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

Bahl, C.; Morisseau, C; Bomberger, J

Cystic fibrosis transmembrane conductance regulator (CFTR) inhibitory factor (Cif) is a virulence factor secreted by Pseudomonas aeruginosa that reduces the quantity of CFTR in the apical membrane of human airway epithelial cells. Initial sequence analysis suggested that Cif is an epoxide hydrolase (EH), but its sequence violates two strictly conserved EH motifs and also is compatible with other {alpha}/{beta} hydrolase family members with diverse substrate specificities. To investigate the mechanistic basis of Cif activity, we have determined its structure at 1.8-{angstrom} resolution by X-ray crystallography. The catalytic triad consists of residues Asp129, His297, and Glu153, which are conserved across themore » family of EHs. At other positions, sequence deviations from canonical EH active-site motifs are stereochemically conservative. Furthermore, detailed enzymatic analysis confirms that Cif catalyzes the hydrolysis of epoxide compounds, with specific activity against both epibromohydrin and cis-stilbene oxide, but with a relatively narrow range of substrate selectivity. Although closely related to two other classes of {alpha}/{beta} hydrolase in both sequence and structure, Cif does not exhibit activity as either a haloacetate dehalogenase or a haloalkane dehalogenase. A reassessment of the structural and functional consequences of the H269A mutation suggests that Cif's effect on host-cell CFTR expression requires the hydrolysis of an extended endogenous epoxide substrate.« less

Voltage control of magnetism in NiZn ferrite/mica/PMNPT heterostructure with giant tunability and narrow linewidth

NASA Astrophysics Data System (ADS)

Wang, Xinjun; Chen, Yunpeng; Chen, Huaihao; Gao, Yuan; He, Yifan; Li, Menghui; Lin, Hwaider; Sun, Neville; Sun, Nian

2018-05-01

Recently, large magnetoelectric coupling of a spinel/piezoelectric heterostructure has been reported. However, the linewidth of the spinel is very large due to lattice mismatch when ferrite is directly deposited on piezoelectric substrates. This indicates a large magnetic loss, which impedes the spinel/piezoelectric heterostructure from useful device applications. Mica is a well-known 2D material, which can be split manually layer by layer without the substrate clamping effect. In this report, NiZn ferrite was deposited on a mica substrate by a spin-spray deposition technique. Spin-spray deposition is a wet chemical synthesis technique involving several chemical reactions for generating high-quality crystalline spinel ferrite films with various compositions directly from an aqueous solution. The thickness of ferrite is 2 μm, and the linewidth of the ferromagnetic resonance (FMR) is 115 Oe which is suitable for RF/microwave devices. The large FMR field tuning of 605 Oe was observed in NiZn ferrite/mica/PMN-PT heterostructures with minimal substrate clamping effect by reducing the thickness of the mica substrate. These multiferroic heterostructures exhibiting combined giant magnetoelectric coupling and narrow ferromagnetic resonance linewidth offer great opportunities for flexible RF magnetic devices.

Stable aqueous based Cu nanoparticle ink for printing well-defined highly conductive features on a plastic substrate.

PubMed

Jeong, Sunho; Song, Hae Chun; Lee, Won Woo; Lee, Sun Sook; Choi, Youngmin; Son, Wonil; Kim, Eui Duk; Paik, Choon Hoon; Oh, Seok Heon; Ryu, Beyong-Hwan

2011-03-15

With the aim of inkjet printing highly conductive and well-defined Cu features on plastic substrates, aqueous based Cu ink is prepared for the first time using water-soluble Cu nanoparticles with a very thin surface oxide layer. Owing to the specific properties, high surface tension and low boiling point, of water, the aqueous based Cu ink endows a variety of advantages over conventional Cu inks based on organic solvents in printing narrow conductive patterns without irregular morphologies. It is demonstrated how the design of aqueous based ink affects the basic properties of printed conductive features such as surface morphology, microstructure, conductivity, and line width. The long-term stability of aqueous based Cu ink against oxidation is analyzed through an X-ray photoelectron spectroscopy (XPS) based investigation on the evolution of the surface oxide layer in the aqueous based ink.

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

NASA Astrophysics Data System (ADS)

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

2015-06-01

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

Lasing characteristics of InAs quantum dot laers on InP substrate

NASA Technical Reports Server (NTRS)

Yang, Y.; Qiu, D.; Uhl, R.; Chacon, R.

2003-01-01

Single-stack InAs self-assembled quantum dots (QD) lasers based on InP substrate have been grown by metalorganic vapor phase epitaxy. The narrow ridge waveguide lasers lased up to 260 K in continuous wave operation, and near room temperature in pulsed mode, with wavelengths between 1.59 to 1.74 mu m.

Identification, expression and characterization of an R-ω-transaminase from Capronia semiimmersa.

PubMed

Iglesias, César; Panizza, Paola; Rodriguez Giordano, Sonia

2017-07-01

Chiral amines are essential precursors in the production of biologically active compounds, including several important drugs. Among the biocatalytic strategies that have been developed for their synthesis, the use of ω-transaminases (ω-TA) appears as an attractive alternative allowing the stereoselective amination of prochiral ketones. However, the problems associated with narrow substrate specificity, unfavourable reaction equilibrium and expensive amine donors still hamper its industrial application. The search for novel enzymes from nature can contribute to expand the catalytic repertoire of ω-TA and help to circumvent some of these problems. A genome mining approach, based on the work described by Höhne et al., was applied for selection of potential R-ω-TA. Additional criteria were used to select an enzyme that differs from previously described ones. A candidate R-ω-TA from Capronia semiimmersa was selected, cloned and expressed in Escherichia coli. Interestingly, alignment of this enzyme with previously reported TA sequences revealed the presence of two additional amino acid residues in a loop close to the active site. The impact of this change was analysed with a structural model based on crystallized R-ω-TAs. Analysis of the substrate specificity of R-ω-TA from C. semiimmersa indicates that it accepts a diversity of ketones as substrates yielding the corresponding amine with good yields and excellent enantioselectivity. The expressed enzyme accepts isopropylamine as amine donor what makes it suitable for industrial processes.

Surface study of graphene ink for fine solid lines printed on BOPP Substrate in micro-flexographic printing using XPS analysis technique

NASA Astrophysics Data System (ADS)

Hassan, S.; Yusof, M. S.; Embong, Z.; Ding, S.; Maksud, M. I.

2018-01-01

Micro-flexographic printing is a combination of flexography and micro-contact printing technique. It is a new printing method for fine solid lines printing purpose. Graphene material has been used as depositing agent or printing ink in other printing technique like inkjet printing. This graphene ink is printed on biaxially oriented polypropylene (BOPP) by using Micro-flexographic printing technique. The choose of graphene as a printing ink is due to its wide application in producing electronic and micro-electronic devices such as Radio-frequency identification (RFID) and printed circuit board. The graphene printed on the surface of BOPP substrate was analyzed using X-Ray Photoelectron Spectroscopy (XPS). The positions for each synthetic component in the narrow scan are referred to the electron binding energy (eV). This research is focused on two narrow scan regions which are C 1s and O 1s. Further discussion of the narrow scan spectrum will be explained in detail. From the narrow scan analysis, it is proposed that from the surface adhesive properties of graphene, it is suitable as an alternative printing ink medium for Micro-flexographic printing technique in printing multiple fine solid lines at micro to nano scale feature.

Low cost microminiature refrigerators for large unit volume applications

NASA Technical Reports Server (NTRS)

Duboc, R. M., Jr.

1983-01-01

Photolithographic techniques were employed to fabricate small Joule-Thomson refrigerators in laminated substrates. The gas passages of a J-T refrigerator are formed by etching channels as narrow as 50 microns and as shallow as 5 microns in glass plates which are laminated together. Circular refrigerators on the order of 1.5 centimeters in diameter and .75 millimeters thick were produced which cool down to cryogenic temperatures in a few seconds, using Argon or Nitrogen, with no vacuum or radiation insulation. Smaller refrigerators are developed for both faster cooldown and low refrigeration capacity applications. By using this technology, custom refrigerators can be designed to meet specific application requirements.

Protein export through the bacterial flagellar type III export pathway.

PubMed

Minamino, Tohru

2014-08-01

For construction of the bacterial flagellum, which is responsible for bacterial motility, the flagellar type III export apparatus utilizes both ATP and proton motive force across the cytoplasmic membrane and exports flagellar proteins from the cytoplasm to the distal end of the nascent structure. The export apparatus consists of a membrane-embedded export gate made of FlhA, FlhB, FliO, FliP, FliQ, and FliR and a water-soluble ATPase ring complex consisting of FliH, FliI, and FliJ. FlgN, FliS, and FliT act as substrate-specific chaperones that do not only protect their cognate substrates from degradation and aggregation in the cytoplasm but also efficiently transfer the substrates to the export apparatus. The ATPase ring complex facilitates the initial entry of the substrates into the narrow pore of the export gate. The export gate by itself is a proton-protein antiporter that uses the two components of proton motive force, the electric potential difference and the proton concentration difference, for different steps of the export process. A specific interaction of FlhA with FliJ located in the center of the ATPase ring complex allows the export gate to efficiently use proton motive force to drive protein export. The ATPase ring complex couples ATP binding and hydrolysis to its assembly-disassembly cycle for rapid and efficient protein export cycle. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey. © 2013 Elsevier B.V. All rights reserved.

Phylogenetic and Functional Substrate Specificity for Endolithic Microbial Communities in Hyper-Arid Environments

PubMed Central

Crits-Christoph, Alexander; Robinson, Courtney K.; Ma, Bing; Ravel, Jacques; Wierzchos, Jacek; Ascaso, Carmen; Artieda, Octavio; Souza-Egipsy, Virginia; Casero, M. Cristina; DiRuggiero, Jocelyne

2016-01-01

Under extreme water deficit, endolithic (inside rock) microbial ecosystems are considered environmental refuges for life in cold and hot deserts, yet their diversity and functional adaptations remain vastly unexplored. The metagenomic analyses of the communities from two rock substrates, calcite and ignimbrite, revealed that they were dominated by Cyanobacteria, Actinobacteria, and Chloroflexi. The relative distribution of major phyla was significantly different between the two substrates and biodiversity estimates, from 16S rRNA gene sequences and from the metagenomic data, all pointed to a higher taxonomic diversity in the calcite community. While both endolithic communities showed adaptations to extreme aridity and to the rock habitat, their functional capabilities revealed significant differences. ABC transporters and pathways for osmoregulation were more diverse in the calcite chasmoendolithic community. In contrast, the ignimbrite cryptoendolithic community was enriched in pathways for secondary metabolites, such as non-ribosomal peptides (NRP) and polyketides (PK). Assemblies of the metagenome data produced population genomes for the major phyla found in both communities and revealed a greater diversity of Cyanobacteria population genomes for the calcite substrate. Draft genomes of the dominant Cyanobacteria in each community were constructed with more than 93% estimated completeness. The two annotated proteomes shared 64% amino acid identity and a significantly higher number of genes involved in iron update, and NRPS gene clusters, were found in the draft genomes from the ignimbrite. Both the community-wide and genome-specific differences may be related to higher water availability and the colonization of large fissures and cracks in the calcite in contrast to a harsh competition for colonization space and nutrient resources in the narrow pores of the ignimbrite. Together, these results indicated that the habitable architecture of both lithic substrates- chasmoendolithic versus cryptoendolithic – might be an essential element in determining the colonization and the diversity of the microbial communities in endolithic substrates at the dry limit for life. PMID:27014224

Modulation of substrate specificities of D-sialic acid aldolase through single mutations of Val-251.

PubMed

Chou, Chien-Yu; Ko, Tzu-Ping; Wu, Kuan-Jung; Huang, Kai-Fa; Lin, Chun-Hung; Wong, Chi-Huey; Wang, Andrew H-J

2011-04-22

In a recent directed-evolution study, Escherichia coli D-sialic acid aldolase was converted by introducing eight point mutations into a new enzyme with relaxed specificity, denoted RS-aldolase (also known formerly as L-3-deoxy-manno-2-octulosonic acid (L-KDO) aldolase), which showed a preferred selectivity toward L-KDO. To investigate the underlying molecular basis, we determined the crystal structures of D-sialic acid aldolase and RS-aldolase. All mutations are away from the catalytic center, except for V251I, which is near the opening of the (α/β)(8)-barrel and proximal to the Schiff base-forming Lys-165. The change of specificity from D-sialic acid to RS-aldolase can be attributed mainly to the V251I substitution, which creates a narrower sugar-binding pocket, but without altering the chirality in the reaction center. The crystal structures of D-sialic acid aldolase·l-arabinose and RS-aldolase·hydroxypyruvate complexes and five mutants (V251I, V251L, V251R, V251W, and V251I/V265I) of the D-sialic acid aldolase were also determined, revealing the location of substrate molecules and how the contour of the active site pocket was shaped. Interestingly, by mutating Val251 alone, the enzyme can accept substrates of varying size in the aldolase reactions and still retain stereoselectivity. The engineered D-sialic acid aldolase may find applications in synthesizing unnatural sugars of C(6) to C(10) for the design of antagonists and inhibitors of glycoenzymes.

Neural activity underlying motor-action preparation and cognitive narrowing in approach-motivated goal states.

PubMed

Gable, Philip A; Threadgill, A Hunter; Adams, David L

2016-02-01

High-approach-motivated (pre-goal) positive affect states encourage tenacious goal pursuit and narrow cognitive scope. As such, high approach-motivated states likely enhance the neural correlates of motor-action preparation to aid in goal acquisition. These neural correlates may also relate to the cognitive narrowing associated with high approach-motivated states. In the present study, we investigated motor-action preparation during pre-goal and post-goal states using an index of beta suppression over the motor cortex. The results revealed that beta suppression was greatest in pre-goal positive states, suggesting that higher levels of motor-action preparation occur during high approach-motivated positive states. Furthermore, beta and alpha suppression in the high approach-motivated positive states predicted greater cognitive narrowing. These results suggest that approach-motivated pre-goal states engage the neural substrates of motor-action preparation and cognitive narrowing. Individual differences in motor-action preparation relate to the degree of cognitive narrowing.

Low-Energy, Hydrogen-Free Method of Diamond Synthesis

NASA Technical Reports Server (NTRS)

Varshney, Deepak (Inventor); Morell, Gerardo (Inventor); Weiner, Brad R. (Inventor); Makarov, Vladimir (Inventor)

2013-01-01

Diamond thin films were deposited on copper substrate by the Vapor Solid (VS) deposition method using a mixture of fullerene C(sub 60) and graphite as the source material. The deposition took place only when the substrate was kept in a narrow temperature range of approximately 550-650 C. Temperatures below and above this range results in the deposition of fullerenes and other carbon compounds, respectively.

CHARACTERIZATION OF A NARROW SPECTRUM ANTIMICROBIAL THAT EXHIBITS SPECIFIC ACTIVITY AGAINST UROPATHOGENIC BACTERIA

DTIC Science & Technology

2017-08-28

NARROW-SPECTRUM ANTIMICROBIAL THAT EXHIBITS SPECIFIC ACTIVITY AGAINST UROPATHOGENIC BACTERIA by Caitlin M. Barrows Courtney M. Cowell Jennifer...From - To) October 2015 – September 2016 4. TITLE AND SUBTITLE CHARACTERIZATION OF A NARROW-SPECTRUM ANTIMICROBIAL THAT EXHIBITS SPECIFIC ACTIVITY ...objective of the work described in this report is to identify a narrow-spectrum antimicrobial that exhibits targeted activity against uropathogenic

Structures of Human DPP7 Reveal the Molecular Basis of Specific Inhibition and the Architectural Diversity of Proline-Specific Peptidases

PubMed Central

Dong, Aiping; Seitova, Almagul; Crombett, Lissete; Shewchuk, Lisa M.; Hassell, Annie M.; Sweitzer, Sharon M.; Sweitzer, Thomas D.; McDevitt, Patrick J.; Johanson, Kyung O.; Kennedy-Wilson, Karen M.; Cossar, Doug; Bochkarev, Alexey; Gruber, Karl; Dhe-Paganon, Sirano

2012-01-01

Proline-specific dipeptidyl peptidases (DPPs) are emerging targets for drug development. DPP4 inhibitors are approved in many countries, and other dipeptidyl peptidases are often referred to as DPP4 activity- and/or structure-homologues (DASH). Members of the DASH family have overlapping substrate specificities, and, even though they share low sequence identity, therapeutic or clinical cross-reactivity is a concern. Here, we report the structure of human DPP7 and its complex with a selective inhibitor Dab-Pip (L-2,4-diaminobutyryl-piperidinamide) and compare it with that of DPP4. Both enzymes share a common catalytic domain (α/β-hydrolase). The catalytic pocket is located in the interior of DPP7, deep inside the cleft between the two domains. Substrates might access the active site via a narrow tunnel. The DPP7 catalytic triad is completely conserved and comprises Ser162, Asp418 and His443 (corresponding to Ser630, Asp708 and His740 in DPP4), while other residues lining the catalytic pockets differ considerably. The “specificity domains” are structurally also completely different exhibiting a β-propeller fold in DPP4 compared to a rare, completely helical fold in DPP7. Comparing the structures of DPP7 and DPP4 allows the design of specific inhibitors and thus the development of less cross-reactive drugs. Furthermore, the reported DPP7 structures shed some light onto the evolutionary relationship of prolyl-specific peptidases through the analysis of the architectural organization of their domains. PMID:22952628

Background correction in forensic photography. II. Photography of blood under conditions of non-uniform illumination or variable substrate color--practical aspects and limitations.

PubMed

Wagner, John H; Miskelly, Gordon M

2003-05-01

The combination of photographs taken at wavelengths at and bracketing the peak of a narrow absorbance band can lead to enhanced visualization of the substance causing the narrow absorbance band. This concept can be used to detect putative bloodstains by division of a linear photographic image taken at or near 415 nm with an image obtained by averaging linear photographs taken at or near 395 and 435 nm. Nonlinear images can also be background corrected by substituting subtraction for the division. This paper details experimental applications and limitations of this technique, including wavelength selection of the illuminant and at the camera. Characterization of a digital camera to be used in such a study is also detailed. Detection limits for blood using the three wavelength correction method under optimum conditions have been determined to be as low as 1 in 900 dilution, although on strongly patterned substrates blood diluted more than twenty-fold is difficult to detect. Use of only the 435 nm photograph to estimate the background in the 415 nm image lead to a twofold improvement in detection limit on unpatterned substrates compared with the three wavelength method with the particular camera and lighting system used, but it gave poorer background correction on patterned substrates.

The safety of lumacaftor and ivacaftor for the treatment of cystic fibrosis.

PubMed

Talamo Guevara, Maria; McColley, Susanna A

2017-11-01

Lumacaftor-ivacaftor is indicated for treatment of cystic fibrosis (CF) in patients homozygous for the Phe-508del cystic fibrosis transmembrane conductance regulator (CFTR) gene mutations. In clinical trials, treated patients showed improved pulmonary function, reduced pulmonary exacerbations, and other benefits. This article reviews safety of this therapy. Areas covered: Safety findings in ivacaftor, lumacaftor and combined therapy trials, and reported subsequently through post-approval evaluation, were accessed by PubMed and Google searches using key words 'VX-770', 'ivacaftor', 'VX-809', and 'lumacaftor'. Transaminitis was seen in ivacaftor and combination trials. Non-congenital cataracts were seen in pre-clinical animal studies and in children taking ivacaftor and combined therapy. Dyspnea occurs in some patients taking lumacaftor and combined therapy and usually resolves without stopping treatment. Lumacaftor is a strong inducer of CYP3A while ivacaftor is a CYP3A sensitive substrate. Combination therapy can decrease systemic exposure of medications that are substrates of CYP3A, decreasing therapeutic effect. Co-administration of lumacaftor-ivacaftor with sensitive CYP3A substrates or CYP3A substrates with narrow therapeutic index is not recommended. Expert opinion: Lumacaftor-ivacaftor therapy may be associated with ocular and hepatic side effects. Specific recommendations for monitoring are available. Dyspnea occurs, especially during initiation of treatment. Potential drug interactions should be evaluated in patients taking combination therapy. The risk benefit ratio of lumacaftor-ivacaftor favors therapy.

Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I

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

Shi, Yuqian; Hellinga, Homme W.; Beese, Lorena S.

Human exonuclease 1 (hExo1) is a member of the RAD2/XPG structure-specific 5'-nuclease superfamily. Its dominant, processive 5'–3' exonuclease and secondary 5'-flap endonuclease activities participate in various DNA repair, recombination, and replication processes. A single active site processes both recessed ends and 5'-flap substrates. By initiating enzyme reactions in crystals, we have trapped hExo1 reaction intermediates that reveal structures of these substrates before and after their exo- and endonucleolytic cleavage, as well as structures of uncleaved, unthreaded, and partially threaded 5' flaps. Their distinctive 5' ends are accommodated by a small, mobile arch in the active site that binds recessed endsmore » at its base and threads 5' flaps through a narrow aperture within its interior. A sequence of successive, interlocking conformational changes guides the two substrate types into a shared reaction mechanism that catalyzes their cleavage by an elaborated variant of the two-metal, in-line hydrolysis mechanism. Coupling of substrate-dependent arch motions to transition-state stabilization suppresses inappropriate or premature cleavage, enhancing processing fidelity. The striking reduction in flap conformational entropy is catalyzed, in part, by arch motions and transient binding interactions between the flap and unprocessed DNA strand. At the end of the observed reaction sequence, hExo1 resets without relinquishing DNA binding, suggesting a structural basis for its processivity.« less

Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I.

PubMed

Shi, Yuqian; Hellinga, Homme W; Beese, Lorena S

2017-06-06

Human exonuclease 1 (hExo1) is a member of the RAD2/XPG structure-specific 5'-nuclease superfamily. Its dominant, processive 5'-3' exonuclease and secondary 5'-flap endonuclease activities participate in various DNA repair, recombination, and replication processes. A single active site processes both recessed ends and 5'-flap substrates. By initiating enzyme reactions in crystals, we have trapped hExo1 reaction intermediates that reveal structures of these substrates before and after their exo- and endonucleolytic cleavage, as well as structures of uncleaved, unthreaded, and partially threaded 5' flaps. Their distinctive 5' ends are accommodated by a small, mobile arch in the active site that binds recessed ends at its base and threads 5' flaps through a narrow aperture within its interior. A sequence of successive, interlocking conformational changes guides the two substrate types into a shared reaction mechanism that catalyzes their cleavage by an elaborated variant of the two-metal, in-line hydrolysis mechanism. Coupling of substrate-dependent arch motions to transition-state stabilization suppresses inappropriate or premature cleavage, enhancing processing fidelity. The striking reduction in flap conformational entropy is catalyzed, in part, by arch motions and transient binding interactions between the flap and unprocessed DNA strand. At the end of the observed reaction sequence, hExo1 resets without relinquishing DNA binding, suggesting a structural basis for its processivity.

Electronic structure of uranium overlayers on magnesium and aluminium

NASA Astrophysics Data System (ADS)

Gouder, T.

1997-06-01

We studied U overlayers on polycrystalline Mg and Al by X-ray and ultra-violet photoelectron spectroscopies (XPS and UPS, respectively), and compared the mode of growth and the evolution of the electronic structure as a function of coverage. The goal of this work was to detect localization, or at least correlation effects, in U overlayers and U substrate near surface alloys, which were expected to occur because of the reduced U 5f bandwidth in these systems. On Mg, U deposits as a pure overlayer without any interdiffusion, while on Al spontaneous interdiffusion takes place. The U 4f spectra of {U}/{Mg} show only weak correlation satellites. Nevertheless, the asymmetrical shape of the U 4f peak indicates 5f band narrowing. On Al, strong correlation satellites are observed in addition to plasmon loss features. It seems that U-substrate interactions promote correlation effects, while the reduced coordination in overlayers plays a less important role. UPS valence-band (VB) spectra of the two systems look remarkably similar. They do not show any correlation satellites. With decreasing overlayer thickness the 5f peak narrows, which is attributed to 5f band narrowing at the surface.

Molecular cloning and functional characterization of psoralen synthase, the first committed monooxygenase of furanocoumarin biosynthesis.

PubMed

Larbat, Romain; Kellner, Sandra; Specker, Silvia; Hehn, Alain; Gontier, Eric; Hans, Joachim; Bourgaud, Frederic; Matern, Ulrich

2007-01-05

Ammi majus L. accumulates linear furanocoumarins by cytochrome P450 (CYP)-dependent conversion of 6-prenylumbelliferone via (+)-marmesin to psoralen. Relevant activities, i.e. psoralen synthase, are induced rapidly from negligible background levels upon elicitation of A. majus cultures with transient maxima at 9-10 h and were recovered in labile microsomes. Expressed sequence tags were cloned from elicited Ammi cells by a nested DD-RT-PCR strategy with CYP-specific primers, and full-size cDNAs were generated from those fragments correlated in abundance with the induction profile of furanocoumarin-specific activities. One of these cDNAs representing a transcript of maximal abundance at 4 h of elicitation was assigned CYP71AJ1. Functional expression in Escherichia coli or yeast cells initially failed but was accomplished eventually in yeast cells after swapping the N-terminal membrane anchor domain with that of CYP73A1. The recombinant enzyme was identified as psoralen synthase with narrow substrate specificity for (+)-marmesin. Psoralen synthase catalyzes a unique carbon-chain cleavage reaction concomitantly releasing acetone by syn-elimination. Related plants, i.e. Heracleum mantegazzianum, are known to produce both linear and angular furanocoumarins by analogous conversion of 8-prenylumbelliferone via (+)-columbianetin to angelicin, and it was suggested that angelicin synthase has evolved from psoralen synthase. However, (+)-columbianetin failed as substrate but competitively inhibited psoralen synthase activity. Analogy modeling and docked solutions defined the conditions for high affinity substrate binding and predicted the minimal requirements to accommodate (+)-columbianetin in the active site cavity. The studies suggested that several point mutations are necessary to pave the road toward angelicin synthase evolution.

Dynamics of reflection high-energy electron diffraction intensity oscillations during molecular beam epitaxial growth of GaAs on (111)B GaAs substrates

NASA Astrophysics Data System (ADS)

Yen, M. Y.; Haas, T. W.

1990-06-01

We have observed intensity oscillations in reflection high-energy electron diffraction during molecular beam epitaxial growth of GaAs on (111)B GaAs substrates. These oscillations only exist over a narrow range of growth conditions and their behavior is strongly dependent on the migration kinetics of group III and the molecular dissociative reaction of group V elements.

Sub-5 nm, globally aligned graphene nanoribbons on Ge(001)

DOE PAGES

Kiraly, Brian; Mannix, Andrew J.; Jacobberger, Robert M.; ...

2016-05-23

Graphene nanoribbons (GNRs) hold great promise for future electronics because of their edge and width dependent electronic bandgaps and exceptional transport properties. While significant progress toward such devices has been made, the field has been limited by difficulties achieving narrow widths, global alignment, and atomically pristine GNR edges on technologically relevant substrates. A recent advance has challenged these limits by using Ge(001) substrates to direct the bottom-up growth of GNRs with nearly pristine armchair edges and widths near ~10 nm via atmospheric pressure chemical vapor deposition. In this work, we extend the growth of GNRs on Ge(001) to ultra-high vacuummore » conditions and realize GNRs narrower than 5 nm. Armchair graphene nanoribbons directed along the Ge <110> surface directions are achieved with excellent width control and relatively large bandgaps. As a result, the bandgap magnitude and electronic uniformity make these new materials excellent candidates for future developments in nanoelectronics.« less

Vertical-Cavity Surface-Emitting Laser Diodes: Design, Growth, Mode Control and Integration by Fluidic Self-Assembly

NASA Astrophysics Data System (ADS)

Hadley, Mark Alfred

Some important problems to overcome in the design and fabrication of vertical-cavity surface-emitting laser diodes (VCSELs) are: narrow design tolerances, molecular beam epitaxy growth control and multiple transverse modes. This dissertation addresses each of these problems. First, optical, electrical and thermal design issues are discussed in detail. Second, a new growth method using the thermal emission from the substrate during growth is described which is used to accurately control the growth of multilayer structures. The third problem addressed is that of multiple transverse modes. For many applications it is desirable for a VCSEL to lase in the lowest-order transverse mode. In most structures, this only occurs at low powers. It is shown that an external cavity can be used to force a VCSEL to lase in a single transverse mode at all power levels. A new type of VCSEL, grown on a p-doped substrate in order to increase injection uniformity, is designed specifically for use in an external cavity. There are two types of external cavities used to control modes: a long external "macro-cavity" and a short external "micro-cavity." These external cavities have been used to obtain peak powers of over 100 mW while remaining in the fundamental mode under pulsed operation. Finally, a more general topic is researched. This topic, called fluidic self-assembly (FSA), is a new integration technique that can be used not only to integrate VCSELs on a separate substrate, but to integrate many different material systems and devices together on the same substrate. The basic concept of FSA is to make a large number of objects of a particular shape. On a separate substrate, holes that match the shape of the objects are also fabricated. By placing the substrate in an inert fluid containing the objects, and recirculating the fluid and the objects over the substrate, it is possible to fill the holes with correctly oriented objects. Results of a FSA study are reported in which 100% fill factors are obtained. Specifically, FSA was used to assemble two different sizes of silicon blocks into holes in a silicon substrate. Fabrication techniques as well as FSA results are included.

CT demonstration of pharyngeal narrowing in adult obstructive sleep apnea

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

Bohlman, M.E.; Haponik, E.F.; Smith, P.L.

Sleep apnea is a major cause of daytime hypersomnolence. Among the proposed etiologies, focal obstruction of the airways at the level of the pharynx has been suggested but not proven. Using computed tomography, the cross-sectional area of the airway can be readily assessed. Thirty-three adults with clinically proven sleep apnea and 12 normal adults underwent systematic computed tomography of the neck. Significant airway narrowing was demonstrated in all the patients with obstructive sleep apnea, whereas no such narrowing was seen in the controls. In 11, the narrowing was at a single level, whereas in 22 patients two or more levelsmore » were affected. This study has shown that a structurally abnormal airway may serve as an anatomic substrate for the development of sleep apnea. On the basis of this evidence, uvulopalatopharyngoplasty has been performed in two patients with relief of symptoms in one.« less

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

Proteolytic activities of kiwifruit actinidin (Actinidia deliciosa cv. Hayward) on different fibrous and globular proteins: a comparative study of actinidin with papain.

PubMed

Chalabi, Maryam; Khademi, Fatemeh; Yarani, Reza; Mostafaie, Ali

2014-04-01

Actinidin, a member of the papain-like family of cysteine proteases, is abundant in kiwifruit. To date, a few studies have been provided to investigate the proteolytic activity and substrate specificity of actinidin on native proteins. Herein, the proteolytic activity of actinidin was compared to papain on several different fibrous and globular proteins under neutral, acidic and basic conditions. The digested samples were subjected to sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and densitometry to assess the proteolytic effect. Furthermore, the levels of free amino nitrogen (FAN) of the treated samples were determined using the ninhydrin colorimetric method. The findings showed that actinidin has no or limited proteolytic effect on globular proteins such as immunoglobulins including sheep IgG, rabbit IgG, chicken IgY and fish IgM, bovine serum albumin (BSA), lipid transfer protein (LTP), and whey proteins (α-lactalbumin and β-lactoglobulin) compared to papain. In contrast to globular proteins, actinidin could hydrolyze collagen and fibrinogen perfectly at neutral and mild basic pHs. Moreover, this enzyme could digest pure α-casein and major subunits of micellar casein especially in acidic pHs. Taken together, the data indicated that actinidin has narrow substrate specificity with the highest enzymatic activity for the collagen and fibrinogen substrates. The results describe the actinidin as a mild plant protease useful for many special applications such as cell isolation from different tissues and some food industries as a mixture formula with other relevant proteases.

Activation of P-glycoprotein and CYP 3A by Coptidis Rhizoma in vivo: Using cyclosporine as a probe substrate in rats.

PubMed

Yu, Chung-Ping; Huang, Ching-Ya; Lin, Shiuan-Pey; Hou, Yu-Chi

2018-04-01

Coptidis Rhizoma (CR), the rhizome of Coptis chinensis FRANCH, is a popular Chinese herb. CR contains plenty of isoquinoline alkaloids such as berberine, coptisine and palmatine. Cyclosporine (CSP), an important immunosuppressant with narrow therapeutic window, is employed as a probe substrate of P-glycoprotein (P-gp) and CYP3A4 in order to investigate the in vivo modulation effect of CR on P-gp and CYP3A4. Three groups of rats were orally administered CSP without and with single dose or repeated dosing of CR in a parallel design. Blood samples were collected at specific time points and the blood CSP concentration was determined by a specific monoclonal fluorescence polarization immunoassay. The results showed that a single dose (1.0 g/kg) and the 7th dose (1.0 g/kg) of CR significantly decreased the C max of CSP by 56.9% and 70.4%, and reduced the AUC 0-540 by 56.4% and 68.7%, respectively. Cell study indicated that CR decoction, berberine, coptisine, palmatine all activated the efflux transport of P-gp. Ex-vivo study showed that the serum metabolites of CR activated CYP 3A4. In conclusion, through using CSP as an in vivo probe substrate, we have verified that oral intake of CR activated the functions of P-gp and CYP3A based on in vivo and in vitro studies. Copyright © 2017. Published by Elsevier B.V.

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

Mohammad, Sabah M., E-mail: Sabahaskari14@gmail.com; Ahmed, Naser M.; Abd-Alghafour, Nabeel M.

Vertically, well-aligned and high density ZnO nanorods were successfully hydrothermally grown on glass and silicon substrates using a simple and low cost system. The mechanism of synthesis of ZnO nanorods, generated with our system under hydrothermal conditions, is investigated in this report. Field-emission scanning electron microscopy indicated that the fabricated ZnO nanorods on both substrates have hexagonal shape with diameters ranging from 20 nm to 70 nm which grew vertically from the substrate. XRD analysis confirms the formation of wurtzite ZnO phase with a preferred orientation along (002) direction perpendicular on the substrate and enhanced crystallinity. The low value ofmore » the tensile strain (0.126 %) revealed that ZnO nanorods preferred to grow along the c-axis for both substrates. Photoluminescence spectra exhibited a strong, sharp UV near band edge emission peak with narrow FWHM values for both samples.« less

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

PubMed

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

2003-05-13

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

Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I

PubMed Central

Shi, Yuqian; Hellinga, Homme W.; Beese, Lorena S.

2017-01-01

Human exonuclease 1 (hExo1) is a member of the RAD2/XPG structure-specific 5′-nuclease superfamily. Its dominant, processive 5′–3′ exonuclease and secondary 5′-flap endonuclease activities participate in various DNA repair, recombination, and replication processes. A single active site processes both recessed ends and 5′-flap substrates. By initiating enzyme reactions in crystals, we have trapped hExo1 reaction intermediates that reveal structures of these substrates before and after their exo- and endonucleolytic cleavage, as well as structures of uncleaved, unthreaded, and partially threaded 5′ flaps. Their distinctive 5′ ends are accommodated by a small, mobile arch in the active site that binds recessed ends at its base and threads 5′ flaps through a narrow aperture within its interior. A sequence of successive, interlocking conformational changes guides the two substrate types into a shared reaction mechanism that catalyzes their cleavage by an elaborated variant of the two-metal, in-line hydrolysis mechanism. Coupling of substrate-dependent arch motions to transition-state stabilization suppresses inappropriate or premature cleavage, enhancing processing fidelity. The striking reduction in flap conformational entropy is catalyzed, in part, by arch motions and transient binding interactions between the flap and unprocessed DNA strand. At the end of the observed reaction sequence, hExo1 resets without relinquishing DNA binding, suggesting a structural basis for its processivity. PMID:28533382

Implications of the Hierarchical Structure of Psychopathology for Psychiatric Neuroimaging.

PubMed

Zald, David H; Lahey, Benjamin B

2017-05-01

Research into the neurobiological substrates of psychopathology has been impeded by heterogeneity within diagnostic categories, comorbidity among mental disorders, and the presence of symptoms that transcend diagnostic categories. Solutions to these issues increasingly focus neurobiological research on isolated or narrow groupings of symptoms or functional constructs rather than categorical diagnoses. Here we argue for a more integrative approach that also incorporates the broad hierarchical structure of psychopathological symptoms and their etiological mechanisms. This approach places clinical neuroscience research in the context of a hierarchy of empirically defined factors of symptoms such as internalizing disorders, externalizing disorders, and the general factor of psychopathology. Application of this hierarchical approach has the potential to reveal neural substrates that nonspecifically contribute to multiple forms of psychopathology and their comorbidity, and in doing so, facilitate the study of mechanisms that are specific to single dimensions and subsets of symptoms. Neurobiological research on the hierarchy of dimensions of psychopathology is only just beginning to emerge, but has the potential to radically alter our understanding of the neurobiology of abnormal behavior.

Implications of the Hierarchical Structure of Psychopathology for Psychiatric Neuroimaging

PubMed Central

Zald, David H.; Lahey, Benjamin B.

2017-01-01

Research into the neurobiological substrates of psychopathology has been impeded by heterogeneity within diagnostic categories, comorbidity among mental disorders, and the presence of symptoms that transcend diagnostic categories. Solutions to these issues increasingly focus neurobiological research on isolated or narrow groupings of symptoms or functional constructs rather than categorical diagnoses. Here we argue for a more integrative approach that also incorporates the broad hierarchical structure of psychopathological symptoms and their etiological mechanisms. This approach places clinical neuroscience research in the context of a hierarchy of empirically defined factors of symptoms such as internalizing disorders, externalizing disorders, and the general factor of psychopathology. Application of this hierarchical approach has the potential to reveal neural substrates that nonspecifically contribute to multiple forms of psychopathology and their comorbidity, and in doing so, facilitate the study of mechanisms that are specific to single dimensions and subsets of symptoms. Neurobiological research on the hierarchy of dimensions of psychopathology is only just beginning to emerge, but has the potential to radically alter our understanding of the neurobiology of abnormal behavior. PMID:28713866

Carbonaceous film coating

DOEpatents

Maya, L.

1988-04-27

A method of making a carbonaceous film comprising heating tris(1,3,2-benzodiazaborolo)borazine or dodecahydro tris(1,3,2)diazaborine(1,2-a:1'2'-c:1''2''-e)borazine in an inert atmosphere in the presence of a substrate to a temperature at which the borazine compound decomposes, and the decomposition products deposit onto the substrate to form a thin, tenacious, highly reflective conductive coating having a narrow band gap which is susceptible of modification and a relatively low coefficient of friction.

Carbonaceous film coating

DOEpatents

Maya, Leon

1989-01-01

A method of making a carbonaceous film comprising heating tris(1,3,2-benzodiazaborolo)borazine or dodecahydro tris[1,3,2]diazaborine[1,2-a:1'2'-c:1"2"-e]borazine in an inert atmosphere in the presence of a substrate to a temperature at which the borazine compound decomposes, and the decomposition products deposit onto the substrate to form a thin, tenacious, highly reflective conductive coating having a narrow band gap which is susceptible of modification and a relatively low coefficient of friction.

Distributed Capacitive Sensor for Sample Mass Measurement

NASA Technical Reports Server (NTRS)

Toda, Risaku; McKinney, Colin; Jackson, Shannon P.; Mojarradi, Mohammad; Manohara, Harish; Trebi-Ollennu, Ashitey

2011-01-01

Previous robotic sample return missions lacked in situ sample verification/ quantity measurement instruments. Therefore, the outcome of the mission remained unclear until spacecraft return. In situ sample verification systems such as this Distributed Capacitive (DisC) sensor would enable an unmanned spacecraft system to re-attempt the sample acquisition procedures until the capture of desired sample quantity is positively confirmed, thereby maximizing the prospect for scientific reward. The DisC device contains a 10-cm-diameter pressure-sensitive elastic membrane placed at the bottom of a sample canister. The membrane deforms under the weight of accumulating planetary sample. The membrane is positioned in close proximity to an opposing rigid substrate with a narrow gap. The deformation of the membrane makes the gap narrower, resulting in increased capacitance between the two parallel plates (elastic membrane and rigid substrate). C-V conversion circuits on a nearby PCB (printed circuit board) provide capacitance readout via LVDS (low-voltage differential signaling) interface. The capacitance method was chosen over other potential approaches such as the piezoelectric method because of its inherent temperature stability advantage. A reference capacitor and temperature sensor are embedded in the system to compensate for temperature effects. The pressure-sensitive membranes are aluminum 6061, stainless steel (SUS) 403, and metal-coated polyimide plates. The thicknesses of these membranes range from 250 to 500 m. The rigid substrate is made with a 1- to 2-mm-thick wafer of one of the following materials depending on the application requirements glass, silicon, polyimide, PCB substrate. The glass substrate is fabricated by a microelectromechanical systems (MEMS) fabrication approach. Several concentric electrode patterns are printed on the substrate. The initial gap between the two plates, 100 m, is defined by a silicon spacer ring that is anodically bonded to the glass substrate. The fabricated proof-of-concept devices have successfully demonstrated tens to hundreds of picofarads of capacitance change when a simulated sample (100 g to 500 g) is placed on the membrane.

Specific features of the spectra and relaxation kinetics of long-wavelength photoconductivity in narrow-gap HgCdTe epitaxial films and heterostructures with quantum wells

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

Rumyantsev, V. V., E-mail: rumyantsev@ipmras.ru; Ikonnikov, A. V.; Antonov, A. V.

2013-11-15

The spectra and relaxation kinetics of interband photoconductivity are investigated in narrow-gap Hg{sub 1-x}Cd{sub x}Te epitaxial films with x = 0.19-0.23 and in structures with HgCdTe-based quantum wells (QWs), having an interband-transition energy in the range of 30-90 meV, grown by molecular-beam epitaxy on GaAs (013) substrates. A long-wavelength sensitivity band caused by impurities or defects is found in the spectra of the structures with quantum wells in addition to the interband photoconductivity. It is shown that the lifetimes of nonequilibrium carriers in the structures with QWs is less than in bulk samples at the same optical-transition energy. From themore » measured carrier lifetimes, the ampere-watt responsivity and the equivalent noise power for a film with x = 0.19 at a wavelength of 19 {mu}m are estimated. When investigating the relaxation kinetics of the photoconductivity at 4.2 K in high excitation regime, it is revealed that radiative recombination is dominant over other mechanisms of nonequilibrium-carrier recombination.« less

Angle resolved x-ray photoelectron spectroscopy (ARXPS) analysis of lanthanum oxide for micro-flexography printing

NASA Astrophysics Data System (ADS)

Hassan, S.; Yusof, M. S.; Embong, Z.; Maksud, M. I.

2016-01-01

Micro-flexography printing was developed in patterning technique from micron to nano scale range to be used for graphic, electronic and bio-medical device on variable substrates. In this work, lanthanum oxide (La2O3) has been used as a rare earth metal candidate as depositing agent. This metal deposit was embedded on Carbon (C) and Silica (Si) wafer substrate using Magnetron Sputtering technique. The choose of Lanthanum as a target is due to its wide application in producing electronic devices such as thin film battery and printed circuit board. The La2O3 deposited on the surface of Si wafer substrate was then analyzed using Angle Resolve X-Ray Photoelectron Spectroscopy (ARXPS). The position for each synthetic component in the narrow scan of Lanthanum (La) 3d and O 1s are referred to the electron binding energy (eV). The La 3d narrow scan revealed that the oxide species of this particular metal is mainly contributed by La2O3 and La(OH)3. The information of oxygen species, O2- component from O 1s narrow scan indicated that there are four types of species which are contributed from the bulk (O2-), two chemisorb component (La2O3) and La(OH)3 and physisorp component (OH). Here, it is proposed that from the adhesive and surface chemical properties of La, it is suitable as an alternative medium for micro-flexography printing technique in printing multiple fine solid lines at nano scale. Hence, this paper will describe the capability of this particular metal as rare earth metal for use in of micro-flexography printing practice. The review of other parameters contributing to print fine lines will also be described later.

Bioprocess development workflow: Transferable physiological knowledge instead of technological correlations.

PubMed

Reichelt, Wieland N; Haas, Florian; Sagmeister, Patrick; Herwig, Christoph

2017-01-01

Microbial bioprocesses need to be designed to be transferable from lab scale to production scale as well as between setups. Although substantial effort is invested to control technological parameters, usually the only true constant parameter is the actual producer of the product: the cell. Hence, instead of solely controlling technological process parameters, the focus should be increasingly laid on physiological parameters. This contribution aims at illustrating a workflow of data life cycle management with special focus on physiology. Information processing condenses the data into physiological variables, while information mining condenses the variables further into physiological descriptors. This basis facilitates data analysis for a physiological explanation for observed phenomena in productivity. Targeting transferability, we demonstrate this workflow using an industrially relevant Escherichia coli process for recombinant protein production and substantiate the following three points: (1) The postinduction phase is independent in terms of productivity and physiology from the preinduction variables specific growth rate and biomass at induction. (2) The specific substrate uptake rate during induction phase was found to significantly impact the maximum specific product titer. (3) The time point of maximum specific titer can be predicted by an easy accessible physiological variable: while the maximum specific titers were reached at different time points (19.8 ± 7.6 h), those maxima were reached all within a very narrow window of cumulatively consumed substrate dSn (3.1 ± 0.3 g/g). Concluding, this contribution provides a workflow on how to gain a physiological view on the process and illustrates potential benefits. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 33:261-270, 2017. © 2016 American Institute of Chemical Engineers.

Samarium electrodeposited acetate and oxide thin films on stainless steel substrate characterized by XPS

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

Myhre, Kristian; Burns, Jonathan; Meyer, Harry

Characterization of a samarium thin film deposited on a stainless steel substrate using molecular electrodeposition was carried out using a Thermo Scientific K-Alpha X-ray photoelectron spectrometer. We studied two types of samarium electrodeposition samples, one as-deposited and one heated to 700 °C in an air flow. Survey scans include peaks coming from the stainless steel substrate, such as Fe and Cr. An X-ray photoelectron spectroscopy (XPS) survey spectrum, Sm 3d, C 1s, and O 1s narrow scans are shown. It was determined that the heating process decomposed the deposited Sm acetate to Sm 2O 3 using XPS.

Samarium electrodeposited acetate and oxide thin films on stainless steel substrate characterized by XPS

DOE PAGES

Myhre, Kristian; Burns, Jonathan; Meyer, Harry; ...

2016-06-01

Characterization of a samarium thin film deposited on a stainless steel substrate using molecular electrodeposition was carried out using a Thermo Scientific K-Alpha X-ray photoelectron spectrometer. We studied two types of samarium electrodeposition samples, one as-deposited and one heated to 700 °C in an air flow. Survey scans include peaks coming from the stainless steel substrate, such as Fe and Cr. An X-ray photoelectron spectroscopy (XPS) survey spectrum, Sm 3d, C 1s, and O 1s narrow scans are shown. It was determined that the heating process decomposed the deposited Sm acetate to Sm 2O 3 using XPS.

Fabrication of an open Au/nanoporous film by water-in-oil emulsion-induced block copolymer micelles.

PubMed

Koh, Haeng-Deog; Kang, Nam-Goo; Lee, Jae-Suk

2007-12-18

Water-in-oil (W/O) emulsion-induced micelles with narrow size distributions of approximately 140 nm were prepared by sonicating the polystyrene-b-poly(2-vinylpyridine) (PS-b-P2VP) block copolymer in the toluene/water (50:1 vol %). The ordered nanoporous block copolymer films with the hydrophilic P2VP interior and the PS matrix were distinctly fabricated by casting the resultant solution on substrates, followed by evaporating the organic solvent and water. The porous diameter was estimated to be about 70 nm. Here, we successfully prepared the open nanoporous nanocomposites, the P2VP domain decorated by Au (5+/-0.4 nm) nanoparticles based on the methodology mentioned. We anticipate that this novelty enhances the specific function of nanoporous films.

Characterization of the 2′,3′ cyclic phosphodiesterase activities of Clostridium thermocellum polynucleotide kinase-phosphatase and bacteriophage λ phosphatase

PubMed Central

Keppetipola, Niroshika; Shuman, Stewart

2007-01-01

Clostridium thermocellum polynucleotide kinase-phosphatase (CthPnkp) catalyzes 5′ and 3′ end-healing reactions that prepare broken RNA termini for sealing by RNA ligase. The central phosphatase domain of CthPnkp belongs to the dinuclear metallophosphoesterase superfamily exemplified by bacteriophage λ phosphatase (λ-Pase). CthPnkp is a Ni2+/Mn2+-dependent phosphodiesterase-monoesterase, active on nucleotide and non-nucleotide substrates, that can be transformed toward narrower metal and substrate specificities via mutations of the active site. Here we characterize the Mn2+-dependent 2′,3′ cyclic nucleotide phosphodiesterase activity of CthPnkp, the reaction most relevant to RNA repair pathways. We find that CthPnkp prefers a 2′,3′ cyclic phosphate to a 3′,5′ cyclic phosphate. A single H189D mutation imposes strict specificity for a 2′,3′ cyclic phosphate, which is cleaved to form a single 2′-NMP product. Analysis of the cyclic phosphodiesterase activities of mutated CthPnkp enzymes illuminates the active site and the structural features that affect substrate affinity and kcat. We also characterize a previously unrecognized phosphodiesterase activity of λ-Pase, which catalyzes hydrolysis of bis-p-nitrophenyl phosphate. λ-Pase also has cyclic phosphodiesterase activity with nucleoside 2′,3′ cyclic phosphates, which it hydrolyzes to yield a mixture of 2′-NMP and 3′-NMP products. We discuss our results in light of available structural and functional data for other phosphodiesterase members of the binuclear metallophosphoesterase family and draw inferences about how differences in active site composition influence catalytic repertoire. PMID:17986465

Characterization of a newly synthesized carbonyl reductase and construction of a biocatalytic process for the synthesis of ethyl (S)-4-chloro-3-hydroxybutanoate with high space-time yield.

PubMed

You, Zhong-Yu; Liu, Zhi-Qiang; Zheng, Yu-Guo

2014-02-01

A carbonyl reductase (SCR2) gene was synthesized and expressed in Escherichia coli after codon optimization to investigate its biochemical properties and application in biosynthesis of ethyl (S)-4-chloro-3-hydroxybutanoate ((S)-CHBE), which is an important chiral synthon for the side chain of cholesterol-lowering drug. The recombinant SCR2 was purified and characterized using ethyl 4-chloro-3-oxobutanoate (COBE) as substrate. The specific activity of purified enzyme was 11.9 U mg(-1). The optimum temperature and pH for enzyme activity were 45 °C and pH 6.0, respectively. The half-lives of recombinant SCR2 were 16.5, 7.7, 2.2, 0.41, and 0.05 h at 30 °C, 35 °C, 40 °C, 45 °C, and 50 °C, respectively, and it was highly stable in acidic environment. This SCR2 displayed a relatively narrow substrate specificity. The apparent K m and V max values of purified enzyme for COBE are 6.4 mM and 63.3 μmol min(-1) mg(-1), respectively. The biocatalytic process for the synthesis of (S)-CHBE was constructed by this SCR2 in an aqueous-organic solvent system with a substrate fed-batch strategy. At the final COBE concentration of 1 M, (S)-CHBE with yield of 95.3% and e.e. of 99% was obtained after 6-h reaction. In this process, the space-time yield per gram of biomass (dry cell weight, DCW) and turnover number of NADP(+) to (S)-CHBE were 26.5 mmol L(-1) h(-1) g(-1) DCW and 40,000 mol/mol, respectively, which were the highest values as compared with other works.

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.

Raman imaging using fixed bandpass filter

NASA Astrophysics Data System (ADS)

Landström, L.; Kullander, F.; Lundén, H.; Wästerby, P.

2017-05-01

By using fixed narrow band pass optical filtering and scanning the laser excitation wavelength, hyperspectral Raman imaging could be achieved. Experimental, proof-of-principle results from the Chemical Warfare Agent (CWA) tabun (GA) as well as the common CWA simulant tributyl phosphate (TBP) on different surfaces/substrates are presented and discussed.

Cyclopentanoid analogs of phosphatidylcholine: susceptibility to phospholipase A2.

PubMed

Lister, M D; Hancock, A J

1988-10-01

Six isomers of dipalmitoylcyclopentanetriol phosphocholine (cyclopentano-lecithin) were tested as potential substrates for phospholipase A2. Since each of these analogs possesses a configuration that mimics a narrow range of conformations of a glycerophospholipid molecule, the analogs were used to assess the enzyme's conformational requirements. Studies showed that all of the analogs containing the phosphocholine at the C-1 (or C-3) position could be hydrolyzed, while only one of the three analogs that contains the polar head group at the C-2 position was susceptible. Kinetic studies, however, revealed that only the all-trans-(1,3/2-1P)-cyclopentano-lecithin gave initial rates of hydrolysis that were measurable by pH-stat. Acyl group specificity of the enzyme towards the all-trans isomer was determined with an analog was acyl groups were distinguishable. The synthesis of this mixed-acid-cyclopentano-PC is described herein. When this analog was enzymatically assayed, results unequivocally showed the enzyme to be specific for C-2 acyl hydrolysis. This specificity, and data showing that the all-trans analog is stereospecifically hydrolyzed, indicate that it is acted on in an analogous manner to dipalmitoylphosphatidylcholine. These studies indicate that although the configuration of the analog is not necessarily a prerequisite for hydrolysis, there does appear to be an optimal spatial orientation for enzymatic activity. The analogy between the susceptibilities of all-trans-(1,3/2-1P)-cyclopentano-lecithin and glycero-lecithin suggests that the conformation of the glycero-lecithin during phospholipase A2-mediated hydrolysis may be best simulated by the all-trans orientation of C-O bonds in the artificial substrate.

Dry season distribution of land crabs, Gecarcinus quadratus (Crustacea: Gecarcinidae), in Corcovado National Park, Costa Rica.

PubMed

Griffiths, Megan E; Mohammad, Basma A; Vega, Andres

2007-03-01

The land crab Gecarcinus quadratus is an engineering species that controls nutrient cycling in tropical forests. Factors regulating their coastal distribution are not fully understood. We quantified land crab distribution during the dry season at Sirena Field Station in Corcovado National Park, Costa Rica, and found that land crab burrow density decreases with increasing distance from the ocean. Leaf litter depth and tree seedling density are negatively correlated with land crab burrow density. Burrows are strongly associated with sand substrate and burrow density is comparatively low in clay substrate. Results suggest that G. quadratus is limited to a narrow coastal zone with sand substrate, and this distribution could have profound effects on plant community structure.

Human Viperin Causes Radical SAM-Dependent Elongation of Escherichia coli, Hinting at Its Physiological Role.

PubMed

Nelp, Micah T; Young, Anthony P; Stepanski, Branden M; Bandarian, Vahe

2017-08-01

Viperin (virus inhibitory protein, endoplasmic reticulum-associated, interferon-inducible) is a widely distributed protein that is expressed in response to infection and causes antiviral effects against a broad spectrum of viruses. Viperin is a member of the radical S-adenosyl-l-methionine (SAM) superfamily of enzymes, which typically employ a 4Fe-4S cluster to reductively cleave SAM to initiate chemistry. Though the specific reaction catalyzed by viperin remains unknown, it has been shown that expression of viperin causes an increase in the fluidity of lipid membranes, which impedes the budding of nascent viral particles from the membrane inhibiting propagation of the infection. Herein, we show that expression of the human viperin homologue induces a dramatically elongated morphology of the host Escherichia coli cells. Mutation of an essential cysteine that coordinates the radical SAM cluster abrogates this effect. Thus, the native radical SAM activity of viperin is likely occurring in the host bacteria, indicating the elusive substrate is shared between both bacteria and humans, significantly narrowing the range of potential candidate substrates and providing a convenient bacterial platform from which future studies can occur.

Deep Sequencing of Random Mutant Libraries Reveals the Active Site of the Narrow Specificity CphA Metallo-β-Lactamase is Fragile to Mutations.

PubMed

Sun, Zhizeng; Mehta, Shrenik C; Adamski, Carolyn J; Gibbs, Richard A; Palzkill, Timothy

2016-09-12

CphA is a Zn(2+)-dependent metallo-β-lactamase that efficiently hydrolyzes only carbapenem antibiotics. To understand the sequence requirements for CphA function, single codon random mutant libraries were constructed for residues in and near the active site and mutants were selected for E. coli growth on increasing concentrations of imipenem, a carbapenem antibiotic. At high concentrations of imipenem that select for phenotypically wild-type mutants, the active-site residues exhibit stringent sequence requirements in that nearly all residues in positions that contact zinc, the substrate, or the catalytic water do not tolerate amino acid substitutions. In addition, at high imipenem concentrations a number of residues that do not directly contact zinc or substrate are also essential and do not tolerate substitutions. Biochemical analysis confirmed that amino acid substitutions at essential positions decreased the stability or catalytic activity of the CphA enzyme. Therefore, the CphA active - site is fragile to substitutions, suggesting active-site residues are optimized for imipenem hydrolysis. These results also suggest that resistance to inhibitors targeted to the CphA active site would be slow to develop because of the strong sequence constraints on function.

Neural Correlates of Multisensory Perceptual Learning

PubMed Central

Powers, Albert R.; Hevey, Matthew A.; Wallace, Mark T.

2012-01-01

The brain’s ability to bind incoming auditory and visual stimuli depends critically on the temporal structure of this information. Specifically, there exists a temporal window of audiovisual integration within which stimuli are highly likely to be perceived as part of the same environmental event. Several studies have described the temporal bounds of this window, but few have investigated its malleability. Recently, our laboratory has demonstrated that a perceptual training paradigm is capable of eliciting a 40% narrowing in the width of this window that is stable for at least one week after cessation of training. In the current study we sought to reveal the neural substrates of these changes. Eleven human subjects completed an audiovisual simultaneity judgment training paradigm, immediately before and after which they performed the same task during an event-related 3T fMRI session. The posterior superior temporal sulcus (pSTS) and areas of auditory and visual cortex exhibited robust BOLD decreases following training, and resting state and effective connectivity analyses revealed significant increases in coupling among these cortices after training. These results provide the first evidence of the neural correlates underlying changes in multisensory temporal binding and that likely represent the substrate for a multisensory temporal binding window. PMID:22553032

Total ionizing dose effect in an input/output device for flash memory

NASA Astrophysics Data System (ADS)

Liu, Zhang-Li; Hu, Zhi-Yuan; Zhang, Zheng-Xuan; Shao, Hua; Chen, Ming; Bi, Da-Wei; Ning, Bing-Xu; Zou, Shi-Chang

2011-12-01

Input/output devices for flash memory are exposed to gamma ray irradiation. Total ionizing dose has been shown great influence on characteristic degradation of transistors with different sizes. In this paper, we observed a larger increase of off-state leakage in the short channel device than in long one. However, a larger threshold voltage shift is observed for the narrow width device than for the wide one, which is well known as the radiation induced narrow channel effect. The radiation induced charge in the shallow trench isolation oxide influences the electric field of the narrow channel device. Also, the drain bias dependence of the off-state leakage after irradiation is observed, which is called the radiation enhanced drain induced barrier lowing effect. Finally, we found that substrate bias voltage can suppress the off-state leakage, while leading to more obvious hump effect.

Subdigital setae of chameleon feet: friction-enhancing microstructures for a wide range of substrate roughness.

PubMed

Spinner, Marlene; Westhoff, Guido; Gorb, Stanislav N

2014-06-27

Hairy adhesive systems of microscopic setae with triangular flattened tips have evolved convergently in spiders, insects and arboreal lizards. The ventral sides of the feet and tails in chameleons are also covered with setae. However, chameleon setae feature strongly elongated narrow spatulae or fibrous tips. The friction enhancing function of these microstructures has so far only been demonstrated in contact with glass spheres. In the present study, the frictional properties of subdigital setae of Chamaeleo calyptratus were measured under normal forces in the physical range on plane substrates having different roughness. We showed that chameleon setae maximize friction on a wide range of substrate roughness. The highest friction was measured on asperities of 1 μm. However, our observations of the climbing ability of Ch. calyptratus on rods of different diameters revealed that also claws and grasping feet are additionally responsible for the force generation on various substrates during locomotion.

Graphene as an atomically thin interface for growth of vertically aligned carbon nanotubes.

PubMed

Rao, Rahul; Chen, Gugang; Arava, Leela Mohana Reddy; Kalaga, Kaushik; Ishigami, Masahiro; Heinz, Tony F; Ajayan, Pulickel M; Harutyunyan, Avetik R

2013-01-01

Growth of vertically aligned carbon nanotube (CNT) forests is highly sensitive to the nature of the substrate. This constraint narrows the range of available materials to just a few oxide-based dielectrics and presents a major obstacle for applications. Using a suspended monolayer, we show here that graphene is an excellent conductive substrate for CNT forest growth. Furthermore, graphene is shown to intermediate growth on key substrates, such as Cu, Pt, and diamond, which had not previously been compatible with nanotube forest growth. We find that growth depends on the degree of crystallinity of graphene and is best on mono- or few-layer graphene. The synergistic effects of graphene are revealed by its endurance after CNT growth and low contact resistances between the nanotubes and Cu. Our results establish graphene as a unique interface that extends the class of substrate materials for CNT growth and opens up important new prospects for applications.

Graphene as an atomically thin interface for growth of vertically aligned carbon nanotubes

PubMed Central

Rao, Rahul; Chen, Gugang; Arava, Leela Mohana Reddy; Kalaga, Kaushik; Ishigami, Masahiro; Heinz, Tony F.; Ajayan, Pulickel M.; Harutyunyan, Avetik R.

2013-01-01

Growth of vertically aligned carbon nanotube (CNT) forests is highly sensitive to the nature of the substrate. This constraint narrows the range of available materials to just a few oxide-based dielectrics and presents a major obstacle for applications. Using a suspended monolayer, we show here that graphene is an excellent conductive substrate for CNT forest growth. Furthermore, graphene is shown to intermediate growth on key substrates, such as Cu, Pt, and diamond, which had not previously been compatible with nanotube forest growth. We find that growth depends on the degree of crystallinity of graphene and is best on mono- or few-layer graphene. The synergistic effects of graphene are revealed by its endurance after CNT growth and low contact resistances between the nanotubes and Cu. Our results establish graphene as a unique interface that extends the class of substrate materials for CNT growth and opens up important new prospects for applications. PMID:23712556

Between Scylla and Charybdis: Hydrophobic Graphene-Guided Water Diffusion on Hydrophilic Substrates

PubMed Central

Kim, Jin-Soo; Choi, Jin Sik; Lee, Mi Jung; Park, Bae Ho; Bukhvalov, Danil; Son, Young-Woo; Yoon, Duhee; Cheong, Hyeonsik; Yun, Jun-Nyeong; Jung, Yousung; Park, Jeong Young; Salmeron, Miquel

2013-01-01

The structure of water confined in nanometer-sized cavities is important because, at this scale, a large fraction of hydrogen bonds can be perturbed by interaction with the confining walls. Unusual fluidity properties can thus be expected in the narrow pores, leading to new phenomena like the enhanced fluidity reported in carbon nanotubes. Crystalline mica and amorphous silicon dioxide are hydrophilic substrates that strongly adsorb water. Graphene, on the other hand, interacts weakly with water. This presents the question as to what determines the structure and diffusivity of water when intercalated between hydrophilic substrates and hydrophobic graphene. Using atomic force microscopy, we have found that while the hydrophilic substrates determine the structure of water near its surface, graphene guides its diffusion, favouring growth of intercalated water domains along the C-C bond zigzag direction. Molecular dynamics and density functional calculations are provided to help understand the highly anisotropic water stripe patterns observed. PMID:23896759

Subdigital setae of chameleon feet: Friction-enhancing microstructures for a wide range of substrate roughness

NASA Astrophysics Data System (ADS)

Spinner, Marlene; Westhoff, Guido; Gorb, Stanislav N.

2014-06-01

Hairy adhesive systems of microscopic setae with triangular flattened tips have evolved convergently in spiders, insects and arboreal lizards. The ventral sides of the feet and tails in chameleons are also covered with setae. However, chameleon setae feature strongly elongated narrow spatulae or fibrous tips. The friction enhancing function of these microstructures has so far only been demonstrated in contact with glass spheres. In the present study, the frictional properties of subdigital setae of Chamaeleo calyptratus were measured under normal forces in the physical range on plane substrates having different roughness. We showed that chameleon setae maximize friction on a wide range of substrate roughness. The highest friction was measured on asperities of 1 μm. However, our observations of the climbing ability of Ch. calyptratus on rods of different diameters revealed that also claws and grasping feet are additionally responsible for the force generation on various substrates during locomotion.

Conceptual development of the Laser Beam Manifold (LBM)

NASA Technical Reports Server (NTRS)

Campbell, W.; Owen, R. B.

1979-01-01

The laser beam manifold, a device for transforming a single, narrow, collimated beam of light into several beams of desired intensity ratios is described. The device consists of a single optical substrate with a metallic coating on both optical surfaces. By changing the entry point, the number of outgoing beams can be varied.

Ridge-width dependence of the threshold of long wavelength (λ ≈ 14 µm) Quantum Cascade lasers with sloped and vertical sidewalls.

PubMed

Huang, Xue; Chiu, Yenting; Charles, William O; Gmachl, Claire

2012-01-30

We investigate the ridge-width dependence of the threshold of Quantum Cascade lasers fabricated by wet and dry etching, respectively. The sloped sidewalls resulting from wet etching affect the threshold in two ways as the ridge gets narrower. First, the transverse modes are deeper in the substrate, hence reducing the optical confinement factor. Second, more important, a non-negligible field exists in the lossy SiO2 insulation layer, as a result of transverse magnetic mode coupling to the surface plamon mode at the insulator/metal surface, which increases the waveguide loss. By contrast, dry etching is anisotropic and leads to waveguides with vertical sidewalls, which avoids the shift of the modes to the substrate layer and coupling to the surface plasmons, resulting in improved threshold compared with wet-etched lasers, e.g., for narrow ridge widths below 20 µm, the threshold of a 14 µm wide λ ≈ 14 µm laser by dry etching is ~60% lower than that of a wet-etched laser of the same width, at 80 K.

Experimental and theoretical study of the buckling of narrow thin plates on an elastic foundation under compression

NASA Astrophysics Data System (ADS)

Kurguzov, V. D.; Demeshkin, A. G.

2016-05-01

The paper describes the processes of elastic deformation of thin films under mechanical loading. The film is modeled longitudinally by a compressed plate arranged on an elastic foundation. A computer model of the buckling of the narrow thin plate with a delamination portion located on an elastic foundation is constructed. This paper also touches upon the supercritical behavior of the plate-substrate system. The experiments on the axial compression of a metal strip adhered to a rubber plate are performed, and 2 to 7 buckling modes are obtained therein. The critical loads and buckling modes obtained in the numerical calculations are compared with the experimental data. It is shown that there is the possibility of progressive delamination of the metal plate from the foundation if the critical load is exceeded. It is found that the use of the proposed approach, which, in contrast to other approaches, accounts for the elastic deformation of the substrate, causes the dependence between the critical bending stress and the stiffness of the foundation.

Group-III nitride VCSEL structures grown by molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Ng, HockMin; Moustakas, Theodore D.

2000-07-01

III-nitride VCSEL structures designed for electron-beam pumping have been grown by molecular beam epitaxy (MBE). The structures consist of a sapphire substrate on which an AlN/GaN distributed Bragg reflector (DBR) with peak reflectance >99% at 402 nm is deposited. The active region consists of a 2-(lambda) cavity with 25 In0.1Ga0.9N/GaN multiquantum wells (MQWs) whose emission coincides with the high reflectance region of the DBR. The thicknesses of the InGaN wells and the GaN barriers are 35 angstrom and 75 angstrom respectively. The top reflector consists of a silver metallic mirror which prevents charging effects during electron-beam pumping. The structure was pumped from the top- side with a cw electron-beam using a modified cathodoluminescence (CL) system mounted on a scanning electron microscope chamber. Light output was collected from the polished sapphire substrate side. Measurements performed at 100 K showed intense emission at 407 nm with narrowing of the linewidth with increasing beam current. A narrow emission linewidth of 0.7 nm was observed indicating the onset of stimulated emission.

The diagnostic value of narrow-band imaging for early and invasive lung cancer: a meta-analysis.

PubMed

Zhu, Juanjuan; Li, Wei; Zhou, Jihong; Chen, Yuqing; Zhao, Chenling; Zhang, Ting; Peng, Wenjia; Wang, Xiaojing

2017-07-01

This study aimed to compare the ability of narrow-band imaging to detect early and invasive lung cancer with that of conventional pathological analysis and white-light bronchoscopy. We searched the PubMed, EMBASE, Sinomed, and China National Knowledge Infrastructure databases for relevant studies. Meta-disc software was used to perform data analysis, meta-regression analysis, sensitivity analysis, and heterogeneity testing, and STATA software was used to determine if publication bias was present, as well as to calculate the relative risks for the sensitivity and specificity of narrow-band imaging vs those of white-light bronchoscopy for the detection of early and invasive lung cancer. A random-effects model was used to assess the diagnostic efficacy of the above modalities in cases in which a high degree of between-study heterogeneity was noted with respect to their diagnostic efficacies. The database search identified six studies including 578 patients. The pooled sensitivity and specificity of narrow-band imaging were 86% (95% confidence interval: 83-88%) and 81% (95% confidence interval: 77-84%), respectively, and the pooled sensitivity and specificity of white-light bronchoscopy were 70% (95% confidence interval: 66-74%) and 66% (95% confidence interval: 62-70%), respectively. The pooled relative risks for the sensitivity and specificity of narrow-band imaging vs the sensitivity and specificity of white-light bronchoscopy for the detection of early and invasive lung cancer were 1.33 (95% confidence interval: 1.07-1.67) and 1.09 (95% confidence interval: 0.84-1.42), respectively, and sensitivity analysis showed that narrow-band imaging exhibited good diagnostic efficacy with respect to detecting early and invasive lung cancer and that the results of the study were stable. Narrow-band imaging was superior to white light bronchoscopy with respect to detecting early and invasive lung cancer; however, the specificities of the two modalities did not differ significantly.

Degradation of misfolded proteins in neurodegenerative diseases: therapeutic targets and strategies.

PubMed

Ciechanover, Aaron; Kwon, Yong Tae

2015-03-13

Mammalian cells remove misfolded proteins using various proteolytic systems, including the ubiquitin (Ub)-proteasome system (UPS), chaperone mediated autophagy (CMA) and macroautophagy. The majority of misfolded proteins are degraded by the UPS, in which Ub-conjugated substrates are deubiquitinated, unfolded and cleaved into small peptides when passing through the narrow chamber of the proteasome. The substrates that expose a specific degradation signal, the KFERQ sequence motif, can be delivered to and degraded in lysosomes via the CMA. Aggregation-prone substrates resistant to both the UPS and the CMA can be degraded by macroautophagy, in which cargoes are segregated into autophagosomes before degradation by lysosomal hydrolases. Although most misfolded and aggregated proteins in the human proteome can be degraded by cellular protein quality control, some native and mutant proteins prone to aggregation into β-sheet-enriched oligomers are resistant to all known proteolytic pathways and can thus grow into inclusion bodies or extracellular plaques. The accumulation of protease-resistant misfolded and aggregated proteins is a common mechanism underlying protein misfolding disorders, including neurodegenerative diseases such as Huntington's disease (HD), Alzheimer's disease (AD), Parkinson's disease (PD), prion diseases and Amyotrophic Lateral Sclerosis (ALS). In this review, we provide an overview of the proteolytic pathways in neurons, with an emphasis on the UPS, CMA and macroautophagy, and discuss the role of protein quality control in the degradation of pathogenic proteins in neurodegenerative diseases. Additionally, we examine existing putative therapeutic strategies to efficiently remove cytotoxic proteins from degenerating neurons.

