Revisiting the Nucleotide and Aminoglycoside Substrate Specificity of the Bifunctional Aminoglycoside Acetyltransferase(6′)-Ie/Aminoglycoside Phosphotransferase(2″)-Ia Enzyme*

PubMed Central

Frase, Hilary; Toth, Marta; Vakulenko, Sergei B.

2012-01-01

The bifunctional aminoglycoside-modifying enzyme aminoglycoside acetyltransferase(6′)-Ie/aminoglycoside phosphotransferase(2″)-Ia, or AAC(6′)-Ie/APH(2″)-Ia, is the major source of aminoglycoside resistance in Gram-positive bacterial pathogens. In previous studies, using ATP as the cosubstrate, it was reported that the APH(2″)-Ia domain of this enzyme is unique among aminoglycoside phosphotransferases, having the ability to inactivate an unusually broad spectrum of aminoglycosides, including 4,6- and 4,5-disubstituted and atypical. We recently demonstrated that GTP, and not ATP, is the preferred cosubstrate of this enzyme. We now show, using competition assays between ATP and GTP, that GTP is the exclusive phosphate donor at intracellular nucleotide levels. In light of these findings, we reevaluated the substrate profile of the phosphotransferase domain of this clinically important enzyme. Steady-state kinetic characterization using the phosphate donor GTP demonstrates that AAC(6′)-Ie/APH(2″)-Ia phosphorylates 4,6-disubstituted aminoglycosides with high efficiency (kcat/Km = 105-107 m−1 s−1). Despite this proficiency, no resistance is conferred to some of these antibiotics by the enzyme in vivo. We now show that phosphorylation of 4,5-disubstituted and atypical aminoglycosides are negligible and thus these antibiotics are not substrates. Instead, these aminoglycosides tend to stimulate an intrinsic GTPase activity of the enzyme. Taken together, our data show that the bifunctional enzyme efficiently phosphorylates only 4,6-disubstituted antibiotics; however, phosphorylation does not necessarily result in bacterial resistance. Hence, the APH(2″)-Ia domain of the bifunctional AAC(6′)-Ie/APH(2″)-Ia enzyme is a bona fide GTP-dependent kinase with a narrow substrate profile, including only 4,6-disubstituted aminoglycosides. PMID:23115238

Chromosome-Encoded Broad-Spectrum Ambler Class A β-Lactamase RUB-1 from Serratia rubidaea

PubMed Central

Didi, Jennifer; Ergani, Ayla; Lima, Sandra

2016-01-01

ABSTRACT Whole-genome sequencing of Serratia rubidaea CIP 103234T revealed a chromosomally located Ambler class A β-lactamase gene. The gene was cloned, and the β-lactamase, RUB-1, was characterized. RUB-1 displayed 74% and 73% amino acid sequence identity with the GIL-1 and TEM-1 penicillinases, respectively, and its substrate profile was similar to that of the latter β-lactamases. Analysis by 5′ rapid amplification of cDNA ends revealed promoter sequences highly divergent from the Escherichia coli σ70 consensus sequence. This work further illustrates the heterogeneity of β-lactamases among Serratia spp. PMID:27956418

Chromosome-Encoded Broad-Spectrum Ambler Class A β-Lactamase RUB-1 from Serratia rubidaea.

PubMed

Bonnin, Rémy A; Didi, Jennifer; Ergani, Ayla; Lima, Sandra; Naas, Thierry

2017-02-01

Whole-genome sequencing of Serratia rubidaea CIP 103234 T revealed a chromosomally located Ambler class A β-lactamase gene. The gene was cloned, and the β-lactamase, RUB-1, was characterized. RUB-1 displayed 74% and 73% amino acid sequence identity with the GIL-1 and TEM-1 penicillinases, respectively, and its substrate profile was similar to that of the latter β-lactamases. Analysis by 5' rapid amplification of cDNA ends revealed promoter sequences highly divergent from the Escherichia coli σ 70 consensus sequence. This work further illustrates the heterogeneity of β-lactamases among Serratia spp. Copyright © 2017 American Society for Microbiology.

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

Nazareth, A.S.; Sood, D.K.; Zmood, R.B.

A focusing grid broad beam Kaufman source, using argon ions on a target of nominal composition Nd{sub 2}Fe{sub 14}B has been employed to sputter deposit magnetic thin films of thicknesses ranging from 800 {angstrom} to 1300 {angstrom} on silicon-(111) substrates at room temperature. These films were characterized for their composition depth profile by Rutherford Backscattering Spectroscopy, while x-ray diffraction was used to study the crystallographic structure. Due to a close match between (111) Si with (220) Nd{sub 2}Fe{sub 14}B lattice spacings, preferred crystallographic texturing was expected, and experimental results showed a greatly enhanced (220) texture. The degradation in magnetic propertiesmore » was attributed to the presence of oxygen in the films as indicated by concentration depth profiles. It is premised that another significant role of oxygen may be to relieve the misfit strain across the interface by its incorporation within the Nd{sub 2}Fe{sub 14}B phase.« less

Substrate Profile and Metal-ion Selectivity of Human Divalent Metal-ion Transporter-1*

PubMed Central

Illing, Anthony C.; Shawki, Ali; Cunningham, Christopher L.; Mackenzie, Bryan

2012-01-01

Divalent metal-ion transporter-1 (DMT1) is a H+-coupled metal-ion transporter that plays essential roles in iron homeostasis. DMT1 exhibits reactivity (based on evoked currents) with a broad range of metal ions; however, direct measurement of transport is lacking for many of its potential substrates. We performed a comprehensive substrate-profile analysis for human DMT1 expressed in RNA-injected Xenopus oocytes by using radiotracer assays and the continuous measurement of transport by fluorescence with the metal-sensitive PhenGreen SK fluorophore. We provide validation for the use of PhenGreen SK fluorescence quenching as a reporter of cellular metal-ion uptake. We determined metal-ion selectivity under fixed conditions using the voltage clamp. Radiotracer and continuous measurement of transport by fluorescence assays revealed that DMT1 mediates the transport of several metal ions that were ranked in selectivity by using the ratio Imax/K0.5 (determined from evoked currents at −70 mV): Cd2+ > Fe2+ > Co2+, Mn2+ ≫ Zn2+, Ni2+, VO2+. DMT1 expression did not stimulate the transport of Cr2+, Cr3+, Cu+, Cu2+, Fe3+, Ga3+, Hg2+, or VO+. 55Fe2+ transport was competitively inhibited by Co2+ and Mn2+. Zn2+ only weakly inhibited 55Fe2+ transport. Our data reveal that DMT1 selects Fe2+ over its other physiological substrates and provides a basis for predicting the contribution of DMT1 to intestinal, nasal, and pulmonary absorption of metal ions and their cellular uptake in other tissues. Whereas DMT1 is a likely route of entry for the toxic heavy metal cadmium, and may serve the metabolism of cobalt, manganese, and vanadium, we predict that DMT1 should contribute little if at all to the absorption or uptake of zinc. The conclusion in previous reports that copper is a substrate of DMT1 is not supported. PMID:22736759

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.

Insights into the evolution of enzyme substrate promiscuity after the discovery of (βα)₈ isomerase evolutionary intermediates from a diverse metagenome.

PubMed

Noda-García, Lianet; Juárez-Vázquez, Ana L; Ávila-Arcos, María C; Verduzco-Castro, Ernesto A; Montero-Morán, Gabriela; Gaytán, Paul; Carrillo-Tripp, Mauricio; Barona-Gómez, Francisco

2015-06-10

Current sequence-based approaches to identify enzyme functional shifts, such as enzyme promiscuity, have proven to be highly dependent on a priori functional knowledge, hampering our ability to reconstruct evolutionary history behind these mechanisms. Hidden Markov Model (HMM) profiles, broadly used to classify enzyme families, can be useful to distinguish between closely related enzyme families with different specificities. The (βα)8-isomerase HisA/PriA enzyme family, involved in L-histidine (HisA, mono-substrate) biosynthesis in most bacteria and plants, but also in L-tryptophan (HisA/TrpF or PriA, dual-substrate) biosynthesis in most Actinobacteria, has been used as model system to explore evolutionary hypotheses and therefore has a considerable amount of evolutionary, functional and structural knowledge available. We searched for functional evolutionary intermediates between the HisA and PriA enzyme families in order to understand the functional divergence between these families. We constructed a HMM profile that correctly classifies sequences of unknown function into the HisA and PriA enzyme sub-families. Using this HMM profile, we mined a large metagenome to identify plausible evolutionary intermediate sequences between HisA and PriA. These sequences were used to perform phylogenetic reconstructions and to identify functionally conserved amino acids. Biochemical characterization of one selected enzyme (CAM1) with a mutation within the functionally essential N-terminus phosphate-binding site, namely, an alanine instead of a glycine in HisA or a serine in PriA, showed that this evolutionary intermediate has dual-substrate specificity. Moreover, site-directed mutagenesis of this alanine residue, either backwards into a glycine or forward into a serine, revealed the robustness of this enzyme. None of these mutations, presumably upon functionally essential amino acids, significantly abolished its enzyme activities. A truncated version of this enzyme (CAM2) predicted to adopt a (βα)6-fold, and thus entirely lacking a C-terminus phosphate-binding site, was identified and shown to have HisA activity. As expected, reconstruction of the evolution of PriA from HisA with HMM profiles suggest that functional shifts involve mutations in evolutionarily intermediate enzymes of otherwise functionally essential residues or motifs. These results are in agreement with a link between promiscuous enzymes and intragenic epistasis. HMM provides a convenient approach for gaining insights into these evolutionary processes.

Optical Properties of ZnCdS:I Orange and ZnSTe:I White Thin Film Phosphor for High Ra White LED

NASA Astrophysics Data System (ADS)

Fujii, Satoshi; Tasaki, Norio; Shinomura, Naohiko; Kurai, Satoshi; Yamada, Yoichi; Taguchi, Tsunemasa

In order to develop visible thin film phosphors, we have for the first time prepared ZnCdS and ZnSTe doped with Iodine (I) using low-pressure MOCVD method. ZnCdS:I, of which Cd composition was calibrated to match the lattice constant to that of substrate and the band gap to absorption peak, showed a orange broad emission consist of yellow near band edge emission and red SA emission. Isoelectronic Te in ZnS indicates strong blue-green emissions, whilst I donor impurity in ZnS shows strong red SA emissions. A typical ZnSTe:I thin film shows two broad emission bands locating at around 500 and 680 nm, respectively, indicating Ra˜90. It was shown that high Ra thin film phosphor can be realized by single material (ZnSTe:I), and that MOCVD method is capable for controlling the thickness and doping profile to obtain uniform white emission pattern.

Maskless deposition technique for the physical vapor deposition of thin film and multilayer coatings with subnanometer precision and accuracy

DOEpatents

Vernon, Stephen P.; Ceglio, Natale M.

2000-01-01

The invention is a method for the production of axially symmetric, graded and ungraded thickness thin film and multilayer coatings that avoids the use of apertures or masks to tailor the deposition profile. A motional averaging scheme permits the deposition of uniform thickness coatings independent of the substrate radius. Coating uniformity results from an exact cancellation of substrate radius dependent terms, which occurs when the substrate moves at constant velocity. If the substrate is allowed to accelerate over the source, arbitrary coating profiles can be generated through appropriate selection and control of the substrate center of mass equation of motion. The radial symmetry of the coating profile is an artifact produced by orbiting the substrate about its center of mass; other distributions are obtained by selecting another rotation axis. Consequently there is a direct mapping between the coating thickness and substrate equation of motion which can be used to tailor the coating profile without the use of masks and apertures.

Rapid and general profiling of protease specificity by using combinatorial fluorogenic substrate libraries

PubMed Central

Harris, Jennifer L.; Backes, Bradley J.; Leonetti, Francesco; Mahrus, Sami; Ellman, Jonathan A.; Craik, Charles S.

2000-01-01

A method is presented for the preparation and use of fluorogenic peptide substrates that allows for the configuration of general substrate libraries to rapidly identify the primary and extended specificity of proteases. The substrates contain the fluorogenic leaving group 7-amino-4-carbamoylmethylcoumarin (ACC). Substrates incorporating the ACC leaving group show kinetic profiles comparable to those with the traditionally used 7-amino-4-methylcoumarin (AMC) leaving group. The bifunctional nature of ACC allows for the efficient production of single substrates and substrate libraries by using 9-fluorenylmethoxycarbonyl (Fmoc)-based solid-phase synthesis techniques. The approximately 3-fold-increased quantum yield of ACC over AMC permits reduction in enzyme and substrate concentrations. As a consequence, a greater number of substrates can be tolerated in a single assay, thus enabling an increase in the diversity space of the library. Soluble positional protease substrate libraries of 137,180 and 6,859 members, possessing amino acid diversity at the P4-P3-P2-P1 and P4-P3-P2 positions, respectively, were constructed. Employing this screening method, we profiled the substrate specificities of a diverse array of proteases, including the serine proteases thrombin, plasmin, factor Xa, urokinase-type plasminogen activator, tissue plasminogen activator, granzyme B, trypsin, chymotrypsin, human neutrophil elastase, and the cysteine proteases papain and cruzain. The resulting profiles create a pharmacophoric portrayal of the proteases to aid in the design of selective substrates and potent inhibitors. PMID:10869434

Laccase versus Laccase-Like Multi-Copper Oxidase: A Comparative Study of Similar Enzymes with Diverse Substrate Spectra

PubMed Central

Reiss, Renate; Ihssen, Julian; Richter, Michael; Eichhorn, Eric; Schilling, Boris; Thöny-Meyer, Linda

2013-01-01

Laccases (EC 1.10.3.2) are multi-copper oxidases that catalyse the one-electron oxidation of a broad range of compounds including substituted phenols, arylamines and aromatic thiols to the corresponding radicals. Owing to their broad substrate range, copper-containing laccases are versatile biocatalysts, capable of oxidizing numerous natural and non-natural industry-relevant compounds, with water as the sole by-product. In the present study, 10 of the 11 multi-copper oxidases, hitherto considered to be laccases, from fungi, plant and bacterial origin were compared. A substrate screen of 91 natural and non-natural compounds was recorded and revealed a fairly broad but distinctive substrate spectrum amongst the enzymes. Even though the enzymes share conserved active site residues we found that the substrate ranges of the individual enzymes varied considerably. The EC classification is based on the type of chemical reaction performed and the actual name of the enzyme often refers to the physiological substrate. However, for the enzymes studied in this work such classification is not feasible, even more so as their prime substrates or natural functions are mainly unknown. The classification of multi-copper oxidases assigned as laccases remains a challenge. For the sake of simplicity we propose to introduce the term “laccase-like multi-copper oxidase” (LMCO) in addition to the term laccase that we use exclusively for the enzyme originally identified from the sap of the lacquer tree Rhus vernicifera. PMID:23755261

Common genes regulate food and ethanol intake in Drosophila.

PubMed

Sekhon, Morgan L; Lamina, Omoteniola; Hogan, Kerry E; Kliethermes, Christopher L

2016-06-01

The abuse liability of alcohol (ethanol) is believed to result in part from its actions on neurobiological substrates that underlie the motivation toward food and other natural reinforcers, and a growing body of evidence indicates that these substrates are broadly conserved among animal phyla. Understanding the extent to which the substrates regulating ethanol and food intake overlap is an important step toward developing therapeutics that selectively reduce ethanol intake. In the current experiments, we measured food and ethanol intake in Recombinant Inbred (RI) lines of Drosophila melanogaster using several assays, and then calculated genetic correlations to estimate the degree to which common genes might underlie behavior in these assays. We found that food intake and ethanol intake as measured in the capillary assay are genetically correlated traits in D. melanogaster, as well as in a panel of 11 Drosophila species that we tested subsequently. RI line differences in food intake in a dyed food assay were genetically unrelated to ethanol intake in the capillary assay or to ethanol preference measured using an olfactory trap apparatus. Using publicly available gene expression data, we found that expression profiles across the RI lines of a number of genes (including the D2-like dopamine receptor, DOPA decarboxylase, and fruitless) correlated with the RI line differences in food and ethanol intake we measured, while the expression profiles of other genes, including NPF, and the NPF and 5-HT2 receptors, correlated only with ethanol intake or preference. Our results suggest that food and ethanol intake are regulated by some common genes in Drosophila, but that other genes regulate ethanol intake independently of food intake. These results have implications toward the development of therapeutics that preferentially reduce ethanol intake. Copyright © 2016 Elsevier Inc. All rights reserved.

Method of fabricating reflection-mode EUV diffraction elements

DOEpatents

Naulleau, Patrick P.

2002-01-01

Techniques for fabricating a well-controlled, quantized-level, engineered surface that serves as substrates for EUV reflection multilayer overcomes problems associated with the fabrication of reflective EUV diffraction elements. The technique when employed to fabricate an EUV diffraction element that includes the steps of: (a) forming an etch stack comprising alternating layers of first and second materials on a substrate surface where the two material can provide relative etch selectivity; (b) creating a relief profile in the etch stack wherein the relief profile has a defined contour; and (c) depositing a multilayer reflection film over the relief profile wherein the film has an outer contour that substantially matches that of the relief profile. For a typical EUV multilayer, if the features on the substrate are larger than 50 nm, the multilayer will be conformal to the substrate. Thus, the phase imparted to the reflected wavefront will closely match that geometrically set by the surface height profile.

Phylogenetic and experimental characterization of an acyl-ACP thioesterase family reveals significant diversity in enzymatic specificity and activity.

PubMed

Jing, Fuyuan; Cantu, David C; Tvaruzkova, Jarmila; Chipman, Jay P; Nikolau, Basil J; Yandeau-Nelson, Marna D; Reilly, Peter J

2011-08-10

Acyl-acyl carrier protein thioesterases (acyl-ACP TEs) catalyze the hydrolysis of the thioester bond that links the acyl chain to the sulfhydryl group of the phosphopantetheine prosthetic group of ACP. This reaction terminates acyl chain elongation of fatty acid biosynthesis, and in plant seeds it is the biochemical determinant of the fatty acid compositions of storage lipids. To explore acyl-ACP TE diversity and to identify novel acyl ACP-TEs, 31 acyl-ACP TEs from wide-ranging phylogenetic sources were characterized to ascertain their in vivo activities and substrate specificities. These acyl-ACP TEs were chosen by two different approaches: 1) 24 TEs were selected from public databases on the basis of phylogenetic analysis and fatty acid profile knowledge of their source organisms; and 2) seven TEs were molecularly cloned from oil palm (Elaeis guineensis), coconut (Cocos nucifera) and Cuphea viscosissima, organisms that produce medium-chain and short-chain fatty acids in their seeds. The in vivo substrate specificities of the acyl-ACP TEs were determined in E. coli. Based on their specificities, these enzymes were clustered into three classes: 1) Class I acyl-ACP TEs act primarily on 14- and 16-carbon acyl-ACP substrates; 2) Class II acyl-ACP TEs have broad substrate specificities, with major activities toward 8- and 14-carbon acyl-ACP substrates; and 3) Class III acyl-ACP TEs act predominantly on 8-carbon acyl-ACPs. Several novel acyl-ACP TEs act on short-chain and unsaturated acyl-ACP or 3-ketoacyl-ACP substrates, indicating the diversity of enzymatic specificity in this enzyme family. These acyl-ACP TEs can potentially be used to diversify the fatty acid biosynthesis pathway to produce novel fatty acids.

Phylogenetic and experimental characterization of an acyl-ACP thioesterase family reveals significant diversity in enzymatic specificity and activity

PubMed Central

2011-01-01

Background Acyl-acyl carrier protein thioesterases (acyl-ACP TEs) catalyze the hydrolysis of the thioester bond that links the acyl chain to the sulfhydryl group of the phosphopantetheine prosthetic group of ACP. This reaction terminates acyl chain elongation of fatty acid biosynthesis, and in plant seeds it is the biochemical determinant of the fatty acid compositions of storage lipids. Results To explore acyl-ACP TE diversity and to identify novel acyl ACP-TEs, 31 acyl-ACP TEs from wide-ranging phylogenetic sources were characterized to ascertain their in vivo activities and substrate specificities. These acyl-ACP TEs were chosen by two different approaches: 1) 24 TEs were selected from public databases on the basis of phylogenetic analysis and fatty acid profile knowledge of their source organisms; and 2) seven TEs were molecularly cloned from oil palm (Elaeis guineensis), coconut (Cocos nucifera) and Cuphea viscosissima, organisms that produce medium-chain and short-chain fatty acids in their seeds. The in vivo substrate specificities of the acyl-ACP TEs were determined in E. coli. Based on their specificities, these enzymes were clustered into three classes: 1) Class I acyl-ACP TEs act primarily on 14- and 16-carbon acyl-ACP substrates; 2) Class II acyl-ACP TEs have broad substrate specificities, with major activities toward 8- and 14-carbon acyl-ACP substrates; and 3) Class III acyl-ACP TEs act predominantly on 8-carbon acyl-ACPs. Several novel acyl-ACP TEs act on short-chain and unsaturated acyl-ACP or 3-ketoacyl-ACP substrates, indicating the diversity of enzymatic specificity in this enzyme family. Conclusion These acyl-ACP TEs can potentially be used to diversify the fatty acid biosynthesis pathway to produce novel fatty acids. PMID:21831316

Cold spraying of aluminum bronze on profiled submillimeter cermet structures formed by laser cladding

NASA Astrophysics Data System (ADS)

Ryashin, N. S.; Malikov, A. G.; Shikalov, V. S.; Gulyaev, I. P.; Kuchumov, B. M.; Klinkov, S. V.; Kosarev, V. F.; Orishich, A. M.

2017-10-01

The paper presents results of the cold spraying of aluminum bronze coatings on substrates profiled with WC/Ni tracks obtained by laser cladding. Reinforcing cermet frames shaped as grids with varied mesh sizes were clad on stainless steel substrates using a CO2 laser machine "Siberia" (ITAM SB RAS, Russia). As a result, surfaces/substrates with heterogeneous shape, composition, and mechanical properties were obtained. Aluminum bronze coatings were deposited from 5lF-NS powder (Oerlikon Metco, Switzerland) on those substrates using cold spraying equipment (ITAM SB RAS). Data of profiling, microstructure diagnostics, EDS analysis, and mechanical tests of obtained composites is reported. Surface relief of the sprayed coatings dependence on substrate structure has been demonstrated.

Geomorphic characterization of the U.S. Atlantic continental margin

USGS Publications Warehouse

Brothers, Daniel S.; ten Brink, Uri S.; Andrews, Brian D.; Chaytor, Jason D.

2013-01-01

The increasing volume of multibeam bathymetry data collected along continental margins is providing new opportunities to study the feedbacks between sedimentary and oceanographic processes and seafloor morphology. Attempts to develop simple guidelines that describe the relationships between form and process often overlook the importance of inherited physiography in slope depositional systems. Here, we use multibeam bathymetry data and seismic reflection profiles spanning the U.S. Atlantic outer continental shelf, slope and rise from Cape Hatteras to New England to quantify the broad-scale, across-margin morphological variation. Morphometric analyses suggest the margin can be divided into four basic categories that roughly align with Quaternary sedimentary provinces. Within each category, Quaternary sedimentary processes exerted heavy modification of submarine canyons, landslide complexes and the broad-scale morphology of the continental rise, but they appear to have preserved much of the pre-Quaternary, across-margin shape of the continental slope. Without detailed constraints on the substrate structure, first-order morphological categorization the U.S. Atlantic margin does not provide a reliable framework for predicting relationships between form and process.

Broadly tunable terahertz difference-frequency generation in quantum cascade lasers on silicon

NASA Astrophysics Data System (ADS)

Jung, Seungyong; Kim, Jae Hyun; Jiang, Yifan; Vijayraghavan, Karun; Belkin, Mikhail A.

2018-01-01

We report broadly tunable terahertz (THz) sources based on intracavity Cherenkov difference-frequency generation in quantum cascade lasers transfer-printed on high-resistivity silicon substrates. Spectral tuning from 1.3 to 4.3 THz was obtained from a 2-mm long laser chip using a modified Littrow external cavity setup. The THz power output and the midinfrared-to-THz conversion efficiency of the devices transferred on silicon are dramatically enhanced, compared with the devices on a native semi-insulating InP substrate. Enhancement is particularly significant at higher THz frequencies, where the tail of the Reststrahlen band results in a strong absorption of THz light in the InP substrate.

Substrate Specificity of Human Protein Arginine Methyltransferase 7 (PRMT7)

PubMed Central

Feng, You; Hadjikyriacou, Andrea; Clarke, Steven G.

2014-01-01

Protein arginine methyltransferase 7 (PRMT7) methylates arginine residues on various protein substrates and is involved in DNA transcription, RNA splicing, DNA repair, cell differentiation, and metastasis. The substrate sequences it recognizes in vivo and the enzymatic mechanism behind it, however, remain to be explored. Here we characterize methylation catalyzed by a bacterially expressed GST-tagged human PRMT7 fusion protein with a broad range of peptide and protein substrates. After confirming its type III activity generating only ω-NG-monomethylarginine and its distinct substrate specificity for RXR motifs surrounded by basic residues, we performed site-directed mutagenesis studies on this enzyme, revealing that two acidic residues within the double E loop, Asp-147 and Glu-149, modulate the substrate preference. Furthermore, altering a single acidic residue, Glu-478, on the C-terminal domain to glutamine nearly abolished the activity of the enzyme. Additionally, we demonstrate that PRMT7 has unusual temperature dependence and salt tolerance. These results provide a biochemical foundation to understanding the broad biological functions of PRMT7 in health and disease. PMID:25294873

An evaluation of direct PCR amplification

PubMed Central

Hall, Daniel E.; Roy, Reena

2014-01-01

Aim To generate complete DNA profiles from blood and saliva samples deposited on FTA® and non-FTA® paper substrates following a direct amplification protocol. Methods Saliva samples from living donors and blood samples from deceased individuals were deposited on ten different FTA® and non-FTA® substrates. These ten paper substrates containing body fluids were kept at room temperature for varying lengths of time ranging from one day to approximately one year. For all assays in this research, 1.2 mm punches were collected from each substrate containing one type of body fluid and amplified with reagents provided in the nine commercial polymerase chain reaction (PCR) amplification kits. The substrates were not subjected to purification reagent or extraction buffer prior to amplification. Results Success rates were calculated for all nine amplification kits and all ten substrates based on their ability to yield complete DNA profiles following a direct amplification protocol. Six out of the nine amplification kits, and four out of the ten paper substrates had the highest success rates overall. Conclusion The data show that it is possible to generate complete DNA profiles following a direct amplification protocol using both standard (non-direct) and direct PCR amplification kits. The generation of complete DNA profiles appears to depend more on the success of the amplification kit rather than the than the FTA®- or non-FTA®-based substrates. PMID:25559837

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.

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.

Super-massive binary black holes and emission lines in active galactic nuclei

NASA Astrophysics Data System (ADS)

Popović, Luka Č.

2012-02-01

It is now agreed that mergers play an essential role in the evolution of galaxies and therefore that mergers of supermassive black holes (SMBHs) must have been common. We see the consequences of past supermassive binary black holes (SMBs) in the light profiles of so-called 'core ellipticals' and a small number of SMBs have been detected. However, the evolution of SMBs is poorly understood. Theory predicts that SMBs should spend a substantial amount of time orbiting at velocities of a few thousand kilometers per second. If the SMBs are surrounded by gas observational effects might be expected from accretion onto one or both of the SMBHs. This could result in a binary Active Galactic Nucleus (AGN) system. Like a single AGN, such a system would emit a broad band electromagnetic spectrum and broad and narrow emission lines. The broad emission spectral lines emitted from AGNs are our main probe of the geometry and physics of the broad line region (BLR) close to the SMBH. There is a group of AGNs that emit very broad and complex line profiles, showing two displaced peaks, one blueshifted and one redshifted from the systemic velocity defined by the narrow lines, or a single such peak. It has been proposed that such line shapes could indicate an SMB system. We discuss here how the presence of an SMB will affect the BLRs of AGNs and what the observational consequences might be. We review previous claims of SMBs based on broad line profiles and find that they may have non-SMB explanations as a consequence of a complex BLR structure. Because of these effects it is very hard to put limits on the number of SMBs from broad line profiles. It is still possible, however, that unusual broad line profiles in combination with other observational effects (line ratios, quasi-periodical oscillations, spectropolarimetry, etc.) could be used for SMBs detection. Some narrow lines (e.g., [O III]) in some AGNs show a double-peaked profile. Such profiles can be caused by streams in the Narrow Line Region (NLR), but may also indicate the presence of a kilo-parsec scale mergers. A few objects indicated as double-peaked narrow line emitters are confirmed as kpc-scale margers, but double-peaked narrow line profiles are mostly caused by the complex NLR geometry. We briefly discuss the expected line profile of broad Fe Kα that probably originated in the accretion disk(s) around SMBs. This line may also be very complex and indicate the complex disk geometry or/and an SMB presence. Finally we consider rare configurations where a SMB system might be gravitationally lensed by a foreground galaxy, and discuss the expected line profiles in these systems.

Method of fabricating reflection-mode EUV diffusers

DOEpatents

Anderson, Erik; Naulleau, Patrick P.

2005-03-01

Techniques for fabricating well-controlled, random relief, engineered surfaces that serve as substrates for EUV optical devices are accomplished with grayscale exposure. The method of fabricating a multilevel EUV optical element includes: (a) providing a substrate; (b) depositing a layer of curable material on a surface of the substrate; (c) creating a relief profile in a layer of cured material from the layer of curable material wherein the relief profile comprises multiple levels of cured material that has a defined contour; and (d) depositing a multilayer reflection film over the relief profile wherein the film has an outer contour that substantially matches that of the relief profile. The curable material can comprise photoresist or a low dielectric constant material.

Overlay coating degradation by simultaneous oxidation and coating/substrate interdiffusion. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Nesbitt, J. A.

1983-01-01

Degradation of NiCrAlZr overlay coatings on various NiCrAl substrates was examined after cyclic oxidation. Concentration/distance profiles were measured in the coating and substrate after various oxidation exposures at 1150 C. For each stubstrate, the Al content in the coating decreased rapidly. The concentration/distance profiles, and particularly that for Al, reflected the oxide spalling resistance of each coated substrate. A numerical model was developed to simulate diffusion associated with overlay-coating degradation by oxidation and coating/substrate interdiffusion. Input to the numerical model consisted of the Cr and Al content of the coating and substrate, ternary diffusivities, and various oxide spalling parameters. The model predicts the Cr and Al concentrations in the coating and substrate after any number of oxidation/thermal cycles. The numerical model also predicts coating failure based on the ability of the coating to supply sufficient Al to the oxide scale. The validity of the model was confirmed by comparison of the predicted and measured concentration/distance profiles. The model was subsequently used to identify the most critical system parameters affecting coating life.

Single Cell Profiling using Ionic Liquid Matrix-Enhanced Secondary Ion Mass Spectrometry for Neuronal Cell Type Differentiation

PubMed Central

Do, Thanh D.; Comi, Troy J.; Dunham, Sage J. B.; Rubakhin, Stanislav S.; Sweedler, Jonathan V.

2017-01-01

A high-throughput single cell profiling method has been developed for matrix-enhanced secondary ion mass spectrometry (ME-SIMS) to investigate the lipid profiles of neuronal cells. Populations of cells are dispersed onto the substrate, their locations determined using optical microscopy, and the cell locations used to guide the acquisition of SIMS spectra from the cells. Up to 2,000 cells can be assayed in one experiment at a rate of 6 s per cell. Multiple saturated and unsaturated phosphatidylcholines (PCs) and their fragments are detected and verified with tandem mass spectrometry from individual cells when ionic liquids are employed as a matrix. Optically guided single cell profiling with ME-SIMS is suitable for a range of cell sizes, from Aplysia californica neurons larger than 75 μm to 7-μm rat cerebellar neurons. ME-SIMS analysis followed by t-distributed stochastic neighbor embedding of peaks in the lipid molecular mass range (m/z 700–850) distinguishes several cell types from the rat central nervous system, largely based on the relative proportions of the four dominant lipids, PC(32:0), PC(34:1), PC(36:1), and PC(38:5). Furthermore, subpopulations within each cell type are tentatively classified consistent with their endogenous lipid ratios. The results illustrate the efficacy of a new approach to classify single cell populations and subpopulations using SIMS profiling of lipid and metabolite contents. These methods are broadly applicable for high throughput single cell chemical analyses. PMID:28194949

Substrate specificity of human protein arginine methyltransferase 7 (PRMT7): the importance of acidic residues in the double E loop.

PubMed

Feng, You; Hadjikyriacou, Andrea; Clarke, Steven G

2014-11-21

Protein arginine methyltransferase 7 (PRMT7) methylates arginine residues on various protein substrates and is involved in DNA transcription, RNA splicing, DNA repair, cell differentiation, and metastasis. The substrate sequences it recognizes in vivo and the enzymatic mechanism behind it, however, remain to be explored. Here we characterize methylation catalyzed by a bacterially expressed GST-tagged human PRMT7 fusion protein with a broad range of peptide and protein substrates. After confirming its type III activity generating only ω-N(G)-monomethylarginine and its distinct substrate specificity for RXR motifs surrounded by basic residues, we performed site-directed mutagenesis studies on this enzyme, revealing that two acidic residues within the double E loop, Asp-147 and Glu-149, modulate the substrate preference. Furthermore, altering a single acidic residue, Glu-478, on the C-terminal domain to glutamine nearly abolished the activity of the enzyme. Additionally, we demonstrate that PRMT7 has unusual temperature dependence and salt tolerance. These results provide a biochemical foundation to understanding the broad biological functions of PRMT7 in health and disease. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Understanding the Broad Substrate Repertoire of Nitroreductase Based on Its Kinetic Mechanism*

PubMed Central

Pitsawong, Warintra; Hoben, John P.; Miller, Anne-Frances

2014-01-01

The oxygen-insensitive nitroreductase from Enterobacter cloacae (NR) catalyzes two-electron reduction of nitroaromatics to the corresponding nitroso compounds and, subsequently, to hydroxylamine products. NR has an unusually broad substrate repertoire, which may be related to protein dynamics (flexibility) and/or a simple non-selective kinetic mechanism. To investigate the possible role of mechanism in the broad substrate repertoire of NR, the kinetics of oxidation of NR by para-nitrobenzoic acid (p-NBA) were investigated using stopped-flow techniques at 4 °C. The results revealed a hyperbolic dependence on the p-NBA concentration with a limiting rate of 1.90 ± 0.09 s−1, indicating one-step binding before the flavin oxidation step. There is no evidence for a distinct binding step in which specificity might be enforced. The reduction of p-NBA is rate-limiting in steady-state turnover (1.7 ± 0.3 s−1). The pre-steady-state reduction kinetics of NR by NADH indicate that NADH reduces the enzyme with a rate constant of 700 ± 20 s−1 and a dissociation constant of 0.51 ± 0.04 mm. Thus, we demonstrate simple transient kinetics in both the reductive and oxidative half-reactions that help to explain the broad substrate repertoire of NR. Finally, we tested the ability of NR to reduce para-hydroxylaminobenzoic acid, demonstrating that the corresponding amine does not accumulate to significant levels even under anaerobic conditions. Thus E. cloacae NR is not a good candidate for enzymatic production of aromatic amines. PMID:24706760

Influence of nitrogen substrates and substrate C:N ratios on the nitrogen isotopic composition of amino acids from the marine bacterium Vibrio harveyi

NASA Astrophysics Data System (ADS)

Maki, K.; Ohkouchi, N.; Chikaraishi, Y.; Fukuda, H.; Miyajima, T.; Nagata, T.

2014-09-01

Nitrogen (N) isotopic compositions of individual hydrolysable amino acids (δ15NAAs) in N pools have been increasingly used for trophic position assessment and evaluation of sources and transformation processes of organic matter in marine environments. However, there are limited data about variability in δ15NAAs patterns and how this variability influences marine bacteria, an important mediator of trophic transfer and organic matter transformation. We explored whether marine bacterial δ15NAAs profiles change depending on the type and C:N ratio of the substrate. The δ15NAAs profile of a marine bacterium, Vibrio harveyi, was examined using medium containing either glutamate, alanine or ammonium as the N source [substrate C:N ratios (range, 3 to 20) were adjusted with glucose]. The data were interpreted as a reflection of isotope fractionations associated with de novo synthesis of amino acids by bacteria. Principal component analysis (PCA) using the δ15N offset values normalized to glutamate + glutamine δ15N revealed that δ15NAAs profiles differed depending on the N source and C:N ratio of the substrate. High variability in the δ15N offset of alanine and valine largely explained this bacterial δ15NAAs profile variability. PCA was also conducted using bacterial and phytoplankton (cyanobacteria and eukaryotic algae) δ15NAAs profile data reported previously. The results revealed that bacterial δ15NAAs patterns were distinct from those of phytoplankton. Therefore, the δ15NAAs profile is a useful indicator of biochemical responses of bacteria to changes in substrate conditions, serving as a potentially useful method for identifying organic matter sources in marine environments.

Characterization of an aryl-alcohol oxidase from the plant saprophytic basidiomycete Coprinopsis cinerea with broad substrate specificity against aromatic alcohols.

PubMed

Tamaru, Yoshiaki; Umezawa, Kiwamu; Yoshida, Makoto

2018-07-01

The aim of the study was to obtain information about the enzymatic properties of aryl-alcohol oxidase from the plant saprophytic basidiomycete Coprinopsis cinerea (rCcAAO), which is classified into the auxiliary activities family 3 subfamily 2 (AA3_2). The gene encoding AAO from the plant saprophytic basidiomycete Coprinopsis cinerea (CcAAO) was cloned, and the recombinant CcAAO (rCcAAO) was heterologously expressed in the methylotrophic yeast Pichia pastoris. The purified rCcAAO showed significant activity not only against trans,trans-2,4-hexadien-1-ol but also against a broad range of aromatic alcohols including aromatic compounds that were reported to be poor substrates for known AAOs. Moreover, site-directed mutagenesis analysis demonstrated that mutants with substitutions from leucine to phenylalanine and tryptophan at position 416 exhibited decreases of activity for aromatic alcohols but still maintained the activity for trans,trans-2,4-hexadien-1-ol. Leucine 416 in CcAAO contributes to the broad substrate specificity against various aromatic alcohols, which is useful for the production of hydrogen peroxide using this enzyme.

Diffraction efficiency of plasmonic gratings fabricated by electron beam lithography using a silver halide film

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

Sudheer,, E-mail: sudheer@rrcat.gov.in, E-mail: sudheer.rrcat@gmail.com; Tiwari, P.; Srivastava, Himanshu

2016-07-28

The silver nanoparticle surface relief gratings of ∼10 μm period are fabricated using electron beam lithography on the silver halide film substrate. Morphological characterization of the gratings shows that the period, the shape, and the relief depth in the gratings are mainly dependent on the number of lines per frame, the spot size, and the accelerating voltage of electron beam raster in the SEM. Optical absorption of the silver nanoparticle gratings provides a broad localized surface plasmon resonance peak in the visible region, whereas the intensity of the peaks depends on the number density of silver nanoparticles in the gratings. Themore » maximum efficiency of ∼7.2% for first order diffraction is observed for the grating fabricated at 15 keV. The efficiency is peaking at 560 nm with ∼380 nm bandwidth. The measured profiles of the diffraction efficiency for the gratings are found in close agreement with the Raman-Nath diffraction theory. This technique provides a simple and efficient method for the fabrication of plasmonic nanoparticle grating structures with high diffraction efficiency having broad wavelength tuning.« less

Effect of nonsinusoidal bias waveforms on ion energy distributions and fluorocarbon plasma etch selectivity

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

Agarwal, Ankur; Kushner, Mark J.; Iowa State University, Department of Electrical and Computer Engineering, 104 Marston Hall, Ames, Iowa 50011-2151

2005-09-15

The distributions of ion energies incident on the wafer significantly influence feature profiles and selectivity during plasma etching. Control of ion energies is typically obtained by varying the amplitude or frequency of a radio frequency sinusoidal bias voltage applied to the substrate. The resulting ion energy distribution (IED), though, is generally broad. Controlling the width and shape of the IED can potentially improve etch selectivity by distinguishing between threshold energies of surface processes. In this article, control of the IED was computationally investigated by applying a tailored, nonsinusoidal bias waveform to the substrate of an inductively coupled plasma. The waveformmore » we investigated, a quasi-dc negative bias having a short positive pulse each cycle, produced a narrow IED whose width was controllable based on the length of the positive spike and frequency. We found that the selectivity between etching Si and SiO{sub 2} in fluorocarbon plasmas could be controlled by adjusting the width and energy of the IED. Control of the energy of a narrow IED enables etching recipes that transition between speed and selectivity without change of gas mixture.« less

A broad pH range indicator-based spectrophotometric assay for true lipases using tributyrin and tricaprylin[S

PubMed Central

Camacho-Ruiz, María de los Angeles; Mateos-Díaz, Juan Carlos; Carrière, Frédéric; Rodriguez, Jorge A.

2015-01-01

A continuous assay is proposed for the screening of acidic, neutral, or alkaline lipases using microtiter plates, emulsified short- and medium-chain TGs, and a pH indicator. The lipase activity measurement is based on the decrease of the pH indicator optical density due to protonation which is caused by the release of FFAs during the hydrolysis of TGs and thus acidification. Purified lipases with distinct pH optima and an esterase were used to validate the method. The rate of lipolysis was found to be linear with time and proportional to the amount of enzyme added in each case. Specific activities measured with this microplate assay method were lower than those obtained by the pH-stat technique. Nevertheless, the pH-dependent profiles of enzymatic activity were similar with both assays. In addition, the substrate preference of each enzyme tested was not modified and this allowed discriminating lipase and esterase activities using tributyrin (low water solubility) and tricaprylin (not water soluble) as substrates. This continuous lipase assay is compatible with a high sample throughput and can be applied for the screening of lipases and lipase inhibitors from biological samples. PMID:25748441

Free-standing sub-10 nm nanostencils for the definition of gaps in plasmonic antennas.

PubMed

Duan, Huigao; Hu, Hailong; Hui, Hui Kim; Shen, Zexiang; Yang, Joel K W

2013-05-10

Nanogaps between metal nanostructures are useful in localizing optical energy in plasmonic antennas, but are challenging to directly pattern. Patterning with the positive-tone polymethyl methacrylate (PMMA) resist causes an undesirable spread in nanogap dimensions. On the other hand, the negative-tone hydrogen silsesquioxane (HSQ) resist possesses the high resolution suited for the definition of nanogaps. However, it requires a hydrofluoric acid solution for liftoff, making it incompatible with the quartz or glass substrates used in optical devices. In this work, we created free-standing nanostencils in HSQ with sub-10 nm dimensions onto PMMA supports, which allow liftoff in organic solvents, thus extending this method to a broad range of substrate materials. The cross-sectional profiles of the nanogaps formed between the gold nanostructures were imaged in a transmission electron microscope and measured to be ~8 nm. We demonstrated the utility of this process in fabricating entire arrays of dimer nanostructures with sub-10 nm gaps. Using a surface enhanced Raman scattering setup, an order of magnitude increase in peak intensity was observed when the fields in the gap were resonantly excited compared to when the fields were localized at the corners of the nanostructures.

Some Lactobacillus l-Lactate Dehydrogenases Exhibit Comparable Catalytic Activities for Pyruvate and Oxaloacetate

PubMed Central

Arai, Kazuhito; Kamata, Takeo; Uchikoba, Hiroyuki; Fushinobu, Shinya; Matsuzawa, Hiroshi; Taguchi, Hayao

2001-01-01

The nonallosteric and allosteric l-lactate dehydrogenases of Lactobacillus pentosus and L. casei, respectively, exhibited broad substrate specificities, giving virtually the same maximal reaction velocity and substrate Km values for pyruvate and oxaloacetate. Replacement of Pro101 with Asn reduced the activity of the L. pentosus enzyme toward these alternative substrates to a greater extent than the activity toward pyruvate. PMID:11114942

Fabricating Blazed Diffraction Gratings by X-Ray Lithography

NASA Technical Reports Server (NTRS)

Mouroulis, Pantazis; Hartley, Frank; Wilson, Daniel

2004-01-01

Gray-scale x-ray lithography is undergoing development as a technique for fabricating blazed diffraction gratings. As such, gray-scale x-ray lithography now complements such other grating-fabrication techniques as mechanical ruling, holography, ion etching, laser ablation, laser writing, and electron-beam lithography. Each of these techniques offers advantages and disadvantages for implementing specific grating designs; no single one of these techniques can satisfy the design requirements for all applications. Gray-scale x-ray lithography is expected to be advantageous for making gratings on steeper substrates than those that can be made by electron-beam lithography. This technique is not limited to sawtooth groove profiles and flat substrates: various groove profiles can be generated on arbitrarily shaped (including highly curved) substrates with the same ease as sawtooth profiles can be generated on flat substrates. Moreover, the gratings fabricated by this technique can be made free of ghosts (spurious diffraction components attributable to small spurious periodicities in the locations of grooves). The first step in gray-scale x-ray lithography is to conformally coat a substrate with a suitable photoresist. An x-ray mask (see Figure 1) is generated, placed between the substrate and a source of collimated x-rays, and scanned over the substrate so as to create a spatial modulation in the exposure of the photoresist. Development of the exposed photoresist results in a surface corrugation that corresponds to the spatial modulation and that defines the grating surface. The grating pattern is generated by scanning an appropriately shaped x-ray area mask along the substrate. The mask example of Figure 1 would generate a blazed grating profile when scanned in the perpendicular direction at constant speed, assuming the photoresist responds linearly to incident radiation. If the resist response is nonlinear, then the mask shape can be modified to account for the nonlinearity and produce a desired groove profile. An example of grating grooves generated by this technique is shown in Figure 2. A maximum relative efficiency of 88 percent has been demonstrated.

Oxidase catalysis via aerobically generated hypervalent iodine intermediates

NASA Astrophysics Data System (ADS)

Maity, Asim; Hyun, Sung-Min; Powers, David C.

2018-02-01

The development of sustainable oxidation chemistry demands strategies to harness O2 as a terminal oxidant. Oxidase catalysis, in which O2 serves as a chemical oxidant without necessitating incorporation of oxygen into reaction products, would allow diverse substrate functionalization chemistry to be coupled to O2 reduction. Direct O2 utilization suffers from intrinsic challenges imposed by the triplet ground state of O2 and the disparate electron inventories of four-electron O2 reduction and two-electron substrate oxidation. Here, we generate hypervalent iodine reagents—a broadly useful class of selective two-electron oxidants—from O2. This is achieved by intercepting reactive intermediates of aldehyde autoxidation to aerobically generate hypervalent iodine reagents for a broad array of substrate oxidation reactions. The use of aryl iodides as mediators of aerobic oxidation underpins an oxidase catalysis platform that couples substrate oxidation directly to O2 reduction. We anticipate that aerobically generated hypervalent iodine reagents will expand the scope of aerobic oxidation chemistry in chemical synthesis.

Evaluation of Direct PCR Amplification Using Various Swabs and Washing Reagents.

PubMed

Altshuler, Hallie; Roy, Reena

2015-11-01

DNA profiles were generated via direct amplification from blood and saliva samples deposited on various types of swab substrates. Each of the six non-FTA substrates used in this research was punched with a Harris 1.2 mm puncher. After 0.1 μL of blood or 0.5 μL saliva, samples were deposited on each of these punches, samples were pretreated with one of four buffers and washing reagents. Amplification was performed using direct and nondirect autosomal and Y-STR kits. Autosomal and Y-STR profiles were successfully generated from most of these substrates when pretreated with buffer or washing reagents. Concordant profiles were obtained within and between the six substrates, the six amplification kits, and all four reagents. The direct amplification of substrates which do not contain lysing agent would be beneficial to the forensic community as the procedure can be used on evidence samples commonly found at crime scenes. © 2015 American Academy of Forensic Sciences.

Constraints on the outer radius of the broad emission line region of active galactic nuclei

NASA Astrophysics Data System (ADS)

Landt, Hermine; Ward, Martin J.; Elvis, Martin; Karovska, Margarita

2014-03-01

Here we present observational evidence that the broad emission line region (BELR) of active galactic nuclei (AGN) generally has an outer boundary. This was already clear for sources with an obvious transition between the broad and narrow components of their emission lines. We show that the narrow component of the higher-order Paschen lines is absent in all sources, revealing a broad emission line profile with a broad, flat top. This indicates that the BELR is kinematically separate from the narrow emission line region. We use the virial theorem to estimate the BELR outer radius from the flat top width of the unblended profiles of the strongest Paschen lines, Paα and Paβ, and find that it scales with the ionizing continuum luminosity roughly as expected from photoionization theory. The value of the incident continuum photon flux resulting from this relationship corresponds to that required for dust sublimation. A flat-topped broad emission line profile is produced by both a spherical gas distribution in orbital motion and an accretion disc wind if the ratio between the BELR outer and inner radius is assumed to be less than ˜100-200. On the other hand, a pure Keplerian disc can be largely excluded, since for most orientations and radial extents of the disc the emission line profile is double-horned.

Method and system using power modulation and velocity modulation producing sputtered thin films with sub-angstrom thickness uniformity or custom thickness gradients

DOEpatents

Montcalm, Claude [Livermore, CA; Folta, James Allen [Livermore, CA; Walton, Christopher Charles [Berkeley, CA

2003-12-23

A method and system for determining a source flux modulation recipe for achieving a selected thickness profile of a film to be deposited (e.g., with highly uniform or highly accurate custom graded thickness) over a flat or curved substrate (such as concave or convex optics) by exposing the substrate to a vapor deposition source operated with time-varying flux distribution as a function of time. Preferably, the source is operated with time-varying power applied thereto during each sweep of the substrate to achieve the time-varying flux distribution as a function of time. Preferably, the method includes the steps of measuring the source flux distribution (using a test piece held stationary while exposed to the source with the source operated at each of a number of different applied power levels), calculating a set of predicted film thickness profiles, each film thickness profile assuming the measured flux distribution and a different one of a set of source flux modulation recipes, and determining from the predicted film thickness profiles a source flux modulation recipe which is adequate to achieve a predetermined thickness profile. Aspects of the invention include a computer-implemented method employing a graphical user interface to facilitate convenient selection of an optimal or nearly optimal source flux modulation recipe to achieve a desired thickness profile on a substrate. The method enables precise modulation of the deposition flux to which a substrate is exposed to provide a desired coating thickness distribution.

Homology modelling of Drosophila cytochrome P450 enzymes associated with insecticide resistance.

PubMed

Jones, Robert T; Bakker, Saskia E; Stone, Deborah; Shuttleworth, Sally N; Boundy, Sam; McCart, Caroline; Daborn, Phillip J; ffrench-Constant, Richard H; van den Elsen, Jean M H

2010-10-01

Overexpression of the cytochrome P450 gene Cyp6g1 confers resistance against DDT and a broad range of other insecticides in Drosophila melanogaster Meig. In the absence of crystal structures of CYP6G1 or complexes with its substrates, structural studies rely on homology modelling and ligand docking to understand P450-substrate interactions. Homology models are presented for CYP6G1, a P450 associated with resistance to DDT and neonicotinoids, and two other enzymes associated with insecticide resistance in D. melanogaster, CYP12D1 and CYP6A2. The models are based on a template of the X-ray structure of the phylogenetically related human CYP3A4, which is known for its broad substrate specificity. The model of CYP6G1 has a much smaller active site cavity than the template. The cavity is also 'V'-shaped and is lined with hydrophobic residues, showing high shape and chemical complementarity with the molecular characteristics of DDT. Comparison of the DDT-CYP6G1 complex and a non-resistant CYP6A2 homology model implies that tight-fit recognition of this insecticide is important in CYP6G1. The active site can accommodate differently shaped substrates ranging from imidacloprid to malathion but not the pyrethroids permethrin and cyfluthrin. The CYP6G1, CYP12D1 and CYP6A2 homology models can provide a structural insight into insecticide resistance in flies overexpressing P450 enzymes with broad substrate specificities.

Seafloor change detection using multibeam echosounder backscatter: case study on the Belgian part of the North Sea

NASA Astrophysics Data System (ADS)

Montereale-Gavazzi, Giacomo; Roche, Marc; Lurton, Xavier; Degrendele, Koen; Terseleer, Nathan; Van Lancker, Vera

2018-06-01

To characterize seafloor substrate type, seabed mapping and particularly multibeam echosounding are increasingly used. Yet, the utilisation of repetitive MBES-borne backscatter surveys to monitor the environmental status of the seafloor remains limited. Often methodological frameworks are missing, and should comprise of a suite of change detection procedures, similarly to those developed in the terrestrial sciences. In this study, pre-, ensemble and post-classification approaches were tested on an eight km2 study site within a Habitat Directive Area in the Belgian part of the North Sea. In this area, gravel beds with epifaunal assemblages were observed. Flourishing of the fauna is constrained by overtopping with sand or increased turbidity levels, which could result from anthropogenic activities. Monitoring of the gravel to sand ratio was hence put forward as an indicator of good environmental status. Seven acoustic surveys were undertaken from 2004 to 2015. The methods allowed quantifying temporal trends and patterns of change of the main substrate classes identified in the study area; namely fine to medium homogenous sand, medium sand with bioclastic detritus and medium to coarse sand with gravel. Results indicated that by considering the entire study area and the entire time series, the gravel to sand ratio fluctuated, but was overall stable. Nonetheless, when only the biodiversity hotspots were considered, net losses and a gradual trend, indicative of potential smothering, was captured by ensemble and post-classification approaches respectively. Additionally, a two-dimensional morphological analysis, based on the bathymetric data, suggested a loss of profile complexity from 2004 to 2015. Causal relationships with natural and anthropogenic stressors are yet to be established. The methodologies presented and discussed are repeatable and can be applied to broad-scale geographical extents given that broad-scale time series datasets become available.

Characterization of a beta-lactamase produced in Mycobacterium fortuitum D316.

PubMed Central

Amicosante, G; Franceschini, N; Segatore, B; Oratore, A; Fattorini, L; Orefici, G; Van Beeumen, J; Frere, J M

1990-01-01

A beta-lactamase from Mycobacterium fortuitum D316 was purified and some physico-chemical properties and substrate profile determined. On the basis of its N-terminal sequence and of its sensitivity to beta-iodopenicillanate inactivation, the enzyme appeared to be a class A beta-lactamase, but its substrate profile was quite unexpected, since nine cephalosporins were among the eleven best substrates. The enzyme also hydrolysed ureidopenicillins and some so-called 'beta-lactamase-stable' cephalosporins. Images Fig. 1. PMID:2123098

Influence of Molecular Shape on Molecular Orientation and Stability of Vapor-Deposited Organic Semiconductors

NASA Astrophysics Data System (ADS)

Walters, Diane M.; Johnson, Noah D.; Ediger, M. D.

Physical vapor deposition is commonly used to prepare active layers in organic electronics. Recently, it has been shown that molecular orientation and packing can be tuned by changing the substrate temperature during deposition, while still producing macroscopically homogeneous films. These amorphous materials can be highly anisotropic when prepared with low substrate temperatures, and they can exhibit exceptional kinetic stability; films retain their favorable packing when heated to high temperatures. Here, we study the influence of molecular shape on molecular orientation and stability. We investigate disc-shaped molecules, such as TCTA and m-MTDATA, nearly spherical molecules, such as Alq3, and linear molecules covering a broad range of aspect ratios, such as p-TTP and BSB-Cz. Disc-shaped molecules have preferential horizontal orientation when deposited at low substrate temperatures, and their orientation can be tuned by changing the substrate temperature. Alq3 forms stable, amorphous films that are optically isotropic when vapor deposited over a broad range of substrate temperatures. This work may guide the choice of material and deposition conditions for vapor-deposited films used in organic electronics and allow for more efficient devices to be fabricated.

Double-peaked broad line emission from the LINER nucleus of NGC 1097

NASA Technical Reports Server (NTRS)

Storchi-Bergmann, Thaisa; Baldwin, Jack A.; Wilson, Andrew S.

1993-01-01

We report the recent appearance of a very broad component in the H-alpha and H-beta emission lines of the weakly active nucleus of the Sersic-Pastoriza galaxy NGC 1097. The FWZI of the broad component is about 21,000 km/s, and its profile is double-peaked; the presence of a blue, featureless continuum in the nucleus is also suggested. The broad component was first observed in H-alpha in November 2, 1991, and confirmed 11 months later. The H-alpha profile and flux did not change in this time interval. Comparison with previously published spectral data indicates that the broad lines have only recently appeared. Together with the relatively high X-ray luminosity and the compact nuclear radio source, our results characterize the presence of a Seyfert 1 nucleus in a galaxy which had previously shown only LINER characteristics. Obscuring material along our line of sight to the nucleus appears to have recently cleared, permitting a direct view of the active nucleus. We discuss two possible structures for the broad line region, biconical outflow and an accretion disk, that could give rise to the observed profile.

Modeling degradation and failure of Ni-Cr-Al overlay coatings

NASA Technical Reports Server (NTRS)

Nesbitt, J. A.; Heckel, R. W.

1984-01-01

Degradation of a Ni-16Cr-25Al-0.06Zr overlay coating on a Ni-22Cr substrate was examined after oxidation accompanied by thermal cycling. Concentration/distance profiles were measured in the coating and substrate after various one-hour cycles at 1150 C. A numerical model was developed to simulate coating degradation by simultaneous oxidation and coating/substrate interdiffusion. The validity of the model was confirmed by comparison of predicted and measured concentration/distance profiles. The ability of the model to identify critical system parameters was demonstrated for the case of the initial Al and Cr content of the coating and substrate.

The Staphylococcus aureus leucine aminopeptidase LAP is localized to the bacterial cytosol and demonstrates a broad substrate range that extends beyond leucine

PubMed Central

Carroll, Ronan K.; Veillard, Florian; Gagne, Danielle T.; Lindenmuth, Jarrod M.; Poreba, Marcin; Drag, Marcin; Potempa, Jan; Shaw, Lindsey N.

2013-01-01

Staphylococcus aureus is a potent pathogen of humans exhibiting a broad disease range, in part, due to an extensive repertoire of secreted virulence factors, including proteases. Recently, we identified the first example of an intracellular protease (leucine aminopeptidase - LAP) that is required for virulence in S. aureus. Disruption of pepZ, the gene encoding LAP, had no affect on the growth rate of bacteria, however, in systemic and localized infection models the pepZ mutant was significantly attenuated in virulence. Recently, a contradictory report has been published, suggesting that LAP is an extracellular enzyme and it is required for growth in S. aureus. Here, we investigate these results and confirm our previous findings that LAP is localized to the bacterial cytosol and is not required for growth. In addition we conduct a biochemical investigation of purified recombinant LAP identifying optimal conditions for enzymatic activity and substrate preference for hydrolysis. Our results show that LAP has a broad substrate range, including activity against the dipeptide cysteine-glycine and that leucine is not the primary target of LAP. PMID:23241672

The biochemical characterization of three imine-reducing enzymes from Streptosporangium roseum DSM43021, Streptomyces turgidiscabies and Paenibacillus elgii.

PubMed

Scheller, Philipp N; Nestl, Bettina M

2016-12-01

Recently imine reductases (IREDs) have emerged as promising biocatalysts for the synthesis of a wide variety of chiral amines. To promote their application, many novel enzymes were reported, but only a few of them were biochemically characterized. To expand the available knowledge about IREDs, we report the characterization of two recently identified (R)-selective IREDs from Streptosporangium roseum DSM43021 and Streptomyces turgidiscabies and one (S)-selective IRED from Paenibacillus elgii. The biochemical properties including pH profiles, temperature stabilities, and activities of the enzymes in the presence of organic solvents were investigated. All three enzymes showed relatively broad pH spectra with maximum activities in the neutral range. While the (R)-selective IREDs displayed only limited thermostabilities, the (S)-selective enzyme was found to be the most thermostable IRED known to date. The activity of this IRED proved also to be most tolerant towards the investigated co-solvents DMSO and methanol. We further studied activities and selectivities towards a panel of cyclic imine model substrates to compare these enzymes with other IREDs. In biotransformations, IREDs showed high conversions and the amine products were obtained with up to 99 % ee. By recording the kinetic constants for these compounds, substrate preferences of the IREDs were investigated and it was shown that the (S)-IRED favors the transformation of bulky imines contrary to the (R)-selective IREDs. Finally, novel exocyclic imine substrates were tested and also high activities and selectivities detected.

X-ray structures of the Pseudomonas cichorii D-tagatose 3-epimerase mutant form C66S recognizing deoxy sugars as substrates.

PubMed

Yoshida, Hiromi; Yoshihara, Akihide; Ishii, Tomohiko; Izumori, Ken; Kamitori, Shigehiro

2016-12-01

Pseudomonas cichorii D-tagatose 3-epimerase (PcDTE), which has a broad substrate specificity, efficiently catalyzes the epimerization of not only D-tagatose to D-sorbose but also D-fructose to D-psicose (D-allulose) and also recognizes the deoxy sugars as substrates. In an attempt to elucidate the substrate recognition and catalytic reaction mechanisms of PcDTE for deoxy sugars, the X-ray structures of the PcDTE mutant form with the replacement of Cys66 by Ser (PcDTE_C66S) in complexes with deoxy sugars were determined. These X-ray structures showed that substrate recognition by the enzyme at the 1-, 2-, and 3-positions is responsible for enzymatic activity and that substrate-enzyme interactions at the 4-, 5-, and 6-positions are not essential for the catalytic reaction of the enzyme leading to the broad substrate specificity of PcDTE. They also showed that the epimerization site of 1-deoxy 3-keto D-galactitol is shifted from C3 to C4 and that 1-deoxy sugars may bind to the catalytic site in the inhibitor-binding mode. The hydrophobic groove that acts as an accessible surface for substrate binding is formed through the dimerization of PcDTE. In PcDTE_C66S/deoxy sugar complex structures, bound ligand molecules in both the linear and ring forms were detected in the hydrophobic groove, while bound ligand molecules in the catalytic site were in the linear form. This result suggests that the sugar-ring opening of a substrate may occur in the hydrophobic groove and also that the narrow channel of the passageway to the catalytic site allows a substrate in the linear form to pass through.

Method and system for producing sputtered thin films with sub-angstrom thickness uniformity or custom thickness gradients

DOEpatents

Folta, James A.; Montcalm, Claude; Walton, Christopher

2003-01-01

A method and system for producing a thin film with highly uniform (or highly accurate custom graded) thickness on a flat or graded substrate (such as concave or convex optics), by sweeping the substrate across a vapor deposition source with controlled (and generally, time-varying) velocity. In preferred embodiments, the method includes the steps of measuring the source flux distribution (using a test piece that is held stationary while exposed to the source), calculating a set of predicted film thickness profiles, each film thickness profile assuming the measured flux distribution and a different one of a set of sweep velocity modulation recipes, and determining from the predicted film thickness profiles a sweep velocity modulation recipe which is adequate to achieve a predetermined thickness profile. Aspects of the invention include a practical method of accurately measuring source flux distribution, and a computer-implemented method employing a graphical user interface to facilitate convenient selection of an optimal or nearly optimal sweep velocity modulation recipe to achieve a desired thickness profile on a substrate. Preferably, the computer implements an algorithm in which many sweep velocity function parameters (for example, the speed at which each substrate spins about its center as it sweeps across the source) can be varied or set to zero.

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.

Development of glycosynthases with broad glycan specificity for the efficient glyco-remodeling of antibodies.

PubMed

Shivatare, Sachin S; Huang, Lin-Ya; Zeng, Yi-Fang; Liao, Jung-Yu; You, Tsai-Hong; Wang, Shi-Yun; Cheng, Ting; Chiu, Chih-Wei; Chao, Ping; Chen, Li-Tzu; Tsai, Tsung-I; Huang, Chiu-Chen; Wu, Chung-Yi; Lin, Nan-Horng; Wong, Chi-Huey

2018-06-12

The first systematic investigation of the effect of high mannose, hybrid, and bi- and tri-antennary complex type glycans on the effector functions of antibodies was achieved by the discovery of novel Endo-S2 mutants generated by site-directed mutagenesis as glycosynthases with broad substrate specificity.

Ubiquitinated Proteome: Ready for Global?*

PubMed Central

Shi, Yi; Xu, Ping; Qin, Jun

2011-01-01

Ubiquitin (Ub) is a small and highly conserved protein that can covalently modify protein substrates. Ubiquitination is one of the major post-translational modifications that regulate a broad spectrum of cellular functions. The advancement of mass spectrometers as well as the development of new affinity purification tools has greatly expedited proteome-wide analysis of several post-translational modifications (e.g. phosphorylation, glycosylation, and acetylation). In contrast, large-scale profiling of lysine ubiquitination remains a challenge. Most recently, new Ub affinity reagents such as Ub remnant antibody and tandem Ub binding domains have been developed, allowing for relatively large-scale detection of several hundreds of lysine ubiquitination events in human cells. Here we review different strategies for the identification of ubiquitination site and discuss several issues associated with data analysis. We suggest that careful interpretation and orthogonal confirmation of MS spectra is necessary to minimize false positive assignments by automatic searching algorithms. PMID:21339389

Biochemical profiling in silico--predicting substrate specificities of large enzyme families.

PubMed

Tyagi, Sadhna; Pleiss, Juergen

2006-06-25

A general high-throughput method for in silico biochemical profiling of enzyme families has been developed based on covalent docking of potential substrates into the binding sites of target enzymes. The method has been tested by systematically docking transition state--analogous intermediates of 12 substrates into the binding sites of 20 alpha/beta hydrolases from 15 homologous families. To evaluate the effect of side chain orientations to the docking results, 137 crystal structures were included in the analysis. A good substrate must fulfil two criteria: it must bind in a productive geometry with four hydrogen bonds between the substrate and the catalytic histidine and the oxyanion hole, and a high affinity of the enzyme-substrate complex as predicted by a high docking score. The modelling results in general reproduce experimental data on substrate specificity and stereoselectivity: the differences in substrate specificity of cholinesterases toward acetyl- and butyrylcholine, the changes of activity of lipases and esterases upon the size of the acid moieties, activity of lipases and esterases toward tertiary alcohols, and the stereopreference of lipases and esterases toward chiral secondary alcohols. Rigidity of the docking procedure was the major reason for false positive and false negative predictions, as the geometry of the complex and docking score may sensitively depend on the orientation of individual side chains. Therefore, appropriate structures have to be identified. In silico biochemical profiling provides a time efficient and cost saving protocol for virtual screening to identify the potential substrates of the members of large enzyme family from a library of molecules.

Method for high-precision multi-layered thin film deposition for deep and extreme ultraviolet mirrors

DOEpatents

Ruffner, Judith Alison

1999-01-01

A method for coating (flat or non-flat) optical substrates with high-reflectivity multi-layer coatings for use at Deep Ultra-Violet ("DUV") and Extreme Ultra-Violet ("EUV") wavelengths. The method results in a product with minimum feature sizes of less than 0.10-.mu.m for the shortest wavelength (13.4-nm). The present invention employs a computer-based modeling and deposition method to enable lateral and vertical thickness control by scanning the position of the substrate with respect to the sputter target during deposition. The thickness profile of the sputter targets is modeled before deposition and then an appropriate scanning algorithm is implemented to produce any desired, radially-symmetric thickness profile. The present invention offers the ability to predict and achieve a wide range of thickness profiles on flat or figured substrates, i.e., account for 1/R.sup.2 factor in a model, and the ability to predict and accommodate changes in deposition rate as a result of plasma geometry, i.e., over figured substrates.

Photoluminescence enhancement of silicon quantum dot monolayer by plasmonic substrate fabricated by nano-imprint lithography

NASA Astrophysics Data System (ADS)

Yanagawa, Hiroto; Inoue, Asuka; Sugimoto, Hiroshi; Shioi, Masahiko; Fujii, Minoru

2017-12-01

Near-field coupling between a silicon quantum dot (Si-QD) monolayer and a plasmonic substrate fabricated by nano-imprint lithography and having broad multiple resonances in the near-infrared (NIR) window of biological substances was studied by precisely controlling the QDs-substrate distance. A strong enhancement of the NIR photoluminescence (PL) of Si-QDs was observed. Detailed analyses of the PL and PL excitation spectra, the PL decay dynamics, and the reflectance spectra revealed that both the excitation cross-sections and the emission rates are enhanced by the surface plasmon resonances, thanks to the broad multiple resonances of the plasmonic substrate, and that the relative contribution of the two enhancement processes depends strongly on the excitation wavelength. Under excitation by short wavelength photons (405 nm), where enhancement of the excitation cross-section is not expected, the maximum enhancement was obtained when the QDs-substrate distance was around 30 nm. On the other hand, under long wavelength excitation (641 nm), where strong excitation cross-section enhancement is expected, the largest enhancement was obtained when the distance was minimum (around 1 nm). The achievement of efficient excitation of NIR luminescence of Si-QDs by long wavelength photons paves the way for the development of Si-QD-based fluorescence bio-sensing devices with a high bound-to-free ratio.

A broad pH range indicator-based spectrophotometric assay for true lipases using tributyrin and tricaprylin.

PubMed

Camacho-Ruiz, María de Los Angeles; Mateos-Díaz, Juan Carlos; Carrière, Frédéric; Rodriguez, Jorge A

2015-05-01

A continuous assay is proposed for the screening of acidic, neutral, or alkaline lipases using microtiter plates, emulsified short- and medium-chain TGs, and a pH indicator. The lipase activity measurement is based on the decrease of the pH indicator optical density due to protonation which is caused by the release of FFAs during the hydrolysis of TGs and thus acidification. Purified lipases with distinct pH optima and an esterase were used to validate the method. The rate of lipolysis was found to be linear with time and proportional to the amount of enzyme added in each case. Specific activities measured with this microplate assay method were lower than those obtained by the pH-stat technique. Nevertheless, the pH-dependent profiles of enzymatic activity were similar with both assays. In addition, the substrate preference of each enzyme tested was not modified and this allowed discriminating lipase and esterase activities using tributyrin (low water solubility) and tricaprylin (not water soluble) as substrates. This continuous lipase assay is compatible with a high sample throughput and can be applied for the screening of lipases and lipase inhibitors from biological samples. Copyright © 2015 by the American Society for Biochemistry and Molecular Biology, Inc.

Orbital Angular Momentum (OAM) Antennas via Mode Combining and Canceling in Near-field.

PubMed

Byun, Woo Jin; Do Choi, Hyung; Cho, Yong Heui

2017-10-09

Orbital angular momentum (OAM) mode combining and canceling in the near-field was investigated using a Cassegrain dual-reflectarray antenna composed of multiple microstrip patches on the main and sub-reflectarrays. Microstrip patches on dielectric substrates were designed to radiate the particular OAM modes for arithmetic mode combining, where two OAM wave-generating reflectarrays are very closely placed in the near-field. We conducted near-field antenna measurements at 18 [GHz] by manually replacing the sub-reflectarray substrates with different OAM mode numbers of 0, ±1, when the OAM mode number of the main reflectarray was fixed to +1. We subsequently checked the azimuthal phase distributions of the reflected total electromagnetic waves in the near-field, and verified that the OAM waves mutually reflected from the main and sub-reflectarrays are added or subtracted to each other according to their OAM mode numbers. Based on our proposal, an OAM mode-canceling reflectarray antenna was designed, and the following measurements indicate that the antenna has a better reflection bandwidth and antenna gain than a conventional reflectarray antenna. The concept of OAM mode canceling in the near-field can contribute widely to a new type of low-profile, broad-reflection bandwidth, and high-gain antenna.

Mechanistic Basis for High Stereoselectivity and Broad Substrate Scope in the (salen)Co(III)-Catalyzed Hydrolytic Kinetic Resolution

PubMed Central

Ford, David D.; Nielsen, Lars P. C.; Zuend, Stephan J.; Jacobsen, Eric N.

