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Sample records for hairpin ribozyme catalysis

  1. Structural studies on an internal loop from a hairpin ribozyme

    Energy Technology Data Exchange (ETDEWEB)

    Cai, Z.; SantaLucia, J. Jr.; Tinoco, I. Jr. [Univ. of California, Berkeley, CA (United States)

    1994-12-01

    Ribozymes, RNA enzymes, catalyze site-specific RNA cleavage and ligation reactions. We are studying the three-dimensional structure of a hairpin ribozyme derived from the minus strand of tobacco ring spot virus satellite RNA ((-)sTRSV), which has been engineering to specifically cleave the HIV-1 RNA. The minimum structure for the catalytic reaction involves a 50-nucleotide ribozyme and a 14-nucleotide substrate. The proposed secondary structure of the ribozyme-substrate complex consists of four short helices separated by two internal loops. The relatively large size (64-nucleotide) of the ribozyme-substrate complex presents formidable problems in solving the structure using NMR. Therefore we are studying smaller structural subunits of the complex. We are determining the high resolution structure of the symmetric internal loop involving the cleavage site and the flanking helices. One strand of the internal loop was selectively {sup 13}C-labeled at C8 of each purine and C6 of each pyrimidine. By using {sup 13}C-edited two-dimensional NMR, the proton NOESY spectrum was greatly simplified. This allowed unambiguous sequential proton resonance assignments along each strand. Three-dimensional {sup 1}-{sup 13}C HMQC-NOESY was used to further facilitate resonance assignments. We are also enzymatically synthesizing the entire 50-nucleotide ribozyme and will combine it with the {sup 13}C-labeled substrate. Through comparison of the NOE connectivities of the labeled nucleotides from the internal loop alone with those from the entire complex, the differences between the two structures can be elucidated.

  2. A four-way junction accelerates hairpin ribozyme folding via a discrete intermediate

    Science.gov (United States)

    Tan, Elliot; Wilson, Timothy J.; Nahas, Michelle K.; Clegg, Robert M.; Lilley, David M. J.; Ha, Taekjip

    2003-01-01

    The natural form of the hairpin ribozyme comprises two major structural elements: a four-way RNA junction and two internal loops carried by adjacent arms of the junction. The ribozyme folds into its active conformation by an intimate association between the loops, and the efficiency of this process is greatly enhanced by the presence of the junction. We have used single-molecule spectroscopy to show that the natural form fluctuates among three distinct states: the folded state and two additional, rapidly interconverting states (proximal and distal) that are inherited from the junction. The proximal state juxtaposes the two loop elements, thereby increasing the probability of their interaction and thus accelerating folding by nearly three orders of magnitude and allowing the ribozyme to fold rapidly in physiological conditions. Therefore, the hairpin ribozyme exploits the dynamics of the junction to facilitate the formation of the active site from its other elements. Dynamic interplay between structural elements, as we demonstrate for the hairpin ribozyme, may be a general theme for other functional RNA molecules. PMID:12883002

  3. Pressure modulates the self-cleavage step of the hairpin ribozyme

    Science.gov (United States)

    Schuabb, Caroline; Kumar, Narendra; Pataraia, Salome; Marx, Dominik; Winter, Roland

    2017-03-01

    The ability of certain RNAs, denoted as ribozymes, to not only store genetic information but also catalyse chemical reactions gave support to the RNA world hypothesis as a putative step in the development of early life on Earth. This, however, might have evolved under extreme environmental conditions, including the deep sea with pressures in the kbar regime. Here we study pressure-induced effects on the self-cleavage of hairpin ribozyme by following structural changes in real-time. Our results suggest that compression of the ribozyme leads to an accelerated transesterification reaction, being the self-cleavage step, although the overall process is retarded in the high-pressure regime. The results reveal that favourable interactions between the reaction site and neighbouring nucleobases are strengthened under pressure, resulting therefore in an accelerated self-cleavage step upon compression. These results suggest that properly engineered ribozymes may also act as piezophilic biocatalysts in addition to their hitherto known properties.

  4. Thermodynamics and kinetics of RNA tertiary structure formation in the junctionless hairpin ribozyme.

    Science.gov (United States)

    White, Neil A; Hoogstraten, Charles G

    2017-09-01

    The hairpin ribozyme consists of two RNA internal loops that interact to form the catalytically active structure. This docking transition is a rare example of intermolecular formation of RNA tertiary structure without coupling to helix annealing. We have used temperature-dependent surface plasmon resonance (SPR) to characterize the thermodynamics and kinetics of RNA tertiary structure formation for the junctionless form of the ribozyme, in which loops A and B reside on separate molecules. We find docking to be strongly enthalpy-driven and to be accompanied by substantial activation barriers for association and dissociation, consistent with the structural reorganization of both internal loops upon complex formation. Comparisons with the parallel analysis of a ribozyme variant carrying a 2'-O-methyl modification at the self-cleavage site and with published data in other systems reveal a surprising diversity of thermodynamic signatures, emphasizing the delicate balance of contributions to the free energy of formation of RNA tertiary structure. Copyright © 2017 Elsevier B.V. All rights reserved.

  5. The influence of junction conformation on RNA cleavage by the hairpin ribozyme in its natural junction form.

    Science.gov (United States)

    Thomson, J B; Lilley, D M

    1999-01-01

    In the natural form of the hairpin ribozyme the two loop-carrying duplexes that comprise the majority of essential bases for activity form two adjacent helical arms of a four-way RNA junction. In the present work we have manipulated the sequence around the junction in a way known to perturb the global folding properties. We find that replacement of the junction by a different sequence that has the same conformational properties as the natural sequence gives closely similar reaction rate and Arrhenius activation energy for the substrate cleavage reaction. By comparison, rotation of the natural sequence in order to alter the three-dimensional folding of the ribozyme leads to a tenfold reduction in the kinetics of cleavage. Replacement with the U1 four-way junction that is resistant to rotation into the antiparallel structure required to allow interaction between the loops also gives a tenfold reduction in cleavage rate. The results indicate that the conformation of the junction has a major influence on the catalytic activity of the ribozyme. The results are all consistent with a role for the junction in the provision of a framework by which the loops are presented for interaction in order to create the active form of the ribozyme. PMID:10024170

  6. Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme

    Czech Academy of Sciences Publication Activity Database

    Mlýnský, V.; Banáš, P.; Šponer, Jiří; van der Kamp, M.W.; Mulholland, A.J.; Otyepka, M.

    2014-01-01

    Roč. 10, č. 4 (2014), s. 1608-1622 ISSN 1549-9618 R&D Projects: GA ČR(CZ) GAP208/12/1878; GA ČR(CZ) GBP301/11/P558; GA MŠk(CZ) ED1.1.00/02.0068 Institutional support: RVO:68081707 Keywords : MOLECULAR-DYNAMICS SIMULATIONS * DELTA-VIRUS RIBOZYME * ACID-BASE CATALYSIS Subject RIV: BO - Biophysics Impact factor: 5.498, year: 2014

  7. Importance of specific nucleotides in the folding of the natural form of the hairpin ribozyme.

    Science.gov (United States)

    Wilson, T J; Zhao, Z Y; Maxwell, K; Kontogiannis, L; Lilley, D M

    2001-02-20

    The hairpin ribozyme in its natural context consists of two loops in RNA duplexes that are connected as arms of a four-way helical junction. Magnesium ions induce folding into the active conformation in which the two loops are in proximity. In this study, we have investigated nucleotides that are important to this folding process. We have analyzed the folding in terms of the cooperativity and apparent affinity for magnesium ions as a function of changes in base sequence and functional groups, using fluorescence resonance energy transfer. Our results suggest that the interaction between the loops is the sum of a number of component interactions. Some sequence variants such as A10U, G+1A, and C25U exhibit loss of cooperativity and reduced affinity of apparent magnesium ion binding. These variants are also very impaired in ribozyme cleavage activity. Nucleotides A10, G+1, and C25 thus appear to be essential in creating the conformational environment necessary for ion binding. The double variant G+1A/C25U exhibits a marked recovery of both folding and catalytic activity compared to either individual variant, consistent with the proposal of a triple-base interaction among A9, G+1, and C25 [Pinard, R., Lambert, D., Walter, N. G., Heckman, J. E., Major, F., and Burke, J. M. (1999) Biochemistry 38, 16035-16039]. However, substitution of A9 leads to relatively small changes in folding properties and cleavage activity, and the double variant G+1DAP/C25U (DAP is 2,6-diaminopurine), which could form an isosteric triple-base interaction, exhibits folding and cleavage activities that are both very impaired compared to those of the natural sequence. Our results indicate an important role for a Watson--Crick base pair between G+1 and C25; this may be buttressed by an interaction with A9, but the loss of this has less significant consequences for folding. 2'-Deoxyribose substitution leads to folding with reduced magnesium ion affinity in the following order: unmodified RNA > dA9

  8. A Conserved Target Site in HIV-1 Gag RNA is Accessible to Inhibition by Both an HDV Ribozyme and a Short Hairpin RNA

    Directory of Open Access Journals (Sweden)

    Robert J Scarborough

    2014-01-01

    Full Text Available Antisense-based molecules targeting HIV-1 RNA have the potential to be used as part of gene or drug therapy to treat HIV-1 infection. In this study, HIV-1 RNA was screened to identify more conserved and accessible target sites for ribozymes based on the hepatitis delta virus motif. Using a quantitative screen for effects on HIV-1 production, we identified a ribozyme targeting a highly conserved site in the Gag coding sequence with improved inhibitory potential compared to our previously described candidates targeting the overlapping Tat/Rev coding sequence. We also demonstrate that this target site is highly accessible to short hairpin directed RNA interference, suggesting that it may be available for the binding of antisense RNAs with different modes of action. We provide evidence that this target site is structurally conserved in diverse viral strains and that it is sufficiently different from the human transcriptome to limit off-target effects from antisense therapies. We also show that the modified hepatitis delta virus ribozyme is more sensitive to a mismatch in its target site compared to the short hairpin RNA. Overall, our results validate the potential of a new target site in HIV-1 RNA to be used for the development of antisense therapies.

  9. Mapping the Chemical Space of the RNA Cleavage and Its Implications for Ribozyme Catalysis

    Czech Academy of Sciences Publication Activity Database

    Mlýnský, V.; Kührová, P.; Jurečka, P.; Šponer, Jiří; Otyepka, M.; Banáš, Pavel

    2017-01-01

    Roč. 121, č. 48 (2017), s. 10828-10840 ISSN 1520-6106 R&D Projects: GA ČR GAP208/12/1878 Institutional support: RVO:68081707 Keywords : delta-virus ribozyme * self-cleaving ribozymes Subject RIV: CF - Physical ; Theoretical Chemistry OBOR OECD: Physical chemistry Impact factor: 3.177, year: 2016

  10. Capturing hammerhead ribozyme structures in action by modulating general base catalysis.

    Directory of Open Access Journals (Sweden)

    Young-In Chi

    2008-09-01

    Full Text Available We have obtained precatalytic (enzyme-substrate complex and postcatalytic (enzyme-product complex crystal structures of an active full-length hammerhead RNA that cleaves in the crystal. Using the natural satellite tobacco ringspot virus hammerhead RNA sequence, the self-cleavage reaction was modulated by substituting the general base of the ribozyme, G12, with A12, a purine variant with a much lower pKa that does not significantly perturb the ribozyme's atomic structure. The active, but slowly cleaving, ribozyme thus permitted isolation of enzyme-substrate and enzyme-product complexes without modifying the nucleophile or leaving group of the cleavage reaction, nor any other aspect of the substrate. The predissociation enzyme-product complex structure reveals RNA and metal ion interactions potentially relevant to transition-state stabilization that are absent in precatalytic structures.

  11. Structural and catalytic effects of an invariant purine substitution in the hammerhead ribozyme: implications for the mechanism of acid–base catalysis

    Science.gov (United States)

    Schultz, Eric P.; Vasquez, Ernesto E.; Scott, William G.

    2014-01-01

    The hammerhead ribozyme catalyzes RNA cleavage via acid–base catalysis. Whether it does so by general acid–base catalysis, in which the RNA itself donates and abstracts protons in the transition state, as is typically assumed, or by specific acid–base catalysis, in which the RNA plays a structural role and proton transfer is mediated by active-site water molecules, is unknown. Previous biochemical and crystallographic experiments implicate an invariant purine in the active site, G12, as the general base. However, G12 may play a structural role consistent with specific base catalysis. To better understand the role of G12 in the mechanism of hammerhead catalysis, a 2.2 Å resolution crystal structure of a hammerhead ribozyme from Schistosoma mansoni with a purine substituted for G12 in the active site of the ribozyme was obtained. Comparison of this structure (PDB entry 3zd4), in which A12 is substituted for G, with three previously determined structures that now serve as important experimental controls, allows the identification of structural perturbations that are owing to the purine substitution itself. Kinetic measurements for G12 purine-substituted schistosomal hammerheads confirm a previously observed dependence of rate on the pK a of the substituted purine; in both cases inosine, which is similar to G in pK a and hydrogen-bonding properties, is unexpectedly inactive. Structural comparisons indicate that this may primarily be owing to the lack of the exocyclic 2-amino group in the G12A and G12I substitutions and its structural effect upon both the nucleotide base and phosphate of A9. The latter involves the perturbation of a previously identified and well characterized metal ion-binding site known to be catalytically important in both minimal and full-length hammerhead ribozyme sequences. The results permit it to be suggested that G12 plays an important role in stabilizing the active-site structure. This result, although not inconsistent with the

  12. Structural and catalytic effects of an invariant purine substitution in the hammerhead ribozyme: implications for the mechanism of acid-base catalysis.

    Science.gov (United States)

    Schultz, Eric P; Vasquez, Ernesto E; Scott, William G

    2014-09-01

    The hammerhead ribozyme catalyzes RNA cleavage via acid-base catalysis. Whether it does so by general acid-base catalysis, in which the RNA itself donates and abstracts protons in the transition state, as is typically assumed, or by specific acid-base catalysis, in which the RNA plays a structural role and proton transfer is mediated by active-site water molecules, is unknown. Previous biochemical and crystallographic experiments implicate an invariant purine in the active site, G12, as the general base. However, G12 may play a structural role consistent with specific base catalysis. To better understand the role of G12 in the mechanism of hammerhead catalysis, a 2.2 Å resolution crystal structure of a hammerhead ribozyme from Schistosoma mansoni with a purine substituted for G12 in the active site of the ribozyme was obtained. Comparison of this structure (PDB entry 3zd4), in which A12 is substituted for G, with three previously determined structures that now serve as important experimental controls, allows the identification of structural perturbations that are owing to the purine substitution itself. Kinetic measurements for G12 purine-substituted schistosomal hammerheads confirm a previously observed dependence of rate on the pK(a) of the substituted purine; in both cases inosine, which is similar to G in pK(a) and hydrogen-bonding properties, is unexpectedly inactive. Structural comparisons indicate that this may primarily be owing to the lack of the exocyclic 2-amino group in the G12A and G12I substitutions and its structural effect upon both the nucleotide base and phosphate of A9. The latter involves the perturbation of a previously identified and well characterized metal ion-binding site known to be catalytically important in both minimal and full-length hammerhead ribozyme sequences. The results permit it to be suggested that G12 plays an important role in stabilizing the active-site structure. This result, although not inconsistent with the potential

  13. General base catalysis for cleavage by the active-site cytosine of the hepatitis delta virus ribozyme: QM/MM calculations establish chemical feasibility

    Czech Academy of Sciences Publication Activity Database

    Banáš, Pavel; Rulíšek, Lubomír; Hánošová, V.; Svozil, Daniel; Walter, N.G.; Šponer, Jiří; Otyepka, Michal

    2008-01-01

    Roč. 112, č. 35 (2008), s. 11177-11187 ISSN 1520-6106 R&D Projects: GA MŠk LC512; GA MŠk(CZ) LC06030; GA AV ČR(CZ) IAA400040802; GA AV ČR 1QS500040581 Grant - others:NIH(US) GM62357 Institutional research plan: CEZ:AV0Z40550506; CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : HDV ribozyme * catalysis * QM/MM calculations Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.189, year: 2008

  14. Reactive Conformation of the Active Site in the Hairpin Ribozyme Achieved by Molecular Dynamics Simulations with epsilon/zeta Force Field Reparametrizations

    Czech Academy of Sciences Publication Activity Database

    Mlýnský, V.; Kuehrova, P.; Zgarbová, M.; Jurečka, P.; Walter, Nils G.; Otyepka, M.; Šponer, Jiří; Banáš, Pavel

    2015-01-01

    Roč. 119, č. 11 (2015), s. 4220-4229 ISSN 1520-6106 R&D Projects: GA ČR(CZ) GAP208/12/1878 Institutional support: RVO:68081707 Keywords : ACID- BASE CATALYSIS * NUCLEIC-ACIDS * RNA CATALYSIS Subject RIV: BO - Biophysics Impact factor: 3.187, year: 2015

  15. A ribozyme transcribed by a ribozyme

    DEFF Research Database (Denmark)

    Bentin, Thomas

    2011-01-01

    Prominent current ideas on how life emerged on Earth include an RNA world hypothesis in which RNA performed informational as well as catalytic functions in the absence of both DNA and protein. Demonstration of a self-replicative system based on ribonucleic acid polymers as both information carriers...... and catalysts would lend support to such a scenario. A pivotal component of this system would be an RNA dependent RNA polymerase ribozyme capable of replicating its own RNA gene. Recent work from the Holliger group at the Laboratory for Molecular Biology in Cambridge has provided synthetic ribozymes1 that just...

  16. Artificial hammerhead ribozymes: engineering and applications

    International Nuclear Information System (INIS)

    Vorobjeva, M A; Davydova, A S; Venyaminova, Aliya G

    2011-01-01

    The properties of hammerhead ribozymes are described. Various hammerhead ribozyme constructs for target RNA cleavage were considered. Approaches to enhancement of the stability of artificial ribozymes in biological media and to regulation of the catalytic activity of hammerhead ribozymes using effector molecules are described. The effect of ribozymes on extended structured natural RNAs is discussed. Applications of artificial hammerhead ribozymes as inhibitors of gene expression at matrix RNA level were considered.

  17. Wobble pairs of the HDV ribozyme play specific roles in stabilization of active site dynamics

    Czech Academy of Sciences Publication Activity Database

    Sripathi, K.N.; Banáš, P.; Réblová, K.; Šponer, Jiří; Otyepka, M.; Walter, Nils G.

    2015-01-01

    Roč. 17, č. 8 (2015), s. 5887-5900 ISSN 1463-9076 R&D Projects: GA ČR GAP208/12/1878 Institutional support: RVO:68081707 Keywords : HEPATITIS -DELTA-VIRUS * SELF-CLEAVING RIBOZYMES * ACID-BASE CATALYSIS Subject RIV: BO - Biophysics Impact factor: 4.449, year: 2015

  18. Lanthanide Cofactors for Triphosphorylation Ribozymes

    Science.gov (United States)

    Sweeney, K. J.; Müller, U. F.

    2017-07-01

    RNA world organisms could have used trimetaphosphate as energy source for thermodynamically unfavorable RNA polymerization. Using in vitro selection we show here that Lanthanides can serve as cofactors for ribozyme-catalyzed RNA triphosphorylation.

  19. Chemical Feasibility of the General Acid/Base Mechanism of glmS Ribozyme Self-Cleavage

    Czech Academy of Sciences Publication Activity Database

    Dubecký, M.; Walter, Nils G.; Šponer, Jiří; Otyepka, M.; Banáš, Pavel

    2015-01-01

    Roč. 103, č. 10 (2015), s. 550-562 ISSN 0006-3525 R&D Projects: GA MŠk(CZ) ED1.1.00/02.0068; GA ČR(CZ) GAP208/12/1878 Institutional support: RVO:68081707 Keywords : MOLECULAR-DYNAMICS SIMULATIONS * ACTIVE-SITE GUANINE * HAIRPIN RIBOZYME Subject RIV: BO - Biophysics Impact factor: 2.248, year: 2015

  20. Competition Between Co(NH3)63+ and Inner Sphere Mg2+ Ions in the HDV Ribozyme

    OpenAIRE

    Gong, Bo; Chen, Jui-Hui; Bevilacqua, Philip C.; Golden, Barbara L.; Carey, Paul R.

    2009-01-01

    Divalent cations play critical structural and functional roles in many RNAs. While the hepatitis delta virus (HDV) ribozyme can undergo self-cleavage in the presence of molar concentrations of monovalent cations, divalent cations such as Mg2+ are required for efficient catalysis under physiological conditions. Moreover, the cleavage reaction can be inhibited with Co(NH3)63+, an analog of Mg(H2O)62+. Here, the binding of Mg2+ and Co(NH3)63+ to the HDV ribozyme are studied by Raman microscopic ...

  1. Complexity in pH-Dependent Ribozyme Kinetics: Dark pKa Shifts and Wavy Rate-pH Profiles.

    Science.gov (United States)

    Frankel, Erica A; Bevilacqua, Philip C

    2018-02-06

    Charged bases occur in RNA enzymes, or ribozymes, where they play key roles in catalysis. Cationic bases donate protons and perform electrostatic catalysis, while anionic bases accept protons. We previously published simulations of rate-pH profiles for ribozymes in terms of species plots for the general acid and general base that have been useful for understanding how ribozymes respond to pH. In that study, we did not consider interaction between the general acid and general base or interaction with other species on the RNA. Since that report, diverse small ribozyme classes have been discovered, many of which have charged nucleobases or metal ions in the active site that can either directly interact and participate in catalysis or indirectly interact as "influencers". Herein, we simulate experimental rate-pH profiles in terms of species plots in which reverse protonated charged nucleobases interact. These analyses uncover two surprising features of pH-dependent enzyme kinetics. (1) Cooperativity between the general acid and general base enhances population of the functional forms of a ribozyme and manifests itself as hidden or "dark" pK a shifts, real pK a shifts that accelerate the reaction but are not readily observed by standard experimental approaches, and (2) influencers favorably shift the pK a s of proton-transferring nucleobases and manifest themselves as "wavy" rate-pH profiles. We identify parallels with the protein enzyme literature, including reverse protonation and wavelike behavior, while pointing out that RNA is more prone to reverse protonation. The complexities uncovered, which arise from simple pairwise interactions, should aid deconvolution of complex rate-pH profiles for RNA and protein enzymes and suggest veiled catalytic devices for promoting catalysis that can be tested by experiment and calculation.

  2. Advancing Polymerase Ribozymes Towards Self-Replication

    Science.gov (United States)

    Tjhung, K. F.; Joyce, G. F.

    2017-07-01

    Autocatalytic replication and evolution in vitro by (i) a cross-chiral RNA polymerase catalyzing polymerization of mononucleotides of the opposite handedness; (ii) non-covalent assembly of component fragments of an existing RNA polymerase ribozyme.

  3. Hammerhead ribozyme activity and oligonucleotide duplex stability in mixed solutions of water and organic compounds

    Directory of Open Access Journals (Sweden)

    Shu-ichi Nakano

    2014-01-01

    Full Text Available Nucleic acids are useful for biomedical targeting and sensing applications in which the molecular environment is different from that of a dilute aqueous solution. In this study, the influence of various types of mixed solutions of water and water-soluble organic compounds on RNA was investigated by measuring the catalytic activity of the hammerhead ribozyme and the thermodynamic stability of an oligonucleotide duplex. The compounds with a net neutral charge, such as poly(ethylene glycol, small primary alcohols, amide compounds, and aprotic solvent molecules, added at high concentrations changed the ribozyme-catalyzed RNA cleavage rate, with the magnitude of the effect dependent on the NaCl concentration. These compounds also changed the thermodynamic stability of RNA base pairs of an oligonucleotide duplex and its dependence on the NaCl concentration. Specific interactions with RNA molecules and reduced water activity could account for the inhibiting effects on the ribozyme catalysis and destabilizing effects on the duplex stability. The salt concentration dependence data correlated with the dielectric constant, but not with water activity, viscosity, and the size of organic compounds. This observation suggests the significance of the dielectric constant effects on the RNA reactions under molecular crowding conditions created by organic compounds.

  4. Chemical fidelity of an RNA polymerase ribozyme

    DEFF Research Database (Denmark)

    Attwater, J.; Tagami, S.; Kimoto, M.

    2013-01-01

    for function. Here we have explored the chemical fidelity, i.e. substrate selectivity and specificity for both single and multiple catalytic steps of the Z RNA polymerase ribozyme-a modern day analogue of the primordial RNA replicase. Using a wide range of nucleotide analogues and ionic conditions, we observe......The emergence of catalytically active RNA enzymes (ribozymes) is widely believed to have been an important transition in the origin of life. In the context of a likely heterogeneous chemical environment, substrate specificity and selectivity of these primordial enzymes would have been critical...

  5. Vesicle Encapsulation Studies Reveal that Single Molecule Ribozyme Heterogeneities Are Intrinsic

    Science.gov (United States)

    Okumus, Burak; Wilson, Timothy J.; Lilley, David M. J.; Ha, Taekjip

    2004-01-01

    Single-molecule measurements have revealed that what were assumed to be identical molecules can differ significantly in their static and dynamic properties. One of the most striking examples is the hairpin ribozyme, which was shown to exhibit two to three orders of magnitude variation in folding kinetics between molecules. Although averaged behavior of single molecules matched the bulk solution data, it was not possible to exclude rigorously the possibility that the variations around the mean values arose from different ways of interacting with the surface environment. To test this, we minimized the molecules' interaction with the surface by encapsulating DNA or RNA molecules inside 100- to 200-nm diameter unilamellar vesicles, following the procedures described by Haran and coworkers. Vesicles were immobilized on a supported lipid bilayer via biotin-streptavidin linkages. We observed no direct binding of DNA or RNA on the supported bilayer even at concentrations exceeding 100 nM, indicating that these molecules do not bind stably on the membrane. Since the vesicle diameter is smaller than the resolution of optical microscopy, the lateral mobility of the molecules is severely constrained, allowing long observation periods. We used fluorescence correlation spectroscopy, nuclease digestion, and external buffer exchange to show that the molecules were indeed encapsulated within the vesicles. When contained within vesicles, the natural form of the hairpin ribozyme exhibited 50-fold variation in both folding and unfolding rates in 0.5 mM Mg2+, which is identical to what was observed from the molecules tethered directly on the surface. This strongly indicates that the observed heterogeneity in dynamic properties does not arise as an artifact of surface attachment, but is intrinsic to the nature of the molecules. PMID:15454471

  6. Cisplatin Targeting of Bacterial Ribosomal RNA Hairpins

    Directory of Open Access Journals (Sweden)

    Gayani N. P. Dedduwa-Mudalige

    2015-09-01

    Full Text Available Cisplatin is a clinically important chemotherapeutic agent known to target purine bases in nucleic acids. In addition to major deoxyribonucleic acid (DNA intrastrand cross-links, cisplatin also forms stable adducts with many types of ribonucleic acid (RNA including siRNA, spliceosomal RNAs, tRNA, and rRNA. All of these RNAs play vital roles in the cell, such as catalysis of protein synthesis by rRNA, and therefore serve as potential drug targets. This work focused on platination of two highly conserved RNA hairpins from E. coli ribosomes, namely pseudouridine-modified helix 69 from 23S rRNA and the 790 loop of helix 24 from 16S rRNA. RNase T1 probing, MALDI mass spectrometry, and dimethyl sulfate mapping revealed platination at GpG sites. Chemical probing results also showed platination-induced RNA structural changes. These findings reveal solvent and structural accessibility of sites within bacterial RNA secondary structures that are functionally significant and therefore viable targets for cisplatin as well as other classes of small molecules. Identifying target preferences at the nucleotide level, as well as determining cisplatin-induced RNA conformational changes, is important for the design of more potent drug molecules. Furthermore, the knowledge gained through studies of RNA-targeting by cisplatin is applicable to a broad range of organisms from bacteria to human.

  7. Molecular characterization of a new member of the lariat capping twin-ribozyme introns

    DEFF Research Database (Denmark)

    Tang, Yunjia; Nielsen, Henrik; Masquida, Benoît

    2014-01-01

    BACKGROUND: Twin-ribozyme introns represent a complex class of mobile group I introns that harbour a lariat capping (LC) ribozyme and a homing endonuclease gene embedded in a conventional self-splicing group I ribozyme (GIR2). Twin-ribozyme introns have so far been confined to nucleolar DNA in Na...

  8. Environmental catalysis

    International Nuclear Information System (INIS)

    Montes Consuelo; Villa, Aida Luz

    1996-01-01

    The term environmental catalysis has been used lately to refer to a variety of applications of the catalysis, those which, they have grouped in the following categories: a) Control of emissions (chimney Gases and gases of the vehicles, Compound Organic Volatile (VOC), Scents, Chlorofluorocarbons) b) Conversion of having undone solids or liquids. C) Selective obtaining of alternating products that replace polluting compounds. d)replacement of catalysis environmentally dangerous And e)Development of catalysts for the obtaining of valuable chemical products without the formation of polluting by-products. In the group of Environmental Catalysis comes working in the first category, Particularly, in the exploration of active catalysts in the decrease of the emissions coming from combustion systems, carbon monoxide, hydrocarbons, nitrogen oxides (NOx), N20 and sulfur (SOx). Our fundamental premise is that the molecular meshes are catalytic potential for the development of a technology environmentally clean. These materials understand a class of inorganic compound with unique properties and intimately related with the structure. The net of the molecular meshes consists on tetrahedral configuration atoms (Al,Si, P, etc.) united to each other by oxygen atoms. As a result they are not formed three-dimensional structures alone with channels and cavities but also, with openings bounded by rings that consist of a certain number of tetrahedral atoms

  9. Involvement of a cytosine side chain in proton transfer in the rate-determining step of ribozyme self-cleavage

    Science.gov (United States)

    Shih, I-hung; Been, Michael D.

    2001-01-01

    Ribozymes of hepatitis delta virus have been proposed to use an active-site cytosine as an acid-base catalyst in the self-cleavage reaction. In this study, we have examined the role of cytosine in more detail with the antigenomic ribozyme. Evidence that proton transfer in the rate-determining step involved cytosine 76 (C76) was obtained from examining cleavage activity of the wild-type and imidazole buffer-rescued C76-deleted (C76Δ) ribozymes in D2O and H2O. In both reactions, a similar kinetic isotope effect and shift in the apparent pKa indicate that the buffer is functionally substituting for the side chain in proton transfer. Proton inventory of the wild-type reaction supported a mechanism of a single proton transfer at the transition state. This proton transfer step was further characterized by exogenous base rescue of a C76Δ mutant with cytosine and imidazole analogues. For the imidazole analogues that rescued activity, the apparent pKa of the rescue reaction, measured under kcat/KM conditions, correlated with the pKa of the base. From these data a Brønsted coefficient (β) of 0.51 was determined for the base-rescued reaction of C76Δ. This value is consistent with that expected for proton transfer in the transition state. Together, these data provide strong support for a mechanism where an RNA side chain participates directly in general acid or general base catalysis of the wild-type ribozyme to facilitate RNA cleavage. PMID:11171978

  10. Competition Between Co(NH3)63+ and Inner Sphere Mg2+ Ions in the HDV Ribozyme

    Science.gov (United States)

    Gong, Bo; Chen, Jui-Hui; Bevilacqua, Philip C.; Golden, Barbara L.; Carey, Paul R.

    2009-01-01

    Divalent cations play critical structural and functional roles in many RNAs. While the hepatitis delta virus (HDV) ribozyme can undergo self-cleavage in the presence of molar concentrations of monovalent cations, divalent cations such as Mg2+ are required for efficient catalysis under physiological conditions. Moreover, the cleavage reaction can be inhibited with Co(NH3)63+, an analog of Mg(H2O)62+. Here, the binding of Mg2+ and Co(NH3)63+ to the HDV ribozyme are studied by Raman microscopic analysis of crystals. Raman difference spectra acquired at different metal ion conditions reveal changes in the ribozyme. When Mg2+ alone is introduced to the ribozyme, inner sphere coordination of Mg(H2O)x2+ (x≤5) to non-bridging PO2− oxygen, and changes in base stretches and phosphodiester group conformation are observed. In addition, binding of Mg2+ induces deprotonation of a cytosine assigned to the general acid C75, consistent with solution studies. When Co(NH3)63+ alone is introduced, deprotonation of C75 is again observed, as are distinctive changes in base vibrational ring modes and phosphodiester backbone conformation. In contrast to Mg2+ binding, Co(NH3)63+ binding does not perturb PO2− group vibrations, consistent with its ability to make only outer sphere contacts. Surprisingly, competitive binding studies reveal that Co(NH3)63+ ions displace some inner sphere-coordinated magnesium species, including ions coordinated to PO2− groups or the N7 of a guanine, likely G1 at the active site. These observations contrast with the tenet that Co(NH3)63+ ions displace only outer sphere magnesium ions. Overall, our data support two classes of inner sphere Mg2+-PO2− binding sites: sites that Co(NH3)63+ can displace, and others it cannot. PMID:19888753

  11. Catalysis studies

    International Nuclear Information System (INIS)

    Taylor, T.N.; Ellis, W.P.

    1977-11-01

    The New Research Initiatives Program (NRIP) project on catalysis in Los Alamos Scientific Laboratory (LASL) Group CMB-8 has made significant progress towards performing the first basic in situ experimental studies of heterogeneous catalysis on solid compound surfaces in a LEED-Auger system. To further understand the surface crystallography of a possible catalyst compound, LEED-Auger measurements were made on UO 2 (approximately 100) vicinal surfaces. These (approximately 100) vicinal surfaces were shown to decompose irreversibly into lower index facets, including prominent (100) facets, at temperatures below those needed for creation of lowest index faceting on (approximately 111) vicinal surfaces. LEED examination of fully faceted surfaces from both types of UO 2 vicinal cuts did not show evidence of cyclopropane or propene chemisorption. The existing LEED-Auger system was modified to allow catalytic reactions at approximately less than 10 -3 torr. A sample holder, specifically designed for catalysis measurements in the modified system, was tested while examining single crystals of CoO and Cr 2 O 3 . Extensive LEED-Auger measurements were made on CoO in vacuo and in the presence of light hydrocarbons and alcohols plus H 2 O, NO, and NH 3 . No chemisorptive behavior was observed except with H 2 O in the presence of the electron beam. Although only examined briefly, the Cr 2 O 3 was remarkable for the sharp LEED features obtained prior to any surface treatment in the vacuum system

  12. A new RNA branching activity: the GIR1 ribozyme

    DEFF Research Database (Denmark)

    Nielsen, Henrik; Johansen, Steinar D

    2006-01-01

    The formation of lariat intermediates during the first step of splicing of group II introns and spliceosomal introns is a well-studied fundamental reaction in molecular biology. Apart from this prominent example, there are surprisingly few occurrences of branched nucleotides or even 2......',5'-phosphodiester bonds in biology. We recently described a new ribozyme, the GIR1 branching ribozyme, which catalyzes the formation of a tiny lariat that caps an mRNA. This new example together with work on artificial branching ribozymes and deoxyribozymes shows that branching is facile and points...... to the possibility that branching reactions could be more prevalent than previously recognized....

  13. Molecular modelling of the GIR1 branching ribozyme gives new insight into evolution of structurally related ribozymes

    DEFF Research Database (Denmark)

    Beckert, Bertrand Dominique; Nielsen, Henrik; Einvik, Christer

    2008-01-01

    a catalytic core showing a different topology from that of group I ribozymes. The differences include a core J8/7 region that has been reduced and is complemented by residues from the pre-lariat fold. These findings provide the basis for an evolutionary mechanism that accounts for the change from group I...... splicing ribozyme to the branching GIR1 architecture. Such an evolutionary mechanism can be applied to other large RNAs such as the ribonuclease P....

  14. Environmental catalysis

    Energy Technology Data Exchange (ETDEWEB)

    Janssen, F.J.J.G.; Santen, R.A. van (eds.)

    1999-04-01

    Catalysts play key roles in the production of clean fuels, the conversion of waste and green raw materials into energy, clean combustion engines including control of NOx and soot production and reduction of greenhouse gases, production of clean water and polymers, as well as reduction from polymers to monometers. This book contains 15 chapters by experts in the field, on the theme of catalysts used to create a sustainable society. Chapters include: catalysts for renewable energy and chemicals, fuel cells, catalytic processes for high-quality transportation fuels; oxidative coupling of methane, methane utilisation via synthesis gas generation, catalytic combustion, catalytical removal of nitrate from water, contribution of catalysis towards the reduction of atmospheric air pollution (CO{sub 2}, CFCs, N{sub 2}O), ozone), emission control from mobile sources and from stationary sources, and deactivation, regeneration and recycling of hydroprocessing catalysts.

  15. Hairpin vortices in turbulent boundary layers

    International Nuclear Information System (INIS)

    Eitel-Amor, G; Schlatter, P; Flores, O

    2014-01-01

    The present work addresses the question whether hairpin vortices are a dominant feature of near-wall turbulence and which role they play during transition. First, the parent-offspring mechanism is investigated in temporal simulations of a single hairpin vortex introduced in a mean shear flow corresponding to turbulent channels and boundary layers up to Re τ = 590. Using an eddy viscosity computed from resolved simulations, the effect of a turbulent background is also considered. Tracking the vortical structure downstream, it is found that secondary hairpins are created shortly after initialization. Thereafter, all rotational structures decay, whereas this effect is enforced in the presence of an eddy viscosity. In a second approach, a laminar boundary layer is tripped to transition by insertion of a regular pattern of hairpins by means of defined volumetric forces representing an ejection event. The idea is to create a synthetic turbulent boundary layer dominated by hairpin-like vortices. The flow for Re τ < 250 is analysed with respect to the lifetime of individual hairpin-like vortices. Both the temporal and spatial simulations demonstrate that the regeneration process is rather short-lived and may not sustain once a turbulent background has formed. From the transitional flow simulations, it is conjectured that the forest of hairpins reported in former DNS studies is an outer layer phenomenon not being connected to the onset of near-wall turbulence.

  16. Kinetic partitioning mechanism of HDV ribozyme folding

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Jiawen; Gong, Sha; Wang, Yujie; Zhang, Wenbing, E-mail: wbzhang@whu.edu.cn [Department of Physics, Wuhan University, Wuhan, Hubei 430072 (China)

    2014-01-14

    RNA folding kinetics is directly tied to RNA biological functions. We introduce here a new approach for predicting the folding kinetics of RNA secondary structure with pseudoknots. This approach is based on our previous established helix-based method for predicting the folding kinetics of RNA secondary structure. In this approach, the transition rates for an elementary step: (1) formation, (2) disruption of a helix stem, and (3) helix formation with concomitant partial melting of an incompatible helix, are calculated with the free energy landscape. The folding kinetics of the Hepatitis delta virus (HDV) ribozyme and the mutated sequences are studied with this method. The folding pathways are identified by recursive searching the states with high net flux-in(out) population starting from the native state. The theory results are in good agreement with that of the experiments. The results indicate that the bi-phasic folding kinetics for the wt HDV sequence is ascribed to the kinetic partitioning mechanism: Part of the population will quickly fold to the native state along the fast pathway, while another part of the population will fold along the slow pathway, in which the population is trapped in a non-native state. Single mutation not only changes the folding rate but also the folding pathway.

  17. A natural fast-cleaving branching ribozyme from the amoeboflagellate Naegleria pringsheimi

    DEFF Research Database (Denmark)

    Tang, Yunjia; Nielsen, Henrik; Birgisdottir, Asa Birna

    2011-01-01

    The GIR1 branching ribozyme constitutes a separate class of naturally occurring ribozymes. Most studies have been performed with the single GIR1 known from the myxomycete Didymium iridis whereas the large number of GIR1s found in the amoeboflagellate Naegleria has remained largely uncharacterized....... Here, we investigate ribozyme cleavage properties of a collection of Naegleria GIR1 ribozymes and define the variant from N. pringsheimi as a suitable model due to its superior activity in vitro. We identify the minimal ribozyme by deletion analysis applying a new RNase R based assay for the branching...

  18. Ionic interactions and the global conformations of the hammerhead ribozyme

    DEFF Research Database (Denmark)

    Bassi, G S; Møllegaard, N E; Murchie, A I

    1995-01-01

    Here we investigate the global conformation of the hammerhead ribozyme. Electrophoretic studies demonstrate that the structure is folded in response to the concentration and type of ions present. Folding based on colinear alignment of arms II and III is suggested, with a variable angle subtended ...

  19. A dynamical mechanism for the hairpin diagram

    International Nuclear Information System (INIS)

    Chang Chaohsi; Guo Xinheng; Li Xueqian.

    1989-09-01

    Based on the non-valence quark-antiquark and gluon constituent structure of mesons we give a reasonable dynamical mechanism which can induce the hairpin diagram without violating the well-observed OZI rule. We calculate the hairpin amplitudes of D deg. → K-bar deg.η and K-bar deg.η' normalized by D deg. → K-bar deg.π deg. and have found that the hairpin diagram can give rise to substantial contribution to the decays where a meson with a SU(3) flavor singlet component is involved in the final state. In this scenario, we also obtain the branching ratio of D deg. → K-bar deg. φ as 0.55% in comparison with the experimental data of 0.83%. (autor). 33 refs, 3 figs

  20. Advances in catalysis

    CERN Document Server

    Gates, Bruce C

    2012-01-01

    Advances in Catalysis fills the gap between the journal papers and the textbooks across the diverse areas of catalysis research. For more than 60 years Advances in Catalysis has been dedicated to recording progress in the field of catalysis and providing the scientific community with comprehensive and authoritative reviews. This series in invaluable to chemical engineers, physical chemists, biochemists, researchers and industrial chemists working in the fields of catalysis and materials chemistry. * In-depth, critical, state-of-the-art reviews * Comprehensive, covers of all as

  1. QM/MM Studies of Hairpin Ribozyme Self-Cleavage Suggest the Feasibility of Multiple Competing Reaction Mechanisms

    Czech Academy of Sciences Publication Activity Database

    Mlýnský, V.; Banáš, P.; Walter, N.G.; Šponer, Jiří; Otyepka, M.

    2011-01-01

    Roč. 115, č. 47 (2011), s. 13911-13924 ISSN 1520-6106 R&D Projects: GA ČR(CZ) GAP208/10/2302; GA ČR(CZ) GA203/09/1476; GA ČR(CZ) GAP208/11/1822 Institutional research plan: CEZ:AV0Z50040702 Institutional support: RVO:68081707 Keywords : TRANSITION-STATE STABILIZATION * BASE-PHOSPHATE INTERACTIONS * DENSITY-FUNCTIONAL THEORY Subject RIV: BO - Biophysics Impact factor: 3.696, year: 2011

  2. Speciation of a group I intron into a lariat capping ribozyme

    DEFF Research Database (Denmark)

    Meyer, Mélanie; Nielsen, Henrik; Oliéric, Vincent

    2014-01-01

    The lariat-capping (LC) ribozyme is a natural ribozyme isolated from eukaryotic microorganisms. Despite apparent structural similarity to group I introns, the LC ribozyme catalyzes cleavage by a 2',5' branching reaction, leaving the 3' product with a 3-nt lariat cap that functionally substitutes ....... The structures also show how conserved interactions twist residues, forming the lariat to join chemical groups involved in branching....

  3. Template-directed ligation of tethered mononucleotides by t4 DNA ligase for kinase ribozyme selection.

    Directory of Open Access Journals (Sweden)

    David G Nickens

    Full Text Available BACKGROUND: In vitro selection of kinase ribozymes for small molecule metabolites, such as free nucleosides, will require partition systems that discriminate active from inactive RNA species. While nucleic acid catalysis of phosphoryl transfer is well established for phosphorylation of 5' or 2' OH of oligonucleotide substrates, phosphorylation of diffusible small molecules has not been demonstrated. METHODOLOGY/PRINCIPAL FINDINGS: This study demonstrates the ability of T4 DNA ligase to capture RNA strands in which a tethered monodeoxynucleoside has acquired a 5' phosphate. The ligation reaction therefore mimics the partition step of a selection for nucleoside kinase (deoxyribozymes. Ligation with tethered substrates was considerably slower than with nicked, fully duplex DNA, even though the deoxynucleotides at the ligation junction were Watson-Crick base paired in the tethered substrate. Ligation increased markedly when the bridging template strand contained unpaired spacer nucleotides across from the flexible tether, according to the trends: A(2>A(1>A(3>A(4>A(0>A(6>A(8>A(10 and T(2>T(3>T(4>T(6 approximately T(1>T(8>T(10. Bridging T's generally gave higher yield of ligated product than bridging A's. ATP concentrations above 33 microM accumulated adenylated intermediate and decreased yields of the gap-sealed product, likely due to re-adenylation of dissociated enzyme. Under optimized conditions, T4 DNA ligase efficiently (>90% joined a correctly paired, or TratioG wobble-paired, substrate on the 3' side of the ligation junction while discriminating approximately 100-fold against most mispaired substrates. Tethered dC and dG gave the highest ligation rates and yields, followed by tethered deoxyinosine (dI and dT, with the slowest reactions for tethered dA. The same kinetic trends were observed in ligase-mediated capture in complex reaction mixtures with multiple substrates. The "universal" analog 5-nitroindole (dNI did not support ligation when

  4. Many Activities, One Structure: Functional Plasticity of Ribozyme Folds

    Directory of Open Access Journals (Sweden)

    Matthew W.L. Lau

    2016-11-01

    Full Text Available Catalytic RNAs, or ribozymes, are involved in a number of essential biological processes, such as replication of RNA genomes and mobile genetic elements, RNA splicing, translation, and RNA degradation. The function of ribozymes requires the formation of active sites decorated with RNA functional groups within defined three-dimensional (3D structures. The genotype (sequence of RNAs ultimately determines what 3D structures they adopt (as a function of their environmental conditions. These 3D structures, in turn, give rise to biochemical activity, which can further elaborate them by catalytic rearrangements or association with other molecules. The fitness landscape of a non-periodic linear polymer, such as RNA, relates its primary structure to a phenotype. Two major challenges in the analysis of ribozymes is to map all possible genotypes to their corresponding catalytic activity (that is, to determine their fitness landscape experimentally, and to understand whether their genotypes and three-dimensional structures can support multiple different catalytic functions. Recently, the combined results of experiments that employ in vitro evolution methods, high-throughput sequencing and crystallographic structure determination have hinted at answers to these two questions: while the fitness landscape of ribozymes is rugged, meaning that their catalytic activity cannot be optimized by a smooth trajectory in sequence space, once an RNA achieves a stable three-dimensional fold, it can be endowed with distinctly different biochemical activities through small changes in genotype. This functional plasticity of highly structured RNAs may be particularly advantageous for the adaptation of organisms to drastic changes in selective pressure, or for the development of new biotechnological tools.

  5. Multicatalyst system in asymmetric catalysis

    CERN Document Server

    Zhou, Jian

    2014-01-01

    This book introduces multi-catalyst systems by describing their mechanism and advantages in asymmetric catalysis.  Helps organic chemists perform more efficient catalysis with step-by-step methods  Overviews new concepts and progress for greener and economic catalytic reactions  Covers topics of interest in asymmetric catalysis including bifunctional catalysis, cooperative catalysis, multimetallic catalysis, and novel tandem reactions   Has applications for pharmaceuticals, agrochemicals, materials, and flavour and fragrance

  6. Local neutral networks help maintain inaccurately replicating ribozymes.

    Science.gov (United States)

    Szilágyi, András; Kun, Ádám; Szathmáry, Eörs

    2014-01-01

    The error threshold of replication limits the selectively maintainable genome size against recurrent deleterious mutations for most fitness landscapes. In the context of RNA replication a distinction between the genotypic and the phenotypic error threshold has been made; where the latter concerns the maintenance of secondary structure rather than sequence. RNA secondary structure is treated as a proxy for function. The phenotypic error threshold allows higher per digit mutation rates than its genotypic counterpart, and is known to increase with the frequency of neutral mutations in sequence space. Here we show that the degree of neutrality, i.e. the frequency of nearest-neighbour (one-step) neutral mutants is a remarkably accurate proxy for the overall frequency of such mutants in an experimentally verifiable formula for the phenotypic error threshold; this we achieve by the full numerical solution for the concentration of all sequences in mutation-selection balance up to length 16. We reinforce our previous result that currently known ribozymes could be selectively maintained by the accuracy known from the best available polymerase ribozymes. Furthermore, we show that in silico stabilizing selection can increase the mutational robustness of ribozymes due to the fact that they were produced by artificial directional selection in the first place. Our finding offers a better understanding of the error threshold and provides further insight into the plausibility of an ancient RNA world.

  7. Prebiotic Factors Influencing the Activity of a Ligase Ribozyme

    Directory of Open Access Journals (Sweden)

    Fabrizio Anella

    2017-04-01

    Full Text Available An RNA-lipid origin of life scenario provides a plausible route for compartmentalized replication of an informational polymer and subsequent division of the container. However, a full narrative to form such RNA protocells implies that catalytic RNA molecules, called ribozymes, can operate in the presence of self-assembled vesicles composed of prebiotically relevant constituents, such as fatty acids. Hereby, we subjected a newly engineered truncated variant of the L1 ligase ribozyme, named tL1, to various environmental conditions that may have prevailed on the early Earth with the objective to find a set of control parameters enabling both tL1-catalyzed ligation and formation of stable myristoleic acid (MA vesicles. The separate and concurrent effects of temperature, concentrations of Mg2+, MA, polyethylene glycol and various solutes were investigated. The most favorable condition tested consists of 100 mM NaCl, 1 mM Mg2+, 5 mM MA, and 4 °C temperature, whereas the addition of Mg2+-chelating solutes, such as citrate, tRNAs, aspartic acid, and nucleoside triphosphates severely inhibits the reaction. These results further solidify the RNA-lipid world hypothesis and stress the importance of using a systems chemistry approach whereby a wide range of prebiotic factors interfacing with ribozymes are considered.

  8. Catalysis seen in action

    NARCIS (Netherlands)

    Tromp, M.

    2015-01-01

    Synchrotron radiation techniques are widely applied in materials research and heterogeneous catalysis. In homogeneous catalysis, its use so far is rather limited despite its high potential. Here, insights in the strengths and limitations of X-ray spectroscopy technique in the field of homogeneous

  9. Monopole catalysis: an overview

    International Nuclear Information System (INIS)

    Dawson, S.

    1983-11-01

    A summary of the talks presented in the topological workshop on monopole catalysis at this conference is given. We place special emphasis on the conservation laws which determine the allowed monopole-fermion interactions and on catalysis as a probe of the structure of a grand unified theory. 11 references

  10. Catalysis of Supramolecular Hydrogelation

    NARCIS (Netherlands)

    Trausel, F.; Versluis, F.; Maity, C.; Poolman, J.M.; Lovrak, M.; van Esch, J.H.; Eelkema, R.

    2016-01-01

    ConspectusOne often thinks of catalysts as chemical tools to accelerate a reaction or to have a reaction run under more benign conditions. As such, catalysis has a role to play in the chemical industry and in lab scale synthesis that is not to be underestimated. Still, the role of catalysis in

  11. Engineering integrated digital circuits with allosteric ribozymes for scaling up molecular computation and diagnostics.

    Science.gov (United States)

    Penchovsky, Robert

    2012-10-19

    Here we describe molecular implementations of integrated digital circuits, including a three-input AND logic gate, a two-input multiplexer, and 1-to-2 decoder using allosteric ribozymes. Furthermore, we demonstrate a multiplexer-decoder circuit. The ribozymes are designed to seek-and-destroy specific RNAs with a certain length by a fully computerized procedure. The algorithm can accurately predict one base substitution that alters the ribozyme's logic function. The ability to sense the length of RNA molecules enables single ribozymes to be used as platforms for multiple interactions. These ribozymes can work as integrated circuits with the functionality of up to five logic gates. The ribozyme design is universal since the allosteric and substrate domains can be altered to sense different RNAs. In addition, the ribozymes can specifically cleave RNA molecules with triplet-repeat expansions observed in genetic disorders such as oculopharyngeal muscular dystrophy. Therefore, the designer ribozymes can be employed for scaling up computing and diagnostic networks in the fields of molecular computing and diagnostics and RNA synthetic biology.

  12. Generation and Development of RNA Ligase Ribozymes with Modular Architecture Through “Design and Selection”

    Directory of Open Access Journals (Sweden)

    Yuki Fujita

    2010-08-01

    Full Text Available In vitro selection with long random RNA libraries has been used as a powerful method to generate novel functional RNAs, although it often requires laborious structural analysis of isolated RNA molecules. Rational RNA design is an attractive alternative to avoid this laborious step, but rational design of catalytic modules is still a challenging task. A hybrid strategy of in vitro selection and rational design has been proposed. With this strategy termed “design and selection,” new ribozymes can be generated through installation of catalytic modules onto RNA scaffolds with defined 3D structures. This approach, the concept of which was inspired by the modular architecture of naturally occurring ribozymes, allows prediction of the overall architectures of the resulting ribozymes, and the structural modularity of the resulting ribozymes allows modification of their structures and functions. In this review, we summarize the design, generation, properties, and engineering of four classes of ligase ribozyme generated by design and selection.

  13. Horizons in catalysis

    Energy Technology Data Exchange (ETDEWEB)

    Idol, J D

    1979-04-21

    A discussion covers a brief historical review of industrial catalysis; a survey of major present-day catalytic processes in the petroleum and petrochemical industries; the outlook for the industrial catalyst applications in coal liquefaction, conversion of coal liquids, shale oil, and other synthetic crude sources for transportation fuels, and synthesis gas-based processes; some important directions for future developments, including phase transfer catalysis, photocatalysis, and advanced techniques for catalyst studies; and the need for closer industry-university and industry-government cooperation in the field of catalysis.

  14. Surface and nanomolecular catalysis

    CERN Document Server

    Richards, Ryan

    2006-01-01

    Using new instrumentation and experimental techniques that allow scientists to observe chemical reactions and molecular properties at the nanoscale, the authors of Surface and Nanomolecular Catalysis reveal new insights into the surface chemistry of catalysts and the reaction mechanisms that actually occur at a molecular level during catalysis. While each chapter contains the necessary background and explanations to stand alone, the diverse collection of chapters shows how developments from various fields each contributed to our current understanding of nanomolecular catalysis as a whole. The

  15. Molecular water oxidation catalysis

    CERN Document Server

    Llobet, Antoni

    2014-01-01

    Photocatalytic water splitting is a promising strategy for capturing energy from the sun by coupling light harvesting and the oxidation of water, in order to create clean hydrogen fuel. Thus a deep knowledge of the water oxidation catalysis field is essential to be able to come up with useful energy conversion devices based on sunlight and water splitting. Molecular Water Oxidation Catalysis: A Key Topic for New Sustainable Energy Conversion Schemes presents a comprehensive and state-of-the-art overview of water oxidation catalysis in homogeneous phase, describing in detail the most importan

  16. On hairpin vortices in a transitional boundary layer

    Directory of Open Access Journals (Sweden)

    Uruba Václav

    2012-04-01

    Full Text Available In the presented paper the results of experiments on transitional boundary layer are presented. The boundary layer was generated on smooth flat wall with zero pressure gradient forming one side of the channel of rectangular cross section. The hairpin vortices, packets of hairpin vortices, turbulent spots and calmed regions were experimentally investigated using time-resolved PIV technique.

  17. Catalysis seen in action.

    Science.gov (United States)

    Tromp, Moniek

    2015-03-06

    Synchrotron radiation techniques are widely applied in materials research and heterogeneous catalysis. In homogeneous catalysis, its use so far is rather limited despite its high potential. Here, insights in the strengths and limitations of X-ray spectroscopy technique in the field of homogeneous catalysis are given, including new technique developments. A relevant homogeneous catalyst, used in the industrially important selective oligomerization of ethene, is taken as a worked-out example. Emphasis is placed on time-resolved operando X-ray absorption spectroscopy with outlooks to novel high energy resolution and emission techniques. All experiments described have been or can be done at the Diamond Light Source Ltd (Didcot, UK). © 2015 The Author(s) Published by the Royal Society. All rights reserved.

  18. Concepts in catalysis

    International Nuclear Information System (INIS)

    Boudart, M.

    1992-01-01

    This paper reports on concept in catalysis which are very important in heterogeneous catalysis, even today, when in spite of surface science, the complexity of events at a real catalytic surface is still evading the understanding necessary for design. In this paper the authors will attempt to give an update on evolving concepts in heterogeneous catalysis. The topics include: counting active centers on metal surfaces; the notion of turnover frequency for a catalytic cycle; the concept of structure (in) sensitive reactions; the ensemble (geometric) vs. The ligand (electronic) effect following Sachtler's school; the idea of a rate determining step and of a most abundant reactive intermediate; the effect of surface non-uniformity on catalytic kinetics; what makes catalytic cycles turnover

  19. Catalysis induced by radiations

    International Nuclear Information System (INIS)

    Jimenez B, J.; Gonzalez J, J. C.

    2010-01-01

    In Mexico is generated a great quantity of residuals considered as dangerous, for its capacity of corrosion, reactivity, toxicity to the environment, inflammability and biological-infectious potential. It is important to mention that the toxic compounds cannot be discharged to the sewerage systems and much less to the receiving bodies of water. The usual treatment that receives the dangerous residuals is the incineration and the bordering. The incineration is an efficient form of treating the residuals, but it can be dioxins source and benzofurans, being the phenol and chloro phenol the precursors of these compounds. At the present time the radiolytic degradation of organic compounds has been broadly studied, especially the 4-chloro phenol and of same form the photo catalysis of organic compounds. However the combination of both processes, called radio catalysis is barely reported. In this work the results of the experiments realized for to degrade the 4-chloro phenol by means of radio catalysis are reported. (Author)

  20. Catalysis for alternative energy generation

    CERN Document Server

    2012-01-01

    Summarizes recent problems in using catalysts in alternative energy generation and proposes novel solutions  Reconsiders the role of catalysis in alternative energy generation  Contributors include catalysis and alternative energy experts from across the globe

  1. Editorial: Nanoscience makes catalysis greener

    KAUST Repository

    Polshettiwar, Vivek; Basset, Jean-Marie; Astruc, Didier

    2012-01-01

    Green chemistry by nanocatalysis: Catalysis is a strategic field of science because it involves new ways of meeting energy and sustainability challenges. The concept of green chemistry, which makes the science of catalysis even more creative, has

  2. Folding of the natural hammerhead ribozyme is enhanced by interaction of auxiliary elements

    Science.gov (United States)

    PENEDO, J. CARLOS; WILSON, TIMOTHY J.; JAYASENA, SUMEDHA D.; KHVOROVA, ANASTASIA; LILLEY, DAVID M.J.

    2004-01-01

    It has been shown that the activity of the hammerhead ribozyme at μM magnesium ion concentrations is markedly increased by the inclusion of loops in helices I and II. We have studied the effect of such loops on the magnesium ion-induced folding of the ribozyme, using fluorescence resonance energy transfer. We find that with the loops in place, folding into the active conformation occurs in a single step, in the μM range of magnesium ion concentration. Disruption of the loop–loop interaction leads to a reversion to two-step folding, with the second stage requiring mM concentrations of magnesium ion. Sodium ions also promote the folding of the natural form of the ribozyme at high concentrations, but the folding occurs as a two-stage process. The loops clearly act as important auxiliary elements in the function of the ribozyme, permitting folding to occur efficiently under physiological conditions. PMID:15100442

  3. Isotopes in heterogeneous catalysis

    CERN Document Server

    Hargreaves, Justin SJ

    2006-01-01

    The purpose of this book is to review the current, state-of-the-art application of isotopic methods to the field of heterogeneous catalysis. Isotopic studies are arguably the ultimate technique in in situ methods for heterogeneous catalysis. In this review volume, chapters have been contributed by experts in the field and the coverage includes both the application of specific isotopes - Deuterium, Tritium, Carbon-14, Sulfur-35 and Oxygen-18 - as well as isotopic techniques - determination of surface mobility, steady state transient isotope kinetic analysis, and positron emission profiling.

  4. Metamorphosis of a Hairpin Vortex into a Young Turbulent Spot

    Science.gov (United States)

    Singer, Bart A.; Joslin, Ronald D.

    1995-01-01

    Direct numerical simulation was used to study the formation and growth of a hairpin vortex in a flat-plate boundary layer and its later development into a young turbulent spot. Fluid injection through a slit in the wall triggered the initial vortex. The legs of the vortex were stretched into a hairpin shape as it traveled downstream. Multiple hairpin vortex heads developed between the stretched legs. New vortices formed beneath the streamwise-elongated vortex legs. The continued development of additional vortices resulted in the formation of a traveling region of highly disturbed ow with an arrowhead shape similar to that of a turbulent spot.

  5. Pollution Control by Catalysis

    DEFF Research Database (Denmark)

    Eriksen, Kim Michael; Fehrmann, Rasmus

    1998-01-01

    The report summarises the results of two years of collaboration supported by INTAS between Department of Chemistry,DTU,DK , IUSTI,Universite de Provence,FR, ICE/HT University 6of Patras,GR, and Boreskov Institute of Catalysis,RU.The project has been concerned with mechanistic studies of deNOx and...

  6. Preface: Catalysis Today

    DEFF Research Database (Denmark)

    Li, Yongdan

    2016-01-01

    This special issue of Catalysis Today with the theme “Sustain-able Energy” results from a great success of the session “Catalytic Technologies Accelerating the Establishment of Sustainable and Clean Energy”, one of the two sessions of the 1st International Symposium on Catalytic Science and Techn...

  7. Advances in catalysis

    International Nuclear Information System (INIS)

    Eley, D.D.; Pine, H.; Weisz, P.B.

    1989-01-01

    This book reports on the current state of knowledge concerning structure and catalysis of metals and metal oxide particles, old and new. It addresses the basic and broad problems of what the catalytically relevant surface structures of metals are, where we stand in techniques capable of attacking this problem, and what the current state of knowledge is. The focus is on long-standing, important, and central problem of general investigative methodology and strategy: the pressure gap is created by the fact that the best techniques of surface analysis require high-vacuum conditions, while useful catalysis is confined to conditions of near ambient or higher pressures. The authors review the basic question of the influence of particle size on catalytic behavior of metal particles which involves questions of the basic sciences as much as practical considerations of catalyst design and use. They discuss preparatory techniques, analytical technology, and methods of characterization of these materials

  8. Solid Base Catalysis

    CERN Document Server

    Ono, Yoshio

    2011-01-01

    The importance of solid base catalysts has come to be recognized for their environmentally benign qualities, and much significant progress has been made over the past two decades in catalytic materials and solid base-catalyzed reactions. The book is focused on the solid base. Because of the advantages over liquid bases, the use of solid base catalysts in organic synthesis is expanding. Solid bases are easier to dispose than liquid bases, separation and recovery of products, catalysts and solvents are less difficult, and they are non-corrosive. Furthermore, base-catalyzed reactions can be performed without using solvents and even in the gas phase, opening up more possibilities for discovering novel reaction systems. Using numerous examples, the present volume describes the remarkable role solid base catalysis can play, given the ever increasing worldwide importance of "green" chemistry. The reader will obtain an overall view of solid base catalysis and gain insight into the versatility of the reactions to whic...

  9. Metallic nanosystems in catalysis

    International Nuclear Information System (INIS)

    Bukhtiyarov, Valerii I; Slin'ko, Mikhail G

    2001-01-01

    The reactivities of metallic nanosystems in catalytic processes are considered. The activities of nanoparticles in catalysis are due to their unique microstructures, electronic properties and high specific surfaces of the active centres. The problems of increasing the selectivities of catalytic processes are discussed using several nanosystems as examples. The mutual effects of components of bimetallic nanoparticles are discussed. The prospects for theoretical and experimental investigations into catalytic nanosystems and the construction of industrial catalysts based on them are evaluated. The bibliography includes 207 references.

  10. Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction

    Science.gov (United States)

    Mir, Aamir; Chen, Ji; Robinson, Kyle; Lendy, Emma; Goodman, Jaclyn; Neau, David; Golden, Barbara L.

    2016-01-01

    The hammerhead ribozyme is a self-cleaving RNA broadly dispersed across all kingdoms of life. Although it was the first of the small, nucleolytic ribozymes discovered, the mechanism by which it catalyzes its reaction remains elusive. The nucleobase of G12 is well positioned to be a general base, but it is unclear if or how this guanine base becomes activated for proton transfer. Metal ions have been implicated in the chemical mechanism, but no interactions between divalent metal ions and the cleavage site have been observed crystallographically. To better understand how this ribozyme functions, we have solved crystal structures of wild-type and G12A mutant ribozymes. We observe a pH-dependent conformational change centered around G12, consistent with this nucleotide becoming deprotonated. Crystallographic and kinetic analysis of the G12A mutant reveals a Zn2+ specificity switch suggesting a direct interaction between a divalent metal ion and the purine at position 12. The metal ion specificity switch and the pH–rate profile of the G12A mutant suggest that the minor imino tautomer of A12 serves as the general base in the mutant ribozyme. We propose a model in which the hammerhead ribozyme rearranges prior to the cleavage reaction, positioning two divalent metal ions in the process. The first metal ion, positioned near G12, becomes directly coordinated to the O6 keto oxygen, to lower the pKa of the general base and organize the active site. The second metal ion, positioned near G10.1, bridges the N7 of G10.1 and the scissile phosphate and may participate directly in the cleavage reaction. PMID:26398724

  11. CATALYSIS OF CHEMICAL PROCESSES: PARTICULAR ...

    African Journals Online (AJOL)

    IICBA01

    secondary/high schools and universities, the inhibition of the chemical reactions is frequently ... As a result, the lesson catalysis is frequently included in chemistry education curricula at ... Misinterpretations in teaching and perception of catalysis ... profile is shown as a dependence of energy on reaction progress, without ...

  12. Spectroscopy in catalysis : an introduction

    NARCIS (Netherlands)

    Niemantsverdriet, J.W.

    2007-01-01

    Spectroscopy in Catalysis is an introduction to the most important analytical techniques that are nowadays used in catalysis and in catalytic surface chemistry. The aim of the book is to give the reader a feeling for the type of information that characterization techniques provide about questions

  13. Hybridization-based biosensor containing hairpin probes and use thereof

    Science.gov (United States)

    Miller, Benjamin L.; Strohsahl, Christopher M.

    2010-10-12

    A sensor chip that includes: a fluorescence quenching surface; a nucleic acid probe that contains first and second ends with the first end bound to the fluorescence quenching surface, and is characterized by being able to self-anneal into a hairpin conformation; and a first fluorophore bound to the second end of the first nucleic acid molecule. When the first nucleic acid molecule is in the hairpin conformation, the fluorescence quenching surface substantially quenches fluorescent emissions by the first fluorophore; and when the first nucleic acid molecule is in a non-hairpin conformation, fluorescent emissions by the fluorophore are substantially free of quenching by the fluorescence quenching surface. Various nucleic acid probes, methods of making the sensor chip, biological sensor devices that contain the sensor chip, and their methods of use are also disclosed.

  14. Characterization of a parallel-stranded DNA hairpin

    International Nuclear Information System (INIS)

    Germann, M.W.; Vogel, H.J.; Pon, R.T.; van de Sande, J.H.

    1989-01-01

    Recently, the authors have shown that synthetic DNA containing homooligomeric A-T base pairs can form a parallel-stranded intramolecular hairpin structure. In the present study, they have employed NMR and optical spectroscopy to investigate the structure of the parallel-stranded (PS) DNA hairpin 3'-d(T) 8 C 4 (A) 8 -3' and the related antiparallel (APS) hair 5'-d(T) 8 C 4 (A) 8 -3'. The parallel orientation of the strands in the PS oligonucleotide is achieved by introducing a 5'-5' phosphodiester linkage in the hairpin loop. Ultraviolet spectroscopic and fluorescence data of drug binding are consistent with the formation of PS and APS structures, respectively, in these two hairpins. Vacuum circular dichroism measurements in combination with theoretical CD calculations indicate that the PS structure forms a right-handed helix. 31 P NMR measurements indicate that the conformation of the phosphodiester backbone of the PS structure is not drastically different from that of the APS control. The presence of slowly exchanging imino protons at 14 ppm and the observation of nuclear Overhauser enhancement between imino protons and the AH-2 protons demonstrate that similar base pairing and base stacking between T and A residues occur in both hairpins. On the basis of NOESY measurements, they find that the orientation of the bases is in the anti region and that the sugar puckering is in the 2'-endo range. The results indicate a B-like conformation for each of the strands in the stem part of the PS hairpin and reverse Watson-Crick base pairing between the T and A residues. These data are consistent with a previously calculated structure for parallel-stranded DNA

  15. The genomic HDV ribozyme utilizes a previously unnoticed U-turn motif to accomplish fast site-specific catalysis

    Czech Academy of Sciences Publication Activity Database

    Šefčíková, J.; Krasovská, Maryna V.; Šponer, Jiří; Walter, N.G.