Crystal structure of the catalytic core domain of the family 6 cellobiohydrolase II, Cel6A, from Humicola insolens, at 1.92 A resolution.

PubMed

Varrot, A; Hastrup, S; Schülein, M; Davies, G J

1999-01-15

The three-dimensional structure of the catalytic core of the family 6 cellobiohydrolase II, Cel6A (CBH II), from Humicola insolens has been determined by X-ray crystallography at a resolution of 1.92 A. The structure was solved by molecular replacement using the homologous Trichoderma reesei CBH II as a search model. The H. insolens enzyme displays a high degree of structural similarity with its T. reesei equivalent. The structure features both O- (alpha-linked mannose) and N-linked glycosylation and a hexa-co-ordinate Mg2+ ion. The active-site residues are located within the enclosed tunnel that is typical for cellobiohydrolase enzymes and which may permit a processive hydrolysis of the cellulose substrate. The close structural similarity between the two enzymes implies that kinetics and chain-end specificity experiments performed on the H. insolens enzyme are likely to be applicable to the homologous T. reesei enzyme. These cast doubt on the description of cellobiohydrolases as exo-enzymes since they demonstrated that Cel6A (CBH II) shows no requirement for non-reducing chain-ends, as had been presumed. There is no crystallographic evidence in the present structure to support a mechanism involving loop opening, yet preliminary modelling experiments suggest that the active-site tunnel of Cel6A (CBH II) is too narrow to permit entry of a fluorescenyl-derivatized substrate, known to be a viable substrate for this enzyme.

Sexual Dimorphisms of Appendicular Musculoskeletal Morphology Related to Social Display in Cuban Anolis Lizards.

PubMed

Anzai, Wataru; Cádiz, Antonio; Endo, Hideki

2015-10-01

In Anolis lizards, sexual dimorphism has been reported in morphological and ecological traits. Males show larger body size and longer limbs related to territorial combat and courtship display with the dewlap. Although functional-anatomical traits are closely related to locomotor behaviors, differences between sexes in musculoskeletal traits on limbs remain unclear. We explored the relationships among sexual dimorphisms in musculoskeletal morphology, habitat, and locomotor traits in Anolis lizards. Specifically, we examined appendicular musculoskeletal morphology in three species of Cuban Anolis by measuring muscle mass and lengths of moment arms. Through comparisons of crossing locomotion, we found that the runner species possessed larger extensors in hindlimbs, which are advantageous for running, whereas the masses of the humeral and femoral retractors were larger in climber species, allowing these lizards to hold up their bodies and occupy tree substrates. Comparisons between the sexes showed different trends among the three species. Males of A. porcatus, which inhabit narrow branches or leaves, had stronger elbow extensors that maintain the display posture. In contrast, males of A. sagrei, which occupy broad surfaces, did not show sexual differences that affected social display. Moreover, A. bartschi indicated sexual differences despite the absence of dewlapping behavior. Our findings suggest that both sexes show fundamentally similar relationships between muscular morphology and locomotor habits to adapt arboreal or terrestrial substrates, and yet sexual dimorphism in forelimb muscles may additionally affected by male specific display with the dewlap.

Oral intake of curcumin markedly activated CYP 3A4: in vivo and ex-vivo studies

PubMed Central

Hsieh, Yow-Wen; Huang, Ching-Ya; Yang, Shih-Ying; Peng, Yu-Hsuan; Yu, Chung-Ping; Chao, Pei-Dawn Lee; Hou, Yu-Chi

2014-01-01

Curcumin, a specific secondary metabolite of Curcuma species, has potentials for a variety of beneficial health effects. It is nowadays used as a dietary supplement. Everolimus (EVL) is an immunosuppressant indicated for allograft rejection and cancer therapy, but with narrow therapeutic window. EVL is a substrate of P-glycoprotein (P-gp) and cytochrome P450 3A4 (CYP3A4). This study investigated the effect of coadministration of curcumin on the pharmacokinetics of EVL in rats and the underlying mechanisms. EVL (0.5 mg/kg) was orally administered without and with 50 and 100 mg/kg of curcumin, respectively, in rats. Blood samples were collected at specific time points and EVL concentrations in blood were determined by QMS® immunoassay. The underlying mechanisms were evaluated using cell model and recombinant CYP 3A4 isozyme. The results indicated that 50 and 100 mg/kg of curcumin significantly decreased the AUC0-540 of EVL by 70.6% and 71.5%, respectively, and both dosages reduced the Cmax of EVL by 76.7%. Mechanism studies revealed that CYP3A4 was markedly activated by curcumin metabolites, which apparently overrode the inhibition effects of curcumin on P-gp. In conclusion, oral intake of curcumin significantly decreased the bioavailability of EVL, a probe substrate of P-gp/CYP 3A4, mainly through marked activation on CYP 3A4. PMID:25300360

Cell Adhesion Minimization by a Novel Mesh Culture Method Mechanically Directs Trophoblast Differentiation and Self-Assembly Organization of Human Pluripotent Stem Cells.

PubMed

Okeyo, Kennedy Omondi; Kurosawa, Osamu; Yamazaki, Satoshi; Oana, Hidehiro; Kotera, Hidetoshi; Nakauchi, Hiromitsu; Washizu, Masao

2015-10-01

Mechanical methods for inducing differentiation and directing lineage specification will be instrumental in the application of pluripotent stem cells. Here, we demonstrate that minimization of cell-substrate adhesion can initiate and direct the differentiation of human pluripotent stem cells (hiPSCs) into cyst-forming trophoblast lineage cells (TLCs) without stimulation with cytokines or small molecules. To precisely control cell-substrate adhesion area, we developed a novel culture method where cells are cultured on microstructured mesh sheets suspended in a culture medium such that cells on mesh are completely out of contact with the culture dish. We used microfabricated mesh sheets that consisted of open meshes (100∼200 μm in pitch) with narrow mesh strands (3-5 μm in width) to provide support for initial cell attachment and growth. We demonstrate that minimization of cell adhesion area achieved by this culture method can trigger a sequence of morphogenetic transformations that begin with individual hiPSCs attached on the mesh strands proliferating to form cell sheets by self-assembly organization and ultimately differentiating after 10-15 days of mesh culture to generate spherical cysts that secreted human chorionic gonadotropin (hCG) hormone and expressed caudal-related homeobox 2 factor (CDX2), a specific marker of trophoblast lineage. Thus, this study demonstrates a simple and direct mechanical approach to induce trophoblast differentiation and generate cysts for application in the study of early human embryogenesis and drug development and screening.

Multicolor Bioluminescence Boosts Malaria Research: Quantitative Dual-Color Assay and Single-Cell Imaging in Plasmodium falciparum Parasites

PubMed Central

2015-01-01

New reliable and cost-effective antimalarial drug screening assays are urgently needed to identify drugs acting on different stages of the parasite Plasmodium falciparum, and particularly those responsible for human-to-mosquito transmission, that is, the P. falciparum gametocytes. Low Z′ factors, narrow dynamic ranges, and/or extended assay times are commonly reported in current gametocyte assays measuring gametocyte-expressed fluorescent or luciferase reporters, endogenous ATP levels, activity of gametocyte enzymes, or redox-dependent dye fluorescence. We hereby report on a dual-luciferase gametocyte assay with immature and mature P. falciparum gametocyte stages expressing red and green-emitting luciferases from Pyrophorus plagiophthalamus under the control of the parasite sexual stage-specific pfs16 gene promoter. The assay was validated with reference antimalarial drugs and allowed to quantitatively and simultaneously measure stage-specific drug effects on parasites at different developmental stages. The optimized assay, requiring only 48 h incubation with drugs and using a cost-effective luminogenic substrate, significantly reduces assay cost and time in comparison to state-of-the-art analogous assays. The assay had a Z′ factor of 0.71 ± 0.03, and it is suitable for implementation in 96- and 384-well microplate formats. Moreover, the use of a nonlysing d-luciferin substrate significantly improved the reliability of the assay and allowed one to perform, for the first time, P. falciparum bioluminescence imaging at single-cell level. PMID:25102353

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

Characterization and functional analysis of the MAL and MPH Loci for maltose utilization in some ale and lager yeast strains.

PubMed

Vidgren, Virve; Ruohonen, Laura; Londesborough, John

2005-12-01

Maltose and maltotriose are the major sugars in brewer's wort. Brewer's yeasts contain multiple genes for maltose transporters. It is not known which of these express functional transporters. We correlated maltose transport kinetics with the genotypes of some ale and lager yeasts. Maltose transport by two ale strains was strongly inhibited by other alpha-glucosides, suggesting the use of broad substrate specificity transporters, such as Agt1p. Maltose transport by three lager strains was weakly inhibited by other alpha-glucosides, suggesting the use of narrow substrate specificity transporters. Hybridization studies showed that all five strains contained complete MAL1, MAL2, MAL3, and MAL4 loci, except for one ale strain, which lacked a MAL2 locus. All five strains also contained both AGT1 (coding a broad specificity alpha-glucoside transporter) and MAL11 alleles. MPH genes (maltose permease homologues) were present in the lager but not in the ale strains. During growth on maltose, the lager strains expressed AGT1 at low levels and MALx1 genes at high levels, whereas the ale strains expressed AGT1 at high levels and MALx1 genes at low levels. MPHx expression was negligible in all strains. The AGT1 sequences from the ale strains encoded full-length (616 amino acid) polypeptides, but those from both sequenced lager strains encoded truncated (394 amino acid) polypeptides that are unlikely to be functional transporters. Thus, despite the apparently similar genotypes of these ale and lager strains revealed by hybridization, maltose is predominantly carried by AGT1-encoded transporters in the ale strains and by MALx1-encoded transporters in the lager strains.

Structure-based Analysis to Hu-DNA Binding

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

Swinger,K.; Rice, P.

2007-01-01

HU and IHF are prokaryotic proteins that induce very large bends in DNA. They are present in high concentrations in the bacterial nucleoid and aid in chromosomal compaction. They also function as regulatory cofactors in many processes, such as site-specific recombination and the initiation of replication and transcription. HU and IHF have become paradigms for understanding DNA bending and indirect readout of sequence. While IHF shows significant sequence specificity, HU binds preferentially to certain damaged or distorted DNAs. However, none of the structurally diverse HU substrates previously studied in vitro is identical with the distorted substrates in the recently publishedmore » Anabaena HU(AHU)-DNA cocrystal structures. Here, we report binding affinities for AHU and the DNA in the cocrystal structures. The binding free energies for formation of these AHU-DNA complexes range from 10-14.5 kcal/mol, representing K{sub d} values in the nanomolar to low picomolar range, and a maximum stabilization of at least 6.3 kcal/mol relative to complexes with undistorted, non-specific DNA. We investigated IHF binding and found that appropriate structural distortions can greatly enhance its affinity. On the basis of the coupling of structural and relevant binding data, we estimate the amount of conformational strain in an IHF-mediated DNA kink that is relieved by a nick (at least 0.76 kcal/mol) and pinpoint the location of the strain. We show that AHU has a sequence preference for an A+T-rich region in the center of its DNA-binding site, correlating with an unusually narrow minor groove. This is similar to sequence preferences shown by the eukaryotic nucleosome.« less

Emission study on the gamma-ray irradiation effects on the ferroelectric Pb(Zr,Ti)O3 thin films

NASA Astrophysics Data System (ADS)

Lee, Yunsang; Lim, Junwhi; Yang, Sun A.; Bu, S. D.

We investigated the photoluminescence of the gammy-ray irradiated Pb(Zr,Ti)O3 (PZT) thin films with the various total doses up to 1000 kGy. The PZT thin films were prepared on the Pt/Ti/SiO2/Si substrates by using a sol-gel method with a spin-coating process. It was found that the visible emission emerges near 550 nm with the gamma-ray irradiation. The intensity of the emission increased with the increasing dose amount. The spectral feature of the gamma-ray induced emission was quite narrow, which was distinguished from that formed by normal defects such as oxygen vacancy. We suggest that the gamma-ray irradiation should generate a specific type of defect state inside the PZT films, which could be detected by the low temperature photoluminescence spectroscopy.

Optical evidence for the effect of gamma-ray irradiation on ferroelectric Pb(Zr0.52Ti0.48)O3 thin films

NASA Astrophysics Data System (ADS)

Lim, Junhwi; Lee, Y. S.; Yang, Sun A.; Bu, Sang Don

2016-06-01

We investigated the visible emission property of Pb(Zr,Ti)O3 (PZT) thin films irradiated with gammy-ray (γ-ray) irradiated at various total doses up to 1000 kGy. The PZT thin films were prepared on Pt/Ti/SiO2/Si substrates by using a sol-gel method with a spin-coating process. The visible emission was found to emerge near 550 nm upon γ-ray irradiation, and the intensity of the emission increased with increasing dose. The spectrum of the γ-ray-induced emission was quite narrow, which was quite different from that due to normal defects such as oxygen vacancies. We suggest that the γ-ray irradiation generates inside the PZT films a specific type of defect state that can be detected by using low-temperature photoluminescence spectroscopy.

Crystal structure of lactose permease in complex with an affinity inactivator yields unique insight into sugar recognition

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

Chaptal, Vincent; Kwon, Seunghyug; Sawaya, Michael R.

Lactose permease of Escherichia coli (LacY) with a single-Cys residue in place of A122 (helix IV) transports galactopyranosides and is specifically inactivated by methanethiosulfonyl-galactopyranosides (MTS-gal), which behave as unique suicide substrates. In order to study the mechanism of inactivation more precisely, we solved the structure of single-Cys122 LacY in complex with covalently bound MTS-gal. This structure exhibits an inward-facing conformation similar to that observed previously with a slight narrowing of the cytoplasmic cavity. MTS-gal is bound covalently, forming a disulfide bond with C122 and positioned between R144 and W151. E269, a residue essential for binding, coordinates the C-4 hydroxyl ofmore » the galactopyranoside moiety. The location of the sugar is in accord with many biochemical studies.« less

Growth of HgCdTe by Modified Molecular Beam Epitaxy

DTIC Science & Technology

1981-06-01

more commonly available substrates, e.g., silicon and germa - nium. If successful, this approach may by-pass the need for large size CdTe technology...the cooling rate is quite slow. 14 C3239A/bw SC5202. 11FR U) I- CL 0 00 CL 6 uiV CLC W- ( n EU (zw*/M) In A1LISN~a H3MOd U 0 4.- rwo 4- CC L- 01a...7 and Fig. 8. The angular distribution of the splashed particles is narrower. By placing the substrate at a wide 22 C3239A/bw ř N SC5202. 11FR I-x

An experimental investigation of high temperature superconducting microstrip antennas at K- and Ka-band frequencies. Ph.D. Thesis Final Report

NASA Technical Reports Server (NTRS)

Richard, Mark A.

1993-01-01

The recent discovery of high temperature superconductors (HTS) has generated a substantial amount of interest in microstrip antenna applications. However, the high permittivity of substrates compatible with HTS results in narrow bandwidths and high patch edge impedances of such antennas. To investigate the performance of superconducting microstrip antennas, three antenna architectures at K and Ka-band frequencies are examined. Superconducting microstrip antennas that are directly coupled, gap coupled, and electromagnetically coupled to a microstrip transmission line were designed and fabricated on lanthanum aluminate substrates using YBa2Cu3O7 superconducting thin films. For each architecture, a single patch antenna and a four element array were fabricated. Measurements from these antennas, including input impedance, bandwidth, patterns, efficiency, and gain are presented. The measured results show usable antennas can be constructed using any of the architectures. All architectures show excellent gain characteristics, with less than 2 dB of total loss in the four element arrays. Although the direct and gap coupled antennas are the simplest antennas to design and fabricate, they suffer from narrow bandwidths. The electromagnetically coupled antenna, on the other hand, allows the flexibility of using a low permittivity substrate for the patch radiator, while using HTS for the feed network, thus increasing the bandwidth while effectively utilizing the low loss properties of HTS. Each antenna investigated in this research is the first of its kind reported.

Growth of InN on Ge substrate by molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Trybus, Elaissa; Namkoong, Gon; Henderson, Walter; Doolittle, W. Alan; Liu, Rong; Mei, Jin; Ponce, Fernando; Cheung, Maurice; Chen, Fei; Furis, Madalina; Cartwright, Alexander

2005-06-01

InN epitaxial growth on a (1 1 1)-oriented, Ga-doped germanium substrate using molecular beam epitaxy is described. X-ray diffraction and transmission electron microscopy investigations have shown that the InN epitaxial layer consists of a wurtzite structure, which has the epitaxial relationship of (0 0 0 1) InN∥(1 1 1) Ge. Transmission electron microscopy shows an intermediate layer at the interface between the InN/Ge substrate. Consistent with recent reports implying a narrow bandgap of InN [Phys. Stat Sol. B 229 (2002) R1, Appl. Phys. Lett. 80 (2002) 3967], a strong photoluminescence with peak energy of 0.69 eV at 15 K was observed for this InN epilayer, in contrast to the peak energy of 0.71 eV for Ga-doped Ge under the same measurement conditions.

X-ray probe of GaN thin films grown on InGaN compliant substrates

NASA Astrophysics Data System (ADS)

Xu, Xiaoqing; Li, Yang; Liu, Jianming; Wei, Hongyuan; Liu, Xianglin; Yang, Shaoyan; Wang, Zhanguo; Wang, Huanhua

2013-04-01

GaN thin films grown on InGaN compliant substrates were characterized by several X-ray technologies: X-ray reciprocal space mapping (RSM), grazing incidence X-ray diffraction (GIXRD), and X-ray photoemission spectrum (XPS). Narrow Lorentz broadening and stress free state were observed for GaN grown on InGaN compliant substrate, while mosaic structure and large tensile stress were observed at the presence of residual indium atoms. RSM disclosed the mosaicity, and the GIXRD was conducted to investigate the depth dependences of crystal quality and strain states. XPS depth profile of indium contents indicated that residual indium atoms deteriorated the crystal quality of GaN not only by producing lattice mismatch at the interface of InGaN and GaN but also by diffusing into GaN overlayers. Accordingly, two solutions were proposed to improve the efficiency of self-patterned lateral epitaxial overgrowth method. This research goes a further step in resolving the urgent substrate problem in GaN fabrication.

Subdigital setae of chameleon feet: Friction-enhancing microstructures for a wide range of substrate roughness

PubMed Central

Spinner, Marlene; Westhoff, Guido; Gorb, Stanislav N.

2014-01-01

Hairy adhesive systems of microscopic setae with triangular flattened tips have evolved convergently in spiders, insects and arboreal lizards. The ventral sides of the feet and tails in chameleons are also covered with setae. However, chameleon setae feature strongly elongated narrow spatulae or fibrous tips. The friction enhancing function of these microstructures has so far only been demonstrated in contact with glass spheres. In the present study, the frictional properties of subdigital setae of Chamaeleo calyptratus were measured under normal forces in the physical range on plane substrates having different roughness. We showed that chameleon setae maximize friction on a wide range of substrate roughness. The highest friction was measured on asperities of 1 μm. However, our observations of the climbing ability of Ch. calyptratus on rods of different diameters revealed that also claws and grasping feet are additionally responsible for the force generation on various substrates during locomotion. PMID:24970387

Free-Flow Zone Electrophoresis of Peptides and Proteins in PDMS Microchip for Narrow pI Range Sample Prefractionation Coupled with Mass Spectrometry

PubMed Central

Song, Yong-Ak; Chan, Michael; Celio, Chris; Tannenbaum, Steven R.; Wishnok, John S.; Han, Jongyoon

2010-01-01

In this paper, we are evaluating the strategy of sorting peptides / proteins based on the charge to mass without resorting to ampholytes and / or isoelectric focusing, using a single- and two-step free-flow zone electrophoresis. We developed a simple fabrication method to create a salt bridge for free-flow zone electrophoresis in PDMS chips by surface printing a hydrophobic layer on a glass substrate. Since the surface-printed hydrophobic layer prevents plasma bonding between the PDMS chip and the substrate, an electrical junction gap can be created for free-flow zone electrophoresis. With this device, we demonstrated a separation of positive and negative peptides and proteins at a given pH in standard buffer systems, and validated the sorting result with LC/MS. Furthermore, we coupled two sorting steps via off-chip titration, and isolated peptides within specific pI ranges from sample mixtures, where the pI range was simply set by the pH values of the buffer solutions. This free-flow zone electrophoresis sorting device, with its simplicity of fabrication, and a sorting resolution of 0.5 pH unit, can potentially be a high-throughput sample fractionation tool for targeted proteomics using LC/MS. PMID:20163146

Characterization of three chalcone synthase-like genes from apple (Malus x domestica Borkh.).

PubMed

Yahyaa, Mosaab; Ali, Samah; Davidovich-Rikanati, Rachel; Ibdah, Muhammad; Shachtier, Alona; Eyal, Yoram; Lewinsohn, Efraim; Ibdah, Mwafaq

2017-08-01

Apple (Malus x domestica Brokh.) is a widely cultivated deciduous tree species of significant economic importance. Apple leaves accumulate high levels of flavonoids and dihydrochalcones, and their formation is dependent on enzymes of the chalcone synthase family. Three CHS genes were cloned from apple leaves and expressed in Escherichia coli. The encoded recombinant enzymes were purified and functionally characterized. In-vitro activity assays indicated that MdCHS1, MdCHS2 and MdCHS3 code for proteins exhibiting polyketide synthase activity that accepted either p-dihydrocoumaroyl-CoA, p-coumaroyl-CoA, or cinnamoyl-CoA as starter CoA substrates in the presence of malonyl-CoA, leading to production of phloretin, naringenin chalcone, and pinocembrin chalcone. MdCHS3 coded a chalcone-dihydrochalcone synthase enzyme with narrower substrate specificity than the previous ones. The apparent Km values of MdCHS3 for p-dihydrocoumaryl-CoA and p-coumaryl-CoA were both 5.0 μM. Expression analyses of MdCHS genes varied according to tissue type. MdCHS1, MdCHS2 and MdCHS3 expression levels were associated with the levels of phloretin accumulate in the respective tissues. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

M-shaped grating by nanoimprinting: a replicable, large-area, highly active plasmonic surface-enhanced Raman scattering substrate with nanogaps.

PubMed

Zhu, Zhendong; Bai, Benfeng; Duan, Huigao; Zhang, Haosu; Zhang, Mingqian; You, Oubo; Li, Qunqing; Tan, Qiaofeng; Wang, Jia; Fan, Shoushan; Jin, Guofan

2014-04-24

Plasmonic nanostructures separated by nanogaps enable strong electromagnetic-field confinement on the nanoscale for enhancing light-matter interactions, which are in great demand in many applications such as surface-enhanced Raman scattering (SERS). A simple M-shaped nanograting with narrow V-shaped grooves is proposed. Both theoretical and experimental studies reveal that the electromagnetic field on the surface of the M grating can be pronouncedly enhanced over that of a grating without such grooves, due to field localization in the nanogaps formed by the narrow V grooves. A technique based on room-temperature nanoimprinting lithography and anisotropic reactive-ion etching is developed to fabricate this device, which is cost-effective, reliable, and suitable for fabricating large-area nanostructures. As a demonstration of the potential application of this device, the M grating is used as a SERS substrate for probing Rhodamine 6G molecules. Experimentally, an average SERS enhancement factor as high as 5×10⁸ has been achieved, which verifies the greatly enhanced light-matter interaction on the surface of the M grating over that of traditional SERS surfaces. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Narrow bandpass steep edge optical filter for the JAST/T80 telescope instrumentation

NASA Astrophysics Data System (ADS)

Reichel, S.; Brauneck, U.; Bourquin, S.; Marín-Franch, A.

2013-09-01

The Observatorio Astrofisico de Javalambre in Spain observes with its JAST/T80 telescope galaxies in the Local Universe in a systematic study. This is accomplished with a multi-band photometric all sky survey called Javalambre Photometric Local Universe Survey (J-PLUS). A wide field camera receives the signals from universe via optical filters. In this presentation the development and design of a narrow bandpass steep edge filter with wide suppression will be shown. The filter has a full width half maximum in the range of 13-15 nm (with <1 nm tolerance) with central wavelengths in the range 350-860nm and an average transmission larger than 90% in the passband. Signals beyond the passband (blocking range) have to be suppressed down to 250nm and up to 1050nm (spectral regime), where a blocking of OD 5 (transmission < 10-5) is required. The edges have to be steep for a small transition width from 5% to 80%. The spectral requirements result in a large number of layers which are deposited with magnetron sputtering. The transmitted wavefront error of the optical filter must be less than lambda/2 over the 100mm aperture and the central wavelength uniformity must be better than +/- 0.4% over the clear aperture. The filter consists of optical filter glass and a coated substrate in order to reach the spectral requirements. The substrate is coated with more than 120 layers. The total filter thickness was specified to be 8.0mm. Results of steep edge narrow bandpass filters will be demonstrated fulfilling all these demanding requirements.

Low-temperature synthesis of single-walled carbon nanotubes with a narrow diameter distribution using size-classified catalyst nanoparticles

NASA Astrophysics Data System (ADS)

Kondo, Daiyu; Sato, Shintaro; Awano, Yuji

2006-05-01

Single-walled carbon nanotubes (SWNTs) with a narrow diameter distribution have been synthesized by hot-filament chemical vapor deposition using acetylene at 590 °C. Iron nanoparticles with diameters of 1.6, 2.0, 2.5, 5.0 and 10 nm (standard deviation: ≈10%) obtained with a differential mobility analyzer were used as a catalyst without any supporting materials on a substrate. SWNTs were obtained from 2.0 nm or smaller particles. The ratio of G band to D band in Raman spectra was as high as 35 without purification, indicating that high-quality SWNTs were synthesized. The SWNT diameters correlated with the particle diameters, demonstrating diameter-controlled SWNT growth.

Photocatalytic activity of self-assembled porous TiO2 nano-columns array fabricated by oblique angle sputter deposition

NASA Astrophysics Data System (ADS)

Shi, Pengjun; Li, Xibo; Zhang, Qiuju; Yi, Zao; Luo, Jiangshan

2018-04-01

A well-separated and oriented TiO2 nano-columns arrays with porous structure were fabricated by the oblique angle sputter deposition technique and subsequently annealing at 450 °C in Ar/O2 mixed atmosphere. The deposited substrate was firstly modified by a template of self-assembled close-packed arrays of 500 nm-diameter silica (SiO2) spheres. Scanning electronic microscopic (SEM) images show that the porous columnar nanostructure is formed as a result of the geometric shadowing effect and surface diffusion of the adatoms in oblique angle deposition (OAD). X-ray diffraction (XRD) measurements reveal that the physically OAD film with annealing treatment are generally mixed phase of rutile and anatase TiO2 polymorphic forms. The morphology induced absorbance and band gap tuning by different substrates was demonstrated by the UV–vis spectroscopy. The well-separated one-dimensional (1D) nano-columns array with specific large porous surface area is beneficial for charge separation in photocatalytic degradation. Compared with compact thin film, such self-assembled porous TiO2 nano-columns array fabricated by oblique angle sputter deposition performed an enhanced visible light induced photocatalytic activity by decomposing methyl orange (MO) solution. The well-designed periodic array-structured porous TiO2 films by using modified patterned substrates has been demonstrated significantly increased absorption edge in the UV-visible light region with a narrower optical band gap, which are expected to be favorable for application in photovoltaic, lithium-ion insertion and photocatalytic, etc.

Measurements of weak interactions between truncated substrates and a hammerhead ribozyme by competitive kinetic analyses: implications for the design of new and efficient ribozymes with high sequence specificity

PubMed Central

Kasai, Yasuhiro; Shizuku, Hideki; Takagi, Yasuomi; Warashina, Masaki; Taira, Kazunari

2002-01-01

Exploitation of ribozymes in a practical setting requires high catalytic activity and strong specificity. The hammerhead ribozyme R32 has considerable potential in this regard since it has very high catalytic activity. In this study, we have examined how R32 recognizes and cleaves a specific substrate, focusing on the mechanism behind the specificity. Comparing rates of cleavage of a substrate in a mixture that included the correct substrate and various substrates with point mutations, we found that R32 cleaved the correct substrate specifically and at a high rate. To clarify the source of this strong specificity, we quantified the weak interactions between R32 and various truncated substrates, using truncated substrates as competitive inhibitors since they were not readily cleaved during kinetic measurements of cleavage of the correct substrate, S11. We found that the strong specificity of the cleavage reaction was due to a closed form of R32 with a hairpin structure. The self-complementary structure within R32 enabled the ribozyme to discriminate between the correct substrate and a mismatched substrate. Since this hairpin motif did not increase the Km (it did not inhibit the binding interaction) or decrease the kcat (it did not decrease the cleavage rate), this kind of hairpin structure might be useful for the design of new ribozymes with strong specificity and high activity. PMID:12034825

Substrate-Specific Differential Gene Expression and RNA editing in the Brown Rot Fungus Fomitopsis pinicola.

PubMed

Wu, Baojun; Gaskell, Jill; Held, Benjamin W; Toapanta, Cristina; Vuong, Thu; Ahrendt, Steven; Lipzen, Anna; Zhang, Jiwei; Schilling, Jonathan S; Master, Emma; Grigoriev, Igor V; Blanchette, Robert A; Cullen, Dan; Hibbett, David S

2018-06-08

Wood-decaying fungi tend to have characteristic substrate ranges that partly define their ecological niche. Fomitopsis pinicola is a brown rot species of Polyporales that is reported on 82 species of softwoods and 42 species of hardwoods. We analyzed gene expression levels and RNA editing profiles of F. pinicola from submerged cultures with ground wood powder (sampled at five days) or solid wood wafers (sampled at ten and thirty days), using aspen, pine, and spruce substrates (aspen was used only in submerged cultures). Fomitopsis pinicola expressed similar sets of wood-degrading enzymes typical of brown rot fungi across all culture conditions and timepoints. Nevertheless, differential gene expression and RNA editing were observed across all pairwise comparisons of substrates and timepoints. Genes exhibiting differential expression and RNA editing encode diverse enzymes with known or potential function in brown rot decay, including laccase, benzoquinone reductase, aryl alcohol oxidase, cytochrome P450s, and various glycoside hydrolases. There was no overlap between differentially expressed and differentially edited genes, suggesting that these may provide F. pinicola with independent mechanisms for responding to different conditions. Comparing transcriptomes from submerged cultures and wood wafers, we found that culture conditions had a greater impact on global expression profiles than substrate wood species. In contrast, the suites of genes subject to RNA editing were much less affected by culture conditions. These findings highlight the need for standardization of culture conditions in studies of gene expression in wood-decaying fungi. IMPORTANCE All species of wood-decaying fungi occur on a characteristic range of substrates (host plants), which may be broad or narrow. Understanding the mechanisms that allow fungi to grow on particular substrates is important for both fungal ecology and applied uses of different feedstocks in industrial processes. We grew the wood-decaying polypore Fomitopsis pinicola on three different wood species, aspen, pine and spruce, under various culture conditions. We examined both gene expression (transcription levels) and RNA editing (post-transcriptional modification of RNA, which can potentially yield different proteins from the same gene). We found that F. pinicola is able to modify both gene expression and RNA editing profiles across different substrate species and culture conditions. Many of the genes involved encode enzymes with known or predicted functions in wood decay. This work provides clues to how wood-decaying fungi may adjust their arsenal of decay enzymes to accommodate different host substrates. Copyright © 2018 American Society for Microbiology.

Condensing Heat Exchanger with Hydrophilic Antimicrobial Coating

NASA Technical Reports Server (NTRS)

Thomas, Christopher M. (Inventor); Ma, Yonghui (Inventor)

2014-01-01

A multi-layer antimicrobial hydrophilic coating is applied to a substrate of anodized aluminum, although other materials may form the substrate. A silver layer is sputtered onto a thoroughly clean anodized surface of the aluminum to about 400 nm thickness. A layer of crosslinked, silicon-based macromolecular structure about 10 nm thickness overlies the silver layer, and the outermost surface of the layer of crosslinked, silicon-based macromolecular structure is hydroxide terminated to produce a hydrophilic surface with a water drop contact angle of less than 10.degree.. The coated substrate may be one of multiple fins in a condensing heat exchanger for use in the microgravity of space, which has narrow channels defined between angled fins such that the surface tension of condensed water moves water by capillary flow to a central location where it is pumped to storage. The antimicrobial coating prevents obstruction of the capillary passages.

Tearing as a test for mechanical characterization of thin adhesive films

NASA Astrophysics Data System (ADS)

Hamm, Eugenio; Reis, Pedro; Leblanc, Michael; Roman, Benoit; Cerda, Enrique

2008-05-01

Thin adhesive films have become increasingly important in applications involving packaging, coating or for advertising. Once a film is adhered to a substrate, flaps can be detached by tearing and peeling, but they narrow and collapse in pointy shapes. Similar geometries are observed when peeling ultrathin films grown or deposited on a solid substrate, or skinning the natural protective cover of a ripe fruit. Here, we show that the detached flaps have perfect triangular shapes with a well-defined vertex angle; this is a signature of the conversion of bending energy into surface energy of fracture and adhesion. In particular, this triangular shape of the tear encodes the mechanical parameters related to these three forms of energy and could form the basis of a quantitative assay for the mechanical characterization of thin adhesive films, nanofilms deposited on substrates or fruit skin.

Tearing as a test for mechanical characterization of thin adhesive films.

PubMed

Hamm, Eugenio; Reis, Pedro; LeBlanc, Michael; Roman, Benoit; Cerda, Enrique

2008-05-01

Thin adhesive films have become increasingly important in applications involving packaging, coating or for advertising. Once a film is adhered to a substrate, flaps can be detached by tearing and peeling, but they narrow and collapse in pointy shapes. Similar geometries are observed when peeling ultrathin films grown or deposited on a solid substrate, or skinning the natural protective cover of a ripe fruit. Here, we show that the detached flaps have perfect triangular shapes with a well-defined vertex angle; this is a signature of the conversion of bending energy into surface energy of fracture and adhesion. In particular, this triangular shape of the tear encodes the mechanical parameters related to these three forms of energy and could form the basis of a quantitative assay for the mechanical characterization of thin adhesive films, nanofilms deposited on substrates or fruit skin.

Lateral epitaxial overgowth of GaAs by organometallic chemical vapor deposition

NASA Technical Reports Server (NTRS)

Gale, R. P.; Mcclelland, R. W.; Fan, J. C. C.; Bozler, C. O.

1982-01-01

Lateral epitaxial overgrowth of GaAs by organometallic chemical vapor deposition has been demonstrated. Pyrolytic decomposition of trimethylgallium and arsine, without the use of HCl, was used to deposit GaAs on substrates prepared by coating (110) GaAs wafers with SiO2, then using photolithography to open narrow stripes in the oxide. Lateral overgrowth was seeded by epitaxial deposits formed on the GaAs surfaces exposed by the stripe openings. The extent of lateral overgrowth was investigated as a function of stripe orientation and growth temperature. Ratios of lateral to vertical growth rates greater than five have been obtained. The lateral growth is due to surface-kinetic control for the two-dimensional growth geometry studied. A continuous epitaxial GaAs layer 3 microns thick has been grown over a patterned mask on a GaAs substrate and then cleaved from the substrate.

Interlocking-based attachment during locomotion in the beetle Pachnoda marginata (Coleoptera, Scarabaeidae)

PubMed Central

Bußhardt, Philipp; Kunze, Daniel; Gorb, Stanislav N.

2014-01-01

The attachment function of tibial spurs and pretarsal claws in the beetle Pachnoda marginata (Coleoptera, Scarabaeidae) during locomotion was examined in this study. First, we measured the angle, at which the beetles detached from substrates with different roughness. At a surface roughness of 12 μm and higher, intact animals were able to cling to a completely tilted platform (180°). Second, we estimated the forces the beetles could exert in walking on smooth and rough cylinders of different diameters, on a plane and also between two plates. To elucidate the role of the individual structures, we ablated them consecutively. We found tibial spurs not to be in use in walking on flat substrates. On some of the curved substrates, ablation of tibial spurs caused an effect. A clear effect of tibial spurs was revealed in walking between two plates. Thus, these structures are probably used for generating propulsion in narrowed spaces. PMID:25385502

Finding pathways to prepare Fe4N thin films at low substrate temperature

NASA Astrophysics Data System (ADS)

Seema, Gupta, Nitiand Mukul

2018-04-01

In Fe-N phase diagram the formation of Fe4N thin films occur in a very narrow region, specially below 573 K. Above this, the range of homogeneity for formation of Fe4N start to increase yielding more favorable conditions for formation of single phase Fe4N. However, when deposited at high substrate temperature (Ts) typically above 650 K, nitrogen (N) tends to diffuse out of the system yielding a N deficient phase. In this work, we attempt to find pathways to deposit Fe4N thin films at low Ts and successfully prepared single phase Fe4N thin films at Ts as low as 423 K. This was achieved by utilizing an underlayer of CrN. We find that such underlayer not only has close lattice matching with Fe4N, it also acts as a diffusion barrier for the film-substrate interface.

Development of a microbalance suitable for space application. [mass measurement device for particulate and vapor deposition measurements

NASA Technical Reports Server (NTRS)

Patashnick, H.; Rupprecht, G.

1977-01-01

The tapered element oscillating microbalance (TEOM), an ultrasensitive mass measurement device which is suitable for both particulate and vapor deposition measurements is described. The device can be used in contamination measurements, surface reaction studies, particulate monitoring systems or any microweighing activity where either laboratory or field monitoring capability is desired. The active element of the TEOM consists of a tube or reed constructed of a material with high mechanical quality factor and having a special taper. The element is firmly mounted at the wide end while the other end supports a substrate surface which can be composed of virtually any material. The tapered element with the substrate at the free (narrow) end is set into oscillation in a clamped free mode. A feedback system maintains the oscillation whose natural frequency will change in relation to the mass deposited on the substrate.

Growth of heterostructures on InAs for high mobility device applications

NASA Astrophysics Data System (ADS)

Contreras-Guerrero, R.; Wang, S.; Edirisooriya, M.; Priyantha, W.; Rojas-Ramirez, J. S.; Bhuwalka, K.; Doornbos, G.; Holland, M.; Oxland, R.; Vellianitis, G.; Van Dal, M.; Duriez, B.; Passlack, M.; Diaz, C. H.; Droopad, R.

2013-09-01

The growth of heterostructures lattice matched to InAs(100) substrates for high mobility electronic devices has been investigated. The oxide removal process and homoepitaxial nucleation depends on the deposition parameters to avoid the formation of surface defects that can propagate through the structure during growth which can result in degraded device performance. The growth parameters for InAs homoepitaxy were found to be within an extremely narrow range when using As4 with a slight increase using As2. High structural quality lattice matched AlAsxSb1-x buffer layer was grown on InAs(100) substrates using a digital growth technique with the AlAs mole fraction adjusted by varying the incident As flux. Using the AlAsxSb1-x buffer layer, the transport properties of thin InAs channel layers were determined on conducting native substrates.

Mass production of holographic transparent components for augmented and virtual reality applications

NASA Astrophysics Data System (ADS)

Russo, Juan Manuel; Dimov, Fedor; Padiyar, Joy; Coe-Sullivan, Seth

2017-06-01

Diffractive optics such as holographic optical elements (HOEs) can provide transparent and narrow band components with arbitrary incident and diffracted angles for near-to-eye commercial electronic products for augmented reality (AR), virtual reality (VR), and smart glass applications. In this paper, we will summarize the operational parameters and general optical geometries relevant for near-to-eye displays, the holographic substrates available for these applications, and their performance characteristics and ease of manufacture. We will compare the holographic substrates available in terms of fabrication, manufacturability, and end-user performance characteristics. Luminit is currently emplacing the manufacturing capacity to serve this market, and this paper will discuss the capabilities and limitations of this unique facility.

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

Microhabitat suitability and niche breadth of common and imperiled Atlantic Slope freshwater mussels

USGS Publications Warehouse

Pandolfo, Tamara J.; Kwak, Thomas J.; Cope, W. Gregory

2016-01-01

Knowledge of the habitat suitability of freshwater mussels (family Unionidae) is necessary for effective decision making in conservation and management. We empirically measured microhabitat use for 10 unionid mussel species, including the U.S. federally endangered Alasmidonta heterodon, at 20 sites in the Tar River basin, North Carolina, USA. We also quantified habitat availability at each site, and calculated habitat suitability for each mussel species. The majority of available habitat across all sites consisted of shallow, slow-moving water with penetrable silt or sand substrate. Among species, mean water depth of occupied habitats ranged 0.23 – 0.54 m, mean bottom velocity ranged 0.001 – 0.055 m/s, average mean-column velocity ranged 0 – 0.055 m/s, and mean substrate penetrability ranged 0.11 – 11.67 on an index scale. The most commonly measured dominant substrate materials were silt, sand, very coarse sand, pea gravel, and coarse gravel. The most common cover types were coarse woody debris and fine woody debris. These findings revealed a relationship between the niche breadth and conservation status of four species. Federally endangered A. heterodon consistently showed a narrower suite of suitable microhabitats than the common mussel Elliptio complanata. The range of suitable habitat characteristics for Fusconaia masoni and Villosa constricta, listed as North Carolina (USA) state endangered and special concern, respectively, was typically narrower than those of E. complanata and wider than those of A. heterodon. These habitat suitability criteria and relationships will be useful to guide identification of suitable sites for habitat protection, mussel relocation, or site restoration.

Ultra-narrow surface lattice resonances in plasmonic metamaterial arrays for biosensing applications.

PubMed

Danilov, Artem; Tselikov, Gleb; Wu, Fan; Kravets, Vasyl G; Ozerov, Igor; Bedu, Frederic; Grigorenko, Alexander N; Kabashin, Andrei V

2018-05-01

When excited over a periodic metamaterial lattice of gold nanoparticles (~ 100nm), localized plasmon resonances (LPR) can be coupled by a diffraction wave propagating along the array plane, which leads to a drastic narrowing of plasmon resonance lineshapes (down to a few nm full-width-at-half-maximum) and the generation of singularities of phase of reflected light. These phenomena look very promising for the improvement of performance of plasmonic biosensors, but conditions of implementation of such diffractively coupled plasmonic resonances, also referred to as plasmonic surface lattice resonances (PSLR), are not always compatible with biosensing arrangement implying the placement of the nanoparticles between a glass substrate and a sample medium (air, water). Here, we consider conditions of excitation and properties of PSLR over arrays of glass substrate-supported single and double Au nanoparticles (~ 100-200nm), arranged in a periodic metamaterial lattice, in direct and Attenuated Total Reflection (ATR) geometries, and assess their sensitivities to variations of refractive index (RI) of the adjacent sample dielectric medium. First, we identify medium (PSLR air , PSLR wat for air and water, respectively) and substrate (PSLR sub ) modes corresponding to the coupling of individual plasmon oscillations at medium- and substrate-related diffraction cut-off edges. We show that spectral sensitivity of medium modes to RI variations is determined by the lattice periodicity in both direct and ATR geometries (~ 320nm per RIU change in our case), while substrate mode demonstrates much lower sensitivity. We also show that phase sensitivity of PSLR can exceed 10 5 degrees of phase shift per RIU change and thus outperform the relevant parameter for all other plasmonic sensor counterparts. We finally demonstrate the applicability of surface lattice resonances in plasmonic metamaterial arrays to biosensing using standard streptavidin-biotin affinity model. Combining advantages of nanoscale architectures, including drastic concentration of electric field, possibility of manipulation at the nanoscale etc, and high phase and spectral sensitivities, PSLRs promise the advancement of current state-of-the-art plasmonic biosensing technology toward single molecule label-free detection. Copyright © 2017 Elsevier B.V. All rights reserved.

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

PubMed Central

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

2017-01-01

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

Effects of electrical conductivity of substrate materials on microstructure of diamond-like carbon films prepared by bipolar-type plasma based ion implantation

NASA Astrophysics Data System (ADS)

Nakao, S.; Sonoda, T.

2013-03-01

Diamond-like carbon (DLC) films are prepared by a bipolar-type plasma based ion implantation, and the structural differences between DLC films deposited on different electrical conductive substrates, i.e., conductive Si wafers and insulating glass plates are examined by Raman spectroscopy and x-ray photo emission spectroscopy (XPS). In the Raman measurements, graphite (G) and disorder (D) peaks are observed for both samples. However, the additional photo luminescence is overlapped on the spectra in the case of on-glass sample. To elucidate the structural difference, the intensity ratio of D to G peak (I(D)/I(G)), G peak position and full width at half maximum (FWHM) are obtained by curve fitting using Gaussian function and linear baseline. It is found that the I(D)/I(G) is lower, G peak position is higher and FWHM of G peak is narrower for on-glass sample than for on-Si sample. According to Robertson [1], lower I(D)/I(G) seems more sp3 C-C bonding in amount for on-glass sample. In contrast, higher G peak position and narrower FWHM of G peak suggest less sp3 C-C bonding in amount for on-glass sample. The results of XPS analysis with C1s spectra reveal that sp3 ratio, i.e., the intensity ratio of sp3/(sp3+sp2) is smaller for on-glass sample than for on-Si sample. The inconsistency of the trend between I(D)/I(G) and other parameters (G peak position and FWHM of G peak) might be caused by the overlap of photo luminescence signal on Raman spectrum as to on-glass sample. From these results, it is considered that sp3 C-C bonding is reduced in amount when using insulating substrate in comparison with conductive substrate.

Meniscus-force-mediated layer transfer technique using single-crystalline silicon films with midair cavity: Application to fabrication of CMOS transistors on plastic substrates

NASA Astrophysics Data System (ADS)

Sakaike, Kohei; Akazawa, Muneki; Nakagawa, Akitoshi; Higashi, Seiichiro

2015-04-01

A novel low-temperature technique for transferring a silicon-on-insulator (SOI) layer with a midair cavity (supported by narrow SiO2 columns) by meniscus force has been proposed, and a single-crystalline Si (c-Si) film with a midair cavity formed in dog-bone shape was successfully transferred to a poly(ethylene terephthalate) (PET) substrate at its heatproof temperature or lower. By applying this proposed transfer technique, high-performance c-Si-based complementary metal-oxide-semiconductor (CMOS) transistors were successfully fabricated on the PET substrate. The key processes are the thermal oxidation and subsequent hydrogen annealing of the SOI layer on the midair cavity. These processes ensure a good MOS interface, and the SiO2 layer works as a “blocking” layer that blocks contamination from PET. The fabricated n- and p-channel c-Si thin-film transistors (TFTs) on the PET substrate showed field-effect mobilities of 568 and 103 cm2 V-1 s-1, respectively.

Monitoring substrate enables real-time regulation of a protein localization pathway.

PubMed

Ito, Koreaki; Mori, Hiroyuki; Chiba, Shinobu

2018-06-01

Protein localization machinery supports cell survival and physiology, suggesting the potential importance of its expression regulation. Here, we summarize a remarkable scheme of regulation, which allows real-time feedback regulation of the machinery expression. A class of regulatory nascent polypeptides, called monitoring substrates, undergoes force-sensitive translation arrest. The resulting ribosome stalling on the mRNA then affects mRNA folding to expose the ribosome-binding site of the downstream target gene and upregulate its translation. The target gene encodes a component of the localization machinery, whose physical action against the monitoring substrate leads to arrest cancellation. Thus, this scheme of feedback loop allows the cell to adjust the amount of the machinery to correlate inversely with the effectiveness of the process at a given moment. The system appears to have emerged late in evolution, in which a narrow range of organisms selected a distinct monitoring substrate-machinery combination. Currently, regulatory systems of SecM-SecA, VemP-SecDF2 and MifM-YidC2 are known to occur in different bacterial species.

Studies to reveal the nature of interactions between catalase and curcumin using computational methods and optical techniques.

PubMed

Mofidi Najjar, Fayezeh; Ghadari, Rahim; Yousefi, Reza; Safari, Naser; Sheikhhasani, Vahid; Sheibani, Nader; Moosavi-Movahedi, Ali Akbar

2017-02-01

Curcumin is an important antioxidant compound, and is widely reported as an effective component for reducing complications of many diseases. However, the detailed mechanisms of its activity remain poorly understood. We found that curcumin can significantly increase catalase activity of BLC (bovine liver catalase). The mechanism of curcumin action was investigated using a computational method. We suggested that curcumin may activate BLC by modifying the bottleneck of its narrow channel. The molecular dynamic simulation data showed that placing curcumin on the structure of enzyme can increase the size of the bottleneck in the narrow channel of BLC, and readily allow the access of substrate to the active site. Because of the increase of the distance between amino acids of the bottleneck in the presence of curcumin, the entrance space of substrate increased from 250Å 3 to 440Å 3 . In addition, the increase in emission of intrinsic fluorescence of BLC in presence of curcumin demonstrated changes in tertiary structure of catalase, and possibility of less quenching. We also used circular dichroism (CD) spectropolarimetry to determine how curcumin may alter the enzyme secondary structure. Catalase spectra in the presence of various concentrations of curcumin showed an increase in the amount of α-helix content. Copyright © 2016 Elsevier B.V. All rights reserved.

Perovskite nanocrystals: across-dimensional attachment, film-scale assembly on a flexible substrate and their fluorescence properties

NASA Astrophysics Data System (ADS)

Huang, Wenyi; Liu, Jiajia; Bai, Bing; Huang, Liu; Xu, Meng; Liu, Jia; Rong, Hongpan; Zhang, Jiatao

2018-03-01

Perovskite nanocrystals (NCs), which are a good fluorescence candidate with excellent photoelectric properties, have opened new avenues in the fabrication of highly efficient solar cells, light-emitting diodes (LEDs), and other optoelectronic devices. Further advances will rely on the multitude of compositional, structural variants that enable the formation of lower-dimensionality layered and three-dimensional (3D) perovskites with architectural innovations. In this work, the perovskite film was fabricated on a flexible substrate using simple dip-coating technology and 3D assemblies of perovskite NCs were obtained through an attachment process. Original perovskite NCs had a rectangular or square morphology with high particle uniformity and the narrow and symmetric fluorescence emission peak was adjustable at 515-527 nm. The controllable self-assembly of the micron size cuboid-like 3D assembly had an apparent enhancement on peak (111) in the x-ray diffraction (XRD) pattern. Surface ligands not only play a role in the attachment process but also keep the independence of each NC in 3D assemblies. Such assembly of the perovskite film maintained the original perovskite NCs fluorescence emission peak and narrow full width at the half-maximum (FWHM), which is of great importance for the investigation of future devices.

Using spectral information in forensic imaging.

PubMed

Miskelly, Gordon M; Wagner, John H

2005-12-20

Improved detection of forensic evidence by combining narrow band photographic images taken at a range of wavelengths is dependent on the substance of interest having a significantly different spectrum from the underlying substrate. While some natural substances such as blood have distinctive spectral features which are readily distinguished from common colorants, this is not true for visualization agents commonly used in forensic science. We now show that it is possible to select reagents with narrow spectral features that lead to increased visibility using digital cameras and computer image enhancement programs even if their coloration is much less intense to the unaided eye than traditional reagents. The concept is illustrated by visualising latent fingermarks on paper with the zinc complex of Ruhemann's Purple, cyanoacrylate-fumed fingerprints with Eu(tta)(3)(phen), and soil prints with 2,6-bis(benzimidazol-2-yl)-4-[4'-(dimethylamino)phenyl]pyridine [BBIDMAPP]. In each case background correction is performed at one or two wavelengths bracketing the narrow absorption or emission band of these compounds. However, compounds with sharp spectral features would also lead to improved detection using more advanced algorithms such as principal component analysis.

Prevalence of Extracranial Venous Narrowing on Magnetic Resonance Venography Is Similar in People With Multiple Sclerosis, Their Siblings, and Unrelated Healthy Controls: A Blinded, Case-Control Study.

PubMed

Martin, Nancy; Traboulsee, Anthony L; Machan, Lindsay; Klass, Darren; Ellchuk, Tasha; Zhao, Yinshan; Knox, Katherine B; Kopriva, David; Lala, Shantilal; Nickel, Darren; Otani, Robert; Perera, Warren R; Rauscher, Alexander; Sadovnick, A Dessa; Szkup, Peter; Li, David K

2017-05-01

The study sought to assess and compare the prevalence of narrowing of the major extracranial veins in subjects with multiple sclerosis and controls, and to assess the sensitivity and specificity of magnetic resonance venography (MRV) for describing extracranial venous narrowing as it applies to the chronic cerebrospinal venous insufficiency theory, using catheter venography (CV) as the gold standard. The jugular and azygos veins were assessed with time-of-flight MRV in this assessor-blinded, case-control study of subjects with multiple sclerosis, their unaffected siblings, and unrelated controls. The veins were evaluated by diameter and area, and compared with CV. Collateral vessels were also analyzed for maximal diameter, as a potential indicator of compensatory flow. A high prevalence of extracranial venous narrowing was demonstrated in all study groups, collectively up to 84% by diameter criteria and 90% by area, with no significant difference between the groups when assessed independently (P = .34 and .63, respectively). There was high interobserver variability in the reporting of vessel narrowing (kappa = 0.32), and poor vessel per vessel correlation between narrowing on MRV and CV (kappa = 0.064). Collateral neck veins demonstrated no convincing difference in maximum size or correlation with jugular narrowing. There is a high prevalence of narrowing of the major extracranial veins on MRV in all 3 study groups, with no significant difference between them. These findings do not support the chronic cerebrospinal venous insufficiency theory. Although MRV has shown a high sensitivity for identifying venous narrowing, time-of-flight imaging demonstrates poor interobserver agreement and poor specificity when compared with the gold standard CV. Copyright © 2016 Canadian Association of Radiologists. Published by Elsevier Inc. All rights reserved.

Quadrilinear CCD sensors for the multispectral channel of spaceborne imagers

NASA Astrophysics Data System (ADS)

Materne, Alex; Gili, Bruno; Laubier, David; Gimenez, Thierry

2001-12-01

The PLEIADES-HR Earth Observation satellites will combine a high resolution panchromatic channel -- 0.7 m at nadir -- and a multispectral channel allowing a 2.8 m resolution. This paper presents the main specifications, design and performances of a 52 microns pitch quadrilinear CCD sensor developed by ATMEL under CNES contract, for the multispectral channel of the PLEIADES-HR instrument. The monolithic CCD device includes four lines of 1500 pixels, each line dedicated to a narrow spectral band within blue to near infra red spectrum. The design of the photodiodes and CCD registers, with larger size than those developed up to now for CNES spaceborne imagers, needed some specific structures to break the large equipotential areas where charge do not flow properly. Results are presented on the options which were experimented to improve sensitivity, maintain transfer efficiency and reduce power dissipation. The four spectral bands are achieved by four stripe filters made by SAGEM-REOSC PRODUCTS on a glass substrate, to be assembled on the sensor window. Line to line spacing on the silicon die takes into account the results of straylight analysis. A mineral layer, with high optical absorption performances is deposited between photosensitive lines to further reduce straylight.

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.

Deposition of vanadium oxide films by direct-current magnetron reactive sputtering

NASA Astrophysics Data System (ADS)

Kusano, E.; Theil, J. A.; Thornton, John A.

1988-06-01

It is demonstrated here that thin films of vanadium oxide can be deposited at modest substrate temperatures by dc reactive sputtering from a vanadium target in an O2-Ar working gas using a planar magnetron source. Resistivity ratios of about 5000 are found between a semiconductor phase with a resistivity of about 5 Ohm cm and a metallic phase with a resistivity of about 0.001 Ohm cm for films deposited onto borosilicate glass substrates at about 400 C. X-ray diffraction shows the films to be single-phase VO2 with a monoclinic structure. The VO2 films are obtained for a narrow range of O2 injection rates which correspond to conditions where cathode poisoning is just starting to occur.

Wide-angle Spectrally Selective Perfect Absorber by Utilizing Dispersionless Tamm Plasmon Polaritons

PubMed Central

Xue, Chun-hua; Wu, Feng; Jiang, Hai-tao; Li, Yunhui; Zhang, Ye-wen; Chen, Hong

2016-01-01

We theoretically investigate wide-angle spectrally selective absorber by utilizing dispersionless Tamm plasmon polaritons (TPPs) under TM polarization. TPPs are resonant tunneling effects occurring on the interface between one-dimensional photonic crystals (1DPCs) and metal slab, and their dispersion properties are essentially determined by that of 1DPCs. Our investigations show that dispersionless TPPs can be excited in 1DPCs containing hyperbolic metamaterials (HMMs) on metal substrate. Based on dispersionless TPPs, electromagnetic waves penetrate into metal substrate and are absorbed entirely by lossy metal, exhibiting a narrow-band and wide-angle perfect absorption for TM polarization. Our results exhibit nearly perfect absorption with a value over 98% in the angle of incidence region of 0–80 degree. PMID:27991565

Robust lanthanide emitters in polyelectrolyte thin films for photonic applications

NASA Astrophysics Data System (ADS)

Greenspon, Andrew S.; Marceaux, Brandt L.; Hu, Evelyn L.

2018-02-01

Trivalent lanthanides provide stable emission sources at wavelengths spanning the ultraviolet through the near infrared with uses in telecommunications, lighting, and biological sensing and imaging. We describe a method for incorporating an organometallic lanthanide complex within polyelectrolyte multilayers, producing uniform, optically active thin films on a variety of substrates. These films demonstrate excellent emission with narrow linewidths, stable over a period of months, even when bound to metal substrates. Utilizing different lanthanides such as europium and terbium, we are able to easily tune the resulting wavelength of emission of the thin film. These results demonstrate the suitability of this platform as a thin film emitter source for a variety of photonic applications such as waveguides, optical cavities, and sensors.

Deposition of vanadium oxide films by direct-current magnetron reactive sputtering

NASA Technical Reports Server (NTRS)

Kusano, E.; Theil, J. A.; Thornton, John A.

1988-01-01

It is demonstrated here that thin films of vanadium oxide can be deposited at modest substrate temperatures by dc reactive sputtering from a vanadium target in an O2-Ar working gas using a planar magnetron source. Resistivity ratios of about 5000 are found between a semiconductor phase with a resistivity of about 5 Ohm cm and a metallic phase with a resistivity of about 0.001 Ohm cm for films deposited onto borosilicate glass substrates at about 400 C. X-ray diffraction shows the films to be single-phase VO2 with a monoclinic structure. The VO2 films are obtained for a narrow range of O2 injection rates which correspond to conditions where cathode poisoning is just starting to occur.

Control of Growth Rate by Initial Substrate Concentration at Values Below Maximum Rate

PubMed Central

Gaudy, Anthony F.; Obayashi, Alan; Gaudy, Elizabeth T.

1971-01-01

The hyperbolic relationship between specific growth rate, μ, and substrate concentration, proposed by Monod and used since as the basis for the theory of steady-state growth in continuous-flow systems, was tested experimentally in batch cultures. Use of a Flavobacterium sp. exhibiting a high saturation constant for growth in glucose minimal medium allowed direct measurement of growth rate and substrate concentration throughout the growth cycle in medium containing a rate-limiting initial concentration of glucose. Specific growth rates were also measured for a wide range of initial glucose concentrations. A plot of specific growth rate versus initial substrate concentration was found to fit the hyperbolic equation. However, the instantaneous relationship between specific growth rate and substrate concentration during growth, which is stated by the equation, was not observed. Well defined exponential growth phases were developed at initial substrate concentrations below that required for support of the maximum exponential growth rate and a constant doubling time was maintained until 50% of the substrate had been used. It is suggested that the external substrate concentration initially present “sets” the specific growth rate by establishing a steady-state internal concentration of substrate, possibly through control of the number of permeation sites. PMID:5137579

Morphology of the limbs in the semi-fossorial desert rodent species of Tympanoctomys (Octodontidae, Rodentia)

PubMed Central

Perez, M. Julieta; Barquez, Ruben M.; Diaz, M. Monica

2017-01-01

Abstract Here, a detailed description of the forelimbs and hindlimbs of all living species of the genus Tympanoctomys are presented. These rodents, highly adapted to desert environments, are semi-fossorial with capacity to move on the surface as well as to build burrows. The shape, structure, and size of the limbs are described. Contrary to what was expected for scratch digging semi-fossorial species, Tympanoctomys have slender humerus, radius and ulna; with narrow epicondyles of the humerus and short olecranon of the ulna with poorly developed processes. Following our descriptions, no intrageneric morphological variation regarding to the configuration of the limbs was detected, probably due to phylogenetic proximity, and not related to specific variations in response to different use of substrates or habits. The obtained results constitute a source of previously unpublished information as well as an important base for future analysis in different studies, such as morphometric, morpho-functional, or phylogenetic researches. PMID:29118644

Gene cloning and characterization of two NADH-dependent 3-quinuclidinone reductases from Microbacterium luteolum JCM 9174.

PubMed

Isotani, Kentaro; Kurokawa, Junji; Suzuki, Fumiko; Nomoto, Syunsuke; Negishi, Takashi; Matsuda, Michiko; Itoh, Nobuya

2013-02-01

We used the resting-cell reaction to screen approximately 200 microorganisms for biocatalysts which reduce 3-quinuclidinone to optically pure (R)-(-)-3-quinuclidinol. Microbacterium luteolum JCM 9174 was selected as the most suitable organism. The genes encoding the protein products that reduced 3-quinuclidinone were isolated from M. luteolum JCM 9174. The bacC gene, which consists of 768 nucleotides corresponding to 255 amino acid residues and is a constituent of the bacilysin synthetic gene cluster, was amplified by PCR based on homology to known genes. The qnr gene consisted of 759 nucleotides corresponding to 252 amino acid residues. Both enzymes belong to the short-chain alcohol dehydrogenase/reductase (SDR) family. The genes were expressed in Escherichia coli as proteins which were His tagged at the N terminus, and the recombinant enzymes were purified and characterized. Both enzymes showed narrow substrate specificity and high stereoselectivity for the reduction of 3-quinuclidinone to (R)-(-)-3-quinuclidinol.

Using 31P NMR spectroscopy at 14.1 Tesla to investigate PARP-1 associated energy failure and metabolic rescue in cerebrocortical slices.

PubMed

Zeng, Jianying; Hirai, Kiyoshi; Yang, Guo-Yuan; Ying, Weihai; Swanson, Raymond A; Kelly, Mark; Mayer, Moriz; James, Thomas L; Litt, Lawrence

2004-08-01

PARP-1 activation by H(2)O(2) in an acute preparation of superfused, respiring, neonatal cerebrocortical slices was assessed from PAR-polymer formation detected with immunohistochemistry and Western blotting. (31)P NMR spectroscopy at 14.1 Tesla of perchloric acid slice extracts was used to assess energy failure in a 1-h H(2)O(2) exposure as well as in a subsequent 4-h recovery period where the superfusate had no H(2)O(2) and specifically chosen metabolic substrates. Although more data are needed to fully characterize different bioenergetic responses, a high NMR spectral resolution (PCr full-width at half-max approximately.01 ppm) and narrow widths for most metabolites (<.2 ppm) permitted accurate quantifications of spectrally resolved resonances for ADP, ATP, NAD(+)/NADH, and other high energy phosphates. It appears possible to use brain slices to quantitatively study PARP-related, NAD-associated energy failure, and rescue with TCA metabolites.

Demonstration of a Monolithic Micro-Spectrometer System

NASA Technical Reports Server (NTRS)

Rajic, S.; Egert, C. M.

1995-01-01

The starting design of a spectrometer based on a modified Czerny-Turner configuration containing five precision surfaces encapsulated in a monolithic structure is described. Since the purpose at the early stages of the development was to demonstrate the feasibility of the technology and not an attempt to address a specific sensing problem, the first substrate material chosen was optical quality polymethyl methacrylate (PMMA). The final system design decision was narrowed down to two possible configurations containing five and six precision surfaces. The five surface design was chosen since it contained one less precision optical surface, yet included multiple off-axis spheres. In this particular design and material system, the mass was kept below 7 g. The wavelength range (bandpass) design goal was 1 micrometer (0.6 - 1.6 micrometers). The PMMA is particularly transparent in this wavelength region and there are interesting effects to monitor within this band. The optical system was designed and optimized using the ZEMAX optical design software program to be entirely alignment free (self aligning).

Fully Packaged Carbon Nanotube Supercapacitors by Direct Ink Writing on Flexible Substrates.

PubMed

Chen, Bolin; Jiang, Yizhou; Tang, Xiaohui; Pan, Yayue; Hu, Shan

2017-08-30

The ability to print fully packaged integrated energy storage components (e.g., supercapacitors) is of critical importance for practical applications of printed electronics. Due to the limited variety of printable materials, most studies on printed supercapacitors focus on printing the electrode materials but rarely the full-packaged cell. This work presents for the first time the printing of a fully packaged single-wall carbon nanotube-based supercapacitor with direct ink writing (DIW) technology. Enabled by the developed ink formula, DIW setup, and cell architecture, the whole printing process is mask free, transfer free, and alignment free with precise and repeatable control on the spatial distribution of all constituent materials. Studies on cell design show that a wider electrode pattern and narrower gap distance between electrodes lead to higher specific capacitance. The as-printed fully packaged supercapacitors have energy and power performances that are among the best in recently reported planar carbon-based supercapacitors that are only partially printed or nonprinted.

Adhesion signals of phospholipid vesicles at an electrified interface.

PubMed

DeNardis, Nadica Ivošević; Žutić, Vera; Svetličić, Vesna; Frkanec, Ruža

2012-09-01

General adhesion behavior of phospholipid vesicles was examined in a wide range of potentials at the mercury electrode by recording time-resolved adhesion signals. It was demonstrated that adhesion-based detection is sensitive to polar headgroups in phospholipid vesicles. We identified a narrow potential window around the point of zero charge of the electrode where the interaction of polar headgroups of phosphatidylcholine vesicles with the substrate is manifested in the form of bidirectional signals. The bidirectional signal is composed of the charge flow due to the nonspecific interaction of vesicle adhesion and spreading and of the charge flow due to a specific interaction of the negatively charged electrode and the most exposed positively charged choline headgroups. These signals are expected to appear only when the electrode surface charge density is less than the surface charge density of the choline groups at the contact interface. In comparison, for the negatively charged phosphatidylserine vesicles, we identified the potential window at the mercury electrode where charge compensation takes place, and bidirectional signals were not detected.

The oligomeric architecture of the archaeal exosome is important for processive and efficient RNA degradation.

PubMed

Audin, Maxime J C; Wurm, Jan Philip; Cvetkovic, Milos A; Sprangers, Remco

2016-04-07

The exosome plays an important role in RNA degradation and processing. In archaea, three Rrp41:Rrp42 heterodimers assemble into a barrel like structure that contains a narrow RNA entrance pore and a lumen that contains three active sites. Here, we demonstrate that this quaternary structure of the exosome is important for efficient RNA degradation. We find that the entrance pore of the barrel is required for nM substrate affinity. This strong interaction is crucial for processive substrate degradation and prevents premature release of the RNA from the enzyme. Using methyl TROSY NMR techniques, we establish that the 3' end of the substrate remains highly flexible inside the lumen. As a result, the RNA jumps between the three active sites that all equally participate in substrate degradation. The RNA jumping rate is, however, much faster than the cleavage rate, indicating that not all active site:substrate encounters result in catalysis. Enzymatic turnover therefore benefits from the confinement of the active sites and substrate in the lumen, which ensures that the RNA is at all times bound to one of the active sites. The evolution of the exosome into a hexameric complex and the optimization of its catalytic efficiency were thus likely co-occurring events. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Novel narrow-host-range vectors for direct cloning of foreign DNA in Pseudomonas.

PubMed

Boivin, R; Bellemare, G; Dion, P

1994-01-01

Narrow-host-range vectors, based on an indigenous replicon and containing a multiple cloning site, have been constructed in a Pseudomonas host capable of growth on unusual substrates. The new cloning vectors yield sufficient amounts of DNA for preparative purposes and belong to an incompatibility group different from that of the incP and incQ broad-host-range vectors. One of these vectors, named pDB47F, was used to clone, directly in Pseudomonas, DNA fragments from Agrobacterium, Pseudomonas, and Rhizobium. A clone containing Agrobacterium and KmR gene sequences was transformed with a higher efficiency than an RSF1010-derived vector (by as much as 1250-fold) in four out of five Pseudomonas strains tested. The considerable efficiency obtained with this system makes possible the direct cloning and phenotypic selection of foreign DNA in Pseudomonas.

Development of Sample Verification System for Sample Return Missions

NASA Technical Reports Server (NTRS)

Toda, Risaku; McKinney, Colin; Jackson, Shannon P.; Mojarradi, Mohammad; Trebi-Ollennu, Ashitey; Manohara, Harish

2011-01-01

This paper describes the development of a proof of-concept sample verification system (SVS) for in-situ mass measurement of planetary rock and soil sample in future robotic sample return missions. Our proof-of-concept SVS device contains a 10 cm diameter pressure sensitive elastic membrane placed at the bottom of a sample canister. The membrane deforms under the weight of accumulating planetary sample. The membrane is positioned in proximity to an opposing substrate with a narrow gap. The deformation of the membrane makes the gap to be narrower, resulting in increased capacitance between the two nearly parallel plates. Capacitance readout circuitry on a nearby printed circuit board (PCB) transmits data via a low-voltage differential signaling (LVDS) interface. The fabricated SVS proof-of-concept device has successfully demonstrated approximately 1pF/gram capacitance change

Photo-Detection on Narrow-Bandgap High-Mobility 2D Semiconductors

NASA Astrophysics Data System (ADS)

Charnas, Adam; Qiu, Gang; Deng, Yexin; Wang, Yixiu; Du, Yuchen; Yang, Lingming; Wu, Wenzhuo; Ye, Peide

Photo-detection and energy harvesting device concepts have been demonstrated widely in 2D materials such as graphene, TMDs, and black phosphorus. In this work, we demonstrate anisotropic photo-detection achieved using devices fabricated from hydrothermally grown narrow-bandgap high-mobility 2D semiconductor. Back-gated FETs were fabricated by transferring the 2D flakes onto a Si/SiO2 substrate and depositing various metal contacts across the flakes to optimize the access resistance for optoelectronic devices. Photo-responsivity was measured and mapped by slightly biasing the devices and shining a laser spot at different locations of the device to observe and map the resulting photo-generated current. Optimization of the Schottky barrier height for both n and p at the metal-2D interfaces using asymmetric contact engineering was performed to improve device performance.

Cushing's syndrome mutant PKA L205R exhibits altered substrate specificity

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

Lubner, Joshua M.; Dodge-Kafka, Kimberly L.; Carlson, Cathrine R.