2013-01-01

In the (salen)Co(III)-catalyzed hydrolytic kinetic resolution (HKR) of terminal epoxides, the rate- and stereoselectivity-determining epoxide ring-opening step occurs by a cooperative bimetallic mechanism with one Co(III) complex acting as a Lewis acid and another serving to deliver the hydroxide nucleophile. In this paper, we analyze the basis for the extraordinarily high stereoselectivity and broad substrate scope observed in the HKR. We demonstrate that the stereochemistry of each of the two (salen)Co(III) complexes in the rate-determining transition structure is important for productive catalysis: a measurable rate of hydrolysis occurs only if the absolute stereochemistry of each of these (salen)Co(III) complexes is the same. Experimental and computational studies provide strong evidence that stereochemical communication in the HKR is mediated by the stepped conformation of the salen ligand, and not the shape of the chiral diamine backbone of the ligand. A detailed computational analysis reveals that the epoxide binds the Lewis acidic Co(III) complex in a well-defined geometry imposed by stereoelectronic, rather than steric effects. This insight serves as the basis of a complete stereochemical and transition structure model that sheds light on the reasons for the broad substrate generality of the HKR. PMID:24041239

Mechanistic basis for high stereoselectivity and broad substrate scope in the (salen)Co(III)-catalyzed hydrolytic kinetic resolution.

PubMed

Ford, David D; Nielsen, Lars P C; Zuend, Stephan J; Musgrave, Charles B; Jacobsen, Eric N

2013-10-16

In the (salen)Co(III)-catalyzed hydrolytic kinetic resolution (HKR) of terminal epoxides, the rate- and stereoselectivity-determining epoxide ring-opening step occurs by a cooperative bimetallic mechanism with one Co(III) complex acting as a Lewis acid and another serving to deliver the hydroxide nucleophile. In this paper, we analyze the basis for the extraordinarily high stereoselectivity and broad substrate scope observed in the HKR. We demonstrate that the stereochemistry of each of the two (salen)Co(III) complexes in the rate-determining transition structure is important for productive catalysis: a measurable rate of hydrolysis occurs only if the absolute stereochemistry of each of these (salen)Co(III) complexes is the same. Experimental and computational studies provide strong evidence that stereochemical communication in the HKR is mediated by the stepped conformation of the salen ligand, and not the shape of the chiral diamine backbone of the ligand. A detailed computational analysis reveals that the epoxide binds the Lewis acidic Co(III) complex in a well-defined geometry imposed by stereoelectronic rather than steric effects. This insight serves as the basis of a complete stereochemical and transition structure model that sheds light on the reasons for the broad substrate generality of the HKR.

Towards substrate engineering of graphene-silicon Schottky diode photodetectors.

PubMed

Selvi, Hakan; Unsuree, Nawapong; Whittaker, Eric; Halsall, Matthew P; Hill, Ernie W; Thomas, Andrew; Parkinson, Patrick; Echtermeyer, Tim J

2018-02-15

Graphene-silicon Schottky diode photodetectors possess beneficial properties such as high responsivities and detectivities, broad spectral wavelength operation and high operating speeds. Various routes and architectures have been employed in the past to fabricate devices. Devices are commonly based on the removal of the silicon-oxide layer on the surface of silicon by wet-etching before deposition of graphene on top of silicon to form the graphene-silicon Schottky junction. In this work, we systematically investigate the influence of the interfacial oxide layer, the fabrication technique employed and the silicon substrate on the light detection capabilities of graphene-silicon Schottky diode photodetectors. The properties of devices are investigated over a broad wavelength range from near-UV to short-/mid-infrared radiation, radiation intensities covering over five orders of magnitude as well as the suitability of devices for high speed operation. Results show that the interfacial layer, depending on the required application, is in fact beneficial to enhance the photodetection properties of such devices. Further, we demonstrate the influence of the silicon substrate on the spectral response and operating speed. Fabricated devices operate over a broad spectral wavelength range from the near-UV to the short-/mid-infrared (thermal) wavelength regime, exhibit high photovoltage responses approaching 10 6 V W -1 and short rise- and fall-times of tens of nanoseconds.

Automated X-ray quality control of catalytic converters

NASA Astrophysics Data System (ADS)

Shashishekhar, N.; Veselitza, D.

2017-02-01

Catalytic converters are devices attached to the exhaust system of automobile or other engines to eliminate or substantially reduce polluting emissions. They consist of coated substrates enclosed in a stainless steel housing. The substrate is typically made of ceramic honeycombs; however stainless steel foil honeycombs are also used. The coating is usually a slurry of alumina, silica, rare earth oxides and platinum group metals. The slurry also known as the wash coat is applied to the substrate in two doses, one on each end of the substrate; in some cases multiple layers of coating are applied. X-ray imaging is used to inspect the applied coating depth on a substrate to confirm compliance with quality requirements. Automated image analysis techniques are employed to measure the coating depth from the X-ray image. Coating depth is assessed by analysis of attenuation line profiles in the image. Edge detection algorithms with noise reduction and outlier rejection are used to calculate the coating depth at a specified point along an attenuation line profile. Quality control of the product is accomplished using several attenuation line profile regions for coating depth measurements, with individual pass or fail criteria specified for each region.

Sorption of VX to Clay Minerals and Soils: Thermodynamic and Kinetic Studies

DTIC Science & Technology

2012-12-01

Suspengel 200, humus , and soil substrates for use in this study. In addition, the authors gratefully acknowledge the support of the ECBC Technical...sorption profiles for VX with clay substrates ..................................55 30. Initial kinetic sorption profiles for VX with humus ...naturally derived garden soil amendment, identified as humus , was purchased from Frey Brothers (Quarryville, PA). Two natural soils, identified as MCL lot

Optically-initiated silicon carbide high voltage switch with contoured-profile electrode interfaces

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

Sullivan, James S.; Hawkins, Steven A.

An improved photoconductive switch having a SiC or other wide band gap substrate material with opposing contoured profile cavities which have a contoured profile selected from one of Rogowski, Bruce, Chang, Harrison, and Ernst profiles, and two electrodes with matching contoured-profile convex interface surfaces.

Subcellular localization of rat CYP2E1 impacts metabolic efficiency toward common substrates.

PubMed

Hartman, Jessica H; Martin, H Cass; Caro, Andres A; Pearce, Amy R; Miller, Grover P

2015-12-02

Cytochrome P450 2E1 (CYP2E1) detoxifies or bioactivates many low molecular-weight compounds. Most knowledge about CYP2E1 activity relies on studies of the enzyme localized to endoplasmic reticulum (erCYP2E1); however, CYP2E1 undergoes transport to mitochondria (mtCYP2E1) and becomes metabolically active. We report the first comparison of in vitro steady-state kinetic profiles for erCYP2E1 and mtCYP2E1 oxidation of probe substrate 4-nitrophenol and pollutants styrene and aniline using subcellular fractions from rat liver. For all substrates, metabolic efficiency changed with substrate concentration for erCYP2E1 reflected in non-hyperbolic kinetic profiles but not for mtCYP2E1. Hyperbolic kinetic profiles for the mitochondrial enzyme were consistent with Michaelis-Menten mechanism in which metabolic efficiency was constant. By contrast, erCYP2E1 metabolism of 4-nitrophenol led to a loss of enzyme efficiency at high substrate concentrations when substrate inhibited the reaction. Similarly, aniline metabolism by erCYP2E1 demonstrated negative cooperativity as metabolic efficiency decreased with increasing substrate concentration. The opposite was observed for erCYP2E1 oxidation of styrene; the sigmoidal kinetic profile indicated increased efficiency at higher substrate concentrations. These mechanisms and CYP2E1 levels in mitochondria and endoplasmic reticulum were used to estimate the impact of CYP2E1 subcellular localization on metabolic flux of pollutants. Those models showed that erCYP2E1 mainly carries out aniline metabolism at all aniline concentrations. Conversely, mtCYP2E1 dominates styrene oxidation at low styrene concentrations and erCYP2E1 at higher concentrations. Taken together, subcellular localization of CYP2E1 results in distinctly different enzyme activities that could impact overall metabolic clearance and/or activation of substrates and thus impact the interpretation and prediction of toxicological outcomes. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Catalytic mechanism and substrate specificity of the β-subunit of the voltage-gated potassium (Kv) channel

PubMed Central

Tipparaju, Srinivas M.; Barski, Oleg A.; Srivastava, Sanjay; Bhatnagar, Aruni

2008-01-01

The β-subunits of voltage-gated potassium (Kv) channels are members of aldo-keto reductase (AKR) superfamily. These proteins regulate inactivation and membrane localization of Kv1 and Kv4 channels. The Kvβ proteins bind to pyridine nucleotides with high affinity; however, their catalytic properties remain unclear. Here we report that recombinant rat Kvβ2 catalyzes the reduction of a wide range of aldehydes and ketones. The rate of catalysis was slower (0.06 to 0.2 min−1) than that of other AKRs, but displayed the expected hyperbolic dependence on substrate concentration, with no evidence of allosteric cooperativity. Catalysis was prevented by site-directed substitution of Tyr-90 with phenylalanine, indicating that the acid-base catalytic residue, identified in other AKRs, has a conserved function in Kvβ2. The protein catalyzed the reduction of a broad range of carbonyls including aromatic carbonyls, electrophilic aldehydes and prostaglandins, phospholipid and sugar aldehydes. Little or no activity was detected with carbonyl steroids. Initial velocity profiles were consistent with an ordered bi-bi rapid-equilibrium mechanism in which NADPH binding precedes carbonyl binding. Significant primary kinetic isotope effects (2.0 – 3.1) were observed under single and multiple turnover conditions, indicating that the bond-breaking chemical step is rate-limiting. Structure-activity relationships with a series of para-substituted benzaldehydes indicated that the electronic interactions predominate during substrate binding and that no significant charge develops during the transition state. These data strengthen the view that Kvβ proteins are catalytically-active AKRs that impart redox-sensitivity to Kv channels. PMID:18672894

pH Dependence of a Mammalian Polyamine Oxidase: Insights into Substrate Specificity and the Role of Lysine 315†

PubMed Central

Pozzi, Michelle Henderson; Gawandi, Vijay; Fitzpatrick, Paul F.

2009-01-01

Mammalian polyamine oxidases (PAO) catalyze the oxidation of N1-acetylspermine and N1-acetylspermidine to produce N-acetyl-3-aminopropanaldehyde and spermidine or putrescine. Structurally, PAO is a member of the monoamine oxidase family of flavoproteins. The effects of pH on kinetic parameters of mouse PAO have been determined to provide insight into the protonation state of the polyamine required for catalysis and the roles of ionizable residues in the active site in amine oxidation. For N1-acetylspermine, N1-acetylspermidine, and spermine, the kcat/Kamine-pH profiles are bell-shaped. In each case the profile agrees with that expected if the productive form of the substrate has a single positively charged nitrogen. The pKi-pH profiles for a series of polyamine analogs are most consistent with the nitrogen at the site of oxidation being neutral and one other nitrogen being positively charged in the reactive form of the substrate. With N1-acetylspermine as substrate, the value of kred, the limiting rate constant for flavin reduction, is pH dependent, decreasing below a pKa value of 7.3, again consistent with the requirement for an uncharged nitrogen for substrate oxidation. Lys315 in PAO corresponds to a conserved active site residue found throughout the monoamine oxidase family. Mutation of Lys315 to methionine has no effect on the kcat/Kamine profile for spermine, the kred value with N1-acetylspermine is only 1.8-fold lower in the mutant protein, and the pKa in the kred-pH profile with N1-acetylspermine shifts to 7.8. These results rule out Lys315 as a source of a pKa in the kcat/Kamine or kcat/kred profiles. They also establish that this residue does not play a critical role in amine oxidation by PAO. PMID:19199575

Self-assembled antireflection coatings for light trapping based on SiGe random metasurfaces

NASA Astrophysics Data System (ADS)

Bouabdellaoui, Mohammed; Checcucci, Simona; Wood, Thomas; Naffouti, Meher; Sena, Robert Paria; Liu, Kailang; Ruiz, Carmen M.; Duche, David; le Rouzo, Judikael; Escoubas, Ludovic; Berginc, Gerard; Bonod, Nicolas; Zazoui, Mimoun; Favre, Luc; Metayer, Leo; Ronda, Antoine; Berbezier, Isabelle; Grosso, David; Gurioli, Massimo; Abbarchi, Marco

2018-03-01

We demonstrate a simple self-assembly method based on solid state dewetting of ultrathin silicon films and germanium deposition for the fabrication of efficient antireflection coatings on silicon for light trapping. We fabricate SiGe islands with a high surface density, randomly positioned and broadly varied in size. This allows one to reduce the reflectance to low values in a broad spectral range (from 500 nm to 2500 nm) and a broad angle (up to 55°) and to trap within the wafer a large portion of the impinging light (˜40 % ) also below the band gap, where the Si substrate is nonabsorbing. Theoretical simulations agree with the experimental results, showing that the efficient light coupling into the substrate is mediated by Mie resonances formed within the SiGe islands. This lithography-free method can be implemented on arbitrarily thick or thin SiO2 layers and its duration only depends on the sample thickness and on the annealing temperature.

Alkyl Aryl Ether Bond Formation with PhenoFluor**

PubMed Central

Shen, Xiao; Neumann, Constanze N.; Kleinlein, Claudia; Claudia, Nathaniel W.; Ritter, Tobias

2015-01-01

An alkyl aryl ether bond formation reaction between phenols and primary and secondary alcohols with PhenoFluor has been developed. The reaction features a broad substrate scope and tolerates many functional groups, and substrates that are challenging for more conventional ether bond forming processes may be coupled. A preliminary mechanistic study indicates reactivity distinct from conventional ether bond formation. PMID:25800679

Direct Y-STR amplification of body fluids deposited on commonly found crime scene substrates.

PubMed

Dargay, Amanda; Roy, Reena

2016-04-01

Body fluids detected on commonly found crime scene substrates require extraction, purification and quantitation of DNA prior to amplification and generation of short tandem repeat (STR) DNA profiles. In this research Y-STR profiles were generated via direct amplification of blood and saliva deposited on 12 different substrates. These included cigarette butts, straws, grass, leaves, woodchips and seven different types of fabric. After depositing either 0.1 μL of blood or 0.5 μL of saliva, each substrate containing the dry body fluid stain was punched using a Harris 1.2 mm micro-punch. Each of these punched substrates, a total of 720 samples, containing minute amount of blood or saliva was either amplified directly without any pre-treatment, or was treated with one of the four washing reagents or buffer. In each of these five experimental groups the substrates containing the body fluid remained in the amplification reagent during the thermal cycling process. Each sample was amplified with the three direct Y-STR amplification kits; AmpFℓSTR(®) Yfiler(®) Direct, Yfiler(®) Plus Amplification Kits and the PowerPlex(®) Y23 System. Complete and concordant Y-STR profiles were successfully obtained from most of these 12 challenging crime scene objects when the stains were analyzed by at least one of the five experimental groups. The reagents and buffer were interchangeable among the three amplification kits, however, pre-treatment with these solutions did not appear to enhance the quality or the number of the full profiles generated with direct amplification. This study demonstrates that blood and saliva deposited on these simulated crime scene objects can be amplified directly. Copyright © 2016 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

Community-level physiological profiling performed with an oxygen-sensitive fluorophore in a microtiter plate

NASA Technical Reports Server (NTRS)

Garland, Jay L.; Roberts, Michael S.; Levine, Lanfang H.; Mills, Aaron L.

2003-01-01

Community-level physiological profiling based upon fluorometric detection of oxygen consumption was performed on hydroponic rhizosphere and salt marsh litter samples by using substrate levels as low as 50 ppm with incubation times between 5 and 24 h. The rate and extent of response were increased in samples acclimated to specific substrates and were reduced by limiting nitrogen availability in the wells.

Mechanistic Studies of the Yeast Polyamine Oxidase Fms1: Kinetic Mechanism, Substrate Specificity, and pH Dependence†

PubMed Central

Adachi, Mariya S.; Torres, Jason M.; Fitzpatrick, Paul F.

2010-01-01

The flavoprotein oxidase Fms1 from Saccharomyces cerevisiae catalyzes the oxidation of spermine and N1-acetylspermine to yield spermidine and 3-aminopropanal or N-acetyl-3-aminopropanal. The kinetic mechanism of the enzyme has been determined with both substrates. The initial velocity patterns are ping-pong, consistent with reduction being kinetically irreversible. Reduction of Fms1 by either substrate is biphasic. The rate constant for the rapid phase varies with the substrate concentration, with limiting rates for reduction of the enzyme of 126 and 1410 s−1 and apparent Kd values of 24.3 and 484 μM for spermine and N1-acetylspermine, respectively. The rapid phase is followed by a concentration-independent phase that is slower than turnover. The reaction of the reduced enzyme with oxygen is monophasic, with a rate constant of 402 mM−1 s−1 with spermine at 25 °C, and 204 mM−1 s−1 with N1-acetylspermine at 4 °C, pH 9.0. This step is followed by rate-limiting product dissociation. The kcat/Kamine-pH profiles are bell-shaped, with an average pKa value of 9.3 with spermine and pKa values of 8.3 and 9.6 with N1-acetylspermine. Both profiles are consistent with the active forms of substrates having two charged nitrogens. The pH profiles for the rate constant for flavin reduction show pKa values of 8.3 and 7.2 for spermine and N1-acetylspermine, respectively, for groups that must be unprotonated; these pKa values are assigned to the substrate N4. The kcat/KO2-pH profiles show pKa values of 7.5 for spermine and 6.8 for N1-acetylspermine. With both substrates, the kcat value decreases when a single residue is protonated. PMID:21067138

Morphology and enzyme production of Trichoderma reesei Rut C-30 are affected by the physical and structural characteristics of cellulosic substrates.

PubMed

Peciulyte, Ausra; Anasontzis, George E; Karlström, Katarina; Larsson, Per Tomas; Olsson, Lisbeth

2014-11-01

The industrial production of cellulolytic enzymes is dominated by the filamentous fungus Trichoderma reesei (anamorph of Hypocrea jecorina). In order to develop optimal enzymatic cocktail, it is of importance to understand the natural regulation of the enzyme profile as response to the growth substrate. The influence of the complexity of cellulose on enzyme production by the microorganisms is not understood. In the present study we attempted to understand how different physical and structural properties of cellulose-rich substrates affected the levels and profiles of extracellular enzymes produced by T. reesei. Enzyme production by T. reesei Rut C-30 was studied in submerged cultures on five different cellulose-rich substrates, namely, commercial cellulose Avicel® and industrial-like cellulosic pulp substrates which consist mainly of cellulose, but also contain residual hemicellulose and lignin. In order to evaluate the hydrolysis of the substrates by the fungal enzymes, the spatial polymer distributions were characterised by cross-polarisation magic angle spinning carbon-13 nuclear magnetic resonance (CP/MAS (13)C-NMR) in combination with spectral fitting. Proteins in culture supernatants at early and late stages of enzyme production were labeled by Tandem Mass Tags (TMT) and protein profiles were analysed by liquid chromatography-tandem mass spectrometry. The data have been deposited to the ProteomeXchange with identifier PXD001304. In total 124 proteins were identified and quantified in the culture supernatants, including cellulases, hemicellulases, other glycoside hydrolases, lignin-degrading enzymes, auxiliary activity 9 (AA9) family (formerly GH61), supporting activities of proteins and enzymes acting on cellulose, proteases, intracellular proteins and several hypothetical proteins. Surprisingly, substantial differences in the enzyme profiles were found even though there were minor differences in the chemical composition between the cellulose-rich substrates. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Method for high-precision multi-layered thin film deposition for deep and extreme ultraviolet mirrors

DOEpatents

Ruffner, J.A.

1999-06-15

A method for coating (flat or non-flat) optical substrates with high-reflectivity multi-layer coatings for use at Deep Ultra-Violet (DUV) and Extreme Ultra-Violet (EUV) wavelengths. The method results in a product with minimum feature sizes of less than 0.10 [micro]m for the shortest wavelength (13.4 nm). The present invention employs a computer-based modeling and deposition method to enable lateral and vertical thickness control by scanning the position of the substrate with respect to the sputter target during deposition. The thickness profile of the sputter targets is modeled before deposition and then an appropriate scanning algorithm is implemented to produce any desired, radially-symmetric thickness profile. The present invention offers the ability to predict and achieve a wide range of thickness profiles on flat or figured substrates, i.e., account for 1/R[sup 2] factor in a model, and the ability to predict and accommodate changes in deposition rate as a result of plasma geometry, i.e., over figured substrates. 15 figs.

Energy metabolic reprogramming in the hypertrophied and early stage failing heart: a multisystems approach.

PubMed

Lai, Ling; Leone, Teresa C; Keller, Mark P; Martin, Ola J; Broman, Aimee T; Nigro, Jessica; Kapoor, Kapil; Koves, Timothy R; Stevens, Robert; Ilkayeva, Olga R; Vega, Rick B; Attie, Alan D; Muoio, Deborah M; Kelly, Daniel P

2014-11-01

An unbiased systems approach was used to define energy metabolic events that occur during the pathological cardiac remodeling en route to heart failure (HF). Combined myocardial transcriptomic and metabolomic profiling were conducted in a well-defined mouse model of HF that allows comparative assessment of compensated and decompensated (HF) forms of cardiac hypertrophy because of pressure overload. The pressure overload data sets were also compared with the myocardial transcriptome and metabolome for an adaptive (physiological) form of cardiac hypertrophy because of endurance exercise training. Comparative analysis of the data sets led to the following conclusions: (1) expression of most genes involved in mitochondrial energy transduction were not significantly changed in the hypertrophied or failing heart, with the notable exception of a progressive downregulation of transcripts encoding proteins and enzymes involved in myocyte fatty acid transport and oxidation during the development of HF; (2) tissue metabolite profiles were more broadly regulated than corresponding metabolic gene regulatory changes, suggesting significant regulation at the post-transcriptional level; (3) metabolomic signatures distinguished pathological and physiological forms of cardiac hypertrophy and served as robust markers for the onset of HF; and (4) the pattern of metabolite derangements in the failing heart suggests bottlenecks of carbon substrate flux into the Krebs cycle. Mitochondrial energy metabolic derangements that occur during the early development of pressure overload-induced HF involve both transcriptional and post-transcriptional events. A subset of the myocardial metabolomic profile robustly distinguished pathological and physiological cardiac remodeling. © 2014 American Heart Association, Inc.

Structural basis for the substrate specificity of PepA from Streptococcus pneumoniae, a dodecameric tetrahedral protease.

PubMed

Kim, Doyoun; San, Boi Hoa; Moh, Sang Hyun; Park, Hyejin; Kim, Dong Young; Lee, Sangho; Kim, Kyeong Kyu

2010-01-01

Regulated cytosolic proteolysis is one of the key cellular processes ensuring proper functioning of a cell. M42 family proteases show a broad spectrum of substrate specificities, but the structural basis for such diversity of the substrate specificities is lagging behind biochemical data. Here we report the crystal structure of PepA from Streptococcus pneumoniae, a glutamyl aminopeptidase belonging to M42 family (SpPepA). We found that Arg-257 in the substrate binding pocket is strategically positioned so that Arg-257 can make electrostatic interactions with the acidic residue of a substrate at its N-terminus. Structural comparison of the substrate binding pocket of the M42 family proteases, along with the structure-based multiple sequence alignment, argues that the appropriate electrostatic interactions contribute to the selective substrate specificity of SpPepA. Copyright 2009 Elsevier Inc. All rights reserved.

COSIM: A Finite-Difference Computer Model to Predict Ternary Concentration Profiles Associated With Oxidation and Interdiffusion of Overlay-Coated Substrates

NASA Technical Reports Server (NTRS)

Nesbitt, James A.

2001-01-01

A finite-difference computer program (COSIM) has been written which models the one-dimensional, diffusional transport associated with high-temperature oxidation and interdiffusion of overlay-coated substrates. The program predicts concentration profiles for up to three elements in the coating and substrate after various oxidation exposures. Surface recession due to solute loss is also predicted. Ternary cross terms and concentration-dependent diffusion coefficients are taken into account. The program also incorporates a previously-developed oxide growth and spalling model to simulate either isothermal or cyclic oxidation exposures. In addition to predicting concentration profiles after various oxidation exposures, the program can also be used to predict coating life based on a concentration dependent failure criterion (e.g., surface solute content drops to 2%). The computer code is written in FORTRAN and employs numerous subroutines to make the program flexible and easily modifiable to other coating oxidation problems.

Functional and Structural Characterization of Purine Nucleoside Phosphorylase from Kluyveromyces lactis and Its Potential Applications in Reducing Purine Content in Food

PubMed Central

Mahor, Durga; Priyanka, Anu; Prasad, Gandham S; Thakur, Krishan Gopal

2016-01-01

Consumption of foods and beverages with high purine content increases the risk of hyperuricemia, which causes gout and can lead to cardiovascular, renal, and other metabolic disorders. As patients often find dietary restrictions challenging, enzymatically lowering purine content in popular foods and beverages offers a safe and attractive strategy to control hyperuricemia. Here, we report structurally and functionally characterized purine nucleoside phosphorylase (PNP) from Kluyveromyces lactis (KlacPNP), a key enzyme involved in the purine degradation pathway. We report a 1.97 Å resolution crystal structure of homotrimeric KlacPNP with an intrinsically bound hypoxanthine in the active site. KlacPNP belongs to the nucleoside phosphorylase-I (NP-I) family, and it specifically utilizes 6-oxopurine substrates in the following order: inosine > guanosine > xanthosine, but is inactive towards adenosine. To engineer enzymes with broad substrate specificity, we created two point variants, KlacPNPN256D and KlacPNPN256E, by replacing the catalytically active Asn256 with Asp and Glu, respectively, based on structural and comparative sequence analysis. KlacPNPN256D not only displayed broad substrate specificity by utilizing both 6-oxopurines and 6-aminopurines in the order adenosine > inosine > xanthosine > guanosine, but also displayed reversal of substrate specificity. In contrast, KlacPNPN256E was highly specific to inosine and could not utilize other tested substrates. Beer consumption is associated with increased risk of developing gout, owing to its high purine content. Here, we demonstrate that KlacPNP and KlacPNPN256D could be used to catalyze a key reaction involved in lowering beer purine content. Biochemical properties of these enzymes such as activity across a wide pH range, optimum activity at about 25°C, and stability for months at about 8°C, make them suitable candidates for food and beverage industries. Since KlacPNPN256D has broad substrate specificity, a combination of engineered KlacPNP and other enzymes involved in purine degradation could effectively lower the purine content in foods and beverages. PMID:27768715

Numerical analysis of high-power broad-area laser diode with improved heat sinking structure using epitaxial liftoff technique

NASA Astrophysics Data System (ADS)

Kim, Younghyun; Sung, Yunsu; Yang, Jung-Tack; Choi, Woo-Young

2018-02-01

The characteristics of high-power broad-area laser diodes with the improved heat sinking structure are numerically analyzed by a technology computer-aided design based self-consistent electro-thermal-optical simulation. The high-power laser diodes consist of a separate confinement heterostructure of a compressively strained InGaAsP quantum well and GaInP optical cavity layers, and a 100-μm-wide rib and a 2000-μm long cavity. In order to overcome the performance deteriorations of high-power laser diodes caused by self-heating such as thermal rollover and thermal blooming, we propose the high-power broad-area laser diode with improved heat-sinking structure, which another effective heat-sinking path toward the substrate side is added by removing a bulk substrate. It is possible to obtain by removing a 400-μm-thick GaAs substrate with an AlAs sacrificial layer utilizing well-known epitaxial liftoff techniques. In this study, we present the performance improvement of the high-power laser diode with the heat-sinking structure by suppressing thermal effects. It is found that the lateral far-field angle as well as quantum well temperature is expected to be improved by the proposed heat-sinking structure which is required for high beam quality and optical output power, respectively.

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 composition.« less

Efficient broad color luminescence from InGaN/GaN single quantum-well nanocolumn crystals on Si (111) substrate

NASA Astrophysics Data System (ADS)

Zhang, Wei; Zhang, Xuehua; Wang, Yongjin; Hu, Fangren

2017-10-01

Nanocolumn InGaN/GaN single quantum well crystals were deposited on Si (111) substrate with nitrified Ga dots as buffer layer. Transmission electron microscopy image shows the crystals' diameter of 100-130 nm and length of about 900 nm. Nanoscale spatial phase separation of cubic and hexagonal GaN was observed by selective area electron diffraction on the quantum well layer. Raman spectrum of the quantum well crystals proved that the crystals were fully relaxed. Room temperature photoluminescence from 450 to 750 nm and full width at half maximum of about 420 meV indicate broad color luminescence covering blue, green, yellow and red emission, which is helpful for the fabrication of tunable optoelectronic devices and colorful light emitting diodes.

A novel non-thermostable deuterolysin from Aspergillus oryzae.

PubMed

Maeda, Hiroshi; Katase, Toru; Sakai, Daisuke; Takeuchi, Michio; Kusumoto, Ken-Ichi; Amano, Hitoshi; Ishida, Hiroki; Abe, Keietsu; Yamagata, Youhei

2016-09-01

Three putative deuterolysin (EC 3.4.24.29) genes (deuA, deuB, and deuC) were found in the Aspergillus oryzae genome database ( http://www.bio.nite.go.jp/dogan/project/view/AO ). One of these genes, deuA, was corresponding to NpII gene, previously reported. DeuA and DeuB were overexpressed by recombinant A. oryzae and were purified. The degradation profiles against protein substrates of both enzymes were similar, but DeuB showed wider substrate specificity against peptidyl MCA-substrates compared with DeuA. Enzymatic profiles of DeuB except for thermostability also resembled those of DeuA. DeuB was inactivated by heat treatment above 80° C, different from thermostable DeuA. Transcription analysis in wild type A. oryzae showed only deuB was expressed in liquid culture, and the addition of the proteinous substrate upregulated the transcription. Furthermore, the NaNO3 addition seems to eliminate the effect of proteinous substrate for the transcription of deuB.

Composite perfluorohydrocarbon membranes, their preparation and use

DOEpatents

Ding, Yong; Bikson, Benjamin

2017-04-04

Composite porous hydrophobic membranes are prepared by forming a perfluorohydrocarbon layer on the surface of a preformed porous polymeric substrate. The substrate can be formed from poly (aryl ether ketone) and a perfluorohydrocarbon layer can be chemically grafted to the surface of the substrate. The membranes can be utilized for a broad range of fluid separations, such as microfiltration, nanofiltration, ultrafiltration as membrane contactors for membrane distillation and for degassing and dewatering of fluids. The membranes can further contain a dense ultra-thin perfluorohydrocarbon layer superimposed on the porous poly (aryl ether ketone) substrate and can be utilized as membrane contactors or as gas separation. membranes for natural gas treatment and gas dehydration.

Electrically pumped 1.3 microm room-temperature InAs/GaAs quantum dot lasers on Si substrates by metal-mediated wafer bonding and layer transfer.

PubMed

Tanabe, Katsuaki; Guimard, Denis; Bordel, Damien; Iwamoto, Satoshi; Arakawa, Yasuhiko

2010-05-10

An electrically pumped InAs/GaAs quantum dot laser on a Si substrate has been demonstrated. The double-hetero laser structure was grown on a GaAs substrate by metal-organic chemical vapor deposition and layer-transferred onto a Si substrate by GaAs/Si wafer bonding mediated by a 380-nm-thick Au-Ge-Ni alloy layer. This broad-area Fabry-Perot laser exhibits InAs quantum dot ground state lasing at 1.31 microm at room temperature with a threshold current density of 600 A/cm(2). (c) 2010 Optical Society of America.

EMISSION SIGNATURES FROM SUB-PARSEC BINARY SUPERMASSIVE BLACK HOLES. I. DIAGNOSTIC POWER OF BROAD EMISSION LINES

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

Nguyen, Khai; Bogdanović, Tamara

Motivated by advances in observational searches for sub-parsec supermassive black hole binaries (SBHBs) made in the past few years, we develop a semi-analytic model to describe spectral emission-line signatures of these systems. The goal of this study is to aid the interpretation of spectroscopic searches for binaries and to help test one of the leading models of binary accretion flows in the literature: SBHB in a circumbinary disk. In this work, we present the methodology and a comparison of the preliminary model with the data. We model SBHB accretion flows as a set of three accretion disks: two mini-disks thatmore » are gravitationally bound to the individual black holes and a circumbinary disk. Given a physically motivated parameter space occupied by sub-parsec SBHBs, we calculate a synthetic database of nearly 15 million broad optical emission-line profiles and explore the dependence of the profile shapes on characteristic properties of SBHBs. We find that the modeled profiles show distinct statistical properties as a function of the semimajor axis, mass ratio, eccentricity of the binary, and the degree of alignment of the triple disk system. This suggests that the broad emission-line profiles from SBHB systems can in principle be used to infer the distribution of these parameters and as such merit further investigation. Calculated profiles are more morphologically heterogeneous than the broad emission lines in observed SBHB candidates and we discuss improved treatment of radiative transfer effects, which will allow a direct statistical comparison of the two groups.« less

A computational study of the dechlorination of β-hexachlorocyclohexane (β-HCH) catalyzed by the haloalkane dehalogenase LinB.

PubMed

Manna, Rabindra Nath; Dybala-Defratyka, Agnieszka

2014-11-15

LinB, a haloalkane dehalogenase from Sphingomonas paucimobilis UT26, is known to metabolize halohydrocarbons to halide ions and the respective alcohols. Its broad substrate specificity allowed its consideration for bioremediation. Herein, we have shown its catalytic action toward β-hexachlorocyclohexane (β-HCH) - an example of large-size substrates that can be accommodated in its active site. We have analyzed the capability of combined QM/MM schemes to describe in detail the SN2 dechlorination reaction between β-HCH and Asp108 in the active site of LinB. Free energy surfaces have been calculated using one and two dimensional potentials of mean force (PMF) obtained at the PM3/MM (MM=amberff99SB, TIP3P) level of theory. The overestimated energetic barriers by the PM3 Hamiltonian were corrected using a DFT functional (M06-2X). The resulted activation energies (16 and 19 kcal mol(-1) from 1D and 2D-PMF profiles, respectively) for the dechlorination reaction of β-HCH in the active site of LinB enzyme are in qualitative agreement with the experimentally determined value of 17 kcal mol(-1). The binding of β-HCH to the active site of LinB has been compared to the binding of smaller 1-chlorobutane (1-CB) and larger δ-hexabromocyclododecane (δ-HBCD). Copyright © 2014 Elsevier Inc. All rights reserved.

Assessment Practices of Child Clinicians.

PubMed

Cook, Jonathan R; Hausman, Estee M; Jensen-Doss, Amanda; Hawley, Kristin M

2017-03-01

Assessment is an integral component of treatment. However, prior surveys indicate clinicians may not use standardized assessment strategies. We surveyed 1,510 clinicians and used multivariate analysis of variance to explore group differences in specific measure use. Clinicians used unstandardized measures more frequently than standardized measures, although psychologists used standardized measures more frequently than nonpsychologists. We also used latent profile analysis to classify clinicians based on their overall approach to assessment and examined associations between clinician-level variables and assessment class or profile membership. A four-profile model best fit the data. The largest profile consisted of clinicians who primarily used unstandardized assessments (76.7%), followed by broad-spectrum assessors who regularly use both standardized and unstandardized assessment (11.9%), and two smaller profiles of minimal (6.0%) and selective assessors (5.5%). Compared with broad-spectrum assessors, unstandardized and minimal assessors were less likely to report having adequate standardized measures training. Implications for clinical practice and training are discussed.

Phosphatidylinositol kinase. A component of the chromaffin-granule membrane

PubMed Central

Phillips, John H.

1973-01-01

Phosphorylation of bovine chromaffin granules by ATP leads to the formation of diphosphoinositide in the granule membrane. Both phosphatidylinositol kinase and its substrate are components of this membrane, and triphosphoinositide is not formed under the conditions of the assay. The reaction is Mg2+-dependent and is stimulated by Mn2+ and F− ions. The initial reaction is rapid, with a broad pH profile and a `transition' temperature for its activation energy at 27°C. The apparent Km for ATP is 5μm. ATP, N-ethylmaleimide, Cu2+ ions and NaIO4 are inhibitory. The phospholipids of chromaffin-granule membranes have been analysed: 6.8% of the lipid P is found in phosphatidylinositol, and only 2–3% in phosphatidylserine. Comparison of the rate of phosphorylation of intact and lysed granules suggests that the sites for phosphorylation are on the outer (cytoplasmic) surface of the granules, and diphosphoinositide may therefore make an important contribution to the charge of the chromaffin granule in vivo. PMID:4360713

The ketogenic diet as broad-spectrum treatment for super-refractory pediatric status epilepticus: challenges in implementation in the pediatric and neonatal intensive care units.

PubMed

Cobo, Nicole H; Sankar, Raman; Murata, Kristina K; Sewak, Sarika L; Kezele, Michele A; Matsumoto, Joyce H

2015-02-01

Refractory status epilepticus carries significant morbidity and mortality. Recent reports have promoted the use of the ketogenic diet as an effective treatment for refractory status epilepticus. We describe our recent experience with instituting the ketogenic diet for 4 critically ill children in refractory status epilepticus, ranging in age from 9 weeks to 13.5 years after failure of traditional treatment. The ketogenic diet allowed these patients to be weaned off continuous infusions of anesthetics without recurrence of status epilepticus, though delayed ketosis and persistently elevated glucose measurements posed special challenges to effective initiation, and none experienced complete seizure cessation. The ease of sustaining myocardial function with fatty acid energy substrates compares favorably over the myocardial toxicity posed by anesthetic doses of barbiturates and contributes to the safety profile of the ketogenic diet. The ketogenic diet can be implemented successfully and safely for the treatment of refractory status epilepticus in pediatric patients. © The Author(s) 2014.

High-Throughput Lectin Microarray-Based Analysis of Live Cell Surface Glycosylation

PubMed Central

Li, Yu; Tao, Sheng-ce; Zhu, Heng; Schneck, Jonathan P.

2011-01-01

Lectins, plant-derived glycan-binding proteins, have long been used to detect glycans on cell surfaces. However, the techniques used to characterize serum or cells have largely been limited to mass spectrometry, blots, flow cytometry, and immunohistochemistry. While these lectin-based approaches are well established and they can discriminate a limited number of sugar isomers by concurrently using a limited number of lectins, they are not amenable for adaptation to a high-throughput platform. Fortunately, given the commercial availability of lectins with a variety of glycan specificities, lectins can be printed on a glass substrate in a microarray format to profile accessible cell-surface glycans. This method is an inviting alternative for analysis of a broad range of glycans in a high-throughput fashion and has been demonstrated to be a feasible method of identifying binding-accessible cell surface glycosylation on living cells. The current unit presents a lectin-based microarray approach for analyzing cell surface glycosylation in a high-throughput fashion. PMID:21400689

Effect of alloy chemistry and exposure conditions on the oxidation of titanium

NASA Technical Reports Server (NTRS)

Unnam, J.; Shenoy, R. N.; Clark, R. K.

1984-01-01

Multiwall is a new thermal protection system concept for advanced space transportation vehicles. The system consists of discrete panels made up of multiple layers of foil gage metal. Titanium is the proposed candidate metal for multiwall panels in the reentry temperature range up to 675 C. Oxidation and embrittlement are the principal concerns related to the use of Ti in heat shield applications. The results of a broad study on the oxidation kinetics of several titanium alloys subjected to different exposure conditions are described. The alloys include commercially pure titanium, Ti-6Al-4V, and Ti-6Al-2Sn-4Zr-2Mo. Oxidation studies were performed on these alloys exposed at 704 C in 5-760 torr air pressure and 0 to 50% relative humidity. The resulting weight gains were correlated with oxide thickness and substrate contamination. The contamination depth and weight gains due to solid solutioning were obtained from microhardness depth profiles and hardness versus weight percent oxygen calibration data.

Ultra-thin high-efficiency mid-infrared transmissive Huygens meta-optics.

PubMed

Zhang, Li; Ding, Jun; Zheng, Hanyu; An, Sensong; Lin, Hongtao; Zheng, Bowen; Du, Qingyang; Yin, Gufan; Michon, Jerome; Zhang, Yifei; Fang, Zhuoran; Shalaginov, Mikhail Y; Deng, Longjiang; Gu, Tian; Zhang, Hualiang; Hu, Juejun

2018-04-16

The mid-infrared (mid-IR) is a strategically important band for numerous applications ranging from night vision to biochemical sensing. Here we theoretically analyzed and experimentally realized a Huygens metasurface platform capable of fulfilling a diverse cross-section of optical functions in the mid-IR. The meta-optical elements were constructed using high-index chalcogenide films deposited on fluoride substrates: the choices of wide-band transparent materials allow the design to be scaled across a broad infrared spectrum. Capitalizing on a two-component Huygens' meta-atom design, the meta-optical devices feature an ultra-thin profile (λ 0 /8 in thickness) and measured optical efficiencies up to 75% in transmissive mode for linearly polarized light, representing major improvements over state-of-the-art. We have also demonstrated mid-IR transmissive meta-lenses with diffraction-limited focusing and imaging performance. The projected size, weight and power advantages, coupled with the manufacturing scalability leveraging standard microfabrication technologies, make the Huygens meta-optical devices promising for next-generation mid-IR system applications.

A family of highly conserved glycosomal 2-hydroxyacid dehydrogenases from Phytomonas sp.

PubMed

Uttaro, A D; Altabe, S G; Rider, M H; Michels, P A; Opperdoes, F R

2000-10-13

Phytomonas sp. contains two malate dehydrogenase isoforms, a mitochondrial isoenzyme with a high specificity for oxaloacetate and a glycosomal isozyme that acts on a broad range of substrates (Uttaro, A. D., and Opperdoes, F.R. (1997) Mol. Biochem. Parasitol. 89, 51-59). Here, we show that the low specificity of the latter isoenzyme is the result of a number of recent gene duplications that gave rise to a family of glycosomal 2-hydroxyacid dehydrogenase genes. Two of these genes were cloned, sequenced, and overexpressed in Escherichia coli. Although both gene products have 322 amino acids, share 90.4% identical residues, and have a similar hydrophobicity profile and net charge, their kinetic properties were strikingly different. One isoform behaved as a real malate dehydrogenase with a high specificity for oxaloacetate, whereas the other showed no activity with oxaloacetate but was able to reduce other oxoacids, such as phenyl pyruvate, 2-oxoisocaproate, 2-oxovalerate, 2-oxobutyrate, 2-oxo-4-methiolbutyrate, and pyruvate.

An optically transparent metasurface for broadband microwave antireflection

NASA Astrophysics Data System (ADS)

Zhao, Jie; Zhang, Cheng; Cheng, Qiang; Yang, Jin; Cui, Tie Jun

2018-02-01

Metamaterial absorbers and diffusers provide powerful routes to decrease the backward reflection significantly with advantages of ultrathin profile and customized bandwidth. Simultaneous control of the absorption and scattering behaviors of the metamaterials which helps to improve the suppression capabilities of backward reflection, however, still remains a challenge. Aiming at this goal, we propose a metasurface constituted by two kinds of elements in a pseudorandom arrangement. By the use of indium tin oxide with moderate sheet resistance in the meta-atoms, enhanced absorption of energy can be achieved in a broad spectrum when interacted with illuminated waves. In the meanwhile, electromagnetic diffusion will be invoked from the destructive interference among the elements, giving rise to significant reduction of specular reflection as a result. Excellent agreements are observed between simulation and experiment with pronounced reflection suppression from 6.8 GHz to 19.4 GHz. In addition, the optical transparence of the patterns and substrates makes the proposed metasurface a promising candidate for future applications like photovoltaic solar cells and electromagnetic shielding glasses.

High voltage photo-switch package module having encapsulation with profiled metallized concavities

DOEpatents

Sullivan, James S; Sanders, David M; Hawkins, Steven A; Sampayan, Stephen A

2015-05-05

A photo-conductive switch package module having a photo-conductive substrate or wafer with opposing electrode-interface surfaces metalized with first metallic layers formed thereon, and encapsulated with a dielectric encapsulation material such as for example epoxy. The first metallic layers are exposed through the encapsulation via encapsulation concavities which have a known contour profile, such as a Rogowski edge profile. Second metallic layers are then formed to line the concavities and come in contact with the first metal layer, to form profiled and metalized encapsulation concavities which mitigate enhancement points at the edges of electrodes matingly seated in the concavities. One or more optical waveguides may also be bonded to the substrate for coupling light into the photo-conductive wafer, with the encapsulation also encapsulating the waveguides.

Amine oxidation by d-arginine dehydrogenase in Pseudomonas aeruginosa.

PubMed

Ouedraogo, Daniel; Ball, Jacob; Iyer, Archana; Reis, Renata A G; Vodovoz, Maria; Gadda, Giovanni

2017-10-15

d-Arginine dehydrogenase from Pseudomonas aeruginosa (PaDADH) is a flavin-dependent oxidoreductase, which is part of a novel two-enzyme racemization system that functions to convert d-arginine to l-arginine. PaDADH contains a noncovalently linked FAD that shows the highest activity with d-arginine. The enzyme exhibits broad substrate specificity towards d-amino acids, particularly with cationic and hydrophobic d-amino acids. Biochemical studies have established the structure and the mechanistic properties of the enzyme. The enzyme is a true dehydrogenase because it displays no reactivity towards molecular oxygen. As established through solvent and multiple kinetic isotope studies, PaDADH catalyzes an asynchronous CH and NH bond cleavage via a hydride transfer mechanism. Steady-state kinetic studies with d-arginine and d-histidine are consistent with the enzyme following a ping-pong bi-bi mechanism. As shown by a combination of crystallography, kinetic and computational data, the shape and flexibility of loop L1 in the active site of PaDADH are important for substrate capture and broad substrate specificity. Copyright © 2017 Elsevier Inc. All rights reserved.

Identification and substrate prediction of new Fragaria x ananassa aquaporins and expression in different tissues and during strawberry fruit development.

PubMed

Merlaen, Britt; De Keyser, Ellen; Van Labeke, Marie-Christine

2018-01-01

The newly identified aquaporin coding sequences presented here pave the way for further insights into the plant-water relations in the commercial strawberry ( Fragaria x ananassa ). Aquaporins are water channel proteins that allow water to cross (intra)cellular membranes. In Fragaria x ananassa , few of them have been identified hitherto, hampering the exploration of the water transport regulation at cellular level. Here, we present new aquaporin coding sequences belonging to different subclasses: plasma membrane intrinsic proteins subtype 1 and subtype 2 (PIP1 and PIP2) and tonoplast intrinsic proteins (TIP). The classification is based on phylogenetic analysis and is confirmed by the presence of conserved residues. Substrate-specific signature sequences (SSSSs) and specificity-determining positions (SDPs) predict the substrate specificity of each new aquaporin. Expression profiling in leaves, petioles and developing fruits reveals distinct patterns, even within the same (sub)class. Expression profiles range from leaf-specific expression over constitutive expression to fruit-specific expression. Both upregulation and downregulation during fruit ripening occur. Substrate specificity and expression profiles suggest that functional specialization exists among aquaporins belonging to a different but also to the same (sub)class.

Fabrication of nanopore and nanoparticle arrays with high aspect ratio AAO masks.

PubMed

Li, Z P; Xu, Z M; Qu, X P; Wang, S B; Peng, J; Mei, L H

2017-03-03

How to use high aspect ratio anodic aluminum oxide (AAO) membranes as an etching and evaporation mask is one of the unsolved problems in the application of nanostructured arrays. Here we describe the versatile utilizations of the highly ordered AAO membranes with a high aspect ratio of more than 20 used as universal masks for the formation of various nanostructure arrays on various substrates. The result shows that the fabricated nanopore and nanoparticle arrays of substrates inherit the regularity of the AAO membranes completely. The flat AAO substrates and uneven AAO frontages were attached to the Si substrates respectively as an etching mask, which demonstrates that the two kinds of replication, positive and negative, represent the replication of the mirroring of Si substrates relative to the flat AAO substrates and uneven AAO frontages. Our work is a breakthrough for the broad research field of surface nano-masking.

Fabrication of nanopore and nanoparticle arrays with high aspect ratio AAO masks

NASA Astrophysics Data System (ADS)

Li, Z. P.; Xu, Z. M.; Qu, X. P.; Wang, S. B.; Peng, J.; Mei, L. H.

2017-03-01

How to use high aspect ratio anodic aluminum oxide (AAO) membranes as an etching and evaporation mask is one of the unsolved problems in the application of nanostructured arrays. Here we describe the versatile utilizations of the highly ordered AAO membranes with a high aspect ratio of more than 20 used as universal masks for the formation of various nanostructure arrays on various substrates. The result shows that the fabricated nanopore and nanoparticle arrays of substrates inherit the regularity of the AAO membranes completely. The flat AAO substrates and uneven AAO frontages were attached to the Si substrates respectively as an etching mask, which demonstrates that the two kinds of replication, positive and negative, represent the replication of the mirroring of Si substrates relative to the flat AAO substrates and uneven AAO frontages. Our work is a breakthrough for the broad research field of surface nano-masking.

Broad Low-Intensity Wings in the Emission-Line Profiles of Four Wolf-Rayet Galaxies

NASA Astrophysics Data System (ADS)

Méndez, David I.; Esteban, César

1997-10-01

High-resolution spectroscopic observations have been obtained for the Wolf-Rayet galaxies He 2-10, II Zw 40, POX 4, and Tol 35. Several subregions have been selected in each slit position in order to investigate possible spatial variations in the line profiles, radial velocities, and ionization conditions of the gas. The most remarkable feature of the spectra is the presence of asymmetric broad low-intensity wings in the profiles of the brightest emission lines. These spectral features are detected farther out from the star-forming knots, showing linear dimensions between 300 pc and 4.1 kpc. The maximum expansion velocity measured for this gas is between 120 and 340 km s-1 and appears to be quite constant along the slit for all the objects. Additional general properties of the spectra are (1) the quoted emission-line ratios are similar in the narrow and broad components, (2) no systematic differences of the behavior of the broad and narrow components have been found along the major and minor axis of the galaxies, and (3) the spatial distribution of the ionized gas is peaked centrally. Different mechanisms capable of producing the observed broad spectral features are discussed: cloud-cloud collisions in virialized gas, ``academic'' superbubbles, champagne flows, and superbubble blowout. It is concluded that superbubble blowout expanding over a cloudy medium can explain the observational properties in a reasonable manner.

Characterisation of the broad substrate specificity 2-keto acid decarboxylase Aro10p of Saccharomyces kudriavzevii and its implication in aroma development.

PubMed

Stribny, Jiri; Romagnoli, Gabriele; Pérez-Torrado, Roberto; Daran, Jean-Marc; Querol, Amparo

2016-03-12

The yeast amino acid catabolism plays an important role in flavour generation since higher alcohols and acetate esters, amino acid catabolism end products, are key components of overall flavour and aroma in fermented products. Comparative studies have shown that other Saccharomyces species, such as S. kudriavzevii, differ during the production of aroma-active higher alcohols and their esters compared to S. cerevisiae. In this study, we performed a comparative analysis of the enzymes involved in the amino acid catabolism of S. kudriavzevii with their potential to improve the flavour production capacity of S. cerevisiae. In silico screening, based on the severity of amino acid substitutions evaluated by Grantham matrix, revealed four candidates, of which S. kudriavzevii Aro10p (SkAro10p) had the highest score. The analysis of higher alcohols and esters produced by S. cerevisiae then revealed enhanced formation of isobutanol, isoamyl alcohol and their esters when endogenous ARO10 was replaced with ARO10 from S. kudriavzevii. Also, significant differences in the aroma profile were found in fermentations of synthetic wine must. Substrate specificities of SkAro10p were compared with those of S. cerevisiae Aro10p (ScAro10p) by their expression in a 2-keto acid decarboxylase-null S. cerevisiae strain. Unlike the cell extracts with expressed ScAro10p which showed greater activity for phenylpyruvate, which suggests this phenylalanine-derivative to be the preferred substrate, the decarboxylation activities measured in the cell extracts with SkAro10p ranged with all the tested substrates at the same level. The activities of SkAro10p towards substrates (except phenylpyruvate) were higher than of those for ScAro10p. The results indicate that the amino acid variations observed between the orthologues decarboxylases encoded by SkARO10 and ScARO10 could be the reason for the distinct enzyme properties, which possibly lead to the enhanced production of several flavour compounds. The knowledge on the important enzyme involved in higher alcohols biosynthesis by S. kudriavzevii could be of scientific as well as of applied interest.

Large-Scale, Lineage-Specific Expansion of a Bric-a-Brac/Tramtrack/Broad Complex Ubiquitin-Ligase Gene Family in Rice[W

PubMed Central

Gingerich, Derek J.; Hanada, Kousuke; Shiu, Shin-Han; Vierstra, Richard D.

2007-01-01

Selective ubiquitination of proteins is directed by diverse families of ubiquitin-protein ligases (or E3s) in plants. One important type uses Cullin-3 as a scaffold to assemble multisubunit E3 complexes containing one of a multitude of bric-a-brac/tramtrack/broad complex (BTB) proteins that function as substrate recognition factors. We previously described the 80-member BTB gene superfamily in Arabidopsis thaliana. Here, we describe the complete BTB superfamily in rice (Oryza sativa spp japonica cv Nipponbare) that contains 149 BTB domain–encoding genes and 43 putative pseudogenes. Amino acid sequence comparisons of the rice and Arabidopsis superfamilies revealed a near equal repertoire of putative substrate recognition module types. However, phylogenetic comparisons detected numerous gene duplication and/or loss events since the rice and Arabidopsis BTB lineages split, suggesting possible functional specialization within individual BTB families. In particular, a major expansion and diversification of a subset of BTB proteins containing Meprin and TRAF homology (MATH) substrate recognition sites was evident in rice and other monocots that likely occurred following the monocot/dicot split. The MATH domain of a subset appears to have evolved significantly faster than those in a smaller core subset that predates flowering plants, suggesting that the substrate recognition module in many monocot MATH-BTB E3s are diversifying to ubiquitinate a set of substrates that are themselves rapidly changing. Intriguing possibilities include pathogen proteins attempting to avoid inactivation by the monocot host. PMID:17720868

Overlapping protective roles for glutathione transferase gene family members in chemical and oxidative stress response in Agrobacterium tumefaciens.

PubMed

Skopelitou, Katholiki; Muleta, Abdi W; Pavli, Ourania; Skaracis, Georgios N; Flemetakis, Emmanouil; Papageorgiou, Anastassios C; Labrou, Nikolaos E

2012-03-01

In the present work, we describe the characterisation of the glutathione transferase (GST) gene family from Agrobacterium tumefaciens C58. A genome survey revealed the presence of eight GST-like proteins in A. tumefaciens (AtuGSTs). Comparison by multiple sequence alignment generated a dendrogram revealing the phylogenetic relationships of AtuGSTs-like proteins. The beta and theta classes identified in other bacterial species are represented by five members in A. tumefaciens C58. In addition, there are three "orphan" sequences that do not fit into any previously recognised GST classes. The eight GST-like genes were cloned, expressed in Escherichia coli and their substrate specificity was determined towards 17 different substrates. The results showed that AtuGSTs catalyse a broad range of reactions, with different members of the family exhibiting quite varied substrate specificity. The 3D structures of AtuGSTs were predicted using molecular modelling. The use of comparative sequence and structural analysis of the AtuGST isoenzymes allowed us to identify local sequence and structural characteristics between different GST isoenzymes and classes. Gene expression profiling was conducted under normal culture conditions as well as under abiotic stress conditions (addition of xenobiotics, osmotic stress and cold and heat shock) to induce and monitor early stress-response mechanisms. The results reveal the constitutive expression of GSTs in A. tumefaciens and a modulation of GST activity after treatments, indicating that AtuGSTs presumably participate in a wide range of functions, many of which are important in counteracting stress conditions. These functions may be relevant to maintaining cellular homeostasis as well as in the direct detoxification of toxic compounds.

Substrate Specifity Profiling of the Aspergillus fumigatus Proteolytic Secretome Reveals Consensus Motifs with Predominance of Ile/Leu and Phe/Tyr

PubMed Central

Watson, Douglas S.; Feng, Xizhi; Askew, David S.; Jambunathan, Kalyani; Kodukula, Krishna; Galande, Amit K.

2011-01-01

Background The filamentous fungus Aspergillus fumigatus (AF) can cause devastating infections in immunocompromised individuals. Early diagnosis improves patient outcomes but remains challenging because of the limitations of current methods. To augment the clinician's toolkit for rapid diagnosis of AF infections, we are investigating AF secreted proteases as novel diagnostic targets. The AF genome encodes up to 100 secreted proteases, but fewer than 15 of these enzymes have been characterized thus far. Given the large number of proteases in the genome, studies focused on individual enzymes may overlook potential diagnostic biomarkers. Methodology and Principal Findings As an alternative, we employed a combinatorial library of internally quenched fluorogenic probes (IQFPs) to profile the global proteolytic secretome of an AF clinical isolate in vitro. Comparative protease activity profiling revealed 212 substrate sequences that were cleaved by AF secreted proteases but not by normal human serum. A central finding was that isoleucine, leucine, phenylalanine, and tyrosine predominated at each of the three variable positions of the library (44.1%, 59.1%, and 57.0%, respectively) among substrate sequences cleaved by AF secreted proteases. In contrast, fewer than 10% of the residues at each position of cleaved sequences were cationic or anionic. Consensus substrate motifs were cleaved by thermostable serine proteases that retained activity up to 50°C. Precise proteolytic cleavage sites were reliably determined by a simple, rapid mass spectrometry-based method, revealing predominantly non-prime side specificity. A comparison of the secreted protease activities of three AF clinical isolates revealed consistent protease substrate specificity fingerprints. However, secreted proteases of A. flavus, A. nidulans, and A. terreus strains exhibited striking differences in their proteolytic signatures. Conclusions This report provides proof-of-principle for the use of protease substrate specificity profiling to define the proteolytic secretome of Aspergillus fumigatus. Expansion of this technique to protease secretion during infection could lead to development of novel approaches to fungal diagnosis. PMID:21695046

Constraining the geometry and kinematics of the quasar broad emission line region using gravitational microlensing. I. Models and simulations

NASA Astrophysics Data System (ADS)

Braibant, L.; Hutsemékers, D.; Sluse, D.; Goosmann, R.

2017-11-01

Recent studies have shown that line profile distortions are commonly observed in gravitationally lensed quasar spectra. Often attributed to microlensing differential magnification, line profile distortions can provide information on the geometry and kinematics of the broad emission line region (BLR) in quasars. We investigate the effect of gravitational microlensing on quasar broad emission line profiles and their underlying continuum, combining the emission from simple representative BLR models with generic microlensing magnification maps. Specifically, we considered Keplerian disk, polar, and equatorial wind BLR models of various sizes. The effect of microlensing has been quantified with four observables: μBLR, the total magnification of the broad emission line; μcont, the magnification of the underlying continuum; as well as red/blue, RBI and wings/core, WCI, indices that characterize the line profile distortions. The simulations showed that distortions of line profiles, such as those recently observed in lensed quasars, can indeed be reproduced and attributed to the differential effect of microlensing on spatially separated regions of the BLR. While the magnification of the emission line μBLR sets an upper limit on the BLR size and, similarly, the magnification of the continuum μcont sets an upper limit on the size of the continuum source, the line profile distortions mainly depend on the BLR geometry and kinematics. We thus built (WCI,RBI) diagrams that can serve as diagnostic diagrams to discriminate between the various BLR models on the basis of quantitative measurements. It appears that a strong microlensing effect puts important constraints on the size of the BLR and on its distance to the high-magnification caustic. In that case, BLR models with different geometries and kinematics are more prone to produce distinctive line profile distortions for a limited number of caustic configurations, which facilitates their discrimination. When the microlensing effect is weak, there is a larger overlap between the characteristics of the line profile distortions produced by the different models, and constraints can only be derived on a statistical basis.

Direct transfer of graphene onto flexible substrates.

PubMed

Martins, Luiz G P; Song, Yi; Zeng, Tingying; Dresselhaus, Mildred S; Kong, Jing; Araujo, Paulo T

2013-10-29

In this paper we explore the direct transfer via lamination of chemical vapor deposition graphene onto different flexible substrates. The transfer method investigated here is fast, simple, and does not require an intermediate transfer membrane, such as polymethylmethacrylate, which needs to be removed afterward. Various substrates of general interest in research and industry were studied in this work, including polytetrafluoroethylene filter membranes, PVC, cellulose nitrate/cellulose acetate filter membranes, polycarbonate, paraffin, polyethylene terephthalate, paper, and cloth. By comparing the properties of these substrates, two critical factors to ensure a successful transfer on bare substrates were identified: the substrate's hydrophobicity and good contact between the substrate and graphene. For substrates that do not satisfy those requirements, polymethylmethacrylate can be used as a surface modifier or glue to ensure successful transfer. Our results can be applied to facilitate current processes and open up directions for applications of chemical vapor deposition graphene on flexible substrates. A broad range of applications can be envisioned, including fabrication of graphene devices for opto/organic electronics, graphene membranes for gas/liquid separation, and ubiquitous electronics with graphene.

Holographic injection locking of a broad area laser diode via a photorefractive thin-film device.

PubMed

van Voorst, P D; de Wit, M R; Offerhaus, H L; Tay, S; Thomas, J; Peyghambarian, N; Boller, K-J

2007-12-24

We demonstrate locking of a high power broad area laser diode to a single frequency using holographic feedback from a photorefractive polymer thin-film device for the first time. A four-wave mixing setup is used to generate feedback for the broad area diode at the wavelength of the single frequency source (Ti:Sapphire laser) while the spatial distribution adapts to the preferred profile of the broad area diode. The result is an injection-locked broad area diode emitting with a linewidth comparable to the Ti:Sapphire laser.

Etch Profile Simulation Using Level Set Methods

NASA Technical Reports Server (NTRS)

Hwang, Helen H.; Meyyappan, Meyya; Arnold, James O. (Technical Monitor)

1997-01-01

Etching and deposition of materials are critical steps in semiconductor processing for device manufacturing. Both etching and deposition may have isotropic and anisotropic components, due to directional sputtering and redeposition of materials, for example. Previous attempts at modeling profile evolution have used so-called "string theory" to simulate the moving solid-gas interface between the semiconductor and the plasma. One complication of this method is that extensive de-looping schemes are required at the profile corners. We will present a 2D profile evolution simulation using level set theory to model the surface. (1) By embedding the location of the interface in a field variable, the need for de-looping schemes is eliminated and profile corners are more accurately modeled. This level set profile evolution model will calculate both isotropic and anisotropic etch and deposition rates of a substrate in low pressure (10s mTorr) plasmas, considering the incident ion energy angular distribution functions and neutral fluxes. We will present etching profiles of Si substrates in Ar/Cl2 discharges for various incident ion energies and trench geometries.

AGN Space Telescope and Optical Reverberation Mapping Project. IV. Velocity-Delay Mapping of Broad Emission Lines in NGC 5548

NASA Astrophysics Data System (ADS)

Horne, Keith D.; Agn Storm Team

2015-01-01

Two-dimensional velocity-delay maps of AGN broad emission line regions can be recovered by modelling observations of reverberating emission-line profiles on the assumption that the line profile variations are driven by changes in ionising radiation from a compact source near the black hole. The observable light travel time delay resolves spatial structure on iso-delay paraboloids, while the doppler shift resolves kinematic structure along the observer's line-of-sight. Velocity-delay maps will be presented and briefly discussed for the Lyman alpha, CIV and Hbeta line profiles based on the HST and ground-based spectrophotometric monitoring of NGC 5548 during the 2014 AGN STORM campaign.

Observations of emission in bright, low redshift quasars

NASA Technical Reports Server (NTRS)

1983-01-01

Ultraviolet, infrared, and optical spectra were combined to obtain a data set sample as broad as possible in the range of hydrogen lines in individual quasars. From the measured Lyman fluxes, coupled with Balmer and Paschen line fluxes measured in these same objects, an effort was made to establish observational constraints that would guide models of the broad emission line regions of quasars. It was found that IUE spectra were generally of sufficiently high quality to derive line profiles of the ultraviolet lines Lyman alpha and CIV 1550 A, which were compared to the Balmer line profiles. The objects observed and the line fluxes are tabulated. Plots of line profiles are included.

Lanthanum tricyanide-catalyzed acyl silane-ketone benzoin additions.

PubMed

Tarr, James C; Johnson, Jeffrey S

2009-09-03

Lanthanum tricyanide efficiently catalyzes a benzoin-type coupling between acyl silanes and ketones. Yields range from moderate to excellent over a broad substrate scope encompassing aryl, alkyl, electron-rich, and sterically hindered ketones.

Anomalous fast dynamics of adsorbate overlayers near an incommensurate structural transition.

PubMed

Granato, Enzo; Ying, S C; Elder, K R; Ala-Nissila, T

2013-09-20

We investigate the dynamics of a compressively strained adsorbed layer on a periodic substrate via a simple two-dimensional model that admits striped and hexagonal incommensurate phases. We show that the mass transport is superfast near the striped-hexagonal phase boundary and in the hexagonal phase. For an initial step profile separating a bare substrate region (or "hole") from the rest of a striped incommensurate phase, the superfast domain wall dynamics leads to a bifurcation of the initial step profile into two interfaces or profiles propagating in opposite directions with a hexagonal phase in between. This yields a theoretical understanding of the recent experiments for the Pb/Si(111) system.

Characterization of a new oligoalginate lyase from marine bacterium Vibrio sp.

PubMed

Yu, Zuochen; Zhu, Benwei; Wang, Wenxia; Tan, Haidong; Yin, Heng

2018-06-01

A new oligoalginate lyase encoding gene, designed oal17A, was cloned from marine bacterium Vibrio sp. W13, and then expressed in Escherichia coli. The recombinant Oal17A was purified by NTA-Ni resin with maximal activity at 30°C and pH7.0. Oal17A exhibited broad substrate specificity, and preferred to degrade alginate than polyM or polyG into monosaccharide acid. The specific activity of Oal17A toward alginate, polyM and polyG was 21.14U/mg, 12.31U/mg and 7.43U/mg, respectively. With features of high-level expression and broad substrate specificity, Oal17A would be a potential tool for alginate monomer production process of alginate utilizing for biofuels and bioethanol production. Copyright © 2018 Elsevier B.V. All rights reserved.

Synthesis and characterization of InN nanocrystals on glass substrate by plasma assisted reactive evaporation

NASA Astrophysics Data System (ADS)

Ganesh, V.; Alizadeh, M.; Shuhaimi, A.; Sundaram, S.; Hakim, K. M.; Goh, B. T.; Rahman, S. A.

2017-07-01

InN nanocrystals were grown on glass substrate by plasma assisted reactive evaporation technique and the quality was compared with InN on Si (111) substrate. Single phase InN was confirmed by X-ray diffraction and micro Raman analysis on both the substrates. Agglomerated and Hexagonal faceting nanocrystals observed by field emission scanning electron microscopy. Energy dispersive X-ray analysis shows InN nanocrystals are nearly stochiometric. Photoluminescence reveals a broad emission near bandedge at 2 .04 eV and defect band at 1.07 eV. The Hall measurement on both the substrates reveals high electron carrier concentration. These encouraging results obtained suggested that high quality single crystalline InN can be obtained on glass substrate further optimizing the growth parameters. This novel growth of InN nanocrystals on glass substrate is an important step towards the development of monolithic, high efficiency low-cost InGaN-based renewable energy sources.

COSIM: A Finite-Difference Computer Model to Predict Ternary Concentration Profiles Associated with Oxidation and Interdiffusion of Overlay-Coated Substrates

NASA Technical Reports Server (NTRS)

Nesbitt, James A.

2000-01-01

A finite-difference computer program (COSIM) has been written which models the one-dimensional, diffusional transport associated with high-temperature oxidation and interdiffusion of overlay-coated substrates. The program predicts concentration profiles for up to three elements in the coating and substrate after various oxidation exposures. Surface recession due to solute loss is also predicted. Ternary cross terms and concentration-dependent diffusion coefficients are taken into account. The program also incorporates a previously-developed oxide growth and spalling model to simulate either isothermal or cyclic oxidation exposures. In addition to predicting concentration profiles after various oxidation exposures, the program can also be used to predict coating fife based on a concentration dependent failure criterion (e.g., surface solute content drops to two percent). The computer code, written in an extension of FORTRAN 77, employs numerous subroutines to make the program flexible and easily modifiable to other coating oxidation problems.

The influence of gravity on the distribution of the deposit formed onto a substrate by sessile, hanging, and sandwiched hanging drop evaporation.

PubMed

Sandu, Ion; Fleaca, Claudiu Teodor

2011-06-15

The focus of the present article is the study of the influence of gravity on the particle deposition profiles on a solid substrate during the evaporation of sessile, hanging and sandwiched hanging drops of colloidal particle suspensions. For concentrations of nanoparticles in the colloidal solutions in the range 0.0001-1 wt.%, highly diluted suspensions will preferentially form rings while concentrated suspensions will preferentially form spots in both sessile and hanging drop evaporation. For intermediary concentrations, the particle deposition profiles will depend on the nanoparticle aggregation dynamics in the suspension during the evaporation process, gravity and on the detailed evaporation geometry. The evaporation of a drop of toluene/carbon nanoparticle suspension hanging from a pendant water drop will leave on the substrate a circular spot with no visible external ring. By contrast, a clear external ring is formed on the substrate by the sessile evaporation of a similar drop of suspension sandwiched between a water drop and the substrate. From the application viewpoint, these processes can be used to create preferential electrical conductive carbon networks and contacts for arrays of self-assembled nanostructures fabricated on solid substrates as well as on flexible polymeric substrates. Copyright © 2011 Elsevier Inc. All rights reserved.

Modular injector integrated linear apparatus with motion profile optimization for spatial atomic layer deposition.

PubMed

Wang, Xiaolei; Li, Yun; Lin, Jilong; Shan, Bin; Chen, Rong

2017-11-01

A spatial atomic layer deposition apparatus integrated with a modular injector and a linear motor has been designed. It consists of four parts: a precursor delivery manifold, a modular injector, a reaction zone, and a driving unit. An injector with multi-layer structured channels is designed to help improve precursor distribution homogeneity. During the back and forth movement of the substrate at high speed, the inertial impact caused by jerk and sudden changes of acceleration will degrade the film deposition quality. Such residual vibration caused by inertial impact will aggravate the fluctuation of the gap distance between the injector and the substrate in the deposition process. Thus, an S-curve motion profile is implemented to reduce the large inertial impact, and the maximum position error could be reduced by 84%. The microstructure of the film under the S-curve motion profile shows smaller root-mean-square and scanning voltage amplitude under an atomic force microscope, which verifies the effectiveness of the S-curve motion profile in reducing the residual vibration and stabilizing the gap distance between the injector and the substrate. The film deposition rate could reach 100 nm/min while maintaining good uniformity without obvious periodic patterns on the surface.

Modular injector integrated linear apparatus with motion profile optimization for spatial atomic layer deposition

NASA Astrophysics Data System (ADS)

Wang, Xiaolei; Li, Yun; Lin, Jilong; Shan, Bin; Chen, Rong

2017-11-01

A spatial atomic layer deposition apparatus integrated with a modular injector and a linear motor has been designed. It consists of four parts: a precursor delivery manifold, a modular injector, a reaction zone, and a driving unit. An injector with multi-layer structured channels is designed to help improve precursor distribution homogeneity. During the back and forth movement of the substrate at high speed, the inertial impact caused by jerk and sudden changes of acceleration will degrade the film deposition quality. Such residual vibration caused by inertial impact will aggravate the fluctuation of the gap distance between the injector and the substrate in the deposition process. Thus, an S-curve motion profile is implemented to reduce the large inertial impact, and the maximum position error could be reduced by 84%. The microstructure of the film under the S-curve motion profile shows smaller root-mean-square and scanning voltage amplitude under an atomic force microscope, which verifies the effectiveness of the S-curve motion profile in reducing the residual vibration and stabilizing the gap distance between the injector and the substrate. The film deposition rate could reach 100 nm/min while maintaining good uniformity without obvious periodic patterns on the surface.

Functional Diversity of Haloacid Dehalogenase Superfamily Phosphatases from Saccharomyces cerevisiae: BIOCHEMICAL, STRUCTURAL, AND EVOLUTIONARY INSIGHTS.

