doi.org/10.7554/eLife.25754.001 PMID:28390173

  11. Substrate specificity and kinetic properties of alpha-galactosidases from Vicia faba.

    PubMed

    Dey, P M; Pridham, J B

    1969-10-01

    1. The hydrolysis of a variety of galactosides and other glycosides by alpha-galactosidases I and II of Vicia faba was studied. 2. The effect of temperature on kinetic parameters was also examined. 3. Both enzymes are inhibited by excess of substrate (p-nitrophenyl alpha-d-galactoside); with enzyme I this is competitive and is caused by the galactosyl moiety. 4. Enzyme I is inhibited by oligosaccharides possessing terminal non-reducing galactose residues and to a smaller extent by l-arabinose and d-fucose. 5. The effect of pH on K(m) and V(max.) values suggests that carboxyl and imidazole groups are involved in the catalytic activity of enzyme I. 6. Photo-oxidation experiments with enzyme I also suggest that an imidazole group is present at the active site.

  12. A practical and efficient cellular substrate for the generation of induced pluripotent stem cells from adults: blood-derived endothelial progenitor cells.

    PubMed

    Geti, Imbisaat; Ormiston, Mark L; Rouhani, Foad; Toshner, Mark; Movassagh, Mehregan; Nichols, Jennifer; Mansfield, William; Southwood, Mark; Bradley, Allan; Rana, Amer Ahmed; Vallier, Ludovic; Morrell, Nicholas W

    2012-12-01

    Induced pluripotent stem cells (iPSCs) have the potential to generate patient-specific tissues for disease modeling and regenerative medicine applications. However, before iPSC technology can progress to the translational phase, several obstacles must be overcome. These include uncertainty regarding the ideal somatic cell type for reprogramming, the low kinetics and efficiency of reprogramming, and karyotype discrepancies between iPSCs and their somatic precursors. Here we describe the use of late-outgrowth endothelial progenitor cells (L-EPCs), which possess several favorable characteristics, as a cellular substrate for the generation of iPSCs. We have developed a protocol that allows the reliable isolation of L-EPCs from peripheral blood mononuclear cell preparations, including frozen samples. As a proof-of-principle for clinical applications we generated EPC-iPSCs from both healthy individuals and patients with heritable and idiopathic forms of pulmonary arterial hypertension. L-EPCs grew clonally; were highly proliferative, passageable, and bankable; and displayed higher reprogramming kinetics and efficiencies compared with dermal fibroblasts. Unlike fibroblasts, the high efficiency of L-EPC reprogramming allowed for the reliable generation of iPSCs in a 96-well format, which is compatible with high-throughput platforms. Array comparative genome hybridization analysis of L-EPCs versus donor-matched circulating monocytes demonstrated that L-EPCs have normal karyotypes compared with their subject's reference genome. In addition, >80% of EPC-iPSC lines tested did not acquire any copy number variations during reprogramming compared with their parent L-EPC line. This work identifies L-EPCs as a practical and efficient cellular substrate for iPSC generation, with the potential to address many of the factors currently limiting the translation of this technology.

  13. Buffer layers on metal alloy substrates for superconducting tapes

    DOEpatents

    Jia, Quanxi; Foltyn, Stephen R.; Arendt, Paul N.; Groves, James R.

    2004-10-05

    An article including a substrate, at least one intermediate layer upon the surface of the substrate, a layer of an oriented cubic oxide material having a rock-salt-like structure upon the at least one intermediate layer, and a layer of a SrRuO.sub.3 buffer material upon the oriented cubic oxide material layer is provided together with additional layers such as a HTS top-layer of YBCO directly upon the layer of a SrRuO.sub.3 buffer material layer. With a HTS top-layer of YBCO upon at least one layer of the SrRuO.sub.3 buffer material in such an article, J.sub.c 's of up to 1.3.times.10.sup.6 A/cm.sup.2 have been demonstrated with projected I.sub.c 's of over 200 Amperes across a sample 1 cm wide.

  14. Structure of a Clostridium botulinum C143S thiaminase I/thiamin complex reveals active site architecture .

    PubMed

    Sikowitz, Megan D; Shome, Brateen; Zhang, Yang; Begley, Tadhg P; Ealick, Steven E

    2013-11-05

    Thiaminases are responsible for the degradation of thiamin and its metabolites. Two classes of thiaminases have been identified based on their three-dimensional structures and their requirements for a nucleophilic second substrate. Although the reactions of several thiaminases have been characterized, the physiological role of thiamin degradation is not fully understood. We have determined the three-dimensional X-ray structure of an inactive C143S mutant of Clostridium botulinum (Cb) thiaminase I with bound thiamin at 2.2 Å resolution. The C143S/thiamin complex provides atomic level details of the orientation of thiamin upon binding to Cb-thiaminase I and the identity of active site residues involved in substrate binding and catalysis. The specific roles of active site residues were probed by using site directed mutagenesis and kinetic analyses, leading to a detailed mechanism for Cb-thiaminase I. The structure of Cb-thiaminase I is also compared to the functionally similar but structurally distinct thiaminase II.

  15. Substrate spacing and thin-film yield in chemical bath deposition of semiconductor thin films

    NASA Astrophysics Data System (ADS)

    Arias-Carbajal Reádigos, A.; García, V. M.; Gomezdaza, O.; Campos, J.; Nair, M. T. S.; Nair, P. K.

    2000-11-01

    Thin-film yield in the chemical bath deposition technique is studied as a function of separation between substrates in batch production. Based on a mathematical model, it is proposed and experimentally verified in the case of CdS thin films that the film thickness reaches an asymptotic maximum with increase in substrate separation. It is shown that at a separation less than 1 mm between substrates the yield, i.e. percentage in moles of a soluble cadmium salt deposited as a thin film of CdS, can exceed 50%. This behaviour is explained on the basis of the existence of a critical layer of solution near the substrate, within which the relevant ionic species have a higher probability of interacting with the thin-film layer than of contributing to precipitate formation. The critical layer depends on the solution composition and the temperature of the bath as well as the duration of deposition. An effective value for the critical layer thickness has been defined as half the substrate separation at which 90% of the maximum film thickness for the particular bath composition, bath temperature and duration of deposition is obtained. In the case of CdS thin films studied as an example, the critical layer is found to extend from 0.5 to 2.5 mm from the substrate surface, depending on the deposition conditions.

  16. Rock-dwelling lizards exhibit less sensitivity of sprint speed to increases in substrate rugosity.

    PubMed

    Collins, Clint E; Self, Jessica D; Anderson, Roger A; McBrayer, Lance D

    2013-06-01

    Effectively moving across variable substrates is important to all terrestrial animals. The effects of substrates on lizard performance have ecological ramifications including the partitioning of habitat according to sprinting ability on different surfaces. This phenomenon is known as sprint sensitivity, or the decrease in sprint speed due to change in substrate. However, sprint sensitivity has been characterized only in arboreal Anolis lizards. Our study measured sensitivity to substrate rugosity among six lizard species that occupy rocky, sandy, and/or arboreal habitats. Lizards that use rocky habitats are less sensitive to changes in substrate rugosity, followed by arboreal lizards, and then by lizards that use sandy habitats. We infer from comparative phylogenetic analysis that forelimb, chest, and tail dimensions are important external morphological features related to sensitivity to changes in substrate rugosity. Copyright © 2013 Elsevier GmbH. All rights reserved.

  17. A general correction to initial rates determined for nonprocessive exo-depolymerases acting on both substrate and product

    USDA-ARS?s Scientific Manuscript database

    We recently reported on the kinetics of the polygalacturonase TtGH28 acting on trimer and dimer substrates. When the starting substrate for hydrolysis is the trimer, the product dimer is also subject to hydrolysis, resulting in discrepancies when either the concentration of dimer or monomer product ...

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

    NASA Astrophysics Data System (ADS)

    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.

  19. Biohydrogen Production from Pineapple Waste: Effect of Substrate Concentration and Acid Pretreatment

    NASA Astrophysics Data System (ADS)

    Cahyari, K.; Putri, A. M.; Oktaviani, E. D.; Hidayat, M. A.; Norajsha, J. D.

    2018-05-01

    Biohydrogen is the ultimate choice of energy carrier in future due to its superior qualities such as fewer greenhouse gases emission, high energy density (142 kJ/gram), and high energy conversion using a fuel cell. Production of biohydrogen from organic waste e.g. pineapple waste offers a simultaneous solution for renewable energy production and waste management. It is estimated that pineapple cultivation in Indonesia generated more than 1 million ton/year comprising of rotten pineapple fruit, leaves, and stems. Majority of this waste is dumped into landfill area without any treatments which lead to many environmental problems. This research was meant to investigate the utilization of pineapple waste i.e. peel and the core of pineapple fruit and leaves to produce biohydrogen through mesophilic dark fermentation (30°C, 1 atm, pH 5.0). Effect of dilute acid treatment and substrate concentration was particularly investigated in these experiments. Peel and core of pineapple waste were subjected to fermentation at 3 various substrate concentration i.e. 8.8, 17.6 and 26.4-gram VS/liter. Meanwhile, pineapple leaves were pretreated using dilute acid (H2SO4) at 0.2, 0.3 and 0.4 N and followed by dark fermentation. Results show that the highest yield of biohydrogen was obtained at a substrate concentration of 26.4-gram VS/liter both for peel and core of the waste. Pretreatment using dilute acid (H2SO4) 0.3 N might improve fermentation process with a higher yield at 0.8 ml/gram VS. Hydrogen percentage in biogas produced during fermentation process was in the range between 5 – 32% of volume ratio. In summary, it is possible to utilize pineapple waste for production of biohydrogen at an optimum substrate concentration of 26.4-gram VS/liter and acid pretreatment (H2SO4) of 0.3 N.

  20. Transport properties and c/a ratio of V{sub 2}O{sub 3} thin films grown on C- and R-plane sapphire substrates by pulsed laser deposition

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Sakai, Joe; Limelette, Patrice; Funakubo, Hiroshi

    2015-12-14

    We prepared V{sub 2}O{sub 3} thin films on C- or R-plane sapphire (Al{sub 2}O{sub 3}) substrates by a pulsed laser deposition method. X-ray diffraction analyses confirmed that single-phase V{sub 2}O{sub 3} films were epitaxially grown on both C- and R-planes under an Ar gas ambient of 2 × 10{sup −2} mbar at a substrate temperature of 873 K. Depending on the deposition conditions, c/a ratios at room temperature of (0001)-oriented V{sub 2}O{sub 3} films widely ranged from 2.79 to 2.88. Among them, the films of 2.81 ≤ c/a ≤ 2.84 showed complex metal (M)–insulator (I)–M transition during cooling from 300 to 10 K, while those of larger c/a ratiosmore » were accompanied by metallic properties throughout this temperature range. All the films on R-plane substrates underwent simple M-I transition at ∼150 K, which was more abrupt than the films on C-plane, whereas their c/a ratios were narrowly distributed. The distinct difference of M-I transition properties between C- and R-plane films is explained by the intrinsic a- and c-axes evolution through the transition from M to I phases.« less

  1. Probing flexible thermoplastic thin films on a substrate using ultrasonic waves to retrieve mechanical moduli and density: Inverse problem

    NASA Astrophysics Data System (ADS)

    Lazri, H.; Ogam, E.; Amar, B.; Fellah, Z. E. A.; Sayoud, N.; Boumaiza, Y.