    2007-01-01

    Roč. 35, č. 6 (2007), s. 1933-1946 ISSN 0305-1048 R&D Projects: GA ČR(CZ) GA203/05/0388; GA ČR(CZ) GA203/05/0009; GA AV ČR(CZ) 1QS500040581; GA AV ČR(CZ) IAA400550701; GA MŠk(CZ) LC512 Institutional research plan: CEZ:AV0Z50040702; CEZ:AV0Z40550506 Keywords : hepatitis delta virus * molecular dynamics * self-cleavage Subject RIV: BO - Biophysics Impact factor: 6.954, year: 2007

  16. Practical Engineering Aspects of Catalysis in Microreactors

    Czech Academy of Sciences Publication Activity Database

    Křišťál, Jiří; Stavárek, Petr; Vajglová, Zuzana; Vondráčková, Magdalena; Pavlorková, Jana; Jiřičný, Vladimír

    2015-01-01

    Roč. 41, č. 12 (2015), s. 9357-9371 ISSN 0922-6168. [Pannonian Symposium on Catalysis /12./. Castle Trest, 16.09.2014-20.09.2014] Institutional support: RVO:67985858 Keywords : heterogeneous catalysis * homogeneous catalysis * photo catalysis Subject RIV: CI - Industrial Chemistry, Chemical Engineering Impact factor: 1.833, year: 2015

  17. Whirlwinds and hairpins in the atmospheric surface layer

    NARCIS (Netherlands)

    Oncley, Steven P.; Hartogensis, O.K.; Tong, Chenning

    2016-01-01

    Vortices in the atmospheric surface layer are characterized using observations at unprecedented resolution from a fixed array of 31 turbulence sensors. During the day, these vortices likely are dust devils, though no visual observations are available for confirmation. At night, hairpin vortices

  18. Modeling the mechanism of CLN025 beta-hairpin formation

    Science.gov (United States)

    McKiernan, Keri A.; Husic, Brooke E.; Pande, Vijay S.

    2017-09-01

    Beta-hairpins are substructures found in proteins that can lend insight into more complex systems. Furthermore, the folding of beta-hairpins is a valuable test case for benchmarking experimental and theoretical methods. Here, we simulate the folding of CLN025, a miniprotein with a beta-hairpin structure, at its experimental melting temperature using a range of state-of-the-art protein force fields. We construct Markov state models in order to examine the thermodynamics, kinetics, mechanism, and rate-determining step of folding. Mechanistically, we find the folding process is rate-limited by the formation of the turn region hydrogen bonds, which occurs following the downhill hydrophobic collapse of the extended denatured protein. These results are presented in the context of established and contradictory theories of the beta-hairpin folding process. Furthermore, our analysis suggests that the AMBER-FB15 force field, at this temperature, best describes the characteristics of the full experimental CLN025 conformational ensemble, while the AMBER ff99SB-ILDN and CHARMM22* force fields display a tendency to overstabilize the native state.

  19. The Drosophila Helicase MLE Targets Hairpin Structures in Genomic Transcripts.

    Directory of Open Access Journals (Sweden)

    Simona Cugusi

    2016-01-01

    Full Text Available RNA hairpins are a common type of secondary structures that play a role in every aspect of RNA biochemistry including RNA editing, mRNA stability, localization and translation of transcripts, and in the activation of the RNA interference (RNAi and microRNA (miRNA pathways. Participation in these functions often requires restructuring the RNA molecules by the association of single-strand (ss RNA-binding proteins or by the action of helicases. The Drosophila MLE helicase has long been identified as a member of the MSL complex responsible for dosage compensation. The complex includes one of two long non-coding RNAs and MLE was shown to remodel the roX RNA hairpin structures in order to initiate assembly of the complex. Here we report that this function of MLE may apply to the hairpins present in the primary RNA transcripts that generate the small molecules responsible for RNA interference. Using stocks from the Transgenic RNAi Project and the Vienna Drosophila Research Center, we show that MLE specifically targets hairpin RNAs at their site of transcription. The association of MLE at these sites is independent of sequence and chromosome location. We use two functional assays to test the biological relevance of this association and determine that MLE participates in the RNAi pathway.

  20. Dicer-independent processing of short hairpin RNAs

    NARCIS (Netherlands)

    Liu, Ying Poi; Schopman, Nick C. T.; Berkhout, Ben

    2013-01-01

    Short hairpin RNAs (shRNAs) are widely used to induce RNA interference (RNAi). We tested a variety of shRNAs that differed in stem length and terminal loop size and revealed strikingly different RNAi activities and shRNA-processing patterns. Interestingly, we identified a specific shRNA design that

  1. The glmS ribozyme cofactor is a general acid-base catalyst.

    Science.gov (United States)

    Viladoms, Júlia; Fedor, Martha J

    2012-11-21

    The glmS ribozyme is the first natural self-cleaving ribozyme known to require a cofactor. The d-glucosamine-6-phosphate (GlcN6P) cofactor has been proposed to serve as a general acid, but its role in the catalytic mechanism has not been established conclusively. We surveyed GlcN6P-like molecules for their ability to support self-cleavage of the glmS ribozyme and found a strong correlation between the pH dependence of the cleavage reaction and the intrinsic acidity of the cofactors. For cofactors with low binding affinities, the contribution to rate enhancement was proportional to their intrinsic acidity. This linear free-energy relationship between cofactor efficiency and acid dissociation constants is consistent with a mechanism in which the cofactors participate directly in the reaction as general acid-base catalysts. A high value for the Brønsted coefficient (β ~ 0.7) indicates that a significant amount of proton transfer has already occurred in the transition state. The glmS ribozyme is the first self-cleaving RNA to use an exogenous acid-base catalyst.

  2. Ribozyme Activity of RNA Nonenzymatically Polymerized from 3 ',5 '-Cyclic GMP

    Czech Academy of Sciences Publication Activity Database

    Pino, S.; Costanzo, G.; Giorgi, A.; Šponer, Jiří; Šponer, Judit E.; Di Mauro, E.

    2013-01-01

    Roč. 15, č. 12 (2013), s. 5362-5383 ISSN 1099-4300 R&D Projects: GA ČR(CZ) GAP208/10/2302; GA MŠk(CZ) ED1.1.00/02.0068 Institutional support: RVO:68081707 Keywords : RNA polymerization * RNA origin * ribozymes Subject RIV: BO - Biophysics Impact factor: 1.564, year: 2013

  3. Magnetic catalysis and inverse magnetic catalysis in QCD

    International Nuclear Information System (INIS)

    Mueller, N.

    2015-01-01

    We investigate the effects of strong magnetic fields on the QCD phase structure at vanishing density by solving the gluon and quark gap equations. The chiral crossover temperature as well as the chiral condensate is computed. For asymptotically large magnetic fields we find magnetic catalysis, while we find inverse magnetic catalysis for intermediate magnetic fields. Moreover, for large magnetic fields the chiral phase transition for massless quarks turns into a crossover. The underlying mechanisms are then investigated analytically within a few simplifications of the full numerical analysis. We find that a combination of gluon screening effects and the weakening of the strong coupling is responsible for the phenomenon of inverse catalysis seen in lattice studies. In turn, the magnetic catalysis at large magnetic field is already indicated by simple arguments based on dimensionality. (author)

  4. Spectroscopy in catalysis : an introduction

    NARCIS (Netherlands)

    Niemantsverdriet, J.W.

    2000-01-01

    Spectroscopy in Catalysis describes the most important modern analytical techniques used to investigate catalytic surfaces. These include electron spectroscopy (XPS, UPS, AES, EELS), ion spectroscopy (SIMS, SNMS, RBS, LEIS), vibrational spectroscopy (infrared, Raman, EELS), temperature-programmed

  5. Hairpin-Hairpin Molecular Beacon Interactions for Detection of Survivin mRNA in Malignant SW480 Cells.

    Science.gov (United States)

    Ratajczak, Katarzyna; Krazinski, Bartlomiej E; Kowalczyk, Anna E; Dworakowska, Beata; Jakiela, Slawomir; Stobiecka, Magdalena

    2018-05-07

    Cancer biomarkers offer unique prospects for the development of cancer diagnostics and therapy. One of such biomarkers, protein survivin (Sur), exhibits strong antiapoptotic and proliferation-enhancing properties and is heavily expressed in multiple cancers. Thus, it can be utilized to provide new modalities for modulating the cell-growth rate, essential for effective cancer treatment. Herein, we have focused on the development of a new survivin-based cancer detection platform for colorectal cancer cells SW480 using a turn-on fluorescence oligonucleotide molecular beacon (MB) probe, encoded to recognize Sur messenger RNA (mRNA). Contrary to the expectations, we have found that both the complementary target oligonucleotide strands as well as the single- and double-mismatch targets, instead of exhibiting the anticipated simple random conformations, preferentially formed secondary structure motifs by folding into small-loop hairpin structures. Such a conformation may interfere with, or even undermine, the biorecognition process. To gain better understanding of the interactions involved, we have replaced the classical Tyagi-Kramer model of interactions between a straight target oligonucleotide strand and a hairpin MB with a new model to account for the hairpin-hairpin interactions as the biorecognition principle. A detailed mechanism of these interactions has been proposed. Furthermore, in experimental work, we have demonstrated an efficient transfection of malignant SW480 cells with SurMB probes containing a fluorophore Joe (SurMB-Joe) using liposomal nanocarriers. The green emission from SurMB-Joe in transfected cancer cells, due to the hybridization of the SurMB-Joe loop with Sur mRNA hairpin target, corroborates Sur overexpression. On the other hand, healthy human-colon epithelial cells CCD 841 CoN show only negligible expression of survivin mRNA. These experiments provide the proof-of-concept for distinguishing between the cancer and normal cells by the proposed

  6. Editorial: Nanoscience makes catalysis greener

    KAUST Repository

    Polshettiwar, Vivek

    2012-01-09

    Green chemistry by nanocatalysis: Catalysis is a strategic field of science because it involves new ways of meeting energy and sustainability challenges. The concept of green chemistry, which makes the science of catalysis even more creative, has become an integral part of sustainability. This special issue is at the interface of green chemistry and nanocatalysis, and features excellent background articles as well as the latest research results. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Molecular ingredients of heterogeneous catalysis

    International Nuclear Information System (INIS)

    Somorjai, G.A.

    1982-06-01

    The purpose of this paper is to present a review and status report to those in theoretical chemistry of the rapidly developing surface science of heterogeneous catalysis. The art of catalysis is developing into science. This profound change provides one with opportunities not only to understand the molecular ingredients of important catalytic systems but also to develop new and improved catalyst. The participation of theorists to find answers to important questions is sorely needed for the sound development of the field. It is the authors hope that some of the outstanding problems of heterogeneous catalysis that are identified in this paper will be investigated. For this purpose the paper is divided into several sections. The brief Introduction to the methodology and recent results of the surface science of heterogeneous catalysis is followed by a review of the concepts of heterogeneous catalysis. Then, the experimental results that identified the three molecular ingredients of catalysis, structure, carbonaceous deposit and the oxidation state of surface atoms are described. Each section is closed with a summary and a list of problems that require theoretical and experimental scrutiny. Finally attempts to build new catalyst systems and the theoretical and experimental problems that appeared in the course of this research are described

  8. Molecular ingredients of heterogeneous catalysis

    Energy Technology Data Exchange (ETDEWEB)

    Somorjai, G.A.

    1982-06-01

    The purpose of this paper is to present a review and status report to those in theoretical chemistry of the rapidly developing surface science of heterogeneous catalysis. The art of catalysis is developing into science. This profound change provides one with opportunities not only to understand the molecular ingredients of important catalytic systems but also to develop new and improved catalyst. The participation of theorists to find answers to important questions is sorely needed for the sound development of the field. It is the authors hope that some of the outstanding problems of heterogeneous catalysis that are identified in this paper will be investigated. For this purpose the paper is divided into several sections. The brief Introduction to the methodology and recent results of the surface science of heterogeneous catalysis is followed by a review of the concepts of heterogeneous catalysis. Then, the experimental results that identified the three molecular ingredients of catalysis, structure, carbonaceous deposit and the oxidation state of surface atoms are described. Each section is closed with a summary and a list of problems that require theoretical and experimental scrutiny. Finally attempts to build new catalyst systems and the theoretical and experimental problems that appeared in the course of this research are described.

  9. A novel strategy for selection of allosteric ribozymes yields RiboReporter™ sensors for caffeine and aspartame

    Science.gov (United States)

    Ferguson, Alicia; Boomer, Ryan M.; Kurz, Markus; Keene, Sara C.; Diener, John L.; Keefe, Anthony D.; Wilson, Charles; Cload, Sharon T.

    2004-01-01

    We have utilized in vitro selection technology to develop allosteric ribozyme sensors that are specific for the small molecule analytes caffeine or aspartame. Caffeine- or aspartame-responsive ribozymes were converted into fluorescence-based RiboReporter™ sensor systems that were able to detect caffeine or aspartame in solution over a concentration range from 0.5 to 5 mM. With read-times as short as 5 min, these caffeine- or aspartame-dependent ribozymes function as highly specific and facile molecular sensors. Interestingly, successful isolation of allosteric ribozymes for the analytes described here was enabled by a novel selection strategy that incorporated elements of both modular design and activity-based selection methods typically used for generation of catalytic nucleic acids. PMID:15026535

  10. Enhanced Micellar Catalysis LDRD.

    Energy Technology Data Exchange (ETDEWEB)

    Betty, Rita G.; Tucker, Mark D; Taggart, Gretchen; Kinnan, Mark K.; Glen, Crystal Chanea; Rivera, Danielle; Sanchez, Andres; Alam, Todd Michael

    2012-12-01

    The primary goals of the Enhanced Micellar Catalysis project were to gain an understanding of the micellar environment of DF-200, or similar liquid CBW surfactant-based decontaminants, as well as characterize the aerosolized DF-200 droplet distribution and droplet chemistry under baseline ITW rotary atomization conditions. Micellar characterization of limited surfactant solutions was performed externally through the collection and measurement of Small Angle X-Ray Scattering (SAXS) images and Cryo-Transmission Electron Microscopy (cryo-TEM) images. Micellar characterization was performed externally at the University of Minnesotas Characterization Facility Center, and at the Argonne National Laboratory Advanced Photon Source facility. A micellar diffusion study was conducted internally at Sandia to measure diffusion constants of surfactants over a concentration range, to estimate the effective micelle diameter, to determine the impact of individual components to the micellar environment in solution, and the impact of combined components to surfactant phase behavior. Aerosolized DF-200 sprays were characterized for particle size and distribution and limited chemical composition. Evaporation rates of aerosolized DF-200 sprays were estimated under a set of baseline ITW nozzle test system parameters.

  11. Targeted cleavage of hepatitis E virus 3' end RNA mediated by hammerhead ribozymes inhibits viral RNA replication

    International Nuclear Information System (INIS)

    Sriram, Bandi; Thakral, Deepshi; Panda, Subrat Kumar

    2003-01-01

    The 3' end of hepatitis E virus (HEV) contains cis-acting regulatory element, which plays an important role in viral replication. To develop specific replication inhibitor at the molecular level, mono- and di-hammerhead ribozymes (Rz) were designed and synthesized against the conserved 3' end sequences of HEV, which cleave at nucleotide positions 7125 and 7112/7125, respectively. Di-hammerhead ribozyme with two catalytic motifs in tandem was designed to cleave simultaneously at two sites spaced 13 nucleotides apart, which increases the overall cleavage efficiency and prevents the development of escape mutants. Specific cleavage products were obtained with both the ribozymes in vitro at physiological conditions. The inactive control ribozymes showed no cleavage. The ribozymes showed specific inhibition of HEV 3' end fused-luciferase reporter gene expression by ∼37 and ∼60%, respectively in HepG2 cells. These results demonstrate a feasible approach to inhibit the HEV replication to a limited extent by targeting the cis-acting 3' end of HEV with hammerhead ribozymes

  12. A Therapeutic Potential of Animal β-hairpin Antimicrobial Peptides.

    Science.gov (United States)

    Panteleev, Pavel V; Balandin, Sergey V; Ivanov, Vadim T; Ovchinnikova, Tatiana V

    2017-01-01

    Endogenous antimicrobial peptides (AMPs) are evolutionary ancient molecular factors of innate immunity that play the key role in host defense. Because of the low resistance rate, AMPs have caught extensive attention as possible alternatives to conventional antibiotics. Over the last years, it has become evident that biological functions of AMPs are beyond direct killing of microbial cells. This review focuses on a relatively small family of animal host defense peptides with the β-hairpin structure stabilized by disulfide bridges. Their small size, rigid structure, stability to proteases, and plethora of biological functions, including antibacterial, antifungal, antiviral, anticancer, endotoxin-binding, metabolism- and immune- modulating activities, make natural β-hairpin AMPs an attractive molecular basis for drug design. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  13. Operando research in heterogeneous catalysis

    CERN Document Server

    Groot, Irene

    2017-01-01

    This book is devoted to the emerging field of techniques for visualizing atomic-scale properties of active catalysts under actual working conditions, i.e. high gas pressures and high temperatures. It explains how to understand these observations in terms of the surface structures and dynamics and their detailed interplay with the gas phase. This provides an important new link between fundamental surface physics and chemistry, and applied catalysis. The book explains the motivation and the necessity of operando studies, and positions these with respect to the more traditional low-pressure investigations on the one hand and the reality of industrial catalysis on the other. The last decade has witnessed a rapid development of new experimental and theoretical tools for operando studies of heterogeneous catalysis. The book has a strong emphasis on the new techniques and illustrates how the challenges introduced by the harsh, operando conditions are faced for each of these new tools. Therefore, one can also read th...

  14. Green chemistry by nano-catalysis

    KAUST Repository

    Polshettiwar, Vivek; Varma, Rajender S.

    2010-01-01

    the homogeneous catalysts. This review focuses on the use of nano-catalysis for green chemistry development including the strategy of using microwave heating with nano-catalysis in benign aqueous reaction media which offers an extraordinary synergistic effect

  15. Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape

    Czech Academy of Sciences Publication Activity Database

    Sripathi, K.N.; Tay, W.W.; Banáš, P.; Otyepka, M.; Šponer, Jiří; Walter, N. G.

    2014-01-01

    Roč. 20, č. 7 (2014), s. 1112-1128 ISSN 1355-8382 R&D Projects: GA MŠk(CZ) ED1.1.00/02.0068; GA ČR(CZ) GAP208/12/1878 Institutional support: RVO:68081707 Keywords : time-resolved FRET * steady-state FRET * small ribozyme Subject RIV: BO - Biophysics Impact factor: 4.936, year: 2014

  16. Positron studies in catalysis research

    International Nuclear Information System (INIS)

    1994-01-01

    During the past eight months, the authors have made progress in several areas relevant to the eventual use of positron techniques in catalysis research. They have come closer to the completion of their positron microscope, and at the same time have performed several studies in their non-microscopic positron spectrometer which should ultimately be applicable to catalysis. The current status of the efforts in each of these areas is summarized in the following sections: Construction of the positron microscope (optical element construction, data collection software, and electronic sub-assemblies); Doppler broadening spectroscopy of metal silicide; Positron lifetime spectroscopy of glassy polymers; and Positron lifetime measurements of pore-sizes in zeolites

  17. Catalysis and sustainable (green) chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Centi, Gabriele; Perathoner, Siglinda [Dipartimento di Chimica Industriale ed Ingegneria dei Materiali, University of Messina, Salita Sperone 31, 98166 Messina (Italy)

    2003-01-15

    Catalysis is a key technology to achieve the objectives of sustainable (green) chemistry. After introducing the concepts of sustainable (green) chemistry and a brief assessment of new sustainable chemical technologies, the relationship between catalysis and sustainable (green) chemistry is discussed and illustrated via an analysis of some selected and relevant examples. Emphasis is also given to the concept of catalytic technologies for scaling-down chemical processes, in order to develop sustainable production processes which reduce the impact on the environment to an acceptable level that allows self-depuration processes of the living environment.

  18. Modulation of individual steps in group I intron catalysis by a peripheral metal ion.

    Science.gov (United States)

    Forconi, Marcello; Piccirilli, Joseph A; Herschlag, Daniel

    2007-10-01

    Enzymes are complex macromolecules that catalyze chemical reactions at their active sites. Important information about catalytic interactions is commonly gathered by perturbation or mutation of active site residues that directly contact substrates. However, active sites are engaged in intricate networks of interactions within the overall structure of the macromolecule, and there is a growing body of evidence about the importance of peripheral interactions in the precise structural organization of the active site. Here, we use functional studies, in conjunction with published structural information, to determine the effect of perturbation of a peripheral metal ion binding site on catalysis in a well-characterized catalytic RNA, the Tetrahymena thermophila group I ribozyme. We perturbed the metal ion binding site by site-specifically introducing a phosphorothioate substitution in the ribozyme's backbone, replacing the native ligands (the pro-R (P) oxygen atoms at positions 307 and 308) with sulfur atoms. Our data reveal that these perturbations affect several reaction steps, including the chemical step, despite the absence of direct contacts of this metal ion with the atoms involved in the chemical transformation. As structural probing with hydroxyl radicals did not reveal significant change in the three-dimensional structure upon phosphorothioate substitution, the effects are likely transmitted through local, rather subtle conformational rearrangements. Addition of Cd(2+), a thiophilic metal ion, rescues some reaction steps but has deleterious effects on other steps. These results suggest that native interactions in the active site may have been aligned by the naturally occurring peripheral residues and interactions to optimize the overall catalytic cycle.

  19. EMSL and Institute for Integrated Catalysis (IIC) Catalysis Workshop

    Energy Technology Data Exchange (ETDEWEB)

    Campbell, Charles T.; Datye, Abhaya K.; Henkelman, Graeme A.; Lobo, Raul F.; Schneider, William F.; Spicer, Leonard D.; Tysoe, Wilfred T.; Vohs, John M.; Baer, Donald R.; Hoyt, David W.; Thevuthasan, Suntharampillai; Mueller, Karl T.; Wang, Chong M.; Washton, Nancy M.; Lyubinetsky, Igor; Teller, Raymond G.; Andersen, Amity; Govind, Niranjan; Kowalski, Karol; Kabius, Bernd C.; Wang, Hongfei; Campbell, Allison A.; Shelton, William A.; Bylaska, Eric J.; Peden, Charles HF; Wang, Yong; King, David L.; Henderson, Michael A.; Rousseau, Roger J.; Szanyi, Janos; Dohnalek, Zdenek; Mei, Donghai; Garrett, Bruce C.; Ray, Douglas; Futrell, Jean H.; Laskin, Julia; DuBois, Daniel L.; Kuprat, Laura R.; Plata, Charity

    2011-05-24

    Within the context of significantly accelerating scientific progress in research areas that address important societal problems, a workshop was held in November 2010 at EMSL to identify specific and topically important areas of research and capability needs in catalysis-related science.

  20. Cyclopalladated complexes in enantioselective catalysis

    Energy Technology Data Exchange (ETDEWEB)

    Dunina, Valeria V; Gorunova, Olga N; Zykov, P A; Kochetkov, Konstantin A

    2011-01-31

    The results of the use of optically active palladacycles in enantioselective catalysis of [3,3]-sigmatropic rearrangements, aldol condensation, the Michael reaction and cross-coupling are analyzed. Reactions with allylic substrates or reagents and some other transformations are considered.

  1. Catalysis in Molten Ionic Media

    DEFF Research Database (Denmark)

    Boghosian, Soghomon; Fehrmann, Rasmus

    2013-01-01

    This chapter deals with catalysis in molten salts and ionic liquids, which are introduced and reviewed briefly, while an in-depth review of the oxidation catalyst used for the manufacturing of sulfuric acid and cleaning of flue gas from electrical power plants is the main topic of the chapter...

  2. Identify Beta-Hairpin Motifs with Quadratic Discriminant Algorithm Based on the Chemical Shifts.

    Directory of Open Access Journals (Sweden)

    Feng YongE

    Full Text Available Successful prediction of the beta-hairpin motif will be helpful for understanding the of the fold recognition. Some algorithms have been proposed for the prediction of beta-hairpin motifs. However, the parameters used by these methods were primarily based on the amino acid sequences. Here, we proposed a novel model for predicting beta-hairpin structure based on the chemical shift. Firstly, we analyzed the statistical distribution of chemical shifts of six nuclei in not beta-hairpin and beta-hairpin motifs. Secondly, we used these chemical shifts as features combined with three algorithms to predict beta-hairpin structure. Finally, we achieved the best prediction, namely sensitivity of 92%, the specificity of 94% with 0.85 of Mathew's correlation coefficient using quadratic discriminant analysis algorithm, which is clearly superior to the same method for the prediction of beta-hairpin structure from 20 amino acid compositions in the three-fold cross-validation. Our finding showed that the chemical shift is an effective parameter for beta-hairpin prediction, suggesting the quadratic discriminant analysis is a powerful algorithm for the prediction of beta-hairpin.

  3. An anti-VEGF ribozyme embedded within the adenoviral VAI sequence inhibits glioblastoma cell angiogenic potential in vitro.

    Science.gov (United States)

    Ciafrè, Silvia Anna; Niola, Francesco; Wannenes, Francesca; Farace, Maria Giulia

    2004-01-01

    Vascular endothelial growth factor (VEGF) plays an important role in tumor angiogenesis, where it functions as one of the major angiogenic factors sustaining growth and draining catabolites. In this study, we developed an anti-VEGF ribozyme targeted to the 5' part of human VEGF mRNA. We endowed this ribozyme with an additional feature expected to improve its activity in vivo, by cloning it into a VAI transcriptional cassette. VAI is originally part of the adenovirus genome, and is characterized by high transcription rates, good stability due to its strong secondary structure and cytoplasmic localization. Transfection of U87 human glioblastoma cells with plasmid vectors encoding for this ribozyme resulted in a strong (-56%) reduction of VEGF secreted in the extracellular medium, indicating a good biological activity of the ribozyme. Moreover, this reduction in VEGF secretion had the important functional consequence of drastically diminishing the formation of tube-like structures of human umbilical vascular endothelial cells in a Matrigel in vitro angiogenesis assay. In conclusion, our VAI-embedded anti-VEGF ribozyme is a good inhibitor of angiogenesis in vitro, in a glioblastoma cell context. Thus, it may represent a useful tool for future applications in vivo, for antiangiogenic gene therapy of glioblastoma and of highly vascularized tumors. Copyright 2004 S. Karger AG, Basel

  4. DiGIR1 and NaGIR1: naturally occurring group I-like ribozymes with unique core organization and evolved biological role

    DEFF Research Database (Denmark)

    Johansen, Steinar; Einvik, Christer; Nielsen, Henrik

    2002-01-01

    introns (twin-ribozyme introns) in distantly related organisms. The Didymium GIR1 (DiGIR1) and Naegleria GIR1 (NaGIR1) share fundamental features in structural organization and reactivity, and display significant differences when compared to the related group I splicing ribozymes. GIR1 lacks...

  5. Molecular catalysis science: Perspective on unifying the fields of catalysis.

    Science.gov (United States)

    Ye, Rong; Hurlburt, Tyler J; Sabyrov, Kairat; Alayoglu, Selim; Somorjai, Gabor A

    2016-05-10

    Colloidal chemistry is used to control the size, shape, morphology, and composition of metal nanoparticles. Model catalysts as such are applied to catalytic transformations in the three types of catalysts: heterogeneous, homogeneous, and enzymatic. Real-time dynamics of oxidation state, coordination, and bonding of nanoparticle catalysts are put under the microscope using surface techniques such as sum-frequency generation vibrational spectroscopy and ambient pressure X-ray photoelectron spectroscopy under catalytically relevant conditions. It was demonstrated that catalytic behavior and trends are strongly tied to oxidation state, the coordination number and crystallographic orientation of metal sites, and bonding and orientation of surface adsorbates. It was also found that catalytic performance can be tuned by carefully designing and fabricating catalysts from the bottom up. Homogeneous and heterogeneous catalysts, and likely enzymes, behave similarly at the molecular level. Unifying the fields of catalysis is the key to achieving the goal of 100% selectivity in catalysis.

  6. New and future developments in catalysis catalysis by nanoparticles

    CERN Document Server

    Suib, Steven L

    2013-01-01

    New and Future Developments in Catalysis is a package of seven books that compile the latest ideas concerning alternate and renewable energy sources and the role that catalysis plays in converting new renewable feedstock into biofuels and biochemicals. Both homogeneous and heterogeneous catalysts and catalytic processes will be discussed in a unified and comprehensive approach. There will be extensive cross-referencing within all volumes. The use of catalysts in the nanoscale offers various advantages (increased efficiency and less byproducts), and these are discussed in this volume along with the various catalytic processes using nanoparticles. However, this is not without any risks and the safety aspects and effects on humans and the environment are still unknown. The present data as well as future needs are all part of this volume along with the economics involved. Offers in-depth coverage of all catalytic topics of current interest and outlines future challenges and research areas A clear and visual descr...

  7. Incorporation of a cationic aminopropyl chain in DNA hairpins: thermodynamics and hydration

    Science.gov (United States)

    Soto, Ana Maria; Kankia, Besik I.; Dande, Prasad; Gold, Barry; Marky, Luis A.

    2001-01-01

    We report on the physicochemical effects resulting from incorporating a 5-(3-aminopropyl) side chain onto a 2′-deoxyuridine (dU) residue in a short DNA hairpin. A combination of spectroscopy, calorimetry, density and ultrasound techniques were used to investigate both the helix–coil transition of a set of  hairpins with the following sequence: d(GCGACTTTTTGNCGC) [N = dU, deoxythymidine (dT) or 5-(3-aminopropyl)-2′-deoxyuridine (dU*)], and the interaction of each hairpin with Mg2+. All three molecules undergo two-state transitions with melting temperatures (TM) independent of strand concentration that indicates their intramolecular hairpin formation. The unfolding of each hairpin takes place with similar TM values of 64–66°C and similar thermodynamic profiles. The unfavorable unfolding free energies of 6.4–6.9 kcal/mol result from the typical compensation of unfavorable enthalpies, 36–39 kcal/mol, and favorable entropies of ∼110 cal/mol. Furthermore, the stability of each hairpin increases as the salt concentration increases, the TM-dependence on salt yielded slopes of 2.3–2.9°C, which correspond to counterion releases of 0.53 (dU and dT) and 0.44 (dU*) moles of Na+ per mole of hairpin. Absolute volumetric and compressibility measurements reveal that all three hairpins have similar hydration levels. The electrostatic interaction of Mg2+ with each hairpin yielded binding affinities in the order: dU > dT > dU*, and a similar release of 2–4 electrostricted water molecules. The main result is that the incorporation of the cationic 3-aminopropyl side chain in the major groove of the hairpin stem neutralizes some local negative charges yielding a hairpin molecule with lower charge density. PMID:11522834

  8. The Role of XPG in Processing (CAGn/(CTGn DNA Hairpins

    Directory of Open Access Journals (Sweden)

    Hou Caixia

    2011-03-01

    Full Text Available Abstract Background During DNA replication or repair, disease-associated (CAGn/(CTGn expansion can result from formation of hairpin structures in the repeat tract of the newly synthesized or nicked DNA strand. Recent studies identified a nick-directed (CAGn/(CTGn hairpin repair (HPR system that removes (CAGn/(CTGn hairpins from human cells via endonucleolytic incisions. Because the process is highly similar to the mechanism by which XPG and XPF endonucleases remove bulky DNA lesions during nucleotide excision repair, we assessed the potential role of XPG in conducting (CAGn/(CTGn HPR. Results To determine if the XPG endonuclease is involved in (CAGn/(CTGn hairpin removal, two XPG-deficient cell lines (GM16024 and AG08802 were examined for their ability to process (CAGn/(CTGn hairpins in vitro. We demonstrated that the GM16024 cell line processes all hairpin substrates as efficiently as HeLa cells, and that the AG08802 cell line is partially defective in HPR. Analysis of repair intermediates revealed that nuclear extracts from both XPG-deficient lines remove CAG/CTG hairpins via incisions, but the incision products are distinct from those generated in HeLa extracts. We also show that purified recombinant XPG protein greatly stimulates HPR in XPG-deficient extracts by promoting an incision 5' to the hairpin. Conclusions Our results strongly suggest that 1 human cells possess multiple pathways to remove (CAGn/(CTGn hairpins located in newly synthesized (or nicked DNA strand; and 2 XPG, although not essential for (CAGn/(CTGn hairpin removal, stimulates HPR by facilitating a 5' incision to the hairpin. This study reveals a novel role for XPG in genome-maintenance and implicates XPG in diseases caused by trinucleotide repeat expansion.

  9. Chemical catalysis in biodiesel production (I): enzymatic catalysis processes

    International Nuclear Information System (INIS)

    Jachmarian, I.; Dobroyan, M.; Veira, J.; Vieitez, I.; Mottini, M.; Segura, N.; Grompone, M.

    2009-01-01

    There are some well known advantages related with the substitution of chemical catalysis by enzymatic catalysis processes.Some commercial immobilized lipases are useful for the catalysis of bio diesel reaction, which permits the achievement of high conversions and the recovery of high purity products, like a high quality glycerine. The main disadvantage of this alternative method is related with the last inactivation of the enzyme (by both the effect of the alcohol and the absorption of glycerol on catalyst surface), which added to the high cost of the catalyst, produces an unfavourable economical balance of the entire process. In the work the efficiency of two commercial immobilized lipases (Lipozyme TL IM y Novozyme 435 NNovozymes-Dinamarca) in the catalysis of the continuous transesterification of sunflower oil with different alcohols was studied. The intersolubility of the different mixturesinvolving reactans (S oil/alkyl esters/alcohol) and products (P mixtures with a higher content of 1% of glycerol,while for ethanol homogeneous mixtures were obtained at 12% of glycerol (44.44 12).Using and ethanolic substrate at the proportion S=19:75:6 and Lipozyme TL IM, it was possible to achieve a 98% of convertion to the corresponding biodiesel.When Novozymes 435 catalyzed the process it was possible to increase the oil concentration in the substrateaccording to proportion S=35:30:35, and a 78% conversion was obtained. The productivity shown by the firt enzyme was 70mg biodiesel g enzime-1, hora-1 while with the second one the productivity increased to 230. Results suggested that the convenient adjustement of substrate composition with the addition of biodiesel to reactants offers an efficient method for maximizing the enzyme productivity, hence improving the profitability of the enzymatic catalyzed process. (author)

  10. Ribozyme Mediated gRNA Generation for In Vitro and In Vivo CRISPR/Cas9 Mutagenesis.

    Science.gov (United States)

    Lee, Raymond Teck Ho; Ng, Ashley Shu Mei; Ingham, Philip W

    2016-01-01

    CRISPR/Cas9 is now regularly used for targeted mutagenesis in a wide variety of systems. Here we report the use of ribozymes for the generation of gRNAs both in vitro and in zebrafish embryos. We show that incorporation of ribozymes increases the types of promoters and number of target sites available for mutagenesis without compromising mutagenesis efficiency. We have tested this by comparing the efficiency of mutagenesis of gRNA constructs with and without ribozymes and also generated a transgenic zebrafish expressing gRNA using a heat shock promoter (RNA polymerase II-dependent promoter) that was able to induce mutagenesis of its target. Our method provides a streamlined approach to test gRNA efficiency as well as increasing the versatility of conditional gene knock out in zebrafish.

  11. Group I-like ribozymes with a novel core organization perform obligate sequential hydrolytic cleavages at two processing sites

    DEFF Research Database (Denmark)

    Einvik, C; Nielsen, Henrik; Westhof, E

    1998-01-01

    A new category of self-splicing group I introns with conserved structural organization and function is found among the eukaryotic microorganisms Didymium and Naegleria. These complex rDNA introns contain two distinct ribozymes with different functions: a regular group I splicing...... available GIR1 sequences and propose a common RNA secondary structure resembling that of group I splicing-ribozymes, but with some important differences. The GIR1s lack most peripheral sequence components, as well as a P1 segment, and, at approximately 160-190 nt, they are the smallest functional group I...... ribozymes known from nature. All GIR1s were found to contain a novel 6-bp pseudoknot (P15) within their catalytic core region. Experimental support of the proposed structure was obtained from the Didymium GIR1 by RNA structure probing and site-directed mutagenesis. Three-dimensional modeling indicates...

  12. Catalysis in the Primordial World

    Directory of Open Access Journals (Sweden)

    Nenad Raos

    2017-11-01

    Full Text Available Catalysis provides orderly prebiotic synthesis and eventually its evolution into autocatalytic (self-reproduction systems. Research on homogeneous catalysis is concerned mostly with random peptide synthesis and the chances to produce catalytic peptide oligomers. Synthesis of ribose via formose reaction was found to be catalysed by B(OH4−, presumably released by weathering of borate minerals. Oxide and clay mineral surfaces provide catalytic sites for the synthesis of oligopeptides and oligonucleotides. Chemoautotrophic or iron-sulphur-world theory assumes that the first (pioneer organisms developed by catalytic processes on (Fe/NiS particles formed near/close hydrothermal vents. The review provides an overlay of possible catalytic reactions in prebiotic environment, discussing their selectivity (regioselectivity, stereoselectivity as well as geological availability of catalytic minerals and geochemical conditions enabling catalytic reactions on early Earth.

  13. Asymmetric cation-binding catalysis

    DEFF Research Database (Denmark)

    Oliveira, Maria Teresa; Lee, Jiwoong

    2017-01-01

    The employment of metal salts is quite limited in asymmetric catalysis, although it would provide an additional arsenal of safe and inexpensive reagents to create molecular functions with high optical purity. Cation chelation by polyethers increases the salts' solubility in conventional organic...... solvents, thus increasing their applicability in synthesis. The expansion of this concept to chiral polyethers led to the emergence of asymmetric cation-binding catalysis, where chiral counter anions are generated from metal salts, particularly using BINOL-based polyethers. Alkali metal salts, namely KF...... highly enantioselective silylation reactions in polyether-generated chiral environments, and leading to a record-high turnover in asymmetric organocatalysis. This can lead to further applications by the asymmetric use of other inorganic salts in various organic transformations....

  14. Effects of a mutation on the folding mechanism of a β-hairpin

    NARCIS (Netherlands)

    Juraszek, J.; Bolhuis, P.G.

    2009-01-01

    The folding mechanism of a protein is determined by its primary sequence. Yet, how the mechanism is changed by a mutation is still poorly understood, even for basic secondary structures such as β-hairpins. We perform an extensive simulation study of the effects of mutating the GB1 β-hairpin into

  15. Compaction of a Bacterial Group I Ribozyme Coincides with the Assembly of Core Helices

    International Nuclear Information System (INIS)

    Perez-Salas, U.; Rangan, P.; Krueger, S.; Briber, R.; Thirumalai, D.; Woodson, S.

    2004-01-01

    Counterions are critical to the self-assembly of RNA tertiary structure because they neutralize the large electrostatic forces which oppose the folding process. Changes in the size and shape of the Azoarcus group I ribozyme as a function of Mg 2+ and Na + concentration were followed by small angle neutron scattering. In low salt buffer, the RNA was expanded, with an average radius of gyration (R g ) of 53 ± 1 Angstroms. A highly cooperative transition to a compact form (R g = 31.5 ± 0.5 Angstroms) was observed between 1.6 and 1.7 mM MgCl 2 . The collapse transition, which is unusually sharp in Mg 2+ , has the characteristics of a first-order phase transition. Partial digestion with ribonuclease T1 under identical conditions showed that this transition correlated with the assembly of double helices in the ribozyme core. Fivefold higher Mg 2+ concentrations were required for self-splicing, indicating that compaction occurs before native tertiary interactions are fully stabilized. No further decrease in Rg was observed between 1.7 and 20 mM MgCl 2 , indicating that the intermediates have the same dimensions as the native ribozyme, within the uncertainty of the data (± 1 Angstroms). A more gradual transition to a final R g of approximately 33.5 Angstroms was observed between 0.45 and 2 M NaCl. This confirms the expectation that monovalent ions not only are less efficient in charge neutralization but also contract the RNA less efficiently than multivalent ions

  16. Cosmic strings and baryon decay catalysis

    Energy Technology Data Exchange (ETDEWEB)

    Gregory, R.; Perkins, W.B.; Davis, A.C.; Brandenberger, R.H. (Fermi National Accelerator Lab., Batavia, IL (USA); Cambridge Univ. (UK); Brown Univ., Providence, RI (USA). Dept. of Physics)

    1989-09-01

    Cosmic strings, like monopoles, can catalyze proton decay. For integer charged fermions, the cross section for catalysis is not amplified, unlike in the case of monopoles. We review the catalysis processes both in the free quark and skyrmion pictures and discuss the implications for baryogenesis. We present a computation of the cross section for monopole catalyzed skyrmion decay using classical physics. We also discuss some effects which can screen catalysis processes. 32 refs., 1 fig.

  17. Magnetic monopole catalysis of proton decay

    International Nuclear Information System (INIS)

    Marciano, W.J.; Salvino, D.

    1986-09-01

    Catalysis of proton decay by GUT magnetic monopoles (the Rubakov-Callan effect) is discussed. Combining a short-distance cross section calculation by Bernreuther and Craigie with the long-distance velocity dependent distortion factors of Arafune and Fukugita, catalysis rate predictions which can be compared with experiment are obtained. At present, hydrogen rich detectors such as water (H 2 O) and methane (CH 4 ) appear to be particularly well suited for observing catalysis by very slow monopoles. 17 refs., 1 fig

  18. Cosmic strings and baryon decay catalysis

    International Nuclear Information System (INIS)

    Gregory, R.; Perkins, W.B.; Davis, A.C.; Brandenberger, R.H.; Cambridge Univ.; Brown Univ., Providence, RI

    1989-09-01

    Cosmic strings, like monopoles, can catalyze proton decay. For integer charged fermions, the cross section for catalysis is not amplified, unlike in the case of monopoles. We review the catalysis processes both in the free quark and skyrmion pictures and discuss the implications for baryogenesis. We present a computation of the cross section for monopole catalyzed skyrmion decay using classical physics. We also discuss some effects which can screen catalysis processes. 32 refs., 1 fig

  19. Cooperative catalysis designing efficient catalysts for synthesis

    CERN Document Server

    Peters, René

    2015-01-01

    Written by experts in the field, this is a much-needed overview of the rapidly emerging field of cooperative catalysis. The authors focus on the design and development of novel high-performance catalysts for applications in organic synthesis (particularly asymmetric synthesis), covering a broad range of topics, from the latest progress in Lewis acid / Br?nsted base catalysis to e.g. metal-assisted organocatalysis, cooperative metal/enzyme catalysis, and cooperative catalysis in polymerization reactions and on solid surfaces. The chapters are classified according to the type of cooperating acti

  20. Solid acid catalysis from fundamentals to applications

    CERN Document Server

    Hattori, Hideshi

    2014-01-01

    IntroductionTypes of solid acid catalystsAdvantages of solid acid catalysts Historical overviews of solid acid catalystsFuture outlookSolid Acids CatalysisDefinition of acid and base -Brnsted acid and Lewis acid-Acid sites on surfacesAcid strengthRole of acid sites in catalysisBifunctional catalysisPore size effect on catalysis -shape selectivity-Characterization of Solid Acid Catalysts Indicator methodTemperature programmed desorption (TPD) of ammoniaCalorimetry of adsorption of basic moleculesInfrare

  1. Short hairpin-loop-structured oligodeoxynucleotides reduce HSV-1 replication

    Directory of Open Access Journals (Sweden)

    Heinrich Jochen

    2009-04-01

    Full Text Available Abstract The Herpes simplex virus (HSV is known as an infectious agent and widespread in the human population. The symptoms of HSV infections can range from mild to life threatening, especially in immune-compromised individuals. HSV infections are commonly treated with the guanosine analogue Aciclovir, but reports of resistance are increasing. Efforts are made to establish single-stranded antisense oligodeoxynucleotides (as and small interfering ribonucleic acids (siRNAs for antiviral treatment. Recently, another class of short interfering nucleic acids, partially double-stranded hairpin loop-structured 54 mer oligodeoxynucleotides (ODNs, was shown to allow hydrolysis of HIV RNA by binding to the viral RNA. This leads to a substrate for the viral RNase H. To assess the potential of such ODNs for inhibition of HSV-1 replication, five partially double-stranded ODNs were designed based on the sequences of known siRNAs against HSV-1 with antiviral activity. Three of them are directed against early and two against leaky late genes. Primary human lung fibroblasts, MRC-5, and African green monkey kidney cells, Vero, were transfected with ODNs and subsequently infected. The effect on HSV-1 replication was determined by analyzing the virus titer in cell culture supernatants by quantitative PCR and plaque assays. An inhibitory effect was observed with all five selected ODNs, with two cases showing statistical significance in both cell types. The observed effect was sequence-specific and dose dependent. In one case the ODN was more efficient than a previously described siRNA directed against the same target site in the mRNA of UL5, a component of the helicase/primase complex. HSV-1 virions and ODNs can be applied simultaneously without transfection reagent, but at a 50-fold higher concentration to Vero cells with similar efficiencies. The results underline the potential of partially double-stranded hairpin loop-structured ODNs as antiviral agents.

  2. Hydrogen Production by Homogeneous Catalysis: Alcohol Acceptorless Dehydrogenation

    DEFF Research Database (Denmark)

    Nielsen, Martin

    2015-01-01

    in hydrogen production from biomass using homogeneous catalysis. Homogeneous catalysis has the advance of generally performing transformations at much milder conditions than traditional heterogeneous catalysis, and hence it constitutes a promising tool for future applications for a sustainable energy sector...

  3. Stereospecificity of oligonucleotide interactions revisited: no evidence for heterochiral hybridization and ribozyme/DNAzyme activity.

    Directory of Open Access Journals (Sweden)

    Kai Hoehlig

    Full Text Available A major challenge for the application of RNA- or DNA-oligonucleotides in biotechnology and molecular medicine is their susceptibility to abundant nucleases. One intriguing possibility to tackle this problem is the use of mirror-image (l-oligonucleotides. For aptamers, this concept has successfully been applied to even develop therapeutic agents, so-called Spiegelmers. However, for technologies depending on RNA/RNA or RNA/DNA hybridization, like antisense or RNA interference, it has not been possible to use mirror-image oligonucleotides because Watson-Crick base pairing of complementary strands is (thought to be stereospecific. Many scientists consider this a general principle if not a dogma. A recent publication proposing heterochiral Watson-Crick base pairing and sequence-specific hydrolysis of natural RNA by mirror-image ribozymes or DNAzymes (and vice versa prompted us to systematically revisit the stereospecificity of oligonucleotides hybridization and catalytic activity. Using hyperchromicity measurements we demonstrate that hybridization only occurs among homochiral anti-parallel complementary oligonucleotide strands. As expected, achiral PNA hybridizes to RNA and DNA irrespective of their chirality. In functional assays we could not confirm an alleged heterochiral hydrolytic activity of ribozymes or DNAzymes. Our results confirm a strict stereospecificity of oligonucleotide hybridization and clearly argue against the possibility to use mirror-image oligonucleotides for gene silencing or antisense applications.

  4. Heat capacity changes in RNA folding: application of perturbation theory to hammerhead ribozyme cold denaturation.

    Science.gov (United States)

    Mikulecky, Peter J; Feig, Andrew L

    2004-01-01

    In proteins, empirical correlations have shown that changes in heat capacity (DeltaC(P)) scale linearly with the hydrophobic surface area buried upon folding. The influence of DeltaC(P) on RNA folding has been widely overlooked and is poorly understood. In addition to considerations of solvent reorganization, electrostatic effects might contribute to DeltaC(P)s of folding in polyanionic species such as RNAs. Here, we employ a perturbation method based on electrostatic theory to probe the hot and cold denaturation behavior of the hammerhead ribozyme. This treatment avoids much of the error associated with imposing two-state folding models on non-two-state systems. Ribozyme stability is perturbed across a matrix of solvent conditions by varying the concentration of NaCl and methanol co-solvent. Temperature-dependent unfolding is then monitored by circular dichroism spectroscopy. The resulting array of unfolding transitions can be used to calculate a DeltaC(P) of folding that accurately predicts the observed cold denaturation temperature. We confirm the accuracy of the calculated DeltaC(P) by using isothermal titration calorimetry, and also demonstrate a methanol-dependence of the DeltaC(P). We weigh the strengths and limitations of this method for determining DeltaC(P) values. Finally, we discuss the data in light of the physical origins of the DeltaC(P)s for RNA folding and consider their impact on biological function.

  5. Sequence-dependent unfolding kinetics of DNA hairpins studied by nanopore force spectroscopy

    International Nuclear Information System (INIS)

    Renner, Stephan; Bessonov, Andrey; Simmel, Friedrich C; Gerland, Ulrich

    2010-01-01

    Nanopore force spectroscopy is used to study the unzipping kinetics of two DNA hairpin molecules with a 12 base pair long stem containing two contiguous stretches of six GC and six AT base pairs in interchanged order. Even though the thermodynamic stabilities of the two structures are nearly the same, they differ greatly in their unzipping kinetics. When the GC segment has to be broken before the AT segment, the unfolding rate is orders of magnitude smaller than in the opposite case. We also investigated hairpins with stem regions consisting only of AT or GC base pairs. The pure AT hairpins translocate much faster than the other hairpins, whereas the pure GC hairpins translocate on similar timescales to the hairpins with only an initial GC segment. For each hairpin, nanopore force spectroscopy is performed for different loading rates and the resulting unzipping distributions are mathematically transformed to a master curve that yields the unfolding rate as a function of applied voltage. This is compared with a stochastic model of the unfolding process for the two sequences for different voltages. The results can be rationalized in terms of the different natures of the free energy landscapes for the unfolding process.

  6. Fundamental concepts in heterogeneous catalysis

    CERN Document Server

    Norskov, Jens K; Abild-Pedersen, Frank; Bligaard, Thomas

    2014-01-01

    This book is based on a graduate course and suitable as a primer for any newcomer to the field, this book is a detailed introduction to the experimental and computational methods that are used to study how solid surfaces act as catalysts.   Features include:First comprehensive description of modern theory of heterogeneous catalysisBasis for understanding and designing experiments in the field   Allows reader to understand catalyst design principlesIntroduction to important elements of energy transformation technologyTest driven at Stanford University over several semesters

  7. DOE Laboratory Catalysis Research Symposium - Abstracts

    Energy Technology Data Exchange (ETDEWEB)

    Dunham, T.

    1999-02-01

    The conference consisted of two sessions with the following subtopics: (1) Heterogeneous Session: Novel Catalytic Materials; Photocatalysis; Novel Processing Conditions; Metals and Sulfides; Nuclear Magnetic Resonance; Metal Oxides and Partial Oxidation; Electrocatalysis; and Automotive Catalysis. (2) Homogeneous Catalysis: H-Transfer and Alkane Functionalization; Biocatalysis; Oxidation and Photocatalysis; and Novel Medical, Methods, and Catalyzed Reactions.

  8. Computational Design of Clusters for Catalysis

    Science.gov (United States)

    Jimenez-Izal, Elisa; Alexandrova, Anastassia N.

    2018-04-01

    When small clusters are studied in chemical physics or physical chemistry, one perhaps thinks of the fundamental aspects of cluster electronic structure, or precision spectroscopy in ultracold molecular beams. However, small clusters are also of interest in catalysis, where the cold ground state or an isolated cluster may not even be the right starting point. Instead, the big question is: What happens to cluster-based catalysts under real conditions of catalysis, such as high temperature and coverage with reagents? Myriads of metastable cluster states become accessible, the entire system is dynamic, and catalysis may be driven by rare sites present only under those conditions. Activity, selectivity, and stability are highly dependent on size, composition, shape, support, and environment. To probe and master cluster catalysis, sophisticated tools are being developed for precision synthesis, operando measurements, and multiscale modeling. This review intends to tell the messy story of clusters in catalysis.

  9. "Nanocrystal bilayer for tandem catalysis"

    Energy Technology Data Exchange (ETDEWEB)

    Yamada, Yusuke; Tsung, Chia Kuang; Huang, Wenyu; Huo, Ziyang; E.Habas, Susan E; Soejima, Tetsuro; Aliaga, Cesar E; Samorjai, Gabor A; Yang, Peidong

    2011-01-24

    Supported catalysts are widely used in industry and can be optimized by tuning the composition and interface of the metal nanoparticles and oxide supports. Rational design of metal-metal oxide interfaces in nanostructured catalysts is critical to achieve better reaction activities and selectivities. We introduce here a new class of nanocrystal tandem catalysts that have multiple metal-metal oxide interfaces for the catalysis of sequential reactions. We utilized a nanocrystal bilayer structure formed by assembling platinum and cerium oxide nanocube monolayers of less than 10 nm on a silica substrate. The two distinct metal-metal oxide interfaces, CeO2-Pt and Pt-SiO2, can be used to catalyse two distinct sequential reactions. The CeO2-Pt interface catalysed methanol decomposition to produce CO and H2, which were subsequently used for ethylene hydroformylation catalysed by the nearby Pt-SiO2 interface. Consequently, propanal was produced selectively from methanol and ethylene on the nanocrystal bilayer tandem catalyst. This new concept of nanocrystal tandem catalysis represents a powerful approach towards designing high-performance, multifunctional nanostructured catalysts

  10. Curvature bound from gravitational catalysis

    Science.gov (United States)

    Gies, Holger; Martini, Riccardo

    2018-04-01

    We determine bounds on the curvature of local patches of spacetime from the requirement of intact long-range chiral symmetry. The bounds arise from a scale-dependent analysis of gravitational catalysis and its influence on the effective potential for the chiral order parameter, as induced by fermionic fluctuations on a curved spacetime with local hyperbolic properties. The bound is expressed in terms of the local curvature scalar measured in units of a gauge-invariant coarse-graining scale. We argue that any effective field theory of quantum gravity obeying this curvature bound is safe from chiral symmetry breaking through gravitational catalysis and thus compatible with the simultaneous existence of chiral fermions in the low-energy spectrum. With increasing number of dimensions, the curvature bound in terms of the hyperbolic scale parameter becomes stronger. Applying the curvature bound to the asymptotic safety scenario for quantum gravity in four spacetime dimensions translates into bounds on the matter content of particle physics models.

  11. Short hairpin RNA interference therapy for ischemic heart disease

    Science.gov (United States)

    Huang, Mei; Chan, Denise; Jia, Fangjun; Xie, Xiaoyan; Li, Zongjin; Hoyt, Grant; Robbins, Robert C.; Chen, Xiaoyuan; Giaccia, Amato; Wu, Joseph C.

    2013-01-01

    Background During hypoxia, upregulation of hypoxia inducible factor-1 alpha (HIF-1α) transcriptional factor can activate several downstream angiogenic genes. However, HIF-1α is naturally degraded by prolyl hydroxylase-2 (PHD2) protein. Here we hypothesize that short hairpin RNA (shRNA) interference therapy targeting PHD2 can be used for treatment of myocardial ischemia and this process can be followed noninvasively by molecular imaging. Methods and Results PHD2 was cloned from mouse embryonic stem (ES) cells by comparing the homolog gene in human and rat. The best candidate shRNA sequence for inhibiting PHD2 was inserted into the pSuper vector driven by the H1 promoter, followed by a separate hypoxia response element (HRE)-incorporated promoter driving a firefly luciferase (Fluc) reporter gene. This construct was used to transfect mouse C2C12 myoblast cell line for in vitro confirmation. Compared to the control short hairpin scramble (shScramble) as control, inhibition of PHD2 increased levels of HIF-1α protein and several downstream angiogenic genes by >30% (P<0.01). Afterwards, shRNA targeting PHD2 (shPHD2) plasmid was injected intramyocardially following ligation of left anterior descending (LAD) artery in mice. Animals were randomized into shPHD2 group (n=20) versus shScramble sequence as control (n=20). Bioluminescence imaging detected transgene expression for 4–5 weeks. Echocardiographic study showed the shPHD2 group had improved fractional shortening compared with the shScramble group at week 4 (33.7%±1.9% vs. 28.4%±2.8%; P<0.05). Postmortem analysis showed increased presence of small capillaries and venules in the infarcted zones by CD31 staining. Finally, Western blot anlaysis of explanted hearts also confirm that animals treated with shPHD2 had significantly higher levels of HIF-1α protein. Conclusions This is the first study to image the biological role of shRNA therapy for improving cardiac function. Inhibition of PHD2 by shRNA led to

  12. Structural and sequence features of two residue turns in beta-hairpins.

    Science.gov (United States)

    Madan, Bharat; Seo, Sung Yong; Lee, Sun-Gu

    2014-09-01

    Beta-turns in beta-hairpins have been implicated as important sites in protein folding. In particular, two residue β-turns, the most abundant connecting elements in beta-hairpins, have been a major target for engineering protein stability and folding. In this study, we attempted to investigate and update the structural and sequence properties of two residue turns in beta-hairpins with a large data set. For this, 3977 beta-turns were extracted from 2394 nonhomologous protein chains and analyzed. First, the distribution, dihedral angles and twists of two residue turn types were determined, and compared with previous data. The trend of turn type occurrence and most structural features of the turn types were similar to previous results, but for the first time Type II turns in beta-hairpins were identified. Second, sequence motifs for the turn types were devised based on amino acid positional potentials of two-residue turns, and their distributions were examined. From this study, we could identify code-like sequence motifs for the two residue beta-turn types. Finally, structural and sequence properties of beta-strands in the beta-hairpins were analyzed, which revealed that the beta-strands showed no specific sequence and structural patterns for turn types. The analytical results in this study are expected to be a reference in the engineering or design of beta-hairpin turn structures and sequences. © 2014 Wiley Periodicals, Inc.

  13. A speculated ribozyme site in the herpes simplex virus type 1 latency-associated transcript gene is not essential for a wild-type reactivation phenotype

    Science.gov (United States)

    Carpenter, Dale; Singh, Sukhpreet; Osorio, Nelson; Hsiang, Chinhui; Jiang, Xianzhi; Jin, Ling; Jones, Clinton; Wechsler, Steven L

    2010-01-01

    During herpes simplex virus-1 (HSV-1) latency in sensory neurons, LAT (latency-associated transcript) is the only abundantly expressed viral gene. LAT plays an important role in the HSV-1 latency-reactivation cycle, because LAT deletion mutants have a significantly decreased reactivation phenotype. Based solely on sequence analysis, it was speculated that LAT encodes a ribozyme that plays an important role in how LAT enhances the virus’ reactivation phenotype. Because LAT ribozyme activity has never been reported, we decided to test the converse hypothesis, namely, that this region of LAT does not encode a ribozyme function important for LAT’s ability to enhance the reactivation phenotype. We constructed a viral mutant (LAT-Rz) in which the speculated ribozyme consensus sequence was altered such that no ribozyme was encoded. We report here that LAT-Rz had a wild-type reactivation phenotype in mice, confirming the hypothesis that the speculated LAT ribozyme is not a dominant factor in stimulating the latency-reactivation cycle in mice. PMID:18982533

  14. Surface science and heterogeneous catalysis

    International Nuclear Information System (INIS)

    Somorjai, G.A.

    1980-05-01

    The catalytic reactions studied include hydrocarbon conversion over platinum, the transition metal-catalyzed hydrogenation of carbon monoxide, and the photocatalyzed dissociation of water over oxide surfaces. The method of combined surface science and catalytic studies is similar to those used in synthetic organic chemistry. The single-crystal models for the working catalyst are compared with real catalysts by comparing the rates of cyclopropane ring opening on platinum and the hydrogenation of carbon monoxide on rhodium single crystal surface with those on practical commercial catalyst systems. Excellent agreement was obtained for these reactions. This document reviews what was learned about heterogeneous catalysis from these surface science approaches over the past 15 years and present models of the active catalyst surface

  15. Tandem catalysis: a new approach to polymers.

    Science.gov (United States)

    Robert, Carine; Thomas, Christophe M

    2013-12-21

    The creation of polymers by tandem catalysis represents an exciting frontier in materials science. Tandem catalysis is one of the strategies used by Nature for building macromolecules. Living organisms generally synthesize macromolecules by in vivo enzyme-catalyzed chain growth polymerization reactions using activated monomers that have been formed within cells during complex metabolic processes. However, these biological processes rely on highly complex biocatalysts, thus limiting their industrial applications. In order to obtain polymers by tandem catalysis, homogeneous and enzyme catalysts have played a leading role in the last two decades. In the following feature article, we will describe selected published efforts to achieve these research goals.

  16. Supported Ionic Liquid Phase (SILP) catalysis

    DEFF Research Database (Denmark)

    Riisager, Anders; Fehrmann, Rasmus; Haumann, Marco

    2006-01-01

    Applications of ionic liquids to replace conventional solvents in homogeneous transition-metal catalysis have increased significantly during the last decade. Biphasic ionic liquid/organic liquid systems offer advantages with regard to product separation, catalyst stability, and recycling...... but utilise in the case of fast chemical reactions only a small amount of expensive ionic liquid and catalyst. The novel Supported Ionic Liquid Phase (SILP) catalysis concept overcomes these drawbacks and allows the use of fixed-bed reactors for continuous reactions. In this Microreview the SILP catalysis...

  17. Relation between Hydrogen Evolution and Hydrodesulfurization Catalysis

    DEFF Research Database (Denmark)

    Šaric, Manuel; Moses, Poul Georg; Rossmeisl, Jan

    2016-01-01

    A relation between hydrogen evolution and hydrodesulfurization catalysis was found by density functional theory calculations. The hydrogen evolution reaction and the hydrogenation reaction in hydrodesulfurization share hydrogen as a surface intermediate and, thus, have a common elementary step...

  18. Special section on Nano-Catalysis

    CSIR Research Space (South Africa)

    Makgwane, PR

    2013-01-01

    Full Text Available to achieve sustainable and green catalytic processes. The special issue contains 40 peer reviewed scientific papers that include four comprehensive review articles contributions from the invited experts in the respective catalysis fields....

  19. Current trends of surface science and catalysis

    CERN Document Server

    Park, Jeong Young

    2014-01-01

    Including detail on applying surface science in renewable energy conversion, this book covers the latest results on model catalysts including single crystals, bridging "materials and pressure gaps", and hot electron flows in heterogeneous catalysis.

  20. Faraday Discussions meeting Catalysis for Fuels.

    Science.gov (United States)

    Fischer, Nico; Kondrat, Simon A; Shozi, Mzamo

    2017-05-02

    Welcome to Africa was the motto when after more than 100 years the flag ship conference series of the Royal Society of Chemistry, the Faraday Discussions was hosted for the first time on the African Continent. Under the fitting topic 'Catalysis for Fuels' over 120 delegates followed the invitation by the conference chair Prof. Graham Hutchings FRS (Cardiff Catalysis Institute), his organizing committee and the co-organizing DST-NRF Centre of Excellence in Catalysis c*change (). In the presentations of 21 invited speakers and 59 posters, cutting edge research in the field of catalysis for fuels, designing new catalysts for synthetic fuels, hydrocarbon conversion in the production of synthetic fuels and novel photocatalysis was presented over the two-day meeting. The scene was set by the opening lecture of Prof. Enrique Iglesias (UC Berkeley) and wrapped-up with the concluding remarks by Philip Gibson (SASOL).

  1. Advancing Sustainable Catalysis with Magnetite Surface ...

    Science.gov (United States)

    This article surveys the recent developments in the synthesis, surface modification, and synthetic applications of magnetitenanoparticles. The emergence of iron(II,III) oxide (triiron tetraoxide or magnetite; Fe3O4, or FeO•Fe2O3) nanoparticles as a sustainable support in heterogeneous catalysis is highlighted. Use of an oxide of earth-abundant iron for various applications in catalysis and environmental remediation.

  2. New developments in oxidation catalysis

    Energy Technology Data Exchange (ETDEWEB)

    Rosowski, F. [BASF SE, Ludwigshafen (Germany)

    2011-07-01

    The impact of heterogeneous catalysis on the economy can be depicted by the global revenue of the chemical industry in 2006, which accounted for 2200 billion Euros with a share of all chemical products produced applying heterogeneous catalysis of about two thirds. [1] The range of products is enormous and they contribute greatly to the quality of our lifes. The advancement in the development of basic and intermediate chemical products is crucially dependent on either the further development of existing catalyst systems or the development of new catalysts and key to success for the chemical industry. Within the context of oxidation catalysis, the following driving forces are guiding research activities: There is a continuous desire to increase the selectivity of a given process in response to both economic as well as ecological needs and taking advantage of higher efficiencies in terms of cost savings and a better utilization of raw materials. A second motivation focuses on raw material change to all abundant and competitive feedstocks requiring both new developments in catalyst design as well as process technology. A more recent motivation refers to the use of metal oxide redox systems which are key to success for the development of novel technologies allowing for the separation of carbon dioxide and the use of carbon dioxide as a feedstock molecule as well as storing renewable energy in a chemical. To date, general ab initio approaches are known for the design of novel catalytic materials only for a few chemical reactions, whereas most industrial catalytic processes have been developed by empirical methods. [2] The development of catalytic materials are either based on the targeted synthesis of catalytic lead structures as well as high throughput methods that allow for the screening of a large range of parameters. [3 - 5] The successful development of catalysts together with reactor technology has led to both significant savings in raw materials and emissions. The

  3. ISOTOPE METHODS IN HOMOGENEOUS CATALYSIS.

    Energy Technology Data Exchange (ETDEWEB)

    BULLOCK,R.M.; BENDER,B.R.

    2000-12-01

    The use of isotope labels has had a fundamentally important role in the determination of mechanisms of homogeneously catalyzed reactions. Mechanistic data is valuable since it can assist in the design and rational improvement of homogeneous catalysts. There are several ways to use isotopes in mechanistic chemistry. Isotopes can be introduced into controlled experiments and followed where they go or don't go; in this way, Libby, Calvin, Taube and others used isotopes to elucidate mechanistic pathways for very different, yet important chemistries. Another important isotope method is the study of kinetic isotope effects (KIEs) and equilibrium isotope effect (EIEs). Here the mere observation of where a label winds up is no longer enough - what matters is how much slower (or faster) a labeled molecule reacts than the unlabeled material. The most careti studies essentially involve the measurement of isotope fractionation between a reference ground state and the transition state. Thus kinetic isotope effects provide unique data unavailable from other methods, since information about the transition state of a reaction is obtained. Because getting an experimental glimpse of transition states is really tantamount to understanding catalysis, kinetic isotope effects are very powerful.

  4. Life extension of MAPS-2 by replacement of boiler hairpin type heat exchangers

    International Nuclear Information System (INIS)

    Tripathi, J.C.; Rastogi, S.K.; Rastogi, A.K.