PubMed

Kuznetsova, Ekaterina; Nocek, Boguslaw; Brown, Greg; Makarova, Kira S; Flick, Robert; Wolf, Yuri I; Khusnutdinova, Anna; Evdokimova, Elena; Jin, Ke; Tan, Kemin; Hanson, Andrew D; Hasnain, Ghulam; Zallot, Rémi; de Crécy-Lagard, Valérie; Babu, Mohan; Savchenko, Alexei; Joachimiak, Andrzej; Edwards, Aled M; Koonin, Eugene V; Yakunin, Alexander F

2015-07-24

The haloacid dehalogenase (HAD)-like enzymes comprise a large superfamily of phosphohydrolases present in all organisms. The Saccharomyces cerevisiae genome encodes at least 19 soluble HADs, including 10 uncharacterized proteins. Here, we biochemically characterized 13 yeast phosphatases from the HAD superfamily, which includes both specific and promiscuous enzymes active against various phosphorylated metabolites and peptides with several HADs implicated in detoxification of phosphorylated compounds and pseudouridine. The crystal structures of four yeast HADs provided insight into their active sites, whereas the structure of the YKR070W dimer in complex with substrate revealed a composite substrate-binding site. Although the S. cerevisiae and Escherichia coli HADs share low sequence similarities, the comparison of their substrate profiles revealed seven phosphatases with common preferred substrates. The cluster of secondary substrates supporting significant activity of both S. cerevisiae and E. coli HADs includes 28 common metabolites that appear to represent the pool of potential activities for the evolution of novel HAD phosphatases. Evolution of novel substrate specificities of HAD phosphatases shows no strict correlation with sequence divergence. Thus, evolution of the HAD superfamily combines the conservation of the overall substrate pool and the substrate profiles of some enzymes with remarkable biochemical and structural flexibility of other superfamily members. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Novel SiO2-deposited CaF2 substrate for vibrational sum-frequency generation (SFG) measurements of chemisorbed monolayers in an aqueous environment.

PubMed

Padermshoke, Adchara; Konishi, Shouta; Ara, Masato; Tada, Hirokazu; Ishibashi, Taka-Aki

2012-06-01

A novel SiO(2)-deposited CaF(2) (SiO(2)/CaF(2)) substrate for measuring vibrational sum-frequency generation (SFG) spectra of silane-based chemisorbed monolayers in aqueous media has been developed. The substrate is suitable for silanization and transparent over a broad range of the infrared (IR) probe. The present work demonstrates the practical application of the SiO(2)/CaF(2) substrate and, to our knowledge, the first SFG spectrum at the solid/water interface of a silanized monolayer observed over the IR fingerprint region (1780-1400 cm(-1)) using a back-side probing geometry. This new substrate can be very useful for SFG studies of various chemisorbed organic molecules, particularly biological compounds, in aqueous environments.

Detailed seamount-scale studies of ferromanganese crusts reveal new insights into their formation and resource assessment.

NASA Astrophysics Data System (ADS)

Murton, B. J.; Lusty, P.; Yeo, I. A.; Howarth, S.

2017-12-01

The seafloor hosts abundant mineral deposits critical for low-carbon economies and emerging technologies. These include ferromanganese crusts (FeMnC) that grow on seamounts. While the broad distribution of FeMnC is known, local controls on growth, composition and formation are not. Here, we describe a detailed study of a gyot in the NE Atlantic (Tropic Seamount) that explores the controls, from the surface to the seafloor, exerted on FeMnC growth from current energy, surface productivity, sediment distribution, seafloor morphology, substrate lithology, sediments mobility and thickness, and seamount subsidence. During cruise JC142 (2016), we mapped the seamount with EM120 multibeam, mapped the 400km2 summit with AUV multibeam, sidescan sonar, sub-bottom profiler and 361,644 photographs. During 28 ROV dives we drilled 58 core and collected 344 individual rock samples. We found FeMnC at all depths, with the thickest (<20cm) located at the greatest depths (3000-4000m). The thinnest are on the summit plateau, with the centre and southern edge having the thickest sediment. FeMnC pavements form many different terraces on the summit. Frequent undercuts expose a calcareous substrate. Elsewhere, cobbles and pebbles form the nucleolus for crusts up to 10cm thick, with growth into the sediment. Many substrates are found to comprise semi-consolidated sediment. The presence of thick crusts at the base of the seamount contradicts accepted understanding of FeMnC deposition just below the oxygen minimum zone (OMZ). In areas on the eastern and western spurs, between 2500m and 1000m, where current energy is greatest, sessile fauna are most abundant. Dense coral debris at these locations appears to inhibit crust formation and coral and sponge `gardens' are frequent on near vertical cliffs. The observation that crusts have grown downwards into and over soft sediment is enigmatic since present understanding requires hard substrates to be exposed to seawater for crusts to grow, and any burial would inhibit such growth. Plume tracking shows reduction to background within 1000m. Our study challenges the view that ferromanganese crusts form at the base of the OMZ and grow upwards on solid substrates. Instead, we see an interplay between crust precipitation, the morphological evolution of the seamount, its hydrography and substrates.

[Substrate specifity in Amoeba proteus].

PubMed

Sopina, V A

2006-01-01

Three different phosphatases ("slow", "middle" and "fast") were found in Amoeba proteus (strain B) after PAGE and a subsequent gel staining in 1-naphthyl phosphate containing incubation mixture (pH 9.0). Substrate specificity of these phosphatases was determined in supernatants of homogenates using inhibitors of phosphatase activity. All phosphatases showed a broad substrate specificity. Of 10 tested compounds, p-nitrophenyl phosphate was a preferable substrate for all 3 phosphatases. All phosphatases were able to hydrolyse bis-p-nitrophenyl phosphate and, hence, displayed phosphodiesterase activity. All phosphatases hydrolysed O-phospho-L-tyrosine to a greater or lesser degree. Only little differences in substrate specificity of phosphatases were noticed: 1) "fast" and "middle" phosphatases hydrolysed naphthyl phosphates and O-phospho-L-tyrosine less efficiently than did "slow" phosphatase; 2) "fast" and "middle" phosphatases hydrolysed 2- naphthyl phosphate to a lesser degree than 1-naphthyl phosphate 3) "fast" and "middle" phosphatases hydrolysed O-phospho-L-serine and O-phospho-L-threonine with lower intensity as compared with "slow" phosphatase; 4) as distinct from "middle" and "slow" phosphatases, the "fast" phosphatase hydrolysed glucose-6-phosphate very poorly. The revealed broad substrate specificity of "slow" phosphatase together with data of inhibitory analysis and results of experiments with reactivation of this phosphatase by Zn2+-ions after its inactivation by EDTA strongly suggest that only the "slow" phosphatase is a true alkaline phosphatase (EC 3.1.3.1). The alkaline phosphatase of A. proteus is secreted into culture medium where its activity is low. The enzyme displays both phosphomono- and phosphodiesterase activities, in addition to supposed protein phosphatase activity. It still remains unknown, to which particular phosphatase class the amoeban "middle" and "fast" phosphatases (pH 9.0) may be assigned.

Flash Study Analysis and the Music Learning Pro-Files Project

ERIC Educational Resources Information Center

Cremata, Radio; Pignato, Joseph; Powell, Bryan; Smith, Gareth Dylan

2016-01-01

This paper introduces the Music Learning Profiles Project, and its methodological approach, flash study analysis. Flash study analysis is a method that draws heavily on extant qualitative approaches to education research, to develop broad understandings of music learning in diverse contexts. The Music Learning Profiles Project (MLPP) is an…

Lanthanum Tricyanide-Catalyzed Acyl Silane-Ketone Benzoin Additions

PubMed Central

Tarr, James C.; Johnson, Jeffrey S.

2009-01-01

Lanthanum tricyanide efficiently catalyzes a benzoin-type coupling between acyl silanes and ketones. Yields range from moderate to excellent over a broad substrate scope encompassing aryl, alkyl, electron-rich, and sterically hindered ketones. PMID:19655731

Direct transfer of graphene onto flexible substrates

PubMed Central

Martins, Luiz G. P.; Song, Yi; Zeng, Tingying; Dresselhaus, Mildred S.; Kong, Jing; Araujo, Paulo T.

2013-01-01

In this paper we explore the direct transfer via lamination of chemical vapor deposition graphene onto different flexible substrates. The transfer method investigated here is fast, simple, and does not require an intermediate transfer membrane, such as polymethylmethacrylate, which needs to be removed afterward. Various substrates of general interest in research and industry were studied in this work, including polytetrafluoroethylene filter membranes, PVC, cellulose nitrate/cellulose acetate filter membranes, polycarbonate, paraffin, polyethylene terephthalate, paper, and cloth. By comparing the properties of these substrates, two critical factors to ensure a successful transfer on bare substrates were identified: the substrate’s hydrophobicity and good contact between the substrate and graphene. For substrates that do not satisfy those requirements, polymethylmethacrylate can be used as a surface modifier or glue to ensure successful transfer. Our results can be applied to facilitate current processes and open up directions for applications of chemical vapor deposition graphene on flexible substrates. A broad range of applications can be envisioned, including fabrication of graphene devices for opto/organic electronics, graphene membranes for gas/liquid separation, and ubiquitous electronics with graphene. PMID:24127582

Glutamic Acid Selective Chemical Cleavage of Peptide Bonds.

PubMed

Nalbone, Joseph M; Lahankar, Neelam; Buissereth, Lyssa; Raj, Monika

2016-03-04

Site-specific hydrolysis of peptide bonds at glutamic acid under neutral aqueous conditions is reported. The method relies on the activation of the backbone amide chain at glutamic acid by the formation of a pyroglutamyl (pGlu) imide moiety. This activation increases the susceptibility of a peptide bond toward hydrolysis. The method is highly specific and demonstrates broad substrate scope including cleavage of various bioactive peptides with unnatural amino acid residues, which are unsuitable substrates for enzymatic hydrolysis.

The first mammalian aldehyde oxidase crystal structure: insights into substrate specificity.

PubMed

Coelho, Catarina; Mahro, Martin; Trincão, José; Carvalho, Alexandra T P; Ramos, Maria João; Terao, Mineko; Garattini, Enrico; Leimkühler, Silke; Romão, Maria João

2012-11-23

Aldehyde oxidases have pharmacological relevance, and AOX3 is the major drug-metabolizing enzyme in rodents. The crystal structure of mouse AOX3 with kinetics and molecular docking studies provides insights into its enzymatic characteristics. Differences in substrate and inhibitor specificities can be rationalized by comparing the AOX3 and xanthine oxidase structures. The first aldehyde oxidase structure represents a major advance for drug design and mechanistic studies. Aldehyde oxidases (AOXs) are homodimeric proteins belonging to the xanthine oxidase family of molybdenum-containing enzymes. Each 150-kDa monomer contains a FAD redox cofactor, two spectroscopically distinct [2Fe-2S] clusters, and a molybdenum cofactor located within the protein active site. AOXs are characterized by broad range substrate specificity, oxidizing different aldehydes and aromatic N-heterocycles. Despite increasing recognition of its role in the metabolism of drugs and xenobiotics, the physiological function of the protein is still largely unknown. We have crystallized and solved the crystal structure of mouse liver aldehyde oxidase 3 to 2.9 Å. This is the first mammalian AOX whose structure has been solved. The structure provides important insights into the protein active center and further evidence on the catalytic differences characterizing AOX and xanthine oxidoreductase. The mouse liver aldehyde oxidase 3 three-dimensional structure combined with kinetic, mutagenesis data, molecular docking, and molecular dynamics studies make a decisive contribution to understand the molecular basis of its rather broad substrate specificity.

Impact of Experimental Conditions on the Evaluation of Interactions between Multidrug and Toxin Extrusion Proteins and Candidate Drugs.

PubMed

Lechner, Christian; Ishiguro, Naoki; Fukuhara, Ayano; Shimizu, Hidetada; Ohtsu, Naoko; Takatani, Masahito; Nishiyama, Kotaro; Washio, Ikumi; Yamamura, Norio; Kusuhara, Hiroyuki

2016-08-01

Multidrug and toxin extrusion transporters (MATEs) have a determining influence on the pharmacokinetic profiles of many drugs and are involved in several clinical drug-drug interactions (DDIs). Cellular uptake assays with recombinant cells expressing human MATE1 or MATE2-K are widely used to investigate MATE-mediated transport for DDI assessment; however, the experimental conditions and used test substrates vary among laboratories. We therefore initially examined the impact of three assay conditions that have been applied for MATE substrate and inhibitor profiling in the literature. One of the tested conditions resulted in significantly higher uptake rates of the three test substrates, [(14)C]metformin, [(3)H]thiamine, and [(3)H]1-methyl-4-phenylpyridinium (MPP(+)), but IC50 values of four tested MATE inhibitors varied only slightly among the three conditions (<2.5-fold difference). Subsequently, we investigated the uptake characteristics of the five MATE substrates: [(14)C]metformin, [(3)H]thiamine, [(3)H]MPP(+), [(3)H]estrone-3-sulfate (E3S), and rhodamine 123, as well as the impact of the used test substrate on the inhibition profiles of 10 MATE inhibitors at one selected assay condition. [(3)H]E3S showed atypical uptake characteristics compared with those observed with the other four substrates. IC50 values of the tested inhibitors were in a similar range (<4-fold difference) when [(14)C]metformin, [(3)H]thiamine, [(3)H]MPP(+), or [(3)H]E3S were used as substrates but were considerably higher with rhodamine 123 (9.8-fold and 4.1-fold differences compared with [(14)C]metformin with MATE1 and MATE2-K, respectively). This study demonstrated for the first time that the impact of assay conditions on IC50 determination is negligible, that kinetic characteristics differ among used test substrates, and that substrate-dependent inhibition exists for MATE1 and MATE2-K, giving valuable insight into the assessment of clinically relevant MATE-mediated DDIs in vitro. Copyright © 2016 by The American Society for Pharmacology and Experimental Therapeutics.

Micro knife-edge optical measurement device in a silicon-on-insulator substrate.

PubMed

Chiu, Yi; Pan, Jiun-Hung

2007-05-14

The knife-edge method is a commonly used technique to characterize the optical profiles of laser beams or focused spots. In this paper, we present a micro knife-edge scanner fabricated in a silicon-on-insulator substrate using the micro-electromechanical-system technology. A photo detector can be fabricated in the device to allow further integration with on-chip signal conditioning circuitry. A novel backside deep reactive ion etching process is proposed to solve the residual stress effect due to the buried oxide layer. Focused optical spot profile measurement is demonstrated.

More vertical etch profile using a Faraday cage in plasma etching

NASA Astrophysics Data System (ADS)

Cho, Byeong-Ok; Hwang, Sung-Wook; Ryu, Jung-Hyun; Moon, Sang Heup

1999-05-01

Scanning electron microscope images of sidewalls obtained by plasma etching of an SiO2 film with and without a Faraday cage have been compared. When the substrate film is etched in the Faraday cage, faceting is effectively suppressed and the etch profile becomes more vertical regardless of the process conditions. This is because the electric potential in the cage is nearly uniform and therefore distortion of the electric field at the convex corner of a microfeature is prevented. The most vertical etch profile is obtained when the cage is used in fluorocarbon plasmas, where faceting is further suppressed due to the decrease in the chemical sputtering yield and the increase in the radical/ion flux on the substrate.

Evaluation of productivity and antioxidant profile of solid-state cultivated macrofungi Pleurotus albidus and Pycnoporus sanguineus.

PubMed

Gambato, Gabriela; Todescato, Kelly; Pavão, Elisa Maria; Scortegagna, Angélica; Fontana, Roselei Claudete; Salvador, Mirian; Camassola, Marli

2016-05-01

The aim of this study was to investigate the production profile of Pleurotus albidus and Pycnoporus sanguineus on different waste substrates containing natural phenolics, and also to investigate whether phenolic-rich substrates can improve the phenolic content of these macrofungi. The medium formulated with Pinus sp. sawdust (PSW) made possible the highest yields (2.62±0.73%) of P. sanguineus. However, the supplementation of PSW with apple waste (AW) resulted in better P. albidus yields (23.94±2.92%). The results indicated that the substrate composition affected macrofungi production, also the chemical composition and the presence of phenolic compounds in the production media influence phenolic content and antioxidant activity in macrofungi. Copyright © 2016 Elsevier Ltd. All rights reserved.

Growth and characterization of V2O5 nanorods deposited by spray pyrolysis at low temperatures

NASA Astrophysics Data System (ADS)

Abd-Alghafour, N. M.; Ahmed, Naser M.; Hassan, Zai.; Mohammad, Sabah M.; Bououdina, M.

2016-07-01

Vanadium pentoxide (V2O5) nanorods were deposited by spray pyrolysis on preheated glass substrates at low temperatures. The influence of substrate temperature on the crystallization of V2O5 has been investigated. X-ray diffraction analysis (XRD) revealed that the films deposited at Tsub = 300°C were orthorhombic structures with preferential along (001) direction. Formation of nanorods from substrate surface which led to the formation of films with small-sized and rod-shaped nanostructure is observed by field scanning electron microscopy. Optical transmittance in the visible range increases to reach a maximum value of about 80% for a substrate temperature of 350°C. PL spectra reveal one main broad peak centered around 540 nm with high intensity.

Allosteric regulation of rhomboid intramembrane proteolysis.

PubMed

Arutyunova, Elena; Panwar, Pankaj; Skiba, Pauline M; Gale, Nicola; Mak, Michelle W; Lemieux, M Joanne

2014-09-01

Proteolysis within the lipid bilayer is poorly understood, in particular the regulation of substrate cleavage. Rhomboids are a family of ubiquitous intramembrane serine proteases that harbour a buried active site and are known to cleave transmembrane substrates with broad specificity. In vitro gel and Förster resonance energy transfer (FRET)-based kinetic assays were developed to analyse cleavage of the transmembrane substrate psTatA (TatA from Providencia stuartii). We demonstrate significant differences in catalytic efficiency (kcat/K0.5) values for transmembrane substrate psTatA (TatA from Providencia stuartii) cleavage for three rhomboids: AarA from P. stuartii, ecGlpG from Escherichia coli and hiGlpG from Haemophilus influenzae demonstrating that rhomboids specifically recognize this substrate. Furthermore, binding of psTatA occurs with positive cooperativity. Competitive binding studies reveal an exosite-mediated mode of substrate binding, indicating allostery plays a role in substrate catalysis. We reveal that exosite formation is dependent on the oligomeric state of rhomboids, and when dimers are dissociated, allosteric substrate activation is not observed. We present a novel mechanism for specific substrate cleavage involving several dynamic processes including positive cooperativity and homotropic allostery for this interesting class of intramembrane proteases. © 2014 The Authors.

Allosteric regulation of rhomboid intramembrane proteolysis

PubMed Central

Arutyunova, Elena; Panwar, Pankaj; Skiba, Pauline M; Gale, Nicola; Mak, Michelle W; Lemieux, M Joanne

2014-01-01

Proteolysis within the lipid bilayer is poorly understood, in particular the regulation of substrate cleavage. Rhomboids are a family of ubiquitous intramembrane serine proteases that harbour a buried active site and are known to cleave transmembrane substrates with broad specificity. In vitro gel and Förster resonance energy transfer (FRET)-based kinetic assays were developed to analyse cleavage of the transmembrane substrate psTatA (TatA from Providencia stuartii). We demonstrate significant differences in catalytic efficiency (kcat/K0.5) values for transmembrane substrate psTatA (TatA from Providencia stuartii) cleavage for three rhomboids: AarA from P. stuartii, ecGlpG from Escherichia coli and hiGlpG from Haemophilus influenzae demonstrating that rhomboids specifically recognize this substrate. Furthermore, binding of psTatA occurs with positive cooperativity. Competitive binding studies reveal an exosite-mediated mode of substrate binding, indicating allostery plays a role in substrate catalysis. We reveal that exosite formation is dependent on the oligomeric state of rhomboids, and when dimers are dissociated, allosteric substrate activation is not observed. We present a novel mechanism for specific substrate cleavage involving several dynamic processes including positive cooperativity and homotropic allostery for this interesting class of intramembrane proteases. PMID:25009246

WOR5, a Novel Tungsten-Containing Aldehyde Oxidoreductase from Pyrococcus furiosus with a Broad Substrate Specificity

PubMed Central

Bevers, Loes E.; Bol, Emile; Hagedoorn, Peter-Leon; Hagen, Wilfred R.

2005-01-01

WOR5 is the fifth and last member of the family of tungsten-containing oxidoreductases purified from the hyperthermophilic archaeon Pyrococcus furiosus. It is a homodimeric protein (subunit, 65 kDa) that contains one [4Fe-4S] cluster and one tungstobispterin cofactor per subunit. It has a broad substrate specificity with a high affinity for several substituted and nonsubstituted aliphatic and aromatic aldehydes with various chain lengths. The highest catalytic efficiency of WOR5 is found for the oxidation of hexanal (Vmax = 15.6 U/mg, Km = 0.18 mM at 60°C). Hexanal-incubated enzyme exhibits S = 1/2 electron paramagnetic resonance signals from [4Fe-4S]1+ (g values of 2.08, 1.93, and 1.87) and W5+ (g values of 1.977, 1.906, and 1.855). Cyclic voltammetry of ferredoxin and WOR5 on an activated glassy carbon electrode shows a catalytic wave upon addition of hexanal, suggesting that ferredoxin can be a physiological redox partner. The combination of WOR5, formaldehyde oxidoreductase, and aldehyde oxidoreductase forms an efficient catalyst for the oxidation of a broad range of aldehydes in P. furiosus. PMID:16199576

Enzyme specificity under dynamic control

NASA Astrophysics Data System (ADS)

Ota, Nobuyuki; Agard, David A.

2002-03-01

The contributions of conformational dynamics to substrate specificity have been examined by the application of principal component analysis to molecular dynamics trajectories of alpha-lytic protease. The wild-type alpha-lytic protease is highly specific for substrates with small hydrophobic side chains at the specificity pocket, while the Met190Ala binding pocket mutant has a much broader specificity, actively hydrolyzing substrates ranging from Ala to Phe. We performed a principal component analysis using 1-nanosecond molecular dynamics simulations using solvent boundary condition. We found that the walls of the wild-type substrate binding pocket move in tandem with one another, causing the pocket size to remain fixed so that only small substrates are recognized. In contrast, the M190A mutant shows uncoupled movement of the binding pocket walls, allowing the pocket to sample both smaller and larger sizes, which appears to be the cause of the observed broad specificity. The results suggest that the protein dynamics of alpha-lytic protease may play a significant role in defining the patterns of substrate specificity.

Structural insights into the cofactor-assisted substrate recognition of yeast methylglyoxal/isovaleraldehyde reductase Gre2.

PubMed

Guo, Peng-Chao; Bao, Zhang-Zhi; Ma, Xiao-Xiao; Xia, Qingyou; Li, Wei-Fang

2014-09-01

Saccharomyces cerevisiae Gre2 (EC1.1.1.283) serves as a versatile enzyme that catalyzes the stereoselective reduction of a broad range of substrates including aliphatic and aromatic ketones, diketones, as well as aldehydes, using NADPH as the cofactor. Here we present the crystal structures of Gre2 from S. cerevisiae in an apo-form at 2.00Å and NADPH-complexed form at 2.40Å resolution. Gre2 forms a homodimer, each subunit of which contains an N-terminal Rossmann-fold domain and a variable C-terminal domain, which participates in substrate recognition. The induced fit upon binding to the cofactor NADPH makes the two domains shift toward each other, producing an interdomain cleft that better fits the substrate. Computational simulation combined with site-directed mutagenesis and enzymatic activity analysis enabled us to define a potential substrate-binding pocket that determines the stringent substrate stereoselectivity for catalysis. Copyright © 2014 Elsevier B.V. All rights reserved.

Elevated gold ellipse nanoantenna dimers as sensitive and tunable surface enhanced Raman spectroscopy substrates

DOE PAGES

Jubb, A. M.; Jiao, Y.; Eres, Gyula; ...

2016-02-15

Here we demonstrate large area arrays of elevated gold ellipse dimers with precisely controlled gaps for use as sensitive and highly controllable surface enhanced Raman scattering (SERS) substrates. The significantly enhanced Raman signal observed with SERS arises from both localized and long range plasmonic effects. By controlling the geometry of a SERS substrate, in this case the size and aspect ratio of individual ellipses, the plasmon resonance can be tuned in a broad wavelength range, providing a method for designing the response of SERS substrates at different excitation wavelengths. Plasmon effects exhibited by the elevated gold ellipse dimer substrates aremore » also demonstrated and confirmed through finite difference time domain (FDTD) simulations. A plasmon resonance red shift with an increase of the ellipse aspect ratio is observed, allowing systematic control of the resulting SERS signal intensity. Optimized elevated ellipse dimer substrates with 10±2 nm gaps exhibit uniform SERS enhancement factors on the order of 10 9 for adsorbed p-mercaptoaniline molecules.« less

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.

Profilometry of thin films on rough substrates by Raman spectroscopy

PubMed Central

Ledinský, Martin; Paviet-Salomon, Bertrand; Vetushka, Aliaksei; Geissbühler, Jonas; Tomasi, Andrea; Despeisse, Matthieu; De Wolf , Stefaan; Ballif , Christophe; Fejfar, Antonín

2016-01-01

Thin, light-absorbing films attenuate the Raman signal of underlying substrates. In this article, we exploit this phenomenon to develop a contactless thickness profiling method for thin films deposited on rough substrates. We demonstrate this technique by probing profiles of thin amorphous silicon stripes deposited on rough crystalline silicon surfaces, which is a structure exploited in high-efficiency silicon heterojunction solar cells. Our spatially-resolved Raman measurements enable the thickness mapping of amorphous silicon over the whole active area of test solar cells with very high precision; the thickness detection limit is well below 1 nm and the spatial resolution is down to 500 nm, limited only by the optical resolution. We also discuss the wider applicability of this technique for the characterization of thin layers prepared on Raman/photoluminescence-active substrates, as well as its use for single-layer counting in multilayer 2D materials such as graphene, MoS2 and WS2. PMID:27922033

In vitro fermentation profiles, gas production rates, and microbiota modulation as affected by certain fructans, galactooligosaccharides, and polydextrose.

PubMed

Hernot, David C; Boileau, Thomas W; Bauer, Laura L; Middelbos, Ingmar S; Murphy, Michael R; Swanson, Kelly S; Fahey, George C

2009-02-25

It is of interest to benefit from the positive intestinal health outcomes of prebiotic consumption but with minimal gas production. This study examined gas production potential, fermentation profile, and microbial modulation properties of several types of oligosaccharides. Substrates studied included short-chain, medium-chain, and long-chain fructooligosaccharides, oligofructose-enriched inulin, galactooligosaccharide, and polydextrose. Each substrate was fermented in vitro using human fecal inoculum, and fermentation characteristics were quantified at 0, 4, 8, and 12 h. Gas and short-chain fatty acid (SCFA) production data showed that short-chain oligosaccharides were more rapidly fermented and produced more SCFA and gas than substrates with greater degrees of polymerization. Lactobacilli increased similarly among substrates. Short-chain oligosaccharides fermentation resulted in the greatest increase in bifidobacteria concentrations. Mixing short- and long-chain oligosaccharides attenuated short-chain oligosaccharide fermentation rate and extent. This study provides new information on the fermentation characteristics of some oligosaccharides used in human nutrition.

Effects of Different Substrates on Lignocellulosic Enzyme Expression, Enzyme Activity, Substrate Utilization and Biological Efficiency of Pleurotus Eryngii.

PubMed

Xie, Chunliang; Yan, Li; Gong, Wenbing; Zhu, Zuohua; Tan, Senwei; Chen, Du; Hu, Zhenxiu; Peng, Yuande

2016-01-01

Pleurotus eryngii is one of the most valued and delicious mushrooms which are commercially cultivated on various agro-wastes. How different substrates affect lignocellulosic biomass degradation, lignocellulosic enzyme production and biological efficiency in Pleurotus eryngii was unclear. In this report, Pleurotus eryngii was cultivated in substrates including ramie stalks, kenaf stalks, cottonseed hulls and bulrush stalks. The results showed that ramie stalks and kenaf stalks were found to best suitable to cultivate Pleurotus eryngii with the biological efficiency achieved at 55% and 57%, respectively. In order to establish correlations between different substrates and lignocellulosic enzymes expression, the extracellular proteins from four substrates were profiled with high throughput TMT-based quantitative proteomic approach. 241 non-redundant proteins were identified and 74 high confidence lignocellulosic enzymes were quantified. Most of the cellulases, hemicellulases and lignin depolymerization enzymes were highly up-regulated when ramie stalks and kenaf stalks were used as carbon sources. The enzyme activities results suggested cellulases, hemicellulases and lignin depolymerization enzymes were significantly induced by ramie stalks and kenaf stalks. The lignocelluloses degradation, most of the lignocellulosic enzymes expressions and activities of Pleurotus eryngii had positive correlation with the biological efficiency, which depend on the nature of lignocellulosic substrates. In addition, the lignocellulosic enzymes expression profiles during Pleurotus eryngii growth in different substrates were obtained. The present study suggested that most of the lignocellulosic enzymes expressions and activities can be used as tools for selecting better performing substrates for commercial mushroom cultivation. © 2016 The Author(s) Published by S. Karger AG, Basel.

Functional protease profiling for diagnosis of malignant disease.

PubMed

Findeisen, Peter; Neumaier, Michael

2012-01-01

Clinical proteomic profiling by mass spectrometry (MS) aims at uncovering specific alterations within mass profiles of clinical specimens that are of diagnostic value for the detection and classification of various diseases including cancer. However, despite substantial progress in the field, the clinical proteomic profiling approaches have not matured into routine diagnostic applications so far. Their limitations are mainly related to high-abundance proteins and their complex processing by a multitude of endogenous proteases thus making rigorous standardization difficult. MS is biased towards the detection of low-molecular-weight peptides. Specifically, in serum specimens, the particular fragments of proteolytically degraded proteins are amenable to MS analysis. Proteases are known to be involved in tumour progression and tumour-specific proteases are released into the blood stream presumably as a result of invasive progression and metastasis. Thus, the determination of protease activity in clinical specimens from patients with malignant disease can offer diagnostic and also therapeutic options. The identification of specific substrates for tumour proteases in complex biological samples is challenging, but proteomic screens for proteases/substrate interactions are currently experiencing impressive progress. Such proteomic screens include peptide-based libraries, differential isotope labelling in combination with MS, quantitative degradomic analysis of proteolytically generated neo-N-termini, monitoring the degradation of exogenous reporter peptides with MS, and activity-based protein profiling. In the present article, we summarize and discuss the current status of proteomic techniques to identify tumour-specific protease-substrate interactions for functional protease profiling. Thereby, we focus on the potential diagnostic use of the respective approaches. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Secondary ion mass spectrometry study of ex situ annealing of epitaxial GaAs grown on Si substrates

NASA Technical Reports Server (NTRS)

Radhakrishnan, G.; Mccullough, O.; Cser, J.; Katz, J.

1988-01-01

Samples of epitaxial GaAs grown on (100) Si substrates using molecular beam epitaxy were annealed at four different temperatures, from 800 to 950 C. Following annealing, the samples were analyzed using secondary ion mass spectrometry. Depth profiles of Ga, As, and Si reveal optimum conditions for annealing, and place a lower limit on a damage threshold for GaAs/Si substrates.

Substrate Specificity of MarP, a Periplasmic Protease Required for Resistance to Acid and Oxidative Stress in Mycobacterium tuberculosis*

PubMed Central

Small, Jennifer L.; O'Donoghue, Anthony J.; Boritsch, Eva C.; Tsodikov, Oleg V.; Knudsen, Giselle M.; Vandal, Omar; Craik, Charles S.; Ehrt, Sabine

2013-01-01

The transmembrane serine protease MarP is important for pH homeostasis in Mycobacterium tuberculosis (Mtb). Previous structural studies revealed that MarP contains a chymotrypsin fold and a disulfide bond that stabilizes the protease active site in the substrate-bound conformation. Here, we determined that MarP is located in the Mtb periplasm and showed that this localization is essential for function. Using the recombinant protease domain of MarP, we identified its substrate specificity using two independent assays: positional-scanning synthetic combinatorial library profiling and multiplex substrate profiling by mass spectrometry. These methods revealed that MarP prefers bulky residues at P4, tryptophan or leucine at P2, arginine or hydrophobic residues at P1, and alanine or asparagine at P1′. Guided by these data, we designed fluorogenic peptide substrates and characterized the kinetic properties of MarP. Finally, we tested the impact of mutating MarP cysteine residues on the peptidolytic activity of recombinant MarP and its ability to complement phenotypes of Mtb ΔMarP. Taken together, our studies provide insight into the enzymatic properties of MarP, its substrate preference, and the importance of its transmembrane helices and disulfide bond. PMID:23504313

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.

Heavy Ion Current Transients in SiGe HBTs

NASA Technical Reports Server (NTRS)

Pellish, Jonathan A.; Reed, Robert A.; Vizkelethy, Gyorgy; McMorrow, Dale; Ferlet-Cavrois, Veronique; Baggio, Jacques; Paillet, Philipe; Duhanel, Olivier; Phillips, Stanley D.; Sutton, Akil K.;

Porous nC-Si/SiOx nanostructured layer on Si substrate with tunable photoluminescent properties fabricated by direct, precursor-free microplasma irradiation in air

NASA Astrophysics Data System (ADS)

Wang, Tao; Hu, Mingshan; Yang, Bin; Wang, Xiaolin; Liu, Jingquan

2018-03-01

Porous nC-Si/SiOx photoluminescent nanostructured layer is fabricated by direct, precursor-free microplasma irradiation on Si substrate in air. It is confirmed that the deposited layer has porous and cluster-like structures by scanning electron microscopy (SEM) and profile scanning. Fourier transform infrared transmission (FTIR), X-ray diffraction (XRD) and X-ray photoelectron spectrum (XPS) results indicate the produced layer is actually composed of nanocrystalline silicon (nC-Si) embedded in SiOx matrix. Transmission electron microscopy (TEM) and Raman results show the mean particle size of nC-Si is mainly between 2 and 4 nm and the highest crystalline volume fraction reaches 86.9%. The photoluminescence (PL) measurement of nC-Si/SiOx layer exhibited a broad band centered at 1.7-1.9 eV, ranging from 1.2-2.4 eV, and could be tuned by varying the applied voltage. The synthetical mechanisms are discussed to explain the PL properties of the layers. We propose that the energetic ions bombing induced by high compressed electric field near the Si surface is the main reason for porous nC-Si/SiOx formation. Maskless deposition of the line pattern of nC-Si/SiOx layer was also successfully fabricated. This simple, maskless, vacuum-free and precursor-free technique could be used in various potential optoelectronics and biological applications in the future.

Metal-free catalytic enantioselective C-B bond formation: (pinacolato)boron conjugate additions to α,β-unsaturated ketones, esters, Weinreb amides, and aldehydes promoted by chiral N-heterocyclic carbenes.

PubMed

Wu, Hao; Radomkit, Suttipol; O'Brien, Jeannette M; Hoveyda, Amir H

2012-05-16

The first broadly applicable metal-free enantioselective method for boron conjugate addition (BCA) to α,β-unsaturated carbonyls is presented. The C-B bond forming reactions are promoted in the presence of 2.5-7.5 mol % of a readily accessible C(1)-symmetric chiral imidazolinium salt, which is converted, in situ, to the catalytically active diastereo- and enantiomerically pure N-heterocyclic carbene (NHC) by the common organic base 1,8-diazabicyclo[5.4.0]undec-7-ene (dbu). In addition to the commercially available bis(pinacolato)diboron [B(2)(pin)(2)], and in contrast to reactions with the less sterically demanding achiral NHCs, the presence of MeOH is required for high efficiency. Acyclic and cyclic α,β-unsaturated ketones, as well as acyclic esters, Weinreb amides, and aldehydes, can serve as suitable substrates; the desired β-boryl carbonyls are isolated in up to 94% yield and >98:2 enantiomer ratio (er). Transformations are often carried out at ambient temperature. In certain cases, such as when the relatively less reactive unsaturated amides are used, elevated temperatures are required (50-66 °C); nonetheless, reactions remain highly enantioselective. The utility of the NHC-catalyzed method is demonstrated through comparison with the alternative Cu-catalyzed protocols; in cases involving a polyfunctional substrate, unique profiles in chemoselectivity are exhibited by the metal-free approach (e.g., conjugate addition vs reaction with an alkyne, allene, or aldehyde).

Microbial community changes as a possible factor controlling carbon sequestration in subsoil

NASA Astrophysics Data System (ADS)

Strücker, Juliane; Jörgensen, Rainer Georg

2015-04-01

In order to gain more knowledge regarding the microbial community and their influence on carbon sequestration in subsoil two depth profiles with different soil organic carbon (SOC) concentrations were sampled. The SOC concentrations developed naturally due to deposition and erosion. This experiment offers the opportunity to investigate to which extend natural SOC availability or other subsoil specific conditions influence the composition and the functional diversity of the microbial community and in return if there is any evidence how the microbial community composition affects carbon sequestration under these conditions. Soil samples were taken at four different depths on two neighbouring arable sites; one Kolluvisol with high SOC concentrations (8-12 g/kg) throughout the profile and one Luvisol with low SOC concentrations (3-4 g/kg) below 30 cm depth. The multi substrate induced respiration (MSIR) method was used to identify shifts in the functional diversity of the microbial community along the depth profiles. Amino sugars Muramic Acid and Glucosamine were measured as indicators for bacterial and fungal residues and ergosterol was determined as marker for saprotrophic fungi. The results of the discriminant analysis of the respiration values obtained from the 17 substrates used in the MSIR show that the substrate use in subsoil is different from the substrate use in topsoil. The amino sugar analysis and the ratio of ergosterol to microbial biomass C indicate that the fungal dominance of the microbial community decreases with depth. The results from this study support previous findings, which also observed decreasing fungal dominance with depth. Furthermore the MSIR approach shows clearly that not only the composition of the microbial community but also their substrate use changes with depth. Thus, a different microbial community with altered substrate requirements could be an important reason for enhanced carbon sequestration in subsoil. The fact that the MSIR was also able to differentiate between the two sites proves the assumption that resources are an important factor controlling the functional diversity of the microbial community, as abiotic factors are very similar for the two profiles, but the sites show a different depth gradient for SOC.

Design of N-acyl homoserine lactonase with high substrate specificity by a rational approach.

PubMed

Kyeong, Hyun-Ho; Kim, Jin-Hyun; Kim, Hak-Sung

2015-06-01

N-Acyl homoserine lactone (AHL) is a major quorum-sensing signaling molecule in many bacterial species. Quorum-quenching (QQ) enzymes, which degrade such signaling molecules, have attracted much attention as an approach to controlling and preventing bacterial virulence and pathogenesis. However, naturally occurring QQ enzymes show a broad substrate spectrum, raising the concern of unintentionally attenuating beneficial effects by symbiotic bacteria. Here we report the rational design of acyl homoserine lactonase with high substrate specificity. Through docking analysis, we identified three key residues which play a key role in the substrate preference of the enzyme. The key residues were changed in a way that increases hydrophobic contact with a substrate having a short acyl chain (C4-AHL) while generating steric clashes with that containing a long acyl chain (C12-AHL). The resulting mutants exhibited a significantly shifted preference toward a substrate with a short acyl chain. Molecular dynamics simulations suggested that the mutations affect the behavior of a flexible loop, allowing tighter binding of a substrate with a short acyl chain.

Interferometric nanoporous anodic alumina photonic coatings for optical sensing

NASA Astrophysics Data System (ADS)

Chen, Yuting; Santos, Abel; Wang, Ye; Kumeria, Tushar; Wang, Changhai; Li, Junsheng; Losic, Dusan

2015-04-01

Herein, we present a systematic study on the development, optical optimization and sensing applicability of colored photonic coatings based on nanoporous anodic alumina films grown on aluminum substrates. These optical nanostructures, so-called distributed Bragg reflectors (NAA-DBRs), are fabricated by galvanostatic pulse anodization process, in which the current density is altered in a periodic manner in order to engineer the effective medium of the resulting photonic coatings. As-prepared NAA-DBR photonic coatings present brilliant interference colors on the surface of aluminum, which can be tuned at will within the UV-visible spectrum by means of the anodization profile. A broad library of NAA-DBR colors is produced by means of different anodization profiles. Then, the effective medium of these NAA-DBR photonic coatings is systematically assessed in terms of optical sensitivity, low limit of detection and linearity by reflectometric interference spectroscopy (RIfS) in order to optimize their nanoporous structure toward optical sensors with enhanced sensing performance. Finally, we demonstrate the applicability of these photonic nanostructures as optical platforms by selectively detecting gold(iii) ions in aqueous solutions. The obtained results reveal that optimized NAA-DBR photonic coatings can achieve an outstanding sensing performance for gold(iii) ions, with a sensitivity of 22.16 nm μM-1, a low limit of detection of 0.156 μM (i.e. 30.7 ppb) and excellent linearity within the working range (0.9983).Herein, we present a systematic study on the development, optical optimization and sensing applicability of colored photonic coatings based on nanoporous anodic alumina films grown on aluminum substrates. These optical nanostructures, so-called distributed Bragg reflectors (NAA-DBRs), are fabricated by galvanostatic pulse anodization process, in which the current density is altered in a periodic manner in order to engineer the effective medium of the resulting photonic coatings. As-prepared NAA-DBR photonic coatings present brilliant interference colors on the surface of aluminum, which can be tuned at will within the UV-visible spectrum by means of the anodization profile. A broad library of NAA-DBR colors is produced by means of different anodization profiles. Then, the effective medium of these NAA-DBR photonic coatings is systematically assessed in terms of optical sensitivity, low limit of detection and linearity by reflectometric interference spectroscopy (RIfS) in order to optimize their nanoporous structure toward optical sensors with enhanced sensing performance. Finally, we demonstrate the applicability of these photonic nanostructures as optical platforms by selectively detecting gold(iii) ions in aqueous solutions. The obtained results reveal that optimized NAA-DBR photonic coatings can achieve an outstanding sensing performance for gold(iii) ions, with a sensitivity of 22.16 nm μM-1, a low limit of detection of 0.156 μM (i.e. 30.7 ppb) and excellent linearity within the working range (0.9983). Electronic supplementary information (ESI) available: The Supporting Information file provides further information about real-time monitoring of ΔOTeff with changes in the refractive index of the medium filling the nanopores, demonstration of visual red shift in a NAA-DBR sample after infiltration with isopropanol and calculations of linearity (R2) for each NAA-DBR coating. See DOI: 10.1039/c5nr00369e

Cellulosic ethanol production via consolidated bioprocessing by a novel thermophilic anaerobic bacterium isolated from a Himalayan hot spring.

PubMed

Singh, Nisha; Mathur, Anshu S; Tuli, Deepak K; Gupta, Ravi P; Barrow, Colin J; Puri, Munish

2017-01-01

Cellulose-degrading thermophilic anaerobic bacterium as a suitable host for consolidated bioprocessing (CBP) has been proposed as an economically suited platform for the production of second-generation biofuels. To recognize the overall objective of CBP, fermentation using co-culture of different cellulolytic and sugar-fermenting thermophilic anaerobic bacteria has been widely studied as an approach to achieving improved ethanol production. We assessed monoculture and co-culture fermentation of novel thermophilic anaerobic bacterium for ethanol production from real substrates under controlled conditions. In this study, Clostridium sp. DBT-IOC-C19, a cellulose-degrading thermophilic anaerobic bacterium, was isolated from the cellulolytic enrichment cultures obtained from a Himalayan hot spring. Strain DBT-IOC-C19 exhibited a broad substrate spectrum and presented single-step conversion of various cellulosic and hemicellulosic substrates to ethanol, acetate, and lactate with ethanol being the major fermentation product. Additionally, the effect of varying cellulose concentrations on the fermentation performance of the strain was studied, indicating a maximum cellulose utilization ability of 10 g L -1 cellulose. Avicel degradation kinetics of the strain DBT-IOC-C19 displayed 94.6% degradation at 5 g L -1 and 82.74% degradation at 10 g L -1 avicel concentration within 96 h of fermentation. In a comparative study with Clostridium thermocellum DSM 1313, the ethanol and total product concentrations were higher by the newly isolated strain on pretreated rice straw at an equivalent substrate loading. Three different co-culture combinations were used on various substrates that presented two-fold yield improvement than the monoculture during batch fermentation. This study demonstrated the direct fermentation ability of the novel thermophilic anaerobic bacteria on various cellulosic and hemicellulosic substrates into ethanol without the aid of any exogenous enzymes, representing CBP-based fermentation approach. Here, the broad substrate utilization spectrum of isolated cellulolytic thermophilic anaerobic bacterium was shown to be of potential utility. We demonstrated that the co-culture strategy involving novel strains is efficient in improving ethanol production from real substrate.

A comparison of stable-isotope probing of DNA and phospholipid fatty acids to study prokaryotic functional diversity in sulfate-reducing marine sediment enrichment slurries.

PubMed

Webster, Gordon; Watt, Lynsey C; Rinna, Joachim; Fry, John C; Evershed, Richard P; Parkes, R John; Weightman, Andrew J

2006-09-01

Marine sediment slurries enriched for anaerobic, sulfate-reducing prokaryotic communities utilizing glucose and acetate were used to provide the first comparison between stable-isotope probing (SIP) of phospholipid fatty acids (PLFA) and DNA (16S rRNA and dsrA genes) biomarkers. Different 13C-labelled substrates (glucose, acetate and pyruvate) at low concentrations (100 microM) were used over a 7-day incubation to follow and identify carbon flow into different members of the community. Limited changes in total PLFA and bacterial 16S rRNA gene DGGE profiles over 7 days suggested the presence of a stable bacterial community. A broad range of PLFA were rapidly labelled (within 12 h) in the 13C-glucose slurry but this changed with time, suggesting the presence of an active glucose-utilizing population and later development of another population able to utilize glucose metabolites. The identity of the major glucose-utilizers was unclear as 13C-enriched PLFA were common (16:0, 16:1, 18:1omega7, highest incorporation) and there was little difference between 12C- and 13C-DNA 16S rRNA gene denaturing gradient gel electrophoresis (DGGE) profiles. Seemingly glucose, a readily utilizable substrate, resulted in widespread incorporation consistent with the higher extent of 13C-incorporation (approximately 10 times) into PLFA compared with 13C-acetate or 13C-pyruvate. 13C-PLFA in the 13C-acetate and 13C-pyruvate slurries were similar to each other and to those that developed in the 13C-glucose slurry after 4 days. These were more diagnostic, with branched odd-chain fatty acids (i15:0, a15:0 and 15:1omega6) possibly indicating the presence of Desulfococcus or Desulfosarcina sulfate-reducing bacteria (SRB) and sequences related to these SRB were in the 13C-acetate-DNA dsrA gene library. The 13C-acetate-DNA 16S rRNA gene library also contained sequences closely related to SRB, but these were the acetate-utilizing Desulfobacter sp., as well as a broad range of uncultured Bacteria. In contrast, analysis of DGGE bands from 13C-DNA demonstrated that the candidate division JS1 and Firmicutes were actively assimilating 13C-acetate. Denaturing gradient gel electrophoresis also confirmed the presence of JS1 in the 13C-DNA from the 13C-glucose slurry. These results demonstrate that JS1, originally found in deep subsurface sediments, is more widely distributed in marine sediments and provides the first indication of its metabolism; incorporation of acetate and glucose (or glucose metabolites) under anaerobic, sulfate-reducing conditions. Here we demonstrate that PLFA- and DNA-SIP can be used together in a sedimentary system, with low concentrations of 13C-substrate and overlapping incubation times (up to 7 days) to provide complementary, although not identical, information on carbon flow and the identity of active members of an anaerobic prokaryotic community.

Study of firefly luciferin oxidation and isomerism as possible inhibition pathways for firefly bioluminescence

NASA Astrophysics Data System (ADS)

Pinto da Silva, Luís; Esteves da Silva, Joaquim C. G.

2014-01-01

Firefly bioluminescence presents a light emitting profile with a form of a flash, due to the firefly luciferase-catalyzed formation of inhibitory products. These impair the binding of the substrate luciferin to the active site of the enzyme. However, this luciferase catalyzed pathways may not be the only ones responsible for the flash profile. The oxidation and isomerisation of the substrate luciferin lead to the formation of compounds that are also known inhibitors of firefly bioluminescence. So, the objective of this Letter was to analyze if these reactions could be capable of interfering with the bioluminescence reaction.

Key Issues Concerning Biolog Use for Aerobic and Anaerobic Freshwater Bacterial Community-Level Physiological Profiling

NASA Astrophysics Data System (ADS)

Christian, Bradley W.; Lind, Owen T.

2006-06-01

Bacterial heterotrophy in aquatic ecosystems is important in the overall carbon cycle. Biolog MicroPlates provide information into the metabolic potential of bacteria involved in carbon cycling. Specifically, Biolog EcoPlatesTM were developed with ecologically relevant carbon substrates to allow investigators to measure carbon substrate utilization patterns and develop community-level physiological profiles from natural bacterial assemblages. However, understanding of the functionality of these plates in freshwater research is limited. We explored several issues of EcoPlate use for freshwater bacterial assemblages including inoculum density, incubation temperature, non-bacterial color development, and substrate selectivity. Each of these has various effects on plate interpretation. We offer suggestions and techniques to resolve these interpretation issues. Lastly we propose a technique to allow EcoPlate use in anaerobic freshwater bacterial studies.

On the levels of enzymatic substrate specificity: Implications for the early evolution of metabolic pathways

NASA Technical Reports Server (NTRS)

Lazcano, A.; Diaz-Villagomez, E.; Mills, T.; Oro, J.

1995-01-01

The most frequently invoked explanation for the origin of metabolic pathways is the retrograde evolution hypothesis. In contrast, according to the so-called 'patchwork' theory, metabolism evolved by the recruitment of relatively inefficient small enzymes of broad specificity that could react with a wide range of chemically related substrates. In this paper it is argued that both sequence comparisons and experimental results on enzyme substrate specificity support the patchwork assembly theory. The available evidence supports previous suggestions that gene duplication events followed by a gradual neoDarwinian accumulation of mutations and other minute genetic changes lead to the narrowing and modification of enzyme function in at least some primordial metabolic pathways.

Printable semiconductor structures and related methods of making and assembling

DOEpatents

Nuzzo, Ralph G.; Rogers, John A.; Menard, Etienne; Lee, Keon Jae; Khang; , Dahl-Young; Sun, Yugang; Meitl, Matthew; Zhu, Zhengtao; Ko, Heung Cho; Mack, Shawn

2013-03-12

The present invention provides a high yield pathway for the fabrication, transfer and assembly of high quality printable semiconductor elements having selected physical dimensions, shapes, compositions and spatial orientations. The compositions and methods of the present invention provide high precision registered transfer and integration of arrays of microsized and/or nanosized semiconductor structures onto substrates, including large area substrates and/or flexible substrates. In addition, the present invention provides methods of making printable semiconductor elements from low cost bulk materials, such as bulk silicon wafers, and smart-materials processing strategies that enable a versatile and commercially attractive printing-based fabrication platform for making a broad range of functional semiconductor devices.

Printable semiconductor structures and related methods of making and assembling

DOEpatents

Nuzzo, Ralph G [Champaign, IL; Rogers, John A [Champaign, IL; Menard, Etienne [Durham, NC; Lee, Keon Jae [Tokyo, JP; Khang, Dahl-Young [Urbana, IL; Sun, Yugang [Westmont, IL; Meitl, Matthew [Raleigh, NC; Zhu, Zhengtao [Rapid City, SD; Ko, Heung Cho [Urbana, IL; Mack, Shawn [Goleta, CA

2011-10-18

The present invention provides a high yield pathway for the fabrication, transfer and assembly of high quality printable semiconductor elements having selected physical dimensions, shapes, compositions and spatial orientations. The compositions and methods of the present invention provide high precision registered transfer and integration of arrays of microsized and/or nanosized semiconductor structures onto substrates, including large area substrates and/or flexible substrates. In addition, the present invention provides methods of making printable semiconductor elements from low cost bulk materials, such as bulk silicon wafers, and smart-materials processing strategies that enable a versatile and commercially attractive printing-based fabrication platform for making a broad range of functional semiconductor devices.

Printable semiconductor structures and related methods of making and assembling

DOEpatents

Nuzzo, Ralph G.; Rogers, John A.; Menard, Etienne; Lee, Keon Jae; Khang, Dahl-Young; Sun, Yugang; Meitl, Matthew; Zhu, Zhengtao; Ko, Heung Cho; Mack, Shawn

2010-09-21

The present invention provides a high yield pathway for the fabrication, transfer and assembly of high quality printable semiconductor elements having selected physical dimensions, shapes, compositions and spatial orientations. The compositions and methods of the present invention provide high precision registered transfer and integration of arrays of microsized and/or nanosized semiconductor structures onto substrates, including large area substrates and/or flexible substrates. In addition, the present invention provides methods of making printable semiconductor elements from low cost bulk materials, such as bulk silicon wafers, and smart-materials processing strategies that enable a versatile and commercially attractive printing-based fabrication platform for making a broad range of functional semiconductor devices.

ZnO buffer layer for metal films on silicon substrates

DOEpatents

Ihlefeld, Jon

2014-09-16

Dramatic improvements in metallization integrity and electroceramic thin film performance can be achieved by the use of the ZnO buffer layer to minimize interfacial energy between metallization and adhesion layers. In particular, the invention provides a substrate metallization method utilizing a ZnO adhesion layer that has a high work of adhesion, which in turn enables processing under thermal budgets typically reserved for more exotic ceramic, single-crystal, or metal foil substrates. Embodiments of the present invention can be used in a broad range of applications beyond ferroelectric capacitors, including microelectromechanical systems, micro-printed heaters and sensors, and electrochemical energy storage, where integrity of metallized silicon to high temperatures is necessary.

Substrate mass transfer: analytical approach for immobilized enzyme reactions

NASA Astrophysics Data System (ADS)

Senthamarai, R.; Saibavani, T. N.

2018-04-01

In this paper, the boundary value problem in immobilized enzyme reactions is formulated and approximate expression for substrate concentration without external mass transfer resistance is presented. He’s variational iteration method is used to give approximate and analytical solutions of non-linear differential equation containing a non linear term related to enzymatic reaction. The relevant analytical solution for the dimensionless substrate concentration profile is discussed in terms of dimensionless reaction parameters α and β.

Metabolic Profile of Wound-Induced Changes in Primary Carbon Metabolism in Sugarbeet Root

USDA-ARS?s Scientific Manuscript database

Injury to plant products induces respiration rate and increases the demand for respiratory substrates. Alterations in primary carbon metabolism are likely to support the elevated demand for respiratory substrates, although the nature of these alterations is unknown. To gain insight into the metabo...

Improved measurement of extracellular enzymatic activities in subsurface sediments using competitive desorption treatment

NASA Astrophysics Data System (ADS)

Hoarfrost, Adrienne; Snider, Rachel; Arnosti, Carol

2017-02-01

Extracellular enzymatic activities initiate microbially-driven heterotrophic carbon cycling in subsurface sediments. While measurement of hydrolytic activities in sediments is fundamental to our understanding of carbon cycling, these measurements are often technically difficult due to sorption of organic substrates to the sediment matrix. Most methods that measure hydrolysis of organic substrates in sediments rely on recovery of a fluorophore or fluorescently-labeled target substrate from a sediment incubation. The tendency for substrates to sorb to sediments results in lower recovery of an added substrate, and can result in data that are unusable or difficult to interpret. We developed a treatment using competitive desorption of a fluorescently-labeled, high molecular weight organic substrate that improves recovery of the labeled substrate from sediment subsamples. Competitive desorption treatment improved recovery of the fluorescent substrate by a median of 66%, expanded the range of sediments for which activity measurements could be made, and was effective in sediments from a broad range of geochemical contexts. More reliable measurements of hydrolytic activities in sediments will yield usable and more easily interpretable data from a wider range of sedimentary environments, enabling better understanding of microbially-catalyzed carbon cycling in subsurface environments.

Universal digital high-resolution melt: a novel approach to broad-based profiling of heterogeneous biological samples.

PubMed

Fraley, Stephanie I; Hardick, Justin; Masek, Billie J; Jo Masek, Billie; Athamanolap, Pornpat; Rothman, Richard E; Gaydos, Charlotte A; Carroll, Karen C; Wakefield, Teresa; Wang, Tza-Huei; Yang, Samuel

2013-10-01

Comprehensive profiling of nucleic acids in genetically heterogeneous samples is important for clinical and basic research applications. Universal digital high-resolution melt (U-dHRM) is a new approach to broad-based PCR diagnostics and profiling technologies that can overcome issues of poor sensitivity due to contaminating nucleic acids and poor specificity due to primer or probe hybridization inaccuracies for single nucleotide variations. The U-dHRM approach uses broad-based primers or ligated adapter sequences to universally amplify all nucleic acid molecules in a heterogeneous sample, which have been partitioned, as in digital PCR. Extensive assay optimization enables direct sequence identification by algorithm-based matching of melt curve shape and Tm to a database of known sequence-specific melt curves. We show that single-molecule detection and single nucleotide sensitivity is possible. The feasibility and utility of U-dHRM is demonstrated through detection of bacteria associated with polymicrobial blood infection and microRNAs (miRNAs) associated with host response to infection. U-dHRM using broad-based 16S rRNA gene primers demonstrates universal single cell detection of bacterial pathogens, even in the presence of larger amounts of contaminating bacteria; U-dHRM using universally adapted Lethal-7 miRNAs in a heterogeneous mixture showcases the single copy sensitivity and single nucleotide specificity of this approach.

ESDA®-Lite collection of DNA from latent fingerprints on documents.

PubMed

Plaza, Dane T; Mealy, Jamia L; Lane, J Nicholas; Parsons, M Neal; Bathrick, Abigail S; Slack, Donia P

2015-05-01

The ability to detect and non-destructively collect biological samples for DNA processing would benefit the forensic community by preserving the physical integrity of evidentiary items for more thorough evaluations by other forensic disciplines. The Electrostatic Detection Apparatus (ESDA®) was systemically evaluated for its ability to non-destructively collect DNA from latent fingerprints deposited on various paper substrates for short tandem repeat (STR) DNA profiling. Fingerprints were deposited on a variety of paper substrates that included resume paper, cotton paper, magazine paper, currency, copy paper, and newspaper. Three DNA collection techniques were performed: ESDA collection, dry swabbing, and substrate cutting. Efficacy of each collection technique was evaluated by the quantity of DNA present in each sample and the percent profile generated by each sample. Both the ESDA and dry swabbing non-destructive sampling techniques outperformed the destructive methodology of substrate cutting. A greater number of full profiles were generated from samples collected with the non-destructive dry swabbing collection technique than were generated from samples collected with the ESDA; however, the ESDA also allowed the user to visualize the area of interest while non-destructively collecting the biological material. The ability to visualize the biological material made sampling straightforward and eliminated the need for numerous, random swabbings/cuttings. Based on these results, the evaluated non-destructive ESDA collection technique has great potential for real-world forensic implementation. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Application Of Optical Processing For Growth Of Silicon Dioxide

DOEpatents

Sopori, Bhushan L.

1997-06-17

A process for producing a silicon dioxide film on a surface of a silicon substrate. The process comprises illuminating a silicon substrate in a substantially pure oxygen atmosphere with a broad spectrum of visible and infrared light at an optical power density of from about 3 watts/cm.sup.2 to about 6 watts/cm.sup.2 for a time period sufficient to produce a silicon dioxide film on the surface of the silicon substrate. An optimum optical power density is about 4 watts/cm.sup.2 for growth of a 100.ANG.-300.ANG. film at a resultant temperature of about 400.degree. C. Deep level transient spectroscopy analysis detects no measurable impurities introduced into the silicon substrate during silicon oxide production and shows the interface state density at the SiO.sub.2 /Si interface to be very low.

CVD diamond substrate for microelectronics. Final report

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

Burden, J.; Gat, R.

1996-11-01

Chemical Vapor Deposition (CVD) of diamond films has evolved dramatically in recent years, and commercial opportunities for diamond substrates in thermal management applications are promising. The objective of this technology transfer initiative (TTI) is for Applied Science and Technology, Inc. (ASTEX) and AlliedSignal Federal Manufacturing and Technologies (FM&T) to jointly develop and document the manufacturing processes and procedures required for the fabrication of multichip module circuits using CVD diamond substrates, with the major emphasis of the project concentrating on lapping/polishing prior to metallization. ASTEX would provide diamond films for the study, and FM&T would use its experience in lapping, polishing,more » and substrate metallization to perform secondary processing on the parts. The primary goal of the project was to establish manufacturing processes that lower the manufacturing cost sufficiently to enable broad commercialization of the technology.« less

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.

Light spectrum modifies the utilization pattern of energy sources in Pseudomonas sp. DR 5-09

PubMed Central

Rosberg, Anna Karin; Windstam, Sofia T.; Karlsson, Maria E.; Bergstrand, Karl-Johan; Khalil, Sammar; Wohanka, Walter

2017-01-01

Despite the overruling impact of light in the phyllosphere, little is known regarding the influence of light spectra on non-phototrophic bacteria colonizing the leaf surface. We developed an in vitro method to study phenotypic profile responses of bacterial pure cultures to different bands of the visible light spectrum using monochromatic (blue: 460 nm; red: 660 nm) and polychromatic (white: 350–990 nm) LEDs, by modification and optimization of a protocol for the Phenotype MicroArray™ technique (Biolog Inc., CA, USA). The new protocol revealed high reproducibility of substrate utilization under all conditions tested. Challenging the non-phototrophic bacterium Pseudomonas sp. DR 5–09 with white, blue, and red light demonstrated that all light treatments affected the respiratory profile differently, with blue LED having the most decisive impact on substrate utilization by impairing respiration of 140 substrates. The respiratory activity was decreased on 23 and 42 substrates under red and white LEDs, respectively, while utilization of one, 16, and 20 substrates increased in the presence of red, blue, and white LEDs, respectively. Interestingly, on four substrates contrasting utilization patterns were found when the bacterium was exposed to different light spectra. Although non-phototrophic bacteria do not rely directly on light as an energy source, Pseudomonas sp. DR 5–09 changed its respiratory activity on various substrates differently when exposed to different lights. Thus, ability to sense and distinguish between different wavelengths even within the visible light spectrum must exist, and leads to differential regulation of substrate usage. With these results, we hypothesize that different light spectra might be a hitherto neglected key stimulus for changes in microbial lifestyle and habits of substrate usage by non-phototrophic phyllospheric microbiota, and thus might essentially stratify leaf microbiota composition and diversity. PMID:29267321

Light spectrum modifies the utilization pattern of energy sources in Pseudomonas sp. DR 5-09.

PubMed

Gharaie, Samareh; Vaas, Lea A I; Rosberg, Anna Karin; Windstam, Sofia T; Karlsson, Maria E; Bergstrand, Karl-Johan; Khalil, Sammar; Wohanka, Walter; Alsanius, Beatrix W

2017-01-01

Despite the overruling impact of light in the phyllosphere, little is known regarding the influence of light spectra on non-phototrophic bacteria colonizing the leaf surface. We developed an in vitro method to study phenotypic profile responses of bacterial pure cultures to different bands of the visible light spectrum using monochromatic (blue: 460 nm; red: 660 nm) and polychromatic (white: 350-990 nm) LEDs, by modification and optimization of a protocol for the Phenotype MicroArray™ technique (Biolog Inc., CA, USA). The new protocol revealed high reproducibility of substrate utilization under all conditions tested. Challenging the non-phototrophic bacterium Pseudomonas sp. DR 5-09 with white, blue, and red light demonstrated that all light treatments affected the respiratory profile differently, with blue LED having the most decisive impact on substrate utilization by impairing respiration of 140 substrates. The respiratory activity was decreased on 23 and 42 substrates under red and white LEDs, respectively, while utilization of one, 16, and 20 substrates increased in the presence of red, blue, and white LEDs, respectively. Interestingly, on four substrates contrasting utilization patterns were found when the bacterium was exposed to different light spectra. Although non-phototrophic bacteria do not rely directly on light as an energy source, Pseudomonas sp. DR 5-09 changed its respiratory activity on various substrates differently when exposed to different lights. Thus, ability to sense and distinguish between different wavelengths even within the visible light spectrum must exist, and leads to differential regulation of substrate usage. With these results, we hypothesize that different light spectra might be a hitherto neglected key stimulus for changes in microbial lifestyle and habits of substrate usage by non-phototrophic phyllospheric microbiota, and thus might essentially stratify leaf microbiota composition and diversity.

PHOENIX IR Spectra of CO in the Sun and the Stars

NASA Astrophysics Data System (ADS)

Ayres, T. R.; Valenti, J. A.; Hinkle, K. H.; Johns-Krull, C. M.; Wiedemann, G. R.

1998-05-01

We report high-resolution (R ~ 5*E(4) ) spectra of the 2143 cm(-1) (4.7 mu m) interval---containing lines from the fundamental (Delta v =1) bands of carbon monoxide---in the Sun and other late-type stars, obtained with the PHOENIX cryogenic infrared spectrometer. The solar work was conducted at the McMath-Pierce telescope during the period 21--26 April 1997, while the stellar observations were obtained on the night of 6 December 1997 at the Kitt Peak 2.1-m. Comparisons of spatially-averaged spectra from the long-slit observations of the Sun with very high-resolution Fourier transform spectrometer scans permitted an evalution of the PHOENIX instrumental profile (affected by flexing of the grating owing to unequal thermal coefficients of the epoxy replica and the silicon substrate). The profile information subsequently was applied in comparisons of the stellar data sets with CO spectra synthesized using a variety of prototype thermal structure models. On the stellar side, we concentrated on bright K-type giants whose broad CO profiles are fully resolved at PHOENIX resolution. Our intent was to test the degree of thermal heterogeneity in the outer layers of the red giant atmospheres; analogous to the ``thermal bifurcation'' effects deduced in the solar context (namely, the dichotomy between classical hot chromosphere and the controversial cool ``COmosphere''). Our spectral analyses provide a preview of the power of PHOENIX for high-resolution infrared spectroscopy of stars; to be realized in the coming months when the original grating is replaced with an improved version. [-2mm] The observations were obtained at the National Optical Astronomy Observatories, which is operated by AURA, Inc., under a cooperative agreement with the National Science Foundation. This work was supported by NSF grant AST-9618505.

Defining efficient enzyme-cofactor pairs for bioorthogonal profiling of protein methylation

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

Islam, Kabirul; Chen, Yuling; Wu, Hong

2013-11-18

Protein methyltransferase (PMT)-mediated posttranslational modification of histone and nonhistone substrates modulates stability, localization, and interacting partners of target proteins in diverse cellular contexts. These events play critical roles in normal biological processes and are frequently deregulated in human diseases. In the course of identifying substrates of individual PMTs, bioorthogonal profiling of protein methylation (BPPM) has demonstrated its merits. In this approach, specific PMTs are engineered to process S-adenosyl-L-methionine (SAM) analogs as cofactor surrogates and label their substrates with distinct chemical modifications for target elucidation. Despite the proof-of-concept advancement of BPPM, few efforts have been made to explore its generality. Withmore » two cancer-relevant PMTs, EuHMT1 (GLP1/KMT1D) and EuHMT2 (G9a/KMT1C), as models, we defined the key structural features of engineered PMTs and matched SAM analogs that can render the orthogonal enzyme–cofactor pairs for efficient catalysis. Here we have demonstrated that the presence of sulfonium-β-sp 2 carbon and flexible, medium-sized sulfonium-δ-substituents are crucial for SAM analogs as BPPM reagents. The bulky cofactors can be accommodated by tailoring the conserved Y1211/Y1154 residues and nearby hydrophobic cavities of EuHMT1/2. Profiling proteome-wide substrates with BPPM allowed identification of >500 targets of EuHMT1/2 with representative targets validated using native EuHMT1/2 and SAM. This finding indicates that EuHMT1/2 may regulate many cellular events previously unrecognized to be modulated by methylation. The present work, therefore, paves the way to a broader application of the BPPM technology to profile methylomes of diverse PMTs and elucidate their downstream functions.« less

Site-selective and stereoselective functionalization of non-activated tertiary C-H bonds

NASA Astrophysics Data System (ADS)

Liao, Kuangbiao; Pickel, Thomas C.; Boyarskikh, Vyacheslav; Bacsa, John; Musaev, Djamaladdin G.; Davies, Huw M. L.

2017-11-01

The synthesis of complex organic compounds usually relies on controlling the reactions of the functional groups. In recent years, it has become possible to carry out reactions directly on the C-H bonds, previously considered to be unreactive. One of the major challenges is to control the site-selectivity because most organic compounds have many similar C-H bonds. The most well developed procedures so far rely on the use of substrate control, in which the substrate has one inherently more reactive C-H bond or contains a directing group or the reaction is conducted intramolecularly so that a specific C-H bond is favoured. A more versatile but more challenging approach is to use catalysts to control which site in the substrate is functionalized. p450 enzymes exhibit C-H oxidation site-selectivity, in which the enzyme scaffold causes a specific C-H bond to be functionalized by placing it close to the iron-oxo haem complex. Several studies have aimed to emulate this enzymatic site-selectivity with designed transition-metal catalysts but it is difficult to achieve exceptionally high levels of site-selectivity. Recently, we reported a dirhodium catalyst for the site-selective functionalization of the most accessible non-activated (that is, not next to a functional group) secondary C-H bonds by means of rhodium-carbene-induced C-H insertion. Here we describe another dirhodium catalyst that has a very different reactivity profile. Instead of the secondary C-H bond, the new catalyst is capable of precise site-selectivity at the most accessible tertiary C-H bonds. Using this catalyst, we modify several natural products, including steroids and a vitamin E derivative, indicating the applicability of this method of synthesis to the late-stage functionalization of complex molecules. These studies show it is possible to achieve site-selectivity at different positions within a substrate simply by selecting the appropriate catalyst. We hope that this work will inspire the design of even more sophisticated catalysts, such that catalyst-controlled C-H functionalization becomes a broadly applied strategy for the synthesis of complex molecules.

Atomic force microscopy and nanoindentation investigation of polydimethylsiloxane elastomeric substrate compliancy for various sputtered thin film morphologies.

PubMed

Maji, Debashis; Das, Soumen

2018-03-01

Crack free electrically continuous metal thin films over soft elastomeric substrates play an integral part in realization of modern day flexible bioelectronics and biosensors. Under nonoptimized deposition conditions, delamination, and/or cracking of the top film as well as the underlying soft substrate hinders optimal performance of these devices. Hence it is very important to understand and control not only the various deposition factors like power, time, or deposition pressure but also investigate the various interfacial physics playing a critical role in assuring thin film adhesion and substrate compliancy. In the present study, various nanomechanical information of the underlying substrate, namely, crack profile, average roughness, Young's modulus, and adhesion force were studied for uncracked and cracked polydimethylsiloxane (PDMS) surfaces along with pristine and conventional plasma treated PDMS samples as control. Quantification of the above parameters were done using three-dimensional surface profiler, scanning electron microscopy, nanoindentation, and atomic force microscopy techniques to elucidate the modulus range, average roughness, and adhesion force. Comparative analysis with control revealed remarkable similarity between increased modulus values, increased surface roughness, and reduced adhesion force accounting for reduced substrate compliancy and resulting in film cracking or buckling which are critical for development of various bioflexible devices. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 106A: 725-737, 2018. © 2017 Wiley Periodicals, Inc.

Dissecting substrate specificities of the mitochondrial AFG3L2 protease.