    2018-05-01

    Flexible, supple thermoplastic thin films (PVB and PET) placed on elastic substrates were probed using ultrasonic waves to identify their mechanical moduli and density. The composite medium immersed in a fluid host medium (water) was excited using a 50 Mhz transducer operating at normal incidence in reflection mode. Elastic wave propagation data from the stratified medium was captured in the host medium as scattered field. These data were used along with theoretical fluid-solid interaction forward models for stratified-media developed using elasticity theory, to solve an inverse problem for the recovery of the model parameters of the thin films. Two configurations were modeled, one considering the substrate as a semi-infinite elastic medium and the second the substrate having a finite thickness and flanked by a semi-infinite host medium. Transverse slip for the sliding interface between the films and substrate was chosen. This was found to agree with the experiments whereby the thin films were just placed on the substrate without bonding. The inverse problems for the recovery of the mechanical parameters were successful in retrieving the thin films’ parameters under the slip boundary condition. The possible improvements to the new method for the characterization of thin films are discussed.

  2. Lapped substrate for enhanced backsurface reflectivity in a thermophotovoltaic energy conversion system

    DOEpatents

    Baldasaro, Paul F; Brown, Edward J; Charache, Greg W; DePoy, David M

    2000-01-01

    A method for fabricating a thermophotovoltaic energy conversion cell including a thin semiconductor wafer substrate (10) having a thickness (.beta.) calculated to decrease the free carrier absorption on a heavily doped substrate; wherein the top surface of the semiconductor wafer substrate is provided with a thermophotovoltaic device (11), a metallized grid (12) and optionally an antireflective (AR) overcoating; and, the bottom surface (10') of the semiconductor wafer substrate (10) is provided with a highly reflecting coating which may comprise a metal coating (14) or a combined dielectric/metal coating (17).

  3. Lapped substrate for enhanced backsurface reflectivity in a thermophotovoltaic energy conversion system

    DOEpatents

    Baldasaro, Paul F; Brown, Edward J; Charache, Greg W; DePoy, David M

    2000-09-05

    A method for fabricating a thermophotovoltaic energy conversion cell including a thin semiconductor wafer substrate (10) having a thickness (.beta.) calculated to decrease the free carrier absorption on a heavily doped substrate; wherein the top surface of the semiconductor wafer substrate is provided with a thermophotovoltaic device (11), a metallized grid (12) and optionally an antireflective (AR) overcoating; and, the bottom surface (10') of the semiconductor wafer substrate (10) is provided with a highly reflecting coating which may comprise a metal coating (14) or a combined dielectric/metal coating (17).

  4. Method of creating a controlled interior surface configuration of passages within a substrate

    DOEpatents

    Dembowski, Peter V.; Schilke, Peter W.

    1983-01-01

    A method of creating a controlled interior surface configuration of passages within a substrate, particularly cooling passages of nozzles or buckets of a gas turbine, involves the hot isostatic pressing of a leachable passage insert whose surface carries the female image of the desired interior surface configuration inside the substrate followed by leaching of the insert from the substrate.

  5. An enzyme-mediated protein-fragment complementation assay for substrate screening of sortase A.

    PubMed

    Li, Ning; Yu, Zheng; Ji, Qun; Sun, Jingying; Liu, Xiao; Du, Mingjuan; Zhang, Wei

    2017-04-29

    Enzyme-mediated protein conjugation has gained great attention recently due to the remarkable site-selectivity and mild reaction condition affected by the nature of enzyme. Among all sorts of enzymes reported, sortase A from Staphylococcus aureus (SaSrtA) is the most popular enzyme due to its selectivity and well-demonstrated applications. Position scanning has been widely applied to understand enzyme substrate specificity, but the low throughput of chemical synthesis of peptide substrates and analytical methods (HPLC, LC-ESI-MS) have been the major hurdle to fully decode enzyme substrate profile. We have developed a simple high-throughput substrate profiling method to reveal novel substrates of SaSrtA 7M, a widely used hyperactive peptide ligase, by modified protein-fragment complementation assay (PCA). A small library targeting the LPATG motif recognized by SaSrtA 7M was generated and screened against proteins carrying N-terminal glycine. Using this method, we have confirmed all currently known substrates of the enzyme, and moreover identified some previously unknown substrates with varying activities. The method provides an easy, fast and highly-sensitive way to determine substrate profile of a peptide ligase in a high-throughput manner. Copyright © 2017 Elsevier Inc. All rights reserved.

  6. Substrate effects on endothelial cell adherence rates.

    PubMed

    Scott, W J; Mann, P

    1990-01-01

    Endothelial cell attachment to a synthetic substrate was studied using an in vitro model system. Attachment rate was defined as the number of tritium-labeled endothelial cells attached to a synthetic substrate after 30 minutes. The surface of the synthetic substrate was chemically modified with either laminin or fibronectin. Labeled endothelial cells attached more rapidly to synthetic substrate, chemically modified with biomolecules, as compared with the untreated substrate controls. Unlabeled endothelial cells were grown to confluency on a second set of modified and untreated substrates. The cells were removed with 1% Triton, and the rate of re-endothelialization with tritium-labeled endothelial cells was determined. The rate was 11-13 times that of the same cells on untreated substrate. These data confirm that biomolecules increase the attachment rate of endothelial cells to synthetic substrate, and also suggest that endothelial cells may secrete a Triton-insoluble product (Sigma, St. Louis, MO) into subendothelial matrix that increases re-endothelialization.

  7. Immobilization of naringin onto chitosan substrates by using ozone activation.

    PubMed

    Li, Chung Hsing; Wang, Jing Wei; Ho, Ming Hua; Shih, Jia Lin; Hsiao, Sheng Wen; Thien, Doan Van Hong

    2014-03-01

    Ozone oxidation can easily produce peroxides containing active free radicals that can be used for the surface modification of biomaterials. This process is highly efficient and nontoxic. In this research, naringin, an HMG-CoA reductase inhibitor that can promote bone formation, was immobilized onto a chitosan film using ozone activation. First, a chitosan film was treated by ozone to produce peroxides; these peroxides were then quantified and their amount was optimized by an iodide assay. For the in vitro delivery of naringin, a chitosan-naringin substrate was immersed in phosphate-buffered saline to quantify the released amount of naringin. It was found that the immobilized naringin was slowly released over the course of two weeks, where its concentration in the medium was controlled by this delivery process. The results of cell culture showed that cell viability and early osteogenic differentiation, as measured by alkaline phosphatase expression, were promoted with the immobilized naringin on chitosan substrates. The expression of osteogenic proteins, including type-I collagen, bone siloprotein, and osteocalcin, were also enhanced. According to the results of Smad1 and Smad6 phosphorylation, immobilized naringin on ozonated chitosan substrates would be able to initiate bone morphogenetic protein-Smad signaling by activating receptor Smad and by suppressing inhibitory Smad. The results in this research demonstrated that the naringin-chitosan substrate produced by biocompatible ozone activation was highly osteoconductive without cytotoxicity. Copyright © 2013 Elsevier B.V. All rights reserved.

  8. Mesoporous silica nanoparticle-based substrates for cell directed delivery of Notch signalling modulators to control myoblast differentiation

    NASA Astrophysics Data System (ADS)

    Böcking, Dominique; Wiltschka, Oliver; Niinimäki, Jenni; Shokry, Hussein; Brenner, Rolf; Lindén, Mika; Sahlgren, Cecilia

    2014-01-01

    Biochemical cues are critical to control stem cell function and can be utilized to develop smart biomaterials for stem cell engineering. The challenge is to deliver these cues in a restricted manner with spatial and temporal control. Here we have developed bilayer films of mesoporous silica nanoparticles for delayed cellular delivery of Notch modulators to promote muscle stem cell differentiation. We demonstrate that drug-loaded particles are internalized from the particle-covered surface, which allows for direct delivery of the drug into the cell and a delayed and confined drug release. Substrates of particles loaded with γ-secretase-inhibitors, which block the Notch signalling pathway, promoted efficient differentiation of myoblasts. The particle substrates were fully biocompatible and did not interfere with the inherent differentiation process. We further demonstrate that impregnating commercially available, biocompatible polymer scaffolds with MSNs allows for a free standing substrate for cell directed drug delivery.Biochemical cues are critical to control stem cell function and can be utilized to develop smart biomaterials for stem cell engineering. The challenge is to deliver these cues in a restricted manner with spatial and temporal control. Here we have developed bilayer films of mesoporous silica nanoparticles for delayed cellular delivery of Notch modulators to promote muscle stem cell differentiation. We demonstrate that drug-loaded particles are internalized from the particle-covered surface, which allows for direct delivery of the drug into the cell and a delayed and confined drug release. Substrates of particles loaded with γ-secretase-inhibitors, which block the Notch signalling pathway, promoted efficient differentiation of myoblasts. The particle substrates were fully biocompatible and did not interfere with the inherent differentiation process. We further demonstrate that impregnating commercially available, biocompatible polymer scaffolds with

  9. Metal oxide nanorod arrays on monolithic substrates

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Gao, Pu-Xian; Guo, Yanbing; Ren, Zheng

    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 includemore » 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.« less

  10. Coupling between apical tension and basal adhesion allow epithelia to collectively sense and respond to substrate topography over long distances.

    PubMed

    Broaders, Kyle E; Cerchiari, Alec E; Gartner, Zev J

    2015-12-01

    Epithelial sheets fold into complex topographies that contribute to their function in vivo. Cells can sense and respond to substrate topography in their immediate vicinity by modulating their interfacial mechanics, but the extent to which these mechanical properties contribute to their ability to sense substrate topography across length scales larger than a single cell has not been explored in detail. To study the relationship between the interfacial mechanics of single cells and their collective behavior as tissues, we grew cell-sheets on substrates engraved with surface features spanning macroscopic length-scales. We found that many epithelial cell-types sense and respond to substrate topography, even when it is locally nearly planar. Cells clear or detach from regions of local negative curvature, but not from regions with positive or no curvature. We investigated this phenomenon using a finite element model where substrate topography is coupled to epithelial response through a balance of tissue contractility and adhesive forces. The model correctly predicts the focal sites of cell-clearing and epithelial detachment. Furthermore, the model predicts that local tissue response to substrate curvature is a function of the surrounding topography of the substrate across long distances. Analysis of cell-cell and cell-substrate contact angles suggests a relationship between these single-cell interfacial properties, epithelial interfacial properties, and collective epithelial response to substrate topography. Finally, we show that contact angles change upon activation of oncogenes or inhibition of cell-contractility, and that these changes correlate with collective epithelial response. Our results demonstrate that in mechanically integrated epithelial sheets, cell contractility can be transmitted through multiple cells and focused by substrate topography to affect a behavioral response at distant sites.

