Advanced Silicon-on-Insulator: Crystalline Silicon on Atomic Layer Deposited Beryllium Oxide.

PubMed

Min Lee, Seung; Hwan Yum, Jung; Larsen, Eric S; Chul Lee, Woo; Keun Kim, Seong; Bielawski, Christopher W; Oh, Jungwoo

2017-10-16

Silicon-on-insulator (SOI) technology improves the performance of devices by reducing parasitic capacitance. Devices based on SOI or silicon-on-sapphire technology are primarily used in high-performance radio frequency (RF) and radiation sensitive applications as well as for reducing the short channel effects in microelectronic devices. Despite their advantages, the high substrate cost and overheating problems associated with complexities in substrate fabrication as well as the low thermal conductivity of silicon oxide prevent broad applications of this technology. To overcome these challenges, we describe a new approach of using beryllium oxide (BeO). The use of atomic layer deposition (ALD) for producing this material results in lowering the SOI wafer production cost. Furthermore, the use of BeO exhibiting a high thermal conductivity might minimize the self-heating issues. We show that crystalline Si can be grown on ALD BeO and the resultant devices exhibit potential for use in advanced SOI technology applications.

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

PubMed Central

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

2012-01-01

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

A robotics platform for automated batch fabrication of high density, microfluidics-based DNA microarrays, with applications to single cell, multiplex assays of secreted proteins

NASA Astrophysics Data System (ADS)

Ahmad, Habib; Sutherland, Alex; Shin, Young Shik; Hwang, Kiwook; Qin, Lidong; Krom, Russell-John; Heath, James R.

2011-09-01

Microfluidics flow-patterning has been utilized for the construction of chip-scale miniaturized DNA and protein barcode arrays. Such arrays have been used for specific clinical and fundamental investigations in which many proteins are assayed from single cells or other small sample sizes. However, flow-patterned arrays are hand-prepared, and so are impractical for broad applications. We describe an integrated robotics/microfluidics platform for the automated preparation of such arrays, and we apply it to the batch fabrication of up to eighteen chips of flow-patterned DNA barcodes. The resulting substrates are comparable in quality with hand-made arrays and exhibit excellent substrate-to-substrate consistency. We demonstrate the utility and reproducibility of robotics-patterned barcodes by utilizing two flow-patterned chips for highly parallel assays of a panel of secreted proteins from single macrophage cells.

A robotics platform for automated batch fabrication of high density, microfluidics-based DNA microarrays, with applications to single cell, multiplex assays of secreted proteins

PubMed Central

Ahmad, Habib; Sutherland, Alex; Shin, Young Shik; Hwang, Kiwook; Qin, Lidong; Krom, Russell-John; Heath, James R.

2011-01-01

Microfluidics flow-patterning has been utilized for the construction of chip-scale miniaturized DNA and protein barcode arrays. Such arrays have been used for specific clinical and fundamental investigations in which many proteins are assayed from single cells or other small sample sizes. However, flow-patterned arrays are hand-prepared, and so are impractical for broad applications. We describe an integrated robotics/microfluidics platform for the automated preparation of such arrays, and we apply it to the batch fabrication of up to eighteen chips of flow-patterned DNA barcodes. The resulting substrates are comparable in quality with hand-made arrays and exhibit excellent substrate-to-substrate consistency. We demonstrate the utility and reproducibility of robotics-patterned barcodes by utilizing two flow-patterned chips for highly parallel assays of a panel of secreted proteins from single macrophage cells. PMID:21974603

A robotics platform for automated batch fabrication of high density, microfluidics-based DNA microarrays, with applications to single cell, multiplex assays of secreted proteins.

PubMed

Ahmad, Habib; Sutherland, Alex; Shin, Young Shik; Hwang, Kiwook; Qin, Lidong; Krom, Russell-John; Heath, James R

2011-09-01

Microfluidics flow-patterning has been utilized for the construction of chip-scale miniaturized DNA and protein barcode arrays. Such arrays have been used for specific clinical and fundamental investigations in which many proteins are assayed from single cells or other small sample sizes. However, flow-patterned arrays are hand-prepared, and so are impractical for broad applications. We describe an integrated robotics/microfluidics platform for the automated preparation of such arrays, and we apply it to the batch fabrication of up to eighteen chips of flow-patterned DNA barcodes. The resulting substrates are comparable in quality with hand-made arrays and exhibit excellent substrate-to-substrate consistency. We demonstrate the utility and reproducibility of robotics-patterned barcodes by utilizing two flow-patterned chips for highly parallel assays of a panel of secreted proteins from single macrophage cells. © 2011 American Institute of Physics

Photoluminescence Study of Gallium Nitride Thin Films Obtained by Infrared Close Space Vapor Transport.

PubMed

Santana, Guillermo; de Melo, Osvaldo; Aguilar-Hernández, Jorge; Mendoza-Pérez, Rogelio; Monroy, B Marel; Escamilla-Esquivel, Adolfo; López-López, Máximo; de Moure, Francisco; Hernández, Luis A; Contreras-Puente, Gerardo

2013-03-15

Photoluminescence (PL) studies in GaN thin films grown by infrared close space vapor transport (CSVT-IR) in vacuum are presented in this work. The growth of GaN thin films was done on a variety of substrates like silicon, sapphire and fused silica. Room temperature PL spectra of all the GaN films show near band-edge emission (NBE) and a broad blue and green luminescence (BL, GL), which can be seen with the naked eye in a bright room. The sample grown by infrared CSVT on the silicon substrate shows several emission peaks from 2.4 to 3.22 eV with a pronounced red shift with respect to the band gap energy. The sample grown on sapphire shows strong and broad ultraviolet emission peaks (UVL) centered at 3.19 eV and it exhibits a red shift of NBE. The PL spectrum of GaN films deposited on fused silica exhibited a unique and strong blue-green emission peak centered at 2.38 eV. The presence of yellow and green luminescence in all samples is related to native defects in the structure such as dislocations in GaN and/or the presence of amorphous phases. We analyze the material quality that can be obtained by CSVT-IR in vacuum, which is a high yield technique with simple equipment set-up, in terms of the PL results obtained in each case.

Photoluminescence Study of Gallium Nitride Thin Films Obtained by Infrared Close Space Vapor Transport

PubMed Central

Santana, Guillermo; de Melo, Osvaldo; Aguilar-Hernández, Jorge; Mendoza-Pérez, Rogelio; Monroy, B. Marel; Escamilla-Esquivel, Adolfo; López-López, Máximo; de Moure, Francisco; Hernández, Luis A.; Contreras-Puente, Gerardo

2013-01-01

Photoluminescence (PL) studies in GaN thin films grown by infrared close space vapor transport (CSVT-IR) in vacuum are presented in this work. The growth of GaN thin films was done on a variety of substrates like silicon, sapphire and fused silica. Room temperature PL spectra of all the GaN films show near band-edge emission (NBE) and a broad blue and green luminescence (BL, GL), which can be seen with the naked eye in a bright room. The sample grown by infrared CSVT on the silicon substrate shows several emission peaks from 2.4 to 3.22 eV with a pronounced red shift with respect to the band gap energy. The sample grown on sapphire shows strong and broad ultraviolet emission peaks (UVL) centered at 3.19 eV and it exhibits a red shift of NBE. The PL spectrum of GaN films deposited on fused silica exhibited a unique and strong blue-green emission peak centered at 2.38 eV. The presence of yellow and green luminescence in all samples is related to native defects in the structure such as dislocations in GaN and/or the presence of amorphous phases. We analyze the material quality that can be obtained by CSVT-IR in vacuum, which is a high yield technique with simple equipment set-up, in terms of the PL results obtained in each case. PMID:28809356

Analysis of Nearly One Thousand Mammalian Mirtrons Reveals Novel Features of Dicer Substrates

PubMed Central

Shenker, Sol; Mohammed, Jaaved; Lai, Eric C.

2015-01-01

Mirtrons are microRNA (miRNA) substrates that utilize the splicing machinery to bypass the necessity of Drosha cleavage for their biogenesis. Expanding our recent efforts for mammalian mirtron annotation, we use meta-analysis of aggregate datasets to identify ~500 novel mouse and human introns that confidently generate diced small RNA duplexes. These comprise nearly 1000 total loci distributed in four splicing-mediated biogenesis subclasses, with 5'-tailed mirtrons as, by far, the dominant subtype. Thus, mirtrons surprisingly comprise a substantial fraction of endogenous Dicer substrates in mammalian genomes. Although mirtron-derived small RNAs exhibit overall expression correlation with their host mRNAs, we observe a subset with substantial differences that suggest regulated processing or accumulation. We identify characteristic sequence, length, and structural features of mirtron loci that distinguish them from bulk introns, and find that mirtrons preferentially emerge from genes with larger numbers of introns. While mirtrons generate miRNA-class regulatory RNAs, we also find that mirtrons exhibit many features that distinguish them from canonical miRNAs. We observe that conventional mirtron hairpins are substantially longer than Drosha-generated pre-miRNAs, indicating that the characteristic length of canonical pre-miRNAs is not a general feature of Dicer substrate hairpins. In addition, mammalian mirtrons exhibit unique patterns of ordered 5' and 3' heterogeneity, which reveal hidden complexity in miRNA processing pathways. These include broad 3'-uridylation of mirtron hairpins, atypically heterogeneous 5' termini that may result from exonucleolytic processing, and occasionally robust decapitation of the 5' guanine (G) of mirtron-5p species defined by splicing. Altogether, this study reveals that this extensive class of non-canonical miRNA bears a multitude of characteristic properties, many of which raise general mechanistic questions regarding the processing of endogenous hairpin transcripts. PMID:26325366

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

Mahadevapuram, Nikhila; Mitra, Indranil; Sridhar, Shyam

Thin films of lamellar poly(styrene-b-methyl methacrylate) (PS-PMMA) block copolymers are widely investigated for surface patterning. These materials can generate dense arrays of nanoscale lines when the lamellar domains are oriented perpendicular to the substrate. To stabilize this preferred domain orientation, we tuned the substrate surface energy using oxidation of hydrophobic silane coatings. This simple approach is effective for a broad range of PS-PMMA film thicknesses when the oxidation time is optimized, which demonstrates that the substrate coating is energetically neutral with respect to PS and PMMA segments. The lamellar films are characterized by high densities of defects that exhibit amore » strong dependence on film thickness: in-plane topological defects disrupt the lateral order in ultrathin films, while lamellar domains in thick films can bend and tilt to large misorientation angles. As a result, the types and densities of these defects are similar to those observed with other classes of neutral substrate coatings, such as random copolymer brushes, which demonstrates that oxidized silanes can be used to control PS-PMMA self assembly in thin films.« less

Ordering of lamellar block copolymers on oxidized silane coatings

DOE PAGES

Mahadevapuram, Nikhila; Mitra, Indranil; Sridhar, Shyam; ...

2016-01-02

Thin films of lamellar poly(styrene-b-methyl methacrylate) (PS-PMMA) block copolymers are widely investigated for surface patterning. These materials can generate dense arrays of nanoscale lines when the lamellar domains are oriented perpendicular to the substrate. To stabilize this preferred domain orientation, we tuned the substrate surface energy using oxidation of hydrophobic silane coatings. This simple approach is effective for a broad range of PS-PMMA film thicknesses when the oxidation time is optimized, which demonstrates that the substrate coating is energetically neutral with respect to PS and PMMA segments. The lamellar films are characterized by high densities of defects that exhibit amore » strong dependence on film thickness: in-plane topological defects disrupt the lateral order in ultrathin films, while lamellar domains in thick films can bend and tilt to large misorientation angles. As a result, the types and densities of these defects are similar to those observed with other classes of neutral substrate coatings, such as random copolymer brushes, which demonstrates that oxidized silanes can be used to control PS-PMMA self assembly in thin films.« less

Preparing high-adhesion silver coating on APTMS modified polyethylene with excellent anti-bacterial performance

NASA Astrophysics Data System (ADS)

Li, Wenfei; Chen, Yunxiang; Wu, Song; Zhang, Jian; Wang, Hao; Zeng, Dawen; Xie, Changsheng

2018-04-01

Silver coating as a broad-spectrum antimicrobial agent was considered to alleviate the inflammation caused by intrauterine device (IUD) in endometrium. In this work, to avoid the damage of silver coating and ensure its antibacterial properties, 3-aminopropyltrimethoxysilane (APTMS) was introduced to modify the polyethylene (PE) substrate for the purpose of improving the adhesion of the silver coating. From the 90° peel test, it could be found that the adhesive strength of silver coating on the APTMS modified PE substrate was nearly 23 times stronger than the silver coating on substrate without surface modification. The dramatically enhanced adhesive strength could be attributed to the formation of continuous chemical bonds between the silver coatings and substrates after surface modification, which had been confirmed by the XPS. Moreover, the standard antibacterial test revealed that the silver coated samples against Staphylococcus aureus (S. aureus) exhibit excellent antibacterial efficacy. Considering the largely enhanced adhesion and the effective antibacterial property, it is reasonable to believe that the silver coating could be considered as a potential candidate for the antibacterial agent in IUD.

Alkylsilyl Peroxides as Alkylating Agents in the Copper-Catalyzed Selective Mono-N-Alkylation of Primary Amides and Arylamines.

PubMed

Sakamoto, Ryu; Sakurai, Shunya; Maruoka, Keiji

2017-07-06

The copper-catalyzed selective mono-N-alkylation of primary amides or arylamines using alkylsilyl peroxides as alkylating agents is reported. The reaction proceeds under mild reaction conditions and exhibits a broad substrate scope with respect to the alkylsilyl peroxides, as well as to the primary amides and arylamines. Mechanistic studies suggest that the present reaction should proceed through a free-radical process that includes alkyl radicals generated from the alkylsilyl peroxides. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Study on the corrosion resistance and anti-infection of modified magnesium alloy.

PubMed

Bai, Ningning; Tan, Cui; Li, Qing; Xi, Zhongxian

2017-01-01

In this paper, a low-cost and multifunctional hydroxyapatite (HA)/pefloxacin (PFLX) drug eluting layer is coated on magnesium (Mg) alloy through a simple hydrothermal and dip process. The drug PFLX could provide effective prevention for bone infection and inflammation due to its broad-spectrum antibacterial property. And HA would promote the growth of new bone and further improve the biocompatibility of implants. Besides, both PFLX and HA exhibits excellent corrosion protection for Mg alloy substrate. This coating is of great value for improving the application of Mg alloy as biomaterials.

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

PubMed

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

2017-01-01

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

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

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

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

2016-07-15

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

Near band edge emission characteristics of sputtered nano-crystalline ZnO films

NASA Astrophysics Data System (ADS)

Kunj, Saurabh; Sreenivas, K.

2016-05-01

Sputtered zinc oxide (ZnO) thin films deposited on unheated glass substrate under different sputtering gas mixtures (Ar+O2) have been investigated using X-ray diffraction and photo luminescence spectroscopy. Earlier reported studies on ZnO films prepared by different techniques exhibit either a sharp/broad near band edge (NBE) emission peak depending on the crystalline quality of the film. In the present study zinc oxide films, grown on unheated substrates, are seen to possess a preferred (002) orientation with a microstructure consisting of clustered nano-sized crystallites. The splitting in the near band edge emission (NBE) into three characteristic peaks is attributed to quantum confinement effect, and is observed specifically under an excitation of 270 nm. Deep level emission (DLE) in the range 400 to 700 nm is not observed indicating absence of deep level radiative defects.

Engineering an enantioselective amine oxidase for the synthesis of pharmaceutical building blocks and alkaloid natural products.

PubMed

Ghislieri, Diego; Green, Anthony P; Pontini, Marta; Willies, Simon C; Rowles, Ian; Frank, Annika; Grogan, Gideon; Turner, Nicholas J

2013-07-24

The development of cost-effective and sustainable catalytic methods for the production of enantiomerically pure chiral amines is a key challenge facing the pharmaceutical and fine chemical industries. This challenge is highlighted by the estimate that 40-45% of drug candidates contain a chiral amine, fueling a demand for broadly applicable synthetic methods that deliver target structures in high yield and enantiomeric excess. Herein we describe the development and application of a "toolbox" of monoamine oxidase variants from Aspergillus niger (MAO-N) which display remarkable substrate scope and tolerance for sterically demanding motifs, including a new variant, which exhibits high activity and enantioselectivity toward substrates containing the aminodiphenylmethane (benzhydrylamine) template. By combining rational structure-guided engineering with high-throughput screening, it has been possible to expand the substrate scope of MAO-N to accommodate amine substrates containing bulky aryl substituents. These engineered MAO-N biocatalysts have been applied in deracemization reactions for the efficient asymmetric synthesis of the generic active pharmaceutical ingredients Solifenacin and Levocetirizine as well as the natural products (R)-coniine, (R)-eleagnine, and (R)-leptaflorine. We also report a novel MAO-N mediated asymmetric oxidative Pictet-Spengler approach to the synthesis of (R)-harmicine.

Biochemical Characterization of CPS-1, a Subclass B3 Metallo-β-Lactamase from a Chryseobacterium piscium Soil Isolate.

PubMed

Gudeta, Dereje Dadi; Pollini, Simona; Docquier, Jean-Denis; Bortolaia, Valeria; Rossolini, Gian Maria; Guardabassi, Luca

2015-12-14

CPS-1 is a subclass B3 metallo-β-lactamase from a Chryseobacterium piscium isolate collected from soil, showing 68% amino acid identity to the GOB-1 enzyme. CPS-1 was overproduced in Escherichia coli Rosetta (DE3), purified by chromatography, and biochemically characterized. This enzyme exhibits a broad-spectrum substrate profile, including penicillins, cephalosporins, and carbapenems, which overall resembles those of L1, GOB-1, and acquired subclass B3 enzymes AIM-1 and SMB-1. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Gate-defined quantum confinement in suspended bilayer graphene

NASA Astrophysics Data System (ADS)

Allen, M. T.; Martin, J.; Yacoby, A.

2012-07-01

Quantum-confined devices that manipulate single electrons in graphene are emerging as attractive candidates for nanoelectronics applications. Previous experiments have employed etched graphene nanostructures, but edge and substrate disorder severely limit device functionality. Here we present a technique that builds quantum-confined structures in suspended bilayer graphene with tunnel barriers defined by external electric fields that open a bandgap, thereby eliminating both edge and substrate disorder. We report clean quantum dot formation in two regimes: at zero magnetic field B using the energy gap induced by a perpendicular electric field and at B>0 using the quantum Hall ν=0 gap for confinement. Coulomb blockade oscillations exhibit periodicity consistent with electrostatic simulations based on local top-gate geometry, a direct demonstration of local control over the band structure of graphene. This technology integrates single electron transport with high device quality and access to vibrational modes, enabling broad applications from electromechanical sensors to quantum bits.

Enantioselective Cyanation of Benzylic C–H Bonds via Copper-Catalyzed Radical Relay

PubMed Central

Zhang, Wen; Wang, Fei; McCann, Scott D.; Wang, Dinghai; Chen, Pinhong; Stahl, Shannon; Liu, Guosheng

2017-01-01

Direct methods for stereoselective functionalization of C(sp3)–H bonds in complex organic molecules could facilitate much more efficient preparation of therapeutics and agrochemicals. Here, we report a copper-catalyzed radical relay pathway for enantioselective conversion of benzylic C–H bonds into benzylic nitriles. Hydrogen-atom abstraction affords an achiral benzylic radical that undergoes asymmetric C(sp3)–CN bond upon reaction with a chiral copper catalyst. The reactions proceed efficiently at room temperature with the benzylic substrate as limiting reagent, exhibit broad substrate scope with high enantioselectivity (typically 90-99% enantiomeric excess), and afford products that are key precursors to important bioactive molecules. Mechanistic studies provide evidence for diffusible organic radicals and highlight the difference between these reactions and C–H oxidations mediated by enzymes and other catalysts that operate via radical rebound pathways. PMID:27701109

Pseudorotational epitaxy of self-assembled octadecyltrichlorosilane monolayers on sapphire (0001)

DOE PAGES

Steinrück, H. -G.; Magerl, A.; Deutsch, M.; ...

2014-10-06

The structure of octadecyltrichlorosilane self-assembled monolayers (SAMs) on sapphire (0001) was studied by Å-resolution surface-specific x-ray scattering methods. The monolayer was found to consist of three sublayers where the outermost layer corresponds to vertically oriented, closely packed alkyl tails. Laterally, the monolayer is hexagonally packed and exhibits pseudorotational epitaxy to the sapphire, manifested by a broad scattering peak at zero relative azimuthal rotation, with long powderlike tails. The lattice mismatch of ~1% – 3% to the sapphire’s and the different length scale introduced by the lateral Si-O-Si bonding prohibit positional epitaxy. However, the substrate induces an intriguing increase in themore » crystalline coherence length of the SAM’s powderlike crystallites when rotationally aligned with the sapphire’s lattice. As a result, the increase correlates well with the rotational dependence of the separation of corresponding substrate-monolayer lattice sites.« less

Release of wine monoterpenes from natural precursors by glycosidases from Oenococcus oeni

PubMed Central

Michlmayr, Herbert; Nauer, Stefan; Brandes, Walter; Schümann, Christina; Kulbe, Klaus D.; del Hierro, Andrés M.; Eder, Reinhard

2012-01-01

It is now well established that wine-related lactic acid bacteria (LAB), especially Oenococcus oeni, possess glycosidase activities that positively contribute to wine aroma through the hydrolysis of grape-derived aroma precursors. In our recent studies, we have identified and characterised several LAB glycosidases with potential in these terms. Here, we report that both a glucosidase and an arabinosidase from O. oeni can release high amounts of monoterpenes from natural substrates under optimal conditions, indicating that these intracellular enzymes might play a significant role in the hydrolysis of aroma precursors during malolactic fermentation. The enzymes from O. oeni exhibited broad substrate specificities (release of both primary/tertiary terpene alcohols) and were even active in grape juice. Further, a sensory panel clearly preferred enzyme-treated Riesling wines over the controls and affirmed that the glycosidases from O. oeni could improve the typical Riesling aroma.

Structural basis of the broad substrate tolerance of the antibody 7B9-catalyzed hydrolysis of p-nitrobenzyl esters.

PubMed

Miyamoto, Naoki; Yoshimura, Miho; Okubo, Yuji; Suzuki-Nagata, Kayo; Tsumuraya, Takeshi; Ito, Nobutoshi; Fujii, Ikuo

2018-05-01

Catalytic antibody 7B9, which was elicited against p-nitrobenzyl phosphonate transition-state analogue (TSA) 1, hydrolyzes a wide range of p-nitrobenzyl monoesters and thus shows broad substrate tolerance. To reveal the molecular basis of this substrate tolerance, the 7B9 Fab fragment complexed with p-nitrobenzyl ethylphosphonate 2 was crystallized and the three-dimensional structure was determined. The crystal structure showed that the strongly antigenic p-nitrobenzyl moiety occupied a relatively shallow antigen-combining site and therefore the alkyl moiety was located outside the pocket. These results support the observed broad substrate tolerance of 7B9 and help rationalize how 7B9 can catalyze various p-nitrobenzyl ester derivatives. The crystal structure also showed that three amino acid residues (Asn H33 , Ser H95 , and Arg L96 ) were placed in key positions to form hydrogen bonds with the phosphonate oxygens of the transitions-state analogue. In addition, the role of these amino acid residues was examined by site-directed mutagenesis to alanine: all mutants (Asn H33 Ala, Ser H95 Ala, and Arg L96 Ala) showed no detectable catalytic activity. Coupling the findings from our structural studies with these mutagenesis results clarified the structural basis of the observed broad substrate tolerance of antibody 7B9-catalyzed hydrolyses. Our findings provide new strategies for the generation of catalytic antibodies that accept a broad range of substrates, aiding their practical application in synthetic organic chemistry. Copyright © 2017 Elsevier Ltd. All rights reserved.

Direct Growth of III-Nitride Nanowire-Based Yellow Light-Emitting Diode on Amorphous Quartz Using Thin Ti Interlayer

NASA Astrophysics Data System (ADS)

Prabaswara, Aditya; Min, Jung-Wook; Zhao, Chao; Janjua, Bilal; Zhang, Daliang; Albadri, Abdulrahman M.; Alyamani, Ahmed Y.; Ng, Tien Khee; Ooi, Boon S.

2018-02-01

Consumer electronics have increasingly relied on ultra-thin glass screen due to its transparency, scalability, and cost. In particular, display technology relies on integrating light-emitting diodes with display panel as a source for backlighting. In this study, we undertook the challenge of integrating light emitters onto amorphous quartz by demonstrating the direct growth and fabrication of a III-nitride nanowire-based light-emitting diode. The proof-of-concept device exhibits a low turn-on voltage of 2.6 V, on an amorphous quartz substrate. We achieved 40% transparency across the visible wavelength while maintaining electrical conductivity by employing a TiN/Ti interlayer on quartz as a translucent conducting layer. The nanowire-on-quartz LED emits a broad linewidth spectrum of light centered at true yellow color ( 590 nm), an important wavelength bridging the green-gap in solid-state lighting technology, with significantly less strain and dislocations compared to conventional planar quantum well nitride structures. Our endeavor highlighted the feasibility of fabricating III-nitride optoelectronic device on a scalable amorphous substrate through facile growth and fabrication steps. For practical demonstration, we demonstrated tunable correlated color temperature white light, leveraging on the broadly tunable nanowire spectral characteristics across red-amber-yellow color regime.

Direct Growth of III-Nitride Nanowire-Based Yellow Light-Emitting Diode on Amorphous Quartz Using Thin Ti Interlayer.

PubMed

Prabaswara, Aditya; Min, Jung-Wook; Zhao, Chao; Janjua, Bilal; Zhang, Daliang; Albadri, Abdulrahman M; Alyamani, Ahmed Y; Ng, Tien Khee; Ooi, Boon S

2018-02-06

Consumer electronics have increasingly relied on ultra-thin glass screen due to its transparency, scalability, and cost. In particular, display technology relies on integrating light-emitting diodes with display panel as a source for backlighting. In this study, we undertook the challenge of integrating light emitters onto amorphous quartz by demonstrating the direct growth and fabrication of a III-nitride nanowire-based light-emitting diode. The proof-of-concept device exhibits a low turn-on voltage of 2.6 V, on an amorphous quartz substrate. We achieved ~ 40% transparency across the visible wavelength while maintaining electrical conductivity by employing a TiN/Ti interlayer on quartz as a translucent conducting layer. The nanowire-on-quartz LED emits a broad linewidth spectrum of light centered at true yellow color (~ 590 nm), an important wavelength bridging the green-gap in solid-state lighting technology, with significantly less strain and dislocations compared to conventional planar quantum well nitride structures. Our endeavor highlighted the feasibility of fabricating III-nitride optoelectronic device on a scalable amorphous substrate through facile growth and fabrication steps. For practical demonstration, we demonstrated tunable correlated color temperature white light, leveraging on the broadly tunable nanowire spectral characteristics across red-amber-yellow color regime.

Extended substrate specificity and first potent irreversible inhibitor/activity-based probe design for Zika virus NS2B-NS3 protease.

PubMed

Rut, Wioletta; Zhang, Linlin; Kasperkiewicz, Paulina; Poreba, Marcin; Hilgenfeld, Rolf; Drąg, Marcin

2017-03-01

Zika virus is spread by Aedes mosquitoes and is linked to acute neurological disorders, especially to microcephaly in newborn children and Guillan-Barré Syndrome. The NS2B-NS3 protease of this virus is responsible for polyprotein processing and therefore considered an attractive drug target. In this study, we have used the Hybrid Combinatorial Substrate Library (HyCoSuL) approach to determine the substrate specificity of ZIKV NS2B-NS3 protease in the P4-P1 positions using natural and a large spectrum of unnatural amino acids. Obtained data demonstrate a high level of specificity of the S3-S1 subsites, especially for basic amino acids. However, the S4 site exhibits a very broad preference toward natural and unnatural amino acids with selected D-amino acids being favored over L enantiomers. This information was used for the design of a very potent phosphonate inhibitor/activity-based probe of ZIKV NS2B-NS3 protease. Copyright © 2016 Elsevier B.V. All rights reserved.

Identification and functional characterization of a Na+-independent neutral amino acid transporter with broad substrate selectivity.

PubMed

Segawa, H; Fukasawa, Y; Miyamoto, K; Takeda, E; Endou, H; Kanai, Y

1999-07-09

We have isolated a cDNA from rat small intestine that encodes a novel Na+-independent neutral amino acid transporter with distinctive characteristics in substrate selectivity and transport property. The encoded protein, designated L-type amino acid transporter-2 (LAT-2), shows amino acid sequence similarity to the system L Na+-independent neutral amino acid transporter LAT-1 (Kanai, Y., Segawa, H., Miyamoto, K., Uchino, H., Takeda, E., and Endou, H. (1998) J. Biol. Chem. 273, 23629-23632) (50% identity) and the system y+L transporters y+LAT-1 (47%) and KIAA0245/y+LAT-2 (45%) (Torrents, D., Estevez, R., Pineda, M., Fernandez, E., Lloberas, J., Shi, Y.-B., Zorzano, A., and Palacin, M. (1998) J. Biol. Chem. 273, 32437-32445). LAT-2 is a nonglycosylated membrane protein. It requires 4F2 heavy chain, a type II membrane glycoprotein, for its functional expression in Xenopus oocytes. LAT-2-mediated transport is not dependent on Na+ or Cl- and is inhibited by a system L-specific inhibitor, 2-aminobicyclo-(2,2,1)-heptane-2-carboxylic acid (BCH), indicating that LAT-2 is a second isoform of the system L transporter. Compared with LAT-1, which prefers large neutral amino acids with branched or aromatic side chains, LAT-2 exhibits remarkably broad substrate selectivity. It transports all of the L-isomers of neutral alpha-amino acids. LAT-2 exhibits higher affinity (Km = 30-50 microM) to Tyr, Phe, Trp, Thr, Asn, Ile, Cys, Ser, Leu, Val, and Gln and relatively lower affinity (Km = 180-300 microM) to His, Ala, Met, and Gly. In addition, LAT-2 mediates facilitated diffusion of substrate amino acids, as distinct from LAT-1, which mediates amino acid exchange. LAT-2-mediated transport is increased by lowering the pH level, with peak activity at pH 6.25, because of the decrease in the Km value without changing the Vmax value. Because of these functional properties and a high level of expression of LAT-2 in the small intestine, kidney, placenta, and brain, it is suggested that the heterodimeric complex of LAT-2 and 4F2 heavy chain is involved in the trans-cellular transport of neutral amino acids in epithelia and blood-tissue barriers.

Plasmin substrate binding site cooperativity guides the design of potent peptide aldehyde inhibitors.

PubMed

Swedberg, Joakim E; Harris, Jonathan M

2011-10-04

Perioperative bleeding is a cause of major blood loss and is associated with increased rates of postoperative morbidity and mortality. To combat this, antifibrinolytic inhibitors of the serine protease plasmin are commonly used to reduce bleeding during surgery. The most effective and previously widely used of these is the broad range serine protease inhibitor aprotinin. However, adverse clinical outcomes have led to use of alternative serine lysine analogues to inhibit plasmin. These compounds suffer from low selectivity and binding affinity. Consequently, a concerted effort to discover potent and selective plasmin inhibitors has developed. This study used a noncombinatorial peptide library to define plasmin's extended substrate specificity and guide the design of potent transition state analogue inhibitors. The various substrate binding sites of plasmin were found to exhibit a higher degree of cooperativity than had previously been appreciated. Peptide sequences capitalizing on these features produced high-affinity inhibitors of plasmin. The most potent of these, Lys-Met(sulfone)-Tyr-Arg-H [KM(O(2))YR-H], inhibited plasmin with a K(i) of 3.1 nM while maintaining 25-fold selectivity over plasma kallikrein. Furthermore, 125 nM (0.16 μg/mL) KM(O(2))YR-H attenuated fibrinolysis in vitro with an efficacy similar to that of 15 nM (0.20 μg/mL) aprotinin. To date, this is the most potent peptide inhibitor of plasmin that exhibits selectivity against plasma kallikrein, making this compound an attractive candidate for further therapeutic development.

[Extracellular proteolytic enzymes of Azospirillum brasilensis strain Sp7 and regulation of their activity by a homologous lectin].

PubMed

Chernyshova, M P; Alen'kina, S A; Nikitina, V E; Ignatov, V V

2005-01-01

It was found that Azospirillum brasilensis strain Sp7 is able to produce extracellular proteolytic enzymes. The enzymes were active within a broad range of pH values, with two peaks of activity being located in the acid and alkaline pH areas; required calcium ions; and exhibited substrate specificity with respect to azogelatin. Zymography allowed at least four proteolytic enzymes with molecular weights of 32, 45, 52, and 174 kDa to be detected in A. brasilense Sp7 culture liquid. It was shown that the lectin from A. brasilense Sp7 can inhibit proteolytic enzymes.

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

NASA Astrophysics Data System (ADS)

Draxl, Claudia

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

Synthesis and Characterization of Methylammonium Lead Iodide Perovskite and its Application in Planar Hetero-junction Devices

NASA Astrophysics Data System (ADS)

Upadhyaya, Aditi; Mohan Singh Negi, Chandra; Yadav, Anjali; Gupta, Saral K.; Singh Verma, Ajay

2018-06-01

The present paper reports on the synthesis and characterization of methylammonium lead iodide perovskite thin film and its applications in heterojunction devices. Perovskite thin films were deposited by a simple spin-coating method using a precursor solution including methyl ammonium iodide and lead iodide onto a glass substrate. The surface morphology study via field emission scanning electron microscopy of the perovskite thin film shows complete surface coverage on glass substrate with negligible pin-holes. UV–visible spectroscopy study revealed a broad absorption range and the exhibition of a band-gap of 1.6 eV. The dark current-voltage (I–V) characteristics of all the devices under study show rectifying behaviour similar to the Schottky diode. Various device parameters such as ideality factor and barrier height are extracted from the I–V curve. At low voltages the devices exhibit Ohmic behaviour, trap free space charge limited conduction governs the charge transport at an intermediate voltage range, while at much higher voltages the devices show trap controlled space charge limited conduction. Furthermore, impedance spectroscopy measurements enable us to extract the various internal parameters of the devices. Correlations between these parameters and I–V characteristics are discussed. The different capacitive process arising in the devices was discussed using the capacitance versus frequency curve.

Highly Stretchable and Conductive Superhydrophobic Coating for Flexible Electronics.

PubMed

Su, Xiaojing; Li, Hongqiang; Lai, Xuejun; Chen, Zhonghua; Zeng, Xingrong

2018-03-28

Superhydrophobic materials integrating stretchability with conductivity have huge potential in the emerging application horizons such as wearable electronic sensors, flexible power storage apparatus, and corrosion-resistant circuits. Herein, a facile spraying method is reported to fabricate a durable superhydrophobic coating with excellent stretchable and electrical performance by combing 1-octadecanethiol-modified silver nanoparticles (M-AgNPs) with polystyrene- b-poly(ethylene- co-butylene)- b-polystyrene (SEBS) on a prestretched natural rubber (NR) substrate. The embedding of M-AgNPs in elastic SEBS matrix and relaxation of prestretched NR substrate construct hierarchical rough architecture and endow the coating with dense charge-transport pathways. The fabricated coating exhibits superhydrophobicity with water contact angle larger than 160° and a high conductivity with resistance of about 10 Ω. The coating not only maintains superhydrophobicity at low/high stretch ratio for the newly generated small/large protuberances but also responds to stretching and bending with good sensitivity, broad sensing range, and stable response cycles. Moreover, the coating exhibits excellent durability to heat and strong acid/alkali and mechanical forces including droplet impact, kneading, torsion, and repetitive stretching-relaxation. The findings conceivably stand out as a new tool to fabricate multifunctional superhydrophobic materials with excellent stretchability and conductivity for flexible electronics under wet or corrosive environments.

Structure of YciA from Haemophilus influenzae (HI0827), a Hexameric Broad Specificity Acyl-Coenzyme A Thioesterase

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

Willis, Mark A.; Zhuang, Zhihao; Song, Feng

2008-04-02

The crystal structure of HI0827 from Haemophilus influenzae Rd KW20, initially annotated 'hypothetical protein' in sequence databases, exhibits an acyl-coenzyme A (acyl-CoA) thioesterase 'hot dog' fold with a trimer of dimers oligomeric association, a novel assembly for this enzyme family. In studies described in the preceding paper [Zhuang, Z., Song, F., Zhao, H., Li, L., Cao, J., Eisenstein, E., Herzberg, O., and Dunaway-Mariano, D. (2008) Biochemistry 47, 2789-2796], HI0827 is shown to be an acyl-CoA thioesterase that acts on a wide range of acyl-CoA compounds. Two substrate binding sites are located across the dimer interface. The binding sites are occupiedmore » by two CoA molecules, one with full occupancy and the second only partially occupied. The CoA molecules, acquired from HI0827-expressing Escherichia coli cells, remained tightly bound to the enzyme through the protein purification steps. The difference in CoA occupancies indicates a different substrate affinity for each of the binding sites, which in turn implies that the enzyme might be subject to allosteric regulation. Mutagenesis studies have shown that the replacement of the putative catalytic carboxylate Asp44 with an alanine residue abolishes activity. The impact of this mutation is seen in the crystal structure of D44A HI0827. Whereas the overall fold and assembly of the mutant protein are the same as those of the wild-type enzyme, the CoA ligands are absent. The dimer interface is perturbed, and the channel that accommodates the thioester acyl chain is more open and wider than that observed in the wild-type enzyme. A model of intact substrate bound to wild-type HI0827 provides a structural rationale for the broad substrate range.« less

aKMT Catalyzes Extensive Protein Lysine Methylation in the Hyperthermophilic Archaeon Sulfolobus islandicus but is Dispensable for the Growth of the Organism *

PubMed Central

Chu, Yindi; Zhu, Yanping; Chen, Yuling; Li, Wei; Zhang, Zhenfeng; Liu, Di; Wang, Tongkun; Ma, Juncai; Deng, Haiteng; Liu, Zhi-Jie; Ouyang, Songying; Huang, Li

2016-01-01

Protein methylation is believed to occur extensively in creanarchaea. Recently, aKMT, a highly conserved crenarchaeal protein lysine methyltransferase, was identified and shown to exhibit broad substrate specificity in vitro. Here, we have constructed an aKMT deletion mutant of the hyperthermophilic crenarchaeon Sulfolobus islandicus. The mutant was viable but showed a moderately slower growth rate than the parental strain under non-optimal growth conditions. Consistent with the moderate effect of the lack of aKMT on the growth of the cell, expression of a small number of genes, which encode putative functions in substrate transportation, energy metabolism, transcriptional regulation, stress response proteins, etc, was differentially regulated by more than twofold in the mutant strain, as compared with that in the parental strain. Analysis of the methylation of total cellular protein by mass spectrometry revealed that methylated proteins accounted for ∼2/3 (1,158/1,751) and ∼1/3 (591/1,757) of the identified proteins in the parental and the mutant strains, respectively, indicating that there is extensive protein methylation in S. islandicus and that aKMT is a major protein methyltransferase in this organism. No significant sequence preference was detected at the sites of methylation by aKMT. Methylated lysine residues, when visible in the structure, are all located on the surface of the proteins. The crystal structure of aKMT in complex with S-adenosyl-l-methionine (SAM) or S-adenosyl homocysteine (SAH) reveals that the protein consists of four α helices and seven β sheets, lacking a substrate recognition domain found in PrmA, a bacterial homolog of aKMT, in agreement with the broad substrate specificity of aKMT. Our results suggest that aKMT may serve a role in maintaining the methylation status of cellular proteins required for the efficient growth of the organism under certain non-optimal conditions. PMID:27329856

Thickness-controlled direct growth of nanographene and nanographite film on non-catalytic substrates

NASA Astrophysics Data System (ADS)

Du, Lei; Yang, Liu; Hu, Zhiting; Zhang, Jiazhen; Huang, Chunlai; Sun, Liaoxin; Wang, Lin; Wei, Dacheng; Chen, Gang; Lu, Wei

2018-05-01

Metal-catalyzed chemical vapor deposition (CVD) has been broadly employed for large-scale production of high-quality graphene. However, a following transfer process to targeted substrates is needed, which is incompatible with current silicon technology. We here report a new CVD approach to form nanographene and nanographite films with accurate thickness control directly on non-catalytic substrates such as silicon dioxide and quartz at 800 °C. The growth time is as short as a few seconds. The approach includes using 9-bis(diethylamino)silylanthracene as the carbon source and an atomic layer deposition (ALD) controlling system. The structure of the formed nanographene and nanographite films were characterized using atomic force microscopy, high resolution transmission electron microscopy, Raman scattering, and x-ray photoemission spectroscopy. The nanographite film exhibits a transmittance higher than 80% at 550 nm and a sheet electrical resistance of 2000 ohms per square at room temperature. A negative temperature-dependence of the resistance of the nanographite film is also observed. Moreover, the thickness of the films can be precisely controlled via the deposition cycles using an ALD system, which promotes great application potential for optoelectronic and thermoelectronic-devices.

Thickness-controlled direct growth of nanographene and nanographite film on non-catalytic substrates.

PubMed

Du, Lei; Yang, Liu; Hu, Zhiting; Zhang, Jiazhen; Huang, Chunlai; Sun, Liaoxin; Wang, Lin; Wei, Dacheng; Chen, Gang; Lu, Wei

2018-05-25

Metal-catalyzed chemical vapor deposition (CVD) has been broadly employed for large-scale production of high-quality graphene. However, a following transfer process to targeted substrates is needed, which is incompatible with current silicon technology. We here report a new CVD approach to form nanographene and nanographite films with accurate thickness control directly on non-catalytic substrates such as silicon dioxide and quartz at 800 °C. The growth time is as short as a few seconds. The approach includes using 9-bis(diethylamino)silylanthracene as the carbon source and an atomic layer deposition (ALD) controlling system. The structure of the formed nanographene and nanographite films were characterized using atomic force microscopy, high resolution transmission electron microscopy, Raman scattering, and x-ray photoemission spectroscopy. The nanographite film exhibits a transmittance higher than 80% at 550 nm and a sheet electrical resistance of 2000 ohms per square at room temperature. A negative temperature-dependence of the resistance of the nanographite film is also observed. Moreover, the thickness of the films can be precisely controlled via the deposition cycles using an ALD system, which promotes great application potential for optoelectronic and thermoelectronic-devices.

Therapeutic effects of remediating autophagy failure in a mouse model of Alzheimer disease by enhancing lysosomal proteolysis.

PubMed

Yang, Dun-Sheng; Stavrides, Philip; Mohan, Panaiyur S; Kaushik, Susmita; Kumar, Asok; Ohno, Masuo; Schmidt, Stephen D; Wesson, Daniel W; Bandyopadhyay, Urmi; Jiang, Ying; Pawlik, Monika; Peterhoff, Corrinne M; Yang, Austin J; Wilson, Donald A; St George-Hyslop, Peter; Westaway, David; Mathews, Paul M; Levy, Efrat; Cuervo, Ana M; Nixon, Ralph A

2011-07-01

The extensive autophagic-lysosomal pathology in Alzheimer disease (AD) brain has revealed a major defect: in the proteolytic clearance of autophagy substrates. Autophagy failure contributes on several levels to AD pathogenesis and has become an important therapeutic target for AD and other neurodegenerative diseases. We recently observed broad therapeutic effects of stimulating autophagic-lysosomal proteolysis in the TgCRND8 mouse model of AD that exhibits defective proteolytic clearance of autophagic substrates, robust intralysosomal amyloid-β peptide (Aβ) accumulation, extracellular β-amyloid deposition and cognitive deficits. By genetically deleting the lysosomal cysteine protease inhibitor, cystatin B (CstB), to selectively restore depressed cathepsin activities, we substantially cleared Aβ, ubiquitinated proteins and other autophagic substrates from autolysosomes/lysosomes and rescued autophagic-lysosomal pathology, as well as reduced total Aβ40/42 levels and extracellular amyloid deposition, highlighting the underappreciated importance of the lysosomal system for Aβ clearance. Most importantly, lysosomal remediation prevented the marked learning and memory deficits in TgCRND8 mice. Our findings underscore the pathogenic significance of autophagic-lysosomal dysfunction in AD and demonstrate the value of reversing this dysfunction as an innovative therapeautic strategy for AD.

Lipase-Secreting Bacillus Species in an Oil-Contaminated Habitat: Promising Strains to Alleviate Oil Pollution.

PubMed

Lee, Li Pin; Karbul, Hudzaifah Mohamed; Citartan, Marimuthu; Gopinath, Subash C B; Lakshmipriya, Thangavel; Tang, Thean-Hock

2015-01-01

Lipases are of great interest for different industrial applications due to their diversity and versatility. Among different lipases, microbial lipases are preferable due to their broad substrate specificity, and higher stability with lower production costs compared to the lipases from plants and animals. In the past, a vast number of bacterial species have been reported as potential lipases producers. In this study, the lipases-producing bacterial species were isolated from an oil spillage area in the conventional night market. Isolated species were identified as Bacillus species by biochemical tests which indicate their predominant establishment, and further screened on the agar solid surfaces using lipid and gelatin as the substrates. Out of the ten strains tested, four potential strains were subjected to comparison analysis of the lipolytic versus proteolytic activities. Strain 10 exhibited the highest lipolytic and proteolytic activity. In all the strains, the proteolytic activity is higher than the lipolytic activity except for strain 8, suggesting the possibility for substrate-based extracellular gene induction. The simultaneous secretion of both the lipase and protease is a mean of survival. The isolated bacterial species which harbour both lipase and protease enzymes could render potential industrial-based applications and solve environmental issues.

A Fungal α-Galactosidase from Tricholoma matsutake with Broad Substrate Specificity and Good Hydrolytic Activity on Raffinose Family Oligosaccharides.

PubMed

Geng, Xueran; Tian, Guoting; Zhao, Yongchang; Zhao, Liyan; Wang, Hexiang; Ng, Tzi Bun

2015-07-24

An acidic α-galactosidase designated as TMG was purified from the fruiting bodies The purification protocol entailed ion exchange chromatography on Q-Sepharose and of Tricholoma matsutake with 136-fold purification and a specific activity of 909 units/mg. Mono-Q and fast protein liquid chromatography on Superdex 75. TMG is a monomeric protein exhibiting a molecular mass of 47 kDa in SDS-PAGE and gel filtration. The purified enzyme was identified by LC-MS/MS and three inner amino acid sequences were obtained. The optimum pH and temperature for TMG with pNPGal as substrate were pH 4.5 and 55 °C, respectively. The α-galactosidase activity was strongly inhibited by K+, Ca2+, Cd2+, Hg2+, Ag+ and Zn2+ ions. The enzyme activity was inhibited by the chemical modification agent N-bromosuccinimide (NBS), indicating the importance of tryptophan residue(s) at or near the active site. Besides hydrolyzing pNPGal, TMG also efficaciously catalyzed the degradation of natural substrates such as stachyose, raffinose, and melibiose. Thus TMG can be exploited commercially for improving the nutritional value of soy milk by degradation of indigestible oligosaccharides.

Plant-expressed cocaine hydrolase variants of butyrylcholinesterase exhibit altered allosteric effects of cholinesterase activity and increased inhibitor sensitivity.

PubMed

Larrimore, Katherine E; Kazan, I Can; Kannan, Latha; Kendle, R Player; Jamal, Tameem; Barcus, Matthew; Bolia, Ashini; Brimijoin, Stephen; Zhan, Chang-Guo; Ozkan, S Banu; Mor, Tsafrir S

2017-09-05

Butyrylcholinesterase (BChE) is an enzyme with broad substrate and ligand specificities and may function as a generalized bioscavenger by binding and/or hydrolyzing various xenobiotic agents and toxicants, many of which target the central and peripheral nervous systems. Variants of BChE were rationally designed to increase the enzyme's ability to hydrolyze the psychoactive enantiomer of cocaine. These variants were cloned, and then expressed using the magnICON transient expression system in plants and their enzymatic properties were investigated. In particular, we explored the effects that these site-directed mutations have over the enzyme kinetics with various substrates of BChE. We further compared the affinity of various anticholinesterases including organophosphorous nerve agents and pesticides toward these BChE variants relative to the wild type enzyme. In addition to serving as a therapy for cocaine addiction-related diseases, enhanced bioscavenging against other harmful agents could add to the practicality and versatility of the plant-derived recombinant enzyme as a multivalent therapeutic.

Thin films of a ferroelectric phenazine/chloranilic acid organic cocrystal

NASA Astrophysics Data System (ADS)

Thompson, Nicholas J.; Jandl, Adam C.; Spalenka, Josef W.; Evans, Paul G.

2011-07-01

Phenazine-chloranilic acid cocrystal thin films can be formed by vacuum evaporation of the component molecules onto cooled substrates. Fluxes of phenazine and chloranilic acid were provided from separate sublimation sources, from which the cocrystalline phase can be formed under a wide range of impingement rates of the component molecules. Substrates consisted of Au or Ni thin films on Si wafers, cooled to 100-140 K during deposition. X-ray diffraction and scanning electron microscopy show that this process yields polycrystalline thin films of the cocrystal with voids between crystalline grains. The relative intensities of X-ray reflections differ from reported intensities of polycrystalline powders, suggesting that the films have an anisotropic distribution of crystallographic orientations. The cocrystalline thin films have an effective dielectric constant of 13 at room temperature, increasing at lower temperatures and exhibiting a broad maximum near 200 K. The means to grow thin films of organic ferroelectric materials will allow the integration of new functionalities into organic electronic device structures, including capacitors and field-effect transistors.

Peptide-Like Molecules (PLMs): A Journey from Peptide Bond Isosteres to Gramicidin S Mimetics and Mitochondrial Targeting Agents

PubMed Central

Wipf, Peter; Xiao, Jingbo; Stephenson, Corey R. J.

2010-01-01

Peptides are natural ligands and substrates for receptors and enzymes and exhibit broad physiological effects. However, their use as therapeutic agents often suffers from poor bioavailability and insufficient membrane permeability. The success of peptide mimicry hinges on the ability of bioisosteres, in particular peptide bond replacements, to adopt suitable secondary structures relevant to peptide strands and position functional groups in equivalent space. This perspective highlights past and ongoing studies in our group that involve new methods development as well as specific synthetic library preparations and applications in chemical biology, with the goal to enhance the use of alkene and cyclopropane peptide bond isosteres. PMID:20725595

Crystal structure and mutational analysis of aminoacylhistidine dipeptidase from Vibrio alginolyticus reveal a new architecture of M20 metallopeptidases.

PubMed

Chang, Chin-Yuan; Hsieh, Yin-Cheng; Wang, Ting-Yi; Chen, Yi-Chin; Wang, Yu-Kuo; Chiang, Ting-Wei; Chen, Yi-Ju; Chang, Cheng-Hsiang; Chen, Chun-Jung; Wu, Tung-Kung

2010-12-10

Aminoacylhistidine dipeptidases (PepD, EC 3.4.13.3) belong to the family of M20 metallopeptidases from the metallopeptidase H clan that catalyze a broad range of dipeptide and tripeptide substrates, including L-carnosine and L-homocarnosine. Homocarnosine has been suggested as a precursor for the neurotransmitter γ-aminobutyric acid (GABA) and may mediate the antiseizure effects of GABAergic therapies. Here, we report the crystal structure of PepD from Vibrio alginolyticus and the results of mutational analysis of substrate-binding residues in the C-terminal as well as substrate specificity of the PepD catalytic domain-alone truncated protein PepD(CAT). The structure of PepD was found to exist as a homodimer, in which each monomer comprises a catalytic domain containing two zinc ions at the active site center for its hydrolytic function and a lid domain utilizing hydrogen bonds between helices to form the dimer interface. Although the PepD is structurally similar to PepV, which exists as a monomer, putative substrate-binding residues reside in different topological regions of the polypeptide chain. In addition, the lid domain of the PepD contains an "extra" domain not observed in related M20 family metallopeptidases with a dimeric structure. Mutational assays confirmed both the putative di-zinc allocations and the architecture of substrate recognition. In addition, the catalytic domain-alone truncated PepD(CAT) exhibited substrate specificity to l-homocarnosine compared with that of the wild-type PepD, indicating a potential value in applications of PepD(CAT) for GABAergic therapies or neuroprotection.

Identification of microplastics by FTIR and Raman microscopy: a novel silicon filter substrate opens the important spectral range below 1300 cm(-1) for FTIR transmission measurements.

PubMed

Käppler, Andrea; Windrich, Frank; Löder, Martin G J; Malanin, Mikhail; Fischer, Dieter; Labrenz, Matthias; Eichhorn, Klaus-Jochen; Voit, Brigitte

2015-09-01

The presence of microplastics in aquatic ecosystems is a topical problem and leads to the need of appropriate and reliable analytical methods to distinctly identify and to quantify these particles in environmental samples. As an example transmission, Fourier transform infrared (FTIR) imaging can be used to analyze samples directly on filters without any visual presorting, when the environmental sample was afore extracted, purified, and filtered. However, this analytical approach is strongly restricted by the limited IR transparency of conventional filter materials. Within this study, we describe a novel silicon (Si) filter substrate produced by photolithographic microstructuring, which guarantees sufficient transparency for the broad mid-infrared region of 4000-600 cm(-1). This filter type features holes with a diameter of 10 μm and exhibits adequate mechanical stability. Furthermore, it will be shown that our Si filter substrate allows a distinct identification of the most common microplastics, polyethylene (PE), and polypropylene (PP), in the characteristic fingerprint region (1400-600 cm(-1)). Moreover, using the Si filter substrate, a differentiation of microparticles of polyesters having quite similar chemical structure, like polyethylene terephthalate (PET) and polybutylene terephthalate (PBT), is now possible, which facilitates a visualization of their distribution within a microplastic sample by FTIR imaging. Finally, this Si filter can also be used as substrate for Raman microscopy-a second complementary spectroscopic technique-to identify microplastic samples.

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

PubMed Central

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

2013-01-01

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

Structural characterization of ZnO thin films grown on various substrates by pulsed laser deposition

NASA Astrophysics Data System (ADS)

Novotný, M.; Čížek, J.; Kužel, R.; Bulíř, J.; Lančok, J.; Connolly, J.; McCarthy, E.; Krishnamurthy, S.; Mosnier, J.-P.; Anwand, W.; Brauer, G.

2012-06-01

ZnO thin films were grown by pulsed laser deposition on three different substrates: sapphire (0 0 0 1), MgO (1 0 0) and fused silica (FS). The structure and morphology of the films were characterized by x-ray diffraction and scanning electron microscopy and defect studies were carried out using slow positron implantation spectroscopy (SPIS). Films deposited on all substrates studied in this work exhibit the wurtzite ZnO structure and are characterized by an average crystallite size of 20-100 nm. However, strong differences in the microstructure of films deposited on various substrates were found. The ZnO films deposited on MgO and sapphire single-crystalline substrates exhibit local epitaxy, i.e. a well-defined relation between film crystallites and the substrate. Domains with different orientation relationships with the substrate were found in both films. On the other hand, the film deposited on the FS substrate exhibits fibre texture with random lateral orientation of crystallites. Extremely high compressive in-plane stress of σ ˜ 14 GPa was determined in the film deposited on the MgO substrate, while the film deposited on sapphire is virtually stress-free, and the film deposited on the FS substrate exhibits a tensile in-plane stress of σ ˜ 0.9 GPa. SPIS investigations revealed that the concentration of open-volume defects in the ZnO films is substantially higher than that in a bulk ZnO single crystal. Moreover, the ZnO films deposited on MgO and sapphire single-crystalline substrates exhibit a significantly higher density of defects than the film deposited on the amorphous FS substrate.

Detoxification function of the Arabidopsis sulphotransferase AtSOT12 by sulphonation of xenobiotics.

PubMed

Chen, Jinhua; Gao, Liqiong; Baek, Dongwon; Liu, Chunlin; Ruan, Ying; Shi, Huazhong

2015-08-01

Cytosolic sulphotransferases have been implicated in inactivation of endogenous steroid hormones and detoxification of xenobiotics in human and animals. Yet, the function of plant sulphotransferases in xenobiotic sulphonation and detoxification has not been reported. In this study, we show that the Arabidopsis sulphotransferase AtSOT12 could sulphonate the bacterial-produced toxin cycloheximide. Loss-of-function mutant sot12 exhibited hypersensitive phenotype to cycloheximide, and expression of AtSOT12 protein in yeast cells conferred resistance to this toxic compound. AtSOT12 exhibited broad specificity and could sulphonate a variety of xenobiotics including phenolic and polycyclic compounds. Enzyme kinetics analysis indicated that AtSOT12 has different selectivity for simple phenolics with different side chains, and the position of the side chain in the simple phenolic compounds affects substrate binding affinity and catalytic efficiency. We proposed that the broad specificity and induced production of AtSOT12 may have rendered this enzyme to not only modify endogenous molecules such as salicylic acid as we previously reported, but also sulphonate pathogen-produced toxic small molecules to protect them from infection. Sulphonation of small molecules in plants may constitute a rapid way to inactivate or change the physiochemical properties of biologically active molecules that could have profound effects on plant growth, development and defence. © 2015 John Wiley & Sons Ltd.

Sub-micrometer yttrium iron garnet LPE films with low ferromagnetic resonance losses

NASA Astrophysics Data System (ADS)

Dubs, Carsten; Surzhenko, Oleksii; Linke, Ralf; Danilewsky, Andreas; Brückner, Uwe; Dellith, Jan

2017-05-01

Using a liquid phase epitaxy (LPE) technique (1 1 1) yttrium iron garnet (YIG) films with thicknesses of  ≈100 nm and surface roughnesses as low as 0.3 nm have been grown on (1 1 1) gadolinium gallium garnet (GGG) substrates as a basic material for spin-wave propagation experiments in microstructured waveguides. The continuously strained films exhibit nearly perfect crystallinity without significant mosaicity and with effective lattice misfits of Δ {{a}\\bot}/{{a}s}≈ {{10}-4} and below. The film/substrate interface is extremely sharp without broad interdiffusion layer formation. All LPE films exhibit a nearly bulk-like saturation magnetization of (1800+/- 20 ) Gs and an ‘easy cone’ anisotropy type with extremely small in-plane coercive fields  <0.2 Oe. There is a rather weak in-plane magnetic anisotropy with a pronounced six-fold symmetry observed for the saturation field  <1.5 Oe. No significant out-of-plane anisotropy is observed, but a weak dependence of the effective magnetization on the lattice misfit is detected. The narrowest ferromagnetic resonance linewidth is determined to be 1.4 Oe @ 6.5 GHz which is the lowest value reported so far for YIG films of 100 nm thicknesses and below. The Gilbert damping coefficient for investigated LPE films is estimated to be close to 1× {{10}-4} .

Dielectric and ferroelectric properties of strain-relieved epitaxial lead-free KNN-LT-LS ferroelectric thin films on SrTiO3 substrates

NASA Astrophysics Data System (ADS)

Abazari, M.; Akdoǧan, E. K.; Safari, A.

2008-05-01

We report the growth of single-phase (K0.44,Na0.52,Li0.04)(Nb0.84,Ta0.10,Sb0.06)O3 thin films on SrRuO3 coated ⟨001⟩ oriented SrTiO3 substrates by using pulsed laser deposition. Films grown at 600°C under low laser fluence exhibit a ⟨001⟩ textured columnar grained nanostructure, which coalesce with increasing deposition temperature, leading to a uniform fully epitaxial highly stoichiometric film at 750°C. However, films deposited at lower temperatures exhibit compositional fluctuations as verified by Rutherford backscattering spectroscopy. The epitaxial films of 400-600nm thickness have a room temperature relative permittivity of ˜750 and a loss tangent of ˜6% at 1kHz. The room temperature remnant polarization of the films is 4μC /cm2, while the saturation polarization is 7.1μC/cm2 at 24kV/cm and the coercive field is ˜7.3kV/cm. The results indicate that approximately 50% of the bulk permittivity and 20% of bulk spontaneous polarization can be retained in submicron epitaxial KNN-LT-LS thin film, respectively. The conductivity of the films remains to be a challenge as evidenced by the high loss tangent, leakage currents, and broad hysteresis loops.