PubMed

Ding, Bojian; Martin, Dwight W; Rampello, Anthony J; Glynn, Steven E

2018-06-22

Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane. Identifying how AFG3L2 selects substrates from the diverse complement of matrix-localized proteins is essential for understanding mitochondrial protein biogenesis and quality control. Here, we create solubilized forms of AFG3L2 to examine the enzyme's substrate specificity mechanisms. We show that conserved residues within the pre-sequence of the mitochondrial ribosomal protein, MrpL32, target the subunit to the protease for processing into a mature form. Moreover, these residues can act as a degron, delivering diverse model proteins to AFG3L2 for degradation. By determining the sequence of degra-dation products from multiple substrates using mass spectrometry, we construct a peptidase specificity pro-file that displays constrained product lengths and is dominated by the identity of the residue at the P1' posi-tion, with a strong preference for hydrophobic and small polar residues. This specificity profile is validated by examining the cleavage of both fluorogenic reporter peptides and full polypeptide substrates bearing different P1' residues. Together, these results demonstrate that AFG3L2 contains multiple modes of specificity, dis-criminating between potential substrates by recognizing accessible degron sequences, and performing peptide bond cleavage at preferred patterns of residues within the compartmental chamber.

Profiles of Discourse Recognition

ERIC Educational Resources Information Center

Singer, Murray

2013-01-01

A discourse recognition theory derived from more general memory formulations would be broad in its psychological implications. This study compared discourse recognition with some established profiles of item recognition. Participants read 10 stories either once or twice each. They then rated their confidence in recognizing explicit, paraphrased,…

Characterization of near-stoichiometric Ti:LiNbO(3) strip waveguides with varied substrate refractive index in the guiding layer.

PubMed

Zhang, De-Long; Zhang, Pei; Zhou, Hao-Jiang; Pun, Edwin Yue-Bun

2008-10-01

We have demonstrated the possibility that near-stoichiometric Ti:LiNbO(3) strip waveguides are fabricated by carrying out vapor transport equilibration at 1060 degrees C for 12 h on a congruent LiNbO(3) substrate with photolithographically patterned 4-8 microm wide, 115 nm thick Ti strips. Optical characterizations show that these waveguides are single mode at 1.5 microm and show a waveguide loss of 1.3 dB/cm for TM mode and 1.1 dB/cm for TE mode. In the width/depth direction of the waveguide, the mode field follows the Gauss/Hermite-Gauss function. Secondary-ion-mass spectrometry (SIMS) was used to study Ti-concentration profiles in the depth direction and on the surface of the 6 microm wide waveguide. The result shows that the Ti profile follows a sum of two error functions along the width direction and a complementary error function in the depth direction. The surface Ti concentration, 1/e width and depth, and mean diffusivities along the width and depth directions of the guide are similar to 3.0 x 10(21) cm(-3), 3.8 microm, 2.6 microm, 0.30 and 0.14 microm(2)/h, respectively. Micro-Raman analysis was carried out on the waveguide endface to characterize the depth profile of Li composition in the guiding layer. The results show that the depth profile of Li composition also follows a complementary error function with a 1/e depth of 3.64 microm. The mean ([Li(Li)]+[Ti(Li)])/([Nb(Nb)]+[Ti(Nb)]) ratio in the waveguide layer is about 0.98. The inhomogeneous Li-composition profile results in a varied substrate index in the guiding layer. A two-dimensional refractive index profile model in the waveguide is proposed by taking into consideration the varied substrate index and assuming linearity between Ti-induced index change and Ti concentration. The net waveguide surface index increments at 1545 nm are 0.0114 and 0.0212 for ordinary and extraordinary rays, respectively. Based upon the constructed index model, the fundamental mode field profile was calculated using the beam propagation method, and the mode sizes and effective index versus the Ti-strip width were calculated for three lower TM and TE modes using the variational method. An agreement between theory and experiment is obtained.

Beam profile and coherence properties of synchrotron beams after reflection on modified multilayer mirrors

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

Rack, Alexander, E-mail: alexander.rack@esrf.fr; Vivo, Amparo; Morawe, Christian

2016-07-27

Multilayer mirrors present an attractive alternative for reflective hard X-ray monochromators due to their increased bandwidth compared with crystal-based systems. An issue remains the strong modulations in the reflected beam profile, i.e. an irregular stripe pattern. This is a major problem for micro-imaging applications, where multilayer-based monochromators are frequently employed to deliver higher photon flux density. A subject of particular interest is how to overcome beam profile modifications, namely the stripe patterns, induced by the reflection on a multilayer. For multilayer coatings in general it is known that the substrate and its surface quality significantly influence the performance of suchmore » kind of mirrors as the coating reproduces to a certain degree roughness and shape of the substrate. Our studies have shown that modified coatings can significantly change the impact of the multilayer reflection on the beam profile. We will present recent results as well as a critical review.« less

Carbon utilization profile of the filamentous fungal species Fusarium fujikuroi, Penicillium decumbens, and Sarocladium strictum isolated from marine coastal environments.

PubMed

Fuentes, Marcelo E; Quiñones, Renato A

Facultative marine filamentous fungi have recently emerged as a functional component in coastal marine systems. However, little is known about their ecological role and functions in biogeochemical cycles. Penicillium decumbens, S. strictum, and F. fujikuroi were isolated from the coastal upwelling zone off south-central Chile. Their carbon profiles were characterized using Biolog FF MicroPlates. These species used a wide range of carbon sources, mainly carbohydrates, but also amino acids, suggesting the use of metabolic routes that include glycolysis/gluconeogenesis. Substrate richness revealed a great capacity for the utilization of nutritional sources, reflected by the following Shannon Indices of utilization of specific substrates: 4.02 for S. strictum, 4.01 for P. decumbes, and 3.91 for F. fujikuroi, which reveals a high physiological capacity for oxidizing different substrates. Significant differences were found between 18 substrates utilized by all three species. Results suggest that filamentous fungi should be considered an integral part of the marine microbial community and included in biogeochemical cycling models of upwelling ecosystems.

Dry texturing of solar cells

DOEpatents

Sopori, B.L.

1994-10-25

A textured backside of a semiconductor device for increasing light scattering and absorption in a semiconductor substrate is accomplished by applying infrared radiation to the front side of a semiconductor substrate that has a metal layer deposited on its backside in a time-energy profile that first produces pits in the backside surface and then produces a thin, highly reflective, low resistivity, epitaxial alloy layer over the entire area of the interface between the semiconductor substrate and a metal contact layer. The time-energy profile includes ramping up to a first energy level and holding for a period of time to create the desired pit size and density and then rapidly increasing the energy to a second level in which the entire interface area is melted and alloyed quickly. After holding the second energy level for a sufficient time to develop the thin alloy layer over the entire interface area, the energy is ramped down to allow epitaxial crystal growth in the alloy layer. The result is a textured backside on an optically reflective, low resistivity alloy interface between the semiconductor substrate and the metal electrical contact layer. 9 figs.

Dry texturing of solar cells

DOEpatents

Sopori, Bhushan L.

1994-01-01

A textured backside of a semiconductor device for increasing light scattering and absorption in a semiconductor substrate is accomplished by applying infrared radiation to the front side of a semiconductor substrate that has a metal layer deposited on its backside in a time-energy profile that first produces pits in the backside surface and then produces a thin, highly reflective, low resistivity, epitaxial alloy layer over the entire area of the interface between the semiconductor substrate and a metal contact layer. The time-energy profile includes ramping up to a first energy level and holding for a period of time to create the desired pit size and density and then rapidly increasing the energy to a second level in which the entire interface area is melted and alloyed quickly. After holding the second energy level for a sufficient time to develop the thin alloy layer over the entire interface area, the energy is ramped down to allow epitaxial crystal growth in the alloy layer. The result is a textured backside an optically reflective, low resistivity alloy interface between the semiconductor substrate and the metal electrical contact layer.

Cross-guide Moreno directional coupler in empty substrate integrated waveguide

NASA Astrophysics Data System (ADS)

Miralles, E.; Belenguer, A.; Esteban, H.; Boria, V.

2017-05-01

Substrate integrated waveguides (SIWs) combine the advantages of rectangular waveguides (low losses) and planar circuits (low cost and low profile). Empty substrate integrated waveguide (ESIW) has been proposed as a novel configuration in SIWs recently. This technology significantly reduces the losses of conventional SIW by removing its inner dielectric. The cross-guide directional coupler is a well-known low-profile design for having a broadband waveguide coupler. In this paper a cross-guide coupler with ESIW technique is proposed. In such a manner, the device can be integrated with microwave circuits and other printed circuit board components. It is the first time that a cross-guide coupler is implemented in ESIW technology. The designed, fabricated, and measured device presents good results as a matter of insertion loss of 1 dB (including transitions), reflection under 20 dB, coupling between 19.5 and 21.5 dB, and directivity higher than 15 dB over targeted frequency range from 12.4 GHz to 18 GHz. The coupler implemented in ESIW improves the directivity when compared to similar solutions in other empty substrate integrated waveguide solutions.

Profiling the changes in signaling pathways in ascorbic acid/β-glycerophosphate-induced osteoblastic differentiation.

PubMed

Chaves Neto, Antonio Hernandes; Queiroz, Karla Cristiana; Milani, Renato; Paredes-Gamero, Edgar Julian; Justo, Giselle Zenker; Peppelenbosch, Maikel P; Ferreira, Carmen Veríssima

2011-01-01

Despite numerous reports on the ability of ascorbic acid and β-glycerophosphate (AA/β-GP) to induce osteoblast differentiation, little is known about the molecular mechanisms involved in this phenomenon. In this work, we used a peptide array containing specific consensus sequences (potential substrates) for protein kinases and traditional biochemical techniques to examine the signaling pathways modulated during AA/β-GP-induced osteoblast differentiation. The kinomic profile obtained after 7 days of treatment with AA/β-GP identified 18 kinase substrates with significantly enhanced or reduced phosphorylation. Peptide substrates for Akt, PI3K, PKC, BCR, ABL, PRKG1, PAK1, PAK2, ERK1, ERBB2, and SYK showed a considerable reduction in phosphorylation, whereas enhanced phosphorylation was observed in substrates for CHKB, CHKA, PKA, FAK, ATM, PKA, and VEGFR-1. These findings confirm the potential usefulness of peptide microarrays for identifying kinases known to be involved in bone development in vivo and in vitro and show that this technique can be used to investigate kinases whose function in osteoblastic differentiation is poorly understood.

Growth and high rate reactive ion etching of epitaxially grown barium hexaferrite films on single crystal silicon carbide substrates

NASA Astrophysics Data System (ADS)

Chen, Zhaohui

Ferrites are an invaluable group of insulating magnetic materials used for high frequency microwave applications in such passive electronic devices as isolators, phase shifters, and circulators. Because of their high permeability, non-reciprocal electromagnetic properties, and low eddy current losses, there are no other materials that serve such a broad range of applications. Until recently, they have been widely employed in bulk form, with little success in thin film-based applications in commercial or military microwave technologies. In today's technology, emerging electronic systems, such as high frequency, high power wireless and satellite communications (GPS, Bluetooth, WLAN, commercial radar, etc) thin film materials are in high demand. It is widely recognized that as high frequency devices shift to microwave frequencies the integration of passive devices with semiconductor electronics holds significant advantages in the realization of miniaturization, broader bandwidths, higher performance, speed, power and lower production costs. Thus, the primary objective of this thesis is to explore the integration of ferrite films with wide band gap semiconductor substrates for the realization of monolithic integrated circuits (MICs). This thesis focuses on two key steps for the integration of barium hexaferrite (Ba M-type or BaM) devices on semiconductor substrates. First, the development of high crystal quality ferrite film growth via pulsed laser deposition on wide band gap silicon carbide semiconductor substrates, and second, the effective patterning of BaM films using dry etching techniques. To address part one, BaM films were deposited on 6H silicon carbide (0001) substrates by Pulsed Laser Deposition. X-ray diffraction showed strong crystallographic alignment while pole figures exhibited reflections consistent with epitaxial growth. After optimized annealing, BaM films have a perpendicular magnetic anisotropy field of 16,900 Oe, magnetization (4piMs) of 4.4 kG, and ferromagnetic resonance peak-to-peak derivative linewidth at 53 GHz of 96 Oe. This combination of properties qualifies these films for microwave device applications. This marks the first growth of a microwave ferrite on SiC substrates and offers a new approach in the design and development of mu-wave and mm-wave monolithic integrated circuits. In part two, high-rate reactive ion etching using CHF3/SF6 gas mixtures was successfully demonstrated on BaM films, resulting in high aspect profile features of less than 50 nm in lateral dimension. These demonstrations enable the future integration of ferrites into MIC devices and technologies.

Engineered jadomycin analogues with altered sugar moieties revealing JadS as a substrate flexible O-glycosyltransferase.

PubMed

Li, Liyuan; Pan, Guohui; Zhu, Xifen; Fan, Keqiang; Gao, Wubin; Ai, Guomin; Ren, Jinwei; Shi, Mingxin; Olano, Carlos; Salas, José A; Yang, Keqian

2017-07-01

Glycosyltransferases (GTs)-mediated glycodiversification studies have drawn significant attention recently, with the goal of generating bioactive compounds with improved pharmacological properties by diversifying the appended sugars. The key to achieving glycodiversification is to identify natural and/or engineered flexible GTs capable of acting upon a broad range of substrates. Here, we report the use of a combinatorial biosynthetic approach to probe the substrate flexibility of JadS, the GT in jadomycin biosynthesis, towards different non-native NDP-sugar substrates, enabling us to identify six jadomycin B analogues with different sugar moieties. Further structural engineering by precursor-directed biosynthesis allowed us to obtain 11 new jadomycin analogues. Our results for the first time show that JadS is a flexible O-GT that can utilize both L- and D- sugars as donor substrates, and tolerate structural changes at the C2, C4 and C6 positions of the sugar moiety. JadS may be further exploited to generate novel glycosylated jadomycin molecules in future glycodiversification studies.

Substrate specificity and pH dependence of homogeneous wheat germ acid phosphatase.

PubMed

Van Etten, R L; Waymack, P P

1991-08-01

The broad substrate specificity of a homogeneous isoenzyme of wheat germ acid phosphatase (WGAP) was extensively investigated by chromatographic, electrophoretic, NMR, and kinetic procedures. WGAP exhibited no divalent metal ion requirement and was unaffected upon incubation with EDTA or o-phenanthroline. A comparison of two catalytically homogeneous isoenzymes revealed little difference in substrate specificity. The specificity of WGAP was established by determining the Michaelis constants for a wide variety of substrates. p-Nitrophenyl phosphate, pyrophosphate, tripolyphosphate, and ATP were preferred substrates while lesser activities were seen toward sugar phosphates, trimetaphosphate, phosphoproteins, and (much less) phosphodiesters. An extensive table of Km and Vmax values is given. The pathway for the hydrolysis of trimetaphosphate was examined by colorimetric and 31P NMR methods and it was found that linear tripolyphosphate is not a free intermediate in the enzymatic reaction. In contrast to literature reports, homogeneous wheat germ acid phosphatase exhibits no measurable carboxylesterase activity, nor does it hydrolyze phenyl phosphonothioate esters or phytic acid at significant rates.

From coffee ring to spherulites ring of poly(ethylene oxide) film from drying droplet

NASA Astrophysics Data System (ADS)

Hu, Yinchun; Zhang, Xuerong; Qiu, Maibo; Wei, Yan; Zhou, Qiong; Huang, Di

2018-03-01

We discuss how the "spherulites ring" morphology and "coffee ring" profile of PEO film formed by the drying droplet at glass substrate with different heating rate. Upon increasing the heating rate of substrate, it is found that deposited PEO film from drying droplet shows the unusually observed "coffee ring" profile and "spherulites ring" morphology. The main mechanism for this phenomenon is proposed to be an enhanced Marangoni convection which is induced by the increased solute concentration gradient and reduced viscous force above 70 °C. A simple formation mechanism of the unusually observed "coffee ring" profile and "spherulites ring" morphology is proposed. These findings can be exploited to trace the center of Marangoni convection, with potential applications in designing the spherulite patterns of crystalline polymer films in ink-jet printing and self-assembly fields.

Unnatural amino acids increase activity and specificity of synthetic substrates for human and malarial cathepsin C.

PubMed

Poreba, Marcin; Mihelic, Marko; Krai, Priscilla; Rajkovic, Jelena; Krezel, Artur; Pawelczak, Malgorzata; Klemba, Michael; Turk, Dusan; Turk, Boris; Latajka, Rafal; Drag, Marcin

2014-04-01

Mammalian cathepsin C is primarily responsible for the removal of N-terminal dipeptides and activation of several serine proteases in inflammatory or immune cells, while its malarial parasite ortholog dipeptidyl aminopeptidase 1 plays a crucial role in catabolizing the hemoglobin of its host erythrocyte. In this report, we describe the systematic substrate specificity analysis of three cathepsin C orthologs from Homo sapiens (human), Bos taurus (bovine) and Plasmodium falciparum (malaria parasite). Here, we present a new approach with a tailored fluorogenic substrate library designed and synthesized to probe the S1 and S2 pocket preferences of these enzymes with both natural and a broad range of unnatural amino acids. Our approach identified very efficiently hydrolyzed substrates containing unnatural amino acids, which resulted in the design of significantly better substrates than those previously known. Additionally, in this study significant differences in terms of the structures of optimal substrates for human and malarial orthologs are important from the therapeutic point of view. These data can be also used for the design of specific inhibitors or activity-based probes.

Effect of Substrate Conversion on Performance of Microbial Fuel Cells and Anodic Microbial Communities.

PubMed

Zhao, Yang-Guo; Zhang, Yi; She, Zonglian; Shi, Yue; Wang, Min; Gao, Mengchun; Guo, Liang

2017-09-01

Performance of microbial fuel cells (MFCs) was monitored during the influent nutrient change from lactate to glucose/acetate/propionate and then to lactate. Meanwhile, anodic microbial communities were characterized by culture-independent molecular biotechnologies. Results showed MFC performance recovered rapidly when the lactate was replaced by one of its metabolic intermediates acetate, while it needed a longer time to recover if lactate substrate was converted to glucose/propionate or acetate to lactate. Secondary lactate feed enhanced the enrichment of bacterial populations dominating in first lactate feed. Electricity-producing bacteria, Geobacter spp., and beneficial helpers, Anaeromusa spp. and Pseudomonas spp., revived from a low abundance as lactate secondary supply, but microbial communities were hard to achieve former profiles in structure and composition. Hence, microbial community profiles tended to recover when outside environmental condition were restored. Different substrates selected unique functional microbial populations.

The X-ray photoelectron spectroscopy depth profiling and tribological characterization of ion-plated gold on various metals

NASA Technical Reports Server (NTRS)

Miyoshi, K.; Spalvins, T.; Buckley, D. H.

1983-01-01

For the case of ion-plated gold, the graded interface between gold and a nickel substrate and a nickel substrate, such tribological properties as friction and microhardness are examined by means of X-ray photoelectron spectroscopy analysis and depth profiling. Sliding was conducted against SiC pins in both the adhesive process, where friction arises from adhesion between sliding surfaces, and abrasion, in which friction is due to pin indentation and groove-plowing. Both types of friction are influenced by coating depth, but with opposite trends: the graded interface exhibited the highest adhesion, but the lowest abrasion. The coefficient of friction due to abrasion is inversely related to hardness. Graded interface microhardness values are found to be the highest, due to an alloying effect. There is almost no interface gradation between the vapor-deposited gold film and the substrate.

AES study on the chemical composition of ferroelectric BaTiO3 thin films RF sputter-deposited on silicon

NASA Technical Reports Server (NTRS)

Dharmadhikari, V. S.; Grannemann, W. W.

1983-01-01

AES depth profiling data are presented for thin films of BaTiO3 deposited on silicon by RF sputtering. By profiling the sputtered BaTiO3/silicon structures, it was possible to study the chemical composition and the interface characteristics of thin films deposited on silicon at different substrate temperatures. All the films showed that external surface layers were present, up to a few tens of angstroms thick, the chemical composition of which differed from that of the main layer. The main layer had stable composition, whereas the intermediate film-substrate interface consisted of reduced TiO(2-x) oxides. The thickness of this intermediate layer was a function of substrate temperature. All the films showed an excess of barium at the interface. These results are important in the context of ferroelectric phenomena observed in BaTiO3 thin films.

Internal structure of copper(II)-phthalocyanine thin films on SiO2/Si substrates investigated by grazing incidence x-ray reflectometry

NASA Astrophysics Data System (ADS)

Brieva, A. C.; Jenkins, T. E.; Jones, D. G.; Strössner, F.; Evans, D. A.; Clark, G. F.

2006-04-01

The internal structure of copper(II)-phthalocyanine (CuPc) thin films grown on SiO2/Si by organic molecular beam deposition has been studied by grazing incidence x-ray reflectometry (GIXR) and atomic force microscopy. The electronic density profile is consistent with a structure formed by successive monolayers of molecules in the α form with the b axis lying in the substrate surface plane. The authors present an electronic density profile model of CuPc films grown on SiO2/Si. The excellent agreement between the model and experimental data allows postdeposition monitoring of the internal structure of the CuPc films with the nondestructive GIXR technique, providing a tool for accurate control of CuPc growth on silicon-based substrates. In addition, since the experiments have been carried out ex situ, they show that these structures can endure ambient conditions.

Mid-infrared tunable metamaterials

DOEpatents

Brener, Igal; Miao, Xiaoyu; Shaner, Eric A.; Passmore, Brandon Scott

2017-07-11

A mid-infrared tunable metamaterial comprises an array of resonators on a semiconductor substrate having a large dependence of dielectric function on carrier concentration and a semiconductor plasma resonance that lies below the operating range, such as indium antimonide. Voltage biasing of the substrate generates a resonance shift in the metamaterial response that is tunable over a broad operating range. The mid-infrared tunable metamaterials have the potential to become the building blocks of chip based active optical devices in mid-infrared ranges, which can be used for many applications, such as thermal imaging, remote sensing, and environmental monitoring.

Mid-infrared tunable metamaterials

DOEpatents

Brener, Igal; Miao, Xiaoyu; Shaner, Eric A; Passmore, Brandon Scott; Jun, Young Chul

2015-04-28

A mid-infrared tunable metamaterial comprises an array of resonators on a semiconductor substrate having a large dependence of dielectric function on carrier concentration and a semiconductor plasma resonance that lies below the operating range, such as indium antimonide. Voltage biasing of the substrate generates a resonance shift in the metamaterial response that is tunable over a broad operating range. The mid-infrared tunable metamaterials have the potential to become the building blocks of chip based active optical devices in mid-infrared ranges, which can be used for many applications, such as thermal imaging, remote sensing, and environmental monitoring.

Partial dust obscuration in active galactic nuclei as a cause of broad-line profile and lag variability, and apparent accretion disc inhomogeneities

NASA Astrophysics Data System (ADS)

Gaskell, C. Martin; Harrington, Peter Z.

2018-04-01

The profiles of the broad emission lines of active galactic nuclei (AGNs) and the time delays in their response to changes in the ionizing continuum ("lags") give information about the structure and kinematics of the inner regions of AGNs. Line profiles are also our main way of estimating the masses of the supermassive black holes (SMBHs). However, the profiles often show ill-understood, asymmetric structure and velocity-dependent lags vary with time. Here we show that partial obscuration of the broad-line region (BLR) by outflowing, compact, dusty clumps produces asymmetries and velocity-dependent lags similar to those observed. Our model explains previously inexplicable changes in the ratios of the hydrogen lines with time and velocity, the lack of correlation of changes in line profiles with variability of the central engine, the velocity dependence of lags, and the change of lags with time. We propose that changes on timescales longer than the light-crossing time do not come from dynamical changes in the BLR, but are a natural result of the effect of outflowing dusty clumps driven by radiation pressure acting on the dust. The motion of these clumps offers an explanation of long-term changes in polarization. The effects of the dust complicate the study of the structure and kinematics of the BLR and the search for sub-parsec SMBH binaries. Partial obscuration of the accretion disc can also provide the local fluctuations in luminosity that can explain sizes deduced from microlensing.

QSO Broad Emission Line Asymmetries: Evidence of Gravitational Redshift?

NASA Astrophysics Data System (ADS)

Corbin, Michael R.

1995-07-01

The broad optical and ultraviolet emission lines of QSOs and active galactic nuclei (AGNs) display both redward and blueward asymmetries. This result is particularly well established for Hβ and C IV λ1549, and it has been found that Hβ becomes increasingly redward asymmetric with increasing soft X-ray luminosity. Two models for the origin of these asymmetries are investigated: (1) Anisotropic line emission from an ensemble of radially moving clouds, and (2) Two-component profiles consisting of a core of intermediate (˜1000-4000 km s-1) velocity width and a very broad (˜5000-20,000 km s-1) base, in which the asymmetries arise due to a velocity difference between the centroids of the components. The second model is motivated by the evidence that the traditional broad-line region is actually composed of an intermediate-line region (ILR) of optically thick clouds and a very broad line region (VBLR) of optically thin clouds lying closer to the central continuum source. Line profiles produced by model (1) are found to be inconsistent with those observed, being asymmetric mainly in their cores, whereas the asymmetries of actual profiles arise mainly from excess emission in their wings. By contrast, numerical fitting to actual Hβ and C IV λ1549 line profiles reveals that the majority can be accurately modeled by two components, either two Gaussians or the combination of a Gaussian base and a logarithmic core. The profile asymmetries in Hβ can be interpreted as arising from a shift of the base component over a range ˜6300 km s-1 relative to systemic velocity as defined by the position of the [O III] λ5007 line. A similar model appears to apply to C IV λ1549. The correlation between Hβ asymmetry and X-ray luminosity may thus be interpreted as a progressive red- shift of the VBLR velocity centroid relative to systemic velocity with increasing X-ray luminosity. This in turn suggests that the underlying effect is gravitational red shift, as soft X-ray emission arises from a region ˜ light-minutes in size and arguably traces the mass of the putative supermassive black hole. Depending on the size of the VBLR and the exact amount of its profile centroid shift, central masses in the range 109-10 Msun are implied for the objects displaying the strongest redward profile asymmetries, consistent with other estimates. The largest VBLR velocity dispersions measured from the two-component modeling are ˜20,000 km s-1, which also yields a virial mass ˜109 Msun for a VBLR size 0.1 pc. The gravitational redshift model does not explain the origin of the blueshift of the VBLR emission among low X-ray luminosity sources, however. This must be interpreted as arising from a competing effect such as electron scattering of line photons in the vicinity of the VBLR. On average, radio-loud objects have redward asymmetric broad-line profiles and stronger intermediate- and narrow-line emission than radio-quiet objects of comparable optical luminosity. Under the gravitational redshift model these differences may be interpreted as the result of black hole and host galaxy masses that are larger on average among the former class, consistent with the evidence that they are merger products.

Community-level physiological profiles of bacteria and fungi: Plate type and incubation temperature influences on contrasting soils

Treesearch

Aimee T. Classen; Sarah I. Boyle; Kristin E. Haskins; Steven T. Overby; Stephen C. Hart

2003-01-01

Temperature sensitivity of community-level physiological profiles (CLPPs) was examined for two semiarid soils from the southwestern United States using five different C-substrate profile microtiter plates (Biolog GN2, GP2, ECO, SFN2, and SFP2) incubated at five different temperature regimes.The CLPPs produced from all plate types were relatively unaffected by these...

Xpo7 is a broad-spectrum exportin and a nuclear import receptor.

PubMed

Aksu, Metin; Pleiner, Tino; Karaca, Samir; Kappert, Christin; Dehne, Heinz-Jürgen; Seibel, Katharina; Urlaub, Henning; Bohnsack, Markus T; Görlich, Dirk

2018-05-10

Exportins bind cargo molecules in a RanGTP-dependent manner inside nuclei and transport them through nuclear pores to the cytoplasm. CRM1/Xpo1 is the best-characterized exportin because specific inhibitors such as leptomycin B allow straightforward cargo validations in vivo. The analysis of other exportins lagged far behind, foremost because no such inhibitors had been available for them. In this study, we explored the cargo spectrum of exportin 7/Xpo7 in depth and identified not only ∼200 potential export cargoes but also, surprisingly, ∼30 nuclear import substrates. Moreover, we developed anti-Xpo7 nanobodies that acutely block Xpo7 function when transfected into cultured cells. The inhibition is pathway specific, mislocalizes export cargoes of Xpo7 to the nucleus and import substrates to the cytoplasm, and allowed validation of numerous tested cargo candidates. This establishes Xpo7 as a broad-spectrum bidirectional transporter and paves the way for a much deeper analysis of exportin and importin function in the future. © 2018 Aksu et al.

The First Mammalian Aldehyde Oxidase Crystal Structure

PubMed Central

Coelho, Catarina; Mahro, Martin; Trincão, José; Carvalho, Alexandra T. P.; Ramos, Maria João; Terao, Mineko; Garattini, Enrico; Leimkühler, Silke; Romão, Maria João

2012-01-01

Aldehyde oxidases (AOXs) are homodimeric proteins belonging to the xanthine oxidase family of molybdenum-containing enzymes. Each 150-kDa monomer contains a FAD redox cofactor, two spectroscopically distinct [2Fe-2S] clusters, and a molybdenum cofactor located within the protein active site. AOXs are characterized by broad range substrate specificity, oxidizing different aldehydes and aromatic N-heterocycles. Despite increasing recognition of its role in the metabolism of drugs and xenobiotics, the physiological function of the protein is still largely unknown. We have crystallized and solved the crystal structure of mouse liver aldehyde oxidase 3 to 2.9 Å. This is the first mammalian AOX whose structure has been solved. The structure provides important insights into the protein active center and further evidence on the catalytic differences characterizing AOX and xanthine oxidoreductase. The mouse liver aldehyde oxidase 3 three-dimensional structure combined with kinetic, mutagenesis data, molecular docking, and molecular dynamics studies make a decisive contribution to understand the molecular basis of its rather broad substrate specificity. PMID:23019336

Effective cleaning of hexagonal boron nitride for graphene devices.

PubMed

Garcia, Andrei G F; Neumann, Michael; Amet, François; Williams, James R; Watanabe, Kenji; Taniguchi, Takashi; Goldhaber-Gordon, David

2012-09-12

Hexagonal boron nitride (h-BN) films have attracted considerable interest as substrates for graphene. ( Dean, C. R. et al. Nat. Nanotechnol. 2010 , 5 , 722 - 6 ; Wang, H. et al. Electron Device Lett. 2011 , 32 , 1209 - 1211 ; Sanchez-Yamagishi, J. et al. Phys. Rev. Lett. 2012 , 108 , 1 - 5 .) We study the presence of organic contaminants introduced by standard lithography and substrate transfer processing on h-BN films exfoliated on silicon oxide substrates. Exposure to photoresist processing adds a large broad luminescence peak to the Raman spectrum of the h-BN flake. This signal persists through typical furnace annealing recipes (Ar/H(2)). A recipe that successfully removes organic contaminants and results in clean h-BN flakes involves treatment in Ar/O(2) at 500 °C.

Application of optical processing for growth of silicon dioxide

DOEpatents

Sopori, B.L.

1997-06-17

A process for producing a silicon dioxide film on a surface of a silicon substrate is disclosed. The process comprises illuminating a silicon substrate in a substantially pure oxygen atmosphere with a broad spectrum of visible and infrared light at an optical power density of from about 3 watts/cm{sup 2} to about 6 watts/cm{sup 2} for a time period sufficient to produce a silicon dioxide film on the surface of the silicon substrate. An optimum optical power density is about 4 watts/cm{sup 2} for growth of a 100{angstrom}-300{angstrom} film at a resultant temperature of about 400 C. Deep level transient spectroscopy analysis detects no measurable impurities introduced into the silicon substrate during silicon oxide production and shows the interface state density at the SiO{sub 2}/Si interface to be very low. 1 fig.

[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.

Efficient calculation of general Voigt profiles

NASA Astrophysics Data System (ADS)

Cope, D.; Khoury, R.; Lovett, R. J.

1988-02-01

An accurate and efficient program is presented for the computation of OIL profiles, generalizations of the Voigt profile resulting from the one-interacting-level model of Ward et al. (1974). These profiles have speed dependent shift and width functions and have asymmetric shapes. The program contains an adjustable error control parameter and includes the Voigt profile as a special case, although the general nature of this program renders it slower than a specialized Voigt profile method. Results on accuracy and computation time are presented for a broad set of test parameters, and a comparison is made with previous work on the asymptotic behavior of general Voigt profiles.

KCTD2, an adaptor of Cullin3 E3 ubiquitin ligase, suppresses gliomagenesis by destabilizing c-Myc

PubMed Central

Kim, Eun-Jung; Kim, Sung-Hak; Jin, Xiong; Jin, Xun; Kim, Hyunggee

2017-01-01

Cullin3 E3 ubiquitin ligase ubiquitinates a wide range of substrates through substrate-specific adaptors Bric-a-brac, Tramtrack, and Broad complex (BTB) domain proteins. These E3 ubiquitin ligase complexes are involved in diverse cellular functions. Our recent study demonstrated that decreased Cullin3 expression induces glioma initiation and correlates with poor prognosis of patients with malignant glioma. However, the substrate recognition mechanism associated with tumorigenesis is not completely understood. Through yeast two-hybrid screening, we identified potassium channel tetramerization domain-containing 2 (KCTD2) as a BTB domain protein that binds to Cullin3. The interaction of Cullin3 and KCTD2 was verified using immunoprecipitation and immunofluorescence. Of interest, KCTD2 expression was markedly decreased in patient-derived glioma stem cells (GSCs) compared with non-stem glioma cells. Depletion of KCTD2 using a KCTD2-specific short-hairpin RNA in U87MG glioma cells and primary Ink4a/Arf-deficient murine astrocytes markedly increased self-renewal activity in addition with an increased expression of stem cell markers, and mouse in vivo intracranial tumor growth. As an underlying mechanism for these KCTD2-mediated phenotypic changes, we demonstrated that KCTD2 interacts with c-Myc, which is a key stem cell factor, and causes c-Myc protein degradation by ubiquitination. As a result, KCTD2 depletion acquires GSC features and affects aerobic glycolysis via expression changes in glycolysis-associated genes through c-Myc protein regulation. Of clinical significance was our finding that patients having a profile of KCTD2 mRNA-low and c-Myc gene signature-high, but not KCTD2 mRNA-low and c-Myc mRNA-high, are strongly associated with poor prognosis. This study describes a novel regulatory mode of c-Myc protein in malignant gliomas and provides a potential framework for glioma therapy by targeting c-Myc function. PMID:28060381

Cloning and characterization of unusual fatty acid desaturases from Anemone leveillei: identification of an acyl-coenzyme A C20 Delta5-desaturase responsible for the synthesis of sciadonic acid.

PubMed

Sayanova, Olga; Haslam, Richard; Venegas Caleron, Monica; Napier, Johnathan A

2007-05-01

The seed oil of Anemone leveillei contains significant amounts of sciadonic acid (20:3Delta(5,11,14); SA), an unusual non-methylene-interrupted fatty acid with pharmaceutical potential similar to arachidonic acid. Two candidate cDNAs (AL10 and AL21) for the C(20) Delta(5cis)-desaturase from developing seeds of A. leveillei were functionally characterized in transgenic Arabidopsis (Arabidopsis thaliana) plants. The open reading frames of both Delta(5)-desaturases showed some similarity to presumptive acyl-coenzyme A (CoA) desaturases found in animals and plants. When expressed in transgenic Arabidopsis, AL21 showed a broad range of substrate specificity, utilizing both saturated (16:0 and 18:0) and unsaturated (18:2, n-6 and 18:3, n-3) substrates. In contrast, AL10 did not show any activity in wild-type Arabidopsis. Coexpression of AL10 or AL21 with a C(18) Delta(9)-elongase in transgenic Arabidopsis plants resulted in the production of SA and juniperonic fatty acid (20:4Delta(5,11,14,17)). Thus, AL10 acted only on C(20) polyunsaturated fatty acids in a manner analogous to "front-end" desaturases. However, neither AL10 nor AL21 contain the cytochrome b(5) domain normally present in this class of enzymes. Acyl-CoA profiling of transgenic Arabidopsis plants and developing A. leveillei seeds revealed significant accumulation of Delta(5)-unsaturated fatty acids as acyl-CoAs compared to the accumulation of these fatty acids in total lipids. Positional analysis of triacylglycerols of A. leveillei seeds showed that Delta(5)-desaturated fatty acids were present in both sn-2 and sn-1 + sn-3 positions, although the majority of 16:1Delta(5), 18:1Delta(5), and SA was present at the sn-2 position. Our data provide biochemical evidence for the A. leveillei Delta(5)-desaturases using acyl-CoA substrates.

The effect of substrate on thermodynamic and kinetic anisotropies in atomic thin films.

PubMed

Haji-Akbari, Amir; Debenedetti, Pablo G

2014-07-14

Glasses have a wide range of technological applications. The recent discovery of ultrastable glasses that are obtained by depositing the vapor of a glass-forming liquid onto the surface of a cold substrate has sparked renewed interest in the effects of confinements on physicochemical properties of liquids and glasses. Here, we use molecular dynamics simulations to study the effect of substrate on thin films of a model glass-forming liquid, the Kob-Andersen binary Lennard-Jones system, and compute profiles of several thermodynamic and kinetic properties across the film. We observe that the substrate can induce large oscillations in profiles of thermodynamic properties such as density, composition, and stress, and we establish a correlation between the oscillations in total density and the oscillations in normal stress. We also demonstrate that the kinetic properties of an atomic film can be readily tuned by changing the strength of interactions between the substrate and the liquid. Most notably, we show that a weakly attractive substrate can induce the emergence of a highly mobile region in its vicinity. In this highly mobile region, structural relaxation is several times faster than in the bulk, and the exploration of the potential energy landscape is also more efficient. In the subsurface region near a strongly attractive substrate, however, the dynamics is decelerated and the sampling of the potential energy landscape becomes less efficient than the bulk. We explain these two distinct behaviors by establishing a correlation between the oscillations in kinetic properties and the oscillations in lateral stress. Our findings offer interesting opportunities for designing better substrates for the vapor deposition process or developing alternative procedures for situations where vapor deposition is not feasible.

Semiconductor quantum dots as Förster resonance energy transfer donors for intracellularly-based biosensors

NASA Astrophysics Data System (ADS)

Field, Lauren D.; Walper, Scott A.; Susumu, Kimihiro; Oh, Eunkeu; Medintz, Igor L.; Delehanty, James B.

2017-02-01

Förster resonance energy transfer (FRET)-based assemblies currently comprise a significant portion of intracellularly based sensors. Although extremely useful, the fluorescent protein pairs typically utilized in such sensors are still plagued by many photophysical issues including significant direct acceptor excitation, small changes in FRET efficiency, and limited photostability. Luminescent semiconductor nanocrystals or quantum dots (QDs) are characterized by many unique optical properties including size-tunable photoluminescence, broad excitation profiles coupled to narrow emission profiles, and resistance to photobleaching, which can cumulatively overcome many of the issues associated with use of fluorescent protein FRET donors. Utilizing QDs for intracellular FRET-based sensing still requires significant development in many areas including materials optimization, bioconjugation, cellular delivery and assay design and implementation. We are currently developing several QD-based FRET sensors for various intracellular applications. These include sensors targeting intracellular proteolytic activity along with those based on theranostic nanodevices for monitoring drug release. The protease sensor is based on a unique design where an intracellularly expressed fluorescent acceptor protein substrate assembles onto a QD donor following microinjection, forming an active complex that can be monitored in live cells over time. In the theranostic configuration, the QD is conjugated to a carrier protein-drug analogue complex to visualize real-time intracellular release of the drug from its carrier in response to an external stimulus. The focus of this talk will be on the design, properties, photophysical characterization and cellular application of these sensor constructs.

GaSb and Ga1-xInxSb Thermophotovoltaic Cells using Diffused Junction Technology in Bulk Substrates

NASA Astrophysics Data System (ADS)

Dutta, P. S.; Borrego, J. M.; Ehsani, H.; Rajagopalan, G.; Bhat, I. B.; Gutmann, R. J.; Nichols, G.; Baldasaro, P. F.

2003-01-01

This paper presents results of experimental and theoretical research on antimonide- based thermophotovoltaic (TPV) materials and cells. The topics discussed include: growth of large diameter ternary GaInSb bulk crystals, substrate preparation, diffused junction processes, cell fabrication and characterization, and, cell modeling. Ternary GaInSb boules up to 2 inches in diameter have been grown using the vertical Bridgman technique with a novel self solute feeding technique. A single step diffusion process followed by precise etching of the diffused layer has been developed to obtain a diffusion profile appropriate for high efficiency, p-n junction GaSb and GaInSb thermophotovoltaic cells. The optimum junction depth to obtain the highest quantum efficiency and open circuit voltage has been identified based on diffusion lengths (or minority carrier lifetimes), carrier mobility and experimental diffused impurity profiles. Theoretical assessment of the performance of ternary (GaInSb) and binary (GaSb) cells fabricated by Zn diffusion in bulk substrates has been performed using PC-1D one-dimensional computer simulations. Several factors affecting the cell performances such as the effects of emitter doping profile, emitter thickness and recombination mechanisms (Auger, radiative and Shockley-Read-Hall), the advantages of surface passivation and the impact of dark current due to the metallic grid will be discussed. The conditions needed for diffused junction cells on ternary and binary substrates to achieve similar performance to the epitaxially grown lattice- matched quaternary cells are identified.

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.

Superintendent Leadership: A Phenomenological Study of Texas Superintendents from Broad Prize Eligible School Districts

ERIC Educational Resources Information Center

Moreno, Jose H.

2014-01-01

The identification of leadership qualities and reform strategies implemented to increase student achievement in urban school districts is vital to closing the achievement gap. The purpose of this phenomenological study was to identify a leadership profile of the Broad Prize superintendent and reform strategies used to leverage systemic change that…

Mapping estuarine distributions of the non-indigenous Japanese Eelgrass Zostera japonica using Color Infrared Aerial Photography

EPA Science Inventory

This presentation describes a technique for mapping distributions of the nonindigenous Japanese eelgrass Zostera japonica in estuarine ecosystems of the Pacific Northwest. The relatively broad distribution of this intertidal plant, often on very soft substrate, makes classical g...

Regulator and enzyme specificities of the TOL plasmid-encoded upper pathway for degradation of aromatic hydrocarbons and expansion of the substrate range of the pathway.

PubMed Central

Abril, M A; Michan, C; Timmis, K N; Ramos, J L

1989-01-01

The TOL plasmid upper pathway operon encodes enzymes involved in the catabolism of aromatic hydrocarbons such as toluene and xylenes. The regulator of the gene pathway, the XylR protein, exhibits a very broad effector specificity, being able to recognize as effectors not only pathway substrates but also a wide variety of mono- and disubstituted methyl-, ethyl-, and chlorotoluenes, benzyl alcohols, and p-chlorobenzaldehyde. Benzyl alcohol dehydrogenase and benzaldehyde dehydrogenase, two upper pathway enzymes, exhibit very broad substrate specificities and transform unsubstituted substrates and m- and p-methyl-, m- and p-ethyl-, and m- and p-chloro-substituted benzyl alcohols and benzaldehydes, respectively, at a high rate. In contrast, toluene oxidase only oxidizes toluene, m- and p-xylene, m-ethyltoluene, and 1,2,4-trimethylbenzene [corrected], also at a high rate. A biological test showed that toluene oxidase attacks m- and p-chlorotoluene, albeit at a low rate. No evidence for the transformation of p-ethyltoluene by toluene oxidase has been found. Hence, toluene oxidase acts as the bottleneck step for the catabolism of p-ethyl- and m- and p-chlorotoluene through the TOL upper pathway. A mutant toluene oxidase able to transform p-ethyltoluene was isolated, and a mutant strain capable of fully degrading p-ethyltoluene was constructed with a modified TOL plasmid meta-cleavage pathway able to mineralize p-ethylbenzoate. By transfer of a TOL plasmid into Pseudomonas sp. strain B13, a clone able to slowly degrade m-chlorotoluene was also obtained. PMID:2687253

Cysteine peptidases in the tomato trypanosomatid Phytomonas serpens: influence of growth conditions, similarities with cruzipain and secretion to the extracellular environment.

PubMed

Elias, Camila G R; Pereira, Fernanda M; Dias, Felipe A; Silva, Thiago L A; Lopes, Angela H C S; d'Avila-Levy, Claudia M; Branquinha, Marta H; Santos, André L S

2008-12-01

We have characterized the cysteine peptidase production by Phytomonas serpens, a tomato trypanosomatid. The parasites were cultivated in four distinct media, since growth conditions could modulate the synthesis of bioactive molecules. The proteolytic profile has not changed qualitatively regardless the media, showing two peptidases of 38 and 40kDa; however, few quantitative changes were observed including a drastic reduction (around 70%) on the 40 and 38kDa peptidase activities when parasites were grown in yeast extract and liver infusion trypticase medium, respectively, in comparison with parasites cultured in Warren medium. The time-span of growth did not significantly alter the protein and peptidase expression. The proteolytic activities were blocked by classical cysteine peptidase inhibitors (E-64, leupeptin, and cystatin), being more active at pH 5.0 and showing complete dependence to reducing agents (dithiothreitol and l-cysteine) for full activity. The cysteine peptidases were able to hydrolyze several proteinaceous substrates, including salivary gland proteins from Oncopeltus fasciatus, suggesting broad substrate utilization. By means of agglutination, fluorescence microscopy, flow cytometry and Western blotting analyses we showed that both cysteine peptidases produced by P. serpens share common epitopes with cruzipain, the major cysteine peptidase of Trypanosoma cruzi. Moreover, our data suggest that the 40kDa cysteine peptidase was located at the P. serpens cell surface, attached to membrane domains via a glycosylphosphatidylinositol anchor. The 40kDa peptidase was also detected in the cell-free culture supernatant, in an active form, which suggests secretion of this peptidase to the extracellular environment.

Global Microarray Analysis of Carbohydrate Use in Alkaliphilic Hemicellulolytic Bacterium Bacillus sp. N16-5

PubMed Central

Song, Yajian; Xue, Yanfen; Ma, Yanhe

2013-01-01

The alkaliphilic hemicellulolytic bacterium Bacillus sp. N16-5 has a broad substrate spectrum and exhibits the capacity to utilize complex carbohydrates such as galactomannan, xylan, and pectin. In the monosaccharide mixture, sequential utilization by Bacillus sp. N16-5 was observed. Glucose appeared to be its preferential monosaccharide, followed by fructose, mannose, arabinose, xylose, and galactose. Global transcription profiles of the strain were determined separately for growth on six monosaccharides (glucose, fructose, mannose, galactose, arabinose, and xylose) and four polysaccharides (galactomannan, xylan, pectin, and sodium carboxymethylcellulose) using one-color microarrays. Numerous genes potentially related to polysaccharide degradation, sugar transport, and monosaccharide metabolism were found to respond to a specific substrate. Putative gene clusters for different carbohydrates were identified according to transcriptional patterns and genome annotation. Identification and analysis of these gene clusters contributed to pathway reconstruction for carbohydrate utilization in Bacillus sp. N16-5. Several genes encoding putative sugar transporters were highly expressed during growth on specific sugars, suggesting their functional roles. Two phosphoenolpyruvate-dependent phosphotransferase systems were identified as candidate transporters for mannose and fructose, and a major facilitator superfamily transporter was identified as a candidate transporter for arabinose and xylose. Five carbohydrate uptake transporter 1 family ATP-binding cassette transporters were predicted to participate in the uptake of hemicellulose and pectin degradation products. Collectively, microarray data improved the pathway reconstruction involved in carbohydrate utilization of Bacillus sp. N16-5 and revealed that the organism precisely regulates gene transcription in response to fluctuations in energy resources. PMID:23326578

Metal-Free Catalytic Enantioselective C–B Bond Formation: (Pinacolato)boron Conjugate Additions to α,β-Unsaturated Ketones, Esters, Weinreb Amides and Aldehydes Promoted by Chiral N-Heterocyclic Carbenes

PubMed Central

Wu, Hao; Radomkit, Suttipol; O’Brien, Jeannette M.; Hoveyda, Amir H.

2012-01-01

The first broadly applicable metal-free enantioselective method for boron conjugate addition (BCA) to α,β-unsaturated carbonyls is presented. The C–B bond forming reactions are promoted in the presence of 2.5–7.5 mol % of a readily accessible C1-symmetric chiral imidazolinium salt, which is converted, in situ, to the catalytically active diastereo- and enantiomerically pure N-heterocyclic carbene (NHC) by the common organic base 1,8-diazabicyclo[5.4.0]undec-7-ene (dbu). In addition to the commercially available bis(pinacolato)diboron [B2(pin)2], and in contrast to reactions with the less sterically demanding achiral NHCs, the presence of MeOH is required for high efficiency. Acyclic and cyclic α,β-unsaturated ketones, as well as acyclic esters, Weinreb amides and aldehydes can serve as suitable substrates; the desired β-boryl carbonyls are isolated in up to 94% yield and >98:2 enantiomer ratio (er). Transformations are often carried out at ambient temperature. In certain cases, such as when the relatively less reactive unsaturated amides are used, elevated temperatures are required (50–66 °C); nonetheless, reactions remain highly enantioselective. The utility of the NHC-catalyzed method is demonstrated through comparison with the alternative Cu-catalyzed protocols; in cases involving a polyfunctional substrate, unique profiles in chemoselectivity are exhibited by the metal-free approach (e.g., conjugate addition vs reaction with an alkyne, allene or aldehyde). PMID:22559866

Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets

PubMed Central

Macosko, Evan Z.; Basu, Anindita; Satija, Rahul; Nemesh, James; Shekhar, Karthik; Goldman, Melissa; Tirosh, Itay; Bialas, Allison R.; Kamitaki, Nolan; Martersteck, Emily M.; Trombetta, John J.; Weitz, David A.; Sanes, Joshua R.; Shalek, Alex K.; Regev, Aviv; McCarroll, Steven A.

2015-01-01

Summary Cells, the basic units of biological structure and function, vary broadly in type and state. Single-cell genomics can characterize cell identity and function, but limitations of ease and scale have prevented its broad application. Here we describe Drop-Seq, a strategy for quickly profiling thousands of individual cells by separating them into nanoliter-sized aqueous droplets, associating a different barcode with each cell’s RNAs, and sequencing them all together. Drop-Seq analyzes mRNA transcripts from thousands of individual cells simultaneously while remembering transcripts’ cell of origin. We analyzed transcriptomes from 44,808 mouse retinal cells and identified 39 transcriptionally distinct cell populations, creating a molecular atlas of gene expression for known retinal cell classes and novel candidate cell subtypes. Drop-Seq will accelerate biological discovery by enabling routine transcriptional profiling at single-cell resolution. PMID:26000488

Systematic identification of substrates for profiling of secreted proteases from Aspergillus species.

PubMed

Schaal, René; Kupfahl, Claudio; Buchheidt, Dieter; Neumaier, Michael; Findeisen, Peter

2007-11-01

Reliable and early diagnosis of life-threatening invasive mycoses in neutropenic patients caused by fungi of the Aspergillus species remains challenging because current clinical diagnostic tools lack in sensitivity and/or specificity. During invasive growth a variety of fungal proteases are secreted into the bloodstream and protease profiling with reporter peptides might improve diagnosis of invasive aspergillosis in serum specimens. To characterise the specific protease activity of Aspergillus fumigatus and Aspergillus niger we analyzed Aspergillus culture supernatants, human serum and the mixture of both. A systematic screening for optimised protease substrates was performed using a random peptide library consisting of 360 synthetic peptides featuring fluorescence resonance energy transfer (FRET). We could identify numerous peptides that are selectively cleaved by fungus-specific proteases. These reporter peptides might be feasible for future protease profiling of serum specimens to improve diagnosis and monitoring of invasive aspergillosis.

Evaluating Factor XIII Specificity for Glutamine-Containing Substrates Using a MALDI-TOF Mass Spectrometry Assay

PubMed Central

Doiphode, Prakash G.; Malovichko, Marina V.; Mouapi, Kelly Njine; Maurer, Muriel C.

2014-01-01

Activated Factor XIII (FXIIIa) catalyzes the formation of γ-glutamyl-ε-lysyl cross-links within the fibrin blood clot network. Although several cross-linking targets have been identified, the characteristic features that define FXIIIa substrate specificity are not well understood. To learn more about how FXIIIa selects its targets, a matrix-assisted laser desorption ionization – time of flight mass spectrometry (MALDI-TOF MS) based assay was developed that could directly follow the consumption of a glutamine-containing substrate and the formation of a cross-linked product with glycine ethylester. This FXIIIa kinetics assay is no longer reliant on a secondary coupled reaction, on substrate labeling, or on detecting the final deacylation portion of the transglutaminase reaction. With the MALDI-TOF MS assay, glutamine-containing peptides derived from α2-antiplasmin, S. Aureus fibronectin binding protein A, and thrombin activatable fibrinolysis inhibitor were examined directly. Results suggest that the FXIIIa active site surface responds to changes in substrate residues following the reactive glutamine. The P-1 substrate position is sensitive to charge character and the P-2 and P-3 to the broad FXIIIa substrate specificity pockets. The more distant P-8 to P-11 region serves as a secondary substrate anchoring point. New knowledge on FXIIIa specificity may be used to design better substrates or inhibitors of this transglutaminase. PMID:24751466

Catalytic properties of thimet oligopeptidase H600A mutant

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

Machado, Mauricio F.M.; Marcondes, Marcelo F.; Rioli, Vanessa

2010-04-02

Thimet oligopeptidase (EC 3.4.24.15, TOP) is a metallo-oligopeptidase that participates in the intracellular metabolism of peptides. Predictions based on structurally analogous peptidases (Dcp and ACE-2) show that TOP can present a hinge-bend movement during substrate hydrolysis, what brings some residues closer to the substrate. One of these residues that in TOP crystallographic structure are far from the catalytic residues, but, moves toward the substrate considering this possible structural reorganization is His{sup 600}. In the present work, the role of His{sup 600} of TOP was investigated by site-directed mutagenesis. TOP H600A mutant was characterized through analysis of S{sub 1} and S{submore » 1}' specificity, pH-activity profile and inhibition by JA-2. Results showed that TOP His{sup 600} residue makes important interactions with the substrate, supporting the prediction that His{sup 600} moves toward the substrate due to a hinge movement similar to the Dcp and ACE-2. Furthermore, the mutation H600A affected both K{sub m} and k{sub cat}, showing the importance of His{sup 600} for both substrate binding and/or product release from active site. Changes in the pH-profile may indicate also the participation of His{sup 600} in TOP catalysis, transferring a proton to the newly generated NH{sub 2}-terminus or helping Tyr{sup 605} and/or Tyr{sup 612} in the intermediate oxyanion stabilization.« less

Beyond brown: polyphenol oxidases as enzymes of plant specialized metabolism

USDA-ARS?s Scientific Manuscript database

Most cloned and/or characterized plant polyphenol oxidases (PPOs) have catecholase activity (i.e., they oxidize o-diphenols to o-quinones) and are localized or predicted to be localized to plastids. As a class, they have broad substrate specificity and are associated with browning of produce and oth...

H α and H β Raman scattering line profiles of the symbiotic star AG Pegasi

NASA Astrophysics Data System (ADS)

Lee, Seong-Jae; Hyung, Siek

2018-04-01

The H α and H β line profiles of the symbiotic star AG Pegasi, observed in 1998 September (phase ϕ = 10.24), display top narrow double Gaussian components and bottom broad components (FWHM = 200-400 km s-1). The photoionization model indicates that the ionized zone, responsible for the hydrogen Balmer and Lyman lines, is radiation-bounded, with a hydrogen gas number density of nH ˜ 109.85 cm-3 and a gas temperature of Te = 12 000-15 000 K. We have carried out Monte Carlo simulations to fit the Raman scattering broad wings, assuming that the hydrogen Ly β and Ly γ lines emitted within the radiation-bounded H II zone around a white dwarf have the same double Gaussian line profile shape as the hydrogen Balmer lines. The simulation shows that the scattering H I zones are attached to (or located just outside) the inner H II shells. The best fit to the observed broad H I line profiles indicates that the column density of the scattering neutral zone is NH ≃ 3-5 × 1019 cm-2. We have examined whether the geometrical structure responsible for the observed H α and H β line profiles is a bipolar conical shell structure, consisting of the radiation-bounded ionized zone and the outer material bounded neutral zone. The expanding bipolar structure might be two opposite regions of the common envelope or the outer shell of the Roche lobe around the hot white dwarf, formed through the mass inflows from the giant star and pushed out by the fast winds from the hot white dwarf.

Design of ultrasensitive probes for human neutrophil elastase through hybrid combinatorial substrate library profiling

PubMed Central

Kasperkiewicz, Paulina; Poreba, Marcin; Snipas, Scott J.; Parker, Heather; Winterbourn, Christine C.; Salvesen, Guy S.; Drag, Marcin

2014-01-01

The exploration of protease substrate specificity is generally restricted to naturally occurring amino acids, limiting the degree of conformational space that can be surveyed. We substantially enhanced this by incorporating 102 unnatural amino acids to explore the S1–S4 pockets of human neutrophil elastase. This approach provides hybrid natural and unnatural amino acid sequences, and thus we termed it the Hybrid Combinatorial Substrate Library. Library results were validated by the synthesis of individual tetrapeptide substrates, with the optimal substrate demonstrating more than three orders of magnitude higher catalytic efficiency than commonly used substrates of elastase. This optimal substrate was converted to an activity-based probe that demonstrated high selectivity and revealed the specific presence of active elastase during the process of neutrophil extracellular trap formation. We propose that this approach can be successfully used for any type of endopeptidase to deliver high activity and selectivity in substrates and probes. PMID:24550277

Broad Halpha Wing Formation in the Planetary Nebula IC 4997.

PubMed

Lee; Hyung

2000-02-10

The young and compact planetary nebula IC 4997 is known to exhibit very broad wings with a width exceeding 5000 km s-1 around Halpha. We propose that the broad wings are formed through Rayleigh-Raman scattering that involves atomic hydrogen, by which Lybeta photons with a velocity width of a few 102 km s-1 are converted to optical photons and fill the Halpha broad wing region. The conversion efficiency reaches 0.6 near the line center, where the scattering optical depth is much larger than 1, and rapidly decreases in the far wings. Assuming that close to the central star there exists an unresolved inner compact core of high density, nH approximately 109-1010 cm-3, we use the photoionization code "CLOUDY" to show that sufficient Lybeta photons for scattering are produced. Using a top-hat-incident profile for the Lybeta flux and a scattering region with a H i column density NHi=2x1020 cm-2 and a substantial covering factor, we perform a profile-fitting analysis in order to obtain a satisfactory fit to the observed flux. We briefly discuss the astrophysical implications of the Rayleigh-Raman processes in planetary nebulae and other emission objects.

The broad autism phenotype predicts relationship outcomes in newly formed college roommates.

PubMed

Faso, Daniel J; Corretti, Conrad A; Ackerman, Robert A; Sasson, Noah J

2016-05-01

Although previous studies have reported that the broad autism phenotype is associated with reduced relationship quality within established relationships, understanding how this association emerges requires assessment prior to relationship development. In the present longitudinal study, college roommates with minimal familiarity prior to cohabitation (N = 162) completed the broad autism phenotype questionnaire and intermittently reported on their relationship quality and interpersonal behaviors toward their roommate over their first 10 weeks of living together. Actor-Partner Interdependence Models demonstrated that roommates mismatched on aloofness (one high and one low) had lower relationship satisfaction than those matched on it, with the interpersonal behavior of warmth mediating this association. Because relationship satisfaction remained high when both roommates were aloof, satisfaction does not appear predicated upon the presence of aloofness generally but rather reflects a product of dissimilarity in aloof profiles between roommates. In contrast, although participants reported less relationship satisfaction and commitment with roommates higher on pragmatic language abnormalities, mismatches on this broad autism phenotype trait, and on rigid personality, were less consequential. In sum, these findings suggest that complementary profiles of social motivation may facilitate relationship quality during the early course of relationship development. © The Author(s) 2015.

Investigation of antenna-coupled Nb5N6 microbolometer THz detector with substrate resonant cavity.

PubMed

Tu, Xuecou; Jiang, Chengtao; Xiao, Peng; Kang, Lin; Zhai, Shimin; Jiang, Zhou; Feng Su, Run; Jia, Xiaoqing; Zhang, Labao; Chen, Jian; Wu, Peiheng

2018-04-02

Fabricating resonant cavities with conventional methods to improve the coupling efficiency of a detector in the terahertz (THz) region is difficult for the wavelength is too long. Here, we propose a solution by using the substrate cavity effect given that the substrate wavelength and thickness of the preparation device are in the same order. The planar dipole antenna-coupled Nb 5 N 6 microbolometers with different substrate thicknesses were fabricated. The interference effect of the substrate cavity on the optical voltage response of the detector is analyzed experimentally and theoretically. The experimental results show that the optical response of the detector is determined by the length of the substrate cavity. Thus, the THz devices with different detection frequencies can be designed by changing the substrate cavity length. Furthermore, on the basis of this substrate cavity effect, an asymmetric coupled Fabry-Pérot (FP) cavity is constituted by simply placing a movable metallic planar mirror at the backside of the Si substrate. The incident THz radiation on the Nb 5 N 6 microbolometer can be effectively manipulated by changing the substrate-mirror distance to modulate the phase relation between the reflect wave and the incident wave. The distinct radiation control can be observed, and the experiments can be well explained by numerically analyzing the responsivity dynamics that highlights the role of the FP cavity effect during radiation. All of the results discussed here can be extended to a broad range of frequency and other type of THz detectors.

Analysis of Substrates of Protein Kinase C Isoforms in Human Breast Cells By The Traceable Kinase Method

PubMed Central

Chen, Xiangyu; Zhao, Xin; Abeyweera, Thushara P.; Rotenberg, Susan A.

2012-01-01

A previous report (Biochemistry 46: 2364–2370, 2007) described the application of The Traceable Kinase Method to identify substrates of PKCα in non-transformed human breast MCF-10A cells. Here, a non-radioactive variation of this method compared the phospho-protein profiles of three traceable PKC isoforms (α, δ and ζ) for the purpose of identifying novel, isoform-selective substrates. Each FLAG-tagged traceable kinase was expressed and co-immunoprecipitated along with high affinity substrates. The isolated kinase and its associated substrates were subjected to an in vitro phosphorylation reaction with traceable kinase-specific N6-phenyl-ATP, and the resulting phospho-proteins were analyzed by Western blot with an antibody that recognizes the phosphorylated PKC consensus site. Phospho-protein profiles generated by PKC-α and -δ were similar and differed markedly from that of PKC-ζ. Mass spectrometry of selected bands revealed known PKC substrates and several potential substrates that included the small GTPase-associated effector protein Cdc42 effector protein-4 (CEP4). Of those potential substrates tested, only CEP4 was phosphorylated by pure PKC-α, –δ, and −ζ isoforms in vitro, and by endogenous PKC isoforms in MCF-10A cells treated with DAG-lactone, a membrane permeable PKC activator. Under these conditions, the stoichiometry of CEP4 phosphorylation was 3.2 ± 0.5 (mol phospho-CEP4/mol CEP4). Following knock-down with isoform-specific shRNA-encoding plasmids, phosphorylation of CEP4 was substantially decreased in response to silencing of each of the three isoforms (PKC–α, –δ, or –ζ), whereas testing of kinase-dead mutants supported a role for only PKC-α and –δ in CEP4 phosphorylation. These findings identify CEP4 as a novel intracellular PKC substrate that is phosphorylated by multiple PKC isoforms. PMID:22897107

A miniature filter on a suspended substrate with a two-sided pattern of strip conductors

NASA Astrophysics Data System (ADS)

Belyaev, B. A.; Voloshin, A. S.; Bulavchuk, A. S.; Galeev, R. G.

2016-06-01

A miniature bandpass filter of new design with original stripline resonators on suspended substrate has been studied. The proposed filters of third to sixth order are distinguished for their high frequency-selective properties and mush smaller size in comparison to analogs. It is shown that a broad stopband extending above three-fold central bandpass frequency is determined by weak coupling of resonators at resonances of the second and third modes. A prototype sixth-order filter with a central frequency of 1 GHz, manufactured on a ceramic substrate with dielectric permittivity ɛ = 80, has contour dimensions of 36.6 × 4.8 × 0.5 mm3. Parametric synthesis of the filter, based on electrodynamic 3D model simulations, showed quite good agreement with the results of measurements.

Associations between Toddler-Age Communication and Kindergarten-Age Self-Regulatory Skills

ERIC Educational Resources Information Center

Aro, Tuija; Laakso, Marja-Leena; Määttä, Sira; Tolvanen, Asko; Poikkeus, Anna-Maija

2014-01-01

Purpose: In this study, the authors aimed at gaining understanding on the associations of different types of early language and communication profiles with later self-regulation skills by using longitudinal data from toddler age to kindergarten age. Method: Children with early language profiles representing expressive delay, broad delay (i.e.,…

School Readiness amongst Urban Canadian Families: Risk Profiles and Family Mediation

ERIC Educational Resources Information Center

Browne, Dillon T.; Wade, Mark; Prime, Heather; Jenkins, Jennifer M.

2018-01-01

There is an ongoing need for literature that identifies the effects of broad contextual risk on school readiness outcomes via family mediating mechanisms. This is especially true amongst diverse and urban samples characterized by variability in immigration history. To address this limitation, family profiles of sociodemographic and contextual risk…

Ohio Marketing Management and Research. Technical Competency Profile (TCP).

ERIC Educational Resources Information Center

Ray, Gayl M.; Wilson, Nick; Mangini, Rick

This document provides a framework for a broad-based secondary and postsecondary curriculum to prepare students for employment in marketing management and research (MMR). The first part of the technical competency profile (TCP) contains the following items: an explanation of the purpose and scope of Ohio's TCPs; college tech prep program…

Ohio Medical Office Management. Technical Competency Profile (TCP).

ERIC Educational Resources Information Center

Ray, Gayl M.; Wilson, Nick; Mangini, Rick

This document provides a framework for a broad-based secondary and postsecondary curriculum to prepare students for employment in medical office management. The first part of the technical competency profile (TCP) contains the following items: an explanation of the purpose and scope of Ohio's TCPs; college tech prep program standards; an overview…

Profiles of For-Profit and Nonprofit Education Management Organizations. Fourteenth Edition--2011-2012

ERIC Educational Resources Information Center

Miron, Gary; Gulosino, Charisse

2013-01-01

Annual "Profiles" reports are comprehensive digests of data on education management organizations. Analysis and interpretation of the data in this report are, for the most part, limited to describing general trends over time. The report is intended for a broad audience. Policymakers, educators, school district officials, and school board…

Evolutionary dynamics of enzymes.

PubMed

Demetrius, L

1995-08-01

This paper codifies and rationalizes the large diversity in reaction rates and substrate specificity of enzymes in terms of a model which postulates that the kinetic properties of present-day enzymes are the consequence of the evolutionary force of mutation and selection acting on a class of primordial enzymes with poor catalytic activity and broad substrate specificity. Enzymes are classified in terms of their thermodynamic parameters, activation enthalpy delta H* and activation entropy delta S*, in their kinetically significant transition states as follows: type 1, delta H* > 0, delta S* < 0; type 2, delta H* < or = 0, delta S* < or = 0; type 3, delta H* > 0, delta S* > 0. We study the evolutionary dynamics of these three classes of enzymes subject to mutation, which acts at the level of the gene which codes for the enzyme and selection, which acts on the organism that contains the enzyme. Our model predicts the following evolutionary trends in the reaction rate and binding specificity for the three classes of molecules. In type 1 enzymes, evolution results in random, non-directional changes in the reaction rate and binding specificity. In type 2 and 3 enzymes, evolution results in a unidirectional increase in both the reaction rate and binding specificity. We exploit these results in order to codify the diversity in functional properties of present-day enzymes. Type 1 molecules will be described by intermediate reaction rates and broad substrate specificity. Type 2 enzymes will be characterized by diffusion-controlled rates and absolute substrate specificity. The type 3 catalysts can be further subdivided in terms of their activation enthalpy into two classes: type 3a (delta H* small) and type 3b (delta H* large). We show that type 3a will be represented by the same functional properties that identify type 2, namely, diffusion-controlled rates and absolute substrate specificity, whereas type 3b will be characterized by non-diffusion-controlled rates and absolute substrate specificity. We infer from this depiction of the three classes of enzymes, a general relation between the two functional properties, reaction rate and substrate specificity, namely, enzymes with diffusion-controlled rates have absolute substrate specificity. By appealing to energetic considerations, we furthermore show that enzymes with diffusion-controlled rates (types 2 and 3a) form a small subset of the class of all enzymes. This codification of present-day enzymes derived from an evolutionary model, essentially relates the structural properties of enzymes, as described by their thermodynamic parameters, to their functional properties, as represented by the reaction rate and substrate specificity.

Neuroimaging and Anxiety: the Neural Substrates of Pathological and Non-pathological Anxiety.

PubMed

Taylor, James M; Whalen, Paul J

2015-06-01

Advances in the use of noninvasive neuroimaging to study the neural correlates of pathological and non-pathological anxiety have shone new light on the underlying neural bases for both the development and manifestation of anxiety. This review summarizes the most commonly observed neural substrates of the phenotype of anxiety. We focus on the neuroimaging paradigms that have shown promise in exposing this relevant brain circuitry. In this way, we offer a broad overview of how anxiety is studied in the neuroimaging laboratory and the key findings that offer promise for future research and a clearer understanding of anxiety.

Optical properties of chitin: surface-enhanced Raman scattering substrates based on antireflection structures on cicada wings

NASA Astrophysics Data System (ADS)

Stoddart, P. R.; Cadusch, P. J.; Boyce, T. M.; Erasmus, R. M.; Comins, J. D.

2006-02-01

The transparent wings of some cicada species present ordered arrays of papillary structures with a spacing of approximately 200 nm. These structures serve an antireflection function, with optical transmission peaking at a value of approximately 98% and rising above 90% over a broad band from 450 to 2500 nm. The dimensions of the papillae are comparable to the roughness scale of surface-enhanced Raman scattering (SERS) substrates. SERS measurements performed on silver- and gold-coated wings display enhancement factors of approximately 106 with no apparent background contribution from the wing.

SEMICONDUCTOR MATERIALS: White light photoluminescence from ZnS films on porous Si substrates

NASA Astrophysics Data System (ADS)

Caifeng, Wang; Qingshan, Li; Bo, Hu; Weibing, Li

2010-03-01

ZnS films were deposited on porous Si (PS) substrates using a pulsed laser deposition (PLD) technique. White light emission is observed in photoluminescence (PL) spectra, and the white light is the combination of blue and green emission from ZnS and red emission from PS. The white PL spectra are broad, intense in a visible band ranging from 450 to 700 nm. The effects of the excitation wavelength, growth temperature of ZnS films, PS porosity and annealing temperature on the PL spectra of ZnS/PS were also investigated.

Photoinduced Miyaura Borylation by a Rare Earth Photoreductant: the Hexachlorocerate(III) Anion.

PubMed

Qiao, Yusen; Yang, Qiaomu; Schelter, Eric

2018-05-12

The first photoinduced sp2 carbon-heteroatom bond forming reaction by a rare earth photoreductant, a Miyaura borylation, has been achieved. This simple, scalable, and novel borylation method that makes use of the hexachlorocerate(III) anion, [CeIIICl6]3-, has a broad substrate scope and functional group tolerance and can be conducted at room temperature. Combined with Suzuki-Miyaura cross-coupling, the methodology is applicable to the synthesis of various biaryl products, including through the use of aryl chloride substrates. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Bacterial Anabaena variabilis phenylalanine ammonia lyase: a biocatalyst with broad substrate specificity.

PubMed

Lovelock, Sarah L; Turner, Nicholas J

2014-10-15

Phenylalanine ammonia lyases (PALs) catalyse the regio- and stereoselective hydroamination of cinnamic acid analogues to yield optically enriched α-amino acids. Herein, we demonstrate that a bacterial PAL from Anabaena variabilis (AvPAL) displays significantly higher activity towards a series of non-natural substrates than previously described eukaryotic PALs. Biotransformations performed on a preparative scale led to the synthesis of the 2-chloro- and 4-trifluoromethyl-phenylalanine derivatives in excellent ee, highlighting the enormous potential of bacterial PALs as biocatalysts for the synthesis of high value, non-natural amino acids. Copyright © 2014 Elsevier Ltd. All rights reserved.

n-BuLi as a highly efficient precatalyst for hydrophosphonylation of aldehydes and unactivated ketones.