The PKA L205R hotspot mutation has been implicated in Cushing's syndrome through hyperactive gain-of-function PKA signaling; however, its influence on substrate specificity has not been investigated. Here, we employ the Proteomic Peptide Library (ProPeL) approach to create high-resolution models for PKA WT and PKA L205R substrate specificity. We reveal that the L205R mutation reduces canonical hydrophobic preference at the substrate P + 1 position, and increases acidic preference in downstream positions. Using these models, we designed peptide substrates that exhibit altered selectivity for specific PKA variants, and demonstrate the feasibility of selective PKA L205R loss-of-function signaling. Through these results, wemore » suggest that substrate rewiring may contribute to Cushing's syndrome disease etiology, and introduce a powerful new paradigm for investigating mutation-induced kinase substrate rewiring in human disease.« less

Cushing's syndrome mutant PKA L205R exhibits altered substrate specificity

DOE PAGES

Lubner, Joshua M.; Dodge-Kafka, Kimberly L.; Carlson, Cathrine R.; ...

2017-02-01

The PKA L205R hotspot mutation has been implicated in Cushing's syndrome through hyperactive gain-of-function PKA signaling; however, its influence on substrate specificity has not been investigated. Here, we employ the Proteomic Peptide Library (ProPeL) approach to create high-resolution models for PKA WT and PKA L205R substrate specificity. We reveal that the L205R mutation reduces canonical hydrophobic preference at the substrate P + 1 position, and increases acidic preference in downstream positions. Using these models, we designed peptide substrates that exhibit altered selectivity for specific PKA variants, and demonstrate the feasibility of selective PKA L205R loss-of-function signaling. Through these results, wemore » suggest that substrate rewiring may contribute to Cushing's syndrome disease etiology, and introduce a powerful new paradigm for investigating mutation-induced kinase substrate rewiring in human disease.« less

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.

Understanding the Specificity and Random Collision of Enzyme-Substrate Interaction

ERIC Educational Resources Information Center

Kin, Ng Hong; Ling, Tan Aik

2016-01-01

The concept of specificity of enzyme action can potentially be abstract for some students as they fail to appreciate how the three-dimensional configuration of enzymes and the active sites confer perfect fit for specific substrates. In science text books, the specificity of enzyme-substrate binding is typically likened to the action of a lock and…

Stabilizing new bismuth compounds in thin film form [Stabilizing new thin film materials in bismuth compounds

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

Chen, Aiping; Zhou, Honghui; Zhu, Yuanyuan

2016-11-10

Growth of unexpected phases from a composite target of BiFeO 3:BiMnO 3 and/or BiFeO 3:BiCrO 3 has been explored using pulsed laser deposition. The Bi 2FeMnO 6 tetragonal phase can be grown directly on SrTiO 3 (STO) substrate, while two phases (S1 and S2) were found to grow on LaAlO 3 (LAO) substrates with narrow growth windows. However, introducing a thin CeO 2 buffer layer effectively broadens the growth window for the pure S1 phase, regardless of the substrate. Moreover, we discovered two new phases (X1 and X2) when growing on STO substrates using a BiFeO 3:BiCrO 3 target. Puremore » X2 phase can be obtained on CeO 2-buffered STO and LAO substrates. This work demonstrates that some unexpected phases can be stabilized in a thin film form by using composite perovskite BiRO 3 (R = Cr, Mn, Fe, Co, Ni) targets. Moreover, it also indicates that CeO 2 can serve as a general template for the growth of bismuth compounds with potential room-temperature multiferroicity.« less

Pulse laser-induced particle separation from polymethyl methacrylate: a mechanistic study

NASA Astrophysics Data System (ADS)

Arif, S.; Armbruster, O.; Kautek, W.

2013-04-01

The separation mechanism of opaque and transparent model micro-particles, graphite and polystyrene copolymer spheres, respectively, from polymethyl methacrylate (PMMA) substrates were investigated employing a ns-pulse laser radiating at 532 nm. The particles transparent in the visible wavelength range could be removed from PMMA efficiently in a very narrow fluence range between 1 and 2 J/cm2 according to a simple 1D thermal expansion model. Above this fluence region, with single pulses, the transparent microspheres caused local ablation of the PMMA substrate in the optical microlens nearfield. This process led to removal of the particles themselves due to the expansion of the ablation plasma. The irregularly shaped graphite particles shaded the underlying substrate from the incoming radiation so that no optical nearfield damage mechanism could be observed. Therefore, a substantial cleaning window between 0.5 and more than 16 J/cm2 was provided. The graphite data suggest an ablation mechanism of the particulates themselves due to a high optical absorption coefficient.

Spectroscopic properties of triangular silver nanoplates immobilized on polyelectrolyte multilayer-modified glass substrates

NASA Astrophysics Data System (ADS)

Rabor, Janice B.; Kawamura, Koki; Muko, Daiki; Kurawaki, Junichi; Niidome, Yasuro

2017-07-01

Fabrication of surface-immobilized silver nanostructures with reproducible plasmonic properties by dip-coating technique is difficult due to shape alteration. To address this challenge, we used a polyelectrolyte multilayer to promote immobilization of as-received triangular silver nanoplates (TSNP) on a glass substrate through electrostatic interaction. The substrate-immobilized TSNP were characterized by absorption spectrophotometry and scanning electron microscopy. The bandwidth and peak position of localized surface plasmon resonance (LSPR) bands can be tuned by simply varying the concentration of the colloidal solution and immersion time. TSNP immobilized from a higher concentration of colloidal solution with longer immersion time produced broadened LSPR bands in the near-IR region, while a lower concentration with shorter immersion time produced narrower bands in the visible region. The shape of the nanoplates was retained even at long immersion time. Analysis of peak positions and bandwidths also revealed the point at which the main species of the immobilization had been changed from isolates to aggregates.

Catalytic nanoporous membranes

DOEpatents

Pellin, Michael J [Naperville, IL; Hryn, John N [Naperville, IL; Elam, Jeffrey W [Elmhurst, IL

2009-12-01

A nanoporous catalytic membrane which displays several unique features including pores which can go through the entire thickness of the membrane. The membrane has a higher catalytic and product selectivity than conventional catalysts. Anodic aluminum oxide (AAO) membranes serve as the catalyst substrate. This substrate is then subjected to Atomic Layer Deposition (ALD), which allows the controlled narrowing of the pores from 40 nm to 10 nm in the substrate by deposition of a preparatory material. Subsequent deposition of a catalytic layer on the inner surfaces of the pores reduces pore sizes to less than 10 nm and allows for a higher degree of reaction selectivity. The small pore sizes allow control over which molecules enter the pores, and the flow-through feature can allow for partial oxidation of reactant species as opposed to complete oxidation. A nanoporous separation membrane, produced by ALD is also provided for use in gaseous and liquid separations. The membrane has a high flow rate of material with 100% selectivity.

Structural, kinetic, and thermodynamic studies of specificity designed HIV-1 protease.

PubMed

Alvizo, Oscar; Mittal, Seema; Mayo, Stephen L; Schiffer, Celia A

2012-07-01

HIV-1 protease recognizes and cleaves more than 12 different substrates leading to viral maturation. While these substrates share no conserved motif, they are specifically selected for and cleaved by protease during viral life cycle. Drug resistant mutations evolve within the protease that compromise inhibitor binding but allow the continued recognition of all these substrates. While the substrate envelope defines a general shape for substrate recognition, successfully predicting the determinants of substrate binding specificity would provide additional insights into the mechanism of altered molecular recognition in resistant proteases. We designed a variant of HIV protease with altered specificity using positive computational design methods and validated the design using X-ray crystallography and enzyme biochemistry. The engineered variant, Pr3 (A28S/D30F/G48R), was designed to preferentially bind to one out of three of HIV protease's natural substrates; RT-RH over p2-NC and CA-p2. In kinetic assays, RT-RH binding specificity for Pr3 increased threefold compared to the wild-type (WT), which was further confirmed by isothermal titration calorimetry. Crystal structures of WT protease and the designed variant in complex with RT-RH, CA-p2, and p2-NC were determined. Structural analysis of the designed complexes revealed that one of the engineered substitutions (G48R) potentially stabilized heterogeneous flap conformations, thereby facilitating alternate modes of substrate binding. Our results demonstrate that while substrate specificity could be engineered in HIV protease, the structural pliability of protease restricted the propagation of interactions as predicted. These results offer new insights into the plasticity and structural determinants of substrate binding specificity of the HIV-1 protease. Copyright © 2012 The Protein Society.

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

PubMed

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

2007-02-01

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

Substrate specificity of the ubiquitin and Ubl proteases

PubMed Central

Ronau, Judith A; Beckmann, John F; Hochstrasser, Mark

2016-01-01

Conjugation and deconjugation of ubiquitin and ubiquitin-like proteins (Ubls) to cellular proteins are highly regulated processes integral to cellular homeostasis. Most often, the C-termini of these small polypeptides are attached to lysine side chains of target proteins by an amide (isopeptide) linkage. Deubiquitinating enzymes (DUBs) and Ubl-specific proteases (ULPs) comprise a diverse group of proteases that recognize and remove ubiquitin and Ubls from their substrates. How DUBs and ULPs distinguish among different modifiers, or different polymeric forms of these modifiers, remains poorly understood. The specificity of ubiquitin/Ubl-deconjugating enzymes for particular substrates depends on multiple factors, ranging from the topography of specific substrate features, as in different polyubiquitin chain types, to structural elements unique to each enzyme. Here we summarize recent structural and biochemical studies that provide insights into mechanisms of substrate specificity among various DUBs and ULPs. We also discuss the unexpected specificities of non-eukaryotic proteases in these families. PMID:27012468

Altered Substrate Specificity of Drug-Resistant Human Immunodeficiency Virus Type 1 Protease

PubMed Central

Dauber, Deborah S.; Ziermann, Rainer; Parkin, Neil; Maly, Dustin J.; Mahrus, Sami; Harris, Jennifer L.; Ellman, Jon A.; Petropoulos, Christos; Craik, Charles S.

2002-01-01

Resistance to human immunodeficiency virus type 1 protease (HIV PR) inhibitors results primarily from the selection of multiple mutations in the protease region. Because many of these mutations are selected for the ability to decrease inhibitor binding in the active site, they also affect substrate binding and potentially substrate specificity. This work investigates the substrate specificity of a panel of clinically derived protease inhibitor-resistant HIV PR variants. To compare protease specificity, we have used positional-scanning, synthetic combinatorial peptide libraries as well as a select number of individual substrates. The subsite preferences of wild-type HIV PR determined by using the substrate libraries are consistent with prior reports, validating the use of these libraries to compare specificity among a panel of HIV PR variants. Five out of seven protease variants demonstrated subtle differences in specificity that may have significant impacts on their abilities to function in viral maturation. Of these, four variants demonstrated up to fourfold changes in the preference for valine relative to alanine at position P2 when tested on individual peptide substrates. This change correlated with a common mutation in the viral NC/p1 cleavage site. These mutations may represent a mechanism by which severely compromised, drug-resistant viral strains can increase fitness levels. Understanding the altered substrate specificity of drug-resistant HIV PR should be valuable in the design of future generations of protease inhibitors as well as in elucidating the molecular basis of regulation of proteolysis in HIV. PMID:11773410

Post-fabrication voltage controlled resonance tuning of nanoscale plasmonic antennas.

PubMed

Lumdee, Chatdanai; Toroghi, Seyfollah; Kik, Pieter G

2012-07-24

Voltage controlled wavelength tuning of the localized surface plasmon resonance of gold nanoparticles on an aluminum film is demonstrated in single particle microscopy and spectroscopy measurements. Anodization of the Al film after nanoparticle deposition forms an aluminum oxide spacer layer between the gold particles and the Al film, modifying the particle-substrate interaction. Darkfield microscopy reveals ring-shaped scattering images from individual Au nanoparticles, indicative of plasmon resonances with a dipole moment normal to the substrate. Single particle scattering spectra show narrow plasmon resonances that can be tuned from ~580 to ~550 nm as the anodization voltage increases to 12 V. All observed experimental trends could be reproduced in numerical simulations. The presented approach could be used as a general postfabrication resonance optimization step of plasmonic nanoantennas and devices.

Stresses and Temperature Stability of Dense Wavelength Division Multiplexing Filters Prepared by Reactive Ion-Assisted E-Gun Evaporation

NASA Astrophysics Data System (ADS)

Wei, Chao-Tsang; Shieh, Han-Ping D.

2005-10-01

In this paper, we report the in situ measurement of the temperature stability of narrow-band-pass filters on different types of substrate, for dense wavelength division multiplexing (DWDM) filters in optical-fiber transmission systems. The DWDM filters were designed as all-dielectric Fabry-Perot filters and fabricated by reactive ion-assisted deposition. Ta2O5 and SiO2 were used as high- and low-refractive-index layers, respectively, for constructing the DWDM filters. The accuracy and stability of the coating process were evaluated for fabricating the DWDM filters for the temperature stability of the center wavelength. The center wavelength shift was determined to be greatly dependent on the coefficient of thermal expansion of the substrate on which the filter is deposited.

Low work function, stable compound clusters and generation process

DOEpatents

Dinh, Long N.; Balooch, Mehdi; Schildbach, Marcus A.; Hamza, Alex V.; McLean, II, William

2000-01-01

Low work function, stable compound clusters are generated by co-evaporation of a solid semiconductor (i.e., Si) and alkali metal (i.e., Cs) elements in an oxygen environment. The compound clusters are easily patterned during deposition on substrate surfaces using a conventional photo-resist technique. The cluster size distribution is narrow, with a peak range of angstroms to nanometers depending on the oxygen pressure and the Si source temperature. Tests have shown that compound clusters when deposited on a carbon substrate contain the desired low work function property and are stable up to 600.degree. C. Using the patterned cluster containing plate as a cathode baseplate and a faceplate covered with phosphor as an anode, one can apply a positive bias to the faceplate to easily extract electrons and obtain illumination.

Room-temperature continuous operation of InAsSb quantum-dot lasers near 2 mu m based on (100) InP substrate

NASA Technical Reports Server (NTRS)

Qui, Y.; Uhl, D.; Keo, S.

2003-01-01

Single-stack InAsSb self-assembled quantum-dot lasers based on (001) InP substrate have been grown by metalorganic vapor-phase epitaxy. The narrow ridge waveguide lasers lased at wavelengths near 2 mu m up to 25 degrees C in continuous-wave operation. At room temperature, a differential quantum efficiency of 13 percent is obtained and the maximum output optical power reaches 3 mW per facet with a threshold current density of 730 A/cm(sup 2). With increasing temperature the emission wavelength is extremely temperature stable, and a very low wavelength temperature sensitivity of 0.05 nm/degrees C is measured, which is even lower than that caused by the refractive index change.

Luminescence properties of ZnxMg1-xSe layers

NASA Astrophysics Data System (ADS)

Bala, Waclaw; Firszt, Franciszek; Dzik, Janusz; Gapinski, Adam; Glowacki, Grzegorz

1995-10-01

This work deals with the study of luminescence properties of ZnxMg1-xSe layers prepared by different methods. ZnxMg1-xSe mixed crystal layers were obtained by: (a) thermal diffusion of Mg metal in the temperature range 1050 K - 1200 K into ZnSe single crystal grown by Bridgman method, and (b) epitaxial growth on (001) GaAs and (111) ZnTe substrates by MBE using elemental Zn, Se and Mg sources. The luminescence spectra of ZnxMg1-xSe layers grown on (001) GaAs and (111) ZnTe substrates are dominated by narrow blue and violet emission bands with maxima positioned at about 3.05 - 3.28 eV, 2.88 - 3.04 eV, and 2.81 - 2.705 eV.

Obtaining Thickness-Limited Electrospray Deposition for 3D Coating.

PubMed

Lei, Lin; Kovacevich, Dylan A; Nitzsche, Michael P; Ryu, Jihyun; Al-Marzoki, Kutaiba; Rodriguez, Gabriela; Klein, Lisa C; Jitianu, Andrei; Singer, Jonathan P

2018-04-04

Electrospray processing utilizes the balance of electrostatic forces and surface tension within a charged spray to produce charged microdroplets with a narrow dispersion in size. In electrospray deposition, each droplet carries a small quantity of suspended material to a target substrate. Past electrospray deposition results fall into two major categories: (1) continuous spray of films onto conducting substrates and (2) spray of isolated droplets onto insulating substrates. A crossover regime, or a self-limited spray, has only been limitedly observed in the spray of insulating materials onto conductive substrates. In such sprays, a limiting thickness emerges, where the accumulation of charge repels further spray. In this study, we examined the parametric spray of several glassy polymers to both categorize past electrospray deposition results and uncover the critical parameters for thickness-limited sprays. The key parameters for determining the limiting thickness were (1) field strength and (2) spray temperature, related to (i) the necessary repulsive field and (ii) the ability for the deposited materials to swell in the carrier solvent vapor and redistribute charge. These control mechanisms can be applied to the uniform or controllably-varied microscale coating of complex three-dimensional objects.

High rate DC-reactive sputter deposition of Y 2O 3 film on the textured metal substrate for the superconducting coated conductor

NASA Astrophysics Data System (ADS)

Kim, Ho-Sup; Park, Chan; Ko, Rock-Kil; Shi, Dongqui; Chung, Jun-Ki; Ha, Hong-Soo; Park, Yu-Mi; Song, Kyu-Jeong; Youm, Do-Jun

2005-10-01

Y2O3 film was directly deposited on Ni-3at%W substrate by DC reactive sputtering. DC reactive sputtering was carried out using metallic Y target and water vapor for oxidizing the elements of metallic target on the substrate. The detailed conditions of DC reactive sputtering for depositions of Y2O3 films were investigated. The window of water vapor for proper growth of Y2O3 films was determined by sufficient oxidations of the Y2O3 films and the non-oxidation of the target surface, which was required for high rate sputtering. The window turned out to be fairly wide in the chamber used. As the sputtering power was raised, the deposition rate increased without narrowing the window. The fabricated Y2O3 films showed good texture qualities and surface morphologies. The YBCO film deposited directly on the Y2O3 buffered Ni-3at%W substrate showed Tc, Ic (77 K, self field), and Jc (77 K, self field) of 89 K, 64 A/cm and 1.1 MA/cm2, respectively.

Enhancing elastic stress relaxation in SiGe/Si heterostructures by Si pillar necking

NASA Astrophysics Data System (ADS)

Isa, F.; Salvalaglio, M.; Arroyo Rojas Dasilva, Y.; Jung, A.; Isella, G.; Erni, R.; Timotijevic, B.; Niedermann, P.; Gröning, P.; Montalenti, F.; von Känel, H.

2016-10-01

We demonstrate that the elastic stress relaxation mechanism in micrometre-sized, highly mismatched heterostructures may be enhanced by employing patterned substrates in the form of necked pillars, resulting in a significant reduction of the dislocation density. Compositionally graded Si1-xGex crystals were grown by low energy plasma enhanced chemical vapour deposition, resulting in tens of micrometres tall, three-dimensional heterostructures. The patterned Si(001) substrates consist of micrometre-sized Si pillars either with the vertical {110} or isotropically under-etched sidewalls resulting in narrow necks. The structural properties of these heterostructures were investigated by defect etching and transmission electron microscopy. We show that the dislocation density, and hence the competition between elastic and plastic stress relaxation, is highly influenced by the shape of the substrate necks and their proximity to the mismatched epitaxial material. The SiGe dislocation density increases monotonically with the crystal width but is significantly reduced by the substrate under-etching. The drop in dislocation density is interpreted as a direct effect of the enhanced compliance of the under-etched Si pillars, as confirmed by the three-dimensional finite element method simulations of the elastic energy distribution.

Thermokinetics of heterogeneous droplet nucleation on conically textured substrates.

PubMed

Singha, Sanat K; Das, Prasanta K; Maiti, Biswajit

2015-11-28

Within the framework of the classical theory of heterogeneous nucleation, a thermokinetic model is developed for line-tension-associated droplet nucleation on conical textures considering growth or shrinkage of the formed cluster due to both interfacial and peripheral monomer exchange and by considering different geometric configurations. Along with the principle of free energy extremization, Katz kinetic approach has been employed to study the effect of substrate conicity and wettability on the thermokinetics of heterogeneous water droplet nucleation. Not only the peripheral tension is found to have a considerable effect on the free energy barrier but also the substrate hydrophobicity and hydrophilicity are observed to switch over their roles between conical crest and trough for different growth rates of the droplet. Besides, the rate of nucleation increases and further promotes nucleation for negative peripheral tension as it diminishes the free energy barrier appreciably. Moreover, nucleation inhibition can be achievable for positive peripheral tension due to the enhancement of the free energy barrier. Analyzing all possible geometric configurations, the hydrophilic narrower conical cavity is found to be the most preferred nucleation site. These findings suggest a physical insight into the context of surface engineering for the promotion or the suppression of nucleation on real or engineered substrates.

Electrochemical photovoltaic cell having ternary alloy film

DOEpatents

Russak, Michael A.

1984-01-01

A thin film compound semiconductor electrode comprising CdSe.sub.1-x Te.sub.x (0.ltoreq.x.ltoreq.1) is deposited on a transparent conductive substrate. An electrolyte contacts the film to form a photoactive site. The semiconductor material has a narrow energy bandgap permitting high efficiency for light conversion. The film may be fabricated by: (1) co-evaporation of two II-VI group compounds with a common cation, or (2) evaporation of three elements, concurrenty.

Cleavage Entropy as Quantitative Measure of Protease Specificity

PubMed Central

Fuchs, Julian E.; von Grafenstein, Susanne; Huber, Roland G.; Margreiter, Michael A.; Spitzer, Gudrun M.; Wallnoefer, Hannes G.; Liedl, Klaus R.

2013-01-01

A purely information theory-guided approach to quantitatively characterize protease specificity is established. We calculate an entropy value for each protease subpocket based on sequences of cleaved substrates extracted from the MEROPS database. We compare our results with known subpocket specificity profiles for individual proteases and protease groups (e.g. serine proteases, metallo proteases) and reflect them quantitatively. Summation of subpocket-wise cleavage entropy contributions yields a measure for overall protease substrate specificity. This total cleavage entropy allows ranking of different proteases with respect to their specificity, separating unspecific digestive enzymes showing high total cleavage entropy from specific proteases involved in signaling cascades. The development of a quantitative cleavage entropy score allows an unbiased comparison of subpocket-wise and overall protease specificity. Thus, it enables assessment of relative importance of physicochemical and structural descriptors in protease recognition. We present an exemplary application of cleavage entropy in tracing substrate specificity in protease evolution. This highlights the wide range of substrate promiscuity within homologue proteases and hence the heavy impact of a limited number of mutations on individual substrate specificity. PMID:23637583

Substrate specificity of sheep liver sorbitol dehydrogenase.

PubMed Central

Lindstad, R I; Köll, P; McKinley-McKee, J S

1998-01-01

The substrate specificity of sheep liver sorbitol dehydrogenase has been studied by steady-state kinetics over the range pH 7-10. Sorbitol dehydrogenase stereo-selectively catalyses the reversible NAD-linked oxidation of various polyols and other secondary alcohols into their corresponding ketones. The kinetic constants are given for various novel polyol substrates, including L-glucitol, L-mannitol, L-altritol, D-altritol, D-iditol and eight heptitols, as well as for many aliphatic and aromatic alcohols. The maximum velocities (kcat) and the substrate specificity-constants (kcat/Km) are positively correlated with increasing pH. The enzyme-catalysed reactions occur by a compulsory ordered kinetic mechanism with the coenzyme as the first, or leading, substrate. With many substrates, the rate-limiting step for the overall reaction is the enzyme-NADH product dissociation. However, with several substrates there is a transition to a mechanism with partial rate-limitation at the ternary complex level, especially at low pH. The kinetic data enable the elucidation of new empirical rules for the substrate specificity of sorbitol dehydrogenase. The specificity-constants for polyol oxidation vary as a function of substrate configuration with D-xylo> D-ribo > L-xylo > D-lyxo approximately L-arabino > D-arabino > L-lyxo. Catalytic activity with a polyol or an aromatic substrate and various 1-deoxy derivatives thereof varies with -CH2OH > -CH2NH2 > -CH2OCH3 approximately -CH3. The presence of a hydroxyl group at each of the remaining chiral centres of a polyol, apart from the reactive C2, is also nonessential for productive ternary complex formation and catalysis. A predominantly nonpolar enzymic epitope appears to constitute an important structural determinant for the substrate specificity of sorbitol dehydrogenase. The existence of two distinct substrate binding regions in the enzyme active site, along with that of the catalytic zinc, is suggested to account for the lack of stereospecificity at C2 in some polyols. PMID:9461546

Duodenal villous morphology assessed using magnification narrow band imaging correlates well with histology in patients with suspected malabsorption syndrome.

PubMed

Dutta, Amit Kumar; Sajith, Kattiparambil Gangadharan; Shah, Gautam; Pulimood, Anna Benjamin; Simon, Ebby George; Joseph, Anjilivelil Joseph; Chacko, Ashok

2014-11-01

Narrow band imaging with magnification enables detailed assessment of duodenal villi and may be useful in predicting the presence of villous atrophy or normal villi. We aimed to assess the morphology of duodenal villi using magnification narrow band imaging and correlate it with histology findings in patients with clinically suspected malabsorption syndrome. Patients with clinical suspicion of malabsorption presenting at a tertiary care center were prospectively recruited in this diagnostic intervention study. Patients underwent upper gastrointestinal endoscopy using magnification narrow band imaging. The villous morphology in the second part of the duodenum was assessed independently by two endoscopists and the presence of normal or atrophic villi was recorded. Biopsy specimen was obtained from the same area and was examined by two pathologists together. The sensitivity and specificity of magnification narrow band imaging in detecting the presence of duodenal villous atrophy was calculated and compared to the histology. One hundred patients with clinically suspected malabsorption were included in this study. Sixteen patients had histologically confirmed villous atrophy. The sensitivity and specificity of narrow band imaging in predicting villous atrophy was 87.5% and 95.2%, respectively, for one endoscopist. The corresponding figures for the second endoscopist were 81.3% and 92.9%, respectively. The interobserver agreement was very good with a kappa value of 0.87. Magnification narrow band imaging performed very well in predicting duodenal villous morphology. This may help in carrying out targeted biopsies and avoiding unnecessary biopsies in patients with suspected malabsorption. © 2014 The Authors. Digestive Endoscopy © 2014 Japan Gastroenterological Endoscopy Society.

Kinetics of reactions of the Actinomadura R39 DD-peptidase with specific substrates.

PubMed

Adediran, S A; Kumar, Ish; Nagarajan, Rajesh; Sauvage, Eric; Pratt, R F

2011-01-25

The Actinomadura R39 DD-peptidase catalyzes the hydrolysis and aminolysis of a number of small peptides and depsipeptides. Details of its substrate specificity and the nature of its in vivo substrate are not, however, well understood. This paper describes the interactions of the R39 enzyme with two peptidoglycan-mimetic substrates 3-(D-cysteinyl)propanoyl-D-alanyl-D-alanine and 3-(D-cysteinyl)propanoyl-D-alanyl-D-thiolactate. A detailed study of the reactions of the former substrate, catalyzed by the enzyme, showed DD-carboxypeptidase, DD-transpeptidase, and DD-endopeptidase activities. These results confirm the specificity of the enzyme for a free D-amino acid at the N-terminus of good substrates and indicated a preference for extended D-amino acid leaving groups. The latter was supported by determination of the structural specificity of amine nucleophiles for the acyl-enzyme generated by reaction of the enzyme with the thiolactate substrate. It was concluded that a specific substrate for this enzyme, and possibly the in vivo substrate, may consist of a partly cross-linked peptidoglycan polymer where a free side chain N-terminal un-cross-linked amino acid serves as the specific acyl group in an endopeptidase reaction. The enzyme is most likely a DD-endopeptidase in vivo. pH-rate profiles for reactions of the enzyme with peptides, the thiolactate named above, and β-lactams indicated the presence of complex proton dissociation pathways with sticky substrates and/or protons. The local structure of the active site may differ significantly for reactions of peptides and β-lactams. Solvent kinetic deuterium isotope effects indicate the presence of classical general acid/base catalysis in both acylation and deacylation; there is no evidence of the low fractionation factor active site hydrogen found previously in class A and C β-lactamases.

E3Net: a system for exploring E3-mediated regulatory networks of cellular functions.

PubMed

Han, Youngwoong; Lee, Hodong; Park, Jong C; Yi, Gwan-Su

2012-04-01

Ubiquitin-protein ligase (E3) is a key enzyme targeting specific substrates in diverse cellular processes for ubiquitination and degradation. The existing findings of substrate specificity of E3 are, however, scattered over a number of resources, making it difficult to study them together with an integrative view. Here we present E3Net, a web-based system that provides a comprehensive collection of available E3-substrate specificities and a systematic framework for the analysis of E3-mediated regulatory networks of diverse cellular functions. Currently, E3Net contains 2201 E3s and 4896 substrates in 427 organisms and 1671 E3-substrate specific relations between 493 E3s and 1277 substrates in 42 organisms, extracted mainly from MEDLINE abstracts and UniProt comments with an automatic text mining method and additional manual inspection and partly from high throughput experiment data and public ubiquitination databases. The significant functions and pathways of the extracted E3-specific substrate groups were identified from a functional enrichment analysis with 12 functional category resources for molecular functions, protein families, protein complexes, pathways, cellular processes, cellular localization, and diseases. E3Net includes interactive analysis and navigation tools that make it possible to build an integrative view of E3-substrate networks and their correlated functions with graphical illustrations and summarized descriptions. As a result, E3Net provides a comprehensive resource of E3s, substrates, and their functional implications summarized from the regulatory network structures of E3-specific substrate groups and their correlated functions. This resource will facilitate further in-depth investigation of ubiquitination-dependent regulatory mechanisms. E3Net is freely available online at http://pnet.kaist.ac.kr/e3net.

Glycan microarray screening assay for glycosyltransferase specificities.

PubMed

Peng, Wenjie; Nycholat, Corwin M; Razi, Nahid

2013-01-01

Glycan microarrays represent a high-throughput approach to determining the specificity of glycan-binding proteins against a large set of glycans in a single format. This chapter describes the use of a glycan microarray platform for evaluating the activity and substrate specificity of glycosyltransferases (GTs). The methodology allows simultaneous screening of hundreds of immobilized glycan acceptor substrates by in situ incubation of a GT and its appropriate donor substrate on the microarray surface. Using biotin-conjugated donor substrate enables direct detection of the incorporated sugar residues on acceptor substrates on the array. In addition, the feasibility of the method has been validated using label-free donor substrate combined with lectin-based detection of product to assess enzyme activity. Here, we describe the application of both procedures to assess the specificity of a recombinant human α2-6 sialyltransferase. This technique is readily adaptable to studying other glycosyltransferases.

Fabrication of superconducting nanowires from ultrathin MgB2 films via focused ion beam milling

NASA Astrophysics Data System (ADS)

Zhang, Chen; Wang, Da; Liu, Zheng-Hao; Zhang, Yan; Ma, Ping; Feng, Qing-Rong; Wang, Yue; Gan, Zi-Zhao

2015-02-01

High quality superconducting nanowires were fabricated from ultrathin MgB2 films by a focused ion beam milling technique. The precursor MgB2 films in 10 nm thick were grown on MgO substrates by using a hybrid physical-chemical vapor deposition method. The nanowires, in widths of about 300-600 nm and lengths of 1 or 10 μm, showed high superconducting critical temperatures (Tc's) above 34 K and narrow superconducting transition widths (ΔTc's) of 1-3 K. The superconducting critical current density Jc of the nanowires was above 5 × 107 A/cm2 at 20 K. The high Tc, narrow ΔTc, and high Jc of the nanowires offered the possibility of making MgB2-based nano-devices such as hot-electron bolometers and superconducting nanowire single-photon detectors with high operating temperatures at 15-20 K.

Microstrip patch antenna receiving array operating in the Ku band

NASA Technical Reports Server (NTRS)

Walcher, Douglas A.

1996-01-01

Microstrip patch antennas were first investigated from the idea that it would be highly advantageous to fabricate radiating elements (antennas) on the same dielectric substrate as RF circuitry and transmission lines. Other advantages were soon discovered to be its lightweight, low profile, conformability to shaped surfaces, and low manufacturing costs. Unfortunately, these same patches continually exhibit narrow bandwidths, wide beamwidths, and low antenna gain. This thesis will present the design and experimental results of a microstrip patch antenna receiving array operating in the Ku band. An antenna array will be designed in an attempt to improve its performance over a single patch. Most Ku band information signals are either wide band television images or narrow band data and voice channels. An attempt to improve the gain of the array by introducing parasitic patches on top of the array will also be presented in this thesis.

Characterizing Protease Specificity: How Many Substrates Do We Need?

PubMed Central

Schauperl, Michael; Fuchs, Julian E.; Waldner, Birgit J.; Huber, Roland G.; Kramer, Christian; Liedl, Klaus R.

2015-01-01

Calculation of cleavage entropies allows to quantify, map and compare protease substrate specificity by an information entropy based approach. The metric intrinsically depends on the number of experimentally determined substrates (data points). Thus a statistical analysis of its numerical stability is crucial to estimate the systematic error made by estimating specificity based on a limited number of substrates. In this contribution, we show the mathematical basis for estimating the uncertainty in cleavage entropies. Sets of cleavage entropies are calculated using experimental cleavage data and modeled extreme cases. By analyzing the underlying mathematics and applying statistical tools, a linear dependence of the metric in respect to 1/n was found. This allows us to extrapolate the values to an infinite number of samples and to estimate the errors. Analyzing the errors, a minimum number of 30 substrates was found to be necessary to characterize substrate specificity, in terms of amino acid variability, for a protease (S4-S4’) with an uncertainty of 5 percent. Therefore, we encourage experimental researchers in the protease field to record specificity profiles of novel proteases aiming to identify at least 30 peptide substrates of maximum sequence diversity. We expect a full characterization of protease specificity helpful to rationalize biological functions of proteases and to assist rational drug design. PMID:26559682

Motor-substrate interactions in mycoplasma motility explains non-Arrhenius temperature dependence.

PubMed

Chen, Jing; Neu, John; Miyata, Makoto; Oster, George

2009-12-02

Mycoplasmas exhibit a novel, substrate-dependent gliding motility that is driven by approximately 400 "leg" proteins. The legs interact with the substrate and transmit the forces generated by an assembly of ATPase motors. The velocity of the cell increases linearly by nearly 10-fold over a narrow temperature range of 10-40 degrees C. This corresponds to an Arrhenius factor that decreases from approximately 45 k(B)T at 10 degrees C to approximately 10 k(B)T at 40 degrees C. On the other hand, load-velocity curves at different temperatures extrapolate to nearly the same stall force, suggesting a temperature-insensitive force-generation mechanism near stall. In this article, we propose a leg-substrate interaction mechanism that explains the intriguing temperature sensitivity of this motility. The large Arrhenius factor at low temperature comes about from the addition of many smaller energy barriers arising from many substrate-binding sites at the distal end of the leg protein. The Arrhenius dependence attenuates at high temperature due to two factors: 1), the reduced effective multiplicity of energy barriers intrinsic to the multiple-site binding mechanism; and 2), the temperature-sensitive weakly facilitated leg release that curtails the power stroke. The model suggests an explanation for the similar steep, sub-Arrhenius temperature-velocity curves observed in many molecular motors, such as kinesin and myosin, wherein the temperature behavior is dominated not by the catalytic biochemistry, but by the motor-substrate interaction.

Motor-Substrate Interactions in Mycoplasma Motility Explains Non-Arrhenius Temperature Dependence

PubMed Central

Chen, Jing; Neu, John; Miyata, Makoto; Oster, George

2009-01-01

Abstract Mycoplasmas exhibit a novel, substrate-dependent gliding motility that is driven by ∼400 “leg” proteins. The legs interact with the substrate and transmit the forces generated by an assembly of ATPase motors. The velocity of the cell increases linearly by nearly 10-fold over a narrow temperature range of 10–40°C. This corresponds to an Arrhenius factor that decreases from ∼45 kBT at 10°C to ∼10 kBT at 40°C. On the other hand, load-velocity curves at different temperatures extrapolate to nearly the same stall force, suggesting a temperature-insensitive force-generation mechanism near stall. In this article, we propose a leg-substrate interaction mechanism that explains the intriguing temperature sensitivity of this motility. The large Arrhenius factor at low temperature comes about from the addition of many smaller energy barriers arising from many substrate-binding sites at the distal end of the leg protein. The Arrhenius dependence attenuates at high temperature due to two factors: 1), the reduced effective multiplicity of energy barriers intrinsic to the multiple-site binding mechanism; and 2), the temperature-sensitive weakly facilitated leg release that curtails the power stroke. The model suggests an explanation for the similar steep, sub-Arrhenius temperature-velocity curves observed in many molecular motors, such as kinesin and myosin, wherein the temperature behavior is dominated not by the catalytic biochemistry, but by the motor-substrate interaction. PMID:19948122

Use of CdS quantum dot-functionalized cellulose nanocrystal films for anti-counterfeiting applications

NASA Astrophysics Data System (ADS)

Chen, L.; Lai, C.; Marchewka, R.; Berry, R. M.; Tam, K. C.

2016-07-01

Structural colors and photoluminescence have been widely used for anti-counterfeiting and security applications. We report for the first time the use of CdS quantum dot (QD)-functionalized cellulose nanocrystals (CNCs) as building blocks to fabricate nanothin films via layer-by-layer (LBL) self-assembly for anti-counterfeiting applications. Both negatively- and positively-charged CNC/QD nanohybrids with a high colloidal stability and a narrow particle size distribution were prepared. The controllable LBL coating process was characterized by scanning electron microscopy and ellipsometry. The rigid structure of CNCs leads to nanoporous structured films on poly(ethylene terephthalate) (PET) substrates with high transmittance (above 70%) over the entire range of visible light and also resulted in increased hydrophilicity (contact angles of ~40 degrees). Nanothin films on PET substrates showed good flexibility and enhanced stability in both water and ethanol. The modified PET films with structural colors from thin-film interference and photoluminescence from QDs can be used in anti-counterfeiting applications.Structural colors and photoluminescence have been widely used for anti-counterfeiting and security applications. We report for the first time the use of CdS quantum dot (QD)-functionalized cellulose nanocrystals (CNCs) as building blocks to fabricate nanothin films via layer-by-layer (LBL) self-assembly for anti-counterfeiting applications. Both negatively- and positively-charged CNC/QD nanohybrids with a high colloidal stability and a narrow particle size distribution were prepared. The controllable LBL coating process was characterized by scanning electron microscopy and ellipsometry. The rigid structure of CNCs leads to nanoporous structured films on poly(ethylene terephthalate) (PET) substrates with high transmittance (above 70%) over the entire range of visible light and also resulted in increased hydrophilicity (contact angles of ~40 degrees). Nanothin films on PET substrates showed good flexibility and enhanced stability in both water and ethanol. The modified PET films with structural colors from thin-film interference and photoluminescence from QDs can be used in anti-counterfeiting applications. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr03039d

Molecular cloning and catalytic characterization of a recombinant tropine biosynthetic tropinone reductase from Withania coagulans leaf.

PubMed

Kushwaha, Amit K; Sangwan, Neelam S; Tripathi, Sandhya; Sangwan, Rajender S

2013-03-10

Tropinone reductases (TRs) are small proteins belonging to the SDR (short chain dehydrogenase/reductase) family of enzymes. TR-I and TR-II catalyze the conversion of tropinone into tropane alcohols (tropine and pseudotropine, respectively). The steps are intermediary enroute to biosynthesis of tropane esters of medicinal importance, hyoscyamine/scopolamine, and calystegins, respectively. Biosynthesis of tropane alkaloids has been proposed to occur in roots. However, in the present report, a tropine forming tropinone reductase (TR-I) cDNA was isolated from the aerial tissue (leaf) of a medicinal plant, Withania coagulans. The ORF was deduced to encode a polypeptide of 29.34 kDa. The complete cDNA (WcTRI) was expressed in E. coli and the recombinant His-tagged protein was purified for functional characterization. The enzyme had a narrow pH range of substantial activity with maxima at 6.6. Relatively superior thermostability of the enzyme (30% retention of activity at 60 °C) was catalytic novelty in consonance with the desert area restricted habitat of the plant. The in vitro reaction kinetics predominantly favoured the forward reaction. The enzyme had wide substrate specificity but did not cover the substrates of other well-known plant SDR related to menthol metabolism. To our knowledge, this pertains to be the first report on any gene and enzyme of secondary metabolism from the commercially and medicinally important vegetable rennet species. Copyright © 2012 Elsevier B.V. All rights reserved.

Angle resolved x-ray photoelectron spectroscopy (ARXPS) analysis of lanthanum oxide for micro-flexography printing

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

Hassan, S., E-mail: suhaimihas@uthm.edu.my; Yusof, M. S., E-mail: mdsalleh@uthm.edu.my; Maksud, M. I., E-mail: midris1973@gmail.com

2016-01-22

Micro-flexography printing was developed in patterning technique from micron to nano scale range to be used for graphic, electronic and bio-medical device on variable substrates. In this work, lanthanum oxide (La{sub 2}O{sub 3}) has been used as a rare earth metal candidate as depositing agent. This metal deposit was embedded on Carbon (C) and Silica (Si) wafer substrate using Magnetron Sputtering technique. The choose of Lanthanum as a target is due to its wide application in producing electronic devices such as thin film battery and printed circuit board. The La{sub 2}O{sub 3} deposited on the surface of Si wafer substratemore » was then analyzed using Angle Resolve X-Ray Photoelectron Spectroscopy (ARXPS). The position for each synthetic component in the narrow scan of Lanthanum (La) 3d and O 1s are referred to the electron binding energy (eV). The La 3d narrow scan revealed that the oxide species of this particular metal is mainly contributed by La{sub 2}O{sub 3} and La(OH){sub 3}. The information of oxygen species, O{sup 2-} component from O 1s narrow scan indicated that there are four types of species which are contributed from the bulk (O{sup 2−}), two chemisorb component (La{sub 2}O{sub 3}) and La(OH){sub 3} and physisorp component (OH). Here, it is proposed that from the adhesive and surface chemical properties of La, it is suitable as an alternative medium for micro-flexography printing technique in printing multiple fine solid lines at nano scale. Hence, this paper will describe the capability of this particular metal as rare earth metal for use in of micro-flexography printing practice. The review of other parameters contributing to print fine lines will also be described later.« less

A Subject-Specific Acoustic Model of the Upper Airway for Snoring Sounds Generation

PubMed Central

Saha, Shumit; Bradley, T. Douglas; Taheri, Mahsa; Moussavi, Zahra; Yadollahi, Azadeh

2016-01-01

Monitoring variations in the upper airway narrowing during sleep is invasive and expensive. Since snoring sounds are generated by air turbulence and vibrations of the upper airway due to its narrowing; snoring sounds may be used as a non-invasive technique to assess upper airway narrowing. Our goal was to develop a subject-specific acoustic model of the upper airway to investigate the impacts of upper airway anatomy, e.g. length, wall thickness and cross-sectional area, on snoring sounds features. To have a subject-specific model for snoring generation, we used measurements of the upper airway length, cross-sectional area and wall thickness from every individual to develop the model. To validate the proposed model, in 20 male individuals, intensity and resonant frequencies of modeled snoring sounds were compared with those measured from recorded snoring sounds during sleep. Based on both modeled and measured results, we found the only factor that may positively and significantly contribute to snoring intensity was narrowing in the upper airway. Furthermore, measured resonant frequencies of snoring were inversely correlated with the upper airway length, which is a risk factor for upper airway collapsibility. These results encourage the use of snoring sounds analysis to assess the upper airway anatomy during sleep. PMID:27210576

Narrow band imaging versus autofluorescence imaging for head and neck squamous cell carcinoma detection: a prospective study.

PubMed

Ni, X-G; Zhang, Q-Q; Wang, G-Q

2016-11-01

This study aimed to compare the diagnostic effectiveness of narrow band imaging and autofluorescence imaging for malignant laryngopharyngeal tumours. Between May 2010 and October 2010, 50 consecutive patients with suspected laryngopharyngeal tumour underwent endoscopic laryngopharynx examination. The morphological characteristics of laryngopharyngeal lesions were analysed using high performance endoscopic systems equipped with narrow band imaging and autofluorescence imaging modes. The diagnostic effectiveness of white light image, narrow band imaging and autofluorescence imaging endoscopy for benign and malignant laryngopharyngeal lesions was evaluated. Under narrow band imaging endoscopy, the superficial microvessels of squamous cell carcinomas appeared as dark brown spots or twisted cords. Under autofluorescence imaging endoscopy, malignant lesions appeared as bright purple. The sensitivity of malignant lesion diagnosis was not significantly different between narrow band imaging and autofluorescence imaging modes, but was better than for white light image endoscopy (χ2 = 12.676, p = 0.002). The diagnostic specificity was significantly better in narrow band imaging mode than in both autofluorescence imaging and white light imaging mode (χ2 = 8.333, p = 0.016). Narrow band imaging endoscopy is the best option for the diagnosis and differential diagnosis of laryngopharyngeal tumours.

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

PubMed

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

2018-01-14

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

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

Buried nanoantenna arrays: versatile antireflection coating.

PubMed

Kabiri, Ali; Girgis, Emad; Capasso, Federico

2013-01-01

Reflection is usually a detrimental phenomenon in many applications such as flat-panel-displays, solar cells, photodetectors, infrared sensors, and lenses. Thus far, to control and suppress the reflection from a substrate, numerous techniques including dielectric interference coatings, surface texturing, adiabatic index matching, and scattering from plasmonic nanoparticles have been investigated. A new technique is demonstrated to manage and suppress reflection from lossless and lossy substrates. It provides a wider flexibility in design versus previous methods. Reflection from a surface can be suppressed over a narrowband, wideband, or multiband frequency range. The antireflection can be dependent or independent of the incident wave polarization. Moreover, antireflection at a very wide incidence angle can be attained. The reflection from a substrate is controlled by a buried nanoantenna array, a structure composed of (1) a subwavelength metallic array and (2) a dielectric cover layer referred to as a superstrate. The material properties and thickness of the superstrate and nanoantennas' geometry and periodicity control the phase and intensity of the wave circulating inside the superstrate cavity. A minimum reflectance of 0.02% is achieved in various experiments in the mid-infrared from a silicon substrate. The design can be integrated in straightforward way in optical devices. The proposed structure is a versatile AR coating to optically impedance matches any substrate to free space in selected any narrow and broadband spectral response across the entire visible and infrared spectrum.

Fabrication and characterization of microstructures created in thermally deposited arsenic trisulfide by multiphoton lithography

NASA Astrophysics Data System (ADS)

Schwarz, Casey M.; Grabill, Chris N.; Richardson, Gerald D.; Labh, Shreya; Lewis, Anna M.; Vyas, Aadit; Gleason, Benn; Rivero-Baleine, Clara; Richardson, Kathleen A.; Pogrebnyakov, Alexej; Mayer, Theresa S.; Kuebler, Stephen M.

2017-04-01

A detailed study of multiphoton lithography (MPL) in arsenic trisulfide (As2S3) films and the effects on nanoscale morphology, chemical networking, and the appearance of the resulting features by the chemical composition, deposition rate, etch processing, and inclusion of an antireflection (AR) layer of As2Se3 between the substrate and the As2S3 layer is reported. MPL was used to photo-pattern nanostructured arrays in single- and multilayer films. The variation in chemical composition for laser-exposed, UV-exposed, and unexposed films is correlated with the etch response, nanostructure formation, and deposition conditions. Reflection of the focused beam at the substrate back into the film produces standing wave interference that modulates the exposure with distance from the substrate and produces nanobead structures. The interference and the modulation can be controlled by the addition of an AR layer of As2Se3 deposited between the substrate and the As2S3 film. Relative to structures produced in a single-layer As2S3 film having no AR layer, photo-patterning in the multilayer As2S3-on-As2Se3 film yields pillar-shaped structures that are closer to the targeted shape and are narrower (120 versus 320 nm), more uniform, and better adhering to the substrate. Processing methods are demonstrated for fabricating large-area arrays with diffractive optical function.

Dynamic locomotor capabilities revealed by early dinosaur trackmakers from southern Africa.

PubMed

Wilson, Jeffrey A; Marsicano, Claudia A; Smith, Roger M H

2009-10-06

A new investigation of the sedimentology and ichnology of the Early Jurassic Moyeni tracksite in Lesotho, southern Africa has yielded new insights into the behavior and locomotor dynamics of early dinosaurs. The tracksite is an ancient point bar preserving a heterogeneous substrate of varied consistency and inclination that includes a ripple-marked riverbed, a bar slope, and a stable algal-matted bar top surface. Several basal ornithischian dinosaurs and a single theropod dinosaur crossed its surface within days or perhaps weeks of one another, but responded to substrate heterogeneity differently. Whereas the theropod trackmaker accommodated sloping and slippery surfaces by gripping the substrate with its pedal claws, the basal ornithischian trackmakers adjusted to the terrain by changing between quadrupedal and bipedal stance, wide and narrow gauge limb support (abduction range = 31 degrees ), and plantigrade and digitigrade foot posture. The locomotor adjustments coincide with changes in substrate consistency along the trackway and appear to reflect 'real time' responses to a complex terrain. It is proposed that these responses foreshadow important locomotor transformations characterizing the later evolution of the two main dinosaur lineages. Ornithischians, which shifted from bipedal to quadrupedal posture at least three times in their evolutionary history, are shown to have been capable of adopting both postures early in their evolutionary history. The substrate-gripping behavior demonstrated by the early theropod, in turn, is consistent with the hypothesized function of pedal claws in bird ancestors.

Single-mode surface plasmon distributed feedback lasers.

PubMed

Karami Keshmarzi, Elham; Tait, R Niall; Berini, Pierre

2018-03-29

Single-mode surface plasmon distributed feedback (DFB) lasers are realized in the near infrared using a two-dimensional non-uniform long-range surface plasmon polariton structure. The surface plasmon mode is excited onto a 20 nm-thick, 1 μm-wide metal stripe (Ag or Au) on a silica substrate, where the stripe is stepped in width periodically, forming a 1st order Bragg grating. Optical gain is provided by optically pumping a 450 nm-thick IR-140 doped PMMA layer as the top cladding, which covers the entire length of the Bragg grating, thus creating a DFB laser. Single-mode lasing peaks of very narrow linewidth were observed for Ag and Au DFBs near 882 nm at room temperature. The narrow linewidths are explained by the low spontaneous emission rate into the surface plasmon lasing mode as well as the high quality factor of the DFB structure. The lasing emission is exclusively TM polarized. Kinks in light-light curves accompanied by spectrum narrowing were observed, from which threshold pump power densities can be clearly identified (0.78 MW cm-2 and 1.04 MW cm-2 for Ag and Au DFB lasers, respectively). The Schawlow-Townes linewidth for our Ag and Au DFB lasers is estimated and very narrow linewidths are predicted for the lasers. The lasers are suitable as inexpensive, recyclable and highly coherent sources of surface plasmons, or for integration with other surface plasmon elements of similar structure.

Giant Electric Field Control of Magnetism and Narrow Ferromagnetic Resonance Linewidth in FeCoSiB/Si/SiO2/PMN PT Multiferroic Heterostructures (Open Access Author’s Manuscript)

DTIC Science & Technology

2016-06-06

the widely used lead zirconate titanate ceramics which have a typical piezoelectric coefficient d31 of ~- 200pC/N, PMN-PT single crystals used in...substrate clamping effect, therefore, a relatively giant tunability can be obtained. However, the normally large roughness of piezoelectric layer...is the saturation magnetostriction constant, Y the Young’s modulus of the magnetic film, deff the effective piezoelectric coefficient, E

Optical humidity sensor

DOEpatents

Tarvin, Jeffrey A.

1987-01-01

An optical dielectric humidity sensor which includes a dielectric mirror having multiple alternating layers of two porous water-adsorbent dielectric materials with differing indices of refraction carried by a translucent substrate. A narrow-band polarized light source is positioned to direct light energy onto the mirror, and detectors are positioned to receive light energy transmitted through and reflected by the mirror. A ratiometer indicates humidity in the atmosphere which surrounds the dielectric mirror as a function of a ratio of light energies incident on the detectors.

Optical humidity sensor

DOEpatents

Tarvin, J.A.

1987-02-10

An optical dielectric humidity sensor is disclosed which includes a dielectric mirror having multiple alternating layers of two porous water-adsorbent dielectric materials with differing indices of refraction carried by a translucent substrate. A narrow-band polarized light source is positioned to direct light energy onto the mirror, and detectors are positioned to receive light energy transmitted through and reflected by the mirror. A ratiometer indicates humidity in the atmosphere which surrounds the dielectric mirror as a function of a ratio of light energies incident on the detectors. 2 figs.

Linewidth Narrowing and Purcell Enhancement in Photonic Crystal Cavities on an Er-Doped Silicon Nitride Platform

DTIC Science & Technology

2010-02-01

Low noise superconducting single photon detectors on silicon,” Appl. Phys. Lett. 93, 131101 (2008). 20. M. T. Tanner, C. M. Natarajan, V. K... wavelength sensitivity in NbTiN superconducting nanowire single-photon detectors fabricated on oxidized silicon substrates,” Proceedings of Single...cavity resonance wavelength and Q-factor for the PC cavity are shown in Figure 3. The data are taken both at low (0.050 mW) pump power and high (30 mW

On the Correlation Between the Self-Organized Island Pattern and Substrate Elastic Anisotropy

DTIC Science & Technology

2007-04-01

eters would be most useful to experimentalists. The kinetic Monte Carlo KMC has been proposed re- cently to study QD island self-organization by many...time ti. 21,25 Based on a proposed coupled KMC , the authors simu- lated the island ordering and narrow size distribution in two dimensions and further...100, 013527 2006pattern has not been studied so far within the coupled KMC algorithm where the long-range strain energy field is in- cluded

Two Predicted Transmembrane Domains Exclude Very Long Chain Fatty acyl-CoAs from the Active Site of Mouse Wax Synthase

PubMed Central

Kawelke, Steffen; Feussner, Ivo

2015-01-01

Wax esters are used as coatings or storage lipids in all kingdoms of life. They are synthesized from a fatty alcohol and an acyl-CoA by wax synthases. In order to get insights into the structure-function relationships of a wax synthase from Mus musculus, a domain swap experiment between the mouse acyl-CoA:wax alcohol acyltransferase (AWAT2) and the homologous mouse acyl-CoA:diacylglycerol O-acyltransferase 2 (DGAT2) was performed. This showed that the substrate specificity of AWAT2 is partially determined by two predicted transmembrane domains near the amino terminus of AWAT2. Upon exchange of the two domains for the respective part of DGAT2, the resulting chimeric enzyme was capable of incorporating up to 20% of very long acyl chains in the wax esters upon expression in S. cerevisiae strain H1246. The amount of very long acyl chains in wax esters synthesized by wild type AWAT2 was negligible. The effect was narrowed down to a single amino acid position within one of the predicted membrane domains, the AWAT2 N36R variant. Taken together, we provide first evidence that two predicted transmembrane domains in AWAT2 are involved in determining its acyl chain length specificity. PMID:26714272

Understanding transporter specificity and the discrete appearance of channel-like gating domains in transporters

PubMed Central

Diallinas, George

2014-01-01

Transporters are ubiquitous proteins mediating the translocation of solutes across cell membranes, a biological process involved in nutrition, signaling, neurotransmission, cell communication and drug uptake or efflux. Similarly to enzymes, most transporters have a single substrate binding-site and thus their activity follows Michaelis-Menten kinetics. Substrate binding elicits a series of structural changes, which produce a transporter conformer open toward the side opposite to the one from where the substrate was originally bound. This mechanism, involving alternate outward- and inward-facing transporter conformers, has gained significant support from structural, genetic, biochemical and biophysical approaches. Most transporters are specific for a given substrate or a group of substrates with similar chemical structure, but substrate specificity and/or affinity can vary dramatically, even among members of a transporter family that show high overall amino acid sequence and structural similarity. The current view is that transporter substrate affinity or specificity is determined by a small number of interactions a given solute can make within a specific binding site. However, genetic, biochemical and in silico modeling studies with the purine transporter UapA of the filamentous ascomycete Aspergillus nidulans have challenged this dogma. This review highlights results leading to a novel concept, stating that substrate specificity, but also transport kinetics and transporter turnover, are determined by subtle intramolecular interactions between a major substrate binding site and independent outward- or cytoplasmically-facing gating domains, analogous to those present in channels. This concept is supported by recent structural evidence from several, phylogenetically and functionally distinct transporter families. The significance of this concept is discussed in relationship to the role and potential exploitation of transporters in drug action. PMID:25309439

Effect of same-temperature GaN cap layer on the InGaN/GaN multiquantum well of green light-emitting diode on silicon substrate.

PubMed

Zheng, Changda; Wang, Li; Mo, Chunlan; Fang, Wenqing; Jiang, Fengyi

2013-01-01

GaN green LED was grown on Si (111) substrate by MOCVD. To enhance the quality of InGaN/GaN MQWs, same-temperature (ST) GaN protection layers with different thickness of 8 Å, 15 Å, and 30 Å were induced after the InGaN quantum wells (QWs) layer. Results show that a relative thicker cap layer is benefit to get InGaN QWs with higher In percent at fixed well temperature and obtain better QW/QB interface. As the cap thickness increases, the indium distribution becomes homogeneous as verified by fluorescence microscope (FLM). The interface of MQWs turns to be abrupt from XRD analysis. The intensity of photoluminescence (PL) spectrum is increased and the FWHM becomes narrow.

Oriented graphene nanoribbons embedded in hexagonal boron nitride trenches

PubMed Central

Chen, Lingxiu; He, Li; Wang, Hui Shan; Wang, Haomin; Tang, Shujie; Cong, Chunxiao; Xie, Hong; Li, Lei; Xia, Hui; Li, Tianxin; Wu, Tianru; Zhang, Daoli; Deng, Lianwen; Yu, Ting; Xie, Xiaoming; Jiang, Mianheng

2017-01-01

Graphene nanoribbons (GNRs) are ultra-narrow strips of graphene that have the potential to be used in high-performance graphene-based semiconductor electronics. However, controlled growth of GNRs on dielectric substrates remains a challenge. Here, we report the successful growth of GNRs directly on hexagonal boron nitride substrates with smooth edges and controllable widths using chemical vapour deposition. The approach is based on a type of template growth that allows for the in-plane epitaxy of mono-layered GNRs in nano-trenches on hexagonal boron nitride with edges following a zigzag direction. The embedded GNR channels show excellent electronic properties, even at room temperature. Such in-plane hetero-integration of GNRs, which is compatible with integrated circuit processing, creates a gapped channel with a width of a few benzene rings, enabling the development of digital integrated circuitry based on GNRs. PMID:28276532

Supported inorganic membranes

DOEpatents

Sehgal, Rakesh; Brinker, Charles Jeffrey

1998-01-01

Supported inorganic membranes capable of molecular sieving, and methods for their production, are provided. The subject membranes exhibit high flux and high selectivity. The subject membranes are substantially defect free and less than about 100 nm thick. The pores of the subject membranes have an average critical pore radius of less than about 5 .ANG., and have a narrow pore size distribution. The subject membranes are prepared by coating a porous substrate with a polymeric sol, preferably under conditions of low relative pressure of the liquid constituents of the sol. The coated substrate is dried and calcined to produce the subject supported membrane. Also provided are methods of derivatizing the surface of supported inorganic membranes with metal alkoxides. The subject membranes find use in a variety of applications, such as the separation of constituents of gaseous streams, as catalysts and catalyst supports, and the like.

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

PubMed

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

2017-12-11

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

Reprogramming caspase-7 specificity by regio-specific mutations and selection provides alternate solutions for substrate recognition

DOE PAGES

Hill, Maureen E.; MacPherson, Derek J.; Wu, Peng; ...

2016-03-31

The ability to routinely engineer protease specificity can allow us to better understand and modulate their biology for expanded therapeutic and industrial applications. In this paper, we report a new approach based on a caged green fluorescent protein (CA-GFP) reporter that allows for flow-cytometry-based selection in bacteria or other cell types enabling selection of intracellular protease specificity, regardless of the compositional complexity of the protease. Here, we apply this approach to introduce the specificity of caspase-6 into caspase-7, an intracellular cysteine protease important in cellular remodeling and cell death. We found that substitution of substrate-contacting residues from caspase-6 into caspase-7more » was ineffective, yielding an inactive enzyme, whereas saturation mutagenesis at these positions and selection by directed evolution produced active caspases. The process produced a number of nonobvious mutations that enabled conversion of the caspase-7 specificity to match caspase-6. The structures of the evolved-specificity caspase-7 (esCasp-7) revealed alternate binding modes for the substrate, including reorganization of an active site loop. Profiling the entire human proteome of esCasp-7 by N-terminomics demonstrated that the global specificity toward natural protein substrates is remarkably similar to that of caspase-6. Because the esCasp-7 maintained the core of caspase-7, we were able to identify a caspase-6 substrate, lamin C, that we predict relies on an exosite for substrate recognition. These reprogrammed proteases may be the first tool built with the express intent of distinguishing exosite dependent or independent substrates. Finally, this approach to specificity reprogramming should also be generalizable across a wide range of proteases.« less

Reprogramming caspase-7 specificity by regio-specific mutations and selection provides alternate solutions for substrate recognition

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

Hill, Maureen E.; MacPherson, Derek J.; Wu, Peng

The ability to routinely engineer protease specificity can allow us to better understand and modulate their biology for expanded therapeutic and industrial applications. In this paper, we report a new approach based on a caged green fluorescent protein (CA-GFP) reporter that allows for flow-cytometry-based selection in bacteria or other cell types enabling selection of intracellular protease specificity, regardless of the compositional complexity of the protease. Here, we apply this approach to introduce the specificity of caspase-6 into caspase-7, an intracellular cysteine protease important in cellular remodeling and cell death. We found that substitution of substrate-contacting residues from caspase-6 into caspase-7more » was ineffective, yielding an inactive enzyme, whereas saturation mutagenesis at these positions and selection by directed evolution produced active caspases. The process produced a number of nonobvious mutations that enabled conversion of the caspase-7 specificity to match caspase-6. The structures of the evolved-specificity caspase-7 (esCasp-7) revealed alternate binding modes for the substrate, including reorganization of an active site loop. Profiling the entire human proteome of esCasp-7 by N-terminomics demonstrated that the global specificity toward natural protein substrates is remarkably similar to that of caspase-6. Because the esCasp-7 maintained the core of caspase-7, we were able to identify a caspase-6 substrate, lamin C, that we predict relies on an exosite for substrate recognition. These reprogrammed proteases may be the first tool built with the express intent of distinguishing exosite dependent or independent substrates. Finally, this approach to specificity reprogramming should also be generalizable across a wide range of proteases.« less

Substrate- and isoform-specific proteome stability in normal and stressed cardiac mitochondria.

PubMed

Lau, Edward; Wang, Ding; Zhang, Jun; Yu, Hongxiu; Lam, Maggie P Y; Liang, Xiangbo; Zong, Nobel; Kim, Tae-Young; Ping, Peipei

2012-04-27

Mitochondrial protein homeostasis is an essential component of the functions and oxidative stress responses of the heart. To determine the specificity and efficiency of proteome turnover of the cardiac mitochondria by endogenous and exogenous proteolytic mechanisms. Proteolytic degradation of the murine cardiac mitochondria was assessed by 2-dimensional differential gel electrophoresis and liquid chromatography-tandem mass spectrometry. Mitochondrial proteases demonstrated a substrate preference for basic protein variants, which indicates a possible recognition mechanism based on protein modifications. Endogenous mitochondrial proteases and the cytosolic 20S proteasome exhibited different substrate specificities. The cardiac mitochondrial proteome contains low amounts of proteases and is remarkably stable in isolation. Oxidative damage lowers the proteolytic capacity of cardiac mitochondria and reduces substrate availability for mitochondrial proteases. The 20S proteasome preferentially degrades specific substrates in the mitochondria and may contribute to cardiac mitochondrial proteostasis.

Effects of low energy E-beam irradiation on graphene and graphene field effect transistors and raman metrology of graphene on split gate test structures

NASA Astrophysics Data System (ADS)

Rao, Gayathri S.

2011-12-01

Apart from its compelling performance in conventional nanoelectronic device geometries, graphene is an appropriate candidate to study certain interesting phenomenon (e.g. the Veselago lens effect) predicted on the basis of its linear electron dispersion relation. A key requirement for the observation of such phenomenon in graphene and for its use in conventional field-effect transistor (FET) devices is the need to minimize defects such as consisting of -- or resulting from -- adsorbates and lattice non-uniformities, and reduce deleterious substrate effects. Consequently the investigation of the origin and interaction of defects in the graphene lattice is essential to improve and tailor graphene-based device performance. In this thesis, optical spectroscopic studies on the influence of low-energy electron irradiation on adsorbate-induced defectivity and doping for substrate supported and suspended graphene were carried out along with spectroscopic and transport measurements on graphene FETs. A comparative investigation of the effects of single-step versus multi-step, low-energy electron irradiation (500 eV) on suspended, substrate supported graphene and on graphene FETs is reported. E-beam irradiation (single-step and multi-step) of substrate-supported graphene resulted in an increase in the Raman ID/IG ratio largely from hydrogenation due to radiolysis of the interfacial water layer between the graphene and the SiO2 substrate and from irradiated surface adsorbates. GFETs subjected to single and multi-step irradiation showed n-doping from CNP (charge neutrality point) shift of ˜ -8 and ˜ -16 V respectively. Correlation of this data with Raman analysis of suspended and supported graphene samples implied a strong role of the substrate and irradiation sequence in determining the level of doping. A correspondingly higher reduction in mobility per incident electron was also observed for GFETs subjected to multi-step irradiation compared to single step, in line with measured Raman ID/IG ratios. Additionally, the Raman G-band DeltaFWHM variation was strongly dependent on the nature of the e-beam irradiation and the presence of the substrate. Single-step irradiated, substrate-supported graphene exhibited substantial broadening while multi-step irradiation resulted in G-band narrowing. This behavior was not observed for suspended graphene which indicated the addition or elimination of substrate-induced phonon-relaxation mechanisms in response to each type of irradiation. The narrowing of the FWHM (G) in the multi-step case is attributed to doping consistent with the Dirac point shift of ˜ -16V and the removal of Landau phonon damping above Ef > ℏwG2 . In strong contrast, single step irradiation of substrate supported graphene yielded a broadening of the FWHM (G) accompanied by a CNP shift of ˜ -8V indicating appreciable n-doping. This reveals the presence of alternate phonon decay channels even when Landau damping above Ef > ℏwG2 is removed. It is proposed in this dissertation that this phenomenon is linked to hybridization of silicon oxide defect states (induced by single-step e-beam irradiation) and graphene electron states. This hybridization promotes a graphene phonon decay channel distinct from Landau damping, the latter being forbidden under sufficient doping. It is proposed that the alternate phonon decay channel involves two-component inelastic scattering, wherein the graphene phonons transfer energy to the carriers in the lattice which in turn couple to the polar phonons of the substrate resulting in mobility reduction. Furthermore, it is proposed that this defect-induced, graphene phonon decay channel is inhibited in multi-step e-beam irradiation due to the presence of adsorbates on the graphene introduced during ambient exposure between radiation cycles. On e-beam irradiation the adsorbates induce polar orientation of water dipoles at the graphene/SiO2 interface. This polar layer shifts the hybridized defect bands closer to the graphene Dirac bands thereby reducing the inelastic scattering and inhibiting the phonon decay medicated by SiO2 surface polar phonons (SPP). This model also explains the enhancement of n-type doping in GFETS observed for multi-step irradiation. These results highlight the impact of substrate defects and interaction of induced defectivity with the e-beam along with the role of interfacial water in impacting graphene device performance. The thesis also presents data on Raman-based characterization of graphene including layer number determination and carrier concentration measurement. Determination of layer number for graphene exfoliates focused on the splitting of the 2D Raman band. In addition, an alternate Raman-based thickness metrology was evaluated for CVD-based, polycrystalline graphene. Both were carried out on split gate test structures as a method for monolayer or bilayer confirmation in device geometries. In addition, carrier concentration measurements of exfoliates on 300nm SiO2 and split-gate test structure substrate have also been characterized with back gate biasing. These measurements made use of the stiffening of the Raman G-band with doping and the narrowing of the G-band FWHM. These results were important for validating conclusions from the e-beam irradiation experiments mentioned above regarding carrier doping.

Relative Expression Levels Rather Than Specific Activity Plays the Major Role in Determining In Vivo AKT Isoform Substrate Specificity

PubMed Central

Lee, Rachel S.; House, Colin M.; Cristiano, Briony E.; Hannan, Ross D.; Pearson, Richard B.; Hannan, Katherine M.

2011-01-01

The AKT protooncogene mediates many cellular processes involved in normal development and disease states such as cancer. The three structurally similar isoforms: AKT1, AKT2, and AKT3 exhibit both functional redundancy and isoform-specific functions; however the basis for their differential signalling remains unclear. Here we show that in vitro, purified AKT3 is ∼47-fold more active than AKT1 at phosphorylating peptide and protein substrates. Despite these marked variations in specific activity between the individual isoforms, a comprehensive analysis of phosphorylation of validated AKT substrates indicated only subtle differences in signalling via individual isoforms in vivo. Therefore, we hypothesise, at least in this model system, that relative tissue/cellular abundance, rather than specific activity, plays the dominant role in determining AKT substrate specificity in situ. PMID:21869924

Involvement of arginine 878 together with Ca2+ in mouse aminopeptidase A substrate specificity for N-terminal acidic amino-acid residues

PubMed Central

Couvineau, Pierre; de Almeida, Hugo; Maigret, Bernard; Llorens-Cortes, Catherine

2017-01-01

Aminopeptidase A (APA) is a membrane-bound zinc metalloprotease cleaving, in the brain, the N-terminal aspartyl residue of angiotensin II to generate angiotensin III, which exerts a tonic stimulatory effect on the control of blood pressure in hypertensive animals. Using a refined APA structure derived from the human APA crystal structure, we docked the specific and selective APA inhibitor, EC33 in the presence of Ca2+. We report the presence in the S1 subsite of Arg-887 (Arg-878 in mouse APA), the guanidinium moiety of which established an interaction with the electronegative sulfonate group of EC33. Mutagenic replacement of Arg-878 with an alanine or a lysine residue decreased the affinity of the recombinant enzymes for the acidic substrate, α-L-glutamyl-β-naphthylamide, with a slight decrease in substrate hydrolysis velocity either with or without Ca2+. In the absence of Ca2+, the mutations modified the substrate specificity of APA for the acidic substrate, the mutated enzymes hydrolyzing more efficiently basic and neutral substrates, although the addition of Ca2+ partially restored the acidic substrate specificity. The analysis of the 3D models of the Arg-878 mutated APAs revealed a change in the volume of the S1 subsite, which may impair the binding and/or the optimal positioning of the substrate in the active site as well as its hydrolysis. These findings demonstrate the key role of Arg-878 together with Ca2 + in APA substrate specificity for N-terminal acidic amino acid residues by ensuring the optimal positioning of acidic substrates during catalysis. PMID:28877217

Catalytic nanoporous membranes

DOEpatents

Pellin, Michael J; Hryn, John N; Elam, Jeffrey W

2013-08-27

A nanoporous catalytic membrane which displays several unique features Including pores which can go through the entire thickness of the membrane. The membrane has a higher catalytic and product selectivity than conventional catalysts. Anodic aluminum oxide (AAO) membranes serve as the catalyst substrate. This substrate is then subjected to Atomic Layer Deposition (ALD), which allows the controlled narrowing of the pores from 40 nm to 10 nm in the substrate by deposition of a preparatory material. Subsequent deposition of a catalytic layer on the inner surfaces of the pores reduces pore sizes to less than 10 nm and allows for a higher degree of reaction selectivity. The small pore sizes allow control over which molecules enter the pores, and the flow-through feature can allow for partial oxidation of reactant species as opposed to complete oxidation. A nanoporous separation membrane, produced by ALD is also provided for use in gaseous and liquid separations. The membrane has a high flow rate of material with 100% selectivity. Also provided is a method for producing a catalytic membrane having flow-through pores and discreet catalytic clusters adhering to the inside surfaces of the pores.