Low-temperature growth of aligned ZnO nanorods: effect of annealing gases on the structural and optical properties.

PubMed

Umar, Ahmad; Hahn, Yoon-Bong; Al-Hajry, A; Abaker, M

2014-06-01

Aligned ZnO nanorods were grown on ZnO/Si substrate via simple aqueous solution process at low-temperature of - 65 degrees C by using zinc nitrate and hexamethylenetetramine (HMTA). The detailed morphological and structural properties measured by FESEM, XRD, EDS and TEM confirmed that the as-grown nanorods are vertically aligned, well-crystalline possessing wurtzite hexagonal phase and grown along the [0001] direction. The room-temperature photoluminescence spectrum of the grown nanorods exhibited a strong and broad green emission and small ultraviolet emission. The as-prepared ZnO nanorods were post-annealed in nitrogen (N2) and oxygen (O2) environments and further characterized in terms of their morphological, structural and optical properties. After annealing the nanorods exhibit well-crystallinity and wurtzite hexagonal phase. Moreover, by annealing the PL spectra show the enhancement in the UV emission and suppression in the green emission. The presented results demonstrate that simply by post-annealing process, the optical properties of ZnO nanostructures can be controlled.

Regioconvergent and Enantioselective Rhodium-Catalyzed Hydroamination of Internal and Terminal Alkynes: A Highly Flexible Access to Chiral Pyrazoles.

PubMed

Haydl, Alexander M; Hilpert, Lukas J; Breit, Bernhard

2016-05-04

The rhodium-catalyzed asymmetric N-selective coupling of pyrazole derivatives with internal and terminal alkynes features an utmost chemo-, regio-, and enantioselective access to enantiopure allylic pyrazoles, readily available for incorporation in small-molecule pharmaceuticals. This methodology is distinguished by a broad substrate scope, resulting in a remarkable compatability with a variety of different functional groups. It furthermore exhibits an intriguing case of regio-, position-, and enantioselectivity in just one step, underscoring the sole synthesis of just one out of up to six possible products in a highly flexible approach to allylated pyrazoles by emanating from various internal and terminal alkynes. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Purification, cloning, functional expression and characterization of perakine reductase: the first example from the AKR enzyme family, extending the alkaloidal network of the plant Rauvolfia.

PubMed

Sun, Lianli; Ruppert, Martin; Sheludko, Yuri; Warzecha, Heribert; Zhao, Yu; Stöckigt, Joachim

2008-07-01

Perakine reductase (PR) catalyzes an NADPH-dependent step in a side-branch of the 10-step biosynthetic pathway of the alkaloid ajmaline. The enzyme was cloned by a "reverse-genetic" approach from cell suspension cultures of the plant Rauvolfia serpentina (Apocynaceae) and functionally expressed in Escherichia coli as the N-terminal His(6)-tagged protein. PR displays a broad substrate acceptance, converting 16 out of 28 tested compounds with reducible carbonyl function which belong to three substrate groups: benzaldehyde, cinnamic aldehyde derivatives and monoterpenoid indole alkaloids. The enzyme has an extraordinary selectivity in the group of alkaloids. Sequence alignments define PR as a new member of the aldo-keto reductase (AKR) super family, exhibiting the conserved catalytic tetrad Asp52, Tyr57, Lys84, His126. Site-directed mutagenesis of each of these functional residues to an alanine residue results in >97.8% loss of enzyme activity, in compounds of each substrate group. PR represents the first example of the large AKR-family which is involved in the biosynthesis of plant monoterpenoid indole alkaloids. In addition to a new esterase, PR significantly extends the Rauvolfia alkaloid network to the novel group of peraksine alkaloids.

Entropic stabilization of a deubiquitinase provides conformational plasticity and slow unfolding kinetics beneficial for functioning on the proteasome

PubMed Central

Lee, Yun-Tzai Cloud; Chang, Chia-Yun; Chen, Szu-Yu; Pan, Yun-Ru; Ho, Meng-Ru; Hsu, Shang-Te Danny

2017-01-01

Human ubiquitin C-terminal hydrolyase UCH-L5 is a topologically knotted deubiquitinase that is activated upon binding to the proteasome subunit Rpn13. The length of its intrinsically disordered cross-over loop is essential for substrate recognition. Here, we showed that the catalytic domain of UCH-L5 exhibits higher equilibrium folding stability with an unfolding rate on the scale of 10−8 s−1, over four orders of magnitudes slower than its paralogs, namely UCH-L1 and -L3, which have shorter cross-over loops. NMR relaxation dynamics analysis confirmed the intrinsic disorder of the cross-over loop. Hydrogen deuterium exchange analysis further revealed a positive correlation between the length of the cross-over loop and the degree of local fluctuations, despite UCH-L5 being thermodynamically and kinetically more stable than the shorter UCHs. Considering the role of UCH-L5 in removing K48-linked ubiquitin to prevent proteasomal degradation of ubiquitinated substrates, our findings offered mechanistic insights into the evolution of UCH-L5. Compared to its paralogs, it is entropically stabilized to withstand mechanical unfolding by the proteasome while maintaining structural plasticity. It can therefore accommodate a broad range of substrate geometries at the cost of unfavourable entropic loss. PMID:28338014

Expression and purification of human and Saccharomyces cerevisiae equilibrative nucleoside transporters.

PubMed

Boswell-Casteel, Rebba C; Johnson, Jennifer M; Roe-Žurž, Zygy; Duggan, Kelli D; Schmitz, Hannah; Hays, Franklin A

2018-02-01

Nucleosides play an essential role in the physiology of eukaryotes by acting as metabolic precursors in de novo nucleic acid synthesis and energy metabolism. Nucleosides also act as ligands for purinergic receptors. Equilibrative nucleoside transporters (ENTs) are polytopic integral membrane proteins that aid in regulating plasmalemmal flux of purine and pyrimidine nucleosides and nucleobases. ENTs exhibit broad substrate selectivity across different isoforms and utilize diverse mechanisms to drive substrate flux across membranes. However, the molecular mechanisms and chemical determinants of ENT-mediated substrate recognition, binding, inhibition, and transport are poorly understood. To determine how ENT-mediated transport occurs at the molecular level, greater chemical insight and assays employing purified protein are essential. This article focuses on the expression and purification of human ENT1, human ENT2, and Saccharomyces cerevisiae ScENT1 using novel expression and purification strategies to isolate recombinant ENTs. ScENT1, hENT1, and hENT2 were expressed in W303 Saccharomyces cerevisiae cells and detergent solubilized from the membrane. After detergent extraction, these ENTs were further purified using immobilized metal affinity chromatography and size exclusion chromatography. This effort resulted in obtaining quantities of purified protein sufficient for future biophysical analysis. Copyright © 2017 Elsevier Inc. All rights reserved.

Biochemical characterisation of the esterase activities of wine lactic acid bacteria.

PubMed

Matthews, Angela; Grbin, Paul R; Jiranek, Vladimir

2007-11-01

Esters are an important group of volatile compounds that can contribute to wine flavour. Wine lactic acid bacteria (LAB) have been shown to produce esterases capable of hydrolysing ester substrates. This study aims to characterise the esterase activities of nine LAB strains under important wine conditions, namely, acidic conditions, low temperature (to 10 degrees C) and in the presence of ethanol (2-18% v/v). Esterase substrate specificity was also examined using seven different ester substrates. The bacteria were generally found to have a broad pH activity range, with the majority of strains showing maximum activity close to pH 6.0. Exceptions included an Oenococcus oeni strain that retained most activity even down to a pH of 4.0. Most strains exhibited highest activity across the range 30-40 degrees C. Increasing ethanol concentration stimulated activity in some of the strains. In particular, O. oeni showed an increase in activity up to a maximum ethanol concentration of around 16%. Generally, strains were found to have greater activity towards short-chained esters (C2-C8) compared to long-chained esters (C10-C18). Even though the optimal physicochemical conditions for enzyme activity differed from those found in wine, these findings are of potential importance to oenology because significant activities remained under wine-like conditions.

Lipase-Secreting Bacillus Species in an Oil-Contaminated Habitat: Promising Strains to Alleviate Oil Pollution

PubMed Central

Lee, Li Pin; Karbul, Hudzaifah Mohamed; Citartan, Marimuthu; Gopinath, Subash C. B.; Lakshmipriya, Thangavel; Tang, Thean-Hock

2015-01-01

Lipases are of great interest for different industrial applications due to their diversity and versatility. Among different lipases, microbial lipases are preferable due to their broad substrate specificity, and higher stability with lower production costs compared to the lipases from plants and animals. In the past, a vast number of bacterial species have been reported as potential lipases producers. In this study, the lipases-producing bacterial species were isolated from an oil spillage area in the conventional night market. Isolated species were identified as Bacillus species by biochemical tests which indicate their predominant establishment, and further screened on the agar solid surfaces using lipid and gelatin as the substrates. Out of the ten strains tested, four potential strains were subjected to comparison analysis of the lipolytic versus proteolytic activities. Strain 10 exhibited the highest lipolytic and proteolytic activity. In all the strains, the proteolytic activity is higher than the lipolytic activity except for strain 8, suggesting the possibility for substrate-based extracellular gene induction. The simultaneous secretion of both the lipase and protease is a mean of survival. The isolated bacterial species which harbour both lipase and protease enzymes could render potential industrial-based applications and solve environmental issues. PMID:26180812

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

NASA Astrophysics Data System (ADS)

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

2018-01-01

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

Photoluminescence and charge-transport characteristics of nano-columnar titanium dioxide films prepared by rf-sputtering on alumina templates

NASA Astrophysics Data System (ADS)

Kheirandish, E.; Hosseini, T.; Yavarishad, N.; King, S.; Kouklin, N.

2018-02-01

The current study presents the synthesis and characterization of poly-crystalline TiO2 thin-film prepared by rf-sputtering on top of a highly regimented nanoporous Au-coated Al2O3 substrate. The film’s physical and electronic properties were characterized via SEM, EDS, x-ray diffraction and RAMAN spectroscopy as well as temperature dependent photoluminescence (PL) and I-V measurements. The films feature a 1D, columnar-like structure and exhibit a medium strength, spectrally-broad light emission in the UV-visible range. PL emission shows a weak T-dependence and is attributed to interband electronic transitions and defect-assisted radiative recombinations. The charge transport is confirmed to be polaronic in nature with both thermally-assisted hopping and quantum mechanical tunneling regulating a charge flow within the columns in the intermediate temperature regime of ˜200-320 K. These results open a door to utilizing nano-textured substrates/scaffolds to produce electronic-grade anatase TiO2 by sputtering for advanced opto-electronic device applications.

Apatite layer growth on glassy Zr48Cu36Al8Ag8 sputtered titanium for potential biomedical applications

NASA Astrophysics Data System (ADS)

Thanka Rajan, S.; Karthika, M.; Bendavid, Avi; Subramanian, B.

2016-04-01

The bioactivity of magnetron sputtered thin film metallic glasses (TFMGs) of Zr48Cu36Al8Ag8 (at.%) on titanium substrates was tested for bio implant applications. The structural and elemental compositions of TFMGs were analyzed by XRD, XPS and EDAX. X-ray diffraction analysis displayed a broad hump around the incident angle of 30-50°, suggesting that the coatings possess a glassy structure. An in situ crystal growth of hydroxyapatite was observed by soaking the sputtered specimen in simulated body fluid (SBF). The nucleation and growth of a calcium phosphate (Ca-P) bone-like hydroxyapatite on Zr48Cu36Al8Ag8 (at.%) TFMG from SBF was investigated by using XRD, AFM and SEM. The presence of calcium and phosphorus elements was confirmed by EDAX and XPS. In vitro electrochemical corrosion studies indicated that the Zr-based TFMG coating sustain in the stimulated body-fluid (SBF), exhibiting superior corrosion resistance with a lower corrosion penetration rate and electrochemical stability than the bare crystalline titanium substrate.

The quorum-quenching lactonase from Alicyclobacter acidoterrestris : purification, kinetic characterization, crystallization and crystallographic analysis

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

Bergonzi, Celine; Schwab, Michael; Chabriere, Eric

Lactonases comprise a class of enzymes that hydrolyze lactones, including acyl-homoserine lactones (AHLs); the latter are used as chemical signaling molecules by numerous Gram-negative bacteria. Lactonases have therefore been demonstrated to quench AHL-based bacterial communication. In particular, lactonases are capable of inhibiting bacterial behaviors that depend on these chemicals, such as the formation of biofilms or the expression of virulence factors. A novel representative from the metallo-β-lactamase superfamily, named AaL, was isolated from the thermoacidophilic bacteriumAlicyclobacter acidoterrestris. Kinetic characterization proves AaL to be a proficient lactonase, with catalytic efficiencies (k cat/K m) against AHLs in the region of 10 5Mmore » -1s -1. AaL exhibits a very broad substrate specificity. Its structure is expected to reveal the molecular determinants for its substrate binding and specificity, as well as to provide grounds for future protein-engineering projects. Here, the expression, purification, characterization, crystallization and X-ray diffraction data collection of AaL at 1.65Å resolution are reported.« less

Smooth, All-Solid, Low-Hysteresis, Omniphobic Surfaces with Enhanced Mechanical Durability.

PubMed

Boban, Mathew; Golovin, Kevin; Tobelmann, Brian; Gupte, Omkar; Mabry, Joseph M; Tuteja, Anish

2018-04-11

The utility of omniphobic surfaces stems from their ability to repel a multitude of liquids, possessing a broad range of surface tensions and polarities, by causing them to bead up and either roll or slide off. These surfaces may be self-cleaning, corrosion-resistant, heat-transfer enhancing, stain-resistant or resistant to mineral- or biofouling. The majority of reported omniphobic surfaces use texture, lubricants, and/or grafted monolayers to engender these repellent properties. Unfortunately, these approaches often produce surfaces with deficiencies in long-term stability, durability, scalability, or applicability to a wide range of substrates. To overcome these limitations, we have fabricated an all-solid, substrate-independent, smooth, omniphobic coating composed of a fluorinated polyurethane and fluorodecyl polyhedral oligomeric silsesquioxane. Liquids of varying surface tension, including water, hexadecane, ethanol, and silicone oil, exhibit low-contact-angle hysteresis (<15°) on these surfaces, allowing liquid droplets to slide off, leaving no residue. Moreover, we demonstrate that these robust surfaces retained their repellent properties more effectively than textured or lubricated omniphobic surfaces after being subjected to mechanical abrasion.

Structural Insights into Drug Processing by Human Carboxylesterase 1: Tamoxifen, Mevastatin, and Inhibition by Benzil

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

Fleming, Christopher D.; Bencharit, Sompop; Edwards, Carol C.

2010-07-19

Human carboxylesterase 1 (hCE1) exhibits broad substrate specificity and is involved in xenobiotic processing and endobiotic metabolism. We present and analyze crystal structures of hCE1 in complexes with the cholesterol-lowering drug mevastatin, the breast cancer drug tamoxifen, the fatty acyl ethyl ester (FAEE) analogue ethyl acetate, and the novel hCE1 inhibitor benzil. We find that mevastatin does not appear to be a substrate for hCE1, and instead acts as a partially non-competitive inhibitor of the enzyme. Similarly, we show that tamoxifen is a low micromolar, partially non-competitive inhibitor of hCE1. Further, we describe the structural basis for the inhibition ofmore » hCE1 by the nanomolar-affinity dione benzil, which acts by forming both covalent and non-covalent complexes with the enzyme. Our results provide detailed insights into the catalytic and non-catalytic processing of small molecules by hCE1, and suggest that the efficacy of clinical drugs may be modulated by targeted hCE1 inhibitors.« less

Structural insights into drug processing by human carboxylesterase 1: tamoxifen, mevastatin, and inhibition by benzil.

PubMed

Fleming, Christopher D; Bencharit, Sompop; Edwards, Carol C; Hyatt, Janice L; Tsurkan, Lyudmila; Bai, Feng; Fraga, Charles; Morton, Christopher L; Howard-Williams, Escher L; Potter, Philip M; Redinbo, Matthew R

2005-09-09

Human carboxylesterase 1 (hCE1) exhibits broad substrate specificity and is involved in xenobiotic processing and endobiotic metabolism. We present and analyze crystal structures of hCE1 in complexes with the cholesterol-lowering drug mevastatin, the breast cancer drug tamoxifen, the fatty acyl ethyl ester (FAEE) analogue ethyl acetate, and the novel hCE1 inhibitor benzil. We find that mevastatin does not appear to be a substrate for hCE1, and instead acts as a partially non-competitive inhibitor of the enzyme. Similarly, we show that tamoxifen is a low micromolar, partially non-competitive inhibitor of hCE1. Further, we describe the structural basis for the inhibition of hCE1 by the nanomolar-affinity dione benzil, which acts by forming both covalent and non-covalent complexes with the enzyme. Our results provide detailed insights into the catalytic and non-catalytic processing of small molecules by hCE1, and suggest that the efficacy of clinical drugs may be modulated by targeted hCE1 inhibitors.

Switchable regioselectivity in amine-catalysed asymmetric cycloadditions

NASA Astrophysics Data System (ADS)

Zhou, Zhi; Wang, Zhou-Xiang; Zhou, Yuan-Chun; Xiao, Wei; Ouyang, Qin; Du, Wei; Chen, Ying-Chun

2017-06-01

Building small-molecule libraries with structural and stereogenic diversity plays an important role in drug discovery. The development of switchable intermolecular cycloaddition reactions from identical substrates in different regioselective fashions would provide an attractive protocol. However, this also represents a challenge in organic chemistry, because it is difficult to control regioselectivity to afford the products exclusively and at the same time achieve high levels of stereoselectivity. Here, we report the diversified cycloadditions of α‧-alkylidene-2-cyclopentenones catalysed by cinchona-derived primary amines. An asymmetric γ,β‧-regioselective intermolecular [6+2] cycloaddition reaction with 3-olefinic (7-aza)oxindoles is realized through the in situ generation of formal 4-aminofulvenes, while a different β,γ-regioselective [2+2] cycloaddition reaction with maleimides to access fused cyclobutanes is disclosed. In contrast, an intriguing α,γ-regioselective [4+2] cycloaddition reaction is uncovered with the same set of substrates, by employing an unprecedented dual small-molecule catalysis of amines and thiols. All of the cycloaddition reactions exhibit excellent regio- and stereoselectivity, producing a broad spectrum of chiral architectures with high structural diversity and molecular complexity.

Substrate Specificity of Human Protein Arginine Methyltransferase 7 (PRMT7)

PubMed Central

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

2014-01-01

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

Tuning the Phase and Microstructural Properties of TiO2 Films Through Pulsed Laser Deposition and Exploring Their Role as Buffer Layers for Conductive Films

NASA Astrophysics Data System (ADS)

Agarwal, S.; Haseman, M. S.; Leedy, K. D.; Winarski, D. J.; Saadatkia, P.; Doyle, E.; Zhang, L.; Dang, T.; Vasilyev, V. S.; Selim, F. A.

2018-04-01

Titanium oxide (TiO2) is a semiconducting oxide of increasing interest due to its chemical and thermal stability and broad applicability. In this study, thin films of TiO2 were deposited by pulsed laser deposition on sapphire and silicon substrates under various growth conditions, and characterized by x-ray diffraction (XRD), atomic force microscopy (AFM), optical absorption spectroscopy and Hall-effect measurements. XRD patterns revealed that a sapphire substrate is more suitable for the formation of the rutile phase in TiO2, while a silicon substrate yields a pure anatase phase, even at high-temperature growth. AFM images showed that the rutile TiO2 films grown at 805°C on a sapphire substrate have a smoother surface than anatase films grown at 620°C. Optical absorption spectra confirmed the band gap energy of 3.08 eV for the rutile phase and 3.29 eV for the anatase phase. All the deposited films exhibited the usual high resistivity of TiO2; however, when employed as a buffer layer, anatase TiO2 deposited on sapphire significantly improves the conductivity of indium gallium zinc oxide thin films. The study illustrates how to control the formation of TiO2 phases and reveals another interesting application for TiO2 as a buffer layer for transparent conducting oxides.

NAD deamidation "a new reaction" by an enzyme from Aspergillus terreus DSM 826.

PubMed

Elzainy, Tahany A; Ali, Thanaa H

2005-02-01

NAD deamidation is a non-previously recognized reaction. This reaction has been found to be catalyzed by extracts of Aspergillus terreus DSM 826. Conversion of NAD to the biosynthetic intermediate, deamido NAD, by these extracts, at the optimum pH and temperature did not exceed about 55 of the amount of the substrate added. Completion of the reaction was achieved when the extracts were pre-heated at 50 degrees C for 15 min in absence of the substrate. In a very similar manner, the extracts catalyzed hydrolytic cleavage of the amide linkages of different biomolecules such as nicotinamide, nicotinamide riboside, nicotinamide mononucleotide, L-glutamine, L-asparagine and acetamide. Polyacrylamide was also deamidated under the same conditions. In addition, complete dephosphorylation of the dinucleotide molecule was also effected by the same extracts. Separation of the NAD deamidating enzyme from the NAD dephosphorylating enzyme was achieved on using either DEAE - Sephadex A-25 or Sephadex G-200 column chromatography. The obtained phosphohydrolase-free-deamidase showed optimum activity at pH 8 of 0.1 M phosphate buffer and 50 degrees C. It exhibited broad substrate specificity and hyperbolic substrate saturation kinetics. It was isosterically inhibited by the product of its activity and this inhibition was prevented by heating the extracts at 50 degrees C for 15 min. Its activity was not affected in presence of sodium fluoride, partially inhibited in presence of magnesium chloride and was retained in the freezer for some months.

The Legionella pneumophila Dot/Icm-secreted Effector PlcC/CegC1 Together with PlcA and PlcB Promotes Virulence and Belongs to a Novel Zinc Metallophospholipase C Family Present in Bacteria and Fungi*

PubMed Central

Aurass, Philipp; Schlegel, Maren; Metwally, Omar; Harding, Clare R.; Schroeder, Gunnar N.; Frankel, Gad; Flieger, Antje

2013-01-01

Legionella pneumophila is a water-borne bacterium that causes pneumonia in humans. PlcA and PlcB are two previously defined L. pneumophila proteins with homology to the phosphatidylcholine-specific phospholipase C (PC-PLC) of Pseudomonas fluorescens. Additionally, we found that Lpg0012 shows similarity to PLCs and has been shown to be a Dot/Icm-injected effector, CegC1, which is designated here as PlcC. It remained unclear, however, whether these L. pneumophila proteins exhibit PLC activity. PlcC expressed in Escherichia coli hydrolyzed a broad phospholipid spectrum, including PC, phosphatidylglycerol (PG), and phosphatidylinositol. The addition of Zn2+ ions activated, whereas EDTA inhibited, PlcC-derived PLC activity. Protein homology search revealed that the three Legionella enzymes and P. fluorescens PC-PLC share conserved domains also present in uncharacterized fungal proteins. Fifteen conserved amino acids were essential for enzyme activity as identified via PlcC mutagenesis. Analysis of defined L. pneumophila knock-out mutants indicated Lsp-dependent export of PG-hydrolyzing PLC activity. PlcA and PlcB exhibited PG-specific activity and contain a predicted Sec signal sequence. In line with the reported requirement of host cell contact for Dot/Icm-dependent effector translocation, PlcC showed cell-associated PC-specific PLC activity after bacterial growth in broth. A PLC triple mutant, but not single or double mutants, exhibited reduced host killing in a Galleria mellonella infection model, highlighting the importance of the three PLCs in pathogenesis. In summary, we describe here a novel Zn2+-dependent PLC family present in Legionella, Pseudomonas, and fungi with broad substrate preference and function in virulence. PMID:23457299

The Legionella pneumophila Dot/Icm-secreted effector PlcC/CegC1 together with PlcA and PlcB promotes virulence and belongs to a novel zinc metallophospholipase C family present in bacteria and fungi.

PubMed

Aurass, Philipp; Schlegel, Maren; Metwally, Omar; Harding, Clare R; Schroeder, Gunnar N; Frankel, Gad; Flieger, Antje

2013-04-19

Legionella pneumophila is a water-borne bacterium that causes pneumonia in humans. PlcA and PlcB are two previously defined L. pneumophila proteins with homology to the phosphatidylcholine-specific phospholipase C (PC-PLC) of Pseudomonas fluorescens. Additionally, we found that Lpg0012 shows similarity to PLCs and has been shown to be a Dot/Icm-injected effector, CegC1, which is designated here as PlcC. It remained unclear, however, whether these L. pneumophila proteins exhibit PLC activity. PlcC expressed in Escherichia coli hydrolyzed a broad phospholipid spectrum, including PC, phosphatidylglycerol (PG), and phosphatidylinositol. The addition of Zn(2+) ions activated, whereas EDTA inhibited, PlcC-derived PLC activity. Protein homology search revealed that the three Legionella enzymes and P. fluorescens PC-PLC share conserved domains also present in uncharacterized fungal proteins. Fifteen conserved amino acids were essential for enzyme activity as identified via PlcC mutagenesis. Analysis of defined L. pneumophila knock-out mutants indicated Lsp-dependent export of PG-hydrolyzing PLC activity. PlcA and PlcB exhibited PG-specific activity and contain a predicted Sec signal sequence. In line with the reported requirement of host cell contact for Dot/Icm-dependent effector translocation, PlcC showed cell-associated PC-specific PLC activity after bacterial growth in broth. A PLC triple mutant, but not single or double mutants, exhibited reduced host killing in a Galleria mellonella infection model, highlighting the importance of the three PLCs in pathogenesis. In summary, we describe here a novel Zn(2+)-dependent PLC family present in Legionella, Pseudomonas, and fungi with broad substrate preference and function in virulence.

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

Crystal Structures of the Novel Cytosolic 5′-Nucleotidase IIIB Explain Its Preference for m7GMP

PubMed Central

Monecke, Thomas; Buschmann, Juliane; Neumann, Piotr; Wahle, Elmar; Ficner, Ralf

2014-01-01

5′-nucleotidases catalyze the hydrolytic dephosphorylation of nucleoside monophosphates. As catabolic enzymes they contribute significantly to the regulation of cellular nucleotide levels; misregulation of nucleotide metabolism and nucleotidase deficiencies are associated with a number of diseases. The seven human 5′-nucleotidases differ with respect to substrate specificity and cellular localization. Recently, the novel cytosolic 5′-nucleotidase III-like protein, or cN-IIIB, has been characterized in human and Drosophila. cN-IIIB exhibits a strong substrate preference for the modified nucleotide 7-methylguanosine monophosphate but the structural reason for this preference was unknown. Here, we present crystal structures of cN-IIIB from Drosophila melanogaster bound to the reaction products 7-methylguanosine or cytidine. The structural data reveal that the cytosine- and 7-methylguanine moieties of the products are stacked between two aromatic residues in a coplanar but off-centered position. 7-methylguanosine is specifically bound through π-π interactions and distinguished from unmodified guanosine by additional cation-π coulomb interactions between the aromatic side chains and the positively charged 7-methylguanine. Notably, the base is further stabilized by T-shaped edge-to-face stacking of an additional tryptophan packing perpendicularly against the purine ring and forming, together with the other aromates, an aromatic slot. The structural data in combination with site-directed mutagenesis experiments reveal the molecular basis for the broad substrate specificity of cN-IIIB but also explain the substrate preference for 7-methylguanosine monophosphate. Analyzing the substrate specificities of cN-IIIB and the main pyrimidine 5′-nucleotidase cN-IIIA by mutagenesis studies, we show that cN-IIIA dephosphorylates the purine m7GMP as well, hence redefining its substrate spectrum. Docking calculations with cN-IIIA and m7GMP as well as biochemical data reveal that Asn69 does not generally exclude the turnover of purine substrates thus correcting previous suggestions. PMID:24603684

Transparent nanotubular capacitors based on transplanted anodic aluminum oxide templates.

PubMed

Zhang, Guozhen; Wu, Hao; Chen, Chao; Wang, Ti; Wu, Wenhui; Yue, Jin; Liu, Chang

2015-03-11

Transparent AlZnO/Al2O3/AlZnO nanocapacitor arrays have been fabricated by atomic layer deposition in anodic aluminum oxide templates transplanted on the AlZnO/glass substrates. A high capacitance density of 37 fF/μm(2) is obtained, which is nearly 5.8 times bigger than that of planar capacitors. The capacitance density almost remains the same in a broad frequency range from 1 kHz to 200 kHz. Moreover, a low leakage current density of 1.7 × 10(-7) A/cm(2) at 1 V has been achieved. The nanocapacitors exhibit an average optical transmittance of more than 80% in the visible range, and thus open the door to practical applications in transparent integrated circuits.

Study of white light emission from ZnS/PS composite system

NASA Astrophysics Data System (ADS)

Wang, Caifeng; Li, Qingshan; Lu, Lei; Zhang, Lichun; Qi, Hongxia

2007-09-01

ZnS films were deposited by pulsed laser deposition (PLD) on porous silicon (PS) substrates formed by electrochemical anodization of p-type (100) silicon wafer. The photoluminescence (PL) spectra of ZnS/PS composites were measured at room temperature. Under different excitation wavelengths, the relative integrated intensities of the red light emission from PS layers and the blue-green emission from ZnS films had different values. After samples were annealed in vacuum at different temperatures (200, 300, and 400 Celsius degree) for 30 min respectively, a new green emission located at around 550 nm appeared in the PL spectra of all ZnS/PS samples, and all of the ZnS/PS composites had a broad PL band (450-700 nm) in the visible region, exhibiting intensively white light emission.

A stretchable electrode array for non-invasive, skin-mounted measurement of electrocardiography (ECG), electromyography (EMG) and electroencephalography (EEG).

PubMed

Ma, Rui; Kim, Dae-Hyeong; McCormick, Martin; Coleman, Todd; Rogers, John

2010-01-01

This paper reports a class of stretchable electrode array capable of intimate, conformal integration onto the curvilinear surfaces of skin on the human body. The designs employ conventional metallic conductors but in optimized mechanical layouts, on soft, thin elastomeric substrates. These devices exhibit an ability to record spontaneous EEG activity even without conductive electrolyte gels, with recorded alpha rhythm responses that are 40% stronger than those collected using conventional tin electrodes and gels under otherwise similar conditions. The same type of device can also measure high quality ECG and EMG signals. The results suggest broad utility for skin-mounted measurements of electrical activity in the body, with advantages in signal levels, wearability and modes of integration compared to alternatives.

Mapping the Substrate Binding Site of Phenylacetone Monooxygenase from Thermobifida fusca by Mutational Analysis▿†

PubMed Central

Dudek, Hanna M.; de Gonzalo, Gonzalo; Torres Pazmiño, Daniel E.; Stępniak, Piotr; Wyrwicz, Lucjan S.; Rychlewski, Leszek; Fraaije, Marco W.

2011-01-01

Baeyer-Villiger monooxygenases catalyze oxidations that are of interest for biocatalytic applications. Among these enzymes, phenylacetone monooxygenase (PAMO) from Thermobifida fusca is the only protein showing remarkable stability. While related enzymes often present a broad substrate scope, PAMO accepts only a limited number of substrates. Due to the absence of a substrate in the elucidated crystal structure of PAMO, the substrate binding site of this protein has not yet been defined. In this study, a structural model of cyclopentanone monooxygenase, which acts on a broad range of compounds, has been prepared and compared with the structure of PAMO. This revealed 15 amino acid positions in the active site of PAMO that may account for its relatively narrow substrate specificity. We designed and analyzed 30 single and multiple mutants in order to verify the role of these positions. Extensive substrate screening revealed several mutants that displayed increased activity and altered regio- or enantioselectivity in Baeyer-Villiger reactions and sulfoxidations. Further substrate profiling resulted in the identification of mutants with improved catalytic properties toward synthetically attractive compounds. Moreover, the thermostability of the mutants was not compromised in comparison to that of the wild-type enzyme. Our data demonstrate that the positions identified within the active site of PAMO, namely, V54, I67, Q152, and A435, contribute to the substrate specificity of this enzyme. These findings will aid in more dedicated and effective redesign of PAMO and related monooxygenases toward an expanded substrate scope. PMID:21724896

The "Transport Specificity Ratio": a structure-function tool to search the protein fold for loci that control transition state stability in membrane transport catalysis

PubMed Central

King, Steven C

2004-01-01

Background In establishing structure-function relationships for membrane transport proteins, the interpretation of phenotypic changes can be problematic, owing to uncertainties in protein expression levels, sub-cellular localization, and protein-folding fidelity. A dual-label competitive transport assay called "Transport Specificity Ratio" (TSR) analysis has been developed that is simple to perform, and circumvents the "expression problem," providing a reliable TSR phenotype (a constant) for comparison to other transporters. Results Using the Escherichia coli GABA (4-aminobutyrate) permease (GabP) as a model carrier, it is demonstrated that the TSR phenotype is largely independent of assay conditions, exhibiting: (i) indifference to the particular substrate concentrations used, (ii) indifference to extreme changes (40-fold) in transporter expression level, and within broad limits (iii) indifference to assay duration. The theoretical underpinnings of TSR analysis predict all of the above observations, supporting that TSR has (i) applicability in the analysis of membrane transport, and (ii) particular utility in the face of incomplete information on protein expression levels and initial reaction rate intervals (e.g., in high-throughput screening situations). The TSR was used to identify gab permease (GabP) variants that exhibit relative changes in catalytic specificity (kcat/Km) for [14C]GABA (4-aminobutyrate) versus [3H]NA (nipecotic acid). Conclusions The TSR phenotype is an easily measured constant that reflects innate molecular properties of the transition state, and provides a reliable index of the difference in catalytic specificity that a carrier exhibits toward a particular pair of substrates. A change in the TSR phenotype, called a Δ(TSR), represents a specificity shift attributable to underlying changes in the intrinsic substrate binding energy (ΔGb) that translocation catalysts rely upon to decrease activation energy (). TSR analysis is therefore a structure-function tool that enables parsimonious scanning for positions in the protein fold that couple to the transition state, creating stability and thereby serving as functional determinants of catalytic power (efficiency, or specificity). PMID:15548327

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

PubMed

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

2014-11-21

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

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

PubMed Central

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

2014-01-01

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

YODA MAP3K kinase regulates plant immune responses conferring broad-spectrum disease resistance.

PubMed

Sopeña-Torres, Sara; Jordá, Lucía; Sánchez-Rodríguez, Clara; Miedes, Eva; Escudero, Viviana; Swami, Sanjay; López, Gemma; Piślewska-Bednarek, Mariola; Lassowskat, Ines; Lee, Justin; Gu, Yangnan; Haigis, Sabine; Alexander, Danny; Pattathil, Sivakumar; Muñoz-Barrios, Antonio; Bednarek, Pawel; Somerville, Shauna; Schulze-Lefert, Paul; Hahn, Michael G; Scheel, Dierk; Molina, Antonio

2018-04-01

Mitogen-activated protein kinases (MAPKs) cascades play essential roles in plants by transducing developmental cues and environmental signals into cellular responses. Among the latter are microbe-associated molecular patterns perceived by pattern recognition receptors (PRRs), which trigger immunity. We found that YODA (YDA) - a MAPK kinase kinase regulating several Arabidopsis developmental processes, like stomatal patterning - also modulates immune responses. Resistance to pathogens is compromised in yda alleles, whereas plants expressing the constitutively active YDA (CA-YDA) protein show broad-spectrum resistance to fungi, bacteria, and oomycetes with different colonization modes. YDA functions in the same pathway as ERECTA (ER) Receptor-Like Kinase, regulating both immunity and stomatal patterning. ER-YDA-mediated immune responses act in parallel to canonical disease resistance pathways regulated by phytohormones and PRRs. CA-YDA plants exhibit altered cell-wall integrity and constitutively express defense-associated genes, including some encoding putative small secreted peptides and PRRs whose impairment resulted in enhanced susceptibility phenotypes. CA-YDA plants show strong reprogramming of their phosphoproteome, which contains protein targets distinct from described MAPKs substrates. Our results suggest that, in addition to stomata development, the ER-YDA pathway regulates an immune surveillance system conferring broad-spectrum disease resistance that is distinct from the canonical pathways mediated by described PRRs and defense hormones. © 2018 Universidad Politécnica de Madrid (UPM) New Phytologist © 2018 New Phytologist Trust.

Characterization of two Listeria innocua chitinases of different sizes that were expressed in Escherichia coli.

PubMed

Honda, Shotaro; Wakita, Satoshi; Sugahara, Yasusato; Kawakita, Masao; Oyama, Fumitaka; Sakaguchi, Masayoshi

2016-09-01

Two putative chitinase genes, lin0153 and lin1996, from the nonpathogenic bacterium Listeria innocua were expressed in Escherichia coli, and the gene products were characterized. The genes were close homologs of chitinases from the pathogenic bacterium Listeria monocytogenes, in which chitinases and chitin-binding proteins play important roles in pathogenesis in mice-infection models. The purified recombinant enzymes that are different in size, LinChi78 (lin0153 product) and LinChi35 (lin1996 product)-with molecular masses of 82 and 38 kDa, including vector-derived additional sequences, respectively-exhibited optimum catalytic activity under neutral and acidic conditions at 50 °C, respectively, and were stable over broad pH (4-11) and temperature (4-40 °C) ranges. LinChi35 displayed higher k cat and K M values for 4-nitrophenyl N,N-diacetyl-β-D-chitobioside [4NP-(GlcNAc)2] than LinChi78. Both enzymes produced primarily dimers from colloidal chitin as a substrate. However, LinChi78 and LinChi35 could hydrolyze oligomeric substrates in a processive exo- and nonprocessive endo-manner, respectively, and showed different reactivity toward oligomeric substrates. Both enzymes could bind chitin beads but were different in their binding ability toward crystalline α-chitin and cellulose. The structure-function relationships of these chitinases are discussed in reference to other bacterial chitinases.

Terahertz MMICs and Antenna-in-Package Technology at 300 GHz for KIOSK Download System

NASA Astrophysics Data System (ADS)

Tajima, Takuro; Kosugi, Toshihiko; Song, Ho-Jin; Hamada, Hiroshi; El Moutaouakil, Amine; Sugiyama, Hiroki; Matsuzaki, Hideaki; Yaita, Makoto; Kagami, Osamu

2016-12-01

Toward the realization of ultra-fast wireless communications systems, the inherent broad bandwidth of the terahertz (THz) band is attracting attention, especially for short-range instant download applications. In this paper, we present our recent progress on InP-based THz MMICs and packaging techniques based on low-temperature co-fibered ceramic (LTCC) technology. The transmitter MMICs are based on 80-nm InP-based high electron mobility transistors (HEMTs). Using the transmitter packaged in an E-plane split-block waveguide and compact lens receiver packaged in LTCC multilayered substrates, we tested wireless data transmission up to 27 Gbps with the simple amplitude key shifting (ASK) modulation scheme. We also present several THz antenna-in-packaging solutions based on substrate integrated waveguide (SIW) technology. A vertical hollow (VH) SIW was applied to a compact medium-gain SIW antenna and low-loss interconnection integrated in LTCC multi-layer substrates. The size of the LTCC antennas with 15-dBi gain is less than 0.1 cm3. For feeding the antenna, we investigated an LTCC-integrated transition and polyimide transition to LTCC VH SIWs. These transitions exhibit around 1-dB estimated loss at 300 GHz and more than 35 GHz bandwidth with 10-dB return loss. The proposed package solutions make antennas and interconnections easy to integrate in a compact LTCC package with an MMIC chip for practical applications.

Phase-Engineered Type-II Multimetal-Selenide Heterostructures toward Low-Power Consumption, Flexible, Transparent, and Wide-Spectrum Photoresponse Photodetectors.

PubMed

Chen, Yu-Ze; Wang, Sheng-Wen; Su, Teng-Yu; Lee, Shao-Hsin; Chen, Chia-Wei; Yang, Chen-Hua; Wang, Kuangye; Kuo, Hao-Chung; Chueh, Yu-Lun

2018-05-01

Phase-engineered type-II metal-selenide heterostructures are demonstrated by directly selenizing indium-tin oxide to form multimetal selenides in a single step. The utilization of a plasma system to assist the selenization facilitates a low-temperature process, which results in large-area films with high uniformity. Compared to single-metal-selenide-based photodetectors, the multimetal-selenide photodetectors exhibit obviously improved performance, which can be attributed to the Schottky contact at the interface for tuning the carrier transport, as well as the type-II heterostructure that is beneficial for the separation of the electron-hole pairs. The multimetal-selenide photodetectors exhibit a response to light over a broad spectrum from UV to visible light with a high responsivity of 0.8 A W -1 and an on/off current ratio of up to 10 2 . Interestingly, all-transparent photodetectors are successfully produced in this work. Moreover, the possibility of fabricating devices on flexible substrates is also demonstrated with sustainable performance, high strain tolerance, and high durability during bending tests. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Oxidase catalysis via aerobically generated hypervalent iodine intermediates

NASA Astrophysics Data System (ADS)

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

2018-02-01

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

Non-specific activities of the major herbicide-resistance gene BAR.

PubMed

Christ, Bastien; Hochstrasser, Ramon; Guyer, Luzia; Francisco, Rita; Aubry, Sylvain; Hörtensteiner, Stefan; Weng, Jing-Ke

2017-12-01

Bialaphos resistance (BAR) and phosphinothricin acetyltransferase (PAT) genes, which convey resistance to the broad-spectrum herbicide phosphinothricin (also known as glufosinate) via N-acetylation, have been globally used in basic plant research and genetically engineered crops 1-4 . Although early in vitro enzyme assays showed that recombinant BAR and PAT exhibit substrate preference toward phosphinothricin over the 20 proteinogenic amino acids 1 , indirect effects of BAR-containing transgenes in planta, including modified amino acid levels, have been seen but without the identification of their direct causes 5,6 . Combining metabolomics, plant genetics and biochemical approaches, we show that transgenic BAR indeed converts two plant endogenous amino acids, aminoadipate and tryptophan, to their respective N-acetylated products in several plant species. We report the crystal structures of BAR, and further delineate structural basis for its substrate selectivity and catalytic mechanism. Through structure-guided protein engineering, we generated several BAR variants that display significantly reduced non-specific activities compared with its wild-type counterpart in vivo. The transgenic expression of enzymes can result in unintended off-target metabolism arising from enzyme promiscuity. Understanding such phenomena at the mechanistic level can facilitate the design of maximally insulated systems featuring heterologously expressed enzymes.

Proximity-activated nanoparticles: in vitro performance of specific structural modification by enzymatic cleavage

PubMed Central

Adam Smith, R; Sewell, Sarah L; Giorgio, Todd D

2008-01-01

The development and in vitro performance of a modular nanoscale system capable of specific structural modification by enzymatic activity is described in this work. Due to its small physical size and adaptable characteristics, this system has the potential for utilization in targeted delivery systems and biosensing. Nanoparticle probes were synthesized containing two distinct fluorescent species including a quantum dot base particle and fluorescently labeled cleavable peptide substrate. Activity of these probes was monitored by gel electrophoresis with quantitative cleavage measurements made by fluorometric analysis. The model proximity-activated nanoparticles studied here exhibit significant susceptibility to cleavage by matrix metalloprotease-7 (MMP-7) at physiologically relevant concentrations, with nearly complete cleavage of available substrate molecules after 24 hours. This response is specific to MMP-7 enzyme activity, as cleavage is completely inhibited with the addition of EDTA. Utilization of enzyme-specific modification is a sensitive approach with broad applications for targeted therapeutics and biosensing. The versatility of this nanoparticle system is highlighted in its modular design, as it has the capability to integrate characteristics for detection, biosensing, targeting, and payload delivery into a single, multifunctional nanoparticle structure. PMID:18488420

Effects of argon addition on a-CNx film deposition by hot carbon filament chemical vapor deposition

NASA Astrophysics Data System (ADS)

Watanabe, Yoshihisa; Aono, Masami; Yamazaki, Ayumi; Kitazawa, Nobuaki; Nakamura, Yoshikazu

2002-07-01

Using a carbon filament which supplies carbon and heat, amorphous carbon nitride (a-CNx) films were prepared on Si (100) substrates by hot filament chemical vapor deposition. Deposition was performed in a low-pressure atmosphere of pure nitrogen and a gas mixture of nitrogen and argon. Effects of argon additions to the nitrogen atmosphere on the film microstructure and interface composition between the film and substrate were studied by field-emission scanning electron microscopy (FESEM) and x-ray photoelectron spectroscopy (XPS). FESEM observations reveal that the film prepared in a pure nitrogen atmosphere has uniform nucleation and a densely packed columnar pieces structure. The film prepared in the nitrogen and argon gas mixture exhibits preferential nucleation and a tapered structure with macroscopic voids. Depth analyses using XPS reveal that the film prepared in pure nitrogen possesses a broad interface, which includes silicon carbide as well as a-CNx, whereas a sharp interface is discerned in the film prepared in the mixed nitrogen and argon gas. We observed that silicon carbide formation is suppressed by an argon addition to the nitrogen atmosphere during deposition. copyright 2002 American Vacuum Society.

Amino Acid Residues That Contribute to Substrate Specificity of Class A β-Lactamase SME-1

PubMed Central

Majiduddin, Fahd K.; Palzkill, Timothy

2005-01-01

Carbapenem antibiotics are used as antibiotics of last resort because they possess a broad spectrum of antimicrobial activity and are not easily hydrolyzed by β-lactamases. Recently, class A enzymes, such as the SME-1, NMC-A, and IMI-1 β-lactamases, have been identified with the capacity to hydrolyze carbapenem antibiotics. Traditional class A β-lactamases, such as TEM-1 and SHV-1, are unable to hydrolyze carbapenem antibiotics and exhibit some differences in sequence from those that are able to hydrolyze carbapenem antibiotics. The positions that differ may contribute to the unique substrate specificity of the class A carbapenemase SME-1. Codons in the SME-1 gene representing residues 104, 105, 132, 167, 237, and 241 were randomized by site-directed mutagenesis, and functional mutants were selected for the ability to hydrolyze imipenem, ampicillin, or cefotaxime. Although several positions are important for hydrolysis of β-lactam antibiotics, no single position was found to uniquely contribute to carbapenem hydrolysis. The results of this study support a model whereby the carbapenemase activity of SME-1 is due to a highly distributed set of interactions that subtly alter the structure of the active-site pocket. PMID:16048956

Amino acid residues that contribute to substrate specificity of class A beta-lactamase SME-1.

PubMed

Majiduddin, Fahd K; Palzkill, Timothy

2005-08-01

Carbapenem antibiotics are used as antibiotics of last resort because they possess a broad spectrum of antimicrobial activity and are not easily hydrolyzed by beta-lactamases. Recently, class A enzymes, such as the SME-1, NMC-A, and IMI-1 beta-lactamases, have been identified with the capacity to hydrolyze carbapenem antibiotics. Traditional class A beta-lactamases, such as TEM-1 and SHV-1, are unable to hydrolyze carbapenem antibiotics and exhibit some differences in sequence from those that are able to hydrolyze carbapenem antibiotics. The positions that differ may contribute to the unique substrate specificity of the class A carbapenemase SME-1. Codons in the SME-1 gene representing residues 104, 105, 132, 167, 237, and 241 were randomized by site-directed mutagenesis, and functional mutants were selected for the ability to hydrolyze imipenem, ampicillin, or cefotaxime. Although several positions are important for hydrolysis of beta-lactam antibiotics, no single position was found to uniquely contribute to carbapenem hydrolysis. The results of this study support a model whereby the carbapenemase activity of SME-1 is due to a highly distributed set of interactions that subtly alter the structure of the active-site pocket.

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

PubMed

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

2010-10-01

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

Metal release and sequestration from black slate mediated by a laccase of Schizophyllum commune.

PubMed

Kirtzel, Julia; Scherwietes, Eric Leon; Merten, Dirk; Krause, Katrin; Kothe, Erika

2018-06-25

Schizophyllum commune is a filamentous basidiomycete which can degrade complex organic macromolecules like lignin by the secretion of a large repertoire of enzymes. One of these white rot enzymes, laccase, exhibits a broad substrate specificity and is able to oxidize a variety of substances including carbonaceous rocks. To investigate the role of laccase in bioweathering, laccase gene lcc2 was overexpressed, and the influence on weathering of black slate, originating from a former alum mine in Schmiedefeld, Germany, was examined. The metal release from the rock material was enhanced, associated with a partial metal accumulation into the mycelium. A sequestration of metals could be shown with fluorescent staining methods, and an accumulation of Zn, Cd, and Pb was visualized in different cell organelles. Additionally, we could show an increased metal resistance of the laccase overexpressing strain.

Identification of a type-D feruloyl esterase from Neurospora crassa.

PubMed

Crepin, V F; Faulds, C B; Connerton, I F

2004-02-01

Feruloyl esterases constitute an interesting group of enzymes that have the potential for use over a broad range of applications in the agri-food industries. In order to expand the range of available enzymes, we have examined the presence of feruoyl esterase genes present in the genome sequence of the filamentous fungus Neurospora crassa. We have identified an orphan gene (contig 3.544), the translation of which shows sequence identity with known feruloyl esterases. This gene was cloned and the corresponding recombinant protein expressed in Pichia pastoris to confirm that the enzyme (NcFaeD-3.544) exhibits feruloyl esterase activity. Unusually the enzyme was capable of p-coumaric acid release from untreated crude plant cell wall materials. The substrate utilisation preferences of the recombinant enzyme place it in the recently recognised type-D sub-class of feruloyl esterase.

Isolation and Physicochemical Characterization of Laccase from Ganoderma lucidum-CDBT1 Isolated from Its Native Habitat in Nepal.

PubMed

Shrestha, Prabin; Joshi, Bishnu; Joshi, Jarina; Malla, Rajani; Sreerama, Lakshmaiah

2016-01-01

At present, few organisms are known to and capable of naturally producing laccases and white rot fungi are one such group. In the present study, three fungal species, namely, Ganoderma lucidum -CDBT1 , Ganoderma japonicum, and Lentinula edodes , isolated from their native habitat in Nepal were screened for laccase production, and G. lucidum -CDBT1 was found to express highest levels of enzyme (day 10 culture media showed 0.92 IU/mg total protein or 92 IU/mL laccase activity with ABTS as substrate). Lignin extracted from rice straw was used in Olga medium for laccase production and isolation from G. lucidum -CDBT1. Presence of lignin (5 g/L) and copper sulfate (30  μ M) in the media increased the extracellular laccase content by 111% and 114%, respectively. The laccase enzyme produced by G. lucidum -CDBT1 was fractionated by ammonium sulfate and purified by DEAE Sepharose anion exchange chromatography. The purified enzyme was found to have a molecular mass of 43 kDa and exhibits optimal activity at pH 5.0 and 30°C. The isolated laccase was thermally stable for up to 70°C for 1 h and exhibited broad pH stability. The kinetic constants, K m , V max , and K cat , determined using 2,2'-azinobis-(-3-ethylbenzothiazoline-6-sulfonic acid) as substrate were found to be 110  μ M, 36  μ mol/min/mg, and 246 min -1 , respectively. The isolated thermostable laccase will be used in future experiments for delignification process.

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

PubMed

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

2016-12-01

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

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

Functional diversity of family 3 β-glucosidases from thermophilic cellulolytic fungus Humicola insolens Y1

PubMed Central

Xia, Wei; Bai, Yingguo; Cui, Ying; Xu, Xinxin; Qian, Lichun; Shi, Pengjun; Zhang, Wei; Luo, Huiying; Zhan, Xiuan; Yao, Bin

2016-01-01

The fungus Humicola insolens is one of the most powerful decomposers of crystalline cellulose. However, studies on the β-glucosidases from this fungus remain insufficient, especially on glycosyl hydrolase family 3 enzymes. In the present study, we analyzed the functional diversity of three distant family 3 β-glucosidases from Humicola insolens strain Y1, which belonged to different evolutionary clades, by heterogeneous expression in Pichia pastoris strain GS115. The recombinant enzymes shared similar enzymatic properties including thermophilic and neutral optima (50–60 °C and pH 5.5–6.0) and high glucose tolerance, but differed in substrate specificities and kinetics. HiBgl3B was solely active towards aryl β-glucosides while HiBgl3A and HiBgl3C showed broad substrate specificities including both disaccharides and aryl β-glucosides. Of the three enzymes, HiBgl3C exhibited the highest specific activity (158.8 U/mg on pNPG and 56.4 U/mg on cellobiose) and catalytic efficiency and had the capacity to promote cellulose degradation. Substitutions of three key residues Ile48, Ile278 and Thr484 of HiBgl3B to the corresponding residues of HiBgl3A conferred the enzyme activity towards sophorose, and vice versa. This study reveals the functional diversity of GH3 β-glucosidases as well as the key residues in recognizing +1 subsite of different substrates. PMID:27271847

The effect of PS porosity on the structure, optical and electrical properties of ZnS/PS

NASA Astrophysics Data System (ADS)

Wang, Cai-Feng; Hu, Bo; Yi, Hou-Hui; Li, Wei-Bing

2014-03-01

ZnS films were deposited on porous silicon (PS) substrates with different porosities by pulsed laser deposition (PLD). The crystalline structure, surface morphology of ZnS films on PS substrates and optical, electrical properties of ZnS/PS composites were studied. The results show that, ZnS films deposited on PS substrates were grown in preferred orientation along β-ZnS (111) direction corresponding to crystalline structure of cubic phase. With the increase of PS porosity, the XRD diffraction peak intensity of ZnS films decreases. Some voids and cracks appear in the films. Compared with as-prepared PS, the PL peak of PS for ZnS/PS has a blueshift. The larger the porosity of PS, the greater the blueshift is. A new green light emission located around 550 nm is observed with increasing PS porosity, which is ascribed to defect-center luminescence of ZnS. The blue, green emission of ZnS combined with the red emission of PS, a broad photoluminescence band (450-750 nm) is formed. ZnS/PS composites exhibited intense white light emission. The I-V characteristics of ZnS/PS heterojunctions showed rectifying behavior. Under forward bias conditions, the current density is large. Under reverse bias conditions, the current density nearly to be zero. The forward current increases with increasing PS porosity. This work lay a foundation for the realization of electroluminescence of ZnS/PS and solid white light emission devices.

Functional diversity of family 3 β-glucosidases from thermophilic cellulolytic fungus Humicola insolens Y1.

PubMed

Xia, Wei; Bai, Yingguo; Cui, Ying; Xu, Xinxin; Qian, Lichun; Shi, Pengjun; Zhang, Wei; Luo, Huiying; Zhan, Xiuan; Yao, Bin

2016-06-08

The fungus Humicola insolens is one of the most powerful decomposers of crystalline cellulose. However, studies on the β-glucosidases from this fungus remain insufficient, especially on glycosyl hydrolase family 3 enzymes. In the present study, we analyzed the functional diversity of three distant family 3 β-glucosidases from Humicola insolens strain Y1, which belonged to different evolutionary clades, by heterogeneous expression in Pichia pastoris strain GS115. The recombinant enzymes shared similar enzymatic properties including thermophilic and neutral optima (50-60 °C and pH 5.5-6.0) and high glucose tolerance, but differed in substrate specificities and kinetics. HiBgl3B was solely active towards aryl β-glucosides while HiBgl3A and HiBgl3C showed broad substrate specificities including both disaccharides and aryl β-glucosides. Of the three enzymes, HiBgl3C exhibited the highest specific activity (158.8 U/mg on pNPG and 56.4 U/mg on cellobiose) and catalytic efficiency and had the capacity to promote cellulose degradation. Substitutions of three key residues Ile48, Ile278 and Thr484 of HiBgl3B to the corresponding residues of HiBgl3A conferred the enzyme activity towards sophorose, and vice versa. This study reveals the functional diversity of GH3 β-glucosidases as well as the key residues in recognizing +1 subsite of different substrates.

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

PubMed

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

2018-06-12

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

Interaction of dopamine beta-mono-oxygenase with substituted imidazoles and pyrazoles. Catalysis and inhibition.

PubMed Central

Sirimanne, S R; Herman, H H; May, S W

1987-01-01

The interaction of dopamine beta-mono-oxygenase (DBM) with substrate analogues possessing either imidazole or pyrazole functionalities at the alkyl chain terminus was investigated. 1-(4-Hydroxybenzyl)imidazole (4-HOBI) is an active substrate for DBM, and it exhibits the expected ascorbate- and fumarate-dependencies and normal kinetic behaviour at concentrations up to 10 mM. 4-Hydroxybenzaldehyde was identified as the product formed from 4-HOBI on the basis of h.p.l.c. and g.c.-m.s. analysis, and its formation exhibits the expected 1:1 stoichiometry with O2 consumption. The 4-HOBI/DBM reaction is kinetically comparable with other DBM activities, and 4-HOBI is the first substrate analogue yet reported that exhibits substantial activity though lacking a terminal amino group. Introduction of a methyl substituent at the 2-position of the imidazole ring abolishes substrate activity, probably through a steric effect. 1-(4-Hydroxybenzyl)pyrazole, where imidazole is replaced by the isomeric pyrazole moiety, is a potent DBM inhibitor, and not a substrate. These results represent the first report of an active heterocyclic substrate or inhibitor for this enzyme, and establish the basis for the design of new classes of DBM substrates and inhibitors. PMID:3593236

Engineered Luciferase Reporter from a Deep Sea Shrimp Utilizing a Novel Imidazopyrazinone Substrate

PubMed Central

2012-01-01

Bioluminescence methodologies have been extraordinarily useful due to their high sensitivity, broad dynamic range, and operational simplicity. These capabilities have been realized largely through incremental adaptations of native enzymes and substrates, originating from luminous organisms of diverse evolutionary lineages. We engineered both an enzyme and substrate in combination to create a novel bioluminescence system capable of more efficient light emission with superior biochemical and physical characteristics. Using a small luciferase subunit (19 kDa) from the deep sea shrimp Oplophorus gracilirostris, we have improved luminescence expression in mammalian cells ∼2.5 million-fold by merging optimization of protein structure with development of a novel imidazopyrazinone substrate (furimazine). The new luciferase, NanoLuc, produces glow-type luminescence (signal half-life >2 h) with a specific activity ∼150-fold greater than that of either firefly (Photinus pyralis) or Renilla luciferases similarly configured for glow-type assays. In mammalian cells, NanoLuc shows no evidence of post-translational modifications or subcellular partitioning. The enzyme exhibits high physical stability, retaining activity with incubation up to 55 °C or in culture medium for >15 h at 37 °C. As a genetic reporter, NanoLuc may be configured for high sensitivity or for response dynamics by appending a degradation sequence to reduce intracellular accumulation. Appending a signal sequence allows NanoLuc to be exported to the culture medium, where reporter expression can be measured without cell lysis. Fusion onto other proteins allows luminescent assays of their metabolism or localization within cells. Reporter quantitation is achievable even at very low expression levels to facilitate more reliable coupling with endogenous cellular processes. PMID:22894855

Elucidating the Role of Residue 67 in IMP-Type Metallo-β-Lactamase Evolution.

PubMed

LaCuran, Alecander E; Pegg, Kevin M; Liu, Eleanor M; Bethel, Christopher R; Ai, Ni; Welsh, William J; Bonomo, Robert A; Oelschlaeger, Peter

2015-12-01

Antibiotic resistance in bacteria is ever changing and adapting, as once-novel β-lactam antibiotics are losing their efficacy, primarily due to the production of β-lactamases. Metallo-β-lactamases (MBLs) efficiently inactivate a broad range of β-lactam antibiotics, including carbapenems, and are often coexpressed with other antibacterial resistance factors. The rapid dissemination of MBLs and lack of novel antibacterials pose an imminent threat to global health. In an effort to better counter these resistance-conferring β-lactamases, an investigation of their natural evolution and resulting substrate specificity was employed. In this study, we elucidated the effects of different amino acid substitutions at position 67 in IMP-type MBLs on the ability to hydrolyze and confer resistance to a range of β-lactam antibiotics. Wild-type β-lactamases IMP-1 and IMP-10 and mutants IMP-1-V67A and IMP-1-V67I were characterized biophysically and biochemically, and MICs for Escherichia coli cells expressing these enzymes were determined. We found that all variants exhibited catalytic efficiencies (kcat/Km) equal to or higher than that of IMP-1 against all tested β-lactams except penicillins, against which IMP-1 and IMP-1-V67I showed the highest kcat/Km values. The substrate-specific effects of the different amino acid substitutions at position 67 are discussed in light of their side chain structures and possible interactions with the substrates. Docking calculations were employed to investigate interactions between different side chains and an inhibitor used as a β-lactam surrogate. The differences in binding affinities determined experimentally and computationally seem to be governed by hydrophobic interactions between residue 67 and the inhibitor and, by inference, the β-lactam substrates. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Substrate-based inhibitors exhibiting excellent protective and therapeutic effects against Botulinum Neurotoxin A intoxication.