PubMed

Liu, Chengwei; Zhang, Yu; Qian, Qinqin; Yuan, Dan; Yao, Yingming

2014-12-05

It was found for the first time that organic alkali metal compounds serve as highly efficient precatalysts for the hydrophosphonylation reactions of aldehydes and unactivated ketones with dialkyl phosphite under mild conditions. For ketone substrates, a reversible reaction was observed, and the influence of catalyst loading and reaction temperature on the reaction equilibrium was studied in detail. Overall, the hydrophosphonylation reactions catalyzed by 0.1 mol % n-BuLi were completed within 5 min for a broad range of substrates and generated a series of α-hydroxy phosphonates in high yields.

Preparation and Properties of High-T(sub c) Bi-Pb-Sr-Ca-Cu-O Thick Film Superconductors on YSZ Substrates

NASA Technical Reports Server (NTRS)

Hooker, Matthew W.

1996-01-01

An evaluation of four firing profiles was performed to determine the optimum processing conditions for producing high-T(sub c) Bi-Pb-Sr-Ca-Cu-O thick films on yttria-stabilized zirconia substrates. Using these four profiles, the effects of sintering temperatures of 830-850 C and soak times of 0.5 to 12 hours were examined. In this study, T-c, zero values of 100 K were obtained using a firing profile in which the films were sintered for 1.5 to 2 hours at 840 to 845 C and then quenched to room temperature. X-ray diffraction analyses of these specimens confirmed the presence of the high-T(sub c) phase. Films which were similarly fired and furnace cooled from the peak processing temperature exhibited a two-step superconductive transition to zero resistance, with T-c,zero values ranging from 85 to 92 K. The other firing profiles evaluated in this investigation yielded specimens which either exhibited critical transition temperatures below 90 K or did not exhibit a superconductive transition above 77 K.

An evaluation method of the profile of plasma-induced defects based on capacitance-voltage measurement

NASA Astrophysics Data System (ADS)

Okada, Yukimasa; Ono, Kouichi; Eriguchi, Koji

2017-06-01

Aggressive shrinkage and geometrical transition to three-dimensional structures in metal-oxide-semiconductor field-effect transistors (MOSFETs) lead to potentially serious problems regarding plasma processing such as plasma-induced physical damage (PPD). For the precise control of material processing and future device designs, it is extremely important to clarify the depth and energy profiles of PPD. Conventional methods to estimate the PPD profile (e.g., wet etching) are time-consuming. In this study, we propose an advanced method using a simple capacitance-voltage (C-V) measurement. The method first assumes the depth and energy profiles of defects in Si substrates, and then optimizes the C-V curves. We applied this methodology to evaluate the defect generation in (100), (111), and (110) Si substrates. No orientation dependence was found regarding the surface-oxide layers, whereas a large number of defects was assigned in the case of (110). The damaged layer thickness and areal density were estimated. This method provides the highly sensitive PPD prediction indispensable for designing future low-damage plasma processes.

Analysis of Functional Coupling: Mitochondrial Creatine Kinase and Adenine Nucleotide Translocase

PubMed Central

Vendelin, Marko; Lemba, Maris; Saks, Valdur A.

2004-01-01

The mechanism of functional coupling between mitochondrial creatine kinase (MiCK) and adenine nucleotide translocase (ANT) in isolated heart mitochondria is analyzed. Two alternative mechanisms are studied: 1), dynamic compartmentation of ATP and ADP, which assumes the differences in concentrations of the substrates between intermembrane space and surrounding solution due to some diffusion restriction and 2), direct transfer of the substrates between MiCK and ANT. The mathematical models based on these possible mechanisms were composed and simulation results were compared with the available experimental data. The first model, based on a dynamic compartmentation mechanism, was not sufficient to reproduce the measured values of apparent dissociation constants of MiCK reaction coupled to oxidative phosphorylation. The second model, which assumes the direct transfer of substrates between MiCK and ANT, is shown to be in good agreement with experiments—i.e., the second model reproduced the measured constants and the estimated ADP flux, entering mitochondria after the MiCK reaction. This model is thermodynamically consistent, utilizing the free energy profiles of reactions. The analysis revealed the minimal changes in the free energy profile of the MiCK-ANT interaction required to reproduce the experimental data. A possible free energy profile of the coupled MiCK-ANT system is presented. PMID:15240503

Reversible Self-Assembly of 3D Architectures Actuated by Responsive Polymers.

PubMed

Zhang, Cheng; Su, Jheng-Wun; Deng, Heng; Xie, Yunchao; Yan, Zheng; Lin, Jian

2017-11-29

An assembly of three-dimensional (3D) architectures with defined configurations has important applications in broad areas. Among various approaches of constructing 3D structures, a stress-driven assembly provides the capabilities of creating 3D architectures in a broad range of functional materials with unique merits. However, 3D architectures built via previous methods are simple, irreversible, or not free-standing. Furthermore, the substrates employed for the assembly remain flat, thus not involved as parts of the final 3D architectures. Herein, we report a reversible self-assembly of various free-standing 3D architectures actuated by the self-folding of smart polymer substrates with programmed geometries. The strategically designed polymer substrates can respond to external stimuli, such as organic solvents, to initiate the 3D assembly process and subsequently become the parts of the final 3D architectures. The self-assembly process is highly controllable via origami and kirigami designs patterned by direct laser writing. Self-assembled geometries include 3D architectures such as "flower", "rainbow", "sunglasses", "box", "pyramid", "grating", and "armchair". The reported self-assembly also shows wide applicability to various materials including epoxy, polyimide, laser-induced graphene, and metal films. The device examples include 3D architectures integrated with a micro light-emitting diode and a flex sensor, indicting the potential applications in soft robotics, bioelectronics, microelectromechanical systems, and others.

Two Distinct Types of E3 Ligases Work in Unison to Regulate Substrate Ubiquitylation.

PubMed

Scott, Daniel C; Rhee, David Y; Duda, David M; Kelsall, Ian R; Olszewski, Jennifer L; Paulo, Joao A; de Jong, Annemieke; Ovaa, Huib; Alpi, Arno F; Harper, J Wade; Schulman, Brenda A

2016-08-25

Hundreds of human cullin-RING E3 ligases (CRLs) modify thousands of proteins with ubiquitin (UB) to achieve vast regulation. Current dogma posits that CRLs first catalyze UB transfer from an E2 to their client substrates and subsequent polyubiquitylation from various linkage-specific E2s. We report an alternative E3-E3 tagging cascade: many cellular NEDD8-modified CRLs associate with a mechanistically distinct thioester-forming RBR-type E3, ARIH1, and rely on ARIH1 to directly add the first UB and, in some cases, multiple additional individual monoubiquitin modifications onto CRL client substrates. Our data define ARIH1 as a component of the human CRL system, demonstrate that ARIH1 can efficiently and specifically mediate monoubiquitylation of several CRL substrates, and establish principles for how two distinctive E3s can reciprocally control each other for simultaneous and joint regulation of substrate ubiquitylation. These studies have broad implications for CRL-dependent proteostasis and mechanisms of E3-mediated UB ligation. Copyright © 2016 Elsevier Inc. All rights reserved.

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.

Probing the substrate specificity of the bacterial Pnkp/Hen1 RNA repair system using synthetic RNAs

PubMed Central

Zhang, Can; Chan, Chio Mui; Wang, Pei; Huang, Raven H.

2012-01-01

Ribotoxins cleave essential RNAs involved in protein synthesis as a strategy for cell killing. RNA repair systems exist in nature to counteract the lethal actions of ribotoxins, as first demonstrated by the RNA repair system from bacteriophage T4 25 yr ago. Recently, we found that two bacterial proteins, named Pnkp and Hen1, form a stable complex and are able to repair ribotoxin-cleaved tRNAs in vitro. However, unlike the well-studied T4 RNA repair system, the natural RNA substrates of the bacterial Pnkp/Hen1 RNA repair system are unknown. Here we present comprehensive RNA repair assays with the recombinant Pnkp/Hen1 proteins from Anabaena variabilis using a total of 33 different RNAs as substrates that might mimic various damaged forms of RNAs present in living cells. We found that unlike the RNA repair system from bacteriophage T4, the bacterial Pnkp/Hen1 RNA repair system exhibits broad substrate specificity. Based on the experimental data presented here, a model of preferred RNA substrates of the Pnkp/Hen1 repair system is proposed. PMID:22190744

Conformal growth of Mo/Si multilayers on grating substrates using collimated ion beam sputtering

NASA Astrophysics Data System (ADS)

Voronov, D. L.; Gawlitza, P.; Cambie, R.; Dhuey, S.; Gullikson, E. M.; Warwick, T.; Braun, S.; Yashchuk, V. V.; Padmore, H. A.

2012-05-01

Deposition of multilayers on saw-tooth substrates is a key step in the fabrication of multilayer blazed gratings (MBG) for extreme ultraviolet and soft x-rays. Growth of the multilayers can be perturbed by shadowing effects caused by the highly corrugated surface of the substrates, which results in distortion of the multilayer stack structure and degradation of performance of MBGs. To minimize the shadowing effects, we used an ion-beam sputtering machine with a highly collimated atomic flux to deposit Mo/Si multilayers on saw-tooth substrates. The sputtering conditions were optimized by finding a balance between smoothening and roughening processes in order to minimize degradation of the groove profile in the course of deposition and at the same time to keep the interfaces of a multilayer stack smooth enough for high efficiency. An optimal value of energy of 200 eV for sputtering Kr+ ions was found by deposition of test multilayers on flat substrates at a range of ion energies. Two saw-tooth substrates were deposited at energies of 200 eV and 700 eV for the sputtering ions. It was found that reduction of the ion energy improved the blazing performance of the MBG and resulted in a 40% gain in the diffraction efficiency due to better replication of the groove profile by the multilayer. As a result of the optimization performed, an absolute diffraction efficiency of 28.8% was achieved for the 2nd blaze order of the MBG with a groove density of 7350 lines/mm at a wavelength of 13.5 nm. Details of the growth behavior of the multilayers on flat and saw-tooth substrates are discussed in terms of the linear continuous model of film growth.

Conformal growth of Mo/Si multilayers on grating substrates using collimated ion beam sputtering

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

Voronov, D. L.; Cambie, R.; Dhuey, S.

2012-05-01

Deposition of multilayers on saw-tooth substrates is a key step in the fabrication of multilayer blazed gratings (MBG) for extreme ultraviolet and soft x-rays. Growth of the multilayers can be perturbed by shadowing effects caused by the highly corrugated surface of the substrates, which results in distortion of the multilayer stack structure and degradation of performance of MBGs. To minimize the shadowing effects, we used an ion-beam sputtering machine with a highly collimated atomic flux to deposit Mo/Si multilayers on saw-tooth substrates. The sputtering conditions were optimized by finding a balance between smoothening and roughening processes in order to minimizemore » degradation of the groove profile in the course of deposition and at the same time to keep the interfaces of a multilayer stack smooth enough for high efficiency. An optimal value of energy of 200 eV for sputtering Kr{sup +} ions was found by deposition of test multilayers on flat substrates at a range of ion energies. Two saw-tooth substrates were deposited at energies of 200 eV and 700 eV for the sputtering ions. It was found that reduction of the ion energy improved the blazing performance of the MBG and resulted in a 40% gain in the diffraction efficiency due to better replication of the groove profile by the multilayer. As a result of the optimization performed, an absolute diffraction efficiency of 28.8% was achieved for the 2nd blaze order of the MBG with a groove density of 7350 lines/mm at a wavelength of 13.5 nm. Details of the growth behavior of the multilayers on flat and saw-tooth substrates are discussed in terms of the linear continuous model of film growth.« less

Conformal growth of Mo/Si multilayers on grating substrates using collimated ion beam sputtering

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

Voronov, D. L.; Gawlitza, Peter; Cambie, Rossana

2012-05-07

Deposition of multilayers on saw-tooth substrates is a key step in the fabrication of multilayer blazed gratings (MBG) for extreme ultraviolet and soft x-rays. Growth of the multilayers can be perturbed by shadowing effects caused by the highly corrugated surface of the substrates, which results in distortion of the multilayer stack structure and degradation of performance of MBGs. In this study, to minimize the shadowing effects, we used an ion-beamsputtering machine with a highly collimated atomic flux to deposit Mo/Si multilayers on saw-tooth substrates. The sputtering conditions were optimized by finding a balance between smoothening and roughening processes in ordermore » to minimize degradation of the groove profile in the course of deposition and at the same time to keep the interfaces of a multilayer stack smooth enough for high efficiency. An optimal value of energy of 200 eV for sputtering Kr + ions was found by deposition of test multilayers on flat substrates at a range of ion energies. Two saw-tooth substrates were deposited at energies of 200 eV and 700 eV for the sputtering ions. It was found that reduction of the ion energy improved the blazing performance of the MBG and resulted in a 40% gain in the diffraction efficiency due to better replication of the groove profile by the multilayer. As a result of the optimization performed, an absolute diffraction efficiency of 28.8% was achieved for the 2nd blaze order of the MBG with a groove density of 7350 lines/mm at a wavelength of 13.5 nm. Lastly, details of the growth behavior of the multilayers on flat and saw-tooth substrates are discussed in terms of the linear continuous model of film growth.« less

A RADIAL VELOCITY TEST FOR SUPERMASSIVE BLACK HOLE BINARIES AS AN EXPLANATION FOR BROAD, DOUBLE-PEAKED EMISSION LINES IN ACTIVE GALACTIC NUCLEI

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

Liu, Jia; Halpern, Jules P.; Eracleous, Michael

2016-01-20

One of the proposed explanations for the broad, double-peaked Balmer emission lines observed in the spectra of some active galactic nuclei (AGNs) is that they are associated with sub-parsec supermassive black hole (SMBH) binaries. Here, we test the binary broad-line region hypothesis through several decades of monitoring of the velocity structure of double-peaked Hα emission lines in 13 low-redshift, mostly radio-loud AGNs. This is a much larger set of objects compared to an earlier test by Eracleous et al. and we use much longer time series for the three objects studied in that paper. Although systematic changes in radial velocitymore » can be traced in many of their lines, they are demonstrably not like those of a spectroscopic binary in a circular orbit. Any spectroscopic binary period must therefore be much longer than the span of the monitoring (assuming a circular orbit), which in turn would require black hole masses that exceed by 1–2 orders of magnitude the values obtained for these objects using techniques such as reverberation mapping and stellar velocity dispersion. Moreover, the response of the double-peaked Balmer line profiles to fluctuations of the ionizing continuum and the shape of the Lyα profiles are incompatible with an SMBH binary. The binary broad-line region hypothesis is therefore disfavored. Other processes evidently shape these line profiles and cause the long-term velocity variations of the double peaks.« less

Electronic structures of GeSi nanoislands grown on pit-patterned Si(001) substrate

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

Ye, Han, E-mail: Dabombyh@aliyun.com; Yu, Zhongyuan

2014-11-15

Patterning pit on Si(001) substrate prior to Ge deposition is an important approach to achieve GeSi nanoislands with high ordering and size uniformity. In present work, the electronic structures of realistic uncapped pyramid, dome, barn and cupola nanoislands grown in (105) pits are systematically investigated by solving Schrödinger equation for heavy-hole, which resorts to inhomogeneous strain distribution and nonlinear composition-dependent band parameters. Uniform, partitioned and equilibrium composition profile (CP) in nanoisland and inverted pyramid structure are simulated separately. We demonstrate the huge impact of composition profile on localization of heavy-hole: wave function of ground state is confined near pit facetsmore » for uniform CP, at bottom of nanoisland for partitioned CP and at top of nanoisland for equilibrium CP. Moreover, such localization is gradually compromised by the size effect as pit filling ratio or pit size decreases. The results pave the fundamental guideline of designing nanoislands on pit-patterned substrates for desired applications.« less

Nondestructive Biological Evidence Collection with Alternative Swabs and Adhesive Lifters.

PubMed

Plaza, Dane T; Mealy, Jamia L; Lane, J Nicholas; Parsons, M Neal; Bathrick, Abigail S; Slack, Donia P

2016-03-01

In forensic science, biological material is typically collected from evidence via wet/dry double swabbing with cotton swabs, which is effective but can visibly damage an item's surface. When an item's appearance must be maintained, dry swabbing and tape-lifting may be employed as collection techniques that are visually nondestructive to substrates' surfaces. This study examined the efficacy of alternative swab matrices and adhesive lifters when collecting blood and fingerprints from glass, painted drywall, 100% cotton, and copy paper. Data were evaluated by determining the percent profile and quality score for each STR profile generated. Hydraflock(®) swabs, BVDA Gellifters(®) , and Scenesafe FAST™ tape performed as well as or better than cotton swabs when collecting fingerprints from painted drywall and 100% cotton. Collection success was also dependent on the type of biological material sampled and the substrate on which it was deposited. These results demonstrated that alternative swabs and adhesive lifters can be effective for nondestructive DNA collection from various substrates. © 2015 American Academy of Forensic Sciences.

X-Ray Fluorescence Solvent Detection at the Substrate-Adhesive Interface

NASA Technical Reports Server (NTRS)

Wurth, Laura; Evans, Kurt; Weber, Bart; Headrick, Sarah

2005-01-01

With environmental regulations limiting the use of volatile organic compounds, low-vapor pressure solvents have replaced traditional degreasing solvents for bond substrate preparation. When used to clean and prepare porous bond substrates such as phenolic composites, low vapor pressure solvents can penetrate deep into substrate pore networks and remain there for extended periods. Trapped solvents can interact with applied adhesives either prior to or during cure, potentially compromising bond properties. Currently, methods for characterizing solvent time-depth profiles in bond substrates are limited to bulk gravimetric or sectioning techniques. While sectioning techniques such as microtome allow construction of solvent depth profiles, their depth resolution and reliability are limited by substrate type. Sectioning techniques are particularly limited near the adhesive-substrate interface where depth resolution is further limited by adhesive-substrate hardness and, in the case of a partially cured adhesive, mechanical properties differences. Additionally, sectioning techniques cannot provide information about lateral solvent diffusion. Cross-section component mapping is an alternative method for measuring solvent migration in porous substrates that eliminates the issues associated with sectioning techniques. With cross-section mapping, the solvent-wiped substrate is sectioned perpendicular rather than parallel to the wiped surface, and the sectioned surface is analyzed for the solvent or solvent components of interest using a two-dimensional mapping or imaging technique. Solvent mapping can be performed using either direct or indirect methods. With a direct method, one or more solvent components are mapped using red or Raman spectroscopy together with a moveable sample stage and/or focal plane array detector. With an indirect method, an elemental "tag" not present in the substrate is added to the solvent before the substrate is wiped. Following cross sectioning, the tag element can then be mapped by its characteristic x-ray emission using either x-ray fluorescence, or electron-beam energy-and wavelength-dispersive x-ray spectrometry. The direct mapping techniques avoid issues of different diffusion or migration rates of solvents and elemental tags, while the indirect techniques avoid spectral resolution issues in cases where solvents and substrates have adjacent or overlapping peaks. In this study, cross-section component indirect mapping is being evaluated as a method for measuring migration of d-limonene based solvents in glass-cloth phenolic composite (GCP) prior to and during subsequent bonding and epoxy adhesive cure.

Extended Lindhard-Scharf-Schiott Theory for Ion Implantation Profiles Expressed with Pearson Function

NASA Astrophysics Data System (ADS)

Suzuki, Kunihiro

2009-04-01

Ion implantation profiles are expressed by the Pearson function with first, second, third, and fourth moment parameters of Rp, ΔRp, γ, and β. We derived an analytical model for these profile moments by solving a Lindhard-Scharf-Schiott (LSS) integration equation using perturbation approximation. This analytical model reproduces Monte Carlo data that were well calibrated to reproduce a vast experimental database. The extended LSS theory is vital for instantaneously predicting ion implantation profiles with any combination of incident ions and substrate atoms including their energy dependence.

When lithography meets self-assembly: a review of recent advances in the directed assembly of complex metal nanostructures on planar and textured surfaces

NASA Astrophysics Data System (ADS)

Hughes, Robert A.; Menumerov, Eredzhep; Neretina, Svetlana

2017-07-01

One of the foremost challenges in nanofabrication is the establishment of a processing science that integrates wafer-based materials, techniques, and devices with the extraordinary physicochemical properties accessible when materials are reduced to nanoscale dimensions. Such a merger would allow for exacting controls on nanostructure positioning, promote cooperative phenomenon between adjacent nanostructures and/or substrate materials, and allow for electrical contact to individual or groups of nanostructures. With neither self-assembly nor top-down lithographic processes being able to adequately meet this challenge, advancements have often relied on a hybrid strategy that utilizes lithographically-defined features to direct the assembly of nanostructures into organized patterns. While these so-called directed assembly techniques have proven viable, much of this effort has focused on the assembly of periodic arrays of spherical or near-spherical nanostructures comprised of a single element. Work directed toward the fabrication of more complex nanostructures, while still at a nascent stage, has nevertheless demonstrated the possibility of forming arrays of nanocubes, nanorods, nanoprisms, nanoshells, nanocages, nanoframes, core-shell structures, Janus structures, and various alloys on the substrate surface. In this topical review, we describe the progress made in the directed assembly of periodic arrays of these complex metal nanostructures on planar and textured substrates. The review is divided into three broad strategies reliant on: (i) the deterministic positioning of colloidal structures, (ii) the reorganization of deposited metal films at elevated temperatures, and (iii) liquid-phase chemistry practiced directly on the substrate surface. These strategies collectively utilize a broad range of techniques including capillary assembly, microcontact printing, chemical surface modulation, templated dewetting, nanoimprint lithography, and dip-pen nanolithography and employ a wide scope of chemical processes including redox reactions, alloying, dealloying, phase separation, galvanic replacement, preferential etching, template-mediated reactions, and facet-selective capping agents. Taken together, they highlight the diverse toolset available when fabricating organized surfaces of substrate-supported nanostructures.

Interfacial development of electrophoretically deposited graphene oxide films on Al alloys

DOE PAGES

Jin, Sumin; Dickerson, James H.; Pham, Viet Hung; ...

2015-07-28

Adhesion between film and substrate is critical for electronic device and coating applications. Interfacial development between electrophoretically deposited graphene oxide films on Al 1100 and Al 5052 alloys were investigated using FT-IR and XPS depth profiling techniques. Obtained results suggest metal ion permeation from the substrates into deposited graphene oxide films. The interface between the films and the substrates were primarily composed of Al-O-C bonds from oxygenated defects on graphene oxide plane rather than expected Al-C formation. Films heat treated at 150 °C had change in microstructure and peak shifts in XPS spectra suggesting change in chemical structure of bondsmore » between the films and the substrates.« less

Fabrication of broadband antireflection coating at terahertz frequency using a hot emboss method

NASA Astrophysics Data System (ADS)

Li, YunZhou; Cai, Bin; Zhu, YiMing

2014-11-01

We fabricated a terahertz anti-reflective structure on a polystylene by using a hot-embossing method. Polystylene was spin-coated onto a silicon substrate and then transformed by using a metallic mould comprising a bunch of Chinese acupuncture needles. The transformation layer yielded gradient refractive index profiles on the substrate which can reduce the surface reflection effectively. The samples were evaluated by a terahertz time-domain spectroscope. Compared with a bare silicon substrate, we observed an increase of ~30% in the transmittance. We also observed broader bandwidth properties compared with a single-layer antireflective structure. The process imposes no substrate limiting; i.e., it has great potential to be applied onto various THz devices.

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.

How Conformational Dynamics of DNA Polymerase Select Correct Substrates: Experiments and Simulations

PubMed Central

Kirmizialtin, Serdal; Nguyen, Virginia; Johnson, Kenneth A.; Elber, Ron

2012-01-01

Summary Nearly every enzyme undergoes a significant change in structure after binding it’s substrate. New experimental and theoretical analyses of the role of changes in HIV reverse transcriptase structure in selecting a correct substrate are presented. Atomically detailed simulations using the Milestoning method predict a rate and free energy profile of the conformational change commensurate with experimental data. A large conformational change occurring on a ms timescale locks the correct nucleotide at the active site, but promotes release of a mismatched nucleotide. The positions along the reaction coordinate that decide the yield of the reaction are not determined by the chemical step. Rather, the initial steps of weak substrate binding and protein conformational transition significantly enrich the yield of a reaction with a correct substrate, while the same steps diminish the reaction probability of an incorrect substrate. PMID:22483109

Preparation of CuIn{sub x}Ga{sub 1{minus}x}Se{sub 2} thin films on Si substrates

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

Yamamoto, Yukio; Yamaguchi, Toshiyuki; Suzuki, Masayoshi

For fabricating efficient tandem solar cells, CuIn{sub x}Ga{sub 1{minus}x}Se{sub 2} thin films have been prepared on Si(100), Si(110) and Si(111) substrates in the temperature range (R.T.{approximately}400 C) by rf sputtering. From EPMA analysis, these sputtered thin films are found to be nearly stoichiometric over the whole substrate temperature range, irrespective of the azimuth plane of the Si substrate. XPS studies showed that the compositional depth profile in these thin films is uniform. X-ray diffraction analysis indicated that all the thin films had a chalcopyrite structure. CuIn{sub x}Ga{sub 1{minus}x}Se{sub 2} thin films were strongly oriented along the (112) plane with increasingmore » the substrate temperature, independent of the azimuth plane of the Si substrate, suggesting the larger grain growth.« less

Synthesis of fructooligosaccharides (FosA) and inulin (InuO) by GH68 fructosyltransferases from Bacillus agaradhaerens strain WDG185.

PubMed

Kralj, Slavko; Leeflang, Chris; Sierra, Estefanía Ibáñez; Kempiński, Błażej; Alkan, Veli; Kolkman, Marc

2018-01-01

Fructooligosaccharides (FOS) and inulin, composed of β-2-1 linked fructose units, have a broad range of industrial applications. They are known to have various beneficial health effects and therefore have broad application potential in nutrition. For (modified) inulin also for non-food purposes more applications are arising. Examples are carboxymethylated inulin as anti-scalant and carboymlated inulin as emulsifiers. Various plants synthesize FOS and/or inulin type of fructans. However, isolating of FOS and inulin from plants is challenging due to for instance varying chains length. There is an increasing demand for FOS and inulin oligosaccharides and alternative procedures for their synthesis are attractive. We identified and characterized two fructosyltransferases from Bacillus agaradhaerens WDG185. FosA, a β-fructofuranosidase, synthesises short chain fructooligosaccharides (GF2-GF4) at high sucrose concentration, whereas InuO, an inulosucrase, synthesises a broad range of inulooligosaccharides (GF2-GF24) from sucrose, very similar to plant derived inulin. FosA and InuO showed activity over a broad pH range from 6 to 10 and optimal temperature at 60°C. Calcium ions and EDTA were found to have no effect on the activity of both enzymes. Kinetic analysis showed that only at relatively low substrate concentrations both enzymes showed Michaelis-Menten type of kinetics for total and transglycosylation activity. Both enzymes showed increased transglycosylation upon increasing substrate concentrations. These are the first examples of the molecular and biochemical characterization of a β-fructofuranosidase (FosA) and an inulosucrase enzyme (InuO) and its product from a Bacillus agaradhaerens strain. Copyright © 2017 Elsevier Ltd. All rights reserved.

Wavelength shift in vertical cavity laser arrays on a patterned substrate

NASA Astrophysics Data System (ADS)

Eng, L. E.; Bacher, K.; Yuen, W.; Larson, M.; Ding, G.; Harris, J. S., Jr.; Chang-Hasnain, C. J.

1995-03-01

The authors demonstrate a spatially chirped emission wavelength in vertical cavity surface emitting laser (VCSEL) arrays grown by molecular beam epitaxy. The wavelength shift is due to a lateral thickness variation in the Al(0.2)Ga(0.8)As cavity, which is induced by a substrate temperature profile during growth. A 20 nm shift in lasing wavelength is obtained in a VCSEL array.

Identifying and Profiling Scholastic Cheaters: Their Personality, Cognitive Ability, and Motivation

ERIC Educational Resources Information Center

Williams, Kevin M.; Nathanson, Craig; Paulhus, Delroy L.

2010-01-01

Despite much research, skepticism remains over the possibility of profiling scholastic cheaters. However, several relevant predictor variables and newer diagnostic tools have been overlooked. We remedy this deficit with a series of three studies. Study 1 was a large-scale survey of a broad range of personality predictors of self-reported cheating.…

Design of 2.5 GHz broad bandwidth microwave bandpass filter at operating frequency of 10 GHz using HFSS

NASA Astrophysics Data System (ADS)

Jasim, S. E.; Jusoh, M. A.; Mahmud, S. N. S.; Zamani, A. H.

2018-04-01

Development of low losses, small size and broad bandwidth microwave bandpass filter operating at higher frequencies is an active area of research. This paper presents a new route used to design and simulate microwave bandpass filter using finite element modelling and realized broad bandwidth, low losses, small dimension microwave bandpass filter operating at 10 GHz frequency using return loss method. The filter circuit has been carried out using Computer Aid Design (CAD), Ansoft HFSS software and designed with four parallel couple line model and small dimension (10 × 10 mm2) using LaAlO3 substrate. The response of the microwave filter circuit showed high return loss -50 dB at operating frequency at 10.4 GHz and broad bandwidth of 2.5 GHz from 9.5 to 12 GHz. The results indicate the filter design and simulation using HFSS is reliable and have the opportunity to transfer from lab potential experiments to the industry.

Plasma membrane dynamics and tetrameric organisation of ABCG2 transporters in mammalian cells revealed by single particle imaging techniques.

PubMed

Wong, Kelvin; Briddon, Stephen J; Holliday, Nicholas D; Kerr, Ian D

2016-01-01

ABCG2 is one of three human ATP binding cassette (ABC) transporters involved in the export from cells of a chemically and structurally diverse range of compounds. This multidrug efflux capability, together with a broad tissue distribution in the body, means that ABCG2 exerts a range of effects on normal physiology such as kidney urate transport, as well as contributing towards the pharmacokinetic profiles of many exogenous drugs. The primary sequence of ABCG2 contains only half the number of domains required for a functioning ABC transporter and so it must oligomerise in order to function, yet its oligomeric state in intact cell membranes remains uncharacterized. We have analysed ABCG2 in living cell membranes using a combination of fluorescence correlation spectroscopy, photon counting histogram analysis, and stepwise photobleaching to demonstrate a predominantly tetrameric structure for ABCG2 in the presence or absence of transport substrates. These results provide the essential basis for exploring pharmacological manipulation of oligomeric state as a strategy to modulate ABCG2 activity in future selective therapeutics. Copyright © 2015 Elsevier B.V. All rights reserved.

Assaying Oxidative Coupling Activity of CYP450 Enzymes.

PubMed

Agarwal, Vinayak

2018-01-01

Cytochrome P450 (CYP450) enzymes are ubiquitous catalysts in natural product biosynthetic schemes where they catalyze numerous different transformations using radical intermediates. In this protocol, we describe procedures to assay the activity of a marine bacterial CYP450 enzyme Bmp7 which catalyzes the oxidative radical coupling of polyhalogenated aromatic substrates. The broad substrate tolerance of Bmp7, together with rearrangements of the aryl radical intermediates leads to a large number of products to be generated by the enzymatic action of Bmp7. The complexity of the product pool generated by Bmp7 thus presents an analytical challenge for structural elucidation. To address this challenge, we describe mass spectrometry-based procedures to provide structural insights into aryl crosslinked products generated by Bmp7, which can complement subsequent spectroscopic experiments. Using the procedures described here, for the first time, we show that Bmp7 can efficiently accept polychlorinated aryl substrates, in addition to the physiological polybrominated substrates for the biosynthesis of polyhalogenated marine natural products. © 2018 Elsevier Inc. All rights reserved.

Enzymatic Detoxication, Conformational Selection, and the Role of Molten Globule Active Sites*

PubMed Central

Honaker, Matthew T.; Acchione, Mauro; Zhang, Wei; Mannervik, Bengt; Atkins, William M.

2013-01-01

The role of conformational ensembles in enzymatic reactions remains unclear. Discussion concerning “induced fit” versus “conformational selection” has, however, ignored detoxication enzymes, which exhibit catalytic promiscuity. These enzymes dominate drug metabolism and determine drug-drug interactions. The detoxication enzyme glutathione transferase A1–1 (GSTA1–1), exploits a molten globule-like active site to achieve remarkable catalytic promiscuity wherein the substrate-free conformational ensemble is broad with barrierless transitions between states. A quantitative index of catalytic promiscuity is used to compare engineered variants of GSTA1–1 and the catalytic promiscuity correlates strongly with characteristics of the thermodynamic partition function, for the substrate-free enzymes. Access to chemically disparate transition states is encoded by the substrate-free conformational ensemble. Pre-steady state catalytic data confirm an extension of the conformational selection model, wherein different substrates select different starting conformations. The kinetic liability of the conformational breadth is minimized by a smooth landscape. We propose that “local” molten globule behavior optimizes detoxication enzymes. PMID:23649628

Substrate promiscuity of a rosmarinic acid synthase from lavender (Lavandula angustifolia L.).

PubMed

Landmann, Christian; Hücherig, Stefanie; Fink, Barbara; Hoffmann, Thomas; Dittlein, Daniela; Coiner, Heather A; Schwab, Wilfried

2011-08-01

One of the most common types of modification of secondary metabolites is the acylation of oxygen- and nitrogen-containing substrates to produce esters and amides, respectively. Among the known acyltransferases, the members of the plant BAHD family are capable of acylating a wide variety of substrates. Two full-length acyltransferase cDNAs (LaAT1 and 2) were isolated from lavender flowers (Lavandula angustifolia L.) by reverse transcriptase-PCR using degenerate primers based on BAHD sequences. Recombinant LaAT1 exhibited a broad substrate tolerance accepting (hydroxy)cinnamoyl-CoAs as acyl donors and not only tyramine, tryptamine, phenylethylamine and anthranilic acid but also shikimic acid and 4-hydroxyphenyllactic acid as acceptors. Thus, LaLT1 forms esters and amides like its phylogenetic neighbors. In planta LaAT1 might be involved in the biosynthesis of rosmarinic acid, the ester of caffeic acid and 3,4-dihydroxyphenyllactic acid, a major constituent of lavender flowers. LaAT2 is one of three members of clade VI with unknown function.

Improved GaSb-based quantum well laser performance through metamorphic growth on GaAs substrates

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

Richardson, Christopher J. K., E-mail: richardson@lps.umd.edu; He, Lei; Apiratikul, Paveen

The promise of the metamorphic growth paradigm is to enable design freedom of the substrate selection criteria beyond current choices that are limited by lattice matching requirements. A demonstration of this emerging degree of freedom is reported here by directly comparing identical laser structures grown both pseudomorphically on a GaSb substrate and metamorphically on a GaAs substrate. Improved thermal performance of the metamorphic laser material enables a higher output power before thermal roll-over begins. These performance gains are demonstrated in minimally processed gain-guided broad-area type-I lasers emitting close to 2-μm wavelengths and mounted p-side up. Continuous wave measurements at roommore » temperature yield a T{sub 0} of 145 K and peak output power of 192 mW from metamorphic lasers, compared to a T{sub 0} of 96 K and peak output power of 164 mW from identical lasers grown pseudomorphically on GaSb.« less

Stereo- and regio-selective one-pot synthesis of triazole-based unnatural amino acids and β- amino triazoles

EPA Science Inventory

Synthesis of triazole based unnatural amino acids and β-amino triazole has been described via stereo and regioselective one-pot multi-component reaction of sulfamidates, sodium azide, and alkynes under MW conditions. The developed method is applicable to a broad substrate scope a...

Oviposition Substrate of the Mountain Fly Drosophila nigrosparsa (Diptera: Drosophilidae)

PubMed Central

Tratter, Magdalena; Bächli, Gerhard; Kirchmair, Martin; Kaufmann, Rüdiger; Arthofer, Wolfgang; Schlick-Steiner, Birgit C.; Steiner, Florian M.

2016-01-01

The survival of insect larvae often depends on the mother’s choice of oviposition substrate, and thus, this choice is an essential part of an insect species’ ecology. Especially species with narrow substrate preferences may suffer from changes in substrate availability triggered by, for example, climate change. Recent climate warming is affecting species directly (e.g., physiology) but also indirectly (e.g., biological interactions) leading to mismatching phenologies and distributions. However, the preferred oviposition substrate is still unknown for many drosophilid species, especially for those at higher elevations. In this study, we investigated the oviposition-substrate preference of the montane-alpine fly Drosophila nigrosparsa in rearing and multiple-choice experiments using natural substrates in the laboratory. Insect emergence from field-collected substrates was tested. More than 650 insects were reared from natural substrates, among them 152 drosophilids but no individual of D. nigrosparsa. In the multiple-choice experiments, D. nigrosparsa preferred ovipositing on mushrooms (> 93% of eggs); additionally, a few eggs were laid on berries but none on other substrates such as cow faeces, rotten plant material, and soil. The flies laid 24 times more eggs per day when mushrooms were included in the substrates than when they were excluded. We infer that D. nigrosparsa is a mushroom breeder with some variation in oviposition choice. The flies favoured some mushrooms over others, but they were not specialised on a single fungal taxon. Although it is unclear if and how climate change will affect D. nigrosparsa, our results indicate that this species will not be threatened by oviposition-substrate limitations in the near future because of the broad altitudinal distribution of the mushrooms considered here, even if the flies will have to shift upwards to withstand increasing temperatures. PMID:27788257

Inkjet-based adaptive planarization (Conference Presentation)

NASA Astrophysics Data System (ADS)

Singhal, Shrawan; Grigas, Michelle M.; Khusnatdinov, Niyaz; Sreenivasan, Srinivasan V.

2017-03-01

Planarization is a critical unit step in the lithography process because it enables patterning of surfaces with versatile pattern density without compromising on the stringent planarity and depth-of-focus requirements. In addition to nanoscale pattern density variation, parasitics such as pre-existing wafer topography, can corrupt the desired process output after planarization. The topography of any surface can be classified in three broad categories, depending upon the amplitude and spatial wavelength of the same [1], [2]: (i) nominal shape, (ii) nanotopography and (iii) roughness. The nominal shape is given by the largest spatial wavelengths, typically < 20mm. For spatial length scales of 1-20mm, height variations at this spatial wavelength range are classified as nanotopography. Roughness usually has lower spatial wavelengths. While the nominal shape of a substrate surface is usually decided by the nature of wafer preparation and the tooling and chucking infrastructure used in the same, roughness is usually mitigated by standard polishing techniques. It is the intermediate nanotopography that is probably the most critical surface topography parameter. This is because most traditional polishing techniques cannot selectively address pre-existing substrate topography, without introducing a parasitic signature at the scale of nanotopography. Moreover, fields with pattern density variation typically also have length scales that are commensurate with nanotopography. It is thus instructive to summarize existing planarization technology to understand current limitations. Spin on Glass and Etch back is one technique used for micron scale device manufacturing [3]. As the name implies, a glass dielectric is spin-coated on the substrate followed by etching in a chemistry that ensures equal etching rates for both the sacrificial glass and the underlying film or substrate material. Photoresists may also be used instead of glass. However, the global planarity that can be achieved by this technique is limited. Also, planarization over a large isolated topographical feature has been studied for the reverse-tone Jet-and-Flash Imprint Lithography process, also known as JFIL-R [4]. This relies on surface tension and capillary effects to smoothen a spin-coated Si containing film that can be etched to obtain a smooth profile. To meet the stringent requirement of planarity in submicron device technologies Chemical Mechanical Planarization (CMP) is the most widely used planarization technology [5], [6]. It uses a combination of abrasive laden chemical slurry and a mechanical pad for achieving planar profiles. The biggest concern with CMP is the dependence of material removal rate on the pattern density of material, leading to the formation of a step between the high density and low-density. The step shows up as a long-range thickness variation in the planarized film, similar in scale to pre-existing substrate topography that should have been polished away. Preventive techniques like dummy fill and patterned resist can be used to reduce the variation in pattern density. These techniques increase the complexity of the planarization process and significantly limit the device design flexibility. Contact Planarization (CP) has also been reported as an alternative to the CMP processing [7], [8]. A substrate is spin coated with a photo curable material and pre baked to remove residual solvent. An ultra-flat surface or an optical flat is pressed on the spin-coated wafer. The material is forced to reflow. Pressure is used to spread out material evenly and achieve global planarization. The substrate is then exposed to UV radiation to harden the photo curable material. Although attractive, this process is not adaptive as it does not account for differences in surface topography of the wafer and the optical flat, nor can it address all the parasitics that arise during the process itself. The optical flat leads to undesirable planarization of even the substrate nominal shape and nanotopography, which corrupts the final film thickness profile. Hence, it becomes extremely difficult to eliminate this signature to a desirable extent without introducing other parasitic signatures. An example of this is shown in Figure 1. In this paper, a novel adaptive planarization process has been presented that potentially addresses the problems associated with planarization of varying pattern density, even in the presence of pre-existing substrate topography [9]. This process is called Inkjet-enabled Adaptive Planarization (IAP). The IAP process uses an inverse optimization scheme, built around a validated fluid mechanics-based forward model [10], that takes the pre-existing substrate topography and pattern layout as inputs. It then generates an inkjet drop pattern with a material distribution that is correlated with the desired planarization film profile. This allows a contiguous film to be formed with the desired thickness variation to cater to the topography and any parasitic signatures caused by the pattern layout. This film is formed by the coercing action of a compliant superstrate, which forces the drops to spread and merge and eliminates any bubble trapping. Then, the film is cured using blanket UV exposure and the superstrate separated to reveal the desired planarized film. The use of an inverse optimization algorithm allows substrate topography to be addressed adaptively. In other words, the algorithm can generate a drop pattern that does not disturb the pre-existing substrate topography substantially, but only caters to the pattern density variation. This process has potential advantages over other planarization techniques because of its adaptive nature. Hence, the IAP process can cater to substrates of varying topographies and pattern densities by changing the inkjetted material distribution, without any changes in hardware. The IAP process can also address pre-existing substrate topography selectively by conforming to the nominal shape while planarizing over the pattern layout. A schematic of the IAP process is shown in Figure 2. The goal of this paper is to present some preliminary results from the IAP process. A test pattern layout has been generated with the help of photolithography, and is shown in Figure 3. For the purpose of this trial, the nanoscale features have not been patterned, as it is expected that the planarization process will be blind to their presence. Thus, areas with nanoscale patterns have been patterned as a single feature of SiO2 with height equal to 100 nm. These features are adjacent to pattern-less areas, thus marking a drastic change in pattern density. As can be seen in Figure 4, the smallest length scale across which pattern density changes, is 70 microns. The goal of the IAP process is to be able to planarize this pattern with a film that conforms to pre-existing substrate topography. The targeted planarity of the film is 95% 3sigma, while the targeted film thickness at the tallest feature is less than 30 nm. In another trial, the inverse tone of the same layout will also be tested. This pattern has features of height equal to 100 nm where the previous pattern did not. The targeted metrics for the inverse layout are the same as the nominal layout.

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

Development of a self-consistent free-form approach for studying the three-dimensional morphology of a thin film

NASA Astrophysics Data System (ADS)

Kozhevnikov, Igor V.; Peverini, Luca; Ziegler, Eric

2012-03-01

A method capable of extracting the depth distribution of the dielectric constant of a thin film deposited on a substrate and the three power spectral density (PSD) functions characterizing its roughness is presented. It is based on the concurrent analysis of x-ray reflectivity and scattering measurements obtained at different glancing angle values of the probe beam so that the effect of roughness is taken into account during reconstruction of the dielectric constant profile. Likewise, the latter is taken into account when determining the PSD functions describing the film roughness. This approach is using a numerical computation iterative procedure that demonstrated a rapid convergence for the overall set of data leading to a precise description of the three-dimensional morphology of a film. In the case of a tungsten thin film deposited by dc-magnetron sputtering onto a silicon substrate and characterized under vacuum, the analysis of the x-ray data showed the tungsten density to vary with depth from 95% of the bulk density at the top of the film to about 80% near the substrate, where the presence of an interlayer, estimated to be 0.7 nm thick, was evidenced. The latter may be due to diffusion and/or implantation of tungsten atoms into the silicon substrate. In the reconstruction of the depth profile, the resolution (minimum feature size correctly reconstructed) was estimated to be of the order of 0.4-0.5 nm. The depth distribution of the dielectric constant was shown to affect the roughness conformity coefficient extracted from the measured x-ray scattering distributions, while the deposition process increased the film roughness at high spatial frequency as compared to the virgin substrate. On the contrary, the roughness showed a weak influence on the dielectric constant depth profile extracted, as the sample used in our particular experiment was extremely smooth.

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.

Community-level physiological profiles of microorganisms inhabiting soil contaminated with heavy metals

NASA Astrophysics Data System (ADS)

Kuźniar, Agnieszka; Banach, Artur; Stępniewska, Zofia; Frąc, Magdalena; Oszust, Karolina; Gryta, Agata; Kłos, Marta; Wolińska, Agnieszka

2018-01-01

The aim of the study was to assess the differences in the bacterial community physiological profiles in soils contaminated with heavy metals versus soils without metal contaminations. The study's contaminated soil originated from the surrounding area of the Szopienice non-ferrous metal smelter (Silesia Region, Poland). The control was soil unexposed to heavy metals. Metal concentration was appraised by flame atomic absorption spectrometry, whereas the the community-level physiological profile was determined with the Biolog EcoPlatesTM system. The soil microbiological activity in both sites was also assessed via dehydrogenase activity. The mean concentrations of metals (Cd and Zn) in contaminated soil samples were in a range from 147.27 to 12265.42 mg kg-1, and the heavy metal contamination brought about a situation where dehydrogenase activity inhibition was observed mostly in the soil surface layers. Our results demonstrated that there is diversity in the physiological profiles of microorganisms inhabiting contaminated and colntrol soils; therefore, for assessment purposes, these were treated as two clusters. Cluster I included colntrol soil samples in which microbial communities utilised most of the available substrates. Cluster II incorporated contaminated soil samples in which a smaller number of the tested substrates was utilised by the contained microorganisms. The physiological profiles of micro-organisms inhabiting the contaminated and the colntrol soils are distinctly different.

Boron depth profiles and residual damage following rapid thermal annealing of low-temperature BSi molecular ion implantation in silicon

NASA Astrophysics Data System (ADS)

Liang, J. H.; Wang, S. C.

2007-08-01

The influence of substrate temperature on both the implantation and post-annealing characteristics of molecular-ion-implanted 5 × 1014 cm-2 77 keV BSi in silicon was investigated in terms of boron depth profiles and damage microstructures. The substrate temperatures under investigation consisted of room temperature (RT) and liquid nitrogen temperature (LT). Post-annealing treatments were performed using rapid thermal annealing (RTA) at 1050 °C for 25 s. Boron depth profiles and damage microstructures in both the as-implanted and as-annealed specimens were determined using secondary ion mass spectrometry (SIMS) and transmission electron microscopy (TEM), respectively. The as-implanted results revealed that, compared to the RT specimen, the LT specimen yields a shallower boron depth profile with a reduced tail into the bulk. An amorphous layer containing a smooth amorphous-to-crystalline (a/c) interface is evident in the LT specimen while just the opposite is true in the as-implanted RT one. The as-annealed results illustrated that the extension of the boron depth profile into the bulk via transient-enhanced diffusion (TED) in the LT specimen is less than it is in the RT one. Only residual defects are visible in the LT specimen while two clear bands of dislocation loops appear in the RT one.

Effect of dactyloscopic powders on DNA profiling from enhanced fingerprints: results from an experimental study.

PubMed

Tozzo, Pamela; Giuliodori, Alice; Rodriguez, Daniele; Caenazzo, Luciana

2014-03-01

We conducted a study on the effect of fingerprint enhancement methods on subsequent short tandem repeat profiling. First, we performed a study typing blood traces deposited on 5 different surfaces, treated with 8 types of dactyloscopic powders. Three different DNA extraction methods were used. Subsequently, we analyzed latent fingerprints on the same 5 surfaces enhanced with the 8 different powders used in the first part of the study. This study has demonstrated that DNA profiling can be performed on fingerprints left on different substrates, and the substrate will affect the amount of DNA that can be recovered for DNA typing. In the first phase of the study, a profile was obtained in 92% of the 120 samples analyzed; in the second part, in 55% of the 80 samples analyzed, we obtained a profile complete in 32.5% of the cases. From the results obtained, it seems that the powders used in latent fingerprints enhancement, rather than having a direct inhibitory effect on extraction and amplification of DNA, may cause partial degradation of DNA, reducing the efficiency of amplification reaction. It should not be forgotten that these results were obtained under laboratory conditions, and in real caseworks, there may still be different problems involved.

Temporal and spectral properties of the songs of the southern green stink bug Nezara viridula (L.) from Slovenia.

PubMed

Cokl, A; Virant-Doberlet, M; Stritih, N

2000-01-01

Substrate born songs of the southern green stinkbug Nezara viridula (L.) from Slovenia were recorded and analysed. The male calling song is composed of narrow-band regularly repeated single pulses and of broad-band frequency modulated pulses grouped into pulse trains. The female calling song is characterised by broad-band pulsed and narrow-band non-pulsed pulse trains. A frequency modulated pre-pulse precedes the narrow-band pulse train. A frequency-modulated post-pulse usually follows the pulse train of the male courtship song. The male calling song triggers broad-band pulse trains of the female courtship song. The female also produces a repelling low-frequency vibration that inhibits male calling and courtship. The male rival song is characterised by prolonged pulses with a typical frequency modulation.

Kinetic analysis of extension of substrate specificity with Xanthomonas maltophilia, Aeromonas hydrophila, and Bacillus cereus metallo-beta-lactamases.

PubMed Central

Felici, A; Amicosante, G

1995-01-01

Twenty beta-lactam molecules, including penicillins, cephalosporins, penems, carbapenems, and monobactams, were investigated as potential substrates for Xanthomonas maltophilia ULA-511, Aeromonas hydrophila AE036, and Bacillus cereus 5/B/6 metallo-beta-lactamases. A detailed analysis of the kinetic parameters examined confirmed these enzymes to be broad-spectrum beta-lactamases with different ranges of catalytic efficiency. Cefoxitin and moxalactam, substrates for the beta-lactamases from X. maltophilia ULA-511 and B. cereus 5/B/6, behaved as inactivators of the A. hydrophila AE036 metallo-beta-lactamase, which appeared to be unique among the enzymes tested in this study. In addition, we report a new, faster, and reliable purification procedure for the B. cereus 5/B/6 metallo-beta-lactamase, cloned in Escherichia coli HB101. PMID:7695305

Chiral poly-rare earth metal complexes in asymmetric catalysis

PubMed Central

Shibasaki, Masakatsu

2006-01-01

Asymmetric catalysis is a powerful component of modern synthetic organic chemistry. To further broaden the scope and utility of asymmetric catalysis, new basic concepts for the design of asymmetric catalysts are crucial. Because most chemical reactions involve bond-formation between two substrates or moieties, high enantioselectivity and catalyst activity should be realized if an asymmetric catalyst can activate two reacting substrates simultaneously at defined positions. Thus, we proposed the concept of bifunctional asymmetric catalysis, which led us to the design of new asymmetric catalysts containing two functionalities (e.g. a Lewis acid and a Brønsted base or a Lewis acid and a Lewis base). These catalysts demonstrated broad reaction applicability with excellent substrate generality. Using our catalytic asymmetric reactions as keys steps, efficient total syntheses of pharmaceuticals and their biologically active lead natural products were achieved. PMID:25792774

Mesonephric (Wolffian) Pseudoendometrioid Carcinoma of the Broad Ligament, Arising From a Papillary Cystadenoma.

PubMed

Moerman, Philippe; Amant, Frederic; Vergote, Ignace

2016-10-01

This article describes the case of a 70-year-old woman with an adnexal cystadenocarcinoma located in the right broad ligament and displaying a striking resemblance to a well-differentiated endometrioid adenocarcinoma. The uniqueness of this pseudoendometrioid carcinoma lies in the fact that its mesonephric nature is revealed by the origin from a papillary cystadenoma of the broad ligament, where remnants of the mesonephric duct are seated, and the immunohistochemical profile, particularly a uniform negativity for estrogen and progesterone receptors, apical-luminal positivity for CD10, and strong nuclear positivity for GATA3. © The Author(s) 2016.

Highly ionized gas absorption in the disk and halo toward HD 167756 at 3.5 kilometers per second resolution

NASA Technical Reports Server (NTRS)

Savage, Blair D.; Sembach, Kenneth R.; Cardelli, Jason A.

1994-01-01

High-resolution spectra of interstellar Si IV, C IV, and N V absorption lines along the 4 kpc path to the inner Galaxy star HD 167756 at z = -0.85 kpc are presented. The spectra were obtained with the echelle mode of Goddard High Resolution Spectrograph (GHRS) aboard the Hubble Space Telescope (HST) and have signal-to-noise ratios ranging from 23 to 38. The high resolution of the measurements full width at half maximum (FWHM = 3.5 km/s) results in fully resolved line profiles for the highly ionized gas absorption. The measurements provide information on the column density per unit velocity, N(v), as a function of velocity for Si IV, C IV, and N V. The C IV and N V profiles extend from -70 to +70 km/s, while the Si IV profiles extend from -40 to +70 km/s. The integrated logarithmic column densities are long N(Si IV) = 13.09 +/- 0.02, log N(C IV) = 13.83 +/- 0.02, and log N(N V) = 13.56 +/- 0.03. The N V profile is broad, asymmetric, and featureless, while the Si IV profile contains narrow absorption components near V(sub LSR) = -19, 0, +20, and +52 km/s with Doppler spread parameters, b about = 10-12 km/s. The C IV profile contains both broad and narrow structure. The high ion feature near +52 km/s is also detected in the low-ionization lines of Ca II, O I, Si II, and Fe II. The other narrow Si IV and C IV components occur within several km/s of components seen in low-ionization species. The sight line contains at least two types of highly ionized gas. One type gives rise to a broad N V profile, and the other results in the more structured Si IV profile. The C IV profile contains contributions from both types of highly ionized gas. The broad but asymmetric N V profile is well represented by a large Galactic scale height gas which is participating in Galactic rotation and has a combination of thermal and turbulent broadening with b(sub tot) about = 42 km/s. The C IV to N V abundance ratio of 1.0 +/- 0.3 for the gas implies T about 1.6 x 10(exp 5) K or about 8 x 10(exp 5) K if the gas is in collisional ionization equilibrium and has a solar carbon to nitrogen abundance ratio. This absorption may be associated with cooling hot gas situated in Galactic shells and supershells along the sight line. The gas producing the narrow Si IV and C IV absorption components has line widths that are compatible with origins in conductive interfaces between the warm and hot interstellar medium. Kinematic flows associated with the photoionized edges of clouds might also produce Si IV and C IV lines with Doppler spread parameters similar to those observed, but the C IV to Si IV ratio in this gas is 3.5, which leads us to favor the conductive interface interpretation.

A study on the evaporation process with multiple point-sources

NASA Astrophysics Data System (ADS)

Jun, Sunghoon; Kim, Minseok; Kim, Suk Han; Lee, Moon Yong; Lee, Eung Ki

2013-10-01

In Organic Light Emitting Display (OLED) manufacturing processes, there is a need to enlarge the mother glass substrate to raise its productivity and enable OLED TV. The larger the size of the glass substrate, the more difficult it is to establish a uniform thickness profile of the organic thin-film layer in the vacuum evaporation process. In this paper, a multiple point-source evaporation process is proposed to deposit a uniform organic layer uniformly. Using this method, a uniformity of 3.75% was achieved along a 1,300 mm length of Gen. 5.5 glass substrate (1300 × 1500 mm2).

Mechanistic and Structural Analyses of the Role of His67 in the Yeast Polyamine Oxidase Fms1†

PubMed Central

Adachi, Mariya S.; Taylor, Alexander B.; Hart, P. John; Fitzpatrick, Paul F.

2012-01-01

The flavoprotein oxidase Fms1 from Saccharomyces cerevisiae catalyzes the oxidation of spermine and N1-acetylspermine to spermidine and 3-aminopropanal or N-acetyl-3-aminopropanal. Within the active site of Fms1, His67 is positioned to form hydrogen bonds with the polyamine substrate. This residue is also conserved in other polyamine oxidases. The catalytic properties of H67Q, H67N, and H67A Fms1 have been characterized to evaluate the role of this residue in catalysis. With both spermine and N1-acetylspermine as the amine substrate, the value of the first-order rate constant for flavin reduction decreases 2–3 orders of magnitude, with the H67Q mutation having the smallest effect and H67N the largest. The kcat/KO2 value changes very little upon mutation with N1-acetylspermine as the amine substrate and decreases only an order of magnitude with spermine. The kcat/KM-pH profiles with N1-acetylspermine are bell-shaped for all the mutants; the similarity to the profile of the wild-type enzyme rules out His67 as being responsible for either of the pKa values. The pH profiles for the rate constant for flavin reduction for all the mutant enzymes similarly show the same pKa as wild-type Fms1, about ~7.4; this pKa is assigned to the substrate N4. The kcat/KO2-pH profiles for wild-type Fms1 and the H67A enzyme both show a pKa of about ~6.9; this suggests His67 is not responsible for this pH behaviour. With the H67Q, H67N, and H67A enzymes the kcat value decreases when a single residue is protonated, as is the case with the wild-type enzyme. The structure of H67Q Fms1 has been determined at a resolution of 2.4 Å. The structure shows that the mutation disrupts a hydrogen bond network in the active site, suggesting that His67 is important both for direct interactions with the substrate and to maintain the overall active site structure. PMID:22642831

Mechanistic and structural analyses of the role of His67 in the yeast polyamine oxidase Fms1.

PubMed

Adachi, Mariya S; Taylor, Alexander B; Hart, P John; Fitzpatrick, Paul F

2012-06-19

The flavoprotein oxidase Fms1 from Saccharomyces cerevisiae catalyzes the oxidation of spermine and N(1)-acetylspermine to spermidine and 3-aminopropanal or N-acetyl-3-aminopropanal. Within the active site of Fms1, His67 is positioned to form hydrogen bonds with the polyamine substrate. This residue is also conserved in other polyamine oxidases. The catalytic properties of H67Q, H67N, and H67A Fms1 have been characterized to evaluate the role of this residue in catalysis. With both spermine and N(1)-acetylspermine as the amine substrate, the value of the first-order rate constant for flavin reduction decreases 2-3 orders of magnitude, with the H67Q mutation having the smallest effect and H67N the largest. The k(cat)/K(O2) value changes very little upon mutation with N(1)-acetylspermine as the amine substrate and decreases only an order of magnitude with spermine. The k(cat)/K(M)-pH profiles with N(1)-acetylspermine are bell-shaped for all the mutants; the similarity to the profile of the wild-type enzyme rules out His67 as being responsible for either of the pK(a) values. The pH profiles for the rate constant for flavin reduction for all the mutant enzymes similarly show the same pK(a) as wild-type Fms1, about ∼7.4; this pK(a) is assigned to the substrate N4. The k(cat)/K(O2)-pH profiles for wild-type Fms1 and the H67A enzyme both show a pK(a) of about ∼6.9; this suggests His67 is not responsible for this pH behavior. With the H67Q, H67N, and H67A enzymes the k(cat) value decreases when a single residue is protonated, as is the case with the wild-type enzyme. The structure of H67Q Fms1 has been determined at a resolution of 2.4 Å. The structure shows that the mutation disrupts a hydrogen bond network in the active site, suggesting that His67 is important both for direct interactions with the substrate and to maintain the overall active site structure.

A resonance-free nano-film airborne ultrasound emitter

NASA Astrophysics Data System (ADS)

Daschewski, Maxim; Harrer, Andrea; Prager, Jens; Kreutzbruck, Marc; Beck, Uwe; Lange, Thorid; Weise, Matthias

2013-01-01

In this contribution we present a novel thermo-acoustic approach for the generation of broad band airborne ultrasound and investigate the applicability of resonance-free thermo-acoustic emitters for very short high pressure airborne ultrasound pulses. We report on measurements of thermo-acoustic emitter consisting of a 30 nm thin metallic film on a usual soda-lime glass substrate, generating sound pressure values of more than 140 dB at 60 mm distance from the transducer and compare the results with conventional piezoelectric airborne ultrasound transducers. Our experimental investigations show that such thermo-acoustic devices can be used as broad band emitters using pulse excitation.

Broad Frequency LTCC Vertical Interconnect Transition for Multichip Modules and System on Package Applications

NASA Technical Reports Server (NTRS)

Decrossas, Emmanuel; Glover, Michael D.; Porter, Kaoru; Cannon, Tom; Mantooth, H. Alan; Hamilton, M. C.

2013-01-01

Various stripline structures and flip chip interconnect designs for high-speed digital communication systems implemented in low temperature co-fired ceramic (LTCC) substrates are studied in this paper. Specifically, two different transition designs from edge launch 2.4 millimeter connectors to stripline transmission lines embedded in LTCC are discussed. After characterizing the DuPont (sup trademark) 9K7 green tape, different designs are proposed to improve signal integrity for high-speed digital data. The full-wave simulations and experimental data validate the presented designs over a broad frequency band from Direct Current to 50 gigahertz and beyond.

Matrix metalloproteinase processing of signaling molecules to regulate inflammation.

PubMed

Butler, Georgina S; Overall, Christopher M

2013-10-01

Inflammation is a complex and highly regulated process that facilitates the clearance of pathogens and mediates tissue repair. Failure to resolve inflammation can lead to chronic inflammatory diseases such as periodontitis. Matrix metalloproteinases are generally thought to be detrimental in disease because degradation of extracellular matrix contributes to pathology. However, proteomic techniques (degradomics) are revealing that matrix metalloproteinases process a diverse array of substrates and therefore have a broad range of functions. Many matrix metalloproteinase substrates modulate inflammation and hence, by processing these proteins, matrix metalloproteinases can orchestrate the inflammatory response. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

The Aldo-Keto Reductase Superfamily and its Role in Drug Metabolism and Detoxification

PubMed Central

Barski, Oleg A.; Tipparaju, Srinivas M.; Bhatnagar, Aruni

2008-01-01

The Aldo-Keto Reductase (AKR) superfamily comprises of several enzymes that catalyze redox transformations involved in biosynthesis, intermediary metabolism and detoxification. Substrates of the family include glucose, steroids, glycosylation end products, lipid peroxidation products, and environmental pollutants. These proteins adopt a (β/α)8 barrel structural motif interrupted by a number of extraneous loops and helixes that vary between proteins and bring structural identity to individual families. The human AKR family differs from the rodent families. Due to their broad substrate specificity, AKRs play an important role in the Phase II detoxification of a large number of pharmaceuticals, drugs, and xenobiotics. PMID:18949601

Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction

PubMed Central

Siegel, Justin B.; Zanghellini, Alexandre; Lovick, Helena M.; Kiss, Gert; Lambert, Abigail R.; St.Clair, Jennifer L.; Gallaher, Jasmine L.; Hilvert, Donald; Gelb, Michael H.; Stoddard, Barry L.; Houk, Kendall N.; Michael, Forrest E.; Baker, David

2011-01-01

The Diels-Alder reaction is a cornerstone in organic synthesis, forming two carbon-carbon bonds and up to four new stereogenic centers in one step. No naturally occurring enzymes have been shown to catalyze bimolecular Diels-Alder reactions. We describe the de novo computational design and experimental characterization of enzymes catalyzing a bimolecular Diels-Alder reaction with high stereoselectivity and substrate specificity. X-ray crystallography confirms that the structure matches the design for the most active of the enzymes, and binding site substitutions reprogram the substrate specificity. Designed stereoselective catalysts for carbon-carbon bond forming reactions should be broadly useful in synthetic chemistry. PMID:20647463

Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction.

PubMed

Siegel, Justin B; Zanghellini, Alexandre; Lovick, Helena M; Kiss, Gert; Lambert, Abigail R; St Clair, Jennifer L; Gallaher, Jasmine L; Hilvert, Donald; Gelb, Michael H; Stoddard, Barry L; Houk, Kendall N; Michael, Forrest E; Baker, David

2010-07-16

The Diels-Alder reaction is a cornerstone in organic synthesis, forming two carbon-carbon bonds and up to four new stereogenic centers in one step. No naturally occurring enzymes have been shown to catalyze bimolecular Diels-Alder reactions. We describe the de novo computational design and experimental characterization of enzymes catalyzing a bimolecular Diels-Alder reaction with high stereoselectivity and substrate specificity. X-ray crystallography confirms that the structure matches the design for the most active of the enzymes, and binding site substitutions reprogram the substrate specificity. Designed stereoselective catalysts for carbon-carbon bond-forming reactions should be broadly useful in synthetic chemistry.

Combustion-Assisted Photonic Annealing of Printable Graphene Inks via Exothermic Binders.

PubMed

Secor, Ethan B; Gao, Theodore Z; Dos Santos, Manuel H; Wallace, Shay G; Putz, Karl W; Hersam, Mark C

2017-09-06

High-throughput and low-temperature processing of high-performance nanomaterial inks is an important technical challenge for large-area, flexible printed electronics. In this report, we demonstrate nitrocellulose as an exothermic binder for photonic annealing of conductive graphene inks, leveraging the rapid decomposition kinetics and built-in energy of nitrocellulose to enable versatile process integration. This strategy results in superlative electrical properties that are comparable to extended thermal annealing at 350 °C, using a pulsed light process that is compatible with thermally sensitive substrates. The resulting porous microstructure and broad liquid-phase patterning compatibility are exploited for printed graphene microsupercapacitors on paper-based substrates.

Carbohydrates as efficient catalysts for the hydration of α-amino nitriles.

PubMed

Chitale, Sampada; Derasp, Joshua S; Hussain, Bashir; Tanveer, Kashif; Beauchemin, André M

2016-11-01

Directed hydration of α-amino nitriles was achieved under mild conditions using simple carbohydrates as catalysts exploiting temporary intramolecularity. A broadly applicable procedure using both formaldehyde and NaOH as catalysts efficiently hydrated a variety of primary and secondary susbtrates, and allowed the hydration of enantiopure substrates to proceed without racemization. This work also provides a rare comparison of the catalytic activity of carbohydrates, and shows that the simple aldehydes at the basis of chemical evolution are efficient organocatalysts mimicking the function of hydratase enzymes. Optimal catalytic efficiency was observed with destabilized aldehydes, and with difficult substrates only simple carbohydrates such as formaldehyde and glycolaldehyde proved reliable.

The Post-polyketide Synthase Steps in iso-Migrastatin Biosynthesis Featuring Tailoring Enzymes with Broad Substrate Specificity

PubMed Central

Ma, Ming; Kwong, Thomas; Lim, Si-Kyu; Ju, Jianhua; Lohman, Jeremy R.; Shen, Ben

2013-01-01

The iso-migrastatin (iso-MGS) biosynthetic gene cluster from Streptomyces platensis NRRL 18993 consists of 11 genes, featuring an acyltransferase (AT)-less type I polyketide synthase (PKS) and three tailoring enzymes MgsIJK. Systematic inactivation of mgsIJK in S. platensis enabled us to (i) identify two nascent products (10 and 13) of the iso-MGS AT-less type I PKS, establishing an unprecedented novel feature for AT-less type I PKSs, and (ii) account for the formation of all known post-PKS biosynthetic intermediates (10-17) generated by the three tailoring enzymes MgsIJK, which possessed significant substrate promiscuities. PMID:23394593

The different origins of high- and low-ionization broad emission lines revealed by gravitational microlensing in the Einstein cross

NASA Astrophysics Data System (ADS)

Braibant, L.; Hutsemékers, D.; Sluse, D.; Anguita, T.

2016-07-01

We investigate the kinematics and ionization structure of the broad emission line region of the gravitationally lensed quasar QSO2237+0305 (the Einstein cross) using differential microlensing in the high- and low-ionization broad emission lines. We combine visible and near-infrared spectra of the four images of the lensed quasar and detect a large-amplitude microlensing effect distorting the high-ionization CIV and low-ionization Hα line profiles in image A. While microlensing only magnifies the red wing of the Balmer line, it symmetrically magnifies the wings of the CIV emission line. Given that the same microlensing pattern magnifies both the high- and low-ionization broad emission line regions, these dissimilar distortions of the line profiles suggest that the high- and low-ionization regions are governed by different kinematics. Since this quasar is likely viewed at intermediate inclination, we argue that the differential magnification of the blue and red wings of Hα favors a flattened, virialized, low-ionization region whereas the symmetric microlensing effect measured in CIV can be reproduced by an emission line formed in a polar wind, without the need of fine-tuned caustic configurations. Based on observations made with the ESO-VLT, Paranal, Chile; Proposals 076.B-0197 and 076.B-0607 (PI: Courbin).

The effects of diurnal Ramadan fasting on energy expenditure and substrate oxidation in healthy men.

PubMed

Alsubheen, Sana'a A; Ismail, Mohammad; Baker, Alicia; Blair, Jason; Adebayo, Adeboye; Kelly, Liam; Chandurkar, Vikram; Cheema, Sukhinder; Joanisse, Denis R; Basset, Fabien A

2017-12-01

The study aimed to examine the effects of diurnal Ramadan fasting (RF) on substrate oxidation, energy production, blood lipids and glucose as well as body composition. Nine healthy Muslim men (fasting (FAST) group) and eight healthy non-practicing men (control (CNT) group) were assessed pre- and post-RF. FAST were additionally assessed at days 10, 20 and 30 of RF in the morning and evening. Body composition was determined by hydrodensitometry, substrate oxidation and energy production by indirect calorimetry, blood metabolic profile by biochemical analyses and energy balance by activity tracker recordings and food log analyses. A significant group×time interaction revealed that chronic RF reduced body mass and adiposity in FAST, without changing lean mass, whereas CNT subjects remained unchanged. In parallel to these findings, a significant main diurnal effect (morning v. evening) of RF on substrate oxidation (a shift towards lipid oxidation) and blood metabolic profile (a decrease in glucose and an increase in total cholesterol and TAG levels, respectively) was observed, which did not vary over the course of the Ramadan. In conclusion, although RF induces diurnal metabolic adjustments (morning v. evening), no carryover effect was observed throughout RF despite the extended daily fasting period (18·0 (sd 0·3) h) and changes in body composition.

Comparative study of myocardial high energy phosphate substrate content in slow and fast growing chicken and in chickens with heart failure and ascites.

PubMed

Olkowski, A A; Nain, S; Wojnarowicz, C; Laarveld, B; Alcorn, J; Ling, B B

2007-09-01

In order to explain the biochemical mechanisms associated with deteriorating heart function in broiler chickens, this study compared myocardial high energy phosphate substrates in leghorns, feed restricted (Broilers-Res) broilers, ad libitum fed broilers (Broilers-AL), and in broilers that developed heart failure and ascites. The profile of adenine nucleotide content in the heart tissue did not differ between leghorns and Broilers-Res, but there were significant differences among Broilers-Res, Broilers-AL, and broilers with ascites. During intensive growth periods, leghorns and Broilers-Res showed increasing trends in heart ATP levels, whereas in fast growing broilers the heart ATP declined (p<0.021). ATP:ADP and ATP:CrP ratios increased with age in both leghorn and Broilers-Res, declined in fast growing broilers, and were the lowest in broilers that developed heart failure. The changes in heart high energy phosphate profile in broilers suggest that the energy demand of the heart during a rapid growth phase may exceed the bird's metabolic capacity to supply adequate levels of high energy phosphate substrate. The insufficiency of energy substrate likely contributes to the declining heart rate. In some individuals this may lead to impaired heart pump function, and in more severe cases may progress to heart pump failure.

Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche

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

Morin, Emmanuelle; Kohler, Annegret; Baker, Adam R.