Structure and substrate ion binding in the sodium/proton antiporter PaNhaP

PubMed Central

Wöhlert, David; Kühlbrandt, Werner; Yildiz, Özkan

2014-01-01

Sodium/proton antiporters maintain intracellular pH and sodium levels. Detailed structures of antiporters with bound substrate ions are essential for understanding how they work. We have resolved the substrate ion in the dimeric, electroneutral sodium/proton antiporter PaNhaP from Pyrococcus abyssi at 3.2 Å, and have determined its structure in two different conformations at pH 8 and pH 4. The ion is coordinated by three acidic sidechains, a water molecule, a serine and a main-chain carbonyl in the unwound stretch of trans-membrane helix 5 at the deepest point of a negatively charged cytoplasmic funnel. A second narrow polar channel may facilitate proton uptake from the cytoplasm. Transport activity of PaNhaP is cooperative at pH 6 but not at pH 5. Cooperativity is due to pH-dependent allosteric coupling of protomers through two histidines at the dimer interface. Combined with comprehensive transport studies, the structures of PaNhaP offer unique new insights into the transport mechanism of sodium/proton antiporters. DOI: http://dx.doi.org/10.7554/eLife.03579.001 PMID:25426802

Improving performance of armchair graphene nanoribbon field effect transistors via boron nitride doping

NASA Astrophysics Data System (ADS)

Goharrizi, A. Yazdanpanah; Sanaeepur, M.; Sharifi, M. J.

2015-09-01

Device performance of 10 nm length armchair graphene nanoribbon field effect transistors with 1.5 nm and 4 nm width (13 and 33 atoms in width respectively) are compared in terms of Ion /Ioff , trans-conductance, and sub-threshold swing. While narrow devices suffer from edge roughness wider devices are subject to more substrate surface roughness and reduced bandgap. Boron Nitride doping is employed to compensate reduced bandgap in wider devices. Simultaneous effects of edge and substrate surface roughness are considered. Results show that in the presence of both the edge and substrate surface roughness the 4 nm wide device with boron nitride doping shows improved performance with respect to the 1.5 nm one (both of which incorporate the same bandgap AGNR as channel material). Electronic simulations are performed via NEGF method along with tight-binding Hamiltonian. Edge and surface roughness are created by means of one and two dimensional auto correlation functions respectively. Electronic characteristics are averaged over a large number of devices due to statistic nature of both the edge and surface roughness.

Effect of substrate temperature and V/III flux ratio on In incorporation for InGaN/GaN heterostructures grown by plasma-assisted molecular-beam epitaxy

NASA Astrophysics Data System (ADS)

O'Steen, M. L.; Fedler, F.; Hauenstein, R. J.

1999-10-01

Reflection high-energy electron diffraction (RHEED) and laterally spatially resolved high resolution x-ray diffraction (HRXRD) have been used to identify and characterize rf plasma-assisted molecular-beam epitaxial growth factors which strongly affect the efficiency of In incorporation into InxGa1-xN epitaxial materials. HRXRD results for InxGa1-xN/GaN superlattices reveal a particularly strong dependence of average alloy composition x¯ upon both substrate growth temperature and incident V/III flux ratio. For fixed flux ratio, results reveal a strong thermally activated behavior, with over an order-of-magnitude decrease in x¯ with increasing growth temperature within the narrow range 590-670 °C. Within this same range, a further strong dependence upon V/III flux ratio is observed. The decreased In incorporation at elevated substrate temperatures is tentatively attributed to In surface-segregation and desorption processes. RHEED observations support this segregation/desorption interpretation to account for In loss.

Influence of deposition temperature on WTiN coatings tribological performance

NASA Astrophysics Data System (ADS)

Londoño-Menjura, R. F.; Ospina, R.; Escobar, D.; Quintero, J. H.; Olaya, J. J.; Mello, A.; Restrepo-Parra, E.

2018-01-01

WTiN films were grown on silicon and stainless-steel substrates using the DC magnetron sputtering technique. The substrate temperature was varied taking values of 100 °C, 200 °C, 300 °C, and 400 °C. X-ray diffraction analysis allowed us to identify a rock salt-type face centered cubic (FCC) structure, with a lattice parameter of approximately 4.2 nm, a relatively low microstrain (deformations at microscopy level, between 4.7% and 6.7%), and a crystallite size of a few nanometers (11.6 nm-31.5 nm). The C1s, N1s, O1s, Ti2p, W4s, W4p, W4d and W4f narrow spectra were obtained using X-ray photoelectron spectroscopy (XPS) and depending on the substrate temperature, the deconvoluted spectra presented different binding energies. Grain sizes and roughness (approximately 4 nm) of films were determined using atomic force microscopy. Scratch and pin on disc tests were conducted, showing better performance of the film grown at 200 °C. This sample exhibited a lower roughness, coefficient of friction, and wear rate.

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

Structural Basis of Substrate Specificity and Regiochemistry in the MycF/TylF Family of Sugar O -Methyltransferases.

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

Bernard, Steffen M.; Akey, David L.; Tripathi, Ashootosh

Sugar moieties in natural products are frequently modified by O-methylation. In the biosynthesis of the macrolide antibiotic mycinamicin, methylation of a 6'-deoxyallose substituent occurs in a stepwise manner first at the 2'- and then the 3'-hydroxyl groups to produce the mycinose moiety in the final product. The timing and placement of the O-methylations impact final stage C-H functionalization reactions mediated by the P450 monooxygenase MycG. The structural basis of pathway ordering and substrate specificity is unknown. A series of crystal structures of MycF, the 3'-O-methyltransferase, including the free enzyme and complexes with S-adenosyl homocysteine (SAH), substrate, product, and unnatural substrates,more » show that SAM binding induces substantial ordering that creates the binding site for the natural substrate, and a bound metal ion positions the substrate for catalysis. A single amino acid substitution relaxed the 2'-methoxy specificity but retained regiospecificity. The engineered variant produced a new mycinamicin analog, demonstrating the utility of structural information to facilitate bioengineering approaches for the chemoenzymatic synthesis of complex small molecules containing modified sugars. Using the MycF substrate complex and the modeled substrate complex of a 4'-specific homolog, active site residues were identified that correlate with the 3'- or 4'- specificity of MycF family members and define the protein and substrate features that direct the regiochemistry of methyltransfer. Lastly, this classification scheme will be useful in the annotation of new secondary metabolite pathways that utilize this family of enzymes.« less

Structural Basis of Substrate Specificity and Regiochemistry in the MycF/TylF Family of Sugar O -Methyltransferases.

DOE PAGES

Bernard, Steffen M.; Akey, David L.; Tripathi, Ashootosh; ...

2015-02-18

Sugar moieties in natural products are frequently modified by O-methylation. In the biosynthesis of the macrolide antibiotic mycinamicin, methylation of a 6'-deoxyallose substituent occurs in a stepwise manner first at the 2'- and then the 3'-hydroxyl groups to produce the mycinose moiety in the final product. The timing and placement of the O-methylations impact final stage C-H functionalization reactions mediated by the P450 monooxygenase MycG. The structural basis of pathway ordering and substrate specificity is unknown. A series of crystal structures of MycF, the 3'-O-methyltransferase, including the free enzyme and complexes with S-adenosyl homocysteine (SAH), substrate, product, and unnatural substrates,more » show that SAM binding induces substantial ordering that creates the binding site for the natural substrate, and a bound metal ion positions the substrate for catalysis. A single amino acid substitution relaxed the 2'-methoxy specificity but retained regiospecificity. The engineered variant produced a new mycinamicin analog, demonstrating the utility of structural information to facilitate bioengineering approaches for the chemoenzymatic synthesis of complex small molecules containing modified sugars. Using the MycF substrate complex and the modeled substrate complex of a 4'-specific homolog, active site residues were identified that correlate with the 3'- or 4'- specificity of MycF family members and define the protein and substrate features that direct the regiochemistry of methyltransfer. Lastly, this classification scheme will be useful in the annotation of new secondary metabolite pathways that utilize this family of enzymes.« less

Pharmacogenomics of CYP2C9: Functional and Clinical Considerations†

PubMed Central

Rettie, Allan E.; Fowler, Douglas M.; Miners, John O.

2017-01-01

CYP2C9 is the most abundant CYP2C subfamily enzyme in human liver and the most important contributor from this subfamily to drug metabolism. Polymorphisms resulting in decreased enzyme activity are common in the CYP2C9 gene and this, combined with narrow therapeutic indices for several key drug substrates, results in some important issues relating to drug safety and efficacy. CYP2C9 substrate selectivity is detailed and, based on crystal structures for the enzyme, we describe how CYP2C9 catalyzes these reactions. Factors relevant to clinical response to CYP2C9 substrates including inhibition, induction and genetic polymorphism are discussed in detail. In particular, we consider the issue of ethnic variation in pattern and frequency of genetic polymorphisms and clinical implications. Warfarin is the most well studied CYP2C9 substrate; recent work on use of dosing algorithms that include CYP2C9 genotype to improve patient safety during initiation of warfarin dosing are reviewed and prospects for their clinical implementation considered. Finally, we discuss a novel approach to cataloging the functional capabilities of rare ‘variants of uncertain significance’, which are increasingly detected as more exome and genome sequencing of diverse populations is conducted. PMID:29283396

Ordered alternating binary polymer nanodroplet array by sequential spin dewetting.

PubMed

Bhandaru, Nandini; Das, Anuja; Salunke, Namrata; Mukherjee, Rabibrata

2014-12-10

We report a facile technique for fabricating an ordered array of nearly equal-sized mesoscale polymer droplets of two constituent polymers (polystyrene, PS and poly(methyl methacrylate), PMMA) arranged in an alternating manner on a topographically patterned substrate. The self-organized array of binary polymers is realized by sequential spin dewetting. First, a dilute solution of PMMA is spin-dewetted on a patterned substrate, resulting in an array of isolated PMMA droplets arranged along the substrate grooves due to self-organization during spin coating itself. The sample is then silanized with octadecyltrichlorosilane (OTS), and subsequently, a dilute solution of PS is spin-coated on to it, which also undergoes spin dewetting. The spin-dewetted PS drops having a size nearly equal to the pre-existing PMMA droplets position themselves between two adjacent PMMA drops under appropriate conditions, forming an alternating binary polymer droplet array. The alternating array formation takes place for a narrow range of solution concentration for both the polymers and depends on the geometry of the substrate. The size of the droplets depends on the extent of confinement, and droplets as small as 100 nm can be obtained by this method, on a suitable template. The findings open up the possibility of creating novel surfaces having ordered multimaterial domains with a potential multifunctional capability.

Process optimization of ultrasonic spray coating of polymer films.

PubMed

Bose, Sanjukta; Keller, Stephan S; Alstrøm, Tommy S; Boisen, Anja; Almdal, Kristoffer

2013-06-11

In this work we have performed a detailed study of the influence of various parameters on spray coating of polymer films. Our aim is to produce polymer films of uniform thickness (500 nm to 1 μm) and low roughness compared to the film thickness. The coatings are characterized with respect to thickness, roughness (profilometer), and morphology (optical microscopy). Polyvinylpyrrolidone (PVP) is used to do a full factorial design of experiments with selected process parameters such as temperature, distance between spray nozzle and substrate, and speed of the spray nozzle. A mathematical model is developed for statistical analysis which identifies the distance between nozzle and substrate as the most significant parameter. Depending on the drying of the sprayed droplets on the substrate, we define two broad regimes, "dry" and "wet". The optimum condition of spraying lies in a narrow window between these two regimes, where we obtain a film of desired quality. Both with increasing nozzle-substrate distance and temperature, the deposition moves from a wet state to a dry regime. Similar results are also achieved for solvents with low boiling points. Finally, we study film formation during spray coating with poly (D,L-lactide) (PDLLA). The results confirm the processing knowledge obtained with PVP and indicate that the observed trends are identical for spraying of other polymer films.

Strain tuning of electronic structure in Bi 4Ti 3O 12-LaCoO 3 epitaxial thin films

DOE PAGES

Choi, Woo Seok; Lee, Ho Nyung

2015-05-08

In this study, we investigated the crystal and electronic structures of ferroelectric Bi 4Ti 3O 12 single-crystalline thin films site-specifically substituted with LaCoO 3 (LCO). The epitaxial films were grown by pulsed laser epitaxy on NdGaO 3 and SrTiO 3 substrates to vary the degree of strain. With increasing the LCO substitution, we observed a systematic increase in the c-axis lattice constant of the Aurivillius phase related with the modification of pseudo-orthorhombic unit cells. These compositional and structural changes resulted in a systematic decrease in the band gap, i.e., the optical transition energy between the oxygen 2p and transition-metal 3dmore » states, based on a spectroscopic ellipsometry study. In particular, the Co 3d state seems to largely overlap with the Ti t 2g state, decreasing the band gap. Interestingly, the applied tensile strain facilitates the band-gap narrowing, demonstrating that epitaxial strain is a useful tool to tune the electronic structure of ferroelectric transition-metal oxides.« less

The Origins of Specificity in the Microcin-Processing Protease TldD/E.

PubMed

Ghilarov, Dmitry; Serebryakova, Marina; Stevenson, Clare E M; Hearnshaw, Stephen J; Volkov, Dmitry S; Maxwell, Anthony; Lawson, David M; Severinov, Konstantin

2017-10-03

TldD and TldE proteins are involved in the biosynthesis of microcin B17 (MccB17), an Escherichia coli thiazole/oxazole-modified peptide toxin targeting DNA gyrase. Using a combination of biochemical and crystallographic methods we show that E. coli TldD and TldE interact to form a heterodimeric metalloprotease. TldD/E cleaves the N-terminal leader sequence from the modified MccB17 precursor peptide, to yield mature antibiotic, while it has no effect on the unmodified peptide. Both proteins are essential for the activity; however, only the TldD subunit forms a novel metal-containing active site within the hollow core of the heterodimer. Peptide substrates are bound in a sequence-independent manner through β sheet interactions with TldD and are likely cleaved via a thermolysin-type mechanism. We suggest that TldD/E acts as a "molecular pencil sharpener": unfolded polypeptides are fed through a narrow channel into the active site and processively truncated through the cleavage of short peptides from the N-terminal end. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Investigation of Dual-Mode Microstrip Bandpass Filter Based on SIR Technique

PubMed Central

Mezaal, Yaqeen S.; Ali, Jawad K.

2016-01-01

In this paper, a new bandpass filter design has been presented using simple topology of stepped impedance square loop resonator. The proposed bandpass filter has been simulated and fabricated using a substrate with an insulation constant of 10.8, thickness of 1.27mm and loss tangent of 0.0023 at center frequency of 5.8 GHz. The simulation results have been evaluated using Sonnet simulator that is extensively adopted in microwave analysis and implementation. The output frequency results demonstrated that the proposed filter has high-quality frequency responses in addition to isolated second harmonic frequency. Besides, this filter has very small surface area and perceptible narrow band response features that represent the conditions of recent wireless communication systems. Various filter specifications have been compared with different magnitudes of perturbation element dimension. Furthermore, phase scattering response and current intensity distribution of the proposed filter have been discussed. The simulated and experimental results are well-matched. Lastly, the features of the proposed filter have been compared with other designed microstrip filters in the literature. PMID:27798675

DdlN from Vancomycin-Producing Amycolatopsis orientalis C329.2 Is a VanA Homologue with d-Alanyl-d-Lactate Ligase Activity

PubMed Central

Marshall, C. Gary; Wright, Gerard D.

1998-01-01

Vancomycin-resistant enterococci acquire high-level resistance to glycopeptide antibiotics through the synthesis of peptidoglycan terminating in d-alanyl-d-lactate. A key enzyme in this process is a d-alanyl-d-alanine ligase homologue, VanA or VanB, which preferentially catalyzes the synthesis of the depsipeptide d-alanyl-d-lactate. We report the overexpression, purification, and enzymatic characterization of DdlN, a VanA and VanB homologue encoded by a gene of the vancomycin-producing organism Amycolatopsis orientalis C329.2. Evaluation of kinetic parameters for the synthesis of peptides and depsipeptides revealed a close relationship between VanA and DdlN in that depsipeptide formation was kinetically preferred at physiologic pH; however, the DdlN enzyme demonstrated a narrower substrate specificity and commensurately increased affinity for d-lactate in the C-terminal position over VanA. The results of these functional experiments also reinforce the results of previous studies that demonstrated that glycopeptide resistance enzymes from glycopeptide-producing bacteria are potential sources of resistance enzymes in clinically relevant bacteria. PMID:9791137

Atrial fibrillation driver mechanisms: Insight from the isolated human heart.

PubMed

Csepe, Thomas A; Hansen, Brian J; Fedorov, Vadim V

2017-01-01

Although there have been great technological advances in the treatment of atrial fibrillation (AF), current therapies remain limited due to a narrow understanding of AF mechanisms in the human heart. This review will highlight our recent studies on explanted human hearts where we developed and employed a novel functional-structural mapping approach by integrating high-resolution simultaneous endo-epicardial and panoramic optical mapping with 3D gadolinium-enhanced MRI to define the spatiotemporal characteristics of AF drivers and their structural substrates. The results allow us to postulate that the primary mechanism of AF maintenance in human hearts is a limited number of localized intramural microanatomic reentrant AF drivers anchored to heart-specific 3D fibrotically insulated myobundle tracks, which may remain hidden to clinical single-surface electrode mapping. We suggest that ex vivo human heart studies, by using an integrated 3D functional and structural mapping approach, will help to reveal defining features of AF drivers as well as validate and improve clinical approaches to detect and target these AF drivers in patients with cardiac diseases. Copyright © 2016 Elsevier Inc. All rights reserved.

Engineering of Pyranose Dehydrogenase for Increased Oxygen Reactivity

PubMed Central

Krondorfer, Iris; Lipp, Katharina; Brugger, Dagmar; Staudigl, Petra; Sygmund, Christoph; Haltrich, Dietmar; Peterbauer, Clemens K.

2014-01-01

Pyranose dehydrogenase (PDH), a member of the GMC family of flavoproteins, shows a very broad sugar substrate specificity but is limited to a narrow range of electron acceptors and reacts extremely slowly with dioxygen as acceptor. The use of substituted quinones or (organo)metals as electron acceptors is undesirable for many production processes, especially of food ingredients. To improve the oxygen reactivity, site-saturation mutagenesis libraries of twelve amino acids around the active site of Agaricus meleagris PDH were expressed in Saccharomyces cerevisiae. We established high-throughput screening assays for oxygen reactivity and standard dehydrogenase activity using an indirect Amplex Red/horseradish peroxidase and a DCIP/D-glucose based approach. The low number of active clones confirmed the catalytic role of H512 and H556. Only one position was found to display increased oxygen reactivity. Histidine 103, carrying the covalently linked FAD cofactor in the wild-type, was substituted by tyrosine, phenylalanine, tryptophan and methionine. Variant H103Y was produced in Pichia pastoris and characterized and revealed a five-fold increase of the oxygen reactivity. PMID:24614932

Site-specific deposition of single gold nanoparticles by individual growth in electrohydrodynamically-printed attoliter droplet reactors.

PubMed

Schneider, Julian; Rohner, Patrik; Galliker, Patrick; Raja, Shyamprasad N; Pan, Ying; Tiwari, Manish K; Poulikakos, Dimos

2015-06-07

Gold nanoparticles with unique electronic, optical and catalytic properties can be efficiently synthesized in colloidal suspensions and are of broad scientific and technical interest and utility. However, their orderly integration on functional surfaces and devices remains a challenge. Here we show that single gold nanoparticles can be directly grown in individually printed, stabilized metal-salt ink attoliter droplets, using a nanoscale electrohydrodynamic printing method with a stable high-frequency dripping mode. This enables controllable sessile droplet nanoreactor formation and sustenance on non-wetting substrates, despite simultaneous rapid evaporation. The single gold nanoparticles can be formed inside such reactors in situ or by subsequent thermal annealing and plasma ashing. With this non-contact technique, single particles with diameters tunable in the range of 5-35 nm and with narrow size distribution, high yield and alignment accuracy are generated on demand and patterned into arbitrary arrays. The nanoparticles feature good catalytic activity as shown by the exemplary growth of silicon nanowires from the nanoparticles and the etching of nanoholes by the printed nanoparticles.

Substrate-specific regulation of ubiquitination by the anaphase-promoting complex

PubMed Central

Song, Ling

2011-01-01

By orchestrating the sequential degradation of a large number of cell cycle regulators, the ubiquitin ligase anaphase-promoting complex (APC/C) is essential for proliferation in all eukaryotes. The correct timing of APC/C-dependent substrate degradation, a critical feature of progression through mitosis, was long known to be controlled by mechanisms targeting the core APC/C-machinery. Recent experiments, however have revealed an important contribution of substrate-specific regulation of the APC/C to achieve accurate cell division. In this perspective, we describe different mechanisms of substrate-specific APC/C-regulation and discuss their importance for cell division. PMID:21191176

Exploring the specific features of interfacial enzymology based on lipase studies.

PubMed

Aloulou, Ahmed; Rodriguez, Jorge A; Fernandez, Sylvie; van Oosterhout, Dirk; Puccinelli, Delphine; Carrière, Frédéric

2006-09-01

Many enzymes are active at interfaces in the living world (such as in the signaling processes at the surface of cell membranes, digestion of dietary lipids, starch and cellulose degradation, etc.), but fundamental enzymology remains largely focused on the interactions between enzymes and soluble substrates. The biochemical and kinetic characterization of lipolytic enzymes has opened up new paths of research in the field of interfacial enzymology. Lipases are water-soluble enzymes hydrolyzing insoluble triglyceride substrates, and studies on these enzymes have led to the development of specific interfacial kinetic models. Structure-function studies on lipases have thrown light on the interfacial recognition sites present in the molecular structure of these enzymes, the conformational changes occurring in the presence of lipids and amphiphiles, and the stability of the enzymes present at interfaces. The pH-dependent activity, substrate specificity and inhibition of these enzymes can all result from both "classical" interactions between a substrate or inhibitor and the active site, as well as from the adsorption of the enzymes at the surface of aggregated substrate particles such as oil drops, lipid bilayers or monomolecular lipid films. The adsorption step can provide an alternative target for improving substrate specificity and developing specific enzyme inhibitors. Several data obtained with gastric lipase, classical pancreatic lipase, pancreatic lipase-related protein 2 and phosphatidylserine-specific phospholipase A1 were chosen here to illustrate these specific features of interfacial enzymology.

Background correction in forensic photography. I. Photography of blood under conditions of non-uniform illumination or variable substrate color--theoretical aspects and proof of concept.

PubMed

Wagner, John H; Miskelly, Gordon M

2003-05-01

The combination of photographs taken at two or three wavelengths at and bracketing an absorbance peak indicative of a particular compound can lead to an image with enhanced visualization of the compound. This procedure works best for compounds with absorbance bands that are narrow compared with "average" chromophores. If necessary, the photographs can be taken with different exposure times to ensure that sufficient light from the substrate is detected at all three wavelengths. The combination of images is readily performed if the images are obtained with a digital camera and are then processed using an image processing program. Best results are obtained if linear images at the peak maximum, at a slightly shorter wavelength, and at a slightly longer wavelength are used. However, acceptable results can also be obtained under many conditions if non-linear photographs are used or if only two wavelengths (one of which is at the peak maximum) are combined. These latter conditions are more achievable by many "mid-range" digital cameras. Wavelength selection can either be by controlling the illumination (e.g., by using an alternate light source) or by use of narrow bandpass filters. The technique is illustrated using blood as the target analyte, using bands of light centered at 395, 415, and 435 nm. The extension of the method to detection of blood by fluorescence quenching is also described.

Deciphering kinase-substrate relationships by analysis of domain-specific phosphorylation network.

PubMed

Damle, Nikhil Prakash; Mohanty, Debasisa

2014-06-15

In silico prediction of site-specific kinase-substrate relationships (ssKSRs) is crucial for deciphering phosphorylation networks by linking kinomes to phosphoproteomes. However, currently available predictors for ssKSRs give rise to a large number of false-positive results because they use only a short sequence stretch around phosphosite as determinants of kinase specificity and do not consider the biological context of kinase-substrate recognition. Based on the analysis of domain-specific kinase-substrate relationships, we have constructed a domain-level phosphorylation network that implicitly incorporates various contextual factors. It reveals preferential phosphorylation of specific domains by certain kinases. These novel correlations have been implemented in PhosNetConstruct, an automated program for predicting target kinases for a substrate protein. PhosNetConstruct distinguishes cognate kinase-substrate pairs from a large number of non-cognate combinations. Benchmarking on independent datasets using various statistical measures demonstrates the superior performance of PhosNetConstruct over ssKSR-based predictors. PhosNetConstruct is freely available at http://www.nii.ac.in/phosnetconstruct.html. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Substrate Specificity and Possible Heterologous Targets of Phytaspase, a Plant Cell Death Protease*

PubMed Central

Galiullina, Raisa A.; Kasperkiewicz, Paulina; Chichkova, Nina V.; Szalek, Aleksandra; Serebryakova, Marina V.; Poreba, Marcin; Drag, Marcin; Vartapetian, Andrey B.

2015-01-01

Plants lack aspartate-specific cell death proteases homologous to animal caspases. Instead, a subtilisin-like serine-dependent plant protease named phytaspase shown to be involved in the accomplishment of programmed death of plant cells is able to hydrolyze a number of peptide-based caspase substrates. Here, we determined the substrate specificity of rice (Oryza sativa) phytaspase by using the positional scanning substrate combinatorial library approach. Phytaspase was shown to display an absolute specificity of hydrolysis after an aspartic acid residue. The preceding amino acid residues, however, significantly influence the efficiency of hydrolysis. Efficient phytaspase substrates demonstrated a remarkable preference for an aromatic amino acid residue in the P3 position. The deduced optimum phytaspase recognition motif has the sequence IWLD and is strikingly hydrophobic. The established pattern was confirmed through synthesis and kinetic analysis of cleavage of a set of optimized peptide substrates. An amino acid motif similar to the phytaspase cleavage site is shared by the human gastrointestinal peptide hormones gastrin and cholecystokinin. In agreement with the established enzyme specificity, phytaspase was shown to hydrolyze gastrin-1 and cholecystokinin at the predicted sites in vitro, thus destroying the active moieties of the hormones. PMID:26283788

Substrate Sorting by a Supercharged Nanoreactor

PubMed Central

2017-01-01

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

Stiffness of hyaluronic acid gels containing liver extracellular matrix supports human hepatocyte function and alters cell morphology.

PubMed

Deegan, Daniel B; Zimmerman, Cynthia; Skardal, Aleksander; Atala, Anthony; Shupe, Thomas D

2015-03-01

Tissue engineering and cell based liver therapies have utilized primary hepatocytes with limited success due to the failure of hepatocytes to maintain their phenotype in vitro. In order to overcome this challenge, hyaluronic acid (HA) cell culture substrates were formulated to closely mimic the composition and stiffness of the normal liver cellular microenvironment. The stiffness of the substrate was modulated by adjusting HA hydrogel crosslinking. Additionally, the repertoire of bioactive molecules within the HA substrate was bolstered by supplementation with normal liver extracellular matrix (ECM). Primary human hepatocyte viability and phenotype were determined over a narrow physiologically relevant range of substrate stiffnesses from 600 to 4600Pa in both the presence and absence of liver ECM. Cell attachment, viability, and organization of the actin cytoskeleton improved with increased stiffness up to 4600Pa. These differences were not evident in earlier time points or substrates containing only HA. However, gene expression for the hepatocyte markers hepatocyte nuclear factor 4 alpha (HNF4α) and albumin significantly decreased on the 4600Pa stiffness at day 7 indicating that cells may not have maintained their phenotype long-term at this stiffness. Function, as measured by albumin secretion, varied with both stiffness and time in culture and peaked at day 7 at the 1200Pa stiffness, slightly below the stiffness of normal liver ECM at 3000Pa. Overall, gel stiffness affected primary human hepatocyte cell adhesion, functional marker expression, and morphological characteristics dependent on both the presence of liver ECM in gel substrates and time in culture. Copyright © 2015 Elsevier Ltd. All rights reserved.

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

Electronic, Magnetic, and Transport Properties of Polyacrylonitrile-Based Carbon Nanofibers of Various Widths: Density-Functional Theory Calculations

NASA Astrophysics Data System (ADS)

Partovi-Azar, P.; Panahian Jand, S.; Kaghazchi, P.

2018-01-01

Edge termination of graphene nanoribbons is a key factor in determination of their physical and chemical properties. Here, we focus on nitrogen-terminated zigzag graphene nanoribbons resembling polyacrylonitrile-based carbon nanofibers (CNFs) which are widely studied in energy research. In particular, we investigate magnetic, electronic, and transport properties of these CNFs as functions of their widths using density-functional theory calculations together with the nonequilibrium Green's function method. We report on metallic behavior of all the CNFs considered in this study and demonstrate that the narrow CNFs show finite magnetic moments. The spin-polarized electronic states in these fibers exhibit similar spin configurations on both edges and result in spin-dependent transport channels in the narrow CNFs. We show that the partially filled nitrogen dangling-bond bands are mainly responsible for the ferromagnetic spin ordering in the narrow samples. However, the magnetic moment becomes vanishingly small in the case of wide CNFs where the dangling-bond bands fall below the Fermi level and graphenelike transport properties arising from the π orbitals are recovered. The magnetic properties of the CNFs as well as their stability have also been discussed in the presence of water molecules and the hexagonal boron nitride substrate.

Axial computed tomography evaluation of the internal nasal valve correlates with clinical valve narrowing and patient complaint.

PubMed

Moche, Jason A; Cohen, Justin C; Pearlman, Steven J

2013-07-01

The objective of this work was to explore the utility of axial computed tomography (CT) imaging to objectively define a narrow internal nasal valve, and compare those findings with clinical examination and patient complaint. Retrospective review from a single facial plastic surgery center. We reviewed 40 consecutive patients evaluated for either sinusitis or nasal airway obstruction for which a CT scan was obtained at a single radiology institution. Thirty-six complete office records were examined for the presence of clinical internal valve narrowing and complaints of nasal obstruction. In total, 72 internal nasal valves were analyzed using axial plane CT and measurements were compared to clinical findings and presence of airway obstruction. Measured valve areas for clinically normal internal nasal valves averaged 0.47 cm(2) vs 0.28 cm(2) for clinically narrow valves, a decrease of 40.4%. In unobstructed nasal airways the valve area averaged 0.51 cm(2) vs 0.38 cm(2) in obstructed airways, a difference of 25.5%. A radiographically measured valve area of <0.30 cm(2) suggests clinical narrowing with a sensitivity of 71.4%, specificity of 88.9%, positive predictive value of 62.5%, and negative predictive value of 92.3%. Using standard axial CT imaging we describe an objective method of radiographically evaluating the nasal valve, demonstrating strong correlation with physical examination and patient complaint. Additionally, radiographic valve areas can be used to screen for clinically narrow nasal valves with good sensitivity and specificity, providing a novel straightforward method for nasal valve assessment. © 2012 ARS-AAOA, LLC.

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.

Engineering the Substrate Specificity of the DhbE Adenylation Domain by Yeast Cell Surface Display

PubMed Central

Zhang, Keya; Nelson, Kathryn M.; Bhuripanyo, Karan; Grimes, Kimberly D.; Zhao, Bo; Aldrich, Courtney C.; Yin, Jun

2013-01-01

SUMMARY The adenylation (A) domains of nonribosomal peptide synthetases (NRPSs) activate aryl acids or amino acids to launch their transfer through the NRPS assembly line for the biosynthesis of many medicinally important natural products. In order to expand the substrate pool of NRPSs, we developed a method based on yeast cell surface display to engineer the substrate specificities of the A-domains. We acquired A-domain mutants of DhbE that have 11- and 6-fold increases in kcat/Km with nonnative substrates 3-hydroxybenzoic acid and 2-aminobenzoic acid, respectively and corresponding 3- and 33-fold decreases in kcat/Km values with the native substrate 2,3-dihydroxybenzoic acid, resulting in a dramatic switch in substrate specificity of up to 200-fold. Our study demonstrates that yeast display can be used as a high throughput selection platform to reprogram the “nonribosomal code” of A-domains. PMID:23352143

Calcium-dependent protein kinases from Arabidopsis show substrate specificity differences in an analysis of 103 substrates.

PubMed

Curran, Amy; Chang, Ing-Feng; Chang, Chia-Lun; Garg, Shilpi; Miguel, Rodriguez Milla; Barron, Yoshimi D; Li, Ying; Romanowsky, Shawn; Cushman, John C; Gribskov, Michael; Harmon, Alice C; Harper, Jeffrey F

2011-01-01

The identification of substrates represents a critical challenge for understanding any protein kinase-based signal transduction pathway. In Arabidopsis, there are more than 1000 different protein kinases, 34 of which belong to a family of Ca(2+)-dependent protein kinases (CPKs). While CPKs are implicated in regulating diverse aspects of plant biology, from ion transport to transcription, relatively little is known about isoform-specific differences in substrate specificity, or the number of phosphorylation targets. Here, in vitro kinase assays were used to compare phosphorylation targets of four CPKs from Arabidopsis (CPK1, 10, 16, and 34). Significant differences in substrate specificity for each kinase were revealed by assays using 103 different substrates. For example CPK16 phosphorylated Serine 109 in a peptide from the stress-regulated protein, Di19-2 with K(M) ∼70 μM, but this site was not phosphorylated significantly by CPKs 1, 10, or 34. In contrast, CPKs 1, 10, and 34 phosphorylated 93 other peptide substrates not recognized by CPK16. Examples of substrate specificity differences among all four CPKs were verified by kinetic analyses. To test the correlation between in vivo phosphorylation events and in vitro kinase activities, assays were performed with 274 synthetic peptides that contained phosphorylation sites previously mapped in proteins isolated from plants (in vivo-mapped sites). Of these, 74 (27%) were found to be phosphorylated by at least one of the four CPKs tested. This 27% success rate validates a robust strategy for linking the activities of specific kinases, such as CPKs, to the thousands of in planta phosphorylation sites that are being uncovered by emerging technologies.

Calcium-Dependent Protein Kinases from Arabidopsis Show Substrate Specificity Differences in an Analysis of 103 Substrates

PubMed Central

Curran, Amy; Chang, Ing-Feng; Chang, Chia-Lun; Garg, Shilpi; Miguel, Rodriguez Milla; Barron, Yoshimi D.; Li, Ying; Romanowsky, Shawn; Cushman, John C.; Gribskov, Michael; Harmon, Alice C.; Harper, Jeffrey F.

2011-01-01

The identification of substrates represents a critical challenge for understanding any protein kinase-based signal transduction pathway. In Arabidopsis, there are more than 1000 different protein kinases, 34 of which belong to a family of Ca2+-dependent protein kinases (CPKs). While CPKs are implicated in regulating diverse aspects of plant biology, from ion transport to transcription, relatively little is known about isoform-specific differences in substrate specificity, or the number of phosphorylation targets. Here, in vitro kinase assays were used to compare phosphorylation targets of four CPKs from Arabidopsis (CPK1, 10, 16, and 34). Significant differences in substrate specificity for each kinase were revealed by assays using 103 different substrates. For example CPK16 phosphorylated Serine 109 in a peptide from the stress-regulated protein, Di19-2 with KM ∼70 μM, but this site was not phosphorylated significantly by CPKs 1, 10, or 34. In contrast, CPKs 1, 10, and 34 phosphorylated 93 other peptide substrates not recognized by CPK16. Examples of substrate specificity differences among all four CPKs were verified by kinetic analyses. To test the correlation between in vivo phosphorylation events and in vitro kinase activities, assays were performed with 274 synthetic peptides that contained phosphorylation sites previously mapped in proteins isolated from plants (in vivo-mapped sites). Of these, 74 (27%) were found to be phosphorylated by at least one of the four CPKs tested. This 27% success rate validates a robust strategy for linking the activities of specific kinases, such as CPKs, to the thousands of in planta phosphorylation sites that are being uncovered by emerging technologies. PMID:22645532

Sugar microarray via click chemistry: molecular recognition with lectins and amyloid β (1-42)

NASA Astrophysics Data System (ADS)

Matsumoto, Erino; Yamauchi, Takahiro; Fukuda, Tomohiro; Miura, Yoshiko

2009-06-01

Sugar microarrays were fabricated on various substrates via click chemistry. Acetylene-terminated substrates were prepared by forming self-assembled monolayers (SAMs) on a gold substrate with alkyl-disulfide and on silicon, quartz and glass substrates with a silane-coupling reagent. The gold substrates were subjected to surface plasmon resonance measurements, and the quartz and glass substrates were subjected to spectroscopy measurements and optical microscopy observation. The saccharide-immobilized substrate on the gold substrate showed specific interaction with the corresponding lectin, and the saccharides showed inert surface properties to other proteins with a high signal-to-noise ratio. We also focused on the saccharide-protein interaction on protein amyloidosis of Alzheimer amyloid β. Amyloid β peptide showed conformation transition on the saccharide-immobilization substrate into a β-sheet, and fibril formation and amyloid aggregates were found on the specific saccharides.

Structure of the carboxypeptidase B complex with N-sulfamoyl-L-phenylalanine - a transition state analog of non-specific substrate.

PubMed

Akparov, Valery; Timofeev, Vladimir; Khaliullin, Ilyas; Švedas, Vytas; Kuranova, Inna

2018-03-01

Carboxypeptidase B (EC 3.4.17.2) (CPB) is commonly used in the industrial insulin production and as a template for drug design. However, its ability to discriminate substrates with hydrophobic, hydrophilic, and charged side chains is not well understood. We report structure of CPB complex with a transition state analog N-sulfamoyl-L-phenylalanine solved at 1.74Å. The study provided an insight into structural basis of CPB substrate specificity. Ligand binding is affected by structure-depended conformational changes of Asp255 in S1'-subsite, interactions with Asn144 and Arg145 in C-terminal binding subsite, and Glu270 in the catalytic center. Side chain of the non-specific substrate analog SPhe in comparison with that of specific substrate analog SArg (reported earlier) not only loses favorable electrostatic interactions and two hydrogen bonds with Asp255 and three fixed water molecules, but is forced to be in the unfavorable hydrophilic environment. Thus, Ser207, Gly253, Tyr248, and Asp255 residues play major role in the substrate recognition by S1'-subsite.

Novel α-L-arabinofuranosidase from Cellulomonas fimi ATCC 484 and its substrate-specificity analysis with the aid of computer.

PubMed

Yang, Ying; Zhang, Lujia; Guo, Mingrong; Sun, Jiaqi; Matsukawa, Shingo; Xie, Jingli; Wei, Dongzhi

2015-04-15

In the process of gene mining for novel α-L-arabinofuranosidases (AFs), the gene Celf_3321 from Cellulomonas fimi ATCC 484 encodes an AF, termed as AbfCelf, with potent activity, 19.4 U/mg under the optimum condition, pH 6.0 and 40 °C. AbfCelf can hydrolyze α-1,5-linked oligosaccharides, sugar beet arabinan, linear 1,5-α-arabinan, and wheat flour arabinoxylan, which is partly different from some previously well-characterized GH 51 AFs. The traditional substrate-specificity analysis for AFs is labor-consuming and money costing, because the substrates include over 30 kinds of various 4-nitrophenol (PNP)-glycosides, oligosaccharides, and polysaccharides. Hence, a preliminary structure and mechanism based method was applied for substrate-specificity analysis. The binding energy (ΔG, kcal/mol) obtained by docking suggested the reaction possibility and coincided with the experimental results. AbfA crystal 1QW9 was used to test the rationality of docking method in simulating the interaction between enzyme and substrate, as well the credibility of the substrate-specificity analysis method in silico.

In silico design, synthesis, and assays of specific substrates for proteinase 3: influence of fluorogenic and charged groups.

PubMed

Narawane, Shailesh; Budnjo, Adnan; Grauffel, Cédric; Haug, Bengt Erik; Reuter, Nathalie

2014-02-13

Neutrophil serine proteases are specific regulators of the immune response, and proteinase 3 is a major target antigen in antineutrophil cytoplasmic antibody-associated vasculitis. FRET peptides containing 2-aminobenzoic acid (Abz) and N-(2,4-dinitrophenyl)ethylenediamine (EDDnp) as fluorophore and quencher groups, respectively, have been widely used to probe proteases specificity. Using in silico design followed by enzymatic assays, we show that Abz and EDDnp significantly contribute to substrate hydrolysis by PR3. We also propose a new substrate specific for PR3.

Substrate Specificities and Conformational Flexibility of 3-Ketosteroid 9α-Hydroxylases*

PubMed Central

Penfield, Jonathan S.; Worrall, Liam J.; Strynadka, Natalie C.; Eltis, Lindsay D.

2014-01-01

KshA is the oxygenase component of 3-ketosteroid 9α-hydroxylase, a Rieske oxygenase involved in the bacterial degradation of steroids. Consistent with its role in bile acid catabolism, KshA1 from Rhodococcus rhodochrous DSM43269 had the highest apparent specificity (kcat/Km) for steroids with an isopropyl side chain at C17, such as 3-oxo-23,24-bisnorcholesta-1,4-diene-22-oate (1,4-BNC). By contrast, the KshA5 homolog had the highest apparent specificity for substrates with no C17 side chain (kcat/Km >105 s−1 m−1 for 4-estrendione, 5α-androstandione, and testosterone). Unexpectedly, substrates such as 4-androstene-3,17-dione (ADD) and 4-BNC displayed strong substrate inhibition (KiS ∼100 μm). By comparison, the cholesterol-degrading KshAMtb from Mycobacterium tuberculosis had the highest specificity for CoA-thioesterified substrates. These specificities are consistent with differences in the catabolism of cholesterol and bile acids, respectively, in actinobacteria. X-ray crystallographic structures of the KshAMtb·ADD, KshA1·1,4-BNC-CoA, KshA5·ADD, and KshA5·1,4-BNC-CoA complexes revealed that the enzymes have very similar steroid-binding pockets with the substrate's C17 oriented toward the active site opening. Comparisons suggest Tyr-245 and Phe-297 are determinants of KshA1 specificity. All enzymes have a flexible 16-residue “mouth loop,” which in some structures completely occluded the substrate-binding pocket from the bulk solvent. Remarkably, the catalytic iron and α-helices harboring its ligands were displaced up to 4.4 Å in the KshA5·substrate complexes as compared with substrate-free KshA, suggesting that Rieske oxygenases may have a dynamic nature similar to cytochrome P450. PMID:25049233

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

The ‘Goldilocks’ effect: preservation bias in vertebrate track assemblages

PubMed Central

Falkingham, P. L.; Bates, K. T.; Margetts, L.; Manning, P. L.

2011-01-01

Finite-element analysis was used to investigate the extent of bias in the ichnological fossil record attributable to body mass. Virtual tracks were simulated for four dinosaur taxa of different sizes (Struthiomimus, Tyrannosaurus, Brachiosaurus and Edmontosaurus), in a range of substrate conditions. Outlines of autopodia were generated based upon osteology and published soft-tissue reconstructions. Loads were applied vertically to the feet equivalent to the weight of the animal, and distributed accordingly to fore- and hindlimbs where relevant. Ideal, semi-infinite elastic–plastic substrates displayed a ‘Goldilocks’ quality where only a narrow range of loads could produce tracks, given that small animals failed to indent the substrate, and larger animals would be unable to traverse the area without becoming mired. If a firm subsurface layer is assumed, a more complete assemblage is possible, though there is a strong bias towards larger, heavier animals. The depths of fossil tracks within an assemblage may indicate thicknesses of mechanically distinct substrate layers at the time of track formation, even when the lithified strata appear compositionally homogeneous. This work increases the effectiveness of using vertebrate tracks as palaeoenvironmental indicators in terms of inferring substrate conditions at the time of track formation. Additionally, simulated undertracks are examined, and it is shown that complex deformation beneath the foot may not be indicative of limb kinematics as has been previously interpreted, but instead ridges and undulations at the base of a track may be a function of sediment displacement vectors and pedal morphology. PMID:21233145

van der Waals epitaxy of CdTe thin film on graphene

NASA Astrophysics Data System (ADS)

Mohanty, Dibyajyoti; Xie, Weiyu; Wang, Yiping; Lu, Zonghuan; Shi, Jian; Zhang, Shengbai; Wang, Gwo-Ching; Lu, Toh-Ming; Bhat, Ishwara B.

2016-10-01

van der Waals epitaxy (vdWE) facilitates the epitaxial growth of materials having a large lattice mismatch with the substrate. Although vdWE of two-dimensional (2D) materials on 2D materials have been extensively studied, the vdWE for three-dimensional (3D) materials on 2D substrates remains a challenge. It is perceived that a 2D substrate passes little information to dictate the 3D growth. In this article, we demonstrated the vdWE growth of the CdTe(111) thin film on a graphene buffered SiO2/Si substrate using metalorganic chemical vapor deposition technique, despite a 46% large lattice mismatch between CdTe and graphene and a symmetry change from cubic to hexagonal. Our CdTe films produce a very narrow X-ray rocking curve, and the X-ray pole figure analysis showed 12 CdTe (111) peaks at a chi angle of 70°. This was attributed to two sets of parallel epitaxy of CdTe on graphene with a 30° relative orientation giving rise to a 12-fold symmetry in the pole figure. First-principles calculations reveal that, despite the relatively small energy differences, the graphene buffer layer does pass epitaxial information to CdTe as the parallel epitaxy, obtained in the experiment, is energetically favored. The work paves a way for the growth of high quality CdTe film on a large area as well as on the amorphous substrates.

Dynamic Locomotor Capabilities Revealed by Early Dinosaur Trackmakers from Southern Africa

PubMed Central

Wilson, Jeffrey A.; Marsicano, Claudia A.; Smith, Roger M. H.

2009-01-01

Background A new investigation of the sedimentology and ichnology of the Early Jurassic Moyeni tracksite in Lesotho, southern Africa has yielded new insights into the behavior and locomotor dynamics of early dinosaurs. Methodology/Principal Findings The tracksite is an ancient point bar preserving a heterogeneous substrate of varied consistency and inclination that includes a ripple-marked riverbed, a bar slope, and a stable algal-matted bar top surface. Several basal ornithischian dinosaurs and a single theropod dinosaur crossed its surface within days or perhaps weeks of one another, but responded to substrate heterogeneity differently. Whereas the theropod trackmaker accommodated sloping and slippery surfaces by gripping the substrate with its pedal claws, the basal ornithischian trackmakers adjusted to the terrain by changing between quadrupedal and bipedal stance, wide and narrow gauge limb support (abduction range = 31°), and plantigrade and digitigrade foot posture. Conclusions/Significance The locomotor adjustments coincide with changes in substrate consistency along the trackway and appear to reflect ‘real time’ responses to a complex terrain. It is proposed that these responses foreshadow important locomotor transformations characterizing the later evolution of the two main dinosaur lineages. Ornithischians, which shifted from bipedal to quadrupedal posture at least three times in their evolutionary history, are shown to have been capable of adopting both postures early in their evolutionary history. The substrate-gripping behavior demonstrated by the early theropod, in turn, is consistent with the hypothesized function of pedal claws in bird ancestors. PMID:19806213

Cleavage-site specificity of prolyl endopeptidase FAP investigated with a full-length protein substrate.

PubMed

Huang, Chih-Hsiang; Suen, Ching-Shu; Lin, Ching-Ting; Chien, Chia-Hui; Lee, Hsin-Ying; Chung, Kuei-Min; Tsai, Ting-Yueh; Jiaang, Weir-Tong; Hwang, Ming-Jing; Chen, Xin

2011-06-01

Fibroblast activation protein (FAP) is a prolyl-cleaving endopeptidase proposed as an anti-cancer drug target. It is necessary to define its cleavage-site specificity to facilitate the identification of its in vivo substrates and to understand its biological functions. We found that the previously identified substrate of FAP, α(2)-anti-plasmin, is not a robust substrate in vitro. Instead, an intracellular protein, SPRY2, is cleavable by FAP and more suitable for investigation of its substrate specificity in the context of the full-length globular protein. FAP prefers uncharged residues, including small or bulky hydrophobic amino acids, but not charged amino acids, especially acidic residue at P1', P3 and P4 sites. Molecular modelling analysis shows that the substrate-binding site of FAP is surrounded by multiple tyrosine residues and some negatively charged residues, which may exert least preference for substrates with acidic residues. This provides an explanation why FAP cannot cleave interleukins, which have a glutamate at either P4 or P2', despite their P3-P2-P1 sites being identical to SPRY2 or α-AP. Our study provided new information on FAP cleavage-site specificity, which differs from the data obtained by profiling with a peptide library or with the denatured protein, gelatin, as the substrate. Furthermore, our study suggests that negatively charged residues should be avoided when designing FAP inhibitors.

Microfluidic transmission surface plasmon resonance enhancement for biosensor applications

NASA Astrophysics Data System (ADS)

Lertvachirapaiboon, Chutiparn; Baba, Akira; Ekgasit, Sanong; Shinbo, Kazunari; Kato, Keizo; Kaneko, Futao

2017-01-01

The microfluidic transmission surface plasmon resonance (MTSPR) constructed by assembling a gold-coated grating substrate with a microchannel was employed for biosensor application. The transmission surface plasmon resonance spectrum obtained from the MTSPR sensor chip showed a strong and narrow surface plasmon resonance (SPR) peak located between 650 and 800 nm. The maximum SPR excitation was observed at an incident angle of 35°. The MTSPR sensor chip was employed for glucose sensor application. Gold-coated grating substrates were functionalized using 3-mercapto-1-propanesulfonic acid sodium salt and subsequently functionalized using a five-bilayer poly(allylamine hydrochloride)/poly(sodium 4-styrenesulfonate) to facilitate the coupling/decoupling of the surface plasmon and to prepare a uniform surface for sensing. The detection limit of our developed system for glucose was 2.31 mM. This practical platform represents a high possibility of further developing several biomolecules, multiplex systems, and a point-of-care assay for practical biosensor applications.

Temporal behavior of RHEED intensity oscillations during molecular beam epitaxial growth of GaAs and AlGaAs on (111)B GaAs substrates

NASA Astrophysics Data System (ADS)

Yen, Ming Y.; Haas, T. W.

1990-10-01

We present the temporal behavior of intensity oscillations in reflection high-energy electron diffraction (RHEED) during molecular beam epitaxial (MBE) growth of GaAs and A1GaAs on (1 1 1)B GaAs substrates. The RHEED intensity oscillations were examined as a function of growth parameters in order to provide the insight into the dynamic characteristics and to identify the optimal condition for the two-dimensional layer-by-layer growth. The most intense RHEED oscillation was found to occur within a very narrow temperature range which seems to optimize the surface migration kinetics of the arriving group III elements and the molecular dissodiative reaction of the group V elements. The appearance of an initial transient of the intensity upon commencement of the growth and its implications are described.

Stackable multi-port gas nozzles

DOEpatents

Poppe, Steve; Rozenzon, Yan; Ding, Peijun

2015-03-03

One embodiment provides a reactor for material deposition. The reactor includes a chamber and at least one gas nozzle. The chamber includes a pair of susceptors, each having a front side and a back side. The front side mounts a number of substrates. The susceptors are positioned vertically so that the front sides of the susceptors face each other, and the vertical edges of the susceptors are in contact with each other, thereby forming a substantially enclosed narrow channel between the substrates mounted on different susceptors. The gas nozzle includes a gas-inlet component situated in the center and a detachable gas-outlet component stacked around the gas-inlet component. The gas-inlet component includes at least one opening coupled to the chamber, and is configured to inject precursor gases into the chamber. The detachable gas-outlet component includes at least one opening coupled to the chamber, and is configured to output exhaust gases from the chamber.

Controlling the interparticle spacing of Au-salt loaded micelles and Au nanoparticles on flat surfaces.

PubMed

Bansmann, J; Kielbassa, S; Hoster, H; Weigl, F; Boyen, H G; Wiedwald, U; Ziemann, P; Behm, R J

2007-09-25

The self-organization of diblock copolymers into micellar structures in an appropriate solvent allows the deposition of well ordered arrays of pure metal and alloy nanoparticles on flat surfaces with narrow distributions in particle size and interparticle spacing. Here we investigated the influence of the materials (substrate and polymer) and deposition parameters (temperature and emersion velocity) on the deposition of metal salt loaded micelles by dip-coating from solution and on the order and inter-particle spacing of the micellar deposits and thus of the metal nanoparticle arrays resulting after plasma removal of the polymer shell. For identical substrate and polymer, variation of the process parameters temperature and emersion velocity enables the controlled modification of the interparticle distance within a certain length regime. Moreover, also the degree of hexagonal order of the final array depends sensitively on these parameters.

Quality improvements of ZnxCdyMg1-x-ySe layers grown on InP substrates by a thin ZnCdSe interfacial layer

NASA Astrophysics Data System (ADS)

Zeng, L.; Yang, B. X.; Tamargo, M. C.; Snoeks, E.; Zhao, L.

1998-03-01

The quality of lattice-matched ZnxCdyMg1-x-ySe epitaxial layers grown on (001) InP substrates with a III-V buffer layer has been improved by initially growing a ZnCdSe interfacial layer (50 Å) at low temperature. The widths of double crystal x-ray rocking curves for ZnxCdyMg1-x-ySe epilayers with band gaps as high as 3.05 eV were reduced to about 70 arcsec. The defect density evaluated from etch pit density and plan-view transmission electron microscopy measurements was reduced by two orders of magnitude, to 106-107cm-2. The photoluminescence band edge emission became more symmetric and slightly narrower. It is proposed that an initial two-dimensional growth mode has been achieved by incorporating such a lattice-matched ZnCdSe layer.

Effect of Same-Temperature GaN Cap Layer on the InGaN/GaN Multiquantum Well of Green Light-Emitting Diode on Silicon Substrate

PubMed Central

Zheng, Changda; Wang, Li; Mo, Chunlan; Fang, Wenqing; Jiang, Fengyi

2013-01-01

GaN green LED was grown on Si (111) substrate by MOCVD. To enhance the quality of InGaN/GaN MQWs, same-temperature (ST) GaN protection layers with different thickness of 8 Å, 15 Å, and 30 Å were induced after the InGaN quantum wells (QWs) layer. Results show that a relative thicker cap layer is benefit to get InGaN QWs with higher In percent at fixed well temperature and obtain better QW/QB interface. As the cap thickness increases, the indium distribution becomes homogeneous as verified by fluorescence microscope (FLM). The interface of MQWs turns to be abrupt from XRD analysis. The intensity of photoluminescence (PL) spectrum is increased and the FWHM becomes narrow. PMID:24369453

Sonoelectrochemical one-pot synthesis of Pt - Carbon black nanocomposite PEMFC electrocatalyst.

PubMed

Karousos, Dionysios S; Desdenakis, Kostantinos I; Sakkas, Petros M; Sourkouni, Georgia; Pollet, Bruno G; Argirusis, Christos

2017-03-01

Simultaneous electrocatalytic Pt-nanoparticle synthesis and decoration of Vulcan XC-72 carbon black substrate was achieved in a novel one-step-process, combining galvanostatic pulsed electrodeposition and pulsed ultrasonication with high power, low-frequency (20kHz) ultrasound. Aqueous chloroplatinic acid precursor baths, as well as carbon black suspensions in the former, were examined and decoration was proven by a combination of characterization methods, namely: dynamic light scattering, transmission electron microscopy, scanning electron microscopy with EDX-analysis and cyclic voltammetry. In particular, PVP was shown to have a beneficial stabilizing effect against free nanoparticle aggregation, ensuring narrow size distributions of the nanoparticles synthesized, but is also postulated to prevent the establishment of a strong metal-substrate interaction. Current pulse amplitude was identified as the most critical nanoparticle size-determining parameters, while only small size particles, under 10nm, appeared to be attached to carbon black. Copyright © 2016 Elsevier B.V. All rights reserved.

Two dimensional radial gas flows in atmospheric pressure plasma-enhanced chemical vapor deposition

NASA Astrophysics Data System (ADS)

Kim, Gwihyun; Park, Seran; Shin, Hyunsu; Song, Seungho; Oh, Hoon-Jung; Ko, Dae Hong; Choi, Jung-Il; Baik, Seung Jae

2017-12-01

Atmospheric pressure (AP) operation of plasma-enhanced chemical vapor deposition (PECVD) is one of promising concepts for high quality and low cost processing. Atmospheric plasma discharge requires narrow gap configuration, which causes an inherent feature of AP PECVD. Two dimensional radial gas flows in AP PECVD induces radial variation of mass-transport and that of substrate temperature. The opposite trend of these variations would be the key consideration in the development of uniform deposition process. Another inherent feature of AP PECVD is confined plasma discharge, from which volume power density concept is derived as a key parameter for the control of deposition rate. We investigated deposition rate as a function of volume power density, gas flux, source gas partial pressure, hydrogen partial pressure, plasma source frequency, and substrate temperature; and derived a design guideline of deposition tool and process development in terms of deposition rate and uniformity.

Using multivalency to tailor the superselective binding of polymers on substrates

NASA Astrophysics Data System (ADS)

Tito, Nicholas; Frenkel, Daan

2014-03-01

Multivalency is a microscopic design concept in which a single nanoscopic entity contains multiple ligands, each of which may bind to multiple receptors on another entity. A useful property of many multivalent systems is ``superselectivity,'' where the fraction of the multivalent species bound to their complementary receptors grows sharply with the total number of receptors available. For example in the past two decades, multivalency has been exploited to develop DNA-coated nanoparticles that self-assemble into aggregates over an extremely narrow temperature window. In this talk, we use analytic and self-consistent field theories to explore the binding of multivalent polymers to receptors on a flat substrate. Discussion will focus on how the sequence, number, and binding strength of ligands along the polymer chain can be used to tune the superselectivity of the system. Comparison with recent experiments on model systems will be presented as time permits. We wish to thank ERC Advanced Grant 227758.

Imbibition with swelling: Capillary rise in thin deformable porous media

NASA Astrophysics Data System (ADS)

Kvick, Mathias; Martinez, D. Mark; Hewitt, Duncan R.; Balmforth, Neil J.

2017-07-01

The imbibition of a liquid into a thin deformable porous substrate driven by capillary suction is considered. The substrate is initially dry and has uniform porosity and thickness. Two-phase flow theory is used to describe how the liquid flows through the pore space behind the wetting front when out-of-plane deformation of the solid matrix is considered. Neglecting gravity and evaporation, standard shallow-layer scalings are used to construct a reduced model of the dynamics. The model predicts convergence to a self-similar behavior in all regions except near the wetting front, where a boundary layer arises whose structure narrows with the advance of the front. Over time, the rise height approaches the similarity scaling of t1 /2, as in the classical Washburn or BCLW law. The results are compared with a series of laboratory experiments using cellulose paper sheets, which provide qualitative agreement.

Bauhinia proteinase inhibitor-based synthetic fluorogenic substrates for enzymes isolated from insect midgut and caterpillar bristles.

PubMed

Andrade, Sonia A; Santomauro-Vaz, Eugênio M; Lopes, Adriana R; Chudzinski-Tavassi, Ana M; Juliano, Maria A; Terra, Walter R; Sampaio, Misako U; Sampaio, Claudio A M; Oliva, Maria Luiza V

2003-03-01

Bauhinia ungulata factor Xa inhibitor (BuXI) inactivates factor Xa and LOPAP, a prothrombin activator proteinase isolated from the venom of Lonomia obliqua caterpillar bristles. The reactive site of the enzyme-inhibitor interaction was explored to design specific substrates for both enzymes. Methionine is crucial for LOPAP and factor Xa substrate interaction, since the change of both Met residues in the substrates abolished the hydrolysis. Synthetic substrates containing the sequence around the reactive site of BbKI, a plasma kallikrein inhibitor, were shown to be specific for trypsin hydrolysis. Therefore, these substrates may be an alternative in studies aiming at a characterization of trypsin-like enzyme activities, especially non-mammalian enzymes.

Cloning and Molecular Characterization of an Alpha-Glucosidase (MalH) from the Halophilic Archaeon Haloquadratum walsbyi.

PubMed

Cuebas-Irizarry, Mara F; Irizarry-Caro, Ricardo A; López-Morales, Carol; Badillo-Rivera, Keyla M; Rodríguez-Minguela, Carlos M; Montalvo-Rodríguez, Rafael

2017-11-21

We report the heterologous expression and molecular characterization of the first extremely halophilic alpha-glucosidase (EC 3.2.1.20) from the archaeon Haloquadratum walsbyi . A 2349 bp region ( Hqrw_2071 ) from the Hqr. walsbyi C23 annotated genome was PCR-amplified and the resulting amplicon ligated into plasmid pET28b(+), expressed in E. coli Rosetta cells, and the resulting protein purified by Ni-NTA affinity chromatography. The recombinant protein showed an estimated molecular mass of 87 kDa, consistent with the expected value of the annotated protein, and an optimal activity for the hydrolysis of α-PNPG was detected at 40 °C, and at pH 6.0. Enzyme activity values were the highest in the presence of 3 M NaCl or 3-4 M KCl. However, specific activity values were two-fold higher in the presence of 3-4 M KCl when compared to NaCl suggesting a cytoplasmic localization. Phylogenetic analyses, with respect to other alpha-glucosidases from members of the class Halobacteria, showed that the Hqr. walsbyi MalH was most similar (up to 41%) to alpha-glucosidases and alpha-xylosidases of Halorubrum . Moreover, computational analyses for the detection of functional domains, active and catalytic sites, as well as 3D structural predictions revealed a close relationship with an E. coli YicI-like alpha-xylosidase of the GH31 family. However, the purified enzyme did not show alpha-xylosidase activity. This narrower substrate range indicates a discrepancy with annotations from different databases and the possibility of specific substrate adaptations of halophilic glucosidases due to high salinity. To our knowledge, this is the first report on the characterization of an alpha-glucosidase from the halophilic Archaea, which could serve as a new model to gain insights into carbon metabolism in this understudied microbial group.

Activin receptor inhibition by Smad2 regulates Drosophila wing disc patterning through BMP-response elements

PubMed Central

Peterson, Aidan J.; O'Connor, Michael B.

2013-01-01

Imaginal disc development in Drosophila requires coordinated cellular proliferation and tissue patterning. In our studies of TGFβ superfamily signaling components, we found that a protein null mutation of Smad2, the only Activin subfamily R-Smad in the fruit fly, produces overgrown wing discs that resemble gain of function for BMP subfamily signaling. The wing discs are expanded specifically along the anterior-posterior axis, with increased proliferation in lateral regions. The morphological defect is not observed in mutants for the TGFβ receptor baboon, and epistasis tests showed that baboon is epistatic to Smad2 for disc overgrowth. Rescue experiments indicate that Baboon binding, but not canonical transcription factor activity, of Smad2 is required for normal disc growth. Smad2 mutant discs generate a P-Mad stripe that is narrower and sharper than the normal gradient, and activation targets are correspondingly expressed in narrowed domains. Repression targets of P-Mad are profoundly mis-regulated, with brinker and pentagone reporter expression eliminated in Smad2 mutants. Loss of expression requires a silencer element previously shown to be controlled by BMP signaling. Epistasis experiments show that Baboon, Mad and Schnurri are required to mediate the ectopic silencer output in the absence of Smad2. Taken together, our results show that loss of Smad2 permits promiscuous Baboon activity, which represses genes subject to control by Mad-dependent silencer elements. The absence of Brinker and Pentagone in Smad2 mutants explains the compound wing disc phenotype. Our results highlight the physiological relevance of substrate inhibition of a kinase, and reveal a novel interplay between the Activin and BMP pathways. PMID:23293296

High resolution on-chip optical filter array based on double subwavelength grating reflectors

DOE PAGES

Horie, Yu; Arbabi, Amir; Han, Seunghoon; ...

2015-11-05

An optical filter array consisting of vertical narrow-band Fabry-Pèrot (FP) resonators formed by two highly reflective high contrast subwavelength grating mirrors is reported. The filters are designed to cover a wide range of operation wavelengths ( Δλ/λ=5%) just by changing the in-plane grating parameters while the device thickness is maintained constant. In conclusion, operation in the telecom band with transmission efficiencies greater than 40% and quality factors greater than 1,000 are measured experimentally for filters fabricated on the same substrate.

AC Loss Minimization in High Temperature Superconductors - U.K.

DTIC Science & Technology

2003-11-07

high currents in high magnetic fields. The DC properties are very attractive, but to reduce the AC losses it is necessary to use a narrow conductor... NiFe in the whole magnetic field region (goHext=0.01 T - 6 T) roughly by a factor of 2, reflecting the sample Jc(B) dependencies. Also the magnetic ...ratio of the tape, there is no visible effect in a parallel magnetic field. Hysteresis losses in metallic substrates - CeO2:Pd/ NiFe and CeO2:Pd/NiCrW

High resolution on-chip optical filter array based on double subwavelength grating reflectors

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

Horie, Yu; Arbabi, Amir; Han, Seunghoon

An optical filter array consisting of vertical narrow-band Fabry-Pèrot (FP) resonators formed by two highly reflective high contrast subwavelength grating mirrors is reported. The filters are designed to cover a wide range of operation wavelengths ( Δλ/λ=5%) just by changing the in-plane grating parameters while the device thickness is maintained constant. In conclusion, operation in the telecom band with transmission efficiencies greater than 40% and quality factors greater than 1,000 are measured experimentally for filters fabricated on the same substrate.

High-Resolution Printing of 3D Structures Using an Electrohydrodynamic Inkjet with Multiple Functional Inks.

PubMed

An, Byeong Wan; Kim, Kukjoo; Lee, Heejoo; Kim, So-Yun; Shim, Yulhui; Lee, Dae-Young; Song, Jun Yeob; Park, Jang-Ung

2015-08-05

Electrohydrodynamic-inkjet-printed high-resolution complex 3D structures with multiple functional inks are demonstrated. Printed 3D structures can have a variety of fine patterns, such as vertical or helix-shaped pillars and straight or rounded walls, with high aspect ratios (greater than ≈50) and narrow diameters (≈0.7 μm). Furthermore, the formation of freestanding, bridge-like Ag wire structures on plastic substrates suggests substantial potentials as high-precision, flexible 3D interconnects. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Insight into the substrate specificity change caused by the Y227H mutation of α-glucosidase III from the European honeybee (Apis mellifera) through molecular dynamics simulations.

PubMed

Na Ayutthaya, Pratchaya Pramoj; Chanchao, Chanpen; Chunsrivirot, Surasak

2018-01-01

Honey from the European honeybee, Apis mellifera, is produced by α-glucosidases (HBGases) and is widely used in food, pharmaceutical, and cosmetic industries. Categorized by their substrate specificities, HBGases have three isoforms: HBGase I, II and III. Previous experimental investigations showed that wild-type HBGase III from Apis mellifera (WT) preferred sucrose to maltose as a substrate, while the Y227H mutant (MT) preferred maltose to sucrose. This mutant can potentially be used for malt hydrolysis because it can efficiently hydrolyze maltose. In this work, to elucidate important factors contributing to substrate specificity of this enzyme and gain insight into how the Y227H mutation causes substrate specificity change, WT and MT homology models were constructed, and sucrose/maltose was docked into active sites of the WT and MT. AMBER14 was employed to perform three independent molecular dynamics runs for these four complexes. Based on the relative binding free energies calculated by the MM-GBSA method, sucrose is better than maltose for WT binding, while maltose is better than sucrose for MT binding. These rankings support the experimentally observed substrate specificity that WT preferred sucrose to maltose as a substrate, while MT preferred maltose to sucrose, suggesting the importance of binding affinity for substrate specificity. We also found that the Y227H mutation caused changes in the proximities between the atoms necessary for sucrose/maltose hydrolysis that may affect enzyme efficiency in the hydrolysis of sucrose/maltose. Moreover, the per-residue binding free energy decomposition results show that Y227/H227 may be a key residue for preference binding of sucrose/maltose in the WT/MT active site. Our study provides important and novel insight into the binding of sucrose/maltose in the active site of Apis mellifera HBGase III and into how the Y227H mutation leads to the substrate specificity change at the molecular level. This knowledge could be beneficial in the design of this enzyme for increased production of desired products.

A hydrodynamic microchip for formation of continuous cell chains

NASA Astrophysics Data System (ADS)

Khoshmanesh, Khashayar; Zhang, Wei; Tang, Shi-Yang; Nasabi, Mahyar; Soffe, Rebecca; Tovar-Lopez, Francisco J.; Rajadas, Jayakumar; Mitchell, Arnan

2014-05-01

Here, we demonstrate the unique features of a hydrodynamic based microchip for creating continuous chains of model yeast cells. The system consists of a disk shaped microfluidic structure, containing narrow orifices that connect the main channel to an array of spoke channels. Negative pressure provided by a syringe pump draws fluid from the main channel through the narrow orifices. After cleaning process, a thin layer of water is left between the glass substrate and the polydimethylsiloxane microchip, enabling leakage beneath the channel walls. A mechanical clamp is used to adjust the operation of the microchip. Relaxing the clamp allows leakage of liquid beneath the walls in a controllable fashion, leading to formation of a long cell chain evenly distributed along the channel wall. The unique features of the microchip are demonstrated by creating long chains of yeast cells and model 15 μm polystyrene particles along the side wall and analysing the hydrogen peroxide induced death of patterned cells.

InP Based Ternary And Quaternary Thin Film Structures On Large Areas Grown By LP-MOVPE

NASA Astrophysics Data System (ADS)

Schmitz, D.; Strauch, , G.; Jurgensen, H.; Heyen, M.; Harde, P.