  11. Hydrological performance of dual-substrate-layer green roofs using porous inert substrates with high sorption capacities.

    PubMed

    Wang, Xiaoou; Tian, Yimei; Zhao, Xinhua; Peng, Chenrui

    2017-06-01

    Given that the common medium in existing green roofs is a single layer composed of organic and inorganic substrates, seven pilot-scale dual-substrate-layer extensive green roofs (G1-G7), which include nutrition and adsorption substrate layers, were constructed in this study. The effectiveness of porous inert substrates (activated charcoal, zeolite, pumice, lava, vermiculite and expanded perlite) used as the adsorption substrate for stormwater retention was investigated. A single-substrate-layer green roof (G8) was built for comparison with G1-G7. Despite the larger total rainfall depth (mm) of six types of simulated rains (43.2, 54.6, 76.2, 87.0, 85.2 and 86.4, respectively), the total percent retention of G1-G7 varied between 14% and 82% with an average of 43%, exhibiting better runoff-retaining capacity than G8 based on the maximum potential rainfall storage depth per unit height of adsorption substrate. Regression analysis showed that there was a logarithmic relationship between cumulative rainfall depth with non-zero runoff and stormwater retention for G1-G4 and a linear relationship for G5-G8. To enhance the water retention capacity and extend the service life of dual-substrate-layer extensive green roofs, the mixture of activated charcoal and/or pumice with expanded perlite and/or vermiculite is more suitable as the adsorption substrate than the mixture containing lava and/or zeolite.

  12. Exploiting the Substrate Promiscuity of Hydroxycinnamoyl-CoA:Shikimate Hydroxycinnamoyl Transferase to Reduce Lignin

    DOE PAGES

    Eudes, Aymerick; Pereira, Jose H.; Yogiswara, Sasha; ...

    2016-02-08

    Lignin poses a major challenge in the processing of plant biomass for agro-industrial applications. For bioengineering purposes, there is a pressing interest in identifying and characterizing the enzymes responsible for the biosynthesis of lignin. Hydroxycinnamoyl-CoA:shikimate hydroxycinnamoyl transferase (HCT; EC 2.3.1.133) is a key metabolic entry point for the synthesis of the most important lignin monomers: coniferyl and sinapyl alcohols. In this study, we investigated the substrate promiscuity of HCT from a bryophyte (Physcomitrella) and from five representatives of vascular plants (Arabidopsis, poplar, switchgrass, pine and Selaginella) using a yeast expression system. We demonstrate for these HCTs a conserved capacity tomore » acylate with p-coumaroyl-CoA several phenolic compounds in addition to the canonical acceptor shikimate normally used during lignin biosynthesis. Using either recombinant HCT from switchgrass (PvHCT2a) or an Arabidopsis stem protein extract, we show evidence of the inhibitory effect of these phenolics on the synthesis of p-coumaroyl shikimate in vitro, which presumably occurs via a mechanism of competitive inhibition. A structural study of PvHCT2a confirmed the binding of a non-canonical acceptor in a similar manner to shikimate in the active site of the enzyme. Finally, we exploited in Arabidopsis the substrate flexibility of HCT to reduce lignin content and improve biomass saccharification by engineering transgenic lines that overproduce one of the HCT non-canonical acceptors. Our results demonstrate conservation of HCT substrate promiscuity and provide support for a new strategy for lignin reduction in the effort to improve the quality of plant biomass for forage and cellulosic biofuels.« less

  13. Structural Snapshots of Heparin Depolymerization by Heparin Lyase I

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Han, Young-Hyun; Garron, Marie-Line; Kim, Hye-Yeon

    2010-01-12

    Heparin lyase I (heparinase I) specifically depolymerizes heparin, cleaving the glycosidic linkage next to iduronic acid. Here, we show the crystal structures of heparinase I from Bacteroides thetaiotaomicron at various stages of the reaction with heparin oligosaccharides before and just after cleavage and product disaccharide. The heparinase I structure is comprised of a {beta}-jellyroll domain harboring a long and deep substrate binding groove and an unusual thumb-resembling extension. This thumb, decorated with many basic residues, is of particular importance in activity especially on short heparin oligosaccharides. Unexpected structural similarity of the active site to that of heparinase II with anmore » ({alpha}/{alpha}){sub 6} fold is observed. Mutational studies and kinetic analysis of this enzyme provide insights into the catalytic mechanism, the substrate recognition, and processivity.« less

  14. The kinetic friction of ZnO nanowires on amorphous SiO2 and SiN substrates

    NASA Astrophysics Data System (ADS)

    Roy, Aditi; Xie, Hongtao; Wang, Shiliang; Huang, Han

    2016-12-01

    ZnO nanowires were bent on amorphous SiO2 and SiN substrates in an ambient atmosphere using optical nanomanipulation. The kinetic friction between the nanowires and substrate was determined from the bent shape of the nanowires. The kinetic friction force per unit area, i.e. frictional shear stress, for the ZnO/SiO2 and ZnO/SiN nanowire/substrate systems being measured were 1.05 ± 0.28 and 2.08 ± 0.33 MPa, respectively. The surface roughness and the Hamaker constant of SiO2 and SiN substrates had significant effect on the frictional stresses.

  15. Yield and size of oyster mushroom grown on rice/wheat straw basal substrate supplemented with cotton seed hull.

    PubMed

    Yang, Wenjie; Guo, Fengling; Wan, Zhengjie

    2013-10-01

    Oyster mushroom (Pleurotus ostreatus) was cultivated on rice straw basal substrate, wheat straw basal substrate, cotton seed hull basal substrate, and wheat straw or rice straw supplemented with different proportions (15%, 30%, and 45% in rice straw substrate, 20%, 30%, and 40% in wheat straw substrate) of cotton seed hull to find a cost effective substrate. The effect of autoclaved sterilized and non-sterilized substrate on growth and yield of oyster mushroom was also examined. Results indicated that for both sterilized substrate and non-sterilized substrate, oyster mushroom on rice straw and wheat basal substrate have faster mycelial growth rate, comparatively poor surface mycelial density, shorter total colonization period and days from bag opening to primordia formation, lower yield and biological efficiency, lower mushroom weight, longer stipe length and smaller cap diameter than that on cotton seed hull basal substrate. The addition of cotton seed hull to rice straw and wheat straw substrate slowed spawn running, primordial development and fruit body formation. However, increasing the amount of cotton seed hull can increase the uniformity and white of mycelium, yield and biological efficiency, and increase mushroom weight, enlarge cap diameter and shorten stipe length. Compared to the sterilized substrate, the non-sterilized substrate had comparatively higher mycelial growth rate, shorter total colonization period and days from bag opening to primordia formation. However, the non-sterilized substrate did not gave significantly higher mushroom yield and biological efficiency than the sterilized substrate, but some undesirable characteristics, i.e. smaller mushroom cap diameter and relatively long stipe length.

  16. Graphene transport mediated by micropatterned substrates

    NASA Astrophysics Data System (ADS)

    Hinnefeld, J. Henry; Gill, Stephen T.; Mason, Nadya

    2018-04-01

    Engineered substrates offer a promising avenue towards graphene devices having tunable properties. In particular, topographically patterned substrates can expose unique behavior due to their ability to induce local variations in strain and electrostatic doping. However, to explore the range of possible science and applications, it is important to create topographic substrates that both have tunable features and are suitable for transport measurements. In this letter, we describe the fabrication of tunable, topographically patterned substrates suitable for transport measurements. We report both optical and transport measurements of graphene devices fabricated on these substrates and demonstrate the characteristic strain and local doping behavior induced by the topographic features.

  17. Biofunctionalization on alkylated silicon substrate surfaces via "click" chemistry.

    PubMed

    Qin, Guoting; Santos, Catherine; Zhang, Wen; Li, Yan; Kumar, Amit; Erasquin, Uriel J; Liu, Kai; Muradov, Pavel; Trautner, Barbara Wells; Cai, Chengzhi

    2010-11-24

    Biofunctionalization of silicon substrates is important to the development of silicon-based biosensors and devices. Compared to conventional organosiloxane films on silicon oxide intermediate layers, organic monolayers directly bound to the nonoxidized silicon substrates via Si-C bonds enhance the sensitivity of detection and the stability against hydrolytic cleavage. Such monolayers presenting a high density of terminal alkynyl groups for bioconjugation via copper-catalyzed azide-alkyne 1,3-dipolar cycloaddition (CuAAC, a "click" reaction) were reported. However, yields of the CuAAC reactions on these monolayer platforms were low. Also, the nonspecific adsorption of proteins on the resultant surfaces remained a major obstacle for many potential biological applications. Herein, we report a new type of "clickable" monolayers grown by selective, photoactivated surface hydrosilylation of α,ω-alkenynes, where the alkynyl terminal is protected with a trimethylgermanyl (TMG) group, on hydrogen-terminated silicon substrates. The TMG groups on the film are readily removed in aqueous solutions in the presence of Cu(I). Significantly, the degermanylation and the subsequent CuAAC reaction with various azides could be combined into a single step in good yields. Thus, oligo(ethylene glycol) (OEG) with an azido tag was attached to the TMG-alkyne surfaces, leading to OEG-terminated surfaces that reduced the nonspecific adsorption of protein (fibrinogen) by >98%. The CuAAC reaction could be performed in microarray format to generate arrays of mannose and biotin with varied densities on the protein-resistant OEG background. We also demonstrated that the monolayer platform could be functionalized with mannose for highly specific capturing of living targets (Escherichia coli expressing fimbriae) onto the silicon substrates.