Agaricus bisporus is the model fungus for the adaptation, persistence, and growth in the humic-rich leaf-litter environment. Aside from its ecological role, A. bisporus has been an important component of the human diet for over 200 y and worldwide cultivation of the button mushroom forms a multibillion dollar industry. We present two A. bisporus genomes, their gene repertoires and transcript profiles on compost and during mushroom formation. The genomes encode a full repertoire of polysaccharide-degrading enzymes similar to that of wood-decayers. Comparative transcriptomics of mycelium grown on defined medium, casing-soil, and compost revealed genes encoding enzymes involved in xylan, cellulose,more » pectin, and protein degradation are more highly expressed in compost. The striking expansion of heme-thiolate peroxidases and etherases is distinctive from Agaricomycotina wood-decayers and suggests a broad attack on decaying lignin and related metabolites found in humic acid-rich environment. Similarly, up-regulation of these genes together with a lignolytic manganese peroxidase, multiple copper radical oxidases, and cytochrome P450s is consistent with challenges posed by complex humic-rich substrates. The gene repertoire and expression of hydrolytic enzymes in A. bisporus is substantially different from the taxonomically related ectomycorrhizal symbiont Laccaria bicolor. A common promoter motif was also identified in genes very highly expressed in humic-rich substrates. These observations reveal genetic and enzymatic mechanisms governing adaptation to the humic-rich ecological niche formed during plant degradation, further defining the critical role such fungi contribute to soil structure and carbon sequestration in terrestrial ecosystems. Genome sequence will expedite mushroom breeding for improved agronomic characteristics.« less

GDSL lipases modulate immunity through lipid homeostasis in rice

PubMed Central

Lam, Sin Man; Tong, Xiaohong; Liu, Jiyun; Wang, Xin; Shui, Guanghou

2017-01-01

Lipids and lipid metabolites play important roles in plant-microbe interactions. Despite the extensive studies of lipases in lipid homeostasis and seed oil biosynthesis, the involvement of lipases in plant immunity remains largely unknown. In particular, GDSL esterases/lipases, characterized by the conserved GDSL motif, are a subfamily of lipolytic enzymes with broad substrate specificity. Here, we functionally identified two GDSL lipases, OsGLIP1 and OsGLIP2, in rice immune responses. Expression of OsGLIP1 and OsGLIP2 was suppressed by pathogen infection and salicylic acid (SA) treatment. OsGLIP1 was mainly expressed in leaf and leaf sheath, while OsGLIP2 showed high expression in elongating internodes. Biochemical assay demonstrated that OsGLIP1 and OsGLIP2 are functional lipases that could hydrolyze lipid substrates. Simultaneous down-regulation of OsGLIP1 and OsGLIP2 increased plant resistance to both bacterial and fungal pathogens, whereas disease resistance in OsGLIP1 and OsGLIP2 overexpression plants was significantly compromised, suggesting that both genes act as negative regulators of disease resistance. OsGLIP1 and OsGLIP2 proteins mainly localize to lipid droplets and the endoplasmic reticulum (ER) membrane. The proper cellular localization of OsGLIP proteins is indispensable for their functions in immunity. Comprehensive lipid profiling analysis indicated that the alteration of OsGLIP gene expression was associated with substantial changes of the levels of lipid species including monogalactosyldiacylglycerol (MGDG) and digalactosyldiacylglycerol (DGDG). We show that MGDG and DGDG feeding could attenuate disease resistance. Taken together, our study indicates that OsGLIP1 and OsGLIP2 negatively regulate rice defense by modulating lipid metabolism, thus providing new insights into the function of lipids in plant immunity. PMID:29131851

Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche

PubMed Central

Morin, Emmanuelle; Kohler, Annegret; Baker, Adam R.; Foulongne-Oriol, Marie; Lombard, Vincent; Nagye, Laszlo G.; Ohm, Robin A.; Patyshakuliyeva, Aleksandrina; Brun, Annick; Aerts, Andrea L.; Bailey, Andrew M.; Billette, Christophe; Coutinho, Pedro M.; Deakin, Greg; Doddapaneni, Harshavardhan; Floudas, Dimitrios; Grimwood, Jane; Hildén, Kristiina; Kües, Ursula; LaButti, Kurt M.; Lapidus, Alla; Lindquist, Erika A.; Lucas, Susan M.; Murat, Claude; Riley, Robert W.; Salamov, Asaf A.; Schmutz, Jeremy; Subramanian, Venkataramanan; Wösten, Han A. B.; Xu, Jianping; Eastwood, Daniel C.; Foster, Gary D.; Sonnenberg, Anton S. M.; Cullen, Dan; de Vries, Ronald P.; Lundell, Taina; Hibbett, David S.; Henrissat, Bernard; Burton, Kerry S.; Kerrigan, Richard W.; Challen, Michael P.; Grigoriev, Igor V.; Martin, Francis

2012-01-01

Agaricus bisporus is the model fungus for the adaptation, persistence, and growth in the humic-rich leaf-litter environment. Aside from its ecological role, A. bisporus has been an important component of the human diet for over 200 y and worldwide cultivation of the “button mushroom” forms a multibillion dollar industry. We present two A. bisporus genomes, their gene repertoires and transcript profiles on compost and during mushroom formation. The genomes encode a full repertoire of polysaccharide-degrading enzymes similar to that of wood-decayers. Comparative transcriptomics of mycelium grown on defined medium, casing-soil, and compost revealed genes encoding enzymes involved in xylan, cellulose, pectin, and protein degradation are more highly expressed in compost. The striking expansion of heme-thiolate peroxidases and β-etherases is distinctive from Agaricomycotina wood-decayers and suggests a broad attack on decaying lignin and related metabolites found in humic acid-rich environment. Similarly, up-regulation of these genes together with a lignolytic manganese peroxidase, multiple copper radical oxidases, and cytochrome P450s is consistent with challenges posed by complex humic-rich substrates. The gene repertoire and expression of hydrolytic enzymes in A. bisporus is substantially different from the taxonomically related ectomycorrhizal symbiont Laccaria bicolor. A common promoter motif was also identified in genes very highly expressed in humic-rich substrates. These observations reveal genetic and enzymatic mechanisms governing adaptation to the humic-rich ecological niche formed during plant degradation, further defining the critical role such fungi contribute to soil structure and carbon sequestration in terrestrial ecosystems. Genome sequence will expedite mushroom breeding for improved agronomic characteristics. PMID:23045686

Blue/pink/purple electroluminescence from metal-oxide-semiconductor devices fabricated by spin-coating of [tantalum:(gadolinium/praseodymium)] and (praseodymium:cerium) organic compounds on silicon

NASA Astrophysics Data System (ADS)

Ohzone, Takashi; Matsuda, Toshihiro; Fukuoka, Ryouhei; Hattori, Fumihiro; Iwata, Hideyuki

2016-08-01

Blue/pink/purple electroluminescence (EL) from metal-oxide-semiconductor (MOS) devices with an indium tin oxide (ITO)/[Gd/(Ta + Gd/Pr)/(Pr + Ce)-Si-O] insulator layer/n+-Si substrate surface is reported. The insulator layers were fabricated from organic liquid sources of Gd or (Ta + Gd/Pr)/(Pr + Ce) mixtures, which were spin-coated on the n+-Si substrate and annealed at 950 °C for 30 min in air. The EL emission could be observed by the naked eye in the dark in the Fowler-Nordheim (FN) tunnel current regions. Peak wavelengths in the measured EL spectra were independent of the positive current. The EL intensity ratio of ultraviolet (UV) to the visible range varied with the composition ratio of the (Ta + Gd) liquids, and an optimum Ta to Gd ratio existed for the strongest blue emission, which could be attributed to the Ta-related oxide/silicate. The pink EL of the device fabricated with the (\\text{Ta}:\\text{Pr} = 6:4) mixture ratio can be explained by EL emission peaks related to the Pr3+ ions. The purple EL observed from the (\\text{Pr}:\\text{Ce} = 6:4) device corresponds to the strong and broad emission profile near the 357 nm peak, which cannot be assigned to Ce3+ ions. The results suggest that the EL can be attributed to the double-layer oxides with different compositions in the MOS devices. The upper layer consists of various Ta-, Gd-, Pr-, and Ce-related oxides and their silicates, while the lower SiO x -rich layer contributes to the FN current due to the high electric field, and thus the various EL colors.

Weak coordination as a powerful means for developing broadly useful C-H functionalization reactions.

PubMed

Engle, Keary M; Mei, Tian-Sheng; Wasa, Masayuki; Yu, Jin-Quan

2012-06-19

Reactions that convert carbon-hydrogen (C-H) bonds into carbon-carbon (C-C) or carbon-heteroatom (C-Y) bonds are attractive tools for organic chemists, potentially expediting the synthesis of target molecules through new disconnections in retrosynthetic analysis. Despite extensive inorganic and organometallic study of the insertion of homogeneous metal species into unactivated C-H bonds, practical applications of this technology in organic chemistry are still rare. Only in the past decade have metal-catalyzed C-H functionalization reactions become more widely utilized in organic synthesis. Research in the area of homogeneous transition metal-catalyzed C-H functionalization can be broadly grouped into two subfields. They reflect different approaches and goals and thus have different challenges and opportunities. One approach involves reactions of completely unfunctionalized aromatic and aliphatic hydrocarbons, which we refer to as "first functionalization". Here the substrates are nonpolar and hydrophobic and thus interact very weakly with polar metal species. To overcome this weak affinity and drive metal-mediated C-H cleavage, chemists often use hydrocarbon substrates in large excess (for example, as solvent). Because highly reactive metal species are needed in first functionalization, controlling the chemoselectivity to avoid overfunctionalization is often difficult. Additionally, because both substrates and products are comparatively low-value chemicals, developing cost-effective catalysts with exceptionally high turnover numbers that are competitive with alternatives (including heterogeneous catalysts) is challenging. Although an exciting field, first functionalization is beyond the scope of this Account. The second subfield of C-H functionalization involves substrates containing one or more pre-existing functional groups, termed "further functionalization". One advantage of this approach is that the existing functional group (or groups) can be used to chelate the metal catalyst and position it for selective C-H cleavage. Precoordination can overcome the paraffin nature of C-H bonds by increasing the effective concentration of the substrate so that it need not be used as solvent. From a synthetic perspective, it is desirable to use a functional group that is an intrinsic part of the substrate so that extra steps for installation and removal of an external directing group can be avoided. In this way, dramatic increases in molecular complexity can be accomplished in a single stroke through stereo- and site-selective introduction of a new functional group. Although reactivity is a major challenge (as with first functionalization), the philosophy in further functionalization differs; the major challenge is developing reactions that work with predictable selectivity in intricately functionalized contexts on commonly occurring structural motifs. In this Account, we focus on an emergent theme within the further functionalization literature: the use of commonly occurring functional groups to direct C-H cleavage through weak coordination. We discuss our motivation for studying Pd-catalyzed C-H functionalization assisted by weakly coordinating functional groups and chronicle our endeavors to bring reactions of this type to fruition. Through this approach, we have developed reactions with a diverse range of substrates and coupling partners, with the broad scope likely stemming from the high reactivity of the cyclopalladated intermediates, which are held together through weak interactions.

Weak Coordination as a Powerful Means for Developing Broadly Useful C–H Functionalization Reactions

PubMed Central

Engle, Keary M.; Mei, Tian-Sheng; Wasa, Masayuki

2011-01-01

Conspectus Reactions that convert carbon–hydrogen (C–H) bonds into carbon–carbon (C–C) or carbon–heteroatom (C–Y) bonds are attractive tools for organic chemists, potentially expediting the synthesis of target molecules through new disconnections in retrosynthetic analysis. Despite extensive inorganic and organometallic study of the insertion of homogeneous metal species into unactivated C–H bonds, practical applications of this technology in organic chemistry are still rare. Only in the past decade have metal-catalyzed C–H functionalization reactions become more widely utilized in organic synthesis. Research in the area of homogeneous transition metal–catalyzed C–H functionalization can be broadly grouped into two subfields. They reflect different approaches and goals and thus have different challenges and opportunities. One approach involves reactions of completely unfunctionalized aromatic and aliphatic hydrocarbons, which we refer to as “first functionalization.” Here the substrates are nonpolar and hydrophobic and thus interact very weakly with polar metal species. To overcome this weak affinity and drive metal-mediated C–H cleavage, chemists often use hydrocarbon substrates in large excess (for example, as solvent). Because highly reactive metal species are needed in first functionalization, controlling the chemoselectivity to avoid over-functionalization is often difficult. Additionally, because both substrates and products are comparatively low-value chemicals, developing cost-effective catalysts with exceptionally high turnover numbers that are competitive with alternatives (including heterogeneous catalysts) is challenging. Although an exciting field, first functionalization is beyond the scope of this Account. The second subfield of C–H functionalization involves substrates containing one or more pre-existing functional groups, termed “further functionalization.” One advantage of this approach is that the existing functional group (or groups) can be used to chelate the metal catalyst and position it for selective C–H cleavage. Precoordination can overcome the paraffin nature of C–H bonds by increasing the effective concentration of the substrate so that it needn't be used as solvent. From a synthetic perspective, it is desirable to use a functional group that is an intrinsic part of the substrate so that extra steps for installation and removal of an external directing group can be avoided. In this way, dramatic increases in molecular complexity can be accomplished in a single stroke through stereo- and site-selective introduction of a new functional group. Although reactivity is a major challenge (as with first functionalization), the philosophy in further functionalization differs—the major challenge is developing reactions that work with predictable selectivity in intricately functionalized contexts on commonly occurring structural motifs. In this Account, we focus on an emergent theme within the further functionalization literature: the use of commonly occurring functional groups to direct C–H cleavage through weak coordinations. We discuss our motivation for studying Pd-catalyzed C–H functionalization assisted by weakly coordinating functional groups and chronicle our endeavors to bring reactions of this type to fruition. Through this approach, we have developed reactions with a diverse range of substrates and coupling partners, with the broad scope likely stemming from higher reactivity of the less stable cyclopalladated intermediates held in place by weak coordinations. PMID:22166158

Substrate stiffness influences high resolution printing of living cells with an ink-jet system.

PubMed

Tirella, Annalisa; Vozzi, Federico; De Maria, Carmelo; Vozzi, Giovanni; Sandri, Tazio; Sassano, Duccio; Cognolato, Livio; Ahluwalia, Arti

2011-07-01

The adaptation of inkjet printing technology for the realisation of controlled micro- and nano-scaled biological structures is of great potential in tissue and biomaterial engineering. In this paper we present the Olivetti BioJet system and its applications in tissue engineering and cell printing. BioJet, which employs a thermal inkjet cartridge, was used to print biomolecules and living cells. It is well known that high stresses and forces are developed during the inkjet printing process. When printing living particles (i.e., cell suspensions) the mechanical loading profile can dramatically damage the processed cells. Therefore computational models were developed to predict the velocity profile and the mechanical load acting on a droplet during the printing process. The model was used to investigate the role of the stiffness of the deposition substrate during droplet impact and compared with experimental investigations on cell viability after printing on different materials. The computational model and the experimental results confirm that impact forces are highly dependent on the deposition substrate and that soft and viscous surfaces can reduce the forces acting on the droplet, preventing cell damage. These results have high relevance for cell bioprinting; substrates should be designed to have a good compromise between substrate stiffness to conserve spatial patterning without droplet coalescence but soft enough to absorb the kinetic energy of droplets in order to maintain cell viability. Copyright © 2011. Published by Elsevier B.V.

Kinetics and mechanism of hydration of o-thioquinone methide in aqueous solution. Rate-determining protonation of sulfur.

PubMed

Chiang, Yvonne; Kresge, A Jerry; Sadovski, Oleg; Zhan, Hao-Qiang

2005-03-04

o-Thioquinone methide, 2, was generated in aqueous solution by flash photolysis of benzothiete, 1, and rates of hydration of this quinone methide to o-mercaptobenzyl alcohol, 3, were measured in perchloric acid solutions, using H2O and D2O as the solvent, and also in acetic acid and tris(hydroxymethyl)methylammonium ion buffers, using H2O as the solvent. The rate profiles constructed from these data show hydronium-ion-catalyzed and uncatalyzed hydration reaction regions, just like the rate profiles based on literature data for hydration of the oxygen analogue, o-quinone methide, of the presently examined substrate. Solvent isotope effects on hydronium-ion catalysis of hydration for the two substrates, however, are quite different: k(H)/k(D) = 0.42 for the oxygen quinone methide, whereas k(H)/k(D) = 1.66 for the sulfur substrate. The inverse nature (k(H)/k(D) < 1) of the isotope effect in the oxygen system indicates that this reaction occurs by a preequilibrium proton-transfer reaction mechanism, with protonation of the substrate on its oxygen atom being fast and reversible and capture of the benzyl-type carbocationic intermediate so formed being rate-determining. The normal direction (k(H)/k(D) > 1) of the isotope effect in the sulfur system, on the other hand, suggests that protonation of the substrate on its sulfur atom is in this case rate-determining, with carbocation capture a fast following step. A semiquantitative argument supporting this hypothesis is presented.

Development of high poloidal beta, steady-state scenario with ITER-like tungsten divertor on EAST

NASA Astrophysics Data System (ADS)

Garofalo, A. M.; Gong, X. Z.; Qian, J.; Chen, J.; Li, G.; Li, K.; Li, M. H.; Zhai, X.; Bonoli, P.; Brower, D.; Cao, L.; Cui, L.; Ding, S.; Ding, W. X.; Guo, W.; Holcomb, C.; Huang, J.; Hyatt, A.; Lanctot, M.; Lao, L. L.; Liu, H.; Lyu, B.; McClenaghan, J.; Peysson, Y.; Ren, Q.; Shiraiwa, S.; Solomon, W.; Zang, Q.; Wan, B.

2017-07-01

Recent experiments on EAST have achieved the first long pulse H-mode (61 s) with zero loop voltage and an ITER-like tungsten divertor, and have demonstrated access to broad plasma current profiles by increasing the density in fully-noninductive lower hybrid current-driven discharges. These long pulse discharges reach wall thermal and particle balance, exhibit stationary good confinement (H 98y2 ~ 1.1) with low core electron transport, and are only possible with optimal active cooling of the tungsten armors. In separate experiments, the electron density was systematically varied in order to study its effect on the deposition profile of the external lower hybrid current drive (LHCD), while keeping the plasma in fully-noninductive conditions and with divertor strike points on the tungsten divertor. A broadening of the current profile is found, as indicated by lower values of the internal inductance at higher density. A broad current profile is attractive because, among other reasons, it enables internal transport barriers at large minor radius, leading to improved confinement as shown in companion DIII-D experiments. These experiments strengthen the physics basis for achieving high performance, steady state discharges in future burning plasmas.

Development of high poloidal beta, steady-state scenario with ITER-like tungsten divertor on EAST

DOE PAGES

Garofalo, Andrea M.; Gong, X. Z.; Qian, J.; ...

2017-06-07

Recent experiments on EAST have achieved the first long pulse H-mode (61 s) with zero loop voltage and an ITER-like tungsten divertor, and have demonstrated access to broad plasma current profiles by increasing the density in fully-noninductive lower hybrid current-driven discharges. These long pulse discharges reach wall thermal and particle balance, exhibit stationary good confinement (H 98y2~1.1) with low core electron transport, and are only possible with optimal active cooling of the tungsten armors. In separate experiments, the electron density was systematically varied in order to study its effect on the deposition profile of the external lower hybrid current drivemore » (LHCD), while keeping the plasma in fully-noninductive conditions and with divertor strike points on the tungsten divertor. A broadening of the current profile is found, as indicated by lower values of the internal inductance at higher density. A broad current profile is attractive because, among other reasons, it enables internal transport barriers at large minor radius, leading to improved confinement as shown in companion DIII-D experiments. These experiments strengthen the physics basis for achieving high performance, steady state discharges in future burning plasmas.« less

Experimental investigation and computational modeling of hot filament diamond chemical vapor deposition

NASA Astrophysics Data System (ADS)

Zumbach, Volker; Schäfer, Jörg; Tobai, Jens; Ridder, Michael; Dreier, Thomas; Schaich, Thomas; Wolfrum, Jürgen; Ruf, Bernhard; Behrendt, Frank; Deutschman, Olaf; Warnatz, Jürgen

1997-10-01

A joint investigation has been undertaken of the gas-phase chemistry taking place in a hot-filament chemical vapor-deposition (HFCVD) process for diamond synthesis on silica surfaces by a detailed comparison of numerical modeling and experimental results. Molecular beam sampling using quadrupole mass spectroscopy and resonance-enhanced multiphoton ionization time of flight mass spectroscopy (REMPI-TOF-MS) has been used to determine absolute concentrations of stable hydrocarbons and radicals. Resulting species of a CH4/H2, a CH4/D2 (both 0.5%/99.5%) and a C2H2/H2 (0.25%/99.75%) feedgas mixture were investigated for varying filament and substrate temperatures. Spatially resolved temperature profiles at various substrate temperatures, obtained from coherent anti-Stokes Raman spectroscopy (CARS) of hydrogen, are used as input parameters for the numerical code to reproduce hydrogen atom, methyl radical, methane, acetylene, and ethylene concentration profiles in the boundary layer of the substrate. In addition, the concentration of vibrationally excited hydrogen is determined by CARS. Results reveal only qualitative agreement between measured data and simulations, concerning concentrations of stable species and radicals probed near the surface, on filament and substrate temperature dependence, respectively. Hydrogen and deuterium experiments show similar behaviour for all species. In the case of CH4 as feedgas the model describes measured concentration profiles of CH3, CH4, and C2H2 qualitatively well. Large differences between model and experiment occur for hydrogen atoms (factor of 2) and C2H4 (factor of 3). For acetylene as feedgas the model is not able to give any predictions because no conversion of C2H2 is seen in the model in contrast to the experiment.

Substrate polarization in enzyme catalysis: QM/MM analysis of the effect of oxaloacetate polarization on acetyl-CoA enolization in citrate synthase.

PubMed

van der Kamp, Marc W; Perruccio, Francesca; Mulholland, Adrian J

2007-11-15

Citrate synthase is an archetypal carbon-carbon bond forming enzyme. It promotes the conversion of oxaloacetate (OAA) to citrate by catalyzing the deprotonation (enolization) of acetyl-CoA, followed by nucleophilic attack of the enolate form of this substrate on OAA to form a citryl-CoA intermediate and subsequent hydrolysis. OAA is strongly bound to the active site and its alpha-carbonyl group is polarized. This polarization has been demonstrated spectroscopically, [(Kurz et al., Biochemistry 1985;24:452-457; Kurz and Drysdale, Biochemistry 1987;26:2623-2627)] and has been suggested to be an important catalytic strategy. Substrate polarization is believed to be important in many enzymes. The first step, formation of the acetyl-CoA enolate intermediate, is thought to be rate-limiting in the mesophilic (pig/chicken) enzyme. We have examined the effects of substrate polarization on this key step using quantum mechanical/molecular mechanical (QM/MM) methods. Free energy profiles have been calculated by AM1/CHARMM27 umbrella sampling molecular dynamics (MD) simulations, together with potential energy profiles. To study the influence of OAA polarization, profiles were calculated with different polarization of the OAA alpha-carbonyl group. The results indicate that OAA polarization influences catalysis only marginally but has a larger effect on intermediate stabilization. Different levels of treatment of OAA are compared (MM or QM), and its polarization in the protein and in water analyzed at the B3LYP/6-31+G(d)/CHARMM27 level. Analysis of stabilization by individual residues shows that the enzyme mainly stabilizes the enolate intermediate (not the transition state) through electrostatic (including hydrogen bond) interactions: these contribute much more than polarization of OAA. (c) 2007 Wiley-Liss, Inc.

Differential Inhibition of Ex-Vivo Tumor Kinase Activity by Vemurafenib in BRAF(V600E) and BRAF Wild-Type Metastatic Malignant Melanoma

PubMed Central

Tahiri, Andliena; Røe, Kathrine; Ree, Anne H.; de Wijn, Rik; Risberg, Karianne; Busch, Christian; Lønning, Per E.; Kristensen, Vessela; Geisler, Jürgen

2013-01-01

Background Treatment of metastatic malignant melanoma patients harboring BRAF(V600E) has improved drastically after the discovery of the BRAF inhibitor, vemurafenib. However, drug resistance is a recurring problem, and prognoses are still very bad for patients harboring BRAF wild-type. Better markers for targeted therapy are therefore urgently needed. Methodology In this study, we assessed the individual kinase activity profiles in 26 tumor samples obtained from patients with metastatic malignant melanoma using peptide arrays with 144 kinase substrates. In addition, we studied the overall ex-vivo inhibitory effects of vemurafenib and sunitinib on kinase activity status. Results Overall kinase activity was significantly higher in lysates from melanoma tumors compared to normal skin tissue. Furthermore, ex-vivo incubation with both vemurafenib and sunitinib caused significant decrease in phosphorylation of kinase substrates, i.e kinase activity. While basal phosphorylation profiles were similar in BRAF wild-type and BRAF(V600E) tumors, analysis with ex-vivo vemurafenib treatment identified a subset of 40 kinase substrates showing stronger inhibition in BRAF(V600E) tumor lysates, distinguishing the BRAF wild-type and BRAF(V600E) tumors. Interestingly, a few BRAF wild-type tumors showed inhibition profiles similar to BRAF(V600E) tumors. The kinase inhibitory effect of vemurafenib was subsequently analyzed in cell lines harboring different BRAF mutational status with various vemurafenib sensitivity in-vitro. Conclusions Our findings suggest that multiplex kinase substrate array analysis give valuable information about overall tumor kinase activity. Furthermore, intra-assay exposure to kinase inhibiting drugs may provide a useful tool to study mechanisms of resistance, as well as to identify predictive markers. PMID:24023633

General method to evaluate substrate surface modification techniques for light extraction enhancement of organic light emitting diodes

NASA Astrophysics Data System (ADS)

Krummacher, B. C.; Mathai, M. K.; Choong, V.; Choulis, S. A.; So, F.; Winnacker, A.

2006-09-01

The external light output of organic light emitting diodes (OLEDs) can be increased by modifying the light emitting surface. The apparent light extraction enhancement is given by the ratio between the efficiency of the unmodified device and the efficiency of the modified device. This apparent light extraction enhancement is dependent on the OLED architecture itself and is not the correct value to judge the effectiveness of a technique to enhance light outcoupling due to substrate surface modification. We propose a general method to evaluate substrate surface modification techniques for light extraction enhancement of OLEDs independent from the device architecture. This method is experimentally demonstrated using green electrophosphorescent OLEDs with different device architectures. The substrate surface of these OLEDs was modified by applying a prismatic film to increase light outcoupling from the device stack. It was demonstrated that the conventionally measured apparent light extraction enhancement by means of the prismatic film does not reflect the actual performance of the light outcoupling technique. Rather, by comparing the light extracted out of the prismatic film to that generated in the OLED layers and coupled into the substrate (before the substrate/air interface), a more accurate evaluation of light outcoupling enhancement can be achieved. Furthermore we show that substrate surface modification can change the output spectrum of a broad band emitting OLED.

Large-scale uniform ZnO tetrapods on catalyst free glass substrate by thermal evaporation method

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

Alsultany, Forat H., E-mail: foratusm@gmail.com; Hassan, Z.; Ahmed, Naser M.

2016-07-15

Highlights: • Investigate the growth of ZnO-Ts on glass substrate by thermal evaporation method. • Glass substrate without any catalyst or a seed layer. • The morphology was controlled by adjusting the temperature of the material and the substrate. • Glass substrate was placed vertically in the quartz tube. - Abstract: Here, we report for the first time the catalyst-free growth of large-scale uniform shape and size ZnO tetrapods on a glass substrate via thermal evaporation method. Three-dimensional networks of ZnO tetrapods have needle–wire junctions, an average leg length of 2.1–2.6 μm, and a diameter of 35–240 nm. The morphologymore » and structure of ZnO tetrapods were investigated by controlling the preparation temperature of each of the Zn powder and the glass substrate under O{sub 2} and Ar gases. Studies were carried out on ZnO tetrapods using X-ray diffraction, field emission scanning electron microscopy, UV–vis spectrophotometer, and a photoluminescence. The results showed that the sample grow in the hexagonal wurtzite structure with preferentially oriented along (002) direction, good crystallinity and high transmittance. The band gap value is about 3.27 eV. Photoluminescence spectrum exhibits a very sharp peak at 378 nm and a weak broad green emission.« less

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

Barnes, Hannah C.; Zuluaga, Manuel D.; Houze, Robert A.

We report the Tropical Rainfall Measurement Mission's (TRMM) Spectral Latent Heating algorithm shows the contributions of different forms of convection to the latent heating profiles of the Madden-Julian Oscillation over the central Indian and West Pacific Oceans. In both oceanic regions, storms containing broad stratiform regions produce increased upper level heating during active Madden-Julian Oscillation (MJO) phases. The largest differences between the central Indian and West Pacific Ocean heating are associated with heating produced by convective elements. Examination of the most extreme forms of convection shows that mesoscale organized convection often produces at least as much latent heat as youngmore » vigorous deep convection. Heating from nonextreme (often midlevel-topped) convection is an important component of the MJO heating in both regions in all stages of the MJO. Over the central Indian Ocean the heating profile changes from having a maximum at 2 km due to nonextreme convection to a profile during the active stage that has two maxima: one at 3 km due to nonextreme convection and 6 km owing to numerous mature mesoscale storms with broad stratiform precipitation components. Lastly, over the West Pacific, the maxima at 3 and 6 km are present in all MJO stages, but the magnitude of the 6 km maximum sharply increases in the active MJO stage due to an increase in the number of storms with broad stratiform precipitation areas.« less

Latent heating characteristics of the MJO computed from TRMM Observations

DOE PAGES

Barnes, Hannah C.; Zuluaga, Manuel D.; Houze, Robert A.

2015-01-14

We report the Tropical Rainfall Measurement Mission's (TRMM) Spectral Latent Heating algorithm shows the contributions of different forms of convection to the latent heating profiles of the Madden-Julian Oscillation over the central Indian and West Pacific Oceans. In both oceanic regions, storms containing broad stratiform regions produce increased upper level heating during active Madden-Julian Oscillation (MJO) phases. The largest differences between the central Indian and West Pacific Ocean heating are associated with heating produced by convective elements. Examination of the most extreme forms of convection shows that mesoscale organized convection often produces at least as much latent heat as youngmore » vigorous deep convection. Heating from nonextreme (often midlevel-topped) convection is an important component of the MJO heating in both regions in all stages of the MJO. Over the central Indian Ocean the heating profile changes from having a maximum at 2 km due to nonextreme convection to a profile during the active stage that has two maxima: one at 3 km due to nonextreme convection and 6 km owing to numerous mature mesoscale storms with broad stratiform precipitation components. Lastly, over the West Pacific, the maxima at 3 and 6 km are present in all MJO stages, but the magnitude of the 6 km maximum sharply increases in the active MJO stage due to an increase in the number of storms with broad stratiform precipitation areas.« less

Fungal Diversity Is Not Determined by Mineral and Chemical Differences in Serpentine Substrates

PubMed Central

Daghino, Stefania; Murat, Claude; Sizzano, Elisa; Girlanda, Mariangela; Perotto, Silvia

2012-01-01

The physico-chemical properties of serpentine soils lead to strong selection of plant species. Whereas many studies have described the serpentine flora, little information is available on the fungal communities dwelling in these sites. Asbestos minerals, often associated with serpentine rocks, can be weathered by serpentine-isolated fungi, suggesting an adaptation to this substrate. In this study, we have investigated whether serpentine substrates characterized by the presence of rocks with distinct mineral composition could select for different fungal communities. Both fungal isolation and 454 pyrosequencing of amplicons obtained from serpentine samples following direct DNA extraction revealed some fungal taxa shared by the four ophiolitic substrates, but also highlighted several substrate-specific taxa. Bootstrap analysis of 454 OTU abundances indicated weak clustering of fungal assemblages from the different substrates, which did not match substrate classification based on exchangeable macronutrients and metals. Intra-substrate variability, as assessed by DGGE profiles, was similar across the four serpentine substrates, and comparable to inter-substrate variability. These findings indicate the absence of a correlation between the substrate (mineral composition and available cations) and the diversity of the fungal community. Comparison of culture-based and culture-independent methods supports the higher taxonomic precision of the former, as complementation of the better performance of the latter. PMID:23028507

Precise micropatterning of silver nanoparticles on plastic substrates

NASA Astrophysics Data System (ADS)

Ammosova, Lena; Jiang, Yu; Suvanto, Mika; Pakkanen, Tapani A.

2017-04-01

Conventional fabrication methods to obtain metal patterns on polymer substrates are restricted by high operating temperature and complex preparation steps. The present study demonstrates a simple yet versatile method for preparation of silver nanoparticle micropatterns on polymer substrates with various surface geometry. With the microworking robot technique, we were able not only to directly structure the surface, but also precisely deposit silver nanoparticle ink on the desired surface location with the minimum usage of ink material. The prepared silver nanoparticle ink, containing silver cations and polyethylene glycol (PEG) as a reducing agent, yields silver nanoparticle micropatterns on plastic substrates at low sintering temperature without any contamination. The influence of the ink behaviour was studied, such as substrate wettability, ink volume, and sintering temperature. The ultraviolet visible (UV-vis), scanning electron microscopy (SEM), and energy dispersive spectroscopy (EDS) measurements revealed the formation of micropatterns with uniformly distributed silver nanoparticles. The prepared patterns are expected to have a broad range of applications in optics, medicine, and sensor devices owing to the unique properties of silver. Furthermore, the deposition of a chemical compound, which is different from the substrate material, not only adds a fourth dimension to the prestructured three-dimensional (3D) surfaces, but also opens new application areas to the conventional surface structures.

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.

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

Designs and Materials for Better Coronagraph Occulting Masks

NASA Technical Reports Server (NTRS)

Balasubramanian, Kunjithapatham

2010-01-01

New designs, and materials appropriate for such designs, are under investigation in an effort to develop coronagraph occulting masks having broad-band spectral characteristics superior to those currently employed. These designs and materials are applicable to all coronagraphs, both ground-based and spaceborne. This effort also offers potential benefits for the development of other optical masks and filters that are required (1) for precisely tailored spatial transmission profiles, (2) to be characterized by optical-density neutrality and phase neutrality (that is, to be characterized by constant optical density and constant phase over broad wavelength ranges), and/or (3) not to exhibit optical- density-dependent phase shifts. The need for this effort arises for the following reasons: Coronagraph occulting masks are required to impose, on beams of light transmitted through them, extremely precise control of amplitude and phase according to carefully designed transmission profiles. In the original application that gave rise to this effort, the concern has been to develop broad-band occulting masks for NASA s Terrestrial Planet Finder coronagraph. Until now, experimental samples of these masks have been made from high-energy-beam-sensitive (HEBS) glass, which becomes locally dark where irradiated with a high-energy electron beam, the amount of darkening depending on the electron-beam energy and dose. Precise mask profiles have been written on HEBS glass blanks by use of electron beams, and the masks have performed satisfactorily in monochromatic light. However, the optical-density and phase profiles of the HEBS masks vary significantly with wavelength; consequently, the HEBS masks perform unsatisfactorily in broad-band light. The key properties of materials to be used in coronagraph occulting masks are their extinction coefficients, their indices of refraction, and the variations of these parameters with wavelength. The effort thus far has included theoretical predictions of performances of masks that would be made from alternative materials chosen because the wavelength dependences of their extinction coefficients and their indices of refraction are such that that the optical-density and phase profiles of masks made from these materials can be expected to vary much less with wavelength than do those of masks made from HEBS glass. The alternative materials considered thus far include some elemental metals such as Pt and Ni, metal alloys such as Inconel, metal nitrides such as TiN, and dielectrics such as SiO2. A mask as now envisioned would include thin metal and dielectric films having stepped or smoothly varying thicknesses (see figure). The thicknesses would be chosen, taking account of the indices of refraction and extinction coefficients, to obtain an acceptably close approximation of the desired spatial transmittance profile with a flat phase profile

Goddard High-Resolution Spectrograph Observations of Procyon and HR1099

NASA Technical Reports Server (NTRS)

Wood, Brian E.; Harper, Graham M.; Linsky, Jeffrey L.; Dempsey, Robert C.

1996-01-01

Goddard High Resolution Spectrograph (GHRS) observations have revealed the presence of broad wings in the transition-region lines of AU Mic and Capella. It has been proposed that these wings are signatures of microflares in the transition regions of these stars and that the solar analog for this phenomenon might be the 'transition region explosive events' discussed by Dere, Bartoe, & Brueckner. We have analyzed GHRS observations of Procyon (F5 IV-V) and HR 1099 (K1 IV + G5 IV) to search for broad wings in the UV emission lines of these stars. We find that the transition-region lines of HR 1099, which are emitted almost entirely by the K1 star, do indeed have broad wings that are even more prominent than those of AU Mic and Capella. This is consistent with the association of the broad wings with microflaring since HR 1099 is a very active binary system. In contrast, the transition-region lines of Procyon, a relatively inactive star, do not show evidence for broad wings, with the possible exception of N v lambda1239. However, Procyon's lines do appear to have excess emission in their blue wings. Linsky et al. found no evidence for broad wings in Capella's chromospheric lines, but we find that the Mg II resonance lines of HR 1099 do have broad wings. The striking resemblance between HR 1099's Mg II and C iv lines suggests that the Mg II line profiles may be regulated by turbulent processes similar to those that control the transition-region line profiles. If this is the case, microflaring may be occurring in the K1 star's chromosphere as well as in its transition region. However, radiative transfer calculations suggest that the broad wings of the Mg II lines can also result from normal chromospheric opacity effects rather than pure turbulence. The prominence of broad wings in the transition region and perhaps even chromospheric lines of active stars suggests that microflaring is very prevalent in the outer atmospheres of active stars.

Pharmaceutical-grade oral films as substrates for printed medicine.

PubMed

Wimmer-Teubenbacher, M; Planchette, C; Pichler, H; Markl, D; Hsiao, W K; Paudel, A; Stegemann, S

2018-05-18

In contact-less printing, such as piezo-electric drop on demand printing used in the study, the drop formation process is independent of the substrate. This means that having developed a printable formulation, printed pharmaceutical dosage forms can be obtained on any pharmaceutical grade substrate, such as polymer-based films. In this work we evaluated eight different oral films based on their suitability as printing substrates for sodium picosulfate. The different polymer films were compared regarding printed spot morphology, chemical stability and dissolution profile. The morphology of printed sodium picosulfate was investigated with scanning electron microscopy and optical coherence tomography. The spreading of the deposited drops was found to be governed by the contact angle of the ink with the substrate. The form of the sodium picosulfate drops changed on microcrystalline cellulose films at ambient conditions over 8 weeks and stayed unchanged on other tested substrates. Sodium picosulfate remained amorphous on all substrates according to small and wide angle X-ray scattering, differential scanning calorimetry and polarized light microscopy measurements. The absence of chemical interactions between the drug and substrates, as indicated by infrared spectroscopy, makes all tested substrates suitable for printing sodium picosulfate onto them. Copyright © 2018 Elsevier B.V. All rights reserved.

Copper-Catalyzed C(sp2)-S Coupling Reactions for the Synthesis of Aryl Dithiocarbamates with Thiuram Disulfide Reagents.

PubMed

Dong, Zhi-Bing; Liu, Xing; Bolm, Carsten

2017-11-03

An efficient protocol for the copper-catalyzed preparation of aryl dithiocarbamates from aryl iodides and inexpensive, environmentally benign tetraalkylthiuram disulfides was developed. The features of mild reaction conditions, high yields, and broad substrate scope render this new approach synthetically attractive for the preparation of potentially biologically active compounds.

DREW-UCLA Breast Cancer Research and Training Program: Molecular/Cellular Pathogenesis Model

DTIC Science & Technology

2007-03-01

system in bovine renal brush- border [13] and in a bovine renal epithelial cell line NBL -1 [14]. In order to highlight the substrate difference with an... NBL -1 expresses a broad specificity Na(+)-dependent neu- tral amino acid transport system (System B0) similar to that in bovine renal brush border

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

Friedmann, T.A.; Tallant, D.R.; Barbour, J.C.

Carbon Nitride (CN{sub x}) films have been grown by ion-assisted pulsed-laser deposition (IAPLD). Graphite targets were laser ablated while bombarding the substrate with ions from a broad-beam Kaufman-type ion source. Ion voltage, current density, substrate temperature, and feed gas composition (N{sub 2} in Ar) were varied. Resultant films were characterized by Raman. Fourier transform infrared (FTIR), and Rutherford back scattering (RBS) spectroscopy. Samples with {approximately} 30% N/C ratio have been fabricated. The corresponding Raman and FTIR spectra indicate that nitrogen is incorporated into the samples by insertion into sp{sup 2}-bonded structures. A low level of C{identical_to}N triple bonds is alsomore » found. As the ion current and voltage are increased with a pure Ar ion beam, Raman peaks associated with nanocrystalline graphite appear in the spectra. Adding low levels of nitrogen to the ion beam first reduces the Raman intensity in the vicinity of the graphite disorder peak without adding detectable amounts of nitrogen to the films (as measured by RBS). At higher nitrogen levels in the ion beam, significant amounts of nitrogen are incorporated into the samples, and the magnitude of the ``disorder`` peak increases. By increasing the temperature of the substrate during deposition, the broad peak due mainly to sp{sup 2}-bonded C-N in the FTIR spectra is shifted to lower wavenumber. This could be interpreted as evidence of single-bonded C-N; however, it is more likely that the character of the sp{sup 2} bonding is changing.« less

Quantification of Transporter and Receptor Proteins in Dog Brain Capillaries and Choroid Plexus: Relevance for the Distribution in Brain and CSF of Selected BCRP and P-gp Substrates.

PubMed

Braun, Clemens; Sakamoto, Atsushi; Fuchs, Holger; Ishiguro, Naoki; Suzuki, Shinobu; Cui, Yunhai; Klinder, Klaus; Watanabe, Michitoshi; Terasaki, Tetsuya; Sauer, Achim

2017-10-02

Transporters at the blood-brain barrier (BBB) and the blood-cerebrospinal fluid barrier (BCSFB) play a pivotal role as gatekeepers for efflux or uptake of endogenous and exogenous molecules. The protein expression of a number of them has already been determined in the brains of rodents, nonhuman primates, and humans using quantitative targeted absolute proteomics (QTAP). The dog is an important animal model for drug discovery and development, especially for safety evaluations. The purpose of the present study was to clarify the relevance of the transporter protein expression for drug distribution in the dog brain and CSF. We used QTAP to examine the protein expression of 17 selected transporters and receptors at the dog BBB and BCSFB. For the first time, we directly linked the expression of two efflux transporters, P-glycoprotein (P-gp) and breast cancer resistance protein (BCRP), to regional brain and CSF distribution using specific substrates. Two cocktails, each containing one P-gp substrate (quinidine or apafant) and one BCRP substrate (dantrolene or daidzein) were infused intravenously prior to collection of the brain. Transporter expression varied only slightly between the capillaries of different brain regions and did not result in region-specific distribution of the investigated substrates. There were, however, distinct differences between brain capillaries and choroid plexus. Largest differences were observed for BCRP and P-gp: both were highly expressed in brain capillaries, but no BCRP and only low amounts of P-gp were detected in the choroid plexus. K p,uu,brain and K p,uu,CSF of both P-gp substrates were indicative of drug efflux. Also, K p,uu,brain for the BCRP substrates was low. In contrast, K p,uu,CSF for both BCRP substrates was close to unity, resulting in K p,uu,CSF /K p,uu,brain ratios of 7 and 8, respectively. We conclude that the drug transporter expression profiles differ between the BBB and BCSFB in dogs, that there are species differences in the expression profiles, and that CSF is not a suitable surrogate for unbound brain concentrations of BCRP substrates in dogs.

Optimization of Cold Spray Deposition of High-Density Polyethylene Powders

NASA Astrophysics Data System (ADS)

Bush, Trenton B.; Khalkhali, Zahra; Champagne, Victor; Schmidt, David P.; Rothstein, Jonathan P.

2017-10-01

When a solid, ductile particle impacts a substrate at sufficient velocity, the resulting heat, pressure and plastic deformation can produce bonding between the particle and the substrate. The use of a cool supersonic gas flow to accelerate these solid particles is known as cold spray deposition. The cold spray process has been commercialized for some metallic materials, but further research is required to unlock the exciting potential material properties possible with polymeric particles. In this work, a combined computational and experimental study was employed to study the cold spray deposition of high-density polyethylene powders over a wide range of particle temperatures and impact velocities. Cold spray deposition of polyethylene powders was demonstrated across a range broad range of substrate materials including several different polymer substrates with different moduli, glass and aluminum. A material-dependent window of successful deposition was determined for each substrate as a function of particle temperature and impact velocity. Additionally, a study of deposition efficiency revealed the optimal process parameters for high-density polyethylene powder deposition which yielded a deposition efficiency close to 10% and provided insights into the physical mechanics responsible for bonding while highlighting paths toward future process improvements.

Comparative interactions of withanolides and sterols with two members of sterol glycosyltransferases from Withania somnifera.

PubMed

Pandey, Vibha; Dhar, Yogeshwar Vikram; Gupta, Parul; Bag, Sumit K; Atri, Neelam; Asif, Mehar Hasan; Trivedi, Prabodh Kumar; Misra, Pratibha

2015-04-16

Sterol glycosyltransferases (SGTs) are ubiquitous but one of the most diverse group of enzymes of glycosyltransferases family. Members of this family modulate physical and chemical properties of secondary plant products important for various physiological processes. The role of SGTs has been demonstrated in the biosynthesis of pharmaceutically important molecules of medicinal plants like Withania somnifera. Analysis suggested conserved behaviour and high similarity in active sites of WsSGTs with other plant GTs. Substrate specificity of WsSGTs were analysed through docking performance of WsSGTs with different substrates (sterols and withanolides). Best docking results of WsSGTL1 in the form of stable enzyme-substrate complex having lowest binding energies were obtained with brassicasterol, transandrosteron and WsSGTL4 with solasodine, stigmasterol and 24-methylene cholesterol. This study reveals topological characters and conserved nature of two SGTs from W. somnifera (WsSGTs) i.e. WsSGTL1 and WsSGTL4. However, besides being ubiquitous in nature and with broad substrate specificity, difference between WsSGTL1 and WsSGTL4 is briefly described by difference in stability (binding energy) of enzyme-substrate complexes through comparative docking.

Proteomic analysis reveals diverse proline hydroxylation-mediated oxygen-sensing cellular pathways in cancer cells

PubMed Central

Liu, Bing; Gao, Yankun; Ruan, Hai-Bin; Chen, Yue

2016-01-01

Proline hydroxylation is a critical cellular mechanism regulating oxygen-response pathways in tumor initiation and progression. Yet, its substrate diversity and functions remain largely unknown. Here, we report a system-wide analysis to characterize proline hydroxylation substrates in cancer cells using an immunoaffinity-purification assisted proteomics strategy. We identified 562 sites from 272 proteins in HeLa cells. Bioinformatic analysis revealed that proline hydroxylation substrates are significantly enriched with mRNA processing and stress-response cellular pathways with canonical and diverse flanking sequence motifs. Structural analysis indicates a significant enrichment of proline hydroxylation participating in the secondary structure of substrate proteins. Our study identified and validated Brd4, a key transcription factor, as a novel proline hydroxylation substrate. Functional analysis showed that the inhibition of proline hydroxylation pathway significantly reduced the proline hydroxylation abundance on Brd4 and affected Brd4-mediated transcriptional activity as well as cell proliferation in AML leukemia cells. Taken together, our study identified a broad regulatory role of proline hydroxylation in cellular oxygen-sensing pathways and revealed potentially new targets that dynamically respond to hypoxia microenvironment in tumor cells. PMID:27764789

A curious case of the accretion-powered X-ray pulsar GX 1+4

NASA Astrophysics Data System (ADS)

Jaisawal, Gaurava K.; Naik, Sachindra; Gupta, Shivangi; Chenevez, Jérôme; Epili, Prahlad

2018-07-01

We present detailed spectral and timing studies using a NuSTAR observation of GX 1+4 in 2015 October during an intermediate-intensity state. The measured spin period of 176.778 s is found to be one of the highest values since its discovery. In contrast to a broad sinusoidal-like pulse profile, a peculiar sharp peak is observed in profiles below ˜25 keV. The profiles at higher energies are found to be significantly phase shifted compared to the soft X-ray profiles. Broad-band energy spectra of GX 1+4, obtained from NuSTAR and Swift observations, are described with various continuum models. Among these, a two-component model consisting of a bremsstrahlung and a blackbody component is found to best fit the phase-averaged and phase-resolved spectra. Physical models are also used to investigate the emission mechanism in the pulsar, which allows us to estimate the magnetic field strength to be in ˜(5-10) × 1012 G range. Phase-resolved spectroscopy of NuSTAR observation shows a strong blackbody emission component in a narrow pulse phase range. This component is interpreted as the origin of the peculiar peak in the pulse profiles below ≤25 keV. The size of emitting region is calculated to be ˜400 m. The bremsstrahlung component is found to dominate in hard X-rays and explains the nature of simple profiles at high energies.

Tribological characteristics of gold films deposited on metals by ion plating and vapor deposition

NASA Technical Reports Server (NTRS)

Miyoshi, K.; Spalvins, T.; Buckley, D. H.

1984-01-01

The graded interface between an ion-plated film and a substrate is discussed as well as the friction and wear properties of ion-plated gold. X-ray photoelectron spectroscopy (XPS) depth profiling and microhardness depth profiling were used to investigate the interface. The friction and wear properties of ion-plated and vapor-deposited gold films were studied both in an ultra high vacuum system to maximize adhesion and in oil to minimize adhesion. The results indicate that the solubility of gold on the substrate material controls the depth of the graded interface. Thermal diffusion and chemical diffusion mechanisms are thought to be involved in the formation of the gold-nickel interface. In iron-gold graded interfaces the gold was primarily dispersed in the iron and thus formed a physically bonded interface. The hardness of the gold film was influenced by its depth and was also related to the composition gradient between the gold and the substrate. The graded nickel-gold interface exhibited the highest hardness because of an alloy hardening effect. The effects of film thickness on adhesion and friction were established.

Tribological characteristics of gold films deposited on metals by ion plating and vapor deposition

NASA Technical Reports Server (NTRS)

Miyoshi, K.; Spalvins, T.; Buckley, D. H.

1986-01-01

The graded interface between an ion-plated film and a substrate is discussed as well as the friction and wear properties of ion-plated gold. X-ray photoelectron spectroscopy (XPS) depth profiling and microhardness depth profiling were used to investigate the interface. The friction and wear properties of ion-plated and vapor-deposited gold films were studied both in an ultra high vacuum system to maximize adhesion and in oil to minimize adhesion. The results indicate that the solubility of gold on the substrate material controls the depth of the graded interface. Thermal diffusion and chemical diffusion mechanisms are thought to be involved in the formation of the gold-nickel interface. In iron-gold graded interfaces the gold was primarily dispersed in the iron and thus formed a physically bonded interface. The hardness of the gold film was influenced by its depth and was also related to the composition gradient between the gold and the substrate. The graded nickel-gold interface exhibited the highest hardness because of an alloy hardening effect. The effects of film thickness on adhesion and friction were established.

The influence of different heat sources on temperature distributions in broad-area diode lasers

NASA Astrophysics Data System (ADS)

Szymanski, Michal; Zbroszczyk, Mariusz; Mroziewicz, Bohdan

2004-09-01

Deep insight into thermal effects in the broad-area lasers is the main condition of obtaining the improved devices. We present the analytical solution of the two-dimensional, stationary heat conduction equation yielding the temperature profile in the laser cross-section in plane parallel to the mirrors. Our approach allows for considering various heating mechanisms and assessing their contribution to the total temperature of the device.

Computational imaging of defects in commercial substrates for electronic and photonic devices

NASA Astrophysics Data System (ADS)

Fukuzawa, Masayuki; Kashiwagi, Ryo; Yamada, Masayoshi

2012-03-01

Computational defect imaging has been performed in commercial substrates for electronic and photonic devices by combining the transmission profile acquired with an imaging type of linear polariscope and the computational algorithm to extract a small amount of birefringence. The computational images of phase retardation δ exhibited spatial inhomogeneity of defect-induced birefringence in GaP, LiNbO3, and SiC substrates, which were not detected by conventional 'visual inspection' based on simple optical refraction or transmission because of poor sensitivity. The typical imaging time was less than 30 seconds for 3-inch diameter substrate with the spatial resolution of 200 μm, while that by scanning polariscope was 2 hours to get the same spatial resolution. Since our proposed technique have been achieved high sensitivity, short imaging time, and wide coverage of substrate materials, which are practical advantages over the laboratory-scale apparatus such as X-ray topography and electron microscope, it is useful for nondestructive inspection of various commercial substrates in production of electronic and photonic devices.

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.

Unnatural amino acids increase sensitivity and provide for the design of highly selective caspase substrates

PubMed Central

Poreba, M; Kasperkiewicz, P; Snipas, S J; Fasci, D; Salvesen, G S; Drag, M

2014-01-01

Traditional combinatorial peptidyl substrate library approaches generally utilize natural amino acids, limiting the usefulness of this tool in generating selective substrates for proteases that share similar substrate specificity profiles. To address this limitation, we synthesized a Hybrid Combinatorial Substrate Library (HyCoSuL) with the general formula of Ac-P4-P3-P2-Asp-ACC, testing the approach on a family of closely related proteases – the human caspases. The power of this library for caspase discrimination extends far beyond traditional PS-SCL approach, as in addition to 19 natural amino acids we also used 110 diverse unnatural amino acids that can more extensively explore the chemical space represented by caspase-active sites. Using this approach we identified and employed peptide-based substrates that provided excellent discrimination between individual caspases, allowing us to simultaneously resolve the individual contribution of the apical caspase-9 and the executioner caspase-3 and caspase-7 in the development of cytochrome-c-dependent apoptosis for the first time. PMID:24832467

Effects of MAR-M247 substrate (modified) composition on coating oxidation coating/substrate interdiffusion. M.S. Thesis. Final Report; [protective coatings for hot section components of gas turbine engines

NASA Technical Reports Server (NTRS)

Pilsner, B. H.

1985-01-01

The effects of gamma+gamma' Mar-M247 substrate composition on gamma+beta Ni-Cr-Al-Zr coating oxidation and coating/substrate interdiffusion were evaluated. These results were also compared to a prior study for a Ni-Cr-Al-Zr coated gamma Ni-Cr-Al substrate with equivalent Al and Cr atomic percentages. Cyclic oxidation behavior at 1130 C was investigated using change in weight curves. Concentration/distance profiles were measured for Al, Cr, Co, W, and Ta. The surface oxides were examined by X-ray diffraction and scanning electron microscopy. The results indicate that variations of Ta and C concentrations in the substrate do not affect oxidation resistance, while additions of grain boundary strengthening elements (Zr, Hf, B) increase oxidation resistance. In addition, the results indicate that oxidation phenomena in gamma+beta/gamma+gamma' Mar-M247 systems have similar characteristics to the l gamma+beta/gamma Ni-Cr-Al system.

The origin of the residual conductivity of GaN films on ferroelectric materials

NASA Astrophysics Data System (ADS)

Lee, Kyoung-Keun; Cai, Zhuhua; Ziemer, Katherine; Doolittle, William Alan

2009-08-01

In this paper, the origin of the conductivity of GaN films grown on ferroelectric materials was investigated using XPS, AES, and XRD analysis tools. Depth profiles confirmed the existence of impurities in the GaN film originating from the substrates. Bonding energy analysis from XPS and AES verified that oxygen impurities from the substrates were the dominant origin of the conductivity of the GaN film. Furthermore, Ga-rich GaN films have a greater chance of enhancing diffusion of lithium oxide from the substrates, resulting in more substrate phase separation and a wider inter-mixed region confirmed by XRD. Therefore, the direct GaN film growth on ferroelectric materials causes impurity diffusion from the substrates, resulting in highly conductive GaN films. Future work needs to develop non-conductive buffer layers for impurity suppression in order to obtain highly resistive GaN films.

Numerical simulations of sessile droplet evaporating on heated substrate

NASA Astrophysics Data System (ADS)

Chen, Xue; Chen, Paul G.; Ouazzani, Jalil; Liu, Qiusheng

2017-04-01

Motivated by the space project EFILE, a 2D axisymmetric numerical model in the framework of ALE method is developed to investigate the coupled physical mechanism during the evaporation of a pinned drop that partially wets on a heated substrate. The model accounts for mass transport in surrounding air, Marangoni convection inside the drop and heat conduction in the substrate as well as moving interface. Numerical results predict simple scaling laws for the evaporation rate which scales linearly with drop radius but follows a power-law with substrate temperature. It is highlighted that thermal effect of the substrate has a great impact on the temperature profile at the drop surface, which leads to a multicellular thermocapillary flow pattern. In particular, the structure of the multicellular flow behavior induced within a heated drop is mainly controlled by a geometric parameter (aspect ratio). A relationship between the number of thermal cells and the aspect ratio is proposed.

Fluorogenic kinetic assay for high-throughput discovery of stereoselective ketoreductases relevant to pharmaceutical synthesis.

PubMed

Thai, Yen-Chi; Szekrenyi, Anna; Qi, Yuyin; Black, Gary W; Charnock, Simon J; Fessner, Wolf-Dieter

2018-04-01

Enantiomerically pure 1-(6-methoxynaphth-2-yl) and 1-(6-(dimethylamino)naphth-2-yl) carbinols are fluorogenic substrates for aldo/keto reductase (KRED) enzymes, which allow the highly sensitive and reliable determination of activity and kinetic constants of known and unknown enzymes, as well as an immediate enantioselectivity typing. Because of its simplicity in microtiter plate format, the assay qualifies for the discovery of novel KREDs of yet unknown specificity among this vast enzyme superfamily. The suitability of this approach for enzyme typing is illustrated by an exemplary screening of a large collection of short-chain dehydrogenase/reductase (SDR) enzymes arrayed from a metagenomic approach. We believe that this assay format should match well the pharmaceutical industry's demand for acetophenone-type substrates and the continuing interest in new enzymes with broad substrate promiscuity for the synthesis of chiral, non-racemic carbinols. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Patterned microstructures formed with MeV Au implantation in Si(1 0 0)

NASA Astrophysics Data System (ADS)

Rout, Bibhudutta; Greco, Richard R.; Zachry, Daniel P.; Dymnikov, Alexander D.; Glass, Gary A.

2006-09-01

Energetic (MeV) Au implantation in Si(1 0 0) (n-type) through masked micropatterns has been used to create layers resistant to KOH wet etching. Microscale patterns were produced in PMMA and SU(8) resist coatings on the silicon substrates using P-beam writing and developed. The silicon substrates were subsequently exposed using 1.5 MeV Au 3+ ions with fluences as high as 1 × 10 16 ions/cm 2 and additional patterns were exposed using copper scanning electron microscope calibration grids as masks on the silicon substrates. When wet etched with KOH microstructures were created in the silicon due to the resistance to KOH etching cause by the Au implantation. The process of combining the fabrication of masked patterns with P-beam writing with broad beam Au implantation through the masks can be a promising, cost-effective process for nanostructure engineering with Si.

Adhesion of Antireflective Coatings in Multijunction Photovoltaics

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

Brock, Ryan; Miller, David C.; Dauskardt, Reinhold H.

2016-11-21

The development of a new composite dual cantilever beam (cDCB) thin-film adhesion testing method is reported, which allows the measurement of adhesion on the fragile thin substrates used in multijunction photovoltaics. We address the adhesion of several antireflective coating systems on multijunction cells. By varying interface chemistry and morphology, we demonstrate the ensuing effects on adhesion and help to develop an understanding of how high adhesion can be achieved, as adhesion values ranging from 0.5 J/m2 to 10 J/m2 were measured. Damp Heat (85 degrees C/85% RH) was used to invoke degradation of interfacial adhesion. We show that even withmore » germanium substrates that fracture easily, quantitative measurements of adhesion can still be made at high test yield. The cDCB test is discussed as an important new methodology, which can be broadly applied to any system that makes use of thin, brittle, or otherwise fragile substrates.« less

Adhesion of Antireflective Coatings in Multijunction Photovoltaics: Preprint

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

Brock, Ryan; Dauskardt, Reinhold H.; Miller, David C.

2016-06-16

The development of a new composite dual cantilever beam (cDCB) thin-film adhesion testing method is reported, which allows the measurement of adhesion on the fragile thin substrates used in multijunction photovoltaics. We address the adhesion of several antireflective coating systems on multijunction cells. By varying interface chemistry and morphology, we demonstrate the ensuing effects on adhesion and help to develop an understanding of how high adhesion can be achieved, as adhesion values ranging from 0.5 J/m2 to 10 J/m2 were measured. Damp Heat (85 degrees C/85% RH) was used to invoke degradation of interfacial adhesion. We show that even withmore » germanium substrates that fracture easily, quantitative measurements of adhesion can still be made at high test yield. The cDCB test is discussed as an important new methodology, which can be broadly applied to any system that makes use of thin, brittle, or otherwise fragile substrates.« less

Broadband omnidirectional antireflection coating based on subwavelength surface Mie resonators

PubMed Central

Spinelli, P.; Verschuuren, M.A.; Polman, A.

2012-01-01

Reflection is a natural phenomenon that occurs when light passes the interface between materials with different refractive index. In many applications, such as solar cells or photodetectors, reflection is an unwanted loss process. Many ways to reduce reflection from a substrate have been investigated so far, including dielectric interference coatings, surface texturing, adiabatic index matching and scattering from plasmonic nanoparticles. Here we present an entirely new concept that suppresses the reflection of light from a silicon surface over a broad spectral range. A two-dimensional periodic array of subwavelength silicon nanocylinders designed to possess strongly substrate-coupled Mie resonances yields almost zero total reflectance over the entire spectral range from the ultraviolet to the near-infrared. This new antireflection concept relies on the strong forward scattering that occurs when a scattering structure is placed in close proximity to a high-index substrate with a high optical density of states. PMID:22353722

A robotics platform for automated batch fabrication of high density, microfluidics-based DNA microarrays, with applications to single cell, multiplex assays of secreted proteins

NASA Astrophysics Data System (ADS)

Ahmad, Habib; Sutherland, Alex; Shin, Young Shik; Hwang, Kiwook; Qin, Lidong; Krom, Russell-John; Heath, James R.

2011-09-01

Microfluidics flow-patterning has been utilized for the construction of chip-scale miniaturized DNA and protein barcode arrays. Such arrays have been used for specific clinical and fundamental investigations in which many proteins are assayed from single cells or other small sample sizes. However, flow-patterned arrays are hand-prepared, and so are impractical for broad applications. We describe an integrated robotics/microfluidics platform for the automated preparation of such arrays, and we apply it to the batch fabrication of up to eighteen chips of flow-patterned DNA barcodes. The resulting substrates are comparable in quality with hand-made arrays and exhibit excellent substrate-to-substrate consistency. We demonstrate the utility and reproducibility of robotics-patterned barcodes by utilizing two flow-patterned chips for highly parallel assays of a panel of secreted proteins from single macrophage cells.

A robotics platform for automated batch fabrication of high density, microfluidics-based DNA microarrays, with applications to single cell, multiplex assays of secreted proteins

PubMed Central

Ahmad, Habib; Sutherland, Alex; Shin, Young Shik; Hwang, Kiwook; Qin, Lidong; Krom, Russell-John; Heath, James R.

2011-01-01

Microfluidics flow-patterning has been utilized for the construction of chip-scale miniaturized DNA and protein barcode arrays. Such arrays have been used for specific clinical and fundamental investigations in which many proteins are assayed from single cells or other small sample sizes. However, flow-patterned arrays are hand-prepared, and so are impractical for broad applications. We describe an integrated robotics/microfluidics platform for the automated preparation of such arrays, and we apply it to the batch fabrication of up to eighteen chips of flow-patterned DNA barcodes. The resulting substrates are comparable in quality with hand-made arrays and exhibit excellent substrate-to-substrate consistency. We demonstrate the utility and reproducibility of robotics-patterned barcodes by utilizing two flow-patterned chips for highly parallel assays of a panel of secreted proteins from single macrophage cells. PMID:21974603

A robotics platform for automated batch fabrication of high density, microfluidics-based DNA microarrays, with applications to single cell, multiplex assays of secreted proteins.

PubMed

Ahmad, Habib; Sutherland, Alex; Shin, Young Shik; Hwang, Kiwook; Qin, Lidong; Krom, Russell-John; Heath, James R

2011-09-01

Microfluidics flow-patterning has been utilized for the construction of chip-scale miniaturized DNA and protein barcode arrays. Such arrays have been used for specific clinical and fundamental investigations in which many proteins are assayed from single cells or other small sample sizes. However, flow-patterned arrays are hand-prepared, and so are impractical for broad applications. We describe an integrated robotics/microfluidics platform for the automated preparation of such arrays, and we apply it to the batch fabrication of up to eighteen chips of flow-patterned DNA barcodes. The resulting substrates are comparable in quality with hand-made arrays and exhibit excellent substrate-to-substrate consistency. We demonstrate the utility and reproducibility of robotics-patterned barcodes by utilizing two flow-patterned chips for highly parallel assays of a panel of secreted proteins from single macrophage cells. © 2011 American Institute of Physics

Revisiting inconsistency in large pharmacogenomic studies

PubMed Central

Safikhani, Zhaleh; Smirnov, Petr; Freeman, Mark; El-Hachem, Nehme; She, Adrian; Rene, Quevedo; Goldenberg, Anna; Birkbak, Nicolai J.; Hatzis, Christos; Shi, Leming; Beck, Andrew H.; Aerts, Hugo J.W.L.; Quackenbush, John; Haibe-Kains, Benjamin

2017-01-01

In 2013, we published a comparative analysis of mutation and gene expression profiles and drug sensitivity measurements for 15 drugs characterized in the 471 cancer cell lines screened in the Genomics of Drug Sensitivity in Cancer (GDSC) and Cancer Cell Line Encyclopedia (CCLE). While we found good concordance in gene expression profiles, there was substantial inconsistency in the drug responses reported by the GDSC and CCLE projects. We received extensive feedback on the comparisons that we performed. This feedback, along with the release of new data, prompted us to revisit our initial analysis. We present a new analysis using these expanded data, where we address the most significant suggestions for improvements on our published analysis — that targeted therapies and broad cytotoxic drugs should have been treated differently in assessing consistency, that consistency of both molecular profiles and drug sensitivity measurements should be compared across cell lines, and that the software analysis tools provided should have been easier to run, particularly as the GDSC and CCLE released additional data. Our re-analysis supports our previous finding that gene expression data are significantly more consistent than drug sensitivity measurements. Using new statistics to assess data consistency allowed identification of two broad effect drugs and three targeted drugs with moderate to good consistency in drug sensitivity data between GDSC and CCLE. For three other targeted drugs, there were not enough sensitive cell lines to assess the consistency of the pharmacological profiles. We found evidence of inconsistencies in pharmacological phenotypes for the remaining eight drugs. Overall, our findings suggest that the drug sensitivity data in GDSC and CCLE continue to present challenges for robust biomarker discovery. This re-analysis provides additional support for the argument that experimental standardization and validation of pharmacogenomic response will be necessary to advance the broad use of large pharmacogenomic screens. PMID:28928933

Comparing the Broad Socio-Cognitive Profile of Youth with Williams Syndrome and 22Q11.2 Deletion Syndrome

ERIC Educational Resources Information Center

Weisman, O.; Feldman, R.; Burg-Malki, M.; Keren, M.; Geva, R.; Diesendruck, G.; Gothelf, D.

2017-01-01

Background: Numerous studies have assessed the socio-cognitive profile in Williams syndrome (WS) and, independently, in 22q11.2 deletion syndrome (22q11.2DS). Yet, a cross-syndrome comparison of these abilities between individuals with these two syndromes with known social deficits has not been conducted. Methods: Eighty-two children participated…

Retrieval and characterization of ozone profiles from solar infrared spectra at the Jungfraujoch

NASA Astrophysics Data System (ADS)

Barret, B.; de MazièRe, M.; Demoulin, P.

2002-12-01

Vertical distributions of ozone from June 1996 to November 2000 have been retrieved from high-resolution Fourier transform infrared (FTIR) solar absorption spectra recorded at the primary Network for Detection of Stratospheric Change station of the Jungfraujoch in the Swiss Alps (46.5°N, 8°E, 3580 m above sea level (asl). The retrievals were performed using the Optimal Estimation Method (OEM), both in a narrow spectral interval (1002.567-1003.2 cm-1) and in a broad spectral interval (1000.0-1005.0 cm-1) in the O3 9.6-μm band. A thorough characterization of the retrievals has been performed following the lines of OEM, including an information content analysis, a study of the correlations between retrieved instrumental parameters and retrieved ozone concentrations, and an evaluation of the O3 profile error budget. It is demonstrated that the information content is significantly higher for spectra in the broad microwindow, resulting in higher vertical resolutions, on the order of 8 km, of the retrieved profiles extending up to 40 km, and less correlations between retrieved parameters. An independent statistical verification of the retrieval results and their characterization has been performed by comparison of the FTIR ozone profiles with independent measurements. These are the ozone profile measurements from balloon soundings at Payerne, from the microwave radiometer at Bern and the lidar at Observatoire de Haute-Provence (OHP), and the total column data from the Dobson spectrophotometer at Arosa. Applying the optimum retrieval procedure in the broad spectral interval, an excellent agreement has been found between the FTIR O3 profile data and the correlative data. The largest offset of the FTIR data in comparison with the correlative data is found with respect to the lidar data in the 24- to 40-km layer, and is on the order of 5%. No systematic biases have been found in the troposphere, neither in the upper troposphere-lower stratosphere (UTLS) up to 18 km. The dispersion of the relative differences between the data sets, if any, is never larger than half of the natural ozone variability.

Integrated Lens Antennas for Multi-Pixel Receivers

NASA Technical Reports Server (NTRS)

Lee, Choonsup; Chattopadhyay, Goutam

2011-01-01

Future astrophysics and planetary experiments are expected to require large focal plane arrays with thousands of detectors. Feedhorns have excellent performance, but their mass, size, fabrication challenges, and expense become prohibitive for very large focal plane arrays. Most planar antenna designs produce broad beam patterns, and therefore require additional elements for efficient coupling to the telescope optics, such as substrate lenses or micromachined horns. An antenna array with integrated silicon microlenses that can be fabricated photolithographically effectively addresses these issues. This approach eliminates manual assembly of arrays of lenses and reduces assembly errors and tolerances. Moreover, an antenna array without metallic horns will reduce mass of any planetary instrument significantly. The design has a monolithic array of lens-coupled, leaky-wave antennas operating in the millimeter- and submillimeter-wave frequencies. Electromagnetic simulations show that the electromagnetic fields in such lens-coupled antennas are mostly confined in approximately 12 15 . This means that one needs to design a small-angle sector lens that is much easier to fabricate using standard lithographic techniques, instead of a full hyper-hemispherical lens. Moreover, this small-angle sector lens can be easily integrated with the antennas in an array for multi-pixel imager and receiver implementation. The leaky antenna is designed using double-slot irises and fed with TE10 waveguide mode. The lens implementation starts with a silicon substrate. Photoresist with appropriate thickness (optimized for the lens size) is spun on the substrate and then reflowed to get the desired lens structure. An antenna array integrated with individual lenses for higher directivity and excellent beam profile will go a long way in realizing multi-pixel arrays and imagers. This technology will enable a new generation of compact, low-mass, and highly efficient antenna arrays for use in multi-pixel receivers and imagers for future planetary and astronomical instruments. These antenna arrays can also be used in radars and imagers for contraband detection at stand-off distances. This will be enabling technology for future balloon-borne, smaller explorer class mission (SMEX), and other missions, and for a wide range of proposed planetary sounders and radars for planetary bodies.

Cloning and Characterization of Unusual Fatty Acid Desaturases from Anemone leveillei: Identification of an Acyl-Coenzyme A C20 Δ5-Desaturase Responsible for the Synthesis of Sciadonic Acid1

PubMed Central

Sayanova, Olga; Haslam, Richard; Venegas Caleron, Monica; Napier, Johnathan A.