1989-11-01

Using low pressure MOVPE and higher linear flow velocities high purity GalnAs/lnP and GalnAsP heterostructures can be prepared. Excellent homogeneity in thickness, composition, and doping on a 2" InP substrate can be realized by this approach for optimized conditions. The low growth rates required for the deposition of very narrow well structures are achieved by selecting reduced pressures of the group III and group V compounds used for deposition. The method yields structures with high electron mobilities of the two dimensional electron gas in the well and narrow PL (i.e. 2.2 meV for 20 nm wells) line widths, which is indicative of low impurity incorporation and abrupt heterojunctions. The observed energy shifts (up to 528 meV) demonstrate the large range of bandgap variation attainable by this method. A study of dopant incorporation shows, that Zn yields steep transitions in InGaAs.

Long-range electrostatic complementarity governs substrate recognition by human chymotrypsin C, a key regulator of digestive enzyme activation.

PubMed

Batra, Jyotica; Szabó, András; Caulfield, Thomas R; Soares, Alexei S; Sahin-Tóth, Miklós; Radisky, Evette S

2013-04-05

Human chymotrypsin C (CTRC) is a pancreatic serine protease that regulates activation and degradation of trypsinogens and procarboxypeptidases by targeting specific cleavage sites within their zymogen precursors. In cleaving these regulatory sites, which are characterized by multiple flanking acidic residues, CTRC shows substrate specificity that is distinct from that of other isoforms of chymotrypsin and elastase. Here, we report the first crystal structure of active CTRC, determined at 1.9-Å resolution, revealing the structural basis for binding specificity. The structure shows human CTRC bound to the small protein protease inhibitor eglin c, which binds in a substrate-like manner filling the S6-S5' subsites of the substrate binding cleft. Significant binding affinity derives from burial of preferred hydrophobic residues at the P1, P4, and P2' positions of CTRC, although acidic P2' residues can also be accommodated by formation of an interfacial salt bridge. Acidic residues may also be specifically accommodated in the P6 position. The most unique structural feature of CTRC is a ring of intense positive electrostatic surface potential surrounding the primarily hydrophobic substrate binding site. Our results indicate that long-range electrostatic attraction toward substrates of concentrated negative charge governs substrate discrimination, which explains CTRC selectivity in regulating active digestive enzyme levels.

Substrate Specificity and Possible Heterologous Targets of Phytaspase, a Plant Cell Death Protease.

PubMed

Galiullina, Raisa A; Kasperkiewicz, Paulina; Chichkova, Nina V; Szalek, Aleksandra; Serebryakova, Marina V; Poreba, Marcin; Drag, Marcin; Vartapetian, Andrey B

2015-10-09

Plants lack aspartate-specific cell death proteases homologous to animal caspases. Instead, a subtilisin-like serine-dependent plant protease named phytaspase shown to be involved in the accomplishment of programmed death of plant cells is able to hydrolyze a number of peptide-based caspase substrates. Here, we determined the substrate specificity of rice (Oryza sativa) phytaspase by using the positional scanning substrate combinatorial library approach. Phytaspase was shown to display an absolute specificity of hydrolysis after an aspartic acid residue. The preceding amino acid residues, however, significantly influence the efficiency of hydrolysis. Efficient phytaspase substrates demonstrated a remarkable preference for an aromatic amino acid residue in the P3 position. The deduced optimum phytaspase recognition motif has the sequence IWLD and is strikingly hydrophobic. The established pattern was confirmed through synthesis and kinetic analysis of cleavage of a set of optimized peptide substrates. An amino acid motif similar to the phytaspase cleavage site is shared by the human gastrointestinal peptide hormones gastrin and cholecystokinin. In agreement with the established enzyme specificity, phytaspase was shown to hydrolyze gastrin-1 and cholecystokinin at the predicted sites in vitro, thus destroying the active moieties of the hormones. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Structural and Kinetic Basis for Substrate Selectivity in Populus tremuloides Sinapyl Alcohol Dehydrogenase

PubMed Central

Bomati, Erin K.; Noel, Joseph P.

2005-01-01

We describe the three-dimensional structure of sinapyl alcohol dehydrogenase (SAD) from Populus tremuloides (aspen), a member of the NADP(H)-dependent dehydrogenase family that catalyzes the last reductive step in the formation of monolignols. The active site topology revealed by the crystal structure substantiates kinetic results indicating that SAD maintains highest specificity for the substrate sinapaldehyde. We also report substantial substrate inhibition kinetics for the SAD-catalyzed reduction of hydroxycinnamaldehydes. Although SAD and classical cinnamyl alcohol dehydrogenases (CADs) catalyze the same reaction and share some sequence identity, the active site topology of SAD is strikingly different from that predicted for classical CADs. Kinetic analyses of wild-type SAD and several active site mutants demonstrate the complexity of defining determinants of substrate specificity in these enzymes. These results, along with a phylogenetic analysis, support the inclusion of SAD in a plant alcohol dehydrogenase subfamily that includes cinnamaldehyde and benzaldehyde dehydrogenases. We used the SAD three-dimensional structure to model several of these SAD-like enzymes, and although their active site topologies largely mirror that of SAD, we describe a correlation between substrate specificity and amino acid substitution patterns in their active sites. The SAD structure thus provides a framework for understanding substrate specificity in this family of enzymes and for engineering new enzyme specificities. PMID:15829607

Structural and kinetic basis for substrate selectivity in Populus tremuloides sinapyl alcohol dehydrogenase.

PubMed

Bomati, Erin K; Noel, Joseph P

2005-05-01

We describe the three-dimensional structure of sinapyl alcohol dehydrogenase (SAD) from Populus tremuloides (aspen), a member of the NADP(H)-dependent dehydrogenase family that catalyzes the last reductive step in the formation of monolignols. The active site topology revealed by the crystal structure substantiates kinetic results indicating that SAD maintains highest specificity for the substrate sinapaldehyde. We also report substantial substrate inhibition kinetics for the SAD-catalyzed reduction of hydroxycinnamaldehydes. Although SAD and classical cinnamyl alcohol dehydrogenases (CADs) catalyze the same reaction and share some sequence identity, the active site topology of SAD is strikingly different from that predicted for classical CADs. Kinetic analyses of wild-type SAD and several active site mutants demonstrate the complexity of defining determinants of substrate specificity in these enzymes. These results, along with a phylogenetic analysis, support the inclusion of SAD in a plant alcohol dehydrogenase subfamily that includes cinnamaldehyde and benzaldehyde dehydrogenases. We used the SAD three-dimensional structure to model several of these SAD-like enzymes, and although their active site topologies largely mirror that of SAD, we describe a correlation between substrate specificity and amino acid substitution patterns in their active sites. The SAD structure thus provides a framework for understanding substrate specificity in this family of enzymes and for engineering new enzyme specificities.

Biophysical assays to probe the mechanical properties of the interphase cell nucleus: substrate strain application and microneedle manipulation.

PubMed

Lombardi, Maria L; Zwerger, Monika; Lammerding, Jan

2011-09-14

In most eukaryotic cells, the nucleus is the largest organelle and is typically 2 to 10 times stiffer than the surrounding cytoskeleton; consequently, the physical properties of the nucleus contribute significantly to the overall biomechanical behavior of cells under physiological and pathological conditions. For example, in migrating neutrophils and invading cancer cells, nuclear stiffness can pose a major obstacle during extravasation or passage through narrow spaces within tissues.(1) On the other hand, the nucleus of cells in mechanically active tissue such as muscle requires sufficient structural support to withstand repetitive mechanical stress. Importantly, the nucleus is tightly integrated into the cellular architecture; it is physically connected to the surrounding cytoskeleton, which is a critical requirement for the intracellular movement and positioning of the nucleus, for example, in polarized cells, synaptic nuclei at neuromuscular junctions, or in migrating cells.(2) Not surprisingly, mutations in nuclear envelope proteins such as lamins and nesprins, which play a critical role in determining nuclear stiffness and nucleo-cytoskeletal coupling, have been shown recently to result in a number of human diseases, including Emery-Dreifuss muscular dystrophy, limb-girdle muscular dystrophy, and dilated cardiomyopathy.(3) To investigate the biophysical function of diverse nuclear envelope proteins and the effect of specific mutations, we have developed experimental methods to study the physical properties of the nucleus in single, living cells subjected to global or localized mechanical perturbation. Measuring induced nuclear deformations in response to precisely applied substrate strain application yields important information on the deformability of the nucleus and allows quantitative comparison between different mutations or cell lines deficient for specific nuclear envelope proteins. Localized cytoskeletal strain application with a microneedle is used to complement this assay and can yield additional information on intracellular force transmission between the nucleus and the cytoskeleton. Studying nuclear mechanics in intact living cells preserves the normal intracellular architecture and avoids potential artifacts that can arise when working with isolated nuclei. Furthermore, substrate strain application presents a good model for the physiological stress experienced by cells in muscle or other tissues (e.g., vascular smooth muscle cells exposed to vessel strain). Lastly, while these tools have been developed primarily to study nuclear mechanics, they can also be applied to investigate the function of cytoskeletal proteins and mechanotransduction signaling.

Thin-Film Solar Cells on Polymer Substrates for Space Power

NASA Technical Reports Server (NTRS)

Hepps, A. F.; McNatt, Jeremiah; Morel, D. L.; Ferckides, C. S.; Jin, M. H.; Orbey, N.; Cushman, M.; Birkmire, R. W.; Shafarman, W. N.; Newton, R.

2004-01-01

Photovoltaic arrays have played a key role in power generation in space. The current technology will continue to evolve but is limited in the important mass specific power metric (MSP or power/weight ratio) because it is based on bulk crystal technology. Solar cells based on thin-film materials offer the promise of much higher MSP and much lower cost. However, for many space applications, a 20% or greater AM0 efficiency (eta) may be required. The leading thin-film materials, amorphous Si, CuInSe, and CdTe have seen significant advances in efficiency over the last decade but will not achieve the required efficiency in the near future. Several new technologies are herein described to maximize both device eta and MSP. We will discuss these technologies in the context of space exploration and commercialization. One novel approach involves the use of very lightweight polyimide substrates. We describe efforts to enable this advance including materials processing and device fabrication and characterization. Another approach involves stacking two cells on top of each other. These tandem devices more effectively utilize solar radiation by passing through non-absorbed longer wavelength light to a narrow-bandgap bottom cell material. Modeling of current devices in tandem format indicates that AM0 efficiencies near 20% can be achieved with potential for 25% in the near future. Several important technical issues need to be resolved to realize the benefits of lightweight technologies for solar arrays, such as: monolithic interconnects, lightweight array structures, and new ultra-light support and deployment mechanisms. Recent advances will be stressed.

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.

Computer Simulations Reveal Substrate Specificity of Glycosidic Bond Cleavage in Native and Mutant Human Purine Nucleoside Phosphorylase.

PubMed

Isaksen, Geir Villy; Hopmann, Kathrin Helen; Åqvist, Johan; Brandsdal, Bjørn Olav

2016-04-12

Purine nucleoside phosphorylase (PNP) catalyzes the reversible phosphorolysis of purine ribonucleosides and 2'-deoxyribonucleosides, yielding the purine base and (2'-deoxy)ribose 1-phosphate as products. While this enzyme has been extensively studied, several questions with respect to the catalytic mechanism have remained largely unanswered. The role of the phosphate and key amino acid residues in the catalytic reaction as well as the purine ring protonation state is elucidated using density functional theory calculations and extensive empirical valence bond (EVB) simulations. Free energy surfaces for adenosine, inosine, and guanosine are fitted to ab initio data and yield quantitative agreement with experimental data when the surfaces are used to model the corresponding enzymatic reactions. The cognate substrates 6-aminopurines (inosine and guanosine) interact with PNP through extensive hydrogen bonding, but the substrate specificity is found to be a direct result of the electrostatic preorganization energy along the reaction coordinate. Asn243 has previously been identified as a key residue providing substrate specificity. Mutation of Asn243 to Asp has dramatic effects on the substrate specificity, making 6-amino- and 6-oxopurines equally good as substrates. The principal effect of this particular mutation is the change in the electrostatic preorganization energy between the native enzyme and the Asn243Asp mutant, clearly favoring adenosine over inosine and guanosine. Thus, the EVB simulations show that this particular mutation affects the electrostatic preorganization of the active site, which in turn can explain the substrate specificity.

Unravelling the mechanisms for plant survival on gypsum soils: an analysis of the chemical composition of gypsum plants from Turkey.

PubMed

Bolukbasi, A; Kurt, L; Palacio, S

2016-03-01

Depending on their specificity to gypsum, plants can be classified as gypsophiles (gypsum exclusive) and gypsovags (non-exclusive). The former may further be segregated into wide and narrow gypsophiles, depending on the breadth of their distribution area. Narrow gypsum endemics have a putative similar chemical composition to plants non-exclusive to gypsum (i.e. gypsovags), which may indicate their similar ecological strategy as stress-tolerant plant refugees on gypsum. However, this hypothesis awaits testing in different regions of the world. We compared the chemical composition of four narrow gypsum endemics, one widely distributed gypsophile and six gypsovags from Turkey. Further, we explored the plasticity in chemical composition of Turkish gypsovags growing on high- and low-gypsum content soils. Differences were explored with multivariate analyses (RDA) and mixed models (REML). Narrow gypsum endemics segregated from gypsovags in their chemical composition according to RDAs (mainly due to higher K and ash content in the former). Nevertheless, differences were small and disappeared when different nutrients were analysed individually. All the gypsovags studied accumulated more S and ash when growing on high-gypsum than on low-gypsum soils. Similar to narrow gypsum endemics from other regions of the world, most local gypsum endemics from Turkey show a similar chemical composition to gypsovags. This may indicate a shared ecological strategy as stress-tolerant plants not specifically adapted to gypsum. Nevertheless, the narrow gypsum endemic Gypsophila parva showed a chemical composition typical of gypsum specialists, indicating that various strategies are feasible within narrowly distributed gypsophiles. © 2015 German Botanical Society and The Royal Botanical Society of the Netherlands.

Resveratrol serves as a protein-substrate interaction stabilizer in human SIRT1 activation

NASA Astrophysics Data System (ADS)

Hou, Xuben; Rooklin, David; Fang, Hao; Zhang, Yingkai

2016-11-01

Resveratrol is a natural compound found in red wine that has been suggested to exert its potential health benefit through the activation of SIRT1, a crucial member of the mammalian NAD+-dependent deacetylases. SIRT1 has emerged as an attractive therapeutic target for many aging related diseases, however, how its activity can only be activated toward some specific substrates by resveratrol has been poorly understood. Herein, by employing extensive molecular dynamics simulations as well as fragment-centric topographical mapping of binding interfaces, we have clarified current controversies in the literature and elucidated that resveratrol plays an important activation role by stabilizing SIRT1/peptide interactions in a substrate-specific manner. This new mechanism highlights the importance of the N-terminal domain in substrate recognition, explains the activity restoration role of resveratrol toward some “loose-binding” substrates of SIRT1, and has significant implications for the rational design of new substrate-specific SIRT1 modulators.

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.

Resveratrol serves as a protein-substrate interaction stabilizer in human SIRT1 activation.

PubMed

Hou, Xuben; Rooklin, David; Fang, Hao; Zhang, Yingkai

2016-11-30

Resveratrol is a natural compound found in red wine that has been suggested to exert its potential health benefit through the activation of SIRT1, a crucial member of the mammalian NAD + -dependent deacetylases. SIRT1 has emerged as an attractive therapeutic target for many aging related diseases, however, how its activity can only be activated toward some specific substrates by resveratrol has been poorly understood. Herein, by employing extensive molecular dynamics simulations as well as fragment-centric topographical mapping of binding interfaces, we have clarified current controversies in the literature and elucidated that resveratrol plays an important activation role by stabilizing SIRT1/peptide interactions in a substrate-specific manner. This new mechanism highlights the importance of the N-terminal domain in substrate recognition, explains the activity restoration role of resveratrol toward some "loose-binding" substrates of SIRT1, and has significant implications for the rational design of new substrate-specific SIRT1 modulators.

Engineering the substrate specificity of the DhbE adenylation domain by yeast cell surface display.

PubMed

Zhang, Keya; Nelson, Kathryn M; Bhuripanyo, Karan; Grimes, Kimberly D; Zhao, Bo; Aldrich, Courtney C; Yin, Jun

2013-01-24

The adenylation (A) domains of nonribosomal peptide synthetases (NRPSs) activate aryl acids or amino acids to launch their transfer through the NRPS assembly line for the biosynthesis of many medicinally important natural products. In order to expand the substrate pool of NRPSs, we developed a method based on yeast cell surface display to engineer the substrate specificities of the A-domains. We acquired A-domain mutants of DhbE that have 11- and 6-fold increases in k(cat)/K(m) with nonnative substrates 3-hydroxybenzoic acid and 2-aminobenzoic acid, respectively and corresponding 3- and 33-fold decreases in k(cat)/K(m) values with the native substrate 2,3-dihydroxybenzoic acid, resulting in a dramatic switch in substrate specificity of up to 200-fold. Our study demonstrates that yeast display can be used as a high throughput selection platform to reprogram the "nonribosomal code" of A-domains. Copyright © 2013 Elsevier Ltd. All rights reserved.

Substrate-Driven Mapping of the Degradome by Comparison of Sequence Logos

PubMed Central

Fuchs, Julian E.; von Grafenstein, Susanne; Huber, Roland G.; Kramer, Christian; Liedl, Klaus R.

2013-01-01

Sequence logos are frequently used to illustrate substrate preferences and specificity of proteases. Here, we employed the compiled substrates of the MEROPS database to introduce a novel metric for comparison of protease substrate preferences. The constructed similarity matrix of 62 proteases can be used to intuitively visualize similarities in protease substrate readout via principal component analysis and construction of protease specificity trees. Since our new metric is solely based on substrate data, we can engraft the protease tree including proteolytic enzymes of different evolutionary origin. Thereby, our analyses confirm pronounced overlaps in substrate recognition not only between proteases closely related on sequence basis but also between proteolytic enzymes of different evolutionary origin and catalytic type. To illustrate the applicability of our approach we analyze the distribution of targets of small molecules from the ChEMBL database in our substrate-based protease specificity trees. We observe a striking clustering of annotated targets in tree branches even though these grouped targets do not necessarily share similarity on protein sequence level. This highlights the value and applicability of knowledge acquired from peptide substrates in drug design of small molecules, e.g., for the prediction of off-target effects or drug repurposing. Consequently, our similarity metric allows to map the degradome and its associated drug target network via comparison of known substrate peptides. The substrate-driven view of protein-protein interfaces is not limited to the field of proteases but can be applied to any target class where a sufficient amount of known substrate data is available. PMID:24244149

Cyclooxygenase Reaction Mechanism of PGHS ------- Evidence for a Reversible Transition between a Pentadienyl Radical and a New Tyrosyl Radical by Nitric Oxide Trapping

PubMed Central

Lü, Jian-Ming; Rogge, Corina E.; Wu, Gang; Kulmacz, Richard J.; van der Donk, Wilfred A.; Tsai, Ah-lim

2011-01-01

Incubation of prostaglandin H synthase-1 (PGHS-1) under anaerobic conditions with peroxide and arachidonic acid leads to two major radical species: a pentadienyl radical and a radical with a narrow EPR spectrum. The proportions of the two radicals are sensitive to temperature, favoring the narrow radical species at 22 °C. The EPR characteristics of this latter radical are somewhat similar to the previously reported narrow-singlet tyrosine radical NS1a and are insensitive to deuterium labeling of AA. To probe the origin and structure of this radical, we combined EPR analysis with nitric oxide (NO) trapping of tyrosine and substrate derived radicals for both PGHS-1 and -2. Formation of 3-nitrotyrosine in the proteins was analyzed by immunoblotting, whereas NO adducts to AA and AA metabolites were analyzed by mass spectrometry and by chromatography of 14C-labeled products. The results indicate that both nitrated tyrosine residues and NO-AA adducts formed upon NO trapping. The NO-AA adduct was predominantly an oxime at C11 of AA with three conjugated double bonds, as indicated by absorption at 275 nm and by mass spectral analysis. This adduct amounted to 10% and 20% of the heme concentration of PGHS-1 and -2, respectively. For PGHS-1, the yield of NO-AA adduct matched the yield of the narrow radical signal obtained in parallel EPR experiments. High frequency EPR characterization of this narrow radical, reported in an accompanying paper, supports assignment to a new tyrosyl radical, NS1c, rather than an AA-based radical. To reconcile the results from EPR and NO-trapping studies, we propose that the NS1c is in equilibrium with an AA pentadienyl radical, and that the latter reacts preferentially with NO. PMID:21403766

Lightweight Electrode For Nickel/Hydrogen Cell

NASA Technical Reports Server (NTRS)

Britton, Doris L.

1994-01-01

Improved substrate for nickel electrode increases specific energy of nickel/hydrogen cell. Consists of 50 percent by weight nickel fiber, 35 percent nickel powder, and 15 percent cobalt powder. Porosity and thickness of nickel electrodes affect specific energy, initial performance, and cycle life of cell. Substrate easily manufactured with much larger porosities than those of heavy-sintered state-of-art nickel substrate.

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

Crosby, Heidi A; Pelletier, Dale A; Hurst, Gregory

Background: Protein acetylation is widespread in prokaryotes. Results: Six new acyl-CoA synthetases whose activities are controlled by acetylation were identified, and their substrate preference established. A new protein acetyltransferase was also identified and its substrate specificity determined. Conclusion: Protein acetyltransferases acetylate a conserved lysine residue in protein substrates. Significance: The R. palustris Pat enzyme specifically acetylates AMP-forming acyl-CoA synthetases and regulates fatty acid metabolism.

Designing PolyHEMA Substrates that Mimic the Viscoelastic Response of Soft Tissue

PubMed Central

Holt, Brian; Tripathi, Anubhav; Morgan, Jeffrey R.

2011-01-01

Matching the mechanical properties of a biomaterial to soft tissue is often overlooked despite the fact that it’s well known that cells respond to and are capable of changing their mechanical environment. In this paper, we used NaCl and alginate beads as porogens to make a series of micro- and macro-porous pHEMA substrates [poly(2-hydroxyethly methacrylate)] and quantified their mechanical behavior under low-magnitude shear loads over physiologically relevant frequencies. Using a stress-controlled rheometer, we performed isothermal (37°C) frequency response experiments between 0.628 and 75.4 rad/s [0.01–12Hz] at 0.1% strain. Both micro- and macro-porous pHEMA substrates were predominately elastic in nature with a narrow range of G′ and G″ values that mimicked the response of human skin. The magnitude of the G′ and G″ values of the macro-porous substrates were designed to closely match human skin. To determine how cell growth might alter their mechanical properties, pHEMA substrates were functionalized and human skin fibroblasts grown on them for fourteen days. As a result of cell growth, the magnitude of G′ and G″ increased at low frequencies while also altering the degree of high frequency dependence, indicating that cellular interactions with the micro-pore infrastructure has a profound effect on the viscoelastic behavior of the substrates. These data could be fit to a mathematical model describing a soft solid. A quantitative understanding of the mechanical behavior of biomaterials in regimes that are physiologically relevant and how these mechanics may change after implantation may aid in the design of new materials. PMID:21496821

Accretion Rate: An Axis Of Agn Unification

NASA Astrophysics Data System (ADS)

Trump, Jonathan R.; Impey, C. D.; Kelly, B. C.

2011-01-01

We show how accretion rate governs the physical properties of broad-line, narrow-line, and lineless active galactic nuclei (AGNs). We avoid the systematic errors plaguing previous studies of AGN accretion rate by using accurate accretion luminosities from well-sampled multiwavelength SEDs from the Cosmic Evolution Survey (COSMOS), and accurate black hole masses derived from virial scaling relations (for broad-line AGNs) or host-AGN relations (for narrow-line and lineless AGNs). In general, broad emission lines are present only at the highest accretion rates (L/L_Edd>0.01), and these rapidly accreting AGNs are observed as broad-line AGNs or possibly as obscured narrow-line AGNs. Narrow-line and lineless AGNs at lower specific accretion rates (L/L_Edd<0.01) are unobscured and yet lack a broad line region. The disappearance of the broad emission lines is caused by an expanding radiatively inefficient accretion flow (RIAF) at the inner radius of the accretion disk. The presence of the RIAF also drives L/L_Edd<0.01 narrow-line and lineless AGNs to be 10-100 times more radio-luminous than broad-line AGNs, since the unbound nature of the RIAF means it is easier to form a radio outflow. The IR torus signature also tends to become weaker or disappear from L/L_Edd<0.01 AGNs, although there may be additional mid-IR synchrotron emission associated with the RIAF. Together these results suggest that specific accretion rate is an important physical "axis" of AGN unification, described by a simple model.

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

PubMed

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

2012-08-31

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

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

PubMed Central

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

2012-01-01

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

PnuC and the utilization of the nicotinamide riboside analog 3-aminopyridine in Haemophilus influenzae.

PubMed

Sauer, Elizabeta; Merdanovic, Melisa; Mortimer, Anne Price; Bringmann, Gerhard; Reidl, Joachim

2004-12-01

The utilization pathway for the uptake of NAD and nicotinamide riboside was previously characterized for Haemophilus influenzae. We now report on the cellular location, topology, and substrate specificity of PnuC. pnuC of H. influenzae is only distantly related to pnuC of Escherichia coli and Salmonella enterica serovar Typhimurium. When E. coli PnuC was expressed in an H. influenzae pnuC mutant, it was able to take up only nicotinamide riboside and not nicotinamide mononucleotide. Therefore, we postulated that PnuC transporters in general possess specificity for nicotinamide riboside. Earlier studies showed that 3-aminopyridine derivatives (e.g., 3-aminopyridine adenine dinucleotide) are inhibitory for H. influenzae growth. By testing characterized strains with mutations in the NAD utilization pathway, we show that 3-aminopyridine riboside is inhibitory to H. influenzae and is taken up by the NAD-processing and nicotinamide riboside route. 3-Aminopyridine riboside is utilized effectively in a pnuC+ background. In addition, we demonstrate that 3-aminopyridine adenine dinucleotide resynthesis is produced by NadR. 3-Aminopyridine riboside-resistant H. influenzae isolates were characterized, and mutations in nadR could be detected. We also tested other species of the family Pasteurellaceae, Pasteurella multocida and Actinobacillus actinomycetemcomitans, and found that 3-aminopyridine riboside does not act as a growth inhibitor; hence, 3-aminopyridine riboside represents an anti-infective agent with a very narrow host range.

LUGOL'S IODINE CHROMOENDOSCOPY VERSUS NARROW BAND IMAGE ENHANCED ENDOSCOPY FOR THE DETECTION OF ESOPHAGEAL CANCER IN PATIENTS WITH STENOSIS SECONDARY TO CAUSTIC/CORROSIVE AGENT INGESTION.

PubMed

Pennachi, Caterina Maria Pia Simoni; Moura, Diogo Turiani Hourneaux de; Amorim, Renato Bastos Pimenta; Guedes, Hugo Gonçalo; Kumbhari, Vivek; Moura, Eduardo Guimarães Hourneaux de

2017-01-01

The diagnosis of corrosion cancer should be suspected in patients with corrosive ingestion if after a latent period of negligible symptoms there is development of dysphagia, or poor response to dilatation, or if respiratory symptoms develop in an otherwise stable patient of esophageal stenosis. Narrow Band Imaging detects superficial squamous cell carcinoma more frequently than white-light imaging, and has significantly higher sensitivity and accuracy compared with white-light. To determinate the clinical applicability of Narrow Band Imaging versus Lugol´s solution chromendoscopy for detection of early esophageal cancer in patients with caustic/corrosive agent stenosis. Thirty-eight patients, aged between 28-84 were enrolled and examined by both Narrow Band Imaging and Lugol´s solution chromendoscopy. A 4.9mm diameter endoscope was used facilitating examination of a stenotic area without dilation. Narrow Band Imaging was performed and any lesion detected was marked for later biopsy. Then, Lugol´s solution chromoendoscopy was performed and biopsies were taken at suspicious areas. Patients who had abnormal findings at the routine, Narrow Band Imaging or Lugol´s solution chromoscopy exam had their stenotic ring biopsied. We detected nine suspicious lesions with Narrow Band Imaging and 14 with Lugol´s solution chromendoscopy. The sensitivity and specificity of the Narrow Band Imaging was 100% and 80.6%, and with Lugol´s chromoscopy 100% and 66.67%, respectively. Five (13%) suspicious lesions were detected both with Narrow Band Imaging and Lugol's chromoscopy, two (40%) of these lesions were confirmed carcinoma on histopathological examination. Narrow Band Imaging is an applicable option to detect and evaluate cancer in patients with caustic /corrosive stenosis compared to the Lugol´s solution chromoscopy.

Selectively Plasmon-Enhanced Second-Harmonic Generation from Monolayer Tungsten Diselenide on Flexible Substrates.

PubMed

Wang, Zhuo; Dong, Zhaogang; Zhu, Hai; Jin, Lei; Chiu, Ming-Hui; Li, Lain-Jong; Xu, Qing-Hua; Eda, Goki; Maier, Stefan A; Wee, Andrew T S; Qiu, Cheng-Wei; Yang, Joel K W

2018-02-27

Monolayer two-dimensional transition-metal dichalcogenides (2D TMDCs) exhibit promising characteristics in miniaturized nonlinear optical frequency converters, due to their inversion asymmetry and large second-order nonlinear susceptibility. However, these materials usually have very short light interaction lengths with the pump laser because they are atomically thin, such that second-harmonic generation (SHG) is generally inefficient. In this paper, we fabricate a judiciously structured 150 nm-thick planar surface consisting of monolayer tungsten diselenide and sub-20 nm-wide gold trenches on flexible substrates, reporting ∼7000-fold SHG enhancement without peak broadening or background in the spectra as compared to WSe 2 on as-grown sapphire substrates. Our proof-of-concept experiment yields effective second-order nonlinear susceptibility of 2.1 × 10 4 pm/V. Three orders of magnitude enhancement is maintained with pump wavelength ranging from 800 to 900 nm, breaking the limitation of narrow pump wavelength range for cavity-enhanced SHG. In addition, SHG amplitude can be dynamically controlled via selective excitation of the lateral gap plasmon by rotating the laser polarization. Such a fully open, flat, and ultrathin profile enables a great variety of functional samples with high SHG from one patterned silicon substrate, favoring scalable production of nonlinear converters. The surface accessibility also enables integration with other optical components for information processing in an ultrathin and flexible form.

Highly Efficient Antibacterial Surfaces Based on Bacterial/Cell Size Selective Microporous Supports.

PubMed

Vargas-Alfredo, Nelson; Santos-Coquillat, Ana; Martínez-Campos, Enrique; Dorronsoro, Ane; Cortajarena, Aitziber L; Del Campo, Adolfo; Rodríguez-Hernández, Juan

2017-12-27

We report on the fabrication of efficient antibacterial substrates selective for bacteria, i.e., noncytotoxic against mammalian cells. The strategy proposed is based on the different size of bacteria (1-4 μm) in comparison with mammalian cells (above 20 μm) that permit the bacteria to enter in contact with the inner part of micrometer-sized pores where the antimicrobial functionality are placed. On the contrary, mammalian cells, larger in terms of size, remain at the top surface, thus reducing adverse cytotoxic effects and improving the biocompatibility of the substrates. For this purpose, we fabricated well-ordered functional microporous substrates (3-5 μm) using the breath figures approach that enabled the selective functionalization of the pore cavity, whereas the rest of the surface remained unaffected. Microporous surfaces were prepared from polymer blends comprising a homopolymer (i.e., polystyrene) and a block copolymer (either polystyrene-b-poly(dimethylaminoethyl methacrylate) (PDMAEMA) or a quaternized polystyrene-b-poly(dimethylaminoethyl methacrylate)). As a result, porous surfaces with a narrow size distribution and a clear enrichment of the PDMAEMA or the quaternized PDMAEMA block inside the pores were obtained that, in the case of the quaternized PDMAEMA, provided an excellent antimicrobial activity to the films.

Selective Binding, Self-Assembly and Nanopatterning of the Creutz-Taube Ion on Surfaces

PubMed Central

Wang, Yuliang; Lieberman, Marya; Hang, Qingling; Bernstein, Gary

2009-01-01

The surface attachment properties of the Creutz-Taube ion, i.e., [(NH3)5Ru(pyrazine)Ru(NH3)5]5+, on both hydrophilic and hydrophobic types of surfaces were investigated using X-ray photoelectron spectroscopy (XPS). The results indicated that the Creutz-Taube ions only bound to hydrophilic surfaces, such as SiO2 and –OH terminated organic SAMs on gold substrates. No attachment of the ions on hydrophobic surfaces such as –CH3 terminated organic SAMs and poly(methylmethacrylate) (PMMA) thin films covered gold or SiO2 substrates was observed. Further ellipsometric, atomic force microscopy (AFM) and time-dependent XPS studies suggested that the attached cations could form an inorganic analog of the self-assembled monolayer on SiO2 substrate with a “lying-down” orientation. The strong electrostatic interaction between the highly charged cations and the anionic SiO2 surface was believed to account for these observations. Based on its selective binding property, patterning of wide (∼200 nm) and narrow (∼35 nm) lines of the Creutz-Taube ions on SiO2 surface were demonstrated through PMMA electron resist masks written by electron beam lithography (EBL). PMID:19333420

Clinical evaluation of P-glycoprotein inhibition by venetoclax: a drug interaction study with digoxin.

PubMed

Chiney, Manoj S; Menon, Rajeev M; Bueno, Orlando F; Tong, Bo; Salem, Ahmed Hamed

2018-09-01

1. Venetoclax is a novel, small molecule B-cell lymphoma-2 (BCL-2) inhibitor that has demonstrated clinical efficacy in a variety of haematological malignancies. Since venetoclax is an inhibitor of P glycoprotein (P-gp) transporter, a study was conducted in healthy, female volunteers to evaluate the effect of venetoclax on the pharmacokinetics of digoxin, a P-gp probe substrate. 2. Volunteers received a single oral dose of digoxin (0.5 mg) with or without a single oral dose of venetoclax (100  mg). Serial blood samples were obtained for pharmacokinetic assessments of digoxin and venetoclax and serial urine samples were obtained for measurement of digoxin concentrations. Safety was assessed throughout the study. 3. Coadministration of digoxin and venetoclax increased digoxin maximum observed plasma concentration (C max ) by 35% and area under the plasma-concentration time curve (AUC 0-∞) by 9%. Digoxin half-life, renal clearance and the fraction excreted unchanged in urine remained relatively similar. The results of this study indicate that venetoclax can increase the concentrations of P-gp substrates. Narrow therapeutic index P-gp substrates should be administered six hours prior to venetoclax to minimise the potential interaction.

Growth kinetics, effect of carbon substrate in biosynthesis of mcl-PHA by Pseudomonas putida Bet001

PubMed Central

Gumel, A.M.; Annuar, M.S.M.; Heidelberg, T.

2014-01-01

Growth associated biosynthesis of medium chain length poly-3-hydroxyalkanoates (mcl-PHA) in Pseudomonas putida Bet001 isolated from palm oil mill effluent was studied. Models with substrate inhibition terms described well the kinetics of its growth. Selected fatty acids (C8:0 to C18:1) and ammonium were used as carbon and nitrogen sources during growth and PHA biosynthesis, resulting in PHA accumulation of about 50 to 69% (w/w) and PHA yields ranging from 10.12 g L−1 to 15.45 g L−1, respectively. The monomer composition of the PHA ranges from C4 to C14, and was strongly influenced by the type of carbon substrate fed. Interestingly, an odd carbon chain length (C7) monomer was also detected when C18:1 was fed. Polymer showed melting temperature (Tm) of 42.0 (± 0.2) °C, glass transition temperature (Tg) of −1.0 (± 0.2) °C and endothermic melting enthalpy of fusion (ΔHf) of 110.3 (± 0.1) J g−1. The molecular weight (Mw) range of the polymer was relatively narrow between 55 to 77 kDa. PMID:25242925

Growth kinetics, effect of carbon substrate in biosynthesis of mcl-PHA by Pseudomonas putida Bet001.

PubMed

Gumel, A M; Annuar, M S M; Heidelberg, T

2014-01-01

Growth associated biosynthesis of medium chain length poly-3-hydroxyalkanoates (mcl-PHA) in Pseudomonas putida Bet001 isolated from palm oil mill effluent was studied. Models with substrate inhibition terms described well the kinetics of its growth. Selected fatty acids (C8:0 to C18:1) and ammonium were used as carbon and nitrogen sources during growth and PHA biosynthesis, resulting in PHA accumulation of about 50 to 69% (w/w) and PHA yields ranging from 10.12 g L(-1) to 15.45 g L(-1), respectively. The monomer composition of the PHA ranges from C4 to C14, and was strongly influenced by the type of carbon substrate fed. Interestingly, an odd carbon chain length (C7) monomer was also detected when C18:1 was fed. Polymer showed melting temperature (T m) of 42.0 (± 0.2) °C, glass transition temperature (T g) of -1.0 (± 0.2) °C and endothermic melting enthalpy of fusion (ΔHf) of 110.3 (± 0.1) J g(-1). The molecular weight (M w) range of the polymer was relatively narrow between 55 to 77 kDa.

Plasmonic and silicon spherical nanoparticle antireflective coatings

NASA Astrophysics Data System (ADS)

Baryshnikova, K. V.; Petrov, M. I.; Babicheva, V. E.; Belov, P. A.

2016-03-01

Over the last decade, plasmonic antireflecting nanostructures have been extensively studied to be utilized in various optical and optoelectronic systems such as lenses, solar cells, photodetectors, and others. The growing interest to all-dielectric photonics as an alternative optical technology along with plasmonics motivates us to compare antireflective properties of plasmonic and all-dielectric nanoparticle coatings based on silver and crystalline silicon respectively. Our simulation results for spherical nanoparticles array on top of amorphous silicon show that both silicon and silver coatings demonstrate strong antireflective properties in the visible spectral range. For the first time, we show that zero reflectance from the structure with silicon coatings originates from the destructive interference of electric- and magnetic-dipole responses of nanoparticle array with the wave reflected from the substrate, and we refer to this reflection suppression as substrate-mediated Kerker effect. We theoretically compare the silicon and silver coating effectiveness for the thin-film photovoltaic applications. Silver nanoparticles can be more efficient, enabling up to 30% increase of the overall absorbance in semiconductor layer. Nevertheless, silicon coatings allow up to 64% absorbance increase in the narrow band spectral range because of the substrate-mediated Kerker effect, and band position can be effectively tuned by varying the nanoparticles sizes.

Plasmonic and silicon spherical nanoparticle antireflective coatings

PubMed Central

Baryshnikova, K. V.; Petrov, M. I.; Babicheva, V. E.; Belov, P. A.

2016-01-01

Over the last decade, plasmonic antireflecting nanostructures have been extensively studied to be utilized in various optical and optoelectronic systems such as lenses, solar cells, photodetectors, and others. The growing interest to all-dielectric photonics as an alternative optical technology along with plasmonics motivates us to compare antireflective properties of plasmonic and all-dielectric nanoparticle coatings based on silver and crystalline silicon respectively. Our simulation results for spherical nanoparticles array on top of amorphous silicon show that both silicon and silver coatings demonstrate strong antireflective properties in the visible spectral range. For the first time, we show that zero reflectance from the structure with silicon coatings originates from the destructive interference of electric- and magnetic-dipole responses of nanoparticle array with the wave reflected from the substrate, and we refer to this reflection suppression as substrate-mediated Kerker effect. We theoretically compare the silicon and silver coating effectiveness for the thin-film photovoltaic applications. Silver nanoparticles can be more efficient, enabling up to 30% increase of the overall absorbance in semiconductor layer. Nevertheless, silicon coatings allow up to 64% absorbance increase in the narrow band spectral range because of the substrate-mediated Kerker effect, and band position can be effectively tuned by varying the nanoparticles sizes. PMID:26926602

Growth and Properties of Lattice Matched GaAsSbN Epilayer on GaAs for Solar Cell Applications

NASA Technical Reports Server (NTRS)

Bharatan, Sudhakar; Iyer, Shanthi; Matney, Kevin; Collis, Ward J.; Nunna Kalyan; Li, Jia; Wu, Liangjin; McGuire, Kristopher; McNeil, Laurie E.

2006-01-01

The growth and properties of GaAsSbN single quantum wells (SQWs) are investigated in this work. The heterostructures were grown on GaAs substrates in an elemental solid source molecular beam epitaxy (MBE) system assisted with a RF plasma nitrogen source. A systematic study has been carried out to determine the influence of various growth conditions, such as the growth temperature and the source shutter-opening sequence, on the quality of the grown layers and the incorporation of N and Sb. The effects of ex situ and in situ annealing under As overpressure on the optical properties of the layers have also been investigated. Substrate temperature in the range of 450-470 C was found to be optimum. Simultaneous opening of the source shutters was found to yield sharper QW interfaces. N and Sb incorporations were found to depend strongly upon substrate temperatures and source shutter opening sequences. A significant increase in PL intensity with a narrowing of PL line shape and blue shift in emission energy were observed on annealing the GaAsSbN/GaAs SQW, with in situ annealing under As overpressure providing better results, compared to ex situ annealing.

Specificity of hammerhead ribozyme cleavage.

PubMed Central

Hertel, K J; Herschlag, D; Uhlenbeck, O C

1996-01-01

To be effective in gene inactivation, the hammerhead ribozyme must cleave a complementary RNA target without deleterious effects from cleaving non-target RNAs that contain mismatches and shorter stretches of complementarity. The specificity of hammerhead cleavage was evaluated using HH16, a well-characterized ribozyme designed to cleave a target of 17 residues. Under standard reaction conditions, HH16 is unable to discriminate between its full-length substrate and 3'-truncated substrates, even when six fewer base pairs are formed between HH16 and the substrate. This striking lack of specificity arises because all the substrates bind to the ribozyme with sufficient affinity so that cleavage occurs before their affinity differences are manifested. In contrast, HH16 does exhibit high specificity towards certain 3'-truncated versions of altered substrates that either also contain a single base mismatch or are shortened at the 5' end. In addition, the specificity of HH16 is improved in the presence of p7 nucleocapsid protein from human immunodeficiency virus (HIV)-1, which accelerates the association and dissociation of RNA helices. These results support the view that the hammerhead has an intrinsic ability to discriminate against incorrect bases, but emphasizes that the high specificity is only observed in a certain range of helix lengths. Images PMID:8670879

Long-range Electrostatic Complementarity Governs Substrate Recognition by Human Chymotrypsin C, a Key Regulator of Digestive Enzyme Activation*

PubMed Central

Batra, Jyotica; Szabó, András; Caulfield, Thomas R.; Soares, Alexei S.; Sahin-Tóth, Miklós; Radisky, Evette S.

2013-01-01

Human chymotrypsin C (CTRC) is a pancreatic serine protease that regulates activation and degradation of trypsinogens and procarboxypeptidases by targeting specific cleavage sites within their zymogen precursors. In cleaving these regulatory sites, which are characterized by multiple flanking acidic residues, CTRC shows substrate specificity that is distinct from that of other isoforms of chymotrypsin and elastase. Here, we report the first crystal structure of active CTRC, determined at 1.9-Å resolution, revealing the structural basis for binding specificity. The structure shows human CTRC bound to the small protein protease inhibitor eglin c, which binds in a substrate-like manner filling the S6-S5′ subsites of the substrate binding cleft. Significant binding affinity derives from burial of preferred hydrophobic residues at the P1, P4, and P2′ positions of CTRC, although acidic P2′ residues can also be accommodated by formation of an interfacial salt bridge. Acidic residues may also be specifically accommodated in the P6 position. The most unique structural feature of CTRC is a ring of intense positive electrostatic surface potential surrounding the primarily hydrophobic substrate binding site. Our results indicate that long-range electrostatic attraction toward substrates of concentrated negative charge governs substrate discrimination, which explains CTRC selectivity in regulating active digestive enzyme levels. PMID:23430245

Substrate specificity of xenobiotic metabolizing esterases in the liver of two catfish species

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

Jaiswal, R.G.; Huang, T.L.; Obih, P.O.

1994-12-31

The preliminary studies were conducted on the characterization of substrate specificity in the liver microsomes and cytosol of two catfish species, Ictalurus punctatus and Ictalurus natalie. A series of five esters of p-nitrophenol were used as calorimetric substrates to assay the carboxylesterases. The substrate specificity of liver microsomal and cytosolic carboxylesterases were remarkably different from each other. The valerate ester of p-nitrophenol was most rapidly hydrolyzed by the microsomal carboxylesterases, whereas the prioponate ester was the best substrate for cytosolic carboxylesterases. The Ictalurus natalie catfish species were obtained from the Devil Swamp site of the Mississippi River Basin which ismore » known to be heavily contaminated with toxic and hazardous industrial wastes. These results will be discussed in relation to the responses of xenobiotic metabolizing esterases to environmental pollutants and their possible use as biomarkers.« less

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

PubMed Central

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

2012-01-01

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

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.

Critical Amino Acids in the Active Site of Meprin Metalloproteinases for Substrate and Peptide Bond Specificity*

PubMed Central

Villa, James P.; Bertenshaw, Greg P.; Bond, Judith S.

2008-01-01

SUMMARY The protease domains of the evolutionarily-related α and ß subunits of meprin metalloproteases are approximately 55% identical at the amino acid level, however, their substrate and peptide bond specificities differ markedly. The meprin ß subunit favors acidic residues proximal to the scissile bond, while the α subunit prefers small or aromatic amino acids flanking the scissile bond. Thus gastrin, a peptide that contains a string of five Glu residues, is an excellent substrate for meprin ß while it is not hydrolyzed by meprin α. Work herein aimed to identify critical amino acids in the meprin active sites that determine the substrate specificity differences. Sequence alignments and homology models, based on the crystal structure of the crayfish astacin, showed electrostatic differences within the meprin active sites. Site-directed mutagenesis of active site residues demonstrated that replacement of a hydrophobic residue by a basic amino acid enabled the meprin α protease to cleave gastrin. The meprin αY199K mutant was most effective; the corresponding mutation of meprin ßK185Y resulted in decreased activity toward gastrin. Peptide cleavage site determinations and kinetic analyses using a variety of peptides extended evidence that meprin αTyr199/ßLys185 are substrate specificity determinants in meprin active sites. These studies shed light on the molecular basis for the substrate specificity differences of astacin metalloproteinases. PMID:12888571

Computational Study on Substrate Specificity of a Novel Cysteine Protease 1 Precursor from Zea mays

PubMed Central

Liu, Huimin; Chen, Liangcheng; Li, Quan; Zheng, Mingzhu; Liu, Jingsheng

2014-01-01

Cysteine protease 1 precursor from Zea mays (zmCP1) is classified as a member of the C1A family of peptidases (papain-like cysteine protease) in MEROPS (the Peptidase Database). The 3D structure and substrate specificity of the zmCP1 is still unknown. This study is the first one to build the 3D structure of zmCP1 by computer-assisted homology modeling. In order to determine the substrate specificity of zmCP1, docking study is used for rapid and convenient analysis of large populations of ligand–enzyme complexes. Docking results show that zmCP1 has preference for P1 position and P2 position for Arg and a large hydrophobic residue (such as Phe). Gly147, Gly191, Cys189, and Asp190 are predicted to function as active residues at the S1 subsite, and the S2 subsite contains Leu283, Leu193, Ala259, Met194, and Ala286. SIFt results indicate that Gly144, Arg268, Trp308, and Ser311 play important roles in substrate binding. Then Molecular Mechanics-Poisson-Boltzmann Surface Area (MM-PBSA) method was used to explain the substrate specificity for P1 position of zmCp1. This study provides insights into the molecular basis of zmCP1 activity and substrate specificity. PMID:24921705

A multiwell format assay for heparanase.

PubMed

Behzad, Farhad; Brenchley, Paul E C

2003-09-15

This assay employs a biotinylated heparan sulfate glycosaminoglycan (HSGAG) substrate that is covalently linked to the surface of 96-well immunoassay plates. The ratio of biotin:HSGAG and the coating concentration of substrate bound to the wells have been optimized and allow removal of biotin HSGAG within 60 min of incubation at 37 degrees C in assay buffer with a standard dilution of bacterial heparitinase or platelet heparanase. Loss of biotin signal from the well surface is detected on incubation with peroxidase-streptavidin followed by color development using 3,3',5,5'-tetramethylbenzidine as the peroxidase substrate. The new assay allows specific detection of heparanase activity in multiple samples in a total time of 3 h including a 1-h substrate digestion step and is a significant improvement with regard to sensitivity, specificity, and ease of handling of multiple samples compared to other described assays. Heparanase specifically degrades the biotinylated HSGAG substrate, when used with an optimized assay buffer. A range of enzymes including collagenase, trypsin, plasmin, pepsin, chondroitinases, hyaluronidase, and neuraminidase show no effect on the substrate under optimized assay conditions. The covalent linkage of the substrate to the well prevents leaching of substrate and allows preparation and long-term storage of substrate-coated plates. The assay can be used to detect heparanase levels in clinical samples and cell culture supernatants and is ideal as a screening method for antagonists of enzyme activity.

Nanoengineered Polystyrene Surfaces with Nanopore Array Pattern Alters Cytoskeleton Organization and Enhances Induction of Neural Differentiation of Human Adipose-Derived Stem Cells.

PubMed

Jung, Ae Ryang; Kim, Richard Y; Kim, Hyung Woo; Shrestha, Kshitiz Raj; Jeon, Seung Hwan; Cha, Kyoung Je; Park, Yong Hyun; Kim, Dong Sung; Lee, Ji Youl

2015-07-01

Human adipose-derived stem cells (hADSCs) can differentiate into various cell types depending on chemical and topographical cues. One topographical cue recently noted to be successful in inducing differentiation is the nanoengineered polystyrene surface containing nanopore array-patterned substrate (NP substrate), which is designed to mimic the nanoscale topographical features of the extracellular matrix. In this study, efficacies of NP and flat substrates in inducing neural differentiation of hADSCs were examined by comparing their substrate-cell adhesion rates, filopodia growth, nuclei elongation, and expression of neural-specific markers. The polystyrene nano Petri dishes containing NP substrates were fabricated by a nano injection molding process using a nickel electroformed nano-mold insert (Diameter: 200 nm. Depth of pore: 500 nm. Center-to-center distance: 500 nm). Cytoskeleton and filopodia structures were observed by scanning electron microscopy and F-actin staining, while cell adhesion was tested by vinculin staining after 24 and 48 h of seeding. Expression of neural specific markers was examined by real-time quantitative polymerase chain reaction and immunocytochemistry. Results showed that NP substrates lead to greater substrate-cell adhesion, filopodia growth, nuclei elongation, and expression of neural specific markers compared to flat substrates. These results not only show the advantages of NP substrates, but they also suggest that further study into cell-substrate interactions may yield great benefits for biomaterial engineering.

Visual cues for woodpeckers: light reflectance of decayed wood varies by decay fungus

USGS Publications Warehouse

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

2018-01-01

The appearance of wood substrates is likely relevant to bird species with life histories that require regular interactions with wood for food and shelter. Woodpeckers detect decayed wood for cavity placement or foraging, and some species may be capable of detecting trees decayed by specific fungi; however, a mechanism allowing for such specificity remains unidentified. We hypothesized that decay fungi associated with woodpecker cavity sites alter the substrate reflectance in a species-specific manner that is visually discriminable by woodpeckers. We grew 10 species of wood decay fungi from pure cultures on sterile wood substrates of 3 tree species. We then measured the relative reflectance spectra of decayed and control wood wafers and compared them using the receptor noise-limited (RNL) color discrimination model. The RNL model has been used in studies of feather coloration, egg shells, flowers, and fruit to model how the colors of objects appear to birds. Our analyses indicated 6 of 10 decayed substrate/control comparisons were above the threshold of discrimination (i.e., indicating differences discriminable by avian viewers), and 12 of 13 decayed substrate comparisons were also above threshold for a hypothetical woodpecker. We conclude that woodpeckers should be capable of visually detecting decayed wood on trees where bark is absent, and they should also be able to detect visually species-specific differences in wood substrates decayed by fungi used in this study. Our results provide evidence for a visual mechanism by which woodpeckers could identify and select substrates decayed by specific fungi, which has implications for understanding ecologically important woodpecker–fungus interactions.

Substrate specificity effects of lipoxygenase products and inhibitors on soybean lipoxygenase-1.

PubMed

Wecksler, Aaron T; Garcia, Natalie K; Holman, Theodore R

2009-09-15

Recently, it has been shown that lipoxygenase (LO) products affect the substrate specificity of human 15-LO. In the current paper, we demonstrate that soybean LO-1 (sLO-1) is not affected by its own products, however, inhibitors which bind the allosteric site, oleyl sulfate (OS) and palmitoleyl sulfate (PS), not only lower catalytic activity, but also change the substrate specificity, by increasing the arachidonic acid (AA)/linoleic acid (LA) ratio to 4.8 and 4.0, respectively. The fact that LO inhibitors can lower activity and also change the LO product ratio is a new concept in lipoxygenase inhibition, where the goal is to not only reduce the catalytic activity but also alter substrate selectivity towards a physiologically beneficial product.

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

PubMed Central

Campbell, T B; Cech, T R

1995-01-01

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

Bio-inspired in situ growth of monolayer silver nanoparticles on graphene oxide paper as multifunctional substrate

NASA Astrophysics Data System (ADS)

Li, Shi-Kuo; Yan, You-Xian; Wang, Jin-Long; Yu, Shu-Hong

2013-11-01

In this study, we report a facile bio-inspired method for large-scale preparation of highly dispersed Ag nanoparticles (NPs) on the surface of flexible reduced graphene oxide (rGO) paper with using dopamine (DA) both as a reductant and a surface modifier. Through the self-polymerization of dopamine, free-standing GO paper can be simultaneously reduced and modified with following in situ growth of monolayer Ag NPs on such a substrate. The spherical Ag NPs with an average diameter of 80 nm have a narrow size distribution and tunable cover density. Such a flexible rGO/Ag hybrid paper presents enhanced antibacterial activity against E. coli and a high active and sensitive SERS response toward Rhodamine 6G (R6G) molecules. The detection signals can be obtained while the R6G concentration is as low as to 10-8 M. This work provides a simple strategy for large-scale fabrication of monolayer Ag NPs on flexible rGO paper as a portable antibacterial substrate and a potential SERS substrate for molecular detection applications.In this study, we report a facile bio-inspired method for large-scale preparation of highly dispersed Ag nanoparticles (NPs) on the surface of flexible reduced graphene oxide (rGO) paper with using dopamine (DA) both as a reductant and a surface modifier. Through the self-polymerization of dopamine, free-standing GO paper can be simultaneously reduced and modified with following in situ growth of monolayer Ag NPs on such a substrate. The spherical Ag NPs with an average diameter of 80 nm have a narrow size distribution and tunable cover density. Such a flexible rGO/Ag hybrid paper presents enhanced antibacterial activity against E. coli and a high active and sensitive SERS response toward Rhodamine 6G (R6G) molecules. The detection signals can be obtained while the R6G concentration is as low as to 10-8 M. This work provides a simple strategy for large-scale fabrication of monolayer Ag NPs on flexible rGO paper as a portable antibacterial substrate and a potential SERS substrate for molecular detection applications. Electronic supplementary information (ESI) available: Preparation of GO aqueous colloid solution; XPS spectra of GO paper and PDA modified rGO paper; SEM images of rGO/Ag hybrid paper after immersed in mercaptoethanol solution or in high alkaline solution; photograph and SEM image of pure rGO paper after reaction with AgNO3 solution. SEM image and TEM graph of the pre-synthesized Ag NPs and their SEM images incubated with PDA modified rGO paper; SERS spectra of R6G (1.0 × 10-4 M) molecules before and after cleaning with concentrated hydrochloric acid liquid taken on rGO/Ag hybrid paper obtained by a reaction with 1.0 M AgNO3 solution; SERS spectra of R6G (1.0 × 10-4 M) molecules with different reusable cycles taken on rGO/Ag hybrid paper obtained by a reaction with 1.0 M AgNO3 solution; comparison between different kinds of substrates with the detection limit toward R6G. See DOI: 10.1039/c3nr03857b

Effect of ferromagnetic exchange field on band gap and spin polarisation of graphene on a TMD substrate

NASA Astrophysics Data System (ADS)

Goswami, Partha

2018-03-01

We calculate the electronic band dispersion of graphene monolayer on a two-dimensional transition metal dichalcogenide substrate (GrTMD) around K and K^' } points by taking into account the interplay of the ferromagnetic impurities and the substrate-induced interactions. The latter are (strongly enhanced) intrinsic spin-orbit interaction (SOI), the extrinsic Rashba spin-orbit interaction (RSOI) and the one related to the transfer of the electronic charge from graphene to substrate. We introduce exchange field ( M) in the Hamiltonian to take into account the deposition of magnetic impurities on the graphene surface. The cavalcade of the perturbations yield particle-hole symmetric band dispersion with an effective Zeeman field due to the interplay of the substrate-induced interactions with RSOI as the prime player. Our graphical analysis with extremely low-lying states strongly suggests the following: The GrTMDs, such as graphene on WY2, exhibit (direct) band-gap narrowing / widening (Moss-Burstein (MB) gap shift) including the increase in spin polarisation ( P) at low temperature due to the increase in the exchange field ( M) at the Dirac points. The polarisation is found to be electric field tunable as well. Finally, there is anticrossing of non-parabolic bands with opposite spins, the gap closing with same spins, etc. around the Dirac points. A direct electric field control of magnetism at the nanoscale is needed here. The magnetic multiferroics, like BiFeO3 (BFO), are useful for this purpose due to the coupling between the magnetic and electric order parameters.

Effect of oxidation of the non-catalytic β-propeller domain on the substrate specificity of prolyl oligopeptidase from Pleurotus eryngii.

PubMed

Tokai, Shota; Bito, Tomohiro; Shimizu, Katsuhiko; Arima, Jiro

2017-05-27

Enzymes belonging to the S9 family of prolyl oligopeptidases are of interest because of their pharmacological importance and have a non-catalytic β-propeller domain. In this study, we found that the oxidation of Met203, which lies on surface of the β-propeller domain, leads to change in the substrate specificity of eryngase, an enzyme from Pleurotus eryngii and a member of the S9 family of prolyl oligopeptidases. The activity of eryngase for L-Phe-p-nitroanilide was maintained following hydrogen peroxide treatment but was dramatically reduced for other p-nitroanilide substrates. MALDI-TOF MS analysis using tryptic peptides of eryngase indicated that the change in substrate specificity was triggered by oxidizing Met203 to methionine sulfoxide. In addition, mutations of Met203 to smaller residues provided specificities similar to those observed following oxidation of the wild-type enzyme. Substitution of Met203 with Phe significantly decreased activity, indicating that Met203 may be involved in substrate gating. Copyright © 2017 Elsevier Inc. All rights reserved.

Photometric Signatures of Starbursts in Interacting Galaxies and the Butcher-Oemler Effect

NASA Technical Reports Server (NTRS)

Rakos, Karl D.; Maindl, Thomas I.; Schombert, James M.

1996-01-01

This paper presents new and synthetic narrow band photometry of ellipticals, spirals, Seyferts and interacting galaxies in an attempt to identify the cause of the unusually high fraction of blue cluster galaxies in distant clusters (the Butcher-Oemler Effect). The properties and distribution of the low redshift sample specifically points to starbursts as the origin of the blue narrow band colors in interacting Arp galaxies.

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

Prospective CO 2 saline resource estimation methodology: Refinement of existing US-DOE-NETL methods based on data availability

DOE PAGES

Goodman, Angela; Sanguinito, Sean; Levine, Jonathan S.

2016-09-28

Carbon storage resource estimation in subsurface saline formations plays an important role in establishing the scale of carbon capture and storage activities for governmental policy and commercial project decision-making. Prospective CO 2 resource estimation of large regions or subregions, such as a basin, occurs at the initial screening stages of a project using only limited publicly available geophysical data, i.e. prior to project-specific site selection data generation. As the scale of investigation is narrowed and selected areas and formations are identified, prospective CO 2 resource estimation can be refined and uncertainty narrowed when site-specific geophysical data are available. Here, wemore » refine the United States Department of Energy – National Energy Technology Laboratory (US-DOE-NETL) methodology as the scale of investigation is narrowed from very large regional assessments down to selected areas and formations that may be developed for commercial storage. In addition, we present a new notation that explicitly identifies differences between data availability and data sources used for geologic parameters and efficiency factors as the scale of investigation is narrowed. This CO 2 resource estimation method is available for screening formations in a tool called CO 2-SCREEN.« less

Weak Broadband Electromagnetic Fields are More Disruptive to Magnetic Compass Orientation in a Night-Migratory Songbird (Erithacus rubecula) than Strong Narrow-Band Fields

PubMed Central

Schwarze, Susanne; Schneider, Nils-Lasse; Reichl, Thomas; Dreyer, David; Lefeldt, Nele; Engels, Svenja; Baker, Neville; Hore, P. J.; Mouritsen, Henrik

2016-01-01

Magnetic compass orientation in night-migratory songbirds is embedded in the visual system and seems to be based on a light-dependent radical pair mechanism. Recent findings suggest that both broadband electromagnetic fields ranging from ~2 kHz to ~9 MHz and narrow-band fields at the so-called Larmor frequency for a free electron in the Earth’s magnetic field can disrupt this mechanism. However, due to local magnetic fields generated by nuclear spins, effects specific to the Larmor frequency are difficult to understand considering that the primary sensory molecule should be organic and probably a protein. We therefore constructed a purpose-built laboratory and tested the orientation capabilities of European robins in an electromagnetically silent environment, under the specific influence of four different oscillating narrow-band electromagnetic fields, at the Larmor frequency, double the Larmor frequency, 1.315 MHz or 50 Hz, and in the presence of broadband electromagnetic noise covering the range from ~2 kHz to ~9 MHz. Our results indicated that the magnetic compass orientation of European robins could not be disrupted by any of the relatively strong narrow-band electromagnetic fields employed here, but that the weak broadband field very efficiently disrupted their orientation. PMID:27047356

Prospective CO 2 saline resource estimation methodology: Refinement of existing US-DOE-NETL methods based on data availability

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

Goodman, Angela; Sanguinito, Sean; Levine, Jonathan S.

Carbon storage resource estimation in subsurface saline formations plays an important role in establishing the scale of carbon capture and storage activities for governmental policy and commercial project decision-making. Prospective CO 2 resource estimation of large regions or subregions, such as a basin, occurs at the initial screening stages of a project using only limited publicly available geophysical data, i.e. prior to project-specific site selection data generation. As the scale of investigation is narrowed and selected areas and formations are identified, prospective CO 2 resource estimation can be refined and uncertainty narrowed when site-specific geophysical data are available. Here, wemore » refine the United States Department of Energy – National Energy Technology Laboratory (US-DOE-NETL) methodology as the scale of investigation is narrowed from very large regional assessments down to selected areas and formations that may be developed for commercial storage. In addition, we present a new notation that explicitly identifies differences between data availability and data sources used for geologic parameters and efficiency factors as the scale of investigation is narrowed. This CO 2 resource estimation method is available for screening formations in a tool called CO 2-SCREEN.« less

Hydrophobic fluorescent probes introduce artifacts into single molecule tracking experiments due to non-specific binding.

PubMed

Zanetti-Domingues, Laura C; Tynan, Christopher J; Rolfe, Daniel J; Clarke, David T; Martin-Fernandez, Marisa

2013-01-01

Single-molecule techniques are powerful tools to investigate the structure and dynamics of macromolecular complexes; however, data quality can suffer because of weak specific signal, background noise and dye bleaching and blinking. It is less well-known, but equally important, that non-specific binding of probe to substrates results in a large number of immobile fluorescent molecules, introducing significant artifacts in live cell experiments. Following from our previous work in which we investigated glass coating substrates and demonstrated that the main contribution to this non-specific probe adhesion comes from the dye, we carried out a systematic investigation of how different dye chemistries influence the behaviour of spectrally similar fluorescent probes. Single-molecule brightness, bleaching and probe mobility on the surface of live breast cancer cells cultured on a non-adhesive substrate were assessed for anti-EGFR affibody conjugates with 14 different dyes from 5 different manufacturers, belonging to 3 spectrally homogeneous bands (491 nm, 561 nm and 638 nm laser lines excitation). Our results indicate that, as well as influencing their photophysical properties, dye chemistry has a strong influence on the propensity of dye-protein conjugates to adhere non-specifically to the substrate. In particular, hydrophobicity has a strong influence on interactions with the substrate, with hydrophobic dyes showing much greater levels of binding. Crucially, high levels of non-specific substrate binding result in calculated diffusion coefficients significantly lower than the true values. We conclude that the physic-chemical properties of the dyes should be considered carefully when planning single-molecule experiments. Favourable dye characteristics such as photostability and brightness can be offset by the propensity of a conjugate for non-specific adhesion.

Hydrophobic Fluorescent Probes Introduce Artifacts into Single Molecule Tracking Experiments Due to Non-Specific Binding

PubMed Central

Rolfe, Daniel J.; Clarke, David T.; Martin-Fernandez, Marisa

2013-01-01

Single-molecule techniques are powerful tools to investigate the structure and dynamics of macromolecular complexes; however, data quality can suffer because of weak specific signal, background noise and dye bleaching and blinking. It is less well-known, but equally important, that non-specific binding of probe to substrates results in a large number of immobile fluorescent molecules, introducing significant artifacts in live cell experiments. Following from our previous work in which we investigated glass coating substrates and demonstrated that the main contribution to this non-specific probe adhesion comes from the dye, we carried out a systematic investigation of how different dye chemistries influence the behaviour of spectrally similar fluorescent probes. Single-molecule brightness, bleaching and probe mobility on the surface of live breast cancer cells cultured on a non-adhesive substrate were assessed for anti-EGFR affibody conjugates with 14 different dyes from 5 different manufacturers, belonging to 3 spectrally homogeneous bands (491 nm, 561 nm and 638 nm laser lines excitation). Our results indicate that, as well as influencing their photophysical properties, dye chemistry has a strong influence on the propensity of dye-protein conjugates to adhere non-specifically to the substrate. In particular, hydrophobicity has a strong influence on interactions with the substrate, with hydrophobic dyes showing much greater levels of binding. Crucially, high levels of non-specific substrate binding result in calculated diffusion coefficients significantly lower than the true values. We conclude that the physic-chemical properties of the dyes should be considered carefully when planning single-molecule experiments. Favourable dye characteristics such as photostability and brightness can be offset by the propensity of a conjugate for non-specific adhesion. PMID:24066121

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

PubMed

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

2017-12-22

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

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.

[Substrate specificities of bile salt hydrolase 1 and its mutants from Lactobacillus salivarius].

PubMed

Bi, Jie; Fang, Fang; Qiu, Yuying; Yang, Qingli; Chen, Jian

2014-03-01

In order to analyze the correlation between critical residues in the catalytic centre of BSH and the enzyme substrate specificity, seven mutants of Lactobacillus salivarius bile salt hydrolase (BSH1) were constructed by using the Escherichia coli pET-20b(+) gene expression system, rational design and site-directed mutagenesis. These BSH1 mutants exhibited different hydrolytic activities against various conjugated bile salts through substrate specificities comparison. Among the residues being tested, Cys2 and Thr264 were deduced as key sites for BSH1 to catalyze taurocholic acid and glycocholic acid, respectively. Moreover, Cys2 and Thr264 were important for keeping the catalytic activity of BSH1. The high conservative Cys2 was not the only active site, other mutant amino acid sites were possibly involved in substrate binding. These mutant residues might influence the space and shape of the substrate-binding pockets or the channel size for substrate passing through and entering active site of BSH1, thus, the hydrolytic activity of BSH1 was changed to different conjugated bile salt.

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.

Recent developments in the clinical pharmacology of rolapitant: subanalyses in specific populations

PubMed Central

Rapoport, Bernardo Leon; Aapro, Matti; Chasen, Martin R; Jordan, Karin; Navari, Rudolph M; Schnadig, Ian; Schwartzberg, Lee

2017-01-01

Knowledge of the involvement of the neurokinin substance P in emesis has led to the development of the neurokinin-1 receptor antagonists (NK-1 RAs) for control of chemotherapy-induced nausea and vomiting (CINV), in combination with serotonin type 3 receptor antagonists and corticosteroids. The NK-1 RA rolapitant, recently approved in oral formulation, has nanomolar affinity for the NK-1 receptor, as do the other commercially available NK-1 RAs, aprepitant and netupitant. Rolapitant is rapidly absorbed and has a long half-life in comparison to aprepitant and netupitant. All three NK-1 RAs undergo metabolism by cytochrome P450 (CYP) 3A4, necessitating caution with the concomitant use of CYP3A4 inhibitors, but in contrast to aprepitant and netupitant, rolapitant does not inhibit or induce CYP3A4. However, rolapitant is a moderate inhibitor of CYP2D6, and concomitant use with CYP2D6 substrates with narrow therapeutic indices should be avoided. Aprepitant, netupitant, and rolapitant have all demonstrated efficacy in the control of delayed CINV in patients receiving moderately and highly emetogenic chemotherapy in randomized controlled trials, including over multiple cycles of chemotherapy. We reviewed recent post hoc analyses of clinical trial data demonstrating that rolapitant is efficacious in the control of CINV in patient populations with specific tumor types, namely, breast cancers, gastrointestinal/colorectal cancers, and lung cancers. In addition, we show that rolapitant has efficacy in the control of CINV in specific age groups of patients receiving chemotherapy (<65 and ≥65 years of age). Overall, the safety profile of rolapitant in these specific patient populations was consistent with that observed in primary analyses of phase 3 trials. PMID:28919712

The diversity and specificity of the extracellular proteome in the cellulolytic bacterium Caldicellulosiruptor bescii is driven by the nature of the cellulosic growth substrate

DOE PAGES

Poudel, Suresh; Giannone, Richard J.; Basen, Mirko; ...