  18. Method and apparatus for coating a patterned thin film on a substrate from a fluid source with continuous feed capability

    DOEpatents

    Burrows, Paul E [Kennewick, WA; Sapochak, Linda S [Kennewick, WA

    2009-09-22

    A method and apparatus for forming patterned coatings of thin film, non-polymerizable compounds on a substrate. A mixture of the non-polymerizable compound and a liquid carrier is pumped into the interior of a heated evaporation box having an internal temperature sufficient to convert substantially all of the non-polymerizable compound and liquid carrier to a gaseous form. The non-polymerizable compound and liquid carrier are then removed from the evaporation box via exit slit in the evaporation box. Adjacent to the exit slit, and maintained in a vacuum, is a first substrate upon which the non-polymerizable compound condenses. The first substrate is in motion, for example on a web roller, thereby allowing a continuous coating of the non-polymerizable compound to be applied to the first substrate. Once the non-polymerizable compound is applied to one side of the first substrate, an energy source is then directed toward the opposite side of the first substrate. In this manner, a portion of the non-polymerizable compound is removed from the first substrate. A second substrate is then provided adjacent to the first substrate, and the non-polymerizable compound is thereby transferred from the first substrate onto the second substrate. By repeatedly transferring portions of the non-polymerizable material from the first substrate to the second substrate in this manner, the thin film, non-polymerizable materials can be formed onto the second substrate in a predetermined pattern, and in a continuous and highly efficient process.

  19. Characterization of substrate binding of the WW domains in human WWP2 protein.

    PubMed

    Jiang, Jiahong; Wang, Nan; Jiang, Yafei; Tan, Hongwei; Zheng, Jimin; Chen, Guangju; Jia, Zongchao

    2015-07-08

    WW domains harbor substrates containing proline-rich motifs, but the substrate specificity and binding mechanism remain elusive for those WW domains less amenable for structural studies, such as human WWP2 (hWWP2). Herein we have employed multiple techniques to investigate the second WW domain (WW2) in hWWP2. Our results show that hWWP2 is a specialized E3 for PPxY motif-containing substrates only and does not recognize other amino acids and phospho-residues. The strongest binding affinity of WW2, and the incompatibility between each WW domain, imply a novel relationship, and our SPR experiment reveals a dynamic binding mode in Class-I WW domains for the first time. The results from alanine-scanning mutagenesis and modeling further point to functionally conserved residues in WW2. Copyright © 2015 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

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

    PubMed

    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.

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

    PubMed Central

    Zhang, Fangzhou; Bordia, Rajendra K.

    2018-01-01

    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. PMID:29584647

  2. Monobromobimane occupies a distinct xenobiotic substrate site in glutathione S-transferase π

    PubMed Central

    Ralat, Luis A.; Colman, Roberta F.

    2003-01-01

    Monobromobimane (mBBr), functions as a substrate of porcine glutathione S-transferase π (GST π): The enzyme catalyzes the reaction of mBBr with glutathione. S-(Hydroxyethyl)bimane, a nonreactive analog of monobromobimane, acts as a competitive inhibitor with respect to mBBr as substrate but does not affect the reaction of GST π with another substrate, 1-chloro-2,4-dinitrobenzene (CDNB). In the absence of glutathione, monobromobimane inactivates GST π at pH 7.0 and 25°C as assayed using mBBr as substrate, with a lesser effect on the enzyme’s use of CDNB as substrate. These results indicate that the sites occupied by CDNB and mBBr are not identical. Inactivation is proportional to the incorporation of 2 moles of bimane/mole of subunit. Modification of GST π with mBBr does not interfere with its binding of 8-anilino-1-naphthalene sulfonate, indicating that this hydrophobic site is not the target of monobromobimane. S-Methylglutathione and S-(hydroxyethyl)bimane each yield partial protection against inactivation and decrease reagent incorporation, while glutathionyl-bimane protects completely against inactivation. Peptide analysis after trypsin digestion indicates that mBBr modifies Cys45 and Cys99 equally. Modification of Cys45 is reduced in the presence of S-methylglutathione, indicating that this residue is at or near the glutathione binding region. In contrast, modification of Cys99 is reduced in the presence of S-(hydroxyethyl)bimane, suggesting that this residue is at or near the mBBr xenobiotic substrate binding site. Modification of Cys99 can best be understood by reaction with monobromobimane while it is bound to its xenobiotic substrate site in an alternate orientation. These results support the concept that glutathione S-transferase accomplishes its ability to react with a diversity of substrates in part by harboring distinct xenobiotic substrate sites. PMID:14573868

  3. Monobromobimane occupies a distinct xenobiotic substrate site in glutathione S-transferase pi.

    PubMed

    Ralat, Luis A; Colman, Roberta F

    2003-11-01

    Monobromobimane (mBBr), functions as a substrate of porcine glutathione S-transferase pi (GST pi): The enzyme catalyzes the reaction of mBBr with glutathione. S-(Hydroxyethyl)bimane, a nonreactive analog of monobromobimane, acts as a competitive inhibitor with respect to mBBr as substrate but does not affect the reaction of GST pi with another substrate, 1-chloro-2,4-dinitrobenzene (CDNB). In the absence of glutathione, monobromobimane inactivates GST pi at pH 7.0 and 25 degrees C as assayed using mBBr as substrate, with a lesser effect on the enzyme's use of CDNB as substrate. These results indicate that the sites occupied by CDNB and mBBr are not identical. Inactivation is proportional to the incorporation of 2 moles of bimane/mole of subunit. Modification of GST pi with mBBr does not interfere with its binding of 8-anilino-1-naphthalene sulfonate, indicating that this hydrophobic site is not the target of monobromobimane. S-Methylglutathione and S-(hydroxyethyl)bimane each yield partial protection against inactivation and decrease reagent incorporation, while glutathionyl-bimane protects completely against inactivation. Peptide analysis after trypsin digestion indicates that mBBr modifies Cys45 and Cys99 equally. Modification of Cys45 is reduced in the presence of S-methylglutathione, indicating that this residue is at or near the glutathione binding region. In contrast, modification of Cys99 is reduced in the presence of S-(hydroxyethyl)bimane, suggesting that this residue is at or near the mBBr xenobiotic substrate binding site. Modification of Cys99 can best be understood by reaction with monobromobimane while it is bound to its xenobiotic substrate site in an alternate orientation. These results support the concept that glutathione S-transferase accomplishes its ability to react with a diversity of substrates in part by harboring distinct xenobiotic substrate sites.

  4. Femtosecond laser-induced formation of submicrometer spikes on a semiconductor substrate

    DOEpatents

    Mazur, Eric; Shen, Mengyan

    2013-12-03

    The present invention generally provides a semiconductor substrates having submicron-sized surface features generated by irradiating the surface with ultra short laser pulses. In one aspect, a method of processing a semiconductor substrate is disclosed that includes placing at least a portion of a surface of the substrate in contact with a fluid, and exposing that surface portion to one or more femtosecond pulses so as to modify the topography of that portion. The modification can include, e.g., generating a plurality of submicron-sized spikes in an upper layer of the surface.

  5. Identification of in vivo substrates of the yeast mitochondrial chaperonins reveals overlapping but non-identical requirement for hsp60 and hsp10.

    PubMed Central

    Dubaquié, Y; Looser, R; Fünfschilling, U; Jenö, P; Rospert, S

    1998-01-01

    The mechanism of chaperonin-assisted protein folding has been mostly analyzed in vitro using non-homologous substrate proteins. In order to understand the relative importance of hsp60 and hsp10 in the living cell, homologous substrate proteins need to be identified and analyzed. We have devised a novel screen to test the folding of a large variety of homologous substrates in the mitochondrial matrix in the absence or presence of functional hsp60 or hsp10. The identified substrates have an Mr of 15-90 kDa and fall into three groups: (i) proteins that require both hsp60 and hsp10 for correct folding; (ii) proteins that completely fail to fold after inactivation of hsp60 but are unaffected by the inactivation of hsp10; and (iii) newly imported hsp60 itself, which is more severely affected by inactivation of hsp10 than by inactivation of pre-existing hsp60. The majority of the identified substrates are group I proteins. For these, the lack of hsp60 function has a more pronounced effect than inactivation of hsp10. We suggest that homologous substrate proteins have differential chaperonin requirements, indicating that hsp60 and hsp10 do not always act as a single functional unit in vivo. PMID:9774331

  6. Substrate-Versatile Approach to Robust Antireflective and Superhydrophobic Coatings with Excellent Self-Cleaning Property in Varied Environments.

    PubMed

    Ren, Tingting; He, Junhui

    2017-10-04

    Robust antireflective and superhydrophobic coatings are highly desired in wide applications, such as optical devices, solar cell panels, architectural and automotive glasses, lab-on chip systems, and windows for electronic devices. Meanwhile, simple, low-cost, and substrate-versatile fabrication is also essential toward real applications of such coatings. Herein, we developed a substrate-versatile strategy to fabricate robust antireflective and superhydrophobic coatings with excellent self-cleaning property in varied environments, including air and oil and after oil contamination. A mixed ethanol suspension, which consists of 1H,1H,2H,2H-perfluorooctyltriethoxysilane modified dual-sized silica nanoparticles and acid-catalyzed silica precursor, was first synthesized. The acid-catalyzed silica precursor could help to form a highly cross-linked silica network by connecting the silica nanoparticles, thus significantly enhancing the robustness of coatings. The as-prepared coatings were able to withstand a water drop impact test, sand abrasion test, tape adhesion test, and knife and pencil scratching tests. More importantly, it was also found that the wettability and self-cleaning property of coatings after oil contamination were surprisingly different from those in air and oil. These observations are explainable by the alteration of interface; i.e., the alteration of interface has significant effects on the functional properties of coatings. Additionally, the mixed suspension could be sprayed onto various hard and soft substrates including glass, polyethylene terephthalate (PET), polycarbonate (PC), and poly(methyl methacrylate) (PMMA), opening up a feasible route toward varied practical applications in solar cell panels, optical devices, architectural and automotive glasses, droplet manipulators, and fluid control.