    2006-01-01

    The steam generating equipment in MAPS-1 and 2 are Hairpin type comprises of eight boiler assemblies arranged in two banks of four boilers each. Each hairpin type heat exchangers consist of 195 Monel-400 tubes of 12.7 mm OD x 1.24 mm WT. One boiler assembly consists of eleven inverted U type heat exchangers (called hairpin type heat exchangers) mounted in parallel on inlet and outlet heavy water manifolds and connected to steam drum through individual short riser. Heavy water flows through these tubes where as feed water enters the shell at the bottom of one leg called pre-heat leg. After commissioning of MAPS-2 in 1985, five hairpins of MAPS-2 developed leak during the course of operation by the year 1999. Absence of physical access for health assessment of steam generator tube and lack of provision for tube sheet cleaning to remove the deposits on feed water side had caused pile and resulted in tube failures by under deposit pitting corrosion. All the 88 hairpins of MAPS-2 were replaced to extend the plant life when MAPS-2 was taken out of grid for En-masse Coolant Channel Replacement job (EMCCR) in the year 2001 - 03. The long shutdown of MAPS units for EMCCR was considered to be cost effective since unscheduled plant shut downs on account of tube leaks could be avoided. (author)

  5. An enzyme-catalyzed multistep DNA refolding mechanism in hairpin telomere formation.

    Directory of Open Access Journals (Sweden)

    Ke Shi

    Full Text Available Hairpin telomeres of bacterial linear chromosomes are generated by a DNA cutting-rejoining enzyme protelomerase. Protelomerase resolves a concatenated dimer of chromosomes as the last step of chromosome replication, converting a palindromic DNA sequence at the junctions between chromosomes into covalently closed hairpins. The mechanism by which protelomerase transforms a duplex DNA substrate into the hairpin telomeres remains largely unknown. We report here a series of crystal structures of the protelomerase TelA bound to DNA that represent distinct stages along the reaction pathway. The structures suggest that TelA converts a linear duplex substrate into hairpin turns via a transient strand-refolding intermediate that involves DNA-base flipping and wobble base-pairs. The extremely compact di-nucleotide hairpin structure of the product is fully stabilized by TelA prior to strand ligation, which drives the reaction to completion. The enzyme-catalyzed, multistep strand refolding is a novel mechanism in DNA rearrangement reactions.

  6. Miniature short hairpin RNA screens to characterize antiproliferative drugs.

    Science.gov (United States)

    Kittanakom, Saranya; Arnoldo, Anthony; Brown, Kevin R; Wallace, Iain; Kunavisarut, Tada; Torti, Dax; Heisler, Lawrence E; Surendra, Anuradha; Moffat, Jason; Giaever, Guri; Nislow, Corey

    2013-08-07

    The application of new proteomics and genomics technologies support a view in which few drugs act solely by inhibiting a single cellular target. Indeed, drug activity is modulated by complex, often incompletely understood cellular mechanisms. Therefore, efforts to decipher mode of action through genetic perturbation such as RNAi typically yields "hits" that fall into several categories. Of particular interest to the present study, we aimed to characterize secondary activities of drugs on cells. Inhibiting a known target can result in clinically relevant synthetic phenotypes. In one scenario, drug perturbation could, for example, improperly activate a protein that normally inhibits a particular kinase. In other cases, additional, lower affinity targets can be inhibited as in the example of inhibition of c-Kit observed in Bcr-Abl-positive cells treated with Gleevec. Drug transport and metabolism also play an important role in the way any chemicals act within the cells. Finally, RNAi per se can also affect cell fitness by more general off-target effects, e.g., via the modulation of apoptosis or DNA damage repair. Regardless of the root cause of these unwanted effects, understanding the scope of a drug's activity and polypharmacology is essential for better understanding its mechanism(s) of action, and such information can guide development of improved therapies. We describe a rapid, cost-effective approach to characterize primary and secondary effects of small-molecules by using small-scale libraries of virally integrated short hairpin RNAs. We demonstrate this principle using a "minipool" composed of shRNAs that target the genes encoding the reported protein targets of approved drugs. Among the 28 known reported drug-target pairs, we successfully identify 40% of the targets described in the literature and uncover several unanticipated drug-target interactions based on drug-induced synthetic lethality. We provide a detailed protocol for performing such screens and for

  7. Specific acid catalysis and Lewis acid catalysis of Diels–Alder reactions in aqueous media

    NARCIS (Netherlands)

    Mubofu, Egid B.; Engberts, Jan B.F.N.

    2004-01-01

    A comparative study of specific acid catalysis and Lewis acid catalysis of Diels–Alder reactions between dienophiles (1, 4 and 6) and cyclopentadiene (2) in water and mixed aqueous media is reported. The reactions were performed in water with copper(II) nitrate as the Lewis acid catalyst whereas

  8. Specific acid catalysis and Lewis acid catalysis of Diels-Alder reactions in aqueous media

    NARCIS (Netherlands)

    Mubofu, E.B.; Engberts, J.B.F.N.

    A comparative study of specific acid catalysis and Lewis acid catalysis of Diells-Alder reactions between dienophiles (1, 4 and 6) and cyclopentadiene (2) in water and mixed aqueous media is reported. The reactions were performed in water with copper(II) nitrate as the Lewis acid catalyst whereas

  9. Discrimination among individual Watson–Crick base pairs at the termini of single DNA hairpin molecules

    Science.gov (United States)

    Vercoutere, Wenonah A.; Winters-Hilt, Stephen; DeGuzman, Veronica S.; Deamer, David; Ridino, Sam E.; Rodgers, Joseph T.; Olsen, Hugh E.; Marziali, Andre; Akeson, Mark

    2003-01-01

    Nanoscale α-hemolysin pores can be used to analyze individual DNA or RNA molecules. Serial examination of hundreds to thousands of molecules per minute is possible using ionic current impedance as the measured property. In a recent report, we showed that a nanopore device coupled with machine learning algorithms could automatically discriminate among the four combinations of Watson–Crick base pairs and their orientations at the ends of individual DNA hairpin molecules. Here we use kinetic analysis to demonstrate that ionic current signatures caused by these hairpin molecules depend on the number of hydrogen bonds within the terminal base pair, stacking between the terminal base pair and its nearest neighbor, and 5′ versus 3′ orientation of the terminal bases independent of their nearest neighbors. This report constitutes evidence that single Watson–Crick base pairs can be identified within individual unmodified DNA hairpin molecules based on their dynamic behavior in a nanoscale pore. PMID:12582251

  10. Hairpin formation within the enhancer region of the human enkephalin gene

    International Nuclear Information System (INIS)

    McMurray, C.T.; Douglass, J.O.; Wilson, W.D.

    1991-01-01

    The 3',5'-cyclic adenosine monophosphate (cAMP)-inducible enhancer of the human enkephaline gene is located within an imperfect palindrom of 23 base pairs. The authors have found that a 23-base-pair oligonucleotide duplex containing the enhancer undergoes a reversible conformational transition from the duplex to two individual hairpin structures each formed from one strand of the duplex. Each individual hairpin forms with mismatched base pairs, one containing two GT pairs and the other containing two AC pairs. The conformational transition is stabilized by proton transfer to the hairpin containing AC mismatched pairs. The unique physical and thermodynamic properties of the enkephalin enhancer DNA suggest a model in which DNA secondary structure within the enhancer region plays and active role incAMP-inducible activation of the human enkephalin gene via formation of cruciform structures

  11. Hairpin formation within the enhancer region of the human enkephalin gene

    Energy Technology Data Exchange (ETDEWEB)

    McMurray, C.T.; Douglass, J.O. (Oregon Health Sciences Univ., Portland (United States)); Wilson, W.D. (Georgia State Univ., Atlanta (United States))

    1991-01-15

    The 3{prime},5{prime}-cyclic adenosine monophosphate (cAMP)-inducible enhancer of the human enkephaline gene is located within an imperfect palindrom of 23 base pairs. The authors have found that a 23-base-pair oligonucleotide duplex containing the enhancer undergoes a reversible conformational transition from the duplex to two individual hairpin structures each formed from one strand of the duplex. Each individual hairpin forms with mismatched base pairs, one containing two GT pairs and the other containing two AC pairs. The conformational transition is stabilized by proton transfer to the hairpin containing AC mismatched pairs. The unique physical and thermodynamic properties of the enkephalin enhancer DNA suggest a model in which DNA secondary structure within the enhancer region plays and active role incAMP-inducible activation of the human enkephalin gene via formation of cruciform structures.

  12. Linear Chromosome-generating System of Agrobacterium tumefaciens C58: Protelomerase Generates and Protects Hairpin Ends

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Wai Mun; DaGloria, Jeanne; Fox, Heather; Ruan, Qiurong; Tillou, John; Shi, Ke; Aihara, Hideki; Aron, John; Casjens, Sherwood (Utah); (UMM)

    2012-09-05

    Agrobacterium tumefaciens C58, the pathogenic bacteria that causes crown gall disease in plants, harbors one circular and one linear chromosome and two circular plasmids. The telomeres of its unusual linear chromosome are covalently closed hairpins. The circular and linear chromosomes co-segregate and are stably maintained in the organism. We have determined the sequence of the two ends of the linear chromosome thus completing the previously published genome sequence of A. tumefaciens C58. We found that the telomeres carry nearly identical 25-bp sequences at the hairpin ends that are related by dyad symmetry. We further showed that its Atu2523 gene encodes a protelomerase (resolvase) and that the purified enzyme can generate the linear chromosomal closed hairpin ends in a sequence-specific manner. Agrobacterium protelomerase, whose presence is apparently limited to biovar 1 strains, acts via a cleavage-and-religation mechanism by making a pair of transient staggered nicks invariably at 6-bp spacing as the reaction intermediate. The enzyme can be significantly shortened at both the N and C termini and still maintain its enzymatic activity. Although the full-length enzyme can uniquely bind to its product telomeres, the N-terminal truncations cannot. The target site can also be shortened from the native 50-bp inverted repeat to 26 bp; thus, the Agrobacterium hairpin-generating system represents the most compact activity of all hairpin linear chromosome- and plasmid-generating systems to date. The biochemical analyses of the protelomerase reactions further revealed that the tip of the hairpin telomere may be unusually polymorphically capable of accommodating any nucleotide.

  13. Nano catalysis: Academic Discipline and Industrial Realities

    International Nuclear Information System (INIS)

    Olveira, S.; Forster, S.P.; Seeger, S.

    2014-01-01

    Nano technology plays a central role in both academic research and industrial applications. Nano enabled products are not only found in consumer markets, but also importantly in business to business markets (B2B). One of the oldest application areas of nano technology is nano catalysis—an excellent example for such a B2 B market. Several existing reviews illustrate the scientific developments in the field of nano catalysis. The goal of the present review is to provide an up-to-date picture of academic research and to extend this picture by an industrial and economic perspective. We therefore conducted an extensive search on several scientific databases and we further analyzed more than 1,500 nano catalysis-related patents and numerous market studies. We found that scientists today are able to prepare nano catalysts with superior characteristics regarding activity, selectivity, durability, and recoverability, which will contribute to solve current environmental, social, and industrial problems. In industry, the potential of nano catalysis is recognized, clearly reflected by the increasing number of nano catalysis-related patents and products on the market. The current nano catalysis research in academic and industrial laboratories will therefore enable a wealth of future applications in the industry

  14. Limits of neutral drift: lessons from the in vitro evolution of two ribozymes.

    Science.gov (United States)

    Petrie, Katherine L; Joyce, Gerald F

    2014-10-01

    The relative contributions of adaptive selection and neutral drift to genetic change are unknown but likely depend on the inherent abundance of functional genotypes in sequence space and how accessible those genotypes are to one another. To better understand the relative roles of selection and drift in evolution, local fitness landscapes for two different RNA ligase ribozymes were examined using a continuous in vitro evolution system under conditions that foster the capacity for neutral drift to mediate genetic change. The exploration of sequence space was accelerated by increasing the mutation rate using mutagenic nucleotide analogs. Drift was encouraged by carrying out evolution within millions of separate compartments to exploit the founder effect. Deep sequencing of individuals from the evolved populations revealed that the distribution of genotypes did not escape the starting local fitness peak, remaining clustered around the sequence used to initiate evolution. This is consistent with a fitness landscape where high-fitness genotypes are sparse and well isolated, and suggests, at least in this context, that neutral drift alone is not a primary driver of genetic change. Neutral drift does, however, provide a repository of genetic variation upon which adaptive selection can act.

  15. Sustainable green catalysis by supported metal nanoparticles.

    Science.gov (United States)

    Fukuoka, Atsushi; Dhepe, Paresh L

    2009-01-01

    The recent progress of sustainable green catalysis by supported metal nanoparticles is described. The template synthesis of metal nanoparticles in ordered porous materials is studied for the rational design of heterogeneous catalysts capable of high activity and selectivity. The application of these materials in green catalytic processes results in a unique activity and selectivity arising from the concerted effect of metal nanoparticles and supports. The high catalytic performances of Pt nanoparticles in mesoporous silica is reported. Supported metal catalysts have also been applied to biomass conversion by heterogeneous catalysis. Additionally, the degradation of cellulose by supported metal catalysts, in which bifunctional catalysis of acid and metal plays the key role for the hydrolysis and reduction of cellulose, is also reported. Copyright 2009 The Japan Chemical Journal Forum and Wiley Periodicals, Inc.

  16. Green chemistry by nano-catalysis

    KAUST Repository

    Polshettiwar, Vivek

    2010-01-01

    Nano-materials are important in many diverse areas, from basic research to various applications in electronics, biochemical sensors, catalysis and energy. They have emerged as sustainable alternatives to conventional materials, as robust high surface area heterogeneous catalysts and catalyst supports. The nano-sized particles increase the exposed surface area of the active component of the catalyst, thereby enhancing the contact between reactants and catalyst dramatically and mimicking the homogeneous catalysts. This review focuses on the use of nano-catalysis for green chemistry development including the strategy of using microwave heating with nano-catalysis in benign aqueous reaction media which offers an extraordinary synergistic effect with greater potential than these three components in isolation. To illustrate the proof-of-concept of this "green and sustainable" approach, representative examples are discussed in this article. © 2010 The Royal Society of Chemistry.

  17. Quantum catalysis : the modelling of catalytic transition states

    NARCIS (Netherlands)

    Hall, M.B.; Margl, P.; Naray-Szabo, G.; Schramm, Vern; Truhlar, D.G.; Santen, van R.A.; Warshel, A.; Whitten, J.L.; Truhlar, D.G.; Morokuma, K.

    1999-01-01

    A review with 101 refs.; we present an introduction to the computational modeling of transition states for catalytic reactions. We consider both homogeneous catalysis and heterogeneous catalysis, including organometallic catalysts, enzymes, zeolites and metal oxides, and metal surfaces. We summarize

  18. Competing role of catalysis-coagulation and catalysis-fragmentation in kinetic aggregation behaviours

    International Nuclear Information System (INIS)

    Li Xiao-Dong; Lin Zhen-Quan; Song Mei-Xia; Ke Jian-Hong

    2010-01-01

    We propose a kinetic aggregation model where species A aggregates evolve by the catalysis-coagulation and the catalysis-fragmentation, while the catalyst aggregates of the same species B or C perform self-coagulation processes. By means of the generalized Smoluchowski rate equation based on the mean-field assumption, we study the kinetic behaviours of the system with the catalysis-coagulation rate kernel K(i,j;l) ∝ l ν and the catalysis-fragmentation rate kernel F(i,j;l) ∝ l μ , where l is the size of the catalyst aggregate, and ν and μ are two parameters reflecting the dependence of the catalysis reaction on the size of the catalyst aggregate. The relation between the values of parameters ν and μ reflects the competing roles between the two catalysis processes in the kinetic evolution of species A. It is found that the competing roles of the catalysis-coagulation and catalysis-fragmentation in the kinetic aggregation behaviours are not determined simply by the relation between the two parameters ν and μ, but also depend on the values of these two parameters. When ν > μ and ν ≥ 0, the kinetic evolution of species A is dominated by the catalysis-coagulation and its aggregate size distribution a k (t) obeys the conventional or generalized scaling law; when ν k (t) approaches the scale-free form; and in other cases, a balance is established between the two competing processes at large times and a k (t) obeys a modified scaling law. (cross-disciplinary physics and related areas of science and technology)

  19. Next-Generation Catalysis for Renewables: Combining Enzymatic with Inorganic Heterogeneous Catalysis for Bulk Chemical Production

    DEFF Research Database (Denmark)

    Vennestrøm, Peter Nicolai Ravnborg; Christensen, C.H.; Pedersen, S.

    2010-01-01

    chemical platform under different conditions than those conventionally employed. Indeed, new process and catalyst concepts need to be established. Both enzymatic catalysis (biocatalysis) and heterogeneous inorganic catalysis are likely to play a major role and, potentially, be combined. One type...... of combination involves one-pot cascade catalysis with active sites from bio- and inorganic catalysts. In this article the emphasis is placed specifically on oxidase systems involving the coproduction of hydrogen peroxide, which can be used to create new in situ collaborative oxidation reactions for bulk...

  20. (CAG)(n)-hairpin DNA binds to Msh2-Msh3 and changes properties of mismatch recognition.

    Science.gov (United States)

    Owen, Barbara A L; Yang, Zungyoon; Lai, Maoyi; Gajec, Maciej; Gajek, Maciez; Badger, John D; Hayes, Jeffrey J; Edelmann, Winfried; Kucherlapati, Raju; Wilson, Teresa M; McMurray, Cynthia T

    2005-08-01

    Cells have evolved sophisticated DNA repair systems to correct damaged DNA. However, the human DNA mismatch repair protein Msh2-Msh3 is involved in the process of trinucleotide (CNG) DNA expansion rather than repair. Using purified protein and synthetic DNA substrates, we show that Msh2-Msh3 binds to CAG-hairpin DNA, a prime candidate for an expansion intermediate. CAG-hairpin binding inhibits the ATPase activity of Msh2-Msh3 and alters both nucleotide (ADP and ATP) affinity and binding interfaces between protein and DNA. These changes in Msh2-Msh3 function depend on the presence of A.A mispaired bases in the stem of the hairpin and on the hairpin DNA structure per se. These studies identify critical functional defects in the Msh2-Msh3-CAG hairpin complex that could misdirect the DNA repair process.

  1. A molecular view of heterogeneous catalysis

    DEFF Research Database (Denmark)

    Christensen, Claus H.; Nørskov, Jens Kehlet

    2008-01-01

    The establishment of a molecular view of heterogeneous catalysis has been hampered for a number of reasons. There are, however, recent developments, which show that we are now on the way towards reaching a molecular-scale picture of the way solids work as catalysts. By a combination of new...... by enabling a rational design of new catalysts. We illustrate this important development in heterogeneous catalysis by highlighting recent examples of catalyst systems for which it has been possible to achieve such a detailed understanding. In particular, we emphasize examples where this progress has made...

  2. Keynotes in energy-related catalysis

    CERN Document Server

    Kaliaguine, S

    2011-01-01

    Catalysis by solid acids, which includes (modified) zeolites, is of special relevance to energy applications. Acid catalysis is highly important in modern petroleum refining operations - large-scale processes such as fluid catalytic cracking, catalytic reforming, alkylation and olefin oligomerization rely on the transformation of hydrocarbons by acid catalysts. (Modified) zeolites are therefore essential for the improvement of existing processes and for technical innovations in the conversion of crude. There can be little doubt that zeolite-based catalysts will play a major role in the futu

  3. Heterogeneous catalysis at nanoscale for energy applications

    CERN Document Server

    Tao, Franklin (Feng); Kamat, Prashant V

    2015-01-01

    This book presents both the fundamentals concepts and latest achievements of a field that is growing in importance since it represents a possible solution for global energy problems.  It focuses on an atomic-level understanding of heterogeneous catalysis involved in important energy conversion processes. It presents a concise picture for the entire area of heterogeneous catalysis with vision at the atomic- and nano- scales, from synthesis, ex-situ and in-situ characterization, catalytic activity and selectivity, to mechanistic understanding based on experimental exploration and theoretical si

  4. Catalysis by nonmetals rules for catalyst selection

    CERN Document Server

    Krylov, Oleg V

    1970-01-01

    Catalysis by Non-metals: Rules of Catalyst Selection presents the development of scientific principles for the collection of catalysts. It discusses the investigation of the mechanism of chemosorption and catalysis. It addresses a series of properties of solid with catalytic activity. Some of the topics covered in the book are the properties of a solid and catalytic activity in oxidation-reduction reactions; the difference of electronegativities and the effective charges of atoms; the role of d-electrons in the catalytic properties of a solid; the color of solids; and proton-acid and proton-ba

  5. Phylogenetic footprinting of non-coding RNA: hammerhead ribozyme sequences in a satellite DNA family of Dolichopoda cave crickets (Orthoptera, Rhaphidophoridae

    Directory of Open Access Journals (Sweden)

    Venanzetti Federica

    2010-01-01

    Full Text Available Abstract Background The great variety in sequence, length, complexity, and abundance of satellite DNA has made it difficult to ascribe any function to this genome component. Recent studies have shown that satellite DNA can be transcribed and be involved in regulation of chromatin structure and gene expression. Some satellite DNAs, such as the pDo500 sequence family in Dolichopoda cave crickets, have a catalytic hammerhead (HH ribozyme structure and activity embedded within each repeat. Results We assessed the phylogenetic footprints of the HH ribozyme within the pDo500 sequences from 38 different populations representing 12 species of Dolichopoda. The HH region was significantly more conserved than the non-hammerhead (NHH region of the pDo500 repeat. In addition, stems were more conserved than loops. In stems, several compensatory mutations were detected that maintain base pairing. The core region of the HH ribozyme was affected by very few nucleotide substitutions and the cleavage position was altered only once among 198 sequences. RNA folding of the HH sequences revealed that a potentially active HH ribozyme can be found in most of the Dolichopoda populations and species. Conclusions The phylogenetic footprints suggest that the HH region of the pDo500 sequence family is selected for function in Dolichopoda cave crickets. However, the functional role of HH ribozymes in eukaryotic organisms is unclear. The possible functions have been related to trans cleavage of an RNA target by a ribonucleoprotein and regulation of gene expression. Whether the HH ribozyme in Dolichopoda is involved in similar functions remains to be investigated. Future studies need to demonstrate how the observed nucleotide changes and evolutionary constraint have affected the catalytic efficiency of the hammerhead.

  6. Strange temperature dependence of the folding rate of a 16-residue β-hairpin

    International Nuclear Information System (INIS)

    Xu Yao; Wang Ting; Gai Feng

    2006-01-01

    The folding/unfolding kinetics of a 16-residue β-hairpin that undergoes cold denaturation at ambient temperatures were investigated by time-resolved infrared spectroscopy coupled with the laser-induced temperature jump (T-jump) initiation method. We found that the relaxation kinetics of this β-hairpin following a T-jump, obtained by probing the amide I' band of the peptide backbone, show strange temperature dependence. At temperatures below approximately 35 deg. C where this β-hairpin mainly exhibits cold denaturation, the T-jump induced relaxation rate is ∼5 μs -1 , whereas at temperatures where heat denaturation takes place, the relaxation rate increases to ∼1 μs -1 . These results cannot be readily explained by a two-state folding model that has been used to describe the folding thermodynamics of this β-hairpin. In addition, these results suggest that the folding free energy barrier separating the cold-denatured state from the folded state is different from that separating the heat-denatured state from the folded state, coinciding with the idea that the mechanism leading to cold denaturation is different from that leading to heat denaturation

  7. Design of a new hairpin DNAzyme: The activity controlled by TMPyP4

    African Journals Online (AJOL)

    Jane

    2011-08-01

    Aug 1, 2011 ... activity and increase cell toxicity (Abdelgany et al., 2007). The hairpin DNAzyme is a ... fixed concentration of 5×10-4M in 50 mM Tris-HCl buffer (pH= 7.5,. 25°C) with 10 mM ..... Functional nucleic acid sensors. Chem. Rev.

  8. Role of the DIS hairpin in replication of human immunodeficiency virus type 1

    NARCIS (Netherlands)

    Berkhout, B.; van Wamel, J. L.

    1996-01-01

    The virion-associated genome of human immunodeficiency virus type 1 consists of a noncovalently linked dimer of two identical, unspliced RNA molecules. A hairpin structure within the untranslated leader transcript is postulated to play a role in RNA dimerization through base pairing of the

  9. Generation of sequence signatures from DNA amplification fingerprints with mini-hairpin and microsatellite primers.

    Science.gov (United States)

    Caetano-Anollés, G; Gresshoff, P M

    1996-06-01

    DNA amplification fingerprinting (DAF) with mini-hairpins harboring arbitrary "core" sequences at their 3' termini were used to fingerprint a variety of templates, including PCR products and whole genomes, to establish genetic relationships between plant tax at the interspecific and intraspecific level, and to identify closely related fungal isolates and plant accessions. No correlation was observed between the sequence of the arbitrary core, the stability of the mini-hairpin structure and DAF efficiency. Mini-hairpin primers with short arbitrary cores and primers complementary to simple sequence repeats present in microsatellites were also used to generate arbitrary signatures from amplification profiles (ASAP). The ASAP strategy is a dual-step amplification procedure that uses at least one primer in each fingerprinting stage. ASAP was able to reproducibly amplify DAF products (representing about 10-15 kb of sequence) following careful optimization of amplification parameters such as primer and template concentration. Avoidance of primer sequences partially complementary to DAF product termini was necessary in order to produce distinct fingerprints. This allowed the combinatorial use of oligomers in nucleic acid screening, with numerous ASAP fingerprinting reactions based on a limited number of primer sequences. Mini-hairpin primers and ASAP analysis significantly increased detection of polymorphic DNA, separating closely related bermudagrass (Cynodon) cultivars and detecting putatively linked markers in bulked segregant analysis of the soybean (Glycine max) supernodulation (nitrate-tolerant symbiosis) locus.

  10. Inhibition of HIV Replication by Cyclic and Hairpin PNAs Targeting the HIV-1 TAR RNA Loop

    Science.gov (United States)

    Upert, Gregory; Di Giorgio, Audrey; Upadhyay, Alok; Manvar, Dinesh; Pandey, Nootan; Pandey, Virendra N.; Patino, Nadia

    2012-01-01

    Human immunodeficiency virus-1 (HIV-1) replication and gene expression entails specific interaction of the viral protein Tat with its transactivation responsive element (TAR), to form a highly stable stem-bulge-loop structure. Previously, we described triphenylphosphonium (TPP) cation-based vectors that efficiently deliver nucleotide analogs (PNAs) into the cytoplasm of cells. In particular, we showed that the TPP conjugate of a linear 16-mer PNA targeting the apical stem-loop region of TAR impedes Tat-mediated transactivation of the HIV-1 LTR in vitro and also in cell culture systems. In this communication, we conjugated TPP to cyclic and hairpin PNAs targeting the loop region of HIV-1 TAR and evaluated their antiviral efficacy in a cell culture system. We found that TPP-cyclic PNAs containing only 8 residues, showed higher antiviral potency compared to hairpin PNAs of 12 or 16 residues. We further noted that the TPP-conjugates of the 8-mer cyclic PNA as well as the 16-mer linear PNA displayed similar antiviral efficacy. However, cyclic PNAs were shown to be highly specific to their target sequences. This communication emphasizes on the importance of small constrained cyclic PNAs over both linear and hairpin structures for targeting biologically relevant RNA hairpins. PMID:23029603

  11. Inhibition of HIV Replication by Cyclic and Hairpin PNAs Targeting the HIV-1 TAR RNA Loop

    Directory of Open Access Journals (Sweden)

    Gregory Upert

    2012-01-01

    Full Text Available Human immunodeficiency virus-1 (HIV-1 replication and gene expression entails specific interaction of the viral protein Tat with its transactivation responsive element (TAR, to form a highly stable stem-bulge-loop structure. Previously, we described triphenylphosphonium (TPP cation-based vectors that efficiently deliver nucleotide analogs (PNAs into the cytoplasm of cells. In particular, we showed that the TPP conjugate of a linear 16-mer PNA targeting the apical stem-loop region of TAR impedes Tat-mediated transactivation of the HIV-1 LTR in vitro and also in cell culture systems. In this communication, we conjugated TPP to cyclic and hairpin PNAs targeting the loop region of HIV-1 TAR and evaluated their antiviral efficacy in a cell culture system. We found that TPP-cyclic PNAs containing only 8 residues, showed higher antiviral potency compared to hairpin PNAs of 12 or 16 residues. We further noted that the TPP-conjugates of the 8-mer cyclic PNA as well as the 16-mer linear PNA displayed similar antiviral efficacy. However, cyclic PNAs were shown to be highly specific to their target sequences. This communication emphasizes on the importance of small constrained cyclic PNAs over both linear and hairpin structures for targeting biologically relevant RNA hairpins.

  12. Vibrational spectral simulation for peptides of mixed secondary structure: Method comparisons with the Trpzip model hairpin

    Czech Academy of Sciences Publication Activity Database

    Bouř, Petr; Keiderling, T. A.

    2005-01-01

    Roč. 109, - (2005), 23687-23697 ISSN 1089-5647 R&D Projects: GA AV ČR(CZ) IAA4055104 Grant - others:NSF(US) CHE03-16014 Institutional research plan: CEZ:AV0Z40550506 Keywords : VCD * trpzin model hairpin * peptides Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.679, year: 2003

  13. Hairpin and duplex formation in DNA fragments CCAATTTTGG, CCAATTTTTTGG, and CCATTTTTGG: a proton NMR study

    International Nuclear Information System (INIS)

    Pramanik, P.; Kanhouwa, N.; Kan, L.

    1988-01-01

    Three DNA fragments, CCAATTTTGG (1), CCAATTTTTTGG (2), AND CCATTTTTGG (3), were studied by proton NMR spectroscopy in aqueous solution. All these oligodeoxyribonucleotides contain common sequences at the 5' and 3' ends (5'-CCA and TGG-3'). 2 as well as 3 forms only hairpin structures with four unpaired thymidylyl units, four and three base pair stems, respectively, in neutral solution under low and high NaCl concentrations. At high salt concentration the oligomer 1 forms a duplex structure with -TT- internal loop. On the other hand, the same oligomer forms a stable hairpin structure at low salt and low strand concentrations at pH 7. The hairpin structure of 1 has a stem containing only three base pairs (CCA x TGG) and a loop containing four nucleotides (-ATTT-) that includes a dissociated A x T base pair. The two secondary structures of 1 coexist in an aqueous solution containing 0.1 M NaCl, at pH 7. The equilibrium shifts to the hairpin side when the temperature is raised. The stabilities and base-stacking modes of all three oligonucleotides in tow different structures are reported

  14. Determination of low-energy structures of a small RNA hairpin using ...

    Indian Academy of Sciences (India)

    In this method, the history of the simulation is used to increase the probability of states less visited in the simulation. It has been found that using both energy and end-to-end distance as the biasing parameters in the simulation, the partially folded structure of the hairpin starting from random structures could be obtained.

  15. Hairpin-like fluorescent probe for imaging of NF-κB transcription factor activity.

    Science.gov (United States)

    Metelev, Valeri; Zhang, Surong; Tabatadze, David; Bogdanov, Alexei

    2011-04-20

    Three oligodeoxyribonucleotides (ODN) covalently labeled with near-infrared (NIR) fluorochromes were synthesized and characterized with a goal of comparing in vitro a hairpin-based and a duplex-based FRET probe designed for the detection of human recombinant NF-κB p50/p65 heterodimer binding to DNA. Using deoxyguanosine phosphoramidite with a phosphorus-linked aminoethylene (diethylene glycol) hydrophilic linker, we synthesized ODNs with internucleoside reactive sites. The hairpin loop amino linker was modified with IRDye 800CW (FRET acceptor), and the 3'-end was modified with Cy5.5 (FRET donor) using a dithio-linker. To obtain a duplex probe, we conjugated Cy5.5 and 800CW to complementary strands at the distance of ten base pairs in the resultant duplex. No quenching of dyes was observed in either probe. The FRET efficiency was higher in the duplex (71%) than in the hairpin (56%) due to a more favorable distance between the donor and the acceptor. However, the hairpin design allowed more precise ratiometric measurement of fluorescence intensity changes as a result of NF-κB p50/p65 binding to the probe. We determined that as a result of binding there was a statistically significant increase of fluorescence intensity of Cy5.5 (donor) due to a decrease of FRET if normalized by 800CW intensity measured independently of FRET. We conclude that the hairpin based probe design allows for the synthesis of a dual fluorescence imaging probe that renders signal changes that are simple to interpret and stoichiometrically correct for detecting transcription factor-DNA interactions.

  16. µ-reactors for Heterogeneous Catalysis

    DEFF Research Database (Denmark)

    Jensen, Robert

    is described in detail. Since heating and temperature measurement is an extremely important point in heterogeneous catalysis an entire chapter is dedicated to this subject. Three different types of heaters have been implemented and tested both for repeatability and homogeneity of the heating as well...

  17. Heterogeneous catalysis in highly sensitive microreactors

    DEFF Research Database (Denmark)

    Olsen, Jakob Lind

    This thesis present a highly sensitive silicon microreactor and examples of its use in studying catalysis. The experimental setup built for gas handling and temperature control for the microreactor is described. The implementation of LabVIEW interfacing for all the experimental parts makes...

  18. Supported ionic liquid-phase (SILP) catalysis

    DEFF Research Database (Denmark)

    Riisager, Anders; Fehrmann, Rasmus; Wasserscheid, P.

    2005-01-01

    The concept of supported ionic liquid-phase (SILP) catalysis has been demonstrated for gas- and liquid-phase continuous fixed-bed reactions using rhodium phosphine catalyzed hydroformylation of propene and 1-octene as examples. The nature of the support had important influence on both the catalytic...

  19. Rate tracer studies of heterogeneous catalysis

    Energy Technology Data Exchange (ETDEWEB)

    Happel, J; Kiang, S

    1977-10-01

    An analysis is presented of the extent to which parameters involved in transient tracing of isotopic species in heterogeneous catalysis can be determined by experiments in which tracer concentrations are measured as a function of time. Different treatments for open and closed systems with the over-all reaction at equilibrium or irreversible were developed.

  20. Transition metal catalysis in confined spaces

    NARCIS (Netherlands)

    Leenders, S.H.A.M.

    2016-01-01

    Chemical reactions are required for the conversion of feedstocks to valuable materials, such as different types of plastics, pharmaceutical ingredients and advanced materials. In order to facilitate the conversion of these feedstocks to a wide array of products, catalysis plays a prominent role.

  1. Asymmetric Aminalization via Cation-Binding Catalysis

    DEFF Research Database (Denmark)

    Park, Sang Yeon; Liu, Yidong; Oh, Joong Suk

    2018-01-01

    Asymmetric cation-binding catalysis, in principle, can generate "chiral" anionic nucleophiles, where the counter cations are coordinated within chiral environments. Nitrogen-nucleophiles are intrinsically basic, therefore, its use as nucleophiles is often challenging and limiting the scope of the...

  2. Design and kinetic analysis of hammerhead ribozyme and DNAzyme that specifically cleave TEL-AML1 chimeric mRNA

    International Nuclear Information System (INIS)

    Choi, Woo-Hyung; Choi, Bo-Ra; Kim, Jae Hyun; Yeo, Woon-Seok; Oh, Sangtaek; Kim, Dong-Eun

    2008-01-01

    In order to develop the oligonucleotides to abolish an expression of TEL-AML1 chimeric RNA, which is a genetic aberration that causes the acute lymphoblastic leukemia (ALL), hammerhead ribozymes and deoxyoligoribozymes that can specifically cleave TEL-AML1 fusion RNA were designed. Constructs of the deoxyribozyme with an asymmetric substrate binding arm (Dz26) and the hammerhead ribozyme with a 4 nt-bulged substrate binding arm in the stem III (buRz28) were able to cleave TEL-AML1 chimeric RNA specifically at sites close to the junction in vitro, without cleaving the normal TEL and AML1 RNA. Single-turnover kinetic analysis under enzyme-excess condition revealed that the buRz28 is superior to the Dz26 in terms of substrate binding and RNA-cleavage. In conjunction with current progress in a gene-delivery technology, the designed oligonucleotides that specifically cleave the TEL-AML1 chimeric mRNA are hoped to be applicable for the treatment of ALL in vivo

  3. Molecular trade-offs in RNA ligases affected the modular emergence of complex ribozymes at the origin of life

    Science.gov (United States)

    Dhar, Nisha; Weinberg, Marc S.; Michod, Richard E.; Durand, Pierre M.

    2017-09-01

    In the RNA world hypothesis complex, self-replicating ribozymes were essential. For the emergence of an RNA world, less is known about the early processes that accounted for the formation of complex, long catalysts from small passively formed molecules. The functional role of small sequences has not been fully explored and, here, a possible role for smaller ligases is demonstrated. An established RNA polymerase model, the R18, was truncated from the 3' end to generate smaller molecules. All the molecules were investigated for self-ligation functions with a set of oligonucleotide substrates without predesigned base pairing. The smallest molecule that exhibited self-ligation activity was a 40-nucleotide RNA. It also demonstrated the greatest functional flexibility as it was more general in the kinds of substrates it ligated to itself although its catalytic efficiency was the lowest. The largest ribozyme (R18) ligated substrates more selectively and with greatest efficiency. With increase in size and predicted structural stability, self-ligation efficiency improved, while functional flexibility decreased. These findings reveal that molecular size could have increased from the activity of small ligases joining oligonucleotides to their own end. In addition, there is a size-associated molecular-level trade-off that could have impacted the evolution of RNA-based life.

  4. Molecular trade-offs in RNA ligases affected the modular emergence of complex ribozymes at the origin of life

    Science.gov (United States)

    Weinberg, Marc S.; Michod, Richard E.

    2017-01-01

    In the RNA world hypothesis complex, self-replicating ribozymes were essential. For the emergence of an RNA world, less is known about the early processes that accounted for the formation of complex, long catalysts from small passively formed molecules. The functional role of small sequences has not been fully explored and, here, a possible role for smaller ligases is demonstrated. An established RNA polymerase model, the R18, was truncated from the 3′ end to generate smaller molecules. All the molecules were investigated for self-ligation functions with a set of oligonucleotide substrates without predesigned base pairing. The smallest molecule that exhibited self-ligation activity was a 40-nucleotide RNA. It also demonstrated the greatest functional flexibility as it was more general in the kinds of substrates it ligated to itself although its catalytic efficiency was the lowest. The largest ribozyme (R18) ligated substrates more selectively and with greatest efficiency. With increase in size and predicted structural stability, self-ligation efficiency improved, while functional flexibility decreased. These findings reveal that molecular size could have increased from the activity of small ligases joining oligonucleotides to their own end. In addition, there is a size-associated molecular-level trade-off that could have impacted the evolution of RNA-based life. PMID:28989747

  5. Approaches to single-nanoparticle catalysis.

    Science.gov (United States)

    Sambur, Justin B; Chen, Peng

    2014-01-01

    Nanoparticles are among the most important industrial catalysts, with applications ranging from chemical manufacturing to energy conversion and storage. Heterogeneity is a general feature among these nanoparticles, with their individual differences in size, shape, and surface sites leading to variable, particle-specific catalytic activity. Assessing the activity of individual nanoparticles, preferably with subparticle resolution, is thus desired and vital to the development of efficient catalysts. It is challenging to measure the activity of single-nanoparticle catalysts, however. Several experimental approaches have been developed to monitor catalysis on single nanoparticles, including electrochemical methods, single-molecule fluorescence microscopy, surface plasmon resonance spectroscopy, X-ray microscopy, and surface-enhanced Raman spectroscopy. This review focuses on these experimental approaches, the associated methods and strategies, and selected applications in studying single-nanoparticle catalysis with chemical selectivity, sensitivity, or subparticle spatial resolution.

  6. ELECTROCHEMICAL PROMOTED CATALYSIS: TOWARDS PRACTICAL UTILIZATION

    Directory of Open Access Journals (Sweden)

    DIMITRIOS TSIPLAKIDES

    2008-07-01

    Full Text Available Electrochemical promotion (EP of catalysis has already been recognized as “a valuable development in catalytic research” (J. Pritchard, 1990 and as “one of the most remarkable advances in electrochemistry since 1950” (J. O’M. Bockris, 1996. Laboratory studies have clearly elucidated the phenomenology of electrochemical promotion and have proven that EP is a general phenomenon at the interface of catalysis and electrochemistry. The major progress toward practical utilization of EP is surveyed in this paper. The focus is given on the electropromotion of industrial ammonia synthesis catalyst, the bipolar EP and the development of a novel monolithic electropromoted reactor (MEPR in conjunction with the electropromotion of thin sputtered metal films. Future perspectives of electrochemical promotion applications in the field of hydrogen technologies are discussed.

  7. Symmetry and asymmetry in mandelate racemase catalysis

    International Nuclear Information System (INIS)

    Whitman, C.P.; Hegeman, G.D.; Cleland, W.W.; Kenyon, G.L.

    1985-01-01

    Kinetic properties of mandelate racemase catalysis (Vmax, Km, deuterium isotope effects, and pH profiles) were all measured in both directions by the circular dichroic assay of Sharp. These results, along with those of studying interactions of mandelate racemase with resolved, enantiomeric competitive inhibitors [(R)- and (S)-alpha-phenylglycerates], indicate a high degree of symmetry in both binding and catalysis. Racemization of either enantiomer of mandelate in D 2 O did not show an overshoot region of molecular ellipticity in circular dichroic measurements upon approach to equilibrium. Both the absence of such an overshoot region and the high degree of kinetic symmetry are consistent with a one-base acceptor mechanism for mandelate racemase. On the other hand, results of irreversible inhibition with partially resolved, enantiomeric affinity labels [(R)- and (S)-alpha-phenylglycidates] reveal a ''functional asymmetry'' at the active site. Mechanistic proposals, consistent with these results, are presented

  8. USD Catalysis Group for Alternative Energy

    Energy Technology Data Exchange (ETDEWEB)

    Hoefelmeyer, James D.; Koodali, Ranjit; Sereda, Grigoriy; Engebretson, Dan; Fong, Hao; Puszynski, Jan; Shende, Rajesh; Ahrenkiel, Phil

    2012-03-13

    The South Dakota Catalysis Group (SDCG) is a collaborative project with mission to develop advanced catalysts for energy conversion with two primary goals: (1) develop photocatalytic systems in which polyfunctionalized TiO2 are the basis for hydrogen/oxygen synthesis from water and sunlight (solar fuels group), (2) develop new materials for hydrogen utilization in fuel cells (fuel cell group). In tandem, these technologies complete a closed chemical cycle with zero emissions.

  9. Impact of Secondary Interactions in Asymmetric Catalysis

    OpenAIRE

    Frölander, Anders

    2007-01-01

    This thesis deals with secondary interactions in asymmetric catalysis and their impact on the outcome of catalytic reactions. The first part revolves around the metal-catalyzed asymmetric allylic alkylation reaction and how interactions within the catalyst affect the stereochemistry. An OH–Pd hydrogen bond in Pd(0)–π-olefin complexes of hydroxy-containing oxazoline ligands was identified by density functional theory computations and helped to rationalize the contrasting results obtained emplo...

  10. Confined catalysis under two-dimensional materials

    OpenAIRE

    Li, Haobo; Xiao, Jianping; Fu, Qiang; Bao, Xinhe

    2017-01-01

    Small spaces in nanoreactors may have big implications in chemistry, because the chemical nature of molecules and reactions within the nanospaces can be changed significantly due to the nanoconfinement effect. Two-dimensional (2D) nanoreactor formed under 2D materials can provide a well-defined model system to explore the confined catalysis. We demonstrate a general tendency for weakened surface adsorption under the confinement of graphene overlayer, illustrating the feasible modulation of su...

  11. Hybrid nuclear reactors and muon catalysis

    International Nuclear Information System (INIS)

    Petrov, Yu.

    1983-01-01

    Three methods are described of the conversion of isotope 238 U to 239 Pu by neutron capture in fast breeder reactors, in the breeding blanket of hybrid thermonuclear reactors using neutrons generated by fusion and electronuclear breeding in which the target is bombarded with 1 GeV protons. Their possible use in power production is discussed. Another prospective energy source is the use of muon catalysis in the fusion of deuterium and tritium nuclei. (J.P.)

  12. Nanoscale Advances in Catalysis and Energy Applications

    Energy Technology Data Exchange (ETDEWEB)

    Li, Yimin; Somorjai, Gabor A.

    2010-05-12

    In this perspective, we present an overview of nanoscience applications in catalysis, energy conversion, and energy conservation technologies. We discuss how novel physical and chemical properties of nanomaterials can be applied and engineered to meet the advanced material requirements in the new generation of chemical and energy conversion devices. We highlight some of the latest advances in these nanotechnologies and provide an outlook at the major challenges for further developments.

  13. Predictive Modeling in Actinide Chemistry and Catalysis

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Ping [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2016-05-16

    These are slides from a presentation on predictive modeling in actinide chemistry and catalysis. The following topics are covered in these slides: Structures, bonding, and reactivity (bonding can be quantified by optical probes and theory, and electronic structures and reaction mechanisms of actinide complexes); Magnetic resonance properties (transition metal catalysts with multi-nuclear centers, and NMR/EPR parameters); Moving to more complex systems (surface chemistry of nanomaterials, and interactions of ligands with nanoparticles); Path forward and conclusions.

  14. Catalysis in micellar and macromoleular systems

    CERN Document Server

    Fendler, Janos

    1975-01-01

    Catalysis in Micellar and Macromolecular Systems provides a comprehensive monograph on the catalyses elicited by aqueous and nonaqueous micelles, synthetic and naturally occurring polymers, and phase-transfer catalysts. It delineates the principles involved in designing appropriate catalytic systems throughout. Additionally, an attempt has been made to tabulate the available data exhaustively. The book discusses the preparation and purification of surfactants; the physical and chemical properties of surfactants and micelles; solubilization in aqueous micellar systems; and the principles of

  15. Observation of hairpin defects in a nematic main-chain polyester

    Science.gov (United States)

    Li, M. H.; Brûlet, A.; Davidson, P.; Keller, P.; Cotton, J. P.

    1993-04-01

    The conformation of a main-chain liquid crystalline polyester in its oriented nematic phase has been determined by small-angle neutron scattering. The data are fitted by a model of rigid cylinder with orientational fluctuations. For a low degree of polymerization (~9) the chain is almost completely elongated in the direction of the nematic field. For a polymer 3 times longer, the existence of two hairpins is shown at high temperature; this number decreases with decreasing temperature.

  16. α-helix to β-hairpin transition of human amylin monomer

    Science.gov (United States)

    Singh, Sadanand; Chiu, Chi-cheng; Reddy, Allam S.; de Pablo, Juan J.

    2013-04-01

    The human islet amylin polypeptide is produced along with insulin by pancreatic islets. Under some circumstances, amylin can aggregate to form amyloid fibrils, whose presence in pancreatic cells is a common pathological feature of Type II diabetes. A growing body of evidence indicates that small, early stage aggregates of amylin are cytotoxic. A better understanding of the early stages of the amylin aggregation process and, in particular, of the nucleation events leading to fibril growth could help identify therapeutic strategies. Recent studies have shown that, in dilute solution, human amylin can adopt an α-helical conformation, a β-hairpin conformation, or an unstructured coil conformation. While such states have comparable free energies, the β-hairpin state exhibits a large propensity towards aggregation. In this work, we present a detailed computational analysis of the folding pathways that arise between the various conformational states of human amylin in water. A free energy surface for amylin in explicit water is first constructed by resorting to advanced sampling techniques. Extensive transition path sampling simulations are then employed to identify the preferred folding mechanisms between distinct minima on that surface. Our results reveal that the α-helical conformer of amylin undergoes a transformation into the β-hairpin monomer through one of two mechanisms. In the first, misfolding begins through formation of specific contacts near the turn region, and proceeds via a zipping mechanism. In the second, misfolding occurs through an unstructured coil intermediate. The transition states for these processes are identified. Taken together, the findings presented in this work suggest that the inter-conversion of amylin between an α-helix and a β-hairpin is an activated process and could constitute the nucleation event for fibril growth.

  17. An approach to the construction of tailor-made amphiphilic peptides that strongly and selectively bind to hairpin RNA targets.

    Science.gov (United States)

    Lee, Su Jin; Hyun, Soonsil; Kieft, Jeffrey S; Yu, Jaehoon

    2009-02-18

    The hairpin RNA motif is one of the most frequently observed secondary structures and is often targeted by therapeutic agents. An amphiphilic peptide with seven lysine and eight leucine residues and its derivatives were designed for use as ligands against RNA hairpin motifs. We hypothesized that variations in both the hydrophobic leucine-rich and hydrophilic lysine-rich spheres of these amphiphilic peptides would create extra attractive interactions with hairpin RNA targets. A series of alanine-scanned peptides were probed to identify the most influential lysine residues in the hydrophilic sphere. The binding affinities of these modified peptides with several hairpins, such as RRE, TAR from HIV, a short hairpin from IRES of HCV, and a hairpin from the 16S A-site stem from rRNA, were determined. Since the hairpin from IRES of HCV was the most susceptible to the initial series of alanine-scanned peptides, studies investigating how further variations in the peptides effect binding employed the IRES hairpin. Next, the important Lys residues were substituted by shorter chain amines, such as ornithine, to place the peptide deeper into the hairpin groove. In a few cases, a 70-fold improved binding was observed for peptides that contained the specifically located shorter amine side chains. To further explore changes in binding affinities brought about by alterations in the hydrophobic sphere, tryptophan residues were introduced in place of leucine. A few peptides with tryptophan in specific positions also displayed 70-fold improved binding affinities. Finally, double mutant peptides incorporating both specifically located shorter amine side chains in the hydrophilic region and tryptophan residues in the hydrophobic region were synthesized. The binding affinities of peptides containing the simple double modification were observed to be 80 times lower, and their binding specificities were increased 40-fold. The results of this effort provide important information about

  18. "Off-on" electrochemical hairpin-DNA-based genosensor for cancer diagnostics.

    Science.gov (United States)

    Farjami, Elaheh; Clima, Lilia; Gothelf, Kurt; Ferapontova, Elena E

    2011-03-01

    A simple and robust "off-on" signaling genosensor platform with improved selectivity for single-nucleotide polymorphism (SNP) detection based on the electronic DNA hairpin molecular beacons has been developed. The DNA beacons were immobilized onto gold electrodes in their folded states through the alkanethiol linker at the 3'-end, while the 5'-end was labeled with a methylene blue (MB) redox probe. A typical "on-off" change of the electrochemical signal was observed upon hybridization of the 27-33 nucleotide (nt) long hairpin DNA to the target DNA, in agreement with all the hitherto published data. Truncation of the DNA hairpin beacons down to 20 nts provided improved genosensor selectivity for SNP and allowed switching of the electrochemical genosensor response from the on-off to the off-on mode. Switching was consistent with the variation in the mechanism of the electron transfer reaction between the electrode and the MB redox label, for the folded beacon being characteristic of the electrochemistry of adsorbed species, while for the "open" duplex structure being formally controlled by the diffusion of the redox label within the adsorbate layer. The relative current intensities of both processes were governed by the length of the formed DNA duplex, potential scan rate, and apparent diffusion coefficient of the redox species. The off-on genosensor design used for detection of a cancer biomarker TP53 gene sequence favored discrimination between the healthy and SNP-containing DNA sequences, which was particularly pronounced at short hybridization times.

  19. Opening of the TAR hairpin in the HIV-1 genome causes aberrant RNA dimerization and packaging

    Directory of Open Access Journals (Sweden)

    Das Atze T

    2012-07-01

    Full Text Available Abstract Background The TAR hairpin is present at both the 5′ and 3′ end of the HIV-1 RNA genome. The 5′ element binds the viral Tat protein and is essential for Tat-mediated activation of transcription. We recently observed that complete TAR deletion is allowed in the context of an HIV-1 variant that does not depend on this Tat-TAR axis for transcription. Mutations that open the 5′ stem-loop structure did however affect the leader RNA conformation and resulted in a severe replication defect. In this study, we set out to analyze which step of the HIV-1 replication cycle is affected by this conformational change of the leader RNA. Results We demonstrate that opening the 5′ TAR structure through a deletion in either side of the stem region caused aberrant dimerization and reduced packaging of the unspliced viral RNA genome. In contrast, truncation of the TAR hairpin through deletions in both sides of the stem did not affect RNA dimer formation and packaging. Conclusions These results demonstrate that, although the TAR hairpin is not essential for RNA dimerization and packaging, mutations in TAR can significantly affect these processes through misfolding of the relevant RNA signals.

  20. 2-Aminopurine hairpin probes for the detection of ultraviolet-induced DNA damage

    International Nuclear Information System (INIS)

    El-Yazbi, Amira F.; Loppnow, Glen R.

    2012-01-01

    Highlights: ► Molecular beacon with 2AP bases detects DNA damage in a simple mix-and-read assay. ► Molecular beacons with 2AP bases detect damage at a 17.2 nM limit of detection. ► The 2AP molecular beacon is linear over a 0–3.5 μM concentration range for damage. - Abstract: Nucleic acid exposure to radiation and chemical insults leads to damage and disease. Thus, detection and understanding DNA damage is important for elucidating molecular mechanisms of disease. However, current methods of DNA damage detection are either time-consuming, destroy the sample, or are too specific to be used for generic detection of damage. In this paper, we develop a fluorescence sensor of 2-aminopurine (2AP), a fluorescent analogue of adenine, incorporated in the loop of a hairpin probe for the quantification of ultraviolet (UV) C-induced nucleic acid damage. Our results show that the selectivity of the 2AP hairpin probe to UV-induced nucleic acid damage is comparable to molecular beacon (MB) probes of DNA damage. The calibration curve for the 2AP hairpin probe shows good linearity (R 2 = 0.98) with a limit of detection of 17.2 nM. This probe is a simple, fast and economic fluorescence sensor for the quantification of UV-induced damage in DNA.

  1. Short hairpin RNA-mediated knockdown of protein expression in Entamoeba histolytica

    Directory of Open Access Journals (Sweden)

    Singh Upinder

    2009-02-01

    Full Text Available Abstract Background Entamoeba histolytica is an intestinal protozoan parasite of humans. The genome has been sequenced, but the study of individual gene products has been hampered by the lack of the ability to generate gene knockouts. We chose to test the use of RNA interference to knock down gene expression in Entamoeba histolytica. Results An episomal vector-based system, using the E. histolytica U6 promoter to drive expression of 29-basepair short hairpin RNAs, was developed to target protein-encoding genes in E. histolytica. The short hairpin RNAs successfully knocked down protein levels of all three unrelated genes tested with this system: Igl, the intermediate subunit of the galactose- and N-acetyl-D-galactosamine-inhibitable lectin; the transcription factor URE3-BP; and the membrane binding protein EhC2A. Igl levels were reduced by 72%, URE3-BP by 89%, and EhC2A by 97%. Conclusion Use of the U6 promoter to drive expression of 29-basepair short hairpin RNAs is effective at knocking down protein expression for unrelated genes in Entamoeba histolytica, providing a useful tool for the study of this parasite.

  2. Short hairpin RNA-mediated knockdown of protein expression in Entamoeba histolytica.

    Science.gov (United States)

    Linford, Alicia S; Moreno, Heriberto; Good, Katelyn R; Zhang, Hanbang; Singh, Upinder; Petri, William A

    2009-02-17

    Entamoeba histolytica is an intestinal protozoan parasite of humans. The genome has been sequenced, but the study of individual gene products has been hampered by the lack of the ability to generate gene knockouts. We chose to test the use of RNA interference to knock down gene expression in Entamoeba histolytica. An episomal vector-based system, using the E. histolytica U6 promoter to drive expression of 29-basepair short hairpin RNAs, was developed to target protein-encoding genes in E. histolytica. The short hairpin RNAs successfully knocked down protein levels of all three unrelated genes tested with this system: Igl, the intermediate subunit of the galactose- and N-acetyl-D-galactosamine-inhibitable lectin; the transcription factor URE3-BP; and the membrane binding protein EhC2A. Igl levels were reduced by 72%, URE3-BP by 89%, and EhC2A by 97%. Use of the U6 promoter to drive expression of 29-basepair short hairpin RNAs is effective at knocking down protein expression for unrelated genes in Entamoeba histolytica, providing a useful tool for the study of this parasite.

  3. Stabilization of a β-hairpin in monomeric Alzheimer's amyloid-β peptide inhibits amyloid formation

    Science.gov (United States)

    Hoyer, Wolfgang; Grönwall, Caroline; Jonsson, Andreas; Ståhl, Stefan; Härd, Torleif

    2008-01-01

    According to the amyloid hypothesis, the pathogenesis of Alzheimer's disease is triggered by the oligomerization and aggregation of the amyloid-β (Aβ) peptide into protein plaques. Formation of the potentially toxic oligomeric and fibrillar Aβ assemblies is accompanied by a conformational change toward a high content of β-structure. Here, we report the solution structure of Aβ(1–40) in complex with the phage-display selected affibody protein ZAβ3, a binding protein of nanomolar affinity. Bound Aβ(1–40) features a β-hairpin comprising residues 17–36, providing the first high-resolution structure of Aβ in β conformation. The positions of the secondary structure elements strongly resemble those observed for fibrillar Aβ. ZAβ3 stabilizes the β-sheet by extending it intermolecularly and by burying both of the mostly nonpolar faces of the Aβ hairpin within a large hydrophobic tunnel-like cavity. Consequently, ZAβ3 acts as a stoichiometric inhibitor of Aβ fibrillation. The selected Aβ conformation allows us to suggest a structural mechanism for amyloid formation based on soluble oligomeric hairpin intermediates. PMID:18375754

  4. Hairpin structures in DNA containing arabinofuranosylcytosine. A combination of nuclear magnetic resonance and molecular dynamics

    International Nuclear Information System (INIS)

    Pieters, J.M.L.; de Vroom, E.; van der Marel, G.A.; van Boom, J.H.; Altona, C.; Koning, T.H.G.; Kaptein, R.

    1990-01-01

    Nuclear magnetic resonance (NMR) and model-building studies were carried out on the hairpin form of the octamer d(CG a CTAGCG) ( a C = arabinofuranosylcytosine), referred to as the TA compound. The nonexchangeable protons of the TA compound were assigned by means of nuclear Overhauser effect spectroscopy (NOESY) and correlated spectroscopy (COSY). Form a detailed analysis of the coupling data and of the NOESY spectra the following conclusions are reached: (i) the hairpin consists of a stem of three Watson-Crick type base pairs, and the two remaining residues, T(4) and dA(5), participate in a loop. (ii) All sugar rings show conformational flexibility although a strong preference for the S-type (C2'-endo) conformer is observed. (iii) The thymine does not stack upon the 3' side of the stem as expected, but swings into the minor groove. (iv) At the 5'-3' loop-stem junction a stacking discontinuity occurs as a consequence of a sharp turn in that part of the backbone, caused by the unusual β + and γ t torsion angles in residue dG(6). (v) The A base slides over the 5' side of the stem to stack upon the a C(3) residue at the 3' side of the stem in an antiparallel fashion. On the basis of J couplings and a set approximate proton-proton distances from NOE cross peaks, a model for the hairpin was constructed

  5. Neutrons for Catalysis: A Workshop on Neutron Scattering Techniques for Studies in Catalysis

    International Nuclear Information System (INIS)

    Overbury, Steven H.; Coates, Leighton; Herwig, Kenneth W.; Kidder, Michelle

    2011-01-01

    This report summarizes the Workshop on Neutron Scattering Techniques for Studies in Catalysis, held at the Spallation Neutron Source (SNS) at Oak Ridge National Laboratory (ORNL) on September 16 and 17, 2010. The goal of the Workshop was to bring experts in heterogeneous catalysis and biocatalysis together with neutron scattering experimenters to identify ways to attack new problems, especially Grand Challenge problems in catalysis, using neutron scattering. The Workshop locale was motivated by the neutron capabilities at ORNL, including the High Flux Isotope Reactor (HFIR) and the new and developing instrumentation at the SNS. Approximately 90 researchers met for 1 1/2 days with oral presentations and breakout sessions. Oral presentations were divided into five topical sessions aimed at a discussion of Grand Challenge problems in catalysis, dynamics studies, structure characterization, biocatalysis, and computational methods. Eleven internationally known invited experts spoke in these sessions. The Workshop was intended both to educate catalyst experts about the methods and possibilities of neutron methods and to educate the neutron community about the methods and scientific challenges in catalysis. Above all, it was intended to inspire new research ideas among the attendees. All attendees were asked to participate in one or more of three breakout sessions to share ideas and propose new experiments that could be performed using the ORNL neutron facilities. The Workshop was expected to lead to proposals for beam time at either the HFIR or the SNS; therefore, it was expected that each breakout session would identify a few experiments or proof-of-principle experiments and a leader who would pursue a proposal after the Workshop. Also, a refereed review article will be submitted to a prominent journal to present research and ideas illustrating the benefits and possibilities of neutron methods for catalysis research.

  6. Neutrons for Catalysis: A Workshop on Neutron Scattering Techniques for Studies in Catalysis

    Energy Technology Data Exchange (ETDEWEB)

    Overbury, Steven {Steve} H [ORNL; Coates, Leighton [ORNL; Herwig, Kenneth W [ORNL; Kidder, Michelle [ORNL

    2011-10-01

    This report summarizes the Workshop on Neutron Scattering Techniques for Studies in Catalysis, held at the Spallation Neutron Source (SNS) at Oak Ridge National Laboratory (ORNL) on September 16 and 17, 2010. The goal of the Workshop was to bring experts in heterogeneous catalysis and biocatalysis together with neutron scattering experimenters to identify ways to attack new problems, especially Grand Challenge problems in catalysis, using neutron scattering. The Workshop locale was motivated by the neutron capabilities at ORNL, including the High Flux Isotope Reactor (HFIR) and the new and developing instrumentation at the SNS. Approximately 90 researchers met for 1 1/2 days with oral presentations and breakout sessions. Oral presentations were divided into five topical sessions aimed at a discussion of Grand Challenge problems in catalysis, dynamics studies, structure characterization, biocatalysis, and computational methods. Eleven internationally known invited experts spoke in these sessions. The Workshop was intended both to educate catalyst experts about the methods and possibilities of neutron methods and to educate the neutron community about the methods and scientific challenges in catalysis. Above all, it was intended to inspire new research ideas among the attendees. All attendees were asked to participate in one or more of three breakout sessions to share ideas and propose new experiments that could be performed using the ORNL neutron facilities. The Workshop was expected to lead to proposals for beam time at either the HFIR or the SNS; therefore, it was expected that each breakout session would identify a few experiments or proof-of-principle experiments and a leader who would pursue a proposal after the Workshop. Also, a refereed review article will be submitted to a prominent journal to present research and ideas illustrating the benefits and possibilities of neutron methods for catalysis research.

  7. Controllable Catalysis with Nanoparticles: Bimetallic Alloy Systems and Surface Adsorbates

    KAUST Repository

    Chen, Tianyou

    2016-05-16

    Transition metal nanoparticles are privileged materials in catalysis due to their high specific surface areas and abundance of active catalytic sites. While many of these catalysts are quite useful, we are only beginning to understand the underlying catalytic mechanisms. Opening the “black box” of nanoparticle catalysis is essential to achieve the ultimate goal of catalysis by design. In this Perspective we highlight recent work addressing the topic of controlled catalysis with bimetallic alloy and “designer” adsorbate-stabilized metal nanoparticles.

  8. Controllable Catalysis with Nanoparticles: Bimetallic Alloy Systems and Surface Adsorbates

    KAUST Repository

    Chen, Tianyou; Rodionov, Valentin

    2016-01-01

    Transition metal nanoparticles are privileged materials in catalysis due to their high specific surface areas and abundance of active catalytic sites. While many of these catalysts are quite useful, we are only beginning to understand the underlying catalytic mechanisms. Opening the “black box” of nanoparticle catalysis is essential to achieve the ultimate goal of catalysis by design. In this Perspective we highlight recent work addressing the topic of controlled catalysis with bimetallic alloy and “designer” adsorbate-stabilized metal nanoparticles.

  9. The PS1 hairpin of Mcm3 is essential for viability and for DNA unwinding in vitro.

    Directory of Open Access Journals (Sweden)

    Simon K W Lam

    Full Text Available The pre-sensor 1 (PS1 hairpin is found in ring-shaped helicases of the AAA+ family (ATPases associated with a variety of cellular activities of proteins and is implicated in DNA translocation during DNA unwinding of archaeal mini-chromosome maintenance (MCM and superfamily 3 viral replicative helicases. To determine whether the PS1 hairpin is required for the function of the eukaryotic replicative helicase, Mcm2-7 (also comprised of AAA+ proteins, we mutated the conserved lysine residue in the putative PS1 hairpin motif in each of the Saccharomyces cerevisiae Mcm2-7 subunits to alanine. Interestingly, only the PS1 hairpin of Mcm3 was essential for viability. While mutation of the PS1 hairpin in the remaining MCM subunits resulted in minimal phenotypes, with the exception of Mcm7 which showed slow growth under all conditions examined, the viable alleles were synthetic lethal with each other. Reconstituted Mcm2-7 containing Mcm3 with the PS1 mutation (Mcm3(K499A had severely decreased helicase activity. The lack of helicase activity provides a probable explanation for the inviability of the mcm3(K499A strain. The ATPase activity of Mcm2-7(3K499A was similar to the wild type complex, but its interaction with single-stranded DNA in an electrophoretic mobility shift assay and its associations in cells were subtly altered. Together, these findings indicate that the PS1 hairpins in the Mcm2-7 subunits have important and distinct functions, most evident by the essential nature of the Mcm3 PS1 hairpin in DNA unwinding.

  10. Fluorescence-based characterization of genetically encoded peptides that fold in live cells: progress toward a generic hairpin scaffold

    Science.gov (United States)

    Cheng, Zihao; Campbell, Robert E.

    2007-02-01

    Binding proteins suitable for expression and high affinity molecular recognition in the cytoplasm or nucleus of live cells have numerous applications in the biological sciences. In an effort to add a new minimal motif to the growing repertoire of validated non-immunoglobulin binding proteins, we have undertaken the development of a generic protein scaffold based on a single β-hairpin that can fold efficiently in the cytoplasm. We have developed a method, based on the measurement of fluorescence resonance energy transfer (FRET) between a genetically fused cyan fluorescent protein (CFP) and yellow fluorescent protein (YFP), that allows the structural stability of recombinant β-hairpin peptides to be rapidly assessed both in vitro and in vivo. We have previously reported the validation of this method when applied to a 16mer tryptophan zipper β-hairpin. We now describe the use of this method to evaluate the potential of a designed 20mer β-hairpin peptide with a 3rd Trp/Trp cross-strand pair to function as a generic protein scaffold. Quantitative analysis of the FRET efficiency, resistance to proteolysis (assayed by loss of FRET), and circular dichroism spectra revealed that the 20mer peptide is significantly more tolerant of destabilizing mutations than the 16mer peptide. Furthermore, we experimentally demonstrate that the in vitro determined β-hairpin stabilities are well correlated with in vivo β-hairpin stabilities as determined by FRET measurements of colonies of live bacteria expressing the recombinant peptides flanked by CFP and YFP. Finally, we report on our progress to develop highly folded 24mer and 28mer β-hairpin peptides through the use of fluorescence-based library screening.

  11. Surface Science Foundations of Catalysis and Nanoscience

    CERN Document Server

    Kolasinski, Kurt K

    2012-01-01

    Surface science has evolved from being a sub-field of chemistry or physics, and has now established itself as an interdisciplinary topic. Knowledge has developed sufficiently that we can now understand catalysis from a surface science perspective. No-where is the underpinning nature of surface science better illustrated than with nanoscience. Now in its third edition, this successful textbook aims to provide students with an understanding of chemical transformations and the formation of structures at surfaces. The chapters build from simple to more advanced principles with each featuring exerc

  12. Catalysis-enhanced strengthening of porous materials

    International Nuclear Information System (INIS)

    Sokolova, L.N.; Shchukin, E.D.; Burenkova, L.N.; Romanovskij, B.V.

    2000-01-01

    Change in the strength of compressed tablets of the catalyst on the basis of ZrO 2 (84 mass %) and Y 2 O 3 (16 mass %) after conducting the endothermal reaction of the methanol and ethanol dehydration at 700-800 deg C is studied. It is shown, that the key factor, determining the strengthening effect by 65-88% is not at all the reaction exothermal nature, which could lead to local heating of the catalyst surface. In reality significant increase in concentration of surface defects, as compared to the equilibrium at the given temperature is achieved on the account of conjugation of processes of catalysis and surface defects formation [ru

  13. Catalysis in electrochemistry: from fundamentals to strategies for fuel cell development

    National Research Council Canada - National Science Library

    Santos, Elizabeth; Schmickler, Wolfgang

    2011-01-01

    "Catalysis in Electrochemistry: From Fundamentals to Strategies for Fuel Cell Development is a modern, comprehensive reference work on catalysis in electrochemistry, including principles, methods, strategies, and applications...