PubMed

Guo, Jiubiao; Wang, Jinglin; Gao, Shan; Ji, Bin; Waichi Chan, Edward; Chen, Sheng

2015-11-20

Potent inhibitors to reverse Botulinum neurotoxins (BoNTs) activity in neuronal cells are currently not available. A better understanding of the substrate recognition mechanism of BoNTs enabled us to design a novel class of peptide inhibitors which were derivatives of the BoNT/A substrate, SNAP25. Through a combination of in vitro, cellular based, and in vivo mouse assays, several potent inhibitors of approximately one nanomolar inhibitory strength both in vitro and in vivo have been identified. These compounds represent the first set of inhibitors that exhibited full protection against BoNT/A intoxication in mice model with undetectable toxicity. Our findings validated the hypothesis that a peptide inhibitor targeting the two BoNT structural regions which were responsible for substrate recognition and cleavage respectively could exhibit excellent inhibitory effect, thereby providing insight on future development of more potent inhibitors against BoNTs.

Visible-blind ultraviolet photodetectors on porous silicon carbide substrates

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

Naderi, N.; Hashim, M.R., E-mail: roslan@usm.my

2013-06-01

Highlights: • Highly reliable UV detectors are fabricated on porous silicon carbide substrates. • The optical properties of samples are enhanced by increasing the current density. • The optimized sample exhibits enhanced sensitivity to the incident UV radiation. - Abstract: Highly reliable visible-blind ultraviolet (UV) photodetectors were successfully fabricated on porous silicon carbide (PSC) substrates. High responsivity and high photoconductive gain were observed in a metal–semiconductor–metal ultraviolet photodetector that was fabricated on an optimized PSC substrate. The PSC samples were prepared via the UV-assisted photo-electrochemical etching of an n-type hexagonal silicon carbide (6H-SiC) substrate using different etching current densities. Themore » optical results showed that the current density is an outstanding etching parameter that controls the porosity and uniformity of PSC substrates. A highly porous substrate was synthesized using a suitable etching current density to enhance its light absorption, thereby improving the sensitivity of UV detector with this substrate. The electrical characteristics of fabricated devices on optimized PSC substrates exhibited enhanced sensitivity and responsivity to the incident radiation.« less

Elastin-like polypeptides: Therapeutic applications for an emerging class of nanomedicines.

PubMed

Despanie, Jordan; Dhandhukia, Jugal P; Hamm-Alvarez, Sarah F; MacKay, J Andrew

2016-10-28

Elastin-like polypeptides (ELPs) constitute a genetically engineered class of 'protein polymers' derived from human tropoelastin. They exhibit a reversible phase separation whereby samples remain soluble below a transition temperature (T t ) but form amorphous coacervates above T t . Their phase behavior has many possible applications in purification, sensing, activation, and nanoassembly. As humanized polypeptides, they are non-immunogenic, substrates for proteolytic biodegradation, and can be decorated with pharmacologically active peptides, proteins, and small molecules. Recombinant synthesis additionally allows precise control over ELP architecture and molecular weight, resulting in protein polymers with uniform physicochemical properties suited to the design of multifunctional biologics. As such, ELPs have been employed for various uses including as anti-cancer agents, ocular drug delivery vehicles, and protein trafficking modulators. This review aims to offer the reader a catalogue of ELPs, their various applications, and potential for commercialization across a broad spectrum of fields. Copyright © 2015. Published by Elsevier B.V.

Core-shell silicon nanowire solar cells

PubMed Central

Adachi, M. M.; Anantram, M. P.; Karim, K. S.

2013-01-01

Silicon nanowires can enhance broadband optical absorption and reduce radial carrier collection distances in solar cell devices. Arrays of disordered nanowires grown by vapor-liquid-solid method are attractive because they can be grown on low-cost substrates such as glass, and are large area compatible. Here, we experimentally demonstrate that an array of disordered silicon nanowires surrounded by a thin transparent conductive oxide has both low diffuse and specular reflection with total values as low as < 4% over a broad wavelength range of 400 nm < λ < 650 nm. These anti-reflective properties together with enhanced infrared absorption in the core-shell nanowire facilitates enhancement in external quantum efficiency using two different active shell materials: amorphous silicon and nanocrystalline silicon. As a result, the core-shell nanowire device exhibits a short-circuit current enhancement of 15% with an amorphous Si shell and 26% with a nanocrystalline Si shell compared to their corresponding planar devices. PMID:23529071

Order-disorder transition in a two-dimensional boron-carbon-nitride alloy

NASA Astrophysics Data System (ADS)

Lu, Jiong; Zhang, Kai; Feng Liu, Xin; Zhang, Han; Chien Sum, Tze; Castro Neto, Antonio H.; Loh, Kian Ping

2013-10-01

Two-dimensional boron-carbon-nitride materials exhibit a spectrum of electronic properties ranging from insulating to semimetallic, depending on their composition and geometry. Detailed experimental insights into the phase separation and ordering in such alloy are currently lacking. Here we report the mixing and demixing of boron-nitrogen and carbon phases on ruthenium (0001) and found that energetics for such processes are modified by the metal substrate. The brick-and-mortar patchwork observed of stoichiometrically percolated hexagonal boron-carbon-nitride domains surrounded by a network of segregated graphene nanoribbons can be described within the Blume-Emery-Griffiths model applied to a honeycomb lattice. The isostructural boron nitride and graphene assumes remarkable fluidity and can be exchanged entirely into one another by a catalytically assistant substitution. Visualizing the dynamics of phase separation at the atomic level provides the premise for enabling structural control in a two-dimensional network for broad nanotechnology applications.

Discovery of piperonal-converting oxidase involved in the metabolism of a botanical aromatic aldehyde

PubMed Central

Doi, Shiori; Hashimoto, Yoshiteru; Tomita, Chiaki; Kumano, Takuto; Kobayashi, Michihiko

2016-01-01

Piperonal-catabolizing microorganisms were isolated from soil, the one (strain CT39-3) exhibiting the highest activity being identified as Burkholderia sp. The piperonal-converting enzyme involved in the initial step of piperonal metabolism was purified from strain CT39-3. Gene cloning of the enzyme and a homology search revealed that the enzyme belongs to the xanthine oxidase family, which comprises molybdoenzymes containing a molybdopterin cytosine dinucleotide cofactor. We found that the piperonal-converting enzyme acts on piperonal in the presence of O2, leading to formation of piperonylic acid and H2O2. The growth of strain CT39-3 was inhibited by higher concentrations of piperonal in the culture medium. Together with this finding, the broad substrate specificity of this enzyme for various aldehydes suggests that it would play an important role in the defense mechanism against antimicrobial compounds derived from plant species. PMID:27905507

Structural and optical properties of semi-polar (11-22) InGaN/GaN green light-emitting diode structure

NASA Astrophysics Data System (ADS)

Zhao, Guijuan; Wang, Lianshan; Li, Huijie; Meng, Yulin; Li, Fangzheng; Yang, Shaoyan; Wang, Zhanguo

2018-01-01

Semi-polar (11-22) InGaN multiple quantum well (MQW) green light-emitting diode (LED) structures have been realized by metal-organic chemical vapor deposition on an m-plane sapphire substrate. By introducing double GaN buffer layers, we improve the crystal quality of semi-polar (11-22) GaN significantly. The vertical alignment of the diffraction peaks in the (11-22) X-ray reciprocal space mapping indicates the fully strained MQW on the GaN layer. The photoluminescence spectra of the LED structure show stronger emission intensity along the [1-100] InGaN/GaN direction. The electroluminescence emission of the LED structure is very broad with peaks around 550 nm and 510 nm at the 100 mA current injection for samples A and B, respectively, and exhibits a significant blue-shift with increasing drive current.

Synthesis of a Bicyclic Azetidine with In Vivo Antimalarial Activity Enabled by Stereospecific, Directed C(sp3)-H Arylation.

PubMed

Maetani, Micah; Zoller, Jochen; Melillo, Bruno; Verho, Oscar; Kato, Nobutaka; Pu, Jun; Comer, Eamon; Schreiber, Stuart L

2017-08-16

The development of new antimalarial therapeutics is necessary to address the increasing resistance to current drugs. Bicyclic azetidines targeting Plasmodium falciparum phenylalanyl-tRNA synthetase comprise one promising new class of antimalarials, especially due to their activities against three stages of the parasite's life cycle, but a lengthy synthetic route to these compounds may affect the feasibility of delivering new therapeutic agents within the cost constraints of antimalarial drugs. Here, we report an efficient synthesis of antimalarial compound BRD3914 (EC 50 = 15 nM) that hinges on a Pd-catalyzed, directed C(sp 3 )-H arylation of azetidines at the C3 position. This newly developed protocol exhibits a broad substrate scope and provides access to valuable, stereochemically defined building blocks. BRD3914 was evaluated in P. falciparum-infected mice, providing a cure after four oral doses.

Three-dimensional conformal graphene microstructure for flexible and highly sensitive electronic skin

NASA Astrophysics Data System (ADS)

Yang, Jun; Ran, Qincui; Wei, Dapeng; Sun, Tai; Yu, Leyong; Song, Xuefen; Pu, Lichun; Shi, Haofei; Du, Chunlei

2017-03-01

We demonstrate a highly stretchable electronic skin (E-skin) based on the facile combination of microstructured graphene nanowalls (GNWs) and a polydimethylsiloxane (PDMS) substrate. The microstructure of the GNWs was endowed by conformally growing them on the unpolished silicon wafer without the aid of nanofabrication technology. Then a stamping transfer method was used to replicate the micropattern of the unpolished silicon wafer. Due to the large contact interface between the 3D graphene network and the PDMS, this type of E-skin worked under a stretching ratio of nearly 100%, and showed excellent mechanical strength and high sensitivity, with a change in relative resistance of up to 6500% and a gauge factor of 65.9 at 99.64% strain. Furthermore, the E-skin exhibited an obvious highly sensitive response to joint movement, eye movement and sound vibration, demonstrating broad potential applications in healthcare, body monitoring and wearable devices.

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Tunable UV-visible absorption of SnS2 layered quantum dots produced by liquid phase exfoliation.

PubMed

Fu, Xiao; Ilanchezhiyan, P; Mohan Kumar, G; Cho, Hak Dong; Zhang, Lei; Chan, A Sattar; Lee, Dong J; Panin, Gennady N; Kang, Tae Won

2017-02-02

4H-SnS 2 layered crystals synthesized by a hydrothermal method were used to obtain via liquid phase exfoliation quantum dots (QDs), consisting of a single layer (SLQDs) or multiple layers (MLQDs). Systematic downshift of the peaks in the Raman spectra of crystals with a decrease in size was observed. The bandgap of layered QDs, estimated by UV-visible absorption spectroscopy and the tunneling current measurements using graphene probes, increases from 2.25 eV to 3.50 eV with decreasing size. 2-4 nm SLQDs, which are transparent in the visible region, show selective absorption and photosensitivity at wavelengths in the ultraviolet region of the spectrum while larger MLQDs (5-90 nm) exhibit a broad band absorption in the visible spectral region and the photoresponse under white light. The results show that the layered quantum dots obtained by liquid phase exfoliation exhibit well-controlled and regulated bandgap absorption in a wide tunable wavelength range. These novel layered quantum dots prepared using an inexpensive method of exfoliation and deposition from solution onto various substrates at room temperature can be used to create highly efficient visible-blind ultraviolet photodetectors and multiple bandgap solar cells.

Substrate stress relaxation regulates cell spreading

NASA Astrophysics Data System (ADS)

Chaudhuri, Ovijit; Gu, Luo; Darnell, Max; Klumpers, Darinka; Bencherif, Sidi A.; Weaver, James C.; Huebsch, Nathaniel; Mooney, David J.

2015-02-01

Studies of cellular mechanotransduction have converged upon the idea that cells sense extracellular matrix (ECM) elasticity by gauging resistance to the traction forces they exert on the ECM. However, these studies typically utilize purely elastic materials as substrates, whereas physiological ECMs are viscoelastic, and exhibit stress relaxation, so that cellular traction forces exerted by cells remodel the ECM. Here we investigate the influence of ECM stress relaxation on cell behaviour through computational modelling and cellular experiments. Surprisingly, both our computational model and experiments find that spreading for cells cultured on soft substrates that exhibit stress relaxation is greater than cells spreading on elastic substrates of the same modulus, but similar to that of cells spreading on stiffer elastic substrates. These findings challenge the current view of how cells sense and respond to the ECM.

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

PubMed Central

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

2012-01-01

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

Substrate Specificity of Cysteine Proteases Beyond the S2 Pocket: Mutagenesis and Molecular Dynamics Investigation of Fasciola hepatica Cathepsins L

PubMed Central

Corvo, Ileana; Ferraro, Florencia; Merlino, Alicia; Zuberbühler, Kathrin; O'Donoghue, Anthony J.; Pastro, Lucía; Pi-Denis, Natalia; Basika, Tatiana; Roche, Leda; McKerrow, James H.; Craik, Charles S.; Caffrey, Conor R.; Tort, José F.

2018-01-01

Cysteine proteases are widespread in all life kingdoms, being central to diverse physiological processes based on a broad range of substrate specificity. Paralogous Fasciola hepatica cathepsin L proteases are essential to parasite invasion, tissue migration and reproduction. In spite of similarities in their overall sequence and structure, these enzymes often exhibit different substrate specificity. These preferences are principally determined by the amino acid composition of the active site's S2 subsite (pocket) of the enzyme that interacts with the substrate P2 residue (Schetcher and Berger nomenclature). Although secreted FhCL1 accommodates aliphatic residues in the S2 pocket, FhCL2 is also efficient in cleaving proline in that position. To understand these differences, we engineered the FhCL1 S2 subsite at three amino acid positions to render it identical to that present in FhCL2. The substitutions did not produce the expected increment in proline accommodation in P2. Rather, they decreased the enzyme's catalytic efficiency toward synthetic peptides. Nonetheless, a change in the P3 specificity was associated with the mutation of Leu67 to Tyr, a hinge residue between the S2 and S3 subsites that contributes to the accommodation of Gly in S3. Molecular dynamic simulations highlighted changes in the spatial distribution and secondary structure of the S2 and S3 pockets of the mutant FhCL1 enzymes. The reduced affinity and catalytic efficiency of the mutant enzymes may be due to a narrowing of the active site cleft that hinders the accommodation of substrates. Because the variations in the enzymatic activity measured could not be exclusively allocated to those residues lining the active site, other more external positions might modulate enzyme conformation, and, therefore, catalytic activity. PMID:29725596

Zero thermal expansion and semiconducting properties in PbTiO 3 –Bi(Co, Ti)O 3 ferroelectric solid solutions

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

Pan, Zhao; Chen, Jun; Jiang, Xingxing

Zero thermal expansion (ZTE) behavior is rare but important for both fundamental studies and practical applications of functional materials. Up to now, most available ZTE materials are either electrical insulating oxides or conductive metallic compounds. Very few ZTE materials exhibit the semiconductor feature. Here we report a ZTE in semiconducting ferroelectric of 0.6PbTiO 3-0.4Bi(Co 0.55Ti 0.45)O 3-δ. Its unit cell volume exhibits a negligible change over a broad temperature range from room temperature to 500 °C. The ZTE is supposed to be correlated with the spontaneous volume ferroelectronstriction. Intriguingly, the present ZTE material also exhibits the semiconducting characteristic accompanied bymore » negative temperature coefficient of resistance. The mechanism of electric conduction is attributed to the electronic hopping from one ionic (Ti 3+) to another (Ti 4+). The semiconductor nature has also been confirmed by the noticeable visible-light absorption with the relative lower band-gap (E g) value of 1.5 eV, while ferroelectric property can be well maintained with large polarization. The first-principles calculations reveal that the drastically narrowed E g is related to the Co-Ti substitution. Finally, the present multifunctional material containing ZTE, semiconducting and ferroelectric properties is suggested to enable new applications such as the substrate for solar conversion devices.« less

Two-dimensional CsPbBr3/PCBM heterojunctions for sensitive, fast and flexible photodetectors boosted by charge transfer

NASA Astrophysics Data System (ADS)

Shen, Yalong; Yu, Dejian; Wang, Xiong; Huo, Chengxue; Wu, Ye; Zhu, Zhengfeng; Zeng, Haibo

2018-02-01

Inorganic halide perovskites exhibited promising potentials for high-performance wide-band photodetectors (PDs) due to their high light absorption coefficients, long carrier diffusion length and wide light absorption ranges. Here, we report two-dimensional (2D) CsPbBr3/PCBM heterojunctions for sensitive, fast and flexible PDs, whose performances can be greatly boosted by the charge transfer through the energy-aligned interface. The 2D CsPbBr3 nanosheets with high crystallinity were fabricated via a simple solution-process at room temperature, and then assembled into flexible heterojunctions films with polymerphenyl-C61-butyric acid methyl ester (PCBM). Significantly, the efficient and fast charge transfer at the heterojunctions interface was evidenced by the obvious photoluminescence quenching and variation of recombination dynamics. Subsequently, such heterojunctions PD exhibited an enhanced responsivity of 10.85 A W-1 and an ultrahigh detectivity of 3.06 × 1013 Jones. In addition, the PD shows a broad linear dynamic range of 73 dB, a fast response speed with rise time of 44 μs and decay time of 390 μs, respectively. Moreover, the PD lying on polyethylene terephthalate substrates exhibited an outstanding mechanical flexibility and a robust electrical stability. These results could provide a new avenue for integration of 2D perovskites and organic functional materials and for high-performance flexible PDs.

Zero thermal expansion and semiconducting properties in PbTiO 3 –Bi(Co, Ti)O 3 ferroelectric solid solutions

DOE PAGES

Pan, Zhao; Chen, Jun; Jiang, Xingxing; ...

2017-02-16

Zero thermal expansion (ZTE) behavior is rare but important for both fundamental studies and practical applications of functional materials. Up to now, most available ZTE materials are either electrical insulating oxides or conductive metallic compounds. Very few ZTE materials exhibit the semiconductor feature. Here we report a ZTE in semiconducting ferroelectric of 0.6PbTiO 3-0.4Bi(Co 0.55Ti 0.45)O 3-δ. Its unit cell volume exhibits a negligible change over a broad temperature range from room temperature to 500 °C. The ZTE is supposed to be correlated with the spontaneous volume ferroelectronstriction. Intriguingly, the present ZTE material also exhibits the semiconducting characteristic accompanied bymore » negative temperature coefficient of resistance. The mechanism of electric conduction is attributed to the electronic hopping from one ionic (Ti 3+) to another (Ti 4+). The semiconductor nature has also been confirmed by the noticeable visible-light absorption with the relative lower band-gap (E g) value of 1.5 eV, while ferroelectric property can be well maintained with large polarization. The first-principles calculations reveal that the drastically narrowed E g is related to the Co-Ti substitution. Finally, the present multifunctional material containing ZTE, semiconducting and ferroelectric properties is suggested to enable new applications such as the substrate for solar conversion devices.« less

Zero Thermal Expansion and Semiconducting Properties in PbTiO3-Bi(Co, Ti)O3 Ferroelectric Solid Solutions.

PubMed

Pan, Zhao; Chen, Jun; Jiang, Xingxing; Lin, Zheshuai; Zhang, Linxing; Fan, Longlong; Rong, Yangchun; Hu, Lei; Liu, Hui; Ren, Yang; Kuang, Xiaojun; Xing, Xianran

2017-03-06

Zero thermal expansion (ZTE) behavior is rare but important for both fundamental studies and practical applications of functional materials. Until now, most available ZTE materials are either electrical insulating oxides or conductive metallic compounds. Very few ZTE materials exhibit the semiconductor feature. Here we report a ZTE in a semiconducting ferroelectric of 0.6PbTiO 3 -0.4Bi(Co 0.55 Ti 0.45 )O 3-δ . Its unit cell volume exhibits a negligible change over a broad temperature range from room temperature to 500 °C. The ZTE is supposed to be correlated with the spontaneous volume ferroelectronstriction. Intriguingly, the present ZTE material also exhibits the semiconducting characteristic accompanied by negative temperature coefficient of resistance. The mechanism of electric conduction is attributed to the electronic hopping from one ion (Ti 3+ ) to another (Ti 4+ ). The semiconductor nature has also been confirmed by the noticeable visible-light absorption with the relatively lower band gap (E g ) value of 1.5 eV, while the ferroelectric property can be well-maintained with large polarization. The first-principles calculations reveal that the drastically narrowed E g is related to the Co-Ti substitution. The present multifunctional material containing ZTE, semiconducting, and ferroelectric properties is suggested to enable new applications such as the substrate for solar conversion devices.

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

PubMed Central

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

2013-01-01

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

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

PubMed

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

2013-10-16

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

2-(Benzothiazol-2-yl)-phenyl-β-d-galactopyranoside derivatives as fluorescent pigment dyeing substrates and their application for the assay of β-d-galactosidase activities.

PubMed

Otsubo, Tadamune; Minami, Akira; Fujii, Haruna; Taguchi, Risa; Takahashi, Tadanobu; Suzuki, Takashi; Teraoka, Fumiteru; Ikeda, Kiyoshi

2013-04-01

2-(Benzothiazol-2-yl)-phenyl-β-d-galactopyranoside derivatives were synthesized as novel artificial fluorescent pigment dyeing substrates for β-d-galactosidase. The substrates, which exhibited non-fluorescence or weak fluorescence in solution phase, were smoothly hydrolyzed by β-d-galactosidase from Aspergillus oryzae and yielded a water-insoluble strong fluorescent pigment. The difference of fluorescent intensity exhibited a linear relationship with the amount of enzyme. Copyright © 2013 Elsevier Ltd. All rights reserved.

Purification and characterization of a novel cytosolic NADP(H)-dependent retinol oxidoreductase from rabbit liver.

PubMed

Huang, D Y; Ichikawa, Y

1997-03-07

Rabbit liver cytosol exhibits very high retinol dehydrogenase activity. At least two retinol dehydrogenases were demonstrated to exist in rabbit liver cytosol, and the major one, a cytosolic NADP(H)-dependent retinol dehydrogenase (systematic name: retinol oxidoreductase) was purified about 1795-fold to electrophoretic and column chromatographic homogeneity by a procedure involving column chromatography on AF-Red Toyopearl twice and then hydroxyapatite. Its molecular mass was estimated to be 34 kDa by SDS-PAGE, and 144 kDa by HPLC gel filtration, suggesting that it is a homo-tetramer. The enzyme uses free retinol and retinal, and their complexes with CRBP as substrates in vitro. The optimum pH values for retinol oxidation of free retinol and CRBP-retinol were 8.8-9.2 and 8.0-9.0, respectively, and those for retinal reduction of free retinal and retinal-CRBP were the same, 7.0-7.6. Km for free retinol and Vmax for retinal formation were 2.8 microM and 2893 nmol/min per mg protein at 37 degrees C (pH 9.0) and the corresponding values with retinol-CRBP as a substrate were 2.5 microM and 2428 nmol/min per mg protein at 37 degrees C (pH 8.6); Km for free retinal and Vmax for retinol formation were 6.5 microM and 4108 nmol/min per mg protein, and the corresponding values with retinal-CRBP as a substrate were 5.1 microM and 3067 nmol/min per mg protein at 37 degrees C, pH 7.4. NAD(H) was not effective as a cofactor. 4-Methylpyrazole was a weak inhibitor (IC50 = 28 mM) of the enzyme, and ethanol was neither a substrate nor an inhibitor of the enzyme. This enzyme exhibits relatively broad aldehyde reductase activity and some ketone reductase activity, the activity for aromatic substitutive aldehydes being especially high and effective. Whereas, except in the case of retinol, oxidative activity toward the corresponding alcohols was not detected. This novel cytosolic enzyme may play an important role in vivo in maintaining the homeostasis of retinal, the substrate of retinoic acid synthesis, at least in rabbit liver, since a high concentration of retinol in liver and the lower Km of the enzyme for retinol force the oxidative reaction, while higher activity of retinal reductase at physiological pH forces the reductive reaction.

Enhanced photothermal lens using a photonic crystal surface

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

Zhao, Yunfei; Liu, Longju; Zhao, Xiangwei

2016-08-15

A photonic crystal (PC)-enhanced photothermal lens (PTL) is demonstrated for the detection of optically thin light absorption materials. The PC-enhanced PTL system is based on a pump-probe scheme consisting of a PC surface, pump laser beam, and probe laser beam. Heated by the pump beam, light absorption materials on the PC surface generate the PTL and cause a substantial change to the guided-mode resonance supported by the PC structure. The change of the PC resonance is detected using the probe laser beam by measuring its reflectivity from the PC surface. When applied to analyze dye molecules deposited on the PCmore » substrate, the developed system is capable of enhancing the PTL signal by 10-fold and reducing the lowest distinguishable concentration by 8-fold, in comparison to measuring without utilizing the PC resonance. The PC-enhanced PTL was also used to detect gold nanoparticles on the PC surface and exhibited a 20-fold improvement of the lowest distinguishable concentration. The PC-enhanced PTL technology offers a potential tool to obtain the absorption signatures of thin films in a broad spectral range with high sensitivity and inexpensive instrumentation. As a result, this technology will enable a broad range of applications of photothermal spectroscopy in chemical analysis and biomolecule sensing.« less

Expression of the Acidothermus cellulolyticus E1 endoglucanase in Caldicellulosiruptor bescii enhances its ability to deconstruct crystalline cellulose

DOE PAGES

Chung, Daehwan; Young, Jenna; Cha, Minseok; ...

2015-08-13

The Caldicellulosiruptor bescii genome encodes a potent set of carbohydrate-active enzymes (CAZymes), found primarily as multi-domain enzymes that exhibit high cellulolytic and hemicellulolytic activity on and allow utilization of a broad range of substrates, including plant biomass without conventional pretreatment. CelA, the most abundant cellulase in the C. bescii secretome, uniquely combines a GH9 endoglucanase and a GH48 exoglucanase in one protein. The most effective commercial enzyme cocktails used in vitro to pretreat biomass are derived from fungal cellulases (cellobiohydrolases, endoglucanases and a β-d-glucosidases) that act synergistically to release sugars for microbial conversion. The C. bescii genome contains six GH5more » domains in five different open reading frames. Four exist in multi-domain proteins and two as single catalytic domains. E1 is a GH5 endoglucanase reported to have high specific activity and simple architecture and is active at the growth temperature of C. bescii. E1 is an endo-1,4-β-glucanase linked to a family 2 carbohydrate-binding module shown to bind primarily to cellulosic substrates. As a result, we tested if the addition of this protein to the C. bescii secretome would improve its cellulolytic activity.« less

Highly sensitive optically controlled tunable capacitor and photodetector based on a metal-insulator-semiconductor on silicon-on-insulator substrates

NASA Astrophysics Data System (ADS)

Mikhelashvili, V.; Cristea, D.; Meyler, B.; Yofis, S.; Shneider, Y.; Atiya, G.; Cohen-Hyams, T.; Kauffmann, Y.; Kaplan, W. D.; Eisenstein, G.

2015-01-01

We describe a new type of optically sensitive tunable capacitor with a wide band response ranging from the ultraviolet (245 nm) to the near infrared (880 nm). It is based on a planar Metal-Oxide-Semiconductor (MOS) structure fabricated on an insulator on silicon substrate where the insulator layer comprises a double layer dielectric stack of SiO2-HfO2. Two operating configurations have been examined, a single diode and a pair of back-to-back connected devices, where either one or both diodes are illuminated. The varactors exhibit, in all cases, very large sensitivities to illumination. Near zero bias, the capacitance dependence on illumination intensity is sub linear and otherwise it is nearly linear. In the back-to-back connected configuration, the reverse biased diode acts as a light tunable resistor whose value affects strongly the capacitance of the second, forward biased, diode and vice versa. The proposed device is superior to other optical varactors in its large sensitivity to illumination in a very broad wavelength range (245 nm-880 nm), the strong capacitance dependence on voltage and the superior current photo responsivity. Above and beyond that structure requires a very simple fabrication process which is CMOS compatible.

Anomalous Elasticity of 4He Films at the Quantum Phase Transition

NASA Astrophysics Data System (ADS)

Shirahama, Keiya; Takahashi, Daisuke; Kogure, Takayuki; Yoshimura, Hitomi; Higashino, Rama

4 He films on solid substrates exhibit a quantum phase transition between localized (nonsuperfluid) and superfluid states by changing coverage n. We have made torsional oscillator (TO) studies for 4He films adsorbed on nanoporous glasses. A TO with localized films showed an apparent ''supersolid'' behavior, an increase in TO frequency f with broad peak in Q-1. Combining with FEM analyses for TO's with different designs, we conclude that the behavior results from the softening of adsorbed 4He films at high temperatures. The features in f and Q-1 are fitted well to a Debye-like activation with a distributed energy gap Δ, so the elasticity is accounted by thermal excitation of localized atoms to an ''extended'' state. As the critical coverage nc approaches the gap decreases to zero with a powerlaw Δ ~(n -nc) 1 . 2 . Assuming that the 4He chemical potential μ (n) is located in the middle of the gap, we can estimate the elastic constant κ-1 =n2 ∂μ / ∂n . The elasticity agrees with shear moduli of 4He films obtained from the FEM analysis within factor of three. The energetics proposed from the elastic behavior naturally explains other properties of He films adsorbed on disordered substrates.

A Novel 5-Enolpyruvylshikimate-3-Phosphate Synthase from Rahnella aquatilis with Significantly Reduced Glyphosate Sensitivity

PubMed Central

Xiong, Ai-Sheng; Zhao, Wei; Fu, Xiao-Yan; Han, Hong-Juan; Chen, Chen; Jin, Xiao-Fen; Yao, Quan-Hong

2012-01-01

The 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS; EC 2.5.1.19) is a key enzyme in the shikimate pathway for the production of aromatic amino acids and chorismate-derived secondary metabolites in plants, fungi, and microorganisms. It is also the target of the broad-spectrum herbicide glyphosate. Natural glyphosate resistance is generally thought to occur within microorganisms in a strong selective pressure condition. Rahnella aquatilis strain GR20, an antagonist against pathogenic agrobacterial strains of grape crown gall, was isolated from the rhizosphere of grape in glyphosate-contaminated vineyards. A novel gene encoding EPSPS was identified from the isolated bacterium by complementation of an Escherichia coli auxotrophic aroA mutant. The EPSPS, named AroAR.aquatilis, was expressed and purified from E. coli, and key kinetic values were determined. The full-length enzyme exhibited higher tolerance to glyphosate than the E. coli EPSPS (AroAE.coli), while retaining high affinity for the substrate phosphoenolpyruvate. Transgenic plants of AroAR.aquatilis were also observed to be more resistant to glyphosate at a concentration of 5 mM than that of AroAE.coli. To probe the sites contributing to increased tolerance to glyphosate, mutant R.aquatilis EPSPS enzymes were produced with the c-strand of subdomain 3 and the f-strand of subdomain 5 (Thr38Lys, Arg40Val, Arg222Gln, Ser224Val, Ile225Val, and Gln226Lys) substituted by the corresponding region of the E. coli EPSPS. The mutant enzyme exhibited greater sensitivity to glyphosate than the wild type R.aquatilis EPSPS with little change of affinity for its first substrate, shikimate-3-phosphate (S3P) and phosphoenolpyruvate (PEP). The effect of the residues on subdomain 5 on glyphosate resistance was more obvious. PMID:22870190

2'-Deoxyribosyltransferase from Leishmania mexicana, an efficient biocatalyst for one-pot, one-step synthesis of nucleosides from poorly soluble purine bases.

PubMed

Crespo, N; Sánchez-Murcia, P A; Gago, F; Cejudo-Sanches, J; Galmes, M A; Fernández-Lucas, Jesús; Mancheño, José Miguel

2017-10-01

Processes catalyzed by enzymes offer numerous advantages over chemical methods although in many occasions the stability of the biocatalysts becomes a serious concern. Traditionally, synthesis of nucleosides using poorly water-soluble purine bases, such as guanine, xanthine, or hypoxanthine, requires alkaline pH and/or high temperatures in order to solubilize the substrate. In this work, we demonstrate that the 2'-deoxyribosyltransferase from Leishmania mexicana (LmPDT) exhibits an unusually high activity and stability under alkaline conditions (pH 8-10) across a broad range of temperatures (30-70 °C) and ionic strengths (0-500 mM NaCl). Conversely, analysis of the crystal structure of LmPDT together with comparisons with hexameric, bacterial homologues revealed the importance of the relationships between the oligomeric state and the active site architecture within this family of enzymes. Moreover, molecular dynamics and docking approaches provided structural insights into the substrate-binding mode. Biochemical characterization of LmPDT identifies the enzyme as a type I NDT (PDT), exhibiting excellent activity, with specific activity values 100- and 4000-fold higher than the ones reported for other PDTs. Interestingly, LmPDT remained stable during 36 h at different pH values at 40 °C. In order to explore the potential of LmPDT as an industrial biocatalyst, enzymatic production of several natural and non-natural therapeutic nucleosides, such as vidarabine (ara A), didanosine (ddI), ddG, or 2'-fluoro-2'-deoxyguanosine, was carried out using poorly water-soluble purines. Noteworthy, this is the first time that the enzymatic synthesis of 2'-fluoro-2'-deoxyguanosine, ara G, and ara H by a 2'-deoxyribosyltransferase is reported.

Isolation and Physicochemical Characterization of Laccase from Ganoderma lucidum-CDBT1 Isolated from Its Native Habitat in Nepal

PubMed Central

Joshi, Jarina; Malla, Rajani

2016-01-01

At present, few organisms are known to and capable of naturally producing laccases and white rot fungi are one such group. In the present study, three fungal species, namely, Ganoderma lucidum-CDBT1, Ganoderma japonicum, and Lentinula edodes, isolated from their native habitat in Nepal were screened for laccase production, and G. lucidum-CDBT1 was found to express highest levels of enzyme (day 10 culture media showed 0.92 IU/mg total protein or 92 IU/mL laccase activity with ABTS as substrate). Lignin extracted from rice straw was used in Olga medium for laccase production and isolation from G. lucidum-CDBT1. Presence of lignin (5 g/L) and copper sulfate (30 μM) in the media increased the extracellular laccase content by 111% and 114%, respectively. The laccase enzyme produced by G. lucidum-CDBT1 was fractionated by ammonium sulfate and purified by DEAE Sepharose anion exchange chromatography. The purified enzyme was found to have a molecular mass of 43 kDa and exhibits optimal activity at pH 5.0 and 30°C. The isolated laccase was thermally stable for up to 70°C for 1 h and exhibited broad pH stability. The kinetic constants, K m, V max, and K cat, determined using 2,2′-azinobis-(-3-ethylbenzothiazoline-6-sulfonic acid) as substrate were found to be 110 μM, 36 μmol/min/mg, and 246 min−1, respectively. The isolated thermostable laccase will be used in future experiments for delignification process. PMID:27822471

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

NASA Astrophysics Data System (ADS)

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

2018-03-01

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

Alkyl Aryl Ether Bond Formation with PhenoFluor**

PubMed Central

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

2015-01-01

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

Cloning and characterization of a novel amidase from Paracoccus sp. M-1, showing aryl acylamidase and acyl transferase activities.

PubMed

Shen, Weiliang; Chen, Honghong; Jia, Kaizhi; Ni, Jun; Yan, Xin; Li, Shunpeng

2012-05-01

A novel amidase gene, designated pamh, was cloned from Paracoccus sp. M-1. Site-directed mutagenesis and bioinformatic analysis showed that the PamH protein belonged to the amidase signature enzyme family. PamH was expressed in Escherichia coli, purified, and characterized. The molecular mass of PamH was determined to be 52 kDa with an isoelectric point of 5.13. PamH displayed its highest enzymatic activity at 45°C and at pH 8.0 and was stable within a pH range of 5.0-10.0. The PamH enzyme exhibited amidase activity, aryl acylamidase activity, and acyl transferase activity, allowing it to function across a very broad substrate spectrum. PamH was highly active on aromatic and short-chain aliphatic amides (benzamide and propionamide), moderately active on amino acid amides, and possessed weak urease activity. Of the anilides examined, only propanil was a good substrate for PamH. For propanil, the k (cat) and K (m) were 2.8 s(-1) and 158 μM, respectively, and the catalytic efficiency value (k (cat)/K (m)) was 0.018 μM(-1) s(-1). In addition, PamH was able to catalyze the acyl transfer reaction to hydroxylamine for both amide and anilide substrates, including acetamide, propanil, and 4-nitroacetanilide; the highest reaction rate was shown with isobutyramide. These characteristics make PamH an excellent candidate for environmental remediation and an important enzyme for the biosynthesis of novel amides.

Characterization of dolichol and dolichyl phosphate phosphatase from soya beans (Glycine max).

PubMed Central

Ravi, K; Rip, J W; Carroll, K K

1983-01-01

A series of polyprenols, ranging in length from 15 to 22 isoprene units, has been isolated from soya beans (Glycine max) and purified by high-pressure liquid chromatography. N.m.r., i.r. and mass spectra of the compounds indicated that they are alpha-saturated polyprenols of the dolichol type. The amount present in dry seeds was about 9 mg/100 g, whereas dolichyl phosphate (Dol-P) was present only in trace amounts. Dol-P phosphatase activity was detected in the microsomal fraction of 5-day-old germinating soya-bean cotyledons. The Dol-P phosphatase activity was linear with respect to time and protein concentration and exhibited a broad pH optimum (pH 7-9). Triton X-100 was necessary for significant enzyme activity. Enzyme activity was slightly enhanced by EDTA, whereas dithiothreitol was without effect. An apparent Km of 5 microM was determined for Dol-P. Bivalent metal ions were not required for enzyme activity. A number of phosphorylated compounds tested as enzyme substrates (including a number of nucleoside phosphates, glucose 6-phosphate, sodium beta-glycerophosphate and Na4P2O7) did not compete with [1-3H]Dol-P as substrate. A number of phospholipids were also tested for their ability to act as Dol-P phosphatase substrates. At 1 mM concentration, phosphatidylcholine, phosphatidylethanolamine, phosphatidic acid and lysophosphatidic acid each inhibited enzymic activity. However, at 0.1 mM concentration, phosphatidylcholine and phosphatidylethanolamine were slightly stimulatory, whereas phosphatidic acid and lysophosphatidic acid were still inhibitory. Phosphatidic acid showed competitive inhibition. PMID:6311165

Multiple Multi-Copper Oxidase Gene Families in Basidiomycetes – What for?

PubMed Central

Kües, Ursula; Rühl, Martin

2011-01-01

Genome analyses revealed in various basidiomycetes the existence of multiple genes for blue multi-copper oxidases (MCOs). Whole genomes are now available from saprotrophs, white rot and brown rot species, plant and animal pathogens and ectomycorrhizal species. Total numbers (from 1 to 17) and types of mco genes differ between analyzed species with no easy to recognize connection of gene distribution to fungal life styles. Types of mco genes might be present in one and absent in another fungus. Distinct types of genes have been multiplied at speciation in different organisms. Phylogenetic analysis defined different subfamilies of laccases sensu stricto (specific to Agaricomycetes), classical Fe2+-oxidizing Fet3-like ferroxidases, potential ferroxidases/laccases exhibiting either one or both of these enzymatic functions, enzymes clustering with pigment MCOs and putative ascorbate oxidases. Biochemically best described are laccases sensu stricto due to their proposed roles in degradation of wood, straw and plant litter and due to the large interest in these enzymes in biotechnology. However, biological functions of laccases and other MCOs are generally little addressed. Functions in substrate degradation, symbiontic and pathogenic intercations, development, pigmentation and copper homeostasis have been put forward. Evidences for biological functions are in most instances rather circumstantial by correlations of expression. Multiple factors impede research on biological functions such as difficulties of defining suitable biological systems for molecular research, the broad and overlapping substrate spectrum multi-copper oxidases usually possess, the low existent knowledge on their natural substrates, difficulties imposed by low expression or expression of multiple enzymes, and difficulties in expressing enzymes heterologously. PMID:21966246

Identification, characterization, immobilization, and mutational analysis of a novel acetylesterase with industrial potential (LaAcE) from Lactobacillus acidophilus.

PubMed

Wang, Ying; Ryu, Bum Han; Yoo, Wanki; Lee, Chang Woo; Kim, Kyeong Kyu; Lee, Jun Hyuck; Kim, T Doohun

2018-01-01

Lactic acid bacteria, which are involved in the fermentation of vegetables, meats, and dairy products, are widely used for the productions of small organic molecules and bioactive peptides. Here, a novel acetylesterase (LaAcE) from Lactobacillus acidophilus NCFM was identified, functionally characterized, immobilized, and subjected to site-directed mutagenesis for biotechnological applications. The enzymatic properties of LaAcE were investigated using biochemical and biophysical methods including native polyacrylamide gel electrophoresis, acetic acid release, biochemical assays, enzyme kinetics, and spectroscopic methods. Interestingly, LaAcE exhibited the ability to act on a broad range of substrates including glucose pentaacetate, glyceryl tributyrate, fish oil, and fermentation-related compounds. Furthermore, immobilization of LaAcE showed good recycling ability and high thermal stability compared with free LaAcE. A structural model of LaAcE was used to guide mutational analysis of hydrophobic substrate-binding region, which was composed of Leu 156 , Phe 164 , and Val 204 . Five mutants (L156A, F164A, V204A, L156A/F164A, and L156A/V204A) were generated and investigated to elucidate the roles of these hydrophobic residues in substrate specificity. This work provided valuable insights into the properties of LaAcE, and demonstrated that LaAcE could be used as a model enzyme of acetylesterase in lactic acid bacteria, making LaAcE a great candidate for industrial applications. Copyright © 2017 Elsevier B.V. All rights reserved.

Static and high frequency magnetic properties of FeGa thin films deposited on convex flexible substrates

NASA Astrophysics Data System (ADS)

Yu, Ying; Zhan, Qingfeng; Wei, Jinwu; Wang, Jianbo; Dai, Guohong; Zuo, Zhenghu; Zhang, Xiaoshan; Liu, Yiwei; Yang, Huali; Zhang, Yao; Xie, Shuhong; Wang, Baomin; Li, Run-Wei

2015-04-01

Magnetostrictive FeGa thin films were deposited on the bowed flexible polyethylene terephthalate (PET) substrates, which were fixed on the convex mold. A compressive stress was induced in FeGa films when the PET substrates were shaped from convex to flat. Due to the effect of magnetostriction, FeGa films exhibit an obvious in-plane uniaxial magnetic anisotropy which could be enhanced by increasing the applied pre-strains on the substrates during growth. Consequently, the ferromagnetic resonance frequency of the films was significantly increased, but the corresponding initial permeability was decreased. Moreover, the films with pre-strains less than 0.78% exhibit a working bandwidth of microwave absorption about 2 GHz. Our investigations demonstrated a convenient method via the pre-strained substrates to tune the high frequency properties of magnetic thin films which could be applied in flexible microwave devices.

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.

The “gating” residues Ile199 and Tyr326 in human monoamine oxidase B function in substrate and inhibitor recognition

PubMed Central

Milczek, Erika M.; Binda, Claudia; Rovida, Stefano; Mattevi, Andrea; Edmondson, Dale E.

2011-01-01

Summary The major structural difference between human monoamine oxidases A (MAO A) and B (MAO B) is that MAO A has a monopartite substrate cavity of ~550 Å3 volume and MAO B contains a dipartite cavity structure with volumes of ~290 Å3 (entrance cavity) and ~400 Å3 (substrate cavity). Ile199 and Tyr326 side chains separate these two cavities in MAO B. To probe the function of these gating residues, Ile199Ala and Ile199Ala Tyr326Ala mutant forms of MAO B were investigated. Structural data on the Ile199Ala MAO B mutant show no alterations in active site geometries compared to WT enzyme while the Ile199Ala-Tyr326Ala MAO B mutant exhibits alterations in residues 100–103 which are part of the loop gating the entrance to the active site. Both mutant enzymes exhibit catalytic properties with increased amine KM but unaltered kcat values. The altered KM values on mutation are attributed to the influence of the cavity structure in the binding and subsequent deprotonation of the amine substrate. Both mutant enzymes exhibit weaker binding affinities relative to WT enzyme for small reversible inhibitors. Ile199Ala MAO B exhibits an increase in binding affinity for reversible MAO B specific inhibitors which bridge both cavities. The Ile199Ala-Tyr326Ala double mutant exhibits inhibitor binding properties more similar to those of MAO A than to MAO B. These results demonstrate the bipartite cavity structure in MAO B plays an important role in substrate and inhibitor recognition to distinguish its specificities from those of MAO A and provides insights into specific reversible inhibitor design for these membrane-bound enzymes. PMID:21978362

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

PubMed Central

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

2016-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2018-02-01

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

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.

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

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

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

2011-04-18

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

Monolayer and/or few-layer graphene on metal or metal-coated substrates

DOEpatents

Sutter, Peter Werner; Sutter, Eli Anguelova

2015-04-14

Disclosed is monolayer and/or few-layer graphene on metal or metal-coated substrates. Embodiments include graphene mirrors. In an example, a mirror includes a substrate that has a surface exhibiting a curvature operable to focus an incident beam onto a focal plane. A graphene layer conformally adheres to the substrate, and is operable to protect the substrate surface from degradation due to the incident beam and an ambient environment.

Extremely Bendable, High-Performance Integrated Circuits Using Semiconducting Carbon Nanotube Networks for Digital, Analog, and Radio-Frequency Applications

DTIC Science & Technology

2012-02-07

circuits on mechanically flexible substrates for digital, analog and radio frequency applications. The asobtained thin-film transistors ( TFTs ) exhibit... flexible substrates for digital, analog and radio frequency applications. The as- obtained thin-film transistors ( TFTs ) exhibit highly uniform device...LCD) and organic light- emitting diode ( OLED ) displays lack the transparency and flexibility and are thus unsuitable for flexible electronic

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

NASA Astrophysics Data System (ADS)

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

2017-10-01

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

Composite perfluorohydrocarbon membranes, their preparation and use

DOEpatents

Ding, Yong; Bikson, Benjamin

2017-04-04

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

Genetically engineered SCN5A mutant pig hearts exhibit conduction defects and arrhythmias

PubMed Central

Park, David S.; Cerrone, Marina; Morley, Gregory; Vasquez, Carolina; Fowler, Steven; Liu, Nian; Bernstein, Scott A.; Liu, Fang-Yu; Zhang, Jie; Rogers, Christopher S.; Priori, Silvia G.; Chinitz, Larry A.; Fishman, Glenn I.

2014-01-01

SCN5A encodes the α subunit of the major cardiac sodium channel NaV1.5. Mutations in SCN5A are associated with conduction disease and ventricular fibrillation (VF); however, the mechanisms that link loss of sodium channel function to arrhythmic instability remain unresolved. Here, we generated a large-animal model of a human cardiac sodium channelopathy in pigs, which have cardiac structure and function similar to humans, to better define the arrhythmic substrate. We introduced a nonsense mutation originally identified in a child with Brugada syndrome into the orthologous position (E558X) in the pig SCN5A gene. SCN5AE558X/+ pigs exhibited conduction abnormalities in the absence of cardiac structural defects. Sudden cardiac death was not observed in young pigs; however, Langendorff-perfused SCN5AE558X/+ hearts had an increased propensity for pacing-induced or spontaneous VF initiated by short-coupled ventricular premature beats. Optical mapping during VF showed that activity often began as an organized focal source or broad wavefront on the right ventricular (RV) free wall. Together, the results from this study demonstrate that the SCN5AE558X/+ pig model accurately phenocopies many aspects of human cardiac sodium channelopathy, including conduction slowing and increased susceptibility to ventricular arrhythmias. PMID:25500882

Surface plasmon resonance and nonlinear optical behavior of pulsed laser-deposited semitransparent nanostructured copper thin films

NASA Astrophysics Data System (ADS)

Kesarwani, Rahul; Khare, Alika

2018-06-01

In this paper, surface plasmon resonance (SPR) and nonlinear optical properties of semitransparent nanostructured copper thin films fabricated on the glass substrate at 400 °C by pulsed laser deposition technique are reported. The thickness, linear absorption coefficient and linear refractive index of the films were measured by spectroscopic ellipsometer. The average particle size as measured via atomic force microscope was in the range of 12.84-26.02 nm for the deposition time ranging from 5 to 10 min, respectively. X-ray diffraction spectra revealed the formation of Cu (111) and Cu (200) planes. All these thin films exhibited broad SPR peak. The third-order optical nonlinearity of all the samples was investigated via modified z-scan technique using cw laser at a wavelength of 632.8 nm. The open aperture z-scan spectra of Cu thin film deposited for 5 min duration exhibited reverse saturation absorption whereas all the other samples displayed saturation absorption behavior. The nonlinear refractive index coefficient of these films showed a positive sign having the magnitude of the order of 10- 4 cm/W. The real and imaginary parts of susceptibilities were also calculated from the z-scan data and found to be of the order of 10- 6 esu.

Recent progress in asymmetric bifunctional catalysis using multimetallic systems.

PubMed

Shibasaki, Masakatsu; Kanai, Motomu; Matsunaga, Shigeki; Kumagai, Naoya

2009-08-18

The concept of bifunctional catalysis, wherein both partners of a bimolecular reaction are simultaneously activated, is very powerful for designing efficient asymmetric catalysts. Catalytic asymmetric processes are indispensable for producing enantiomerically enriched compounds in modern organic synthesis, providing more economical and environmentally benign results than methods requiring stoichiometric amounts of chiral reagents. Extensive efforts in this field have produced many asymmetric catalysts, and now a number of reactions can be rendered asymmetric. We have focused on the development of asymmetric catalysts that exhibit high activity, selectivity, and broad substrate generality under mild reaction conditions. Asymmetric catalysts based on the concept of bifunctional catalysis have emerged as a particularly effective class, enabling simultaneous activation of multiple reaction components. Compared with conventional catalysts, bifunctional catalysts generally exhibit enhanced catalytic activity and higher levels of stereodifferentiation under milder reaction conditions, attracting much attention as next-generation catalysts for prospective practical applications. In this Account, we describe recent advances in enantioselective catalysis with bifunctional catalysts. Since our identification of heterobimetallic rare earth-alkali metal-BINOL (REMB) complexes, we have developed various types of bifunctional multimetallic catalysts. The REMB catalytic system is effective for catalytic asymmetric Corey-Chaykovsky epoxidation and cyclopropanation. A dinucleating Schiff base has emerged as a suitable multidentate ligand for bimetallic catalysts, promoting catalytic syn-selective nitro-Mannich, anti-selective nitroaldol, and Mannich-type reactions. The sugar-based ligand GluCAPO provides a suitable platform for polymetallic catalysts; structural elucidation revealed that their higher order polymetallic structures are a determining factor for their function in the catalytic asymmetric Strecker reaction. Rational design identified a related ligand, FujiCAPO, which exhibits superior performance in catalytic asymmetric conjugate addition of cyanide to enones and a catalytic asymmetric Diels-Alder-type reaction. The combination of an amide-based ligand with a rare earth metal constitutes a unique catalytic system: the ligand-metal association is in equilibrium because of structural flexibility. These catalytic systems are effective for asymmetric amination of highly coordinative substrate as well as for Mannich-type reaction of alpha-cyanoketones, in which hydrogen bonding cooperatively contributes to substrate activation and stereodifferentiation. Most of the reactions described here generate stereogenic tetrasubstituted carbons or quaternary carbons, noteworthy accomplishments even with modern synthetic methods. Several reactions have been incorporated into the asymmetric synthesis of therapeutics (or their candidate molecules) such as Tamiflu, AS-3201 (ranirestat), GRL-06579A, and ritodrine, illustrating the usefulness of bifunctional asymmetric catalysis.

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

PubMed

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

2017-03-03

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

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

NASA Astrophysics Data System (ADS)

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

2017-03-01

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

Impacts of zeolite nanoparticles on substrate properties of thin film nanocomposite membranes for engineered osmosis

NASA Astrophysics Data System (ADS)

Salehi, Tahereh Mombeini; Peyravi, Majid; Jahanshahi, Mohsen; Lau, Woei-Jye; Rad, Ali Shokuhi

2018-04-01

In this work, microporous substrates modified by zeolite nanoparticles were prepared and used for composite membrane making with the aim of reducing internal concentration polarization (ICP) effect of membranes during engineered osmosis applications. Nanocomposite substrates were fabricated via phase inversion technique by embedding nanostructured zeolite (clinoptilolite) in the range of 0-0.6 wt% into matrix of polyethersulfone (PES) substrate. Of all the substrates prepared, the PES0.4 substrate (with 0.4 wt% zeolite) exhibited unique characteristics, i.e., increased surface porosity, lower structural parameter ( S) (from 0.78 to 0.48 mm), and enhanced water flux. The thin film nanocomposite (TFN) membrane made of this optimized substrate was also reported to exhibit higher water flux compared to the control composite membrane during forward osmosis (FO) and pressure-retarded osmosis (PRO) test, without compromising reverse solute flux. The water flux of such TFN membrane was 43% higher than the control TFC membrane (1.93 L/m2 h bar) with salt rejection recorded at 94.7%. An increment in water flux is ascribed to the reduction in structural parameter, leading to reduced ICP effect.

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

PubMed Central

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

2007-01-01

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

Tracing the 4000 year history of organic thin films: From monolayers on liquids to multilayers on solidsa)

NASA Astrophysics Data System (ADS)

Greene, J. E.

2015-03-01

The recorded history of organic monolayer and multilayer thin films spans approximately 4000 years. Fatty-acid-based monolayers were deposited on water by the ancients for applications ranging from fortune telling in King Hammurabi's time (˜1800 BC, Mesopotamia) to stilling choppy waters for sailors and divers as reported by the Roman philosopher Pliny the Elder in ˜78 AD, and then much later (1774) by the peripatetic American statesman and natural philosopher Benjamin Franklin, to Japanese "floating-ink" art (suminagashi) developed ˜1000 years ago. The modern science of organic monolayers began in the late-1800s/early-1900s with experiments by Lord Rayleigh and the important development by Agnes Pockels, followed two decades later by Irving Langmuir, of the tools and technology to measure the surface tension of liquids, the surface pressure of organic monolayers deposited on water, interfacial properties, molecular conformation of the organic layers, and phase transitions which occur upon compressing the monolayers. In 1935, Katherine Blodgett published a landmark paper showing that multilayers can be synthesized on solid substrates, with controlled thickness and composition, using an apparatus now known as the Langmuir-Blodgett (L-B) trough. A disadvantage of LB films for some applications is that they form weak physisorbed bonds to the substrate. In 1946, Bigelow, Pickett, and Zisman demonstrated, in another seminal paper, the growth of organic self-assembled monolayers (SAMs) via spontaneous adsorption from solution, rather than from the water/air interface, onto SiO2 and metal substrates. SAMs are close-packed two-dimensional organic crystals which exhibit strong covalent bonding to the substrate. The first multicomponent adsorbed monolayers and multilayer SAMs were produced in the early 1980s. Langmuir monolayers, L-B multilayers, and self-assembled mono- and multilayers have found an extraordinarily broad range of applications including controlled wetting, adhesion, electrochemistry, biocompatibility, molecular recognition, biosensing, cell biology, non-linear optics, molecular electronics, solar cells, read/write/erase memory, and magnetism.

Preparation and Characterization of Ferroelectric BaTi0.91(Hf0.5, Zr0.5)0.09O3 Thin Films by Sol-Gel Process Using Titanium and Zirconium Alkoxides

NASA Astrophysics Data System (ADS)

Thongrueng, Jirawat; Nishio, Keishi; Nagata, Kunihiro; Tsuchiya, Toshio

2000-09-01

Sol-gel-derived BaTi0.91(Hf0.5, Zr0.5)0.09O3 (BTHZ-9) thin films have been successfully prepared on Pt and Pt(111)/Ti/SiO2/Si(100) substrates by spin-coating and sintering from 550 to 900°C for 2 h in oxygen ambient. X-ray diffraction measurement indicated that the single perovskite phase of the BTHZ-9 thin films was obtained at heat treatment above 650°C. The formation temperature of the double-alkoxy-derived BTHZ-9 thin films was lower by at least 80°C than that of the films prepared from only titanium alkoxide. The microstructure of the films was observed by atomic force microscopy and scanning electron microscopy. The grain size of the films increased from 70 to 200 nm with increasing sintering temperature ranging from 650 to 850°C. The maximum peak for the dielectric constant, corresponding to the Curie point (87°C), was broad and lower in magnitude compared with that of the BTHZ-9 bulk ceramics. Tensile stresses resulting from the differences between thermal expansion coefficients of the substrate and the film caused poor electrical properties. BTHZ-9 thin films exhibited a well-saturated polarization-electric field hysteresis loop. The polarization and coercive field for the 850-nm-thick BTHZ-9 thin film prepared on Pt/Ti/SiO2/Si substrate at 750°C were determined to be 8 μC/cm2 and 15 kV/cm, respectively. Those of the BTHZ-9 thin film prepared on Pt substrate at 850°C were found to be 9 μC/cm2 and 18 kV/cm, respectively.

Alteration of Substrate and Inhibitor Specificity of Feline Immunodeficiency Virus Protease

PubMed Central

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

2000-01-01

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

A Novel GH7 Endo-β-1,4-Glucanase from Neosartorya fischeri P1 with Good Thermostability, Broad Substrate Specificity and Potential Application in the Brewing Industry.

PubMed

Liu, Yun; Dun, Baoqing; Shi, Pengjun; Ma, Rui; Luo, Huiying; Bai, Yingguo; Xie, Xiangming; Yao, Bin

2015-01-01

An endo-β-1,4-glucanase gene, cel7A, was cloned from the thermophilic cellulase-producing fungus Neosartorya fischeri P1 and expressed in Pichia pastoris. The 1,410-bp full-length gene encodes a polypeptide of 469 amino acids consisting of a putative signal peptide at residues 1-20, a catalytic domain of glycoside hydrolase family 7 (GH7), a short Thr/Ser-rich linker and a family 1 carbohydrate-binding module (CBM 1). The purified recombinant Cel7A had pH and temperature optima of pH 5.0 and 60°C, respectively, and showed broad pH adaptability (pH 3.0-6.0) and excellent stability at pH3.0-8.0 and 60°C. Belonging to the group of nonspecific endoglucanases, Cel7A exhibited the highest activity on barley β-glucan (2020 ± 9 U mg-1), moderate on lichenan and CMC-Na, and weak on laminarin, locust bean galactomannan, Avicel, and filter paper. Under simulated mashing conditions, addition of Cel7A (99 μg) reduced the mash viscosity by 9.1% and filtration time by 24.6%. These favorable enzymatic properties make Cel7A as a good candidate for applications in the brewing industry.

Semi-contact-writing of polymer molds for prototyping PDMS chips with low surface roughness, sharp edges and locally varying channel heights

NASA Astrophysics Data System (ADS)

Gutzweiler, Ludwig; Stumpf, Fabian; Tanguy, Laurent; Roth, Guenter; Koltay, Peter; Zengerle, Roland; Riegger, Lutz

2016-04-01

Microfluidic systems fabricated in polydimethylsiloxane (PDMS) enable a broad variety of applications and are widespread in the field of Lab-on-a-Chip. Here we demonstrate semi-contact-writing, a novel method for fabrication of polymer based molds for casting microfluidic PDMS chips in a highly flexible, time and cost-efficient manner. The method is related to direct-writing of an aqueous polymer solution on a planar glass substrate and substitutes conventional, time- and cost-consuming UV-lithography. This technique facilitates on-demand prototyping in a low-cost manner and is therefore ideally suited for rapid chip layout iterations. No cleanroom facilities and less expertise are required. Fabrication time from scratch to ready-to-use PDMS-chip is less than 5 h. This polymer writing method enables structure widths down to 140 μm and controllable structure heights ranging from 5.5 μm for writing single layers up to 98 μm by stacking. As a unique property, freely selectable height variations across a substrate can be achieved by application of local stacking. Furthermore, the molds exhibit low surface roughness (R a   =  24 nm, R RMS  =  28 nm) and high fidelity edge sharpness. We validated the method by fabrication of molds to cast PDMS chips for droplet based flow-through PCR with single-cell sensitivity.