  7. Virtual substrate method for nanomaterials characterization

    PubMed Central

    Da, Bo; Liu, Jiangwei; Yamamoto, Mahito; Ueda, Yoshihiro; Watanabe, Kazuyuki; Cuong, Nguyen Thanh; Li, Songlin; Tsukagoshi, Kazuhito; Yoshikawa, Hideki; Iwai, Hideo; Tanuma, Shigeo; Guo, Hongxuan; Gao, Zhaoshun; Sun, Xia; Ding, Zejun

    2017-01-01

    Characterization techniques available for bulk or thin-film solid-state materials have been extended to substrate-supported nanomaterials, but generally non-quantitatively. This is because the nanomaterial signals are inevitably buried in the signals from the underlying substrate in common reflection-configuration techniques. Here, we propose a virtual substrate method, inspired by the four-point probe technique for resistance measurement as well as the chop-nod method in infrared astronomy, to characterize nanomaterials without the influence of underlying substrate signals from four interrelated measurements. By implementing this method in secondary electron (SE) microscopy, a SE spectrum (white electrons) associated with the reflectivity difference between two different substrates can be tracked and controlled. The SE spectrum is used to quantitatively investigate the covering nanomaterial based on subtle changes in the transmission of the nanomaterial with high efficiency rivalling that of conventional core-level electrons. The virtual substrate method represents a benchmark for surface analysis to provide ‘free-standing' information about supported nanomaterials. PMID:28548114

  8. A PP2A-B55 recognition signal controls substrate dephosphorylation kinetics during mitotic exit

    PubMed Central

    Cundell, Michael J.; Holder, James

    2016-01-01

    PP2A-B55 is one of the major phosphatases regulating cell division. Despite its importance for temporal control during mitotic exit, how B55 substrates are recognized and differentially dephosphorylated is unclear. Using phosphoproteomics combined with kinetic modeling to extract B55-dependent rate constants, we have systematically identified B55 substrates and assigned their temporal order in mitotic exit. These substrates share a bipartite polybasic recognition determinant (BPR) flanking a Cdk1 phosphorylation site. Experiments and modeling show that dephosphorylation rate is encoded into B55 substrates, including its inhibitor ENSA, by cooperative action of basic residues within the BPR. A complementary acidic surface on B55 decodes this signal, supporting a cooperative electrostatic mechanism for substrate selection. A further level of specificity is encoded into B55 substrates because B55 displays selectivity for phosphothreonine. These simple biochemical properties, combined with feedback control of B55 activity by the phosphoserine-containing substrate/inhibitor ENSA, can help explain the temporal sequence of events during exit from mitosis. PMID:27551054

  9. Photovoltaic cell with nano-patterned substrate

    DOEpatents

    Cruz-Campa, Jose Luis; Zhou, Xiaowang; Zubia, David

    2016-10-18

    A photovoltaic solar cell comprises a nano-patterned substrate layer. A plurality of nano-windows are etched into an intermediate substrate layer to form the nano-patterned substrate layer. The nano-patterned substrate layer is positioned between an n-type semiconductor layer composed of an n-type semiconductor material and a p-type semiconductor layer composed of a p-type semiconductor material. Semiconductor material accumulates in the plurality of nano-windows, causing a plurality of heterojunctions to form between the n-type semiconductor layer and the p-type semiconductor layer.

  10. Femtosecond laser-induced formation of submicrometer spikes on a semiconductor substrate

    DOEpatents

    Mazur, Eric [Concord, MA; Shen, Mengyan [Arlington, MA

    2008-10-28

    The present invention generally provides semiconductor substrates having submicron-sized surface features generated by irradiating the surface with ultra short laser pulses. In one aspect, a method of processing a semiconductor substrate is disclosed that includes placing at least a portion of a surface of the substrate in contact with a fluid, and exposing that surface portion to one or more femtosecond pulses so as to modify the topography of that portion. The modification can include, e.g., generating a plurality of submicron-sized spikes in an upper layer of the surface.

  11. Femtosecond laser-induced formation of submicrometer spikes on a semiconductor substrate

    DOEpatents

    Mazur, Eric; Shen, Mengyan

    2015-09-15

    The present invention generally provides semiconductor substrates having submicronsized surface features generated by irradiating the surface with ultra short laser pulses. In one aspect, a method of processing a semiconductor substrate is disclosed that includes placing at least a portion of a surface of the substrate in contact with a fluid, and exposing that surface portion to one or more femtosecond pulses so as to modify the topography of that portion. The modification can include, e.g., generating a plurality of submicron-sized spikes in an upper layer of the surface.

  12. Femtosecond laser-induced formation of submicrometer spikes on a semiconductor substrate

    DOEpatents

    Mazur, Eric , Shen; Mengyan, [Belmont, MA

    2011-02-08

    The present invention generally provides semiconductor substrates having submicron-sized surface features generated by irradiating the surface with ultra short laser pulses. In one aspect, a method of processing a semiconductor substrate is disclosed that includes placing at least a portion of a surface of the substrate in contact with a fluid, and exposing that surface portion to one or more femtosecond pulses so as to modify the topography of that portion. The modification can include, e.g., generating a plurality of submicron-sized spikes in an upper layer of the surface.

  13. Thermally Stable, Piezoelectric and Pyroelectric Polymeric Substrates

    NASA Technical Reports Server (NTRS)

    Simpson, Joycely O. (Inventor); St.Clair, Terry L. (Inventor)

    1999-01-01

    A thermally stable, piezoelectric and pyroelectric polymeric substrate was prepared. This thermally stable, piezoelectric and pyroelectric polymeric substrate may be used to prepare electromechanical transducers, thermomechanical transducers, accelerometers. acoustic sensors, infrared sensors, pressure sensors, vibration sensors, impact sensors, in-situ temperature sensors, in-situ stress/strain sensors, micro actuators, switches, adjustable fresnel lenses, speakers, tactile sensors. weather sensors, micro positioners, ultrasonic devices, power generators, tunable reflectors, microphones, and hydrophones. The process for preparing these polymeric substrates includes: providing a polymeric substrate having a softening temperature greater than 1000 C; depositing a metal electrode material onto the polymer film; attaching a plurality of electrical leads to the metal electrode coated polymeric substrate; heating the metal electrode coated polymeric substrate in a low dielectric medium; applying a voltage to the heated metal electrode coated polymeric substrate to induce polarization; and cooling the polarized metal electrode coated polymeric electrode while maintaining a constant voltage.

  14. A flexible and transparent graphene/ZnO nanorod hybrid structure fabricated by exfoliating a graphite substrate.

    PubMed

    Nam, Gwang-Hee; Baek, Seong-Ho; Cho, Chang-Hee; Park, Il-Kyu

    2014-10-21

    We demonstrate the fabrication of a graphene/ZnO nanorod (NR) hybrid structure by mechanical exfoliation of ZnO NRs grown on a graphite substrate. We confirmed the existence of graphene sheets on the hybrid structure by analyzing the Raman spectra and current-voltage (I-V) characteristics. The Raman spectra of the exfoliated graphene/ZnO NR hybrid structure show G and 2D band peaks that are shifted to lower wavenumbers, indicating that the exfoliated graphene layer exists under a significant amount of strain. The I-V characteristics of the graphene/ZnO NR hybrid structure show current flow through the graphene layer, while no current flow is observed on the ZnO NR/polydimethylsiloxane (PDMS) composite without graphene, thereby indicating that the few-layer graphene was successfully transferred onto the hybrid structure. A piezoelectric nanogenerator is demonstrated by using the fabricated graphene/ZnO NR hybrid structure. The nanogenerator exhibits stable output voltage up to 3.04 V with alternating current output characteristics.

  15. Cohesive detachment of an elastic pillar from a dissimilar substrate

    NASA Astrophysics Data System (ADS)

    Fleck, N. A.; Khaderi, S. N.; McMeeking, R. M.; Arzt, E.

    The adhesion of micron-scale surfaces due to intermolecular interactions is a subject of intense interest spanning electronics, biomechanics and the application of soft materials to engineering devices. The degree of adhesion is sensitive to the diameter of micro-pillars in addition to the degree of elastic mismatch between pillar and substrate. Adhesion-strength-controlled detachment of an elastic circular cylinder from a dissimilar substrate is predicted using a Dugdale-type of analysis, with a cohesive zone of uniform tensile strength emanating from the interface corner. Detachment initiates when the opening of the cohesive zone attains a critical value, giving way to crack formation. When the cohesive zone size at crack initiation is small compared to the pillar diameter, the initiation of detachment can be expressed in terms of a critical value Hc of the corner stress intensity. The estimated pull-off force is somewhat sensitive to the choice of stick/slip boundary condition used on the cohesive zone, especially when the substrate material is much stiffer than the pillar material. The analysis can be used to predict the sensitivity of detachment force to the size of pillar and to the degree of elastic mismatch between pillar and substrate.

  16. Conformational state interactions provide clues to the pharmacochaperone potential of serotonin transporter partial substrates

    PubMed Central

    Bhat, Shreyas; Hasenhuetl, Peter S.; Kasture, Ameya; El-Kasaby, Ali; Baumann, Michael H.; Blough, Bruce E.; Sucic, Sonja; Sandtner, Walter; Freissmuth, Michael

    2017-01-01

    Point mutations in SLC6 transporters cause misfolding, which can be remedied by pharmacochaperones. The serotonin transporter (SERT/SLC6A4) has a rich pharmacology including inhibitors, releasers (amphetamines, which promote the exchange mode), and more recently, discovered partial substrates. We hypothesized that partial substrates trapped the transporter in one or several states of the transport cycle. This conformational trapping may also be conducive to folding. We selected naphthylpropane-2-amines of the phenethylamine library (PAL) including the partial substrate PAL1045 and its congeners PAL287 and PAL1046. We analyzed their impact on the transport cycle of SERT by biochemical approaches and by electrophysiological recordings; substrate-induced peak currents and steady-state currents monitored the translocation of substrate and co-substrate Na+ across the lipid bilayer and the transport cycle, respectively. These experiments showed that PAL1045 and its congeners bound with different affinities (ranging from nm to μm) to various conformational intermediates of SERT during the transport cycle. Consistent with the working hypothesis, PAL1045 was the most efficacious compound in restoring surface expression and transport activity to the folding-deficient mutant SERT-601PG602-AA. These experiments provide a proof-of-principle for a rational search for pharmacochaperones, which may be useful to restore function to clinically relevant folding-deficient transporter mutants. PMID:28842491

  17. A hot-spot-active magnetic graphene oxide substrate for microRNA detection based on cascaded chemiluminescence resonance energy transfer

    NASA Astrophysics Data System (ADS)

    Bi, Sai; Chen, Min; Jia, Xiaoqiang; Dong, Ying

    2015-02-01

    Herein, a cascaded chemiluminescence resonance energy transfer (C-CRET) process was demonstrated from horseradish peroxidase (HRP)-mimicking DNAzyme-catalyzed luminol-H2O2 to fluorescein and further to graphene oxide (GO) when HRP-mimicking DNAzyme/fluorescein was in close proximity to the GO surface. The proposed C-CRET system was successfully implemented to construct three modes of C-CRET hot-spot-active substrates (modes I, II and III) by covalently immobilizing HRP-mimicking DNAzyme/fluorescein-labeled hairpin DNAs (hot-spot-generation probes) on magnetic GO (MGO), resulting in a signal ``off'' state due to the quenching of the luminol/H2O2/HRP-mimicking DNAzyme/fluorescein CRET system by GO. Upon the introduction of microRNA-122 (miRNA-122), the targets (mode I) or the new triggers that were generated through a strand displacement reaction (SDR) initiated by miRNA-122 (modes II and III) hybridized with the loop domains of hairpin probes on MGO to form double-stranded (modes I and II) or triplex-stem structures (mode III), causing an ``open'' configuration of the hairpin probe and a CRET signal ``on'' state, thus achieving sensitive and selective detection of miRNA-122. More importantly, the substrate exhibited excellent controllability, reversibility and reproducibility through SDR and magnetic separation (modes II and III), especially sequence-independence for hairpin probes in mode III, holding great potential for the development of a versatile platform for optical biosensing.Herein, a cascaded chemiluminescence resonance energy transfer (C-CRET) process was demonstrated from horseradish peroxidase (HRP)-mimicking DNAzyme-catalyzed luminol-H2O2 to fluorescein and further to graphene oxide (GO) when HRP-mimicking DNAzyme/fluorescein was in close proximity to the GO surface. The proposed C-CRET system was successfully implemented to construct three modes of C-CRET hot-spot-active substrates (modes I, II and III) by covalently immobilizing HRP-mimicking DNAzyme

  18. [Preparation and Performance of Ultrafast γ-CuI Scintillation Conversion Screen].