  14. The nature of the active site in heterogeneous metal catalysis

    DEFF Research Database (Denmark)

    Nørskov, Jens Kehlet; Bligaard, Thomas; Larsen, Britt Hvolbæk

    2008-01-01

    This tutorial review, of relevance for the surface science and heterogeneous catalysis communities, provides a molecular-level discussion of the nature of the active sites in metal catalysis. Fundamental concepts such as "Bronsted-Evans-Polanyi relations'' and "volcano curves'' are introduced...

  15. UV Catalysis, Cyanotype Photography, and Sunscreens

    Science.gov (United States)

    Lawrence, Glen D.; Fishelson, Stuart

    1999-09-01

    This laboratory experiment is intended for a chemistry course for non-science majors. The experiment utilizes one of the earliest photographic processes, the cyanotype process, to demonstrate UV catalysis of chemical reactions. In addition to making photographic prints from negatives, the process can be used to test the effectiveness of sunscreens and the relative efficacy of the SPF (sun protection factor) rating of sunscreens. This is an inexpensive process, requiring solutions of ammonium ferric citrate and potassium ferricyanide, with options to use hydrogen peroxide and ammonium hydroxide solutions. Students can prepare their own UV-sensitized paper with the indicated chemicals and watch the photographic image appear as it is exposed to sunlight or fluorescent UV lamps in a light box designed for use in this experiment. The laboratory experiment should stimulate discussion of UV catalysis, photographic processes and photochemistry, sunscreens, and UV damage to biological organisms. The chemicals used are relatively nontoxic, and the procedure is simple enough to be used by groups of diverse ages and abilities.

  16. Liquid crystal polymers: evidence of hairpin defects in nematic main chains, comparison with side chain polymers

    Science.gov (United States)

    Li, M. H.; Brûlet, A.; Keller, P.; Cotton, J. P.

    1996-09-01

    This article describes the conformation of two species of liquid crystalline polymers as revealed by small angle neutron scattering. The results obtained with side chain polymers are recalled. The procedure used to analyze the scattering data of main chains in the nematic phase is reported in this paper. It permits a demonstration of the existence of hairpins. Comparison of both polymer species shows that in the isotropic phase, the two polymers adopt a random coil conformation. In the nematic phase, the conformations are very different; the side chains behave as a melt of penetrable random coils whereas the main chains behave as a nematic phase of non penetrable cylinders.

  17. Effect of secondary structure on the thermodynamics and kinetics of PNA hybridization to DNA hairpins

    DEFF Research Database (Denmark)

    Kushon, S A; Jordan, J P; Seifert, J L

    2001-01-01

    The binding of a series of PNA and DNA probes to a group of unusually stable DNA hairpins of the tetraloop motif has been observed using absorbance hypochromicity (ABS), circular dichroism (CD), and a colorimetric assay for PNA/DNA duplex detection. These results indicate that both stable PNA...... structures in both target and probe molecules are shown to depress the melting temperatures and free energies of the probe-target duplexes. Kinetic analysis of hybridization yields reaction rates that are up to 160-fold slower than hybridization between two unstructured strands. The thermodynamic and kinetic...

  18. Non-Covalent Fluorescent Labeling of Hairpin DNA Probe Coupled with Hybridization Chain Reaction for Sensitive DNA Detection.

    Science.gov (United States)

    Song, Luna; Zhang, Yonghua; Li, Junling; Gao, Qiang; Qi, Honglan; Zhang, Chengxiao

    2016-04-01

    An enzyme-free signal amplification-based assay for DNA detection was developed using fluorescent hairpin DNA probes coupled with hybridization chain reaction (HCR). The hairpin DNAs were designed to contain abasic sites in the stem moiety. Non-covalent labeling of the hairpin DNAs was achieved when a fluorescent ligand was bound to the abasic sites through hydrogen bonding with the orphan cytosine present on the complementary strand, accompanied by quench of ligand fluorescence. As a result, the resultant probes, the complex formed between the hairpin DNA and ligand, showed almost no fluorescence. Upon hybridization with target DNA, the probe underwent a dehybridization of the stem moiety containing an abasic site. The release of ligand from the abasic site to the solution resulted in an effective fluorescent enhancement, which can be used as a signal. Compared with a sensing system without HCR, a 20-fold increase in the sensitivity was achieved using the sensing system with HCR. The fluorescent intensity of the sensing system increased with the increase in target DNA concentration from 0.5 nM to 100 nM. A single mismatched target ss-DNA could be effectively discriminated from complementary target DNA. Genotyping of a G/C single-nucleotide polymorphism of polymerase chain reaction (PCR) products was successfully demonstrated with the sensing system. Therefore, integrating HCR strategy with non-covalent labeling of fluorescent hairpin DNA probes provides a sensitive and cost-effective DNA assay. © The Author(s) 2016.

  19. A regenerative electrochemical biosensor for mercury(II) by using the insertion approach and dual-hairpin-based amplification

    International Nuclear Information System (INIS)

    Jia, Jing; Ling, Yu; Gao, Zhong Feng; Lei, Jing Lei; Luo, Hong Qun; Li, Nian Bing

    2015-01-01

    Highlights: • The dual-hairpin structure as a signal amplifier is label-free and handy. • The strategy uses the insertion approach to improve the hybridization efficiency. • This biosensor has a low detection limit (28 pM) for detection of Hg 2+ . • This biosensor can be easily regenerated by using L-cysteine. - Abstract: A simple and effective biosensor for Hg 2+ determination was investigated. The novel biosensor was prepared by the insertion approach that the moiety-labeled DNA inserted into a loosely packed cyclic-dithiothreitol (DTT) monolayer, improving the hybridization efficiency. Electrochemical impedance spectroscopy studies of two biosensors (single-hairpin and dual-hairpin structure DNA modified electrodes) used for Hg 2+ detection indicated that the dual-hairpin modified electrode had a larger electron transfer resistance change (ΔR ct ). Consequently, the dual-hairpin structure was used as a signal amplifier for the preparation of a selective Hg 2+ biosensor. This biosensor exhibited an excellent selectivity toward Hg 2+ over Cd 2+ , Pd 2+ , Co 2+ etc. Also, a linear relation was observed between the ΔR ct and Hg 2+ concentrations in a range from 0.1 nM to 5 μM with a detection limit of 28 pM under optimum conditions. Moreover, the biosensor can be reused by using L-cysteine and successfully applied for detecting Hg 2+ in real samples

  20. Identification of a key structural element for protein folding within beta-hairpin turns.

    Science.gov (United States)

    Kim, Jaewon; Brych, Stephen R; Lee, Jihun; Logan, Timothy M; Blaber, Michael

    2003-05-09

    Specific residues in a polypeptide may be key contributors to the stability and foldability of the unique native structure. Identification and prediction of such residues is, therefore, an important area of investigation in solving the protein folding problem. Atypical main-chain conformations can help identify strains within a folded protein, and by inference, positions where unique amino acids may have a naturally high frequency of occurrence due to favorable contributions to stability and folding. Non-Gly residues located near the left-handed alpha-helical region (L-alpha) of the Ramachandran plot are a potential indicator of structural strain. Although many investigators have studied mutations at such positions, no consistent energetic or kinetic contributions to stability or folding have been elucidated. Here we report a study of the effects of Gly, Ala and Asn substitutions found within the L-alpha region at a characteristic position in defined beta-hairpin turns within human acidic fibroblast growth factor, and demonstrate consistent effects upon stability and folding kinetics. The thermodynamic and kinetic data are compared to available data for similar mutations in other proteins, with excellent agreement. The results have identified that Gly at the i+3 position within a subset of beta-hairpin turns is a key contributor towards increasing the rate of folding to the native state of the polypeptide while leaving the rate of unfolding largely unchanged.

  1. β-Hairpin of Islet Amyloid Polypeptide Bound to an Aggregation Inhibitor

    Science.gov (United States)

    Mirecka, Ewa A.; Feuerstein, Sophie; Gremer, Lothar; Schröder, Gunnar F.; Stoldt, Matthias; Willbold, Dieter; Hoyer, Wolfgang

    2016-01-01

    In type 2 diabetes, the formation of islet amyloid consisting of islet amyloid polypeptide (IAPP) is associated with reduction in β-cell mass and contributes to the failure of islet cell transplantation. Rational design of inhibitors of IAPP amyloid formation has therapeutic potential, but is hampered by the lack of structural information on inhibitor complexes of the conformationally flexible, aggregation-prone IAPP. Here we characterize a β-hairpin conformation of IAPP in complex with the engineered binding protein β-wrapin HI18. The β-strands correspond to two amyloidogenic motifs, 12-LANFLVH-18 and 22-NFGAILS-28, which are connected by a turn established around Ser-20. Besides backbone hydrogen bonding, the IAPP:HI18 interaction surface is dominated by non-polar contacts involving hydrophobic side chains of the IAPP β-strands. Apart from monomers, HI18 binds oligomers and fibrils and inhibits IAPP aggregation and toxicity at low substoichiometric concentrations. The IAPP β-hairpin can serve as a molecular recognition motif enabling control of IAPP aggregation. PMID:27641459

  2. New and future developments in catalysis catalysis for remediation and environmental concerns

    CERN Document Server

    Suib, Steven L

    2013-01-01

    New and Future Developments in Catalysis is a package of seven books that compile the latest ideas concerning alternate and renewable energy sources and the role that catalysis plays in converting new renewable feedstock into biofuels and biochemicals. Both homogeneous and heterogeneous catalysts and catalytic processes will be discussed in a unified and comprehensive approach. There will be extensive cross-referencing within all volumes. The various sources of environmental pollution are the theme of this volume. The volume lists all current environmentally friendly catalytic chemical processes used for environmental remediation and critically compares their economic viability. Offers in-depth coverage of all catalytic topics of current interest and outlines future challenges and research areas A clear and visual description of all parameters and conditions, enabling the reader to draw conclusions for a particular case Outlines the catalytic processes applicable to energy generation and design of green proce...

  3. Transient β-hairpin formation in α-synuclein monomer revealed by coarse-grained molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Hang; Ma, Wen [Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (United States); Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (United States); Han, Wei [Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (United States); Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (United States); Schulten, Klaus, E-mail: kschulte@ks.uiuc.edu [Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (United States); Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (United States); Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (United States)

    2015-12-28

    Parkinson’s disease, originating from the intrinsically disordered peptide α-synuclein, is a common neurodegenerative disorder that affects more than 5% of the population above age 85. It remains unclear how α-synuclein monomers undergo conformational changes leading to aggregation and formation of fibrils characteristic for the disease. In the present study, we perform molecular dynamics simulations (over 180 μs in aggregated time) using a hybrid-resolution model, Proteins with Atomic details in Coarse-grained Environment (PACE), to characterize in atomic detail structural ensembles of wild type and mutant monomeric α-synuclein in aqueous solution. The simulations reproduce structural properties of α-synuclein characterized in experiments, such as secondary structure content, long-range contacts, chemical shifts, and {sup 3}J(H{sub N}H{sub C{sub α}})-coupling constants. Most notably, the simulations reveal that a short fragment encompassing region 38-53, adjacent to the non-amyloid-β component region, exhibits a high probability of forming a β-hairpin; this fragment, when isolated from the remainder of α-synuclein, fluctuates frequently into its β-hairpin conformation. Two disease-prone mutations, namely, A30P and A53T, significantly accelerate the formation of a β-hairpin in the stated fragment. We conclude that the formation of a β-hairpin in region 38-53 is a key event during α-synuclein aggregation. We predict further that the G47V mutation impedes the formation of a turn in the β-hairpin and slows down β-hairpin formation, thereby retarding α-synuclein aggregation.

  4. Structural and dynamic characterization of the upper part of the HIV-1 cTAR DNA hairpin

    OpenAIRE

    Zargarian, Loussin?; Kanevsky, Igor; Bazzi, Ali; Boynard, Jonathan; Chaminade, Fran?oise; Foss?, Philippe; Mauffret, Olivier

    2009-01-01

    First strand transfer is essential for HIV-1 reverse transcription. During this step, the TAR RNA hairpin anneals to the cTAR DNA hairpin; this annealing reaction is promoted by the nucleocapsid protein and involves an initial loop?loop interaction between the apical loops of TAR and cTAR. Using NMR and probing methods, we investigated the structural and dynamic properties of the top half of the cTAR DNA (mini-cTAR). We show that the upper stem located between the apical and the internal loop...

  5. Microbial electro-catalysis in fuel cell

    International Nuclear Information System (INIS)

    Dumas, Claire

    2007-01-01

    Microbial fuel cells (MFC) are devices that ensure the direct conversion of organic matter into electricity using bacterial bio-films as the catalysts of the electrochemical reactions. This study aims at improving the comprehension of the mechanisms involved in electron transfer pathways between the adhered bacteria and the electrodes. This optimization of the MFC power output could be done, for example, in exploring and characterizing various electrode materials. The electrolysis experiments carried out on Geobacter sulfurreducens deal with the microbial catalysis of the acetate oxidation, on the one hand, and the catalysis of the fumarate reduction on the other hand. On the anodic side, differences in current densities appeared on graphite, DSA R and stainless steel (8 A/m 2 , 5 A/m 2 and 0.7 A/m 2 respectively). These variations were explained more by materials roughness differences rather than their nature. Impedance spectroscopy study shows that the electro-active bio-film developed on stainless steel does not seem to modify the evolution of the stainless steel oxide layer, only the imposed potential remains determining. On the cathodic side, stainless steel sustained current densities more than twenty times higher than those obtained with graphite electrodes. The adhesion study of G. sulfurreducens on various materials in a flow cell, suggests that the bio-films resist to the hydrodynamic constraints and are not detached under a shear stress threshold value. The installation of two MFC prototypes, one in a sea station and the other directly in Genoa harbour (Italy) confirms some results obtained in laboratory and were promising for a MFC scale-up. (author) [fr

  6. Prebiotic RNA Synthesis by Montmorillonite Catalysis

    Directory of Open Access Journals (Sweden)

    Sohan Jheeta

    2014-08-01

    Full Text Available This review summarizes our recent findings on the role of mineral salts in prebiotic RNA synthesis, which is catalyzed by montmorillonite clay minerals. The clay minerals not only catalyze the synthesis of RNA but also facilitate homochiral selection. Preliminary data of these findings have been presented at the “Horizontal Gene Transfer and the Last Universal Common Ancestor (LUCA” conference at the Open University, Milton Keynes, UK, 5–6 September 2013. The objective of this meeting was to recognize the significance of RNA in LUCA. We believe that the prebiotic RNA synthesis from its monomers must have been a simple process. As a first step, it may have required activation of the 5'-end of the mononucleotide with a leaving group, e.g., imidazole in our model reaction (Figure 1. Wide ranges of activating groups are produced from HCN under plausible prebiotic Earth conditions. The final step is clay mineral catalysis in the presence of mineral salts to facilitate selective production of functional RNA. Both the clay minerals and mineral salts would have been abundant on early Earth. We have demonstrated that while montmorillonite (pH 7 produced only dimers from its monomers in water, addition of sodium chloride (1 M enhanced the chain length multifold, as detected by HPLC. The effect of monovalent cations on RNA synthesis was of the following order: Li+ > Na+ > K+. A similar effect was observed with the anions, enhancing catalysis in the following order: Cl− > Br− > I−. The montmorillonite-catalyzed RNA synthesis was not affected by hydrophobic or hydrophilic interactions. We thus show that prebiotic synthesis of RNA from its monomers was a simple process requiring only clay minerals and a small amount of salt.

  7. Density functional theory studies of transition metal nanoparticles in catalysis

    DEFF Research Database (Denmark)

    Greeley, Jeffrey Philip; Rankin, Rees; Zeng, Zhenhua

    2013-01-01

    Periodic Density Functional Theory calculations are capable of providing powerful insights into the structural, energetics, and electronic phenomena that underlie heterogeneous catalysis on transition metal nanoparticles. Such calculations are now routinely applied to single crystal metal surfaces...... and to subnanometer metal clusters. Descriptions of catalysis on truly nanosized structures, however, are generally not as well developed. In this talk, I will illustrate different approaches to analyzing nanocatalytic phenomena with DFT calculations. I will describe case studies from heterogeneous catalysis...... and electrocatalysis, in which single crystal models are combined with Wulff construction-based ideas to produce descriptions of average nanocatalyst behavior. Then, I will proceed to describe explicitly DFT-based descriptions of catalysis on truly nanosized particles (

  8. Bridging heterogeneous and homogeneous catalysis concepts, strategies, and applications

    CERN Document Server

    Li, Can

    2014-01-01

    This unique handbook fills the gap in the market for an up-to-date work that links both homogeneous catalysis applied to organic reactions and catalytic reactions on surfaces of heterogeneous catalysts.

  9. Nanostructured Membranes for Green Synthesis of Nanoparticles and Enzyme Catalysis

    Science.gov (United States)

    Macroporous membranes functionalized with ionizable macromolecules provide promising applications in toxic metal capture at high capacity, nanoparticle synthesis, and catalysis. Our low‐pressure membrane approach is marked by reaction and separation selectivity and their tunabili...

  10. Nanostructured Membranes for Enzyme Catalysis and Green Synthesis of Nanoparticles

    Science.gov (United States)

    Macroporous membranes functionalized with ionizable macromolecules provide promising applications in toxic metal capture at high capacity, nanoparticle synthesis, and catalysis. Our low-pressure membrane approach is marked by reaction and separation selectivity and their tunabil...

  11. Catalysis by metallic nanoparticles in solution: Thermosensitive microgels as nanoreactors

    OpenAIRE

    Roa, Rafael; Angioletti-Uberti, Stefano; Lu, Yan; Dzubiella, Joachim; Piazza, Francesco; Ballauff, Matthias

    2018-01-01

    Metallic nanoparticles have been used as catalysts for various reactions, and the huge literature on the subject is hard to overlook. In many applications, the nanoparticles must be affixed to a colloidal carrier for easy handling during catalysis. These "passive carriers" (e.g., dendrimers) serve for a controlled synthesis of the nanoparticles and prevent coagulation during catalysis. Recently, hybrids from nanoparticles and polymers have been developed that allow us to change the catalytic ...

  12. 3. International conference on catalysis in membrane reactors

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1998-09-01

    The 3. International Conference on Catalysis in Membrane Reactors, Copenhagen, Denmark, is a continuation of the previous conferences held in Villeurbanne 1994 and Moscow 1996 and will deal with the rapid developments taking place within membranes with emphasis on membrane catalysis. The approx. 80 contributions in form of plenary lectures and posters discuss hydrogen production, methane reforming into syngas, selectivity and specificity of various membranes etc. The conference is organised by the Danish Catalytic Society under the Danish Society for Chemical Engineering. (EG)

  13. Melting of a beta-Hairpin Peptide Using Isotope-Edited 2D IR Spectroscopy and Simulations

    NARCIS (Netherlands)

    Smith, Adam W.; Lessing, Joshua; Ganim, Ziad; Peng, Chunte Sam; Tokmakoff, Andrei; Roy, Santanu; Jansen, Thomas L. C.; Knoester, Jasper

    2010-01-01

    Isotope-edited two-dimensional infrared spectroscopy has been used! to characterize the conformational heterogeneity of the beta-hairpin peptide TrpZip2 (17.2) across its thermal unfolding transition Four isotopologues were synthesized to probe hydrogen bonding and solvent exposure of the beta-turn

  14. Melting of a beta-hairpin peptide using isotope-edited 2D IR spectroscopy and simulations.

    NARCIS (Netherlands)

    Smith, A.W.; Lessing, J.; Ganim, Z.; Peng, C.S.; Tokmakoff, A.; Roy, S.; Jansen, T.L.Th.A.; Knoester, J.

    2010-01-01

    Isotope-edited two-dimensional infrared spectroscopy has been used to characterize the conformational heterogeneity of the beta-hairpin peptide TrpZip2 (TZ2) across its thermal unfolding transition. Four isotopologues were synthesized to probe hydrogen bonding and solvent exposure of the beta-turn

  15. One-step isothermal detection of multiple KRAS mutations by forming SNP specific hairpins on a gold nanoshell.

    Science.gov (United States)

    Chung, Chan Ho; Kim, Joong Hyun

    2018-04-24

    We developed a one-step isothermal method for typing multiple KRAS mutations using a designed set of primers to form a hairpin on a gold nanoshell upon being ligated by a SNP specific DNA ligase after binding of targets. As a result, we could detect as low as 20 attomoles of KRAS mutations within 1 h.

  16. Detection of innersphere interactions between magnesium hydrate and the phosphate backbone of the HDV ribozyme using Raman crystallography.

    Science.gov (United States)

    Gong, Bo; Chen, Yuanyuan; Christian, Eric L; Chen, Jui-Hui; Chase, Elaine; Chadalavada, Durga M; Yajima, Rieko; Golden, Barbara L; Bevilacqua, Philip C; Carey, Paul R

    2008-07-30

    A Raman microscope and Raman difference spectroscopy are used to detect the vibrational signature of RNA-bound magnesium hydrate in crystals of hepatitis delta virus (HDV) ribozyme and to follow the effects of magnesium hydrate binding to the nonbridging phosphate oxygens in the phosphodiester backbone. There is a correlation between the Raman intensity of the innersphere magnesium hydrate signature peak, near 322 cm-1, and the intensity of the PO2- symmetric stretch, near 1100 cm-1, perturbed by magnesium binding, demonstrating direct observation of -PO2-...Mg2+(H2O)x innersphere complexes. The complexes may be pentahydrates (x = 5) and tetrahydrates (x = 4). The assignment of the Raman feature near 322 cm-1 to a magnesium hydrate species is confirmed by isotope shifts observed in D2O and H218O that are semiquantitatively reproduced by calculations. The standardized intensity changes in the 1100 cm-1 PO2- feature seen upon magnesium hydrate binding indicates that there are approximately 5 innersphere Mg2+...-O2P contacts per HDV molecule when the crystal is exposed to a solution containing 20 mM magnesium.

  17. RNA polymerase II mediated transcription from the polymerase III promoters in short hairpin RNA expression vector

    International Nuclear Information System (INIS)

    Rumi, Mohammad; Ishihara, Shunji; Aziz, Monowar; Kazumori, Hideaki; Ishimura, Norihisa; Yuki, Takafumi; Kadota, Chikara; Kadowaki, Yasunori; Kinoshita, Yoshikazu

    2006-01-01

    RNA polymerase III promoters of human ribonuclease P RNA component H1, human U6, and mouse U6 small nuclear RNA genes are commonly used in short hairpin RNA (shRNA) expression vectors due their precise initiation and termination sites. During transient transfection of shRNA vectors, we observed that H1 or U6 promoters also express longer transcripts enough to express several reporter genes including firefly luciferase, green fluorescent protein EGFP, and red fluorescent protein JRed. Expression of such longer transcripts was augmented by upstream RNA polymerase II enhancers and completely inhibited by downstream polyA signal sequences. Moreover, the transcription of firefly luciferase from human H1 promoter was sensitive to RNA polymerase II inhibitor α-amanitin. Our findings suggest that commonly used polymerase III promoters in shRNA vectors are also prone to RNA polymerase II mediated transcription, which may have negative impacts on their targeted use

  18. Detection of DNA damage by using hairpin molecular beacon probes and graphene oxide.

    Science.gov (United States)

    Zhou, Jie; Lu, Qian; Tong, Ying; Wei, Wei; Liu, Songqin

    2012-09-15

    A hairpin molecular beacon tagged with carboxyfluorescein in combination with graphene oxide as a quencher reagent was used to detect the DNA damage by chemical reagents. The fluorescence of molecular beacon was quenched sharply by graphene oxide; while in the presence of its complementary DNA the quenching efficiency decreased because their hybridization prevented the strong adsorbability of molecular beacon on graphene oxide. If the complementary DNA was damaged by a chemical reagent and could not form intact duplex structure with molecular beacon, more molecular beacon would adsorb on graphene oxide increasing the quenching efficiency. Thus, damaged DNA could be detected based on different quenching efficiencies afforded by damaged and intact complementary DNA. The damage effects of chlorpyrifos-methyl and three metabolites of styrene such as mandelieaeids, phenylglyoxylieaeids and epoxystyrene on DNA were studied as models. The method for detection of DNA damage was reliable, rapid and simple compared to the biological methods. Copyright © 2012 Elsevier B.V. All rights reserved.

  19. Synthetic, structural mimetics of the β-hairpin flap of HIV-1 protease inhibit enzyme function.

    Science.gov (United States)

    Chauhan, Jay; Chen, Shen-En; Fenstermacher, Katherine J; Naser-Tavakolian, Aurash; Reingewertz, Tali; Salmo, Rosene; Lee, Christian; Williams, Emori; Raje, Mithun; Sundberg, Eric; DeStefano, Jeffrey J; Freire, Ernesto; Fletcher, Steven

    2015-11-01

    Small-molecule mimetics of the β-hairpin flap of HIV-1 protease (HIV-1 PR) were designed based on a 1,4-benzodiazepine scaffold as a strategy to interfere with the flap-flap protein-protein interaction, which functions as a gated mechanism to control access to the active site. Michaelis-Menten kinetics suggested our small-molecules are competitive inhibitors, which indicates the mode of inhibition is through binding the active site or sterically blocking access to the active site and preventing flap closure, as designed. More generally, a new bioactive scaffold for HIV-1PR inhibition has been discovered, with the most potent compound inhibiting the protease with a modest K(i) of 11 μM. Copyright © 2015 Elsevier Ltd. All rights reserved.

  20. Dedicated Beamline Facilities for Catalytic Research. Synchrotron Catalysis Consortium (SCC)

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Jingguang [Columbia Univ., New York, NY; Frenkel, Anatoly [Yeshiva Univ., New York, NY (United States); Rodriguez, Jose [Brookhaven National Lab. (BNL), Upton, NY (United States); Adzic, Radoslav [Brookhaven National Lab. (BNL), Upton, NY (United States); Bare, Simon R. [UOP LLC, Des Plaines, IL (United States); Hulbert, Steve L. [Brookhaven National Lab. (BNL), Upton, NY (United States); Karim, Ayman [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Mullins, David R. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Overbury, Steve [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2015-03-04

    Synchrotron spectroscopies offer unique advantages over conventional techniques, including higher detection sensitivity and molecular specificity, faster detection rate, and more in-depth information regarding the structural, electronic and catalytic properties under in-situ reaction conditions. Despite these advantages, synchrotron techniques are often underutilized or unexplored by the catalysis community due to various perceived and real barriers, which will be addressed in the current proposal. Since its establishment in 2005, the Synchrotron Catalysis Consortium (SCC) has coordinated significant efforts to promote the utilization of cutting-edge catalytic research under in-situ conditions. The purpose of the current renewal proposal is aimed to provide assistance, and to develop new sciences/techniques, for the catalysis community through the following concerted efforts: Coordinating the implementation of a suite of beamlines for catalysis studies at the new NSLS-II synchrotron source; Providing assistance and coordination for catalysis users at an SSRL catalysis beamline during the initial period of NSLS to NSLS II transition; Designing in-situ reactors for a variety of catalytic and electrocatalytic studies; Assisting experimental set-up and data analysis by a dedicated research scientist; Offering training courses and help sessions by the PIs and co-PIs.

  1. Short, multiple-stranded β-hairpin peptides have antimicrobial potency with high selectivity and salt resistance.

    Science.gov (United States)

    Chou, Shuli; Shao, Changxuan; Wang, Jiajun; Shan, Anshan; Xu, Lin; Dong, Na; Li, Zhongyu

    2016-01-01

    The β-hairpin structure has been proposed to exhibit potent antimicrobial properties with low cytotoxicity, thus, multiple β-hairpin structures have been proved to be highly stable in structures containing tightly packed hydrophobic cores. The aim of this study was to develop peptide-based synthetic strategies for generating short, but effective AMPs as inexpensive antimicrobial agents. Multiple-stranded β-hairpin peptides with the same β-hairpin unit, (WRXxRW)n where n=1, 2, 3, or 4 and Xx represent the turn sequence, were synthesized, and their potential as antimicrobial agents was evaluated. Owning to the tightly packed hydrophobic core and paired Trp of this multiple-stranded β-hairpin structure, all the 12-residues peptides exhibited high cell selectivity towards bacterial cells over human red blood cells (hRBCs), and the peptide W2 exhibited stronger antimicrobial activities with the MIC values of 2-8μM against various tested bacteria. Not only that, but W2 also showed obvious synergy with streptomycin and chloramphenicol against Escherichia coli, and displayed synergy with ciprofloxacin against Staphylococcus aureus with the FICI values ⩽0.5. Fluorescence spectroscopy and electron microscopy analyses indicated that W2 kills microbial cells by permeabilizing the cell membrane and damaging membrane integrity. Collectively, based on the multiple β-hairpin peptides, the ability to develop libraries of short and effective peptides will be a powerful approach to the discovery of novel antimicrobial agents. We successfully screened a peptide W2 ((WRPGRW)2) from a series of multiple-stranded β-hairpin antimicrobial peptides based on the "S-shaped" motif that induced the formation of a globular structure, and Trp zipper was used to replace the disulfide bonds to reduce the cost of production. This novel structure applied to AMPs improved cell selectivity and salt stability. The findings of this study will promote the development of peptide

  2. Combinatorial pattern discovery approach for the folding trajectory analysis of a beta-hairpin.

    Directory of Open Access Journals (Sweden)

    Laxmi Parida

    2005-06-01

    Full Text Available The study of protein folding mechanisms continues to be one of the most challenging problems in computational biology. Currently, the protein folding mechanism is often characterized by calculating the free energy landscape versus various reaction coordinates, such as the fraction of native contacts, the radius of gyration, RMSD from the native structure, and so on. In this paper, we present a combinatorial pattern discovery approach toward understanding the global state changes during the folding process. This is a first step toward an unsupervised (and perhaps eventually automated approach toward identification of global states. The approach is based on computing biclusters (or patterned clusters-each cluster is a combination of various reaction coordinates, and its signature pattern facilitates the computation of the Z-score for the cluster. For this discovery process, we present an algorithm of time complexity c in RO((N + nm log n, where N is the size of the output patterns and (n x m is the size of the input with n time frames and m reaction coordinates. To date, this is the best time complexity for this problem. We next apply this to a beta-hairpin folding trajectory and demonstrate that this approach extracts crucial information about protein folding intermediate states and mechanism. We make three observations about the approach: (1 The method recovers states previously obtained by visually analyzing free energy surfaces. (2 It also succeeds in extracting meaningful patterns and structures that had been overlooked in previous works, which provides a better understanding of the folding mechanism of the beta-hairpin. These new patterns also interconnect various states in existing free energy surfaces versus different reaction coordinates. (3 The approach does not require calculating the free energy values, yet it offers an analysis comparable to, and sometimes better than, the methods that use free energy landscapes, thus validating the

  3. Combinatorial Pattern Discovery Approach for the Folding Trajectory Analysis of a beta-Hairpin.

    Directory of Open Access Journals (Sweden)

    2005-06-01

    Full Text Available The study of protein folding mechanisms continues to be one of the most challenging problems in computational biology. Currently, the protein folding mechanism is often characterized by calculating the free energy landscape versus various reaction coordinates, such as the fraction of native contacts, the radius of gyration, RMSD from the native structure, and so on. In this paper, we present a combinatorial pattern discovery approach toward understanding the global state changes during the folding process. This is a first step toward an unsupervised (and perhaps eventually automated approach toward identification of global states. The approach is based on computing biclusters (or patterned clusters-each cluster is a combination of various reaction coordinates, and its signature pattern facilitates the computation of the Z-score for the cluster. For this discovery process, we present an algorithm of time complexity cinRO((N + nm log n, where N is the size of the output patterns and (n x m is the size of the input with n time frames and m reaction coordinates. To date, this is the best time complexity for this problem. We next apply this to a beta-hairpin folding trajectory and demonstrate that this approach extracts crucial information about protein folding intermediate states and mechanism. We make three observations about the approach: (1 The method recovers states previously obtained by visually analyzing free energy surfaces. (2 It also succeeds in extracting meaningful patterns and structures that had been overlooked in previous works, which provides a better understanding of the folding mechanism of the beta-hairpin. These new patterns also interconnect various states in existing free energy surfaces versus different reaction coordinates. (3 The approach does not require calculating the free energy values, yet it offers an analysis comparable to, and sometimes better than, the methods that use free energy landscapes, thus validating the

  4. Water isotope effect on the thermostability of a polio viral RNA hairpin: A metadynamics study

    Science.gov (United States)

    Pathak, Arup K.; Bandyopadhyay, Tusar

    2017-04-01

    Oral polio vaccine is considered to be the most thermolabile of all the common childhood vaccines. Despite heavy water (D2O) having been known for a long time to stabilise attenuated viral RNA against thermodegradation, the molecular underpinnings of its mechanism of action are still lacking. Whereas, understanding the basis of D2O action is an important step that might reform the way other thermolabile drugs are stored and could possibly minimize the cold chain problem. Here using a combination of parallel tempering and well-tempered metadynamics simulation in light water (H2O) and in D2O, we have fully described the free energy surface associated with the folding/unfolding of a RNA hairpin containing a non-canonical basepair motif, which is conserved within the 3'-untranslated region of poliovirus-like enteroviruses. Simulations reveal that in heavy water (D2O) there is a considerable increase of the stability of the folded basin as monitored through an intramolecular hydrogen bond (HB), size, shape, and flexibility of RNA structures. This translates into a higher melting temperature in D2O by 41 K when compared with light water (H2O). We have explored the hydration dynamics of the RNA, hydration shell around the RNA surface, and spatial dependence of RNA-solvent collective HB dynamics in the two water systems. Simulation in heavy water clearly showed that D2O strengthens the HB network in the solvent, lengthens inter-residue water-bridge lifetime, and weakens dynamical coupling of the hairpin to its solvation environment, which enhances the rigidity of solvent exposed sites of the native configurations. The results might suggest that like other added osmoprotectants, D2O can act as a thermostabilizer when used as a solvent.

  5. Short Hairpin RNA (shRNA): Design, Delivery, and Assessment of Gene Knockdown

    Science.gov (United States)

    Moore, Chris B.; Guthrie, Elizabeth H.; Huang, Max Tze-Han; Taxman, Debra J.

    2013-01-01

    Shortly after the cellular mechanism of RNA interference (RNAi) was first described, scientists began using this powerful technique to study gene function. This included designing better methods for the successful delivery of small interfering RNAs (siRNAs) and short hairpin RNAs (shRNAs) into mammalian cells. While the simplest method for RNAi is the cytosolic delivery of siRNA oligonucleotides, this technique is limited to cells capable of transfection and is primarily utilized during transient in vitro studies. The introduction of shRNA into mammalian cells through infection with viral vectors allows for stable integration of shRNA and long-term knockdown of the targeted gene; however, several challenges exist with the implementation of this technology. Here we describe some well-tested protocols which should increase the chances of successful design, delivery, and assessment of gene knockdown by shRNA. We provide suggestions for designing shRNA targets and controls, a protocol for sequencing through the secondary structure of the shRNA hairpin structure, and protocols for packaging and delivery of shRNA lentiviral particles. Using real-time PCR and functional assays we demonstrate the successful knockdown of ASC, an inflammatory adaptor molecule. These studies demonstrate the practicality of including two shRNAs with different efficacies of knockdown to provide an additional level of control and to verify dose dependency of functional effects. Along with the methods described here, as new techniques and algorithms are designed in the future, shRNA is likely to include further promising application and continue to be a critical component of gene discovery. PMID:20387148

  6. Turn stability in beta-hairpin peptides: Investigation of peptides containing 3:5 type I G1 bulge turns.

    Science.gov (United States)

    Blandl, Tamas; Cochran, Andrea G; Skelton, Nicholas J

    2003-02-01

    The turn-forming ability of a series of three-residue sequences was investigated by substituting them into a well-characterized beta-hairpin peptide. The starting scaffold, bhpW, is a disulfide-cyclized 10-residue peptide that folds into a stable beta-hairpin with two antiparallel strands connected by a two-residue reverse turn. Substitution of the central two residues with the three-residue test sequences leads to less stable hairpins, as judged by thiol-disulfide equilibrium measurements. However, analysis of NMR parameters indicated that each molecule retains a significant folded population, and that the type of turn adopted by the three-residue sequence is the same in all cases. The solution structure of a selected peptide with a PDG turn contained an antiparallel beta-hairpin with a 3:5 type I + G1 bulge turn. Analysis of the energetic contributions of individual turn residues in the series of peptides indicates that substitution effects have significant context dependence, limiting the predictive power of individual amino acid propensities for turn formation. The most stable and least stable sequences were also substituted into a more stable disulfide-cyclized scaffold and a linear beta-hairpin scaffold. The relative stabilities remained the same, suggesting that experimental measurements in the bhpW context are a useful way to evaluate turn stability for use in protein design projects. Moreover, these scaffolds are capable of displaying a diverse set of turns, which can be exploited for the mimicry of protein loops or for generating libraries of reverse turns.

  7. A regenerative electrochemical biosensor for mercury(II) by using the insertion approach and dual-hairpin-based amplification

    Energy Technology Data Exchange (ETDEWEB)

    Jia, Jing; Ling, Yu; Gao, Zhong Feng [Key Laboratory of Eco-Environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715 (China); Lei, Jing Lei [College of Chemistry and Chemical Engineering, Chongqing University, Chongqing 400044 (China); Luo, Hong Qun, E-mail: luohq@swu.edu.cn [Key Laboratory of Eco-Environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715 (China); Li, Nian Bing, E-mail: linb@swu.edu.cn [Key Laboratory of Eco-Environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715 (China)

    2015-09-15

    Highlights: • The dual-hairpin structure as a signal amplifier is label-free and handy. • The strategy uses the insertion approach to improve the hybridization efficiency. • This biosensor has a low detection limit (28 pM) for detection of Hg{sup 2+}. • This biosensor can be easily regenerated by using L-cysteine. - Abstract: A simple and effective biosensor for Hg{sup 2+} determination was investigated. The novel biosensor was prepared by the insertion approach that the moiety-labeled DNA inserted into a loosely packed cyclic-dithiothreitol (DTT) monolayer, improving the hybridization efficiency. Electrochemical impedance spectroscopy studies of two biosensors (single-hairpin and dual-hairpin structure DNA modified electrodes) used for Hg{sup 2+} detection indicated that the dual-hairpin modified electrode had a larger electron transfer resistance change (ΔR{sub ct}). Consequently, the dual-hairpin structure was used as a signal amplifier for the preparation of a selective Hg{sup 2+} biosensor. This biosensor exhibited an excellent selectivity toward Hg{sup 2+} over Cd{sup 2+}, Pd{sup 2+}, Co{sup 2+} etc. Also, a linear relation was observed between the ΔR{sub ct} and Hg{sup 2+} concentrations in a range from 0.1 nM to 5 μM with a detection limit of 28 pM under optimum conditions. Moreover, the biosensor can be reused by using L-cysteine and successfully applied for detecting Hg{sup 2+} in real samples.

  8. Tandem rhodium catalysis: exploiting sulfoxides for asymmetric transition-metal catalysis.

    Science.gov (United States)

    Kou, K G M; Dong, V M

    2015-06-07

    Sulfoxides are uncommon substrates for transition-metal catalysis due to their propensity to inhibit catalyst turnover. In a collaborative effort with Ken Houk, we developed the first dynamic kinetic resolution (DKR) of allylic sulfoxides using asymmetric rhodium-catalyzed hydrogenation. A detailed mechanistic analysis of this transformation using both experimental and theoretical methods revealed rhodium to be a tandem catalyst that promoted both hydrogenation of the alkene and racemization of the allylic sulfoxide. Using a combination of deuterium labelling and DFT studies, a novel mode of allylic sulfoxide racemization via a Rh(III)-π-allyl intermediate was identified.

  9. Loop residues and catalysis in OMP synthase

    DEFF Research Database (Denmark)

    Wang, Gary P.; Hansen, Michael Riis; Grubmeyer, Charles

    2012-01-01

    binding of OMP or PRPP in binary complexes was affected little by loop mutation, suggesting that the energetics of ground-state binding have little contribution from the catalytic loop, or that a favorable binding energy is offset by costs of loop reorganization. Pre-steady-state kinetics for mutants...... values for all four substrate molecules. The 20% (i.e., 1.20) intrinsic [1?-3H]OMP kinetic isotope effect (KIE) for WT is masked because of high forward and reverse commitment factors. K103A failed to express intrinsic KIEs fully (1.095 ± 0.013). In contrast, H105A, which has a smaller catalytic lesion...... (preceding paper in this issue, DOI 10.1021/bi300083p)]. The full expression of KIEs by H105A and E107A may result from a less secure closure of the catalytic loop. The lower level of expression of the KIE by K103A suggests that in these mutant proteins the major barrier to catalysis is successful closure...

  10. Catalysis in high-temperature fuel cells.

    Science.gov (United States)

    Föger, K; Ahmed, K

    2005-02-17

    Catalysis plays a critical role in solid oxide fuel cell systems. The electrochemical reactions within the cell--oxygen dissociation on the cathode and electrochemical fuel combustion on the anode--are catalytic reactions. The fuels used in high-temperature fuel cells, for example, natural gas, propane, or liquid hydrocarbons, need to be preprocessed to a form suitable for conversion on the anode-sulfur removal and pre-reforming. The unconverted fuel (economic fuel utilization around 85%) is commonly combusted using a catalytic burner. Ceramic Fuel Cells Ltd. has developed anodes that in addition to having electrochemical activity also are reactive for internal steam reforming of methane. This can simplify fuel preprocessing, but its main advantage is thermal management of the fuel cell stack by endothermic heat removal. Using this approach, the objective of fuel preprocessing is to produce a methane-rich fuel stream but with all higher hydrocarbons removed. Sulfur removal can be achieved by absorption or hydro-desulfurization (HDS). Depending on the system configuration, hydrogen is also required for start-up and shutdown. Reactor operating parameters are strongly tied to fuel cell operational regimes, thus often limiting optimization of the catalytic reactors. In this paper we discuss operation of an authothermal reforming reactor for hydrogen generation for HDS and start-up/shutdown, and development of a pre-reformer for converting propane to a methane-rich fuel stream.

  11. Ferroelectric based catalysis: Switchable surface chemistry

    Science.gov (United States)

    Kakekhani, Arvin; Ismail-Beigi, Sohrab

    2015-03-01

    We describe a new class of catalysts that uses an epitaxial monolayer of a transition metal oxide on a ferroelectric substrate. The ferroelectric polarization switches the surface chemistry between strongly adsorptive and strongly desorptive regimes, circumventing difficulties encountered on non-switchable catalytic surfaces where the Sabatier principle dictates a moderate surface-molecule interaction strength. This method is general and can, in principle, be applied to many reactions, and for each case the choice of the transition oxide monolayer can be optimized. Here, as a specific example, we show how simultaneous NOx direct decomposition (into N2 and O2) and CO oxidation can be achieved efficiently on CrO2 terminated PbTiO3, while circumventing oxygen (and sulfur) poisoning issues. One should note that NOx direct decomposition has been an open challenge in automotive emission control industry. Our method can expand the range of catalytically active elements to those which are not conventionally considered for catalysis and which are more economical, e.g., Cr (for NOx direct decomposition and CO oxidation) instead of canonical precious metal catalysts. Primary support from Toyota Motor Engineering and Manufacturing, North America, Inc.

  12. Center for Catalysis at Iowa State University

    Energy Technology Data Exchange (ETDEWEB)

    Kraus, George A.

    2006-10-17

    The overall objective of this proposal is to enable Iowa State University to establish a Center that enjoys world-class stature and eventually enhances the economy through the transfer of innovation from the laboratory to the marketplace. The funds have been used to support experimental proposals from interdisciplinary research teams in areas related to catalysis and green chemistry. Specific focus areas included: • Catalytic conversion of renewable natural resources to industrial materials • Development of new catalysts for the oxidation or reduction of commodity chemicals • Use of enzymes and microorganisms in biocatalysis • Development of new, environmentally friendly reactions of industrial importance These focus areas intersect with barriers from the MYTP draft document. Specifically, section 2.4.3.1 Processing and Conversion has a list of bulleted items under Improved Chemical Conversions that includes new hydrogenation catalysts, milder oxidation catalysts, new catalysts for dehydration and selective bond cleavage catalysts. Specifically, the four sections are: 1. Catalyst development (7.4.12.A) 2. Conversion of glycerol (7.4.12.B) 3. Conversion of biodiesel (7.4.12.C) 4. Glucose from starch (7.4.12.D) All funded projects are part of a soybean or corn biorefinery. Two funded projects that have made significant progress toward goals of the MYTP draft document are: Catalysts to convert feedstocks with high fatty acid content to biodiesel (Kraus, Lin, Verkade) and Conversion of Glycerol into 1,3-Propanediol (Lin, Kraus). Currently, biodiesel is prepared using homogeneous base catalysis. However, as producers look for feedstocks other than soybean oil, such as waste restaurant oils and rendered animal fats, they have observed a large amount of free fatty acids contained in the feedstocks. Free fatty acids cannot be converted into biodiesel using homogeneous base-mediated processes. The CCAT catalyst system offers an integrated and cooperative catalytic

  13. A hairpin within YAP mRNA 3′UTR functions in regulation at post-transcription level

    Energy Technology Data Exchange (ETDEWEB)

    Gao, Yuen; Wang, Yuan; Feng, Jinyan; Feng, Guoxing; Zheng, Minying; Yang, Zhe; Xiao, Zelin; Lu, Zhanping [State Key Laboratory of Medicinal Chemical Biology, Department of Cancer Research, College of Life Sciences, Nankai University, Tianjin 300071 (China); Ye, Lihong [State Key Laboratory of Medicinal Chemical Biology, Department of Biochemistry, College of Life Sciences, Nankai University, Tianjin 300071 (China); Zhang, Xiaodong, E-mail: zhangxd@nankai.edu.cn [State Key Laboratory of Medicinal Chemical Biology, Department of Cancer Research, College of Life Sciences, Nankai University, Tianjin 300071 (China)

    2015-04-03

    The central dogma of gene expression is that DNA is transcribed into messenger RNAs, which in turn serve as the template for protein synthesis. Recently, it has been reported that mRNAs display regulatory roles that rely on their ability to compete for microRNA binding, independent of their protein-coding function. However, the regulatory mechanism of mRNAs remains poorly understood. Here, we report that a hairpin within YAP mRNA 3′untranslated region (3′UTR) functions in regulation at post-transcription level through generating endogenous siRNAs (esiRNAs). Bioinformatics analysis for secondary structure showed that YAP mRNA displayed a hairpin structure (termed standard hairpin, S-hairpin) within its 3′UTR. Surprisingly, we observed that the overexpression of S-hairpin derived from YAP 3′UTR (YAP-sh) increased the luciferase reporter activities of transcriptional factor NF-κB and AP-1 in 293T cells. Moreover, we identified that a fragment from YAP-sh, an esiRNA, was able to target mRNA 3′UTR of NF2 (a member of Hippo-signaling pathway) and YAP mRNA 3′UTR itself in hepatoma cells. Thus, we conclude that the YAP-sh within YAP mRNA 3′UTR may serve as a novel regulatory element, which functions in regulation at post-transcription level. Our finding provides new insights into the mechanism of mRNAs in regulatory function. - Highlights: • An S-hairpin within YAP mRNA 3′UTR possesses regulatory function. • YAP-sh acts as a regulatory element for YAP at post-transcription level. • YAP-sh-3p20, an esiRNA derived from YAP-sh, targets mRNAs of YAP and NF2. • YAP-sh-3p20 depresses the proliferation of HepG2 cells in vitro.

  14. A hairpin within YAP mRNA 3′UTR functions in regulation at post-transcription level

    International Nuclear Information System (INIS)

    Gao, Yuen; Wang, Yuan; Feng, Jinyan; Feng, Guoxing; Zheng, Minying; Yang, Zhe; Xiao, Zelin; Lu, Zhanping; Ye, Lihong; Zhang, Xiaodong

    2015-01-01

    The central dogma of gene expression is that DNA is transcribed into messenger RNAs, which in turn serve as the template for protein synthesis. Recently, it has been reported that mRNAs display regulatory roles that rely on their ability to compete for microRNA binding, independent of their protein-coding function. However, the regulatory mechanism of mRNAs remains poorly understood. Here, we report that a hairpin within YAP mRNA 3′untranslated region (3′UTR) functions in regulation at post-transcription level through generating endogenous siRNAs (esiRNAs). Bioinformatics analysis for secondary structure showed that YAP mRNA displayed a hairpin structure (termed standard hairpin, S-hairpin) within its 3′UTR. Surprisingly, we observed that the overexpression of S-hairpin derived from YAP 3′UTR (YAP-sh) increased the luciferase reporter activities of transcriptional factor NF-κB and AP-1 in 293T cells. Moreover, we identified that a fragment from YAP-sh, an esiRNA, was able to target mRNA 3′UTR of NF2 (a member of Hippo-signaling pathway) and YAP mRNA 3′UTR itself in hepatoma cells. Thus, we conclude that the YAP-sh within YAP mRNA 3′UTR may serve as a novel regulatory element, which functions in regulation at post-transcription level. Our finding provides new insights into the mechanism of mRNAs in regulatory function. - Highlights: • An S-hairpin within YAP mRNA 3′UTR possesses regulatory function. • YAP-sh acts as a regulatory element for YAP at post-transcription level. • YAP-sh-3p20, an esiRNA derived from YAP-sh, targets mRNAs of YAP and NF2. • YAP-sh-3p20 depresses the proliferation of HepG2 cells in vitro

  15. Generating carbyne equivalents with photoredox catalysis

    Science.gov (United States)

    Wang, Zhaofeng; Herraiz, Ana G.; Del Hoyo, Ana M.; Suero, Marcos G.

    2018-02-01

    Carbon has the unique ability to bind four atoms and form stable tetravalent structures that are prevalent in nature. The lack of one or two valences leads to a set of species—carbocations, carbanions, radicals and carbenes—that is fundamental to our understanding of chemical reactivity. In contrast, the carbyne—a monovalent carbon with three non-bonded electrons—is a relatively unexplored reactive intermediate; the design of reactions involving a carbyne is limited by challenges associated with controlling its extreme reactivity and the lack of efficient sources. Given the innate ability of carbynes to form three new covalent bonds sequentially, we anticipated that a catalytic method of generating carbynes or related stabilized species would allow what we term an ‘assembly point’ disconnection approach for the construction of chiral centres. Here we describe a catalytic strategy that generates diazomethyl radicals as direct equivalents of carbyne species using visible-light photoredox catalysis. The ability of these carbyne equivalents to induce site-selective carbon-hydrogen bond cleavage in aromatic rings enables a useful diazomethylation reaction, which underpins sequencing control for the late-stage assembly-point functionalization of medically relevant agents. Our strategy provides an efficient route to libraries of potentially bioactive molecules through the installation of tailored chiral centres at carbon-hydrogen bonds, while complementing current translational late-stage functionalization processes. Furthermore, we exploit the dual radical and carbene character of the generated carbyne equivalent in the direct transformation of abundant chemical feedstocks into valuable chiral molecules.

  16. Catalysis-by-design impacts assessment

    Energy Technology Data Exchange (ETDEWEB)

    Fassbender, L L; Young, J K [Pacific Northwest Lab., Richland, WA (USA); Sen, R K [Sen (R.K.) and Associates, Washington, DC (USA)

    1991-05-01

    Catalyst researchers have always recognized the need to develop a detailed understanding of the mechanisms of catalytic processes, and have hoped that it would lead to developing a theoretical predictive base to guide the search for new catalysts. This understanding allows one to develop a set of hierarchical models, from fundamental atomic-level ab-initio models to detailed engineering simulations of reactor systems, to direct the search for optimized, efficient catalyst systems. During the last two decades, the explosions of advanced surface analysis techniques have helped considerably to develop the building blocks for understanding various catalytic reactions. An effort to couple these theoretical and experimental advances to develop a set of hierarchical models to predict the nature of catalytic materials is a program entitled Catalysis-by-Design (CRD).'' In assessing the potential impacts of CBD on US industry, the key point to remember is that the value of the program lies in developing a novel methodology to search for new catalyst systems. Industrial researchers can then use this methodology to develop proprietary catalysts. Most companies involved in catalyst R D have two types of ongoing projects. The first type, what we call market-driven R D,'' are projects that support and improve upon a company's existing product lines. Project of the second type, technology-driven R D,'' are longer term, involve the development of totally new catalysts, and are initiated through scientists' research ideas. The CBD approach will impact both types of projects. However, this analysis indicates that the near-term impacts will be on market-driven'' projects. The conclusions and recommendations presented in this report were obtained by the authors through personal interviews with individuals involved in a variety of industrial catalyst development programs and through the three CBD workshops held in the summer of 1989. 34 refs., 7 figs., 7 tabs.

  17. Biodiesel forming reactions using heterogeneous catalysis

    Science.gov (United States)

    Liu, Yijun

    Biodiesel synthesis from biomass provides a means for utilizing effectively renewable resources, a way to convert waste vegetable oils and animal fats to a useful product, a way to recycle carbon dioxide for a combustion fuel, and production of a fuel that is biodegradable, non-toxic, and has a lower emission profile than petroleum-diesel. Free fatty acid (FFA) esterification and triglyceride (TG) transesterification with low molecular weight alcohols constitute the synthetic routes to prepare biodiesel from lipid feedstocks. This project was aimed at developing a better understanding of important fundamental issues involved in heterogeneous catalyzed biodiesel forming reactions using mainly model compounds, representing part of on-going efforts to build up a rational base for assay, design, and performance optimization of solid acids/bases in biodiesel synthesis. As FFA esterification proceeds, water is continuously formed as a byproduct and affects reaction rates in a negative manner. Using sulfuric acid (as a catalyst) and acetic acid (as a model compound for FFA), the impact of increasing concentrations of water on acid catalysis was investigated. The order of the water effect on reaction rate was determined to be -0.83. Sulfuric acid lost up to 90% activity as the amount of water present increased. The nature of the negative effect of water on esterification was found to go beyond the scope of reverse hydrolysis and was associated with the diminished acid strength of sulfuric acid as a result of the preferential solvation by water molecules of its catalytic protons. The results indicate that as esterification progresses and byproduct water is produced, deactivation of a Bronsted acid catalyst like H2SO4 occurs. Using a solid composite acid (SAC-13) as an example of heterogeneous catalysts and sulfuric acid as a homogeneous reference, similar reaction inhibition by water was demonstrated for homogeneous and heterogeneous catalysis. This similarity together with

  18. Kinetic evolutionary behavior of catalysis-select migration

    International Nuclear Information System (INIS)

    Wu Yuan-Gang; Lin Zhen-Quan; Ke Jian-Hong

    2012-01-01

    We propose a catalysis-select migration driven evolution model of two-species (A- and B-species) aggregates, where one unit of species A migrates to species B under the catalysts of species C, while under the catalysts of species D the reaction will become one unit of species B migrating to species A. Meanwhile the catalyst aggregates of species C perform self-coagulation, as do the species D aggregates. We study this catalysis-select migration driven kinetic aggregation phenomena using the generalized Smoluchowski rate equation approach with C species catalysis-select migration rate kernel K(k;i,j) = Kkij and D species catalysis-select migration rate kernel J(k;i,j)= Jkij. The kinetic evolution behaviour is found to be dominated by the competition between the catalysis-select immigration and emigration, in which the competition is between JD 0 and KC 0 (D 0 and C 0 are the initial numbers of the monomers of species D and C, respectively). When JD 0 −KC 0 > 0, the aggregate size distribution of species A satisfies the conventional scaling form and that of species B satisfies a modified scaling form. And in the case of JD 0 −KC 0 0 −KC 0 > 0 case. (interdisciplinary physics and related areas of science and technology)

  19. Novel guanidinylated bioresponsive poly(amidoamines designed for short hairpin RNA delivery

    Directory of Open Access Journals (Sweden)

    Yu J

    2016-12-01

    Full Text Available Jiankun Yu,1 Jinmin Zhang,1 Haonan Xing,1 Yanping Sun,1 Zhen Yang,1 Tianzhi Yang,2 Cuifang Cai,1 Xiaoyun Zhao,3 Li Yang,1 Pingtian Ding1 1School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, China; 2Department of Basic Pharmaceutical Sciences, School of Pharmacy, Husson University, Bangor, ME, USA; 3Department of Microbiology and Cell Biology, School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, China Abstract: Two different disulfide (SS-containing poly(amidoamine (PAA polymers were constructed using guanidino (Gua-containing monomers (ie, arginine [Arg] and agmatine [Agm] and N,N'-cystamine bisacrylamide (CBA by Michael-addition polymerization. In order to characterize these two Gua-SS-PAA polymers and investigate their potentials as short hairpin RNA (shRNA-delivery carriers, pSilencer 4.1-CMV FANCF shRNA was chosen as a model plasmid DNA to form complexes with these two polymers. The Gua-SS-PAAs and plasmid DNA complexes were determined with particle sizes less than 90 nm and positive ζ-potentials under 20 mV at nucleic acid:polymer weight ratios lower than 1:24. Bioresponsive release of plasmid DNA was observed from both newly constructed complexes. Significantly lower cytotoxicity was observed for both polymer complexes compared with polyethylenimine and Lipofectamine 2000, two widely used transfection reagents as reference carriers. Arg-CBA showed higher transfection efficiency and gene-silencing efficiency in MCF7 cells than Agm-CBA and the reference carriers. In addition, the cellular uptake of Arg-CBA in MCF7 cells was found to be higher and faster than Agm-CBA and the reference carriers. Similarly, plasmid DNA transport into the nucleus mediated by Arg-CBA was more than that by Agm-CBA and the reference carriers. The study suggested that guanidine and carboxyl introduced into Gua-SS-PAAs polymers resulted in a better nuclear localization effect, which played a key role in the

  20. 1H and 31P resonance assignments and secondary structure of hairpin conformer of IA mismatched oligonucleotide d-GGTACIAGTACC

    International Nuclear Information System (INIS)

    Chary, K.V.R.; Rastogi, V.K.; Govil, Girjesh

    1994-01-01

    Almost complete 1 H and 31 P resonance assignments of two coexisting conformers, duplex and an hairpin, of d-GGTACIAGTACC at 1.25mM concentration and 305 K have been achieved. The results demonstrate that the hairpin conformer has a structure with two purines I6 and A7 forming a two-base loop on a B-DNA stem. Stacking is continued on the 5'-side of the loop, with the I6 stacked upon C5. The base A7, on the 3'-side of the loop stacks partially with I6. The glycosidic angle for G8 is in the anti domain and it maintains normal Watson-Crick base-pairing with the opposite C5. (author). 28 refs., 7 figs., 2 tabs

  1. Francois Garin: Pioneer work in catalysis through synchrotron radiation

    International Nuclear Information System (INIS)

    Bazin, Dominique

    2014-01-01

    Starting from the late seventies, the progressively increased availability of beamlines dedicated to X-ray absorption spectroscopy allowed the execution of experiments in chemistry. In this manuscript, I describe the contribution of Francois Garin at the frontier of heterogeneous catalysis and synchrotron radiation. Working at LURE as a scientific in charge of a beamline dedicated to X-ray absorption spectroscopy during almost twenty years and thus, having the opportunity to discuss with research groups working in heterogeneous catalysis in Europe as well as in the United States, it was quite easy to show that his work is clearly at the origin of current research in heterogeneous catalysis, not only in France, but in different synchrotron radiation centres. (authors)

  2. 2008 Gordon Research Conference on Catalysis [Conference summary report

    Energy Technology Data Exchange (ETDEWEB)

    Soled, Stuart L.; Gray, Nancy Ryan

    2009-01-01

    The GRC on Catalysis is one of the most prestigious catalysis conferences as it brings together leading researchers from around the world to discuss their latest, most exciting work in catalysis. The 2008 conference will continue this tradition. The conference will cover a variety of themes including new catalytic materials, theoretical and experimental approaches to improve understanding of kinetics and transport phenomena, and state of the art nanoscale characterization probes to monitor active sites. The conference promotes interactions among established researchers and young scientists. It provides a venue for students to meet, talk to and learn from some of the world leading researchers in the area. It also gives them a platform for displaying their own work during the poster sessions. The informal nature of the meeting, excellent quality of the presentations and posters, and ability to meet many outstanding colleagues makes this an excellent conference.

  3. Lentiviral Delivery of a Vesicular Glutamate Transporter 1 (VGLUT1)-Targeting Short Hairpin RNA Vector Into the Mouse Hippocampus Impairs Cognition

    NARCIS (Netherlands)

    King, Madeleine V.; Kurian, Nisha; Qin, Si; Papadopoulou, Nektaria; Westerink, Ben H. C.; Cremers, Thomas I.; Epping-Jordan, Mark P.; Le Poul, Emmanuel; Ray, David E.; Fone, Kevin C. F.; Kendall, David A.; Marsden, Charles A.; Sharp, Tyson V.

    Glutamate is the principle excitatory neurotransmitter in the mammalian brain, and dysregulation of glutamatergic neurotransmission is implicated in the pathophysiology of several psychiatric and neurological diseases. This study utilized novel lentiviral short hairpin RNA (shRNA) vectors to target

  4. Mutational analysis of an archaeal minichromosome maintenance protein exterior hairpin reveals critical residues for helicase activity and DNA binding

    Directory of Open Access Journals (Sweden)

    Brewster Aaron S

    2010-08-01

    Full Text Available Abstract Background The mini-chromosome maintenance protein (MCM complex is an essential replicative helicase for DNA replication in Archaea and Eukaryotes. While the eukaryotic complex consists of six homologous proteins (MCM2-7, the archaeon Sulfolobus solfataricus has only one MCM protein (ssoMCM, six subunits of which form a homohexamer. We have recently reported a 4.35Å crystal structure of the near full-length ssoMCM. The structure reveals a total of four β-hairpins per subunit, three of which are located within the main channel or side channels of the ssoMCM hexamer model generated based on the symmetry of the N-terminal Methanothermobacter thermautotrophicus (mtMCM structure. The fourth β-hairpin, however, is located on the exterior of the hexamer, near the exit of the putative side channels and next to the ATP binding pocket. Results In order to better understand this hairpin's role in DNA binding and helicase activity, we performed a detailed mutational and biochemical analysis of nine residues on this exterior β-hairpin (EXT-hp. We examined the activities of the mutants related to their helicase function, including hexamerization, ATPase, DNA binding and helicase activities. The assays showed that some of the residues on this EXT-hp play a role for DNA binding as well as for helicase activity. Conclusions These results implicate several current theories regarding helicase activity by this critical hexameric enzyme. As the data suggest that EXT-hp is involved in DNA binding, the results reported here imply that the EXT-hp located near the exterior exit of the side channels may play a role in contacting DNA substrate in a manner that affects DNA unwinding.

  5. RPA coordinates DNA end resection and prevents formation of DNA hairpins.

    Science.gov (United States)

    Chen, Huan; Lisby, Michael; Symington, Lorraine S

    2013-05-23

    Replication protein A (RPA) is an essential eukaryotic single-stranded DNA binding protein with a central role in DNA metabolism. RPA directly participates in DNA double-strand break repair by stimulating 5'-3' end resection by the Sgs1/BLM helicase and Dna2 endonuclease in vitro. Here we investigated the role of RPA in end resection in vivo, using a heat-inducible degron system that allows rapid conditional depletion of RPA in Saccharomyces cerevisiae. We found that RPA depletion eliminated both the Sgs1-Dna2- and Exo1-dependent extensive resection pathways and synergized with mre11Δ to prevent end resection. The short single-stranded DNA tails formed in the absence of RPA were unstable due to 3' strand loss and the formation of fold-back hairpin structures that required resection initiation and Pol32-dependent DNA synthesis. Thus, RPA is required to generate ssDNA, and also to protect ssDNA from degradation and inappropriate annealing that could lead to genome rearrangements. Copyright © 2013 Elsevier Inc. All rights reserved.

  6. Multi-resistance strategy for viral diseases and short hairpin RNA verification method in pigs

    Directory of Open Access Journals (Sweden)

    Jong-nam Oh

    2018-04-01

    Full Text Available Objective Foot and mouth disease (FMD and porcine reproductive and respiratory syndrome (PRRS are major diseases that interrupt porcine production. Because they are viral diseases, vaccinations are of only limited effectiveness in preventing outbreaks. To establish an alternative multi-resistant strategy against FMD virus (FMDV and PRRS virus (PRRSV, the present study introduced two genetic modification techniques to porcine cells. Methods First, cluster of differentiation 163 (CD163, the PRRSV viral receptor, was edited with the clustered regularly interspaced short palindromic repeats-CRISPR-associated protein 9 technique. The CD163 gene sequences of edited cells and control cells differed. Second, short hairpin RNA (shRNAs were integrated into the cells. The shRNAs, targeting the 3D gene of FMDV and the open reading frame 7 (ORF7 gene of PRRSV, were transferred into fibroblasts. We also developed an in vitro shRNA verification method with a target gene expression vector. Results shRNA activity was confirmed in vitro with vectors that expressed the 3D and ORF7 genes in the cells. Cells containing shRNAs showed lower transcript levels than cells with only the expression vectors. The shRNAs were integrated into CD163-edited cells to combine the two techniques, and the viral genes were suppressed in these cells. Conclusion We established a multi-resistant strategy against viral diseases and an in vitro shRNA verification method.

  7. Biological Applications of Designed Hairpin Peptides: As Antimicrobials and as Inhibitors of Amyloidogenesis

    Science.gov (United States)

    Sivanesam, Kalkena

    More than 40 diseases have been associated with the misfolding of peptides (or proteins) that form fibrils with a very specific morphology. These peptides classified as amyloidogenic peptides have been implicated in the development of Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, Hungtinton's Disease etc. To date, these diseases have no cure, only therapies that can ameliorate the symptoms to a degree. Inhibition of the amyloidogenesis of these peptides has been proposed as a possible treatment option. While small molecules have been heavily tested as inhibitors of amyloidogenesis, peptides have emerged as potential inhibitors. In this work, the ability of a set of designed hairpin peptides to inhibit the amyloidogenesis of two different systems, alpha-synuclein (implicated in Parkinson's Disease) and human amylin (implicated in Type II Diabetes) is tested. Using circular dichroism and thioflavin T fluorescence, the ability of these peptides to inhibit amyloidogenesis is tested. The binding loci of these inhibitors to alpha-synuclein are also explored. The use of peptides as antimicrobials on the other hand is not a novel concept. However, most antimicrobial peptides, both natural and designed, rely heavily on covalent stabilizations in order to maintain secondary structure. In this study, non-covalent stabilizations are applied to a couple of natural as well as designed antimicrobials in order to study the effects of secondary structure stabilization on biological activity.

  8. Hairpin RNA Targeting Multiple Viral Genes Confers Strong Resistance to Rice Black-Streaked Dwarf Virus

    Directory of Open Access Journals (Sweden)

    Fangquan Wang

    2016-05-01

    Full Text Available Rice black-streaked dwarf virus (RBSDV belongs to the genus Fijivirus in the family of Reoviridae and causes severe yield loss in rice-producing areas in Asia. RNA silencing, as a natural defence mechanism against plant viruses, has been successfully exploited for engineering virus resistance in plants, including rice. In this study, we generated transgenic rice lines harbouring a hairpin RNA (hpRNA construct targeting four RBSDV genes, S1, S2, S6 and S10, encoding the RNA-dependent RNA polymerase, the putative core protein, the RNA silencing suppressor and the outer capsid protein, respectively. Both field nursery and artificial inoculation assays of three generations of the transgenic lines showed that they had strong resistance to RBSDV infection. The RBSDV resistance in the segregating transgenic populations correlated perfectly with the presence of the hpRNA transgene. Furthermore, the hpRNA transgene was expressed in the highly resistant transgenic lines, giving rise to abundant levels of 21–24 nt small interfering RNA (siRNA. By small RNA deep sequencing, the RBSDV-resistant transgenic lines detected siRNAs from all four viral gene sequences in the hpRNA transgene, indicating that the whole chimeric fusion sequence can be efficiently processed by Dicer into siRNAs. Taken together, our results suggest that long hpRNA targeting multiple viral genes can be used to generate stable and durable virus resistance in rice, as well as other plant species.