Leishmania UDP-sugar pyrophosphorylase: the missing link in galactose salvage?

PubMed

Damerow, Sebastian; Lamerz, Anne-Christin; Haselhorst, Thomas; Führing, Jana; Zarnovican, Patricia; von Itzstein, Mark; Routier, Françoise H

2010-01-08

The Leishmania parasite glycocalyx is rich in galactose-containing glycoconjugates that are synthesized by specific glycosyltransferases that use UDP-galactose as a glycosyl donor. UDP-galactose biosynthesis is thought to be predominantly a de novo process involving epimerization of the abundant nucleotide sugar UDP-glucose by the UDP-glucose 4-epimerase, although galactose salvage from the environment has been demonstrated for Leishmania major. Here, we present the characterization of an L. major UDP-sugar pyrophosphorylase able to reversibly activate galactose 1-phosphate into UDP-galactose thus proving the existence of the Isselbacher salvage pathway in this parasite. The ordered bisubstrate mechanism and high affinity of the enzyme for UTP seem to favor the synthesis of nucleotide sugar rather than their pyrophosphorolysis. Although L. major UDP-sugar pyrophosphorylase preferentially activates galactose 1-phosphate and glucose 1-phosphate, the enzyme is able to act on a variety of hexose 1-phosphates as well as pentose 1-phosphates but not hexosamine 1-phosphates and hence presents a broad in vitro specificity. The newly identified enzyme exhibits a low but significant homology with UDP-glucose pyrophosphorylases and conserved in particular is the pyrophosphorylase consensus sequence and residues involved in nucleotide and phosphate binding. Saturation transfer difference NMR spectroscopy experiments confirm the importance of these moieties for substrate binding. The described leishmanial enzyme is closely related to plant UDP-sugar pyrophosphorylases and presents a similar substrate specificity suggesting their common origin.

Enzymatic properties and substrate specificity of a bacterial phosphatidylcholine synthase.

PubMed

Aktas, Meriyem; Köster, Stefan; Kizilirmak, Sarah; Casanova, Javier C; Betz, Heidi; Fritz, Christiane; Moser, Roman; Yildiz, Özkan; Narberhaus, Franz

2014-08-01

Phosphatidylcholine (PC) is a rare membrane lipid in bacteria, but is crucial for virulence of the plant pathogen Agrobacterium tumefaciens and various other pathogens. Agrobacterium tumefaciens uses two independent PC biosynthesis pathways. One is dependent on the integral membrane protein PC synthase (Pcs), which catalyzes the conversion of cytidine diphosphate-diacylglycerol (CDP-DAG) and choline to PC, thereby releasing a cytidine monophosphate (CMP). Here, we show that Pcs consists of eight transmembrane segments with its N- and C-termini located in the cytoplasm. A cytoplasmic loop between the second and third membrane helix contains the majority of the conserved amino acids of a CDP-alcohol phosphotransferase motif (DGX2 ARX12 GX3 DX3 D). Using point mutagenesis, we provide evidence for a crucial role of this motif in choline binding and enzyme activity. To study the catalytic features of the enzyme, we established a purification protocol for recombinant Pcs. The enzyme forms stable oligomers and exhibits broad substrate specificity towards choline derivatives. The presence of CDP-DAG and manganese is a prerequisite for cooperative binding of choline. PC formation by Pcs is reversible and proceeds via two successive reactions. In a first choline- and manganese-independent reaction, CDP-DAG is hydrolyzed releasing a CMP molecule. The resulting phosphatidyl intermediate reacts with choline in a second manganese-dependent step to form PC. Pcs and Pcs bind by molecular sieving (1, 2, 3). © 2014 FEBS.

The multigene family of lysophosphatidate acyltransferase (LPAT)-related enzymes in Ricinus communis: cloning and molecular characterization of two LPAT genes that are expressed in castor seeds.

PubMed

Arroyo-Caro, José María; Chileh, Tarik; Kazachkov, Michael; Zou, Jitao; Alonso, Diego López; García-Maroto, Federico

2013-02-01

The multigene family encoding proteins related to lysophosphatidyl-acyltransferases (LPATs) has been analyzed in the castor plant Ricinus communis. Among them, two genes designated RcLPAT2 and RcLPATB, encoding proteins with LPAT activity and expressed in the developing seed, have been cloned and characterized in some detail. RcLPAT2 groups with well characterized members of the so-called A-class LPATs and it shows a generalized expression pattern in the plant and along seed development. Enzymatic assays of RcLPAT2 indicate a preference for ricinoleoyl-CoA over other fatty acid thioesters when ricinoleoyl-LPA is used as the acyl acceptor, while oleoyl-CoA is the preferred substrate when oleoyl-LPA is employed. RcLPATB groups with B-class LPAT enzymes described as seed specific and selective for unusual fatty acids. However, RcLPATB exhibit a broad specificity on the acyl-CoAs, with saturated fatty acids (12:0-16:0) being the preferred substrates. RcLPATB is upregulated coinciding with seed triacylglycerol accumulation, but its expression is not restricted to the seed. These results are discussed in the light of a possible role for LPAT isoenzymes in the channelling of ricinoleic acid into castor bean triacylglycerol. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Directing enzyme devolution for biosynthesis of alkanols and 1,n-alkanediols from natural polyhydroxy compounds.

PubMed

Dai, Lu; Tao, Fei; Tang, Hongzhi; Guo, Yali; Shen, Yaling; Xu, Ping

2017-11-01

Primordial enzymes are proposed to possess broad specificities. Through divergence and evolution, enzymes have been refined to exhibit specificity towards one reaction or substrate, and are thus commonly assumed as "specialists". However, some enzymes are "generalists" that catalyze a range of substrates and reactions. This property has been defined as enzyme promiscuity and is of great importance for the evolution of new functions. The promiscuities of two enzymes, namely glycerol dehydratase and diol dehydratase, were herein exploited for catalyzing long-chain polyols, including 1,2-butanediol, 1,2,4-butanetriol, erythritol, 1,2-pentanediol, 1,2,5-pentanetriol, and 1,2,6-hexanetriol. The specific activities required for catalyzing these six long-chain polyols were studied via in vitro enzyme assays, and the catalytic efficiencies were increased through protein engineering. The promiscuous functions were subsequently applied in vivo to establish 1,4-butanediol pathways from lignocellulose derived compounds, including xylose and erythritol. In addition, a pathway for 1-pentanol production from 1,2-pentanediol was also constructed. The results suggest that exploiting enzyme promiscuity is promising for exploring new catalysts, which would expand the repertoire of genetic elements available to synthetic biology and may provide a starting point for designing and engineering novel pathways for valuable chemicals. Copyright © 2017 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

Effects of hydrogenated TiO2 nanotube arrays on protein adsorption and compatibility with osteoblast-like cells.

PubMed

Lu, Ran; Wang, Caiyun; Wang, Xin; Wang, Yuji; Wang, Na; Chou, Joshua; Li, Tao; Zhang, Zhenting; Ling, Yunhan; Chen, Su

2018-01-01

Modified titanium (Ti) substrates with titanium dioxide (TiO 2 ) nanotubes have broad usage as implant surface treatments and as drug delivery systems. To improve drug-loading capacity and accelerate bone integration with titanium, in this study, we hydrogenated anodized titanium dioxide nanotubes (TNTs) by a thermal treatment. Three groups were examined, namely: hydrogenated TNTs (H 2 -TNTs, test), unmodified TNTs (air-TNTs, control), and Ti substrates (Ti, control). Our results showed that oxygen vacancies were present in all the nanotubes. The quantity of -OH groups greatly increased after hydrogenation. Furthermore, the protein adsorption and loading capacity of the H 2 -TNTs were considerably enhanced as compared with the properties of the air-TNTs ( P <0.05). Additionally, time-of-flight secondary ion mass spectrometry (TOF-SIMS) was used to investigate the interactions of TNTs with proteins. During the protein-loading process, the H 2 -TNTs not only enabled rapid protein adsorption, but also decreased the rate of protein elution compared with that of the air-TNTs. We found that the H 2 -TNTs exhibited better biocompatibility than the air-TNT and Ti groups. Both cell adhesion activity and alkaline phosphatase activity were significantly improved toward MG-63 human osteoblast-like cells as compared with the control groups ( P <0.05). We conclude that hydrogenated TNTs could greatly improve the loading capacity of bioactive molecules and MG-63 cell proliferation.

Electrostatic powder coatings of pristine graphene: A new approach for coating of granular and fibril substrates

NASA Astrophysics Data System (ADS)

Nine, Md J.; Kabiri, Shervin; Tung, Tran Thanh; Tran, Diana N. H.; Losic, Dusan

2018-05-01

The use of pristine graphene (pG) based on solution processed coating technologies is often limited by their poor dispersibility in water and organic solvents which prevents to achieve the best performing properties of pG in coating applications. To address these limitations, we developed a dispersant-free coating approach of pG based on their intrinsic solid-lubricity and interlayer electrostatic interactions. The "rotating drum" method was established to provide suitable conditions for electrostatic deposition of pG-powder which is demonstrated on two model substrates with granular and fibril morphologies (urea and acrylic fibers) to improve their physical and electrical properties. The results showed that the pG coating enables to minimize moisture induced caking tendency of commercial urea prills at a relative humidity (RH) of 85% (higher than critical humidity) exhibiting greater moisture rejection ability (∼2 times higher than uncoated urea) and to improve their anti-abrasive properties. The pG-powder coating applied on nonconductive acrylic fibers provides a stable conductive layer (∼0.8 ± 0.1 kΩ/sq) which made them suitable for using in wearable electronics, sensors and electromagnetic interference (EMI) shielding. The developed coating method for pG-powder based on "rotating drum" is generic, simple, eco-friendly, low-cost, and scalable for broad range of coating applications.

Direct transfer of graphene onto flexible substrates.

PubMed

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

2013-10-29

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

Field nanoemitter: One-dimension Al4C3 ceramics

NASA Astrophysics Data System (ADS)

Sun, Y.; Cui, H.; Gong, L.; Chen, Jian; Shen, P. K.; Wang, C. X.

2011-07-01

As a kind of ionic (or salt-like) carbide, Al4C3 hardly any active functions have been found except for structure material purposes. However, considering the unique characteristic features of its crystal structure, we think Al4C3 in fact might have huge potential for exhibiting active functionality on field-emission application. Herein, we report for the first time the catalyst-free synthesis and excellent field emission properties of Al4C3 one-dimension (1-D) nanostructures. The 1-D nanostructures acting as cold electron emitters display excellent field emission performance with the turn-on field as low as 1.4-2.0 V μm-1 and the threshold field down to 4.2-4.4 V μm-1. Such emitters are technologically useful, because they can be easily fabricated on large substrates, and the synthesis process is simple and broadly applicable. The findings conceptually provide new opportunities for the application of Al4C3 ceramic material in vacuum microelectronic devices.

Production of Sporotrichum thermophile xylanase by solid state fermentation utilizing deoiled Jatropha curcas seed cake and its application in xylooligosachharide synthesis.

PubMed

Sadaf, Ayesha; Khare, S K

2014-02-01

De-oiled Jatropha curcas seed cake, a plentiful by-product of biodiesel industry was used as substrate for the production of a useful xylanase from Sporotrichum thermophile in solid state fermentation. Under the optimized conditions, 1025U xylanase/g (deoiled seed cake) was produced. The xylanase exhibited half life of 4h at 45°C and 71.44min at 50°C respectively. It was stable in a broad pH range of 7.0-11.0. Km and Vmax were 12.54mg/ml and 454.5U/ml/min respectively. S. thermophile xylanase is an endoxylanase free of exoxylanase activity, hence advantageous for xylan hydrolysis to produce xylooligosachharides. Hydrolysis of oat spelt xylan by S. thermophile xylanase yielded 73% xylotetraose, 15.4% xylotriose and 10% xylobiose. The S. thermophile endoxylanase thus seem potentially useful in the food industries. Copyright © 2013 Elsevier Ltd. All rights reserved.

Topologically knotted deubiquitinases exhibit unprecedented mechanostability to withstand the proteolysis by an AAA+ protease.

PubMed

Sriramoju, Manoj Kumar; Chen, Yen; Lee, Yun-Tzai Cloud; Hsu, Shang-Te Danny

2018-05-04

More than one thousand knotted protein structures have been identified so far, but the functional roles of these knots remain elusive. It has been postulated that backbone entanglement may provide additional mechanostability. Here, we employed a bacterial proteasome, ClpXP, to mechanically unfold 5 2 -knotted human ubiquitin C-terminal hydrolase (UCH) paralogs from their C-termini, followed by processive translocation into the proteolytic chamber for degradation. Our results revealed unprecedentedly slow kinetics of ClpXP-mediated proteolysis for the proteasome-associated UCHL5: ten thousand times slower than that of a green fluorescence protein (GFP), which has a comparable size to the UCH domain but much higher chemical and thermal stabilities. The ClpXP-dependent mechanostability positively correlates with the intrinsic unfolding rates of the substrates, spanning over several orders of magnitude for the UCHs. The broad range of mechanostability within the same protein family may be associated with the functional requirements for their differential malleabilities.

Interferometric 2D Sum Frequency Generation Spectroscopy Reveals Structural Heterogeneity of Catalytic Monolayers on Transparent Materials.

PubMed

Vanselous, Heather; Stingel, Ashley M; Petersen, Poul B

2017-02-16

Molecular monolayers exhibit structural and dynamical properties that are different from their bulk counterparts due to their interaction with the substrate. Extracting these distinct properties is crucial for a better understanding of processes such as heterogeneous catalysis and interfacial charge transfer. Ultrafast nonlinear spectroscopic techniques such as 2D infrared (2D IR) spectroscopy are powerful tools for understanding molecular dynamics in complex bulk systems. Here, we build on technical advancements in 2D IR and heterodyne-detected sum frequency generation (SFG) spectroscopy to study a CO 2 reduction catalyst on nanostructured TiO 2 with interferometric 2D SFG spectroscopy. Our method combines phase-stable heterodyne detection employing an external local oscillator with a broad-band pump pulse pair to provide the first high spectral and temporal resolution 2D SFG spectra of a transparent material. We determine the overall molecular orientation of the catalyst and find that there is a static structural heterogeneity reflective of different local environments at the surface.

Large area nanoscale metal meshes for use as transparent conductive layers.

PubMed

Jin, Yuanhao; Li, Qunqing; Chen, Mo; Li, Guanhong; Zhao, Yudan; Xiao, Xiaoyang; Wang, Jiaping; Jiang, Kaili; Fan, Shoushan

2015-10-21

We report on the experimental realization of using super-aligned carbon nanotubes (SACNTs) as etching masks for the fabrication of large area nanoscale metal meshes. This method can easily be extended to different metals on both rigid and flexible substrates. The as-fabricated metal meshes, including the ones made of gold, copper, and aluminum, are suitable for use as transparent conductive layers (TCLs). The metal meshes, which are similar to the SACNT networks in their dimensional features of tens of nanometers, exhibit compatible performance in terms of optical transmittance and sheet resistance. Moreover, because the metal meshes are fabricated as an integrated material, there is no junction resistance between the interconnected metal nanostructures, which markedly lowers their sheet resistance at high temperatures. The fabrication of such an effective etching mask involves a simple drawing process of the SACNT networks prepared and a common deposition process. This approach should be easy to extend to various research fields and has broad prospects in commercial applications.

Chlorodifluoromethane-triggered formation of difluoromethylated arenes catalysed by palladium

NASA Astrophysics Data System (ADS)

Feng, Zhang; Min, Qiao-Qiao; Fu, Xia-Ping; An, Lun; Zhang, Xingang

2017-09-01

Difluoromethylated aromatic compounds are of increasing importance in pharmaceuticals, agrochemicals and materials. Chlorodifluoromethane (ClCF2H), an inexpensive, abundant and widely used industrial raw material, represents the ideal and most straightforward difluoromethylating reagent, but introduction of the difluoromethyl group (CF2H) from ClCF2H into aromatics has not been reported. Here, we describe a direct palladium-catalysed difluoromethylation method for coupling ClCF2H with arylboronic acids and esters to generate difluoromethylated arenes with high efficiency. The reaction exhibits a remarkably broad substrate scope, including heteroarylboronic acids, and was used for difluoromethylation of a range of pharmaceuticals and biologically active compounds. Preliminary mechanistic studies revealed that a palladium difluorocarbene intermediate is involved in the reaction. Although numerous metal-difluorocarbene complexes have been prepared, the catalytic synthesis of difluoromethylated or difluoromethylenated compounds involving metal-difluorocarbene complexes has not received much attention. This new reaction therefore also opens the door to understand metal-difluorocarbene complex catalysed reactions.

Light Management in Flexible Glass by Wood Cellulose Coating

PubMed Central

Fang, Zhi-Qiang; Zhu, Hong-Li; Li, Yuan-Yuan; Liu, Zhen; Dai, Jia-Qi; Preston, Colin; Garner, Sean; Cimo, Pat; Chai, Xin-Sheng; Chen, Gang; Hu, Liang-Bing

2014-01-01

Ultra-thin flexible glass with high transparency is attractive for a broad range of display applications; however, substrates with low optical haze are not ideal for thin film solar cells, since most of the light will go through the semiconductor layer without scattering, and the length of light travelling path in the active layer is small. By simply depositing a layer of TEMPO (2,2,6,6-tetramethylpiperidine-1-oxyl radical)-oxidized wood fibers (TOWFs), we are able to tailor the optical properties of flexible glass dramatically from exhibiting low haze (<1%) to high haze (~56%) without compromising the total forward transmittance (~90%). The influence of the TOWFs morphology on the optical properties of TOWFs-coated flexible glass is investigated. As the average fiber length decreases, the transmission haze of TOWF-coated flexible glass illustrates a decreasing trend. Earth-abundant natural materials for transparent, hazy, and flexible glass have tremendous applicability in the fabrication of flexible optoelectronics with tunable light scattering effects by enabling inexpensive and large-scale processes. PMID:25068486

Effect of annealing on morphology and photoluminescence of beta-Ga2O3 nanostructures.

PubMed

Zhang, Shiying; Zhuang, Huizhao; Xue, Chengshan; Li, Baoli

2008-07-01

A novel method was applied to prepare one-dimensional beta-Ga2O3 nanostructure films. In this method, beta-Ga2O3 nanostructures have been successfully synthesized on Si(111) substrates through annealing sputtered Ga22O3/Mo films for differernt time under flowing ammonia. The as-synthesized beta-Ga2O3 nanostructures were characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM) and photoluminescence (PL) spectrum. The results show that the formed nanostructures are single-crystalline Ga2O3 with monoclinic structure. The annealing time of the samples has an evident influence on the morphology and optical property of the nanostructured beta-Ga2O3 synthesized. The representative photoluminescence spectrum at room temperature exhibits a strong and broad emission band centered at 411.5 nm and a relatively weak emission peak located at 437.6 nm. The growth mechanism of the beta-Ga2O3 nanostructured materials is also discussed briefly.

Some Properties of Extracellular Acetylxylan Esterase Produced by the Yeast Rhodotorula mucilaginosa†

PubMed Central

Lee, Hung; To, Rebecca J. B.; Latta, Roger K.; Biely, Peter; Schneider, Henry

1987-01-01

The red yeast Rhodotorula mucilaginosa produced an esterase that accumulated in the culture supernatant on induction with triacetin. The enzyme was specific for substrates bearing an O-acetyl group, but was relatively nonspecific for the rest of the molecule, which could consist of a phenol, a monosaccharide, a polysaccharide, or an aliphatic alcohol. The esterase was more active against acetylxylan and glucose β-d-pentaacetate than were a number of esterases from plant and animal sources, when activities on 4-nitrophenyl acetate were compared. The enzyme exhibited Michaelis-Menten kinetics and was active over a broad pH range (5.5 to 9.2), with an optimum between pH 8 and 10. In addition, the enzyme retained its activity for 2 h at 55°C. The yeast that produced the enzyme did not produce xylanase and, hence, is of interest for the production of acetylxylan esterase that is free of xylanolytic activity. PMID:16347498

Plasmonic hole arrays for combined photon and electron management

DOE PAGES

Liapis, Andreas C.; Sfeir, Matthew Y.; Black, Charles T.

2016-11-14

Material architectures that balance optical transparency and electrical conductivity are highly sought after for thin-film device applications. However, these are competing properties, since the electronic structure that gives rise to conductivity typically also leads to optical opacity. Nanostructured metal films that exhibit extraordinary optical transmission, while at the same time being electrically continuous, offer considerable flexibility in the design of their transparency and resistivity. In this paper, we present design guidelines for metal films perforated with arrays of nanometer-scale holes, discussing the consequences of the choice of nanostructure dimensions, of the type of metal, and of the underlying substrate onmore » their electrical, optical, and interfacial properties. We experimentally demonstrate that such films can be designed to have broad-band optical transparency while being an order of magnitude more conductive than indium tin oxide. Finally, prototypical photovoltaic devices constructed with perforated metal contacts convert ~18% of the incident photons, compared to <1% for identical devices having contacts without the hole array.« less

Lanthanum tricyanide-catalyzed acyl silane-ketone benzoin additions.

PubMed

Tarr, James C; Johnson, Jeffrey S

2009-09-03

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

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

NASA Astrophysics Data System (ADS)

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

2017-07-01

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

Fully integrated carbon nanotube composite thin film strain sensors on flexible substrates for structural health monitoring

NASA Astrophysics Data System (ADS)

Burton, A. R.; Lynch, J. P.; Kurata, M.; Law, K. H.

2017-09-01

Multifunctional thin film materials have opened many opportunities for novel sensing strategies for structural health monitoring. While past work has established methods of optimizing multifunctional materials to exhibit sensing properties, comparatively less work has focused on their integration into fully functional sensing systems capable of being deployed in the field. This study focuses on the advancement of a scalable fabrication process for the integration of multifunctional thin films into a fully integrated sensing system. This is achieved through the development of an optimized fabrication process that can create a broad range of sensing systems using multifunctional materials. A layer-by-layer deposited multifunctional composite consisting of single walled carbon nanotubes (SWNT) in a polyvinyl alcohol and polysodium-4-styrene sulfonate matrix are incorporated with a lithography process to produce a fully integrated sensing system deposited on a flexible substrate. To illustrate the process, a strain sensing platform consisting of a patterned SWNT-composite thin film as a strain-sensitive element within an amplified Wheatstone bridge sensing circuit is presented. Strain sensing is selected because it presents many of the design and processing challenges that are core to patterning multifunctional thin film materials into sensing systems. Strain sensors fabricated on a flexible polyimide substrate are experimentally tested under cyclic loading using standard four-point bending coupons and a partial-scale steel frame assembly under lateral loading. The study reveals the material process is highly repeatable to produce fully integrated strain sensors with linearity and sensitivity exceeding 0.99 and 5 {{V}}/{ε }, respectively. The thin film strain sensors are robust and are capable of high strain measurements beyond 3000 μ {ε }.

The Crystal Structure of the Ring-Hydroxylating Dioxygenase from Sphingomonas CHY-1

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

Jakoncic,J.; Jouanneau, Y.; Meyer, C.

The ring-hydroxylating dioxygenase (RHD) from Sphingomonas CHY-1 is remarkable due to its ability to initiate the oxidation of a wide range of polycyclic aromatic hydrocarbons (PAHs), including PAHs containing four- and five-fused rings, known pollutants for their toxic nature. Although the terminal oxygenase from CHY-1 exhibits limited sequence similarity with well characterized RHDs from the naphthalene dioxygenase family, the crystal structure determined to 1.85 {angstrom} by molecular replacement revealed the enzyme to share the same global {alpha}{sub 3}{beta}{sub 3} structural pattern. The catalytic domain distinguishes itself from other bacterial non-heme Rieske iron oxygenases by a substantially larger hydrophobic substrate bindingmore » pocket, the largest ever reported for this type of enzyme. While residues in the proximal region close to the mononuclear iron atom are conserved, the central region of the catalytic pocket is shaped mainly by the side chains of three amino acids, Phe350, Phe404 and Leu356, which contribute to the rather uniform trapezoidal shape of the pocket. Two flexible loops, LI and LII, exposed to the solvent seem to control the substrate access to the catalytic pocket and control the pocket length. Compared with other naphthalene dioxygenases residues Leu223 and Leu226, on loop LI, are moved towards the solvent, thus elongating the catalytic pocket by at least 2 {angstrom}. An 11 {angstrom} long water channel extends from the interface between the {alpha} and {beta} subunits to the catalytic site. The comparison of these structures with other known oxygenases suggests that the broad substrate specificity presented by the CHY-1 oxygenase is primarily due to the large size and particular topology of its catalytic pocket and provided the basis for the study of its reaction mechanism.« less

Expanding the Catalytic Triad in Epoxide Hydrolases and Related Enzymes.

PubMed

Amrein, Beat A; Bauer, Paul; Duarte, Fernanda; Janfalk Carlsson, Åsa; Naworyta, Agata; Mowbray, Sherry L; Widersten, Mikael; Kamerlin, Shina C L

2015-10-02

Potato epoxide hydrolase 1 exhibits rich enantio- and regioselectivity in the hydrolysis of a broad range of substrates. The enzyme can be engineered to increase the yield of optically pure products as a result of changes in both enantio- and regioselectivity. It is thus highly attractive in biocatalysis, particularly for the generation of enantiopure fine chemicals and pharmaceuticals. The present work aims to establish the principles underlying the activity and selectivity of the enzyme through a combined computational, structural, and kinetic study using the substrate trans -stilbene oxide as a model system. Extensive empirical valence bond simulations have been performed on the wild-type enzyme together with several experimentally characterized mutants. We are able to computationally reproduce the differences between the activities of different stereoisomers of the substrate and the effects of mutations of several active-site residues. In addition, our results indicate the involvement of a previously neglected residue, H104, which is electrostatically linked to the general base H300. We find that this residue, which is highly conserved in epoxide hydrolases and related hydrolytic enzymes, needs to be in its protonated form in order to provide charge balance in an otherwise negatively charged active site. Our data show that unless the active-site charge balance is correctly treated in simulations, it is not possible to generate a physically meaningful model for the enzyme that can accurately reproduce activity and selectivity trends. We also expand our understanding of other catalytic residues, demonstrating in particular the role of a noncanonical residue, E35, as a "backup base" in the absence of H300. Our results provide a detailed view of the main factors driving catalysis and regioselectivity in this enzyme and identify targets for subsequent enzyme design efforts.

Solution NMR characterization of magnetic/electronic properties of azide and cyanide-inhibited substrate complexes of human heme oxygenase: implications for steric ligand tilt.

PubMed

Peng, Dungeng; Ogura, Hiroshi; Ma, Li-Hua; Evans, John P; de Montellano, Paul R Ortiz; La Mar, Gerd N

2013-04-01

Solution 2D (1)H NMR was carried out on the azide-ligated substrate complex of human heme oxygenase, hHO, to provide information on the active site molecular structure, chromophore electronic/magnetic properties, and the distal H-bond network linked to the exogenous ligand by catalytically relevant oriented water molecules. While 2D NMR exhibited very similar patterns of two-dimensional nuclear Overhauser spectroscopy cross peaks of residues with substrate and among residues as the previously characterized cyanide complex, significant, broadly distributed chemical shift differences were observed for both labile and non-labile protons. The anisotropy and orientation of the paramagnetic susceptibility tensor, χ, were determined for both the azide and cyanide complexes. The most significant difference observed is the tilt of the major magnetic axes from the heme normal, which is only half as large for the azide than cyanide ligand, with each ligand tilted toward the catalytically cleaved α-meso position. The difference in chemical shifts is quantitatively correlated with differences in dipolar shifts in the respective complexes for all but the distal helix. The necessity of considering dipolar shifts, and hence determination of the orientation/anisotropy of χ, in comparing chemical shifts involving paramagnetic complexes, is emphasized. The analysis shows that the H-bond network cannot detect significant differences in H-bond acceptor properties of cyanide versus azide ligands. Lastly, significant retardation of distal helix labile proton exchange upon replacing cyanide with azide indicates that the dynamic stability of the distal helix is increased upon decreasing the steric interaction of the ligand with the distal helix. Copyright © 2013. Published by Elsevier Inc.

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

PubMed

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

2012-03-01

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

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

PubMed

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

2012-06-01

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

[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.

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.

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.

Lanthanum Tricyanide-Catalyzed Acyl Silane-Ketone Benzoin Additions

PubMed Central

Tarr, James C.; Johnson, Jeffrey S.

2009-01-01

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

Direct transfer of graphene onto flexible substrates

PubMed Central

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

2013-01-01

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

Glutamic Acid Selective Chemical Cleavage of Peptide Bonds.

PubMed

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

2016-03-04

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

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

PubMed

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

2012-11-23

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

A High-yield Two-step Transfer Printing Method for Large-scale Fabrication of Organic Single-crystal Devices on Arbitrary Substrates

PubMed Central

Deng, Wei; Zhang, Xiujuan; Pan, Huanhuan; Shang, Qixun; Wang, Jincheng; Zhang, Xiaohong; Zhang, Xiwei; Jie, Jiansheng

2014-01-01

Single-crystal organic nanostructures show promising applications in flexible and stretchable electronics, while their applications are impeded by the large incompatibility with the well-developed photolithography techniques. Here we report a novel two-step transfer printing (TTP) method for the construction of organic nanowires (NWs) based devices onto arbitrary substrates. Copper phthalocyanine (CuPc) NWs are first transfer-printed from the growth substrate to the desired receiver substrate by contact-printing (CP) method, and then electrode arrays are transfer-printed onto the resulting receiver substrate by etching-assisted transfer printing (ETP) method. By utilizing a thin copper (Cu) layer as sacrificial layer, microelectrodes fabricated on it via photolithography could be readily transferred to diverse conventional or non-conventional substrates that are not easily accessible before with a high transfer yield of near 100%. The ETP method also exhibits an extremely high flexibility; various electrodes such as Au, Ti, and Al etc. can be transferred, and almost all types of organic devices, such as resistors, Schottky diodes, and field-effect transistors (FETs), can be constructed on planar or complex curvilinear substrates. Significantly, these devices can function properly and exhibit closed or even superior performance than the device counterparts fabricated by conventional approach. PMID:24942458

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

PubMed Central

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

2011-01-01

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

Enhanced flux of substrates into polyamine biosynthesis but not ethylene in tomato fruit engineered with yeast S-adenosylmethionine decarboxylase gene

Treesearch

Yi Lasanajak; Rakesh Minocha; Subhash C. Minocha; Ravinder Goyal; Tahira Fatima; Avtar K. Handa; Autar K. Mattoo

2014-01-01

S-adenosylmethionine (SAM), a major substrate in 1-C metabolism is a common precursor in the biosynthetic pathways of polyamines and ethylene, two important plant growth regulators, which exhibit opposing developmental effects, especially during fruit ripening. However, the flux of various substrates including SAM into the two competing pathways in...

Quantitative isotope incorporation reveals substrate partitioning in a coastal microbial community.

PubMed

Mayali, Xavier; Weber, Peter K

2018-05-01

To quantitatively link microbial identity with biogeochemical function, we carried out 14 simultaneous stable isotope probing experiments with organic and inorganic C and N substrates to measure the isotope incorporation by over one hundred co-occurring eukaryotic and prokaryotic populations in a coastal community. We found that nitrate was the most commonly incorporated substrate, and that light-driven carbon fixation was carried out by some bacterial taxa from the Flavobacteriales and OM60 (NOR5) clade, in addition to photoautotrophic phytoplankton. We found that organisms that incorporated starch, maltose, glucose, lactose and bicarbonate were phylogenetically clustered, suggesting that specific bacterial lineages specialized in the incorporation of these substrates. The data further revealed that coastal microorganisms spanned a range of resource utilization strategies from generalists to specialists and demonstrated a high level of substrate partitioning, with two thirds of taxa exhibiting unique substrate incorporation patterns and the remaining third shared by no more than three OTUs each. Specialists exhibited more extreme incorporation levels (high or low), whereas generalists displayed more intermediate activity levels. These results shed valuable insights into the bottom-up ecological strategies enabling the persistence of high microbial diversity in aquatic ecosystems.

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

NASA Astrophysics Data System (ADS)

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

2016-07-01

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

Allosteric regulation of rhomboid intramembrane proteolysis.

PubMed

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

2014-09-01

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

Allosteric regulation of rhomboid intramembrane proteolysis

PubMed Central

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

2014-01-01

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

Enzyme specificity under dynamic control

NASA Astrophysics Data System (ADS)

Ota, Nobuyuki; Agard, David A.

2002-03-01

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

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

PubMed

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

2014-09-01

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

Structural and kinetic properties of a novel purple acid phosphatase from phosphate-starved tomato (Lycopersicon esculentum) cell cultures.

PubMed Central

Bozzo, Gale G; Raghothama, Kashchandra G; Plaxton, William C

2004-01-01

An intracellular acid phosphatase (IAP) from P(i)-starved (-P(i)) tomato ( Lycopersicon esculentum ) suspension cells has been purified to homogeneity. IAP is a purple acid phosphatase (PAP), as the purified protein was violet in colour (lambda(max)=546 nm) and was insensitive to L-tartrate. PAGE, periodic acid-Schiff staining and peptide mapping demonstrated that the enzyme exists as a 142 kDa heterodimer composed of an equivalent ratio of glycosylated and structurally dissimilar 63 (alpha-subunit) and 57 kDa (beta-subunit) polypeptides. However, the nine N-terminal amino acids of the alpha- and beta-subunits were identical, exhibiting similarity to the deduced N-terminal portions of several putative plant PAPs. Quantification of immunoblots probed with rabbit anti-(tomato acid phosphatase) immune serum revealed that the 4-fold increase in IAP activity due to P(i)-deprivation was correlated with similar increases in the amount of antigenic IAP alpha- and beta-subunits. IAP displayed optimal activity at pH 5.1, was activated 150% by 10 mM Mg(2+), but was potently inhibited by Zn(2+), Cu(2+), Fe(3+), molybdate, vanadate, fluoride and P(i). Although IAP demonstrated broad substrate selectivity, its specificity constant ( V (max)/ K (m)) with phosphoenolpyruvate was >250% greater than that obtained with any other substrate. IAP exhibited significant peroxidase activity, which was optimal at pH 9.0 and insensitive to Mg(2+) or molybdate. This IAP is proposed to scavenge P(i) from intracellular phosphate esters in -P(i) tomato. A possible secondary IAP role in the metabolism of reactive oxygen species is discussed. IAP properties are compared with those of two extracellular PAP isoenzymes that are secreted into the medium of -P(i) tomato cells [Bozzo, Raghothama and Plaxton (2002) Eur. J. Biochem. 269, 6278-6286]. PMID:14521509

Purification and characterization of xylitol dehydrogenase with l-arabitol dehydrogenase activity from the newly isolated pentose-fermenting yeast Meyerozyma caribbica 5XY2.

PubMed

Sukpipat, Wiphat; Komeda, Hidenobu; Prasertsan, Poonsuk; Asano, Yasuhisa

2017-01-01

Meyerozyma caribbica strain 5XY2, which was isolated from an alcohol fermentation starter in Thailand, was found to catabolize l-arabinose as well as d-glucose and d-xylose. The highest production amounts of ethanol from d-glucose, xylitol from d-xylose, and l-arabitol from l-arabinose were 0.45 g/g d-glucose, 0.60 g/g d-xylose, and 0.61 g/g l-arabinose with 21.7 g/L ethanol, 20.2 g/L xylitol, and 30.3 g/l l-arabitol, respectively. The enzyme with l-arabitol dehydrogenase (LAD) activity was purified from the strain and found to exhibit broad specificity to polyols, such as xylitol, d-sorbitol, ribitol, and l-arabitol. Xylitol was the preferred substrate with K m =16.1 mM and k cat /K m =67.0 min -1 mM -1 , while l-arabitol was also a substrate for the enzyme with K m =31.1 mM and k cat /K m =6.5 min -1  mM -1 . Therefore, this enzyme from M. caribbica was named xylitol dehydrogenase (McXDH). McXDH had an optimum temperature and pH at 40°C and 9.5, respectively. The McXDH gene included a coding sequence of 1086 bp encoding a putative 362 amino acid protein of 39 kDa with an apparent homopentamer structure. Native McXDH and recombinant McXDH exhibited relative activities toward l-arabitol of approximately 20% that toward xylitol, suggesting the applicability of this enzyme with the functions of XDH and LAD to the development of pentose-fermenting Saccharomyces cerevisiae. Copyright © 2016 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Isolation and characterization of Bacillus subtilis strain BY-3, a thermophilic and efficient cellulase-producing bacterium on untreated plant biomass.

PubMed

Meng, F; Ma, L; Ji, S; Yang, W; Cao, B

2014-09-01

Bioconversion of biomass, particularly crop wastes, into biofuels is being developed as an alternative approach in meeting the high energy demand. In this study, a thermophilic bacterial strain BY-3 that exhibits cellulolytic potential was isolated from faecal samples of Tibetan pigs; this strain was identified as Bacillus subtilis. The strain can produce cellulase when grown on various substrates, including carboxymethyl cellulose, rice straw, corn stover, soluble starch and wheat bran. The maximum cellulase activity of the strain was up to 4·323 ± 0·065 U ml(-1) when cultivated in the medium containing corn stover (30 g l(-1) ) for 24 h. The results demonstrated that corn stover is the most suitable substrate for cellulase production by the strain BY-3. The crude cellulase of strain BY-3 was most active at pH 5·5 and 60°C, and the enzyme in acetate buffer (50 mmol l(-1) ) demonstrated a good stability at 60°C for at least 1 h. The crude cellulase exhibited a strong antibacterial activity against Staphylococcus aureus. The strain can be used in cost-efficient cellulase production for bioconversion of agricultural residual biomass into biofuels. The increased consumption of fossil fuels has caused serious energy crisis and environmental problem. Thus, an alternative energy source is necessary. Bioconversion of biomass, particularly agricultural residuals, into value-added bioproducts, such as biofuels and chemical solvents, has received considerable attention. In this study, the newly isolated thermophilic Bacillus subtilis strain BY-3 produces cellulase efficiently with the use of untreated corn stover as a sole carbon source. This strain possesses the thermostable cellulase that is active with diverse crop wastes with a broad pH range and is a highly promising candidate for agricultural waste management. © 2014 The Society for Applied Microbiology.

On sub-T(g) dewetting of nanoconfined liquids and autophobic dewetting of crystallites.

PubMed

Souda, Ryutaro

2012-03-28

The glass transition temperature (T(g)) of thin films is reduced by nanoconfinement, but it is also influenced by the free surface and substrate interface. To gain more insights into their contributions, dewetting behaviors of n-pentane, 3-methylpentane, and toluene films are investigated on various substrates as functions of temperature and film thickness. It is found that monolayers of these molecules exhibit sub-T(g) dewetting on a perfluoro-alkyl modified Ni substrate, which is attributable to the evolution of a 2D liquid. The onset temperature of dewetting increases with film thickness because fluidity evolves via cooperative motion of many molecules; sub-T(g) dewetting is observed for films thinner than 5 monolayers. In contrast, monolayers wet substrates of graphite, silicon, and amorphous solid water until crystallization occurs. The crystallites exhibit autophobic dewetting on the substrate covered with a wetting monolayer. The presence of premelting layers is inferred from the fact that n-pentane crystallites disappear on amorphous solid water via intermixing. Thus, the properties of quasiliquid formed on the crystallite surface differ significantly from those of the 2D liquid formed before crystallization.

Multifunctional epitaxial systems on silicon substrates

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

Singamaneni, Srinivasa Rao, E-mail: ssingam@ncsu.edu; Materials Science Division, Army Research Office, Research Triangle Park, North Carolina 27709; Department of Physics, The University of Texas at El Paso, El Paso, Texas 79968

2016-09-15

Multifunctional heterostructures can exhibit a wide range of functional properties, including colossal magneto-resistance, magnetocaloric, and multiferroic behavior, and can display interesting physical phenomena including spin and charge ordering and strong spin-orbit coupling. However, putting this functionality to work remains a challenge. To date, most of the work reported in the literature has dealt with heterostructures deposited onto closely lattice matched insulating substrates such as DyScO{sub 3}, SrTiO{sub 3} (STO), or STO buffered Si(100) using concepts of lattice matching epitaxy (LME). However, strain in heterostructures grown by LME is typically not fully relaxed and the layers contain detrimental defects such asmore » threading dislocations that can significantly degrade the physical properties of the films and adversely affect the device characteristics. In addition, most of the substrates are incompatible with existing CMOS-based technology, where Si (100) substrates dominate. This review discusses recent advances in the integration of multifunctional oxide and non-oxide materials onto silicon substrates. An alternative thin film growth approach, called “domain matching epitaxy,” is presented which identifies approaches for minimizing lattice strain and unwanted defects in large misfit systems (7%–25% and higher). This approach broadly allows for the integration of multifunctional materials onto silicon substrates, such that sensing, computation, and response functions can be combined to produce next generation “smart” devices. In general, pulsed laser deposition has been used to epitaxially grow these materials, although the concepts developed here can be extended to other deposition techniques, as well. It will be shown that TiN and yttria-stabilized zirconia template layers provide promising platforms for the integration of new functionality into silicon-based computer chips. This review paper reports on a number of thin-film heterostructure systems that span a variety of ferroelectric, multiferroic, magnetic, photocatalytic, and smart materials. Their properties have been extensively investigated and their functionality found to be comparable to films grown on single-crystal oxide substrates previously reported by researchers in this field. In addition, this review explores the utility of using laser processing to introduce stable defects in a controlled way and induce magnetism and engineer the optical and electrical properties of nonmagnetic oxides such as BaTiO{sub 3}, VO{sub 2}, NiO, and TiO{sub 2} as an alternative for incorporating additional magnetic and conducting layers into the structure. These significant materials advancements herald a flurry of exciting new advances in CMOS-compatible multifunctional devices.« less

Heavy Ion Current Transients in SiGe HBTs

NASA Technical Reports Server (NTRS)

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

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

Schmidtbauer, Jan; Bansen, Roman; Heimburger, Robert

Germanium nanowires (NWs) were grown onto Ge(111) substrates by the vapor-liquid-solid process using gold droplets. The growth was carried out in a molecular beam epitaxy chamber at substrate temperatures between 370 Degree-Sign C and 510 Degree-Sign C. The resulting nanowire growth rate turns out to be highly dependent on the substrate temperature exhibiting the maximum at T = 430 Degree-Sign C. The temperature dependence of growth rate can be attributed to surface diffusion both along the substrate and nanowire sidewalls. Analyzing the diffusive material transport yields a diffusion length of 126 nm at a substrate temperature of 430 Degree-Sign C.

Method for forming metallic silicide films on silicon substrates by ion beam deposition

DOEpatents

Zuhr, Raymond A.; Holland, Orin W.

1990-01-01

Metallic silicide films are formed on silicon substrates by contacting the substrates with a low-energy ion beam of metal ions while moderately heating the substrate. The heating of the substrate provides for the diffusion of silicon atoms through the film as it is being formed to the surface of the film for interaction with the metal ions as they contact the diffused silicon. The metallic silicide films provided by the present invention are contaminant free, of uniform stoichiometry, large grain size, and exhibit low resistivity values which are of particular usefulness for integrated circuit production.

Thermal Stability of Silver Paste Sintering on Coated Copper and Aluminum Substrates

NASA Astrophysics Data System (ADS)

Pei, Chun; Chen, Chuantong; Suganuma, Katsuaki; Fu, Guicui

2018-01-01

The thermal stability of silver (Ag) paste sintering on coated copper (Cu) and aluminum (Al) substrates has been investigated. Instead of conventional zincating or nickel plating, magnetron sputtering was used to achieve coating with titanium (Ti) and Ag. Silicon (Si) chips were bonded to coated Cu and Al substrates using a mixture of submicron Ag flakes and particles under 250°C and 0.4 MPa for 30 min. The joints were then subject to aging testing at 250°C for duration of 200 h, 500 h, and 1000 h. Two types of joints exhibited satisfactory initial shear strength above 45 MPa. However, the shear strength of the joints on Al substrate decreased to 28 MPa after 1000 h of aging, while no shear strength decline was detected for the joints on Cu substrate. Fracture surface analysis revealed that the vulnerable points of the two types of joints were (1) the Ag layer and (2) the interface between the Ti layer and Cu substrate. Based on the results of scanning electron microscopy (SEM), energy-dispersive x-ray spectroscopy (EDS), and simulations, cracks in the Ag layer were identified as the cause of the shear strength degradation in the joints on Al substrate. The interface evolution of the joints on Cu substrate was ascribed to Cu migration and discontinuity points that initialized in the Ti layer. This study reveals that Al exhibited superior thermal stability with sintered Ag paste.

P-glycoprotein substrate transport assessed by comparing cellular and vesicular ATPase activity.

PubMed

Nervi, Pierluigi; Li-Blatter, Xiaochun; Aänismaa, Päivi; Seelig, Anna

2010-03-01

We compared the P-glycoprotein ATPase activity in inside-out plasma membrane vesicles and living NIH-MDR1-G185 cells with the aim to detect substrate transport. To this purpose we used six substrates which differ significantly in their passive influx through the plasma membrane. In cells, the cytosolic membrane leaflet harboring the substrate binding site of P-glycoprotein has to be approached by passive diffusion through the lipid membrane, whereas in inside-out plasma membrane vesicles, it is accessible directly from the aqueous phase. Compounds exhibiting fast passive influx compared to active efflux by P-glycoprotein induced similar ATPase activity profiles in cells and inside-out plasma membrane vesicles, because their concentrations in the cytosolic leaflets were similar. Compounds exhibiting similar influx as efflux induced in contrast different ATPase activity profiles in cells and inside-out vesicles. Their concentration was significantly lower in the cytosolic leaflet of cells than in the cytosolic leaflet of inside-out membrane vesicles, indicating that P-glycoprotein could cope with passive influx. P-glycoprotein thus transported all compounds at a rate proportional to ATP hydrolysis (i.e. all compounds were substrates). However, it prevented substrate entry into the cytosol only if passive influx of substrates across the lipid bilayer was in a similar range as active efflux. Copyright 2009 Elsevier B.V. All rights reserved.

Study of Nanoscale Friction Behaviors of Graphene on Gold Substrates Using Molecular Dynamics

NASA Astrophysics Data System (ADS)

Zhu, Pengzhe; Li, Rui

2018-02-01

In this paper, we investigate the friction behaviors of graphene flakes sliding on a gold substrate using molecular dynamics simulations. The effects of flake size, flake shape, relative rotation angle between flake and substrate, and crystal orientation of substrate on the friction process are thoroughly studied. It is found that under the same load, the average friction forces per atom are smaller for a bigger graphene flake, which exhibits an obvious size effect. It is also shown that flake shape is critical in determining the friction in the sliding process. The average friction forces per atom for the square flake are much bigger than those for the triangular and round flakes. Moreover, the average friction forces per atom for the triangular flake are the smallest. We also find that the orientation of graphene flake relative to gold substrate plays a vital role in the friction process. The friction forces for the graphene flake sliding along the armchair direction are much bigger than those for the flakes with rotation. In addition, it is also found that single crystalline gold substrate exhibits a significant anisotropic effect of friction, which is attributed to the anisotropic effect of potential energy corrugation. These understandings not only shed light on the underlying mechanisms of graphene flake sliding on the gold substrates but also may guide the design and fabrication of nanoscale graphene-based devices.

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

NASA Technical Reports Server (NTRS)

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

1995-01-01

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

Printable semiconductor structures and related methods of making and assembling

DOEpatents

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

2013-03-12

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

Printable semiconductor structures and related methods of making and assembling

DOEpatents

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

2011-10-18

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

Printable semiconductor structures and related methods of making and assembling

DOEpatents

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

2010-09-21

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

ZnO buffer layer for metal films on silicon substrates

DOEpatents

Ihlefeld, Jon

2014-09-16

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

High sensitivity Schottky junction diode based on monolithically grown aligned polypyrrole nanofibers: Broad range detection of m-dihydroxybenzene.

PubMed

Ameen, Sadia; Akhtar, M Shaheer; Seo, Hyung-Kee; Shin, Hyung Shik

2015-07-30

Aligned p-type polypyrrole (PPy) nanofibers (NFs) thin film was grown on n-type silicon (100) substrate by an electrochemical technique to fabricate Schottky junction diode for the efficient detection of m-dihydroxybenzene chemical. The highly dense and well aligned PPy NFs with the average diameter (∼150-200 nm) were grown on n-type Si substrate. The formation of aligned PPy NFs was confirmed by elucidating the structural, compositional and the optical properties. The electrochemical behavior of the fabricated Pt/p-aligned PPy NFs/n-silicon Schottky junction diode was evaluated by cyclovoltametry (CV) and current (I)-voltage (V) measurements with the variation of m-dihydroxybenzene concentration in the phosphate buffer solution (PBS). The fabricated Pt/p-aligned PPy NFs/n-silicon Schottky junction diode exhibited the rectifying behavior of I-V curve with the addition of m-dihydroxybenzene chemical, while a weak rectifying I-V behavior was observed without m-dihydroxybenzene chemical. This non-linear I-V behavior suggested the formation of Schottky barrier at the interface of Pt layer and p-aligned PPy NFs/n-silicon thin film layer. By analyzing the I-V characteristics, the fabricated Pt/p-aligned PPy NFs/n-silicon Schottky junction diode displayed reasonably high sensitivity ∼23.67 μAmM(-1)cm(-2), good detection limit of ∼1.51 mM with correlation coefficient (R) of ∼0.9966 and short response time (10 s). Copyright © 2015 Elsevier B.V. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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

2018-03-01

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

Colloid-Interface-Assisted Laser Irradiation of Nanocrystals Superlattices to be Scalable Plasmonic Superstructures with Novel Activities.

PubMed

Huang, Liu; Wan, Xiaodong; Rong, Hongpan; Yao, Yuan; Xu, Meng; Liu, Jia; Ji, Muwei; Liu, Jiajia; Jiang, Lan; Zhang, Jiatao

2018-04-01

High-efficient charge and energy transfer between nanocrystals (NCs) in a bottom-up assembly are hard to achieve, resulting in an obstacle in application. Instead of the ligands exchange strategies, the advantage of a continuous laser is taken with optimal wavelength and power to irradiate the film-scale NCs superlattices at solid-liquid interfaces. Owing to the Au-based NCs' surface plasmon resonance (SPR) effect, the gentle laser irradiation leads the Au NCs or Au@CdS core/shell NCs to attach each other with controlled pattern at the interfaces between solid NCs phase and liquid ethanol/ethylene glycol. A continuous wave 532 nm laser (6.68-13.37 W cm -2 ), to control Au-based superlattices, is used to form the monolayer with uniformly reduced interparticle distance followed by welded superstructures. Considering the size effect to Au NCs' melting, when decreasing the Au NCs size to ≈5 nm, stronger welding nanostructures are obtained with diverse unprecedented shapes which cannot be achieved by normal colloidal synthesis. With the help of facile scale-up and formation at solid-liquid interfaces, and a good connection of crystalline between NCs, the obtained plasmonic superstructured films that could be facilely transferred onto different substrates exhibit broad SPR absorption in the visible and near-infrared regime, enhanced electric conductivities, and wide applications as surface enhanced Raman scattering (SERS)-active substrates. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

2,4-Dinitrotoluene dioxygenase from Burkholderia sp. strain DNT: similarity to naphthalene dioxygenase.

PubMed Central

Suen, W C; Haigler, B E; Spain, J C

1996-01-01

2,4-Dinitrotoluene (DNT) dioxygenase from Burkholderia sp. strain DNT catalyzes the initial oxidation of DNT to form 4-methyl-5-nitrocatechol (MNC) and nitrite. The displacement of the aromatic nitro group by dioxygenases has only recently been described, and nothing is known about the evolutionary origin of the enzyme systems that catalyze these reactions. We have shown previously that the gene encoding DNT dioxygenase is localized on a degradative plasmid within a 6.8-kb NsiI DNA fragment (W.-C. Suen and J. C. Spain, J. Bacteriol. 175:1831-1837, 1993). We describe here the sequence analysis and the substrate range of the enzyme system encoded by this fragment. Five open reading frames were identified, four of which have a high degree of similarity (59 to 78% identity) to the components of naphthalene dioxygenase (NDO) from Pseudomonas strains. The conserved amino acid residues within NDO that are involved in cofactor binding were also identified in the gene encoding DNT dioxygenase. An Escherichia coli clone that expressed DNT dioxygenase converted DNT to MNC and also converted naphthalene to (+)-cis-(1R,2S)-dihydroxy-1,2-dihydronaphthalene. In contrast, the E. coli clone that expressed NDO did not oxidize DNT. Furthermore, the enzyme systems exhibit similar broad substrate specificities and can oxidize such compounds as indole, indan, indene, phenetole, and acenaphthene. These results suggest that DNT dioxygenase and the NDO enzyme system share a common ancestor. PMID:8759857

Purification and biochemical characterization of feruloyl esterases from Aspergillus terreus MTCC 11096.

PubMed

Kumar, C Ganesh; Kamle, Avijeet; Kamal, Ahmed

2013-01-01

Aspergillus terreus MTCC 11096 isolated from the soils of agricultural fields cultivating sweet sorghum was previously identified to produce feruloyl esterases (FAEs). The enzymes responsible for feruloyl esterase activity were purified to homogeneity and named as AtFAE-1, AtFAE-2, and AtFAE-3. The enzymes were monomeric having molecular masses of 74, 23 and 36 kDa, respectively. Active protein bands were identified by a developed pH-dependent zymogram on native PAGE. The three enzymes exhibited variation in pH tolerance ranging between pH 5-8 and thermostability of up to 55°C. Inhibition studies revealed that the serine residue was essential for feruloyl esterase activity; moreover aspartyl and glutamyl residues are not totally involved at the active site. Metal ions such as Ca(2+), K(+), and Mg(2+) stabilized the enzyme activity for all three FAEs. Kinetic data indicated that all three enzymes showed catalytic efficiencies (k(cat) /K(m)) against different synthesized alkyl and aryl esters indicating their broad substrate specificity. The peptide mass fingerprinting by MALDI/TOF-MS analysis and enzyme affinity toward methoxy and hydroxy substituents on the benzene ring revealed that the AtFAE-1 belonged to type A while AtFAE-2 and AtFAE-3 were type C FAE. The FAEs could release 65 to 90% of ferulic acid from agrowaste substrates in the presence of xylanase. © 2013 American Institute of Chemical Engineers.

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

PubMed

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

2012-05-16

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

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

NASA Astrophysics Data System (ADS)

Hoarfrost, Adrienne; Snider, Rachel; Arnosti, Carol

2017-02-01

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

Anisotropy-based crystalline oxide-on-semiconductor material

DOEpatents

McKee, Rodney Allen; Walker, Frederick Joseph

2000-01-01

A semiconductor structure and device for use in a semiconductor application utilizes a substrate of semiconductor-based material, such as silicon, and a thin film of a crystalline oxide whose unit cells are capable of exhibiting anisotropic behavior overlying the substrate surface. Within the structure, the unit cells of the crystalline oxide are exposed to an in-plane stain which influences the geometric shape of the unit cells and thereby arranges a directional-dependent quality of the unit cells in a predisposed orientation relative to the substrate. This predisposition of the directional-dependent quality of the unit cells enables the device to take beneficial advantage of characteristics of the structure during operation. For example, in the instance in which the crystalline oxide of the structure is a perovskite, a spinel or an oxide of similarly-related cubic structure, the structure can, within an appropriate semiconductor device, exhibit ferroelectric, piezoelectric, pyroelectric, electro-optic, ferromagnetic, antiferromagnetic, magneto-optic or large dielectric properties that synergistically couple to the underlying semiconductor substrate.

Ultra-Smooth, Fully Solution-Processed Large-Area Transparent Conducting Electrodes for Organic Devices

PubMed Central

Jin, Won-Yong; Ginting, Riski Titian; Ko, Keum-Jin; Kang, Jae-Wook

2016-01-01

A novel approach for the fabrication of ultra-smooth and highly bendable substrates consisting of metal grid-conducting polymers that are fully embedded into transparent substrates (ME-TCEs) was successfully demonstrated. The fully printed ME-TCEs exhibited ultra-smooth surfaces (surface roughness ~1.0 nm), were highly transparent (~90% transmittance at a wavelength of 550 nm), highly conductive (sheet resistance ~4 Ω ◻−1), and relatively stable under ambient air (retaining ~96% initial resistance up to 30 days). The ME-TCE substrates were used to fabricate flexible organic solar cells and organic light-emitting diodes exhibiting devices efficiencies comparable to devices fabricated on ITO/glass substrates. Additionally, the flexibility of the organic devices did not degrade their performance even after being bent to a bending radius of ~1 mm. Our findings suggest that ME-TCEs are a promising alternative to indium tin oxide and show potential for application toward large-area optoelectronic devices via fully printing processes. PMID:27808221

Ultra-Smooth, Fully Solution-Processed Large-Area Transparent Conducting Electrodes for Organic Devices

NASA Astrophysics Data System (ADS)

Jin, Won-Yong; Ginting, Riski Titian; Ko, Keum-Jin; Kang, Jae-Wook

2016-11-01

A novel approach for the fabrication of ultra-smooth and highly bendable substrates consisting of metal grid-conducting polymers that are fully embedded into transparent substrates (ME-TCEs) was successfully demonstrated. The fully printed ME-TCEs exhibited ultra-smooth surfaces (surface roughness ~1.0 nm), were highly transparent (~90% transmittance at a wavelength of 550 nm), highly conductive (sheet resistance ~4 Ω ◻-1), and relatively stable under ambient air (retaining ~96% initial resistance up to 30 days). The ME-TCE substrates were used to fabricate flexible organic solar cells and organic light-emitting diodes exhibiting devices efficiencies comparable to devices fabricated on ITO/glass substrates. Additionally, the flexibility of the organic devices did not degrade their performance even after being bent to a bending radius of ~1 mm. Our findings suggest that ME-TCEs are a promising alternative to indium tin oxide and show potential for application toward large-area optoelectronic devices via fully printing processes.

Ultra-Smooth, Fully Solution-Processed Large-Area Transparent Conducting Electrodes for Organic Devices.

PubMed

Jin, Won-Yong; Ginting, Riski Titian; Ko, Keum-Jin; Kang, Jae-Wook

2016-11-03

A novel approach for the fabrication of ultra-smooth and highly bendable substrates consisting of metal grid-conducting polymers that are fully embedded into transparent substrates (ME-TCEs) was successfully demonstrated. The fully printed ME-TCEs exhibited ultra-smooth surfaces (surface roughness ~1.0 nm), were highly transparent (~90% transmittance at a wavelength of 550 nm), highly conductive (sheet resistance ~4 Ω ◻ -1 ), and relatively stable under ambient air (retaining ~96% initial resistance up to 30 days). The ME-TCE substrates were used to fabricate flexible organic solar cells and organic light-emitting diodes exhibiting devices efficiencies comparable to devices fabricated on ITO/glass substrates. Additionally, the flexibility of the organic devices did not degrade their performance even after being bent to a bending radius of ~1 mm. Our findings suggest that ME-TCEs are a promising alternative to indium tin oxide and show potential for application toward large-area optoelectronic devices via fully printing processes.

Substrates suitable for deposition of superconducting thin films

DOEpatents

Feenstra, Roeland; Boatner, Lynn A.

1993-01-01

A superconducting system for the lossless transmission of electrical current comprising a thin film of superconducting material Y.sub.1 Ba.sub.2 Cu.sub.3 O.sub.7-x epitaxially deposited upon a KTaO.sub.3 substrate. The KTaO.sub.3 is an improved substrate over those of the prior art since the it exhibits small lattice constant mismatch and does not chemically react with the superconducting film.