    PubMed

    Xia, Ming; Gu, Mu; Liu, Xiao-lin; Liu, Bo; Huang, Shi-ming; Ni, Chen

    2015-04-01

    Micro-columnar structured γ-CuI scintillation conversion screen with columnar diameter in the micrometer and thickness about 17 µm were prepared by thermal evaporation method on quartz substrates with different temperatures. X-ray excited luminescence spectra of the screens show two peaks located at 430 nm and near 700 nm, which correspond to the fast and slow emission components, respectively. The fast one dominated. The intensity of 430 nm peak decreased as the substrate temperature rose from 170 °C to 210 °C. At the same time the intensity of 700 nm band increased. The changes may be attributed to the iodine loss from screen caused by the substrate temperature. The phenomenon of iodine loss was observed by the Rutherford backscattering experiment. The crystal structure of the screens presents (111) preferred orientation, which is independent of the substrate temperature. As the temperature rose to 210 °C, two weak additional peaks of (220) and (420) γ-CuI crystal planes in X-ray diffraction patterns appeared due to the increase in kinetic energy of CuI molecules. The scanning electron microscopy images of the screens showed that the columnar structure was improved when the substrate temperature increased from 170 °C to 190 °C, but it would be degenerated when the temperature continued to rise to 210 °C because of the surface and bulk diffusion effects of the depositing molecules. Finally, the spatial resolution of the γ-CuI scintillation screens was measured by knife-edge method, and they are 4.5, 7.2 and 5.6lp · mm(-1) for the screens prepared at the substrates temperatures of 170, 190 and 210 °C, respectively. The result shows that micro-column structure could improve the spatial resolution of γ-CuI scintillation screen.

  19. Semiconductor films on flexible iridium substrates

    DOEpatents

    Goyal, Amit

    2005-03-29

    A laminate semiconductor article includes a flexible substrate, an optional biaxially textured oxide buffer system on the flexible substrate, a biaxially textured Ir-based buffer layer on the substrate or the buffer system, and an epitaxial layer of a semiconductor. Ir can serve as a substrate with an epitaxial layer of a semiconductor thereon.

  20. Adhesion of single- and multi-walled carbon nanotubes to silicon substrate: atomistic simulations and continuum analysis

    NASA Astrophysics Data System (ADS)

    Yuan, Xuebo; Wang, Youshan

    2017-10-01

    The radial deformation of carbon nanotubes (CNTs) adhering to a substrate may prominently affect their mechanical and physical properties. In this study, both classical atomistic simulations and continuum analysis are carried out, to investigate the lateral adhesion of single-walled CNTs (SWCNTs) and multi-walled CNTs (MWCNTs) to a silicon substrate. A linear elastic model for analyzing the adhesion of 2D shells to a rigid semi-infinite substrate is constructed in the framework of continuum mechanics. Good agreement is achieved between the cross-section profiles of adhesive CNTs obtained by the continuum model and by the atomistic simulation approach. It is found that the adhesion of a CNT to the silicon substrate is significantly influenced by its initial diameter and the number of walls. CNTs with radius larger than a certain critical radius are deformed radially on the silicon substrate with flat contact regions. With increasing number of walls, the extent of radial deformation of a MWCNT on the substrate decreases dramatically, and the flat contact area reduces—and eventually vanishes—due to increasing equivalent bending stiffness. It is analytically predicted that large-diameter MWCNTs with a large number of walls are likely to ‘stand’ on the silicon substrate. The present work can be useful for understanding the radial deformation of CNTs adhering to a solid planar substrate.

  1. Amending pine bark with alternative substrates

    USDA-ARS?s Scientific Manuscript database

    Due to a number of factors, pine bark supplies have significantly decreased over the past few years. While alternative substrates are being evaluated, many growers are asking if these alternative substrates can be used to stretch existing PB supplies. In this study, two alternative substrates, “Cl...

  2. Bacterial growth and substrate degradation by BTX-oxidizing culture in response to salt stress.

    PubMed

    Lee, Chi-Yuan; Lin, Ching-Hsing

    2006-01-01

    Interactions between microbial growth and substrate degradation are important in determining the performance of trickle-bed bioreactors (TBB), especially when salt is added to reduce biomass formation in order to alleviate media clogging. This study was aimed at quantifying salinity effects on bacterial growth and substrate degradation, and at acquiring kinetic information in order to improve the design and operation of TBB. Experiment works began by cultivating a mixed culture in a chemostat reactor receiving artificial influent containing a mixture of benzene, toluene, and xylene (BTX), followed by using the enrichment culture to degrade the individual BTX substrates under a particular salinity, which ranged 0-50 g l(-1) in batch mode. Then, the measured concentrations of biomass and residual substrate versus time were analyzed with the microbial kinetics; moreover, the obtained microbial kinetic constants under various salinities were modeled using noncompetitive inhibition kinetics. For the three substrates the observed bacterial yields appeared to be decreased from 0.51-0.74 to 0.20-0.22 mg mg(-1) and the maximum specific rate of substrate utilization, q, declined from 0.25-0.42 to 0.07-0.11 h(-1), as the salinity increased from 0 to 50 NaCl g l(-1). The NaCl acted as noncompetitive inhibitor, where the modeling inhibitions of the coefficients, K ( T(S)), were 22.7-29.7 g l(-1) for substrate degradation and K ( T(mu)), 13.0-19.0 g l(-1), for biomass formation. The calculated ratios for the bacterial maintenance rate, m (S), to q, further indicated that the percentage energy spent on maintenance increased from 19-24 to 86-91% as salinity level increased from 0 to 50 g l(-1). These results revealed that the bacterial growth was more inhibited than substrate degradation by the BTX oxidizers under the tested salinity levels. The findings from this study demonstrate the potential of applying NaCl salt to control excessive biomass formation in biotrickling filters.

  3. Boiling regimes of impacting drops on a heated substrate under reduced pressure

    NASA Astrophysics Data System (ADS)

    van Limbeek, Michiel A. J.; Hoefnagels, Paul B. J.; Shirota, Minori; Sun, Chao; Lohse, Detlef

    2018-05-01

    We experimentally investigate the boiling behavior of impacting ethanol drops on a heated smooth sapphire substrate at pressures ranging from P =0.13 bar to atmospheric pressure. We employ frustrated total internal reflection imaging to study the wetting dynamics of the contact between the drop and the substrate. The spreading drop can be in full contact (contact boiling), it can partially touch (transition boiling), or the drop can be fully levitated (Leidenfrost boiling). We show that the temperature of the boundary between contact and transition boiling shows at most a weak dependence on the impact velocity, but a significant decrease with decreasing ambient gas pressure. A striking correspondence is found between the temperature of this boundary and the static Leidenfrost temperature for all pressures. We therefore conclude that both phenomena share the same mechanism and are dominated by the dynamics taking place at the contact line. On the other hand, the boundary between transition boiling and Leidenfrost boiling, i.e., the dynamic Leidenfrost temperature, increases for increasing impact velocity for all ambient gas pressures. Moreover, the dynamic Leidenfrost temperature coincides for pressures between P =0.13 and 0.54 bar, whereas for atmospheric pressure the dynamic Leidenfrost temperature is slightly elevated. This indicates that the dynamic Leidenfrost temperature is at most weakly dependent on the enhanced evaporation by the lower saturation temperature of the liquid.

  4. HIV-1 RT Inhibitors with a Novel Mechanism of Action: NNRTIs that Compete with the Nucleotide Substrate

    PubMed Central

    Maga, Giovanni; Radi, Marco; Gerard, Marie-Aline; Botta, Maurizio; Ennifar, Eric

    2010-01-01

    HIV-1 reverse transcriptase (RT) inhibitors currently used in antiretroviral therapy can be divided into two classes: (i) nucleoside analog RT inhibitors (NRTIs), which compete with natural nucleoside substrates and act as terminators of proviral DNA synthesis, and (ii) non-nucleoside RT inhibitors (NNRTIs), which bind to a hydrophobic pocket close to the RT active site. In spite of the efficiency of NRTIs and NNRTIs, the rapid emergence of multidrug-resistant mutations requires the development of new RT inhibitors with an alternative mechanism of action. Recently, several studies reported the discovery of novel non-nucleoside inhibitors with a distinct mechanism of action. Unlike classical NNRTIs, they compete with the nucleotide substrate, thus forming a new class of RT inhibitors: nucleotide-competing RT inhibitors (NcRTIs). In this review, we discuss current progress in the understanding of the peculiar behavior of these compounds. PMID:21994659

  5. Stress Corrosion Cracking Susceptibility of 304L Substrate and 308L Weld Metal Exposed to a Salt Spray

    PubMed Central

    Hsu, Chia-Hao; Chen, Tai-Cheng; Huang, Rong-Tan; Tsay, Leu-Wen

    2017-01-01

    304 stainless steels (SS) were considered as the materials for a dry storage canister. In this study, ER (Electrode Rod) 308L was utilized as the filler metal for the groove and overlay welds of a 304L stainless steel substrate, which was prepared via a gas tungsten arc-welding process in multiple passes. The electron backscatter diffraction (EBSD) map was used to identify the inherent microstructures in distinct specimens. U-bend and weight-loss tests were conducted by testing the 304L substrates and welds in a salt spray containing 5 wt % NaCl at 80 °C to evaluate their susceptibility to stress corrosion cracking (SCC). Generally, the weight loss of the ER 308L deposit was higher than that of the 304L substrate in a salt spray in the same sample-prepared condition. The dissolution of the skeletal structure in the fusion zone (FZ) was responsible for a greater weight loss of the 308L deposit, especially for the cold-rolled and sensitized specimen. Cold rolling was detrimental and sensitization after cold rolling was very harmful to the SCC resistance of the 304L substrate and 308L deposit. Overall, the SCC susceptibility of each specimen was correlated with its weight loss in each group. PMID:28772547