  9. Hairpin RNA Targeting Multiple Viral Genes Confers Strong Resistance to Rice Black-Streaked Dwarf Virus.

    Science.gov (United States)

    Wang, Fangquan; Li, Wenqi; Zhu, Jinyan; Fan, Fangjun; Wang, Jun; Zhong, Weigong; Wang, Ming-Bo; Liu, Qing; Zhu, Qian-Hao; Zhou, Tong; Lan, Ying; Zhou, Yijun; Yang, Jie

    2016-05-11

    Rice black-streaked dwarf virus (RBSDV) belongs to the genus Fijivirus in the family of Reoviridae and causes severe yield loss in rice-producing areas in Asia. RNA silencing, as a natural defence mechanism against plant viruses, has been successfully exploited for engineering virus resistance in plants, including rice. In this study, we generated transgenic rice lines harbouring a hairpin RNA (hpRNA) construct targeting four RBSDV genes, S1, S2, S6 and S10, encoding the RNA-dependent RNA polymerase, the putative core protein, the RNA silencing suppressor and the outer capsid protein, respectively. Both field nursery and artificial inoculation assays of three generations of the transgenic lines showed that they had strong resistance to RBSDV infection. The RBSDV resistance in the segregating transgenic populations correlated perfectly with the presence of the hpRNA transgene. Furthermore, the hpRNA transgene was expressed in the highly resistant transgenic lines, giving rise to abundant levels of 21-24 nt small interfering RNA (siRNA). By small RNA deep sequencing, the RBSDV-resistant transgenic lines detected siRNAs from all four viral gene sequences in the hpRNA transgene, indicating that the whole chimeric fusion sequence can be efficiently processed by Dicer into siRNAs. Taken together, our results suggest that long hpRNA targeting multiple viral genes can be used to generate stable and durable virus resistance in rice, as well as other plant species.

  10. Buckwheat trypsin inhibitor with helical hairpin structure belongs to a new family of plant defence peptides.

    Science.gov (United States)

    Oparin, Peter B; Mineev, Konstantin S; Dunaevsky, Yakov E; Arseniev, Alexander S; Belozersky, Mikhail A; Grishin, Eugene V; Egorov, Tsezi A; Vassilevski, Alexander A

    2012-08-15

    A new peptide trypsin inhibitor named BWI-2c was obtained from buckwheat (Fagopyrum esculentum) seeds by sequential affinity, ion exchange and reversed-phase chromatography. The peptide was sequenced and found to contain 41 amino acid residues, with four cysteine residues involved in two intramolecular disulfide bonds. Recombinant BWI-2c identical to the natural peptide was produced in Escherichia coli in a form of a cleavable fusion with thioredoxin. The 3D (three-dimensional) structure of the peptide in solution was determined by NMR spectroscopy, revealing two antiparallel α-helices stapled by disulfide bonds. Together with VhTI, a trypsin inhibitor from veronica (Veronica hederifolia), BWI-2c represents a new family of protease inhibitors with an unusual α-helical hairpin fold. The linker sequence between the helices represents the so-called trypsin inhibitory loop responsible for direct binding to the active site of the enzyme that cleaves BWI-2c at the functionally important residue Arg(19). The inhibition constant was determined for BWI-2c against trypsin (1.7×10(-1)0 M), and the peptide was tested on other enzymes, including those from various insect digestive systems, revealing high selectivity to trypsin-like proteases. Structural similarity shared by BWI-2c, VhTI and several other plant defence peptides leads to the acknowledgement of a new widespread family of plant peptides termed α-hairpinins.

  11. Comparison of Cytotoxic Activity in Leukemic Lineages Reveals Important Features of β-Hairpin Antimicrobial Peptides.

    Science.gov (United States)

    Buri, Marcus V; Torquato, Heron F Vieira; Barros, Carlos Castilho; Ide, Jaime S; Miranda, Antonio; Paredes-Gamero, Edgar J

    2017-07-01

    Several reports described different modes of cell death triggered by antimicrobial peptides (AMPs) due to direct effects on membrane disruption, and more recently by apoptosis and necrosis-like patterns. Cytotoxic curves of four β-hairpin AMPs (gomesin, protegrin, tachyplesin, and polyphemusin) were obtained from several human leukemic lineages and normal monocytes and Two cell lines were then selected based on their cytotoxic sensitivity. One was sensitive to AMPs (K562) and the other resistant (KG-1) and their effect compared between these lineages. Thus, these lineages were chosen to further investigate biological features related with their cytotoxicities to AMPs. Stimulation with AMPs produced cell death, with activation of caspase-3, in K562 lineage. Increase on the fluidity of plasmatic membrane by reducing cholesterol potentiated cytotoxicity of AMPs in both lineages. Quantification of internal and external gomesin binding to the cellular membrane of both K562 and KG-1 cells showed that more peptide is accumulated inside of K562 cells. Additionally, evaluation of multi-drug resistant pumps activity showed that KG-1 has more activity than K562 lineage. A comparison of intrinsic gene patterns showed great differences between K562 and KG-1, but stimulation with gomesin promoted few changes in gene expression patterns. Differences in internalization process through the plasma membrane, multidrug resistance pumps activity, and gene expression pattern are important features to AMPs regulated cell death. J. Cell. Biochem. 118: 1764-1773, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  12. Covalent Bonding of Pyrrolobenzodiazepines (PBDs) to Terminal Guanine Residues within Duplex and Hairpin DNA Fragments

    Science.gov (United States)

    Mantaj, Julia; Jackson, Paul J. M.; Karu, Kersti; Rahman, Khondaker M.; Thurston, David E.

    2016-01-01

    Pyrrolobenzodiazepines (PBDs) are covalent-binding DNA-interactive agents with growing importance as payloads in Antibody Drug Conjugates (ADCs). Until now, PBDs were thought to covalently bond to C2-NH2 groups of guanines in the DNA-minor groove across a three-base-pair recognition sequence. Using HPLC/MS methodology with designed hairpin and duplex oligonucleotides, we have now demonstrated that the PBD Dimer SJG-136 and the C8-conjugated PBD Monomer GWL-78 can covalently bond to a terminal guanine of DNA, with the PBD skeleton spanning only two base pairs. Control experiments with the non-C8-conjugated anthramycin along with molecular dynamics simulations suggest that the C8-substituent of a PBD Monomer, or one-half of a PBD Dimer, may provide stability for the adduct. This observation highlights the importance of PBD C8-substituents, and also suggests that PBDs may bind to terminal guanines within stretches of DNA in cells, thus representing a potentially novel mechanism of action at the end of DNA strand breaks. PMID:27055050

  13. Isoporphyrin Intermediate in Heme Oxygenase Catalysis

    Science.gov (United States)

    Evans, John P.; Niemevz, Fernando; Buldain, Graciela; de Montellano, Paul Ortiz

    2008-01-01

    Human heme oxygenase-1 (hHO-1) catalyzes the O2- and NADPH-dependent oxidation of heme to biliverdin, CO, and free iron. The first step involves regiospecific insertion of an oxygen atom at the α-meso carbon by a ferric hydroperoxide and is predicted to proceed via an isoporphyrin π-cation intermediate. Here we report spectroscopic detection of a transient intermediate during oxidation by hHO-1 of α-meso-phenylheme-IX, α-meso-(p-methylphenyl)-mesoheme-III, and α-meso-(p-trifluoromethylphenyl)-mesoheme-III. In agreement with previous experiments (Wang, J., Niemevz, F., Lad, L., Huang, L., Alvarez, D. E., Buldain, G., Poulos, T. L., and Ortiz de Montellano, P. R. (2004) J. Biol. Chem. 279, 42593–42604), only the α-biliverdin isomer is produced with concomitant formation of the corresponding benzoic acid. The transient intermediate observed in the NADPH-P450 reductase-catalyzed reaction accumulated when the reaction was supported by H2O2 and exhibited the absorption maxima at 435 and 930 nm characteristic of an isoporphyrin. Product analysis by reversed phase high performance liquid chromatography and liquid chromatography electrospray ionization mass spectrometry of the product generated with H2O2 identified it as an isoporphyrin that, on quenching, decayed to benzoylbiliverdin. In the presence of H218O2, one labeled oxygen atom was incorporated into these products. The hHO-1-isoporphyrin complexes were found to have half-lives of 1.7 and 2.4 h for the p-trifluoromethyl- and p-methyl-substituted phenylhemes, respectively. The addition of NADPH-P450 reductase to the H2O2-generated hHO-1-isoporphyrin complex produced α-biliverdin, confirming its role as a reaction intermediate. Identification of an isoporphyrin intermediate in the catalytic sequence of hHO-1, the first such intermediate observed in hemoprotein catalysis, completes our understanding of the critical first step of heme oxidation. PMID:18487208

  14. The Development of Visible-Light Photoredox Catalysis in Flow.

    Science.gov (United States)

    Garlets, Zachary J; Nguyen, John D; Stephenson, Corey R J

    2014-04-01

    Visible-light photoredox catalysis has recently emerged as a viable alternative for radical reactions otherwise carried out with tin and boron reagents. It has been recognized that by merging photoredox catalysis with flow chemistry, slow reaction times, lower yields, and safety concerns may be obviated. While flow reactors have been successfully applied to reactions carried out with UV light, only recent developments have demonstrated the same potential of flow reactors for the improvement of visible-light-mediated reactions. This review examines the initial and continuing development of visible-light-mediated photoredox flow chemistry by exemplifying the benefits of flow chemistry compared with conventional batch techniques.

  15. New and future developments in catalysis activation of carbon dioxide

    CERN Document Server

    Suib, Steven L

    2013-01-01

    New and Future Developments in Catalysis is a package of books that compile the latest ideas concerning alternate and renewable energy sources and the role that catalysis plays in converting new renewable feedstock into biofuels and biochemicals. Both homogeneous and heterogeneous catalysts and catalytic processes will be discussed in a unified and comprehensive approach. There will be extensive cross-referencing within all volumes. This volume presents a complete picture of all carbon dioxide (CO2) sources, outlines the environmental concerns regarding CO2, and critica

  16. KCC1: First Nanoparticle developed by KAUST Catalysis Center

    KAUST Repository

    Basset, Jean-Marie

    2010-08-01

    KCC1 is the first Nanoparticle developed by KAUST Catalysis Center. Director of KAUST Catalysis Center, Dr. Jean-Marie Basset, Senior Research Scientist at KCC, Dr. Vivek Polshettiwar, and Dr. Dongkyu Cha of the Advanced Nanofabrication Imaging & Characterization Core Laboratory discuss the details of this recent discovery. This video was produced by KAUST Visualization Laboratory and KAUST Technology Transfer and Innovation - Terence McElwee, Director, Technology Transfer and Innovation - IP@kaust.edu.sa This technology is part of KAUST\\'s technology commercialization program that seeks to stimulate development and commercial use of KAUST-developed technologies. For more information email us at ip@kaust.edu.sa.

  17. Probing the Gaseous Structure of a β-Hairpin Peptide with H/D Exchange and Electron Capture Dissociation.

    Science.gov (United States)

    Straus, Rita N; Jockusch, Rebecca A

    2017-02-01

    An improved understanding of the extent to which native protein structure is retained upon transfer to the gas phase promises to enhance biological mass spectrometry, potentially streamlining workflows and providing fundamental insights into hydration effects. Here, we investigate the gaseous conformation of a model β-hairpin peptide using gas-phase hydrogen-deuterium (H/D) exchange with subsequent electron capture dissociation (ECD). Global gas-phase H/D exchange levels, and residue-specific exchange levels derived from ECD data, are compared among the wild type 16-residue peptide GB1p and several variants. High protection from H/D exchange observed for GB1p, but not for a truncated version, is consistent with the retention of secondary structure of GB1p in the gas phase or its refolding into some other compact structure. Four alanine mutants that destabilize the hairpin in solution show levels of protection similar to that of GB1p, suggesting collapse or (re)folding of these peptides upon transfer to the gas phase. These results offer a starting point from which to understand how a key secondary structural element, the β-hairpin, is affected by transfer to the gas phase. This work also demonstrates the utility of a much-needed addition to the tool set that is currently available for the investigation of the gaseous conformation of biomolecules, which can be employed in the future to better characterize gaseous proteins and protein complexes. Graphical Abstract ᅟ.

  18. Seventh BES [Basic Energy Sciences] catalysis and surface chemistry research conference

    International Nuclear Information System (INIS)

    1990-03-01

    Research programs on catalysis and surface chemistry are presented. A total of fifty-seven topics are included. Areas of research include heterogeneous catalysis; catalysis in hydrogenation, desulfurization, gasification, and redox reactions; studies of surface properties and surface active sites; catalyst supports; chemical activation, deactivation; selectivity, chemical preparation; molecular structure studies; sorption and dissociation. Individual projects are processed separately for the data bases

  19. Seventh BES (Basic Energy Sciences) catalysis and surface chemistry research conference

    Energy Technology Data Exchange (ETDEWEB)

    1990-03-01

    Research programs on catalysis and surface chemistry are presented. A total of fifty-seven topics are included. Areas of research include heterogeneous catalysis; catalysis in hydrogenation, desulfurization, gasification, and redox reactions; studies of surface properties and surface active sites; catalyst supports; chemical activation, deactivation; selectivity, chemical preparation; molecular structure studies; sorption and dissociation. Individual projects are processed separately for the data bases. (CBS)

  20. DNA-based asymmetric organometallic catalysis in water

    NARCIS (Netherlands)

    Oelerich, Jens; Roelfes, Gerard

    2013-01-01

    Here, the first examples of DNA-based organometallic catalysis in water that give rise to high enantioselectivities are described. Copper complexes of strongly intercalating ligands were found to enable the asymmetric intramolecular cyclopropanation of alpha-diazo-beta-keto sulfones in water. Up to

  1. Density functional theory in surface science and heterogeneous catalysis

    DEFF Research Database (Denmark)

    Nørskov, Jens Kehlet; Scheffler, M.; Toulhoat, H.

    2006-01-01

    Solid surfaces are used extensively as catalysts throughout the chemical industry, in the energy sector, and in environmental protection. Recently, density functional theory has started providing new insight into the atomic-scale mechanisms of heterogeneous catalysis, helping to interpret the large...

  2. International symposium on 'applications of zeolites in heterogeneous catalysis'

    Energy Technology Data Exchange (ETDEWEB)

    1978-11-01

    The International Symposium on applications of zeolites in heterogeneous catalysis, organized by the Hungarian Chemical Society (Szeged, Hung. 9/11-14/78), included 48 papers, which were published in the Vertical Bar3Vertical BarActa Phys. Chem. (Szeged) 24.

  3. Molecular catalysis and high-volume organic synthesis

    Energy Technology Data Exchange (ETDEWEB)

    Khidekel, M L; Vasserberg, V E

    1977-01-01

    The field of catalysis is very wide. The properties of catalysts are briefly reviewed and compared with the properties of enzymes. Various uses of enxymes in industry (sugar from corn, cellulose breakdown, etc.) are pointed out. The types of homogeneous and heterogeneous catalysts for use in organic synthesis are discussed. 48 refs. (SJR)

  4. Pincer-porphyrin hybrids : Synthesis, self-assembly, and catalysis

    NARCIS (Netherlands)

    Suijkerbuijk, B.M.J.M.

    2007-01-01

    Metal complexes play an important role in established research areas such as catalysis and materials chemistry as well as in emerging fields of chemical exploration such as bioinorganic chemistry. Changes in the metal center's ligand environment, i.e., the nature and number of the Lewis basic atoms

  5. Sustainable Catalysis_Energy efficient reactions and Applications

    Science.gov (United States)

    This book chapter discusses various catalysts for environmental remediation. Detailed information on catalysis using ferrate and ferrite oxidation, TiO2 photocatalysis, and new catalysts (i.e., graphene, perovskites and graphitic carbon nitride) is provided for the degradation of...

  6. Examining the role of glutamic acid 183 in chloroperoxidase catalysis

    NARCIS (Netherlands)

    Yi, X.; Conesa, A.; Punt, P.J.; Hager, L.P.

    2003-01-01

    Site-directed mutagenesis has been used to investigate the role of glutamic acid 183 in chloroperoxidase catalysis. Based on the x-ray crystallographic structure of chloroperoxidase, Glu-183 is postulated to function on distal side of the heme prosthetic group as an acid-base catalyst in

  7. Alkylation of hydrothiophosphoryl compounds in conditions of interphase catalysis

    International Nuclear Information System (INIS)

    Aladzheva, I.M.; Odinets, I.L.; Petrovskij, P.V.; Mastryukova, T.A.; Kabachkin, M.I.

    1993-01-01

    A method of interphase catalysis permitted to develop a common method for synthesis of compounds with thiophosphoryl group. The effect of nature of hydrothiophosphoryl compound, alkylating agent, two-phase system and reaction conditions on alkylation product yields was investigated in detail

  8. Towards a generic model of catalysis | Grayson | Bulletin of the ...

    African Journals Online (AJOL)

    We consider polarizabilities and hardness/softness parameters to see how local polarizations of the electron density may also be responsible for activation of a localised area of a large molecule. KEY WORDS: Electrostatic catalysis, Geometrical strain, Environment strain, Entasis, Polarizability, Hardness and softness. Bull.

  9. bond activation and catalysis by Ru -pac complexes

    Indian Academy of Sciences (India)

    and their reactivity towards oxidation of a few organic compounds. Keywords. Kinetics; catalysis; -O–O- bond activation; Ru-pac complex; oxidation. 1. Introduction. Ru-pac complexes exhibit catalytic properties,1 in homogeneous conditions in the presence of oxygen atom donors, that mimic the biological enzymatic oxi-.

  10. Nitrogen doped carbon nanotubes : synthesis, characterization and catalysis

    NARCIS (Netherlands)

    van Dommele, S.

    2008-01-01

    Nitrogen containing Carbon Nanotubes (NCNT) have altered physical- and chemical properties with respect to polarity, conductivity and reactivity as compared to conventional carbon nanotubes (CNT) and have potential for use in electronic applications or catalysis. In this thesis the incorporation of

  11. Role of catalysis in sustainable production of synthetic elastomers

    Indian Academy of Sciences (India)

    productions, the impact of synthetic elastomer business cannot be overlooked. The need of ... Keywords. Elastomers; catalysis; tyres and automobiles; mechanism; manufacturing process. 1. ..... level fractional factorial design model was also developed to ..... Polybutadiene can be manufactured by a number of pro- cesses ...

  12. Two-dimensional zeolites in catalysis: current status and perspectives

    Czech Academy of Sciences Publication Activity Database

    Opanasenko, Maksym; Roth, Wieslaw Jerzy; Čejka, Jiří

    2016-01-01

    Roč. 6, č. 8 (2016), s. 2467-2484 ISSN 2044-4753 R&D Projects: GA ČR GP13-17593P; GA ČR(CZ) GAP106/12/0189 Institutional support: RVO:61388955 Keywords : mesoporous molecular sieves * catalysis * acylation reactions Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 5.773, year: 2016

  13. Function and anatomy of plant siRNA pools derived from hairpin transgenes

    Directory of Open Access Journals (Sweden)

    Lee Kevin AW

    2007-11-01

    Full Text Available Abstract Background RNA interference results in specific gene silencing by small-interfering RNAs (siRNAs. Synthetic siRNAs provide a powerful tool for manipulating gene expression but high cost suggests that novel siRNA production methods are desirable. Strong evolutionary conservation of siRNA structure suggested that siRNAs will retain cross-species function and that transgenic plants expressing heterologous siRNAs might serve as useful siRNA bioreactors. Here we report a detailed evaluation of the above proposition and present evidence regarding structural features of siRNAs extracted from plants. Results Testing the gene silencing capacity of plant-derived siRNAs in mammalian cells proved to be very challenging and required partial siRNA purification and design of a highly sensitive assay. Using the above assay we found that plant-derived siRNAs are ineffective for gene silencing in mammalian cells. Plant-derived siRNAs are almost exclusively double-stranded and most likely comprise a mixture of bona fide siRNAs and aberrant partially complementary duplexes. We also provide indirect evidence that plant-derived siRNAs may contain a hitherto undetected physiological modification, distinct from 3' terminal 2-O-methylation. Conclusion siRNAs produced from plant hairpin transgenes and extracted from plants are ineffective for gene silencing in mammalian cells. Thus our findings establish that a previous claim that transgenic plants offer a cost-effective, scalable and sustainable source of siRNAs is unwarranted. Our results also indicate that the presence of aberrant siRNA duplexes and possibly a plant-specific siRNA modification, compromises the gene silencing capacity of plant-derived siRNAs in mammalian cells.

  14. Characterization of cis-Acting RNA Elements of Zika Virus by Using a Self-Splicing Ribozyme-Dependent Infectious Clone.

    Science.gov (United States)

    Liu, Zhong-Yu; Yu, Jiu-Yang; Huang, Xing-Yao; Fan, Hang; Li, Xiao-Feng; Deng, Yong-Qiang; Ji, Xue; Cheng, Meng-Li; Ye, Qing; Zhao, Hui; Han, Jian-Feng; An, Xiao-Ping; Jiang, Tao; Zhang, Bo; Tong, Yi-Gang; Qin, Cheng-Feng

    2017-11-01

    Zika virus (ZIKV) has caused significant outbreaks and epidemics in the Americas recently, raising global concern due to its ability to cause microcephaly and other neurological complications. A stable and efficient infectious clone of ZIKV is urgently needed. However, the instability and toxicity of flavivirus cDNA clones in Escherichia coli hosts has hindered the development of ZIKV infectious clones. Here, using a novel self-splicing ribozyme-based strategy, we generated a stable infectious cDNA clone of a contemporary ZIKV strain imported from Venezuela to China in 2016. The constructed clone contained a modified version of the group II self-splicing intron P.li.LSUI2 near the junction between the E and NS1 genes, which were removed from the RNA transcripts by an easy-to-establish in vitro splicing reaction. Transfection of the spliced RNAs into BHK-21 cells led to the production of infectious progeny virus that resembled the parental virus. Finally, potential cis -acting RNA elements in ZIKV genomic RNA were identified based on this novel reverse genetics system, and the critical role of 5'-SLA promoter and 5'-3' cyclization sequences were characterized by a combination of different assays. Our results provide another stable and reliable reverse genetics system for ZIKV that will help study ZIKV infection and pathogenesis, and the novel self-splicing intron-based strategy could be further expanded for the construction of infectious clones from other emerging and reemerging flaviviruses. IMPORTANCE The ongoing Zika virus (ZIKV) outbreaks have drawn global concern due to the unexpected causal link to fetus microcephaly and other severe neurological complications. The infectious cDNA clones of ZIKV are critical for the research community to study the virus, understand the disease, and inform vaccine design and antiviral screening. A panel of existing technologies have been utilized to develop ZIKV infectious clones. Here, we successfully generated a stable

  15. Hybridization chain reaction-based colorimetric aptasensor of adenosine 5'-triphosphate on unmodified gold nanoparticles and two label-free hairpin probes.

    Science.gov (United States)

    Gao, Zhuangqiang; Qiu, Zhenli; Lu, Minghua; Shu, Jian; Tang, Dianping

    2017-03-15

    This work designs a new label-free aptasensor for the colorimetric determination of small molecules (adenosine 5'-triphosphate, ATP) by using visible gold nanoparticles as the signal-generation tags, based on target-triggered hybridization chain reaction (HCR) between two hairpin DNA probes. The assay is carried out referring to the change in the color/absorbance by salt-induced aggregation of gold nanoparticles after the interaction with hairpins, gold nanoparticles and ATP. To construct such an assay system, two hairpin DNA probes with a short single-stranded DNA at the sticky end are utilized for interaction with gold nanoparticles. In the absence of target ATP, the hairpin DNA probes can prevent gold nanoparticles from the salt-induced aggregation through the interaction of the single-stranded DNA at the sticky end with gold nanoparticles. Upon target ATP introduction, the aptamer-based hairpin probe is opened to expose a new sticky end for the strand-displacement reaction with another complementary hairpin, thus resulting in the decreasing single-stranded DNA because of the consumption of hairpins. In this case, gold nanoparticles are uncovered owing to the formation of double-stranded DNA, which causes their aggregation upon addition of the salt, thereby leading to the change in the red-to-blue color. Under the optimal conditions, the HCR-based colorimetric assay presents good visible color or absorbance responses for the determination of target ATP at a concentration as low as 1.0nM. Importantly, the methodology can be further extended to quantitatively or qualitatively monitor other small molecules or biotoxins by changing the sequence of the corresponding aptamer. Copyright © 2016 Elsevier B.V. All rights reserved.

  16. The mitochondrial genomes of sponges provide evidence for multiple invasions by Repetitive Hairpin-forming Elements (RHE

    Directory of Open Access Journals (Sweden)

    Lavrov Dennis V

    2009-12-01

    Full Text Available Abstract Background The mitochondrial (mt genomes of sponges possess a variety of features, which appear to be intermediate between those of Eumetazoa and non-metazoan opisthokonts. Among these features is the presence of long intergenic regions, which are common in other eukaryotes, but generally absent in Eumetazoa. Here we analyse poriferan mitochondrial intergenic regions, paying particular attention to repetitive sequences within them. In this context we introduce the mitochondrial genome of Ircinia strobilina (Lamarck, 1816; Demospongiae: Dictyoceratida and compare it with mtDNA of other sponges. Results Mt genomes of dictyoceratid sponges are identical in gene order and content but display major differences in size and organization of intergenic regions. An even higher degree of diversity in the structure of intergenic regions was found among different orders of demosponges. One interesting observation made from such comparisons was of what appears to be recurrent invasions of sponge mitochondrial genomes by repetitive hairpin-forming elements, which cause large genome size differences even among closely related taxa. These repetitive hairpin-forming elements are structurally and compositionally divergent and display a scattered distribution throughout various groups of demosponges. Conclusion Large intergenic regions of poriferan mt genomes are targets for insertions of repetitive hairpin- forming elements, similar to the ones found in non-metazoan opisthokonts. Such elements were likely present in some lineages early in animal mitochondrial genome evolution but were subsequently lost during the reduction of intergenic regions, which occurred in the Eumetazoa lineage after the split of Porifera. Porifera acquired their elements in several independent events. Patterns of their intra-genomic dispersal can be seen in the mt genome of Vaceletia sp.

  17. Hairpin stabilized fluorescent silver nanoclusters for quantitative detection of NAD+ and monitoring NAD+/NADH based enzymatic reactions.

    Science.gov (United States)

    Jain, Priyamvada; Chakma, Babina; Patra, Sanjukta; Goswami, Pranab

    2017-03-01

    A set of 90 mer long ssDNA candidates, with different degrees of cytosine (C-levels) (% and clusters) was analyzed for their function as suitable Ag-nanocluster (AgNC) nucleation scaffolds. The sequence (P4) with highest C-level (42.2%) emerged as the only candidate supporting the nucleation process as evident from its intense fluorescence peak at λ 660 nm . Shorter DNA subsets derived from P4 with only stable hairpin structures could support the AgNC formation. The secondary hairpin structures were confirmed by PAGE, and CD studies. The number of base pairs in the stem region also contributes to the stability of the hairpins. A shorter 29 mer sequence (Sub 3) (ΔG = -1.3 kcal/mol) with 3-bp in the stem of a 7-mer loop conferred highly stable AgNC. NAD + strongly quenched the fluorescence of Sub 3-AgNC in a concentration dependent manner. Time resolved photoluminescence studies revealed the quenching involves a combined static and dynamic interaction where the binding constant and number of binding sites for NAD + were 0.201 L mol -1 and 3.6, respectively. A dynamic NAD + detection range of 50-500 μM with a limit of detection of 22.3 μM was discerned. The NAD + mediated quenching of AgNC was not interfered by NADH, NADP + , monovalent and divalent ions, or serum samples. The method was also used to follow alcohol dehydrogenase and lactate dehydrogenase catalyzed physiological reactions in a turn-on and turn-off assay, respectively. The proposed method with ssDNA-AgNC could therefore be extended to monitor other NAD + /NADH based enzyme catalyzed reactions in a turn-on/turn-off approach. Copyright © 2016 Elsevier B.V. All rights reserved.

  18. Molecular-Level Design of Heterogeneous Chiral Catalysis

    International Nuclear Information System (INIS)

    Zaera, Francisco

    2012-01-01

    The following is a proposal to continue our multi-institutional research on heterogeneous chiral catalysis. Our team combines the use of surface-sensitive analytical techniques for the characterization of model systems with quantum and statistical mechanical calculations to interpret experimental data and guide the design of future research. Our investigation focuses on the interrelation among the three main mechanisms by which enantioselectivity can be bestowed to heterogeneous catalysts, namely: (1) by templating chirality via the adsorption of chiral supramolecular assemblies, (2) by using chiral modifiers capable of forming chiral complexes with the reactant and force enantioselective surface reactions, and (3) by forming naturally chiral surfaces using imprinting chiral agents. Individually, the members of our team are leaders in these various aspects of chiral catalysis, but the present program provides the vehicle to generate and exploit the synergies necessary to address the problem in a comprehensive manner. Our initial work has advanced the methodology needed for these studies, including an enantioselective titration procedure to identify surface chiral sites, infrared spectroscopy in situ at the interface between gases or liquids and solids to mimic realistic catalytic conditions, and DFT and Monte Carlo algorithms to simulate and understand chirality on surfaces. The next step, to be funded by the monies requested in this proposal, is to apply those methods to specific problems in chiral catalysis, including the identification of the requirements for the formation of supramolecular surface structures with enantioselective behavior, the search for better molecules to probe the chiral nature of the modified surfaces, the exploration of the transition from supramolecular to one-to-one chiral modification, the correlation of the adsorption characteristics of one-to-one chiral modifiers with their physical properties, in particular with their configuration

  19. An O(n(5)) algorithm for MFE prediction of kissing hairpins and 4-chains in nucleic acids.

    Science.gov (United States)

    Chen, Ho-Lin; Condon, Anne; Jabbari, Hosna

    2009-06-01

    Efficient methods for prediction of minimum free energy (MFE) nucleic secondary structures are widely used, both to better understand structure and function of biological RNAs and to design novel nano-structures. Here, we present a new algorithm for MFE secondary structure prediction, which significantly expands the class of structures that can be handled in O(n(5)) time. Our algorithm can handle H-type pseudoknotted structures, kissing hairpins, and chains of four overlapping stems, as well as nested substructures of these types.

  20. Stabilization of the beta-hairpin in Mason-Pfizer monkey virus capsid protein- a critical step for infectivity

    Czech Academy of Sciences Publication Activity Database

    Obr, M.; Hadravová, Romana; Doležal, Michal; Křížová, Ivana; Papoušková, V.; Žídek, L.; Hrabal, R.; Ruml, T.; Rumlová, Michaela

    2014-01-01

    Roč. 11, Oct 30 (2014), 94/1-94/14 ISSN 1742-4690 R&D Projects: GA ČR(CZ) GA14-15326S; GA MŠk LO1302 Grant - others:GA MŠk(CZ) ED1.1.00/02.0068; Seventh Framework Programme of the European Union(XE) FP7-261863 Program:ED Institutional support: RVO:61388963 Keywords : retrovirus * assembly * M-PMV * capsid protein * maturation * beta-hairpin Subject RIV: EE - Microbiology, Virology Impact factor: 4.185, year: 2014 http://www.retrovirology.com/content/11/1/94

  1. Targeting of human interleukin-12B by small hairpin RNAs in xenografted psoriatic skin

    Directory of Open Access Journals (Sweden)

    Jakobsen Maria

    2011-02-01

    Full Text Available Abstract Background Psoriasis is a chronic inflammatory skin disorder that shows as erythematous and scaly lesions. The pathogenesis of psoriasis is driven by a dysregulation of the immune system which leads to an altered cytokine production. Proinflammatory cytokines that are up-regulated in psoriasis include tumor necrosis factor alpha (TNFα, interleukin-12 (IL-12, and IL-23 for which monoclonal antibodies have already been approved for clinical use. We have previously documented the therapeutic applicability of targeting TNFα mRNA for RNA interference-mediated down-regulation by anti-TNFα small hairpin RNAs (shRNAs delivered by lentiviral vectors to xenografted psoriatic skin. The present report aims at targeting mRNA encoding the shared p40 subunit (IL-12B of IL-12 and IL-23 by cellular transduction with lentiviral vectors encoding anti-IL12B shRNAs. Methods Effective anti-IL12B shRNAs are identified among a panel of shRNAs by potency measurements in cultured cells. The efficiency and persistency of lentiviral gene delivery to xenografted human skin are investigated by bioluminescence analysis of skin treated with lentiviral vectors encoding the luciferase gene. shRNA-expressing lentiviral vectors are intradermally injected in xenografted psoriatic skin and the effects of the treatment evaluated by clinical psoriasis scoring, by measurements of epidermal thickness, and IL-12B mRNA levels. Results Potent and persistent transgene expression following a single intradermal injection of lentiviral vectors in xenografted human skin is reported. Stable IL-12B mRNA knockdown and reduced epidermal thickness are achieved three weeks after treatment of xenografted psoriatic skin with lentivirus-encoded anti-IL12B shRNAs. These findings mimick the results obtained with anti-TNFα shRNAs but, in contrast to anti-TNFα treatment, anti-IL12B shRNAs do not ameliorate the psoriatic phenotype as evaluated by semi-quantitative clinical scoring and by

  2. Heterogeneous Catalysis of Polyoxometalate Based Organic–Inorganic Hybrids

    Directory of Open Access Journals (Sweden)

    Yuanhang Ren

    2015-03-01

    Full Text Available Organic–inorganic hybrid polyoxometalate (POM compounds are a subset of materials with unique structures and physical/chemical properties. The combination of metal-organic coordination complexes with classical POMs not only provides a powerful way to gain multifarious new compounds but also affords a new method to modify and functionalize POMs. In parallel with the many reports on the synthesis and structure of new hybrid POM compounds, the application of these compounds for heterogeneous catalysis has also attracted considerable attention. The hybrid POM compounds show noteworthy catalytic performance in acid, oxidation, and even in asymmetric catalytic reactions. This review summarizes the design and synthesis of organic–inorganic hybrid POM compounds and particularly highlights their recent progress in heterogeneous catalysis.

  3. Value-added Chemicals from Biomass by Heterogeneous Catalysis

    DEFF Research Database (Denmark)

    Voss, Bodil

    feedstock, having retained one C-C bond originating from the biomass precursor, the aspects of utilising heterogeneous catalysis for its conversion to value added chemicals is investigated. Through a simple analysis of known, but not industrialised catalytic routes, the direct conversion of ethanol....... The results of the thesis, taking one example of biomass conversion, show that the utilisation of biomass in the production of chemicals by heterogeneous catalysis is promising from a technical point of view. But risks of market price excursions dominated by fossil based chemicals further set a criterion...... been implemented. The subject on chemical production has received less attention. This thesis describes and evaluates the quest for an alternative conversion route, based on a biomass feedstock and employing a heterogeneous catalyst capable of converting the feedstock, to a value-added chemical...

  4. Magnetic Catalysis of Chiral Symmetry Breaking: A Holographic Prospective

    International Nuclear Information System (INIS)

    Filev, V.; Rashkov, R.; Rashkov, R.

    2010-01-01

    We review a recent investigation of the effect of magnetic catalysis of mass generation in holographic Yang-Mills theories. We aim at a self-contained and pedagogical form of the review. We provide a brief field theory background and review the basics of holographic flavordynamics. The main part of the paper investigates the influence of external magnetic field to holographic gauge theories dual to the D3/D5- and D3/D7-brane intersections. Among the observed phenomena are the spontaneous breaking of a global internal symmetry, Zeeman splitting of the energy levels, and the existence of pseudo, Goldstone modes. An analytic derivation of the Gell-Mann-Oaks-Renner relation for the D3/D7 set up is reviewed. In the D3/D5 case, the pseudo-Goldstone modes satisfy nonrelativistic dispersion relation. The studies reviewed confirm the universal nature of the magnetic catalysis of mass generation.

  5. Hydrogen Tunneling Links Protein Dynamics to Enzyme Catalysis

    Science.gov (United States)

    Klinman, Judith P.; Kohen, Amnon

    2014-01-01

    The relationship between protein dynamics and function is a subject of considerable contemporary interest. Although protein motions are frequently observed during ligand binding and release steps, the contribution of protein motions to the catalysis of bond making/breaking processes is more difficult to probe and verify. Here, we show how the quantum mechanical hydrogen tunneling associated with enzymatic C–H bond cleavage provides a unique window into the necessity of protein dynamics for achieving optimal catalysis. Experimental findings support a hierarchy of thermodynamically equilibrated motions that control the H-donor and -acceptor distance and active-site electrostatics, creating an ensemble of conformations suitable for H-tunneling. A possible extension of this view to methyl transfer and other catalyzed reactions is also presented. The impact of understanding these dynamics on the conceptual framework for enzyme activity, inhibitor/drug design, and biomimetic catalyst design is likely to be substantial. PMID:23746260

  6. Homogeneous Catalysis with Metal Complexes Fundamentals and Applications

    CERN Document Server

    Duca, Gheorghe

    2012-01-01

    The book about homogeneous catalysis with metal complexes deals with the description of the reductive-oxidative, metal complexes  in a liquid phase (in polar solvents, mainly in water, and less in nonpolar solvents). The exceptional importance of the redox processes in chemical systems, in the reactions occuring in living organisms, the environmental processes, atmosphere, water, soil, and in industrial technologies (especially in food-processing industries) is discussed. The detailed practical aspects of the established regularities are explained for solving the specific practical tasks in various fields of industrial chemistry, biochemistry, medicine, analytical chemistry and ecological chemistry. The main scope of the book is the survey and systematization of the latest advances in homogeneous catalysis with metal complexes. It gives an overview of the research results and practical experience accumulated by the author during the last decade.

  7. Bionic catalysis of porphyrin for electrochemical detection of nucleic acids

    International Nuclear Information System (INIS)

    Li Jie; Lei Jianping; Wang Quanbo; Wang Peng; Ju Huangxian

    2012-01-01

    Highlights: ► This is the first application of bionic catalysis of porphyrin as detection probe in bioanalysis. ► Porphyrin–DNA–gold nanoparticle probe is synthesized. ► Binding model between FeTMPyP and DNA is verified. ► The detection probe shows excellent electrocatalytic behaviors toward the reduction of O 2 . ► The biosensor exhibited good performance with wide linear range and high specificity. - Abstract: A novel electrochemical strategy was designed for the detection of DNA based on the bionic catalysis of porphyrin. The detection probe was prepared via the assembly of thiolated double strand DNA (dsDNA) with gold nanoparticles (AuNPs), and then interacted with cationic iron (III) meso-tetrakis (N-methylphyridinum-4-yl) porphyrin (FeTMPyP) via groove binding along the dsDNA surface. The resulting nanocomplex was characterized with transmission electron microscopy, UV–vis absorption and circular dichroism spectroscopy. The FeTMPyP–DNA–AuNPs probe on gold electrode demonstrated the excellent electrocatalytic behaviors toward the reduction of O 2 due to the largely loading of FeTMPyP and good conductivity. Based on bionic catalysis of porphyrin for the reduction of O 2 , the resulting biosensor exhibited a good performance for the detection of DNA with a wide linear range from 1 × 10 −12 to 1 × 10 −8 mol L −1 and detection limit of 2.5 × 10 −13 mol L −1 at the signal/noise of 3. More importantly, the biosensor presented excellent ability to discriminate the perfectly complementary target and the mismatched stand. This strategy could be conveniently extended for detection of other biomolecules. To the best of our knowledge, this is the first application of bionic catalysis of porphyrin as detection probe and opens new opportunities for sensitive detection of biorecognition events.

  8. Heterogeneous Catalysis: Understanding for Designing, and Designing for Applications

    OpenAIRE

    Corma Canós, Avelino

    2016-01-01

    Despite the introduction of high-throughput and combinatorial methods that certainly can be useful in the process of catalysts optimization, it is recognized that the generation of fundamental knowledge at the molecular level is key for the development of new concepts and for reaching the final objective of solid catalysts by design … Corma Canós, A. (2016). Heterogeneous Catalysis: Understanding for Designing, and Designing for Applications. Angewandte Chemie International Edition. 55(21)...

  9. Cooperative catalysis by silica-supported organic functional groups

    OpenAIRE

    Margelefsky, Eric L.; Zeidan, Ryan K.; Davis, Mark E.

    2008-01-01

    Hybrid inorganic–organic materials comprising organic functional groups tethered from silica surfaces are versatile, heterogeneous catalysts. Recent advances have led to the preparation of silica materials containing multiple, different functional groups that can show cooperative catalysis; that is, these functional groups can act together to provide catalytic activity and selectivity superior to what can be obtained from either monofunctional materials or homogeneous catalysts. This tutorial...

  10. Chemistry of Fluorinated Carbon Acids: Synthesis, Physicochemical Properties, and Catalysis.

    Science.gov (United States)

    Yanai, Hikaru

    2015-01-01

    The bis[(trifluoromethyl)sulfonyl]methyl (Tf2CH; Tf=SO2CF3) group is known to be one of the strongest carbon acid functionalities. The acidity of such carbon acids in the gas phase is stronger than that of sulfuric acid. Our recent investigations have demonstrated that this type of carbon acids work as novel acid catalysts. In this paper, recent achievements in carbon acid chemistry by our research group, including synthesis, physicochemical properties, and catalysis, are summarized.

  11. Understanding plasma catalysis through modelling and simulation—a review

    International Nuclear Information System (INIS)

    Neyts, E C; Bogaerts, A

    2014-01-01

    Plasma catalysis holds great promise for environmental applications, provided that the process viability can be maximized in terms of energy efficiency and product selectivity. This requires a fundamental understanding of the various processes taking place and especially the mutual interactions between plasma and catalyst. In this review, we therefore first examine the various effects of the plasma on the catalyst and of the catalyst on the plasma that have been described in the literature. Most of these studies are purely experimental. The urgently needed fundamental understanding of the mechanisms underpinning plasma catalysis, however, may also be obtained through modelling and simulation. Therefore, we also provide here an overview of the modelling efforts that have been developed already, on both the atomistic and the macroscale, and we identify the data that can be obtained with these models to illustrate how modelling and simulation may contribute to this field. Last but not least, we also identify future modelling opportunities to obtain a more complete understanding of the various underlying plasma catalytic effects, which is needed to provide a comprehensive picture of plasma catalysis. (paper)

  12. Crown ethers and phase transfer catalysis in polymer science

    CERN Document Server

    Carraher, Charles

    1984-01-01

    Phase transfer catalysis or interfacial catalysis is a syn­ thetic technique involving transport of an organic or inorganic salt from a solid or aqueous phase into an organic liquid where reaction with an organic-soluble substrate takes place. Over the past 15 years there has been an enormous amount of effort invested in the development of this technique in organic synthe­ sis. Several books and numerous review articles have appeared summarizing applications in which low molecular weight catalysts are employed. These generally include either crown ethers or onium salts of various kinds. While the term phase transfer catalysis is relatively new, the concept of using a phasetrans­ fer agent (PTA) is much older~ Both Schnell and Morgan employed such catalysts in synthesis of polymeric species in the early 1950's. Present developments are really extensions of these early applications. It has only been within the last several years that the use of phase transfer processes have been employed in polymer synthesis...

  13. Expanding the peptide beta-turn in alphagamma hybrid sequences: 12 atom hydrogen bonded helical and hairpin turns.

    Science.gov (United States)

    Chatterjee, Sunanda; Vasudev, Prema G; Raghothama, Srinivasarao; Ramakrishnan, Chandrasekharan; Shamala, Narayanaswamy; Balaram, Padmanabhan

    2009-04-29

    Hybrid peptide segments containing contiguous alpha and gamma amino acid residues can form C(12) hydrogen bonded turns which may be considered as backbone expanded analogues of C(10) (beta-turns) found in alphaalpha segments. Exploration of the regular hydrogen bonded conformations accessible for hybrid alphagamma sequences is facilitated by the use of a stereochemically constrained gamma amino acid residue gabapentin (1-aminomethylcyclohexaneacetic acid, Gpn), in which the two torsion angles about C(gamma)-C(beta) (theta(1)) and C(beta)-C(alpha) (theta(2)) are predominantly restricted to gauche conformations. The crystal structures of the octapeptides Boc-Gpn-Aib-Gpn-Aib-Gpn-Aib-Gpn-Aib-OMe (1) and Boc-Leu-Phe-Val-Aib-Gpn-Leu-Phe-Val-OMe (2) reveal two distinct conformations for the Aib-Gpn segment. Peptide 1 forms a continuous helix over the Aib(2)-Aib(6) segment, while the peptide 2 forms a beta-hairpin structure stabilized by four cross-strand hydrogen bonds with the Aib-Gpn segment forming a nonhelical C(12) turn. The robustness of the helix in peptide 1 in solution is demonstrated by NMR methods. Peptide 2 is conformationally fragile in solution with evidence of beta-hairpin conformations being obtained in methanol. Theoretical calculations permit delineation of the various C(12) hydrogen bonded structures which are energetically feasible in alphagamma and gammaalpha sequences.

  14. Dynamics of bleomycin interaction with a strongly bound hairpin DNA substrate, and implications for cleavage of the bound DNA.

    Science.gov (United States)

    Bozeman, Trevor C; Nanjunda, Rupesh; Tang, Chenhong; Liu, Yang; Segerman, Zachary J; Zaleski, Paul A; Wilson, W David; Hecht, Sidney M

    2012-10-31

    Recent studies involving DNAs bound strongly by bleomycins have documented that such DNAs are degraded by the antitumor antibiotic with characteristics different from those observed when studying the cleavage of randomly chosen DNAs in the presence of excess Fe·BLM. In the present study, surface plasmon resonance has been used to characterize the dynamics of BLM B(2) binding to a strongly bound hairpin DNA, to define the effects of Fe(3+), salt, and temperature on BLM-DNA interaction. One strong primary DNA binding site, and at least one much weaker site, were documented. In contrast, more than one strong cleavage site was found, an observation also made for two other hairpin DNAs. Evidence is presented for BLM equilibration between the stronger and weaker binding sites in a way that renders BLM unavailable to other, less strongly bound DNAs. Thus, enhanced binding to a given site does not necessarily result in increased DNA degradation at that site; i.e., for strongly bound DNAs, the facility of DNA cleavage must involve other parameters in addition to the intrinsic rate of C-4' H atom abstraction from DNA sugars.

  15. HTS dual-band bandpass filters using stub-loaded hair-pin resonators for mobile communication systems

    Energy Technology Data Exchange (ETDEWEB)

    Sekiya, N., E-mail: nsekiya@yamanashi.ac.jp; Sugiyama, S.

    2014-09-15

    Highlights: • We have developed a HTS five-pole dual-band bandpass filter using stub-loaded hair-pin resonators. • The proposed dual-band BPF can independently control of the center frequency. • Flexibly adjustment of the bandwidth can be achieved by the H-shaped waveguide. • The proposed BPF is evaluated by simulation and measurement with good agreement. - Abstract: A HTS dual-band bandpass filter is developed to obtain sharp-cut off characteristics for mobile communication systems. The filter is composed of five stub-loaded hair-pin resonators with H-shaped waveguides between them. The main advantage of the proposed filter is to allow independent control of the center frequency of the first and second bands. The bandwidths can be flexibly adjusted using the H-shaped waveguide. An electromagnetic simulator was used to design and analyze the filter, which have a 3.5-GHz center frequency and a 70-MHz (2%) bandwidth for the first band and a 5.0-GHz center frequency and a 100-MHz (2%) bandwidth for the second band. The filter was fabricated using YBa{sub 2}Cu{sub 3}O{sub y} thin film on an Al{sub 2}O{sub 3} substrate. Ground plane was fabricated using Au thin film. The measured frequency responses of the filter tally well with the simulated ones.

  16. The haloarchaeal MCM proteins: bioinformatic analysis and targeted mutagenesis of the β7-β8 and β9-β10 hairpin loops and conserved zinc binding domain cysteines.

    Science.gov (United States)

    Kristensen, Tatjana P; Maria Cherian, Reeja; Gray, Fiona C; MacNeill, Stuart A

    2014-01-01

    The hexameric MCM complex is the catalytic core of the replicative helicase in eukaryotic and archaeal cells. Here we describe the first in vivo analysis of archaeal MCM protein structure and function relationships using the genetically tractable haloarchaeon Haloferax volcanii as a model system. Hfx. volcanii encodes a single MCM protein that is part of the previously identified core group of haloarchaeal MCM proteins. Three structural features of the N-terminal domain of the Hfx. volcanii MCM protein were targeted for mutagenesis: the β7-β8 and β9-β10 β-hairpin loops and putative zinc binding domain. Five strains carrying single point mutations in the β7-β8 β-hairpin loop were constructed, none of which displayed impaired cell growth under normal conditions or when treated with the DNA damaging agent mitomycin C. However, short sequence deletions within the β7-β8 β-hairpin were not tolerated and neither was replacement of the highly conserved residue glutamate 187 with alanine. Six strains carrying paired alanine substitutions within the β9-β10 β-hairpin loop were constructed, leading to the conclusion that no individual amino acid within that hairpin loop is absolutely required for MCM function, although one of the mutant strains displays greatly enhanced sensitivity to mitomycin C. Deletions of two or four amino acids from the β9-β10 β-hairpin were tolerated but mutants carrying larger deletions were inviable. Similarly, it was not possible to construct mutants in which any of the conserved zinc binding cysteines was replaced with alanine, underlining the likely importance of zinc binding for MCM function. The results of these studies demonstrate the feasibility of using Hfx. volcanii as a model system for reverse genetic analysis of archaeal MCM protein function and provide important confirmation of the in vivo importance of conserved structural features identified by previous bioinformatic, biochemical and structural studies.

  17. The haloarchaeal MCM proteins: bioinformatic analysis and targeted mutagenesis of the β7-β8 and β9-β10 hairpin loops and conserved zinc binding domain cysteines

    Directory of Open Access Journals (Sweden)

    Tatjana P Kristensen

    2014-03-01

    Full Text Available The hexameric MCM complex is the catalytic core of the replicative helicase in eukaryotic and archaeal cells. Here we describe the first in vivo analysis of archaeal MCM protein structure and function relationships using the genetically tractable haloarchaeon Haloferax volcanii as a model system. Hfx. volcanii encodes a single MCM protein that is part of the previously identified core group of haloarchaeal MCM proteins. Three structural features of the N-terminal domain of the Hfx. volcanii MCM protein were targeted for mutagenesis: the β7-β8 and β9-β10 β-hairpin loops and putative zinc binding domain. Five strains carrying single point mutations in the β7-β8 β-hairpin loop were constructed, none of which displayed impaired cell growth under normal conditions or when treated with the DNA damaging agent mitomycin C. However, short sequence deletions within the β7-β8 β-hairpin were not tolerated and neither was replacement of the highly conserved residue glutamate 187 with alanine. Six strains carrying paired alanine substitutions within the β9-β10 β-hairpin loop were constructed, leading to the conclusion that no individual amino acid within that hairpin loop is absolutely required for MCM function, although one of the mutant strains displays greatly enhanced sensitivity to mitomycin C. Deletions of two or four amino acids from the β9-β10 β-hairpin were tolerated but mutants carrying larger deletions were inviable. Similarly, it was not possible to construct mutants in which any of the conserved zinc binding cysteines was replaced with alanine, underlining the likely importance of zinc binding for MCM function. The results of these studies demonstrate the feasibility of using Hfx. volcanii as a model system for reverse genetic analysis of archaeal MCM protein function and provide important confirmation of the in vivo importance of conserved structural features identified by previous bioinformatic, biochemical and structural

  18. Acyclic peptides incorporating the d-Phe-2-Abz turn motif: Investigations on antimicrobial activity and propensity to adopt β-hairpin conformations.

    Science.gov (United States)

    Cameron, Alan J; Varnava, Kyriakos G; Edwards, Patrick J B; Harjes, Elena; Sarojini, Vijayalekshmi

    2018-06-14

    Three linear peptides incorporating d-Phe-2-Abz as the turn motif are reported. Peptide 1, a hydrophobic β-hairpin, served as a proof of principle for the design strategy with both NMR and CD spectra strongly suggesting a β-hairpin conformation. Peptides 2 and 3, designed as amphipathic antimicrobials, exhibited broad spectrum antimicrobial activity, with potency in the nanomolar range against Staphylococcus aureus. Both compounds possess a high degree of selectivity, proving non-haemolytic at concentrations 500 to 800 times higher than their respective minimal inhibitory concentrations (MICs) against S. aureus. Peptide 2 induced cell membrane and cell wall disintegration in both S. aureus and Pseudomonas aeruginosa as observed by transmission electron microscopy. Peptide 2 also demonstrated moderate antifungal activity against Candida albicans with an MIC of 50 μM. Synergism was observed with sub-MIC levels of amphotericin B (AmB), leading to nanomolar MICs against C. albicans for peptide 2. Based on circular dichroism spectra, both peptides 2 and 3 appear to exist as a mixture of conformers with the β-hairpin as a minor conformer in aqueous solution, and a slight increase in hairpin population in 50% trifluoroethanol, which was more pronounced for peptide 3. NMR spectra of peptide 2 in a 1:1 CD 3 CN/H 2 O mixture and 30 mM deuterated sodium dodecyl sulfate showed evidence of an extended backbone conformation of the β-strand residues. However, inter-strand rotating frame Overhauser effects (ROE) could not be detected and a loosely defined divergent hairpin structure resulted from ROE structure calculation in CD 3 CN/H 2 O. The loosely defined hairpin conformation is most likely a result of the electrostatic repulsions between cationic strand residues which also probably contribute towards maintaining low haemolytic activity. Copyright © 2018 European Peptide Society and John Wiley & Sons, Ltd.

  19. RNA Catalysis, Thermodynamics and the Origin of Life

    Directory of Open Access Journals (Sweden)

    William G. Scott

    2014-04-01

    Full Text Available The RNA World Hypothesis posits that the first self-replicating molecules were RNAs. RNA self-replicases are, in general, assumed to have employed nucleotide 5ʹ-polyphosphates (or their analogues as substrates for RNA polymerization. The mechanism by which these substrates might be synthesized with sufficient abundance to supply a growing and evolving population of RNAs is problematic for evolutionary hypotheses because non-enzymatic synthesis and assembly of nucleotide 5ʹ-triphosphates (or other analogously activated phosphodiester species is inherently difficult. However, nucleotide 2ʹ,3ʹ-cyclic phosphates are also phosphodiesters, and are the natural and abundant products of RNA degradation. These have previously been dismissed as viable substrates for prebiotic RNA synthesis. We propose that the arguments for their dismissal are based on a flawed assumption, and that nucleotide 2ʹ,3ʹ-cyclic phosphates in fact possess several significant, advantageous properties that indeed make them particularly viable substrates for prebiotic RNA synthesis. An RNA World hypothesis based upon the polymerization of nucleotide 2ʹ,3ʹ-cyclic phosphates possesses additional explanatory power in that it accounts for the observed ribozyme “fossil record”, suggests a viable mechanism for substrate transport across lipid vesicle boundaries of primordial proto-cells, circumvents the problems of substrate scarcity and implausible synthetic pathways, provides for a primitive but effective RNA replicase editing mechanism, and definitively explains why RNA, rather than DNA, must have been the original catalyst. Finally, our analysis compels us to propose that a fundamental and universal property that drives the evolution of living systems, as well as pre-biotic replicating molecules (be they composed of RNA or protein, is that they exploit chemical reactions that already possess competing kinetically-preferred and thermodynamically-preferred pathways in a

  20. Mutation in the β-hairpin of the Bordetella pertussis adenylate cyclase toxin modulates N-lobe conformation in calmodulin

    International Nuclear Information System (INIS)

    Springer, Tzvia I.; Goebel, Erich; Hariraju, Dinesh; Finley, Natosha L.

    2014-01-01

    Highlights: • Bordetella pertussis adenylate cyclase toxin modulates bi-lobal structure of CaM. • The structure and stability of the complex rely on intermolecular associations. • A novel mode of CaM-dependent activation of the adenylate cyclase toxin is proposed. - Abstract: Bordetella pertussis, causative agent of whooping cough, produces an adenylate cyclase toxin (CyaA) that is an important virulence factor. In the host cell, the adenylate cyclase domain of CyaA (CyaA-ACD) is activated upon association with calmodulin (CaM), an EF-hand protein comprised of N- and C-lobes (N-CaM and C-CaM, respectively) connected by a flexible tether. Maximal CyaA-ACD activation is achieved through its binding to both lobes of intact CaM, but the structural mechanisms remain unclear. No high-resolution structure of the intact CaM/CyaA-ACD complex is available, but crystal structures of isolated C-CaM bound to CyaA-ACD shed light on the molecular mechanism by which this lobe activates the toxin. Previous studies using molecular modeling, biochemical, and biophysical experiments demonstrate that CyaA-ACD’s β-hairpin participates in site-specific interactions with N-CaM. In this study, we utilize nuclear magnetic resonance (NMR) spectroscopy to probe the molecular association between intact CaM and CyaA-ACD. Our results indicate binding of CyaA-ACD to CaM induces large conformational perturbations mapping to C-CaM, while substantially smaller structural changes are localized primarily to helices I, II, and IV, and the metal-binding sites in N-CaM. Site-specific mutations in CyaA-ACD’s β-hairpin structurally modulate N-CaM, resulting in conformational perturbations in metal binding sites I and II, while no significant structural modifications are observed in C-CaM. Moreover, dynamic light scattering (DLS) analysis reveals that mutation of the β-hairpin results in a decreased hydrodynamic radius (R h ) and reduced thermal stability in the mutant complex. Taken together

  1. Mutation in the β-hairpin of the Bordetella pertussis adenylate cyclase toxin modulates N-lobe conformation in calmodulin

    Energy Technology Data Exchange (ETDEWEB)

    Springer, Tzvia I.; Goebel, Erich; Hariraju, Dinesh [Department of Microbiology, Miami University, Oxford, OH 45056 (United States); Finley, Natosha L., E-mail: finleynl@miamioh.edu [Department of Microbiology, Miami University, Oxford, OH 45056 (United States); Cell, Molecular, and Structural Biology Program, Miami University, Oxford, OH 45056 (United States)

    2014-10-10

    Highlights: • Bordetella pertussis adenylate cyclase toxin modulates bi-lobal structure of CaM. • The structure and stability of the complex rely on intermolecular associations. • A novel mode of CaM-dependent activation of the adenylate cyclase toxin is proposed. - Abstract: Bordetella pertussis, causative agent of whooping cough, produces an adenylate cyclase toxin (CyaA) that is an important virulence factor. In the host cell, the adenylate cyclase domain of CyaA (CyaA-ACD) is activated upon association with calmodulin (CaM), an EF-hand protein comprised of N- and C-lobes (N-CaM and C-CaM, respectively) connected by a flexible tether. Maximal CyaA-ACD activation is achieved through its binding to both lobes of intact CaM, but the structural mechanisms remain unclear. No high-resolution structure of the intact CaM/CyaA-ACD complex is available, but crystal structures of isolated C-CaM bound to CyaA-ACD shed light on the molecular mechanism by which this lobe activates the toxin. Previous studies using molecular modeling, biochemical, and biophysical experiments demonstrate that CyaA-ACD’s β-hairpin participates in site-specific interactions with N-CaM. In this study, we utilize nuclear magnetic resonance (NMR) spectroscopy to probe the molecular association between intact CaM and CyaA-ACD. Our results indicate binding of CyaA-ACD to CaM induces large conformational perturbations mapping to C-CaM, while substantially smaller structural changes are localized primarily to helices I, II, and IV, and the metal-binding sites in N-CaM. Site-specific mutations in CyaA-ACD’s β-hairpin structurally modulate N-CaM, resulting in conformational perturbations in metal binding sites I and II, while no significant structural modifications are observed in C-CaM. Moreover, dynamic light scattering (DLS) analysis reveals that mutation of the β-hairpin results in a decreased hydrodynamic radius (R{sub h}) and reduced thermal stability in the mutant complex. Taken

  2. Catalysis as a foundational pillar of green chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Anastas, Paul T. [White House Office of Science and Technology Policy, Department of Chemistry, University of Nottingham Nottingham, (United Kingdom); Kirchhoff, Mary M. [U.S. Environmental Protection Agency and Trinity College, Washington, DC (United States); Williamson, Tracy C. [U.S. Environmental Protection Agency, Washington, DC (United States)

    2001-11-30

    Catalysis is one of the fundamental pillars of green chemistry, the design of chemical products and processes that reduce or eliminate the use and generation of hazardous substances. The design and application of new catalysts and catalytic systems are simultaneously achieving the dual goals of environmental protection and economic benefit. Green chemistry, the design of chemical products and processes that reduce or eliminate the use and generation of hazardous substances, is an overarching approach that is applicable to all aspects of chemistry. From feedstocks to solvents, to synthesis and processing, green chemistry actively seeks ways to produce materials in a way that is more benign to human health and the environment. The current emphasis on green chemistry reflects a shift away from the historic 'command-and-control' approach to environmental problems that mandated waste treatment and control and clean up through regulation, and toward preventing pollution at its source. Rather than accepting waste generation and disposal as unavoidable, green chemistry seeks new technologies that are cleaner and economically competitive. Utilizing green chemistry for pollution prevention demonstrates the power and beauty of chemistry: through careful design, society can enjoy the products on which we depend while benefiting the environment. The economic benefits of green chemistry are central drivers in its advancement. Industry is adopting green chemistry methodologies because they improve the corporate bottom line. A wide array of operating costs are decreased through the use of green chemistry. When less waste is generated, environmental compliance costs go down. Treatment and disposal become unnecessary when waste is eliminated. Decreased solvent usage and fewer processing steps lessen the material and energy costs of manufacturing and increase material efficiency. The environmental, human health, and the economic advantages realized through green chemistry

  3. Radio catalysis application in degradation of complex organic samples

    International Nuclear Information System (INIS)

    Moreno L, A.

    2014-01-01

    The generation of wastewater is a consequence of human activities, industries to be the generators of a large part of these discharges. These contaminated waters can be processed for their remediation; however the recalcitrant organic compounds are hardly removed through conventional treatments applied, so that new technologies have been developed for disposal such as the advanced oxidation technologies or processes. With the aim of the study is to apply ionizing radiation as a method of remediation in wastewater, in this work were carried out experiments of radiolysis and radio catalysis, which are techniques considered advanced oxidation technologies, that consist in irradiate with 60 Co gamma radiation solutions of 4- chloro phenol and methylene blue, applied at different concentrations and using as process control measurements of the compound not degraded by UV-vis spectrophotometry at 507 and 664 nm for 4-chloro phenol and methylene blue respectively. At doses greater than 2.5 kGy were near-zero degradation. Degradation experiments were also conducted by photo catalysis by irradiation with a UV lamp of 354 nm wavelength. For 4-chloro phenol results showed that degradation is efficient (39%). With those previous results, these techniques were applied to degrade complex mixtures of organic compounds from samples of wastewater from a sewage treatment plant, where was considered as process control measurement of the dissolved organic carbon obtained by a spectrophotometric analysis at 254 nm, and a maximum of 26% degradation was obtained by applying 80 kGy. On the other hand, a series of experiments fractionating the irradiations at intervals of 20 kGy to obtain a cumulative dose of 80 kGy, which was 2.8 times greater with respect to degradation by radio catalysis with continuous irradiation. (Author)

  4. Organocatalysis: Fundamentals and Comparisons to Metal and Enzyme Catalysis

    Directory of Open Access Journals (Sweden)

    Pierre Vogel

    2016-08-01

    Full Text Available Catalysis fulfills the promise that high-yielding chemical transformations will require little energy and produce no toxic waste. This message is carried by the study of the evolution of molecular catalysis of some of the most important reactions in organic chemistry. After reviewing the conceptual underpinnings of catalysis, we discuss the applications of different catalysts according to the mechanism of the reactions that they catalyze, including acyl group transfers, nucleophilic additions and substitutions, and C–C bond forming reactions that employ umpolung by nucleophilic additions to C=O and C=C double bonds. We highlight the utility of a broad range of organocatalysts other than compounds based on proline, the cinchona alkaloids and binaphthyls, which have been abundantly reviewed elsewhere. The focus is on organocatalysts, although a few examples employing metal complexes and enzymes are also included due to their significance. Classical Brønsted acids have evolved into electrophilic hands, the fingers of which are hydrogen donors (like enzymes or other electrophilic moieties. Classical Lewis base catalysts have evolved into tridimensional, chiral nucleophiles that are N- (e.g., tertiary amines, P- (e.g., tertiary phosphines and C-nucleophiles (e.g., N-heterocyclic carbenes. Many efficient organocatalysts bear electrophilic and nucleophilic moieties that interact simultaneously or not with both the electrophilic and nucleophilic reactants. A detailed understanding of the reaction mechanisms permits the design of better catalysts. Their construction represents a molecular science in itself, suggesting that sooner or later chemists will not only imitate Nature but be able to catalyze a much wider range of reactions with high chemo-, regio-, stereo- and enantioselectivity. Man-made organocatalysts are much smaller, cheaper and more stable than enzymes.

  5. An amplified graphene oxide-based fluorescence aptasensor based on target-triggered aptamer hairpin switch and strand-displacement polymerization recycling for bioassays.

    Science.gov (United States)

    Hu, Kun; Liu, Jinwen; Chen, Jia; Huang, Yong; Zhao, Shulin; Tian, Jianniao; Zhang, Guohai

    2013-04-15

    An amplified graphene oxide (GO) based fluorescence aptasensor based on target-triggered aptamer hairpin switch and strand-displacement polymerization recycling is developed for bioassays. The dye-labeled single-strand DNA (aptamer hairpin) was adsorbed on the surface of GO, which result in the fluorescence quenching of dye, and exhibiting minimal background fluorescence. Upon the target, primer and polymerase, the stem of the aptamer hairpin was opened, and binds with the primer to triggers the circular target strand-displacement polymerization reaction, which produces huge amounts of duplex helixes DNA and lead to strong fluorescence emission due to shielding of nucelobases within its double-helix structure. During the polymerization reaction, the primer was extended, and target was displaced. And the displaced target recognizes and hybridizes with another hairpin probe, triggering the next round of polymerization reaction, and the circle process induces fluorescence signal amplification for the detection of analyte. To test the feasibility of the aptasensor systems, interferon-gamma (IFN-γ) was employed as a model analyte. A detection limit as low as 1.5 fM is obtained based on the GO aptasensor with a linear range of three orders of magnitude. The present method was successfully applied for the detection of IFN-γ in human plasma. Copyright © 2012 Elsevier B.V. All rights reserved.

  6. Plasma Chemistry and Catalysis in Gases and Liquids

    CERN Document Server

    Parvulescu, Vasile I; Lukes, Petr

    2012-01-01

    Filling the gap for a book that not only covers gases but also plasma methods in liquids, this is all set to become the standard reference on the topic. It considers the central aspects in plasma chemistry and plasma catalysis by focusing on the green and environmental applications, while also taking into account their practical and economic viability. With the topics addressed by an international group of major experts, this is a must-have for researchers, PhD students and postdocs specializing in the field.

  7. Charge Transfer and Catalysis at the Metal Support Interface

    Energy Technology Data Exchange (ETDEWEB)

    Baker, Lawrence Robert [Univ. of California, Berkeley, CA (United States)

    2012-07-31

    Kinetic, electronic, and spectroscopic characterization of model Pt–support systems are used to demonstrate the relationship between charge transfer and catalytic activity and selectivity. The results show that charge flow controls the activity and selectivity of supported metal catalysts. This dissertation builds on extensive existing knowledge of metal–support interactions in heterogeneous catalysis. The results show the prominent role of charge transfer at catalytic interfaces to determine catalytic activity and selectivity. Further, this research demonstrates the possibility of selectively driving catalytic chemistry by controlling charge flow and presents solid-state devices and doped supports as novel methods for obtaining electronic control over catalytic reaction kinetics.

  8. Coal-related research, organic chemistry, and catalysis

    International Nuclear Information System (INIS)

    Anon.