Superconducting thin films on potassium tantalate substrates

DOEpatents

Feenstra, Roeland; Boatner, Lynn A.

1992-01-01

A superconductive system for the lossless transmission of electrical current comprising a thin film of superconducting material Y.sub.1 Ba.sub.2 Cu.sub.3 O.sub.7-x epitaxially deposited upon a KTaO.sub.3 substrate. The KTaO.sub.3 is an improved substrate over those of the prior art since the it exhibits small lattice constant mismatch and does not chemically react with the superconducting film.

Foldable graphene electronic circuits based on paper substrates.

PubMed

Hyun, Woo Jin; Park, O Ok; Chin, Byung Doo

2013-09-14

Graphene electronic circuits are prepared on paper substrates by using graphene nanoplates and applied to foldable paper-based electronics. The graphene circuits show a small change in conductance under various folding angles and maintain an electronic path on paper substrates after repetition of folding and unfolding. Foldable paper-based applications with graphene circuits exhibit excellent folding stability. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Wear Characteristics of Ni-Based Hardfacing Alloy Deposited on Stainless Steel Substrate by Laser Cladding

NASA Astrophysics Data System (ADS)

Awasthi, Reena; Limaye, P. K.; Kumar, Santosh; Kushwaha, Ram P.; Viswanadham, C. S.; Srivastava, Dinesh; Soni, N. L.; Patel, R. J.; Dey, G. K.

2015-03-01

In this study, dry sliding wear characteristics of the Ni-based hardfacing alloy (Ni-Mo-Cr-Si) deposited on stainless steel SS316L substrate by laser cladding have been presented. Dry sliding wear behavior of the laser clad layer was evaluated against two different counter bodies, AISI 52100 chromium steel (~850 VHN) and tungsten carbide ball (~2200 VHN) to study both adhesive and abrasive wear characteristics, in comparison with the substrate SS316L using ball on plate reciprocating wear tester. The wear resistance was evaluated as a function of load and sliding speed for a constant sliding amplitude and sliding distance. The wear mechanisms were studied on the basis of wear surface morphology and microchemical analysis of the wear track using SEM-EDS. Laser clad layer of Ni-Mo-Cr-Si on SS316L exhibited much higher hardness (~700 VHN) than that of substrate SS316L (~200 VHN). The laser clad layer exhibited higher wear resistance as compared to SS316L substrate while sliding against both the counterparts. However, the improvement in the wear resistance of the clad layer as compared to the substrate was much higher while sliding against AISI 52100 chromium steel than that while sliding against WC, at the same contact stress intensity.

Deposition of Cubic AlN Films on MgO (100) Substrates by Laser Molecular Beam Epitaxy

NASA Astrophysics Data System (ADS)

Mo, Z. K.; Yang, W. J.; Weng, Y.; Fu, Y. C.; He, H.; Shen, X. M.

2017-12-01

Cubic AlN (c-AlN) films were deposited on MgO (100) substrates by laser molecular beam epitaxy (LMBE) technique. The crystal structure and surface morphology of deposited films with various laser pulse energy and substrate temperature were investigated. The results indicate that c-AlN films exhibit the (200) preferred orientation, showing a good epitaxial relationship with the substrate. The surface roughness of c-AlN films increases when the laser pulse energy and substrate temperature increase. The film grown at laser pulse energy of 150 mJ and substrate temperature of 700 °C shows the best crystalline quality and relatively smooth surface.

Application Of Optical Processing For Growth Of Silicon Dioxide

DOEpatents

Sopori, Bhushan L.

1997-06-17

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

CVD diamond substrate for microelectronics. Final report

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

Burden, J.; Gat, R.

1996-11-01

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

Combination of inverted pyramidal nanovoid with silver nanoparticles to obtain further enhancement and its detection for ricin

NASA Astrophysics Data System (ADS)

Wang, Meng; Wang, Bin; Wu, Shixuan; Guo, Tingke; Li, Haoyu; Guo, Zhaoqing; Wu, Junhua; Jia, Peiyuan; Wang, Yuxia; Xu, Xiaoxuan; Wang, Yufang; Zhang, Cunzhou

2015-02-01

We have obtained the surface-enhanced Raman scattering substrate by depositing silver nanoparticles on the surface of the inverted pyramidal nanovoid in order to improve the enhance effects. Experimental results showed that the combined substrate exhibited greater enhancement than the nanovoid substrate or nanoparticles. In order to test the SERS activity of the combined substrates, Rh6G and ricin toxin were used as Raman probes. Finite element method was employed to simulate electric field and induced charge distribution of the substrates, which have been used to explore the interaction between nanoparticles and nanovoid as well as mechanism of the great enhancement.

Effect of substrate preheating treatment on the microstructure and ultrasonic cavitation erosion behavior of plasma-sprayed YSZ coatings.

PubMed

Deng, Wen; An, Yulong; Hou, Guoliang; Li, Shuangjian; Zhou, Huidi; Chen, Jianmin

2018-09-01

Inconel 718 was used as the substrate and preheated at different temperatures to deposit yttrium stabilized zirconia (denoted as YSZ) coatings by atmospheric plasma spraying. The microstructure of the as-deposited YSZ coatings and those after cavitation-erosion tests were characterized by field emission scanning electron microscopy, Raman spectroscopy, and their hardness and toughness as well as cavitation-erosion resistance were evaluated in relation to the effect of substrate preheating temperature. Results indicate that the as-deposited YSZ coatings exhibit typical layered structure and consist of columnar crystals. With the increase of the substrate preheating temperature, the compactness and cohesion strength of coatings are obviously enhanced, which result in the increases in the hardness, elastic modulus and toughness as well as cavitation-erosion resistance of the ceramic coatings therewith. Particularly, the YSZ coating deposited at a substrate preheating temperature of 800 °C exhibits the highest hardness and toughness as well as the strongest lamellar interfacial bonding and cavitation-erosion resistance (its cavitation-erosion life is as much as 8 times than that of deposited at room temperature). Copyright © 2018 Elsevier B.V. All rights reserved.

Environmentally Benign and Permanent Modifications to Prevent Biofouling on Marine and Hydrokinetic Devices

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

Zheng Zhang

2012-04-19

Semprus Biosciences is developing environmentally benign and permanent modifications to prevent biofouling on Marine and Hydrokinetic (MHK) devices. Biofouling, including growth on external surfaces by bacteria, algae, barnacles, mussels, and other marine organisms, accumulate quickly on MHK devices, causing mechanical wear and changes in performance. Biofouling on crucial components of hydrokinetic devices, such as rotors, generators, and turbines, imposes substantial mass and hydrodynamic loading with associated efficiency loss and maintenance costs. Most antifouling coatings leach toxic ingredients, such as copper and tributyltin, through an eroding process, but increasingly stringent regulation of biocides has led to interest in the development ofmore » non-biocidal technologies to control fouling. Semprus Biosciences research team is developing modifications to prevent fouling from a broad spectrum of organisms on devices of all shapes, sizes, and materials for the life of the product. The research team designed and developed betaine-based polymers as novel underwater coatings to resist the attachment of marine organisms. Different betaine-based monomers and polymers were synthesized and incorporated within various coating formulations. The formulations and application methods were developed on aluminum panels with required adhesion strength and mechanical properties. The coating polymers were chemically stable under UV, hydrolytic and oxidative environments. The sulfobetaine formulations are applicable as nonleaching and stable underwater coatings. For the first time, coating formulations modified with highly packed sulfobetaine polymers were prepared and demonstrated resistance to a broad spectrum of marine organisms. Assays for comparing nonfouling performance were developed to evaluate protein adsorption and bacteria attachment. Barnacle settlement and removal were evaluated and a 60-day field test was performed. Silicone substrates including a commercial fouling release coating were used for comparison. Compared with the unmodified silicone substrates, the sulfobetaine-modified formulations were able to exhibit a 98% reduction in fibrinogen adsorption, 97.0% (E. coli), 99.6% (S. aureus), and 99.5% (C. lytica) reduction in bacteria attachment, and 100% reduction in barnacles cyprid attachment. In addition to the significant improvement in fouling resistance of various organisms, the 60-day field test also showed an evident efficacy from visual assessment, foul rating, and fouling removal test. The research confirmed that the novel antifouling mechanism of betaine polymers provides a new avenue for marine coating development. The developed coatings out-performed currently used nontoxic underwater coatings in a broad spectrum of fouling resistance. By further developing formulations and processing methods for specific devices, the technology is ready for the next stage of development with demonstration in MHK systems.« less

Superconductive microstrip exhibiting negative differential resistivity

DOEpatents

Huebener, R.P.; Gallus, D.E.

1975-10-28

A device capable of exhibiting negative differential electrical resistivity over a range of values of current and voltage is formed by vapor- depositing a thin layer of a material capable of exhibiting superconductivity on an insulating substrate, establishing electrical connections at opposite ends of the deposited strip, and cooling the alloy into its superconducting range. The device will exhibit negative differential resistivity when biased in the current- induced resistive state.

Growth and elemental content of two tree species growing on abandoned coal fly ash basins. [Liquidambar styraciflua L. ; Platanus occidentalis

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

Carlson, C.L.; Adriano, D.C.

Differences in aboveground tissue concentrations of trace elements were assessed for sweetgum (Liquidambar styraciflua L.) and sycamore (Plantanus occidentalis L.) growing on two abandoned coal fly ash basins and a control soil. The wet basin (pH = 5.58) had originally received precipitator ash in an ash-water slurry, while the dry basin (pH = 8.26) had received both precipitator and bottom ash in dry form. In general, trees from the wet basin exhibited elevated trace element concentrations in comparison to the controls, while the dry basin trees exhibited reduced concentrations. On eof the most striking differenced in elemental concentrations among themore » ash basin and control trees was observed for Mn, with the control trees exhibiting concentrations orders of magnitude greater than the ash basin trees. Differences in foliar trace element concentrations among the sites can generally be explained by differences in substrate trace element concentrations and/or substrate pH. While trees from the wet ash basin generally had the highest trace element concentrations, these trees also attained the greatest height and diameter growth, suggesting that the elevated trace element concentrations in the wet basin substrate are not limiting the establishment of these two species. The greater height and diameter growth of the wet basin trees is presumably a result of the greater water-holding capacity of the substrate on this site. Differences in growth and tissue concentrations between sweetgum and sycamore highlight the importance of using more than one species when assessing metal toxicity or deficiency on a given substrate.« less

Switchable vanadium oxide films by a sol-gel process

NASA Astrophysics Data System (ADS)

Partlow, D. P.; Gurkovich, S. R.; Radford, K. C.; Denes, L. J.

1991-07-01

Thin polycrystalline films of VO2 and V2O3 were deposited on a variety of substrates using a sol-gel process. The orientation, microstructure, optical constants, and optical and electrical switching behavior are presented. These films exhibited sharp optical switching behavior even on an amorphous substrate such as fused silica. The method yields reproducible results and is amenable to the coating of large substrates and curved surfaces such as mirrors and lenses.

Tribological synthesis method for producing low-friction surface film coating

DOEpatents

Ajayi, Oyelayo O.; Lorenzo-Martin, Maria De La; Fenske, George R.

2016-10-25

An article of method of manufacture of a low friction tribological film on a substrate. The article includes a substrate of a steel or ceramic which has been tribologically processed with a lubricant containing selected additives and the additives, temperature, load and time of processing can be selectively controlled to bias formation of a film on the substrate where the film is an amorphous structure exhibiting highly advantageous low friction properties.

High performance and reusable SERS substrates using Ag/ZnO heterostructure on periodic silicon nanotube substrate

NASA Astrophysics Data System (ADS)

Lai, Yi-Chen; Ho, Hsin-Chia; Shih, Bo-Wei; Tsai, Feng-Yu; Hsueh, Chun-Hway

2018-05-01

Surface-enhanced Raman scattering (SERS) substrate with a higher surface area, enhanced light harvesting, multiple hot spots and strong electromagnetic field enhancements would exhibit enhanced Raman signals. Herein, the Ag nanoparticle/ZnO nanowire heterostructure decorated periodic silicon nanotube (Ag@ZnO@SiNT) substrate was proposed and fabricated. The proposed structure employed as SERS-active substrate was examined, and the results showed both the high performance in terms of high sensitivity and good reproducibility. Furthermore, the Ag@ZnO@SiNT substrate demonstrated the self-cleaning performance through the photocatalytic degradation of probed molecules upon UV-irradiation. The results showed that the proposed nanostructure had high performance, good reproducibility and reusability, and it is a promising SERS-active substrate for molecular sensing and cleaning.

Zinc-ion-dependent acid phosphatase exhibits magnesium-ion-dependent myo-inositol-1-phosphatase activity.

PubMed

Fujimoto, S; Okano, I; Tanaka, Y; Sumida, Y; Tsuda, J; Kawakami, N; Shimohama, S

1996-06-01

We have purified bovine brain Zn(2+)-dependent acid phosphatase (Zn(2+)-APase), which requires Zn2+ ions to hydrolyze the substrate p-nitrophenyl phosphate (pNPP) in an acidic environment. The substrate specificity and metal requirement of Zn(2+)-APase at a physiological pH was also studied. The enzyme exhibited hydrolytic activity on myo-inositol-1- and -2-monophosphates, 2'-adenosine monophosphate, 2'-guanosine monophosphate, and the alpha- and beta-glycerophosphates, glucose-1-phosphate, and fructose-6-phosphate in 50 mM Tris-HCl buffer (pH 7.4) in the presence of Mg2+ ions, but not on pNPP and phosphotyrosine. Zn2+, Mn2+ and Co2+ ions were less effective for activation. Among the above substrates, myo-inositol-1-phosphate was the most susceptible to hydrolysis by the enzyme in the presence of 3 mM Mg2+ ions. The enzyme exhibited an optimum pH at around 8 for myo-inositol-1-phosphate in the presence of 3 mM Mg2+ ions. The Mg(2+)-dependent myo-inositol-1-phosphatase activity of the enzyme was significantly inhibited by Li+ ions. The Zn(2+)-dependent p-nitrophenyl phosphatase activity and Mg(2+)-dependent myo-inositol-1-phosphatase activity of the purified enzyme fraction exhibited similar behavior on Sephadex G-100 and Mono Q colomns. These findings suggest that Zn(2+)-APase also exhibits Mg(2+)-dependent myo-inositol-1-phosphatase activity under physiological conditions.

Superhydrophobic hybrid inorganic-organic thiol-ene surfaces fabricated via spray-deposition and photopolymerization.

PubMed

Sparks, Bradley J; Hoff, Ethan F T; Xiong, Li; Goetz, James T; Patton, Derek L

2013-03-13

We report a simple and versatile method for the fabrication of superhydrophobic inorganic-organic thiol-ene coatings via sequential spray-deposition and photopolymerization under ambient conditions. The coatings are obtained by spray-deposition of UV-curable hybrid inorganic-organic thiol-ene resins consisting of pentaerythritol tetra(3-mercaptopropionate) (PETMP), triallyl isocyanurate (TTT), 2,4,6,8-tetramethyl-2,4,6,8-tetravinylcyclotetrasiloxane (TMTVSi), and hydrophobic fumed silica nanoparticles. The spray-deposition process and nanoparticle agglomeration/dispersion provide surfaces with hierarchical morphologies exhibiting both micro- and nanoscale roughness. The wetting behavior, dependent on the concentration of TMTVSi and hydrophobic silica nanoparticles, can be varied over a broad range to ultimately provide coatings with high static water contact angles (>150°), low contact angle hysteresis, and low roll off angles (<5°). The cross-linked thiol-ene coatings are solvent resistant, stable at low and high pH, and maintain superhydrophobic wetting behavior after extended exposure to elevated temperatures. We demonstrate the versatility of the spray-deposition and UV-cure process on a variety of substrate surfaces including glass, paper, stone, and cotton fabric.

Intrinsic and extrinsic dielectric responses of CaCu3Ti4O12 thin films

NASA Astrophysics Data System (ADS)

Rubinger, C. P. L.; Moreira, R. L.; Ribeiro, G. M.; Matinaga, F. M.; Autier Laurent, S.; Mercey, B.; Lobo, R. P. S. M.

2011-10-01

CaCu3Ti4O12 thin films were epitaxially grown on (001) LaAlO3 substrates by pulsed laser deposition under optimized growth conditions. The crystal structure and sample morphology were characterized by x-ray diffraction, AFM, TEM, ellipsometry, and Raman spectroscopy. The dielectric responses of the films were investigated in a large temperature range (5 to 375 K) by infrared reflectivity and impedance spectroscopies. The films exhibited a colossal dielectric response, with the dielectric permittivity reaching 104 at 100 Hz. The results obtained in a broad frequency range allowed us to investigate the behavior of intrinsic and extrinsic dielectric responses of this material. The room temperature centrosymmetrical cubic structure remains stable down to 5 K, though softening of the lower frequency infrared phonon modes indicates an incipient ferroelectric character. The radio frequency dielectric response reveals two relaxations of extrinsic origin, a primary higher frequency relaxation responsible for the colossal dielectric behavior and a secondary one of lower frequency. The activation energies of these processes are compatible with the presence of shallow defect levels created by oxygen vacancies.

Diversity and natural functions of antibiotics produced by beneficial and plant pathogenic bacteria.

PubMed

Raaijmakers, Jos M; Mazzola, Mark

2012-01-01

Soil- and plant-associated environments harbor numerous bacteria that produce antibiotic metabolites with specific or broad-spectrum activities against coexisting microorganisms. The function and ecological importance of antibiotics have long been assumed to yield a survival advantage to the producing bacteria in the highly competitive but resource-limited soil environments through direct suppression. Although specific antibiotics may enhance producer persistence when challenged by competitors or predators in soil habitats, at subinhibitory concentrations antibiotics exhibit a diversity of other roles in the life history of the producing bacteria. Many processes modulated by antibiotics may be inherently critical to the producing bacterium, such as the acquisition of substrates or initiation of developmental changes that will ensure survival under stressful conditions. Antibiotics may also have roles in more complex interactions, including in virulence on host plants or in shaping the outcomes of multitrophic interactions. The innate functions of antibiotics to producing bacteria in their native ecosystem are just beginning to emerge, but current knowledge already reveals a breadth of activities well beyond the historical perspective of antibiotics as weaponry in microbial conflicts.

Preferential paths in yield stress fluid flow through a porous medium

NASA Astrophysics Data System (ADS)

Guasto, Jeffrey; Waisbord, Nicolas; Stoop, Norbert; Dunkel, Jörn

2016-11-01

A broad range of biological, geological, and industrial materials with complex rheological properties are subjected to flow through porous media in applications ranging from oil recovery to food manufacturing. In this experimental study, we examine the flow of a model yield stress fluid (Carbopol micro-gel) through a quasi-2D porous medium, fabricated in a microfluidic channel. The flow is driven by applying a precisely-controlled pressure gradient and measured by particle tracking velocimetry, and our observations are complemented by a pore-network model of the yield stress fluid flow. While remaining unyielded at small applied pressure, the micro-gel begins to yield at a critical pressure gradient, exhibiting a single preferential flow path that percolates through the porous medium. As the applied pressure gradient increases, we observe a subsequent coarsening and invasion of the yielded, fluidized network. An examination of both the yielded network topology and pore-scale flow reveal that two cooperative phenomena are involved in sculpting the preferential flow paths: (1) the geometry of the porous microstructure, and (2) the adhesive surface interactions between the micro-gel and substrate. NSF CBET-1511340.

Photocrosslinkable biodegradable elastomers based on cinnamate-functionalized polyesters.

PubMed

Zhu, Congcong; Kustra, Stephen R; Bettinger, Christopher J

2013-07-01

Synthetic biodegradable elastomers are an emerging class of materials that play a critical role in supporting innovations in bioabsorbable medical implants. This paper describes the synthesis and characterization of poly(glycerol-co-sebacate)-cinnamate (PGS-CinA), a biodegradable elastomer based on hyperbranched polyesters derivatized with pendant cinnamate groups. PGS-CinA can be prepared via photodimerization in the absence of photoinitiators using monomers that are found in common foods. The resulting network exhibits a Young's modulus of 50.5-152.1kPa and a projected in vitro degradation half-life time between 90 and 140days. PGS-CinA elastomers are intrinsically cell-adherent and support rapid proliferation of fibroblasts. Spreading and proliferation of fibroblasts are loosely governed by the substrate stiffness within the range of Young's moduli in PGS-CinA networks that were prepared. The thermo-mechanical properties, biodegradability and intrinsic support of cell attachment and proliferation suggest that PGS-CinA networks are broadly applicable for use in next generation bioabsorable materials including temporary medical devices and scaffolds for soft tissue engineering. Copyright © 2013 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Isolation and characterization of a novel glycosyl hydrolase family 74 (GH74) cellulase from the black goat rumen metagenomic library.

PubMed

Song, Yun-Hee; Lee, Kyung-Tai; Baek, Jin-Young; Kim, Min-Ju; Kwon, Mi-Ra; Kim, Young-Joo; Park, Mi-Rim; Ko, Haesu; Lee, Jin-Sung; Kim, Keun-Sung

2017-05-01

This study aimed to isolate and characterize a novel cellulolytic enzyme from black goat rumen by using a culture-independent approach. A metagenomic fosmid library was constructed from black goat rumen contents and screened for a novel cellulase. The KG37 gene encoding a protein of 858 amino acid residues (92.7 kDa) was isolated. The deduced protein contained a glycosyl hydrolase family 74 (GH74) domain and showed 77% sequence identity to two endo-1,4-β-glucanases from Fibrobacter succinogenes. The novel GH74 cellulase gene was overexpressed in Escherichia coli, and its protein product was functionally characterized. The recombinant GH74 cellulase showed a broad substrate spectrum. The enzyme exhibited its optimum activity at pH 5.0 and temperature range of 20-50 °C. The enzyme was thermally stable at pH 5.0 and at a temperature of 20-40 °C. The novel GH74 cellulase can be practically exploited to convert lignocellulosic biomass to value-added products in various industrial applications in future.

S phase activation of the histone H2B promoter by OCA-S, a coactivator complex that contains GAPDH as a key component.

PubMed

Zheng, Lei; Roeder, Robert G; Luo, Yan

2003-07-25

We have isolated and functionally characterized a multicomponent Oct-1 coactivator, OCA-S which is essential for S phase-dependent histone H2B transcription. The p38 component of OCA-S binds directly to Oct-1, exhibits potent transactivation potential, is selectively recruited to the H2B promoter in S phase, and is essential for S phase-specific H2B transcription in vivo and in vitro. Surprisingly, p38 represents a nuclear form of glyceraldehyde-3-phosphate dehydrogenase, and binding to Oct-1, as well as OCA-S function, is stimulated by NAD(+) but inhibited by NADH. OCA-S also interacts with NPAT, a cyclin E/cdk2 substrate that is broadly involved in histone gene transcription. These studies thus link the H2B transcriptional machinery to cell cycle regulators, and possibly to cellular metabolic state (redox status), and set the stage for studies of the underlying mechanisms and the basis for coordinated histone gene expression and coupling to DNA replication.

Initial Study on Thin Film Preparation of Carbon Nanodots Composites as Luminescence Material

NASA Astrophysics Data System (ADS)

Iskandar, F.; Aimon, A. H.; Akmaluddin, A. R.; Nuryadin, B. W.; Abdullah, M.

2016-08-01

Nowadays, the developments of phosphors materials require elements without noble metals and simple production process. Carbon nanodots (C-dots) are one of phosphor materials with wide range of emission band, and high biocompatibility. In this research thin film carbon nanodots composite have been prepared by spin coating method. Prior deposition, powder carbon nanodots were synthesized from a mixture of commercial urea as the nitrogen sources and citric acid as a carbon source by using hydrothermal and microwave-assisted heating method. The prepared powder was dispersed in transparent epoxy resin and then coated on glass substrate. The photoluminescence result for sample with 0.035 g citric acid exhibited an intense, single, homogeneous and broad spectrum with yellowish emission upon excitation at 365 nm. The Fourier Transform Infrared Spectroscopy (FTIR) result showed the existences of C=C, C-H, C=O, N-H and O-H functional groups which confirmed the quality of the sample. Further, based on UV-Vis measurement, the prepared thin film was highly transparent (transmittance 90%) with estimated film thickness around 764 nm. This result may open an opportunity for optoelectronic devices.

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

Goldsmith, Steven Y.; Spires, Shannon V.

There are currently two proposed standards for agent communication languages, namely, KQML (Finin, Lobrou, and Mayfield 1994) and the FIPA ACL. Neither standard has yet achieved primacy, and neither has been evaluated extensively in an open environment such as the Internet. It seems prudent therefore to design a general-purpose agent communications facility for new agent architectures that is flexible yet provides an architecture that accepts many different specializations. In this paper we exhibit the salient features of an agent communications architecture based on distributed metaobjects. This architecture captures design commitments at a metaobject level, leaving the base-level design and implementationmore » up to the agent developer. The scope of the metamodel is broad enough to accommodate many different communication protocols, interaction protocols, and knowledge sharing regimes through extensions to the metaobject framework. We conclude that with a powerful distributed object substrate that supports metaobject communications, a general framework can be developed that will effectively enable different approaches to agent communications in the same agent system. We have implemented a KQML-based communications protocol and have several special-purpose interaction protocols under development.« less

Production of high activity Aspergillus niger BCC4525 β-mannanase in Pichia pastoris and its application for mannooligosaccharides production from biomass hydrolysis.

PubMed

Harnpicharnchai, Piyanun; Pinngoen, Waraporn; Teanngam, Wanwisa; Sornlake, Warasirin; Sae-Tang, Kittapong; Manitchotpisit, Pennapa; Tanapongpipat, Sutipa

2016-12-01

A cDNA encoding β-mannanase was cloned from Aspergillus niger BCC4525 and expressed in Pichia pastoris KM71. The secreted enzyme hydrolyzed locust bean gum substrate with very high activity (1625 U/mL) and a relatively high k cat /K m (461 mg -1 s -1  mL). The enzyme is thermophilic and thermostable with an optimal temperature of 70 °C and 40% retention of endo-β-1,4-mannanase activity after preincubation at 70 °C. In addition, the enzyme exhibited broad pH stability with an optimal pH of 5.5. The recombinant enzyme hydrolyzes low-cost biomass, including palm kernel meal (PKM) and copra meal, to produce mannooligosaccharides, which is used as prebiotics to promote the growth of beneficial microflora in animals. An in vitro digestibility test simulating the gastrointestinal tract system of broilers suggested that the recombinant β-mannanase could effectively liberate reducing sugars from PKM-containing diet. These characteristics render this enzyme suitable for utilization as a feed additive to improve animal performance.

Spray deposition of highly transparent fluorine doped cadmium oxide thin films

NASA Astrophysics Data System (ADS)

Deokate, R. J.; Pawar, S. M.; Moholkar, A. V.; Sawant, V. S.; Pawar, C. A.; Bhosale, C. H.; Rajpure, K. Y.

2008-01-01

The cadmium oxide (CdO) and F:CdO films have been deposited by spray pyrolysis method using cadmium acetate and ammonium fluoride as precursors for Cd and F ions, respectively. The effect of temperature and F doping on the structural, morphological, optical and Hall effect properties of sprayed CdO thin films was investigated using X-ray diffraction (XRD), scanning electron microscopy (SEM), atomic force microscopy (AFM), optical absorption and electrical measurement techniques. TGA and DTA studies, indicates the formation of CdO by decomposition of cadmium acetate after 250 °C. XRD patterns reveal that samples are polycrystalline with cubic structure and exhibits (2 0 0) preferential orientation. Considerable broading of (2 0 0) peak, simultaneous shifting of corresponding Bragg's angle have been observed with respect to F doping level. SEM and AFM show the heterogeneous distribution of cubical grains all over the substrate, which are randomly distributed. F doping shifts the optical gap along with the increase in the transparency of CdO films. The Hall effect measurement indicates that the resistivity and mobility decrease up to 4% F doping.

Novel Dehalogenase Mechanism for 2,3-Dichloro-1-Propanol Utilization in Pseudomonas putida Strain MC4

PubMed Central

Arif, Muhammad Irfan; Samin, Ghufrana; van Leeuwen, Jan G. E.; Oppentocht, Jantien

2012-01-01

A Pseudomonas putida strain (MC4) that can utilize 2,3-dichloro-1-propanol (DCP) and several aliphatic haloacids and haloalcohols as sole carbon and energy source for growth was isolated from contaminated soil. Degradation of DCP was found to start with oxidation and concomitant dehalogenation catalyzed by a 72-kDa monomeric protein (DppA) that was isolated from cell lysate. The dppA gene was cloned from a cosmid library and appeared to encode a protein equipped with a signal peptide and that possessed high similarity to quinohemoprotein alcohol dehydrogenases (ADHs), particularly ADH IIB and ADH IIG from Pseudomonas putida HK. This novel dehalogenating dehydrogenase has a broad substrate range, encompassing a number of nonhalogenated alcohols and haloalcohols. With DCP, DppA exhibited a kcat of 17 s−1. 1H nuclear magnetic resonance experiments indicated that DCP oxidation by DppA in the presence of 2,6-dichlorophenolindophenol (DCPIP) and potassium ferricyanide [K3Fe(CN)6] yielded 2-chloroacrolein, which was oxidized to 2-chloroacrylic acid. PMID:22752160

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

PubMed

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

2017-07-01

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

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.

Molecular and enzymatic characterization of alkaline lipase from Bacillus amyloliquefaciens E1PA isolated from lipid-rich food waste.

PubMed

Saengsanga, Thanakorn; Siripornadulsil, Wilailak; Siripornadulsil, Surasak

2016-01-01

Bacillus amyloliquefaciens E1PA is a lipase-producing strain that was originally isolated from lipid-rich food waste, and the production of its lipase was found to be induced by vegetable oils. The E1PA lipase was successfully expressed and secreted in a heterologous Escherichia coli host and was ultimately purified. The conserved pentapeptide motif Ala-His-Ser-Met-Gly was observed at positions 108-112. The purified recombinant lipase was stable over a pH range of 4.0-11.0 at 40 °C and exhibited maximal activity at pH 10. The recombinant E1PA lipase hydrolyzed a wide range of acyl esters (C4-C18). However, the highest activity (3.5 units mg(-1)) was observed when the p-nitrophenyl ester of myristate (C14) was used as a substrate. Compared to the lipases produced by Bacillus spp., the E1PA lipase displayed a structural molecular mass excluding the leader sequence (19.22 kDa) and a pI (9.82) that were similar to those reported for B. amyloliquefaciens lipases and lipase subfamily I.4 but that were quite distinct from those of lipase subfamily I.5 (approximately 43 kDa, pI 6). These results suggested that Bacillus lipases are closely related. Although the recombinant E1PA lipase digested only certain oils, the wild-type E1PA lipase degraded a variety of oils, including blended and re-used cooking oils. The recombinant and wild-type forms of the E1PA lipase were able to digest heterogeneous lipid-rich food waste at similar levels; this result suggests that this lipase can function even when it solely consists of its structural enzyme component. The enzyme exhibited lipid hydrolysis ability as either an intracellular domain of the recombinant protein or an extracellular domain secreted by the E1PA strain. However, the recombinant lipase showed higher activity than the wild-type E1PA lipase, indicating that the recombinant protein from E. coli possessed effective lipase activity. Thus, the inducible alkaline E1PA lipase exhibited the ability to act on a broad spectrum of substrates, and the effective form produced in the heterogeneous host can be further developed for several applications, such as biodiesel production and lipase production. Copyright © 2015 Elsevier Inc. All rights reserved.

Biochemical Characterization and Relative Expression Levels of Multiple Carbohydrate Esterases of the Xylanolytic Rumen Bacterium Prevotella ruminicola 23 Grown on an Ester-Enriched Substrate ▿ †

PubMed Central

Kabel, Mirjam A.; Yeoman, Carl J.; Han, Yejun; Dodd, Dylan; Abbas, Charles A.; de Bont, Jan A. M.; Morrison, Mark; Cann, Isaac K. O.; Mackie, Roderick I.

2011-01-01

We measured expression and used biochemical characterization of multiple carbohydrate esterases by the xylanolytic rumen bacterium Prevotella ruminicola 23 grown on an ester-enriched substrate to gain insight into the carbohydrate esterase activities of this hemicellulolytic rumen bacterium. The P. ruminicola 23 genome contains 16 genes predicted to encode carbohydrate esterase activity, and based on microarray data, four of these were upregulated >2-fold at the transcriptional level during growth on an ester-enriched oligosaccharide (XOSFA,Ac) from corn relative to a nonesterified fraction of corn oligosaccharides (AXOS). Four of the 16 esterases (Xyn10D-Fae1A, Axe1-6A, AxeA1, and Axe7A), including the two most highly induced esterases (Xyn10D-Fae1A and Axe1-6A), were heterologously expressed in Escherichia coli, purified, and biochemically characterized. All four enzymes showed the highest activity at physiologically relevant pH (6 to 7) and temperature (30 to 40°C) ranges. The P. ruminicola 23 Xyn10D-Fae1A (a carbohydrate esterase [CE] family 1 enzyme) released ferulic acid from methylferulate, wheat bran, corn fiber, and XOSFA,Ac, a corn fiber-derived substrate enriched in O-acetyl and ferulic acid esters, but exhibited negligible activity on sugar acetates. As expected, the P. ruminicola Axe1-6A enzyme, which was predicted to possess two distinct esterase family domains (CE1 and CE6), released ferulic acid from the same substrates as Xyn10D-Fae1 and was also able to cleave O-acetyl ester bonds from various acetylated oligosaccharides (AcXOS). The P. ruminicola 23 AxeA1, which is not assigned to a CE family, and Axe7A (CE7) were found to be acetyl esterases that had activity toward a broad range of mostly nonpolymeric acetylated substrates along with AcXOS. All enzymes were inhibited by the proximal location of other side groups like 4-O-methylglucuronic acid, ferulic acid, or acetyl groups. The unique diversity of carbohydrate esterases in P. ruminicola 23 likely gives it the ability to hydrolyze substituents on the xylan backbone and enhances its capacity to efficiently degrade hemicellulose. PMID:21742923

Mid-infrared tunable metamaterials

DOEpatents

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

2017-07-11

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

Mid-infrared tunable metamaterials

DOEpatents

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

2015-04-28

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

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

NASA Astrophysics Data System (ADS)

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

2017-11-01

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

Tracing the 4000 year history of organic thin films: From monolayers on liquids to multilayers on solids

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

Greene, J. E.; Linköping University, 581 83 Linköping; National Taiwan University of Science and Technology, Taipei 10607, Taiwan

The recorded history of organic monolayer and multilayer thin films spans approximately 4000 years. Fatty-acid-based monolayers were deposited on water by the ancients for applications ranging from fortune telling in King Hammurabi's time (∼1800 BC, Mesopotamia) to stilling choppy waters for sailors and divers as reported by the Roman philosopher Pliny the Elder in ∼78 AD, and then much later (1774) by the peripatetic American statesman and natural philosopher Benjamin Franklin, to Japanese “floating-ink” art (suminagashi) developed ∼1000 years ago. The modern science of organic monolayers began in the late-1800s/early-1900s with experiments by Lord Rayleigh and the important development bymore » Agnes Pockels, followed two decades later by Irving Langmuir, of the tools and technology to measure the surface tension of liquids, the surface pressure of organic monolayers deposited on water, interfacial properties, molecular conformation of the organic layers, and phase transitions which occur upon compressing the monolayers. In 1935, Katherine Blodgett published a landmark paper showing that multilayers can be synthesized on solid substrates, with controlled thickness and composition, using an apparatus now known as the Langmuir-Blodgett (L-B) trough. A disadvantage of LB films for some applications is that they form weak physisorbed bonds to the substrate. In 1946, Bigelow, Pickett, and Zisman demonstrated, in another seminal paper, the growth of organic self-assembled monolayers (SAMs) via spontaneous adsorption from solution, rather than from the water/air interface, onto SiO{sub 2} and metal substrates. SAMs are close-packed two-dimensional organic crystals which exhibit strong covalent bonding to the substrate. The first multicomponent adsorbed monolayers and multilayer SAMs were produced in the early 1980s. Langmuir monolayers, L-B multilayers, and self-assembled mono- and multilayers have found an extraordinarily broad range of applications including controlled wetting, adhesion, electrochemistry, biocompatibility, molecular recognition, biosensing, cell biology, non-linear optics, molecular electronics, solar cells, read/write/erase memory, and magnetism.« less

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.

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

PubMed

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

2018-05-10

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

The First Mammalian Aldehyde Oxidase Crystal Structure

PubMed Central

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

2012-01-01

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

Effective cleaning of hexagonal boron nitride for graphene devices.

PubMed

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

2012-09-12

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

Application of optical processing for growth of silicon dioxide

DOEpatents

Sopori, B.L.

1997-06-17

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

[Biogas production from cellulose-containing substrates: a review].

PubMed

Tsavkelova, E A; Netrusov, A I

2012-01-01

Anaerobic microbial conversion of organic substrates to various biofuels is one of the alternative energy sources attracting the greatest attention of scientists. The advantages of biogas production over other technologies are the ability of methanogenic communities to degrade a broad range of substrates and concomitant benefits: neutralization of organic waste, reduction of greenhouse gas emission, and fertilizer production. Cellulose-containing materials are a good substrate, but their full-scale utilization encounters a number of problems, including improvement of the quality and amount ofbiogas produced and maintenance of the stability and high efficiency of microbial communities. We review data on microorganisms that form methanogenic cellulolytic communities, enzyme complexes of anaerobes essential for cellulose fiber degradation, and feedstock pretreatment, as biodegradation is hindered in the presence of lignin. Methods for improving biogas production by optimization of microbial growth conditions are considered on the examples of biogas formation from various types of plant and paper materials: writing paper and cardboard.

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

NASA Astrophysics Data System (ADS)

Chen, Zhaohui

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

Biochemical characterization of a thermophilic β-mannanase from Talaromyces leycettanus JCM12802 with high specific activity.

PubMed

Wang, Caihong; Luo, Huiying; Niu, Canfang; Shi, Pengjun; Huang, Huoqing; Meng, Kun; Bai, Yingguo; Wang, Kun; Hua, Huifang; Yao, Bin

2015-02-01

Thermophilic β-mannanases are of increasing importance for wide industrial applications. In the current study, gene cloning, functional expression in Pichia pastoris, and characterization of a thermophilic β-mannanase (Man5A) from thermophilic Talaromyces leycettanus JCM12802 are reported. Deduced Man5A exhibits the highest identity with a putative β-mannanase from Talaromyces stipitatus ATCC10500 (70.3 %) and is composed of an N-terminal signal peptide, a fungal-type carbohydrate-binding module (CBM) of family 1, and a catalytic domain of glycosyl hydrolase (GH) family 5 at the C-terminus. Two recombinant proteins with different glycosylation levels, termed Man5A1 (72 kDa) and Man5A2 (60 kDa), were identified after purification. Both enzymes were thermophilic, exhibiting optimal activity at 85-90 °C, and were highly stable at 70 °C. Man5A1 and Man5A2 had a pH optimum of 4.5 and 4.0, respectively, and were highly stable over the broad pH range of 3.0-10.0. Most metal ions and sodium dodecyl sulfate (SDS) had no effect on the enzymatic activities. Man5A1 and Man5A2 exhibited high specific activity (2,160 and 1,800 U/mg, respectively) when using locust bean gum as the substrate. The CBM1 and two key residues D191 and R286 were found to affect Man5A thermostability. Man5A displays a classical four-site-binding mode, hydrolyzing mannooligosaccharides into smaller units, galactomannan into mannose and mannobiose, and glucomanman into mannose, mannobiose, and mannopentaose, respectively. All these properties make Man5A a good candidate for extensive applications in the bioconversion, pulp bleaching, textile, food, and feed industries.

Laser generation in microdisc resonators with InAs/GaAs quantum dots transferred on a silicon substrate

NASA Astrophysics Data System (ADS)

Nadtochiy, A. M.; Kryzhanovskaya, N. V.; Maximov, M. V.; Zhukov, A. E.; Moiseev, E. I.; Kulagina, M. M.; Vashanova, K. A.; Zadiranov, Yu. M.; Mukhin, I. S.; Arakcheeva, E. M.; Livshits, D.; Lipovskii, A. A.

2013-09-01

Microdisc resonators based on InAs/GaAs quantum dots separated from a GaAs substrate by selective etching and fixed to a silicon substrate by epoxy glue are studied using luminescence spectroscopy. A disc resonator 6 μm in diameter exhibits quasi-single-mode laser generation at a temperature of 78 K with a threshold power of 320 μW and λ/Δλ ˜ 27000.

ZnO deposition on metal substrates: Relating fabrication, morphology, and wettability

NASA Astrophysics Data System (ADS)

Beaini, Sara S.; Kronawitter, Coleman X.; Carey, Van P.; Mao, Samuel S.

2013-05-01

It is not common practice to deposit thin films on metal substrates, especially copper, which is a common heat exchanger metal and practical engineering material known for its heat transfer properties. While single crystal substrates offer ideal surfaces with uniform structure for compatibility with oxide deposition, metallic surfaces needed for industrial applications exhibit non-idealities that complicate the fabrication of oxide nanostructure arrays. The following study explored different ZnO fabrication techniques to deposit a (super)hydrophobic thin film of ZnO on a metal substrate, specifically copper, in order to explore its feasibility as an enhanced condensing surface. ZnO was selected for its non-toxicity, ability to be made (super)hydrophobic with hierarchical roughness, and its photoinduced hydrophilicity characteristic, which could be utilized to pattern it to have both hydrophobic-hydrophilic regions. We investigated the variation of ZnO's morphology and wetting state, using SEMs and sessile drop contact angle measurements, as a function of different fabrication techniques: sputtering, pulsed laser deposition (PLD), electrodeposition and annealing Zn. We successfully fabricated (super)hydrophobic ZnO on a mirror finish, commercially available copper substrate using the scalable electrodeposition technique. PLD for ZnO deposition did not prove viable, as the ZnO samples on metal substrates were hydrophilic and the process does not lend itself to scalability. The annealed Zn sheets did not exhibit consistent wetting state results.

The Identification of Congeners and Aliens by Drosophila Larvae.

PubMed

Del Pino, Francisco; Jara, Claudia; Pino, Luis; Medina-Muñoz, María Cristina; Alvarez, Eduardo; Godoy-Herrera, Raúl

2015-01-01

We investigated the role of Drosophila larva olfactory system in identification of congeners and aliens. We discuss the importance of these activities in larva navigation across substrates, and the implications for allocation of space and food among species of similar ecologies. Wild type larvae of cosmopolitan D. melanogaster and endemic D. pavani, which cohabit the same breeding sites, used species-specific volatiles to identify conspecifics and aliens moving toward larvae of their species. D. gaucha larvae, a sibling species of D. pavani that is ecologically isolated from D. melanogaster, did not respond to melanogaster odor cues. Similar to D. pavani larvae, the navigation of pavani female x gaucha male hybrids was influenced by conspecific and alien odors, whereas gaucha female x pavani male hybrid larvae exhibited behavior similar to the D. gaucha parent. The two sibling species exhibited substantial evolutionary divergence in processing the odor inputs necessary to identify conspecifics. Orco (Or83b) mutant larvae of D. melanogaster, which exhibit a loss of sense of smell, did not distinguish conspecific from alien larvae, instead moving across the substrate. Syn97CS and rut larvae of D. melanogaster, which are unable to learn but can smell, moved across the substrate as well. The Orco (Or83b), Syn97CS and rut loci are necessary to orient navigation by D. melanogaster larvae. Individuals of the Trana strain of D. melanogaster did not respond to conspecific and alien larval volatiles and therefore navigated randomly across the substrate. By contrast, larvae of the Til-Til strain used larval volatiles to orient their movement. Natural populations of D. melanogaster may exhibit differences in identification of conspecific and alien larvae. Larval locomotion was not affected by the volatiles.

Micro and nanocrystalline diamond formation on reticulated vitreous carbon substrate

NASA Astrophysics Data System (ADS)

Diniz, A. V.; Trava-Airoldi, V. J.; Corat, E. J.; Ferreira, N. G.

2005-10-01

High diamond nucleation and a three-dimensional growth on reticulated vitreous carbon substrate are obtained by chemical vapor deposition. Scanning electron microscopy images show continuous films covering the whole substrate including the center of 3.5 mm thick porous samples. It is evident the nanocrystalline diamond (NCD) film formation on deeper substrate regions. The grain size can vary from nano to micro scale for deposition time of 20 h. Raman spectra of sample regions closer to filaments exhibit well-defined diamond line. For central regions of sample (depth between 1.0 and 2.0 mm) Raman spectra also confirm NCD film.

Identification of Inonotus obliquus polysaccharide with broad-spectrum antiviral activity against multi-feline viruses.

PubMed

Tian, Jin; Hu, Xiaoliang; Liu, Dafei; Wu, Hongxia; Qu, Liandong

2017-02-01

Inonotus obliquus polysaccharides (IOPs) are a potential drug for the prevention and treatment of cancer, cardiopathy, diabetes, AIDs, pancreatitis and other diseases. In this study, we found that IOP can act as a broad-spectrum antiviral drug against feline viruses in the in vitro experiment. Using cell models of feline calicivirus (FCV), we demonstrated that IOP treatment was capable of exhibiting anti-FCV strain F9 activity in cell-based assays and also showed low cytotoxicity. Investigation of the mechanism of action of the compound revealed that IOP treatment induces its inhibitory actions directly on virus particles through blocking viral binding/absorpting. The inhibitory activity against other FCV isolates from China was also identified. More importantly, we found that IOP exhibited broad-spectrum antiviral activity against the feline herpesvirus 1, feline influenza virus H3N2 and H5N6, feline panleukopenia virus and feline infectious peritonitis virus that can contribute to respiratory and gastrointestinal diseases in cats. These findings suggest that IOP may be a potential broad-spectrum antiviral drug against feline viruses. Copyright © 2016 Elsevier B.V. All rights reserved.

Purification and characterization of a cobalt-activated carboxypeptidase from the hyperthermophilic archaeon Pyrococcus furiosus.

PubMed Central

Cheng, T. C.; Ramakrishnan, V.; Chan, S. I.

1999-01-01

A novel metallocarboxypeptidase (PfuCP) has been purified to homogeneity from the hyperthermophilic archaeon, Pyrococcus furiosus, with its intended use in C-terminal ladder sequencing of proteins and peptides at elevated temperatures. PfuCP was purified in its inactive state by the addition of ethylenediaminetetraacetic acid (EDTA) and dithiothreitol (DTT) to purification buffers, and the activity was restored by the addition of divalent cobalt (K, = 24 +/- 4 microM at 80 degrees C). The serine protease inhibitor phenylmethylsulfonyl fluoride (PMSF) had no effect on the activity. The molecular mass of monomeric PfuCP is 59 kDa as determined by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) and 58 kDa by SDS-PAGE analysis. In solution, PfuCP exists as a homodimer of approximately 128 kDa as determined by gel filtration chromatography. The activity of PfuCP exhibits a temperature optimum exceeding 90 degrees C under ambient pressure, and a narrow pH optimum of 6.2-6.6. Addition of Co2+ to the apoPfuCP at room temperature does not alter its far-UV circular dichroism (CD) or its intrinsic fluorescence spectrum. Even when the CoPfuCP is heated to 80 degrees C, its far-UV CD shows a minimal change in the global conformation and the intrinsic fluorescence of aromatic residues shows only a partial quenching. Changes in the intrinsic fluorescence appear essentially reversible with temperature. Finally, the far-UV CD and intrinsic fluorescence data suggest that the overall structure of the holoenzyme is extremely thermostable. However, the activities of both the apo and holo enzyme exhibit a similar second-order decay over time, with 50% activity remaining after approximately 40 min at 80 degrees C. The N-blocked synthetic dipeptide, N-carbobenzoxy-Ala-Arg (ZAR), was used in the purification assay. The kinetic parameters at 80 degrees C with 0.4 mM CoCl2 were: Km, 0.9 +/- 0.1 mM; Vmax, 2,300 +/- 70 U mg(-1); and turn over number, 600 +/- 20 s(-1). Activity against other ZAX substrates (X = V, L, I, M, W, Y, F, N, A, S, H, K) revealed a broad specificity for neutral, aromatic, polar, and basic C-terminal residues. This broad specificity was confirmed by the C-terminal ladder sequencing of several synthetic and natural peptides, including porcine N-acetyl-renin substrate, for which we have observed (by MALDI-TOF MS) stepwise hydrolysis by PfuCP of up to seven residues from the C-terminus: Ac-Asp-Arg-Val-Tyr-Ile-His-Pro-Phe-His-Leu-Leu-Val-Tyr-Ser. PMID:10595552

Interfacial nanobubbles on atomically flat substrates with different hydrophobicities.

PubMed

Wang, Xingya; Zhao, Binyu; Ma, Wangguo; Wang, Ying; Gao, Xingyu; Tai, Renzhong; Zhou, Xingfei; Zhang, Lijuan

2015-04-07

The dependence of the morphology of interfacial nanobubbles on atomically flat substrates with different wettability ranges was investigated by using PeakForce quantitative nanomechanics. Interfacial nanobubbles were formed and imaged on silicon nitride (Si3N4), mica, and highly ordered pyrolytic graphite (HOPG) substrates that were partly covered by reduced graphene oxide (rGO). The contact angles and sizes of those nanobubbles were measured under the same conditions. Nanobubbles with the same lateral width exhibited different heights on the different substrates, with the order Si3N4≈mica>rGO>HOPG, which is consistent with the trend of the hydrophobicity of the substrates. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Substrate-Influenced Thermo-Mechanical Fatigue of Copper Metallizations: Limits of Stoney’s Equation

PubMed Central

Bigl, Stephan; Wurster, Stefan; Cordill, Megan J.

2017-01-01

Rapid progress in the reduction of substrate thickness for silicon-based microelectronics leads to a significant reduction of the device bending stiffness and the need to address its implication for the thermo-mechanical fatigue behavior of metallization layers. Results on 5 µm thick Cu films reveal a strong substrate thickness-dependent microstructural evolution. Substrates with hs = 323 and 220 µm showed that the Cu microstructure exhibits accelerated grain growth and surface roughening. Moreover, curvature-strain data indicates that Stoney’s simplified curvature-stress relation is not valid for thin substrates with regard to the expected strains, but can be addressed using more sophisticated plate bending theories. PMID:29120407

Deposition of thermal and hot-wire chemical vapor deposition copper thin films on patterned substrates.

PubMed

Papadimitropoulos, G; Davazoglou, D

2011-09-01

In this work we study the hot-wire chemical vapor deposition (HWCVD) of copper films on blanket and patterned substrates at high filament temperatures. A vertical chemical vapor deposition reactor was used in which the chemical reactions were assisted by a tungsten filament heated at 650 degrees C. Hexafluoroacetylacetonate Cu(I) trimethylvinylsilane (CupraSelect) vapors were used, directly injected into the reactor with the aid of a liquid injection system using N2 as carrier gas. Copper thin films grown also by thermal and hot-wire CVD. The substrates used were oxidized silicon wafers on which trenches with dimensions of the order of 500 nm were formed and subsequently covered with LPCVD W. HWCVD copper thin films grown at filament temperature of 650 degrees C showed higher growth rates compared to the thermally ones. They also exhibited higher resistivities than thermal and HWCVD films grown at lower filament temperatures. Thermally grown Cu films have very uniform deposition leading to full coverage of the patterned substrates while the HWCVD films exhibited a tendency to vertical growth, thereby creating gaps and incomplete step coverage.

Constructing Free Standing Metal Organic Framework MIL-53 Membrane Based on Anodized Aluminum Oxide Precursor

PubMed Central

Zhang, Yunlu; Gao, Qiuming; Lin, Zhi; Zhang, Tao; Xu, Jiandong; Tan, Yanli; Tian, Weiqian; Jiang, Lei

2014-01-01

Metal organic framework (MOF) materials have attracted great attention due to their well-ordered and controllable pores possessing of prominent potentials for gas molecule sorption and separation performances. Organizing the MOF crystals to a continuous membrane with a certain scale will better exhibit their prominent potentials. Reports in recent years concentrate on well grown MOF membranes on specific substrates. Free standing MOF membranes could have more important applications since they are independent from the substrates. However, the method to prepare such a membrane has been a great challenge because good mechanical properties and stabilities are highly required. Here, we demonstrate a novel and facile technique for preparing the free standing membrane with a size as large as centimeter scale. The substrate we use proved itself not only a good skeleton but also an excellent precursor to fulfill the reaction. This kind of membrane owns a strong mechanical strength, based on the fact that it is much thinner than the composite membranes grown on substrates and it could exhibit good property of gas separation. PMID:24821299

Spatially resolved mapping of electrical conductivity across individual domain (grain) boundaries in graphene.

PubMed

Clark, Kendal W; Zhang, X-G; Vlassiouk, Ivan V; He, Guowei; Feenstra, Randall M; Li, An-Ping

2013-09-24

All large-scale graphene films contain extended topological defects dividing graphene into domains or grains. Here, we spatially map electronic transport near specific domain and grain boundaries in both epitaxial graphene grown on SiC and CVD graphene on Cu subsequently transferred to a SiO2 substrate, with one-to-one correspondence to boundary structures. Boundaries coinciding with the substrate step on SiC exhibit a significant potential barrier for electron transport of epitaxial graphene due to the reduced charge transfer from the substrate near the step edge. Moreover, monolayer-bilayer boundaries exhibit a high resistance that can change depending on the height of substrate step coinciding at the boundary. In CVD graphene, the resistance of a grain boundary changes with the width of the disordered transition region between adjacent grains. A quantitative modeling of boundary resistance reveals the increased electron Fermi wave vector within the boundary region, possibly due to boundary induced charge density variation. Understanding how resistance change with domain (grain) boundary structure in graphene is a crucial first step for controlled engineering of defects in large-scale graphene films.

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

EPA Science Inventory

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

Ride or Die

ERIC Educational Resources Information Center

Denmead, Tyler; Brown, Ruth-Nicole

2014-01-01

In this Instructional Resource, Denmead and Brown consider how "Ruffneck Constructivists," an exhibition curated by Kara Walker at the Institute for Contemporary Art (ICA), University of Pennsylvania, can disturb and provoke young creatives and art education more broadly. For this exhibition, Walker draws on the figure that MC Lyte…

Investigation of high-speed Si photodetectors in standard CMOS technology

NASA Astrophysics Data System (ADS)

Wang, Huaqiang; Guo, Xia

2018-05-01

In this paper, the frequency response characteristics of the photodetector(PD) were studied considering intrinsic and extrinsic effects. Then we designed the interdigitated p-i-n PD on Silicon-on-Insulator (SOI) and epitaxial (EPI) substrates with photosensitive area of 30-μm diameter, fabricated by CMOS process. The 2-μm finger-spacing devices exhibited a 205 MHz bandwidth at a reverse bias of 3 V processed on 2-μm SOI substrates. EPI devices with 1 μm finger spacing exhibited a 131 MHz bandwidth under -3 V. Responsivity of 0.051 A/W and 0.21 A/W were measured at 850 nm on SOI and EPI substrates, respectively. Compared with the bulk silicon PD, the bandwidth is greatly improved. The PD gains the high cost performance ratio, which can be widely used in short distance communication such as visible light communication and free space optical communication.

Molecular dynamics studies of interfacial water at the alumina surface.

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

Argyris, Dr. Dimitrios; Ho, Thomas; Cole, David

2011-01-01

Interfacial water properties at the alumina surface were investigated via all-atom equilibrium molecular dynamics simulations at ambient temperature. Al-terminated and OH-terminated alumina surfaces were considered to assess the structural and dynamic behavior of the first few hydration layers in contact with the substrates. Density profiles suggest water layering up to {approx}10 {angstrom} from the solid substrate. Planar density distribution data indicate that water molecules in the first interfacial layer are organized in well-defined patterns dictated by the atomic terminations of the alumina surface. Interfacial water exhibits preferential orientation and delayed dynamics compared to bulk water. Water exhibits bulk-like behavior atmore » distances greater than {approx}10 {angstrom} from the substrate. The formation of an extended hydrogen bond network within the first few hydration layers illustrates the significance of water?water interactions on the structural properties at the interface.« less

III-nitride core–shell nanorod array on quartz substrates

PubMed Central

Bae, Si-Young; Min, Jung-Wook; Hwang, Hyeong-Yong; Lekhal, Kaddour; Lee, Ho-Jun; Jho, Young-Dahl; Lee, Dong-Seon; Lee, Yong-Tak; Ikarashi, Nobuyuki; Honda, Yoshio; Amano, Hiroshi

2017-01-01

We report the fabrication of near-vertically elongated GaN nanorods on quartz substrates. To control the preferred orientation and length of individual GaN nanorods, we combined molecular beam epitaxy (MBE) with pulsed-mode metal–organic chemical vapor deposition (MOCVD). The MBE-grown buffer layer was composed of GaN nanograins exhibiting an ordered surface and preferred orientation along the surface normal direction. Position-controlled growth of the GaN nanorods was achieved by selective-area growth using MOCVD. Simultaneously, the GaN nanorods were elongated by the pulsed-mode growth. The microstructural and optical properties of both GaN nanorods and InGaN/GaN core–shell nanorods were then investigated. The nanorods were highly crystalline and the core–shell structures exhibited optical emission properties, indicating the feasibility of fabricating III-nitride nano-optoelectronic devices on amorphous substrates. PMID:28345641

``The Princess and the Pea'' at the Nanoscale: Wrinkling and Delamination of Graphene on Nanoparticles

NASA Astrophysics Data System (ADS)

Yamamoto, Mahito; Pierre-Louis, Olivier; Huang, Jia; Fuhrer, Michael S.; Einstein, Theodore L.; Cullen, William G.

2012-10-01

Thin membranes exhibit complex responses to external forces or geometrical constraints. A familiar example is the wrinkling, exhibited by human skin, plant leaves, and fabrics, that results from the relative ease of bending versus stretching. Here, we study the wrinkling of graphene, the thinnest and stiffest known membrane, deposited on a silica substrate decorated with silica nanoparticles. At small nanoparticle density, monolayer graphene adheres to the substrate, detached only in small regions around the nanoparticles. With increasing nanoparticle density, we observe the formation of wrinkles which connect nanoparticles. Above a critical nanoparticle density, the wrinkles form a percolating network through the sample. As the graphene membrane is made thicker, global delamination from the substrate is observed. The observations can be well understood within a continuum-elastic model and have important implications for strain-engineering the electronic properties of graphene.

Base-metal saturation of refractory carbide coatings produced by enhanced ceramic jets in electrothermally exploded powder spray

NASA Astrophysics Data System (ADS)

Tamura, Hideki; Itaya, Masanobu

2000-09-01

Tungsten carbide and tantalum carbide were sprayed onto substrates of mild steel by the electrothermally exploded powder spray (ELTEPS) process. High-speed x-ray radiography revealed that tungsten-carbide jets of molten particles guided inside a nozzle exhibited denser flow than unguided jets at the substrate. The velocity of the jet was approximately 800 m/s at the early stage of jetting. The ceramic coatings obtained from the guided spray consisted of carbides of a few to tens of micrometers in size, which were saturated by the base metal up to the top of the coating. The coatings exhibited diffusion of the sprayed ceramics and base metal at the interface of the deposit and substrate. The enhancement of the jet flow formed a microstructure of the ceramic coating, which was saturated by the base metal even without post heat treatment.

Friction and hardness of gold films deposited by ion plating and evaporation

NASA Technical Reports Server (NTRS)

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

1983-01-01

Sliding friction experiments were conducted with ion-plated and vapor-deposited gold films on various substrates in contact with a 0.025-mm-radius spherical silicon carbide rider in mineral oil. Hardness measurements were also made to examine the hardness depth profile of the coated gold on the substrate. The results indicate that the hardness is influenced by the depth of the gold coating from the surface. The hardness increases with an increase in the depth. The hardness is also related to the composition gradient in the graded interface between the gold coating and the substrate. The graded interface exhibited the highest hardness resulting from an alloy hardening effect. The coefficient of friction is inversely related to the hardness, namely, the load carrying capacity of the surface. The greater the hardness that the metal surface possesses, the lower is the coefficient of friction. The graded interface exhibited the lowest coefficient of friction.