  6. Substrate-bound structure of the E. coli multidrug resistance transporter MdfA

    PubMed Central

    Heng, Jie; Zhao, Yan; Liu, Ming; Liu, Yue; Fan, Junping; Wang, Xianping; Zhao, Yongfang; Zhang, Xuejun C

    2015-01-01

    Multidrug resistance is a serious threat to public health. Proton motive force-driven antiporters from the major facilitator superfamily (MFS) constitute a major group of multidrug-resistance transporters. Currently, no reports on crystal structures of MFS antiporters in complex with their substrates exist. The E. coli MdfA transporter is a well-studied model system for biochemical analyses of multidrug-resistance MFS antiporters. Here, we report three crystal structures of MdfA-ligand complexes at resolutions up to 2.0 Å, all in the inward-facing conformation. The substrate-binding site sits proximal to the conserved acidic residue, D34. Our mutagenesis studies support the structural observations of the substrate-binding mode and the notion that D34 responds to substrate binding by adjusting its protonation status. Taken together, our data unveil the substrate-binding mode of MFS antiporters and suggest a mechanism of transport via this group of transporters. PMID:26238402

  7. Substituent effect on the oxidation of phenols and aromatic amines by horseradish peroxidase compound I.

    PubMed

    Job, D; Dunford, H B

    1976-07-15

    A stopped-flow kinetic study shows that the reduction rate of horseradish peroxidase compound I by phenols and aromatic amines is greatly dependent upon the substituent effect on the benzene ring. Morever it has been possible to relate the reduction rate constants of monosubstituted substrates by a linear free-energy relationship (Hammett equation). The correlation of log (rate constants) with sigma values (Hammett equation) and the absence of correlation with sigma+ values (Okamoto-Brown equation) can be explained by a mechanism of aromatic substrate oxidations, in which the substrate gives an electron to the enzyme compound I and simultaneously loses a proton. The analogy which has been made with oxidation potentials of phenols or anilines strengthens the view that the reaction is only dependent on the relative ease of oxidation of the substrate. The rate constant obtained for p-aminophenol indicates that a value of 2.3 X 10(8) M-1 S-1 probably approaches the diffusion-controlled limit for a bimolecular reaction involving compound I and an aromatic substrate.

  8. A Mechanistic Pharmacokinetic Model for Liver Transporter Substrates Under Liver Cirrhosis Conditions

    PubMed Central

    Li, R; Barton, HA; Maurer, TS

    2015-01-01

    Liver cirrhosis is a disease characterized by the loss of functional liver mass. Physiologically based pharmacokinetic (PBPK) modeling was applied to interpret and predict how the interplay among physiological changes in cirrhosis affects pharmacokinetics. However, previous PBPK models under cirrhotic conditions were developed for permeable cytochrome P450 substrates and do not directly apply to substrates of liver transporters. This study characterizes a PBPK model for liver transporter substrates in relation to the severity of liver cirrhosis. A published PBPK model structure for liver transporter substrates under healthy conditions and the physiological changes for cirrhosis are combined to simulate pharmacokinetics of liver transporter substrates in patients with mild and moderate cirrhosis. The simulated pharmacokinetics under liver cirrhosis reasonably approximate observations. This analysis includes meta-analysis to obtain system-dependent parameters in cirrhosis patients and a top-down approach to improve understanding of the effect of cirrhosis on transporter-mediated drug disposition under cirrhotic conditions. PMID:26225262

  9. Effect of External Electric Field on Substrate Transport of a Secondary Active Transporter.

    PubMed

    Zhang, Ji-Long; Zheng, Qing-Chuan; Yu, Li-Ying; Li, Zheng-Qiang; Zhang, Hong-Xing

    2016-08-22

    Substrate transport across a membrane accomplished by a secondary active transporter (SAT) is essential to the normal physiological function of living cells. In the present research, a series of all-atom molecular dynamics (MD) simulations under different electric field (EF) strengths was performed to investigate the effect of an external EF on the substrate transport of an SAT. The results show that EF both affects the interaction between substrate and related protein's residues by changing their conformations and tunes the timeline of the transport event, which collectively reduces the height of energy barrier for substrate transport and results in the appearance of two intermediate conformations under the existence of an external EF. Our work spotlights the crucial influence of external EFs on the substrate transport of SATs and could provide a more penetrating understanding of the substrate transport mechanism of SATs.

  10. Methylene blue stimulates substrate-level phosphorylation catalysed by succinyl-CoA ligase in the citric acid cycle.

    PubMed

    Komlódi, T; Tretter, L

    2017-09-01

    Methylene blue (MB), a potential neuroprotective agent, is efficient in various neurodegenerative disease models. Beneficial effects of MB have been attributed to improvements in mitochondrial functions. Substrate-level phosphorylation (SLP) results in the production of ATP independent from the ATP synthase (ATP-ase). In energetically compromised mitochondria, ATP produced by SLP can prevent the reversal of the adenine nucleotide translocase and thus the hydrolysis of glycolytic ATP. The aim of the present study was to investigate the effect of MB on mitochondrial SLP catalysed by succinyl-CoA ligase. Measurements were carried out on isolated guinea pig cortical mitochondria respiring on α-ketoglutarate, glutamate, malate or succinate. The mitochondrial functions and parameters like ATP synthesis, oxygen consumption, membrane potential, and NAD(P)H level were followed online, in parallel with the redox state of MB. SLP-mediated ATP synthesis was measured in the presence of inhibitors for ATP-ase and adenylate kinase. In the presence of the ATP-ase inhibitor oligomycin MB stimulated respiration with all of the respiratory substrates. However, the rate of ATP synthesis increased only with substrates α-ketoglutarate and glutamate (forming succinyl-CoA). MB efficiently stimulated SLP and restored the membrane potential in mitochondria also with the combined inhibition of Complex I and ATP synthase. ATP formed by SLP alleviated the energetic insufficiency generated by the lack of oxidative phosphorylation. Thus, the MB-mediated stimulation of SLP might be important in maintaining the energetic competence of mitochondria and in preventing the mitochondrial hydrolysis of glycolytic ATP. The mitochondrial effects of MB are explained by the ability to accept electrons from reducing equivalents and transfer them to cytochrome c bypassing the respiratory Complexes I and III. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. Substrate-binding specificity of chitinase and chitosanase as revealed by active-site architecture analysis.

    PubMed

    Liu, Shijia; Shao, Shangjin; Li, Linlin; Cheng, Zhi; Tian, Li; Gao, Peiji; Wang, Lushan

    2015-12-11

    Chitinases and chitosanases, referred to as chitinolytic enzymes, are two important categories of glycoside hydrolases (GH) that play a key role in degrading chitin and chitosan, two naturally abundant polysaccharides. Here, we investigate the active site architecture of the major chitosanase (GH8, GH46) and chitinase families (GH18, GH19). Both charged (Glu, His, Arg, Asp) and aromatic amino acids (Tyr, Trp, Phe) are observed with higher frequency within chitinolytic active sites as compared to elsewhere in the enzyme structure, indicating significant roles related to enzyme function. Hydrogen bonds between chitinolytic enzymes and the substrate C2 functional groups, i.e. amino groups and N-acetyl groups, drive substrate recognition, while non-specific CH-π interactions between aromatic residues and substrate mainly contribute to tighter binding and enhanced processivity evident in GH8 and GH18 enzymes. For different families of chitinolytic enzymes, the number, type, and position of substrate atoms bound in the active site vary, resulting in different substrate-binding specificities. The data presented here explain the synergistic action of multiple enzyme families at a molecular level and provide a more reasonable method for functional annotation, which can be further applied toward the practical engineering of chitinases and chitosanases. Copyright © 2015 Elsevier Ltd. All rights reserved.

  12. Gold Nanoparticle Labels and Heterogeneous Immunoassays: The Case for the Inverted Substrate.

    PubMed

    Crawford, Alexis C; Young, Colin C; Porter, Marc D

    2018-06-15

    This paper examines how the difference in the spatial orientation of the capture substrate influences the analytical sensitivity and limits of detection for immunoassays that use gold nanoparticle labels (AuNPs) and rely on diffusion in quiet solution in the antigen capture and labeling steps. Ideally, the accumulation of both reactants should follow a dependence governed by the rate in which diffusion delivers reactants to the capture surface. In other words, the accumulation of reactants should increase with the square root of the incubation time, i.e., t1/2. The work herein shows, however, that this expectation is only obeyed when the capture substrate is oriented to direct the gravity-induced sedimentation of the AuNP labels away from the substrate. Using an assay for human IgG, the results show that circumventing the sedimentation of the gold nanoparticle labels by substrate inversion enables the dependence of the labeling step on diffusion, reduces nonspecific label adsorption, and improves the estimated detection limit by ~30×. High-density maps of the signal across the two types of substrates also demonstrate that inversion in the labeling step results in a more uniform distribution of AuNP labels across the surface, which translates to a greater measurement reproducibility. These results, which are supported by model simulations via the Mason-Weaver sedimentation-diffusion equation, and their potential implications when using other nanoparticle labels and related materials in diagnostic tests and other applications, are briefly discussed.

  13. Quantitative isotope incorporation reveals substrate partitioning in a coastal microbial community.

    PubMed

    Mayali, Xavier; Weber, Peter K

    2018-05-01

    To quantitatively link microbial identity with biogeochemical function, we carried out 14 simultaneous stable isotope probing experiments with organic and inorganic C and N substrates to measure the isotope incorporation by over one hundred co-occurring eukaryotic and prokaryotic populations in a coastal community. We found that nitrate was the most commonly incorporated substrate, and that light-driven carbon fixation was carried out by some bacterial taxa from the Flavobacteriales and OM60 (NOR5) clade, in addition to photoautotrophic phytoplankton. We found that organisms that incorporated starch, maltose, glucose, lactose and bicarbonate were phylogenetically clustered, suggesting that specific bacterial lineages specialized in the incorporation of these substrates. The data further revealed that coastal microorganisms spanned a range of resource utilization strategies from generalists to specialists and demonstrated a high level of substrate partitioning, with two thirds of taxa exhibiting unique substrate incorporation patterns and the remaining third shared by no more than three OTUs each. Specialists exhibited more extreme incorporation levels (high or low), whereas generalists displayed more intermediate activity levels. These results shed valuable insights into the bottom-up ecological strategies enabling the persistence of high microbial diversity in aquatic ecosystems.