2007-01-01

The seed oil of Anemone leveillei contains significant amounts of sciadonic acid (20:3Δ5,11,14; SA), an unusual non-methylene-interrupted fatty acid with pharmaceutical potential similar to arachidonic acid. Two candidate cDNAs (AL10 and AL21) for the C20 Δ5cis-desaturase from developing seeds of A. leveillei were functionally characterized in transgenic Arabidopsis (Arabidopsis thaliana) plants. The open reading frames of both Δ5-desaturases showed some similarity to presumptive acyl-coenzyme A (CoA) desaturases found in animals and plants. When expressed in transgenic Arabidopsis, AL21 showed a broad range of substrate specificity, utilizing both saturated (16:0 and 18:0) and unsaturated (18:2, n-6 and 18:3, n-3) substrates. In contrast, AL10 did not show any activity in wild-type Arabidopsis. Coexpression of AL10 or AL21 with a C18 Δ9-elongase in transgenic Arabidopsis plants resulted in the production of SA and juniperonic fatty acid (20:4Δ5,11,14,17). Thus, AL10 acted only on C20 polyunsaturated fatty acids in a manner analogous to “front-end” desaturases. However, neither AL10 nor AL21 contain the cytochrome b5 domain normally present in this class of enzymes. Acyl-CoA profiling of transgenic Arabidopsis plants and developing A. leveillei seeds revealed significant accumulation of Δ5-unsaturated fatty acids as acyl-CoAs compared to the accumulation of these fatty acids in total lipids. Positional analysis of triacylglycerols of A. leveillei seeds showed that Δ5-desaturated fatty acids were present in both sn-2 and sn-1 + sn-3 positions, although the majority of 16:1Δ5, 18:1Δ5, and SA was present at the sn-2 position. Our data provide biochemical evidence for the A. leveillei Δ5-desaturases using acyl-CoA substrates. PMID:17384161

Substrate optimization and clinical validation of reporter peptides for MS-based protease profiling in serum specimens: a new approach for diagnosis of malignant disease.

PubMed

Yepes, Diego; Jacob, Anette; Dauber, Marc; Costina, Victor; Hofheinz, Ralf; Neumaier, Michael; Findeisen, Peter

2011-07-01

The progression of many solid tumors is characterized by the release of tumor-associated proteases, such as cancer procoagulant, MMP2 and MMP7. Consequently, the detection of tumor-specific proteolytic activity in serum specimens has recently been proposed as a new diagnostic tool in oncology. However, tumor-associated proteases are highly diluted in serum specimens and it is challenging to identify substrates that are specifically cleaved. In this study, we describe the systematic optimization of a synthetic peptide substrate using a positional scanning synthetic combinatorial library (PS-SCL) approach. The initial reporter peptide (RP) comprises of the cleavage site, WKPYDAAD, that is part of the coagulation factor X, the natural substrate of the tumor-associated cysteine protease cancer procoagulant (EC 3.4.22.26). Specifically, the amino acid substitution of aspartatic acid (D) in position P1' against asparagine (N) improved the processing of respective RPs in serum specimens from patients with colorectal tumors compared to healthy controls. Proteolytic fragments of RPs accumulated during prolonged incubation with serum specimens and were quantified with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Finally, the optimized RP with the cleaved motif WKPYNAAD was combined with the RPs, VPLSLTMG and IPVSLRSG, that were cleaved by the tumor-associated proteases, MMP2 and MMP7, respectively. The diagnostic accuracy of MS-based protease profiling was evaluated for this triplex RP mix in a cohort of 50 serum specimens equally divided into colorectal cancer patients and healthy control individuals. Multiparametric analysis showed an AUC value of 0.90 for the receiver operating characteristic curve and was superior to the classification accuracy of the single markers. Our results demonstrate that RPs for MS-based protease profiling can systematically be optimized with a PS-SCL. Furthermore, the combination of different RPs can additionally increase the classification accuracy of functional protease profiling, and this in turn could lead to improved diagnosis, monitoring and prognosis of malignant disease.

Broad H3K4me3 is associated with increased transcription elongation and enhancer activity at tumor suppressor genes

PubMed Central

Chen, Kaifu; Chen, Zhong; Wu, Dayong; Zhang, Lili; Lin, Xueqiu; Su, Jianzhong; Rodriguez, Benjamin; Xi, Yuanxin; Xia, Zheng; Chen, Xi; Shi, Xiaobing; Wang, Qianben; Li, Wei

2016-01-01

Tumor suppressors are mostly defined by inactivating mutations in tumors, yet little is known about their epigenetic features in normal cells. Through integrative analysis of 1,134 genome-wide epigenetic profiles, mutations from >8,200 tumor-normal pairs, and our experimental data from clinical samples, we discovered broad H3K4me3 (wider than 4 kb) as the first epigenetic signature for tumor suppressors in normal cells. Broad H3K4me3 is associated with increased transcription elongation and enhancer activity together leading to exceptionally high gene expression, and is distinct from other broad epigenetic features, such as super-enhancers. Broad H3K4me3 conserved across normal cells may represent pan-cancer tumor suppressors, such as P53 and PTEN, whereas cell-type-specific broad H3K4me3 may indicate cell-identity genes and cell-type-specific tumor suppressors. Furthermore, widespread shortening of broad H3K4me3 in cancers is associated with repression of tumor suppressors. Together, the broad H3K4me3 epigenetic signature provides mutation-independent information for the discovery and characterization of novel tumor suppressors. PMID:26301496

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.

Influence of surface morphology on adsorption of potassium stearate molecules on diamond-like carbon substrate: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Guo, Shusen; Cao, Yongzhi; Sun, Tao; Zhang, Junjie; Gu, Le; Zhang, Chuanwei; Xu, Zhiqiang

2018-05-01

Molecular dynamics (MD) simulations were used to provide insights into the influence of nano-scale surface morphology on adsorptive behavior of Potassium stearate molecules on diamond-like carbon (DLC) substrates. Particular focus was given to explain that how the distinctive geometric properties of different surface morphologies affect the equilibrium structures and substrate-molecules interactions of monolayers, which was achieved through adsorptive analysis methods including adsorptive process, density profile, density distribution and surface potential energy. Analysis on surface potential energy demonstrated that the adsorptivity of amorphous smooth substrate is uniformly distributed over the surface, while DLC substrates with different surface morphologies appear to be more potentially corrugated, which improves the adsorptivity significantly. Because of the large distance of molecules from carbon atoms located at the square groove bottom, substrate-molecules interactions vanish significantly, and thus potassium stearate molecules cannot penetrate completely into the square groove. It can be observed that the equilibrium substrate-molecules interactions of triangle groove and semi-circle groove are much more powerful than that of square groove due to geometrically advantageous properties. These findings provided key information of optimally design of solid substrates with controllable adsorptivity.

Allosteric Control of Substrate Specificity of the Escherichia coli ADP-glucose Pyrophosphorylase

NASA Astrophysics Data System (ADS)

Ebrecht, Ana C.; Solamen, Ligin; Hill, Benjamin L.; Iglesias, Alberto A.; Olsen, Kenneth W.; Ballicora, Miguel A.

2017-06-01

The substrate specificity of enzymes is crucial to control the fate of metabolites to different pathways. However, there is growing evidence that many enzymes can catalyze alternative reactions. This promiscuous behavior has important implications in protein evolution and the acquisition of new functions. The question is how the undesirable outcomes of in vivo promiscuity can be prevented. ADP-glucose pyrophosphorylase from Escherichia coli is an example of an enzyme that needs to select the correct substrate from a broad spectrum of alternatives. This selection will guide the flow of carbohydrate metabolism towards the synthesis of reserve polysaccharides. Here, we show that the allosteric activator fructose-1,6-bisphosphate plays a role in such selection by increasing the catalytic efficiency of the enzyme towards the use of ATP rather than other nucleotides. In the presence of fructose-1,6-bisphosphate, the kcat/S0.5 for ATP was near 600-fold higher that other nucleotides, whereas in the absence of activator was only 3-fold higher. We propose that the allosteric regulation of certain enzymes is an evolutionary mechanism of adaptation for the selection of specific substrates.

Solid-substrate bioprocessing of cow dung for the production of carboxymethyl cellulase by Bacillus halodurans IND18.

PubMed

Vijayaraghavan, P; Prakash Vincent, S G; Dhillon, G S

2016-02-01

The production of carboxymethyl cellulase (CMCase) by Bacillus halodurans IND18 under solid substrate fermentation (SSF) using cow dung was optimized through two level full factorial design and second order response surface methodology (RSM). The central composite design (CCD) was employed to optimize the vital fermentation parameters, such as pH of the substrate, concentration of nitrogen source (peptone) and ion (sodium dihydrogen phosphate) sources in medium for achieving higher enzyme production. The optimum medium composition was found to be 1.46% (w/w) peptone, 0.095% (w/w) sodium dihydrogen phosphate and pH 8.0. The model prediction of 4210IU/g enzyme activity at optimum conditions was verified experimentally as 4140IU/g. The enzyme was active over a broad temperature range (40-60±1°C) and pH (7.0-9.0) with maximal activity at 60±1°C and pH 8.0. This study demonstrated the potential of cow dung as novel substrate for CMCase production. Copyright © 2015 Elsevier Ltd. All rights reserved.

A method to restrain the charging effect on an insulating substrate in high energy electron beam lithography

NASA Astrophysics Data System (ADS)

Mingyan, Yu; Shirui, Zhao; Yupeng, Jing; Yunbo, Shi; Baoqin, Chen

2014-12-01

Pattern distortions caused by the charging effect should be reduced while using the electron beam lithography process on an insulating substrate. We have developed a novel process by using the SX AR-PC 5000/90.1 solution as a spin-coated conductive layer, to help to fabricate nanoscale patterns of poly-methyl-methacrylate polymer resist on glass for phased array device application. This method can restrain the influence of the charging effect on the insulating substrate effectively. Experimental results show that the novel process can solve the problems of the distortion of resist patterns and electron beam main field stitching error, thus ensuring the accuracy of the stitching and overlay of the electron beam lithography system. The main characteristic of the novel process is that it is compatible to the multi-layer semiconductor process inside a clean room, and is a green process, quite simple, fast, and low cost. It can also provide a broad scope in the device development on insulating the substrate, such as high density biochips, flexible electronics and liquid crystal display screens.

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

Mahadevapuram, Nikhila; Mitra, Indranil; Sridhar, Shyam

Thin films of lamellar poly(styrene-b-methyl methacrylate) (PS-PMMA) block copolymers are widely investigated for surface patterning. These materials can generate dense arrays of nanoscale lines when the lamellar domains are oriented perpendicular to the substrate. To stabilize this preferred domain orientation, we tuned the substrate surface energy using oxidation of hydrophobic silane coatings. This simple approach is effective for a broad range of PS-PMMA film thicknesses when the oxidation time is optimized, which demonstrates that the substrate coating is energetically neutral with respect to PS and PMMA segments. The lamellar films are characterized by high densities of defects that exhibit amore » strong dependence on film thickness: in-plane topological defects disrupt the lateral order in ultrathin films, while lamellar domains in thick films can bend and tilt to large misorientation angles. As a result, the types and densities of these defects are similar to those observed with other classes of neutral substrate coatings, such as random copolymer brushes, which demonstrates that oxidized silanes can be used to control PS-PMMA self assembly in thin films.« less

Ordering of lamellar block copolymers on oxidized silane coatings

DOE PAGES

Mahadevapuram, Nikhila; Mitra, Indranil; Sridhar, Shyam; ...

2016-01-02

Thin films of lamellar poly(styrene-b-methyl methacrylate) (PS-PMMA) block copolymers are widely investigated for surface patterning. These materials can generate dense arrays of nanoscale lines when the lamellar domains are oriented perpendicular to the substrate. To stabilize this preferred domain orientation, we tuned the substrate surface energy using oxidation of hydrophobic silane coatings. This simple approach is effective for a broad range of PS-PMMA film thicknesses when the oxidation time is optimized, which demonstrates that the substrate coating is energetically neutral with respect to PS and PMMA segments. The lamellar films are characterized by high densities of defects that exhibit amore » strong dependence on film thickness: in-plane topological defects disrupt the lateral order in ultrathin films, while lamellar domains in thick films can bend and tilt to large misorientation angles. As a result, the types and densities of these defects are similar to those observed with other classes of neutral substrate coatings, such as random copolymer brushes, which demonstrates that oxidized silanes can be used to control PS-PMMA self assembly in thin films.« less

Preparing high-adhesion silver coating on APTMS modified polyethylene with excellent anti-bacterial performance

NASA Astrophysics Data System (ADS)

Li, Wenfei; Chen, Yunxiang; Wu, Song; Zhang, Jian; Wang, Hao; Zeng, Dawen; Xie, Changsheng

2018-04-01

Silver coating as a broad-spectrum antimicrobial agent was considered to alleviate the inflammation caused by intrauterine device (IUD) in endometrium. In this work, to avoid the damage of silver coating and ensure its antibacterial properties, 3-aminopropyltrimethoxysilane (APTMS) was introduced to modify the polyethylene (PE) substrate for the purpose of improving the adhesion of the silver coating. From the 90° peel test, it could be found that the adhesive strength of silver coating on the APTMS modified PE substrate was nearly 23 times stronger than the silver coating on substrate without surface modification. The dramatically enhanced adhesive strength could be attributed to the formation of continuous chemical bonds between the silver coatings and substrates after surface modification, which had been confirmed by the XPS. Moreover, the standard antibacterial test revealed that the silver coated samples against Staphylococcus aureus (S. aureus) exhibit excellent antibacterial efficacy. Considering the largely enhanced adhesion and the effective antibacterial property, it is reasonable to believe that the silver coating could be considered as a potential candidate for the antibacterial agent in IUD.

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.

Green oxidations of furans--initiated by molecular oxygen--that give key natural product motifs.

PubMed

Montagnon, Tamsyn; Noutsias, Dimitris; Alexopoulou, Ioanna; Tofi, Maria; Vassilikogiannakis, Georgios

2011-04-07

In this article, we explore how changes in the positioning of pendant hydroxyl functionalities in the photooxygenation substrate dramatically alter the course of furan oxidations that are initiated by singlet oxygen; and, how these different reactivities can be harnessed through cascade reaction sequences to access, rapidly and effectively, a broad range of important natural product motifs.

Pd-catalyzed intramolecular oxidative C-H amination: synthesis of carbazoles.

PubMed

Youn, So Won; Bihn, Joon Hyung; Kim, Byung Seok

2011-07-15

A Pd-catalyzed oxidative C-H amination of N-Ts-2-arylanilines under ambient temperature using Oxone as an inexpensive, safe, and easy-to-handle oxidant has been developed. This process represents a green and practical method for the facile construction of carbazoles with a broad substrate scope and wide functional group tolerance. © 2011 American Chemical Society

Ion-Deposited Polished Coatings

NASA Technical Reports Server (NTRS)

Banks, B. A.

1986-01-01

Polished, dense, adherent coatings relatively free of imperfections. New process consists of using broad-beam ion source in evacuated chamber to ion-clean rotating surface that allows grazing incidence of ion beam. This sputter cleans off absorbed gases, organic contaminants, and oxides of mirror surface. In addition to cleaning, surface protrusions sputter-etched away. Process particularly adaptable to polishing of various substrates for optical or esthetic purposes.

Catalytic Conia-ene and related reactions.

PubMed

Hack, Daniel; Blümel, Marcus; Chauhan, Pankaj; Philipps, Arne R; Enders, Dieter

2015-10-07

Since its initial inception, the Conia-ene reaction, known as the intramolecular addition of enols to alkynes or alkenes, has experienced a tremendous development and appealing catalytic protocols have emerged. This review fathoms the underlying mechanistic principles rationalizing how substrate design, substrate activation, and the nature of the catalyst work hand in hand for the efficient synthesis of carbocycles and heterocycles at mild reaction conditions. Nowadays, Conia-ene reactions can be found as part of tandem reactions, and the road for asymmetric versions has already been paved. Based on their broad applicability, Conia-ene reactions have turned into a highly appreciated synthetic tool with impressive examples in natural product synthesis reported in recent years.

GO-Cu7S4 catalyzed ortho-aminomethylation of phenol derivatives with N,N-dimethylbenzylamines: site-selective oxidative CDC.

PubMed

Gupta, Sonu; Chandna, Nisha; Dubey, Pooja; Singh, Ajai K; Jain, Nidhi

2018-06-21

Copper chalcogenide nanoparticles (Cu7S4) supported on graphene oxide (GO) have been synthesized for the first time from Cu2S, and used as highly efficient heterogeneous catalysts for oxidative ortho-selective C-H aminomethylation of phenols with N,N-dimethylbenzylamines. The NPs (30-80 nm) have been characterized by HRTEM, SEM-EDX, PXRD, FTIR, Raman, ICP-AES and XPS analyses. The NP catalyzed sp2-sp3 cross dehydrogenative coupling (CDC) features a broad substrate scope, excellent functional group tolerance, high yields, use of an inexpensive and reusable copper catalyst, mild conditions, and no need for pre-functionalization of substrates.

Transferable self-welding silver nanowire network as high performance transparent flexible electrode.

PubMed

Zhu, Siwei; Gao, Yuan; Hu, Bin; Li, Jia; Su, Jun; Fan, Zhiyong; Zhou, Jun

2013-08-23

High performance transparent electrodes (TEs) with figures-of-merit as high as 471 were assembled using ultralong silver nanowires (Ag NWs). A room-temperature plasma was employed to enhance the conductivity of the Ag NW TEs by simultaneously removing the insulating PVP layer coating on the NWs and welding the junctions tightly. Furthermore, we developed a general way to fabricate TEs regardless of substrate limitations by transferring the as-fabricated Ag NW network onto various substrates directly, and the transmittance can remain as high as 91% with a sheet resistivity of 13 Ω/sq. The highly robust and stable flexible TEs will have broad applications in flexible optoelectronic and electronic devices.

Discovery of a metalloenzyme-like cooperative catalytic system of metal nanoclusters and catechol derivatives for the aerobic oxidation of amines.

PubMed

Yuan, Hao; Yoo, Woo-Jin; Miyamura, Hiroyuki; Kobayashi, Shū

2012-08-29

We have discovered a new class of cooperative catalytic system, consisting of heterogeneous polymer-immobilized bimetallic Pt/Ir alloyed nanoclusters (NCs) and 4-tert-butylcatechol, for the aerobic oxidation of amines to imines under ambient conditions. After optimization, the desired imines were obtained in good to excellent yields with broad substrate scope. The reaction rate was determined to be first-order with respect to the substrate and catechol and zero-order for the alloyed Pt/Ir NC catalyst. Control studies revealed that both the heterogeneous NC catalyst and 4-tert-butylcatechol are essential and act cooperatively to facilitate the aerobic oxidation under mild conditions.

Scope and mechanism in palladium-catalyzed isomerizations of highly substituted allylic, homoallylic, and alkenyl alcohols.

PubMed

Larionov, Evgeny; Lin, Luqing; Guénée, Laure; Mazet, Clément

2014-12-03

Herein we report the palladium-catalyzed isomerization of highly substituted allylic alcohols and alkenyl alcohols by means of a single catalytic system. The operationally simple reaction protocol is applicable to a broad range of substrates and displays a wide functional group tolerance, and the products are usually isolated in high chemical yield. Experimental and computational mechanistic investigations provide complementary and converging evidence for a chain-walking process consisting of repeated migratory insertion/β-H elimination sequences. Interestingly, the catalyst does not dissociate from the substrate in the isomerization of allylic alcohols, whereas it disengages during the isomerization of alkenyl alcohols when additional substituents are present on the alkyl chain.

Computer-assisted enzyme immunoassays and simplified immunofluorescence assays: applications for the diagnostic laboratory and the veterinarian's office.

PubMed

Jacobson, R H; Downing, D R; Lynch, T J

1982-11-15

A computer-assisted enzyme-linked immunosorbent assay (ELISA) system, based on kinetics of the reaction between substrate and enzyme molecules, was developed for testing large numbers of sera in laboratory applications. Systematic and random errors associated with conventional ELISA technique were identified leading to results formulated on a statistically validated, objective, and standardized basis. In a parallel development, an inexpensive system for field and veterinary office applications contained many of the qualities of the computer-assisted ELISA. This system uses a fluorogenic indicator (rather than the enzyme-substrate interaction) in a rapid test (15 to 20 minutes' duration) which promises broad application in serodiagnosis.

Structural, optical and Carrier dynamics of self-assembled InGaN nanocolumns on Si(111)

NASA Astrophysics Data System (ADS)

Kumar, Praveen; Devi, Pooja; Soto Rodriguez, P. E. D.; Jain, Rishabh; Jaggi, Neena; Sinha, R. K.; Kumar, Mahesh

2018-05-01

We investigated the morphological, structural, optical, electrical and carrier relaxation dynamic changes on the self-assembled grown InGaN nanocolumns (NCs) directly on p-Si(111) substrate at two different substrate temperature, namely 580 °C (A) and 500 °C (B). The emission wavelength of comparably low temperature (LT) grown NCs was red-shifted from 3.2eV to 2.4eV. First observations on the charge carrier dynamics of these directly grown NCs show comparable broad excited state absorption (ESA) for LT gown NCs, which manifest bi-exponential decay due to the radiative defects generated during the coalescence of these NCs.

Arabidopsis BPM proteins function as substrate adaptors to a cullin3-based E3 ligase to affect fatty acid metabolism in plants.

PubMed

Chen, Liyuan; Lee, Joo Hyun; Weber, Henriette; Tohge, Takayuki; Witt, Sandra; Roje, Sanja; Fernie, Alisdair R; Hellmann, Hanjo

2013-06-01

Regulation of transcriptional processes is a critical mechanism that enables efficient coordination of the synthesis of required proteins in response to environmental and cellular changes. Transcription factors require accurate activity regulation because they play a critical role as key mediators assuring specific expression of target genes. In this work, we show that cullin3-based E3 ligases have the potential to interact with a broad range of ethylene response factor (ERF)/APETALA2 (AP2) transcription factors, mediated by Math-BTB/POZ (for Meprin and TRAF [tumor necrosis factor receptor associated factor] homolog)-Broad complex, Tramtrack, Bric-a-brac/Pox virus and Zinc finger) proteins. The assembly with an E3 ligase causes degradation of their substrates via the 26S proteasome, as demonstrated for the wrinkled1 ERF/AP2 protein. Furthermore, loss of Math-BTB/POZ proteins widely affects plant development and causes altered fatty acid contents in mutant seeds. Overall, this work demonstrates a link between fatty acid metabolism and E3 ligase activities in plants and establishes CUL3-based E3 ligases as key regulators in transcriptional processes that involve ERF/AP2 family members.

Synthesis and properties of SiN coatings as stable fluorescent markers on vertically aligned carbon nanofibers

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

Pearce, Ryan; Klein, Kate L; Ivanov, Ilia N

2014-01-01

The growth of vertically aligned carbon nanofibers (VACNFs) in a catalytic dc ammonia/acetylene plasma process on silicon substrates is often accompanied by sidewall deposition of material that contains mostly Si and N. In fluorescent microscopy experiments, imaging VACNF interfacing to live cell cultures it turned out that this material is broadly fluorescent, which made VACNFs useful as spatial markers, or created nuisance when DNA-labeling got masked. In this paper we provide insight into nature of this silicon/nitrogen in situ coatings. Here we have proposed a potential mechanism for deposition of SiNx coating on the sidewalls of VACNFs during PECVD synthesismore » in addition to exploring the origin of the coatings fluorescence. It seems most likely that the substrate reacts with the process gases through both processes similar to reactive sputtering and CVD to form silane and other silicon bearing compounds before being deposited isotropically as a SiNx coating onto the VACNFs. The case for the presence of Si-NCs is made strong through a combination of the strong fluorescence and elemental analysis of the samples. These broadly luminescent fibers can prove useful as registry markers in fluorescent cellular studies.« less

Optical gradients in a-Si:H thin films detected using real-time spectroscopic ellipsometry with virtual interface analysis

NASA Astrophysics Data System (ADS)

Junda, Maxwell M.; Karki Gautam, Laxmi; Collins, Robert W.; Podraza, Nikolas J.

2018-04-01

Virtual interface analysis (VIA) is applied to real time spectroscopic ellipsometry measurements taken during the growth of hydrogenated amorphous silicon (a-Si:H) thin films using various hydrogen dilutions of precursor gases and on different substrates during plasma enhanced chemical vapor deposition. A procedure is developed for optimizing VIA model configurations by adjusting sampling depth into the film and the analyzed spectral range such that model fits with the lowest possible error function are achieved. The optimal VIA configurations are found to be different depending on hydrogen dilution, substrate composition, and instantaneous film thickness. A depth profile in the optical properties of the films is then extracted that results from a variation in an optical absorption broadening parameter in a parametric a-Si:H model as a function of film thickness during deposition. Previously identified relationships are used linking this broadening parameter to the overall shape of the optical properties. This parameter is observed to converge after about 2000-3000 Å of accumulated thickness in all layers, implying that similar order in the a-Si:H network can be reached after sufficient thicknesses. In the early stages of growth, however, significant variations in broadening resulting from substrate- and processing-induced order are detected and tracked as a function of bulk layer thickness yielding an optical property depth profile in the final film. The best results are achieved with the simplest film-on-substrate structures while limitations are identified in cases where films have been deposited on more complex substrate structures.

Leveraging Crystal Anisotropy for Deterministic Growth of InAs Quantum Dots with Narrow Optical Linewidths

DTIC Science & Technology

2013-08-29

similar layer thicknesses. This offset indicates that the electric field profile of our Schottky diode is different than for unpatterned samples, implying...sacrificing uniformity by further optimizing the substrate Figure 3. (a) Schematic of the Schottky diode heterostructure, indicating the patterned substrate...and negative (X−) trions are indicated . (c) Distribution of linewidths for 80 PL lines from dots grown in high density arrays such as those in Figure 2b

High efficiency, low cost, thin film silicon solar cell design and method for making

DOEpatents

Sopori, Bhushan L.

2001-01-01

A semiconductor device having a substrate, a conductive intermediate layer deposited onto said substrate, wherein the intermediate layer serves as a back electrode, an optical reflector, and an interface for impurity gettering, and a semiconductor layer deposited onto said intermediate layer, wherein the semiconductor layer has a grain size at least as large as the layer thickness, and preferably about ten times the layer thickness. The device is formed by depositing a metal layer on a substrate, depositing a semiconductive material on the metal-coated substrate to produce a composite structure, and then optically processing the composite structure by illuminating it with infrared electromagnetic radiation according to a unique time-energy profile that first produces pits in the backside surface of the semiconductor material, then produces a thin, highly reflective, low resistivity alloy layer over the entire area of the interface between the semiconductor material and the metal layer, and finally produces a grain-enhanced semiconductor layer. The time-energy profile includes increasing the energy to a first energy level to initiate pit formation and create the desired pit size and density, then ramping up to a second energy level in which the entire device is heated to produce an interfacial melt, and finally reducing the energy to a third energy level and holding for a period of time to allow enhancement in the grain size of the semiconductor layer.

High efficiency low cost thin film silicon solar cell design and method for making

DOEpatents

Sopori, Bhushan L.

1999-01-01

A semiconductor device having a substrate, a conductive intermediate layer deposited onto said substrate, wherein the intermediate layer serves as a back electrode, an optical reflector, and an interface for impurity gettering, and a semiconductor layer deposited onto said intermediate layer, wherein the semiconductor layer has a grain size at least as large as the layer thickness, and preferably about ten times the layer thickness. The device is formed by depositing a metal layer on a substrate, depositing a semiconductive material on the metal-coated substrate to produce a composite structure, and then optically processing the composite structure by illuminating it with infrared electromagnetic radiation according to a unique time-energy profile that first produces pits in the backside surface of the semiconductor material, then produces a thin, highly reflective, low resistivity alloy layer over the entire area of the interface between the semiconductor material and the metal layer, and finally produces a grain-enhanced semiconductor layer. The time-energy profile includes increasing the energy to a first energy level to initiate pit formation and create the desired pit size and density, then ramping up to a second energy level in which the entire device is heated to produce an interfacial melt, and finally reducing the energy to a third energy level and holding for a period of time to allow enhancement in the grain size of the semiconductor layer.

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

Use of Activity-Based Probes to Develop High Throughput Screening Assays That Can Be Performed in Complex Cell Extracts

PubMed Central

Deu, Edgar; Yang, Zhimou; Wang, Flora; Klemba, Michael; Bogyo, Matthew

2010-01-01

Background High throughput screening (HTS) is one of the primary tools used to identify novel enzyme inhibitors. However, its applicability is generally restricted to targets that can either be expressed recombinantly or purified in large quantities. Methodology and Principal Findings Here, we described a method to use activity-based probes (ABPs) to identify substrates that are sufficiently selective to allow HTS in complex biological samples. Because ABPs label their target enzymes through the formation of a permanent covalent bond, we can correlate labeling of target enzymes in a complex mixture with inhibition of turnover of a substrate in that same mixture. Thus, substrate specificity can be determined and substrates with sufficiently high selectivity for HTS can be identified. In this study, we demonstrate this method by using an ABP for dipeptidyl aminopeptidases to identify (Pro-Arg)2-Rhodamine as a specific substrate for DPAP1 in Plasmodium falciparum lysates and Cathepsin C in rat liver extracts. We then used this substrate to develop highly sensitive HTS assays (Z’>0.8) that are suitable for use in screening large collections of small molecules (i.e >300,000) for inhibitors of these proteases. Finally, we demonstrate that it is possible to use broad-spectrum ABPs to identify target-specific substrates. Conclusions We believe that this approach will have value for many enzymatic systems where access to large amounts of active enzyme is problematic. PMID:20700487

Analysis of Scattering from Archival Pulsar Data using a CLEAN-based Method

NASA Astrophysics Data System (ADS)

Tsai, -Wei, Jr.; Simonetti, John H.; Kavic, Michael

2017-02-01

In this work, we adopted a CLEAN-based method to determine the scatter time, τ, from archived pulsar profiles under both the thin screen and uniform medium scattering models and to calculate the scatter time frequency scale index α, where τ \\propto {ν }α . The value of α is -4.4, if a Kolmogorov spectrum of the interstellar medium turbulence is assumed. We deconvolved 1342 profiles from 347 pulsars over a broad range of frequencies and dispersion measures. In our survey, in the majority of cases the scattering effect was not significant compared to pulse profile widths. For a subset of 21 pulsars scattering at the lowest frequencies was large enough to be measured. Because reliable scatter time measurements were determined only for the lowest frequency, we were limited to using upper limits on scatter times at higher frequencies for the purpose of our scatter time frequency slope estimation. We scaled the deconvolved scatter time to 1 GHz assuming α =-4.4 and considered our results in the context of other observations which yielded a broad relation between scatter time and dispersion measure.

Three-dimensional architecture for solid state radiation detectors

DOEpatents

Parker, S.

1999-03-30

A radiation-damage resistant radiation detector is formed on a substrate formed of a material doped with a first conductivity type dopant. The detector includes at least one first electrode formed of first conductivity type dopant, and at least one second electrode that is spaced-apart from the first electrode and formed of a second conductivity type dopant. Each first and second electrode penetrates into the substrate from a substrate surface, and one or more electrodes may penetrate entirely through the substrate, that is traversing from one surface to the other surface. Particulate and/or electromagnetic radiation penetrating at least a surface of the substrate releases electrons and holes in substrate regions. Because the electrodes may be formed entirely through the substrate thickness, the released charges will be a relatively small distance from at least a portion of such an electrode, e.g., a distance less than the substrate thickness. The electrons and/or holes traverse the small distance and are collected by said electrodes, thus promoting rapid detection of the radiation. By providing one or more electrodes with a dopant profile radially graded in a direction parallel to a substrate surface, an electric field results that promotes rapid collection of released electrons and said holes. Monolithic combinations of such detectors may be fabricated including CMOS electronics to process radiation signals. 45 figs.

Three-dimensional architecture for solid state radiation detectors

DOEpatents

Parker, Sherwood

1999-01-01

A radiation-damage resistant radiation detector is formed on a substrate formed of a material doped with a first conductivity type dopant. The detector includes at least one first electrode formed of first conductivity type dopant, and at least one second electrode that is spaced-apart from the first electrode and formed of a second conductivity type dopant. Each first and second electrode penetrates into the substrate from a substrate surface, and one or more electrodes may penetrate entirely through the substrate, that is traversing from one surface to the other surface. Particulate and/or electromagnetic radiation penetrating at least a surface of the substrate releases electrons and holes in substrate regions. Because the electrodes may be formed entirely through the substrate thickness, the released charges will be a relatively small distance from at least a portion of such an electrode, e.g., a distance less than the substrate thickness. The electrons and/or holes traverse the small distance and are collected by said electrodes, thus promoting rapid detection of the radiation. By providing one or more electrodes with a dopant profile radially graded in a direction parallel to a substrate surface, an electric field results that promotes rapid collection of released electrons and said holes. Monolithic combinations of such detectors may be fabricated including CMOS electronics to process radiation signals.

Broad Redshifted Line as a Signature of Outflow

NASA Astrophysics Data System (ADS)

Titarchuk, Lev; Kazanas, Demos; Becker, Peter A.

2003-11-01

We formulate and solve the diffusion problem of line photon propagation in a bulk outflow from a compact object (black hole or neutron star) using a generic assumption regarding the distribution of line photons within the outflow. Thomson scattering of the line photons within the expanding flow leads to a decrease of their energy which is of first order in v/c, where v is the outflow velocity and c is the speed of light. We demonstrate that the emergent line profile is closely related to the time distribution of photons diffusing through the flow (the light curve) and consists of a broad redshifted feature. We analyzed the line profiles for the general case of outflow density distribution. We emphasize that the redshifted lines are intrinsic properties of the powerful outflow that are supposed to be in many compact objects.

Broad Red-Shifted Lines as a Signature of Outflow

NASA Astrophysics Data System (ADS)

Kazanas, Demosthenes; Titarchuk, Lev; Becker, Peter A.

2004-07-01

We formulate and solve the diffusion problem of line photon propagation in a bulk outflow from a compact object (black hole or neutron star) using a generic assumption regarding the distribution of line photons within the outflow. Thomson scattering of the line photons within the expanding flow leads to a decrease of their energy which is of first order in v/c, where v is the outflow velocity and c the speed of light. We demonstrate that the emergent line profile is closely related to the time distribution of photons diffusing through the flow (the light curve) and consists of a broad redshifted feature. We analyzed the line profiles for the general case of outflow density distribution. We emphasize that the redshifted lines are intrinsic properties of the powerful outflow that are supposed to be in many compact objects.

Broad Red-Shifted Lines as a Signature of Outflows

NASA Astrophysics Data System (ADS)

Titarchuck, Lev; Kazanas, Demos; Becker, Peter A.

2006-02-01

We formulate and solve the diffusion problem of line photon propagation in a bulk outflow from a compact object (black hole or neutron star) using a generic assumption regarding the distribution of line photons within the outflow. Thomson scattering of the line photons within the expanding flow leads to a decrease of their energy which is of first order in υ/c, where υ the outflow velocity and c is the speed of light. We demonstrate that the emergent line profile is closely related to the time distribution of photons diffusing through the flow (the light curve) and consists of a broad redshifted feature. We analyzed the line profiles for the general case of outflow density distribution. We emphasize that the redshifted lines are intrinsic properties of the powerful outflow that are supposed to be in many compact objects.

Spliceosome Profiling Visualizes Operations of a Dynamic RNP at Nucleotide Resolution.

PubMed

Burke, Jordan E; Longhurst, Adam D; Merkurjev, Daria; Sales-Lee, Jade; Rao, Beiduo; Moresco, James J; Yates, John R; Li, Jingyi Jessica; Madhani, Hiten D

2018-05-03

Tools to understand how the spliceosome functions in vivo have lagged behind advances in the structural biology of the spliceosome. Here, methods are described to globally profile spliceosome-bound pre-mRNA, intermediates, and spliced mRNA at nucleotide resolution. These tools are applied to three yeast species that span 600 million years of evolution. The sensitivity of the approach enables the detection of canonical and non-canonical events, including interrupted, recursive, and nested splicing. This application of statistical modeling uncovers independent roles for the size and position of the intron and the number of introns per transcript in substrate progression through the two catalytic stages. These include species-specific inputs suggestive of spliceosome-transcriptome coevolution. Further investigations reveal the ATP-dependent discard of numerous endogenous substrates after spliceosome assembly in vivo and connect this discard to intron retention, a form of splicing regulation. Spliceosome profiling is a quantitative, generalizable global technology used to investigate an RNP central to eukaryotic gene expression. Copyright © 2018 Elsevier Inc. All rights reserved.

Fabrication and stabilization of silicon-based photonic crystals with tuned morphology for multi-band optical filtering

NASA Astrophysics Data System (ADS)

Salem, Mohamed Shaker; Abdelaleem, Asmaa Mohamed; El-Gamal, Abear Abdullah; Amin, Mohamed

2017-01-01

One-dimensional silicon-based photonic crystals are formed by the electrochemical anodization of silicon substrates in hydrofluoric acid-based solution using an appropriate current density profile. In order to create a multi-band optical filter, two fabrication approaches are compared and discussed. The first approach utilizes a current profile composed of a linear combination of sinusoidal current waveforms having different frequencies. The individual frequency of the waveform maps to a characteristic stop band in the reflectance spectrum. The stopbands of the optical filter created by the second approach, on the other hand, are controlled by stacking multiple porous silicon rugate multilayers having different fabrication conditions. The morphology of the resulting optical filters is tuned by controlling the electrolyte composition and the type of the silicon substrate. The reduction of sidelobes arising from the interference in the multilayers is observed by applying an index matching current profile to the anodizing current waveform. In order to stabilize the resulting optical filters against natural oxidation, atomic layer deposition of silicon dioxide on the pore wall is employed.

Verification of the modified model of the drying process of a polymer liquid film on a flat substrate by experiment (2): through more accurate experiment

NASA Astrophysics Data System (ADS)

Kagami, Hiroyuki

2006-05-01

We have proposed and modified a model of drying process of polymer solution coated on a flat substrate for flat polymer film fabrication and have presented the fruits through Photomask Japan 2002, 2003, 2004 and so on. And for example numerical simulation of the model qualitatively reappears a typical thickness profile of the polymer film formed after drying, that is, the profile that the edge of the film is thicker and just the region next to the edge's bump is thinner. Then we have clarified dependence of distribution of polymer molecules on a flat substrate on a various parameters based on analysis of many numerical simulations. Then we done a few kinds of experiments so as to verify the modified model and reported the initial result of them through Photomask Japan 2005. Through the initial result we could observe some results supporting the modified model. But we could not observe a characteristic region of a valley next to the edge's bump of a polymer film after drying because a shape of a solution's film coated on a substrate in the experiment was different from one in resists' coating and drying process or imagined in the modified model. In this study, we improved above difference between experiment and the model and did experiments for verification again with a shape of a solution's film coated on a substrate coincident with one imagined in the modified model and using molar concentration. As a result, some were verified more strongly and some need to be examined again. That is, we could confirm like results of last experiment that the smaller average molecular weight of Metoloses was, the larger the gradient of thickness profile of a polymer thin film was. But we could not observe a depression just inside the edge of the thin film also in this improved experiment. We may be able to enumerate the fact that not an organic solution but an aqueous solution was used in the experiment as the cause of non-formation of the depression.

Effect of lipophilicity modulation on inhibition of human rhinovirus capsid binders.

PubMed

Morley, Andrew; Tomkinson, Nicholas; Cook, Andrew; MacDonald, Catherine; Weaver, Richard; King, Sarah; Jenkinson, Lesley; Unitt, John; McCrae, Christopher; Phillips, Tim

2011-10-15

To try and generate broad spectrum human rhinovirus VP1 inhibitors with more attractive physicochemical, DMPK and safety profiles, we explored the current SAR of known VP1 compounds. This lead to the identification of specific structural regions where reduction in polarity can be achieved, so guiding chemistry to analogues with significantly superior profiles to previously reported inhibitors. Copyright © 2011 Elsevier Ltd. All rights reserved.

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

A PROFILE ANALYSIS OF RAMAN-SCATTERED O VI BANDS AT 6825 Å AND 7082 Å IN SANDULEAK’S STAR

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

Heo, Jeong-Eun; Lee, Hee-Won; Angeloni, Rodolfo

2016-12-20

We present a detailed modeling of the two broad bands observed at 6825 and 7082 Å in Sanduleak’s star, a controversial object in the Large Magellanic Cloud. These bands are known to originate from Raman scattering of O vi  λ λ 1032 and 1038 photons with atomic hydrogen and are only observed in bona fide symbiotic stars. Our high-resolution spectrum obtained with the Magellan Inamori Kyocera Echelle spectrograph at the Magellan-Clay Telescope reveals, quite surprisingly, that the profiles of the two bands look very different: while the Raman 6825 Å band shows a single broad profile with a redward extendedmore » bump, the Raman 7082 Å band exhibits a distinct triple-peak profile. Our model suggests that the O vi emission nebula can be decomposed into a red, blue, and central emission region from an accretion disk, a bipolar outflow, and a further compact, optically thick region. We also perform Monte Carlo simulations with the aim of fitting the observed flux ratio F (6825)/ F (7082) ∼ 4.5, which indicates that the neutral region in Sanduleak’s star is characterized by the column density N{sub Hi} ∼ 1 × 10{sup 23} cm{sup −2}.« less

Towards a Neurobehavioral Profile of Fetal Alcohol Spectrum Disorders

PubMed Central

Mattson, Sarah N.; Roesch, Scott C.; Fagerlund, Åse; Autti-Rämö, Ilona; Jones, Kenneth Lyons; May, Philip A.; Adnams, Colleen M.; Konovalova, Valentina; Riley, Edward P.

2010-01-01

Background A primary goal of recent research is the development of neurobehavioral profiles that specifically define fetal alcohol spectrum disorders (FASD), which may assist differential diagnosis or improve treatment. In the current study we define a preliminary profile using neuropsychological data from a multisite study. Methods Data were collected using a broad neurobehavioral protocol from two sites of a multisite study of FASD. Subjects were children with heavy prenatal alcohol exposure and unexposed controls. The alcohol-exposed group included children with and with out fetal alcohol syndrome (FAS). From 547 neuropsychological, 22 variables were selected for analysis based on their ability to distinguish children with heavy prenatal alcohol exposure from nonexposed controls. These data were analyzed using latent profile analysis (LPA). Results The results indicated that a 2-class model best fit the data. The resulting profile was successful at distinguishing subjects with FAS from nonexposed controls without FAS with 92% overall accuracy; 87.8% of FAS cases and 95.7% of controls were correctly classified. The same analysis was repeated with children with heavy prenatal alcohol exposure but without FAS and non-exposed controls with similar results. The overall accuracy was 84.7%; 68.4% of alcohol-exposed cases and 95% of controls were correctly classified. In both analyses, the profile based on neuropsychological variables was more successful at distinguishing the groups than was IQ alone. Conclusions We used data from two sites of a multisite study and a broad neuropsychological test battery to determine a profile that could be used to accurately identify children affected by prenatal alcohol exposure. Results indicated that measures of executive function and spatial processing are especially sensitive to prenatal alcohol exposure. PMID:20569243

Mechanistic and Structural Analyses of the Role of His67 in the Yeast Polyamine Oxidase Fms1

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

Adachi, Mariya S.; Taylor, Alexander B.; Hart, P. John

2012-07-25

The flavoprotein oxidase Fms1 from Saccharomyces cerevisiae catalyzes the oxidation of spermine and N1-acetylspermine to spermidine and 3-aminopropanal or N-acetyl-3-aminopropanal. Within the active site of Fms1, His67 is positioned to form hydrogen bonds with the polyamine substrate. This residue is also conserved in other polyamine oxidases. The catalytic properties of H67Q, H67N, and H67A Fms1 have been characterized to evaluate the role of this residue in catalysis. With both spermine and N1-acetylspermine as the amine substrate, the value of the first-order rate constant for flavin reduction decreases 2-3 orders of magnitude, with the H67Q mutation having the smallest effect andmore » H67N the largest. The k{sub cat}/K{sub O2} value changes very little upon mutation with N{sup 1}-acetylspermine as the amine substrate and decreases only an order of magnitude with spermine. The k{sub cat}/K{sub M}-pH profiles with N{sup 1}-acetylspermine are bell-shaped for all the mutants; the similarity to the profile of the wild-type enzyme rules out His67 as being responsible for either of the pK{sub a} values. The pH profiles for the rate constant for flavin reduction for all the mutant enzymes similarly show the same pK{sub a} as wild-type Fms1, about {approx}7.4; this pK{sub a} is assigned to the substrate N4. The k{sub cat}/K{sub O2}-pH profiles for wild-type Fms1 and the H67A enzyme both show a pK{sub a} of about {approx}6.9; this suggests His67 is not responsible for this pH behavior. With the H67Q, H67N, and H67A enzymes the k{sub cat} value decreases when a single residue is protonated, as is the case with the wild-type enzyme. The structure of H67Q Fms1 has been determined at a resolution of 2.4 {angstrom}. The structure shows that the mutation disrupts a hydrogen bond network in the active site, suggesting that His67 is important both for direct interactions with the substrate and to maintain the overall active site structure.« less

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.

Characterisation of diode-connected SiGe BiCMOS HBTs for space applications

NASA Astrophysics Data System (ADS)

Venter, Johan; Sinha, Saurabh; Lambrechts, Wynand

2016-02-01

Silicon-germanium (SiGe) bipolar complementary metal-oxide semiconductor (BiCMOS) transistors have vertical doping profiles reaching deeper into the substrate when compared to lateral CMOS transistors. Apart from benefiting from high-speed, high current gain and low-output resistance due to its vertical profile, BiCMOS technology is increasingly becoming a preferred technology for researchers to realise next-generation space-based optoelectronic applications. BiCMOS transistors have inherent radiation hardening, to an extent predictable cryogenic performance and monolithic integration potential. SiGe BiCMOS transistors and p-n junction diodes have been researched and used as a primary active component for over the last two decades. However, further research can be conducted with diode-connected heterojunction bipolar transistors (HBTs) operating at cryogenic temperatures. This work investigates these characteristics and models devices by adapting standard fabrication technology components. This work focuses on measurements of the current-voltage relationship (I-V curves) and capacitance-voltage relationships (C-V curves) of diode-connected HBTs. One configuration is proposed and measured, which is emitterbase shorted. The I-V curves are measured for various temperature points ranging from room temperature (300 K) to the temperature of liquid nitrogen (77 K). The measured datasets are used to extract a model of the formed diode operating at cryogenic temperatures and used as a standard library component in computer aided software designs. The advantage of having broad-range temperature models of SiGe transistors becomes apparent when considering implementation of application-specific integrated circuits and silicon-based infrared radiation photodetectors on a single wafer, thus shortening interconnects and lowering parasitic interference, decreasing the overall die size and improving on overall cost-effectiveness. Primary applications include space-based geothermal radiation sensing and cryogenic terahertz radiation sensing.

Light Regulation of the Arabidopsis Respiratory Chain. Multiple Discrete Photoreceptor Responses Contribute to Induction of Type II NAD(P)H Dehydrogenase Genes1

PubMed Central

Escobar, Matthew A.; Franklin, Keara A.; Svensson, Å. Staffan; Salter, Michael G.; Whitelam, Garry C.; Rasmusson, Allan G.

2004-01-01

Controlled oxidation reactions catalyzed by the large, proton-pumping complexes of the respiratory chain generate an electrochemical gradient across the mitochondrial inner membrane that is harnessed for ATP production. However, several alternative respiratory pathways in plants allow the maintenance of substrate oxidation while minimizing the production of ATP. We have investigated the role of light in the regulation of these energy-dissipating pathways by transcriptional profiling of the alternative oxidase, uncoupling protein, and type II NAD(P)H dehydrogenase gene families in etiolated Arabidopsis seedlings. Expression of the nda1 and ndc1 NAD(P)H dehydrogenase genes was rapidly up-regulated by a broad range of light intensities and qualities. For both genes, light induction appears to be a direct transcriptional effect that is independent of carbon status. Mutant analyses demonstrated the involvement of two separate photoreceptor families in nda1 and ndc1 light regulation: the phytochromes (phyA and phyB) and an undetermined blue light photoreceptor. In the case of the nda1 gene, the different photoreceptor systems generate distinct kinetic induction profiles that are integrated in white light response. Primary transcriptional control of light response was localized to a 99-bp region of the nda1 promoter, which contains an I-box flanked by two GT-1 elements, an arrangement prevalent in the promoters of photosynthesis-associated genes. Light induction was specific to nda1 and ndc1. The only other substantial light effect observed was a decrease in aox2 expression. Overall, these results suggest that light directly influences the respiratory electron transport chain via photoreceptor-mediated transcriptional control, likely for supporting photosynthetic metabolism. PMID:15333756

Structure of YciA from Haemophilus influenzae (HI0827), a Hexameric Broad Specificity Acyl-Coenzyme A Thioesterase

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

Willis, Mark A.; Zhuang, Zhihao; Song, Feng

2008-04-02

The crystal structure of HI0827 from Haemophilus influenzae Rd KW20, initially annotated 'hypothetical protein' in sequence databases, exhibits an acyl-coenzyme A (acyl-CoA) thioesterase 'hot dog' fold with a trimer of dimers oligomeric association, a novel assembly for this enzyme family. In studies described in the preceding paper [Zhuang, Z., Song, F., Zhao, H., Li, L., Cao, J., Eisenstein, E., Herzberg, O., and Dunaway-Mariano, D. (2008) Biochemistry 47, 2789-2796], HI0827 is shown to be an acyl-CoA thioesterase that acts on a wide range of acyl-CoA compounds. Two substrate binding sites are located across the dimer interface. The binding sites are occupiedmore » by two CoA molecules, one with full occupancy and the second only partially occupied. The CoA molecules, acquired from HI0827-expressing Escherichia coli cells, remained tightly bound to the enzyme through the protein purification steps. The difference in CoA occupancies indicates a different substrate affinity for each of the binding sites, which in turn implies that the enzyme might be subject to allosteric regulation. Mutagenesis studies have shown that the replacement of the putative catalytic carboxylate Asp44 with an alanine residue abolishes activity. The impact of this mutation is seen in the crystal structure of D44A HI0827. Whereas the overall fold and assembly of the mutant protein are the same as those of the wild-type enzyme, the CoA ligands are absent. The dimer interface is perturbed, and the channel that accommodates the thioester acyl chain is more open and wider than that observed in the wild-type enzyme. A model of intact substrate bound to wild-type HI0827 provides a structural rationale for the broad substrate range.« less

aKMT Catalyzes Extensive Protein Lysine Methylation in the Hyperthermophilic Archaeon Sulfolobus islandicus but is Dispensable for the Growth of the Organism *

PubMed Central

Chu, Yindi; Zhu, Yanping; Chen, Yuling; Li, Wei; Zhang, Zhenfeng; Liu, Di; Wang, Tongkun; Ma, Juncai; Deng, Haiteng; Liu, Zhi-Jie; Ouyang, Songying; Huang, Li

2016-01-01

Protein methylation is believed to occur extensively in creanarchaea. Recently, aKMT, a highly conserved crenarchaeal protein lysine methyltransferase, was identified and shown to exhibit broad substrate specificity in vitro. Here, we have constructed an aKMT deletion mutant of the hyperthermophilic crenarchaeon Sulfolobus islandicus. The mutant was viable but showed a moderately slower growth rate than the parental strain under non-optimal growth conditions. Consistent with the moderate effect of the lack of aKMT on the growth of the cell, expression of a small number of genes, which encode putative functions in substrate transportation, energy metabolism, transcriptional regulation, stress response proteins, etc, was differentially regulated by more than twofold in the mutant strain, as compared with that in the parental strain. Analysis of the methylation of total cellular protein by mass spectrometry revealed that methylated proteins accounted for ∼2/3 (1,158/1,751) and ∼1/3 (591/1,757) of the identified proteins in the parental and the mutant strains, respectively, indicating that there is extensive protein methylation in S. islandicus and that aKMT is a major protein methyltransferase in this organism. No significant sequence preference was detected at the sites of methylation by aKMT. Methylated lysine residues, when visible in the structure, are all located on the surface of the proteins. The crystal structure of aKMT in complex with S-adenosyl-l-methionine (SAM) or S-adenosyl homocysteine (SAH) reveals that the protein consists of four α helices and seven β sheets, lacking a substrate recognition domain found in PrmA, a bacterial homolog of aKMT, in agreement with the broad substrate specificity of aKMT. Our results suggest that aKMT may serve a role in maintaining the methylation status of cellular proteins required for the efficient growth of the organism under certain non-optimal conditions. PMID:27329856

One-pot synthesis of active copper-containing carbon dots with laccase-like activities

NASA Astrophysics Data System (ADS)

Ren, Xiangling; Liu, Jing; Ren, Jun; Tang, Fangqiong; Meng, Xianwei

2015-11-01

Herein, an effective strategy for designing a new type of nanozyme, blue fluorescent laccase mimics, is reported. Active copper-containing carbon dots (Cu-CDs) were synthesized through a simple, nontoxic and one-pot hydrothermal method, which showed favorable photoluminescence properties and good photostability under high-salt conditions or in a broad pH range (3.0-13.5). The Cu-CDs possessed intrinsic laccase-like activities and could catalyze the oxidation of the laccase substrate p-phenylenediamine (PPD) to produce a typical color change from colorless to brown. Poly(methacrylic acid sodium salt) (PMAA) not only was used as the carbon source and reducing agent, but also provided carboxyl groups to assist flocculation between Cu-CDs and polyacrylamide, which facilitated the removal of PPD. Importantly, the intrinsic fluorescence of the as-prepared Cu-CDs could indicate the presence of hydroquinone, one of the substrates of laccases, based on laccase mimics and fluorescence quenching.Herein, an effective strategy for designing a new type of nanozyme, blue fluorescent laccase mimics, is reported. Active copper-containing carbon dots (Cu-CDs) were synthesized through a simple, nontoxic and one-pot hydrothermal method, which showed favorable photoluminescence properties and good photostability under high-salt conditions or in a broad pH range (3.0-13.5). The Cu-CDs possessed intrinsic laccase-like activities and could catalyze the oxidation of the laccase substrate p-phenylenediamine (PPD) to produce a typical color change from colorless to brown. Poly(methacrylic acid sodium salt) (PMAA) not only was used as the carbon source and reducing agent, but also provided carboxyl groups to assist flocculation between Cu-CDs and polyacrylamide, which facilitated the removal of PPD. Importantly, the intrinsic fluorescence of the as-prepared Cu-CDs could indicate the presence of hydroquinone, one of the substrates of laccases, based on laccase mimics and fluorescence quenching. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr04685h

Method and system using power modulation for maskless vapor deposition of spatially graded thin film and multilayer coatings with atomic-level precision and accuracy

DOEpatents

Montcalm, Claude [Livermore, CA; Folta, James Allen [Livermore, CA; Tan, Swie-In [San Jose, CA; Reiss, Ira [New City, NY

2002-07-30

A method and system for producing a film (preferably a thin film with highly uniform or highly accurate custom graded thickness) on a flat or graded substrate (such as concave or convex optics), by sweeping the substrate across a vapor deposition source operated with time-varying flux distribution. In preferred embodiments, the source is operated with time-varying power applied thereto during each sweep of the substrate to achieve the time-varying flux distribution as a function of time. A user selects a source flux modulation recipe for achieving a predetermined desired thickness profile of the deposited film. The method relies on precise modulation of the deposition flux to which a substrate is exposed to provide a desired coating thickness distribution.

Assessing Carbon-Based Anodes for Lithium-Ion Batteries: A Universal Description of Charge-Transfer Binding

DOE PAGES

Liu, Yuanyue; Wang, Y. Morris; Yakobson, Boris I.; ...

2014-07-11

Many key performance characteristics of carbon-based lithium-ion battery anodes are largely determined by the strength of binding between lithium (Li) and sp 2 carbon (C), which can vary significantly with subtle changes in substrate structure, chemistry, and morphology. We use density functional theory calculations to investigate the interactions of Li with a wide variety of sp 2 C substrates, including pristine, defective, and strained graphene, planar C clusters, nanotubes, C edges, and multilayer stacks. In almost all cases, we find a universal linear relation between the Li-C binding energy and the work required to fill previously unoccupied electronic states withinmore » the substrate. This suggests that Li capacity is predominantly determined by two key factors—namely, intrinsic quantum capacitance limitations and the absolute placement of the Fermi level. This simple descriptor allows for straightforward prediction of the Li-C binding energy and related battery characteristics in candidate C materials based solely on the substrate electronic structure. It further suggests specific guidelines for designing more effective C-based anodes. Furthermore, this method should be broadly applicable to charge-transfer adsorption on planar substrates, and provides a phenomenological connection to established principles in supercapacitor and catalyst design.« less

Re-Os geochronology and coupled Os-Sr isotope constraints on the Sturtian snowball Earth.

PubMed

Rooney, Alan D; Macdonald, Francis A; Strauss, Justin V; Dudás, Francis Ö; Hallmann, Christian; Selby, David

2014-01-07

After nearly a billion years with no evidence for glaciation, ice advanced to equatorial latitudes at least twice between 717 and 635 Mya. Although the initiation mechanism of these Neoproterozoic Snowball Earth events has remained a mystery, the broad synchronicity of rifting of the supercontinent Rodinia, the emplacement of large igneous provinces at low latitude, and the onset of the Sturtian glaciation has suggested a tectonic forcing. We present unique Re-Os geochronology and high-resolution Os and Sr isotope profiles bracketing Sturtian-age glacial deposits of the Rapitan Group in northwest Canada. Coupled with existing U-Pb dates, the postglacial Re-Os date of 662.4 ± 3.9 Mya represents direct geochronological constraints for both the onset and demise of a Cryogenian glaciation from the same continental margin and suggests a 55-My duration of the Sturtian glacial epoch. The Os and Sr isotope data allow us to assess the relative weathering input of old radiogenic crust and more juvenile, mantle-derived substrate. The preglacial isotopic signals are consistent with an enhanced contribution of juvenile material to the oceans and glacial initiation through enhanced global weatherability. In contrast, postglacial strata feature radiogenic Os and Sr isotope compositions indicative of extensive glacial scouring of the continents and intense silicate weathering in a post-Snowball Earth hothouse.

Moxidectin: a review of chemistry, pharmacokinetics and use in horses

PubMed Central

Cobb, Rami; Boeckh, Albert

2009-01-01

This article reviews the current knowledge of the use of moxidectin (MOX) in horses, including its mode of action, pharmacokinetic and pharmacodynamic properties, efficacy, safety and resistance profile. Moxidectin is a second generation macrocyclic lactone (ML) with potent endectocide activity. It is used for parasite control in horses in an oral gel formulation. The principal mode of action of MOX and of other MLs is binding to gamma-aminobutyric (GABA) and glutamate-gated chloride channels. Moxidectin is different from other MLs in that it is a poor substrate for P-glycoproteins (P-gps) and therefore less susceptible to elimination from parasite cells through this mechanism. Due to its unique physicochemical and pharmacokinetic characteristics, MOX provides broad distribution into tissues, long half-life, significant residual antiparasitic activity, and high efficacy against encysted cyathostomin larvae. These characteristics allow for high efficacy and longer treatment interval against all important nematodes, when compared to other equine anthelmintics. A combination of MOX with praziquantel provides expanded spectrum of activity by adding activity against cestodes. Appropriate use of MOX allows for the development of strategic anthelmintic programmes that are different from those with conventional anthelmintics. Fewer treatments are required over a period of time, and therefore impose less frequent selection pressure for resistance. PMID:19778466

Surface assessment and modification of concrete using abrasive blasting

NASA Astrophysics Data System (ADS)

Millman, Lauren R.

Composite systems are applied to concrete substrates to strengthen and extend the service life. Successful restoration or rehabilitation requires surface preparation prior to the application of the overlay. Surface coatings, waterproofing systems, and other external surface applications also require surface preparation prior to application. Abrasive blast media is often used to clean and uniformly roughen the substrate. The appropriate surface roughness is necessary to facilitate a strong bond between the existing substrate and overlay. Thus, surface modification using abrasive blast media (sand and dry ice), their respective environmental effects, surface roughness characterization prior to and after blasting, and the adhesion between the substrate and overlay are the focus of this dissertation. This dissertation is comprised of an introduction, a literature review, and four chapters, the first of which addresses the environmental effects due to abrasive blasting using sand, water, and dry ice. The assessment considered four response variables: carbon dioxide (CO2) emissions, fuel and energy consumption, and project duration. The results indicated that for sand blasting and water jetting, the primary factor contributing to environmental detriment was CO22 emissions from vehicular traffic near the construction site. The second chapter is an analysis of the International Concrete Repair Institute's (ICRI) concrete surface profiles (CSPs) using 3-D optical profilometry. The primary objective was to evaluate the suitability of approximating the 3-D surface (areal) parameters with those extracted from 2-D (linear) profiles. Four profile directions were considered: two diagonals, and lines parallel and transverse to the longitudinal direction of the mold. For any CSP mold, the estimation of the 3-D surface roughness using a 2-D linear profile resulted in underestimation and overestimation errors exceeding 50%, demonstrating the inadequacy of 2-D linear profiles to approximate the 3-D concrete surface profiles. The errors were reduced when a weighted average of the four linear profiles approximated the corresponding 3-D parameter. The following chapter considers the parametric and sensitivity of concrete surface topography measurements. The weighted average of the four 2-D profiles consistently resulted in underestimation of the corresponding 3-D parameters: the dispersion of surface elevations (Sq) and the roughness (Sa). Results indicated the 3-D parameter, Sq, had the least sensitivity to data point reduction. The final chapter investigated surface modification using dry ice and sand blasting. The overall objective was to evaluate the change in the 3-D surface roughness (Sa) following blasting as functions of mix design and as induced by freeze-thaw cycling, and to compare the results obtained using dry ice with those obtained using sand as the blasting media. In general, sand blasting produced larger changes in Sa compared to dry ice blasting for the concrete mix designs considered. The primary mechanism responsible for altering the surface topography of the concrete was the scaling of the superficial cement paste layer on the exposed surface, which was due to freeze-thaw cycling. The largest relative change in roughness following blasting occurred in the control samples, which had not undergone freeze-thaw cycling.

Ultra-broad gain quantum cascade lasers tunable from 6.5 to 10.4 μm.

PubMed

Xie, Feng; Caneau, C; Leblanc, H; Ho, M-T; Zah, C

2015-09-01

We present a quantum cascade laser structure with an ultra-broad gain profile that covers the wavelength range from 6.5 to 10.4 μm. In a grating-tuned external cavity, we demonstrated continuous tuning from 1027  cm(-1) to 1492  cm(-1) with this broad gain laser chip. We also fabricated distributed feedback quantum cascade laser arrays with this active region design and varied grating periods. We demonstrated single wavelength lasing from 962 (10.4) to 1542  cm(-1) (6.5 μm). The frequency coverage (580  cm(-1)) is about 46% of center frequency.

Formation of high-Tc YBa2Cu3O(7-delta) films on Y2BaCuO5 substrate

NASA Astrophysics Data System (ADS)

Wang, W. N.; Lu, H. B.; Lin, W. J.; Yao, P. C.; Hsu, H. E.

1988-07-01

High-Tc superconducting YBa2Cu3O(7-delta) films have been successfully prepared on green Y2BaCuO5 (2115) ceramic substrate. The films have been formed by RF sputtering and screen printing with post annealing at 925 C. Regarding superconducting features, the sharp resistivity drop with Tc onset around 95 K (midpoint 84 K) and 99 K (midpoint 89 K) has been observed for RF sputtered and printed films respectively. Both films show the excellent adhesion towards the 2115 substrate. Powder X-ray diffraction profiles indicate a majority of 1237 phase with preferred orientation for RF sputtered thin film.

Quantitative and Comparative Profiling of Protease Substrates through a Genetically Encoded Multifunctional Photocrosslinker.

PubMed

He, Dan; Xie, Xiao; Yang, Fan; Zhang, Heng; Su, Haomiao; Ge, Yun; Song, Haiping; Chen, Peng R

2017-11-13

A genetically encoded, multifunctional photocrosslinker was developed for quantitative and comparative proteomics. By bearing a bioorthogonal handle and a releasable linker in addition to its photoaffinity warhead, this probe enables the enrichment of transient and low-abundance prey proteins after intracellular photocrosslinking and prey-bait separation, which can be subject to stable isotope dimethyl labeling and mass spectrometry analysis. This quantitative strategy (termed isoCAPP) allowed a comparative proteomic approach to be adopted to identify the proteolytic substrates of an E. coli protease-chaperone dual machinery DegP. Two newly identified substrates were subsequently confirmed by proteolysis experiments. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Use of GC/MS and Microtome Techniques as Methods to Evaluate ODC Free Cleaner Diffusion and Evaporation in Insulation and Phenolic Case Material

NASA Technical Reports Server (NTRS)

Biegert, L. L.

2001-01-01

Because of the 1990 Clean Air Act Amendment (CAAA) many chlorinated solvents used in the aerospace industry are being phased out. Replacement of the ODC (ozone-depleting chemicals) with less volatile, non-ozone depleting cleaners has been extensively studied over the past seven years at Thiokol Propulsion, a Division of Cordant Technologies, Inc. The down selection of ODC replacement cleaners has been based on several factors including the diffusion evaporation of the cleaners in selected substrates. Methodologies were developed to evaluate the cleaner content in substrates. Methods of cutting thin slices of material (microtoming) were combined with GC/MS (gas chromatography/mass spectroscopy) analysis. Substrates evaluated in this study include potential solid rocket motor materials: ASNBR (asbestos-filled nitrile butadiene rubber) and CFEPDM (carbon-filled ethylene propylene dimonomer) insulation and glass (GCP), carbon (CCP) and silica (SCP) cloth phenolic substrates with fibers either parallel (0 deg) or perpendicular (90 deg) to the surface. Residue profiles indicate both cleaner and substrate composition affect the diffusion and subsequent evaporation of the cleaner from the substrate surface.

Buckling analysis of stiff thin films suspended on a substrate with tripod surface relief structure

NASA Astrophysics Data System (ADS)

Yu, Qingmin; Chen, Furong; Li, Ming; Cheng, Huanyu

2017-09-01

A wavy configuration is a simple yet powerful structural design strategy, which has been widely used in flexible and stretchable electronics. A buckled structure created from a prestretch-contact-release process represents an early effort. Substrates with engineered surface relief structures (e.g., rectangular islands or tripod structure) have enabled stretchability to the devices without sacrificing their electric performance (e.g., high areal coverage for LEDs/photovoltaics/batteries/supercapacitors). In particular, the substrate with a tripod surface relief structure allows wrinkled devices to be suspended on a soft tripod substrate. This minimizes the contact area between devices and the deformed substrate, which contributes to a significantly reduced interfacial stress/strain. To uncover the underlying mechanism of such a design, we exploit the energy method to analytically investigate the buckling and postbuckling behaviors of stiff films suspended on a stretchable polymeric substrate with a tripod surface relief structure. Validated by finite element analysis, the predications from such an analytical study elucidate the deformed profile and maximum strain in the buckled and postbuckled stiff thin device films, providing a useful toolkit for future experimental designs.

Direct microfabrication of oxide patterns by local electrodeposition of precisely positioned electrolyte: the case of Cu2O

PubMed Central

Wang, P.; Roberts, R. C.; Ngan, A. H. W.

2016-01-01

An efficient technique for writing 2D oxide patterns on conductive substrates is proposed and demonstrated in this paper. The technique concerns a novel concept for selective electrodeposition, in which a minimum quantity of liquid electrolyte, through an extrusion nozzle, is delivered and manipulated into the desired shape on the substrate, meanwhile being electrodeposited into the product by an applied voltage across the nozzle and substrate. Patterns of primarily Cu2O with 80~90% molar fraction are successfully fabricated on stainless steel substrates using this method. A key factor that allows the solid product to be primarily oxide Cu2O instead of metal Cu – the product predicted by the equilibrium Pourbaix diagram given the unusually large absolute deposition voltage used in this method, is the non-equilibrium condition involved in the process due to the short deposition time. Other factors including the motion of the extrusion nozzle relative to the substrate and the surface profile of the substrate that influence the electrodeposition performance are also discussed. PMID:27255188

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.

Enzyme-substrate relationships in the ubiquitin system: approaches for identifying substrates of ubiquitin ligases.

PubMed

O'Connor, Hazel F; Huibregtse, Jon M

2017-09-01

Protein ubiquitylation is an important post-translational modification, regulating aspects of virtually every biochemical pathway in eukaryotic cells. Hundreds of enzymes participate in the conjugation and deconjugation of ubiquitin, as well as the recognition, signaling functions, and degradation of ubiquitylated proteins. Regulation of ubiquitylation is most commonly at the level of recognition of substrates by E3 ubiquitin ligases. Characterization of the network of E3-substrate relationships is a major goal and challenge in the field, as this expected to yield fundamental biological insights and opportunities for drug development. There has been remarkable success in identifying substrates for some E3 ligases, in many instances using the standard protein-protein interaction techniques (e.g., two-hybrid screens and co-immunoprecipitations paired with mass spectrometry). However, some E3s have remained refractory to characterization, while others have simply not yet been studied due to the sheer number and diversity of E3s. This review will discuss the range of tools and techniques that can be used for substrate profiling of E3 ligases.

Development and Validation of the Role Profile of the Nurse Continence Specialist: A Project of the International Continence Society.

PubMed

Paterson, Janice; Ostaszkiewicz, Joan; Suyasa, I Gede Putu Darma; Skelly, Jennifer; Bellefeuille, Lesley

Although nurses have specialized in the management of incontinence, bladder, bowel, and pelvic floor dysfunction for more than 30 years, there is a lack of awareness and underutilization of their role. This article describes a 6-year project to define, characterize, and validate a role profile of the Nurse Continence Specialist. Data collection used a 2-phase, mixed-methods design. Phase 1 of the project resulted in a draft Nurse Continence Specialist role profile and Phase 2 led to validation of the draft profile. The result was a broad consensus about what constitutes the specific skill set for Nurse Continence Specialist specialization within nursing.

Complementary use of ion beam elastic backscattering and recoil detection analysis for the precise determination of the composition of thin films made of light elements

NASA Astrophysics Data System (ADS)

Climent-Font, A.; Cervera, M.; Hernández, M. J.; Muñoz-Martín, A.; Piqueras, J.

2008-04-01

Rutherford backscattering spectrometry (RBS) is a well known powerful technique to obtain depth profiles of the constituent elements in a thin film deposited on a substrate made of lighter elements. In its standard use the probing beam is typically 2 MeV He. Its capabilities to obtain precise composition profiles are severely diminished when the overlaying film is made of elements lighter than the substrate. In this situation the analysis of the energy of the recoiled element from the sample in the elastic scattering event, the ERDA technique may be advantageous. For the detection of light elements it is also possible to use beams at specific energies producing elastic resonances with these light elements to be analyzed, with a much higher scattering cross sections than the Rutherford values. This technique may be called non-RBS. In this work we report on the complementary use of ERDA with a 30 MeV Cl beam and non-RBS with 1756 keV H ions to characterize thin films made of boron, carbon and nitrogen (BCN) deposited on Si substrates.

Chemical mechanism of D-amino acid oxidase from Rhodotorula gracilis: pH dependence of kinetic parameters.