2018-03-23

Background: Caldicellulosiruptor bescii is a thermophilic cellulolytic bacterium that efficiently deconstructs lignocellulosic biomass into sugars, which subsequently can be fermented into alcohols, such as ethanol, and other products. Deconstruction of complex substrates by C. bescii involves a myriad of highly abundant, substrate-specific extracellular solute binding proteins (ESBPs) and carbohydrate-active enzymes (CAZymes) containing carbohydrate-binding modules (CBMs). Mass spectrometry-based proteomics was employed to investigate how these substrate recognition proteins and enzymes vary as a function of lignocellulosic substrates.Results:Proteomic analysis revealed several key extracellular proteins that respond specifically to either C5 or C6 mono- and polysaccharides. These include proteins of unknown functions (PUFs),more » ESBPs, and CAZymes. ESBPs that were previously shown to interact more efficiently with hemicellulose and pectin were detected in high abundance during growth on complex C5 substrates, such as switchgrass and xylan. Some proteins, such as Athe_0614 and Athe_2368, whose functions are not well defined were predicted to be involved in xylan utilization and ABC transport and were significantly more abundant in complex and C5 substrates, respectively. The proteins encoded by the entire glucan degradation locus (GDL; Athe_1857, 1859, 1860, 1865, 1867, and 1866) were highly abundant under all growth conditions, particularly when C. bescii was grown on cellobiose, switchgrass, or xylan. In contrast, the glycoside hydrolases Athe_0609 (Pullulanase) and 0610, which both possess CBM20 and a starch binding domain, appear preferential to C5/complex substrate deconstruction. Some PUFs, such as Athe_2463 and 2464, were detected as highly abundant when grown on C5 substrates (xylan and xylose), also suggesting C5-substrate specificity. In conclusion, this study reveals the protein membership of the C. bescii secretome and demonstrates its plasticity based on the complexity (mono-/disaccharides vs. polysaccharides) and type of carbon (C5 vs. C6) available to the microorganism. The presence or increased abundance of extracellular proteins as a response to specific substrates helps to further elucidate C. bescii’s utilization and conversion of lignocellulosic biomass to biofuel and other valuable products. This includes improved characterization of extracellular proteins that lack discrete functional roles and are poorly/not annotated.« less

The diversity and specificity of the extracellular proteome in the cellulolytic bacterium Caldicellulosiruptor bescii is driven by the nature of the cellulosic growth substrate

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

Poudel, Suresh; Giannone, Richard J.; Basen, Mirko

Background: Caldicellulosiruptor bescii is a thermophilic cellulolytic bacterium that efficiently deconstructs lignocellulosic biomass into sugars, which subsequently can be fermented into alcohols, such as ethanol, and other products. Deconstruction of complex substrates by C. bescii involves a myriad of highly abundant, substrate-specific extracellular solute binding proteins (ESBPs) and carbohydrate-active enzymes (CAZymes) containing carbohydrate-binding modules (CBMs). Mass spectrometry-based proteomics was employed to investigate how these substrate recognition proteins and enzymes vary as a function of lignocellulosic substrates.Results:Proteomic analysis revealed several key extracellular proteins that respond specifically to either C5 or C6 mono- and polysaccharides. These include proteins of unknown functions (PUFs),more » ESBPs, and CAZymes. ESBPs that were previously shown to interact more efficiently with hemicellulose and pectin were detected in high abundance during growth on complex C5 substrates, such as switchgrass and xylan. Some proteins, such as Athe_0614 and Athe_2368, whose functions are not well defined were predicted to be involved in xylan utilization and ABC transport and were significantly more abundant in complex and C5 substrates, respectively. The proteins encoded by the entire glucan degradation locus (GDL; Athe_1857, 1859, 1860, 1865, 1867, and 1866) were highly abundant under all growth conditions, particularly when C. bescii was grown on cellobiose, switchgrass, or xylan. In contrast, the glycoside hydrolases Athe_0609 (Pullulanase) and 0610, which both possess CBM20 and a starch binding domain, appear preferential to C5/complex substrate deconstruction. Some PUFs, such as Athe_2463 and 2464, were detected as highly abundant when grown on C5 substrates (xylan and xylose), also suggesting C5-substrate specificity. In conclusion, this study reveals the protein membership of the C. bescii secretome and demonstrates its plasticity based on the complexity (mono-/disaccharides vs. polysaccharides) and type of carbon (C5 vs. C6) available to the microorganism. The presence or increased abundance of extracellular proteins as a response to specific substrates helps to further elucidate C. bescii’s utilization and conversion of lignocellulosic biomass to biofuel and other valuable products. This includes improved characterization of extracellular proteins that lack discrete functional roles and are poorly/not annotated.« less

The diversity and specificity of the extracellular proteome in the cellulolytic bacterium Caldicellulosiruptor bescii is driven by the nature of the cellulosic growth substrate.

PubMed

Poudel, Suresh; Giannone, Richard J; Basen, Mirko; Nookaew, Intawat; Poole, Farris L; Kelly, Robert M; Adams, Michael W W; Hettich, Robert L

2018-01-01

Caldicellulosiruptor bescii is a thermophilic cellulolytic bacterium that efficiently deconstructs lignocellulosic biomass into sugars, which subsequently can be fermented into alcohols, such as ethanol, and other products. Deconstruction of complex substrates by C. bescii involves a myriad of highly abundant, substrate-specific extracellular solute binding proteins (ESBPs) and carbohydrate-active enzymes (CAZymes) containing carbohydrate-binding modules (CBMs). Mass spectrometry-based proteomics was employed to investigate how these substrate recognition proteins and enzymes vary as a function of lignocellulosic substrates. Proteomic analysis revealed several key extracellular proteins that respond specifically to either C5 or C6 mono- and polysaccharides. These include proteins of unknown functions (PUFs), ESBPs, and CAZymes. ESBPs that were previously shown to interact more efficiently with hemicellulose and pectin were detected in high abundance during growth on complex C5 substrates, such as switchgrass and xylan. Some proteins, such as Athe_0614 and Athe_2368, whose functions are not well defined were predicted to be involved in xylan utilization and ABC transport and were significantly more abundant in complex and C5 substrates, respectively. The proteins encoded by the entire glucan degradation locus (GDL; Athe_1857, 1859, 1860, 1865, 1867, and 1866) were highly abundant under all growth conditions, particularly when C. bescii was grown on cellobiose, switchgrass, or xylan. In contrast, the glycoside hydrolases Athe_0609 (Pullulanase) and 0610, which both possess CBM20 and a starch binding domain, appear preferential to C5/complex substrate deconstruction. Some PUFs, such as Athe_2463 and 2464, were detected as highly abundant when grown on C5 substrates (xylan and xylose), also suggesting C5-substrate specificity. This study reveals the protein membership of the C. bescii secretome and demonstrates its plasticity based on the complexity (mono-/disaccharides vs. polysaccharides) and type of carbon (C5 vs. C6) available to the microorganism. The presence or increased abundance of extracellular proteins as a response to specific substrates helps to further elucidate C. bescii 's utilization and conversion of lignocellulosic biomass to biofuel and other valuable products. This includes improved characterization of extracellular proteins that lack discrete functional roles and are poorly/not annotated.

Self-organized micro-holes on titania based sol-gel films under continuous direct writing with a continuous wave ultraviolet laser

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

Bakhti, S.; Destouches, N.; Gamet, E.

The microstructuring of titania based sol-gel films is investigated by direct writing with a continuous wave ultraviolet laser beam emitting at 244 nm. Depending on the exposure conditions, the films exhibit a volume expansion, a volume shrinkage, a self-shaped delamination, or are damaged. This paper is mainly focused on the regime where spontaneous local delamination occurs, which corresponds to a narrow range of laser irradiances and writing speeds. In this regime, self-organized round-shape micro-holes opened on the substrate are generated.

Anomalous complete opaqueness in a sparse array of gold nanoparticle chains

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

Bai Benfeng; Tsinghua-Foxconn Nanotechnology Research Center, Tsinghua University, Beijing 100084; Department of Physics and Mathematics, University of Eastern Finland, P.O. Box 111, FI-80101 Joensuu

2011-08-22

We report on an anomalous polarization-switching extinction effect in a sparse array of gold nanoparticle chains: under normal incidence of light, the array is almost transparent for one polarization; whereas it is fully opaque (with nearly zero transmittance) for the orthogonal polarization within a narrow band, even though the nanoparticles cover only a tiny fraction (say, 3.5%) of the transparent substrate surface. We reveal that the strong polarization-dependent short-range dipolar coupling and long-range radiative coupling of gold nanoparticles in this highly asymmetric array is responsible for this extraordinary effect.

Generation and oxidation of aerosol deposited PdAg nanoparticles

NASA Astrophysics Data System (ADS)

Blomberg, S.; Gustafson, J.; Martin, N. M.; Messing, M. E.; Deppert, K.; Liu, Z.; Chang, R.; Fernandes, V. R.; Borg, A.; Grönbeck, H.; Lundgren, E.

2013-10-01

PdAg nanoparticles with a diameter of 10 nm have been generated by an aerosol particle method, and supported on a silica substrate. By using a combination of X-ray Energy Dispersive Spectroscopy and X-ray Photoelectron Spectroscopy it is shown that the size distribution of the particles is narrow and that the two metals form an alloy with a mixture of 75% Pd and 25% Ag. Under oxidizing conditions, Pd is found to segregate to the surface and a thin PdO like oxide is formed similar to the surface oxide previously reported on extended PdAg and pure Pd surfaces.

Field effect transistor and method of construction thereof

NASA Technical Reports Server (NTRS)

Fletner, W. R. (Inventor)

1978-01-01

A field effect transistor is constructed by placing a semi-conductor layer on an insulating substrate so that the gate region is separated from source and drain regions. The gate electrode and gate region of the layer are of generally reduced length, the gate region being of greatest length on its surface closest to the gate electrode. This is accomplished by initially creating a relatively large gate region of one polarity, and then reversing the polarity of a central portion of this gate region by ion bombardment, thus achieving a narrower final gate region of the stated configuration.

Controlling the width of self-assembled dysprosium silicide nanowires on the Si(001) surface.

PubMed

Cui, Y; Chung, J; Nogami, J

2012-02-01

We present STM data that show that it is possible to use a metal induced 2 × 7 reconstruction of Si(001) to narrow the width distribution of Dy silicide nanowires. This behavior is distinct from the effect of the 7 × 7 reconstruction on the Si(111) surface, where the 7 × 7 serves as a static template and the deposited metal avoids the unit cell boundaries on the substrate. In this case, the 2 × 7 is a dynamic template, and the nanowires nucleate at anti-phase boundaries between 2 × 7 reconstruction domains.

Analysis of ABCB phosphoglycoproteins (PGPs) and their contribution to monocot biomass, structural stability, and productivity

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

Murphy, Angus Stuart

2014-09-23

Efforts to manipulate production of plant secondary cell walls to improve the quality of biofuel feedstocks are currently limited by an inability to regulate the transport of small molecule components out of the cell. Plant ABCB p-glycoproteins are a small family of plasma membrane organic molecule transporters that have become primary targets for this effort, as they can potentially be harnessed to control the export of aromatic compounds and organic acids. However, unlike promiscuous mammalian ABCBs that function in multidrug resistance, all plant ABCB proteins characterized to date exhibit relatively narrow substrate specificity. Although ABCBs exhibit a highly conserved architecture,more » efforts to modify ABCB activity have been hampered by a lack of structural information largely because an eukaryotic ABCB protein crystal structure has yet to be obtained. Structure/ function analyses have been further impeded by the lack of a common heterologous expression system that can be used to characterize recombinant ABCB proteins, as many cannot be functionally expressed in S. cereviseae or other systems where proteins with analogous function can be readily knocked out. Using experimentally-determined plant ABCB substrate affinities and the crystal structure of the bacterial Sav1866 “half” ABC transporter, we have developed sequence/structure models for ABCBs that provide a testable context for mutational analysis of plant ABCB transporters. We have also developed a flexible heterologous expression system in Schizosaccharomyces pombe in which all endogenous ABC transporters have been knocked out. The effectiveness of this system for transport studies has been demonstrated by the successful functional expression all of the known PIN, AUX/LAX and ABCB auxin transporters. Our central hypothesis is that the domains of the ABCB proteins that we have identified as substrate docking sites and regulators of transport directionality can be altered or swapped to alter the transport characteristics of the proteins. We propose to combine computer modelling, mutational analyses, and complementation of well characterized Arabidopsis abcb4,14,and 19 mutants to elucidate ABCB function. The long term objective of this project is to enhance ABCB transport of cell wall components, to manipulate the direction of ABCB substrate transport, and, ultimately, to produce “designer” ABC transporters that can be used to modify plant feedstock quality.« less

Combining affinity proteomics and network context to identify new phosphatase substrates and adapters in growth pathways

PubMed Central

Sacco, Francesca; Boldt, Karsten; Calderone, Alberto; Panni, Simona; Paoluzi, Serena; Castagnoli, Luisa; Ueffing, Marius; Cesareni, Gianni

2014-01-01

Protein phosphorylation homoeostasis is tightly controlled and pathological conditions are caused by subtle alterations of the cell phosphorylation profile. Altered levels of kinase activities have already been associated to specific diseases. Less is known about the impact of phosphatases, the enzymes that down-regulate phosphorylation by removing the phosphate groups. This is partly due to our poor understanding of the phosphatase-substrate network. Much of phosphatase substrate specificity is not based on intrinsic enzyme specificity with the catalytic pocket recognizing the sequence/structure context of the phosphorylated residue. In addition many phosphatase catalytic subunits do not form a stable complex with their substrates. This makes the inference and validation of phosphatase substrates a non-trivial task. Here, we present a novel approach that builds on the observation that much of phosphatase substrate selection is based on the network of physical interactions linking the phosphatase to the substrate. We first used affinity proteomics coupled to quantitative mass spectrometry to saturate the interactome of eight phosphatases whose down regulations was shown to affect the activation of the RAS-PI3K pathway. By integrating information from functional siRNA with protein interaction information, we develop a strategy that aims at inferring phosphatase physiological substrates. Graph analysis is used to identify protein scaffolds that may link the catalytic subunits to their substrates. By this approach we rediscover several previously described phosphatase substrate interactions and characterize two new protein scaffolds that promote the dephosphorylation of PTPN11 and ERK by DUSP18 and DUSP26, respectively. PMID:24847354

Assessing the Utility of Compound Trait Estimates of Narrow Personality Traits.

PubMed

Credé, Marcus; Harms, Peter D; Blacksmith, Nikki; Wood, Dustin

2016-01-01

It has been argued that approximations of narrow traits can be made through linear combinations of broad traits such as the Big Five personality traits. Indeed, Hough and Ones ( 2001 ) used a qualitative analysis of scale content to arrive at a taxonomy of how Big Five traits might be combined to approximate various narrow traits. However, the utility of such compound trait approximations has yet to be established beyond specific cases such as integrity and customer service orientation. Using data from the Eugene-Springfield Community Sample (Goldberg, 2008 ), we explore the ability of linear composites of scores on Big Five traits to approximate scores on 127 narrow trait measures from 5 well-known non-Big-Five omnibus measures of personality. Our findings indicate that individuals' standing on more than 30 narrow traits can be well estimated from 3 different types of linear composites of scores on Big Five traits without a substantial sacrifice in criterion validity. We discuss theoretical accounts for why such relationships exist as well as the theoretical and practical implications of these findings for researchers and practitioners.

Enhancing the visibility of injuries with narrow-banded beams of light within the visible light spectrum.

PubMed

Limmen, Roxane M; Ceelen, Manon; Reijnders, Udo J L; Joris Stomp, S; de Keijzer, Koos C; Das, Kees

2013-03-01

The use of narrow-banded visible light sources in improving the visibility of injuries has been hardly investigated, and studies examining the extent of this improvement are lacking. In this study, narrow-banded beams of light within the visible light spectrum were used to explore their ability in improving the visibility of external injuries. The beams of light were induced by four crime-lites(®) providing narrow-banded beams of light between 400 and 550 nm. The visibility of the injuries was assessed through specific long-pass filters supplied with the set of crime-lites(®) . Forty-three percent of the examined injuries improved in visibility by using the narrow-banded visible light. In addition, injuries were visualized that were not visible or just barely visible to the naked eye. The improvements in visibility were particularly marked with the use of crime-lites(®) "violet" and "blue" covering the spectrum between 400-430 and 430-470 nm. The simple noninvasive method showed a great potential contribution in injury examination. © 2012 American Academy of Forensic Sciences.

BOK-Printed Electronics

NASA Technical Reports Server (NTRS)

Ghaffarian, Reza

2013-01-01

The use of printed electronics technologies (PETs), 2D or 3D printing approaches either by conventional electronic fabrication or by rapid graphic printing of organic or nonorganic electronic devices on various small or large rigid or flexible substrates, is projected to grow exponentially in commercial industry. This has provided an opportunity to determine whether or not PETs could be applicable for low volume and high-reliability applications. This report presents a summary of literature surveyed and provides a body of knowledge (BOK) gathered on the current status of organic and printed electronics technologies. It reviews three key industry roadmaps- on this subject-OE-A, ITRS, and iNEMI-each with a different name identification for this emerging technology. This followed by a brief review of the status of the industry on standard development for this technology, including IEEE and IPC specifications. The report concludes with key technologies and applications and provides a technology hierarchy similar to those of conventional microelectronics for electronics packaging. Understanding key technology roadmaps, parameters, and applications is important when judicially selecting and narrowing the follow-up of new and emerging applicable technologies for evaluation, as well as the low risk insertion of organic, large area, and printed electronics.

Tailored Fano resonance and localized electromagnetic field enhancement in Ag gratings

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

Li, Zhaozhu; Klopf, J. Michael; Wang, Lei

Metallic gratings can support Fano resonances when illuminated with EM radiation, and their characteristic reflectivity versus incident angle lineshape can be greatly affected by the surrounding dielectric environment and the grating geometry. By using conformal oblique incidence thin film deposition onto an optical grating substrate, it is possible to increase the grating amplitude due to shadowing effects, thereby enabling tailoring of the damping processes and electromagnetic field couplings of the Fano resonances, hence optimizing the associated localized electric field intensity. To investigate these effects we compare the optical reflectivity under resonance excitation in samples prepared by oblique angle deposition (OAD)more » and under normal deposition (ND) onto the same patterned surfaces. We observe that by applying OAD method, the sample exhibits a deeper and narrower reflectivity dip at resonance than that obtained under ND. This can be explained in terms of a lower damping of Fano resonance on obliquely deposited sample and leads to a stronger localized electric field. This approach opens a fabrication path for applications where tailoring the electromagnetic field induced by Fano resonance can improve the figure of merit of specific device characteristics, e.g. quantum efficiency (QE) in grating-based metallic photocathodes.« less

Tailored Fano resonance and localized electromagnetic field enhancement in Ag gratings

DOE PAGES

Li, Zhaozhu; Klopf, J. Michael; Wang, Lei; ...

2017-03-14

Metallic gratings can support Fano resonances when illuminated with EM radiation, and their characteristic reflectivity versus incident angle lineshape can be greatly affected by the surrounding dielectric environment and the grating geometry. By using conformal oblique incidence thin film deposition onto an optical grating substrate, it is possible to increase the grating amplitude due to shadowing effects, thereby enabling tailoring of the damping processes and electromagnetic field couplings of the Fano resonances, hence optimizing the associated localized electric field intensity. To investigate these effects we compare the optical reflectivity under resonance excitation in samples prepared by oblique angle deposition (OAD)more » and under normal deposition (ND) onto the same patterned surfaces. We observe that by applying OAD method, the sample exhibits a deeper and narrower reflectivity dip at resonance than that obtained under ND. This can be explained in terms of a lower damping of Fano resonance on obliquely deposited sample and leads to a stronger localized electric field. This approach opens a fabrication path for applications where tailoring the electromagnetic field induced by Fano resonance can improve the figure of merit of specific device characteristics, e.g. quantum efficiency (QE) in grating-based metallic photocathodes.« less

Periodic domain boundary ordering in a dense molecular adlayer: Sub-saturation carbon monoxide on Pd(111)

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

Xu, Pan; Liu, Shizhong; Hong, Sung -Young

Here, we describe a previously unreported ordered phase of carbon monoxide adsorbed on the (111) facet of single crystal palladium at near-saturation coverage. The adlayer superstructure is identified from low energy electron diffraction to be c(16×2) with respect to the underlying Pd(111) surface net. The ideal coverage is determined to be 0.6875 ML, approximately 92% of the 0.75–ML saturation coverage. Density functional theory calculations support a model for the molecular packing characterized by strips of locally-saturated (2×2) regions, with the CO bound near high-symmetry surface sites, separated by antiphase domain boundaries. The structure exists in a narrow coverage range andmore » is prepared by heating the saturated adlayer to desorb a small fraction of the CO. Comparison of the c(16×2) domain-boundary structure with structural motifs at lower coverages suggests that between 0.6 and 0.6875 ML the adlayer order may be more strongly influenced by interadsorbate repulsion than by adsorption-site-specific interactions. The system is an example of the structural complexity that results from the compromise between adsorbate–substrate and adsorbate–adsorbate interactions.« less

Periodic domain boundary ordering in a dense molecular adlayer: Sub-saturation carbon monoxide on Pd(111)

DOE PAGES

Xu, Pan; Liu, Shizhong; Hong, Sung -Young; ...

2016-12-31

Here, we describe a previously unreported ordered phase of carbon monoxide adsorbed on the (111) facet of single crystal palladium at near-saturation coverage. The adlayer superstructure is identified from low energy electron diffraction to be c(16×2) with respect to the underlying Pd(111) surface net. The ideal coverage is determined to be 0.6875 ML, approximately 92% of the 0.75–ML saturation coverage. Density functional theory calculations support a model for the molecular packing characterized by strips of locally-saturated (2×2) regions, with the CO bound near high-symmetry surface sites, separated by antiphase domain boundaries. The structure exists in a narrow coverage range andmore » is prepared by heating the saturated adlayer to desorb a small fraction of the CO. Comparison of the c(16×2) domain-boundary structure with structural motifs at lower coverages suggests that between 0.6 and 0.6875 ML the adlayer order may be more strongly influenced by interadsorbate repulsion than by adsorption-site-specific interactions. The system is an example of the structural complexity that results from the compromise between adsorbate–substrate and adsorbate–adsorbate interactions.« less

Kleptothermy: an additional category of thermoregulation, and a possible example in sea kraits (Laticauda laticaudata, Serpentes).

PubMed

Brischoux, François; Bonnet, Xavier; Shine, Richard

2009-12-23

Lacking the capacity for thermogenesis, most ectotherms inhabiting thermally heterogeneous environments rely instead upon exploiting that ambient heterogeneity. In many cases they maintain body temperatures within a narrow range despite massive spatial and temporal variation in ambient conditions. Reliance on diverse thermal opportunities is reflected in specific terms for organisms that bask in sunlight to regulate their temperature (heliotherms), or that press their bodies against warm substrates to facilitate heat flow (thigmotherms), or that rely on large body mass to maintain thermal constancy (gigantothermy). We propose an additional category of thermoregulators: kleptotherms, which regulate their own temperature by 'stealing' heat from other organisms. This concept involves two major conditions: the thermal heterogeneity created by the presence of a warm organism in a cool environment and the selective use of that heterogeneity by another animal to maintain body temperatures at higher (and more stable) levels than would be possible elsewhere in the local area. Kleptothermy occurs in endotherms also, but is usually reciprocal (rather than unilateral as in ectotherms). Thermal monitoring on a small tropical island documents a possible example of kleptothermy, based on high stable temperatures of a sea snake (Laticauda laticaudata) inside a burrow occupied by seabirds.

Heparin/heparan sulfate 6-O-sulfatase from Flavobacterium heparinum: integrated structural and biochemical investigation of enzyme active site and substrate specificity.

PubMed

Myette, James R; Soundararajan, Venkataramanan; Shriver, Zachary; Raman, Rahul; Sasisekharan, Ram

2009-12-11

Heparin and heparan sulfate glycosaminoglycans (HSGAGs) comprise a chemically heterogeneous class of sulfated polysaccharides. The development of structure-activity relationships for this class of polysaccharides requires the identification and characterization of degrading enzymes with defined substrate specificity and enzymatic activity. Toward this end, we report here the molecular cloning and extensive structure-function analysis of a 6-O-sulfatase from the Gram-negative bacterium Flavobacterium heparinum. In addition, we report the recombinant expression of this enzyme in Escherichia coli in a soluble, active form and identify it as a specific HSGAG sulfatase. We further define the mechanism of action of the enzyme through biochemical and structural studies. Through the use of defined substrates, we investigate the kinetic properties of the enzyme. This analysis was complemented by homology-based molecular modeling studies that sought to rationalize the substrate specificity of the enzyme and mode of action through an analysis of the active-site topology of the enzyme including identifying key enzyme-substrate interactions and assigning key amino acids within the active site of the enzyme. Taken together, our structural and biochemical studies indicate that 6-O-sulfatase is a predominantly exolytic enzyme that specifically acts on N-sulfated or N-acetylated 6-O-sulfated glucosamines present at the non-reducing end of HSGAG oligosaccharide substrates. This requirement for the N-acetyl or N-sulfo groups on the glucosamine substrate can be explained through eliciting favorable interactions with key residues within the active site of the enzyme. These findings provide a framework that enables the use of 6-O-sulfatase as a tool for HSGAG structure-activity studies as well as expand our biochemical and structural understanding of this important class of enzymes.

Study of education disparities and health information seeking behavior.

PubMed

Lorence, Daniel; Park, Heeyoung

2007-02-01

This exploratory technology assessment examines how educational characteristics of health information seekers are associated with access to computers, the Internet, and online health information. Specifically, we examine (1) if there exists significant variation across identified health technology user groups regarding access to online health information, and (2) if differences between education levels have narrowed, remained constant, or widened over recent years, following national educational initiatives to narrow the technology gap for low-education user groups. Using a stratified sample from national tracking survey data, we find that recent policy initiatives under national technology access and other programs have demonstrated little effect in narrowing the digital divide for low-education users of web-based technologies.

Switchable narrow linewidth fiber laser with LP11 transverse mode output

NASA Astrophysics Data System (ADS)

Shen, Ya; Ren, Guobin; Yang, Yuguang; Yao, Shuzhi; Wu, Yue; Jiang, Youchao; Xu, Yao; Jin, Wenxing; Zhu, Bofeng; Jian, Shuisheng

2018-01-01

We experimentally demonstrate a switchable narrow linewidth single-longitudinal-mode (SLM) erbium-doped fiber (EDF) ring laser with LP11 transverse mode output. The laser is based on a mode selective all-fiber fused coupler which is composed of a single-mode fiber (SMF) and a two-mode fiber (TMF). By controlling the polarization state of the output light, the laser can provide narrow linewidth SLM output with LP11 transverse mode at two specific wavelengths, which correspond to two transmission peaks of the chirped moiré fiber grating (CMFBG). The 20 dB linewidth of the fiber laser for each wavelength is approximately 7.2 and 6.4 kHz.

The trimethylammonium headgroup of choline is a major determinant for substrate binding and specificity in choline oxidase.

PubMed

Gadda, Giovanni; Powell, Nichole L N; Menon, Prashanthi

2004-10-15

Choline oxidase catalyzes the oxidation of choline to glycine betaine via two sequential flavin-linked transfers of hydride equivalents to molecular oxygen and formation of a betaine aldehyde intermediate. In the present study, choline and glycine betaine analogs were used as substrates and inhibitors for the enzyme to investigate the structural determinants that are relevant for substrate recognition and specificity. Competitive inhibition patterns with respect to choline were determined for a number of substituted amines at pH 6.5 and 25 degrees C. The Kis values for the carboxylate-containing ligands glycine betaine, N,N-dimethylglycine, and N-methylglycine increased monotonically with decreasing number of methyl groups, consistent with the trimethylammonium portion of the ligand being important for binding. In contrast, the acetate portion of glycine betaine did not contribute to binding, as suggested by lack of changes in the Kis values upon substituting glycine betaine with inhibitors containing methyl, ethyl, allyl, and 2-amino-ethyl side chains. In agreement with the inhibition data, the specificity of the enzyme for the organic substrate (kcat/Km value) decreased when N,N-dimethylethanolamine, N-methylethanolamine, and the isosteric substrate 3,3-dimethyl-1-butanol were used as substrate instead of choline; a contribution of approximately 7 kcal mol(-1) toward substrate discrimination was estimated for the interaction of the trimethylammonium portion of the substrate with the active site of choline oxidase.

Peptide microarray analysis of substrate specificity of the transmembrane Ser/Thr kinase KPI-2 reveals reactivity with cystic fibrosis transmembrane conductance regulator and phosphorylase.

PubMed

Wang, Hong; Brautigan, David L

2006-11-01

Human lemur (Lmr) kinases are predicted to be Tyr kinases based on sequences and are related to neurotrophin receptor Trk kinases. This study used homogeneous recombinant KPI-2 (Lmr2, LMTK2, Cprk, brain-enriched protein kinase) kinase domain and a library of 1,154 peptides on a microarray to analyze substrate specificity. We found that KPI-2 is strictly a Ser/Thr kinase that reacts with Ser either preceded by or followed by Pro residues but unlike other Pro-directed kinases does not strictly require an adjacent Pro residue. The most reactive peptide in the library corresponds to Ser-737 of cystic fibrosis transmembrane conductance regulator, and the recombinant R domain of cystic fibrosis transmembrane conductance regulator was a preferred substrate. Furthermore the KPI-2 kinase phosphorylated peptides corresponding to the single site in phosphorylase and purified phosphorylase b, making this only the second known phosphorylase b kinase. Phosphorylase was used as a specific substrate to show that KPI-2 is inhibited in living cells by addition of nerve growth factor or serum. The results demonstrate the utility of the peptide library to probe specificity and discover kinase substrates and offer a specific assay that reveals hormonal regulation of the activity of this unusual transmembrane kinase.

Ultra-low roughness magneto-rheological finishing for EUV mask substrates

NASA Astrophysics Data System (ADS)

Dumas, Paul; Jenkins, Richard; McFee, Chuck; Kadaksham, Arun J.; Balachandran, Dave K.; Teki, Ranganath

2013-09-01

EUV mask substrates, made of titania-doped fused silica, ideally require sub-Angstrom surface roughness, sub-30 nm flatness, and no bumps/pits larger than 1 nm in height/depth. To achieve the above specifications, substrates must undergo iterative global and local polishing processes. Magnetorheological finishing (MRF) is a local polishing technique which can accurately and deterministically correct substrate figure, but typically results in a higher surface roughness than the current requirements for EUV substrates. We describe a new super-fine MRF® polishing fluid whichis able to meet both flatness and roughness specifications for EUV mask blanks. This eases the burden on the subsequent global polishing process by decreasing the polishing time, and hence the defectivity and extent of figure distortion.

Multi-tap complex-coefficient incoherent microwave photonic filters based on optical single-sideband modulation and narrow band optical filtering.

PubMed

Sagues, Mikel; García Olcina, Raimundo; Loayssa, Alayn; Sales, Salvador; Capmany, José

2008-01-07

We propose a novel scheme to implement tunable multi-tap complex coefficient filters based on optical single sideband modulation and narrow band optical filtering. A four tap filter is experimentally demonstrated to highlight the enhanced tuning performance provided by complex coefficients. Optical processing is performed by the use of a cascade of four phase-shifted fiber Bragg gratings specifically fabricated for this purpose.

QM/MM Investigation of Substrate and Product Specificities of Suv4-20h2: How Does This Enzyme Generate Dimethylated H4K20 from Monomethylated Substrate?

PubMed

Qian, Ping; Guo, Haobo; Wang, Liang; Guo, Hong

2017-06-13

Protein lysine methyltransferases (PKMTs) catalyze the methylation of lysine residues on histone proteins in the regulation of chromatin structure and gene expression. In contrast to many other PKMTs for which unmodified lysine is the methylation target, the enzymes in the Suv4-20 family are able to generate dimethylated product (H4K20me2) based exclusively on the monomethylated H4K20 substrate (H4K20me1). The origin of such substrate/product specificity is still not clear. Here, molecular dynamics (MD) and free energy (potential of mean force) simulations are undertaken using quantum mechanical/molecular mechanical (QM/MM) potentials to understand the substrate/product specificities of Suv4-20h2, a member of the Suv4-20 family. The free energy barriers for mono-, di-, and trimethylation in Suv4-20h2 obtained from the simulations are found to be well correlated with the specificities observed experimentally with the allowed dimethylation based on the H4K20me1 substrate and prohibited monomethylation and trimethylation based on H4K20 and H4K20me2, respectively. It is demonstrated that the reason for the relatively efficient dimethylation is an effective transition state (TS) stabilization through strengthening the CH···O interactions as well as the presence of a cation-π interaction at the transition state. The simulations also show that the failures of Suv4-20h2 to catalyze monomethylation and trimethylation are due, respectively, to a less effective TS stabilization and inability of the reactant complex containing H4K20me2 to adopt a reactive (near attack) configuration for methyl transfer. The results suggest that care must be exercised in the prediction of the substrate specificity based only on the existence of near attack configurations in substrate complexes.

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

PubMed

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

2016-06-08

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

Insights into the Specificity of Lysine Acetyltransferases

DOE PAGES

Tucker, Alex C.; Taylor, Keenan C.; Rank, Katherine C.; ...

2014-11-07

Reversible lysine acetylation by protein acetyltransferases is a conserved regulatory mechanism that controls diverse cellular pathways. Gcn5-related N-acetyltransferases (GNATs), named after their founding member, are found in all domains of life. GNATs are known for their role as histone acetyltransferases, but non-histone bacterial protein acetytransferases have been identified. Only structures of GNAT complexes with short histone peptide substrates are available in databases. Given the biological importance of this modification and the abundance of lysine in polypeptides, how specificity is attained for larger protein substrates is central to understanding acetyl-lysine-regulated networks. In this paper, we report the structure of a GNATmore » in complex with a globular protein substrate solved to 1.9 Å. GNAT binds the protein substrate with extensive surface interactions distinct from those reported for GNAT-peptide complexes. Finally, our data reveal determinants needed for the recognition of a protein substrate and provide insight into the specificity of GNATs.« less

Substrate-specific modifications on magnetic iron oxide nanoparticles as an artificial peroxidase for improving sensitivity in glucose detection.

PubMed

Liu, Yanping; Yu, Faquan

2011-04-08

Magnetic iron oxide nanoparticles (MION) were recently found to act as a peroxidase with intrinsic advantages over natural counterparts. Their limited affinity toward catalysis substrates, however, dramatically reduces their utility. In this paper, some effective groups were screened out and conjugated on MION as substrate-specific modifications for improving MION's affinity to substrates and hence utility. Nanoparticles of four different superficial structures were synthesized and characterized by TEM, size, zeta potential and SQUID, and assayed for peroxidase activity. Glucose detection was selected as an application model system to evaluate the bonus thereof. Catalysis was found to follow Michaelis-Menten kinetics. Sulfhydryl groups incorporated on MION (SH-MION) notably improve the affinity toward a substrate (hydrogen peroxide) and so do amino groups (NH₂-MION) toward another substrate, proved by variation in the determined kinetic parameters. A synergistically positive effect was observed and an apparently elevated detection sensitivity and a significantly lowered detection limit of glucose were achieved when integrated with both sulfhydryl and amino groups (SH-NH₂-MION). Our findings suggest that substrate-specific surface modifications are a straightforward and robust strategy to improve MION peroxidase-like activity. The high activity extends magnetic nanoparticles to wide applications other than glucose detection.

Low energy electron catalyst: the electronic origin of catalytic strategies.

PubMed

Davis, Daly; Sajeev, Y

2016-10-12

Using a low energy electron (LEE) as a catalyst, the electronic origin of the catalytic strategies corresponding to substrate selectivity, reaction specificity and reaction rate enhancement is investigated for a reversible unimolecular elementary reaction. An electronic energy complementarity between the catalyst and the substrate molecule is the origin of substrate selectivity and reaction specificity. The electronic energy complementarity is induced by tuning the electronic energy of the catalyst. The energy complementarity maximizes the binding forces between the catalyst and the molecule. Consequently, a new electronically metastable high-energy reactant state and a corresponding new low barrier reaction path are resonantly created for a specific reaction of the substrate through the formation of a catalyst-substrate transient adduct. The LEE catalysis also reveals a fundamental structure-energy correspondence in the formation of the catalyst-substrate transient adduct. Since the energy complementarities corresponding to the substrate molecules of the forward and the backward steps of the reversible reactions are not the same due to their structural differences, the LEE catalyst exhibits a unique one-way catalytic strategy, i.e., the LEE catalyst favors the reversible reaction more effectively in one direction. A characteristic stronger binding of the catalyst to the transition state of the reaction than in the initial reactant state and the final product state is the molecular origin of barrier lowering.

Comparison of Scheimpflug imaging and spectral domain anterior segment optical coherence tomography for detection of narrow anterior chamber angles.

PubMed

Grewal, D S; Brar, G S; Jain, R; Grewal, S P S

2011-05-01

To compare the performance of anterior chamber volume (ACV) and anterior chamber depth (ACD) obtained using Scheimpflug imaging with angle opening distance (AOD500) and trabecular-iris space area (TISA500) obtained using spectral domain anterior segment optical coherence tomography (SD-ASOCT) in detecting narrow angles classified using gonioscopy. In this prospective, cross-sectional observational study, 265 eyes of 265 consecutive patients underwent sequential Scheimpflug imaging, SD-ASOCT imaging, and gonioscopy. Correlations between gonioscopy grading, ACV, ACD, AOD500, and TISA500 were evaluated. Area under receiver operating characteristic curve (AUC), sensitivity, specificity, and likelihood ratios (LRs) were calculated to assess the performance of ACV, ACD, AOD500, and TISA500 in detecting narrow angles (defined as Shaffer grade ≤1 in all quadrants). SD-ASOCT images were obtained at the nasal and temporal quadrants only. Twenty-eight eyes (10.6%) were classified as narrow angles on gonioscopy. ACV correlated with gonioscopy grading (P<0.001) for temporal (r=0.204), superior (r=0.251), nasal (r=0.213), and inferior (r=0.236) quadrants. ACV correlated with TISA500 for nasal (r=0.135, P=0.029) and temporal (P=0.160, P=0.009) quadrants and also with AOD500 for nasal (r=0.498, P<0.001) and temporal (r=0.517, P<0.001) quadrants. For detection of narrow angles, ACV (AUC=0.935; 95% confidence interval (CI) =0.898-0.961) performed similar to ACD (AUC=0.88, P=0.06) and significantly better than AOD500 nasal (AUC=0.761, P=0.001), AOD500 temporal (AUC=0.808, P<0.001), TISA500 nasal (AUC=0.756, P<0.001), and TISA500 temporal (AUC=0.738, P<0.001). Using a cutoff of 113 mm(3), ACV had 90% sensitivity and 88% specificity for detecting narrow angles. Positive and negative LRs for ACV were 8.63 (95% CI=7.4-10.0) and 0.11 (95% CI=0.03-0.4), respectively. ACV measurements using Scheimpflug imaging outperformed AOD500 and TISA500 using SD-ASOCT for detecting narrow angles.

Structural and kinetic studies of a novel nerol dehydrogenase from Persicaria minor, a nerol-specific enzyme for citral biosynthesis.

PubMed

Tan, Cheng Seng; Hassan, Maizom; Mohamed Hussein, Zeti Azura; Ismail, Ismanizan; Ho, Kok Lian; Ng, Chyan Leong; Zainal, Zamri

2018-02-01

Geraniol degradation pathway has long been elucidated in microorganisms through bioconversion studies, yet weakly characterised in plants; enzyme with specific nerol-oxidising activity has not been reported. A novel cDNA encodes nerol dehydrogenase (PmNeDH) was isolated from Persicaria minor. The recombinant PmNeDH (rPmNeDH) is a homodimeric enzyme that belongs to MDR (medium-chain dehydrogenases/reductases) superfamily that catalyses the first oxidative step of geraniol degradation pathway in citral biosynthesis. Kinetic analysis revealed that rPmNeDH has a high specificity for allylic primary alcohols with backbone ≤10 carbons. rPmNeDH has ∼3 fold higher affinity towards nerol (cis-3,7-dimethyl-2,6-octadien-1-ol) than its trans-isomer, geraniol. To our knowledge, this is the first alcohol dehydrogenase with higher preference towards nerol, suggesting that nerol can be effective substrate for citral biosynthesis in P. minor. The rPmNeDH crystal structure (1.54 Å) showed high similarity with enzyme structures from MDR superfamily. Structure guided mutation was conducted to describe the relationships between substrate specificity and residue substitutions in the active site. Kinetics analyses of wild-type rPmNeDH and several active site mutants demonstrated that the substrate specificity of rPmNeDH can be altered by changing any selected active site residues (Asp 280 , Leu 294 and Ala 303 ). Interestingly, the L294F, A303F and A303G mutants were able to revamp the substrate preference towards geraniol. Furthermore, mutant that exhibited a broader substrate range was also obtained. This study demonstrates that P. minor may have evolved to contain enzyme that optimally recognise cis-configured nerol as substrate. rPmNeDH structure provides new insights into the substrate specificity and active site plasticity in MDR superfamily. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Scopolin-hydrolyzing beta-glucosidases in roots of Arabidopsis.

PubMed

Ahn, Young Ock; Shimizu, Bun-ichi; Sakata, Kanzo; Gantulga, Dashzeveg; Zhou, Changhe; Zhou, Zhanghe; Bevan, David R; Esen, Asim

2010-01-01

Three beta-glucosidases (At1g66270-BGLU21, At1g66280-BGLU22, and At3g09260-BGLU23) were purified from the roots of Arabidopsis and their cDNAs were expressed in insect cells. In addition, two beta-glucosidase binding protein cDNAs (At3g16420; PBPI and At3g16430; PBPII) were expressed in Escherichia coli and their protein products purified. These binding proteins interact with beta-glucosidases and activate them. BGLU21, 22 and 23 hydrolyzed the natural substrate scopolin specifically and also hydrolyzed to some extent substrates whose aglycone moiety is similar to scopolin (e.g. esculin and 4-MU-glucoside). In contrast, they hydrolyzed poorly DIMBOA-glucoside and did not hydrolyze pNP- and oNP-glucosides. We determined the physicochemical properties of native and recombinant BGLUs, and found no differences between them. They were stable in a narrow pH range (5-7.5) and had temperature and pH optima for activity at 35 degrees C and pH 5.5, respectively. As for thermostability, >95% of their activity was retained at 40 degrees C but dramatically decreased at >50 degrees C. The apparent K(m) of native and recombinant enzymes for scopolin was 0.73 and 0.81 mM, respectively, and it was 5.8 and 9.7 mM, respectively, for esculin. Western blot analysis showed that all three enzymes were exclusively expressed in roots of seedlings but not in any other plant part or organ under normal conditions. Furthermore, spatial expression patterns of all eight genes belonging to subfamily 3 were investigated at the transcription level by RT-PCR.

Measurements of the absorption coefficient of stratospheric aerosols

NASA Technical Reports Server (NTRS)

Ogren, J. A.; Ahlquist, N. C.; Clarke, A. D.; Charlson, R. J.

1981-01-01

The absorption coefficients of stratospheric aerosols are measured using a variation on the integrating plate method. The technique is based on the decrease in the transparency of a substrate when an absorbing aerosol is deposited on it. A Lambert scatterer is placed behind the substrate to integrate forward scattered light and minimize the effect of scattering on the measurement. The low pressure in the stratosphere is used for the direct impaction of particles onto a narrow strip of opal glass. The eight samples collected had a median value of 4 x 10 to the -9th m with an uncertainty of + or - 5 x 10 to the -9th m. If this absorption is due to graphitic carbon, then its concentration is estimated at about 0.4 ng/cu m, or about 0.25% of the total aerosol mass concentration. Estimates of the aerosol scattering coefficients based on satellite extinction inversions result in an aerosol single-scattering albedo in the range of 0.96-1.0.

Flexible organic transistors and circuits with extreme bending stability

NASA Astrophysics Data System (ADS)

Sekitani, Tsuyoshi; Zschieschang, Ute; Klauk, Hagen; Someya, Takao

2010-12-01

Flexible electronic circuits are an essential prerequisite for the development of rollable displays, conformable sensors, biodegradable electronics and other applications with unconventional form factors. The smallest radius into which a circuit can be bent is typically several millimetres, limited by strain-induced damage to the active circuit elements. Bending-induced damage can be avoided by placing the circuit elements on rigid islands connected by stretchable wires, but the presence of rigid areas within the substrate plane limits the bending radius. Here we demonstrate organic transistors and complementary circuits that continue to operate without degradation while being folded into a radius of 100μm. This enormous flexibility and bending stability is enabled by a very thin plastic substrate (12.5μm), an atomically smooth planarization coating and a hybrid encapsulation stack that places the transistors in the neutral strain position. We demonstrate a potential application as a catheter with a sheet of transistors and sensors wrapped around it that enables the spatially resolved measurement of physical or chemical properties inside long, narrow tubes.

Terahertz radiation in graphene hyperbolic medium excited by an electric dipole.

PubMed

Feng, Xiaodong; Gong, Sen; Zhong, Renbin; Zhao, Tao; Hu, Min; Zhang, Chao; Liu, Shenggang

2018-03-01

In this Letter, the enhanced and directional radiation in a wide terahertz (THz) frequency range in a graphene hyperbolic medium excited by an electric dipole is presented. The numerical simulations and theoretical analyses indicate that the enhanced radiation comes from the strong surface plasmon couplings in the graphene hyperbolic medium, consisting of alternative graphene and dielectric substrate layers. The simulation results also show that the peak power flow of the enhanced THz radiation in the graphene hyperbolic medium is dramatically enhanced by more than 1 order of magnitude over that in a general medium within a certain distance from the dipole, and the electromagnetic fields are strongly concentrated in a narrow angle. Also, the radiation fields can be manipulated, and the fields' angular distributions can be tuned by adjusting the dielectric permittivity and thickness of the substrates, and the chemical potential of graphene. Accordingly, it provides a good opportunity for developing miniature, integratable, high-power-density, and tunable radiation sources in the THz band at room temperature.

Front-Side Microstrip Line Feeding a Raised Antenna Patch

NASA Technical Reports Server (NTRS)

Hodges, Richard; Hoppe, Daniel

2005-01-01

An improved design concept for a printed-circuit patch antenna and the transmission line that feeds the patch calls for (1) a microstrip transmission line on the front (radiative) side of a printed-circuit board based on a thin, high-permittivity dielectric substrate; (2) using the conductor covering the back side of the circuit board as a common ground plane for both the microstrip line and the antenna patch; (3) supporting the antenna patch in front of the circuit board on a much thicker, lower-permittivity dielectric spacer layer; and (4) connecting the microstrip transmission line to the patch by use of a thin wire or narrow ribbon that extends through the thickness of the spacer and is oriented perpendicularly to the circuit-board plane. The thickness of the substrate is typically chosen so that a microstrip transmission line of practical width has an impedance between 50 and 100 ohms. The advantages of this design concept are best understood in the context of the disadvantages of prior design concepts, as explained

Sodium-coupled neutral amino acid (System N/A) transporters of the SLC38 gene family.

PubMed

Mackenzie, Bryan; Erickson, Jeffrey D

2004-02-01

The sodium-coupled neutral amino acid transporters (SNAT) of the SLC38 gene family resemble the classically-described System A and System N transport activities in terms of their functional properties and patterns of regulation. Transport of small, aliphatic amino acids by System A subtypes (SNAT1, SNAT2, and SNAT4) is rheogenic and pH sensitive. The System N subtypes SNAT3 and SNAT5 also countertransport H(+), which may be key to their operation in reverse, and have narrower substrate profiles than do the System A subtypes. Glutamine emerges as a favored substrate throughout the family, except for SNAT4. The SLC38 transporters undoubtedly play many physiological roles including the transfer of glutamine from astrocyte to neuron in the CNS, ammonia detoxification and gluconeogenesis in the liver, and the renal response to acidosis. Probing their regulation has revealed additional roles, and recent work has considered SLC38 transporters as therapeutic targets in neoplasia.

A metal-insulator transition study of VO 2 thin films grown on sapphire substrates

DOE PAGES

Yu, Shifeng; Wang, Shuyu; Lu, Ming; ...

2017-12-15

In this paper, vanadium thin films were deposited on sapphire substrates by DC magnetron sputtering and then oxidized in a tube furnace filled with oxygen under different temperatures and oxygen flow rates. The significant influence of the oxygen flow rate and oxidation temperature on the electrical and structural properties of the vanadium oxide thin films were investigated systematically. It shows the pure vanadium dioxide (VO 2) state can only be obtained in a very narrow temperature and oxygen flow rate range. The resistivity change during the metal-insulator transition varies from 0.2 to 4 orders of magnitude depending on the oxidationmore » condition. Large thermal hysteresis during the metal-insulator phase transition was observed during the transition compared to the results in literature. Proper oxidation conditions can significantly reduce the thermal hysteresis. Finally, the fabricated VO 2 thin films showed the potential to be applied in the development of electrical sensors and other smart devices.« less

Sensitive SERS detection at the single-particle level based on nanometer-separated mushroom-shaped plasmonic dimers

NASA Astrophysics Data System (ADS)

Xiang, Quan; Li, Zhiqin; Zheng, Mengjie; Liu, Qing; Chen, Yiqin; Yang, Lan; Jiang, Tian; Duan, Huigao

2018-03-01

Elevated metallic nanostructures with nanogaps (<10 nm) possess advantages for surface enhanced Raman scattering (SERS) via the synergic effects of nanogaps and efficient decoupling from the substrate through an elevated three-dimensional (3D) design. In this work, we demonstrate a pattern-transfer-free process to reliably define elevated nanometer-separated mushroom-shaped dimers directly from 3D resist patterns based on the gap-narrowing effect during the metallic film deposition. By controlling the initial size of nanogaps in resist structures and the following deposited film thickness, metallic nanogaps could be tuned at the sub-10 nm scale with single-digit nanometer precision. Both experimental and simulated results revealed that gold dimer on mushroom-shaped pillars have the capability to achieve higher SERS enhancement factor comparing to those plasmonic dimers on cylindrical pillars or on a common SiO2/Si substrate, implying that the nanometer-gapped elevated dimer is an ideal platform to achieve the highest possible field enhancement for various plasmonic applications.

Structure of a Type-1 Secretion System ABC Transporter.

PubMed

Morgan, Jacob L W; Acheson, Justin F; Zimmer, Jochen

2017-03-07

Type-1 secretion systems (T1SSs) represent a widespread mode of protein secretion across the cell envelope in Gram-negative bacteria. The T1SS is composed of an inner-membrane ABC transporter, a periplasmic membrane-fusion protein, and an outer-membrane porin. These three components assemble into a complex spanning both membranes and providing a conduit for the translocation of unfolded polypeptides. We show that ATP hydrolysis and assembly of the entire T1SS complex is necessary for protein secretion. Furthermore, we present a 3.15-Å crystal structure of AaPrtD, the ABC transporter found in the Aquifex aeolicus T1SS. The structure suggests a substrate entry window just above the transporter's nucleotide binding domains. In addition, highly kinked transmembrane helices, which frame a narrow channel not observed in canonical peptide transporters, are likely involved in substrate translocation. Overall, the AaPrtD structure supports a polypeptide transport mechanism distinct from alternating access. Copyright © 2017 Elsevier Ltd. All rights reserved.

Analysis of epitaxial drift field N on P silicon solar cells

NASA Technical Reports Server (NTRS)

Baraona, C. R.; Brandhorst, H. W., Jr.

1976-01-01

The performance of epitaxial drift field silicon solar cell structures having a variety of impurity profiles was calculated. These structures consist of a uniformly doped P-type substrate layer, and a P-type epitaxial drift field layer with a variety of field strengths. Several N-layer structures were modeled. A four layer solar cell model was used to calculate efficiency, open circuit voltage and short circuit current. The effect on performance of layer thickness, doping level, and diffusion length was determined. The results show that peak initial efficiency of 18.1% occurs for a drift field thickness of about 30 micron with the doping rising from 10 to the 17th power atoms/cu cm at the edge of the depletion region to 10 to the 18th power atoms/cu cm in the substrate. Stronger drift fields (narrow field regions) allowed very high performance (17% efficiency) even after irradiation to 3x10 to the 14th power 1 MeV electrons/sq cm.

Growth characteristics of (100)HgCdTe layers in low-temperature MOVPE with ditertiarybutyltelluride

NASA Astrophysics Data System (ADS)

Yasuda, K.; Hatano, H.; Ferid, T.; Minamide, M.; Maejima, T.; Kawamoto, K.

1996-09-01

Low-temperature growth of (100)HgCdTe (MCT) layers in MOVPE has been studied using ditertiarybutyltelluride (DtBTe), dimethylcadmium (DMCd), and elementary mercury as precursors. MCT layers were grown at 275°C on (100)GaAs substrates. Growths were carried out in a vertical growth cell which has a narrow spacing between the substrate and cell ceiling. Using the growth cell, the Cd-composition ( x) of MCT layers was controlled over a wide range from 0 to 0.98 by the DMCd flow. The growth rate of the MCT layers was constant at 5 μm h -1 for the increased DMCd flow. Preferential Cd-incorporation into MCT layers and an increase of the growth rate were observed in the presence of mercury vapor. The growth characteristics were considered to be due to the alkyl-exchange reaction between DMCd and mercury. The electrical properties and crystallinity of grown layers were also evaluated, which showed that layers with high quality can be grown at 275°C.

Highly oriented Bi-based thin films with zero resistance at 106 K

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

Kula, W.; Sobolewski, R.; Gorecka, J.

1991-03-01

This paper reports on fabrication and characterization of nearly single-phase superconducting Bi{sub 2}Sr{sub 2}Ca{sub 2}Cu{sub 3}O{sub x} thin films. The films were dc magnetron sputtered from heavily Pb-doped (Pb/Bi molar ratios up to 1.25), sintered targets on unheated MgO, SrTiO{sub 3}, CaNdAlO{sub 4}, and SrLaAlO{sub 4} single crystals. For the films grown on the (100) oriented MgO substrate, less than 1 hour of annealing in air at 870{degrees} C was sufficient to obtain more than 90% of the 110-K-phase material, with highly c-axis oriented crystalline structure and zero resistivity at 106 K. The films fabricated on the other substrates alsomore » exhibited a narrow superconducting transition and were fully superconducting above 100 K, but they consisted of a mixed-phase material with a large percentage of the 80 K phase.« less

Electrical characterizations of MIS structures based on variable-gap n(p)-HgCdTe grown by MBE on Si(0 1 3) substrates

NASA Astrophysics Data System (ADS)

Voitsekhovskii, A. V.; Nesmelov, S. N.; Dzyadukh, S. M.; Varavin, V. S.; Dvoretskii, S. A.; Mikhailov, N. N.; Yakushev, M. V.; Sidorov, G. Yu.

2017-12-01

Metal-insulator-semiconductor (MIS) structures based on n(p)-Hg1-xCdxTe (x = 0.22-0.40) with near-surface variable-gap layers were grown by the molecular-beam epitaxy (MBE) technique on the Si (0 1 3) substrates. Electrical properties of MIS structures were investigated experimentally at various temperatures (9-77 K) and directions of voltage sweep. The ;narrow swing; technique was used to determine the spectra of fast surface states with the exception of hysteresis effects. It is established that the density of fast surface states at the MCT/Al2O3 interface at a minimum does not exceed 3 × 1010 eV-1 × cm-2. For MIS structures based on n-MCT/Si(0 1 3), the differential resistance of the space-charge region in strong inversion mode in the temperature range 50-90 K is limited by the Shockley-Read-Hall generation in the space-charge region.

Low resistance thin film organic solar cell electrodes

DOEpatents

Forrest, Stephen [Princeton, NJ; Xue, Jiangeng [Piscataway, NJ

2008-01-01

A method which lower the series resistance of photosensitive devices includes providing a transparent film of a first electrically conductive material arranged on a transparent substrate; depositing and patterning a mask over the first electrically conductive material, such that openings in the mask have sloping sides which narrow approaching the substrate; depositing a second electrically conductive material directly onto the first electrically conductive material exposed in the openings of the mask, at least partially filling the openings; stripping the mask, leaving behind reentrant structures of the second electrically conductive material which were formed by the deposits in the openings of the mask; after stripping the mask, depositing a first organic material onto the first electrically conductive material in between the reentrant structures; and directionally depositing a third electrically conductive material over the first organic material deposited in between the reentrant structures, edges of the reentrant structures aligning deposition so that the third electrically conductive material does not directly contact the first electrically conductive material, and does not directly contact the second electrically conductive material.

Encapsulation of Polymer Colloids in a Sol-Gel Matrix. Direct-Writing of Coassembling Organic-Inorganic Hybrid Photonic Crystals.

PubMed

Mikosch, Annabel; Kuehne, Alexander J C

2016-03-22

The spontaneous self-assembly of polymer colloids into ordered arrangements provides a facile strategy for the creation of photonic crystals. However, these structures often suffer from defects and insufficient cohesion, which result in flaking and delamination from the substrate. A coassembly process has been developed for convective assembly, resulting in large-area encapsulated colloidal crystals. However, to generate patterns or discrete deposits in designated places, convective assembly is not suitable. Here we experimentally develop conditions for direct-writing of coassembling monodisperse dye-doped polystyrene particles with a sol-gel precursor to form solid encapsulated photonic crystals. In a simple procedure the colloids are formulated in a sol-gel precursor solution, drop-cast on a flat substrate, and dried. We here establish the optimal parameters to form reproducible highly ordered photonic crystals with good optical performance. The obtained photonic crystals interact with light in the visible spectrum with a narrow optical stop-gap.

High aspect ratio nano-fabrication of photonic crystal structures on glass wafers using chrome as hard mask.

PubMed

Hossain, Md Nazmul; Justice, John; Lovera, Pierre; McCarthy, Brendan; O'Riordan, Alan; Corbett, Brian

2014-09-05

Wafer-scale nano-fabrication of silicon nitride (Si x N y ) photonic crystal (PhC) structures on glass (quartz) substrates is demonstrated using a thin (30 nm) chromium (Cr) layer as the hard mask for transferring the electron beam lithography (EBL) defined resist patterns. The use of the thin Cr layer not only solves the charging effect during the EBL on the insulating substrate, but also facilitates high aspect ratio PhCs by acting as a hard mask while deep etching into the Si x N y . A very high aspect ratio of 10:1 on a 60 nm wide grating structure has been achieved while preserving the quality of the flat top of the narrow lines. The presented nano-fabrication method provides PhC structures necessary for a high quality optical response. Finally, we fabricated a refractive index based PhC sensor which shows a sensitivity of 185 nm per RIU.

Photodetectors based on single-walled carbon nanotubes and thiamonomethinecyanine J-aggregates on flexible substrates

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

Fedorov, I. V., E-mail: i-v-fedorov@mail.ru; Emel’yanov, A. V.; Romashkin, A. V.

2015-09-15

The present paper is devoted to observations of the photoresistive effect in multilayer structures with a sensitive layer of J-aggregates of thiamonomethinecyanine polymethine dye and a transparent electrode of a conductive carbon-nanotube network on a flexible polyethylenenaphtalate substrate. The effect of narrow-band emission with a wavelength of 465 nm on a change in the conductivity of the fabricated structures is studied. The prepared samples are studied by atomic-force microscopy, Raman spectroscopy, and spectrophotometry methods. It is shown that these structures are photosensitive to the indicated spectral region, and the dye layer is a film of dye J-aggregates. The change inmore » the sample conductivity upon exposure to light one hundred times exceeds the dark conductivity. In general, the principal possibility of developing a photoresistive detector based on J-aggregates of cyanine dyes on flexible supports on account of the use of transparent and conductive carbon-nanotube layers is shown.« less

Use of CdS quantum dot-functionalized cellulose nanocrystal films for anti-counterfeiting applications.

PubMed

Chen, L; Lai, C; Marchewka, R; Berry, R M; Tam, K C

2016-07-21

Structural colors and photoluminescence have been widely used for anti-counterfeiting and security applications. We report for the first time the use of CdS quantum dot (QD)-functionalized cellulose nanocrystals (CNCs) as building blocks to fabricate nanothin films via layer-by-layer (LBL) self-assembly for anti-counterfeiting applications. Both negatively- and positively-charged CNC/QD nanohybrids with a high colloidal stability and a narrow particle size distribution were prepared. The controllable LBL coating process was characterized by scanning electron microscopy and ellipsometry. The rigid structure of CNCs leads to nanoporous structured films on poly(ethylene terephthalate) (PET) substrates with high transmittance (above 70%) over the entire range of visible light and also resulted in increased hydrophilicity (contact angles of ∼40 degrees). Nanothin films on PET substrates showed good flexibility and enhanced stability in both water and ethanol. The modified PET films with structural colors from thin-film interference and photoluminescence from QDs can be used in anti-counterfeiting applications.

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

A universal small molecule, inorganic phosphate, restricts the substrate specificity of Dicer-2 in small RNA biogenesis

PubMed Central

Fukunaga, Ryuya; Zamore, Phillip D

2014-01-01

The enzyme Dicer is central to the production of small silencing RNAs such as microRNAs (miRNAs) and small interfering RNAs (siRNAs). Like other insects, Drosophila melanogaster uses different Dicers to make siRNAs and miRNAs: Dicer-1 produces miRNAs from pre-miRNAs, whereas Dicer-2 generates siRNAs from long double-stranded RNA (dsRNA). How do the 2 Dicers achieve their substrate specificity? Here, we review recent findings that inorganic phosphate restricts the substrate specificity of Dicer-2 to long dsRNA. Inorganic phosphate inhibits Dicer-2 from binding and cleaving pre-miRNAs, without affecting the processing of long dsRNA. Crystal structures of a fragment of human Dicer in complex with an RNA duplex identify a phosphate-binding pocket that recognizes both the 5′-monophosphate of a substrate RNA and inorganic phosphate. We propose that inorganic phosphate occupies the phosphate-binding pocket in the fly Dicer-2, blocking binding of pre-miRNA and restricting pre-miRNA processing to Dicer-1. Thus, a small molecule can alter the substrate specificity of a nucleic acid-processing enzyme. PMID:24787225

Mammalian Protein Arginine Methyltransferase 7 (PRMT7) Specifically Targets RXR Sites in Lysine- and Arginine-rich Regions*

PubMed Central

Feng, You; Maity, Ranjan; Whitelegge, Julian P.; Hadjikyriacou, Andrea; Li, Ziwei; Zurita-Lopez, Cecilia; Al-Hadid, Qais; Clark, Amander T.; Bedford, Mark T.; Masson, Jean-Yves; Clarke, Steven G.

2013-01-01

The mammalian protein arginine methyltransferase 7 (PRMT7) has been implicated in roles of transcriptional regulation, DNA damage repair, RNA splicing, cell differentiation, and metastasis. However, the type of reaction that it catalyzes and its substrate specificity remain controversial. In this study, we purified a recombinant mouse PRMT7 expressed in insect cells that demonstrates a robust methyltransferase activity. Using a variety of substrates, we demonstrate that the enzyme only catalyzes the formation of ω-monomethylarginine residues, and we confirm its activity as the prototype type III protein arginine methyltransferase. This enzyme is active on all recombinant human core histones, but histone H2B is a highly preferred substrate. Analysis of the specific methylation sites within intact histone H2B and within H2B and H4 peptides revealed novel post-translational modification sites and a unique specificity of PRMT7 for methylating arginine residues in lysine- and arginine-rich regions. We demonstrate that a prominent substrate recognition motif consists of a pair of arginine residues separated by one residue (RXR motif). These findings will significantly accelerate substrate profile analysis, biological function study, and inhibitor discovery for PRMT7. PMID:24247247

Mammalian protein arginine methyltransferase 7 (PRMT7) specifically targets RXR sites in lysine- and arginine-rich regions.

PubMed

Feng, You; Maity, Ranjan; Whitelegge, Julian P; Hadjikyriacou, Andrea; Li, Ziwei; Zurita-Lopez, Cecilia; Al-Hadid, Qais; Clark, Amander T; Bedford, Mark T; Masson, Jean-Yves; Clarke, Steven G

2013-12-27

The mammalian protein arginine methyltransferase 7 (PRMT7) has been implicated in roles of transcriptional regulation, DNA damage repair, RNA splicing, cell differentiation, and metastasis. However, the type of reaction that it catalyzes and its substrate specificity remain controversial. In this study, we purified a recombinant mouse PRMT7 expressed in insect cells that demonstrates a robust methyltransferase activity. Using a variety of substrates, we demonstrate that the enzyme only catalyzes the formation of ω-monomethylarginine residues, and we confirm its activity as the prototype type III protein arginine methyltransferase. This enzyme is active on all recombinant human core histones, but histone H2B is a highly preferred substrate. Analysis of the specific methylation sites within intact histone H2B and within H2B and H4 peptides revealed novel post-translational modification sites and a unique specificity of PRMT7 for methylating arginine residues in lysine- and arginine-rich regions. We demonstrate that a prominent substrate recognition motif consists of a pair of arginine residues separated by one residue (RXR motif). These findings will significantly accelerate substrate profile analysis, biological function study, and inhibitor discovery for PRMT7.

Narrow bandgap semiconducting silicides: Intrinsic infrared detectors on a silicon chip

NASA Technical Reports Server (NTRS)

Mahan, John E.

1989-01-01

Polycrystalline thin films of CrSi2, LaSi2, and ReSi2 were grown on silicon substrates. Normal incidence optical transmittance and reflectance measurements were made as a function of wavelength. It was demonstrated that LaSi2 is a metallic conductor, but that CrSi2 and ReSi2 are, in fact, narrow bandgap semiconductors. For CrSi2, the complex index of refraction was determined by computer analysis of the optical data. From the imaginary part, the optical absorption coefficient was determined as a function of photon energy. It was shown that CrSi2 possesses an indirect forbidden energy gap of slightly less than 0.31 eV, and yet it is a very strong absorber of light above the absorption edge. On the other hand, the ReSi2 films exhibit an absorption edge in the vicinity of 0.2 eV. Measurements of the thermal activation energy of resistivity for ReSi2 indicate a bandgap of 0.18 eV. It is concluded that the semiconducting silicides merit further investigation for development as new silicon-compatible infrared detector materials.

Using oriented peptide array libraries to evaluate methylarginine-specific antibodies and arginine methyltransferase substrate motifs

PubMed Central

Gayatri, Sitaram; Cowles, Martis W.; Vemulapalli, Vidyasiri; Cheng, Donghang; Sun, Zu-Wen; Bedford, Mark T.

2016-01-01

Signal transduction in response to stimuli relies on the generation of cascades of posttranslational modifications that promote protein-protein interactions and facilitate the assembly of distinct signaling complexes. Arginine methylation is one such modification, which is catalyzed by a family of nine protein arginine methyltransferases, or PRMTs. Elucidating the substrate specificity of each PRMT will promote a better understanding of which signaling networks these enzymes contribute to. Although many PRMT substrates have been identified, and their methylation sites mapped, the optimal target motif for each of the nine PRMTs has not been systematically addressed. Here we describe the use of Oriented Peptide Array Libraries (OPALs) to methodically dissect the preferred methylation motifs for three of these enzymes – PRMT1, CARM1 and PRMT9. In parallel, we show that an OPAL platform with a fixed methylarginine residue can be used to validate the methyl-specific and sequence-specific properties of antibodies that have been generated against different PRMT substrates, and can also be used to confirm the pan nature of some methylarginine-specific antibodies. PMID:27338245

Design and isolation of ribozyme-substrate pairs using RNase P-based ribozymes containing altered substrate binding sites.

PubMed Central

Mobley, E M; Pan, T

1999-01-01

Substrate recognition and cleavage by the bacterial RNase P RNA requires two domains, a specificity domain, or S-domain, and a catalytic domain, or C-domain. The S-domain binds the T stem-loop region in a pre-tRNA substrate to confer specificity for tRNA substrates. In this work, the entire S-domain of the Bacillus subtilis RNase P RNA is replaced with an artificial substrate binding module. New RNA substrates are isolated by in vitro selection using two libraries containing random regions of 60 nt. At the end of the selection, the cleavage rates of the substrate library are approximately 0.7 min(-1)in 10 mM MgCl(2)at 37 degrees C, approximately 4-fold better than the cleavage of a pre-tRNA substrate by the wild-type RNase P RNA under the same conditions. The contribution of the S-domain replacement to the catalytic efficiency is from 6- to 22 000-fold. Chemical and nuclease mapping of two ribozyme-product complexes shows that this contribution correlates with direct interactions between the S-domain replacement and the selected substrate. These results demonstrate the feasibility of design and isolation of RNase P-based, matching ribozyme-substrate pairs without prior knowledge of the sequence or structure of the interactive modules in the ribozyme or substrate. PMID:10518624

Structural insights into the difference in substrate recognition of two mannoside phosphorylases from two GH130 subfamilies.

PubMed

Ye, Yuxin; Saburi, Wataru; Odaka, Rei; Kato, Koji; Sakurai, Naofumi; Komoda, Keisuke; Nishimoto, Mamoru; Kitaoka, Motomitsu; Mori, Haruhide; Yao, Min

2016-03-01

In Ruminococcus albus, 4-O-β-D-mannosyl-D-glucose phosphorylase (RaMP1) and β-(1,4)-mannooligosaccharide phosphorylase (RaMP2) belong to two subfamilies of glycoside hydrolase family 130. The two enzymes phosphorolyze β-mannosidic linkages at the nonreducing ends of their substrates, and have substantially diverse substrate specificity. The differences in their mechanism of substrate binding have not yet been fully clarified. In the present study, we report the crystal structures of RaMP1 with/without 4-O-β-D-mannosyl-d-glucose and RaMP2 with/without β-(1→4)-mannobiose. The structures of the two enzymes differ at the +1 subsite of the substrate-binding pocket. Three loops are proposed to determine the different substrate specificities. One of these loops is contributed from the adjacent molecule of the oligomer structure. In RaMP1, His245 of loop 3 forms a hydrogen-bond network with the substrate through a water molecule, and is indispensible for substrate binding. © 2016 Federation of European Biochemical Societies.

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.

Integrating gastrocnemius force-length properties, in vivo activation and operating lengths reveals how Anolis deal with ecological challenges.

PubMed

Foster, Kathleen L; Higham, Timothy E

2017-03-01

A central question in biology is how animals successfully behave under complex natural conditions. Although changes in locomotor behaviour, motor control and force production in relation to incline are commonly examined, a wide range of other factors, including a range of perch diameters, pervades arboreal habitats. Moving on different substrate diameters requires considerable alteration of body and limb posture, probably causing significant shifts in the lengths of the muscle-tendon units powering locomotion. Thus, how substrate shape impacts in vivo muscle function remains an important but neglected question in ecophysiology. Here, we used high-speed videography, electromyography, in situ contractile experiments and morphology to examine gastrocnemius muscle function during arboreal locomotion in the Cuban knight anole, Anolis equestris The gastrocnemius contributes more to the propulsive effort on broad surfaces than on narrow surfaces. Surprisingly, substrate inclination affected the relationship between the maximum potential force and fibre recruitment; the trade-off that was present between these variables on horizontal surfaces became a positive relationship on inclined surfaces. Finally, the biarticular nature of the gastrocnemius allows it to generate force isometrically, regardless of substrate diameter and incline, despite the fact that the tendons are incapable of stretching during cyclical locomotion. Our results emphasize the importance of considering ecology and muscle function together, and the necessity of examining both mechanical and physiological properties of muscles to understand how animals move in their environment. © 2017. Published by The Company of Biologists Ltd.

Development of a self-packaged 2D MEMS thermal wind sensor for low power applications

NASA Astrophysics Data System (ADS)

Zhu, Yan-qing; Chen, Bei; Qin, Ming; Huang, Jian-qiu; Huang, Qing-an

2015-08-01

This article describes the design, fabrication, and testing of a self-packaged 2D thermal wind sensor. The sensor consists of four heaters and nine thermistors. A central thermistor senses the average heater temperature, whereas the other eight, which are distributed symmetrically around the heaters, measure the temperature differences between the upstream and downstream surface of the sensor. The sensor was realized on one side of a silicon-in-glass (SIG) substrate. Vertical silicon vias in the substrate ensure good thermal contact between the sensor and the airflow and the glass effectively isolates the heaters from the thermistors. The substrate was fabricated by using a glass reflow process, after which the sensor was realized by a lift-off process. The sensor’s geometry was investigated with the help of simulations. These show that narrow heaters, moderate heater spacing, and thin substrates all improve the sensor’s sensitivity. Finally, the sensor was tested and calibrated in a wind tunnel by using a linear interpolation algorithm. At a constant heating power of 24.5 mW, measurement results show that the sensor can detect airflow speeds of up to 25 m s-1, with an accuracy of 0.1 m s-1 at low speeds and 0.5 m s-1 at high speeds. Airflow direction can be determined in a range of 360° with an accuracy of ±6°.