  14. Impact resistance performance of diamond film on a curved molybdenum substrate

    NASA Astrophysics Data System (ADS)

    Chen, Yang; Gou, Li

    2017-08-01

    Diamond films with different thicknesses were deposited on flat and curved molybdenum substrate by the microwave plasma chemical vapour deposition (MPCVD) method. Scanning electronic microscopy, atomic force microscopy and Raman spectroscopy were employed to characterise the morphology, the surface roughness and the composition of the films, respectively. A NanoTest system was used for hardness, elastic modulus and nanoimpact tests. The curved surface and ductility of the molybdenum substrate allow large deformation for the thinner films. The substrate has less effect on impact for the thicker film, the deformation of which is mainly determined by the film composition. Under a load of 50 mN and 75 cycles, less deformation occurred for the 22 μm thick film on the curved molybdenum substrate.

  15. Masking ability of a zirconia ceramic on composite resin substrate shades.

    PubMed

    Tabatabaian, Farhad; Shabani, Sima; Namdari, Mahshid; Sadeghpour, Koroush

    2017-01-01

    Masking ability of a restorative material plays an important role to cover discolored tooth structure; however, this ability has not yet been well understood in zirconia-based restorations. This study assessed the masking ability of a zirconia ceramic on composite resin substrates with different shades. Ten zirconia disc specimens, with 0.5 mm thickness and 10 mm diameter, were fabricated by a computer-aided design/computer-aided manufacturing system. A white substrate (control) and six composite resin substrates with different shades including A1, A2, A3, B2, C2, and D3 were prepared. The substrates had a cylindrical shape with 10 mm diameter and height. The specimens were placed onto the substrates for spectrophotometric evaluation. A spectrophotometer measured the L*, a*, and b* values for the specimens. ΔE values were calculated to determine the color differences between the groups and the control and then were compared with a perceptional threshold (ΔE = 2.6). Repeated measures ANOVA and Bonferroni tests were used for data analysis ( P < 0.05). The mean and standard deviation of ΔE values for A1, A2, A3, B2, C2, and D3 groups were 6.78 ± 1.59, 8.13 ± 1.66, 9.81 ± 2.64, 9.61 ± 1.38, 9.59 ± 2.63, and 8.13 ± 1.89, respectively. A significant difference was found among the groups in the ΔE values ( P = 0.006). The ΔE values were more than the perceptional threshold in all the groups ( P < 0.0001). Within the limitations of this study, it can be concluded that the tested zirconia ceramic could not thoroughly mask different shades of the composite resin substrates. Moreover, color masking of zirconia depends on the shade of substrate.

  16. Effects of Substrate Addition on Soil Respiratory Carbon Release Under Long-Term Warming and Clipping in a Tallgrass Prairie

    PubMed Central

    Jia, Xiaohong; Zhou, Xuhui; Luo, Yiqi; Xue, Kai; Xue, Xian; Xu, Xia; Yang, Yuanhe; Wu, Liyou; Zhou, Jizhong

    2014-01-01

    Regulatory mechanisms of soil respiratory carbon (C) release induced by substrates (i.e., plant derived substrates) are critical for predicting ecosystem responses to climate change, but the mechanisms are not well understood. In this study, we sampled soils from a long-term field manipulative experiment and conducted a laboratory incubation to explore the role of substrate supply in regulating the differences in soil C release among the experimental treatments, including control, warming, clipping, and warming plus clipping. Three types of substrates (glucose, C3 and C4 plant materials) were added with an amount equal to 1% of soil dry weight under the four treatments. We found that the addition of all three substrates significantly stimulated soil respiratory C release in all four warming and clipping treatments. In soils without substrate addition, warming significantly stimulated soil C release but clipping decreased it. However, additions of glucose and C3 plant materials (C3 addition) offset the warming effects, whereas C4 addition still showed the warming-induced stimulation of soil C release. Our results suggest that long-term warming may inhibit microbial capacity for decomposition of C3 litter but may enhance it for decomposition of C4 litter. Such warming-induced adaptation of microbial communities may weaken the positive C-cycle feedback to warming due to increased proportion of C4 species in plant community and decreased litter quality. In contrast, clipping may weaken microbial capacity for warming-induced decomposition of C4 litter but may enhance it for C3 litter. Warming- and clipping-induced shifts in microbial metabolic capacity may be strongly associated with changes in plant species composition and could substantially influence soil C dynamics in response to global change. PMID:25490701

  17. Effects of substrate addition on soil respiratory carbon release under long-term warming and clipping in a tallgrass prairie.

    PubMed

    Jia, Xiaohong; Zhou, Xuhui; Luo, Yiqi; Xue, Kai; Xue, Xian; Xu, Xia; Yang, Yuanhe; Wu, Liyou; Zhou, Jizhong

    2014-01-01

    Regulatory mechanisms of soil respiratory carbon (C) release induced by substrates (i.e., plant derived substrates) are critical for predicting ecosystem responses to climate change, but the mechanisms are not well understood. In this study, we sampled soils from a long-term field manipulative experiment and conducted a laboratory incubation to explore the role of substrate supply in regulating the differences in soil C release among the experimental treatments, including control, warming, clipping, and warming plus clipping. Three types of substrates (glucose, C3 and C4 plant materials) were added with an amount equal to 1% of soil dry weight under the four treatments. We found that the addition of all three substrates significantly stimulated soil respiratory C release in all four warming and clipping treatments. In soils without substrate addition, warming significantly stimulated soil C release but clipping decreased it. However, additions of glucose and C3 plant materials (C3 addition) offset the warming effects, whereas C4 addition still showed the warming-induced stimulation of soil C release. Our results suggest that long-term warming may inhibit microbial capacity for decomposition of C3 litter but may enhance it for decomposition of C4 litter. Such warming-induced adaptation of microbial communities may weaken the positive C-cycle feedback to warming due to increased proportion of C4 species in plant community and decreased litter quality. In contrast, clipping may weaken microbial capacity for warming-induced decomposition of C4 litter but may enhance it for C3 litter. Warming- and clipping-induced shifts in microbial metabolic capacity may be strongly associated with changes in plant species composition and could substantially influence soil C dynamics in response to global change.

  18. Soft lithography using perfluorinated polyether molds and PRINT technology for fabrication of 3-D arrays on glass substrates

    NASA Astrophysics Data System (ADS)

    Wiles, Kenton B.; Wiles, Natasha S.; Herlihy, Kevin P.; Maynor, Benjamin W.; Rolland, Jason P.; DeSimone, Joseph M.

    2006-03-01

    The fabrication of nanometer size structures and complex devices for microelectronics is of increasing importance so as to meet the challenges of large-scale commercial applications. Soft lithography typically employs elastomeric polydimethylsiloxane (PDMS) molds to replicate micro- and nanoscale features. However, the difficulties of PDMS for nanoscale fabrication include inherent incompatibility with organic liquids and the production of a residual scum or flash layer that link features where the nano-structures meet the substrate. An emerging technologically advanced technique known as Pattern Replication in Non-wetting Templates (PRINT) avoids both of these dilemmas by utilizing photocurable perfluorinated polyether (PFPE) rather than PDMS as the elastomeric molding material. PFPE is a liquid at room temperature that exhibits low modulus and high gas permeability when cured. The highly fluorinated PFPE material allows for resistance to swelling by organic liquids and very low surface energies, thereby preventing flash layer formation and ease of separation of PFPE molds from the substrates. These enhanced characteristics enable easy removal of the stamp from the molded material, thereby minimizing damage to the nanoscale features. Herein we describe that PRINT can be operated in two different modes depending on whether the objects to be molded are to be removed and harvested (i.e. to make shape specific organic particles) or whether scum free objects are desired which are adhered onto the substrate (i.e. for scum free pattern generation using imprint lithography). The former can be achieved using a non-reactive, low surface energy substrate (PRINT: Particle Replication in Non-wetting Templates) and the latter can be achieved using a reactive, low surface energy substrate (PRINT: Pattern Replication in Non-wetting Templates). We show that the PRINT technology can been used to fabricate nano-particle arrays covalently bound to a glass substrate with no scum layer

  19. Is substrate composition a suitable predictor for deep-water coral occurrence on fine scales?

    NASA Astrophysics Data System (ADS)

    Bennecke, Swaantje; Metaxas, Anna

    2017-06-01

    Species distribution modelling can be applied to identify potentially suitable habitat for species with largely unknown distributions, such as many deep-water corals. Important variables influencing species occurrence in the deep sea, e.g. substrate composition, are often not included in these modelling approaches because high-resolution data are unavailable. We investigated the relationship between substrate composition and the occurrence of the two deep-water octocoral species Primnoa resedaeformis and Paragorgia arborea, which require hard substrate for attachment. On a scale of 10s of metres, we analysed images of the seafloor taken at two locations inside the Northeast Channel Coral Conservation Area in the Northwest Atlantic. We interpolated substrate composition over the sampling areas and determined the contribution of substrate classes, depth and slope to describe habitat suitability using maximum entropy modelling (Maxent). Substrate composition was similar at both sites - dominated by pebbles in a matrix of sand (>80%) with low percentages of suitable substrate for coral occurrence. Coral abundance was low at site 1 (0.9 colonies of P. resedaeformis per 100 m2) and high at site 2 (63 colonies of P. resedaeformis per 100 m2) indicating that substrate alone is not sufficient to explain varying patterns in coral occurrence. Spatial interpolations of substrate classes revealed the difficulty to accurately resolve sparsely distributed boulders (3-5% of substrate). Boulders were by far the most important variable in the habitat suitability model (HSM) for P. resedaeformis at site 1, indicating the fundamental influence of a substrate class that is the least abundant. At site 2, HSMs identified cobbles and sand/pebble as the most important variables for habitat suitability. However, substrate classes were correlated making it difficult to determine the influence of individual variables. To provide accurate information on habitat suitability for the two coral

  20. Choosing co-substrates to supplement biogas production from animal slurry--a life cycle assessment of the environmental consequences.

    PubMed

    Croxatto Vega, Giovanna Catalina; ten Hoeve, Marieke; Birkved, Morten; Sommer, Sven G; Bruun, Sander

    2014-11-01

    Biogas production from animal slurry can provide substantial contributions to reach renewable energy targets, yet due to the low methane potential of slurry, biogas plants depend on the addition of co-substrates to make operations profitable. The environmental performance of three underexploited co-substrates, straw, organic household waste and the solid fraction of separated slurry, were assessed against slurry management without biogas production, using LCA methodology. The analysis showed straw, which would have been left on arable fields, to be an environmentally superior co-substrate. Due to its low nutrient content and high methane potential, straw yields the lowest impacts for eutrophication and the highest climate change and fossil depletion savings. Co-substrates diverted from incineration to biogas production had fewer environmental benefits, due to the loss of energy production, which is then produced from conventional fossil fuels. The scenarios can often provide benefits for one impact category while causing impacts in another. Copyright © 2014 Elsevier Ltd. All rights reserved.