    1980-01-01

    Coal chemistry research topics included: H exchange at 400 0 C, breaking C-C bonds in coal, molecular weight estimation using small-angle neutron scattering, 13 C NMR spectra of coals, and tunneling during H/D isotope effects. Studies of coal conversion chemistry included thermolysis of bibenzyl and 1-naphthol, heating of coals in phenol, advanced indirect liquefaction based on Koelbel slurry Fischer-Tropsch reactor, and plasma oxidation of coal minerals. Reactions of PAHs in molten SbCl 3 , a hydrocracking catalyst, were studied. Finally, heterogeneous catalysis (desulfurization etc.) was studied using Cu, Au, and Ni surfaces. 7 figures, 6 tables

  9. Molecular complexity from polyunsaturated substrates: the gold catalysis approach.

    Science.gov (United States)

    Fensterbank, Louis; Malacria, Max

    2014-03-18

    Over the last two decades, electrophilic catalysis relying on platinum(II), gold(I), and gold(III) salts has emerged as a remarkable synthetic methodology. Chemists have discovered a large variety of organic transformations that convert a great assortment of highly functionalized precursors into valuable final products. In many cases, these methodologies offer unique features, allowing access to unprecedented molecular architectures. Due to the mild reaction conditions and high function compatibility, scientists have successfully developed applications in total synthesis of natural products, as well as in asymmetric catalysis. In addition, all these developments have been accompanied by the invention of well-tailored catalysts, so that a palette of different electrophilic agents is now commercially available or readily synthesized at the bench. In some respects, researchers' interests in developing homogeneous gold catalysis can be compared with the Californian gold rush of the 19th century. It has attracted into its fervor thousands of scientists, providing a huge number of versatile and important reports. More notably, it is clear that the contribution to the art of organic synthesis is very valuable, though the quest is not over yet. Because they rely on the intervention of previously unknown types of intermediates, new retrosynthetic disconnections are now possible. In this Account, we discuss our efforts on the use of readily available polyunsaturated precursors, such as enynes, dienynes, allenynes, and allenenes to give access to highly original polycyclic structures in a single operation. These transformations transit via previously undescribed intermediates A, B, D, F, and H that will be encountered later on. All these intermediates have been determined by both ourselves and others by DFT calculations and in some cases have been confirmed on the basis of experimental data. In addition, dual gold activation can be at work in some of these transformations

  10. Inorganic Chemistry in Hydrogen Storage and Biomass Catalysis

    Energy Technology Data Exchange (ETDEWEB)

    Thorn, David [Los Alamos National Laboratory

    2012-06-13

    Making or breaking C-H, B-H, C-C bonds has been at the core of catalysis for many years. Making or breaking these bonds to store or recover energy presents us with fresh challenges, including how to catalyze these transformations in molecular systems that are 'tuned' to minimize energy loss and in molecular and material systems present in biomass. This talk will discuss some challenging transformations in chemical hydrogen storage, and some aspects of the inorganic chemistry we are studying in the development of catalysts for biomass utilization.

  11. USD Catalysis Group for Alternative Energy - Final report

    Energy Technology Data Exchange (ETDEWEB)

    Hoefelmeyer, James

    2014-10-03

    I. Project Summary Catalytic processes are a major technological underpinning of modern society, and are essential to the energy sector in the processing of chemical fuels from natural resources, fine chemicals synthesis, and energy conversion. Advances in catalyst technology are enormously valuable since these lead to reduced chemical waste, reduced energy loss, and reduced costs. New energy technologies, which are critical to future economic growth, are also heavily reliant on catalysts, including fuel cells and photo-electrochemical cells. Currently, the state of South Dakota is underdeveloped in terms of research infrastructure related to catalysis. If South Dakota intends to participate in significant economic growth opportunities that result from advances in catalyst technology, then this area of research needs to be made a high priority for investment. To this end, a focused research effort is proposed in which investigators from The University of South Dakota (USD) and The South Dakota School of Mines and Technology (SDSMT) will contribute to form the South Dakota Catalysis Group (SDCG). The multidisciplinary team of the (SDCG) include: (USD) Dan Engebretson, James Hoefelmeyer, Ranjit Koodali, and Grigoriy Sereda; (SDSMT) Phil Scott Ahrenkiel, Hao Fong, Jan Puszynski, Rajesh Shende, and Jacek Swiatkiewicz. The group is well suited to engage in a collaborative project due to the resources available within the existing programs. Activities within the SDCG will be monitored through an external committee consisting of three distinguished professors in chemistry. The committee will provide expert advice and recommendations to the SDCG. Advisory meetings in which committee members interact with South Dakota investigators will be accompanied by individual oral and poster presentations in a materials and catalysis symposium. The symposium will attract prominent scientists, and will enhance the visibility of research in the state of South Dakota. The SDCG requests

  12. Short-hairpin RNA-mediated stable silencing of Grb2 impairs cell growth and DNA synthesis

    International Nuclear Information System (INIS)

    Di Fulvio, Mauricio; Henkels, Karen M.; Gomez-Cambronero, Julian

    2007-01-01

    Grb2 is an SH2-SH3 protein adaptor responsible for linking growth factor receptors with intracellular signaling cascades. To study the role of Grb2 in cell growth, we have generated a new COS7 cell line (COS7 shGrb2 ), based on RNAi technology, as null mutations in mammalian Grb2 genes are lethal in early development. This novel cell line continuously expresses a short hairpin RNA that targets endogenous Grb2. Stable COS7 shGrb2 cells had the shGrb2 integrated into the genomic DNA and carried on SiL construct (made refractory to the shRNA-mediated interference), but not with an SH2-deficient mutant (R86K). Thus, a viable knock-down and rescue protocol has demonstrated that Grb2 is crucial for cell proliferation

  13. Electronic Detection of DNA Hybridization by Coupling Organic Field-Effect Transistor-Based Sensors and Hairpin-Shaped Probes

    Directory of Open Access Journals (Sweden)

    Corrado Napoli

    2018-03-01

    Full Text Available In this paper, the electronic transduction of DNA hybridization is presented by coupling organic charge-modulated field-effect transistors (OCMFETs and hairpin-shaped probes. These probes have shown interesting properties in terms of sensitivity and selectivity in other kinds of assays, in the form of molecular beacons (MBs. Their integration with organic-transistor based sensors, never explored before, paves the way to a new class of low-cost, easy-to-use, and portable genetic sensors with enhanced performances. Thanks to the peculiar characteristics of the employed sensor, measurements can be performed at relatively high ionic strengths, thus optimizing the probes’ functionality without affecting the detection ability of the device. A complete electrical characterization of the sensor is reported, including calibration with different target concentrations in the measurement environment and selectivity evaluation. In particular, DNA hybridization detection for target concentration as low as 100 pM is demonstrated.

  14. Visual detection of STAT5B gene expression in living cell using the hairpin DNA modified gold nanoparticle beacon.

    Science.gov (United States)

    Xue, Jianpeng; Shan, Lingling; Chen, Haiyan; Li, Yang; Zhu, Hongyan; Deng, Dawei; Qian, Zhiyu; Achilefu, Samuel; Gu, Yueqing

    2013-03-15

    Signal transducer and activator of transcription 5B (STAT5B) is an important protein in JAK-STAT signaling pathway that is responsible for the metastasis and proliferation of tumor cells. Determination of the STAT5B messenger Ribonucleic Acid (mRNA) relating to the STAT5B expression provides insight into the mechanism of tumor progression. In this study, we designed and used a special hairpin deoxyribonucleic acid (DNA) for human STAT5B mRNA to functionalize gold nanoparticles, which served as a beacon for detecting human STAT5B expression. Up to 90% quenching efficiency was achieved. Upon hybridizing with the target mRNA, the hairpin DNA modified gold nanoparticle beacons (hDAuNP beacons) release the fluorophores attached at 5' end of the oligonucleotide sequence. The fluorescence properties of the beacon before and after the hybridization with the complementary DNA were confirmed in vitro. The stability of hDAuNP beacons against degradation by DNase I and GSH indicated that the prepared beacon is stable inside cells. The detected fluorescence in MCF-7 cancer cells correlates with the specific STAT5B mRNA expression, which is consistent with the result from PCR measurement. Fluorescence microscopy showed that the hDAuNP beacons internalized in cells without using transfection agents, with intracellular distribution in the cytoplasm rather than the nucleus. The results demonstrated that this beacon could directly provide quantitative measurement of the intracellular STAT5B mRNA in living cells. Compared to the previous approaches, this beacon has advantages of higher target to background ratio of detection and an increased resistance to nuclease degradation. The strategy reported in this study is a promising approach for the intracellular measurement of RNA or protein expression in living cells, and has great potential in the study of drug screening and discovery. Copyright © 2012 Elsevier B.V. All rights reserved.

  15. Differential RNAi responses of Nicotiana benthamiana individuals transformed with a hairpin-inducing construct during Plum pox virus challenge.

    Science.gov (United States)

    Montes, Christian; Castro, Álvaro; Barba, Paola; Rubio, Julia; Sánchez, Evelyn; Carvajal, Denisse; Aguirre, Carlos; Tapia, Eduardo; DelÍ Orto, Paola; Decroocq, Veronique; Prieto, Humberto

    2014-10-01

    Gene silencing and large-scale small RNA analysis can be used to develop RNA interference (RNAi)-based resistance strategies for Plum pox virus (PPV), a high impact disease of Prunus spp. In this study, a pPPViRNA hairpin-inducing vector harboring two silencing motif-rich regions of the PPV coat protein (CP) gene was evaluated in transgenic Nicotiana benthamiana (NB) plants. Wild-type NB plants infected with a chimeric PPV virus (PPV::GFP) exhibited affected leaves with mosaic chlorosis congruent to GFP fluorescence at 21 day post-inoculation; transgenic lines depicted a range of phenotypes from fully resistant to susceptible. ELISA values and GFP fluorescence intensities were used to select transgenic-resistant (TG-R) and transgenic-susceptible (TG-S) lines for further characterization of small interfering RNAs (siRNAs) by large-scale small RNA sequencing. In infected TG-S and untransformed (WT) plants, the observed siRNAs were nearly exclusively 21- and 22-nt siRNAs that targeted the whole PPV::GFP genome; 24-nt siRNAs were absent in these individuals. Challenged TG-R plants accumulated a full set of 21- to 24-nt siRNAs that were primarily associated with the selected motif-rich regions, indicating that a trans-acting siRNAs process prevented viral multiplication. BLAST analysis identified 13 common siRNA clusters targeting the CP gene. 21-nt siRNA sequences were associated with the 22-nt siRNAs and the scarce 23- and 24-nt molecules in TG-S plants and with most of the observed 22-, 23-, and 24-nt siRNAs in TG-R individuals. These results validate the use of a multi-hot spot silencing vector against PPV and elucidate the molecules by which hairpin-inducing vectors initiate RNAi in vivo.

  16. A study of the influence of charged residues on β-hairpin formation by nuclear magnetic resonance and molecular dynamics.

    Science.gov (United States)

    Makowska, Joanna; Zmudzińska, Wioletta; Uber, Dorota; Chmurzyński, Lech

    2014-12-01

    Chain reversals are often nucleation sites in protein folding. The β-hairpins of FBP28 WW domain and IgG are stable and have been proved to initiate the folding and are, therefore, suitable for studying the influence of charged residues on β-hairpin conformation. In this paper, we carried out NMR examination of the conformations in solution of two fragments from the FPB28 protein (PDB code: 1E0L) (N-terminal part) namely KTADGKT-NH2 (1E0L 12-18, D7) and YKTADGKTY-NH2 (1E0L 11-19, D9), one from the B3 domain of the protein G (PDB code: 1IGD), namely DDATKT-NH2 (1IGD 51-56) (Dag1), and three variants of Dag1 peptide: DVATKT-NH2 (Dag2), OVATKT-NH2 (Dag3) and KVATKT-NH2 (Dag4), respectively, in which the original charged residue were replaced with non-polar residues or modified charged residues. It was found that both the D7 and D9 peptides form a large fraction bent conformations. However, no hydrophobic contacts between the terminal Tyr residues of D9 occur, which suggests that the presence of a pair of like-charged residues stabilizes chain reversal. Conversely, only the Dag1 and Dag2 peptides exhibit some chain reversal; replacing the second aspartic-acid residue with a valine and the first one with a basic residue results in a nearly extended conformation. These results suggest that basic residues farther away in sequence can result in stabilization of chain reversal owing to screening of the non-polar core. Conversely, smaller distance in sequence prohibits this screening, while the presence oppositely-charged residues can stabilize a turn because of salt-bridge formation.

  17. On the origin of the cobalt particle size effects in Fischer−Tropsch catalysis

    NARCIS (Netherlands)

    den Breejen, J.P.|info:eu-repo/dai/nl/304837318; Radstake, P.B.|info:eu-repo/dai/nl/304829587; Bezemer, G.L.; Bitter, J.H.|info:eu-repo/dai/nl/160581435; Froseth, V.; Holmen, A.; de Jong, K.P.|info:eu-repo/dai/nl/06885580X

    2009-01-01

    The effects of metal particle size in catalysis are of prime scientific and industrial importance and call for a better understanding. In this paper the origin of the cobalt particle size effects in Fischer−Tropsch (FT) catalysis was studied. Steady-State Isotopic Transient Kinetic Analysis (SSITKA)

  18. [Prediction of common buffer catalysis in hydrolysis of fenchlorazole-ethyl].

    Science.gov (United States)

    Lin, Jing; Chen, Jing-wen; Zhang, Si-yu; Cai, Xi-yun; Qiao, Xian-liang

    2008-09-01

    The purpose of this study was to elucidate the effects of temperatures, pH levels and buffer catalysis on the hydrolysis of FCE. The hydrolysis of FCE follows first-order kinetics at different pH levels and temperatures. FCE hydrolysis rates are greatly increased at elevated pH levels and temperatures. The maximum contribution of buffer catalysis to the hydrolysis of FCE was assessed based on application of the Bronsted equations for general acid-base catalysis. The results suggest that the buffer solutions play an obvious catalysis role in hydrolysis of FCE and the hydrolysis rates of FCE are quickened by the buffer solutions. Besides, the buffer catalysis capacity of different buffer solutions is diverse, and the buffer catalysis capacity at different pH levels with the same buffer solutions is different, too. The phosphate buffer at pH = 7 shows the maximal buffer catalysis capacity. The hydrolysis rate constants of FCE as a function of temperature and pH, which were remedied by the buffer catalysis factor, were mathematically combined to predict the hydrolytic dissipation of FCE. The equation suggests that the hydrolysis half-lives of FCE ranged from 7 d to 790 d. Hydrolysis metabolites of FCE were identified by liquid chromatography-mass spectrometry. In basic conditions (pH 8-10), fenchlorazole was formed via breakdown of the ester bond of the safener.

  19. Asymmetric Aldol Additions: A Guided-Inquiry Laboratory Activity on Catalysis

    Science.gov (United States)

    King, Jorge H. Torres; Wang, Hong; Yezierski, Ellen J.

    2018-01-01

    Despite the importance of asymmetric catalysis in both the pharmaceutical and commodity chemicals industries, asymmetric catalysis is under-represented in undergraduate chemistry laboratory curricula. A novel guided-inquiry experiment based on the asymmetric aldol addition was developed. Students conduct lab work to compare the effectiveness of…

  20. Curcumin stably interacts with DNA hairpin through minor groove binding and demonstrates enhanced cytotoxicity in combination with FdU nucleotides.

    Science.gov (United States)

    Ghosh, Supratim; Mallick, Sumana; Das, Upasana; Verma, Ajay; Pal, Uttam; Chatterjee, Sabyasachi; Nandy, Abhishek; Saha, Krishna D; Maiti, Nakul Chandra; Baishya, Bikash; Suresh Kumar, G; Gmeiner, William H

    2018-03-01

    We report, based on biophysical studies and molecular mechanical calculations that curcumin binds DNA hairpin in the minor groove adjacent to the loop region forming a stable complex. UV-Vis and fluorescence spectroscopy indicated interaction of curcumin with DNA hairpin. In this novel binding motif, two ɣ H of curcumin heptadiene chain are closely positioned to the A 16 -H8 and A 17 -H8, while G 12 -H8 is located in the close proximity of curcumin α H. Molecular dynamics (MD) simulations suggest, the complex is stabilized by noncovalent forces including; π-π stacking, H-bonding and hydrophobic interactions. Nuclear magnetic resonance (NMR) spectroscopy in combination with molecular dynamics simulations indicated curcumin is bound in the minor groove, while circular dichroism (CD) spectra suggested minute enhancement in base stacking and a little change in DNA helicity, without significant conformational change of DNA hairpin structure. The DNA:curcumin complex formed with FdU nucleotides rather than Thymidine, demonstrated enhanced cytotoxicity towards oral cancer cells relative to the only FdU substituted hairpin. Fluorescence co-localization demonstrated stability of the complex in biologically relevant conditions, including its cellular uptake. Acridine orange/EtBr staining further confirmed the enhanced cytotoxic effects of the complex, suggesting apoptosis as mode of cell death. Thus, curcumin can be noncovalently complexed to small DNA hairpin for cellular delivery and the complex showed increased cytotoxicity in combination with FdU nucleotides, demonstrating its potential for advanced cancer therapy. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Catalysis of heat-to-work conversion in quantum machines

    Science.gov (United States)

    Ghosh, A.; Latune, C. L.; Davidovich, L.; Kurizki, G.

    2017-11-01

    We propose a hitherto-unexplored concept in quantum thermodynamics: catalysis of heat-to-work conversion by quantum nonlinear pumping of the piston mode which extracts work from the machine. This concept is analogous to chemical reaction catalysis: Small energy investment by the catalyst (pump) may yield a large increase in heat-to-work conversion. Since it is powered by thermal baths, the catalyzed machine adheres to the Carnot bound, but may strongly enhance its efficiency and power compared with its noncatalyzed counterparts. This enhancement stems from the increased ability of the squeezed piston to store work. Remarkably, the fraction of piston energy that is convertible into work may then approach unity. The present machine and its counterparts powered by squeezed baths share a common feature: Neither is a genuine heat engine. However, a squeezed pump that catalyzes heat-to-work conversion by small investment of work is much more advantageous than a squeezed bath that simply transduces part of the work invested in its squeezing into work performed by the machine.

  2. Structural basis for catalysis at the membrane-water interface.

    Science.gov (United States)

    Dufrisne, Meagan Belcher; Petrou, Vasileios I; Clarke, Oliver B; Mancia, Filippo

    2017-11-01

    The membrane-water interface forms a uniquely heterogeneous and geometrically constrained environment for enzymatic catalysis. Integral membrane enzymes sample three environments - the uniformly hydrophobic interior of the membrane, the aqueous extramembrane region, and the fuzzy, amphipathic interfacial region formed by the tightly packed headgroups of the components of the lipid bilayer. Depending on the nature of the substrates and the location of the site of chemical modification, catalysis may occur in each of these environments. The availability of structural information for alpha-helical enzyme families from each of these classes, as well as several beta-barrel enzymes from the bacterial outer membrane, has allowed us to review here the different ways in which each enzyme fold has adapted to the nature of the substrates, products, and the unique environment of the membrane. Our focus here is on enzymes that process lipidic substrates. This article is part of a Special Issue entitled: Bacterial Lipids edited by Russell E. Bishop. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Acid-base catalysis of N-[(morpholine)methylene]daunorubicin.

    Science.gov (United States)

    Krause, Anna; Jelińska, Anna; Cielecka-Piontek, Judyta; Klawitter, Maria; Zalewski, Przemysław; Oszczapowicz, Irena; Wąsowska, Małgorzata

    2012-08-01

    The stability of N-[(morpholine)methylene]-daunorubicin hydrochloride (MMD) was investigated in the pH range 0.44-13.54, at 313, 308, 303 and 298 K. The degradation of MMD as a result of hydrolysis is a pseudo-first-order reaction described by the following equation: ln c = ln c(0) - k(obs)• t. In the solutions of hydrochloric acid, sodium hydroxide, borate, acetate and phosphate buffers, k(obs) = k(pH) because general acid-base catalysis was not observed. Specific acid-base catalysis of MMD comprises the following reactions: hydrolysis of the protonated molecules of MMD catalyzed by hydrogen ions (k(1)) and spontaneous hydrolysis of MMD molecules other than the protonated ones (k(2)) under the influence of water. The total rate of the reaction is equal to the sum of partial reactions: k(pH) = k(1) • a(H)+ • f(1) + k(2) • f(2) where: k(1) is the second-order rate constant (mol(-1) l s(-1)) of the specific hydrogen ion-catalyzed degradation of the protonated molecules of MMD; k(2) is the pseudo-first-order rate constant (s(-1)) of the water-catalyzed degradation of MMD molecules other than the protonated ones, f(1) - f(2) are fractions of the compound. MMD is the most stable at approx. pH 2.5.

  4. Conformational Dynamics of Thermus aquaticus DNA Polymerase I during Catalysis

    Science.gov (United States)

    Suo, Zucai

    2014-01-01

    Despite the fact that DNA polymerases have been investigated for many years and are commonly used as tools in a number of molecular biology assays, many details of the kinetic mechanism they use to catalyze DNA synthesis remain unclear. Structural and kinetic studies have characterized a rapid, pre-catalytic open-to-close conformational change of the Finger domain during nucleotide binding for many DNA polymerases including Thermus aquaticus DNA polymerase I (Taq Pol), a thermostable enzyme commonly used for DNA amplification in PCR. However, little has been done to characterize the motions of other structural domains of Taq Pol or any other DNA polymerase during catalysis. Here, we used stopped-flow Förster resonance energy transfer (FRET) to investigate the conformational dynamics of all five structural domains of the full-length Taq Pol relative to the DNA substrate during nucleotide binding and incorporation. Our study provides evidence for a rapid conformational change step induced by dNTP binding and a subsequent global conformational transition involving all domains of Taq Pol during catalysis. Additionally, our study shows that the rate of the global transition was greatly increased with the truncated form of Taq Pol lacking the N-terminal domain. Finally, we utilized a mutant of Taq Pol containing a de novo disulfide bond to demonstrate that limiting protein conformational flexibility greatly reduced the polymerization activity of Taq Pol. PMID:24931550

  5. Oxidase catalysis via aerobically generated hypervalent iodine intermediates

    Science.gov (United States)

    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.

  6. Characterization techniques for graphene-based materials in catalysis

    Directory of Open Access Journals (Sweden)

    Maocong Hu

    2017-06-01

    Full Text Available Graphene-based materials have been studied in a wide range of applications including catalysis due to the outstanding electronic, thermal, and mechanical properties. The unprecedented features of graphene-based catalysts, which are believed to be responsible for their superior performance, have been characterized by many techniques. In this article, we comprehensively summarized the characterization methods covering bulk and surface structure analysis, chemisorption ability determination, and reaction mechanism investigation. We reviewed the advantages/disadvantages of different techniques including Raman spectroscopy, X-ray photoelectron spectroscopy (XPS, Fourier transform infrared spectroscopy (FTIR and Diffuse Reflectance Fourier Transform Infrared Spectroscopy (DRIFTS, X-Ray diffraction (XRD, X-ray absorption near edge structure (XANES and X-ray absorption fine structure (XAFS, atomic force microscopy (AFM, scanning electron microscopy (SEM, transmission electron microscopy (TEM, high-resolution transmission electron microscopy (HRTEM, ultraviolet-visible spectroscopy (UV-vis, X-ray fluorescence (XRF, inductively coupled plasma mass spectrometry (ICP, thermogravimetric analysis (TGA, Brunauer–Emmett–Teller (BET, and scanning tunneling microscopy (STM. The application of temperature-programmed reduction (TPR, CO chemisorption, and NH3/CO2-temperature-programmed desorption (TPD was also briefly introduced. Finally, we discussed the challenges and provided possible suggestions on choosing characterization techniques. This review provides key information to catalysis community to adopt suitable characterization techniques for their research.

  7. Stabilizing ultrasmall Au clusters for enhanced photoredox catalysis.

    Science.gov (United States)

    Weng, Bo; Lu, Kang-Qiang; Tang, Zichao; Chen, Hao Ming; Xu, Yi-Jun

    2018-04-18

    Recently, loading ligand-protected gold (Au) clusters as visible light photosensitizers onto various supports for photoredox catalysis has attracted considerable attention. However, the efficient control of long-term photostability of Au clusters on the metal-support interface remains challenging. Herein, we report a simple and efficient method for enhancing the photostability of glutathione-protected Au clusters (Au GSH clusters) loaded on the surface of SiO 2 sphere by utilizing multifunctional branched poly-ethylenimine (BPEI) as a surface charge modifying, reducing and stabilizing agent. The sequential coating of thickness controlled TiO 2 shells can further significantly improve the photocatalytic efficiency, while such structurally designed core-shell SiO 2 -Au GSH clusters-BPEI@TiO 2 composites maintain high photostability during longtime light illumination conditions. This joint strategy via interfacial modification and composition engineering provides a facile guideline for stabilizing ultrasmall Au clusters and rational design of Au clusters-based composites with improved activity toward targeting applications in photoredox catalysis.

  8. Contrast and Synergy between Electrocatalysis and Heterogeneous Catalysis

    Directory of Open Access Journals (Sweden)

    Andrzej Wieckowski

    2011-01-01

    Full Text Available The advances in spectroscopy and theory that have occurred over the past two decades begin to provide detailed in situ resolution of the molecular transformations that occur at both gas/metal as well as aqueous/metal interfaces. These advances begin to allow for a more direct comparison of heterogeneous catalysis and electrocatalysis. Such comparisons become important, as many of the current energy conversion strategies involve catalytic and electrocatalytic processes that occur at fluid/solid interfaces and display very similar characteristics. Herein, we compare and contrast a few different catalytic and electrocatalytic systems to elucidate the principles that cross-cut both areas and establish characteristic differences between the two with the hope of advancing both areas.

  9. REALCAT: A New Platform to Bring Catalysis to the Lightspeed

    Directory of Open Access Journals (Sweden)

    Paul Sébastien

    2015-03-01

    Full Text Available Catalysis, irrespective of its form can be considered as one of the most important pillars of today’s chemical industry. The development of new catalysts with improved performances is therefore a highly strategic issue. However, the a priori theoretical design of the best catalyst for a desired reaction is not yet possible and a time- and money-consuming experimental phase is still needed to develop a new catalyst for a given reaction. The REALCAT platform described in this paper consists in a complete, unique, integrated and top-level high-throughput technologies workflow that allows a significant acceleration of this kind of research. This is illustrated by some preliminary results of optimization of the operating conditions of glycerol dehydration to acrolein over an heteropolyacid-based supported catalyst. It is shown that using REALCAT high-throughput tools a more than 10-fold acceleration of the operating conditions optimization process is obtained.

  10. Advanced electron microscopy characterization of nanomaterials for catalysis

    Directory of Open Access Journals (Sweden)

    Dong Su

    2017-04-01

    Full Text Available Transmission electron microscopy (TEM has become one of the most powerful techniques in the fields of material science, inorganic chemistry and nanotechnology. In terms of resolutions, advanced TEM may reach a high spatial resolution of 0.05 nm, a high energy-resolution of 7 meV. In addition, in situ TEM can help researchers to image the process happened within 1 ms. This paper reviews the recent technical progresses of applying advanced TEM characterization on nanomaterials for catalysis. The text is organized based on the perspective of application: for example, size, composition, phase, strain, and morphology. The electron beam induced effect and in situ TEM are also introduced. I hope this review can help the scientists in related fields to take advantage of advanced TEM to their own researches. Keywords: Advanced TEM, Nanomaterials, Catalysts, In situ

  11. Gravitational catalysis of merons in Einstein-Yang-Mills theory

    Science.gov (United States)

    Canfora, Fabrizio; Oh, Seung Hun; Salgado-Rebolledo, Patricio

    2017-10-01

    We construct regular configurations of the Einstein-Yang-Mills theory in various dimensions. The gauge field is of meron-type: it is proportional to a pure gauge (with a suitable parameter λ determined by the field equations). The corresponding smooth gauge transformation cannot be deformed continuously to the identity. In the three-dimensional case we consider the inclusion of a Chern-Simons term into the analysis, allowing λ to be different from its usual value of 1 /2 . In four dimensions, the gravitating meron is a smooth Euclidean wormhole interpolating between different vacua of the theory. In five and higher dimensions smooth meron-like configurations can also be constructed by considering warped products of the three-sphere and lower-dimensional Einstein manifolds. In all cases merons (which on flat spaces would be singular) become regular due to the coupling with general relativity. This effect is named "gravitational catalysis of merons".

  12. Catalysis by Dust Grains in the Solar Nebula

    Science.gov (United States)

    Kress, Monika E.; Tielens, Alexander G. G. M.

    1996-01-01

    In order to determine whether grain-catalyzed reactions played an important role in the chemistry of the solar nebula, we have applied our time-dependent model of methane formation via Fischer-Tropsch catalysis to pressures from 10(exp -5) to 1 bar and temperatures from 450 to 650 K. Under these physical conditions, the reaction 3H2 + CO yields CH4 + H2O is readily catalyzed by an iron or nickel surface, whereas the same reaction is kinetically inhibited in the gas phase. Our model results indicate that under certain nebular conditions, conversion of CO to methane could be extremely efficient in the presence of iron-nickel dust grains over timescales very short compared to the lifetime of the solar nebula.

  13. Enzymatic catalysis treatment method of meat industry wastewater using lacasse.

    Science.gov (United States)

    Thirugnanasambandham, K; Sivakumar, V

    2015-01-01

    The process of meat industry produces in a large amount of wastewater that contains high levels of colour and chemical oxygen demand (COD). So they must be pretreated before their discharge into the ecological system. In this paper, enzymatic catalysis (EC) was adopted to treat the meat wastewater. Box-Behnken design (BBD), an experimental design for response surface methodology (RSM), was used to create a set of 29 experimental runs needed for optimizing of the operating conditions. Quadratic regression models with estimated coefficients were developed to describe the colour and COD removals. The experimental results show that EC could effectively reduce colour (95 %) and COD (86 %) at the optimum conditions of enzyme dose of 110 U/L, incubation time of 100 min, pH of 7 and temperature of 40 °C. RSM could be effectively adopted to optimize the operating multifactors in complex EC process.

  14. Catalysis and Downsizing in Mg-Based Hydrogen Storage Materials

    Directory of Open Access Journals (Sweden)

    Jianding Li

    2018-02-01

    Full Text Available Magnesium (Mg-based materials are promising candidates for hydrogen storage due to the low cost, high hydrogen storage capacity and abundant resources of magnesium for the realization of a hydrogen society. However, the sluggish kinetics and strong stability of the metal-hydrogen bonding of Mg-based materials hinder their application, especially for onboard storage. Many researchers are devoted to overcoming these challenges by numerous methods. Here, this review summarizes some advances in the development of Mg-based hydrogen storage materials related to downsizing and catalysis. In particular, the focus is on how downsizing and catalysts affect the hydrogen storage capacity, kinetics and thermodynamics of Mg-based hydrogen storage materials. Finally, the future development and applications of Mg-based hydrogen storage materials is discussed.

  15. Catalysis by metal-organic frameworks: fundamentals and opportunities.

    Science.gov (United States)

    Ranocchiari, Marco; van Bokhoven, Jeroen Anton

    2011-04-14

    Crystalline porous materials are extremely important for developing catalytic systems with high scientific and industrial impact. Metal-organic frameworks (MOFs) show unique potential that still has to be fully exploited. This perspective summarizes the properties of MOFs with the aim to understand what are possible approaches to catalysis with these materials. We categorize three classes of MOF catalysts: (1) those with active site on the framework, (2) those with encapsulated active species, and (3) those with active sites attached through post-synthetic modification. We identify the tunable porosity, the ability to fine tune the structure of the active site and its environment, the presence of multiple active sites, and the opportunity to synthesize structures in which key-lock bonding of substrates occurs as the characteristics that distinguish MOFs from other materials. We experience a unique opportunity to imagine and design heterogeneous catalysts, which might catalyze reactions previously thought impossible.

  16. Quantifying the limits of transition state theory in enzymatic catalysis.

    Science.gov (United States)

    Zinovjev, Kirill; Tuñón, Iñaki

    2017-11-21

    While being one of the most popular reaction rate theories, the applicability of transition state theory to the study of enzymatic reactions has been often challenged. The complex dynamic nature of the protein environment raised the question about the validity of the nonrecrossing hypothesis, a cornerstone in this theory. We present a computational strategy to quantify the error associated to transition state theory from the number of recrossings observed at the equicommittor, which is the best possible dividing surface. Application of a direct multidimensional transition state optimization to the hydride transfer step in human dihydrofolate reductase shows that both the participation of the protein degrees of freedom in the reaction coordinate and the error associated to the nonrecrossing hypothesis are small. Thus, the use of transition state theory, even with simplified reaction coordinates, provides a good theoretical framework for the study of enzymatic catalysis. Copyright © 2017 the Author(s). Published by PNAS.

  17. Cooperative catalysis with block copolymer micelles: A combinatorial approach

    KAUST Repository

    Bukhryakov, Konstantin V.

    2015-02-09

    A rapid approach to identifying complementary catalytic groups using combinations of functional polymers is presented. Amphiphilic polymers with "clickable" hydrophobic blocks were used to create a library of functional polymers, each bearing a single functionality. The polymers were combined in water, yielding mixed micelles. As the functional groups were colocalized in the hydrophobic microphase, they could act cooperatively, giving rise to new modes of catalysis. The multipolymer "clumps" were screened for catalytic activity, both in the presence and absence of metal ions. A number of catalyst candidates were identified across a wide range of model reaction types. One of the catalytic systems discovered was used to perform a number of preparative-scale syntheses. Our approach provides easy access to a range of enzyme-inspired cooperative catalysts.

  18. Molecular surface science of heterogeneous catalysis. History and perspective

    International Nuclear Information System (INIS)

    Somorjai, G.A.

    1983-08-01

    A personal account is given of how the author became involved with modern surface science and how it was employed for studies of the chemistry of surfaces and heterogeneous catalysis. New techniques were developed for studying the properties of the surface monolayers: Auger electron spectroscopy, LEED, XPS, molecular beam surface scattering, etc. An apparatus was developed and used to study hydrocarbon conversion reactions on Pt, CO hydrogenation on Rh and Fe, and NH 3 synthesis on Fe. A model has been developed for the working Pt reforming catalyst. The three molecular ingredients that control catalytic properties are atomic surface structure, an active carbonaceous deposit, and the proper oxidation state of surface atoms. 40 references, 21 figures

  19. Molecular surface science of heterogeneous catalysis. History and perspective

    Energy Technology Data Exchange (ETDEWEB)

    Somorjai, G.A.

    1983-08-01

    A personal account is given of how the author became involved with modern surface science and how it was employed for studies of the chemistry of surfaces and heterogeneous catalysis. New techniques were developed for studying the properties of the surface monolayers: Auger electron spectroscopy, LEED, XPS, molecular beam surface scattering, etc. An apparatus was developed and used to study hydrocarbon conversion reactions on Pt, CO hydrogenation on Rh and Fe, and NH/sub 3/ synthesis on Fe. A model has been developed for the working Pt reforming catalyst. The three molecular ingredients that control catalytic properties are atomic surface structure, an active carbonaceous deposit, and the proper oxidation state of surface atoms. 40 references, 21 figures. (DLC)

  20. Cooperative catalysis with block copolymer micelles: A combinatorial approach

    KAUST Repository

    Bukhryakov, Konstantin V.; Desyatkin, Victor G.; O'Shea, John Paul; Almahdali, Sarah; Solovyeva, Vera; Rodionov, Valentin

    2015-01-01

    A rapid approach to identifying complementary catalytic groups using combinations of functional polymers is presented. Amphiphilic polymers with "clickable" hydrophobic blocks were used to create a library of functional polymers, each bearing a single functionality. The polymers were combined in water, yielding mixed micelles. As the functional groups were colocalized in the hydrophobic microphase, they could act cooperatively, giving rise to new modes of catalysis. The multipolymer "clumps" were screened for catalytic activity, both in the presence and absence of metal ions. A number of catalyst candidates were identified across a wide range of model reaction types. One of the catalytic systems discovered was used to perform a number of preparative-scale syntheses. Our approach provides easy access to a range of enzyme-inspired cooperative catalysts.

  1. A solvable two-species catalysis-driven aggregation model

    CERN Document Server

    Ke Jian Hong

    2003-01-01

    We study the kinetics of a two-species catalysis-driven aggregation system, in which an irreversible aggregation between any two clusters of one species occurs only with the catalytic action of another species. By means of a generalized mean-field rate equation, we obtain the asymptotic solutions of the cluster mass distributions in a simple process with a constant rate kernel. For the case without any consumption of the catalyst, the cluster mass distribution of either species always approaches a conventional scaling law. However, the evolution behaviour of the system in the case with catalyst consumption is complicated and depends crucially on the relative data of the initial concentrations of the two species.

  2. Mesostructure-Induced Selectivity in CO2 Reduction Catalysis.

    Science.gov (United States)

    Hall, Anthony Shoji; Yoon, Youngmin; Wuttig, Anna; Surendranath, Yogesh

    2015-12-02

    Gold inverse opal (Au-IO) thin films are active for CO2 reduction to CO with high efficiency at modest overpotentials and high selectivity relative to hydrogen evolution. The specific activity for hydrogen evolution diminishes by 10-fold with increasing porous film thickness, while CO evolution activity is largely unchanged. We demonstrate that the origin of hydrogen suppression in Au-IO films stems from the generation of diffusional gradients within the pores of the mesostructured electrode rather than changes in surface faceting or Au grain size. For electrodes with optimal mesoporosity, 99% selectivity for CO evolution can be obtained at overpotentials as low as 0.4 V. These results establish electrode mesostructuring as a complementary method for tuning selectivity in CO2-to-fuels catalysis.

  3. Atomically precise cluster catalysis towards quantum controlled catalysts

    International Nuclear Information System (INIS)

    Watanabe, Yoshihide

    2014-01-01

    Catalysis of atomically precise clusters supported on a substrate is reviewed in relation to the type of reactions. The catalytic activity of supported clusters has generally been discussed in terms of electronic structure. Several lines of evidence have indicated that the electronic structure of clusters and the geometry of clusters on a support, including the accompanying cluster-support interaction, are strongly correlated with catalytic activity. The electronic states of small clusters would be easily affected by cluster–support interactions. Several studies have suggested that it is possible to tune the electronic structure through atomic control of the cluster size. It is promising to tune not only the number of cluster atoms, but also the hybridization between the electronic states of the adsorbed reactant molecules and clusters in order to realize a quantum-controlled catalyst. (review)

  4. Catalysis. Innovative applications in petrochemistry and refining. Preprints

    Energy Technology Data Exchange (ETDEWEB)

    Ernst, S.; Balfanz, U.; Jess, A.; Lercher, J.A.; Lichtscheidl, J.; Marchionna, M.; Nees, F.; Santacesaria, E. (eds.)

    2011-07-01

    Within the DGMK conference at 4th to 6th October, 2011 in Dresden (Federal Republic of Germany) the following lectures were held: (1) Developing linear-alpha-olefins technology - From laboratory to a commercial plant (A. Meiswinkel); (2) New developments in oxidation catalysis (F. Rosowski); (3) Study of the performance of vanadium based catalysts prepared by grafting in the oxidative dehydrogenation of propane (E. Santacesaria); (4) Hydrocracking for oriented conversion of heavy oils: recent trends for catalyst development (F. Bertoncini); (5) Acidic ionic liquids for n-alkane isomerization in a liquid-liquid or slurry-phase reaction mode (C. Meyer); (6) Dual catalyst system for the hydrocracking of heavy oils and residues (G. Bellussi); (7) Understanding hydrodenitrogenation on novel unsupported sulphide Mo-W-Ni catalysts (J. Hein); (8) Hydrocracking of ethyllaurate on bifunctional micro-/mesoporous composite materials (M. Adam); (9) Catalytic dehydration of ethanol to ethylene (Ying Zhu); (10) The Evonik-Uhde HPPO process for propylene oxide production (B. Jaeger); (11) A green two-step process for adipic acid production from cyclohexene: A study on parameters affecting selectivity (F. Cavani); (12) DISY: The direct synthesis of hydrogen peroxide, a bridge for innovative applications (R, Buzzoni); (13) Solid catalyst with ionic liquid layer (SCILL) - A concept to improve the selectivity of selective hydrogenations (A. Jess); (14) Co-Zn-Al based hydrotalcites as catalysts for Fischer-Tropsch process (C.L. Bianchi); (15) Honeycomb supports with high thermal conductivity for the Fischer-Tropsch synthesis (C.G. Visconti); (16) How to make Fischer-Tropsch catalyst scale-up fully reliable (L. Fischer); (17) New developments in FCC catalysis (C.P. Kelkar); (18) The potential of medium-pore zeolites for improved propene yields from catalytic cracking (F. Bager).

  5. Catalysis Science Initiative: Catalyst Design by Discovery Informatics

    Energy Technology Data Exchange (ETDEWEB)

    Delgass, William Nicholas [Purdue Univ., West Lafayette, IN (United States). Chemical Engineering; Abu-Omar, Mahdi [Purdue Univ., West Lafayette, IN (United States) Department of Chemistry; Caruthers, James [Purdue Univ., West Lafayette, IN (United States). Chemical Engineering; Ribeiro, Fabio [Purdue Univ., West Lafayette, IN (United States). Chemical Engineering; Thomson, Kendall [Purdue Univ., West Lafayette, IN (United States). Chemical Engineering; Schneider, William [Univ. of Notre Dame, IN (United States)

    2016-07-08

    Catalysts selectively enhance the rates of chemical reactions toward desired products. Such reactions provide great benefit to society in major commercial sectors such as energy production, protecting the environment, and polymer products and thereby contribute heavily to the country’s gross national product. Our premise is that the level of fundamental understanding of catalytic events at the atomic and molecular scale has reached the point that more predictive methods can be developed to shorten the cycle time to new processes. The field of catalysis can be divided into two regimes: heterogeneous and homogeneous. For the heterogeneous catalysis regime, we have used the water-gas shift (WGS) reaction (CO + H2O + CO2 + H2O) over supported metals as a test bed. Detailed analysis and strong coupling of theory with experiment have led to the following conclusions: • The sequence of elementary steps goes through a COOH intermediate • The CO binding energy is a strong function of coverage of CO adsorbed on the surface in many systems • In the case of Au catalysts, the CO adsorption is generally too weak on surface with close atomic packing, but the enhanced binding at corner atoms (which are missing bonding partners) of cubo-octahedral nanoparticles increases the energy to a near optimal value and produces very active catalysts. • Reaction on the metal alone cannot account for the experimental results. The reaction is dual functional with water activation occurring at the metal-support interface. It is clear from our work that the theory component is essential, not only for prediction of new systems, but also for reconciling data and testing hypotheses regarding potential descriptors. Particularly important is the finding that the interface between nano-sized metal particles and the oxides that are used to support them represent a new state of matter in the sense that the interfacial bonding perturbs the chemical state of both metals atoms and the support

  6. Phe783, Thr797, and Asp804 in transmembrane hairpin M5-M6 of Na+,K+-ATPase play a key role in ouabain binding.

    Science.gov (United States)

    Qiu, Li Yan; Koenderink, Jan B; Swarts, Herman G P; Willems, Peter H G M; De Pont, Jan Joep H H M

    2003-11-21

    Ouabain is a glycoside that binds to and inhibits the action of Na+,K+-ATPase. Little is known, however, about the specific requirements of the protein surface for glycoside binding. Using chimeras of gastric H+,K+-ATPase and Na+,K+-ATPase, we demonstrated previously that the combined presence of transmembrane hairpins M3-M4 and M5-M6 of Na+,K+-ATPase in a backbone of H+,K+-ATPase (HN34/56) is both required and sufficient for high affinity ouabain binding. Since replacement of transmembrane hairpin M3-M4 by the N terminus up to transmembrane segment 3 (HNN3/56) resulted in a low affinity ouabain binding, hairpin M5-M6 seems to be essential for ouabain binding. To assess which residues of M5-M6 are required for ouabain action, we divided this transmembrane hairpin in seven parts and individually replaced these parts by the corresponding sequences of H+,K+-ATPase in chimera HN34/56. Three of these chimeras failed to bind ouabain following expression in Xenopus laevis oocytes. Altogether, these three chimeras contained 7 amino acids that were specific for Na+,K+-ATPase. Individual replacement of these 7 amino acids by the corresponding amino acids in H+,K+-ATPase revealed a dramatic loss of ouabain binding for F783Y, T797C, and D804E. As a proof of principle, the Na+,K+-ATPase equivalents of these 3 amino acids were introduced in different combinations in chimera HN34. The presence of all 3 amino acids appeared to be required for ouabain action. Docking of ouabain onto a three-dimensional-model of Na+,K+-ATPase suggests that Asp804, in contrast to Phe783 and Thr797, does not actually form part of the ouabain-binding pocket. Most likely, the presence of this amino acid is required for adopting of the proper conformation for ouabain binding.

  7. Is TNF-a-targeted short hairpin RNA (shRNA) a novel potential therapeutic tool in psoriasis treatment?

    DEFF Research Database (Denmark)

    Stenderup, Karin; Jakobsen, Maria; Rosada, Cecilia

    2008-01-01

      TNF-α is a well known target in psoriasis treatment and biological treatments targeting TNF-a are already clinically used against psoriasis and psoriasis arthritis. Attention is however given to a novel therapeutic tool: RNA interference that controls gene silencing. This study investigates...... the efficiency of targeting TNF-a with specific short hairpin RNA (shRNA) and explores its potential in treating psoriasis. ShRNAs targeting human TNF-α mRNA were generated. Their efficiency in down-regulating TNF-a protein expression was evaluated using a Renilla luciferase screening-assay and a transient co...... TNF-a shRNA was used to transduce HEK293 cells and verify vector-derived TNF-a knockdown in vitro. In vivo, psoriasis skin was exposed to lentiviral TNF-a shRNAs by a single intra-dermal injection. Psoriasis skin for the in vivo study was obtained from psoriatic plaque skin biopsies that were...

  8. An optimized lentiviral vector system for conditional RNAi and efficient cloning of microRNA embedded short hairpin RNA libraries.

    Science.gov (United States)

    Adams, Felix F; Heckl, Dirk; Hoffmann, Thomas; Talbot, Steven R; Kloos, Arnold; Thol, Felicitas; Heuser, Michael; Zuber, Johannes; Schambach, Axel; Schwarzer, Adrian

    2017-09-01

    RNA interference (RNAi) and CRISPR-Cas9-based screening systems have emerged as powerful and complementary tools to unravel genetic dependencies through systematic gain- and loss-of-function studies. In recent years, a series of technical advances helped to enhance the performance of virally delivered RNAi. For instance, the incorporation of short hairpin RNAs (shRNAs) into endogenous microRNA contexts (shRNAmiRs) allows the use of Tet-regulated promoters for synchronous onset of gene knockdown and precise interrogation of gene dosage effects. However, remaining challenges include lack of efficient cloning strategies, inconsistent knockdown potencies and leaky expression. Here, we present a simple, one-step cloning approach for rapid and efficient cloning of miR-30 shRNAmiR libraries. We combined a human miR-30 backbone retaining native flanking sequences with an optimized all-in-one lentiviral vector system for conditional RNAi to generate a versatile toolbox characterized by higher doxycycline sensitivity, reduced leakiness and enhanced titer. Furthermore, refinement of existing shRNA design rules resulted in substantially improved prediction of powerful shRNAs. Our approach was validated by accurate quantification of the knockdown potency of over 250 single shRNAmiRs. To facilitate access and use by the scientific community, an online tool was developed for the automated design of refined shRNA-coding oligonucleotides ready for cloning into our system. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. Pathogenic effects of Rift Valley fever virus NSs gene are alleviated in cultured cells by expressed antiviral short hairpin RNAs.

    Science.gov (United States)

    Scott, Tristan; Paweska, Janusz T; Arbuthnot, Patrick; Weinberg, Marc S

    2012-01-01

    Rift Valley fever virus (RVFV), a member of the Bunyaviridae family, may cause severe hepatitis, encephalitis and haemorrhagic fever in humans. There are currently no available licensed vaccines or therapies to treat the viral infection in humans. RNA interference (RNAi)-based viral gene silencing offers a promising approach to inhibiting replication of this highly pathogenic virus. The small (S) segment of the RVFV tripartite genome carries the genetic determinates for pathogenicity during infection. This segment encodes the non-structural S (NSs) and essential nucleocapsid (N) genes. To advance RNAi-based inhibition of RVFV replication, we designed several Pol III short hairpin RNA (shRNA) expression cassettes against the NSs and N genes, including a multimerized plasmid vector that included four shRNA expression cassettes. Effective target silencing was demonstrated using full- and partial-length target reporter assays, and confirmed by western blot analysis of exogenous N and NSs expression. Small RNA northern blots showed detectable RNAi guide strand formation from single and multimerized shRNA constructs. Using a cell culture model of RVFV replication, shRNAs targeting the N gene decreased intracellular nucleocapsid protein concentration and viral replication. The shRNAs directed against the NSs gene reduced NSs protein concentrations and alleviated NSs-mediated cytotoxicity, which may be caused by host transcription suppression. These data are the first demonstration that RNAi activators have a potential therapeutic benefit for countering RVFV infection.

  10. Fast and quantitative differentiation of single-base mismatched DNA by initial reaction rate of catalytic hairpin assembly.

    Science.gov (United States)

    Li, Chenxi; Li, Yixin; Xu, Xiao; Wang, Xinyi; Chen, Yang; Yang, Xiaoda; Liu, Feng; Li, Na

    2014-10-15

    The widely used catalytic hairpin assembly (CHA) amplification strategy generally needs several hours to accomplish one measurement based on the prevailingly used maximum intensity detection mode, making it less practical for assays where high throughput or speed is desired. To make the best use of the kinetic specificity of toehold domain for circuit reaction initiation, we developed a mathematical model and proposed an initial reaction rate detection mode to quantitatively differentiate the single-base mismatch. Using the kinetic mode, assay time can be reduced substantially to 10 min for one measurement with the comparable sensitivity and single-base mismatch differentiating ability as were obtained by the maximum intensity detection mode. This initial reaction rate based approach not only provided a fast and quantitative differentiation of single-base mismatch, but also helped in-depth understanding of the CHA system, which will be beneficial to the design of highly sensitive and specific toehold-mediated hybridization reactions. Copyright © 2014 Elsevier B.V. All rights reserved.

  11. Target-induced structure switching of hairpin aptamers for label-free and sensitive fluorescent detection of ATP via exonuclease-catalyzed target recycling amplification.

    Science.gov (United States)

    Xu, Yunying; Xu, Jin; Xiang, Yun; Yuan, Ruo; Chai, Yaqin

    2014-01-15

    In this work, we described the development of a new label-free, simple and sensitive fluorescent ATP sensing platform based on exonuclease III (Exo III)-catalyzed target recycling (ECTR) amplification and SYBR Green I indicator. The hairpin aptamer probes underwent conformational structure switching and re-configuration in the presence of ATP, which led to catalytic cleavage of the re-configured aptamers by Exo III to release ATP and to initiate the ECTR process. Such ECTR process resulted in the digestion of a significant number of the hairpin aptamer probes, leading to much less intercalation of SYBR Green I to the hairpin stems and drastic suppression of the fluorescence emission for sensitive ATP detection down to the low nanomolar level. Due to the highly specific affinity bindings between aptamers and ATP, the developed method exhibited excellent selectivity toward ATP against other analogous molecules. Besides, our ATP sensing approach used un-modified aptamer probes and could be performed in a "mix-and-detect" fashion in homogenous solutions. All these distinct advantages of the developed method thus made it hold great potential for the development of simple and robust sensing strategies for the detection of other small molecules. © 2013 Elsevier B.V. All rights reserved.

  12. Effects of secondary structure on pre-mRNA splicing: hairpins sequestering the 5' but not the 3' splice site inhibit intron processing in Nicotiana plumbaginifolia.

    Science.gov (United States)

    Liu, H X; Goodall, G J; Kole, R; Filipowicz, W

    1995-01-16

    We have performed a systematic study of the effect of artificial hairpins on pre-mRNA splicing in protoplasts of a dicot plant, Nicotiana plumbaginifolia. Hairpins with a potential to form 18 or 24 bp stems strongly inhibit splicing when they sequester the 5' splice site or are placed in the middle of short introns. However, similar 24 bp hairpins sequestering the 3' splice site do not prevent this site from being used as an acceptor. Utilization of the stem-located 3' site requires that the base of the stem is separated from the upstream 5' splice site by a minimum of approximately 45 nucleotides and that another 'helper' 3' splice site is present downstream of the stem. The results indicate that the spliceosome or factors associated with it may have a potential to unfold secondary structure present in the downstream portion of the intron, prior to or at the step of the 3' splice site selection. The finding that the helper 3' site is required for utilization of the stem-located acceptor confirms and extends previous observations, obtained with HeLa cell in vitro splicing systems, indicating that the 3' splice site may be recognized at least twice during spliceosome assembly.

  13. DNA hairpin structures in solution: 500-MHz two-dimensional 1H NMR studies on d(CGCCGCAGC) and d(CGCCGTAGC)

    International Nuclear Information System (INIS)

    Gupta, G.; Sarma, M.H.; Sarma, R.H.

    1987-01-01

    A hairpin structure contains two conformationally distinct domains: a double-helical stem with Watson-Crick base pairs and a single-stranded loop that connects the two arms of the stem. By extensive 1D and 2D 500-MHz 1 H NMR studies in H 2 O and D 2 O, it has been demonstrated that the DNA oligomers d(CGCCGCAGC) and d(CGCCGTAGC) form hairpin structures under conditions of low concentration, 0.5 mM in DNA strand, and low salt (20 mM NaCl, pH 7). From examination of the nuclear Overhauser effect (NOE) between base protons H8/H6 and sugar protons H1' and H2'/H2'', it was concluded that in D(CGCCGCAGC) and d(CGCCCTAGC) all the nine nucleotides display average (C2'-endo,anti) geometry. The NMR data in conjunction with molecular model building and solvent accessibility studies were used to derive a working model for the hairpins

  14. Coupling chemical and biological catalysis: a flexible paradigm for producing biobased chemicals.

    Science.gov (United States)

    Schwartz, Thomas J; Shanks, Brent H; Dumesic, James A

    2016-04-01

    Advances in metabolic engineering have allowed for the development of new biological catalysts capable of selectively de-functionalizing biomass to yield platform molecules that can be upgraded to biobased chemicals using high efficiency continuous processing allowed by heterogeneous chemical catalysis. Coupling these disciplines overcomes the difficulties of selectively activating COH bonds by heterogeneous chemical catalysis and producing petroleum analogues by biological catalysis. We show that carboxylic acids, pyrones, and alcohols are highly flexible platforms that can be used to produce biobased chemicals by this approach. More generally, we suggest that molecules with three distinct functionalities may represent a practical upper limit on the extent of functionality present in the platform molecules that serve as the bridge between biological and chemical catalysis. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. Core–shell nanoparticles: synthesis and applications in catalysis and electrocatalysis

    Science.gov (United States)

    Core–shell nanoparticles (CSNs) are a class of nanostructured materials that have recently received increased attention owing to their interesting properties and broad range of applications in catalysis, biology, materials chemistry and sensors. By rationally tuning the cores as ...

  16. Ir/Sn dual-reagent catalysis towards highly selective alkylation of ...

    Indian Academy of Sciences (India)

    Wintec

    Organometallic; bimetallic; catalysis; alkylation; benzyl alcohol; iridium, tin. 1. Introduction ... cording to our proposal, the oxidative addition of tin(IV) halides across a ..... 33. 4. Conclusion. In summary, we have demonstrated here an Ir/Sn.

  17. Support for U.S. Participants at the 16th International Congress on Catalysis

    Energy Technology Data Exchange (ETDEWEB)

    Wachs, Israel E. [Lehigh Univ., Bethlehem, PA (United States)

    2017-01-17

    The enclosed report highlights the travel grant awarded to offset the cost of foreign travel of several faculty and students to attend the 16th International Congress on Catalysis (ICC) held in Beijing, China, July 3-8, 2016.

  18. Combination of sunlight irradiated oxidative processes for landfill leachate: heterogeneous catalysis (TiO2 versus homogeneous catalysis (H2O2

    Directory of Open Access Journals (Sweden)

    Oswaldo Luiz Cobra Guimarães

    2013-04-01

    Full Text Available The objective of this work was to study the treatment of landfill leachate liquid in nature, after the use of a combination of advanced oxidation processes. More specifically, it compared heterogeneous catalysis with TiO2 to homogeneous catalysis with H2O2, both under photo-irradiated sunlight. The liquid used for the study was the leachate from the landfill of the city of Cachoeira Paulista, São Paulo State, Brazil. The experiments were conducted in a semi-batch reactor open to the absorption of solar UV radiation, with 120 min reaction time. The factors and their respective levels (-1, 0 and 1 were distributed in a experimental design 24-1 with duplicate and triplicate in the central point, resulting in an array with 19 treatment trials. The studied factors in comparing the two catalytic processes were: liquid leachate dilution, TiO2 concentration on the reactor plate, the H2O2 amount and pH level. The leachate had low photo-catalytic degradability, with NOPC reductions ranging from 1% to a maximum of 24.9%. When considering each factor alone, neither homogeneous catalysis with H2O2, nor heterogeneous catalysis with TiO2, could degrade the percolated liquid without significant reductions (5% level in total NOPC. On the other hand, the combined use of homogenous catalysis with H2O2 and heterogeneous catalysis H2O2 resulted in the greatest reductions in NOPC. The optimum condition for the NOPC reduction was obtained at pH 7, dilution of percolated:water at 1:1 (v v-1 rate; excess of 12.5% H2O2 and coating plate reactor with 0.025 g cm-2 TiO2.

  19. Liquid phase oxidation via heterogeneous catalysis organic synthesis and industrial applications

    CERN Document Server

    Clerici, Mario G

    2013-01-01

    Sets the stage for environmentally friendly industrial organic syntheses From basic principles to new and emerging industrial applications, this book offers comprehensive coverage of heterogeneous liquid-phase selective oxidation catalysis. It fully examines the synthesis, characterization, and application of catalytic materials for environmentally friendly organic syntheses. Readers will find coverage of all the important classes of catalysts, with an emphasis on their stability and reusability. Liquid Phase Oxidation via Heterogeneous Catalysis features contributions from an internation

  20. Adenoviral short hairpin RNA therapy targeting phosphodiesterase 5a relieves cardiac remodeling and dysfunction following myocardial infarction

    Science.gov (United States)

    Li, Longhu; Haider, Husnain Kh.; Wang, Linlin; Lu, Gang

    2012-01-01

    We previously showed that treatment with tadalafil, a long-acting phosphodiesterase-5a (PDE5a) inhibitor, effectively prevented adverse left ventricular (LV) remodeling of the infarcted heart. We hypothesized that short-hairpin RNA (shRNA) therapy targeting PDE5a would simulate the effects of pharmacological intervention for treatment of postinfarction LV remodeling and dysfunction. Experimental model of myocardial infarction was developed in female mice by permanent ligation of left coronary artery. Immediately after that, an adenoviral vector encoding for shRNA sequence targeting PDE5a (Ad-shPDE5a) was injected intramyocardially, which specifically inhibited PDE5a in the heart. Four weeks later, Ad-shPDE5a treated mice showed significant mitigation of the left ventricle (LV) dilatation and dysfunction as indicated by smaller LV cavity and more preserved ejection fraction and fractional shortening. Infarction size and fibrosis were significantly reduced in Ad-shPDE5a-treated mice. Additionally, more salvaged cardiomyocytes, significantly reduced collagen contents, and higher blood vessel density were observed in Ad-shPDE5a-treated mice. The cytoprotective effects of Ad-shPDE5a were demonstrated in vitro in Ad-shPDE5a transfected cardiomyocytes cultured under oxygen glucose deprivation. Among downstream mediators of PDE5a signaling, cyclic GMP (cGMP) and cGMP-dependent protein kinase G (PKG) were activated with concomitant reduction in caspase-3 activity. However, no significant change in PKA and cAMP activities were observed in Ad-shPDE5a-treated hearts. Inhibition with shRNA improved cardiac remodeling and dysfunction by reducing infarction size and cardiac fibrosis and increased cGMP and PKG activity. These findings suggest that PDE5 inhibition with Ad-shPDE5a is a novel approach for treatment of myocardial infarction. PMID:22447941

  1. Hairpin DNA-Templated Silver Nanoclusters as Novel Beacons in Strand Displacement Amplification for MicroRNA Detection.

    Science.gov (United States)

    Zhang, Jingpu; Li, Chao; Zhi, Xiao; Ramón, Gabriel Alfranca; Liu, Yanlei; Zhang, Chunlei; Pan, Fei; Cui, Daxiang

    2016-01-19

    MicroRNA (miRNA) biomarkers display great potential for cancer diagnosis and prognosis. The development of rapid and specific methods for miRNA detection has become a hotspot. Herein, hairpin DNA-templated silver nanoclusters (AgNCs/HpDNA) were prepared and integrated into strand-displacement amplification (SDA) as a novel beacon for miRNA detection. The light-up platform was established based on guanine (G)-rich fluorescence enhancement that essentially converted the excitation/emission pair of AgNCs/HpDNAs from a shorter wavelength to a longer wavelength, and then achieved fluorescent enhancement at longer wavelength. On the basis of the validation of the method, the single and duplex detection were conducted in two plasma biomarkers (miR-16-5p and miR-19b-3p) for the diagnosis of gastric cancer. The probe (AgNCs/RED 16(7s)C) utilized for miR-16-5p detection adopted a better conformation with high specificity to recognize single-base mismatches by producing dramatically opposite signals (increase or decrease at 580 nm ex/640 nm em) while the probe (AgNCs/GRE 19b(5s)C) for miR-19b-3p generated dual signals (increase at 490 nm ex/570 nm em and decrease at 430 nm ex/530 nm em) with bright fluorescence in one reaction during the amplification, but unexpectedly was partially digested. This is for the first time to allow the generation of enhanced fluorescent AgNCs and the target recognition integrated into a single process, which offers great opportunity for specific miRNA detection in an easy and rapid way.

  2. Optimization of Critical Hairpin Features Allows miRNA-based Gene Knockdown Upon Single-copy Transduction

    Directory of Open Access Journals (Sweden)

    Renier Myburgh

    2014-01-01

    Full Text Available Gene knockdown using micro RNA (miRNA-based vector constructs is likely to become a prominent gene therapy approach. It was the aim of this study to improve the efficiency of gene knockdown through optimizing the structure of miRNA mimics. Knockdown of two target genes was analyzed: CCR5 and green fluorescent protein. We describe here a novel and optimized miRNA mimic design called mirGE comprising a lower stem length of 13 base pairs (bp, positioning of the targeting strand on the 5′ side of the miRNA, together with nucleotide mismatches in upper stem positions 1 and 12 placed on the passenger strand. Our mirGE proved superior to miR-30 in four aspects: yield of targeting strand incorporation into RNA-induced silencing complex (RISC; incorporation into RISC of correct targeting strand; precision of cleavage by Drosha; and ratio of targeting strand over passenger strand. A triple mirGE hairpin cassette targeting CCR5 was constructed. It allowed CCR5 knockdown with an efficiency of over 90% upon single-copy transduction. Importantly, single-copy expression of this construct rendered transduced target cells, including primary human macrophages, resistant to infection with a CCR5-tropic strain of HIV. Our results provide new insights for a better knockdown efficiency of constructs containing miRNA. Our results also provide the proof-of-principle that cells can be rendered HIV resistant through single-copy vector transduction, rendering this approach more compatible with clinical applications.

  3. Short Hairpin RNA Silencing of PHD-2 Improves Neovascularization and Functional Outcomes in Diabetic Wounds and Ischemic Limbs.

    Directory of Open Access Journals (Sweden)

    Kevin J Paik

    Full Text Available The transcription factor hypoxia-inducible factor 1-alpha (HIF-1α is responsible for the downstream expression of over 60 genes that regulate cell survival and metabolism in hypoxic conditions as well as those that enhance angiogenesis to alleviate hypoxia. However, under normoxic conditions, HIF-1α is hydroxylated by prolyl hydroxylase 2, and subsequently degraded, with a biological half-life of less than five minutes. Here we investigated the therapeutic potential of inhibiting HIF-1α degradation through short hairpin RNA silencing of PHD-2 in the setting of diabetic wounds and limb ischemia. Treatment of diabetic mouse fibroblasts with shPHD-2 in vitro resulted in decreased levels of PHD-2 transcript demonstrated by qRT-PCR, higher levels of HIF-1α as measured by western blot, and higher expression of the downstream angiogenic genes SDF-1 and VEGFα, as measured by qRT-PCR. In vivo, shPHD-2 accelerated healing of full thickness excisional wounds in diabetic mice compared to shScr control, (14.33 ± 0.45 days vs. 19 ± 0.33 days and was associated with an increased vascular density. Delivery of shPHD-2 also resulted in improved perfusion of ischemic hind limbs compared to shScr, prevention of distal digit tip necrosis, and increased survival of muscle tissue. Knockdown of PHD-2 through shRNA treatment has the potential to stimulate angiogenesis through overexpression of HIF-1α and upregulation of pro-angiogenic genes downstream of HIF-1α, and may represent a viable, non-viral approach to gene therapy for ischemia related applications.

  4. Preparative semiconductor photoredox catalysis: An emerging theme in organic synthesis

    Directory of Open Access Journals (Sweden)

    David W. Manley

    2015-09-01

    Full Text Available Heterogeneous semiconductor photoredox catalysis (SCPC, particularly with TiO2, is evolving to provide radically new synthetic applications. In this review we describe how photoactivated SCPCs can either (i interact with a precursor that donates an electron to the semiconductor thus generating a radical cation; or (ii interact with an acceptor precursor that picks up an electron with production of a radical anion. The radical cations of appropriate donors convert to neutral radicals usually by loss of a proton. The most efficient donors for synthetic purposes contain adjacent functional groups such that the neutral radicals are resonance stabilized. Thus, ET from allylic alkenes and enol ethers generated allyl type radicals that reacted with 1,2-diazine or imine co-reactants to yield functionalized hydrazones or benzylanilines. SCPC with tertiary amines enabled electron-deficient alkenes to be alkylated and furoquinolinones to be accessed. Primary amines on their own led to self-reactions involving C–N coupling and, with terminal diamines, cyclic amines were produced. Carboxylic acids were particularly fruitful affording C-centered radicals that alkylated alkenes and took part in tandem addition cyclizations producing chromenopyrroles; decarboxylative homo-dimerizations were also observed. Acceptors initially yielding radical anions included nitroaromatics and aromatic iodides. The latter led to hydrodehalogenations and cyclizations with suitable precursors. Reductive SCPC also enabled electron-deficient alkenes and aromatic aldehydes to be hydrogenated without the need for hydrogen gas.

  5. Hydrogen and methane synthesis through radiation catalysis. Final report

    International Nuclear Information System (INIS)

    DuBow, J.

    1980-09-01

    The goal of this research was to evaluate the potential for using reactor wastes to synthesize useful products in quasi-photochemical configuration. It was found that semiconductor oxides act as heterogenous catalysts for the formation of H 2 in aqueous media under 60 Co irradiation. The principle of a gamma-ray solar cell was demonstrated experimentally. Experiments with ultraviolet irradiated TiO 2 and ZnO grains demonstrated that both H 2 and H 2 O 2 were formed, in contrast to the results of work by previous authors. These results were rationalized by energy band diagram representations and by applying principles of semiconductor photoelectrochemistry. The concept of gamma-ray assisted desulfurization of coal through radiological degradation and heterogenous catalysis was experimentally demonstrated. The proof-of-concept experiments in the present study provide the basis for further fundamental and applied investigations, particularly in a potentially efficient system with a fresh source and 1.5 m path length

  6. Gold Nanofilm Redox Catalysis for Oxygen Reduction at Soft Interfaces

    International Nuclear Information System (INIS)

    Smirnov, Evgeny; Peljo, Pekka; Scanlon, Micheál D.; Girault, Hubert H.