The Structure of Lombricine Kinase

PubMed Central

Bush, D. Jeffrey; Kirillova, Olga; Clark, Shawn A.; Davulcu, Omar; Fabiola, Felcy; Xie, Qing; Somasundaram, Thayumanasamy; Ellington, W. Ross; Chapman, Michael S.

2011-01-01

Lombricine kinase is a member of the phosphagen kinase family and a homolog of creatine and arginine kinases, enzymes responsible for buffering cellular ATP levels. Structures of lombricine kinase from the marine worm Urechis caupo were determined by x-ray crystallography. One form was crystallized as a nucleotide complex, and the other was substrate-free. The two structures are similar to each other and more similar to the substrate-free forms of homologs than to the substrate-bound forms of the other phosphagen kinases. Active site specificity loop 309–317, which is disordered in substrate-free structures of homologs and is known from the NMR of arginine kinase to be inherently dynamic, is resolved in both lombricine kinase structures, providing an improved basis for understanding the loop dynamics. Phosphagen kinases undergo a segmented closing on substrate binding, but the lombricine kinase ADP complex is in the open form more typical of substrate-free homologs. Through a comparison with prior complexes of intermediate structure, a correlation was revealed between the overall enzyme conformation and the substrate interactions of His178. Comparative modeling provides a rationale for the more relaxed specificity of these kinases, of which the natural substrates are among the largest of the phosphagen substrates. PMID:21212263

Sentan: A Novel Specific Component of the Apical Structure of Vertebrate Motile Cilia

PubMed Central

Yuba-Kubo, Akiko; Tsukita, Sachiko; Tsukita, Shoichiro; Amagai, Masayuki

2008-01-01

Human respiratory and oviductal cilia have specific apical structures characterized by a narrowed distal portion and a ciliary crown. These structures are conserved among vertebrates that have air respiration systems; however, the molecular components of these structures have not been defined, and their functions are unknown. To identify the molecular component(s) of the cilia apical structure, we screened EST libraries to identify gene(s) that are exclusively expressed in ciliated tissues, are transcriptionally up-regulated during in vitro ciliogenesis, and are not expressed in testis (because sperm flagella have no such apical structures). One of the identified gene products, named sentan, was localized to the distal tip region of motile cilia. Using anti-sentan polyclonal antibodies and electron microscopy, sentan was shown to localize exclusively to the bridging structure between the cell membrane and peripheral singlet microtubules, which specifically exists in the narrowed distal portion of cilia. Exogenously expressed sentan showed affinity for the membrane protrusions, and a protein–lipid binding assay revealed that sentan bound to phosphatidylserine. These findings suggest that sentan is the first molecular component of the ciliary tip to bridge the cell membrane and peripheral singlet microtubules, making the distal portion of the cilia narrow and stiff to allow for better airway clearance or ovum transport. PMID:18829862

Rapid change with depth in megabenthic structure-forming communities of the Makapu'u deep-sea coral bed

NASA Astrophysics Data System (ADS)

Long, Dustin J.; Baco, Amy R.

2014-01-01

Seamounts are largely unexplored undersea mountains rising abruptly from the ocean floor, which can support an increased abundance and diversity of organisms. Deep-sea corals are important benthic structure-formers on current-swept hard substrates in these habitats. While depth is emerging as a factor structuring the fauna of seamounts on a large spatial scale, most work addressing deep-sea coral and seamount community structure has not considered the role of small-scale variation in species distributions. Video from six ROV dives over a depth range of ~320-530 m were analyzed to assess the diversity and density of benthic megafaunal invertebrates across the Makapu'u deep-sea coral bed, offshore of Oahu, Hawaii. At the same time, the physical environment along the dive track was surveyed to relate biotic patterns with abiotic variables including depth, aspect, rugosity, substrate, slope and relief to test the factors structuring community assemblages. Despite the narrow range examined, depth was found to be the strongest structuring gradient, and six unique macrobenthic communities were found, with a 93% faunal dissimilarity over the depth surveyed. Relief, rugosity and slope were also factors in the final model. Alcyonacean octocorals were the dominant macrofaunal invertebrates at all but the deepest depth zone. The commercially harvested precious coral C. secundum was the dominant species at depths 370-470 m, with a distribution that is on average deeper than similar areas. This may be artificial due to the past harvesting of this species on the shallower portion of its range. Primnoid octocorals were the most abundant octocoral family overall. This work yields new insight on the spatial ecology of seamounts, pointing out that community changes can occur over narrow depth ranges and that communities can be structured by small-scale physiography.

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.

The association of foot structure and footwear fit with disability in children and adolescents with Down syndrome.

PubMed

Lim, Polly Qx; Shields, Nora; Nikolopoulos, Nikolaos; Barrett, Joanna T; Evans, Angela M; Taylor, Nicholas F; Munteanu, Shannon E

2015-01-01

Foot deformity, flat feet, and the use of ill-fitting footwear are common in children and adolescents with Down syndrome (DS). The aim of this study was to determine whether these observations are associated with foot-specific disability in this group. A cross-sectional study design. Foot structure (foot posture determined using the Arch Index, presence of hallux valgus and lesser toe deformities) and footwear fit (determined by length and width percentage differences between the participant's foot and footwear) were assessed in 50 participants with DS (22 females, 28 males) aged five to 18 with a mean (SD) age of 10.6 (3.9) years. Foot-specific disability was determined using the parent-reported Oxford Ankle Foot Questionnaire for Children (OxAFQ-C). Associations between foot structure and footwear fit with the four domains (Physical, School and play, Emotional and Footwear) of the OxAFQ-C were determined using multivariate regression modelling. The mean (SD) Arch Index was 0.29 (0.08), and the prevalence of flat feet, hallux valgus and lesser toe deformities was 76%, 10% and 12% respectively. Few participants wore footwear that was too short (10%), but the use of footwear that was too narrow was common (58%). The presence of hallux valgus was significantly associated with increased disability for the OxAFQ-C School and play domain scores. The use of narrow-fitting footwear was significantly associated with increased levels of disability for the OxAFQ-C Physical, School and play, and Emotional domains. However, these variables only explained between 10% to 14% of the variance in the OxAFQ-C domain scores. There were no significant associations between foot structure and footwear fit with the OxAFQ-C Footwear domain scores. Flatter feet and lesser toe deformities are not associated with foot-specific disability in children and adolescents with DS. Hallux valgus is associated with foot-specific disability during school and play activities. Ill-fitting footwear (too narrow) is common and is associated with foot-specific disability. Further research is required to identify if the relationship between narrow-fitting footwear and foot-specific disability is causal, and to identify other factors associated with foot-specific disability in children and adolescents with DS.

Sensitive kinase assay linked with phosphoproteomics for identifying direct kinase substrates

PubMed Central

Xue, Liang; Wang, Wen-Horng; Iliuk, Anton; Hu, Lianghai; Galan, Jacob A.; Yu, Shuai; Hans, Michael; Geahlen, Robert L.; Tao, W. Andy

2012-01-01

Our understanding of the molecular control of many disease pathologies requires the identification of direct substrates targeted by specific protein kinases. Here we describe an integrated proteomic strategy, termed kinase assay linked with phosphoproteomics, which combines a sensitive kinase reaction with endogenous kinase-dependent phosphoproteomics to identify direct substrates of protein kinases. The unique in vitro kinase reaction is carried out in a highly efficient manner using a pool of peptides derived directly from cellular kinase substrates and then dephosphorylated as substrate candidates. The resulting newly phosphorylated peptides are then isolated and identified by mass spectrometry. A further comparison of these in vitro phosphorylated peptides with phosphopeptides derived from endogenous proteins isolated from cells in which the kinase is either active or inhibited reveals new candidate protein substrates. The kinase assay linked with phosphoproteomics strategy was applied to identify unique substrates of spleen tyrosine kinase (Syk), a protein-tyrosine kinase with duel properties of an oncogene and a tumor suppressor in distinctive cell types. We identified 64 and 23 direct substrates of Syk specific to B cells and breast cancer cells, respectively. Both known and unique substrates, including multiple centrosomal substrates for Syk, were identified, supporting a unique mechanism that Syk negatively affects cell division through its centrosomal kinase activity. PMID:22451900

Surface-assisted laser desorption/ionization time-of-flight mass spectrometry of small drug molecules and high molecular weight synthetic/biological polymers using electrospun composite nanofibers.

PubMed

Bian, Juan; Olesik, Susan V

2017-03-27

Polyacrylonitrile/Nafion®/carbon nanotube (PAN/Nafion®/CNT) composite nanofibers were prepared using electrospinning. These electrospun nanofibers were studied as possible substrates for surface-assisted laser desorption/ionization (SALDI) and matrix-enhanced surface-assisted laser desorption/ionization time-of-flight mass spectrometry (ME-SALDI/TOF-MS) for the first time in this paper. Electrospinning provides this novel substrate with a uniform morphology and a narrow size distribution, where CNTs were evenly and firmly immobilized on polymeric nanofibers. The results show that PAN/Nafion®/CNT nanofibrous mats are good substrates for the analysis of both small drug molecules and high molecular weight polymers with high sensitivity. Markedly improved reproducibility was observed relative to MALDI. Due to the composite formation between the polymers and the CNTs, no contamination of the carbon nanotubes to the mass spectrometer was observed. Furthermore, electrospun nanofibers used as SALDI substrates greatly extended the duration of ion signals of target analytes compared to the MALDI matrix. The proposed SALDI approach was successfully used to quantify small drug molecules with no interference in the low mass range. The results show that verapamil could be detected with a surface concentration of 220 femtomoles, indicating the high detection sensitivity of this method. Analysis of peptides and proteins with the electrospun composite substrate using matrix assisted-SALDI was improved and a low limit of detection of approximately 6 femtomoles was obtained for IgG. Both SALDI and ME-SALDI analyses displayed high reproducibility with %RSD ≤ 9% for small drug molecules and %RSD ≤ 14% for synthetic polymers and proteins.

Accessing the dynamics of end-grafted flexible polymer chains by atomic force-electrochemical microscopy. Theoretical modeling of the approach curves by the elastic bounded diffusion model and Monte Carlo simulations. Evidence for compression-induced lateral chain escape.

PubMed

Abbou, Jeremy; Anne, Agnès; Demaille, Christophe

2006-11-16

The dynamics of a molecular layer of linear poly(ethylene glycol) (PEG) chains of molecular weight 3400, bearing at one end a ferrocene (Fc) label and thiol end-grafted at a low surface coverage onto a gold substrate, is probed using combined atomic force-electrochemical microscopy (AFM-SECM), at the scale of approximately 100 molecules. Force and current approach curves are simultaneously recorded as a force-sensing microelectrode (tip) is inserted within the approximately 10 nm thick, redox labeled, PEG chain layer. Whereas the force approach curve gives access to the structure of the compressed PEG layer, the tip-current, resulting from tip-to-substrate redox cycling of the Fc head of the chain, is controlled by chain dynamics. The elastic bounded diffusion model, which considers the motion of the Fc head as diffusion in a conformational field, complemented by Monte Carlo (MC) simulations, from which the chain conformation can be derived for any degree of confinement, allows the theoretical tip-current approach curve to be calculated. The experimental current approach curve can then be very satisfyingly reproduced by theory, down to a tip-substrate separation of approximately 2 nm, using only one adjustable parameter characterizing the chain dynamics: the effective diffusion coefficient of the chain head. At closer tip-substrate separations, an unpredicted peak is observed in the experimental current approach curve, which is shown to find its origin in a compression-induced escape of the chain from within the narrowing tip-substrate gap. MC simulations provide quantitative support for lateral chain elongation as the escape mechanism.

Wet-chemical passivation of atomically flat and structured silicon substrates for solar cell application

NASA Astrophysics Data System (ADS)

Angermann, H.; Rappich, J.; Korte, L.; Sieber, I.; Conrad, E.; Schmidt, M.; Hübener, K.; Polte, J.; Hauschild, J.

2008-04-01

Special sequences of wet-chemical oxidation and etching steps were optimised with respect to the etching behaviour of differently oriented silicon to prepare very smooth silicon interfaces with excellent electronic properties on mono- and poly-crystalline substrates. Surface photovoltage (SPV) and photoluminescence (PL) measurements, atomic force microscopy (AFM) and scanning electron microscopy (SEM) investigations were utilised to develop wet-chemical smoothing procedures for atomically flat and structured surfaces, respectively. Hydrogen-termination as well as passivation by wet-chemical oxides were used to inhibit surface contamination and native oxidation during the technological processing. Compared to conventional pre-treatments, significantly lower micro-roughness and densities of surface states were achieved on mono-crystalline Si(100), on evenly distributed atomic steps, such as on vicinal Si(111), on silicon wafers with randomly distributed upside pyramids, and on poly-crystalline EFG ( Edge-defined Film-fed- Growth) silicon substrates. The recombination loss at a-Si:H/c-Si interfaces prepared on c-Si substrates with randomly distributed upside pyramids was markedly reduced by an optimised wet-chemical smoothing procedure, as determined by PL measurements. For amorphous-crystalline hetero-junction solar cells (ZnO/a-Si:H(n)/c-Si(p)/Al) with textured c-Si substrates the smoothening procedure results in a significant increase of short circuit current Isc, fill factor and efficiency η. The scatter in the cell parameters for measurements on different cells is much narrower, as compared to conventional pre-treatments, indicating more well-defined and reproducible surface conditions prior to a-Si:H emitter deposition and/or a higher stability of the c-Si surface against variations in the a-Si:H deposition conditions.

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

PubMed Central

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

2009-01-01

Background Members of the Casein Kinase I (CKI) family of serine/threonine kinases regulate diverse biological pathways. The seven mammalian CKI isoforms contain a highly conserved kinase domain and divergent amino- and carboxy-termini. Although they share a preferred target recognition sequence and have overlapping expression patterns, individual isoforms often have specific substrates. In an effort to determine how substrates recognize differences between CKI isoforms, we have examined the interaction between CKIε and two substrates from different signaling pathways. Methodology/Principal Findings CKIε, but not CKIα, binds to and phosphorylates two proteins: Period, a transcriptional regulator of the circadian rhythms pathway, and Disheveled, an activator of the planar cell polarity pathway. We use GST-pull-down assays data to show that two key residues in CKIα's kinase domain prevent Disheveled and Period from binding. We also show that the unique C-terminus of CKIε does not determine Dishevelled's and Period's preference for CKIε nor is it essential for binding, but instead plays an auxillary role in stabilizing the interactions of CKIε with its substrates. We demonstrate that autophosphorylation of CKIε's C-terminal tail prevents substrate binding, and use mass spectrometry and chemical crosslinking to reveal how a phosphorylation-dependent interaction between the C-terminal tail and the kinase domain prevents substrate phosphorylation and binding. Conclusions/Significance The biochemical interactions between CKIε and Disheveled, Period, and its own C-terminus lead to models that explain CKIε's specificity and regulation. PMID:19274088

Detection of trace explosives on relevant substrates using a mobile platform for photothermal infrared imaging spectroscopy (PT-IRIS)

NASA Astrophysics Data System (ADS)

Kendziora, Christopher A.; Furstenberg, Robert; Papantonakis, Michael; Nguyen, Viet; Byers, Jeff; McGill, R. Andrew

2015-05-01

This manuscript describes the results of recent tests regarding standoff detection of trace explosives on relevant substrates using a mobile platform. We are developing a technology for detection based on photo-thermal infrared (IR) imaging spectroscopy (PT-IRIS). This approach leverages one or more microfabricated IR quantum cascade lasers, tuned to strong absorption bands in the analytes and directed to illuminate an area on a surface of interest. An IR focal plane array is used to image the surface thermal emission upon laser illumination. The PT-IRIS signal is processed as a hyperspectral image cube comprised of spatial, spectral and temporal dimensions as vectors within a detection algorithm. Increased sensitivity to explosives and selectivity between different analyte types is achieved by narrow bandpass IR filters in the collection path. We have previously demonstrated the technique at several meters of stand-off distance indoors and in field tests, while operating the lasers below the infrared eye-safe intensity limit (100 mW/cm2). Sensitivity to explosive traces as small as a single 10 μm diameter particle (~1 ng) has been demonstrated. Analytes tested here include RDX, TNT, ammonium nitrate and sucrose. The substrates tested in this current work include metal, plastics, glass and painted car panels.

Direct spontaneous growth and interfacial structural properties of inclined GaN nanopillars on r-plane sapphire

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

Adikimenakis, A.; Aretouli, K. E.; Tsagaraki, K.

2015-06-28

The spontaneous growth of GaN nanopillars (NPs) by direct plasma-assisted molecular beam epitaxy on nitridated r-plane sapphire substrates has been studied. The emanation of metal-polarity NPs from inside an a-plane nonpolar GaN film was found to depend on both the substrate nitridation and the growth conditions. The density of NPs increased with increasing the duration of the nitridation process and the power applied on the radio-frequency plasma source, as well as the III/V flux ratio, while variation of the first two parameters enhanced the roughness of the substrate's surface. Transmission electron microscopy (TEM) techniques were employed to reveal the structuralmore » characteristics of the NPs and their nucleation mechanism from steps on the sapphire surface and/or interfacial semipolar GaN nanocrystals. Lattice strain measurements showed a possible Al enrichment of the first 5–6 monolayers of the NPs. By combining cross-sectional and plan-view TEM observations, the three-dimensional model of the NPs was constructed. The orientation relationship and interfacial accommodation between the NPs and the nonpolar a-plane GaN film were also elucidated. The NPs exhibited strong and narrow excitonic emission, suggesting an excellent structural quality.« less

Optical cross-talk and surface characterization of SERS nanoimaging bundle substrates

NASA Astrophysics Data System (ADS)

Kiser, John B.; Cullum, Brian M.

2010-04-01

Due to the narrow vibrational bandwidths and unique molecular fingerprints, Raman spectroscopy can be an information rich transduction technique for chemical imaging. Dynamic systems are often difficult to measure using spontaneous Raman due to the relatively weak scattering cross-sections. Using a Raman enhancement mechanism such as surface enhanced Raman scattering (SERS), exposure times can be reduced to a reasonable level for dynamic imaging, due to the increased Raman signal intensity. This paper will discuss the development of a novel SERS substrate, fabricated on the tips of fiber-optic imaging bundles, which can be integrated into a multispectral imaging system for non-scanning chemical imaging. These substrates are fabricated by mechanically tapering a polished fiber optic imaging bundle consisting of 30,000 individual elements; producing 100-nm or smaller diameter core elements on the distal tip. Chemical etching with hydrofluoric acid creates uniform cladding spikes onto which a SERS active metal is vacuum deposited, forming the SERS active surface. By varying the size of the silver islands deposited on the cladding peaks active, surface plasmons can be tuned to various excitation frequencies. The surface of these tapered fiber optic probes will be evaluated by analysis of the SERS signal, location and shape of the active surface plasmons. The cross talk between the fiber elements will also be evaluated.

III/V nano ridge structures for optical applications on patterned 300 mm silicon substrate

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

Kunert, B.; Guo, W.; Mols, Y.

We report on an integration approach of III/V nano ridges on patterned silicon (Si) wafers by metal organic vapor phase epitaxy (MOVPE). Trenches of different widths (≤500 nm) were processed in a silicon oxide (SiO{sub 2}) layer on top of a 300 mm (001) Si substrate. The MOVPE growth conditions were chosen in a way to guarantee an efficient defect trapping within narrow trenches and to form a box shaped ridge with increased III/V volume when growing out of the trench. Compressively strained InGaAs/GaAs multi-quantum wells with 19% indium were deposited on top of the fully relaxed GaAs ridges as an activemore » material for optical applications. Transmission electron microcopy investigation shows that very flat quantum well (QW) interfaces were realized. A clear defect trapping inside the trenches is observed whereas the ridge material is free of threading dislocations with only a very low density of planar defects. Pronounced QW photoluminescence (PL) is detected from different ridge sizes at room temperature. The potential of these III/V nano ridges for laser integration on Si substrates is emphasized by the achieved ridge volume which could enable wave guidance and by the high crystal quality in line with the distinct PL.« less

Mapping Strain Gradients in the FIB-Structured InGaN/GaN Multilayered Films with 3D X-ray Microbeam

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

Barabash, Rozaliya; Gao, Yanfei; Ice, Gene E

2010-01-01

This research presents a combined experimental-modeling study of lattice rotations and deviatoric strain gradients induced by focused-ion beam (FIB) milling in nitride heterostructures. 3D X-ray polychromatic microdiffraction (PXM) is used to map the local lattice orientation distribution in FIB-structured areas. Results are discussed in connection with microphotoluminescence ({mu}-PL), fluorescent analysis, scanning electron microscopy (SEM) and transmission electron microscopy (TEM) data. It is demonstrated that FIB-milling causes both direct and indirect damage to the InGaN/GaN layers. In films subjected to direct ion beam impact, a narrow amorphidized top layer is formed. Near the milling area, FIB-induced stress relaxation and formation ofmore » complicated 3D strain fields are observed. The resulting lattice orientation changes are found to correlate with a decrease and/or loss of PL intensity, and agree well with finite element simulations of the three-dimensional strain fields near the relaxed trenches. Experimentally, it is found that the lattice surface normal has an in-plane rotation, which only appears in simulations when the GaN-substrate lattice mismatch annihilates the InGaN-substrate mismatch. This behavior further supports the notion that the film/substrate interface is incoherent.« less

Mapping strain gradients in the FIB-structured InGaN/GaN multilayered films with 3D x-ray microbeam.

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

Barabash, R. I.; Gao, Y. F.; Ice, G. E.

2010-11-25

This research presents a combined experimental-modeling study of lattice rotations and deviatoric strain gradients induced by focused-ion beam (FIB) milling in nitride heterostructures. 3D X-ray polychromatic microdiffraction (PXM) is used to map the local lattice orientation distribution in FIB-structured areas. Results are discussed in connection with microphotoluminescence ({mu}-PL), fluorescent analysis, scanning electron microscopy (SEM) and transmission electron microscopy (TEM) data. It is demonstrated that FIB-milling causes both direct and indirect damage to the InGaN/GaN layers. In films subjected to direct ion beam impact, a narrow amorphidized top layer is formed. Near the milling area, FIB-induced stress relaxation and formation ofmore » complicated 3D strain fields are observed. The resulting lattice orientation changes are found to correlate with a decrease and/or loss of PL intensity, and agree well with finite element simulations of the three-dimensional strain fields near the relaxed trenches. Experimentally, it is found that the lattice surface normal has an in-plane rotation, which only appears in simulations when the GaN-substrate lattice mismatch annihilates the InGaN-substrate mismatch. This behavior further supports the notion that the film/substrate interface is incoherent.« less

Effect of Sophora flavescens on the pharmacokinetics of carbamazepine in rats.

PubMed

Shi, Lei; Dang, Xue-Liang; Liu, Xin-You; Wei, Hua-Mei; Yang, Meng-Meng; Zhang, Yan

2014-12-01

Carbamazepine (CBZ), an antiepileptic with narrow therapeutic window, is a substrate of CYP 3A4 which metabolizes CBZ to carbamazepine-10,11-epoxide (CBZE). CBZE is an active and toxicity metabolite, and it is a substrate of MRP-2. Using CBZ for a long time can cause hepatic injury. Sophora flavescens (SF) is a medicinal herb used for the protected hepatic injury. This study investigated the acute and chronic effects of SF on the pharmacokinetics of CBZ in rats. The concentrations of CBZ and CBZE in plasma and tissues were determined by HPLC method. The results showed that SF which significantly decreased the AUC0-t of CBZ, increased CBZE conversely. Tissue analysis showed that the concentrations of CBZ and CBZE in brain and liver were decreased by SF. In addition, the distribution of CBZE in kidney was reduced significantly, which influenced the CBZE excretion and increased the drug toxic potentially. Results in the current study suggest that patients using CBZ might be cautioned in the use of SF extract or Sophora-derived products. Meanwhile, patients receiving drugs which are substrates of CYP 3A4 and/or MRP-2 should be advised of the potential herb-drug interaction to reduce the risk of therapeutic failure or increased toxicity of conventional drug therapy.

Laser Cladding of Ultra-Thin Nickel-Based Superalloy Sheets.

PubMed

Gabriel, Tobias; Rommel, Daniel; Scherm, Florian; Gorywoda, Marek; Glatzel, Uwe

2017-03-10

Laser cladding is a well-established process to apply coatings on metals. However, on substrates considerably thinner than 1 mm it is only rarely described in the literature. In this work 200 µm thin sheets of nickel-based superalloy 718 are coated with a powder of a cobalt-based alloy, Co-28Cr-9W-1.5Si, by laser cladding. The process window is very narrow, therefore, a precisely controlled Yb fiber laser was used. To minimize the input of energy into the substrate, lines were deposited by setting single overlapping points. In a design of experiments (DoE) study, the process parameters of laser power, laser spot area, step size, exposure time, and solidification time were varied and optimized by examining the clad width, weld penetration, and alloying depth. The microstructure of the samples was investigated by optical microscope (OM) and scanning electron microscopy (SEM), combined with electron backscatter diffraction (EBSD) and energy dispersive X-ray spectroscopy (EDX). Similarly to laser cladding of thicker substrates, the laser power shows the highest influence on the resulting clad. With a higher laser power, the clad width and alloying depth increase, and with a larger laser spot area the weld penetration decreases. If the process parameters are controlled precisely, laser cladding of such thin sheets is manageable.

Laser Cladding of Ultra-Thin Nickel-Based Superalloy Sheets

PubMed Central

Gabriel, Tobias; Rommel, Daniel; Scherm, Florian; Gorywoda, Marek; Glatzel, Uwe

2017-01-01

Laser cladding is a well-established process to apply coatings on metals. However, on substrates considerably thinner than 1 mm it is only rarely described in the literature. In this work 200 µm thin sheets of nickel-based superalloy 718 are coated with a powder of a cobalt-based alloy, Co–28Cr–9W–1.5Si, by laser cladding. The process window is very narrow, therefore, a precisely controlled Yb fiber laser was used. To minimize the input of energy into the substrate, lines were deposited by setting single overlapping points. In a design of experiments (DoE) study, the process parameters of laser power, laser spot area, step size, exposure time, and solidification time were varied and optimized by examining the clad width, weld penetration, and alloying depth. The microstructure of the samples was investigated by optical microscope (OM) and scanning electron microscopy (SEM), combined with electron backscatter diffraction (EBSD) and energy dispersive X-ray spectroscopy (EDX). Similarly to laser cladding of thicker substrates, the laser power shows the highest influence on the resulting clad. With a higher laser power, the clad width and alloying depth increase, and with a larger laser spot area the weld penetration decreases. If the process parameters are controlled precisely, laser cladding of such thin sheets is manageable. PMID:28772639

Effects of substrate concentrations on the growth of heterotrophic bacteria and algae in secondary facultative ponds.

PubMed

Kayombo, S; Mbwette, T S A; Katima, J H Y; Jorgensen, S E

2003-07-01

This paper presents the effect of substrate concentration on the growth of a mixed culture of algae and heterotrophic bacteria in secondary facultative ponds (SFPs) utilizing settled domestic sewage as a sole source of organic carbon. The growth of the mixed culture was studied at the concentrations ranging between 200 and 800 mg COD/l in a series of batch chemostat reactors. From the laboratory data, the specific growth rate (micro) was determined using the modified Gompertz model. The maximum specific growth rate ( micro(max)) and half saturation coefficients (K(s)) were calculated using the Monod kinetic equation. The maximum observed growth rate ( micro(max)) for heterotrophic bacteria was 3.8 day(-1) with K(s) of 200 mg COD/l. The micro(max) for algal biomass based on suspended volatile solids was 2.7 day(-1) with K(s) of 110 mg COD/l. The micro(max) of algae based on the chlorophyll-a was 3.5 day(-1) at K(s) of 50mg COD/l. The observed specific substrate removal by heterotrophic bacteria varied between the concentrations of substrate used and the average value was 0.82 (mg COD/mg biomass). The specific substrate utilization rate in the bioreactors was direct proportional to the specific growth rate. Hence, the determined Monod kinetic parameters are useful for the definition of the operation of SFPs.

A Haloalkane Dehalogenase from a Marine Microbial Consortium Possessing Exceptionally Broad Substrate Specificity.

PubMed

Buryska, Tomas; Babkova, Petra; Vavra, Ondrej; Damborsky, Jiri; Prokop, Zbynek

2018-01-15

The haloalkane dehalogenase enzyme DmmA was identified by marine metagenomic screening. Determination of its crystal structure revealed an unusually large active site compared to those of previously characterized haloalkane dehalogenases. Here we present a biochemical characterization of this interesting enzyme with emphasis on its structure-function relationships. DmmA exhibited an exceptionally broad substrate specificity and degraded several halogenated environmental pollutants that are resistant to other members of this enzyme family. In addition to having this unique substrate specificity, the enzyme was highly tolerant to organic cosolvents such as dimethyl sulfoxide, methanol, and acetone. Its broad substrate specificity, high overexpression yield (200 mg of protein per liter of cultivation medium; 50% of total protein), good tolerance to organic cosolvents, and a broad pH range make DmmA an attractive biocatalyst for various biotechnological applications. IMPORTANCE We present a thorough biochemical characterization of the haloalkane dehalogenase DmmA from a marine metagenome. This enzyme with an unusually large active site shows remarkably broad substrate specificity, high overexpression, significant tolerance to organic cosolvents, and activity under a broad range of pH conditions. DmmA is an attractive catalyst for sustainable biotechnology applications, e.g., biocatalysis, biosensing, and biodegradation of halogenated pollutants. We also report its ability to convert multiple halogenated compounds to corresponding polyalcohols. Copyright © 2018 American Society for Microbiology.

UFD4 lacking the proteasome-binding region catalyses ubiquitination but is impaired in proteolysis.

PubMed

Xie, Youming; Varshavsky, Alexander

2002-12-01

The ubiquitin system recognizes degradation signals of protein substrates through E3-E2 ubiquitin ligases, which produce a substrate-linked multi-ubiquitin chain. Ubiquitinated substrates are degraded by the 26S proteasome, which consists of the 20S protease and two 19S particles. We previously showed that UBR1 and UFD4, two E3 ligases of the yeast Saccharomyces cerevisiae, interact with specific proteasomal subunits. Here we advance this analysis for UFD4 and show that it interacts with RPT4 and RPT6, two subunits of the 19S particle. The 201-residue amino-terminal region of UFD4 is essential for its binding to RPT4 and RPT6. UFD4(DeltaN), which lacks this N-terminal region, adds ubiquitin to test substrates with apparently wild-type activity, but is impaired in conferring short half-lives on these substrates. We propose that interaction of a targeted substrate with the 26S proteasome involves contacts of specific proteasomal subunits with the substrate-bound ubiquitin ligase, with the substrate-linked multi-ubiquitin chain and with the substrate itself. This multiple-site binding may function to slow down dissociation of the substrate from the proteasome and to facilitate the unfolding of substrate through ATP-dependent movements of the chaperone subunits of the 19S particle.

Exploration of CIGAS Alloy System for Thin-Film Photovoltaics on Novel Lightweight and Flexible Substrates

NASA Technical Reports Server (NTRS)

Woods, Lawrence M.; Kalla, Ajay; Ribelin, Rosine

2007-01-01

Thin-film photovoltaics (TFPV) on lightweight and flexible substrates offer the potential for very high solar array specific power (W/kg). ITN Energy Systems, Inc. (ITN) is developing flexible TFPV blanket technology that has potential for specific power greater than 2000 W/kg (including space coatings) that could result in solar array specific power between 150 and 500 W/kg, depending on array size, when mated with mechanical support structures specifically designed to take advantage of the lightweight and flexible substrates.(1) This level of specific power would far exceed the current state of the art for spacecraft PV power generation, and meet the needs for future spacecraft missions.(2) Furthermore the high specific power would also enable unmanned aircraft applications and balloon or high-altitude airship (HAA) applications, in addition to modular and quick deploying tents for surface assets or lunar base power, as a result of the high power density (W/sq m) and ability to be integrated into the balloon, HAA or tent fabric. ITN plans to achieve the high specific power by developing single-junction and two-terminal monolithic tandem-junction PV cells using thin-films of high-efficiency and radiation resistant CuInSe2 (CIS) partnered with bandgap-tunable CIS-alloys with Ga (CIGS) or Al (CIAS) on novel lightweight and flexible substrates. Of the various thin-film technologies, single-junction and radiation resistant CIS and associated alloys with gallium, aluminum and sulfur have achieved the highest levels of TFPV device performance, with the best efficiency reaching 19.5% under AM1.5 illumination conditions and on thick glass substrates.(3) Thus, it is anticipated that single- and tandem-junction devices with flexible substrates and based on CIS and related alloys will achieve the highest levels of thin-film space and HAA solar array performance.

Engineering Nucleotide Specificity of Succinyl-CoA Synthetase in Blastocystis: The Emerging Role of Gatekeeper Residues.

PubMed

Vashisht, Kapil; Verma, Sonia; Gupta, Sunita; Lynn, Andrew M; Dixit, Rajnikant; Mishra, Neelima; Valecha, Neena; Hamblin, Karleigh A; Maytum, Robin; Pandey, Kailash C; van der Giezen, Mark

2017-01-24

Charged, solvent-exposed residues at the entrance to the substrate binding site (gatekeeper residues) produce electrostatic dipole interactions with approaching substrates, and control their access by a novel mechanism called "electrostatic gatekeeper effect". This proof-of-concept study demonstrates that the nucleotide specificity can be engineered by altering the electrostatic properties of the gatekeeper residues outside the binding site. Using Blastocystis succinyl-CoA synthetase (SCS, EC 6.2.1.5), we demonstrated that the gatekeeper mutant (ED) resulted in ATP-specific SCS to show high GTP specificity. Moreover, nucleotide binding site mutant (LF) had no effect on GTP specificity and remained ATP-specific. However, via combination of the gatekeeper mutant with the nucleotide binding site mutant (ED+LF), a complete reversal of nucleotide specificity was obtained with GTP, but no detectable activity was obtained with ATP. This striking result of the combined mutant (ED+LF) was due to two changes; negatively charged gatekeeper residues (ED) favored GTP access, and nucleotide binding site residues (LF) altered ATP binding, which was consistent with the hypothesis of the "electrostatic gatekeeper effect". These results were further supported by molecular modeling and simulation studies. Hence, it is imperative to extend the strategy of the gatekeeper effect in a different range of crucial enzymes (synthetases, kinases, and transferases) to engineer substrate specificity for various industrial applications and substrate-based drug design.

Monomer functionalized silica coated with Ag nanoparticles for enhanced SERS hotspots

NASA Astrophysics Data System (ADS)

Newmai, M. Boazbou; Verma, Manoj; Kumar, P. Senthil

2018-05-01

Mesoporous silica (SiO2) spheres are well-known for their excellent chromatographic properties such as the relatively high specific surface, large pore volume, uniform particle size, narrow pore size distribution with favorable pore connectivity; whereas the noble metal Ag nanoparticles have unique size/shape dependant surface plasmon resonance with wide ranging applications. Thus, the desire to synchronize both their properties for specific applications has naturally prompted research in the design and synthesis of core-shell type novel nanoAg@mesoSiO2 nanocomposites, which display potential utility in applications such as photothermal therapy, photocatalysis, molecular sensing, and photovoltaics. In the present work, SiO2 spheres were carefully functionalized with the monomer, N-vinyl pyrrolidone (NVP), which cohesively controls the uniform mass transfer of Ag+ metal ions, thereby enabling its sequential reduction to zerovalent Ag (in the presence of slightly excess NaOH) by electron transfer from nucleophilic attack of the NVP vinyl group by the water molecules even under ambient conditions. Complete metal nanoshell coverage of the silica surface was obtained after multiple Ag deposition cycles, as systematically confirmed from the BET, TEM, optical and FTIR characterization. Our present Ag-coated silica spheres were directly utilized as viable SERS substrates with high sensitivity in contrast with other long chain polymer/surfactant coated silica spheres, owing to the presence of significant number of nanogaps enhanced SERS 'hotspots', which were methodically analyzed utilizing two example analytes, such as crystal violet (CV) and calendula officinalis (CaF).

Kinetic modeling of lactic acid production from batch submerged fermentation of cheese whey

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

Tango, M.S.A.; Ghaly, A.E.

1999-12-01

A kinetic model for the production of lactic acid through batch submerged fermentation of cheese whey using Lactobacillus helveticus was developed. The model accounts for the effect of substrate limitation, substrate inhibition, lactic acid inhibition, maintenance energy and cell death on the cell growth, substrate utilization, and lactic acid production during the fermentation process. The model was evaluated using experimental data from Tango and Ghaly (1999). The predicted results obtained from the model compared well with experimental (R{sup 2} = 0.92--0.98). The model was also used to investigate the effect of the initial substrate concentration on the lag period, fermentationmore » time, specific growth rate, and cell productivity during batch fermentation. The maximum specific growth rate ({micro}{sub m}), the saturation constant (K{sub S}), the substrate inhibition constant (K{sub IS}), and the lactic acid inhibition constant (K{sub IP}) were found to be 0.25h{sup {minus}1}, 0.9 g/L, 250.0 g/L, and 60.0 g/L, respectively. High initial lactose concentration in cheese whey reduced both the specific growth rate and substrate utilization rate due to the substrate inhibition phenomenon. The maximum lactic acid production occurred at about 100 g/L initial lactose concentration after 40 h of fermentation. The maximum lactic acid concentration above which Lactobacillus helveticus did not grow was found to be 80.0 g/L.« less

Comparison of the health-related quality of life in patients with narrow gastric tube and whole stomach reconstruction after oncologic esophagectomy: a prospective randomized study.

PubMed

Zhang, M; Wu, Q C; Li, Q; Jiang, Y J; Zhang, C; Chen, D

2013-01-01

To compare the health-related quality of life in patients with narrow gastric tube and whole stomach reconstructions after oncologic esophagectomy. In a prospective randomized single-center study from 2007 to 2008, 104 patients underwent esophagectomy for cancer. To assess health-related quality of life, the questionnaire (European Organization for Research and Treatment of Cancer Quality of Life Questionnaire Core 30 and the Oesophagus-Specific Quality of Life Questionnaire 18) was administered at 3 weeks, 6 months, 1 year, and 2 years after surgery. The perioperative complication rate was 26.9% in narrow gastric tube group and 48.1% in whole stomach group (P = 0.31). At the time of 3 weeks after surgery, the reflux and dyspnea scores were higher in whole stomach group than in narrow gastric tube group, which meant that the patients in whole stomach group suffered more severe problem. At the time of 6 months and 1 year after surgery, the reflux scores were lower in narrow gastric tube group than in whole stomach group, which revealed that there were less problems of reflux in the patients of narrow gastric tube group; meanwhile, the score of physical function scale in narrow gastric tube group was higher conversely, which suggested that the patients gain a better status in physical function. Nausea and vomiting is the only notable symptom that was worse in whole stomach group at the time of 2 years after surgery, which suggested that patients in whole stomach group suffered more severe nausea and vomiting. Narrow gastric tube reconstruction may be a good alternative choice for patients undergoing oncologic esophagectomy in view of better health-related quality of life after the surgery.

Molecular Basis for the Relative Substrate Specificity of Human Immunodeficiency Virus Type 1 and Feline Immunodeficiency Virus Proteases

PubMed Central

Beck, Zachary Q.; Lin, Ying-Chuan; Elder, John H.

2001-01-01

We have used a random hexamer phage library to delineate similarities and differences between the substrate specificities of human immunodeficiency virus type 1 (HIV-1) and feline immunodeficiency virus (FIV) proteases (PRs). Peptide sequences were identified that were specifically cleaved by each protease, as well as sequences cleaved equally well by both enzymes. Based on amino acid distinctions within the P3-P3′ region of substrates that appeared to correlate with these cleavage specificities, we prepared a series of synthetic peptides within the framework of a peptide sequence cleaved with essentially the same efficiency by both HIV-1 and FIV PRs, Ac-KSGVF↓VVNGLVK-NH2 (arrow denotes cleavage site). We used the resultant peptide set to assess the influence of specific amino acid substitutions on the cleavage characteristics of the two proteases. The findings show that when Asn is substituted for Val at the P2 position, HIV-1 PR cleaves the substrate at a much greater rate than does FIV PR. Likewise, Glu or Gln substituted for Val at the P2′ position also yields peptides specifically susceptible to HIV-1 PR. In contrast, when Ser is substituted for Val at P1′, FIV PR cleaves the substrate at a much higher rate than does HIV-1 PR. In addition, Asn or Gln at the P1 position, in combination with an appropriate P3 amino acid, Arg, also strongly favors cleavage by FIV PR over HIV PR. Structural analysis identified several protease residues likely to dictate the observed specificity differences. Interestingly, HIV PR Asp30 (Ile-35 in FIV PR), which influences specificity at the S2 and S2′ subsites, and HIV-1 PR Pro-81 and Val-82 (Ile-98 and Gln-99 in FIV PR), which influence specificity at the S1 and S1′ subsites, are residues which are often involved in development of drug resistance in HIV-1 protease. The peptide substrate KSGVF↓VVNGK, cleaved by both PRs, was used as a template for the design of a reduced amide inhibitor, Ac-GSGVFΨ(CH2NH)VVNGL-NH2. This compound inhibited both FIV and HIV-1 PRs with approximately equal efficiency. These findings establish a molecular basis for distinctions in substrate specificity between human and feline lentivirus PRs and offer a framework for development of efficient broad-based inhibitors. PMID:11533208

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.

Chemical probing of the human sirtuin 5 active site reveals its substrate acyl specificity and peptide-based inhibitors.

PubMed

Roessler, Claudia; Nowak, Theresa; Pannek, Martin; Gertz, Melanie; Nguyen, Giang T T; Scharfe, Michael; Born, Ilona; Sippl, Wolfgang; Steegborn, Clemens; Schutkowski, Mike

2014-09-26

Sirtuins are NAD(+)-dependent deacetylases acting as sensors in metabolic pathways and stress response. In mammals there are seven isoforms. The mitochondrial sirtuin 5 is a weak deacetylase but a very efficient demalonylase and desuccinylase; however, its substrate acyl specificity has not been systematically analyzed. Herein, we investigated a carbamoyl phosphate synthetase 1 derived peptide substrate and modified the lysine side chain systematically to determine the acyl specificity of Sirt5. From that point we designed six potent peptide-based inhibitors that interact with the NAD(+) binding pocket. To characterize the interaction details causing the different substrate and inhibition properties we report several X-ray crystal structures of Sirt5 complexed with these peptides. Our results reveal the Sirt5 acyl selectivity and its molecular basis and enable the design of inhibitors for Sirt5. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

ATP-independent reversal of a membrane protein aggregate by a chloroplast SRP

PubMed Central

Jaru-Ampornpan, Peera; Shen, Kuang; Lam, Vinh Q.; Ali, Mona; Doniach, Sebastian; Jia, Tony Z.; Shan, Shu-ou

2010-01-01

Membrane proteins impose enormous challenges to cellular protein homeostasis during their post-translational targeting, and require chaperones to keep them soluble and translocation-competent. Here we show that a novel targeting factor in the chloroplast Signal Recognition Particle (cpSRP), cpSRP43, is a highly specific molecular chaperone that efficiently reverses the aggregation of its substrate proteins. In contrast to AAA+-chaperones, cpSRP43 utilizes specific binding interactions with its substrate to mediate its disaggregase activity. This ‘disaggregase’ capability can allow targeting machineries to more effectively capture their protein substrates, and emphasizes a close connection between protein folding and trafficking processes. Moreover, cpSRP43 provides the first example of an ATP-independent disaggregase, and demonstrates that efficient reversal of protein aggregation can be attained by specific binding interactions between a chaperone and its substrate. PMID:20424608

Specific minor groove solvation is a crucial determinant of DNA binding site recognition

PubMed Central

Harris, Lydia-Ann; Williams, Loren Dean; Koudelka, Gerald B.

2014-01-01

The DNA sequence preferences of nearly all sequence specific DNA binding proteins are influenced by the identities of bases that are not directly contacted by protein. Discrimination between non-contacted base sequences is commonly based on the differential abilities of DNA sequences to allow narrowing of the DNA minor groove. However, the factors that govern the propensity of minor groove narrowing are not completely understood. Here we show that the differential abilities of various DNA sequences to support formation of a highly ordered and stable minor groove solvation network are a key determinant of non-contacted base recognition by a sequence-specific binding protein. In addition, disrupting the solvent network in the non-contacted region of the binding site alters the protein's ability to recognize contacted base sequences at positions 5–6 bases away. This observation suggests that DNA solvent interactions link contacted and non-contacted base recognition by the protein. PMID:25429976

Precise measurement of ultra-narrow laser linewidths using the strong coherent envelope

NASA Astrophysics Data System (ADS)

Huang, Shihong; Zhu, Tao; Liu, Min; Huang, Wei

2017-02-01

Laser linewidth narrowing down to kHz or even Hz is an important topic in areas like clock synchronization technology, laser radars, quantum optics, and high-precision detection. Conventional decoherence measurement methods like delayed self-heterodyne/homodyne interferometry cannot measure such narrow linewidths accurately. This is because a broadening of the Gaussian spectrum, which hides the laser’s intrinsic Lorentzian linewidth, cannot be avoided. Here, we introduce a new method using the strong coherent envelope to characterize the laser’s intrinsic linewidth through self-coherent detection. This method can eliminate the effect of the broadened Gaussian spectrum induced by the 1/f frequency noise. We analyze, in detail, the relationship between intrinsic laser linewidth, contrast difference with the second peak and the second trough (CDSPST) of the strong coherent envelope, and the length of the delaying fiber. The correct length for the delaying fiber can be chosen by combining the estimated laser linewidth (Δfest) with a specific CDSPST (ΔS) to obtain the accurate laser linewidth (Δf). Our results indicate that this method can be used as an accurate detection tool for measurements of narrow or super-narrow linewidths.

Experimental study on occupant evacuation in narrow seat aisle

NASA Astrophysics Data System (ADS)

Huang, Shenshi; Lu, Shouxiang; Lo, Siuming; Li, Changhai; Guo, Yafei

2018-07-01

Narrow seat aisle is an important area in the train car interior due to the large passenger population, however evacuation therein has not gained enough concerns. In this experimental study, the occupant evacuation of the narrow seat aisle area is investigated, with the aisle width of 0.4-0.6 m and the evacuation direction of forward and backward. The evacuation behaviors are analyzed based on the video record, and the discussion is carried out in the aspect of evacuation time, crowdedness, evacuation order, and aisle conflicts. The result shows that with the increasing aisle width, total evacuation time and the average specific evacuation rate decrease. The aisle is crowded for some time, with a large linear occupant densities. The evacuation order of each occupant is mainly related to the seat position. Moreover, it is found that the aisle conflicts can be well described by Burstedde's model. This study gives a useful benchmark for evacuation simulation of narrow seat aisle, and provides reference to safety design of seat area in train cars.

[Constitutional narrowing of the cervical spinal canal. Radiological and clinical findings].

PubMed

Ritter, G; Rittmeyer, K; Hopf, H C

1975-02-21

A constitutional narrowing of the cervical spinal canal was seen in 31 patients with neurological disorders. The ratio of the inner diameter of the spinal canal to the diameter of the vertebral body was smaller than 1 (normal greater than 1). Clinical signs were observed from 45 years upwards where reactivedegenerative changes cause additional narrowing. The majority of patients were male, predominantly heavy manual labourers. There is often a trauma preceding. On myelography multilocular deformations of the spinal subarachnoid space and nerve roots are seen. On the mechanical narrowing of the spinal canal a vascular factor supervenes, caused by exostoses, intervertebral disc protrusions, and fibrosing processes. Clinically a chronic progressive spinal transection syndrome (cervical myelopathy) dominates besides a multilocular root involvement. Posterior column sensibility is predominantly lost. Pain in the extemities and the cervical column is an early symptom. Non-specific CSF changes occur frequently. In case of root involvement the electromyogram is pathological. The prognosis is bad. Operation can only remove reactive processes but not the constitutional anomaly.

Analytical Applications Of High-Resolution Molecular Fluorescence Spectroscopy In Low Temperature Solid Matrices

NASA Astrophysics Data System (ADS)

Hofstraat, Johannes W.; van Zeijl, W. J.; Smedes, F.; Ariese, Freek; Gooijer, Cees; Velthorst, Nel H.; Locher, R.; Renn, Alois; Wild, Urs P.

1989-05-01

High-resolution fluorescence spectroscopy may be used to obtain highly specific, vibrationally resolved spectral signatures of molecules. Two techniques are presented that both make use of low temperature, solid matrices. In Shpol'skii spectroscopy highly resolved spectra are obtained by employing n-alkanes as solvents that form neat crystalline matrices at low temperatures in which the guest molecules occupy well defined substitutional sites. Fluorescence line-narrowing spectroscopy is based on the application of selective (mostly laser-) excitation of the guest molecules. Principles and analytical applications of both techniques will be discussed. Specific attention will be paid to the determination of pyrene in bird meat by means of Shpol'skii spectroscopy and to the possibilities of applying two-dimensional fluorescence line-narrowing spectroscopy.

Regulation of the Deposition Morphology of Inkjet-Printed Crystalline Materials via Polydopamine Functional Coatings for Highly Uniform and Electrically Conductive Patterns.

PubMed

Liu, Liang; Ma, Siyuan; Pei, Yunheng; Xiong, Xiao; Sivakumar, Preeth; Singler, Timothy J

2016-08-24

We report a method to achieve highly uniform inkjet-printed silver nitrate (AgNO3) and a reactive silver precursor patterns on rigid and flexible substrates functionalized with polydopamine (PDA) coatings. The printed AgNO3 patterns on PDA-coated substrates (glass and polyethylene terephthalate (PET)) exhibit a narrow thickness distribution ranging between 0.9 and 1 μm in the line transverse direction and uniform deposition profiles in the line axial direction. The deposited reactive silver precursor patterns on PDA-functionalized substrates also show "dome-shaped" morphology without "edge-thickened" structure due to "coffee-stain" effect. We posit that the highly uniform functional ink deposits formed on PDA-coated substrates are attributable to the strong binding interaction between the abundant catecholamine moieties at the PDA surface and the metallic silver cations (Ag(+) or Ag(NH3)(2+)) in the solutal inks. During printing of the ink rivulet and solvent evaporation, the substrate-liquid ink (S-L) interface is enriched with the silver-based cations and a solidification at the S/L interface is induced. The preferential solidification initiated at the S-L interface is further verified by the in situ visualization of the dynamic solidification process during solvent evaporation, and results suggest an enhanced crystal nucleation and growth localized at the S-L interface on PDA functionalized substrates. This interfacial interaction mediates solute transport in the liquid phase, resulting in the controlled enrichment of solute at the S-L interface and mitigated solute precipitation in both the contact line region and the liquid ink-vapor (L-V) interface due to evaporation. This mediated transport contributes to the final uniform solid deposition for both types of ink systems. This technique provides a complementary strategy for achieving highly uniform inkjet-printed crystalline structures, and can serve as an innovative foundation for high-precision additive delivery of functional materials.

Evidence for proton tunneling and a transient covalent flavin-substrate adduct in choline oxidase S101A.

PubMed

Uluisik, Rizvan; Romero, Elvira; Gadda, Giovanni

2017-11-01

The effect of temperature on the reaction of alcohol oxidation catalyzed by choline oxidase was investigated with the S101A variant of choline oxidase. Anaerobic enzyme reduction in a stopped-flow spectrophotometer was biphasic using either choline or 1,2-[ 2 H 4 ]-choline as a substrate. The limiting rate constants k lim1 and k lim2 at saturating substrate were well separated (k lim1 /k lim2 >9), and were >15-fold slower than for wild-type choline oxidase. Solvent deuterium kinetic isotope effects (KIEs) ~4 established that k lim1 probes the proton transfer from the substrate hydroxyl to a catalytic base. Primary substrate deuterium KIEs ≥7 demonstrated that k lim2 reports on hydride transfer from the choline alkoxide to the flavin. Between 15°C and 39°C the k lim1 and k lim2 values increased with increasing temperature, allowing for the analyses of H + and H - transfers using Eyring and Arrhenius formalisms. Temperature-independent KIE on the k lim1 value ( H2O k lim1 / D2O k lim1 ) suggests that proton transfer occurs within a highly reorganized tunneling-ready-state with a narrow distribution of donor-acceptor distances. Eyring analysis of the k lim2 value gave lines with the slope (choline) >slope (D-choline) , suggesting kinetic complexity. Spectral evidence for the transient occurrence of a covalent flavin-substrate adduct during the first phase of the anaerobic reaction of S101A CHO with choline is presented, supporting the notion that an important role of amino acid residues in the active site of flavin-dependent enzymes is to eliminate alternative reactions of the versatile enzyme-bound flavin for the reaction that needs to be catalyzed. Copyright © 2017 Elsevier B.V. All rights reserved.

Effects of ion and nanosecond-pulsed laser co-irradiation on the surface nanostructure of Au thin films on SiO{sub 2} glass substrates

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

Yu, Ruixuan; Meng, Xuan; Takayanagi, Shinya

2014-04-14

Ion irradiation and short-pulsed laser irradiation can be used to form nanostructures on the surfaces of substrates. This work investigates the synergistic effects of ion and nanosecond-pulsed laser co-irradiation on surface nanostructuring of Au thin films deposited under vacuum on SiO{sub 2} glass substrates. Gold nanoparticles are randomly formed on the surface of the substrate after nanosecond-pulsed laser irradiation under vacuum at a wavelength of 532 nm with a repetition rate of 10 Hz and laser energy density of 0.124 kJ/m{sup 2}. Gold nanoparticles are also randomly formed on the substrate after 100-keV Ar{sup +} ion irradiation at doses of upmore » to 3.8 × 10{sup 15} ions/cm{sup 2}, and nearly all of these nanoparticles are fully embedded in the substrate. With increasing ion irradiation dose (number of incident laser pulses), the mean diameter of the Au nanoparticles decreases (increases). However, Au nanoparticles are only formed in a periodic surface arrangement after co-irradiation with 6000 laser pulses and 3.8 × 10{sup 15} ions/cm{sup 2}. The periodic distance is ∼540 nm, which is close to the wavelength of the nanosecond-pulsed laser, and the mean diameter of the Au nanoparticles remains at ∼20 nm with a relatively narrow distribution. The photoabsorption peaks of the ion- or nanosecond-pulsed laser-irradiated samples clearly correspond to the mean diameter of Au nanoparticles. Conversely, the photoabsorption peaks for the co-irradiated samples do not depend on the mean nanoparticle diameter. This lack of dependence is likely caused by the periodic nanostructure formed on the surface by the synergistic effects of co-irradiation.« less

Characterization of the Serratia marcescens SdeCDE multidrug efflux pump studied via gene knockout mutagenesis.

PubMed

Begic, Sanela; Worobec, Elizabeth A

2008-05-01

Serratia marcescens is an important nosocomial agent having high antibiotic resistance. A major mechanism for S. marcescens antibiotic resistance is active efflux. To ascertain the substrate specificity of the S. marcescens SdeCDE efflux pump, we constructed pump gene deletion mutants. sdeCDE knockout strains showed no change in antibiotic susceptibility in comparison with the parental strains for any of the substrates, with the exception of novobiocin. In addition, novobiocin was the only antibiotic to be accumulated by sdeCDE-deficient strains. Based on the substrates used in our study, we conclude that SdeCDE is a Resistance-Nodulation-Cell Division family pump with limited substrate specificity.

Identification of Residues Involved in Substrate Specificity and Cytotoxicity of Two Closely Related Cutinases from Mycobacterium tuberculosis

PubMed Central

Dedieu, Luc; Serveau-Avesque, Carole; Canaan, Stéphane

2013-01-01

The enzymes belonging to the cutinase family are serine enzymes active on a large panel of substrates such as cutin, triacylglycerols, and phospholipids. In the M. tuberculosis H37Rv genome, seven genes coding for cutinase-like proteins have been identified with strong immunogenic properties suggesting a potential role as vaccine candidates. Two of these enzymes which are secreted and highly homologous, possess distinct substrates specificities. Cfp21 is a lipase and Cut4 is a phospholipase A2, which has cytotoxic effects on macrophages. Structural overlay of their three-dimensional models allowed us to identify three areas involved in the substrate binding process and to shed light on this substrate specificity. By site-directed mutagenesis, residues present in these Cfp21 areas were replaced by residues occurring in Cut4 at the same location. Three mutants acquired phospholipase A1 and A2 activities and the lipase activities of two mutants were 3 and 15 fold greater than the Cfp21 wild type enzyme. In addition, contrary to mutants with enhanced lipase activity, mutants that acquired phospholipase B activities induced macrophage lysis as efficiently as Cut4 which emphasizes the relationship between apparent phospholipase A2 activity and cytotoxicity. Modification of areas involved in substrate specificity, generate recombinant enzymes with higher activity, which may be more immunogenic than the wild type enzymes and could therefore constitute promising candidates for antituberculous vaccine production. PMID:23843969

Identification of residues involved in substrate specificity and cytotoxicity of two closely related cutinases from Mycobacterium tuberculosis.

PubMed

Dedieu, Luc; Serveau-Avesque, Carole; Canaan, Stéphane

2013-01-01

The enzymes belonging to the cutinase family are serine enzymes active on a large panel of substrates such as cutin, triacylglycerols, and phospholipids. In the M. tuberculosis H37Rv genome, seven genes coding for cutinase-like proteins have been identified with strong immunogenic properties suggesting a potential role as vaccine candidates. Two of these enzymes which are secreted and highly homologous, possess distinct substrates specificities. Cfp21 is a lipase and Cut4 is a phospholipase A2, which has cytotoxic effects on macrophages. Structural overlay of their three-dimensional models allowed us to identify three areas involved in the substrate binding process and to shed light on this substrate specificity. By site-directed mutagenesis, residues present in these Cfp21 areas were replaced by residues occurring in Cut4 at the same location. Three mutants acquired phospholipase A1 and A2 activities and the lipase activities of two mutants were 3 and 15 fold greater than the Cfp21 wild type enzyme. In addition, contrary to mutants with enhanced lipase activity, mutants that acquired phospholipase B activities induced macrophage lysis as efficiently as Cut4 which emphasizes the relationship between apparent phospholipase A2 activity and cytotoxicity. Modification of areas involved in substrate specificity, generate recombinant enzymes with higher activity, which may be more immunogenic than the wild type enzymes and could therefore constitute promising candidates for antituberculous vaccine production.

[Substrate-inhibitory analysis of monoamine oxidase from hepatopancreas of the octopus Bathypolypus arcticus].

PubMed

Basova, I N; Iagodina, O V

2012-01-01

Study of the substrate-inhibitory specificity of mitochondrial monoamine oxidase (MAO) of hepatopancreas of the octopus Bathypolypus arcticus revealed distinctive peculiarities of catalytic properties of this enzyme. The studied enzyme, on one hand, like the classic MAO of homoiothermal animals, is able to deaminate tyramine, serotonin, benzylamine, tryptamine, beta-phenylethylamine, while, on the other hand, deaminates histamine and does not deaminate putrescine--classic substrates of diamine oxidase (DAO). Results of the substrate-inhibitory analysis with use of chlorgiline and deprenyl are indirect proofs of the existence in the octopus hepatopancreas of one molecular MAO form. Semicarbazide and pyronine G turned out to be weak irreversible inhibitors, four derivatives of acridine--irreversible inhibitors of the intermediate effectiveness with respect to the octopus hepatopancreas MAO; specificity of action of inhibitors at deamination of different substrates was equal.

Millimeter-wave/infrared rectenna development at Georgia Tech

NASA Technical Reports Server (NTRS)

Gouker, Mark A.

1989-01-01

The key design issues of the Millimeter Wave/Infrared (MMW/IR) monolithic rectenna have been resolved. The work at Georgia Tech in the last year has focused on increasing the power received by the physically small MMW rectennas in order to increase the rectification efficiency. The solution to this problem is to place a focusing element on the back side of the substrate. The size of the focusing element can be adjusted to help maintain the optimum input power density not only for different power densities called for in various mission scenarios, but also for the nonuniform power density profile of a narrow EM-beam.

Terraced-heterostructure large-optical-cavity AlGaAs diode laser - A new type of high-power CW single-mode device

NASA Technical Reports Server (NTRS)

Botez, D.; Connolly, J. C.

1982-01-01

A new terraced lateral wave confining structure is obtained by liquid phase epitaxy over channeled substrates misoriented perpendicular to the channels' direction. Single spatial and longitudinal mode CW operation is achieved to 50 mW from one facet, in large spot sizes (2 x 7.5 micron, 1/e squared points in intensity) and narrow beams (6 deg x 23 deg), full width half-power). At 70 C ambient temperature CW lasing is obtained to 15 mW from one facet. Weak mode confinement in an asymmetric lateral waveguides provides discrimination against high-order mode oscillation.

Plasmon-Induced Transparency Based on Triple Arc-Ring Resonators.

PubMed

Dong, Guang-Xi; Xie, Qin; Zhang, Qi; Wang, Ben-Xin; Huang, Wei-Qing

2018-06-06

This paper presents a plasmon-induced transparency (PIT) using an easy-fabricating metamaterial composed of three pieces of metallic arc-rings on top of a dielectric substrate. The transmission of the transparent peak of 1.32 THz reaches approximately 93%. The utilization of the coupled Lorentzian oscillator model and the distribution of electromagnetic fields together explain the cause of the transparent peak. The simulation results further demonstrate that the bandwidth of the transmission peak can be narrowed by changing the sizes of the arc-rings. Moreover, an on/off effect based on the transparent peak is discussed by introducing photosensitive silicon into the air gaps of the suggested metamaterial structure.

Coexistence of non-volatile bi-polar resistive switching and tunneling magnetoresistance in spatially confined La0.3Pr0.4Ca0.3MnO3 films

NASA Astrophysics Data System (ADS)

Jeon, J.; Jung, J.; Chow, K. H.

2017-12-01

We report the coexistence of non-volatile bi-polar resistive switching (RS) and tunneling magnetoresistance (TMR) in spatially confined La0.3Pr0.4Ca0.3MnO3 films grown on LaAlO3 substrates. At certain temperatures, the arrangement of electronic phase domains in these narrow systems mimics those found in heterostructured metal-insulator-metal devices. The relative spin orientations between adjacent ferromagnetic metallic phase domains enable the TMR effect, while the creation/annihilation of conduction filaments between the metallic phase domains produces the RS effect.

Long-range dielectric-loaded surface plasmon polariton waveguides operating at telecommunication wavelengths.

PubMed

Volkov, Valentyn S; Han, Zhanghua; Nielsen, Michael G; Leosson, Kristjan; Keshmiri, Hamid; Gosciniak, Jacek; Albrektsen, Ole; Bozhevolnyi, Sergey I

2011-11-01

We report on the realization of long-range dielectric-loaded surface plasmon polariton waveguides (LR-DLSPPWs) consisting of straight and bent subwavelength dielectric ridges deposited on thin and narrow metal stripes supported by a dielectric buffer layer covering a low-index substrate. Using imaging with a near-field optical microscope and end-fire coupling with a tapered fiber connected to a tunable laser at telecommunication wavelengths (1425-1545 nm), we demonstrate low-loss (propagation length ∼500 μm) and well-confined (mode width ∼1 μm) LR-DLSPPW mode guiding and determine the propagation and bend loss.

Quantum dots for GaAs-based surface emitting lasers at 1300 nm

NASA Astrophysics Data System (ADS)

Grundmann, M.; Ledentsov, N. N.; Hopfer, F.; Heinrichsdorff, F.; Guffarth, F.; Bimberg, D.; Ustinov, V. M.; Zhukov, A. E.; Kovsh, A. R.; Maximov, M. V.; Musikhin, Yu. G.; Alferov, Zh. I.; Lott, J. A.; Zhakharov, N. D.; Werner, P.

InGaAs quantum dots (QD's) on GaAs substrate have been fabricated using metal-organic chemical vapor deposition (MOCVD) and molecular beam epitaxy (MBE) for the use in vertical cavity surface emitting laser diodes. Similar recombination spectra are obtained by employing the two different approaches of seeding and overgrowth with a quantum well. Despite the shift to larger wavelengths a large separation (=80 meV) between excited states is maintained. The introduction of such QD's into a vertical cavity leads to strong narrowing of the emission spectrum. Lasing from a 1300 nm InGaAs quantum dot VCSEL is reported.

Structure and Activity Analyses of Escherichia coli K-12 NagD Provide Insight into the Evolution of Biochemical Function in the Haloakanoic Acid Dehlogenase Superfamily

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

Tremblay,L.; Dunaway-Mariano, D.; Allen, K.

2006-01-01

The HAD superfamily is a large superfamily of proteins which share a conserved core domain that provides those active site residues responsible for the chemistry common to all family members. The superfamily is further divided into the four subfamilies I, IIA, IIB, and III, based on the topology and insertion site of a cap domain that provides substrate specificity. This structural and functional division implies that members of a given HAD structural subclass may target substrates that have similar structural characteristics. To understand the structure/function relationships in all of the subfamilies, a type IIA subfamily member, NagD from Escherichia colimore » K-12, was selected (type I, IIB, and III members have been more extensively studied). The structure of the NagD protein was solved to 1.80 Angstroms with R{sub work} = 19.8% and R{sub free} = 21.8%. Substrate screening and kinetic analysis showed NagD to have high specificity for nucleotide monophosphates with kcat/Km = 3.12 x 10{sup 4} and 1.28 x 10{sup 4} {micro}M{sup -1} s{sup -1} for UMP and GMP, respectively. This specificity is consistent with the presence of analogues of NagD that exist as fusion proteins with a nucleotide pyrophosphatase from the Nudix family. Docking of the nucleoside substrate in the active site brings it in contact with conserved residues from the cap domain that can act as a substrate specificity loop (NagD residues 144-149) in the type IIA subfamily. NagD and other subfamily IIA and IIB members show the common trait that substrate specificity and catalytic efficiencies (k{sub cat}/K{sub m}) are low (1 x 10{sup 4} M{sup -1} s{sup -1}) and the boundaries defining physiological substrates are somewhat overlapping. The ability to catabolize other related secondary metabolites indicates that there is regulation at the genetic level.« less

DbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications.

PubMed

Lu, Cheng-Tsung; Huang, Kai-Yao; Su, Min-Gang; Lee, Tzong-Yi; Bretaña, Neil Arvin; Chang, Wen-Chi; Chen, Yi-Ju; Chen, Yu-Ju; Huang, Hsien-Da

2013-01-01

Protein modification is an extremely important post-translational regulation that adjusts the physical and chemical properties, conformation, stability and activity of a protein; thus altering protein function. Due to the high throughput of mass spectrometry (MS)-based methods in identifying site-specific post-translational modifications (PTMs), dbPTM (http://dbPTM.mbc.nctu.edu.tw/) is updated to integrate experimental PTMs obtained from public resources as well as manually curated MS/MS peptides associated with PTMs from research articles. Version 3.0 of dbPTM aims to be an informative resource for investigating the substrate specificity of PTM sites and functional association of PTMs between substrates and their interacting proteins. In order to investigate the substrate specificity for modification sites, a newly developed statistical method has been applied to identify the significant substrate motifs for each type of PTMs containing sufficient experimental data. According to the data statistics in dbPTM, >60% of PTM sites are located in the functional domains of proteins. It is known that most PTMs can create binding sites for specific protein-interaction domains that work together for cellular function. Thus, this update integrates protein-protein interaction and domain-domain interaction to determine the functional association of PTM sites located in protein-interacting domains. Additionally, the information of structural topologies on transmembrane (TM) proteins is integrated in dbPTM in order to delineate the structural correlation between the reported PTM sites and TM topologies. To facilitate the investigation of PTMs on TM proteins, the PTM substrate sites and the structural topology are graphically represented. Also, literature information related to PTMs, orthologous conservations and substrate motifs of PTMs are also provided in the resource. Finally, this version features an improved web interface to facilitate convenient access to the resource.

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.

The Structure of Lombricine Kinase: Implications for Phosphagen Conformational Changes

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

Bush, D. Jeffrey; Kirillova, Olga; Clark, Shawn A.

2012-05-29

Lombricine kinase is a member of the phosphagen kinase family and a homolog of creatine and arginine kinases, enzymes responsible for buffering cellular ATP levels. Structures of lombricine kinase from the marine worm Urechis caupo were determined by x-ray crystallography. One form was crystallized as a nucleotide complex, and the other was substrate-free. The two structures are similar to each other and more similar to the substrate-free forms of homologs than to the substrate-bound forms of the other phosphagen kinases. Active site specificity loop 309-317, which is disordered in substrate-free structures of homologs and is known from the NMR ofmore » arginine kinase to be inherently dynamic, is resolved in both lombricine kinase structures, providing an improved basis for understanding the loop dynamics. Phosphagen kinases undergo a segmented closing on substrate binding, but the lombricine kinase ADP complex is in the open form more typical of substrate-free homologs. Through a comparison with prior complexes of intermediate structure, a correlation was revealed between the overall enzyme conformation and the substrate interactions of His{sup 178}. Comparative modeling provides a rationale for the more relaxed specificity of these kinases, of which the natural substrates are among the largest of the phosphagen substrates.« less

A Measure of the Broad Substrate Specificity of Enzymes Based on ‘Duplicate’ Catalytic Residues

PubMed Central

Chakraborty, Sandeep; Ásgeirsson, Bjarni; Rao, Basuthkar J.