DICER-ARGONAUTE2 Complex in Continuous Fluorogenic Assays of RNA Interference Enzymes

PubMed Central

Bernard, Mark A.; Wang, Leyu; Tachado, Souvenir D.

2015-01-01

Mechanistic studies of RNA processing in the RNA-Induced Silencing Complex (RISC) have been hindered by lack of methods for continuous monitoring of enzymatic activity. “Quencherless” fluorogenic substrates of RNAi enzymes enable continuous monitoring of enzymatic reactions for detailed kinetics studies. Recombinant RISC enzymes cleave the fluorogenic substrates targeting human thymidylate synthase (TYMS) and hypoxia-inducible factor 1-α subunit (HIF1A). Using fluorogenic dsRNA DICER substrates and fluorogenic siRNA, DICER+ARGONAUTE2 mixtures exhibit synergistic enzymatic activity relative to either enzyme alone, and addition of TRBP does not enhance the apparent activity. Titration of AGO2 and DICER in enzyme assays suggests that AGO2 and DICER form a functional high-affinity complex in equimolar ratio. DICER and DICER+AGO2 exhibit Michaelis-Menten kinetics with DICER substrates. However, AGO2 cannot process the fluorogenic siRNA without DICER enzyme, suggesting that AGO2 cannot self-load siRNA into its active site. The DICER+AGO2 combination processes the fluorogenic siRNA substrate (K m=74 nM) with substrate inhibition kinetics (K i=105 nM), demonstrating experimentally that siRNA binds two different sites that affect Dicing and AGO2-loading reactions in RISC. This result suggests that siRNA (product of DICER) bound in the active site of DICER may undergo direct transfer (as AGO2 substrate) to the active site of AGO2 in the DICER+AGO2 complex. Competitive substrate assays indicate that DICER+AGO2 cleavage of fluorogenic siRNA is specific, since unlabeled siRNA and DICER substrates serve as competing substrates that cause a concentration-dependent decrease in fluorescent rates. Competitive substrate assays of a series of DICER substrates in vitro were correlated with cell-based assays of HIF1A mRNA knockdown (log-log slope=0.29), suggesting that improved DICER substrate designs with 10-fold greater processing by the DICER+AGO2 complex can provide a strong (~2800-fold) improvement in potency for mRNA knockdown. This study lays the foundation of a systematic biochemical approach to optimize nucleic acid-based therapeutics for Dicing and ARGONAUTE2-loading for improving efficacy. PMID:25793518

Purification and characterization of two distinct acidic phytases with broad pH stability from Aspergillus niger NCIM 563.

PubMed

Soni, S K; Magdum, A; Khire, J M

2010-11-01

Aspergillus niger NCIM 563 produced two different extracellular phytases (Phy I and Phy II) under submerged fermentation conditions at 30°C in medium containing dextrin-glucose-sodium nitrate-salts. Both the enzymes were purified to homogeneity using Rotavapor concentration, Phenyl-Sepharose column chromatography and Sephacryl S-200 gel filtration. The molecular mass of Phy I and II as determined by SDS-PAGE and gel filtration were 66, 264, 150 and 148 kDa respectively, indicating that Phy I consists of four identical subunits and Phy II is a monomer. The pI values of Phy I and II were 3.55 and 3.91, respectively. Phy I was highly acidic with optimum pH of 2.5 and was stable over a broad pH range (1.5-9.0) while Phy II showed a pH optimum of 5.0 with stability in the range of pH 3.5-9.0. Phy I exhibited very broad substrate specificity while Phy II was more specific for sodium phytate. Similarly Phy II was strongly inhibited by Ag(+), Hg(2+) (1 mM) metal ions and Phy I was partially inhibited. Peptide analysis by Mass Spectrometry (MS) MALDI-TOF also indicated that both the proteins were totally different. The K(m) for Phy I and II for sodium phytate was 2.01 and 0.145 mM while V(max) was 5,018 and 1,671 μmol min(-1) mg(-1), respectively. The N-terminal amino acid sequences of Phy I and Phy II were FSYGAAIPQQ and GVDERFPYTG, respectively. Phy II showed no homology with Phy I and any other known phytases from the literature suggesting its unique nature. This, according to us, is the first report of two distinct novel phytases from Aspergillus niger.

Purification, Cloning, Characterization, and N-Glycosylation Analysis of a Novel β-Fructosidase from Aspergillus oryzae FS4 Synthesizing Levan- and Neolevan-Type Fructooligosaccharides

PubMed Central

Lu, Lili; Jin, Lan; Liu, Jiawei; Song, Deyong; Guo, Zhongwu; Xiao, Min

2014-01-01

β-Fructosidases are a widespread group of enzymes that catalyze the hydrolysis of terminal fructosyl units from various substrates. These enzymes also exhibit transglycosylation activity when they function with high concentrations of sucrose, which is used to synthesize fructooligosaccharides (FOS) in the food industry. A β-fructosidase (BfrA) with high transglycosylation activity was purified from Aspergillus oryzae FS4 as a monomeric glycoprotein. Compared with the most extensively studied Aspergillus spp. fructosidases that synthesize inulin-type β-(2-1)-linked FOS, BfrA has unique transfructosylating property of synthesizing levan- and neolevan-type β-(2-6)-linked FOS. The coding sequence (bfrAFS4, 1.86 kb) of BfrA was amplified and expressed in Escherichia coli and Pichia pastoris. Both native and recombinant proteins showed transfructosylation and hydrolyzation activities with broad substrate specificity. These proteins could hydrolyze the following linkages: Glc α-1, 2-β Fru; Glc α-1, 3-α Fru; and Glc α-1, 5-β Fru. Compared with the unglycosylated E. coli-expressed BfrA (E.BfrA), the N-glycosylated native (N.BfrA) and the P. pastoris-expressed BfrA (P.BfrA) were highly stable at a wide pH range (pH 4 to 11), and significantly more thermostable at temperatures up to 50°C with a maximum activity at 55°C. Using sucrose as substrate, the Km and kcat values for total activity were 37.19±5.28 mM and 1.0016±0.039×104 s−1 for N.BfrA. Moreover, 10 of 13 putative N-glycosylation sites were glycosylated on N.BfrA, and N-glycosylation was essential for enzyme thermal stability and optima activity. Thus, BfrA has demonstrated as a well-characterized A. oryzae fructosidase with unique transfructosylating capability of synthesizing levan- and neolevan-type FOS. PMID:25501957

Cloning and characterization of a novel acidic cutinase from Sirococcus conigenus.

PubMed

Nyyssölä, Antti; Pihlajaniemi, Ville; Häkkinen, Mari; Kontkanen, Hanna; Saloheimo, Markku; Nakari-Setälä, Tiina

2014-04-01

A cutinase gene (ScCut1) was amplified by PCR from the genomic DNA of the ascomycetous plant pathogen Sirococcous conigenus VTT D-04989 using degenerate primers designed on the basis of conserved segments of known cutinases and cutinase-like enzymes. No introns or N- or O-glycosylation sites could be detected by analysis of the ScCut1 gene sequence. The alignment of ScCut1 with other fungal cutinases indicated that ScCut1 contained the conserved motif G-Y-S-Q-G surrounding the active site serine as well as the aspartic acid and histidine residues of the cutinase active site. The gene was expressed in Pichia pastoris, and the recombinantly produced ScCut1 enzyme was purified to homogeneity by immobilized metal affinity chromatography exploiting a C-terminal His-tag translationally fused to the protein. The purified ScCut1 exhibited activity at acidic pH. The K(m) and V(max) values determined for pNP-butyrate esterase activity at pH 4.5 were 1.7 mM and 740 nkat mg⁻¹, respectively. Maximal activities were determined at between pH 4.7 and 5.2 and at between pH 4.1 and 4.6 with pNP-butyrate and tritiated cutin as the substrates, respectively. With both substrates, the enzyme was active over a broad pH range (between pH 3.0 and 7.5). Activity could still be detected at pH 3.0 both with tritiated cutin and with p-nitrophenyl butyrate (relative activity of 25 %) as the substrates. ScCut1 showed activity towards shorter (C2 to C3) fatty acid esters of p-nitrophenol than towards longer ones. Circular dichroism analysis suggested that the denaturation of ScCut1 by heating the protein sample to 80 °C was to a great extent reversible.

Two-dimensional models for the optical response of thin films

NASA Astrophysics Data System (ADS)

Li, Yilei; Heinz, Tony F.

2018-04-01

In this work, we present a systematic study of 2D optical models for the response of thin layers of material under excitation by normally incident light. The treatment, within the framework of classical optics, analyzes a thin film supported by a semi-infinite substrate, with both the thin layer and the substrate assumed to exhibit local, isotropic linear response. Starting from the conventional three-dimensional (3D) slab model of the system, we derive a two-dimensional (2D) sheet model for the thin film in which the optical response is described by a sheet optical conductivity. We develop criteria for the applicability of this 2D sheet model for a layer with an optical thickness far smaller than the wavelength of the light. We examine in detail atomically thin semi-metallic and semiconductor van-der-Waals layers and ultrathin metal films as representative examples. Excellent agreement of the 2D sheet model with the 3D slab model is demonstrated over a broad spectral range from the radio frequency limit to the near ultraviolet. A linearized version of system response for the 2D model is also presented for the case where the influence of the optically thin layer is sufficiently weak. Analytical expressions for the applicability and accuracy of the different optical models are derived, and the appropriateness of the linearized treatment for the materials is considered. We discuss the advantages, as well as limitations, of these models for the purpose of deducing the optical response function of the thin layer from experiment. We generalize the theory to take into account in-plane anisotropy, layered thin film structures, and more general substrates. Implications of the 2D model for the transmission of light by the thin film and for the implementation of half- and totally absorbing layers are discussed.

Structure of fructose bisphosphate aldolase from Encephalitozoon cuniculi

PubMed Central

Gardberg, Anna; Sankaran, Banumathi; Davies, Doug; Bhandari, Janhavi; Staker, Bart; Stewart, Lance

2011-01-01

Fructose bisphosphate aldolose (FBPA) enzymes have been found in a broad range of eukaryotic and prokaryotic organisms. FBPA catalyses the cleavage of fructose 1,6-bisphosphate into glyceraldehyde 3-phosphate and dihydroxy­acetone phosphate. The SSGCID has reported several FBPA structures from pathogenic sources. Bioinformatic analysis of the genome of the eukaryotic microsporidian parasite Encephalitozoon cuniculi revealed an FBPA homolog. The structures of this enzyme in the presence of the native substrate FBP and also with the partial substrate analog phosphate are reported. The purified enzyme crystallized in 90 mM Bis-Tris propane pH 6.5, 18% PEG 3350, 18 mM NaKHPO4, 10 mM urea for the phosphate-bound form and 100 mM Bis-Tris propane pH 6.5, 20% PEG 3350, 20 mM fructose 1,6-­bisphosphate for the FBP-bound form. In both cases protein was present at 25 mg ml−1 and the sitting-drop vapour-diffusion method was used. For the FBP-bound form, a data set to 2.37 Å resolution was collected from a single crystal at 100 K. The crystal belonged to the orthorhombic space group C2221, with unit-cell parameters a = 121.46, b = 135.82, c = 61.54 Å. The structure was refined to a final free R factor of 20.8%. For the phosphate-bound form, a data set was collected to 2.00 Å resolution. The space group was also C2221 and the unit-cell parameters were a = 121.96, b = 137.61, c = 62.23 Å. The structure shares the typical barrel tertiary structure reported for previous FBPA structures and exhibits the same Schiff base in the active site. The quaternary structure is dimeric. This work provides a direct experimental result for the substrate-binding conformation of the product state of E. cuniculi FBPA. PMID:21904050

Structure of fructose bisphosphate aldolase from Encephalitozoon cuniculi.

PubMed

Gardberg, Anna; Sankaran, Banumathi; Davies, Doug; Bhandari, Janhavi; Staker, Bart; Stewart, Lance

2011-09-01

Fructose bisphosphate aldolose (FBPA) enzymes have been found in a broad range of eukaryotic and prokaryotic organisms. FBPA catalyses the cleavage of fructose 1,6-bisphosphate into glyceraldehyde 3-phosphate and dihydroxyacetone phosphate. The SSGCID has reported several FBPA structures from pathogenic sources. Bioinformatic analysis of the genome of the eukaryotic microsporidian parasite Encephalitozoon cuniculi revealed an FBPA homolog. The structures of this enzyme in the presence of the native substrate FBP and also with the partial substrate analog phosphate are reported. The purified enzyme crystallized in 90 mM Bis-Tris propane pH 6.5, 18% PEG 3350, 18 mM NaKHPO(4), 10 mM urea for the phosphate-bound form and 100 mM Bis-Tris propane pH 6.5, 20% PEG 3350, 20 mM fructose 1,6-bisphosphate for the FBP-bound form. In both cases protein was present at 25 mg ml(-1) and the sitting-drop vapour-diffusion method was used. For the FBP-bound form, a data set to 2.37 Å resolution was collected from a single crystal at 100 K. The crystal belonged to the orthorhombic space group C222(1), with unit-cell parameters a=121.46, b=135.82, c=61.54 Å. The structure was refined to a final free R factor of 20.8%. For the phosphate-bound form, a data set was collected to 2.00 Å resolution. The space group was also C222(1) and the unit-cell parameters were a=121.96, b=137.61, c=62.23 Å. The structure shares the typical barrel tertiary structure reported for previous FBPA structures and exhibits the same Schiff base in the active site. The quaternary structure is dimeric. This work provides a direct experimental result for the substrate-binding conformation of the product state of E. cuniculi FBPA.

Multi-substrate flavonol O-glucosyltransferases from strawberry (Fragaria×ananassa) achene and receptacle

PubMed Central

Griesser, Markus; Vitzthum, Florian; Fink, Barbara; Bellido, Mari Luz; Raasch, Constanze; Munoz-Blanco, Juan; Schwab, Wilfried

2008-01-01

In an effort to characterize fruit ripening-related genes functionally, two glucosyltransferases, FaGT6 and FaGT7, were cloned from a strawberry (Fragaria×ananassa) cDNA library and the full-length open reading frames were amplified by rapid amplification of cDNA ends. FaGT6 and FaGT7 were expressed heterologously as fusion proteins in Escherichia coli and target protein was purified using affinity chromatography. Both recombinant enzymes exhibited a broad substrate tolerance in vitro, accepting numerous flavonoids, hydroxycoumarins, and naphthols. FaGT6 formed 3-O-glucosides and minor amounts of 7-O-, 4′-O-, and 3′-O-monoglucosides and one diglucoside from flavonols such as quercetin. FaGT7 converted quercetin to the 3-O-glucoside and 4′-O-glucoside and minor levels of the 7- and 3′-isomers but formed no diglucoside. Gene expression studies showed that both genes are strongly expressed in achenes of small-sized green fruits, while the expression levels were generally lower in the receptacle. Significant levels of quercetin 3-O-, 7-O-, and 4′-O-glucosides, kaempferol 3-O- and 7-O-glucosides, as well as isorhamnetin 7-O-glucoside, were identified in achenes and the receptacle. In the receptacle, the expression of both genes is negatively controlled by auxin which correlates with the ripening-related gene expression in this tissue. Salicylic acid, a known signal molecule in plant defence, induces the expression of both genes. Thus, it appears that FaGT6 and FaGT7 are involved in the glucosylation of flavonols and may also participate in xenobiotic metabolism. The latter function is supported by the proven ability of strawberries to glucosylate selected unnatural substrates injected in ripe fruits. This report presents the first biochemical characterization of enzymes mainly expressed in strawberry achenes and provides the foundation of flavonoid metabolism in the seeds. PMID:18487633

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

Two Polyhydroxyalkanoate Synthases from Distinct Classes from the Aromatic Degrader Cupriavidus pinatubonensis JMP134 Exhibit the Same Substrate Preference.

PubMed

Jiang, Xuan; Luo, Xi; Zhou, Ning-Yi

2015-01-01

Cupriavidus pinatubonensis JMP134 utilizes a variety of aromatic substrates as sole carbon sources, including meta-nitrophenol (MNP). Two polyhydroxyalkanoate (PHA) synthase genes, phaC1 and phaC2, were annotated and categorized as class I and class II PHA synthase genes, respectively. In this study, both His-tagged purified PhaC1 and PhaC2 were shown to exhibit typical class I PHA synthase substrate specificity to make short-chain-length (SCL) PHA from 3-hydroxybutyryl-CoA and failed to make medium-chain-length (MCL) PHA from 3-hydroxyoctanoyl-CoA. The phaC1 or phaC2 deletion strain could also produce SCL PHA when grown in fructose or octanoate, but the double mutant of phaC1 and phaC2 lost this ability. The PhaC2 also exhibited substrate preference towards SCL substrates when expressed in Pseudomonas aeruginosa PAO1 phaC mutant strain. On the other hand, the transcriptional level of phaC1 was 70-fold higher than that of phaC2 in MNP-grown cells, but 240-fold lower in octanoate-grown cells. Further study demonstrated that only phaC1 was involved in PHA synthesis in MNP-grown cells. These findings suggested that phaC1 and phaC2 genes were differentially regulated under different growth conditions in this strain. Within the phaC2-containing gene cluster, a single copy of PHA synthase gene was present clustering with genes encoding enzymes in the biosynthesis of PHA precursors. This is markedly different from the genetic organization of all other previously reported class II PHA synthase gene clusters and this cluster likely comes from a distinct evolutionary path.

Two Polyhydroxyalkanoate Synthases from Distinct Classes from the Aromatic Degrader Cupriavidus pinatubonensis JMP134 Exhibit the Same Substrate Preference

PubMed Central

Jiang, Xuan; Luo, Xi; Zhou, Ning-Yi

2015-01-01

Cupriavidus pinatubonensis JMP134 utilizes a variety of aromatic substrates as sole carbon sources, including meta-nitrophenol (MNP). Two polyhydroxyalkanoate (PHA) synthase genes, phaC1 and phaC2, were annotated and categorized as class I and class II PHA synthase genes, respectively. In this study, both His-tagged purified PhaC1 and PhaC2 were shown to exhibit typical class I PHA synthase substrate specificity to make short-chain-length (SCL) PHA from 3-hydroxybutyryl-CoA and failed to make medium-chain-length (MCL) PHA from 3-hydroxyoctanoyl-CoA. The phaC1 or phaC2 deletion strain could also produce SCL PHA when grown in fructose or octanoate, but the double mutant of phaC1 and phaC2 lost this ability. The PhaC2 also exhibited substrate preference towards SCL substrates when expressed in Pseudomonas aeruginosa PAO1 phaC mutant strain. On the other hand, the transcriptional level of phaC1 was 70-fold higher than that of phaC2 in MNP-grown cells, but 240-fold lower in octanoate-grown cells. Further study demonstrated that only phaC1 was involved in PHA synthesis in MNP-grown cells. These findings suggested that phaC1 and phaC2 genes were differentially regulated under different growth conditions in this strain. Within the phaC2-containing gene cluster, a single copy of PHA synthase gene was present clustering with genes encoding enzymes in the biosynthesis of PHA precursors. This is markedly different from the genetic organization of all other previously reported class II PHA synthase gene clusters and this cluster likely comes from a distinct evolutionary path. PMID:26544851

Heterologous expression and characterization of two chitinase 5 enzymes from the migratory locust Locusta migratoria.

PubMed

Li, Ying-Long; Song, Hui-Fang; Zhang, Xue-Yao; Li, Da-Qi; Zhang, Ting-Ting; Ma, En-Bo; Zhang, Jian-Zhen

2016-06-01

Insect chitinases are involved in degradation of chitin from the exoskeleton or peritrophic metrix of midgut. In Locusta migratoria, two duplicated Cht5s (LmCht5-1 and LmCht5-2) have been shown to have distinct molecular characteristics and biological roles. To explore the protein properties of the two LmCht5s, we heterologously expressed both enzymes using baculovirus expression system in SF9 cells, and characterized kinetic and carbohydrate-binding properties of purified enzymes. LmCht5-1 and LmCht5-2 exhibited similar pH and temperature optimums. LmCht5-1 has lower Km value for the oligomeric substrate (4MU-(GlcNAc)3 ), and higher Km value for the longer substrate (CM-Chitin-RBV) compared with LmCht5-2. A comparison of amino acids and homology modeling of catalytic domain presented similar TIM barrel structures and differentiated amino acids between two proteins. LmCht5-1 has a chitin-binding domain (CBD) tightly bound to colloidal chitin, but LmCht5-2 does not have a CBD for binding to colloidal chitin. Our results suggested both LmCht5-1 and LmCht5-2, which have the critical glutamate residue in region II of catalytic domain, exhibited chitinolytic activity cleaving both polymeric and oligomeric substrates. LmCht5-1 had relatively higher activity against the oligomeric substrate, 4MU-(GlcNAc)3 , whereas LmCht5-2 exhibited higher activity toward the longer substrate, CM-Chitin-RBV. These findings are helpful for further research to clarify their different roles in insect growth and development. © 2016 Institute of Zoology, Chinese Academy of Sciences.

Dynamic impact testing of hedgehog spines using a dual-arm crash pendulum.

PubMed

Swift, Nathan B; Hsiung, Bor-Kai; Kennedy, Emily B; Tan, Kwek-Tze

2016-08-01

Hedgehog spines are a potential model for impact resistant structures and material. While previous studies have examined static mechanical properties of individual spines, actual collision tests on spines analogous to those observed in the wild have not previously been investigated. In this study, samples of roughly 130 keratin spines were mounted vertically in thin substrates to mimic the natural spine layout on hedgehogs. A weighted crash pendulum was employed to induce and measure the effects of repeated collisions against samples, with the aim to evaluate the influence of various parameters including humidity effect, impact energy, and substrate hardness. Results reveal that softer samples-due to humidity conditioning and/or substrate material used-exhibit greater durability over multiple impacts, while the more rigid samples exhibit greater energy absorption performance at the expense of durability. This trend is exaggerated during high-energy collisions. Comparison of the results to baseline tests with industry standard impact absorbing foam, wherein the spines exhibit similar energy absorption, verifies the dynamic impact absorption capabilities of hedgehog spines and their candidacy as a structural model for engineered impact technology. Copyright © 2016 Elsevier Ltd. All rights reserved.

Investigation of Hexagonal Ferrite Film Growth Techniques for Millimeter-Wave Systems Applications.

DTIC Science & Technology

1987-03-15

hexaferrite LPE layer on CoGa 204 substrate. Some areas of the film exhibit a terraced structure .................................... 32 Figure 17 (a) Layer...49 G), which is the standard substrate for yttrium iron garnet epitaxial film growth. The dielectric constant is slightly larger than values for...Details are given ’.- in Appendices III a:d IV. 4.1 INTIODUCTION In LPE , a small lattice mismatch between film and substrate is .r..r ial tc gro.w good

Threonine deaminase from extremely halophilic bacteria - Cooperative substrate kinetics and salt dependence.

NASA Technical Reports Server (NTRS)

Lieberman, M. M.; Lanyi, J. K.

1972-01-01

The effect of salt on the activity, stability, and allosteric properties of catabolic threonine deaminase from Halobacterium cutirubrum was studied. The enzyme exhibits sigmoidal kinetics with the substrate, threonine. The Hill slope is 1.55 at pH 10. The enzyme is activated by ADP at low substrate concentrations. In the presence of this effector, sigmoidal kinetics are no longer observed. At pH 10, in the absence of ADP, enzyme activity increases with increasing NaCl concentration from 0 to 4 M.

Temporal succession in carbon incorporation from macromolecules by particle-attached bacteria in marine microcosms: Particle-attached bacteria incorporating organic carbon

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

Mayali, Xavier; Stewart, Benjamin; Mabery, Shalini

Here, we investigated bacterial carbon assimilation from stable isotope-labelled macromolecular substrates (proteins; lipids; and two types of polysaccharides, starch and cellobiose) while attached to killed diatom detrital particles during laboratory microcosms incubated for 17 days. Using Chip-SIP (secondary ion mass spectrometry analysis of RNA microarrays), we identified generalist operational taxonomic units (OTUs) from the Gammaproteobacteria, belonging to the genera Colwellia, Glaciecola, Pseudoalteromonas and Rheinheimera, and from the Bacteroidetes, genera Owenweeksia and Maribacter, that incorporated the four tested substrates throughout the incubation period. Many of these OTUs exhibited the highest isotope incorporation relative to the others, indicating that they were likelymore » the most active. Additional OTUs from the Gammaproteobacteria, Bacteroidetes and Alphaproteobacteria exhibited generally (but not always) lower activity and did not incorporate all tested substrates at all times, showing species succession in organic carbon incorporation. We also found evidence to suggest that both generalist and specialist OTUs changed their relative substrate incorporation over time, presumably in response to changing substrate availability as the particles aged. This pattern was demonstrated by temporal succession from relatively higher starch incorporation early in the incubations, eventually switching to higher cellobiose incorporation after 2 weeks.« less

Magnetic anisotropy modulation of epitaxial Fe3O4 films on MgO substrates

NASA Astrophysics Data System (ADS)

Chichvarina, O.; Herng, T. S.; Xiao, W.; Hong, X.; Ding, J.

2015-05-01

Fe3O4 has been widely studied because of its great potential in spintronics and other applications. As a magnetic electrode, it is highly desired if magnetic anisotropy can be controlled. Here, we report the results from our systematic study on the magnetic properties of magnetite (Fe3O4) thin films epitaxially grown on various MgO substrates. Strikingly, we observed a prominent perpendicular magnetic anisotropy in Fe3O4 film deposited on MgO (111) substrate. When measured in out-of-plane direction, the film (40 nm thick) exhibits a well-defined square hysteresis loop with coercivity (Hc) above 1 kOe, while much lower coercivity was obtained in the in-plane orientation. In sharp contrast, the films deposited onto MgO (100) and MgO (110) substrates show in-plane magnetic anisotropy. These films exhibit a typical soft magnet characteristic—Hc lies within the range of 200-400 Oe. All the films showed a clear Verwey transition near 120 K—a characteristic of Fe3O4 material. In addition, a series of magnetoresistance (MR) measurements is performed and the MR results are in good agreement with the magnetic observations. The role of the substrate orientation and film thickness dependency is also investigated.

Self-Stacked Reduced Graphene Oxide Nanosheets Coated with Cobalt-Nickel Hydroxide by One-Step Electrochemical Deposition toward Flexible Electrochromic Supercapacitors.

PubMed

Grote, Fabian; Yu, Zi-You; Wang, Jin-Long; Yu, Shu-Hong; Lei, Yong

2015-09-01

The implementation of an optical function into supercapacitors is an innovative approach to make energy storage devices smarter and to meet the requirements of smart electronics. Here, it is reported for the first time that nickel-cobalt hydroxide on reduced graphene oxide can be utilized for flexible electrochromic supercapacitors. A new and straightforward one-step electrochemical deposition process is introduced that is capable of simultaneously reducing GO and depositing amorphous Co(1-x)Ni(x)(OH)2 on the rGO. It is shown that the rGO nanosheets are homogeneously coated with metal hydroxide and are vertically stacked. No high temperature processes are used so that flexible polymer-based substrates can be coated. The synthesized self-stacked rGO-Co(1-x)Ni(x)(OH)2 nanosheet material exhibits pseudocapacitive charge storage behavior with excellent rate capability, high Columbic efficiency, and nondiffusion limited behavior. It is shown that the electrochemical behavior of the Ni(OH)2 can be modulated, by simultaneously depositing nickel and cobalt hydroxide, into broad oxidization and reduction bands. Further, the material exhibits electrochromic property and can switch between a bleached and transparent state. Literature comparison reveals that the performance characteristics of the rGO-Co(1-x)Ni(x)(OH)2 nanosheet material, in terms of gravimetric capacitance, areal capacitance, and long-term cycling stability, are among the highest reported values of supercapacitors with electrochromic property. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Beyond brown: polyphenol oxidases as enzymes of plant specialized metabolism

USDA-ARS?s Scientific Manuscript database

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

Biochemical properties and subcellular localization of tyrosine aminotransferases in Arabidopsis thaliana.

PubMed

Wang, Minmin; Toda, Kyoko; Maeda, Hiroshi A

2016-12-01

Plants produce various L-tyrosine (Tyr)-derived compounds that are of pharmaceutical or nutritional importance to humans. Tyr aminotransferase (TAT) catalyzes the reversible transamination between Tyr and 4-hydroxyphenylpyruvate (HPP), the initial step in the biosynthesis of many Tyr-derived plant natural products. Herein reported is the biochemical characterization and subcellular localization of TAT enzymes from the model plant Arabidopsis thaliana. Phylogenetic analysis showed that Arabidopsis has at least two homologous TAT genes, At5g53970 (AtTAT1) and At5g36160 (AtTAT2). Their recombinant enzymes showed distinct biochemical properties: AtTAT1 had the highest activity towards Tyr, while AtTAT2 exhibited a broad substrate specificity for both amino and keto acid substrates. Also, AtTAT1 favored the direction of Tyr deamination to HPP, whereas AtTAT2 preferred transamination of HPP to Tyr. Subcellular localization analysis using GFP-fusion proteins and confocal microscopy showed that AtTAT1, AtTAT2, and HPP dioxygenase (HPPD), which catalyzes the subsequent step of TAT, are localized in the cytosol, unlike plastid-localized Tyr and tocopherol biosynthetic enzymes. Furthermore, subcellular fractionation indicated that, while HPPD activity is restricted to the cytosol, TAT activity is detected in both cytosolic and plastidic fractions of Arabidopsis leaf tissue, suggesting that an unknown aminotransferase(s) having TAT activity is also present in the plastids. Biochemical and cellular analyses of Arabidopsis TATs provide a fundamental basis for future in vivo studies and metabolic engineering for enhanced production of Tyr-derived phytochemicals in plants. Copyright © 2016 Elsevier Ltd. All rights reserved.

Abiotic influences on bicarbonate use in the giant kelp, Macrocystis pyrifera, in the Monterey Bay.

PubMed

Drobnitch, Sarah Tepler; Nickols, Kerry; Edwards, Matthew

2017-02-01

In the Monterey Bay region of central California, the giant kelp Macrocystis pyrifera experiences broad fluctuations in wave forces, temperature, light availability, nutrient availability, and seawater carbonate chemistry, all of which may impact their productivity. In particular, current velocities and light intensity may strongly regulate the supply and demand of inorganic carbon (Ci) as substrates for photosynthesis. Macrocystis pyrifera can acquire and utilize both CO 2 and bicarbonate (HCO 3 - ) as Ci substrates for photosynthesis and growth. Given the variability in carbon delivery (due to current velocities and varying [DIC]) and demand (in the form of saturating irradiance), we hypothesized that the proportion of CO 2 and bicarbonate utilized is not constant for M. pyrifera, but a variable function of their fluctuating environment. We further hypothesized that populations acclimated to different wave exposure and irradiance habitats would display different patterns of bicarbonate uptake. To test these hypotheses, we carried out oxygen evolution trials in the laboratory to measure the proportion of bicarbonate utilized by M. pyrifera via external CA under an orthogonal cross of velocity, irradiance, and acclimation treatments. Our Monterey Bay populations of M. pyrifera exhibited proportionally higher external bicarbonate utilization in high irradiance and high flow velocity conditions than in sub-saturating irradiance or low flow velocity conditions. However, there was no significant difference in proportional bicarbonate use between deep blades and canopy blades, nor between individuals from wave-exposed versus wave-protected sites. This study contributes a new field-oriented perspective on the abiotic controls of carbon utilization physiology in macroalgae. © 2016 Phycological Society of America.

Temperature controlled evolution of monoclinic to super-tetragonal phase of epitaxial BiFeO3 thin films on La0.67Sr0.33MnO3 buffered SrTiO3 substrate

NASA Astrophysics Data System (ADS)

Singh, Anar; Kaifeng, Dong; Chen, Jing-Sheng

2018-03-01

Epitaxial BiFeO3 thin films of 130nm were deposited by pulsed laser deposition (PLD) technique on La0.67Sr0.33MnO3 buffered SrTiO3 (001) substrate at various temperatures under different ambient oxygen pressures. Reciprocal space mapping reveals that, with decreasing temperature and oxygen pressure, the broadly reported monoclinic phase (MA) of BiFeO3 thin film initially transforms to a tetragonal phase (T1) with c/a =1.05 (1) in a narrow girth of deposition condition and then to a super-tetragonal phase (T2) with giant c/a = 1.24 (1), as confirmed by reciprocal space mapping using high resolution x-ray diffraction. The surface morphology of the films reveals the island growth of the BiFeO3 films deposited at low temperatures. We propose that the transformation from monoclinic to the super-tetragonal phase is essentially due to the manifestation of excess local strain as a result of the island growth. This study offers a recipe to grow the super-tetragonal phase of BiFeO3, with giant c/a =1.24 (1) which exhibits exceptionally large ferroelectric polarization, on ferromagnetic layer La0.67Sr0.33MnO3. This phase of BiFeO3 can be utilized for the ferroelectric control of magnetism at the interface of BiFeO3 and La0.67Sr0.33MnO3.

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

PubMed Central

Song, Yajian; Xue, Yanfen; Ma, Yanhe

2013-01-01

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

Blastobotrys (Arxula) adeninivorans: a promising alternative yeast for biotechnology and basic research.

PubMed

Malak, Anna; Baronian, Kim; Kunze, Gotthard

2016-10-01

Blastobotrys adeninivorans (syn. Arxula adeninivorans) is a non-conventional, non-pathogenic, imperfect, haploid yeast, belonging to the subphylum Saccharomycotina, which has to date received comparatively little attention from researchers. It possesses unusual properties such as thermo- and osmotolerance, and a broad substrate spectrum. Depending on the cultivation temperature B. (A.) adeninivorans exhibits different morphological forms and various post-translational modifications and protein expression properties that are strongly correlated with the morphology. The genome has been completely sequenced and, in addition, there is a well-developed transformation/expression platform, which makes rapid, simple gene manipulations possible. This yeast species is a very good host for homologous and heterologous gene expression and is also a useful gene donor. Blastobotrys (A.) adeninivorans is able to use a very wide range of substrates as carbon and/or nitrogen sources and is an interesting organism owing to the presence of many metabolic pathways, for example degradation of n-butanol, purines and tannin. In addition, its unusual properties and robustness make it a useful bio-component for whole cell biosensors. There are currently a number of products on the market produced by B. (A.) adeninivorans and further investigation may contribute further innovative solutions for current challenges that exist in the biotechnology industry. Additionally it may become a useful alternative to existing commercial yeast strains and as a model organism in research. In this review we present information relevant to the exploitation of B. (A.) adeninivorans in research and industrial settings. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

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

PubMed Central

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

2012-01-01

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

Structural and magnetic properties of Ni nanofilms on Ge(001) by molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Bocirnea, Amelia Elena; Costescu, Ruxandra Maria; Pasuk, Iuliana; Lungu, George Adrian; Teodorescu, Cristian Mihail

2017-12-01

Ni films of 20 nm nominal thickness were grown on Ge(001) substrates by molecular beam epitaxy at several different temperatures from room temperature up to 400 °C. X-ray diffraction and X-ray photoelectron spectroscopy reveal the nucleation of Ni-Ge compounds (NiGe, Ni2Ge, Ni5Ge2) as well as a departure from the fcc Ni structure exhibited by the films at and beyond a temperature of 100 °C. The binding energy of the Ni 2p peak increases from the RT value (852.7 eV) by 0.5-1.1 eV for the Ni/Ge(001) samples, while the Ge 2p binding energy changes by 0.6-0.7 eV after Ni growth compared to a clean Ge(001) substrate (there is only a ±0.15 eV shift among the samples grown on substrates at higher temperatures). By increasing substrate temperature, we obtained higher intermixing of Ni and Ge, but rather than both Ni and Ge interdiffusing, we find that Ni diffuses further into the germanium with higher substrate temperature, forming increasingly Ni-rich Ni-Ge compounds diluted into the Ge matrix. Based on Magneto-optic Kerr Effect measurements, Ni/Ge(001) grown on substrates at 100 and 200 °C does not exhibit a hysteresis loop, while the samples on 300 and 400 °C substrates show magnetic behavior, which we attribute to the magnetic character of hexagonal Ni5Ge2 (which is determined here for the first time to be a ferromagnetic phase).

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

PubMed

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

2018-04-02

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

Gold nanoparticle-embedded silk protein-ZnO nanorod hybrids for flexible bio-photonic devices

NASA Astrophysics Data System (ADS)

Gogurla, Narendar; Kundu, Subhas C.; Ray, Samit K.

2017-04-01

Silk protein has been used as a biopolymer substrate for flexible photonic devices. Here, we demonstrate ZnO nanorod array hybrid photodetectors on Au nanoparticle-embedded silk protein for flexible optoelectronics. Hybrid samples exhibit optical absorption at the band edge of ZnO as well as plasmonic energy due to Au nanoparticles, making them attractive for selective UV and visible wavelength detection. The device prepared on Au-silk protein shows a much lower dark current and a higher photo to dark-current ratio of ∼105 as compared to the control sample without Au nanoparticles. The hybrid device also exhibits a higher specific detectivity due to higher responsivity arising from the photo-generated hole trapping by Au nanoparticles. Sharp pulses in the transient photocurrent have been observed in devices prepared on glass and Au-silk protein substrates due to the light induced pyroelectric effect of ZnO, enabling the demonstration of self-powered photodetectors at zero bias. Flexible hybrid detectors have been demonstrated on Au-silk/polyethylene terephthalate substrates, exhibiting characteristics similar to those fabricated on rigid glass substrates. A study of the performance of photodetectors with different bending angles indicates very good mechanical stability of silk protein based flexible devices. This novel concept of ZnO nanorod array photodetectors on a natural silk protein platform provides an opportunity to realize integrated flexible and self-powered bio-photonic devices for medical applications in near future.

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

NASA Astrophysics Data System (ADS)

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

2016-06-01

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

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.

Lattice Transparency of Graphene.

PubMed

Chae, Sieun; Jang, Seunghun; Choi, Won Jin; Kim, Youn Sang; Chang, Hyunju; Lee, Tae Il; Lee, Jeong-O

2017-03-08

Here, we demonstrated the transparency of graphene to the atomic arrangement of a substrate surface, i.e., the "lattice transparency" of graphene, by using hydrothermally grown ZnO nanorods as a model system. The growth behaviors of ZnO nanocrystals on graphene-coated and uncoated substrates with various crystal structures were investigated. The atomic arrangements of the nucleating ZnO nanocrystals exhibited a close match with those of the respective substrates despite the substrates being bound to the other side of the graphene. By using first-principles calculations based on density functional theory, we confirmed the energetic favorability of the nucleating phase following the atomic arrangement of the substrate even with the graphene layer present in between. In addition to transmitting information about the atomic lattice of the substrate, graphene also protected its surface. This dual role enabled the hydrothermal growth of ZnO nanorods on a Cu substrate, which otherwise dissolved in the reaction conditions when graphene was absent.

A comparative analysis of characteristic floral scent compounds in Prunus mume and related species.

PubMed

Hao, Ruijie; Du, Dongliang; Wang, Tao; Yang, Weiru; Wang, Jia; Zhang, Qixiang

2014-01-01

In order to investigate the difference in their characteristic floral scents between Prunus mume Siebold & Zucc. and the related Prunus species, their headspace volatiles and endogenous extraction were analyzed by gas chromatography-mass spectrometry. The efficiency of substrate utilization of the flowers was studied by incubating them with different alcohol substrates. Our results indicated that benzyl acetate is a dominant compound influencing the characteristic floral scent of P. mume. An alcohol substrate concentration of 4 mmol L(-1) and a reaction time of 2 h were constituted the reaction condition for catalysis of exogenous alcohol substrates by the flowers. Under these conditions, Prunus sibirica exhibited the highest utilization efficiency for benzyl alcohol substrate while the utilization efficiency of Prunus persica was the lowest. Comparative analysis of several alcohol substrates indicated that the flowers of the tested species had selective specificity for benzyl alcohol substrates.

Rock-dwelling lizards exhibit less sensitivity of sprint speed to increases in substrate rugosity.

PubMed

Collins, Clint E; Self, Jessica D; Anderson, Roger A; McBrayer, Lance D

2013-06-01

Effectively moving across variable substrates is important to all terrestrial animals. The effects of substrates on lizard performance have ecological ramifications including the partitioning of habitat according to sprinting ability on different surfaces. This phenomenon is known as sprint sensitivity, or the decrease in sprint speed due to change in substrate. However, sprint sensitivity has been characterized only in arboreal Anolis lizards. Our study measured sensitivity to substrate rugosity among six lizard species that occupy rocky, sandy, and/or arboreal habitats. Lizards that use rocky habitats are less sensitive to changes in substrate rugosity, followed by arboreal lizards, and then by lizards that use sandy habitats. We infer from comparative phylogenetic analysis that forelimb, chest, and tail dimensions are important external morphological features related to sensitivity to changes in substrate rugosity. Copyright © 2013 Elsevier GmbH. All rights reserved.

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

PubMed

Taylor, James M; Whalen, Paul J

2015-06-01

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

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

NASA Astrophysics Data System (ADS)

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

2006-02-01

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

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

NASA Astrophysics Data System (ADS)

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

2010-03-01

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

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

PubMed

Qiao, Yusen; Yang, Qiaomu; Schelter, Eric

2018-05-12

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

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

PubMed

Lovelock, Sarah L; Turner, Nicholas J

2014-10-15

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

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

PubMed

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

2014-12-05

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

Seed germination of roundleaf buffaloberry (Shepherdia rotundifolia) and silver buffaloberry (Shepherdia argentea) in three substrates

Treesearch

Taun Beddes; Heidi A. Kratsch

2009-01-01

Many western native plant species occur in areas characterized by well-drained soils low in organic matter. Some drought-tolerant native plant species exhibit poor seed germination. It was hypothesized that traditional growing substrates high in organic matter may impede their germination; therefore, stratified seeds of roundleaf buffaloherry (Shepherdia rotundifolia)...

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

PubMed

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

2017-11-29

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

High-performance carbon nanotube thin-film transistors on flexible paper substrates

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

Liu, Na; Yun, Ki Nam; Yu, Hyun-Yong

Single-walled carbon nanotubes (SWCNTs) are promising materials as active channels for flexible transistors owing to their excellent electrical and mechanical properties. However, flexible SWCNT transistors have never been realized on paper substrates, which are widely used, inexpensive, and recyclable. In this study, we fabricated SWCNT thin-film transistors on photo paper substrates. The devices exhibited a high on/off current ratio of more than 10{sup 6} and a field-effect mobility of approximately 3 cm{sup 2}/V·s. The proof-of-concept demonstration indicates that SWCNT transistors on flexible paper substrates could be applied as low-cost and recyclable flexible electronics.

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

PubMed

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

2016-08-25

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

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

PubMed

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

2018-04-15

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

Optical and mechanical properties of nanocrystalline ZrC thin films grown by pulsed laser deposition.

DOE PAGES

Craciun, D.; Socol, G.; Lambers, E.; ...

2015-01-17

Thin ZrC films (<500 nm) were grown on (100) Si substrates at a substrate temperature of 500 °C by the pulsed laser deposition (PLD) technique using a KrF excimer laser under different CH 4 pressures. Glancing incidence X-ray diffraction showed that films were nanocrystalline, while X-ray reflectivity studies found out films were very dense and exhibited a smooth surface morphology. Optical spectroscopy data shows that the films have high reflectivity (>90%) in the infrared region, characteristic of metallic behavior. Nanoindentation results indicated that films deposited under lower CH 4 pressures exhibited slightly higher nanohardness and Young modulus values than filmsmore » deposited under higher pressures. As a result, tribological characterization revealed that these films exhibited relatively high wear resistance and steady-state friction coefficients on the order of μ = 0.4.« less

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

NASA Astrophysics Data System (ADS)

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

2017-07-01

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

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

Ligand complex structures of l-amino acid oxidase/monooxygenase from Pseudomonas sp. AIU 813 and its conformational change.

PubMed

Im, Dohyun; Matsui, Daisuke; Arakawa, Takatoshi; Isobe, Kimiyasu; Asano, Yasuhisa; Fushinobu, Shinya

2018-03-01

l-Amino acid oxidase/monooxygenase from Pseudomonas sp. AIU 813 (l-AAO/MOG) catalyzes both the oxidative deamination and oxidative decarboxylation of the α-group of l-Lys to produce a keto acid and amide, respectively. l-AAO/MOG exhibits limited specificity for l-amino acid substrates with a basic side chain. We previously determined its ligand-free crystal structure and identified a key residue for maintaining the dual activities. Here, we determined the structures of l-AAO/MOG complexed with l-Lys, l-ornithine, and l-Arg and revealed its substrate recognition. Asp238 is located at the ceiling of a long hydrophobic pocket and forms a strong interaction with the terminal, positively charged group of the substrates. A mutational analysis on the D238A mutant indicated that the interaction is critical for substrate binding but not for catalytic control between the oxidase/monooxygenase activities. The catalytic activities of the D238E mutant unexpectedly increased, while the D238F mutant exhibited altered substrate specificity to long hydrophobic substrates. In the ligand-free structure, there are two channels connecting the active site and solvent, and a short region located at the dimer interface is disordered. In the l-Lys complex structure, a loop region is displaced to plug the channels. Moreover, the disordered region in the ligand-free structure forms a short helix in the substrate complex structures and creates the second binding site for the substrate. It is assumed that the amino acid substrate enters the active site of l-AAO/MOG through this route. The atomic coordinates and structure factors (codes 5YB6, 5YB7, and 5YB8) have been deposited in the Protein Data Bank (http://wwpdb.org/). 1.4.3.2 (l-amino acid oxidase), 1.13.12.2 (lysine 2-monooxygenase).

Elastic hydrogel substrate supports robust expansion of murine myoblasts and enhances their engraftment

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

Ding, Ke, E-mail: dk1118@yeah.net; Yang, Zhong; Xu, Jian-zhong, E-mail: xjzspine@163.com

The application of satellite cell-derived myoblasts in regenerative medicine has been restricted by the rapid loss of stemness during in vitro cell expansion using traditional culture systems. However, studies published in the past decade have highlighted the influence of substrate elasticity on stem cell fate and revealed that culture on a soft hydrogel substrate can promote self-renewal and prolong the regenerative potential of muscle stem cells. Whether hydrogel substrates have similar effects after long-term robust expansion remains to be determined. Herein we prepared an elastic chitosan/beta-glycerophosphate/collagen hydrogel mimicking the soft microenvironment of muscle tissues for use as the substrate formore » satellite cell culture and investigated its influence on long-term cell expansion. After 20 passages in culture, satellite cell-derived myoblasts cultured on our hydrogel substrate exhibited significant improvements in proliferation capability, cell viability, colony forming frequency, and potential for myogenic differentiation compared to those cultured on a routine rigid culture surface. Immunochemical staining and western blot analysis both confirmed that myoblasts cultured on the hydrogel substrate expressed higher levels of several differentiation-related markers, including Pax7, Pax3, and SSEA-1, and a lower level of MyoD compared to myoblasts cultured on rigid culture plates (all p<0.05). After transplantation into the tibialis anterior of nude mice, myoblasts that had been cultured on the hydrogel substrate demonstrated a significantly greater engraftment efficacy than those cultured on the traditional surface. Collectively, these results indicate that the elastic hydrogel substrate supported robust expansion of murine myoblasts and enhanced their engraftment in vivo. - Highlights: • An elastic hydrogel was designed to mimic the pliable muscle tissue microenvironment. • Myoblasts retained their stemness in long-term culture on the elastic hydrogels. • Myoblasts expanded on the elastic hydrogel exhibited enhanced in vivo engraftment.« less

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

PubMed

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

2018-01-01

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

Effects of Inductively Coupled Plasma Hydrogen on Long-Wavelength Infrared HgCdTe Photodiodes

NASA Astrophysics Data System (ADS)

Boieriu, P.; Buurma, C.; Bommena, R.; Blissett, C.; Grein, C.; Sivananthan, S.

2013-12-01

Bulk passivation of semiconductors with hydrogen continues to be investigated for its potential to improve device performance. In this work, hydrogen-only inductively coupled plasma (ICP) was used to incorporate hydrogen into long-wavelength infrared HgCdTe photodiodes grown by molecular-beam epitaxy. Fully fabricated devices exposed to ICP showed statistically significant increases in zero-bias impedance values, improved uniformity, and decreased dark currents. HgCdTe photodiodes on Si substrates passivated with amorphous ZnS exhibited reductions in shunt currents, whereas devices on CdZnTe substrates passivated with polycrystalline CdTe exhibited reduced surface leakage, suggesting that hydrogen passivates defects in bulk HgCdTe and in CdTe.

Black GE based on crystalline/amorphous core/shell nanoneedle arrays

DOEpatents

Javey, Ali; Chueh, Yu-Lun; Fan, Zhiyong

2014-03-04

Direct growth of black Ge on low-temperature substrates, including plastics and rubber is reported. The material is based on highly dense, crystalline/amorphous core/shell Ge nanoneedle arrays with ultrasharp tips (.about.4 nm) enabled by the Ni catalyzed vapor-solid-solid growth process. Ge nanoneedle arrays exhibit remarkable optical properties. Specifically, minimal optical reflectance (<1%) is observed, even for high angles of incidence (.about.75.degree.) and for relatively short nanoneedle lengths (.about.1 .mu.m). Furthermore, the material exhibits high optical absorption efficiency with an effective band gap of .about.1 eV. The reported black Ge can have important practical implications for efficient photovoltaic and photodetector applications on nonconventional substrates.

High transmittance hetero junctions based on n-ITO/p-CuO bilayer thin films

NASA Astrophysics Data System (ADS)

Jaya, T. P.; Pradyumnan, P. P.

2016-12-01

Oxide based bilayered n-ITO/p-CuO crystalline diodes were fabricated by plasma vapor deposition using radio frequency magnetron sputtering. The p-n hetero junction diodes were highly transparent in the visible region and exhibits rectifying I-V characteristics. The substrate temperature during fabrication of p-layer CuO was found to have a profound influence on I-V characteristics. The films deposited at substrate temperature of 150 °C and 230 °C exhibited diode ideality factors of (η value) 1.731 and 1.862 respectively. This high ideality factor, combined with an optical transparency of above 70% suggests the potential use of these bi-layers in optoelectronic applications.

Pd/V.sub.2O.sub.5 device for colorimetric H.sub.2 detection

DOEpatents

Liu, Ping [San Diego, CA; Tracy, C Edwin [Golden, CO; Pitts, J Roland [Lakewood, CO; Smith, II, R. Davis; Lee, Se-Hee [Lakewood, CO

2008-09-02

A sensor structure for chemochromic optical detection of hydrogen gas over a wide response range, that exhibits stability during repeated coloring/bleaching cycles upon exposure and removal of hydrogen gas, comprising: a glass substrate (20); a vanadium oxide layer (21) coated on the glass substrate; and a palladium layer (22) coated on the vanadium oxide layer.

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

NASA Astrophysics Data System (ADS)

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

2018-04-01

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

Nanowire surface fastener fabrication on flexible substrate.

PubMed

Toku, Yuhki; Uchida, Keita; Morita, Yasuyuki; Ju, Yang

2018-07-27

The market for wearable devices has increased considerably in recent years. In response to this demand, flexible electronic circuit technology has become more important. The conventional bonding technology in electronic assembly depends on high-temperature processes such as reflow soldering, which result in undesired thermal damages and residual stress at a bonding interface. In addition, it exhibits poor compatibility with bendable or stretchable device applications. Therefore, there is an urgent requirement to attach electronic parts on printed circuit boards with good mechanical and electrical properties at room temperature. Nanowire surface fasteners (NSFs) are candidates for resolving these problems. This paper describes the fabrication of an NSF on a flexible substrate, which can be used for room temperature conductive bonding. The template method is used for preparing high-density nanowire arrays. A Cu thin film is layered on the template as the flexible substrate. After etching the template, a Cu NSF is obtained on the Cu film substrate. In addition, the electrical and mechanical properties of the Cu NSF are studied under various fabrication conditions. The Cu NSF exhibits high shear adhesion strength (∼234 N cm -2 ) and low contact resistivity (2.2 × 10 -4 Ω cm 2 ).

Nanowire surface fastener fabrication on flexible substrate

NASA Astrophysics Data System (ADS)

Toku, Yuhki; Uchida, Keita; Morita, Yasuyuki; Ju, Yang

2018-07-01

The market for wearable devices has increased considerably in recent years. In response to this demand, flexible electronic circuit technology has become more important. The conventional bonding technology in electronic assembly depends on high-temperature processes such as reflow soldering, which result in undesired thermal damages and residual stress at a bonding interface. In addition, it exhibits poor compatibility with bendable or stretchable device applications. Therefore, there is an urgent requirement to attach electronic parts on printed circuit boards with good mechanical and electrical properties at room temperature. Nanowire surface fasteners (NSFs) are candidates for resolving these problems. This paper describes the fabrication of an NSF on a flexible substrate, which can be used for room temperature conductive bonding. The template method is used for preparing high-density nanowire arrays. A Cu thin film is layered on the template as the flexible substrate. After etching the template, a Cu NSF is obtained on the Cu film substrate. In addition, the electrical and mechanical properties of the Cu NSF are studied under various fabrication conditions. The Cu NSF exhibits high shear adhesion strength (∼234 N cm‑2) and low contact resistivity (2.2 × 10‑4 Ω cm2).

The XPS depth profiling and tribological characterization of ion-plated gold on various metals

NASA Technical Reports Server (NTRS)

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

1983-01-01

Friction properties were measured with a gold film; the graded interface between gold and nickel substrate; and the nickel substrate. All sliding was conducted against hard silicon carbide pins in two processes. In the adhesive process, friction arises primarily from adhesion between sliding surfaces. In the abrasion process, friction occurs as a result of the hard pin sliding against the film, indenting into it, and plowing a series of grooves. Copper and 440 C stainless steel substrates were also used. Results indicate that the friction related to both adhesion and abrasion is influenced by coating depth. The trends in friction behavior as a function of film depth are, however, just the opposite. The graded interface exhibited the highest adhesion and friction, while the graded interface resulted in the lowest abrasion and friction. The coefficient of friction due to abrasion is inversely related to the hardness. The greater the hardness of the surface, the lower is the abrasion and friction. The microhardness in the graded interface exhibited the highest hardness due to an alloy hardening effect. Almost no graded interface between the vapor-deposited gold film and the substrates was detected.

Assaying Oxidative Coupling Activity of CYP450 Enzymes.

PubMed

Agarwal, Vinayak

2018-01-01

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

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

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

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

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

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

EPA Science Inventory

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

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

PubMed Central

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

2016-01-01

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

Uniform modeling of bacterial colony patterns with varying nutrient and substrate

NASA Astrophysics Data System (ADS)

Schwarcz, Deborah; Levine, Herbert; Ben-Jacob, Eshel; Ariel, Gil

2016-04-01

Bacteria develop complex patterns depending on growth condition. For example, Bacillus subtilis exhibit five different patterns depending on substrate hardness and nutrient concentration. We present a unified integro-differential model that reproduces the entire experimentally observed morphology diagram at varying nutrient concentrations and substrate hardness. The model allows a comprehensive and quantitative comparison between experimental and numerical variables and parameters, such as colony growth rate, nutrient concentration and diffusion constants. As a result, the role of the different physical mechanisms underlying and regulating the growth of the colony can be evaluated.

α-Diazo-β-ketonitriles: uniquely reactive substrates for arene and alkene cyclopropanation.

PubMed

Nani, Roger R; Reisman, Sarah E

2013-05-15

An investigation of the intramolecular cyclopropanation reactions of α-diazo-β-ketonitriles is reported. These studies reveal that α-diazo-β-ketonitriles exhibit unique reactivity in their ability to undergo arene cyclopropanation reactions; other similar acceptor-acceptor-substituted diazo substrates instead produce mixtures of C-H insertion and dimerization products. α-Diazo-β-ketonitriles also undergo highly efficient intramolecular cyclopropanation of tri- and tetrasubstituted alkenes. In addition, the α-cyano-α-ketocyclopropane products are demonstrated to serve as substrates for SN2, SN2', and aldehyde cycloaddition reactions.

Multilevel robustness

NASA Astrophysics Data System (ADS)

Girard, Henri-Louis; Khan, Sami; Varanasi, Kripa K.

2018-03-01

A combination of hard, soft and nanoscale organic components results in robust superhydrophobic surfaces that can withstand mechanical abrasion and chemical oxidation, and exhibit excellent substrate adhesion.

The negative impact of α-ketoglutarate dehydrogenase complex deficiency on matrix substrate-level phosphorylation

PubMed Central

Kiss, Gergely; Konrad, Csaba; Doczi, Judit; Starkov, Anatoly A.; Kawamata, Hibiki; Manfredi, Giovanni; Zhang, Steven F.; Gibson, Gary E.; Beal, M. Flint; Adam-Vizi, Vera; Chinopoulos, Christos

2013-01-01

A decline in α-ketoglutarate dehydrogenase complex (KGDHC) activity has been associated with neurodegeneration. Provision of succinyl-CoA by KGDHC is essential for generation of matrix ATP (or GTP) by substrate-level phosphorylation catalyzed by succinyl-CoA ligase. Here, we demonstrate ATP consumption in respiration-impaired isolated and in situ neuronal somal mitochondria from transgenic mice with a deficiency of either dihydrolipoyl succinyltransferase (DLST) or dihydrolipoyl dehydrogenase (DLD) that exhibit a 20–48% decrease in KGDHC activity. Import of ATP into the mitochondrial matrix of transgenic mice was attributed to a shift in the reversal potential of the adenine nucleotide translocase toward more negative values due to diminished matrix substrate-level phosphorylation, which causes the translocase to reverse prematurely. Immunoreactivity of all three subunits of succinyl-CoA ligase and maximal enzymatic activity were unaffected in transgenic mice as compared to wild-type littermates. Therefore, decreased matrix substrate-level phosphorylation was due to diminished provision of succinyl-CoA. These results were corroborated further by the finding that mitochondria from wild-type mice respiring on substrates supporting substrate-level phosphorylation exhibited ∼30% higher ADP-ATP exchange rates compared to those obtained from DLST+/− or DLD+/− littermates. We propose that KGDHC-associated pathologies are a consequence of the inability of respiration-impaired mitochondria to rely on “in-house” mitochondrial ATP reserves.—Kiss, G., Konrad, C., Doczi, J., Starkov, A. A., Kawamata, H., Manfredi, G., Zhang, S. F., Gibson, G. E., Beal, M. F., Adam-Vizi, V., Chinopoulos, C. The negative impact of α-ketoglutarate dehydrogenase complex deficiency on matrix substrate-level phosphorylation. PMID:23475850

Substrate nitridation induced modulations in transport properties of wurtzite GaN/p-Si (100) heterojunctions grown by molecular beam epitaxy

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

Bhat, Thirumaleshwara N.; Rajpalke, Mohana K.; Krupanidhi, S. B.

Phase pure wurtzite GaN films were grown on Si (100) substrates by introducing a silicon nitride layer followed by low temperature GaN growth as buffer layers. GaN films grown directly on Si (100) were found to be phase mixtured, containing both cubic ({beta}) and hexagonal ({alpha}) modifications. The x-ray diffraction (XRD), scanning electron microscopy (SEM), photoluminescence (PL) spectroscopy studies reveal that the significant enhancement in the structural as well as in the optical properties of GaN films grown with silicon nitride buffer layer grown at 800 deg. C when compared to the samples grown in the absence of silicon nitridemore » buffer layer and with silicon nitride buffer layer grown at 600 deg. C. Core-level photoelectron spectroscopy of Si{sub x}N{sub y} layers reveals the sources for superior qualities of GaN epilayers grown with the high temperature substrate nitridation process. The discussion has been carried out on the typical inverted rectification behavior exhibited by n-GaN/p-Si heterojunctions. Considerable modulation in the transport mechanism was observed with the nitridation conditions. The heterojunction fabricated with the sample of substrate nitridation at high temperature exhibited superior rectifying nature with reduced trap concentrations. Lowest ideality factors ({approx}1.5) were observed in the heterojunctions grown with high temperature substrate nitridation which is attributed to the recombination tunneling at the space charge region transport mechanism at lower voltages and at higher voltages space charge limited current conduction is the dominating transport mechanism. Whereas, thermally generated carrier tunneling and recombination tunneling are the dominating transport mechanisms in the heterojunctions grown without substrate nitridation and low temperature substrate nitridation, respectively.« less

Influence of substrate metal alloy type on the properties of hydroxyapatite coatings deposited using a novel ambient temperature deposition technique.