    2016-01-01

    ABSTRACT: Functionalization of a soft or liquid-liquid interface by a one gold nanoparticle thick “nanofilm” provides a conductive pathway to facilitate interfacial electron transfer from a lipophilic electron donor to a hydrophilic electron acceptor in a process known as interfacial redox catalysis. The gold nanoparticles in the nanofilm are charged by Fermi level equilibration with the lipophilic electron donor and act as an interfacial reservoir of electrons. Additional thermodynamic driving force can be provided by electrochemically polarising the interface. Using these principles, the biphasic reduction of oxygen by a lipophilic electron donor, decamethylferrocene, dissolved in α,α,α-trifluorotoluene was catalysed at a gold nanoparticle nanofilm modified water-oil interface. A recently developed microinjection technique was utilised to modify the interface reproducibly with the mirror-like gold nanoparticle nanofilm, while the oxidised electron donor species and the reduction product, hydrogen peroxide, were detected by ion transfer voltammetry and UV/vis spectroscopy, respectively. Metallization of the soft interface allowed the biphasic oxygen reduction reaction to proceed via an alternative mechanism with enhanced kinetics and at a significantly lower overpotential in comparison to a bare soft interface. Weaker lipophilic reductants, such as ferrocene, were capable of charging the interfacial gold nanoparticle nanofilm but did not have sufficient thermodynamic driving force to significantly elicit biphasic oxygen reduction.

  7. Bacterial and Fungal Proteolytic Enzymes: Production, Catalysis and Potential Applications.

    Science.gov (United States)

    da Silva, Ronivaldo Rodrigues

    2017-09-01

    Submerged and solid-state bioprocesses have been extensively explored worldwide and employed in a number of important studies dealing with microbial cultivation for the production of enzymes. The development of these production technologies has facilitated the generation of new enzyme-based products with applications in pharmaceuticals, food, bioactive peptides, and basic research studies, among others. The applicability of microorganisms in biotechnology is potentiated because of their various advantages, including large-scale production, short time of cultivation, and ease of handling. Currently, several studies are being conducted to search for new microbial peptidases with peculiar biochemical properties for industrial applications. Bioprospecting, being an important prerequisite for research and biotechnological development, is based on exploring the microbial diversity for enzyme production. Limited information is available on the production of specific proteolytic enzymes from bacterial and fungal species, especially on the subgroups threonine and glutamic peptidases, and the seventh catalytic type, nonhydrolytic asparagine peptide lyase. This gap in information motivated the present study about these unique biocatalysts. In this study, the biochemical and biotechnological aspects of the seven catalytic types of proteolytic enzymes, namely aspartyl, cysteine, serine, metallo, glutamic, and threonine peptidase, and asparagine peptide lyase, are summarized, with an emphasis on new studies, production, catalysis, and application of these enzymes.

  8. Mineral catalysis of oil producing reactions in coal liquefaction

    Energy Technology Data Exchange (ETDEWEB)

    Shridharani, K.G.

    1983-01-01

    This work was concerned primarily with the development of a relatively inexpensive, readily available, high activity catalyst that can be used as a disposable catalyst in coal liquefaction processes. For a fair evaluation of the developmental mineral catalyst (presulfided iron oxide), it was necessary to determine at different stages of this work, whether catalyst inhibition, deactivation or activity was the limiting factor in coal liquefaction catalysis. First, different routes were explored to prepare a high hydrogenation activity, iron-based catalyst. Naphthalene hydrogenation was used as a model reaction to rate the hydrogenation activities of different additives. Presulfiding of iron oxide with H/sub 2/S, under controlled conditions, rendered the highest hydrogenation activity mineral catalyst, which had a hydrogenation activity even greater than that of commercial CoMo/Al/sub 2/O/sub 3/ catalyst sulfided with creosote oil and hydrogen. Sulfiding of CoMo/Al/sub 2/O/sub 3/ catalyst with H/sub 2/S remarkably improved its initial hydrogenation activity. Second, the catalyst inhibition and deactivation during liquefaction were studied. Liquefaction-process solvents contain a number of compounds that can either deactivate or inhibit the hydrogenation activity of a catalyst. Finally, the hydrocracking activity of the presulfided iron oxide catalyst was compared with that of commercial catalysts, CoMo/Al/sub 2/O/sub 3/ and low alumina FCC catalyst.

  9. Ferroelectrics: A pathway to switchable surface chemistry and catalysis

    Science.gov (United States)

    Kakekhani, Arvin; Ismail-Beigi, Sohrab; Altman, Eric I.

    2016-08-01

    It has been known for more than six decades that ferroelectricity can affect a material's surface physics and chemistry thereby potentially enhancing its catalytic properties. Ferroelectrics are a class of materials with a switchable electrical polarization that can affect surface stoichiometry and electronic structure and thus adsorption energies and modes; e.g., molecular versus dissociative. Therefore, ferroelectrics may be utilized to achieve switchable surface chemistry whereby surface properties are not fixed but can be dynamically controlled by, for example, applying an external electric field or modulating the temperature. Several important examples of applications of ferroelectric and polar materials in photocatalysis and heterogeneous catalysis are discussed. In photocatalysis, the polarization direction can control band bending at water/ferroelectric and ferroelectric/semiconductor interfaces, thereby facilitating charge separation and transfer to the electrolyte and enhancing photocatalytic activity. For gas-surface interactions, available results suggest that using ferroelectrics to support catalytically active transition metals and oxides is another way to enhance catalytic activity. Finally, the possibility of incorporating ferroelectric switching into the catalytic cycle itself is described. In this scenario, a dynamic collaboration of two polarization states can be used to drive reactions that have been historically challenging to achieve on surfaces with fixed chemical properties (e.g., direct NOx decomposition and the selective partial oxidation of methane). These predictions show that dynamic modulation of the polarization can help overcome some of the fundamental limitations on catalytic activity imposed by the Sabatier principle.

  10. Anatomy of the magnetic catalysis by renormalization-group method

    Science.gov (United States)

    Hattori, Koichi; Itakura, Kazunori; Ozaki, Sho

    2017-12-01

    We first examine the scaling argument for a renormalization-group (RG) analysis applied to a system subject to the dimensional reduction in strong magnetic fields, and discuss the fact that a four-Fermi operator of the low-energy excitations is marginal irrespective of the strength of the coupling constant in underlying theories. We then construct a scale-dependent effective four-Fermi interaction as a result of screened photon exchanges at weak coupling, and establish the RG method appropriately including the screening effect, in which the RG evolution from ultraviolet to infrared scales is separated into two stages by the screening-mass scale. Based on a precise agreement between the dynamical mass gaps obtained from the solutions of the RG and Schwinger-Dyson equations, we discuss an equivalence between these two approaches. Focusing on QED and Nambu-Jona-Lasinio model, we clarify how the properties of the interactions manifest themselves in the mass gap, and point out an importance of respecting the intrinsic energy-scale dependences in underlying theories for the determination of the mass gap. These studies are expected to be useful for a diagnosis of the magnetic catalysis in QCD.

  11. Retinal Photoisomerization in Rhodopsin: Electrostatic and Steric Catalysis

    International Nuclear Information System (INIS)

    Tomasello, Gaia; Altoe, Piero; Stenta, Marco; Olaso-Gonzalez, Gloria; Garavelli, Marco; Orlandi, Giorgio

    2007-01-01

    Excited state QM(CASPT2//CASSCF)/MM(GAFF) calculations, by our recently developed code COBRAMM (Computations at Bologna Relating Ab-initio and Molecular Mechanic Methods), were carried out in rhodopsin to investigate on the steric and electrostatic effects in retinal photoisomerization catalysis due to the β-ionone ring and glutammate 181 (GLU 181), respectively. The excited state photoisomerization channel has been mapped and a new christallographyc structure (2.2 Aa resolution) has been used for this purpose. Two different set-ups have been used to evaluate the electrostatic effects of GLU 181 (which is very close to the central double bond of the chromophore): the first with a neutral GLU 181 (as commonly accepted), the second with a negatively charged (i.e. deprotonated) GLU 181 (as very recent experimental findings seem to suggest). On the other hand, β-ionone ring steric effects were evaluated by calculating the photoisomerization path of a modified chromophore, where the ring double bond has been saturated. Spectroscopic properties were calculated and compared with the available experimental data

  12. Anatomy of the magnetic catalysis by renormalization-group method

    Directory of Open Access Journals (Sweden)

    Koichi Hattori

    2017-12-01

    Full Text Available We first examine the scaling argument for a renormalization-group (RG analysis applied to a system subject to the dimensional reduction in strong magnetic fields, and discuss the fact that a four-Fermi operator of the low-energy excitations is marginal irrespective of the strength of the coupling constant in underlying theories. We then construct a scale-dependent effective four-Fermi interaction as a result of screened photon exchanges at weak coupling, and establish the RG method appropriately including the screening effect, in which the RG evolution from ultraviolet to infrared scales is separated into two stages by the screening-mass scale. Based on a precise agreement between the dynamical mass gaps obtained from the solutions of the RG and Schwinger–Dyson equations, we discuss an equivalence between these two approaches. Focusing on QED and Nambu–Jona-Lasinio model, we clarify how the properties of the interactions manifest themselves in the mass gap, and point out an importance of respecting the intrinsic energy-scale dependences in underlying theories for the determination of the mass gap. These studies are expected to be useful for a diagnosis of the magnetic catalysis in QCD.

  13. The Applications of Morphology Controlled ZnO in Catalysis

    Directory of Open Access Journals (Sweden)

    Yuhai Sun

    2016-11-01

    Full Text Available Zinc oxide (ZnO, with the unique chemical and physical properties of high chemical stability, broad radiation absorption range, high electrochemical coupling coefficient, and high photo-stability, is an attractive multifunctional material which has promoted great interest in many fields. What is more, its properties can be tuned by controllable synthesized morphologies. Therefore, after the success of the abundant morphology controllable synthesis, both the morphology-dependent ZnO properties and their related applications have been extensively investigated. This review concentrates on the properties of morphology-dependent ZnO and their applications in catalysis, mainly involved reactions on green energy and environmental issues, such as CO2 hydrogenation to fuels, methanol steam reforming to generate H2, bio-diesel production, pollutant photo-degradation, etc. The impressive catalytic properties of ZnO are associated with morphology tuned specific microstructures, defects or abilities of electron transportation, etc. The main morphology-dependent promotion mechanisms are discussed and summarized.

  14. Studies of Metal-Metal Bonded Compounds in Catalysis

    Energy Technology Data Exchange (ETDEWEB)

    Berry, John F. [Univ. of Wisconsin, Madison, WI (United States)

    2018-01-19

    The overall goals of this research are (1) to define the fundamental coordination chemistry underlying successful catalytic transformations promoted by metal-metal bonded compounds, and (2) to explore new chemical transformations that occur at metal-metal bonded sites that could lead to the discovery of new catalytic processes. Transformations of interest include metal-promoted reactions of carbene, nitrene, or nitrido species to yield products with new C–C and C–N bonds, respectively. The most promising suite of transition metal catalysts for these transformations is the set of metal-metal bonded coordination compounds of Ru and Rh of the general formula M2(ligand)4, where M = Ru or Rh and ligand = a monoanionic, bridging ligand such as acetate. Development of new catalysts and improvement of catalytic conditions have been stymied by a general lack of knowledge about the nature of highly reactive intermediates in these reactions, the knowledge that is to be supplied by this work. Our three specific objectives for this year have been (A) to trap, isolate, and characterize new reactive intermediates of general relevance to catalysis, (B) to explore the electronic structure and reactivity of these unusual species, and how these two properties are interrelated, and (C) to use our obtained mechanistic knowledge to design new catalysts with a focus on Earth-abundant first-row transition metal compounds.

  15. Catalysis as an Enabling Science for Sustainable Polymers.

    Science.gov (United States)

    Zhang, Xiangyi; Fevre, Mareva; Jones, Gavin O; Waymouth, Robert M

    2018-01-24

    The replacement of current petroleum-based plastics with sustainable alternatives is a crucial but formidable challenge for the modern society. Catalysis presents an enabling tool to facilitate the development of sustainable polymers. This review provides a system-level analysis of sustainable polymers and outlines key criteria with respect to the feedstocks the polymers are derived from, the manner in which the polymers are generated, and the end-of-use options. Specifically, we define sustainable polymers as a class of materials that are derived from renewable feedstocks and exhibit closed-loop life cycles. Among potential candidates, aliphatic polyesters and polycarbonates are promising materials due to their renewable resources and excellent biodegradability. The development of renewable monomers, the versatile synthetic routes to convert these monomers to polyesters and polycarbonate, and the different end-of-use options for these polymers are critically reviewed, with a focus on recent advances in catalytic transformations that lower the technological barriers for developing more sustainable replacements for petroleum-based plastics.

  16. Sequential rhodium/palladium catalysis: enantioselective formation of dihydroquinolinones in the presence of achiral and chiral ligands.

    Science.gov (United States)

    Zhang, Lei; Qureshi, Zafar; Sonaglia, Lorenzo; Lautens, Mark

    2014-12-08

    Compatible combinations of achiral and chiral ligands can be used in rhodium/palladium catalysis to achieve highly enantioselective domino reactions. The difference in rates of catalysis and minimal effects of ligand interference confer control in the domino sequence. The "all-in-one" 1,4-conjugate arylation and C-N cross-coupling through sequential Rh/Pd catalysis provides access to enantioenriched dihydroquinolinone building blocks. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Probing adenine rings and backbone linkages using base specific isotope-edited Raman spectroscopy: application to group II intron ribozyme domain V.

    Science.gov (United States)

    Chen, Yuanyuan; Eldho, Nadukkudy V; Dayie, T Kwaku; Carey, Paul R

    2010-04-27

    with the differences in hydration radii. These subtle differences in electrostatic interactions may be related to observed variations in catalytic activity. For a reconstructed ribozyme comprising domains 1-3 (D123) connected in cis plus domain 5 (D5) supplied in trans, cleavage of spliced exon substrates in the presence of magnesium and K(+) or Cs(+) is more efficient than that in the presence of magnesium with Na(+) or Li(+).

  18. Electrostatic catalysis of a Diels-Alder reaction

    Science.gov (United States)

    Aragonès, Albert C.; Haworth, Naomi L.; Darwish, Nadim; Ciampi, Simone; Bloomfield, Nathaniel J.; Wallace, Gordon G.; Diez-Perez, Ismael; Coote, Michelle L.

    2016-03-01

    It is often thought that the ability to control reaction rates with an applied electrical potential gradient is unique to redox systems. However, recent theoretical studies suggest that oriented electric fields could affect the outcomes of a range of chemical reactions, regardless of whether a redox system is involved. This possibility arises because many formally covalent species can be stabilized via minor charge-separated resonance contributors. When an applied electric field is aligned in such a way as to electrostatically stabilize one of these minor forms, the degree of resonance increases, resulting in the overall stabilization of the molecule or transition state. This means that it should be possible to manipulate the kinetics and thermodynamics of non-redox processes using an external electric field, as long as the orientation of the approaching reactants with respect to the field stimulus can be controlled. Here, we provide experimental evidence that the formation of carbon-carbon bonds is accelerated by an electric field. We have designed a surface model system to probe the Diels-Alder reaction, and coupled it with a scanning tunnelling microscopy break-junction approach. This technique, performed at the single-molecule level, is perfectly suited to deliver an electric-field stimulus across approaching reactants. We find a fivefold increase in the frequency of formation of single-molecule junctions, resulting from the reaction that occurs when the electric field is present and aligned so as to favour electron flow from the dienophile to the diene. Our results are qualitatively consistent with those predicted by quantum-chemical calculations in a theoretical model of this system, and herald a new approach to chemical catalysis.

  19. New Ir Bis-Carbonyl Precursor for Water Oxidation Catalysis

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Daria L. [Department of Chemistry, Yale University, 225; Beltrán-Suito, Rodrigo [Department of Chemistry, Yale University, 225; Thomsen, Julianne M. [Department of Chemistry, Yale University, 225; Hashmi, Sara M. [Department of Chemical and Environmental; Materna, Kelly L. [Department of Chemistry, Yale University, 225; Sheehan, Stafford W. [Catalytic Innovations LLC, 70 Crandall; Mercado, Brandon Q. [Department of Chemistry, Yale University, 225; Brudvig, Gary W. [Department of Chemistry, Yale University, 225; Crabtree, Robert H. [Department of Chemistry, Yale University, 225

    2016-02-05

    This paper introduces IrI(CO)2(pyalc) (pyalc = (2-pyridyl)-2-propanoate) as an atom-efficient precursor for Ir-based homogeneous oxidation catalysis. This compound was chosen to simplify analysis of the water oxidation catalyst species formed by the previously reported Cp*IrIII(pyalc)OH water oxidation precatalyst. Here, we present a comparative study on the chemical and catalytic properties of these two precursors. Previous studies show that oxidative activation of Cp*Ir-based precursors with NaIO4 results in formation of a blue IrIV species. This activation is concomitant with the loss of the placeholder Cp* ligand which oxidatively degrades to form acetic acid, iodate, and other obligatory byproducts. The activation process requires substantial amounts of primary oxidant, and the degradation products complicate analysis of the resulting IrIV species. The species formed from oxidation of the Ir(CO)2(pyalc) precursor, on the other hand, lacks these degradation products (the CO ligands are easily lost upon oxidation) which allows for more detailed examination of the resulting Ir(pyalc) active species both catalytically and spectroscopically, although complete structural analysis is still elusive. Once Ir(CO)2(pyalc) is activated, the system requires acetic acid or acetate to prevent the formation of nanoparticles. Investigation of the activated bis-carbonyl complex also suggests several Ir(pyalc) isomers may exist in solution. By 1H NMR, activated Ir(CO)2(pyalc) has fewer isomers than activated Cp*Ir complexes, allowing for advanced characterization. Future research in this direction is expected to contribute to a better structural understanding of the active species. A diol crystallization agent was needed for the structure determination of 3.

  20. Horse Liver Alcohol Dehydrogenase: Zinc Coordination and Catalysis

    Energy Technology Data Exchange (ETDEWEB)

    Plapp, Bryce V.; Savarimuthu, Baskar Raj; Ferraro, Daniel J.; Rubach, Jon K.; Brown, Eric N.; Ramaswamy, S. (Iowa)

    2017-07-07

    During catalysis by liver alcohol dehydrogenase (ADH), a water bound to the catalytic zinc is replaced by the oxygen of the substrates. The mechanism might involve a pentacoordinated zinc or a double-displacement reaction with participation by a nearby glutamate residue, as suggested by studies of human ADH3, yeast ADH1, and some other tetrameric ADHs. Zinc coordination and participation of water in the enzyme mechanism were investigated by X-ray crystallography. The apoenzyme and its complex with adenosine 5'-diphosphoribose have an open protein conformation with the catalytic zinc in one position, tetracoordinated by Cys-46, His-67, Cys-174, and a water molecule. The bidentate chelators 2,2'-bipyridine and 1,10-phenanthroline displace the water and form a pentacoordinated zinc. The enzyme–NADH complex has a closed conformation similar to that of ternary complexes with coenzyme and substrate analogues; the coordination of the catalytic zinc is similar to that found in the apoenzyme, except that a minor, alternative position for the catalytic zinc is ~1.3 Å from the major position and closer to Glu-68, which could form the alternative coordination to the catalytic zinc. Complexes with NADH and N-1-methylhexylformamide or N-benzylformamide (or with NAD+ and fluoro alcohols) have the classical tetracoordinated zinc, and no water is bound to the zinc or the nicotinamide rings. The major forms of the enzyme in the mechanism have a tetracoordinated zinc, where the carboxylate group of Glu-68 could participate in the exchange of water and substrates on the zinc. Hydride transfer in the Michaelis complexes does not involve a nearby water.

  1. Highly conserved small subunit residues influence rubisco large subunit catalysis.

    Science.gov (United States)

    Genkov, Todor; Spreitzer, Robert J

    2009-10-30

    The chloroplast enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyzes the rate-limiting step of photosynthetic CO(2) fixation. With a deeper understanding of its structure-function relationships and competitive inhibition by O(2), it may be possible to engineer an increase in agricultural productivity and renewable energy. The chloroplast-encoded large subunits form the active site, but the nuclear-encoded small subunits can also influence catalytic efficiency and CO(2)/O(2) specificity. To further define the role of the small subunit in Rubisco function, the 10 most conserved residues in all small subunits were substituted with alanine by transformation of a Chlamydomonas reinhardtii mutant that lacks the small subunit gene family. All the mutant strains were able to grow photosynthetically, indicating that none of the residues is essential for function. Three of the substitutions have little or no effect (S16A, P19A, and E92A), one primarily affects holoenzyme stability (L18A), and the remainder affect catalysis with or without some level of associated structural instability (Y32A, E43A, W73A, L78A, P79A, and F81A). Y32A and E43A cause decreases in CO(2)/O(2) specificity. Based on the x-ray crystal structure of Chlamydomonas Rubisco, all but one (Glu-92) of the conserved residues are in contact with large subunits and cluster near the amino- or carboxyl-terminal ends of large subunit alpha-helix 8, which is a structural element of the alpha/beta-barrel active site. Small subunit residues Glu-43 and Trp-73 identify a possible structural connection between active site alpha-helix 8 and the highly variable small subunit loop between beta-strands A and B, which can also influence Rubisco CO(2)/O(2) specificity.

  2. Solar photo-catalysis to remove paper mill wastewater pollutants

    Energy Technology Data Exchange (ETDEWEB)

    Amat, A.M.; Arques, A. [Departamento de Ingenieria Textil y Papelera, Universidad Politecnica de Valencia, EPSA-UPV, Paseo del Viaducto 1, E-03801 Alcoy (Spain); Lopez, F. [Departamento de Ingenieria Quimica y Nuclear, Universidad Politecnica de Valencia, EPSA-UPV, Paseo del Viaducto 1, E-03801 Alcoy (Spain); Miranda, M.A. [Departamento de Quimica, Instituto de Tecnologia Quimica, Universidad Politecnica de Valencia, UPV-CSIC, 46071 Valencia (Spain)

    2005-10-01

    Solar degradation of effluents in board paper industries has been studied using different photo-catalysts: Fenton reagent and TiO{sub 2}. p-Toluenesulfonic acid was chosen as a model compound for sulfonated pollutants already present in the incoming waters. The abatement of a 0.005M solution of this pollutant after 6h was found to be 47% for photo-Fenton and 27% for TiO{sub 2} (pseudo-first-order rate constants 0.002 and 0.001min{sup -1}, respectively). Eugenol and guaiacol were chosen as models for lignin degradation products. They were efficiently degraded by both photo-catalysts, and reaction rates were higher for eugenol (0.0024min{sup -1}) than for guaiacol (0.0018min{sup -1}). A solution of sodium acetate, sodium butyrate and d-glucose was chosen to study the effect of photo-catalysis towards volatile fatty acids and saccharides arising from starch degradation. In this case a clearly worse performance was observed: only 20% degradation was observed after 7h of treatment. When the real wastewater was treated with photo-catalytic methods, the best performance was obtained in closed circuits, when the COD values were higher. This fact can be explained by taking into account that closure of the circuits results in an accumulation of reluctant phenolic pollutants, while starch derivatives are continuously degraded by microorganisms in the circuits; as phenolic compounds are more easily degraded by photo-catalytic means, these methods are suitable for closed circuits. Finally, changes in the BOD{sub st} were determined by means of active sludges respirometry. A noticeable BOD{sub st} increase (30-50%) was observed in all cases, attributable to chemical oxidation of biodegradable species. (author)

  3. Core-shell nanoreactors for efficient aqueous biphasic catalysis.

    Science.gov (United States)

    Zhang, Xuewei; Cardozo, Andrés F; Chen, Si; Zhang, Wenjing; Julcour, Carine; Lansalot, Muriel; Blanco, Jean-François; Gayet, Florence; Delmas, Henri; Charleux, Bernadette; Manoury, Eric; D'Agosto, Franck; Poli, Rinaldo

    2014-11-17

    Water-borne phosphine-functionalized core-cross-linked micelles (CCM) consisting of a hydrophobic core and a hydrophilic shell were obtained as stable latexes by reversible addition-fragmentation chain transfer (RAFT) in water in a one-pot, three-step process. Initial homogeneous aqueous-phase copolymerization of methacrylic acid (MAA) and poly(ethylene oxide) methyl ether methacrylate (PEOMA) is followed by copolymerization of styrene (S) and 4-diphenylphosphinostyrene (DPPS), yielding P(MAA-co-PEOMA)-b-P(S-co-DPPS) amphiphilic block copolymer micelles (M) by polymerization-induced self-assembly (PISA), and final micellar cross-linking with a mixture of S and diethylene glycol dimethacrylate. The CCM were characterized by dynamic light scattering and NMR spectroscopy to evaluate size, dispersity, stability, and the swelling ability of various organic substrates. Coordination of [Rh(acac)(CO)2 ] (acac=acetylacetonate) to the core-confined phosphine groups was rapid and quantitative. The CCM and M latexes were then used, in combination with [Rh(acac)(CO)2 ], to catalyze the aqueous biphasic hydroformylation of 1-octene, in which they showed high activity, recyclability, protection of the activated Rh center by the polymer scaffold, and low Rh leaching. The CCM latex gave slightly lower catalytic activity but significantly less Rh leaching than the M latex. A control experiment conducted in the presence of the sulfoxantphos ligand pointed to the action of the CCM as catalytic nanoreactors with substrate and product transport into and out of the polymer core, rather than as a surfactant in interfacial catalysis. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Stabilization of the H,K-ATPase M5M6 membrane hairpin by K+ ions. Mechanistic significance for p2-type atpases.

    Science.gov (United States)

    Gatto, C; Lutsenko, S; Shin, J M; Sachs, G; Kaplan, J H

    1999-05-14

    The integral membrane protein, the gastric H,K-ATPase, is an alpha-beta heterodimer, with 10 putative transmembrane segments in the alpha-subunit and one such segment in the beta-subunit. All transmembrane segments remain within the membrane domain following trypsinization of the intact gastric H,K-ATPase in the presence of K+ ions, identified as M1M2, M3M4, M5M6, and M7, M8, M9, and M10. Removal of K+ ions from this digested preparation results in the selective loss of the M5M6 hairpin from the membrane. The release of the M5M6 fragment is directed to the extracellular phase as evidenced by the accumulation of the released M5M6 hairpin inside the sealed inside out vesicles. The stabilization of the M5M6 hairpin in the membrane phase by the transported cation as well as loss to the aqueous phase in the absence of the transported cation has been previously observed for another P2-type ATPase, the Na, K-ATPase (Lutsenko, S., Anderko, R., and Kaplan, J. H. (1995) Proc. Natl. Acad. Sci. U. S. A. 92, 7936-7940). Thus, the effects of the counter-transported cation on retention of the M5M6 segment in the membrane as compared with the other membrane pairs may be a general feature of P2-ATPase ion pumps, reflecting a flexibility of this region that relates to the mechanism of transport.

  5. Binding, folding and insertion of a β-hairpin peptide at a lipid bilayer surface: Influence of electrostatics and lipid tail packing.

    Science.gov (United States)

    Reid, Keon A; Davis, Caitlin M; Dyer, R Brian; Kindt, James T

    2018-03-01

    Antimicrobial peptides (AMPs) act as host defenses against microbial pathogens. Here we investigate the interactions of SVS-1 (KVKVKVKV d P l PTKVKVKVK), an engineered AMP and anti-cancer β-hairpin peptide, with lipid bilayers using spectroscopic studies and atomistic molecular dynamics simulations. In agreement with literature reports, simulation and experiment show preferential binding of SVS-1 peptides to anionic over neutral bilayers. Fluorescence and circular dichroism studies of a Trp-substituted SVS-1 analogue indicate, however, that it will bind to a zwitterionic DPPC bilayer under high-curvature conditions and folds into a hairpin. In bilayers formed from a 1:1 mixture of DPPC and anionic DPPG lipids, curvature and lipid fluidity are also observed to promote deeper insertion of the fluorescent peptide. Simulations using the CHARMM C36m force field offer complementary insight into timescales and mechanisms of folding and insertion. SVS-1 simulated at an anionic mixed POPC/POPG bilayer folded into a hairpin over a microsecond, the final stage in folding coinciding with the establishment of contact between the peptide's valine sidechains and the lipid tails through a "flip and dip" mechanism. Partial, transient folding and superficial bilayer contact are seen in simulation of the peptide at a zwitterionic POPC bilayer. Only when external surface tension is applied does the peptide establish lasting contact with the POPC bilayer. Our findings reveal the influence of disruption to lipid headgroup packing (via curvature or surface tension) on the pathway of binding and insertion, highlighting the collaborative effort of electrostatic and hydrophobic interactions on interaction of SVS-1 with lipid bilayers. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. Proximity hybridization-regulated catalytic DNA hairpin assembly for electrochemical immunoassay based on in situ DNA template-synthesized Pd nanoparticles

    International Nuclear Information System (INIS)

    Zhou, Fuyi; Yao, Yao; Luo, Jianjun; Zhang, Xing; Zhang, Yu; Yin, Dengyang; Gao, Fenglei; Wang, Po

    2017-01-01

    Novel hybridization proximity-regulated catalytic DNA hairpin assembly strategy has been proposed for electrochemical immunoassay based on in situ DNA template-synthesized Pd nanoparticles as signal label. The DNA template-synthesized Pd nanoparticles were characterized with atomic force microscopic and X-ray photoelectron spectroscopy. The highly efficient electrocatalysis by DNA template synthesized Pd nanoparticles for NaBH 4 oxidation produced an intense detection signal. The label-free electrochemical method achieved the detection of carcinoembryonic antigen (CEA) with a linear range from 10 −15 to 10 −11  g mL −1 and a detection limit of 0.43 × 10 −15  g mL −1 . Through introducing a supersandwich reaction to increase the DNA length, the electrochemical signal was further amplified, leading to a detection limit of 0.52 × 10 −16  g mL −1 . And it rendered satisfactory analytical performance for the determination of CEA in serum samples. Furthermore, it exhibited good reproducibility and stability; meanwhile, it also showed excellent specificity due to the specific recognition of antigen by antibody. Therefore, the DNA template synthesized Pd nanoparticles based signal amplification approach has great potential in clinical applications and is also suitable for quantification of biomarkers at ultralow level. - Graphical abstract: A novel label-free and enzyme-free electrochemical immunoassay based on proximity hybridization-regulated catalytic DNA hairpin assemblies for recycling of the CEA. - Highlights: • A novel enzyme-free electrochemical immunosensor was developed for detection of CEA. • The signal amplification was based on catalytic DNA hairpin assembly and DNA-template-synthesized Pd nanoparticles. • The biosensor could detect CEA down to 0.52 × 10 −16  g mL −1 level with a dynamic range spanning 5 orders of magnitude.

  7. Metschnikowia Species Share a Pool of Diverse rRNA Genes Differing in Regions That Determine Hairpin-Loop Structures and Evolve by Reticulation.

    Directory of Open Access Journals (Sweden)

    Matthias Sipiczki

    Full Text Available Modern taxonomy of yeasts is mainly based on phylogenetic analysis of conserved DNA and protein sequences. By far the most frequently used sequences are those of the repeats of the chromosomal rDNA array. It is generally accepted that the rDNA repeats of a genome have identical sequences due to the phenomenon of sequence homogenisation and can thus be used for identification and barcoding of species. Here we show that the rDNA arrays of the type strains of Metschnikowia andauensis and M. fructicola are not homogenised. Both have arrays consisting of diverse repeats that differ from each other in the D1/D2 domains by up to 18 and 25 substitutions. The variable sites are concentrated in two regions that correspond to back-folding stretches of hairpin loops in the predicted secondary structure of the RNA molecules. The substitutions do not alter significantly the overall hairpin-loop structure due to wobble base pairing at sites of C-T transitions and compensatory mutations in the complementary strand of the hairpin stem. The phylogenetic and network analyses of the cloned sequences revealed that the repeats had not evolved in a vertical tree-like way but reticulation might have shaped the rDNA arrays of both strains. The neighbour-net analysis of all cloned sequences of the type strains and the database sequences of different strains further showed that these species share a continuous pool of diverse repeats that appear to evolve by reticulate evolution.

  8. Cu and Cu-Based Nanoparticles: Synthesis and Applications in Catalysis.

    Science.gov (United States)

    Gawande, Manoj B; Goswami, Anandarup; Felpin, François-Xavier; Asefa, Tewodros; Huang, Xiaoxi; Silva, Rafael; Zou, Xiaoxin; Zboril, Radek; Varma, Rajender S

    2016-03-23

    The applications of copper (Cu) and Cu-based nanoparticles, which are based on the earth-abundant and inexpensive copper metal, have generated a great deal of interest in recent years, especially in the field of catalysis. The possible modification of the chemical and physical properties of these nanoparticles using different synthetic strategies and conditions and/or via postsynthetic chemical treatments has been largely responsible for the rapid growth of interest in these nanomaterials and their applications in catalysis. In addition, the design and development of novel support and/or multimetallic systems (e.g., alloys, etc.) has also made significant contributions to the field. In this comprehensive review, we report different synthetic approaches to Cu and Cu-based nanoparticles (metallic copper, copper oxides, and hybrid copper nanostructures) and copper nanoparticles immobilized into or supported on various support materials (SiO2, magnetic support materials, etc.), along with their applications in catalysis. The synthesis part discusses numerous preparative protocols for Cu and Cu-based nanoparticles, whereas the application sections describe their utility as catalysts, including electrocatalysis, photocatalysis, and gas-phase catalysis. We believe this critical appraisal will provide necessary background information to further advance the applications of Cu-based nanostructured materials in catalysis.

  9. Towards an atomic level understanding of niobia based catalysts and catalysis by combining the science of catalysis with surface science

    Directory of Open Access Journals (Sweden)

    Martin Schmal

    2009-06-01

    Full Text Available The science of catalysis and surface science have developed, independently, key information for understanding catalytic processes. One might argue: is there anything fundamental to be discovered through the interplay between catalysis and surface science? Real catalysts of monometallic and bimetallic Co/Nb2O5 and Pd-Co/Nb2O5 catalysts showed interesting selectivity results on the Fischer-Tropsch synthesis (Noronha et al. 1996, Rosenir et al. 1993. The presence of a noble metal increased the C+5 selectivity and decreased the methane formation depending of the reduction temperature. Model catalyst of Co-Pd supported on niobia and alumina were prepared and characterized at the atomic level, thus forming the basis for a comparison with "real" support materials. Growth, morphology and structure of both pure metal and alloy particles were studied. It is possible to support the strong metal support interaction suggested by studies on real catalysts via the investigation of model systems for niobia in comparison to alumina support in which this effect does not occur. Formation of Co2+ penetration into the niobia lattice was suggested on the basis of powder studies and can be fully supported on the basis of model studies. It is shown for both real catalysts and model systems that oxidation state of Co plays a key role in controlling the reactivity in Fischer-Tropsch reactions systems and that the addition of Pd is a determining factor for the stability of the catalyst. It is demonstrated that the interaction with unsaturated hydrocarbons depends strongly on the state of oxidation.As ciências da catálise e da superfície têm desenvolvido independentemente temas básicos para o entendimento de processos catalíticos. Pode-se até questionar se há ainda algo fundamental para ser descoberto através da interface entre catálise eciência da superfície? Catalisadores mono e bimetálicos de Co/Nb2O5 e Pd-Co/ Nb2O5 apresentaram resultados interessantes de

  10. Extremely efficient catalysis of carbon-carbon bond formation using "click" dendrimer-stabilized palladium nanoparticles.

    Science.gov (United States)

    Astruc, Didier; Ornelas, Cátia; Diallo, Abdou K; Ruiz, Jaime

    2010-07-20

    This article is an account of the work carried out in the authors' laboratory illustrating the usefulness of dendrimer design for nanoparticle palladium catalysis. The "click" synthesis of dendrimers constructed generation by generation by 1-->3 C connectivity, introduces 1,2,3-triazolyl ligands insides the dendrimers at each generation. Complexation of the ligands by Pd(II) followed by reduction to Pd(0) forms dendrimer-stabilized Pd nanoparticles (PdNPs) that are extremely reactive in the catalysis of olefin hydrogenation and C-C bond coupling reactions. The stabilization can be outer-dendritic for the small zeroth-generation dendrimer or intra-dendritic for the larger first- and second-generation dendrimers. The example of the Miyaura-Suzuki reaction that can be catalyzed by down to 1 ppm of PdNPs with a "homeopathic" mechanism (the less, the better) is illustrated here, including catalysis in aqueous solvents.

  11. Morphology-controlled synthesis of silver nanostructures via a seed catalysis process

    Science.gov (United States)

    Chen, Chang; Wang, Li; Yu, Haojie; Wang, Jianjun; Zhou, Junfeng; Tan, Qiaohua; Deng, Libo

    2007-03-01

    A novel, effective strategy named 'seed catalysis' has been described here to synthesize silver nanostructures with controllable morphology. Typically, we added Na2S into the reaction system and the Ag2S semiconductor colloids formed at the initial stage would act as both seeds and catalyst in the silver reduction. The morphology of products is controlled by the concentration of Na2S added to the system. Low concentration of Na2S gives nanocubes of 40-50 nm in size, while a high concentration of Na2S is of benefit to obtain nanowires. The growth of the silver crystal is also accelerated by the catalysis of Ag2S. Electron microscopy and UV-vis absorption spectra have been used to investigate the evolution of silver nanowires, and a reasonable mechanism to explain the role of Ag2S seeds has also been suggested. This semiconductor seed catalysis strategy will provide wide applications in the fabrication of metal nanomaterials.

  12. A new class of PN3-pincer ligands for metal–ligand cooperative catalysis

    KAUST Repository

    Li, Huaifeng

    2014-12-01

    Work on a new class of PN3-pincer ligands for metal-ligand cooperative catalysis is reviewed. While the field of the pyridine-based PN3-transition metal pincer complexes is still relatively young, many important applications of these complexes have already emerged. In several cases, the PN3-pincer complexes for metal-ligand cooperative catalysis result in significantly improved or unprecedented activities. The synthesis and coordination chemistry of PN3-pincer ligands are briefly summarized first to cover the synthetic routes for their preparation, followed by a focus review on their applications in catalysis. A specific emphasis is placed on the later section about the role of PN3-pincer ligands\\' dearomatization-rearomatization steps during the catalytic cycles. The mechanistic insights from density functional theory (DFT) calculations are also discussed.

  13. Morphology-controlled synthesis of silver nanostructures via a seed catalysis process

    International Nuclear Information System (INIS)

    Chen Chang; Wang Li; Yu Haojie; Wang Jianjun; Zhou Junfeng; Tan Qiaohua; Deng Libo

    2007-01-01

    A novel, effective strategy named 'seed catalysis' has been described here to synthesize silver nanostructures with controllable morphology. Typically, we added Na 2 S into the reaction system and the Ag 2 S semiconductor colloids formed at the initial stage would act as both seeds and catalyst in the silver reduction. The morphology of products is controlled by the concentration of Na 2 S added to the system. Low concentration of Na 2 S gives nanocubes of 40-50 nm in size, while a high concentration of Na 2 S is of benefit to obtain nanowires. The growth of the silver crystal is also accelerated by the catalysis of Ag 2 S. Electron microscopy and UV-vis absorption spectra have been used to investigate the evolution of silver nanowires, and a reasonable mechanism to explain the role of Ag 2 S seeds has also been suggested. This semiconductor seed catalysis strategy will provide wide applications in the fabrication of metal nanomaterials

  14. A new class of PN3-pincer ligands for metal–ligand cooperative catalysis

    KAUST Repository

    Li, Huaifeng; Zheng, Bin; Huang, Kuo-Wei

    2014-01-01

    Work on a new class of PN3-pincer ligands for metal-ligand cooperative catalysis is reviewed. While the field of the pyridine-based PN3-transition metal pincer complexes is still relatively young, many important applications of these complexes have already emerged. In several cases, the PN3-pincer complexes for metal-ligand cooperative catalysis result in significantly improved or unprecedented activities. The synthesis and coordination chemistry of PN3-pincer ligands are briefly summarized first to cover the synthetic routes for their preparation, followed by a focus review on their applications in catalysis. A specific emphasis is placed on the later section about the role of PN3-pincer ligands' dearomatization-rearomatization steps during the catalytic cycles. The mechanistic insights from density functional theory (DFT) calculations are also discussed.

  15. Converting Homogeneous to Heterogeneous in Electrophilic Catalysis using Monodisperse Metal Nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Witham, Cole A.; Huang, Wenyu; Tsung, Chia-Kuang; Kuhn, John N.; Somorjai, Gabor A.; Toste, F. Dean

    2009-10-15

    A continuing goal in catalysis is the transformation of processes from homogeneous to heterogeneous. To this end, nanoparticles represent a new frontier in heterogeneous catalysis, where this conversion is supplemented by the ability to obtain new or divergent reactivity and selectivity. We report a novel method for applying heterogeneous catalysts to known homogeneous catalytic reactions through the design and synthesis of electrophilic platinum nanoparticles. These nanoparticles are selectively oxidized by the hypervalent iodine species PhICl{sub 2}, and catalyze a range of {pi}-bond activation reactions previously only homogeneously catalyzed. Multiple experimental methods are utilized to unambiguously verify the heterogeneity of the catalytic process. The discovery of treatments for nanoparticles that induce the desired homogeneous catalytic activity should lead to the further development of reactions previously inaccessible in heterogeneous catalysis. Furthermore, our size and capping agent study revealed that Pt PAMAM dendrimer-capped nanoparticles demonstrate superior activity and recyclability compared to larger, polymer-capped analogues.

  16. 2010 CATALYSIS GORDON RESEARCH CONFERENCE, JUNE 27 - JULY 2, 2010, NEW LONDON, NEW HAMPSHIRE

    Energy Technology Data Exchange (ETDEWEB)

    Abhaya Datye

    2010-07-02

    Catalysis is a key technology for improving the quality of life while simultaneously reducing the adverse impact of human activities on the environment. The discovery of new catalytic processes and the improvement of existing ones are also critically important for securing the nation's energy supply. The GRC on Catalysis is considered one the most prestigious conference for catalysis research, bringing together leading researchers from both academia, industry and national labs to discuss the latest, most exciting research in catalysis and the future directions for the field. The 2010 GRC on Catalysis will follow time-honored traditions and feature invited talks from the world's leading experts in the fundamentals and applications of catalytic science and technology. We plan to have increased participation from industry. The extended discussions in the company of outstanding thinkers will stimulate and foster new science. The conference will include talks in the following areas: Alternative feedstocks for chemicals and fuels, Imaging and spectroscopy, Design of novel catalysts, Catalyst preparation fundamentals, Molecular insights through theory, Surface Science, Catalyst stability and dynamics. In 2010, the Catalysis conference will move to a larger conference room with a new poster session area that will allow 40 posters per session. The dorm rooms provide single and double accommodations, free WiFi and the registration fee includes all meals and the famous lobster dinner on Thursday night. Afternoons are open to enjoy the New England ambiance with opportunities for hiking, sailing, golf and tennis to create an outstanding conference that will help you network with colleagues, and make long lasting connections.

  17. Treatment of the liquid waste of the laboratories of the engineering Department by means of photo catalysis

    International Nuclear Information System (INIS)

    Porras, Paula; Avalos, Yasmin; Mejia, Gloria; Penuela, Gustavo

    2000-01-01

    In this paper are showed the results of wastewater treatment of CIA and ISA laboratories of engineering Department. Photo catalysis was used in treatment of wastewater, with a removal between 52% and 68% as chemical oxygen demand (COD) during 6 hours of photo degradation. In photo catalysis, TiO 2 , hydrogen peroxide and ultraviolet light were used

  18. Respiratory-aspirated 35-mm hairpin successfully retrieved with a Teflon® snare system under fluoroscopic guidance via a split endotracheal tube: a useful technique in cases of failed extraction by bronchoscopy and avoiding the need for a thoracotomy.

    Science.gov (United States)

    Gill, S S; Pease, R A; Ashwin, C J; Gill, S S; Tait, N P

    2012-09-01

    Respiratory foreign body aspiration (FBA) is a common global health problem requiring prompt recognition and early treatment to prevent potentially fatal complications. The majority of FBAs are due to organic objects and treatment is usually via either endoscopic or surgical extraction. FBA of a straight hairpin has been described as a unique entity in the literature, occurring most commonly in females, particularly during adolescence. In the process of inserting hairpins, the pins will typically be between the teeth with the head tilted backwards, while tying their hair with both hands. This position increases the risk of aspiration, particularly if there is any sudden coughing or laughing. To our knowledge, this is the first case report of a 35-mm straight metallic hairpin foreign body that has been successfully retrieved by a radiological snare system under fluoroscopic guidance. This was achieved with the use of a split endotracheal tube, and therefore avoided the need for a thoracotomy in an adolescent female patient.

  19. Catalysis by Design Using Surface Organometallic Nitrogen-Containing Fragments

    KAUST Repository

    Hamzaoui, Bilel

    2016-06-14

    The aim of this thesis is to explore the chemistry of well-defined silica-supported group 4 and group 5 complexes that contain one or more multiply-bonded nitrogen atoms. Such species have been recognized as crucial intermediates in many catalytic reactions (e.g. hydroaminoalkylation, olefin hydrogenation, imine metathesis…). The first chapter provided a bibliographic overview of the preparation and the reactivity of group 4 and 5 complexes towards hydroaminoalkylation and imine metathesis catalysis. The second chapter deals with the isolation and the characterization of a series of well-defined group 4 ƞ2-imine complexes surfaces species. 2D solid-state NMR (1H–13C HETCOR, Multiple Quantum) experiments have revealed consistently a unique structural rearrangement, viz azametallacycle occurring on the immobilized metal-amido ligands. Hydrogenolysis of the sole Zr-C bond in such species gives selectively a silica-supported zirconium monohydride that can perform the catalytic hydrogenation of olefins. The third chapter examines the mechanistic studies of the intermolecular hydroaminoalkylation using SOMC to identify the key metallacyclic surface intermediates (silica-supported three-membred and five-membered). The catalyst was regenerated by protonolysis and afforded pure amine. Catalytic testing of a selection of amine compounds with variable electronic properties was carried out. The fourth chapter deals with the generation and the characterization of well-defined silica-supported zirconium-imido complexes. The resulting species effectively catalyzes imine/imine cross-metathesis and thus considered as the first heterogeneous catalysts active for imine metathesis reaction. The fifth chapter studies the reaction of SBA15.1100 ºC with dry aniline and derivatives leading to opening strained siloxane bridges into acid-base paired functionalities (formation of N-phenylsilanamine-silanol pairs). This approach was successfully applied to the design of a series of

  20. Perspectives on electrostatics and conformational motions in enzyme catalysis.

    Science.gov (United States)

    Hanoian, Philip; Liu, C Tony; Hammes-Schiffer, Sharon; Benkovic, Stephen

    2015-02-17

    CONSPECTUS: Enzymes are essential for all living organisms, and their effectiveness as chemical catalysts has driven more than a half century of research seeking to understand the enormous rate enhancements they provide. Nevertheless, a complete understanding of the factors that govern the rate enhancements and selectivities of enzymes remains elusive, due to the extraordinary complexity and cooperativity that are the hallmarks of these biomolecules. We have used a combination of site-directed mutagenesis, pre-steady-state kinetics, X-ray crystallography, nuclear magnetic resonance (NMR), vibrational and fluorescence spectroscopies, resonance energy transfer, and computer simulations to study the implications of conformational motions and electrostatic interactions on enzyme catalysis in the enzyme dihydrofolate reductase (DHFR). We have demonstrated that modest equilibrium conformational changes are functionally related to the hydride transfer reaction. Results obtained for mutant DHFRs illustrated that reductions in hydride transfer rates are correlated with altered conformational motions, and analysis of the evolutionary history of DHFR indicated that mutations appear to have occurred to preserve both the hydride transfer rate and the associated conformational changes. More recent results suggested that differences in local electrostatic environments contribute to finely tuning the substrate pKa in the initial protonation step. Using a combination of primary and solvent kinetic isotope effects, we demonstrated that the reaction mechanism is consistent across a broad pH range, and computer simulations suggested that deprotonation of the active site Tyr100 may play a crucial role in substrate protonation at high pH. Site-specific incorporation of vibrational thiocyanate probes into the ecDHFR active site provided an experimental tool for interrogating these microenvironments and for investigating changes in electrostatics along the DHFR catalytic cycle

  1. Nanoporous gold membranes: From morphological control to fuel cell catalysis

    Science.gov (United States)

    Ding, Yi

    Porous noble metals are particularly attractive for scientific research and industrial applications such as catalysis, sensing, and filtration. In this thesis, I will discuss the fabrication, characterization, and application of a new class of porous metals, called nanoporous metals (NPM). NPM is made during selective dissolution (also called dealloying) of reactive components (e.g., silver) from multi-component alloys (e.g., Ag/Au alloy). Commercially available white gold leaf (Ag65Au35) can, for example, be etched into nanoporous gold (NPG) membrane by simply floating the leaf on concentrated nitric acid for periods of a few minutes. NPG leaf adopts a single crystal porous structure within individual grains. The microstructure of NPG, such as the pore size, is tunable between a few nanometers to sub-micron length scale by either thermal annealing or post-treatment in nitric acid for extended period of time. A new gas-liquid-solid interface electroless plating technique is developed to uniformly cover the NPG surface with other metals, such as silver and platinum. This technique allows new opportunities of making functionalized nanostructures. We show that a combination of silver plating and dealloying can be used to make multimodal porous metals, which are expected to have application in sensing field. Electroless platinum plating onto NPG shows very usual growth mode. TEM observation indicates that the platinum layer on NPG surface takes a novel form of layer-islanding growth (Stranski-Krastanov growth). Annealing the Pt/NPG composite smoothens the Pt islands and forms a 1 nm coherent Pt layer on the NPG backbone, possibly with dislocation formation at the Pt/Au interface. Furthermore, it was found that we could dissolve the gold away in aqueous gold etchant, leaving behind the 1 nm-thick Pt shell, a structure we call nanotubular mesoporous platinum (NMP). Pt plated NPG has a series of unique structural properties, such as high active surface area, thermally

  2. Metal nanoparticles in liquid phase catalysis; from recent advances to future goals.

    Science.gov (United States)

    Zahmakıran, Mehmet; Ozkar, Saim

    2011-09-01

    Metal nanoparticles have attracted much attention over the last decade owing to their unique properties, different to their bulk counterparts, which pave the way for their application in different fields from materials science and engineering to biomedical applications. Of particular interest, the use of metal nanoparticles in catalysis has brought superior efficiency in terms of activity, selectivity and lifetime to heterogeneous catalysis. This article reviews the recent developments in the synthesis routes and the catalytic performance of metal nanoparticles depending on the solvent used for various organic and inorganic transformations. Additionally, we also discuss the prevalent complications and their possible solutions plus future prospects in the field of nanocatalysis.

  3. Growth mechanism of graphene on platinum: Surface catalysis and carbon segregation

    International Nuclear Information System (INIS)

    Sun, Jie; Lindvall, Niclas; Yurgens, August; Nam, Youngwoo; Cole, Matthew T.; Teo, Kenneth B. K.; Woo Park, Yung

    2014-01-01

    A model of the graphene growth mechanism of chemical vapor deposition on platinum is proposed and verified by experiments. Surface catalysis and carbon segregation occur, respectively, at high and low temperatures in the process, representing the so-called balance and segregation regimes. Catalysis leads to self-limiting formation of large area monolayer graphene, whereas segregation results in multilayers, which evidently “grow from below.” By controlling kinetic factors, dominantly monolayer graphene whose high quality has been confirmed by quantum Hall measurement can be deposited on platinum with hydrogen-rich environment, quench cooling, tiny but continuous methane flow and about 1000 °C growth temperature

  4. Enzyme catalysis: a new definition accounting for noncovalent substrate- and product-like states.

    Science.gov (United States)

    Purich, D L

    2001-07-01

    Biological catalysis frequently causes changes in noncovalent bonding. By building on Pauling's assertion that any long-lived, chemically distinct interaction is a chemical bond, this article redefines enzyme catalysis as the facilitated making and/or breaking of chemical bonds, not just of covalent bonds. It is also argued that nearly every ATPase or GTPase is misnamed as a hydrolase and actually belongs to a distinct class of enzymes, termed here 'energases'. By transducing covalent bond energy into mechanical work, energases mediate such fundamental processes as protein folding, self-assembly, G-protein interactions, DNA replication, chromatin remodeling and even active transport.

  5. Effect of a Dual Charge on the DNA-Conjugated Redox Probe on DNA Sensing by Short Hairpin Beacons Tethered to Gold Electrodes.

    Science.gov (United States)

    Kékedy-Nagy, László; Shipovskov, Stepan; Ferapontova, Elena E

    2016-08-16

    Charges of redox species can critically affect both the interfacial state of DNA and electrochemistry of DNA-conjugated redox labels and, as a result, the electroanalytical performance of those systems. Here, we show that the kinetics of electron transfer (ET) between the gold electrode and methylene blue (MB) label conjugated to a double-stranded (ds) DNA tethered to gold strongly depend on the charge of the MB molecule, and that affects the performance of genosensors exploiting MB-labeled hairpin DNA beacons. Positively charged MB binds to dsDNA via electrostatic and intercalative/groove binding, and this binding allows the DNA-mediated electrochemistry of MB intercalated into the duplex and, as a result, a complex mode of the electrochemical signal change upon hairpin hybridization to the target DNA, dominated by the "on-off" signal change mode at nanomolar levels of the analyzed DNA. When MB bears an additional carboxylic group, the negative charge provided by this group prevents intimate interactions between MB and DNA, and then the ET in duplexes is limited by the diffusion of the MB-conjugated dsDNA (the phenomenon first shown in Farjami , E. ; Clima , L. ; Gothelf , K. ; Ferapontova , E. E. Anal. Chem. 2011 , 83 , 1594 ) providing the robust "off-on" nanomolar DNA sensing. Those results can be extended to other intercalating redox probes and are of strategic importance for design and development of electrochemical hybridization sensors exploiting DNA nanoswitchable architectures.

  6. Stability of monomeric Cro variants: Isoenergetic transformation of a type I' to a type II' beta-hairpin by single amino acid replacements.

    Science.gov (United States)

    Mollah, A K M M; Stennis, Rhonda L; Mossing, Michael C

    2003-05-01

    The thermodynamic stabilities of three monomeric variants of the bacteriophage lambda Cro repressor that differ only in the sequence of two amino acids at the apex of an engineered beta-hairpin have been determined. The sequences of the turns are EVK-XX-EVK, where the two central residues are DG, GG, and GT, respectively. Standard-state unfolding free energies, determined from circular dichroism measurements as a function of urea concentration, range from 2.4 to 2.7 kcal/mole, while those determined from guanidine hydrochloride range from 2.8 to 3.3 kcal/mole for the three proteins. Thermal denaturation yields van't Hoff unfolding enthalpies of 36 to 40 kcal /mole at midpoint temperatures in the range of 53 to 58 degrees C. Extrapolation of the thermal denaturation free energies with heat capacities of 400 to 600 cal/mole deg gives good agreement with the parameters determined in denaturant titrations. As predicted from statistical surveys of amino acid replacements in beta-hairpins, energetic barriers to transformation from a type I' turn (DG) to a type II' turn (GT) can be quite small.

  7. Asymmetric catalysis in the cyclopropanation of olefins; Catalise assimetrica na ciclopropanacao de olefinas

    Energy Technology Data Exchange (ETDEWEB)

    Leao, Raquel A.C.; Ferreira, Vitor F.; Pinheiro, Sergio [Universidade Federal Fluminense (UFF), Niteroi, RJ (Brazil). Dept. de Quimica Organica]. E-mail: cegvito@vm.uff.br

    2007-07-01

    The main methodologies in the asymmetric cyclopropanation of alkenes with emphasis on asymmetric catalysis are covered. Examples are the Simmons-Smith reaction, the use of diazoalkanes and reactions carried out by decomposition of alpha-diazoesters in the presence of transition metals. (author)

  8. Theoretical mo delling of nanoparticles with applications to catalysis and sustainable energy

    DEFF Research Database (Denmark)

    Brodersen, Simon Hedegaard

    The aim of this thesis is to gain a better understanding of the shape and structure of nanoparticles. Nanoparticles are important in heterogeneous catalysis, where the chemical reaction happens at the surface, since they maximise the available surface area for a given amount of catalyst. Studies...

  9. A spectral study of the elementary step of proton transfer in heterogeneous acid catalysis

    Energy Technology Data Exchange (ETDEWEB)

    Kazanskii, V B

    1977-09-01

    A spectral study of the elementary step of proton transfer in heterogeneous acid catalysis involved a determination of the potential curves of the OH bond in surface hydroxyl groups (e.g., those on silica, NaHY zeolite, or glass) of differing acidity from IR stretching frequency data in the overtone region; a calculation of the activation energies for proton transfer during acid catalysis from the changes in the curve forms after adsorption of various molecules (e.g., water, ammonia, benzene, toluene, xylenes, acetone, and cyclohexane); and a comparison of the IR predictions with quantum-chemical calculations of the potential curves. The results appear to furnish a new criterion for the coordinate of reactions involving Broensted sites: if the activation energy measured during actual catalysis is close to that calculated from the IR stretching data, the reaction proceeds by the stepwise mechanism of acid catalysis; but if these values differ greatly, the reaction involves a concerted mechanism (i.e., activation of the adsorbed molecule without involvement of OH groups). Tables, graphs, and 15 references.

  10. Synergistic dual activation catalysis by palladium nanoparticles for epoxide ring opening with phenols.

    Science.gov (United States)

    Seth, Kapileswar; Roy, Sudipta Raha; Pipaliya, Bhavin V; Chakraborti, Asit K

    2013-07-04

    Synergistic dual activation catalysis has been devised for epoxide phenolysis wherein palladium nanoparticles induce electrophilic activation via coordination with the epoxide oxygen followed by nucleophilic activation through anion-π interaction with the aromatic ring of the phenol, and water (reaction medium) also renders assistance through 'epoxide-phenol' dual activation.

  11. Catalysis in flow microreactors with wall coatings of acidic polymer brushes and dendrimer-encapsulated nanoparticles

    NARCIS (Netherlands)

    Ricciardi, R.

    2015-01-01

    Continuous-flow microreactors are an invaluable tool to carry out organic reactions owing to their numerous advantages with respect to batch scale synthesis. In particular, supported catalysts enable heterogeneous catalysis to be conducted in an efficient way. In this thesis, the development and

  12. Green catalysis by nanoparticulate catalysts developed for flow processing? case study of glucose hydrogenation

    NARCIS (Netherlands)

    Gericke, D.; Ott-Reinhardt, D.; Matveeva, V.; Sulman, E.M.; Aho, A.; Murzin, D.Y.; Roggan, S.; Danilova, L.; Hessel, V.; Löb, P.; Kralisch, D.

    2015-01-01

    Heterogeneous catalysis, flow chemistry, continuous processing, green solvents, catalyst immobilization and recycling are some of the most relevant, emerging key technologies to achieve green synthesis. However, a quantification of potential effects on a case to case level is required to provide a

  13. The role of Fischer-Tropsch catalysis in solar nebula chemistry

    NARCIS (Netherlands)

    Kress, ME; Tielens, AGGM

    Fischer-Tropsch catalysis, the iron/nickel catalyzed conversion of CO and H(2) to hydrocarbons, would have been the only thermally-driven pathway available in the solar nebula to convert CO into other forms of carbon. A major issue in meteoritics is to determine the origin of meteoritic organics:

  14. Catalysis looks to the future. Panel on new directions in catalytic science and technology

    Energy Technology Data Exchange (ETDEWEB)

    1992-12-31

    Catalysts play a vital role in providing society with fuels, commodity and fine chemicals, pharmaceuticals, and means for protecting the environment. To be useful, a good catalyst must have a high turnover frequency (activity), produce the right kind of product (selectivity), and have a long life (durability), all at an acceptable cost. Research in the field of catalysis provides the tools and understanding required to facilitate and accelerate the development of improved catalysts and to open opportunities for the discovery of new catalytic processes. The aim of this report is to identify the research opportunities and challenges for catalysis in the coming decades and to detail the resources necessary to ensure steady progress. Chapter 2 discusses opportunities for developing new catalysts to meet the demands of the chemical and fuel industries, and the increasing role of catalysis in environmental protection. The intellectual challenges for advancing the frontiers of catalytic science are outlined in Chapter 3. The human and institutional resources available in the US for carrying out research on catalysis are summarized in Chapter 4. The findings and recommendations of the panel for industry, academe, the national laboratories, and the federal government are presented in Chapter 5.

  15. Applications of secondary ion mass spectrometry in catalysis and surface chemistry

    NARCIS (Netherlands)

    Borg, H.J.; Niemantsverdriet, J.W.; Spivey, J.J.; Agarwal, S.K.

    1994-01-01

    A review with 182 refs. is given on phys. phenomena such as sputtering, ion emission, ionization and neutralization which are involved in SIMS. Applications of SIMS in catalysis and obtaining information about catalysts interactions with gases promoters and poisons are described. Also applications

  16. Enzyme-Like Catalysis of the Nazarov Cyclization by Supramolecular Encapsulation

    Energy Technology Data Exchange (ETDEWEB)

    Hastings, Courtney; Pluth, Michael; Bergman, Robert; Raymond, Kenneth

    2010-03-29

    A primary goal in the design and synthesis of molecular hosts has been the selective recognition and binding of a variety of guests using non-covalent interactions. Supramolecular catalysis, which is the application of such hosts towards catalysis, has much in common with many enzymatic reactions, chiefly the use of both spatially appropriate binding pockets and precisely oriented functional groups to recognize and activate specific substrate molecules. Although there are now many examples which demonstrate how selective encapsulation in a host cavity can enhance the reactivity of a bound guest, all have failed to reach the degree of increased reactivity typical of enzymes. We now report the catalysis of the Nazarov cyclization by a self-assembled coordination cage, a carbon-carbon bond-forming reaction which proceeds under mild, aqueous conditions. The acceleration in this system is over a million-fold, and represents the first example of supramolecular catalysis that achieves the level of rate enhancement comparable to that observed in several enzymes. We explain the unprecedented degree of rate increase as due to the combination of (a) preorganization of the encapsulated substrate molecule, (b) stabilization of the transition state of the cyclization by constrictive binding, and (c) increase in the basicity of the complexed alcohol functionality.

  17. Influence of temperature and hydroxide concentration on the settling time of hydroxy-catalysis bonds

    International Nuclear Information System (INIS)

    Reid, S.; Cagnoli, G.; Elliffe, E.; Faller, J.; Hough, J.; Martin, I.; Rowan, S.

    2007-01-01

    Many applications using bonded optical components have stringent requirements on the strength, rigidity, stability and alignment of the bonds. Hydroxy-catalysis bonding fulfills these requirements. Here we investigate methods by which the bonding time may be extended to better aid the precise prealignment of optical components through controlling the temperature and concentration of the bonding solution

  18. Pop-It Beads to Introduce Catalysis of Reaction Rate and Substrate Depletion Effects

    Science.gov (United States)

    Gehret, Austin U.

    2017-01-01

    A kinesthetic classroom activity was designed to help students understand enzyme activity and catalysis of reaction rate. Students served the role of enzymes by manipulating Pop-It Beads as the catalytic event. This activity illuminates the relationship between reaction rate and reaction progress by allowing students to experience first-hand the…

  19. Challenges and perspectives for catalysis in production of diesel from biomass

    DEFF Research Database (Denmark)

    Madsen, Anders Theilgaard; Søndergaard, Helle; Fehrmann, Rasmus

    2011-01-01

    oils or waste fats with methanol is the most prominent and has been applied industrially for a decade. Homogeneous acid and base catalysis is normally used, but solid acids, solid bases, ionic liquids and lipases are being developed as replacements. Hydrodeoxygenation of vegetable oils has likewise...

  20. Chemical Ligation and Isotope Labeling to Locate Dynamic Effects during Catalysis by Dihydrofolate Reductase.

    Science.gov (United States)

    Luk, Louis Y P; Ruiz-Pernía, J Javier; Adesina, Aduragbemi S; Loveridge, E Joel; Tuñón, Iñaki; Moliner, Vincent; Allemann, Rudolf K

    2015-07-27

    Chemical ligation has been used to alter motions in specific regions of dihydrofolate reductase from E. coli and to investigate the effects of localized motional changes on enzyme catalysis. Two isotopic hybrids were prepared; one with the mobile N-terminal segment containing heavy isotopes ((2) H, (13) C, (15) N) and the remainder of the protein with natural isotopic abundance, and the other one with only the C-terminal segment isotopically labeled. Kinetic investigations indicated that isotopic substitution of the N-terminal segment affected only a physical step of catalysis, whereas the enzyme chemistry was affected by protein motions from the C-terminal segment. QM/MM studies support the idea that dynamic effects on catalysis mostly originate from the C-terminal segment. The use of isotope hybrids provides insights into the microscopic mechanism of dynamic coupling, which is difficult to obtain with other studies, and helps define the dynamic networks of intramolecular interactions central to enzyme catalysis. © 2015 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

  1. ISHHC XIII International Symposium on the Relations betweenHomogeneous and Heterogeneous Catalysis

    Energy Technology Data Exchange (ETDEWEB)

    Somorjai (Ed.), G.A.

    2007-06-11

    The International Symposium on Relations between Homogeneous and Heterogeneous Catalysis (ISHHC) has a long and distinguished history. Since 1974, in Brussels, this event has been held in Lyon, France (1977), Groeningen, The Netherlands (1981); Asilomar, California (1983); Novosibirsk, Russia (1986); Pisa, Italy (1989); Tokyo, Japan (1992); Balatonfuered, Hungary (1995); Southampton, United Kingdom (1999); Lyon, France (2001); Evanston, Illinois (2001) and Florence, Italy (2005). The aim of this international conference in Berkeley is to bring together practitioners in the three fields of catalysis, heterogeneous, homogeneous and enzyme, which utilize mostly nanosize particles. Recent advances in instrumentation, synthesis and reaction studies permit the nanoscale characterization of the catalyst systems, often for the same reaction, under similar experimental conditions. It is hoped that this circumstance will permit the development of correlations of these three different fields of catalysis on the molecular level. To further this goal we aim to uncover and focus on common concepts that emerge from nanoscale studies of structures and dynamics of the three types of catalysts. Another area of focus that will be addressed is the impact on and correlation of nanosciences with catalysis. There is information on the electronic and atomic structures of nanoparticles and their dynamics that should have importance in catalyst design and catalytic activity and selectivity.

  2. Chemistry, spectroscopy and the role of supported vanadium oxides in heterogeneous catalysis

    NARCIS (Netherlands)

    Weckhuysen, B.M.; Keller, D.E.

    2003-01-01

    Supported vanadium oxide catalysts are active in a wide range of applications. In this review, an overview is given of the current knowledge available about vanadium oxide-based catalysts. The review starts with the importance of vanadium in heterogeneous catalysis, a discussion of the molecular

  3. Interrelation of chemistry and process design in biodiesel manufacturing by heterogeneous catalysis

    NARCIS (Netherlands)

    Dimian, A.C.; Srokol, Z.W.; Mittelmeijer-Hazeleger, M.C.; Rothenberg, G.

    2010-01-01

    The pros and cons of using heterogeneous catalysis for biodiesel manufacturing are introduced, and explained from a chemistry and engineering viewpoint. Transesterification reactions of various feed types are then compared in batch and continuous process operation modes. The results show that the

  4. Eroding dipoles and vorticity growth for Euler flows in {{{R}}}^{3}: the hairpin geometry as a model for finite-time blowup

    Science.gov (United States)

    Childress, Stephen; Gilbert, Andrew D.