PubMed Central

Ramón, F; Castillón, M; De La Mata, I; Acebal, C

1998-01-01

The variation of kinetic parameters of d-amino acid oxidase from Rhodotorula gracilis with pH was used to gain information about the chemical mechanism of the oxidation of D-amino acids catalysed by this flavoenzyme. d-Alanine was the substrate used. The pH dependence of Vmax and Vmax/Km for alanine as substrate showed that a group with a pK value of 6.26-7.95 (pK1) must be unprotonated and a group with a pK of 10.8-9.90 (pK2) must be protonated for activity. The lower pK value corresponded to a group on the enzyme involved in catalysis and whose protonation state was not important for binding. The higher pK value was assumed to be the amino group of the substrate. Profiles of pKi for D-aspartate as competitive inhibitor showed that binding is prevented when a group on the enzyme with a pK value of 8.4 becomes unprotonated; this basic group was not detected in Vmax/Km profiles suggesting its involvement in binding of the beta-carboxylic group of the inhibitor. PMID:9461524

Strain transfer through film-substrate interface and surface curvature evolution during a tensile test

NASA Astrophysics Data System (ADS)

He, Wei; Han, Meidong; Goudeau, Philippe; Bourhis, Eric Le; Renault, Pierre-Olivier; Wang, Shibin; Li, Lin-an

2018-03-01

Uniaxial tensile tests on polyimide-supported thin metal films are performed to respectively study the macroscopic strain transfer through an interface and the surface curvature evolution. With a dual digital image correlation (DIC) system, the strains of the film and the substrate can be simultaneously measured in situ during the tensile test. For the true strains below 2% (far beyond the films' elastic limit), a complete longitudinal strain transfer is present irrespective of the film thickness, residual stresses and microstructure. By means of an optical surface profiler, the three-dimensional (3D) topography of film surface can be obtained during straining. As expected, the profile of the specimen center remains almost flat in the tensile direction. Nevertheless, a relatively significant curvature evolution (of the same order with the initial curvature induced by residual stresses) is observed along the transverse direction as a result of a Poisson's ratio mismatch between the film and the substrate. Furthermore, finite element method (FEM) has been performed to simulate the curvature evolution considering the geometric nonlinearity and the perfect strain transfer at the interface, which agrees well with the experimental results.

Transcriptome of an Armillaria root disease pathogen reveals candidate genes involved in host substrate utilization at the host­-pathogen interface

Treesearch

A. L. Ross-Davis; J. E. Stewart; J. W. Hanna; M.-S. Kim; B. J. Knaus; R. Cronn; H. Rai; B. A. Richardson; G. I. McDonald; N. B. Klopfenstein

2013-01-01

Armillaria species display diverse ecological roles ranging from beneficial saprobe to virulent pathogen. Armillaria solidipes (formerly A. ostoyae), a causal agent of Armillaria root disease, is a virulent primary pathogen with a broad host range of woody plants across the Northern Hemisphere. This white-rot pathogen grows between trees as rhizomorphs and attacks...

Highly sensitive and adaptable fluorescence-quenched pair discloses the substrate specificity profiles in diverse protease families

PubMed Central

Poreba, Marcin; Szalek, Aleksandra; Rut, Wioletta; Kasperkiewicz, Paulina; Rutkowska-Wlodarczyk, Izabela; Snipas, Scott J.; Itoh, Yoshifumi; Turk, Dusan; Turk, Boris; Overall, Christopher M.; Kaczmarek, Leszek; Salvesen, Guy S.; Drag, Marcin

2017-01-01

Internally quenched fluorescent (IQF) peptide substrates originating from FRET (Förster Resonance Energy Transfer) are powerful tool for examining the activity and specificity of proteases, and a variety of donor/acceptor pairs are extensively used to design individual substrates and combinatorial libraries. We developed a highly sensitive and adaptable donor/acceptor pair that can be used to investigate the substrate specificity of cysteine proteases, serine proteases and metalloproteinases. This novel pair comprises 7-amino-4-carbamoylmethylcoumarin (ACC) as the fluorophore and 2,4-dinitrophenyl-lysine (Lys(DNP)) as the quencher. Using caspase-3, caspase-7, caspase-8, neutrophil elastase, legumain, and two matrix metalloproteinases (MMP2 and MMP9), we demonstrated that substrates containing ACC/Lys(DNP) exhibit 7 to 10 times higher sensitivity than conventional 7-methoxy-coumarin-4-yl acetic acid (MCA)/Lys(DNP) substrates; thus, substantially lower amounts of substrate and enzyme can be used for each assay. We therefore propose that the ACC/Lys(DNP) pair can be considered a novel and sensitive scaffold for designing substrates for any group of endopeptidases. We further demonstrate that IQF substrates containing unnatural amino acids can be used to investigate protease activities/specificities for peptides containing post-translationally modified amino acids. Finally, we used IQF substrates to re-investigate the P1-Asp characteristic of caspases, thus demonstrating that some human caspases can also hydrolyze substrates after glutamic acid. PMID:28230157

Non-steady state simulation of BOM removal in drinking water biofilters: model development.

PubMed

Hozalski, R M; Bouwer, E J

2001-01-01

A numerical model was developed to simulate the non-steady-state behavior of biologically-active filters used for drinking water treatment. The biofilter simulation model called "BIOFILT" simulates the substrate (biodegradable organic matter or BOM) and biomass (both attached and suspended) profiles in a biofilter as a function of time. One of the innovative features of BIOFILT compared to previous biofilm models is the ability to simulate the effects of a sudden loss in attached biomass or biofilm due to filter backwash on substrate removal performance. A sensitivity analysis of the model input parameters indicated that the model simulations were most sensitive to the values of parameters that controlled substrate degradation and biofilm growth and accumulation including the substrate diffusion coefficient, the maximum rate of substrate degradation, the microbial yield coefficient, and a dimensionless shear loss coefficient. Variation of the hydraulic loading rate or other parameters that controlled the deposition of biomass via filtration did not significantly impact the simulation results.

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

PubMed

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

2018-06-13

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

Contact Electrification of Individual Dielectric Microparticles Measured by Optical Tweezers in Air.

PubMed

Park, Haesung; LeBrun, Thomas W

2016-12-21

We measure charging of single dielectric microparticles after interaction with a glass substrate using optical tweezers to control the particle, measure its charge with a sensitivity of a few electrons, and precisely contact the particle with the substrate. Polystyrene (PS) microparticles adhered to the substrate can be selected based on size, shape, or optical properties and repeatedly loaded into the optical trap using a piezoelectric (PZT) transducer. Separation from the substrate leads to charge transfer through contact electrification. The charge on the trapped microparticles is measured from the response of the particle motion to a step excitation of a uniform electric field. The particle is then placed onto a target location of the substrate in a controlled manner. Thus, the triboelectric charging profile of the selected PS microparticle can be measured and controlled through repeated cycles of trap loading followed by charge measurement. Reversible optical trap loading and manipulation of the selected particle leads to new capabilities to study and control successive and small changes in surface interactions.

Metabolomics Reveal Optimal Grain Preprocessing (Milling) toward Rice Koji Fermentation.

PubMed

Lee, Sunmin; Lee, Da Eun; Singh, Digar; Lee, Choong Hwan

2018-03-21

A time-correlated mass spectrometry (MS)-based metabolic profiling was performed for rice koji made using the substrates with varying degrees of milling (DOM). Overall, 67 primary and secondary metabolites were observed as significantly discriminant among different samples. Notably, a higher abundance of carbohydrate (sugars, sugar alcohols, organic acids, and phenolic acids) and lipid (fatty acids and lysophospholipids) derived metabolites with enhanced hydrolytic enzyme activities were observed for koji made with DOM of 5-7 substrates at 36 h. The antioxidant secondary metabolites (flavonoids and phenolic acid) were relatively higher in koji with DOM of 0 substrates, followed by DOM of 5 > DOM of 7 > DOM of 9 and 11 at 96 h. Hence, we conjecture that the rice substrate preprocessing between DOM of 5 and 7 was potentially optimal toward koji fermentation, with the end product being rich in distinctive organoleptic, nutritional, and functional metabolites. The study rationalizes the substrate preprocessing steps vital for commercial koji making.

Design of Selective Substrates and Activity-Based Probes for Hydrolase Important for Pathogenesis 1 (HIP1) from Mycobacterium tuberculosis.

PubMed

Lentz, Christian S; Ordonez, Alvaro A; Kasperkiewicz, Paulina; La Greca, Florencia; O'Donoghue, Anthony J; Schulze, Christopher J; Powers, James C; Craik, Charles S; Drag, Marcin; Jain, Sanjay K; Bogyo, Matthew

2016-11-11

Although serine proteases are important mediators of Mycobacterium tuberculosis (Mtb) virulence, there are currently no tools to selectively block or visualize members of this family of enzymes. Selective reporter substrates or activity-based probes (ABPs) could provide a means to monitor infection and response to therapy using imaging methods. Here, we use a combination of substrate selectivity profiling and focused screening to identify optimized reporter substrates and ABPs for the Mtb "Hydrolase important for pathogenesis 1" (Hip1) serine protease. Hip1 is a cell-envelope-associated enzyme with minimal homology to host proteases, making it an ideal target for probe development. We identified substituted 7-amino-4-chloro-3-(2-bromoethoxy)isocoumarins as irreversible inhibitor scaffolds. Furthermore, we used specificity data to generate selective reporter substrates and to further optimize a selective chloroisocoumarin inhibitor. These new reagents are potentially useful in delineating the roles of Hip1 during pathogenesis or as diagnostic imaging tools for specifically monitoring Mtb infections.

Design of Selective Substrates and Activity-Based Probes for Hydrolase Important for Pathogenesis 1 (HIP1) from Mycobacterium tuberculosis

PubMed Central

2016-01-01

Although serine proteases are important mediators of Mycobacterium tuberculosis (Mtb) virulence, there are currently no tools to selectively block or visualize members of this family of enzymes. Selective reporter substrates or activity-based probes (ABPs) could provide a means to monitor infection and response to therapy using imaging methods. Here, we use a combination of substrate selectivity profiling and focused screening to identify optimized reporter substrates and ABPs for the Mtb “Hydrolase important for pathogenesis 1” (Hip1) serine protease. Hip1 is a cell-envelope-associated enzyme with minimal homology to host proteases, making it an ideal target for probe development. We identified substituted 7-amino-4-chloro-3-(2-bromoethoxy)isocoumarins as irreversible inhibitor scaffolds. Furthermore, we used specificity data to generate selective reporter substrates and to further optimize a selective chloroisocoumarin inhibitor. These new reagents are potentially useful in delineating the roles of Hip1 during pathogenesis or as diagnostic imaging tools for specifically monitoring Mtb infections. PMID:27739665

Broad H3K4me3 is associated with increased transcription elongation and enhancer activity at tumor-suppressor genes.

PubMed

Chen, Kaifu; Chen, Zhong; Wu, Dayong; Zhang, Lili; Lin, Xueqiu; Su, Jianzhong; Rodriguez, Benjamin; Xi, Yuanxin; Xia, Zheng; Chen, Xi; Shi, Xiaobing; Wang, Qianben; Li, Wei

2015-10-01

Tumor suppressors are mostly defined by inactivating mutations in tumors, yet little is known about their epigenetic features in normal cells. Through integrative analysis of 1,134 genome-wide epigenetic profiles, mutations from >8,200 tumor-normal pairs and our experimental data from clinical samples, we discovered broad peaks for trimethylation of histone H3 at lysine 4 (H3K4me3; wider than 4 kb) as the first epigenetic signature for tumor suppressors in normal cells. Broad H3K4me3 is associated with increased transcription elongation and enhancer activity, which together lead to exceptionally high gene expression, and is distinct from other broad epigenetic features, such as super-enhancers. Genes with broad H3K4me3 peaks conserved across normal cells may represent pan-cancer tumor suppressors, such as TP53 and PTEN, whereas genes with cell type-specific broad H3K4me3 peaks may represent cell identity genes and cell type-specific tumor suppressors. Furthermore, widespread shortening of broad H3K4me3 peaks in cancers is associated with repression of tumor suppressors. Thus, the broad H3K4me3 epigenetic signature provides mutation-independent information for the discovery and characterization of new tumor suppressors.

Is there a link between selectivity and binding thermodynamics profiles?

PubMed

Tarcsay, Ákos; Keserű, György M

2015-01-01

Thermodynamics of ligand binding is influenced by the interplay between enthalpy and entropy contributions of the binding event. The impact of these binding free energy components, however, is not limited to the primary target only. Here, we investigate the relationship between binding thermodynamics and selectivity profiles by combining publicly available data from broad off-target assay profiling and the corresponding thermodynamics measurements. Our analysis indicates that compounds binding their primary targets with higher entropy contributions tend to hit more off-targets compared with those ligands that demonstrated enthalpy-driven binding. Copyright © 2014 Elsevier Ltd. All rights reserved.

Assessment of factors regulating the thermal lens profile and lateral brightness in high power diode lasers

NASA Astrophysics Data System (ADS)

Rieprich, J.; Winterfeldt, M.; Tomm, J.; Kernke, R.; Crump, P.

2017-02-01

The lateral beam parameter product, BPPlat, and resulting lateral brightness of GaAs-based high-power broad-area diode lasers is strongly influenced by the thermal lens profile. We present latest progress in efforts using FEM simulation to interpret how variation in chip construction influences the thermal lens profile, itself determined experimentally using thermography (thermal camera). Important factors are shown to include the vertical (epitaxial) structure, the properties of the submount and the transition between chip and submount, whose behavior is shown to be consistent with the presence of a significant thermal barrier.

Automated Microbial Metabolism Laboratory

NASA Technical Reports Server (NTRS)

1973-01-01

Development of the automated microbial metabolism laboratory (AMML) concept is reported. The focus of effort of AMML was on the advanced labeled release experiment. Labeled substrates, inhibitors, and temperatures were investigated to establish a comparative biochemical profile. Profiles at three time intervals on soil and pure cultures of bacteria isolated from soil were prepared to establish a complete library. The development of a strategy for the return of a soil sample from Mars is also reported.

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.

Determination of defect content and defect profile in semiconductor heterostructures

NASA Astrophysics Data System (ADS)

Zubiaga, A.; Garcia, J. A.; Plazaola, F.; Zúñiga-Pérez, J.; Muñoz-Sanjosé, V.

2011-01-01

In this article we present an overview of the technique to obtain the defects depth profile and width of a deposited layer and multilayer based on positron annihilation spectroscopy. In particular we apply the method to ZnO and ZnO/ZnCdO layers deposited on sapphire substrates. After introducing some terminology we first calculate the trend that the W/S parameters of the Doppler broadening measurements must follow, both in a qualitative and quantitative way. From this point we extend the results to calculate the width and defect profiles in deposited layer samples.

Deciphering Phosphotyrosine-Dependent Signaling Networks in Cancer by SH2 Profiling

PubMed Central

Machida, Kazuya; Khenkhar, Malik

2012-01-01

It has been a decade since the introduction of SH2 profiling, a modular domain-based molecular diagnostics tool. This review covers the original concept of SH2 profiling, different analytical platforms, and their applications, from the detailed analysis of single proteins to broad screening in translational research. Illustrated by practical examples, we discuss the uniqueness and advantages of the approach as well as its limitations and challenges. We provide guidance for basic researchers and oncologists who may consider SH2 profiling in their respective cancer research, especially for those focusing on tyrosine phosphoproteomics. SH2 profiling can serve as an alternative phosphoproteomics tool to dissect aberrant tyrosine kinase pathways responsible for individual malignancies, with the goal of facilitating personalized diagnostics for the treatment of cancer. PMID:23226573

The Case for Optically Thick High-Velocity Broad-Line Region Gas in Active Galactic Nuclei

NASA Astrophysics Data System (ADS)

Snedden, Stephanie A.; Gaskell, C. Martin

2007-11-01

A combined analysis of the profiles of the main broad quasar emission lines in both Hubble Space Telescope and optical spectra shows that while the profiles of the strong UV lines are quite similar, there is frequently a strong increase in the Lyα/Hα ratio in the high-velocity gas. We show that the suggestion that the high-velocity gas is optically thin presents many problems. We show that the relative strengths of the high-velocity wings arise naturally in an optically thick BLR component. An optically thick model successfully explains the equivalent widths of the lines, the Lyα/Hα ratios and flatter Balmer decrements in the line wings, the strengths of C III] and the λ1400 blend, and the strong variability in flux of high-velocity, high-ionization lines (especially He II and He I).

Beam shaping in high-power broad-area quantum cascade lasers using optical feedback

PubMed Central

Ferré, Simon; Jumpertz, Louise; Carras, Mathieu; Ferreira, Robson; Grillot, Frédéric

2017-01-01

Broad-area quantum cascade lasers with high output powers are highly desirable sources for various applications including infrared countermeasures. However, such structures suffer from strongly deteriorated beam quality due to multimode behavior, diffraction of light and self-focusing. Quantum cascade lasers presenting high performances in terms of power and heat-load dissipation are reported and their response to a nonlinear control based on optical feedback is studied. Applying optical feedback enables to efficiently tailor its near-field beam profile. The different cavity modes are sequentially excited by shifting the feedback mirror angle. Further control of the near-field profile is demonstrated using spatial filtering. The impact of an inhomogeneous gain as well as the influence of the cavity width are investigated. Compared to existing technologies, that are complex and costly, beam shaping with optical feedback is a more flexible solution to obtain high-quality mid-infrared sources. PMID:28287175

Beam shaping in high-power broad-area quantum cascade lasers using optical feedback.

PubMed

Ferré, Simon; Jumpertz, Louise; Carras, Mathieu; Ferreira, Robson; Grillot, Frédéric

2017-03-13

Broad-area quantum cascade lasers with high output powers are highly desirable sources for various applications including infrared countermeasures. However, such structures suffer from strongly deteriorated beam quality due to multimode behavior, diffraction of light and self-focusing. Quantum cascade lasers presenting high performances in terms of power and heat-load dissipation are reported and their response to a nonlinear control based on optical feedback is studied. Applying optical feedback enables to efficiently tailor its near-field beam profile. The different cavity modes are sequentially excited by shifting the feedback mirror angle. Further control of the near-field profile is demonstrated using spatial filtering. The impact of an inhomogeneous gain as well as the influence of the cavity width are investigated. Compared to existing technologies, that are complex and costly, beam shaping with optical feedback is a more flexible solution to obtain high-quality mid-infrared sources.

Substrate and pH-Dependent Kinetic Profile of 3-Mercaptopropionate Dioxygenase from Pseudomonas aeruginosa.

PubMed

Fellner, Matthias; Aloi, Sekotilani; Tchesnokov, Egor P; Wilbanks, Sigurd M; Jameson, Guy N L

2016-03-08

Thiol dioxygenases catalyze the synthesis of sulfinic acids in a range of organisms from bacteria to mammals. A thiol dioxygenase from the bacterium Pseudomonas aeruginosa oxidizes both 3-mercaptopropionic acid and cysteine, with a ∼70 fold preference for 3-mercaptopropionic acid over all pHs. This substrate reactivity is widened compared to other thiol dioxygenases and was exploited in this investigation of the residues important for activity. A simple model incorporating two protonation events was used to fit profiles of the Michaelis-Menten parameters determined at different pH values for both substrates. The pKs determined using plots of k(cat)/Km differ at low pH, but not in a way easily attributable to protonation of the substrate alone and share a common value at higher pH. Plots of k(cat) versus pH are also quite different at low pH showing the monoprotonated ES complexes with 3-mercaptopropionic acid and cysteine have different pKs. At higher pH, k(cat) decreases sigmoidally with a similar pK regardless of substrate. Loss of reactivity at high pH is attributed to deprotonation of tyrosine 159 and its influence on dioxygen binding. A mechanism is proposed by which deprotonation of tyrosine 159 both blocks oxygen binding and concomitantly promotes cystine formation. Finally, the role of tyrosine 159 was further probed by production of a G95C variant that is able to form a cysteine-tyrosine crosslink homologous to that found in mammalian cysteine dioxygenases. Activity of this variant is severely impaired. Crystallography shows that when un-crosslinked, the cysteine thiol excludes tyrosine 159 from its native position, while kinetic analysis shows that the thioether bond impairs reactivity of the crosslinked form.

Distinct signalling properties of insulin receptor substrate (IRS)-1 and IRS-2 in mediating insulin/IGF-1 action.

PubMed

Rabiee, Atefeh; Krüger, Marcus; Ardenkjær-Larsen, Jacob; Kahn, C Ronald; Emanuelli, Brice

2018-07-01

Insulin/IGF-1 action is driven by a complex and highly integrated signalling network. Loss-of-function studies indicate that the major insulin/IGF-1 receptor substrate (IRS) proteins, IRS-1 and IRS-2, mediate different biological functions in vitro and in vivo, suggesting specific signalling properties despite their high degree of homology. To identify mechanisms contributing to the differential signalling properties of IRS-1 and IRS-2 in the mediation of insulin/IGF-1 action, we performed comprehensive mass spectrometry (MS)-based phosphoproteomic profiling of brown preadipocytes from wild type, IRS-1 -/- and IRS-2 -/- mice in the basal and IGF-1-stimulated states. We applied stable isotope labeling by amino acids in cell culture (SILAC) for the accurate quantitation of changes in protein phosphorylation. We found ~10% of the 6262 unique phosphorylation sites detected to be regulated by IGF-1. These regulated sites included previously reported substrates of the insulin/IGF-1 signalling pathway, as well as novel substrates including Nuclear Factor I X and Semaphorin-4B. In silico prediction suggests the protein kinase B (PKB), protein kinase C (PKC), and cyclin-dependent kinase (CDK) as the main mediators of these phosphorylation events. Importantly, we found preferential phosphorylation patterns depending on the presence of either IRS-1 or IRS-2, which was associated with specific sets of kinases involved in signal transduction downstream of these substrates such as PDHK1, MAPK3, and PKD1 for IRS-1, and PIN1 and PKC beta for IRS-2. Overall, by generating a comprehensive phosphoproteomic profile from brown preadipocyte cells in response to IGF-1 stimulation, we reveal both common and distinct insulin/IGF-1 signalling events mediated by specific IRS proteins. Copyright © 2018 Elsevier Inc. All rights reserved.

Water-mediated interactions enable smooth substrate transport in a bacterial efflux pump.

PubMed

Vargiu, Attilio Vittorio; Ramaswamy, Venkata Krishnan; Malvacio, Ivana; Malloci, Giuliano; Kleinekathöfer, Ulrich; Ruggerone, Paolo

2018-04-01

Efflux pumps of the Resistance-Nodulation-cell Division superfamily confer multi-drug resistance to Gram-negative bacteria. The most-studied polyspecific transporter belonging to this class is the inner-membrane trimeric antiporter AcrB of Escherichia coli. In previous studies, a functional rotation mechanism was proposed for its functioning, according to which the three monomers undergo concerted conformational changes facilitating the extrusion of substrates. However, the molecular determinants and the energetics of this mechanism still remain unknown, so its feasibility must be proven mechanistically. A computational protocol able to mimic the functional rotation mechanism in AcrB was developed. By using multi-bias molecular dynamics simulations we characterized the translocation of the substrate doxorubicin driven by conformational changes of the protein. In addition, we estimated for the first time the free energy profile associated to this process. We provided a molecular view of the process in agreement with experimental data. Moreover, we showed that the conformational changes occurring in AcrB enable the formation of a layer of structured waters on the internal surface of the transport channel. This water layer, in turn, allows for a fairly constant hydration of the substrate, facilitating its diffusion over a smooth free energy profile. Our findings reveal a new molecular mechanism of polyspecific transport whereby water contributes by screening potentially strong substrate-protein interactions. We provided a mechanistic understanding of a fundamental process related to multi-drug transport. Our results can help rationalizing the behavior of other polyspecific transporters and designing compounds avoiding extrusion or inhibitors of efflux pumps. Copyright © 2018 The Author(s). Published by Elsevier B.V. All rights reserved.

Atypical profiles and modulations of heme-enzymes catalyzed outcomes by low amounts of diverse additives suggest diffusible radicals' obligatory involvement in such redox reactions.

PubMed

Manoj, Kelath Murali; Parashar, Abhinav; Venkatachalam, Avanthika; Goyal, Sahil; Satyalipsu; Singh, Preeti Gunjan; Gade, Sudeep K; Periyasami, Kalaiselvi; Jacob, Reeba Susan; Sardar, Debosmita; Singh, Shanikant; Kumar, Rajan; Gideon, Daniel A

2016-06-01

Peroxidations mediated by heme-enzymes have been traditionally studied under a single-site (heme distal pocket), non-sequential (ping-pong), two-substrates binding scheme of Michaelis-Menten paradigm. We had reported unusual modulations of peroxidase and P450 reaction outcomes and explained it invoking diffusible reactive species [Manoj, 2006; Manoj et al., 2010; Andrew et al., 2011, Parashar et al., 2014 & Venkatachalam et al., 2016]. A systematic investigation of specific product formation rates was undertaken to probe the hypothesis that involvement of diffusible reactive species could explain undefined substrate specificities and maverick modulations (sponsored by additives) of heme-enzymes. When the rate of specific product formation was studied as a function of reactants' concentration or environmental conditions, we noted marked deviations from normal profiles. We report that heme-enzyme mediated peroxidations of various substrates are inhibited (or activated) by sub-equivalent concentrations of diverse redox-active additives and this is owing to multiple redox equilibriums in the milieu. At low enzyme and peroxide concentrations, the enzyme is seen to recycle via a one-electron (oxidase) cycle, which does not require the substrate to access the heme centre. Schemes are provided that explain the complex mechanistic cycle, kinetics & stoichiometry. It is not obligatory for an inhibitor or substrate to interact with the heme centre for influencing overall catalysis. Roles of diffusible reactive species explain catalytic outcomes at low enzyme and reactant concentrations. The current work highlights the scope/importance of redox enzyme reactions that could occur "out of the active site" in biological or in situ systems. Copyright © 2016 Elsevier B.V. and Société française de biochimie et biologie Moléculaire (SFBBM). All rights reserved.

Controlling astigmatism and polarization in a stripe heterojunction laser

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

Boroshnev, A.V.; Gorshkova, O.A.; Kobyakova, M.S.

1985-02-01

It is shown that it is possible to change the waveguide properties of a heterojunction laser and to control its optical characteristics in a single heterostructure fabricated on a substrate with a terraced profile. (AIP)

Oxybenzone oxidation following solar irradiation of skin: photoprotection versus antioxidant inactivation.

PubMed

Schallreuter, K U; Wood, J M; Farwell, D W; Moore, J; Edwards, H G

1996-03-01

We used noninvasive Fourier transform (FT) Raman spectroscopy to follow the fate of the broadly used ultraviolet UVA sun blocker, oxybenzone, after topical application to the skin. Our results showed that oxybenzone is rapidly photo-oxidized, yielding oxybenzone semiquinone, a potent electrophile, which reacts with thiol groups on important anti-oxidant enzymes and substrates, such as thioredoxin reductase and reduced glutathione, respectively. Although oxybenzone is an excellent broad spectrum UVA filter, its rapid oxidation followed by the inactivation of important antioxidant systems indicates that this substance may be rather harmful to the homeostasis of the epidermis. Furthermore, these results demonstrate that FT-Raman spectroscopy is a useful method for studying the transport and metabolism of active ingredients in topical preparations.

Two-dimensional analytical modeling of a linear variable filter for spectral order sorting.

PubMed

Ko, Cheng-Hao; Wu, Yueh-Hsun; Tsai, Jih-Run; Wang, Bang-Ji; Chakraborty, Symphony

2016-06-10

A two-dimensional thin film thickness model based on the geometry of a commercial coater which can calculate more effectively the profiles of linear variable filters (LVFs) has been developed. This is done by isolating the substrate plane as an independent coordinate (local coordinate), while the rotation and translation matrices are used to establish the coordinate transformation and combine the characteristic vector with the step function to build a borderline which can conclude whether the local mask will block the deposition or not. The height of the local mask has been increased up to 40 mm in the proposed model, and two-dimensional simulations are developed to obtain a thin film profile deposition on the substrate inside the evaporation chamber to achieve the specific request of producing a LVF zone width in a more economical way than previously reported [Opt. Express23, 5102 (2015)OPEXFF1094-408710.1364/OE.23.005102].

Analytical solutions for the profile of two-dimensional droplets with finite-length precursor films

NASA Astrophysics Data System (ADS)

Perazzo, Carlos Alberto; Mac Intyre, J. R.; Gomba, J. M.

2017-12-01

By means of the lubrication approximation we obtain the full family of static bidimensional profiles of a liquid resting on a substrate under partial-wetting conditions imposed by a disjoining-conjoining pressure. We show that for a set of quite general disjoining-conjoining pressure potentials, the free surface can adopt only five nontrivial static patterns; in particular, we find solutions when the height goes to zero which describe satisfactorily the complete free surface for a finite amount of fluid deposited on a substrate. To test the extension of the applicability of our solutions, we compare them with those obtained when the lubrication approximations are not employed and under conditions where the lubrication hypothesis are not strictly valid, and also with axisymmetric solutions. For a given disjoining-conjoining potential, we report a new analytical solution that accounts for all the five possible solutions.

Evaluation of the effect of process variables on the fatty acid profile of single cell oil produced by Mortierella using solid-state fermentation.

PubMed

Asadi, Seyedeh Zeinab; Khosravi-Darani, Kianoush; Nikoopour, Houshang; Bakhoda, Hossein

2015-03-01

This article reviews some of the aspects of single cell oil (SCO) production using solid-state fermentation (SSF) by fungi of the genus Mortierella. This article provides an overview of the advantages of SSF for SCO formation by the aforementioned fungus and demonstrates that the content of the polyunsaturated fatty acids (PUFA) depend on the type of fermentation media and culture conditions. Process variables that influence lipid accumulation by Mortierella spp. and the profile of the fatty acids are discussed, including incubation temperature, time, aeration, growth phase of the mycelium, particle size of the substrate, carbon to nitrogen ratio, initial moisture content and pH as well as supplementation of the substrate with nitrogen and oil. Finally, the article highlights future research trends for the scaled-up production of PUFAs in SSF.

Quasi-Bessel beams from asymmetric and astigmatic illumination sources.

PubMed

Müller, Angelina; Wapler, Matthias C; Schwarz, Ulrich T; Reisacher, Markus; Holc, Katarzyna; Ambacher, Oliver; Wallrabe, Ulrike

2016-07-25

We study the spatial intensity distribution and the self-reconstruction of quasi-Bessel beams produced from refractive axicon lenses with edge emitting laser diodes as asymmetric and astigmatic illumination sources. Comparing these to a symmetric mono-mode fiber source, we find that the asymmetry results in a transition of a quasi-Bessel beam into a bow-tie shaped pattern and eventually to a line shaped profile at a larger distance along the optical axis. Furthermore, we analytically estimate and discuss the effects of astigmatism, substrate modes and non-perfect axicons. We find a good agreement between experiment, simulation and analytic considerations. Results include the derivation of a maximal axicon angle related to astigmatism of the illuminating beam, impact of laser diode beam profile imperfections like substrate modes and a longitudinal oscillation of the core intensity and radius caused by a rounded axicon tip.

Epitaxial solar cells fabrication

NASA Technical Reports Server (NTRS)

Daiello, R. V.; Robinson, P. H.; Kressel, H.

1975-01-01

Silicon epitaxy has been studied for the fabrication of solar cell structures, with the intent of optimizing efficiency while maintaining suitability for space applications. SiH2CL2 yielded good quality layers and junctions with reproducible impurity profiles. Diode characteristics and lifetimes in the epitaxial layers were investigated as a function of epitaxial growth conditions and doping profile, as was the effect of substrates and epitaxial post-gettering on lifetime. The pyrolytic decomposition of SiH4 was also used in the epitaxial formation of highly doped junction layers on bulk Si wafers. The effects of junction layer thickness and bulk background doping level on cell performance, in particular, open-circuit voltage, were investigated. The most successful solar cells were fabricated with SiH2 CL2 to grow p/n layers on n(+) substrates. The best performance was obtained from a p(+)/p/n/n(+) structure grown with an exponential grade in the n-base layer.

Enantioselective photochemistry via Lewis acid catalyzed triplet energy transfer

PubMed Central

Blum, Travis R.; Miller, Zachary D.; Bates, Desiree M.; Guzei, Ilia A.; Yoon, Tehshik P.

2017-01-01

Relatively few catalytic systems are able to control the stereochemistry of electronically excited organic intermediates. Here we report the discovery that a chiral Lewis acid complex can catalyze triplet energy transfer from an electronically excited photosensitizer. This strategy is applied to asymmetric [2+2] photocycloadditions of 2′-hydroxychalcones using tris(bipyridyl) ruthenium(II) as a sensitizer. A variety of electrochemical, computational, and spectroscopic data rule out substrate activation via photoinduced electron transfer and instead support a mechanism in which Lewis acid coordination dramatically lowers the triplet energy of the chalcone substrate. We expect that this approach will enable chemists to more broadly apply their detailed understanding of chiral Lewis acid catalysis to stereocontrol in reactions of electronically excited states. PMID:27980203

Recent Advances in the Structural Mechanisms of DNA Glycosylases

PubMed Central

Brooks, Sonja C.; Adhikary, Suraj; Rubinson, Emily H.; Eichman, Brandt F.

2012-01-01

DNA glycosylases safeguard the genome by locating and excising a diverse array of aberrant nucleobases created from oxidation, alkylation, and deamination of DNA. Since the discovery 28 years ago that these enzymes employ a base flipping mechanism to trap their substrates, six different protein architectures have been identified to perform the same basic task. Work over the past several years has unraveled details for how the various DNA glycosylases survey DNA, detect damage within the duplex, select for the correct modification, and catalyze base excision. Here, we provide a broad overview of these latest advances in glycosylase mechanisms gleaned from structural enzymology, highlighting features common to all glycosylases as well as key differences that define their particular substrate specificities. PMID:23076011

Studies on nickel-tungsten oxide thin films

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

Usha, K. S.; Sivakumar, R., E-mail: krsivakumar1979@yahoo.com; Sanjeeviraja, C.

2014-10-15

Nickel-Tungsten oxide (95:5) thin films were prepared by rf sputtering at 200W rf power with various substrate temperatures. X-ray diffraction study reveals the amorphous nature of films. The substrate temperature induced decrease in energy band gap with a maximum transmittance of 71%1 was observed. The Micro-Raman study shows broad peaks at 560 cm{sup −1} and 1100 cm{sup −1} correspond to Ni-O vibration and the peak at 860 cm{sup −1} can be assigned to the vibration of W-O-W bond. Photoluminescence spectra show two peaks centered on 420 nm and 485 nm corresponding to the band edge emission and vacancies created duemore » to the addition of tungsten, respectively.« less

Modifying Yeast Tolerance to Inhibitory Conditions of Ethanol Production Processes

PubMed Central

Caspeta, Luis; Castillo, Tania; Nielsen, Jens

2015-01-01

Saccharomyces cerevisiae strains having a broad range of substrate utilization, rapid substrate consumption, and conversion to ethanol, as well as good tolerance to inhibitory conditions are ideal for cost-competitive ethanol production from lignocellulose. A major drawback to directly design S. cerevisiae tolerance to inhibitory conditions of lignocellulosic ethanol production processes is the lack of knowledge about basic aspects of its cellular signaling network in response to stress. Here, we highlight the inhibitory conditions found in ethanol production processes, the targeted cellular functions, the key contributions of integrated -omics analysis to reveal cellular stress responses according to these inhibitors, and current status on design-based engineering of tolerant and efficient S. cerevisiae strains for ethanol production from lignocellulose. PMID:26618154

Mechanistic and Structural Analyses of the Roles of Active Site Residues in the Yeast Polyamine Oxidase Fms1: Characterization of the N195A and D94N Enzymes†

PubMed Central

Adachi, Mariya S.; Taylor, Alexander B.; Hart, P. John; Fitzpatrick, Paul F.

2012-01-01

The flavoprotein Fms1 from Saccharomyces cerevisiae catalyzes the oxidation of spermine in the biosynthetic pathway for pantothenic acid. The same reaction is catalyzed by the mammalian polyamine and spermine oxidases. The active site of Fms1 contains three amino acid residues positioned to interact with the polyamine substrate, His67, Asn195, and Asp94. These three residues form a hydrogen-bonding triad with Asn195 the central residue. Previous studies of the effects of mutating His67 are consistent with that residue being important both for interacting with the substrate and for maintaining the hydrogen bonds in the triad (Adachi, M. S., Taylor, A. B., Hart, P. J., and Fitzpatrick, P. F. (2012) Biochemistry 51, 4888-4897). The N195A and D94N enzymes have now been characterized to evaluate their roles in catalysis. Both mutations primarily affect the reductive half-reaction. With N1-acetylspermine as substrate, the rate constant for flavin reduction decreases ~450-fold for both mutations; the effects with spermine as substrate are smaller, 20- to 40-fold. The kcat/Kamine and kcat pH profiles with N1acetylspermine are only slightly changed from the profiles for the wild-type enzyme, consistent with the pKa values arising from the amine substrate or product and not from active site residues. The structure of the N195A enzyme was determined at a resolution of 2.0 Å. The structure shows a molecule of tetraethylene glycol in the active site and establishes that the mutation has no effect on the protein structure. Overall, the results are consistent with the role of Asn195 and Asp94 being to properly position the polyamine substrate for oxidation. PMID:23034052

Mechanistic and structural analyses of the roles of active site residues in yeast polyamine oxidase Fms1: characterization of the N195A and D94N enzymes.

PubMed

Adachi, Mariya S; Taylor, Alexander B; Hart, P John; Fitzpatrick, Paul F

2012-10-30

Flavoprotein Fms1 from Saccharomyces cerevisiae catalyzes the oxidation of spermine in the biosynthetic pathway for pantothenic acid. The same reaction is catalyzed by the mammalian polyamine and spermine oxidases. The active site of Fms1 contains three amino acid residues positioned to interact with the polyamine substrate, His67, Asn195, and Asp94. These three residues form a hydrogen-bonding triad with Asn195 being the central residue. Previous studies of the effects of mutating His67 are consistent with that residue being important both for interacting with the substrate and for maintaining the hydrogen bonds in the triad [Adachi, M. S., Taylor, A. B., Hart, P. J., and Fitzpatrick, P. F. (2012) Biochemistry 51, 4888-4897]. The N195A and D94N enzymes have now been characterized to evaluate their roles in catalysis. Both mutations primarily affect the reductive half-reaction. With N(1)-acetylspermine as the substrate, the rate constant for flavin reduction decreases ~450-fold for both mutations; the effects with spermine as the substrate are smaller, 20-40-fold. The k(cat)/K(amine)- and k(cat)-pH profiles with N(1)-acetylspermine are only slightly changed from the profiles for the wild-type enzyme, consistent with the pK(a) values arising from the amine substrate or product and not from active site residues. The structure of the N195A enzyme was determined at a resolution of 2.0 Å. The structure shows a molecule of tetraethylene glycol in the active site and establishes that the mutation has no effect on the protein structure. Overall, the results are consistent with the role of Asn195 and Asp94 being to properly position the polyamine substrate for oxidation.

Characterization and identification of ubiquitin conjugation sites with E3 ligase recognition specificities.

PubMed

Nguyen, Van-Nui; Huang, Kai-Yao; Huang, Chien-Hsun; Chang, Tzu-Hao; Bretaña, Neil; Lai, K; Weng, Julia; Lee, Tzong-Yi

2015-01-01

In eukaryotes, ubiquitin-conjugation is an important mechanism underlying proteasome-mediated degradation of proteins, and as such, plays an essential role in the regulation of many cellular processes. In the ubiquitin-proteasome pathway, E3 ligases play important roles by recognizing a specific protein substrate and catalyzing the attachment of ubiquitin to a lysine (K) residue. As more and more experimental data on ubiquitin conjugation sites become available, it becomes possible to develop prediction models that can be scaled to big data. However, no development that focuses on the investigation of ubiquitinated substrate specificities has existed. Herein, we present an approach that exploits an iteratively statistical method to identify ubiquitin conjugation sites with substrate site specificities. In this investigation, totally 6259 experimentally validated ubiquitinated proteins were obtained from dbPTM. After having filtered out homologous fragments with 40% sequence identity, the training data set contained 2658 ubiquitination sites (positive data) and 5532 non-ubiquitinated sites (negative data). Due to the difficulty in characterizing the substrate site specificities of E3 ligases by conventional sequence logo analysis, a recursively statistical method has been applied to obtain significant conserved motifs. The profile hidden Markov model (profile HMM) was adopted to construct the predictive models learned from the identified substrate motifs. A five-fold cross validation was then used to evaluate the predictive model, achieving sensitivity, specificity, and accuracy of 73.07%, 65.46%, and 67.93%, respectively. Additionally, an independent testing set, completely blind to the training data of the predictive model, was used to demonstrate that the proposed method could provide a promising accuracy (76.13%) and outperform other ubiquitination site prediction tool. A case study demonstrated the effectiveness of the characterized substrate motifs for identifying ubiquitination sites. The proposed method presents a practical means of preliminary analysis and greatly diminishes the total number of potential targets required for further experimental confirmation. This method may help unravel their mechanisms and roles in E3 recognition and ubiquitin-mediated protein degradation.

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.

Structural basis for the substrate selectivity of a HAD phosphatase from Thermococcus onnurineus NA1.

PubMed

Ngo, Tri Duc; Van Le, Binh; Subramani, Vinod Kumar; Thi Nguyen, Chi My; Lee, Hyun Sook; Cho, Yona; Kim, Kyeong Kyu; Hwang, Hye-Yeon

2015-05-22

Proteins in the haloalkaloic acid dehalogenase (HAD) superfamily, which is one of the largest enzyme families, is generally composed of a catalytic core domain and a cap domain. Although proteins in this family show broad substrate specificities, the mechanisms of their substrate recognition are not well understood. In this study, we identified a new substrate binding motif of HAD proteins from structural and functional analyses, and propose that this motif might be crucial for interacting with hydrophobic rings of substrates. The crystal structure of TON_0338, one of the 17 putative HAD proteins identified in a hyperthermophilic archaeon, Thermococcus onnurineus NA1, was determined as an apo-form at 2.0 Å resolution. In addition, we determined the crystal structure TON_0338 in complex with Mg(2+) or N-cyclohexyl-2-aminoethanesulfonic acid (CHES) at 1.7 Å resolution. Examination of the apo-form and CHES-bound structures revealed that CHES is sandwiched between Trp58 and Trp61, suggesting that this Trp sandwich might function as a substrate recognition motif. In the phosphatase assay, TON_0338 was shown to have high activity for flavin mononucleotide (FMN), and the docking analysis suggested that the flavin of FMN may interact with Trp58 and Trp61 in a way similar to that observed in the crystal structure. Moreover, the replacement of these tryptophan residues significantly reduced the phosphatase activity for FMN. Our results suggest that WxxW may function as a substrate binding motif in HAD proteins, and expand the diversity of their substrate recognition mode. Copyright © 2015 Elsevier Inc. All rights reserved.

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.

Molecular aspect ratio and anchoring strength effects in a confined Gay-Berne liquid crystal

NASA Astrophysics Data System (ADS)

Cañeda-Guzmán, E.; Moreno-Razo, J. A.; Díaz-Herrera, E.; Sambriski, E. J.

2014-04-01

Phase diagrams for Gay-Berne (GB) fluids were obtained from molecular dynamics simulations for GB(2, 5, 1, 2) (i.e. short mesogens) and GB(3, 5, 1, 2) (i.e. long mesogens), which yield isotropic, nematic, and smectic-B phases. The long-mesogen fluid also yields the smectic-A phase. Ordered phases of the long-mesogen fluid form at higher temperatures and lower densities when compared to those of the short-mesogen fluid. The effect of confinement under weak and strong substrate couplings in slab geometry was investigated. Compared to the bulk, the isotropic-nematic transition does not shift in temprature significantly for the weakly coupled substrate in either mesogen fluid. However, the strongly coupled substrate shifts the transition to lower temperature. Confinement induces marked stratification in the short-mesogen fluid. This effect diminishes with distance from the substrate, yielding bulk-like behaviour in the slab central region. Fluid stratification is very weak for the long-mesogen fluid, but the strongly coupled substrate induces 'smectisation', an ordering effect that decays with distance. Orientation of the fluid on the substrate depends on the mesogen. There is no preferred orientation in a plane parallel to the substrate for the weakly coupled case. In the strongly coupled case, the mesogen orientation mimics that of adjacent fluid layers. Planar anchoring is observed with a broad distribution of orientations in the weakly coupled case. In the strongly coupled case, the distribution leans toward planar orientations for the short-mesogen fluid, while a marginal preference for tilting persists in the long-mesogen fluid.

Angiotensin-I converting enzyme (ACE): structure, biological roles, and molecular basis for chloride ion dependence.

PubMed

Masuyer, Geoffrey; Yates, Christopher J; Sturrock, Edward D; Acharya, K Ravi

2014-10-01

Somatic angiotensin-I converting enzyme (sACE) has an essential role in the regulation of blood pressure and electrolyte fluid homeostasis. It is a zinc protease that cleaves angiotensin-I (AngI), bradykinin, and a broad range of other signalling peptides. The enzyme activity is provided by two homologous domains (N- and C-), which display clear differences in substrate specificities and chloride activation. The presence of chloride ions in sACE and its unusual role in activity was identified early on in the characterisation of the enzyme. The molecular mechanisms of chloride activation have been investigated thoroughly through mutagenesis studies and shown to be substrate-dependent. Recent results from X-ray crystallography structural analysis have provided the basis for the intricate interactions between ACE, its substrate and chloride ions. Here we describe the role of chloride ions in human ACE and its physiological consequences. Insights into the chloride activation of the N- and C-domains could impact the design of improved domain-specific ACE inhibitors.

Comparative reactivity of different types of stable cyclic and acyclic mono- and diamino carbenes with simple organic substrates.

PubMed

Martin, David; Canac, Yves; Lavallo, Vincent; Bertrand, Guy

2014-04-02

A series of stable carbenes, featuring a broad range of electronic properties, were reacted with simple organic substrates. The N,N-dimesityl imidazolylidene (NHC) does not react with isocyanides, whereas anti-Bredt di(amino)carbene (pyr-NHC), cyclic (alkyl)(amino)carbene (CAAC), acyclic di(amino)carbene (ADAC), and acyclic (alkyl)(amino)carbene (AAAC) give rise to the corresponding ketenimines. NHCs are known to promote the benzoin condensation, and we found that the CAAC, pyr-NHC, and ADAC react with benzaldehyde to give the ketone tautomer of the Breslow intermediate, whereas the AAAC first gives the corresponding epoxide and ultimately the Breslow intermediate, which can be isolated. Addition of excess benzaldehyde to the latter does not lead to benzoin but to a stable 1,3-dioxolane. Depending on the electronic properties of carbenes, different products are also obtained with methyl acrylate as a substrate. The critical role of the carbene electrophilicity on the outcome of reactions is discussed.

Multiple chitinases of an endophytic Serratia proteamaculans 568 generate chitin oligomers.

PubMed

Purushotham, Pallinti; Sarma, P V S R N; Podile, Appa Rao

2012-05-01

Serratia proteamaculans 568 genome revealed the presence of four family 18 chitinases (Sp ChiA, Sp ChiB, Sp ChiC, and Sp ChiD). Heterologous expression and characterization of Sp ChiA, Sp ChiB, and Sp ChiC showed that these enzymes were optimally active at pH 6.0-7.0, and 40°C. The three Sp chitinases displayed highest activity/binding to β-chitin and showed broad range of substrate specificities, and released dimer as major end product from oligomeric and polymeric substrates. Longer incubation was required for hydrolysis of trimer for the three Sp chitinases. The three Sp chitinases released up to tetramers from colloidal chitin substrate. Sp ChiA and Sp ChiB were processive chitinases, while Sp ChiC was a non-processive chitinase. Based on the known structures of ChiA and ChiB from S. marcescens, 3D models of Sp ChiA and Sp ChiB were generated. Copyright © 2012 Elsevier Ltd. All rights reserved.

Transparent and conductive indium doped cadmium oxide thin films prepared by pulsed filtered cathodic arc deposition

DOE PAGES

Zhu, Yuankun; Mendelsberg, Rueben J.; Zhu, Jiaqi; ...

2012-11-26

Indium doped cadmium oxide (CdO:In) films with different In concentrations were prepared on low-cost glass substrates by pulsed filtered cathodic arc deposition (PFCAD). In this study, it is shown that polycrystalline CdO:In films with smooth surface and dense structure are obtained. In-doping introduces extra electrons leading to remarkable improvements of electron mobility and conductivity, as well as improvement in the optical transmittance due to the Burstein Moss effect. CdO:In films on glass substrates with thickness near 230 nm show low resistivity of 7.23 x 10 -5 Ωcm, high electron mobility of 142 cm 2/Vs, and mean transmittance over 80% frommore » 500-1250 nm (including the glass substrate). These high quality pulsed arc-grown CdO:In films are potentially suitable for high efficiency multi-junction solar cells that harvest a broad range of the solar spectrum.« less

Substrateless Welding of Self-Assembled Silver Nanowires at Air/Water Interface.

PubMed

Hu, Hang; Wang, Zhongyong; Ye, Qinxian; He, Jiaqing; Nie, Xiao; He, Gufeng; Song, Chengyi; Shang, Wen; Wu, Jianbo; Tao, Peng; Deng, Tao

2016-08-10

Integrating connected silver nanowire networks with flexible polymers has appeared as a popular way to prepare flexible electronics. To reduce the contact resistance and enhance the connectivity between silver nanowires, various welding techniques have been developed. Herein, rather than welding on solid supporting substrates, which often requires complicated transferring operations and also may pose damage to heat-sensitive substrates, we report an alternative approach to prepare easily transferrable conductive networks through welding of self-assembled silver nanowires at the air/water interface using plasmonic heating. The intriguing welding behavior of partially aligned silver nanowires was analyzed with combined experimental observation and theoretical modeling. The underlying water not only physically supports the assembled silver nanowires but also buffers potential overheating during the welding process, thereby enabling effective welding within a broad range of illumination power density and illumination duration. The welded networks could be directly integrated with PDMS substrates to prepare high-performance stable flexible heaters that are stretchable, bendable, and can be easily patterned to explore selective heating applications.

Quantitative adhesion characterization of antireflective coatings in multijunction photovoltaics

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

Brock, Ryan; Rewari, Raunaq; Novoa, Fernando D.

We discuss the development of a new composite dual cantilever beam (cDCB) thin-film adhesion testing method, which enables the quantitative measurement of adhesion on the thin and fragile substrates used in multijunction photovoltaics. In particular, we address the adhesion of several 2- and 3-layer antireflective coating systems on multijunction cells. By varying interface chemistry and morphology through processing, we demonstrate the marked effects on adhesion and help to develop an understanding of how high adhesion can be achieved, as adhesion values ranging from 0.5 J/m2 to 10 J/m2 were measured. Damp heat (85 degrees C/85% RH) was used to invokemore » degradation of interfacial adhesion. We demonstrate that even with germanium substrates that fracture relatively easily, quantitative measurements of adhesion can be made at high test yield. The cDCB test is discussed as an important new methodology, which can be broadly applied to any system that makes use of thin, brittle, or otherwise fragile substrates.« less

Impact of nanoscale topography on genomics and proteomics of adherent bacteria.

PubMed

Rizzello, Loris; Sorce, Barbara; Sabella, Stefania; Vecchio, Giuseppe; Galeone, Antonio; Brunetti, Virgilio; Cingolani, Roberto; Pompa, Pier Paolo

2011-03-22

Bacterial adhesion onto inorganic/nanoengineered surfaces is a key issue in biotechnology and medicine, because it is one of the first necessary steps to determine a general pathogenic event. Understanding the molecular mechanisms of bacteria-surface interaction represents a milestone for planning a new generation of devices with unanimously certified antibacterial characteristics. Here, we show how highly controlled nanostructured substrates impact the bacterial behavior in terms of morphological, genomic, and proteomic response. We observed by atomic force microscopy (AFM) and scanning electron microscopy (SEM) that type-1 fimbriae typically disappear in Escherichia coli adherent onto nanostructured substrates, as opposed to bacteria onto reference glass or flat gold surfaces. A genetic variation of the fimbrial operon regulation was consistently identified by real time qPCR in bacteria interacting with the nanorough substrates. To gain a deeper insight into the molecular basis of the interaction mechanisms, we explored the entire proteomic profile of E. coli by 2D-DIGE, finding significant changes in the bacteria adherent onto the nanorough substrates, such as regulations of proteins involved in stress processes and defense mechanisms. We thus demonstrated that a pure physical stimulus, that is, a nanoscale variation of surface topography, may play per se a significant role in determining the morphological, genetic, and proteomic profile of bacteria. These data suggest that in depth investigations of the molecular processes of microorganisms adhering to surfaces are of great importance for the design of innovative biomaterials with active biological functionalities.

High efficiency low cost thin film silicon solar cell design and method for making

DOEpatents

Sopori, B.L.

1999-04-27

A semiconductor device is described having a substrate, a conductive intermediate layer deposited onto said substrate, wherein the intermediate layer serves as a back electrode, an optical reflector, and an interface for impurity gettering, and a semiconductor layer deposited onto said intermediate layer, wherein the semiconductor layer has a grain size at least as large as the layer thickness, and preferably about ten times the layer thickness. The device is formed by depositing a metal layer on a substrate, depositing a semiconductive material on the metal-coated substrate to produce a composite structure, and then optically processing the composite structure by illuminating it with infrared electromagnetic radiation according to a unique time-energy profile that first produces pits in the backside surface of the semiconductor material, then produces a thin, highly reflective, low resistivity alloy layer over the entire area of the interface between the semiconductor material and the metal layer, and finally produces a grain-enhanced semiconductor layer. The time-energy profile includes increasing the energy to a first energy level to initiate pit formation and create the desired pit size and density, then ramping up to a second energy level in which the entire device is heated to produce an interfacial melt, and finally reducing the energy to a third energy level and holding for a period of time to allow enhancement in the grain size of the semiconductor layer. 9 figs.

Effect of high-oleic canola and flaxseed oils on energy expenditure and body composition in hypercholesterolemic subjects.

PubMed

Gillingham, Leah G; Robinson, Kimberley S; Jones, Peter J H

2012-11-01

The fatty acid profile of dietary fats may contribute to its channelling toward oxidation versus storage, influencing energy and weight balance. Our objective was to compare the effects of diets enriched with high-oleic canola oil (HOCO), alone or blended with flaxseed oil (FXCO), on energy expenditure, substrate utilization, and body composition versus a typical Western diet (WD). Using a randomized crossover design, 34 hypercholesterolemic subjects (n=22 females) consumed 3 controlled diets for 28 days containing ~49% energy from carbohydrate, 14% energy from protein, and 37% energy from fat, of which 70% of fat was provided by HOCO rich in oleic acid, FXCO rich in alpha-linolenic acid, or WD rich in saturated fat. Indirect calorimetry measured energy expenditure and substrate oxidation. Body composition was analyzed by dual-energy x-ray absorptiometry. After 28 days, resting and postprandial energy expenditure and substrate oxidation were not different after consumption of the HOCO or FXCO diets compared with a typical Western diet. No significant changes in body composition measures were observed between diets. However, the android-to-gynoid ratio tended to increase (P=.055) after the FXCO diet compared with the HOCO diet. The data suggest that substituting a typical Western dietary fatty acid profile with HOCO or FXCO does not significantly modulate energy expenditure, substrate oxidation or body composition in hypercholesterolemic males and females. Copyright © 2012 Elsevier Inc. All rights reserved.

Efficacy of Enzyme and Substrate Reduction Therapy with a Novel Antagonist of Glucosylceramide Synthase for Fabry Disease

PubMed Central

Ashe, Karen M; Budman, Eva; Bangari, Dinesh S; Siegel, Craig S; Nietupski, Jennifer B; Wang, Bing; Desnick, Robert J; Scheule, Ronald K; Leonard, John P; Cheng, Seng H; Marshall, John

2015-01-01

Fabry disease, an X-linked glycosphingolipid storage disorder, is caused by the deficient activity of α-galactosidase A (α-Gal A). This results in the lysosomal accumulation in various cell types of its glycolipid substrates, including globotriaosylceramide (GL-3) and lysoglobotriaosylceramide (globotriaosyl lysosphingolipid, lyso-GL-3), leading to kidney, heart, and cerebrovascular disease. To complement and potentially augment the current standard of care, biweekly infusions of recombinant α-Gal A, the merits of substrate reduction therapy (SRT) by selectively inhibiting glucosylceramide synthase (GCS) were examined. Here, we report the development of a novel, orally available GCS inhibitor (Genz-682452) with pharmacological and safety profiles that have potential for treating Fabry disease. Treating Fabry mice with Genz-682452 resulted in reduced tissue levels of GL-3 and lyso-GL-3 and a delayed loss of the thermal nociceptive response. Greatest improvements were realized when the therapeutic intervention was administered to younger mice before they developed overt pathology. Importantly, as the pharmacologic profiles of α-Gal A and Genz-682452 are different, treating animals with both drugs conferred the greatest efficacy. For example, because Genz-682452, but not α-Gal A, can traverse the blood–brain barrier, levels of accumulated glycosphingolipids were reduced in the brain of Genz-682452–treated but not α-Gal A–treated mice. These results suggest that combining substrate reduction and enzyme replacement may confer both complementary and additive therapeutic benefits in Fabry disease. PMID:25938659

Genome-Wide Characterization of Major Intrinsic Proteins in Four Grass Plants and Their Non-Aqua Transport Selectivity Profiles with Comparative Perspective

PubMed Central

Azad, Abul Kalam; Ahmed, Jahed; Alum, Md. Asraful; Hasan, Md. Mahbub; Ishikawa, Takahiro; Sawa, Yoshihiro; Katsuhara, Maki

2016-01-01

Major intrinsic proteins (MIPs), commonly known as aquaporins, transport not only water in plants but also other substrates of physiological significance and heavy metals. In most of the higher plants, MIPs are divided into five subfamilies (PIPs, TIPs, NIPs, SIPs and XIPs). Herein, we identified 68, 42, 38 and 28 full-length MIPs, respectively in the genomes of four monocot grass plants, specifically Panicum virgatum, Setaria italica, Sorghum bicolor and Brachypodium distachyon. Phylogenetic analysis showed that the grass plants had only four MIP subfamilies including PIPs, TIPs, NIPs and SIPs without XIPs. Based on structural analysis of the homology models and comparing the primary selectivity-related motifs [two NPA regions, aromatic/arginine (ar/R) selectivity filter and Froger's positions (FPs)] of all plant MIPs that have been experimentally proven to transport non-aqua substrates, we predicted the transport profiles of all MIPs in the four grass plants and also in eight other plants. Groups of MIP subfamilies based on ar/R selectivity filter and FPs were linked to the non-aqua transport profiles. We further deciphered the substrate selectivity profiles of the MIPs in the four grass plants and compared them with their counterparts in rice, maize, soybean, poplar, cotton, Arabidopsis thaliana, Physcomitrella patens and Selaginella moellendorffii. In addition to two NPA regions, ar/R filter and FPs, certain residues, especially in loops B and C, contribute to the functional distinctiveness of MIP groups. Expression analysis of transcripts in different organs indicated that non-aqua transport was related to expression of MIPs since most of the unexpressed MIPs were not predicted to facilitate the transport of non-aqua molecules. Among all MIPs in every plant, TIP (BdTIP1;1, SiTIP1;2, SbTIP2;1 and PvTIP1;2) had the overall highest mean expression. Our study generates significant information for understanding the diversity, evolution, non-aqua transport profiles and insight into comparative transport selectivity of plant MIPs, and provides tools for the development of transgenic plants. PMID:27327960

Genome-Wide Characterization of Major Intrinsic Proteins in Four Grass Plants and Their Non-Aqua Transport Selectivity Profiles with Comparative Perspective.

PubMed

Azad, Abul Kalam; Ahmed, Jahed; Alum, Md Asraful; Hasan, Md Mahbub; Ishikawa, Takahiro; Sawa, Yoshihiro; Katsuhara, Maki

2016-01-01

Major intrinsic proteins (MIPs), commonly known as aquaporins, transport not only water in plants but also other substrates of physiological significance and heavy metals. In most of the higher plants, MIPs are divided into five subfamilies (PIPs, TIPs, NIPs, SIPs and XIPs). Herein, we identified 68, 42, 38 and 28 full-length MIPs, respectively in the genomes of four monocot grass plants, specifically Panicum virgatum, Setaria italica, Sorghum bicolor and Brachypodium distachyon. Phylogenetic analysis showed that the grass plants had only four MIP subfamilies including PIPs, TIPs, NIPs and SIPs without XIPs. Based on structural analysis of the homology models and comparing the primary selectivity-related motifs [two NPA regions, aromatic/arginine (ar/R) selectivity filter and Froger's positions (FPs)] of all plant MIPs that have been experimentally proven to transport non-aqua substrates, we predicted the transport profiles of all MIPs in the four grass plants and also in eight other plants. Groups of MIP subfamilies based on ar/R selectivity filter and FPs were linked to the non-aqua transport profiles. We further deciphered the substrate selectivity profiles of the MIPs in the four grass plants and compared them with their counterparts in rice, maize, soybean, poplar, cotton, Arabidopsis thaliana, Physcomitrella patens and Selaginella moellendorffii. In addition to two NPA regions, ar/R filter and FPs, certain residues, especially in loops B and C, contribute to the functional distinctiveness of MIP groups. Expression analysis of transcripts in different organs indicated that non-aqua transport was related to expression of MIPs since most of the unexpressed MIPs were not predicted to facilitate the transport of non-aqua molecules. Among all MIPs in every plant, TIP (BdTIP1;1, SiTIP1;2, SbTIP2;1 and PvTIP1;2) had the overall highest mean expression. Our study generates significant information for understanding the diversity, evolution, non-aqua transport profiles and insight into comparative transport selectivity of plant MIPs, and provides tools for the development of transgenic plants.

Capillary wave theory of adsorbed liquid films and the structure of the liquid-vapor interface

NASA Astrophysics Data System (ADS)

MacDowell, Luis G.

2017-08-01

In this paper we try to work out in detail the implications of a microscopic theory for capillary waves under the assumption that the density is given along lines normal to the interface. Within this approximation, which may be justified in terms of symmetry arguments, the Fisk-Widom scaling of the density profile holds for frozen realizations of the interface profile. Upon thermal averaging of capillary wave fluctuations, the resulting density profile yields results consistent with renormalization group calculations in the one-loop approximation. The thermal average over capillary waves may be expressed in terms of a modified convolution approximation where normals to the interface are Gaussian distributed. In the absence of an external field we show that the phenomenological density profile applied to the square-gradient free energy functional recovers the capillary wave Hamiltonian exactly. We extend the theory to the case of liquid films adsorbed on a substrate. For systems with short-range forces, we recover an effective interface Hamiltonian with a film height dependent surface tension that stems from the distortion of the liquid-vapor interface by the substrate, in agreement with the Fisher-Jin theory of short-range wetting. In the presence of long-range interactions, the surface tension picks up an explicit dependence on the external field and recovers the wave vector dependent logarithmic contribution observed by Napiorkowski and Dietrich. Using an error function for the intrinsic density profile, we obtain closed expressions for the surface tension and the interface width. We show the external field contribution to the surface tension may be given in terms of the film's disjoining pressure. From literature values of the Hamaker constant, it is found that the fluid-substrate forces may be able to double the surface tension for films in the nanometer range. The film height dependence of the surface tension described here is in full agreement with results of the capillary wave spectrum obtained recently in computer simulations, and the predicted translation mode of surface fluctuations reproduces to linear order in field strength an exact solution of the density correlation function for the Landau-Ginzburg-Wilson Hamiltonian in an external field.

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.

Quantitative SIMS depth profiling of diffusion barrier gate-oxynitride structures in TFT-LCDs.

PubMed

Dreer, Sabine; Wilhartitz, Peter; Piplits, Kurt; Mayerhofer, Karl; Foisner, Johann; Hutter, Herbert

2004-06-01

Gate oxynitride structures of TFT-LCDs were investigated by SIMS, and successful solutions are demonstrated to overcome difficulties arising due to the charging effects of the multilayer systems, the matrix effect of the method, and the small pattern sizes of the samples. Because of the excellent reproducibility achieved by applying exponential relative sensitivity functions for quantitative analysis, minor differences in the barrier gate-oxynitride composition deposited on molybdenum capped aluminium-neodymium metallisation electrodes were determined between the centre and the edge of the TFT-LCD substrates. No differences were found for molybdenum-tungsten metallisations. Furthermore, at the edge of the glass substrates, aluminium, neodymium, and molybdenum SIMS depth profiles show an exponential trend. With TEM micrographs an inhomogeneous thickness of the molybdenum capping is revealed as the source of this effect, which influences the electrical behaviour of the device. The production process was improved after these results and the aging behaviour of TFT-LCDs was investigated in order to explain the change in control voltage occurring during the lifetime of the displays. SIMS and TEM show an enrichment of neodymium at the interface to the molybdenum layer, confirming good diffusion protection of the molybdenum barrier during accelerated aging. The reason for the shift of the control voltage was finally located by semi-quantitative depth profiling of the sodium diffusion originating from the glass substrate. Molybdenum-tungsten was a much better buffer for the highly-mobile charge carriers than aluminium-neodymium. Best results were achieved with PVD silicon oxynitride as diffusion barrier and gate insulator deposited on aluminium-neodymium metallisation layers.

Proteomic validation of protease drug targets: pharmacoproteomics of matrix metalloproteinase inhibitor drugs using isotope-coded affinity tag labelling and tandem mass spectrometry.

PubMed

Butler, G S; Overall, C M

2007-01-01

We illustrate the use of quantitative proteomics, namely isotope-coded affinity tag labelling and tandem mass spectrometry, to assess the targets and effects of the blockade of matrix metalloproteinases by an inhibitor drug in a breast cancer cell culture system. Treatment of MT1-MMP-transfected MDA-MB-231 cells with AG3340 (Prinomastat) directly affected the processing a multitude of matrix metalloproteinase substrates, and indirectly altered the expression of an array of other proteins with diverse functions. Therefore, broad spectrum blockade of MMPs has wide-ranging biological consequences. In this human breast cancer cell line, secreted substrates accumulated uncleaved in the conditioned medium and plasma membrane protein substrates were retained on the cell surface, due to reduced processing and shedding of these proteins (cell surface receptors, growth factors and bioactive molecules) to the medium in the presence of the matrix metalloproteinase inhibitor. Hence, proteomic investigation of drug-perturbed cellular proteomes can identify new protease substrates and at the same time provides valuable information for target validation, drug efficacy and potential side effects prior to commitment to clinical trials.

Fluorescent Labeling of COS-7 Expressing SNAP-tag Fusion Proteins for Live Cell Imaging

PubMed Central

Provost, Christopher R.; Sun, Luo

2010-01-01

SNAP-tag and CLIP-tag protein labeling systems enable the specific, covalent attachment of molecules, including fluorescent dyes, to a protein of interest in live cells. These systems offer a broad selection of fluorescent substrates optimized for a range of imaging instrumentation. Once cloned and expressed, the tagged protein can be used with a variety of substrates for numerous downstream applications without having to clone again. There are two steps to using this system: cloning and expression of the protein of interest as a SNAP-tag fusion, and labeling of the fusion with the SNAP-tag substrate of choice. The SNAP-tag is a small protein based on human O6-alkylguanine-DNA-alkyltransferase (hAGT), a DNA repair protein. SNAP-tag labels are dyes conjugated to guanine or chloropyrimidine leaving groups via a benzyl linker. In the labeling reaction, the substituted benzyl group of the substrate is covalently attached to the SNAP-tag. CLIP-tag is a modified version of SNAP-tag, engineered to react with benzylcytosine rather than benzylguanine derivatives. When used in conjunction with SNAP-tag, CLIP-tag enables the orthogonal and complementary labeling of two proteins simultaneously in the same cells. PMID:20485262

Engineering an enantioselective amine oxidase for the synthesis of pharmaceutical building blocks and alkaloid natural products.

PubMed

Ghislieri, Diego; Green, Anthony P; Pontini, Marta; Willies, Simon C; Rowles, Ian; Frank, Annika; Grogan, Gideon; Turner, Nicholas J

2013-07-24

The development of cost-effective and sustainable catalytic methods for the production of enantiomerically pure chiral amines is a key challenge facing the pharmaceutical and fine chemical industries. This challenge is highlighted by the estimate that 40-45% of drug candidates contain a chiral amine, fueling a demand for broadly applicable synthetic methods that deliver target structures in high yield and enantiomeric excess. Herein we describe the development and application of a "toolbox" of monoamine oxidase variants from Aspergillus niger (MAO-N) which display remarkable substrate scope and tolerance for sterically demanding motifs, including a new variant, which exhibits high activity and enantioselectivity toward substrates containing the aminodiphenylmethane (benzhydrylamine) template. By combining rational structure-guided engineering with high-throughput screening, it has been possible to expand the substrate scope of MAO-N to accommodate amine substrates containing bulky aryl substituents. These engineered MAO-N biocatalysts have been applied in deracemization reactions for the efficient asymmetric synthesis of the generic active pharmaceutical ingredients Solifenacin and Levocetirizine as well as the natural products (R)-coniine, (R)-eleagnine, and (R)-leptaflorine. We also report a novel MAO-N mediated asymmetric oxidative Pictet-Spengler approach to the synthesis of (R)-harmicine.

Computing Generalized Matrix Inverse on Spiking Neural Substrate.

PubMed

Shukla, Rohit; Khoram, Soroosh; Jorgensen, Erik; Li, Jing; Lipasti, Mikko; Wright, Stephen

2018-01-01

Emerging neural hardware substrates, such as IBM's TrueNorth Neurosynaptic System, can provide an appealing platform for deploying numerical algorithms. For example, a recurrent Hopfield neural network can be used to find the Moore-Penrose generalized inverse of a matrix, thus enabling a broad class of linear optimizations to be solved efficiently, at low energy cost. However, deploying numerical algorithms on hardware platforms that severely limit the range and precision of representation for numeric quantities can be quite challenging. This paper discusses these challenges and proposes a rigorous mathematical framework for reasoning about range and precision on such substrates. The paper derives techniques for normalizing inputs and properly quantizing synaptic weights originating from arbitrary systems of linear equations, so that solvers for those systems can be implemented in a provably correct manner on hardware-constrained neural substrates. The analytical model is empirically validated on the IBM TrueNorth platform, and results show that the guarantees provided by the framework for range and precision hold under experimental conditions. Experiments with optical flow demonstrate the energy benefits of deploying a reduced-precision and energy-efficient generalized matrix inverse engine on the IBM TrueNorth platform, reflecting 10× to 100× improvement over FPGA and ARM core baselines.

Origin of low sodium capacity in graphite and generally weak substrate binding of Na and Mg among alkali and alkaline earth metals.

PubMed

Liu, Yuanyue; Merinov, Boris V; Goddard, William A

2016-04-05

It is well known that graphite has a low capacity for Na but a high capacity for other alkali metals. The growing interest in alternative cation batteries beyond Li makes it particularly important to elucidate the origin of this behavior, which is not well understood. In examining this question, we find a quite general phenomenon: among the alkali and alkaline earth metals, Na and Mg generally have the weakest chemical binding to a given substrate, compared with the other elements in the same column of the periodic table. We demonstrate this with quantum mechanics calculations for a wide range of substrate materials (not limited to C) covering a variety of structures and chemical compositions. The phenomenon arises from the competition between trends in the ionization energy and the ion-substrate coupling, down the columns of the periodic table. Consequently, the cathodic voltage for Na and Mg is expected to be lower than those for other metals in the same column. This generality provides a basis for analyzing the binding of alkali and alkaline earth metal atoms over a broad range of systems.

Caenorhabditis elegans PRMT-7 and PRMT-9 Are Evolutionarily Conserved Protein Arginine Methyltransferases with Distinct Substrate Specificities.

PubMed

Hadjikyriacou, Andrea; Clarke, Steven G

2017-05-23

Caenorhabditis elegans protein arginine methyltransferases PRMT-7 and PRMT-9 are two evolutionarily conserved enzymes, with distinct orthologs in plants, invertebrates, and vertebrates. Biochemical characterization of these two enzymes reveals that they share much in common with their mammalian orthologs. C. elegans PRMT-7 produces only monomethylarginine (MMA) and preferentially methylates R-X-R motifs in a broad collection of substrates, including human histone peptides and RG-rich peptides. In addition, the activity of the PRMT-7 enzyme is dependent on temperature, the presence of metal ions, and the reducing agent dithiothreitol. C. elegans PRMT-7 has a substrate specificity and a substrate preference different from those of mammalian PRMT7, and the available X-ray crystal structures of the PRMT7 orthologs show differences in active site architecture. C. elegans PRMT-9, on the other hand, produces symmetric dimethylarginine and MMA on SFTB-2, the conserved C. elegans ortholog of human RNA splicing factor SF3B2, indicating a possible role in the regulation of nematode splicing. In contrast to PRMT-7, C. elegans PRMT-9 appears to be biochemically indistinguishable from its human ortholog.