PubMed

Barry, J N; Cowley, A; McNally, P J; Dowling, D P

2014-03-01

Hydroxyapatite (HA) coatings are applied widely to enhance the level of osteointegration onto orthopedic implants. Atmospheric plasma spray (APS) is typically used for the deposition of these coatings; however, HA crystalline changes regularly occur during this high-thermal process. This article reports on the evaluation of a novel low-temperature (<47°C) HA deposition technique, called CoBlast, for the application of crystalline HA coatings. To-date, reports on the CoBlast technique have been limited to titanium alloy substrates. This study addresses the suitability of the CoBlast technique for the deposition of HA coatings on a number of alternative metal alloys utilized in the fabrication of orthopedic devices. In addition to titanium grade 5, both cobalt chromium and stainless steel 316 were investigated. In this study, HA coatings were deposited using both the CoBlast and the plasma sprayed techniques, and the resultant HA coating and substrate properties were evaluated and compared. The CoBlast-deposited HA coatings were found to present similar surface morphologies, interfacial properties, and composition irrespective of the substrate alloy type. Coating thickness however displayed some variation with the substrate alloy, ranging from 2.0 to 3.0 μm. This perhaps is associated with the electronegativity of the metal alloys. The APS-treated samples exhibited evidence of both coating, and significantly, substrate phase alterations for two metal alloys; titanium grade 5 and cobalt chrome. Conversely, the CoBlast-processed samples exhibited no phase changes in the substrates after depositions. The APS alterations were attributed to the brief, but high-intensity temperatures experienced during processing. Copyright © 2013 Wiley Periodicals, Inc.

Hotspots engineering by grafting Au@Ag core-shell nanoparticles on the Au film over slightly etched nanoparticles substrate for on-site paraquat sensing.

PubMed

Wang, Chaoguang; Wu, Xuezhong; Dong, Peitao; Chen, Jian; Xiao, Rui

2016-12-15

Paraquat (PQ) pollutions are ultra-toxic to human beings and hard to be decomposed in the environment, thus requiring an on-site detection strategy. Herein, we developed a robust and rapid PQ sensing strategy based on the surface-enhanced Raman scattering (SERS) technique. A hybrid SERS substrate was prepared by grafting the Au@Ag core-shell nanoparticles (NPs) on the Au film over slightly etched nanoparticles (Au FOSEN). Hotspots were engineered at the junctions as indicated by the finite difference time domain calculation. SERS performance of the hybrid substrate was explored using p-ATP as the Raman probe. The hybrid substrate gives higher enhancement factor comparing to either the Au FOSEN substrate or the Au@Ag core-shell NPs, and exhibits excellent reproducibility, homogeneity and stability. The proposed SERS substrates were prepared in batches for the practical PQ sensing. The total analysis time for a single sample, including the pre-treatment and measurement, was less than 5min with a PQ detection limit of 10nM. Peak intensities of the SERS signal were plotted as a function of the PQ concentrations to calibrate the sensitivity by fitting the Hill's equation. The plotted calibration curve showed a good log-log linearity with the coefficient of determination of 0.98. The selectivity of the sensing proposal was based on the "finger print" Raman spectra of the analyte. The proposed substrate exhibited good recovery when it applied to real water samples, including lab tap water, bottled water, and commercially obtained apple juice and grape juice. This SERS-based PQ detection method is simple, rapid, sensitive and selective, which shows great potential in pesticide residue and additives abuse monitoring. Copyright © 2016 Elsevier B.V. All rights reserved.

A novel bifunctional Ni-doped TiO2 inverse opal with enhanced SERS performance and excellent photocatalytic activity

NASA Astrophysics Data System (ADS)

Li, Xuehong; Wu, Yun; Shen, Yuhua; Sun, Yan; Yang, Ying; Xie, Anjian

2018-01-01

Three-dimensional inverse opal photonic microarray (IOPM) structure exhibits good qualities in structural regularity and interconnectivity, such as high specific surface area, large pore volume, uniform pore size, and ordered periodic construction. Here, a novel nickel-doped titanium dioxide IOPM (Ni-TiO2 IOPM) was fabricated for the first time as a bifunctional material for the applications of surface-enhanced Raman scattering (SERS) substrate and photocatalyst. The Ni doping could change the defect concentration of the substrate to enhance the SERS effect, and could increase the light absorption of the substrate in visible region. The synergistic effect of Ni doping and the periodically ordered porous structure enhanced both SERS sensitivity and photocatalytic activity. As a SERS substrate, the Ni-TiO2 IOPM exhibited highly sensitive detection capability for 4-mercaptobenzoic acid (4-MBA) at a concentration as low as 1 × 10-11 M. Under simulated sunlight, about 95% of the methylene blue (MB) was degraded within 90 min when Ni-TiO2 IOPM was used as the photocatalytst. The Ni-TiO2 IOPM prepared in this work may be a promising bifunctional SERS substrate candidate for organic sewage detection and environment protection. In addition, the fabrication strategy can be extended to synthesize other nanomaterials with orderly and porous structure.

Microstructural study of codeposited pentacene:perfluoropentacene grown on KCl by TEM techniques

NASA Astrophysics Data System (ADS)

Félix, Rocío; Breuer, Tobias; Witte, Gregor; Volz, Kerstin; Gries, Katharina I.

2017-08-01

Transmission electron microscopy techniques have been used as a research tool to derive information on structure and orientation of organic semiconductor blends. Within this work, we have studied the structure and morphology of pentacene (PEN, C22H14) and perfluoropentacene (PFP, C22F14) blends grown with [2:1] and [1:2] mixing ratios on KCl substrates. The [2:1] mixture exhibits a uniform layer on the substrate with domains that are rotated in-plane by 90° towards each other. Electron diffraction experiments revealed that these domains are formed by a crystalline mixed phase (consisting of PEN and PFP) and a PEN phase in excess whose lattice parameters are rather similar. By contrast, in the [1:2] blend, two different arrangements were found. The majority of the sample exhibits some spicular fibers on a background layer lying on top of the KCl substrate. The microstructural characterization revealed that these fibers consist of pure PFP in excess while the background layer is formed by the mixed phase. The other arrangement, which is present to a lesser extent, consists of a PFP film that is in direct contact with the KCl substrate. Using electron diffraction experiments, the orientation of the different phases with respect to each other and in some cases relative to the KCl substrate has been determined.

Material growth and characterization for solid state devices

NASA Technical Reports Server (NTRS)

Stefanakos, E. K.; Collis, W. J.; Abul-Fadl, A.; Iyer, S.

1984-01-01

During the reporting period, InGaAs was grown on Fe-doped (semi-insulating) (100) InP substrates by current controlled liquid phase epitaxy (CCLPE) at 640 C and current densities of 2.5A sq/cm to 5 A/sq cm for periods from 5 to 30 minutes. Special efforts were made to reduce the background carrier concentration in the grown layers as much as possible. The best layers exhibited carrier concentrations in the mid-10 to the 15th power/cu cm range and up to 10,900 sq cm/V-sec room temperature mobility. InGaAsP quaternary layers of energy gap corresponding to wavelengths of approximately 1.5 microns and 1.3 microns were grown on (100) InP substrates by CCLPE. In the device fabrication area, work was directed toward processing MISFET's using InGaAs. SiO2, Si3N4 and Al2O3 were deposited by ion beam sputtering, electron beam evaporation and chemical vapor reaction on Si, GaAs, and InGaAs substrates. SiO2 and Si3N4 sputtered layers were found to possess a high density of pinhole defects that precluded capacitance-voltage analysis. Chemical vapor deposited Al2O3 layers on Si, GaAs and InGaAs substrates also exhibited a large number of pinhole defects. This prevented achieving good MIS devices over most of the substrate surface area.

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.

Analysis of effect of nanoporous alumina substrate coated with polypyrrole nanowire on cell morphology based on AFM topography.

PubMed

El-Said, Waleed Ahmed; Yea, Cheol-Heon; Jung, Mi; Kim, Hyuncheol; Choi, Jeong-Woo

2010-05-01

In this study, in situ electrochemical synthesis of polypyrrole nanowires with nanoporous alumina template was described. The formation of highly ordered porous alumina substrate was demonstrated with Atomic Force Microscopy (AFM) and Scanning Electron Microscopy (SEM). In addition, Fourier transform infrared analysis confirmed that polypyrrole (PP) nanowires were synthesized by direct electrochemical oxidation of pyrrole. HeLa cancer cells and HMCF normal cells were immobilized on the polypyrrole nanowires/nanoporous alumina substrates to determine the effects of the substrate on the cell morphology, adhesion and proliferation as well as the biocompatibility of the substrate. Cell adhesion and proliferation were characterized using a standard MTT assay. The effects of the polypyrrole nanowires/nanoporous alumina substrate on the cell morphology were studied by AFM. The nanoporous alumina coated with polypyrrole nanowires was found to exhibit better cell adhesion and proliferation than polystyrene petridish, aluminum foil, 1st anodized and uncoated 2nd anodized alumina substrate. This study showed the potential of the polypyrrole nanowires/nanoporous alumina substrate as biocompatibility electroactive polymer substrate for both healthy and cancer cell cultures applications.

Flexible organic light emitting diodes fabricated on biocompatible silk fibroin substrate

NASA Astrophysics Data System (ADS)

Liu, Yuqiang; Xie, Yuemin; Liu, Yuan; Song, Tao; Zhang, Ke-Qin; Liao, Liangsheng; Sun, Baoquan

2015-10-01

Flexible and biodegradable electronics are currently under extensive investigation for biocompatible and environmentally-friendly applications. Synthetic plastic foils are widely used as substrates for flexible electronics. But typical plastic substrates such as polyethylene naphthalate (PEN) could not be degraded in a natural bio-environment. A great demand still exists for a next-generation biocompatible and biodegradable substrate for future application. For example, electronic devices can be potentially integrated into the human body. In this work, we demonstrate that the biocompatible and biodegradable natural silk fibroin (SF) films embedded with silver nanowires (AgNWs) mesh could be employed as conductive transparent substrates to fabricate flexible organic light emitting diodes (OLEDs). Compared with commercial PEN substrates coated with indium tin oxide, the AgNWs/SF composite substrates exhibit a similar sheet resistance of 12 Ω sq-1, a lower surface roughness, as well as a broader light transmission range. Flexible OLEDs based on AgNWs/SF substrates achieve a current efficiency of 19 cd A-1, demonstrating the potential of the flexible AgNWs/SF films as conductive and transparent substrates for next-generation biodegradable devices.

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

PubMed Central

Felici, A; Amicosante, G

1995-01-01

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

Chiral poly-rare earth metal complexes in asymmetric catalysis

PubMed Central

Shibasaki, Masakatsu

2006-01-01

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

Measurement of Nonribosomal Peptide Synthetase Adenylation Domain Activity Using a Continuous Hydroxylamine Release Assay.

PubMed

Duckworth, Benjamin P; Wilson, Daniel J; Aldrich, Courtney C

2016-01-01

Adenylation is a crucial enzymatic process in the biosynthesis of nonribosomal peptide synthetase (NRPS) derived natural products. Adenylation domains are considered the gatekeepers of NRPSs since they select, activate, and load the carboxylic acid substrate onto a downstream peptidyl carrier protein (PCP) domain of the NRPS. We describe a coupled continuous kinetic assay for NRPS adenylation domains that substitutes the PCP domain with hydroxylamine as the acceptor molecule. The pyrophosphate released from the first-half reaction is then measured using a two-enzyme coupling system, which detects conversion of the chromogenic substrate 7-methylthioguanosine (MesG) to 7-methylthioguanine. From profiling substrate specificity of unknown or engineered adenylation domains to studying chemical inhibition of adenylating enzymes, this robust assay will be of widespread utility in the broad field NRPS enzymology.

Fabrication of Single Crystal Gallium Phosphide Thin Films on Glass.

PubMed

Emmer, Hal; Chen, Christopher T; Saive, Rebecca; Friedrich, Dennis; Horie, Yu; Arbabi, Amir; Faraon, Andrei; Atwater, Harry A

2017-07-05

Due to its high refractive index and low absorption coefficient, gallium phosphide is an ideal material for photonic structures targeted at the visible wavelengths. However, these properties are only realized with high quality epitaxial growth, which limits substrate choice and thus possible photonic applications. In this work, we report the fabrication of single crystal gallium phosphide thin films on transparent glass substrates via transfer bonding. GaP thin films on Si (001) and (112) grown by MOCVD are bonded to glass, and then the growth substrate is removed with a XeF 2 vapor etch. The resulting GaP films have surface roughnesses below 1 nm RMS and exhibit room temperature band edge photoluminescence. Magnesium doping yielded p-type films with a carrier density of 1.6 × 10 17  cm -3 that exhibited mobilities as high as 16 cm 2 V -1 s -1 . Due to their unique optical properties, these films hold much promise for use in advanced optical devices.

Fabrication of Single Crystal Gallium Phosphide Thin Films on Glass

DOE PAGES

Emmer, Hal; Chen, Christopher T.; Saive, Rebecca; ...

2017-07-05

Due to its high refractive index and low absorption coefficient, gallium phosphide is an ideal material for photonic structures targeted at the visible wavelengths. However, these properties are only realized with high quality epitaxial growth, which limits substrate choice and thus possible photonic applications. In this work, we report the fabrication of single crystal gallium phosphide thin films on transparent glass substrates via transfer bonding. GaP thin films on Si (001) and (112) grown by MOCVD are bonded to glass, and then the growth substrate is removed with a XeF 2 vapor etch. The resulting GaP films have surface roughnessesmore » below 1 nm RMS and exhibit room temperature band edge photoluminescence. Magnesium doping yielded p-type films with a carrier density of 1.6 × 10 17 cm -3 that exhibited mobilities as high as 16 cm 2V -1s -1. Therefore, due to their unique optical properties, these films hold much promise for use in advanced optical devices.« less

Surface modification of 316L stainless steel with magnetron sputtered TiN/VN nanoscale multilayers for bio implant applications.

PubMed

Subramanian, B; Ananthakumar, R; Kobayashi, Akira; Jayachandran, M

2012-02-01

Nanoscale multilayered TiN/VN coatings were developed by reactive dc magnetron sputtering on 316L stainless steel substrates. The coatings showed a polycrystalline cubic structure with (111) preferential growth. XPS analysis indicated the presence of peaks corresponding to Ti2p, V2p, N1s, O1s, and C1s. Raman spectra exhibited the characteristic peaks in the acoustic range of 160-320 cm(-1) and in the optic range between 480 and 695 cm(-1). Columnar structure of the coatings was observed from TEM analysis. The number of adherent platelets on the surface of the TiN/VN multilayer, VN, TiN single layer coating exhibit fewer aggregation and pseudopodium than on substrates. The wear resistance of the multilayer coatings increases obviously as a result of their high hardness. Tafel plots in simulated bodily fluid showed lower corrosion rate for the TiN/VN nanoscale multilayer coatings compared to single layer and bare 316L SS substrate.

Fabrication of Single Crystal Gallium Phosphide Thin Films on Glass

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

Emmer, Hal; Chen, Christopher T.; Saive, Rebecca

Due to its high refractive index and low absorption coefficient, gallium phosphide is an ideal material for photonic structures targeted at the visible wavelengths. However, these properties are only realized with high quality epitaxial growth, which limits substrate choice and thus possible photonic applications. In this work, we report the fabrication of single crystal gallium phosphide thin films on transparent glass substrates via transfer bonding. GaP thin films on Si (001) and (112) grown by MOCVD are bonded to glass, and then the growth substrate is removed with a XeF 2 vapor etch. The resulting GaP films have surface roughnessesmore » below 1 nm RMS and exhibit room temperature band edge photoluminescence. Magnesium doping yielded p-type films with a carrier density of 1.6 × 10 17 cm -3 that exhibited mobilities as high as 16 cm 2V -1s -1. Therefore, due to their unique optical properties, these films hold much promise for use in advanced optical devices.« less

The Influence of Chitosan Substrate and Its Nanometric Form Toward the Green Power Generation in Sediment Microbial Fuel Cell.

PubMed

Karthikeyan, C; Sathishkumar, Y; Lee, Yang Soo; Kim, Ae Rhan; Yoo, Dong Jin; Kumar, G Gnana

2017-01-01

A simple, environmental friendly and biologically important sediment interfaced fuel cell was developed for the green energy generation. The soil sediment used for the study is enriched of rich anthropogenic free organic carbon, sufficient manganese and high level potassium contents as evidenced from the geochemical characterizations. The saccharides produced by the catalytic reaction of substrate chitosan were utilized for the growth of microorganisms and electron shuttling processes. Chitosan substrate influenced sediment microbial fuel cells exhibited the nearly two fold power increment over the substrate free fuel cells. The fuel cell efficiencies were further increased by bringing the substrate chitosan at nanometric level, which is nearly three and two fold higher than that of substrate free and chitosan influenced sediment microbial fuel cells, respectively, and the influential parameters involved in the power and longevity issues were addressed with different perspectives.

Spectroscopy on the wing: naturally inspired SERS substrates for biochemical analysis.

PubMed

Garrett, Natalie L; Vukusic, Peter; Ogrin, Feodor; Sirotkin, Evgeny; Winlove, C Peter; Moger, Julian

2009-03-01

We show that naturally occurring chitinous nanostructures found on the wings of the Graphium butterfly can be used as substrates for surface-enhanced Raman scattering when coated with a thin film of gold or silver. The substrates were found to exhibit excellent biocompatibility and sensitivity, making them ideal for protein assaying. An assay using avidin/biotin binding showed that the substrates could be used to quantify protein binding directly from changes in the surface-enhanced Raman scattering (SERS) spectra and were sensitive over a concentration range comparable with a typical enzyme-linked immunosorbent assays (ELISA) assay. A biomimetic version of the wing nanostructures produced using a highly reproducible, large-scale fabrication process, yielded comparable enhancement factors and biocompatibility. The excellent biocompatibility of the wings and biomimetic substrates is unparalleled by other lithographically produced substrates, and this could pave the way for widespread application of ultrasensitive SERS-based bioassays.

Structure and magnetic properties of spinel-perovskite nanocomposite thin films on SrTiO3 (111) substrates

NASA Astrophysics Data System (ADS)

Kim, Dong Hun; Yang, Junho; Kim, Min Seok; Kim, Tae Cheol

2016-09-01

Epitaxial CoFe2O4-BiFeO3 nanocomposite thin films were synthesized on perovskite structured SrTiO3 (001) and (111) substrates by combinatorial pulsed laser deposition and characterized using scanning electron microscopy, x-ray diffraction, and vibrating sample magnetometer. Triangular BiFeO3 nanopillars were formed in a CoFe2O4 matrix on (111) oriented SrTiO3 substrates, while CoFe2O4 nanopillars with rectangular or square top surfaces grew in a BiFeO3 matrix on (001) substrates. The magnetic hysteresis loops of nanocomposites on (111) oriented SrTiO3 substrates showed isotropic properties due to the strain relaxation while those of films on SrTiO3 (001) substrates exhibited a strong out-of-plane anisotropy originated from shape and strain effects.

Substrate temperature effect on structural and optical properties of Bi2Te3 thin films

NASA Astrophysics Data System (ADS)

Jariwala, B. S.; Shah, D. V.; Kheraj, Vipul

2012-06-01

Structural and optical properties of Bi2Te3 thin films, thermally evaporated on well-cleaned glass substrates at different substrate temperatures, are reported here. X-ray diffraction was carried out for the structural characterization. XRD patterns of the films exhibit preferential orientation along the [0 1 5] direction for the films deposited at all the substrate temperatures together with other supported planes [2 0 5] & [1 1 0]. All other deposition conditions like thickness, deposition rate and pressure were maintained same throughout the experiment. X-ray diffraction lines confirm that the grown films are polycrystalline in nature with hexagonal crystal structure. The effect of substrate temperature on lattice constants, grain size, micro strain, number of crystallites and dislocation density have been investigated and reported in this paper. Also the substrate temperature effect on the optical property has been also investigated using the FTIR spectroscopy.

Nanocrystal-based complementary inverters constructed on flexible plastic substrates.

PubMed

Jang, Jaewon; Cho, Kyoungah; Yun, Junggwon; Kim, Sangsig

2013-05-01

We demonstrate a nanocrystal (NC)-based complementary inverter constructed on a flexible plastic substrate. The NC-based complementary inverter consists of n-type HgSe NC- and p-type HgTe NC-based thin-film transistors (TFTs). Solid films on a plastic substrate obtained from HgSe and HgTe nanocrystals by thermal transformation are utilized as the n- and p-channel layers in these TFTs, respectively. The electrical properties of these component TFTs on unstrained and strained substrates are characterized and the performance of the inverter on the flexible substrate is investigated. The inverter on the unstrained substrate exhibits a logic gain of about 8, a logic swing of 90%, and a noise margin of 2.0 V. The characteristics of the inverter are changed under tensile and compressive strains, but not very significantly. Moreover, a comparison of the electrical characteristics of the n- and p-channel TFTs and the inverter is made in this paper.

Method of making an apparatus for transpiration cooling of substrates such as turbine airfoils

DOEpatents

Alvin, Mary Anne; Anderson, Iver; Heidlof, Andy; White, Emma; McMordie, Bruce

2017-02-28

A method and apparatus for generating transpiration cooling using an oxidized porous HTA layer metallurgically bonded to a substrate having micro-channel architectures. The method and apparatus generates a porous HTA layer by spreading generally spherical HTA powder particles on a substrate, partially sintering under O.sub.2 vacuum until the porous HTA layer exhibits a porosity between 20% and 50% and a neck size ratio between 0.1 and 0.5, followed by a controlled oxidation generating an oxidation layer of alumina, chromia, or silica at a thickness of about 20 to about 500 nm. In particular embodiments, the oxidized porous HTA layer and the substrate comprise Ni as a majority element. In other embodiments, the oxidized porous HTA layer and the substrate further comprise Al, and in additional embodiments, the oxidized porous HTA layer and the substrate comprise .gamma.-Ni+.gamma.'-Ni.sub.3Al.

Low dielectric polyimide aerogels as substrates for lightweight patch antennas.

PubMed

Meador, Mary Ann B; Wright, Sarah; Sandberg, Anna; Nguyen, Baochau N; Van Keuls, Frederick W; Mueller, Carl H; Rodríguez-Solís, Rafael; Miranda, Félix A

2012-11-01

The dielectric properties and loss tangents of low-density polyimide aerogels have been characterized at various frequencies. Relative dielectric constants as low as 1.16 were measured for polyimide aerogels made from 2,2'-dimethylbenzidine (DMBZ) and biphenyl 3,3',4,4'-tetracarbozylic dianhydride (BPDA) cross-linked with 1,3,5-triaminophenoxybenzene (TAB). This formulation was used as the substrate to fabricate and test prototype microstrip patch antennas and benchmark against state of practice commercial antenna substrates. The polyimide aerogel antennas exhibited broader bandwidth, higher gain, and lower mass than the antennas made using commercial substrates. These are very encouraging results, which support the potential advantages of the polyimide aerogel-based antennas for aerospace applications.

Improved out-coupling efficiency of organic light emitting diodes fabricated on a TiO2 planarization layer with embedded Si oxide nanostructures

NASA Astrophysics Data System (ADS)

Sung, Young Hoon; Jung, Pil-Hoon; Han, Kyung-Hoon; Kim, Yang Doo; Kim, Jang-Joo; Lee, Heon

2017-10-01

In order to increase the out-coupling efficiency of organic light emitting diodes, conical Si oxide nanostructures were formed on a glass substrate using nanoimprint lithography with hydrogen silsesquioxane. Then, the substrate was planarized with TiO2 nanoparticles. Since TiO2 nanoparticles have a higher refractive index than Si oxide, the surface of substrate is physically flat, but optically undulated in a manner that enables optical scattering and suppression of total internal reflection. Subsequently, OLEDs formed on a substrate with nanostructured Si oxide and a TiO2 planarization layer exhibit a 25% increase in out-coupling efficiency by suppressing total internal reflection.

Use of a fluorescent radiolabeled triacylglycerol as a substrate for lipoprotein lipase and hepatic triglyceride lipase

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

Dousset, N.; Negre, A.; Salvayre, R.

1988-06-01

A fluorescent radiolabeled triacylglycerol has been synthesized by using a fluorescent fatty acid (pyrene decanoic acid) and a radiolabeled oleic acid. This analog of the natural substrate, 1(3)pyrene decanoic-2,3 (1,2)-dioleoyl-sn-glycerol, has been tested as substrate for determining lipoprotein lipase and hepatic triacylglycerol lipase activities in post-heparin plasma. Optimal conditions for the determination of the two post-heparin plasma lipases were similar to those using radiolabeled triolein. Using this substrate, both post-heparin lipases exhibited their characteristic properties (pH optimum and effect of inhibitors) and attacked external ester bonds (1 or 3) containing pyrene decanoic and oleic acids at a similar rate.

Activity Augmentation of Amphioxus Peptidoglycan Recognition Protein BbtPGRP3 via Fusion with a Chitin Binding Domain

PubMed Central

Wang, Wen-Jie; Cheng, Wang; Luo, Ming; Yan, Qingyu; Yu, Hong-Mei; Li, Qiong; Cao, Dong-Dong; Huang, Shengfeng; Xu, Anlong; Mariuzza, Roy A.; Chen, Yuxing; Zhou, Cong-Zhao

2015-01-01

Peptidoglycan recognition proteins (PGRPs), which have been identified in most animals, are pattern recognition molecules that involve antimicrobial defense. Resulting from extraordinary expansion of innate immune genes, the amphioxus encodes many PGRPs of diverse functions. For instance, three isoforms of PGRP encoded by Branchiostoma belcheri tsingtauense, termed BbtPGRP1~3, are fused with a chitin binding domain (CBD) at the N-terminus. Here we report the 2.7 Å crystal structure of BbtPGRP3, revealing an overall structure of an N-terminal hevein-like CBD followed by a catalytic PGRP domain. Activity assays combined with site-directed mutagenesis indicated that the individual PGRP domain exhibits amidase activity towards both DAP-type and Lys-type peptidoglycans (PGNs), the former of which is favored. The N-terminal CBD not only has the chitin-binding activity, but also enables BbtPGRP3 to gain a five-fold increase of amidase activity towards the Lys-type PGNs, leading to a significantly broadened substrate spectrum. Together, we propose that modular evolution via domain shuffling combined with gene horizontal transfer makes BbtPGRP1~3 novel PGRPs of augmented catalytic activity and broad recognition spectrum. PMID:26479246

The elastase-PK101 structure: Mechanism of an ultrasensitive activity-based probe revealed

DOE PAGES

Lechtenberg, Bernhard C.; Robinson, Howard R.; Kasperkiewicz, Paulina; ...

2015-01-22

Human neutrophil elastase (HNE) plays a central role in neutrophil host defense, but its broad specificity makes HNE a difficult target for both inhibitor and probe development. Recently, we identified the unnatural amino acid containing activity-based probe PK101, which exhibits astounding sensitivity and selectivity for HNE, yet completely lacks mechanistic explanation for its unique characteristics. Here, we present the crystal structure of the HNE-PK101 complex which not only reveals the basis for PK101 ultrasensitivity but also uncovers so far unrecognized HNE features. Strikingly, the Nle( O-Bzl) function in the P4 position of PK101 reveals and leverages an “exo-pocket” on HNEmore » as a critical factor for selectivity. Furthermore, the PK101 P3 position harbors a methionine dioxide function, which mimics a post-translationally oxidized methionine residue and forms a critical hydrogen bond to the backbone amide of Gly219 of HNE. Gly219 resides in a Gly–Gly motif that is unique to HNE, yet compulsory for this interaction. Consequently, this feature enables HNE to accommodate substrates that have undergone methionine oxidation, which constitutes a hallmark post-translational modification of neutrophil signaling.« less

Optimized mid-infrared thermal emitters for applications in aircraft countermeasures

NASA Astrophysics Data System (ADS)

Lorenzo, Simón G.; You, Chenglong; Granier, Christopher H.; Veronis, Georgios; Dowling, Jonathan P.

2017-12-01

We introduce an optimized aperiodic multilayer structure capable of broad angle and high temperature thermal emission over the 3 μm to 5 μm atmospheric transmission band. This aperiodic multilayer structure composed of alternating layers of silicon carbide and graphite on top of a tungsten substrate exhibits near maximal emittance in a 2 μm wavelength range centered in the mid-wavelength infrared band traditionally utilized for atmospheric transmission. We optimize the layer thicknesses using a hybrid optimization algorithm coupled to a transfer matrix code to maximize the power emitted in this mid-infrared range normal to the structure's surface. We investigate possible applications for these structures in mimicking 800-1000 K aircraft engine thermal emission signatures and in improving countermeasure effectiveness against hyperspectral imagers. We find these structures capable of matching the Planck blackbody curve in the selected infrared range with relatively sharp cutoffs on either side, leading to increased overall efficiency of the structures. Appropriately optimized multilayer structures with this design could lead to matching a variety of mid-infrared thermal emissions. For aircraft countermeasure applications, this method could yield a flare design capable of mimicking engine spectra and breaking the lock of hyperspectral imaging systems.

Ultrafine Pt Nanoparticles and Amorphous Nickel Supported on 3D Mesoporous Carbon Derived from Cu-Metal-Organic Framework for Efficient Methanol Oxidation and Nitrophenol Reduction.

PubMed

Wu, Xue-Qian; Zhao, Jun; Wu, Ya-Pan; Dong, Wen-Wen; Li, Dong-Sheng; Li, Jian-Rong; Zhang, Qichun

2018-04-18

The development of novel strategy to produce new porous carbon materials is extremely important because these materials have wide applications in energy storage/conversion, mixture separation, and catalysis. Herein, for the first time, a novel 3D carbon substrate with hierarchical pores derived from commercially available Cu-MOF (metal-organic framework) (HKUST-1) through carbonization and chemical etching has been employed as the catalysts' support. Highly dispersed Pt nanoparticles and amorphous nickel were evenly dispersed on the surface or embedded within carbon matrix. The corresponding optimal composite catalyst exhibits a high mass-specific peak current of 1195 mA mg -1 Pt and excellent poison resistance capacity ( I F / I B = 1.58) for methanol oxidation compared to commercial Pt/C (20%). Moreover, both composite catalysts manifest outstanding properties in the reduction of nitrophenol and demonstrate diverse selectivities for 2/3/4-nitrophenol, which can be attributed to different integrated forms between active species and carbon matrix. This attractive route offers broad prospects for the usage of a large number of available MOFs in fabricating functional carbon materials as well as highly active carbon-based electrocatalysts and heterogeneous organic catalysts.

Immobilized Subpopulations of Leaf Epidermal Mitochondria Mediate PENETRATION2-Dependent Pathogen Entry Control in Arabidopsis

PubMed Central

Klapprodt, Christine; Hause, Gerd; Lipka, Volker

2016-01-01

The atypical myrosinase PENETRATION2 (PEN2) is required for broad-spectrum invasion resistance to filamentous plant pathogens. Previous localization studies suggested PEN2-GFP association with peroxisomes. Here, we show that PEN2 is a tail-anchored protein with dual-membrane targeting to peroxisomes and mitochondria and that PEN2 has the capacity to form homo-oligomer complexes. We demonstrate pathogen-induced recruitment and immobilization of mitochondrial subpopulations at sites of attempted fungal invasion and show that mitochondrial arrest is accompanied by peripheral accumulation of GFP-tagged PEN2. PEN2 substrate production by the cytochrome P450 monooxygenase CYP81F2 is localized to the surface of the endoplasmic reticulum, which focally reorganizes close to the immobilized mitochondria. Exclusive targeting of PEN2 to the outer membrane of mitochondria complements the pen2 mutant phenotype, corroborating the functional importance of the mitochondrial PEN2 protein subpool for controlled local production of PEN2 hydrolysis products at subcellular plant-microbe interaction domains. Moreover, live-cell imaging shows that mitochondria arrested at these domains exhibit a pathogen-induced redox imbalance, which may lead to the production of intracellular signals. PMID:26721862

How UV photolysis accelerates the biodegradation and mineralization of sulfadiazine (SD).

PubMed

Pan, Shihui; Yan, Ning; Liu, Xinyue; Wang, Wenbing; Zhang, Yongming; Liu, Rui; Rittmann, Bruce E

2014-11-01

Sulfadiazine (SD), one of broad-spectrum antibiotics, exhibits limited biodegradation in wastewater treatment due to its chemical structure, which requires initial mono-oxygenation reactions to initiate its biodegradation. Intimately coupling UV photolysis with biodegradation, realized with the internal loop photobiodegradation reactor, accelerated SD biodegradation and mineralization by 35 and 71 %, respectively. The main organic products from photolysis were 2-aminopyrimidine (2-AP), p-aminobenzenesulfonic acid (ABS), and aniline (An), and an SD-photolysis pathway could be identified using C, N, and S balances. Adding An or ABS (but not 2-AP) into the SD solution during biodegradation experiments (no UV photolysis) gave SD removal and mineralization rates similar to intimately coupled photolysis and biodegradation. An SD biodegradation pathway, based on a diverse set of the experimental results, explains how the mineralization of ABS and An (but not 2-AP) provided internal electron carriers that accelerated the initial mono-oxygenation reactions of SD biodegradation. Thus, multiple lines of evidence support that the mechanism by which intimately coupled photolysis and biodegradation accelerated SD removal and mineralization was through producing co-substrates whose oxidation produced electron equivalents that stimulated the initial mono-oxygenation reactions for SD biodegradation.

Co-metabolic degradation of diazo dye- reactive blue 160 by enriched mixed cultures BDN.

PubMed

Balapure, Kshama H; Jain, Kunal; Chattaraj, Sananda; Bhatt, Nikhil S; Madamwar, Datta

2014-08-30

Mixed cultures BDN (BDN) proficient in decolourizing diazo dye-reactive blue 160 (RB160) consist of eight bacterial strains, was developed through culture enrichment method from soil samples contaminated with anthropogenic activities. The synthrophic interactions of BDN have led to complete decolourization and degradation of RB160 (100mg/L) within 4h along with co-metabolism of yeast extract (0.5%) in minimal medium. BDN microaerophilicaly decolourized even 1500mg/L of RB160 under high saline conditions (20g/L NaCl) at 37°C and pH 7.0. BDN exhibited broad substrate specificity and decolourized 27 structurally different dyes. The reductase enzymes symmetrically cleaved RB160 and oxidative enzymes further metabolised the degraded products and five different intermediates were identified using FTIR, (1)HNMR and GC-MS. The phytotoxicity assay confirmed that intact RB160 was more toxic than dye degraded intermediates. The BDN was able to colonize and decolourized RB160 in soil model system in presence of indigenous miocroflora as well as in sterile soil without any amendment of additional nutrients, which signifies it useful and potential application in bioremediation. Copyright © 2014 Elsevier B.V. All rights reserved.

Structure of fructose bisphosphate aldolase from Bartonella henselae bound to fructose 1,6-bisphosphate.

PubMed

Gardberg, Anna; Abendroth, Jan; Bhandari, Janhavi; Sankaran, Banumathi; Staker, Bart

2011-09-01

Fructose bisphosphate aldolase (FBPA) enzymes have been found in a broad range of eukaryotic and prokaryotic organisms. FBPA catalyses the cleavage of fructose 1,6-bisphosphate into glyceraldehyde 3-phosphate and dihydroxyacetone phosphate. The SSGCID has reported several FBPA structures from pathogenic sources, including the bacterium Brucella melitensis and the protozoan Babesia bovis. Bioinformatic analysis of the Bartonella henselae genome revealed an FBPA homolog. The B. henselae FBPA enzyme was recombinantly expressed and purified for X-ray crystallographic studies. The purified enzyme crystallized in the apo form but failed to diffract; however, well diffracting crystals could be obtained by cocrystallization in the presence of the native substrate fructose 1,6-bisphosphate. A data set to 2.35 Å resolution was collected from a single crystal at 100 K. The crystal belonged to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a=72.39, b=127.71, c=157.63 Å. The structure was refined to a final free R factor of 22.2%. The structure shares the typical barrel tertiary structure and tetrameric quaternary structure reported for previous FBPA structures and exhibits the same Schiff base in the active site.

Hot-Volumes as Uniform and Reproducible SERS-Detection Enhancers in Weakly-Coupled Metallic Nanohelices

NASA Astrophysics Data System (ADS)

Caridad, José M.; Winters, Sinéad; McCloskey, David; Duesberg, Georg S.; Donegan, John F.; Krstić, Vojislav

2017-03-01

Reproducible and enhanced optical detection of molecules in low concentrations demands simultaneously intense and homogeneous electric fields acting as robust signal amplifiers. To generate such sophisticated optical near-fields, different plasmonic nanostructures were investigated in recent years. These, however, exhibit either high enhancement factor (EF) or spatial homogeneity but not both. Small interparticle gaps or sharp nanostructures show enormous EFs but no near-field homogeneity. Meanwhile, approaches using rounded and separated monomers create uniform near-fields with moderate EFs. Here, guided by numerical simulations, we show how arrays of weakly-coupled Ag nanohelices achieve both homogeneous and strong near-field enhancements, reaching even the limit forreproducible detection of individual molecules. The unique near-field distribution of a single nanohelix consists of broad hot-spots, merging with those from neighbouring nanohelices in specific array configurations and generating a wide and uniform detection zone (“hot-volume”). We experimentally assessed these nanostructures via surface-enhanced Raman spectroscopy, obtaining a corresponding EF of ~107 and a relative standard deviation <10%. These values demonstrate arrays of nanohelices as state-of-the-art substrates for reproducible optical detection as well as compelling nanostructures for related fields such as near-field imaging.

Purification and characterization of caffeine synthase from tea leaves.

PubMed

Kato, M; Mizuno, K; Fujimura, T; Iwama, M; Irie, M; Crozier, A; Ashihara, H

1999-06-01

Caffeine synthase (CS), the S-adenosylmethionine-dependent N-methyltransferase involved in the last two steps of caffeine biosynthesis, was extracted from young tea (Camellia sinensis) leaves; the CS was purified 520-fold to apparent homogeneity and a final specific activity of 5.7 nkat mg-1 protein by ammonium sulfate fractionation and hydroxyapatite, anion-exchange, adenosine-agarose, and gel-filtration chromatography. The native enzyme was monomeric with an apparent molecular mass of 61 kD as estimated by gel-filtration chromatography and 41 kD as analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The enzyme displayed a sharp pH optimum of 8.5. The final preparation exhibited 3- and 1-N-methyltransferase activity with a broad substrate specificity, showing high activity toward paraxanthine, 7-methylxanthine, and theobromine and low activity with 3-methylxanthine and 1-methylxanthine. However, the enzyme had no 7-N-methyltransferase activity toward xanthosine and xanthosine 5'-monophosphate. The Km values of CS for paraxanthine, theobromine, 7-methylxanthine, and S-adenosylmethionine were 24, 186, 344, and 21 microM, respectively. The possible role and regulation of CS in purine alkaloid biosynthesis in tea leaves are discussed. The 20-amino acid N-terminal sequence for CS showed little homology with other methyltransferases.

A resonance-free nano-film airborne ultrasound emitter

NASA Astrophysics Data System (ADS)

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

2013-01-01

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

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

NASA Technical Reports Server (NTRS)

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

2013-01-01

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

Matrix metalloproteinase processing of signaling molecules to regulate inflammation.

PubMed

Butler, Georgina S; Overall, Christopher M

2013-10-01

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

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

PubMed Central

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

2008-01-01

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

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

PubMed Central

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

2011-01-01

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

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

PubMed

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

2010-07-16

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

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

PubMed

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

2017-09-06

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

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

PubMed

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

2016-11-01

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

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

PubMed Central

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

2013-01-01

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

Draft Genome Sequence of Streptomyces sp. Strain Wb2n-11, a Desert Isolate with Broad-Spectrum Antagonism against Soilborne Phytopathogens

DOE PAGES

Köberl, Martina; White, Richard A.; Erschen, Sabine; ...

2015-08-06

Streptomyces sp. strain Wb2n-11, isolated from native desert soil, exhibited broad-spectrum antagonism against plant pathogenic fungi, bacteria, and nematodes. The 8.2-Mb draft genome reveals genes putatively responsible for its promising biocontrol activity and genes which enable the soil bacterium to directly interact beneficially with plants.

Flow variation and substrate type affect dislodgement of the freshwater polychaete, Manayunkia speciosa

USGS Publications Warehouse

Malakauskas, David M.; Wilson, Sarah J.; Wilzbach, Margaret A.; Som, Nicholas A.

2013-01-01

We quantified microscale flow forces and their ability to entrain the freshwater polychaete, Manayunkia speciosa, the intermediate host for 2 myxozoan parasites (Ceratomyxa shasta and Parvicapsula minibicornis) that cause substantial mortalities in salmonid fishes in the Pacific Northwest. In a laboratory flume, we measured the shear stress associated with 2 mean flow velocities and 3 substrates and quantified associated dislodgement of polychaetes, evaluated survivorship of dislodged polychaetes, and observed behavioral responses of the polychaetes in response to increased flow. We used a generalized linear mixed model to estimate the probability of polychaete dislodgement for treatment combinations of velocity (mean flow velocity  =  55 cm/s with a shear velocity  =  3 cm/s, mean flow velocity  =  140 cm/s with a shear velocity  =  5 cm/s) and substrate type (depositional sediments and analogs of rock faces and the filamentous alga, Cladophora). Few polychaetes were dislodged at shear velocities <3 cm/s on any substrate. Above this level of shear, probability of dislodgement was strongly affected by both substrate type and velocity. After accounting for substrate, odds of dislodgement were 8× greater at the higher flow. After accounting for velocity, probability of dislodgement was greatest from fine sediments, intermediate from rock faces, and negligible from Cladophora. Survivorship of dislodged polychaetes was high. Polychaetes exhibited a variety of behaviors for avoiding increases in flow, including extrusion of mucus, burrowing into sediments, and movement to lower-flow microhabitats. Our findings suggest that polychaete populations probably exhibit high resilience to flow-mediated disturbances.

Microstructure, Tensile Adhesion Strength and Thermal Shock Resistance of TBCs with Different Flame-Sprayed Bond Coat Materials Onto BMI Polyimide Matrix Composite

NASA Astrophysics Data System (ADS)

Abedi, H. R.; Salehi, M.; Shafyei, A.

2017-10-01

In this study, thermal barrier coatings (TBCs) composed of different bond coats (Zn, Al, Cu-8Al and Cu-6Sn) with mullite top coats were flame-sprayed and air-plasma-sprayed, respectively, onto bismaleimide matrix composites. These polyimide matrix composites are of interest to replace PMR-15, due to concerns about the toxicity of the MDA monomer from which PMR-15 is made. The results showed that pores and cracks appeared at the bond coat/substrate interface for the Al-bonded TBC because of its high thermal conductivity and diffusivity resulting in transferring of high heat flux and temperature to the polymeric substrate during top coat deposition. The other TBC systems due to the lower conductivity and diffusivity of bonding layers could decrease the adverse thermal effect on the polymer substrate during top coat deposition and exhibited adhesive bond coat/substrate interfaces. The tensile adhesion test showed that the adhesion strength of the coatings to the substrate is inversely proportional to the level of residual stress in the coatings. However, the adhesion strength of Al bond-coated sample decreased strongly after mullite top coat deposition due to thermal damage at the bond coat/substrate interface. TBC system with the Cu-6Sn bond coat exhibited the best thermal shock resistance, while Al-bonded TBC showed the lowest. It was inferred that thermal mismatch stresses and oxidation of the bond coats were the main factors causing failure in the thermal shock test.

Highly adhesive and high fatigue-resistant copper/PET flexible electronic substrates

NASA Astrophysics Data System (ADS)

Park, Sang Jin; Ko, Tae-Jun; Yoon, Juil; Moon, Myoung-Woon; Oh, Kyu Hwan; Han, Jun Hyun

2018-01-01

A voidless Cu/PET substrate is fabricated by producing a superhydrophilic PET surface comprised of nanostructures with large width and height and then by Cu electroless plating. Effect of PET surface nanostructure size on the failure mechanism of the Cu/PET substrate is studied. The fabricated Cu/PET substrate exhibits a maximum peel strength of 1300 N m-1 without using an interlayer, and virtually no increase in electrical resistivity under the extreme cyclic bending condition of 1 mm curvature radius after 300 k cycles. The authors find that there is an optimum nanostructure size for the highest Cu/PET adhesion strength, and the failure mechanism of the Cu/PET flexible substrate depends on the PET surface nanostructure size. Thus, this work presents the possibility to produce flexible metal/polymer electronic substrates that have excellent interfacial adhesion between the metal and polymer and high fatigue resistance against repeated bending. Such metal/polymer substrates provides new design opportunities for wearable electronic devices that can withstand harsh environments and have extended lifetimes.

Biodegradation of Oil Slicks on the Marine Environment.

DTIC Science & Technology

1976-11-01

Ransenula, Candida, Rho4o~torula and Penicillium . The substrate range of these organisms wasevaluated on 11 aliphatic , alicyclic and aromatic...and aromatic compounds (TR 1, ],97C). On the basis of the above substrate range tests and growth, characteristic., a Flavobacteri um sp . and a...incubation. ~ -Paraff Ins served as the bestsubstrates for both organisms, but Plavobacteriua sp . exhibited higher rates of mineralization. Branching

Ceramic capacitor exhibiting graceful failure by self-clearing, method for fabricating self-clearing capacitor

DOEpatents

Kaufman, David Y [Chicago, IL; Saha, Sanjib [Santa Clara, CA

2006-08-29

A short-resistant capacitor comprises an electrically conductive planar support substrate having a first thickness, a ceramic film deposited over the support substrate, thereby defining a ceramic surface; and a metallic film deposited over the ceramic surface, said film having a second thickness which is less than the first thickness and which is between 0.01 and 0.1 microns.

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

PubMed

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

2012-06-19

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

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

PubMed Central

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

2011-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2006-09-01

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

Tet(L) and Tet(K) Tetracycline-Divalent Metal/H+ Antiporters: Characterization of Multiple Catalytic Modes and a Mutagenesis Approach to Differences in Their Efflux Substrate and Coupling Ion Preferences

PubMed Central

Jin, Jie; Guffanti, Arthur A.; Bechhofer, David H.; Krulwich, Terry A.

2002-01-01

The Tet(L) protein encoded in the Bacillus subtilis chromosome and the closely related Tet(K) protein from Staphylococcus aureus plasmids are multifunctional antiporters that have three cytoplasmic efflux substrates: a tetracycline-divalent metal (TC-Me2+) complex that bears a net single positive charge, Na+, and K+. Tet(L) and Tet(K) had been shown to couple efflux of each of these substrates to influx of H+ as the coupling ion. In this study, competitive cross-inhibition between K+ and other cytoplasmic efflux substrates was demonstrated. Tet(L) and Tet(K) had also been shown to use K+ as an alternate coupling ion in support of Na+ or K+ efflux. Here they were shown to couple TC-Me2+ efflux to K+ uptake as well, exhibiting greater use of K+ as a coupling ion as the external pH increased. The substrate and coupling ion preferences of the two Tet proteins differed, especially in the higher preference of Tet(K) than Tet(L) for K+, both as a cytoplasmic efflux substrate and as an external coupling ion. Site-directed mutagenesis was employed to test the hypothesis that some feature of the putative “antiporter motif,” motif C, of Tet proteins would be involved in these characteristic preferences. Mutation of the A157 in Tet(L) to a hydroxyamino acid resulted in a more Tet(K)-like K+ preference both as coupling ion and efflux substrate. A reciprocal S157A mutant of Tet(K) exhibited reduced K+ preference. Competitive inhibition among substrates and the parallel effects of the single mutation upon K+ preference, as both an efflux substrate and coupling ion, are compatible with a model in which a single translocation pathway through the Tet(L) and Tet(K) transporters is used both for the cytoplasmic efflux substrates and for the coupling ions, in an alternating fashion. However, the effects of the A157 and other mutations of Tet(L) indicate that even if there are a shared binding site and translocation pathway, some elements of that pathway are used by all substrates and others are important only for particular substrates. PMID:12169596

Precise micropatterning of silver nanoparticles on plastic substrates

NASA Astrophysics Data System (ADS)

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

2017-04-01

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

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

PubMed

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

2014-09-01

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

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

PubMed Central

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

2014-01-01

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

Preparations, Properties, and Applications of Periodic Nano Arrays using Anodized Aluminum Oxide and Di-block Copolymer

NASA Astrophysics Data System (ADS)

Noh, Kunbae

2011-12-01

Self-ordered arrangements observed in various materials systems such as anodic aluminum oxide, polystyrene nanoparticles, and block copolymer are of great interest in terms of providing new opportunities in nanofabrication field where lithographic techniques are broadly used in general. Investigations on self-assembled nano arrays to understand how to obtain periodic nano arrays in an efficient yet inexpensive way, and how to realize advanced material and device systems thereof, can lead to significant impacts on science and technology for many forefront device applications. In this thesis, various aspects of periodic nano-arrays have been discussed including novel preparations, properties and applications of anodized aluminum oxide (AAO) and PS-b-P4VP (S4VP) di-block copolymer self-assembly. First, long-range ordered AAO arrays have been demonstrated. Nanoimprint lithography (NIL) process allowed a faithful pattern transfer of the imprint mold pattern onto Al thin film, and interesting self-healing and pattern tripling phenomena were observed, which could be applicable towards fabrication of the NIL master mold having highly dense pattern over large area, useful for fabrication of a large-area substrate for predictable positioning of arrayed devices. Second, S4VP diblock copolymer self-assembly and S4VP directed AAO self-assembly have been demonstrated in the Al thin film on Si substrate. Such a novel combination of two dissimilar self-assembly techniques demonstrated a potential as a versatile tool for nanopatterning formation on a Si substrate, capable of being integrated into Si process technology. As exemplary applications, vertically aligned Ni nanowires have been synthesized into an S4VP-guided AAO membrane on a Si substrate in addition to anti-dot structured [Co/Pd]n magnetic multilayer using S4VP self assembly. Third, a highly hexagonally ordered, vertically parallel aluminum oxide nanotube array was successfully fabricated via hard anodization technique. The Al2O3 nanotube arrays so fabricated exhibit a uniform and reproducible dimension, and a quite high aspect ratio of greater than ˜1,000. Such high-aspect-ratio, mechanically robust, large-surface-area nanotube array structure can be useful for many technical applications. As a potential application in biomedical research, drug storage/controlled drug release from such AAO nanotubes was investigated, and the advantageous potential of using AAO nanotubes for biological implant surface coatings alternative to TiO2 nanotubes has been discussed.

Combining Dynamic Stretch and Tunable Stiffness to Probe Cell Mechanobiology In Vitro

PubMed Central

Throm Quinlan, Angela M.; Sierad, Leslie N.; Capulli, Andrew K.; Firstenberg, Laura E.; Billiar, Kristen L.

2011-01-01

Cells have the ability to actively sense their mechanical environment and respond to both substrate stiffness and stretch by altering their adhesion, proliferation, locomotion, morphology, and synthetic profile. In order to elucidate the interrelated effects of different mechanical stimuli on cell phenotype in vitro, we have developed a method for culturing mammalian cells in a two-dimensional environment at a wide range of combined levels of substrate stiffness and dynamic stretch. Polyacrylamide gels were covalently bonded to flexible silicone culture plates and coated with monomeric collagen for cell adhesion. Substrate stiffness was adjusted from relatively soft (G′ = 0.3 kPa) to stiff (G′ = 50 kPa) by altering the ratio of acrylamide to bis-acrylamide, and the silicone membranes were stretched over circular loading posts by applying vacuum pressure to impart near-uniform stretch, as confirmed by strain field analysis. As a demonstration of the system, porcine aortic valve interstitial cells (VIC) and human mesenchymal stem cells (hMSC) were plated on soft and stiff substrates either statically cultured or exposed to 10% equibiaxial or pure uniaxial stretch at 1Hz for 6 hours. In all cases, cell attachment and cell viability were high. On soft substrates, VICs cultured statically exhibit a small rounded morphology, significantly smaller than on stiff substrates (p<0.05). Following equibiaxial cyclic stretch, VICs spread to the extent of cells cultured on stiff substrates, but did not reorient in response to uniaxial stretch to the extent of cells stretched on stiff substrates. hMSCs exhibited a less pronounced response than VICs, likely due to a lower stiffness threshold for spreading on static gels. These preliminary data demonstrate that inhibition of spreading due to a lack of matrix stiffness surrounding a cell may be overcome by externally applied stretch suggesting similar mechanotransduction mechanisms for sensing stiffness and stretch. PMID:21858051

Substrate specificity characterization for eight putative nudix hydrolases. Evaluation of criteria for substrate identification within the Nudix family.

PubMed

Nguyen, Vi N; Park, Annsea; Xu, Anting; Srouji, John R; Brenner, Steven E; Kirsch, Jack F

2016-12-01

The nearly 50,000 known Nudix proteins have a diverse array of functions, of which the most extensively studied is the catalyzed hydrolysis of aberrant nucleotide triphosphates. The functions of 171 Nudix proteins have been characterized to some degree, although physiological relevance of the assayed activities has not always been conclusively demonstrated. We investigated substrate specificity for eight structurally characterized Nudix proteins, whose functions were unknown. These proteins were screened for hydrolase activity against a 74-compound library of known Nudix enzyme substrates. We found substrates for four enzymes with k cat /K m values >10,000 M -1  s -1 : Q92EH0_LISIN of Listeria innocua serovar 6a against ADP-ribose, Q5LBB1_BACFN of Bacillus fragilis against 5-Me-CTP, and Q0TTC5_CLOP1 and Q0TS82_CLOP1 of Clostridium perfringens against 8-oxo-dATP and 3'-dGTP, respectively. To ascertain whether these identified substrates were physiologically relevant, we surveyed all reported Nudix hydrolytic activities against NTPs. Twenty-two Nudix enzymes are reported to have activity against canonical NTPs. With a single exception, we find that the reported k cat /K m values exhibited against these canonical substrates are well under 10 5 M -1  s -1 . By contrast, several Nudix enzymes show much larger k cat /K m values (in the range of 10 5 to >10 7 M -1  s -1 ) against noncanonical NTPs. We therefore conclude that hydrolytic activities exhibited by these enzymes against canonical NTPs are not likely their physiological function, but rather the result of unavoidable collateral damage occasioned by the enzymes' inability to distinguish completely between similar substrate structures. Proteins 2016; 84:1810-1822. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Site-directed mutagenesis maps interactions that enhance cognate and limit promiscuous catalysis by an alkaline phosphatase superfamily phosphodiesterase.

PubMed

Wiersma-Koch, Helen; Sunden, Fanny; Herschlag, Daniel

2013-12-23

Catalytic promiscuity, an evolutionary concept, also provides a powerful tool for gaining mechanistic insights into enzymatic reactions. Members of the alkaline phosphatase (AP) superfamily are highly amenable to such investigation, with several members having been shown to exhibit promiscuous activity for the cognate reactions of other superfamily members. Previous work has shown that nucleotide pyrophosphatase/phosphodiesterase (NPP) exhibits a >10⁶-fold preference for the hydrolysis of phosphate diesters over phosphate monoesters, and that the reaction specificity is reduced 10³-fold when the size of the substituent on the transferred phosphoryl group of phosphate diester substrates is reduced to a methyl group. Here we show additional specificity contributions from the binding pocket for this substituent (herein termed the R' substituent) that account for an additional ~250-fold differential specificity with the minimal methyl substituent. Removal of four hydrophobic side chains suggested on the basis of structural inspection to interact favorably with R' substituents decreases phosphate diester reactivity 10⁴-fold with an optimal diester substrate (R' = 5'-deoxythymidine) and 50-fold with a minimal diester substrate (R' = CH₃). These mutations also enhance the enzyme's promiscuous phosphate monoesterase activity by nearly an order of magnitude, an effect that is traced by mutation to the reduction of unfavorable interactions with the two residues closest to the nonbridging phosphoryl oxygen atoms. The quadruple R' pocket mutant exhibits the same activity toward phosphate diester and phosphate monoester substrates that have identical leaving groups, with substantial rate enhancements of ~10¹¹-fold. This observation suggests that the Zn²⁺ bimetallo core of AP superfamily enzymes, which is equipotent in phosphate monoester and diester catalysis, has the potential to become specialized for the hydrolysis of each class of phosphate esters via addition of side chains that interact with the substrate atoms and substituents that project away from the Zn²⁺ bimetallo core.

Take To the Streets: Guide To Planning Outdoor, Public Exhibits.

ERIC Educational Resources Information Center

Cutting, Jennifer McGregor; And Others

Placing exhibits in public places provides a unique opportunity to reach a broad non-museum-going audience. It offers marketing and publicity opportunities as well as the potential to develop relationships with agencies and individuals who are stakeholders in the public site. The purpose of this guidebook is to describe the steps in creating an…

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

PubMed

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

2017-11-03

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

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

DTIC Science & Technology

2007-03-01

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

A survey of the kinetic parameters of class C beta-lactamases. Penicillins.

PubMed Central

Galleni, M; Frère, J M

1988-01-01

The interaction between six class C beta-lactamases and various penicillins has been studied. All the enzymes behaved in a very uniform manner. Benzylpenicillin exhibited relatively low kcat. values (14-75 s-1) but low values of Km resulted in high catalytic efficiencies [kcat./Km = 10 X 10(6)-75 X 10(6) M-1.s-1]. The kcat. values for ampicillin were 10-100-fold lower. Carbenicillin, oxacillin cloxacillin and methicillin were very poor substrates, exhibiting kcat. values between 1 x 10(-3) and 0.1 s-1. The Km values were correspondingly small. It could safely be hypothesized that, with all the tested substrates, deacylation was rate-limiting, resulting in acyl-enzyme accumulation. PMID:3264154

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

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

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

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

Germanium-Assisted Direct Growth of Graphene on Arbitrary Dielectric Substrates for Heating Devices

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

Wang, Ziwen; Xue, Zhongying; Zhang, Miao

Direct growth of graphene on dielectric substrates is a prerequsite for the development of graphene-based electronic and optoelectronic devices. However, the current graphene synthesis directly on dielectric substrates always involves metal contamination problem, and the direct production of graphene patterns still remains unattainable and challenging. We propose herein a semiconducting Ge-assisted chemical vapor deposition approach to directly grow monolayer graphene on arbitrary dielectric substrates. By pre-patterning of catalytic Ge layer, the graphene with desired pattern can be achieved with extreme ease. Due to the catalysis of Ge, monolayer graphene is able to form on Ge covered dielectric substrates including SiOmore » 2/Si, quartz glass and sapphire substrates. Optimization of the process parameters leads to the complete sublimation of catalytic Ge layer during or immediately after monolayer graphene formation, thus resulting in direct deposition of large-area continuous graphene on dielectric substrates. The large-area, highly conductive graphene synthesized on transparent dielectric substrate using the proposed approach has exhibited wide applications, e.g., in defogger and in thermochromic displays, with both devices possessing excellent performances.« less

Germanium-Assisted Direct Growth of Graphene on Arbitrary Dielectric Substrates for Heating Devices

DOE PAGES

Wang, Ziwen; Xue, Zhongying; Zhang, Miao; ...

2017-05-31

Direct growth of graphene on dielectric substrates is a prerequsite for the development of graphene-based electronic and optoelectronic devices. However, the current graphene synthesis directly on dielectric substrates always involves metal contamination problem, and the direct production of graphene patterns still remains unattainable and challenging. We propose herein a semiconducting Ge-assisted chemical vapor deposition approach to directly grow monolayer graphene on arbitrary dielectric substrates. By pre-patterning of catalytic Ge layer, the graphene with desired pattern can be achieved with extreme ease. Due to the catalysis of Ge, monolayer graphene is able to form on Ge covered dielectric substrates including SiOmore » 2/Si, quartz glass and sapphire substrates. Optimization of the process parameters leads to the complete sublimation of catalytic Ge layer during or immediately after monolayer graphene formation, thus resulting in direct deposition of large-area continuous graphene on dielectric substrates. The large-area, highly conductive graphene synthesized on transparent dielectric substrate using the proposed approach has exhibited wide applications, e.g., in defogger and in thermochromic displays, with both devices possessing excellent performances.« less

Cladonia lichens on extensive green roofs: evapotranspiration, substrate temperature, and albedo.