    2018-02-01

    A theory of an eroding ‘hairpin’ vortex dipole structure in three-dimensions is developed, extending our previous study of an axisymmetric eroding dipole without swirl. The axisymmetric toroidal dipole was found to lead to maximal growth of vorticity, as {t}4/3. The hairpin is here similarly proposed as a model to produce large ‘self-stretching’ of vorticity, with the possibility of finite-time blow-up. We derive a system of partial differential equations of ‘generalized’ form, involving contour averaging of a locally two-dimensional Euler flow. We do not attempt here to solve the system exactly, but point out that non-existence of physically acceptable solutions would most probably be a result of the axial flow. Because of the axial flow the vorticity distribution within the dipole eddies is no longer of the simple Sadovskii type (vorticity constant over a cross-section) obtained in the axisymmetric problem. Thus the solution of the system depends upon the existence of a larger class of propagating two-dimensional dipoles. The hairpin model is obtained by formal asymptotic analysis. As in the axisymmetric problem a local transformation to ‘shrinking’ coordinates is introduced, but now in a self-similar form appropriate to the study of a possible finite-time singularity. We discuss some properties of the model, including a study of the helicity and a first step in iterating toward a solution from the Sadovskii structure. We also present examples of two-dimensional propagating dipoles not previously studied, which have a vorticity profile consistent with our model. Although no rigorous results can be given, and analysis of the system is only partial, the formal calculations are consistent with the possibility of a finite time blowup of vorticity at a point of vanishing circulation of the dipole eddies, but depending upon the existence of the necessary two-dimensional propagating dipole. Our results also suggest that conservation of kinetic energy as

  5. Proximity hybridization-regulated catalytic DNA hairpin assembly for electrochemical immunoassay based on in situ DNA template-synthesized Pd nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Fuyi [School of Chemistry and Chemical Engineering, Jiangsu Normal University, Xuzhou 221116 (China); Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical College, 221004, Xuzhou (China); Yao, Yao; Luo, Jianjun; Zhang, Xing; Zhang, Yu; Yin, Dengyang [Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical College, 221004, Xuzhou (China); Gao, Fenglei, E-mail: jsxzgfl@sina.com [Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical College, 221004, Xuzhou (China); Wang, Po, E-mail: wangpo@jsnu.edu.cn [School of Chemistry and Chemical Engineering, Jiangsu Normal University, Xuzhou 221116 (China)

    2017-05-29

    Novel hybridization proximity-regulated catalytic DNA hairpin assembly strategy has been proposed for electrochemical immunoassay based on in situ DNA template-synthesized Pd nanoparticles as signal label. The DNA template-synthesized Pd nanoparticles were characterized with atomic force microscopic and X-ray photoelectron spectroscopy. The highly efficient electrocatalysis by DNA template synthesized Pd nanoparticles for NaBH{sub 4} oxidation produced an intense detection signal. The label-free electrochemical method achieved the detection of carcinoembryonic antigen (CEA) with a linear range from 10{sup −15} to 10{sup −11} g mL{sup −1} and a detection limit of 0.43 × 10{sup −15} g mL{sup −1}. Through introducing a supersandwich reaction to increase the DNA length, the electrochemical signal was further amplified, leading to a detection limit of 0.52 × 10{sup −16} g mL{sup −1}. And it rendered satisfactory analytical performance for the determination of CEA in serum samples. Furthermore, it exhibited good reproducibility and stability; meanwhile, it also showed excellent specificity due to the specific recognition of antigen by antibody. Therefore, the DNA template synthesized Pd nanoparticles based signal amplification approach has great potential in clinical applications and is also suitable for quantification of biomarkers at ultralow level. - Graphical abstract: A novel label-free and enzyme-free electrochemical immunoassay based on proximity hybridization-regulated catalytic DNA hairpin assemblies for recycling of the CEA. - Highlights: • A novel enzyme-free electrochemical immunosensor was developed for detection of CEA. • The signal amplification was based on catalytic DNA hairpin assembly and DNA-template-synthesized Pd nanoparticles. • The biosensor could detect CEA down to 0.52 × 10{sup −16} g mL{sup −1} level with a dynamic range spanning 5 orders of magnitude.

  6. Uma perspectiva computacional sobre catálise enzimática A computational perspective on enzymatic catalysis

    Directory of Open Access Journals (Sweden)

    Guilherme M. Arantes

    2008-01-01

    Full Text Available Enzymes are extremely efficient catalysts. Here, part of the mechanisms proposed to explain this catalytic power will be compared to quantitative experimental results and computer simulations. Influence of the enzymatic environment over species along the reaction coordinate will be analysed. Concepts of transition state stabilisation and reactant destabilisation will be confronted. Divided site model and near-attack conformation hypotheses will also be discussed. Molecular interactions such as covalent catalysis, general acid-base catalysis, electrostatics, entropic effects, steric hindrance, quantum and dynamical effects will also be analysed as sources of catalysis. Reaction mechanisms, in particular that catalysed by protein tyrosine phosphatases, illustrate the concepts.

  7. Disulfide-stabilized Helical Hairpin Structure and Activity of a Novel Antifungal Peptide EcAMP1 from Seeds of Barnyard Grass (Echinochloa crus-galli)*

    Science.gov (United States)

    Nolde, Svetlana B.; Vassilevski, Alexander A.; Rogozhin, Eugene A.; Barinov, Nikolay A.; Balashova, Tamara A.; Samsonova, Olga V.; Baranov, Yuri V.; Feofanov, Alexey V.; Egorov, Tsezi A.; Arseniev, Alexander S.; Grishin, Eugene V.

    2011-01-01

    This study presents purification, activity characterization, and 1H NMR study of the novel antifungal peptide EcAMP1 from kernels of barnyard grass Echinochloa crus-galli. The peptide adopts a disulfide-stabilized α-helical hairpin structure in aqueous solution and thus represents a novel fold among naturally occurring antimicrobial peptides. Micromolar concentrations of EcAMP1 were shown to inhibit growth of several fungal phytopathogens. Confocal microscopy revealed intensive EcAMP1 binding to the surface of fungal conidia followed by internalization and accumulation in the cytoplasm without disturbance of membrane integrity. Close spatial structure similarity between EcAMP1, the trypsin inhibitor VhTI from seeds of Veronica hederifolia, and some scorpion and cone snail toxins suggests natural elaboration of different functions on a common fold. PMID:21561864

  8. Disulfide-stabilized helical hairpin structure and activity of a novel antifungal peptide EcAMP1 from seeds of barnyard grass (Echinochloa crus-galli).

    Science.gov (United States)

    Nolde, Svetlana B; Vassilevski, Alexander A; Rogozhin, Eugene A; Barinov, Nikolay A; Balashova, Tamara A; Samsonova, Olga V; Baranov, Yuri V; Feofanov, Alexey V; Egorov, Tsezi A; Arseniev, Alexander S; Grishin, Eugene V

    2011-07-15

    This study presents purification, activity characterization, and (1)H NMR study of the novel antifungal peptide EcAMP1 from kernels of barnyard grass Echinochloa crus-galli. The peptide adopts a disulfide-stabilized α-helical hairpin structure in aqueous solution and thus represents a novel fold among naturally occurring antimicrobial peptides. Micromolar concentrations of EcAMP1 were shown to inhibit growth of several fungal phytopathogens. Confocal microscopy revealed intensive EcAMP1 binding to the surface of fungal conidia followed by internalization and accumulation in the cytoplasm without disturbance of membrane integrity. Close spatial structure similarity between EcAMP1, the trypsin inhibitor VhTI from seeds of Veronica hederifolia, and some scorpion and cone snail toxins suggests natural elaboration of different functions on a common fold.

  9. Analysis of cis and trans Requirements for DNA Replication at the Right-End Hairpin of the Human Bocavirus 1 Genome.

    Science.gov (United States)

    Shen, Weiran; Deng, Xuefeng; Zou, Wei; Engelhardt, John F; Yan, Ziying; Qiu, Jianming

    2016-09-01

    Parvoviruses are single-stranded DNA viruses that use the palindromic structures at the ends of the viral genome for their replication. The mechanism of parvovirus replication has been studied mostly in the dependoparvovirus adeno-associated virus 2 (AAV2) and the protoparvovirus minute virus of mice (MVM). Here, we used human bocavirus 1 (HBoV1) to understand the replication mechanism of bocaparvovirus. HBoV1 is pathogenic to humans, causing acute respiratory tract infections, especially in young children under 2 years old. By using the duplex replicative form of the HBoV1 genome in human embryonic kidney 293 (HEK293) cells, we identified the HBoV1 minimal replication origin at the right-end hairpin (OriR). Mutagenesis analyses confirmed the putative NS1 binding and nicking sites within the OriR. Of note, unlike the large nonstructural protein (Rep78/68 or NS1) of other parvoviruses, HBoV1 NS1 did not specifically bind OriR in vitro, indicating that other viral and cellular components or the oligomerization of NS1 is required for NS1 binding to the OriR. In vivo studies demonstrated that residues responsible for NS1 binding and nicking are within the origin-binding domain. Further analysis identified that the small nonstructural protein NP1 is required for HBoV1 DNA replication at OriR. NP1 and other viral nonstructural proteins (NS1 to NS4) colocalized within the viral DNA replication centers in both OriR-transfected cells and virus-infected cells, highlighting a direct involvement of NP1 in viral DNA replication at OriR. Overall, our study revealed the characteristics of HBoV1 DNA replication at OriR, suggesting novel characteristics of autonomous parvovirus DNA replication. Human bocavirus 1 (HBoV1) causes acute respiratory tract infections in young children. The duplex HBoV1 genome replicates in HEK293 cells and produces progeny virions that are infectious in well-differentiated airway epithelial cells. A recombinant AAV2 vector pseudotyped with an HBoV1

  10. Resonance hairpin and Langmuir probe-assisted laser photodetachment measurements of the negative ion density in a pulsed dc magnetron discharge

    Energy Technology Data Exchange (ETDEWEB)

    Bradley, James W.; Dodd, Robert; You, S.-D.; Sirse, Nishant; Karkari, Shantanu Kumar [Department of Electrical Engineering and Electronics, University of Liverpool, Liverpool (United Kingdom); National Centre for Plasma Science and Technology, Dublin City University, Dublin 9, Republic of Ireland (Ireland); National Centre for Plasma Science and Technology, Dublin City University, Dublin 9, Republic of Ireland and Institute for Plasma Research, Bhat Gandhinagar, Gujarat (India)

    2011-05-15

    The time-resolved negative oxygen ion density n{sub -} close to the center line in a reactive pulsed dc magnetron discharge (10 kHz and 50% duty cycle) has been determined for the first time using a combination of laser photodetachment and resonance hairpin probing. The discharge was operated at a power of 50 W in 70% argon and 30% oxygen gas mixtures at 1.3 Pa pressure. The results show that the O{sup -} density remains pretty constant during the driven phase of the discharge at values typically below 5x10{sup 14} m{sup -3}; however, in the off-time, the O{sup -} density grows reaching values several times those in the on-time. This leads to the negative ion fraction (or degree of electronegativity) {alpha}=n{sub -}/n{sub e} being higher in the off phase (maximum value {alpha}{approx}1) than in the on phase ({alpha}=0.05-0.3). The authors also see higher values of {alpha} at positions close to the magnetic null than in the more magnetized region of the plasma. This fractional increase in negative ion density during the off-phase is attributed to the enhanced dissociative electron attachment of highly excited oxygen molecules in the cooling plasma. The results show that close to the magnetic null the photodetached electron density decays quickly after the laser pulse, followed by a slow decay over a few microseconds governed by the negative ion temperature. However, in the magnetized regions of the plasma, this decay is more gradual. This is attributed to the different cross-field transport rates for electrons in these two regions. The resonance hairpin probe measurements of the photoelectron densities are compared directly to photoelectron currents obtained using a conventional Langmuir probe. There is good agreement in the general trends, particularly in the off-time.

  11. Enzyme-free electrochemical detection of microRNA-21 using immobilized hairpin probes and a target-triggered hybridization chain reaction amplification strategy

    International Nuclear Information System (INIS)

    Liu, Hongying; Bei, Xiaoqiong; Xia, Qiuting; Fu, Yan; Zhang, Shi; Liu, Maochuan; Fan, Kai; Zhang, Mingzhen; Yang, Yong

    2016-01-01

    We describe a sensitive enzyme-free bioassay for the determination of microRNA-21. It is based on a combination of target-triggered hybridization chain reaction, tagging with CdTe quantum dots (QDs), and anodic stripping voltammetry. Firstly, a thiolated capture hairpin probe SH-HP1 was immobilized on the surface of a gold electrode. HP1 unfolds in the presence of microRNA-21. If hairpin probe 2 (HP2) is present, a HP1-HP2 complex will be formed which possesses an exposed stem of HP2, and microRNA is released in parallel. The released microRNA-21 triggers a hybridization chain reaction and this leads to form an exposed DNA segment of HP2 and cycle use microRNA-21. With the aid of assistant DNA A1 and A2, the exposed DNA segment of HP2 progressed to a long double strand. The strand is rich in CdTe QDs with the help of QDs-A1. Then, the attached QDs were dissolved with HNO 3 to give dissolved Cd(II) ions. Finally, the corresponding electrochemical current response of Cd(II) is monitored by anodic stripping voltammetry and used to quantify the concentration of microRNA-21. More microRNA-21 participated in this reaction increases the number of CdTe QDs, which results in increased electrochemical current. Thus, an ultrasensitive detection of microRNA-21 is accomplished by anodic stripping voltammetry. This gene assay displays a detection limit as low as 33 aM. It can discriminate between complementary DNA sequence and single-base mismatched DNA, indicating its high specificity. (author)

  12. Adeno-Associated Viral Vector-Mediated mTOR Inhibition by Short Hairpin RNA Suppresses Laser-Induced Choroidal Neovascularization

    Directory of Open Access Journals (Sweden)

    Tae Kwann Park

    2017-09-01

    Full Text Available Choroidal neovascularization (CNV is the defining characteristic feature of the wet subtype of age-related macular degeneration (AMD and may result in irreversible blindness. Based on anti-vascular endothelial growth factor (anti-VEGF, the current therapeutic approaches to CNV are fraught with difficulties, and mammalian target of rapamycin (mTOR has recently been proposed as a possible therapeutic target, although few studies have been conducted. Here, we show that a recombinant adeno-associated virus-delivered mTOR-inhibiting short hairpin RNA (rAAV-mTOR shRNA, which blocks the activity of both mTOR complex 1 and 2, represents a promising therapeutic approach for the treatment of CNV. Eight-week-old male C57/B6 mice were treated with the short hairpin RNA (shRNA after generating CNV lesions in the eyes via laser photocoagulation. The recombinant adeno-associated virus (rAAV delivery vehicle was able to effectively transduce cells in the inner retina, and significantly fewer inflammatory cells and less extensive CNV were observed in the animals treated with rAAV-mTOR shRNA when compared with control- and rAAV-scrambled shRNA-treated groups. Presumably related to the reduction of CNV, increased autophagy was detected in CNV lesions treated with rAAV-mTOR shRNA, whereas significantly fewer apoptotic cells detected in the outer nuclear layer around the CNV indicate that mTOR inhibition may also have neuroprotective effects. Taken together, these results demonstrate the therapeutic potential of mTOR inhibition, resulting from rAAV-mTOR shRNA activity, in the treatment of AMD-related CNV. Keywords: retinal neovascularization, choroidal neovascularization, adeno-associated virus, mTOR, RNA interference, mTOR shRNA, autophagy

  13. Charge Transfer and Support Effects in Heterogeneous Catalysis

    Energy Technology Data Exchange (ETDEWEB)

    Hervier, Antoine [Univ. of California, Berkeley, CA (United States)

    2011-12-21

    The kinetic, electronic and spectroscopic properties of two-dimensional oxide-supported catalysts were investigated in order to understand the role of charge transfer in catalysis. Pt/TiO2 nanodiodes were fabricated and used as catalysts for hydrogen oxidation. During the reaction, the current through the diode, as well as its I-V curve, were monitored, while gas chromatography was used to measure the reaction rate. The current and the turnover rate were found to have the same temperature dependence, indicating that hydrogen oxidation leads to the non-adiabatic excitation of electrons in Pt. A fraction of these electrons have enough energy to ballistically transport through Pt and overcome the Schottky barrier at the interface with TiO2. The yield for this phenomenon is on the order of 10-4 electrons per product molecule formed, similar to what has been observed for CO oxidation and for the adsorption of many different molecules. The same Pt/TiO2 system was used to compare currents in hydrogen oxidation and deuterium oxidation. The current through the diode under deuterium oxidation was found to be greater than under hydrogen oxidation by a factor of three. Weighted by the difference in turnover frequencies for the two isotopes, this would imply a chemicurrent yield 5 times greater for D2 compared to H2, contrary to what is expected given the higher mass of D2. Reversible changes in the rectification factor of the diode are observed when switching between D2 and H2. These changes are a likely cause for the differences in current between the two isotopes. In the nanodiode experiments, surface chemistry leads to charge flow, suggesting the possibility of creating charge flow to tune surface chemistry. This was done first by exposing a Pt/Si diode to visible light while using it as a catalyst for H2 oxidation. Absorption of the light in the Si, combined with

  14. Spiegelzymes® mirror-image hammerhead ribozymes and mirror-image DNAzymes, an alternative to siRNAs and microRNAs to cleave mRNAs in vivo?

    Directory of Open Access Journals (Sweden)

    Eliza Wyszko

    Full Text Available With the discovery of small non-coding RNA (ncRNA molecules as regulators for cellular processes, it became intriguing to develop technologies by which these regulators can be applied in molecular biology and molecular medicine. The application of ncRNAs has significantly increased our knowledge about the regulation and functions of a number of proteins in the cell. It is surprising that similar successes in applying these small ncRNAs in biotechnology and molecular medicine have so far been very limited. The reasons for these observations may lie in the high complexity in which these RNA regulators function in the cells and problems with their delivery, stability and specificity. Recently, we have described mirror-image hammerhead ribozymes and DNAzymes (Spiegelzymes® which can sequence-specifically hydrolyse mirror-image nucleic acids, such as our mirror-image aptamers (Spiegelmers discovered earlier. In this paper, we show for the first time that Spiegelzymes are capable of recognising complementary enantiomeric substrates (D-nucleic acids, and that they efficiently hydrolyse them at submillimolar magnesium concentrations and at physiologically relevant conditions. The Spiegelzymes are very stable in human sera, and do not require any protein factors for their function. They have the additional advantages of being non-toxic and non-immunogenic. The Spiegelzymes can be used for RNA silencing and also as therapeutic and diagnostic tools in medicine. We performed extensive three-dimensional molecular modelling experiments with mirror-image hammerhead ribozymes and DNAzymes interacting with D-RNA targets. We propose a model in which L/D-double helix structures can be formed by natural Watson-Crick base pairs, but where the nucleosides of one of the two strands will occur in an anticlinal conformation. Interestingly enough, the duplexes (L-RNA/D-RNA and L-DNA/D-RNA in these models can show either right- or left-handedness. This is a very new

  15. Build/Couple/Pair and Multifunctional Catalysis Strategies for the Synthesis of Heterocycles from Simple Starting Materials

    DEFF Research Database (Denmark)

    Ascic, Erhad

    . Multifunctional Catalysis: Synthesis of Heterocycles from Simple Starting Materials A multifunctional catalysis approach, involving a ruthenium-catalyzed tandem ringclosing metathesis/isomerization/N-acyliminium cyclization sequence, is described. Double bonds created during ring-closing metathesis isomerize......, a series of interesting indolizidinones are formed in good yields with excellent diastereoselectivities, including a formal total synthesis of the antiparasitic natural product harmicine and the first total synthesis of mescalotam. Furthermore, preliminary asymmetric variants of the tandem process have...

  16. Comparison of the role that entropy has played in processes of non-enzymatic and enzymatic catalysis

    International Nuclear Information System (INIS)

    Dixon Pineda, Manuel Tomas

    2012-01-01

    The function that entropy has played is compared in processes of non-enzymatic and enzymatic catalysis. The processes followed are showed: the kinetics of the acid hydrolysis of 3-pentyl acetate and cyclopentyl acetate catalyzed by hydrochloric acid and enzymatic hydrolysis of ethyl acetate and γ-butyrolactone catalyzed by pig liver esterase. The activation parameters of Eyring were determined for each process and interpreted the contribution of the entropy of activation for catalysis in this type of model reactions. (author) [es

  17. Complexes with charge transfer and ion-radical salts in catalysis

    Energy Technology Data Exchange (ETDEWEB)

    Krylov, O V [AN SSSR, Moscow. Inst. Khimicheskoj Fiziki

    1978-01-01

    Considered are the data experimentally proving formation of complexes with charge transfer as intermediate complexes in homogeneous and heterogeneous catalysis. Catalytic activity correlations with charge transfer energy (and in heterogeneous catalysis with width of semiconductor forbidden band can be useful while selection of catalysts (MoO/sub 3//MgO; V/sub 2/O/sub 5//MgO; MoO/sub 3//Al/sub 2/O/sub 3/; V/sub 2/O/sub 5//Al/sub 2/O/sub 3/). A review of papers on catalytic activity of the previously prepared complexes with charge transfer and ion-radical salts is given. The use of alkali metal complexes with aromatic compounds showed their high activity in hydrogenation reactions and proved principle possibility of activation of hydrogen and hydrocarbons by the systems which do not contain transfer metals.

  18. Sustainable preparation of supported metal nanoparticles and their applications in catalysis.

    Science.gov (United States)

    Campelo, Juan M; Luna, Diego; Luque, Rafael; Marinas, José M; Romero, Antonio A

    2009-01-01

    Metal nanoparticles have attracted much attention over the last decade owing to their unique properties as compared to their bulk metal equivalents, including a large surface-to-volume ratio and tunable shapes. To control the properties of nanoparticles with particular respect to shape, size and dispersity is imperative, as these will determine the activity in the desired application. Supported metal nanoparticles are widely employed in catalysis. Recent advances in controlling the shape and size of nanoparticles have opened the possibility to optimise the particle geometry for enhanced catalytic activity, providing the optimum size and surface properties for specific applications. This Review describes the state of the art with respect to the preparation and use of supported metal nanoparticles in catalysis. The main groups of such nanoparticles (noble and transition metal nanoparticles) are highlighted and future prospects are discussed.

  19. First Principles Molecular Dynamics Study of Catalysis for Polyolefins: the Ziegler-Natta Heterogeneous System.

    Directory of Open Access Journals (Sweden)

    Michele Parrinello

    2002-04-01

    Full Text Available Abstract: We review part of our recent ab initio molecular dynamics study on the Ti-based Ziegler-Natta supported heterogeneous catalysis of α-olefins. The results for the insertion of ethylene in the metal-carbon bond are discussed as a fundamental textbook example of polymerization processes. Comparison with the few experimental data available has shown that simulation can reproduce activation barriers and the overall energetics of the reaction with sufficient accuracy. This puts these quantum dynamical simulations in a new perspective as a virtual laboratory where the microscopic picture of the catalysis, which represents an important issue that still escapes experimental probes, can be observed and understood. These results are then discussed in comparison with a V-based catalyst in order to figure out analogies and differences with respect to the industrially more successful Tibased systems.

  20. New and future developments in catalysis batteries, hydrogen storage and fuel cells

    CERN Document Server

    Suib, Steven L

    2013-01-01

    New and Future Developments in Catalysis is a package of seven books that compile the latest ideas concerning alternate and renewable energy sources and the role that catalysis plays in converting new renewable feedstock into biofuels and biochemicals. Both homogeneous and heterogeneous catalysts and catalytic processes will be discussed in a unified and comprehensive approach. There will be extensive cross-referencing within all volumes. Batteries and fuel cells are considered to be environmentally friendly devices for storage and production of electricity, and they are gaining considerable attention. The preparation of the feed for fuel cells (fuel) as well as the catalysts and the various conversion processes taking place in these devices are covered in this volume, together with the catalytic processes for hydrogen generation and storage. An economic analysis of the various processes is also part of this volume and enables an informed choice of the most suitable process. Offers in-depth coverage of all ca...

  1. Cp2 TiX Complexes for Sustainable Catalysis in Single-Electron Steps.

    Science.gov (United States)

    Richrath, Ruben B; Olyschläger, Theresa; Hildebrandt, Sven; Enny, Daniel G; Fianu, Godfred D; Flowers, Robert A; Gansäuer, Andreas

    2018-04-25

    We present a combined electrochemical, kinetic, and synthetic study with a novel and easily accessible class of titanocene catalysts for catalysis in single-electron steps. The tailoring of the electronic properties of our Cp 2 TiX-catalysts that are prepared in situ from readily available Cp 2 TiX 2 is achieved by varying the anionic ligand X. Of the complexes investigated, Cp 2 TiOMs proved to be either equal or substantially superior to the best catalysts developed earlier. The kinetic and thermodynamic properties pertinent to catalysis have been determined. They allow a mechanistic understanding of the subtle interplay of properties required for an efficient oxidative addition and reduction. Therefore, our study highlights that efficient catalysts do not require the elaborate covalent modification of the cyclopentadienyl ligands. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Major Successes of Theory-and-Experiment-Combined Studies in Surface Chemistry and Heterogeneous Catalysis.

    Energy Technology Data Exchange (ETDEWEB)

    Somorjai, Gabor A.; Li, Yimin

    2009-11-21

    Experimental discoveries followed by theoretical interpretations that pave the way of further advances by experimentalists is a developing pattern in modern surface chemistry and catalysis. The revolution of modern surface science started with the development of surface-sensitive techniques such as LEED, XPS, AES, ISS and SIMS, in which the close collaboration between experimentalists and theorists led to the quantitative determination of surface structure and composition. The experimental discovery of the chemical activity of surface defects and the trends in the reactivity of transitional metals followed by the explanations from the theoretical studies led to the molecular level understanding of active sites in catalysis. The molecular level knowledge, in turn, provided a guide for experiments to search for new generation of catalysts. These and many other examples of successes in experiment-and-theory-combined studies demonstrate the importance of the collaboration between experimentalists and theorists in the development of modern surface science.

  3. Reactivating Catalytic Surface: Insights into the Role of Hot Holes in Plasmonic Catalysis.

    Science.gov (United States)

    Peng, Tianhuan; Miao, Junjian; Gao, Zhaoshuai; Zhang, Linjuan; Gao, Yi; Fan, Chunhai; Li, Di

    2018-03-01

    Surface plasmon resonance of coinage metal nanoparticles is extensively exploited to promote catalytic reactions via harvesting solar energy. Previous efforts on elucidating the mechanisms of enhanced catalysis are devoted to hot electron-induced photothermal conversion and direct charge transfer to the adsorbed reactants. However, little attention is paid to roles of hot holes that are generated concomitantly with hot electrons. In this work, 13 nm spherical Au nanoparticles with small absorption cross-section are employed to catalyze a well-studied glucose oxidation reaction. Density functional theory calculation and X-ray absorption spectrum analysis reveal that hot holes energetically favor transferring catalytic intermediates to product molecules and then desorbing from the surface of plasmonic catalysts, resulting in the recovery of their catalytic activities. The studies shed new light on the use of the synergy of hot holes and hot electrons for plasmon-promoted catalysis. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Evaluation of commercial and sulfated ZrO_2 aiming application catalysis

    International Nuclear Information System (INIS)

    Silva, F.N.; Dantas, J.; Costa, A.C.F.M.; Pallone, E.M.J.A.; Dutra, R.C.L.

    2014-01-01

    This study evaluates the performance of commercial and sulfated ZrO_2 for future application in catalysis. Commercial ZrO_2 was provided by the company Saint-Gobain Zirpro. The sulfation occurred with SO_4"-"2 ion content of 30% compared to the mass of ZrO_2. The samples were characterized by XRD, FTIR, EDX and GD. The results revealed the formation of a monoclinic phase for the commercial sample, and a monoclinic major phase with tetragonal traces for the sulfated sample. The commercial ZrO_2 showed a narrow, bimodal and asymmetric agglomerates distribution, while the sulfated sample showed a narrow, tetramodal and asymmetric agglomerates distribution. The presence of traces of the tetragonal phase in the SO_4"-"2/ZrO_2 XRD, and the presence of SO_3 in the EDX were good indicators for future use in catalysis to provide ester. (author)

  5. Synergy between experimental and theoretical methods in the exploration of homogeneous transition metal catalysis

    DEFF Research Database (Denmark)

    Lupp, Daniel; Christensen, Niels Johan; Fristrup, Peter

    2014-01-01

    n this Perspective, we will focus on the use of both experimental and theoretical methods in the exploration of reaction mechanisms in homogeneous transition metal catalysis. We briefly introduce the use of Hammett studies and kinetic isotope effects (KIE). Both of these techniques can be complem......n this Perspective, we will focus on the use of both experimental and theoretical methods in the exploration of reaction mechanisms in homogeneous transition metal catalysis. We briefly introduce the use of Hammett studies and kinetic isotope effects (KIE). Both of these techniques can...... be complemented by computational chemistry – in particular in cases where interpretation of the experimental results is not straightforward. The good correspondence between experiment and theory is only possible due to recent advances within the applied theoretical framework. We therefore also highlight...

  6. Camphor as Chiral Motif in Ligand Design - Applications in Catalysis and Complexation Gas-Chromatography

    OpenAIRE

    Spallek, Markus Jürgen

    2012-01-01

    This thesis is intended to further extend the scope of camphor and camphor-derived building blocks in the synthesis of chiral ligands, catalysts and selectors, their successful application in catalysis and in enantioseparation sciences. The thesis is divided into four independent chapters each focusing on the development of novel camphor-based compounds and their application as catalysts or metal-selectors. A short introduction is given for each chapter dealing with recent progress in the fie...

  7. On the mechanism of hydrogen evolution catalysis by proteins: A case study with bovine serum albumin

    Czech Academy of Sciences Publication Activity Database

    Doneux, T.; Ostatná, Veronika; Paleček, Emil

    2011-01-01

    Roč. 56, č. 25 (2011), s. 9337-9343 ISSN 0013-4686 R&D Projects: GA MŠk(CZ) ME09038; GA MŠk(CZ) LC06035 Grant - others:GA ČR(CZ) GAP301/11/2055 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : hydrogen evolution reaction * mediated catalysis * proton transfer Subject RIV: BO - Biophysics Impact factor: 3.832, year: 2011

  8. Multi-Scale Computational Enzymology: Enhancing Our Understanding of Enzymatic Catalysis

    OpenAIRE

    Rami Gherib; Hisham M. Dokainish; James W. Gauld

    2013-01-01

    Elucidating the origin of enzymatic catalysis stands as one the great challenges of contemporary biochemistry and biophysics. The recent emergence of computational enzymology has enhanced our atomistic-level description of biocatalysis as well the kinetic and thermodynamic properties of their mechanisms. There exists a diversity of computational methods allowing the investigation of specific enzymatic properties. Small or large density functional theory models allow the comparison of a pleth...

  9. Chiral phosphites as ligands in asymmetric metal complex catalysis and synthesis of coordination compounds

    International Nuclear Information System (INIS)

    Gavrilov, Konstantin N; Bondarev, Oleg G; Polosukhin, Aleksei I

    2004-01-01

    The data published during the last five years on the application of chiral derivatives of phosphorous acid in coordination chemistry and enantioselective catalysis are summarised and discussed. The effect of the nature of these ligands on the structure of metal complexes and on the efficiency of catalytic organic syntheses is shown. Hydroformylation, hydrogenation, allylic substitution and conjugate addition catalysed by transition metal complexes with optically active phosphites and hydrophosphoranes are considered. The prospects for the development of this field of research are demonstrated.

  10. Planar, Polysilazane?Derived Porous Ceramic Supports for Membrane and Catalysis Applications

    OpenAIRE

    Konegger, Thomas; Williams, Lee F.; Bordia, Rajendra K.

    2015-01-01

    Porous, silicon carbonitride?based ceramic support structures for potential membrane and catalysis applications were generated from a preceramic polysilazane precursor in combination with spherical, ultrahigh?molecular weight polyethylene microparticles through a sacrificial filler approach. A screening evaluation was used for the determination of the impact of both porogen content and porogen size on pore structure, strength, and permeability characteristics of planar specimens. By optimizin...

  11. Selective polymerization catalysis: controlling the metal chain end group to prepare block copolyesters.

    Science.gov (United States)

    Zhu, Yunqing; Romain, Charles; Williams, Charlotte K

    2015-09-30

    Selective catalysis is used to prepare block copolyesters by combining ring-opening polymerization of lactones and ring-opening copolymerization of epoxides/anhydrides. By using a dizinc complex with mixtures of up to three different monomers and controlling the chemistry of the Zn-O(polymer chain) it is possible to select for a particular polymerization route and thereby control the composition of block copolyesters.

  12. Kokes Awards for the 23rd North American Catalysis Society Meeting

    Energy Technology Data Exchange (ETDEWEB)

    Jacobs, Gary [University of Kentucky Research Foundation, Lexington, KY (United States)

    2014-01-31

    The Tri-State Catalysis Society awarded 107 Kokes Travel Awards. The program was very successful and to date this was the most Kokes Travel Awards ever awarded at a North American Catalysis Society Meeting. It provided students who merited an award the opportunity to attend the meeting, present a paper in the form of either an oral presentation or a poster presentation, and to serve the North American Catalysis Society by participating in the organization of the meeting. Students worked very hard during the week of the meeting to make it a success. Financial support for the Kokes awards was provided by DOE, NSF, NACS, as well as the Tri-State Catalysis Society, the latter through fund raising activities, and other donations. AT the meeting, each student received over $1050 in kind to offset the costs of registration fees ($260), hotel accommodations ($295.7), transportation ($400 travel allowance), as well as T-shirts ($20), and banquet tickets ($95 provided by donations from society members). In addition, for the first time, students received certificates that were signed by the President of NACS, Professor Enrique Iglesia, and by the Kokes Awards Chair, Gary Jacobs (see last page). A list of meeting co-chairs (i.e., Uschi M. Graham, Umit S. Ozkan, and Madan Bhassin) and the honorary chair (Burtron H. Davis) was also included on the certificate, along with the name of the recipient. The awardees were chosen on a merit-based guideline which also included the requirements of having a presentation accepted at the meeting and being a student at a North American University. The Richard J. Kokes Student Travel Award Committee (Gary Jacobs, Rodney Andrews, and Peter Smirniotis) with help from the Organizing Committee were able to secure money from four sources as detailed in Table 1. As detailed by our Treasurer, Dr. Helge Toufar of Clariant, the total amount spent was $105,000.

  13. Recent Progress in Asymmetric Catalysis and Chromatographic Separation by Chiral Metal–Organic Frameworks

    Directory of Open Access Journals (Sweden)

    Suchandra Bhattacharjee

    2018-03-01

    Full Text Available Metal–organic frameworks (MOFs, as a new class of porous solid materials, have emerged and their study has established itself very quickly into a productive research field. This short review recaps the recent advancement of chiral MOFs. Here, we present simple, well-ordered instances to classify the mode of synthesis of chiral MOFs, and later demonstrate the potential applications of chiral MOFs in heterogeneous asymmetric catalysis and enantioselective separation. The asymmetric catalysis sections are subdivided based on the types of reactions that have been successfully carried out recently by chiral MOFs. In the part on enantioselective separation, we present the potentiality of chiral MOFs as a stationary phase for high-performance liquid chromatography (HPLC and high-resolution gas chromatography (GC by considering fruitful examples from current research work. We anticipate that this review will provide interest to researchers to design new homochiral MOFs with even greater complexity and effort to execute their potential functions in several fields, such as asymmetric catalysis, enantiomer separation, and chiral recognition.

  14. Converting homogeneous to heterogeneous in electrophilic catalysis using monodisperse metal nanoparticles.

    Science.gov (United States)

    Witham, Cole A; Huang, Wenyu; Tsung, Chia-Kuang; Kuhn, John N; Somorjai, Gabor A; Toste, F Dean

    2010-01-01

    A continuing goal in catalysis is to unite the advantages of homogeneous and heterogeneous catalytic processes. To this end, nanoparticles represent a new frontier in heterogeneous catalysis, where this unification can also be supplemented by the ability to obtain new or divergent reactivity and selectivity. We report a novel method for applying heterogeneous catalysts to known homogeneous catalytic reactions through the design and synthesis of electrophilic platinum nanoparticles. These nanoparticles are selectively oxidized by the hypervalent iodine species PhICl(2), and catalyse a range of π-bond activation reactions previously only catalysed through homogeneous processes. Multiple experimental methods are used to unambiguously verify the heterogeneity of the catalytic process. The discovery of treatments for nanoparticles that induce the desired homogeneous catalytic activity should lead to the further development of reactions previously inaccessible in heterogeneous catalysis. Furthermore, a size and capping agent study revealed that Pt PAMAM dendrimer-capped nanoparticles demonstrate superior activity and recyclability compared with larger, polymer-capped analogues.

  15. Cheese whey protein recovery by ultrafiltration through transglutaminase (TG) catalysis whey protein cross-linking.

    Science.gov (United States)

    Wen-Qiong, Wang; Lan-Wei, Zhang; Xue, Han; Yi, Lu

    2017-01-15

    In whey ultrafiltration (UF) production, two main problems are whey protein recovery and membrane fouling. In this study, membrane coupling protein transglutaminase (TG) catalysis protein cross-linking was investigated under different conditions to find out the best treatment. We found that the optimal conditions for protein recovery involved catalyzing whey protein cross-linking with TG (40U/g whey proteins) at 40°C for 60min at pH 5.0. Under these conditions, the recovery rate was increased 15-20%, lactose rejection rate was decreased by 10%, and relative permeate flux was increase 30-40% compared to the sample without enzyme treatment (control). It was noticeable that the total resistance and cake resistance were decreased after enzyme catalysis. This was mainly due to the increased particle size and decreased zeta potential. Therefore, membrane coupling enzyme catalysis protein cross-linking is a potential means for further use. Copyright © 2016. Published by Elsevier Ltd.

  16. NMR Computational Studies of Solid Acidity/Fundamental Studies of Catalysis by Solid Acids

    Energy Technology Data Exchange (ETDEWEB)

    James F. Haw

    2008-06-28

    This project focused on catalysis by zeolites and the synergy of spectroscopic characterization and theoretical modeling. In collaboration with the Waroquier group in Belgium we used state-of-the-art quantum chemical simulations on a supramolecular model of both the HZSM-5 zeolite and the co-catalytic hydrocarbon pool species and calculated a full catalytic cycle (including all rate constants) for methanol-to-olefin (MTO) catalysis involving a hydrocarbon pool species. This work not only represents the most robust computational analysis of a successful MTO route to date, but it also succeeds in tying together the many experimental clues. That work was featured on the cover of Angewandte Chemie. More recently we elucidated several unsuspected roles for formaldehyde in methanol to olefin catalysis. Formaldehyde proves to be a key species responsible for both the growth of the catalytically active hydrocarbon pool and its inevitable aging into deactivated polycyclic aromatic species. The apparent inevitability of formaldehyde formation at high temperatures, in particular in contact with active metal or metal oxide surfaces, may put some fundamental limitations on the economic potential of conversion of methanol to olefins.

  17. Generating single-photon catalyzed coherent states with quantum-optical catalysis

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Xue-xiang, E-mail: xuxuexiang@jxnu.edu.cn [Center for Quantum Science and Technology, Jiangxi Normal University, Nanchang 330022 (China); Yuan, Hong-chun [College of Electrical and Optoelectronic Engineering, Changzhou Institute of Technology, Changzhou 213002 (China)

    2016-07-15

    We theoretically generate single-photon catalyzed coherent states (SPCCSs) by means of quantum-optical catalysis based on the beam splitter (BS) or the parametric amplifier (PA). These states are obtained in one of the BS (or PA) output channels if a coherent state and a single-photon Fock state are present in two input ports and a single photon is registered in the other output port. The success probabilities of the detection (also the normalization factors) are discussed, which is different for BS and PA catalysis. In addition, we prove that the generated states catalyzed by BS and PA devices are actually the same quantum states after analyzing photon number distribution of the SPCCSs. The quantum properties of the SPCCSs, such as sub-Poissonian distribution, anti-bunching effect, quadrature squeezing effect, and the negativity of the Wigner function are investigated in detail. The results show that the SPCCSs are non-Gaussian states with an abundance of nonclassicality. - Highlights: • We generate single-photon catalyzed coherent states with quantum-optical catalysis. • We prove the equivalent effects of the lossless beam splitter and the non-degenerate parametric amplifier. • Some nonclassical properties of the generated states are investigated in detail.

  18. Morphology-controlled synthesis of silver nanostructures via a seed catalysis process

    Energy Technology Data Exchange (ETDEWEB)

    Chen Chang; Wang Li; Yu Haojie; Wang Jianjun; Zhou Junfeng; Tan Qiaohua; Deng Libo [State Key Laboratory of Polymer Reaction Engineering, Zhejiang University, Hangzhou 310027 (China)

    2007-03-21

    A novel, effective strategy named 'seed catalysis' has been described here to synthesize silver nanostructures with controllable morphology. Typically, we added Na{sub 2}S into the reaction system and the Ag{sub 2}S semiconductor colloids formed at the initial stage would act as both seeds and catalyst in the silver reduction. The morphology of products is controlled by the concentration of Na{sub 2}S added to the system. Low concentration of Na{sub 2}S gives nanocubes of 40-50 nm in size, while a high concentration of Na{sub 2}S is of benefit to obtain nanowires. The growth of the silver crystal is also accelerated by the catalysis of Ag{sub 2}S. Electron microscopy and UV-vis absorption spectra have been used to investigate the evolution of silver nanowires, and a reasonable mechanism to explain the role of Ag{sub 2}S seeds has also been suggested. This semiconductor seed catalysis strategy will provide wide applications in the fabrication of metal nanomaterials.

  19. FATTY ACID ETHYL ESTERS FROM MICROALGAE OF Scenedesmus ecornis BY ENZYMATIC AND ACID CATALYSIS

    Directory of Open Access Journals (Sweden)

    Gabryelle F. de Almeida

    Full Text Available Microalgae are an indispensable food source for the various growth stages of mollusks, crustaceans, and several fish species. Using a microalgae biomass present in the Amazonian ecosystem (Macapá-AP, we study extraction methods for fatty acid such as solvent extraction (magnetic stirring and/or Soxhlet and/or hydrolysis (acid and/or enzymatic catalysis followed by esterification and/or direct transesterification. Extraction of crude triacylglycerides by mechanical stirring at room temperature was more efficient than continuous reflux (Soxhlet. Subsequently, the lipid extract was subject to transesterification with ethanol and CAL-B as a biocatalyst, leading to production of fatty acid ethyl esters (FAEE. Additionally, FAEEs were prepared by hydrolysis of crude triacylglycerides followed by acid-mediated esterification or enzymatic catalysis (lipase. In this case, the type of catalyst did not significantly influence FAEE yields. In the lipid extract, we identified palmitic, linoleic, oleic, and stearic acids with palmitic acid being the most abundant. Our results suggest that enzymatic catalysis is a viable method for the extraction of lipids in the microalga, Scenedesmus ecornis.

  20. Kinetic Studies on the Selective Oxidation of Benzyl Alcohols in Organic Medium under Phase Transfer Catalysis

    Directory of Open Access Journals (Sweden)

    K. Bijudas

    2014-07-01

    Full Text Available Kinetic studies on the oxidation of benzyl alcohol and substituted benzyl alcohols in benzene as the reaction medium have been studied by using potassium dichromate under phase transfer catalysis (PTC. The phase transfer catalysts (PT catalysts used were tetrabutylammonium bromide (TBAB and tetrabutylphosphonium bromide (TBPB.  Benzyl alcohols were selectively oxidised to corresponding benzaldehydes in good yield (above 90%.  The order of reactivity among the studied benzyl alcohols is p - OCH3 > p - CH3 > - H > p - Cl.  Plots of log k2 versus Hammett's substituent constant (s has been found to be curve shaped and this suggests that there should be a continuous change in transition state with changes in substituent present in the substrate from electron donating to electron withdrawing. A suitable mechanism has been suggested in which the rate determining step involves both C - H bond cleavage and C - O bond formations in concerted manner. © 2014 BCREC UNDIP. All rights reserved.Received: 16th March 2014; Revised: 18th May 2014; Accepted: 18th May 2014[How to Cite: Bijudas, K., Bashpa, P., Nair, T.D.R. (2014. Kinetic Studies on the Selective Oxidation of Benzyl Alcohol and Substituted Benzyl Alcohols in Organic Medium under Phase Transfer Catalysis. Bulletin of Chemical Reaction Engineering & Catalysis, 9 (2: 142-147. (doi:10.9767/bcrec.9.2.6476.142-147][Permalink/DOI: http://dx.doi.org/10.9767/bcrec.9.2.6476.142-147] 

  1. Expression of self-complementary hairpin RNA under the control of the rolC promoter confers systemic disease resistance to plum pox virus without preventing local infection.

    Science.gov (United States)

    Pandolfini, Tiziana; Molesini, Barbara; Avesani, Linda; Spena, Angelo; Polverari, Annalisa

    2003-06-25

    Homology-dependent selective degradation of RNA, or post-transcriptional gene silencing (PTGS), is involved in several biological phenomena, including adaptative defense mechanisms against plant viruses. Small interfering RNAs mediate the selective degradation of target RNA by guiding a multicomponent RNAse. Expression of self-complementary hairpin RNAs within two complementary regions separated by an intron elicits PTGS with high efficiency. Plum pox virus (PPV) is the etiological agent of sharka disease in Drupaceae, although it can also be transmitted to herbaceous species (e.g. Nicotiana benthamiana). Once inside the plant, PPV is transmitted via plasmodesmata from cell to cell, and at longer distances, via phloem. The rolC promoter drives expression in phloem cells. RolC expression is absent in both epidermal and mesophyll cells. The aim of the present study was to confer systemic disease resistance without preventing local viral infection. In the ihprolC-PP197 gene (intron hair pin rolC PPV 197), a 197 bp sequence homologous to the PPV RNA genome (from base 134 to 330) was placed as two inverted repeats separated by the DNA sequence of the rolA intron. This hairpin construct is under the control of the rolC promoter.N. benthamiana plants transgenic for the ihprolC-PP197 gene contain siRNAs homologous to the 197 bp sequence. The transgenic progeny of ihprolC-PP197 plants are resistant to PPV systemic infection. Local infection is unaffected. Most (80%) transgenic plants are virus free and symptomless. Some plants (20%) contain virus in uninoculated apical leaves; however they show only mild symptoms of leaf mottling. PPV systemic resistance cosegregates with the ihprolC-PP197 transgene and was observed in progeny plants of all independent transgenic lines analyzed. SiRNAs of 23-25 nt homologous to the PPV sequence used in the ihprolC-PP197 construct were detected in transgenic plants before and after inoculation. Transitivity of siRNAs was observed in

  2. Expression of self-complementary hairpin RNA under the control of the rolC promoter confers systemic disease resistance to plum pox virus without preventing local infection

    Directory of Open Access Journals (Sweden)

    Spena Angelo

    2003-06-01

    Full Text Available Abstract Background Homology-dependent selective degradation of RNA, or post-transcriptional gene silencing (PTGS, is involved in several biological phenomena, including adaptative defense mechanisms against plant viruses. Small interfering RNAs mediate the selective degradation of target RNA by guiding a multicomponent RNAse. Expression of self-complementary hairpin RNAs within two complementary regions separated by an intron elicits PTGS with high efficiency. Plum pox virus (PPV is the etiological agent of sharka disease in Drupaceae, although it can also be transmitted to herbaceous species (e.g. Nicotiana benthamiana. Once inside the plant, PPV is transmitted via plasmodesmata from cell to cell, and at longer distances, via phloem. The rolC promoter drives expression in phloem cells. RolC expression is absent in both epidermal and mesophyll cells. The aim of the present study was to confer systemic disease resistance without preventing local viral infection. Results In the ihprolC-PP197 gene (intron hair pin rolC PPV 197, a 197 bp sequence homologous to the PPV RNA genome (from base 134 to 330 was placed as two inverted repeats separated by the DNA sequence of the rolA intron. This hairpin construct is under the control of the rolC promoter.N. benthamiana plants transgenic for the ihprolC-PP197 gene contain siRNAs homologous to the 197 bp sequence. The transgenic progeny of ihprolC-PP197 plants are resistant to PPV systemic infection. Local infection is unaffected. Most (80% transgenic plants are virus free and symptomless. Some plants (20% contain virus in uninoculated apical leaves; however they show only mild symptoms of leaf mottling. PPV systemic resistance cosegregates with the ihprolC-PP197 transgene and was observed in progeny plants of all independent transgenic lines analyzed. SiRNAs of 23–25 nt homologous to the PPV sequence used in the ihprolC-PP197 construct were detected in transgenic plants before and after inoculation

  3. Understanding of catalysis on early transition metal oxide-based catalysts through exploration of surface structure and chemistry during catalysis using in-situ approaches

    Energy Technology Data Exchange (ETDEWEB)

    Tao, Franklin [Univ. of Kansas, Lawrence, KS (United States). Dept. of Chemical and Petroleum Engineering. Dept. of Chemistry

    2015-09-14

    Two main categories of heterogeneous catalysts are metal and metal oxide which catalyze 80% chemical reactions at solid-gas and solid-liquid interfaces. Metal oxide catalysts are much more complicated than metal catalysts. The reason is that the cations of the metal atoms could exhibit a few different oxidation states on surface of the same catalyst particle such as Co3O4 or change of their oxidation states under different reactive environments. For a metal catalyst, there is only one oxidation state typically. In addition, surface of a metal oxide can be terminated with multiple surface functionalities including O atoms with different binding configurations and OH group. For metal, only metal atoms are exposed typically. Obviously, the complication of surface chemistry and structure of a metal oxide makes studies of surface of an oxide catalyst very challenging. Due to the complication of surface of a meal oxide, the electronic and geometric structures of surface of a metal oxide and the exposed species have received enormous attention since oxide catalysts catalyze at least 1/3 chemical reactions in chemical and energy industries. Understanding of catalytic reactions on early transition metal oxide-based catalysts is fundamentally intriguing and of great practical interest in energy- and environment-related catalysis. Exploration of surface chemistry of oxide-based catalysts at molecular level during catalysis has remained challenging though it is critical in deeply understanding catalysis on oxide-based catalysts and developing oxide-based catalysts with high activity and selectivity. Thus, the overall objective of this project is to explore surface chemistry and structure of early transition metal oxide-based catalysts through in-situ characterization of surface of catalysts, measurements of catalytic performances, and then build an intrinsic correlation of surface chemistry and structure with their catalytic performances in a few

  4. Specific interaction of the nonstructural protein NS1 of minute virus of mice (MVM) with [ACCA](2) motifs in the centre of the right-end MVM DNA palindrome induces hairpin-primed viral DNA replication.

    Science.gov (United States)

    Willwand, Kurt; Moroianu, Adela; Hörlein, Rita; Stremmel, Wolfgang; Rommelaere, Jean

    2002-07-01

    The linear single-stranded DNA genome of minute virus of mice (MVM) is replicated via a double-stranded replicative form (RF) intermediate DNA. Amplification of viral RF DNA requires the structural transition of the right-end palindrome from a linear duplex into a double-hairpin structure, which serves for the repriming of unidirectional DNA synthesis. This conformational transition was found previously to be induced by the MVM nonstructural protein NS1. Elimination of the cognate NS1-binding sites, [ACCA](2), from the central region of the right-end palindrome next to the axis of symmetry was shown to markedly reduce the efficiency of hairpin-primed DNA replication, as measured in a reconstituted in vitro replication system. Thus, [ACCA](2) sequence motifs are essential as NS1-binding elements in the context of the structural transition of the right-end MVM palindrome.

  5. Crystal Structure of the Full-Length Feline Immunodeficiency Virus Capsid Protein Shows an N-Terminal β-Hairpin in the Absence of N-Terminal Proline

    Directory of Open Access Journals (Sweden)

    Christelle Folio

    2017-11-01

    Full Text Available Feline immunodeficiency virus (FIV is a member of the Retroviridae family. It is the causative agent of an acquired immunodeficiency syndrome (AIDS in cats and wild felines. Its capsid protein (CA drives the assembly of the viral particle, which is a critical step in the viral replication cycle. Here, the first atomic structure of full-length FIV CA to 1.67 Å resolution is determined. The crystallized protein exhibits an original tetrameric assembly, composed of dimers which are stabilized by an intermolecular disulfide bridge induced by the crystallogenesis conditions. The FIV CA displays a standard α-helical CA topology with two domains, separated by a linker shorter than other retroviral CAs. The β-hairpin motif at its amino terminal end, which interacts with nucleotides in HIV-1, is unusually long in FIV CA. Interestingly, this functional β-motif is formed in this construct in the absence of the conserved N-terminal proline. The FIV CA exhibits a cis Arg–Pro bond in the CypA-binding loop, which is absent in known structures of lentiviral CAs. This structure represents the first tri-dimensional structure of a functional, full-length FIV CA.

  6. Structure and conformational dynamics of the domain 5 RNA hairpin of a bacterial group II intron revealed by solution nuclear magnetic resonance and molecular dynamics simulations.

    Science.gov (United States)

    Pechlaner, Maria; Sigel, Roland K O; van Gunsteren, Wilfred F; Dolenc, Jožica

    2013-10-08

    Nuclear magnetic resonance (NMR) nuclear Overhauser enhancement (NOE) data obtained for a 35-nucleotide RNA segment of a bacterial group II intron indicate a helical hairpin structure in which three parts, a terminal pentaloop, a bulge, and a G-A mismatch, display no Watson-Crick base pairing. The 668 NOE upper distance bounds for atom pairs are insufficient to uniquely determine the conformation of these segments. Therefore, molecular dynamics simulations including time-averaged distance restraints have been used to obtain a conformational ensemble compatible with the observed NMR data. The ensemble shows alternating hydrogen bonding patterns for the mentioned segments. In particular, in the pentaloop and in the bulge, the hydrogen bonding networks correspond to distinct conformational clusters that could not be captured by using conventional single-structure refinement techniques. This implies that, to obtain a realistic picture of the conformational ensemble of such flexible biomolecules, it is necessary to properly account for the conformational variability in the structure refinement of RNA fragments.

  7. Preclinical safety and efficacy of an anti–HIV-1 lentiviral vector containing a short hairpin RNA to CCR5 and the C46 fusion inhibitor

    Directory of Open Access Journals (Sweden)

    Orit Wolstein

    2014-01-01

    Full Text Available Gene transfer has therapeutic potential for treating HIV-1 infection by generating cells that are resistant to the virus. We have engineered a novel self-inactivating lentiviral vector, LVsh5/C46, using two viral-entry inhibitors to block early steps of HIV-1 cycle. The LVsh5/C46 vector encodes a short hairpin RNA (shRNA for downregulation of CCR5, in combination with the HIV-1 fusion inhibitor, C46. We demonstrate here the effective delivery of LVsh5/C46 to human T cell lines, peripheral blood mononuclear cells, primary CD4+ T lymphocytes, and CD34+ hematopoietic stem/progenitor cells (HSPC. CCR5-targeted shRNA (sh5 and C46 peptide were stably expressed in the target cells and were able to effectively protect gene-modified cells against infection with CCR5- and CXCR4-tropic strains of HIV-1. LVsh5/C46 treatment was nontoxic as assessed by cell growth and viability, was noninflammatory, and had no adverse effect on HSPC differentiation. LVsh5/C46 could be produced at a scale sufficient for clinical development and resulted in active viral particles with very low mutagenic potential and the absence of replication-competent lentivirus. Based on these in vitro results, plus additional in vivo safety and efficacy data, LVsh5/C46 is now being tested in a phase 1/2 clinical trial for the treatment of HIV-1 disease.

  8. Efficient immortalization of primary human cells by p16INK4a-specific short hairpin RNA or Bmi-1, combined with introduction of hTERT.

    Science.gov (United States)

    Haga, Kei; Ohno, Shin-ichi; Yugawa, Takashi; Narisawa-Saito, Mako; Fujita, Masatoshi; Sakamoto, Michiie; Galloway, Denise A; Kiyono, Tohru

    2007-02-01

    Activation of telomerase is sufficient for immortalization of some types of human cells but additional factors may also be essential. It has been proposed that stress imposed by inadequate culture conditions induces senescence due to accumulation of p16(INK4a). Here, we present evidence that many human cell types undergo senescence by activation of the p16(INK4a)/Rb pathway, and that introduction of Bmi-1 can inhibit p16(INK4a) expression and extend the life span of human epithelial cells derived from skin, mammary gland and lung. Introduction of p16(INK4a)-specific short hairpin RNA, as well as Bmi-1, suppressed p16(INK4a) expression in human mammary epithelial cells without promoter methylation, and extended their life span. Subsequent introduction of hTERT, the telomerase catalytic subunit, into cells with low p16(INK4a) levels resulted in efficient immortalization of three cell types without crisis or growth arrest. The majority of the human mammary epithelial cells thus immortalized showed almost normal ploidy as judged by G-banding and spectral karyotyping analysis. Our data suggest that inhibition of p16(INK4a) and introduction of hTERT can immortalize many human cell types with little chromosomal instability.

  9. Short hairpin RNA targeting 2B gene of coxsackievirus B3 exhibits potential antiviral effects both in vitro and in vivo

    Directory of Open Access Journals (Sweden)

    Yao Hailan

    2012-08-01

    Full Text Available Abstract Background Coxsackievirus B3 is an important infectious agent of viral myocarditis, pancreatitis and aseptic meningitis, but there are no specific antiviral therapeutic reagents in clinical use. RNA interference-based technology has been developed to prevent the viral infection. Methods To evaluate the impact of RNA interference on viral replication, cytopathogenicity and animal survival, short hairpin RNAs targeting the viral 2B region (shRNA-2B expressed by a recombinant vector (pGCL-2B or a recombinant lentivirus (Lenti-2B were tansfected in HeLa cells or transduced in mice infected with CVB3. Results ShRNA-2B exhibited a significant effect on inhibition of viral production in HeLa cells. Furthermore, shRNA-2B improved mouse survival rate, reduced the viral tissues titers and attenuated tissue damage compared with those of the shRNA-NC treated control group. Lenti-2B displayed more effective role in inhibition of viral replication than pGCL-2B in vivo. Conclusions Coxsackievirus B3 2B is an effective target of gene silencing against coxsackievirus B3 infection, suggesting that shRNA-2B is a potential agent for further development into a treatment for enterviral diseases.

  10. Asymmetric catalysis in Brazil: development and potential for advancement of Brazilian chemical industry

    International Nuclear Information System (INIS)

    Braga, Antonio Luiz; Luedtke, Diogo Seibert; Schneider, Paulo Henrique; Andrade, Leandro Helgueira; Paixao, Marcio Weber

    2013-01-01

    The preparation of enantiomerically pure or enriched substances is of fundamental importance to pharmaceutical, food, agrochemical, and cosmetics industries and involves a growing market of hundreds of billions of dollars. However, most chemical processes used for their production are not environmentally friendly because in most cases, stoichiometric amounts of chiral inductors are used and substantial waste is produced. In this context, asymmetric catalysis has emerged as an efficient tool for the synthesis of enantiomerically enriched compounds using chiral catalysts. More specifically, considering the current scenario in the Brazilian chemical industry, especially that of pharmaceuticals, the immediate prospect for the use of synthetic routes developed in Brazil in an enantioselective fashion or even the discovery of new drugs is practically null. Currently, the industrial production of drugs in Brazil is primarily focused on the production of generic drugs and is basically supported by imports of intermediates from China and India. In order to change this panorama and move forward toward the gradual incorporation of genuinely Brazilian synthetic routes, strong incentive policies, especially those related to continuous funding, will be needed. These incentives could be a breakthrough once we establish several research groups working in the area of organic synthesis and on the development and application of chiral organocatalysts and ligands in asymmetric catalysis, thus contributing to boost the development of the Brazilian chemical industry. Considering these circumstances, Brazil can benefit from this opportunity because we have a wide biodiversity and a large pool of natural resources that can be used as starting materials for the production of new chiral catalysts and are creating competence in asymmetric catalysis and related areas. This may decisively contribute to the growth of chemistry in our country. (author)

  11. Bicarbonate catalysis of exchange synthesis of [51Cr]Cr(III)-EDTA and other chromium complexes

    International Nuclear Information System (INIS)

    Aronson, F.L.; Strashun, A.M.; Lopez, C.; Steigman, J.

    1993-01-01

    Exchange syntheses of trivalent chromium complexes often require heating, thus limiting tagging of heat-sensitive biological compounds with 51 Cr. Bicarbonate at pH 6, accelerates the formation of mM Cr-EDTA. Accordingly, room temperature catalysis with [ 51 Cr]Cr(III) at 10 -7 -10 -8 M was investigated. Complexes were successfully formed with EDTA and iminodiacetic acid (electrophoretic analysis) and acetylacetone and tropolone (analyzed by chloroform extraction). The formation of these complexes normally requires extensive heating. (author)

  12. Conversion of CO2 via Visible Light Promoted Homogeneous Redox Catalysis

    Directory of Open Access Journals (Sweden)

    Bernhard Rieger

    2012-11-01

    Full Text Available This review gives an overview on the principles of light-promoted homogeneous redox catalysis in terms of applications in CO2 conversion. Various chromophores and the advantages of different structures and metal centers as well as optimization strategies are discussed. All aspects of the reduction catalyst site are restricted to CO2 conversion. An important focus of this review is the question of a replacement of the sacrificial donor which is found in most of the current publications. Furthermore, electronic parameters of supramolecular systems are reviewed with reference to the requisite of chromophores, oxidation and reduction sites.

  13. Hierarchical zeolites: Enhanced utilisation of microporous crystals in catalysis by advances in materials design

    DEFF Research Database (Denmark)

    Perez-Ramirez, Javier; Christensen, Claus H.; Egeblad, Kresten

    2008-01-01

    The introduction of synthetic zeolites has led to a paradigm shift in catalysis, separations, and adsorption processes, due to their unique properties such as crystallinity, high-surface area, acidity, ion-exchange capacity, and shape-selective character. However, the sole presence of micropores...... the properties of the resulting materials and the catalytic function. We particularly dwell on the exciting field of hierarchical zeolites, which couple in a single material the catalytic power of micropores and the facilitated access and improved transport consequence of a complementary mesopore network...

  14. Search for Erzion nuclear catalysis chains from cosmic ray Erzions stopping in organic scintillator

    International Nuclear Information System (INIS)

    Bazhutov, Yu.N.; Pletnikov, E.V.

    2006-01-01

    In the framework of Erzion model, charged cosmic ray Erzions stopping in organic substance begin to create Erzion nuclear catalysis chains with frequency of ∼ 100 MHz during ∼ 10-100 ms. Using an organic substance (plastic) scintillator we can observe long and flat (10-100 ms) pulses of large amplitude (∼100 MeV). No elementary particle can imitate such pulses. It is expected that such pulses in a plastic scintillator with mass of 100 kg will appear at the sea level every week. Such pulses can be observed every day with the Spectrometric Scintillation Super-Telescope (SSTIS) built at IZMIRAN for cosmic rays monitoring. (authors)

  15. Synthesis, Characterization and Applications in Catalysis of Polyoxometalate/Zeolite Composites

    Directory of Open Access Journals (Sweden)

    Frédéric Lefebvre

    2016-05-01

    Full Text Available An overview of the synthesis, characterization and catalytic applications of polyoxometalates/zeolites composites is given. The solids obtained by direct synthesis of the polyoxometalate in the presence of the zeolite are first described with their applications in catalysis. Those obtained by a direct mixing of the two components are then reviewed. In all cases, special care is taken in the localization of the polyoxometalate, inside the zeolite crystal, in mesopores or at the external surface of the crystals, as deduced from the characterization methods.

  16. Exploring Cooperative Effects in Oxidative NHC Catalysis: Regioselective Acylation of Carbohydrates.

    Science.gov (United States)

    Cramer, David L; Bera, Srikrishna; Studer, Armido

    2016-05-23

    The utility of oxidative NHC catalysis for both the regioselective and chemoselective functionalization of carbohydrates is explored. Chiral NHCs allow for the highly regioselective oxidative esterification of various carbohydrates using aldehydes as acylation precursors. The transformation was also shown to be amenable to both cis/trans diol isomers, free amino groups, and selective for specific sugar epimers in competition experiments. Efficiency and regioselectivity of the acylation can be improved upon using two different NHC catalysts that act cooperatively. The potential of the method is documented by the regioselective acylation of an amino-linked neodisaccharide. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Metal-organic frameworks and their applications in catalysis; Redes metalorganicas e suas aplicacoes em catalise

    Energy Technology Data Exchange (ETDEWEB)

    Ramos, Andre Luis Dantas, E-mail: aldramos@ufs.br [Universidade Federal de Sergipe (UFSE), Sao Cristovao, SE (Brazil). Departamento de Engenharia Quimica; Tanase, Stefania; Rothenberg, Gadi [Van' t Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam (Netherlands)

    2014-07-01

    Metal-organic frameworks (MOFs) form a new class of materials with well-defined yet tunable properties. These are crystalline, highly porous and exhibit strong metal-ligand interactions. Importantly, their physical and chemical properties, including pore size, pore structure, acidity, and magnetic and optical characteristics, can be tailored by choosing the appropriate ligands and metal precursors. Here we review the key aspects of synthesis and characterization of MOFs, focusing on lanthanide-based and vanadium-based materials. We also outline some of their applications in catalysis and materials science. (author)

  18. Catalysis Research of Relevance to Carbon Management: Progress, Challenges, and Opportunities

    Energy Technology Data Exchange (ETDEWEB)

    Arakawa, Hironori; Aresta, Michele; Armor, John; Barteau, Mark; Beckman, Eric J.; Bell, Alexis T.; Bercaw, John E.; Creutz, Carol; Dinjus, Eckhard; Dixon, David A.; Domen, Kazunari; Dubois, Daniel L.; Eckert, Juergen; Fujita, Etsuko; Gibson, Dorothy H.; Goddard, William A.; Goodman, Wayne D.; Keller, Jay; Kubas, Gregory J.; Kung, Harold H.; Lyons, James E.; Manzer, Leo; Marks, Tobin J.; Morokuma, Keiji; Nicholas, Kenneth M.; Periana, Roy; Que, Lawrence; Rostrup-Nielson, Jens; Sachtler, Woflgang M H.; Schmidt, Lanny D.; Sen, Ayusman; Somorjai, Gabor A.; Stair, Peter C.; Stults, Bailey R.; Tumas, William

    2001-04-11

    The goal of the 'Opportunities for Catalysis Research in Carbon Management' workshop was to review within the context of greenhouse gas/carbon issues the current state of knowledge, barriers to further scientific and technological progress, and basic scientific research needs in the areas of H{sub 2} generation and utilization, light hydrocarbon activation and utilization, carbon dioxide activation, utilization, and sequestration, emerging techniques and research directions in relevant catalysis research, and in catalysis for more efficient transportation engines. Several overarching themes emerge from this review. First and foremost, there is a pressing need to better understand in detail the catalytic mechanisms involved in almost every process area mentioned above. This includes the structures, energetics, lifetimes, and reactivities of the species thought to be important in the key catalytic cycles. As much of this type of information as is possible to acquire would also greatly aid in better understanding perplexing, incomplete/inefficient catalytic cycles and in inventing new, efficient ones. The most productive way to attack such problems must include long-term, in-depth fundamental studies of both commercial and model processes, by conventional research techniques and, importantly, by applying various promising new physicochemical and computational approaches which would allow incisive, in situ elucidation of reaction pathways. There is also a consensus that more exploratory experiments, especially high-risk, unconventional catalytic and model studies, should be undertaken. Such an effort will likely require specialized equipment, instrumentation, and computational facilities. The most expeditious and cost-effective means to carry out this research would be by close coupling of academic, industrial, and national laboratory catalysis efforts worldwide. Completely new research approaches should be vigorously explored, ranging from novel compositions

  19. Transition processes in the novel method of the muon catalysis investigation

    International Nuclear Information System (INIS)

    Filchenkov, V.V.

    1997-01-01

    The problem of modifying the interpretation of the results to be obtained with the novel method of muon catalysis investigation to take the fast transition processes into account is first considered. The results of exploring the process kinetics are compared with the ones found from the analysis of the appropriate Monte Carlo distributions. The calculation programs simulate both the kinetics and the registration system of the experiment which is now performed in the frame of the large international project TRITON. The main conclusion is that the multiplicity distribution of the fusion neutrons is 'invariant' under any assumptions of the fast transition stage

  20. Electric-field enhanced performance in catalysis and solid-state devices involving gases

    Science.gov (United States)

    Blackburn, Bryan M.; Wachsman, Eric D.; Van Assche, IV, Frederick Martin

    2015-05-19

    Electrode configurations for electric-field enhanced performance in catalysis and solid-state devices involving gases are provided. According to an embodiment, electric-field electrodes can be incorporated in devices such as gas sensors and fuel cells to shape an electric field provided with respect to sensing electrodes for the gas sensors and surfaces of the fuel cells. The shaped electric fields can alter surface dynamics, system thermodynamics, reaction kinetics, and adsorption/desorption processes. In one embodiment, ring-shaped electric-field electrodes can be provided around sensing electrodes of a planar gas sensor.