2012-01-01

The ability of an enzyme to select and act upon a specific class of compounds with unerring precision and efficiency is an essential feature of life. Simultaneously, these enzymes often catalyze the reaction of a range of similar substrates of the same class, and also have promiscuous activities on unrelated substrates. Previously, we have established a methodology to quantify promiscuous activities in a wide range of proteins. In the current work, we quantitatively characterize the active site for the ability to catalyze distinct, yet related, substrates (BRASS). A protein with known structure and active site residues provides the framework for computing ‘duplicate’ residues, each of which results in slightly modified replicas of the active site scaffold. Such spatial congruence is supplemented by Finite difference Poisson Boltzmann analysis which filters out electrostatically unfavorable configurations. The congruent configurations are used to compute an index (BrassIndex), which reflects the broad substrate profile of the active site. We identify an acetylhydrolase and a methyltransferase as having the lowest and highest BrassIndex, respectively, from a set of non-homologous proteins extracted from the Catalytic Site Atlas. The acetylhydrolase, a regulatory enzyme, is known to be highly specific for platelet-activating factor. In the methyltransferase (PDB: 1QAM), various combinations of glycine (Gly38/40/42), asparagine (Asn101/11) and glutamic acid (Glu59/36) residues having similar spatial and electrostatic profiles with the specified scaffold (Gly38, Asn101 and Glu59) exemplifies the broad substrate profile such an active site may provide. ‘Duplicate’ residues identified by relaxing the spatial and/or electrostatic constraints can be the target of directed evolution methodologies, like saturation mutagenesis, for modulating the substrate specificity of proteins. PMID:23166637

QM/MM Free Energy Simulations of Salicylic Acid Methyltransferase: Effects of Stabilization of TS-like Structures on Substrate Specificity

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

Yao, Jianzhuang; Xu, Qin; Chen, Feng

2010-01-01

Salicylic acid methyltransferases (SAMTs) synthesize methyl salicylate (MeSA) using salicylate as the substrate. MeSA synthesized in plants may function as an airborne signal to activate the expression of defense-related genes and could also be a critical mobile signaling molecule that travels from the site of plant infection to establish systemic immunity in the induction of disease resistance. Here the results of QM/MM free energy simulations for the methyl transfer process in Clarkia breweri SAMT (CbSAMT) are reported to determine the origin of the substrate specificity of SAMTs. The free energy barrier for the methyl transfer from S-adenosyl-l-methionine (AdoMet) to 4-hydroxybenzoatemore » in CbSAMT is found to be about 5 kcal/mol higher than that from AdoMet to salicylate, consistent with the experimental observations. It is suggested that the relatively high efficiency for the methylation of salicylate compared to 4-hydroxybenzoate is due, at least in part, to the reason that a part of the stabilization of the transition state (TS) configuration is already reflected in the reactant complex, presumably, through the binding. The results seem to indicate that the creation of the substrate complex (e.g., through mutagenesis and substrate modifications) with its structure closely resembling TS might be fruitful for improving the catalytic efficiency for some enzymes. The results show that the computer simulations may provide important insights into the origin of the substrate specificity for the SABATH family and could be used to help experimental efforts in generating engineered enzymes with altered substrate specificity.« less

Substrate Specificities of MexAB-OprM, MexCD-OprJ, and MexXY-OprM Efflux Pumps in Pseudomonas aeruginosa

PubMed Central

Masuda, Nobuhisa; Sakagawa, Eiko; Ohya, Satoshi; Gotoh, Naomasa; Tsujimoto, Hideto; Nishino, Takeshi

2000-01-01

To find the exact substrate specificities of three species of tripartite efflux systems of Pseudomonas aeruginosa, MexAB-OprM, MexCD-OprJ, and MexXY-OprM, we constructed a series of isogenic mutants, each of which constitutively overproduced one of the three efflux systems and lacked the other two, and their isogenic mutants, which lacked all these systems. Comparison of the susceptibilities of the constructed mutants to 52 antimicrobial agents belonging to various groups suggested the following substrate specificities. All of the efflux systems extrude a wide variety of antimicrobial agent groups, i.e., quinolones, macrolides, tetracyclines, lincomycin, chloramphenicol, most penicillins (all but carbenicillin and sulbenicillin), most cephems (all but cefsulodin and ceftazidime), meropenem, and S-4661, but none of them extrude polymyxin B or imipenem. Extrusion of aminoglycosides is specific to MexXY-OprM, and extrusion of a group of the β-lactams, i.e., carbenicillin, sulbenicillin, ceftazidime, moxalactam, and aztreonam, is specific to MexAB-OprM. Moreover, MexAB-OprM and MexCD-OprJ extrude novobiocin, cefsulodin, and flomoxef, while MexXY-OprM does not. These substrate specificities are distinct from those reported previously. PMID:11083635

Reconstructed ancestral enzymes reveal that negative selection drove the evolution of substrate specificity in ADP-dependent kinases.

PubMed

Castro-Fernandez, Víctor; Herrera-Morande, Alejandra; Zamora, Ricardo; Merino, Felipe; Gonzalez-Ordenes, Felipe; Padilla-Salinas, Felipe; Pereira, Humberto M; Brandão-Neto, Jose; Garratt, Richard C; Guixe, Victoria

2017-09-22

One central goal in molecular evolution is to pinpoint the mechanisms and evolutionary forces that cause an enzyme to change its substrate specificity; however, these processes remain largely unexplored. Using the glycolytic ADP-dependent kinases of archaea, including the orders Thermococcales , Methanosarcinales , and Methanococcales , as a model and employing an approach involving paleoenzymology, evolutionary statistics, and protein structural analysis, we could track changes in substrate specificity during ADP-dependent kinase evolution along with the structural determinants of these changes. To do so, we studied five key resurrected ancestral enzymes as well as their extant counterparts. We found that a major shift in function from a bifunctional ancestor that could phosphorylate either glucose or fructose 6-phosphate (fructose-6-P) as a substrate to a fructose 6-P-specific enzyme was started by a single amino acid substitution resulting in negative selection with a ground-state mode against glucose and a subsequent 1,600-fold change in specificity of the ancestral protein. This change rendered the residual phosphorylation of glucose a promiscuous and physiologically irrelevant activity, highlighting how promiscuity may be an evolutionary vestige of ancestral enzyme activities, which have been eliminated over time. We also could reconstruct the evolutionary history of substrate utilization by using an evolutionary model of discrete binary characters, indicating that substrate uses can be discretely lost or acquired during enzyme evolution. These findings exemplify how negative selection and subtle enzyme changes can lead to major evolutionary shifts in function, which can subsequently generate important adaptive advantages, for example, in improving glycolytic efficiency in Thermococcales . © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

[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.

MnO2-Based Electrochemical Supercapacitors on Flexible Carbon Substrates

NASA Astrophysics Data System (ADS)

Tadjer, Marko J.; Mastro, Michael A.; Rojo, José M.; Mojena, Alberto Boscá; Calle, Fernando; Kub, Francis J.; Eddy, Charles R.

2014-04-01

Manganese dioxide films were grown on large area flexible carbon aerogel substrates. Characterization by x-ray diffraction confirmed α-MnO2 growth. Three types of films were compared as a function of hexamethylenetetramine (HMTA) concentration during growth. The highest concentration of HM TA produced MnO2 flower-like films, as observed by scanning electron microscopy, whose thickness and surface coverage lead to both a higher specific capacitance and higher series resistance. Specific capacitance was measured to be 64 F/g using a galvanostatic setup, compared to the 47 F/g-specific capacitance of the carbon aerogel substrate. Such supercapacitor devices can be fabricated on large area sheets of carbon aerogel to achieve high total capacitance.

Hydrolytic properties and substrate specificity of the foot-and-mouth disease leader protease.

PubMed

Santos, Jorge A N; Gouvea, Iuri E; Júdice, Wagner A S; Izidoro, Mario A; Alves, Fabiana M; Melo, Robson L; Juliano, Maria A; Skern, Tim; Juliano, Luiz

2009-08-25

Foot-and-mouth disease virus, a global animal pathogen, possesses a single-stranded RNA genome that, on release into the infected cell, is immediately translated into a single polyprotein. This polyprotein product is cleaved during synthesis by proteinases contained within it into the mature viral proteins. The first cleavage is performed by the leader protease (Lb(pro)) between its own C-terminus and the N-terminus of VP4. Lb(pro) also specifically cleaves the two homologues of cellular eukaryotic initiation factor (eIF) 4G, preventing translation of capped mRNA. Viral protein synthesis is initiated internally and is thus unaffected. We used a panel of specifically designed FRET peptides to examine the effects of pH and ionic strength on Lb(pro) activity and investigate the size of the substrate binding site and substrate specificity. Compared to the class prototypes, papain and the cathepsins, Lb(pro) possesses several unusual characteristics, including a high sensitivity to salt and a very specific substrate binding site extending up to P(7). Indeed, almost all substitutions investigated were detrimental to Lb(pro) activity. Analysis of structural data showed that Lb(pro) binds residues P(1)-P(3) in an extended conformation, whereas residues P(4)-P(7) are bound in a short 3(10) helix. The specificity of Lb(pro) as revealed by the substituted peptides could be explained for all positions except P(5). Strikingly, Lb(pro) residues L178 and L143 contribute to the architecture of more than one substrate binding pocket. The diverse functions of these two Lb(pro) residues explain why Lb(pro) is one of the smallest, but simultaneously most specific, papain-like enzymes.

Substrate-binding specificity of chitinase and chitosanase as revealed by active-site architecture analysis.

PubMed

Liu, Shijia; Shao, Shangjin; Li, Linlin; Cheng, Zhi; Tian, Li; Gao, Peiji; Wang, Lushan

2015-12-11

Chitinases and chitosanases, referred to as chitinolytic enzymes, are two important categories of glycoside hydrolases (GH) that play a key role in degrading chitin and chitosan, two naturally abundant polysaccharides. Here, we investigate the active site architecture of the major chitosanase (GH8, GH46) and chitinase families (GH18, GH19). Both charged (Glu, His, Arg, Asp) and aromatic amino acids (Tyr, Trp, Phe) are observed with higher frequency within chitinolytic active sites as compared to elsewhere in the enzyme structure, indicating significant roles related to enzyme function. Hydrogen bonds between chitinolytic enzymes and the substrate C2 functional groups, i.e. amino groups and N-acetyl groups, drive substrate recognition, while non-specific CH-π interactions between aromatic residues and substrate mainly contribute to tighter binding and enhanced processivity evident in GH8 and GH18 enzymes. For different families of chitinolytic enzymes, the number, type, and position of substrate atoms bound in the active site vary, resulting in different substrate-binding specificities. The data presented here explain the synergistic action of multiple enzyme families at a molecular level and provide a more reasonable method for functional annotation, which can be further applied toward the practical engineering of chitinases and chitosanases. Copyright © 2015 Elsevier Ltd. All rights reserved.

Reactive ion etched substrates and methods of making and using

DOEpatents

Rucker, Victor C [San Francisco, CA; Shediac, Rene [Oakland, CA; Simmons, Blake A [San Francisco, CA; Havenstrite, Karen L [New York, NY

2007-08-07

Disclosed herein are substrates comprising reactive ion etched surfaces and specific binding agents immobilized thereon. The substrates may be used in methods and devices for assaying or isolating analytes in a sample. Also disclosed are methods of making the reactive ion etched surfaces.

Substrate Material for Holographic Emulsions Utilizing Fluorinated Polyimide Film

NASA Technical Reports Server (NTRS)

Gierow, Paul A. (Inventor); Clayton, William R. (Inventor); St.Clair, Anne K. (Inventor)

1999-01-01

A new holographic substrate utilizing flexible. optically transparent fluorinated polyimides. Said substrates have 0 extremely low birefringence which results in a high signal to noise ratio in subsequent holograms. Specific examples of said fluorinated polyimides include 6FDA+APB and 6FDA+4BDAF.

Synthesis and evaluation of fluorogenic triglycerides as lipase assay substrates.

PubMed

Andersen, Rokhsana J; Brask, Jesper

2016-06-01

Three racemic fluorogenic triglycerides are synthesized and evaluated as lipase assay substrates. The presented synthesis route goes through a key triglyceride intermediate which can be chemoselectively functionalized with a wide range of different probes. Hence the substrate can be tailor-made for a specific assay, or focus can be on low cost in larger scale for applications in high-throughput screening (HTS) assays. In the specific examples, TG-ED, TG-FD and TG-F2 are assembled with the Edans-Dabcyl or the fluorescein-Dabcyl FRET pair, or relying on fluorescein self-quenching, respectively. Proof-of-concept assays allowed determination of 1st order kinetic parameters (kcat/KM) of 460s(-1)M(-1), 59s(-1)M(-1) and 346s(-1)M(-1), respectively, for the three substrates. Commercially available EnzChek lipase substrate provided 204s(-1)M(-1). Substrate concentration was identified as a critical parameter, with measured reaction rates decreasing at higher concentrations when intermolecular quenching becomes significant. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Regulation of Proteolysis by Human Deubiquitinating Enzymes

PubMed Central

Eletr, Ziad M.; Wilkinson, Keith D.

2013-01-01

The post-translational attachment of one or several ubiquitin molecules to a protein generates a variety of targeting signals that are used in many different ways in the cell. Ubiquitination can alter the activity, localization, protein-protein interactions or stability of the targeted protein. Further, a very large number of proteins are subject to regulation by ubiquitin-dependent processes, meaning that virtually all cellular functions are impacted by these pathways. Nearly a hundred enzymes from five different gene families (the deubiquitinating enzymes or DUBs), reverse this modification by hydrolyzing the (iso)peptide bond tethering ubiquitin to itself or the target protein. Four of these families are thiol proteases and one is a metalloprotease. DUBs of the Ubiquitin C-terminal Hydrolase (UCH) family act on small molecule adducts of ubiquitin, process the ubiquitin proprotein, and trim ubiquitin from the distal end of a polyubiquitin chain. Ubiquitin Specific Proteases (USP) tend to recognize and encounter their substrates by interaction of the variable regions of their sequence with the substrate protein directly, or with scaffolds or substrate adapters in multiprotein complexes. Ovarian Tumor (OTU) domain DUBs show remarkable specificity for different Ub chain linkages and may have evolved to recognize substrates on the basis of those linkages. The Josephin family of DUBs may specialize in distinguishing between polyubiquitin chains of different lengths. Finally, the JAB1/MPN+/MOV34 (JAMM) domain metalloproteases cleave the isopeptide bond near the attachment point of polyubiquitin and substrate, as well as being highly specific for the K63 poly-Ub linkage. These DUBs regulate proteolysis by: directly interacting with and co-regulating E3 ligases; altering the level of substrate ubiquitination; hydrolyzing or remodeling ubiquitinated and poly-ubiquitinated substrates; acting in specific locations in the cell and altering the localization of the target protein; and acting on proteasome bound substrates to facilitate or inhibit proteolysis. Thus, the scope and regulation of the ubiquitin pathway is very similar to that of phosphorylation, with the DUBs serving the same functions as the phosphatase. PMID:23845989

Classical Swine Fever Virus Glycoprotein Erns Is an Endoribonuclease with an Unusual Base Specificity

PubMed Central

Hausmann, Yvonne; Roman-Sosa, Gleyder; Thiel, Heinz-Jürgen; Rümenapf, Till

2004-01-01

The glycoprotein Erns of pestiviruses is a virion-associated and -secreted RNase that is involved in virulence. The requirements at the cleavage site in heteropolymeric RNA substrates were studied for Erns. Limited digestion of heteropolymeric RNA substrates indicated a cleavage 5′ of uridine residues irrespective of the preceding nucleotide (Np/U). To further study specificity radiolabeled RNA, molecules of 45 to 56 nucleotides in length were synthesized that contained no or a single Np/U cleavage site. Cleavage was only observed in substrates containing an ApU, CpU, GpU, or UpU dinucleotide and occurred in two steps, an initial NpU-specific and a consecutive unspecific degradation. The NpU-specific cleavage was resistant to 7 M urea while the second-order cleavage was sensitive to denaturation. Kinetic analyses revealed that Erns is a highly active endoribonuclease (kcat/Km = 2 × 106 to 10 × 106 M−1 s−1) with a strong affinity to NpU containing single-stranded RNA substrates (Km = 85 to 260 nM). PMID:15113930

CNG site-specific and methyl-sensitive endonuclease WEN1 from wheat seedlings.

PubMed

Fedoreyeva, L I; Vanyushin, B F

2011-06-01

Endonuclease WEN1 with apparent molecular mass about 27 kDa isolated from cytoplasmic vesicular fraction of aging coleoptiles of wheat seedlings has expressed site specificity action. This is a first detection and isolation of a site-specific endonuclease from higher eukaryotes, in general, and higher plants, in particular. The enzyme hydrolyzes deoxyribooligonucleotides of different composition on CNG (N is G, A, C, or T) sites by splitting the phosphodiester bond between C and N nucleotide residues in CNG sequence independent from neighbor nucleotide context except for CCCG. WEN1 prefers to hydrolyze methylated λ phage DNA and double-stranded deoxyribooligonucleotides containing 5-methylcytosine sites (m(5)CAG, m(5)CTG) compared with unmethylated substrates. The enzyme is also able to hydrolyze single-stranded substrates, but in this case it splits unmethylated substrates predominantly. Detection in wheat seedlings of WEN1 endonuclease that is site specific, sensitive to the substrate methylation status, and modulated with S-adenosyl-L-methionine indicates that in higher plants restriction--modification systems or some of their elements, at least, may exist.

Mutant fatty acid desaturase

DOEpatents

Shanklin, John; Cahoon, Edgar B.

2004-02-03

The present invention relates to a method for producing mutants of a fatty acid desaturase having a substantially increased activity towards fatty acid substrates with chains containing fewer than 18 carbons relative to an unmutagenized precursor desaturase having an 18 carbon atom chain length substrate specificity. The method involves inducing one or more mutations in the nucleic acid sequence encoding the precursor desaturase, transforming the mutated sequence into an unsaturated fatty acid auxotroph cell such as MH13 E. coli, culturing the cells in the absence of supplemental unsaturated fatty acids, thereby selecting for recipient cells which have received and which express a mutant fatty acid desaturase with an elevated specificity for fatty acid substrates having chain lengths of less than 18 carbon atoms. A variety of mutants having 16 or fewer carbon atom chain length substrate specificities are produced by this method. Mutant desaturases produced by this method can be introduced via expression vectors into prokaryotic and eukaryotic cells and can also be used in the production of transgenic plants which may be used to produce specific fatty acid products.

The effect of substrate composition and storage time on urine specific gravity in dogs.

PubMed

Steinberg, E; Drobatz, K; Aronson, L

2009-10-01

The purpose of this study is to evaluate the effects of substrate composition and storage time on urine specific gravity in dogs. A descriptive cohort study of 15 dogs. The urine specific gravity of free catch urine samples was analysed during a 5-hour time period using three separate storage methods; a closed syringe, a diaper pad and non-absorbable cat litter. The urine specific gravity increased over time in all three substrates. The syringe sample had the least change from baseline and the diaper sample had the greatest change from baseline. The urine specific gravity for the litter and diaper samples had a statistically significant increase from the 1-hour to the 5-hour time point. The urine specific gravity from canine urine stored either on a diaper or in a non-absorbable litter increased over time. Although the change was found to be statistically significant over the 5-hour study period it is unlikely to be clinically significant.

Efflux-Mediated Resistance to Tigecycline (GAR-936) in Pseudomonas aeruginosa PAO1

PubMed Central

Dean, Charles R.; Visalli, Melissa A.; Projan, Steven J.; Sum, Phaik-Eng; Bradford, Patricia A.

2003-01-01

Pseudomonas aeruginosa strains are less susceptible to tigecycline (previously GAR-936; MIC, 8 μg/ml) than many other bacteria (P. J. Petersen, N. V. Jacobus, W. J. Weiss, P. E. Sum, and R. T. Testa, Antimicrob. Agents Chemother. 43:738-744, 1999). To elucidate the mechanism of resistance to tigecycline, P. aeruginosa PAO1 strains defective in the MexAB-OprM and/or MexXY (OprM) efflux pumps were tested for susceptibility to tigecycline. Increased susceptibility to tigecycline (MIC, 0.5 to 1 μg/ml) was specifically associated with loss of MexXY. Transcription of mexX and mexY was also responsive to exposure of cells to tigecycline. To test for the emergence of compensatory efflux pumps in the absence of MexXY-OprM, mutants lacking MexXY-OprM were plated on medium containing tigecycline at 4 or 6 μg/ml. Resistant mutants were readily recovered, and these also had decreased susceptibility to several other antibiotics, suggesting efflux pump recruitment. One representative carbenicillin-resistant strain overexpressed OprM, the outer membrane channel component of the MexAB-OprM efflux pump. The mexAB-oprM repressor gene, mexR, from this strain contained a 15-bp in-frame deletion. Two representative chloramphenicol-resistant strains showed expression of an outer membrane protein slightly larger than OprM. The mexCD-OprJ repressor gene, nfxB, from these mutants contained a 327-bp in-frame deletion and an IS element insertion, respectively. Together, these data indicated drug efflux mediated by MexCD-OprJ. The MICs of the narrower-spectrum semisynthetic tetracyclines doxycycline and minocycline increased more substantially than did those of tigecycline and other glycylcyclines against the MexAB-OprM- and MexCD-OprJ-overexpressing mutant strains. This suggests that glycylcyclines, although they are subject to efflux from P. aeruginosa, are generally inferior substrates for P. aeruginosa efflux pumps than are narrower-spectrum tetracyclines. PMID:12604529

Comparison of Scheimpflug imaging and spectral domain anterior segment optical coherence tomography for detection of narrow anterior chamber angles

PubMed Central

Grewal, D S; Brar, G S; Jain, R; Grewal, S P S

2011-01-01

Purpose To compare the performance of anterior chamber volume (ACV) and anterior chamber depth (ACD) obtained using Scheimpflug imaging with angle opening distance (AOD500) and trabecular-iris space area (TISA500) obtained using spectral domain anterior segment optical coherence tomography (SD-ASOCT) in detecting narrow angles classified using gonioscopy. Methods In this prospective, cross-sectional observational study, 265 eyes of 265 consecutive patients underwent sequential Scheimpflug imaging, SD-ASOCT imaging, and gonioscopy. Correlations between gonioscopy grading, ACV, ACD, AOD500, and TISA500 were evaluated. Area under receiver operating characteristic curve (AUC), sensitivity, specificity, and likelihood ratios (LRs) were calculated to assess the performance of ACV, ACD, AOD500, and TISA500 in detecting narrow angles (defined as Shaffer grade ≤1 in all quadrants). SD-ASOCT images were obtained at the nasal and temporal quadrants only. Results Twenty-eight eyes (10.6%) were classified as narrow angles on gonioscopy. ACV correlated with gonioscopy grading (P<0.001) for temporal (r=0.204), superior (r=0.251), nasal (r=0.213), and inferior (r=0.236) quadrants. ACV correlated with TISA500 for nasal (r=0.135, P=0.029) and temporal (P=0.160, P=0.009) quadrants and also with AOD500 for nasal (r=0.498, P<0.001) and temporal (r=0.517, P<0.001) quadrants. For detection of narrow angles, ACV (AUC=0.935; 95% confidence interval (CI) =0.898–0.961) performed similar to ACD (AUC=0.88, P=0.06) and significantly better than AOD500 nasal (AUC=0.761, P=0.001), AOD500 temporal (AUC=0.808, P<0.001), TISA500 nasal (AUC=0.756, P<0.001), and TISA500 temporal (AUC=0.738, P<0.001). Using a cutoff of 113 mm3, ACV had 90% sensitivity and 88% specificity for detecting narrow angles. Positive and negative LRs for ACV were 8.63 (95% CI=7.4–10.0) and 0.11 (95% CI=0.03–0.4), respectively. Conclusions ACV measurements using Scheimpflug imaging outperformed AOD500 and TISA500 using SD-ASOCT for detecting narrow angles. PMID:21336254

Insight into the role of substrate-binding residues in conferring substrate specificity for the multifunctional polysaccharide lyase Smlt1473.

PubMed

MacDonald, Logan C; Berger, Bryan W

2014-06-27

Anionic polysaccharides are of growing interest in the biotechnology industry due to their potential pharmaceutical applications in drug delivery and wound treatment. Chemical composition and polymer length strongly influence the physical and biological properties of the polysaccharide and thus its potential industrial and medical applications. One promising approach to determining monomer composition and controlling the degree of polymerization involves the use of polysaccharide lyases, which catalyze the depolymerization of anionic polysaccharides via a β-elimination mechanism. Utilization of these enzymes for the production of custom-made oligosaccharides requires a high degree of control over substrate specificity. Previously, we characterized a polysaccharide lyase (Smlt1473) from Stenotrophomonas maltophilia k279a, which exhibited significant activity against hyaluronan (HA), poly-β-d-glucuronic acid (poly-GlcUA), and poly-β-d-mannuronic acid (poly-ManA) in a pH-regulated manner. Here, we utilize a sequence structure guided approach based on a homology model of Smlt1473 to identify nine putative substrate-binding residues and examine their effect on substrate specificity via site-directed mutagenesis. Interestingly, single point mutations H221F and R312L resulted in increased activity and specificity toward poly-ManA and poly-GlcUA, respectively. Furthermore, a W171A mutant nearly eliminated HA activity, while increasing poly-ManA and poly-GlcUA activity by at least 35%. The effect of these mutations was analyzed by comparison with the high resolution structure of Sphingomonas sp. A1-III alginate lyase in complex with poly-ManA tetrasaccharide and by taking into account the structural differences between HA, poly-GlcUA, and poly-ManA. Overall, our results demonstrate that even minor changes in active site architecture have a significant effect on the substrate specificity of Smlt1473, whose structural plasticity could be applied to the design of highly active and specific polysaccharide lyases. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

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.

Correlation between radiographic findings of osteoarthritis and arthroscopic findings of articular cartilage degeneration within the patellofemoral joint.

PubMed

Kijowski, Richard; Blankenbaker, Donna; Stanton, Paul; Fine, Jason; De Smet, Arthur

2006-12-01

To correlate radiographic findings of osteoarthritis on axial knee radiographs with arthroscopic findings of articular cartilage degeneration within the patellofemoral joint in patients with chronic knee pain. The study group consisted of 104 patients with osteoarthritis of the patellofemoral joint and 30 patients of similar age with no osteoarthritis of the patellofemoral joint. All patients in the study group had an axial radiograph of the knee performed prior to arthroscopic knee surgery. At the time of arthroscopy, each articular surface of the patellofemoral joint was graded using the Noyes classification system. Two radiologists retrospectively reviewed the knee radiographs to determine the presence of marginal osteophytes, joint-space narrowing, subchondral sclerosis, and subchondral cysts. The sensitivity and specificity of the various radiographic features of osteoarthritis for the detection of articular cartilage degeneration within the patellofemoral joint were determined. The sensitivity of marginal osteophytes, joint-space narrowing, subchondral sclerosis, and subchondral cysts for the detection of articular cartilage degeneration within the patellofemoral joint was 73%, 37%, 4%, and 0% respectively. The specificity of marginal osteophytes, joint-space narrowing, subchondral sclerosis, and subchondral cysts for the detection of articular cartilage degeneration within the patellofemoral joint was 67%, 90%, 100%, and 100% respectively. Marginal osteophytes were the most sensitive radiographic feature for the detection of articular cartilage degeneration within the patellofemoral joint. Joint-space narrowing, subchondral sclerosis, and subchondral cysts were insensitive radiographic features of osteoarthritis, and rarely occurred in the absence of associated osteophyte formation.

Strategies for narrowing the maize yield gap of household farms through precision fertigation under irrigated conditions using CERES-Maize model.

PubMed

Liu, Jiangang; Wang, Guangyao; Chu, Qingquan; Chen, Fu

2017-07-01

Nitrogen (N) application significantly increases maize yield; however, the unreasonable use of N fertilizer is common in China. The analysis of crop yield gaps can reveal the limiting factors for yield improvement, but there is a lack of practical strategies for narrowing yield gaps of household farms. The objectives of this study were to assess the yield gap of summer maize using an integrative method and to develop strategies for narrowing the maize yield gap through precise N fertilization. The results indicated that there was a significant difference in maize yield among fields, with a low level of variation. Additionally, significant differences in N application rate were observed among fields, with high variability. Based on long-term simulation results, the optimal N application rate was 193 kg ha -1 , with a corresponding maximum attainable yield (AY max ) of 10 318 kg ha -1 . A considerable difference between farmers' yields and AY max was observed. Low agronomic efficiency of applied N fertilizer (AE N ) in farmers' fields was exhibited. The integrative method lays a foundation for exploring the specific factors constraining crop yield gaps at the field scale and for developing strategies for rapid site-specific N management. Optimization strategies to narrow the maize yield gap include increasing N application rates and adjusting the N application schedule. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

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

Cloning and characterization of a new broadspecific β-glucosidase from Lactococcus sp. FSJ4.

PubMed

Fang, Shujun; Chang, Jie; Lee, Yong Seok; Guo, Weiliang; Choi, Yong Lark; Zhou, Yongcan

2014-01-01

A β-glucosidase gene bglX was cloned from Lactococcus sp. FSJ4 by the method of shotgun. The bglX open reading frame consisted of 1,437 bp, encoding 478 amino acids. SDS-PAGE showed a recombinant bglX monomer of 54 kDa. Substrate specificity study revealed that the enzyme exhibited multifunctional catalysis activity against pNPG, pNPX and pNPGal. This enzyme shows higher activity against aryl glycosides of xylose than those of glucose or galactose. The enzyme exhibited the maximal activity at 40 °C, and the optimal pH was 6.0 with pNPG and 6.5 with pNPX as the substrates. Molecular modeling and substrate docking showed that there should be one active center responsible for the mutifuntional activity in this enzyme, since the active site pocket was substantially wide to allow the entry of pNPG, pNPX and pNPGal, which elucidated the structure-function relationship in substrate specificities. Substrate docking results indicated that Glu180 and Glu377 were the essential catalytic residues of the enzyme. The CDOCKER_ENERGY values obtained by substrate docking indicated that the enzyme has higher activity against pNPX than those of pNPG and pNPGal. These observations are in conformity with the results obtained from experimental investigation. Therefore, such substrate specificity makes this β-glucosidase of great interest for further study on physiological and catalytic reaction processes.

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

Molecular mechanisms of substrate recognition and specificity of botulinum neurotoxin serotype F.

PubMed

Chen, Sheng; Wan, Hoi Ying

2011-01-15

BoNTs (botulinum neurotoxins) are both deadly neurotoxins and natural toxins that are widely used in protein therapies to treat numerous neurological disorders of dystonia and spinal spasticity. Understanding the mechanism of action and substrate specificity of BoNTs is a prerequisite to develop antitoxin and novel BoNT-derived protein therapy. To date, there is a lack of detailed information with regard to how BoNTs recognize and hydrolyse the substrate VAMP-2 (vesicle-associated membrane protein 2), even though it is known to be cleaved by four of the seven BoNT serotypes, B, D, F, G and TeNT (tetanus neurotoxin). In the present study we dissected the molecular mechanisms of VAMP-2 recognition by BoNT serotype F for the first time. The initial substrate recognition was mediated through sequential binding of VAMP-2 to the B1, B2 and B3 pockets in LC/F (light chain of BoNT serotype F), which directed VAMP-2 to the active site of LC/F and stabilized the active site substrate recognition, where the P2, P1' and P2' sites of VAMP-2 were specifically recognized by the S2, S1' and S2' pockets of LC/F to promote substrate hydrolysis. The understanding of the molecular mechanisms of LC/F substrate recognition provides insights into the development of antitoxins and engineering novel BoNTs to optimize current therapy and extend therapeutic interventions.

Mismatch repair factor MSH2-MSH3 binds and alters the conformation of branched DNA structures predicted to form during genetic recombination.

PubMed

Surtees, Jennifer A; Alani, Eric

2006-07-14

Genetic studies in Saccharomyces cerevisiae predict that the mismatch repair (MMR) factor MSH2-MSH3 binds and stabilizes branched recombination intermediates that form during single strand annealing and gene conversion. To test this model, we constructed a series of DNA substrates that are predicted to form during these recombination events. We show in an electrophoretic mobility shift assay that S. cerevisiae MSH2-MSH3 specifically binds branched DNA substrates containing 3' single-stranded DNA and that ATP stimulates its release from these substrates. Chemical footprinting analyses indicate that MSH2-MSH3 specifically binds at the double-strand/single-strand junction of branched substrates, alters its conformation and opens up the junction. Therefore, MSH2-MSH3 binding to its substrates creates a unique nucleoprotein structure that may signal downstream steps in repair that include interactions with MMR and nucleotide excision repair factors.

Aerobic biological treatment of leachates from municipal solid waste landfill.

PubMed

Andrés, P; Gutierrez, F; Arrabal, C; Cortijo, M

2004-01-01

The main objective of the study was to improve chemical oxygen demand (COD) elimination by secondary biological treatment from leachate of municipal solid waste landfill. This effluent was a supernatant liquid obtained after physicochemical processes and coagulating with Al3+ followed by ammoniacal stripping. First, respirometric assays were carried out to determine the substrate biodegradability. Specific sludge respiration rate (R(s)) vs. concentration of substrate (S), showed an increasing specific rate of assimilation of substrate (Rs), which reached the highest value, when the substrate concentration (COD) was between 75 and 200 mg O2 L(-1). Second, continuous experiments were made in an aerobic digester to test the previous respirometric data and the results showed removal efficiency of COD between 83 and 69%, and a substrate assimilation rate between 1.3 and 3.1 g COD g(-1) volatile suspended solids d(-1).

Resistance modulation in VO2 nanowires induced by an electric field via air-gap gates

NASA Astrophysics Data System (ADS)

Kanki, Teruo; Chikanari, Masashi; Wei, Tingting; Tanaka, Hidekazu; The Institute of Scientific; Industrial Research Team

Vanadium dioxide (VO2) shows huge resistance change with metal-insulator transition (MIT) at around room temperature. Controlling of the MIT by applying an electric field is a topical ongoing research toward the realization of Mott transistor. In this study, we have successfully switched channel resistance of VO2 nano-wire channels by a pure electrostatic field effect using a side-gate-type field-effect transistor (SG-FET) viaair gap and found that single crystalline VO2 nanowires and the channels with narrower width enhance transport modulation rate. The rate of change in resistance ((R0-R)/R, where R0 and R is the resistance of VO2 channel with off state and on state gate voltage (VG) , respectively) was 0.42 % at VG = 30 V in in-plane poly-crystalline VO2 channels on Al2O3(0001) substrates, while the rate in single crystalline channels on TiO2 (001) substrates was 3.84 %, which was 9 times higher than that using the poly-crystalline channels. With reducing wire width from 3000 nm to 400 nm of VO2 on TiO2 (001) substrate, furthermore, resistance modulation ratio enhanced from 0.67 % to 3.84 %. This change can not be explained by a simple free-electron model. In this presentation, we will compare the electronic properties between in-plane polycrystalline VO2 on Al2O3 (0001) and single crystalline VO2 on TiO2 (001) substrates, and show experimental data in detail..

Appropriate salt concentration of nanodiamond colloids for electrostatic self-assembly seeding of monosized individual diamond nanoparticles on silicon dioxide surfaces.

PubMed

Yoshikawa, Taro; Zuerbig, Verena; Gao, Fang; Hoffmann, René; Nebel, Christoph E; Ambacher, Oliver; Lebedev, Vadim

2015-05-19

Monosized (∼4 nm) diamond nanoparticles arranged on substrate surfaces are exciting candidates for single-photon sources and nucleation sites for ultrathin nanocrystalline diamond film growth. The most commonly used technique to obtain substrate-supported diamond nanoparticles is electrostatic self-assembly seeding using nanodiamond colloidal suspensions. Currently, monodisperse nanodiamond colloids, which have a narrow distribution of particle sizes centering on the core particle size (∼4 nm), are available for the seeding technique on different substrate materials such as Si, SiO2, Cu, and AlN. However, the self-assembled nanoparticles tend to form small (typically a few tens of nanometers or even larger) aggregates on all of those substrate materials. In this study, this major weakness of self-assembled diamond nanoparticles was solved by modifying the salt concentration of nanodiamond colloidal suspensions. Several salt concentrations of colloidal suspensions were prepared using potassium chloride as an inserted electrolyte and were examined with respect to seeding on SiO2 surfaces. The colloidal suspensions and the seeded surfaces were characterized by dynamic light scattering and atomic force microscopy, respectively. Also, the interaction energies between diamond nanoparticles in each of the examined colloidal suspensions were compared on the basis of the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory. From these investigations, it became clear that the appropriate salt concentration suppresses the formation of small aggregates during the seeding process owing to the modified electrostatic repulsive interaction between nanoparticles. Finally, monosized (<10 nm) individual diamond nanoparticles arranged on SiO2 surfaces have been successfully obtained.

Emplacement of rock avalanche material across saturated sediments, Southern Alp, New Zealand

NASA Astrophysics Data System (ADS)

Dufresne, A.; Davies, T. R.; McSaveney, M. J.

2012-04-01

The spreading of material from slope failure events is not only influenced by the volume and nature of the source material and the local topography, but also by the materials encountered in the runout path. In this study, evidence of complex interactions between rock avalanche and sedimentary runout path material were investigated at the 45 x 106 m3 long-runout (L: 4.8 km) Round Top rock avalanche deposit, New Zealand. It was sourced within myolinitic schists of the active strike-slip Alpine Fault. The narrow and in-failure-direction elongate source scarp is deep-seated, indicating slope failure was triggered by strong seismic activity. The most striking morphological deposit features are longitudinal ridges aligned radially to source. Trenching and geophysical surveys show bulldozed and sheared substrate material at ridge termini and laterally displaced sedimentary strata. The substrate failed at a minimum depth of 3 m indicating a ploughing motion of the ridges into the saturated material below. Internal avalanche compression features suggest deceleration behind the bulldozed substrate obstacle. Contorted fabric in material ahead of the ridge document substrate disruption by the overriding avalanche material deposited as the next down-motion hummock. Comparison with rock avalanches of similar volume but different emplacement environments places Round Top between longer runout avalanches emplaced over e.g. playa lake sediments and those with shorter travel distances, whose runout was apparently retarded by topographic obstacles or that entrained high-friction debris. These empirical observations indicate the importance of runout path materials on tentative trends in rock avalanche emplacement dynamics and runout behaviour.

Radiative transfer modeling of dust-coated Pancam calibration target materials: Laboratory visible/near-infrared spectrogoniometry

USGS Publications Warehouse

Johnson, J. R.; Sohl-Dickstein, J.; Grundy, W.M.; Arvidson, R. E.; Bell, J.F.; Christensen, P.R.; Graff, T.; Guinness, E.A.; Kinch, K.; Morris, Robert; Shepard, M.K.

2006-01-01

Laboratory visible/near-infrared multispectral observations of Mars Exploration Rover Pancam calibration target materials coated with different thicknesses of Mars spectral analog dust were acquired under variable illumination geometries using the Bloomsburg University Goniometer. The data were fit with a two-layer radiative transfer model that combines a Hapke formulation for the dust with measured values of the substrate interpolated using a He-Torrance approach. We first determined the single-scattering albedo, phase function, opposition effect width, and amplitude for the dust using the entire data set (six coating thicknesses, three substrates, four wavelengths, and phase angles 3??-117??). The dust exhibited single-scattering albedo values similar to other Mars analog soils and to Mars Pathfinder dust and a dominantly forward scattering behavior whose scattering lobe became narrower at longer wavelengths. Opacity values for each dust thickness corresponded well to those predicted from the particles sizes of the Mars analog dust. We then restricted the number of substrates, dust thicknesses, and incidence angles input to the model. The results suggest that the dust properties are best characterized when using substrates whose reflectances are brighter and darker than those of the deposited dust and data that span a wide range of dust thicknesses. The model also determined the dust photometric properties relatively well despite limitations placed on the range of incidence angles. The model presented here will help determine the photometric properties of dust deposited on the MER rovers and to track the multiple episodes of dust deposition and erosion that have occurred at both landing sites. Copyright 2006 by the American Geophysical Union.

Effect of tacticity on the structure and glass transition temperature of polystyrene adsorbed onto solid surfaces

NASA Astrophysics Data System (ADS)

Negash, Solomon; Tatek, Yergou B.; Tsige, Mesfin

2018-04-01

We have carried out atomistic (all-atom) molecular dynamics simulations to investigate the effect of tacticity on the structure and glass transition temperature (Tg) of polystyrene (PS) thin films adsorbed on two distinct types of solid substrates. The systems consist of thin films made of atactic, isotactic, and syndiotactic PS chains supported by graphite or hydroxylated α-quartz substrates, which are known to be atomically flat but chemically and structurally different. We have observed a marked dependence of the film structure on substrate type as well as on tacticity. For instance, rings' orientation near substrate surfaces depends on substrate type for atactic PS and isotactic PS films, while no such dependence is observed for syndiotactic PS films whose interfacial structure seems to result from their propensity to adopt the trans conformation rather than their specific interaction with the substrates. Moreover, our results indicate that glass transition temperatures of substrate supported polystyrene films are higher compared to those of the corresponding free-standing films. More specifically, PS films on graphite exhibit larger Tg values than those on α-quartz, and we have noticed that syndiotactic PS has the largest Tg irrespective of the substrate type. Furthermore, the local Tg in the region of the film in contact with the substrates shows a strong tacticity and substrate dependence, whereas no dependencies were found for the local Tg in the middle of the film. Substrate-film interaction energy and chains' dynamics near substrate-film interfaces were subsequently investigated in order to substantiate the obtained Tgs, and it was found that films with higher Tgs are strongly adsorbed on the substrates and/or exhibit smaller interfacial chains' dynamics essentially due to steric hindrance.

Whole-animal imaging of bacterial infection using endoscopic excitation of β-lactamase (BlaC)-specific fluorogenic probe

NASA Astrophysics Data System (ADS)

Nooshabadi, Fatemeh; Yang, Hee-Jeong; Cheng, Yunfeng; Xie, Hexin; Rao, Jianghong; Cirillo, Jeffrey D.; Maitland, Kristen C.

2016-03-01

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains one of the most frequent causes of death worldwide. The slow growth rate of Mtb limits progress toward understanding tuberculosis including diagnosis of infections and evaluating therapeutic efficacy. Development of near-infrared (NIR) β-lactamase (BlaC)-specific fluorogenic substrate has made a significant breakthrough in the whole-animal imaging to detect Mtb infection. The reporter enzyme fluorescence (REF) system using a BlaC-specific fluorogenic substrate has improved the detection sensitivity in whole-animal optical imaging down to ~104 colony forming units (CFU) of bacteria, about 100-fold improvement over recombinant strains. However, improvement of detection sensitivity is strongly needed for clinical diagnosis of early stage infection at greater tissue depth. In order to improve detection sensitivity, we have integrated a fiber-based microendoscpe into a whole-animal imaging system to transmit the excitation light from the fiber bundle to the fluorescent target directly and measure fluorescent level using BlaC-specific REF substrate in the mouse lung. REF substrate, CNIR800, was delivered via aerosol route to the pulmonary infected mice with M. bovis BCG strain at 24 hours post-infection and groups of mice were imaged at 1-4 hours post-administration of the substrate using the integrated imaging system. In this study we evaluated the kinetics of CNIR800 substrate using REF technology using the integrated imaging system. Integration of these technologies has great promise for improved detection sensitivity allowing pre-clinical imaging for evaluation of new therapeutic agents.

Specific surface to evaluate the efficiencies of milling and pretreatment of wood for enzymatic saccharification

Treesearch

Junyong Zhu; G.S. Wang; X.J. Pan; Roland Gleisner

2009-01-01

Sieving methods have been almost exclusively used for feedstock size-reduction characterization in the biomass refining literature. This study demonstrates a methodology to properly characterize specific surface of biomass substrates through two dimensional measurement of each fiber of the substrate using a wet imaging technique. The methodology provides more...

Experimental observation of phase-flip transitions in the brain

NASA Astrophysics Data System (ADS)

Dotson, Nicholas M.; Gray, Charles M.

2016-10-01

The phase-flip transition has been demonstrated in a host of coupled nonlinear oscillator models, many pertaining directly to understanding neural dynamics. However, there is little evidence that this phenomenon occurs in the brain. Using simultaneous microelectrode recordings in the nonhuman primate cerebral cortex, we demonstrate the presence of phase-flip transitions between oscillatory narrow-band local field potential signals separated by several centimeters. Specifically, we show that sharp transitions between in-phase and antiphase synchronization are accompanied by a jump in synchronization frequency. These findings are significant for two reasons. First, they validate predictions made by model systems. Second, they have potentially far reaching implications for our understanding of the mechanisms underlying corticocortical communication, which are thought to rely on narrow-band oscillatory synchronization with specific relative phase relationships.

Phospholipid substrate-specificity of the L-serine base-exchange enzyme in rat liver microsomal fraction.

PubMed Central

Bjerve, K S

1984-01-01

The specificity of the L-serine base-exchange enzyme towards the fatty acid composition of the phospholipid substrate was investigated with a rat liver microsomal fraction. The relative rates of L-serine incorporation into saturated-hexaenoic, saturated-pentaenoic, saturated-tetraenoic, saturated-trienoic, dienoic-dienoic, monoenoic-dienoic, saturated-dienoic and saturated-monoenoic + saturated-saturated phosphatidylserine molecular species were 42, 5, 23, 4, 5, 4, 5 and 11% respectively. This is similar to, but not identical with, the relative mass abundance of these molecular species in total liver cell phosphatidylserines. The results indicate that the substrate-specificity of the L-serine base-exchange enzyme can at least in part explain the observed fatty acid composition of rat liver phosphatidylserines. PMID:6430274

Probing mammalian spermine oxidase enzyme-substrate complex through molecular modeling, site-directed mutagenesis and biochemical characterization.

PubMed

Tavladoraki, Paraskevi; Cervelli, Manuela; Antonangeli, Fabrizio; Minervini, Giovanni; Stano, Pasquale; Federico, Rodolfo; Mariottini, Paolo; Polticelli, Fabio

2011-04-01

Spermine oxidase (SMO) and acetylpolyamine oxidase (APAO) are FAD-dependent enzymes that are involved in the highly regulated pathways of polyamine biosynthesis and degradation. Polyamine content is strictly related to cell growth, and dysfunctions in polyamine metabolism have been linked with cancer. Specific inhibitors of SMO and APAO would allow analyzing the precise role of these enzymes in polyamine metabolism and related pathologies. However, none of the available polyamine oxidase inhibitors displays the desired characteristics of selective affinity and specificity. In addition, repeated efforts to obtain structural details at the atomic level on these two enzymes have all failed. In the present study, in an effort to better understand structure-function relationships, SMO enzyme-substrate complex has been probed through a combination of molecular modeling, site-directed mutagenesis and biochemical studies. Results obtained indicate that SMO binds spermine in a similar conformation as that observed in the yeast polyamine oxidase FMS1-spermine complex and demonstrate a major role for residues His82 and Lys367 in substrate binding and catalysis. In addition, the SMO enzyme-substrate complex highlights the presence of an active site pocket with highly polar characteristics, which may explain the different substrate specificity of SMO with respect to APAO and provide the basis for the design of specific inhibitors for SMO and APAO.

Comprehensive structural and substrate specificity classification of the Saccharomyces cerevisiae methyltransferome.

PubMed

Wlodarski, Tomasz; Kutner, Jan; Towpik, Joanna; Knizewski, Lukasz; Rychlewski, Leszek; Kudlicki, Andrzej; Rowicka, Maga; Dziembowski, Andrzej; Ginalski, Krzysztof

2011-01-01

Methylation is one of the most common chemical modifications of biologically active molecules and it occurs in all life forms. Its functional role is very diverse and involves many essential cellular processes, such as signal transduction, transcriptional control, biosynthesis, and metabolism. Here, we provide further insight into the enzymatic methylation in S. cerevisiae by conducting a comprehensive structural and functional survey of all the methyltransferases encoded in its genome. Using distant homology detection and fold recognition, we found that the S. cerevisiae methyltransferome comprises 86 MTases (53 well-known and 33 putative with unknown substrate specificity). Structural classification of their catalytic domains shows that these enzymes may adopt nine different folds, the most common being the Rossmann-like. We also analyzed the domain architecture of these proteins and identified several new domain contexts. Interestingly, we found that the majority of MTase genes are periodically expressed during yeast metabolic cycle. This finding, together with calculated isoelectric point, fold assignment and cellular localization, was used to develop a novel approach for predicting substrate specificity. Using this approach, we predicted the general substrates for 24 of 33 putative MTases and confirmed these predictions experimentally in both cases tested. Finally, we show that, in S. cerevisiae, methylation is carried out by 34 RNA MTases, 32 protein MTases, eight small molecule MTases, three lipid MTases, and nine MTases with still unknown substrate specificity.

Investigating Commercial Cellulase Performances Toward Specific Biomass Recalcitrance Factors Using Reference Substrates

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

Ju, Xiaohui; Bowden, Mark E.; Engelhard, Mark H.

Three commercial cellulase preparations, Novozymes Cellic® Ctec2, Dupont Accellerase® 1500, and DSM Cytolase CL, were evaluated for their hydrolytic activity using a set of reference biomass substrates with controlled substrate characteristics. It was found that lignin remains a significant recalcitrance factor to all the preparations, although different enzyme preparations respond to the inhibitory effect of lignin differently. Also, different types of biomass lignin can inhibit cellulose enzymes in different manners. Enhancing enzyme activity toward biomass fiber swelling is an area significantly contributing to potential improvement in cellulose performance. While the degree of polymerization of cellulose in the reference substrates didmore » not present a major recalcitrance factor to Novozymes Cellic® Ctec2, cellulose crystallite has been shown to have a significant lower reactivity toward all enzyme mixtures. The presence of polysaccharide monooxygenases (PMOs) in Novozymes Ctec2 appears to enhance enzyme activity toward decrystallization of cellulose. This study demonstrated that reference substrates with controlled chemical and physical characteristics of structural features can be applied as an effective and practical strategy to identify cellulosic enzyme activities toward specific biomass recalcitrance factor(s) and provide specific targets for enzyme improvement.« less

Specific Inhibition of β-Secretase Processing of the Alzheimer Disease Amyloid Precursor Protein.

PubMed

Ben Halima, Saoussen; Mishra, Sabyashachi; Raja, K Muruga Poopathi; Willem, Michael; Baici, Antonio; Simons, Kai; Brüstle, Oliver; Koch, Philipp; Haass, Christian; Caflisch, Amedeo; Rajendran, Lawrence

2016-03-08

Development of disease-modifying therapeutics is urgently needed for treating Alzheimer disease (AD). AD is characterized by toxic β-amyloid (Aβ) peptides produced by β- and γ-secretase-mediated cleavage of the amyloid precursor protein (APP). β-secretase inhibitors reduce Aβ levels, but mechanism-based side effects arise because they also inhibit β-cleavage of non-amyloid substrates like Neuregulin. We report that β-secretase has a higher affinity for Neuregulin than it does for APP. Kinetic studies demonstrate that the affinities and catalytic efficiencies of β-secretase are higher toward non-amyloid substrates than toward APP. We show that non-amyloid substrates are processed by β-secretase in an endocytosis-independent manner. Exploiting this compartmentalization of substrates, we specifically target the endosomal β-secretase by an endosomally targeted β-secretase inhibitor, which blocked cleavage of APP but not non-amyloid substrates in many cell systems, including induced pluripotent stem cell (iPSC)-derived neurons. β-secretase inhibitors can be designed to specifically inhibit the Alzheimer process, enhancing their potential as AD therapeutics without undesired side effects. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Different substrates and starter inocula govern microbial community structures in biogas reactors.

PubMed

Satpathy, Preseela; Steinigeweg, Sven; Cypionka, Heribert; Engelen, Bert

2016-01-01

The influence of different starter inocula on the microbial communities in biogas batch reactors fed with fresh maize and maize silage as substrates was investigated. Molecular biological analysis by Denaturing Gradient Gel Electrophoresis (DGGE) of 16S rRNA gene fragments showed that each inoculum bore specific microbial communities with varying predominant phylotypes. Both, bacterial and archaeal DGGE profiles displayed three distinct communities that developed depending on the type of inoculum. Although maize and silage are similar substrates, different communities dominated the lactate-rich silage compared to lactate-free fresh maize. Cluster analysis of DGGE gels showed the communities of the same substrates to be stable with their respective inoculum. Bacteria-specific DGGE analysis revealed a rich diversity with Firmicutes being predominant. The other abundant phylotypes were Bacteroidetes and Synergistetes. Archaea-specific DGGE analysis displayed less diverse community structures, identifying members of the Methanosarcinales as the dominant methanogens present in all the three biogas digesters. In general, the source of inoculum played a significant role in shaping microbial communities. Adaptability of the inoculum to the substrates fed also influenced community compositions which further impacted the rates of biogas production.

Roles of s3 site residues of nattokinase on its activity and substrate specificity.

PubMed

Wu, Shuming; Feng, Chi; Zhong, Jin; Huan, Liandong

2007-09-01

Nattokinase (Subtilisin NAT, NK) is a bacterial serine protease with high fibrinolytic activity. To probe their roles on protease activity and substrate specificity, three residues of S3 site (Gly(100), Ser(101) and Leu(126)) were mutated by site-directed mutagenesis. Kinetics parameters of 20 mutants were measured using tetrapeptides as substrates, and their fibrinolytic activities were determined by fibrin plate method. Results of mutation analysis showed that Gly(100) and Ser(101) had reverse steric and electrostatic effects. Residues with bulky or positively charged side chains at position 100 decreased the substrate binding and catalytic activity drastically, while residues with the same characters at position 101 could obviously enhance protease and fibrinolytic activity of NK. Mutation of Leu(126) might impair the structure of the active cleft and drastically decreased the activity of NK. Kinetics studies of the mutants showed that S3 residues were crucial to keep protease activity while they moderately affected substrate specificity of NK. The present study provided some original insight into the P3-S3 interaction in NK and other subtilisins, as well as showed successful protein engineering cases to improve NK as a potential therapeutic agent.

Investigating commercial cellulase performances toward specific biomass recalcitrance factors using reference substrates.

PubMed

Ju, Xiaohui; Bowden, Mark; Engelhard, Mark; Zhang, Xiao

2014-05-01

Three commercial cellulase preparations, Novozymes Cellic(®) Ctec2, Dupont Accellerase(®) 1500, and DSM Cytolase CL, were evaluated for their hydrolytic activity using a set of reference biomass substrates with controlled substrate characteristics. It was found that lignin remains a significant recalcitrance factor to all the preparations, although different enzyme preparations respond to the inhibitory effect of lignin differently. Also, different types of biomass lignin can inhibit cellulase enzymes in different manners. Enhancing enzyme activity toward biomass fiber swelling is an area significantly contributing to potential improvement in cellulase performance. While the degree of polymerization of cellulose in the reference substrates did not present a major recalcitrance factor to Novozymes Cellic(®) Ctec2, cellulose crystallite has been shown to have a significant lower reactivity toward all enzyme mixtures. The presence of polysaccharide monooxygenases (PMOs) in Novozymes Ctec2 appears to enhance enzyme activity toward decrystallization of cellulose. This study demonstrated that reference substrates with controlled chemical and physical characteristics of structural features can be applied as an effective and practical strategy to identify cellulosic enzyme activities toward specific biomass recalcitrance factor(s) and provide specific targets for enzyme improvement.

Light Quality Dependent Changes in Morphology, Antioxidant Capacity, and Volatile Production in Sweet Basil (Ocimum basilicum)

PubMed Central

Carvalho, Sofia D.; Schwieterman, Michael L.; Abrahan, Carolina E.; Colquhoun, Thomas A.; Folta, Kevin M.

2016-01-01

Narrow-bandwidth light treatments may be used to manipulate plant growth, development and metabolism. In this report LED-based light treatments were used to affect yield and metabolic content of sweet basil (Ocimum basilicum L. cv “Ceasar”) grown in controlled environments. This culinary herb produces an aroma highly appreciated by consumers, primarily composed of terpenes/terpenoids, phenylpropanoids, and fatty-acid- derived volatile molecules. Basil plants were grown under narrow-bandwidth light conditions, and leaf area, height, mass, antioxidant capacity and volatile emissions were measured at various time points. The results indicate reproducible significant differences in specific volatiles, and in biochemical classes of volatiles, compared to greenhouse grown plants. For example, basil plants grown under blue/red/yellow or blue/red/green wavelengths emit higher levels of a subset of monoterpenoid volatiles, while a blue/red/far-red treatment leads to higher levels of most sesquiterpenoid volatile molecules. Specific light treatments increase volatile content, mass, and antioxidant capacity. The results show that narrow-bandwidth illumination can induce discrete suites of volatile classes that affect sensory quality in commercial herbs, and may be a useful tool in improving commercial production. PMID:27635127

Light Quality Dependent Changes in Morphology, Antioxidant Capacity, and Volatile Production in Sweet Basil (Ocimum basilicum).

PubMed

Carvalho, Sofia D; Schwieterman, Michael L; Abrahan, Carolina E; Colquhoun, Thomas A; Folta, Kevin M

2016-01-01

Narrow-bandwidth light treatments may be used to manipulate plant growth, development and metabolism. In this report LED-based light treatments were used to affect yield and metabolic content of sweet basil (Ocimum basilicum L. cv "Ceasar") grown in controlled environments. This culinary herb produces an aroma highly appreciated by consumers, primarily composed of terpenes/terpenoids, phenylpropanoids, and fatty-acid- derived volatile molecules. Basil plants were grown under narrow-bandwidth light conditions, and leaf area, height, mass, antioxidant capacity and volatile emissions were measured at various time points. The results indicate reproducible significant differences in specific volatiles, and in biochemical classes of volatiles, compared to greenhouse grown plants. For example, basil plants grown under blue/red/yellow or blue/red/green wavelengths emit higher levels of a subset of monoterpenoid volatiles, while a blue/red/far-red treatment leads to higher levels of most sesquiterpenoid volatile molecules. Specific light treatments increase volatile content, mass, and antioxidant capacity. The results show that narrow-bandwidth illumination can induce discrete suites of volatile classes that affect sensory quality in commercial herbs, and may be a useful tool in improving commercial production.

Analysis of factors affecting the accuracy, reproducibility, and interpretation of microbial community carbon source utilization patterns

USGS Publications Warehouse

Haack, S.K.; Garchow, H.; Klug, M.J.; Forney, L.J.

1995-01-01

We determined factors that affect responses of bacterial isolates and model bacterial communities to the 95 carbon substrates in Biolog microliter plates. For isolates and communities of three to six bacterial strains, substrate oxidation rates were typically nonlinear and were delayed by dilution of the inoculum. When inoculum density was controlled, patterns of positive and negative responses exhibited by microbial communities to each of the carbon sources were reproducible. Rates and extents of substrate oxidation by the communities were also reproducible but were not simply the sum of those exhibited by community members when tested separately. Replicates of the same model community clustered when analyzed by principal- components analysis (PCA), and model communities with different compositions were clearly separated un the first PCA axis, which accounted for >60% of the dataset variation. PCA discrimination among different model communities depended on the extent to which specific substrates were oxidized. However, the substrates interpreted by PCA to be most significant in distinguishing the communities changed with reading time, reflecting the nonlinearity of substrate oxidation rates. Although whole-community substrate utilization profiles were reproducible signatures for a given community, the extent of oxidation of specific substrates and the numbers or activities of microorganisms using those substrates in a given community were not correlated. Replicate soil samples varied significantly in the rate and extent of oxidation of seven tested substrates, suggesting microscale heterogeneity in composition of the soil microbial community.

Molecular basis for allosteric specificity regulation in class Ia ribonucleotide reductase from Escherichia coli

PubMed Central

Zimanyi, Christina M; Chen, Percival Yang-Ting; Kang, Gyunghoon; Funk, Michael A; Drennan, Catherine L

2016-01-01

Ribonucleotide reductase (RNR) converts ribonucleotides to deoxyribonucleotides, a reaction that is essential for DNA biosynthesis and repair. This enzyme is responsible for reducing all four ribonucleotide substrates, with specificity regulated by the binding of an effector to a distal allosteric site. In all characterized RNRs, the binding of effector dATP alters the active site to select for pyrimidines over purines, whereas effectors dGTP and TTP select for substrates ADP and GDP, respectively. Here, we have determined structures of Escherichia coli class Ia RNR with all four substrate/specificity effector-pairs bound (CDP/dATP, UDP/dATP, ADP/dGTP, GDP/TTP) that reveal the conformational rearrangements responsible for this remarkable allostery. These structures delineate how RNR ‘reads’ the base of each effector and communicates substrate preference to the active site by forming differential hydrogen bonds, thereby maintaining the proper balance of deoxynucleotides in the cell. DOI: http://dx.doi.org/10.7554/eLife.07141.001 PMID:26754917

A multicomponent complex is required for the AAUAAA-dependent cross-linking of a 64-kilodalton protein to polyadenylation substrates.

PubMed Central

Wilusz, J; Shenk, T; Takagaki, Y; Manley, J L

1990-01-01

A 64-kilodalton (kDa) polypeptide that is cross-linked by UV light specifically to polyadenylation substrate RNAs containing a functional AAUAAA element has been identified previously. Fractionated HeLa nuclear components that can be combined to regenerate efficient and accurate polyadenylation in vitro have now been screened for the presence of the 64-kDa protein. None of the individual components contained an activity which could generate the 64-kDa species upon UV cross-linking in the presence of substrate RNA. It was necessary to mix two components, cleavage stimulation factor and specificity factor, to reconstitute 64-kDa protein-RNA cross-linking. The addition of cleavage factors to this mixture very efficiently reconstituted the AAUAAA-specific 64-kDa protein-RNA interaction. The 64-kDa protein, therefore, is present in highly purified, reconstituted polyadenylation reactions. However, it is necessary to form a multicomponent complex to efficiently cross-link the protein to a substrate RNA. Images PMID:2304466

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

Aich, Sanjukta; Prasad, Lata; Delbaere, Louis T.J.

GTP-dependent phosphoenolpyruvate carboxykinase (PCK) is the key enzyme that controls the blood glucose level during fasting in higher animals. Here we report the first substrate-free structure of a GTP-dependent phosphoenolpyruvate (PEP) carboxykinase from a bacterium, Corynebacterium glutamicum (CgPCK). The protein crystallizes in space group P2{sub 1} with four molecules per asymmetric unit. The 2.3 {angstrom} resolution structure was solved by molecular replacement using the human cytosolic PCK (hcPCK) structure (PDB ID: 1KHF) as the starting model. The four molecules in the asymmetric unit pack as two dimers, and is an artifact of crystal packing. However, the P-loop and the guaninemore » binding loop of the substrate-free CgPCK structure have different conformations from the other published GTP-specific PCK structures, which all have bound substrates and/or metal ions. It appears that a change in the P-loop and guanine binding loop conformation is necessary for substrate binding in GTP-specific PCKs, as opposed to overall domain movement in ATP-specific PCKs.« less

Substrate specificity and copper loading of the manganese-oxidizing multicopper oxidase Mnx from Bacillus sp. PL-12.

PubMed

Butterfield, Cristina N; Tebo, Bradley M

2017-02-22

Manganese(ii) oxidation in the environment is thought to be driven by bacteria because enzymatic catalysis is many orders of magnitude faster than the abiotic processes. The heterologously purified Mn oxidase (Mnx) from marine Bacillus sp. PL-12 is made up of the multicopper oxidase (MCO) MnxG and two small Cu and heme-binding proteins of unknown function, MnxE and MnxF. Mnx binds Cu and oxidizes both Mn(ii) and Mn(iii), generating Mn(iv) oxide minerals that resemble those found on the Bacillus spore surface. Spectroscopic techniques have illuminated details about the metallo-cofactors of Mnx, but very little is known about their requirement for catalytic activity, and even less is known about the substrate specificity of Mnx. Here we quantify the canonical MCO Cu and persistent peripheral Cu bound to Mnx, and test Mnx oxidizing ability toward different substrates at varying pH. Mn(ii) appears to be the best substrate in terms of k cat , but its oxidation does not follow Michaelis-Menten kinetics, instead showing a sigmoidal cooperative behavior. Mnx also oxidizes Fe(ii) substrate, but in a Michaelis-Menten manner and with a decreased activity, as well as organic substrates. The reduced metals are more rapidly consumed than the larger organic substrates, suggesting the hypothesis that the Mnx substrate site is small and tuned for metal oxidation. Of biological relevance is the result that Mnx has the highest catalytic efficiency for Mn(ii) at the pH of sea water, especially when the protein is loaded with greater than the requisite four MCO copper atoms, suggesting that the protein has evolved specifically for Mn oxidation.

Simultaneous Distinction of Monospecific and Mixed DFS70 Patterns During ANA Screening with a Novel HEp-2 ELITE/DFS70 Knockout Substrate

PubMed Central

Malyavantham, Kishore S.; Suresh, Lakshmanan

2018-01-01

Systemic autoimmune connective tissue disorders are characterized by circulating antinuclear antibodies (ANA). Although there are several technologies available for ANA screening, indirect immunofluorescence (IIF) using Human epithelial cells-2 (HEp-2) substrate remains the primary and recommended method because of its superior sensitivity. HEp-2 substrates can detect a multitude of patterns resulting from autoantibody binding to various protein and nucleic acid autoantigens distributed throughout the nucleus and cytoplasm of the cells. The great diversity of monospecific and mixed patterns resulting from positive reactions on HEp-2 substrate also complicate the interpretation and accuracy of reporting. One specific example which received utmost attention recently is the dense fine speckled 70 (DFS70) pattern resulting from autoantibodies that specifically bind to a protein called lens epithelium derived growth factor (LEDGF). Lack of clear association with a specific systemic autoimmune disease and high prevalence in healthy populations have made accurate interpretation of DFS70 pattern important. Accurate distinction of DFS70 pattern from disease-associated patterns using conventional HEp-2 substrate is challenging. Moreover, frequent co-occurrence of DFS70 pattern along with disease-associated patterns such as homogeneous, speckled, and mixed homogeneous-speckled patterns complicate the IIF interpretation. The goal of this paper is to demonstrate the utility of a novel engineered HEp-2 IIF substrate that retains all advantages of conventional HEp-2 substrate while simultaneously providing the ability to distinguish DFS70 pattern with high confidence in both monospecific and mixed ANA positive examples. The new substrate is further able to unmask disease-associated ANA patterns previously concealed by DFS70 pattern. PMID:29364249

alpha-1,4-Glucan lyase, a new class of starch/glycogen degrading enzyme. III. Substrate specificity, mode of action, and cleavage mechanism.

PubMed

Yu, S; Ahmad, T; Kenne, L; Pedersén, M

1995-05-11

The alpha-1,4-glucan lyase (EC 4.2.2.-), purified from the red alga Gracilariopsis lemaneiformis, is a single polypeptide with a molecular mass of 116,654 Da as determined by matrix-assisted laser-desorption mass spectrometry. It degraded maltose, maltosaccharides, amylose, amylopectin and glycogen, forming 1,5-anhydro-D-fructose from the non-reducing end groups. The substrate specificity, mode of action, and cleavage mechanism of the enzyme were studied by using various naturally occurring and synthesized substrates. This enzyme was highly specific for the alpha-1,4-D-glucosidic bond. When a linear alpha-1,4-glucan was used as substrate, the enzyme split the substrate from the non-reducing end and released 1,5-anhydro-D-fructose successively until only one glucose unit was left. When a branched pentasaccharide of 6(2)-alpha-maltosylmaltotriose, obtained from glycogen by alpha-amylase limitation, was used as substrate, the glucose group in the 4-position of the 4,6-branched residue was not cleaved off. Using maltoheptaose as substrate and following the reaction with HPLC and 1H-NMR spectroscopy, it was found that the action mode of the lyase followed a multichain attack mechanism. 1H- and 13C-NMR spectroscopic studies on unlabelled and labelled amylose (1-2H, 2-2H, 1-13C) as substrates indicated that the lyase cleaved the C-(1')-O(4) bond forming a double bond between C-1' and C-2', thus forming the enol form of 1,5-anhydro-D-fructose. It also indicated that the catalytic process of the lyase involved proton exchanges among C-1, C-2, C-3 and the solvent.

Photometric Characterization of the Reductive Amination Scope of the Imine Reductases from Streptomyces tsukubaensis and Streptomyces ipomoeae.

PubMed

Matzel, Philipp; Krautschick, Lukas; Höhne, Matthias

2017-10-18

Imine reductases (IREDs) have emerged as promising enzymes for the asymmetric synthesis of secondary and tertiary amines starting from carbonyl substrates. Screening the substrate specificity of the reductive amination reaction is usually performed by time-consuming GC analytics. We found two highly active IREDs in our enzyme collection, IR-20 from Streptomyces tsukubaensis and IR-Sip from Streptomyces ipomoeae, that allowed a comprehensive substrate screening with a photometric NADPH assay. We screened 39 carbonyl substrates combined with 17 amines as nucleophiles. Activity data from 663 combinations provided a clear picture about substrate specificity and capabilities in the reductive amination of these enzymes. Besides aliphatic aldehydes, the IREDs accepted various cyclic (C 4 -C 8 ) and acyclic ketones, preferentially with methylamine. IR-Sip also accepted a range of primary and secondary amines as nucleophiles. In biocatalytic reactions, IR-Sip converted (R)-3-methylcyclohexanone with dimethylamine or pyrrolidine with high diastereoselectivity (>94-96 % de). The nucleophile acceptor spectrum depended on the carbonyl substrate employed. The conversion of well-accepted substrates could also be detected if crude lysates were employed as the enzyme source. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Cold Gas-Sprayed Deposition of Metallic Coatings onto Ceramic Substrates Using Laser Surface Texturing Pre-treatment

NASA Astrophysics Data System (ADS)

Kromer, R.; Danlos, Y.; Costil, S.

2018-04-01

Cold spraying enables a variety of metals dense coatings onto metal surfaces. Supersonic gas jet accelerates particles which undergo with the substrate plastic deformation. Different bonding mechanisms can be created depending on the materials. The particle-substrate contact time, contact temperature and contact area upon impact are the parameters influencing physicochemical and mechanical bonds. The resultant bonding arose from plastic deformation of the particle and substrate and temperature increasing at the interface. The objective was to create specific topography to enable metallic particle adhesion onto ceramic substrates. Ceramic did not demonstrate deformation during the impact which minimized the intimate bonds. Laser surface texturing was hence used as prior surface treatment to create specific topography and to enable mechanical anchoring. Particle compressive states were necessary to build up coating. The coating deposition efficiency and adhesion strength were evaluated. Textured surface is required to obtain strong adhesion of metallic coatings onto ceramic substrates. Consequently, cold spray coating parameters depend on the target material and a methodology was established with particle parameters (diameters, velocities, temperatures) and particle/substrate properties to adapt the surface topography. Laser surface texturing is a promising tool to increase the cold spraying applications.

Modified Acyl-ACP desaturase

DOEpatents

Cahoon, Edgar B.; Shanklin, John; Lindqvist, Ylva; Schneider, Gunter

1999-03-30

Disclosed is a method for modifying the chain length and double bond positional specificities of a soluble plant fatty acid desaturase. More specifically, the method involves modifying amino acid contact residues in the substrate binding channel of the soluble fatty acid desaturase which contact the fatty acid. Specifically disclosed is the modification of an acyl-ACP desaturase. Amino acid contact residues which lie within the substrate binding channel are identified, and subsequently replaced with different residues to effect the modification of activity.

Modified acyl-ACP desaturase

DOEpatents

Cahoon, Edgar B.; Shanklin, John; Lindgvist, Ylva; Schneider, Gunter

1998-01-06

Disclosed is a methods for modifying the chain length and double bond positional specificities of a soluble plant fatty acid desaturase. More specifically, the method involves modifying amino acid contact residues in the substrate binding channel of the soluble fatty acid desaturase which contact the fatty acid. Specifically disclosed is the modification of an acyl-ACP desaturase. Amino acid contact residues which lie within the substrate binding channel are identified, and subsequently replaced with different residues to effect the modification of activity.