PubMed

Heim, Amy; Lundholm, Jeremy

2013-01-01

Green roofs are constructed ecosystems that provide ecosystem services in urban environments. Shallow substrate green roofs subject the vegetation layer to desiccation and other environmental extremes, so researchers have evaluated a variety of stress-tolerant vegetation types for green roof applications. Lichens can be found in most terrestrial habitats.  They are able to survive extremely harsh conditions, including frequent cycles of desiccation and rehydration, nutrient-poor soil, fluctuating temperatures, and high UV intensities. Extensive green roofs (substrate depth <20cm) exhibit these harsh conditions, making lichens possible candidates for incorporation into the vegetation layer on extensive green roofs.  In a modular green roof system, we tested the effect of Cladonia lichens on substrate temperature, water loss, and albedo compared to a substrate-only control. Overall, the Cladonia modules had significantly cooler substrate temperatures during the summer and significantly warmer temperatures during the fall.  Additionally, the Cladonia modules lost significantly less water than the substrate-only control. This implies that they may be able to benefit neighboring vascular plant species by reducing water loss and maintaining favorable substrate temperatures.

Effect of charged impurities and morphology on oxidation reactivity of graphene

NASA Astrophysics Data System (ADS)

Yamamoto, Mahito; Cullen, William; Einstein, Theodore; Fuhrer, Michael

2012-02-01

Chemical reactivity of single layer graphene supported on a substrate is observed to be enhanced over thicker graphene. Possible mechanisms for the enhancement are Fermi level fluctuations due to ionized impurities on the substrate, and structural deformation of graphene induced by coupling to the substrate geometry. Here, we study the substrate-dependent oxidation reactivity of graphene, employing various substrates such as SiO2, mica, SiO2 nanoparticle thin film, and hexagonal boron nitride, which exhibit different charged impurity concentrations and surface roughness. Graphene is prepared on each substrate via mechanical exfoliation and oxidized in Ar/O2 mixture at temperatures from 400-600 ^oC. After oxidation, the Raman spectrum of graphene is measured, and the Raman D to G peak ratio is used to quantify the density of point defects introduced by oxidation. We will discuss the correlations among the defect density in oxidized graphene, substrate charge inhomogeneity, substrate corrugations, and graphene layer thickness. This work has been supported by the University of Maryland NSF-MRSEC under Grant No. DMR 05-20471 with supplemental funding from NRI, and NSF-DMR 08-04976.

Optimization of Cold Spray Deposition of High-Density Polyethylene Powders

NASA Astrophysics Data System (ADS)

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

2017-10-01

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

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

PubMed

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

2015-04-16

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

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

PubMed Central

Liu, Bing; Gao, Yankun; Ruan, Hai-Bin; Chen, Yue

2016-01-01

Proline hydroxylation is a critical cellular mechanism regulating oxygen-response pathways in tumor initiation and progression. Yet, its substrate diversity and functions remain largely unknown. Here, we report a system-wide analysis to characterize proline hydroxylation substrates in cancer cells using an immunoaffinity-purification assisted proteomics strategy. We identified 562 sites from 272 proteins in HeLa cells. Bioinformatic analysis revealed that proline hydroxylation substrates are significantly enriched with mRNA processing and stress-response cellular pathways with canonical and diverse flanking sequence motifs. Structural analysis indicates a significant enrichment of proline hydroxylation participating in the secondary structure of substrate proteins. Our study identified and validated Brd4, a key transcription factor, as a novel proline hydroxylation substrate. Functional analysis showed that the inhibition of proline hydroxylation pathway significantly reduced the proline hydroxylation abundance on Brd4 and affected Brd4-mediated transcriptional activity as well as cell proliferation in AML leukemia cells. Taken together, our study identified a broad regulatory role of proline hydroxylation in cellular oxygen-sensing pathways and revealed potentially new targets that dynamically respond to hypoxia microenvironment in tumor cells. PMID:27764789

Wettability of partially suspended graphene

DOE PAGES

Ondarçuhu, Thierry; Thomas, Vincent; Nuñez, Marc; ...

2016-04-13

Dependence on the wettability of graphene on the nature of the underlying substrate remains only partially understood. We systematically investigate the role of liquid-substrate interactions on the wettability of graphene by varying the area fraction of suspended graphene from 0 to 95% by means of nanotextured substrates. We find that completely suspended graphene exhibits the highest water contact angle (85° ± 5°) compared to partially suspended or supported graphene, regardless of the hydrophobicity (hydrophilicity) of the substrate. Moreover, 80% of the long-range water-substrate interactions are screened by the graphene monolayer, the wettability of which is primarily determined by short-range graphene-liquidmore » interactions. By its well-defined chemical and geometrical properties, supported graphene therefore provides a model system to elucidate the relative contribution of short and long range interactions to the macroscopic contact angle.« less

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

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.

Mechanical and wear properties of aluminum coating prepared by cold spraying

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

Yusof, Siti Nurul Akmal, E-mail: em-leo277@yahoo.com; Manap, Abreeza, E-mail: Abreeza@uniten.edu.my; Afandi, Nurfanizan Mohd

In this study, aluminum (Al) powders were deposited onto Al substrates using cold spray to form a coating. The main objective is to investigate and compare the microstructure, mechanical and wear properties of Al coating to that of the Al substrate. The microstructure of the coating and substrate were observed using Scanning Electron Microscope (SEM). Hardness was evaluated using the Vickers Hardness test and wear properties were investigated using a pin-on-disk wear test machine. The elemental composition of the coating and substrate was determined using Energy-dispersive X-ray spectroscopy (EDX). Results showed that the friction coefficient and specific wear rate decreasedmore » while wear rate increased linearly with increasing load. It was found that the coating exhibit slightly better mechanical and wear properties compared to the substrate.« less

Influence of airway wall compliance on epithelial cell injury and adhesion during interfacial flows

PubMed Central

Higuita-Castro, Natalia; Mihai, Cosmin; Hansford, Derek J.

2014-01-01

Interfacial flows during cyclic airway reopening are an important source of ventilator-induced lung injury. However, it is not known how changes in airway wall compliance influence cell injury during airway reopening. We used an in vitro model of airway reopening in a compliant microchannel to investigate how airway wall stiffness influences epithelial cell injury. Epithelial cells were grown on gel substrates with different rigidities, and cellular responses to substrate stiffness were evaluated in terms of metabolic activity, mechanics, morphology, and adhesion. Repeated microbubble propagations were used to simulate cyclic airway reopening, and cell injury and detachment were quantified via live/dead staining. Although cells cultured on softer gels exhibited a reduced elastic modulus, these cells experienced less plasma membrane rupture/necrosis. Cells on rigid gels exhibited a minor, but statistically significant, increase in the power law exponent and also exhibited a significantly larger height-to-length aspect ratio. Previous studies indicate that this change in morphology amplifies interfacial stresses and, therefore, correlates with the increased necrosis observed during airway reopening. Although cells cultured on stiff substrates exhibited more plasma membrane rupture, these cells experienced significantly less detachment and monolayer disruption during airway reopening. Western blotting and immunofluorescence indicate that this protection from detachment and monolayer disruption correlates with increased focal adhesion kinase and phosphorylated paxillin expression. Therefore, changes in cell morphology and focal adhesion structure may govern injury responses during compliant airway reopening. In addition, these results indicate that changes in airway compliance, as occurs during fibrosis or emphysema, may significantly influence cell injury during mechanical ventilation. PMID:25213636

Genetic abolishment of hepatocyte proliferation activates hepatic stem cells.

PubMed

Endo, Yoko; Zhang, Mingjun; Yamaji, Sachie; Cang, Yong

2012-01-01

Quiescent hepatic stem cells (HSCs) can be activated when hepatocyte proliferation is compromised. Chemical injury rodent models have been widely used to study the localization, biomarkers, and signaling pathways in HSCs, but these models usually exhibit severe promiscuous toxicity and fail to distinguish damaged and non-damaged cells. Our goal is to establish new animal models to overcome these limitations, thereby providing new insights into HSC biology and application. We generated mutant mice with constitutive or inducible deletion of Damaged DNA Binding protein 1 (DDB1), an E3 ubiquitin ligase, in hepatocytes. We characterized the molecular mechanism underlying the compensatory activation and the properties of oval cells (OCs) by methods of mouse genetics, immuno-staining, cell transplantation and gene expression profiling. We show that deletion of DDB1 abolishes self-renewal capacity of mouse hepatocytes in vivo, leading to compensatory activation and proliferation of DDB1-expressing OCs. Partially restoring proliferation of DDB1-deficient hepatocytes by ablation of p21, a substrate of DDB1 E3 ligase, alleviates OC proliferation. Purified OCs express both hepatocyte and cholangiocyte markers, form colonies in vitro, and differentiate to hepatocytes after transplantation. Importantly, the DDB1 mutant mice exhibit very minor liver damage, compared to a chemical injury model. Microarray analysis reveals several previously unrecognized markers, including Reelin, enriched in oval cells. Here we report a genetic model in which irreversible inhibition of hepatocyte duplication results in HSC-driven liver regeneration. The DDB1 mutant mice can be broadly applied to studies of HSC differentiation, HSC niche and HSCs as origin of liver cancer.

Improving Glyphosate Oxidation Activity of Glycine Oxidase from Bacillus cereus by Directed Evolution

PubMed Central

Zhan, Tao; Zhang, Kai; Chen, Yangyan; Lin, Yongjun; Wu, Gaobing; Zhang, Lili; Yao, Pei; Shao, Zongze; Liu, Ziduo

2013-01-01

Glyphosate, a broad spectrum herbicide widely used in agriculture all over the world, inhibits 5-enolpyruvylshikimate-3-phosphate synthase in the shikimate pathway, and glycine oxidase (GO) has been reported to be able to catalyze the oxidative deamination of various amines and cleave the C-N bond in glyphosate. Here, in an effort to improve the catalytic activity of the glycine oxidase that was cloned from a glyphosate-degrading marine strain of Bacillus cereus (BceGO), we used a bacteriophage T7 lysis-based method for high-throughput screening of oxidase activity and engineered the gene encoding BceGO by directed evolution. Six mutants exhibiting enhanced activity toward glyphosate were screened from two rounds of error-prone PCR combined with site directed mutagenesis, and the beneficial mutations of the six evolved variants were recombined by DNA shuffling. Four recombinants were generated and, when compared with the wild-type BceGO, the most active mutant B3S1 showed the highest activity, exhibiting a 160-fold increase in substrate affinity, a 326-fold enhancement in catalytic efficiency against glyphosate, with little difference between their pH and temperature stabilities. The role of these mutations was explored through structure modeling and molecular docking, revealing that the Arg51 mutation is near the active site and could be an important residue contributing to the stabilization of glyphosate binding, while the role of the remaining mutations is unclear. These results provide insight into the application of directed evolution in optimizing glycine oxidase function and have laid a foundation for the development of glyphosate-tolerant crops. PMID:24223901

Genetic Abolishment of Hepatocyte Proliferation Activates Hepatic Stem Cells

PubMed Central

Endo, Yoko; Zhang, Mingjun; Yamaji, Sachie; Cang, Yong

2012-01-01

Quiescent hepatic stem cells (HSCs) can be activated when hepatocyte proliferation is compromised. Chemical injury rodent models have been widely used to study the localization, biomarkers, and signaling pathways in HSCs, but these models usually exhibit severe promiscuous toxicity and fail to distinguish damaged and non-damaged cells. Our goal is to establish new animal models to overcome these limitations, thereby providing new insights into HSC biology and application. We generated mutant mice with constitutive or inducible deletion of Damaged DNA Binding protein 1 (DDB1), an E3 ubiquitin ligase, in hepatocytes. We characterized the molecular mechanism underlying the compensatory activation and the properties of oval cells (OCs) by methods of mouse genetics, immuno-staining, cell transplantation and gene expression profiling. We show that deletion of DDB1 abolishes self-renewal capacity of mouse hepatocytes in vivo, leading to compensatory activation and proliferation of DDB1-expressing OCs. Partially restoring proliferation of DDB1-deficient hepatocytes by ablation of p21, a substrate of DDB1 E3 ligase, alleviates OC proliferation. Purified OCs express both hepatocyte and cholangiocyte markers, form colonies in vitro, and differentiate to hepatocytes after transplantation. Importantly, the DDB1 mutant mice exhibit very minor liver damage, compared to a chemical injury model. Microarray analysis reveals several previously unrecognized markers, including Reelin, enriched in oval cells. Here we report a genetic model in which irreversible inhibition of hepatocyte duplication results in HSC-driven liver regeneration. The DDB1 mutant mice can be broadly applied to studies of HSC differentiation, HSC niche and HSCs as origin of liver cancer. PMID:22384083

Ultrafast Flame Annealing of TiO2 Paste for Fabricating Dye-Sensitized and Perovskite Solar Cells with Enhanced Efficiency.

PubMed

Kim, Jung Kyu; Chai, Sung Uk; Cho, Yoonjun; Cai, Lili; Kim, Sung June; Park, Sangwook; Park, Jong Hyeok; Zheng, Xiaolin

2017-11-01

Mesoporous TiO 2 nanoparticle (NP) films are broadly used as electrodes in photoelectrochemical cells, dye-sensitized solar cells (DSSCs), and perovskite solar cells (PSCs). State-of-the-art mesoporous TiO 2 NP films for these solar cells are fabricated by annealing TiO 2 paste-coated fluorine-doped tin oxide glass in a box furnace at 500 °C for ≈30 min. Here, the use of a nontraditional reactor, i.e., flame, is reported for the high throughput and ultrafast annealing of TiO 2 paste (≈1 min). This flame-annealing method, compared to conventional furnace annealing, exhibits three distinct benefits. First, flame removes polymeric binders in the initial TiO 2 paste more completely because of its high temperature (≈1000 °C). Second, flame induces strong interconnections between TiO 2 nanoparticles without affecting the underlying transparent conducting oxide substrate. Third, the flame-induced carbothermic reduction on the TiO 2 surface facilitates charge injection from the dye/perovskite to TiO 2 . Consequently, when the flame-annealed mesoporous TiO 2 film is used to fabricate DSSCs and PSCs, both exhibit enhanced charge transport and higher power conversion efficiencies than those fabricated using furnace-annealed TiO 2 films. Finally, when the ultrafast flame-annealing method is combined with a fast dye-coating method to fabricate DSSC devices, its total fabrication time is reduced from over 3 h to ≈10 min. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Distinct roles of N- and O-glycans in cellulase activity and stability

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

Amore, Antonella; Knott, Brandon C.; Supekar, Nitin T.

In nature, many microbes secrete mixtures of glycoside hydrolases, oxidoreductases, and accessory enzymes to deconstruct polysaccharides and lignin in plants. These enzymes are often decorated with N- and O-glycosylation, the roles of which have been broadly attributed to protection from proteolysis, as the extracellular milieu is an aggressive environment. Glycosylation has been shown to sometimes affect activity, but these effects are not fully understood. In this paper, we examine N- and O-glycosylation on a model, multimodular glycoside hydrolase family 7 cellobiohydrolase (Cel7A), which exhibits an O-glycosylated carbohydrate-binding module (CBM) and an O-glycosylated linker connected to an N- and O-glycosylated catalyticmore » domain (CD) - a domain architecture common to many biomass-degrading enzymes. We report consensus maps for Cel7A glycosylation that include glycan sites and motifs. Additionally, we examine the roles of glycans on activity, substrate binding, and thermal and proteolytic stability. N-glycan knockouts on the CD demonstrate that N-glycosylation has little impact on cellulose conversion or binding, but does have major stability impacts. O-glycans on the CBM have little impact on binding, proteolysis, or activity in the whole-enzyme context. However, linker O-glycans greatly impact cellulose conversion via their contribution to proteolysis resistance. Molecular simulations predict an additional role for linker O-glycans, namely that they are responsible for maintaining separation between ordered domains when Cel7A is engaged on cellulose, as models predict a-helix formation and decreased cellulose interaction for the nonglycosylated linker. In conclusion, this study reveals key roles for N- and O-glycosylation that are likely broadly applicable to other plant cell-wall-degrading enzymes.« less

Novel Materials, Processing and Device Technologies for Space Exploration with Potential Dual-Use Applications

NASA Technical Reports Server (NTRS)

Hepp, A. F.; Bailey, S. G.; McNatt, J. S.; Chandrashekhar, M. V. S.; Harris, J. D.; Rusch, A. W.; Nogales, K. A.; Goettsche, K.V.; Hanson, W.; Amos, D.;

Novel Materials, Processing, and Device Technologies for Space Exploration with Potential Dual-Use Applications

NASA Technical Reports Server (NTRS)

Hepp, A. F.; Bailey, S. G.; McNatt, J. S.; Chandrashekhar, M. V. S.; Harris, J. D.; Rusch, A. W.; Nogales, K. A.; Goettsche, K. V.; Hanson, W.; Amos, D.;

FIM-1, a new acquired metallo-β-lactamase from a Pseudomonas aeruginosa clinical isolate from Italy.

PubMed

Pollini, Simona; Maradei, Simona; Pecile, Patrizia; Olivo, Giuseppe; Luzzaro, Francesco; Docquier, Jean-Denis; Rossolini, Gian Maria

2013-01-01

Acquired metallo-β-lactamases (MBLs) are resistance determinants of increasing clinical importance in Gram-negative bacterial pathogens, which confer a broad-spectrum β-lactam resistance, including carbapenems. Several such enzymes have been described since the 1990s. In the present study, a novel acquired MBL, named FIM-1, was identified and characterized. The bla(FIM-1) gene was cloned from a multidrug-resistant Pseudomonas aeruginosa clinical isolate (FI-14/157) cultured from a patient with a vascular graft infection in Florence, Italy. The isolate belonged in the sequence type 235 epidemic clonal lineage. The FIM-1 enzyme is a member of subclass B1 and, among acquired MBLs, exhibited the highest similarity (ca. 40% amino acid identity) with NDM-type enzymes. In P. aeruginosa FI-14/157, the bla(FIM-1) gene was apparently inserted into the chromosome and associated with ISCR19-like elements that were likely involved in the capture and mobilization of this MBL gene. Transfer experiments of the bla(FIM-1) gene to an Escherichia coli strain or another P. aeruginosa strain by conjugation or electrotransformation were not successful. The FIM-1 protein was produced in E. coli and purified by two chromatography steps. Analysis of the kinetic parameters, carried out with the purified enzyme, revealed that FIM-1 has a broad substrate specificity, with a preference for penicillins (except the 6α-methoxy derivative temocillin) and carbapenems. Aztreonam was not hydrolyzed. Detection of this novel type of acquired MBL in a P. aeruginosa clinical isolate underscores the increasing diversity of such enzymes that can be encountered in the clinical setting.

Distinct roles of N- and O-glycans in cellulase activity and stability

DOE PAGES

Amore, Antonella; Knott, Brandon C.; Supekar, Nitin T.; ...

2017-12-11

In nature, many microbes secrete mixtures of glycoside hydrolases, oxidoreductases, and accessory enzymes to deconstruct polysaccharides and lignin in plants. These enzymes are often decorated with N- and O-glycosylation, the roles of which have been broadly attributed to protection from proteolysis, as the extracellular milieu is an aggressive environment. Glycosylation has been shown to sometimes affect activity, but these effects are not fully understood. In this paper, we examine N- and O-glycosylation on a model, multimodular glycoside hydrolase family 7 cellobiohydrolase (Cel7A), which exhibits an O-glycosylated carbohydrate-binding module (CBM) and an O-glycosylated linker connected to an N- and O-glycosylated catalyticmore » domain (CD) - a domain architecture common to many biomass-degrading enzymes. We report consensus maps for Cel7A glycosylation that include glycan sites and motifs. Additionally, we examine the roles of glycans on activity, substrate binding, and thermal and proteolytic stability. N-glycan knockouts on the CD demonstrate that N-glycosylation has little impact on cellulose conversion or binding, but does have major stability impacts. O-glycans on the CBM have little impact on binding, proteolysis, or activity in the whole-enzyme context. However, linker O-glycans greatly impact cellulose conversion via their contribution to proteolysis resistance. Molecular simulations predict an additional role for linker O-glycans, namely that they are responsible for maintaining separation between ordered domains when Cel7A is engaged on cellulose, as models predict a-helix formation and decreased cellulose interaction for the nonglycosylated linker. In conclusion, this study reveals key roles for N- and O-glycosylation that are likely broadly applicable to other plant cell-wall-degrading enzymes.« less

Cascade detection for the extraction of localized sequence features; specificity results for HIV-1 protease and structure-function results for the Schellman loop.

PubMed

Newell, Nicholas E

2011-12-15

The extraction of the set of features most relevant to function from classified biological sequence sets is still a challenging problem. A central issue is the determination of expected counts for higher order features so that artifact features may be screened. Cascade detection (CD), a new algorithm for the extraction of localized features from sequence sets, is introduced. CD is a natural extension of the proportional modeling techniques used in contingency table analysis into the domain of feature detection. The algorithm is successfully tested on synthetic data and then applied to feature detection problems from two different domains to demonstrate its broad utility. An analysis of HIV-1 protease specificity reveals patterns of strong first-order features that group hydrophobic residues by side chain geometry and exhibit substantial symmetry about the cleavage site. Higher order results suggest that favorable cooperativity is weak by comparison and broadly distributed, but indicate possible synergies between negative charge and hydrophobicity in the substrate. Structure-function results for the Schellman loop, a helix-capping motif in proteins, contain strong first-order features and also show statistically significant cooperativities that provide new insights into the design of the motif. These include a new 'hydrophobic staple' and multiple amphipathic and electrostatic pair features. CD should prove useful not only for sequence analysis, but also for the detection of multifactor synergies in cross-classified data from clinical studies or other sources. Windows XP/7 application and data files available at: https://sites.google.com/site/cascadedetect/home. nacnewell@comcast.net Supplementary information is available at Bioinformatics online.

Phospholipid flippase activity of the reconstituted P-glycoprotein multidrug transporter.

PubMed

Romsicki, Y; Sharom, F J

2001-06-12

The P-glycoprotein multidrug transporter acts as an ATP-powered efflux pump for a large variety of hydrophobic drugs, natural products, and peptides. The protein is proposed to interact with its substrates within the hydrophobic interior of the membrane. There is indirect evidence to suggest that P-glycoprotein can also transport, or "flip", short chain fluorescent lipids between leaflets of the membrane. In this study, we use a fluorescence quenching technique to directly show that P-glycoprotein reconstituted into proteoliposomes translocates a wide variety of NBD lipids from the outer to the inner leaflet of the bilayer. Flippase activity depended on ATP hydrolysis at the outer surface of the proteoliposome, and was inhibited by vanadate. P-Glycoprotein exhibited a broad specificity for phospholipids, and translocated phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, and sphingomyelin. Lipid derivatives that were flipped included molecules with long, short, unsaturated, and saturated acyl chains and species with the NBD group covalently linked to either acyl chains or the headgroup. The extent of lipid translocation from the outer to the inner leaflet in a 20 min period at 37 degrees C was directly estimated, and fell in the range of 0.36-1.83 nmol/mg of protein. Phospholipid flipping was inhibited in a concentration-dependent, saturable fashion by various substrates and modulators, including vinblastine, verapamil, and cyclosporin A, and the efficiency of inhibition correlated well with the affinity of binding to Pgp. Taken together, these results suggest that P-glycoprotein carries out both lipid translocation and drug transport by the same path. The transporter may be a generic flippase for hydrophobic molecules with the correct steric attributes that are present within the membrane interior.

Mining lipolytic enzymes in community DNA from high Andean soils using a targeted approach.

PubMed

Borda-Molina, Daniel; Montaña, José Salvador; Zambrano, María Mercedes; Baena, Sandra

2017-08-01

Microbial enrichments cultures are a useful strategy to speed up the search for enzymes that can be employed in industrial processes. Lipases have gained special attention because they show unique properties such as: broad substrate specificity, enantio- and regio-selectivity and stability in organic solvents. A major goal is to identify novel lipolytic enzymes from microorganisms living in cold extreme environments such as high Andean soils, of relevance to our study being their capability be used in industrial processes. Paramo and glacier soils from the Nevados National Park in Colombia were sampled and microbial communities enriched through a fed-batch fermentation using olive oil as an inductor substrate. After 15 days of enrichment under aerobic conditions, total DNA was extracted. Subsequently, metagenomic libraries were constructed in the cosmid vector pWEB-TNC™. After functional screening, twenty and eighteen lipolytic clones were obtained from Paramo and Glacier soil enrichments, respectively. Based on lipid hydrolysis halo dimensions, the clone (Gla1) from a glacier enrichment was selected. A gene related to lipolytic activity was subcloned to evaluate enzyme properties. Phylogenetic analysis of the identified gene showed that the encoded lipase belongs to the family GDSL from a Ralstonia-like species. Interestingly, the secreted enzyme exhibited stability at high temperature and alkaline conditions, specifically the preferred conditions at 80 °C and pH 9.0. Thus, with the identification of an enzyme with non-expected properties, in this study is shown the potential of extreme cold environments to be explored for new catalytic molecules, using current molecular biology techniques, with applications in industrial processes, which demand stability under harsh conditions.

Purification and Characterization of an Inverting Stereo- and Enantioselective sec-Alkylsulfatase from the Gram-Positive Bacterium Rhodococcus ruber DSM 44541

PubMed Central

Pogorevc, Mateja; Faber, Kurt

2003-01-01

Whole cells of Rhodococcus ruber DSM 44541 were found to hydrolyze (±)-2-octyl sulfate in a stereo- and enantiospecific fashion. When growing on a complex medium, the cells produced two sec-alkylsulfatases and (at least) one prim-alkylsulfatase in the absence of an inducer, such as a sec-alkyl sulfate or a sec-alcohol. From the crude cell-free lysate, two proteins responsible for sulfate ester hydrolysis (designated RS1 and RS2) were separated from each other based on their different hydrophobicities and were subjected to further chromatographic purification. In contrast to sulfatase RS1, enzyme RS2 proved to be reasonably stable and thus could be purified to homogeneity. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed a single band at a molecular mass of 43 kDa. Maximal enzyme activity was observed at 30°C and at pH 7.5. Sulfatase RS2 showed a clear preference for the hydrolysis of linear secondary alkyl sulfates, such as 2-, 3-, or 4-octyl sulfate, with remarkable enantioselectivity (an enantiomeric ratio of up to 21 [23]). Enzymatic hydrolysis of (R)-2-octyl sulfate furnished (S)-2-octanol without racemization, which revealed that the enzymatic hydrolysis proceeded through inversion of the configuration at the stereogenic carbon atom. Screening of a broad palette of potential substrates showed that the enzyme exhibited limited substrate tolerance; while simple linear sec-alkyl sulfates (C7 to C10) were freely accepted, no activity was found with branched and mixed aryl-alkyl sec-sulfates. Due to the fact that prim-sulfates were not accepted, the enzyme was classified as sec-alkylsulfatase (EC 3.1.6.X). PMID:12732552

Self-organized broadband light trapping in thin film amorphous silicon solar cells.

PubMed

Martella, C; Chiappe, D; Delli Veneri, P; Mercaldo, L V; Usatii, I; Buatier de Mongeot, F

2013-06-07

Nanostructured glass substrates endowed with high aspect ratio one-dimensional corrugations are prepared by defocused ion beam erosion through a self-organized gold (Au) stencil mask. The shielding action of the stencil mask is amplified by co-deposition of gold atoms during ion bombardment. The resulting glass nanostructures enable broadband anti-reflection functionality and at the same time ensure a high efficiency for diffuse light scattering (Haze). It is demonstrated that the patterned glass substrates exhibit a better photon harvesting than the flat glass substrate in p-i-n type thin film a-Si:H solar cells.

Unraveling orbital hybridization of triplet emitters at the metal-organic interface.

PubMed

Ewen, Pascal R; Sanning, Jan; Doltsinis, Nikos L; Mauro, Matteo; Strassert, Cristian A; Wegner, Daniel

2013-12-27

We have investigated the structural and electronic properties of phosphorescent planar platinum(II) complexes at the interface of Au(111) with submolecular resolution using combined scanning tunneling microscopy and spectroscopy as well as density functional theory. Our analysis shows that molecule-substrate coupling and lateral intermolecular interactions are weak. While the ligand orbitals remain essentially unchanged upon contact with the substrate, we found modified electronic behavior at the Pt atom due to local hybridization and charge transfer to the substrate. Thus, this novel class of phosphorescent molecules exhibits well-defined and tunable interaction with its local environment.

Fabrication of flexible and vertical silicon nanowire electronics.

PubMed

Weisse, Jeffrey M; Lee, Chi Hwan; Kim, Dong Rip; Zheng, Xiaolin

2012-06-13

Vertical silicon nanowire (SiNW) array devices directly connected on both sides to metallic contacts were fabricated on various non-Si-based substrates (e.g., glass, plastics, and metal foils) in order to fully exploit the nanomaterial properties for final applications. The devices were realized with uniform length Ag-assisted electroless etched SiNW arrays that were detached from their fabrication substrate, typically Si wafers, reattached to arbitrary substrates, and formed with metallic contacts on both sides of the NW array. Electrical characterization of the SiNW array devices exhibits good current-voltage characteristics consistent with the SiNW morphology.

Direct Coating of Nanocrystalline Diamond on Steel

NASA Astrophysics Data System (ADS)

Tsugawa, Kazuo; Kawaki, Shyunsuke; Ishihara, Masatou; Hasegawa, Masataka

2012-09-01

Nanocrystalline diamond films have been successfully deposited on stainless steel substrates without any substrate pretreatments to promote diamond nucleation, including the formation of interlayers. A low-temperature growth technique, 400 °C or lower, in microwave plasma chemical vapor deposition using a surface-wave plasma has cleared up problems in diamond growth on ferrous materials, such as the surface graphitization, long incubation time, substrate softening, and poor adhesion. The deposited nanocrystalline diamond films on stainless steel exhibit good adhesion and tribological properties, such as a high wear resistance, a low friction coefficient, and a low aggression strength, at room temperature in air without lubrication.

SERS substrates fabricated using ceramic filters for the detection of bacteria: Eliminating the citrate interference

NASA Astrophysics Data System (ADS)

Mosier-Boss, P. A.; Sorensen, K. C.; George, R. D.; Sims, P. C.; O'braztsova, A.

2017-06-01

It was found that spectra obtained for bacteria on SERS substrates fabricated by filtering citrate-generated Ag nanoparticles (NPs) onto rigid, ceramic filters exhibited peaks due to citrate as well as the bacteria. In many cases the citrate spectrum overwhelmed that of the bacteria. Given the simplicity of the method to prepare these substrates, means of eliminating this citrate interference were explored. It was found that allowing a mixture of bacteria suspension and citrate-generated Ag NPs to incubate prior to filtering onto the ceramic filter eliminated this interference.

Evaluating Education and Science at the KSC Visitor Complex

NASA Technical Reports Server (NTRS)

Erickson, Lance K.

2002-01-01

As part of a two-year NASA-ASEE project, a preliminary evaluation and subsequent recommendations were developed to improve the education and science content of the Kennedy Space Center Visitor Complex exhibits. Recommendations for improvements in those exhibits were based on qualitative descriptions of the exhibits, on comparisons to similar exhibit collections, and on available evaluation processes. Because of the subjective nature of measuring content in a broad group of exhibits and displays, emphasis is placed on employing a survey format for a follow-on, more quantitative evaluation. The use of an external organization for this evaluation development is also recommended to reduce bias and increase validity.

Evaluating Education and Science at the KSC Visitor Complex

NASA Technical Reports Server (NTRS)

Erickson, Lance K.

2001-01-01

As part of a two-year NASA-ASEE project, a preliminary evaluation and subsequent recommendations were developed to improve the education and science content of the Kennedy Space Center Visitor Complex exhibits. Recommendations for improvements in those exhibits were based on qualitative descriptions of the exhibits, on comparisons to similar exhibit collections, and on available evaluation processes. Because of the subjective nature of measuring content in a broad group of exhibits and displays, emphasis is placed on employing a survey format for a follow-on, more quantitative evaluation. The use of an external organization for this evaluation development is also recommended to reduce bias and increase validity.

Fluorogenic kinetic assay for high-throughput discovery of stereoselective ketoreductases relevant to pharmaceutical synthesis.

PubMed

Thai, Yen-Chi; Szekrenyi, Anna; Qi, Yuyin; Black, Gary W; Charnock, Simon J; Fessner, Wolf-Dieter

2018-04-01

Enantiomerically pure 1-(6-methoxynaphth-2-yl) and 1-(6-(dimethylamino)naphth-2-yl) carbinols are fluorogenic substrates for aldo/keto reductase (KRED) enzymes, which allow the highly sensitive and reliable determination of activity and kinetic constants of known and unknown enzymes, as well as an immediate enantioselectivity typing. Because of its simplicity in microtiter plate format, the assay qualifies for the discovery of novel KREDs of yet unknown specificity among this vast enzyme superfamily. The suitability of this approach for enzyme typing is illustrated by an exemplary screening of a large collection of short-chain dehydrogenase/reductase (SDR) enzymes arrayed from a metagenomic approach. We believe that this assay format should match well the pharmaceutical industry's demand for acetophenone-type substrates and the continuing interest in new enzymes with broad substrate promiscuity for the synthesis of chiral, non-racemic carbinols. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Patterned microstructures formed with MeV Au implantation in Si(1 0 0)

NASA Astrophysics Data System (ADS)

Rout, Bibhudutta; Greco, Richard R.; Zachry, Daniel P.; Dymnikov, Alexander D.; Glass, Gary A.

2006-09-01

Energetic (MeV) Au implantation in Si(1 0 0) (n-type) through masked micropatterns has been used to create layers resistant to KOH wet etching. Microscale patterns were produced in PMMA and SU(8) resist coatings on the silicon substrates using P-beam writing and developed. The silicon substrates were subsequently exposed using 1.5 MeV Au 3+ ions with fluences as high as 1 × 10 16 ions/cm 2 and additional patterns were exposed using copper scanning electron microscope calibration grids as masks on the silicon substrates. When wet etched with KOH microstructures were created in the silicon due to the resistance to KOH etching cause by the Au implantation. The process of combining the fabrication of masked patterns with P-beam writing with broad beam Au implantation through the masks can be a promising, cost-effective process for nanostructure engineering with Si.

Adhesion of Antireflective Coatings in Multijunction Photovoltaics

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

Brock, Ryan; Miller, David C.; Dauskardt, Reinhold H.

2016-11-21

The development of a new composite dual cantilever beam (cDCB) thin-film adhesion testing method is reported, which allows the measurement of adhesion on the fragile thin substrates used in multijunction photovoltaics. We address the adhesion of several antireflective coating systems on multijunction cells. By varying interface chemistry and morphology, we demonstrate the ensuing effects on adhesion and help to develop an understanding of how high adhesion can be achieved, as adhesion values ranging from 0.5 J/m2 to 10 J/m2 were measured. Damp Heat (85 degrees C/85% RH) was used to invoke degradation of interfacial adhesion. We show that even withmore » germanium substrates that fracture easily, quantitative measurements of adhesion can still be made at high test yield. The cDCB test is discussed as an important new methodology, which can be broadly applied to any system that makes use of thin, brittle, or otherwise fragile substrates.« less

Adhesion of Antireflective Coatings in Multijunction Photovoltaics: Preprint

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

Brock, Ryan; Dauskardt, Reinhold H.; Miller, David C.

2016-06-16

The development of a new composite dual cantilever beam (cDCB) thin-film adhesion testing method is reported, which allows the measurement of adhesion on the fragile thin substrates used in multijunction photovoltaics. We address the adhesion of several antireflective coating systems on multijunction cells. By varying interface chemistry and morphology, we demonstrate the ensuing effects on adhesion and help to develop an understanding of how high adhesion can be achieved, as adhesion values ranging from 0.5 J/m2 to 10 J/m2 were measured. Damp Heat (85 degrees C/85% RH) was used to invoke degradation of interfacial adhesion. We show that even withmore » germanium substrates that fracture easily, quantitative measurements of adhesion can still be made at high test yield. The cDCB test is discussed as an important new methodology, which can be broadly applied to any system that makes use of thin, brittle, or otherwise fragile substrates.« less

Broadband omnidirectional antireflection coating based on subwavelength surface Mie resonators

PubMed Central

Spinelli, P.; Verschuuren, M.A.; Polman, A.

2012-01-01

Reflection is a natural phenomenon that occurs when light passes the interface between materials with different refractive index. In many applications, such as solar cells or photodetectors, reflection is an unwanted loss process. Many ways to reduce reflection from a substrate have been investigated so far, including dielectric interference coatings, surface texturing, adiabatic index matching and scattering from plasmonic nanoparticles. Here we present an entirely new concept that suppresses the reflection of light from a silicon surface over a broad spectral range. A two-dimensional periodic array of subwavelength silicon nanocylinders designed to possess strongly substrate-coupled Mie resonances yields almost zero total reflectance over the entire spectral range from the ultraviolet to the near-infrared. This new antireflection concept relies on the strong forward scattering that occurs when a scattering structure is placed in close proximity to a high-index substrate with a high optical density of states. PMID:22353722

Dewetting and spreading transitions for active matter on random pinning substrates.

PubMed

Sándor, Cs; Libál, A; Reichhardt, C; Olson Reichhardt, C J

2017-05-28

We show that sterically interacting self-propelled disks in the presence of random pinning substrates exhibit transitions among a variety of different states. In particular, from a phase separated cluster state, the disks can spread out and homogeneously cover the substrate in what can be viewed as an example of an active matter wetting transition. We map the location of this transition as a function of activity, disk density, and substrate strength, and we also identify other phases including a cluster state, coexistence between a cluster and a labyrinth wetted phase, and a pinned liquid. Convenient measures of these phases include the cluster size, which dips at the wetting-dewetting transition, and the fraction of sixfold coordinated particles, which drops when dewetting occurs.

Enhancement of magnetostrictive properties of Galfenol thin films

NASA Astrophysics Data System (ADS)

Nivedita, Lalitha Raveendran; Manivel, Palanisamy; Pandian, Ramanathaswamy; Murugesan, S.; Morley, Nicola Ann; Asokan, K.; Rajendra Kumar, Ramasamy Thangavelu

2018-04-01

The present study investigates the role of substrate temperatures on the structural, morphological, magnetic and magnetostrictive properties of DC sputtered FeGa thin films grown on Si substrates. These films were deposited at various substrate temperatures between 50 and 350 °C. The structural characterization of the films revealed columnar growth and the transformation of surface morphology from prismatic to spherical at high substrate temperatures. Both L12 and B2 phases of FeGa existed in the films, with the L12 phase dominating. The in-plane and out-of-plane vibration sample magnetometry measurements showed the evolution of magnetic anisotropy in these films. It was revealed from the magnetostriction measurements that the films deposited at 250 °C exhibited the maximum value of 59 ppm.

Prolonged bioluminescence imaging in living cells and mice using novel pro-substrates for Renilla luciferase.

PubMed

Yuan, Mingliang; Ma, Xiaojie; Jiang, Tianyu; Gao, Yuqi; Cui, Yuanyuan; Zhang, Chaochao; Yang, Xingye; Huang, Yun; Du, Lupei; Yampolsky, Ilia; Li, Minyong

2017-12-13

The prodrug or caged-luciferin strategy affords an excellent platform for persistent bioluminescence imaging. In the current work, we designed and synthesized ten novel pro-substrates for Renilla luciferase by introducing ester protecting groups of different sizes into the carbonyl group of the free luciferin 1. Taking advantage of intracellular esterases, lipases, and nucleophilic substances, the ester protecting groups were hydrolyzed, resulting in the release of a free luciferin and a bioluminescence signal turn-on. Among the tested pro-substrates, the butyryloxymethyl luciferin 7 exhibited low cytotoxicity and a prolonged luminescence signal both in cellulo and in vivo. Therefore, the butyryloxymethyl luciferin 7 can act as a promising substrate for noninvasive extended imaging in diagnostic and therapeutic fields.

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

NASA Astrophysics Data System (ADS)

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

1992-12-01

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

Characterization of a novel thermostable Mn(II)-dependent 2,3-dihydroxybiphenyl 1,2-dioxygenase from a polychlorinated biphenyl- and naphthalene-degrading Bacillus sp. JF8.

PubMed

Hatta, Takashi; Mukerjee-Dhar, Gouri; Damborsky, Jiri; Kiyohara, Hohzoh; Kimbara, Kazuhide

2003-06-13

A novel thermostable Mn(II)-dependent 2,3-dihydroxybiphenyl-1,2-dioxygenase (BphC_JF8) catalyzing the meta-cleavage of the hydroxylated biphenyl ring was purified from the thermophilic biphenyl and naphthalene degrader, Bacillus sp. JF8, and the gene was cloned. The native and recombinant BphC enzyme was purified to homogeneity. The enzyme has a molecular mass of 125 +/- 10 kDa and was composed of four identical subunits (35 kDa). BphC_JF8 has a temperature optimum of 85 degrees C and a pH optimum of 7.5. It exhibited a half-life of 30 min at 80 degrees C and 81 min at 75 degrees C, making it the most thermostable extradiol dioxygenase studied. Inductively coupled plasma mass spectrometry analysis confirmed the presence of 4.0-4.8 manganese atoms per enzyme molecule. The EPR spectrum of BphC_JF8 exhibited g = 2.02 and g = 4.06 signals having the 6-fold hyperfine splitting characteristic of Mn(II). The enzyme can oxidize a wide range of substrates, and the substrate preference was in the order 2,3-dihydroxybiphenyl > 3-methylcatechol > catechol > 4-methylcatechol > 4-chlorocatechol. The enzyme is resistant to denaturation by various chelators and inhibitors (EDTA, 1,10-phenanthroline, H2O2, 3-chlorocatechol) and did not exhibit substrate inhibition even at 3 mm 2,3-dihydroxybiphenyl. A decrease in Km accompanied an increase in temperature, and the Km value of 0.095 microm for 2,3-dihydroxybiphenyl (at 60 degrees C) is among the lowest reported. The kinetic properties and thermal stability of the native and recombinant enzyme were identical. The primary structure of BphC_JF8 exhibits less than 25% sequence identity to other 2,3-dihydroxybiphenyl 1,2-dioxygenases. The metal ligands and active site residues of extradiol dioxygenases are conserved, although several amino acid residues found exclusively in enzymes that preferentially cleave bicyclic substrates are missing in BphC_JF8. A three-dimensional homology model of BphC_JF8 provided a basis for understanding the substrate specificity, quaternary structure, and stability of the enzyme.

High-power 0.87-micron channel substrate planar lasers for spaceborne communications

NASA Technical Reports Server (NTRS)

Connolly, J. C.; Stewart, T. R.; Gilbert, D. B.; Slavin, S. E.; Carlin, D. B.

1988-01-01

High-power single-mode channeled-substrate planar AlGaAs diode lasers are being developed for reliable high-power operation for use as sources in spaceborne optical communication systems. The CSP laser structure has been optimized for operation at an emission wavelength of 870 nm. Such devices have exhibited output powers in excess of 80 mW CW at an operating temperature of 80 C.

Design analysis of phosphor-free monolithic white light-emitting-diodes with InGaN/ InGaN multiple quantum wells on ternary InGaN substrates

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

Ooi, Yu Kee, E-mail: Yu.Kee.Ooi@rit.edu; Zhang, Jing, E-mail: Jing.Zhang@rit.edu

2015-05-15

Phosphor-free monolithic white light emitting diodes (LEDs) based on InGaN/ InGaN multiple quantum wells (MQWs) on ternary InGaN substrates are proposed and analyzed in this study. Simulation studies show that LED devices composed of multi-color-emitting InGaN/ InGaN quantum wells (QWs) employing ternary InGaN substrate with engineered active region exhibit stable white color illumination with large output power (∼ 170 mW) and high external quantum efficiency (EQE) (∼ 50%). The chromaticity coordinate for the investigated monolithic white LED devices are located at (0.30, 0.28) with correlated color temperature (CCT) of ∼ 8200 K at J = 50 A/cm{sup 2}. A referencemore » LED device without any nanostructure engineering exhibits green color emission shows that proper engineered structure is essential to achieve white color illumination. This proof-of-concept study demonstrates that high-efficiency and cost-effective phosphor-free monolithic white LED is feasible by the use of InGaN/ InGaN MQWs on ternary InGaN substrate combined with nanostructure engineering, which would be of great impact for solid state lighting.« less

Enhanced super-hydrophobic and switching behavior of ZnO nanostructured surfaces prepared by simple solution--immersion successive ionic layer adsorption and reaction process.

PubMed

Suresh Kumar, P; Sundaramurthy, J; Mangalaraj, D; Nataraj, D; Rajarathnam, D; Srinivasan, M P

2011-11-01

A simple and cost-effective successive ionic layer adsorption and reaction (SILAR) method was adopted to fabricate hydrophobic ZnO nanostructured surfaces on transparent indium-tin oxide (ITO), glass and polyethylene terephthalate (PET) substrates. ZnO films deposited on different substrates show hierarchical structures like spindle, flower and spherical shape with diameters ranging from 30 to 300 nm. The photo-induced switching behaviors of ZnO film surfaces between hydrophobic and hydrophilic states were examined by water contact angle and X-ray photoelectron spectroscopy (XPS) analysis. ZnO nanostructured films had contact angles of ~140° and 160°±2 on glass and PET substrates, respectively, exhibiting hydrophobic behavior without any surface modification or treatment. Upon exposure to ultraviolet (UV) illumination, the films showed hydrophilic behavior (contact angle: 15°±2), which upon low thermal stimuli revert back to its original hydrophobic nature. Such reversible and repeatable switching behaviors were observed upon cyclical exposure to ultraviolet radiation. These biomimetic ZnO surfaces exhibit good anti-reflective properties with lower reflectance of 9% for PET substrates. Thus, the present work is significant in terms of its potential application in switching devices, solar coatings and self-cleaning smart windows. Copyright © 2011 Elsevier Inc. All rights reserved.

A non-modular type B feruloyl esterase from Neurospora crassa exhibits concentration-dependent substrate inhibition.

PubMed Central

Crepin, Valerie F; Faulds, Craig B; Connerton, Ian F

2003-01-01

Feruloyl esterases, a subclass of the carboxylic acid esterases (EC 3.1.1.1), are able to hydrolyse the ester bond between the hydroxycinnamic acids and sugars present in the plant cell wall. The enzymes have been classified as type A or type B, based on their substrate specificity for aromatic moieties. We show that Neurospora crassa has the ability to produce multiple ferulic acid esterase activities depending upon the length of fermentation with either sugar beet pulp or wheat bran substrates. A gene identified on the basis of its expression on sugar beet pulp has been cloned and overexpressed in Pichia pastoris. The gene encodes a single-domain ferulic acid esterase, which represents the first report of a non-modular type B enzyme (fae-1 gene; GenBank accession no. AJ293029). The purified recombinant protein has been shown to exhibit concentration-dependent substrate inhibition (K(m) 0.048 mM, K (i) 2.5 mM and V(max) 8.2 units/mg against methyl 3,4-dihydroxycinnamate). The kinetic behaviour of the non-modular enzyme is discussed in terms of the diversity in the roles of the feruloyl esterases in the mobilization of plant cell wall materials and their respective modes of action. PMID:12435269

Unraveling the stereochemical and dynamic aspects of the catalytic site of bacterial peptidyl-tRNA hydrolase

PubMed Central

Kabra, Ashish; Shahid, Salman; Pal, Ravi Kant; Yadav, Rahul; Pulavarti, S.V.S. Rama Krishna; Jain, Anupam; Tripathi, Sarita; Arora, Ashish

2017-01-01

Bacterial peptidyl-tRNA hydrolase (Pth; EC 3.1.1.29) hydrolyzes the peptidyl-tRNAs accumulated in the cytoplasm and thereby prevents cell death by alleviating tRNA starvation. X-ray and NMR studies of Vibrio cholerae Pth (VcPth) and mutants of its key residues involved in catalysis show that the activity and selectivity of the protein depends on the stereochemistry and dynamics of residues H24, D97, N118, and N14. D97-H24 interaction is critical for activity because it increases the nucleophilicity of H24. The N118 and N14 have orthogonally competing interactions with H24, both of which reduce the nucleophilicity of H24 and are likely to be offset by positioning of a peptidyl-tRNA substrate. The region proximal to H24 and the lid region exhibit slow motions that may assist in accommodating the substrate. Helix α3 exhibits a slow wobble with intermediate time scale motions of its N-cap residue N118, which may work as a flypaper to position the scissile ester bond of the substrate. Overall, the dynamics of interactions between the side chains of N14, H24, D97, and N118, control the catalysis of substrate by this enzyme. PMID:28096445

Wzx flippases exhibiting complex O-unit preferences require a new model for Wzx-substrate interactions.

PubMed

Liu, Michael A; Morris, Paraskevi; Reeves, Peter R

2018-06-10

The Wzx flippase is a critical component of the O-antigen biosynthesis pathway, being responsible for the translocation of oligosaccharide O units across the inner membrane in Gram-negative bacteria. Recent studies have shown that Wzx has a strong preference for its cognate O unit, but the types of O-unit structural variance that a given Wzx can accommodate are poorly understood. In this study, we identified two Yersinia pseudotuberculosis Wzx that can distinguish between different terminal dideoxyhexose sugars on a common O-unit main-chain, despite both being able to translocate several other structurally-divergent O units. We also identified other Y. pseudotuberculosis Wzx that can translocate a structurally divergent foreign O unit with high efficiency, and thus exhibit an apparently relaxed substrate preference. It now appears that Wzx substrate preference is more complex than previously suggested, and that not all O-unit residues are equally important determinants of translocation efficiency. We propose a new "Structure-Specific Triggering" model in which Wzx translocation proceeds at a low level for a wide variety of substrates, with high-frequency translocation only being triggered by Wzx interacting with one or more preferred O-unit structural elements found on its cognate O unit(s). © 2018 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

A dye-decolorizing peroxidase from Bacillus subtilis exhibiting substrate-dependent optimum temperature for dyes and β-ether lignin dimer

PubMed Central

Min, Kyoungseon; Gong, Gyeongtaek; Woo, Han Min; Kim, Yunje; Um, Youngsoon

2015-01-01

In the biorefinery using lignocellulosic biomass as feedstock, pretreatment to breakdown or loosen lignin is important step and various approaches have been conducted. For biological pretreatment, we screened Bacillus subtilis KCTC2023 as a potential lignin-degrading bacterium based on veratryl alcohol (VA) oxidation test and the putative heme-containing dye-decolorizing peroxidase was found in the genome of B. subtilis KCTC2023. The peroxidase from B. subtilis KCTC2023 (BsDyP) was capable of oxidizing various substrates and atypically exhibits substrate-dependent optimum temperature: 30°C for dyes (Reactive Blue19 and Reactive Black5) and 50°C for high redox potential substrates (2,2′-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid [ABTS], VA, and veratryl glycerol-β-guaiacyl ether [VGE]) over +1.0 V vs. normal hydrogen electrode. At 50°C, optimum temperature for high redox potential substrates, BsDyP not only showed the highest VA oxidation activity (0.13 Umg−1) among the previously reported bacterial peroxidases but also successfully achieved VGE decomposition by cleaving Cα-Cβ bond in the absence of any oxidative mediator with a specific activity of 0.086 Umg−1 and a conversion rate of 53.5%. Based on our results, BsDyP was identified as the first bacterial peroxidase capable of oxidizing high redox potential lignin-related model compounds, especially VGE, revealing a previously unknown versatility of lignin degrading biocatalyst in nature. PMID:25650125

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

Carbon Source Preference in Chemosynthetic Hot Spring Communities

PubMed Central

Urschel, Matthew R.; Kubo, Michael D.; Hoehler, Tori M.; Peters, John W.

2015-01-01

Rates of dissolved inorganic carbon (DIC), formate, and acetate mineralization and/or assimilation were determined in 13 high-temperature (>73°C) hot springs in Yellowstone National Park (YNP), Wyoming, in order to evaluate the relative importance of these substrates in supporting microbial metabolism. While 9 of the hot spring communities exhibited rates of DIC assimilation that were greater than those of formate and acetate assimilation, 2 exhibited rates of formate and/or acetate assimilation that exceeded those of DIC assimilation. Overall rates of DIC, formate, and acetate mineralization and assimilation were positively correlated with spring pH but showed little correlation with temperature. Communities sampled from hot springs with similar geochemistries generally exhibited similar rates of substrate transformation, as well as similar community compositions, as revealed by 16S rRNA gene-tagged sequencing. Amendment of microcosms with small (micromolar) amounts of formate suppressed DIC assimilation in short-term (<45-min) incubations, despite the presence of native DIC concentrations that exceeded those of added formate by 2 to 3 orders of magnitude. The concentration of added formate required to suppress DIC assimilation was similar to the affinity constant (Km) for formate transformation, as determined by community kinetic assays. These results suggest that dominant chemoautotrophs in high-temperature communities are facultatively autotrophic or mixotrophic, are adapted to fluctuating nutrient availabilities, and are capable of taking advantage of energy-rich organic substrates when they become available. PMID:25819970

Gold Nanoparticles on Functionalized Silicon Substrate under Coulomb Blockade Regime: An Experimental and Theoretical Investigation.

PubMed

Pluchery, Olivier; Caillard, Louis; Dollfus, Philippe; Chabal, Yves J

2018-01-18

Single charge electronics offer a way for disruptive technology in nanoelectronics. Coulomb blockade is a realistic way for controlling the electric current through a device with the accuracy of one electron. In such devices the current exhibits a step-like increase upon bias which reflects the discrete nature of the fundamental charge. We have assembled a double tunnel junction on an oxide-free silicon substrate that exhibits Coulomb staircase characteristics using gold nanoparticles (AuNPs) as Coulomb islands. The first tunnel junction is an insulating layer made of a grafted organic monolayer (GOM) developed for this purpose. The GOM also serves for attaching AuNPs covalently. The second tunnel junction is made by the tip of an STM. We show that this device exhibits reproducible Coulomb blockade I-V curves at 40 K in vacuum. We also show that depending on the doping of the silicon substrate, the whole Coulomb staircase can be adjusted. We have developed a simulation approach based on the orthodox theory that was completed by calculating the bias dependent tunnel barriers and by including an accurate calculation of the band bending. This model accounts for the experimental data and the doping dependence of Coulomb oscillations. This study opens new perspectives toward designing new kind of single electron transistors (SET) based on this dependence of the Coulomb staircase with the charge carrier concentration.

The mechanistic exploration of porous activated graphene sheets-anchored SnO2 nanocrystals for application in high-performance Li-ion battery anodes.

PubMed

Yang, Yingchang; Ji, Xiaobo; Lu, Fang; Chen, Qiyuan; Banks, Craig E

2013-09-28

Porous activated graphene sheets have been for the first time exploited herein as encapsulating substrates for lithium ion battery (LIB) anodes. The as-fabricated SnO2 nanocrystals-porous activated graphene sheet (AGS) composite electrode exhibits improved electrochemical performance as an anode material for LIBs, such as better cycle performance and higher rate capability in comparison with graphene sheets, activated graphene sheets, bare SnO2 and SnO2-graphene sheet composites. The superior electrochemical performances of the designed anode can be ascribed to the porous AGS substrate, which improves the electrical conductivity of the electrode, inhibits agglomeration between particles and effectively buffers the strain from the volume variation during Li(+)-intercalation-de-intercalation and provides more cross-plane diffusion channels for Li(+) ions. As a result, the designed anode exhibits an outstanding capacity of up to 610 mA h g(-1) at a current density of 100 mA g(-1) after 50 cycles and a good rate performance of 889, 747, 607, 482 and 372 mA h g(-1) at a current density of 100, 200, 500, 1000, and 2000 mA g(-1), respectively. This work is of importance for energy storage as it provides a new substrate for the design and implementation of next-generation LIBs exhibiting exceptional electrochemical performances.

RNA-Cleaving DNA Enzymes with Altered Regio- or Enantioselectivity

NASA Technical Reports Server (NTRS)

Ordoukhanian, Phillip; Joyce, Gerald F.

2002-01-01

In vitro evolution methods were used to obtain DNA enzymes that cleave either a 2',5' - phosphodiester following a wibonucleotide or a 3',5' -phosphodiester following an L-ribonucleotide. Both enzymes can operate in an intermolecular reaction format with multiple turnover. The DNA enzyme that cleaves a 2',5' -phosphodiester exhibits a k(sub cat) of approx. 0.01/ min and catalytic efficiency, k(sub cat)/k(sub m) of approx. 10(exp 5)/ M min. The enzyme that cleaves an L-ribonudeotide is about 10-fold slower and has a catalytic efficiency of approx. 4 x 10(exp 5)/ M min. Both enzymes require a divalent metal cation for their activity and have optimal catalytic rate at pH 7-8 and 35-50 C. In a comparison of each enzyme s activity with either its corresponding substrate that contains an unnatural ribonudeotide or a substrate that instead contains a standard ribonucleotide, the 2',5' -phosphodiester-deaving DNA enzyme exhibited a regioselectivity of 6000- fold, while the L-ribonucleotide-cleaving DNA enzyme exhibited an enantioselectivity of 50-fold. These molecules demonstrate how in vitro evolution can be used to obtain regio- and enantioselective catalysts that exhibit specificities for nonnatural analogues of biological compounds.

Allosteric Control of Substrate Specificity of the Escherichia coli ADP-glucose Pyrophosphorylase

NASA Astrophysics Data System (ADS)

Ebrecht, Ana C.; Solamen, Ligin; Hill, Benjamin L.; Iglesias, Alberto A.; Olsen, Kenneth W.; Ballicora, Miguel A.

2017-06-01

The substrate specificity of enzymes is crucial to control the fate of metabolites to different pathways. However, there is growing evidence that many enzymes can catalyze alternative reactions. This promiscuous behavior has important implications in protein evolution and the acquisition of new functions. The question is how the undesirable outcomes of in vivo promiscuity can be prevented. ADP-glucose pyrophosphorylase from Escherichia coli is an example of an enzyme that needs to select the correct substrate from a broad spectrum of alternatives. This selection will guide the flow of carbohydrate metabolism towards the synthesis of reserve polysaccharides. Here, we show that the allosteric activator fructose-1,6-bisphosphate plays a role in such selection by increasing the catalytic efficiency of the enzyme towards the use of ATP rather than other nucleotides. In the presence of fructose-1,6-bisphosphate, the kcat/S0.5 for ATP was near 600-fold higher that other nucleotides, whereas in the absence of activator was only 3-fold higher. We propose that the allosteric regulation of certain enzymes is an evolutionary mechanism of adaptation for the selection of specific substrates.

Solid-substrate bioprocessing of cow dung for the production of carboxymethyl cellulase by Bacillus halodurans IND18.

PubMed

Vijayaraghavan, P; Prakash Vincent, S G; Dhillon, G S

2016-02-01

The production of carboxymethyl cellulase (CMCase) by Bacillus halodurans IND18 under solid substrate fermentation (SSF) using cow dung was optimized through two level full factorial design and second order response surface methodology (RSM). The central composite design (CCD) was employed to optimize the vital fermentation parameters, such as pH of the substrate, concentration of nitrogen source (peptone) and ion (sodium dihydrogen phosphate) sources in medium for achieving higher enzyme production. The optimum medium composition was found to be 1.46% (w/w) peptone, 0.095% (w/w) sodium dihydrogen phosphate and pH 8.0. The model prediction of 4210IU/g enzyme activity at optimum conditions was verified experimentally as 4140IU/g. The enzyme was active over a broad temperature range (40-60±1°C) and pH (7.0-9.0) with maximal activity at 60±1°C and pH 8.0. This study demonstrated the potential of cow dung as novel substrate for CMCase production. Copyright © 2015 Elsevier Ltd. All rights reserved.